Thom Group Wiki - User contributions [en]

Group List

2025-04-09T12:13:57Z

Ksp31:

<div style="text-align: center;">
<timeline>
# Constants
Define $width = 1200
Define $height = 1100
Define $headerx = -520 # -width/2 + 80
Define $headery = -3

Define $bigbang = 01/01/2010
Define $bigcrunch = 15/04/2025

# Canvas settings
ImageSize = width:$width height:$height
PlotArea = right:20 left:150 bottom:100 top:0
AlignBars = justify
Legend = columns:4 left:220 top:50 columnwidth:160
DateFormat = dd/mm/yyyy
Period = from:$bigbang till:$bigcrunch
TimeAxis = orientation:horizontal

# Colors
Colors =
id:canvas value:gray(0.95) # background for whole image
id:bars value:white # background for bars
id:grid1 value:gray(0.6) # major grid
id:grid2 value:gray(0.85) # minor grid
id:gray value:gray(0.5) # for colophon
id:lgray value:gray(0.7)
id:odd value:rgb(0.941, 0.796, 0.647) # orange for odd grid
id:even value:rgb(0.486, 0.733, 1) # blue for even grid

id:Leader value:rgb(0.501,0,0.125) legend:Group_leader
id:Postdoc value:rgb(0.231,0.278,0.968) legend:Postdoctoral_researcher
id:PhD value:rgb(0.192,0.470,0.450) legend:PhD_student
id:MPhil value:rgb(0.392,0.770,0.750) legend:MPhil_student
id:PartIII value:rgb(1,0.580,0.2) legend:Part_III_student
id:Visitor value:rgb(0.2,0.8,1) legend:Visiting_researcher
id:StudentVisitor value:rgb(0.968,0.231,0.294) legend:Visiting_student
id:Summer value:rgb(1,0.521,0.909) legend:Summer_intern
id:Undergrad value:rgb(1,0.821,0.969) legend:Undergraduate_student

# Grids
ScaleMajor = unit:year grid:grid1 increment:1 start:01/01/2010
#ScaleMinor = unit:month grid:grid2 increment:1 start:01/01/2010

# Presets
Define $GroupLeader = color:Leader width:0.1in
Define $Postdoc = color:Postdoc width:0.1in
Define $PhD = color:PhD width:0.1in
Define $MPhil = color:MPhil width:0.1in
Define $PartIII = color:PartIII width:0.1in
Define $Visitor = color:Visitor width:0.1in
Define $StudentVisitor = color:StudentVisitor width:0.1in
Define $Summer = color:Summer width:0.1in
Define $Undergrad = color:Undergrad width:0.1in
Define $guide = color:gray width:0.1
Define $break = color:gray width:2.5 from:$bigbang till:$bigcrunch fontsize:M shift:($headerx,$headery) align:right

# Plotdata generated using Python 3
# Script and data can be found at `thom-fs-common/group/groupwiki`.
# Paste content of plotscript.txt after the next line.
#######################################################
BarData = # Current
bar:current
bar:AT0 text:Dr_Alex Thom
bar:CL0 text:_Chiara Leadbeater
bar:JT0 text:_Jack Taylor
bar:RP0 text:_Rowan Poklewski-Koziell
bar:LCT0 text:_Lila Cadi Tazi
bar:BC0 text:_Bence Csakany
bar:RH0 text:_Reka Horvath
bar:DC0 text:_Dylan Counsell
bar:CW0 text:_Charlie Wheelwright
# Past
bar:past
bar:AZ0 text:Dr_Alberto Zoccante
bar:WV0 text:Dr_William Vigor
bar:JK0 text:Dr_Jonathan Kimmitt
bar:SC0 text:Dr_Salvatore Cardamone
bar:DG0 text:Dr_Daniel Graf
bar:RF0 text:_Ruth Franklin
bar:CS0 text:Dr_Charles Scott
bar:VN0 text:Dr_Verena Neufeld
bar:HB0 text:Dr_Hugh Burton
bar:BCH0 text:Dr_Bang C. Huynh
bar:DI0 text:Dr_David Izuogu
bar:FA0 text:Dr_Fabio Albertani
bar:MF0 text:Dr_Maria-Andreea Filip
bar:KP0 text:Dr_Kripa Panchagnula
bar:HT0 text:_Henry Tran
bar:AC0 text:_Alexander Card
bar:AS0 text:_Arta Safari
bar:BZ0 text:_Brian Zhao
bar:HYLN0 text:_Heng You Lee (Nicholas)
bar:YS0 text:_Yi Sun
bar:LW0 text:_Lijun Wang
bar:BS0 text:_Benjamin Shires
bar:SC1 text:_Seonghoon Choi
bar:LB0 text:_Letitia-Iona Birnoschi
bar:AG0 text:_Alexander Gunasekera
bar:GB0 text:_George Bateman
bar:EG0 text:_Elizabeth Guest
bar:HX0 text:_Hang Xu
bar:IJ0 text:_Isha Janbakhsh
bar:MZT0 text:_Minghao Zhang (Tiger)
bar:EW0 text:_Eline Welling
bar:JFP0 text:_Juan Fernandez Pottecher
bar:RC0 text:_Raphael Colman
bar:JF0 text:_James Farrell
bar:RDR0 text:Dr_Roberto Di Remigio
bar:TI0 text:_Tomohiro Ichiba
bar:RZ0 text:_Rhiannon Zarotiadis
bar:CF0 text:_Cesar Feniou
bar:TB0 text:_Tarik Benyahia
bar:BM0 text:_Benjamin Mokhtar
bar:MB0 text:_Moritz Baumgarten
bar:CK0 text:_Constance Kraay
bar:AB0 text:_Anna Bui
bar:ZW0 text:_Zian Wang
bar:RB0 text:_Raz Benson
bar:TS0 text:_Tom Sayer
bar:AP0 text:_Adam Prada
bar:JB0 text:_Jamie Buck
bar:KJ0 text:_Kris Jensen
bar:JE0 text:_Jiri Etrych
bar:IW0 text:_Ian Wu
bar:ZWR0 text:_Zhipeng Wang (Richard)
bar:DK0 text:_David Kovacs
bar:JL0 text:_Jimin Li
bar:TA0 text:_Toby Antipaas
bar:DR0 text:_Douglas Russell
bar:KL0 text:_King Lam
bar:MH0 text:_Max Howe
bar:MY0 text:_Motoki Yamano
bar:TH0 text:_Theo Hatcher
bar:MA0 text:_Miriam Al-Hadithi
bar:PY0 text:_Peter Yang

PlotData =
align:center textcolor:black fontsize:S shift:(0,-5)

# Current
bar:current text:Current_members $break
bar:AT0 from: 01/10/2010 till: 04/04/2025 $GroupLeader text:
bar:CL0 from: 01/10/2021 till: 04/04/2025 $PhD text:
bar:JT0 from: 01/10/2022 till: 04/04/2025 $PhD text:Joint with Forse group
bar:RP0 from: 25/04/2023 till: 04/04/2025 $PhD text:
bar:LCT0 from: 08/02/2022 till: 30/09/2022 $StudentVisitor text:
bar:LCT0 from: 01/10/2022 till: 30/09/2023 $MPhil text:
bar:LCT0 from: 01/10/2023 till: 04/04/2025 $PhD text:
bar:BC0 from: 12/07/2023 till: 01/09/2023 $Summer text:
bar:BC0 from: 01/10/2023 till: 30/09/2024 $PartIII text:
bar:BC0 from: 01/10/2024 till: 04/04/2025 $PhD text:
bar:RH0 from: 01/10/2024 till: 04/04/2025 $PhD text:
bar:DC0 from: 01/10/2024 till: 04/04/2025 $MPhil text:
bar:CW0 from: 01/10/2024 till: 04/04/2025 $PartIII text:

# Past
bar:past text:Past_members $break
bar:AZ0 from: 15/08/2012 till: 14/08/2013 $Postdoc text:
bar:WV0 from: 01/10/2011 till: 01/10/2015 $PhD text:Imperial College London
bar:WV0 from: 01/10/2015 till: 01/10/2016 $Postdoc text:Imperial College London
bar:JK0 from: 02/11/2015 till: 31/12/2017 $Postdoc text:
bar:SC0 from: 01/10/2016 till: 30/09/2018 $Postdoc text:
bar:DG0 from: 01/04/2022 till: 30/04/2024 $Postdoc text:
bar:RF0 from: 01/10/2014 till: 01/10/2017 $PhD text:
bar:CS0 from: 01/10/2014 till: 30/06/2015 $PartIII text:
bar:CS0 from: 05/09/2015 till: 30/09/2019 $PhD text:
bar:VN0 from: 05/10/2015 till: 31/10/2019 $PhD text:
bar:HB0 from: 01/07/2014 till: 30/09/2014 $Summer text:
bar:HB0 from: 01/07/2015 till: 30/09/2015 $Summer text:
bar:HB0 from: 26/09/2016 till: 30/09/2020 $PhD text:
bar:BCH0 from: 01/10/2016 till: 30/06/2017 $PartIII text:
bar:BCH0 from: 02/10/2017 till: 30/09/2021 $PhD text:
bar:DI0 from: 09/10/2017 till: 31/12/2021 $PhD text:
bar:FA0 from: 01/10/2018 till: 30/11/2022 $PhD text:
bar:MF0 from: 01/08/2017 till: 30/09/2017 $Summer text:
bar:MF0 from: 01/10/2018 till: 05/09/2022 $PhD text:
bar:KP0 from: 12/08/2019 till: 30/09/2019 $Summer text:
bar:KP0 from: 01/10/2019 till: 30/06/2020 $PartIII text:
bar:KP0 from: 01/10/2020 till: 27/09/2024 $PhD text:
bar:KP0 from: 27/09/2024 till: 14/04/2025 $Visitor text:
bar:HT0 from: 30/09/2016 till: 17/08/2017 $MPhil text:
bar:AC0 from: 05/10/2016 till: 30/08/2017 $MPhil text:
bar:AS0 from: 01/10/2020 till: 30/09/2021 $MPhil text:
bar:BZ0 from: 15/07/2021 till: 30/09/2021 $Summer text:
bar:BZ0 from: 01/10/2021 till: 30/08/2022 $MPhil text:
bar:HYLN0 from: 29/07/2019 till: 30/09/2019 $Summer text:
bar:HYLN0 from: 06/07/2020 till: 30/09/2020 $Summer text:
bar:HYLN0 from: 01/10/2020 till: 30/06/2021 $Undergrad text:
bar:HYLN0 from: 15/07/2021 till: 30/09/2021 $Summer text:
bar:HYLN0 from: 01/10/2021 till: 30/09/2022 $MPhil text:
bar:YS0 from: 01/10/2022 till: 11/08/2023 $MPhil text:
bar:LW0 from: 01/10/2023 till: 30/09/2024 $MPhil text:
bar:BS0 from: 04/10/2016 till: 30/06/2017 $PartIII text:
bar:SC1 from: 01/07/2016 till: 30/09/2016 $Summer text:
bar:SC1 from: 04/10/2016 till: 30/06/2017 $PartIII text:
bar:LB0 from: 02/10/2017 till: 30/06/2018 $PartIII text:
bar:AG0 from: 01/10/2018 till: 30/06/2019 $PartIII text:
bar:GB0 from: 01/10/2019 till: 30/06/2020 $PartIII text:
bar:EG0 from: 06/07/2020 till: 30/09/2020 $Summer text:
bar:EG0 from: 01/10/2020 till: 30/06/2021 $PartIII text:
bar:HX0 from: 06/07/2020 till: 30/09/2020 $Summer text:
bar:HX0 from: 01/10/2020 till: 30/06/2021 $PartIII text:
bar:IJ0 from: 01/10/2020 till: 30/06/2021 $PartIII text:
bar:MZT0 from: 02/08/2019 till: 30/09/2019 $Summer text:
bar:MZT0 from: 20/07/2020 till: 30/09/2020 $Summer text:
bar:MZT0 from: 01/10/2020 till: 30/06/2021 $PartIII text:
bar:EW0 from: 01/10/2022 till: 30/06/2023 $PartIII text:
bar:JFP0 from: 01/07/2022 till: 01/09/2022 $Summer text:
bar:JFP0 from: 01/10/2022 till: 30/06/2023 $PartIII text:
bar:RC0 from: 18/08/2015 till: 16/09/2015 $Visitor text:
bar:JF0 from: 01/11/2015 till: 17/10/2016 $Visitor text:
bar:RDR0 from: 05/01/2018 till: 02/02/2018 $Visitor text:
bar:TI0 from: 16/04/2018 till: 01/10/2018 $StudentVisitor text:
bar:RZ0 from: 04/03/2019 till: 29/07/2019 $StudentVisitor text:
bar:CF0 from: 08/02/2021 till: 31/08/2021 $StudentVisitor text:
bar:TB0 from: 08/02/2021 till: 31/08/2021 $StudentVisitor text:
bar:BM0 from: 12/04/2021 till: 30/09/2021 $StudentVisitor text:
bar:MB0 from: 16/09/2022 till: 01/05/2023 $StudentVisitor text:
bar:CK0 from: 06/07/2020 till: 30/09/2020 $Summer text:
bar:CK0 from: 01/10/2020 till: 30/09/2021 $Undergrad text:
bar:AB0 from: 15/07/2021 till: 30/09/2021 $Undergrad text:
bar:ZW0 from: 15/07/2021 till: 30/09/2021 $Undergrad text:
bar:RB0 from: 01/08/2016 till: 30/09/2016 $Summer text:
bar:TS0 from: 01/08/2016 till: 30/09/2016 $Summer text:
bar:AP0 from: 01/08/2017 till: 30/09/2017 $Summer text:
bar:JB0 from: 01/08/2017 till: 30/09/2017 $Summer text:
bar:KJ0 from: 07/08/2017 till: 29/09/2017 $Summer text:
bar:JE0 from: 25/06/2018 till: 04/09/2018 $Summer text:
bar:IW0 from: 07/08/2018 till: 30/09/2018 $Summer text:
bar:ZWR0 from: 03/09/2018 till: 01/10/2018 $Summer text:
bar:DK0 from: 29/07/2019 till: 30/09/2019 $Summer text:
bar:JL0 from: 06/07/2020 till: 30/09/2020 $Summer text:
bar:TA0 from: 06/07/2020 till: 30/09/2020 $Summer text:
bar:DR0 from: 18/07/2022 till: 01/09/2022 $Summer text:
bar:KL0 from: 18/07/2022 till: 01/09/2022 $Summer text:
bar:MH0 from: 18/07/2022 till: 01/09/2022 $Summer text:
bar:MY0 from: 18/07/2022 till: 01/09/2022 $Summer text:
bar:TH0 from: 18/07/2022 till: 01/09/2022 $Summer text:
bar:TH0 from: 24/07/2023 till: 01/09/2023 $Summer text:
bar:MA0 from: 10/07/2023 till: 01/09/2023 $Summer text:
bar:PY0 from: 10/07/2023 till: 01/09/2023 $Summer text:

# Guidelines
LineData =
layer:back width:0.1
from: $bigbang till: $bigcrunch atpos:113.0 color:even
from: $bigbang till: $bigcrunch atpos:126.7 color:odd
from: $bigbang till: $bigcrunch atpos:140.4 color:even
from: $bigbang till: $bigcrunch atpos:154.1 color:odd
from: $bigbang till: $bigcrunch atpos:167.8 color:even
from: $bigbang till: $bigcrunch atpos:181.5 color:odd
from: $bigbang till: $bigcrunch atpos:195.2 color:even
from: $bigbang till: $bigcrunch atpos:208.89999999999998 color:odd
from: $bigbang till: $bigcrunch atpos:222.6 color:even
from: $bigbang till: $bigcrunch atpos:236.3 color:odd
from: $bigbang till: $bigcrunch atpos:250.0 color:even
from: $bigbang till: $bigcrunch atpos:263.7 color:odd
from: $bigbang till: $bigcrunch atpos:277.4 color:even
from: $bigbang till: $bigcrunch atpos:291.1 color:odd
from: $bigbang till: $bigcrunch atpos:304.79999999999995 color:even
from: $bigbang till: $bigcrunch atpos:318.5 color:odd
from: $bigbang till: $bigcrunch atpos:332.2 color:even
from: $bigbang till: $bigcrunch atpos:345.9 color:odd
from: $bigbang till: $bigcrunch atpos:359.6 color:even
from: $bigbang till: $bigcrunch atpos:373.3 color:odd
from: $bigbang till: $bigcrunch atpos:387.0 color:even
from: $bigbang till: $bigcrunch atpos:400.7 color:odd
from: $bigbang till: $bigcrunch atpos:414.4 color:even
from: $bigbang till: $bigcrunch atpos:428.09999999999997 color:odd
from: $bigbang till: $bigcrunch atpos:441.79999999999995 color:even
from: $bigbang till: $bigcrunch atpos:455.5 color:odd
from: $bigbang till: $bigcrunch atpos:469.2 color:even
from: $bigbang till: $bigcrunch atpos:482.9 color:odd
from: $bigbang till: $bigcrunch atpos:496.59999999999997 color:even
from: $bigbang till: $bigcrunch atpos:510.29999999999995 color:odd
from: $bigbang till: $bigcrunch atpos:524.0 color:even
from: $bigbang till: $bigcrunch atpos:537.7 color:odd
from: $bigbang till: $bigcrunch atpos:551.4 color:even
from: $bigbang till: $bigcrunch atpos:565.0999999999999 color:odd
from: $bigbang till: $bigcrunch atpos:578.8 color:even
from: $bigbang till: $bigcrunch atpos:592.5 color:odd
from: $bigbang till: $bigcrunch atpos:606.2 color:even
from: $bigbang till: $bigcrunch atpos:619.9 color:odd
from: $bigbang till: $bigcrunch atpos:633.6 color:even
from: $bigbang till: $bigcrunch atpos:647.3 color:odd
from: $bigbang till: $bigcrunch atpos:661.0 color:even
from: $bigbang till: $bigcrunch atpos:674.6999999999999 color:odd
from: $bigbang till: $bigcrunch atpos:688.4 color:even
from: $bigbang till: $bigcrunch atpos:702.1 color:odd
from: $bigbang till: $bigcrunch atpos:715.8 color:even
from: $bigbang till: $bigcrunch atpos:729.5 color:odd
from: $bigbang till: $bigcrunch atpos:743.1999999999999 color:even
from: $bigbang till: $bigcrunch atpos:756.9 color:odd
from: $bigbang till: $bigcrunch atpos:770.5999999999999 color:even
from: $bigbang till: $bigcrunch atpos:784.3 color:odd
from: $bigbang till: $bigcrunch atpos:798.0 color:even
from: $bigbang till: $bigcrunch atpos:811.6999999999999 color:odd
from: $bigbang till: $bigcrunch atpos:825.4 color:even
from: $bigbang till: $bigcrunch atpos:839.0999999999999 color:odd
from: $bigbang till: $bigcrunch atpos:852.8 color:even
from: $bigbang till: $bigcrunch atpos:866.5 color:odd
from: $bigbang till: $bigcrunch atpos:880.1999999999999 color:even
from: $bigbang till: $bigcrunch atpos:893.9 color:odd
from: $bigbang till: $bigcrunch atpos:907.5999999999999 color:even
from: $bigbang till: $bigcrunch atpos:921.3 color:odd
from: $bigbang till: $bigcrunch atpos:935.0 color:even
from: $bigbang till: $bigcrunch atpos:948.6999999999999 color:odd
from: $bigbang till: $bigcrunch atpos:962.4 color:even
from: $bigbang till: $bigcrunch atpos:976.0999999999999 color:odd
from: $bigbang till: $bigcrunch atpos:989.8 color:even
from: $bigbang till: $bigcrunch atpos:1003.5 color:odd
from: $bigbang till: $bigcrunch atpos:1017.1999999999999 color:even
from: $bigbang till: $bigcrunch atpos:1030.9 color:odd
from: $bigbang till: $bigcrunch atpos:1044.6 color:even
from: $bigbang till: $bigcrunch atpos:1058.3 color:odd
from: $bigbang till: $bigcrunch atpos:1072.0 color:even
from: $bigbang till: $bigcrunch atpos:1085.6999999999998 color:odd

# Academic years
LineData =
layer:back color:gray width:0.1
at:01/10/2010
at:01/10/2011
at:01/10/2012
at:01/10/2013
at:01/10/2014
at:01/10/2015
at:01/10/2016
at:01/10/2017
at:01/10/2018
at:01/10/2019
at:01/10/2020
at:01/10/2021
at:01/10/2022
at:01/10/2023
at:01/10/2024
#######################################################
# Paste content of plotscript.txt until the above line.

# Updated on 9th April 2025 by Kripa Panchagnula.
# To edit, please refer to thom-fs-common/group/groupwiki.

</timeline>
</div>

Sandbox

2025-04-08T15:53:11Z

Ksp31:

Main Page

2025-04-08T13:55:08Z

Ksp31: /* To-do list for the Wiki */

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</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every <s>other</s> <s>Monday</s> <s>Friday</s> Thursday at <s>2pm</s> 3.30pm.

===Lent 2025===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|23rd January || INFORMAL || Chiara
|-
|30th January || Bence || Charlie
|-
|6th February || INFORMAL || Reka
|-
|13th February || Rowan || Lila
|-
|20th February || INFORMAL || Jack
|-
|27th February || Reka || Jack
|-
|6th March || Rowan || Reka
|-
|20th March || Charlie || Rowan and Chiara
|}

Link to Chemistry Room bookings [https://bookings.ch.cam.ac.uk/lecture-theatres/mrbs/ Here]

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2024-25===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 30 October 2024 || Bence || [https://www.nature.com/articles/s41586-023-06747-5 Solving olympiad geometry without human demonstrations]
|-
| 25 Nov 2024 || Jack || [https://doi.org/10.1103/PhysRevLett.106.040503 Sustained Quantum Coherence and Entanglement in the Avian Compass]
|-
| 22 Jan 2025 || Alex || [https://doi.org/10.1103/PhysRevE.110.064138 Nonuniversality for crossword puzzle percolation]
|-
| 13 Feb 2025 || Charlie || [https://doi.org/10.48550/arXiv.2102.02540 Starquakes in millisecond pulsars and gravitational waves emission]
|}

=Potentially Interesting Seminar Series=

* Leverhulme Centre for Life in the Universe Coffee Meetings https://www.lclu.cam.ac.uk/events/coffee-meetings
* Quantum Information Seminars https://lists.cam.ac.uk/sympa/subscribe/phy-cavendish-quantum-info?previous_action=info

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=

Past Summer Interns [[Past Summer Interns|here]].

===Summer availability:===

{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 20ex;" | '''Away'''
|-
|Chiara || 22-27 June (WATOC)
|-
|...|| ...
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Project_Ideas | Project Ideas]] =
Based on recent talks etc.

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:AJWT_group_photo_07_11_24_taken_by_Nathan_Pitt_University_of_Cambridge_R6B_8515_1_carousel.jpg|1000px|thumb|center]]
[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux

(NB you need to search a bit for the .deb file as the default download is a .rpm. As at 2025/01/25 I found '''slack-desktop-4.41.105-amd64.deb''')
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/scratch/<b>crsid</b>/slack/usr/lib/slack/slack %U
Icon=/scratch/<b>crsid</b>/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Run to register slack://foo.bar urls (necessary for browser integration with the desktop app)
xdg-mime default launch-slack.desktop x-scheme-handler/slack
# <li value="5"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- <s>A Pretty picture for the $wgLogo</s>

Main Page

2025-04-08T13:31:43Z

Ksp31: /* Lent 2025 */

Main Page

2025-04-08T13:31:37Z

Ksp31: /* Lent 2025 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every <s>other</s> <s>Monday</s> <s>Friday</s> Thursday at <s>2pm</s> 3.30pm.

===Lent 2025===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|23rd January || INFORMAL || Chiara
|-
|30th January || Bence || Charlie
|-
|6th February || INFORMAL || Reka
|-
|13th February || Rowan || Lila
|-
|20th February || INFORMAL || Jack
|-
|27th February || Reka || Jack
|-
|6th March || Rowan || Reka
|-
|20th March || Charlie || Rowan and Chiara.
|}

Link to Chemistry Room bookings [https://bookings.ch.cam.ac.uk/lecture-theatres/mrbs/ Here]

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2024-25===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 30 October 2024 || Bence || [https://www.nature.com/articles/s41586-023-06747-5 Solving olympiad geometry without human demonstrations]
|-
| 25 Nov 2024 || Jack || [https://doi.org/10.1103/PhysRevLett.106.040503 Sustained Quantum Coherence and Entanglement in the Avian Compass]
|-
| 22 Jan 2025 || Alex || [https://doi.org/10.1103/PhysRevE.110.064138 Nonuniversality for crossword puzzle percolation]
|-
| 13 Feb 2025 || Charlie || [https://doi.org/10.48550/arXiv.2102.02540 Starquakes in millisecond pulsars and gravitational waves emission]
|}

=Potentially Interesting Seminar Series=

* Leverhulme Centre for Life in the Universe Coffee Meetings https://www.lclu.cam.ac.uk/events/coffee-meetings
* Quantum Information Seminars https://lists.cam.ac.uk/sympa/subscribe/phy-cavendish-quantum-info?previous_action=info

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=

Past Summer Interns [[Past Summer Interns|here]].

===Summer availability:===

{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 20ex;" | '''Away'''
|-
|Chiara || 22-27 June (WATOC)
|-
|...|| ...
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Project_Ideas | Project Ideas]] =
Based on recent talks etc.

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:AJWT_group_photo_07_11_24_taken_by_Nathan_Pitt_University_of_Cambridge_R6B_8515_1_carousel.jpg|1000px|thumb|center]]
[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux

(NB you need to search a bit for the .deb file as the default download is a .rpm. As at 2025/01/25 I found '''slack-desktop-4.41.105-amd64.deb''')
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/scratch/<b>crsid</b>/slack/usr/lib/slack/slack %U
Icon=/scratch/<b>crsid</b>/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Run to register slack://foo.bar urls (necessary for browser integration with the desktop app)
xdg-mime default launch-slack.desktop x-scheme-handler/slack
# <li value="5"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Computer and Storage List

2025-04-01T09:10:51Z

Ksp31: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!info updated
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Software
!Purchased
|-
|carpathia
|379
|
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|<b>QChem</b>
For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|376
|
|Andreea
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 22.04
|
|
|
|2015
|-
|sandstone
|378
|01/04/2025
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 22.04.5
| GTX 750 Ti
|
|<b>QChem</b>
source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG11
|
|Lijun, [Theo, Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG03a
|
|Charlie [Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|<b>QChem</b>
export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|<b>QChem</b>
source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|360
|
|Reka, [Daniel, Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|<b>QChem</b>
. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|
|[Yi, Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|/scratch2 has 18Tb of scratch
|<b>QChem</b>
source /home/maf63/qchem-public/qcsetup

<b>MRCC</b>

source /home/ajwt3/code/mrcc
|2020
|-
|nemesis
|378
|
|Constance
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 20.04.5
|-
|chiron
|UG03A
|
|Chiara
|10
|Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz
|96GB
|Ubuntu 20.04
|
|
|
|2021
|-
|topaz
|360
|
|Lila
|8
|Intel Core i9-11900 2.5GHz 8 Core
|128GB
|Ubuntu 20.04
|NVIDIA GeForce RTX 3080
|
|
|2022
|-
|[https://www.ch.cam.ac.uk/computing/cerebro-compute-server cerebro]
|
|
|Alavi & Thom Groups
|12 x 20
16 x 3 [currently]
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|48GB
64GB
|Rocks 6.2 (CentOS 6.9) SLURM queuing
|
|
|<b>QChem</b>
source /home/hynl2/code/qchemsetup.bash

<b>MRCC</b>

source /home/ajwt3/code/mrcc_2023
|-
|[https://www.hpc.cam.ac.uk/high-performance-computing CSD3]
|
|
|University Tier-2
|Cacade Lake 56 x 672
76 x 544 Ice Lake
|2x Intel(R) Xeon Platinum CPU 8276 @ 2.20GHz
2x Intel(R) Xeon(R) Platinum 8368Q CPU @ 2.60GHz
|192 or 384GB
256 or 512GB
|Rocky Linux 8 SLURM queuing (36h max)
|
|Free core hours are available - talk to AJWT
|<b>QChem</b>
source /rds/project/ajwt3/rds-ajwt3-thom1/qchem_public/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/nest-compute-server nest]
|
|
|CUC3 Group cluster
|40 x 20
|2x Cascade Lake Intel(R) Xeon Gold CPU 6248 @ 2.50GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|
|
|<b>QChem</b>
source /home/maf63/code/qcsetup.sh
|-
|[https://www.ch.cam.ac.uk/computing/rogue-gpu-server rogue]
|
|
|CUC3 Group cluster
|(8 nVidia V100 + 32 CPU) x 2
|2x Sky Lake Intel(R) Xeon Gold CPU 6130 @ 2.10GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|-
|[https://www.archer2.ac.uk/ archer-2]
|
|National Tier-1 Supercomputer
| 128 x 5848
|2 x AMD EPYC Zen2 (Rome) 64-core CPUs @ 2.2GHz
|256GB and 512GB
|
|}

Machine status can be monitored at : https://hobbit.ch.cam.ac.uk/xymon/workstations/workstationsThom/workstationsThomLinux/

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

NB the number of 'processors' may be different from the number of cores owing to hyperthreading. The 'cpu cores' value is the one to take for single CPU machines.

[http://hobbit.ch.cam.ac.uk/xymon/workstations/workstationsThom/workstationsThomLinux/ Hobbit] may also have some useful information.

[https://www.ch.cam.ac.uk/computing/group-computer-representatives Group computer reps] can manage group entries in the department [https://chemdb.ch.cam.ac.uk/hotwire3/chemistry/ database] and there's a [https://apps.ch.cam.ac.uk/computer-reps/group-computers.php hardware inventory] and a [https://apps.ch.cam.ac.uk/space-management/space-report.php space report] too.

=Storage=
A common cause of running out of storage on your workstation is anaconda which puts stuff in /home. This can be safely moved to /scratch and a symbolic link.

cd $HOME
mv .conda /scratch/$USER
ln -s /scratch/$USER/.conda

To find out how much storage you have available and what files/directories are taking up space, the following commands are useful. The first one shows how much space is used/available on each partition, and the second shows the size of everything in the current directory.

df -h
du -sh * | sort -hr

If you can't find any fiiles in /scratch/$USER/thom-fs-common you might need to authenticate with a password. You can do this if you are using key authentication with

ssh -oPubkeyauthentication=no localhost

{| class="wikitable"
!Name
!Type
!Amount
!Notes
|-
|/home/$USER
|local disk
|~50Gb per person (changed to ~100GB after upgrade to 20.04)
|Backed up with snapshots - Theory RIG policy
|-
|/scratch/$USER
|local disk
|~1Tb+ depending on computer
|NOT BACKED UP
|-
|/scratch/$USER/thom-fs-nethome
/scratch/$USER/thom-fs-common
|Chemistry network drive
|2.3T
|Backed up with snapshots - Theory RIG policy
|-
|/scratch/$USER/ifs-thom
|Former UIS Mount - now located at /scratch/$USER/thom-fs/old-ifs-thom
|6144Gb
|Read-only
|-
|/scratch/$USER/theory-fs
|Chemistry network drive
|~50Gb per person
|Backed up with snapshots - Theory RIG policy
|-
|cerebro:/filestore
|Local RAID array
|36950Gb
|Backed up with snapshots - Theory RIG policy
|}

=Theory RIG backup policy=
From https://www.ch.cam.ac.uk/computing/managed-linux-workstations-faq

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

then, about one backup per month for the previous few months

Main Page

2025-02-19T12:20:48Z

Ksp31: /* Group Meetings */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every <s>other</s> <s>Monday</s> <s>Friday</s> Thursday at <s>2pm</s> 3.30pm.

===Lent 2025===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|23rd January || INFORMAL || Chiara
|-
|30th January || Bence || Charlie
|-
|6th February || INFORMAL || Reka
|-
|13th February || Rowan || Lila
|-
|20th February || INFORMAL || Jack
|-
|27th February || Reka ||
|-
|6th March || INFORMAL ||
|-
|20th March || Charlie ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2024-25===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 30 October 2024 || Bence || [https://www.nature.com/articles/s41586-023-06747-5 Solving olympiad geometry without human demonstrations]
|-
| 25 Nov 2024 || Jack || [https://doi.org/10.1103/PhysRevLett.106.040503 Sustained Quantum Coherence and Entanglement in the Avian Compass]
|-
| 22 Jan 2025 || Alex || [https://doi.org/10.1103/PhysRevE.110.064138 Nonuniversality for crossword puzzle percolation]
|-
| 13 Feb 2025 || Charlie || [https://doi.org/10.48550/arXiv.2102.02540 Starquakes in millisecond pulsars and gravitational waves emission]
|}

=Potentially Interesting Seminar Series=

* Leverhulme Centre for Life in the Universe Coffee Meetings https://www.lclu.cam.ac.uk/events/coffee-meetings
* Quantum Information Seminars https://lists.cam.ac.uk/sympa/subscribe/phy-cavendish-quantum-info?previous_action=info

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=

Past Summer Interns [[Past Summer Interns|here]].

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Project_Ideas | Project Ideas]] =
Based on recent talks etc.

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:AJWT_group_photo_07_11_24_taken_by_Nathan_Pitt_University_of_Cambridge_R6B_8515_1_carousel.jpg|1000px|thumb|center]]
[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux

(NB you need to search a bit for the .deb file as the default download is a .rpm. As at 2025/01/25 I found '''slack-desktop-4.41.105-amd64.deb''')
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/scratch/<b>crsid</b>/slack/usr/lib/slack/slack %U
Icon=/scratch/<b>crsid</b>/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Run to register slack://foo.bar urls (necessary for browser integration with the desktop app)
xdg-mime default launch-slack.desktop x-scheme-handler/slack
# <li value="5"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Group Meetings

2025-02-19T12:20:36Z

Ksp31: /* Past Group Meetings */

=Past Group Meetings=

===Michaelmas 2024===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|3rd October || INFORMAL || Alex
|-
|24th October || Alex || Jack
|-
|31st October || INFORMAL || Charlie
|-
|7th November || Andreea || Lila
|-
|14th November || INFORMAL || Bence
|-
|21st November || Hugh || Kripa
|-
|28th November || INFORMAL || Reka
|-
|5th December || Rowan || Charlie
|}

===Easter 2024===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th April || Jack || Alex
|-
|9th May || Chiara || Jack
|-
|23th May || Lijun || Lijun
|-
|6th June || Lila || Kripa
|}

===Lent 2024===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th January || Alex || Lila
|-
|8th February || Kripa || Bence
|-
|22th February || Daniel || Jack
|-
|7th March || Bence || Kripa
|}

===Michaelmas 2023===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|13th October || Lila || Chiara
|-
|27th October || Rowan || Rowan
|-
|10th November || Hugh || Kripa
|-
|24th November || Chiara || Alex (Mince Pies)
|}

===Summer 2023===
{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|2nd August || Summer Interns || Lila
|-
|21st August || Jack || Andreea
|-
|1st September || Summer Interns || Miriam
|-
|18th September || Kripa || Alex
|}

===Easter 2023===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|1st May || Chiara || Andreea
|-
|15th May || Lila || Kripa
|-
|26th May || Yi Sun || Jack
|-
|12th June || Daniel || Alex
|}

===Lent 2023===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|23rd January || Kripa || Moritz
|-
|6th February || Jack || Alex
|-
|20th February || Andreea || Juan
|-
|6th March || Eline + Juan || Kripa
|}

===Michaelmas 2022===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|10th October || Yi Sun || Kripa
|-
|24th October || Chiara|| Andreea
|-
|7th November || Lila || Eline
|-
|21st November || Moritz || Alex (Mince Pies)
|}

===Summer 2022===
{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th July || WATOC Review & IPLU Discussion ||
|-
|8th August || Brian || Andreea
|-
|30th August || Nick || Daniel
|-
|12th September|| Interns || Alex
|}

===Easter 2022===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|9th May || Lila || Andreea
|-
|23rd May || Daniel || Brian
|-
|13th June|| Benjamin || Kripa
|-
|20th June|| Kripa || Lila
|}

===Lent 2022===
{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|24th January || Fabio || Andreea
|-
|7th February || Andreea || Kripa
|-
|21st February|| Nick || Brian
|-
|21st March|| Brian || Chiara
|}
=== Michaelmas 2021===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|4th October|| INFORMAL ||
|-
|18th October || Nick || Fabio
|-
|1st November || Kripa || Andreea
|-
|15th November|| Chiara || Nick
|-
|29th November|| David || Kripa
|}

===Summer 2021===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|12th July 2021 || INFORMAL ||
|-
|20th July 2021 || INFORMAL ||
|-
|27th July 2021 || - ||
|-
|3rd August 2021 || Cesar & Tarik || Chelsea Buns
|-
|9th August 2021 || Constance || Brian
|-
|16th August 2021 || INFORMAL ||
|-
|23rd August 2021|| Benjamin || Andreea
|-
|30th August 2021|| INFORMAL ||
|-
|6th September 2021 || Arta || Kripa
|-
|13th September 2021 || Anna, Brian & Zian|| Nick
|}
===Easter 2021===

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|19th April 2021 || INFORMAL ||
|-
|26th April 2021 || INFORMAL ||
|-
|3rd May 2021 || INFORMAL ||
|-
|10th May 2021 || Andreea || Fruit based
|-
|17th May 2021 || INFORMAL ||
|-
|24th May 2021 || Nick Blunt || Cheesecake
|-
|31st May 2021|| INFORMAL ||
|-
|7th June 2021|| Fabio|| (Boston) Cream Pie
|-
|14th June 2021|| Benjamin ||
|}

==Lent 2021==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|18th January 2021 || INFORMAL || -
|-
|25th January 2021 || INFORMAL || Shortbread
|-
|1st February 2021 || Bang || Non-trivial Symmetry Element
|-
|8th February 2021 || INFORMAL ||
|-
|15th February 2021 || César and Tarik || Carrot Cake
|-
|22th February 2021 || INFORMAL ||
|-
|1st March 2021|| Kripa || Doughnuts (Krispy Kreme)
|-
|8th March 2021|| Hang & Tiger (Part III) || Date Loaf
|-
|15th March 2021|| Elizabeth & Isha (Part III) || Mother's Choice
|}
==Michaelmas 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|12th October 2020 || Andreea || Kripa
|-
|19th October 2020 || INFORMAL || Andreea
|-
|26th October 2020 || Fabio || Bang
|-
|2nd November 2020 || INFORMAL || Fabio
|-
|9th November 2020 || INFORMAL|| Bang
|-
|16th November 2020 || Kripa || Elizabeth
|-
|23rd November 2020|| Arta || Arta
|-
|30th November 2020 || INFORMAL || Andreea
|}

==Summer 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake & Recipe'''
|-
|20th July 2020 || Nick || [https://en.wikipedia.org/wiki/Kiev_cake Kiev cake]
|-
|10th August 2020 || Hugh || Crumble
|-
|24th August 2020 || Constance, Hang, Jimin||
|-
|7 September 2020|| Elizabeth, (Nick), Tiger, Toby ||
|}

==Easter 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake & Recipe'''
|-
|4th May 2020 || Andreea || Tiramisu
|-
|18th May 2020 || David || Carrot
|-
|1st June 2020 || Hugh || Chocolate & Ginger
|-
|15 June 2020|| Bang || Salted Caramel
|}

==Lent 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|27th January 2020 || Bang || Alex
|-
|10th February 2020 || Alex || Kripa & George
|-
|24th February 2020 || Fabio || Bang
|-
|10th March 2020|| Kripa & George || Andreea
|}

==Michaelmas 2019==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|21st October 2019 || Fabio || Hugh
|-
|4th November 2019 || Andreea || David
|-
|18th November 2019 || David || Andreea
|-
|2nd December 2019 || Hugh || Fabio
|}

==Summer Vacation 2019==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|22nd July 2019 || Rhiannon || David
|-
|19th August 2019 || Hugh || Fabio
|-
|2nd September 2019 || Bang || Summer Students
|-
|16th September 2019 || Summer Students || Alex
|}

==Easter Term 2019==

{|
|'''Date''' || '''Talk''' ||| '''Cake'''
|-
|2nd May 2019 || Rhiannon || Fabio
|-
|13th May 2019 || David || Bang
|-
|27th May 2019|| Andreea || Alex
|-
|10th June 2019 || Fabio || Rhiannon
|}

==Easter Vacation 2019==

{|
|'''Date''' || '''Talk''' ||| '''Cake'''
|-
|8th April 2019 || The Boss || Andreea
|}

==Lent Term 2019==

{|
|'''Date''' || '''Talk''' ||| '''Cake'''
|-
|7th January 2019 || Hugh || Alex
|-
|21st January 2019 || Bang || Andreea
|-
|4th February 2019 || Verena || Alex G
|-
|18th February 2019 || Charlie || Alex
|-
|4th March 2019 || Alex G || Verena
|}

==Michaelmas Term 2018==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|1st October 2018 || Bang ||
|-
|15th October 2018 || Alex T || Verena
|-
|30th October 2018 || David || Alex
|-
|12th November 2018 || [Alex T away]
|-
|26th November 2018 ||
|}

==Long Vacation 2018==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|'''3.30pm Tue''' 28th August 2018 || Jirka || Bang
|-
|Mon 10th September 2018 || Verena & Charlie || Alex
|-
|'''Tue''' 25th September 2018 || Richard & Ian
|}

==Easter Term 2018==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|7th May 2018 || Letitia - Alex and Sav no longer in Crete that day. || Alex to bring Greek gifts
|-
|14th May 2018 || David
|-
|4th June 2018 || Bang
|-
|11th June 2018 || Verena (cancelled)
|}

==Lent Term 2018==
{|
|+
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|22nd January 2018 || Letitia || Bang
|-
|5th February 2018 || Alex ||
|-
|19th February 2018 || Flash talks || Alex
|-
|5th March 2018 || [Electronic Structure meeting]
|-
|19th March 2018 || [Scientific Computing Day]
|}

==Michaelmas Term 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|2nd October || Kris || Verena
|-
|16th October || Sav || Charlie
|-
|30th October || David || Hugh?
|-
|13th November || Bang || ?
|-
|27th November || Jonathan || Alex T
|-
|11th December || Hugh || Sav
|}

==Research Period 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|8th August || ? || ?
|-
|22nd August || Adam/Andreea/Jamie/Kris || ?
|-
|5th September || Charlie & Hugh || ?
|-
|19th September || Verena || Kris
|}

==Easter Term 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|24th April || Sav || Alex T
|-
|8th May || Hugh || Sav
|-
|30th May|| Charlie || ?
|-
|12th June || Verena || ?
|}

==Lent Term 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|9th January || Sav || Charlie & Verena
|-
|23rd January || Henry & Alex C || Ruth
|-
|13th February || Choi & Ben || Alex T
|-
|27th February || Bang || Alex C
|-
|13th March || Verena || Ben
|}

==Michaelmas Term 2016==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|10th October 2016 || Charlie || Hugh
|-
|24th October 2016 || Verena || Sav
|-
|7th November 2016 || Choi || Alex
|-
|21st November 2016 || Ruth || Bang & Verena
|-
|5th December 2016 || [AJWT away]
|-
|19th December 2016 || Hugh || Choi
|}

==Research Period 2016==
{|
|+
|'''Date''' || '''Mini-talk'''
|-
|15th August 2016 || Jonathan
|-
|30th August 2016 || Charlie
|-
|12th September 2016 || James
|-
|26th September 2016 || CANCELLED
|}

Main Page

2025-02-19T12:20:21Z

Ksp31: /* Group Meetings */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every <s>other</s> <s>Monday</s> <s>Friday</s> Thursday at <s>2pm</s> 3.30pm.

===Lent 2025===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|23rd January || INFORMAL || Chiara
|-
|30th January || Bence || Charlie
|-
|6th February || INFORMAL || Reka
|-
|13th February || Rowan || Lila
|-
|20th February || INFORMAL || Jack
|-
|27th February || Reka ||
|-
|6th March || INFORMAL ||
|-
|20th March || Charlie ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2024-25===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 30 October 2024 || Bence || [https://www.nature.com/articles/s41586-023-06747-5 Solving olympiad geometry without human demonstrations]
|-
| 25 Nov 2024 || Jack || [https://doi.org/10.1103/PhysRevLett.106.040503 Sustained Quantum Coherence and Entanglement in the Avian Compass]
|-
| 22 Jan 2025 || Alex || [https://doi.org/10.1103/PhysRevE.110.064138 Nonuniversality for crossword puzzle percolation]
|-
| 13 Feb 2025 || Charlie || [https://doi.org/10.48550/arXiv.2102.02540 Starquakes in millisecond pulsars and gravitational waves emission]
|}

=Potentially Interesting Seminar Series=

* Leverhulme Centre for Life in the Universe Coffee Meetings https://www.lclu.cam.ac.uk/events/coffee-meetings
* Quantum Information Seminars https://lists.cam.ac.uk/sympa/subscribe/phy-cavendish-quantum-info?previous_action=info

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=

Past Summer Interns [[Past Summer Interns|here]].

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Project_Ideas | Project Ideas]] =
Based on recent talks etc.

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:AJWT_group_photo_07_11_24_taken_by_Nathan_Pitt_University_of_Cambridge_R6B_8515_1_carousel.jpg|1000px|thumb|center]]
[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux

(NB you need to search a bit for the .deb file as the default download is a .rpm. As at 2025/01/25 I found '''slack-desktop-4.41.105-amd64.deb''')
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/scratch/<b>crsid</b>/slack/usr/lib/slack/slack %U
Icon=/scratch/<b>crsid</b>/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Run to register slack://foo.bar urls (necessary for browser integration with the desktop app)
xdg-mime default launch-slack.desktop x-scheme-handler/slack
# <li value="5"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2025-02-19T12:19:50Z

Ksp31: /* Group List */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every <s>other</s> <s>Monday</s> <s>Friday</s> Thursday at <s>2pm</s> 3.30pm.

===Michaelmas 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|3rd October || INFORMAL || Alex
|-
|24th October || Alex || Jack
|-
|31st October || INFORMAL || Charlie
|-
|7th November || Andreea || Lila
|-
|14th November || INFORMAL || Bence
|-
|21st November || Hugh || Kripa
|-
|28th November || INFORMAL || Reka
|-
|5th December || Rowan || Charlie
|}

===Lent 2025===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|23rd January || INFORMAL || Chiara
|-
|30th January || Bence || Charlie
|-
|6th February || INFORMAL || Reka
|-
|13th February || Rowan || Lila
|-
|20th February || INFORMAL || Jack
|-
|27th February || Reka ||
|-
|6th March || INFORMAL ||
|-
|20th March || Charlie ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2024-25===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 30 October 2024 || Bence || [https://www.nature.com/articles/s41586-023-06747-5 Solving olympiad geometry without human demonstrations]
|-
| 25 Nov 2024 || Jack || [https://doi.org/10.1103/PhysRevLett.106.040503 Sustained Quantum Coherence and Entanglement in the Avian Compass]
|-
| 22 Jan 2025 || Alex || [https://doi.org/10.1103/PhysRevE.110.064138 Nonuniversality for crossword puzzle percolation]
|-
| 13 Feb 2025 || Charlie || [https://doi.org/10.48550/arXiv.2102.02540 Starquakes in millisecond pulsars and gravitational waves emission]
|}

=Potentially Interesting Seminar Series=

* Leverhulme Centre for Life in the Universe Coffee Meetings https://www.lclu.cam.ac.uk/events/coffee-meetings
* Quantum Information Seminars https://lists.cam.ac.uk/sympa/subscribe/phy-cavendish-quantum-info?previous_action=info

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=

Past Summer Interns [[Past Summer Interns|here]].

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Project_Ideas | Project Ideas]] =
Based on recent talks etc.

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:AJWT_group_photo_07_11_24_taken_by_Nathan_Pitt_University_of_Cambridge_R6B_8515_1_carousel.jpg|1000px|thumb|center]]
[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux

(NB you need to search a bit for the .deb file as the default download is a .rpm. As at 2025/01/25 I found '''slack-desktop-4.41.105-amd64.deb''')
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/scratch/<b>crsid</b>/slack/usr/lib/slack/slack %U
Icon=/scratch/<b>crsid</b>/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Run to register slack://foo.bar urls (necessary for browser integration with the desktop app)
xdg-mime default launch-slack.desktop x-scheme-handler/slack
# <li value="5"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2025-02-19T12:18:31Z

Ksp31: /* Installing Slack on department machines */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every <s>other</s> <s>Monday</s> <s>Friday</s> Thursday at <s>2pm</s> 3.30pm.

===Michaelmas 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|3rd October || INFORMAL || Alex
|-
|24th October || Alex || Jack
|-
|31st October || INFORMAL || Charlie
|-
|7th November || Andreea || Lila
|-
|14th November || INFORMAL || Bence
|-
|21st November || Hugh || Kripa
|-
|28th November || INFORMAL || Reka
|-
|5th December || Rowan || Charlie
|}

===Lent 2025===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|23rd January || INFORMAL || Chiara
|-
|30th January || Bence || Charlie
|-
|6th February || INFORMAL || Reka
|-
|13th February || Rowan || Lila
|-
|20th February || INFORMAL || Jack
|-
|27th February || Reka ||
|-
|6th March || INFORMAL ||
|-
|20th March || Charlie ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2024-25===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 30 October 2024 || Bence || [https://www.nature.com/articles/s41586-023-06747-5 Solving olympiad geometry without human demonstrations]
|-
| 25 Nov 2024 || Jack || [https://doi.org/10.1103/PhysRevLett.106.040503 Sustained Quantum Coherence and Entanglement in the Avian Compass]
|-
| 22 Jan 2025 || Alex || [https://doi.org/10.1103/PhysRevE.110.064138 Nonuniversality for crossword puzzle percolation]
|-
| 13 Feb 2025 || Charlie || [https://doi.org/10.48550/arXiv.2102.02540 Starquakes in millisecond pulsars and gravitational waves emission]
|}

=Potentially Interesting Seminar Series=

* Leverhulme Centre for Life in the Universe Coffee Meetings https://www.lclu.cam.ac.uk/events/coffee-meetings
* Quantum Information Seminars https://lists.cam.ac.uk/sympa/subscribe/phy-cavendish-quantum-info?previous_action=info

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=

Past Summer Interns [[Past Summer Interns|here]].

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Project_Ideas | Project Ideas]] =
Based on recent talks etc.

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:AJWT_group_photo_07_11_24_taken_by_Nathan_Pitt_University_of_Cambridge_R6B_8515_1_carousel.jpg]]
[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux

(NB you need to search a bit for the .deb file as the default download is a .rpm. As at 2025/01/25 I found '''slack-desktop-4.41.105-amd64.deb''')
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/scratch/<b>crsid</b>/slack/usr/lib/slack/slack %U
Icon=/scratch/<b>crsid</b>/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Run to register slack://foo.bar urls (necessary for browser integration with the desktop app)
xdg-mime default launch-slack.desktop x-scheme-handler/slack
# <li value="5"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-10-31T17:01:37Z

Ksp31: /* Michaelmas 2024 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every <s>other</s> <s>Monday</s> <s>Friday</s> Thursday at <s>2pm</s> 3.30pm.

===Michaelmas 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|3rd October || INFORMAL ||
|-
|24th October || Alex || Jack
|-
|31st October || INFORMAL || Charlie
|-
|7th November || Andreea || Lila
|-
|14th November || INFORMAL || Bence
|-
|21st November || Hugh ||
|-
|28th November || INFORMAL ||
|-
|5th December || Rowan ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|-
| 13 Feb 2024 || Bence || [https://arxiv.org/pdf/2203.16580 What’s for Lunch? A systematic ordering of foods in the Soup-Salad-Sandwich phase space]
|-
| 12 Mar 2024 || Alex || [https://iopscience.iop.org/article/10.3847/2041-8213/acf577/pdf Carbon-bearing Molecules in a Possible Hycean Atmosphere]
|}

=Potentially Interesting Seminar Series=

* Leverhulme Centre for Life in the Universe Coffee Meetings https://www.lclu.cam.ac.uk/events/coffee-meetings
* Quantum Information Seminars https://lists.cam.ac.uk/sympa/subscribe/phy-cavendish-quantum-info?previous_action=info

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=

Past Summer Interns [[Past Summer Interns|here]].

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Project_Ideas | Project Ideas]] =
Based on recent talks etc.

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Run to register slack://foo.bar urls (necessary for browser integration with the desktop app)
xdg-mime default launch-slack.desktop x-scheme-handler/slack
# <li value="5"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-09-09T10:30:20Z

Ksp31: /* Michaelmas 2024 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every <s>other</s> <s>Monday</s> <s>Friday</s> Thursday at <s>2pm</s> 3.30pm.

===Michaelmas 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|3rd October || INFORMAL ||
|-
|24th October || ||
|-
|31st October || INFORMAL ||
|-
|7th November || Andreea ||
|-
|14th November || INFORMAL ||
|-
|21st November || Hugh ||
|-
|28th November || INFORMAL ||
|-
|5th December || Rowan ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|-
| 13 Feb 2024 || Bence || [https://arxiv.org/pdf/2203.16580 What’s for Lunch? A systematic ordering of foods in the Soup-Salad-Sandwich phase space]
|-
| 12 Mar 2024 || Alex || [https://iopscience.iop.org/article/10.3847/2041-8213/acf577/pdf Carbon-bearing Molecules in a Possible Hycean Atmosphere]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=

Past Summer Interns [[Past Summer Interns|here]].

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-08-12T11:17:01Z

Ksp31: /* Michaelmas 2024 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every <s>other</s> <s>Monday</s> <s>Friday</s> Thursday at <s>2pm</s> 3.30pm.

===Michaelmas 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|3rd October || INFORMAL ||
|-
|24th October || ||
|-
|31st October || INFORMAL ||
|-
|7th November || ||
|-
|14th November || INFORMAL ||
|-
|21st November || ||
|-
|28th November || INFORMAL ||
|-
|5th December || ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|-
| 13 Feb 2024 || Bence || [https://arxiv.org/pdf/2203.16580 What’s for Lunch? A systematic ordering of foods in the Soup-Salad-Sandwich phase space]
|-
| 12 Mar 2024 || Alex || [https://iopscience.iop.org/article/10.3847/2041-8213/acf577/pdf Carbon-bearing Molecules in a Possible Hycean Atmosphere]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=

Past Summer Interns [[Past Summer Interns|here]].

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-08-12T11:16:49Z

Ksp31: /* Michaelmas 2024 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every <s>other</s> <s>Monday</s> <s>Friday</s> Thursday at <s>2pm</s> 3.30pm.

===Michaelmas 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|3rd October || INFORMAL ||
|-
|24th October || ||
|-
|31st October || INFORMAL ||
|-
|7th November || ||
|-
|14th November II INFORMAL ||
|-
|21st November || ||
|-
|28th November || INFORMAL ||
|-
|5th December || ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|-
| 13 Feb 2024 || Bence || [https://arxiv.org/pdf/2203.16580 What’s for Lunch? A systematic ordering of foods in the Soup-Salad-Sandwich phase space]
|-
| 12 Mar 2024 || Alex || [https://iopscience.iop.org/article/10.3847/2041-8213/acf577/pdf Carbon-bearing Molecules in a Possible Hycean Atmosphere]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=

Past Summer Interns [[Past Summer Interns|here]].

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Group Meetings

2024-08-12T11:13:17Z

Ksp31: /* Past Group Meetings */

=Past Group Meetings=

===Easter 2024===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th April || Jack || Alex
|-
|9th May || Chiara || Jack
|-
|23th May || Lijun || Lijun
|-
|6th June || Lila || Kripa
|}

===Lent 2024===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th January || Alex || Lila
|-
|8th February || Kripa || Bence
|-
|22th February || Daniel || Jack
|-
|7th March || Bence || Kripa
|}

===Michaelmas 2023===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|13th October || Lila || Chiara
|-
|27th October || Rowan || Rowan
|-
|10th November || Hugh || Kripa
|-
|24th November || Chiara || Alex (Mince Pies)
|}

===Summer 2023===
{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|2nd August || Summer Interns || Lila
|-
|21st August || Jack || Andreea
|-
|1st September || Summer Interns || Miriam
|-
|18th September || Kripa || Alex
|}

===Easter 2023===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|1st May || Chiara || Andreea
|-
|15th May || Lila || Kripa
|-
|26th May || Yi Sun || Jack
|-
|12th June || Daniel || Alex
|}

===Lent 2023===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|23rd January || Kripa || Moritz
|-
|6th February || Jack || Alex
|-
|20th February || Andreea || Juan
|-
|6th March || Eline + Juan || Kripa
|}

===Michaelmas 2022===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|10th October || Yi Sun || Kripa
|-
|24th October || Chiara|| Andreea
|-
|7th November || Lila || Eline
|-
|21st November || Moritz || Alex (Mince Pies)
|}

===Summer 2022===
{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th July || WATOC Review & IPLU Discussion ||
|-
|8th August || Brian || Andreea
|-
|30th August || Nick || Daniel
|-
|12th September|| Interns || Alex
|}

===Easter 2022===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|9th May || Lila || Andreea
|-
|23rd May || Daniel || Brian
|-
|13th June|| Benjamin || Kripa
|-
|20th June|| Kripa || Lila
|}

===Lent 2022===
{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|24th January || Fabio || Andreea
|-
|7th February || Andreea || Kripa
|-
|21st February|| Nick || Brian
|-
|21st March|| Brian || Chiara
|}
=== Michaelmas 2021===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|4th October|| INFORMAL ||
|-
|18th October || Nick || Fabio
|-
|1st November || Kripa || Andreea
|-
|15th November|| Chiara || Nick
|-
|29th November|| David || Kripa
|}

===Summer 2021===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|12th July 2021 || INFORMAL ||
|-
|20th July 2021 || INFORMAL ||
|-
|27th July 2021 || - ||
|-
|3rd August 2021 || Cesar & Tarik || Chelsea Buns
|-
|9th August 2021 || Constance || Brian
|-
|16th August 2021 || INFORMAL ||
|-
|23rd August 2021|| Benjamin || Andreea
|-
|30th August 2021|| INFORMAL ||
|-
|6th September 2021 || Arta || Kripa
|-
|13th September 2021 || Anna, Brian & Zian|| Nick
|}
===Easter 2021===

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|19th April 2021 || INFORMAL ||
|-
|26th April 2021 || INFORMAL ||
|-
|3rd May 2021 || INFORMAL ||
|-
|10th May 2021 || Andreea || Fruit based
|-
|17th May 2021 || INFORMAL ||
|-
|24th May 2021 || Nick Blunt || Cheesecake
|-
|31st May 2021|| INFORMAL ||
|-
|7th June 2021|| Fabio|| (Boston) Cream Pie
|-
|14th June 2021|| Benjamin ||
|}

==Lent 2021==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|18th January 2021 || INFORMAL || -
|-
|25th January 2021 || INFORMAL || Shortbread
|-
|1st February 2021 || Bang || Non-trivial Symmetry Element
|-
|8th February 2021 || INFORMAL ||
|-
|15th February 2021 || César and Tarik || Carrot Cake
|-
|22th February 2021 || INFORMAL ||
|-
|1st March 2021|| Kripa || Doughnuts (Krispy Kreme)
|-
|8th March 2021|| Hang & Tiger (Part III) || Date Loaf
|-
|15th March 2021|| Elizabeth & Isha (Part III) || Mother's Choice
|}
==Michaelmas 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|12th October 2020 || Andreea || Kripa
|-
|19th October 2020 || INFORMAL || Andreea
|-
|26th October 2020 || Fabio || Bang
|-
|2nd November 2020 || INFORMAL || Fabio
|-
|9th November 2020 || INFORMAL|| Bang
|-
|16th November 2020 || Kripa || Elizabeth
|-
|23rd November 2020|| Arta || Arta
|-
|30th November 2020 || INFORMAL || Andreea
|}

==Summer 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake & Recipe'''
|-
|20th July 2020 || Nick || [https://en.wikipedia.org/wiki/Kiev_cake Kiev cake]
|-
|10th August 2020 || Hugh || Crumble
|-
|24th August 2020 || Constance, Hang, Jimin||
|-
|7 September 2020|| Elizabeth, (Nick), Tiger, Toby ||
|}

==Easter 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake & Recipe'''
|-
|4th May 2020 || Andreea || Tiramisu
|-
|18th May 2020 || David || Carrot
|-
|1st June 2020 || Hugh || Chocolate & Ginger
|-
|15 June 2020|| Bang || Salted Caramel
|}

==Lent 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|27th January 2020 || Bang || Alex
|-
|10th February 2020 || Alex || Kripa & George
|-
|24th February 2020 || Fabio || Bang
|-
|10th March 2020|| Kripa & George || Andreea
|}

==Michaelmas 2019==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|21st October 2019 || Fabio || Hugh
|-
|4th November 2019 || Andreea || David
|-
|18th November 2019 || David || Andreea
|-
|2nd December 2019 || Hugh || Fabio
|}

==Summer Vacation 2019==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|22nd July 2019 || Rhiannon || David
|-
|19th August 2019 || Hugh || Fabio
|-
|2nd September 2019 || Bang || Summer Students
|-
|16th September 2019 || Summer Students || Alex
|}

==Easter Term 2019==

{|
|'''Date''' || '''Talk''' ||| '''Cake'''
|-
|2nd May 2019 || Rhiannon || Fabio
|-
|13th May 2019 || David || Bang
|-
|27th May 2019|| Andreea || Alex
|-
|10th June 2019 || Fabio || Rhiannon
|}

==Easter Vacation 2019==

{|
|'''Date''' || '''Talk''' ||| '''Cake'''
|-
|8th April 2019 || The Boss || Andreea
|}

==Lent Term 2019==

{|
|'''Date''' || '''Talk''' ||| '''Cake'''
|-
|7th January 2019 || Hugh || Alex
|-
|21st January 2019 || Bang || Andreea
|-
|4th February 2019 || Verena || Alex G
|-
|18th February 2019 || Charlie || Alex
|-
|4th March 2019 || Alex G || Verena
|}

==Michaelmas Term 2018==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|1st October 2018 || Bang ||
|-
|15th October 2018 || Alex T || Verena
|-
|30th October 2018 || David || Alex
|-
|12th November 2018 || [Alex T away]
|-
|26th November 2018 ||
|}

==Long Vacation 2018==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|'''3.30pm Tue''' 28th August 2018 || Jirka || Bang
|-
|Mon 10th September 2018 || Verena & Charlie || Alex
|-
|'''Tue''' 25th September 2018 || Richard & Ian
|}

==Easter Term 2018==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|7th May 2018 || Letitia - Alex and Sav no longer in Crete that day. || Alex to bring Greek gifts
|-
|14th May 2018 || David
|-
|4th June 2018 || Bang
|-
|11th June 2018 || Verena (cancelled)
|}

==Lent Term 2018==
{|
|+
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|22nd January 2018 || Letitia || Bang
|-
|5th February 2018 || Alex ||
|-
|19th February 2018 || Flash talks || Alex
|-
|5th March 2018 || [Electronic Structure meeting]
|-
|19th March 2018 || [Scientific Computing Day]
|}

==Michaelmas Term 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|2nd October || Kris || Verena
|-
|16th October || Sav || Charlie
|-
|30th October || David || Hugh?
|-
|13th November || Bang || ?
|-
|27th November || Jonathan || Alex T
|-
|11th December || Hugh || Sav
|}

==Research Period 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|8th August || ? || ?
|-
|22nd August || Adam/Andreea/Jamie/Kris || ?
|-
|5th September || Charlie & Hugh || ?
|-
|19th September || Verena || Kris
|}

==Easter Term 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|24th April || Sav || Alex T
|-
|8th May || Hugh || Sav
|-
|30th May|| Charlie || ?
|-
|12th June || Verena || ?
|}

==Lent Term 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|9th January || Sav || Charlie & Verena
|-
|23rd January || Henry & Alex C || Ruth
|-
|13th February || Choi & Ben || Alex T
|-
|27th February || Bang || Alex C
|-
|13th March || Verena || Ben
|}

==Michaelmas Term 2016==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|10th October 2016 || Charlie || Hugh
|-
|24th October 2016 || Verena || Sav
|-
|7th November 2016 || Choi || Alex
|-
|21st November 2016 || Ruth || Bang & Verena
|-
|5th December 2016 || [AJWT away]
|-
|19th December 2016 || Hugh || Choi
|}

==Research Period 2016==
{|
|+
|'''Date''' || '''Mini-talk'''
|-
|15th August 2016 || Jonathan
|-
|30th August 2016 || Charlie
|-
|12th September 2016 || James
|-
|26th September 2016 || CANCELLED
|}

Main Page

2024-08-12T11:13:02Z

Ksp31: /* Group Meetings */

<div style="text-align: center;">
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#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
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''
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<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
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</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every <s>other</s> <s>Monday</s> <s>Friday</s> Thursday at <s>2pm</s> 3.30pm.

===Easter 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th April || Jack || Alex
|-
|9th May || Chiara || Jack
|-
|23th May || Lijun || Lijun
|-
|6th June || Lila || Kripa
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|-
| 13 Feb 2024 || Bence || [https://arxiv.org/pdf/2203.16580 What’s for Lunch? A systematic ordering of foods in the Soup-Salad-Sandwich phase space]
|-
| 12 Mar 2024 || Alex || [https://iopscience.iop.org/article/10.3847/2041-8213/acf577/pdf Carbon-bearing Molecules in a Possible Hycean Atmosphere]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=

Past Summer Interns [[Past Summer Interns|here]].

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-05-09T15:06:47Z

Ksp31: /* Easter 2024 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> <s>Friday</s> Thursday at <s>3.30pm</s> 2pm.

===Easter 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th April || Jack || Alex
|-
|9th May || Chiara || Jack
|-
|23th May || Lijun || Lijun
|-
|6th June || Lila || Kripa
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|-
| 13 Feb 2024 || Bence || [https://arxiv.org/pdf/2203.16580 What’s for Lunch? A systematic ordering of foods in the Soup-Salad-Sandwich phase space]
|-
| 12 Mar 2024 || Alex || [https://iopscience.iop.org/article/10.3847/2041-8213/acf577/pdf Carbon-bearing Molecules in a Possible Hycean Atmosphere]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-04-25T15:19:57Z

Ksp31: /* Easter 2024 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> <s>Friday</s> Thursday at <s>3.30pm</s> 2pm.

===Easter 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th April || Jack || Alex
|-
|9th May || Lila || Jack
|-
|23th May || Andrew/Lijun ||
|-
|6th June || Chiara || Kripa
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|-
| 13 Feb 2024 || Bence || [https://arxiv.org/pdf/2203.16580 What’s for Lunch? A systematic ordering of foods in the Soup-Salad-Sandwich phase space]
|-
| 12 Mar 2024 || Alex || [https://iopscience.iop.org/article/10.3847/2041-8213/acf577/pdf Carbon-bearing Molecules in a Possible Hycean Atmosphere]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-04-25T15:19:50Z

Ksp31: /* Easter 2024 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> <s>Friday</s> Thursday at <s>3.30pm</s> 2pm.

===Easter 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th April || Jack || Alex
|-
|9th May || Lila || Jack
|-
|23th May || Andrew/Lijun ||
|-
|6th June || Chiara ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|-
| 13 Feb 2024 || Bence || [https://arxiv.org/pdf/2203.16580 What’s for Lunch? A systematic ordering of foods in the Soup-Salad-Sandwich phase space]
|-
| 12 Mar 2024 || Alex || [https://iopscience.iop.org/article/10.3847/2041-8213/acf577/pdf Carbon-bearing Molecules in a Possible Hycean Atmosphere]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-04-24T10:12:32Z

Ksp31: /* Easter 2024 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> <s>Friday</s> Thursday at <s>3.30pm</s> 2pm.

===Easter 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th April || Jack || Alex
|-
|9th May || Lila ||
|-
|23th May || Andrew/Lijun ||
|-
|6th June || Chiara ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|-
| 13 Feb 2024 || Bence || [https://arxiv.org/pdf/2203.16580 What’s for Lunch? A systematic ordering of foods in the Soup-Salad-Sandwich phase space]
|-
| 12 Mar 2024 || Alex || [https://iopscience.iop.org/article/10.3847/2041-8213/acf577/pdf Carbon-bearing Molecules in a Possible Hycean Atmosphere]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Computer and Storage List

2024-04-23T21:24:40Z

Ksp31:

=Computer List=
{| class="wikitable sortable"
!name
!office
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Software
!Purchased
|-
|carpathia
|379
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|<b>QChem</b>
For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|G.05
|Andreea, George [César]
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|
|2015
|-
|sandstone
|378
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04.4
|
|
|<b>QChem</b>
source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG03a
|Lijun, Theo [Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG11
|Haoshan [Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|<b>QChem</b>
export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|<b>QChem</b>
source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|UG03A
|Daniel, [Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|<b>QChem</b>
. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|Yi [Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|
|<b>QChem</b>
source /home/maf63/qchem-public/qcsetup

<b>MRCC</b>

source /home/ajwt3/code/mrcc
|2020
|-
|nemesis
|378
|Constance
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 20.04.5
|-
|chiron
|UG03A
|Chiara
|10
|Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz
|96GB
|Ubuntu 20.04
|
|
|
|2021
|-
|topaz
|360
|Lila
|8
|Intel Core i9-11900 2.5GHz 8 Core
|128GB
|Ubuntu 20.04
|NVIDIA GeForce RTX 3080
|
|
|2022
|-
|[https://www.ch.cam.ac.uk/computing/cerebro-compute-server cerebro]
|
|Alavi & Thom Groups
|12 x 20
16 x 8
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|48GB
64GB
|Rocks 6.2 (CentOS 6.9) SLURM queuing
|
|
|<b>QChem</b>
source /home/hynl2/code/qchemsetup.bash

<b>MRCC</b>

source /home/ajwt3/code/mrcc_2023
|-
|[https://www.hpc.cam.ac.uk/high-performance-computing CSD3]
|
|University Tier-2
|32 x 1152
56 x 672
|2x Intel(R) Xeon Gold CPU 6142 @ 2.60GHz
2x Intel(R) Xeon Platinum CPU 8276 @ 2.20GHz
|192 or 384GB
192 or 384GB
|Scientific Linux release 7.9 (Nitrogen) SLURM queuing
|
|
|<b>QChem</b>
source /rds/project/ajwt3/rds-ajwt3-thom1/qchem_public/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/nest-compute-server nest]
|
|CUC3 Group cluster
|40 x 20
|2x Cascade Lake Intel(R) Xeon Gold CPU 6248 @ 2.50GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|
|
|<b>QChem</b>
source /home/maf63/code/qcsetup.sh
|-
|[https://www.ch.cam.ac.uk/computing/rogue-gpu-server rogue]
|
|CUC3 Group cluster
|(8 nVidia V100 + 32 CPU) x 2
|2x Sky Lake Intel(R) Xeon Gold CPU 6130 @ 2.10GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|-
|[https://www.archer2.ac.uk/ archer-2]
|
|National Tier-1 Supercomputer
| 128 x 5848
|2 x AMD EPYC Zen2 (Rome) 64-core CPUs @ 2.2GHz
|256GB and 512GB
|
|}

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

NB the number of 'processors' may be different from the number of cores owing to hyperthreading. The 'cpu cores' value is the one to take for single CPU machines.

[http://hobbit.ch.cam.ac.uk/xymon/workstations/workstationsThom/workstationsThomLinux/ Hobbit] may also have some useful information.

[https://www.ch.cam.ac.uk/computing/group-computer-representatives Group computer reps] can manage group entries in the department [https://chemdb.ch.cam.ac.uk/hotwire3/chemistry/ database] and there's a [https://apps.ch.cam.ac.uk/computer-reps/group-computers.php hardware inventory] and a [https://apps.ch.cam.ac.uk/space-management/space-report.php space report] too.

=Storage=
A common cause of running out of storage on your workstation is anaconda which puts stuff in /home. This can be safely moved to /scratch and a symbolic link.

cd $HOME
mv .conda /scratch/$USER
ln -s /scratch/$USER/.conda

To find out how much storage you have available and what files/directories are taking up space, the following commands are useful. The first one shows how much space is used/available on each partition, and the second shows the size of everything in the current directory.

df -h
du -sh * | sort -hr

If you can't find any fiiles in /scratch/$USER/thom-fs-common you might need to authenticate with a password. You can do this if you are using key authentication with

ssh -oPubkeyauthentication=no localhost

{| class="wikitable"
!Name
!Type
!Amount
!Notes
|-
|/home/$USER
|local disk
|~50Gb per person (changed to ~100GB after upgrade to 20.04)
|Backed up with snapshots - Theory RIG policy
|-
|/scratch/$USER
|local disk
|~1Tb+ depending on computer
|NOT BACKED UP
|-
|/scratch/$USER/thom-fs-nethome
/scratch/$USER/thom-fs-common
|Chemistry network drive
|2.3T
|Backed up with snapshots - Theory RIG policy
|-
|/scratch/$USER/ifs-thom
|Former UIS Mount - now located at /scratch/$USER/thom-fs/old-ifs-thom
|6144Gb
|Read-only
|-
|/scratch/$USER/theory-fs
|Chemistry network drive
|~50Gb per person
|Backed up with snapshots - Theory RIG policy
|-
|cerebro:/filestore
|Local RAID array
|36950Gb
|Backed up with snapshots - Theory RIG policy
|}

=Theory RIG backup policy=
From https://www.ch.cam.ac.uk/computing/managed-linux-workstations-faq

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

then, about one backup per month for the previous few months

Computer and Storage List

2024-04-11T10:39:01Z

Ksp31: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Q-Chem?
!Purchased
|-
|carpathia
|379
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|G.05
|Andreea, George [César]
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|
|2015
|-
|sandstone
|378
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04.4
|
|
|source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG03a
|Lijun, Theo [Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG11
|Haoshan [Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|UG03A
|Daniel, [Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|Yi [Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|
|source /home/maf63/qchem-public/qcsetup
|2020
|-
|nemesis
|378
|Constance
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 20.04.5
|-
|chiron
|UG03A
|Chiara
|10
|Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz
|96GB
|Ubuntu 20.04
|
|
|
|2021
|-
|topaz
|360
|Lila
|8
|Intel Core i9-11900 2.5GHz 8 Core
|128GB
|Ubuntu 20.04
|NVIDIA GeForce RTX 3080
|
|
|2022
|-
|[https://www.ch.cam.ac.uk/computing/cerebro-compute-server cerebro]
|
|Alavi & Thom Groups
|12 x 20
16 x 8
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|48GB
64GB
|Rocks 6.2 (CentOS 6.9) SLURM queuing
|
|
| source /home/hynl2/code/qchemsetup.bash
|-
|[https://www.hpc.cam.ac.uk/high-performance-computing CSD3]
|
|University Tier-2
|32 x 1152
56 x 672
|2x Intel(R) Xeon Gold CPU 6142 @ 2.60GHz
2x Intel(R) Xeon Platinum CPU 8276 @ 2.20GHz
|192 or 384GB
192 or 384GB
|Scientific Linux release 7.9 (Nitrogen) SLURM queuing
|
|
|source /rds/project/ajwt3/rds-ajwt3-thom1/qchem_public/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/nest-compute-server nest]
|
|CUC3 Group cluster
|40 x 20
|2x Cascade Lake Intel(R) Xeon Gold CPU 6248 @ 2.50GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|
|
|source /home/maf63/code/qcsetup.sh
|-
|[https://www.ch.cam.ac.uk/computing/rogue-gpu-server rogue]
|
|CUC3 Group cluster
|(8 nVidia V100 + 32 CPU) x 2
|2x Sky Lake Intel(R) Xeon Gold CPU 6130 @ 2.10GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|-
|[https://www.archer2.ac.uk/ archer-2]
|
|National Tier-1 Supercomputer
| 128 x 5848
|2 x AMD EPYC Zen2 (Rome) 64-core CPUs @ 2.2GHz
|256GB and 512GB
|
|}

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

NB the number of 'processors' may be different from the number of cores owing to hyperthreading. The 'cpu cores' value is the one to take for single CPU machines.

[http://hobbit.ch.cam.ac.uk/xymon/workstations/workstationsThom/workstationsThomLinux/ Hobbit] may also have some useful information.

[https://www.ch.cam.ac.uk/computing/group-computer-representatives Group computer reps] can manage group entries in the department [https://chemdb.ch.cam.ac.uk/hotwire3/chemistry/ database] and there's a [https://apps.ch.cam.ac.uk/computer-reps/group-computers.php hardware inventory] and a [https://apps.ch.cam.ac.uk/space-management/space-report.php space report] too.

=Storage=
A common cause of running out of storage on your workstation is anaconda which puts stuff in /home. This can be safely moved to /scratch and a symbolic link.

cd $HOME
mv .conda /scratch/$USER
ln -s /scratch/$USER/.conda

To find out how much storage you have available and what files/directories are taking up space, the following commands are useful. The first one shows how much space is used/available on each partition, and the second shows the size of everything in the current directory.

df -h
du -sh * | sort -hr

If you can't find any fiiles in /scratch/$USER/thom-fs-common you might need to authenticate with a password. You can do this if you are using key authentication with

ssh -oPubkeyauthentication=no localhost

{| class="wikitable"
!Name
!Type
!Amount
!Notes
|-
|/home/$USER
|local disk
|~50Gb per person (changed to ~100GB after upgrade to 20.04)
|Backed up with snapshots - Theory RIG policy
|-
|/scratch/$USER
|local disk
|~1Tb+ depending on computer
|NOT BACKED UP
|-
|/scratch/$USER/thom-fs-nethome
/scratch/$USER/thom-fs-common
|Chemistry network drive
|2.3T
|Backed up with snapshots - Theory RIG policy
|-
|/scratch/$USER/ifs-thom
|Former UIS Mount - now located at /scratch/$USER/thom-fs/old-ifs-thom
|6144Gb
|Read-only
|-
|/scratch/$USER/theory-fs
|Chemistry network drive
|~50Gb per person
|Backed up with snapshots - Theory RIG policy
|-
|cerebro:/filestore
|Local RAID array
|36950Gb
|Backed up with snapshots - Theory RIG policy
|}

=Theory RIG backup policy=
From https://www.ch.cam.ac.uk/computing/managed-linux-workstations-faq

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

then, about one backup per month for the previous few months

Main Page

2024-03-20T10:26:40Z

Ksp31: /* Easter 2024 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> <s>Friday</s> Thursday at <s>3.30pm</s> 2pm.

===Easter 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th April || Jack ||
|-
|9th May || Lila ||
|-
|23th May || Andrew/Lijun ||
|-
|6th June || Chiara ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|-
| 13 Feb 2024 || Bence || [https://arxiv.org/pdf/2203.16580 What’s for Lunch? A systematic ordering of foods in the Soup-Salad-Sandwich phase space]
|-
| 12 Mar 2024 || Alex || [https://iopscience.iop.org/article/10.3847/2041-8213/acf577/pdf Carbon-bearing Molecules in a Possible Hycean Atmosphere]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-03-08T10:18:41Z

Ksp31: /* 2023-24 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> <s>Friday</s> Thursday at <s>3.30pm</s> 2pm.

===Easter 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th April || Jack ||
|-
|9th May || Lila ||
|-
|23th May || Chiara/Andrew/Lijun ||
|-
|6th June || Chiara/Andrew/Lijun ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|-
| 13 Feb 2024 || Bence || [https://arxiv.org/pdf/2203.16580 What’s for Lunch? A systematic ordering of foods in the Soup-Salad-Sandwich phase space]
|-
| 12 Mar 2024 || Alex || [https://iopscience.iop.org/article/10.3847/2041-8213/acf577/pdf Carbon-bearing Molecules in a Possible Hycean Atmosphere]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-03-08T10:17:23Z

Ksp31: /* Easter 2024 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> <s>Friday</s> Thursday at <s>3.30pm</s> 2pm.

===Easter 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th April || Jack ||
|-
|9th May || Lila ||
|-
|23th May || Chiara/Andrew/Lijun ||
|-
|6th June || Chiara/Andrew/Lijun ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|-
| 13 Feb 2024 || Bence || [https://arxiv.org/pdf/2203.16580 What’s for Lunch? A systematic ordering of foods in the Soup-Salad-Sandwich phase space]
|-
| 12 Mar 2024 || Alex ||
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Group Meetings

2024-03-08T10:15:58Z

Ksp31: /* Past Group Meetings */

=Past Group Meetings=

===Lent 2024===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th January || Alex || Lila
|-
|8th February || Kripa || Bence
|-
|22th February || Daniel || Jack
|-
|7th March || Bence || Kripa
|}

===Michaelmas 2023===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|13th October || Lila || Chiara
|-
|27th October || Rowan || Rowan
|-
|10th November || Hugh || Kripa
|-
|24th November || Chiara || Alex (Mince Pies)
|}

===Summer 2023===
{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|2nd August || Summer Interns || Lila
|-
|21st August || Jack || Andreea
|-
|1st September || Summer Interns || Miriam
|-
|18th September || Kripa || Alex
|}

===Easter 2023===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|1st May || Chiara || Andreea
|-
|15th May || Lila || Kripa
|-
|26th May || Yi Sun || Jack
|-
|12th June || Daniel || Alex
|}

===Lent 2023===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|23rd January || Kripa || Moritz
|-
|6th February || Jack || Alex
|-
|20th February || Andreea || Juan
|-
|6th March || Eline + Juan || Kripa
|}

===Michaelmas 2022===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|10th October || Yi Sun || Kripa
|-
|24th October || Chiara|| Andreea
|-
|7th November || Lila || Eline
|-
|21st November || Moritz || Alex (Mince Pies)
|}

===Summer 2022===
{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th July || WATOC Review & IPLU Discussion ||
|-
|8th August || Brian || Andreea
|-
|30th August || Nick || Daniel
|-
|12th September|| Interns || Alex
|}

===Easter 2022===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|9th May || Lila || Andreea
|-
|23rd May || Daniel || Brian
|-
|13th June|| Benjamin || Kripa
|-
|20th June|| Kripa || Lila
|}

===Lent 2022===
{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|24th January || Fabio || Andreea
|-
|7th February || Andreea || Kripa
|-
|21st February|| Nick || Brian
|-
|21st March|| Brian || Chiara
|}
=== Michaelmas 2021===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|4th October|| INFORMAL ||
|-
|18th October || Nick || Fabio
|-
|1st November || Kripa || Andreea
|-
|15th November|| Chiara || Nick
|-
|29th November|| David || Kripa
|}

===Summer 2021===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|12th July 2021 || INFORMAL ||
|-
|20th July 2021 || INFORMAL ||
|-
|27th July 2021 || - ||
|-
|3rd August 2021 || Cesar & Tarik || Chelsea Buns
|-
|9th August 2021 || Constance || Brian
|-
|16th August 2021 || INFORMAL ||
|-
|23rd August 2021|| Benjamin || Andreea
|-
|30th August 2021|| INFORMAL ||
|-
|6th September 2021 || Arta || Kripa
|-
|13th September 2021 || Anna, Brian & Zian|| Nick
|}
===Easter 2021===

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|19th April 2021 || INFORMAL ||
|-
|26th April 2021 || INFORMAL ||
|-
|3rd May 2021 || INFORMAL ||
|-
|10th May 2021 || Andreea || Fruit based
|-
|17th May 2021 || INFORMAL ||
|-
|24th May 2021 || Nick Blunt || Cheesecake
|-
|31st May 2021|| INFORMAL ||
|-
|7th June 2021|| Fabio|| (Boston) Cream Pie
|-
|14th June 2021|| Benjamin ||
|}

==Lent 2021==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|18th January 2021 || INFORMAL || -
|-
|25th January 2021 || INFORMAL || Shortbread
|-
|1st February 2021 || Bang || Non-trivial Symmetry Element
|-
|8th February 2021 || INFORMAL ||
|-
|15th February 2021 || César and Tarik || Carrot Cake
|-
|22th February 2021 || INFORMAL ||
|-
|1st March 2021|| Kripa || Doughnuts (Krispy Kreme)
|-
|8th March 2021|| Hang & Tiger (Part III) || Date Loaf
|-
|15th March 2021|| Elizabeth & Isha (Part III) || Mother's Choice
|}
==Michaelmas 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|12th October 2020 || Andreea || Kripa
|-
|19th October 2020 || INFORMAL || Andreea
|-
|26th October 2020 || Fabio || Bang
|-
|2nd November 2020 || INFORMAL || Fabio
|-
|9th November 2020 || INFORMAL|| Bang
|-
|16th November 2020 || Kripa || Elizabeth
|-
|23rd November 2020|| Arta || Arta
|-
|30th November 2020 || INFORMAL || Andreea
|}

==Summer 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake & Recipe'''
|-
|20th July 2020 || Nick || [https://en.wikipedia.org/wiki/Kiev_cake Kiev cake]
|-
|10th August 2020 || Hugh || Crumble
|-
|24th August 2020 || Constance, Hang, Jimin||
|-
|7 September 2020|| Elizabeth, (Nick), Tiger, Toby ||
|}

==Easter 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake & Recipe'''
|-
|4th May 2020 || Andreea || Tiramisu
|-
|18th May 2020 || David || Carrot
|-
|1st June 2020 || Hugh || Chocolate & Ginger
|-
|15 June 2020|| Bang || Salted Caramel
|}

==Lent 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|27th January 2020 || Bang || Alex
|-
|10th February 2020 || Alex || Kripa & George
|-
|24th February 2020 || Fabio || Bang
|-
|10th March 2020|| Kripa & George || Andreea
|}

==Michaelmas 2019==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|21st October 2019 || Fabio || Hugh
|-
|4th November 2019 || Andreea || David
|-
|18th November 2019 || David || Andreea
|-
|2nd December 2019 || Hugh || Fabio
|}

==Summer Vacation 2019==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|22nd July 2019 || Rhiannon || David
|-
|19th August 2019 || Hugh || Fabio
|-
|2nd September 2019 || Bang || Summer Students
|-
|16th September 2019 || Summer Students || Alex
|}

==Easter Term 2019==

{|
|'''Date''' || '''Talk''' ||| '''Cake'''
|-
|2nd May 2019 || Rhiannon || Fabio
|-
|13th May 2019 || David || Bang
|-
|27th May 2019|| Andreea || Alex
|-
|10th June 2019 || Fabio || Rhiannon
|}

==Easter Vacation 2019==

{|
|'''Date''' || '''Talk''' ||| '''Cake'''
|-
|8th April 2019 || The Boss || Andreea
|}

==Lent Term 2019==

{|
|'''Date''' || '''Talk''' ||| '''Cake'''
|-
|7th January 2019 || Hugh || Alex
|-
|21st January 2019 || Bang || Andreea
|-
|4th February 2019 || Verena || Alex G
|-
|18th February 2019 || Charlie || Alex
|-
|4th March 2019 || Alex G || Verena
|}

==Michaelmas Term 2018==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|1st October 2018 || Bang ||
|-
|15th October 2018 || Alex T || Verena
|-
|30th October 2018 || David || Alex
|-
|12th November 2018 || [Alex T away]
|-
|26th November 2018 ||
|}

==Long Vacation 2018==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|'''3.30pm Tue''' 28th August 2018 || Jirka || Bang
|-
|Mon 10th September 2018 || Verena & Charlie || Alex
|-
|'''Tue''' 25th September 2018 || Richard & Ian
|}

==Easter Term 2018==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|7th May 2018 || Letitia - Alex and Sav no longer in Crete that day. || Alex to bring Greek gifts
|-
|14th May 2018 || David
|-
|4th June 2018 || Bang
|-
|11th June 2018 || Verena (cancelled)
|}

==Lent Term 2018==
{|
|+
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|22nd January 2018 || Letitia || Bang
|-
|5th February 2018 || Alex ||
|-
|19th February 2018 || Flash talks || Alex
|-
|5th March 2018 || [Electronic Structure meeting]
|-
|19th March 2018 || [Scientific Computing Day]
|}

==Michaelmas Term 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|2nd October || Kris || Verena
|-
|16th October || Sav || Charlie
|-
|30th October || David || Hugh?
|-
|13th November || Bang || ?
|-
|27th November || Jonathan || Alex T
|-
|11th December || Hugh || Sav
|}

==Research Period 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|8th August || ? || ?
|-
|22nd August || Adam/Andreea/Jamie/Kris || ?
|-
|5th September || Charlie & Hugh || ?
|-
|19th September || Verena || Kris
|}

==Easter Term 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|24th April || Sav || Alex T
|-
|8th May || Hugh || Sav
|-
|30th May|| Charlie || ?
|-
|12th June || Verena || ?
|}

==Lent Term 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|9th January || Sav || Charlie & Verena
|-
|23rd January || Henry & Alex C || Ruth
|-
|13th February || Choi & Ben || Alex T
|-
|27th February || Bang || Alex C
|-
|13th March || Verena || Ben
|}

==Michaelmas Term 2016==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|10th October 2016 || Charlie || Hugh
|-
|24th October 2016 || Verena || Sav
|-
|7th November 2016 || Choi || Alex
|-
|21st November 2016 || Ruth || Bang & Verena
|-
|5th December 2016 || [AJWT away]
|-
|19th December 2016 || Hugh || Choi
|}

==Research Period 2016==
{|
|+
|'''Date''' || '''Mini-talk'''
|-
|15th August 2016 || Jonathan
|-
|30th August 2016 || Charlie
|-
|12th September 2016 || James
|-
|26th September 2016 || CANCELLED
|}

Main Page

2024-02-23T11:48:55Z

Ksp31: /* 2023-24 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> <s>Friday</s> Thursday at <s>3.30pm</s> 2pm.

===Lent 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th January || Alex || Lila
|-
|8th February || Kripa || Bence
|-
|22th February || Daniel || Jack
|-
|7th March || Bence || Kripa
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|-
| 13 Feb 2024 || Bence || [https://arxiv.org/pdf/2203.16580 What’s for Lunch? A systematic ordering of foods in the Soup-Salad-Sandwich phase space]
|-
| 12 Mar 2024 || Alex ||
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

Planning of upcoming seminars happens [[Quantum Club Plans|here]].

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-02-18T22:34:09Z

Ksp31: /* Lent 2024 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> <s>Friday</s> Thursday at <s>3.30pm</s> 2pm.

===Lent 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th January || Alex || Lila
|-
|8th February || Kripa || Bence
|-
|22th February || Daniel || Jack
|-
|7th March || Bence || Kripa
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|-
| 13 Feb 2024 || Bence || [https://arxiv.org/pdf/2203.16580 What’s for Lunch? A systematic ordering of foods in the Soup-Salad-Sandwich phase space]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

Planning of upcoming seminars happens [[Quantum Club Plans|here]].

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-02-06T13:49:37Z

Ksp31: /* 2023-24 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> <s>Friday</s> Thursday at <s>3.30pm</s> 2pm.

===Lent 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th January || Alex || Lila
|-
|8th February || Kripa || Bence
|-
|22th February || Daniel ||
|-
|7th March || Bence ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|-
| 13 Feb 2024 || Bence || [https://arxiv.org/pdf/2203.16580 What’s for Lunch? A systematic ordering of foods in the Soup-Salad-Sandwich phase space]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found here: [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-02-06T12:14:16Z

Ksp31: /* Lent 2024 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> <s>Friday</s> Thursday at <s>3.30pm</s> 2pm.

===Lent 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th January || Alex || Lila
|-
|8th February || Kripa || Bence
|-
|22th February || Daniel ||
|-
|7th March || Bence ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found here: [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-01-25T15:49:52Z

Ksp31: /* Lent 2024 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> <s>Friday</s> Thursday at <s>3.30pm</s> 2pm.

===Lent 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th January || Alex || Lila
|-
|8th February || Daniel || Bence
|-
|22th February || Kripa ||
|-
|7th March || Bence ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found here: [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-01-16T11:24:27Z

Ksp31: /* Lent 2024 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> <s>Friday</s> Thursday at <s>3.30pm</s> 2pm.

===Lent 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th January || Alex || Lila
|-
|8th February || Daniel ||
|-
|22th February || Kripa ||
|-
|7th March || Bence ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found here: [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2023-11-28T14:36:40Z

Ksp31: /* 2023-24 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> <s>Friday</s> Thursday at <s>3.30pm</s> 2pm.

===Lent 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th January || Alex ||
|-
|8th February || Daniel ||
|-
|22th February || Kripa ||
|-
|7th March || Bence ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 1 Nov 2023 || Lila || [https://www.nature.com/articles/s41586-023-06306-y Solid-body trajectoids shaped to roll along desired pathways]
|-
| 29 Nov 2023 || Kripa || [https://arxiv.org/abs/2006.01855 Aligning Superhuman AI with Human Behavior: Chess as a Model System]
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found here: [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do
# Mathematical Physics Lectures by Frederic Schuller: [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxTi6kS4vCmv4ZKm9u8g5yic Geometrical Anatomy of Theoretical Physics] and [https://www.youtube.com/playlist?list=PLPH7f_7ZlzxQVx5jRjbfRGEzWY_upS5K6 Lectures on Quantum Theory]
# Mathematical Physics Lectures by Carl Bender: [https://www.youtube.com/playlist?list=PL43B1963F261E6E47 Perturbation and Asymptotic Series]

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2023-11-24T15:27:40Z

Ksp31: /* Group Meetings */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> <s>Friday</s> Thursday at <s>3.30pm</s> 2pm.

===Lent 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th January || Alex ||
|-
|8th February || Daniel ||
|-
|22th February || Kripa ||
|-
|7th March || Bence ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| || ||
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found here: [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2023-11-24T15:27:10Z

Ksp31: /* Michaelmas 2023 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> Friday at 3.30pm.

===Lent 2024===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th January || Alex ||
|-
|8th February || Daniel ||
|-
|22th February || Kripa ||
|-
|7th March || Bence ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| || ||
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found here: [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Group Meetings

2023-11-24T15:26:03Z

Ksp31: /* Past Group Meetings */

=Past Group Meetings=

===Michaelmas 2023===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|13th October || Lila || Chiara
|-
|27th October || Rowan || Rowan
|-
|10th November || Hugh || Kripa
|-
|24th November || Chiara || Alex (Mince Pies)
|}

===Summer 2023===
{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|2nd August || Summer Interns || Lila
|-
|21st August || Jack || Andreea
|-
|1st September || Summer Interns || Miriam
|-
|18th September || Kripa || Alex
|}

===Easter 2023===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|1st May || Chiara || Andreea
|-
|15th May || Lila || Kripa
|-
|26th May || Yi Sun || Jack
|-
|12th June || Daniel || Alex
|}

===Lent 2023===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|23rd January || Kripa || Moritz
|-
|6th February || Jack || Alex
|-
|20th February || Andreea || Juan
|-
|6th March || Eline + Juan || Kripa
|}

===Michaelmas 2022===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|10th October || Yi Sun || Kripa
|-
|24th October || Chiara|| Andreea
|-
|7th November || Lila || Eline
|-
|21st November || Moritz || Alex (Mince Pies)
|}

===Summer 2022===
{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th July || WATOC Review & IPLU Discussion ||
|-
|8th August || Brian || Andreea
|-
|30th August || Nick || Daniel
|-
|12th September|| Interns || Alex
|}

===Easter 2022===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|9th May || Lila || Andreea
|-
|23rd May || Daniel || Brian
|-
|13th June|| Benjamin || Kripa
|-
|20th June|| Kripa || Lila
|}

===Lent 2022===
{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|24th January || Fabio || Andreea
|-
|7th February || Andreea || Kripa
|-
|21st February|| Nick || Brian
|-
|21st March|| Brian || Chiara
|}
=== Michaelmas 2021===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|4th October|| INFORMAL ||
|-
|18th October || Nick || Fabio
|-
|1st November || Kripa || Andreea
|-
|15th November|| Chiara || Nick
|-
|29th November|| David || Kripa
|}

===Summer 2021===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|12th July 2021 || INFORMAL ||
|-
|20th July 2021 || INFORMAL ||
|-
|27th July 2021 || - ||
|-
|3rd August 2021 || Cesar & Tarik || Chelsea Buns
|-
|9th August 2021 || Constance || Brian
|-
|16th August 2021 || INFORMAL ||
|-
|23rd August 2021|| Benjamin || Andreea
|-
|30th August 2021|| INFORMAL ||
|-
|6th September 2021 || Arta || Kripa
|-
|13th September 2021 || Anna, Brian & Zian|| Nick
|}
===Easter 2021===

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|19th April 2021 || INFORMAL ||
|-
|26th April 2021 || INFORMAL ||
|-
|3rd May 2021 || INFORMAL ||
|-
|10th May 2021 || Andreea || Fruit based
|-
|17th May 2021 || INFORMAL ||
|-
|24th May 2021 || Nick Blunt || Cheesecake
|-
|31st May 2021|| INFORMAL ||
|-
|7th June 2021|| Fabio|| (Boston) Cream Pie
|-
|14th June 2021|| Benjamin ||
|}

==Lent 2021==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|18th January 2021 || INFORMAL || -
|-
|25th January 2021 || INFORMAL || Shortbread
|-
|1st February 2021 || Bang || Non-trivial Symmetry Element
|-
|8th February 2021 || INFORMAL ||
|-
|15th February 2021 || César and Tarik || Carrot Cake
|-
|22th February 2021 || INFORMAL ||
|-
|1st March 2021|| Kripa || Doughnuts (Krispy Kreme)
|-
|8th March 2021|| Hang & Tiger (Part III) || Date Loaf
|-
|15th March 2021|| Elizabeth & Isha (Part III) || Mother's Choice
|}
==Michaelmas 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|12th October 2020 || Andreea || Kripa
|-
|19th October 2020 || INFORMAL || Andreea
|-
|26th October 2020 || Fabio || Bang
|-
|2nd November 2020 || INFORMAL || Fabio
|-
|9th November 2020 || INFORMAL|| Bang
|-
|16th November 2020 || Kripa || Elizabeth
|-
|23rd November 2020|| Arta || Arta
|-
|30th November 2020 || INFORMAL || Andreea
|}

==Summer 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake & Recipe'''
|-
|20th July 2020 || Nick || [https://en.wikipedia.org/wiki/Kiev_cake Kiev cake]
|-
|10th August 2020 || Hugh || Crumble
|-
|24th August 2020 || Constance, Hang, Jimin||
|-
|7 September 2020|| Elizabeth, (Nick), Tiger, Toby ||
|}

==Easter 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake & Recipe'''
|-
|4th May 2020 || Andreea || Tiramisu
|-
|18th May 2020 || David || Carrot
|-
|1st June 2020 || Hugh || Chocolate & Ginger
|-
|15 June 2020|| Bang || Salted Caramel
|}

==Lent 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|27th January 2020 || Bang || Alex
|-
|10th February 2020 || Alex || Kripa & George
|-
|24th February 2020 || Fabio || Bang
|-
|10th March 2020|| Kripa & George || Andreea
|}

==Michaelmas 2019==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|21st October 2019 || Fabio || Hugh
|-
|4th November 2019 || Andreea || David
|-
|18th November 2019 || David || Andreea
|-
|2nd December 2019 || Hugh || Fabio
|}

==Summer Vacation 2019==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|22nd July 2019 || Rhiannon || David
|-
|19th August 2019 || Hugh || Fabio
|-
|2nd September 2019 || Bang || Summer Students
|-
|16th September 2019 || Summer Students || Alex
|}

==Easter Term 2019==

{|
|'''Date''' || '''Talk''' ||| '''Cake'''
|-
|2nd May 2019 || Rhiannon || Fabio
|-
|13th May 2019 || David || Bang
|-
|27th May 2019|| Andreea || Alex
|-
|10th June 2019 || Fabio || Rhiannon
|}

==Easter Vacation 2019==

{|
|'''Date''' || '''Talk''' ||| '''Cake'''
|-
|8th April 2019 || The Boss || Andreea
|}

==Lent Term 2019==

{|
|'''Date''' || '''Talk''' ||| '''Cake'''
|-
|7th January 2019 || Hugh || Alex
|-
|21st January 2019 || Bang || Andreea
|-
|4th February 2019 || Verena || Alex G
|-
|18th February 2019 || Charlie || Alex
|-
|4th March 2019 || Alex G || Verena
|}

==Michaelmas Term 2018==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|1st October 2018 || Bang ||
|-
|15th October 2018 || Alex T || Verena
|-
|30th October 2018 || David || Alex
|-
|12th November 2018 || [Alex T away]
|-
|26th November 2018 ||
|}

==Long Vacation 2018==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|'''3.30pm Tue''' 28th August 2018 || Jirka || Bang
|-
|Mon 10th September 2018 || Verena & Charlie || Alex
|-
|'''Tue''' 25th September 2018 || Richard & Ian
|}

==Easter Term 2018==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|7th May 2018 || Letitia - Alex and Sav no longer in Crete that day. || Alex to bring Greek gifts
|-
|14th May 2018 || David
|-
|4th June 2018 || Bang
|-
|11th June 2018 || Verena (cancelled)
|}

==Lent Term 2018==
{|
|+
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|22nd January 2018 || Letitia || Bang
|-
|5th February 2018 || Alex ||
|-
|19th February 2018 || Flash talks || Alex
|-
|5th March 2018 || [Electronic Structure meeting]
|-
|19th March 2018 || [Scientific Computing Day]
|}

==Michaelmas Term 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|2nd October || Kris || Verena
|-
|16th October || Sav || Charlie
|-
|30th October || David || Hugh?
|-
|13th November || Bang || ?
|-
|27th November || Jonathan || Alex T
|-
|11th December || Hugh || Sav
|}

==Research Period 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|8th August || ? || ?
|-
|22nd August || Adam/Andreea/Jamie/Kris || ?
|-
|5th September || Charlie & Hugh || ?
|-
|19th September || Verena || Kris
|}

==Easter Term 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|24th April || Sav || Alex T
|-
|8th May || Hugh || Sav
|-
|30th May|| Charlie || ?
|-
|12th June || Verena || ?
|}

==Lent Term 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|9th January || Sav || Charlie & Verena
|-
|23rd January || Henry & Alex C || Ruth
|-
|13th February || Choi & Ben || Alex T
|-
|27th February || Bang || Alex C
|-
|13th March || Verena || Ben
|}

==Michaelmas Term 2016==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|10th October 2016 || Charlie || Hugh
|-
|24th October 2016 || Verena || Sav
|-
|7th November 2016 || Choi || Alex
|-
|21st November 2016 || Ruth || Bang & Verena
|-
|5th December 2016 || [AJWT away]
|-
|19th December 2016 || Hugh || Choi
|}

==Research Period 2016==
{|
|+
|'''Date''' || '''Mini-talk'''
|-
|15th August 2016 || Jonathan
|-
|30th August 2016 || Charlie
|-
|12th September 2016 || James
|-
|26th September 2016 || CANCELLED
|}

Main Page

2023-11-13T22:12:59Z

Ksp31: /* Michaelmas 2023 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> Friday at 3.30pm.

===Michaelmas 2023===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|13th October || Lila || Chiara
|-
|27th October || Rowan || Rowan
|-
|10th November || Hugh || Kripa
|-
|24th November || Chiara || Alex (Mince Pies)
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| || ||
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found here: [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice
===Installing Slack on department machines ===
====Ubuntu====
# Download "Slack.deb" from:
https://slack.com/intl/en-gb/downloads/linux
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/<b>crsid</b>/slack
dpkg -x Slack.deb /scratch/<b>crsid</b>/slack
# <li value="3"> Install the desktop shortcut by pasting the following text into '''~/.local/share/applications/slack.desktop'''
[Desktop Entry]
Type=Application
Exec=/home/<b>crsid</b>/scratch/slack/usr/lib/slack/slack %U
Icon=/home/<b>crsid</b>/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2023-11-06T17:56:10Z

Ksp31: /* Michaelmas 2023 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> Friday at 3.30pm.

===Michaelmas 2023===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|13th October || Lila || Chiara
|-
|27th October || Rowan || Rowan
|-
|10th November || Hugh || Kripa
|-
|24th November || Chiara ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| || ||
|}

=Quantum Computing Resources=
==Quantum Club==
Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group .

==Quantum Brainstorm==
Informal quantum discussions taking place at 10am on Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

==Quantum computing Open Questions==
Outstanding questions, along with answers and helpful reading material, can be found here: [[Open Questions|here]].

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Computer and Storage List

2023-11-02T14:47:54Z

Ksp31: /* Computer List */

=Computer List=
{| class="wikitable"
!name
!office
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Q-Chem?
|-
|carpathia
|379
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|-
|liminal
|379
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|-
|hypatia
|356
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|-
|serenity
|376
|Andreea, George [César]
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|-
|sandstone
|378
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04.4
|
|
|source /home/hynl2/code/qcsetup.bash
|-
|gritstone
|360
|Lijun, Theo [Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|-
|moonraker
|378
|Haoshan [Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|-
|obsidian
|378
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|32GB
|Ubuntu 20.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|-
|hylas
|378
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|32GB
|Ubuntu 20.04
|
|-
|cerberus
|356
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|source /home/maf63/qchem-public/qcsetup
|-
|chesterian
|362
|Daniel, [Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|-
|behemoth
|378
|Yi [Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|
|source /home/maf63/qchem-public/qcsetup
|-
|nemesis
|378
|Constance
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 20.04.5
|-
|chiron
|360
|Chiara
|10
|Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz
|96GB
|Ubuntu 20.04
|-
|topaz
|360
|Lila
|8
|Intel Core i9-11900 2.5GHz 8 Core
|128GB
|Ubuntu 20.04
|NVIDIA GeForce RTX 3080
|-
|[https://www.ch.cam.ac.uk/computing/cerebro-compute-server cerebro]
|
|Alavi & Thom Groups
|12 x 20
16 x 8
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|48GB
64GB
|Rocks 6.2 (CentOS 6.9) SLURM queuing
|
|
| source /home/hynl2/code/qchemsetup.bash
|-
|[https://www.hpc.cam.ac.uk/high-performance-computing CSD3]
|
|University Tier-2
|32 x 1152
56 x 672
|2x Intel(R) Xeon Gold CPU 6142 @ 2.60GHz
2x Intel(R) Xeon Platinum CPU 8276 @ 2.20GHz
|192 or 384GB
192 or 384GB
|Scientific Linux release 7.9 (Nitrogen) SLURM queuing
|
|
|source /rds/project/ajwt3/rds-ajwt3-thom1/qchem_public/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/nest-compute-server nest]
|
|CUC3 Group cluster
|40 x 20
|2x Cascade Lake Intel(R) Xeon Gold CPU 6248 @ 2.50GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|
|
|source /home/maf63/code/qcsetup.sh
|-
|[https://www.ch.cam.ac.uk/computing/rogue-gpu-server rogue]
|
|CUC3 Group cluster
|(8 nVidia V100 + 32 CPU) x 2
|2x Sky Lake Intel(R) Xeon Gold CPU 6130 @ 2.10GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|-
|[https://www.archer2.ac.uk/ archer-2]
|
|National Tier-1 Supercomputer
| 128 x 5848
|2 x AMD EPYC Zen2 (Rome) 64-core CPUs @ 2.2GHz
|256GB and 512GB
|
|}

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

NB the number of 'processors' may be different from the number of cores owing to hyperthreading. The 'cpu cores' value is the one to take for single CPU machines.

[http://hobbit.ch.cam.ac.uk/xymon/workstations/workstationsThom/workstationsThomLinux/ Hobbit] may also have some useful information.

[https://www.ch.cam.ac.uk/computing/group-computer-representatives Group computer reps] can manage group entries in the department [https://chemdb.ch.cam.ac.uk/hotwire3/chemistry/ database] and there's a [https://apps.ch.cam.ac.uk/computer-reps/group-computers.php hardware inventory] and a [https://apps.ch.cam.ac.uk/space-management/space-report.php space report] too.

=Storage=
A common cause of running out of storage on your workstation is anaconda which puts stuff in /home. This can be safely moved to /scratch and a symbolic link.

cd $HOME
mv .conda /scratch/$USER
ln -s /scratch/$USER/.conda

To find out how much storage you have available and what files/directories are taking up space, the following commands are useful. The first one shows how much space is used/available on each partition, and the second shows the size of everything in the current directory.

df -h
du -sh * | sort -hr

If you can't find any fiiles in /scratch/$USER/thom-fs-common you might need to authenticate with a password. You can do this if you are using key authentication with

ssh -oPubkeyauthentication=no localhost

{| class="wikitable"
!Name
!Type
!Amount
!Notes
|-
|/home/$USER
|local disk
|~50Gb per person (changed to ~100GB after upgrade to 20.04)
|Backed up with snapshots - Theory RIG policy
|-
|/scratch/$USER
|local disk
|~1Tb+ depending on computer
|NOT BACKED UP
|-
|/scratch/$USER/thom-fs-nethome
/scratch/$USER/thom-fs-common
|Chemistry network drive
|2.3T
|Backed up with snapshots - Theory RIG policy
|-
|/scratch/$USER/ifs-thom
|Former UIS Mount - now located at /scratch/$USER/thom-fs/old-ifs-thom
|6144Gb
|Read-only
|-
|/scratch/$USER/theory-fs
|Chemistry network drive
|~50Gb per person
|Backed up with snapshots - Theory RIG policy
|-
|cerebro:/filestore
|Local RAID array
|36950Gb
|Backed up with snapshots - Theory RIG policy
|}

=Theory RIG backup policy=
From https://www.ch.cam.ac.uk/computing/managed-linux-workstations-faq

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

then, about one backup per month for the previous few months

Main Page

2023-10-17T10:22:12Z

Ksp31: /* Michaelmas 2023 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> Friday at 3.30pm.

===Michaelmas 2023===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|13th October || Lila || Chiara
|-
|27th October || Rowan || Rowan
|-
|10th November || Hugh ||
|-
|24th November || Chiara ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| || ||
|}

Quantum Computing for Quantum Chemistry journal club info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2023-10-05T14:00:54Z

Ksp31: /* Group Meetings */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other <s>Monday</s> Friday at 3.30pm.

===Michaelmas 2023===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|13th October || Lila || Chiara
|-
|27th October || Rowan || Rowan
|-
|10th November || Hugh/Chiara ||
|-
|24th November || Hugh/Chiara ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| || ||
|}

Quantum Computing for Quantum Chemistry journal club info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2023-09-26T08:18:20Z

Ksp31: /* Michaelmas 2023 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other Monday at 3.30pm.

===Michaelmas 2023===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|13th October || Lila || Chiara
|-
|27th October || Rowan || Rowan
|-
|10th November || Hugh/Chiara ||
|-
|24th November || Hugh/Chiara ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| || ||
|}

Quantum Computing for Quantum Chemistry journal club info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2023-09-26T08:17:31Z

Ksp31: /* Michaelmas 2023 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other Monday at 3.30pm.

===Michaelmas 2023===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|20th October || Lila || Chiara
|-
|27th October || Rowan || Rowan
|-
|10th November || Hugh/Chiara ||
|-
|24th November || Hugh/Chiara ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| || ||
|}

Quantum Computing for Quantum Chemistry journal club info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2023-09-22T10:14:45Z

Ksp31: /* Michaelmas 2023 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other Monday at 3.30pm.

===Michaelmas 2023===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|20th October || Rowan || Chiara
|-
|27th October || Hugh/Lila/Chiara ||
|-
|10th November || Hugh/Lila/Chiara ||
|-
|24th November || Hugh/Lila/Chiara ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| || ||
|}

Quantum Computing for Quantum Chemistry journal club info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2023-09-20T10:19:32Z

Ksp31: /* Summer 2023 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other Monday at 3.30pm.

===Michaelmas 2023===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|13th October || Rowan || Chiara
|-
|27th October || Hugh/Lila/Chiara ||
|-
|10th November || Hugh/Lila/Chiara ||
|-
|24th November || Hugh/Lila/Chiara ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| || ||
|}

Quantum Computing for Quantum Chemistry journal club info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Group Meetings

2023-09-20T10:18:04Z

Ksp31: /* Past Group Meetings */

=Past Group Meetings=

===Summer 2023===
{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|2nd August || Summer Interns || Lila
|-
|21st August || Jack || Andreea
|-
|1st September || Summer Interns || Miriam
|-
|18th September || Kripa || Alex
|}

===Easter 2023===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|1st May || Chiara || Andreea
|-
|15th May || Lila || Kripa
|-
|26th May || Yi Sun || Jack
|-
|12th June || Daniel || Alex
|}

===Lent 2023===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|23rd January || Kripa || Moritz
|-
|6th February || Jack || Alex
|-
|20th February || Andreea || Juan
|-
|6th March || Eline + Juan || Kripa
|}

===Michaelmas 2022===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|10th October || Yi Sun || Kripa
|-
|24th October || Chiara|| Andreea
|-
|7th November || Lila || Eline
|-
|21st November || Moritz || Alex (Mince Pies)
|}

===Summer 2022===
{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|25th July || WATOC Review & IPLU Discussion ||
|-
|8th August || Brian || Andreea
|-
|30th August || Nick || Daniel
|-
|12th September|| Interns || Alex
|}

===Easter 2022===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|9th May || Lila || Andreea
|-
|23rd May || Daniel || Brian
|-
|13th June|| Benjamin || Kripa
|-
|20th June|| Kripa || Lila
|}

===Lent 2022===
{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|24th January || Fabio || Andreea
|-
|7th February || Andreea || Kripa
|-
|21st February|| Nick || Brian
|-
|21st March|| Brian || Chiara
|}
=== Michaelmas 2021===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|4th October|| INFORMAL ||
|-
|18th October || Nick || Fabio
|-
|1st November || Kripa || Andreea
|-
|15th November|| Chiara || Nick
|-
|29th November|| David || Kripa
|}

===Summer 2021===

{|
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|12th July 2021 || INFORMAL ||
|-
|20th July 2021 || INFORMAL ||
|-
|27th July 2021 || - ||
|-
|3rd August 2021 || Cesar & Tarik || Chelsea Buns
|-
|9th August 2021 || Constance || Brian
|-
|16th August 2021 || INFORMAL ||
|-
|23rd August 2021|| Benjamin || Andreea
|-
|30th August 2021|| INFORMAL ||
|-
|6th September 2021 || Arta || Kripa
|-
|13th September 2021 || Anna, Brian & Zian|| Nick
|}
===Easter 2021===

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|19th April 2021 || INFORMAL ||
|-
|26th April 2021 || INFORMAL ||
|-
|3rd May 2021 || INFORMAL ||
|-
|10th May 2021 || Andreea || Fruit based
|-
|17th May 2021 || INFORMAL ||
|-
|24th May 2021 || Nick Blunt || Cheesecake
|-
|31st May 2021|| INFORMAL ||
|-
|7th June 2021|| Fabio|| (Boston) Cream Pie
|-
|14th June 2021|| Benjamin ||
|}

==Lent 2021==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|18th January 2021 || INFORMAL || -
|-
|25th January 2021 || INFORMAL || Shortbread
|-
|1st February 2021 || Bang || Non-trivial Symmetry Element
|-
|8th February 2021 || INFORMAL ||
|-
|15th February 2021 || César and Tarik || Carrot Cake
|-
|22th February 2021 || INFORMAL ||
|-
|1st March 2021|| Kripa || Doughnuts (Krispy Kreme)
|-
|8th March 2021|| Hang & Tiger (Part III) || Date Loaf
|-
|15th March 2021|| Elizabeth & Isha (Part III) || Mother's Choice
|}
==Michaelmas 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|12th October 2020 || Andreea || Kripa
|-
|19th October 2020 || INFORMAL || Andreea
|-
|26th October 2020 || Fabio || Bang
|-
|2nd November 2020 || INFORMAL || Fabio
|-
|9th November 2020 || INFORMAL|| Bang
|-
|16th November 2020 || Kripa || Elizabeth
|-
|23rd November 2020|| Arta || Arta
|-
|30th November 2020 || INFORMAL || Andreea
|}

==Summer 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake & Recipe'''
|-
|20th July 2020 || Nick || [https://en.wikipedia.org/wiki/Kiev_cake Kiev cake]
|-
|10th August 2020 || Hugh || Crumble
|-
|24th August 2020 || Constance, Hang, Jimin||
|-
|7 September 2020|| Elizabeth, (Nick), Tiger, Toby ||
|}

==Easter 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake & Recipe'''
|-
|4th May 2020 || Andreea || Tiramisu
|-
|18th May 2020 || David || Carrot
|-
|1st June 2020 || Hugh || Chocolate & Ginger
|-
|15 June 2020|| Bang || Salted Caramel
|}

==Lent 2020==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|27th January 2020 || Bang || Alex
|-
|10th February 2020 || Alex || Kripa & George
|-
|24th February 2020 || Fabio || Bang
|-
|10th March 2020|| Kripa & George || Andreea
|}

==Michaelmas 2019==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|21st October 2019 || Fabio || Hugh
|-
|4th November 2019 || Andreea || David
|-
|18th November 2019 || David || Andreea
|-
|2nd December 2019 || Hugh || Fabio
|}

==Summer Vacation 2019==

{|
|'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|22nd July 2019 || Rhiannon || David
|-
|19th August 2019 || Hugh || Fabio
|-
|2nd September 2019 || Bang || Summer Students
|-
|16th September 2019 || Summer Students || Alex
|}

==Easter Term 2019==

{|
|'''Date''' || '''Talk''' ||| '''Cake'''
|-
|2nd May 2019 || Rhiannon || Fabio
|-
|13th May 2019 || David || Bang
|-
|27th May 2019|| Andreea || Alex
|-
|10th June 2019 || Fabio || Rhiannon
|}

==Easter Vacation 2019==

{|
|'''Date''' || '''Talk''' ||| '''Cake'''
|-
|8th April 2019 || The Boss || Andreea
|}

==Lent Term 2019==

{|
|'''Date''' || '''Talk''' ||| '''Cake'''
|-
|7th January 2019 || Hugh || Alex
|-
|21st January 2019 || Bang || Andreea
|-
|4th February 2019 || Verena || Alex G
|-
|18th February 2019 || Charlie || Alex
|-
|4th March 2019 || Alex G || Verena
|}

==Michaelmas Term 2018==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|1st October 2018 || Bang ||
|-
|15th October 2018 || Alex T || Verena
|-
|30th October 2018 || David || Alex
|-
|12th November 2018 || [Alex T away]
|-
|26th November 2018 ||
|}

==Long Vacation 2018==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|'''3.30pm Tue''' 28th August 2018 || Jirka || Bang
|-
|Mon 10th September 2018 || Verena & Charlie || Alex
|-
|'''Tue''' 25th September 2018 || Richard & Ian
|}

==Easter Term 2018==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|7th May 2018 || Letitia - Alex and Sav no longer in Crete that day. || Alex to bring Greek gifts
|-
|14th May 2018 || David
|-
|4th June 2018 || Bang
|-
|11th June 2018 || Verena (cancelled)
|}

==Lent Term 2018==
{|
|+
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|22nd January 2018 || Letitia || Bang
|-
|5th February 2018 || Alex ||
|-
|19th February 2018 || Flash talks || Alex
|-
|5th March 2018 || [Electronic Structure meeting]
|-
|19th March 2018 || [Scientific Computing Day]
|}

==Michaelmas Term 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|2nd October || Kris || Verena
|-
|16th October || Sav || Charlie
|-
|30th October || David || Hugh?
|-
|13th November || Bang || ?
|-
|27th November || Jonathan || Alex T
|-
|11th December || Hugh || Sav
|}

==Research Period 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|8th August || ? || ?
|-
|22nd August || Adam/Andreea/Jamie/Kris || ?
|-
|5th September || Charlie & Hugh || ?
|-
|19th September || Verena || Kris
|}

==Easter Term 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|24th April || Sav || Alex T
|-
|8th May || Hugh || Sav
|-
|30th May|| Charlie || ?
|-
|12th June || Verena || ?
|}

==Lent Term 2017==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|9th January || Sav || Charlie & Verena
|-
|23rd January || Henry & Alex C || Ruth
|-
|13th February || Choi & Ben || Alex T
|-
|27th February || Bang || Alex C
|-
|13th March || Verena || Ben
|}

==Michaelmas Term 2016==
{|
|'''Date''' || '''Mini-talk''' ||| '''Cake'''
|-
|10th October 2016 || Charlie || Hugh
|-
|24th October 2016 || Verena || Sav
|-
|7th November 2016 || Choi || Alex
|-
|21st November 2016 || Ruth || Bang & Verena
|-
|5th December 2016 || [AJWT away]
|-
|19th December 2016 || Hugh || Choi
|}

==Research Period 2016==
{|
|+
|'''Date''' || '''Mini-talk'''
|-
|15th August 2016 || Jonathan
|-
|30th August 2016 || Charlie
|-
|12th September 2016 || James
|-
|26th September 2016 || CANCELLED
|}

Main Page

2023-08-28T19:41:35Z

Ksp31: /* Summer 'Interns' */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other Monday at 3.30pm.

===Summer 2023===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|2nd August || Summer Interns || Lila
|-
|21st August || Jack || Andreea
|-
|1st September || Summer Interns || Miriam
|-
|18th September || Kripa ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| || ||
|}

Quantum Computing for Quantum Chemistry journal club info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group

=Summer 'Interns'=
{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2023-08-28T19:36:18Z

Ksp31: /* Summer 2023 */

<div style="text-align: center;">
''
# _________ # ___ ___ # ______ # ___ __ __ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \#
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/#
# # # # #
''
</div>
<div style="text-align: center;">
''
# _______ # ______ # ______ # __ __ # ______ #
#/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # #
''
</div>

Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)

In this Wiki you can find various pieces of useful information, such as when group meetings are, who is going to bring cake, how to run a particular calculation or perform a certain computer trick, who's using which computer in the group, and so on. You can also see how fun we are as a group by looking at our various photos.

=Group Calendar=
https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745

{{Special:IframePage}}

=Group Expectations=

The Group Expectations document is available on overleaf https://www.overleaf.com/read/yddfjrvpjckj

=Group Meetings=

Past Group Meetings [[Past Group Meetings|here]]. Group Meetings (usually) take place every other Monday at 3.30pm.

===Summer 2023===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|2nd August || Summer Interns || Lila
|-
|21st August || Jack || Andreea
|-
|1st September || Summer Interns || Miriam
|-
|18th September || Kripa ||
|}

=Journal Club=
12pm in the cybercafe with pizza provided (alternative possible).

Past Journal Clubs [[Journal Clubs|here]].
===2023-24===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| || ||
|}

Quantum Computing for Quantum Chemistry journal club info available at https://www.ch.cam.ac.uk/group/thom/quantum-computing-quantum-chemistry-discussion-group

=Summer 'Interns'=
{| class="wikitable"
! style="width: 40ex;" |'''Name''' || style="width: 50ex;" | '''Project''' || style="width: 24ex;" | '''Machine'''
|-
| Theo Hatcher || Excited States and RevQCMagic || gritstone
|-
| Bence Csakany || Quantum Computing on GPUs and FPGAs || obsidian
|-
| Miriam Al-Hadithi || LCLU Astrochemistry || hylas
|-
| Peter Yang || Hamiltonian decomopositions in Quantum Computing || chiron
|}

Past Summer Interns [[Past Summer Interns|here]].

=Summer Dates=
{| class="wikitable"
! Name
! 3rd July
! 10th July
! 17th July
! 24th July
! 31st July
! 7th August
! 14th August
! 21st August
! 28th August
! 4th September
! 11th September
! 18th September
! 25th September
|-
| Alex || London IChO || || Zurich IChO || Zurich until Tuesday || || || || || || || LJC meeting || || ||
|-
| Theo || || || ||Starts Monday || || || || || || || || Finishes Friday ||
|-
| Bence || || Starts Wednesday || || || || || || || || Finishes Tuesday || || ||
|-
| Miriam || || Starts Wednesday (or Monday?)|| || || || || || || Finishes Friday || || || ||
|-
| Peter || || Starts Monday || || || || || || || Finishes Friday || || || ||
|}

=Dissertations=
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]

= [[Group_List | Group List]] =
The full timeline of all current and past group members is available [https://wikis.ch.cam.ac.uk/thom/wiki/index.php/Group_List here]. NB autogenerated by `thom-fs-common/group/groupwiki`

An up to date list of group members is also available [http://www.ch.cam.ac.uk/group/thom here].

[[File:Wales.jpg|1000px|thumb|center|Thom Group Retreat, Wales, Lent 2023]]
[[File:Snowdon0.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]
[[File:Snowdon1.jpeg|1000px|thumb|center|Thom Group Retreat, Snowdon, Lent 2023]]

[[File:GroupPhotoJul2022.jpg|1000px|thumb|center|Thom Group photo Summer 2022]]

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip<br>
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom<br>
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar
</div>

[[File:AJWT_group_photo_2_5_19-4926_taken_by_Nathan_Pitt_University_of_Cambridge-tighter.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019]]
[[File:AJWT_Group_photo-5470_taken_by_Nathan_Pitt_University_of_Cambridge.jpg|500px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017]]

= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.

- Clusters available.

- Storage available.

= Computing Setup Guide =
Anaconda takes up a lot of space on /home so it's worth running

mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda

= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:

# General bash commands
# Setting up cygwin
# Setting up [https://git-scm.com/book/en/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key ssh keys] and general bash commands what are helpful
# Setting up ssh config files
# using [[GIT]]
# [[The Ten Git-mmandments]]
# Useful cerebro queue commands
# Some [[vim]] tidbits

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

# Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
# In the terminal run the command ''ssh -X crsid@citadel.ch.cam.ac.uk''
# When prompted input your Admitto username (crsid) and password
# Once this has worked run the command ''ssh -X crsid@machinename'' in the terminal to log into a particular machine

Set up logging in without a password:

# Generate an ssh key by running the command ''ssh-keygen'' in the terminal, as described in detail in the section "Introduction to basic shell commands"
# Use ''cd ~/.ssh'' to navigate to the directory holding the keys, and copy the text from the file "id_rsa.pub" beginning with ssh-rsa. This is your public ssh key
# Log into the department citadel machine, and create / navigate to a directory called .ssh
# Use ''chmod 700 .ssh'' to set permissions for the directory
# Input ''vi authorized_keys'' to open up the vi text editor. Press i, then paste in your public ssh key. Press escape, then type '':wq'' and press enter to write and quit the editor
# Log into the particular machine you want to ssh to, and repeat steps 3 to 5
# Exit back to your machine and navigate to the home directory
# Input ''vi .ssh/config'' to open the vi text editor. Press i, then paste in the following, with your crsid and machine name in the places given:
Host citadel
User crsid
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host machinename
Hostname machinename
ProxyCommand ssh citadel -W %h:%p
User crsid
ForwardAgent yes
ServerAliveInterval 60
ServerAliveCountMax 10

Press escape, then input '':wq'' followed by enter to exit the editor.
You can now log straight into citadel with ''ssh citadel'' or straight into your machine with ''ssh machinename''. The last two commands stop the ssh being killed if you are idle for too long. The ''ServerAliveInterval'' is how many seconds to ping a null packet, and the ''ServerAliveCountMax'' are how many consecutive times it needs to fail for the ssh to be killed.

===File Transfer Protocol===

You may want to transfer files between department machines and your computer. The standard way is to ''scp'' via the terminal with commands :
UPLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" LocalPath/FileName crsid@machinename.ch.cam.ac.uk:/RemotePath
DOWNLOAD :
scp -o ProxyCommand="ssh crsid@citadel.ch.cam.ac.uk nc machinename 22" crsid@machinename.ch.cam.ac.uk:/RemotePath/FileName LocalPath

However, a more convenient way is to set up a File Transfer Protocol (FTP) between machines. It can come with a graphic user interface, where you can drag and drop files from the department machine to your computer.

====Windows====

I recommend the WinSCP software. You can download it from [https://winscp.net/eng/download.php here].
Once installed, click ''New Session'', and choose ''SFTP'' protocol with :
Hostname = machinename
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Then click on ''Advanced...'', ''Tunnel'' tab, check the ''Connect through SSH tunnel'' tickbox and enter:
Hostname = citadel.ch.cam.ac.uk
Port number = 22
Username = crsid
Leave 'Password' entry empty.
Click ''OK'' and click ''Save'', and finally ''Login''. Enter your admitto password twice.
You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

====Mac/Linux====

You can download FileZilla for [https://filezilla-project.org/download.php?platform=osx MacOS] or [https://filezilla-project.org/download.php?platform=linux64 linux].
The problem is that FileZilla does not support tunnel ssh. To open the connection, you need to use a ssh client like puTTY.
On MacOS please follow [https://phoenixnap.com/kb/install-putty-on-mac this guide].

On Linux you can do :
sudo apt-get install -y putty
Open it by typing ''putty'' on the terminal. The interface should open.
Type the following entries :

in the ''SSH/Tunnels'' tab :
Source Port = 3111
Destination = machinename:22
local
auto
and click ''Add''. (source port can be any number > 1024)

in the ''session'' tab :
Host Name = citadel.ch.cam.ac.uk
port = 22
connection type = SSH
Enter a name for this connection in the ''saved sessions'' entry, and click ''Save''.

Now click ''Open''.
A terminal should open, type your crsid and your admitto password, you're now logged into Citadel (it's normal that it's not your machine).

Now open FileZilla, and enter :
Host = sftp://localhost
username = crsid
password = admitto password
port = 3111
and click ''Quickconnect''. (port needs to be the same as source port in puTTY).

A window will open (Unknown host key), click ''OK''. Hopefully the connection is successful.

You can now navigate in the directories of the remote machine on the right tab, and of your local computer on the left tab, and you can transfer files between the two with a drag and drop. Enjoy !

=== Using VSCode Remote ===
====Windows====
# Find your wsl ssh config file as a Windows path, for example ''''\\wsl.localhost\Ubuntu\home\<name>\.ssh\config'''''
# Make sure you have the 'Remote SSH' extension installed in VSCode
# In your config file, instead of using the layout above, change it to
Host citadel
User <crsid>
Hostname citadel.ch.cam.ac.uk
ForwardAgent yes
ProxyCommand none
Host <machinename>
Hostname <machinename>
ProxyJump citadel
User <crsid>
ServerAliveInterval 60
ServerAliveCountMax 10
(this has removed the ForwardAgent and ProxyCommand lines and replaced with ProxyJump instead)

# <li value="4">In VSCode, set your ssh config file manually to your path. Your wsl ssh folder can be copied into a Windows path (C:\Users\<user>\<blah>)if VSCode is not happy with the wsl path.</li>
# At the bottom left, the green arrows is where you will be able to connect to remote machines. Click on it, and it should recognise all the hosts in your config file
# Select your host, and you will need to enter your password twice

= Useful Software =
# Using [[QChem]]
# Using [[QCMagic]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]

= Useful Information =
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# Backed-up [[Storage]]
# [[How to get IQMol to run a local version of Q-Chem via SSH]]
# [[Slow ubuntu dash]]
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[The Ten Git-mmandments]]: what NOT to do

= [[Archiving_data | Archiving data for the university repository]] =

= [[Website_to_do | To-do list for the Thom Group Website]] =

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

- Sandbox for safe editing : [[Sandbox| Sandbox]]

- A pretty picture

- A "How to:" page on setting up cygwin, ssh keys and general bash commands what are helpful

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Sandbox

2023-08-21T18:37:22Z

Ksp31: