Thom Group Wiki - User contributions [en]

Main Page

2026-05-28T14:48:41Z

Lc892: /* Research Data Management */

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<pre style="display:inline-block; text-align:left; white-space:pre; margin:0; padding:1em 1.5em; border:2px solid #7c3aed; border-radius:12px; background:#0f172a; box-shadow:0 0 12px rgba(124,58,237,0.45);">
<span style="color:#d62828;"> _________ ___ ___ ______ ___ __ __ </span>
<span style="color:#f77f00;">/________/\ /__/\ /__/\ /_____/\ /__//_//_/\ </span>
<span style="color:#fcbf49;">\__.::.__\/ \::\ \\ \ \ \:::_ \ \ \::\| \| \ \ </span>
<span style="color:#2a9d8f;"> \::\ \ \::\/_\ .\ \ \:\ \ \ \ \:. \ \ </span>
<span style="color:#457b9d;"> \::\ \ \:: ___::\ \ \:\ \ \ \ \:.\-/\ \ \ </span>
<span style="color:#6a4c93;"> \::\ \ \: \ \\::\ \ \:\_\ \ \ \. \ \ \ \ </span>
<span style="color:#8338ec;"> \__\/ \__\/ \::\/ \_____\/ \__\/ \__\/ </span>
</pre>
</div>

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<pre style="display:inline-block; text-align:left; white-space:pre; margin:0; padding:1em 1.5em; border:2px solid #7c3aed; border-radius:12px; background:#0f172a; box-shadow:0 0 12px rgba(124,58,237,0.45);">
<span style="color:#ff0000;"> _______ ______ ______ __ __ ______ </span>
<span style="color:#ff7f00;">/______/\ /_____/\ /_____/\ /_/\/_/\ /_____/\ </span>
<span style="color:#ffff00;">\::::__\/__ \:::_ \ \ \:::_ \ \ \:\ \:\ \ \:::_ \ \ </span>
<span style="color:#00cc00;"> \:\ /____/\ \:(_) ) )_ \:\ \ \ \ \:\ \:\ \ \:(_) \ \ </span>
<span style="color:#0099ff;"> \:\\_ _\/ \: __ `\ \ \:\ \ \ \ \:\ \:\ \ \: ___\/ </span>
<span style="color:#4b0082;"> \:\_\ \ \ \ \ `\ \ \ \:\_\ \ \ \:\_\:\ \ \ \ \ </span>
<span style="color:#8b00ff;"> \_____\/ \_\/ \_\/ \_____\/ \_____\/ \_\/ </span>
</pre>
</div>

</div>

=About=

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. For members of the group please feel free to edit the contents of the wiki and fix any errors that you are bound to spot.

== [[Group_List | Group List and Photos]] ==

Here you can find photos of the group in various locations. There is also a helpful Gantt chart illustrating the storied group history. The chart should ideally be updated termly, the current chart maintainer is Luke Wright and you should email him with any complaints.

== [[Summer_Interns | Summer Interns]] ==

Email theory-sec@ch.cam.ac.uk for summer internship opportunities in the group. You are welcome to suggest ideas for a project you would like to do, but ideas are also available for assignment.

==[https://www.overleaf.com/read/yddfjrvpjckj Group Expectations]==

The Group Expectations document is available on Overleaf above. The rules outlined must be obeyed at all costs, if not, the consequences are dire.

=Events=

This section contains information and dates about all regularly or spontaneously scheduled academic events.

==[https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745 Group Calendar]==
The group calendar is available at the link above. For maximum group efficiency you should add this calendar to your personal calendar. Instructions for how to do this are pending if I can be bothered to write them.

{{Special:IframePage}}

==[[Past Group Meetings|Group Meetings]]==

Group Meetings take place every Thursday at 15.30 in U203. For anyone who needs to book a room for group meetings (or otherwise), follow this link [https://bookings.ch.cam.ac.uk/lecture-theatres/mrbs/ here] to see room availability. The current term's group meetings are available below, so that you need not click the above link (which contains past group meetings).

===Easter 2026===
{| class="wikitable"
! style="width: 20ex;" | Date
! style="width: 18ex;" | Talk
! style="width: 18ex;" | Cake
|-
| 30 April || Luke + Corey + Katrina || Luke
|-
| 7 May || Informal || Lila
|-
| 14 May || Free time ||
|-
| 21 May || Dylan (Jesus MCR?) ||
|-
| 28 May || Emil || Jack
|-
| 4 June || Informal ||
|-
| 11 June || Reka ||
|-
| 18 June || Informal ||
|}

==Journal Club==
Journal Club occurs about twice a term, it usually occurs at 12pm in one of the Cybercafe rooms (U202 or U203) pizza or alternatives are provided. Upcoming and Past Journal Clubs are found [[Journal Clubs|here]].

==Seminars==

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

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

==Quantum Computing Brainstorm==
From Easter 2026, informal quantum discussions taking place at 10am on Thursdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

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

==Forthcoming Conferences==
{| class="wikitable"
! style="width: 20ex;" | Dates
! style="width: 18ex;" | Name
! style="width: 18ex;" | Where
! style="width: 18ex;" | Attending?
|-
| 31st May - 6th Jun 2026 || [https://www.icqc2026.org/ International Congress of Quantum Chemistry] || Berkeley, California || Andreea
|-
| 7th Sep - 11tb Sep 2026 || [https://copl.ethz.ch/events/origins-federation-conference.html Origins Federation] || Zurich, Switzerland || Alex, Bence
|-
| 13th Sep - 18th Sep 2026 || [https://qce.quantum.ieee.org/2026/ IEEE Quantum Week] || Toronto, Canada || Lila
|-
| 14th Sep - 16th Sep 2026 || [https://www.rsc.org/events/find-an-event/molecular-excited-states-theory-and-experiment-faraday-discussion Excited States Faraday Discussion] || Cambridge, UK|| Alex
|-
| 15th Sep - 18th Sep 2026 || [https://www.girton.cam.ac.uk/events/foundations-quantum-technologies Foundations of Quantum Technologies] || Girton College, Cambridge, UK ||
|-
| 19th Sep - 23rd Sep 2026 || [https://www.mes2026.com/ Molecular Electronic Structure 2026] || Kamena Vourla, Greece ||
|-
| 9th Jan - 14th Jan 2028 || [https://watoc2028.org/ World Association of Theoretical and Computational Chemists 2028]|| Mérida, México ||
|}

==Forthcoming Workshops and Schools==
{| class="wikitable"
! style="width: 20ex;" | Dates
! style="width: 18ex;" | Name
! style="width: 18ex;" | Where
! style="width: 18ex;" | Attending?
|-
| 1st July - 3rd July 2026 || [https://ccp-qc.ac.uk/ws_mb/ Tackling the Many‑Body Problem in Condensed Matter with Quantum Computing] || University of Strathclyde, Glasgow || Lila
|-
| 28th Sep - 2nd Oct 2026 || Lennard-Jones Centre Summer School || Cambridge, UK||
|-
| 14th Sep - 18th Sep 2026 || [https://www.quantinuum.com/inquanto-summer-school Inquanto Summer School] || Cambridge, UK||
|}

= Research and Projects =

== [[Project_Ideas | Project Ideas]] ==
Based on recent talks and conferences. Contains both project ideas and more general questions that would be nice to answer.

== Dissertations ==
Please upload any missing documents to these folders such that these contain a complete history of every project or work completed in the group.
* [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]
* [https://www.overleaf.com/read/ffdvzskxvnbm#2e9673 Template for L<sup>A</sup>T<sub>E</sub>X poster]

= Computers =

This section contains all information you could ever need about computers and how to use them.

== [[Computer_and_Storage_List | Computing Resources]] ==

See this section for what computers the group members are using, what compute clusters are available, and where you can store files.

== [[Introduction | Introduction to basic shell commands]] ==
There are a number of tutorials available which document basic operations that are useful. Some highlights include setting up SSH keys, X-forwarding, or how to use vim. Click the hyperlink for the full list.

== [[Connecting_Machines | How to connect to department machines]] ==

It can be useful often to connect to computers in department remotely. Please keep your work-life balance in mind.

== [[Installing_Slack | How to install Slack on department machines ]] ==

Group communication is done primarily through Slack, it may be useful to install it. Alternatively we could begin using pigeon-mail or smoke signals.

== Software Tutorials==
# [[QChem]]
# [[SimpleDMC]]
# [[MRCC]]
# [[GAMESS]]
# [[RevQCMagic]]

== [[Research_Data| Research Data Management ]] ==

= Uncategorisable =

The following sections could not be given a heading in the great wiki organisation of 2026 and thus are labelled as uncategorisable. See [https://en.wikipedia.org/wiki/Russell%27s_paradox Russell's paradox] for more details.

== Useful Information ==

Here are some things that were deemed as useful once upon a time. Please add to the list.

# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# Where to get [[Travel Money]]
# [[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]] ==

For publications data must be archived in accordance with university policy, instructions are here.

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

If there are desired wiki changes but the will to implement is not there they can be written here.

= Archive =

Anything not updated for more than 5 years should be put into this section.

== [[Group_activities | Group Activities]] ==

2026-03-24T12:45:16Z

Lc892: /* Tutorial */

[[File:git.png|link:http://xkcd.com/1597/]]

A GIT repository is a data management system for your files. It is useful for version control.

#First of all, in the directory you wish to make the repository, type 'git ''init'''
#To add a file to the repository, type 'git add ''filename'''
#To commit changes to the repository, type 'git commit ''filename'''. This will bring up a text file where it is possible to record details of the changes.
#To retrieve a file from the repository, type 'git checkout ''filename'''

==Tutorial==

There are many tutorials available. Here are two that look interesting

https://www.vogella.com/tutorials/Git/article.html

https://www.atlassian.com/git/tutorials/

This website will teach you git in a gamified, visual way

https://learngitbranching.js.org

== Group gitlab server ==

# Accessible at https://gitlab.developers.cam.ac.uk/ch/thom

It's '''essential''' to create an additional non-Raven identity by Editing your profile, which enables gitlab access after having left.

A useful piece of workflow advice: If you want to suggest some specific code changes to a Merge request, you can branch off the branch and create a new (sub-)merge request to merge into the original

==Git prompts==
If you wish to reach a higher level of git mastery, it's often helpful to have git show what your current checked out branch is in your command line.
You'll need to put the .gitprompt.bash script your home directory. [There may be updates available to this if anybody would like to look]

<pre>
scp carpathia:~ajwt3/.gitprompt.bash ~
</pre>

I have these lines in my .bashrc (which invoke a little more magic than just git prompt)

<pre>
. ~/.gitprompt.bash
export UN=`uname -r |sed 's/(.*)//'`
export PS1='\[\e]0;\u@\h:\w\a\]\n\[\e[32m\]\u@\h:\[\e[33m\]\w$(__git_ps1 " [%s]")\[\e[0m\]\$ '
</pre>

--[[User:Ajwt3|ajwt3]] ([[User talk:Ajwt3|talk]]) 10:20, 13 September 2016 (BST)

2025-08-04T09:03:15Z

Lc892:

Main Page

2025-08-04T09:02:56Z

Lc892: /* 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.

===Easter 2025===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|1 May || Rowan/Charlie || Andreea
|-
|8 May || Informal || Alex
|-
|15 May || Jack || Jack
|-
|22 May || Chiara || Reka
|-
|29 May || Dylan || Lila
|-
|5 June || Informal || Rowan
|-
|12 June || Informal || Dylan
|-
|19 June || Lila ||
|}

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 Wednesdays 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 interns start dates:===

{| class="wikitable"
! style="width: 20ex;" |'''Name''' || style="width: 20ex;" | '''Start date''' || style="width: 20ex;" | '''End date'''
|-
|Tom Edwards|| 7th July || 29th August
|-
|Nestor Novakovic || 30th June || 5th September
|-
|Petar Panayotov|| 15th July || 15th September
|-
|Divye Baid|| 30th June || 22nd August
|-
|...|| ...
|}

=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:Group_Punting_2025.jpg|1000px|thumb|center|Thom Group Punting Trip, river Cam, Summer 2025]]

[[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
# The bastion host barbican.ch.cam.ac.uk requires ssh keys and an MFA token to log in. Instructions can be found here: https://www.ch.cam.ac.uk/computing/network-bastion-host
# In the terminal run the command ''ssh -X crsid@barbican.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>

Group List

2025-06-23T11:44:38Z

Lc892:

<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 = 30/07/2025

# 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)
id:even value:rgb(0.486, 0.733, 1)
id:textblack value:rgb(0,0,0)

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:NN0 text:_Nestor Novakovic
bar:TE0 text:_Tom Edwards
bar:DB0 text:_Divye Baid
bar:PP0 text:_Petar Panayotov
# 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:CW0 text:_Charlie Wheelwright
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: 20/07/2025 $GroupLeader text:
bar:CL0 from: 01/10/2021 till: 20/07/2025 $PhD text:
bar:JT0 from: 01/10/2022 till: 20/07/2025 $PhD text:Joint with Forse group
bar:RP0 from: 25/04/2023 till: 20/07/2025 $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: 20/07/2025 $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: 20/07/2025 $PhD text:
bar:RH0 from: 01/10/2024 till: 20/07/2025 $PhD text:
bar:DC0 from: 01/10/2024 till: 20/07/2025 $MPhil text:
bar:NN0 from: 30/06/2025 till: 20/07/2025 $Summer text:
bar:TE0 from: 07/07/2025 till: 20/07/2025 $Summer text:
bar:DB0 from: 15/07/2025 till: 20/07/2025 $Summer text:
bar:PP0 from: 15/07/2025 till: 20/07/2025 $Summer 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:CW0 from: 01/10/2024 till: 30/06/2025 $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:125.8 color:odd
from: $bigbang till: $bigcrunch atpos:138.6 color:even
from: $bigbang till: $bigcrunch atpos:151.4 color:odd
from: $bigbang till: $bigcrunch atpos:164.2 color:even
from: $bigbang till: $bigcrunch atpos:177.0 color:odd
from: $bigbang till: $bigcrunch atpos:189.8 color:even
from: $bigbang till: $bigcrunch atpos:202.60000000000002 color:odd
from: $bigbang till: $bigcrunch atpos:215.4 color:even
from: $bigbang till: $bigcrunch atpos:228.2 color:odd
from: $bigbang till: $bigcrunch atpos:241.0 color:even
from: $bigbang till: $bigcrunch atpos:253.8 color:odd
from: $bigbang till: $bigcrunch atpos:266.6 color:even
from: $bigbang till: $bigcrunch atpos:279.4 color:odd
from: $bigbang till: $bigcrunch atpos:292.20000000000005 color:even
from: $bigbang till: $bigcrunch atpos:305.0 color:odd
from: $bigbang till: $bigcrunch atpos:317.8 color:even
from: $bigbang till: $bigcrunch atpos:330.6 color:odd
from: $bigbang till: $bigcrunch atpos:343.4 color:even
from: $bigbang till: $bigcrunch atpos:356.20000000000005 color:odd
from: $bigbang till: $bigcrunch atpos:369.0 color:even
from: $bigbang till: $bigcrunch atpos:381.8 color:odd
from: $bigbang till: $bigcrunch atpos:394.6 color:even
from: $bigbang till: $bigcrunch atpos:407.40000000000003 color:odd
from: $bigbang till: $bigcrunch atpos:420.20000000000005 color:even
from: $bigbang till: $bigcrunch atpos:433.0 color:odd
from: $bigbang till: $bigcrunch atpos:445.8 color:even
from: $bigbang till: $bigcrunch atpos:458.6 color:odd
from: $bigbang till: $bigcrunch atpos:471.40000000000003 color:even
from: $bigbang till: $bigcrunch atpos:484.20000000000005 color:odd
from: $bigbang till: $bigcrunch atpos:497.0 color:even
from: $bigbang till: $bigcrunch atpos:509.8 color:odd
from: $bigbang till: $bigcrunch atpos:522.6 color:even
from: $bigbang till: $bigcrunch atpos:535.4000000000001 color:odd
from: $bigbang till: $bigcrunch atpos:548.2 color:even
from: $bigbang till: $bigcrunch atpos:561.0 color:odd
from: $bigbang till: $bigcrunch atpos:573.8 color:even
from: $bigbang till: $bigcrunch atpos:586.6 color:odd
from: $bigbang till: $bigcrunch atpos:599.4000000000001 color:even
from: $bigbang till: $bigcrunch atpos:612.2 color:odd
from: $bigbang till: $bigcrunch atpos:625.0 color:even
from: $bigbang till: $bigcrunch atpos:637.8000000000001 color:odd
from: $bigbang till: $bigcrunch atpos:650.6 color:even
from: $bigbang till: $bigcrunch atpos:663.4 color:odd
from: $bigbang till: $bigcrunch atpos:676.2 color:even
from: $bigbang till: $bigcrunch atpos:689.0 color:odd
from: $bigbang till: $bigcrunch atpos:701.8000000000001 color:even
from: $bigbang till: $bigcrunch atpos:714.6 color:odd
from: $bigbang till: $bigcrunch atpos:727.4000000000001 color:even
from: $bigbang till: $bigcrunch atpos:740.2 color:odd
from: $bigbang till: $bigcrunch atpos:753.0 color:even
from: $bigbang till: $bigcrunch atpos:765.8000000000001 color:odd
from: $bigbang till: $bigcrunch atpos:778.6 color:even
from: $bigbang till: $bigcrunch atpos:791.4000000000001 color:odd
from: $bigbang till: $bigcrunch atpos:804.2 color:even
from: $bigbang till: $bigcrunch atpos:817.0 color:odd
from: $bigbang till: $bigcrunch atpos:829.8000000000001 color:even
from: $bigbang till: $bigcrunch atpos:842.6 color:odd
from: $bigbang till: $bigcrunch atpos:855.4000000000001 color:even
from: $bigbang till: $bigcrunch atpos:868.2 color:odd
from: $bigbang till: $bigcrunch atpos:881.0 color:even
from: $bigbang till: $bigcrunch atpos:893.8000000000001 color:odd
from: $bigbang till: $bigcrunch atpos:906.6 color:even
from: $bigbang till: $bigcrunch atpos:919.4000000000001 color:odd
from: $bigbang till: $bigcrunch atpos:932.2 color:even
from: $bigbang till: $bigcrunch atpos:945.0 color:odd
from: $bigbang till: $bigcrunch atpos:957.8000000000001 color:even
from: $bigbang till: $bigcrunch atpos:970.6 color:odd
from: $bigbang till: $bigcrunch atpos:983.4000000000001 color:even
from: $bigbang till: $bigcrunch atpos:996.2 color:odd
from: $bigbang till: $bigcrunch atpos:1009.0 color:even
from: $bigbang till: $bigcrunch atpos:1021.8000000000001 color:odd
from: $bigbang till: $bigcrunch atpos:1034.6 color:even
from: $bigbang till: $bigcrunch atpos:1047.4 color:odd
from: $bigbang till: $bigcrunch atpos:1060.2 color:even
from: $bigbang till: $bigcrunch atpos:1073.0 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 23rd June 2025 by Lila.
# To edit, please refer to thom-fs-common/group/groupwiki.

</timeline>
</div>

Sandbox

2025-06-23T11:43:44Z

Lc892:

Sandbox

2025-06-23T11:13:30Z

Lc892: Undo revision 1351 by Lc892 (talk)

Sandbox

2025-06-23T11:12:45Z

Lc892:

<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 = 01/12/2023

# 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)
id:even value:rgb(0.486, 0.733, 1)
id:textblack value:rgb(0,0,0)

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: 23/06/2025 $GroupLeader text:
bar:CL0 from: 01/10/2021 till: 23/06/2025 $PhD text:
bar:JT0 from: 01/10/2022 till: 23/06/2025 $PhD text:Joint with Forse group
bar:RP0 from: 25/04/2023 till: 23/06/2025 $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: 23/06/2025 $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: 23/06/2025 $PhD text:
bar:RH0 from: 01/10/2024 till: 23/06/2025 $PhD text:
bar:DC0 from: 01/10/2024 till: 23/06/2025 $MPhil text:
bar:CW0 from: 01/10/2024 till: 23/06/2025 $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 8th April 2025 by Kripa Panchagnula.
# This is testing the missing name labels on the left, using only "current" data.
# To edit, please refer to thom-fs-common/group/groupwiki.

</timeline>
</div>

Main Page

2024-11-21T10:20:56Z

Lc892: /* Group List */

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

===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
|}

=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 || []
|-
| TBC || || []
|-
| TBC || || []
|}

=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
# <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

2024-11-21T10:20:49Z

Lc892: /* 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
|}

=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 || []
|-
| TBC || || []
|-
| TBC || || []
|}

=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
# <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

2023-12-01T18:35:07Z

Lc892:

<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 = 01/12/2023

# 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)
id:even value:rgb(0.486, 0.733, 1)

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:DG0 text:Dr_Daniel Graf
bar:KP0 text:_Kripa Panchagnula
bar:CL0 text:_Chiara Leadbeater
bar:JT0 text:_Jack Taylor
bar:RP0 text:_Rowan Poklewski-Koziell
bar:LCT0 text:_Lila Cadi Tazi
bar:LW0 text:_Lijun Wang
bar:BC0 text:_Bence Csakany
# 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: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: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: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: 01/12/2023 $GroupLeader text:
bar:DG0 from: 01/04/2022 till: 01/12/2023 $Postdoc 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: 01/12/2023 $PhD text:
bar:CL0 from: 01/10/2021 till: 01/12/2023 $PhD text:
bar:JT0 from: 01/10/2022 till: 01/12/2023 $PhD text:Joint with Forse group
bar:RP0 from: 25/04/2023 till: 01/12/2023 $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: 01/12/2023 $PhD text:
bar:LW0 from: 01/10/2023 till: 01/12/2023 $MPhil text:
bar:BC0 from: 12/07/2023 till: 01/09/2023 $Summer text:
bar:BC0 from: 01/10/2023 till: 01/12/2023 $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: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: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: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:127.1 color:odd
from: $bigbang till: $bigcrunch atpos:141.2 color:even
from: $bigbang till: $bigcrunch atpos:155.3 color:odd
from: $bigbang till: $bigcrunch atpos:169.4 color:even
from: $bigbang till: $bigcrunch atpos:183.5 color:odd
from: $bigbang till: $bigcrunch atpos:197.6 color:even
from: $bigbang till: $bigcrunch atpos:211.7 color:odd
from: $bigbang till: $bigcrunch atpos:225.8 color:even
from: $bigbang till: $bigcrunch atpos:239.89999999999998 color:odd
from: $bigbang till: $bigcrunch atpos:254.0 color:even
from: $bigbang till: $bigcrunch atpos:268.1 color:odd
from: $bigbang till: $bigcrunch atpos:282.2 color:even
from: $bigbang till: $bigcrunch atpos:296.29999999999995 color:odd
from: $bigbang till: $bigcrunch atpos:310.4 color:even
from: $bigbang till: $bigcrunch atpos:324.5 color:odd
from: $bigbang till: $bigcrunch atpos:338.6 color:even
from: $bigbang till: $bigcrunch atpos:352.7 color:odd
from: $bigbang till: $bigcrunch atpos:366.79999999999995 color:even
from: $bigbang till: $bigcrunch atpos:380.9 color:odd
from: $bigbang till: $bigcrunch atpos:395.0 color:even
from: $bigbang till: $bigcrunch atpos:409.09999999999997 color:odd
from: $bigbang till: $bigcrunch atpos:423.2 color:even
from: $bigbang till: $bigcrunch atpos:437.3 color:odd
from: $bigbang till: $bigcrunch atpos:451.4 color:even
from: $bigbang till: $bigcrunch atpos:465.5 color:odd
from: $bigbang till: $bigcrunch atpos:479.59999999999997 color:even
from: $bigbang till: $bigcrunch atpos:493.7 color:odd
from: $bigbang till: $bigcrunch atpos:507.8 color:even
from: $bigbang till: $bigcrunch atpos:521.9 color:odd
from: $bigbang till: $bigcrunch atpos:536.0 color:even
from: $bigbang till: $bigcrunch atpos:550.0999999999999 color:odd
from: $bigbang till: $bigcrunch atpos:564.2 color:even
from: $bigbang till: $bigcrunch atpos:578.3 color:odd
from: $bigbang till: $bigcrunch atpos:592.4 color:even
from: $bigbang till: $bigcrunch atpos:606.5 color:odd
from: $bigbang till: $bigcrunch atpos:620.5999999999999 color:even
from: $bigbang till: $bigcrunch atpos:634.6999999999999 color:odd
from: $bigbang till: $bigcrunch atpos:648.8 color:even
from: $bigbang till: $bigcrunch atpos:662.9 color:odd
from: $bigbang till: $bigcrunch atpos:677.0 color:even
from: $bigbang till: $bigcrunch atpos:691.1 color:odd
from: $bigbang till: $bigcrunch atpos:705.1999999999999 color:even
from: $bigbang till: $bigcrunch atpos:719.3 color:odd
from: $bigbang till: $bigcrunch atpos:733.4 color:even
from: $bigbang till: $bigcrunch atpos:747.5 color:odd
from: $bigbang till: $bigcrunch atpos:761.6 color:even
from: $bigbang till: $bigcrunch atpos:775.6999999999999 color:odd
from: $bigbang till: $bigcrunch atpos:789.8 color:even
from: $bigbang till: $bigcrunch atpos:803.9 color:odd
from: $bigbang till: $bigcrunch atpos:818.0 color:even
from: $bigbang till: $bigcrunch atpos:832.1 color:odd
from: $bigbang till: $bigcrunch atpos:846.1999999999999 color:even
from: $bigbang till: $bigcrunch atpos:860.3 color:odd
from: $bigbang till: $bigcrunch atpos:874.4 color:even
from: $bigbang till: $bigcrunch atpos:888.5 color:odd
from: $bigbang till: $bigcrunch atpos:902.6 color:even
from: $bigbang till: $bigcrunch atpos:916.6999999999999 color:odd
from: $bigbang till: $bigcrunch atpos:930.8 color:even
from: $bigbang till: $bigcrunch atpos:944.9 color:odd
from: $bigbang till: $bigcrunch atpos:959.0 color:even
from: $bigbang till: $bigcrunch atpos:973.1 color:odd
from: $bigbang till: $bigcrunch atpos:987.1999999999999 color:even
from: $bigbang till: $bigcrunch atpos:1001.3 color:odd
from: $bigbang till: $bigcrunch atpos:1015.4 color:even
from: $bigbang till: $bigcrunch atpos:1029.5 color:odd
from: $bigbang till: $bigcrunch atpos:1043.6 color:even
from: $bigbang till: $bigcrunch atpos:1057.6999999999998 color:odd
from: $bigbang till: $bigcrunch atpos:1071.8 color:even

# 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

#######################################################
# Paste content of plotscript.txt until the above line.

# Updated on 16th August 2023 by Lila CT.
# To edit, please refer to thom-fs-common/group/groupwiki.

</timeline>
</div>

Sandbox

2023-12-01T17:56:54Z

Lc892:

2023-10-25T13:09:08Z

Lc892: /* Journal Clubs */

<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 Club=
Quantum Computing for Quantum Chemistry journal club 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.
Notes available [[Quantum Brainstorm|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

Main Page

2023-08-17T16:56:27Z

Lc892: /* To-do list for the Wiki */

<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 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 || Chiara
|-
|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