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''
<div style="overflow-x:auto; max-width:100%;">
# _________ # ___ ___ # ______ # ___ __ __ # # _______ # ______ # ______ # __ __ # ______ #
<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>
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<div style="overflow-x:auto; max-width:100%;">
Hello, Guten Abend, and Bienvenue to the new Thom Group Wiki. (Apparently evenings are good times to read the Wiki.)
<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>
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.


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


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.
{{Special:IframePage}}


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


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.
Past Group Meetings [[Past Group Meetings|here]].


== [[Summer_Interns | Summer Interns]] ==
===Lent 2022===


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


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


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"
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 36ex;" | '''Paper'''
! style="width: 20ex;" | Date
! style="width: 18ex;" | Talk
! style="width: 18ex;" | Cake
|-
|-
| 30 April || Luke + Corey + Katrina || Luke
| 8 Oct 2021 || Kripa || [https://arxiv.org/pdf/1712.01815.pdf/ Mastering Chess and Shogi by Self-Play with a General Reinforcement Learning Algorithm]
|-
|-
| 7 May || Informal ||
| 5 Nov 2021 || Brian || [https://pubs.acs.org/doi/10.1021/acs.jpca.1c05962 Neat, Simple and Wrong: Debunking Electrostatic Fallacies Regarding Noncovalent Interactions]
|-
|-
| 14 May || Reka ||
| 6 Dec 2021 || Kripa || [https://pubs.acs.org/doi/10.1021/acs.jpclett.1c03214 Quantum Algorithm for Full Configuration Interaction Calculations without Controlled Time Evolutions]
|-
|-
| 21 May || Informal ||
| 11 Feb 2022 || Nick || [https://www.nature.com/articles/s41598-021-00053-8 Mapping the NFT revolution: market trends, trade networks, and visual features]
|-
|-
| 28 May || MPhil ||
| 11 Mar 2022 || Andreea || [https://link.springer.com/article/10.1007/BF02650179 Simulating physics with computers]
|}

=Summer 'Interns'=
Past Summer Interns [[Past Summer Interns|here]].
==2021==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
| Anna Bui || 19th Jul - 17th Sep || NOCI Carbon Capture || hypatia
|-
|-
| 4 June || Informal ||
| Zian Wang || 19th Jul - 17th Sep || NOCI Photochemistry || obsidian
|-
|-
| 11 June || Dylan ||
| Brian Zhao || 19th Jul - 17th Sep || Stochastic Coupled Cluster || gritstone
|-
|-
| 18 June || Informal ||
| Nick Lee || 19th Jul - 17th Sep || NOCI Singlet Fission || moonraker
|}
|}


==Journal Club==
= [[Group_List | Group List]] =
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]].
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].


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


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


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


Outstanding questions, along with answers and helpful reading material, can be found [[Open Questions|here]].
= [[Computer_and_Storage_List | Computing Resources]] =
- Group computers available.


= Research and Projects =
- Clusters available.


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


== Dissertations ==
= Computing Setup Guide =
Please upload any missing documents to these folders such that these contain a complete history of every project or work completed in the group.
Anaconda takes up a lot of space on /home so it's worth running
* [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 =
mv ~/.conda /scratch/$USER/.conda
ln -s /scratch/$USER/.conda ~/.conda


This section contains all information you could ever need about computers and how to use them.
= [[Introduction | Introduction to basic shell commands]] =
- There are a number of tutorials available which document basic operations that are useful including:


== [[Computer_and_Storage_List | Computing Resources]] ==
# 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]]
# Useful cerebro queue commands
# Some [[vim]] tidbits


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


== [[Introduction | Introduction to basic shell commands]] ==
= How to connect to department machines =
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]] ==
'''On Mac/WSL:'''


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


== [[Installing_Slack | How to install Slack on department machines ]] ==
Set up logging in without a password:


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


== Software Tutorials==

# [[QChem]]
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.

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

= 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.


= Useful Information =
# Guidelines on [[Code Review]]
# Guidelines on [[Code Review]]
# How to do things relating to [[HANDE]]
# How to do things relating to [[HANDE]]
# How to run PySCF or other [[Python software on Archer]]
# How to run PySCF or other [[Python software on Archer]]
# How to run QChem on [[darwin]]
# Where to get [[Travel Money]]
# 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
# [[Persistent X]] sessions for remote working
# [[Paper submission]]
# [[Paper submission]]
# [[Getting Started with cerebro]]
# [[Getting Started with cerebro]]
# [[Things to do before leaving]]
# [[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]] =
== [[Archiving_data | Archiving data for the university repository]] ==

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


For publications data must be archived in accordance with university policy, instructions are here.
= [[Group_activities | Group Activities]] =


= To-do list for the Wiki=
== [[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.
- A pretty picture


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


Anything not updated for more than 5 years should be put into this section.
- A "How to:" page on using qchem


== [[Group_activities | Group Activities]] ==
- A Pretty picture for the $wgLogo

Latest revision as of 16:43, 31 March 2026

 _________   ___   ___      ______       ___ __ __      
/________/\ /__/\ /__/\    /_____/\     /__//_//_/\     
\__.::.__\/ \::\ \\  \ \   \:::_ \ \    \::\| \| \ \    
   \::\ \    \::\/_\ .\ \   \:\ \ \ \    \:.      \ \   
    \::\ \    \:: ___::\ \   \:\ \ \ \    \:.\-/\  \ \  
     \::\ \    \: \ \\::\ \   \:\_\ \ \    \. \  \  \ \ 
      \__\/     \__\/ \::\/    \_____\/     \__\/ \__\/ 

 _______      ______        ______       __  __       ______     
/______/\    /_____/\      /_____/\     /_/\/_/\     /_____/\    
\::::__\/__  \:::_ \ \     \:::_ \ \    \:\ \:\ \    \:::_ \ \   
 \:\ /____/\  \:(_) ) )_    \:\ \ \ \    \:\ \:\ \    \:(_) \ \  
  \:\\_  _\/   \: __ `\ \    \:\ \ \ \    \:\ \:\ \    \: ___\/  
   \:\_\ \ \    \ \ `\ \ \    \:\_\ \ \    \:\_\:\ \    \ \ \    
    \_____\/     \_\/ \_\/     \_____\/     \_____\/     \_\/

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 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

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.

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.

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.

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 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

Date Talk Cake
30 April Luke + Corey + Katrina Luke
7 May Informal
14 May Reka
21 May Informal
28 May MPhil
4 June Informal
11 June Dylan
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 here.

Seminars

QCQCDG

Quantum Computing for Quantum Chemistry Discussion Group (QCQCDG) info available here.

Quantum Computing Brainstorm

From Easter 2026, informal quantum discussions taking place at 10am on Thursdays in the supervision area. Notes available here.

Outstanding questions, along with answers and helpful reading material, can be found here.

Research and Projects

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.

Computers

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

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 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.

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.

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

  1. QChem
  2. SimpleDMC
  3. MRCC
  4. GAMESS
  5. RevQCMagic

Uncategorisable

The following sections could not be given a heading in the great wiki organisation of 2026 and thus are labelled as uncategorisable. See 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.

  1. Guidelines on Code Review
  2. How to do things relating to HANDE
  3. How to run PySCF or other Python software on Archer
  4. Where to get Travel Money
  5. Persistent X sessions for remote working
  6. Paper submission
  7. Getting Started with cerebro
  8. Things to do before leaving
  9. The Ten Git-mmandments: what NOT to do
  10. Mathematical Physics Lectures by Frederic Schuller: Geometrical Anatomy of Theoretical Physics and Lectures on Quantum Theory
  11. Mathematical Physics Lectures by Carl Bender: Perturbation and Asymptotic Series

Archiving data for the university repository

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

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

Retrieved from "http://wikis.ch.cam.ac.uk/thom/wiki/index.php?title=Main_Page&oldid=1568"