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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

Group Meetings

Past Group Meetings here.

Summer 2022

Date	Talk	Cake
25th July	WATOC Review & IPLU Discussion
8th August	Brian
29th August	Nick
12th September	Interns

Journal Club

Date	Contributor	Paper
8 Oct 2021	Kripa	Mastering Chess and Shogi by Self-Play with a General Reinforcement Learning Algorithm
5 Nov 2021	Brian	Neat, Simple and Wrong: Debunking Electrostatic Fallacies Regarding Noncovalent Interactions
6 Dec 2021	Kripa	Quantum Algorithm for Full Configuration Interaction Calculations without Controlled Time Evolutions
11 Feb 2022	Nick	Mapping the NFT revolution: market trends, trade networks, and visual features
11 Mar 2022	Andreea	Simulating physics with computers
27 Apr 2022	Fabio	Rethinking Superdeterminism
25 May 2022	Kripa	The experience of mathematical beauty and its neural correlates

Summer 'Interns'

Past Summer Interns here.

2022

Name	Dates	Project	Machine
Douglas Russell	-	IPLU	hypatia
Theo Hatcher	-	IPLU	chucksty
Motoki Yamano	-	IPLU	hypatia
King Lam	-	IPLU	chucksty
Juan Fernandez Pottecher	-	Strong Correlation	hylas
Max Howe	-	Singlet Fission	moonraker

Group List

The full timeline of all current and past group members is available here. NB autogenerated by `ifs-thom/cbh31/groupwiki`

An up to date list of group members is also available here.

Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021

Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip
Back row, right to left: David Izuogu, Kripa Panchagnula, Zian Wang, Dr Alex Thom
Not in picture: Fabio Albertani, Nicholas Lee, Tarik Benyahia, César Feniou, Benjamin Mokhtar

Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, May 2019

Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, November 2017

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 to basic shell commands

- There are a number of tutorials available which document basic operations that are useful including:

1. General bash commands
2. Setting up cygwin
3. Setting up ssh keys and general bash commands what are helpful
4. Setting up ssh config files
5. using GIT
6. Useful cerebro queue commands
7. Some vim tidbits

Currently undergoing construction.

How to connect to department machines

On Mac/WSL:

1. Check you have an Admitto account and collect your password from https://www.ch.cam.ac.uk/computing/admitto-service
2. In the terminal run the command ssh -X crsid@citadel.ch.cam.ac.uk
3. When prompted input your Admitto username (crsid) and password
4. 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:

1. 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"
2. 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
3. Log into the department citadel machine, and create / navigate to a directory called .ssh
4. Use chmod 700 .ssh to set permissions for the directory
5. 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
6. Log into the particular machine you want to ssh to, and repeat steps 3 to 5
7. Exit back to your machine and navigate to the home directory
8. 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.

Convenient 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 convenient tool FOR WINDOWS ONLY is the WinSCP software that allows to set up a File Transfer Protocol (FTP) between machines. It has a graphic user interface, where you can drag and drop files from the department machine to your computer. You can download it from https://winscp.net/eng/download.php . 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 !

Useful Software

1. Using QChem
2. Using QCMagic
3. SimpleDMC
4. MRCC
5. GAMESS

Useful Information

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. How to run QChem on darwin
5. Where to get Travel Money
6. Backed-up Storage
7. How to get IQMol to run a local version of Q-Chem via SSH
8. Slow ubuntu dash
9. Persistent X sessions for remote working
10. Paper submission
11. Getting Started with cerebro
12. Things to do before leaving

To-do list for the Wiki

- 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