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Bc528: /* Lent 2025 */

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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

{{Special:IframePage}}

=Group Expectations=

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

=Group Meetings=

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

===Michaelmas 2024===

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

===Lent 2025===

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

=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