Thom Group Wiki - User contributions [en]

Main Page

2026-06-06T10:28:04Z

Ajwt3: /* Forthcoming Conferences */

<div style="display:flex; flex-wrap:wrap; justify-content:center; gap:1em; align-items:flex-start; margin:1em 0;">

<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);">
 _________ ___ ___ ______ ___ __ __ 
/________/\ /__/\ /__/\ /_____/\ /__//_//_/\ 
\__.::.__\/ \::\ \\ \ \ \:::_ \ \ \::\| \| \ \ 
 \::\ \ \::\/_\ .\ \ \:\ \ \ \ \:. \ \ 
 \::\ \ \:: ___::\ \ \:\ \ \ \ \:.\-/\ \ \ 
 \::\ \ \: \ \\::\ \ \:\_\ \ \ \. \ \ \ \ 
 \__\/ \__\/ \::\/ \_____\/ \__\/ \__\/ 
</pre>
</div>

<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);">
 _______ ______ ______ __ __ ______ 
/______/\ /_____/\ /_____/\ /_/\/_/\ /_____/\ 
\::::__\/__ \:::_ \ \ \:::_ \ \ \:\ \:\ \ \:::_ \ \ 
 \:\ /____/\ \:(_) ) )_ \:\ \ \ \ \:\ \:\ \ \:(_) \ \ 
 \:\\_ _\/ \: __ `\ \ \:\ \ \ \ \:\ \:\ \ \: ___\/ 
 \:\_\ \ \ \ \ `\ \ \ \:\_\ \ \ \:\_\:\ \ \ \ \ 
 \_____\/ \_\/ \_\/ \_____\/ \_____\/ \_\/ 
</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 ||
|-
| 27th May - 1st Jun 2029|| ICQC 2029|| Qingdao, China||
|}

==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 LATEX 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]] ==

Main Page

2026-06-06T10:27:51Z

Ajwt3: /* Forthcoming Conferences */

<div style="display:flex; flex-wrap:wrap; justify-content:center; gap:1em; align-items:flex-start; margin:1em 0;">

<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);">
 _________ ___ ___ ______ ___ __ __ 
/________/\ /__/\ /__/\ /_____/\ /__//_//_/\ 
\__.::.__\/ \::\ \\ \ \ \:::_ \ \ \::\| \| \ \ 
 \::\ \ \::\/_\ .\ \ \:\ \ \ \ \:. \ \ 
 \::\ \ \:: ___::\ \ \:\ \ \ \ \:.\-/\ \ \ 
 \::\ \ \: \ \\::\ \ \:\_\ \ \ \. \ \ \ \ 
 \__\/ \__\/ \::\/ \_____\/ \__\/ \__\/ 
</pre>
</div>

<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);">
 _______ ______ ______ __ __ ______ 
/______/\ /_____/\ /_____/\ /_/\/_/\ /_____/\ 
\::::__\/__ \:::_ \ \ \:::_ \ \ \:\ \:\ \ \:::_ \ \ 
 \:\ /____/\ \:(_) ) )_ \:\ \ \ \ \:\ \:\ \ \:(_) \ \ 
 \:\\_ _\/ \: __ `\ \ \:\ \ \ \ \:\ \:\ \ \: ___\/ 
 \:\_\ \ \ \ \ `\ \ \ \:\_\ \ \ \:\_\:\ \ \ \ \ 
 \_____\/ \_\/ \_\/ \_____\/ \_____\/ \_\/ 
</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 ||
|-
| 27th May - 1st Jun 2029|| ICQC 2029| Qingdao, China||
|}

==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 LATEX 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]] ==

Summer Interns

2026-05-21T10:24:19Z

Ajwt3: /* 2026 */

==2026==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
|James Johnson|| 27th July - 25th September || - ||
|-
|Frankie Bregazzi || 29th June - 21st August || ||
|-
|Eve Wall|| 15th July - 15th September || Emergence of Autocatalytic Cycles in HCN-Derived Prebiotic Chemistry: An Ab Initio Network Study ||
|-
|}

==2025==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
|Tom Edwards|| 7th July - 29th August || - || Hypatia
|-
|Nestor Novakovic || 30th June - 5th September || Why is glycine not found in space? || Moonraker
|-
|Petar Panayotov|| 15th July - 15th September || Predicting Coupled Cluster Amplitudes || Sandstone
|-
|Divye Baid|| 30th June - 22nd August || - || Sandstone
|-
|}

==2023==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''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
|}

==2022==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''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
|}

==2021==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
| Anna Bui || 19th July - 17th September || NOCI Carbon Capture || Hypatia
|-
| Zian Wang || 19th July - 17th September || NOCI Photochemistry || Obsidian
|-
| Brian Zhao || 19th July - 17th September || Stochastic Coupled Cluster || Gritstone
|-
| Nick Lee || 19th July - 17th September || NOCI Singlet Fission || Moonraker
|}

==2020==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
|Elizabeth Guest || - || Astrochemistry || Hypatia
|-
|Hang Xu || - || EOM-CC || Gritstone
|-
|Jimin Li || - || holoHubbard || Gritstone
|-
|Constance Kraay || - || Embedded NOCI || Nemesis
|-
|Toby Antipaas || - || SMM || Sandstone
|-
|Tiger Zhang || - || TM Symmetry || Sandstone
|-
|Nicholas Lee || - || Singlet Fission || Moonraker
|}

==2019==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
|Kripa Panchagnula || 12th August - 27th September || Astrochemistry || -
|-
|Tiger Zhang || 2nd August - 20th September || Frustrated Lewis Pairs || -
|-
|David Kovacs || 29th July - 27th September (excluding 20-26th Aug) || Solid-state Coupled Cluster || -
|-
|Nicholas Lee || 29th July - 27th September (excluding 4-9th Aug) || Singlet-Triplet Fission || -
|}

Main Page

2026-05-16T14:31:07Z

Ajwt3: /* Forthcoming Conferences */

<div style="display:flex; flex-wrap:wrap; justify-content:center; gap:1em; align-items:flex-start; margin:1em 0;">

<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);">
 _________ ___ ___ ______ ___ __ __ 
/________/\ /__/\ /__/\ /_____/\ /__//_//_/\ 
\__.::.__\/ \::\ \\ \ \ \:::_ \ \ \::\| \| \ \ 
 \::\ \ \::\/_\ .\ \ \:\ \ \ \ \:. \ \ 
 \::\ \ \:: ___::\ \ \:\ \ \ \ \:.\-/\ \ \ 
 \::\ \ \: \ \\::\ \ \:\_\ \ \ \. \ \ \ \ 
 \__\/ \__\/ \::\/ \_____\/ \__\/ \__\/ 
</pre>
</div>

<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);">
 _______ ______ ______ __ __ ______ 
/______/\ /_____/\ /_____/\ /_/\/_/\ /_____/\ 
\::::__\/__ \:::_ \ \ \:::_ \ \ \:\ \:\ \ \:::_ \ \ 
 \:\ /____/\ \:(_) ) )_ \:\ \ \ \ \:\ \:\ \ \:(_) \ \ 
 \:\\_ _\/ \: __ `\ \ \:\ \ \ \ \:\ \:\ \ \: ___\/ 
 \:\_\ \ \ \ \ `\ \ \ \:\_\ \ \ \:\_\:\ \ \ \ \ 
 \_____\/ \_\/ \_\/ \_____\/ \_____\/ \_\/ 
</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 ||
|-
| 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
|-
| 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
|-
| 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?
|-
| 28th Sep - 2nd Oct 2026 || Lennard-Jones Centre 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 LATEX 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]]

= 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]] ==

Main Page

2026-05-16T14:27:11Z

Ajwt3: /* Events */

<div style="display:flex; flex-wrap:wrap; justify-content:center; gap:1em; align-items:flex-start; margin:1em 0;">

<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);">
 _________ ___ ___ ______ ___ __ __ 
/________/\ /__/\ /__/\ /_____/\ /__//_//_/\ 
\__.::.__\/ \::\ \\ \ \ \:::_ \ \ \::\| \| \ \ 
 \::\ \ \::\/_\ .\ \ \:\ \ \ \ \:. \ \ 
 \::\ \ \:: ___::\ \ \:\ \ \ \ \:.\-/\ \ \ 
 \::\ \ \: \ \\::\ \ \:\_\ \ \ \. \ \ \ \ 
 \__\/ \__\/ \::\/ \_____\/ \__\/ \__\/ 
</pre>
</div>

<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);">
 _______ ______ ______ __ __ ______ 
/______/\ /_____/\ /_____/\ /_/\/_/\ /_____/\ 
\::::__\/__ \:::_ \ \ \:::_ \ \ \:\ \:\ \ \:::_ \ \ 
 \:\ /____/\ \:(_) ) )_ \:\ \ \ \ \:\ \:\ \ \:(_) \ \ 
 \:\\_ _\/ \: __ `\ \ \:\ \ \ \ \:\ \:\ \ \: ___\/ 
 \:\_\ \ \ \ \ `\ \ \ \:\_\ \ \ \:\_\:\ \ \ \ \ 
 \_____\/ \_\/ \_\/ \_____\/ \_____\/ \_\/ 
</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 ||
|-
| 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 || International Congress of Quantum Chemistry || Berkeley, California || Andreea
|-
| 7th Sep - 11tb Sep 2026 || Origins Federation || Zurich, Switzerland || Alex, Bence
|-
| 14th Sep - 16th Sep 2026 || Excited States Faraday Discussion || Cambridge, UK|| Alex
|-
| 19th Sep - 23rd Sep 2026 || 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?
|-
| 28th Sep - 2nd Oct 2026 || Lennard-Jones Centre 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 LATEX 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]]

= 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]] ==

Summer Interns

2026-05-12T14:20:24Z

Ajwt3:

==2026==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
|James Johnson|| 27th July - 25th September || - ||
|-
|Frankie Bregazzi || || ||
|-
|Eve Wall|| 15th July - 15th September || Emergence of Autocatalytic Cycles in HCN-Derived Prebiotic Chemistry: An Ab Initio Network Study ||
|-
|}

==2025==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
|Tom Edwards|| 7th July - 29th August || - || Hypatia
|-
|Nestor Novakovic || 30th June - 5th September || Why is glycine not found in space? || Moonraker
|-
|Petar Panayotov|| 15th July - 15th September || Predicting Coupled Cluster Amplitudes || Sandstone
|-
|Divye Baid|| 30th June - 22nd August || - || Sandstone
|-
|}

==2023==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''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
|}

==2022==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''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
|}

==2021==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
| Anna Bui || 19th July - 17th September || NOCI Carbon Capture || Hypatia
|-
| Zian Wang || 19th July - 17th September || NOCI Photochemistry || Obsidian
|-
| Brian Zhao || 19th July - 17th September || Stochastic Coupled Cluster || Gritstone
|-
| Nick Lee || 19th July - 17th September || NOCI Singlet Fission || Moonraker
|}

==2020==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
|Elizabeth Guest || - || Astrochemistry || Hypatia
|-
|Hang Xu || - || EOM-CC || Gritstone
|-
|Jimin Li || - || holoHubbard || Gritstone
|-
|Constance Kraay || - || Embedded NOCI || Nemesis
|-
|Toby Antipaas || - || SMM || Sandstone
|-
|Tiger Zhang || - || TM Symmetry || Sandstone
|-
|Nicholas Lee || - || Singlet Fission || Moonraker
|}

==2019==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
|Kripa Panchagnula || 12th August - 27th September || Astrochemistry || -
|-
|Tiger Zhang || 2nd August - 20th September || Frustrated Lewis Pairs || -
|-
|David Kovacs || 29th July - 27th September (excluding 20-26th Aug) || Solid-state Coupled Cluster || -
|-
|Nicholas Lee || 29th July - 27th September (excluding 4-9th Aug) || Singlet-Triplet Fission || -
|}

Summer Interns

2026-05-12T14:17:27Z

Ajwt3: /* 2025 */

==2025==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
|Tom Edwards|| 7th July - 29th August || - || Hypatia
|-
|Nestor Novakovic || 30th June - 5th September || Why is glycine not found in space? || Moonraker
|-
|Petar Panayotov|| 15th July - 15th September || Predicting Coupled Cluster Amplitudes || Sandstone
|-
|Divye Baid|| 30th June - 22nd August || - || Sandstone
|-
|}

==2023==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''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
|}

==2022==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''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
|}

==2021==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
| Anna Bui || 19th July - 17th September || NOCI Carbon Capture || Hypatia
|-
| Zian Wang || 19th July - 17th September || NOCI Photochemistry || Obsidian
|-
| Brian Zhao || 19th July - 17th September || Stochastic Coupled Cluster || Gritstone
|-
| Nick Lee || 19th July - 17th September || NOCI Singlet Fission || Moonraker
|}

==2020==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
|Elizabeth Guest || - || Astrochemistry || Hypatia
|-
|Hang Xu || - || EOM-CC || Gritstone
|-
|Jimin Li || - || holoHubbard || Gritstone
|-
|Constance Kraay || - || Embedded NOCI || Nemesis
|-
|Toby Antipaas || - || SMM || Sandstone
|-
|Tiger Zhang || - || TM Symmetry || Sandstone
|-
|Nicholas Lee || - || Singlet Fission || Moonraker
|}

==2019==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
|Kripa Panchagnula || 12th August - 27th September || Astrochemistry || -
|-
|Tiger Zhang || 2nd August - 20th September || Frustrated Lewis Pairs || -
|-
|David Kovacs || 29th July - 27th September (excluding 20-26th Aug) || Solid-state Coupled Cluster || -
|-
|Nicholas Lee || 29th July - 27th September (excluding 4-9th Aug) || Singlet-Triplet Fission || -
|}

Main Page

2026-03-31T16:43:34Z

Ajwt3:

<div style="display:flex; flex-wrap:wrap; justify-content:center; gap:1em; align-items:flex-start; margin:1em 0;">

<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);">
 _________ ___ ___ ______ ___ __ __ 
/________/\ /__/\ /__/\ /_____/\ /__//_//_/\ 
\__.::.__\/ \::\ \\ \ \ \:::_ \ \ \::\| \| \ \ 
 \::\ \ \::\/_\ .\ \ \:\ \ \ \ \:. \ \ 
 \::\ \ \:: ___::\ \ \:\ \ \ \ \:.\-/\ \ \ 
 \::\ \ \: \ \\::\ \ \:\_\ \ \ \. \ \ \ \ 
 \__\/ \__\/ \::\/ \_____\/ \__\/ \__\/ 
</pre>
</div>

<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);">
 _______ ______ ______ __ __ ______ 
/______/\ /_____/\ /_____/\ /_/\/_/\ /_____/\ 
\::::__\/__ \:::_ \ \ \:::_ \ \ \:\ \:\ \ \:::_ \ \ 
 \:\ /____/\ \:(_) ) )_ \:\ \ \ \ \:\ \:\ \ \:(_) \ \ 
 \:\\_ _\/ \: __ `\ \ \:\ \ \ \ \:\ \:\ \ \: ___\/ 
 \:\_\ \ \ \ \ `\ \ \ \:\_\ \ \ \:\_\:\ \ \ \ \ 
 \_____\/ \_\/ \_\/ \_____\/ \_____\/ \_\/ 
</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 ||
|-
| 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 [[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]].

= 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 LATEX 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]]

= 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]] ==

Main Page

2026-03-31T16:41:52Z

Ajwt3: /* Quantum Brainstorm */

<div style="display:flex; flex-wrap:wrap; justify-content:center; gap:1em; align-items:flex-start; margin:1em 0;">

<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);">
 _________ ___ ___ ______ ___ __ __ 
/________/\ /__/\ /__/\ /_____/\ /__//_//_/\ 
\__.::.__\/ \::\ \\ \ \ \:::_ \ \ \::\| \| \ \ 
 \::\ \ \::\/_\ .\ \ \:\ \ \ \ \:. \ \ 
 \::\ \ \:: ___::\ \ \:\ \ \ \ \:.\-/\ \ \ 
 \::\ \ \: \ \\::\ \ \:\_\ \ \ \. \ \ \ \ 
 \__\/ \__\/ \::\/ \_____\/ \__\/ \__\/ 
</pre>
</div>

<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);">
 _______ ______ ______ __ __ ______ 
/______/\ /_____/\ /_____/\ /_/\/_/\ /_____/\ 
\::::__\/__ \:::_ \ \ \:::_ \ \ \:\ \:\ \ \:::_ \ \ 
 \:\ /____/\ \:(_) ) )_ \:\ \ \ \ \:\ \:\ \ \:(_) \ \ 
 \:\\_ _\/ \: __ `\ \ \:\ \ \ \ \:\ \:\ \ \: ___\/ 
 \:\_\ \ \ \ \ `\ \ \ \:\_\ \ \ \:\_\:\ \ \ \ \ 
 \_____\/ \_\/ \_\/ \_____\/ \_____\/ \_\/ 
</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 ||
|-
| 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 [[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 Brainstorm==
From Easter 2026, informal quantum discussions taking place at 10am on Thursdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

= 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 LATEX poster]

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

= 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]]

= 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]] ==

QCMagic

2025-10-13T09:24:50Z

Ajwt3:

NB This is for the old (deprecated) version of qcmagic using python 2. You should not use this.

Use https://gitlab.developers.cam.ac.uk/ch/thom/RevQCMagic instead

QCMagic is a set of Python libraries and scripts to manipulate Q-Chem output files. To get access to QCMagic, visit

https://gitlab.developers.cam.ac.uk/ch/thom/qcmagic

and log in with your Raven account. If you do not have permissions to this site, please send an email to Alex Thom to request access. Once you have logged on to the GitLab Repository, go to <code>Settings -> SSH Keys</code> and follow the instructions to add your own public key to the Repository. Once done, you will be able to clone QCMagic with

git clone git@gitlab.developers.cam.ac.uk:ch/thom/qcmagic.git

The current main branch is <code>master</code>. If you wish to develop QCMagic, you need to create your own branch using

git checkout -b yourNewBranch

and then verify that you are indeed on your own branch:

git status

==Installation==
Having cloned QCMagic, install it by executing the following:

cd qcmagic
./setup.sh

which will automatically generate necessary executable files in a new directory called <code>bin</code> and also add the following lines to your <code>.bashrc</code> or <code>.zshrc</code>:

<pre>
if [[ -d $HOME/qcmagic/bin ]]; then
export PATH=$PATH:$HOME/path/to/qcmagic/bin
export PYTHONPATH=$PYTHONPATH:$HOME/path/to/qcmagic
export VMDSIMPLEGRAPHICS=1
fi</pre>

The last is to ensure you can open a VMD window (provided X forwarding is enabled, and you have VMD installed locally).

If there are problems using VMD via SSH, try using [[xpra]]. <code>makePlots</code> now has an option <code>--xpra</code> that starts VMD in xpra automatically.

If you are using XQuartz and xpra does not seem to work, try the following:
On your local terminal, run this in the command line:

<code>defaults write org.macosforge.xquartz.X11 enable_iglx -bool true</code>

Reload your remote terminal and you might be able to launch remote XQuartz sessions.

Source: https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmdl/28503.html

==Usage==

Probably the best way to explore the capabilities of qcmagic is to use iPython. Say you have a Q-Chem output file myfile.out containing a single job; in iPython type:

from QCManager import *
O = OutputFile('myfile.out') # The class OutputFile is defined in QCOutput.py
O.Parse() # Extract data from myfile.out. Returns False if no Q-Chem errors are found.

Some data will be stored as values in a container, which is a special type of dictionary defined in QCSupport.py, whilst others are regular attributes of O. For example, if myfile.out is the result of a Q-Chem optimisation ('jobtype opt'), you could find the initial and final energies with:

Ei = O.Steps[0]['InternalEnergy']
Ef = O.Steps[-1]['InternalEnergy']

and the initial and final geometries with:

Xi = O.Steps[0]['System'].Atoms
Xf = O.Steps[-1]['System'].Atoms
# Or equivalently:
Xf = O.System.Atoms

==makePlots.py==
'''Note''' This currently appears to work with qchem input files, but not output files.

Example command:

runmakePlots.py my_qchem_file.inp -T tag

This runs a qchem calculation on my_qchem_file.inp and plots the orbitals in VMD. Output files will be saved to a new directory ''tag'', or ''Unnamed'' if tag is unspecified. Run with <code>--help</code> to view all possible options.

Once the plot is up, the display can be controlled entirely from the terminal. For example, view orbital #3 by typing <code>3</code>. Type <code>help</code> to view all available commands.

==scanSurface.py==
===Overview===
A general command for <code>scanSurface</code> has the following form:

runscanSurface.py [options] qchem_file [qchem_file_2 ...] Tag

where <code>qchem_file</code>'s are old Q-Chem input or output files whose inputs are used as the system (and assumed to be setup as above). If these files contain saved minima, they are stored and relocated. Outputs from <code>scanSurface</code> are stored in <code>Tag.sd</code> (a pickled Python data structure containing all calculation results), <code>Tag.dat</code> (a printout of energies at different geometries), and when necessary, <code>Tag.dat2</code> (a printout of NOCI energies at different geometries).

The principle of working of <code>scanSurface</code> is rather simple: from the initial geometry of the system supplied in the old Q-Chem inputs or outputs, each electronic state requested will be followed as the geometry of the molecule is varied. The electron density of the state at the previous geometry is read in as the initial guess for the convergence procedure performed by Q-Chem at the current geometry. Upon convergence, a state distance is calculated between the electron densities at the current and previous geometry, so that only when the new density is located within a certain maximum threshold of the old density can it be accepted as belonging to the same state. <code>scanSurface</code> saves the Q-Chem output file for every calculation as <code>Run*.out</code>.

An example command is:

runscanSurface.py --stretch=0,1,1,0.01 my_qchem_file.out Tag

which runs a scan on a molecule specified in the input section of <code>my_qchem_file.out</code>, calling Q-Chem at points on a surface defined by the stretching of the bond between atom0 and atom1 by 10 units in steps of 0.01, and writing the results to <code>Tag.sd</code> and <code>Tag.dat</code>.

If multiple options are used, such as

runscanSurface.py --stretch=0,1,1,0.01 --stretch=0,2,1,0.01 my_qchem_file.out Tag

the scan will zigzag to cover the whole surface.

===Options===
<code>scanSurface</code> can be run with <code>--help</code> to view all possible options. In this Section, important remarks for some options are presented.
====<code>--read-minima</code>====
This option is used to specify the minima located by metadynamics in the specified Q-Chem output file that <code>scanSurface</code> should read in and follow. It must be noted that this is one-based and ''not'' zero-based, so <code>--read-minima=1</code> ensures only the ''first'' minimum located by metadynamics is scanned. On the other hand, <code>--read-minima=0</code> would have no effect on the scan. For example,

runscanSurface.py --read-minima=1,2,6 --stretch=0,1,1,0.01 my_qchem_file.out Tag

instructs <code>scanSurface</code> to read in minima 1, 2 and 6 from the old Q-Chem output file <code>my_qchem_file.out</code>, follow each of them as the bond between atom0 and atom1 is stretched by 1 unit in steps of 0.01, then store the results as states 0, 1 and 2 in Tag.sd and print out the energies in Tag.dat.

Note that in order for <code>scanSurface</code> to read in the requested minima, the Q-Chem output file must have been generated with the <code>rem</code> option <code>print_orbitals</code> set to <code>true</code>.

====<code>--read-only</code>====
If on, <code>scanSurface</code> only reads and stores the states from the Q-Chem output file to an SD file without trying to reconverge to any of them. This is useful when one seeks to export the states located by metadynamics in a Q-Chem output file to an SD file for further manipulation, analysis or extraction.

====<code>--normal-rotate</code>====
This option may be used in simple cases to change a single bond angle. It relies on being able to work out the connectivity from knowledge of the bond lengths and VDW radii, so can be problematic if (a) the bond lengths are unusual, and (b) there are multiple paths between two atoms. For example,

<code>--normal-rotate=0,1,2,90,0.1</code>

will:
* split the molecule between atom0 and atom1;
* check if each of the other atoms is connected to atom0; if they are, group them with atom0 and if not, group them with atom1; and
* rotate the group of atoms containing atom1 about an axis '''through''' atom1, and '''normal to the plane containing atom0, atom1 and atom2'''.

====<code>--tie</code>====

This option allows multiple parameters to change in sync with one another. For example, one might want to investigate the effect of varying two bond lengths at the same time, but would like to ignore what happens when one is stretched and the other unchanged. This could be very useful in the context of molecular vibrations, or when certain symmetry elements need to be preserved.

For each parameter that needs to be tied, two integers are required:
* one referring to the option:
<blockquote>
ext_charge -- 0, scale -- 1, stretch -- 2, rotate -- 3, normal_rotate -- 4, orth_rotate -- 5, all_normal_rotate -- 6, rotate_axis -- 7;
</blockquote>
* another one specifying the particular instance of said option (zero-based).

An example of a command using --tie:

runscanSurface.py '''--stretch=0,1,1,0.01''' ''--rotate=2,3,90,0.9'' --scale=2 --tie='''2,0''',''3,0'' my_qchem_file.out Tag

This will:
* simultaneously stretch bond atom0-atom1 by 1 unit, and rotate about bond atom2-atom3 by 90°, in 100 steps;
* scale the whole molecule up to twice its original size. As the <code>--scale</code> option is not tied, <code>scanSurface</code> will scale separately every possible geometry allowed by the previous (tied) options.

''Note that an equal number of steps for each tied parameter must be ensured in order for <code>--tie</code> to work correctly!''

====<code>--focus</code>====
If this flag is on, once <code>scanSurface</code> fails to locate the correct minimum at a geometry, it will not attempt to find other minima at that geometry but move on to the next geometry instead, where it will use the minimum on the same state at the last well-converged geometry as reference. If <code>scanSurface</code> locates the correct minimum after a few other minima that belong to different states, only the correct minimum is saved and used as reference for the next geometry, while all other superfluous minima are discarded.

This option is useful when following states that pass through regions of discontinuity (and non-convergence), as it prevents <code>scanSurface</code> from getting trapped in a cascading landslide where it tries to look for other minima and follow them, only to be stuck in more regions of discontinuity (and non-convergence) of these new minima later on, halting the state-tracking process altogether.

==qcSDExtract.py==
''Currently <code>qcSDExtract</code> only works with traditional, non-augmented SDS objects (i.e. those that do not contain variations in exchange-correlation).''
===Overview===
<code>qcSDExtract</code> reads in states stored in a single SD file generated by <code>scanSurface</code>, performs further calculations on them if need be, and extracts out their energies, atomic charges and spins from Mulliken analysis, as well as oxidation states of individual atoms from LOBA analysis. <code>qcSDExtract</code> can parametrise geometries using multiple bond lengths, bond angles, and dihedral angles, allowing multi-dimensional surfaces to be traced out.

A general command for <code>qcSDExtract</code> has the following form:

runqcSDExtract.py [options] SDfile Tag

where <code>SD_file</code> is an SD file containing information of all states read in and possibly followed by <code>scanSurface</code>. Several output files are generated by <code>qcSDExtract</code>:
* Tag.energy, containing all geometrical parameters requested and the energies of the associated states;
* Tag.atomi.charge, containing all geometrical parameters requested and the Mullikan charges of atomi in the associated states;
* Tag.atomi.spinz, containing all geometrical parameters requested and the Mullikan spin charges (''i.e.'' spin imbalances) of atomi in the associated states; and
* Tag.atomi.oxstate, containing all geometrical parameters requested and the LOBA oxidation states of atomi in the associated states.

An example command is:

runqcSDExtract.py --read-minima=0,1,2 --read-geometries=0,1,2,3,4 --bondlength=0,1,0,2,1,2 --bondangle=1,0,2 --rem="LOBA 12" --atoms=0 mydata.sd Tag

which:
* reads in states 0, 1 and 2 at geometries 0, 1, 2, 3 and 4 stored in my_data.sd;
* parametrises these geometries using bond lengths atom0--atom1, atom0--atom2, atom1--atom2, and bond angle atom1--atom0--atom2;
* performs additional LOBA 12 calculations on these minima; and
* outputs Tag.energy, Tag.atom0.charge, Tag.atom0.spinz and Tag.atom0.oxstate, where the three latter files contain details for atom0.

In addition, the actual Q-Chem output file generated when qcSDExtract calls Q-Chem to reconverge into state ''j'' at geometry ''i'' (''i'' and ''j'' are 0-based indices) and/or to perform additional calculations is saved as _SDfile.gi.sj.out (note the underscore prefix).

===Options===

====<code>--read-minima</code>====
At least one 0-based index of one or more states to read in from the SD file must be specified. Multiple indices are separated by commas. For example,

--read-minima=0,1,2

instructs <code>qcSDExtract</code> to read in minima 0, 1 and 2 from the SD file.

''Q: How do I know which (1-based) minimum in the original Q-Chem output file corresponds to which (0-based) minimum in the SD file after <code>scanSurface</code> has been run?''

''A: Examine the stdout of <code>scanSurface</code> and look for the pattern "Old min XYZ -> New sol ABC" which shows the mapping of the (1-based) indices in the original Q-Chem output file, XYZ, to the (0-based) indices in the SD file, ABC.''

====<code>--read-geometries</code>====
This option allows one to specify the 0-based indices of one or more geometries to be examined, separated by commas. If no indices are specified, or if this option is omitted altogether, all geometries will be scanned. For example, if only geometries with indices 0, 5 and 10 are needed, one should specify

--read-geometries=0,5,10

which is useful when only certain interesting portions of the surface are required to be examined.

====<code>--atoms</code>====
This option allows the specification of a list of atom indices (0-based) from which chemical properties are extracted. If this option is omitted, properties will be extracted from only atom0. For example, to extract chemical properties of atom0 and atom1 along state 0 at all geometries, one would use the command

runqcSDExtract.py --read-minima=0 --atoms=0,1 --rem="LOBA 12" my_file.sd Tag

====<code>--bondlength</code>====
This is where one can specify the bond lengths that should be used to parametrise the geometries. This, together with the following two options, <code>--bondangle</code> and <code>--bonddihedral</code>, provides a workaround to construct a full multi-dimensional surface from the flatten-down one-dimensional storage of geometries originally implemented in <code>scanSurface</code>.

Here, one specifies a list of 0-based indices of pairs of atoms whose bond lengths will be used to parametrise the geometries. Therefore, the list must contain an even number of elements, otherwise <code>qcSDExtract</code> will exit with an error. For example,

--bondlength=0,1,0,2,1,2

parametrises the geometries using three bond lengths: atom0--atom1, atom0--atom2, and atom1--atom2. If this option is omitted, atom0--atom1 bond length will be used by default.

====<code>--bondangle</code>====
Here, one specifies a list of 0-based indices of triplets of atoms whose bond angles will be used to parametrise the geometries. The list must contain a multiple of three of elements. In each triplet, the middle index is the centre atom. For example,

--bondangle=1,0,2,1,0,3

uses the bond angles atom1--atom0--atom2 and atom1--atom0--atom3 to parametrise the geometries. There is no default for this option.

====<code>--bonddihedral</code>====
This option specifies a list of 0-based indices of triplets of atoms whose bond dihedrals will be used to parametrise the geometries. The list must contain a multiple of four of elements. In each quartet, the first three atoms form the initial plane. For example,

--bonddihedral=0,1,2,3

uses the dihedral angle between the two planes atom0--atom1--atom2 and atom1--atom2--atom3 to parametrise the geometries. There is no default for this option.

==varyXCB.py==
===Overview===
<code>varyXCB</code> reads in minima from a Q-Chem output file or an SD file (traditional or augmented) and follows them as exchange-correlation functionals are varied, or as basis sets are changed.

A general command for <code>varyXCB</code> has the following form:

runvaryXCB.py [options] file Tag

where <code>file</code> is a Q-Chem output file or an SD file containing minima to be read in. If the SD file contains an instance of class <code>SystemDataSet</code>, it will be augmented to an instance of class <code>SystemDataSetXC</code>, placing all existing minima at exchange-correlation functional index 0 (see later). However, if the SD file already contains a <code>SystemDataSetXC</code> object, it will be read in as-is, but an index for exchange-correlation functionals must be specified via <code>--read-xc</code> so that <code>varyXCB</code> will know which minima to follow (see later).

When run in exchange-correlation following mode, <code>varyXCB</code> outputs the energies of the minima along the parametrised path in the exchange-correlation space in <code>Tag.gi.sj.dat</code>, and stores all minima at all exchange-correlation functionals along the path in <code>Tag.xc.sd</code>, which contains a <code>SystemDataSetXC</code> object. On the other hand, when run in basis projection mode, <code>varyXCB</code> outputs the energies of the minima in the new basis set in Tag.newbasis.gi.sj.dat, and stores all minima in the new basis set in <code>Tag.b.sd</code>, which contains a <code>SystemDataSetXC</code> object.

An example command for exchange-correlation following mode is:

runvaryXCB.py --xc-template=xctemplate --read-minima=1,2,3 --para=lambda,0,1,0.1 my_qchem_file.out Tag

which:
* reads in minima 1, 2 and 3 from my_qchem_file.out and stores them at exchange-correlation functional index 0 of states 0, 1 and 2 respectively in the <code>SystemDataSetXC</code> object in <code>Tag.xc.sd</code>;
* uses the content of <code>xctemplate</code> as a template for <code>$xc_functional</code> section in Q-Chem runs;
* understands that <code>lambda</code> in <code>xctemplate</code> represents a variable parameter that needs to be increased from 0 to 1 in steps of 0.1 to define a path in the exchange-correlation space;
* runs Q-Chem at different exchange-correlation functionals; and
* stores all calculation results in <code>Tag.xc.sd</code> and outputs <code>Tag.gi.sj.dat</code> for ''j''=0,1,2 which contains the energies of states 1, 2 and 3 (read from the Q-Chem output file) as followed along the specified exchange-correlation path.

Another example command for basis projection mode is:

runvaryXCB.py --basis-template=changebasis.template --purecart=1112 --read-minima=0,2,5 --read-geometries=0 --read-xc=1
--rem="SCF_MAX_CYCLES 100" --rem="SCF_MINFIND_READDISTTHRESH 00500" file.sd Tag

which:
* reads in minima 0, 2 and 5 at geometry 0 and exchange-correlation functional index 1 from <code>file.sd</code> and stores them at exchange-correlation functional index 0 of states 0, 1 and 2 respectively in the <code>SystemDataSetXC</code> object in <code>Tag.b.sd</code>;
* reads in the new basis set specified in <code>changebasis.template</code>;
* uses purecart specification <code>1112</code> for the new basis set;
* runs basis projection calculations with additional rem options;
* outputs Tag.newbasis.g0.si.dat containing the energies of state ''i''=0,1,2 at geometry 0 in the old and new basis sets;
* outputs Run-new_basis.gi.sj.xc1.out which is the Q-Chem output file for the actual basis-set projection calculation of state ''i''=0,1,2 at geometry 0 and exchange-correlation 1; and
* stores all calculated data in <code>Tag.b.sd</code>.

===Structure of a <code>QCSystemData.SystemDataSetXC</code> Object ''(for developers only)''===
<code>QCSystemData.SystemDataSetXC</code> (<code>SystemDataSetXC</code> for short) inherits from the base class <code>QCSystemData.SystemDataSet</code> (<code>SystemDataSet</code> for short) with some existing methods overridden and some new methods implemented to cope with the incorporation of exchange-correlation functional variations.

An SD file is a pickled Python '''dictionary''' containing three keys: <code>'Output'</code>, <code>'Job'</code> and <code>'SysData'</code>. Let us call this dictionary <code>D</code>. <code>D['SysData']</code> is then an instance of the class <code>SystemDataSet</code> or the class <code>SystemDataSetXC</code>, depending on how it has been constructed. Here we will only focus on the latter case.

<code>D['SysData']</code> contains various useful methods and variables. However, all important calculation information is contained within the two variables <code>GeomList</code> and <code>StateList</code>.

=====<code>GeomList</code>=====
<code>GeomList</code> is a one-dimensional '''list''' containing elements which are instances of class <code>QCMolecule.System</code>. Each element therefore carries attributes for describing and manipulating a particular geometry (''i.e.'' atom arrangement) of the system. For example, <code>GeomList</code> could contain successive geometries of a diatomic molecule, XY, where the bond length X--Y is gradually increased in a particular range.

In other words, if <code>GL</code> is a <code>GeomList</code>, then <code>GL[i]</code> is an instance of class <code>QCMolecule.System</code> and contains information of geometry with index <code>i</code>.

=====<code>StateList</code>=====
<code>StateList</code> is a one-dimensional '''list''' containing elements which are '''dictionaries'''. Each dictionary then contains key-value pairs, each of which corresponds to a state whose the index is given by the key. The corresponding value is yet another '''list''' whose elements are instances of <code>QCSystemData.SCFStateRich</code> (a class inheriting from <code>QCSystemData.SCFState</code> and able to store more information such as LOBA oxidation states, atomic charges and spins, as well as exchange-correlation functionals) and describe the state at different exchange-correlation functionals.

In other words, if <code>SL</code> is a <code>StateList</code>, then
* <code>SL</code> is a list with a one-to-one correspondence to <code>GL</code>;
* <code>SL[i]</code> is a dictionary containing information of all states at geometry with index <code>i</code>, <code>GL[i]</code>;
* <code>SL[i][j]</code> is a list containing information at all exchange-correlation functionals of state with index <code>j</code> at geometry with index <code>i</code>; and
* <code>SL[i][j][k]</code> is an instance of <code>QCSystemData.SCFStateRich</code> containing information at exchange-correlation functional with index <code>k</code> of state with index <code>j</code> at geometry with index <code>i</code>.

===Options===
<code>varyXCB</code> can be run with <code>-h</code> or <code>--help</code> to display all options supported and how to use them. Here we explain the two most important options that control the working of <code>varyXCB</code>.

====<code>--xc-template</code>====
In this option, the path to the template file containing specifications of exchange and correlation functionals in terms of parameters is specified. There is no default value for this option, so if it is omitted, no exchange-correlation tracking will be carried out. The template file must have the following format:

$xc_functional
X exchange_functional_name parametrised_expression
...
C correlation_functional_name parametrised_expression
...
K parametrised_expression !This is an alternative specification for Hartree-Fock exchange -- see Q-Chem manual
$end

The file must begin with <code>$xc_functional</code> and end with <code>$end</code>, and its format must follow that of the <code>$xc_functional</code> section in Q-Chem inputs, noting that the parametrised expressions must '''contain no white spaces''', e.g.

1-(0.80*lambda)+gamma

where lambda and gamma are parameters. Any parameters used in the template file must then be declared using the <code>--para</code> option of <code>varyXCB</code> in order for <code>varyXCB</code> to parse the template file correctly. Therefore, for a template file containing the above expression, the following options must be present:

--para=gamma,0,1,0.5 --para=lambda,0,1,0.1

====<code>--basis-template</code>====
In this option, the path to the template file containing the specification of a general, larger basis set is indicated. There is no default value for this option, so if it is omitted, no basis set projection will be carried out. This file must begin with <code>$basis</code> and end with <code>$end</code>, and its format must follow that of the <code>$basis</code> section in Q-Chem inputs. In particular,

$basis
general_basis_set_specification
$end

When run in basis projection mode, <code>varyXCB</code> reads in minima in the smaller basis set ('''this must be one of the standard basis sets in Q-Chem and not a general basis set''') and projects them into the larger, general basis set specified in the template file.

''Note that the option <code>--purecart</code> MUST be specified when <code>--basis-template</code> is used, so that Q-Chem will know what types of functions (pure or Cartesian) to use for the general basis set.''

==SymmetryTools==
<code>SymmetryTools</code> is a package within <code>QCMagic</code> that allows users to determine the point group of a molecule and use the symmetry elements of the group to generate and analyse symmetry-related and necessarily degenerate single determinants from those already obtained through SCF calculations. <code>SymmetryTools</code> supports proper and improper rotations involving both spatial and spin degrees of freedom. This allows us to generate a complete set of degenerate symmetry-related SCF single determinants and ultimately identify the irreducible representations spanned by them. The full workflow from obtaining multiple SCF solutions using metadynamics to determining the irreducible representations spanned by any one solution and its symmetry partners is shown below.

=== Step 1: Generating multiple SCF solutions using metadynamics ===
We begin with obtaining several (say, <math>N</math>) SCF solutions using metadynamics in Q-Chem. This involves running an SCF job with <code>SCF_SAVEMINIMA N</code> as a <code>$rem</code> variable where <math>N \geq 1</math>. Note that metadynamics is technically when <math>N > 1</math>. However, when <math>N = 1</math>, only a single SCF determinant will be saved, just like a normal SCF calculation, but the <code>$rem</code> variable <code>SCF_SAVEMINIMA</code> is needed so that this SCF determinant is outputted in a format that is readable by <code>QCMagic</code>. A sample input named <code>BH3.inp</code> for metadynamics on Q-Chem which prints out 5 energy minima for a borane molecule is shown below.

''
$molecule
0 1
B -3.7312212 1.6982695 0.0000000
H -4.8515376 1.3242015 0.0000000
H -3.4950153 2.8555260 0.0000000
H -2.8471106 0.9150809 0.0000000
$end
$rem
BASIS STO-3G
EXCHANGE hf
SCF_GUESS sad
SCF_CONVERGENCE 7
UNRESTRICTED true
SCF_SAVEMINIMA 5
SCF_MAX_CYCLES 1000
MOM_START 1
PRINT_ORBITALS true
SCF_MINFIND_INITNORM 09000
SCF_MINFIND_INITLAMBDA 00200
SCF_MINFIND_INCREASEFACTOR 10100
SCF_MINFIND_RANDOMMIXING -15708
SCF_MINFIND_NRANDOMMIXES 1
SCF_MINFIND_MIXMETHOD 1
SCF_MINFIND_MIXENERGY 00100
SYMMETRY off
DIIS_SEPARATE_ERRVEC true
SYM_IGNORE true
$end
''

We then run

$ qchem BH3.inp BH3.out

The above job finishes successfully, printing 5 minima in the output file <code>BH3.out</code>. We can briefly examine these minima by their energies. Executing

$ grep "Saving Minimum" BH3.out

gives

''
7 -26.0698458670 3.16E-09 00000 Saving Minimum 1
60 -23.8075357551 8.98E-08 00000 Saving Minimum 2
102 -23.5547974285 4.13E-08 00000 Saving Minimum 3
129 -23.5596201123 9.30E-08 00000 Saving Minimum 4
145 -25.3032615669 1.80E-08 00000 Saving Minimum 5
''

Your metadynamics run might find different solutions due to the random nature of metadynamics. Nevertheless, it should still be able to locate five minima fairly easily. We will proceed to determine the irreducible representations spanned by each of these minima together with its symmetry partners. If you wish to separate the minima into different directories, follow step 2 below. If not, you can jump directly to step 3.

=== Step 2a (optional): Extracting SCF minima from the output file ===

It might be convenient to extract the minima from the original Q-Chem output file into separate directories for easier management and manipulation. This, however, is not essential for the use of <code>SymmetryTools</code>. To this end, we first need to ask QCMagic to read in the minima from the output file and store them in a <code>.sd</code> file that can be easily re-read in by QCMagic later on. This is done via

$ runscanSurface.py --read-minima=1,2,3,4,5 --read-only BH3.out BH3-extracted > terminal.out

where
* <code>--read-minima=1,2,3,4,5</code> instructs <code>runscanSurface.py</code> to read in minima 1--5 from the supplied Q-Chem output file. You can include only the minimum or minima that you are interested in here, and you need not use all minima in the output file. To determine which minima are of interest, you can examine their energies and select those within a certain energy window that you are interested in;
* <code>--read-only</code> instructs <code>runscanSurface.py</code> to only read and store the minima without trying to reconverge into them;
* <code>BH3.out</code> tells <code>runscanSurface.py</code> which output file to read in;
* <code>BH3-extracted</code> specifies the tag name for output files generated by <code>runscanSurface.py</code> (No file extension is needed);
* <code>> terminal.out</code> redirects <code>stdout</code> from <code>runscanSurface.py</code> to <code>terminal.out</code>. This is needed to determine which minima in the <code>.sd</code> file the original minima in the output file have been mapped to.

The above command produces <code>BH3-extracted.dat</code>, <code>BH3-extracted.dat2</code>, <code>BH3-extracted.sd</code>, and <code>terminal.out</code>. <code>BH3-extracted.dat</code> and <code>BH3-extracted.dat2</code> are empty and need not concern us further since we did not run any reconvergence calculations. <code>BH3-extracted.sd</code> contains the minima extracted from <code>BH3.out</code>. <code>terminal.out</code> contains print statements from <code>runscanSurface.py</code> that are useful for debugging purposes, but most importantly, it contains statements of the form

Old min <math>x</math> -> New sol <math>y</math>

which tells us that minimum <math>x</math> in the Q-Chem output file is now minimum <math>y</math> in the <code>.sd</code> file produced. For example, minima 1--5 in <code>BH3.out</code> have changed to minima 0--4 in <code>BH3-extracted.sd</code>. We then extracts these statements into a file, say <code>oldminnewsol</code>, to be used by a script called <code>runrearrangeSolutions.py</code> later on.

$ grep "Old min" terminal.out > oldminnewsol

=== Step 2b (optional): Reconverging into each solution separately ===

The <code>.sd</code> file generated in step 2a contains all extracted minima. We could in principle use this <code>.sd</code> file for symmetry analysis, but we could also reconverge into each minimum separately, with possible changes to reconvergence criteria (''e.g.'', higher <code>SCF_CONVERGENCE</code>).

As an example, using <code>BH3-extracted.sd</code> from step 2a, we run

$ runqcSDExtract.py --reconverge --rem="SCF_CONVERGENCE 10" BH3-extracted.sd BH3-highconv

which tries to reconverge into every minimum in <code>BH3-extracted.sd</code> in separate output files. Hence, the number of output files generated is dependent on the number of minima present in the <code>.sd</code> file. In our example, we will have 5 such files:

BH3-highconv.g0.s<math>y</math>.xc0.reconverged.out

where <math>y</math> specifies the solution index number and should corresponds to the <math>y</math> in <code>Old min <math>x</math> -> New sol <math>y</math></code> obtained earlier.

In addition, the following files are also produced:

* <code>BH3-highconv.xc0.atom0.charge.dat</code> provides the Mulliken net atomic charge on atom 0 for all minima (by default of <code>runqcSDExtract.py</code>);
* <code>BH3-highconv.xc0.atom0.oxstate.dat</code> provides the oxidation state of atom 0 from a LOBA calculation (LOBA is off by default);
* <code>BH3-highconv.xc0.atom0.spinz.dat</code> provides the Mulliken net spinZ (<math>S_z</math>) on atom 0 (by default of <code>runqcSDExtract.py</code>);
* <code>BH3-highconv.xc0.energy.dat</code> provides the energy of all minima.

Most of the produced <code>.dat</code> files contain information extracted from the various output files and can be used for inspection purposes. At the end of the day, however, only the <code>.out</code> files <code>BH3-highconv.g0.s<math>y</math>.xc0.reconverged.out</code> are needed to fully describe the minima as they contain the full set of orbital coefficients.

=== Step 2c (optional): Separating output files into different directories ===

It is good practice to analyse each minimum in a separate, properly labelled directory. The script <code>runrearrangeSolutions.py</code> can do this automatically, provided that the files to be moved into a directory called <code>o<math>x</math></code> contain the string <code>.s<math>y</math>.</code> in their names, and that the mapping <code><math>x</math> -> <math>y</math></code> is supplied as a line with the format <code>Old min <math>x</math> -> New sol <math>y</math></code> in the input file passed in to <code>runrearrangeSolutions.py</code>.

For our example, run

$ runrearrangeSolutions.py oldminnewsol

to arrange each of the <code>BH3-highconv.g0.s<math>y</math>.xc0.reconverged.out</code> files into separate directories called <code>o<math>x</math></code>, where the mappings <code><math>x</math> -> <math>y</math></code> are provided in <code>oldminnewsol</code> in the correct format specified above.

=== Step 3: Determining the point group and identifying all symmetry elements of the system ===

In order to apply symmetry operations on the minima and find the irreducible representations spanned by them, we first need to determine the underlying spatial point group set up by the nuclear framework of the system. This then allows us to identify the symmetry elements present. In our earlier example, since all five solutions come from the same system (''i.e.'', same geometry and basis set), we only need to obtain the point group and symmetry elements from one of them. To this end, run

$ cd o1
$ rungeneralisedTransformQCMinima.py foobar BH3-highconv.g0.s0.xc0.reconverged.out BH3-sym

where

* <code>foobar</code> is just a placeholder to satisfy a compulsory positional argument that we do not need or have at the moment;
* <code>BH3-highconv.g0.s0.xc0.reconverged.out</code> is the Q-Chem output file containing all system information, as well as information for state <code>o1</code>;
* <code>BH3-sym</code> specifies the tag name for the files produced by <code>rungeneralisedTransformQCMinima.py</code>.

This produces the following:

* <code>BH3-sym.sym</code> contains an object that has all symmetry and basis information for this system. We will need this object for all symmetry manipulation on all states of this system;
* <code>BH3-sym.g0.sym.summary</code> provides a human-readable summary of the point group and symmetry elements located for this system;
* <code>BH3-sym.sym.sd</code> and <code>BH3-sym.all.transformed.sd</code> do not contain any other useful information for us at the moment.

It is instructive to inspect <code>BH3-sym.g0.sym.summary</code> and check if <code>rungeneralisedTransformQCMinima.py</code> has found a sensible point group and located all expected symmetry elements for the system. In our example, part of this file looks like

''
*********************************************************************************************************
SYMMETRY INFORMATION
*********************************************************************************************************
Rotational symmetry: Symmetric Top - Oblate, Planar
Point group: D3h
Distance threshold: 1.00E-02
*********************************************************************************************************

*********************************************************************************************************
SYMMETRY ELEMENTS LOCATED
*********************************************************************************************************
Proper rotation axes (Cn axes)
Order: 2
Index x y z alpha/pi beta/pi gamma/pi n,i,power
0 -0.9485234 -0.3167072 0.0000000 1.0000000 1.0000000 -1.0000000 2,0,p
1 -0.7485381 0.6630918 0.0000000 0.0000000 1.0000000 -0.0000000 2,1,p
2 -0.1999852 -0.9797989 0.0000000 0.9359106 1.0000000 -0.9359106 2,2,p

Order: 3
Index x y z alpha/pi beta/pi gamma/pi n,i,power
0 0.0000000 0.0000000 -1.0000000 0.0000000 0.0000000 0.6666667 3,0,p

Mirror planes (S1 axes)
Index x y z n,i,power
0 0.0000000 0.0000000 -1.0000000 1,0,p
1 0.3167072 -0.9485234 0.0000000 1,1,p
2 -0.6630918 -0.7485381 -0.0000000 1,2,p
3 0.9797989 -0.1999852 0.0000000 1,3,p

Improper rotation axes (Sn axes)
Order: 3
Index x y z n,i,power
0 0.0000000 0.0000000 -1.0000000 3,0,p
***********************************************************
''

We note the following:

* The point group of the system is found to be <math>D_{3h}</math>, which is correct.
* Apart from the identity <math>E</math> which is not shown, there are three <math>C_2</math> axes, one <math>C_3</math> axis, four <math>\sigma</math> planes (one <math>\sigma_h</math> and three <math>\sigma_v</math>), and one <math>S_3</math> axis, as expected for <math>D_{3h}</math>.
* Each symmetry element is specified by whether it is proper or improper (<math>C</math> or <math>S</math>), its order <math>n</math>, and its index <math>i</math>. These are summarised in the column <code>n,i,power</code> for each symmetry element. The role of the power <math>p</math> will become clear later.
* All symmetry elements are defined with respect to the recentred coordinates where the centre of mass of the molecule has been translated to <math>(0,0,0)</math>. Each axis of rotation (proper or improper) passes through the centre of mass and is parallel to the vector whose components are given in the <code>x</code>, <code>y</code>, and <code>z</code> columns.
* Additionally, the Euler angles for the proper rotations are given in <math>\pi \; \mathrm{rad}</math> following the Whitaker convention in the <code>alpha/pi</code>, <code>beta/pi</code>, and <code>gamma/pi</code> columns.

=== Step 4: Constructing the symmetry operation instruction file ===

Given a minimum that is a single determinant, we seek to generate other symmetry-related single determinants. To this end, we must first tell <code>rungeneralisedTransformQCMinima.py</code> what symmetry operations it will need to use to generate new single determinants. This is done by means of a file that can contain several lines, each of which contains instructions for several symmetry operations to be applied consecutively from the right to generate a single symmetry-equivalent determinant. More detailed information can be found by running

$ rungeneralisedTransformQCMinima.py

without any arguments.

For our BH3 example, however, we shall use a very simple instruction file that contains all spatial symmetry operations (except the trivial identity) in <math>D_{3h}</math> to illustrate how this file should be constructed. Prior to constructing this file, it is important to consult the <code>BH3-sym.g0.sym.summary</code> file generated in step 3 in conjunction with the Character Table for <math>D_{3h}</math>. Assuming that that has been done, let us call this file <code>transform.instructions.full</code> whose content is shown below.

''
# Proper rotations
(C,2,0,1)
(C,2,1,1)
(C,2,2,1)
(C,3,0,1)
(C,-3,0,1)
# Improper rotations
(S,1,0,1) # sigmah
(S,1,1,1) # sigmav
(S,1,2,1) # sigmav
(S,1,3,1) # sigmav
(S,3,0,1)
(S,-3,0,1)

''

We note the following:

* There are 11 non-comment lines in the file corresponding to the 11 non-identity symmetry operations in <math>D_{3h}</math>. We are using all symmetry operations in <math>D_{3h}</math> as we want to generate all possible symmetry-related determinants from any reference SCF determinant obtained for this system. Repeated determinants manifested as linear dependence will be projected out later.
* Anything following <code>#</code> until <code>eol</code> is not considered.
* Each spatial symmetry operation is specified by <code>(signature,order,index,power)</code>, where
** <code>signature</code> gives the type of symmetry operation to be carried out. For our example, <code>signature</code> is either <code>C</code> or <code>S</code> for proper or improper rotations, respectively;
** <code>order</code> gives the order of rotation. This is given by <math>n</math> in <code>BH3-sym.g0.sym.summary</code>. If <math>-n</math> is used, the '''inverse''' of the corresponding rotation with order <math>n</math> is carried out instead;
** <code>index</code> gives the index of the rotation axis (to distinguish between various axes of the same order. This is given by <math>i</math> in <code>BH3-sym.g0.sym.summary</code>;
** <code>power</code> gives the number of times the operation is applied.
* Each <math>C_2</math> axis gives rise to only one <math>\hat{C}_2</math> operation because, for spatial transformations, <math>\hat{C}_2 = \hat{C}_2^{-1}</math>. The same applies to mirror planes (<math>S_1</math> axes) and inversion centres (<math>S_2</math> axes).
* Multiple symmetry operations can be strung together using <code>.</code> and the rightmost symmetry operation is applied first. For example, since <math>\hat{C}_3^{-1} = \hat{C}_{2,1} \cdot \hat{C}_{2,2}</math> in our example (try inspecting the effects of these operations based on their axes defined in <code>BH3-sym.g0.sym.summary</code>), we could replace <code>(C,-3,0,1)</code> with <code>(C,2,1,1).(C,2,2,1)</code>.

=== Step 5: Generating symmetry-related determinants ===

Now that we have identified the symmetry elements present for the system and determined which symmetry operations we would like to apply to a reference determinant, we can proceed to actually generating symmetry-related determinants. This is achieved by running

$ rungeneralisedTransformQCMinima.py -p 6 --read-minima=1 --symmetry=BH3-sym.sym --reconverge transform.instructions.full BH3-highconv.g0.s0.xc0.reconverged.out BH3-highconv.o1

where
* <code>--read-minima=1</code> and <code>BH3-highconv.g0.s0.xc0.reconverged.out</code> instruct <code>rungeneralisedTransformQCMinima.py</code> to use minimum 1 in the Q-Chem output file as the reference determinant. These can be changed to supply different reference determinants to <code>rungeneralisedTransformQCMinima.py</code>. More than one reference determinant can be used, in which case <code>rungeneralisedTransformQCMinima.py</code> will generate and collate symmetry-related determinants for each reference determinant into a separate <code>.sd</code> file (see below);
* <code>--symmetry=BH3-sym.sym</code> points <code>rungeneralisedTransformQCMinima.py</code> to the symmetry object generated earlier and containing all symmetry information of the system;
* <code>--reconverge</code> is optional. This option instructs <code>rungeneralisedTransformQCMinima.py</code> to use the coefficients generated from <code>SymmetryTools</code> as guesses for Q-Chem runs, seek reconvergence, and use the reconverged coefficients as coefficients for the corresponding symmetry-related determinants. This is so that one can verify that a determinant generated by symmetry is indeed an SCF solution. This should be the case for spatial-symmetry-related determinants but need not be so for more exotic transformations involving spins or selected orbitals;
* <code>transform.instructions.full</code> specifies the symmetry operation instruction file constructed in step 4;
* <code>BH3-highconv.o1</code> specifies the tag name for the files produced by <code>rungeneralisedTransformQCMinima.py</code>.

This produces the following:
* <code>BH3-highconv.o1.g0.s0.xc0.(*).out</code> are Q-Chem output files for the reconvergence runs. It is worth running <code>grep "Saving Minimum" BH3-highconv.o1.g0.s0.xc0.*.out</code> and verifying that all reconvergence runs completed successfully and that all reconverged determinants are degenerate to the reference determinant as required by symmetry;
* <code>BH3-highconv.o1.g0.s0.transformed.sd</code> contains the reference determinant together with all symmetry-related ones;
* <code>BH3-highconv.o1.all.transformed.sd</code> need not concern us at the moment.

In what will follow, we will need <code>BH3-highconv.o1.g0.s0.transformed.sd</code> to perform symmetry analyses.

=== Step 6a: Obtaining the <math>\mathbf{S}_\mathrm{AO}</math> matrix from Q-Chem ===

Most symmetry analyses need to compute various overlap and Hamiltonian matrix elements between non-orthogonal determinants. This requires the knowledge of the overlap matrix (<math>\mathbf{S}</math>) of the underlying atomic orbital (<math>\mathrm{AO}</math>) basis functions used. Q-Chem's integral engine is very efficient at computing this, so there is no need for QCMagic to recalculate it. We just need to ask Q-Chem to print it out for QCMagic to read in.

==Basis Set Projection using BASIS2==
<code>BASIS2</code> does not work well with metadynamics. Assuming that you have ran a metadynamics calculation and wish to project your basis to one with more functions, use the following steps:

=== Step 1: Find the appropriate bases ===
Refer to https://www.q-chem.com/qchem-website/manual/qchem43_manual/sect-dualbasis.html and get your corresponding basis.
<code> BASIS2 </code> should be the basis you are currently working with (the basis in which the metadynamics calculation was ran)
<code> BASIS </code> would be the projected basis

===Step 2: Template file (optional) ===
It might be helpful to use a template file as there are quite a few rem variables to be changed.
In your template file, the following should be added:
rem['basis2'] = '<your original basis>'
rem['basis'] = '<projected basis>'
rem['basisprojtype'] = 'ovprojection'
rem['scf_guess'] = 'read'
(If there are unexpected failures, you can add rem['scf_print'] = 2 and rem['scf_guess_print'] = 2 to increase the amount of printouts for debugging purposes)

In addition, do not add rems that runs metadynamics such as scf_saveminima

NOTE: If you are using <code> rem['basis2'] = '6-31g*' </code> and <code> rem['basis'] = '6-311g**' </code>, you will need to add the following rem:
rem['purecart'] = 2. This forces QChem to use cartesian bases to represent the d functions for 6-311G** (This is required because cartesian bases are used for d functions in 6-31G*, rather than the spherical d functions).

=== Step 3: Using runscanSurface ===
Using <code> BASIS2 </code>, there will be difficulties reading in minima from metadynamics calculations. As such, one can use the following code in the command line

<code> runscanSurface.py -p 6 --write-guess --template=<template file> <outfile> <tagfile> </code>

The option --write-guess reads in the minima as if it was a scf_guess read rather than a scf_readminima. This makes it compatible with <code> BASIS2 </code>.

==Useful Classes ''(for developers only)''==

QCMagic includes a number of useful python classes that may be used to generate or analyse data from Q-Chem calculations. Some of the more useful classes and their functions are listed below. <code>QCManager</code> imports most of these and thus importing <code>QCManager</code> sets up QCMagic for easy usage.

'''<code>QCMolecule.Atom</code>'''

A class used to keep track of atoms and their positions via <code>self.Position</code>.

'''<code>QCMolecule.System</code>'''

As a relatively fundamental class in QCMagic, this is used to keep track of a set of atoms contained in self.Atoms, and can be initiated with no inputs followed by addition of atoms, either individually or from a <code>.xyz</code> file/text. Most noteworthy are:
* numerous methods for moving and rotating both the entire system and individual atoms;
* and the method <code>MakeInput()</code> for generating a <code>$molecule</code> section of a Q-Chem input file and <code>self.Charge</code>, <code>self.SpinZ</code> to keep track of spin and charge.

'''<code>QCSystemData.SystemDataSet</code>'''

This class is used to keep track of multiple systems and their associated electronic states. Systems can be added either from SCF states (<code>QCSystemData.SCFState(system,minimum)</code>) or from a <code>QCOutput.OutputFile</code> object. Some important methods and variables in the class are:
* <code>self.GeomList</code> is an instance variable, which is a list of all systems contained in the SDS;
* <code>self.StateList</code> is another instance variable, which is the corresponding list of dictionaries (dicts) with each dictionary (dict) containing the minima (electronic states) associated with that system. Each state has a unique <code>StateList</code> index;
* <code>RunQChem()</code> is a class method for running a Q-Chem calculation. This takes as arguments a Queue and Job (see below), the geometry index (<code>GI</code>) of the <code>System</code> for which the calculation is to be performed, as well as a list (<code>FindMinima</code>) of minima to use as initial guesses given by their <code>StateList</code> indices. if <code>OverwriteGeom=True</code>, the geometry of the <code>GI</code> will be used, otherwise the geometry from the the next pending Job will be used.

'''<code>QCOutput.OutputFile</code>'''

As the name suggests, this is a class used for analysing Q-Chem output files. the <code>Parse()</code> method extracts data from the output file and adds it to <code>self.Outputs</code>. If only one calculation has been performed, <code>self.Outputs[0]</code> contains the data of interest. This includes steps; a list of steps corresponding to the different geometries of ''e.g.'' a geometry optimisation and the corresponding <code>System</code> classes can be extracted. Each step (and <code>CurStep</code> / <code>Steps[-1]</code> for a single point calculation) contains a list of Minima which can be used to instantiate a <code>QCSystemData.SCFState</code> object and add to an SDS. The Minima also contain orbital coefficients and distance metrics.

'''<code>QCInput.Input</code>'''

A class used to generate and manipulate inputs for Q-Chem calculations. An instance of this class contains a section list, <code>self.Sections</code>, and a section dictionary, <code>self.SectionDict</code>, which contain sections to be added to a Q-Chem input file. The <code>rem</code> section is also added as a dictionary and its elements may be changed by ''e.g.'' <code>self.Rem['jobtype']='opt'</code>. Sections can be added, removed or edited. <code>self.System</code> contains the <code>System</code> for which an input is to be written; ''n.b.'' this overwrites any changes to the <code>molecule</code> section! <code>MakeInputText()</code> generates the text that goes into a Q-Chem input file, but jobs may more easily be submitted directly via QCMagic.

'''<code>newJob.Job</code>'''

A class used to managed Q-Chem jobs. A new input can be added to the job with the <code>AddInput()</code> method. This input is automatically added to <code>self.Pending</code> from which jobs are run when the <code>Job</code> class instance is used to do a Q-Chem calculation.

'''<code>QCQueue.QCQueue</code>'''

A class used for running Q-Chem calculations. This is where input files, submission scripts, scratch directories ''etc.'' are actually written and the job submitted. This is also where details about nodes and cores are determined and may need some editing as the hardware and software used to run the calculations is changed.

'''<code>QCRegisterOptions.RegisterOptions</code>'''

Made to register options for <code>scanSurface</code> calculations (see below) but can be partly copied, imitated or imported for easy addition of own options to new scripts.

A useful way of saving and loading such class instances is to use the pickle module.

Fast Randomized Iteration

2025-09-14T07:45:50Z

Ajwt3: Created page with "= Project Title = Fast Randomized Iteration approach to Coupled Cluster = Project Phase = proto == Project aims/abstract == L.-H. Lim and J. Weare, Fast randomized iteration: diffusion Monte Carlo through the lens of numerical linear algebra, SIAM Rev. 59 (2017), 547–587, DOI 10.1137/15M1040827. J. Lu and Z. Wang, The full configuration interaction quantum Monte Carlo method through the lens of inexact power iteration, SIAM J. Sci. Comput. 42 (2020), B1–B29, DOI 1..."

= Project Title =
Fast Randomized Iteration approach to Coupled Cluster

= Project Phase =
proto

== Project aims/abstract ==
L.-H. Lim and J. Weare, Fast randomized iteration: diffusion Monte Carlo through the lens of numerical linear algebra, SIAM Rev. 59 (2017), 547–587, DOI 10.1137/15M1040827.

J. Lu and Z. Wang, The full configuration interaction quantum Monte Carlo method through the lens of inexact power iteration, SIAM J. Sci. Comput. 42 (2020), B1–B29, DOI 10.1137/18M1166626.

S. M. Greene, R. J. Webber, T. C. Berkelbach, and J. Weare, Approximating matrix eigenvalues by subspace iteration with repeated random sparsification, SIAM J. Sci. Comput. 44 (2022), A3067–A3097, DOI 10.1137/21M1422513.

S. M. Greene, R. J. Webber, J. E. T. Smith, J. Weare, and T. C. Berkelbach, Full configuration interaction excited-state energies in large active spaces from subspace iteration with repeated random sparsification, J. Chem. Theory Comput. 18 (2022), 7218–7232, DOI 10.1021/acs.jctc.2c00435.

S. M. Greene, R. J. Webber, J. Weare, and T. C. Berkelbach, Beyond walkers in stochastic quantum chemistry: reducing error using fast randomized iteration, J. Chem. Theory Comput. 15 (2019), 4834–4850, DOI 10.1021/acs.jctc.9b00422.

S. M. Greene, R. J. Webber, J. Weare, and T. C. Berkelbach, Improved fast randomized iteration approach to full configuration interaction, J. Chem. Theory Comput. 16 (2020), 5572–5585, DOI 10.1021/acs.jctc.0c00437.

As a consequence, FRI produces solutions as accurate as FCIQMC with a number of time steps that is smaller by a factor of 10---10000
Randomly sparsified Richardson iteration: A dimension-independent sparse linear solver
Jonathan Weare, Robert J. Webber
First published: 08 September 2025 https://doi.org/10.1002/cpa.70012

== Current state of the project and next steps ==

== Useful skills and knowledge ==
This project requires the knowledge of the following:

=== Theoretical ===
* Familiarity with the integral types of electronic structure theory (including their symmetries), and the efficient process of integral transformation
* Basic notions of linear algebra, and matrix decomposition techniques
* Understanding the mindset of scaling arguments (memory and computational)
* Understanding of Hartree-Fock and MP2 theory, and the basic notions of coupled cluster theory (derivation is not required)

=== Practical ===
* Basic understanding of the C++ syntax (or understanding the syntax of another programming language (e.g., Python) and willingness to explore how the other language works)
* Some familiarity with terminal commands, bash scripting, and the VI editor

== Learning outcomes ==

=== Theoretical ===
* Navigating electronic structure literature on integrals, and finding relevant information for understanding/implementation purposes
* Knowledge on existing approximation techniques that are extensively used in concurrent literature
* Understanding the context of fitting (where and why we use it in the methods we are interested in, and what the advantage/limitations of the proposed technique are)
* Knowledge on relevant statistical measures for performance testing

=== Practical ===
* Knowledge on C++ specific structures
* Familiarity and usage of the OpenMP/MPI parallelisation techniques in practice
* Efficiency optimisation of codes: using relevant matrix operation packages, and appropriate computational algorithms
* Efficient ways of dealing with test sets and extracting data (bash/Python scripting)
* Using Linux-based systems, computer clusters and schedulers

== Interesting references ==
# O. Vahtras, J. Almlöf, and M. W. Feyereisen, ''Chem. Phys. Lett.'' 213, 5–6, 514–518 (1993).
# M. Vose, ''IEEE Transactions on Software Engineering'' 17, 9, 972–975 (1991).
# [https://www.keithschwarz.com/darts-dice-coins/ Practical account on the alias method]
# T. Y. Takeshita, W. A. de Jong, D. Neuhauser, R. Baer, and E. Rabani, ''J. Chem. Theory Comput.'' 13, 4605–4610 (2017).

Project List

2025-09-14T07:41:27Z

Ajwt3:

= Various Projects =
[[Template]]

== Stochastic Coupled Cluster ==
[[Stochastic Density Fitting]]

Stochastic Coupled Cluster Perturbation

Scaling and Benchmarking studies

[[Fast Randomized Iteration]]
== He Bubbles ==

ab initio studies of excited states of clusters

== Quantum Computing ==

== holo and NOCI ==

Project List

2025-09-09T11:22:15Z

Ajwt3: /* Various Projects */

= Various Projects =
[[Template]]

== Stochastic Coupled Cluster ==
[[Stochastic Density Fitting]]

Stochastic Coupled Cluster Perturbation

Scaling and Benchmarking studies

== He Bubbles ==

ab initio studies of excited states of clusters

== Quantum Computing ==

== holo and NOCI ==

Template

2025-09-09T11:08:40Z

Ajwt3: Created page with "= Project Title = == Project aims/abstract == == Current state of the project and next steps == == Useful skills and knowledge == This project requires the knowledge of the following: === Theoretical === * Familiarity with the integral types of electronic structure theory (including their symmetries), and the efficient process of integral transformation * Basic notions of linear algebra, and matrix decomposition techniques * Understanding the mindset of scaling a..."

= Project Title =

== Project aims/abstract ==

== Current state of the project and next steps ==

== Useful skills and knowledge ==
This project requires the knowledge of the following:

=== Theoretical ===
* Familiarity with the integral types of electronic structure theory (including their symmetries), and the efficient process of integral transformation
* Basic notions of linear algebra, and matrix decomposition techniques
* Understanding the mindset of scaling arguments (memory and computational)
* Understanding of Hartree-Fock and MP2 theory, and the basic notions of coupled cluster theory (derivation is not required)

=== Practical ===
* Basic understanding of the C++ syntax (or understanding the syntax of another programming language (e.g., Python) and willingness to explore how the other language works)
* Some familiarity with terminal commands, bash scripting, and the VI editor

== Learning outcomes ==

=== Theoretical ===
* Navigating electronic structure literature on integrals, and finding relevant information for understanding/implementation purposes
* Knowledge on existing approximation techniques that are extensively used in concurrent literature
* Understanding the context of fitting (where and why we use it in the methods we are interested in, and what the advantage/limitations of the proposed technique are)
* Knowledge on relevant statistical measures for performance testing

=== Practical ===
* Knowledge on C++ specific structures
* Familiarity and usage of the OpenMP/MPI parallelisation techniques in practice
* Efficiency optimisation of codes: using relevant matrix operation packages, and appropriate computational algorithms
* Efficient ways of dealing with test sets and extracting data (bash/Python scripting)
* Using Linux-based systems, computer clusters and schedulers

== Interesting references ==
# O. Vahtras, J. Almlöf, and M. W. Feyereisen, ''Chem. Phys. Lett.'' 213, 5–6, 514–518 (1993).
# M. Vose, ''IEEE Transactions on Software Engineering'' 17, 9, 972–975 (1991).
# [https://www.keithschwarz.com/darts-dice-coins/ Practical account on the alias method]
# T. Y. Takeshita, W. A. de Jong, D. Neuhauser, R. Baer, and E. Rabani, ''J. Chem. Theory Comput.'' 13, 4605–4610 (2017).

Stochastic Density Fitting

2025-09-09T11:07:19Z

Ajwt3: Created page with "= Development of stochastic density fitting approaches = == Project aims/abstract == One of the main bottlenecks in practical applications of quantum chemistry is the storage and the AO-MO transformation of two-electron integrals. These processes are highly memory intensive, which makes calculations challenging for systems of chemical interest. In this project, we implement a tensor-factorisation-based technique, and exploit the inherent sparsity of the resulting inter..."

= Development of stochastic density fitting approaches =

== Project aims/abstract ==
One of the main bottlenecks in practical applications of quantum chemistry is the storage and the AO-MO transformation of two-electron integrals. These processes are highly memory intensive, which makes calculations challenging for systems of chemical interest.

In this project, we implement a tensor-factorisation-based technique, and exploit the inherent sparsity of the resulting intermediates to decrease this requirement. The procedure will be based on the “RI-type” density fitting technique, and we sample a set of small but still non-negligible integrals in order to decrease the number of integrals stored.

The method developed will be tested in the framework of deterministic methods (Hartree-Fock and MP2), and its performance features will be compared to existing techniques. In addition, the technique will be implemented with the coupled cluster quantum Monte Carlo technique, which – requiring only good enough estimators to the exact values – is expected to have a larger tolerance to integral errors, and hence, the application of this technique can provide an even more powerful way of extending feasibility in this framework.

== Current state of the project and next steps ==
Past steps of this development process involved a review on the different types of density fitting techniques, and the choice of a deterministic variant that provided a basis for the stochastic algorithm. In addition, a density fitting Hartree-Fock and MP2 code has been developed in C++, which now is compatible with various proposed algorithms for the stochastic fitting. These explore different combinations of sampling the objects resulting from tensor decomposition, and the effect of contraction order. The algorithm now is based on the Vose-Alias method, and explicitly uses the integral values, which means that this does not yet lead to the desired memory advantage (though the gain in fitting time is currently half of the original technique).

Next steps in the project would be to facilitate integral screening, the estimation of selection probabilities based on bounds (without calculating the explicit integral values), and the parallelisation of the sampling process. After this, we will determine general thresholds for choosing the stochastic integrals based on test set results, and examine the performance of the resulting method both for deterministic and stochastic methods.

== Useful skills and knowledge ==
This project requires the knowledge of the followings (and hence this is what you can prepare with if you would like):

=== Theoretical ===
* Familiarity with the integral types of electronic structure theory (including their symmetries), and the efficient process of integral transformation
* Basic notions of linear algebra, and matrix decomposition techniques
* Understanding the mindset of scaling arguments (memory and computational)
* Understanding of Hartree-Fock and MP2 theory, and the basic notions of coupled cluster theory (derivation is not required)

=== Practical ===
* Basic understanding of the C++ syntax (or understanding the syntax of another programming language (e.g., Python) and willingness to explore how the other language works)
* Some familiarity with terminal commands, bash scripting, and the VI editor

== Learning outcomes ==

=== Theoretical ===
* Navigating electronic structure literature on integrals, and finding relevant information for understanding/implementation purposes
* Knowledge on existing approximation techniques that are extensively used in concurrent literature
* Understanding the context of fitting (where and why we use it in the methods we are interested in, and what the advantage/limitations of the proposed technique are)
* Knowledge on relevant statistical measures for performance testing

=== Practical ===
* Knowledge on C++ specific structures
* Familiarity and usage of the OpenMP/MPI parallelisation techniques in practice
* Efficiency optimisation of codes: using relevant matrix operation packages, and appropriate computational algorithms
* Efficient ways of dealing with test sets and extracting data (bash/Python scripting)
* Using Linux-based systems, computer clusters and schedulers

== Interesting references ==
# O. Vahtras, J. Almlöf, and M. W. Feyereisen, ''Chem. Phys. Lett.'' 213, 5–6, 514–518 (1993).
# M. Vose, ''IEEE Transactions on Software Engineering'' 17, 9, 972–975 (1991).
# [https://www.keithschwarz.com/darts-dice-coins/ Practical account on the alias method]
# T. Y. Takeshita, W. A. de Jong, D. Neuhauser, R. Baer, and E. Rabani, ''J. Chem. Theory Comput.'' 13, 4605–4610 (2017).

Project List

2025-09-09T11:07:12Z

Ajwt3: /* Various Projects */

= Various Projects =

[[Template]]

[[Stochastic Density Fitting]]

Project List

2025-09-09T11:06:06Z

Ajwt3: Created page with "= Various Projects ="

= Various Projects =

Computer and Storage List

2025-08-01T08:33:53Z

Ajwt3: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!info updated
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Software
!Purchased
|-
|carpathia
|379
|
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|376
|
|Andreea
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 22.04
|
|
|
|2015
|-
|sandstone
|378
|01/04/2025
|Divye, Petar [Kripa]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 22.04.5
| GTX 750 Ti
|
|QChem
source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG11
|Offline 30/6/25
|Lijun, [Theo, Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG03a
|
|Nestor [Charlie, Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|QChem
export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|28/04/2025
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 22.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|
|Rowan, Tom [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|360
|
|Reka, [Daniel, Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|
|[Yi, Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|/scratch2 has 18Tb of scratch
|QChem
source /home/maf63/qchem-public/qcsetup

MRCC

source /home/ajwt3/code/mrcc
|2020
|-
|nemesis
|378
|Retired 2025
|Constance
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 20.04.5
|-
|chiron
|UG03A
|
|Chiara
|10
|Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz
|96GB
|Ubuntu 20.04
|
|
|
|2021
|-
|topaz
|360
|
|Lila
|8
|Intel Core i9-11900 2.5GHz 8 Core
|128GB
|Ubuntu 20.04
|NVIDIA GeForce RTX 3080
|
|
|2022
|-
|[https://www.ch.cam.ac.uk/computing/cerebro-compute-server cerebro]
|
|
|Alavi & Thom Groups
|12 x 20
16 x 3 [currently]
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|24GB
64GB
|Rocks 6.2 (CentOS 6.9) SLURM queuing
|
|
|QChem
source /home/hynl2/code/qchemsetup.bash
source /sharedscratch/bc528/qchem/qcsetup.bash
MRCC

source /home/ajwt3/code/mrcc_2023
|-
|[https://www.hpc.cam.ac.uk/high-performance-computing CSD3]
|
|
|University Tier-2
|Cacade Lake 56 x 672
76 x 544 Ice Lake
|2x Intel(R) Xeon Platinum CPU 8276 @ 2.20GHz
2x Intel(R) Xeon(R) Platinum 8368Q CPU @ 2.60GHz
|192 or 384GB
256 or 512GB
|Rocky Linux 8 SLURM queuing (36h max)
|
|Free core hours are available - talk to AJWT
|QChem
source /rds/project/ajwt3/rds-ajwt3-thom1/qchem_public/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/nest-compute-server nest]
|
|
|CUC3 Group cluster
|40 x 20
|2x Cascade Lake Intel(R) Xeon Gold CPU 6248 @ 2.50GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|
|
|QChem
source /home/maf63/code/qcsetup.sh

source /sharedscratch/bc528/qchem/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/rogue-gpu-server rogue]
|
|
|CUC3 Group cluster
|(8 nVidia V100 + 32 CPU) x 2
|2x Sky Lake Intel(R) Xeon Gold CPU 6130 @ 2.10GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|-
|[https://www.archer2.ac.uk/ archer-2]
|
|National Tier-1 Supercomputer
| 128 x 5848
|2 x AMD EPYC Zen2 (Rome) 64-core CPUs @ 2.2GHz
|256GB and 512GB
|
|}

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

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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

Main Page

2025-07-30T09:11:31Z

Ajwt3: /* Quantum Brainstorm */

<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: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 
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
</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/crsid/slack
dpkg -x Slack.deb /scratch/crsid/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/crsid/slack/usr/lib/slack/slack %U
Icon=/scratch/crsid/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>

Computer and Storage List

2025-06-30T17:08:31Z

Ajwt3: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!info updated
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Software
!Purchased
|-
|carpathia
|379
|
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|376
|
|Andreea
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 22.04
|
|
|
|2015
|-
|sandstone
|378
|01/04/2025
|Divye, Petar [Kripa]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 22.04.5
| GTX 750 Ti
|
|QChem
source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG11
|Offline 30/6/25
|Lijun, [Theo, Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG03a
|
|Nestor [Charlie, Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|QChem
export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|28/04/2025
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 22.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|
|Rowan, Tom [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|360
|
|Reka, [Daniel, Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|
|[Yi, Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|/scratch2 has 18Tb of scratch
|QChem
source /home/maf63/qchem-public/qcsetup

MRCC

source /home/ajwt3/code/mrcc
|2020
|-
|nemesis
|378
|
|Constance
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 20.04.5
|-
|chiron
|UG03A
|
|Chiara
|10
|Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz
|96GB
|Ubuntu 20.04
|
|
|
|2021
|-
|topaz
|360
|
|Lila
|8
|Intel Core i9-11900 2.5GHz 8 Core
|128GB
|Ubuntu 20.04
|NVIDIA GeForce RTX 3080
|
|
|2022
|-
|[https://www.ch.cam.ac.uk/computing/cerebro-compute-server cerebro]
|
|
|Alavi & Thom Groups
|12 x 20
16 x 3 [currently]
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|24GB
64GB
|Rocks 6.2 (CentOS 6.9) SLURM queuing
|
|
|QChem
source /home/hynl2/code/qchemsetup.bash
source /sharedscratch/bc528/qchem/qcsetup.bash
MRCC

source /home/ajwt3/code/mrcc_2023
|-
|[https://www.hpc.cam.ac.uk/high-performance-computing CSD3]
|
|
|University Tier-2
|Cacade Lake 56 x 672
76 x 544 Ice Lake
|2x Intel(R) Xeon Platinum CPU 8276 @ 2.20GHz
2x Intel(R) Xeon(R) Platinum 8368Q CPU @ 2.60GHz
|192 or 384GB
256 or 512GB
|Rocky Linux 8 SLURM queuing (36h max)
|
|Free core hours are available - talk to AJWT
|QChem
source /rds/project/ajwt3/rds-ajwt3-thom1/qchem_public/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/nest-compute-server nest]
|
|
|CUC3 Group cluster
|40 x 20
|2x Cascade Lake Intel(R) Xeon Gold CPU 6248 @ 2.50GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|
|
|QChem
source /home/maf63/code/qcsetup.sh

source /sharedscratch/bc528/qchem/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/rogue-gpu-server rogue]
|
|
|CUC3 Group cluster
|(8 nVidia V100 + 32 CPU) x 2
|2x Sky Lake Intel(R) Xeon Gold CPU 6130 @ 2.10GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|-
|[https://www.archer2.ac.uk/ archer-2]
|
|National Tier-1 Supercomputer
| 128 x 5848
|2 x AMD EPYC Zen2 (Rome) 64-core CPUs @ 2.2GHz
|256GB and 512GB
|
|}

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

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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

Computer and Storage List

2025-06-30T17:07:15Z

Ajwt3: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!info updated
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Software
!Purchased
|-
|carpathia
|379
|
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|376
|
|Andreea
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 22.04
|
|
|
|2015
|-
|sandstone
|378
|01/04/2025
|Divye, Petar [Kripa]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 22.04.5
| GTX 750 Ti
|
|QChem
source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG11
|Offline 30/6/25
|Lijun, [Theo, Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG03a
|
|Nestor [Charlie, Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|QChem
export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|28/04/2025
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 22.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|360
|
|Reka, [Daniel, Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|
|[Yi, Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|/scratch2 has 18Tb of scratch
|QChem
source /home/maf63/qchem-public/qcsetup

MRCC

source /home/ajwt3/code/mrcc
|2020
|-
|nemesis
|378
|
|Constance
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 20.04.5
|-
|chiron
|UG03A
|
|Chiara
|10
|Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz
|96GB
|Ubuntu 20.04
|
|
|
|2021
|-
|topaz
|360
|
|Lila
|8
|Intel Core i9-11900 2.5GHz 8 Core
|128GB
|Ubuntu 20.04
|NVIDIA GeForce RTX 3080
|
|
|2022
|-
|[https://www.ch.cam.ac.uk/computing/cerebro-compute-server cerebro]
|
|
|Alavi & Thom Groups
|12 x 20
16 x 3 [currently]
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|24GB
64GB
|Rocks 6.2 (CentOS 6.9) SLURM queuing
|
|
|QChem
source /home/hynl2/code/qchemsetup.bash
source /sharedscratch/bc528/qchem/qcsetup.bash
MRCC

source /home/ajwt3/code/mrcc_2023
|-
|[https://www.hpc.cam.ac.uk/high-performance-computing CSD3]
|
|
|University Tier-2
|Cacade Lake 56 x 672
76 x 544 Ice Lake
|2x Intel(R) Xeon Platinum CPU 8276 @ 2.20GHz
2x Intel(R) Xeon(R) Platinum 8368Q CPU @ 2.60GHz
|192 or 384GB
256 or 512GB
|Rocky Linux 8 SLURM queuing (36h max)
|
|Free core hours are available - talk to AJWT
|QChem
source /rds/project/ajwt3/rds-ajwt3-thom1/qchem_public/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/nest-compute-server nest]
|
|
|CUC3 Group cluster
|40 x 20
|2x Cascade Lake Intel(R) Xeon Gold CPU 6248 @ 2.50GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|
|
|QChem
source /home/maf63/code/qcsetup.sh

source /sharedscratch/bc528/qchem/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/rogue-gpu-server rogue]
|
|
|CUC3 Group cluster
|(8 nVidia V100 + 32 CPU) x 2
|2x Sky Lake Intel(R) Xeon Gold CPU 6130 @ 2.10GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|-
|[https://www.archer2.ac.uk/ archer-2]
|
|National Tier-1 Supercomputer
| 128 x 5848
|2 x AMD EPYC Zen2 (Rome) 64-core CPUs @ 2.2GHz
|256GB and 512GB
|
|}

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

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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

Computer and Storage List

2025-06-30T10:41:37Z

Ajwt3: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!info updated
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Software
!Purchased
|-
|carpathia
|379
|
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|376
|
|Andreea
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 22.04
|
|
|
|2015
|-
|sandstone
|378
|01/04/2025
|Divye, Petar [Kripa]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 22.04.5
| GTX 750 Ti
|
|QChem
source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG11
|
|Lijun, [Theo, Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG03a
|
|Nestor [Charlie, Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|QChem
export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|28/04/2025
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 22.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|360
|
|Reka, [Daniel, Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|
|[Yi, Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|/scratch2 has 18Tb of scratch
|QChem
source /home/maf63/qchem-public/qcsetup

MRCC

source /home/ajwt3/code/mrcc
|2020
|-
|nemesis
|378
|
|Constance
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 20.04.5
|-
|chiron
|UG03A
|
|Chiara
|10
|Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz
|96GB
|Ubuntu 20.04
|
|
|
|2021
|-
|topaz
|360
|
|Lila
|8
|Intel Core i9-11900 2.5GHz 8 Core
|128GB
|Ubuntu 20.04
|NVIDIA GeForce RTX 3080
|
|
|2022
|-
|[https://www.ch.cam.ac.uk/computing/cerebro-compute-server cerebro]
|
|
|Alavi & Thom Groups
|12 x 20
16 x 3 [currently]
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|24GB
64GB
|Rocks 6.2 (CentOS 6.9) SLURM queuing
|
|
|QChem
source /home/hynl2/code/qchemsetup.bash
source /sharedscratch/bc528/qchem/qcsetup.bash
MRCC

source /home/ajwt3/code/mrcc_2023
|-
|[https://www.hpc.cam.ac.uk/high-performance-computing CSD3]
|
|
|University Tier-2
|Cacade Lake 56 x 672
76 x 544 Ice Lake
|2x Intel(R) Xeon Platinum CPU 8276 @ 2.20GHz
2x Intel(R) Xeon(R) Platinum 8368Q CPU @ 2.60GHz
|192 or 384GB
256 or 512GB
|Rocky Linux 8 SLURM queuing (36h max)
|
|Free core hours are available - talk to AJWT
|QChem
source /rds/project/ajwt3/rds-ajwt3-thom1/qchem_public/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/nest-compute-server nest]
|
|
|CUC3 Group cluster
|40 x 20
|2x Cascade Lake Intel(R) Xeon Gold CPU 6248 @ 2.50GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|
|
|QChem
source /home/maf63/code/qcsetup.sh

source /sharedscratch/bc528/qchem/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/rogue-gpu-server rogue]
|
|
|CUC3 Group cluster
|(8 nVidia V100 + 32 CPU) x 2
|2x Sky Lake Intel(R) Xeon Gold CPU 6130 @ 2.10GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|-
|[https://www.archer2.ac.uk/ archer-2]
|
|National Tier-1 Supercomputer
| 128 x 5848
|2 x AMD EPYC Zen2 (Rome) 64-core CPUs @ 2.2GHz
|256GB and 512GB
|
|}

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

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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

Computer and Storage List

2025-06-30T10:28:51Z

Ajwt3: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!info updated
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Software
!Purchased
|-
|carpathia
|379
|
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|376
|
|Andreea
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 22.04
|
|
|
|2015
|-
|sandstone
|378
|01/04/2025
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 22.04.5
| GTX 750 Ti
|
|QChem
source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG11
|
|Lijun, [Theo, Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG03a
|
|Nestor [Charlie, Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|QChem
export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|28/04/2025
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 22.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|360
|
|Reka, [Daniel, Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|
|[Yi, Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|/scratch2 has 18Tb of scratch
|QChem
source /home/maf63/qchem-public/qcsetup

MRCC

source /home/ajwt3/code/mrcc
|2020
|-
|nemesis
|378
|
|Constance
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 20.04.5
|-
|chiron
|UG03A
|
|Chiara
|10
|Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz
|96GB
|Ubuntu 20.04
|
|
|
|2021
|-
|topaz
|360
|
|Lila
|8
|Intel Core i9-11900 2.5GHz 8 Core
|128GB
|Ubuntu 20.04
|NVIDIA GeForce RTX 3080
|
|
|2022
|-
|[https://www.ch.cam.ac.uk/computing/cerebro-compute-server cerebro]
|
|
|Alavi & Thom Groups
|12 x 20
16 x 3 [currently]
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|24GB
64GB
|Rocks 6.2 (CentOS 6.9) SLURM queuing
|
|
|QChem
source /home/hynl2/code/qchemsetup.bash
source /sharedscratch/bc528/qchem/qcsetup.bash
MRCC

source /home/ajwt3/code/mrcc_2023
|-
|[https://www.hpc.cam.ac.uk/high-performance-computing CSD3]
|
|
|University Tier-2
|Cacade Lake 56 x 672
76 x 544 Ice Lake
|2x Intel(R) Xeon Platinum CPU 8276 @ 2.20GHz
2x Intel(R) Xeon(R) Platinum 8368Q CPU @ 2.60GHz
|192 or 384GB
256 or 512GB
|Rocky Linux 8 SLURM queuing (36h max)
|
|Free core hours are available - talk to AJWT
|QChem
source /rds/project/ajwt3/rds-ajwt3-thom1/qchem_public/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/nest-compute-server nest]
|
|
|CUC3 Group cluster
|40 x 20
|2x Cascade Lake Intel(R) Xeon Gold CPU 6248 @ 2.50GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|
|
|QChem
source /home/maf63/code/qcsetup.sh

source /sharedscratch/bc528/qchem/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/rogue-gpu-server rogue]
|
|
|CUC3 Group cluster
|(8 nVidia V100 + 32 CPU) x 2
|2x Sky Lake Intel(R) Xeon Gold CPU 6130 @ 2.10GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|-
|[https://www.archer2.ac.uk/ archer-2]
|
|National Tier-1 Supercomputer
| 128 x 5848
|2 x AMD EPYC Zen2 (Rome) 64-core CPUs @ 2.2GHz
|256GB and 512GB
|
|}

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

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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

Main Page

2025-06-16T10:03:03Z

Ajwt3: /* Summer interns start dates: */

<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 Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

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

=Summer 'Interns'=

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

===Summer interns start dates:===

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

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

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

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

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

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

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

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip 
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
</div>

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

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

- Clusters available.

- Storage available.

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

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

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

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

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

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

Set up logging in without a password:

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

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

===File Transfer Protocol===

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

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

====Windows====

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

====Mac/Linux====

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

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

- A pretty picture

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

- A "How to:" page on using qchem

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

Main Page

2025-06-16T10:02:14Z

Ajwt3: /* Summer interns start dates: */

<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 Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

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

=Summer 'Interns'=

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

===Summer interns start dates:===

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

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

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

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

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

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

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

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip 
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
</div>

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

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

- Clusters available.

- Storage available.

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

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

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

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

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

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

Set up logging in without a password:

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

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

===File Transfer Protocol===

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

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

====Windows====

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

====Mac/Linux====

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

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

- A pretty picture

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

- A "How to:" page on using qchem

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

Main Page

2025-06-06T09:49:31Z

Ajwt3: /* Summer interns start dates: */

<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 Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

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

=Summer 'Interns'=

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

===Summer interns start dates:===

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

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

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

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

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

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

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

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip 
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
</div>

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

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

- Clusters available.

- Storage available.

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

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

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

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

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

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

Set up logging in without a password:

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

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

===File Transfer Protocol===

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

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

====Windows====

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

====Mac/Linux====

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

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

- A pretty picture

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

- A "How to:" page on using qchem

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

Main Page

2025-06-06T09:48:56Z

Ajwt3: /* Summer interns start dates: */

<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 Tuesdays in the supervision area.
Notes available [[Quantum Brainstorm|here]].

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

=Summer 'Interns'=

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

===Summer interns start dates:===

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

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

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

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

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

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

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

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip 
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
</div>

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

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

- Clusters available.

- Storage available.

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

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

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

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

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

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

Set up logging in without a password:

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

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

===File Transfer Protocol===

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

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

====Windows====

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

====Mac/Linux====

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

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

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

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

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

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

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

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

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

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

(NB you need to search a bit for the .deb file as the default download is a .rpm. As at 2025/01/25 I found '''slack-desktop-4.41.105-amd64.deb''')
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/crsid/slack
dpkg -x Slack.deb /scratch/crsid/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/crsid/slack/usr/lib/slack/slack %U
Icon=/scratch/crsid/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>

Computer and Storage List

2025-04-02T15:30:11Z

Ajwt3: /* Computer List */

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

MRCC

source /home/ajwt3/code/mrcc
|2020
|-
|nemesis
|378
|
|Constance
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 20.04.5
|-
|chiron
|UG03A
|
|Chiara
|10
|Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz
|96GB
|Ubuntu 20.04
|
|
|
|2021
|-
|topaz
|360
|
|Lila
|8
|Intel Core i9-11900 2.5GHz 8 Core
|128GB
|Ubuntu 20.04
|NVIDIA GeForce RTX 3080
|
|
|2022
|-
|[https://www.ch.cam.ac.uk/computing/cerebro-compute-server cerebro]
|
|
|Alavi & Thom Groups
|12 x 20
16 x 3 [currently]
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|24GB
64GB
|Rocks 6.2 (CentOS 6.9) SLURM queuing
|
|
|QChem
source /home/hynl2/code/qchemsetup.bash

MRCC

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

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

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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

Computer and Storage List

2025-04-01T08:23:32Z

Ajwt3: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!info updated
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Software
!Purchased
|-
|carpathia
|379
|
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|376
|
|Andreea
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|
|2015
|-
|sandstone
|378
|
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04.4
|
|
|QChem
source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG11
|
|Lijun, [Theo, Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG03a
|
|Charlie [Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|QChem
export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|360
|
|Reka, [Daniel, Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|
|[Yi, Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|/scratch2 has 18Tb of scratch
|QChem
source /home/maf63/qchem-public/qcsetup

MRCC

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

MRCC

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

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

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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

Main Page

2025-01-24T09:31:29Z

Ajwt3: /* Installing Slack on department machines */

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

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

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

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

{{Special:IframePage}}

=Group Expectations=

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

=Group Meetings=

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

===Michaelmas 2024===

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

===Lent 2025===

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

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

Past Journal Clubs [[Journal Clubs|here]].
===2024-25===
{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Contributor''' || style="width: 54ex;" | '''Paper'''
|-
| 30 October 2024 || Bence || [https://www.nature.com/articles/s41586-023-06747-5 Solving olympiad geometry without human demonstrations]
|-
| 25 Nov 2024 || Jack || []
|-
| 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 
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
</div>

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

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

- Clusters available.

- Storage available.

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

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

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

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

Currently undergoing construction.

= How to connect to department machines =

===On Mac/WSL===

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

Set up logging in without a password:

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

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

===File Transfer Protocol===

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

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

====Windows====

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

====Mac/Linux====

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

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

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

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

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

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

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

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

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

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

(NB you need to search a bit for the .deb file as the default download is a .rpm. As at 2025/01/25 I found '''slack-desktop-4.41.105-amd64.deb''')
# <li value="2"> Make a directory and run dpkg replacing the with the appropriate file name.
mkdir /scratch/crsid/slack
dpkg -x Slack.deb /scratch/crsid/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/crsid/scratch/slack/usr/lib/slack/slack %U
Icon=/home/crsid/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

2024-10-31T17:02:08Z

Ajwt3: /* Michaelmas 2024 */

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

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

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

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

{{Special:IframePage}}

=Group Expectations=

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

=Group Meetings=

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

===Michaelmas 2024===

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

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

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

=Potentially Interesting Seminar Series=

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

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

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

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

=Summer 'Interns'=

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

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

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

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

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

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

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

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip 
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
</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/crsid/slack
dpkg -x Slack.deb /scratch/crsid/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/crsid/scratch/slack/usr/lib/slack/slack %U
Icon=/home/crsid/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

Project Ideas

2024-10-25T09:01:13Z

Ajwt3: /* October 2024 based on ISTCP 2024 */

= Project Ideas =

Initiated by AJWT and uncurated. Contact to discuss, or do edit or add discussion and links.
== October 2024 based on [https://www.istcp2024.com/web/progress.html ISTCP 2024 ] ==

P: 14/10/24 Martin Head Gordon. local orbitals for MP2 with fixed sparsity pattern. Some thresholding but generally very good and local. JCP 158 064105 '23 || Use these orbitals for CCMC

P: Check size consistency of CCMC (on Ne, Ne2 etc)

P: 14/10/24 Jeremy Richardson: "Breaking down the Barrier between Quantum and Classical." MASH (a deterministic version of surface hopping which couples a fictitious degree of freedom to decide which of two surfaces to hop on). Nat Commun. 15 4335 '24. JCP 158 104111 '23. || Use SCF diabatic-like states for this.

P 14/10/24 Troy van Voorhis "Bootstrap embedding". QuEmb software on GitHub to do this. || Use to look at He in clusters.

TODO Advertise HANDE hackathons on website

P: [post ByteDance] Understanding the Nodal surface - evaluate FermiNet's Nodal surface for quality (somehow)

P: [post ByteDance] Resolution of the Identity or density fitting to get HANDE 2e integrals.

P: [post ByteDance] Can we use the S+|Psi>=0 requirement to enforce Spin symmetry (S^2)

TODO: Read Pfau Science 2024

Q: How exactly are internally and externally contracted defined [Siegbahn 1980, 1983]

L: Quantum Course - Schmidt decomposition and properties of the Density Matrix

L: Quantum Course - Adiabatic connection used in DFT and ADC - how?

TODO: Interact more with Yi Sun on this Bootsctrap embedding

Q: Do complex nuclear coordinates lead to plane wave boundary conditions?

P: Do DMC on Fullerenes

P: 15/10/24 Janus Erikson: "Exact symmetrixation of localied MOs in MBE-FCI." || He has cc-pVTZ benzene results. || Do CCMCSDTQ5/pVDZ CCSDTQ/pVTZ on benzene at his geoms with Chebyshev.

P: biradicals JCP 147 164120 '20

Q: 15/10/24 Weitao Yang: "Delta SCF Excited state approaches: THeoretical Foudnations, Linear conditions for fractional charges and physical meaning of orbital energies". Delta SCF is justified by the correspondence between exact (n, w(r)) <-> (n_s, w_s(r)) correspondence (state number, potential). Functional is not of density but of n,w or 1PDM. 2403.04604. The numbering of states between n_s and n may differ. || What happens when two states cross (i.e. switch n_s value)?

Q: 15/10/24 Andy Teale: "Adiabatic Connection and reaction barriers". He defined a quantity \cal R_\lambda which corresponds to difference in adiabatic connection's W_\labda for a barrier. Shapes of this for forward and backward barriers of H_N2->HN2 very different. changing amount of HF exchange just shifts energies up and down (i.e. you get any result you want). ||Why do forward and backward barriers differ?

P: What barriers are bad in DFT and why?▒▒

P: Separating Static and Dynamic Correlation: MCPDFT and others (Gagliardi, Pernal)

Q: What is a restricted Boltzman Machine useful for?

P: Understanding UCC. How different are the different Anstzes and what effects do they have.

P: Simulate decoherence in quantum computing by coupling to a bath?

P: 16/10/24 Jiali Gao: "Multistate DFT and Applications". JPCL 13 7762 '22, JCTC 18 7403 '23. JCTC 20 8474 '24. JCTC 18 6407 '22|| Can apply this approach directly to the hDFT code or hNOCI code in RevQCMagic.▒

Q: Is MS-DFT for the HF functional just NOCI?

Q: 17/10/24. Wei Wu: "MRDFT with VB methods". Acc. Chem. Res. 54 3895 '21. KCP 157 084106 '22. JCTC 8 1608 '12.| Where are the F+...F- states in hHF/hDFT. How do they compare to the VB states?

TODO: Review of Multireference DFT

Q: 17/10/24 Chen Li: "Improving DFAs through exact constraints and exact WFs." cf Gori Giorgi PRA 75 042511 '07. hbar-> is like strong correlation. || Can we do complex scaling or tracking y changing hbar? Do NOCI with solutions with different hbar values

Q: Can we interact fragments' HF solutions by e-e-scaling the electrons? Is this just the same as bringing them in from infinity?

Q: How can we DAMP CCMC so it foesn't explode into the whole of CC space (so not needing an explicit truncation) Is it because we are not in spin eigenfunctions so we always spawn heavily into higher levels?

P: In the true CC solution, is there a lot of cancellation which might not be visible in a spin-symmetry broken stochastic snapshot (i.e. fluctuation induced sym breaking casuses lots of particles which do't cancel'

Q: 17/10/24 Piotr Piecuch: "Converging High-level CC energetics in Semistochastic, CIPSI-driven & adaptive CC(P;Q)". JCP 159 084108 '23. JCP 154 124103 '21. CCpy code availale on GitHub. ||How do the CC(P;Q) moment corrections actually work?

Q: For Ne@C70, what level of CC(P;Q) would be beeded to get <1cm-1 accuracy?

TODO: Buy "Interacting Electrons".

P: Calculate the diabaticity <Psi_\mu|\grad|Psi_nu> of different SCF states.

Q: Can the concept of diabaticity be applied to DFT? Can we calculate these adiabatic couplings in terms of densities?

== September 2024 ==
Finite Temperature holomorphic Hartree--Fock and DFT

This may alleviate some of the challenges of solutions coalescing

A Language for Electron Correlation

In order to use a generative AI language model to help tackle electron correlation, we need a language to do it in which is mostly transferrable between different molecules (and ceratinly within the same molecule). It should probably be based on localised orbitals in some way, but what is the best way of doing this? Can it be a simple type of decorator saying: correlate these orbitals? This might be a good fast starting guess for something at least.

Lindh Gradient Enhanced Kriging. JCPA for orbital version

Jiuli Gao: Mutistate DFT
SOme H matrix of Densities
Theophilou Subspace Theorem (1979)
JPCL 2022, 13, 7762. JCTC 2022 18 6407. JPCL 12 7409 '21. JCTC 4c00545. JCPL 4838 8 2017.

Kasia Pernal: Ontop Pair Density Functional for WF THeories
Apply to hNOCI

Automated construction of hHF states from dissociated atoms

tetracene noci calcs

NOCI in a larger context - water clusters

pysurf for dynamics - with NOCI? Shirin Faraji

NOCI + Piris Global Natural Orbital Functioonal

CCMC+f12 - generate the 3-e integrals from libint? Use FOrm like Ten-NO pTC2.

To Code:
AFQMC

Project Ideas

2024-10-25T08:58:04Z

Ajwt3: /* October 2024 based on ISTCP 2024 */

= Project Ideas =

Initiated by AJWT and uncurated. Contact to discuss, or do edit or add discussion and links.
== October 2024 based on ISTCP 2024 ==

P: 14/10/24 Martin Head Gordon. local orbitals for MP2 with fixed sparsity pattern. Some thresholding but generally very good and local. JCP 158 064105 '23 || Use these orbitals for CCMC

P: Check size consistency of CCMC (on Ne, Ne2 etc)

P: 14/10/24 Jeremy Richardson: "Breaking down the Barrier between Quantum and Classical." MASH (a deterministic version of surface hopping which couples a fictitious degree of freedom to decide which of two surfaces to hop on). Nat Commun. 15 4335 '24. JCP 158 104111 '23. || Use SCF diabatic-like states for this.

P 14/10/24 Troy van Voorhis "Bootstrap embedding". QuEmb software on GitHub to do this. || Use to look at He in clusters.

TODO Advertise HANDE hackathons on website

P: [post ByteDance] Understanding the Nodal surface - evaluate FermiNet's Nodal surface for quality (somehow)

P: [post ByteDance] Resolution of the Identity or density fitting to get HANDE 2e integrals.

P: [post ByteDance] Can we use the S+|Psi>=0 requirement to enforce Spin symmetry (S^2)

TODO: Read Pfau Science 2024

Q: How exactly are internally and externally contracted defined [Siegbahn 1980, 1983]

L: Quantum Course - Schmidt decomposition and properties of the Density Matrix

L: Quantum Course - Adiabatic connection used in DFT and ADC - how?

TODO: Interact more with Yi Sun on this Bootsctrap embedding

Q: Do complex nuclear coordinates lead to plane wave boundary conditions?

P: Do DMC on Fullerenes

P: 15/10/24 Janus Erikson: "Exact symmetrixation of localied MOs in MBE-FCI." || He has cc-pVTZ benzene results. || Do CCMCSDTQ5/pVDZ CCSDTQ/pVTZ on benzene at his geoms with Chebyshev.

P: biradicals JCP 147 164120 '20

Q: 15/10/24 Weitao Yang: "Delta SCF Excited state approaches: THeoretical Foudnations, Linear conditions for fractional charges and physical meaning of orbital energies". Delta SCF is justified by the correspondence between exact (n, w(r)) <-> (n_s, w_s(r)) correspondence (state number, potential). Functional is not of density but of n,w or 1PDM. 2403.04604. The numbering of states between n_s and n may differ. || What happens when two states cross (i.e. switch n_s value)?

Q: 15/10/24 Andy Teale: "Adiabatic Connection and reaction barriers". He defined a quantity \cal R_\lambda which corresponds to difference in adiabatic connection's W_\labda for a barrier. Shapes of this for forward and backward barriers of H_N2->HN2 very different. changing amount of HF exchange just shifts energies up and down (i.e. you get any result you want). ||Why do forward and backward barriers differ?

P: What barriers are bad in DFT and why?▒▒

P: Separating Static and Dynamic Correlation: MCPDFT and others (Gagliardi, Pernal)

Q: What is a restricted Boltzman Machine useful for?

P: Understanding UCC. How different are the different Anstzes and what effects do they have.

P: Simulate decoherence in quantum computing by coupling to a bath?

P: 16/10/24 Jiali Gao: "Multistate DFT and Applications". JPCL 13 7762 '22, JCTC 18 7403 '23. JCTC 20 8474 '24. JCTC 18 6407 '22|| Can apply this approach directly to the hDFT code or hNOCI code in RevQCMagic.▒

Q: Is MS-DFT for the HF functional just NOCI?

Q: 17/10/24. Wei Wu: "MRDFT with VB methods". Acc. Chem. Res. 54 3895 '21. KCP 157 084106 '22. JCTC 8 1608 '12.| Where are the F+...F- states in hHF/hDFT. How do they compare to the VB states?

TODO: Review of Multireference DFT

Q: 17/10/24 Chen Li: "Improving DFAs through exact constraints and exact WFs." cf Gori Giorgi PRA 75 042511 '07. hbar-> is like strong correlation. || Can we do complex scaling or tracking y changing hbar? Do NOCI with solutions with different hbar values

Q: Can we interact fragments' HF solutions by e-e-scaling the electrons? Is this just the same as bringing them in from infinity?

Q: How can we DAMP CCMC so it foesn't explode into the whole of CC space (so not needing an explicit truncation) Is it because we are not in spin eigenfunctions so we always spawn heavily into higher levels?

P: In the true CC solution, is there a lot of cancellation which might not be visible in a spin-symmetry broken stochastic snapshot (i.e. fluctuation induced sym breaking casuses lots of particles which do't cancel'

Q: 17/10/24 Piotr Piecuch: "Converging High-level CC energetics in Semistochastic, CIPSI-driven & adaptive CC(P;Q)". JCP 159 084108 '23. JCP 154 124103 '21. CCpy code availale on GitHub. ||How do the CC(P;Q) moment corrections actually work?

Q: For Ne@C70, what level of CC(P;Q) would be beeded to get <1cm-1 accuracy?

TODO: Buy "Interacting Electrons".

P: Calculate the diabaticity <Psi_\mu|\grad|Psi_nu> of different SCF states.

Q: Can the concept of diabaticity be applied to DFT? Can we calculate these adiabatic couplings in terms of densities?

== September 2024 ==
Finite Temperature holomorphic Hartree--Fock and DFT

This may alleviate some of the challenges of solutions coalescing

A Language for Electron Correlation

In order to use a generative AI language model to help tackle electron correlation, we need a language to do it in which is mostly transferrable between different molecules (and ceratinly within the same molecule). It should probably be based on localised orbitals in some way, but what is the best way of doing this? Can it be a simple type of decorator saying: correlate these orbitals? This might be a good fast starting guess for something at least.

Lindh Gradient Enhanced Kriging. JCPA for orbital version

Jiuli Gao: Mutistate DFT
SOme H matrix of Densities
Theophilou Subspace Theorem (1979)
JPCL 2022, 13, 7762. JCTC 2022 18 6407. JPCL 12 7409 '21. JCTC 4c00545. JCPL 4838 8 2017.

Kasia Pernal: Ontop Pair Density Functional for WF THeories
Apply to hNOCI

Automated construction of hHF states from dissociated atoms

tetracene noci calcs

NOCI in a larger context - water clusters

pysurf for dynamics - with NOCI? Shirin Faraji

NOCI + Piris Global Natural Orbital Functioonal

CCMC+f12 - generate the 3-e integrals from libint? Use FOrm like Ten-NO pTC2.

To Code:
AFQMC

Project Ideas

2024-10-25T08:55:51Z

Ajwt3: Created page with "= Project Ideas = Initiated by AJWT and uncurated. Contact to discuss, or do edit or add discussion and links. == October 2024 based on ISTCP 2024 == P: 14/10/24 Martin Hea..."

= Project Ideas =

Initiated by AJWT and uncurated. Contact to discuss, or do edit or add discussion and links.
== October 2024 based on ISTCP 2024 ==

P: 14/10/24 Martin Head Gordon. local orbitals for MP2 with fixed sparsity pattern. Some thresholding but generally very good and local. JCP 158 064105 '23 || Use these orbitals for CCMC

P: Check size consistency of CCMC (on Ne, Ne2 etc)

P: 14/10/24 Jeremy Richardson: "Breaking down the Barrier between Quantum and Classical." MASH (a deterministic version of surface hopping which couples a fictitious degree of freedom to decide which of two surfaces to hop on). Nat Commun. 15 4335 '24. JCP 158 104111 '23. || Use SCF diabatic-like states for this.

P 14/10/24 Troy van Voorhis "Bootstrap embedding". QuEmb software on GitHub to do this. || Use to look at He in clusters.

TODO Advertise HANDE hackathons on website

P: [post ByteDance] Understanding the Nodal surface - evaluate FermiNet's Nodal surface for quality (somehow)

P: [post ByteDance] Resolution of the Identity or density fitting to get HANDE 2e integrals.

P: [post ByteDance] Can we use the S+|Psi>=0 requirement to enforce Spin symmetry (S^2)

TODO: Read Pfau Science 2024

Q: How exactly are internally and externally contracted defined [Siegbahn 1980, 1983]

L: Quantum Course - Schmidt decomposition and properties of the Density Matrix

L: Quantum Course - Adiabatic connection used in DFT and ADC - how?

TODO: Interact more with Yi Sun on this Bootsctrap embedding

Q: Do complex nuclear coordinates lead to plane wave boundary conditions?

P: Do DMC on Fullerenes

P: 15/10/24 Janus Erikson: "Exact symmetrixation of localied MOs in MBE-FCI." || He has cc-pVTZ benzene results. || Do CCMCSDTQ5/pVDZ CCSDTQ/pVTZ on benzene at his geoms with Chebyshev.

P: biradicals JCP 147 164120 '20

Q: 15/10/24 Weitao Yang: "Delta SCF Excited state approaches: THeoretical Foudnations, Linear conditions for fractional charges and physical meaning of orbital energies". Delta SCF is justified by the correspondence between exact (n, w(r)) <-> (n_s, w_s(r)) correspondence (state number, potential). Functional is not of density but of n,w or 1PDM. 2403.04604. The numbering of states between n_s and n may differ. || What happens when two states cross (i.e. switch n_s value)?

Q: 15/10/24 Andy Teale: "Adiabatic Connection and reaction barriers". He defined a quantity \cal R_\lambda which corresponds to difference in adiabatic connection's W_\labda for a barrier. Shapes of this for forward and backward barriers of H_N2->HN2 very different. changing amount of HF exchange just shifts energies up and down (i.e. you get any result you want). ||Why do forward and backward barriers differ?

P: What barriers are bad in DFT and why?▒▒

P: Separating Static and Dynamic Correlation: MCPDFT and others (Gagliardi, Pernal)

Q: What is a restricted Boltzman Machine

P: Understanding UCC. How different are the different Anstzes and what effects do they have.

P: Simulate decoherence in quantum computing by coupling to a bath?

P: 16/10/24 Jiali Gao: "Multistate DFT and Applications". JPCL 13 7762 '22, JCTC 18 7403 '23. JCTC 20 8474 '24. JCTC 18 6407 '22|| Can apply this approach directly to the hDFT code or hNOCI code in RevQCMagic.▒

Q: Is MS-DFT for the HF functional just NOCI?

Q: 17/10/24. Wei Wu: "MRDFT with VB methods". Acc. Chem. Res. 54 3895 '21. KCP 157 084106 '22. JCTC 8 1608 '12.| Where are the F+...F- states in hHF/hDFT. How do they compare to the VB states?

TODO: Review of Multireference DFT

Q: 17/10/24 Chen Li: "Improving DFAs through exact constraints and exact WFs." cf Gori Giorgi PRA 75 042511 '07. hbar-> is like strong correlation. || Can we do complex scaling or tracking y changing hbar? Do NOCI with solutions with different hbar values

Q: Can we interact fragments' HF solutions by e-e-scaling the electrons? Is this just the same as bringing them in from infinity?

Q: How can we DAMP CCMC so it foesn't explode into the whole of CC space (so not needing an explicit truncation) Is it because we are not in spin eigenfunctions so we always spawn heavily into higher levels?

P: In the true CC solution, is there a lot of cancellation which might not be visible in a spin-symmetry broken stochastic snapshot (i.e. fluctuation induced sym breaking casuses lots of particles which do't cancel'

Q: 17/10/24 Piotr Piecuch: "Converging High-level CC energetics in Semistochastic, CIPSI-driven & adaptive CC(P;Q)". JCP 159 084108 '23. JCP 154 124103 '21. CCpy code availale on GitHub. ||How do the CC(P;Q) moment corrections actually work?

Q: For Ne@C70, what level of CC(P;Q) would be beeded to get <1cm-1 accuracy?

TODO: Buy "Interacting Electrons".

P: Calculate the diabaticity <Psi_\mu|\grad|Psi_nu> of different SCF states.

Q: Can the concept of diabaticity be applied to DFT? Can we calculate these adiabatic couplings in terms of densities?

== September 2024 ==
Finite Temperature holomorphic Hartree--Fock and DFT

This may alleviate some of the challenges of solutions coalescing

A Language for Electron Correlation

In order to use a generative AI language model to help tackle electron correlation, we need a language to do it in which is mostly transferrable between different molecules (and ceratinly within the same molecule). It should probably be based on localised orbitals in some way, but what is the best way of doing this? Can it be a simple type of decorator saying: correlate these orbitals? This might be a good fast starting guess for something at least.

Lindh Gradient Enhanced Kriging. JCPA for orbital version

Jiuli Gao: Mutistate DFT
SOme H matrix of Densities
Theophilou Subspace Theorem (1979)
JPCL 2022, 13, 7762. JCTC 2022 18 6407. JPCL 12 7409 '21. JCTC 4c00545. JCPL 4838 8 2017.

Kasia Pernal: Ontop Pair Density Functional for WF THeories
Apply to hNOCI

Automated construction of hHF states from dissociated atoms

tetracene noci calcs

NOCI in a larger context - water clusters

pysurf for dynamics - with NOCI? Shirin Faraji

NOCI + Piris Global Natural Orbital Functioonal

CCMC+f12 - generate the 3-e integrals from libint? Use FOrm like Ten-NO pTC2.

To Code:
AFQMC

Main Page

2024-10-25T08:52:12Z

Ajwt3:

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

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

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

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

{{Special:IframePage}}

=Group Expectations=

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

=Group Meetings=

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

===Michaelmas 2024===

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

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

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

=Potentially Interesting Seminar Series=

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

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

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

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

=Summer 'Interns'=

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

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

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

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

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

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

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

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip 
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
</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/crsid/slack
dpkg -x Slack.deb /scratch/crsid/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/crsid/scratch/slack/usr/lib/slack/slack %U
Icon=/home/crsid/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

2024-10-25T08:50:53Z

Ajwt3: /* Michaelmas 2024 */

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

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

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

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

{{Special:IframePage}}

=Group Expectations=

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

=Group Meetings=

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

===Michaelmas 2024===

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

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

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

=Potentially Interesting Seminar Series=

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

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

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

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

=Summer 'Interns'=

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

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

= [[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 
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
</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/crsid/slack
dpkg -x Slack.deb /scratch/crsid/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/crsid/scratch/slack/usr/lib/slack/slack %U
Icon=/home/crsid/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

Computer and Storage List

2024-10-22T08:04:41Z

Ajwt3: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Software
!Purchased
|-
|carpathia
|379
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|376
|Andreea, George [César]
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|
|2015
|-
|sandstone
|378
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04.4
|
|
|QChem
source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG03a
|Lijun, [Theo, Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG11
|Charlie [Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|QChem
export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|UG03A
|Reka, [Daniel, Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|[Yi, Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|/scratch2 has 18Tb of scratch
|QChem
source /home/maf63/qchem-public/qcsetup

MRCC

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

MRCC

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

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

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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

Computer and Storage List

2024-10-22T08:03:29Z

Ajwt3: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Software
!Purchased
|-
|carpathia
|379
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|376
|Andreea, George [César]
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|
|2015
|-
|sandstone
|378
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04.4
|
|
|QChem
source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG03a
|Lijun, [Theo, Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG11
|Charlie [Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|QChem
export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|UG03A
|Reka, [Daniel, Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|[Yi, Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|/scratch2 has 18Tb of scratch
|QChem
source /home/maf63/qchem-public/qcsetup

MRCC

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

MRCC

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

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

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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

Computer and Storage List

2024-09-25T06:45:32Z

Ajwt3: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Software
!Purchased
|-
|carpathia
|379
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|G.05
|Andreea, George [César]
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|
|2015
|-
|sandstone
|378
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04.4
|
|
|QChem
source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG03a
|Lijun, [Theo, Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG11
|Charlie [Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|QChem
export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|UG03A
|Reka, [Daniel, Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|[Yi, Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|/scratch2 has 18Tb of scratch
|QChem
source /home/maf63/qchem-public/qcsetup

MRCC

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

MRCC

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

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

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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

Main Page

2024-09-24T08:57:12Z

Ajwt3:

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

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

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

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

{{Special:IframePage}}

=Group Expectations=

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

=Group Meetings=

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

===Michaelmas 2024===

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

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

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

=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]

= [[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 
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
</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/crsid/slack
dpkg -x Slack.deb /scratch/crsid/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/crsid/scratch/slack/usr/lib/slack/slack %U
Icon=/home/crsid/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

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

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

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

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

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

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

- A pretty picture

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

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-09-24T08:56:35Z

Ajwt3:

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

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

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

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

{{Special:IframePage}}

=Group Expectations=

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

=Group Meetings=

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

===Michaelmas 2024===

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

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

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

=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]

= [[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 
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
</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/crsid/slack
dpkg -x Slack.deb /scratch/crsid/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/crsid/scratch/slack/usr/lib/slack/slack %U
Icon=/home/crsid/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

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

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

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

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

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

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

- A pretty picture

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

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Computer and Storage List

2024-09-24T07:25:49Z

Ajwt3: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Software
!Purchased
|-
|carpathia
|379
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|G.05
|Andreea, George [César]
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|
|2015
|-
|sandstone
|378
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04.4
|
|
|QChem
source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG03a
|Lijun, Theo [Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG11
|Haoshan [Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|QChem
export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|UG03A
|Daniel, [Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|[Yi, Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|/scratch2 has 18Tb of scratch
|QChem
source /home/maf63/qchem-public/qcsetup

MRCC

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

MRCC

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

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

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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

Computer and Storage List

2024-09-24T06:43:03Z

Ajwt3: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Software
!Purchased
|-
|carpathia
|379
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|G.05
|Andreea, George [César]
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|
|2015
|-
|sandstone
|378
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04.4
|
|
|QChem
source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG03a
|Lijun, Theo [Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG11
|Haoshan [Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|QChem
export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|UG03A
|Daniel, [Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|[Yi, Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|/scratch2 has 18Tb of scratch
|QChem
source /home/maf63/qchem-public/qcsetup

MRCC

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

MRCC

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

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

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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

Computer and Storage List

2024-08-16T08:38:36Z

Ajwt3: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Software
!Purchased
|-
|carpathia
|379
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|G.05
|Andreea, George [César]
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|
|2015
|-
|sandstone
|378
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04.4
|
|
|QChem
source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG03a
|Lijun, Theo [Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG11
|Haoshan [Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|QChem
export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|UG03A
|Daniel, [Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|QChem
. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|[Yi, Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|/scratch2 has 18Tb of scratch
|QChem
source /home/maf63/qchem-public/qcsetup

MRCC

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

MRCC

source /home/ajwt3/code/mrcc_2023
|-
|[https://www.hpc.cam.ac.uk/high-performance-computing CSD3]
|
|University Tier-2
|32 x 1152
56 x 672
|2x Intel(R) Xeon Gold CPU 6142 @ 2.60GHz
2x Intel(R) Xeon Platinum CPU 8276 @ 2.20GHz
|192 or 384GB
192 or 384GB
|Scientific Linux release 7.9 (Nitrogen) SLURM queuing
|
|
|QChem
source /rds/project/ajwt3/rds-ajwt3-thom1/qchem_public/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/nest-compute-server nest]
|
|CUC3 Group cluster
|40 x 20
|2x Cascade Lake Intel(R) Xeon Gold CPU 6248 @ 2.50GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|
|
|QChem
source /home/maf63/code/qcsetup.sh
|-
|[https://www.ch.cam.ac.uk/computing/rogue-gpu-server rogue]
|
|CUC3 Group cluster
|(8 nVidia V100 + 32 CPU) x 2
|2x Sky Lake Intel(R) Xeon Gold CPU 6130 @ 2.10GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|-
|[https://www.archer2.ac.uk/ archer-2]
|
|National Tier-1 Supercomputer
| 128 x 5848
|2 x AMD EPYC Zen2 (Rome) 64-core CPUs @ 2.2GHz
|256GB and 512GB
|
|}

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

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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

Main Page

2024-06-26T11:14:35Z

Ajwt3:

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

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

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

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

{{Special:IframePage}}

=Group Expectations=

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

=Group Meetings=

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

===Easter 2024===

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

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

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

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

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

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

=Summer 'Interns'=

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

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

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

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

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

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

[[File:AJWT_group_8_21_taken_by_Nathan Pitt_©University_of_Cambridge_1274_M.jpg|1000px|thumb|center|Thom Group photo - taken by Nathan Pitt, ©University of Cambridge, August 2021]]
<div style="text-align: center;">
Front row, left to right: Anna Bui, Brian Zhao, Bang C. Huynh, Arta Safari, Maria-Andreea Filip 
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
</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/crsid/slack
dpkg -x Slack.deb /scratch/crsid/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/crsid/scratch/slack/usr/lib/slack/slack %U
Icon=/home/crsid/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

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

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

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

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

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

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

- A pretty picture

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

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Main Page

2024-06-26T11:13:35Z

Ajwt3: /* Summer 'Interns' */

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

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

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

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

{{Special:IframePage}}

=Group Expectations=

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

=Group Meetings=

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

===Easter 2024===

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

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

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

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

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

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

=Summer 'Interns'=

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 
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
</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/crsid/slack
dpkg -x Slack.deb /scratch/crsid/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/crsid/scratch/slack/usr/lib/slack/slack %U
Icon=/home/crsid/scratch/slack/usr/share/pixmaps/slack.png
Name=Slack
Terminal=false
StartupWMClass=Slack
Comment=Slack Desktop
GenericName=Slack Client for Linux
StartupNotify=true
Categories=GNOME;GTK;Network;InstantMessaging;
MimeType=x-scheme-handler/slack;
# <li value="4"> Log out then in and it should show up in the search bar (Windows button). Right click to pin to favorites (task bar)
Make sure you've replaced "crsid" with your crsid.

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

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

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

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

= [[Group_activities | Group Activities]] =

= To-do list for the Wiki=

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

- A pretty picture

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

- A "How to:" page on using qchem

- A Pretty picture for the $wgLogo

Past Summer Interns

2024-06-26T11:13:30Z

Ajwt3: /* Past Summer Interns */

=Past Summer Interns=

===2023===
{| 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
|}

===2022===
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''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
|}

===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
|-
| Zian Wang || 19th Jul - 17th Sep || NOCI Photochemistry || obsidian
|-
| Brian Zhao || 19th Jul - 17th Sep || Stochastic Coupled Cluster || gritstone
|-
| Nick Lee || 19th Jul - 17th Sep || NOCI Singlet Fission || moonraker
|}

===2020===
{| class="wikitable"
! style="width: 25ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 18ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
|Elizabeth Guest || || Astrochemistry || hypatia
|-
|Hang Xu || || EOM-CC || gritstone
|-
|Jimin Li || || holoHubbard || gritstone
|-
|Constance Kraay || || Embedded NOCI || nemesis
|-
|Toby Antipaas || || SMM || sandstone
|-
|Tiger Zhang || || TM Symmetry || sandstone
|-
|Nicholas Lee || || Singlet Fission || moonraker
|}
===2019===
{| class="wikitable"
! style="width: 25ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 18ex;" | '''Project'''
|-
|Kripa Panchagnula || 12th August - 27th September || Astrochemistry
|-
|Tiger Zhang || 2nd August - 20th September || Frustrated Lewis Pairs
|-
|David Kovacs || 29th July - 27th September (ex 20-26th Aug)|| Solid-state Coupled Cluster
|-
|Nicholas Lee || 29th July - 27th September (ex 4-9th Aug)|| Singlet-Triplet Fission
|}

Computer and Storage List

2024-04-17T16:03:28Z

Ajwt3: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Q-Chem?
!Purchased
|-
|carpathia
|379
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|G.05
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|G.05
|Andreea, George [César]
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|
|2015
|-
|sandstone
|378
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04.4
|
|
|source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|UG03a
|Lijun, Theo [Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|UG11
|Haoshan [Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|64GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|UG11
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|UG03A
|Daniel, [Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|128GB
|Ubuntu 20.04.5
|
|
|. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|Yi [Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|
|source /home/maf63/qchem-public/qcsetup
|2020
|-
|nemesis
|378
|Constance
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 20.04.5
|-
|chiron
|UG03A
|Chiara
|10
|Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz
|96GB
|Ubuntu 20.04
|
|
|
|2021
|-
|topaz
|360
|Lila
|8
|Intel Core i9-11900 2.5GHz 8 Core
|128GB
|Ubuntu 20.04
|NVIDIA GeForce RTX 3080
|
|
|2022
|-
|[https://www.ch.cam.ac.uk/computing/cerebro-compute-server cerebro]
|
|Alavi & Thom Groups
|12 x 20
16 x 8
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|48GB
64GB
|Rocks 6.2 (CentOS 6.9) SLURM queuing
|
|
| source /home/hynl2/code/qchemsetup.bash
|-
|[https://www.hpc.cam.ac.uk/high-performance-computing CSD3]
|
|University Tier-2
|32 x 1152
56 x 672
|2x Intel(R) Xeon Gold CPU 6142 @ 2.60GHz
2x Intel(R) Xeon Platinum CPU 8276 @ 2.20GHz
|192 or 384GB
192 or 384GB
|Scientific Linux release 7.9 (Nitrogen) SLURM queuing
|
|
|source /rds/project/ajwt3/rds-ajwt3-thom1/qchem_public/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/nest-compute-server nest]
|
|CUC3 Group cluster
|40 x 20
|2x Cascade Lake Intel(R) Xeon Gold CPU 6248 @ 2.50GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|
|
|source /home/maf63/code/qcsetup.sh
|-
|[https://www.ch.cam.ac.uk/computing/rogue-gpu-server rogue]
|
|CUC3 Group cluster
|(8 nVidia V100 + 32 CPU) x 2
|2x Sky Lake Intel(R) Xeon Gold CPU 6130 @ 2.10GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|-
|[https://www.archer2.ac.uk/ archer-2]
|
|National Tier-1 Supercomputer
| 128 x 5848
|2 x AMD EPYC Zen2 (Rome) 64-core CPUs @ 2.2GHz
|256GB and 512GB
|
|}

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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

Computer and Storage List

2024-03-15T11:30:40Z

Ajwt3: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Q-Chem?
!Purchased
|-
|carpathia
|379
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|356
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|
|2014
|-
|serenity
|G.05
|Andreea, George [César]
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|
|2015
|-
|sandstone
|378
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04.4
|
|
|source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|360
|Lijun, Theo [Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|378
|Haoshan [Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|32GB
|Ubuntu 20.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|32GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|356
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|362
|Daniel, [Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|Yi [Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|
|source /home/maf63/qchem-public/qcsetup
|2020
|-
|nemesis
|378
|Constance
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 20.04.5
|-
|chiron
|360
|Chiara
|10
|Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz
|96GB
|Ubuntu 20.04
|
|
|
|2021
|-
|topaz
|360
|Lila
|8
|Intel Core i9-11900 2.5GHz 8 Core
|128GB
|Ubuntu 20.04
|NVIDIA GeForce RTX 3080
|
|
|2022
|-
|[https://www.ch.cam.ac.uk/computing/cerebro-compute-server cerebro]
|
|Alavi & Thom Groups
|12 x 20
16 x 8
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|48GB
64GB
|Rocks 6.2 (CentOS 6.9) SLURM queuing
|
|
| source /home/hynl2/code/qchemsetup.bash
|-
|[https://www.hpc.cam.ac.uk/high-performance-computing CSD3]
|
|University Tier-2
|32 x 1152
56 x 672
|2x Intel(R) Xeon Gold CPU 6142 @ 2.60GHz
2x Intel(R) Xeon Platinum CPU 8276 @ 2.20GHz
|192 or 384GB
192 or 384GB
|Scientific Linux release 7.9 (Nitrogen) SLURM queuing
|
|
|source /rds/project/ajwt3/rds-ajwt3-thom1/qchem_public/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/nest-compute-server nest]
|
|CUC3 Group cluster
|40 x 20
|2x Cascade Lake Intel(R) Xeon Gold CPU 6248 @ 2.50GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|
|
|source /home/maf63/code/qcsetup.sh
|-
|[https://www.ch.cam.ac.uk/computing/rogue-gpu-server rogue]
|
|CUC3 Group cluster
|(8 nVidia V100 + 32 CPU) x 2
|2x Sky Lake Intel(R) Xeon Gold CPU 6130 @ 2.10GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|-
|[https://www.archer2.ac.uk/ archer-2]
|
|National Tier-1 Supercomputer
| 128 x 5848
|2 x AMD EPYC Zen2 (Rome) 64-core CPUs @ 2.2GHz
|256GB and 512GB
|
|}

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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

Computer and Storage List

2024-03-15T11:30:07Z

Ajwt3: /* Computer List */

=Computer List=
{| class="wikitable sortable"
!name
!office
!user
!cores
!processor
!RAM
!OS
!Video Ports
!Displays
!Q-Chem?
!Purchased
|-
|carpathia
|379
| Tests
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.5
|
|
|
|2014
|-
|liminal
|379
|Alex
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|For FCIDUMPS: export QC=qclocal; . ~ajwt3/code/qchem/qcsetup.bash NB(22/12/22) non-canonical RHF integral dumps may be incorrect (use a UHF calc and read it in to RHF).
|2017
|-
|hypatia
|356
|NCP [Doug, Tom, Anna]
|6
|Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz
|32GB
|Ubuntu 20.04.6
|
|
|2014
|-
|serenity
|G.05
|Andreea, George [César]
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|
|2015
|-
|sandstone
|378
|Kripa
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04.4
|
|
|source /home/hynl2/code/qcsetup.bash
|2015
|-
|gritstone
|360
|Lijun, Theo [Brian]
|6
|Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
|32GB
|Ubuntu 20.04
|
|
|
|2015
|-
|moonraker
|378
|Haoshan [Moritz, Max, Nick
Benjamin]
|4
|Intel(R) Xeon(R) CPU E3-1270 v5 @ 3.60GHz
|64GB
|Ubuntu 20.04.5
|
|
|export QC_EXT_LIBS=/home/hynl2/code/extlib; source /home/hynl2/.qcsetup
|2016
|-
|obsidian
|378
|Bence [Eline, Lila, Isha, Zian]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|32GB
|Ubuntu 20.04.5
|NVIDIA GeForce GTX 750 Ti
(Compute Capability 5.0)
|
|
|2016
|-
|hylas
|378
|Rowan [Juan, Fabio]
|6
|Intel(R) Core(TM) i7-6800K CPU @ 3.40GHz
|32GB
|Ubuntu 20.04
|
|
|
|2016
|-
|cerberus
|356
|Alex, Bence
|6
|Intel(R) Core(TM) i7-5930K CPU @ 3.50GHz
|32GB
|CentOS 7 [FPGA development board host]
|-
|chucksty
|110
|Jack, [Theo, King, David]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|source /home/maf63/qchem-public/qcsetup
|2017
|-
|chesterian
|362
|Daniel, [Bang, Tarik]
|6
|Intel(R) Core(TM) i7-7800X CPU @ 3.50GHz
|64GB
|Ubuntu 20.04.5
|
|
|. /home/cbh31/code/qcsetup.public/qcselectversion.sh
|2017
|-
|behemoth
|378
|Yi [Brian, Arta]
|8
|Intel(R) Xeon(R) Silver 4208 CPU @ 2.10GHz
|256GB
|Ubuntu 20.04.5
|
|
|source /home/maf63/qchem-public/qcsetup
|2020
|-
|nemesis
|378
|Constance
|6
|Intel(R) Core(TM) i7-4930X CPU @ 3.40GHz
|16GB
|Ubuntu 20.04.5
|-
|chiron
|360
|Chiara
|10
|Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz
|96GB
|Ubuntu 20.04
|
|
|
|2021
|-
|topaz
|360
|Lila
|8
|Intel Core i9-11900 2.5GHz 8 Core
|128GB
|Ubuntu 20.04
|NVIDIA GeForce RTX 3080
|
|
|2022
|-
|[https://www.ch.cam.ac.uk/computing/cerebro-compute-server cerebro]
|
|Alavi & Thom Groups
|12 x 20
16 x 8
|2x Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
2x Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
|48GB
64GB
|Rocks 6.2 (CentOS 6.9) SLURM queuing
|
|
| source /home/hynl2/code/qchemsetup.bash
|-
|[https://www.hpc.cam.ac.uk/high-performance-computing CSD3]
|
|University Tier-2
|32 x 1152
56 x 672
|2x Intel(R) Xeon Gold CPU 6142 @ 2.60GHz
2x Intel(R) Xeon Platinum CPU 8276 @ 2.20GHz
|192 or 384GB
192 or 384GB
|Scientific Linux release 7.9 (Nitrogen) SLURM queuing
|
|
|source /rds/project/ajwt3/rds-ajwt3-thom1/qchem_public/qcsetup.bash
|-
|[https://www.ch.cam.ac.uk/computing/nest-compute-server nest]
|
|CUC3 Group cluster
|40 x 20
|2x Cascade Lake Intel(R) Xeon Gold CPU 6248 @ 2.50GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|
|
|source /home/maf63/code/qcsetup.sh
|-
|[https://www.ch.cam.ac.uk/computing/rogue-gpu-server rogue]
|
|CUC3 Group cluster
|(8 nVidia V100 + 32 CPU) x 2
|2x Sky Lake Intel(R) Xeon Gold CPU 6130 @ 2.10GHz
|192GB
|CentOS Linux release 7.9.2009 (Core) SLURM queuing
|-
|[https://www.archer2.ac.uk/ archer-2]
|
|National Tier-1 Supercomputer
| 128 x 5848
|2 x AMD EPYC Zen2 (Rome) 64-core CPUs @ 2.2GHz
|256GB and 512GB
|
|}

=Notes=

To find out your OS version, run

lsb_release -a

To determine the RAM, run

head -1 /proc/meminfo

To find out core counts, run

cat /proc/cpuinfo

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

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

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

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

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

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

df -h
du -sh * | sort -hr

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

ssh -oPubkeyauthentication=no localhost

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

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

have a few backups taken over the last 24 hours

then, about one backup per day for the previous week

then, about one backup per week for the previous month

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