<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);">
<span style="color:#d62828;"> _________ ___ ___ ______ ___ __ __ </span>
<span style="color:#f77f00;">/________/\ /__/\ /__/\ /_____/\ /__//_//_/\ </span>
<span style="color:#fcbf49;">\__.::.__\/ \::\ \\ \ \ \:::_ \ \ \::\| \| \ \ </span>
<span style="color:#2a9d8f;"> \::\ \ \::\/_\ .\ \ \:\ \ \ \ \:. \ \ </span>
<span style="color:#457b9d;"> \::\ \ \:: ___::\ \ \:\ \ \ \ \:.\-/\ \ \ </span>
<span style="color:#6a4c93;"> \::\ \ \: \ \\::\ \ \:\_\ \ \ \. \ \ \ \ </span>
<span style="color:#8338ec;"> \__\/ \__\/ \::\/ \_____\/ \__\/ \__\/ </span>
</pre>
</div>

<div style="overflow-x:auto; max-width:100%;">
<pre style="display:inline-block; text-align:left; white-space:pre; margin:0; padding:1em 1.5em; border:2px solid #7c3aed; border-radius:12px; background:#0f172a; box-shadow:0 0 12px rgba(124,58,237,0.45);">
<span style="color:#ff0000;"> _______ ______ ______ __ __ ______ </span>
<span style="color:#ff7f00;">/______/\ /_____/\ /_____/\ /_/\/_/\ /_____/\ </span>
<span style="color:#ffff00;">\::::__\/__ \:::_ \ \ \:::_ \ \ \:\ \:\ \ \:::_ \ \ </span>
<span style="color:#00cc00;"> \:\ /____/\ \:(_) ) )_ \:\ \ \ \ \:\ \:\ \ \:(_) \ \ </span>
<span style="color:#0099ff;"> \:\\_ _\/ \: __ `\ \ \:\ \ \ \ \:\ \:\ \ \: ___\/ </span>
<span style="color:#4b0082;"> \:\_\ \ \ \ \ `\ \ \ \:\_\ \ \ \:\_\:\ \ \ \ \ </span>
<span style="color:#8b00ff;"> \_____\/ \_\/ \_\/ \_____\/ \_____\/ \_\/ </span>
</pre>
</div>

</div>

<div style="width:100%; box-sizing:border-box;">

<div style="
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border-radius:10px;
box-shadow:0 3px 12px rgba(15,23,42,0.08);
">

<div style="margin:-0.55em 0 -0.15em;">
== About ==
</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. 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.

</div>

<div style="display:flex; flex-wrap:wrap; gap:1em; align-items:stretch; margin-bottom:0.8em;">

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border-radius:9px;
">

<div style="margin:-0.55em 0 -0.1em;">
=== [[Group_List | Group List and Photos]] ===
</div>

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.

</div>

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border-radius:9px;
">

<div style="margin:-0.55em 0 -0.1em;">
=== [[Summer_Interns | Summer Interns]] ===
</div>

Email [theory-sec@ch.cam.ac.uk](mailto: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.

</div>

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border-radius:9px;
">

<div style="margin:-0.55em 0 -0.1em;">
=== [https://www.overleaf.com/read/yddfjrvpjckj Group Expectations] ===
</div>

The Group Expectations document is available on [https://www.overleaf.com/read/yddfjrvpjckj Overleaf] as above. The rules outlined must be obeyed at all costs, if not, the consequences are dire.

</div>

</div>

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<div style="margin:-0.55em 0 -0.1em;">
=== Roles ===
</div>

Currently allocated Group Roles are
{| class="wikitable"
! style="width: 20ex;" | Role
! style="width: 18ex;" | Name
! style="width: 18ex;" | From
|-
| Webmaster || Lila ||
|-
| Social Media Master || Lila ||
|-
| Quantum Computing Discussion Group Lead || Lila ||
|-
| Group Meeting Convener || Bence ||
|-
| Group IT Rep || Bence ||
|-
| Group Social Sec || Tamara ||
|}

</div>

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border-radius:9px;
">

<div style="margin:-0.55em 0 -0.15em;">
== Events ==
</div>

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

</div>

<div style="
width:100%;
box-sizing:border-box;
margin-bottom:0.8em;
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<div style="margin:-0.55em 0 -0.1em;">
=== [https://calendar.google.com/calendar/render?mode=day&date=20160601T153539#main_7%7Cday-1+23745+23745+23745 Group Calendar] ===
</div>

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.

<div style="width:100%; max-width:100%; overflow-x:auto;">
{{Special:IframePage}}
</div>

</div>

<div style="display:flex; flex-wrap:wrap; gap:1em; align-items:stretch;">

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flex:1 1 460px;
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padding:0.65em 1em 0.8em;
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border-radius:9px;
">

<div style="margin:-0.55em 0 -0.1em;">
=== [[Past Group Meetings|Group Meetings]] ===
</div>

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).

</div>

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border-radius:9px;
">

<div style="margin:-0.55em 0 -0.1em;">
=== Journal Club ===
</div>

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]].

</div>

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border-radius:9px;
">

<div style="margin:-0.55em 0 -0.1em;">
=== Seminars ===
</div>

* [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]

</div>

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border-radius:9px;
">

<div style="margin:-0.55em 0 -0.1em;">
=== QCQCDG ===
</div>

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].

</div>

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<div style="margin:-0.55em 0 -0.1em;">
=== Quantum Computing Brainstorm ===
</div>

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]].

</div>

</div>

<div style="
margin:0.8em 0;
padding:0.75em 1em 1em;
overflow-x:auto;
background:#f1faf8;
border:1px solid #a9d8ce;
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border-radius:9px;
">

<div style="margin:-0.55em 0 -0.1em;">
=== Forthcoming Conferences ===
</div>

{| 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 || Dylan, Alex
|-
| 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||
|}

</div>

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padding:0.75em 1em 1em;
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border-radius:9px;
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<div style="margin:-0.55em 0 -0.1em;">
=== Forthcoming Workshops and Schools ===
</div>

{| 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||
|}

</div>

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<div style="margin:-0.55em 0 -0.15em;">
== Research and Projects ==
</div>

</div>

<div style="display:flex; flex-wrap:wrap; gap:1em; align-items:stretch;">

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<div style="margin:-0.55em 0 -0.1em;">
=== [[Templated_Projects | Templated Projects ]] ===
</div>

Projects detailed as according to a template.

</div>

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<div style="margin:-0.55em 0 -0.1em;">
=== [[Project_Ideas | Project Ideas and Questions]] ===
</div>

Based on recent talks and conferences. Contains both project ideas and more general questions that would be nice to answer.

</div>

<div style="
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<div style="margin:-0.55em 0 -0.1em;">
=== [[Project_Template | Project Template ]] ===
</div>

The aforementioned template.

</div>

<div style="
flex:1 1 100%;
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border-radius:9px;
">

<div style="margin:-0.55em 0 -0.1em;">
=== Dissertations (Completed Projects) ===
</div>

Please upload any missing documents to these folders such that these contain a complete history of every project or work completed in the group.

* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Dissertations/Forms/AllItems.aspx Dissertations] - Part III Reports, MPhil Theses, First Year Reports, PhD Theses
* [https://universityofcambridgecloud.sharepoint.com/sites/CHEM_ThomGroup/Group%20Meetings/Forms/AllItems.aspx Group Meeting Presentations]
* [https://www.overleaf.com/read/ffdvzskxvnbm#2e9673 Template for L<sup>A</sup>T<sub>E</sub>X poster]

</div>

</div>

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padding:0.45em 1.1em 0.7em;
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<div style="margin:-0.55em 0 -0.15em;">
== Computers ==
</div>

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

</div>

<div style="display:flex; flex-wrap:wrap; gap:1em; align-items:stretch;">

<div style="
flex:1 1 300px;
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padding:0.65em 1em 0.8em;
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border-radius:9px;
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<div style="margin:-0.55em 0 -0.1em;">
=== [[Computer_and_Storage_List | Computing Resources]] ===
</div>

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

</div>

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<div style="margin:-0.55em 0 -0.1em;">
=== [[Introduction | Introduction to basic shell commands]] ===
</div>

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.

</div>

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border-radius:9px;
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<div style="margin:-0.55em 0 -0.1em;">
=== [[Connecting_Machines | How to connect to department machines]] ===
</div>

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

</div>

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border-radius:9px;
">

<div style="margin:-0.55em 0 -0.1em;">
=== [[Transferring_files_between_computers | Transferring files between computers ]] ===
</div>

You might want to do this sometimes.

</div>

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border-radius:9px;
">

<div style="margin:-0.55em 0 -0.1em;">
=== [[Installing_Slack | How to install Slack on department machines ]] ===
</div>

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

</div>

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border-radius:9px;
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<div style="margin:-0.55em 0 -0.1em;">
=== Software Tutorials ===
</div>

# [[QChem]]

# [[SimpleDMC]]

# [[MRCC]]

# [[GAMESS]]

# [[RevQCMagic]]

</div>

</div>

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<div style="margin:-0.55em 0 -0.15em;">
== Uncategorisable ==
</div>

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.

</div>

<div style="display:flex; flex-wrap:wrap; gap:1em; align-items:stretch;">

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flex:1 1 470px;
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padding:0.65em 1em 0.8em;
background:#fffbed;
border:1px solid #ead99a;
border-top:5px solid #fcbf49;
border-radius:9px;
">

<div style="margin:-0.55em 0 -0.1em;">
=== Useful Information ===
</div>

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

# [[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]

# [https://roombookingsystem.cam.ac.uk/Account/Login?ReturnUrl=%2F Link to book meeting pods].

</div>

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border-radius:9px;
">

<div style="margin:-0.55em 0 -0.1em;">
=== [[Archiving_data | Archiving data for the university repository]] ===
</div>

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

</div>

<div style="
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border-radius:9px;
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<div style="margin:-0.55em 0 -0.1em;">
=== [[Website_to_do | To-do list for the Thom Group Website]] ===
</div>

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

</div>

</div>

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border-radius:9px;
">

<div style="margin:-0.55em 0 -0.15em;">
== Archive ==
</div>

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

</div>

<div style="display:flex; flex-wrap:wrap; gap:0.7em; margin-bottom:1.5em;">

<div style="
flex:1 1 220px;
box-sizing:border-box;
padding:0.45em 0.8em 0.6em;
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border-radius:8px;
text-align:center;
">

<div style="margin:-0.55em 0 -0.1em;">
=== [[Group_activities | Group Activities]] ===
</div>

</div>

<div style="
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<div style="margin:-0.55em 0 -0.1em;">
=== [[Website_to_do | Website to do]] ===
</div>

</div>

<div style="
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<div style="margin:-0.55em 0 -0.1em;">
=== [[Darwin | Darwin]] ===
</div>

</div>

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<div style="margin:-0.55em 0 -0.1em;">
=== [[Queuing | Queuing]] ===
</div>

</div>

<div style="
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background:#f3f7fa;
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Main Page

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QCMagic

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Drc71: Drc71 moved page QCMagic to QCMagic (Legacy)

#REDIRECT [[QCMagic (Legacy)]]

QCMagic (Legacy)

2026-07-23T11:57:12Z

Drc71: Drc71 moved page QCMagic to QCMagic (Legacy)

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 BH<sub>3</sub> 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.

2026-07-23T11:52:50Z

Drc71: 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).

Main Page

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Templated Projects

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= Various Projects =

== 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

Templated Projects

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2026-03-25T15:36:51Z

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