Thom Group Wiki - User contributions [en]

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2021-08-19T15:43:49Z

Zw357: /* Summer 2021 */

''
# _________ # ___ ___ # ______ # ___ __ __ # # _______ # ______ # ______ # __ __ # ______ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ # #/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ # #\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ # # \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ # # \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \# # \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/# # \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # # # # # # #
''

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 Meetings=

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

===Summer 2021===

{| class="wikitable"
! style="width: 20ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|12th July 2021 || INFORMAL ||
|-
|20th July 2021 || INFORMAL ||
|-
|27th July 2021 || - ||
|-
|3rd August 2021 || Cesar & Tarik || Chelsea Buns
|-
|9th August 2021 || Constance || Brian
|-
|16th August 2021 || INFORMAL ||
|-
|23rd August 2021|| Benjamin || Andreea
|-
|30th August 2021|| INFORMAL ||
|-
|6th September 2021 || Arta & Anna ||
|-
|13th September 2021 || Brian & Zian||
|}

=Summer 'Interns'=
Past Summer Interns [[Past Summer Interns|here]].
==2021==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
| Anna Bui || 19th Jul - 17th Sep || NOCI Carbon Capture || hypatia
|-
| 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
|}

= [[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].

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

[[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_List | Computer List]] =
- Group computers available.

= [[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]]
# 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.

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

= 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]]

= [[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=

- 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

QChem

2021-07-20T09:00:47Z

Zw357: /* Troubleshooting SCF Metadynamics Calculations */

Q-Chem is a commercial quantum chemistry package available for use in our group.

= Fragment Guesses with multiple bases =
To uses basis set projection and fragment guesses you have to run the smaller basis set calculation with fragments first, and then read this into a second calculation which does the projection
<code>
$molecule
0 1
--
0 1
H 0.000000 -0.115747 1.133769
H 0.000000 1.109931 -0.113383
O 0.000000 0.005817 -0.020386
--
0 1
He 10000 0 0
$end
$rem
JOBTYPE sp
EXCHANGE b3lyp
BASIS cc-pVDZ
scf_guess fragmo
CORRELATION none
SYMMETRY false
SYM_IGNORE true
$end
@@@
$molecule
read
$end
$rem
scf_guess read
JOBTYPE sp
EXCHANGE b3lyp
BASIS cc-pVTZ
BASIS2 cc-pVDZ
CORRELATION none
MAX_SCF_CYCLES 600
SYMMETRY false
SYM_IGNORE true
basisprojtype ovprojection
$end
</code>

==INTDUMP / FCIDUMP ==

To create files in the FCIDUMP format (used e.g. by Hande) create a QChem input file:

<pre>
$molecule
0 1
H 0 0 0
H 1 0 0
$end

$rem
correlation idump
exchange hf
basis sto-3G
use_abelian_subgroup true
scf_guess_print 9999
$end
</pre>

and use the version of QChem currently (2020-02-20) available from:
<pre>
[you@liminal] $ export QC=public_o
[you@liminal] $ source ~ajwt3/code/qchem/qcsetup.bash
[you@liminal] $ qchem your-input-file.in
</pre>

This should produce a file called <code>INTDUMP</code>
<pre>
&FCI NORB= 2,NELEC= 2,MS2= 0
ORBSYM=1,6,
ISYM=1 UHF=.FALSE.
&END
0.62640249948715 1 1 1 1
0.19679058349422 1 2 1 2
0.6217067630807 2 2 1 1
0.19679058349422 2 1 1 2
0.19679058349422 2 1 2 1
0.65307074688898 2 2 2 2
-1.1108441795661 1 1 0 0
-0.58912100326925 2 2 0 0
-0.39980670964291 1 0 0 0
0.37823811728909 2 0 0 0
0.52917721026434 0 0 0 0
</pre>

==Troubleshooting SCF Metadynamics Calculations==

If a calculation repeatedly converges on the same solution, adjusting one or more of these keywords can help to find different solutions.

* Increasing <code>SCF_MINFIND_INITNORM</code>, <code>SCF_MINFIND_INITLAMBDA</code> and <code>SCF_MINFIND_INCREASEFACTOR</code> can help get out of the minimum. However, setting <code>SCF_MINFIND_INITLAMBDA</code> too high can result in SCF solutions with very high energies, and <code>SCF_MINFIND_INITNORM</code> can get in the way of convergence, particularly when reading in a solution (in that case, set it to zero).
* Increasing <code>SCF_MINFIND_RESTARTSTEPS</code> helps if a solution is close to another minima but does not converge before the calculation restarts with new orbitals
* Changing <code>SCF_MINFIND_RANDOMMIXING</code> is generally helpful. +/- 15708 and 31416 are sensible values to try, and 07854 (which corresponds to halfway between swapping the orbitals) can also help.

If the resulting solutions are too high in energy,
* decreasing <code>SCF_MINFIND_INITNORM</code>
* decreasing <code>SCF_MINFIND_INITLAMBDA</code>
* decreasing <code>SCF_MINFIND_MIXENERGY</code> (even to 00005)
* adjusting <code>MOM_START</code>
* and using <code>SCF_MINFIND_MIXMETHOD</code> 1 or 2
can help to find lower-energy excited states.

Main Page

2021-07-13T10:35:56Z

Zw357: /* 2021 */

''
# _________ # ___ ___ # ______ # ___ __ __ # # _______ # ______ # ______ # __ __ # ______ #
#/________/\ #/__/\ /__/\ #/_____/\ #/__//_//_/\ # #/______/\ #/_____/\ #/_____/\ #/_/\/_/\ #/_____/\ #
#\__.::.__\/ #\::\ \\ \ \ #\:::_ \ \ #\::\| \| \ \ # #\::::__\/__ #\:::_ \ \ #\:::_ \ \ #\:\ \:\ \ #\:::_ \ \ #
# \::\ \ # \::\/_\ .\ \ # \:\ \ \ \ # \:. \ \ # # \:\ /____/\ # \:(_) ) )_ # \:\ \ \ \ # \:\ \:\ \ # \:(_) \ \ #
# \::\ \ # \:: ___::\ \ # \:\ \ \ \ # \:.\-/\ \ \ # # \:\\_ _\/ # \: __ `\ \ # \:\ \ \ \ # \:\ \:\ \ # \: ___\/ #
# \::\ \ # \: \ \\::\ \# \:\_\ \ \ # \. \ \ \ \# # \:\_\ \ \ # \ \ `\ \ \ # \:\_\ \ \ # \:\_\:\ \ # \ \ \ #
# \__\/ # \__\/ \::\/# \_____\/ # \__\/ \__\/# # \_____\/ # \_\/ \_\/ # \_____\/ # \_____\/ # \_\/ #
# # # # # # # # # # #
''

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 Meetings=

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

===Summer 2021===

{| class="wikitable"
! style="width: 18ex;" |'''Date''' || style="width: 18ex;" | '''Talk''' || style="width: 18ex;" | '''Cake'''
|-
|12th July 2021 || INFORMAL ||
|-
|20th July 2021 || INFORMAL ||
|-
|27th July 2021 || Cesar & Tarik ||
|-
|3rd August 2021 || Constance ||
|-
|9th August 2021 || INFORMAL ||
|-
|16th August 2021 || INFORMAL ||
|-
|23rd August 2021|| Benjamin ||
|-
|30th August 2021|| INFORMAL ||
|}

=Summer 'Interns'=
Past Summer Interns [[Past Summer Interns|here]].
==2021==
{| class="wikitable"
! style="width: 18ex;" |'''Name''' || style="width: 18ex;" | '''Dates''' || style="width: 25ex;" | '''Project'''|| style="width: 18ex;" | '''Machine'''
|-
| Anna Bui || 19th Jul - 17th Sep || NOCI Carbon Capture || -
|-
| Zian Wang || 19th Jul - 17th Sep || NOCI Photochemistry || -
|-
|| Brian Zhao || 19th Jul - 17th Sep || Stochastic Coupled Cluster || -
|}

= [[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].

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

[[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_List | Computer List]] =
- Group computers available.

= [[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]]
# 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.

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

= 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]]

= [[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=

- 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