QCMagic - Revision history

Ajwt3 at 09:24, 13 October 2025

2025-10-13T09:24:50Z

← Older revision		Revision as of 09:24, 13 October 2025
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			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		QCMagic is a set of Python libraries and scripts to manipulate Q-Chem output files. To get access to QCMagic, visit

Btb32: /* Options */

2021-07-22T12:01:21Z

Options

← Older revision		Revision as of 12:01, 22 July 2021
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	runscanSurface.py --read-minima=1,2,6 --stretch=0,1,1,0.01 my_qchem_file.out Tag		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 10 ~~units~~ 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.		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>.		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>.

Cbh31 at 18:15, 3 August 2020

2020-08-03T18:15:39Z

← Older revision		Revision as of 18:15, 3 August 2020
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	==Installation==		==Installation==
	Having cloned QCMagic, ~~assuming~~ it is ~~in your home directory, add~~ the following ~~to your <code>.bashrc</code>~~:		Having cloned QCMagic, install it by executing the following:

	if ~~<nowiki>[[~~ ~~-d $HOME/~~qcmagic~~/bin ]];</nowiki> then~~		cd qcmagic
			./setup.sh
⚫	export PATH=$PATH:$HOME/qcmagic/bin

⚫	export PYTHONPATH=$PYTHONPATH:$HOME/qcmagic
			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		export VMDSIMPLEGRAPHICS=1
	fi		fi</pre>

	The last is to ensure you can open a VMD window (provided X forwarding is enabled, and you have VMD installed locally).		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 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:		If you are using XQuartz and xpra does not seem to work, try the following:

Hynl2 at 15:21, 1 July 2020

2020-07-01T15:21:14Z

← Older revision		Revision as of 15:21, 1 July 2020
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	Having cloned QCMagic, assuming it is in your home directory, add the following to your <code>.bashrc</code>:		Having cloned QCMagic, assuming it is in your home directory, add the following to your <code>.bashrc</code>:

	if [[ -d $HOME/qcmagic/bin ]]; then		if <nowiki>[[ -d $HOME/qcmagic/bin ]];</nowiki> then
	export PATH=$PATH:$HOME/qcmagic/bin		export PATH=$PATH:$HOME/qcmagic/bin
	export PYTHONPATH=$PYTHONPATH:$HOME/qcmagic		export PYTHONPATH=$PYTHONPATH:$HOME/qcmagic

Hynl2 at 15:19, 1 July 2020

2020-07-01T15:19:52Z

← Older revision		Revision as of 15:19, 1 July 2020
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	Having cloned QCMagic, assuming it is in your home directory, add the following to your <code>.bashrc</code>:		Having cloned QCMagic, assuming it is in your home directory, add the following to your <code>.bashrc</code>:

	~~export~~ ~~PATH=$PATH:~~$HOME/qcmagic		if [[ -d $HOME/qcmagic/bin ]]; then
	export ~~PYTHONPATH~~=$~~PYTHONPATH~~:$HOME/qcmagic		export PATH=$PATH:$HOME/qcmagic/bin
			export PYTHONPATH=$PYTHONPATH:$HOME/qcmagic
	export VMDSIMPLEGRAPHICS=1		export VMDSIMPLEGRAPHICS=1
			fi

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

Hynl2 at 15:13, 1 July 2020

2020-07-01T15:13:07Z

← Older revision		Revision as of 15:13, 1 July 2020
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	Example command:		Example command:

	~~python makePlots~~.py my_qchem_file.inp -T tag		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.		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.
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	A general command for <code>scanSurface</code> has the following form:		A general command for <code>scanSurface</code> has the following form:

	~~scanSurface~~.py [options] qchem_file [qchem_file_2 ...] Tag		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).		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).
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	An example command is:		An example command is:

	~~scanSurface~~.py --stretch=0,1,1,0.01 my_qchem_file.out Tag		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>.		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>.
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	If multiple options are used, such as		If multiple options are used, such as

	~~scanSurface~~.py --stretch=0,1,1,0.01 --stretch=0,2,1,0.01 my_qchem_file.out Tag		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.		the scan will zigzag to cover the whole surface.
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	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,		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,

	~~scanSurface~~.py --read-minima=1,2,6 --stretch=0,1,1,0.01 my_qchem_file.out Tag		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 10 units 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.		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 10 units 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.
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	An example of a command using --tie:		An example of a command using --tie:

	~~scanSurface~~.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		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:		This will:
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	A general command for <code>qcSDExtract</code> has the following form:		A general command for <code>qcSDExtract</code> has the following form:

	~~qcSDExtract~~.py [options] SDfile Tag		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>:		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>:
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	An example command is:		An example command is:

	~~qcSDExtract~~.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		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:		which:
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	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		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

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

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

	~~varyXCB~~.py [options] file Tag		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).		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).
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	An example command for exchange-correlation following mode is:		An example command for exchange-correlation following mode is:

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

	which:		which:
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	Another example command for basis projection mode is:		Another example command for basis projection mode is:

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

Hynl2 at 11:18, 19 September 2019

2019-09-19T11:18:22Z

← Older revision		Revision as of 11:18, 19 September 2019
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	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.		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)''==		==Useful Classes ''(for developers only)''==

Hynl2 at 09:17, 16 September 2019

2019-09-16T09:17:25Z

← Older revision		Revision as of 09:17, 16 September 2019
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	If you are using XQuartz and xpra does not seem to work, try the following:		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>~~		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.		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		Source: https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmdl/28503.html

Hynl2 at 09:16, 16 September 2019

2019-09-16T09:16:44Z

← Older revision		Revision as of 09:16, 16 September 2019
Line 27:		Line 27:

	If you are using XQuartz and xpra does not seem to work, try the following:		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:		On your local terminal, run this in the command line: <code>defaults write org.macosforge.xquartz.X11 enable_iglx -bool true</code>
	<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.		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		Source: https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmdl/28503.html

Hynl2 at 09:16, 16 September 2019

2019-09-16T09:16:16Z

← Older revision		Revision as of 09:16, 16 September 2019
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	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 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==		==Usage==