CamCASP/Notes/7 - Revision history

import>Am592: /* Searching using batch_search.pl */

2009-03-17T19:26:43Z

Searching using batch_search.pl

← Older revision		Revision as of 19:26, 17 March 2009
Line 235:		Line 235:
	File benzene2_27/OUT/benzene2_27.out not found		File benzene2_27/OUT/benzene2_27.out not found
	File benzene2_28/OUT/benzene2_28.out not found		File benzene2_28/OUT/benzene2_28.out not found
	INDEX Rx Ry Rz alpha Nx Ny Nz elst ind2C ~~disp2C exch exind2C exdisp2C~~		INDEX Rx Ry Rz alpha Nx Ny Nz elst ind2C
			disp2C exch exind2C exdisp2C
	0 1 2 3 4 5 6 7 8 9 10 11 12 13
	1 ~~14.589~~ ~~0.000~~ ~~0.000~~ ~~180.000~~ ~~1.000~~ ~~0.000~~ ~~0.000~~ ~~0.852~~ ~~-----~~ ~~-----~~ ~~0.536~~ ~~-----~~ ~~-----~~		0 1 2 3 4 5 6 7 8 9
			10 11 12 13
⚫	2 13.463 0.000 0.000 180.000 1.000 0.000 0.000 0.953 ~~----- ----- 4.269 ----- -----~~
	3 -9.~~173~~ 0.000 5.~~296~~ 180.000 -0.~~707~~ 0.000 -0.~~707~~ ~~-1.606~~ ~~----- ----- 8~~.~~368 -----~~ ~~-----~~		1 14.589 0.000 0.000 180.000 1.000 0.000 0.000 0.852
			----- ----- 0.536 ----- -----
		⚫	2 13.463 0.000 0.000 180.000 1.000 0.000 0.000 0.953
			----- ----- 4.269 ----- -----
			3 -9.173 0.000 5.296 180.000 -0.707 0.000 -0.707 -1.606
			----- ----- 8.368 ----- -----
	...		...
	...		...
	40 -6.659 -4.450 8.280 141.980 0.516 0.712 -0.476 ----- ~~----- ----- ----- ----- -----~~		40 -6.659 -4.450 8.280 141.980 0.516 0.712 -0.476 -----
			----- ----- ----- ----- -----
	</pre>		</pre>
	NOTES:		NOTES:
Line 269:		Line 275:
	END-FILE		END-FILE
	</pre>		</pre>
	which is just the format used by the '''ENERGY-SCAN''' module, so this output can be read using that module. But you will need to fill up the molecule names and units used.		which is just the format used by the '''ENERGY-SCAN''' module, so this output can be read using that module. But you will need to fill up the molecule names and units used.

	==ORIENT jobs using batch_ORIENT.pl==		==ORIENT jobs using batch_ORIENT.pl==

import>Am592: /* ORIENT jobs using batch_ORIENT.pl */

2009-03-17T18:33:05Z

ORIENT jobs using batch_ORIENT.pl

← Older revision		Revision as of 18:33, 17 March 2009
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	==ORIENT jobs using batch_ORIENT.pl==		==ORIENT jobs using batch_ORIENT.pl==
			<pre>
			$ batch_ORIENT.pl

			Usage:
			batch_ORIENT.pl [-j] job [-geom name] [-ornt name] [-pot name]
			[ -iter iterations ] [ -rank rank ] [ -damp beta ] [-d digits]
			</pre>

import>Am592 at 18:29, 17 March 2009

2009-03-17T18:29:45Z

← Older revision		Revision as of 18:29, 17 March 2009
Line 211:		Line 211:

	You will need to search through all these directories for the results. This can be done using the '''batch_search.pl''' script.		You will need to search through all these directories for the results. This can be done using the '''batch_search.pl''' script.

			==Searching using batch_search.pl==
			Once you have the result of batch_SAPT.pl ready you will want to search for energies. This is most conveniently done using the batch_search.pl script that is a wrapper for the search.pl script. It accepts the flags:
			<pre>
			$ batch_search.pl

			Usage:
			batch_search.pl [-j] job [-geom name] [-keys file] [-d digits]
			[-camcasp]

			If the keys file is not present, it is created with the default SAPT(DFT) key.

			To get the energies in the order used by the ENERGY-SCAN module in CamCASP use
			key 'saptdft-camcasp' and six digits with '-d 6'.
			</pre>
			The ''-camcasp'' option writes out the results in almost the same format used by module '''ENERGY-SCAN''', so it can be then read back into CamCASP using the '''ENERGY-SCAN''' module.

			So, to search for SAPT(DFT) interaction energies calculated in benzene dimer example above we would use a keys file containing the line:
			<pre>
			$ more keys
			saptdft-camcasp
			$ batch_search.pl benzene2 -geom random-grid_points.dat -keys keys -d 3
			File benzene2_27/OUT/benzene2_27.out not found
			File benzene2_28/OUT/benzene2_28.out not found
			INDEX Rx Ry Rz alpha Nx Ny Nz elst ind2C disp2C exch exind2C exdisp2C
			0 1 2 3 4 5 6 7 8 9 10 11 12 13
			1 14.589 0.000 0.000 180.000 1.000 0.000 0.000 0.852 ----- ----- 0.536 ----- -----
			2 13.463 0.000 0.000 180.000 1.000 0.000 0.000 0.953 ----- ----- 4.269 ----- -----
			3 -9.173 0.000 5.296 180.000 -0.707 0.000 -0.707 -1.606 ----- ----- 8.368 ----- -----
			...
			...
			40 -6.659 -4.450 8.280 141.980 0.516 0.712 -0.476 ----- ----- ----- ----- ----- -----
			</pre>
			NOTES:
			* If a jobs failed the script will say that it cannot file a file.
			* Energies not calculated in the scan are written as '-----'

			Now if you had used the ''-camcasp'' flag you would get the following:
			<pre>
			$ batch_search.pl benzene2 -geom random-grid_points.dat -keys keys -d 3 -camcasp
			File benzene2_27/OUT/benzene2_27.out not found
			File benzene2_28/OUT/benzene2_28.out not found
			TITLE
			MOL-A
			MOL-B
			POINTS 40
			Energy-units kJ/mol
			LENGTH-UNITS
			ANGLE-UNITS
			LABELS INDEX Rx Ry Rz alpha Nx Ny Nz E(1)elst E(2)ind ...
			1 1.459E+01 0.000E+00 0.000E+00 1.800E+02 1.000E+00 0.000E+00 0.000E+00 8.521E-01 0.0E+00 ...
			2 1.346E+01 0.000E+00 0.000E+00 1.800E+02 1.000E+00 0.000E+00 0.000E+00 9.528E-01 0.0E+00 ...
			...
			...
			40 -6.659E+00 -4.450E+00 8.280E+00 1.420E+02 5.156E-01 7.124E-01 -4.760E-01 0.0E+00 0.0E+00 ...
			END
			END-FILE
			</pre>
			which is just the format used by the '''ENERGY-SCAN''' module, so this output can be read using that module. But you will need to fill up the molecule names and units used.

			==ORIENT jobs using batch_ORIENT.pl==

import>Am592: /* Obtaining the geometry file */

2009-03-17T18:14:55Z

Obtaining the geometry file

← Older revision		Revision as of 18:14, 17 March 2009
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	LENGTH-UNITS BOHR		LENGTH-UNITS BOHR
	ANGLE-UNITS DEGREES		ANGLE-UNITS DEGREES
	LABELS INDEX Rx Ry Rz alpha Nx Ny Nz E(1)elst E(2)ind ~~E(2)disp E(1)exch E(2)exind E(2)exdisp TotOverlap Elst-Asymp Ind2-Asymp Disp-Asymp Delta~~		LABELS INDEX Rx Ry Rz alpha Nx Ny Nz E(1)elst E(2)ind ...
	1 0.145892E+02 0.000000E+00 0.000000E+00 0.180000E+03 0.100000E+01 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.~~000000E+00 0~~.~~000000E+00 0~~.~~000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00~~		1 0.145892E+02 0.000000E+00 0.000000E+00 0.180000E+03 0.100000E+01 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 ...
	2 0.134629E+02 0.000000E+00 0.000000E+00 0.180000E+03 0.100000E+01 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.~~000000E+00 0~~.~~000000E+00 0~~.~~000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00~~		2 0.134629E+02 0.000000E+00 0.000000E+00 0.180000E+03 0.100000E+01 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 ...
	...		...
	...		...
	40 -0.665925E+01 -0.444957E+01 0.827950E+01 0.141980E+03 0.515613E+00 0.712421E+00 -0.476025E+00 0.000000E+00 0.000000E+00 0.~~000000E+00 0~~.~~000000E+00 0~~.~~000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00~~		40 -0.665925E+01 -0.444957E+01 0.827950E+01 0.141980E+03 0.515613E+00 0.712421E+00 -0.476025E+00 0.000000E+00 0.000000E+00 ...
	END		END
	END-FILE		END-FILE
	</pre>		</pre>
			Yes, it has many columns and all we need are the first few that contain the geometry.
	* Now we need to make small changed to '''random.dat''' in order to get it in a form suitable for the batch scripts. Do the following. Copy it to '''random.geom''' (could be any name really, but let's use this). Now edit random.geom so that it looks like:		* Now we need to make small changed to '''random.dat''' in order to get it in a form suitable for the batch scripts. Do the following. Copy it to '''random.geom''' (could be any name really, but let's use this). Now edit random.geom so that it looks like:
	<pre>		<pre>

import>Am592: /* Obtaining the geometry file */

2009-03-17T18:13:25Z

Obtaining the geometry file

@@ Line 62: / Line 62: @@
 FINISH
 </pre>
-The new bits are the '''ENERGY-SCAN''' commands and those indicated by '***'. The '''Skip MOs''' command is needed to get CamCASP to go on without reading in the molecular orbitals. The '''ENERGY-SCAN''' module probes the first molecule (benzene1) with the second (benzene2). The order is important. But all we need are the geometries, so we '''Scan Nothing'''. The results of the energy scan will be in file '''random.dat'''.
+The new bits are the '''ENERGY-SCAN''' commands and those indicated by '***'. The '''Skip MOs''' command is needed to get CamCASP to go on without reading in the molecular orbitals. The '''ENERGY-SCAN''' module probes the first molecule (benzene1) with the second (benzene2). The order is important. But all we need are the geometries, so we '''Scan Nothing'''. The results of the energy scan will be in file '''random.dat'''. This file looks like:
 ==SAPT(DFT) jobs with batch_SAPT.pl==

import>Am592: /* Obtaining the geometry file */

2009-03-17T18:06:19Z

Obtaining the geometry file

@@ Line 5: / Line 5: @@
 ==Obtaining the geometry file==
 The batch scripts all use a geometry file that contains the translation and rotation parameters needed to construct the dimer. This file is constructed by CamCASP as follows.
 ==SAPT(DFT) jobs with batch_SAPT.pl==

import>Am592 at 17:58, 17 March 2009

2009-03-17T17:58:49Z

← Older revision		Revision as of 17:58, 17 March 2009
Line 3:		Line 3:
	The ''${CAMCASP}/bin/'' folder contains a few batch scripts for running sets of jobs at various dimer geometries.		The ''${CAMCASP}/bin/'' folder contains a few batch scripts for running sets of jobs at various dimer geometries.

			==Obtaining the geometry file==
			The batch scripts all use a geometry file that contains the translation and rotation parameters needed to construct the dimer. This file is constructed by CamCASP as follows.


	==SAPT(DFT) jobs with batch_SAPT.pl==		==SAPT(DFT) jobs with batch_SAPT.pl==
	You cannot always perform an energy scan using the '''ENERGY-SCAN''' module in CamCASP as this module requires you to use the MC type of basis. If you need to use the MC+, DC or DC+ types of bases, then you will need to use the '''batch_SAPT.pl''' script. What this script does is to use a template CLUSTER command file and a file containing the translation and rotation parameters that define the dimer in order to run a batch of SAPT(DFT) (and also SAPT) calculations in an automatic way.		You cannot always perform an energy scan using the '''ENERGY-SCAN''' module in CamCASP as this module requires you to use the MC type of basis. If you need to use the MC+, DC or DC+ types of bases, then you will need to use the '''batch_SAPT.pl''' script. What this script does is to use a template CLUSTER command file and a file containing the translation and rotation parameters that define the dimer in order to run a batch of SAPT(DFT) (and also SAPT) calculations in an automatic way.

import>Am592: /* The template CLUSTER file */

2009-03-17T17:57:30Z

The template CLUSTER file

← Older revision		Revision as of 17:57, 17 March 2009
Line 91:		Line 91:
	</pre>		</pre>
	and will be replaced by the actual job name by the batch_SAPT.pl script. The actual job name will be the job name given to this script and an additional '_###' numerical index taken from the geometry file. This helps to keep the runs distinct from each other.		and will be replaced by the actual job name by the batch_SAPT.pl script. The actual job name will be the job name given to this script and an additional '_###' numerical index taken from the geometry file. This helps to keep the runs distinct from each other.

			So you can now run the job using
			<pre>
			batch_SAPT.pl benzene2 -clt benzene2.clt -geom random.geom -b mc+ -ipa 0.3397 -ipb 0.3397 -q intel.q -M 3000
			</pre>
			where my geometries are in file ''random.geom''.

			As jobs finish, they are copied to your main directory (from where the command was issued) to sub-folders ''benzene2_001'', ''benzene2_002'', etc. The actual indices used will depend on the geometry indices in the geometry file. This is handy as, should you split the geometry file into pieces to run on multiple nodes of your machine, the file names used will not clash.

			You will need to search through all these directories for the results. This can be done using the '''batch_search.pl''' script.

import>Am592: /* SAPT(DFT) jobs with batch_SAPT.pl */

2009-03-17T17:51:28Z

SAPT(DFT) jobs with batch_SAPT.pl

@@ Line 15: / Line 15: @@
 You need to supply:
 * The job name. For example, this might be ''benzene2''.
-* The name of the geometry file. More on this below. The default name will be ''jobname.geom'', so if this file is called ''benzene2.geom'', then there is no need to specify it explicitly.
+* The name of the geometry file. The default name will be ''jobname.geom'', so if this file is called ''benzene2.geom'', then there is no need to specify it explicitly.
 * The name of the CLUSTER command file. See below. As with the geometry file, there is a default value of ''jobname.clt''.
 * The type of basis to be used. (Is this now obsolete?)
@@ Line 21: / Line 21: @@
 * The name of the queue. As always, there are special 'queues': ''bg'' says run the job in the background. The other special 'queue' ''none'' may not be usable.
 * You can also specify the memory to be used. This memory (in MB) will be passed to DALTON. The memory given to CamCASP should be in the CLUSTER file.

import>Am592: /* SAPT(DFT) jobs with '''batch_SAPT.pl''' */

2009-03-17T17:37:27Z

SAPT(DFT) jobs with '''batch_SAPT.pl'''

← Older revision		Revision as of 17:37, 17 March 2009
Line 3:		Line 3:
	The ''${CAMCASP}/bin/'' folder contains a few batch scripts for running sets of jobs at various dimer geometries.		The ''${CAMCASP}/bin/'' folder contains a few batch scripts for running sets of jobs at various dimer geometries.

	==SAPT(DFT) jobs with ~~'''~~batch_SAPT.pl~~'''~~==		==SAPT(DFT) jobs with batch_SAPT.pl==
	You cannot always perform an energy scan using the '''ENERGY-SCAN''' module in CamCASP as this module requires you to use the MC type of basis. If you need to use the MC+, DC or DC+ types of bases, then you will need to use the '''batch_SAPT.pl''' script. What this script does is to use a template CLUSTER command file and a file containing the translation and rotation parameters that define the dimer in order to run a batch of SAPT(DFT) (and also SAPT) calculations in an automatic way.		You cannot always perform an energy scan using the '''ENERGY-SCAN''' module in CamCASP as this module requires you to use the MC type of basis. If you need to use the MC+, DC or DC+ types of bases, then you will need to use the '''batch_SAPT.pl''' script. What this script does is to use a template CLUSTER command file and a file containing the translation and rotation parameters that define the dimer in order to run a batch of SAPT(DFT) (and also SAPT) calculations in an automatic way.

Line 13:		Line 13:
	-ipa IP(A) -ipb IP(B) [-q queue] [-M memory in MB]		-ipa IP(A) -ipb IP(B) [-q queue] [-M memory in MB]
	</pre>		</pre>
			You need to supply:
			* The job name. For example, this might be ''benzene2''.
			* The name of the geometry file. More on this below. The default name will be ''jobname.geom'', so if this file is called ''benzene2.geom'', then there is no need to specify it explicitly.
			* The name of the CLUSTER command file. See below. As with the geometry file, there is a default value of ''jobname.clt''.
			* The type of basis to be used. (Is this now obsolete?)
			* The ionisation potentials of the two monomers.
			* The name of the queue. As always, there are special 'queues': ''bg'' says run the job in the background. The other special 'queue' ''none'' may not be usable.
			* You can also specify the memory to be used. This memory (in MB) will be passed to DALTON. The memory given to CamCASP should be in the CLUSTER file.