Dalton - Revision history

import>Ajwt3: /* MOLECULEn */

2007-02-05T16:41:00Z

MOLECULEn

← Older revision		Revision as of 16:41, 5 February 2007
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	:The ''n''th line of the Z-matrix for the molecule. This is comma-separated, and can contain variables and references to atoms on previous lines.		:The ''n''th line of the Z-matrix for the molecule. This is comma-separated, and can contain variables and references to atoms on previous lines.
	;var''n''=val''n'' [;CALC]		;var''n''=val''n'' [;CALC]
	:Variable definitions. Distance variables begin with r, and angular begin with a. val''n'' is an evaluable expression comprising of previously defined variables. All distance and angle variable are liable to a scan if DISTVAR or ANGVAR are specified in the header except if ;CALC is appended to the definition.		:Variable definitions. Distance variables begin with r, and angular begin with a. val''n'' is an evaluable expression comprising of previously defined variables. All distance and angle variable are liable to a scan if DISTVAR or ANGVAR are specified in the header except if ;CALC is appended to the definition. Distances must be specified in Angstroms.

import>Ajwt3 at 09:52, 11 January 2007

2007-01-11T09:52:11Z

← Older revision		Revision as of 09:52, 11 January 2007
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	Usage:<br>		Usage:<br>
	./molrun.pl BASIS MOLLIST FROZEN QUEUE QSIZE<br>		./molrun.pl BASIS MOLLIST FROZEN QUEUE QSIZE<br>
	*DALTEMPLATE - specifies a template .dal file		;DALTEMPLATE: specifies a template .dal file
	*BASIS - specification of basis (e.g. cc-pVDZ). Must be as specified for MOLPRO		;BASIS: specification of basis (e.g. cc-pVDZ). Must be as specified for MOLPRO
	*TAG - tag for root of directory and FCIDUMP FILE		;TAG: tag for root of directory and FCIDUMP FILE
	*MOLLIST - optional list of specific molecules rather than all. e.g. "HOH NN"		;MOLLIST: optional list of specific molecules rather than all. e.g. "HOH NN"
	*FROZEN - 0 if not freezing cores, or 1 if freezing cores		;FROZEN: 0 if not freezing cores, or 1 if freezing cores
	*QUEUE - queue. If queue has a q prepended, jobs are batched.		;QUEUE: queue. If queue has a q prepended, jobs are batched.

	== MOLECULES file ==		== MOLECULES file ==

import>Ajwt3 at 17:37, 9 January 2007

2007-01-09T17:37:31Z

← Older revision		Revision as of 17:37, 9 January 2007
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	*FROZEN - 0 if not freezing cores, or 1 if freezing cores		*FROZEN - 0 if not freezing cores, or 1 if freezing cores
	*QUEUE - queue. If queue has a q prepended, jobs are batched.		*QUEUE - queue. If queue has a q prepended, jobs are batched.

			== MOLECULES file ==

			A file containing a list of molecules and geometries to run. Routines to read and interpret it are in mols.pm. The format is as follows

			<pre>
			HEADER

			MOLECULE1

			MOLECULE2

			...
			</pre>
			=== HEADER ===
			The header contains a list of input parameters to the script, which may be the following:
			; SCALE=''s1,s2''
			: This gives two possible values for a scale parameter, ''s''. All distance measurements are multiplied by ''s''. If ''s1=s2'' then only the single value is used.
			; DISTVAR=''dpc,npts''
			: This allows a scan over distance variables. For each distance variable, ''d'', choose ''npts'' points ranging from <math>d(1-dpc)</math> to <math>d(1+dpc)</math>.
			; ANGVAR=''apc,npts''
			: This allows a scan over angle variables. For each angle variable, ''a'', choose ''npts'' points ranging from <math>a(1-apc)</math> to <math>a(1+apc)</math>.
			; LSHS
			: If present, use low-spin values at scale ''s1'', and high-spin values at scale ''s2''.

			=== MOLECULEn ===
			Each molecule specification consists of the following lines:
			<pre>
			NAME NEL NCORE HSSPIN HSSYM
			ZMAT1;ZMAT2;ZMAT3;...;ZMATn
			var1=val1 [;CALC]
			...
			varn=valn [;CALC]

			</pre>
			These have the following meanings
			; NAME
			: A moniker given to the molecule. This is used to tag all FCIDUMP files and run directories.
			; NEL
			: The total number of electrons in the molecule
			; NCORE
			: The number of core electrons in the molecule (used when frozen-core calculations are performed)
			;HSSPIN
			: The value of 2*Ms for a high-spin state (used with LSHS) (untested with Dalton])
			;HSSYM
			: The MOLPRO symmetry specification for a high-spin state (used with LSHS) (untested with Dalton)
			;ZMAT''n''
			:The ''n''th line of the Z-matrix for the molecule. This is comma-separated, and can contain variables and references to atoms on previous lines.
			;var''n''=val''n'' [;CALC]
			:Variable definitions. Distance variables begin with r, and angular begin with a. val''n'' is an evaluable expression comprising of previously defined variables. All distance and angle variable are liable to a scan if DISTVAR or ANGVAR are specified in the header except if ;CALC is appended to the definition.

import>Ajwt3 at 16:17, 9 January 2007

2007-01-09T16:17:45Z

New page

Dalton is an ''ab initio'' package installed on destiny. Comprehensive documentation can be found at [http://www.kjemi.uio.no/software/dalton/dalton.html].

AJWT has written a number of scripts to simplify running Dalton, and in particular extracting the four-index integrals required as input to NECI. These are available at
destiny:~ajwt3/dalton

== run.pl ==
run.pl [DALTON] 
Parse an input file substituting a placeholder for a series of values,
and then call ./submit.sh.2 for each value with the appropriate specification for dirroot (placeholders changed etc.) and queue. tag is a tag to append to the output filename. submit.sh.2 runs Dalton, and then the postprocessing scripts to produce an FCIDUMP file. As well as the file.mol containing the placeholder, the filename can also contain it.

Usage: 
run.pl file.mol placeholder start end step dirroot tag frozen queue 
or 
run.pl file.mol placeholder listofvalues 0 0 dirroot tag frozen queue 

== molrun.pl ==
molrun.pl [DALTON] 
Perform a series of runs for a set of molecules specified in a MOLECULES file.

Usage: 
./molrun.pl BASIS MOLLIST FROZEN QUEUE QSIZE 
*DALTEMPLATE - specifies a template .dal file
*BASIS - specification of basis (e.g. cc-pVDZ). Must be as specified for MOLPRO
*TAG - tag for root of directory and FCIDUMP FILE
*MOLLIST - optional list of specific molecules rather than all. e.g. "HOH NN"
*FROZEN - 0 if not freezing cores, or 1 if freezing cores
*QUEUE - queue. If queue has a q prepended, jobs are batched.