Dalton

Dalton is an ab initio package installed on destiny. Comprehensive documentation can be found at [1].

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.

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

HEADER

MOLECULE1

MOLECULE2

...

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:

NAME NEL NCORE HSSPIN HSSYM
ZMAT1;ZMAT2;ZMAT3;...;ZMATn
var1=val1 [;CALC]
...
varn=valn [;CALC]

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)

ZMATn

The nth line of the Z-matrix for the molecule. This is comma-separated, and can contain variables and references to atoms on previous lines.

varn=valn [;CALC]

Variable definitions. Distance variables begin with r, and angular begin with a. valn 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.