The first calculation with DALTON

If we have made two input files, one corresponding to DALTON.INP and one corresponding to the MOLECULE input file, we are ready to do our first calculation. Examples of input files can also be found in the dalton/test directory hidden inside the test jobs. You can execute one of the individual test jobs without the TEST script, for example:

> ./energy_nosymm

This will create four files, but right now we are just interested in the .dal and the .mol files. In this particular example they will be energy_nosymm.dal and energy_nosymm.mol. Have a look at some of these input files to get a head-on start on running different kinds of DALTON jobs.

Calculations with DALTON is most conveniently done using the supplied shell script dalton. Thus, to run a calculation of $\beta$ (first hyperpolarizability) with input available as beta.dal on the HCl molecule, and with molecule input available as hcl.mol, you would type

> dalton beta hcl

assuming dalton is available in your path. When the job is finished, the output is copied back as beta_hcl.out. In case that the dalton- and molecule-input has the same name we may write dalton energy_nosymm, and the corresponding output file will be named energy_nosymm.out. In addition, the program will copy back a file named beta_hcl.tar.gz. This file contains, in tar'ed and gzip'ed form, a number of useful interface and post-processing files needed for post-DALTON programs, or needed when restarting calculations.

There are several options to this script, which can be viewed by typing dalton -h or just dalton. These options include:

-b directory

Prepend this directory to the list of directories where the program should look for basis sets. Needed in case you want to use local modifications of a given basis. The job directory and the DALTON basis set library will always be included in the basis set directory list (in that search order).

-d

Removes the contents of the scratch directory before a calculation starts in order to avoid inconsistencies between files.

-D

Do not remove the content of the scratch directory. By default the scratch directory will be deleted. However, in order to do a restart you may want to keep all files in this directory, and you then need to add the -D option when submitting the job.

-e ext

Change the extension to the output file from .out to .ext.

-f

Copy the gzipped-file containing a variety of useful interface files from your home directory to the scratch directory before a calculation starts. This is needed in order to be able to restart DALTON calculations, or if you want to use converged response vectors in a different response calculations for the same molecule.

-M mb

Change the default size of the scratch memory space to mb Mbytes.

-N nodes

Number of nodes to be used in a parallel MPI calculation controlled by running mpirun (or using mpiexec).

-lam file

Call "lamboot file" and "wipe file" before and after mpirun.

-o filename

Redirect the output normally printed in the DALTON.OUT file in the temporary directory to the file ``filename'' in the WRKDIR directory. On a computer system with distributed scratch disk but a commonly mounted home directory, this allows you to follow the calculation without having to log into the compute nodes.

-t tmpdir

Change the TMPDIR (the scratch disc area) to tmpdir from the default scratch directory determined at install-time.

-w wrkdir

Change the working directory to ``wrkdir'', that is, change the directory in which the program searches for input files and places the DALTON.OUT file to ``wrkdir''.

In most cases, the DALTON.OUT file will contain all the information needed about a given calculations. However, in certain cases, additional information may be wanted, and this is contained in various sets of auxiliary files. These files are copied back in the tar'ed and gzip'ed file. This file may include the following set of different files:

DALTON.BAS

Contains a dump of a complete molecule input file. This file take maximum advantage of formatted input, yet differences may occur compared to the basis sets obtained from the basis set library due to the restricted number of digits available in the standard-format output.

DALTON.CM

An output file that contains the most essential information needed for calculation of shielding polarizabilities and magnetizability polarizabilities. Most easily used together with the analyzing program ODCPRG.f supplied in the tools directory.

DALTON.HES

If the keyword .HESPUN has been specified in the *VIBANA input module, the molecular Hessian will be written to this file in a standard format, which may be used as a start Hessian in an first-order geometry optimization, or as input to a ROA or VCD analysis with different basis sets/level of correlation for the intensity operators and the force field. See also the FChk2HES.f program in the tools directory.

DALTON.IRC

Contains information obtained from an Intrinsic Reaction Coordinate (IRC) calculation, as described in Sec. 7.2.1.

DALTON.MOL

Contains the information needed by the MOLPLT-program for visualizing the molecular geometry. The MOLPLT-program is distributed with the GAMESS-US program package.

DALTON.MOPUN

Contains the molecular-orbital coefficients printed in a standard format allowing the transfer of molecular orbitals coefficients from one computer to another.

DALTON.NCA

Contains the information needed by the MOLPLT-program for visualizing normal coordinates.

DALTON.ORB

Contains information about basis set and MO-coefficients so that MO density plots may be generated using the PLTORB program that comes with the GAMESS-US distribution. Currently not supported.

DALTON.TRJ

Contains trajectory information from a direct dynamics calculation as described in Sec. 7.2.2.

DALTON.WLK

Contains information from the walk-procedure, and is needed when restarting a walk (e.g. a numerical differentiation).

molden.inp

Contains the input required for visualizing the results of the calculation using the MOLDEN program (http://http://www.cmbi.ru.nl/molden/molden.html). Please also note that Jmol (http://jmol.sourceforge.net) also can visualize many aspects of a DALTON calculation, including an intrisic reaction coordinate calculation. Jmol uses the DALTON output file (DALTON.OUT) for it's visualization.

RESULTS.RSP

Contains a brief summary of the results obtained form the response functions that have finished. The program may use this information to skip response equations that have already been solved (for instance if the calculation crashed for some reason during the calculation of a set of cubic response functions).

RSPVEC

Contains the converged response equations. The program may use this to avoid repeating linear response equations. Thus, one may use the converged response vectors of a linear response equation in the calculation of quadratic response function, and there may then be no need to solve additional response equations.

SIRIUS.IFC

Interface file between the wave function part of the program and the property modules. Contains all the information required about the optimized molecular wave function.

SIRIUS.RST

Contains restart information needed in case one needs to restart the wave function part of the program.