Quantum 1 Modules

C       DMol³--Running in Standalone

This appendix discusses the basic steps for setting up and running a DMol³ calculation in standalone mode (that is, outside the Cerius²·DMol³ interface). DMol³ may be run in standalone mode directly or by executing a DMol³ run script.

Detailed documentation of the standalone keywords, which are contained in the .input file, is contained in DMol³--Keyword Descriptions.

Methodology

Creating and modifying input files

You should create the initial model structure and the DMol³ input file by using the Cerius²·DMol³ module.

You can write the input file with a text editor. However, it is much easier to create an input from the Cerius²·DMol³ interface. Then save this file by opening the DMol3 Input File control panel (Handling and naming DMol³ input files) and clicking the Save DMol3 Input File action button. This creates a run_name.input file which you can edit if needed.

Computational environment

You also have to set your computational environment so as to access the license files and DMol³ data files. (This task can be handled by a run script instead, see below.)

Running DMol³ directly

If dmol3 is a link to the DMol³ executable, then you can run the program directly by entering at the UNIX prompt:

>	dmol3 run_name 

>	dmol3 h2o

If you need to specify point charges, a Hessian file, a restart file for energy, geometry optimization, or frequency calculations, and/or the starting orbital occupancy, then additional input files are needed.

Handling such runs, as well as cleaning up various scratch files, is facilitated by Running DMol³ from a run script.

Running DMol³ from a run script

It is usually easier to run standalone DMol³ from a run script, rather than directly using just an input file and a structure file. You can create a DMol³ run script by using the Cerius²·DMol³ module.

Alternatively, you can start from an existing DMol³ run script. An example run script called dmol3.run is located in the DMol³ data directory and is printed in the next section.

Once a run script called dmol3.run is ready, it can be used to submit a DMol³ job by entering at the UNIX prompt, for example:

>	dmol3.run  h2o

Example run script

#! /bin/csh -f


##############################################################


#  $NAME Run script designated to run DMol3 background job


##############################################################


#


#  User is encouraged to customize this script


#  WARNING: this script will remove most of the restart and


#  result files. The only surviving files are  .outmol


#  new geometry (.car), 


#  hessian files (.hesswk, .hessian),


#  SCF vectors (.tpvec),


#  history of oprimization (.arc),


#  original .car and .hessian files (.orig),


#  MD history file (.his),


#  files for ploting (.grid)


#


###############################################################


#


#  To run dmol3 standalone just type:


#


#    dmol3.run run_name  &


#


#  where run_name is the NAME of the system


#


#  DMol3 expects that at least NAME.car and NAME.input exist


#  in the cwd, running directory.


#  Optionally you may need to provide specific files to restart


#  DMol3 run.





###############################################################








# Unalias commands, just in case


unalias rm


unalias cp





set NAME  = $1





#


setenv C2DIR /cx4/release/irix64.x11/cerius2_c38





# License setup


source $C2DIR/install/lic_setup





# Set some environmental variables


setenv DMOL3_DATA $C2DIR/res/DMOL3


setenv DMOL3 $C2DIR/exec/dmol3





# Check that the executable of DMol3 exists


if ( -e $DMOL3 ) then


  # Remove existing outfile, if it exists


  if ( -e $NAME.outmol ) /bin/rm $NAME.outmol





  # Save an orignal copy of the car file


  if ( ! -e $NAME.car.orig ) then


    /bin/cp $NAME.car $NAME.car.orig


  endif





  # Save an orignal copy of the hessian file


  if ( ! -e $NAME.hessian.orig ) then


    if ( -e $NAME.hessian ) then


      /bin/cp $NAME.hessian $NAME.hessian.orig


    endif


  endif





  # Now, run the $NAME executable


  $DMOL3  $NAME





else


  echo `The DMOL3 executable cannot be located.'


  echo `Alternatively, there may be a problem with your Cerius2 installation.'


endif








# the following section has to be checked very carefuly before running


# the script, so the only not needed files are removed


#


# restart for frequency


#if ( -e $NAME.hesswk ) then


#   rm $NAME.hesswk


#endif





# restart for optimization


#if ( -e $NAME.hessian ) then


#   rm $NAME.hessian


#endif





# SCF restart file


#if ( -e $NAME.tpvec ) then


#   rm $NAME.tpvec


#endif





# history of optimization


#if ( -e $NAME.arc ) then


#   rm $NAME.arc


#endif





# MD history file


#if ( -e $NAME.his ) then


#   rm $NAME.his


#endif





# old restart for SCF


if ( -e $NAME.tpotl ) then


   rm $NAME.tpotl


endif





# restart for volumetric properties


if ( -e $NAME.tmesh ) then


   rm $NAME.tmesh


endif


if ( -e $NAME.tpsmx ) then


   rm $NAME.tpsmx


endif





# results of properties run


# density of states


if ( -e $NAME.dos ) then


   rm $NAME.dos


endif


# optical absorption


if ( -e $NAME.optabs) then


   rm $NAME.optabs


endif


# remove all the plot files


#  rm *.grd





# Occupancy file


if ( -e $NAME.occup ) then


   rm $NAME.occup


endif





# Remove the following scratch files


if ( -e $NAME.basis ) then


   rm $NAME.basis


endif


if ( -e $NAME.grad ) then


   rm $NAME.grad


endif


if ( -e $NAME.inatm ) then


   rm $NAME.inatm


endif


if ( -e $NAME.incoor ) then


   rm $NAME.incoor


endif


if ( -e $NAME.opt ) then


   rm $NAME.opt


endif


if ( -e $NAME.outatom ) then


   rm $NAME.outatom


endif


if ( -e $NAME.pchk ) then


   rm $NAME.pchk


endif


if ( -e $NAME.startspin ) then


   rm $NAME.startspin


endif


if ( -e $NAME.sym ) then


   rm $NAME.sym


endif


if ( -e $NAME.symdec ) then


   rm $NAME.symdec


endif


if ( -e $NAME.symdv ) then


   rm $NAME.symdv 


endif


if ( -e $NAME.torder ) then


   rm $NAME.torder


endif


if ( -e $NAME.tpdiis ) then


   rm $NAME.tpdiis


endif


if ( -e $NAME.tpdiisk ) then


   rm $NAME.tpdiisk


endif


if ( -e $NAME.tplev1 ) then


   rm $NAME.tplev1


endif


if ( -e $NAME.tplev2 ) then


   rm $NAME.tplev2


endif


if ( -e $NAME.fwv ) then


   rm $NAME.fwv


endif


if ( -e $NAME.amat ) then


   rm $NAME.amat


endif


if ( -e $NAME.prf ) then


   rm $NAME.prf


endif

For an IBM, the following modification of the dmol3.run file is needed, for example:

setenv C2DIR /cx4/release/ibmrios.x11/cerius2

Upon completion of the run, the main results are written to a file called run_name.outmol.

DMol file use and creation during a run

DMol³ uses input files which reside in the DMOL3_DATA directory.

A DMol³ run begins with parsing of the .input file. This may result in creating auxiliary files .startspin and .opt. The .opt file contains input data for the optimization module.

The .car file is read and a DMol³ internal geometry file .incoor is created.

Next, the symmetry of the molecule is investigated. This results in the creating of two symmetry files .sym and .symdec.

The basis set is created automatically using .inatm input and the result is placed in a .basis file. The output of the atom run is stored in an .outatom file.

The .torder file contains information on molecular grid generation.

The .fwv file is created only during an indirect run of DMol³.

Several files are always created during SCF, energy calculations. These are .tpotl, .tpvec, .tpsmx, .tmesh, and .occup. The .tpotl file contains an analytic representation of the Coulomb potential, .tpvec file stores SCF eigenvectors and eigenvalues together with occupation numbers, .tpsmx contains the kinetic energy and overlap matrix, and .tmesh file has the numerical grid information needed for restarting a properties calculation. The .occup file contains information on the occupation of the orbitals.

If the level shift technique is used, then .tplev1 and .tplev2 scratch files are needed.

Typically, SCF convergence is attained using the DIIS procedure. This results in production of a .tpdiis file.

Geometry optimization leads to the formation of several files: .grad contains gradient information, .pchk contains the history of optimization, .hessian is an updated Hessian, and .arc accumulates consecutive .car files generated during geometry optimization.

Molecular dynamics and simulated annealing runs lead to the formation of .arc and .his files which contain the history of the run.

A frequency calculation results in a .hesswk file, which stores gradient data from all finite-difference calculations of the Hessian.

Properties calculations may result in several plot files (.grd), an optical absorption spectrum and intensity file (.optabs), and density-of-states information (.dos).

COSMO calculations lead to the formation of a .cosmo file, which contains information about the COSMO charge density on the cavity surface surrounding the molecule. Also, a large file .amat is created which contains the A matrix of the COSMO run. This is a scratch file and is removed by the running DMol3 script.