Amsterdam Density Functional (ADF)

Introduction :

The Amsterdam Density Functional (ADF) package is software for first-principles electronic structure calculations. ADF is used by academic and industrial researchers worldwide in such diverse fields as pharmacochemistry and materials science. It is currently particularly popular in the research areas of:

Homogeneous and heterogeneous catalysis
Inorganic chemistry
Heavy element chemistry
Various types of spectroscopy
Biochemistry

For further details please check the official website for the software, www.scm.com.

Vendor : Amstersdam Density Functional Software

Supplier : Seascape Learning

Version : 2010.01

Following Software products of ADF are installed at SERC :

ADF version 2010.99

ADF-GUI version 2010.99

BAND version 2010.99

BAND-GUI version 2010.99

GUI version 2010.99

NBO version 2010.99

Utils version 2010.99

License: Node Locked

ADF 2010.01 version consists of:

The Molecular ADF program
The periodic structure program BAND
A Graphical user interface (GUI) for ADF and BAND
Natural Bond Orbital (NBO)

SCM Product Information

Availability

This software is installed on Tesla Cluster and five hplx machines based machines ( hostname: hplx1_4 to hplx1_8). The software is node locked and hence can be used only on these machines. The user can inform system administrator to enable the SERC loginid to use the software on these machines.

Procedure to use ADF SOFTWARE

Environmental Setup required

For csh/tcsh

source /home/pkg/lic/chemistry/adf2010.01/adfrc.csh

For Bash/Sh

source /home/pkg/lic/chemistry/adf2010.01/adfrc.sh

One has to create a run file for using adf or band

Sample run scripts for ADF and BAND are $ADFHOME/examples directory.

How to submit a PBS job for serial and parallel

A sample script to submit an adf job to PBS scheduler is shown below

On the hplx machines adf jobs can use only one cpu and are to be submitted through PBS. You may run adfGUI / bandGUI interactively on hplx1_4 to hplx1_8 machines locally.

For Serial Job, PBS script information:

-----------File myjob.sh-------------------------------------

#!/bin/csh
#PBS -l select=1:ADF=True
#PBS -V
#PBS -S /bin/csh
#PBS -N ADF-Serial

source /home/pkg/lic/chemistry/adf2010.01/adfrc.csh

setenv SCM_TMPDIR /global/utemp/loginid/ADF

cd /global/utemp/loginid/ADF/examples/adf/GO_H2O
./GO_H2O.run > GO_H2O.output

-----------End of the File myjob.sh------------------------

On Tesla Cluster users have to submit jobs to PBS job scheduler. Users have to create a script file to submit to PBS batch system. Below is an example script that can be used to submit an ADF job using 4 cpus.

For Parallel Job, PBS script information:

-----------File myjob.sh-------------------------------------

#!/bin/csh
#PBS -l select=1:ncpus=8:mpiprocs=8
#PBS -l place=pack
#PBS -V
#PBS -S /bin/csh
#PBS -N ADF-Parallel

source /home/pkg/lic/chemistry/adf2010.01/adfrc.csh

# -----------------------------------
setenv SCM_USETMPDIR yes
setenv SCM_TMPDIR /global/utemp/loginid/ADF
setenv NSCM 8
setenv MPI_IC_ORDER "TCP"
# -----------------------------------

cd /global/utemp/loginid/ADF/examples/adf/CuH+_S-squared
./CuH+_S-squared.run > CuH+_S-squared.output

-----------End of the file myjob.sh-------------------------------------

Where ncpus and NSCM must be equal.

For 8 Processor ADF Job, edit Job Script as follows:

#PBS -l select=1:ncpus=8:mpiprocs=8 and NSCM 8

For 14 Processor ADF Job, edit Job Script as follows:

#PBS -l select=1:ncpus=14:mpiprocs=14 and NSCM 14

To use ADF-GUI, ssh to one of the hplx machines and set the DISPLAY environment
variable. The basic commands are given below:

Name of the ADF software invocation
Commands

ADF INPUT adfinput

ADF LEVELS adflevels

BAND INPUT bandinput

BAND STRUCTURE bandstructure

VIEW adfview

MOVIE adfmovie

LOGFILE adftail

OUTPUT adfoutput

SPECTRA adfspectra

DOS adfdos

Preferences guiprefs