Amsterdam Density Functional (ADF)
by Scientific Computing and Modelling
ADF is a Density Functional Theory (DFT) software
package for computational quantum chemistry. It enables
first-principles electronic structure calculations and is
used by theoretical and computational chemists
worldwide, both in industry and in academia.
ADF is used in virtually all areas of chemistry, and is
particularly popular in catalysis, inorganic and heavy
element chemistry, as well as in spectroscopy. It can be
applied to all systems from proteins, solvents, polymers,
surfaces, and solids, to simple molecules in the gas phase.
ADF PROGRAM FEATURES:
- The ADF package can be applied to isolated molecules, polymers, slabs, solids, molecules in solvents, and molecules in protein environments.
- It can treat all elements of the periodic table and contains state-of-the-art relativistic methods (ZORA and spin-orbit coupling) to treat heavy nuclei.
- ADF is especially suited for applications to transition metal compounds.
- It is efficient due to a combination of linear scaling and parallelization techniques.
- ADF contains many standard methods for studying potential energy surfaces.
- ADF can treat a wide range of molecular properties.
- Chemically relevant analysis methods are available (including bond energy decomposition, fragment orbitals and charge decomposition).
- The QM/MM implementation enables the treatment of protein environments with many thousands of atoms.
- ADF includes the very latest meta-GGA exchange-correlation functionals as well as a full range of standard functionals.
For more information about ADF, please visit
http://www.scm.com/Products/ADFInfo.html
ADF-BAND PROGRAM FEATURES:
- BAND is a first-principles periodic structure program for the study of bulk crystals, polymers, as well as surfaces.
- It performs electronic structure calculations based on Density Functional Theory.
- It uses numerical and Slater atomic orbitals.
- BAND avoids pseudo-potential approximations.
- BAND is often used in heterogeneous catalysis studies.
- BAND provides densities-of-states (total, partial, population) analyses.
- It can provide the Potential Energy Surface (PES) of, for instance, a chemisorption system or a chemical reaction at a metal surface.
- BAND offers a variety of density functionals.
- It enables both spin-restricted or spin-unrestricted calculations.
- It provides an analysis of the "bonding" (cohesive) energy in conceptually useful components.
- BAND calculates Mulliken-type population analyses and the charge density Fourier analysis (form factors).
- A fragment analysis feature is available for decomposition of Density-of-States data in terms of the molecular orbitals of (molecular) fragments.
- BAND uses the same relativistic methods (ZORA and spin-orbit) as ADF and is well suited to treat heavy nuclei.
- A time-dependent DFT implementation will enable the accurate calculation of frequency-dependent dielectric functions (contact adf for the current status).
For more information about ADF-BAND, please visit
http://www.scm.com/Products/BANDInfo.html
Running ADF and ADF-BAND on cosmos
To run the newest version of ADF/ADF-BAND on cosmos, you will need to add the following lines to your pbs job file:
ADFHOME=/usr/local/lms/ADF/ADF2005.01b
export ADFHOME
ADFBIN=$ADFHOME/bin
export ADFBIN
ADFRESOURCES=$ADFHOME/atomicdata
export ADFRESOURCES
SCMLICENSE=$ADFHOME/license
export SCMLICENSE
To run adfview:
alias adfview="$ADFBIN/adfview"
# The following NSCM setting determines the number of processors that you are going to use
# Make sure that NSCM=n (n=1-8 depending on the queue) matches the ncpus=n setting in your PBS settings
NSCM=2
export NSCM
DIRAC=$ADFBIN/dirac
export DIRAC
SCM_TMPDIR=$TMPDIR
export SCM_TMPDIR
SCM_USETMPDIR=yes
export SCM_USETMPDIR
Here is a sample job file:
#! /bin/bash
#
#PBS -l ncpus=4,mem=2gb,walltime=24:00:00
# You will need to change sample to the appropriate filename (This sample assumes that your input file ends with adfin: sample.adfin)
file=sample
export file
ADFHOME=/usr/local/lms/ADF/ADF2005.01b
export ADFHOME
ADFBIN=$ADFHOME/bin
export ADFBIN
ADFRESOURCES=$ADFHOME/atomicdata
export ADFRESOURCES
SCMLICENSE=$ADFHOME/license
export SCMLICENSE
NSCM=4
export NSCM
DIRAC=$ADFBIN/dirac
export DIRAC
SCM_TMPDIR=$TMPDIR
export SCM_TMPDIR
SCM_USETMPDIR=yes
export SCM_USETMPDIR
env
date
cd $TMPDIR
chmod u+x $PBS_O_WORKDIR/$file.adfin
$PBS_O_WORKDIR/$file.adfin >> $PBS_O_WORKDIR/$file.out
mv -f ./$file.t21 $PBS_O_WORKDIR/.
date
exit
For information on how to obtain an account on cosmos.tamu.edu please visit the SuperComputing Web site
http://sc.tamu.edu/
Trouble-shooting:
If you you receive the error:
Xlib: connection to "labmol4.chem.tamu.edu:0.0" refused by server
Xlib: Client is not authorized to connect to Server
Error: Can't open display:labmol4.chem.tamu.edu:0.0
(where labmol4 will be replaced by the local machine name)
You need to make sure that you use the -Y flag when you ssh to cosmos (
ssh -Y username@cosmos.tamu.edu )
If you get an error about an unknown flag -Y, try using -X instead when you ssh to the remote machine.
