ADF
Introduction
ADF (The Amsterdam Density Functional package) is a software for first-principles electronic structure calculations. It is particularly popular in the research areas of homogeneous and heterogeneous catalysis, inorganic chemistry, heavy element chemistry, various types of spectroscopy, and biochemistry.
BAND, also called ADF-BAND, is the name of a software package closely related to ADF. BAND can be used to study periodic systems: solids, surfaces, slabs, polymers, and reactions on surfaces. BAND is a part of ADF package here.
Running ADF on Graham
ADF 2016.106 and 2017.207 are installed on Graham cluster and available through the modules system. You can load them using either of.
[name@server $] module load adf/2016.106
[name@server $] module load adf/2017.207
Job Submission
Graham uses the Slurm scheduler; for details about submitting jobs, see Running jobs.
Single adf or band run
The following example is a full-node ADF job script, mysub.sh:
#!/bin/bash
#SBATCH --nodes=1 --ntasks-per-node=32 # 1 node with 32 cpus, you can modify it
#SBATCH --mem-per-cpu=2G # memory, should be <4G for full node job
#SBATCH --time=00-03:00 # time (DD-HH:MM)
#SBATCH --output=adf_test.log # output .log file
module load adf/2017.207
ADF adf_test.inp # ADF command
The following is an example for the input file, adf_test.inp:
Title WATER Geometry Optimization with Delocalized Coordinates
Atoms
O 0.000000 0.000000 0.000000
H 0.000000 -0.689440 -0.578509
H 0.000000 0.689440 -0.578509
End
Basis
Type TZP
Core Small
End
Geometry
Optim Deloc
Converge 0.0000001
End
End Input
Multi adf or band runs within one input file
The following script is an example for a full-node multi-ADF runs, GO_H2O.sh:
#!/bin/bash
#SBATCH --nodes=1 --ntasks-per-node=32 # 1 node with 32 cpus, you can modify it
#SBATCH --mem-per-cpu=2G # memory, should be <4G for full node job
#SBATCH --time=00-03:00 # time (DD-HH:MM)
#SBATCH --output=adf_test.log # output .log file
module load adf/2017.207
./GO_H2O.run # run the input file, GO_H2O.run must be executable
Example for several adf runs within one the input file, GO_H2O.run
#!/bin/bash
if test -z "$SCM_TESTOUTPUT" ; then SCM_TESTOUTPUT=GO_H2O.out; fi
$ADFBIN/adf << eor > $SCM_TESTOUTPUT
Title WATER Geometry Optimization with Delocalized Coordinates
Atoms
O 0.000000 0.000000 0.000000
H 0.000000 -0.689440 -0.578509
H 0.000000 0.689440 -0.578509
End
Basis
Type TZP
Core Small
End
Geometry
Optim Deloc
Converge 0.0000001
End
End Input
eor
rm TAPE21 logfile
$ADFBIN/adf << eor >> $SCM_TESTOUTPUT
Title WATER Geometry Optimization in Cartesians with new optimizer
Atoms
O 0.000000 0.000000 0.000000
H 0.000000 -0.689440 -0.578509
H 0.000000 0.689440 -0.578509
End
Basis
Type TZP
Core Small
End
Geometry
Optim Cartesian
Branch New
Converge 0.0000001
End
End Input
eor
rm TAPE21 logfile
$ADFBIN/adf << eor >> $SCM_TESTOUTPUT
Title WATER Geometry Optimization with Internal Coordinates
Atoms Z-Matrix
1. O 0 0 0
2. H 1 0 0 rOH
3. H 1 2 0 rOH theta
End
Basis
Type TZP
Core Small
End
GeoVar
rOH=0.9
theta=100
End
Geometry
Converge 0.0000001
End
End Input
eor
rm TAPE21 logfile
$ADFBIN/adf << eor >> $SCM_TESTOUTPUT
Title WATER optimization with (partial) specification of Hessian
Atoms Z-Matrix
1. O 0 0 0
2. H 1 0 0 rOH
3. H 1 2 0 rOH theta
End
GeoVar
rOH=0.9
theta=100
End
HessDiag rad=1.0 ang=0.1
Fragments
H t21.H
O t21.O
End
Geometry
Converge 0.0000001
End
End Input
eor
rm TAPE21 logfile
$ADFBIN/adf << eor >> $SCM_TESTOUTPUT
Title WATER Geometry Optimization in Cartesians
Geometry
Optim Cartesian
Converge 0.0000001
End
Define
rOH=0.9
theta=100
End
Atoms Z-Matrix
1. O 0 0 0
2. H 1 0 0 rOH
3. H 1 2 0 rOH theta
End
Fragments
H t21.H
O t21.O
End
End Input
eor
mv TAPE21 H2O.t21
Examples
Examples for adf_test can be found on Graham under
/home/jemmyhu/tests/test_ADF/2017.207/test_adf/
Some user may do multi-step ADF runs within one job, see GO_H2O.run and GO_H2O.sh examples under
/home/jemmyhu/tests/test_ADF/2017.207/test_adf/
The same procedure applies to BAND job, see band_test.inp and band_test.sh examples under
/home/jemmyhu/tests/test_ADF/2017.207/test_band