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:

File : 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:

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:

File : 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

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

Example input/output for ADF can be found on Graham 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