ADF

Amsterdam Density Functional

Introduction

ADF (Amsterdam Density Functional) is an accurate, parallelized, powerful computational chemistry program to understand and predict chemical structure and reactivity with density functional theory. Heavy elements and transition metals are accurately modeled with ADF's reliable relativistic ZORA approach and all-electron basis sets for the whole periodic table (H-Uuo). A vast range of spectroscopic properties and comprehensive analysis tools yield invaluable insight in chemical structure and reactivity. DFT calculations are easily prepared and analyzed with our GUI.

License

ADF is a licensed software. The license file is installed on all nodes of the partition mendoza_q. Currently only members of Professor Jose Mendoza Cortes' research group have access to this software.

Note. The GUI tool of ADF is not installed on the computing nodes of the HPC.

Usage of ADF at the RCC

There are two versions of ADF installed on the HPC cluster, 2014.07 and 2016.101.

To use ADF, first, load the module for the version of ADF you want to use. To use the latest 2016 version (the default),

$ module load adf

To use the older 2014 version instead,

$ module load adf/2014.07

Note. The two versions should NOT be used together. Consequently, only one module file should be loaded. To unload a module use a syntax like the following,

 $ module unload adf/2014.07

To check if this module is successfully loaded,

$ module list

(You should find adf in the outputs of the above command).

To check if you have the correct environment set up,

$ which dirac

(If you can not find dirac, them something is wrong).

To check license information

$ dirac check

The last line should say License Ready.

Scratch Space

Some ADF jobs need large scratch disk space. By default, the scratch directory was set to be

     /panfs/storage.local/engineering/mendozagroup/scratch/adf/$USER/2014

for the 2014 version, and

    /panfs/storage.local/engineering/mendozagroup/scratch/adf/$USER/2016

for the 2016 version, respectively. In the above $USER is your rcc user name.

If you want a specific scratch directory for each Slurm job, you can redefine the scratch dicrectory like the following

module load adf
export SCM_TMPDIR=${SCM_TMPDIR}/${SLURM_JOBID}
echo   $SCM_TMPDIR
if [ ! -d $SCM_TMPDIR ]; then
    mkdir -p $SCM_TMPDIR
fi

Note. In the above, we need to create the new scratch directory ${SLURM_JOBID} since it does not exist.

Example of ADF job

The following is a simple example SLURM job submission script (asking for 3 cores) :

#!/bin/bash
#SBATCH -J "adf_test" 
#SBATCH -n 3
#SBATCH -N 1
#SBATCH -o test-%J.o 
#SBATCH -e test-%J.e
#SBATCH -p mendoza_q
#SBATCH --mail-type=ALL
#SBATCH -t 15:00

cd $SLURM_SUBMIT_DIR
module purge
module load adf
export SCM_TMPDIR=${SCM_TMPDIR}/${SLURM_JOBID}
echo   $SCM_TMPDIR

if [ ! -d $SCM_TMPDIR ]; then
    mkdir -p $SCM_TMPDIR
fi
if [ ! -d $SCM_TMPDIR ]; then
  echo "temporary scratch directory could not be created"
  exit
fi

export NSCM=3
echo  $NSCM
which adf

adf -n 3 < HCN_4P.inp  > HCN_4P.out

The input data file HCN_4P.inp is

Title    HCN Linear Transit, first part
NoPrint  SFO, Frag, Functions, Computation

Atoms      Internal
  1 C  0 0 0       0    0    0
  2 N  1 0 0       1.3  0    0
  3 H  1 2 0       1.0  th  0
End

Basis
  Type DZP
End

Symmetry NOSYM

Integration 6.0 6.0

Geometry
  Branch Old
  LinearTransit  10
  Iterations     30  4
  Converge   Grad=3e-2,  Rad=3e-2,  Angle=2  
END

Geovar
  th   180    0
End

End Input

Upon successful run, you will see in the slurm error output file test-280037.e

NORMAL TERMINATION
NORMAL TERMINATION  
NORMAL TERMINATION
NORMAL TERMINATION
NORMAL TERMINATION
NORMAL TERMINATION

The slurm standout file test-280037.o

/panfs/storage.local/engineering/mendozagroup/scratch/adf/bchen3/2521776
3
/panfs/storage.local/engineering/mendozagroup/ADF/2016/openmpi/adf2016.101/bin/adf
...

To check if adf has run in parallel

 $ cat HCN_4P.out | grep Nodes

You will find at least one line like the following:

 ADF 2016  RunTime: Apr11-2016 11:19:24  Nodes: 1  Procs: 3

Note. Only the CPU-intensive part of the job will be run in parallel. So you will also see some lines like the following

ADF 2016  RunTime: Apr11-2016 11:19:22  Nodes: 1  Procs: 1

Example of Band Job

First, copy the example to your directory

$ cp -r  /panfs/storage.local/engineering/mendozagroup/ADF/2016/openmpi/adf2016.101/examples/band/BasisDefaults .
$ cd BasisDefaults
$ ls   
   BasisDefaults_orig.out  BasisDefaults.run

Next, create a band job slurm script, band.sub

#!/bin/bash
#SBATCH -J "bandjob"
#SBATCH -n 1
#SBATCH -N 1
#SBATCH -o test-%J.oe
#SBATCH -p mendoza_q
#SBATCH --mail-type=ALL
#SBATCH -t 15:00

cd $SLURM_SUBMIT_DIR

module purge
module load adf
export SCM_TMPDIR=${SCM_TMPDIR}/${SLURM_JOBID}
echo   $SCM_TMPDIR

if [ ! -d $SCM_TMPDIR ]; then
    mkdir -p $SCM_TMPDIR
fi
if [ ! -d $SCM_TMPDIR ]; then
     echo "temporary scratch directory could not be created"
    exit
fi

dirac check
./BasisDefaults.run

Submit the job using

sbatch band.sub

The SLURM output fill will be like

/panfs/storage.local/engineering/mendozagroup/scratch/adf/bchen3/2016/2522139

 Checked:
 /panfs/storage.local/engineering/mendozagroup/ADF/2016/openmpi/adf2016.101/license.txt

 License termination date (mm/dd/yyyy):  4/ 1/2017

 ....

 <Apr11-2016> <11:03:41>  NORMAL TERMINATION
 <Apr11-2016> <11:03:41>  END
NORMAL TERMINATION