ADF

Category

Chemistry, Quantum chemistry, DFT

Description

ADF is used in many areas of chemistry and materials science. ADF is particularly strong in molecular properties and inorganic chemistry. The periodic DFT code BAND shares a lot of functionality with ADF. Slabs are treated as real 2D systems, and nanotubes with proper 1D periodicity. DFTB and MOPAC are fast approximate methods to study large molecules and big periodic systems, employing DFT-based and semi-empirical data, respectively. Reaction dynamics in large complex systems can be studied with bond order based ReaxFF. COSMO-RS uses quantum mechanical data from ADF to predict thermodynamic properties of solutions and mixtures (LogP, VLE, pKa, …)

Available versions (Euler, old software stack)

Legacy versions	Supported versions	New versions
2012.01, 2013.01	2014.07	2016.107

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Environment modules (Euler, old software stack)

Version	Module load command	Additional modules loaded automatically
2012.01	module load legacy adf/2012.01
2013.01	module load legacy adf/2013.01
2014.07	module load adf/2014.07
2016.107	module load new adf/2016.07

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

How to submit a job

Usually, the ADF input file is a shell script, that has the ending .run and contains all instructions to perform the simulation with ADF (you can find an example for such an input file below in the example section). You can submit your ADF job with the following command:

sbatch [Slurm options] < my_ADF_input_file.run

Here you need to replace [Slurm options] with Slurm parameters for the resource requirements of the job. Please find a documentation about the parameters of sbatch on the wiki page about the batch system.

Example

As an example for an ADF job, we are performing a geometry optimization for a water molecule. Please note that you explicitly need to set the number of cores used when calling $ADFBIN/adf, otherwise ADF will try to use all available cores.

[sfux@eu-login-01 ~]$ cat h2o.run 
#! /bin/sh
$ADFBIN/adf -n 1 <<eor
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
End

End Input
eor
[sfux@eu-login-01 ~]$ module load adf/2014.07
[sfux@eu-login-01 ~]$ bsub -n 1 -W 2:00 -R "rusage[mem=2048]" < h2o.run 
Generic job.
Job <28422473> is submitted to queue <normal.4h>.
[sfux@eu-login-01 ~]$ bjobs
JOBID      USER        STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
28422473   leonhard    PEND  normal.4h  euler01                 *Input;eor Sep 22 08:22
[sfux@eu-login-01 ~]$ bjobs
JOBID      USER        STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
28422473   leonhard    RUN   normal.4h  euler01     e3341       *Input;eor Sep 22 08:22
[sfux@eu-login-01 ~]$ bjobs
No unfinished job found
[sfux@eu-login-01 ~]$ grep -A 5 "Final Geometry" lsf.o28422473 
 <Sep22-2016> <08:23:18>  Calculating Energy Terms for Final Geometry
  Coordinates in Geometry Cycle 6
    Atom         X           Y           Z   (Angstrom)
    1.O         0.000000    0.000000    0.002108
    2.H         0.000000   -0.769922   -0.595236
    3.H         0.000000    0.769922   -0.595236

All important information about the geometry optimization of the water molecule can be found in the lsf.o28422473 logfile.

License information

Commercial (provided by D-CHAB).
License terms

Links

https://www.scm.com/

https://www.pyadf.org/
https://en.wikipedia.org/wiki/Amsterdam_Density_Functional
https://www.youtube.com/channel/UCS7kQGtEgwSf8jjyTIdUqgQ