CategoryChemistry, Quantum chemistry, DFT
DescriptionADF 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|
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|
How to submit a jobUsually, 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:
bsub [LSF options] < my_ADF_input_file.runHere you need to replace [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the wiki page about the batch system.
ExampleAs 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 -0.595236All important information about the geometry optimization of the water molecule can be found in the lsf.o28422473 logfile.
License informationCommercial (provided by D-CHAB).