AMS

The Amsterdam Modeling Suite offers DFT, semi-empirical, reactive force fields and fluid thermodynamics all with an integrated GUI, a powerful AMS driver and python scripting tool PLAMS. The main compute engines are ADF and BAND for electronic structure calculations (DFT), DFTB and MOPAC for more approximate methods to study larger systems.

Available

  • Puhti: AMS2019, ADF2019, BAND2019, DFTB2019, MOPAC2019, ReaxFF2019 , Version 2019.301

License

  • The license entitles software usage by any academic researcher or student of an academic institute where "Academic" means "belonging to a degree-granting institute".
  • The license does not include the right for employees of government labs or other non-academic non-profit research institutes to use the software.
  • The license only allows non-profit non-commercial use.
  • The license excludes all forms of contract research, royalty-bearing activities and other activities leading to monetary benefits.

Usage

Initialise AMS on Puhti like this:

module load adf/2019.301

Example batch script for Puhti

#!/bin/bash
#SBATCH --partition=test
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=40 # MPI tasks per node
#SBATCH --account=<project>  # insert here the project to be billed 
#SBATCH --time=00:10:00           # time as hh:mm:ss

ulimit -s unlimited
export SCM_TMPDIR=$PWD/SCM_TMP_$SLURM_JOB_ID
mkdir -p $SCM_TMPDIR
export SCM_USE_LOCAL_IMPI=yes
module purge
module load intel/19.0.4 intel-mpi/18.0.5 
module load adf/2019.301

$ADFBIN/adf < methane_dimer_dispersion.inp > methane_dimer_dispersion.log
seff $SLURM_JOBID

Note

Particularly some property calculations can be very disk I/O intensive. Such jobs benefit from using the fast local storage on Puhti. Using local disk for such jobs will also reduce the load on the Lustre parallel file system.

Example batch script for Puhti using local disk

#!/bin/bash
#SBATCH --partition=large
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=40 # MPI tasks per node
#SBATCH --account=<project>  # insert here the project to be billed
#SBATCH --time=00:10:00      # time as hh:mm:ss
#SBATCH --gres=nvme:100      # requested local disk space in GB 
ulimit -s unlimited
export SCM_TMPDIR=$LOCAL_SCRATCH/$SLURM_JOB_ID
mkdir -p $SCM_TMPDIR
export SCM_USE_LOCAL_IMPI=yes
module purge
module load intel/19.0.4 intel-mpi/18.0.5
module load adf/2019.301

$ADFBIN/adf < methane_dimer_dispersion.inp > methane_dimer_dispersion.log
seff $SLURM_JOBID

The AMS-GUIs

The Graphical User Interfaces (GUIs) that are installed on Puhti can be used via NoMachine. For an even better user experience it is also possible to install the GUIs on your own workstation. For details contact CSC servicedesk@csc.fi . In order to manage remote jobs you need to set up an ssh key pair between your workstation and Puhti, for details see "Managing remote jobs". For Windows users there is a helpful video on how to do the setup. In both cases the actual calculations should be done as batch jobs. Example queuing settings that can be used in the GUI: Slurm settings

References

Depending on your usage, be careful to properly cite the AMS driver, used calculation engines as well as feature references. For details, see the relevant documentation

More information