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AMS

The Amsterdam Modeling Suite (AMS) is a comprehensive suite of computational chemistry software. It comes with a graphical user interface, AMS-GUI that provides an intuitive way for setting up, running, and analyzing simulations.

Available

  • Puhti: ADF, Version 2024.102
  • Mahti: ADF, Version 2024.102

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.
  • Research groups which need other modules of the AMS suite can obtain a license for themselves to run the programs on the CSC computers.

Usage

Initialize AMS:

module load ams/2024.102

Example batch scripts

Note

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

#!/bin/bash
#SBATCH --partition=test
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=40      # MPI tasks per node
#SBATCH --account=yourproject     # insert here the project to be billed 
#SBATCH --time=00:15:00           # time as `hh:mm:ss`
#SBATCH --mem-per-cpu=1500        # requested memory per process in MB
module purge
module load ams/2024.102
export SCM_TMPDIR=$PWD/$SLURM_JOB_ID
mkdir -p $SCM_TMPDIR
# Create an example input file from the examples 
sed '1,4d;$d;/Print/,/End/d' $AMSHOME/examples/Benchmarks/ADF/Si35_TZ2P/Si35_TZ2P.run  > ./Si35_TZ2P.inp
"$AMSBIN/ams" < ./Si35_TZ2P.inp > ./Si35_TZ2P.log

#!/bin/bash
#SBATCH --partition=large
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=40      # MPI tasks per node
#SBATCH --account=yourproject     # insert here the project to be billed
#SBATCH --time=00:15:00           # time as `hh:mm:ss`
#SBATCH --mem-per-cpu=1500        # requested memory per process in MB
#SBATCH --gres=nvme:100           # requested local disk space in GB
module load ams/2024.102
export SCM_TMPDIR=$LOCAL_SCRATCH
# Create an example input file from the examples
sed '1,4d;$d;/Print/,/End/d' $AMSHOME/examples/Benchmarks/ADF/Si35_TZ2P/Si35_TZ2P.run  > ./Si35_TZ2P.inp
"$AMSBIN/ams" < ./Si35_TZ2P.inp > ./Si35_TZ2P.log

#!/bin/bash
#SBATCH --partition=medium
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=128 # MPI tasks per node
#SBATCH --account=yourproject # insert here the project to be billed
#SBATCH --time=00:20:00       # time as `hh:mm:ss`
module purge
module load ams/2024.102
export SCM_TMPDIR=$PWD/$SLURM_JOB_ID
mkdir -p $SCM_TMPDIR

# Create an example input file from the examples
sed '1,4d;$d;/Print/,/End/d' $AMSHOME/examples/Benchmarks/ADF/Si35_TZ2P/Si35_TZ2P.run  > ./Si35_TZ2P.inp
"$AMSBIN/ams" < ./Si35_TZ2P.inp > ./Si35_TZ2P.log

The AMS-GUI

AMS comes with an integrated Graphical User Interface, AMS-GUI that makes it easy to set up, run and analyze modelling tasks. You can test the GUI via the Puhti web interface, but for more extensive use we recommend installing the GUI on your own laptop/workstation. For detailed instructions, see the AMS-GUI documentation.

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 AMS documentation

More information