AMS (Amsterdam Modeling Suite), originally named ADF (Amsterdam Density Functional), is the SCM Software for Chemistry and Materials. AMS offers powerful computational chemistry tools for many research areas such as homogeneous and heterogeneous catalysis, inorganic chemistry, heavy element chemistry, various types of spectroscopy, and biochemistry.
Compute Canada users have access to the full SCM module products:
Running AMS on Graham
ams module is installed on Graham only due to license restrictions. To check what versions are available use the
module spider command as follows:
[name@server $] module spider ams
For module commands, please see Using modules.
Graham uses the Slurm scheduler; for details about submitting jobs, see Running jobs.
Example scripts for a adf job
This H2O_adf.sh script is for a whole-node job.
#!/bin/bash #SBATCH --account=def-pi #SBATCH --nodes=1 #SBATCH --ntasks-per-node=32 # 1 node with all 32 cpus, MPI job #SBATCH --mem=0 # request all memory on node #SBATCH --time=00-01:00 # time (DD-HH:MM) #SBATCH --output=H2O_adf-%j.log # output .log file module unload openmpi module load ams/2020.102 bash H2O_adf.run # run the input script
This is the input file used in the script:
#!/bin/sh # This is a shell script for AMS2020 # You should use '$AMSBIN/ams' instead of '$ADFBIN/adf' AMS_JOBNAME=H2O_adf $AMSBIN/ams <<eor # Input options for the AMS driver: System Atoms O 0.000000 0.000000 0.000000 H 0.000000 -0.689440 -0.578509 H 0.000000 0.689440 -0.578509 End End Task GeometryOptimization GeometryOptimization Convergence gradients=1e-4 End # The input options for ADF, which are described in this manual, # should be specified in the 'Engine ADF' block: Engine ADF Basis Type TZP End XC GGA PBE End EndEngine eor
Example scripts for a band job
#!/bin/sh # The calculation of the electric field gradient is invoked by the EFG key block # Since Sn is quite an heavy atom we use the scalar relativistic option. $AMSBIN/ams <<eor Task SinglePoint System FractionalCoords True Lattice 3.8029 0.0 0.0 0.0 3.8029 0.0 0.0 0.0 4.8382 End Atoms O 0.0 0.0 0.0 O 0.5 0.5 0.0 Sn 0.0 0.5 0.2369 Sn 0.5 0.0 -0.2369 End End Engine Band Title SnO EFG NumericalQuality Basic ! Only for speed Tails bas=1e-8 ! Only for reproducibility with nr. of cores ! useful for Moessbauer spectroscopy: density and coulomb pot. at nuclei PropertiesAtNuclei End EFG Enabled True End Basis Type DZ Core none End EndEngine eor
The following slurm script is similar to the one used for a single adf run (H2O_adf.sh), except it's not a whole-node job.
#!/bin/bash #SBATCH --account=def-pi #SBATCH --nodes=1 #SBATCH --ntasks-per-node=16 # a 16 cpus MPI job #SBATCH --mem-per-cpu=3G # memory; 3G per cpu in this example #SBATCH --time=00-10:00 # time (DD-HH:MM) #SBATCH --output=SnO_EFG_band-%j.log module unload openmpi module load ams/2020.102 bash SnO_EFG_band.run # run the input file
- The input for AMS is different from ADF, the previous ADF input file will not run for the new AMS. Some examples can be found in /opt/software/ams/2020.102/examples/
- Except the output .log file, other files are all saved in a subdirectory AMS_JOBNAME.results. If AMS_JOBNAME is not defined in the input .run file, the default name is ams.results
- The restart file name is ams.rkf instead of the TAPE13 in previous ADF versions.
For more usage information, please check the manuals in SCM Support
Rendering over an SSH connection with X11 forwarding is very slow for GUI applications such as AMS-GUI. We recommend you use VNC to connect if you will be running AMS-GUI.
AMS can be run interactively in graphical mode on a Graham compute node (3hr time limit) over TigerVNC with these steps:
- Install a TigerVNC client on your desktop
- Connect to a compute node with vncviewer
module load ams
AMS can be run interactively in graphical mode on gra-vdi (no connection time limit) over TigerVNC with these steps: