AMS/en

Introduction

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.

The full SCM module products are available: * ADF * ADF-GUI * BAND * BAND-GUI * DFTB * ReaxFF * COSMO-RS * QE-GUI * NBO6

Running AMS on Nibi

The ams module is installed on Nibi. The license is an Academic Computing Centre license owned by SHARCNET. You may not use the Software for consulting services nor for purposes that have a commercial nature. To check what versions are available, use the module spider command as follows:

module spider ams

For module commands, please see Using modules.

Job submission

The clusters use the Slurm scheduler; for details about submitting jobs, see Running jobs.

Example scripts for an AMS job

This H2O_adf.sh example script is to request 32 CPUs on one node. Please use a reasonable number of CPUs instead of simply running a full-node job on Nibi, unless you have demonstrated that your job can scale efficiently to 192 CPUs.

#!/bin/bash
#SBATCH --account=def-pi
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=32          # 32 cpus on 1 node, MPI job
#SBATCH --mem-per-cpu=3G              # memory per cpu
#SBATCH --time=00-01:00               # time (DD-HH:MM)
#SBATCH --output=H2O_adf-%j.log       # output .log file

module unload openmpi
module load ams/2025.102
export SCM_TMPDIR=$SLURM_TMPDIR      # use the local disk
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 AMS
# 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

Notes

Important AMS Usage Notes

1. 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/2025.102/examples/.
2. Except for 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.
3. 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.

Running AMS-GUI

Nibi

AMS can be run interactively in graphical mode on a Nibi compute node (8hr time limit) via OnDemand with these steps:

1. Log in to ondemand.sharcnet.ca
2. Select Nibi Desktop from Compute on the top.
3. Select your options (select 1 core for visualization purposes, don't select Enable VirtualGL) and press Launch.
4. Select Launch Nibi Desktop once your job starts.
5. Right-click on the desktop and pick Open it Terminal.
6. Pick MATE Terminal from the System Tools menu under the Applications menu.
7. module unload openmpi
8. module load ams
9. amsinput & (to make AMS input)
10. amsview & (for AMS result visualization)

If you need to select Enable VirtualGL for some other program that you are using, you will have to disable it for just AMS by starting it with LD_PRELOAD= amsinput.

Warning

OnDemand Nibi Desktop is intended for AMS-GUI applications, such as making input files and visualizing results. Please do not use it to run regular jobs or long interactive jobs. Select a single core and reasonable memory and runtime.