AMS

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.

H2O_adf.sh

#!/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:

H2O_adf.run

#!/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

SnO_EFG_band.run

#!/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

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 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 on Nibi

AMS can be run graphically on Nibi using an OnDemand Compute Node Desktop as follows:

1. Log into ondemand.sharcnet.ca
2. Select Compute Node then Compute Desktop from the top menu pulldown
3. Specify Computers=1, Cores=1, GPU=None for visualization then press Launch
4. Once the Desktop changes from Queued to Running press Launch Nibi Desktop
5. When your Desktop starts click Applications -> System Tools -> MATE Terminal
6. module unload openmpi
7. module load ams, (loads the latest version)
8. export SCM_OPENGL_SOFTWARE=1 (enables software rendering)
9. Then execute either amsinput or amsview.

Alternative for GPU-enabled Desktops

If you specified GPU=t4 (15GB) when starting your OnDemand Nibi Desktop then instead do: LD_PRELOAD= amsinput or LD_PRELOAD= amsview

Tip

To select one or more atoms in the GUI, press SHIFT then click.