Introduction¶

AMS (Amsterdam Modeling Suite), originally named ADF, 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:

name@server $ 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.md].

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.

```bash 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:

```text 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¶

```bash 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¶

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/
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

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:

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

Usage Guidelines

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.