AMS/ADF

The Amsterdam Modeling Suite (AMS) is an integrated quantum chemistry and materials modeling software package developed by SCM. It provides a flexible and unified simulation framework for performing electronic-structure calculations, molecular property predictions, and spectroscopy simulations across a wide range of molecular and condensed-phase systems. Within the AMS, the Amsterdam Density Functional (ADF) program serves as a dedicated quantum chemistry engine responsible for carrying out Density Functional Theory (DFT) calculations.

Installed Versions

AMS 2023.101

Instructions can be accessed from AMS/ADF Manual

Input Example

The following AMS input (h2o.ams.in) performs a geometry optimization of a water molecule using DFT with the PBE functional and the TZP basis set, and subsequently computes the vibrational normal modes (frequency analysis) at the optimized structure:

task GeometryOptimization

System
 Atoms
   O   0.000   0.000   0.000
   H   0.758   0.000   0.504
   H  -0.758   0.000   0.504
 End
End

Properties
 NormalModes Yes
End

Engine ADF
 Basis
   Type TZP
 End

 XC
   GGA PBE
 End
EndEngine

Some AMS builds may be sensitive to keyword capitalization (e.g., Task vs task). The batch script provided below automatically normalizes this to avoid parser errors.

Batch Submission (SLURM Script for AMS/ADF)

To run AMS/ADF calculations in batch mode, create a SLURM submission script (subADF.sh) such as:

#!/bin/bash
#SBATCH --job-name=AMS_ADF
#SBATCH --partition=cpu
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --time=00:10:00
#SBATCH --mem=4G
#SBATCH --output=ams.%j.out
#SBATCH --error=ams.%j.err

set -euo pipefail

# -------- Input --------
INPUT_ABS="${1:-h2o.ams.in}"
INPUT_ABS="$(realpath "$INPUT_ABS")"

# -------- Modules / Environment --------
module purge 2>/dev/null || true
module load intel/mpi 2>/dev/null || true

# Initialize scratch and results directories
export SCM_TMPDIR="${SCM_TMPDIR:-/tmp/$USER/ams.$SLURM_JOB_ID}"
export SCM_RESULTSDIR="${SCM_RESULTSDIR:-$PWD/${SLURM_JOB_ID}.results}"
mkdir -p "$SCM_TMPDIR" "$SCM_RESULTSDIR"

# Load AMS environment
source /opt/software/packages/ams2023.101/amsbashrc.sh

export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"

# Explicit AMS executable setup
export AMSBIN="/opt/software/packages/ams2023.101/bin"
export AMSEXE="$AMSBIN/ams.exe"
export AMS_JOBNAME="job_${SLURM_JOB_ID}"
export SCM_RUNNAME="$AMS_JOBNAME"
export SCM_RESULTSDIR="$PWD/${SLURM_JOB_ID}.results"
mkdir -p "$SCM_RESULTSDIR"

# -------- Sanity Prints --------
echo "HOST=$(hostname)"
echo "PWD=$PWD"
echo "INPUT_ABS=$INPUT_ABS"
echo "AMSEXE=$AMSEXE"
echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
echo "SCM_TMPDIR=$SCM_TMPDIR"
echo "SCM_RESULTSDIR=$SCM_RESULTSDIR"

# -------- Keyword Normalization --------
sed -i '1s/^Task /task /' "$INPUT_ABS"

echo "=== Input Preview ==="
head -n 40 "$INPUT_ABS"

# -------- Run AMS --------
echo "=== Running AMS ==="

set +e
srun --mpi=pmix_v5 "$AMSEXE" < "$INPUT_ABS" \
    > "${SLURM_JOB_ID}.stdout" \
    2> "${SLURM_JOB_ID}.stderr"
RC=$?
set -e

echo "Return code = $RC"

# -------- Post-processing --------
echo "=== Results Directory ==="
ls -lah "$SCM_RESULTSDIR"

echo "=== Key Output Files ==="
find "$SCM_RESULTSDIR" -maxdepth 1 -type f \
    \( -name "ams.log" -o -name "*.rkf" -o -name "adf.rkf" -o -name "results.xml" \) \
    -ls

# Optional scratch cleanup
rm -rf "$SCM_TMPDIR"

exit "$RC"

Submitting the Job

To submit with an AMS input:

sbatch subADF.sh h2o.ams.in

Typical AMS/ADF Output Files

Results are written by default to <JOBID>.results/

File	Content	Visualization Tools
`ams.log`	Plain text log file containing SCF convergence, runtime messages, and job progress.	Text editor, `grep`
`adf.rkf`	Main binary results database produced by the ADF engine (energies, orbitals, densities, properties).	AMSview, `rkfread`, AMS Python API
`*.rkf`	Additional binary RKF databases for extended modules (vibrations, thermodynamics, trajectories).	`rkfinfo`, `rkfread`
`results.xml`	Structured XML summary of key results for interoperability and workflow integration.	XML parsers, workflow tools

How to Cite AMS/ADF

ADF2023.1, SCM Theoretical Chemistry, Vrije Universiteit, Amsterdam, The Netherlands, http://www.scm.com. There is no corresponding record for this reference.

te Velde, G.; Bickelhaupt, F. M.; Baerends, E. J.; Fonseca Guerra, C.; van Gisbergen, S. J. A.; Snijders, J. G.; Ziegler, T. Chemistry with ADF. J. Comput. Chem. 2001, 22, 931– 967, DOI: 10.1002/jcc.1056 (https://onlinelibrary.wiley.com/doi/10.1002/jcc.1056)

Last update by Milán SZŐRI: 2026-01-27