Computational Chemistry and Material Science¶
ABINIT¶
ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be computed within the Many-Body Perturbation Theory (the GW approximation and the Bethe-Salpeter equation), and Time-Dependent Density Functional Theory (for molecules). In addition to the main ABINIT code, different utility programs are provided.
Licensing Terms and Conditions
GNU General Public License License
List available versions
module avail abinit
CP2K¶
CP2K is a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. It provides a general framework for different methods such as e.g., density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) and classical pair and many-body potentials.
Key characteristics of CP2K:
- Fist: classical molecular dynamics
- Kim-Gordon Models
- Quickstep: Density functional calculations
Licensing Terms and Conditions
The sources of CP2K are free for all users (GPL license), and all versions of the code are available from the CP2K SVN repository.
Publications of results obtained with CP2K should acknowledge its use by an appropriate citation (see CP2K Homepage).
Run
List available versions
module avail cp2k
module load cp2k
DALTON¶
The Dalton suite consists of two separate executables, Dalton and LSDalton. The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory, whereas LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilites. Any published work arising from use of one of the programs must acknowledge that by a proper reference. The following list of capabilities of the Dalton and LSDalton programs should give you some indication of whether or not the Dalton suite is able to meet your requirements.
List available versions
module avail dalton
module load dalton
GROMACS¶
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
Licensing Terms and Conditions
Gromacs is a joint effort, with contributions from developers around the world: users agree to acknowledge use of GROMACS in any reports or publications of results obtained with the Software (see GROMACS Homepage for details).
Usage
List available versions
module avail gromacs
module load gromacs
Usage GPU
module load gromacs/2025.0
#SBATCH --cpus-per-task=1
#SBATCH --ntasks-per-node=20
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
srun gmx_mpi_cuda -s ... -gpu_id=00000000001111111111 -ntomp 1 -.......
or
#SBATCH --cpus-per-task=10
#SBATCH --ntasks-per-node=2
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
srun gmx_mpi_cuda -s ... -gpu_id=01 -ntomp 10 -.......
The argument of -gpu_id is a string of digits (without delimiter) representing device id-s of the GPUs to be used. For example, “01” specifies using GPUs 0 and 1 in the first and second PP ranks per compute node respectively. To select different sets of GPU-s on different nodes of a compute cluster, use the GMX_GPU_ID environment variable instead. The format for GMX_GPU_ID is identical to -gpu_id, with the difference that an environment variable can have different values on different compute nodes. Multiple MPI ranks on each node can share GPUs. This is accomplished by specifying the id(s) of the GPU(s) multiple times, e.g. “0011” for four ranks sharing two GPUs in this node. This works within a single simulation, or a multi-simulation, with any form of MPI.
http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html
GPAW¶
GPAW: DFT and beyond within the projector-augmented wave method GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). The wave functions can be described with:
Plane-waves (pw) Real-space uniform grids, multigrid methods and the finite-difference approximation (fd) Atom-centered basis-functions (lcao)
List available versions
module avail gpaw
module load gpaw
LAMMPS¶
LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using a variety of force fields and boundary conditions. The current version of LAMMPS is written in C++.
Licensing Terms and Conditions
LAMMPS is a freely-available open-source code, distributed under the terms of the GNU Public License.
List available versions
module avail lammps
module load lammps
Usage GPU
srun lmp_hybrid_GPU -sf gpu -pk gpu 2 -in in.script
LIGGGHTS¶
https://www.cfdem.com/liggghtsr-open-source-discrete-element-method-particle-simulation-code
LIGGGHTS(R)-PUBLIC is an Open Source Discrete Element Method Particle Simulation Software, distributed by DCS Computing GmbH, Linz, Austria. LIGGGHTS (R) and CFDEM(R) are registered trade marks of DCS Computing GmbH, the producer of the LIGGGHTS (R) software and the CFDEM(R)coupling software
Licensing Terms and Conditions
List available versions
module avail liggghts
module load liggghts
LSDALTON¶
The Dalton suite consists of two separate executables, Dalton and LSDalton. The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory, whereas LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilites. Any published work arising from use of one of the programs must acknowledge that by a proper reference. The following list of capabilities of the Dalton and LSDalton programs should give you some indication of whether or not the Dalton suite is able to meet your requirements.
List available versions
module avail lsdalton
module load lsdalton
MOLDEN¶
https://www.theochem.ru.nl/molden/
Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format. Molden reads all the required information from the GAMESS / GAUSSIAN outputfile. Molden is capable of displaying Molecular Orbitals, the electron density and the Molecular minus Atomic density. Either the spherically averaged atomic density or the oriented ground state atomic density can be subtracted for a number of standard basis sets.
Licensing Terms and Conditions
List available versions
module avail molden
module load molden
NAMD¶
http://www.ks.uiuc.edu/Research/namd/
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on [Charm++][charm++] parallel objects, NAMD scales to hundreds of cores for typical simulations and uses the molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.
Licensing Terms and Conditions
NAMD is distributed free of charge with source code. Users agree to acknowledge use of NAMD in any reports or publications of results obtained with the Software (see NAMD Homepage for details).
Run
List available versions
- multicore: distributed + shared memory
- multicore-gpu: distributed + shared memory + GPU
- purempi: distributed memory
module avail namd
Usage GPU
#!/bin/ -l
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --cpus-per-task=4
#SBATCH -p gpu
#SBATCH --gres=gpu:1g.10gb:1
module purge
module load fftw/3.3.10 cuda/11.8 namd/3.0.1/multicore-gpu
PPN=`expr $SLURM_CPUS_PER_TASK - 1`
P="$(($PPN * $SLURM_NNODES * $SLURM_NTASKS_PER_NODE ))"
PROCSPERNODE="$(($SLURM_CPUS_PER_TASK * $SLURM_NTASKS_PER_NODE))"
totalcores=`echo "$SLURM_NNODES*$SLURM_NTASKS_PER_NODE*$SLURM_CPUS_PER_TASK" | bc -l`
for n in `echo $SLURM_NODELIST | scontrol show hostnames`; do echo "host $n ++cpus $PROCSPERNODE" >> nodelist.$SLURM_JOB_ID
done;
NAMDEXE=`which namd2_gpu`
charmrun_gpu ++mpiexec ++p $P ++ppn $PPN ++nodelist ./nodelist.$SLURM_JOB_ID $NAMDEXE +devices $CUDA_VISIBLE_DEVICES input.namd > logfile
rm -f nodelist.$SLURM_JOB_ID
NWChem¶
http://www.nwchem-sw.org/index.php/Main_Page
NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources. NWChem has been developed by the Molecular Sciences Software group of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). Most of the implementation has been funded by the EMSL Construction Project.
Licensing Terms and Conditions
NWChem is available free of charge, subject to the terms and conditions of the EMSL Software User Agreement (see NWChem Homepage for details).
Run
List available versions
module avail nwchem
module load nwchem
#!/bin/bash -l
#SBATCH --nodes=2
module purge
module load oneAPI/2025.0.1 tbb/2022.0 compiler-rt/2025.0.4 mkl/2025.0 openmpi/4.1.8/gnu nwchem/7.2.3
nwchem input.nw > output.nwout
OPENBABEL¶
https://openbabel.org/index.html
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
Licensing Terms and Conditions
List available versions
module avail openbabel
module load openbabel
Quantum ESPRESSO¶
http://www.quantum-espresso.org/
Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials:
PWscf (Plane-Wave Self-Consistent Field) FPMD (First Principles Molecular Dynamics) CP (Car-Parrinello) Licensing Terms and Conditions
Quantum ESPRESSO is an Open Source distribution initiative of the DEMOCRITOS National Simulation Center(Trieste) and SISSA (Trieste), in collaboration with CINECA National Supercomputing Center, the Ecole Polytechnique Fédérale de Lausanne, Université Pierre et Marie Curie, Princeton University, and Oxford University. Scientific work done using Quantum ESPRESSO should contain an explicit acknowledgment and reference to the main papers (see Quantum Espresso Homepage for the details).
Run
List available versions
module avail quantum-espresso
module load quantum-espresso