Atomsk
The Swiss-army knife of atomic simulations
The Swiss-army knife of atomic simulations
Atomsk is not alone! A lot of very useful tools exist out there. Below is a list of other codes that can create, transform, visualize, and/or convert files for atomic systems.
OpenBabel
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.
Pymatgen
Pymatgen (Python Materials Genomics) is a robust, open-source Python library for materials analysis.
Aten
Aten is a tool to create, edit, and visualise coordinates.
AtomMan
AtomMan: the Atomistic Manipulation Toolkit is a Python library for interacting with large-scale atomic systems. The focus of the package is to facilitate the rapid design and development of simulations that are fully documented and easily adaptable to new potentials/atomic arrangements/etc.
ASE (Atomic Simulation Environment)
ASE provides Python modules for manipulating atoms, analyzing simulations, visualization etc.
Avogadro
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
Babel
A Fortran program to insert dislocation in atomistic simulations, calculate their elastic energy, extract the Nye tensors, and much more...
CIF2CELL
CIF2Cell is a tool to generate the geometrical setup for various electronic structure codes from a CIF (Crystallographic Information Framework) file.
Moltemplate
Moltemplate is a cross-platform text-based molecule builder for LAMMPS. It is typically used for building coarse-grained toy molecular models.
nanoSCULPT
NanoSCULPT is a tool/methodology to generate complex and realistic structures for atomistic simulations.
Packmol
Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations.
Pizza.py Toolkit
Pizza.py is a loosely integrated collection of tools, many of which provide pre- and post-processing capability for the LAMMPS molecular dynamics, ChemCell cell modeling, and SPPARKS kinetic Monte Carlo packages.
TopoTools
TopoTools is a VMD plugin for manipulating topology information.
AtomEye
AtomEye is an atomistic configuration viewer.
ddplot
Ddplot visualizes dislocations in crystals using the so-called differential displacement maps.
gdis
GDIS is a scientific visualization program for the display, manipulation, and analysis of isolated molecules and periodic structures.
Jmol
Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry.
Open RasMol
Open RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules.
OVITO (Open VIsualization TOol)
OVITO is a scientific visualization and analysis software for atomistic simulation data.
VESTA (Visualization for Electronic and STructure Analysis)
VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies.
VMD (Visual Molecular Dynamics)
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
XCrySDen (X-window CRYstalline Structures and DENsities)
XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.
XMol
XMol is a utility for creating and viewing graphic images of molecules.
