DISCUS

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

An open source application to simulate crystal structures and to calculate and refine against diffraction pattern and the pair distribution function. A special emphasis placed is on the simulation of materials with disorder and the package provides many tools to create and distribute defects throughout the crystal. Another strong feature is the simulation of nanoparticles.

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OVITO

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

An open-source application for visualization of atoms and molecules developed for molecular dynamics. This application supports a number of input file formats for molecular configration, and can perform visualization of three-dimensional atom configration as well as creation of a animation. The main feature of this application is that various useful analysis tools can be used by intuitive control of a graphical user interface (GUI).

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EVO

  • Level of openness 3 ★★★
  • Document quality 1 ★☆☆

An application for structure prediction based on the evolutionary algorithm. From an input of the atomic position in a unit cell and possible elements at each atomic position, this application predicts the stable structure and composition from the first-principles calculation and molecular dynamics in combination with the evolutionary algorithm. This application is written in Python, and uses Quantum ESPRESSO and GULP as an external program.

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Open Babel

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

An open-source application for translating chemical structure format files. More than 110 formats are supported. This application is actively being developed taking into account use and construction of database and application to infomational technology in chemistry (chemoinformatics). A graphical user interface is alsp provided for Windows.

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CrySPY

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

CrySPY is a crystal structure prediction tool by utilizing first-principles calculations and a classical MD program. Only by inputting chemical composition, crystal structures can be automatically generated and searched. In ver. 0.6.1, random search, Bayesian optimization, and LAQA are available as searching algorithms. CrySPY is interfaced with VASP, Quantum ESPRESSO, and LAMMPS.

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HOOMD-blue

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

An open-source multi-purpose application for many-particle simulation. This application prepares various kinds of statistical methods and potentials, and can perform simulation of rigid-body mechanics, Langevin dynamics, dissipative-particle dynamics, nonequilibrium molecular dynamics, and so on. It prepares python scripts for production of initial conditions, job submission, and analysis of results.

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GENESIS

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

An open-source application for molecular dynamics simulation of biomolecules. This application is optimized for massive parallel computing environments such as the K-computer, and can perform high-speed molecular dynamical simulation of proteins and biomolecules. This application supports both all atoms calculation and coarse-grained model calculation, and can treat extended ensemble such as a replica exchange method. This code is released under GPL license.

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MDACP

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

MDACP (Molecular Dynamics code for Avogadro Challenge Project) is an efficient implementations of classical molecular dynamics (MD) method for the Lennard-Jones particle systems. MDACP Ver. 1.xx adopts flat-MPI and Ver. 2.xx adopts MPI+OpenMP hybrid parallelization.

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OpenKIM

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

Open-source tools and a database for molecular simulation. Data of molecular models (interatomic potentials and force fields), result data of molecular simulation, and test tools can be downloaded freely. API (Application Programming Interface) for exchanging information between atomistic simulation codes and interatomic models is also provided.

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MARBLE

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

An open-source application for molecular dynamics to simulate biopolymers such as proteins and nuclear acids. This application can perform high-speed molecular dynamics simulation by hybrid parallel computing maintaining high-accuracy energy conservation. This application also support high-speed calculation of long-range interaction based on the particle mesh Ewald method. The code is released under GPL lisense.

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