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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LAMMPS

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

A general-purpose open-source application for classical molecular dynamics simulation, distributed under the GPL license. This package can perform molecular dynamics calculation of various systems such as soft matters, solids, and mesoscopic systems. It can be used as a simulator of classical dynamics of realistic atoms as well as general model particles. It supports parallel computing through spatial divisions. Its codes are designed so that their modification and extension are easy.

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NWChem

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

An open-source application for general-purpose quantum chemical calculation, laying emphasis on excited states and time evolution. It is based on time-dependent density functional theory (TDDFT) and the QM/MM calculation. It enables efficient massive parallel computing up to one hundred thousands processes. It supports the relativistic effect and offers the basis choice between the Gaussian basis and the plane-wave basis.

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PIMD

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

An open-source application for molecular simulations. This application supports various methods such as classical and ab initio molecular dynamics, path integral simulations, replica exchange simulations, metadynamics, string method, surface hopping dynamics, QM/MM simulations, and so on. A hierarchical parallelization between molecular structures (replicas) and force fields (adiabatic potentials) enables fast and efficient computation.

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MateriApps Installer

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

A collection of shell scripts for installing open-source applications and tools for computational materials science to macOS, Linux PC, cluster workstations, and major supercomputer systems in Japan. Major applications are preinstalled to the nation-wide joint-use supercomputer system at Institute for Solid State Physics, University of Tokyo by using MateriApps Installer.

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