J-OCTA

  • Level of openness 0 ☆☆☆
  • Document quality 3 ★★★

A unified application for soft materials simulation. This is a commercial application based on OCTA, and includes modeling/analysis tools for individual simulation engines, use-case databases, tools for structure-property relationship analysis as well as basic functions of OCTA. In particular, VSOP, an original solver for molecular dynamics, is added for fast simulation by MPI parallel computing.

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MateriApps LIVE!

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

Debian Live Linux System that contains OS, editors, materials science application software, visualization tools, etc. An environment needed to perform materials science simulations is provided as a one package. By booting up on VirtualBox virtual machine, one can start simulations, such as the first-principles calculation, molecular dynamics, quantum chemical calculation, lattice model calculation, etc, immediately.

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OCTA

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

OCTA is an integrated simulation system for soft materials developed by the joint project of industry and academia funded by Ministry of Economy, Trade and Industry(METI), Japan. OCTA consists of four simulation engines named COGNAC(Molecular dynamics simulation), PASTA(rheology simulation), SUSHI(mean field theory), MUFFIN(continuum theory) and a simulation platform (GOURMET).

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Harlem

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

An open-source multi-purpose application for modeling and visualizing molecules (biomolecules, in particular). This application has been developed for multi-scale molecular simulation, and also provides a simple GUI for AMBER and Gaussian. It also implements exchange of protein residues and the Pathways model for the electron transfer in proteins. It calls rasmol for visualization of atoms and molecules.

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NequIP

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

Open source software for building and using machine learning potentials based on E(3)-equivariant graph neural networks, which can be trained on output files of simulation codes that can be read by ASE. Molecular dynamics calculations with LAMMPS can be performed using the trained potentials.

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GASP

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

An application for structure prediction based on the genetic algorithm. This application can predict the structure and composition of stable phase of crystals, molecules, atomic clusters, and so on by using first-principles calculation and molecular dynamics. This application implements interfaces with various programs such as VASP, LAMMPS, MOPAC, GULP, JDFTx, etc, and runs efficiently on parallel computing architectures.

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Allegro

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

Open source software for constructing the Allegro potential model based on E(3)-equivariant graph neural networks and using the potential model for molecular dynamics simulations. The code depends on NequIP and can be run in a similar manner. Allegro scales better than NequIP since it doesn’t rely on message passing and the architecture is strictly local with respect to atom-wise environments.

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NAP

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

A group of applications that perform molecular dynamics, hybrid quantum/classical mechanical simulation, search of chemical reaction path by the nudged elastic band method, and potential parameter fitting. The molecular dynamics code includes interatomic potentials for several metals and semiconductors, and is capable of parallel computation based of spatial decomposition.

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pacemaker

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

Software tool for constructing interatomic potentials based on nonlinear atomic cluster expansion. It requires the user to either prepare a fitting dataset based on pandas and ASE, or it can automatically extract data from VASP calculation results. The obtained potentials can be used for molecular dynamics simulations using LAMMPS, and it also provides the capability to calculate extrapolation grades for on-the-fly active learning.

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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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