kmos

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

Application for specifying and simulating lattice kinetic Monte Carlo models. It has been developed in the context of simulating heterogeneous catalysis. Models can be specified using provided python APIs or through a simple GUI.

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LOBSTER

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

A post-processor of first-principles calculations for performing COHP (crystal orbital Hamilton population) and COOP (crystal orbital overlap population) chemical bonding analysis. It works with VASP, ABINIT and Quantum ESPRESSO output. The program is provided under an academic-only license.

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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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DeePMD-kit

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

Python/C++ based software package that employs deep learning techniques for construction of interatomic potentials. It implements the Deep Potential, which defines atomic environment descriptors with respect to a local reference frame. The output of many first-principles and molecular dynamics applications can be used as training data, and the trained potentials can be used for molecular dynamics calculations using LAMMPS and path integral molecular dynamics calculations using i-PI.

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BigDFT

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

An open-source application for first-principles calculation based on pseudopotential and wavelet basis. Electronic state calculation of massive systems is performed with high accuracy and high efficiency by using adaptive mesh. Parallel computing by MPI, OpenMP, and GPU is also supported.

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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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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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wxMacMolPlt

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

An open-source application for visualization developed for input and output of GAMESS. This application supports various types of input formats such as GAMESS, XYZ, MolDel, pdb, and CML as well as input by GUI and the Z-matrix format. It can visualize molecular orbitals, electron densities, electrostatic potentials, and normal modes, and can output results into various formats.

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TeNeS

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

A solver program for two dimensional quantum lattice model based on a projected entangled pair state wavefunction and the corner transfer matrix renormalization group method.
This works on a massively parallel machine because tensor operations are OpenMP/MPI parallelized.

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PubChem

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

Open Chemistry database that has been in operation since 2004 under the National Institutes of Health (NIH) in the United States. It mainly targets data for small molecules, but information on large molecules such as lipids and peptides are also collected. The database can be accessed via web browser or PUG REST API. The data can be also downloaded from an FTP site.

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