A simple open-source application for visualization compatible to Protein Data Bank (PDB) format. This application also supports other formats such as Sybyl, Molden, Mopac, and CHARMM. It is a pioneering piece of software as an interactive PDB viewer.
An open-source library for machine learning. Various functions on deep learning based on neural network can be used by this package. This package is especially customised for image identification, and a number of sample codes are prepared. Users can also use pre-trained models, which are open in Caffe Model Zoo. Since this package is written in C++, high-speed operation is realised.
An open-source application for dynamical simulation of open quantum systems. It supports a wide range of Hamiltonians such as quantum optics, ion traps, and superconducting circuits. The time evolution of quantum states is evaluated by a master equation. These calculation library can be called from Python via a user-friendly interface.
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.
ERmod is software for calculating the free energy in soft, molecular aggregate. This program rapidly and accurately calculates the free energy of binding of a molecule in the aggregate through combination of the molecular dynamics simulation and the energy-representation theory of solvation. The solubility of a molecule can be determined with ERmod in arbitrary solvent including supercritical fluid and ionic liquid. Assessment is also possible for the binding strength and site of a molecule in micelle, lipid membrane or protein.
An exact diagonalization package for a wide range of quantum lattice models (e.g. multi-orbital Hubbard model, Heisenberg model, Kondo lattice model). HΦ also supports the massively parallel computations. The Lanczos algorithm for obtaining the ground state and thermal pure quantum state method for finite-temperature calculations are implemented. In addition, dynamical Green’s functions can be calculated using Kω, which is a library of the shifted Krylov subspace method. It is possible to perform simulations for real-time evolution from ver. 3.0.
A first principles calculation program using all electron mixture based approach. It targets broad physical systems such as isolated systems, surfaces and interfaces, and crystals, and it calculates all electronic states from core electrons to valence electrons. It deals with calculation methods such as the GW method, and also deals with parallel calculations. It can execute with high accuracy molecular dynamics calculations for electronic excited states based on time dependent density functional theory.
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.
An open source application implementing path-integral Monte Carlo method based on Stochastic Green function method. Finite temperature calculation of extended Bose Hubbard model and Heisenberg model with finite field can be treated. JSON and YAML formats are adopted for data I/O.
An open-source library for machine learning. Various functions on machine learning/deep learning are implemented in this package. Using flexible user-friendly description, various types of networks from simple to complex ones can be implemented. GPGPU parallel computation based on CUDA is also supported.