An application for molecular science simulation. This application covers not only traditional simulation methods implemented in existing applications but also a number of novel methods for quantum chemical calculation. It can perform ab-initio electronic state calculation for a few thousands atoms/molecules as well as trace calculation of transition states in chemical reaction for a few hundreds atoms/molecules. It can also perform high-efficient massively parallel computing on large-scale parallel computers such as the K-computer.
Payware for visualization of computational fluid dynamics and general numerical simulation. This application provides an integrated environment for two- and three- dimensional graph drawing, and supports interactive visualization of data with many options such as slices, contours, and stream traces. It also supports visualization of large-scale data and efficient comparison between many data sets.
Library for calculating Pfaffian (square root of determinant), which is defined for skew-symmetric matrices. Algorithms are implemented in several languages (Fortran, Python, Matlab, Mathematica) and users can choose favorite one. Interfaces for C are also provided.
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.
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.
2DMAT is a framework for applying a search algorithm to a direct problem solver to find the optimal solution. In version 1.0, for solving a direct problem, 2DMAT offers the wrapper of the solver for the total-reflection high-energy positron diffraction (TRHEPD) experiment. As algorithms, it offers the Nelder-Mead method, the grid search method, the Bayesian optimization method, and the replica exchange Monte Carlo method. Users can define original direct problem solvers or the search algorithms.
Fortran codes for computing the specified k-th eigenvalue and eigenvector for generalized symmetric definite eigenvalue problems. Sylvester’s law of inertia is employed as the fundamental principle in computations, and the sparse direct linear solver (MUMPS) is used in the main routine. By inputting Hamiltonian and its overlap matrices, user can compute electron’s energy and its wave function in the specified k-th energy level.