An open-source application for visualization of atoms and molecules developed for molecular dynamics. This application supports a number of input file formats for molecular configration, and can perform visualization of three-dimensional atom configration as well as creation of a animation. The main feature of this application is that various useful analysis tools can be used by intuitive control of a graphical user interface (GUI).
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.
PAICS is a program of quantum chemical calculation. In this program, fragment molecular orbital (FMO) method is adopted, by which large molecules including biomolecular systems can be treated with several quantum chemical approaches including HF and MP2 methods. At the same time, PaicsView has been developed, which is a supporting program for making input files and analyzing calculation results.
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.
A structure database for proteins and nuclear acids. Three-dimensional structure data of proteins and nuclear acids (atomic coordinates determined experimentally by X-ray crystal analysis, NMR, etc.) can be downloaded. The data reposited in PDB are in the public domain, and can be accessed by everyone freely.
An open-source application for quantum chemical calculation. This package implements various methods for quantum chemical calculation such as Hartree-Fock approximation, density functional theory, coupled-cluster method, and CI (configuration interaction) method. The package is written in C++, and provides API for Python, by which users can perform for preparation of setting and execution of calculation.
A python library for materials analysis. Flexible classes for representation of materials are prepared, and data for crystal structures and various material properties can be handled efficiently. This application can performs analysis of phase diagrams, Pourbaix diagrams, diffusion analyses etc. as well as electronic structure analyses such as density of states and band structures. This software is being actively developed keeping close relation with Materials Project.
An application for ab initio quantum chemical calculation. This application can calculate molecular structures, chemical reactivity, frequency analysis, electron spectrum, and NMR spectrum with high accuracy. It implements the density functional theory, the Hartree-Fock(HF) method as well as recently developed methods such as the post-HF correlation method. It also has GUI for molecular modeling and a tool for preparation of input files.
An open-source application for first-principles molecular dynamics based on a pseudopotential method using plane bases. This application can perform electronic-state calculation and molecular dynamics employing the Car-Parrinello method. It implements MPI parallelization, which enables us to perform efficient parallel computing in various environments including large-scale parallel computers. The program is written in C++, and is distributed in source form under the GPL license.
An open-source application for obtaining optimized many-body wavefunctions expressed by matrix product states (MPS). By using a second-generation density matrix renormalization group (DMRG) algorithm, many-body wave functions can be efficiently optimized. The quantum-chemical operators are represented by matrix product operators (MPOs), which provides flexibility to accommodate various symmetries and relativistic effects.