Open source library to record execution and communication time during specified regions in user’s program. C/C++ and Fortran API are provided. This can profile MPI & OpenMP hybrid parallel programs as well as serial ones.
PHYSBO is a Python library for researchers mainly in the materials science field to perform fast and scalable Bayesian optimization based on COMBO (Common Bayesian Optimization). Users can search the candidate with the largest objective function value from candidates listed in advance by using machine learning prediction. PHYSBO can handle a larger amount of data compared with standard implementations such as scikit-learn.
An application for three-dimensional visualization with the ray tracing method. This application can visualize arbitrary positions and shapes of objects such as spheres and cubes. It can visualize three-dimensional data obtained from computational fluid dynamics etc. by volume rendering. It can also be used for simple three-dimensional graphical simulator with macro functions.
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.
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 visualization of biopolymers. This application can visualize biopolymers by using its original command line and graphical user interface, more than 600 settings for visualization, and more than 20 visualization schemes. This application also supports more than 30 file formats such as PDB and multi-SDF, and can utilize sophisticated visualization methods such as the ray tracing.
An open-source application for analysis and visualization of two- and three-dimensional data. The function of this application can be used not only by interactive operation with three-dimensional display, but also by batch processing. This application supports various environments such as Windows, Mac, and Linux from a desktop PC to a supercomputer performing large scale parallel computation.
An open source library to calculate free energy in molecular dynamics simulation. It supports several famous molecular dynamics software packages such as Amber and Lammps.
Parsec is a DFT program package based on real space basis and norm-conserving pseudopotential.
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.