A collection of shell scripts for installing open-source applications and tools for computational materials science to macOS, Linux PC, cluster workstations, and major supercomputer systems in Japan. Major applications are preinstalled to the nation-wide joint-use supercomputer system at Institute for Solid State Physics, University of Tokyo by using MateriApps Installer.
Mm2cML is a web application that structure files can be generated from molecular model images. By carrying out three-dimensional reconstruction using OpenMVG and OpenMVS from molecular model images photographed by smartphones or digital cameras, and arranging atoms on the basis of them, users can obtain structure files (CML format) usable for molecular simulation. The simulation can be carried out on the basis of the structure examined using the molecular model in the real world.
An open-source application for pre- and post-processing for quantum chemistry calculation. This application can handle outputs from Gaussian, GAMESS, and MOPAC as well as the result of other applications via the Molden format. It supports many graphical interfaces such as Postscript, XWindows, VRML, and OpenGL, and performs visualization of molecular orbitals and electron density. It also produces animation videos of molecular vibration.
Tool for performing analytical continuation for many-body Green’s functions by using the maximum entropy method. From the data of the Green functions on the imaginary axis, users can obtain the values of the Green’s functions on the real axis. This tool supports the several different Green’s functions (Bozonic, Fermionic, anomalous, etc.).
An open-source application for molecular modeling and visualization. This application supports data formats of Gaussian, GAMESS, ADF, and Molden, and has various options for drawing such as orbital, electron density, solvent accessible surface, van der Waals radii, and so on. It implements high-speed and high-quality rendering technology, and runs on Windows, Mac, and Linux.
Payware for first-principles quantum chemical calculation. This application performs molecular orbital calculation based on Hartree-Fock approximation, density functional method, and post-HF methods such as MP, f12, multi-configuration SCF, and coupled cluster method. It also implements calculation by path-integral instanton, quantum Monte Carlo, and density-matrix renormalization group method.
MDACP (Molecular Dynamics code for Avogadro Challenge Project) is an efficient implementations of classical molecular dynamics (MD) method for the Lennard-Jones particle systems. MDACP Ver. 1.xx adopts flat-MPI and Ver. 2.xx adopts MPI+OpenMP hybrid parallelization.
An open-source application for semi-empirical quantum chemical calculation based on NDDO (neglect of diatomic differential overlap) approximation. This program calculates, for a given molecule or a crystal, molecular orbits and atomic forces, as well as vibration spectra, thermal quantities (heat of formation etc.), isotopic exchange effect, force constant, and so on. It can also treat radicals and ions.
An application for atomic multiplet calculation used in X-ray spectroscopies. This application consists of several calculation modules and graphical user interface, and can perform multiplet calculation of atoms. It can take into account effect of crystal fields and charge transfer, both of which are important in transition-metal compounds, and can provide useful information to interpret experimental results obtained in various inner-shell electron X-ray spectroscopies.
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.