A set of python modules for modeling atomic structures, running simulations, and visualizing results. These modules provide interfaces for various application of first-principles calculation, classical molecular dynamics, and quantum chemical calculation through GUI, command line, or python scripts. The source code is available under the LGPL.
This application can produce input files of various applications for density functional theory (DFT) calculations via user-friendly parameter adjustment using three-dimensional computer graphics (3DCG) and graphical user interfaces (GUI). Input-file conversion between different applications is also possible.
An application for prediction of stable and metastable structures from a chemical composition. This application applies particle swarm optimization to predict material structures from results of the first-principles calculation by external packages (VASP, CASTEP, Quantum Espresso, GULP, SIESTA, CP2k). It has been applied to predict not only three-dimensional crystal structures, but also those of clusters and surfaces.
An application for structure prediction based on the genetic algorithm. This application can predict the structure and composition of stable phase of crystals, molecules, atomic clusters, and so on by using first-principles calculation and molecular dynamics. This application implements interfaces with various programs such as VASP, LAMMPS, MOPAC, GULP, JDFTx, etc, and runs efficiently on parallel computing architectures.
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.
Debian Live Linux System that contains OS, editors, materials science application software, visualization tools, etc. An environment needed to perform materials science simulations is provided as a one package. By booting up on VirtualBox virtual machine, one can start simulations, such as the first-principles calculation, molecular dynamics, quantum chemical calculation, lattice model calculation, etc, immediately.
A support application for preparing input files of molecular dynamics calculation. This application supports manual input of atomic coordinates and bond informations, reading files of protain structure database, and editing data by graphical user interface. It also implements various functions such as addition of hydrogen atoms and composition of data. and can treat a large number of atoms using only a moderate memory cost.
A pre/post-processing application for SIESTA and TranSIESTA. This application can calculate phonon frequencies, electron-phonon coupling, and contributions of inelastic scattering to the conductance. It also provides a Python interface for accessing data in the Hamiltonian output from SIESTA.
An application for data analysis of X-ray absorption fine structure (XAFS). By interactive operation using a command line, experimental data of XAFS can be analyzed by various analysis methods. This application also supports various useful functions such as high-speed Fourier analysis, fitting in the radial/k-space coordinates, and data plotting.
An open-source framework for execution management of numerical simulation. By registering target simulators, information at the time of execution (parameters, date and time, hostname, version of simulators, etc.) and calculation results are saved automatically on database. Job submission and browse of job status can be performed efficiently from web browsers.