A collection of C++ interfaces for simulation of mesoscale properties based on grid data. By using provided header files, one can easily construct programs for simulation of various phenomena such as solidification, crystal growth, and spinodal decomposition, based on a Monte Carlo method, cellar automaton, and a phase-field method. This interface supports parallel computing by MPI, and also provides converters of output files for visualization software such as ParaView.
An open-source application for modeling, visualization, and analysis of biomolecule systems such as proteins, nuclear acids, and lipid bilayers. This application visualizes biomolecules by reading Protein Data Bank (PDB) files. It supports various options in rendering and coloring of molecules, and also can animate the result of a molecular dynamics simulation.
NetKet is an open-source project delivering cutting-edge methods for the study of many-body quantum systems with artificial neural networks and machine learning techniques. Users can perform machine learning algorithms to find the ground-state of many-body Hamiltonians such as supervised learning of a given state and optimization of neural network states by using the variational Monte Carlo method.
A python tool for generating symmetry-inequivalent supercell structures from a CIF file containing site occupancy information. SHRY can be used as a command-line tool as well as a module in a python script.
Web server that offers various crystallographic tools free of charge. The server offers over 70 tools/utilities related to space group, magnetic space group, representation theory, scattering theory, etc. The tools are accessed through a web interface.
An open-source application for visualization of many-particle systems. With simple operation by graphical user interface (GUI) or by command line, this application can visualize particle positions obtained from molecular dynamics simulation as well as three-dimensional scalar quantities such as potential energies. It supports various display options on kinds and shapes of particles, and can also visualize bond formation between particles.
An open-source application for simulation of one-dimensional interacting electron models based on a tensor product wavefunction method. This application supports not only electronic models but also spin and bosonic models, and can evaluate various physical quantities for ground states and low-lying excited states. This application also supports time evolution, and can treat models with long-range interactions.
EDlib is an app for performing finite-temperature exact diagonalizations for quantum many-body systems. EDlib is written in C++ and it is possible to obtain finite-temperature properties such as the one-body Green’s function in the Hubbard model and the Anderson model.
FORTRAN-based software package developed by the Behler Group for implementing Behler-Parinello neural network potentials. Potentials can be constructed, evaluated, and used for molecular dynamics simulations using LAMMPS. The newest generation of neural network potentials that take into account long-range electrostatic interactions are implemented.
An open-source application for simulation based on the density-matrix renormalization group (DMRG). This application can perform high-speed calculation of low-dimensional quantum systems with high accuracy. It implements generic programming techniques in the C++ language, and can easily extend simulation to new models and geometries. It is developed putting emphasis on user-friendly interfaces and low dependences on environments.