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.
ERmod is software for calculating the free energy in soft, molecular aggregate. This program rapidly and accurately calculates the free energy of binding of a molecule in the aggregate through combination of the molecular dynamics simulation and the energy-representation theory of solvation. The solubility of a molecule can be determined with ERmod in arbitrary solvent including supercritical fluid and ionic liquid. Assessment is also possible for the binding strength and site of a molecule in micelle, lipid membrane or protein.
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.
An open-source application for molecular dynamics simulation of biomolecules, especially designed for massively parallel computing. This package enables us to perform efficient parallel calculation on parallel computers ranging from 100 to 20,000 cores. For preparation of calculation and analysis of orbits, it uses visualization software VMD. It supports file formats compatible with other applications such as AMBER and CHARMM, and can be used on various computing environments.
The fragment molecular orbital (FMO) method can efficiently do quantum-mechanical calculations of large molecular systems by splitting the whole system into small fragments. The FMO program is distributed within quantum-chemical program suite GAMESS-US. FMO can provide various information regarding the structure and function of biopolymers, such as the interaction between a protein and a ligand.
An open-source solver for the impurity problem based on the continuous-time quantum Monte Carlo method. Imaginary-time Green’s functions of the impurity Anderson model and the effective impurity model in the dynamical mean-field approximation can be calculated with high speed by using an efficient Monte Carlo algorithm. The main programs are written by C++, and can be called from Python scripts.
CCCM is a high-order CCM (coupled cluster method) code for lattice spin systems. It is possible to obtain the ground state and its energy of quantum spin systems in two or three dimensions.
A program package for physical properties related to magnetism. This application can evaluate various physical quantities of magnetics such as crystal fields, magnetic structures, thermodynamic quantities (magnetization, specific heat, etc.), and magnetic excitation. This package can also perform fitting analysis of neutron diffraction experiments and resonant X-ray diffraction experiments, and is helpful to experimentalists.
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 exact diagonalization package for a wide range of quantum lattice models (e.g. multi-orbital Hubbard model, Heisenberg model, Kondo lattice model). HΦ also supports the massively parallel computations. The Lanczos algorithm for obtaining the ground state and thermal pure quantum state method for finite-temperature calculations are implemented. In addition, dynamical Green’s functions can be calculated using Kω, which is a library of the shifted Krylov subspace method. It is possible to perform simulations for real-time evolution from ver. 3.0.