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 application for adding a function of the replica exchange method to the existing applications for molecular dynamics simulation such as MODYLAS, AMBER, and CHARMM. Without changing original programs of molecular dynamics, the replica exchange method can be implemented easily. This application also shows high performance in massive parallel computing by the K-computer.
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 application for calculating transport coefficients based on the Boltzman equation. Within the relaxation time approximation, transport coefficients such as the Hall coefficient and the Seebeck coefficient can be evaluated from the output of the first principles calculation applications (Wien2k, ABINIT, SIESTA, quantum ESPRESSO, VASP). If users can measure relaxation time experimentally, electric conductivity can also be evaluated.
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.
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 application for evaluating superconducting gaps from resutls of the first-principles calculation by Quantum ESPRESSO. By calculating electron-phonon interaction and screened Coulomb interaction from the first-principles calculation, superconducting gaps can be obtained from the gap equation. Quasiparticle densities of states and ultrasonic attenuation rates can also be calculated.
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.
A package including patches and scripts for adding transition-state calculation to the first-principles calculation application VASP. This package adds new functions to VASP such as calculation of reaction paths, transition-state structures, and rate constants, as well as a set of scripts for setting up calculations and analyzing results. A program for the Bader analysis for atomic charge assignment is also included.
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.