A payware for modeling and visualizing molecules. This software includes a standard editor, ChemDraw, and can perform modeling from chemical structural formula. It implements structure optimization and molecular dynamics by molecular mechanics, and provides useful GUIs for MOPAC, Jaguar, GAMESS, and Gaussian. It can also perform spectroscopy analysis. It is included in high-end packages such as ChemBioOffice and ChemOffice.
Application for specifying and simulating lattice kinetic Monte Carlo models. It has been developed in the context of simulating heterogeneous catalysis. Models can be specified using provided python APIs or through a simple GUI.
An open-source application for all-electron first-principles calculation based on augmented plane-wave basis. It performs electronic-state calculation such as band calculation of solids and structure optimization. The all-electron method, which treats core electrons explicitly, improves accuracy compared with pseudo-potential methods. This package can also treat strong electronic correlations by combining electronic-state calculation with the dynamical mean-field approximation.
2DMAT is a framework for applying a search algorithm to a direct problem solver to find the optimal solution. In version 1.0, for solving a direct problem, 2DMAT offers the wrapper of the solver for the total-reflection high-energy positron diffraction (TRHEPD) experiment. As algorithms, it offers the Nelder-Mead method, the grid search method, the Bayesian optimization method, and the replica exchange Monte Carlo method. Users can define original direct problem solvers or the search algorithms.
Software package to implement Behler-Parinello neural network potentials. Potentials can be trained from structure-energy/ interatomic forces/stress data, and molecular dynamics calculations using LAMMPS can also be performed using learned potentials. A prediction uncertainty measure can also be calculated simultaneously.
Fitting data to a scaling law of critical phenomena, we automatically estimate critical point and indices. Since Bayesian method is flexible, we can use all data in a critical region.
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.
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 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.
An open-source application for first-principles calculation utilizing pseudo-potentials and plane-wave basis sets. This application is capable of performing electronic structure calculations of a wide range of physical systems such as crystals and surfaces/interfaces. It supports structure relaxation, phonon-dispersion calculation, and molecular dynamics simulation, and can deal with systems with the spin-orbit interaction.