Open source software for massively parallel quantum chemistry calculations. Energies and geometries of nano-sized molecules can be calculated without fragmentation. The program supports Hartree-Fock, density functional theory, and second-order Møller-Plesset perturbation theory calculations. The input format, execution method, and program structure are simple, and frequently used routines can be easily extracted.
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 general-purpose open-source application for classical molecular dynamics simulation, distributed under the GPL license. This package can perform molecular dynamics calculation of various systems such as soft matters, solids, and mesoscopic systems. It can be used as a simulator of classical dynamics of realistic atoms as well as general model particles. It supports parallel computing through spatial divisions. Its codes are designed so that their modification and extension are easy.
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.
Software package that implements Behler-Parinello type neural network potential. The package provides tools for training and evaluating potentials based on given structure-energy data. It also provides an interface with LAMMPS for performing molecular dynamics calculations.
An open-source application for quantum chemical calculation based on the density-matrix renormalization group (DMRG). For systems with a number of atomic orbitals, low-lying energy eigenvalues can be calculated in high accuracy of order of 1kcal/mol. This application is suitable especially to calculation of multi-orbital systems with one-dimensional topology such as chain-like or circular-like configuration of orbits.
An open-source multi-purpose application for modeling and visualizing molecules (biomolecules, in particular). This application has been developed for multi-scale molecular simulation, and also provides a simple GUI for AMBER and Gaussian. It also implements exchange of protein residues and the Pathways model for the electron transfer in proteins. It calls rasmol for visualization of atoms and molecules.
Libtetrabz is a library which perform efficiently the Brillouin-zone integration in the electronic structure calculation in a solid by using the tetrahedron method.
An open-source application for the first-principles calculation based on the all-electron method with localized bases. By adopting the full-potential LMTO method, high-speed electronic state calculation can be performed with a less number of bases compared with the standard all-electron method. There is no restriction on symmetries as in the LMTO-ASA method, and spin polarization and spin-orbit interaction can also be treated.
An exact diagonalization package for efficiently solving quantum spin 1/2 lattice models in almost fully spin-polarized sectors. QS3 can treat such systems with quite large system sizes, over 1000 sites. It supports calculations of wavenumber-dependence of energy-dispersion and dynamical spin structure factor.