Software tool for constructing interatomic potentials based on nonlinear atomic cluster expansion. It requires the user to either prepare a fitting dataset based on pandas and ASE, or it can automatically extract data from VASP calculation results. The obtained potentials can be used for molecular dynamics simulations using LAMMPS, and it also provides the capability to calculate extrapolation grades for on-the-fly active learning.
PAICS is a program of quantum chemical calculation. In this program, fragment molecular orbital (FMO) method is adopted, by which large molecules including biomolecular systems can be treated with several quantum chemical approaches including HF and MP2 methods. At the same time, PaicsView has been developed, which is a supporting program for making input files and analyzing calculation results.
Parsec is a DFT program package based on real space basis and norm-conserving pseudopotential.
peps-torch is a python library for calculation of quantum many-body problems on two dimensional lattices. Variational principles calculation is used with an infinite PEPS (iPEPS) as the trial wave function. Therefore, the ground state is obtained in the form of the element tensor of the iPEPS. The energy of the trial state is estimated by the corner transfer matrix method (CTM), and its gradient with respect to the element tensor is computed through automatic differentiation provided by pytorch. Functions/classes for exploiting the system’s symmetry are provided for reducing the computational cost if possible. While general models and lattices are not supported, many examples of stand-alone codes would make it relatively easy for users to write their own codes to suit their needs. pytorch is required.
An electronic structure calculation program based on the density functional theory and the pseudo potential scheme with a plane wave basis set. This is a powerful tool to predict the physical properties of unknown materials and to simulate experimental results such as STM and EELS. This also enables users to perform long time molecular dynamics simulations and to analyze chemical reaction processes. This program is available on a wide variety of computers from single-core PCs to massive parallel computers like K computer. The whole source code is open to public.
Software to calculate physical quantities related to phonon in solids from result calculated using first principles calculation software. Results calculated from first principles calculation software such as VASP and Wien2k are used as an input.
An open-source application for molecular simulations. This application supports various methods such as classical and ab initio molecular dynamics, path integral simulations, replica exchange simulations, metadynamics, string method, surface hopping dynamics, QM/MM simulations, and so on. A hierarchical parallelization between molecular structures (replicas) and force fields (adiabatic potentials) enables fast and efficient computation.
A structure database for proteins and nuclear acids. Three-dimensional structure data of proteins and nuclear acids (atomic coordinates determined experimentally by X-ray crystal analysis, NMR, etc.) can be downloaded. The data reposited in PDB are in the public domain, and can be accessed by everyone freely.
An open-source application for quantum chemical calculation. This package implements various methods for quantum chemical calculation such as Hartree-Fock approximation, density functional theory, coupled-cluster method, and CI (configuration interaction) method. The package is written in C++, and provides API for Python, by which users can perform for preparation of setting and execution of calculation.
Open Chemistry database that has been in operation since 2004 under the National Institutes of Health (NIH) in the United States. It mainly targets data for small molecules, but information on large molecules such as lipids and peptides are also collected. The database can be accessed via web browser or PUG REST API. The data can be also downloaded from an FTP site.