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.
Library for calculating Pfaffian (square root of determinant), which is defined for skew-symmetric matrices. Algorithms are implemented in several languages (Fortran, Python, Matlab, Mathematica) and users can choose favorite one. Interfaces for C are also provided.
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.
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.
Python code for a chemical database, PubChem. Users can search data in PubChem by compound name, structural information and so on. It is also possible to receive outputs as a Pandas DataFrame.
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.
Python-based simulations of chemistry framework (PySCF) is a general-purpose electronic structure platform written in Python. Users can perform mean-field and post-mean-field methods with standard Gaussian basis functions. This package also provides several interfaces to other software such as BLOCK and Libxc.
A python package for the tight-binding method. PythTB supports tight-binding calculations of electronic structures and Berry phase in various kinds of systems. Users can use ab initio parameters obtained by Wannier90.