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.
A python library for pre- and post-processing of first-principles electronic structure calculations. As a pre-processing tool, it can automatically generate k-point pathways for first-principles calculations of band structures based on the crystal symmetry. It can also post-process first-principles calculation results to generate band structure and density of states plots with atomic species and orbital contributions, or visualize spin textures and Fermi surfaces. It also provides a functionality for band unfolding.
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.
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.
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.
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.
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.
PHYSBO is a Python library for researchers mainly in the materials science field to perform fast and scalable Bayesian optimization based on COMBO (Common Bayesian Optimization). Users can search the candidate with the largest objective function value from candidates listed in advance by using machine learning prediction. PHYSBO can handle a larger amount of data compared with standard implementations such as scikit-learn.
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.
PolyParGen is a free web application that automatically generates OPLS force field for molecular dynamics calculations. It is possible to create OPLS-AA parameters of macromolecules such as fullerenes with complex crosslinking structures, graphene and cyclic molecules. The generated OPLS-AA force field parameter file in Gromacs format is automatically sent to users.