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.
Python tool for automatic extraction of chemical substance information from literature. Based on natural language processing algorithms, it can extract substance names and related physical/chemical properties such as melting points and spectra from documents written in English.
Python wrapper to manage jobs for the ab initio Monte Carlo package TurboRVB. By combining with a workflow management application, TurboWorkflows, users can perform high-throughput calculations based on TurboRVB.
A highly efficient framework for crystal structure exploration and property prediction dedicated to material science calculations. This application can automate the setup, execution, and analysis of the results of calculations based primarily on the density functional theory. It provides data on more than millions of crystal structures and can be used for high throughput calculations for material exploration. It also interfaces with various DFT codes (VASP, Quantum ESPRESSO, etc.).
A library related to the symmetry of crystal structures. By providing a crystal structure, Spglib can detect information related to the symmetry of the structure, such as symmetry operations, a space group and a primitive cell. It can also generate irreducible wave numbers. Spglib is written in C, but various interfaces are available, including Python, Fortran, and Rust.
Script generation tools to manage large-scale computations on supercomputers and clusters. Moller is provided as part of the HTP-Tools package, designed to support high-throughput computations. It is a tool for generating batch job scripts for supercomputers and clusters, allowing parallel execution of programs under a series of computational conditions, such as parameter parallelism.
DDMRG (DynamicalDMRG) is a program for analyzing the dynamical properties of one-dimensional electron systems by using the density matrix renormalization group method. It simulates excited or photo-induced quantum phenomena in Mott insulators, spin-Peierls materials, organic materials, etc. Parallel computational procedures for linear and non-linear responses in low dimensional electron systems and analyzing routines for relaxation processes of excited states induced by photo-irradiation are available.
This software is for constructing inter-atomic force fields that mostly fit the results of ab-initio calculations, using multi-canonical molecular dynamic simulations. Various potential functions such as silicon, ionic crystal, and water have been pre-installed, and the user’s potential function can also be used. The default ab initio calculation solver is xTAPP and other calculation libraries are also applicable.
A set of routines for real-symmetric dense eigenproblems in supercomputers or massively parallel machines. Both of standard and general eigenproblems are supported. A fast computation is achieved by optimal hybrid solvers among eigenproblem libraries of ELPA, EigenExa and ScaLAPACK. The package includes a mini-appli that can be used in a benchmark test.