/tools

XtalNet is an end-to-end tool for predicting crystal structures based on Powder X-Ray Diffraction data. It utilizes advanced deep learning techniques to generate and evaluate crystal structures, making it significant for materials science and molecular modeling.

TBPLaS (Tight-Binding Package for Large-scale Simulation) is a software package designed for building and solving tight-binding models, emphasizing large systems. It provides various methods for electronic structure calculations and simulations, including exact diagonalization and tight-binding propagation methods.

DefiNet is a tool designed for processing datasets related to high-density and low-density defects in materials. It includes functionalities for data preprocessing, model training, and predicting relaxed structures, making it relevant for molecular simulations and materials science.

This repository contains a reaxFF LAMMPS script designed to simulate the oxidation of nanomaterials, followed by thermal equilibration and tensile testing. It aims to investigate how oxidation impacts the tensile strength of materials, making it relevant for studies in molecular dynamics and materials science.

ChemDataExtractor TADF is a specialized toolkit for extracting chemical information from scientific literature, particularly for TADF materials. It allows users to perform text mining and data extraction, which can be useful for predicting molecular properties and understanding material behavior.

HybridMD is a computational tool designed to solve the Poisson equation for closely-packed dielectric sphere composites. It integrates analytical methods with a mesh-free approach to enhance the efficiency of molecular dynamics simulations involving dielectric nanoparticles.

Material Explorer 1.0 is a specialized assistant for material science research that helps users explore material properties, crystal structures, and computational simulations. It provides data from various sources to assist in material selection and application.

The Electron-Phonon Averaged (EPA) Approximation tool is designed to compute electron-phonon coupling and transport properties in materials. It utilizes a computational workflow involving Quantum ESPRESSO and BoltzTraP to analyze the electronic properties of materials like silicon and half-Heusler compounds.

The 'scalar_codes' repository contains Python codes designed to automate standard VASP calculations, focusing on molecular simulations and geometry optimization. It includes functionalities for analyzing molecular properties and performing various computational tasks related to atomistic systems.

MATLADY is a MATLAB toolkit designed for lattice dynamics calculations based on empirical potentials. It allows users to calculate phonon dispersion for materials like silicon and graphene, making it a useful tool for studying molecular properties in solid-state physics.

TED-Gen is a framework designed for generating and analyzing atomic structures at van der Waals interfaces using a generative model. It utilizes experimental and simulated data to create high-quality training datasets and offers tools for training models to analyze stacking patterns in materials.

GEMCODE is a pipeline for automated screening and design of co-crystals aimed at enhancing tabletability. It utilizes generative AI and evolutionary optimization to facilitate de novo design, making it a valuable tool for molecular design in pharmaceutical applications.

AMDAT is a C++ toolkit for high-performance analysis of molecular dynamics trajectories, focusing on amorphous, glass-forming, and polymer systems. It offers robust analyses such as clustering, mean-square displacements, and radial distribution functions, facilitating advanced molecular modeling studies.

PoreMapper is a Python tool that inflates a balloon inside a molecular cavity to analyze pore shapes and sizes. It provides methods for measuring pore characteristics and visualizing the results, making it useful for molecular simulations and modeling of porous materials.

This tool provides supporting code for optimizing the retrosynthesis of gold nanoparticles using Bayesian optimization techniques. It includes a simulator for generating target distributions and iteratively improves the synthesis process through optimization methods.

PseudoPotentialIO.jl is a Julia package designed to support the reading and writing of pseudopotentials used in density functional theory. It allows users to handle various pseudopotential file formats, facilitating electronic structure calculations in computational chemistry.

This repository contains a solution for the 2022 Samsung AI Challenge, focusing on materials discovery through molecular property prediction. It utilizes a modified GeoGNN architecture to model energy states of molecules and includes methods for training and ensemble modeling.

CrystalFormer-CSP is a tool designed for predicting crystal structures using an autoregressive transformer model. It allows for the generation of crystal structures based on chemical formulas and includes functionalities for sampling, relaxation, and energy calculations.

Kugupu is a molecular network generator designed to study charge transport pathways in organic materials. It utilizes molecular dynamics trajectories for postprocessing, making it a useful tool in the field of computational chemistry and materials science.

PyCD is an open-source application designed for lattice-based kinetic Monte Carlo simulations in crystalline systems. It provides tools for modeling charge dynamics, making it useful for researchers in computational materials science.

LAMMPS-LMFF is an extension of the LAMMPS molecular dynamics package, designed to study layered materials like graphene and boron hexanitride. It includes optimizations for performance on supercomputers, enabling efficient simulations of large atomic systems.

AtomsBuilder.jl is a Julia package designed for the convenient building of atomic structures. It allows users to generate bulk materials and load molecular structures from PubChem, making it useful for molecular design and cheminformatics applications.

The chem-ant repository provides a method to select materials and generate molecules that are similar to a specified target molecule using Monte Carlo Tree Search (MCTS) and Genetic Programming techniques. This tool is part of a larger project and is relevant for molecular design and cheminformatics applications.

Pdn-CO-Dynamics is a repository that provides tools for performing Lattice Kinetic Monte Carlo simulations to study the dynamics of subnanometer palladium clusters under carbon monoxide pressure. It includes sample input files, processed output files, and visualizations of simulation results.