codes and guides to generate the results used in the paper "AI-driven prediction of SARS-CoV-2 variant binding trends from atomistic simulations"
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Updated
Jun 4, 2021 - Jupyter Notebook
codes and guides to generate the results used in the paper "AI-driven prediction of SARS-CoV-2 variant binding trends from atomistic simulations"
Scripts related to the Alloy Theoretic Automated Toolkit
A Python library for the easy implementation of atomistic Monte Carlo algorithms for simulations with LAMMPS.
LAMMPS compute to obtain the per-atom vector from atom to centroid of Voronoi cell.
Fully loaded atomistic modeling environment
Generate, naively, an atomic polycrystalline sample.
Library for handling atomistic graph datasets focusing on transformer-based implementations. It provides utilities for training various models, experimenting with different pre-training tasks, and a suite of pre-trained models with huggingface integrations.
Modular package for atomistic simulations based on Python.
Spring
Ionic Dynamics on GPU (variant of atomistic simulation for ionic crystals like UO2, CaF2, etc.)
A series of recipes and tutorials on how to use python scripting with OVITO
basic monte carlo and molecular dynamics
ASE-compatible calculator for DFTK
Material simulation tutorial on DFT for high school students to find alternative, green energy source to fossil fuels.
Scripts related to the General Utility Lattice Program
A python package for fast building amorphous solids and liquid mixtures from https://materialsproject.org computed structures and machine learning interatomic potentials
Wrapper around ASE Atoms object following the AtomsBase interface
An Atomistic Toolbox - A VUE.js app for having the most important parameters on your screen
Script to smooth xyz and cube file trajectories. Applies spline interpolation to the trajectory
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