Python Molecular-simulation Resources

LitMatter A template for rapid experimentation and scaling deep learning models on molecular and crystal graphs. How to use Clone this repository and

Junction Tree Variational Autoencoder for Molecular Graph Generation Official implementation of our Junction Tree Variational Autoencoder https://arxi

Disimpy Disimpy is a Python package for generating simulated diffusion-weighted MR signals that can be useful in the development and validation of dat

BFSP [v1.05] Bitflip Fault Simulation Platform by Daniele Rizzieri (2021) The platform injects a random bitflip in each of N copies of a binary file.

Cloth Simulation via Taichi

Ultra-Fast Force Fields (UF3) S. R. Xie, M. Rupp, and R. G. Hennig, "Ultra-fast interpretable machine-learning potentials", preprint arXiv:2110.00624

SelfDrive_AI Reinforcement learning for self-driving in a 3D simulation (Created using UNITY-3D) 1. Requirements for the SelfDrive_AI Gym You need Pyt

Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures Code for the Multiplex Molecular Graph Neural Network (M

Knowledge-enhanced Contrastive Learning (KCL) Molecular Contrastive Learning with Chemical Element Knowledge Graph [ AAAI 2022 ]. We construct a Chemi

Attractors A small module that provides functions and classes for very efficient simulation and rendering of iterated function systems; dynamical syst

ONE PIECE is a Japanese manga of great international success. The story turns inhabited in a fictional world, tells the adventures of a young man whose body gained rubber properties after accidentally eating a devil fruit (AKUMA NO MI).

JAX Gravity This repo contains a demo of how to use JAX to create a simple gravity simulation. It uses JAX's experimental ode package to solve the dif

Miniattack Simulate Attacks With Mininet And Hping3 It measures network load with bwm-ng when the net is under attack and plots the result. This demo

ReacNetGenerator An automatic reaction network generator for reactive molecular dynamics simulation. ReacNetGenerator: an automatic reaction network g

MoT - Molecular Transformer Large-scale Pretraining for Molecular Property Prediction Samsung AI Challenge for Scientific Discovery This repository is

Cooperative Driving Dataset (CODD) The Cooperative Driving dataset is a synthetic dataset generated using CARLA that contains lidar data from multiple

Step by step development of a vending coffee machine project, including tkinter, sqlite3, simulation, etc.

Verification of Monty Hall problem by experimental simulation. |中文|English| In the process of learning causal inference, I learned about the Monty Hal

PyMPDATA PyMPDATA is a high-performance Numba-accelerated Pythonic implementation of the MPDATA algorithm of Smolarkiewicz et al. used in geophysical

Description Small wrapper around 3dmol.js and html2canvas for creating self-contained HTML files that display a 3D molecular representation. Double cl

Factorized Fourier Neural Operators This repository contains the code to reproduce the results in our NeurIPS 2021 ML4PS workshop paper, Factorized Fo

Molecular Sets (MOSES): A benchmarking platform for molecular generation models Deep generative models are rapidly becoming popular for the discovery

tmm_fast tmm_fast or transfer-matrix-method_fast is a lightweight package to speed up optical planar multilayer thin-film device computation. It is es

ltempy ltempy is a set of tools for Lorentz TEM data analysis, simulation, and presentation. Features Single Image Transport of Intensity Equation (SI

IROS21 information To test the code and reproduce the experiments, follow the installation steps in Installation.md. Afterwards, follow the steps in E

Robotics Toolbox for Python A Python implementation of the Robotics Toolbox for MATLAB® GitHub repository Documentation Wiki (examples and details) Sy

Fluid Simulation Usage Download this repo and store it in your computer. Open a terminal and go to the root directory of this folder. Make sure you ha

HSPICE can not perform Monte Carlo (MC) simulations while considering aging effects. I developed a python wrapper that automatically performs MC and aging simulations using HPSICE to save engineering hours.

tcaledger PVE with tcaledger app for payments and simulation of payment requests. The purpose of this API is to empower users to accept cryptocurrenci

This is a a CSMA/CA simulator written in Python based on simulator of the same type found the link https://github.com/StevenSLXie/CSMA-Simulator with

In this repository, the code to use Udacity's self driving car simulator as a testbed for training an autonomous car are provided.

Ohm-s-Law-Visualizer It's an application to calculate I from v and r using Ohm's Law. It can also plot a graph between V vs I. Story I'm doing my Unde

Simulation Dataset for BBHnet NOTE: OLD README, UPDATE IN PROGRESS We generate simulation dataset to train BBHnet, our deep learning framework for det

CaloGAN Simulating 3D High Energy Particle Showers in Multi-Layer Electromagnetic Calorimeters with Generative Adversarial Networks. This repository c

Location-Aware Generative Adversarial Networks (LAGAN) for Physics Synthesis This repository contains all the code used in L. de Oliveira (@lukedeo),

COVID-19-simulation Simulation of early COVID-19 using SIR model and variants (SEIR ...). Made by the Laboratory of Sustainable Life Assessment (GYRO)

Scalable Intervention Target Estimation in Linear Models Implementation of the paper Scalable Intervention Target Estimation in Linear Models (NeurIPS

MuMMI RAS v0.1 Released: Nov 16, 2021 MuMMI RAS is the application component of the MuMMI framework developed to create large-scale ML-driven multisca

Web service load balancing simulation experiment.

High Performance Molecular Dynamics Logging into CINECA's computer systems To logon to the M100 system use the following command from an SSH client ss

scheil A Scheil-Gulliver simulation tool using pycalphad. import matplotlib.pyplot as plt from pycalphad import Database, variables as v from scheil i

freud Overview The freud Python library provides a simple, flexible, powerful set of tools for analyzing trajectories obtained from molecular dynamics

pytools is an open source library containing general machine learning and visualisation utilities for reuse, including: Basic tools for API developmen

AutomaticUSnavigation Investigating automatic navigation towards standard US views integrating MARL with the virtual US environment developed in CT2US

A small fun project to simulate Conway's Game of Life, created in Python. Conway's Game of Life simulates a grid of cells, where the state of each cell consists of whether the cell is alive or dead.

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

Autonomous Ground Vehicle Navigation and Control Simulation Examples in Python THIS PROJECT IS CURRENTLY A WORK IN PROGRESS AND THUS THIS REPOSITORY I

Almacenes Para clonar el Repositorio: Vaya a la terminal de Linux o Mac, o a la cmd en Windows y ejecute:

README: GromacsWrapper A primitive Python wrapper around the Gromacs tools. The library is tested with GROMACS 4.6.5, 2018.x, 2019.x, 2020.x, and 2021

Documentation OWPHydroTools GitHub pages documentation Motivation We developed OWPHydroTools with data scientists in mind. We attempted to ensure the

Agent-based model simulation for air quality and pandemic risk assessment in architectural spaces. User Guide archABM is a fast and open source agent-

Molecular Orbital Transitions (MOT) Animate molecular orbital transitions using Psi4 and Blender Author: Maximilian Paradiz Dominguez, University of A

Molecular Sets (MOSES): A benchmarking platform for molecular generation models Deep generative models are rapidly becoming popular for the discovery

elmer_circuitbuilder Python module for creating the circuit simulation definitions for Elmer FEM. The circuit definitions enable easy setup of coils (

A totally unrealistic cell growth/reproduction simulation.

This repository contains code for training and evaluating FlingBot in both simulation and real-world settings on a dual-UR5 robot arm setup for Ubuntu 18.04

Learning 3D Representations of Molecular Chirality with Invariance to Bond Rotations This directory contains the model architectures and experimental

AMAZ3DSim AMAZ3DSim is a lightweight python-based 3D network multi-agent simulator. It uses a cell-based congestion model. It calculates risk, battery

solar-system-pygame Controls UP/DOWN for Emulation Speed Control ESC for Pause/Unpause q to Quit c or ESC again to Continue LEFT CLICK to Add an orbit

Ackermann Line Follower Robot This is a simulation of a line follower robot that works with steering control based on Stanley: The Robot That Won the

FaPro Free,Cross-platform,Single-file mass network protocol server simulator 中文Readme Description FaPro is a Fake Protocol Server tool, Can easily sta

Welcome to arknights-gacha repository This is my shameless attempt of simulating Arknights gacha. Current supported banner types (with potential bugs)

Python Rapid Artificial Intelligence Ab Initio Molecular Dynamics

dm_control: DeepMind Infrastructure for Physics-Based Simulation. DeepMind's software stack for physics-based simulation and Reinforcement Learning en

PyTorch code for DriveGAN: Towards a Controllable High-Quality Neural Simulation

Robotic Arm Simulation in ROS2 and Gazebo General Overview This repository includes: First, how to simulate a 6DoF Robotic Arm from scratch using GAZE

No RL No Simulation (NRNS) Official implementation of the NRNS paper: No RL, No Simulation: Learning to Navigate without Navigating NRNS is a heriarch

About The Project This is a simple DHCP server and client simulation. I implemented it for computer network course spring 2021 The client can request

Anomaly Detection in Multi-Agent Trajectories for Automated Driving This is the official project page including the paper, code, simulation, baseline

Pendulum project, built using pygame and math modules.

Mathematical modeling is a powerful method for the analysis of complex biological systems. Although there are many researches devoted on produ

pulse2percept: A Python-based simulation framework for bionic vision Retinal degenerative diseases such as retinitis pigmentosa and macular degenerati

SmartSim Example Zoo This repository contains CrayLabs and user contibuted examples of using SmartSim for various simulation and machine learning appl

Simulation-based inference for the Galactic Center Excess Siddharth Mishra-Sharma and Kyle Cranmer Abstract The nature of the Fermi gamma-ray Galactic

IsoGCN The official implementation of IsoGCN, presented in the ICLR2021 paper Isometric Transformation Invariant and Equivariant Graph Convolutional N

一款基于Qt与OpenCV的仿真数字示波器

Abstract We present extensive empirical evidence showing that current Bayesian simulation-based inference algorithms are inadequate for the falsificat

A Final Year Project in CUHK, Autumn 2021 Network Dynaimcs Simulation Files param.h edit all the variables & settings here simulate.c the main program

AWS DeepRacer Overview The AWS DeepRacer Evo vehicle is a 1/18th scale Wi-Fi enabled 4-wheel ackermann steering platform that features two RGB cameras

Python-Orbit-Sim A 2D physics sim for orbits. Made using pygame and tkinter. High degree of intractability, allowing you to create celestial bodies of

3D-Transformer: Molecular Representation with Transformer in 3D Space

Overview of liionpack liionpack takes a 1D PyBaMM model and makes it into a pack. You can either specify the configuration e.g. 16 cells in parallel a

PhyCRNet Physics-informed convolutional-recurrent neural networks for solving spatiotemporal PDEs Paper link: [ArXiv] By: Pu Ren, Chengping Rao, Yang

SurRoL IROS 2021 SurRoL: An Open-source Reinforcement Learning Centered and dVRK Compatible Platform for Surgical Robot Learning Features dVRK compati

An event-based multi-device simulation framework providing configuration and orchestration of complex multi-device simulations.

mc3g Monte Carlo simulation of 3G rules This project contains the Python code to do simulations of events according to the 3G rule (in German: "Geimpf

solar-system Simulation of the solar system using various nummerical methods Download the repo Make shure matplotlib, scipy etc. are installed execute

Automatic Differentiation Multipole Moment Molecular Forcefield Performance notes On a single gpu, using waterbox_31ang.pdb example from MPIDplugin wh

BEM(building energy model)-SIM-APP The is a web app presenting my research in BEM(building energy model) calibration. You can play around with some pa

MolEncoder Molecular AutoEncoder in PyTorch Install $ git clone https://github.com/cxhernandez/molencoder.git && cd molencoder $ python setup.py insta

LiDAR fog simulation Created by Martin Hahner at the Computer Vision Lab of ETH Zurich. This is the official code release of the paper Fog Simulation

DockStream Description DockStream is a docking wrapper providing access to a collection of ligand embedders and docking backends. Docking execution an

JANUS: Parallel Tempered Genetic Algorithm Guided by Deep Neural Networks for Inverse Molecular Design This repository contains code for the paper: JA

OpenCDA OpenCDA is a SIMULATION tool integrated with a prototype cooperative driving automation (CDA; see SAE J3216) pipeline as well as regular autom

Evidential Deep Learning for Guided Molecular Property Prediction and Discovery Ava Soleimany*, Alexander Amini*, Samuel Goldman*, Daniela Rus, Sangee

attractors Attractors is a package for simulation and visualization of strange attractors. Installation The simplest way to install the module is via

NeuralWOZ This code is official implementation of "NeuralWOZ: Learning to Collect Task-Oriented Dialogue via Model-based Simulation". Sungdong Kim, Mi

Accelerating Antimicrobial Discovery with Controllable Deep Generative Models and Molecular Dynamics This work will be published in Nature Biomedical

Brax is a differentiable physics engine that simulates environments made up of rigid bodies, joints, and actuators. It's also a suite of learning algorithms to train agents to operate in these environments (PPO, SAC, evolutionary strategy, and direct trajectory optimization are implemented).

Squidpy is a tool for the analysis and visualization of spatial molecular data. It builds on top of scanpy and anndata, from which it inherits modularity and scalability. It provides analysis tools that leverages the spatial coordinates of the data, as well as tissue images if available.