Search Results for "chemistry"
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Showing 849 open source projects for "chemistry"
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Avogadro 2
Avogadro libraries provide 3D rendering, visualization, and analysis
AvogadroLibs is the core C++ library behind Avogadro 2, an open-source molecular editor and visualization platform used in chemistry, materials science, and education. It provides the essential tools for constructing, analyzing, and visualizing molecular structures in 2D and 3D. Designed for extensibility, AvogadroLibs supports plugins for quantum chemistry computations, molecular mechanics, and surface rendering. It interfaces with multiple chemistry formats and data sources, making it a versatile backbone for scientific applications and custom visualization tools. -
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TikZ
TikZ figures for concepts in physics/chemistry/ML
Collection of 111 standalone TikZ figures for illustrating concepts in physics, chemistry, and machine learning. Check out janosh.github.io to search, sort, open in Overleaf, and download figures (PDF/SVG/PNG) from this collection. -
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The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java. The main home page of the CDK is now at: http://cdk.github.io
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LAMMPS
Public development project of the LAMMPS MD software package
...It is designed for high-performance computing and can run efficiently on desktops, clusters, and supercomputers. The software is widely used in materials science, chemistry, physics, nanotechnology, soft matter, and computational engineering. It supports many interaction models, including pair potentials, many-body potentials, reactive force fields, bonded interactions, long-range electrostatics, and user-extendable packages. LAMMPS is script-driven, so users can define simulation geometry, force fields, integration methods, output, and analysis behavior through input files. ... -
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Fermi.jl
Fermi quantum chemistry program
Fermi.jl is a quantum chemistry framework written in pure Julia. This code is developed at the Center for Computational Quantum Chemistry at the University of Georgia under the supervision of Dr. Justin M. Turney and Prof. Henry F. Schaefer. This work is supported by the U.S. National Science Foundation under grant number CHE-1661604. Fermi focuses on post Hartree--Fock methods. -
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Tequila
A High-Level Abstraction Framework for Quantum Algorithms
Tequila is an abstraction framework for (variational) quantum algorithms. It operates on abstract data structures allowing the formulation, combination, automatic differentiation and optimization of generalized objectives. Tequila can execute the underlying quantum expectation values on state-of-the-art simulators as well as on real quantum devices. -
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FairChem
FAIR Chemistry's library of machine learning methods for chemistry
FAIRChem is a unified library for machine learning in chemistry and materials, consolidating data, pretrained models, demos, and application code into a single, versioned toolkit. Version 2 modernizes the stack with a cleaner core package and breaking changes relative to V1, focusing on simpler installs and a stable API surface for production and research. The centerpiece models (e.g., UMA variants) plug directly into the ASE ecosystem via a FAIRChem calculator, so users can run relaxations, molecular dynamics, spin-state energetics, and surface catalysis workflows with the same pretrained network by switching a task flag. ... -
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Claude Scientific Skills
A set of ready to use Agent Skills for research, science, engineering
Claude Scientific Skills is a large open source collection of ready-to-use scientific capabilities that extend AI coding agents into full research assistants. The project provides more than 170 curated skills covering domains such as genomics, drug discovery, medical imaging, physics, and advanced data analysis. Each skill bundles documentation, examples, and tool integrations so agents can reliably execute complex multi-step scientific workflows. The framework follows the open Agent Skills... -
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OpenScience
The open-source AI workbench for scientific research
...The project includes research agents, domain specialists, critique agents, literature-review agents, and more than 290 scientific skills. OpenScience is especially useful for machine learning, biology, physics, chemistry, and research automation workflows that need tool use and provenance. -
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OpenFermion
The electronic structure package for quantum computers
OpenFermion is an open source library for compiling and analyzing quantum algorithms to simulate fermionic systems, including quantum chemistry. Among other functionalities, this version features data structures and tools for obtaining and manipulating representations of fermionic and qubit Hamiltonians. For more information, see our release paper. Currently, OpenFermion is tested on Mac, Windows, and Linux. We recommend using Mac or Linux because the electronic structure plugins are only compatible on these platforms. ... -
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GROMACS
Public/backup repository of the GROMACS molecular simulation toolkit
...It includes tools for system preparation, running simulations, trajectory processing, analysis, and workflow automation. GROMACS is especially strong in computational biophysics and chemistry, but it can also be used for broader molecular modeling tasks. Its main value is giving researchers a fast, mature, and extensively documented platform for studying molecular motion and interactions over time. -
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Scientific Agent Skills
A set of ready to use Agent Skills for research, science, engineering
Scientific Agent Skills is an open-source collection of ready-to-use agent skills designed to turn AI coding assistants into stronger research, science, engineering, and analysis partners. It supports any AI agent compatible with the Agent Skills standard, including tools such as Cursor, Claude Code, Codex, and Gemini CLI. The repository includes 135 skills across scientific domains such as genomics, cheminformatics, clinical research, medical imaging, machine learning, physics, materials... -
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ESPResSo
The ESPResSo package
ESPResSo is a simulation package for molecular dynamics and Monte Carlo simulations of soft matter systems. It is designed for coarse-grained and bead-spring models used in physics, chemistry, and molecular biology. The software can model systems such as polymers, colloids, liquid crystals, ferrofluids, DNA, lipid membranes, and other complex fluids. It includes a broad range of interaction potentials and algorithms for electrostatics, hydrodynamics, and coupled particle-field behavior. ESPResSo is controlled through Python, which makes it flexible for custom simulation setup and analysis. ... -
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DL_POLY
General purpose classical molecular dynamics (MD) simulation software
...It has evolved from older replicated-memory designs into a distributed-memory code suitable for modern parallel computing. The software can be built in serial form or with MPI for larger simulations. It is used for molecular modeling in chemistry, physics, materials science, and condensed-matter research. DL_POLY provides a mature simulation environment for studying atomic and molecular systems under classical force-field descriptions. Its main value is offering a long-running, research-grade MD package with a strong focus on parallel execution and general scientific use. -
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HomotopyContinuation.jl
A Julia package for solving systems of polynomials
HomotopyContinuation.jl is a Julia package for solving systems of polynomial equations by numerical homotopy continuation. Many models in the sciences and engineering are expressed as sets of real solutions to systems of polynomial equations. We can optimize any objective whose gradient is an algebraic function using homotopy methods by computing all critical points of the objective function. An important special case is when the objective function is the euclidean distance to a given point.... -
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tm5
4DVAR data assimilation system using TM5
Model for the simulation of atmospheric tracer transport & chemistry. Allows Zooming. 4D-variational data-assimilation is possible based on the adjoint of the transport code (including zoom). -
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Molsketch
2D molecule editor
Molsketch is a 2D molecular editing tool. Its goal is to help you draw molecules quick and easily. Of course you're creation can be exported afterwards in high quality in a number of vector and bitmap formats. -
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XDrawChem
XDrawChem is an application for chemistry drawing and analysis.
XDrawChem is an application for drawing and analyzing chemical structures and reactions. Please visit the website for full details. Download source and binary releases here, and clone the source from GitHub at the external link above. -
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Stand-alone application and Python tools for interactive and/or batch processing analysis of X-Ray Fluorescence Spectra. Graphical user interface (GUI) and batch processing capabilities provided.
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Kekule
Kekule is a molecular visualization app for the 64-bit Windows
Kekule is a fork of Roger Sayle's old 16-bit Windows 3.1 RasMol 2.6 app, last updated and released in 1995. Kekule is meant to aid high school and college chemistry students in their organic and inorganic chemistry studies by allowing you to visualize molecules in 3 dimensions on your laptops. This will greatly increase a chemistry student's understanding of molecules and their structures. -
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CVSim
Cyclic Voltammetry Simulation Program for Research and Education
This a cyclic voltammetry (CV) program created for teaching CV undergraduate chemistry students. For research, download the version from https://sourceforge.net/projects/cvsimplus/ . CVSim uses the implicit method to simulate diffusion. Development of new methods for more accurate simulation of the diffusion is under way. For more details and discussion contact me at akeramid@ucy.ac.cy. -
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Avogadro
An intuitive molecular editor and visualization tool
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture. -
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smina
Scoring and Minimization with AutoDock Vina
A fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project. -
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nmrshiftdb2 is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. The nmrshiftdb2 software is open source, the data is published under an open content license. The core of nmrshitdb2 are fully assigned spectra with raw data and peak lists (we have pure peak lists as well). Those datasets are peer reviewed by a...
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MSCC Applications Support
Materials and Computational Chemistry applications on HPC platform
Five software i.e. AMDKIIT , ANN-CI, LITESOPH, MTASpec, and µ2mech are developed as an outcome of the Materials and Computational Chemistry (MSCC) project under the National Supercomputing Mission (NSM). These are the set of codes (software) developed by the investigators to perform the computations to study the properties of atoms, molecules, clusters, alloys, bio-molecules, and composite materials using high-performance computing (HPC). For more information on the softwares developed under MSCC please go to: https://sourceforge.net/p/mscc-applications-nsm/wiki/ To download the versions of the MSCC softwares installed on NSM HPC systems please go to: https://github.com/mscc07/mscc To download the test input dataset please go to: https://github.com/mscc07/mscc-testinput For training material please go to: http://www.youtube.com/@mscctraining
