lammps
awesome-python-chemistry
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lammps | awesome-python-chemistry | |
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7 | 2 | |
2,049 | 1,026 | |
3.9% | - | |
10.0 | 4.9 | |
1 day ago | about 1 month ago | |
C++ | ||
GNU General Public License v3.0 only | GNU General Public License v3.0 or later |
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lammps
- Lammps – A flexible simulation tool for particle-based materials modeling
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Efficiently spreading 1K + agents
Look into verlet lists or cell lists for your task, which are typically used with a discrete element method such as LAMMPS for what you seem to be describing.
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Where to find a dynamic charge density animation/simulation?
Your choices are an n-body simulation (e.g., LAMMPS) with Coulomb interactions or, if your electrons are sufficiently sparse, a particle-in-cell (e.g., Starfish). Your best bets for visualization are going to be matplotlib or something more user-friendly like Visit or Paraview. Without a neutralizing background, however, your electrons are just going to repel each other, hit the walls, and disappear - there's not going to be much interesting to visualize. What are you actually trying to simulate? With more information maybe you could receive some more targeted advice.
- Lammps Molecular Dynamics Simulator
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👀 Chem.py has started development 🎉 A python library for doing chemistry simulations!! It's open-source too!!!!
Is this just a personal /learning project? I see "chemical simulations" and think quantum-espresso, LAMMPS, NWChem, etc. If this is a personal project, I apologize for my bluntness above.
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If we invert the velocity of all molecules in a closed system, can we reverse its entropy?
Actually, the LAMMPS website has a similar example: Just hover over the "LAMMPS" logo in yellow and blue.
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Active Matter Simulation using LAMMPS
Modify the file to add what you need. In your case, modify the post_force functions in the files, since those will allow you to define the integration steps for the Vicsek model and its variations.
awesome-python-chemistry
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Seeking library recommendation for 3D visualization of crystal structure
Also I'd take a look through https://github.com/lmmentel/awesome-python-chemistry because I have a hard time believing this isn't a "solved problem" where you just need to find the right existing library.
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HELP ME FIND MOLECULAR OUTLIERS USING PYTHON (pandas)
This list of packages is probably a good place to start. It's a little unclear what your dataset looks like but at a guess you're going to need to parse molecular formulas and perhaps structures (you'll need to convert those into some machine-readable format like InChI). Sounds like you also need to consider molecular weight so you'll need a mass calculator if you don't have those values; you could build your own or leverage one of many available.
What are some alternatives?
espresso - The ESPResSo package
Q6 - Q6 Repository -- EVB, FEP and LIE simulator.
senpai - Molecular dynamics simulation software [Moved to: https://github.com/Chelsea486MHz/senpai]
xtb - Semiempirical Extended Tight-Binding Program Package
Blender-FLIP-Fluids - The FLIP Fluids addon is a tool that helps you set up, run, and render high quality liquid fluid effects all within Blender, the free and open source 3D creation suite.
nwchem - NWChem: Open Source High-Performance Computational Chemistry
The-Powder-Toy - Written in C++ and using SDL, The Powder Toy is a desktop version of the classic 'falling sand' physics sandbox, it simulates air pressure and velocity as well as heat.
pyvista - 3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK)
chemispy - A library for using chemistry in your applications
VisPy - Main repository for Vispy
openmm - OpenMM is a toolkit for molecular simulation using high performance GPU code.
radium-formula-parser