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Interactive, GPU-accelerated Molecular Dynamics using the Taichi programming language

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- calculate_hessian.pdf
- fig1.png
- fig2.png
- fig3.png
- fig4.png
- integrator_benchmark.py
- movie.gif
- plots.ipynb
- readme.md
- result_chain.json
- result_lj.json
- __init__.py
- analyzer.py
- common.py
- consts.py
- examples.py
- forcefield.py
- graphics.py
- grid.py
- integrator.py
- interaction.py
- molecule.py
- system.py
- t3mini.py
- ui.py
LICENSE
mpm28.py
mpm48.py
mpm99.gif
preview.gif
propane.gif
README.md
run_examples.py

// repository documentation

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# TaichiMD
Interactive, GPU-accelerated Molecular (& Macroscopic) Dynamics using the Taichi programming language

(05/26/2022) TaichiMD is now made compatible with taichi v1.0.

![](https://raw.githubusercontent.com/victoriacity/taichimd/master/propane.gif)![](https://raw.githubusercontent.com/victoriacity/taichimd/master/mpm99.gif)

## Goals
* To extend capabilities of the Taichi programming language in computer graphics to molecular simulation education and research
* To achieve interactive, real-time particle-based simulations accelerated by GPUs
* To provide a platform for rapid implementation of novel simulation algorithms and machine-learned simulations

## Examples

### Molecular simulation examples
`python run_examples.py [-h] example ensemble`

positional arguments:
```
  example     [lj | mixlj | biglj | ho | chain | pr]
              lj: Lenneard-Jones system with 4096 molecules, in reduced units; 
              biglj: Lenneard-Jones system with 0.26 million molecules, in reduced units;
              mixlj: 3-component Lenneard-Jones mixture with 6000 molecules, in reduced units;
              ho: Harmonic oscillator around the center of the simulation box; 
              chain: 5 harmonic-bond chain molecules with 100 atoms each, bond bending and torsion not included, in real
              units
              pr: 512 propane molecules using the TraPPE-UA force field with a harmonic bond
              stretching potential at 423 K in a 50*50*50 angstrom box
  ensemble    [NVE | NVT] 
              NVE ensemble with Verlet integration or NVT ensemble with Nose-Hoover thermostat
```
optional arguments: `-h, --help  show help message and exit`

### Macroscopic simulation examples
`mpm28.py`: The MPM88 Taichi example (fluid simulation) in 3 dimensions.
`mpm48.py`: The MPM99 Taichi example (fluid, jelly and snow) in 3 dimensions.

## Graphics
TaichiMD ships with a miniature static version of [`taichi_three`](https://github.com/taichi-dev/taichi_three) for rendering graphics, which requires the `taichi_glsl` package. If the renderer was not imported correctly, the example simulations will use the Taichi GUI canvas for graphics.

## Possible extensions
### Microscopic forces
* Add support for torsional potentials as cosine series
* Add Coulomb forces between charged atoms
### Acceleration algorithms
* Implement Ewald summation and/or fast multipole method for long-range forces (Coulomb)
### Macroscopic forces
* Implement gravity and wall boundaries
* Incorporate macroscopic particle simulation algorithms (SPH, etc.)
* Incorporate agent-based simulation algorithms (crowd simulation, particle swarm) and optimization-based integrators

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