hoomd-mimse

Usage

# setup simulation

# Setup FIRE sim with Mimse force
fire = hoomd.md.minimize.FIRE(1e-2, 1e-7, 1.0, 1e-7)

nve = hoomd.md.methods.ConstantVolume(filter=hoomd.filter.All())
mimse_force = mimse.Mimse(1.0, 1.0)
fire.forces.append(mimse_force)
# create and append any additional forces 

fire.methods.append(nve)
sim.operations.integrator = fire

# run fire until converged
while not fire.converged:
    sim.run(1000)

# then perform MIMSE protocol for some number of iterations
n_iter = 10

for _ in range(n_iter):
    # place new bias and kick the system in some direction
    bias_pos = sim.state.get_snapshot().particles.position
    mimse_force.push_back(bias_pos)
    mimse_force.random_kick(0.1)

    # now converge to minima
    fire.reset()
    while not fire.converged:
        sim.run(1000)

Development

Dependencies

• HOOMD-blue >= 4.6.0
• CUDA >= 12.0

Setup

First, setup a python environment with conda (or some alternative, I like micromamba). Follow the instructions in extern/README.md to create a python environment with the correct dependencies and install hoomd. You may need to install ninja using your package manager, or through some python environment (system or dev environment). We use ninja since it allows for easy incremental builds.

Build-loop

Now to build the project, ensure the python environment is activated and run the following commands:

./config-misme.sh
./build-mimse.sh
./install-mimse.sh

This will build the project and install it into the python environment. If you make changes to the source code, you can run the build and install scripts again.

Do not run ./config-mimse.sh again unless you want to start the build process againfrom scratch! This would only be necessary if you want to change cmake variables!

./build-mimse.sh && ./install-mimse.sh

Testing

With any recent changes built and installed to the development environment, you can run pytest on the mimse source folder

pytest mimse

Benchmarking

python3 -m benchmarks.mimse_lj --device GPU

Caveats 🚧👷

At the moment, this project absolutely does not work with MPI, and WILL GIVE WRONG RESULTS!