bimol_test

Test the model for bimolecular annihilation A+A->0

For the reaction A + A -> 0.

Create data directories

Run the included Python script

python create_data_dirs.py

Running

First use cmake:

mkdir build
cd build
cmake ..

Input data

This requires the stochastic simulations in the bimol_test_stoch_sim directory, and a trained model in the bimol_train directory.

Trajectories for both models

In bimol_test_stoch_sim, new initial conditions are sampled. To evolve these forward in time using the learned differential equation model in bimol_train, run the following commands.

From the build directory, for the visible model:

make learned_trajs_visible
cd ../bin
./learned_trajs_visible

and for the hidden model:

make learned_trajs_visible
cd ../bin
./learned_trajs_visible

The data is written to data_learned_hidden/trajs and data_learned_visible/trajs.

The resulting trajectories can be visualized using the learned_trajs_hidden and learned_trajs_visible notebooks in the mathematica directory.

Sample the learned trajectories

To sample lattices from the learned trajectories, run from the build directory:

make sample_hidden
cd ../bin
./sample_hidden

or

make sample_visible
cd ../bin
./sample_visible

The data is written to data_learned_hidden/samples and data_learned_visible/samples.

Calculate RMSE

To calculate the RMSE between the stochastic simulations in bimol_test_stoch_sim and the moments calculated from the sampled lattices in data_learned_hidden/samples and data_learned_visible/samples, use the mse notebook in the mathematica directory.

Paper figures

Paper figures are created using the mse notebook in the mathematica directory.