Installation/Usage

To install synd:

cd </path/to/synd>

conda env create -f environment.yml

or, to install it into an existing conda environment:

cd </path/to/synd>

conda env update --name <your environment> --file environment.yml

Model building and trajectory generation

from synd.models.discrete.markov import MarkovGenerator
from examples.data.simple_model import transition_matrix, initial_distribution, n_steps, backmapper


if __name__ == '__main__':

    synmd_model = MarkovGenerator(
        transition_matrix=transition_matrix,
        backmapper=backmapper
    )

    trajectory = synmd_model.generate_trajectory(
        initial_states=initial_distribution,
        n_steps=n_steps
    )

    print(trajectory)

Model building and saving

from synd.models.discrete.markov import MarkovGenerator
from examples.data.simple_model import transition_matrix, backmapper


if __name__ == '__main__':

    synmd_model = MarkovGenerator(
        transition_matrix=transition_matrix,
        backmapper=backmapper
    )

    synmd_model.save("simple_synmd_model.dat")

Using a saved model file

from synd.core import load_model
from examples.data.simple_model import initial_distribution

n_steps = 10

if __name__ == '__main__':

    synmd_model = load_model("simple_synmd_model.dat")

    trajectory = synmd_model.generate_trajectory(
        initial_states=initial_distribution,
        n_steps=n_steps
    )

    print(trajectory)

WESTPA Integration

See the examples/westpa directory for an example of WESTPA with a SynD propagator.