openbread

A python 3 implementation of OPENFPM based brownian reaction dynamics.

Requirements

**This module was developed in Python 3.5, and it is recommended to run Python 3.5

This module requires `OPENFPM http://openfpm.mpi-cbg.de/`_ to work properly.

Container-based install

We recommend to use this package inside of the provided container. The docker/ subfolder has all the necessary information and source files to set it up.

Quick start

from openbread.core import *


# Construct species in the model

A = Species(    name = 'A',
                diffusion_constant = 100e-12,
                collision_radius   = 2e-9,
                mass = 1 )

B = Species(    name = 'B',
                diffusion_constant = 100e-12,
                collision_radius   = 2e-9,
                mass = 1 )

C = Species(    name = 'C',
                diffusion_constant = 50e-12,
                collision_radius   = 4e-9,
                mass = 2 )


# Rate constant
k = 1e12


# Setup particle simulation environemnt
volume = 10e-18 # (0.1 mum)^3 in L

medium = ParticleModel.Medium(  viscosity=0.7e-3, # Pa s
                                temperatur=310.15)
volume_fraction = 0.0

crowding = ParticleModel.Crowding( volume_fraction = volume_fraction,
                                   mu = np.log(31.9),
                                   sigma = 0.825,
                                   max_size = 10e-3)

particle_model = ParticleModel(medium,
                               crowding,
                               volume)

particle_model.add_reaction(Reaction('A+B->C', {A:-1,B:-1,C:1},  k ))


# Define initial conditions
particle_model.initial_conditions['A'] = 50e-6
particle_model.initial_conditions['B'] = 50e-6


result = particle_model.simulate(   dt=1e-9,
                                    max_time=1e-5,
                                    log_step=10,
                                    random_seed=1,
                                    is_hardsphere=False,
                                    is_constant_state=False,
                                    t_equlibriate=0.0)

License

The software in this repository is put under an APACHE-2.0 licensing scheme - please see the LICENSE file for more details.