From e02d01a8f59aa04be456b0d04ff27f1b7380e69a Mon Sep 17 00:00:00 2001 From: "spaceBearAmadeus (Alex)" Date: Thu, 14 Nov 2024 12:31:32 -0500 Subject: [PATCH] chore: add kwargs to readdy gen --- worker/data_generator.py | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/worker/data_generator.py b/worker/data_generator.py index b40822173..5b585f052 100644 --- a/worker/data_generator.py +++ b/worker/data_generator.py @@ -217,24 +217,27 @@ def run_readdy( # add species via spec species_names = [] for config in species_config: - for species_name, species_difc in config.items(): - species_names.append(species_name) - system.add_species(species_name, float(species_difc)) + species_name = config["name"] + species_difc = config["diffusion_constant"] + species_names.append(species_name) + system.add_species(species_name, diffusion_constant=float(species_difc)) # add reactions via spec for config in reactions_config: - for reaction_scheme, reaction_rate in config.items(): - system.reactions.add(reaction_scheme, float(reaction_rate)) + reaction_scheme = config["scheme"] + reaction_rate = config["rate"] + system.reactions.add(reaction_scheme, rate=float(reaction_rate)) # configure simulation outputs simulation = system.simulation(kernel="CPU") simulation.output_file = "out.h5" simulation.reaction_handler = "UncontrolledApproximation" - # set initial particle state + # set initial particle state and configure observations for config in particles_config: - for particle_name, particle_positions in config.items(): - simulation.add_particles(particle_name, particle_positions) + particle_name = config["name"] + particle_positions = config["positions"] + simulation.add_particles(particle_name, particle_positions) simulation.observe.number_of_particles( stride=1, types=list(set(species_names))