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Fixes #313 - broken stochastic diffusion #314

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Merged
BryanRumsey merged 1 commit into from
Aug 11, 2022
Merged

Fixes #313 - broken stochastic diffusion #314

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17 changes: 8 additions & 9 deletions spatialpy/solvers/solver.py
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Original file line number Diff line number Diff line change
Expand Up @@ -262,27 +262,26 @@ def __get_input_constants(self, nspecies, ncells, stoich_matrix, dep_graph):
input_constants += outstr

num_types = len(self.model.domain.listOfTypeIDs)
outstr = f"const int input_num_subdomain = {num_types};\n"
outstr = f"const int input_num_subdomain = {num_types-1};\n" # the backend ignores type_id=0 (a.k.a. unassigned)
input_constants += outstr

outstr = f"const double input_subdomain_diffusion_matrix[{len(self.model.listOfSpecies) * num_types}] = "
outstr += "{"
outstr = f"const double input_subdomain_diffusion_matrix[{len(self.model.listOfSpecies) * (num_types-1)}] = "
outvec = []
for i, species in enumerate(self.model.listOfSpecies.values()):
for j, type_id in enumerate(self.model.domain.typeNdxMapping.keys()):
if i + j > 0:
outstr += ','
if j==0: continue # do not process type_id=0 in diffusion
try:
if species not in self.model.listOfDiffusionRestrictions or \
type_id in self.model.listOfDiffusionRestrictions[species]:
outstr += f"{species.diffusion_coefficient}"
outvec.append(f"{species.diffusion_coefficient}")
else:
outstr += "0.0"
outvec.append("0.0")
except KeyError as err:
print(f"error: {err}")
print(self.model.listOfDiffusionRestrictions)
raise SimulationError(f"error: {self.model.listOfDiffusionRestrictions}") from err

outstr += "};\n"
outstr += "{"+",".join(outvec)+"};\n"
input_constants += outstr

return input_constants
Expand Down Expand Up @@ -376,7 +375,7 @@ def __get_system_config(self, num_types, num_chem_species, num_chem_rxns,
num_stoch_species, num_stoch_rxns, num_data_fn):
system_config = f"debug_flag = {self.debug_level};\n"
system_config += "ParticleSystem *system = new ParticleSystem("
system_config += f"{num_types},{num_chem_species},{num_chem_rxns},"
system_config += f"{num_types-1},{num_chem_species},{num_chem_rxns},"
system_config += f"{num_stoch_species},{num_stoch_rxns},{num_data_fn});\n"
system_config += f"system->static_domain = {int(self.model.staticDomain)};\n"
if len(self.model.listOfSpecies) > 0:
Expand Down