# GillesPy2 is a modeling toolkit for biochemical simulation.
# Copyright (C) 2019-2024 GillesPy2 developers.
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import numpy as np
from gillespy2.solvers.cpp.c_decoder import IterativeSimDecoder
from gillespy2.solvers.utilities import solverutils as cutils
from gillespy2.core import GillesPySolver, Model
from gillespy2.core.gillespyError import *
from gillespy2.core import Results
from .c_solver import CSolver, SimulationReturnCode
[docs]class ODECSolver(GillesPySolver, CSolver):
"""
This Solver produces the deterministic continuous solution via Ordinary Differential Equations.
Uses integrators from SUNDIALS to perform calculations used to produce solutions.
"""
name = "ODECSolver"
target = "ode"
[docs] @staticmethod
def get_supported_integrator_options():
return {
"rtol",
"atol",
"max_step",
}
[docs] @classmethod
def get_solver_settings(cls):
"""
Returns a list of arguments supported by odc_c_solver.run.
:returns: Tuple of strings, denoting all keyword argument for this solvers run() method.
:rtype: tuple
"""
return ('model', 't', 'number_of_trajectories', 'timeout', 'increment', 'seed', 'debug', 'profile')
[docs] def run(self=None, model: Model = None, t: int = None, number_of_trajectories: int = 1, timeout: int = 0,
increment: int = None, seed: int = None, debug: bool = False, profile: bool = False, variables={},
resume=None, live_output: str = None, live_output_options: dict = {}, integrator_options: "dict[str, float]" = None, **kwargs):
"""
:param model: The model on which the solver will operate. (Deprecated)
:type model: gillespy2.Model
:param t: End time of simulation.
:type t: int
:param number_of_trajectories: Number of trajectories to simulate.
This is deterministic and will always have same results.
:type number_of_trajectories: int
:param timeout: If set, if simulation takes longer than timeout, will exit.
:type timeout: int
:param increment: Time step increment for plotting.
:type increment: float
:param seed: The random seed for the simulation. Optional, defaults to None.
:type seed: int
:param variables: Dictionary of species and their data that will override existing species data.
:type variables: dict
:param resume: Result of a previously run simulation, to be resumed.
:type resume: gillespy2.Results
:param live_output: The type of output to be displayed by solver. Can be "progress", "text", or "graph".
:type live_output: str
:param live_output_options: Dictionary that contains options for live_output. By default {"interval":1}.
"interval" specifies seconds between displaying.
"clear_output" specifies if display should be refreshed with each display.
:type live_output_options: dict
:returns: A result object containing the results of the simulation.
:rtype: gillespy2.Results
"""
from gillespy2 import log
if self is None:
# Post deprecation block
# raise SimulationError("ODECSolver must be instantiated to run the simulation")
# Pre deprecation block
log.warning(
"""
`gillespy2.Model.run(solver=ODECSolver)` is deprecated.
You should use `gillespy2.Model.run(solver=ODECSolver(model=gillespy2.Model))
Future releases of GillesPy2 may not support this feature.
"""
)
self = ODECSolver(model, resume=resume)
if model is not None:
log.warning('model = gillespy2.model is deprecated. Future releases '
'of GillesPy2 may not support this feature.')
if self.model is None:
if model is None:
raise SimulationError("A model is required to run the simulation.")
self._set_model(model=model)
self.model.compile_prep()
self.validate_model(self.model, model)
self.validate_sbml_features(model=self.model)
self.validate_tspan(increment=increment, t=t)
if increment is None:
increment = self.model.tspan[-1] - self.model.tspan[-2]
if t is None:
t = self.model.tspan[-1]
# Validate parameters prior to running the model.
self._validate_type(variables, dict, "'variables' argument must be a dictionary.")
self._validate_resume(t, resume)
self._validate_kwargs(**kwargs)
if resume is not None:
t = abs(t - int(resume["time"][-1]))
number_timesteps = int(round(t / increment + 1))
args = {
"timesteps": number_timesteps,
"end": t,
"increment": increment,
"interval": str(number_timesteps),
}
if self.variable:
populations = cutils.update_species_init_values(self.model.listOfSpecies, self.species, variables, resume)
parameter_values = cutils.change_param_values(self.model.listOfParameters, self.parameters, self.model.volume, variables)
args.update({
"init_pop": populations,
"parameters": parameter_values
})
elif variables:
log.warning("'variables' argument ignored, because solver has variable=False.")
if integrator_options is not None:
integrator_options = ODECSolver.validate_integrator_options(integrator_options)
args.update(integrator_options)
seed = self._validate_seed(seed)
if seed is not None:
args.update({
"seed": seed
})
if live_output is not None:
live_output_options['type'] = live_output
display_args = {
"model": self.model, "number_of_trajectories": number_of_trajectories, "timeline": np.linspace(0, t, number_timesteps),
"live_output_options": live_output_options, "resume": bool(resume)
}
else:
display_args = None
args = self._make_args(args)
decoder = IterativeSimDecoder.create_default(1, number_timesteps, len(self.model.listOfSpecies))
sim_exec = self._build(self.model, self.target, self.variable, False)
sim_status = self._run(sim_exec, args, decoder, timeout, display_args)
if sim_status == SimulationReturnCode.FAILED:
raise ExecutionError("Error encountered while running simulation C++ file:\n"
f"Return code: {int(sim_status)}.\n")
trajectories, time_stopped = decoder.get_output()
simulation_data = self._format_output(trajectories)
if sim_status == SimulationReturnCode.PAUSED:
simulation_data = self._make_resume_data(time_stopped, simulation_data, t)
if resume is not None:
simulation_data = self._update_resume_data(resume, simulation_data, time_stopped)
self.result = simulation_data
self.rc = int(sim_status)
return sum([Results.build_from_solver_results(self, live_output_options)] * number_of_trajectories)
