gillespy2/solvers/numpy/ode_solver.py
# GillesPy2 is a modeling toolkit for biochemical simulation.
# Copyright (C) 2019-2023 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/>.
"""GillesPy2 Solver for ODE solutions."""
import copy
from threading import Thread, Event
from scipy.integrate import ode
from collections import OrderedDict
import numpy as np
from gillespy2.core import GillesPySolver, log, gillespyError, SimulationError
from gillespy2.solvers.utilities import solverutils as nputils
from gillespy2.core.results import Results
class ODESolver(GillesPySolver):
"""
This solver produces the deterministic continuous solution via Ordinary Differential Equations.
Uses integrators from scipy.integrate.ode to perform calculations used to produce solutions.
:param model: The model on which the solver will operate.
:type model: gillespy2.Model
"""
name = "ODESolver"
rc = 0
stop_event = None
result = None
pause_event = None
def __init__(self, model=None):
if model is None:
raise SimulationError("A model is required to run the simulation.")
name = "ODESolver"
rc = 0
stop_event = None
pause_event = None
result = None
self.model = copy.deepcopy(model)
self.is_instantiated = True
@staticmethod
def __f(t, y, curr_state, model, c_prop):
"""
The right hand side of the differential equation, uses scipy.integrate ode
:param t: time as a numpy array
:param y: species pops as a list
:param curr_state: dictionary of eval variables
:param model: model being simulated
:param c_prop: precompiled reaction propensity function
:returns: integration step
"""
curr_state[0]['t'] = t
state_change = OrderedDict()
for i, species in enumerate(model.listOfSpecies):
curr_state[0][species] = y[i]
state_change[species] = 0
propensity = OrderedDict()
for r_name, reaction in model.listOfReactions.items():
propensity[r_name] = eval(c_prop[r_name], curr_state[0])
for react, stoich in reaction.reactants.items():
state_change[react.name] -= propensity[r_name] * stoich
for prod, stoich in reaction.products.items():
state_change[prod.name] += propensity[r_name] * stoich
state_change = list(state_change.values())
return state_change
@classmethod
def get_solver_settings(cls):
"""
Returns a list of arguments supported by ode_solver.run.
:returns: Tuple of strings, denoting all keyword argument for this solvers run() method.
:rtype: tuple
"""
return ('model', 't', 'number_of_trajectories', 'increment', 'integrator', 'integrator_options',
'timeout')
def run(self=None, model=None, t=None, number_of_trajectories=1, increment=None, integrator='lsoda',
integrator_options={}, live_output=None, live_output_options={}, timeout=None, resume=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 or float
:param number_of_trajectories: Number of trajectories to simulate. By default number_of_trajectories = 1.
This is deterministic and will always have same results.
:type number_of_trajectories: int
:param increment: Time step increment for plotting.
:type increment: float
:param integrator: integrator to be used from scipy.integrate.ode. Options include 'vode', 'zvode', 'lsoda',
'dopri5', and 'dop853'. For more details,
see https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.ode.html
:type integrator: str
:param integrator_options: a dictionary containing options to the scipy integrator. for a list of options,
see https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.ode.html.
Example use: {max_step : 0, rtol : .01}
:type integrator_options: dict
: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 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
:param timeout: If set, if simulation takes longer than timeout, will exit.
:type timeout: int
:param resume: Result of a previously run simulation, to be resumed.
:type resume: gillespy2.Results
: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("ODESolver must be instantiated to run the simulation")
# Pre deprecation block
log.warning(
"""
`gillespy2.Model.run(solver=ODESolver)` is deprecated.
You should use `gillespy2.Model.run(solver=ODESolver(model=gillespy2.Model))
Future releases of GillesPy2 may not support this feature.
"""
)
self = ODESolver(model=model)
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.model = copy.deepcopy(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]
self.stop_event = Event()
self.pause_event = Event()
if timeout is not None and timeout <= 0:
timeout = None
if len(kwargs) > 0:
for key in kwargs:
log.warning('Unsupported keyword argument to {0} solver: {1}'.format(self.name, key))
if number_of_trajectories > 1:
log.warning("Generating duplicate trajectories for model with ODE Solver. "
"Consider running with only 1 trajectory.")
if resume is not None:
# start where we last left off if resuming a simulation
lastT = resume['time'][-1]
step = lastT - resume['time'][-2]
timeline = np.arange(lastT, t+step, step)
else:
timeline = np.linspace(0, t, int(round(t / increment + 1)))
species = list(self.model._listOfSpecies.keys())
trajectory_base, tmpSpecies = nputils.numpy_trajectory_base_initialization(self.model, number_of_trajectories,
timeline, species, resume=resume)
# curr_time and curr_state are list of len 1 so that __run receives reference
if resume is not None:
curr_time = [resume['time'][-1]]
else:
curr_time = [0] # Current Simulation Time
curr_state = [None]
live_grapher = [None]
sim_thread = Thread(target=self.___run, args=(curr_state, curr_time, timeline, trajectory_base,
tmpSpecies, live_grapher,), kwargs={'t': t,
'number_of_trajectories':
number_of_trajectories,
'increment': increment,
'resume': resume,
'integrator': integrator,
'integrator_options':
integrator_options, })
try:
time = 0
sim_thread.start()
if live_output is not None:
import gillespy2.core.liveGraphing
live_output_options['type'] = live_output
gillespy2.core.liveGraphing.valid_graph_params(live_output_options)
if resume is not None:
resumeTest = True # If resuming, relay this information to live_grapher
else:
resumeTest = False
live_grapher[0] = gillespy2.core.liveGraphing.LiveDisplayer(self.model, timeline, number_of_trajectories,
live_output_options, resume=resumeTest)
display_timer = gillespy2.core.liveGraphing.RepeatTimer(live_output_options['interval'],
live_grapher[0].display,
args=(curr_state, curr_time, trajectory_base,live_output))
display_timer.start()
if timeout is not None:
while sim_thread.is_alive():
sim_thread.join(.1)
time += .1
if time >= timeout:
break
else:
while sim_thread.is_alive():
sim_thread.join(.1)
if live_grapher[0] is not None:
display_timer.cancel()
self.stop_event.set()
while self.result is None:
pass
except KeyboardInterrupt:
if live_output:
display_timer.pause = True
display_timer.cancel()
self.pause_event.set()
while self.result is None:
pass
if hasattr(self, 'has_raised_exception'):
raise SimulationError(
f"Error encountered while running simulation:\nReturn code: {int(self.rc)}.\n"
) from self.has_raised_exception
return Results.build_from_solver_results(self, live_output_options)
def ___run(self, curr_state, curr_time, timeline, trajectory_base, tmpSpecies, live_grapher, t=20,
number_of_trajectories=1, increment=0.05, integrator='lsoda',
integrator_options={}, resume=None, **kwargs):
try:
self.__run(curr_state, curr_time, timeline, trajectory_base, tmpSpecies, live_grapher, t,
number_of_trajectories, increment, integrator, integrator_options, resume,
**kwargs)
except Exception as e:
self.has_raised_exception = e
self.result = []
return [], -1
def __run(self, curr_state, curr_time, timeline, trajectory_base, tmpSpecies, live_grapher, t=20,
number_of_trajectories=1, increment=0.05, integrator='lsoda',
integrator_options={}, resume=None, **kwargs):
timeStopped = 0
if resume is not None:
if resume[0].model != self.model:
raise gillespyError.ModelError('When resuming, one must not alter the model being resumed.')
if t < resume['time'][-1]:
raise gillespyError.ExecutionError(
"'t' must be greater than previous simulations end time, or set in the run() method as the "
"simulations next end time")
# compile reaction propensity functions for eval
c_prop = OrderedDict()
for r_name, reaction in self.model.listOfReactions.items():
c_prop[r_name] = compile(reaction.ode_propensity_function, '<string>', 'eval')
result = trajectory_base[0]
entry_count = 0
y0 = [0] * len(self.model.listOfSpecies)
curr_state[0] = OrderedDict()
if resume is not None:
for i, s in enumerate(tmpSpecies):
curr_state[0][s] = tmpSpecies[s]
y0[i] = tmpSpecies[s]
else:
for i, s in enumerate(self.model.listOfSpecies.values()):
curr_state[0][s.name] = s.initial_value
y0[i] = s.initial_value
for p_name, param in self.model.listOfParameters.items():
curr_state[0][p_name] = param.value
if 'vol' not in curr_state[0]:
curr_state[0]['vol'] = 1.0
rhs = ode(ODESolver.__f).set_integrator(integrator, **integrator_options)
rhs.set_initial_value(y0, curr_time[0]).set_f_params(curr_state, self.model, c_prop)
while entry_count < timeline.size - 1:
if self.stop_event.is_set():
self.rc = 33
break
if self.pause_event.is_set():
timeStopped = timeline[entry_count]
break
int_time = curr_time[0] + increment
entry_count += 1
y0 = rhs.integrate(int_time)
curr_time[0] += increment
for i, spec in enumerate(self.model.listOfSpecies):
curr_state[0][spec] = y0[i]
result[entry_count][i+1] = curr_state[0][spec]
results_as_dict = {
'time': timeline
}
for i, species in enumerate(self.model.listOfSpecies):
results_as_dict[species] = result[:, i+1]
results = [results_as_dict] * number_of_trajectories
if timeStopped != 0 or resume is not None:
results = nputils.numpy_resume(timeStopped, results, resume=resume)
self.result = results
return results, self.rc