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test_hybrid_c_events.py
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# 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 os
import sys
sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
import unittest
import gillespy2
from gillespy2 import TauHybridCSolver
import numpy as np
class EventFeatures(unittest.TestCase):
def create_base_event_model(s1, s2, rate):
model = gillespy2.Model(name="BasicEventModel")
s1 = gillespy2.Species(name="S1", initial_value=s1, mode="continuous")
s2 = gillespy2.Species(name="S2", initial_value=s2, mode="continuous")
model.add_species([s1, s2])
rate = gillespy2.Parameter(name="k1", expression=rate)
model.add_parameter(rate)
r1 = gillespy2.Reaction(
name="r1", reactants={s1: 1}, products={s2: 1}, rate=rate,
)
model.add_reaction(r1)
return model
def test_event_with_time_trigger(self):
model = EventFeatures.create_base_event_model(s1=0, s2=0, rate=0.0)
event = gillespy2.Event(name="ev1", assignments=[
gillespy2.EventAssignment(variable=model.get_species('S1'), expression="100.0"),
gillespy2.EventAssignment(variable=model.get_parameter('k1'), expression="1.0")
], trigger=gillespy2.EventTrigger(expression="t>5"))
model.add_event(event)
solver = TauHybridCSolver(model=model)
result = model.run(solver=solver)[0]
s1, s2 = result["S1"][-1], result["S2"][-1]
self.assertGreater(s2, s1, "Expected S2 > S1")
self.assertGreater(s1, 0.0, "Expected S1 > 0")
self.assertAlmostEqual(s1 + s2, 100.0, places=1)
def test_event_with_species_trigger(self):
model = EventFeatures.create_base_event_model(s1=100, s2=0, rate=10.0)
event = gillespy2.Event(name="ev1", assignments=[
gillespy2.EventAssignment(variable=model.get_species('S1'), expression="100.0"),
gillespy2.EventAssignment(variable=model.get_parameter('k1'), expression="0.0")
], trigger=gillespy2.EventTrigger(expression="S1<90"))
model.add_event(event)
solver = TauHybridCSolver(model=model)
result = model.run(solver=solver)[0]
s1, s2 = result["S1"][-1], result["S2"][-1]
self.assertEqual(s1, 100, "Expected S1 == 100 (trigger set S1 to 100 and rate to 0")
self.assertGreater(s2, 0, "Expected S2 > 0")
self.assertFalse(np.any(result["S1"] <= 90.0), "Expected S1 > 90 for entire simulation")
def test_delay_trigger_persistent(self):
model = EventFeatures.create_base_event_model(s1=100, s2=0, rate=1.0)
event1 = gillespy2.Event(name="ev1", assignments=[
gillespy2.EventAssignment(variable=model.get_species('S1'), expression="0"),
gillespy2.EventAssignment(variable=model.get_species('S2'), expression="0"),
gillespy2.EventAssignment(variable=model.get_parameter('k1'), expression="0.0")
], trigger=gillespy2.EventTrigger(expression="S1<60 and S2<S1", persistent=False), delay="t+1.0")
event2 = gillespy2.Event(name="ev2", assignments=[
gillespy2.EventAssignment(variable=model.get_species('S1'), expression="200"),
gillespy2.EventAssignment(variable=model.get_species('S2'), expression="200"),
gillespy2.EventAssignment(variable=model.get_parameter('k1'), expression="0.0"),
], trigger=gillespy2.EventTrigger(expression="S2>90 and t<3.5", persistent=True), delay="1.0")
model.add_event([event1, event2])
solver = TauHybridCSolver(model=model)
result = model.run(solver=solver)[0]
s1, s2 = result["S1"][-1], result["S2"][-1]
# If delay is working correctly:
# * event1 is never triggered. event1 sets everything to 0.
# If event1 fires, event2 can never fire.
# * event2 is triggered, setting everything to 100 (and rate to 0).
self.assertNotIn(0, [s1, s2], "Non-persistent event fired unexpectedly")
self.assertEqual(s1, 200, "Persistent event failed to fire")
self.assertEqual(s2, 200, "Persistent event failed to fire")
def test_trigger_priorities(self):
model = EventFeatures.create_base_event_model(s1=100, s2=0, rate=1.0)
event1 = gillespy2.Event(name="ev1", assignments=[
gillespy2.EventAssignment(variable=model.get_species('S1'), expression="100"),
gillespy2.EventAssignment(variable=model.get_species('S2'), expression="100"),
], trigger=gillespy2.EventTrigger(expression="S1 < 50"), priority="2*t*S1")
event2 = gillespy2.Event(name="ev2", assignments=[
gillespy2.EventAssignment(variable=model.get_species('S1'), expression="0"),
], trigger=gillespy2.EventTrigger(expression="S1 < 50"), priority="t*S1")
model.add_event([event1, event2])
solver = TauHybridCSolver(model=model)
result = model.run(solver=solver)[0]
s1, s2 = result["S1"][-1], result["S2"][-1]
# If priority is working correctly, event2 should ALWAYS fire before event1.
# Proper result is S1 = 0, S2 = 100, so no further reactions are possible.
self.assertEqual(s1, 0, "Events fired in an incorrect order")
self.assertEqual(s2, 100, "Events fired in an incorrect order")
def test_use_values_from_trigger_time(self):
model = EventFeatures.create_base_event_model(s1=100, s2=0, rate=1.0)
event = gillespy2.Event(name="ev1", assignments=[
gillespy2.EventAssignment(variable=model.get_species('S1'), expression="S2"),
gillespy2.EventAssignment(variable=model.get_parameter('k1'), expression="0.0"),
], trigger=gillespy2.EventTrigger(expression="S1 < 60"), delay="1.5", use_values_from_trigger_time=True)
model.add_event(event)
solver = TauHybridCSolver(model=model)
result = model.run(solver=solver)[0]
s1, s2 = result["S1"][-1], result["S2"][-1]
self.assertGreater(s2, s1, "Event assignment did not assign values from trigger time")
def test_initial_values(self):
model = EventFeatures.create_base_event_model(s1=0, s2=100.0, rate=1.0)
event = gillespy2.Event(name="ev1", assignments=[
gillespy2.EventAssignment(variable=model.get_species('S1'), expression="S2/2"),
], trigger=gillespy2.EventTrigger(expression="S1==0", initial_value=False))
model.add_event(event)
solver = TauHybridCSolver(model=model)
result = model.run(solver=solver)
s1, s2 = result["S1"][-1], result["S2"][-1]
self.assertAlmostEqual(s1 + s2, 150.0, places=1, msg="Event assignment assigned incorrect value")
self.assertGreater(s2, 100, "Event with initial condition did not fire")
self.assertEqual(result["S1"][0], 50, "Event assignment with initial condition failed to fire at t=0")