def test_delayed_choice(self):
inpil = """
length a = 5
length b = 15
length c = 15
length d = 15
length e = 15
length z = 15
RC1 = d( e( z ) ) b*( a* + ) c( + ) d @i 1e-8 M
RC1b = d e( z ) d*( b*( a* + ) c( + ) ) @i 1e-8 M
R0 = a b c @i 1e-7 M
R21 = b c( + ) d @i 0 M
R22 = d( e( z ) ) b*( a*( + ) ) c @i 0 M
R31 = b c @i 0 M
RC32b = d e( z ) d*( b*( a*( + ) ) c( + ) ) @i 0 M
RC32 = d( e( z ) ) b*( a*( + ) ) c( + ) d @i 0 M
TC1 = a( b c + b( c( + ) d + d( e( z ) ) ) ) @i 0 M
TC2 = a( b c + b( c( + ) d( + d e( z ) ) ) ) @i 0 M
TC3 = a( b( c + b c( + ) d( + d e( z ) ) ) ) @i 0 M
"""
enum, out = enumerate_pil(inpil, is_file=False, condensed=True)
xml = write_sbml(enum, condensed=True)
rr = RoadRunner()
rr.load(xml)
ExecutableModel = rr.model
RC32 = 'RC32' if 'RC32' in rr.model.getFloatingSpeciesIds(
) else 'RC32b'
RC1 = 'RC1' if 'RC1' in rr.model.getFloatingSpeciesIds() else 'RC1b'
# Compartment
assert ExecutableModel.getCompartmentVolumes() == 1.
assert ExecutableModel.getNumCompartments() == 1
assert ExecutableModel.getCompartmentIds() == ['TestTube']
# Species
speciesIDs = ['R0', RC32, 'R22', 'R31', 'R21', RC1]
ini_spIDs = sorted('init({})'.format(x) for x in speciesIDs)
concIDs = [
'[R0]', '[' + RC32 + ']', '[R22]', '[R31]', '[R21]',
'[' + RC1 + ']'
]
ini_coIDs = sorted('init({})'.format(x) for x in concIDs)
assert ExecutableModel.getNumFloatingSpecies() == len(speciesIDs)
assert sorted(
ExecutableModel.getFloatingSpeciesIds()) == sorted(speciesIDs)
assert sorted(
ExecutableModel.getFloatingSpeciesInitAmountIds()) == sorted(
ini_spIDs)
assert sorted(ExecutableModel.getFloatingSpeciesInitConcentrationIds()
) == sorted(ini_coIDs)
#print(sorted(ini_coIDs))
#print(ExecutableModel.getFloatingSpeciesInitAmounts())
#print(ExecutableModel.getFloatingSpeciesInitConcentrations())
# Reactions
rxnIDs = [
'R0_' + RC1 + '__' + RC32 + '_R31', 'R0_' + RC1 + '__R22_R21'
]
assert ExecutableModel.getNumReactions() == len(rxnIDs)
assert sorted(ExecutableModel.getReactionIds()) == sorted(rxnIDs)
assert rr.model[RC32] == 0
assert rr.model[RC1] == 2e-8
# simulate deterministic
rr.model['init([R0])'] = 1e-8
assert rr.model['init(R0)'] == 1e-8
Vol = 1.66e-15
rr.model.setCompartmentVolumes([Vol])
rr.model['init([R0])'] = 1e-8 * Vol
rr.model[f'init({RC1})'] = 2e-8 * Vol
rr.integrator.absolute_tolerance = 1e-12 * Vol
rr.integrator.relative_tolerance = 1e-12 * Vol
rr.integrator.initial_time_step = 0.00001
result = rr.simulate(0, 500, steps=100)
#print(result)
#rr.plot() # look at it if you like!
# NOTE: something is off with the units with stochastic simulations, weird...
#print(rr.model.getCompartmentVolumes())
#print(rr.model.getFloatingSpeciesInitConcentrations())
#print(rr.model.getFloatingSpeciesInitAmounts())
#print(rr.model.getFloatingSpeciesConcentrations())
#print(rr.model.getFloatingSpeciesAmounts())
rr.reset()
