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reactors.py
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reactors.py
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#!/usr/bin/env python3
###############################################################################
# #
# RMG - Reaction Mechanism Generator #
# #
# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), #
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) #
# #
# Permission is hereby granted, free of charge, to any person obtaining a #
# copy of this software and associated documentation files (the 'Software'), #
# to deal in the Software without restriction, including without limitation #
# the rights to use, copy, modify, merge, publish, distribute, sublicense, #
# and/or sell copies of the Software, and to permit persons to whom the #
# Software is furnished to do so, subject to the following conditions: #
# #
# The above copyright notice and this permission notice shall be included in #
# all copies or substantial portions of the Software. #
# #
# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR #
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, #
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE #
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER #
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING #
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER #
# DEALINGS IN THE SOFTWARE. #
# #
###############################################################################
"""
Contains classes for building RMS simulations
"""
import numpy as np
import sys
import logging
import itertools
if __debug__:
try:
from os.path import dirname, abspath, join, exists
path_rms = dirname(dirname(dirname(abspath(__file__))))
from julia.api import Julia
jl = Julia(sysimage=join(path_rms, "rms.so")) if exists(join(path_rms, "rms.so")) else Julia(compiled_modules=False)
from pyrms import rms
from diffeqpy import de
from julia import Main
except Exception as e:
import warnings
warnings.warn("Unable to import Julia dependencies, original error: " + str(e), RuntimeWarning)
else:
from pyrms import rms
from diffeqpy import de
from julia import Main
from rmgpy.species import Species
from rmgpy.molecule.fragment import Fragment
from rmgpy.reaction import Reaction
from rmgpy.thermo.nasa import NASAPolynomial, NASA
from rmgpy.thermo.wilhoit import Wilhoit
from rmgpy.thermo.thermodata import ThermoData
from rmgpy.kinetics.arrhenius import Arrhenius, ArrheniusEP, ArrheniusBM, PDepArrhenius, MultiArrhenius, MultiPDepArrhenius
from rmgpy.kinetics.kineticsdata import KineticsData
from rmgpy.kinetics.falloff import Troe, ThirdBody, Lindemann
from rmgpy.kinetics.chebyshev import Chebyshev
from rmgpy.data.solvation import SolventData
from rmgpy.kinetics.surface import StickingCoefficient
from rmgpy.solver.termination import TerminationTime, TerminationConversion, TerminationRateRatio
from rmgpy.data.kinetics.family import TemplateReaction
from rmgpy.data.kinetics.depository import DepositoryReaction
class PhaseSystem:
"""
Class for tracking and managing all the phases and interfaces of species/reactions
needed to run a simulation
will typically have a core and edge PhaseSystem where the edge PhaseSystem
contains all species/reactions in the core PhaseSystem
"""
def __init__(self, phases, interfaces):
self.phases = phases
self.interfaces = interfaces
self.species_dict = dict()
def remove_species(self, spc):
"""
If the species is found
removes that species and any reactions it is involved in
from the PhaseSystem and its Phases/Interfaces
"""
for key, phase in self.phases.items():
rms_spc = phase.remove_species(spc.label)
if rms_spc:
for key, interface in self.interfaces.items():
interface.remove_species(rms_spc)
if spc.label in self.species_dict:
del self.species_dict[spc.label]
def add_reaction(self, rxn, species_list):
"""
adds reaction to the appropriate phase/interface
within PhaseSystem
"""
spclabels = [r.label for r in rxn.reactants + rxn.products]
phaseinv = []
for plabel, phase in self.phases.items():
out = [label for label in spclabels if label in phase.names]
if len(out) > 0:
phaseinv.append(phase)
rms_species_list = self.get_rms_species_list()
if len(phaseinv) == 1:
phaseinv[0].add_reaction(rxn, species_list, rms_species_list)
else:
phases = set(phaseinv)
for interface in self.interfaces:
if interface.phaseset == phases:
interface.add_reaction(rxn, species_list, rms_species_list)
break
def pass_species(self, label, phasesys):
"""
Adds a species from self to the input phase system phasesys
(usually adding an edge species to the core PhaseSystem)
also adds any reactions whose participating species are now all
in the core to the core PhaseSystem
reorders edge species ordering to match that of the core
"""
spc = None
for plabel, phase in self.phases.items():
phase_label = plabel
spc = phase.get_species(label)
if spc is not None:
break
assert spc.name not in phasesys.phases[phase_label].names, spc.name
phasesys.phases[phase_label].species.append(spc)
phasesys.phases[phase_label].names.append(label)
phasesys.species_dict[label] = self.species_dict[label]
self.phases[phase_label].species.remove(spc)
self.phases[phase_label].names.remove(label)
self.phases[phase_label].species.insert(len(phasesys.phases[phase_label].species) - 1, spc)
self.phases[phase_label].names.insert(len(phasesys.phases[phase_label].species) - 1, label)
rxnlist = []
for i, rxn in enumerate(self.phases[phase_label].reactions):
if (spc.name in [spec.name for spec in rxn.reactants + rxn.products]) and all(
[spec.name in phasesys.species_dict for spec in rxn.reactants + rxn.products]
):
rxnlist.append(rxn)
for i, rxn in enumerate(rxnlist):
phasesys.phases[phase_label].reactions.append(rxn)
self.phases[phase_label].reactions.remove(rxn)
self.phases[phase_label].reactions.insert(len(phasesys.phases[phase_label].reactions) - 1, rxn)
for key, interface in self.interfaces.items():
rxnlist = []
for i, rxn in enumerate(interface.reactions):
if (
(spc in rxn.reactants or spc in rxn.products)
and all([spec in phasesys.interfaces[key].species for spec in rxn.reactants])
and all([spec in phasesys.interfaces[key].species for spec in rxn.products])
):
rxnlist.append(rxn)
for i, rxn in enumerate(rxnlist):
phasesys.interfaces[key].reactions.append(rxn)
self.interfaces[key].reactions.remove(rxn)
self.interfaces[key].reactions.insert(len(phasesys.interfaces[key].reactions) - 1, rxn)
return
def get_species(self, label):
"""
Retrieve rms species associated with the input label
"""
for plabel, phase in self.phases.items():
spc = phase.get_species(label)
if spc is not None:
return spc
else:
return None
def get_rms_species_list(self):
rms_species_list = []
for phase in self.phases.values():
rms_species_list += phase.species
return rms_species_list
def get_species_names(self):
names = []
for phase in self.phases.values():
names += phase.names
return names
class Phase:
"""
Class containing all species, reactions and properties necessary to describe
kinetics within a specific phase of a simulation
"""
def __init__(self, label="", solvent=None, site_density=None):
self.label = label
self.species = []
self.reactions = []
self.names = []
self.species_dict = dict()
self.add_later_reactions = []
self.rmg_species = []
if solvent:
self.solvent = to_rms(solvent)
if site_density:
self.site_density = site_density
def get_species(self, label):
"""
Retrieve rms species associated with the input label
"""
try:
ind = self.names.index(label)
return self.species[ind]
except (IndexError, ValueError):
return None
def set_solvent(self, solvent):
"""
Set the solvent of the phase
"""
self.solvent = to_rms(solvent)
def add_reaction(self, rxn, edge_phase=None):
"""
add a reaction to the phase
"""
reactions_to_remove = []
if self.add_later_reactions != []:
for reaction in self.add_later_reactions:
added = False
try:
rms_rxn = to_rms(reaction, species_names=self.names, rms_species_list=self.species, rmg_species=self.rmg_species)
self.reactions.append(rms_rxn)
reactions_to_remove.append(reaction)
added = True
except ValueError:
pass
if added and edge_phase is not None:
# If edge phase is provided, then self is the core phase, and this rxn was directly added to the core so not yet exist in edge
# Only add the corresponding rms_rxn to edge if it's successfully added to the core, otherwise this edge phase reaction maybe passed from the edge phase to core phase in pass_species and double added here again
edge_phase.reactions.insert(len(self.reactions) - 1, rms_rxn)
for reaction in reactions_to_remove:
self.add_later_reactions.remove(reaction)
added = False
try:
rms_rxn = to_rms(rxn, species_names=self.names, rms_species_list=self.species, rmg_species=self.rmg_species)
self.reactions.append(rms_rxn)
added = True
except ValueError: # often reactions with efficiencies from seed mechanisms can't be fully constructed until input species are added
if rxn not in self.add_later_reactions:
self.add_later_reactions.append(rxn)
if added and edge_phase is not None:
edge_phase.reactions.insert(len(self.reactions) - 1, rms_rxn)
return
def add_species(self, spc, edge_phase=None):
"""
add a species to the phase
if an edge_phase is given the
edge phase species order is reordered to match
that of self
"""
if spc.label in self.names: # already exists
label = spc.label
logging.debug(f"species {label} was already in phase skipping...")
return
self.rmg_species.append(spc)
label = spc.label
spec = to_rms(spc)
self.species.append(spec)
self.names.append(spc.label)
if edge_phase is not None:
edge_phase.species.insert(len(self.species) - 1, spec)
edge_phase.names.insert(len(self.species) - 1, label)
def remove_species(self, label):
"""
Remove species and associated reactions from the phase
"""
try:
ind = self.names.index(label)
except ValueError:
return
spc = self.species[ind]
rxninds = []
for i, rxn in enumerate(self.reactions):
for spc2 in itertools.chain(rxn.reactants, rxn.products):
if label == spc2.name:
rxninds.append(i)
break
del self.species[ind]
del self.names[ind]
for ind in reversed(rxninds):
del self.reactions[ind]
return spc
class Interface:
"""
Class containing all reactions and properties necessary to describe
kinetics within an interface between two phases in a simulation
"""
def __init__(self, phases, reactions=[]):
self.reactions = reactions or []
self.phaseset = set(phases)
def add_reaction(self, rxn, species_names, rms_species_list):
"""
add a reaction to the interface
"""
self.reactions.append(to_rms(rxn, species_names=species_names, rms_species_list=rms_species_list))
def remove_species(self, spc):
"""
Remove reactions associated with the input species from the interface
"""
rxninds = []
for i, rxn in enumerate(self.reactions):
for spc2 in itertools.chain(rxn.reactants, rxn.products):
if spc.name == spc2.name:
rxninds.append(i)
break
for ind in reversed(rxninds):
del self.reactions[ind]
return
class Reactor:
"""
Super class for running edge analysis
Subclasses implement generate_reactor methods for
generating the necessary RMS phase/domain/reactor objects
"""
def __init__(self, core_phase_system, edge_phase_system, initial_conditions, terminations, constant_species=[]):
self.core_phase_system = core_phase_system
self.edge_phase_system = edge_phase_system
self.initial_conditions = initial_conditions
self.const_spc_names = constant_species
self.n_sims = 1
self.tf = 1.0e6
for term in terminations:
if isinstance(term, TerminationTime):
self.tf = term.time.value_si
self.terminations = [to_rms(term) for term in terminations]
def get_const_spc_indices(self, spcs=None):
rms_species_names = [spc.name for spc in self.core_phase_system.get_rms_species_list()]
return [rms_species_names.index(name) for name in self.const_spc_names]
def finish_termination_criteria(self):
"""
Convert tuples into TerminationConversion objects
this is necessary because in input.py some species objects
are created before they can be converted to rms Species objects
so we construct the rms TerminationConversion objects later
"""
for i, term in enumerate(self.terminations):
if isinstance(term, tuple):
self.terminations[i] = to_rms(TerminationConversion(term[0], term[1]))
def reset_max_edge_species_rate_ratios(self):
"""
This function sets max_edge_species_rate_ratios back to zero
for pruning of ranged reactors it is important to avoid doing this
every initialization
"""
self.max_edge_species_rate_ratios = np.zeros((len(self.prunable_species)), float)
def simulate(self, model_settings, simulator_settings, conditions):
"""
Run edge analysis of the reactor system
"""
# We have to build the edge phase first, because the efficiencies dictionary in any kinetics that has
# efficiencies gets re-written every time we build a phase. If we build the edge phase later, the
# nameefficiencies will contain edge species, and the efficienies dictionary will have edge species index,
# which ultimately cause the core simulation to crash.
edge_react, edge_domains, edge_interfaces, edge_p = self.generate_reactor(self.edge_phase_system)
core_react, core_domains, core_interfaces, core_p = self.generate_reactor(self.core_phase_system)
(
terminated,
resurrected,
invalid_objects,
unimolecular_threshold,
bimolecular_threshold,
trimolecular_threshold,
max_edge_species_rate_ratios,
t,
x,
) = rms.selectobjects(
core_react,
edge_react,
edge_domains,
edge_interfaces,
core_domains,
core_interfaces,
core_p,
edge_p,
model_settings.tol_move_to_core,
model_settings.tol_rad_move_to_core,
model_settings.tol_interrupt_simulation,
model_settings.ignore_overall_flux_criterion,
model_settings.filter_reactions,
model_settings.max_num_objects_per_iter,
model_settings.tol_branch_rxn_to_core,
model_settings.branching_ratio_max,
model_settings.branching_index,
model_settings.terminate_at_max_objects,
self.terminations,
model_settings.filter_threshold,
model_settings.transitory_tol_dict,
model_settings.transitory_step_period,
model_settings.tol_rxn_to_core_deadend_radical,
atol=simulator_settings.atol,
rtol=simulator_settings.rtol,
solver=de.CVODE_BDF(),
)
return (
terminated,
resurrected,
invalid_objects,
unimolecular_threshold,
bimolecular_threshold,
trimolecular_threshold,
max_edge_species_rate_ratios,
t,
x,
)
class ConstantVIdealGasReactor(Reactor):
def __init__(self, core_phase_system, edge_phase_system, initial_conditions, terminations, constant_species=[]):
super().__init__(core_phase_system, edge_phase_system, initial_conditions, terminations, constant_species=[])
def generate_reactor(self, phase_system):
"""
Setup an RMS simulation for EdgeAnalysis
"""
phase = phase_system.phases["Default"]
ig = rms.IdealGas(phase.species, phase.reactions)
domain, y0, p = rms.ConstantVDomain(phase=ig, initialconds=self.initial_conditions)
react = rms.Reactor(domain, y0, (0.0, self.tf), p=p)
return react, domain, [], p
class ConstantTLiquidSurfaceReactor(Reactor):
def __init__(self, core_phase_system, edge_phase_system, initial_conditions, terminations, constant_species):
super().__init__(core_phase_system, edge_phase_system, initial_conditions, terminations, constant_species)
def generate_reactor(self, phase_system):
"""
Setup an RMS simulation for EdgeAnalysis
"""
liq = phase_system.phases["Default"]
surf = phase_system.phases["Surface"]
interface = list(phase_system.interfaces.values())[0]
liq = rms.IdealDiluteSolution(liq.species, liq.reactions, liq.solvent, name="liquid")
surf = rms.IdealSurface(surf.species, surf.reactions, surf.site_density, name="surface")
liq_constant_species = [cspc for cspc in self.const_spc_names if cspc in [spc.name for spc in liq.species]]
cat_constant_species = [cspc for cspc in self.const_spc_names if cspc in [spc.name for spc in surf.species]]
domainliq, y0liq, pliq = rms.ConstantTVDomain(phase=liq, initialconds=self.initial_conditions["liquid"], constantspecies=liq_constant_species)
domaincat, y0cat, pcat = rms.ConstantTAPhiDomain(
phase=surf, initialconds=self.initial_conditions["surface"], constantspecies=cat_constant_species
)
if interface.reactions == []:
inter, pinter = rms.ReactiveInternalInterfaceConstantTPhi(
domainliq,
domaincat,
Main.eval("using ReactionMechanismSimulator; Vector{ElementaryReaction}()"),
self.initial_conditions["liquid"]["T"],
self.initial_conditions["surface"]["A"],
)
else:
inter, pinter = rms.ReactiveInternalInterfaceConstantTPhi(
domainliq, domaincat, interface.reactions, self.initial_conditions["liquid"]["T"], self.initial_conditions["surface"]["A"]
)
react, y0, p = rms.Reactor((domainliq, domaincat), (y0liq, y0cat), (0.0, self.tf), (inter,), (pliq, pcat, pinter))
return react, (domainliq, domaincat), (inter,), p
class ConstantTVLiquidReactor(Reactor):
def __init__(
self,
core_phase_system,
edge_phase_system,
initial_conditions,
terminations,
constant_species=[],
inlet_conditions=dict(),
outlet_conditions=dict(),
evap_cond_conditions=dict(),
):
super().__init__(core_phase_system, edge_phase_system, initial_conditions, terminations, constant_species=constant_species)
self.inlet_conditions = inlet_conditions
self.outlet_conditions = outlet_conditions
self.evap_cond_conditions = evap_cond_conditions
def generate_reactor(self, phase_system):
"""
Setup an RMS simulation for EdgeAnalysis
"""
phase = phase_system.phases["Default"]
liq = rms.IdealDiluteSolution(phase.species, phase.reactions, phase.solvent)
domain, y0, p = rms.ConstantTVDomain(phase=liq, initialconds=self.initial_conditions, constantspecies=self.const_spc_names)
interfaces = []
if self.inlet_conditions:
inlet_conditions = {key: value for (key, value) in self.inlet_conditions.items() if key != "F"}
total_molar_flow_rate = self.inlet_conditions["F"]
inlet = rms.Inlet(domain, inlet_conditions, Main.eval("x->" + str(total_molar_flow_rate)))
interfaces.append(inlet)
if self.outlet_conditions:
total_volumetric_flow_rate = self.outlet_conditions["Vout"]
outlet = rms.VolumetricFlowRateOutlet(domain, Main.eval("x->" + str(total_volumetric_flow_rate)))
interfaces.append(outlet)
if self.evap_cond_conditions:
kLA_kH_evap_cond = rms.kLAkHCondensationEvaporationWithReservoir(domain, self.evap_cond_conditions)
interfaces.append(kLA_kH_evap_cond)
react = rms.Reactor(domain, y0, (0.0, self.tf), interfaces, p=p)
return react, domain, interfaces, p
class ConstantTPIdealGasReactor(Reactor):
def __init__(self, core_phase_system, edge_phase_system, initial_conditions, terminations, constant_species=None):
if constant_species is None:
constant_species = []
super().__init__(core_phase_system, edge_phase_system, initial_conditions, terminations, constant_species=[])
def generate_reactor(self, phase_system):
"""
Setup an RMS simulation for EdgeAnalysis
"""
phase = phase_system.phases["Default"]
ig = rms.IdealGas(phase.species, phase.reactions)
domain, y0, p = rms.ConstantTPDomain(phase=ig, initialconds=self.initial_conditions)
react = rms.Reactor(domain, y0, (0.0, self.tf), p=p)
return react, domain, [], p
def to_rms(obj, species_names=None, rms_species_list=None, rmg_species=None):
"""
Generate corresponding rms object
"""
if isinstance(obj, ThermoData):
obj = obj.to_nasa(Tmin=298, Tmax=2500, Tint=1000)
if isinstance(obj, Arrhenius):
if obj._T0.value_si != 1:
A = obj._A.value_si / (obj._T0.value_si) ** obj._n.value_si
else:
A = obj._A.value_si
n = obj._n.value_si
Ea = obj._Ea.value_si
return rms.Arrhenius(A, n, Ea, rms.EmptyRateUncertainty())
elif isinstance(obj, PDepArrhenius):
Ps = obj._pressures.value_si
arrs = [to_rms(arr) for arr in obj.arrhenius]
return rms.PdepArrhenius(Ps, arrs, rms.EmptyRateUncertainty())
elif isinstance(obj, MultiArrhenius):
arrs = [to_rms(arr) for arr in obj.arrhenius]
return rms.MultiArrhenius(arrs, rms.EmptyRateUncertainty())
elif isinstance(obj, MultiPDepArrhenius):
parrs = [to_rms(parr) for parr in obj.arrhenius]
return rms.MultiPdepArrhenius(parrs, rms.EmptyRateUncertainty())
elif isinstance(obj, Chebyshev):
Tmin = obj.Tmin.value_si
Tmax = obj.Tmax.value_si
Pmin = obj.Pmin.value_si
Pmax = obj.Pmax.value_si
coeffs = obj.coeffs.value_si.tolist()
return rms.Chebyshev(coeffs, Tmin, Tmax, Pmin, Pmax)
elif isinstance(obj, ThirdBody):
arrstr = arrhenius_to_julia_string(obj.arrheniusLow)
efficiencies = {rmg_species[i].label: float(val) for i, val in enumerate(obj.get_effective_collider_efficiencies(rmg_species)) if val != 1}
dstr = "Dict{String,Float64}(["
for key, value in efficiencies.items():
dstr += '"' + key + '"' "=>" + str(value) + ","
dstr += "])"
return Main.eval(
"using ReactionMechanismSimulator; ThirdBody(" + arrstr + ", Dict{Int64,Float64}([]), " + dstr + "," + "EmptyRateUncertainty())"
)
elif isinstance(obj, Lindemann):
arrlow = arrhenius_to_julia_string(obj.arrheniusLow)
arrhigh = arrhenius_to_julia_string(obj.arrheniusHigh)
efficiencies = {rmg_species[i].label: float(val) for i, val in enumerate(obj.get_effective_collider_efficiencies(rmg_species)) if val != 1}
dstr = "Dict{String,Float64}(["
for key, value in efficiencies.items():
dstr += '"' + key + '"' "=>" + str(value) + ","
dstr += "])"
return Main.eval(
"using ReactionMechanismSimulator; Lindemann("
+ arrhigh
+ ","
+ arrlow
+ ","
+ "Dict{Int64,Float64}([]),"
+ dstr
+ ","
+ "EmptyRateUncertainty())"
)
elif isinstance(obj, Troe):
arrlow = arrhenius_to_julia_string(obj.arrheniusLow)
arrhigh = arrhenius_to_julia_string(obj.arrheniusHigh)
efficiencies = {rmg_species[i].label: float(val) for i, val in enumerate(obj.get_effective_collider_efficiencies(rmg_species)) if val != 1}
alpha = obj.alpha
T1 = obj._T1.value_si if obj._T1 is not None else 0.0
T2 = obj._T2.value_si if obj._T2 is not None else 0.0
T3 = obj._T3.value_si if obj._T3 is not None else 0.0
dstr = "Dict{String,Float64}(["
for key, value in efficiencies.items():
dstr += '"' + key + '"' "=>" + str(value) + ","
dstr += "])"
return Main.eval(
"using ReactionMechanismSimulator; Troe("
+ arrhigh
+ ","
+ arrlow
+ ","
+ str(alpha)
+ ","
+ str(T3)
+ ","
+ str(T1)
+ ","
+ str(T2)
+ ","
+ "Dict{Int64,Float64}([]),"
+ dstr
+ ","
+ "EmptyRateUncertainty())"
)
elif isinstance(obj, StickingCoefficient):
if obj._T0.value_si != 1:
A = obj._A.value_si / (obj._T0.value_si) ** obj._n.value_si
else:
A = obj._A.value_si
n = obj._n.value_si
Ea = obj._Ea.value_si
return rms.StickingCoefficient(A, n, Ea, rms.EmptyRateUncertainty())
elif isinstance(obj, NASAPolynomial):
return rms.NASApolynomial(obj.coeffs, obj.Tmin.value_si, obj.Tmax.value_si)
elif isinstance(obj, NASA):
return rms.NASA([to_rms(poly) for poly in obj.polynomials], rms.EmptyThermoUncertainty())
elif isinstance(obj, Species):
if isinstance(obj.molecule[0], Fragment):
obj.molecule[0].assign_representative_molecule()
mol = obj.molecule[0].mol_repr
else:
mol = obj.molecule[0]
atomnums = dict()
for atm in mol.atoms:
if atomnums.get(atm.element.symbol):
atomnums[atm.element.symbol] += 1
else:
atomnums[atm.element.symbol] = 1
bondnum = len(mol.get_all_edges())
if not obj.molecule[0].contains_surface_site():
rad = rms.getspeciesradius(atomnums, bondnum)
diff = rms.StokesDiffusivity(rad)
th = obj.get_thermo_data()
thermo = to_rms(th)
if obj.henry_law_constant_data:
kH = rms.TemperatureDependentHenryLawConstant(Ts=obj.henry_law_constant_data.Ts, kHs=obj.henry_law_constant_data.kHs)
else:
kH = rms.EmptyHenryLawConstant()
if obj.liquid_volumetric_mass_transfer_coefficient_data:
kLA = rms.TemperatureDependentLiquidVolumetricMassTransferCoefficient(
Ts=obj.liquid_volumetric_mass_transfer_coefficient_data.Ts, kLAs=obj.liquid_volumetric_mass_transfer_coefficient_data.kLAs
)
else:
kLA = rms.EmptyLiquidVolumetricMassTransferCoefficient()
return rms.Species(
name=obj.label,
index=obj.index,
inchi="",
smiles="",
adjlist="",
thermo=thermo,
atomnums=atomnums,
bondnum=bondnum,
diffusion=diff,
radius=rad,
radicalelectrons=obj.molecule[0].multiplicity - 1,
molecularweight=obj.molecular_weight.value_si,
henrylawconstant=kH,
liquidvolumetricmasstransfercoefficient=kLA,
comment=obj.thermo.comment,
)
else:
th = obj.get_thermo_data()
thermo = to_rms(th)
return rms.Species(
name=obj.label,
index=obj.index,
inchi="",
smiles="",
adjlist="",
thermo=thermo,
atomnums=atomnums,
bondnum=bondnum,
diffusion=rms.EmptyDiffusivity(),
radius=0.0,
radicalelectrons=obj.molecule[0].multiplicity - 1,
molecularweight=0.0,
henrylawconstant=rms.EmptyHenryLawConstant(),
liquidvolumetricmasstransfercoefficient=rms.EmptyLiquidVolumetricMassTransferCoefficient(),
comment=obj.thermo.comment,
)
elif isinstance(obj, Reaction):
reactantinds = [species_names.index(spc.label) for spc in obj.reactants]
productinds = [species_names.index(spc.label) for spc in obj.products]
reactants = [rms_species_list[i] for i in reactantinds]
products = [rms_species_list[i] for i in productinds]
kinetics = to_rms(obj.kinetics, species_names=species_names, rms_species_list=rms_species_list, rmg_species=rmg_species)
radchange = sum([spc.molecule[0].multiplicity - 1 for spc in obj.products]) - sum([spc.molecule[0].multiplicity - 1 for spc in obj.reactants])
electronchange = 0 # for now
return rms.ElementaryReaction(
index=obj.index,
reactants=reactants,
reactantinds=reactantinds,
products=products,
productinds=productinds,
kinetics=kinetics,
electronchange=electronchange,
radicalchange=radchange,
reversible=obj.reversible,
pairs=[],
comment=obj.kinetics.comment,
)
elif isinstance(obj, SolventData):
return rms.Solvent("solvent", rms.RiedelViscosity(float(obj.A), float(obj.B), float(obj.C), float(obj.D), float(obj.E)))
elif isinstance(obj, TerminationTime):
return rms.TerminationTime(obj.time.value_si)
elif isinstance(obj, TerminationConversion):
return rms.TerminationConversion(to_rms(obj.species), obj.conversion)
elif isinstance(obj, TerminationRateRatio):
return rms.TerminationRateRatio(obj.ratio)
elif isinstance(obj, tuple): # Handle TerminationConversion when the obj doesn't have thermo yet
return obj
else:
errortype = type(obj)
raise ValueError(f"Couldn't convert object of type {errortype} to an RMS object")
def arrhenius_to_julia_string(obj):
return "Arrhenius(" + str(obj.A.value_si) + "," + str(obj.n.value_si) + "," + str(obj.Ea.value_si) + ", EmptyRateUncertainty())"