From b1824150b43442a1984251e1beebe403dd21286d Mon Sep 17 00:00:00 2001 From: Richard West Date: Wed, 5 Jun 2024 22:55:21 -0400 Subject: [PATCH 1/6] Save cantera files that were made from chemkin files to a separate folder. So they don't over-write the ones that are being written directly. --- rmgpy/rmg/main.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rmgpy/rmg/main.py b/rmgpy/rmg/main.py index 88ea75ff4c..06ea73e428 100644 --- a/rmgpy/rmg/main.py +++ b/rmgpy/rmg/main.py @@ -1812,7 +1812,7 @@ def generate_cantera_files(self, chemkin_file, **kwargs): """ transport_file = os.path.join(os.path.dirname(chemkin_file), "tran.dat") file_name = os.path.splitext(os.path.basename(chemkin_file))[0] + ".yaml" - out_name = os.path.join(self.output_directory, "cantera", file_name) + out_name = os.path.join(self.output_directory, "cantera_from_ck", file_name) if "surface_file" in kwargs: out_name = out_name.replace("-gas.", ".") cantera_dir = os.path.dirname(out_name) From 581613332a975e86e105c1265572794a3345b70b Mon Sep 17 00:00:00 2001 From: Nora Khalil Date: Wed, 15 Jun 2022 14:59:52 -0400 Subject: [PATCH 2/6] Rename yml to yaml_rms, because it was specific to RMS This allows the Cantera yaml writer to live alongside it --- rmgpy/rmg/main.py | 2 +- rmgpy/{yml.py => yaml_rms.py} | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) rename rmgpy/{yml.py => yaml_rms.py} (98%) diff --git a/rmgpy/rmg/main.py b/rmgpy/rmg/main.py index 06ea73e428..4b76b598ec 100644 --- a/rmgpy/rmg/main.py +++ b/rmgpy/rmg/main.py @@ -83,7 +83,7 @@ from rmgpy.thermo.thermoengine import submit from rmgpy.tools.plot import plot_sensitivity from rmgpy.tools.uncertainty import Uncertainty, process_local_results -from rmgpy.yml import RMSWriter +from rmgpy.yaml_rms import RMSWriter ################################################################################ diff --git a/rmgpy/yml.py b/rmgpy/yaml_rms.py similarity index 98% rename from rmgpy/yml.py rename to rmgpy/yaml_rms.py index 8b6e9f771f..fd8d73fae2 100644 --- a/rmgpy/yml.py +++ b/rmgpy/yaml_rms.py @@ -49,7 +49,7 @@ from rmgpy.util import make_output_subdirectory -def convert_chemkin_to_yml(chemkin_path, dictionary_path=None, output="chem.rms"): +def convert_chemkin_to_rms(chemkin_path, dictionary_path=None, output="chem.rms"): if dictionary_path: spcs, rxns = load_chemkin_file(chemkin_path, dictionary_path=dictionary_path) else: @@ -57,7 +57,7 @@ def convert_chemkin_to_yml(chemkin_path, dictionary_path=None, output="chem.rms" write_yml(spcs, rxns, path=output) -def write_yml(spcs, rxns, solvent=None, solvent_data=None, path="chem.yml"): +def write_rms(spcs, rxns, solvent=None, solvent_data=None, path="chem.rms"): result_dict = get_mech_dict(spcs, rxns, solvent=solvent, solvent_data=solvent_data) with open(path, 'w') as f: yaml.dump(result_dict, stream=f) @@ -279,5 +279,5 @@ def update(self, rmg): solvent_data = None if rmg.solvent: solvent_data = rmg.database.solvation.get_solvent_data(rmg.solvent) - write_yml(rmg.reaction_model.core.species, rmg.reaction_model.core.reactions, solvent=rmg.solvent, solvent_data=solvent_data, + write_rms(rmg.reaction_model.core.species, rmg.reaction_model.core.reactions, solvent=rmg.solvent, solvent_data=solvent_data, path=os.path.join(self.output_directory, 'rms', 'chem{}.rms').format(len(rmg.reaction_model.core.species))) From 7931ac135bdb4fb8a777bbcab5954628b5759d85 Mon Sep 17 00:00:00 2001 From: Nora Khalil Date: Mon, 13 Jun 2022 12:15:01 -0400 Subject: [PATCH 3/6] Enable Cantera-YAML writing. Nora did most of the work. Richard did some cleanup. Nick fixed species_to_dict function to use correct parameter as rxn species. Co-authored-by: Nora Khalil Co-authored-by: Richard West Co-authored-by: Nicholas Tietje --- rmgpy/rmg/main.py | 3 +- rmgpy/yaml_cantera.py | 378 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 380 insertions(+), 1 deletion(-) create mode 100644 rmgpy/yaml_cantera.py diff --git a/rmgpy/rmg/main.py b/rmgpy/rmg/main.py index 4b76b598ec..150b055c2f 100644 --- a/rmgpy/rmg/main.py +++ b/rmgpy/rmg/main.py @@ -84,6 +84,7 @@ from rmgpy.tools.plot import plot_sensitivity from rmgpy.tools.uncertainty import Uncertainty, process_local_results from rmgpy.yaml_rms import RMSWriter +from rmgpy.yaml_cantera import CanteraWriter ################################################################################ @@ -773,7 +774,7 @@ def register_listeners(self, requires_rms=False): self.attach(ChemkinWriter(self.output_directory)) self.attach(RMSWriter(self.output_directory)) - + self.attach(CanteraWriter(self.output_directory)) if self.generate_output_html: self.attach(OutputHTMLWriter(self.output_directory)) diff --git a/rmgpy/yaml_cantera.py b/rmgpy/yaml_cantera.py new file mode 100644 index 0000000000..c4684bf320 --- /dev/null +++ b/rmgpy/yaml_cantera.py @@ -0,0 +1,378 @@ +#!/usr/bin/env python3 + +############################################################################### +# # +# RMG - Reaction Mechanism Generator # +# # +# Copyright (c) 2002-2024 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. # +# # +############################################################################### + +""" +This file defines functions for outputting the RMG generated mechanism to +a yaml file that can be read by Cantera +""" + + +import os +import yaml + +from rmgpy.species import Species +from rmgpy.kinetics.arrhenius import ( + MultiArrhenius, + MultiPDepArrhenius, +) +from rmgpy.util import make_output_subdirectory +from datetime import datetime +from rmgpy.chemkin import get_species_identifier + + +def write_cantera( + spcs, + rxns, + surface_site_density=None, + solvent=None, + solvent_data=None, + path="chem.yml", +): + """ + Writes yaml file depending on the type of system (gas-phase, catalysis). + Writes beginning lines of yaml file, then uses yaml.dump(result_dict) to write species/reactions info. + """ + + # intro to file will change depending on the presence of surface species + is_surface = False + for spc in spcs: + if spc.contains_surface_site(): + is_surface = True + if is_surface: + result_dict = get_mech_dict_surface( + spcs, rxns, solvent=solvent, solvent_data=solvent_data + ) + phases_block, elements_block = get_phases_elements_with_surface( + spcs, surface_site_density + ) + else: + result_dict = get_mech_dict_nonsurface( + spcs, rxns, solvent=solvent, solvent_data=solvent_data + ) + phases_block, elements_block = get_phases_elements_gas_only(spcs) + + with open(path, "w") as f: + # generator line + f.write("generator: RMG\n") + + # datetime object containing current date and time + now = datetime.now() + dt_string = now.strftime("%a, %d %b %Y %H:%M:%S") + f.write(f"date: {dt_string}\n") + + # units line + f.write( + "\nunits: {length: cm, time: s, quantity: mol, activation-energy: kcal/mol}\n\n" + ) + + f.write(phases_block) + f.write(elements_block) + + yaml.dump(result_dict, stream=f, sort_keys=False) + + +def get_phases_elements_gas_only(spcs): + """ + Returns 'phases' and 'elements' sections for a file + with only gas-phase species/reactions. + """ + sorted_species = sorted(spcs, key=lambda spcs: spcs.index) + species_to_write = [get_species_identifier(spec) for spec in sorted_species] + # make sure species with "[" or "]" is in quotes + species_to_write = [ + f"'{s}'" if "[" in s or "{" in s or "]" in s or "}" in s else s + for s in species_to_write + ] + phases_block = f""" +phases: +- name: gas + thermo: ideal-gas + elements: [H, D, T, C, Ci, O, Oi, N, Ne, Ar, He, Si, S, F, Cl, Br, I] + species: [{', '.join(species_to_write)}] + kinetics: gas + transport: mixture-averaged + state: {{T: 300.0, P: 1 atm}} +""" + + elements_block = """ +elements: +- symbol: Ci + atomic-weight: 13.003 +- symbol: D + atomic-weight: 2.014 +- symbol: Oi + atomic-weight: 17.999 +- symbol: T + atomic-weight: 3.016 + +""" + return phases_block, elements_block + + +def get_phases_elements_with_surface(spcs, surface_site_density): + """ + Yaml files with surface species begin with the following blocks of text, + which includes TWO phases instead of just one. + Returns 'phases' and 'elements' sections. + """ + surface_species = [] + gas_species = [] + for spc in spcs: + + if spc.contains_surface_site(): + surface_species.append(spc) + else: + gas_species.append(spc) + + sorted_surface_species = sorted( + surface_species, key=lambda surface_species: surface_species.index + ) + + surface_species_to_write = [ + get_species_identifier(s) for s in sorted_surface_species + ] + + # make sure species with "[" or "]" is in quotes + surface_species_to_write = [ + f"'{s}'" if "[" in s or "{" in s or "]" in s or "}" in s else s + for s in surface_species_to_write + ] + + sorted_gas_species = sorted(gas_species, key=lambda gas_species: gas_species.index) + gas_species_to_write = [get_species_identifier(s) for s in sorted_gas_species] + + # make sure species with "[" or "]" is in quotes + gas_species_to_write = [ + f"'{s}'" if "[" in s or "{" in s or "]" in s or "}" in s else s + for s in gas_species_to_write + ] + + phases_block = f""" +phases: +- name: gas + thermo: ideal-gas + elements: [H, D, T, C, Ci, O, Oi, N, Ne, Ar, He, Si, S, F, Cl, Br, I] + species: [{', '.join(gas_species_to_write)}] + kinetics: gas + reactions: [gas_reactions] + transport: mixture-averaged + state: {{T: 300.0, P: 1 atm}} + +- name: {surface_species[0].smiles.replace("[","").replace("]","")}_surface + thermo: ideal-surface + adjacent-phases: [gas] + elements: [H, D, T, C, Ci, O, Oi, N, Ne, Ar, He, Si, S, F, Cl, Br, I, X] + species: [{', '.join(surface_species_to_write)}] + kinetics: surface + reactions: [surface_reactions] + site-density: {surface_site_density * 1e-4 } +""" + # surface_site_density * 1e-4 #in units of mol/cm^2 + + elements_block = """ +elements: +- symbol: Ci + atomic-weight: 13.003 +- symbol: D + atomic-weight: 2.014 +- symbol: Oi + atomic-weight: 17.999 +- symbol: T + atomic-weight: 3.016 +- symbol: X + atomic-weight: 195.083 + +""" + return phases_block, elements_block + + +def get_mech_dict_surface(spcs, rxns, solvent="solvent", solvent_data=None): + """ + For systems with surface species/reactions. + Adds 'species', 'gas-reactions', and 'surface-reactions' to result_dict. + """ + gas_rxns = [] + surface_rxns = [] + for rxn in rxns: + if rxn.is_surface_reaction(): + surface_rxns.append(rxn) + else: + gas_rxns.append(rxn) + + names = [x.label for x in spcs] + for i, name in enumerate(names): # fix duplicate names + if names.count(name) > 1: + names[i] += "-" + str(names.count(name)) + + result_dict = dict() + result_dict["species"] = [species_to_dict(x, spcs, names=names) for x in spcs] + + # separate gas and surface reactions + + gas_reactions = [] + for rmg_rxn in gas_rxns: + gas_reactions.extend(reaction_to_dicts(rmg_rxn, spcs)) + result_dict["gas_reactions"] = gas_reactions + + surface_reactions = [] + for rmg_rxn in surface_rxns: + surface_reactions.extend(reaction_to_dicts(rmg_rxn, spcs)) + result_dict["surface_reactions"] = surface_reactions + + return result_dict + + +def get_mech_dict_nonsurface(spcs, rxns, solvent="solvent", solvent_data=None): + """ + For gas-phase systems. + Adds 'species' and 'reactions' to result_dict. + """ + names = [x.label for x in spcs] + for i, name in enumerate(names): # fix duplicate names + if names.count(name) > 1: + names[i] += "-" + str(names.count(name)) + + result_dict = dict() + result_dict["species"] = [species_to_dict(x, spcs, names=names) for x in spcs] + + reactions = [] + for rmg_rxn in rxns: + reactions.extend(reaction_to_dicts(rmg_rxn, spcs)) + result_dict["reactions"] = reactions + + return result_dict + + +def reaction_to_dicts(obj, spcs): + """ + Takes an RMG reaction object (obj), returns a list of dictionaries + for YAML properties. For most reaction objects the list will be of + length 1, but a MultiArrhenius or MultiPDepArrhenius will be longer. + """ + + reaction_list = [] + if isinstance(obj.kinetics, MultiArrhenius) or isinstance( + obj.kinetics, MultiPDepArrhenius + ): + list_of_cantera_reactions = obj.to_cantera(use_chemkin_identifier=True) + else: + list_of_cantera_reactions = [obj.to_cantera(use_chemkin_identifier=True)] + + for reaction in list_of_cantera_reactions: + reaction_data = reaction.input_data + efficiencies = getattr(obj.kinetics, "efficiencies", {}) + if efficiencies: + reaction_data["efficiencies"] = { + spcs[i].to_chemkin(): float(val) + for i, val in enumerate( + obj.kinetics.get_effective_collider_efficiencies(spcs) + ) + if val != 1 + } + reaction_list.append(reaction_data) + + return reaction_list + + +def species_to_dict(obj, spc, names=None, label="solvent"): + """ + Takes an RMG species object (obj), returns a list of dictionaries + for YAML properties. Also adds in the number of surface sites + ('sites') to dictionary. + """ + + result_dict = dict() + + if isinstance(obj, Species): + s = obj.to_cantera(use_chemkin_identifier=True) + species_data = s.input_data + try: + result_dict["note"] = obj.transport_data.comment + except: + pass + if "size" in species_data: + sites = species_data["size"] + species_data.pop("size", None) + species_data["sites"] = sites + species_data.update(result_dict) + return ( + species_data # returns composition, name, thermo, and transport, and note + ) + else: + raise Exception("Species object must be an RMG Species object") + + +class CanteraWriter(object): + """ + This class listens to a RMG subject + and writes an YAML file with the current state of the RMG model, + to a yaml subfolder. + + + A new instance of the class can be appended to a subject as follows: + + rmg = ... + listener = CanteraWriter(outputDirectory) + rmg.attach(listener) + + Whenever the subject calls the .notify() method, the + .update() method of the listener will be called. + + To stop listening to the subject, the class can be detached + from its subject: + + rmg.detach(listener) + + """ + + def __init__(self, output_directory=""): + super(CanteraWriter, self).__init__() + self.output_directory = output_directory + make_output_subdirectory(output_directory, "cantera") + + def update(self, rmg): + + solvent_data = None + if rmg.solvent: + solvent_data = rmg.database.solvation.get_solvent_data(rmg.solvent) + + surface_site_density = None + if rmg.reaction_model.surface_site_density: + surface_site_density = rmg.reaction_model.surface_site_density.value_si + + write_cantera( + rmg.reaction_model.core.species, + rmg.reaction_model.core.reactions, + surface_site_density=surface_site_density, + solvent=rmg.solvent, + solvent_data=solvent_data, + path=os.path.join(self.output_directory, "cantera", "chem{}.yaml").format( + len(rmg.reaction_model.core.species) + ), + ) From 712d349dccc7ad49bb8f381334045b43e225fb4c Mon Sep 17 00:00:00 2001 From: Richard West Date: Fri, 2 Aug 2024 10:59:36 -0400 Subject: [PATCH 4/6] Minor: Fix a Cython declaration in a Reaction method. Although Atom is a subclass of Vertex, it adds an element attribute. This leads to more efficient Cython code (and quietens a warning in vscode). --- rmgpy/reaction.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rmgpy/reaction.py b/rmgpy/reaction.py index 1997824afc..1530001f42 100644 --- a/rmgpy/reaction.py +++ b/rmgpy/reaction.py @@ -1439,7 +1439,7 @@ def is_balanced(self): from rmgpy.molecule.element import element_list from rmgpy.molecule.fragment import CuttingLabel, Fragment - cython.declare(reactant_elements=dict, product_elements=dict, molecule=Graph, atom=Vertex, element=Element, + cython.declare(reactant_elements=dict, product_elements=dict, molecule=Molecule, atom=Atom, element=Element, reactants_net_charge=cython.int, products_net_charge=cython.int) reactant_elements = {} From a10543f4701853c200a190222d1695c6a466cd51 Mon Sep 17 00:00:00 2001 From: Richard West Date: Fri, 2 Aug 2024 14:43:01 -0400 Subject: [PATCH 5/6] Reworking the Elements blocks in cantera yaml writer. Basing it on the Chemkin version. For now only evaluate it once, and include everything. --- rmgpy/yaml_cantera.py | 79 +++++++++++++++++++++---------------------- 1 file changed, 39 insertions(+), 40 deletions(-) diff --git a/rmgpy/yaml_cantera.py b/rmgpy/yaml_cantera.py index c4684bf320..96a39c52be 100644 --- a/rmgpy/yaml_cantera.py +++ b/rmgpy/yaml_cantera.py @@ -68,14 +68,14 @@ def write_cantera( result_dict = get_mech_dict_surface( spcs, rxns, solvent=solvent, solvent_data=solvent_data ) - phases_block, elements_block = get_phases_elements_with_surface( + phases_block = get_phases_with_surface( spcs, surface_site_density ) else: result_dict = get_mech_dict_nonsurface( spcs, rxns, solvent=solvent, solvent_data=solvent_data ) - phases_block, elements_block = get_phases_elements_gas_only(spcs) + phases_block = get_phases_gas_only(spcs) with open(path, "w") as f: # generator line @@ -92,14 +92,40 @@ def write_cantera( ) f.write(phases_block) - f.write(elements_block) - yaml.dump(result_dict, stream=f, sort_keys=False) + f.write(ELEMENTS_BLOCK) + yaml.dump(result_dict, stream=f, sort_keys=False) -def get_phases_elements_gas_only(spcs): +def get_elements_block(): + """ + Returns the 'elements' section, and elements list for a phase """ - Returns 'phases' and 'elements' sections for a file + from rmgpy.molecule.element import get_element + elements_list = ['H', 'C', 'O', 'N', 'Ne', 'Ar', 'He', 'Si', 'S', + 'F', 'Cl', 'Br', 'I'] + isotopes = (('H', 2), ('H', 3), ('C', 13),('O', 18)) + elements_block_list = ['', 'elements:'] + for symbol, isotope in isotopes: + element = get_element(symbol, isotope=isotope) + chemkin_name = element.chemkin_name + mass = 1000 * element.mass + elements_block_list.append(f"- symbol: {chemkin_name}\n atomic-weight: {mass:f}") + elements_list.append(chemkin_name) + # Surface sites + elements_list.append('X') + elements_block_list.append("- symbol: X\n atomic-weight: 195.083\n\n") + elements_block = '\n'.join(elements_block_list) + elements_line = f"elements: [{', '.join(elements_list)}]" + return elements_block, elements_line +# For now this is not dynamic, and includes everything, so we just evaluate it +# once and use it for all files. +ELEMENTS_BLOCK, ELEMENTS_LINE = get_elements_block() + + +def get_phases_gas_only(spcs): + """ + Returns 'phases' sections for a file with only gas-phase species/reactions. """ sorted_species = sorted(spcs, key=lambda spcs: spcs.index) @@ -113,33 +139,20 @@ def get_phases_elements_gas_only(spcs): phases: - name: gas thermo: ideal-gas - elements: [H, D, T, C, Ci, O, Oi, N, Ne, Ar, He, Si, S, F, Cl, Br, I] + {ELEMENTS_LINE} species: [{', '.join(species_to_write)}] kinetics: gas transport: mixture-averaged state: {{T: 300.0, P: 1 atm}} """ + return phases_block - elements_block = """ -elements: -- symbol: Ci - atomic-weight: 13.003 -- symbol: D - atomic-weight: 2.014 -- symbol: Oi - atomic-weight: 17.999 -- symbol: T - atomic-weight: 3.016 -""" - return phases_block, elements_block - - -def get_phases_elements_with_surface(spcs, surface_site_density): +def get_phases_with_surface(spcs, surface_site_density): """ Yaml files with surface species begin with the following blocks of text, which includes TWO phases instead of just one. - Returns 'phases' and 'elements' sections. + Returns 'phases' sections. """ surface_species = [] gas_species = [] @@ -177,7 +190,7 @@ def get_phases_elements_with_surface(spcs, surface_site_density): phases: - name: gas thermo: ideal-gas - elements: [H, D, T, C, Ci, O, Oi, N, Ne, Ar, He, Si, S, F, Cl, Br, I] + {ELEMENTS_LINE} species: [{', '.join(gas_species_to_write)}] kinetics: gas reactions: [gas_reactions] @@ -187,7 +200,7 @@ def get_phases_elements_with_surface(spcs, surface_site_density): - name: {surface_species[0].smiles.replace("[","").replace("]","")}_surface thermo: ideal-surface adjacent-phases: [gas] - elements: [H, D, T, C, Ci, O, Oi, N, Ne, Ar, He, Si, S, F, Cl, Br, I, X] + {ELEMENTS_LINE} species: [{', '.join(surface_species_to_write)}] kinetics: surface reactions: [surface_reactions] @@ -195,21 +208,7 @@ def get_phases_elements_with_surface(spcs, surface_site_density): """ # surface_site_density * 1e-4 #in units of mol/cm^2 - elements_block = """ -elements: -- symbol: Ci - atomic-weight: 13.003 -- symbol: D - atomic-weight: 2.014 -- symbol: Oi - atomic-weight: 17.999 -- symbol: T - atomic-weight: 3.016 -- symbol: X - atomic-weight: 195.083 - -""" - return phases_block, elements_block + return phases_block def get_mech_dict_surface(spcs, rxns, solvent="solvent", solvent_data=None): From a5936e7a488f971e29f86f586b18d3e93e0f8106 Mon Sep 17 00:00:00 2001 From: Lekia Prosper Date: Mon, 3 Mar 2025 13:57:40 -0500 Subject: [PATCH 6/6] add yaml writer test to compare yaml file generated by RMG and the yaml file converted from chemkin files --- .../yaml_writer_data/cantera/chem47.yaml | 2778 +++++++++++++++++ .../chemkin/chem0047-gas.yaml | 1117 +++++++ .../rmgpy/yaml_writer/compare_yaml_outputs.py | 137 + test/rmgpy/yaml_writer/test_yaml.py | 23 + 4 files changed, 4055 insertions(+) create mode 100644 test/rmgpy/test_data/yaml_writer_data/cantera/chem47.yaml create mode 100644 test/rmgpy/test_data/yaml_writer_data/chemkin/chem0047-gas.yaml create mode 100644 test/rmgpy/yaml_writer/compare_yaml_outputs.py create mode 100644 test/rmgpy/yaml_writer/test_yaml.py diff --git a/test/rmgpy/test_data/yaml_writer_data/cantera/chem47.yaml b/test/rmgpy/test_data/yaml_writer_data/cantera/chem47.yaml new file mode 100644 index 0000000000..8b24f4d1c7 --- /dev/null +++ b/test/rmgpy/test_data/yaml_writer_data/cantera/chem47.yaml @@ -0,0 +1,2778 @@ +generator: RMG +date: Tue, 18 Feb 2025 15:33:45 + +units: {length: cm, time: s, quantity: mol, activation-energy: kcal/mol} + + +phases: +- name: gas + thermo: ideal-gas + elements: [H, C, O, N, Ne, Ar, He, Si, S, F, Cl, Br, I, D, T, CI, OI, X] + species: [Ar, Ne, N2, CH4(2), H2O(3), CO2(4), H2(5), CO(6), O2(7), C2H6(8), CH3(9), CH3OH(10), C2H4(11), CH3CHO(12), C3H6O(13), C2H6O(14), CH3COOCH3(15)] + kinetics: gas + reactions: [gas_reactions] + transport: mixture-averaged + state: {T: 300.0, P: 1 atm} + +- name: Pt_surface + thermo: ideal-surface + adjacent-phases: [gas] + elements: [H, C, O, N, Ne, Ar, He, Si, S, F, Cl, Br, I, D, T, CI, OI, X] + species: [X(1), HX(16), OX(17), CX(18), COX(19), CHX(20), CH2X(21), HCOX(22), HCOHX(23), CH3OX(24), CH3COOX(25), CH2COX(26), CH2COX2(27), CH3COOHX(28), C2H4X(29), C2H4X2(30), COOHX(31), CH3X(32), HOX(33), OCXOX(34), HOCXO(35), CO2X(36), H2OX(43), 'C.[Pt](84)', C2H3X(88), CHOX2(110), C2H3X2(120), 'CC#[Pt](307)', C2H2X2(338), 'C#C.[Pt](513)'] + kinetics: surface + reactions: [surface_reactions] + site-density: 3.148e-09 + +elements: +- symbol: D + atomic-weight: 2.014102 +- symbol: T + atomic-weight: 3.016049 +- symbol: CI + atomic-weight: 13.003354 +- symbol: OI + atomic-weight: 17.999159 +- symbol: X + atomic-weight: 195.083 + +species: +- name: Ar + composition: + Ar: 1.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 200.0 + - 1000.0 + - 6000.0 + data: + - - 2.5 + - 0.0 + - 0.0 + - 0.0 + - 0.0 + - -745.375 + - 4.37967 + - - 2.5 + - 0.0 + - 0.0 + - 0.0 + - 0.0 + - -745.375 + - 4.37967 + transport: + model: gas + geometry: atom + diameter: 3.3300000000000005 + well-depth: 136.50054988458677 + note: GRI-Mech +- name: Ne + composition: + Ne: 1.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 200.0 + - 1000.0 + - 6000.0 + data: + - - 2.5 + - 0.0 + - 0.0 + - 0.0 + - 0.0 + - -745.375 + - 3.35532 + - - 2.5 + - 0.0 + - 0.0 + - 0.0 + - 0.0 + - -745.375 + - 3.35532 + transport: + model: gas + geometry: atom + diameter: 3.7580000000000005 + well-depth: 148.6 + note: Epsilon & sigma estimated with fixed Lennard Jones Parameters. This is the + fallback method! Try improving transport databases! +- name: N2 + composition: + N: 2.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 200.0 + - 1000.0 + - 6000.0 + data: + - - 3.53101 + - -0.000123661 + - -5.02999e-07 + - 2.43531e-09 + - -1.40881e-12 + - -1046.98 + - 2.96747 + - - 2.95258 + - 0.0013969 + - -4.92632e-07 + - 7.8601e-11 + - -4.60755e-15 + - -923.949 + - 5.87189 + transport: + model: gas + geometry: linear + diameter: 3.6210000000000013 + well-depth: 97.53030619382686 + polarizability: 1.7600000000000011 + rotational-relaxation: 4.0 + note: GRI-Mech +- name: X(1) + composition: + X: 1.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 298.0 + - 1000.0 + - 2000.0 + data: + - - 0.0 + - 0.0 + - 0.0 + - 0.0 + - 0.0 + - 0.0 + - 0.0 + - - 0.0 + - 0.0 + - 0.0 + - 0.0 + - 0.0 + - 0.0 + - 0.0 +- name: CH4(2) + composition: + C: 1.0 + H: 4.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 100.0 + - 1084.1187337643662 + - 5000.0 + data: + - - 4.205416196255041 + - -0.005355584631145938 + - 2.5112363572294852e-05 + - -2.137632989042285e-08 + - 5.9752576676099345e-12 + - -10161.943346777867 + - -0.9212827273392239 + - - 0.9082602129576632 + - 0.011454094892455498 + - -4.5717433924635545e-06 + - 8.291928595922759e-10 + - -5.6631586824980706e-14 + - -9719.972022902222 + - 13.993125635097375 + transport: + model: gas + geometry: nonlinear + diameter: 3.746000000000001 + well-depth: 141.400440100105 + polarizability: 2.600000000000002 + rotational-relaxation: 13.0 + note: GRI-Mech +- name: H2O(3) + composition: + H: 2.0 + O: 1.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 100.0 + - 1130.243284919479 + - 5000.0 + data: + - - 4.057636221872408 + - -0.0007879402524835726 + - 2.9087893225841516e-06 + - -1.4752057824605237e-09 + - 2.1284959599833601e-13 + - -30281.586653679737 + - -0.3113654695330764 + - - 2.843247813270488 + - 0.0027510897463440443 + - -7.810338827223348e-07 + - 1.0724419204775164e-10 + - -5.793967385714403e-15 + - -29958.611588952655 + - 5.910434907048865 + transport: + model: gas + geometry: nonlinear + diameter: 2.6050000000000004 + well-depth: 572.4019516813576 + dipole: 1.8439999999999999 + rotational-relaxation: 4.0 + note: GRI-Mech +- name: CO2(4) + composition: + C: 1.0 + O: 2.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 100.0 + - 978.2164247415373 + - 5000.0 + data: + - - 3.280844236561561 + - 0.002501860004866126 + - 8.08190843915926e-06 + - -1.2051019574327036e-08 + - 4.665419284125267e-12 + - -48400.830312852784 + - 6.00081543904009 + - - 4.6742752757606745 + - 0.0026096268846741164 + - -9.856820820173133e-07 + - 1.957120153217903e-10 + - -1.4983471395230124e-14 + - -48951.21731066457 + - -2.1107803190827465 + transport: + model: gas + geometry: linear + diameter: 3.763 + well-depth: 244.00106224424113 + polarizability: 2.650000000000001 + rotational-relaxation: 2.1 + note: GRI-Mech +- name: H2(5) + composition: + H: 2.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 100.0 + - 1959.08462230851 + - 5000.0 + data: + - - 3.4353643375690575 + - 0.00021270843056734023 + - -2.7862068251219974e-07 + - 3.4026374586351706e-10 + - -7.760235284610629e-14 + - -1031.3598528421899 + - -3.908418170766748 + - - 2.7881426891855945 + - 0.000587671007977702 + - 1.5899634118409258e-07 + - -5.527107765047777e-11 + - 4.342903937188434e-15 + - -596.1306154450648 + - 0.11286983601569868 + transport: + model: gas + geometry: linear + diameter: 2.9200000000000004 + well-depth: 38.00012796964137 + polarizability: 0.7900000000000005 + rotational-relaxation: 280.0 + note: GRI-Mech +- name: CO(6) + composition: + C: 1.0 + O: 1.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 100.0 + - 1571.6593741294669 + - 5000.0 + data: + - - 3.5683789993113204 + - -0.0008521161385230426 + - 2.489153078746991e-06 + - -1.5632874127406197e-09 + - 3.1358850739748245e-13 + - -14284.254889750642 + - 3.5791254751491537 + - - 2.913095893090424 + - 0.0016465367644801375 + - -6.885940678175395e-07 + - 1.210329274784425e-10 + - -7.839840585892357e-15 + - -14180.899929543586 + - 6.710287418337844 + transport: + model: gas + geometry: linear + diameter: 3.6500000000000004 + well-depth: 98.10027624123336 + polarizability: 1.9500000000000008 + rotational-relaxation: 1.8 + note: GRI-Mech +- name: O2(7) + composition: + O: 2.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 100.0 + - 1074.5555114962035 + - 5000.0 + data: + - - 3.537321799907554 + - -0.0012157092105349748 + - 5.316177942590317e-06 + - -4.894433842532746e-09 + - 1.4584502658366455e-12 + - -1038.5884607015485 + - 4.683684088842607 + - - 3.1538242933344125 + - 0.001678037943720445 + - -7.699709798598658e-07 + - 1.5127470439159983e-10 + - -1.0878179254258219e-14 + - -1040.818802796597 + - 6.16753858679826 + transport: + model: gas + geometry: linear + diameter: 3.4580000000000015 + well-depth: 107.40032560095216 + polarizability: 1.6000000000000008 + rotational-relaxation: 3.8 + note: GRI-Mech +- name: C2H6(8) + composition: + C: 2.0 + H: 6.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 100.0 + - 1012.4143908176864 + - 5000.0 + data: + - - 3.7224027214290585 + - 0.0016507216851436085 + - 3.4417964169825765e-05 + - -3.768635653272928e-08 + - 1.2445292179204619e-11 + - -11557.590566943427 + - 4.682444888027526 + - - 2.8284402467294902 + - 0.017304128331706716 + - -6.733383493412886e-06 + - 1.2374299067889905e-09 + - -8.656844034734494e-14 + - -11997.790083232097 + - 5.938355682638575 + transport: + model: gas + geometry: nonlinear + diameter: 4.3020000000000005 + well-depth: 252.30104810022812 + rotational-relaxation: 1.5 + note: GRI-Mech +- name: CH3(9) + composition: + C: 1.0 + H: 3.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 100.0 + - 697.6534741766965 + - 5000.0 + data: + - - 3.9604315909856713 + - 0.0005929325518967126 + - 8.785780906372586e-06 + - -9.880343260208576e-09 + - 3.6323637393909093e-12 + - 16421.88173561743 + - 0.33986347561181546 + - - 3.095112437831353 + - 0.005554297527849976 + - -1.8815877454521128e-06 + - 3.1333480061460194e-10 + - -2.051949923202252e-14 + - 16542.619031157636 + - 4.202975724684728 + transport: + model: gas + geometry: nonlinear + diameter: 3.8 + well-depth: 144.00072548202698 + note: GRI-Mech +- name: CH3OH(10) + composition: + C: 1.0 + H: 4.0 + O: 1.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 100.0 + - 1035.7423959466812 + - 5000.0 + data: + - - 3.840067829214246 + - 0.0013823530072473104 + - 1.916695141756019e-05 + - -2.0157162318442508e-08 + - 6.391145984999754e-12 + - -25608.308954921802 + - 5.909760961217521 + - - 2.7918159589998375 + - 0.011582830476657863 + - -4.515545111036702e-06 + - 8.212127607375687e-10 + - -5.6706824178167993e-14 + - -25721.155782524937 + - 9.410768406918132 + transport: + model: gas + geometry: nonlinear + diameter: 3.626000000000001 + well-depth: 481.802091582003 + rotational-relaxation: 1.0 + note: GRI-Mech +- name: C2H4(11) + composition: + C: 2.0 + H: 4.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 100.0 + - 979.3618095206666 + - 5000.0 + data: + - - 3.974701280059024 + - -0.004758264205082085 + - 4.167773383176862e-05 + - -4.5138395334516856e-08 + - 1.5422102566698024e-11 + - 4915.408091071431 + - 3.624361133438067 + - - 3.5566615930688514 + - 0.011062651497825246 + - -4.170135867268412e-06 + - 7.85573759380627e-10 + - -5.700500153666173e-14 + - 4320.441720817992 + - 2.1768826469836897 + transport: + model: gas + geometry: nonlinear + diameter: 3.9710000000000005 + well-depth: 280.80075319274636 + rotational-relaxation: 1.5 + note: GRI-Mech +- name: CH3CHO(12) + composition: + C: 2.0 + H: 4.0 + O: 1.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 100.0 + - 1028.8023918717618 + - 5000.0 + data: + - - 3.5799294150648864 + - 0.005189770481773756 + - 2.2689973566565946e-05 + - -2.7374551494008247e-08 + - 9.284917028878933e-12 + - -21369.737609745825 + - 8.969696167185589 + - - 4.085613942096295 + - 0.013906161620516692 + - -5.593725835684122e-06 + - 1.0460983036639744e-09 + - -7.387431892572972e-14 + - -22039.12378460797 + - 3.768155983239756 + transport: + model: gas + geometry: nonlinear + diameter: 3.9700000000000006 + well-depth: 436.0012277388149 + rotational-relaxation: 2.0 + note: GRI-Mech +- name: C3H6O(13) + composition: + C: 3.0 + H: 6.0 + O: 1.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 100.0 + - 1023.9482752714948 + - 5000.0 + data: + - - 3.011401597809541 + - 0.015468379714093743 + - 2.1500989201259812e-05 + - -3.246115535830465e-08 + - 1.1787411835246626e-11 + - -27871.24318665779 + - 13.220327873565262 + - - 5.795918074341681 + - 0.02007633488334714 + - -7.934302252265999e-06 + - 1.4730506707783468e-09 + - -1.037754392188254e-13 + - -29253.28867814445 + - -4.243346340276008 + transport: + model: gas + geometry: nonlinear + diameter: 5.329790656420617 + well-depth: 385.40650221034775 + note: Epsilon & sigma estimated with Tc=500.53 K, Pc=48.02 bar (from Joback method) +- name: C2H6O(14) + composition: + C: 2.0 + H: 6.0 + O: 1.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 100.0 + - 984.001074254348 + - 5000.0 + data: + - - 3.2402595276101858 + - 0.01048595781146264 + - 2.6396769615238197e-05 + - -3.692935677602931e-08 + - 1.3671059764757759e-11 + - -29990.284414834074 + - 11.143301888722519 + - - 5.6849415341883915 + - 0.016131329022904588 + - -5.9636574154952995e-06 + - 1.0889720834413842e-09 + - -7.696209026654223e-14 + - -31225.821127246145 + - -4.444891933810413 + transport: + model: gas + geometry: nonlinear + diameter: 4.530000000000001 + well-depth: 362.6 + rotational-relaxation: 1.5 + note: NOx2018 +- name: CH3COOCH3(15) + composition: + C: 3.0 + H: 6.0 + O: 2.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 100.0 + - 1154.014016522329 + - 5000.0 + data: + - - 2.7506220700391415 + - 0.022081307138984107 + - 1.2174217632822808e-05 + - -2.192140560818284e-08 + - 7.336202259824892e-12 + - -51179.369924439074 + - 16.500243824317018 + - - 5.625264379169836 + - 0.026109980413376352 + - -1.1250095321623012e-05 + - 2.1176510350057785e-09 + - -1.4768311053277557e-13 + - -52774.57988068857 + - -1.8169541985155664 + transport: + model: gas + geometry: nonlinear + diameter: 5.472740943122795 + well-depth: 385.6333050074991 + note: Epsilon & sigma estimated with Tc=500.82 K, Pc=44.39 bar (from Joback method) +- name: HX(16) + composition: + H: 1.0 + X: 1.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 298.0 + - 1000.0 + - 2000.0 + data: + - - -2.0151091 + - 0.0127747196 + - -1.36892852e-05 + - 6.6707688e-09 + - -1.15946694e-12 + - -5530.52906 + - 8.4468689 + - - -0.184968995 + - 0.00605229805 + - -4.83715532e-06 + - 1.81340221e-09 + - -2.61948776e-13 + - -5915.33033 + - -0.504191778 +- name: OX(17) + composition: + O: 1.0 + X: 1.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 298.0 + - 1000.0 + - 2000.0 + data: + - - 0.195855852 + - 0.0116923252 + - -2.02271203e-05 + - 1.61601691e-08 + - -4.90070914e-12 + - -26918.9243 + - -2.01768707 + - - 2.9043837 + - -0.000274871763 + - 5.38558858e-07 + - -3.03946989e-10 + - 5.63969783e-14 + - -27441.1389 + - -14.894415 +- name: CX(18) + composition: + C: 1.0 + X: 1.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 298.0 + - 1000.0 + - 2000.0 + data: + - - -0.573265619 + - 0.0144803183 + - -2.45704673e-05 + - 1.93668551e-08 + - -5.81642502e-12 + - 14766.1073 + - 1.2024425 + - - 2.71617577 + - 1.99967762e-05 + - 3.4803163e-07 + - -2.47205634e-10 + - 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COOHX(31) + composition: + C: 1.0 + H: 2.0 + O: 2.0 + X: 1.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 100.0 + - 1005.0397573487588 + - 5000.0 + data: + - - 3.530067790015102 + - 0.004559423098264702 + - 2.3765659789292852e-05 + - -3.194061446233701e-08 + - 1.1684384295981981e-11 + - -55712.21822313507 + - -7.021210403346891 + - - 6.300815846986892 + - 0.008206156270655643 + - -3.577860107664541e-06 + - 7.243419313446359e-10 + - -5.45315780959017e-14 + - -57010.28215992336 + - -24.089422976242908 +- name: CH3X(32) + composition: + C: 1.0 + H: 3.0 + X: 1.0 + thermo: + model: NASA7 + reference-pressure: 10000.0 + temperature-ranges: + - 298.0 + - 1000.0 + - 2000.0 + data: + - - -0.552219087 + - 0.0264420133 + - -3.55617257e-05 + - 2.60043628e-08 + - -7.52706787e-12 + - -4433.46585 + - 0.692144274 + - - 3.62557353 + - 0.00739511955 + - -2.43797398e-06 + - 1.86159414e-10 + - 3.64849549e-14 + - -5187.22188 + - -18.9668272 +- name: HOX(33) + 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data: + - - 3.838841732956421 + - -0.008209687907563478 + - 6.656228164395793e-05 + - -8.223152517465067e-08 + - 3.138335541616925e-11 + - -3285.263195765613 + - -19.460852187070447 + - - 8.291164052355008 + - 0.0027943034954819776 + - 3.102600442580014e-07 + - -6.343890134318942e-11 + - -1.0080105464031819e-15 + - -5420.926456665365 + - -47.63786342878039 + sites: 2.0 +gas_reactions: +- equation: 2 CH3(9) <=> C2H6(8) + rate-constant: + A: 945000000000.0001 + b: -0.538 + Ea: 565258.4 +- equation: CH4(2) + CO(6) <=> CH3CHO(12) + rate-constant: + A: 65.60000000000001 + b: 2.86 + Ea: 363590000.0000001 +- equation: C2H6(8) + CO(6) <=> C3H6O(13) + rate-constant: + A: 0.538 + b: 3.29 + Ea: 437228000.00000006 +- equation: C2H4(11) + H2O(3) <=> C2H6O(14) + rate-constant: + A: 0.5880000000000001 + b: 2.94 + Ea: 222170000.00000006 +- equation: C2H6(8) + CO2(4) <=> CH3COOCH3(15) + rate-constant: + A: 0.292 + b: 3.13 + Ea: 486722822.00474715 +surface_reactions: +- equation: H2(5) + 2 X(1) <=> 2 HX(16) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.032 + b: 0.0 + Ea: 0.0 +- equation: O2(7) + 2 X(1) <=> 2 OX(17) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.0436 + b: -0.206 + Ea: 1500000.0 +- equation: CO(6) + X(1) <=> COX(19) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.5 + b: 0.0 + Ea: 0.0 +- equation: COX(19) + X(1) <=> CX(18) + OX(17) + type: interface-Arrhenius + rate-constant: + A: 1750000000000.0 + b: 0.0 + Ea: 116200000.0 +- equation: 2 COX(19) <=> CO2(4) + CX(18) + X(1) + type: interface-Arrhenius + rate-constant: + A: 16200000000000.0 + b: 0.5 + Ea: 241700000.00000003 +- equation: COX(19) + OX(17) <=> CO2(4) + 2 X(1) + type: interface-Arrhenius + rate-constant: + A: 2.0e+18 + b: 0.0 + Ea: 123600000.00000001 +- equation: CX(18) + HX(16) <=> CHX(20) + X(1) + type: interface-Arrhenius + rate-constant: + A: 1.7e+23 + b: -0.5 + Ea: 157900000.0 +- equation: COX(19) + HX(16) <=> CHX(20) + OX(17) + type: interface-Arrhenius + rate-constant: + A: 1.26e+19 + b: 0.073 + Ea: 191627199.99999997 +- equation: CHX(20) + HX(16) <=> CH2X(21) + X(1) + type: interface-Arrhenius + rate-constant: + A: 9.77e+23 + b: -0.087 + Ea: 81000000.00000001 +- equation: CX(18) + H2(5) <=> CH2X(21) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.04 + b: 0.0 + Ea: 29700000.0 +- equation: CHX(20) + OX(17) <=> HCOX(22) + X(1) + type: interface-Arrhenius + rate-constant: + A: 4.59e+19 + b: 0.0 + Ea: 109900000.00000001 +- equation: HCOX(22) + X(1) <=> COX(19) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 3.71e+20 + b: 0.0 + Ea: 0.0 +- equation: CH3X(32) + HX(16) <=> CH4(2) + 2 X(1) + type: interface-Arrhenius + rate-constant: + A: 1.44e+21 + b: -0.087 + Ea: 63400000.00000001 +- equation: CH2X(21) + HX(16) <=> CH3X(32) + X(1) + type: interface-Arrhenius + rate-constant: + A: 3.09e+22 + b: -0.087 + Ea: 57200000.0 +- equation: CH3(9) + X(1) <=> CH3X(32) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.16 + b: -0.099 + Ea: 0.0 +- equation: CX(18) + HOX(33) <=> COX(19) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 3.88e+24 + b: 0.188 + Ea: 62500000.0 +- equation: CH3X(32) + HOX(33) <=> CH4(2) + OX(17) + X(1) + type: interface-Arrhenius + rate-constant: + A: 2.98e+21 + b: 0.101 + Ea: 25800000.0 +- equation: CH2X(21) + HOX(33) <=> CH3X(32) + OX(17) + type: interface-Arrhenius + rate-constant: + A: 1.39e+20 + b: 0.101 + Ea: 19000000.0 +- equation: CHX(20) + HOX(33) <=> CH2X(21) + OX(17) + type: interface-Arrhenius + rate-constant: + A: 4.4e+21 + b: 0.101 + Ea: 42400000.0 +- equation: CX(18) + HOX(33) <=> CHX(20) + OX(17) + type: interface-Arrhenius + rate-constant: + A: 2.43e+20 + b: -0.312 + Ea: 118900000.0 +- equation: HOX(33) + HX(16) <=> H2O(3) + 2 X(1) + type: interface-Arrhenius + rate-constant: + A: 1.85e+19 + b: 0.086 + Ea: 41500000.0 +- equation: HOX(33) + X(1) <=> HX(16) + OX(17) + type: interface-Arrhenius + rate-constant: + A: 2.25e+19 + b: 0.188 + Ea: 29600000.000000004 +- equation: 2 HOX(33) <=> H2O(3) + OX(17) + X(1) + type: interface-Arrhenius + rate-constant: + A: 2.34e+19 + b: 0.274 + Ea: 92300000.00000001 +- equation: HCOX(22) + HOX(33) <=> HOCXO(35) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 2.28e+19 + b: 0.263 + Ea: 15900000.000000002 +- equation: HOCXO(35) + X(1) <=> COX(19) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 1.46e+23 + b: -0.213 + Ea: 54300000.0 +- equation: HOCXO(35) + X(1) <=> CO2(4) + HX(16) + X(1) + type: interface-Arrhenius + rate-constant: + A: 3.73e+19 + b: 0.475 + Ea: 33600000.0 +- equation: 2 COX(19) <=> CO2X(36) + CX(18) + type: interface-Arrhenius + rate-constant: + A: 16200000000000.0 + b: 0.5 + Ea: 241700000.00000003 +- equation: CO2(4) + X(1) <=> CO2X(36) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.005 + b: 0.0 + Ea: 0.0 +- equation: COX(19) + OX(17) <=> CO2X(36) + X(1) + type: interface-Arrhenius + rate-constant: + A: 3.7e+20 + b: 0.0 + Ea: 117600000.00000001 +- equation: COX(19) + HOX(33) <=> CO2X(36) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 1.0e+18 + b: 0.0 + Ea: 38700000.0 +- equation: HOCXO(35) + X(1) <=> CO2X(36) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 4.27e+18 + b: 0.549 + Ea: 4184000.0 +- equation: CO2X(36) + HOX(33) <=> HOCXO(35) + OX(17) + type: interface-Arrhenius + rate-constant: + A: 2.15e+18 + b: 0.097 + Ea: 110876000.0 +- equation: CH2COX2(27) <=> CH2X(21) + COX(19) + type: interface-Arrhenius + rate-constant: + A: 4220000000000.0 + b: 0.0 + Ea: 104000000.00000001 +- equation: CH2COX(26) + X(1) <=> CH2COX2(27) + type: interface-Arrhenius + rate-constant: + A: 2.0e+20 + b: 0.0 + Ea: 0.0 +- equation: C2H4(11) + X(1) <=> C2H4X(29) + type: sticking-Arrhenius + sticking-coefficient: + A: 7.0e-06 + b: 0.0 + Ea: 0.0 +- equation: C2H4(11) + 2 X(1) <=> C2H4X2(30) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.69 + b: 0.0 + Ea: 0.0 +- equation: 2 CH2X(21) <=> C2H4X2(30) + type: interface-Arrhenius + rate-constant: + A: 9.89e+22 + b: 0.0 + Ea: 154000000.0 +- equation: C2H4X(29) + X(1) <=> C2H4X2(30) + type: interface-Arrhenius + rate-constant: + A: 1.78e+20 + b: 0.0 + Ea: 12000000.0 +- equation: CO2(4) + 2 X(1) <=> OCXOX(34) + type: sticking-Arrhenius + sticking-coefficient: + A: 1.66 + b: 0.0 + Ea: 0.0 +- equation: OCXOX(34) <=> COX(19) + OX(17) + type: interface-Arrhenius + rate-constant: + A: 4220000000000.0 + b: 0.0 + Ea: 133318492.10043974 +- equation: CO2X(36) + X(1) <=> OCXOX(34) + type: interface-Arrhenius + rate-constant: + A: 4.0e+20 + b: 0.0 + Ea: 0.0 +- equation: C2H6(8) + 2 X(1) <=> 2 CH3X(32) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.015 + b: 0.0 + Ea: 23107338.64226449 +- equation: CH3OH(10) + 2 X(1) <=> CH3X(32) + HOX(33) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.015 + b: 0.0 + Ea: 5000000.0 +- equation: CH3OH(10) + 2 X(1) <=> CH3OX(24) + HX(16) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.099 + b: 0.0 + Ea: 76543362.59050444 +- equation: C2H4(11) + 2 X(1) <=> 2 CH2X(21) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.01 + b: 0.0 + Ea: 41840000.00000001 +- equation: CH3CHO(12) + 2 X(1) <=> CH3X(32) + HCOX(22) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.015 + b: 0.0 + Ea: 5000000.0 +- equation: C2H6O(14) + 2 X(1) <=> CH3OX(24) + CH3X(32) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.015 + b: 0.0 + Ea: 10548863.324930396 +- equation: HCOHX(23) + X(1) <=> CHX(20) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 1.46e+23 + b: -0.213 + Ea: 54300000.00000001 +- equation: HCOHX(23) + X(1) <=> HCOX(22) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 58232049.1536672 +- equation: CH3OX(24) + X(1) <=> CH2X(21) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 1.46e+23 + b: -0.213 + Ea: 54300000.00000001 +- equation: CH3OX(24) + X(1) <=> HCOHX(23) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 7.42e+20 + b: 0.0 + Ea: 0.0 +- equation: CH3COOX(25) + X(1) <=> CH2X(21) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 152862746.7252149 +- equation: CH3COOX(25) + X(1) <=> CH2COX(26) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 1.5392202847961747e+20 + b: 0.1314545095819981 + Ea: 76771524.3146206 +- equation: CH2COX(26) + X(1) <=> CH2X(21) + COX(19) + type: interface-Arrhenius + rate-constant: + A: 3.282e+19 + b: 0.0 + Ea: 241213355.90675473 +- equation: CH3COOHX(28) + X(1) <=> CH3X(32) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 142367281.8074835 +- equation: CH3COOHX(28) + X(1) <=> CH3COOX(25) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 2116349673557.9387 + b: 2.0707027167582193 + Ea: 135191101.8241696 +- equation: C2H4X(29) + X(1) <=> 2 CH2X(21) + type: interface-Arrhenius + rate-constant: + A: 3.282e+19 + b: 0.0 + Ea: 241213355.90675473 +- equation: COOHX(31) + X(1) <=> HCOHX(23) + OX(17) + type: interface-Arrhenius + rate-constant: + A: 1.641e+19 + b: 0.0 + Ea: 241213355.90675473 +- equation: COOHX(31) + X(1) <=> HCOX(22) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 1.781e+20 + b: 0.0 + Ea: 157271108.0512041 +- equation: HOCXO(35) + HX(16) <=> COOHX(31) + X(1) + type: interface-Arrhenius + rate-constant: + A: 2.308e+21 + b: 0.0 + Ea: 70434299.92477237 +- equation: HOCXO(35) + 2 X(1) <=> HX(16) + OCXOX(34) + type: interface-Arrhenius + rate-constant: + A: 1.8566666666666664e+27 + b: 0.0 + Ea: 46000000.00000001 +- equation: CH2X(21) + COOHX(31) <=> CH3COOX(25) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 3.9663639242219776e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: HCOX(22) + OX(17) <=> COX(19) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 3.298e+20 + b: 0.0 + Ea: 0.0 +- equation: HCOHX(23) + OX(17) <=> HCOX(22) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 0.0 +- equation: HCOHX(23) + HOX(33) <=> CH3OX(24) + OX(17) + type: interface-Arrhenius + rate-constant: + A: 1.39e+20 + b: 0.101 + Ea: 19000000.0 +- equation: CH2COX2(27) + OX(17) <=> CH2X(21) + OCXOX(34) + type: interface-Arrhenius + rate-constant: + A: 3.298e+20 + b: 0.0 + Ea: 0.0 +- equation: CH3COOHX(28) + OX(17) <=> CH3COOX(25) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 4.215e+23 + b: -0.101 + Ea: 92700000.00000001 +- equation: COOHX(31) + OX(17) <=> HOCXO(35) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 1.405e+23 + b: -0.101 + Ea: 92700000.00000001 +- equation: CH2X(21) + CX(18) <=> 2 CHX(20) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 64390227.63121586 +- equation: CX(18) + HCOX(22) <=> CHX(20) + COX(19) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 36249036.34728507 +- equation: CX(18) + HCOHX(23) <=> CHX(20) + HCOX(22) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 24052724.51607596 +- equation: CH3OX(24) + CX(18) <=> CHX(20) + HCOHX(23) + type: interface-Arrhenius + rate-constant: + A: 7.425803660210784e+20 + b: 0.0 + Ea: 37291008.396549925 +- equation: CH3COOHX(28) + CX(18) <=> CH3COOX(25) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 1.1899091772665933e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: COOHX(31) + CX(18) <=> CHX(20) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 3.9663639242219776e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: CH3X(32) + CX(18) <=> CH2X(21) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 9.894e+20 + b: 0.0 + Ea: 0.0 +- equation: CHX(20) + HCOX(22) <=> CH2X(21) + COX(19) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 71158808.71606924 +- equation: CHX(20) + HOCXO(35) <=> COX(19) + HCOHX(23) + type: interface-Arrhenius + rate-constant: + A: 4.4e+21 + b: 0.101 + Ea: 42400000.0 +- equation: COX(19) + HCOHX(23) <=> 2 HCOX(22) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 184236253.79594633 +- equation: CH2X(21) + HOCXO(35) <=> CH3OX(24) + COX(19) + type: interface-Arrhenius + rate-constant: + A: 1.39e+20 + b: 0.101 + Ea: 19000000.0 +- equation: HCOHX(23) + HCOX(22) <=> CH3OX(24) + COX(19) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 60967019.55418524 +- equation: CH3COOX(25) + COX(19) <=> CH2COX(26) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 257841657.858039 +- equation: CH3COOHX(28) + COX(19) <=> CH3COOX(25) + HCOX(22) + type: interface-Arrhenius + rate-constant: + A: 1.1899091772665933e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: CH2COX2(27) + CH2X(21) <=> C2H4X2(30) + COX(19) + type: interface-Arrhenius + rate-constant: + A: 1.39e+20 + b: 0.101 + Ea: 19000000.0 +- equation: COOHX(31) + COX(19) <=> HCOX(22) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 3.9663639242219776e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 + duplicate: true +- equation: COOHX(31) + COX(19) <=> HCOX(22) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 3.9663639242219776e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 + duplicate: true +- equation: CH2X(21) + HCOX(22) <=> CH3X(32) + COX(19) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 55966956.128033236 +- equation: COX(19) + HOCXO(35) <=> CO2X(36) + HCOX(22) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 167509689.74174654 +- equation: CHX(20) + HCOHX(23) <=> CH2X(21) + HCOX(22) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 112742416.48001407 +- equation: CH2X(21) + HCOHX(23) <=> CH3OX(24) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 1.39e+20 + b: 0.101 + Ea: 19000000.0 + duplicate: true +- equation: CH2X(21) + HCOHX(23) <=> CH3OX(24) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 89108210.838116 + duplicate: true +- equation: CH3COOHX(28) + CHX(20) <=> CH2X(21) + CH3COOX(25) + type: interface-Arrhenius + rate-constant: + A: 1.1899091772665933e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: CHX(20) + COOHX(31) <=> HCOHX(23) + HCOX(22) + type: interface-Arrhenius + rate-constant: + A: 2.3606654387125515e+20 + b: -0.07441820738726125 + Ea: 118482473.58896875 +- equation: CHX(20) + COOHX(31) <=> CH2X(21) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 3.9663639242219776e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: 2 CH2X(21) <=> CH3X(32) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 84108147.41196401 +- equation: CH2X(21) + HCOHX(23) <=> CH3OX(24) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 1.39e+20 + b: 0.101 + Ea: 19000000.0 + duplicate: true +- equation: CH2X(21) + HCOHX(23) <=> CH3OX(24) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 89108210.838116 + duplicate: true +- equation: CH2X(21) + HCOHX(23) <=> CH3X(32) + HCOX(22) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 74146899.09419289 +- equation: CH2X(21) + CH3OX(24) <=> CH3X(32) + HCOHX(23) + type: interface-Arrhenius + rate-constant: + A: 7.425803660210784e+20 + b: 0.0 + Ea: 47149968.286924005 +- equation: CH2X(21) + CH3COOX(25) <=> CH2COX(26) + CH3OX(24) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 227644252.94263765 +- equation: CH2X(21) + CH3COOHX(28) <=> CH3COOX(25) + CH3X(32) + type: interface-Arrhenius + rate-constant: + A: 3.9663639242219776e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 + duplicate: true +- equation: CH2X(21) + CH3COOHX(28) <=> CH3COOX(25) + CH3X(32) + type: interface-Arrhenius + rate-constant: + A: 1.1899091772665933e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 + duplicate: true +- equation: CH2X(21) + COOHX(31) <=> CH3OX(24) + HCOX(22) + type: interface-Arrhenius + rate-constant: + A: 3.9663639242219776e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: CH2X(21) + COOHX(31) <=> CH3X(32) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 3.9663639242219776e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: CH2X(21) + HOCXO(35) <=> CH3X(32) + CO2X(36) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 57420335.03999308 +- equation: 2 HCOHX(23) <=> CH3OX(24) + HCOX(22) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 86849762.93360609 +- equation: CH3COOX(25) + HCOX(22) <=> CH2COX(26) + COOHX(31) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 130858280.6458121 +- equation: COOHX(31) + COX(19) <=> HCOX(22) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 3.9663639242219776e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 + duplicate: true +- equation: COOHX(31) + COX(19) <=> HCOX(22) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 3.9663639242219776e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 + duplicate: true +- equation: CH3COOHX(28) + HCOHX(23) <=> CH3COOX(25) + CH3OX(24) + type: interface-Arrhenius + rate-constant: + A: 1.1899091772665933e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: COOHX(31) + HCOHX(23) <=> CH3OX(24) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 3.9663639242219776e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: HCOHX(23) + HOCXO(35) <=> CH3OX(24) + CO2X(36) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 70123198.87940632 +- equation: CH3COOHX(28) + HOCXO(35) <=> CH3COOX(25) + COOHX(31) + type: interface-Arrhenius + rate-constant: + A: 1.254e+21 + b: 0.0 + Ea: 131383021.93699808 +- equation: CH2X(21) + CH3COOHX(28) <=> CH3COOX(25) + CH3X(32) + type: interface-Arrhenius + rate-constant: + A: 1.1899091772665933e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 + duplicate: true +- equation: CH2X(21) + CH3COOHX(28) <=> CH3COOX(25) + CH3X(32) + type: interface-Arrhenius + rate-constant: + A: 3.9663639242219776e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 + duplicate: true +- equation: CH3COOX(25) + HOCXO(35) <=> CH3COOHX(28) + CO2X(36) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 64004883.585984856 +- equation: 2 HOCXO(35) <=> CO2X(36) + COOHX(31) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 65511750.51913242 +- equation: CH4(2) + HOX(33) + X(1) <=> CH3X(32) + H2OX(43) + type: sticking-Arrhenius + sticking-coefficient: + A: 1.0 + b: 0.0 + Ea: 10000000.0 +- equation: H2O(3) + X(1) <=> H2OX(43) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.75 + b: 0.0 + Ea: 0.0 +- equation: H2OX(43) + X(1) <=> HOX(33) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 1.15e+18 + b: 0.0 + Ea: 101400000.00000001 +- equation: H2OX(43) + OX(17) <=> 2 HOX(33) + type: interface-Arrhenius + rate-constant: + A: 1.0e+19 + b: 0.0 + Ea: 90500000.0 +- equation: COX(19) + H2OX(43) <=> HOCXO(35) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 4.43e+18 + b: 0.492 + Ea: 99160800.0 +- equation: CO2X(36) + H2OX(43) <=> HOCXO(35) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 3.48e+18 + b: -0.031 + Ea: 91434774.13589227 +- equation: CH2X(21) + H2OX(43) <=> CH3X(32) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 3.3e+18 + b: 0.099 + Ea: 58994400.00000001 +- equation: CHX(20) + H2OX(43) <=> CH2X(21) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 7.29e+18 + b: 0.269 + Ea: 142256000.0 +- equation: CX(18) + H2OX(43) <=> CHX(20) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 4.19e+18 + b: 0.09 + Ea: 65270400.00000001 +- equation: CHX(20) + H2OX(43) <=> HCOHX(23) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 7.932727848443955e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: CH2X(21) + H2OX(43) <=> CH3OX(24) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 7.932727848443955e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: HCOX(22) + HOX(33) <=> COX(19) + H2OX(43) + type: interface-Arrhenius + rate-constant: + A: 3.261e+20 + b: 0.0 + Ea: 28945602.70881056 +- equation: H2OX(43) + HCOHX(23) <=> CH3OX(24) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 7.932727848443955e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: CH3COOHX(28) + HOX(33) <=> CH3COOX(25) + H2OX(43) + type: interface-Arrhenius + rate-constant: + A: 1.254e+21 + b: 0.0 + Ea: 109509900.89857398 +- equation: COOHX(31) + HOX(33) <=> H2OX(43) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 107426878.96157578 +- equation: CH4(2) + X(1) <=> C.[Pt](84) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.008 + b: 0.0 + Ea: 0.0 +- equation: C.[Pt](84) + X(1) <=> CH3X(32) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 1.54e+20 + b: 0.087 + Ea: 55800000.000000015 +- equation: C.[Pt](84) + CX(18) <=> CH3X(32) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 1.586545569688791e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C.[Pt](84) + CHX(20) <=> CH2X(21) + CH3X(32) + type: interface-Arrhenius + rate-constant: + A: 1.586545569688791e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C.[Pt](84) + COX(19) <=> CH3X(32) + HCOX(22) + type: interface-Arrhenius + rate-constant: + A: 1.586545569688791e+18 + b: -0.047836414774522495 + Ea: 160116599.8927413 +- equation: C.[Pt](84) + HCOHX(23) <=> CH3OX(24) + CH3X(32) + type: interface-Arrhenius + rate-constant: + A: 1.586545569688791e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: CH3COOHX(28) + CH3X(32) <=> C.[Pt](84) + CH3COOX(25) + type: interface-Arrhenius + rate-constant: + A: 1.254e+21 + b: 0.0 + Ea: 80600444.07764292 +- equation: CH3X(32) + COOHX(31) <=> C.[Pt](84) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 78517422.1406448 +- equation: C.[Pt](84) + CH2X(21) <=> 2 CH3X(32) + type: interface-Arrhenius + rate-constant: + A: 1.586545569688791e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C.[Pt](84) + OX(17) <=> CH3X(32) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 5.62e+23 + b: -0.101 + Ea: 92700000.00000001 +- equation: CH3X(32) + HOCXO(35) <=> C.[Pt](84) + CO2X(36) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 28775417.599598866 +- equation: CH3X(32) + H2OX(43) <=> C.[Pt](84) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 100390543.17906903 +- equation: CH3COOHX(28) + CX(18) <=> CC#[Pt](307) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 2.3606654387125515e+20 + b: -0.07441820738726125 + Ea: 118482473.58896875 +- equation: CC#[Pt](307) + X(1) <=> CH3X(32) + CX(18) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 197242288.50492182 +- equation: C.[Pt](84) + CX(18) <=> CC#[Pt](307) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 1.586545569688791e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C2H2X2(338) <=> 2 CHX(20) + type: interface-Arrhenius + rate-constant: + A: 7930000000000.0 + b: 0.0 + Ea: 90000000.00000001 +- equation: HCOX(22) + X(1) <=> CHOX2(110) + type: interface-Arrhenius + rate-constant: + A: 1.0e+20 + b: 0.0 + Ea: 0.0 +- equation: HCOHX(23) + 2 X(1) <=> CHOX2(110) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 1.8566666666666664e+27 + b: 0.0 + Ea: 46000000.00000001 +- equation: CHX(20) + OX(17) <=> CHOX2(110) + type: interface-Arrhenius + rate-constant: + A: 6.54e+20 + b: 0.0 + Ea: 142000000.0 +- equation: CHOX2(110) + COX(19) <=> CHX(20) + OCXOX(34) + type: interface-Arrhenius + rate-constant: + A: 1.39e+20 + b: 0.101 + Ea: 19000000.0 +- equation: C2H2X2(338) + OX(17) <=> CHOX2(110) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 6.596e+20 + b: 0.0 + Ea: 0.0 +- equation: C#C.[Pt](513) + X(1) <=> C2H2X2(338) + type: interface-Arrhenius + rate-constant: + A: 1.0e+20 + b: 0.0 + Ea: 0.0 +- equation: C2H4(11) + 2 X(1) <=> C2H3X(88) + HX(16) + type: sticking-Arrhenius + sticking-coefficient: + A: 0.1 + b: 0.0 + Ea: 49942316.1792833 +- equation: C2H4X(29) + X(1) <=> C2H3X(88) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 10479056557881.693 + b: 1.6009912295246733 + Ea: 79448444.9235931 +- equation: C2H4X(29) + OX(17) <=> C2H3X(88) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 5.62e+23 + b: -0.101 + Ea: 92700000.00000001 +- equation: C2H4X(29) + CX(18) <=> C2H3X(88) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 1.586545569688791e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C2H4X(29) + COX(19) <=> C2H3X(88) + HCOX(22) + type: interface-Arrhenius + rate-constant: + A: 1.586545569688791e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C2H3X(88) + X(1) <=> CH2X(21) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 145637492.82208303 +- equation: C2H4X(29) + CHX(20) <=> C2H3X(88) + CH2X(21) + type: interface-Arrhenius + rate-constant: + A: 1.586545569688791e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C2H4X(29) + CH2X(21) <=> C2H3X(88) + CH3X(32) + type: interface-Arrhenius + rate-constant: + A: 1.586545569688791e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C2H4X(29) + HCOHX(23) <=> C2H3X(88) + CH3OX(24) + type: interface-Arrhenius + rate-constant: + A: 1.586545569688791e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C2H4X(29) + CH3COOX(25) <=> C2H3X(88) + CH3COOHX(28) + type: interface-Arrhenius + rate-constant: + A: 1.672e+21 + b: 0.0 + Ea: 135491449.11999902 +- equation: C2H4X(29) + CH3X(32) <=> C.[Pt](84) + C2H3X(88) + type: interface-Arrhenius + rate-constant: + A: 1.672e+21 + b: 0.0 + Ea: 86791893.19764192 +- equation: C2H4X(29) + HOX(33) <=> C2H3X(88) + H2OX(43) + type: interface-Arrhenius + rate-constant: + A: 1.672e+21 + b: 0.0 + Ea: 115701350.01857296 +- equation: C2H4X(29) + HOCXO(35) <=> C2H3X(88) + COOHX(31) + type: interface-Arrhenius + rate-constant: + A: 1.672e+21 + b: 0.0 + Ea: 137574471.05699712 +- equation: C2H3X(88) + HOCXO(35) <=> C2H4X(29) + CO2X(36) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 59525962.94598559 +- equation: C2H3X(88) + 2 X(1) <=> C2H2X2(338) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 1.8566666666666664e+27 + b: 0.0 + Ea: 46000000.00000001 +- equation: C2H3X(88) + CH3COOX(25) <=> C#C.[Pt](513) + CH3COOHX(28) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 188214833.61283815 +- equation: 2 C2H3X(88) <=> C#C.[Pt](513) + C2H4X(29) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 183735912.9728388 +- equation: C2H3X(88) + HOCXO(35) <=> C#C.[Pt](513) + COOHX(31) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 189721700.54598567 +- equation: C2H3X(88) + HOX(33) <=> C#C.[Pt](513) + H2OX(43) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 173898591.70967877 +- equation: C2H3X(88) + CH3X(32) <=> C#C.[Pt](513) + C.[Pt](84) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 152985367.6264521 +- equation: C2H4X2(30) + X(1) <=> C2H3X2(120) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 2.225e+20 + b: 0.0 + Ea: 59000000.00000001 +- equation: C2H3X2(120) + HOX(33) <=> C2H4X2(30) + OX(17) + type: interface-Arrhenius + rate-constant: + A: 1.39e+20 + b: 0.101 + Ea: 19000000.0 +- equation: C2H4X2(30) + CX(18) <=> C2H3X2(120) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 1.4851607320421568e+21 + b: 0.0 + Ea: 39186738.0315976 +- equation: C2H3X2(120) + HCOX(22) <=> C2H4X2(30) + COX(19) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 57175560.28408988 +- equation: C2H3X2(120) <=> CH2X(21) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 27400000000000.0 + b: 0.0 + Ea: 140000000.00000003 +- equation: CH2COX2(27) + CHX(20) <=> C2H3X2(120) + COX(19) + type: interface-Arrhenius + rate-constant: + A: 4.4e+21 + b: 0.101 + Ea: 42400000.0 +- equation: C2H3X2(120) + CH2X(21) <=> C2H4X2(30) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 1.39e+20 + b: 0.101 + Ea: 19000000.0 + duplicate: true +- equation: C2H3X2(120) + CH2X(21) <=> C2H4X2(30) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 85316751.56802069 + duplicate: true +- equation: C2H4X2(30) + CH2X(21) <=> C2H3X2(120) + CH3X(32) + type: interface-Arrhenius + rate-constant: + A: 1.4851607320421568e+21 + b: 0.0 + Ea: 49045697.92197167 +- equation: C2H3X2(120) + HCOHX(23) <=> C2H4X2(30) + HCOX(22) + type: interface-Arrhenius + rate-constant: + A: 4.18e+20 + b: 0.0 + Ea: 77217406.95012063 +- equation: C2H3X2(120) + CH3OX(24) <=> C2H4X2(30) + HCOHX(23) + type: interface-Arrhenius + rate-constant: + A: 7.425803660210784e+20 + b: 0.0 + Ea: 47754270.364952326 +- equation: C2H3X2(120) + CH3COOHX(28) <=> C2H4X2(30) + CH3COOX(25) + type: interface-Arrhenius + rate-constant: + A: 1.1899091772665933e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C.[Pt](84) + C2H3X2(120) <=> C2H4X2(30) + CH3X(32) + type: interface-Arrhenius + rate-constant: + A: 1.586545569688791e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C2H3X2(120) + H2OX(43) <=> C2H4X2(30) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 7.932727848443955e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C2H3X2(120) + COOHX(31) <=> C2H4X2(30) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 3.9663639242219776e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C2H3X2(120) + X(1) <=> C2H2X2(338) + HX(16) + type: interface-Arrhenius + rate-constant: + A: 4.7500000000000007e+20 + b: 0.0 + Ea: 72000000.0 +- equation: C2H3X2(120) + CX(18) <=> C2H2X2(338) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 61189750.20487869 + duplicate: true +- equation: C2H3X2(120) + CHX(20) <=> C2H2X2(338) + CH2X(21) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 149879442.16881678 + duplicate: true +- equation: C2H2X2(338) + CH2X(21) <=> C2H3X2(120) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 2.78e+20 + b: 0.101 + Ea: 19000000.0 + duplicate: true +- equation: C2H3X2(120) + COX(19) <=> C2H2X2(338) + HCOX(22) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 221373279.48474905 + duplicate: true +- equation: C2H2X2(338) + HCOHX(23) <=> C2H3X2(120) + HCOX(22) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 92162974.31119731 +- equation: C2H3X2(120) + HCOHX(23) <=> C2H2X2(338) + CH3OX(24) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 123986788.6224088 + duplicate: true +- equation: C2H2X2(338) + CH3COOHX(28) <=> C2H3X2(120) + CH3COOX(25) + type: interface-Arrhenius + rate-constant: + A: 2.3798183545331866e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C2H2X2(338) + C2H4X(29) <=> C2H3X(88) + C2H3X2(120) + type: interface-Arrhenius + rate-constant: + A: 3.173091139377582e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: 2 C2H3X2(120) <=> C2H2X2(338) + C2H4X2(30) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 114354432.63892333 + duplicate: true +- equation: C2H2X2(338) + COOHX(31) <=> C2H3X2(120) + HOCXO(35) + type: interface-Arrhenius + rate-constant: + A: 7.932727848443955e+17 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C2H3X2(120) + CH2X(21) <=> C2H2X2(338) + CH3X(32) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 111283924.7829956 + duplicate: true +- equation: C2H3X2(120) + OX(17) <=> C2H2X2(338) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 140986479.30347368 + duplicate: true +- equation: C2H2X2(338) + H2OX(43) <=> C2H3X2(120) + HOX(33) + type: interface-Arrhenius + rate-constant: + A: 1.586545569688791e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C.[Pt](84) + C2H2X2(338) <=> C2H3X2(120) + CH3X(32) + type: interface-Arrhenius + rate-constant: + A: 3.173091139377582e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: CH2X(21) + CHOX2(110) <=> C2H3X2(120) + OX(17) + type: interface-Arrhenius + rate-constant: + A: 1.39e+20 + b: 0.101 + Ea: 19000000.0 +- equation: C2H3X(88) + X(1) <=> C2H3X2(120) + type: interface-Arrhenius + rate-constant: + A: 7.15e+19 + b: 0.0 + Ea: 3000000.0 +- equation: C2H3X2(120) + C2H4X(29) <=> C2H3X(88) + C2H4X2(30) + type: interface-Arrhenius + rate-constant: + A: 1.586545569688791e+18 + b: -0.047836414774522495 + Ea: 144264947.1779375 +- equation: C2H2X2(338) + HOX(33) <=> C2H3X2(120) + OX(17) + type: interface-Arrhenius + rate-constant: + A: 2.78e+20 + b: 0.101 + Ea: 19000000.0 + duplicate: true +- equation: C2H3X2(120) + CX(18) <=> C2H2X2(338) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 7.425803660210784e+20 + b: 0.0 + Ea: 36245323.178619735 + duplicate: true +- equation: C2H2X2(338) + HCOX(22) <=> C2H3X2(120) + COX(19) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 63058389.99004559 + duplicate: true +- equation: C2H2X2(338) + CH2X(21) <=> C2H3X2(120) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 2.78e+20 + b: 0.101 + Ea: 19000000.0 + duplicate: true +- equation: C2H2X2(338) + CH2X(21) <=> C2H3X2(120) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 1.672e+21 + b: 0.0 + Ea: 91199581.2739764 + duplicate: true +- equation: C2H3X2(120) + CH2X(21) <=> C2H2X2(338) + CH3X(32) + type: interface-Arrhenius + rate-constant: + A: 7.425803660210784e+20 + b: 0.0 + Ea: 46104283.068993814 + duplicate: true +- equation: C2H3X2(120) + CH2X(21) <=> C2H4X2(30) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 1.39e+20 + b: 0.101 + Ea: 19000000.0 + duplicate: true +- equation: C2H3X2(120) + CH2X(21) <=> C2H4X2(30) + CHX(20) + type: interface-Arrhenius + rate-constant: + A: 8.36e+20 + b: 0.0 + Ea: 85316751.56802069 + duplicate: true +- equation: C2H2X2(338) + CH3OX(24) <=> C2H3X2(120) + HCOHX(23) + type: interface-Arrhenius + rate-constant: + A: 1.4851607320421568e+21 + b: 0.0 + Ea: 50695685.21793019 + duplicate: true +- equation: 2 C2H3X2(120) <=> C2H2X2(338) + C2H4X2(30) + type: interface-Arrhenius + rate-constant: + A: 7.425803660210784e+20 + b: 0.0 + Ea: 46708585.147022136 + duplicate: true diff --git a/test/rmgpy/test_data/yaml_writer_data/chemkin/chem0047-gas.yaml b/test/rmgpy/test_data/yaml_writer_data/chemkin/chem0047-gas.yaml new file mode 100644 index 0000000000..c1fd72df89 --- /dev/null +++ b/test/rmgpy/test_data/yaml_writer_data/chemkin/chem0047-gas.yaml @@ -0,0 +1,1117 @@ +generator: ck2yaml +input-files: [chem0047-gas.inp, chem0047-surface.inp, tran.dat] +cantera-version: 3.2.0a1 +date: Fri, 21 Feb 2025 07:38:38 -0500 + +units: {length: cm, time: s, quantity: mol, activation-energy: kcal/mol} + +phases: +- name: gas + thermo: ideal-gas + elements: [H, D, T, C, Ci, O, Oi, N, Ne, Ar, He, Si, S, F, Cl, Br, I, + X] + species: [Ar, Ne, N2, CH4(2), H2O(3), CO2(4), H2(5), CO(6), O2(7), C2H6(8), + CH3(9), CH3OH(10), C2H4(11), CH3CHO(12), C3H6O(13), C2H6O(14), CH3COOCH3(15)] + kinetics: gas + reactions: + - gas-reactions + transport: mixture-averaged + state: {T: 300.0, P: 1 atm} +- name: site0 + thermo: ideal-surface + adjacent-phases: [gas] + elements: [H, D, T, C, Ci, O, Oi, N, Ne, Ar, He, Si, S, F, Cl, Br, I, + X] + species: [X(1), HX(16), OX(17), CX(18), COX(19), CHX(20), CH2X(21), HCOX(22), + HCOHX(23), CH3OX(24), CH3COOX(25), CH2COX(26), CH2COX2(27), CH3COOHX(28), + C2H4X(29), C2H4X2(30), COOHX(31), CH3X(32), HOX(33), OCXOX(34), HOCXO(35), + CO2X(36), H2OX(43), 'C.[Pt](84)', C2H3X(88), CHOX2(110), C2H3X2(120), + 'CC#[Pt](307)', C2H2X2(338), 'C#C.[Pt](513)'] + site-density: 3.148e-09 + kinetics: surface + reactions: + - site0-reactions + state: {T: 300.0, P: 1 atm} + +elements: +- symbol: Ci + atomic-weight: 13.003 +- symbol: D + atomic-weight: 2.014 +- symbol: Oi + atomic-weight: 17.999 +- symbol: T + atomic-weight: 3.016 +- symbol: X + atomic-weight: 195.083 + +species: +- name: Ar + composition: {Ar: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 6000.0] + data: + - [2.5, 0.0, 0.0, 0.0, 0.0, -745.375, 4.37967] + transport: + model: gas + geometry: atom + well-depth: 136.501 + diameter: 3.33 + note: GRI-Mech +- name: Ne + composition: {Ne: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 6000.0] + data: + - [2.5, 0.0, 0.0, 0.0, 0.0, -745.375, 3.35532] + transport: + model: gas + geometry: atom + well-depth: 148.6 + diameter: 3.758 + note: Epsilon & sigma estimated with fixed Lennard Jones Parameters. + This is the fallback method! Try improving transport databases! +- name: N2 + composition: {N: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 6000.0] + data: + - [3.53101, -1.23661e-04, -5.02999e-07, 2.43531e-09, -1.40881e-12, -1046.98, + 2.96747] + - [2.95258, 1.3969e-03, -4.92632e-07, 7.8601e-11, -4.60755e-15, -923.949, + 5.87189] + transport: + model: gas + geometry: linear + well-depth: 97.53 + diameter: 3.621 + polarizability: 1.76 + rotational-relaxation: 4.0 + note: GRI-Mech +- name: CH4(2) + composition: {C: 1, H: 4} + thermo: + model: NASA7 + temperature-ranges: [100.0, 1084.12, 5000.0] + data: + - [4.2054162, -5.35558463e-03, 2.51123636e-05, -2.13763299e-08, 5.97525767e-12, + -1.01619433e+04, -0.921282727] + - [0.908260213, 0.0114540949, -4.57174339e-06, 8.2919286e-10, -5.66315868e-14, + -9719.97202, 13.9931256] + transport: + model: gas + geometry: nonlinear + well-depth: 141.4 + diameter: 3.746 + polarizability: 2.6 + rotational-relaxation: 13.0 + note: GRI-Mech +- name: H2O(3) + composition: {H: 2, O: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 1130.24, 5000.0] + data: + - [4.05763622, -7.87940252e-04, 2.90878932e-06, -1.47520578e-09, 2.12849596e-13, + -3.02815867e+04, -0.31136547] + - [2.84324781, 2.75108975e-03, -7.81033883e-07, 1.07244192e-10, -5.79396739e-15, + -2.99586116e+04, 5.91043491] + transport: + model: gas + geometry: nonlinear + well-depth: 572.402 + diameter: 2.605 + dipole: 1.844 + rotational-relaxation: 4.0 + note: GRI-Mech +- name: CO2(4) + composition: {C: 1, O: 2} + thermo: + model: NASA7 + temperature-ranges: [100.0, 978.22, 5000.0] + data: + - [3.28084424, 2.50186e-03, 8.08190844e-06, -1.20510196e-08, 4.66541928e-12, + -4.84008303e+04, 6.00081544] + - [4.67427528, 2.60962688e-03, -9.85682082e-07, 1.95712015e-10, -1.49834714e-14, + -4.89512173e+04, -2.11078032] + transport: + model: gas + geometry: linear + well-depth: 244.001 + diameter: 3.763 + polarizability: 2.65 + rotational-relaxation: 2.1 + note: GRI-Mech +- name: H2(5) + composition: {H: 2} + thermo: + model: NASA7 + temperature-ranges: [100.0, 1959.08, 5000.0] + data: + - [3.43536434, 2.12708431e-04, -2.78620683e-07, 3.40263746e-10, -7.76023528e-14, + -1031.35985, -3.90841817] + - [2.78814269, 5.87671008e-04, 1.58996341e-07, -5.52710777e-11, 4.34290394e-15, + -596.130615, 0.112869836] + transport: + model: gas + geometry: linear + well-depth: 38.0 + diameter: 2.92 + polarizability: 0.79 + rotational-relaxation: 280.0 + note: GRI-Mech +- name: CO(6) + composition: {C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 1571.66, 5000.0] + data: + - [3.568379, -8.52116139e-04, 2.48915308e-06, -1.56328741e-09, 3.13588507e-13, + -1.42842549e+04, 3.57912548] + - [2.91309589, 1.64653676e-03, -6.88594068e-07, 1.21032927e-10, -7.83984059e-15, + -1.41808999e+04, 6.71028742] + transport: + model: gas + geometry: linear + well-depth: 98.1 + diameter: 3.65 + polarizability: 1.95 + rotational-relaxation: 1.8 + note: GRI-Mech +- name: O2(7) + composition: {O: 2} + thermo: + model: NASA7 + temperature-ranges: [100.0, 1074.56, 5000.0] + data: + - [3.5373218, -1.21570921e-03, 5.31617794e-06, -4.89443384e-09, 1.45845027e-12, + -1038.58846, 4.68368409] + - [3.15382429, 1.67803794e-03, -7.6997098e-07, 1.51274704e-10, -1.08781793e-14, + -1040.8188, 6.16753859] + transport: + model: gas + geometry: linear + well-depth: 107.4 + diameter: 3.458 + polarizability: 1.6 + rotational-relaxation: 3.8 + note: GRI-Mech +- name: C2H6(8) + composition: {C: 2, H: 6} + thermo: + model: NASA7 + temperature-ranges: [100.0, 1012.41, 5000.0] + data: + - [3.72240272, 1.65072169e-03, 3.44179642e-05, -3.76863565e-08, 1.24452922e-11, + -1.15575906e+04, 4.68244489] + - [2.82844025, 0.0173041283, -6.73338349e-06, 1.23742991e-09, -8.65684403e-14, + -1.19977901e+04, 5.93835568] + transport: + model: gas + geometry: nonlinear + well-depth: 252.301 + diameter: 4.302 + rotational-relaxation: 1.5 + note: GRI-Mech +- name: CH3(9) + composition: {C: 1, H: 3} + thermo: + model: NASA7 + temperature-ranges: [100.0, 697.65, 5000.0] + data: + - [3.96043159, 5.92932552e-04, 8.78578091e-06, -9.88034326e-09, 3.63236374e-12, + 1.64218817e+04, 0.339863476] + - [3.09511244, 5.55429753e-03, -1.88158775e-06, 3.13334801e-10, -2.05194992e-14, + 1.6542619e+04, 4.20297572] + transport: + model: gas + geometry: nonlinear + well-depth: 144.001 + diameter: 3.8 + note: GRI-Mech +- name: CH3OH(10) + composition: {C: 1, H: 4, O: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 1035.74, 5000.0] + data: + - [3.84006783, 1.38235301e-03, 1.91669514e-05, -2.01571623e-08, 6.39114598e-12, + -2.5608309e+04, 5.90976096] + - [2.79181596, 0.0115828305, -4.51554511e-06, 8.21212761e-10, -5.67068242e-14, + -2.57211558e+04, 9.41076841] + transport: + model: gas + geometry: nonlinear + well-depth: 481.802 + diameter: 3.626 + rotational-relaxation: 1.0 + note: GRI-Mech +- name: C2H4(11) + composition: {C: 2, H: 4} + thermo: + model: NASA7 + temperature-ranges: [100.0, 979.36, 5000.0] + data: + - [3.97470128, -4.75826421e-03, 4.16777338e-05, -4.51383953e-08, 1.54221026e-11, + 4915.40809, 3.62436113] + - [3.55666159, 0.0110626515, -4.17013587e-06, 7.85573759e-10, -5.70050015e-14, + 4320.44172, 2.17688265] + transport: + model: gas + geometry: nonlinear + well-depth: 280.801 + diameter: 3.971 + rotational-relaxation: 1.5 + note: GRI-Mech +- name: CH3CHO(12) + composition: {C: 2, H: 4, O: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 1028.8, 5000.0] + data: + - [3.57992942, 5.18977048e-03, 2.26899736e-05, -2.73745515e-08, 9.28491703e-12, + -2.13697376e+04, 8.96969617] + - [4.08561394, 0.0139061616, -5.59372584e-06, 1.0460983e-09, -7.38743189e-14, + -2.20391238e+04, 3.76815598] + transport: + model: gas + geometry: nonlinear + well-depth: 436.001 + diameter: 3.97 + rotational-relaxation: 2.0 + note: GRI-Mech +- name: C3H6O(13) + composition: {C: 3, H: 6, O: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 1023.95, 5000.0] + data: + - [3.0114016, 0.0154683797, 2.15009892e-05, -3.24611554e-08, 1.17874118e-11, + -2.78712432e+04, 13.2203279] + - [5.79591807, 0.0200763349, -7.93430225e-06, 1.47305067e-09, -1.03775439e-13, + -2.92532887e+04, -4.24334634] + transport: + model: gas + geometry: nonlinear + well-depth: 385.407 + diameter: 5.33 + note: Epsilon & sigma estimated with Tc=500.53 K, Pc=48.02 bar (from + Joback method) +- name: C2H6O(14) + composition: {C: 2, H: 6, O: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 984.0, 5000.0] + data: + - [3.24025953, 0.0104859578, 2.63967696e-05, -3.69293568e-08, 1.36710598e-11, + -2.99902844e+04, 11.1433019] + - [5.68494153, 0.016131329, -5.96365742e-06, 1.08897208e-09, -7.69620903e-14, + -3.12258211e+04, -4.44489193] + transport: + model: gas + geometry: nonlinear + well-depth: 362.6 + diameter: 4.53 + rotational-relaxation: 1.5 + note: NOx2018 +- name: CH3COOCH3(15) + composition: {C: 3, H: 6, O: 2} + thermo: + model: NASA7 + temperature-ranges: [100.0, 1154.01, 5000.0] + data: + - [2.75062207, 0.0220813071, 1.21742176e-05, -2.19214056e-08, 7.33620226e-12, + -5.11793699e+04, 16.5002438] + - [5.62526438, 0.0261099804, -1.12500953e-05, 2.11765104e-09, -1.47683111e-13, + -5.27745799e+04, -1.8169542] + transport: + model: gas + geometry: nonlinear + well-depth: 385.633 + diameter: 5.473 + note: Epsilon & sigma estimated with Tc=500.82 K, Pc=44.39 bar (from + Joback method) +- name: X(1) + composition: {X: 1} + thermo: + model: NASA7 + temperature-ranges: [298.0, 2000.0] + data: + - [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] +- name: HX(16) + composition: {H: 1, X: 1} + thermo: + model: NASA7 + temperature-ranges: [298.0, 1000.0, 2000.0] + data: + - [-2.0151091, 0.0127747196, -1.36892852e-05, 6.6707688e-09, -1.15946694e-12, + -5530.52906, 8.4468689] + - [-0.184968995, 6.05229805e-03, -4.83715532e-06, 1.81340221e-09, -2.61948776e-13, + -5915.33033, -0.504191778] +- name: OX(17) + composition: {O: 1, X: 1} + thermo: + model: NASA7 + temperature-ranges: [298.0, 1000.0, 2000.0] + data: + - [0.195855852, 0.0116923252, -2.02271203e-05, 1.61601691e-08, -4.90070914e-12, + -2.69189243e+04, -2.01768707] + - [2.9043837, -2.74871763e-04, 5.38558858e-07, -3.03946989e-10, 5.63969783e-14, + -2.74411389e+04, -14.894415] +- name: CX(18) + composition: {C: 1, X: 1} + thermo: + model: NASA7 + temperature-ranges: [298.0, 1000.0, 2000.0] + data: + - [-0.573265619, 0.0144803183, -2.45704673e-05, 1.93668551e-08, -5.81642502e-12, + 1.47661073e+04, 1.2024425] + - [2.71617577, 1.99967762e-05, 3.4803163e-07, -2.47205634e-10, 5.00169813e-14, + 1.41308872e+04, -14.4477318] +- name: COX(19) + composition: {C: 1, O: 1, X: 1} + thermo: + model: NASA7 + temperature-ranges: [298.0, 1000.0, 2000.0] + data: + - [3.13851368, 7.37719433e-03, -1.21673211e-05, 1.06231734e-08, -3.55085256e-12, + -3.01011015e+04, -14.0684039] + - [4.39015575, 1.21423223e-03, 2.26543548e-08, -2.74772156e-10, 6.84375847e-14, + -3.03339593e+04, -19.9186406] +- name: CHX(20) + composition: {C: 1, H: 1, X: 1} + thermo: + model: NASA7 + temperature-ranges: [298.0, 1000.0, 2000.0] + data: + - [0.444067538, 7.15965809e-03, -6.05381899e-06, 4.41670377e-09, -1.57758787e-12, + 2484.09325, -2.97930741] + - [0.470984781, 6.44724983e-03, -3.18677769e-06, 7.11925015e-10, -5.43593812e-14, + 2479.24869, -3.03223839] +- name: CH2X(21) + composition: {C: 1, H: 2, X: 1} + thermo: + model: NASA7 + temperature-ranges: [298.0, 1000.0, 2000.0] + data: + - [-0.719249342, 0.0165071735, -1.7499851e-05, 1.09676908e-08, -2.88981251e-12, + 1684.1105, 2.01831094] + - [0.983780574, 8.78623452e-03, -4.38766259e-06, 1.09400822e-09, -1.10409266e-13, + 1383.36061, -5.98458146] +- name: HCOX(22) + composition: {C: 1, H: 1, O: 1, X: 1} + thermo: + model: NASA7 + temperature-ranges: [298.0, 1000.0, 2000.0] + data: + - [1.67902911, 0.0139424587, -1.51013698e-05, 9.67718274e-09, -2.69733533e-12, + -2.16030349e+04, -8.23427981] + - [3.03186697, 8.02892147e-03, -4.79702422e-06, 1.39761897e-09, -1.61417712e-13, + -2.18711786e+04, -14.692113] +- name: HCOHX(23) + composition: {C: 1, H: 2, O: 1, X: 1} + thermo: + model: NASA7 + temperature-ranges: [298.0, 1000.0, 2000.0] + data: + - [4.61466774, 1.97736658e-03, 1.13520606e-05, -1.28686112e-08, 4.2885424e-12, + -2.08405084e+04, -18.3405542] + - [2.12897595, 0.0131031973, -8.04327296e-06, 2.48752777e-09, -3.12401921e-13, + -2.03714667e+04, -6.56664446] +- name: CH3OX(24) + composition: {C: 1, H: 3, O: 1, X: 1} + thermo: + model: NASA7 + temperature-ranges: [298.0, 1000.0, 2000.0] + data: + - [1.7232417, 0.0246490814, -2.80859624e-05, 1.72678472e-08, -4.26645223e-12, + -2.48262518e+04, -8.86801544] + - [5.35800551, 9.63360342e-03, -4.83501645e-06, 1.27341188e-09, -1.42248592e-13, + -2.55298238e+04, -26.2856418] +- name: CH3COOX(25) + composition: {C: 2, H: 3, O: 2, X: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 984.45, 5000.0] + data: + - [3.02828539, 0.0110970672, 3.41082297e-05, -5.16093316e-08, 1.99821439e-11, + -5.45206963e+04, -8.73048049] + - [9.44448672, 0.0106736832, -4.32452634e-06, 8.80622118e-10, -6.79718867e-14, + -5.70267527e+04, -45.8963898] +- name: CH2COX(26) + composition: {C: 2, H: 2, O: 1, X: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 961.81, 5000.0] + data: + - [3.22979879, 0.0140344939, -3.56351755e-06, -6.07820031e-09, 3.58358908e-12, + -1.63752671e+04, -9.06405904] + - [6.75419818, 6.25332972e-03, -2.15210043e-06, 3.76495412e-10, -2.61805748e-14, + -1.73712808e+04, -27.5834188] +- name: CH2COX2(27) + composition: {C: 2, H: 2, O: 1, X: 2} + thermo: + model: NASA7 + temperature-ranges: [100.0, 931.96, 5000.0] + data: + - [3.26076086, 8.7928684e-03, 2.17502605e-05, -3.77663092e-08, 1.60291613e-11, + -2.76935704e+04, -15.9429794] + - [8.93173327, 3.51833532e-03, -4.46393644e-07, 6.27459976e-11, -6.93713499e-15, + -2.95785579e+04, -47.3445934] + sites: 2.0 +- name: CH3COOHX(28) + composition: {C: 2, H: 4, O: 2, X: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 1048.69, 5000.0] + data: + - [2.87239041, 0.0186927828, 1.0088838e-05, -2.2522588e-08, 8.70045824e-12, + -5.86586621e+04, -3.00900633] + - [7.28794498, 0.0162041238, -6.88201857e-06, 1.31748685e-09, -9.41982125e-14, + -6.03740403e+04, -28.2845346] +- name: C2H4X(29) + composition: {C: 2, H: 4, X: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 976.84, 5000.0] + data: + - [3.68521618, 1.29459688e-03, 3.31761373e-05, -3.98904869e-08, 1.42375526e-11, + -4431.57003, -13.4989988] + - [4.82101323, 0.0111302021, -4.17185101e-06, 7.79847051e-10, -5.63879306e-14, + -5344.63674, -22.4897119] +- name: C2H4X2(30) + composition: {C: 2, H: 4, X: 2} + thermo: + model: NASA7 + temperature-ranges: [100.0, 945.14, 5000.0] + data: + - [3.75453554, -5.06560113e-03, 6.10124816e-05, -7.41721149e-08, 2.76310662e-11, + -8730.58083, -18.7893661] + - [7.0112633, 7.95379231e-03, -2.18738926e-06, 4.10888303e-10, -3.33917238e-14, + -1.05433116e+04, -40.6504605] + sites: 2.0 +- name: COOHX(31) + composition: {C: 1, H: 2, O: 2, X: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 1005.04, 5000.0] + data: + - [3.53006779, 4.5594231e-03, 2.37656598e-05, -3.19406145e-08, 1.16843843e-11, + -5.57122182e+04, -7.0212104] + - [6.30081585, 8.20615627e-03, -3.57786011e-06, 7.24341931e-10, -5.45315781e-14, + -5.70102822e+04, -24.089423] +- name: CH3X(32) + composition: {C: 1, H: 3, X: 1} + thermo: + model: NASA7 + temperature-ranges: [298.0, 1000.0, 2000.0] + data: + - [-0.552219087, 0.0264420133, -3.55617257e-05, 2.60043628e-08, -7.52706787e-12, + -4433.46585, 0.692144274] + - [3.62557353, 7.39511955e-03, -2.43797398e-06, 1.86159414e-10, 3.64849549e-14, + -5187.22188, -18.9668272] +- name: HOX(33) + composition: {H: 1, O: 1, X: 1} + thermo: + model: NASA7 + temperature-ranges: [298.0, 1000.0, 2000.0] + data: + - [1.58477686, 3.87867982e-03, 1.34107764e-06, -3.93949585e-09, 1.68540254e-12, + -2.90977259e+04, -7.42452379] + - [1.42377797, 5.57119676e-03, -3.3929338e-06, 1.09513419e-09, -1.46734126e-13, + -2.90972119e+04, -6.85806991] +- name: OCXOX(34) + composition: {C: 1, O: 2, X: 2} + thermo: + model: NASA7 + temperature-ranges: [100.0, 924.81, 5000.0] + data: + - [2.99016038, 3.95026566e-03, 2.32709252e-05, -3.78809105e-08, 1.60937226e-11, + -7.26325759e+04, -13.5698649] + - [8.52643192, -1.29139803e-03, 1.43612907e-06, -2.72457525e-10, 1.56499624e-14, + -7.44564313e+04, -44.1708301] + sites: 2.0 +- name: HOCXO(35) + composition: {C: 1, H: 1, O: 2, X: 1} + thermo: + model: NASA7 + temperature-ranges: [298.0, 1000.0, 2000.0] + data: + - [0.700750147, 0.0322756606, -4.70618414e-05, 3.45557357e-08, -1.00331658e-11, + -5.18553737e+04, -4.52637913] + - [6.47849692, 7.149868e-03, -4.22981914e-06, 1.15767979e-09, -1.19086295e-13, + -5.29808669e+04, -32.0736929] +- name: CO2X(36) + composition: {C: 1, O: 2, X: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 1008.22, 5000.0] + data: + - [2.99486686, 9.1859654e-03, -4.12216169e-06, -1.93581616e-09, 1.52889555e-12, + -5.52644684e+04, -8.95864383] + - [5.5544293, 3.15500565e-03, -1.28472914e-06, 2.44776789e-10, -1.77304007e-14, + -5.59901848e+04, -22.3674392] +- name: H2OX(43) + composition: {H: 2, O: 1, X: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 992.64, 5000.0] + data: + - [3.76908588, 6.11563654e-03, -9.97117455e-06, 9.22181366e-09, -3.06918553e-12, + -3.63110221e+04, -15.097954] + - [3.72684086, 3.24910958e-03, -1.05058226e-06, 1.4868916e-10, -7.88009793e-15, + -3.61530243e+04, -14.1408565] +- name: C.[Pt](84) + composition: {C: 1, H: 4, X: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 1348.93, 5000.0] + data: + - [3.88778247, 2.73614901e-03, 9.4539386e-06, -8.27597758e-09, 2.02464154e-12, + -1.52760571e+04, -16.0790121] + - [2.18944665, 0.0116179596, -4.69896427e-06, 8.32126369e-10, -5.50758229e-14, + -1.51677557e+04, -8.67409218] +- name: C2H3X(88) + composition: {C: 2, H: 3, X: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 938.98, 5000.0] + data: + - [3.81685519, -4.95931081e-03, 5.14561017e-05, -6.31488072e-08, 2.37947355e-11, + 486.184087, -15.8827955] + - [6.91814077, 4.84563155e-03, -9.74675469e-07, 1.80928841e-10, -1.67111339e-14, + -1110.88612, -36.0524171] +- name: CHOX2(110) + composition: {C: 1, H: 1, O: 1, X: 2} + thermo: + model: NASA7 + temperature-ranges: [100.0, 926.62, 5000.0] + data: + - [3.83288765, -1.66030981e-03, 2.65567139e-05, -3.48666745e-08, 1.36873378e-11, + -3.03571213e+04, -16.1403346] + - [6.41356232, 8.72293869e-04, 3.23559931e-07, -6.87494619e-11, 2.59893837e-15, + -3.14223679e+04, -31.5612771] + sites: 2.0 +- name: C2H3X2(120) + composition: {C: 2, H: 3, X: 2} + thermo: + model: NASA7 + temperature-ranges: [100.0, 931.26, 5000.0] + data: + - [3.83884173, -8.20968791e-03, 6.65622816e-05, -8.22315252e-08, 3.13833554e-11, + -3285.2632, -19.4608522] + - [8.29116405, 2.7943035e-03, 3.10260044e-07, -6.34389013e-11, -1.00801055e-15, + -5420.92646, -47.6378634] + sites: 2.0 +- name: CC#[Pt](307) + composition: {C: 2, H: 3, X: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 1264.64, 5000.0] + data: + - [3.48625379, 9.84987882e-03, -1.12672006e-06, -2.61528606e-09, 9.94677768e-13, + -1928.44075, 2.78657041] + - [4.86544012, 8.67860765e-03, -3.5223538e-06, 6.42820852e-10, -4.38235056e-14, + -2532.45047, -5.19990243] +- name: C2H2X2(338) + composition: {C: 2, H: 2, X: 2} + thermo: + model: NASA7 + temperature-ranges: [100.0, 928.31, 5000.0] + data: + - [3.24504151, -2.17602793e-03, 3.97905523e-05, -5.17087642e-08, 2.01509093e-11, + 258.438338, -18.4980145] + - [6.79698348, 2.4664034e-03, 5.71681686e-08, -2.66859189e-11, -1.21979217e-15, + -1260.51216, -39.9991896] + sites: 2.0 +- name: C#C.[Pt](513) + composition: {C: 2, H: 2, X: 1} + thermo: + model: NASA7 + temperature-ranges: [100.0, 946.82, 5000.0] + data: + - [3.06056828, 7.58728095e-03, 2.14479983e-06, -8.0788862e-09, 3.69953519e-12, + 1.90210409e+04, -9.52387326] + - [4.94027909, 4.78722202e-03, -1.56395445e-06, 2.67276194e-10, -1.84169549e-14, + 1.8434649e+04, -19.7065975] + +gas-reactions: +- equation: CH3(9) + CH3(9) <=> C2H6(8) # Reaction 1 + rate-constant: {A: 9.45e+14, b: -0.538, Ea: 0.135} +- equation: CO(6) + CH4(2) <=> CH3CHO(12) # Reaction 2 + rate-constant: {A: 6.56e+04, b: 2.86, Ea: 86.9} +- equation: CO(6) + C2H6(8) <=> C3H6O(13) # Reaction 3 + rate-constant: {A: 538.0, b: 3.29, Ea: 104.5} +- equation: H2O(3) + C2H4(11) <=> C2H6O(14) # Reaction 4 + rate-constant: {A: 588.0, b: 2.94, Ea: 53.1} +- equation: CO2(4) + C2H6(8) <=> CH3COOCH3(15) # Reaction 5 + rate-constant: {A: 292.0, b: 3.13, Ea: 116.33} + +site0-reactions: +- equation: X(1) + X(1) + H2(5) <=> HX(16) + HX(16) # Reaction 1 + sticking-coefficient: {A: 0.032, b: 0.0, Ea: 0.0} +- equation: X(1) + X(1) + O2(7) <=> OX(17) + OX(17) # Reaction 2 + sticking-coefficient: {A: 0.0436, b: -0.206, Ea: 0.359} +- equation: X(1) + CO(6) <=> COX(19) # Reaction 3 + sticking-coefficient: {A: 0.5, b: 0.0, Ea: 0.0} +- equation: X(1) + COX(19) <=> OX(17) + CX(18) # Reaction 4 + rate-constant: {A: 1.75e+13, b: 0.0, Ea: 27.772} +- equation: COX(19) + COX(19) <=> X(1) + CX(18) + CO2(4) # Reaction 5 + rate-constant: {A: 1.62e+14, b: 0.5, Ea: 57.768} +- equation: OX(17) + COX(19) <=> X(1) + X(1) + CO2(4) # Reaction 6 + rate-constant: {A: 2.0e+19, b: 0.0, Ea: 29.541} +- equation: HX(16) + CX(18) <=> X(1) + CHX(20) # Reaction 7 + rate-constant: {A: 1.7e+24, b: -0.5, Ea: 37.739} +- equation: HX(16) + COX(19) <=> OX(17) + CHX(20) # Reaction 8 + rate-constant: {A: 1.26e+20, b: 0.073, Ea: 45.8} +- equation: HX(16) + CHX(20) <=> X(1) + CH2X(21) # Reaction 9 + rate-constant: {A: 9.77e+24, b: -0.087, Ea: 19.359} +- equation: H2(5) + CX(18) <=> CH2X(21) # Reaction 10 + sticking-coefficient: {A: 0.04, b: 0.0, Ea: 7.098} +- equation: OX(17) + CHX(20) <=> X(1) + HCOX(22) # Reaction 11 + rate-constant: {A: 4.59e+20, b: 0.0, Ea: 26.267} +- equation: X(1) + HCOX(22) <=> HX(16) + COX(19) # Reaction 12 + rate-constant: {A: 3.71e+21, b: 0.0, Ea: 0.0} +- equation: HX(16) + CH3X(32) <=> X(1) + X(1) + CH4(2) # Reaction 13 + rate-constant: {A: 1.44e+22, b: -0.087, Ea: 15.153} +- equation: HX(16) + CH2X(21) <=> X(1) + CH3X(32) # Reaction 14 + rate-constant: {A: 3.09e+23, b: -0.087, Ea: 13.671} +- equation: X(1) + CH3(9) <=> CH3X(32) # Reaction 15 + sticking-coefficient: {A: 0.16, b: -0.099, Ea: 0.0} +- equation: HOX(33) + CX(18) <=> HX(16) + COX(19) # Reaction 16 + rate-constant: {A: 3.88e+25, b: 0.188, Ea: 14.938} +- equation: HOX(33) + CH3X(32) <=> X(1) + OX(17) + CH4(2) # Reaction 17 + rate-constant: {A: 2.98e+22, b: 0.101, Ea: 6.166} +- equation: HOX(33) + CH2X(21) <=> OX(17) + CH3X(32) # Reaction 18 + rate-constant: {A: 1.39e+21, b: 0.101, Ea: 4.541} +- equation: HOX(33) + CHX(20) <=> OX(17) + CH2X(21) # Reaction 19 + rate-constant: {A: 4.4e+22, b: 0.101, Ea: 10.134} +- equation: HOX(33) + CX(18) <=> OX(17) + CHX(20) # Reaction 20 + rate-constant: {A: 2.43e+21, b: -0.312, Ea: 28.418} +- equation: HX(16) + HOX(33) <=> X(1) + X(1) + H2O(3) # Reaction 21 + rate-constant: {A: 1.85e+20, b: 0.086, Ea: 9.919} +- equation: X(1) + HOX(33) <=> OX(17) + HX(16) # Reaction 22 + rate-constant: {A: 2.25e+20, b: 0.188, Ea: 7.075} +- equation: HOX(33) + HOX(33) <=> X(1) + OX(17) + H2O(3) # Reaction 23 + rate-constant: {A: 2.34e+20, b: 0.274, Ea: 22.06} +- equation: HOX(33) + HCOX(22) <=> HX(16) + HOCXO(35) # Reaction 24 + rate-constant: {A: 2.28e+20, b: 0.263, Ea: 3.8} +- equation: X(1) + HOCXO(35) <=> HOX(33) + COX(19) # Reaction 25 + rate-constant: {A: 1.46e+24, b: -0.213, Ea: 12.978} +- equation: X(1) + HOCXO(35) <=> X(1) + HX(16) + CO2(4) # Reaction 26 + rate-constant: {A: 3.73e+20, b: 0.475, Ea: 8.031} +- equation: COX(19) + COX(19) <=> CX(18) + CO2X(36) # Reaction 27 + rate-constant: {A: 1.62e+14, b: 0.5, Ea: 57.768} +- equation: X(1) + CO2(4) <=> CO2X(36) # Reaction 28 + sticking-coefficient: {A: 5.0e-03, b: 0.0, Ea: 0.0} +- equation: OX(17) + COX(19) <=> X(1) + CO2X(36) # Reaction 29 + rate-constant: {A: 3.7e+21, b: 0.0, Ea: 28.107} +- equation: HOX(33) + COX(19) <=> HX(16) + CO2X(36) # Reaction 30 + rate-constant: {A: 1.0e+19, b: 0.0, Ea: 9.25} +- equation: X(1) + HOCXO(35) <=> HX(16) + CO2X(36) # Reaction 31 + rate-constant: {A: 4.27e+19, b: 0.549, Ea: 1.0} +- equation: HOX(33) + CO2X(36) <=> OX(17) + HOCXO(35) # Reaction 32 + rate-constant: {A: 2.15e+19, b: 0.097, Ea: 26.5} +- equation: CH2COX2(27) <=> COX(19) + CH2X(21) # Reaction 33 + rate-constant: {A: 4.22e+12, b: 0.0, Ea: 24.857} +- equation: X(1) + CH2COX(26) <=> CH2COX2(27) # Reaction 34 + rate-constant: {A: 2.0e+21, b: 0.0, Ea: 0.0} +- equation: X(1) + C2H4(11) <=> C2H4X(29) # Reaction 35 + sticking-coefficient: {A: 7.0e-06, b: 0.0, Ea: 0.0} +- equation: X(1) + X(1) + C2H4(11) <=> C2H4X2(30) # Reaction 36 + sticking-coefficient: {A: 0.69, b: 0.0, Ea: 0.0} +- equation: CH2X(21) + CH2X(21) <=> C2H4X2(30) # Reaction 37 + rate-constant: {A: 9.89e+23, b: 0.0, Ea: 36.807} +- equation: X(1) + C2H4X(29) <=> C2H4X2(30) # Reaction 38 + rate-constant: {A: 1.78e+21, b: 0.0, Ea: 2.868} +- equation: X(1) + X(1) + CO2(4) <=> OCXOX(34) # Reaction 39 + sticking-coefficient: {A: 1.66, b: 0.0, Ea: 0.0} +- equation: OCXOX(34) <=> OX(17) + COX(19) # Reaction 40 + rate-constant: {A: 4.22e+12, b: 0.0, Ea: 31.864} +- equation: X(1) + CO2X(36) <=> OCXOX(34) # Reaction 41 + rate-constant: {A: 4.0e+21, b: 0.0, Ea: 0.0} +- equation: X(1) + X(1) + C2H6(8) <=> CH3X(32) + CH3X(32) # Reaction 42 + sticking-coefficient: {A: 0.015, b: 0.0, Ea: 5.523} +- equation: X(1) + X(1) + CH3OH(10) <=> HOX(33) + CH3X(32) # Reaction 43 + sticking-coefficient: {A: 0.015, b: 0.0, Ea: 1.195} +- equation: X(1) + X(1) + CH3OH(10) <=> HX(16) + CH3OX(24) # Reaction 44 + sticking-coefficient: {A: 0.099, b: 0.0, Ea: 18.294} +- equation: X(1) + X(1) + C2H4(11) <=> CH2X(21) + CH2X(21) # Reaction 45 + sticking-coefficient: {A: 0.01, b: 0.0, Ea: 10.0} +- equation: X(1) + X(1) + CH3CHO(12) <=> HCOX(22) + CH3X(32) # Reaction 46 + sticking-coefficient: {A: 0.015, b: 0.0, Ea: 1.195} +- equation: X(1) + X(1) + C2H6O(14) <=> CH3X(32) + CH3OX(24) # Reaction 47 + sticking-coefficient: {A: 0.015, b: 0.0, Ea: 2.521} +- equation: X(1) + HCOHX(23) <=> HOX(33) + CHX(20) # Reaction 48 + rate-constant: {A: 1.46e+24, b: -0.213, Ea: 12.978} +- equation: X(1) + HCOHX(23) <=> HX(16) + HCOX(22) # Reaction 49 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 13.918} +- equation: X(1) + CH3OX(24) <=> HOX(33) + CH2X(21) # Reaction 50 + rate-constant: {A: 1.46e+24, b: -0.213, Ea: 12.978} +- equation: X(1) + CH3OX(24) <=> HX(16) + HCOHX(23) # Reaction 51 + rate-constant: {A: 7.42e+21, b: 0.0, Ea: 0.0} +- equation: X(1) + CH3COOX(25) <=> HOCXO(35) + CH2X(21) # Reaction 52 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 36.535} +- equation: X(1) + CH3COOX(25) <=> HOX(33) + CH2COX(26) # Reaction 53 + rate-constant: {A: 1.53922e+21, b: 0.131, Ea: 18.349} +- equation: X(1) + CH2COX(26) <=> COX(19) + CH2X(21) # Reaction 54 + rate-constant: {A: 3.282e+20, b: 0.0, Ea: 57.651} +- equation: X(1) + CH3COOHX(28) <=> HOCXO(35) + CH3X(32) # Reaction 55 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 34.027} +- equation: X(1) + CH3COOHX(28) <=> HX(16) + CH3COOX(25) # Reaction 56 + rate-constant: {A: 2.11635e+13, b: 2.071, Ea: 32.311} +- equation: X(1) + C2H4X(29) <=> CH2X(21) + CH2X(21) # Reaction 57 + rate-constant: {A: 3.282e+20, b: 0.0, Ea: 57.651} +- equation: X(1) + COOHX(31) <=> OX(17) + HCOHX(23) # Reaction 58 + rate-constant: {A: 1.641e+20, b: 0.0, Ea: 57.651} +- equation: X(1) + COOHX(31) <=> HOX(33) + HCOX(22) # Reaction 59 + rate-constant: {A: 1.781e+21, b: 0.0, Ea: 37.589} +- equation: HX(16) + HOCXO(35) <=> X(1) + COOHX(31) # Reaction 60 + rate-constant: {A: 2.308e+22, b: 0.0, Ea: 16.834} +- equation: X(1) + X(1) + HOCXO(35) <=> HX(16) + OCXOX(34) # Reaction 61 + rate-constant: {A: 1.856667e+29, b: 0.0, Ea: 10.994} +- equation: CH2X(21) + COOHX(31) <=> HX(16) + CH3COOX(25) # Reaction 62 + rate-constant: {A: 3.966364e+18, b: -0.048, Ea: 34.48} +- equation: OX(17) + HCOX(22) <=> HOX(33) + COX(19) # Reaction 63 + rate-constant: {A: 3.298e+21, b: 0.0, Ea: 0.0} +- equation: OX(17) + HCOHX(23) <=> HOX(33) + HCOX(22) # Reaction 64 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 0.0} +- equation: HOX(33) + HCOHX(23) <=> OX(17) + CH3OX(24) # Reaction 65 + rate-constant: {A: 1.39e+21, b: 0.101, Ea: 4.541} +- equation: OX(17) + CH2COX2(27) <=> OCXOX(34) + CH2X(21) # Reaction 66 + rate-constant: {A: 3.298e+21, b: 0.0, Ea: 0.0} +- equation: OX(17) + CH3COOHX(28) <=> HOX(33) + CH3COOX(25) # Reaction 67 + rate-constant: {A: 4.215e+24, b: -0.101, Ea: 22.156} +- equation: OX(17) + COOHX(31) <=> HOX(33) + HOCXO(35) # Reaction 68 + rate-constant: {A: 1.405e+24, b: -0.101, Ea: 22.156} +- equation: CX(18) + CH2X(21) <=> CHX(20) + CHX(20) # Reaction 69 + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 15.39} +- equation: CX(18) + HCOX(22) <=> COX(19) + CHX(20) # Reaction 70 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 8.664} +- equation: CX(18) + HCOHX(23) <=> CHX(20) + HCOX(22) # Reaction 71 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 5.749} +- equation: CX(18) + CH3OX(24) <=> CHX(20) + HCOHX(23) # Reaction 72 + rate-constant: {A: 7.425804e+21, b: 0.0, Ea: 8.913} +- equation: CX(18) + CH3COOHX(28) <=> CHX(20) + CH3COOX(25) # Reaction 73 + rate-constant: {A: 1.189909e+19, b: -0.048, Ea: 34.48} +- equation: CX(18) + COOHX(31) <=> CHX(20) + HOCXO(35) # Reaction 74 + rate-constant: {A: 3.966364e+18, b: -0.048, Ea: 34.48} +- equation: CX(18) + CH3X(32) <=> CHX(20) + CH2X(21) # Reaction 75 + rate-constant: {A: 9.894e+21, b: 0.0, Ea: 0.0} +- equation: CHX(20) + HCOX(22) <=> COX(19) + CH2X(21) # Reaction 76 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 17.007} +- equation: CHX(20) + HOCXO(35) <=> COX(19) + HCOHX(23) # Reaction 77 + rate-constant: {A: 4.4e+22, b: 0.101, Ea: 10.134} +- equation: COX(19) + HCOHX(23) <=> HCOX(22) + HCOX(22) # Reaction 78 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 44.034} +- equation: HOCXO(35) + CH2X(21) <=> COX(19) + CH3OX(24) # Reaction 79 + rate-constant: {A: 1.39e+21, b: 0.101, Ea: 4.541} +- equation: HCOX(22) + HCOHX(23) <=> COX(19) + CH3OX(24) # Reaction 80 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 14.571} +- equation: COX(19) + CH3COOX(25) <=> HOCXO(35) + CH2COX(26) # Reaction 81 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 61.626} +- equation: COX(19) + CH3COOHX(28) <=> HCOX(22) + CH3COOX(25) # Reaction 82 + rate-constant: {A: 1.189909e+19, b: -0.048, Ea: 34.48} +- equation: CH2X(21) + CH2COX2(27) <=> COX(19) + C2H4X2(30) # Reaction 83 + rate-constant: {A: 1.39e+21, b: 0.101, Ea: 4.541} +- equation: COX(19) + COOHX(31) <=> HCOX(22) + HOCXO(35) # Reaction 84 + duplicate: true + rate-constant: {A: 3.966364e+18, b: -0.048, Ea: 34.48} +- equation: COX(19) + COOHX(31) <=> HCOX(22) + HOCXO(35) # Reaction 85 + duplicate: true + rate-constant: {A: 3.966364e+18, b: -0.048, Ea: 34.48} +- equation: HCOX(22) + CH2X(21) <=> COX(19) + CH3X(32) # Reaction 86 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 13.376} +- equation: COX(19) + HOCXO(35) <=> CO2X(36) + HCOX(22) # Reaction 87 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 40.036} +- equation: CHX(20) + HCOHX(23) <=> HCOX(22) + CH2X(21) # Reaction 88 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 26.946} +- equation: CH2X(21) + HCOHX(23) <=> CHX(20) + CH3OX(24) # Reaction 89 + duplicate: true + rate-constant: {A: 1.39e+21, b: 0.101, Ea: 4.541} +- equation: CH2X(21) + HCOHX(23) <=> CHX(20) + CH3OX(24) # Reaction 90 + duplicate: true + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 21.297} +- equation: CHX(20) + CH3COOHX(28) <=> CH2X(21) + CH3COOX(25) # Reaction 91 + rate-constant: {A: 1.189909e+19, b: -0.048, Ea: 34.48} +- equation: CHX(20) + COOHX(31) <=> HCOX(22) + HCOHX(23) # Reaction 92 + rate-constant: {A: 2.360665e+21, b: -0.074, Ea: 28.318} +- equation: CHX(20) + COOHX(31) <=> HOCXO(35) + CH2X(21) # Reaction 93 + rate-constant: {A: 3.966364e+18, b: -0.048, Ea: 34.48} +- equation: CH2X(21) + CH2X(21) <=> CHX(20) + CH3X(32) # Reaction 94 + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 20.102} +- equation: CH2X(21) + HCOHX(23) <=> CHX(20) + CH3OX(24) # Reaction 95 + duplicate: true + rate-constant: {A: 1.39e+21, b: 0.101, Ea: 4.541} +- equation: CH2X(21) + HCOHX(23) <=> CHX(20) + CH3OX(24) # Reaction 96 + duplicate: true + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 21.297} +- equation: CH2X(21) + HCOHX(23) <=> HCOX(22) + CH3X(32) # Reaction 97 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 17.722} +- equation: CH2X(21) + CH3OX(24) <=> HCOHX(23) + CH3X(32) # Reaction 98 + rate-constant: {A: 7.425804e+21, b: 0.0, Ea: 11.269} +- equation: CH2X(21) + CH3COOX(25) <=> CH3OX(24) + CH2COX(26) # Reaction 99 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 54.408} +- equation: CH2X(21) + CH3COOHX(28) <=> CH3X(32) + CH3COOX(25) # Reaction 100 + duplicate: true + rate-constant: {A: 3.966364e+18, b: -0.048, Ea: 34.48} +- equation: CH2X(21) + CH3COOHX(28) <=> CH3X(32) + CH3COOX(25) # Reaction 101 + duplicate: true + rate-constant: {A: 1.189909e+19, b: -0.048, Ea: 34.48} +- equation: CH2X(21) + COOHX(31) <=> HCOX(22) + CH3OX(24) # Reaction 102 + rate-constant: {A: 3.966364e+18, b: -0.048, Ea: 34.48} +- equation: CH2X(21) + COOHX(31) <=> HOCXO(35) + CH3X(32) # Reaction 103 + rate-constant: {A: 3.966364e+18, b: -0.048, Ea: 34.48} +- equation: HOCXO(35) + CH2X(21) <=> CO2X(36) + CH3X(32) # Reaction 104 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 13.724} +- equation: HCOHX(23) + HCOHX(23) <=> HCOX(22) + CH3OX(24) # Reaction 105 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 20.758} +- equation: HCOX(22) + CH3COOX(25) <=> COOHX(31) + CH2COX(26) # Reaction 106 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 31.276} +- equation: COX(19) + COOHX(31) <=> HCOX(22) + HOCXO(35) # Reaction 107 + duplicate: true + rate-constant: {A: 3.966364e+18, b: -0.048, Ea: 34.48} +- equation: COX(19) + COOHX(31) <=> HCOX(22) + HOCXO(35) # Reaction 108 + duplicate: true + rate-constant: {A: 3.966364e+18, b: -0.048, Ea: 34.48} +- equation: HCOHX(23) + CH3COOHX(28) <=> CH3OX(24) + CH3COOX(25) # Reaction 109 + rate-constant: {A: 1.189909e+19, b: -0.048, Ea: 34.48} +- equation: HCOHX(23) + COOHX(31) <=> HOCXO(35) + CH3OX(24) # Reaction 110 + rate-constant: {A: 3.966364e+18, b: -0.048, Ea: 34.48} +- equation: HOCXO(35) + HCOHX(23) <=> CO2X(36) + CH3OX(24) # Reaction 111 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 16.76} +- equation: HOCXO(35) + CH3COOHX(28) <=> COOHX(31) + CH3COOX(25) # Reaction 112 + rate-constant: {A: 1.254e+22, b: 0.0, Ea: 31.401} +- equation: CH2X(21) + CH3COOHX(28) <=> CH3X(32) + CH3COOX(25) # Reaction 113 + duplicate: true + rate-constant: {A: 1.189909e+19, b: -0.048, Ea: 34.48} +- equation: CH2X(21) + CH3COOHX(28) <=> CH3X(32) + CH3COOX(25) # Reaction 114 + duplicate: true + rate-constant: {A: 3.966364e+18, b: -0.048, Ea: 34.48} +- equation: HOCXO(35) + CH3COOX(25) <=> CO2X(36) + CH3COOHX(28) # Reaction 115 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 15.298} +- equation: HOCXO(35) + HOCXO(35) <=> CO2X(36) + COOHX(31) # Reaction 116 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 15.658} +- equation: X(1) + HOX(33) + CH4(2) <=> H2OX(43) + CH3X(32) # Reaction 117 + sticking-coefficient: {A: 1.0, b: 0.0, Ea: 2.39} +- equation: X(1) + H2O(3) <=> H2OX(43) # Reaction 118 + sticking-coefficient: {A: 0.75, b: 0.0, Ea: 0.0} +- equation: X(1) + H2OX(43) <=> HX(16) + HOX(33) # Reaction 119 + rate-constant: {A: 1.15e+19, b: 0.0, Ea: 24.235} +- equation: OX(17) + H2OX(43) <=> HOX(33) + HOX(33) # Reaction 120 + rate-constant: {A: 1.0e+20, b: 0.0, Ea: 21.63} +- equation: H2OX(43) + COX(19) <=> HX(16) + HOCXO(35) # Reaction 121 + rate-constant: {A: 4.43e+19, b: 0.492, Ea: 23.7} +- equation: H2OX(43) + CO2X(36) <=> HOX(33) + HOCXO(35) # Reaction 122 + rate-constant: {A: 3.48e+19, b: -0.031, Ea: 21.853} +- equation: H2OX(43) + CH2X(21) <=> HOX(33) + CH3X(32) # Reaction 123 + rate-constant: {A: 3.3e+19, b: 0.099, Ea: 14.1} +- equation: H2OX(43) + CHX(20) <=> HOX(33) + CH2X(21) # Reaction 124 + rate-constant: {A: 7.29e+19, b: 0.269, Ea: 34.0} +- equation: H2OX(43) + CX(18) <=> HOX(33) + CHX(20) # Reaction 125 + rate-constant: {A: 4.19e+19, b: 0.09, Ea: 15.6} +- equation: H2OX(43) + CHX(20) <=> HX(16) + HCOHX(23) # Reaction 126 + rate-constant: {A: 7.932728e+18, b: -0.048, Ea: 34.48} +- equation: H2OX(43) + CH2X(21) <=> HX(16) + CH3OX(24) # Reaction 127 + rate-constant: {A: 7.932728e+18, b: -0.048, Ea: 34.48} +- equation: HOX(33) + HCOX(22) <=> H2OX(43) + COX(19) # Reaction 128 + rate-constant: {A: 3.261e+21, b: 0.0, Ea: 6.918} +- equation: H2OX(43) + HCOHX(23) <=> HOX(33) + CH3OX(24) # Reaction 129 + rate-constant: {A: 7.932728e+18, b: -0.048, Ea: 34.48} +- equation: HOX(33) + CH3COOHX(28) <=> H2OX(43) + CH3COOX(25) # Reaction 130 + rate-constant: {A: 1.254e+22, b: 0.0, Ea: 26.173} +- equation: HOX(33) + COOHX(31) <=> H2OX(43) + HOCXO(35) # Reaction 131 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 25.676} +- equation: X(1) + CH4(2) <=> C.[Pt](84) # Reaction 132 + sticking-coefficient: {A: 8.0e-03, b: 0.0, Ea: 0.0} +- equation: X(1) + C.[Pt](84) <=> HX(16) + CH3X(32) # Reaction 133 + rate-constant: {A: 1.54e+21, b: 0.087, Ea: 13.337} +- equation: CX(18) + C.[Pt](84) <=> CHX(20) + CH3X(32) # Reaction 134 + rate-constant: {A: 1.586546e+19, b: -0.048, Ea: 34.48} +- equation: CHX(20) + C.[Pt](84) <=> CH2X(21) + CH3X(32) # Reaction 135 + rate-constant: {A: 1.586546e+19, b: -0.048, Ea: 34.48} +- equation: COX(19) + C.[Pt](84) <=> HCOX(22) + CH3X(32) # Reaction 136 + rate-constant: {A: 1.586546e+19, b: -0.048, Ea: 38.269} +- equation: HCOHX(23) + C.[Pt](84) <=> CH3X(32) + CH3OX(24) # Reaction 137 + rate-constant: {A: 1.586546e+19, b: -0.048, Ea: 34.48} +- equation: CH3X(32) + CH3COOHX(28) <=> C.[Pt](84) + CH3COOX(25) # Reaction 138 + rate-constant: {A: 1.254e+22, b: 0.0, Ea: 19.264} +- equation: COOHX(31) + CH3X(32) <=> HOCXO(35) + C.[Pt](84) # Reaction 139 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 18.766} +- equation: CH2X(21) + C.[Pt](84) <=> CH3X(32) + CH3X(32) # Reaction 140 + rate-constant: {A: 1.586546e+19, b: -0.048, Ea: 34.48} +- equation: OX(17) + C.[Pt](84) <=> HOX(33) + CH3X(32) # Reaction 141 + rate-constant: {A: 5.62e+24, b: -0.101, Ea: 22.156} +- equation: HOCXO(35) + CH3X(32) <=> CO2X(36) + C.[Pt](84) # Reaction 142 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 6.877} +- equation: H2OX(43) + CH3X(32) <=> HOX(33) + C.[Pt](84) # Reaction 143 + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 23.994} +- equation: CX(18) + CH3COOHX(28) <=> HOCXO(35) + CC#[Pt](307) # Reaction 144 + rate-constant: {A: 2.360665e+21, b: -0.074, Ea: 28.318} +- equation: X(1) + CC#[Pt](307) <=> CX(18) + CH3X(32) # Reaction 145 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 47.142} +- equation: CX(18) + C.[Pt](84) <=> HX(16) + CC#[Pt](307) # Reaction 146 + rate-constant: {A: 1.586546e+19, b: -0.048, Ea: 34.48} +- equation: C2H2X2(338) <=> CHX(20) + CHX(20) # Reaction 147 + rate-constant: {A: 7.93e+12, b: 0.0, Ea: 21.511} +- equation: X(1) + HCOX(22) <=> CHOX2(110) # Reaction 148 + rate-constant: {A: 1.0e+21, b: 0.0, Ea: 0.0} +- equation: X(1) + X(1) + HCOHX(23) <=> HX(16) + CHOX2(110) # Reaction 149 + rate-constant: {A: 1.856667e+29, b: 0.0, Ea: 10.994} +- equation: OX(17) + CHX(20) <=> CHOX2(110) # Reaction 150 + rate-constant: {A: 6.54e+21, b: 0.0, Ea: 33.939} +- equation: COX(19) + CHOX2(110) <=> OCXOX(34) + CHX(20) # Reaction 151 + rate-constant: {A: 1.39e+21, b: 0.101, Ea: 4.541} +- equation: OX(17) + C2H2X2(338) <=> CHX(20) + CHOX2(110) # Reaction 152 + rate-constant: {A: 6.596e+21, b: 0.0, Ea: 0.0} +- equation: X(1) + C#C.[Pt](513) <=> C2H2X2(338) # Reaction 153 + rate-constant: {A: 1.0e+21, b: 0.0, Ea: 0.0} +- equation: X(1) + X(1) + C2H4(11) <=> HX(16) + C2H3X(88) # Reaction 154 + sticking-coefficient: {A: 0.1, b: 0.0, Ea: 11.937} +- equation: X(1) + C2H4X(29) <=> HX(16) + C2H3X(88) # Reaction 155 + rate-constant: {A: 1.047906e+14, b: 1.601, Ea: 18.989} +- equation: OX(17) + C2H4X(29) <=> HOX(33) + C2H3X(88) # Reaction 156 + rate-constant: {A: 5.62e+24, b: -0.101, Ea: 22.156} +- equation: CX(18) + C2H4X(29) <=> CHX(20) + C2H3X(88) # Reaction 157 + rate-constant: {A: 1.586546e+19, b: -0.048, Ea: 34.48} +- equation: COX(19) + C2H4X(29) <=> HCOX(22) + C2H3X(88) # Reaction 158 + rate-constant: {A: 1.586546e+19, b: -0.048, Ea: 34.48} +- equation: X(1) + C2H3X(88) <=> CHX(20) + CH2X(21) # Reaction 159 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 34.808} +- equation: CHX(20) + C2H4X(29) <=> CH2X(21) + C2H3X(88) # Reaction 160 + rate-constant: {A: 1.586546e+19, b: -0.048, Ea: 34.48} +- equation: CH2X(21) + C2H4X(29) <=> CH3X(32) + C2H3X(88) # Reaction 161 + rate-constant: {A: 1.586546e+19, b: -0.048, Ea: 34.48} +- equation: HCOHX(23) + C2H4X(29) <=> CH3OX(24) + C2H3X(88) # Reaction 162 + rate-constant: {A: 1.586546e+19, b: -0.048, Ea: 34.48} +- equation: CH3COOX(25) + C2H4X(29) <=> C2H3X(88) + CH3COOHX(28) # Reaction 163 + rate-constant: {A: 1.672e+22, b: 0.0, Ea: 32.383} +- equation: CH3X(32) + C2H4X(29) <=> C.[Pt](84) + C2H3X(88) # Reaction 164 + rate-constant: {A: 1.672e+22, b: 0.0, Ea: 20.744} +- equation: HOX(33) + C2H4X(29) <=> H2OX(43) + C2H3X(88) # Reaction 165 + rate-constant: {A: 1.672e+22, b: 0.0, Ea: 27.653} +- equation: HOCXO(35) + C2H4X(29) <=> COOHX(31) + C2H3X(88) # Reaction 166 + rate-constant: {A: 1.672e+22, b: 0.0, Ea: 32.881} +- equation: HOCXO(35) + C2H3X(88) <=> CO2X(36) + C2H4X(29) # Reaction 167 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 14.227} +- equation: X(1) + X(1) + C2H3X(88) <=> HX(16) + C2H2X2(338) # Reaction 168 + rate-constant: {A: 1.856667e+29, b: 0.0, Ea: 10.994} +- equation: C2H3X(88) + CH3COOX(25) <=> C#C.[Pt](513) + CH3COOHX(28) # Reaction 169 + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 44.984} +- equation: C2H3X(88) + C2H3X(88) <=> C#C.[Pt](513) + C2H4X(29) # Reaction 170 + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 43.914} +- equation: HOCXO(35) + C2H3X(88) <=> COOHX(31) + C#C.[Pt](513) # Reaction 171 + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 45.345} +- equation: HOX(33) + C2H3X(88) <=> H2OX(43) + C#C.[Pt](513) # Reaction 172 + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 41.563} +- equation: CH3X(32) + C2H3X(88) <=> C.[Pt](84) + C#C.[Pt](513) # Reaction 173 + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 36.564} +- equation: X(1) + C2H4X2(30) <=> HX(16) + C2H3X2(120) # Reaction 174 + rate-constant: {A: 2.225e+21, b: 0.0, Ea: 14.101} +- equation: HOX(33) + C2H3X2(120) <=> OX(17) + C2H4X2(30) # Reaction 175 + rate-constant: {A: 1.39e+21, b: 0.101, Ea: 4.541} +- equation: CX(18) + C2H4X2(30) <=> CHX(20) + C2H3X2(120) # Reaction 176 + rate-constant: {A: 1.485161e+22, b: 0.0, Ea: 9.366} +- equation: HCOX(22) + C2H3X2(120) <=> COX(19) + C2H4X2(30) # Reaction 177 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 13.665} +- equation: C2H3X2(120) <=> CHX(20) + CH2X(21) # Reaction 178 + rate-constant: {A: 2.74e+13, b: 0.0, Ea: 33.461} +- equation: CHX(20) + CH2COX2(27) <=> COX(19) + C2H3X2(120) # Reaction 179 + rate-constant: {A: 4.4e+22, b: 0.101, Ea: 10.134} +- equation: CH2X(21) + C2H3X2(120) <=> CHX(20) + C2H4X2(30) # Reaction 180 + duplicate: true + rate-constant: {A: 1.39e+21, b: 0.101, Ea: 4.541} +- equation: CH2X(21) + C2H3X2(120) <=> CHX(20) + C2H4X2(30) # Reaction 181 + duplicate: true + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 20.391} +- equation: CH2X(21) + C2H4X2(30) <=> CH3X(32) + C2H3X2(120) # Reaction 182 + rate-constant: {A: 1.485161e+22, b: 0.0, Ea: 11.722} +- equation: HCOHX(23) + C2H3X2(120) <=> HCOX(22) + C2H4X2(30) # Reaction 183 + rate-constant: {A: 4.18e+21, b: 0.0, Ea: 18.455} +- equation: CH3OX(24) + C2H3X2(120) <=> HCOHX(23) + C2H4X2(30) # Reaction 184 + rate-constant: {A: 7.425804e+21, b: 0.0, Ea: 11.414} +- equation: C2H3X2(120) + CH3COOHX(28) <=> CH3COOX(25) + C2H4X2(30) # Reaction 185 + rate-constant: {A: 1.189909e+19, b: -0.048, Ea: 34.48} +- equation: C.[Pt](84) + C2H3X2(120) <=> CH3X(32) + C2H4X2(30) # Reaction 186 + rate-constant: {A: 1.586546e+19, b: -0.048, Ea: 34.48} +- equation: H2OX(43) + C2H3X2(120) <=> HOX(33) + C2H4X2(30) # Reaction 187 + rate-constant: {A: 7.932728e+18, b: -0.048, Ea: 34.48} +- equation: COOHX(31) + C2H3X2(120) <=> HOCXO(35) + C2H4X2(30) # Reaction 188 + rate-constant: {A: 3.966364e+18, b: -0.048, Ea: 34.48} +- equation: X(1) + C2H3X2(120) <=> HX(16) + C2H2X2(338) # Reaction 189 + rate-constant: {A: 4.75e+21, b: 0.0, Ea: 17.208} +- equation: CX(18) + C2H3X2(120) <=> CHX(20) + C2H2X2(338) # Reaction 190 + duplicate: true + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 14.625} +- equation: CHX(20) + C2H3X2(120) <=> CH2X(21) + C2H2X2(338) # Reaction 191 + duplicate: true + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 35.822} +- equation: CH2X(21) + C2H2X2(338) <=> CHX(20) + C2H3X2(120) # Reaction 192 + duplicate: true + rate-constant: {A: 2.78e+21, b: 0.101, Ea: 4.541} +- equation: COX(19) + C2H3X2(120) <=> HCOX(22) + C2H2X2(338) # Reaction 193 + duplicate: true + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 52.909} +- equation: HCOHX(23) + C2H2X2(338) <=> HCOX(22) + C2H3X2(120) # Reaction 194 + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 22.027} +- equation: HCOHX(23) + C2H3X2(120) <=> CH3OX(24) + C2H2X2(338) # Reaction 195 + duplicate: true + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 29.634} +- equation: C2H2X2(338) + CH3COOHX(28) <=> C2H3X2(120) + CH3COOX(25) # Reaction 196 + rate-constant: {A: 2.379818e+19, b: -0.048, Ea: 34.48} +- equation: C2H2X2(338) + C2H4X(29) <=> C2H3X(88) + C2H3X2(120) # Reaction 197 + rate-constant: {A: 3.173091e+19, b: -0.048, Ea: 34.48} +- equation: C2H3X2(120) + C2H3X2(120) <=> C2H2X2(338) + C2H4X2(30) # Reaction 198 + duplicate: true + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 27.331} +- equation: COOHX(31) + C2H2X2(338) <=> HOCXO(35) + C2H3X2(120) # Reaction 199 + rate-constant: {A: 7.932728e+18, b: -0.048, Ea: 34.48} +- equation: CH2X(21) + C2H3X2(120) <=> CH3X(32) + C2H2X2(338) # Reaction 200 + duplicate: true + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 26.597} +- equation: OX(17) + C2H3X2(120) <=> HOX(33) + C2H2X2(338) # Reaction 201 + duplicate: true + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 33.697} +- equation: H2OX(43) + C2H2X2(338) <=> HOX(33) + C2H3X2(120) # Reaction 202 + rate-constant: {A: 1.586546e+19, b: -0.048, Ea: 34.48} +- equation: C.[Pt](84) + C2H2X2(338) <=> CH3X(32) + C2H3X2(120) # Reaction 203 + rate-constant: {A: 3.173091e+19, b: -0.048, Ea: 34.48} +- equation: CHOX2(110) + CH2X(21) <=> OX(17) + C2H3X2(120) # Reaction 204 + rate-constant: {A: 1.39e+21, b: 0.101, Ea: 4.541} +- equation: X(1) + C2H3X(88) <=> C2H3X2(120) # Reaction 205 + rate-constant: {A: 7.15e+20, b: 0.0, Ea: 0.717} +- equation: C2H3X2(120) + C2H4X(29) <=> C2H3X(88) + C2H4X2(30) # Reaction 206 + rate-constant: {A: 1.586546e+19, b: -0.048, Ea: 34.48} +- equation: HOX(33) + C2H2X2(338) <=> OX(17) + C2H3X2(120) # Reaction 207 + duplicate: true + rate-constant: {A: 2.78e+21, b: 0.101, Ea: 4.541} +- equation: CX(18) + C2H3X2(120) <=> CHX(20) + C2H2X2(338) # Reaction 208 + duplicate: true + rate-constant: {A: 7.425804e+21, b: 0.0, Ea: 8.663} +- equation: HCOX(22) + C2H2X2(338) <=> COX(19) + C2H3X2(120) # Reaction 209 + duplicate: true + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 15.071} +- equation: CH2X(21) + C2H2X2(338) <=> CHX(20) + C2H3X2(120) # Reaction 210 + duplicate: true + rate-constant: {A: 2.78e+21, b: 0.101, Ea: 4.541} +- equation: CH2X(21) + C2H2X2(338) <=> CHX(20) + C2H3X2(120) # Reaction 211 + duplicate: true + rate-constant: {A: 1.672e+22, b: 0.0, Ea: 21.797} +- equation: CH2X(21) + C2H3X2(120) <=> CH3X(32) + C2H2X2(338) # Reaction 212 + duplicate: true + rate-constant: {A: 7.425804e+21, b: 0.0, Ea: 11.019} +- equation: CH2X(21) + C2H3X2(120) <=> CHX(20) + C2H4X2(30) # Reaction 213 + duplicate: true + rate-constant: {A: 1.39e+21, b: 0.101, Ea: 4.541} +- equation: CH2X(21) + C2H3X2(120) <=> CHX(20) + C2H4X2(30) # Reaction 214 + duplicate: true + rate-constant: {A: 8.36e+21, b: 0.0, Ea: 20.391} +- equation: CH3OX(24) + C2H2X2(338) <=> HCOHX(23) + C2H3X2(120) # Reaction 215 + duplicate: true + rate-constant: {A: 1.485161e+22, b: 0.0, Ea: 12.117} +- equation: C2H3X2(120) + C2H3X2(120) <=> C2H2X2(338) + C2H4X2(30) # Reaction 216 + duplicate: true + rate-constant: {A: 7.425804e+21, b: 0.0, Ea: 11.164} diff --git a/test/rmgpy/yaml_writer/compare_yaml_outputs.py b/test/rmgpy/yaml_writer/compare_yaml_outputs.py new file mode 100644 index 0000000000..80d77e21bf --- /dev/null +++ b/test/rmgpy/yaml_writer/compare_yaml_outputs.py @@ -0,0 +1,137 @@ +import os +import yaml +import pandas as pd +import re + +class YamlAnalyst: + def __init__(self, path_to_chemkin_yaml, chemkin_yaml_file): + self.path_to_chemkin_yaml = path_to_chemkin_yaml + self.chemkin_yaml_file = chemkin_yaml_file + + def get_absolute_path(self): + return os.path.join(os.getcwd(), self.path_to_chemkin_yaml, self.chemkin_yaml_file) + + def load_yaml_file(self): + with open(self.get_absolute_path(), 'r') as file: + return yaml.safe_load(file) + + def get_species(self): + return self.load_yaml_file()['species'] + + def get_species_count(self): + return len(self.get_species()) + + def get_species_names(self): + return [specie['name'] for specie in self.get_species()] + + def get_species_count_per_phase(self): + return {f"specie_count_{phase['name']}": len(phase['species']) for phase in self.load_yaml_file()['phases']} + + def get_reactions_dict(self): + reactions_dict = {} + for key, values in self.load_yaml_file().items(): + if key in [f"{phase['name']}-reactions" for phase in self.load_yaml_file()['phases']]: + reactions_dict[key] = self.load_yaml_file()[key] + elif key == 'gas_reactions': + reactions_dict['gas_reactions'] = self.load_yaml_file()['gas_reactions'] + elif key == 'surface_reactions': + reactions_dict['surface_reactions'] = self.load_yaml_file()['surface_reactions'] + return reactions_dict + + def create_reaction_df(self, reactions): + data = [] + for reaction in reactions: + row = {'equation': reaction['equation']} + if 'rate-constant' in reaction: + row.update(reaction['rate-constant']) + elif 'sticking-coefficient' in reaction: + row.update(reaction['sticking-coefficient']) + data.append(row) + return pd.DataFrame(data) + def get_reaction_df(self): + reaction_dfs = {key: self.create_reaction_df(value) for key, value in self.get_reactions_dict().items()} + return reaction_dfs + + def get_reaction_count(self): + return {key: len(value) for key, value in self.get_reactions_dict().items()} + +class CompareYaml: + ''' + Takes a dictionary with keys yaml1 and yaml2, and values a + list of the directory and file name of the yaml files. + + e.g. + + yaml_files = { + 'yaml1': [yaml1_file_directory, file1.yaml], + 'yaml2': [yaml2_file_directory, file2.yaml] + } + ''' + def __init__(self, yaml_files): + self.yaml1 = YamlAnalyst(yaml_files['yaml1'][0], yaml_files['yaml1'][1]) + self.yaml2 = YamlAnalyst(yaml_files['yaml2'][0], yaml_files['yaml2'][1]) + + def compare_species_count(self): + count1 = self.yaml1.get_species_count() + count2 = self.yaml2.get_species_count() + if count1 - count2 == 0: + return True + else: + return False + + def compare_species_names(self): + names1 = set(self.yaml1.get_species_names()) + names2 = set(self.yaml2.get_species_names()) + if set(names1) == set(names2): + return True + else: + return False + + def compare_species_count_per_phase(self): + count_per_phase1 = self.yaml1.get_species_count_per_phase() + count_per_phase2 = self.yaml2.get_species_count_per_phase() + phase_names1 = [phase['name'] for phase in self.yaml1.load_yaml_file()['phases']] + phase_names2 = [phase['name'] for phase in self.yaml2.load_yaml_file()['phases']] + all_phase_names = set(phase_names1).union(set(phase_names2)) + count_diff = {'gas': count_per_phase1[f"specie_count_{phase_names1[0]}"] - count_per_phase2[f"specie_count_{phase_names2[0]}"], + 'surface': count_per_phase1[f"specie_count_{phase_names1[1]}"] - count_per_phase2[f"specie_count_{phase_names2[1]}"] + } + if count_diff['gas'] == 0 and count_diff['surface'] == 0: + return True + else: + return False + + def normalize_equation(self, equation): + def process_side(side): + components = side.split(' + ') + normalized_components = [] + for component in components: + # Remove any prefix integers/coefficients + normalized_component = re.sub(r'^\d*\s*', '', component).strip() + normalized_components.append(normalized_component) + return ' + '.join(sorted(set(normalized_components))) + + reactants, products = equation.split('<=>') + normalized_reactants = process_side(reactants) + normalized_products = process_side(products) + return f"{normalized_reactants} <=> {normalized_products}" + + def compare_reactions(self): + reactions1 = self.yaml1.get_reaction_df() + reactions2 = self.yaml2.get_reaction_df() + comparison_results = {} + + for key1, df1 in reactions1.items(): + df1['normalized_equation'] = df1['equation'].apply(self.normalize_equation) + for key2, df2 in reactions2.items(): + df2['normalized_equation'] = df2['equation'].apply(self.normalize_equation) + merged_df = pd.merge(df1, df2, on='normalized_equation', suffixes=('_1', '_2'), how='inner') + if not merged_df.empty: + merged_df['A_diff'] = merged_df['A_1'].round(2) - merged_df['A_2'].round(2) + merged_df['b_diff'] = merged_df['b_1'].round(2) - merged_df['b_2'].round(2) + merged_df['Ea_diff'] = merged_df['Ea_1'].round(2) - merged_df['Ea_2'].round(2) + comparison_results[f'{key1}_{key2}'] = merged_df[['normalized_equation', 'A_diff', 'b_diff', 'Ea_diff']] + for key, df in comparison_results.items(): + if not (df['A_diff'].eq(0).all() and df['b_diff'].eq(0).all() and df['Ea_diff'].eq(0).all()): + return False + return True diff --git a/test/rmgpy/yaml_writer/test_yaml.py b/test/rmgpy/yaml_writer/test_yaml.py new file mode 100644 index 0000000000..ef9970815d --- /dev/null +++ b/test/rmgpy/yaml_writer/test_yaml.py @@ -0,0 +1,23 @@ +from compare_yaml_outputs import * +import pytest + +@pytest.fixture +def compare_manager(): + '''Create instance of a Compare Yaml before each test''' + yaml_files = { + 'yaml1': ['RMG_yaml_writer_addition/RMG-Py/test/rmgpy/test_data/yaml_writer_data/chemkin/', 'chem0047-gas.yaml'], + 'yaml2': ['RMG_yaml_writer_addition/RMG-Py/test/rmgpy/test_data/yaml_writer_data/cantera/', 'chem47.yaml'] + } + return CompareYaml(yaml_files) + +def test_compare_number_of_species(compare_manager): + assert compare_manager.compare_species_count() == True + +def test_compare_species_names(compare_manager): + assert compare_manager.compare_species_names() == True + +def test_compare_species_count_per_phase(compare_manager): + assert compare_manager.compare_species_count_per_phase() == True + +def test_compare_reactions(compare_manager): + assert compare_manager.compare_reactions() == True \ No newline at end of file