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July 7, 2022, 12:24 |
Cantera .cti to chemkin openFOAM conversion
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#1 |
Member
Join Date: Jun 2020
Posts: 49
Rep Power: 6 |
Hello everyone,
I have a chemical mechanism in the Cantera .cti format, which I want to convert either directly into the Openfoam format for transport properties and reactions or into Chemkin format. I found some tools online, none of which worked so far. Does anyone know how to do this? Thank you very much in advance! |
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December 23, 2022, 15:08 |
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#2 |
Member
abdo
Join Date: Apr 2018
Posts: 42
Rep Power: 7 |
Hello bro,
did you solve the problem or not yet? |
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December 23, 2022, 15:33 |
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#3 |
Member
Join Date: Jun 2020
Posts: 49
Rep Power: 6 |
Not in the way I intended to, sadly. I ended up manually translating the reaction data into openfoam format. Took quite a while, but I couldn't get anything else to work.
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December 24, 2022, 06:04 |
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#4 |
Senior Member
Join Date: Oct 2017
Posts: 124
Rep Power: 8 |
You can use the development (!) version of Cantera to convert it from CTI to YAML (cti2yaml) and then from YAML to CK (yaml2ck). I did it this way myself to be able to use a reaction mechanism in Fluent.
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December 24, 2022, 17:56 |
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#5 | |
Member
abdo
Join Date: Apr 2018
Posts: 42
Rep Power: 7 |
Quote:
Thank you for your comment, I try what you said before, so I use cti2yaml mymech.cti to convert from .cti to YAML but I didn't find the script that should use to convert from YAML to ck. you mention (yaml2ck) to do this but I don't find it in the directory path where I install python, even in the internet I don't find the yaml2ck.py. Could you help me with this? |
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December 25, 2022, 05:02 |
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#6 |
Senior Member
Join Date: Oct 2017
Posts: 124
Rep Power: 8 |
Did you compile Cantera from source? See: https://cantera.org/install/compilin...#sec-compiling
yaml2ck is not yet included in the stable version. |
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December 25, 2022, 15:54 |
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#7 | |
Member
abdo
Join Date: Apr 2018
Posts: 42
Rep Power: 7 |
Quote:
Ps: I use wind10. (base) PS C:\Users\DELL\cantera> scons build scons: Reading SConscript files ... SCons 4.4.0 is using the following Python interpreter: C:\Users\DELL\anaconda3\python.exe (Python 3.9) Compiling with MSVC version 14.3 Compiling with MSVC toolset 14.3 (default) Compiling for architecture: amd64 Compiling using the following toolchain(s): ['default'] INFO: Compiling on 'Intel64 Family 6 Model 94 Stepping 3, GenuineIntel' INFO: Building Cantera from git commit '2ce92eac2' INFO: Configuration variables read from 'cantera.conf' and command line: INFO: Adding conda include and library paths: C:\Users\DELL\anaconda3 Checking for C++ header file cmath... yes Checking for C++ header file fmt/ostream.h... no INFO: Using private installation of fmt library. INFO: Found fmt version 6.2.1 Checking for YAML::Node().Mark()... no INFO: Using private installation of yaml-cpp library. Checking for C++ header file gtest/gtest.h... yes Checking for C++ header file gmock/gmock.h... yes INFO: Using system installation of Googletest Checking for C++ header file eigen3/Eigen/Dense... no Checking for C++ header file Eigen/Dense... no INFO: Using private installation of Eigen. INFO: Found Eigen version Checking whether __GLIBCXX__ is declared... no Checking whether _LIBCPP_VERSION is declared... no Checking whether __clang__ is declared... no Checking for C++ library iomp5... no Checking for C++ library omp... no Checking for C++ library gomp... no ERROR: Boost could not be found. Install Boost headers or set 'boost_inc_dir' to point to the boost headers. I try to install Boost headers but no thing happened. |
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December 26, 2022, 05:04 |
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#8 |
Senior Member
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December 26, 2022, 06:25 |
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#9 | |
Member
abdo
Join Date: Apr 2018
Posts: 42
Rep Power: 7 |
Quote:
Last edited by khaledhmz; December 26, 2022 at 13:13. |
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December 27, 2022, 15:08 |
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#10 |
Senior Member
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Maybe you should try the prebuilt windows binaries: https://sourceforge.net/projects/boo...naries/1.81.0/. Otherwise I am not able to help you with this problem.
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January 2, 2023, 04:38 |
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#11 | |
Member
abdo
Join Date: Apr 2018
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Quote:
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July 5, 2023, 02:27 |
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#12 |
New Member
LyLy
Join Date: Jan 2019
Posts: 14
Rep Power: 7 |
I know this is old post but I found an easier way to get this done.
I found a conversion tool in a Python package called pyMARS Link. Pretty straightforward, install it and executable are available for file conversion This one works too. Link Or you could use this Python code to convert your files: Code:
import os from operator import attrgetter import logging from textwrap import fill import numpy as np import cantera as ct from cantera import ck2cti # number of calories in 1000 Joules CALORIES_CONSTANT = 4184.0 # Conversion from 1 debye to coulomb-meters DEBEYE_CONVERSION = 3.33564e-30 def build_arrhenius(rate, reaction_order, reaction_type): """Builds Arrhenius coefficient string based on reaction type. Parameters ---------- rate : cantera.Arrhenius Arrhenius-form reaction rate coefficient reaction_order : int or float Order of reaction (sum of reactant stoichiometric coefficients) reaction_type : {cantera.ElementaryReaction, cantera.ThreeBodyReaction, cantera.PlogReaction} Type of reaction Returns ------- str String with Arrhenius coefficients """ if reaction_type in [ct.ElementaryReaction, ct.PlogReaction]: pre_exponential_factor = rate.pre_exponential_factor * 1e3**(reaction_order - 1) elif reaction_type == ct.ThreeBodyReaction: pre_exponential_factor = rate.pre_exponential_factor * 1e3**reaction_order elif reaction_type in [ct.FalloffReaction, ct.ChemicallyActivatedReaction]: raise ValueError('Function does not support falloff or chemically activated reactions') else: raise NotImplementedError('Reaction type not supported: ', reaction_type) arrhenius = [f'{pre_exponential_factor:.4e}', f'{rate.temperature_exponent:.3f}', f'{(rate.activation_energy / CALORIES_CONSTANT):.2f}' ] return ' '.join(arrhenius) def build_falloff_arrhenius(rate, reaction_order, reaction_type, pressure_limit): """Builds Arrhenius coefficient strings for falloff and chemically-activated reactions. Parameters ---------- rate : cantera.Arrhenius Arrhenius-form reaction rate coefficient reaction_order : int or float Order of reaction (sum of reactant stoichiometric coefficients) reaction_type : {ct.FalloffReaction, ct.ChemicallyActivatedReaction} Type of reaction pressure_limit : {'high', 'low'} string designating pressure limit Returns ------- str Arrhenius coefficient string """ assert pressure_limit in ['low', 'high'], 'Pressure range needs to be high or low' # Each needs more complicated handling due if high- or low-pressure limit if reaction_type == ct.FalloffReaction: if pressure_limit == 'low': pre_exponential_factor = rate.pre_exponential_factor * 1e3**(reaction_order) elif pressure_limit == 'high': pre_exponential_factor = rate.pre_exponential_factor * 1e3**(reaction_order - 1) elif reaction_type == ct.ChemicallyActivatedReaction: if pressure_limit == 'low': pre_exponential_factor = rate.pre_exponential_factor * 1e3**(reaction_order - 1) elif pressure_limit == 'high': pre_exponential_factor = rate.pre_exponential_factor * 1e3**(reaction_order - 2) else: raise ValueError('Reaction type not supported: ', reaction_type) arrhenius = [f'{pre_exponential_factor:.4e}', f'{rate.temperature_exponent:.3f}', f'{(rate.activation_energy / CALORIES_CONSTANT):.3e}' ] return ' '.join(arrhenius) def build_falloff(parameters, falloff_function): """Creates falloff reaction Troe parameter string Parameters ---------- parameters : numpy.ndarray Array of falloff parameters; length varies based on ``falloff_function`` falloff_function : {'Troe', 'SRI'} Type of falloff function Returns ------- falloff_string : str String of falloff parameters """ if falloff_function == 'Troe': falloff_string = ('TROE / ' + f'{parameters[0]} {parameters[1]} ' f'{parameters[2]} {parameters[3]} /\n' ) elif falloff_function == 'SRI': falloff_string = ('SRI / ' + f'{parameters[0]} {parameters[1]} ' + f'{parameters[2]} {parameters[3]} {parameters[4]} /\n' ) else: raise NotImplementedError(f'Falloff function not supported: {falloff_function}') return falloff_string def write_thermo_data(species_list, filename='generated_thermo.dat'): """Writes thermodynamic data to Chemkin-format file. Parameters ---------- species_list : list of cantera.Species List of species objects filename : str, optional Filename for new Chemkin thermodynamic database file """ with open(filename, 'w') as the_file: the_file.write('THERMO\n' + ' 300.000 1000.000 5000.000\n' ) # write data for each species in the Solution object for species in species_list: composition_string = ''.join([f'{s:2}{int(v):>3}' for s, v in species.composition.items() ]) # first line has species name, space for notes/date, elemental composition, # phase, thermodynamic range temperatures (low, high, middle), and a "1" # total length should be 80 species_string = ( f'{species.name:<18}' + 6*' ' + # date/note field f'{composition_string:<20}' + 'G' + # only supports gas phase f'{species.thermo.min_temp:10.3f}' + f'{species.thermo.max_temp:10.3f}' + f'{species.thermo.coeffs[0]:8.2f}' + 6*' ' + # unused atomic symbols/formula, and blank space '1\n' ) # second line has first five coefficients of high-temperature range, # ending with a "2" in column 79 species_string += ( ''.join([f'{c:15.8e}' for c in species.thermo.coeffs[1:6]]) + ' ' + '2\n' ) # third line has the last two coefficients of the high-temperature range, # first three coefficients of low-temperature range, and "3" species_string += ( ''.join([f'{c:15.8e}' for c in species.thermo.coeffs[6:8]]) + ''.join([f'{c:15.8e}' for c in species.thermo.coeffs[8:11]]) + ' ' + '3\n' ) # fourth and last line has the last four coefficients of the # low-temperature range, and "4" species_string += ( ''.join([f'{c:15.8e}' for c in species.thermo.coeffs[11:15]]) + 19*' ' + '4\n' ) the_file.write(species_string) the_file.write('END\n') def write_transport_data(species_list, filename='generated_transport.dat'): """Writes transport data to Chemkin-format file. Parameters ---------- species_list : list of cantera.Species List of species objects filename : str, optional Filename for new Chemkin transport database file """ geometry = {'atom': '0', 'linear': '1', 'nonlinear': '2'} with open(filename, 'w') as the_file: # write data for each species in the Solution object for species in species_list: # each line contains the species name, integer representing # geometry, Lennard-Jones potential well depth in K, # Lennard-Jones collision diameter in angstroms, # dipole moment in Debye, # polarizability in cubic angstroms, and # rotational relaxation collision number at 298 K. species_string = ( f'{species.name:<16}' + f'{geometry[species.transport.geometry]:>4}' + f'{(species.transport.well_depth / ct.boltzmann):>10.3f}' + f'{(species.transport.diameter * 1e10):>10.3f}' + f'{(species.transport.dipole / DEBEYE_CONVERSION):>10.3f}' + f'{(species.transport.polarizability * 1e30):>10.3f}' + f'{species.transport.rotational_relaxation:>10.3f}' + '\n' ) the_file.write(species_string) def write(solution, output_filename='', path='', skip_thermo=False, skip_transport=False ): """Writes Cantera solution object to Chemkin-format file. Parameters ---------- solution : cantera.Solution Model to be written output_filename : str, optional Name of file to be written; if not provided, use ``solution.name`` path : str, optional Path for writing file. skip_thermo : bool, optional Flag to skip writing thermo data in separate file skip_transport : bool, optional Flag to skip writing transport data in separate file Returns ------- output_file_name : str Name of output model file (.inp) Examples -------- >>> gas = cantera.Solution('gri30.cti') >>> soln2ck.write(gas) reduced_gri30.inp """ if output_filename: output_filename = os.path.join(path, output_filename) else: output_filename = os.path.join(path, f'{solution.name}.inp') if os.path.isfile(output_filename): os.remove(output_filename) with open(output_filename, 'w') as the_file: # Write title block to file the_file.write(f'!Chemkin file converted from solution object: {solution.name}\n\n') # write species and element lists to file element_names = ' '.join(solution.element_names) the_file.write( 'ELEMENTS\n' + f'{element_names}\n' + 'END\n\n' ) species_names = fill( ' '.join(solution.species_names), width=60, break_long_words=False, break_on_hyphens=False ) the_file.write( 'SPECIES\n' + f'{species_names}\n' 'END\n\n' ) # Write reactions to file the_file.write('REACTIONS\n') #write data for each reaction in the Solution Object for reaction in solution.reactions(): reaction_string = f'{reaction.equation:<51}' # The Arrhenius parameters that follow the equation string on the main line # depend on the type of reaction. if type(reaction) in [ct.ElementaryReaction, ct.ThreeBodyReaction]: arrhenius = build_arrhenius( reaction.rate, sum(reaction.reactants.values()), type(reaction) ) elif type(reaction) == ct.FalloffReaction: # high-pressure limit is included on the main reaction line arrhenius = build_falloff_arrhenius( reaction.high_rate, sum(reaction.reactants.values()), ct.FalloffReaction, 'high' ) elif type(reaction) == ct.ChemicallyActivatedReaction: # low-pressure limit is included on the main reaction line arrhenius = build_falloff_arrhenius( reaction.low_rate, sum(reaction.reactants.values()), ct.ChemicallyActivatedReaction, 'low' ) elif type(reaction) == ct.ChebyshevReaction: arrhenius = '1.0e0 0.0 0.0' elif type(reaction) == ct.PlogReaction: arrhenius = build_arrhenius( reaction.rates[0][1], sum(reaction.reactants.values()), ct.PlogReaction ) else: raise NotImplementedError(f'Unsupported reaction type: {type(reaction)}') reaction_string += arrhenius + '\n' # need to trim and print third-body efficiencies, if present if type(reaction) in [ct.ThreeBodyReaction, ct.FalloffReaction, ct.ChemicallyActivatedReaction ]: # trims efficiencies list reduced_efficiencies = {s:reaction.efficiencies[s] for s in reaction.efficiencies if s in solution.species_names } efficiencies_str = ' '.join([f'{s}/{v}/' for s, v in reduced_efficiencies.items()]) if efficiencies_str: reaction_string += efficiencies_str + '\n' # now write any auxiliary information for the reaction if type(reaction) == ct.FalloffReaction: # for falloff reaction, need to write low-pressure limit Arrhenius expression arrhenius = build_falloff_arrhenius( reaction.low_rate, sum(reaction.reactants.values()), ct.FalloffReaction, 'low' ) reaction_string += f'LOW / {arrhenius} /\n' # need to print additional falloff parameters if present if reaction.falloff.parameters.size > 0: falloff_str = build_falloff(reaction.falloff.parameters, reaction.falloff.type) reaction_string += falloff_str elif type(reaction) == ct.ChemicallyActivatedReaction: # for chemically activated reaction, need to write high-pressure expression arrhenius = build_falloff_arrhenius( reaction.low_rate, sum(reaction.reactants.values()), ct.ChemicallyActivatedReaction, 'high' ) reaction_string += f'HIGH / {arrhenius} /\n' # need to print additional falloff parameters if present if reaction.falloff.parameters.size > 0: falloff_str = build_falloff(reaction.falloff.parameters, reaction.falloff.type) reaction_string += falloff_str elif type(reaction) == ct.PlogReaction: # just need one rate per line for rate in reaction.rates: pressure = f'{rate[0] / ct.one_atm}' arrhenius = build_arrhenius(rate[1], sum(reaction.reactants.values()), ct.PlogReaction ) reaction_string += f'PLOG / {pressure} {arrhenius} /\n' elif type(reaction) == ct.ChebyshevReaction: reaction_string += ( f'TCHEB / {reaction.Tmin} {reaction.Tmax} /\n' + f'PCHEB / {reaction.Pmin / ct.one_atm} {reaction.Pmax / ct.one_atm} /\n' + f'CHEB / {reaction.nTemperature} {reaction.nPressure} /\n' ) for coeffs in reaction.coeffs: coeffs_row = ' '.join([f'{c:.6e}' for c in coeffs]) reaction_string += f'CHEB / {coeffs_row} /\n' if reaction.duplicate: reaction_string += 'DUPLICATE\n' the_file.write(reaction_string) the_file.write('END') basename = os.path.splitext(output_filename)[0] outputs = [output_filename] # write thermo data if not skip_thermo: write_thermo_data(solution.species(), basename + '_thermo.dat') outputs.append(basename + '_thermo.dat') # TODO: more careful check for presence of transport data? if not skip_transport and all(sp.transport for sp in solution.species()): write_transport_data(solution.species(), basename + '_transport.dat') outputs.append(basename + '_transport.dat') return outputs def convert(model_file, thermo_file=None, transport_file=None, path=''): """Function to convert between Cantera and Chemkin model formats. Parameters ---------- model_file : str Input model file (Cantera .cti or Chemkin) thermo_file : str, optional Chemkin thermodynamic properties file transport_file : str, optional Chemkin transport data file path : str, optional Path for writing file Returns ------- str or list Path to converted file, or list of files (for Chemkin) Example ------- >>> convert('gri30.inp') gri30.cti >>> convert('gri30.cti') [gri30.inp, gri30_thermo.dat, gri30_transport.dat] """ # check whether Chemkin or Cantera model basename = os.path.splitext(os.path.basename(model_file))[0] extension = os.path.splitext(os.path.basename(model_file))[1] # Chemkin files can have multiple extensions, so easier to check if Cantera if extension == '.cti': # Convert from Cantera to Chemkin format. logging.info('Converter detected Cantera input model: ' + model_file) logging.info('Converting to Chemkin format.') solution = ct.Solution(model_file) converted_files = write(solution, basename + '.inp', path=path) return converted_files else: # Convert from Chemkin to Cantera format. logging.info('Converter detected Chemkin input model: ' + model_file) logging.info('Converting to Cantera format.') converted_file = os.path.join(path, basename + '.cti') # calls ck2cti based on given files args = [f'--input={model_file}'] if thermo_file: args.append(f'--thermo={thermo_file}') if transport_file: args.append(f'--transport={transport_file}') args.append(f'--output={converted_file}') # generally Chemkin files have issues (redundant species, etc.) that require this argument args.append('--permissive') ck2cti.main(args) return converted_file convertedFile = convert("/path/to/your/file/your_file.cti") Last edited by harshabose; July 5, 2023 at 06:47. |
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October 26, 2023, 11:09 |
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#13 | |
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