Converting Chemkin-format files¶
If you want to convert a Chemkin-format file to YAML format, or you'rehaving errors when you try to do so, this section will help.
ck2yaml¶
Many existing reaction mechanism files are in CK format, by which we meanthe input file format developed for use with the Chemkin-II software package(and subsequent releases) as specified in the report describing the Chemkinsoftware [SAND89].
Cantera comes with a converter utility program ck2yaml (or ck2yaml.py)that converts CK format into Cantera format. This program should be run fromthe command line first to convert any CK files you plan to use into Canteraformat (YAML format). (New in Cantera 2.5)
Usage:
ck2yaml [--input=<filename>] [--thermo=<filename>] [--transport=<filename>] [--surface=<filename>] [--name=<name>] [--extra=<filename>] [--output=<filename>] [--single-intermediate-temperature] [--permissive] [--quiet] [--no-validate] [-d | --debug]
Each of the terms in square brackets is an option that can be passed on thecommand line to ck2yaml.
--input: This is the chemistry input file, containing a list of all theelement names that are used, a list of all the species names, and a list ofall the reactions to be considered between the species. This file can alsooptionally contain thermodynamic information for the species.--thermo: If the--inputfile does not contain the thermodynamic data,a separate file containing this information must be specified to the--thermooption.--transport: The--inputfile can also optionally contain transportinformation for the species. If it does not, and the user wishes to use a partof Cantera that relies on some transport properties, the--transportoption must be used to specify the file containing all the transport data forthe species.--surface: For surface mechanisms, this file defines the surface speciesand reactions occurring on the surface. Gas phase species and reactions aredefined in the file specified by the--inputoption.--name: This specifies the name of the phase in the resulting YAML file.The default isgas.--extra: This option specifies a YAML file which can be used to add to thedescriptionfield or to define custom fields that are included in the YAMLoutput.--output: Specifies the output file name. By default, the output file nameis the input file name with the extension changed to.yaml.--single-intermediate-temperature: This option should be used with thermo datawhere only a single break temperature is used and the last value in the first line ofeach species thermo entry is the molecular weight instead.--permissive: This option allows certain recoverable parsing errors (forexample, duplicate thermo data) to be ignored.--quiet: Suppresses warning messages, such those about duplicate thermodata.--no-validate: Disables the validation step, where the YAML mechanism is importedin Cantera to check for errors such as unlabeled duplicate reactions and discontinuousthermodynamic data.--debug: Enables additional debugging output that may be helpful in identifyingproblems in the input files orck2yamlitself.
Example:
ck2yaml --input=chem.inp --thermo=therm.dat --transport=tran.dat
If the ck2yaml script is not on your path but the Cantera Python module is,ck2yaml can also be used by running:
python -m cantera.ck2yaml --input=chem.inp --thermo=therm.dat --transport=tran.dat
An input file containing only species definitions (which can be referenced fromphase definitions in other input files) can be created by specifying only athermo file.
Debugging common errors in CK files¶
Note
Many existing CK format files cause errors in ck2yaml when they areprocessed. Some of these errors may be avoided by specifying the--permissive option. This option allows certain recoverable parsing errors(for example, duplicate transport or thermodynamic data) to be ignored. Othererrors may be caused by incorrect formatting of lines in one or more of theinput files.
When ck2yaml encounters an error, it attempts to print the surroundinginformation to help you to locate the error. Many of the most common errorsare due to an inconsistency of the input files from their standard, as definedin the report for Chemkin referenced above. These errors include:
Each section of the input files must start with a keyword representing thatsection and end with the keyword
END. Keywords that may begin a sectioninclude:ELEMENTSorELEMSPECIESorSPECTHERMOorTHERMO ALLREACTIONSorREACTRANSPORT
The thermodynamic data is read in a fixed format. This means that eachcolumn of the input has a particular meaning. Many common errors aregenerated because information is missing or in the wrong column. Checkthoroughly for extraneous or missing spaces. The format for eachthermodynamic entry should be as follows:
N2 N 2 G200.000 6000.000 1000.00 1 2.95258000E+00 1.39690000E-03-4.92632000E-07 7.86010000E-11-4.60755000E-15 2-9.23949000E+02 5.87189000E+00 3.53101000E+00-1.23661000E-04-5.02999000E-07 3 2.43531000E-09-1.40881000E-12-1.04698000E+03 2.96747000E+00 4
The following table is adapted from the Chemkin manual [SAND89] to describe thecolumn positioning of each required part of the entry. Empty columns should befilled with spaces.
Line No.
Contents
Column
1
Species Name
1–18
1
Date (Optional)
19–24
1
Atomic Symbols and formula
25–44
1
Phase of species (S, L, G)
45
1
Low temperature
46–55
1
High temperature
56–65
1
Common temperature
66–73
1
Additional Atomic Symbols
74–78
1
The integer
180
2
Coefficients \(a_1\)to \(a_5\) for the uppertemperature interval
1–75
2
The integer
280
3
Coefficients \(a_6,\ a_7\)for the upper temperature interval,and \(a_1,\ a_2,\ a_3\) forthe lower temperature interval
1–75
3
The integer
380
4
Coefficients \(a_4\) through\(a_7\) for the lowertemperature interval
1–60
4
The integer
480
The first 18 columns are reserved for the species name. The name assignedto the species in the thermodynamic data must be the same as the speciesname defined in the
SPECIESsection. If the species name is shorterthan 18 characters, the rest of the characters should be filled by spaces.The next six columns (columns 19–24) are typically used to write a date;they are not used further. The next 20 columns (25–44) are used tospecify the elemental composition of the species. In column 45, the phaseof the species (S,L, orGfor solid, liquid, or gasrespectively) should be specified. The next 28 columns are reserved forthe temperatures that delimit the ranges of the polynomials specified onthe next several lines. The first two temperatures have a width of 10columns each (46–55 and 56–65), and represent the lowest temperature andhighest temperature for which the polynomials are valid. The lasttemperature has a width of 8 columns (66–73) and is the commontemperature, where the switch from low to high occurs. The next 5 columns(74–78) are reserved for atomic symbols and are usually left blank forthe default behavior. Column 79 is blank and finally, the row is ended incolumn 80 with the integer1.The next three lines of the thermodynamic entry have a similar format.They contain the coefficients of the polynomial described inThermodynamic Property Models for the NASA7-coefficient polynomial formulation.The second row of the thermo entry (the first after the information row)contains the first five coefficients that apply to the temperature rangebetween the midpoint and the upper limit. 15 columns are alloted for eachcoefficient (for a total of 75 columns), with no spaces between them.Although the entry above shows spaces between positive coefficients, it isto be noted that this is done only for formatting consistency with otherlines that contain negative numbers. After the coefficients, four spacesin columns 76–79 are followed by the integer
2in column 80. On thenext line, the last two coefficients for the upper temperature range andthe first three coefficients for the lower temperature range arespecified. Once again, this takes up the first 75 columns, columns 76–79are blank, and the integer3is in column 80. Finally, on the lastline of a particular entry, the last four coefficients of the lowertemperature range are specified in columns 1–60, 19 blank spaces arepresent, and the integer4is in column 80. The 19 blank spaces in thelast line are part of the standard. However, since the original Chemkininterpreter ignored those spaces, researchers began using that space tostore additional information that was not necessary for the input file.Although these numbers create an error inck2yamlif present, they areharmless and can be ignored by using the--permissiveoption.If the number of atoms of an element in a thermodynamic entry has more than 3digits, it will cause a conversion error. To avoid the error, the elementsymbol should have a
0in the first line of the entry. An ampersand(&) is added after the index of the first line, and the element symbolsand their amounts should be written on the next line as follows:BIN6J PYRENEJ1 C 0H 0 0 0G 300.000 5000.000 1401.000 1&C 778 H 263 3.63345177E+01 3.13968020E-02-1.09044660E-05 1.71125597E-09-1.00056355E-13 2 4.05143093E+04-1.77494305E+02-1.20603441E+01 1.59247554E-01-1.41562602E-04 3 6.26071650E-08-1.09305161E-11 5.56473533E+04 7.68451211E+01 4
or on separate lines with ampersand (
&) as the last character on the line:BIN6 PYRENE C 0H 0 0 0G 300.000 5000.000 1401.000 1&C 778&H 264 3.65839677E+01 3.36764102E-02-1.16783938E-05 1.83077466E-09-1.06963777E-13 2 9.29809483E+03-1.81272070E+02-1.29758980E+01 1.63790064E-01-1.43851166E-04 3 6.31057915E-08-1.09568047E-11 2.48866399E+04 7.94950474E+01 4
It may be the case that scientific formatted numbers are missing the
E.In this case, numbers often show up as1.1+01, when they should be1.1E+01. You can fix this with a Regular Expression "find and replace":Find: (\d+\.\d+)([+-]\d+)Replace: \1E\2
The transport data file also has a specified format, as described in[SAND98], although the format is not as strict as for the thermodynamicentries. In particular, the first 15 columns of a line are reserved forthe species name. One common source of errors is a species that is presentin the transport data file, but not in the thermodynamic data or inthe species list; or a species that is present in the species list butnot the transport data file. The rest of the columns on a given line haveno particular format, but must be present in the following order:
Parameter Number
Parameter Name
1
An integer with value 0, 1, or 2 indicatingmonatomic, linear, or non-linear molecular geometry.
2
The Lennard-Jones potential well depth\(\varepsilon/k_B\) in Kelvin
3
The Lennard-Jones collision diameter \(\sigma\)in Angstrom
4
The dipole moment \(\mu\) in Debye
5
The polarizability \(\alpha\) in Angstroms cubed
6
The rotational relaxation collision number\(Z_{rot}\) at 298 K
Another common error is if all 6 of these numbers are not present for everyspecies.
- SAND89(1,2)
See R. J. Kee, F. M. Rupley, and J. A. Miller, Sandia NationalLaboratories Report SAND89-8009 (1989).http://www.osti.gov/scitech/biblio/5681118
- SAND98
See R. J. Kee, G. Dixon-Lewis, J. Warnatz, M. E. Coltrin, J. A. Miller,H. K. Moffat, Sandia National Laboratories Report SAND86-8246B (1998).
