ck2yaml¶

Many existing reaction mechanism files are in CK format, by which we mean the input file format developed for use with the Chemkin-II software package (and subsequent releases) as specified in the report describing the Chemkin software [SAND89].

Cantera comes with a converter utility program ck2yaml (or ck2yaml.py) that converts CK format into Cantera format. This program should be run from the command line first to convert any CK files you plan to use into Cantera format (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 the command line to ck2yaml.

• --input: This is the chemistry input file, containing a list of all the element names that are used, a list of all the species names, and a list of all the reactions to be considered between the species. This file can also optionally contain thermodynamic information for the species.

• --thermo: If the --input file does not contain the thermodynamic data, a separate file containing this information must be specified to the --thermo option.

• --transport: The --input file can also optionally contain transport information for the species. If it does not, and the user wishes to use a part of Cantera that relies on some transport properties, the --transport option must be used to specify the file containing all the transport data for the species.

• --surface: For surface mechanisms, this file defines the surface species and reactions occurring on the surface. Gas phase species and reactions are defined in the file specified by the --input option.

• --name: This specifies the name of the phase in the resulting YAML file. The default is gas.

• --extra: This option specifies a YAML file which can be used to add to the description field or to define custom fields that are included in the YAML output.

• --output: Specifies the output file name. By default, the output file name is the input file name with the extension changed to .yaml.

• --single-intermediate-temperature: This option should be used with thermo data where only a single break temperature is used and the last value in the first line of each species thermo entry is the molecular weight instead.

• --permissive: This option allows certain recoverable parsing errors (for example, duplicate thermo data) to be ignored.

• --quiet: Suppresses warning messages, such those about duplicate thermo data.

• --no-validate: Disables the validation step, where the YAML mechanism is imported in Cantera to check for errors such as unlabeled duplicate reactions and discontinuous thermodynamic data.

• --debug: Enables additional debugging output that may be helpful in identifying problems in the input files or ck2yaml itself.

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 from phase definitions in other input files) can be created by specifying only a thermo file.

Debugging common errors in CK files¶

When ck2yaml encounters an error, it attempts to print the surrounding information to help you to locate the error. Many of the most common errors are due to an inconsistency of the input files from their standard, as defined in the report for Chemkin referenced above. These errors include:

• Each section of the input files must start with a keyword representing that section and end with the keyword END. Keywords that may begin a section include:

  • ELEMENTS or ELEM

  • SPECIES or SPEC

  • THERMO or THERMO ALL

  • REACTIONS or REAC

  • TRANSPORT

• The thermodynamic data is read in a fixed format. This means that each column of the input has a particular meaning. Many common errors are generated because information is missing or in the wrong column. Check thoroughly for extraneous or missing spaces. The format for each thermodynamic 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 the column positioning of each required part of the entry. Empty columns should be filled 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 1	80
  2	Coefficients \(a_1\) to \(a_5\) for the upper temperature interval	1–75
  2	The integer 2	80
  3	Coefficients \(a_6,\ a_7\) for the upper temperature interval, and \(a_1,\ a_2,\ a_3\) for the lower temperature interval	1–75
  3	The integer 3	80
  4	Coefficients \(a_4\) through \(a_7\) for the lower temperature interval	1–60
  4	The integer 4	80

  The first 18 columns are reserved for the species name. The name assigned to the species in the thermodynamic data must be the same as the species name defined in the SPECIES section. If the species name is shorter than 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 to specify the elemental composition of the species. In column 45, the phase of the species (S, L, or G for solid, liquid, or gas respectively) should be specified. The next 28 columns are reserved for the temperatures that delimit the ranges of the polynomials specified on the next several lines. The first two temperatures have a width of 10 columns each (46–55 and 56–65), and represent the lowest temperature and highest temperature for which the polynomials are valid. The last temperature has a width of 8 columns (66–73) and is the common temperature, where the switch from low to high occurs. The next 5 columns (74–78) are reserved for atomic symbols and are usually left blank for the default behavior. Column 79 is blank and finally, the row is ended in column 80 with the integer 1.

  The next three lines of the thermodynamic entry have a similar format. They contain the coefficients of the polynomial described in Thermodynamic Property Models for the NASA 7-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 range between the midpoint and the upper limit. 15 columns are alloted for each coefficient (for a total of 75 columns), with no spaces between them. Although the entry above shows spaces between positive coefficients, it is to be noted that this is done only for formatting consistency with other lines that contain negative numbers. After the coefficients, four spaces in columns 76–79 are followed by the integer 2 in column 80. On the next line, the last two coefficients for the upper temperature range and the first three coefficients for the lower temperature range are specified. Once again, this takes up the first 75 columns, columns 76–79 are blank, and the integer 3 is in column 80. Finally, on the last line of a particular entry, the last four coefficients of the lower temperature range are specified in columns 1–60, 19 blank spaces are present, and the integer 4 is in column 80. The 19 blank spaces in the last line are part of the standard. However, since the original Chemkin interpreter ignored those spaces, researchers began using that space to store additional information that was not necessary for the input file. Although these numbers create an error in ck2yaml if present, they are harmless and can be ignored by using the --permissive option.

  If the number of atoms of an element in a thermodynamic entry has more than 3 digits, it will cause a conversion error. To avoid the error, the element symbol should have a 0 in the first line of the entry. An ampersand (&) is added after the index of the first line, and the element symbols and 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 as 1.1+01, when they should be 1.1E+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 thermodynamic entries. In particular, the first 15 columns of a line are reserved for the species name. One common source of errors is a species that is present in the transport data file, but not in the thermodynamic data or in the species list; or a species that is present in the species list but not the transport data file. The rest of the columns on a given line have no particular format, but must be present in the following order:

  Parameter Number	Parameter Name
  1	An integer with value 0, 1, or 2 indicating monatomic, 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 every species.

SAND89(1,2)

See R. J. Kee, F. M. Rupley, and J. A. Miller, Sandia National Laboratories 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).