Chemkin-II input

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- Chemkin-II input MIYOSHI Group, Univ. Tokyo

Chemkin-II inputs
This document describes the format of the chemkin-II input files.

Contents
Chemkin Interpreter input (chem.inp) Input-file structure Elements block Species block Thermo block Reactions block Senkin input (senk.inp) Senkin Binary-CSV converter input (sb2c.inp) Rxn Contrib tool input (rxnc.inp) Thermodynamic data (therm.dat)

Chemkin Interpreter input

For the complete description of the Chemkin Interpreter input file, see the following document. 'Chemkin-II: A Fortran Chemical Kinetics Package for the Analysis of Gas-Phase Chemical Kinetics,' R. J. Kee, F. M. Rupley, and J. A. Miller, Sandia Report, SAND89-8009B (1995).

Input-file structure
Below is an example input. !----------------------------------------------------------------------! 'exmHCO01.inp' ! C-H-O system machanism based on ... !----------------------------------------------------------------------ELEMENTS H C N O END !----------------------------------------------------------------------SPECIES H2 H O2 O OH HO2 H2O2 H2O N2 CH3 CH4 ...(snip)... END !----------------------------------------------------------------------THERMO CH3 121286C 1H 3 G 0300.00 5000.00 1000.00 0.02844051E+02 0.06137974E-01-0.02230345E-04 0.03785161E-08-0.02452159E-12 0.16437809E+05 0.05452697E+02 0.02430442E+02 0.11124099E-01-0.01680220E-03 0.16218288E-07-0.05864952E-10 0.16423781E+05 0.06789794E+02 END !----------------------------------------------------------------------REACTIONS KJOULES/MOLE MOLECULES H + CH3 (+M) = CH4 (+M) 3.50E-10 0. 0. !94CEC (300-1000K) LOW /1.726E-24 -1.8 0./ ! for M=Ar TROE /0.63 61. 3315./ ...(snip)... END !----------------------------------------------------------------------The input should be in the following order. The thermo block may be skipped. Elements block 'ELEMENTS' ~ 'END' Species block 'SPECIES' ~ 'END' Thermo block

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'THERMO' ~ 'END' Reactions block 'REACTIONS' ~ 'END' At any position in the format-free part, an exclamation mark, '!', can be inserted. From the exclamation mark to the end of the line is skipped by the parser as a comment. Not allowed in the thermo block which is a fixed-format part.

Elements block
List all the elements contained in the species (that is, atoms and molecules) to be considered. Place the symbols of elements delimited by a space (may be multiple spaces) or a line-feed between 'ELEMENTS' and 'END'. For element symbols, either of upper, lower, or mixed case (e.g. 'AR' 'ar' or 'Ar') is allowed but it must be case-sensitively identical with that used in the thermodata. example-1 ELEMENTS H O AR CL END example-2 ELEMENTS H O C N HE END

Species block
List all the species (atoms and molecules) to be considered. Similarly to the elements, place the names of the species delimited by spaces or a line-feed between 'SPECIES' and 'END'. The species name cannot exceed 16 charactors, and the first letter should not be numeric, '+', nor '='. It does not need to be a chemcal formula such as CH4' or 'C2H6', but should be identical with the name in the therm.dat or thermo block. (For example, formyl radical in the default therm.dat is named as 'HCO', not 'CHO') When the chemical formula is not enough to identify the species, refer to The Chemkin Thermodynamic Data Base (SAND87-8215B). For example, there are three species with C3H4 chemcal formula in therm.dat. They are named as 'C3H4', 'C3H4C', and 'C3H4P' corresponding to allene, cyclopropene, and propyne, respectively.

Thermo block
This block is an option. When the all species in the Species Block are registered in the therm.dat, and if you choose to use them, this block can be skipped. Place the coefficients for thermodynamic functions in four-lines fixed-format per one species between 'THERMO' and 'END'. The format is identical with that of therm.dat and refer to the Thermodata file (therm.dat) section for details. With Chemkin, thermodynamic data should be given for all the species considered. Since thermodynamic functions are required to calculate the rate constants for reverse reactions (See Reactions block) and the heat balance. In an exceptional case, when no reverse reaction should be considered and the temperature change can be negligible (which may no be rare as the condition of the laboratory kinetic experiments ...), thermodynamic data is not necessary. However, even for the isothermic calculation without any reversible reaction, Chemkin requests the thermodata. In such a case, one may register dummy (may be totally inaccurate) thermodata to avoid the error of Chemikin. For this case, do not modify the therm.dat with dummy data, but register it in here in the Thermo block.

Reactions block
List reaction equations with rate parameters for the reactions to be considered in this block. The 'REACTIONS' or 'END' statement should appear as an independent line, and one reaction should be described in a line. A reaction should be described in the order of the reaction equation and rate parameters.

Reaction equation
A reaction equation can be given as the following format. reac1 + reac2 + reac3 = prod1 + prod1 + prod3 The number of the reactants or the products must be no less than one and no more than three. The name of the reactant or product must be identical with the one declared in the Species Block except for the following exceptions. exception-1 A reaction with two or more identical reactants or products may be written as the following example. 2OH = H2O2

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exception-2 M is a special third-body reactant (and product) representing the all the species. It may be used as the following example. H + H + M = H2 + M Details of the reactions with third-body will be given below. One of the following separators can be used between the reactants and products. => Indicates an irreversible reaction, that is, only the forward reaction is considered. = or <=> Indicates an reversible reaction. The rate constant for the reverse reaction is calculated from the thermodynamic data unless it is specified by using REV keyword.

Rate constants and unit

Rate constants are calculated by the modified Arrhenius equation, (1) The parameters, A, b, and Ea should be specified in this order separated by space charactors. In the top line of the Reactions Block, two keywords specifying units for the activation energy and preexponential factor may placed after 'REACTIONS' delimited with space charactors. The default is cal/mol for the activation energy and mol-cm-s-K for the preexponential factor. The acceptable keywords are as follows. CAL/MOLE, KCAL/MOLE, JOULES/MOLE, KJOULES/MOLE, KELVINS MOLES, MOLECULES The unit for the preexponential factor may be either mol-cm-s-K (default, MOLES) or molecules-cm-s-K (MOLECULES). No choice for the unit such as mol/l (= mol dm3).

Reactions involving third-body

Depending on how the rate constants changes with the pressure, on of the following three forms is used. In scientific papers, the reaction involving the third-body always written with the apparent 'M' irrespective of the pressure dependence of the rate constant. The Chemkin input form is a convenience to clarify the way to calculate the pressure dependence of the rate constants and do not confuse. form-1 A + B => C Rate constant is considered to be independent of pressure. form-2 A + B + M => C + M Rate constant is assumed to be in low-pressure limiting region. form-3 A + B (+ M) => C (+ M) Rate constant is in the fall-off region. Auxiliary input is required to specify the formula for the pressure dependence. Auxiliary input for the pressure dependence is required when the form-3 above is specified. The following auxiliary inputs are accepted. Lindemann formula Evaluate the pressure dependence by using the Lindemann formula, (2) where X is a reduce pressure normalized by the fall-off pressure [M]c. (3), (4)

Write A, b, and Ea for the high-pressure limit in the reaction equation line. The rate parameters for the low-pressure limit should be given in the next line by using LOW keyword as follows. A + B (+ M) = C (+ M) 2.3E14 0.0 156.2 LOW/ 6.3E27 -2.6 -54.3 / Troe's formula Evaluate the pressure dependence by using the Troe's formula,

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(5)

(6)

(7) (8) (9) (10) Similarly to the case of Lindemann formula, give the rate parameters for high-pressure and low-pressure limits in the first and second lines, and in the third line, give the parameters a, T***, T*, and T**, in this order by using TROE keyword. The last parameter, T**, is optional and the last term of eq. (10) will be omitted when this parameter is omitted. Below is an example. A + B (+ M) = C (+ M) 2.3E14 0.0 156.2 LOW/ 6.3E27 -2.6 -54.3 / TROE/ 0.604 6980. 132. / In general, the rate parameters for the low-pressure limit or the low-pressure part of the fall-off region depends largely on the buffer gas. This effect can be specified as an enhancement factor. Here is an example. A + B + M = C + M 6.3E27 -2.6 -54.3 CO/1.9/ H2/1.7/ CO2/3./ H2O/5./ In this example, the low-pressure limiting rate constant is multiplied by 1.9, 1.7, 3., and 5. for CO, H2, CO2, and H2O, respectively. Similar input can be added for the fall-off reactions.

Senkin inputs
For the complete description of the Senkin input file format, See the following document. 'SENKIN: A Fortran Program for Predicting Homogeneous Gas Phase Chemical Kinetics with Sensitivity Analysis,' A. E. Lutz, R. J. Kee, and J. A. Miller, Sandia Report, SAND87-8248 (1995).

Sample input
A sample input is shown below. SENS CONP PRES TEMP TIME DELT REAC REAC REAC END

1.0 1000. 2.E-4 1.E-4 H2 2 O2 1 N2 4

Place one keyword per line. Lines beginning with '.' (period), '/' (slash), or '!' (exclamation mark) are skipped as comments. Place 'END' indicating the end of input in the last line. Space character cannot be inserted at the beginning of a line.

Sensitivity option
To perform the sensitivity analysis, place 'SENS' in the first line. When no sensitivity analysis is needed, the problem selection keyword described below will appear at the first line.

Problem selection
One (and only one) of the problem selection keyword is necessary at the first input except for the 'SENS' keyword. The acceptable keywords are as follows. CONP CONstant Pressure & adiabatic

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CONV CONT ICEN

CONstant Volume & adiabatic CONstant Temperature & constant pressure Internal Combustion ENgine (zero-dimensional) Adiabatic compression and expansion with a constant speed crank-piston mechanism.

CGME Core Gas Model Extention Core gas model calculation for a rapid compression machine. VTIM# Volume as a function of TIMe & adiabatic

PRGT* PRoGrammed Temperature & constant pressure TTIM# Temperature as a function of TIMe & constant pressure

* ICEN, CGME, and PRGT are extended keywords which are not valid in the original Senkin.
# When the 'VTIM' or 'TTIM' is specified, the soubroutine VOLT or TEMPT in the senkin driver (skdriver.f) must be

properly written so as it calculates the volume or the temperature, respectively, at a given time. The keywords below may be placed at any line between the problem selection keyword and 'END'.

Initial conditions
The following keywords can be used to specify the initial consitions (required). TEMP Initial temperature [K] PRES REAC Initial pressure [atm] Name of the reactant and moles. May present as many as needed. The name must be registered in the Species Block of chem.inp. The mole fractions will be normalized in senkin.

Integration control
The following keywords can be used to control the integration (required). TIME Final time [s] for integration DELT Time interval [s] for the console and tign.out output. In save.bin, irrespective of this parameter, results for all integration steps are stored.

Options
Keywords for restart, precision of the integration, etc. Use if required. REST Restart The initial condition will be read from the rest.bin. The keywords TEMP, PRES, and REAC are no longer necessary and are ignored if present. Initial time [s] for restart Usually, the initial time for restart is read from the rest.bin. This may be changed by the 'TRES' keyword. Absolute tolerance of variables. It should be noted that the mass fraction of chemical species is integrated in the senkin. Default is 1E-20.

TRES ATOL

RTOL Relative tolerance of variables. (Default : 1E-8) ATLS Absolute and relative tolerance of sensitivity coefficients, respectively. (Default : 1E-5) RTLS TLIM Ignition criterial temperature (Default : initial temperautre + 400 K)

ICEN options
When the 'ICEN' is selected for the problem, the following options may be specified. For details, see ICEN Extension to SENKIN Code (pdf). CMPR K RPM N LOLR R Compression Ratio Ratio of the maximum cylinder volume to minimum volume. Default is 18.4 Rotation speed [rpm] (Default : 1500) Ratio of connecting rod length to crank radius (Default : 3)

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VOLC Vc DEG0 0

Clearance volume [cm3] Cylinder volume at the TDC (top dead center). When no heat loss is considered, this value does not affect the calculation essentially, except for the output of the total mass. (Default : 100 cm3) Initial crank angle [Unit: degree / TDC = 0] (Default : 180)

Heat loss parameters Give the coefficients for the relation of Nusselt number with the Reynolds and Prandtl numbers, ICHT a m n B Tw Nu = a Re m Pr n cylinder bore, B [cm], and cylinder wall temperature, Tw [K]. It should be noted that the cylinder surface area is calculate by using Vc.

CGME options
When the 'CGME' is selected as a problem, the following optional parameters may be specified. Parameters for the volume change after the compression
(Core-Gas Model Coefficients for Volume Function)

The virtual volume change after compression by core gas model is approximated by the following empirical equation. CCVF c1 k1 c2 k 2 c3 k 3 V1 c1exp(k 1t) + c2exp(k 2t) + c3exp(k 3t) + 1 Note that only the relative change of volume is needed and the last term can always be given as unity. The unit of k i is s1. When the following CCVC option is NOT specified, the calculation starts from the temperature and pressure of the compressed gas specified by TEMP and PRES. Parameters for the volume change during the compression
(Core-Gas Model Coefficients for Volume Change during Compression)

The virtual volume change during the compression by core gas model is approximated by the following empirical equations. t<0: 0t< t1 : t1 t < t2 : t2 t < t3 : t3 t < t4 : CCVC t1 V1 t2 V2 t3 V3 t4 V4 t4 t : V=1 V1 = b1t2 + 1 V = b2(t t1) + V1 V1 = b3(t t2) + V21 V1 = b4(t t4)2 + V41 V = b5 / [c1exp(k 1t') + c2exp(k 2t') + c3exp(k 3t') + 1] where t' = t t4 b1 = (V11 1) / t12 b2 = (V2 V1) / (t2 t1) b3 = (V31 V21) / (t3 t2) b4 = (V31 V41) / (t3 t4)2 b5 = V4(c1 + c2 + c3 + 1)

The parameters for the valume change after the compression (c1 ~ c3, k 1 ~ k 3) are also used, and should also be specified by the CCVF option. In these equations, the volume is the core-gas model volume divided by the initial volume before compression. It should be unity (1) at time = 0. The unit of the time t is s [second]. When this option is specified, the initial temperature (TEMP) and pressure (PRES) should be those before the compression. The profile of the volume change specified by the CCVC and CCVF options is shown in the figure to the right. CCVC option specifies (ti , Vi ) pairs at the switching points of the function forms. The time = 0 should be defined so that the V1 in the first part can be well approximated by a quadratic. In the second and third parts, V and V1 are approximated by straight lines, respectively. In the fourth part, V1 is quadratic. After t4, V1 is approximated by the decay function specified by CCVF.

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PRGT option
When the 'PRGT' is selected as a problem, the following optional parameter may be specified. Temperature Point Gives the temperature T [K] at the time t [s]. The temperature profile can be specified by using multiple TPNT t T 'TPNT' options. With PRGT extension, the temperatures between points are given by linear interpolation. The temperature at time = 0 is always the temperature specified by the 'TEMP' keyword. Therefore, the time t of this option cannot be 0 or negative.

Senkin binary-CSV coverter input

Example input
An example input is shown below. ===== sb2c (sbin2csv.f) [ TIME OUTPUT CONTROL: us mind=1e-6 maxd=1e-5 [ CONC OUTPUT CONTROL: molecules/cc selonly H O OH HO2 H2 O2 [ SENS OUTPUT CONTROL: H O TEMP Control file ===== (s ms us) atol=# rtol=# mind=# maxd=# sent=# ] atol=1e-15 rtol=.05 all selonly none molecules/cc molefrac ] all none (or species name list) ]

In three blocks (TIME OUTPUT CONTROL, CONC OUTPUT CONTROL, SENS OUTPUT CONTROL), specify the control parameters. The first line and the lines beginning with '[' are comment lines and may be modified, but should not be deleted. Though the keywords are case insensitive, the species names are case sensitive.

TIME OUTPUT CONTROL (one line)

Specify the unit of the time output and the frequency of the output. Although the save.bin contains the all the results for every integration steps, they are not always necessary, for example, for the plotting. Since the converting all the time steps into CSV files often results in an extremely large file size and/or slow plotting, they are skipped properly. The skipping is controlled by the parameters here. When the variation of the variables (mostly concentrations) is small, the output interval may be large. Such a control can be done with atol and rtol. Also, for example for plotting, the resolution of the abscissa is limited to certain value. The minimum time resolution is controlled by mind. One of the followings can be specified as the unit of time. When omitted, default is 's' (seconds). s seconds

ms milliseconds

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us

microseconds

Following output controls can be specified. Absolute tolerance The species with mole fractions less than atol is not considered for the output frequency control. For example, with atol=1e-15, species with mole fraction less than 11015 are ignored in the output frequency determination. If omitted, default is 1.0E-16. Relative tolerance The output is done when the relative change of the any of the variable exceeds rtol from the last output. For example, rtol=.05 sets the relative torelance to be 5%. If not specified, default is 0.1 (10%).

atol

rtol

Minimum t (Unit: seconds) Irrespective of atol or rtol, the output interval is controlled to be larger than or equal to mind mind. For example, mind=5e-6 forces the minimum output interval to be 5 microseconds. When omitted, dafault value 1.0E-05 (10 microseconds) is adopted. Maximum t (Unit: seconds) Irrespective of atol or rtol, the output interval is controlled to be smaller than or equal to maxd maxd. It should be noted that the minimum output interval is determined by the internal time integration step. When omitted, dafault value 1.0E+03 (1000 seconds) is adopted. Time for sensitivity output (Unit: seconds) Sensitivity output is generated for the all time points that satisfy the other output control options without this option. When this option is specified, the sensitivity output is generated only for the specified time point.

sent

CONC OUTPUT CONTROL (one or two line[s])

Specify the unit of concentration output and the species to be output. The following units can be accepted. (Default : molecules/cc). molecules/cc molecules cm3 molefrac mole fraction

One of the following species output control can be specified. (Default : 'all'). none none (output is generated for temperature and pressure)

selonly selected species only all all the species

The second line is allowed only when the selonly is specified in the first line. List the name of species delimied by spaces in the second line. In the example above, concentrations of only H, O, OH, HO2, H2, and O2 are output in molecules cm3 unit.

SENS OUTPUT CONTROL (one line)

Specify none, all as below, or list the variable names delimited by spaces. Variable names are the speceis names or 'TEMP' (temperature). In the example above, sensitivity coefficients are output for the species H and O, and temperature. Though this input is meaningful only when the 'SENS' is specified in senk.inp, but should never be deleted in other cases. (leave 'none', for example.) none no output all output for all the variables

Rxn Contrib tool input

Example
Below is an example. ===== rxnc (rxncntrb.f) Control Input File ===== [ (Time points to be investigated in s) time1, time2, ... ] 2.5e-4 1.78e-4 5e-5 1.e-6

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[ (species to be investigated) name1, name2, ... ] H O HO2 [ options (atol, min%, top#, sbin, ocsv) ] atol=1e-20 min%=0.1 sbin=save.bin The third, fifth, and seventh lines specifies the time, species, and option, respectively. In the time specification, the time to be analyzed is specified in the unit of seconds. Multiple values are allowed. In the species line, the names of the chemical species must be listed. In the option line, following input with the form of keyword=value can be accepted. sbin=file name specifies the file name of the senkin binary to be read. Default is save.bin.

top#=n (integer) List the top n reactions with highest contribution. min%=r (real) atol=ATOL ocsv List the reactions with the contribution no less than r %. Input the same number as in the senkin input. Default is the default adopted by senkin, that is, 1E-20. When this option is specified, the contribution output is also generated in the .csv files.

Thermodynamic data
For the complete description of the thermodynamic data format, See the following document. 'The Chemkin Thermodynamic Data Base,' R. J. Kee, F. M. Rupley, and J. A. Miller, Sandia Report, SAND87-8215B (1994). Thermodynamic functions are represented with the NASA polynomials, (11) (12) (13) Usually, two sets of the coefficients are prepared for two temperature ranges, 300~1000 K and 1000~5000 K. The thermodynamic data consist of a1, a2, ..., a7 for high temperature and those for low temperature (totally 14 coefficients). The first line consist of the name of the chemcial species, chemical formula etc. For details, see the document shown above. Below is an example. AR 120186AR 1 G 0300.00 5000.00 1000.00 0.02500000E+02 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 -0.07453750E+04 0.04366000E+02 0.02500000E+02 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00-0.07453750E+04 0.04366000E+02 1 2 3 4

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