KUCRS-User's Guide
(c) 2002–2023 by A. Miyoshi
All rights reserved.
KUCRS
– Knowledge-basing Utilities for Complex Reaction Systems –
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KUCRS User's Guide

  The KUCRS run_comb is a command-prompt batch file which invokes several programs during its execution.   Here, these programs and related programs are introduced.

List of the Components

  The run_comb invokes the following programs.
combust Main program of run_comb autogenerator
thermgen Batch version of the THERM [#1] program
thermpac Program to extrapolate thermodynamic functions up to 5000 K by fitting to HOE
pac99m Thermodata generator included in NASA-CEA2 [#2]
(modified for batch processing)
c97to7m Program to covert formats of thermodata
chemgen Processor of macro reaction inputs
trangen Generator of transport data for Chemkin
  The followings are utility programs.
mollib Molecular library maintainance program
mol2smiles Internal format to SMILES converter
smiles2mol SMILES to internal format converter

Example of Using KUCRS components with sample input files

  Below is an example of the usage of KUCRS components with sample input files provided in KUCRS\work\sample.

1. Preparation

  Prepare the environment according to the Getting Started with KUCRS, execute envKUCRS in KUCRS\work, and change directory to KUCRS\work\sample.

2. Generating additivity group data from SMILES

  Below is the contents of the file KUCRS\work\sample\samp.inp. 
iC4H9OO             [O]OCC(C)C
C4H8OOHit           OOC[C](C)C
C4H8OOHii           OOCC(C)[CH2]
Each line contains a name of the chemical species and its SIMLES representation.   By typing,
c:\KUCRS\work\sample> smiles2mol samp.inp samp_mol.dat -t
the program smiles2mol converts the SMILES chemical structures in samp.inp to KUCRS's unique internal representations and stores them into samp_mol.dat.   It also print out human readable chemical structures and additivity groups for the thermodynamic data estimation to console. 
KUCRS rev. 2021.08.23a
...
-----------------------------------------------------------
 name:    iC4H9OO
 formula: C4H9O2
 SMILES:  [O]OCC(C)C
 struct:
 O.- O - C - C - C 
             |_- C 
 groups:  iC4H9OO R C 4 H 9 O 2 $ C/C/H2/O 1 C/C/H3 2 C/C3/H 1 O/C/O 1 O/H/O 1 $ ALPEROX 4 9
 code:    a0008066 (ROO)
-----------------------------------------------------------
...
The option "-t" to smiles2mol may be used to store the "groups:" information in another file, named samp_thg.inp.   Below is the contents of samp_thg.inp. 
Thermodata generated by smiles2mol (Feb 04, 2011)
 iC4H9OO R C 4 H 9 O 2 $ C/C/H2/O 1 C/C/H3 2 C/C3/H 1 O/C/O 1 O/H/O 1 $ ALPEROX 4 9
 C4H8OOHit R C 4 H 9 O 2 $ C/C/H2/O 1 C/C/H3 2 C/C3/H 1 O/C/O 1 O/H/O 1 $ T 5 18
 C4H8OOHii R C 4 H 9 O 2 $ C/C/H2/O 1 C/C/H3 2 C/C3/H 1 O/C/O 1 O/H/O 1 $ P 5 6

3. Generating thermodynamic data from additivity group data

  To generate the thermodynamic data, type as follows.
c:\KUCRS\work\sample> thermgen samp_thg.inp samp_thg.lst
Below is the contents of the samp_thg.lst file created here. 
  UNITS:KJ
 Thermodata generated by smiles2mol (Feb 04, 2011)
 SPECIES       Hf       S    Cp 300     400     500     600     800     1000     1500     DATE        ELEMENTS
 iC4H9OO     -67.36   379.80   121.21  149.45  173.59  194.43  226.81  252.55                 thgen    C   4 H   9 O   2     0 G 4
 C4H8OOHit   -32.64   395.04   126.52  150.96  173.59  194.18  226.69  252.34                 thgen    C   4 H   9 O   2     0 G 5
 C4H8OOHii   -13.39   393.17   126.57  155.64  180.46  201.50  233.34  257.69                 thgen    C   4 H   9 O   2     0 G 5
These data in the list format of the THERM program can be coverted to the NASA polynomial format by using the thermpac and pac99m.  To execute thermpac, type,
c:\KUCRS\work\sample> thermpac samp_thg.lst samp_thg.i97
then a file named samp_thg.i97 containing the following input for pac99m will be created. 
NAME  iC4H9OO         
C4H9O2                  HF298     -67.3600KJOULE
DATE  thgen 
LSTS  OLD
OUTP  MFIG              LSQS              ATM
METH  READIN            JOULES            ATM
      T         200.0000CP/R       11.5533H-H0RT     10.8142S/R        40.5599
      T         298.1500CP/R       14.5122H-H0RT     11.5077S/R        45.6795
      T         300.0000CP/R       14.5769H-H0RT     11.5265S/R        45.7694
      T         400.0000CP/R       17.9773H-H0RT     12.7212S/R        50.4367
      T         500.0000CP/R       20.8915H-H0RT     14.0726S/R        54.7711
 :
      T        4600.0000CP/R       40.2119H-H0RT     34.0938S/R       128.7897
      T        5000.0000CP/R       40.3301H-H0RT     34.5882S/R       132.1477
FINISH
NAME  C4H8OOHit       
 :
Execute pac99m by typing,
c:\KUCRS\work\sample> pac99m samp_thg
The thermodynamic data formed in samp_thg.c97 should be reformatted.  Type as below,
c:\KUCRS\work\sample> c97to7m < samp_thg.c97 > samp_thg.dat
The reformatted file (samp_thg.dat) will look like: 
THERMO
   200.000  1000.000  5000.000
iC4H9OO           thgen C   4H   9O   2     G   200.00   5000.00  1000.00      1
 1.01467873E+01 3.05538270E-02-1.24407750E-05 2.30628955E-09-1.59891993E-13    2
-1.32467955E+04-2.26594992E+01 7.47214966E+00 6.10466106E-03 9.24718413E-05    3
-1.29154051E-07 5.35116356E-11-1.11876674E+04-1.78866742E+00                   4
C4H8OOHit         thgen C   4H   9O   2     G   200.00   5000.00  1000.00      1
 1.03491111E+01 3.03505002E-02-1.24974449E-05 2.33498675E-09-1.62788316E-13    2
-9.12155685E+03-2.18765280E+01 1.18358510E+01-1.49152863E-02 1.28251416E-04    3
-1.54673866E-07 5.98762503E-11-7.64728496E+03-1.99286829E+01                   4
C4H8OOHii         thgen C   4H   9O   2     G   200.00   5000.00  1000.00      1
 1.22743731E+01 2.84317160E-02-1.17144065E-05 2.18973048E-09-1.52718166E-13    2
-7.49654463E+03-3.30242364E+01 8.22486738E+00 3.40269298E-03 1.04442186E-04    3
-1.44956105E-07 5.99150535E-11-4.87848708E+03-4.06884648E+00                   4
END

4. Generating transport data from additivity group data

  The program trangen generates transport data from additivity group data.   Type as follows,
c:\KUCRS\work\sample> trangen samp_thg.inp --no_append
and then a file samp_trn.dat containing the following will be generated. 
!
! generated by KUCRS rev. 2021.08.23a (c) 2002-2021 by A. Miyoshi
!  on Aug 25, 2021.
!
! Transport data generated by trangen (Aug 25, 2021)
iC4H9OO            2   453.6     5.358     0.0       0.0      1.0
C4H8OOHit          2   453.6     5.358     0.0       0.0      1.0
C4H8OOHii          2   453.6     5.358     0.0       0.0      1.0

5. Generating the reaction mechanism in Chemkin format

  The chemgen processes a reaction list in macro representation and generates a reaction mechanism in Chemkin format.  The macro's should be defined in KUCRS\libdata\rxn_macr.dat.   Below is a part of macro definitions in the KUCRS\libdata\rxn_macr.dat. 
 Isom/RO2/5pt         6.95E+11    0.     27150.
 Isom/RO2/6pp         3.07E+11    0.     22960.
The first line above defines a macro named "Isom/RO2/5pt", which means the intramolecular tertiary hydrogen abstraction reaction of a primary RO2 radical via a five-membered ring transition state, with the parameters for the modified Arrhenius expression, A = 6.95E+11, n = 0., and Ea = 27150.   The reaction list in macro representation written in KUCRS\work\sample\samp_chg.inp is shown below. 
 iC4H9OO = C4H8OOHit $ Isom/RO2/5pt 0 1 Y
 iC4H9OO = C4H8OOHii $ Isom/RO2/6pp 0 2 Y
One reaction is written in one line.   The part until "$" is a reaction equation and list reactants to the left of "=" and products to the right.  In the right to "$", write a macro name, a shift value of the activation energy, a multiplication of an preexponential factor, and a flag to indicate whether the reverse reaction is taken into account or not.  For the second reaction in the above example, two times of the rate constant defined by "Isom/RO2/6pp" (for a single methyl group) is assigned since i-butylperoxy has two equivalent methyl groups.   To process this input by the chemgen, Type as follows.
c:\KUCRS\work\sample> chemgen samp_chg.inp samp_thg.dat --no_append
c:\KUCRS\work\sample> mol2smiles samp_mol.dat samp.smiles -l
c:\KUCRS\work\sample> bsmiles samp_thm.dat samp_sp_.csv samp_the.dat
c:\KUCRS\work\sample> copy /b samp_spc.inp + samp_the.dat + samp_rxn.inp samp_chm.inp
The file samp_chm.inp contains the full reaction mechanism needed for Chemkin as shown below. (The other files are the temporary files during the generation of this file, and may be deleted.) 
!
! generated by KUCRS rev. 2021.08.23a (c) 2002-2021 by A. Miyoshi
!  on Aug 25, 2021.
!
elements
 H HE C N O AR
end
species
 iC4H9OO C4H8OOHit C4H8OOHii
end
thermo all
   300.000  1000.000  5000.000
!
! [_ SMILES="[O]OCC(C)C" _]
iC4H9OO           thgen C   4H   9O   2     G   200.00   5000.00  1000.00      1
 1.01467873E+01 3.05538270E-02-1.24407750E-05 2.30628955E-09-1.59891993E-13    2
-1.32467955E+04-2.26594992E+01 7.47214966E+00 6.10466106E-03 9.24718413E-05    3
-1.29154051E-07 5.35116356E-11-1.11876674E+04-1.78866742E+00                   4
!
! [_ SMILES="OOC[C](C)C" _]
C4H8OOHit         thgen C   4H   9O   2     G   200.00   5000.00  1000.00      1
 1.03491111E+01 3.03505002E-02-1.24974449E-05 2.33498675E-09-1.62788316E-13    2
-9.12155685E+03-2.18765280E+01 1.18358510E+01-1.49152863E-02 1.28251416E-04    3
-1.54673866E-07 5.98762503E-11-7.64728496E+03-1.99286829E+01                   4
!
! [_ SMILES="OOCC(C)[CH2]" _]
C4H8OOHii         thgen C   4H   9O   2     G   200.00   5000.00  1000.00      1
 1.22743731E+01 2.84317160E-02-1.17144065E-05 2.18973048E-09-1.52718166E-13    2
-7.49654463E+03-3.30242364E+01 8.22486738E+00 3.40269298E-03 1.04442186E-04    3
-1.44956105E-07 5.99150535E-11-4.87848708E+03-4.06884648E+00                   4
end
reactions      cal/mole  moles
 iC4H9OO=C4H8OOHit                                6.950e+11   0.000   27150.0
                                           rev /  3.884e+10   0.123   18626.1 /
 iC4H9OO=C4H8OOHii                                6.140e+11   0.000   22960.0
                                           rev /  1.094e+12  -0.375   10050.0 /
end
For the execution of the chemgen, one should prepare a table of thermodynamic data, as well as the macro representation input (samp_chg.inp in the example above).   The samp_thg.dat generated by the preceeding processes are used in this example.   The thermodynamic data are required to calculate the rate parameters for the reverse reactions.
[#1] E. R. Ritter and J. W. Bozzelli, "THERM: Thermodynamic Property Estimation for Gas Phase Radicals and Molecules," Int. J. Chem. Kinet., 23, 767-778 (1991).
[#2] S. Gordon and B. J. McBride, "Computer Program for Calculation of Complex Chemical Equilibrium Compositions and Applications," NASA Reference Publication 1311 (1996).