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GPOP reference manual - gpop4thf
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GPOP reference manual - gpop4thf

Synopsis

gpop4thf basename[.gpo/.tst] [temperature-file]

Description

  The program gpop4thf reads a GPOP-format file, basename.gpo, calculates thermodynamic functions, and output results to a CSV file, basename.csv.   A temperature file name may be specified on the command line to override the default temperatures for calculations.
  When an auxiliary input file (basename.ath) presents in the current directory, the program also generates an input file (basename.i97) for pac99 program which can generates 7-coefficients NASA format thermodynamic data.  The programs pac99 is a part of a program suite CEA2.  This program and a program for formatting c97to7 are included in both binary and source-code distributions of GPOP.
* It also generates a list file named basename.lst, which can be used as an input to THERMFIT program, for the compatibility with the older version of this program.
* Note that gpop4thf calculates thermodynamic functions at pressure of 1 bar (NOT at 1 atm) according to the recent standard state definition.   Thermodynamic function is calculated at 1 atm by Gaussian by default, and the entropy calculated by gpop4thf is larger than that by Gaussian by 0.1094 J K−1 mol−1 = R ln(1.01325) even in the case that all vibrations are treated as harmonic vibrations.
* Note that the vibrational frequencies are scaled when GPOP detects known method for calculation. See Frequency scaling and zero-point energy in gpop1scf reference manual.

Input

  The program expects following two input files in the current directory.
1) A GPOP-format file, basename.gpo.
  Note: basename.gpo should be pre-processed by gpop3tst before using gpop4thf.   Even in the case that no modification is needed, it must be pre-processed with null basename.mod.
2) A temperature file (optional).
3) An auxiliary thermodynamic input file named basename.ath (optional).
Temperature File Format
  The temperature file may contain any combination of the following three types of specifications;
tempRange T_start T_end T_step
tempRecipRange numer start end step
tempGauChebGrd T_min T_max nT
tempList T1 T2 T3 ...
The key 'tempRange' sets an equally spaced temperatures list from T_start to T_end, with step T_step.   The next type with a key 'tempRecipRange' sets a list of temperature equally spaced in the reciprocal of temperature, that is, they are equally spaced in the Arrhenius plot.   Like the convention used for the abscissa of the Arrhenius plots, the reciprocal temperature may be specified in the form of: 1000/T, 10000/T, or etc. by setting the numer (numerator) to 1000, 10000, or etc.   For example,
tempRecipRange 10000 5 40 1
sets a list of temperatures corresponding to 10000/T = 5, 6, 7, ..., 40.   The key starting with 'tempGauChebGrd' sets the list of the temperatures suitable for Chebyshev-polynomial fit of RRKM rate coefficients.   For the projected temperature in [−1, 1] from the temperature range [Tmin, Tmax],
,       (1)
it generates the temperature in the Gauss-Chebyshev grid,
.       (2)
This is useful for tstrate and vtst programs when they are used to generate high-pressure limiting rate coefficients which will be used with the RRKM branching fractions calculated by SSUMES programs.   For the detailed description of the Chebyshev polynomials and Gauss-Chebyshev grid, see the of the manual of SSUMES programs.   The last type starting with 'tempList' sets a list of temperatures simply as they listed after the key.
DEFAULT: Default is equivalent to the following input.
tempRang 300. 1500. 100.
Auxiliary Thermodynamic Input File Format
  The auxiliary thermodynamic input file can contain the following four types of keys: 
speciesName name
DH298_kJ ΔH298
DH298_RT ΔH298/RT
numIntRotors nIntRot
The key 'speciesName' sets the name of the chemical species used in the NASA 7-coefficients thermodynamic data.   The keys 'DH298_kJ' and 'DH298_RT' can be used to give the standard enthalpy of formation at 298.15 K in the unit of kJ/mol (DH298_kJ) or by a dimensionless value of ΔfH298° / RT (DH298_RT).   The last key 'numIntRotors' sets the number of internal rotors used in the HOE extrapolation in the THERMFIT program.   Usually, this number is the number of rotatable (single) bonds connecting the molecular moieties.
DEFAULT: The base file name is set to speciesName when this key is missing.   Zero (0) is used for numIntRotors if this key is omitted.   There is NO default to ΔfH298° and the input is mandatory.

Output

The results are written to a csv-format file, basename.csv. Here is an example for ethyl radical calculated from sample files, ethyl500.log and ethyl500.mod.
An example of the .lst output is shown below.
  UNITS:KJ
 Thermodata generated by gpop
 SPECIES       Hf       S    Cp 300     400     500     600     800     1000     1500     DATE        ELEMENTS
 C2H5        120.90   248.12    51.77   62.56   72.74   81.72   96.54  108.12  126.86          gpop    C   2 H   5     0     0 G 1
An example of the .i97 output is shown below.   The statement "LSTS OLD" specifies old 7-coefficient temperature exponents to be used.   Removing this line will results in the generation of new 9-coefficient thermodata. 
NAME  C2H5
C2H5                    HF298     120900.0JOULES
DATE  gpop
LSTS  OLD
OUTP  MFIG              LSQS              ATM
METH  READIN            KJOULE            BAR
      T          200.000CP/R        5.1122H-H0RT   0.0044246S/R        27.6213
      T          298.150CP/R        6.2037H-H0RT   0.0048212S/R        29.8545
      T          300.000CP/R        6.2270H-H0RT   0.0048298S/R        29.8930
      T          400.000CP/R        7.5240H-H0RT   0.0053408S/R        31.8615
      T          500.000CP/R        8.7482H-H0RT   0.0059021S/R        33.6745
      T          600.000CP/R        9.8284H-H0RT   0.0064685S/R        35.3671
      T          700.000CP/R       10.7757H-H0RT   0.0070176S/R        36.9549
      T          800.000CP/R       11.6115H-H0RT   0.0075407S/R        38.4495
      T          900.000CP/R       12.3508H-H0RT   0.0080349S/R        39.8607
      T         1000.000CP/R       13.0041H-H0RT   0.0084998S/R        41.1965
      T         1100.000CP/R       13.5795H-H0RT   0.0089360S/R        42.4635
      T         1200.000CP/R       14.0851H-H0RT   0.0093445S/R        43.6672
      T         1300.000CP/R       14.5285H-H0RT   0.0097266S/R        44.8125
      T         1400.000CP/R       14.9173H-H0RT   0.0100838S/R        45.9038
      T         1500.000CP/R       15.2583H-H0RT   0.0104176S/R        46.9448
      T         1600.000CP/R       15.5578H-H0RT   0.0107297S/R        47.9393
      T         1800.000CP/R       16.0540H-H0RT   0.0112949S/R        49.8017
      T         2000.000CP/R       16.4421H-H0RT   0.0117910S/R        51.5140
      T         2200.000CP/R       16.7493H-H0RT   0.0122283S/R        53.0961
      T         2400.000CP/R       16.9954H-H0RT   0.0126157S/R        54.5644
      T         2600.000CP/R       17.1949H-H0RT   0.0129605S/R        55.9329
      T         2800.000CP/R       17.3584H-H0RT   0.0132690S/R        57.2134
      T         3000.000CP/R       17.4938H-H0RT   0.0135463S/R        58.4157
      T         3300.000CP/R       17.6568H-H0RT   0.0139129S/R        60.0910
      T         3600.000CP/R       17.7838H-H0RT   0.0142304S/R        61.6331
      T         3900.000CP/R       17.8846H-H0RT   0.0145077S/R        63.0607
      T         4200.000CP/R       17.9658H-H0RT   0.0147519S/R        64.3891
      T         4600.000CP/R       18.0516H-H0RT   0.0150353S/R        66.0275
      T         5000.000CP/R       18.1184H-H0RT   0.0152794S/R        67.5355
FINISH

NASA 7-coefficients file generation

Execute pac99 program by typing:
pac99
Then type in the base filename of the .i97 input for pac99, for example for the ethyl500.i97 created above,
ethyl500
An example of the .c97 output is shown below.
C2H5                                                                      
 2 gpop   C   2.00H   5.00    0.00    0.00    0.00 0   29.0611000     120900.000
    200.000  1000.000 5  0.0  1.0  2.0  3.0  4.0  0.0  0.0  0.0        11951.616
 4.011619340D+00-1.214955554D-03 4.282907140D-05-5.350346100D-08 2.089711494D-11
 0.000000000D+00 0.000000000D+00 0.000000000D+00 1.311625678D+04 5.874770650D+00
   1000.000  5000.000 5  0.0  1.0  2.0  3.0  4.0  0.0  0.0  0.0        11951.616
 3.509988000D+00 1.413735304D-02-5.567846340D-06 1.008695468D-09-6.880105140D-14
 0.000000000D+00 0.000000000D+00 0.000000000D+00 1.263918381D+04 5.256827620D+00
Then convert the .c97 coefficients file (new CEA-format) to an older Chemkin-format file as,
c97to7 < ethyl500.c97 > ethyl500.dat
The resultant ethyl500.dat will look like:
C2H5              gpop  C   2H   5          G   200.00   5000.00  1000.00      1
 3.50998800E+00 1.41373530E-02-5.56784634E-06 1.00869547E-09-6.88010514E-14    2
 1.26391838E+04 5.25682762E+00 4.01161934E+00-1.21495555E-03 4.28290714E-05    3
-5.35034610E-08 2.08971149E-11 1.31162568E+04 5.87477065E+00                   4

NASA 9-coefficients file generation

Remove "LSTS OLD" in ethyl500.i97 and save it as ethyl500new.i97.   Then execute pac99 and enter "ethyl500new".   A file named ethyl500new.c97 will be created as shown below.
C2H5                                                                      
 2 gpop   C   2.00H   5.00    0.00    0.00    0.00 0   29.0611000     120900.000
    200.000  1000.000 7 -2.0 -1.0  0.0  1.0  2.0  3.0  4.0  0.0        11951.616
-1.287212127D+05 2.509706238D+03-1.433034199D+01 6.329530310D-02-7.249837920D-05
 4.664756280D-08-1.249131619D-11 0.000000000D+00 1.823363059D+03 1.031468101D+02
   1000.000  5000.000 7 -2.0 -1.0  0.0  1.0  2.0  3.0  4.0  0.0        11951.616
 4.164493570D+06-1.644116308D+04 2.772803501D+01-2.933955205D-03 5.367610840D-07
-5.247265900D-11 2.114822254D-15 0.000000000D+00 1.129120735D+05-1.620314187D+02
Do NEVER try to convert this file to 7-coefficient format by c97to7 which just converts the formatting.