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GPOP - Quick Start step-2
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GPOP - Quick Start step-2

  Followings are the examples of calculation of thermodynamic functions and equilibrium constants.

Pre-processing

  1. Similar to step-1, execute gpop1scf for ethyl500.log and etln500.log as
    gpop1scf ethyl500
    gpop1scf etln500

Processing GPOP format files

  The GPOP-format files, *.gpo, can be directly used by diagnostics and analysis tools named as gpop5* or gpop6*.   However, FURTHER INFORMATION, such as the energy and information of the hindered rotor, is required for the thermodynamics and rate constants calculations (gpop4thf, tstrate, vtst, and prepum).   Additional informations must be provided in the modification information files, *.mod, and the GPOP-format files SHOULD be re-processed (modified) by gpop3tst program before they are used for gpop4thf, tstrate, etc.
  1. Investigate the modification information files, ethyl500.mod and etln500.mod, provided in the sample directory, and compare them with the template modification files generated by gpop1scf, ethyl500_.mod and etln500_.mod.
      Note that gpop1scf creates a template *.mod file as ethyl500.mod for ethyl500.gpo, but, when *.mod file with the same name already exists, a template is generated with different name, for example, ethyl500_.mod.
  2. In this example, ethyl500.mod adds a internal rotator, and the file is different from the automatically generated template, ethyl500_.mod, while etln500.mod is used as generated.
  3. Make modifications to ethyl500.gpo and etln500.gpo as
    gpop3tst ethyl500
    gpop3tst etln500
    The reason why this step is separated from the pre-processing is that there is nearly always something to do in this step with .mod file.   At least, the energy (energyTST) must be provided here, unless you happen to use CBS-QB3 method for energy evaluation.   For other methods, gpop1scf generates useSCFenergy+ZPE key in *.mod files, however, this is usually not satisfactory.
  4. Create the GPOP format file for hydrogen atom as
    gpop3atm hatom500
    Note that this is nothing to do with the Gaussian output.   If you have already calculated the energy of H-atom by some method, you must set it in the .mod, manually.   The pre-processor cannot read out the Gaussian output for atomic species since it does not contain useful infomation such as the structure of the molecule or the vibrational frequency.
  5. Three GPOP-format files, ethyl500.gpo, etln500.gpo, and hatom500.gpo, are now ready for thermodynamic calculations.

Calculating thermodynamic functions for a single species

  1. To calculate the thermodynamic functions for ethyl radical, type;
    gpop4thf ethyl500
  2. A CSV-format file, ethyl500.csv, which contains the thermodynamic calculation results, should be created if the calculations were done successfully.   This will also create ethyl500.lst which can be used as an input to THERMFIT program (developed by Prof. Bozzelli; available in THERM program suit) which generates 7-coefficient NASA polynomial format file for thermodynamic data, which is commonly used by the softwares such as Chemkin.

Calculating equilibrium constants for a reaction

  1. A reaction specification sample file, ethylCHdissoc.rxn, must be in the current directory.
  2. Invoke tstrate program as;
    tstrate ethylCHdissoc
  3. The calculated equilibrium constants can be found in a CSV-format file, ethylCHdissoc.csv.

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