Copyright © 2002–2016 by A. Miyoshi
GPOP reference manual - vtst

GPOP reference manual - vtst


vtst basename


  The program vtst reads a VTST reaction input file, basename.rxv, and GPOP-format files for molecules or atoms described in the VTST reaction input.   Multiple GPOP-format files created from the frequency jobs along the reaction coordinate are read in, and the canonical VTST rate constants are evaluated by interpolation.   Calculated rate constants and equilibrium constants are written in a CSV file, basename.csv.
* 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. However, the imaginary frequency for the tunneling correction, it is used UNSCALED.


  The program expects following input files in the current directory.
1) A VTST reaction input file, basename.rxv
2) GPOP-format files (*.gpo)
  Note: All of the .gpo files should be pre-processed by gpop3tst before using them with vtst.   Even in the case that no modification is needed, it must be pre-processed with null .mod files.   The energetics must be specified explicitly in the .rxv file or by the energyTST in the .mod file before the processing by gpop3tst.
VTSV reaction input file format
  The VTST reaction input file, basename.rxv, is similar to a .rxn file for tstrate.   It should contain a reactants block and at least two varTS lines.   Optionally, a products block may be placed.   The following is an example input for the C–H bond fission reaction of 1H-benzocylobutadiene.   The calculation is done in the reverse direction (recombination).
energyUnit kJ/mol
  file hatom500 bzcycb2en500
  energy 0
  file bzcycb2en1H500
  energy -252.224
varTS  1.8  bzcycb2en1Dr018 -54.708
varTS  1.9  bzcycb2en1Dr019 -31.200
varTS  2.0  bzcycb2en1Dr020 -15.864
varTS  2.1  bzcycb2en1Dr021  -7.521
varTS  2.2  bzcycb2en1Dr022  -3.386
varTS  2.3  bzcycb2en1Dr023  -1.407
varTS  2.4  bzcycb2en1Dr024  -0.502
varTS  2.5  bzcycb2en1Dr025  -0.124
varTS  2.6  bzcycb2en1Dr026   0.017
varTS  2.7  bzcycb2en1Dr027   0.081
varTS  2.8  bzcycb2en1Dr028   0.214
The reactants or products block should contain at least one file key, specifying the name of '.gpo' file(s) to be read.   Unlike the .rxn file, the file name and energy along the reaction coordinates are specified by a line beginning with varTS by the following format.
varTS coord filename [energy]
Here, coord is the reaction coordinate in arbitrary unit, filename is the base name of a .gpo file, and energy is the zero-point energy adiabatic energy at this position in the unit specified by energyUnit.   If the energy to be used is already set in each .gpo file using energyTST by gpop3tst, the last parameter may be omitted.   The varTS should appear in the increasing order of the coordinate.   All valid keys in the blocks or the outside the blocks will be described in detail below.
Keys valid outside the blocks
energyUnit unit
  Changes the unit for energy key in the blocks. Note that this NEVER override the unit of energyTST key in '.gpo' files, which is always hartree. Values may be one of 'hartree' (default), 'kJ/mol', and 'cm-1'.
tempRange T_start T_end T_step
tempRecipRange numer start end step
tempGauChebGrd T_min T_max nT
tempList T1 T2 T3 ...
  Temperatures for calculation. Either tempRange or tempList can be used. Same as these keys in the temperature file format in gpop4thf.
fileType ftyp
  The file type for molecular property input. Valid values are 'gpo' (default) and 'tst'. This is retained for older compatibility.
Keys valid in the reactants and products blocks
file filename1 [filename2 ...]
  This key is used specify the base file name(s) of the reactants or products.   The extension of the file names is fixed (usually .gpo).
energy engy
  This key overrides the sum of the energies of the molecules (or atoms) in the block.   The unit of the energy may be changed by 'energyUnit' key outside the block.


  The results are written to a csv-format file, basename.csv.   An example output is shown below.
  The first three rows exist only when the products were specified in the .rxv file, and show the internal energy change at 0 K (dE0), enthalpy change at 298.15 K (dH298), and entropy change at 298.15 K (dS298) of the reaction.   The fifth to eighth rows show the activation internal energy at 0 K (dE*0), activation enthalpy at 298.15 K (dH*298), and activation entropy at 298.15 K (dS*298) at each coordinate.   It is recommended to check these values, especiallly when you are to use the energy already set in the .gpo files.
  The next block of the rows show the essential results of the VTST calculations.   The units for equilibrium constants (Keq) and rate constants (k) are in (molecules cm−3) – s units.   The vtst program searches for the minimum ln(k) along the reaction coordinate by the third-order natural spline interpolation.   The coord output at each temperature must be carefully checked for not being the either edge of the input coordinates, which suggests the true minimum will be outside the input range of the coordinate.   The last output block contains the rate constant calculated at each coordinate.   This is also helpful to check whether the minimum is located in the input range of the coordinate.