GPOP reference manual

GPOP reference manual - prepum

The program prepum reads a unimolecular reaction input file, basename.um, and GPOP-format files for molecules or atoms described in the unimolecular reaction input. An input file for UNIMOL rrkmth is created in basename_rrkm.inp.

* 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 frequencies for tunneling correction are NOT scaled.

The program expects following two input files in the current directory.

1)	A unimolecular reaction input file, `basename.um`.
2)	A GPOP-format file(s) (`*.gpo`).
		Note: `basename.gpo` should be pre-processed by `gpop3tst` before using `prepum`. Even in the case that no modification is needed, it must be pre-processed with null `basename.mod`.

Unimolecular reaction input file format

The unimolecular reaction input file, basename.um, is similar to the reaction input file, basename.rxn, for tstrate. It should contain one reactant block [1] and at least one channel block. The channel block should contain one transitionState sub-block. The channel block may be placed as many times as you want, though, of course, it cannot exceed the channel-number limit of the UNIMOL rrkmth program. A products sub-block can also be placed in a channel block in order specify the energy of the products, which is required for the asymmetric Eckart tunneling treatment. An example of the unimolecular reaction input file is shown below.

bufferByName N2
collMolec 4.5 500.
reactant{
  file etp500
}
channel{
  transitionState{
    file tsho501
  }
  products{
    file hoo500 etln500
  }
}

Valid keys in the blocks or the outside the blocks will be described in detail below.

Keys valid outside the blocks

title title_string

A title string written in the first line of the UNIMOL input.

bufferByName buffer_gas_name

Specify the buffer gas by a name. Valid names are, N2 (nitrogen, N₂), He (helium), and Ar (argon). Collision parameters used for these buffer gases are listed below.

Table 1. Parameters used for registered buffer gases
buffer gas	molW	sigma	epsK
N₂	28.0134	3.798	71.4
He	4.002602	2.551	10.22
Ar	39.948	3.542	93.3

When neither of this nor buffer key was found, the buffer gas is assumed to be N₂.

buffer molW sigma epsK

Specify the buffer gas by its molecular weight (molW), collision diameter (sigma, in Å), and well depth (epsK; in K).

collMolec sigma epsK

Specify the collision parameters for the reactant molecule, similarly to the buffer key. The molecular weight is calculated from the chemical formula of the reactant. The collision parameters for the buffer-molecule pair are calculated by an arithmetic mean for sigma and geometric mean for epsK as,

σ_pair = (σ_molec + σ_buffer) / 2
ε_pair = (ε_molec ε_buffer)^1/2

If neither of this key nor collPair key is not found, sigma and epsK of the molecule are assumed to be those of N₂, though this default is not recommended usually.

collPair sigma epsK [molW_buffer]

Specify the collision parameters for the pair of the reactant molecule and buffer, similarly to the collMolec key. The molecular weight of the reactant molecule is calculated from the chemical formula of the reactant. The molecular weight of the buffer gas should be specified as the third optional argument molW_buffer, or by buffer or bufferByName key, otherwise, the default molecular weight for N₂ is used. If neither of this key nor collMolec key is not found, sigma and epsK of the molecule are assumed to be those of N₂, though this default is not recommended usually.

energyUnit unit

Changes the unit for energy and alignBaseEnergy keys. Note that this affects the energy key input in ".um" file only, and it NEVER affect 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.

grainSize gsize

Set the grain size in UNIMOL rrkmth input file. The unit is always cm⁻¹ and is not affected by the energyUnit setting. Default is 100 cm⁻¹.

alignBaseEnergy aBaseE

This option is required only when you are to use the UNIMOL rrkmth output files for SSUMES (Steady-State Unimolecular Master-Equation Solver) components. With this option, all of the threshold energies are aligned properly into the grain-size units in order to avoid the asymmetry problem detected by SSUMES components. The absolute base energy, aBaseE, is usually chosen to be the zero-point energy corrected hartree energy of the lowest-energy well.

Keys valid in the reactant, transitionState, and products blocks

file file_name [file_name2 ...]

A key to specify the GPOP-format file for reactant or the transition states.

energy engy

This key overrides the sum of the energies in the molecules (or atoms) in the block. The unit of the energy may be changed by 'energyUnit' key outside the block.

imagFreqTS imgfrq

This key is valid only in a transitionState block, and is used to override the imaginary frequency used for tunneling corrections. Note that the value should be real and positive, that is, the absolute figure of the imaginary frequency in cm^–1 unit.

The UNIMOL rrkmth inputs are written to a file, basename_rrkm.inp. An output from the sample input EtO2concHO2elim.um is shown below.

ethylperoxy radical concerted HO2 elimination (created by GPOP rev. 2009.08.12)
 5000 10  7 7  1  0
 20 21
 31.256
 1 1
 -0.1637744 -0.1743829
 1 1
 0.4917683 1 1 0 0
 0.5931488 1 1 0 0
 4.149 61.028954 28.013400 188.9
 212 1
 348 1
 467 1
 502 1
 624 1
 810 1
 863 1
 975 1
 1010 1
 1192 1
 1266 1
 1276 1
 1301 1
 1426 1
 1524 1
 1558 1
 3006 1
 3063 1
 3082 1
 3149 1
 113 1
 228 1
 347 1
 514 1
 777 1
 819 1
 964 1
 1065 1
 1117 1
 1166 1
 1269 1
 1336 1
 1367 1
 1438 1
 1442 1
 1461 1
 2949 1
 2973 1
 3012 1
 3020 1
 3039 1
 76. 760. 7.6E+3 7.6E+4 7.6E+8 7.6E+11 7.6E+14
 1200.000 1100.000 1000.000 900.000 800.000 700.000 600.000
 1
 20.586 1098 1
 1 2
  1 0
  2 0  1 20

[1]	Note that the block name should be singular, `reactant`, while it is plural, `reactants`, for tstrate input. Number of reactant molecules is always one for a unimolecular reaction.