Copyright © 1998–2020 by A. Miyoshi
SSUMES - Quick Start step-1
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SSUMES - Quick Start step-1
Preparation

Fig. Q1
  1. Build SSUMES and UNIMOL components from source files or unpack the pre-built binaries for MS-Windows according to the instructions in the Installation section.
  2. Set PATH to the directories where SSUMES and UNIMOL executables reside.   (Or place the executables in the current directory by copying / moving them.)
  3. Place sample input files in the current directory. (Either by copying them or by changing directory.   Note that, if you chose not to set the PATH, you must copy sample input files into the current directory where binary executables reside.)
Example problem-1
  The first example problem is an addition reaction of phenyl radical to acetylene (C2H2).   As an example for single-well problem, only the first well for this reaction is considered here as shown in Fig. Q1.   The master-equation is solved for chemical activation problem in order to evaluate the overall rate coefficients as well as the branching fractions for stabilization and the formation of phenylacetylene + H.
RRKM input
  The sample file, rc2h2ph_s_rrkm.inp, is an input file for the rrkmth program, which is a modified version of RRKM program in UNIMOL.   The file contains all necessary information (vibrational frequencies, rotational constatnts, etc.) on the (adduct) molecule and transition states for dissociation reactions.   The RRKM input can be prepared manually or by gpop program suite.   The files used to create rc2h2ph_s_rrkm.inp by prepum program in gpop can be found in sample/gpop directory.
Creating MASTER input file containing ρ(E) and k(E)
  Here the rrkmth program is used to prepare a file rc2h2ph_s_mas.dat from an input file rc2h2ph_s_rrkm.inp.   The MASTER input file, rc2h2ph_s_mas.dat, contains the density of states and microscopic rate constants for a well necessary for the master-equation calculations.
  1. Run rrkmth with rc2h2ph_s_rrkm.inp by typing:
    rrkmth < rc2h2ph_s_rrkm.inp > rc2h2ph_s_rrkm.out
  2. Six files, mas1t.dat, ratnum.csv, ratnum.dat, ratthm.csv, rc2h2ph_s_rrkm.out, and tunnel.dat must have been created in the current directory.
  3. Move (rename) mas1t.dat to rc2h2ph_s_mas.dat by typing:
    mv mas1t.dat rc2h2ph_s_mas.dat
    on Unix or
    ren mas1t.dat rc2h2ph_s_mas.dat
    on Windows.   (Or, use move command on recent Windows.)
  4. Other files are not needed below and may be removed.
Control input
  An additional control input file, rc2h2ph_s_ca.inp, is required to provide the information on the chemical activation reaction and calculation parameters.   Its contents is short and is shown below.
# phenyl-c2h2 single-well model - chemical activation

tempRecipRange 100000 50 331 20
! 10 atm (default unit of pressure is Torr)
pressList 7600

well{
  filename rc2h2ph_s_mas
  recombChan 2
  truncate 50
}
The lines beginning with '#' or '!' are comments.   The first two lines except for the comments and blank lines specifies the temperatures and pressures for calculation.   The block input beginning with 'well{' contains the information on the well: the name of the MASTER input file containing the density of states and microscopic rate constants, the channel number where the reactive flux comes in ('recombChan'), and the number of the grains to be truncated ('truncate').   This is required to consider the stabilization process, and the polulation that goes into the lower grains, for which the number of grains is specified by 'truncate', are considered to be stabilized.   The level of 'truncate' is also shown in Fig. Q1.
Solving master-equation for chemical activation problem
  1. Run carate as:
    carate rc2h2ph_s_ca
  2. The following diagnostic messages are printed to the console, indicating the progress of the calculation:
    carate - SSUMES rev. yyyy.mm.dd
listWells::alignSize absTop = 792
well-1: err3 = 1e-009
kEthInt / kEthOut = 1e-064 / 1e-064
well-1: recombChan = 2
well-1: truncate = 50
umolProb::initMW psiz = 742
T = 2000 [K], p = 7600 [Torr]:
T = 1428.57 [K], p = 7600 [Torr]:
  :
T = 303.03 [K], p = 7600 [Torr]:
  3. When the console output is needed for later investigation – it will be surely needed when you run the programs in batch – it can be redirected to a file like:
    carate rc2h2ph_s_ca > rc2h2ph_s_ca_carate.log
  4. A file, rc2h2ph_s_ca_carate_out.csv is created in the current directory.   It contains the essential results of calculations.   Part of the rc2h2ph_s_ca_carate_out.csv is shown below.
  5. Usually, the results needed are the branching fractions, f1 (branching fraction to channel-1), f2(back) (channel-2), and fstab (stablization).   Due to the input regulation of rrkmth, the channels are always numbered consecutively from that with the lowest threshold energy, E0, to higher ones.   So, the channel-1 in this case is the dissociation to phenylacetylene + H and channel-2 is the dissociation to phenyl + acetylene, that is, back dissociation to the reactants (thus it is indicated as f2(back)).   It should be noted that the rate coefficients in this output, k1, k2(back), kstab, and ktot are unimolecular rate constants for the intermediate in steady-state internal energy distribution, and they are NOT the bimolecular rate coefficients for phenyl + C2H2.
  6. The bimolecular rate coefficients can be calculated by multiplying the high-pressure limiting rate coefficients for the addition reaction, kadd∞, to the branching fractions, f1 and fstab.   The high-pressure limiting rate coefficients must be calculated separately.   For example, they can be calculated by tstrate program in gpop.   Example files for tstrate and results (r_add.csv) can be found in sample/gpop directory.   An example of the calculation of the bimolecular rate coefficients is shown below.
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