Copyright © 1998–2020 by A. Miyoshi
SSUMES - Quick Start step-1
SSUMES - Quick Start step-1
Preparation
![](img/c2h2ph_1.gif)
Fig. Q1
- 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.
- Set PATH to the directories where SSUMES and UNIMOL executables
reside.
(Or place the executables in the current directory by copying
/ moving them.)
- 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.
- Run rrkmth with
rc2h2ph_s_rrkm.inp
by
typing:
rrkmth < rc2h2ph_s_rrkm.inp > rc2h2ph_s_rrkm.out
- 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.
- 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.)
- 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
- Run carate as:
carate rc2h2ph_s_ca
- 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]:
- 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
- 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.
- 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.
- 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.