SSUMES - Quick Start step-3

In the following examples, we will treat the multiple-well problem shown in Fig. Q2. The single-well problem in the previous examples (shown in Fig. Q1) was the subset of this problem. Two low-energy isomerization routes of 2-phenylvinyl radical (well-1) are additionally considered in this problem. Thery are:

the direct ring-closure to well-3 followed by the dissociation to benzocyclobutadiene + H,
and H-transfer to well-2 followed by the ring-closure to well-4 and dissociation.

The isomerization reaction between well-3 and well-4 is also included. It should be noted that these are still only the part of the potential energy surface for this complicated reaction system. See: [I. V. Tokmakov and M. C. Lin, J. Am. Chem. Soc., 125, 11397–11408 (2003).] for more details.

Fig. Q2

Example problem-3

The first example for this multiple-well system is the chemical activation problem starting from phenyl radical + C₂H₂ channel. Four MASTER input files containing ρ(E) and k(E) can be found in the sample directory (rc2h2ph_mwX_mas.dat, X = 1, 2, 3, and 4). They were created by rrkmth program except for the one for well-4, in which the last channel do not have a pronounced barrier and k(E) for this channel was calculated according to the microcanonical VTST using the rdmas and frmmas tools.

Control input

The contents of the control input file, rc2h2ph_m_ca.inp, is shown below.

# phenyl-c2h2 quadruple-well model - chemical activation

tempRecipRange 100000 50 331 20
pressUnit atm
pressList 10

well{
  index 1
  filename rc2h2ph_mw1_mas
  offset 27
  recombChan 4
  connect 2 1       ! connect to well-2 via channel-1
  connect 3 2       ! connect to well-3 via channel-2
  truncate 38
}

well{
  index 2
  filename rc2h2ph_mw2_mas
  offset 23
  connect 1 1       ! connect to well-1 via channel-1
  connect 4 2       ! connect to well-4 via channel-2
  truncate 38
}

well{
  index 3
  filename rc2h2ph_mw3_mas
  offset 71
  connect 1 1       ! connect to well-1 via channel-1
  connect 4 2       ! connect to well-4 via channel-2
  truncate 30
}

well{
  index 4
  filename rc2h2ph_mw4_mas
  offset 0
  connect 2 1       ! connect to well-2 via channel-1
  connect 3 2       ! connect to well-2 via channel-2
  truncate 46
}

The first few lines contains a comment, temperatures and pressures for calculation similar to the previous examples. In the well{...} block, new keywords appear to specify the relations between the wells.

The key index is used to number the well,
connect is used to specify how wells are connected via isomerization channels, and
offset is used to tell the program how much (in energy grain unit) the bottom of the well is offset.

Solving master-equation for multiple-well chemical activation problem

Run carate as: (This may take a minute.)
carate rc2h2ph_m_ca > rc2h2ph_m_ca_carate.log
The file, rc2h2ph_m_ca_carate_out.csv, contains the essential results of calculations as shown below.
As in the previous example (example-1), the required output is usually the branching fractions, which can be found in the block of columns indicated by 'out-going-&-stab-fractions' (shown above). The rest of the output consists of the blocks named, 'out-going-&-stab-rates', 'internal-rates', and 'internal-populations' (shown above), which may not be of interest as results, but may be useful for diagnostic and analysis.
Since the entrance (activation) channel is the same as in example-1, the required bimolecular rate coefficients can be also calculated by multiplying the high-pressure limiting rate constants found in r_add.csv in sample/gpop directory. The results should look like:
Again, it should be noted in order to avoid misunderstanding that the rate coefficients found in the block 'out-going-&-stab-rates' are the unimolecular rate coefficients of the molecule with the steady-state internal energy population, and are NOT the bimolecular rate coefficients usually needed. None of the input files contains the information on the reactants, phenyl radical and acetylene, the bimolecular rate coefficients cannot be computed in the carate program.

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