Copyright © 1998–2009 by A. Miyoshi, Univ. Tokyo
SSUMES reference manual - carate/diseig/dislit
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SSUMES reference manual - carate/diseig/dislit

Synopsis

carate basename[.ext]
diseig basename[.ext] [-e]
dislit basename[.ext]

Description

  The SSUMES component programs carate/diseig/dislit read in MASTER input file(s) containing ρ(E) and k(E) and calculate the steady-state solution to the master-equation for chemically activated (carate) and unimolecular dissociation and/or isomerization reactions (diseig & dislit).   A control input file named basename.inp(.ext) is used to specify the informations on the wells, names of the MASTER input files, temperature and pressure, etc.   The results are written to a CSV file named basename_progname_out.csv.
  The programs expect following two types of input files usually in the current directory.
1) A control file: basename.inp(.ext)
2) MASTER file(s)
The format of the MASTER file is described in the reference manual for mas55c3 and original manual for UNIMOL suite.   The structure and allowed keywords in the control file is described in detail in this manual, and different behavior of the SSUMES program from mas55c3 in reading MASTER input file(s) is described here.

Control input – structure

The structure of the control input is shown below.
# comments
key value [value2, ...]
well{                    ! comments
  key value [value2]
}
well{
  :
}
At least, one well-block enclosed by 'well{' and '}' describing the information of a well must present.   The well-block must contain a 'filename' key specifying the MASTER file name for the well.   For the chemically activated reaction solved by carate, One and not more than one well should contain a 'recombChan' key described below.
Comment
Any charactors after and including '!' or '#' to the end of the line are ignored as comments.   There is no difference between the comments starting with '!' and '#'.

Keys valid outside blocks

Temperature specifications
Any number of temperature specifications are allowed outside the well-blocks.   There are three types of epecifications listed below. (unit: K)
tempRange T_start T_end T_step
tempRecipRange numer start end step
tempList T1 T2 T3 ...
The key 'tempRange' sets an equally spaced temperatures list from T_start to T_end, with step T_step.   The next type with a key 'tempRecipRange' sets a list of temperature equally spaced in the reciprocal of temperature, that is, they are equally spaced in the Arrhenius plot.   Like the convention used for the abscissa of the Arrhenius plots, the reciprocal temperature may be specified in the form of: 1000/T, 10000/T, or etc. by setting the numer (numerator) to 1000, 10000, or etc.   For example,
tempRecipRange 10000 5 40 1
sets a list of temperatures corresponding to 10000/T = 5, 6, 7, ..., 40.   The last type starting with 'tempList' sets a list of temperatures simply as they listed after the key.   If multiple temperature specifications as given, the merged list of temperatures is used.   For example,
tempRange 300 600 100
tempList 298
sets list of temperatures as: { 298, 300, 400, 500, 600 }.
DEFAULT: If no temperature specification is given, programs read them from the MASTER file(s) and the merged list of them are used.
Pressure specifications
Following four types of pressure specifications are allowed.   Default unit is Torr.
pressUnit p_unit
pressRange p_start p_end p_step
pressLog10Range log10p_start log10p_end log10p_step
pressList p1 p2 p3 ...
The key 'pressUnit' changes the unit of pressure.   Allowed units are; 'Torr' (dafault), 'atm', 'Pa', 'kPa', 'MPa', and 'bar'.   This key affects the pressure specification after it.   So, the pressures may be specified with differnt unit within a control file.   For example,
pressUnit atm
pressList 1
pressUnit Torr
pressList 0.1 1 10
set the list of pressures as: { 0.1, 1, 10, 760 }. The key 'pressRange' sets an equally spaced pressure list from p_start to p_end, with step p_step.   The next type with a key 'pressLog10Range' sets a list of pressures equally spaced in logarithmic scale.   For example,
pressLog10Range -2 2 1
sets the list as: { 0.01, 0.1, 1, 10, 100 }.   The unit is affected by the last 'pressUnit' key before it.   The key 'tempList' sets a list of pressures simply as they listed after the key.   When multiple specifications as given, the merged list of them is used.
DEFAULT: If no pressure specification is given, programs read them from the MASTER file(s) and the merged list of them are used.
Solver controls
err3 err
topCut ntop
maxCyc cyc
The parameter 'err3' is the truncation threshold of the collisional energy transfer probability to make the mastre-equation matrix banded.   The dafualt is the 1/1000 of the ERR3 in the MASTER file.   If a MASTER file is generated by rrkmth, ERR3 inside it is 1E-6, and, thus, the default is 1×10−9.   So it may be different from well to well, though there is no physical background to do so.   It should be noted that this parameters must be set at reasonably small in order to calculate rate paramters at very high pressure such as 1010 atm, which is unrealistic but often needed to obtain the complete fall-off curves.   However, it should not be too small in order to calculate the steady-state dissociation rate coefficient at low temperatures.
  The parameter 'topCut' specifies the number of grains at top energy to be eliminated from master-equation.   The dafault is 10, which is a reasonable value needed to eliminates the problem of assymetric isomerization k(E) calculated with different number of grains.   The parameter is usually used to reduce the problem size to speed up the calculation.   Note that the default rrkmth generates rather too much number of grains to avoid the problems at high-temperature, but it is not always the best choice.
  The parameter 'maxCyc' specifies the maximum number of iteration in dislit program.   Other program never read or use this.   The dafault is 300.
Output controls
output opt1 [opt2 ...]
verbose lev
The key 'output' is used to specify the optional outputs.   Allowed options are 'vector', 'HPL', and 'HPLonly'.   The 'vector' option specifies the output of steady-state internal population vector, into the file named basename_progname_vec.csv.   The option 'HPL' tells the program to compute high-pressure limiting (HPL) rate constants by numerical integration and they are written in a file named basename_progname_hpl.csv.   The 'HPLolly' option can be used to compute HPL rates only.   The options, 'HPL' and 'HPLonly' are allowed only for diseig and dislit.  
  The key 'verbose' sets the level of the output of diagnostic messages.   The dafault level is 0 and available levels are 0, 1, 2.

Keys valid inside blocks

Solver control
recombChan ichan
reactant
The key 'recombChan' specifies the recombination channel number where the reactive flux for chemically activated reaction comes in for the program carate.   Othre programs never read or use it.   ichan is the channel number in the corresponding MASTER file.   Due to the restriction of the rrkmth program, the channels are numbered consecutively from that of the lowest to threshold energy to higher.   This key must present in one (and only one) of the well in the program carate.
  The key 'reactant' (it takes no value) specifies the reactant well for dislit in order to solve the steady-state problem of a type of eq (5) in introduction to SSUMES.   The program dislit can be invoked without any 'reactant' key to solve the problem of type of eq (4) in introduction to SSUMES.   However, the key can be specified in only one well.
Well properties and attributes
index idx
filename MASTERfile_name
connect idxWell ichan
offset noff
truncate ntrunc
  The key 'index' is an optional key to assign indices to the wells.   The well-indices are used in specifying the connection between wells by 'connect' keyword as well as in the outputs.   The indices should be integer numbers, but not necessarily the consecutive numbers.   If omitted, indices are automatically assigned consecutively in the order of appearacne in the control input, starting from 1.   However, it is not recommended to use this default indices in specifyinf well-connections in many-well problems, since, for example, when you want to remove well-3 from the 10-well system, you will need to renumber many indices in many connection specifications.
  The name of the MASTER input file corresponding to the well should to be specified by 'filename' key for each well.   The extension '.dat' is assumed when no extension is given in the file name.   A file with an extension other than '.dat' may be specified by explicitly specifying the full file name, but, there is no way to specify the file name without extension.
  The key 'connect' is used to specify the connections between wells via isomerization reactions.   The connection specifications may appear as many times as required in a well.   The first argument ideWell is the index of the well to be connected, and the second argument ichan is the channel number via which the connection is made.   The connections must be consistent in the two-well connected.   The SSUMES programs strictly check the microscopic equilibrium between the microscopic rate coefficients of the two wells, and the properties of the transition state connecting between them must be given exactly the same in the RRKM inputs for two wells.
  The 'offset' key is used to tell the programs about the difference of the energy between vibrationless (ground) states of isomeric molecules (wells) in the units of grain size, typically, 100 cm−1.   The value noff must be an integer number.   Since only the differences of noff's among the wells matter, they may be calculated from any origin, but the origin should be common among the wells.   Usually, the energy of the lowest well is taken to be the origin, that is, offset 0.
  The 'truncate' key can be used to define the lower-energy truncation of each well for carate solver in order to include stabilization process.   For example, 'truncate 10' means the lowest ten grains of the well are eliminated from the master-equation.   The population flux going into the lowest ten grains never comes back, and is treated as stabilized.   This key is never read nor used by diseig and dislit.   The default is zero (truncate 0) for all the wells, that is, no stablization process is included.

Parameters imported from MASTER input file(s)

  The SSUMES component programs carate/diseig/dislit read in MASTER input file(s) compatible for mas55c3.   Some of the calculation parameters are imported from the MASTER input file(s) and some of them can be overridden by corresponding keys in the control input.   See the reference manual for mas55c3 for the detailed description of the MASTER input file.   The different behavior of the SSUMES programs from mas55c3 are summarized below.
The parameters indicated by bold Sans-Serif fonts are used by SSUMES programs.   Others are ignored by SSUMES.
1. TITLE
2. INC,NCHAN,INCCHK
  INCCHK: Read as grain size (cm−1) by SSUMES.
3. ERR1,ERR2,ERR3
  ERR3: tolerance for truncation of P(E,E') is set to ERR3/1000.
4. E0
5. NALPHA
  The number of ALPHAV's read in the next sequence is always 1, irrespective of this value.
If input as positive (NALPHA > 0) or zero (NALPHA = 0), constant (templerature independent) α is assumed.
If input as negative (NALPHA < 0), mas55c3 does calculations assuming the temperature dependent α = α0(T / 1000)β, where α0 is read as ALPHAV(1) and β = |NALPHA| / 2.   For this case, only one value of α is read in the next input.
6. ALPHAV
  Value of α or α0 (cm−1).
7. IXV,JXV
  The functional form of P(E,E') is always exponential-down model irrespective of this input in SSUMES.
8. NP
  number of pressures.
9. PR(I),I=1,NP
  array of pressures, in torr.
10. PALMT
11. JAV
12. NTEMP
  number of input temperatures.
13. TEMPV(I),I=1,NTEMP
  array of input temperatures (K).
14. SGMA,WT1,WT2,EPS
  See RRKM input.
15. IOPTHT,IOPTPR
16. NDEGS
  no. of ρ(E) values to be read in.
17. RHO(I),I=1,NDEGS
  array of ρ(E) values.
18. TEMPV(I),CORRAT(I),I=1,NTEMP
22. NRATES
  no. of microscopic rate coefficients k(E) to be input.
- Input no. 25 looped through IN=1,NCHAN
25. Rn(I),I=1,NRATES
  list of k(E) for channel n.

Output

  The results are written to a csv-format file, basename_progname_out.csv.   They are self-instructive.   See Quick-Start for examples and some instructions.