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 '#'.

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
tempGauChebGrd T_min T_max nT
tempList T1 T2 T3 ...
T0 T0

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 key starting with 'tempGauChebGrd' sets the list of temperatures at the Gauss-Chebyshev grid which is suitable for Chebyshev-polynomial fit of RRKM rate coefficients.   The range of temperature is specified by T_min and T_min, and nT is the number of grid points.   For the detailed description of the Chebyshev polynomials and Gauss-Chebyshev grid, see Chebyshev-polynomial fit section.   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.

The key 'T0' sets initial temperature for distim solver, and only valid in the distim input.  Default is 298.15 K.

T0 300

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
pressGauChebGrd p_min p_max np
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 different 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 starting with 'pressGauChebGrd' sets the list of pressures at the Gauss-Chebyshev grid which is suitable for Chebyshev-polynomial fit of RRKM rate coefficients.   The range of pressure is specified by p_min and p_min, and np is the number of grid points.   For the detailed description of the Chebyshev polynomials and Gauss-Chebyshev grid, see Chebyshev-polynomial fit section.   The last 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.

revPressOrd

This key is only valid in dislit program.   This key inverts the pressure order of calculation, that is, lower pressure to higher.   This is sometimes useful to get converge the desired solution.

Following four types of time specifications are allowed for catime and distim in order specify the output times.   The unit of time is second and the default time base is 1 (s).   Any number of time specifications are allowed outside the well-blocks.

timeBase t_base
timeRange t_start t_end t_step
timeLog10Range log10t_start log10t_end log10t_step
timeList t1 t2 t3 ...

The key 'timeBase' sets the time base used in the subsequent inputs.   for example,

timeBase 1e-6
timeList 1 2 5
timeBase 1e-3
timeRange 3 9 3

sets the output times to 1, 2, and 5 µs and 3, 6, and 9 ms.   The usages of 'timeRange', 'timeLog10Range', and 'timeList' are similar to corresponding pressure specifications.

DEFAULT: equivalent to 'timeLog10Range -6 -1 1'.

err3 err
alphaTdep alpha1000 beta
kEthInt kEmin_internal
kEthOut kEmin_outgoing
topCut ntop
maxCyc cyc
sizeLSDSRW size_fact

The parameter 'err3' is the truncation threshold of the collisional energy transfer probability to make the mastre-equation matrix banded.   The default 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 key 'alphaTdep' can be used specify a temperature-dependent equation for the collisional energy transfer parameter α (alpha).   The α is calculated by the equation, α = α₁₀₀₀ (T / 1000)^β, with α₁₀₀₀ specified by alpha1000 and β specified by beta.   This key overwrites NALPHA and ALPHAV specified in the MASTER input file(s) for all the wells.   The beta in this key can be any floating-point number, while it must be an integer or a half-integer in MASTER input.

  The parameter 'kEthInt' and 'kEthOut' are used to remove out very small microscopic rate constants, k(E), which sometimes make the solver unstable.   Internal k(E)'s, that is, those for isomerization between wells, smaller than kEmin_internal are set to 0 (zero).   Similarly, external k(E)'s, that is, those for dissociation or isomerization to species not included as wells, smaller than kEmin_outgoing are removed.   The default is 1×10⁻⁶⁴ for both kEmin_internal and kEmin_outgoing.

  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.

  The key 'sizeLSDSRW' specifies the factor to the size of working array for DLSODES routine used in catime and distim programs.   The default is 0.3.   Usually there is no need to adjust this parameter unless the DLSODES error on the RWORK size is encountered.

condition cond

The key 'condition' is used to specify the condition for the time-dependent solution calculated by catime (only).   The value 'const' (default) invokes the calculation for the constant flux condition; k_in = const. and n(t = 0) = 0, for the master equation, The value 'init' invokes the calculation for the initial value problem; k_in = 0 and n(t = 0) = r.

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.   When this option is used for carate, the incoming-flux vector is also written in basename_carate_rfxvec.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.   When the 'HPL' option is specified together with the 'vector' option for diseig or dislit, the Boltzmann distribution vector is written in basename_progname_hplvec.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.

recombChan ichan
reactant
excitGrain excitation_grain
excitArbit activation_flux_filename

The key 'recombChan' specifies the recombination channel number where the reactive flux for chemically activated reaction comes in for the program carate.   Other 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.

New feature in version 2018.06.14   The key 'excitGrain' specifies that the activation flux comes from a single grain specified by its number for carate and catime.   This correspond to monochromatic photo-excitation followed by internal conversion which produces highly vibirationally excited ground state molecule.   By the use of 'excitArbit' key, one may specify an arbitrary initial distribution of a molecule.   See activation.csv in sample folder for the format of the input file.   It should be a simple vector of distribution starting from the ground state of the specified well.

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 appearance in the control input, starting from 1.   However, it is not recommended to use this default indices in specifying 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.   In order to avoid the asymmetry error issued by the SSUMES programs, it is highly recommended to prepare the RRKM input files with 'alignBaseEnergy' keyword by prepum program in GPOP.

  The 'truncate' key can be used to define the lower-energy truncation of each well for carate and dislit solvers 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.   The default is zero (truncate 0) for all the wells, that is, no stabilization process is included.