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RunKMC Input File Specification

The RunKMC input file is a plain text file (.txt) consisting of four required sections, each terminated with an end keyword.

  1. Parameters
  2. Species
  3. Rate Constants
  4. Reactions

1. Parameters Section

Defines the simulation parameters for the Kinetic Monte Carlo simulation.

Example:

parameters
    num_units = 1e10
    termination_time = 50,000
    analysis_time = 500.0
end

Required parameters:

  • num_units: integer
    • Total number of particles/molecules
  • termination_time: float
    • When to stop the simulation
  • analysis_time: float
    • How frequently to output/analyze data

Note: the units for termination_time and analysis_time are arbitrary but should be consistent.

2. Species Section

Defines all chemical species in the system with

Example:

species
    # Syntax
    # {type} {name} [C0]={concentration} [FW]={molecular_weight} {optional_params}
    
    I   AIBN    [C0]=0.01   FW=164.2   f=0.50
    U   R       [C0]=0.0    FW=82.1
    M   A       [C0]=2.1    FW=104.2
    M   B       [C0]=0.9    FW=100.1
    P   PA
    P   PB
    P   PA|PB
end

Species Types

  • I = Initiator species
  • M = Monomer species
  • U = Generic unit species
  • P = Polymer species

Species Options:

  • [C0] = Initial concentration (mol/L). If not set, defaults to zero.
  • [FW] = Formula weight (g/mol). Mostly used for monomers (M) for molecular weight calculations.
  • f = Initiator efficiency (0, 1]. Required for all initiators (I).

Parameter Groups:

Another way to define a polymer species is by defining it as a

P PA
P PB
P P PA|PB

What's the difference between defining PA and P[A]?

  • P[X] = Polymer ending with X (~~X)
  • P[X.Y] = Polymer ending with XY (~~XY)
  • P[X.Y.Z] = Polymer ending with XYZ (~~XYZ)

This notation is used for specifying sequence, which is necessary for considering depropagation reactions. Currently, it is not strictly necessary for systems without depropagation.

Wildcard notation

  • P[-.A] P[R.A]|P[A.A]|P[B.A]

This statement says that P[R.A], P[A.A], P[B.A] are all considered P[-.A]. So if a reaction involves P[-.A], any one of the above species can be used.

Examples:

I   AIBN    [C0]=0.01   FW=X    f=0.5
M   A       [C0]=8.7    FW=X
M   B       [C0]=1.3    FW=X
U   R       
P   PA
P   PB
P   D

3. Rate Constants Section

Defines all kinetic parameters:

rateconstants
    kd      = {float}   # Initiator decomposition
    kpAA    = {float}   # Propagation PA + A
    ktcAA   = {float}   # Termination (comb.) of PA + PA
    ...
end

4. Reactions Section

Defines the reaction network. Suppored reactions can be found here.

reactions
    ID AIBN -kd-> R + R
    IN R + A -kpAA-> P
    ...
end