modern_egfrd/samples/powerspectrum/powerspectrum.gfrd at master · gfrd/modern_egfrd · GitHub

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; eGFRD power-spectrum simulation


[Variables]
V = 1e-15                              ; 1 femto liter
c = 0.4E-6                             ; Concentration in Molar
N = round(concentration(c, V))         ; Number of particles

[Simulator]
        EndTime = 60.0                ; sec.
MaintenanceStep = 1000000
MaintenanceFile = sim_dump.out

[World]
Matrix = 8
Size = (1e-3 * V) ^ (1/3)              ; Liter to cube-length in meter

[SpeciesType]
Name = A
   r = 5e-9                            ; m
   D = 0                               ; fixed

[SpeciesType]
Name = B
   r = 5e-9                            ; m
   D = 1e-12                           ; m^2*s^-1

[SpeciesType]
Name = C
   r = 1e-8                            ; m
   D = 0                               ; fixed

[ReactionRule]
Rule = A + B <=> C
  ka = 9.16639e-19                     ; m^3*s^-1
  kd = 220.8                           ; s^-1

[Particles]
A = 1
B = N
C = 0

[ReactionRecord]
File = power_rec.dat

[Progress]
Width = 60