DoiDriverOptions.nml

! This input file implements the A+B<->C reversible association model

&DoiDriverOptions
   basename = "ABC" ! Base filename for output files
   ! Total number of time steps:
   nSteps = 10
   ! Number of steps between two consecutive sets of data in HydroGridAnalysis.
   nSampleStep = 1 ! Set to 0 if no data are to be saved.
   ! Number of steps between two consecutive sets of data printed to file and screen.
   nOutputStep = 1 !  Set to 0 if no data are to be printed.
   ! Number of equilibration steps to be skipped without saving data to files.
   nEquilibrationStep = 1
   ! Number of steps between two consecutive writings of HydroGrid statistics. 
   nStatsStep = 1 ! Set to 0 if only written at the end.
   seed = 0 ! Set to zero for unpredictable seed based on clock
/


&DoiBoxOptions
   problem_type = 2 ! Select initialization: 0=uniform, 1=half A's, half B's (interface), 2=stripe

   !-------------------------------
   ! Physical parameters:
   ! Enter reactionRate(nReactions)
   reactionRate = 1
   ! Enter stochiometric coefficients reactionNetwork(nSpecies,2,nReactions)
   reactionNetwork = 2, 0
   reactionScheme = 1 ! 0 for RDME, 1 for IRDME
   ! Enter speciesDiffusivity(nSpecies)
   speciesDiffusivity = 1
   ! Enter speciesDiameter(nSpecies)
   speciesDiameter = 0.3
   ! Enter initial number densities numberDensity(nSpecies)
   numberDensity = 10
   
   !-------------------------------
   ! Domain parameters:
   ! Domain size is (nBlockingSample * nHydroCells * sampleCellLength)
   ! It is divided into (nBlockingCollision * nHydroCells) DOI cells used to process reactions
   ! This means that the grid spacing used to process collisions is:
   ! dx = nBlockingSample * sampleCellLength / nBlockingCollision
   sampleCellLength(1:3) = 1.0 1.0 1.0 ! size: nMaxDimensions=3
   nHydroCells(1:3) = 3 3 3 ! size: nMaxDimensions=3
   nBlockingCollision = 1 1 1 ! Number of DOI cells per block of sampling cells
   nBlockingSample = 1 1 1 ! Smallest possible division (block) of sampling grid
   
   !-------------------------------   
   ! Time stepping:
   inputTimestep = 1.0 ! Time step size dt
   strangSplitting = .true. ! Use Strang (T) or Lie (F) splitting
   
   ! Initial conditions:
   !-------------------------------      
   addDensityFluctuations = F ! For initial fillings of cells. If set to true=T the initial state will have fluctuations
   usePoisson = T ! Initialize with Poisson (T) or Gaussian (F) fluctuations if addDensityFluctuations=T

   ! Other parameters:
   !-------------------------------      
   fractionExtraParticles = 1 ! The code will allocate space for (1+fractionExtraParticles) times the initial number of particles
   nMaxParticlesPerCell = 0 ! Set to zero to estimate numerically: Used to accelerate the building of some data structures
   randomShift = .true. ! Should we randomly shift the reaction grid in S-BD-RME (T) or keep it fixed (F)
   diffuseByHopping = 0 ! How do particles diffuse: 0=continuous walk, 1=discrete walk, 2=remain on lattice
/

   namelist / DoiBoxOptions / reactionRate, reactionNetwork, reactionScheme, numberDensity, &
      speciesDiffusivity, speciesDiameter, sampleCellLength, nSampleCells, &
      nBlockingSample, nBlockingCollision, fractionExtraParticles, &
      usePoisson, wallBCs, addDensityFluctuations, reservoirThickness, &
      inputTimestep, strangSplitting, randomShift, &
      nMaxParticlesPerCell, randomShift, diffuseByHopping, problem_type



! This is used by HydroGrid library, see its documentation
&HydroAnalysisOptions
   storeConserved=F
   
   writeSnapshotVTK=T ! Save snapshots of the instantaneous fields

   ! Means file: column 1=y, 2=rho, 3=v_x, 4=v_y, 5=T, 6=c
   writeMeansVTK = F ! Write the means to a VTK file

   ! Variances
   writeVariancesVTK = F ! Should we save a VTK file
   nVariances = 0 ! How many co-variances to calculate and save
   !correlationCell = 5 5 1 ! The index of the special cell, if calculating correlations in real space
      ! If so, then use a negative integer for the first variable in variancePairs
      ! By default correlationCell is the cell in the center of the domain
   variancePairs = ""
      ! species1 variable1 species2 variable2
   
   ! Static structure factors
   writeSpectrumVTK = T
   writeAbsValue = T ! Only write absolute values of complex values to VTK file?
   nStructureFactors = 0
   structureFactorPairs = "0"
      ! species1 variable1 species2 variable2
   
   ! Dynamic structure factors:
   nWavenumbers=0
   ! Shape (2,nWavenumbers) if 2D (Nz=1), or (3,nWavenumbers):
   selectedWavenumbers=""
   nSavedSnapshots=100
   
   outputFolder = "./"
   filePrefix = "RDME" ! Prefix for all file names
   axisToPrint = 2 ! 1=x, 2=y, 3=z axis
   periodic = T ! Is the system periodic along the y axes

/