config.txt

{
//global setting
	"Device": 0, // device to be used
	"startStage": 0, // 0 for physics stage, 1 for prechemical stage, 2 for chemical stage, 3 for DNA searching
	"outputDir": "./output/",
	"NPART": 262144,
	"NRAND": 262144,
	"NTHREAD_PER_BLOCK": 256,
	"verbose":3,
	"targetEneDep": 2.5e6, //eV, 
//physics stage
	"GPUBaseMemory":300, // in MB
	"nSecondPer100keV":5000,
	"nRadicalsPer100keV":8000, // increase them if encounter memory issues

	"pCSData":"./tables/physics/totalProtonCS3.dat",
	"eDACSData":"./tables/physics/DACS.txt",
	"eIonCSData":"./tables/physics/ionizationCS.txt",
	"eExcCSData":"./tables/physics/excitationCS.txt",
	"eElaCSData":"./tables/physics/elasticCS.txt",
	"eElaDCSData":"./tables/physics/elasticDCS.txt",

	"eECutoff": 7.5, //eV
	"pECutoff": 100,
	
	"physicsWorldShape":1, // 0 for sphere with radius= physicsWorldSizeX, 1 for box with ROISizeX=the side length along x axis
	"physicsWorldSizeX":0.01, // in cm
	"physicsWorldSizeY":0.01,
	"physicsWorldSizeZ":0.01,
	"physicsWorldCenterX":0, // in cm
	"physicsWorldCenterY":0,
	"physicsWorldCenterZ":0,
 //define ROI
 	"ROIShape":1, // 0 for sphere with radius=ROISizeX, 1 for box with ROISizeX=the side length along x axis
	"ROISizeX":5.5,// in um
	"ROISizeY":5.5,
	"ROISizeZ":5.5,
	"ROICenterX":0, // in um
	"ROICenterY":0,
	"ROICenterZ":0,


	"nPar": 1, // particle number per run
  "maxRun": 1, // maximal runs. Maximal particle simulated=nPar*nRun
	"sourceModel": 1, // 0 for PSF file, 1 for random in sphere. 
	"sourceEnergyModel": 0, // only works if sourceModel!=0. 0 for not using histogram files and uniform inside emin and emax
	// 1 for using histogram files
	"sourceFile":"./input/source.txt", // PSF filename if sourceModel=0, histogram file name if (sourceModel!=0 && sourceEnergyModel==1)
	// The following five parameters only work when sourceModel!=0, i.e., not using PSF files.
	"sourceSampleDim": 0.0001, // unit cm, radius for sourceModel=1, 
	// for other distributions, please reload physicsList::iniParticle()
	"sourcePType": 1,
	"sourceA": 1, // 1 for proton and 0.0054 for electron 
	"sourceEmin":20e7, //eV
	"sourceEmax":20e7,
	
	"fileForIntOutput":"./output/phyint.dat",
	"fileForFloatOutput":"./output/phyfloat.dat",
	"fileForTotalEvent":"./output/totalphy.dat",
	"fileForEnergy":"./output/phyEne.txt",

//physicochemcial stage
	"fileForBranchInfo": "./tables/prechem/branchInfo_prechem_org.txt",
	"fileForRecombineInfo": "./tables/prechem/thermRecombInfo_prechem.txt",
	"fileForIntInput": "./output/phyint.dat",
	"fileForFloatInput": "./output/phyfloat.dat", //default by physics stage
	"fileForOutput":"./output/prechemRes.dat",

//chemical stage	
	"fileForSpecInfo":"./tables/chem/RadiolyticSpecies.txt",
	"fileForReactionInfo":"./tables/chem/Type1_ReactionInfo.txt",
	"useConstantRadius":0, // reaction radius changes with time step? 1 for no 0 for yes
	"fileForRadicalInfo":"./output/prechemRes.dat", // if followingprechemical stage, the name should be the same as "fileForOutput" for prechemical stage
	"chemicalTime":2500, //2500, //unit ps, t_c in the paper
	"DNAReactTime":100, //unit ps, t_i in the paper

	"timeFileForNvsTime":"./output/Time.dat",
	"numberFileForNvsTime":"./output/nRadical.dat",
	"saveInterval":5, //ps
	"chemROI": 5500, //nm

	"fileForChemOutput":"./output/chemRes.dat",
//DNA related
	"bentChromatin":"./tables/dna/BentChromatinFiberUnitTable.txt", // files for reading DNA structure
	"bentHistone":"./tables/dna/BentHistonesTable.txt",
	"straightChromatin":"./tables/dna/StraightChromatinFiberUnitTable.txt",
	"straightHistone":"./tables/dna/StraightHistonesTable.txt",
	"wholeDNA":"./tables/dna/WholeNucleoChromosomesTable.bin",

	"fileForChemPos":"./output/chemRes.dat",
	"fileForOutputDamage":"./output/finalstat.txt",
	"compareEnergy":8711450, // in eV
	"repTimes":1,

	"probChem":0.1
}