Warning, /geant4/examples/advanced/dna/moleculardna/human_cell.mac is written in an unsupported language. File is not indexed.
0001 ### Human cell default geometry
0002
0003 #
0004 # See more details on moleculardna specific UI commands:
0005 # - https://geant4-dna.github.io/molecular-docs/docs/overview/configuration
0006 # - https://geant4-dna.github.io/molecular-docs/docs/overview/macro-anatomy
0007 # - the README file
0008 # - the messenger classes of the moleculardna example
0009 #
0010
0011 # Physics: choice of thermalization model
0012 /process/dna/e-SolvationSubType Meesungnoen2002
0013 #/process/dna/e-SolvationSubType Ritchie1994
0014 #/process/dna/e-SolvationSubType Terrisol1990
0015
0016 # Verbosity: settings
0017 /run/verbose 1
0018 /control/verbose 1
0019
0020 # Chemistry: selection of IRT_syn
0021 /process/chem/TimeStepModel IRT_syn
0022
0023 # Chemistry: end time of chemistry stage
0024 /scheduler/endTime 5.0 ns
0025
0026 # Chemistry: set maximum allowed zero time steps
0027 /scheduler/maxNullTimeSteps 10000000
0028
0029 # Geometry: size of World volume
0030 /world/worldSize 50 um
0031
0032 # Geometry: shape of the cell
0033 /cell/radiusSize 14 2.5 14 um
0034
0035 # Geometry: creation
0036 # See https://geant4-dna.github.io/molecular-docs/docs/examples/bacterial-cell
0037 # - Side length for each placement
0038 /dnageom/placementSize 75 75 75 nm
0039 # - Scaling of XYZ in fractal definition file
0040 /dnageom/fractalScaling 75 75 75 nm
0041 # - Path to file that defines placement locations
0042 /dnageom/definitionFile geometries/cube-centred-X-8.txt
0043 # - Set placement volumes
0044 /dnageom/placementVolume turn geometries/turned_solenoid_750_withHistone.txt
0045 /dnageom/placementVolume turntwist geometries/turned_twisted_solenoid_750_withHistone.txt true
0046 /dnageom/placementVolume straight geometries/straight_solenoid_750_withHistone.txt
0047
0048 # Geometry: distance from base pairs at which radicals are killed
0049 /dnageom/radicalKillDistance 9 nm
0050
0051 # Geometry: deposited energy accumulation range limit to start recording SBs from direct effects
0052 /dnageom/interactionDirectRange 2.0 angstrom
0053
0054 # Damage: model settings
0055 /dnadamage/directDamageLower 5 eV
0056 /dnadamage/directDamageUpper 37.5 eV
0057
0058 /dnadamage/indirectOHBaseChance 1.0
0059 /dnadamage/indirectOHStrandChance 0.405
0060 /dnadamage/inductionOHChance 0.0
0061
0062 /dnadamage/indirectHBaseChance 1.0
0063 /dnadamage/indirectHStrandChance 0.0
0064 /dnadamage/inductionHChance 0.0
0065
0066 /dnadamage/indirectEaqBaseChance 1.0
0067 /dnadamage/indirectEaqStrandChance 0.0
0068 /dnadamage/inductionEaqChance 0.0
0069
0070 # Analysis: add ellipsoid chromosomal region of interest, with the name "cell"
0071 /chromosome/add cell ellipse 7100 2500 7100 0 0 0 nm 0 0 0
0072
0073 # Run: initialization
0074 /run/initialize
0075
0076 # Run: print progress
0077 /run/printProgress 10
0078
0079 # Source geometry
0080 /gps/pos/type Plane
0081 /gps/pos/shape Circle
0082 /gps/pos/centre 0 3000 0 nm
0083 /gps/pos/rot1 0 0 1
0084 /gps/pos/rot2 1 0 0
0085 /gps/pos/radius 7100 nm
0086 /gps/direction 0 -1 0
0087
0088 # Source particle
0089 /gps/particle e-
0090
0091 # Analysis: set ROOT output file name
0092 #/analysisDNA/fileName 50MeV
0093
0094 # Source energy
0095 /gps/energy 0.662 MeV
0096
0097 # Beam on
0098 /run/beamOn 2
