Warning, /geant4/examples/advanced/dna/moleculardna/phage.mac is written in an unsupported language. File is not indexed.
0001 ### Phage 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 /tracking/verbose 0
0019 /control/verbose 1
0020 #/dnageom/verbose 3
0021
0022 # Chemistry: selection of IRT_syn
0023 /process/chem/TimeStepModel IRT_syn
0024
0025 # Chemistry: activation
0026 /chem/activate true
0027
0028 # Chemistry: verbosity
0029 /scheduler/verbose 0
0030
0031 # Chemistry: end time of chemistry stage
0032 /scheduler/endTime 5 ns
0033
0034 # Geometry: size of World volume
0035 /world/worldSize 9 um
0036
0037 # Geometry: size of cell volume
0038 # See https://geant4-dna.github.io/molecular-docs/docs/examples/parameter-study
0039 /cell/radiusSize 4 4 4 um
0040
0041 # Geometry: optimisation of voxelisation
0042 #/dnageom/setSmartVoxels 100
0043
0044 # Geometry: creation
0045 # See https://geant4-dna.github.io/molecular-docs/docs/examples/parameter-study
0046 # - Side length for each placement
0047 /dnageom/placementSize 50 50 50 nm
0048 # - Scaling of XYZ in fractal definition file
0049 /dnageom/fractalScaling 50 50 50 nm
0050 # - Path to file that defines placement locations
0051 /dnageom/definitionFile geometries/phage.txt
0052 # - Set placement volumes
0053 /dnageom/placementVolume turn geometries/1strand_50nm_turn.txt
0054 /dnageom/placementVolume turntwist geometries/1strand_50nm_turn.txt true
0055 /dnageom/placementVolume straight geometries/1strand_50nm_straight.txt
0056
0057 # Geometry: draw cell/chromosome volumes rather than DNA
0058 #/dnageom/drawCellVolumes false
0059
0060 # Geometry: deposited energy accumulation range limit to start recording SBs from direct effects
0061 /dnageom/interactionDirectRange 4.0 angstrom
0062
0063 # Geometry: distance from base pairs at which radicals are killed
0064 /dnageom/radicalKillDistance 4 nm
0065
0066 # Damage: model settings
0067 /dnadamage/directDamageLower 5 eV
0068 /dnadamage/directDamageUpper 37.5 eV
0069
0070 /dnadamage/indirectOHBaseChance 1.0
0071 /dnadamage/indirectOHStrandChance 0.405
0072 /dnadamage/inductionOHChance 0.00
0073
0074 /dnadamage/indirectHBaseChance 1.0
0075 /dnadamage/indirectHStrandChance 0.0
0076 /dnadamage/inductionHChance 0.00
0077
0078 /dnadamage/indirectEaqBaseChance 1.0
0079 /dnadamage/indirectEaqStrandChance 0.0
0080 /dnadamage/inductionEaqChance 0.00
0081
0082 # Analysis: add cylindrical chromosomal region of interest, with the name "phage"
0083 /chromosome/add phage cyl 3500 7000 0 0 0 nm 0 0 0
0084
0085 # Run: initialization
0086 /run/initialize
0087
0088 # Run: progress display
0089 /run/printProgress 10
0090
0091 # Source geometry
0092 /gps/pos/type Plane
0093 /gps/pos/shape Circle
0094 /gps/pos/centre 0 7000 0 nm
0095 /gps/pos/rot1 0 0 1
0096 /gps/pos/rot2 1 0 0
0097 /gps/pos/radius 3500 nm
0098
0099 # Source particle, energy and angular distribution
0100 /gps/particle proton
0101 /gps/energy 2.5 MeV
0102 /gps/direction 0 -1 0
0103
0104 # Beam on
0105 /run/beamOn 10000
