Gabriele Cosmo
106 lines
2.9 KiB
Plaintext
106 lines
2.9 KiB
Plaintext
### Phage default geometry
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#
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# See more details on moleculardna specific UI commands:
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# - https://geant4-dna.github.io/molecular-docs/docs/overview/configuration
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# - https://geant4-dna.github.io/molecular-docs/docs/overview/macro-anatomy
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# - the README file
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# - the messenger classes of the moleculardna example
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#
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# Physics: choice of thermalization model
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/process/dna/e-SolvationSubType Meesungnoen2002
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#/process/dna/e-SolvationSubType Ritchie1994
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#/process/dna/e-SolvationSubType Terrisol1990
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# Verbosity: settings
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/run/verbose 1
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/tracking/verbose 0
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/control/verbose 1
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#/dnageom/verbose 3
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# Chemistry: selection of IRT_syn
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/process/chem/TimeStepModel IRT_syn
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# Chemistry: activation
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/chem/activate true
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# Chemistry: verbosity
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/scheduler/verbose 0
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# Chemistry: end time of chemistry stage
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/scheduler/endTime 5 ns
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# Geometry: size of World volume
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/world/worldSize 9 um
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# Geometry: size of cell volume
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# See https://geant4-dna.github.io/molecular-docs/docs/examples/parameter-study
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/cell/radiusSize 4 4 4 um
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# Geometry: optimisation of voxelisation
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#/dnageom/setSmartVoxels 100
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# Geometry: creation
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# See https://geant4-dna.github.io/molecular-docs/docs/examples/parameter-study
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# - Side length for each placement
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/dnageom/placementSize 50 50 50 nm
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# - Scaling of XYZ in fractal definition file
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/dnageom/fractalScaling 50 50 50 nm
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# - Path to file that defines placement locations
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/dnageom/definitionFile geometries/phage.txt
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# - Set placement volumes
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/dnageom/placementVolume turn geometries/1strand_50nm_turn.txt
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/dnageom/placementVolume turntwist geometries/1strand_50nm_turn.txt true
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/dnageom/placementVolume straight geometries/1strand_50nm_straight.txt
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# Geometry: draw cell/chromosome volumes rather than DNA
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#/dnageom/drawCellVolumes false
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# Geometry: deposited energy accumulation range limit to start recording SBs from direct effects
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/dnageom/interactionDirectRange 4.0 angstrom
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# Geometry: distance from base pairs at which radicals are killed
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/dnageom/radicalKillDistance 4 nm
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# Damage: model settings
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/dnadamage/directDamageLower 5 eV
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/dnadamage/directDamageUpper 37.5 eV
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/dnadamage/indirectOHBaseChance 1.0
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/dnadamage/indirectOHStrandChance 0.405
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/dnadamage/inductionOHChance 0.00
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/dnadamage/indirectHBaseChance 1.0
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/dnadamage/indirectHStrandChance 0.0
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/dnadamage/inductionHChance 0.00
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/dnadamage/indirectEaqBaseChance 1.0
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/dnadamage/indirectEaqStrandChance 0.0
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/dnadamage/inductionEaqChance 0.00
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# Analysis: add cylindrical chromosomal region of interest, with the name "phage"
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/chromosome/add phage cyl 3500 7000 0 0 0 nm 0 0 0
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# Run: initialization
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/run/initialize
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# Run: progress display
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/run/printProgress 10
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# Source geometry
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/gps/pos/type Plane
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/gps/pos/shape Circle
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/gps/pos/centre 0 7000 0 nm
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/gps/pos/rot1 0 0 1
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/gps/pos/rot2 1 0 0
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/gps/pos/radius 3500 nm
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# Source particle, energy and angular distribution
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/gps/particle proton
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/gps/energy 2.5 MeV
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/gps/direction 0 -1 0
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# Beam on
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/run/beamOn 10000
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