Gabriele Cosmo
102 lines
2.8 KiB
Plaintext
102 lines
2.8 KiB
Plaintext
### Human cell 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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/control/verbose 1
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# Chemistry: selection of IRT_syn
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/process/chem/TimeStepModel IRT_syn
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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 5.0 ns
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# Chemistry: set maximum allowed zero time steps
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/scheduler/maxNullTimeSteps 10000000
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# Geometry: size of World volume
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/world/worldSize 50 um
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# Geometry: shape of the cell
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/cell/radiusSize 14 2.5 14 um
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# Geometry: creation
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# See https://geant4-dna.github.io/molecular-docs/docs/examples/bacterial-cell
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# - Side length for each placement
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/dnageom/placementSize 75 75 75 nm
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# - Scaling of XYZ in fractal definition file
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/dnageom/fractalScaling 75 75 75 nm
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# - Path to file that defines placement locations
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/dnageom/definitionFile geometries/cube-centred-X-8.txt
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# - Set placement volumes
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/dnageom/placementVolume turn geometries/turned_solenoid_750_withHistone.txt
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/dnageom/placementVolume turntwist geometries/turned_twisted_solenoid_750_withHistone.txt true
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/dnageom/placementVolume straight geometries/straight_solenoid_750_withHistone.txt
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# Geometry: distance from base pairs at which radicals are killed
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/dnageom/radicalKillDistance 9 nm
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# Geometry: deposited energy accumulation range limit to start recording SBs from direct effects
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/dnageom/interactionDirectRange 2.0 angstrom
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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 0.0
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/dnadamage/indirectHBaseChance 1.0
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/dnadamage/indirectHStrandChance 0.0
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/dnadamage/inductionHChance 0.0
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/dnadamage/indirectEaqBaseChance 1.0
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/dnadamage/indirectEaqStrandChance 0.0
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/dnadamage/inductionEaqChance 0.0
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# Analysis: add ellipsoid chromosomal region of interest, with the name "cell"
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/chromosome/add cell ellipse 7100 2500 7100 0 0 0 nm 0 0 0
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# Run: initialization
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/run/initialize
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# Run: print progress
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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 3000 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 7100 nm
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/gps/direction 0 -1 0
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# Source particle
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/gps/particle e-
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# Analysis: set ROOT output file name
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#/analysisDNA/fileName 50MeV
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# Source energy
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/gps/energy 0.662 MeV
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# Beam on
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/run/beamOn 2
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