### Phage default geometry

#
# See more details on moleculardna specific UI commands:
# - https://geant4-dna.github.io/molecular-docs/docs/overview/configuration
# - https://geant4-dna.github.io/molecular-docs/docs/overview/macro-anatomy
# - the README file
# - the messenger classes of the moleculardna example
#

# Physics: choice of thermalization model
/process/dna/e-SolvationSubType Meesungnoen2002
#/process/dna/e-SolvationSubType Ritchie1994
#/process/dna/e-SolvationSubType Terrisol1990

# Verbosity: settings
/run/verbose 1
/tracking/verbose 0
/control/verbose 1
#/dnageom/verbose 3

# Chemistry: selection of IRT_syn
/process/chem/TimeStepModel IRT_syn

# Chemistry: activation
/chem/activate true

# Chemistry: verbosity
/scheduler/verbose 0

# Chemistry: end time of chemistry stage
/scheduler/endTime 5 ns

# Geometry: size of World volume
/world/worldSize 9 um

# Geometry: size of cell volume
# See https://geant4-dna.github.io/molecular-docs/docs/examples/parameter-study
/cell/radiusSize 4 4 4 um

# Geometry: optimisation of voxelisation
#/dnageom/setSmartVoxels 100

# Geometry: creation
# See https://geant4-dna.github.io/molecular-docs/docs/examples/parameter-study
#  - Side length for each placement
/dnageom/placementSize 50 50 50 nm
#  - Scaling of XYZ in fractal definition file
/dnageom/fractalScaling 50 50 50 nm
#  - Path to file that defines placement locations
/dnageom/definitionFile geometries/phage.txt
#  - Set placement volumes
/dnageom/placementVolume turn geometries/1strand_50nm_turn.txt
/dnageom/placementVolume turntwist geometries/1strand_50nm_turn.txt true
/dnageom/placementVolume straight geometries/1strand_50nm_straight.txt

# Geometry: draw cell/chromosome volumes rather than DNA
#/dnageom/drawCellVolumes false

# Geometry: deposited energy accumulation range limit to start recording SBs from direct effects
/dnageom/interactionDirectRange 4.0 angstrom

# Geometry: distance from base pairs at which radicals are killed
/dnageom/radicalKillDistance 4 nm

# Damage: model settings
/dnadamage/directDamageLower 5 eV
/dnadamage/directDamageUpper 37.5 eV

/dnadamage/indirectOHBaseChance 1.0
/dnadamage/indirectOHStrandChance 0.405
/dnadamage/inductionOHChance 0.00

/dnadamage/indirectHBaseChance 1.0
/dnadamage/indirectHStrandChance 0.0
/dnadamage/inductionHChance 0.00

/dnadamage/indirectEaqBaseChance 1.0
/dnadamage/indirectEaqStrandChance 0.0
/dnadamage/inductionEaqChance 0.00

# Analysis: add cylindrical chromosomal region of interest, with the name "phage"
/chromosome/add phage cyl 3500 7000 0 0 0 nm 0 0 0

# Run: initialization
/run/initialize

# Run: progress display
/run/printProgress 10

# Source geometry
/gps/pos/type Plane
/gps/pos/shape Circle
/gps/pos/centre 0 7000 0 nm
/gps/pos/rot1 0 0 1
/gps/pos/rot2 1 0 0
/gps/pos/radius 3500 nm

# Source particle, energy and angular distribution
/gps/particle  proton
/gps/energy 2.5 MeV
/gps/direction 0 -1 0

# Beam on
/run/beamOn 10000