### Plasmid 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 2
/tracking/verbose 0
/control/verbose 1
/dnageom/verbose 1

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

# Chemistry: activation
/chem/activate true

# Chemistry: verbosity
/scheduler/verbose 0

# Material: verbosity
/material/verbose 2

# Geometry: size of World volume
/world/worldSize 4.84 um

# Geometry: optimisation of voxelisation
/dnageom/setSmartVoxels 1
/dnageom/checkOverlaps false

# Geometry: creation
# See https://geant4-dna.github.io/molecular-docs/docs/examples/bacterial-cell
#  - Side length for each placement
/dnageom/placementSize 200 200 200 nm
#  - Scaling of XYZ in fractal definition file
/dnageom/fractalScaling 1 1 1 nm
#  - Path to file that defines placement locations
/dnageom/definitionFile geometries/prisms_plasmids_positions_500ngpul.txt
#  - Set placement volumes
/dnageom/placementVolume prism geometries/plasmid_4367.txt

# Geometry: take the angles in the voxel placement file as multiples of pi
/dnageom/setVoxelPlacementAnglesAsMultiplesOfPi false

# Geometry: enable custom molecule sizes
/dnageom/useCustomMoleculeSizes false

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

# Geometry: distance from base pairs at which radicals are killed
/dnageom/radicalKillDistance 9 nm

# Geometry: deposited energy accumulation range limit to start recording SBs from direct effects
/dnageom/interactionDirectRange 5.5 angstrom

# Geometry: activate Histone scavenging function
/dnageom/activateHistoneScavenging true

# Analysis: add box chromosomal region of interest, with the name "plasmid"
/chromosome/add plasmid box 2.21 2.21 2.42 0 0 0 um

# Damage: model settings
/dnadamage/directDamageLower 17.5 eV
/dnadamage/directDamageUpper 17.5 eV

/dnadamage/indirectOHBaseChance 1.0
/dnadamage/indirectOHStrandChance 0.65
/dnadamage/inductionOHChance 0.0

/dnadamage/indirectHBaseChance 1.0
/dnadamage/indirectHStrandChance 0.65
/dnadamage/inductionHChance 0.00

/dnadamage/indirectEaqBaseChance 1.0
/dnadamage/indirectEaqStrandChance 0.65
/dnadamage/inductionEaqChance 0.00

# Analysis: set whether strands ought be saved
/analysisDNA/saveStrands false

# Analysis: gap between DNA fragments in base pair
#  Set to zero to score placement volumes independently
/analysisDNA/fragmentGap 0  # do not join

# Draw cell/chromosome volumes rather than DNA (makes DNA invisible)
/dnageom/drawCellVolumes false

# Run: initialization
/run/initialize

# --> Unit tests
#/dnatests/uniqueid
#/dnatests/basepairs
#/dnatests/chromosome
#/analysisDNA/testClassifier
# --> End unit tests

# Run: progress display
/run/printProgress 100

# Source geometry
/gps/pos/type Plane
/gps/pos/shape Square
/gps/pos/centre 0 0 -2.42 um
/gps/pos/halfx 2.21 um
/gps/pos/halfy 2.21 um

# Source particle, energy and angular distribution
/gps/particle proton
/gps/energy 3 MeV
/gps/direction 0 0 1

# Beam on
/run/beamOn 10