### Single DNA fiber visualization

#
# 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
#

# Verbosity: settings
/control/verbose 1
/run/verbose 2
/material/verbose 2
/dnageom/verbose 1

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

# Chemistry: activation
/chem/activate false

# Chemistry: verbosity
/scheduler/verbose 0

# Chemistry: end time of chemistry stage
/scheduler/endTime 1 us

# Geometry: size of World volume
/world/worldSize 300 nm

# Geometry: size of cell volume
# See https://geant4-dna.github.io/molecular-docs/docs/examples/parameter-study
/cell/radiusSize 100 100 100 nm

# Geometry: optimisation of voxelisation
/dnageom/setSmartVoxels 1

# Geometry: check overlaps in DNA geometry region
/dnageom/checkOverlaps false

# Geometry: creation
# See https://geant4-dna.github.io/molecular-docs/docs/examples/parameter-study
#  - Side length for each placement
/dnageom/placementSize 30 30 100 nm
#  - Scaling of XYZ in fractal definition file
/dnageom/fractalScaling 1 1 1 nm
#  - Path to file that defines placement locations
/dnageom/definitionFile geometries/prisms1.txt
#  - Set a placement volume
/dnageom/placementVolume prism geometries/straight-216-0.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 6 angstrom

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

# 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 0.0

/dnadamage/indirectEaqBaseChance 1.0
/dnadamage/indirectEaqStrandChance 0.65
/dnadamage/inductionEaqChance 0.0

# Analysis: add spherical chromosomal region of interest, with the name "fiber"
/chromosome/add fiber sphere 2000 0 0 0 nm

# 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

# Analysis: save the position of hits histones only on one chain
#/analysisDNA/diagnosticChain

# Run: initialization
/run/initialize

# Visualization: to visualize fiber DNA geometry
# - uncomment the next line and save
/control/execute vis.mac
# - then, run ./moleculardna -t 1 -v 1
# - then, in the Session window of the Qt interface, do /control/execute fiber.mac

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

# Run: progress display
/run/printProgress 100

# Source geometry
#/gps/pos/type Volume
#/gps/pos/shape Sphere
#/gps/pos/radius 500 nm
#/gps/pos/centre 0 0 0 nm

# Source particle, energy and angular distribution
/gps/particle e-
/gps/energy 100 eV
/gps/ang/type iso

# Beam on
/tracking/verbose 0
/run/beamOn 10