Control Options

There are many options, that can be used in an input file to control a simulation. In the list below, the default values are given.

Radiobiology

By default, when an RBE model is activated, FRED writes only the corresponding biological dose map. For instance, if McNamara RBE model for protons is activated (lRBE_McNamara=t), then FRED will save the bio dose in out/RBE/DoseBio_McNamara.mhd. Other maps can be optionally requested for checking and/or post-processing FRED output. These maps are the local alpha and beta parameters, and the RBE computed by the requested model.

lRBE_write_DoseBio = t

write biological dose

lRBE_write_Alpha = f

write alpha parameter

lRBE_write_Beta = f

write beta parameter

lRBE_write_RBE = f

write RBE values

Verbosity

The level of output verbosity can be controlled in many ways, e.g. using a command line option, or an environment variable, or setting it directly in the input file.

The levels are varying from 0 (=minimal) to 5 (=debugging).

The sequence that defines the verbosity level is the following:

  1. the level is set to 3 (mid verbosity)

  2. level is taken from FRED_VERBOSE env variable (if present)

  3. level can then be finely tuned in input file using verbose: directives

  4. cmdline option -V0…-V5 override any previous settings

# quick and dirty
verbose: 0

# equivalent form
verbose: all 0

# incremental on multiple lines
verbose: 0
verbose: delivery 1
verbose: geometry source 3

# oneliner
verbose: 0 delivery 1 geometry source 3

# quick oneliner without changing the input file
export FRED_VERBOSE='0 delivery 1 geometry source 3'

The verbose: directive can be used to set the verbosity level separately for each module. The modules that can be controlled are: physics, delivery, plugin, source, geometry, environment, input, materials, radiobiology.

Example of detailed manipulation of verbosity level:

verbose: all 0
verbose: physics 3
verbose: delivery 2
verbose: plugin 5
verbose: source 1
verbose: geometry 3
verbose: environment 0
verbose: input 4
verbose: materials 2
verbose: radiobiology 5

Other control options

lplotray = bool (default = false)

Activate/deactivate output of detailed track information for each traced particle. It can be used for geometry checking and visual debugging of a simulation using sceneViewerFred.py script.

Important

When lplotray=t, the code automatically switches to serial execution on a single process on the CPU. Hence use it with just a few primaries per pencil beam, since the tracking rate will be very low and FRED will produce large text files containing all steps of the tracks.

proton tracks

Tracks of primary and secondary particles in a water phantom irradiated by 100 MeV proton beam.

allowOverlapping = [region1 region2 ...]

The directive allows to define with regions can overlap and which one is the master region to track the particles in, in case of overlap. For instance, it can be useful to define the gantry regions (range shifters, extendable nozzle, etc.) overlapping with the patient CT (Phantom). In this case, the directive allowOverlapping: gantry phantom will force FRED to track particles inside the gantry region containing all the nozzle elements, even if it intersects with the patient CT, which can happen when the extendable nozzle is used and it is moved close to the patient body.

ijFormatVersion = int (default = 20)

Determines the version of the influence matrix file format. See Influence Matrix File Format for more details.

lAllowHUClamping = bool (default = false)

TODO

lWriteIJPerPrim = bool (default = true)

Normalize the influence matrix results for a given quantity per primary