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.


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


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


lplotray = [F|t]

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 script.


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: gantry phantom