How to read Phase Space Files (PSF) in molecularDNA

This guide explains how to use Phase Space Files (PSF) as a particle source for simulations with molecularDNA.

Supported PSF formats

molecularDNA supports PSF files in the following formats: ROOT, text, CSV

Example files and macros

They are located in the phase_space sub-directory.

  • ROOT and text: examples of PSF (example.root and example.txt, containing 100 particles each) and ROOT conversion macros (txtToRoot.C and rootToTxt.C) are available. The ecoli_PSF.mac macro can be used (derived from the ecoli.mac macro).
  • CSV: can be used by GRAS Two-Stage Analysis. Example file (phase_space.csv, containing 20 electrons of 45 keV) and macro (phase_space_test.mac, derived from the cylders.mac macro) are provided. This approach does not work in MT-mode.

Reading PSF files in simulations

Replace the source with PSF particles 

/psf/pattern PSFName
  • Can be use to replace the simulation source with particles from the specified PSF file (PSFName).
  • If no /run/beamOn nOfEvents is specified, the entire PSF is read automatically.
  • If /run/beamOn nOfEvents is issued:
    • The simulation shoots nOfEvents particles from the PSF.
    • If nOfEvents exceeds the number of particles in the PSF, the simulation reuses the PSF from the beginning.

Set the sampling mode 

/psf/samplingMode Mode
  • Default: Sequential reading of the PSF.
  • Sampling: Randomly samples particles without replacement (no particle is reused unless nOfEvents > total particles).
  • Sampling_wRplc: Randomly samples particles with replacement (particles can be reused).

Specify the ROOT NTuple name 

/psf/NTupleName NTupleName
  • Defines the title of the Root NTuple in the PSF file.
  • Default: "PSF".
  • The particles in this NTuple will serve as the simulation source.

Store the number of primaries 

/psf/nOriginal numberOfPrimaries

If the entry PSF has been generated using a previous simulation, this command can be used to store the number of primaries of the previous simulation in a variable (not used yet).