KAHIBARO
43.5. Physics Problems
Table of Contents
Missing interactions
When a simulation runs without the expected physical interactions, the problem is usually in the physics configuration, the production cuts, or the energy and geometry setup. For debugging, always start by asking what interactions you expect to see in a given material, at the given energy, over the given distance.
Begin with the physics list configuration. In GATE, you select physics lists and optional modules, which determine which interaction processes are available to each particle. If you simulate low energy photons in water but no interactions occur, verify that an electromagnetic physics list suitable for medical energies is enabled. For example, lists based on Geant4 low energy electromagnetic models are often used in medical imaging and dosimetry. If you omit hadronic physics, then protons or neutrons will not undergo the nuclear reactions you may expect. Likewise, if optical physics is not enabled, scintillation, Cerenkov production, and optical transport will simply not exist in the simulation even though particles deposit energy.
Next, examine production cuts. Even with the correct physics list, Geant4 and therefore GATE create secondary particles only if they exceed user-defined range cuts. These cuts are specified in length units but internally converted to energy thresholds that depend on material and particle type. If the electron or photon range cuts are set too large, low energy secondaries will never be produced or tracked. In a thin detector or small phantom this can make it look like there are no interactions at all. Use small, medically reasonable cuts in sensitive regions, such as detector crystals and dose scoring volumes, and coarser cuts in less important regions to save time. Region-based cuts allow you to refine this. If a particular detector shows no Compton electrons, for instance, check whether that volume is part of a region with overly coarse cuts.
Geometry and materials can also hide interactions. If the material of a volume is accidentally set to vacuum or air instead of water, bone, or a scintillator, photons may cross it with very few or no interactions. Similarly, if your source and detector are placed incorrectly, particles may never reach the region where you expect interactions. Use geometry visualization to confirm that volumes are where you think they are, and that the material names are correct and present in the material database. A common mistake is a typo in a material name, which silently falls back to a default or fails creation, depending on the configuration.
Source configuration must be checked as well. If your photons have extremely high energies, they may traverse thin detectors with little chance of interacting, particularly in low Z materials. Conversely, if the energy is so low that photons are absorbed before they ever reach a detector, it can appear that nothing happens. Verify the particle type, energy, direction, and position, and check with a simple actor that particles actually pass through the target volume. If your simulation uses radioactive sources, confirm that the decay physics is enabled, that the radionuclide is correctly specified, and that the time window is sufficient to generate decays.
Always verify that an appropriate physics list is enabled, that production cuts are small enough in sensitive regions, that materials are correct, and that the source actually sends particles into the volume of interest. Missing interactions almost always trace back to one of these points.
Actors are useful for diagnosing missing interactions. An energy deposition actor attached to a suspect volume can show whether any energy is deposited there. A phase space or fluence actor upstream and downstream of a volume can reveal whether particles enter and leave without interaction. For more detailed debugging, enable step or track verbose output for a few events and examine whether the processes you expect, such as Compton scattering or ionization, ever appear in the printed step information.
Unexpected particle transport
Unexpected particle transport problems manifest as particles traveling too far, stopping too early, changing direction oddly, or generating unanticipated secondaries. These issues usually originate from inappropriate physics options, transport parameters, material definitions, or geometry overlaps.
Begin by revisiting the chosen physics models. Some physics lists include approximations tuned for speed rather than detailed transport at the energies of interest. For example, if electrons appear to lose energy too slowly in soft tissue, the electromagnetic model selection may not match your energy range. For hadronic particles, certain inelastic or elastic models become active only in specific energy intervals, so ensure that the proton or neutron energies you simulate are covered by processes in the selected list. If secondary production seems excessive or too sparse, check optional modules that control processes like fluorescence, Auger electrons, or ionization models.
Transport parameters and production cuts directly influence how far particles travel. Large range cuts suppress creation of soft secondaries, which can make tracks appear smoother and longer, since many small-angle scatters are not represented by individual secondary tracks. Step limitations and multiple scattering parameters also play a role. If particles appear to jump large distances, it might be due to a large maximum step length in certain regions, which can hide fine details in trajectories. Conversely, if particles stop too early, the cuts or thresholds may prematurely remove them when their remaining range is less than the cut value. For precise studies of stopping behavior, in particular for charged particles, pay close attention to these parameters in the relevant regions.
Materials must be physically realistic. If the density of a material is wrong by a factor of ten, particles will either slow down and stop too quickly or travel much too far. Incorrect elemental composition will also change scattering angles and reaction probabilities. For instance, a scintillator crystal with its composition mistakenly swapped for water will exhibit very different attenuation and energy loss behavior. Always confirm densities and compositions against reliable references or the Geant4 material database entries when available.
Geometry overlaps are another frequent cause of strange transport. If two volumes overlap, Geant4 may repeatedly move a particle across boundaries, causing unusual stepping patterns, or it may consider a particle to be inside the wrong material during part of its trajectory. This can look like particles reflecting from invisible walls or skipping regions entirely. Use GATE or Geant4 overlap checking tools to detect and resolve overlaps, especially in complex detector assemblies and voxelized geometries.
Unrealistic ranges, stopping behavior, or trajectories usually arise from mismatched physics lists, inappropriate cuts or step limits, incorrect material densities or compositions, or geometry overlaps. Always verify these aspects before suspecting deeper problems.
To diagnose transport anomalies, track-level debugging is very effective. Enable verbose stepping for a small number of events and inspect where particles start, which volumes they traverse, what materials they see, and which physical processes act at each step. Check that energy decreases smoothly where expected, that scattering angles look reasonable, and that secondaries appear in appropriate locations. Complement this with visualization of particle tracks in a simplified geometry to see trajectories directly.
Finally, remember that Monte Carlo transport includes statistical fluctuations. Individual tracks can show rare but physically allowed behavior. Focus on systematic patterns across many events when deciding that transport is truly unexpected, and use statistical summaries of range, energy deposition depth, and scattering angles to compare simulation behavior with analytical expectations or experimental benchmarks.
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