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PHITS simulations of neutron and gamma-ray production from and transport of 70–250 MeV protons in heterogeneous 1D tissue phantoms

Ratliff, Hunter; Blangiardi, Francesco; Kögler, Toni

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  <identifier identifierType="DOI">10.14278/rodare.3997</identifier>
  <creators>
    <creator>
      <creatorName>Ratliff, Hunter</creatorName>
      <givenName>Hunter</givenName>
      <familyName>Ratliff</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-3761-5415</nameIdentifier>
      <affiliation>Department of Computer science, Electrical engineering and Mathematical sciences, Western Norway University of Applied Sciences, Inndalsveien 28, Bergen, 5063, Vestland, Norway</affiliation>
    </creator>
    <creator>
      <creatorName>Blangiardi, Francesco</creatorName>
      <givenName>Francesco</givenName>
      <familyName>Blangiardi</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0009-0006-7725-6751</nameIdentifier>
      <affiliation>Technology Methods and Systems Data Based Methods, Fraunhofer ENAS, Technologie Campus 3, Chemnitz, 09126, Saxony, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Kögler, Toni</creatorName>
      <givenName>Toni</givenName>
      <familyName>Kögler</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-9501-0898</nameIdentifier>
      <affiliation>Helmholtz-Zentrum Dresden - Rossendorf</affiliation>
    </creator>
  </creators>
  <titles>
    <title>PHITS simulations of neutron and gamma-ray production from and transport of 70–250 MeV protons in heterogeneous 1D tissue phantoms</title>
  </titles>
  <publisher>Rodare</publisher>
  <publicationYear>2025</publicationYear>
  <subjects>
    <subject>proton therapy</subject>
    <subject>treatment verification</subject>
    <subject>particle transport calculations</subject>
    <subject>PHITS</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2025-09-24</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://rodare.hzdr.de/record/3997</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsIdenticalTo">https://www.hzdr.de/publications/Publ-43014</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.14278/rodare.3996</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://rodare.hzdr.de/communities/novo</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://rodare.hzdr.de/communities/rodare</relatedIdentifier>
  </relatedIdentifiers>
  <version>1.0.0</version>
  <rightsList>
    <rights rightsURI="info:eu-repo/semantics/restrictedAccess">Restricted Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;strong&gt;Introduction&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;This dataset corresponds to the PHITS simulation data used in &amp;quot;Fast Phase Space Reconstruction for Proton Beam Traversal and Neutron Emission in Proton Therapy using Fourier Neural Operators&amp;quot;.&lt;br&gt;
A concise description of the simulation setup is provided here; please refer to the paper for detailed discussion, discription, analysis, and further results derived from this dataset.&lt;/p&gt;

&lt;p&gt;&lt;br&gt;
&lt;strong&gt;Description of simulations&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;This dataset consists of &lt;a href="https://phits.jaea.go.jp/"&gt;PHITS&lt;/a&gt; simulations for 47 different proton energies from 70 MeV to 250 MeV incident upon different &amp;quot;1D&amp;quot; heterogeneous cylindrical phantoms (varied materials every 0.5 mm in length, uniform radially and rotationally) whose composition (materials and sequence along length) are taken from randomly sampled rays cast through a 3D CT phantom [CITE] with CT number mapped to material composition and density via the&amp;nbsp;&lt;em&gt;HumanVoxelTable-KumamotoUniv.data&lt;/em&gt;&amp;nbsp;conversion table within the RT-PHITS utilitydistributed with PHITS.&amp;nbsp;&lt;br&gt;
Included tallies score spatial distributions of energy deposition, LET, proton current (with an additional angular dimension), neutron production, gamma-ray production, and a variety of diagnostic tallies.&amp;nbsp;&lt;br&gt;
Event-by-event &amp;quot;list-mode&amp;quot; data is scored for neutron and gamma-ray production, called &amp;quot;dump&amp;quot; tallies in PHITS.&lt;/p&gt;

&lt;p&gt;Given the objective of these simulations was for AI model development, the 47 energies are divided into 37 &lt;strong&gt;training&lt;/strong&gt; energies (70 MeV to 250 MeV in 5 MeV steps) and 10 &lt;strong&gt;testing&lt;/strong&gt; energies (73 MeV to 245.8 MeV in 19.2 MeV steps).&amp;nbsp;&lt;br&gt;
For each energy, two simulations were ran: (1) a simulation with &lt;strong&gt;1E8&lt;/strong&gt; protons simulated where all &lt;strong&gt;tallies&lt;/strong&gt; (including &lt;strong&gt;dump&lt;/strong&gt; tallies) were included/enabled and (2) a simulation with &lt;strong&gt;1E9&lt;/strong&gt; protons simulated (available on request) but with only &lt;strong&gt;dump&lt;/strong&gt; tallies enabled (other tallies disabled to reduce memory consumption and increase simulation speed).&amp;nbsp;&lt;br&gt;
Furthermore, all of the above was actually performed twice: (1) initially with purely &lt;strong&gt;monoenergetic&lt;/strong&gt; beam energies and with a spatial spread of 2.5 mm and (2) a second &amp;quot;more realistic&amp;quot; set with &lt;strong&gt;Gaussian-distributed&lt;/strong&gt; energies (with energy-dependent FWHM) and slightly wider 4.0 mm beam spread.&lt;/p&gt;

&lt;p&gt;All simulation outputs were automatically processed from the plaintext and binary files produced by PHITS into compressed pickle file objects (NumPy arrays, Pandas DataFrames, dictionaries) using the &lt;a href="https://github.com/Lindt8/PHITS-Tools"&gt;PHITS Tools&lt;/a&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;Python utility.&amp;nbsp;&lt;br&gt;
These Python objects were then utilized in the subsequent analysis of the paper this simulation set was generated for.&lt;/p&gt;

&lt;p&gt;&lt;br&gt;
&lt;strong&gt;Structure of this repository&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;The volume of data present in this repository is quite substantial (~ 700 GB).&amp;nbsp;&lt;br&gt;
Therefore, the repository has been structured in a way to allow flexibility in only downloading data of interest.&lt;/p&gt;

&lt;p&gt;The root directory of this repository consists of 39 top-level directories whose names indicate their contents.&lt;br&gt;
Within each are two directories:&amp;nbsp;&lt;em&gt;training&lt;/em&gt; and&amp;nbsp;&lt;em&gt;testing&lt;/em&gt;.&lt;br&gt;
Within each of these are directories of the format &lt;em&gt;???_MeV&lt;/em&gt;, where &lt;em&gt;???&lt;/em&gt; is replaced by three digits specifying the nominal beam energy in MeV.&amp;nbsp;&lt;br&gt;
(This is &lt;em&gt;???p?&lt;/em&gt; for the energies of the testing dataset, with &lt;em&gt;p&lt;/em&gt; in place of a decimal point.)&lt;br&gt;
Thus, each &lt;em&gt;training&lt;/em&gt; directory contains 37 subdirectories, and each &lt;em&gt;testing&lt;/em&gt; directory contains 10 subdirectories.&lt;br&gt;
(One should note that there are no setup differences between &lt;em&gt;training&lt;/em&gt; and &lt;em&gt;testing&lt;/em&gt; data; they are simply divided here in the same way as in the paper.)&lt;br&gt;
Each &lt;em&gt;???_MeV&lt;/em&gt;/&lt;em&gt;???p?_MeV&lt;/em&gt; directory contains simulation input/output and/or PHITS Tools processed output, depending on the top-level directory it is contained within.&lt;br&gt;
Input and output file names do not differ between different energies; directory structure is used to keep them distinguished/separated.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;PHITS input information&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;One top-level directory differs from all of the others, and this is common_inputs.&lt;br&gt;
As the name suggests, this directory contains all PHITS input information used in generating all of the simulation outputs.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;The core two PHITS input files used are &lt;em&gt;beam-on-target_phits-input_MonoE.inp&lt;/em&gt; for the monoenergetic beam simulation set and &lt;em&gt;beam-on-target_phits-input_GaussE.inp&lt;/em&gt; for the Gaussian-distributed beam energy simulation set.&lt;br&gt;
Within these inputs are lines using the PHITS insert file function &lt;em&gt;infl:{*}&lt;/em&gt;; all inserted files used in the PHITS simulations are also contained within this &lt;em&gt;common_inputs&lt;/em&gt; directory.&lt;br&gt;
The single exception to this is &lt;em&gt;PARAMETERS_files-1-and-7.txt&lt;/em&gt;, which is simply the &lt;em&gt;file(1)&lt;/em&gt; and &lt;em&gt;file(7)&lt;/em&gt; PHITS &lt;em&gt;[Parameters]&lt;/em&gt; arguments and will be system-specific paths to PHITS installation/data files.&lt;br&gt;
Also note that relative paths are used in the &lt;em&gt;infl:{*}&lt;/em&gt; commands; these relative paths differ to how this repository is structured given the repository has been restructured in post for distribution convenience.&amp;nbsp;&lt;br&gt;
File names are still unique and can be found in this &lt;em&gt;common_inputs&lt;/em&gt; directory.&lt;br&gt;
The &lt;em&gt;CELL&lt;/em&gt; subdirectory contains the &lt;em&gt;[Cell]&lt;/em&gt; sections used for the varied phantom compositions, and the &lt;em&gt;MAPPINGS_OF_ENERGY_TO_CELL_FILES.csv&lt;/em&gt; file details how these files are paired with the 47 different beam energies.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;PHITS outputs (raw and processed)&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;The remaining 38 top-level directories contain simulation/processed output.&lt;br&gt;
When these simulations were ran, all output was contained in each &lt;em&gt;???_MeV&lt;/em&gt; directory.&amp;nbsp;&lt;br&gt;
As detailed earlier, these have been split into various top-level directories here to allow more convenient download of only desired files.&lt;br&gt;
Nominally, each of these &lt;em&gt;???_MeV&lt;/em&gt; directories contained the following before being split:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;a &lt;em&gt;beam-on-target_phits-input.inp&lt;/em&gt; PHITS input file (and a simple &lt;em&gt;phits.in&lt;/em&gt; pointing to this input file, needed for parallel running of PHITS); note that these inputs have all specific source energy information populated within this file&lt;/li&gt;
	&lt;li&gt;a &lt;em&gt;phantom_composition_info.csv&lt;/em&gt; file also detailing the phantom composition used for that beam energy&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;tphits*.out&lt;/em&gt; file(s),&lt;strong&gt;&amp;nbsp;raw&lt;/strong&gt;&amp;nbsp;summary output files generated by PHITS&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;*.out&lt;/em&gt; &lt;strong&gt;raw&lt;/strong&gt; plaintext tally output files from PHITS&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;*.eps&lt;/em&gt; &lt;strong&gt;graphical&lt;/strong&gt; visualizations of tally output, generated by PHITS&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;*_dmp.out*&lt;/em&gt; &lt;strong&gt;raw&lt;/strong&gt; binary tally &lt;strong&gt;dump&lt;/strong&gt; files from PHITS&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;*.pickle.xz&lt;/em&gt; &lt;strong&gt;processed&lt;/strong&gt; tally output (and &lt;em&gt;phits.out&lt;/em&gt; metadata) from PHITS Tools, LZMA-compressed pickle files&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;*_dmp_namedtuple_list.pickle.xz&lt;/em&gt; &lt;strong&gt;processed&lt;/strong&gt; tally &lt;strong&gt;dump&lt;/strong&gt; output from PHITS Tools, formatted as a NumPy record array (np.recarray)&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;*_dmp_Pandas_df.pickle.xz&lt;/em&gt; &lt;strong&gt;processed&lt;/strong&gt; tally &lt;strong&gt;dump&lt;/strong&gt; output from PHITS Tools, formatted as a Pandas DataFrame (same numerical data as in NumPy recarray)&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;*.png&lt;/em&gt; and &lt;em&gt;*.pdf&lt;/em&gt; &lt;strong&gt;graphical&lt;/strong&gt; visualizations of tally output, generated by PHITS Tools&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;The top-level directories of this repository are named in a way to detail (1) which simulations their contents pertain to and (2) which output files are contained within them.&lt;br&gt;
The directories are named using an underscore-delimited pattern whose components have the following names and meanings:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Beam type:&amp;nbsp;
	&lt;ul&gt;
		&lt;li&gt;&amp;nbsp;&lt;strong&gt;MonoE&lt;/strong&gt; refers to simulations with the monoenergetic beams with 2.5 mm spread&lt;/li&gt;
		&lt;li&gt;&amp;nbsp;&lt;strong&gt;GaussE&lt;/strong&gt;&amp;nbsp;refers to simulations with the Gaussian-distributed energies and 4.0 mm spread&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
	&lt;li&gt;Simulated number of protons:
	&lt;ul&gt;
		&lt;li&gt;&lt;strong&gt;1E8&lt;/strong&gt;&amp;nbsp;refers to simulations with 10&lt;sup&gt;8&lt;/sup&gt; (one hundred million) protons simulated&amp;nbsp;&lt;/li&gt;
		&lt;li&gt;&lt;strong&gt;1E9&lt;/strong&gt; refers to simulations with 10&lt;sup&gt;9&lt;/sup&gt; (one billion) protons simulated (only available on request)&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
	&lt;li&gt;Output source/type:
	&lt;ul&gt;
		&lt;li&gt;&lt;strong&gt;raw&lt;/strong&gt; refers to the PHITS input and PHITS-generated output&amp;nbsp;&lt;/li&gt;
		&lt;li&gt;&lt;strong&gt;processed&lt;/strong&gt;&amp;nbsp;refers to the Python-formatted processed output produced by PHITS Tools&lt;/li&gt;
		&lt;li&gt;&lt;strong&gt;plots&lt;/strong&gt; refers to the &lt;em&gt;*.eps&lt;/em&gt; files produced by PHITS and the &lt;em&gt;*.png&lt;/em&gt; and &lt;em&gt;*.pdf&lt;/em&gt; files produced by PHITS Tools, all containing graphical plots of tally output (only relevant to &lt;strong&gt;1E8&lt;/strong&gt; simulations)&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
	&lt;li&gt;Other labels:
	&lt;ul&gt;
		&lt;li&gt;&lt;strong&gt;proton-tally&lt;/strong&gt;&amp;nbsp;refers to output from the huge &lt;em&gt;[T-Cross]&lt;/em&gt; tally used only in &lt;strong&gt;1E8&lt;/strong&gt;&amp;nbsp;simulations for scoring proton phase space as a function of energy, position, and direction (separated from others owing to its considerable size)&lt;/li&gt;
		&lt;li&gt;&lt;strong&gt;neutron-dump&lt;/strong&gt; refers to the event-by-event neutron production data scored by a &lt;em&gt;[T-Product]&lt;/em&gt; tally&amp;#39;s &amp;quot;dump&amp;quot; option&lt;/li&gt;
		&lt;li&gt;&lt;strong&gt;NumPy&lt;/strong&gt; and &lt;strong&gt;Pandas&lt;/strong&gt;&amp;nbsp;to denote if &lt;strong&gt;processed&lt;/strong&gt;&amp;nbsp;contents are formatted as NumPy record arrays or Pandas Dataframes&amp;nbsp;&lt;/li&gt;
		&lt;li&gt;&lt;strong&gt;gamma-dump&lt;/strong&gt; refers to the event-by-event gamma-ray production data scored by a &lt;em&gt;[T-Product]&lt;/em&gt; tally&amp;#39;s &amp;quot;dump&amp;quot; option&lt;/li&gt;
		&lt;li&gt;&lt;strong&gt;NumPy&lt;/strong&gt;&amp;nbsp;and &lt;strong&gt;Pandas&lt;/strong&gt; to denote if &lt;strong&gt;processed&lt;/strong&gt;&amp;nbsp;contents are formatted as NumPy record arrays or Pandas Dataframes&amp;nbsp;&lt;/li&gt;
		&lt;li&gt;&lt;strong&gt;other&lt;/strong&gt; refers to output from all other tallies aside from the above three (energy deposition, LET, diagnostic tallies, etc.; only relevant to &lt;strong&gt;1E8&lt;/strong&gt;&amp;nbsp;simulations given all tallies except dump tallies were disabled for &lt;strong&gt;1E9&lt;/strong&gt; simulations) along with (for &lt;strong&gt;raw&lt;/strong&gt;&amp;nbsp;directories) PHITS input-related files and &lt;em&gt;phits*.out&lt;/em&gt; file(s).&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;All put together, this results in the following top-level directories contained in this repository:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;&lt;em&gt;common_inputs&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E8_raw_proton-tally&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E8_raw_neutron-dump&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E8_raw_gamma-dump&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E8_raw_other&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E9_raw_neutron-dump&amp;nbsp;&lt;strong&gt;(upon request)&lt;/strong&gt;&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E9_raw_gamma-dump&amp;nbsp;&lt;strong&gt;(upon request)&lt;/strong&gt;&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E9_raw_other&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E8_processed_proton-tally&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E8_processed_neutron-dump_NumPy&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E8_processed_neutron-dump_Pandas&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E8_processed_gamma-dump_NumPy&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E8_processed_gamma-dump_Pandas&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E8_processed_other&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E9_processed_neutron-dump_NumPy &lt;strong&gt;(upon request)&lt;/strong&gt;&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E9_processed_neutron-dump_Pandas&lt;strong&gt;&amp;nbsp;(upon request)&lt;/strong&gt;&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E9_processed_gamma-dump_NumPy&lt;strong&gt;&amp;nbsp;(upon request)&lt;/strong&gt;&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E9_processed_gamma-dump_Pandas&amp;nbsp;&lt;strong&gt;(upon request)&lt;/strong&gt;&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E9_processed_other&amp;nbsp;&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;GaussE_1E8_plots&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E8_raw_proton-tally&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E8_raw_neutron-dump&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E8_raw_gamma-dump&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E8_raw_other&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E9_raw_neutron-dump&lt;strong&gt;&amp;nbsp;(upon request)&lt;/strong&gt;&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E9_raw_gamma-dump&amp;nbsp;&lt;strong&gt;(upon request)&lt;/strong&gt;&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E9_raw_other&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E8_processed_proton-tally&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E8_processed_neutron-dump_NumPy&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E8_processed_neutron-dump_Pandas&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E8_processed_gamma-dump_NumPy&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E8_processed_gamma-dump_Pandas&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E8_processed_other&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E9_processed_neutron-dump_NumPy&amp;nbsp;&lt;strong&gt;(upon request)&lt;/strong&gt;&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E9_processed_neutron-dump_Pandas&amp;nbsp;&lt;strong&gt;(upon request)&lt;/strong&gt;&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E9_processed_gamma-dump_NumPy&amp;nbsp;&lt;strong&gt;(upon request)&lt;/strong&gt;&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E9_processed_gamma-dump_Pandas&lt;strong&gt;&amp;nbsp;(upon request)&lt;/strong&gt;&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E9_processed_other&lt;/em&gt;&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;MonoE_1E8_plots&lt;/em&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;And, as stated earlier, each of these top-level directories is divided into a &lt;em&gt;training&lt;/em&gt; subdirectory (containing 37 &lt;em&gt;???_MeV&lt;/em&gt; directories) and a &lt;em&gt;testing&lt;/em&gt; subdirectory (containing 10 &lt;em&gt;???p?_MeV &lt;/em&gt;directories), where the &lt;em&gt;???[p?]_MeV&lt;/em&gt; directories only (1) contain particular files (2) relevant to certain simulations&amp;amp;mdash;as specified by the top-level directory&amp;#39;s name.&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;As a note to anyone surveying the &lt;em&gt;raw&lt;/em&gt; files, all &lt;em&gt;GaussE&lt;/em&gt; simulations were ran with OpenMP parallelization with 10 processes.&lt;br&gt;
For&lt;em&gt; 1E8 &lt;/em&gt;simulations, this was conducted as ten PHITS runs of 1E7 protons each; for&lt;em&gt; 1E9 &lt;/em&gt;simulations, this was conducted as twenty runs of 5E7 protons each.&lt;br&gt;
(PHITS runs can be &amp;quot;chained&amp;quot; as &amp;quot;restart calculations&amp;quot;, where one run can resume from where a previous run ended.)&lt;br&gt;
In these simulations, the generated&lt;em&gt; phits.out&lt;/em&gt; files from each run were renamed to &lt;em&gt;phits-#.out&lt;/em&gt; (where &lt;em&gt;#&lt;/em&gt; is the run number,&lt;em&gt; 0&lt;/em&gt; to&lt;em&gt; 19&lt;/em&gt;) and moved into a &lt;em&gt;phitsout&lt;/em&gt; subdirectory after each run&amp;#39;s completion.&lt;br&gt;
However, this was less uniform for the &lt;em&gt;MonoE&lt;/em&gt; simulations; for those, the strategy was to complete each simulation in a single run of PHITS.&amp;nbsp;&lt;br&gt;
This generally involved using a hybrid OpenMP + MPI parallelization with anywhere from 80 to 160 processes each, split between OMP and MPI (noting that some&lt;em&gt; 1E9 &lt;/em&gt;runs were conducted with only MPI parallelization).&lt;br&gt;
None of this influences the output format of the standard tally outputs.&lt;br&gt;
However, the number of dump files produced is equal to the number of MPI processes utilized.&lt;br&gt;
This means that each &lt;em&gt;GaussE&lt;/em&gt; simulation only has one dump file per dump tally owing to only using OpenMP parallelization (which merges its dump files at the end of calculation) while the&lt;em&gt; MonoE &lt;/em&gt;simulations contain a varied number of dump files per dump tally owing to varriations in parallelization strategies employed in those simulations.&lt;br&gt;
PHITS Tools ultimately merges all dump outputs back together in its processing, meaning if looking at the &lt;em&gt;processed&lt;/em&gt; output this quirk of how simulations were conducted should not be apparent at all.&lt;/p&gt;

&lt;p&gt;&lt;br&gt;
Given PHITS Tools was under ongoing development as this dataset was being produced, the &lt;em&gt;GaussE&lt;/em&gt; directories contain some extra output not present in the &lt;em&gt;MonoE&lt;/em&gt; directories.&amp;nbsp; Most notably, only for the &lt;em&gt;GaussE&lt;/em&gt; simulations do the &lt;em&gt;plot&lt;/em&gt; directories contain PNG and PDF plot files generated by PHITS Tools and the &lt;em&gt;*_processed_*&lt;/em&gt; directories contain dictionary objects of the processed &lt;em&gt;phits*.out&lt;/em&gt; files.&lt;/p&gt;

&lt;p&gt;Note that, for convenience, the &lt;em&gt;phits*.out&lt;/em&gt; file(s) for each simulation are also copied to all &lt;em&gt;*_raw_*&lt;/em&gt; directories.&amp;nbsp; The &lt;em&gt;phits*.out&lt;/em&gt; file(s) contain the full PHITS input echo, among other information about the simulation.&amp;nbsp; For the &lt;em&gt;GaussE&lt;/em&gt; simulations, these are within a further &lt;em&gt;phitsout&lt;/em&gt; subdirectory for each beam energy.&amp;nbsp; Also for all &lt;em&gt;GaussE_*_processed_*&lt;/em&gt; directories, the processed &lt;em&gt;phits*.out&lt;/em&gt; file(s), &lt;em&gt;phits*_out.pickle.xz&lt;/em&gt;, are included too.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;&lt;em&gt;TO BE POPULATED&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Acknowledgements&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;The NOVO project has received funding from the European Innovation Council (EIC) under grant agreement No. 101130979. The EIC receives support from the European Union&amp;#39;s Horizon Europe research and innovation programme. Partners from The University of Manchester has received funding from UK Research and Innovation under grant agreement No. 10102118&amp;nbsp;&lt;/p&gt;</description>
  </descriptions>
</resource>
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Publication date:
September 24, 2025
DOI:
10.14278/rodare.3997

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proton therapy treatment verification particle transport calculations PHITS
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