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FILEMAP
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Descriptions of the files and folders included in the MARLEY source code
distribution are given below.
Root folder
-----------
* CITATION.bib: Recommended citations to use when referring to MARLEY in
academic work. These are given in BibTeX format. See README.rst or
http://www.marleygen.org/citing.html for further details.
* COPYING: Contains the text of version 3 of the GNU General Public License
(GNU GPL v3). MARLEY is distributed under the terms of this license.
* FILEMAP: This is the file that you are currently reading. Descriptions are
given herein for all files and folders in the MARLEY source code
distribution.
* GUIDELINES: Contains the text of the MCnet Guidelines for Event Generator
Authors and Users. These guidelines are a non-binding supplement to the GNU
GPL v3 and provide suggestions for how event generator software should be
used and distributed.
* README.rst: Main "readme" file explaining the purpose of the code and its
basic usage. Links are provided to more detailed documentation. This file
is written in the reStructuredText (reST) markup language to allow re-use
of the text on the official MARLEY website (http://www.marleygen.org) and
GitHub repository webpage (http://github.com/MARLEY-MC/marley).
* setup_marley.sh: Bash shell script which sets up the MARLEY runtime
environment. Usage instructions are given in README.rst and
http://www.marleygen.org/getting_started.html.
The following files are intended for use by MARLEY developers only:
* .VERSION: For tagged releases of MARLEY, this text file contains the
version number. It should not be present in development versions of the code.
* .gitignore: Lists files that are intentionally not tracked by the Git
version control system. Similar .gitignore files may be found in other
folders including build/.
* .travis.yml: Build script for the Travis Continuous Integration system used
for testing MARLEY.
build/ folder
-------------
MARLEY executables and shared libraries will appear in this folder when the
code is successfully built.
* Makefile: Script used by GNU Make to build MARLEY from the source code.
data/ folder
------------
* gs_spin_parity_table.txt: Contains a table of ground-state
spin-parities for a large number of nuclides. Each line of the file includes
a nuclear PDG code followed by an integer equal to two times the total nuclear
spin. Each line terminates with either a + or - character used to represent a
parity value.
* mass_table.js: Contains a table of particle and atomic masses in a JSON-like
format. The data sources and units used are documented in the file itself.
data/react/ folder
~~~~~~~~~~~~~~~~~~
This folder stores reaction input files which are used to configure the active
scattering processes in a MARLEY simulation. Documentation for these is given
in section 6.4.1 of the MARLEY implementation paper
(http://arxiv.org/abs/2101.11867).
data/structure/ folder
~~~~~~~~~~~~~~~~~~~~~~
This folder contains many data files organized by element. Each one contains
tables of discrete nuclear energy levels and gamma-rays given in a format
described in appendix B of the MARLEY implementation paper
(http://arxiv.org/abs/2101.11867). Most of these tables are reformatted
versions of files originally distributed with version 1.6 of the TALYS code
(https://tendl.web.psi.ch/tendl_2019/talys.html). In addition to the nuclear
structure data tables, this folder also contains several other files:
* nuclide_index.txt: An "index" file used by MARLEY when retrieving nuclear
data at runtime. Each line contains a nuclear PDG code and the name of
the file which contains the corresponding structure data.
* README.md: A "readme" file which documents the nuclear structure data. It
is written in the Markdown markup language.
* TALYS-CITATION.bib: Provides a BibTeX-format citation for TALYS. This
citation should be included in academic publications that use the default
nuclear structure data files distributed with MARLEY.
data/tests/ folder
~~~~~~~~~~~~~~~~~~
This folder contains configuration files needed to run Catch2-based unit tests
of the code. They are intended to be used by MARLEY developers only.
docs/ folder
------------
Contains the source files needed to generate HTML web pages for the official
MARLEY website. Instructions for those who wish to build a local copy of the
website for offline viewing can be found at
http://www.marleygen.org/dev_docs.html#api-and-meta-documentation.
examples/ folder
----------------
This folder provides various resources that may be useful to new MARLEY users.
examples/config/ folder
~~~~~~~~~~~~~~~~~~~~~~~
Contains example job configuration files which may be used when running the
main ``marley`` executable. Further details about them are given in
setion 5.4 of the MARLEY implementation paper (http://arxiv.org/abs/2101.11867).
examples/executables/ folder
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Provides the source code for several example programs that may be built against
the MARLEY shared libraries. Further details about these are given in
sections 5.5.1, 7.3.3, and 7.4.2 of the MARLEY implementation paper
(http://arxiv.org/abs/2101.11867).
examples/macros/ folder
~~~~~~~~~~~~~~~~~~~~~~~
Contains example macros intended for use with the ROOT data analysis framework
(http://root.cern.ch). Descriptions of all of the examples are given in
examples/macros/README.md and section 7.3.4 of the MARLEY implementation
paper (http://arxiv.org/abs/2101.11867).
examples/marg4/ folder
~~~~~~~~~~~~~~~~~~~~~~
Provides the source code for an example program which interfaces MARLEY
with the Geant4 particle transport code (http://geant4.web.cern.ch).
Documentation for this program is given in section 8.2 of the MARLEY
implementation paper (http://arxiv.org/abs/2101.11867).
include/ folder
---------------
Contains the MARLEY C++ header files. Those in the catch2/ and fftpack4/
subfolders belong to the external packages Catch2
(https://github.com/catchorg/Catch2) and FFTPACK4
(https://people.sc.fsu.edu/~jburkardt/c_src/fftpack4/fftpack4.html),
respectively. These are distributed together with the MARLEY source code.
Header files written specifically for MARLEY may be found in the marley/
subfolder. The marley/tests/ subfolder includes header files intended solely
for use in Catch2-based unit tests by developers.
src/ folder
-----------
Contains the MARLEY C++ implementation files. The scripts/ subfolder contains
some miscellaneous helper scripts. The tests/ subfolder includes C++
implementation files which are used only for Catch2-based unit tests.
.git/ folder
------------
Contains files managed automatically by the Git version control system, which
is used for MARLEY development.