new docs

Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

bibs/mavric.bib

+
+@phdthesis{wagner_acceleration_1997,
+	type = {{PhD} {Thesis}},
+	title = {Acceleration of {Monte} {Carlo} shielding calculations with an automated variance reduction technique and parallel processing},
+	school = {Pennsylvania State University},
+	author = {Wagner, John C.},
+	year = {1997},
+	file = {Full Text:/Users/john/Zotero/storage/VHWL9S7A/Wagner - 1997 - Acceleration of Monte Carlo shielding calculations.pdf:application/pdf}
+}
+
+@article{wagner_automated_1998,
+	title = {Automated variance reduction of {Monte} {Carlo} shielding calculations using the discrete ordinates adjoint function},
+	volume = {128},
+	number = {2},
+	journal = {Nuclear Science and Engineering},
+	author = {Wagner, John C. and Haghighat, Alireza},
+	year = {1998},
+	note = {Publisher: Taylor \& Francis},
+	pages = {186--208},
+	file = {Full Text:/Users/john/Zotero/storage/G5CXY458/Wagner and Haghighat - 1998 - Automated variance reduction of Monte Carlo shield.pdf:application/pdf;Snapshot:/Users/john/Zotero/storage/E28TYP5Z/NSE98-2.html:text/html}
+}
+
+@inproceedings{wagner_automated_2002,
+	title = {An automated deterministic variance reduction generator for {Monte} {Carlo} shielding applications},
+	booktitle = {Proceedings of the {American} {Nuclear} {Society} 12th {Biennial} {RPSD} {Topical} {Meeting}},
+	publisher = {Citeseer},
+	author = {Wagner, John C.},
+	year = {2002},
+	pages = {14--18},
+	file = {Full Text:/Users/john/Zotero/storage/TWA7ZMVP/Wagner - 2002 - An automated deterministic variance reduction gene.pdf:application/pdf}
+}
+
+@article{haghighat_monte_2003,
+	title = {Monte {Carlo} variance reduction with deterministic importance functions},
+	volume = {42},
+	number = {1},
+	journal = {Progress in Nuclear Energy},
+	author = {Haghighat, Alireza and Wagner, John C.},
+	year = {2003},
+	note = {Publisher: Elsevier},
+	pages = {25--53},
+	file = {Snapshot:/Users/john/Zotero/storage/QBPZ9SX9/S0149197002000021.html:text/html}
+}
+
+@article{evans_denovo_2010,
+	title = {Denovo: {A} {New} {Three}-{Dimensional} {Parallel} {Discrete} {Ordinates} {Code} in {SCALE}},
+	volume = {171},
+	issn = {0029-5450},
+	shorttitle = {Denovo},
+	url = {https://doi.org/10.13182/NT171-171},
+	doi = {10.13182/NT171-171},
+	abstract = {Denovo is a new, three-dimensional, discrete ordinates (SN) transport code that uses state-of-the-art solution methods to obtain accurate solutions to the Boltzmann transport equation. Denovo uses the Koch-Baker-Alcouffe parallel sweep algorithm to obtain high parallel efficiency on O(100) processors on XYZ orthogonal meshes. As opposed to traditional SN codes that use source iteration, Denovo uses nonstationary Krylov methods to solve the within-group equations. Krylov methods are far more efficient than stationary schemes. Additionally, classic acceleration schemes (diffusion synthetic acceleration) do not suffer stability problems when used as a preconditioner to a Krylov solver. Denovo’s generic programming framework allows multiple spatial discretization schemes and solution methodologies. Denovo currently provides diamond-difference, theta-weighted diamond-difference, linear-discontinuous finite element, trilinear-discontinuous finite element, and step characteristics spatial differencing schemes. Also, users have the option of running traditional source iteration instead of Krylov iteration. Multigroup upscatter problems can be solved using Gauss-Seidel iteration with transport, two-grid acceleration. A parallel first-collision source is also available. Denovo solutions to the Kobayashi benchmarks are in excellent agreement with published results. Parallel performance shows excellent weak scaling up to 20000 cores and good scaling up to 40000 cores.},
+	number = {2},
+	urldate = {2020-06-26},
+	journal = {Nuclear Technology},
+	author = {Evans, Thomas M. and Stafford, Alissa S. and Slaybaugh, Rachel N. and Clarno, Kevin T.},
+	month = aug,
+	year = {2010},
+	note = {Publisher: Taylor \& Francis
+\_eprint: https://doi.org/10.13182/NT171-171},
+	pages = {171--200},
+	file = {Full Text PDF:/Users/john/Zotero/storage/X2FYELX4/Evans et al. - 2010 - Denovo A New Three-Dimensional Parallel Discrete .pdf:application/pdf;Snapshot:/Users/john/Zotero/storage/UGRT59ZH/NT171-171.html:text/html}
+}
+
+@article{peplow_monte_2011,
+	title = {Monte {Carlo} shielding analysis capabilities with {MAVRIC}},
+	volume = {174},
+	number = {2},
+	journal = {Nuclear Technology},
+	author = {Peplow, Douglas E.},
+	year = {2011},
+	note = {Publisher: Taylor \& Francis},
+	pages = {289--313},
+	file = {Full Text:/Users/john/Zotero/storage/M868U2TW/Peplow - 2011 - Monte Carlo shielding analysis capabilities with M.pdf:application/pdf;Snapshot:/Users/john/Zotero/storage/LZSX7SAG/NT174-289.html:text/html}
+}
+
+@article{wagner_forward-weighted_2007,
+	title = {Forward-weighted {CADIS} method for global variance reduction},
+	volume = {97},
+	journal = {Transactions-American Nuclear Society},
+	author = {Wagner, John C. and Blakeman, Edward D. and Peplow, Douglas E.},
+	year = {2007},
+	note = {Publisher: American Nuclear Society},
+	pages = {630},
+	file = {Full Text:/Users/john/Zotero/storage/6SQ8JVAA/Wagner et al. - 2007 - Forward-weighted CADIS method for global variance .pdf:application/pdf}
+}
+
+@article{warsa_krylov_2004,
+	title = {Krylov iterative methods and the degraded effectiveness of diffusion synthetic acceleration for multidimensional {SN} calculations in problems with material discontinuities},
+	volume = {147},
+	number = {3},
+	journal = {Nuclear science and engineering},
+	author = {Warsa, James S. and Wareing, Todd A. and Morel, Jim E.},
+	year = {2004},
+	note = {Publisher: Taylor \& Francis},
+	pages = {218--248},
+	file = {Full Text:/Users/john/Zotero/storage/A529V79G/Warsa et al. - 2004 - Krylov iterative methods and the degraded effectiv.pdf:application/pdf;Snapshot:/Users/john/Zotero/storage/EZLF6FEH/NSE02-14.html:text/html}
+}
+
+@article{baker_sn_1998,
+	title = {An {Sn} algorithm for the massively parallel {CM}-200 computer},
+	volume = {128},
+	number = {3},
+	journal = {Nuclear Science and Engineering},
+	author = {Baker, Randal S. and Koch, Kenneth R.},
+	year = {1998},
+	note = {Publisher: Taylor \& Francis},
+	pages = {312--320},
+	file = {Full Text:/Users/john/Zotero/storage/Z7E97YNE/Baker and Koch - 1998 - An Sn algorithm for the massively parallel CM-200 .pdf:application/pdf;Snapshot:/Users/john/Zotero/storage/F2WS2BXA/NSE98-1.html:text/html}
+}
+
+@techreport{willenbring_trilinos_2003,
+	title = {Trilinos users guide.},
+	number = {SAND2003-2952},
+	institution = {Sandia National Laboratories},
+	author = {Willenbring, James M. and Heroux, Michael Allen},
+	year = {2003},
+	file = {Snapshot:/Users/john/Zotero/storage/JHTCLF2E/918334.html:text/html}
+}
+
+@techreport{rhoades_tort_1997,
+	title = {The {TORT} three-dimensional discrete ordinates neutron/photon transport code ({TORT} version 3)},
+	institution = {Oak Ridge National Lab., TN (United States)},
+	author = {Rhoades, Wayne A. and Simpson, D. B.},
+	year = {1997},
+	file = {Full Text:/Users/john/Zotero/storage/9NMXH9MX/Rhoades and Simpson - 1997 - The TORT three-dimensional discrete ordinates neut.pdf:application/pdf;Snapshot:/Users/john/Zotero/storage/MT3V26GI/582265.html:text/html}
+}
+
+@article{rhoades_doors_1998,
+	title = {{DOORS} 3.2, one-, two-, three-dimensional discrete ordinates neutron/photon transport code system},
+	volume = {300},
+	journal = {RSICC, Oak Ridge National Laboratory},
+	author = {Rhoades, W. A. and Childs, R. L.},
+	year = {1998},
+	pages = {650}
+}
+
+@article{ibrahim_improving_2009,
+	title = {Improving the {Mesh} {Generation} {Capabilities} in the {SCALE} {Hybrid} {Shielding} {Analysis} {Sequence}},
+	volume = {100},
+	journal = {Trans. Am. Nucl. Soc},
+	author = {Ibrahim, Ahmad M. and Peplow, Douglas E. and Evans, Thomas M. and Wagner, John C. and Wilson, Paul PH},
+	year = {2009},
+	pages = {302},
+	file = {Full Text:/Users/john/Zotero/storage/3FTFPWIZ/Ibrahim et al. - 2009 - Improving the Mesh Generation Capabilities in the .pdf:application/pdf}
+}
+
+@inproceedings{johnson_fast_2013,
+	title = {Fast mix table construction for material discretization},
+	booktitle = {Proceedings of the 2013 {International} {Conference} on {Mathematics} and {Computational} {Methods} {Applied} to {Nuclear} {Science} and {Engineering}-{M} and {C} 2013},
+	author = {Johnson, Seth R.},
+	year = {2013},
+	file = {Snapshot:/Users/john/Zotero/storage/9AF5ECPR/search.html:text/html}
+}
+
+@article{lathrop_ray_1968,
+	title = {Ray effects in discrete ordinates equations},
+	volume = {32},
+	number = {3},
+	journal = {Nuclear Science and Engineering},
+	author = {Lathrop, Kaye D.},
+	year = {1968},
+	note = {Publisher: Taylor \& Francis},
+	pages = {357--369},
+	file = {Snapshot:/Users/john/Zotero/storage/AUTNT6LP/NSE68-4.html:text/html}
+}
+
+@article{lathrop_remedies_1971,
+	title = {Remedies for ray effects},
+	volume = {45},
+	number = {3},
+	journal = {Nuclear Science and Engineering},
+	author = {Lathrop, K. D.},
+	year = {1971},
+	note = {Publisher: Taylor \& Francis},
+	pages = {255--268},
+	file = {Snapshot:/Users/john/Zotero/storage/VBYCXEHT/NSE45-03-255.html:text/html}
+}
+
+@article{gardner_monte_1991,
+	title = {Monte {Carlo} nuclear well logging benchmark problems with preliminary intercomparison results},
+	volume = {5},
+	number = {4},
+	journal = {Nuclear Geophysics},
+	author = {Gardner, R. P. and Verghese, K.},
+	year = {1991},
+	pages = {429--438},
+	file = {Snapshot:/Users/john/Zotero/storage/2Q8F6M7I/search.html:text/html}
+}
+
+@article{wagner_automated_2020,
+	title = {Automated {Variance} {Reduction} {Applied} to {Nuclear} {Well}-{Logging} {Problems}},
+	journal = {Nuclear Science and Engineering},
+	author = {Wagner, John C. and Peplow, Douglas E. and Evans, Thomas M.},
+	year = {2020},
+	file = {Snapshot:/Users/john/Zotero/storage/GZAECFRM/article-9309.html:text/html}
+}
+
+@article{wiarda_development_2009,
+	title = {Development and {Testing} of {Endf}/b-vi. 8 and {Endf}/b-vii. 0 {Coupled} {Neutron}-gamma {Libraries} for {Scale} 6},
+	journal = {ORNL/TM-2008/047 (in press, 2008)},
+	author = {Wiarda, Dorothea and Dunn, Michael E. and Peplow, Douglas E. and Miller, Thomas M. and Akkurt, Hatice},
+	year = {2009}
+}

conf.py

+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'SCALE test documentation'
+copyright = '2020, John Batson'
+author = 'John Batson'
+
+# The full version, including alpha/beta/rc tags
+release = '0.0.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+import sys, os
+sys.path.append(os.path.abspath('extensions'))
+
+import sphinx_rtd_theme
+
+extensions = ['sphinxcontrib.bibtex', "sphinx_rtd_theme"]
+
+numfig = True
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

index.rst

+.. SCALE test documentation documentation master file, created by
+   sphinx-quickstart on Thu Jun 25 13:47:50 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to SCALE test documentation!
+====================================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   MAVRIC

make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

requirements.txt

+sphinxcontrib.bibtex