First major ROLLO PR with source code, tests, and one example problem

README.md

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-# generative-reactor-designs
-Repository to hold the framework and code to produce generative reactor designs. 
+# ROLLO (Reactor evOLutionary aLgorithm Optimizer)
+
+ROLLO is a Python package that applies evolutionary algorithm techniques to optimize nuclear reactor design.
+
+Documentation on the usage of ROLLO is hosted at: ## INSERT WEBSITE ##
+
+## Installation 
+`python -m pip install rollo`
+
+## Running ROLLO 
+`python -m rollo -i <input file> -c <checkpoint file>`
+
+Command line flags: 
+| Flag | Description | Mandatory ? |
+| ----------- | ----------- | ----------- |
+| -i | name of input file | Yes |
+| -c| name of checkpoint file | No |
+
+The checkpoint file holds the results from the ROLLO simulation and also acts 
+as a restart file. Thus, if a ROLLO simulation ends prematurely, the checkpoint 
+file can be used to restart the code from the most recent population and 
+continue the simulation.
+
+## To build documentation 
+`cd docs` 
+
+`make html`
+
+## To upload to PyPI
+`python3 -m build`
+
+`python3 -m twine upload dist/*`
+
+## License 
+ROLLO is distributed under the 3-Clause BSD License.

docs/Makefile

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+# 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     = source
+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)

docs/source/conf.py

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+# 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
+import sphinx_rtd_theme
+
+sys.path.insert(0, os.path.abspath("../../rollo"))
+
+# -- Project information -----------------------------------------------------
+
+project = "rollo"
+copyright = "2021, Gwendolyn J.Y. Chee"
+author = "Gwendolyn J.Y. Chee"
+
+# The full version, including alpha/beta/rc tags
+release = "v0.0.1"
+
+
+# -- 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.
+extensions = [
+    "sphinx_rtd_theme",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.napoleon",
+]
+
+
+# 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 = []
+
+
+# -- 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"]

docs/source/index.rst

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+Welcome to rollo's documentation!
+=================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/modules.rst

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+rollo
+=====
+
+.. toctree::
+   :maxdepth: 4
+
+   rollo

docs/source/rollo.rst

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+rollo package
+=============
+
+Submodules
+----------
+
+rollo.algorithm module
+----------------------
+
+.. automodule:: rollo.algorithm
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+rollo.backend module
+--------------------
+
+.. automodule:: rollo.backend
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+rollo.constraints module
+------------------------
+
+.. automodule:: rollo.constraints
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+rollo.evaluation module
+-----------------------
+
+.. automodule:: rollo.evaluation
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+rollo.executor module
+---------------------
+
+.. automodule:: rollo.executor
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+rollo.input\_validation module
+------------------------------
+
+.. automodule:: rollo.input_validation
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+rollo.moltres\_evaluation module
+--------------------------------
+
+.. automodule:: rollo.moltres_evaluation
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+rollo.openmc\_evaluation module
+-------------------------------
+
+.. automodule:: rollo.openmc_evaluation
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+rollo.special\_variables module
+-------------------------------
+
+.. automodule:: rollo.special_variables
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+rollo.toolbox\_generator module
+-------------------------------
+
+.. automodule:: rollo.toolbox_generator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: rollo
+   :members:
+   :undoc-members:
+   :show-inheritance:

examples/fhr-slab/README.md

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+**ROLLO input file and supporting OpenMC templating scripts for maximizing keff
+in a FHR fuel slab by varying the slab's TRISO fuel particle distribution.**
+
+`rollo_input.json`: ROLLO input file 
+
+`openmc_input.py`: OpenMC templating script 
+
+`constants.py`: Supporting functions for `openmcinp.py`

examples/fhr-slab/constants.py

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+import openmc
+from numpy import pi
+
+# Constants
+T_r1 = 2135e-5
+T_r2 = 3135e-5
+T_r3 = 3485e-5
+T_r4 = 3835e-5
+T_r5 = 4235e-5
+T_pitch = 0.09266
+
+uoc_9 = openmc.Material()
+uoc_9.set_density("g/cc", 11)
+uoc_9.add_nuclide("U235", 2.27325e-3)
+uoc_9.add_nuclide("U238", 2.269476e-2)
+uoc_9.add_nuclide("O16", 3.561871e-2)
+uoc_9.add_nuclide("C0", 9.79714e-3)
+uoc_9.temperature = 1110
+uoc_9.volume = 4 / 3 * pi * (T_r1 ** 3) * 101 * 210 * 4 * 36
+
+por_c = openmc.Material()
+por_c.set_density("g/cc", 1)
+por_c.add_nuclide("C0", 5.013980e-2)
+por_c.temperature = 948
+
+si_c = openmc.Material()
+si_c.set_density("g/cc", 3.2)
+si_c.add_nuclide("Si28", 4.431240e-2)
+si_c.add_nuclide("Si29", 2.25887e-3)
+si_c.add_nuclide("Si30", 1.48990e-3)
+si_c.add_nuclide("C0", 4.806117e-2)
+si_c.temperature = 948
+
+graphite = openmc.Material()
+graphite.set_density("g/cc", 1.8)
+graphite.add_nuclide("C0", 9.025164e-2)
+graphite.temperature = 948
+
+triso_4_layers = openmc.Material()
+triso_4_layers.add_nuclide("C0", 0.06851594519357823)
+triso_4_layers.add_nuclide("Si28", 0.009418744960032735)
+triso_4_layers.add_nuclide("Si29", 0.00048013017638108395)
+triso_4_layers.add_nuclide("Si30", 0.0003166830980933728)
+triso_4_layers.set_density("sum")
+triso_4_layers.temperature = 948
+
+lm_graphite = openmc.Material()
+lm_graphite.set_density("g/cc", 1.8)
+lm_graphite.add_nuclide("C0", 9.025164e-2)
+lm_graphite.temperature = 948
+
+flibe = openmc.Material()
+flibe.set_density("g/cc", 1.95)
+flibe.add_nuclide("Li6", 1.383014e-6)
+flibe.add_nuclide("Li7", 2.37132e-2)
+flibe.add_nuclide("Be9", 1.18573e-2)
+flibe.add_nuclide("F19", 4.74291e-2)
+flibe.temperature = 948
+
+mats = openmc.Materials(
+    (uoc_9, por_c, si_c, graphite, lm_graphite, flibe, triso_4_layers)
+)
+
+# 4 layer triso
+two_spheres = [openmc.Sphere(r=r) for r in [T_r1, T_r5]]
+two_triso_cells = [
+    openmc.Cell(fill=uoc_9, region=-two_spheres[0]),
+    openmc.Cell(fill=triso_4_layers, region=+two_spheres[0] & -two_spheres[1]),
+    openmc.Cell(fill=lm_graphite, region=+two_spheres[1]),
+]
+two_triso_univ = openmc.Universe(cells=two_triso_cells)
+
+
+def create_prism(left, right, left_refl, right_refl):
+    if left_refl:
+        xplane_left = +openmc.XPlane(x0=left, boundary_type="reflective")
+    else:
+        xplane_left = +openmc.XPlane(x0=left)
+    if right_refl:
+        xplane_right = -openmc.XPlane(x0=right, boundary_type="reflective")
+    else:
+        xplane_right = -openmc.XPlane(x0=right)
+    prism = (
+        xplane_left &
+        xplane_right &
+        +openmc.YPlane(y0=0.35) &
+        -openmc.YPlane(y0=0.35 + 2.55) &
+        +openmc.ZPlane(z0=0, boundary_type="reflective") &
+        -openmc.ZPlane(z0=T_pitch * 20, boundary_type="reflective")
+    )
+    return prism
+
+
+def create_prism_vertical(bot, top):
+    yplane_bot = +openmc.YPlane(y0=bot)
+    yplane_top = -openmc.YPlane(y0=top)
+    prism = (
+        +openmc.XPlane(x0=2) &
+        -openmc.XPlane(x0=2 + 23.1) &
+        yplane_bot &
+        yplane_top &
+        +openmc.ZPlane(z0=0, boundary_type="reflective") &
+        -openmc.ZPlane(z0=T_pitch * 20, boundary_type="reflective")
+    )
+    return prism
+
+
+def create_lattice(region, pf):
+    try:
+        centers_1 = openmc.model.pack_spheres(radius=T_r5, region=region, pf=pf)
+        trisos_1 = [openmc.model.TRISO(T_r5, two_triso_univ, c) for c in centers_1]
+        prism = openmc.Cell(region=region)
+        lower_left_1, upper_right_1 = prism.region.bounding_box
+        shape = tuple(((upper_right_1 - lower_left_1) / 0.4).astype(int))
+        pitch_1 = (upper_right_1 - lower_left_1) / shape
+        lattice_1 = openmc.model.create_triso_lattice(
+            trisos_1, lower_left_1, pitch_1, shape, lm_graphite
+        )
+        prism.fill = lattice_1
+    except:
+        prism = openmc.Cell(region=region)
+        prism.fill = lm_graphite
+    return prism