OpenMC general output processing for simple tokamak model

[sbradnam]

Description

This is a first pass at implementing output data processing for a general computational benchmark in OpenMC. The approach uses the OpenMC. API to generate a native pandas dataframe for each tally, with subsequent post-processing conducted to formulate consistently with other simulation outputs. Further work is required to correctly normalize OpenMC. tally outputs, for example, applying volume corrections, and combining photon, positron and electron contributions for photon heating tallies. So far, this has been demonstrated for the new Simple Tokamak benchmark.

Type of change

Please select what type of change this is.

• Bug fix (non-breaking change which fixes an issue)
• New benchmark
  • Non-breaking change which entirely uses exisiting classes, structure etc
  • Breaking change which has implemented new/modified classes etc
• New feature
  • Non-breaking change which adds functionality
  • Breaking change fix or feature that would cause existing functionality to not work as expected

Testing

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

• tests/output_test : test_single_output_openmc has been updated to mimic test_single_output_mcnp. Previously, this test was merely a skeleton test to check OpenMC. metadata and code version parsing.

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• General testing
  • New and existing unit tests pass locally with my changes
  • Coverage is >80%

[codecov]

Codecov Report

Attention: Patch coverage is 91.56939% with 65 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
jade/sphereoutput.py	90.72%	32 Missing ⚠️
jade/output.py	93.41%	21 Missing ⚠️
jade/expoutput.py	91.56%	7 Missing ⚠️
jade/postprocess.py	28.57%	5 Missing ⚠️

Files with missing lines	Coverage Δ
jade/openmc.py	95.53% <100.00%> (+0.58%)	⬆️
jade/postprocess.py	34.83% <28.57%> (-1.64%)	⬇️
jade/expoutput.py	93.60% <91.56%> (+0.11%)	⬆️
jade/output.py	92.78% <93.41%> (+17.85%)	⬆️
jade/sphereoutput.py	94.72% <90.72%> (-1.41%)	⬇️

[dodu94]

before considering approving we need to go through the type hint and docstring of output.py, expoutput.py and sphereoutput.py

[alexvalentine94]

Changes to increase level of abstraction and first implementation for capability to process OpenMC outputs using the API. Very nice additions plus substantial improvement to docstrings across codebase.