Prepare Simulation and App classes for OpenMC support, rework input file structure

[yardasol]

Summary of changes

This PR has ballooned to be non-atomic. It was quicker when making the changes to do it all at once, but in the future I should
really try to keep the number of changes in a single PR down.

Because this PR is so big, we can divvy up the work into assignments.

• Assignment 1:

• doc/installation.rst

• environment.yml

• examples/msbr/msbr.serpent

• examples/tap/tap.serpent

• examples/tap/tap_plot.serpent

• requirements.txt

• saltproc/reactor.py

• Assignment 2:

• saltproc/input_schema.json

• saltproc/version.py

• saltproc/app.py

• saltproc/tests/test.json

• saltproc/tests/test_app.py

• saltproc/tests/integration_tests/const_repr/test_const_reproc_run.py

• saltproc/tests/integration_tests/const_repr/tap_main_test.json

• saltproc/examples/tap/tap_main.json

• saltproc/examples/msbr/msbr_main.json

• Assignment 3:

• saltproc/depcode.py

• saltproc/tests/test_depcode.py

• saltproc/tests/test_materialflow.py

• saltproc/tests/test_process.py

• saltproc/tests/test_separator.py

• saltproc/tests/test_sparger.py

• Assignment 4:

• saltproc/simulation.py

• saltproc/tests/test_simulation.py

• saltproc/tests/integration_tests/no_repro/test_no_reproc_run.py

This PR addresses the issues and snags listed in #96 and #97.
This PR also resolves #77 and #42.
Resolves the rest of #44

The changes this PR makes do not preserve the current API. A comprehensive list of changes is below.

This PR adds the following tests for previously untested functions in simulation.py:

• test_check_switch_geo_trigger
• test_store_after_repr
• test_store_mat_data
• test_store_run_init_info
• test_store_run_step_info

This PR completely restructures the input file structure using a verifiable JSON schema. I have updated all examples, unit tests, and integration tests accordingly

API change
This PR adds, edits, and changes the location of, the following class methods:

• App.check_restart() -> Simulation.check_restart()
• Simulation.switch_to_next_geometry -> DepcodeSerpent.switch_to_next_geometry
• Simulation.runsim_no_reproc -> test/integration_tests/test_no_reproc_run.py::runsim_no_reproc
• Simulation.store_run_step_info
• Simulation.store_run_init_info
• (new) -> Depcode.switch_to_next_geometry
• (new) -> Depcode.read_depcode_info
• (new) -> Depcode.read_repcode_step_param
• DepcodeSerpent.sss_meta_zzz -> DepcodeSerpent.convert_nuclide_name_serpent_to_zam
• DepcodeSerpent.get_tra_or_dec -> DepcodeSerpent.create_nuclide_name_map_zam_to_serpent
• DepcodeSerpent.read_depcode_template -> DepcodeSerpent.read_plaintext_file`

API change
This PR moves (renames/adds where applicable) the following global variables from the saltproc input file into the:

• App.depcode_inp dictionary
• • (new) -> App.depcode_inp['codename']
• • App.exec_path
• • App.template_file
• • App.neutron_pop -> App.depcode_inp['npop']
• • App.active_cycles
• • App.inactive_cycles
• • App.geo_file -> App.depcode_inp['geo_file_paths']
• App.simulation_inp dictionary:
• • (new) -> App.simulation['sim_name']
• • App.db_file -> App.simulation['db_name']
• • App.restart_flag
• • App.adjust_geo
• App.reactor_inp dictionary
• • (new) -> App.reactor_inp['volume']
• • (new) -> App.reactor_inp['mass_flowrate']
• • App.power_levels
• • App.depl_hist -> App.reactor_inp['dep_step_length_cumulative']

This PR also renames the following global variables in app.py:
-depsteps -> num_depsteps

This PR changes, adds, and removes (where needed) the following attributes of the

• Depcode class:
• • template_path -> template_inputfile_path
• • input_path -> iter_inputfile
• • geo_file -> geo_files
• Simulation class:
• • h5_file -> db_path
• • (new) -> restart_flag
• • (new) -> adjust_geo
• • iter_matfile -> (removed)

API change
This PR changes the signatures of the following functions to better make use of object data encapsulation (breaks backwards compatibility:

• Depcode.read_dep_comp
• Depcode.write_depcode_input
• Depcode.write_mat_file
• DepcodeSerpent.read_plaintext_file
• DepcodeSerpent.create_nuclide_map_serpent_to_zam

This PR also fixes a previously unknown bug that wrote material data to the incorrect field in the .h5 database. This bug was caused by a typo I made in app.py in the second call to store_mat_data.

This PR also renames test_no_reproc_run.py::test_integration_3step_saltproc_no_reproc_heavy() to test_no_reproc_run.py::test_integration_2step_saltproc_no_reproc_heavy() because this integration test actually is checking the composition bases on two depletion steps rather than three.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Required for Merging

• I have read the CONTRIBUTING document.
• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have added tests to cover my changes.
• All new and existing tests passed.
  • CI tests pass
  • Local tests pass (including Serpent2 integration tests)

Associated Issues and PRs

• Issue: closes Update Simulation for OpenMC support #96
• Issue: closes [Bug]: No unit tests exist for several functions in simulation.py #97
• Issue: closes Creat JSON schema for input #42
• Issue: closes Feature: Modify input file structure to include Depletion code name #77
• Issue: closes Separation of concerns #44
• PR: merge after Versioned documenation hosting #104

Associated Developers

• Dev: @munkm

Checklist for Reviewers

Reviewers should use this link to get to the
Review Checklist before they begin their review.

[pep8speaks]

Hello @yardasol! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2022-02-07 21:09:28 UTC

[gwenchee]

@gwenchee raised the point that the function get_tra_or_dec isn't very well named. I agree and looked into it. In the function body, this line indicates that the function reads the .out file created by Serpent:

out_file = os.path.join('%s.out' % input_file)
        file = open(out_file, 'r')

The corresponding page on the serpent wiki tells us that this file contains the nuclide and material data. Looking inside a sample .out file, these lines give us some insight into the meaning of the function's name:

 Columns:

  1. Index
  2. Level (first occurence in transmutation paths)
  3. Name (nuclide identifier data)
  4. Library ID
  5. Primary data type: TRA = transport
                        DOS = dosimetry
                        SAB = thermal scattering
                        DEC = only decay data
                        STR = only structural data (mass)
                        PHO = photon interaction data

As stated in the function's docstring, get_tra_or_dec creates an isotope map to transform the serpent2 naming convention (zzzaaa.ttc) to "zzaaam" format.

So perhaps instead of get_tra_or_dec, a more appropriate name would be create_nuclide_map_zam_to_serpent or something similar? Thoughts @gwenchee?

Based on your description, shouldn't it be create_nuclide_map_serpent_to_zam?

[LukeSeifert]

Assignment 2 files look good!

[yardasol]

@gwenchee raised the point that the function get_tra_or_dec isn't very well named. I agree and looked into it. In the function body, this line indicates that the function reads the .out file created by Serpent:

out_file = os.path.join('%s.out' % input_file)
        file = open(out_file, 'r')

The corresponding page on the serpent wiki tells us that this file contains the nuclide and material data. Looking inside a sample .out file, these lines give us some insight into the meaning of the function's name:

 Columns:

  1. Index
  2. Level (first occurence in transmutation paths)
  3. Name (nuclide identifier data)
  4. Library ID
  5. Primary data type: TRA = transport
                        DOS = dosimetry
                        SAB = thermal scattering
                        DEC = only decay data
                        STR = only structural data (mass)
                        PHO = photon interaction data

As stated in the function's docstring, get_tra_or_dec creates an isotope map to transform the serpent2 naming convention (zzzaaa.ttc) to "zzaaam" format.
So perhaps instead of get_tra_or_dec, a more appropriate name would be create_nuclide_map_zam_to_serpent or something similar? Thoughts @gwenchee?

Based on your description, shouldn't it be create_nuclide_map_serpent_to_zam?

I made a mistake when I wrote that description. The function does indeed map nuclide names of 'zzaaam' format into Serpent 2 format:

.
.
.
                 line = line.split() 
                 iname, zzaaam = self.get_nuc_name(line[2]) 
                 map_dict.update({zzaaam: line[2]})
.
.
.

[gwenchee]

@yardasol Once, you rename the function, assignment 3 looks good to me for merging

[yardasol]

Will merge once I verify integration tests still work with the new changes.

[ZoeRichter]

I think my biggest question/comment was about indexing in the testing functions, so if those comments are resolved/not applicable, or you think it would be better to fix in a different PR, I think everything looks good to go.

[yardasol]

@ZoeRichter can you check over the most recent commits and then merge?

[ZoeRichter]

I think I only have the comment I just left - once that gets cleared up we should be good!