Prepare `Simulation` and `App` classes for OpenMC support, rework input file structure #98

yardasol · 2022-01-13T20:44:33Z

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.

…files

pep8speaks · 2022-01-13T20:44:39Z

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 · 2022-02-04T21:33:42Z

@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 · 2022-02-04T21:58:56Z

@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 · 2022-02-04T22:18:44Z

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

yardasol · 2022-02-07T16:16:57Z

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

ZoeRichter · 2022-02-07T19:58:14Z

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.

This reverts commit ad86976.

yardasol · 2022-02-07T21:09:45Z

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

ZoeRichter · 2022-02-07T21:25:45Z

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

…e-simulation Prepare `Simulation` and `App` classes for OpenMC support, rework input file structure d82e4f4

yardasol added 20 commits January 10, 2022 13:52

add codename parameter to App.py

9da4e00

typo fixes

4c493f2

update test and example input files

3cfd4b0

remove un needed codename parameter

4168ce4

fix throw to raise

833969f

fix typos in test input file

95a6131

add test for codename

c7a2ac1

fix overlength line

25e0b60

pep8 fixes

0a0bb5f

more pep8 fixes

538bbfc

update Simulation docstring

d7531a9

update __init__ docstring

b2af45c

h5_file -> db_path

21b1fa3

compression -> compression_params

c27c82b

update run_sim_no_reproc docstring

826e119

update store_after_reproc docstring

5bedb32

dts -> dep_step in app.py

b321e2c

update store_mat_data docstring

6399e59

dts, d_step -> dep_step in simulation.py

18c3599

moment -> store_at_end (int -> bool); make necesary changes in other …

ac606b7

…files

yardasol added 9 commits January 13, 2022 17:05

started writing tests for remaining simulation.py functions

e2f1b6c

rework + finish test_store_mat_data

e360c6c

add test_store_run_init_info; restructure test_store_mat_data

2554e63

fix up test_write_store_run_init_info

aac559e

Added test_store_run_step_info

d51cd78

added test_check_switch_geo_trigger

4035363

typo fixes

639cf22

make code consistnet w/ docstrings

47a8af6

Added test_store_after_reproc

ee689ea

yardasol added 6 commits February 4, 2022 13:05

fix typo in test_app.py

1fafe34

apply changes from fdc4842 to test.json

a272b56

sss_meta_zzz -> convert_nuclide_name_serpent_to_zam

4676880

get_tra_or_dec -> create_nuclide_name_map_zam_to_serpent

3527e7d

fix missing '{' in input_schema.json

a285361

read_depcode_template -> read_plaintext_file

0774592

yardasol requested review from LukeSeifert, ZoeRichter, abachma2 and gwenchee February 4, 2022 20:06

yardasol added 2 commits February 4, 2022 14:13

pep8 fixes

4c8fce1

more pep8 fixes

3082496

LukeSeifert approved these changes Feb 4, 2022

View reviewed changes

update docstring for create_nuclide_name_map_zam_to_serpent

a44d419

yardasol added 2 commits February 7, 2022 14:50

Revert "make nsteps in runsim_no_reproc match its docstring definition"

7d75b04

This reverts commit ad86976.

3step -> 2step

98e90c6

ZoeRichter merged commit d82e4f4 into arfc:master Feb 7, 2022

github-actions bot pushed a commit that referenced this pull request Feb 7, 2022

update docs at commit: Merge pull request #98 from yardasol/generaliz…

050720d

…e-simulation Prepare `Simulation` and `App` classes for OpenMC support, rework input file structure d82e4f4

This was referenced Feb 7, 2022

[Bug]: Update 0.4.0 release notes #121

Closed

Fix v0.4.0 releasenotes + templates #122

Merged

Missing docs #124

Merged

yardasol removed the Status:5-In Review label Feb 11, 2022

yardasol deleted the generalize-simulation branch March 9, 2022 19:00

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Prepare `Simulation` and `App` classes for OpenMC support, rework input file structure #98

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Required for Merging

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