Serpent Interface Upgrade #2290

alfoa · 2024-03-27T15:53:01Z

Pull Request Description

What issue does this change request address? (Use "#" before the issue to link it, i.e., #42.)

Closes #2289

What are the significant changes in functionality due to this change request?

This merge request is aimed to upgrade and make the SERPENT interface fully functional and flexible.

Addition of support for eigen/criticality calculations (not only burnup)
Usage of open source tool (serpentTools: https://serpent-tools.readthedocs.io/en/master/index.html) to parse results from serpent. The serpentTools library is not installed if a user does not invoke the serpent interface.
Utility Function to create RAVEN variable groups has been rewritten to leverage Serpent output parser directly (if a modification of the parser is performed, the script is able to get it directly)
Addition of embedded reactivity calculation
Support of multiple output files (Result files, Detector outputs, Depletion outputs, Micro XS reader)
Bumat support has been disabled since Serpent is removing (deprecated) such output format and all the info are already contained in the Depletion output (*dep.m format)
Consistency checks in the input files (if an output is requested, the flags in the input are checked accordingly)

For Change Control Board: Change Request Review

The following review must be completed by an authorized member of the Change Control Board.

1. Review all computer code.
2. If any changes occur to the input syntax, there must be an accompanying change to the user manual and xsd schema. If the input syntax change deprecates existing input files, a conversion script needs to be added (see Conversion Scripts).
3. Make sure the Python code and commenting standards are respected (camelBack, etc.) - See on the wiki for details.
4. Automated Tests should pass, including run_tests, pylint, manual building and xsd tests. If there are changes to Simulation.py or JobHandler.py the qsub tests must pass.
5. If significant functionality is added, there must be tests added to check this. Tests should cover all possible options. Multiple short tests are preferred over one large test. If new development on the internal JobHandler parallel system is performed, a cluster test must be added setting, in XML block, the node <internalParallel> to True.
6. If the change modifies or adds a requirement or a requirement based test case, the Change Control Board's Chair or designee also needs to approve the change. The requirements and the requirements test shall be in sync.
7. The merge request must reference an issue. If the issue is closed, the issue close checklist shall be done.
8. If an analytic test is changed/added is the the analytic documentation updated/added?
9. If any test used as a basis for documentation examples (currently found in raven/tests/framework/user_guide and raven/docs/workshop) have been changed, the associated documentation must be reviewed and assured the text matches the example.

…iles

…test machine centos8 (since by default it stills uses python 2 for initial installation of plugins

...framework/CodeInterfaceClasses/SERPENT/utilityForCreatingVariables/generateRavenVariables.py

…Variables/generateRavenVariables.py

ravenframework/CodeInterfaceClasses/SERPENT/SerpentInterface.py

ravenframework/CodeInterfaceClasses/SERPENT/serpentOutputParser.py

fixed some exceptions

…n into alfoa/serpentModifications

wangcj05

@alfoa I have several general comments for you to consider.

wangcj05 · 2024-04-02T02:42:27Z

ravenframework/CodeInterfaceClasses/SERPENT/SerpentInterface.py

+    self._fileTypesToRead = ['ResultsReader'] # container of file types to read
+    # in case of burnup calc, the interface can compute the time at which FOMs (e.g. keff) crosses
+    # a target. For example (default), we can compute the time (burnDays) at which absKeff crosses 1.0
+    self.EOLtarget = {'absKeff':1.0}


I kind do not like the naming here, but I do not have a better suggestion here.

maybe eolTarget?

yeah. EOL is the acronym for "End Of Life". I changed it following your suggestion above.

wangcj05 · 2024-04-02T02:50:39Z

ravenframework/CodeInterfaceClasses/SERPENT/serpentOutputParser.py

+      #if 'set mdep' not in data:
+      #  raise Exception("MicroXSReader file type has been requested but no 'mdep' flag has been set in the input file!")


Do you want to keep these lines?

Yes I would like to keep those lines because are "ready" to be used once a "defect" in serpentTools is addressed

wangcj05 · 2024-04-02T02:50:54Z

ravenframework/CodeInterfaceClasses/SERPENT/serpentOutputParser.py

+      #if 'set his' not in data:
+      #  raise Exception("HistoryReader file type has been requested but no 'his' flag has been set in the input file!")
+      #else:
+      #  optionSet = data.split('set his')[1].strip()
+      #  if not optionSet.startswith('1'):
+      #    raise Exception("HistoryReader file type has been requested but 'set his' flag is not set to '1'!")
+


Do you want to keep these lines?

Yes I would like to keep those lines because are "ready" to be used once a "defect" in serpentTools is addressed

wangcj05 · 2024-04-02T02:52:05Z

ravenframework/CodeInterfaceClasses/SERPENT/serpentOutputParser.py

+      #elif ft == 'HistoryReader':
+      #  results.update(self._historyReader(nSteps))
+      #elif ft == 'MicroXSReader':
+      #  results.update(self._microXSReader(nSteps))


Do you want to keep these lines?

Yes I would like to keep those lines because are "ready" to be used once a "defect" in serpentTools is addressed

wangcj05 · 2024-04-02T02:53:01Z

ravenframework/CodeInterfaceClasses/SERPENT/serpentOutputParser.py

-    @ Out, None
-  """
+      if 'keff' in k.lower() and k.lower() != 'anakeff':
+        rho_sigma, rhoLog_sigma = None,  None


camelBack for these variables.

wangcj05 · 2024-04-02T02:53:29Z

ravenframework/CodeInterfaceClasses/SERPENT/serpentOutputParser.py

+        rho, rhoLog = (v[0] - 1) / v[0],  np.log(v[0])
+        if v.shape[0] > 1:
+          # we have sigma
+          rho_sigma, rhoLog_sigma = (v[1] / v[0]) * rho,  (v[1] / v[0]) * rhoLog


camelBack for these variables.

wangcj05 · 2024-04-02T02:56:01Z

...framework/CodeInterfaceClasses/SERPENT/utilityForCreatingVariables/generateRavenVariables.py

@@ -0,0 +1,62 @@
+


please add copyright info

wangcj05 · 2024-04-02T03:03:57Z

ravenframework/Models/PostProcessors/BasicStatistics.py

+      try:
+        sigmaAdjusted = calculations['sigma'][list(needed[metric]['targets'])]/np.sqrt(calculations['equivalentSamples'][list(needed[metric]['targets'])])
+      except:
+        sigmaAdjusted = calculations['sigma'][list(needed[metric]['targets'])]/np.sqrt(self.sampleSize)


Can you put the error type in the "except"? it seems to me these changes may not be the right fix for the issue. I guess equivalentSamples may not computed for certain cases.

Added the error type. What the right fix you have in mind?

I guess maybe we need to figure why equivalentSamples is not calculated in certain case.

The equivalentSamples is not computed when self.pbPresent is False.

I guess we need to assign uniform weight in this case, reset self.pbPressent, and raise a warning for user.

Can you guys do it in another MR? It is not really related to this MR. I can revert the fix if you want.

definitely, you do not need to revert the changes. By the way, I have already approved your PR.

Wonderful.
Thanks a lot!!!

wangcj05 · 2024-04-02T03:06:44Z

ravenframework/utils/utils.py

+def importOrInstall(package):
+  """
+    Method to import or install (if not found) a library named "package"
+    @ In, package, str, the package name to import
+    @ Out, pckImport, module, the imported module
+
+    NOTE: This method should be used only by developers
+          since it silently install packages
+          if not found
+  """
+  pckImport = None
+  try:
+    pckImport = __import__(package)
+  except ImportError:
+    print("(            ) "+UreturnPrintTag('UTILS')+": "+UreturnPrintPostTag('Message') + " -> Python package "+package+"not found. Trying to install it via pip!")
+    import subprocess
+    s = subprocess.getstatusoutput("python -m pip install " + package)
+    if int(s[0]) == 0:
+      print("(            ) "+ UreturnPrintTag('UTILS')+": "+ UreturnPrintPostTag('Message') + " -> Installation succeded!")
+      pckImport = __import__(package)
+    else:
+      print("(            ) " + UreturnPrintTag('UTILS')+ ": " + UreturnPrintPostTag('Message') + " -> Installation failed with error: " + s[1] )
+  return pckImport


As stated, this method should be used only by developers. Can you add the package through RAVEN dependencies file? You may use optional attribute if you do not want to force to install it.

Done. And also modified the test to check for that library (if not found, the tests should be skipped)

@wangcj05 I don't remember. Are the "optional" libraries installed in any machine? (If not, the serpent regression tests are never run)

We do have one unix machine to test optional, however, for your situation, the library serpentTools is not installed. It seems something is wrong with the scripts/library_handler.py, the optional library is not added to pip for some reason. I would suggest you update the script to handle the pip with optional.

I guess the problem is located in the following lines, the addOptional is set to False when using pip within conda.

It seems that serpentTools is now installed.

wangcj05

changes are good.

wangcj05

changes are good.

moosebuild · 2024-04-03T17:56:19Z

Job Test qsubs sawtooth on a5b2cd7 : invalidated by @wangcj05

very slow in removing packages

moosebuild · 2024-04-04T03:46:08Z

Job Test qsubs sawtooth on a5b2cd7 : invalidated by @wangcj05

library issue

wangcj05 · 2024-04-04T14:57:26Z

checklist passed. PR can be merged.

alfoa · 2024-04-04T17:47:15Z

@wangcj05 Thanks a lot!!!

alfoa added 18 commits January 11, 2024 07:05

serpent modifications

0d84018

fixed subdomain statistics

0e17293

Updated Serpent Interface to use serpent tools and parse new output f…

466dd41

…iles

fixed error msg

5ad99b2

Merge branch 'devel' into alfoa/serpentModifications

2b35e6b

new utility script

72a3550

fixed parser

c22bffe

added documentation

9b7dda6

updated test

7aa3706

removed bumat

f8e30fe

remove iso file

7aae099

new input

765edc8

Merge branch 'devel' into alfoa/serpentModifications

c55ead7

Merge branch 'devel' into alfoa/serpentModifications

44f1d32

added EOL if burn up calc

1d96034

added eol

8015339

modified reactivity

3bc7b3f

added tests

33afc32

alfoa requested a review from wangcj05 March 27, 2024 15:53

alfoa added 3 commits March 27, 2024 10:13

in utils only python 2 syntax is allowed

23f3159

fixed typo

b24408b

still some python3 syntax in utils that is not allowed in regression …

80e1659

…test machine centos8 (since by default it stills uses python 2 for initial installation of plugins