Serpent Interface Upgrade (#2290)

* serpent modifications

* fixed subdomain statistics

* Updated Serpent Interface to use serpent tools and parse new output files

* fixed error msg

* new utility script

* fixed parser

* added documentation

* updated test

* removed bumat

* remove iso file

* new input

* added EOL if burn up calc

* added eol

* modified reactivity

* added tests

* in utils only python 2 syntax is allowed

* fixed typo

* still some python3 syntax in utils that is not allowed in regression test machine centos8 (since by default it stills uses python 2 for initial installation of plugins

* Update ravenframework/CodeInterfaceClasses/SERPENT/utilityForCreatingVariables/generateRavenVariables.py

* Update ravenframework/CodeInterfaceClasses/SERPENT/SerpentInterface.py

* Apply suggestions from code review

fixed some exceptions

* removed file of iso list that is not used anymore

* Added doc for EOL parameter

* addressed Wang's comments

* add optional to pip

dependencies.xml

@@ -89,6 +89,7 @@ Note all install methods after "main" take
     <liblapack skip_check='True' os='mac' machine='x86_64'>3.9.0=20_osx64_openblas</liblapack>
     <!-- source="mamba" are the ones installed when mamba is installed -->
     <mamba source="mamba" skip_check='True'/>
+    <serpentTools optional='True' source="pip"/>
   </main>
   <alternate name="pip">
     <hdf5>remove</hdf5>

doc/user_manual/raven_user_manual.tex

@@ -292,7 +292,7 @@
 \\Alp Tezbasaran (new external code interface)
 \\Anthoney A. Griffith (Bayesian optimization)
 \\Jacob A. Bryan (TSA module)
-\\Haoyu Wang (DMD amd DMDc)
+\\Haoyu Wang (DMDc)
 \\Khang Nguyen (new external code interface)
 }
 

ravenframework/CodeInterfaceClasses/SERPENT/SerpentInterface.py

@@ -16,33 +16,41 @@
 """
 #External Modules--------------------begin
 import os
-import sys
 #External Modules--------------------end
 
 #Internal Modules--------------------begin
+from ravenframework.utils import utils
 from ..Generic.GenericCodeInterface import GenericCode
 from . import serpentOutputParser as op
 #Internal Modules--------------------end
 
 class SERPENT(GenericCode):
   """
     Provides code to interface RAVEN to SERPENT
-    This class is used as a code interface for SERPENT in RAVEN.  It expects
-    input parameters to be specified by input file, input files be specified by either
-    command line or in a main input file, and produce a csv output.
-    It is based on the code interface developed by jbae11 and mostly re-written.
+    The class has been upgraded since its first version to allow
+    the usage of the interface for both steadystate and depletion calculations.
+    The output parsing is performed leveraging the library
+    serpentTools (https://serpent-tools.readthedocs.io/en/master/index.html)
+    Multiple output formats are now processable (both for steady state and depletion)
   """
   def __init__(self):
     """
       Initializes the SERPENT Interface.
       @ In, None
       @ Out, None
     """
+    # check if serpentTools is available, raise error it otherwise
+    try:
+      import serpentTools
+    except ImportError:
+      raise ImportError("serpentTools not found and SERPENT Interface has been invoked. Install serpentTools through pip!")
+    # intialize code interface
     GenericCode.__init__(self)
-    self.printTag         = 'SERPENT'# Print Tag
-    self.isotope_list_f   = None     # isotope list file (if any)
-    self.isotopes         = []       # isotopes to collect
-    self.traceCutOff      = 1.e-7    # cutoff threshold for ignoring isotopes
+    self.printTag         = 'SERPENT'         # Print Tag
+    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}
 
   def _findInputFile(self, inputFiles):
     """
@@ -67,21 +75,28 @@ def _readMoreXML(self,xmlNode):
       @ In, xmlNode, xml.etree.ElementTree.Element, Xml element node
       @ Out, None.
     """
-    isotopeList = xmlNode.find("isotope_list")
+    eolNodes = xmlNode.findall("EOL")
+    for eolNode in eolNodes:
+      if eolNode is not None:
+        target = eolNode.attrib.get('target')
+        if target is None:
+          raise ValueError(self.printTag+' ERROR: "target" attribute in <EOL> must be present if <EOL> node is inputted')
+        value = float(eolNode.text)
+        self.eolTarget[target] = value
 
-    if isotopeList is None:
-      raise IOError(self.printTag+' ERROR: <isotope_list> node not inputted!!')
-    body = isotopeList.text.strip()
-    if "," in body:
-      self.isotopes = [iso.strip() for iso in body.split(",")]
-    else:
-      if not body.strip().endswith(".csv"):
-        raise IOError(self.printTag+' ERROR: <isotope_list> file must be a CSV!!')
-      self.isotope_list_f = body
-    cutOff = xmlNode.find("traceCutOff")
-
-    if cutOff is not None:
-      self.traceCutOff = float(cutOff.text)
+    # by default only the "_res.m" file is read.
+    # if additional files are required, the user should request them here
+    addFileTypes = xmlNode.find("additionalFileTypes")
+    if addFileTypes is not None:
+      serpentFileTypes = [ft.strip().lower() for ft in addFileTypes.text.split(",")]
+      if 'ResultsReader' in  serpentFileTypes:
+        # we pop this because it is the default
+        serpentFileTypes.pop(serpentFileTypes.index('ResultsReader'))
+      for ft in serpentFileTypes:
+        if ft not in op.serpentOutputAvailableTypes:
+          raise ValueError(self.printTag+f' ERROR: <Serpent File Type> {ft} not supported! Available types are "'
+                        f'{", ".join(op.serpentOutputAvailableTypes)}!!')
+      self._fileTypesToRead += serpentFileTypes
 
   def initialize(self, runInfo, oriInputFiles):
     """
@@ -90,15 +105,9 @@ def initialize(self, runInfo, oriInputFiles):
       @ In, oriInputFiles, list, list of the original input files
       @ Out, None
     """
-    # read the isotopes
-    if self.isotope_list_f is not None:
-      self.isotopes = []
-      if not os.path.isabs(self.isotope_list_f):
-        self.isotope_list_f = os.path.join(runInfo['WorkingDir'], self.isotope_list_f)
-      lines = open(self.isotope_list_f,"r").readlines()
-      for line in lines:
-        self.isotopes+= [elm.strip() for elm in line.split(",")]
     inputFile = self._findInputFile(oriInputFiles)
+    # check if all the output files will be actually generated by the provided input
+    op.checkCompatibilityFileTypesAndInputFile(inputFile, self._fileTypesToRead)
     # set the extension
     self.setInputExtension([inputFile.getExt()])
 
@@ -136,19 +145,8 @@ def finalizeCodeOutput(self, command, output, workDir):
       @ In, workDir, string, working directory path
       @ Out, None
     """
-    # resfile would be 'input.serpent_res.m'
-    # this is the file produced by RAVEN
     inputRoot = output.replace("_res","")
-    resfile = os.path.join(workDir, output+".m")
-    inputFile = os.path.join(workDir,inputRoot)
-    inbumatfile = os.path.join(workDir, inputRoot+".bumat0")
-    outbumatfile = os.path.join(workDir, inputRoot+".bumat1")
-    # parse files into dictionary
-    keffDict = op.searchKeff(resfile)
-    # the second argument is the percent cutoff
-    inBumatDict = op.bumatRead(inbumatfile, self.traceCutOff)
-    outBumatDict = op.bumatRead(outbumatfile, self.traceCutOff)
+    outputParser = op.SerpentOutputParser(self._fileTypesToRead, os.path.join(workDir,inputRoot), self.eolTarget)
+    results = outputParser.processOutputs()
+    return results
 
-    outputPath = os.path.join(workDir, output+'.csv')
-    op.makeCsv(outputPath, inBumatDict, outBumatDict,
-                keffDict, self.isotopes, inputFile)