Commit 1d82195b authored by Patrick Shriwise's avatar Patrick Shriwise
Browse files

Adding mesh block parsing and checking

parent c3ad6f37

pygriffin/config.py

+1 −1
Original line number Diff line number Diff line
@@ -142,7 +142,7 @@ class PyGriffinConfig: 


    @property

    def griffin_dir(self):

        return self.griffin_exec.parent

        return Path(self.griffin_exec).parent



    @property

    def griffin_exec(self):

pygriffin/isoxml_reader.py

+12 −2
Original line number Diff line number Diff line
@@ -3,15 +3,25 @@ import sys 
from xml.etree import ElementTree as ET





def parse_isoxml(isoxml_file):

def parse_isoxml(isoxml_file, library):

    """

    Extracts names of all isotopes from the XML file

    """

    tree = ET.parse(isoxml_file)

    root = tree.getroot()



    # find the indicated library name

    child_node = None

    for child in root:

        if child.attrib['Name'] == library:

            child_node = child



    if child_node is None:

        raise RuntimeError("Could lot locate library '{}' in "

                           "the ISOXML file".format(library))



    # find all "Isotope" elements

    isotopes = list(root.iter('Isotope'))

    isotopes = list(child_node.iter('Isotope'))

    return [isotope.attrib["Name"] for isotope in isotopes]



if __name__ == '__main__':

pygriffin/moose_parser.py

+43 −8
Original line number Diff line number Diff line
@@ -20,9 +20,10 @@ def parse_moose_materials(input_text): 
        Returns

        -------

        dict

            A dictionary with material names as keys and lists of isotope names

            as values

            A dictionary with material names as keys and values that are tuples

            containing a list of isotopes and the material mesh block

        """

        library_name = None

        mat_block = []

        isotopes = []

        accumulate_lines = False
@@ -36,7 +37,13 @@ def parse_moose_materials(input_text): 


            # once the end of the block has been reached, exit loop

            if accumulate_lines and '[]' == line.replace('\n', ''):

                break

                accumulate_lines = False



            if 'library_name' in line:

                library_name = line.split('=')[-1].strip()



        if library_name is None:

            raise ValueError("Could not detect a library name in the Griffin input files")



        # remove header and footer from material block

        mat_block = mat_block[1:-1]
@@ -55,11 +62,11 @@ def parse_moose_materials(input_text): 
            # detect close of a block

            if _has_moose_block_close(line):

                # get material information upon close of a material block

                mat_name, isotopes = parse_moose_material(mat_lines)

                materials[mat_name] = isotopes

                mat_name, isotopes, block = parse_moose_material(mat_lines)

                materials[mat_name] = (isotopes, block)

                mat_lines = []



        return materials

        return library_name, materials





def parse_moose_material(material_txt):
@@ -88,7 +95,7 @@ def parse_moose_material(material_txt): 
            material_name = material_name.split('/')[-1]



        if 'isotope' in line:

            isotope = line.split(" ")[-1]

            isotope = line.split("=")[-1].strip()

            if '\\' in isotope:

                isotope = isotope[:isotope.find('\\')]

            isotope = isotope.replace('"', '')
@@ -96,4 +103,32 @@ def parse_moose_material(material_txt): 
            isotope = isotope.rstrip('\n')

            isotopes.append(isotope)



    return material_name, isotopes
 
        if 'block' in line:

            block = line.split("=")[-1].strip().strip("'")



    return material_name, isotopes, block





def parse_mesh_blocks(mesh_input):

    """

    Parses mesh blocks from a mesh input file



    Parameters

    ----------



    mesh_input : list of str

        Lines of text containing the MOOSE mesh description



    Returns

    -------

    list

        Sorted list of block IDs

    """

    blocks = set()



    for line in mesh_input:

        if 'block_id' in line:

            block_id = line.split('=')[-1].strip()

            blocks.add(block_id)



    return sorted(list(blocks))

pygriffin/pygriffin.py

+46 −6
Original line number Diff line number Diff line
@@ -9,7 +9,7 @@ import warnings 
from . import checkvalue as cv

from .config import PyGriffinConfig

from .isoxml_reader import parse_isoxml

from .moose_parser import parse_moose_materials

from .moose_parser import parse_moose_materials, parse_mesh_blocks

from .util import run_in_tmpdir
@@ -130,15 +130,19 @@ class PyGriffin: 
        """

        Prints materials assigned and available ISOXML isotopes to screen

        """

        mesh_materials = self.get_material_assignments()

        mat_str = "Materials applied in the Griffin mesh:\n"

        for material, isotopes in mesh_materials.items():

        library, mesh_materials = self.get_material_assignments()

        assigned_mesh_blocks = set()

        mat_str = "Materials applied in the Griffin mesh:\n\n"

        mat_str += "\tLibrary: {}\n".format(library)

        for material, (isotopes, block) in mesh_materials.items():

            mat_str += "\tMaterial Name: {}\n".format(material)

            mat_str += "\tBlock: {}\n".format(block)

            mat_str += "\tIsotopes:\n"

            mat_str += ''.join('\t\t{}\n'.format(i) for i in isotopes)

            assigned_mesh_blocks.add(block)

        print(mat_str)



        isoxml_materials = parse_isoxml(self.process_xs())

        isoxml_materials = parse_isoxml(self.process_xs(), library)

        isotope_str = "Isotopes available in the ISOXML library:\n"

        isotope_str += ''.join('\t{}\n'.format(m) for m in isoxml_materials)

        print(isotope_str)
@@ -148,6 +152,20 @@ class PyGriffin: 
        for isos in mesh_materials.values():

            (mesh_set.update(i) for i in isos)



        mesh_blocks = set(self.get_mesh_blocks())



        unassigned_mesh_blocks = mesh_blocks - assigned_mesh_blocks



        if unassigned_mesh_blocks:

            print('The following mesh blocks are unassigned:\n')

            print(', '.join(sorted(list(unassigned_mesh_blocks))))



        incorrect_mesh_blocks = assigned_mesh_blocks - mesh_blocks



        if incorrect_mesh_blocks:

            print('The following material blocks are not present in the mesh:\n')

            print(', '.join(sorted(list(incorrect_mesh_blocks))))



        # determine materials used in the mesh that are not

        # not present in the ISOXML file

        if not isoxml_set.issuperset(mesh_set):
@@ -161,9 +179,31 @@ class PyGriffin: 


        return invalid_mats, unused_mats



    def get_mesh_blocks(self):

        """

        Get all mesh blocks in the Griffin problem



        Returns

        -------

        list

            A list of sorted mesh block IDs

        """

        # open the mesh file

        if self.mesh.endswith('.i'):

            with open(self.mesh, 'r') as fh:

                return parse_mesh_blocks(fh.readlines())



        return []



    def get_material_assignments(self):

        """

        Concatenate all MOOSE inputs and

        Get all assigned materials in the Griffin problem



        Returns

        -------

        dict

            A dictionary with material names as keys and values that are tuples

            containing a list of isotopes and the material mesh block

        """

        # open the mesh and options files

        lines = []

workbench_runner.py

+1 −2
Original line number Diff line number Diff line
@@ -48,7 +48,6 @@ if __name__ == '__main__': 
    print("Done")

    sys.stdout.flush()





    if griffin_block.simulate is None or str(son_obj.griffin.simulate.value) == '"true"':

        print("Running PyGriffin...")

        sys.stdout.flush()