FENDL-3.2b Retrofitting

src/DataLib/fendl32B_retrofit/activation_analysis.py

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+# Import packages
+import pandas as pd
+from tendl_preprocessing import extract_cross_sections
+
+def iterate_MTs(MTs, file_obj, mt_dict, pKZA):
+    # Initialize lists
+    cross_sections_by_MT = []
+    emitted_particles_list = []
+    dKZAs = []
+    groups = []
+
+    # Extract data for each MT
+    for MT in MTs:
+        sigma_list = extract_cross_sections(file_obj, MT)
+        if not sigma_list:
+            continue
+        dKZA = pKZA - mt_dict[str(MT)]['delKZA']
+        emitted_particles = mt_dict[str(MT)]['Emitted Particles']
+        if dKZA is None:
+            continue
+        cross_sections_by_MT.append(sigma_list)
+        dKZAs.append(dKZA)
+        emitted_particles_list.append(emitted_particles)
+        groups.append(len(sigma_list))
+
+
+    # Store data in a Pandas DataFrame
+    gendf_data = pd.DataFrame({
+        'Parent KZA': [pKZA] * len(dKZAs),
+        'Daughter KZA': dKZAs,
+        'Emitted Particles': emitted_particles_list,
+        'Non-Zero Groups' : groups,
+        'Cross Sections': cross_sections_by_MT
+    })
+
+    return gendf_data

src/DataLib/fendl32B_retrofit/fendl3_retrofit.py

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+# Import packages
+import tendl_preprocessing as tpp
+import activation_analysis
+from logging_config import logger
+import groupr_tools
+import sys
+import argparse
+import asyncio
+import pandas as pd
+import reaction_data as rxd
+
+def fendl_args():
+    """
+    Configure Argument Parser for the FENDL 3.2-b/TENDL 2017 retroffiting,
+        including options for user input of GENDF files that have already
+        been processed using the NJOY GROUPR module or downloading and
+        processing TENDL/PENDF files from the TENDL 2017 database.
+
+        Note: If the user opts to select the "Loclal file input" option,
+        they must ensure that the GENDF file is properly formatted and
+        contains activation, and not transport data, themselves.
+
+    Arguments:
+        None
+
+    Returns:
+        args (argparse.Namespace): Argparse object that contains the user
+            specified arguments for executing the program.
+    """
+
+    parser = argparse.ArgumentParser()
+
+    # Subparsers for 'I' and 'D'
+    subparsers = parser.add_subparsers(dest='method', required=True)
+    parser_I = subparsers.add_parser('I', help='''Local file input.
+                                        Note: This option should only be 
+                                        selected if the user already has
+                                        properly formatted GENDF activation 
+                                        files that have been processed using 
+                                        the NJOY GROUPR module for a
+                                    Vitmain-J group structure with a
+                                        Vitamin-E weight function.''')
+    parser_I.add_argument('--paths', '-p',
+                        required=True,
+                        nargs= '+',
+                        help='Path to the local GENDF file.')
+    parser_D = subparsers.add_parser('D', help='''Download TENDL/PENDF files
+                                        from the TENDL 2017 neutron activation
+                                        database.''')
+    parser_D.add_argument('--element', '-e',
+                        required=True,
+                        help= 'Chemical symbol for selected element (i.e. Ti).')
+    parser_D.add_argument('--A', '-a',
+                        required=True,
+                        help= '''Mass number for selected isotope (i.e. 48).
+                                    If the target is an isomer, type
+                                    "m" after the mass number (i.e. 48m).
+                                    To automatically iterate over all of
+                                    the isotopes for the target element,
+                                    select "all" as the option for --A.
+                                    ''')
+
+    args = parser.parse_args()
+    return args
+
+def handle_local_file_input(mt_dict, cumulative_data, gendf_paths = None, args = None):
+    """
+    Method for extracting and analyzing data from preprocessed GENDF files
+        that the user already has saved locally. Called when the argument
+        for the main function -- fendl3_2b_retrofit() -- is specified as 'I'.
+
+    Arguments:
+        args (argparse.Namespace): Argparse object that contains the user
+            specified arguments for executing the program.
+        mt_dict (dict): Dictionary formatted data structure for mt_table.csv 
+    """
+
+    # Format gendf_paths parameter
+    if gendf_paths is None:
+        gendf_paths = args.paths
+    elif type(gendf_paths) is not list:
+        gendf_paths = [gendf_paths]
+
+    for gendf_path in gendf_paths:
+        # Extract fundamental data from the GENDF file
+        pKZA = tpp.extract_gendf_pkza(gendf_path)
+        matb, MTs, file_obj = tpp.extract_endf_specs(gendf_path, 'gendf')
+
+        logger.info(f"GENDF file path: {gendf_path}")
+        logger.info(f"Parent KZA (pKZA): {pKZA}")
+        logger.info(f'MTs: {MTs}')
+
+        # Extract and save specific data for each MT
+        gendf_data = activation_analysis.iterate_MTs(MTs, file_obj, mt_dict, pKZA)
+        cumulative_data = pd.concat([cumulative_data, gendf_data], ignore_index= True)
+    return cumulative_data
+
+def handle_download_file(args, mt_dict, cumulative_df):
+    """
+    Method for downloading ENDF/PENDF files from the TENDL 2017 database,
+        using the NJOY GROUPR module to convert these to a group-wise file,
+        and then extracting and analyzing the resultant data. Called when
+        the argument for the main function -- fendl3_2b_retrofit() --
+        is specified as 'D'.
+
+    Arguments:
+        args (argparse.Namespace): Argparse object that contains the user
+            specified arguments for executing the program.
+        mt_dict (dict): Dictionary formatted data structure for mt_table.csv 
+    """
+
+    # Establish parameters from the user arguments
+    element = args.element
+    A = args.A
+    if A == 'all':
+        A_vals = asyncio.run(tpp.identify_tendl_isotopes(element))
+        logger.info(
+            f'All isotopes of {element} in the TENDL database: {A_vals}'
+        )
+    else:
+        A_vals = [A]
+
+    # Iterate over all isotopes/isomers, as specified by arguments
+    gendf_paths = []
+    for A in A_vals:
+        endf_path = tpp.download_tendl(element, A, 'endf')
+        pendf_path = tpp.download_tendl(element, A, 'pendf')
+
+        material_id, MTs = tpp.extract_endf_specs(endf_path, 'endf')
+
+        card_deck = groupr_tools.groupr_input_file_format(material_id, MTs,
+                                                        element, A, mt_dict)
+        groupr_tools.groupr_input_file_writer(card_deck, MTs)
+
+        gendf_path = groupr_tools.run_njoy(card_deck, element, A, material_id)
+        gendf_paths.append(gendf_path)
+
+        groupr_tools.njoy_file_cleanup()
+        logger.info(f'Finished iterating for {element}-{A} \n \n')
+
+    return gendf_paths
+
+##############################################################################
+
+def fendl3_2b_retrofit():
+    """
+    Main method when run as a command line script.
+    """
+
+    # Initialize arguments, DataFrame to store data, and load in MT reference
+    args = fendl_args()
+    gendf_paths = []
+    cumulative_data = rxd.initialize_dataframe()
+    mt_dict = rxd.process_mt_table('mt_table.csv')
+
+    # Execute file handling
+    if args.method == 'D':
+        gendf_paths = handle_download_file(args, mt_dict, cumulative_data)
+        args = None
+    cumulative_data = handle_local_file_input(mt_dict,
+                                              cumulative_data,
+                                              gendf_paths = gendf_paths,
+                                              args = args)
+
+    # Save to CSV
+    cumulative_data.to_csv('gendf_data.csv', index=False)
+    logger.info("Saved gendf_data.csv")
+
+##############################################################################
+
+if __name__ == '__main__':
+    fendl3_2b_retrofit()