Uq workflow

models/fng_str/openmc_model.py

@@ -9,16 +9,19 @@
 def _parse_args():
     """Parse and return commandline arguments"""
     parser = argparse.ArgumentParser()
-    parser.add_argument("-b", "--batches", type=int, default=100)
-    parser.add_argument("-p", "--particles", type=int, default=int(1e8))
-    parser.add_argument("-s", "--threads", type=int)
+    parser.add_argument("-b", "--batches", type=int, default=100,
+                        help='Number of batches to simulate (int)')
+    parser.add_argument("-p", "--particles", type=int,
+                        default=int(1e8), help='Number of particles per batch (int)')
+    parser.add_argument("-s", "--threads", type=int,
+                        help='Number of threads to use in the simulation (int)')
     group = parser.add_argument_group("tallies")
     group.add_argument("-r", "--reaction_rates_onaxis", action='store_true',
-                       default=False)
+                       default=False, help='Calculate the reaction rates on-axis case')
     group.add_argument("-o", "--reaction_rates_offaxis", action='store_true',
-                       default=False)
+                       default=False, help='Calculate the reaction rates off-axis case')
     group.add_argument("-d", "--heating", action='store_true',
-                       default=False)
+                       default=False, help='Calculate the nuclear heating case')
 
     args = parser.parse_args()
 
@@ -2177,13 +2180,11 @@ def main():
     settings.batches = args.batches
     settings.particles = args.particles
     settings.source = source
+    settings.weight_windows = openmc.wwinp_to_wws("weight_windows.cadis.wwinp")
     if args.heating:
         settings.survival_biasing = True
         settings.photon_transport = True
         settings.electron_treatment = 'ttb'
-        settings.weight_windows = openmc.wwinp_to_wws("ww_heating.cadis.wwinp")
-    else:
-        settings.weight_windows = openmc.wwinp_to_wws("ww_rr.cadis.wwinp")
     settings.output = {'tallies': False}
 
     ############################################################################

models/fng_str/postprocessing.ipynb

@@ -39,10 +39,10 @@
    "outputs": [],
    "source": [
     "# read sinbad data\n",
-    "experiment_file = ofb.ResultsFromDatabase('experiment.h5', path='results_database')\n",
-    "mcnp_eff3_file = ofb.ResultsFromDatabase('mcnp-4a-b_eff3.h5', path='results_database')\n",
-    "mcnp_fendl1_file = ofb.ResultsFromDatabase('mcnp-4a-b_fendl1.h5', path='results_database')\n",
-    "mcnp_fendl2_file = ofb.ResultsFromDatabase('mcnp-4a-b_fendl2.h5', path='results_database')"
+    "experiment_file = ofb.ResultsFromDatabase('results_database/experiment.h5')\n",
+    "mcnp_eff3_file = ofb.ResultsFromDatabase('results_database/mcnp-4a-b_eff3.h5')\n",
+    "mcnp_fendl1_file = ofb.ResultsFromDatabase('results_database/mcnp-4a-b_fendl1.h5')\n",
+    "mcnp_fendl2_file = ofb.ResultsFromDatabase('results_database/mcnp-4a-b_fendl2.h5')"
    ]
   },
   {
@@ -52,9 +52,9 @@
    "outputs": [],
    "source": [
     "# read openmc results in results_database/\n",
-    "openmc_fendl3_file = ofb.ResultsFromDatabase('openmc-0-14-0_fendl32b.h5', path='results_database')\n",
-    "openmc_endfb8_file = ofb.ResultsFromDatabase('openmc-0-14-0_endfb80.h5', path='results_database')\n",
-    "openmc_jeff3_file = ofb.ResultsFromDatabase('openmc-0-14-0_jeff33.h5', path='results_database')"
+    "openmc_fendl3_file = ofb.ResultsFromDatabase('results_database/openmc-0-14-0_fendl32b.h5')\n",
+    "openmc_endfb8_file = ofb.ResultsFromDatabase('results_database/openmc-0-14-0_endfb80.h5')\n",
+    "openmc_jeff3_file = ofb.ResultsFromDatabase('results_database/openmc-0-14-0_jeff33.h5')"
    ]
   },
   {

models/fng_str/run_and_store.py

@@ -6,7 +6,6 @@
 import numpy as np
 import pandas as pd
 from pathlib import Path
-import h5py
 
 # ignore NaturalNameWarnings
 import warnings
@@ -17,9 +16,12 @@
 def _parse_args():
     """Parse and return commandline arguments"""
     parser = argparse.ArgumentParser()
-    parser.add_argument("-x", "--xslib", type=str)
-    parser.add_argument("-t", "--when", type=str, default='n/a')
-    parser.add_argument("-w", "--where", type=str, default='n/a')
+    parser.add_argument("-x", "--xslib", type=str,
+                        help="Strign with Cross section library name and version (e.g. 'FENDL-2.3')")
+    parser.add_argument("-t", "--when", type=str, default='n/a',
+                        help="String with the month and year the simulation is run as (e.g. 'June 2021')")
+    parser.add_argument("-w", "--where", type=str, default='n/a',
+                        help="String with the place/institution where the simulation is run (e.g. 'MIT-PSFC')")
 
     args = parser.parse_args()
 
@@ -60,10 +62,10 @@ def main():
 
     # read statepoint file
     onaxis_file = ofb.ResultsFromOpenmc(
-        'statepoint.100.h5', 'reaction_rates_onaxis')
+        'reaction_rates_onaxis/statepoint.100.h5')
     offaxis_file = ofb.ResultsFromOpenmc(
-        'statepoint.100.h5', 'reaction_rates_offaxis')
-    heating_file = ofb.ResultsFromOpenmc('statepoint.100.h5', 'heating')
+        'reaction_rates_offaxis/statepoint.100.h5')
+    heating_file = ofb.ResultsFromOpenmc('heating/statepoint.100.h5')
 
     # openmc hdf file
     filename = ofb.build_hdf_filename(
@@ -132,22 +134,13 @@ def main():
     tally_df = pd.DataFrame(d)
 
     path_to_file = Path('results_database') / filename
-
-    # write the tally in the hdf file
-    tally_df.to_hdf(path_to_file, tally_name, mode='a',
-                    format='table', data_columns=True, index=False)
     code_version = 'openmc-' + \
         '.'.join(map(str, heating_file.get_openmc_version))
 
-    # write attributes to the hdf file
-    with h5py.File(path_to_file, 'a') as f:
-        f[tally_name + '/table'].attrs['x_axis'] = xaxis_name
-        f.attrs['code_version'] = code_version
-        f.attrs['xs_library'] = args.xslib.strip().replace(' ', '')
-        f.attrs['batches'] = heating_file.get_batches
-        f.attrs['particles_per_batch'] = heating_file.get_particles_per_batch
-        f.attrs['when'] = args.when
-        f.attrs['where'] = args.where
+    xs_library = args.xslib.strip().replace(' ', '')
+    ofb.to_hdf(tally_df, path_to_file, tally_name, xs_library, xaxis_name,
+               args.when, args.where, code_version,
+               heating_file.get_batches, heating_file.get_particles_per_batch)
 
 
 if __name__ == "__main__":

models/fng_w/openmc_model.py

@@ -9,14 +9,17 @@
 def _parse_args():
     """Parse and return commandline arguments"""
     parser = argparse.ArgumentParser()
-    parser.add_argument("-b", "--batches", type=int, default=100)
-    parser.add_argument("-p", "--particles", type=int, default=int(1e7))
-    parser.add_argument("-s", "--threads", type=int)
+    parser.add_argument("-b", "--batches", type=int, default=100,
+                        help='Number of batches to simulate (int)')
+    parser.add_argument("-p", "--particles", type=int,
+                        default=int(1e7), help='Number of particles per batch (int)')
+    parser.add_argument("-s", "--threads", type=int,
+                        help='Number of threads to use in the simulation (int)')
     group = parser.add_argument_group("tallies")
     group.add_argument("-r", "--reaction_rates", action='store_true',
-                       default=False)
+                       default=False, help='Calculate the reaction rates case')
     group.add_argument("-d", "--heating", action='store_true',
-                       default=False)
+                       default=False, help='Calculate the nuclear heating case')
 
     args = parser.parse_args()
 

models/fng_w/run_and_store.py

@@ -3,10 +3,8 @@
 import subprocess
 import openmc_fusion_benchmarks as ofb
 import helpers
-import numpy as np
 import pandas as pd
 from pathlib import Path
-import h5py
 
 # ignore NaturalNameWarnings
 import warnings
@@ -17,9 +15,12 @@
 def _parse_args():
     """Parse and return commandline arguments"""
     parser = argparse.ArgumentParser()
-    parser.add_argument("-x", "--xslib", type=str)
-    parser.add_argument("-t", "--when", type=str, default='n/a')
-    parser.add_argument("-w", "--where", type=str, default='n/a')
+    parser.add_argument("-x", "--xslib", type=str,
+                        help="Strign with Cross section library name and version (e.g. 'FENDL-2.3')")
+    parser.add_argument("-t", "--when", type=str, default='n/a',
+                        help="String with the month and year the simulation is run as (e.g. 'June 2021')")
+    parser.add_argument("-w", "--where", type=str, default='n/a',
+                        help="String with the place/institution where the simulation is run (e.g. 'MIT-PSFC')")
 
     args = parser.parse_args()
 
@@ -50,8 +51,8 @@ def main():
 
     # read statepoint file
     reaction_rates_file = ofb.ResultsFromOpenmc(
-        'statepoint.100.h5', 'reaction_rates')
-    heating_file = ofb.ResultsFromOpenmc('statepoint.100.h5', 'heating')
+        'reaction_rates/statepoint.100.h5')
+    heating_file = ofb.ResultsFromOpenmc('heating/statepoint.100.h5')
 
     # generate openmc hdf file
     filename = ofb.build_hdf_filename(
@@ -79,22 +80,13 @@ def main():
     tally_df = pd.DataFrame(d)
 
     path_to_file = Path('results_database') / filename
-
-    # write the tally in the hdf file
-    tally_df.to_hdf(path_to_file, tally_name, mode='a',
-                    format='table', data_columns=True, index=False)
     code_version = 'openmc-' + \
         '.'.join(map(str, heating_file.get_openmc_version))
 
-    # write attributes to the hdf file
-    with h5py.File(path_to_file, 'a') as f:
-        f[tally_name + '/table'].attrs['x_axis'] = xaxis_name
-        f.attrs['code_version'] = code_version
-        f.attrs['xs_library'] = args.xslib.strip().replace(' ', '')
-        f.attrs['batches'] = heating_file.get_batches
-        f.attrs['particles_per_batch'] = heating_file.get_particles_per_batch
-        f.attrs['when'] = args.when
-        f.attrs['where'] = args.where
+    xs_library = args.xslib.strip().replace(' ', '')
+    ofb.to_hdf(tally_df, path_to_file, tally_name, xs_library, xaxis_name,
+               args.when, args.where, code_version,
+               heating_file.get_batches, heating_file.get_particles_per_batch)
 
 
 if __name__ == "__main__":

models/fns_clean_w/openmc_model.py

@@ -10,9 +10,12 @@
 def _parse_args():
     """Parse and return commandline arguments"""
     parser = argparse.ArgumentParser()
-    parser.add_argument("-b", "--batches", type=int, default=100)
-    parser.add_argument("-p", "--particles", type=int, default=int(1e7))
-    parser.add_argument("-s", "--threads", type=int)
+    parser.add_argument("-b", "--batches", type=int, default=100,
+                        help='Number of batches to simulate (int)')
+    parser.add_argument("-p", "--particles", type=int,
+                        default=int(1e7), help='Number of particles per batch (int)')
+    parser.add_argument("-s", "--threads", type=int,
+                        help='Number of threads to use in the simulation (int)')
 
     args = parser.parse_args()
 

models/fns_clean_w/postprocessing.ipynb

@@ -44,7 +44,7 @@
    "outputs": [],
    "source": [
     "# read sinbad data\n",
-    "experiment_file = ofb.ResultsFromDatabase('experiment.h5', path='results_database')"
+    "experiment_file = ofb.ResultsFromDatabase('results_database/experiment.h5')"
    ]
   },
   {
@@ -54,7 +54,7 @@
    "outputs": [],
    "source": [
     "# read openmc results in results_database/\n",
-    "openmc_fendl3_file = ofb.ResultsFromDatabase('openmc-0-14-0_fendl32b.h5', path='results_database')"
+    "openmc_fendl3_file = ofb.ResultsFromDatabase('results_database/openmc-0-14-0_fendl32b.h5')"
    ]
   },
   {

models/fns_clean_w/run_and_store.py

@@ -17,9 +17,12 @@
 def _parse_args():
     """Parse and return commandline arguments"""
     parser = argparse.ArgumentParser()
-    parser.add_argument("-x", "--xslib", type=str)
-    parser.add_argument("-t", "--when", type=str, default='n/a')
-    parser.add_argument("-w", "--where", type=str, default='n/a')
+    parser.add_argument("-x", "--xslib", type=str,
+                        help="Strign with Cross section library name and version (e.g. 'FENDL-2.3')")
+    parser.add_argument("-t", "--when", type=str, default='n/a',
+                        help="String with the month and year the simulation is run as (e.g. 'June 2021')")
+    parser.add_argument("-w", "--where", type=str, default='n/a',
+                        help="String with the place/institution where the simulation is run (e.g. 'MIT-PSFC')")
 
     args = parser.parse_args()
 
@@ -45,7 +48,7 @@ def main():
     p.wait()
 
     # read statepoint file
-    openmc_file = ofb.ResultsFromOpenmc('statepoint.100.h5', 'results')
+    openmc_file = ofb.ResultsFromOpenmc('results/statepoint.100.h5')
 
     # openmc hdf file
     filename = ofb.build_hdf_filename(

models/fns_duct/openmc_model.py

@@ -10,10 +10,12 @@
 def _parse_args():
     """Parse and return commandline arguments"""
     parser = argparse.ArgumentParser()
-    parser.add_argument("-b", "--batches", type=int, default=100)
-    parser.add_argument("-p", "--particles", type=int, default=int(1e9))
-    parser.add_argument("-s", "--threads", type=int)
-    parser.add_argument("-c", "--cwd", type=str)
+    parser.add_argument("-b", "--batches", type=int, default=100,
+                        help='Number of batches to simulate (int)')
+    parser.add_argument("-p", "--particles", type=int,
+                        default=int(1e9), help='Number of particles per batch (int)')
+    parser.add_argument("-s", "--threads", type=int,
+                        help='Number of threads to use in the simulation (int)')
 
     args = parser.parse_args()
 

models/fns_duct/postprocessing.ipynb

@@ -41,9 +41,9 @@
    "outputs": [],
    "source": [
     "# read sinbad data\n",
-    "experiment_file = ofb.ResultsFromDatabase('experiment.h5', path='results_database')\n",
-    "mcnp_jendl33_file = ofb.ResultsFromDatabase('mcnp-4b-c_jendl33.h5', path='results_database')\n",
-    "mcnp_fendl2_file = ofb.ResultsFromDatabase('mcnp-4b-c_fendl2.h5', path='results_database')"
+    "experiment_file = ofb.ResultsFromDatabase('results_database/experiment.h5')\n",
+    "mcnp_jendl33_file = ofb.ResultsFromDatabase('results_database/mcnp-4b-c_jendl33.h5')\n",
+    "mcnp_fendl2_file = ofb.ResultsFromDatabase('results_database/mcnp-4b-c_fendl2.h5')"
    ]
   },
   {
@@ -53,8 +53,8 @@
    "outputs": [],
    "source": [
     "# read openmc results in results_database/\n",
-    "openmc_fendl3_file = ofb.ResultsFromDatabase('openmc-0-14-0_fendl32b.h5', path='results_database')\n",
-    "openmc_endfb8_file = ofb.ResultsFromDatabase('openmc-0-14-0_endfb80.h5', path='results_database')"
+    "openmc_fendl3_file = ofb.ResultsFromDatabase('results_database/openmc-0-14-0_fendl32b.h5')\n",
+    "openmc_endfb8_file = ofb.ResultsFromDatabase('results_database/openmc-0-14-0_endfb80.h5')"
    ]
   },
   {

models/fns_duct/run_and_store.py

@@ -13,9 +13,12 @@
 def _parse_args():
     """Parse and return commandline arguments"""
     parser = argparse.ArgumentParser()
-    parser.add_argument("-x", "--xslib", type=str)
-    parser.add_argument("-t", "--when", type=str, default='n/a')
-    parser.add_argument("-w", "--where", type=str, default='n/a')
+    parser.add_argument("-x", "--xslib", type=str,
+                        help="Strign with Cross section library name and version (e.g. 'FENDL-2.3')")
+    parser.add_argument("-t", "--when", type=str, default='n/a',
+                        help="String with the month and year the simulation is run as (e.g. 'June 2021')")
+    parser.add_argument("-w", "--where", type=str, default='n/a',
+                        help="String with the place/institution where the simulation is run (e.g. 'MIT-PSFC')")
 
     args = parser.parse_args()
 
@@ -41,7 +44,7 @@ def main():
     p.wait()
 
     # read statepoint file
-    openmc_file = ofb.ResultsFromOpenmc('statepoint.100.h5', 'results')
+    openmc_file = ofb.ResultsFromOpenmc('results/statepoint.100.h5')
 
     # store activation foil results
     xaxis_name = 'Detector No.'

notebooks/plotting_results.ipynb

@@ -33,10 +33,10 @@
    "outputs": [],
    "source": [
     "# experimental results\n",
-    "experiment_file = ofb.ResultsFromDatabase(filename='experiment.h5', path='example_database')\n",
+    "experiment_file = ofb.ResultsFromDatabase(file='example_database/experiment.h5')\n",
     "experiment_results = experiment_file.get_tally_dataframe(tally_name='rr_nb93')\n",
     "# mcnp results \n",
-    "mcnp_file = ofb.ResultsFromDatabase('mcnp-4b-c_fendl2.h5', path='example_database')\n",
+    "mcnp_file = ofb.ResultsFromDatabase(file='example_database/mcnp-4b-c_fendl2.h5')\n",
     "mcnp_results = mcnp_file.get_tally_dataframe(tally_name='rr_nb93')"
    ]
   },

notebooks/push_openmc_to_database.ipynb

@@ -31,7 +31,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "openmc_results = ofb.ResultsFromOpenmc(statepoint_file='example_statepoint.100.h5', path='example_results')"
+    "openmc_results = ofb.ResultsFromOpenmc(file='example_results/example_statepoint.100.h5')"
    ]
   },
   {
@@ -472,7 +472,7 @@
     }
    ],
    "source": [
-    "openmc_file = ofb.ResultsFromDatabase(filename='openmc-0-13-3_fendl32b.h5', path='example_database')\n",
+    "openmc_file = ofb.ResultsFromDatabase(file='example_database/openmc-0-13-3_fendl32b.h5')\n",
     "openmc_file.get_tally_dataframe(tally_name='rr_onaxis1_nb93')"
    ]
   },