Adds ENDF/B-VII.1 (emission probability and half-life) data and JEFF-3.1.1 (cumulative fission yield) data

.gitignore

@@ -182,6 +182,15 @@ cython_debug/
 /examples/msre/postproc.json
 /examples/msre/images/*
 
+/examples/pure_endfb71/*.csv
+/examples/pure_endfb71/postproc.json
+/examples/pure_endfb71/images/*
+
+/examples/iaea_matching/*.csv
+/examples/iaea_matching/postproc.json
+/examples/iaea_matching/images/*
+
+
 /examples/prelim_results/*
 !/examples/prelim_results/input.json
 !/examples/prelim_results/results_generator.py

README.md

@@ -1,6 +1,9 @@
 # MoSDeN
-Molten Salt Delayed Neutron (MoSDeN) is a tool used for reconstruction of 
+Molten Salt Delayed Neutron (MoSDeN) is a tool used for generation of 
 delayed neutron precursor groups in molten salt reactors.
+This tool can also be used for traditional light water reactors, as users
+can adjust ex-core residence times of fissile samples to be zero and chemical
+removal rates to be zero.
 
 ## History
 This tool had a previous version in this repository accessible with 
@@ -26,9 +29,12 @@ The exact organization of raw, unprocessed data is flexible, with some notable
 exceptions:
 - OpenMC chain files to be should all be in a subdirectory labeled with 
 "omcchain" (see `preprocessing.py` for all keywords)
-- ENDF NFY data should all be in a subdirectory labeled `nfy`
+- ENDF fission yield data should all be in a subdirectory labeled `nfy`
+- JEFF fission yield data should all be in a subdirectory labeled `nfpy`
 - ENDF NFY files should be named "nfy-<ZZZ>_<ID>_<AAA>.csv", so 235U would be 
 `nfy-092_U_235.csv`.
+- JEFF NFPY files should be named "nfpy_<NUMS>_<ZZ>-<ID>-<AAA>.dat", so 235U
+would be `nfpy_3542_92-U-235.dat` (the `NUMS` value meaning is unclear).
 - IAEA beta-delayed neutron emission data should be in a directory `iaea` and 
 be called `eval.csv` (default when downloading data).
 

download_data.sh

@@ -18,6 +18,7 @@ roman_to_int() {
 }
 
 DATA_DIR="mosden/data/unprocessed"
+mkdir -p "$DATA_DIR"
 
 # ENDF --------------------------------------------------------------------
 ENDF_VERSION="VII.1"
@@ -29,8 +30,6 @@ if [[ ! " ${ALLOWED_VERSIONS[*]} " =~ " ${ENDF_VERSION} " ]]; then
     exit 1
 fi
 
-mkdir -p "$DATA_DIR"
-
 LOWERCASE_VERSION=$(echo "${ENDF_VERSION//./}" | tr '[:upper:]' '[:lower:]')
 
 ROMAN_PART="${LOWERCASE_VERSION//[0-9]/}"
@@ -40,27 +39,80 @@ LOWERCASE_VERSION="${INTEGER_VALUE}${DIGIT_PART}"
 
 ENDF_DIR="${DATA_DIR}/endfb${LOWERCASE_VERSION}"
 NFY_DIR="${ENDF_DIR}"
+decay_DIR="${ENDF_DIR}"
 mkdir -p "$NFY_DIR"
 
 if [[ "${ENDF_VERSION}" == "VII.1" ]]; then
   SEPARATOR="-"
+  decay_SEPARATOR="-"
 elif [[ "${ENDF_VERSION}" == "VIII.0" ]]; then
   SEPARATOR="_"
+  decay_SEPARATOR="_"
 fi
 
 NFY_ZIP_NAME="ENDF-B-${ENDF_VERSION}${SEPARATOR}nfy.zip"
-NFY_URL="https://www.nndc.bnl.gov/endf-b7.1/zips/${NFY_ZIP_NAME}"
+NFY_URL="https://www.nndc.bnl.gov/endf-b${INTEGER_VALUE}.${DIGIT_PART}/zips/${NFY_ZIP_NAME}"
 
 echo "Downloading NFY data for ENDF/B-${ENDF_VERSION}..."
 TEMP_ZIP="${NFY_DIR}/${NFY_ZIP_NAME}"
+echo "Accessing ${NFY_URL}"
 wget --show-progress -O "$TEMP_ZIP" "$NFY_URL"
 echo "Extracting NFY data..."
 unzip "$TEMP_ZIP" -d "$NFY_DIR"
 rm "$TEMP_ZIP"
 echo "NFY data handled"
 
+decay_ZIP_NAME="ENDF-B-${ENDF_VERSION}${decay_SEPARATOR}decay.zip"
+decay_URL="https://www.nndc.bnl.gov/endf-b${INTEGER_VALUE}.${DIGIT_PART}/zips/${decay_ZIP_NAME}"
+
+echo "Downloading decay data for ENDF/B-${ENDF_VERSION}..."
+TEMP_ZIP="${decay_DIR}/${decay_ZIP_NAME}"
+echo "Accessing ${decay_URL}"
+wget --show-progress -O "$TEMP_ZIP" "$decay_URL"
+echo "Extracting decay data..."
+unzip "$TEMP_ZIP" -d "$decay_DIR"
+rm "$TEMP_ZIP"
+echo "Decay data handled"
+
 # /ENDF --------------------------------------------------------------------
 
+
+
+# JEFF --------------------------------------------------------------------
+JEFF_VERSION="3.1.1"
+ALLOWED_VERSIONS=("3.1.1")
+
+if [[ ! " ${ALLOWED_VERSIONS[*]} " =~ " ${JEFF_VERSION} " ]]; then
+    echo "Error: Invalid JEFF version '${JEFF_VERSION}'"
+    echo "Allowed versions: ${ALLOWED_VERSIONS[*]}"
+    exit 1
+fi
+JEFF_VERSION_NOP="${JEFF_VERSION//./}"
+
+JEFF_DIR="${DATA_DIR}/jeff${JEFF_VERSION_NOP}"
+NFY_DIR="${JEFF_DIR}/nfpy/"
+mkdir -p "$NFY_DIR"
+echo "Saving data to ${NFY_DIR}"
+
+if [[ "${JEFF_VERSION}" == "3.1.1" ]]; then
+  JEFF_URL="https://www-nds.iaea.org/public/download-endf/JEFF-${JEFF_VERSION}/nfpy/"
+fi
+
+
+echo "Downloading NFY data for JEFF-${JEFF_VERSION}..."
+echo "Accessing ${JEFF_URL}"
+wget --show-progress --recursive --no-parent --accept "*.zip" --no-host-directories --cut-dirs=3 -P "${JEFF_DIR}" "$JEFF_URL"
+echo "Extracting NFY data..."
+for f in "$NFY_DIR"/*.zip; do
+    unzip "$f" -d "$NFY_DIR"
+done
+echo "Removing zip files..."
+rm "$NFY_DIR"/*.zip
+echo "NFY data handled"
+
+
+# /JEFF --------------------------------------------------------------------
+
 # IAEA --------------------------------------------------------------------
 IAEA_DIR="${DATA_DIR}/iaea"
 IAEA_FILE="$IAEA_DIR/eval.csv"

examples/empty_run/input.json

@@ -0,0 +1 @@
+{}

examples/iaea_matching/input.json

@@ -0,0 +1,49 @@
+{
+    "name": "IAEA",
+    "file_options": {
+        "overwrite": {
+            "preprocessing": true,
+            "concentrations": true,
+            "count_rate": true,
+            "group_fitting": true,
+            "postprocessing": true,
+            "logger": true
+        },
+        "unprocessed_data_dir": "/home/luke/github/mosden/mosden/data/unprocessed/",
+        "log_level": 20
+    },
+    "data_options": {
+        "half_life": "iaea/eval.csv",
+        "cross_section": "",
+        "emission_probability": "iaea/eval.csv",
+        "fission_yield": "jeff311/nfpy/",
+        "decay_time_spacing": "log",
+        "temperature_K": 920,
+        "density_g_cm3": 2.3275,
+        "energy_MeV": 0.0253e-6,
+        "fissile_fractions": {
+            "U235": 1.0
+        }
+    },
+    "modeling_options": {
+        "parent_feeding": false,
+        "concentration_handling": "CFY",
+        "count_rate_handling": "data",
+        "reprocessing_locations": ["excore"],
+        "reprocessing": {
+            "Xe": 0.0
+        },
+        "irrad_type": "saturation",
+        "incore_s": 10,
+        "excore_s": 0,
+        "net_irrad_s": 420,
+        "decay_time": 1200,
+        "num_decay_times": 800
+    },
+    "group_options": {
+        "num_groups": 6,
+        "method": "nlls",
+        "samples": 5000,
+        "sample_func": "normal"
+    }
+}

examples/prelim_results/contribution_plots.py

@@ -34,7 +34,6 @@
 
 all_data = [yields, counts, concs]
 all_nucs = [
-    'Other',
     'Ge86',
     'I137',
     'As86',
@@ -45,7 +44,8 @@
     'Br88',
     'Br87',
     'Cs141',
-    'Te136'
+    'Te136',
+    'Other'
 ]
 all_nucs.reverse()
 postobj = PostProcess(None)
@@ -63,18 +63,13 @@
         colors.append(color_nucs[k])
         if k != 'Other':
             k = postobj._convert_nuc_to_latex(k)
-        labels.append(k)
+        labels.append(k + ', ' + str(round(v)) + '\%')
 
-    fig, ax = plt.subplots()
-    _, _, autotexts = ax.pie(sizes, labels=labels, autopct='%1.1f%%',
-            pctdistance=0.7, labeldistance=1.1,
+    fig, ax = plt.subplots(subplot_kw=dict(aspect='equal'))
+    _, _ = ax.pie(sizes, labels=labels, labeldistance=1.1,
             colors=colors)
     ax.axis('equal')
 
-    for i, autotext in enumerate(autotexts):
-        autotext.set_color('black')
-        autotext.set_path_effects([path_effects.Stroke(linewidth=2.0, foreground='white'),
-                                   path_effects.Normal()])
     plt.tight_layout()
     fig.savefig(f'{counter}dnp_yield.png')
     plt.close()

examples/pure_endfb71/input.json

@@ -0,0 +1,55 @@
+{
+    "name": "ENDFB71 Data",
+    "file_options": {
+        "overwrite": {
+            "preprocessing": true,
+            "concentrations": true,
+            "count_rate": true,
+            "group_fitting": true,
+            "postprocessing": true,
+            "logger": true
+        },
+        "unprocessed_data_dir": "/home/luke/github/mosden/mosden/data/unprocessed/",
+        "processed_data_dir": "/home/luke/github/mosden/examples/pure_endfb71/",
+        "output_dir": "/home/luke/github/mosden/examples/pure_endfb71/",
+        "log_level": 20,
+        "log_file": "/home/luke/github/mosden/examples/pure_endfb71/log.log"
+    },
+    "data_options": {
+        "half_life": "endfb71/decay/",
+        "cross_section": "",
+        "emission_probability": "endfb71/decay/",
+        "fission_yield": "endfb71/nfy/",
+        "decay_time_spacing": "log",
+        "temperature_K": 920,
+        "density_g_cm3": 2.3275,
+        "energy_MeV": 0.0253e-6,
+        "fissile_fractions": {
+            "U235": 1.0
+        }
+    },
+    "modeling_options": {
+        "parent_feeding": false,
+        "concentration_handling": "CFY",
+        "count_rate_handling": "data",
+        "reprocessing_locations": ["excore"],
+        "reprocessing": {
+            "Xe": 0.0
+        },
+        "irrad_type": "saturation",
+        "incore_s": 10,
+        "excore_s": 0,
+        "net_irrad_s": 420,
+        "decay_time": 1200,
+        "num_decay_times": 800
+    },
+    "group_options": {
+        "num_groups": 6,
+        "method": "nlls",
+        "samples": 5000,
+        "sample_func": "normal"
+    },
+    "post_options": {
+        "sensitivity_subplots": true
+    }
+}

mosden/base.py

@@ -20,8 +20,9 @@ def __init__(self, input_path: str) -> None:
             Path to the input file
         """
         self.omc_data_words: list[str] = ['omcchain']
-        self.endf_data_words: list[str] = ['nfy']
+        self.endf_data_words: list[str] = ['nfy', 'decay']
         self.iaea_data_words: list[str] = ['iaea']
+        self.jeff_data_words: list[str] = ['jeff']
 
         self.input_path: str = input_path
         self.input_handler: InputHandler = InputHandler(input_path)

mosden/groupfit.py

@@ -9,6 +9,7 @@
 from time import time
 import warnings
 from tqdm import tqdm
+from scipy.linalg import svd
 
 
 class Grouper(BaseClass):
@@ -97,6 +98,7 @@ def _residual_function(
             parameters: np.ndarray[float],
             times: np.ndarray[float],
             counts: np.ndarray[float],
+            count_err: np.ndarray[float],
             fit_func: Callable) -> float:
         """
         Calculate the residual of the current set of parameters
@@ -108,7 +110,9 @@ def _residual_function(
         times : np.ndarray[float]
             List of times
         counts : np.ndarray[float]
-            List of nominal times
+            List of delayed neutron counts
+        count_err : np.ndarray[float]
+            List of count errors
         fit_func : Callable
             Function that takes times and parameters to return list of counts
 
@@ -117,7 +121,7 @@ def _residual_function(
         residual : float
             Value of the residual
         """
-        residual = (counts - fit_func(times, parameters)) / (counts + 1e-12)
+        residual = (counts - fit_func(times, parameters)) / (counts)
         return residual
 
     def _pulse_fit_function(self,
@@ -267,20 +271,24 @@ def _nonlinear_least_squares(self,
                                xtol=1e-12,
                                verbose=0,
                                max_nfev=1e5,
-                               args=(times, counts, fit_function))
-
+                               args=(times, counts, count_err, fit_function))
+        J = result.jac
+        s = svd(J, compute_uv=False)
+        condition_number = s[0] / s[-1]
+        self.logger.info(f'{condition_number = }')
         sampled_params: list[float] = list()
         tracked_counts: list[float] = list()
         sorted_params = self._sort_params_by_half_life(result.x)
         sampled_params.append(sorted_params)
         countrate = CountRate(self.input_path)
         self.logger.info(f'Currently using {self.sample_func} sampling')
         for _ in tqdm(range(1, self.MC_samples), desc='Solving least-squares'):
-            data = countrate.calculate_count_rate(
-                MC_run=True, sampler_func=self.sample_func)
-            count_sample = data['counts']
             with warnings.catch_warnings():
                 warnings.simplefilter('ignore')
+                data = countrate.calculate_count_rate(
+                    MC_run=True, sampler_func=self.sample_func)
+                count_sample = data['counts']
+                count_sample_err = data['sigma counts']
                 result = least_squares(
                     self._residual_function,
                     result.x,
@@ -294,6 +302,7 @@ def _nonlinear_least_squares(self,
                     args=(
                         times,
                         count_sample,
+                        count_sample_err,
                         fit_function))
             tracked_counts.append([i for i in count_sample])
             sorted_params = self._sort_params_by_half_life(result.x)