Merge pull request #39 from LukeSeifert/cleanup

Cleanup

Author: bryanjp05

.gitignore

@@ -174,10 +174,6 @@ cython_debug/
 /examples/huynh_2014/postproc.json
 /examples/huynh_2014/images/*
 
-/examples/empty_run/*.csv
-/examples/empty_run/postproc.json
-/examples/empty_run/images/*
-
 /examples/msre/*.csv
 /examples/msre/postproc.json
 /examples/msre/images/*

README.md

@@ -47,6 +47,20 @@ cumulative fission yields (with energy dependence based on nearest energy)
 - [IAEA data](https://www-nds.iaea.org/beta-delayed-neutron/database.html): 
 these give emission probabilities and half-lives
 
+Some data are provided without additional downloading steps.
+These data include: chemical reprocessing schemes and group parameter data.
+- Chemical removal rates provided should represent *scaled* removal (the removal
+rate applied to the entire volume). This is generally how the data is presented 
+in the literature. The scripts assume the data is in this form. The user input 
+captures this effect via the `base_removal_scaling`. This term represents, as a 
+value from 0 to 1, the ex-core fraction (assuming chemical removal in the that 
+region). Whatever chemical removal rates are used, this term should represent 
+the scaling that has been applied to that data (for example, if the removal 
+occurs everywhere in the primary loop, then the scaling would be 1.0 since this 
+term captures the spatial component.)
+- The group parameter data from the literature should be given as absolute 
+yields (calculable from the relative yield and total yield values).
+
 ### Processing
 Processing consists of three steps:
 1. Generate concentrations (or collect fission yield data).
@@ -73,11 +87,9 @@ including analysis of each step.
 ## Using the tool from source
 Download the repository from GitHub.
 The environment will also to be created by running 
-`conda env create -f environment.yml`.
+`mamba env create -f environment.yml`.
 This should be followed with `conda activate mosdenv` to activate 
 the environment.
-Run `pip install -e .` to make the package available to use on the command line 
-as `mosden` in the `mosdenv` environment.
 Download the data used in tests by running `bash download_data.sh`.
 Check that tests pass by running `pytest` or `pytest -m "not slow"` for the 
 faster version.
@@ -103,4 +115,4 @@ various debug outputs.
 - [<20] is the info level (This is the suggested level)
 - [<30] is the warning level
 - [<40] is the error level
-- [<50] is the critical level
+- [<50] is the critical level

download_data.sh

@@ -56,7 +56,7 @@ NFY_URL="https://www.nndc.bnl.gov/endf-b${INTEGER_VALUE}.${DIGIT_PART}/zips/${NF
 echo "Downloading NFY data for ENDF/B-${ENDF_VERSION}..."
 TEMP_ZIP="${NFY_DIR}/${NFY_ZIP_NAME}"
 echo "Accessing ${NFY_URL}"
-wget --show-progress -O "$TEMP_ZIP" "$NFY_URL"
+wget -4 --show-progress -O "$TEMP_ZIP" "$NFY_URL"
 echo "Extracting NFY data..."
 unzip "$TEMP_ZIP" -d "$NFY_DIR"
 rm "$TEMP_ZIP"
@@ -68,7 +68,7 @@ decay_URL="https://www.nndc.bnl.gov/endf-b${INTEGER_VALUE}.${DIGIT_PART}/zips/${
 echo "Downloading decay data for ENDF/B-${ENDF_VERSION}..."
 TEMP_ZIP="${decay_DIR}/${decay_ZIP_NAME}"
 echo "Accessing ${decay_URL}"
-wget --show-progress -O "$TEMP_ZIP" "$decay_URL"
+wget -4 --show-progress -O "$TEMP_ZIP" "$decay_URL"
 echo "Extracting decay data..."
 unzip "$TEMP_ZIP" -d "$decay_DIR"
 rm "$TEMP_ZIP"
@@ -101,7 +101,7 @@ 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}" "$JEFF_URL"
+wget -4 --show-progress --recursive --no-parent --accept "*.zip" --no-host-directories --cut-dirs=3 -P "${JEFF_DIR}" "$JEFF_URL"
 echo "Extracting NFY data..."
 for f in "$NFY_DIR"/*.zip; do
     unzip "$f" -d "$NFY_DIR"
@@ -120,20 +120,20 @@ IAEA_URL="https://www-nds.iaea.org/relnsd/delayedn/eval.csv"
 mkdir -p "$IAEA_DIR"
 
 echo "Downloading IAEA delayed neutron data..."
-wget -q --show-progress -O "$IAEA_FILE" "$IAEA_URL"
+wget -4 -q --show-progress -O "$IAEA_FILE" "$IAEA_URL"
 echo "Saved to $IAEA_FILE"
 
 # /IAEA --------------------------------------------------------------------
 
 # OpenMC --------------------------------------------------------------------
 OPENMC_DIR="${ENDF_DIR}/omcchain/"
 mkdir -p "$OPENMC_DIR"
-wget -q --show-progress -O "${OPENMC_DIR}chain_casl_pwr.xml" "https://anl.box.com/shared/static/3nvnasacm2b56716oh5hyndxdyauh5gs.xml"
-wget -q --show-progress -O "${OPENMC_DIR}chain_casl_sfr.xml" "https://anl.box.com/shared/static/9fqbq87j0tx4m6vfl06pl4ccc0hwamg9.xml"
+wget -4 -q --show-progress -O "${OPENMC_DIR}chain_casl_pwr.xml" "https://anl.box.com/shared/static/3nvnasacm2b56716oh5hyndxdyauh5gs.xml"
+wget -4 -q --show-progress -O "${OPENMC_DIR}chain_casl_sfr.xml" "https://anl.box.com/shared/static/9fqbq87j0tx4m6vfl06pl4ccc0hwamg9.xml"
 if [[ "${ENDF_VERSION}" == "VII.1" ]]; then
-  wget -q --show-progress -O "${OPENMC_DIR}chain_endfb71_pwr.xml" "https://anl.box.com/shared/static/os1u896bwsbopurpgas72bi6aij2zzdc.xml"
-  wget -q --show-progress -O "${OPENMC_DIR}chain_endfb71_sfr.xml" "https://anl.box.com/shared/static/9058zje1gm0ekd93hja542su50pccvj0.xml"
+  wget -4 -q --show-progress -O "${OPENMC_DIR}chain_endfb71_pwr.xml" "https://anl.box.com/shared/static/os1u896bwsbopurpgas72bi6aij2zzdc.xml"
+  wget -4 -q --show-progress -O "${OPENMC_DIR}chain_endfb71_sfr.xml" "https://anl.box.com/shared/static/9058zje1gm0ekd93hja542su50pccvj0.xml"
 elif [[ "${ENDF_VERSION}" == "VIII.0" ]]; then
-  wget -q --show-progress -O "${OPENMC_DIR}chain_endfb71_pwr.xml" "https://anl.box.com/shared/static/nyezmyuofd4eqt6wzd626lqth7wvpprr.xml"
-  wget -q --show-progress -O "${OPENMC_DIR}chain_endfb71_sfr.xml" "https://anl.box.com/shared/static/x3kp739hr5upmeqpbwx9zk9ep04fnmtg.xml"
+  wget -4 -q --show-progress -O "${OPENMC_DIR}chain_endfb71_pwr.xml" "https://anl.box.com/shared/static/nyezmyuofd4eqt6wzd626lqth7wvpprr.xml"
+  wget -4 -q --show-progress -O "${OPENMC_DIR}chain_endfb71_sfr.xml" "https://anl.box.com/shared/static/x3kp739hr5upmeqpbwx9zk9ep04fnmtg.xml"
 fi

environment.yml

@@ -1,158 +1,17 @@
 name: mosdenv
 channels:
   - conda-forge
-  - defaults
 dependencies:
-  - _libgcc_mutex=0.1
-  - _openmp_mutex=4.5
-  - asttokens=3.0.0
-  - blosc=1.21.6
-  - brotli=1.1.0
-  - brotli-bin=1.1.0
-  - bzip2=1.0.8
-  - c-ares=1.34.5
-  - ca-certificates=2025.10.5
-  - cached-property=1.5.2
-  - cached_property=1.5.2
-  - colorama=0.4.6
-  - contourpy=1.3.3
-  - cycler=0.12.1
-  - dagmc=3.2.4
-  - decorator=5.2.1
-  - eigen=3.4.0
-  - endf=0.1.4
-  - exceptiongroup=1.3.0
-  - executing=2.2.0
-  - fonttools=4.59.0
-  - freetype=2.13.3
-  - future=1.0.0
-  - h5py=3.13.0
-  - hdf4=4.2.15
-  - hdf5=1.14.3
-  - iniconfig=2.0.0
-  - ipython=9.4.0
-  - ipython_pygments_lexers=1.1.1
-  - jedi=0.19.2
-  - jinja2=3.1.6
-  - keyutils=1.6.1
-  - kiwisolver=1.4.8
-  - krb5=1.21.3
-  - lcms2=2.17
-  - ld_impl_linux-64=2.44
-  - lerc=4.0.0
-  - libaec=1.1.4
-  - libblas=3.9.0
-  - libbrotlicommon=1.1.0
-  - libbrotlidec=1.1.0
-  - libbrotlienc=1.1.0
-  - libcblas=3.9.0
-  - libcurl=8.14.1
-  - libdeflate=1.24
-  - libedit=3.1.20250104
-  - libev=4.33
-  - libexpat=2.7.1
-  - libffi=3.4.6
-  - libfreetype=2.13.3
-  - libfreetype6=2.13.3
-  - libgcc=15.1.0
-  - libgcc-ng=15.1.0
-  - libgfortran=15.1.0
-  - libgfortran5=15.1.0
-  - libgomp=15.1.0
-  - libiconv=1.18
-  - libjpeg-turbo=3.1.0
-  - liblapack=3.9.0
-  - liblzma=5.8.1
-  - libnetcdf=4.9.2
-  - libnghttp2=1.64.0
-  - libnsl=2.0.1
-  - libopenblas=0.3.30
-  - libpng=1.6.50
-  - libsqlite=3.50.4
-  - libssh2=1.11.1
-  - libstdcxx=15.1.0
-  - libstdcxx-ng=15.1.0
-  - libtiff=4.7.0
-  - libuuid=2.38.1
-  - libwebp-base=1.6.0
-  - libxcb=1.17.0
-  - libxcrypt=4.4.36
-  - libxml2=2.13.8
-  - libxslt=1.1.43
-  - libzip=1.11.2
-  - libzlib=1.3.1
-  - lxml=6.0.0
-  - lz4-c=1.10.0
-  - markupsafe=3.0.2
-  - matplotlib-base=3.10.5
-  - matplotlib-inline=0.1.7
-  - metis=5.1.0
-  - moab=5.5.1
-  - munkres=1.1.4
-  - ncrystal=4.2.6
-  - ncrystal-core=4.2.6
-  - ncrystal-lib=4.2.6
-  - ncrystal-python=4.2.6
-  - ncurses=6.5
-  - njoy2016=2016.78
-  - numpy=2.3.2
-  - openjpeg=2.5.3
-  - openmc=0.15.2
-  - openssl=3.5.4
-  - packaging=25.0
-  - pandas=2.3.1
-  - parso=0.8.4
-  - patsy=1.0.1
-  - pexpect=4.9.0
-  - pickleshare=0.7.5
-  - pillow=11.3.0
-  - pip=25.2
-  - pluggy=1.6.0
-  - prompt-toolkit=3.0.51
-  - pthread-stubs=0.4
-  - ptyprocess=0.7.0
-  - pure_eval=0.2.3
-  - pygments=2.19.2
-  - pyparsing=3.2.3
-  - pytest=8.4.1
-  - python=3.12.11
-  - python-dateutil=2.9.0.post0
-  - python-tzdata=2025.2
-  - python_abi=3.12
-  - pytz=2025.2
-  - qhull=2020.2
-  - readline=8.2
-  - scipy=1.16.0
-  - seaborn=0.13.2
-  - seaborn-base=0.13.2
-  - setuptools=80.9.0
-  - six=1.17.0
-  - snappy=1.2.2
-  - stack_data=0.6.3
-  - statsmodels=0.14.5
-  - tempest-remap=2.2.0
-  - tk=8.6.13
-  - tomli=2.2.1
-  - tqdm=4.67.1
-  - traitlets=5.14.3
-  - typing_extensions=4.14.1
-  - tzdata=2025b
-  - uncertainties=3.2.3
-  - unicodedata2=16.0.0
-  - wcwidth=0.2.13
-  - wheel=0.45.1
-  - xorg-libxau=1.0.12
-  - xorg-libxdmcp=1.1.5
-  - zlib=1.3.1
-  - zstd=1.5.7
+  - python=3.12
+  - numpy
+  - pip
+  - pytest
+  - pandas
+  - uncertainties
+  - scipy
+  - tqdm
+  - openmc
+  - seaborn
   - pip:
-    - https://github.com/terrapower/armi/archive/main.zip
-    - coverage==7.10.5
-    - ordered-set==4.1.0
-    - pydoe==0.3.8
-    - pyevtk==1.6.0
-    - ruamel-yaml==0.18.15
-    - ruamel-yaml-clib==0.2.12
-    - toml==0.10.2
-    - voluptuous==0.15.2
-    - yamlize==0.7.1
+      - -e .
+      - https://github.com/terrapower/armi/archive/main.zip

examples/empty_run/input.json

@@ -37,13 +37,13 @@
         "incore_s": 10,
         "excore_s": 0,
         "net_irrad_s": 420,
-        "decay_time": 1200,
+        "decay_time": 120,
         "num_decay_times": 800
     },
     "group_options": {
         "num_groups": 6,
         "method": "nlls",
-        "samples": 5000,
+        "samples": 1,
         "sample_func": "normal"
     }
 }

examples/iaea_matching/input.json

@@ -46,7 +46,7 @@
     "group_options": {
         "num_groups": 6,
         "method": "nlls",
-        "samples": 1000,
+        "samples": 100,
         "sample_func": "uniform"
     }
-}
+}

examples/keepin_1957/input.json

@@ -17,7 +17,7 @@
         "cross_section": "",
         "emission_probability": "iaea/eval.csv",
         "fission_yield": "endfb71/nfy/",
-        "decay_time_spacing": "log",
+        "decay_time_spacing": "linear",
         "temperature_K": 920,
         "density_g_cm3": 2.3275,
         "energy_MeV": 0.0253e-6,

examples/prelim_results/input.json

@@ -5,7 +5,7 @@
 import shutil
 from copy import deepcopy
 import subprocess
-from mosden.utils.chemical_schemes import MSBR_scheme
+from mosden.utils.chemical_schemes import Reprocessing
 
 base_input_file = './input.json'
 analysis_list = list()
@@ -32,8 +32,8 @@
         'run_post': False,
         'overwrite': True
     },
-    'reprocessing': [MSBR_scheme(),
-                     MSBR_scheme(include_long=False)],
+    'reprocessing': [Reprocessing(base_input_file).removal_scheme(),
+                     Reprocessing(base_input_file).removal_scheme(include_long=False)],
     'incore_s': [10],
     'excore_s': [10],
     'multi_id': [name]
@@ -48,8 +48,8 @@
         'run_post': False,
         'overwrite': True
     },
-    'reprocessing': [MSBR_scheme(),
-                     MSBR_scheme(rate_scaling=0.0)],
+    'reprocessing': [Reprocessing(base_input_file).removal_scheme(),
+                     Reprocessing(base_input_file).removal_scheme(rate_scaling=0.0)],
     'incore_s': [10],
     'excore_s': [10],
     'multi_id': [name]
@@ -77,7 +77,7 @@
         'run_post': False,
         'overwrite': True
     },
-    'num_decay_times': [50, 100, 200, 400, 800],
+    'num_decay_times': [50, 100, 150, 200, 250, 400, 800],
     'multi_id': [name]
 }
 analysis_list.append(decay_times_analysis)
@@ -99,8 +99,8 @@
 detailed_decay_analysis = {
     'meta': {
         'name': name,
-        'run_full': True,
-        'run_post': False,
+        'run_full': False,
+        'run_post': True,
         'overwrite': True
     },
     'decay_time': [1200, 2400],