Merge branch 'gpr_implementation'

.gitignore

@@ -2,4 +2,7 @@ build
 misc
 commit_msg
 __pycache__
+
+*.egg-info
 *.swp
+*.json

CMakeLists.txt

@@ -120,11 +120,20 @@ FIND_PACKAGE(COIN REQUIRED)
 SET(STUB_INCLUDE_DIRS ${STUB_INCLUDE_DIRS} ${COIN_INCLUDE_DIR})
 set(LIBS ${LIBS} ${COIN_LIBRARIES})
 
+# Find Python and python.h
+FIND_PACKAGE(PythonLibs REQUIRED)
+SET(STUB_INCLUDE_DIRS ${STUB_INCLUDE_DIRS} ${PYTHON_INCLUDE_DIRS})
+
+# Find Niels Lohmann's 'JSON for Modern C++' package
+FIND_PACKAGE(nlohmann_json REQUIRED)
+# The line below does not work!
+# For unknown reasons, CMake does not find the include directories
+# and nlohmann_json_INCLUDE_DIRS is an unset variable.
+SET(STUB_INCLUDE_DIRS ${STUB_INCLUDE_DIRS} ${nlohmann_json_INCLUDE_DIRS})
 
 # include all the directories we just found
 INCLUDE_DIRECTORIES(${STUB_INCLUDE_DIRS})
 
-
 # add the agents
 ADD_SUBDIRECTORY(src)
 

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2020, RWTH Aachen University Nuclear Verification and Disarmament Group
+Copyright (c) 2020-2021, RWTH Aachen University Nuclear Verification and Disarmament Group
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -1,19 +1,34 @@
 # misoenrichment: a Cyclus multi component isotope enrichment module
 
 `misoenrichment` is a module developed at the [Nuclear Verification and Disarmament Group](https://www.nvd.rwth-aachen.de/) at RWTH Aachen University for the nuclear fuel cycle simulator
-[Cyclus](http://fuelcycle.org). It provides a Cyclus facility that enriches 
-uranium streams composed of two or more isotopes taking into account the 
+[Cyclus](http://fuelcycle.org). It currently provides two Cyclus facilities. 
+
+`MIsoEnrich` is an enrichment facility that enriches 
+streams composed of two or more uranium isotopes taking into account the 
 different enrichment behaviour of minor isotopes such as <sup>234</sup>U (present in
 natural as well as in reprocessed uranium) or <sup>236</sup>U (present in 
 reprocessed uranium from spent nuclear fuel). The tracking of minor
 isotopes makes this module suitable for nuclear archaeology, see, e.g., Ref 3.
 
+`GprReactor` is a Cyclus reactor facility that uses Gaussian Process 
+Regression (GPR) to calculate the composition of the irradiated fuel depending
+on various input parameters. Generally, this implementation works for any
+reactor type and any input parameters. However, one needs the appropriate
+GPR model (which needs to be generated using training data) and depending 
+on which input parameters are chosen, the source code of `GprReactor` may
+need minor tweaking. Additional information on this issue will be given
+in future commits.
+
 Table of Contents
-- [Getting Started](#getting-started)
-- [Theoretical background](#theoretical-background)
+- [MIsoEnrich](#misoenrich)
+  - [Getting Started](#getting-started)
+  - [Theoretical background](#theoretical-background)
+- [GprReactor](#gprreactor)
+  - [Requirements](#requirements)
 - [References](#references)
 
-## Getting started
+## MIsoEnrich
+### Getting started
 An example input file is found in `input/main.py` featuring a
 `cycamore::Source` source agent, a `MIsoEnrich` enrichment facility and two
 `cycamore::Sink` agents, one for enriched and one for depleted uranium. 
@@ -34,7 +49,7 @@ level, as explained above) and then blending the product with uranium from
 the feed. This procedure is only performed if the `use_downblending`
 variable is set to `True` in the input file.
 
-## Theoretical background
+### Theoretical background
 The implementation of the facility itself and the interaction with Cyclus'
 Dynamic Resource Exchange is based on the binary enrichment facility from 
 the [Cycamore](https://github.com/cyclus/cycamore) package.
@@ -44,6 +59,31 @@ Ref 1 derives the mathematical formalism of a matched abundance ratio cascade
 using constant overall stage separation factors while Ref 2 gives a new 
 physically founded approach to calculating said separation factors.
 
+## GprReactor
+### Requirements
+This facility needs Niels Lohmann's [JSON for Modern C++](https://json.nlohmann.me/)
+library. It can be downloaded from his [GitHub repository](https://github.com/nlohmann/json)
+or using one of the many package managers, see [here](https://github.com/nlohmann/json#package-managers).
+Successfully tested using `conda install -c conda-forge nlohmann_json` and using `CMake`.
+When using `CMake`, then the package needs to be installed globally 
+(i.e., under `/usr/local`), as shown in the following:
+```
+$ git clone https://github.com/nlohmann/json
+$ cd json
+$ mkdir build
+$cd build
+$ cmake ..
+$ make
+$ sudo make install
+```
+While it _should_ be possible to install `JSON for Modern C++` locally,
+i.e. in `~/.local`, this results in `CMake` not finding `nlohmann/json.hpp`
+during the `misoenrichment` installation. I will hopefully manage to 
+fix this in future versions.
+
+Additionally, one needs `Python3` in combination with the `NumPy` and 
+`SciPy` packages.
+
 ## References
 
 1. E. von Halle, _Multicomponent Isotope Separation in Matched Abundance 

input/archetypes.py

@@ -5,7 +5,9 @@ def archetypes():
              {"lib": "agents", "name": "NullRegion"},
              {"lib": "cycamore", "name": "Sink"},
              {"lib": "cycamore", "name": "Source"},
-             {"lib": "misoenrichment", "name":"MIsoEnrich"}
+             {"lib": "cycamore", "name": "Storage"},
+             {"lib": "misoenrichment", "name": "GprReactor"},
+             {"lib": "misoenrichment", "name": "MIsoEnrich"}
            ]
          }}
 

input/control.py

@@ -2,8 +2,8 @@ def control():
     d = {"control": {
            "startyear": 2020,
            "startmonth": 1,
-           "duration": 12,
-           "dt": 2629846, # duration of a time step in seconds, here: 1 month
+           "duration": 365,
+           "dt": 86400, # duration of a time step in seconds, here: 1 day
            "simhandle": "misoenrichment tutorial file",
            }
         }

input/facility.py

@@ -5,14 +5,13 @@ def facility():
             "config": {"Source": {
               "outcommod": "NaturalU",
               "outrecipe": "NaturalURecipe",
-              "throughput": 2000
+              "throughput": 10000
             }}
           },
           {
-            "name": "EnrichedUSink",
+            "name": "SpentFuelSink",
             "config": {"Sink": {
-              "in_commods": {"val": ["EnrichedU"]},
-              "recipe_name": "EnrichedURecipe"
+              "in_commods": {"val": ["SpentFuel"]}
             }}
           },
           {
@@ -22,6 +21,15 @@ def facility():
               "recipe_name": "DepletedURecipe"
             }}
           },
+          {
+            "name": "FreshFuelStorage",
+            "config": {"Storage": {
+              "in_commods": {"val": ["EnrichedU"]},
+              "out_commods": {"val": ["FreshFuel"]},
+              "in_recipe": ["EnrichedURecipe"],
+              "residence_time": 0
+            }}
+          },
           {
             "name": "EnrichmentFacility",
             "config": {"MIsoEnrich": {
@@ -31,13 +39,28 @@ def facility():
               "tails_commod": "DepletedU",
               "tails_assay": 0.003,
               "initial_feed": 0,
-              "max_feed_inventory": 10000,
+              "max_feed_inventory": 1e299,
               "gamma_235": 1.35,
               "swu_capacity": 1e299,
-              "swu_capacity_vals": {"val": [1e5, 1000, 2000]},
+              "swu_capacity_vals": {"val": [1e5, 5e4, 5e5]},
               "swu_capacity_times": {"val": [0, 5, 6]},
               "use_downblending": True
             }}
+          },
+          {
+            "name": "SavannahRiverReactor",
+            "config": {"GprReactor": {
+              "in_commods": {"val": ["FreshFuel"]},
+              "out_commods": {"val": ["SpentFuel"]},
+              "in_recipes": {"val": ["EnrichedURecipe"]},
+              "n_assem_core": 1,
+              "n_assem_batch": 1,
+              "assem_size": 110820,
+              "cycle_time": 88,
+              "refuel_time": 6,
+              "power_output": 2400,
+              "temperature": 350
+            }}
           }
         ]}
     return d

input/recipe.py

@@ -4,17 +4,19 @@ def recipe():
             "name": "NaturalURecipe",
             "basis": "mass",
             "nuclide": [
-              {"id": "U234", "comp": 5.5e-3},
+              # At the moment (May 2021), U234 is not taken into
+              # account by the Gpr model.
+              #{"id": "U234", "comp": 5.5e-3},
               {"id": "U235", "comp": 0.711},
-              {"id": "U238", "comp": 100 - 0.711 - 5.5e-3}
+              {"id": "U238", "comp": 100 - 0.711}
             ]
           },
           {
             "name": "EnrichedURecipe",
             "basis": "mass",
             "nuclide": [
-              {"id": "U235", "comp": 90},
-              {"id": "U238", "comp": 10}
+              {"id": "U235", "comp": 1.1},
+              {"id": "U238", "comp": 98.9}
             ]
           },
           {

install.py

@@ -37,6 +37,11 @@ def install(args):
     root_dir = os.path.split(__file__)[0]
     makefile = os.path.join(args.build_dir, 'Makefile')
 
+    print("Installing Python (sub)module 'spentfuelgpr'...")
+    spent_fuel_gpr_dir = os.path.join(root_dir, "spentfuelgpr")
+    subprocess.check_call(["pip3", "install", "-e", spent_fuel_gpr_dir])
+    print()
+
     if not os.path.exists(makefile):
         rtn = subprocess.call(['which', 'cmake'], shell=(os.name == 'nt'))
         if rtn != 0:

spentfuelgpr/setup.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from setuptools import setup
+
+def main():
+    setup(
+        name="spentfuelgpr",
+        version="0.1",
+        description="Python part of the MIsoEnrichment module",
+        author="Nuclear Verification and Disarmament Group, RWTH Aachen University",
+        url="https://github.com/maxschalz/miso_enrichment/",
+        license="BSD-3-Clause",
+        packages=["spentfuelgpr"],
+        classifiers=["License :: OSI Approved :: BSD-3-Clause License",
+                     "Programming Language :: Python :: 3"],
+        install_requires=["numpy", "scipy"]
+    )
+    return
+
+if __name__=="__main__":
+    main()

spentfuelgpr/spentfuelgpr/__init__.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Calculate the composition of spent fuel based on a set of trained GPRs.
+
+This module is part of the misoenrichment module for Cyclus, see
+https://github.com/maxschalz/miso_enrichment/ .
+
+The module is strongly based on Antonio Figueroa's work, who kindly
+provided the original code. For more information, please see
+https://doi.org/10.1016/j.anucene.2020.108085
+or https://arxiv.org/abs/2006.12921
+or https://github.com/FigueroaAC/GPs-for-SpentFuel
+"""
+
+__author__ = "Nuclear Verification and Disarmament Group, RWTH Aachen University"
+__copyright__ = "Copyright 2020-2021, Nuclear Verification and Disarmament Group, RWTH Aachen University"
+__credits__ = ["Antonio Figueroa", "Max Schalz"]
+__license__ = "BSD-3-Clause"
+__version__ = "2.0"
+__maintainer__ = "Max Schalz"
+
+from .kernel import *
+from .predict_posterior import *