Making the NE case a little more robust and clean.

test/core/flux/FuelFitFluxHandlerTester.cpp

@@ -29,10 +29,44 @@ BOOST_AUTO_TEST_CASE(checkComputeIncidentFlux)
 {
 	// Create the option to create a network
 	xolotl::options::ConfOptions opts;
+
+	// Create a file with reaction data.
+	std::ofstream reactionFile("reaction.dat");
+	reactionFile
+		<< "0 0 1 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "0 1 0 -0.160789024638881 -12.7387253625273 4.2488E+11 4.23317"
+		<< std::endl
+		<< "0 2 0 2.87060634573234 -8.37649260139129 9.9337E+11 3.43830674"
+		<< std::endl
+		<< "1 0 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 1 0 3.14296517286615 -1.4324963007117 0 0" << std::endl
+		<< "1 2 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 3 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 4 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 5 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 6 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 7 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 8 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "Reactions" << std::endl
+		<< "0 0 1 0.00596" << std::endl
+		<< "0 1 0 0.00596" << std::endl
+		<< "0 2 0 0.00596" << std::endl;
+	reactionFile.close();
+
 	// Create a good parameter file
 	std::string parameterFile = "param.txt";
 	std::ofstream paramFile(parameterFile);
 	paramFile << "netParam=5 0 0 5 1" << std::endl
+			  << "reactionFilePath=reaction.dat" << std::endl
 			  << "tempParam=1500" << std::endl;
 	paramFile.close();
 
@@ -61,6 +95,9 @@ BOOST_AUTO_TEST_CASE(checkComputeIncidentFlux)
 	std::vector<NetworkType::SubdivisionRatio> subdivRatios = {
 		{maxXe + 1, maxV + 1, maxI + 1}};
 	NetworkType network(maxSpeciesAmounts, subdivRatios, 1, opts);
+
+	std::remove("reaction.dat");
+
 	// Get its size
 	const int dof = network.getDOF();
 

test/core/network/AlloyNetworkTester.cpp

@@ -1185,7 +1185,7 @@ BOOST_AUTO_TEST_CASE(traits)
 	BOOST_REQUIRE_EQUAL(toNameString(Spec::Frank), "Frank");
 
 	// parseSpeciesId / getSpeciesLabel / getSpeciesName
-    auto network = NetworkType();
+	auto network = NetworkType();
 	auto sid = network.parseSpeciesId("V");
 	BOOST_REQUIRE(sid.cast<Spec>() == Spec::V);
 	BOOST_REQUIRE_EQUAL(network.getSpeciesLabel(sid), "V");

test/core/network/NetworkTester.cpp

@@ -33,6 +33,38 @@ using network_types =
 
 BOOST_AUTO_TEST_CASE_TEMPLATE(defaut_constructor, T, network_types)
 {
+	// Create a file with reaction data for NE.
+	std::ofstream reactionFile("reaction.dat");
+	reactionFile
+		<< "0 0 1 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "0 1 0 -0.160789024638881 -12.7387253625273 4.2488E+11 4.23317"
+		<< std::endl
+		<< "0 2 0 2.87060634573234 -8.37649260139129 9.9337E+11 3.43830674"
+		<< std::endl
+		<< "1 0 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 1 0 3.14296517286615 -1.4324963007117 0 0" << std::endl
+		<< "1 2 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 3 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 4 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 5 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 6 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 7 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 8 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "Reactions" << std::endl
+		<< "0 0 1 0.00596" << std::endl
+		<< "0 1 0 0.00596" << std::endl
+		<< "0 2 0 0.00596" << std::endl;
+	reactionFile.close();
+
 	using NetworkType = T;
 	constexpr auto speciesRange = NetworkType::getSpeciesRange();
 	std::vector<typename NetworkType::AmountType> maxSpeciesAmounts;
@@ -43,6 +75,9 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(defaut_constructor, T, network_types)
 	NetworkType network =
 		NetworkType(maxSpeciesAmounts, 1, xolotl::options::ConfOptions{});
 
+	// Remove the file because it is not needed anymore
+	std::remove("reaction.dat");
+
 	BOOST_REQUIRE(network.getNumClusters() > 0);
 	BOOST_REQUIRE(network.getDOF() > 0);
 	BOOST_REQUIRE(network.getDeviceMemorySize() > 0);

test/interface/InterfaceTester.cpp

@@ -21,6 +21,38 @@ BOOST_AUTO_TEST_SUITE(Interface_testSuite)
 
 BOOST_AUTO_TEST_CASE(simple0D)
 {
+	// Create a file with reaction data.
+	std::ofstream reactionFile("reaction.dat");
+	reactionFile
+		<< "0 0 1 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "0 1 0 -0.160789024638881 -12.7387253625273 4.2488E+11 4.23317"
+		<< std::endl
+		<< "0 2 0 2.87060634573234 -8.37649260139129 9.9337E+11 3.43830674"
+		<< std::endl
+		<< "1 0 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 1 0 3.14296517286615 -1.4324963007117 0 0" << std::endl
+		<< "1 2 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 3 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 4 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 5 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 6 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 7 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "1 8 0 11.2375337876032 22.3998792567472 4.0767E+11 4.08453089"
+		<< std::endl
+		<< "Reactions" << std::endl
+		<< "0 0 1 0.00596" << std::endl
+		<< "0 1 0 0.00596" << std::endl
+		<< "0 2 0 0.00596" << std::endl;
+	reactionFile.close();
+
 	// Create the parameter file
 	std::string parameterFile = "param.txt";
 	std::ofstream paramFile(parameterFile);
@@ -42,6 +74,7 @@ BOOST_AUTO_TEST_CASE(simple0D)
 			  << "material=Fuel" << std::endl
 			  << "dimensions=0" << std::endl
 			  << "process=reaction" << std::endl
+			  << "reactionFilePath=reaction.dat" << std::endl
 			  << "netParam=5 0 0 5 1" << std::endl;
 	paramFile.close();
 
@@ -55,11 +88,13 @@ BOOST_AUTO_TEST_CASE(simple0D)
 	// Get data to check
 	auto concVector = interface.getConcVector();
 	BOOST_REQUIRE_EQUAL(concVector[0][0][0][0].first, 0);
-	BOOST_REQUIRE_CLOSE(concVector[0][0][0][0].second, 400000000, 0.01);
+	BOOST_REQUIRE_CLOSE(concVector[0][0][0][0].second, 220899.426, 0.01);
 	BOOST_REQUIRE_EQUAL(concVector[0][0][0][10].first, 10);
-	BOOST_REQUIRE_EQUAL(concVector[0][0][0][10].second, 0);
+	BOOST_REQUIRE_CLOSE(
+		concVector[0][0][0][10].second, -1.1602146071246332e-23, 0.01);
 
 	std::remove(parameterFile.c_str());
+	std::remove("reaction.dat");
 }
 
 BOOST_AUTO_TEST_SUITE_END()

xolotl/core/include/xolotl/core/Constants.h

@@ -97,9 +97,6 @@ constexpr double alphaZrCSinkStrength = 2.25e-8; // Single crystal
 // constexpr double alphaZrASinkStrength = 2e-5; //cold-worked Zr
 // constexpr double alphaZrCSinkStrength = 5e-6; //cold-worked Zr
 
-constexpr double uConcentration = 24.44;
-// constexpr double uConcentration = 1.0;
-
 constexpr double zFactor = 100.0;
 
 // Tungsten density in nm^-3

xolotl/core/include/xolotl/core/flux/FuelFitFluxHandler.h

@@ -43,6 +43,9 @@ class FuelFitFluxHandler : public FluxHandler
 	// The temperature
 	double temperature;
 
+	// The uranium concentration
+	double uConc;
+
 	// The list of pure vacancy indices
 	std::vector<IdType> pureDefectIds;
 	std::vector<double> pureDefectFactors;
@@ -75,6 +78,9 @@ class FuelFitFluxHandler : public FluxHandler
 	initializeFluxHandler(network::IReactionNetwork& network, int surfacePos,
 		std::vector<double> grid) override
 	{
+		// Get the uranium concentration
+		uConc = 1.0 / network.getAtomicVolume();
+
 		// Set the grid
 		xGrid = grid;
 
@@ -220,7 +226,6 @@ class FuelFitFluxHandler : public FluxHandler
 		auto yield = defectYield;
 		auto xenonYield = xeYield;
 		auto ids = this->fluxIds;
-		auto uConc = core::uConcentration;
 
 		Kokkos::parallel_for(
 			1, KOKKOS_LAMBDA(std::size_t) {

xolotl/core/include/xolotl/core/network/NEReactionNetwork.h

@@ -56,11 +56,11 @@ class NEReactionNetwork : public ReactionNetwork<NEReactionNetwork>
 	getReactionGenerator() const noexcept;
 
 	void
-	readClusters(const std::string filename = "reactionRates.txt");
+	readClusters(const std::string filename = "reaction.dat");
 
 	void
 	readReactions(
-		double temperature, const std::string filename = "reactionRates.txt");
+		double temperature, const std::string filename = "reaction.dat");
 };
 
 namespace detail

xolotl/core/include/xolotl/core/network/ReactionNetwork.h

@@ -762,11 +762,11 @@ class ReactionNetwork : public ReactionNetworkInterface<TImpl>::Type
 	generateClusterData(const ClusterGenerator& generator);
 
 	void
-	readClusters(const std::string filename = "reactionRates.txt");
+	readClusters(const std::string filename = "reaction.dat");
 
 	void
 	readReactions(
-		double temperature, const std::string filename = "reactionRates.txt");
+		double temperature, const std::string filename = "reaction.dat");
 
 	void
 	defineReactions(Connectivity& connectivity);

xolotl/core/src/network/NEReactionNetwork.cpp

@@ -99,7 +99,9 @@ NEReactionNetwork::readClusters(const std::string filename)
 	std::ifstream reactionFile;
 	reactionFile.open(filename);
 	if (!reactionFile.good()) {
-		return;
+		throw std::string("\nIncorrect filename for reading reactions! \n"
+						  "Either provide reaction.dat or set the file path "
+						  "with the reactionFilePath option.");
 	}
 
 	// First find how big of an object we need to create

xolotl/options/src/ConfOptions.cpp

@@ -212,10 +212,10 @@ ConfOptions::readParams(int argc, const char* argv[])
 		bpo::value<fs::path>(&fluxDepthProfileFilePath),
 		"The path to the custom flux profile file; the default is an empty "
 		"string that will use the default material associated flux handler.")(
-		"reactionFilePath", bpo::value<fs::path>(&reactionFilePath),
-		"The path to the reaction rates file; the default is an empty "
-		"string.")("basalPortion",
-		bpo::value<double>(&basalPortion)->default_value(0.1),
+		"reactionFilePath",
+		bpo::value<fs::path>(&reactionFilePath)->default_value("reaction.dat"),
+		"The path to the reaction rates file; the default is reaction.dat .")(
+		"basalPortion", bpo::value<double>(&basalPortion)->default_value(0.1),
 		"The value of the basal portion generated for each V (0.1 by "
 		"default).")("transitionSize",
 		bpo::value<int>(&transitionSize)->default_value(325),

xolotl/options/src/JSONOptions.cpp

@@ -515,7 +515,7 @@ JSONOptions::defineHandlers()
 		.add(
 			"reactionFilePath", ElemType::string,
 			"The path to the reaction rates file.\n"
-			"(default = \"\")",
+			"(default = \"reaction.dat\")",
 			JSON_ELEM_HANDLER { checkSetParam(tree, name, reactionFilePath); })
 		.add(
 			"basalPortion", ElemType::real,

xolotl/options/src/Options.cpp

@@ -86,7 +86,8 @@ Options::Options() :
 	basalPortion(0.1),
 	transitionSize(325),
 	cascadeDose(-1.0),
-	cascadeEfficiency(0.0)
+	cascadeEfficiency(0.0),
+	reactionFilePath("reaction.dat")
 {
 }