Added option for initial dilsocation density and skeleton of dislo de…

…nsity equation in the PSI network (ORNL-Fusion#112).
vshah3011 · Aug 17, 2023 · d293466 · d293466
1 parent 3bad2aa
commit d293466
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Showing 21 changed files with 376 additions and 26 deletions.
diff --git a/test/options/OptionsTester.cpp b/test/options/OptionsTester.cpp
@@ -125,6 +125,7 @@ BOOST_AUTO_TEST_CASE(goodParamFile)
 		<< "fissionYield=0.3" << std::endl
 		<< "heVRatio=5.0" << std::endl
 		<< "migrationThreshold=1.0" << std::endl
+		<< "disloDensity=0.5" << std::endl
 		<< "fluxDepthProfileFilePath=path/to/the/flux/profile/file.txt"
 		<< std::endl;
 	goodParamFile.close();
@@ -229,6 +230,9 @@ BOOST_AUTO_TEST_CASE(goodParamFile)
 	// Check the migration threshold option
 	BOOST_REQUIRE_EQUAL(opts.getMigrationThreshold(), 1.0);
 
+	// Check the initial dislocation density option
+	BOOST_REQUIRE_EQUAL(opts.getDislocationDensity(), 0.5);
+
 	// Check the network filename
 	BOOST_REQUIRE_EQUAL(opts.getFluxDepthProfileFilePath(),
 		"path/to/the/flux/profile/file.txt");

diff --git a/xolotl/core/include/xolotl/core/network/AlloyReactionNetwork.h b/xolotl/core/include/xolotl/core/network/AlloyReactionNetwork.h
@@ -39,6 +39,12 @@ class AlloyReactionNetwork : public ReactionNetwork<AlloyReactionNetwork>
 	{
 	}
 
+	KOKKOS_INLINE_FUNCTION
+	void
+	setConnectivity(Connectivity)
+	{
+	}
+
 private:
 	double
 	checkLatticeParameter(double latticeParameter);

diff --git a/xolotl/core/include/xolotl/core/network/FeReactionNetwork.h b/xolotl/core/include/xolotl/core/network/FeReactionNetwork.h
@@ -35,6 +35,12 @@ class FeReactionNetwork : public ReactionNetwork<FeReactionNetwork>
 	IndexType
 	checkLargestClusterId();
 
+	KOKKOS_INLINE_FUNCTION
+	void
+	setConnectivity(Connectivity)
+	{
+	}
+
 private:
 	double
 	checkLatticeParameter(double latticeParameter);

diff --git a/xolotl/core/include/xolotl/core/network/IReactionNetwork.h b/xolotl/core/include/xolotl/core/network/IReactionNetwork.h
@@ -317,6 +317,9 @@ class IReactionNetwork
 	virtual IndexType
 	getLargestClusterId() = 0;
 
+	virtual IndexType
+	getDisloDensityId() = 0;
+
 	/**
 	 * @brief Returns an object representing the the bounds of each
 	 * cluster in each dimension of the phase space.

diff --git a/xolotl/core/include/xolotl/core/network/NEReactionNetwork.h b/xolotl/core/include/xolotl/core/network/NEReactionNetwork.h
@@ -36,6 +36,12 @@ class NEReactionNetwork : public ReactionNetwork<NEReactionNetwork>
 	IndexType
 	checkLargestClusterId();
 
+	KOKKOS_INLINE_FUNCTION
+	void
+	setConnectivity(Connectivity)
+	{
+	}
+
 private:
 	double
 	checkLatticeParameter(double latticeParameter);

diff --git a/xolotl/core/include/xolotl/core/network/PSIReactionNetwork.h b/xolotl/core/include/xolotl/core/network/PSIReactionNetwork.h
@@ -43,6 +43,7 @@ class PSIReactionNetwork :
 	using IndexType = typename Superclass::IndexType;
 	using ConcentrationsView = typename Superclass::ConcentrationsView;
 	using FluxesView = typename Superclass::FluxesView;
+	using Connectivity = typename Superclass::Connectivity;
 
 	using Superclass::Superclass;
 
@@ -134,6 +135,9 @@ class PSIReactionNetwork :
 	updateDesorptionLeftSideRate(
 		ConcentrationsView concentrations, IndexType gridIndex);
 
+	KOKKOS_INLINE_FUNCTION
+	void setConnectivity(Connectivity);
+
 private:
 	double
 	checkLatticeParameter(double latticeParameter);
@@ -154,6 +158,25 @@ class PSIReactionNetwork :
 		return detail::PSIReactionGenerator<Species>{*this};
 	}
 
+	KOKKOS_INLINE_FUNCTION
+	double
+	getClimbVelocity(ConcentrationsView concentrations, IndexType gridIndex);
+
+	KOKKOS_INLINE_FUNCTION
+	double
+	getClimbVelocityPartialRho(
+		ConcentrationsView concentrations, IndexType gridIndex);
+
+	KOKKOS_INLINE_FUNCTION
+	double
+	getClimbVelocityPartialV(
+		ConcentrationsView concentrations, IndexType gridIndex);
+
+	KOKKOS_INLINE_FUNCTION
+	double
+	getClimbVelocityPartialI(ConcentrationsView concentrations,
+		IndexType gridIndex, IndexType clusterId);
+
 private:
 	std::unique_ptr<detail::TrapMutationHandler> _tmHandler;
 };
@@ -173,6 +196,7 @@ class PSIReactionGenerator :
 	using Subpaving = typename NetworkType::Subpaving;
 	using IndexType = typename NetworkType::IndexType;
 	using AmountType = typename NetworkType::AmountType;
+	using Connectivity = typename NetworkType::Connectivity;
 
 	using Superclass = ReactionGenerator<PSIReactionNetwork<TSpeciesEnum>,
 		PSIReactionGenerator<TSpeciesEnum>>;
@@ -189,6 +213,9 @@ class PSIReactionGenerator :
 	void
 	addSinks(IndexType i, TTag tag) const;
 
+	void
+	addConnectivity(Connectivity& conn);
+
 private:
 	ReactionCollection<NetworkType>
 	getReactionCollection() const;

diff --git a/xolotl/core/include/xolotl/core/network/ReactionNetwork.h b/xolotl/core/include/xolotl/core/network/ReactionNetwork.h
@@ -336,6 +336,12 @@ class ReactionNetwork : public ReactionNetworkInterface<TImpl>::Type
 		return asDerived()->checkLargestClusterId();
 	}
 
+	IndexType
+	getDisloDensityId() override
+	{
+		return getClusterDataMirror().DisloId();
+	}
+
 	Bounds
 	getAllClusterBounds() override;
 
@@ -695,6 +701,7 @@ class ReactionNetwork : public ReactionNetworkInterface<TImpl>::Type
 	std::map<std::string, SpeciesId> _speciesLabelMap;
 
 	ConnectivitiesView _constantConns;
+	Kokkos::View<IndexType*> _connEntries;
 
 	double _currentTime;
 };

diff --git a/xolotl/core/include/xolotl/core/network/ZrReactionNetwork.h b/xolotl/core/include/xolotl/core/network/ZrReactionNetwork.h
@@ -49,6 +49,12 @@ class ZrReactionNetwork : public ReactionNetwork<ZrReactionNetwork>
 	void
 	initializeExtraClusterData(const options::IOptions& options);
 
+	KOKKOS_INLINE_FUNCTION
+	void
+	setConnectivity(Connectivity)
+	{
+	}
+
 private:
 	double
 	checkLatticeParameter(double latticeParameter);
@@ -66,9 +72,6 @@ class ZrReactionNetwork : public ReactionNetwork<ZrReactionNetwork>
 
 	detail::ZrReactionGenerator
 	getReactionGenerator() const noexcept;
-
-	void
-	defineReactions(Connectivity& connectivity);
 };
 
 namespace detail

diff --git a/xolotl/core/include/xolotl/core/network/detail/ClusterData.h b/xolotl/core/include/xolotl/core/network/detail/ClusterData.h
@@ -144,8 +144,8 @@ struct ClusterDataCommon
 	};
 
 	enum IntValsIndex : int
-	{ 
-	    DISLO_ID = 0,
+	{
+		DISLO_ID = 0,
 		HELIUM_DISLO_ID,
 		HELIUM_GB_ID,
 		NUM_INT_VALS
@@ -224,7 +224,7 @@ struct ClusterDataCommon
 	{
 		setVal(_floatVals, ZETA, val);
 	}
-	
+
 	KOKKOS_INLINE_FUNCTION
 	IndexType
 	DisloId() const
@@ -238,7 +238,6 @@ struct ClusterDataCommon
 		setVal(_intVals, DISLO_ID, val);
 	}
 
-
 	KOKKOS_INLINE_FUNCTION
 	IndexType
 	heliumDisloId() const

diff --git a/xolotl/core/include/xolotl/core/network/detail/ReactionGenerator.h b/xolotl/core/include/xolotl/core/network/detail/ReactionGenerator.h
@@ -137,6 +137,13 @@ class ReactionGeneratorBase
 		return _connectivity;
 	}
 
+	KOKKOS_INLINE_FUNCTION
+	void
+	addConnectivity(Connectivity& conn)
+	{
+		return;
+	}
+
 protected:
 	TDerived*
 	asDerived()

diff --git a/xolotl/core/include/xolotl/core/network/detail/impl/ReactionGenerator.tpp b/xolotl/core/include/xolotl/core/network/detail/impl/ReactionGenerator.tpp
@@ -196,8 +196,10 @@ ReactionGeneratorBase<TNetwork, TDerived>::generateConnectivity(
 			DEVICE_LAMBDA(
 				auto&& reaction) { reaction.contributeConnectivity(tmpConn); });
 	}
-
 	Kokkos::fence();
+
+	this->asDerived()->addConnectivity(tmpConn);
+
 	// Get row map
 	auto counts = tmpConn.row_map;
 	auto nEntries =
@@ -242,6 +244,8 @@ ReactionGeneratorBase<TNetwork, TDerived>::generateConnectivity(
 	}
 	Kokkos::fence();
 
+	this->asDerived()->addConnectivity(tmpConn);
+
 	// Shrink to fit
 	Connectivity connectivity;
 	Kokkos::count_and_fill_crs(

diff --git a/xolotl/core/include/xolotl/core/network/impl/PSIReaction.tpp b/xolotl/core/include/xolotl/core/network/impl/PSIReaction.tpp
@@ -309,7 +309,7 @@ KOKKOS_INLINE_FUNCTION
 double
 PSIDisloSinkReaction<TSpeciesEnum>::getSinkStrength()
 {
-    constexpr double pi = ::xolotl::core::pi;
+	constexpr double pi = ::xolotl::core::pi;
 	double grainSize = 50000.0; // 50 um
 	return 1.0 / (pi * grainSize * grainSize);
 }
@@ -324,8 +324,8 @@ PSIDisloSinkReaction<TSpeciesEnum>::computeRate(
 	double dc = cl.getDiffusionCoefficient(gridIndex);
 
 	// Define the dislocation density
-	double disl = 1E-6;   // #/nm-2
- 
+	double disl = 1E-6; // #/nm-2
+
 	// Dislocation sink strength
 	double disl_strength = this->asDerived()->getSinkBias() * disl * dc;