Manually resolve two rebase conflicts. (9a5d8fd1) · Commits · 郑智淋 / lammps

lib/atc/ATC_Coupling.cpp

+25 −25

Original line number	Diff line number	Diff line
		@@ -30,26 +30,26 @@ namespace ATC {
		useFeMdMassMatrix_(false),
		trackCharge_(false),
		temperatureDef_(NONE),
		prescribedDataMgr_(NULL),
		physicsModel_(NULL),
		prescribedDataMgr_(nullptr),
		physicsModel_(nullptr),
		extrinsicModelManager_(this),
		atomicRegulator_(NULL),
		atomicRegulator_(nullptr),
		atomQuadForInternal_(true),
		elementMask_(NULL),
		elementMaskMass_(NULL),
		elementMaskMassMd_(NULL),
		nodalAtomicMass_(NULL),
		nodalAtomicCount_(NULL),
		nodalAtomicHeatCapacity_(NULL),
		internalToMask_(NULL),
		internalElement_(NULL),
		ghostElement_(NULL),
		nodalGeometryType_(NULL),
		elementMask_(nullptr),
		elementMaskMass_(nullptr),
		elementMaskMassMd_(nullptr),
		nodalAtomicMass_(nullptr),
		nodalAtomicCount_(nullptr),
		nodalAtomicHeatCapacity_(nullptr),
		internalToMask_(nullptr),
		internalElement_(nullptr),
		ghostElement_(nullptr),
		nodalGeometryType_(nullptr),
		bndyIntType_(NO_QUADRATURE),
		bndyFaceSet_(NULL),
		atomicWeightsMask_(NULL),
		shpFcnMask_(NULL),
		shpFcnDerivsMask_(NULL),
		bndyFaceSet_(nullptr),
		atomicWeightsMask_(nullptr),
		shpFcnMask_(nullptr),
		shpFcnDerivsMask_(nullptr),
		sourceIntegration_(FULL_DOMAIN)
		{
		// size the field mask
		@@ -68,7 +68,7 @@ namespace ATC {
		ATC_Coupling::~ATC_Coupling()
		{
		interscaleManager_.clear();
		if (feEngine_) { delete feEngine_; feEngine_ = NULL; }
		if (feEngine_) { delete feEngine_; feEngine_ = nullptr; }
		if (physicsModel_) delete physicsModel_;
		if (atomicRegulator_) delete atomicRegulator_;
		if (prescribedDataMgr_) delete prescribedDataMgr_;
		@@ -127,7 +127,7 @@ namespace ATC {
		argIdx++;
		parse_field(arg,argIdx,thisField,thisIndex);
		string nsetName(arg[argIdx++]);
		XT_Function * f = NULL;
		XT_Function * f = nullptr;
		// parse constant
		if (narg == argIdx+1) {
		f = XT_Function_Mgr::instance()->constant_function(atof(arg[argIdx]));
		@@ -164,7 +164,7 @@ namespace ATC {
		argIdx++;
		parse_field(arg,argIdx,thisField,thisIndex);
		string nsetName(arg[argIdx++]);
		XT_Function * f = NULL;
		XT_Function * f = nullptr;
		// fix current value
		if (narg == argIdx) {
		set<int> nodeSet = (feEngine_->fe_mesh())->nodeset(nsetName);
		@@ -258,7 +258,7 @@ namespace ATC {
		argIdx++;
		parse_field(arg,argIdx,thisField,thisIndex);
		string esetName(arg[argIdx++]);
		XT_Function * f = NULL;
		XT_Function * f = nullptr;
		// parse constant
		if (narg == argIdx+1) {
		string a(arg[argIdx]);
		@@ -367,7 +367,7 @@ namespace ATC {
		argIdx++;
		parse_field(arg,argIdx,thisField,thisIndex);
		string fsetName(arg[argIdx++]);
		XT_Function * f = NULL;
		XT_Function * f = nullptr;
		// parse constant
		if (narg == argIdx+1) {
		f = XT_Function_Mgr::instance()->constant_function(atof(arg[argIdx]));
		@@ -529,7 +529,7 @@ namespace ATC {
		argIdx++;
		parse_field(arg,argIdx,thisField,thisIndex);
		string fsetName(arg[argIdx++]);
		UXT_Function * f = NULL;
		UXT_Function * f = nullptr;
		// parse linear
		if (narg == argIdx+2) {
		f = UXT_Function_Mgr::instance()->linear_function(atof(arg[argIdx]),atof(arg[argIdx+1]));
		@@ -760,7 +760,7 @@ namespace ATC {
		WeakEquation::PDE_Type ATC_Coupling::pde_type(const FieldName fieldName) const
		{
		const WeakEquation * weakEq = physicsModel_->weak_equation(fieldName);
		if (weakEq == NULL) return WeakEquation::PROJECTION_PDE;
		if (weakEq == nullptr) return WeakEquation::PROJECTION_PDE;
		return weakEq->type();
		}
		//--------------------------------------------------
		@@ -768,7 +768,7 @@ namespace ATC {
		bool ATC_Coupling::is_dynamic(const FieldName fieldName) const
		{
		const WeakEquation * weakEq = physicsModel_->weak_equation(fieldName);
		if (weakEq == NULL) return false;
		if (weakEq == nullptr) return false;
		return (physicsModel_->weak_equation(fieldName)->type() == WeakEquation::DYNAMIC_PDE);
		}

lib/atc/ATC_Coupling.h

+12 −12

Original line number	Diff line number	Diff line
		@@ -114,10 +114,10 @@ namespace ATC {
		FIELDS &rhs,
		const Array< std::set <int> > atomMaterialGroups,
		const VectorDependencyManager<SPAR_MAT * > * shpFcnDerivs,
		const SPAR_MAN * shpFcn = NULL,
		const DIAG_MAN * atomicWeights = NULL,
		const MatrixDependencyManager<DenseMatrix, bool> * elementMask = NULL,
		const SetDependencyManager<int> * nodeSet = NULL);
		const SPAR_MAN * shpFcn = nullptr,
		const DIAG_MAN * atomicWeights = nullptr,
		const MatrixDependencyManager<DenseMatrix, bool> * elementMask = nullptr,
		const SetDependencyManager<int> * nodeSet = nullptr);
		/** access to full right hand side / forcing vector */
		FIELDS &rhs() {return rhs_;};
		Array2D <bool> rhs_mask() const {
		@@ -152,14 +152,14 @@ namespace ATC {
		const FIELDS &fields,
		FIELDS &rhs,
		const IntegrationDomainType domain, // = FULL_DOMAIN
		const PhysicsModel * physicsModel=NULL);
		const PhysicsModel * physicsModel=nullptr);
		/** wrapper for FE_Engine's compute_tangent_matrix */
		void compute_rhs_tangent(const std::pair<FieldName,FieldName> row_col,
		const RHS_MASK & rhsMask,
		const FIELDS & fields,
		SPAR_MAT & stiffness,
		const IntegrationDomainType integrationType,
		const PhysicsModel * physicsModel=NULL);
		const PhysicsModel * physicsModel=nullptr);
		void tangent_matrix(const std::pair<FieldName,FieldName> row_col,
		const RHS_MASK & rhsMask,
		const PhysicsModel * physicsModel,
		@@ -197,7 +197,7 @@ namespace ATC {
		return & (it->second).quantity();
		}
		else {
		return NULL;
		return nullptr;
		}
		}
		else {
		@@ -206,7 +206,7 @@ namespace ATC {
		return & (it->second).quantity();
		}
		else {
		return NULL;
		return nullptr;
		}
		}
		}
		@@ -233,7 +233,7 @@ namespace ATC {
		/** access to time integrator */
		const TimeIntegrator * time_integrator(const FieldName & field) const {
		_ctiIt_ = timeIntegrators_.find(field);
		if (_ctiIt_ == timeIntegrators_.end()) return NULL;
		if (_ctiIt_ == timeIntegrators_.end()) return nullptr;
		return _ctiIt_->second;
		};

		@@ -322,7 +322,7 @@ namespace ATC {
		void compute_flux(const Array2D<bool> & rhs_mask,
		const FIELDS &fields,
		GRAD_FIELD_MATS &flux,
		const PhysicsModel * physicsModel=NULL,
		const PhysicsModel * physicsModel=nullptr,
		const bool normalize = false);
		/** evaluate rhs on the atomic domain which is near the FE region */
		void masked_atom_domain_rhs_integral(const Array2D<bool> & rhs_mask,
		@@ -334,7 +334,7 @@ namespace ATC {
		const FIELDS &fields,
		FIELDS &rhs,
		const IntegrationDomainType domain,
		const PhysicsModel * physicsModel=NULL);
		const PhysicsModel * physicsModel=nullptr);
		/** access to boundary fluxes */
		DENS_MAT &get_boundary_flux(FieldName thisField){return boundaryFlux_[thisField].set_quantity();};
		DENS_MAN &boundary_flux(FieldName thisField){return boundaryFlux_[thisField];};
		@@ -352,7 +352,7 @@ namespace ATC {
		// mass matrix filtering
		void delete_mass_mat_time_filter(FieldName thisField);
		/** compute mass matrix for requested field */
		void compute_mass_matrix(FieldName thisField, PhysicsModel * physicsModel = NULL);
		void compute_mass_matrix(FieldName thisField, PhysicsModel * physicsModel = nullptr);
		/** updates filtering of MD contributions */
		void update_mass_matrix(FieldName thisField);
		/** compute the mass matrix components coming from MD integration */

lib/atc/ATC_CouplingEnergy.cpp

+3 −3

Original line number	Diff line number	Diff line
		@@ -30,8 +30,8 @@ namespace ATC {
		string matParamFile,
		ExtrinsicModelType extrinsicModel)
		: ATC_Coupling(groupName,perAtomArray,thisFix),
		nodalAtomicKineticTemperature_(NULL),
		nodalAtomicConfigurationalTemperature_(NULL)
		nodalAtomicKineticTemperature_(nullptr),
		nodalAtomicConfigurationalTemperature_(nullptr)
		{
		// Allocate PhysicsModel
		create_physics_model(THERMAL, matParamFile);
		@@ -103,7 +103,7 @@ namespace ATC {

		// always need kinetic energy
		AtomicEnergyForTemperature * atomicTwiceKineticEnergy = new TwiceKineticEnergy(this);
		AtomicEnergyForTemperature * atomEnergyForTemperature = NULL;
		AtomicEnergyForTemperature * atomEnergyForTemperature = nullptr;

		// Appropriate per-atom quantity based on desired temperature definition
		if (temperatureDef_==KINETIC) {

lib/atc/ATC_CouplingMomentumEnergy.cpp

+3 −3

Original line number	Diff line number	Diff line
		@@ -32,8 +32,8 @@ namespace ATC {
		string matParamFile,
		ExtrinsicModelType extrinsicModel)
		: ATC_Coupling(groupName,perAtomArray,thisFix),
		nodalAtomicKineticTemperature_(NULL),
		nodalAtomicConfigurationalTemperature_(NULL),
		nodalAtomicKineticTemperature_(nullptr),
		nodalAtomicConfigurationalTemperature_(nullptr),
		refPE_(0)
		{
		// Allocate PhysicsModel
		@@ -190,7 +190,7 @@ namespace ATC {
		FieldManager fieldManager(this);
		PerAtomQuantity<double> * fluctuatingAtomicVelocity = fieldManager.per_atom_quantity("AtomicFluctuatingVelocity"); // also creates ProlongedVelocity
		AtomicEnergyForTemperature * atomicTwiceKineticEnergy = new TwiceKineticEnergy(this,fluctuatingAtomicVelocity);
		AtomicEnergyForTemperature * atomEnergyForTemperature = NULL;
		AtomicEnergyForTemperature * atomEnergyForTemperature = nullptr;

		// Appropriate per-atom quantity based on desired temperature definition
		if (temperatureDef_==KINETIC) {

lib/atc/ATC_Method.cpp

+26 −26

Original line number	Diff line number	Diff line
		@@ -35,37 +35,37 @@ using std::pair;
		namespace ATC {

		ATC_Method::ATC_Method(string groupName, double ** & perAtomArray, LAMMPS_NS::Fix * thisFix) :
		nodalAtomicVolume_(NULL),
		nodalAtomicVolume_(nullptr),
		needReset_(true),
		lammpsInterface_(LammpsInterface::instance()),
		interscaleManager_(this),
		timeFilterManager_(this),
		integrateInternalAtoms_(false),
		atomTimeIntegrator_(NULL),
		atomTimeIntegrator_(nullptr),
		ghostManager_(this),
		feEngine_(NULL),
		feEngine_(nullptr),
		initialized_(false),
		meshDataInitialized_(false),
		localStep_(0),
		sizeComm_(8), // 3 positions + 1 material id * 2 for output
		atomCoarseGrainingPositions_(NULL),
		atomGhostCoarseGrainingPositions_(NULL),
		atomProcGhostCoarseGrainingPositions_(NULL),
		atomReferencePositions_(NULL),
		atomCoarseGrainingPositions_(nullptr),
		atomGhostCoarseGrainingPositions_(nullptr),
		atomProcGhostCoarseGrainingPositions_(nullptr),
		atomReferencePositions_(nullptr),
		nNodes_(0),
		nsd_(lammpsInterface_->dimension()),
		xref_(NULL),
		xref_(nullptr),
		readXref_(false),
		needXrefProcessorGhosts_(false),
		trackDisplacement_(false),
		needsAtomToElementMap_(true),
		atomElement_(NULL),
		atomGhostElement_(NULL),
		atomElement_(nullptr),
		atomGhostElement_(nullptr),
		internalElementSet_(""),
		atomMasses_(NULL),
		atomPositions_(NULL),
		atomVelocities_(NULL),
		atomForces_(NULL),
		atomMasses_(nullptr),
		atomPositions_(nullptr),
		atomVelocities_(nullptr),
		atomForces_(nullptr),
		parallelConsistency_(true),
		outputNow_(false),
		outputTime_(true),
		@@ -79,13 +79,13 @@ namespace ATC {
		sizeVector_(0),
		scalarVectorFreq_(0),
		sizePerAtomCols_(4),
		perAtomOutput_(NULL),
		perAtomOutput_(nullptr),
		perAtomArray_(perAtomArray),
		extScalar_(0),
		extVector_(0),
		extList_(NULL),
		extList_(nullptr),
		thermoEnergyFlag_(0),
		atomVolume_(NULL),
		atomVolume_(nullptr),
		atomicWeightsWriteFlag_(false),
		atomicWeightsWriteFrequency_(0),
		atomWeightType_(LATTICE),
		@@ -103,12 +103,12 @@ namespace ATC {
		mdMassNormalization_(false),
		kernelBased_(false),
		kernelOnTheFly_(false),
		kernelFunction_(NULL),
		kernelFunction_(nullptr),
		bondOnTheFly_(false),
		accumulant_(NULL),
		accumulantMol_(NULL),
		accumulantMolGrad_(NULL),
		accumulantWeights_(NULL),
		accumulant_(nullptr),
		accumulantMol_(nullptr),
		accumulantMolGrad_(nullptr),
		accumulantWeights_(nullptr),
		accumulantInverseVolumes_(&invNodeVolumes_),
		accumulantBandwidth_(0),
		useRestart_(false),
		@@ -117,7 +117,7 @@ namespace ATC {
		setRefPEvalue_(false),
		refPEvalue_(0.),
		readRefPE_(false),
		nodalRefPotentialEnergy_(NULL),
		nodalRefPotentialEnergy_(nullptr),
		simTime_(0.0),
		stepCounter_(0)
		{
		@@ -1122,7 +1122,7 @@ pecified
		FieldName & thisField, int & thisIndex)
		{
		string thisName = args[argIdx++];
		if (args[argIdx] == NULL) {
		if (args[argIdx] == nullptr) {
		throw ATC_Error("Need to give field '"+thisName+"' more args");
		}
		thisField = string_to_field(thisName);
		@@ -1282,7 +1282,7 @@ pecified
		if (this->reset_methods()) {
		// clear memory manager
		interscaleManager_.clear_temporary_data();
		atomVolume_ = NULL;
		atomVolume_ = nullptr;

		// reference positions and energy
		if (!initialized_) {
		@@ -1517,7 +1517,7 @@ pecified
		}
		else {
		// set variables to compute atomic weights
		DENS_MAN * nodalVolume(NULL);
		DENS_MAN * nodalVolume(nullptr);
		switch (atomWeightType_) {
		case USER:
		atomVolume_ = new AtomVolumeUser(this,Valpha_);

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