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<center><a href="FEMProblem.hh">Actual source code: FEMProblem.hh</a></center><br>
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<head>
<title></title>
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<meta name="date" content="2010-04-08T19:54:51+00:00">
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<pre width="80"><a name="line1"> 1: </a><font color="#A020F0">#ifndef __FEMProblem</font>
<a name="line4"> 4: </a><font color="#B22222">/*</font>
<a name="line5"> 5: </a><font color="#B22222"> </font>
<a name="line6"> 6: </a><font color="#B22222"> Framework for solving a FEM problem using sieve.</font>
<a name="line7"> 7: </a><font color="#B22222"> </font>
<a name="line8"> 8: </a><font color="#B22222"> The Discretization objects are WAY too embedded into the way things are done; we will have to create ways of </font>
<a name="line10"> 10: </a><font color="#B22222">This includes derived types doing what indicesExcluded does for all things marked with a boundary marker.</font>
<a name="line12"> 12: </a><font color="#B22222">*/</font>
<a name="line14"> 14: </a><font color="#A020F0">#include <Mesh.hh></font>
<a name="line16"> 16: </a>namespace ALE {
<a name="line17"> 17: </a> namespace Problem {
<a name="line19"> 19: </a> <font color="#B22222">/*</font>
<a name="line20"> 20: </a><font color="#B22222"> This class defines a basic interface to a subproblem; all data the type needs will be set at initialization and be</font>
<a name="line21"> 21: </a><font color="#B22222"> members of the derived types</font>
<a name="line23"> 23: </a><font color="#B22222"> The recommended use for a given problem is to define a subproblem class for doing the data initialization for the</font>
<a name="line24"> 24: </a><font color="#B22222"> form, as well as the postprocessing one for doing the boundary handling and setting, and one for dealing with the</font>
<a name="line25"> 25: </a><font color="#B22222"> process of the solve. Work can be broken up as needed; however for the sake of simplicity one should probably</font>
<a name="line26"> 26: </a><font color="#B22222"> have various forms in various subproblems to assemble. This could of course include facet integrals or problems</font>
<a name="line27"> 27: </a><font color="#B22222"> over part of the domain. Look at the examples provided in UFCProblem, which use the UFC form compiler to assemble</font>
<a name="line28"> 28: </a><font color="#B22222"> subproblems of a form.</font>
<a name="line30"> 30: </a><font color="#B22222"> */</font>
<a name="line32"> 32: </a> class SubProblem : public ParallelObject {
<a name="line33"> 33: </a><strong><font color="#FF0000"> public:</font></strong>
<a name="line35"> 35: </a> <font color="#4169E1">typedef</font> std::string name_type;
<a name="line37"> 37: </a> SubProblem(<A href="../../docs/manualpages/Sys/MPI_Comm.html#MPI_Comm">MPI_Comm</A> comm, const int debug = 0) : ParallelObject(comm, debug) {};
<a name="line38"> 38: </a> virtual ~SubProblem() {};
<a name="line40"> 40: </a> };
<a name="line42"> 42: </a> <font color="#B22222">/*</font>
<a name="line43"> 43: </a><font color="#B22222"> Below is a helper derived class of subproblem; the persistently limiting and annoying discretization object in</font>
<a name="line44"> 44: </a><font color="#B22222"> Sieve must be excised; Here are subproblem objects containing the helper functions that are presently in the</font>
<a name="line45"> 45: </a><font color="#B22222"> monster called PETSC_MESH_TYPE, but with references to the discretization object stolen. virtual functions to be</font>
<a name="line46"> 46: </a><font color="#B22222"> filled in in further derived classes are marked. This is meant to be a stepping stone towards generalized use of</font>
<a name="line47"> 47: </a><font color="#B22222"> problem creation objects with multiple fields and interesting boundary conditions. This type can be branched into</font>
<a name="line49"> 49: </a><font color="#B22222"> */</font>
<a name="line51"> 51: </a> //creates a discretization-like thing <font color="#4169E1">for</font> this particular <font color="#4169E1">case</font>; from this we can use the helper functions in the
<a name="line52"> 52: </a> //generalformsubproblem to set up the discretization across the mesh as one might expect in the <font color="#4169E1">case</font> of a
<a name="line55"> 55: </a><font color="#A020F0">#if 0</font>
<a name="line57"> 57: </a> //we really can't use this <font color="#4169E1">for</font> finite elements with UFC
<a name="line59"> 59: </a> class GeneralCell : public ParallelObject {
<a name="line60"> 60: </a><strong><font color="#FF0000"> private:</font></strong>
<a name="line61"> 61: </a> int _embedded_dimension; //the fiberdimension of the coordinate section
<a name="line62"> 62: </a> int closureSize; //the size of the closure
<a name="line63"> 63: </a><strong><font color="#FF0000"> std:</font></strong>:map<int, int> _closure_order; //all that really matters; assume interpolated as the order should be the same
<a name="line64"> 64: </a> int _num_vertices; //necessary to allocate the coordinate array.
<a name="line65"> 65: </a> double * _coordinates; //the coordinate array in order based upon the local topology
<a name="line67"> 67: </a> GeneralCell() {
<a name="line68"> 68: </a> _num_vertices = 0;
<a name="line69"> 69: </a> _coordinates = <A href="../../docs/manualpages/Sys/PETSC_NULL.html#PETSC_NULL">PETSC_NULL</A>;
<a name="line70"> 70: </a> }
<a name="line72"> 72: </a> GeneralCell(int embedded_dimension, int num_vertices) {
<a name="line73"> 73: </a> _embedded_dimension = embedded_dimension;
<a name="line74"> 74: </a> _num_vertices = _num_vertices;
<a name="line75"> 75: </a> _coordinates = new double[_embedded_dimension*_num_vertices];
<a name="line76"> 76: </a> }
<a name="line78"> 78: </a> virtual ~GeneralCell() {
<a name="line79"> 79: </a> <font color="#4169E1">if</font> (_coordinates)
<a name="line80"> 80: </a> delete _coordinates;
<a name="line81"> 81: </a> }
<a name="line83"> 83: </a> virtual void setMeshCell(Obj<PETSC_MESH_TYPE> mesh, PETSC_MESH_TYPE::point_type cell) {
<a name="line84"> 84: </a> throw Exception(<font color="#666666">"GeneralCell->setCell(): Unimplemented base class"</font>);
<a name="line85"> 85: </a> <font color="#4169E1">return</font>;
<a name="line86"> 86: </a> }
<a name="line87"> 87: </a> virtual void setClosureOrder(int subcell, int map) {
<a name="line88"> 88: </a> _closure_order[subcell] = map;
<a name="line89"> 89: </a> }
<a name="line90"> 90: </a> virtual int getClosureOrder(int subcell) {
<a name="line91"> 91: </a> <font color="#4169E1">return</font> _closure_order[subcell];
<a name="line92"> 92: </a> }
<a name="line93"> 93: </a> };
<a name="line95"> 95: </a><font color="#A020F0">#endif</font>
<a name="line97"> 97: </a> class GeneralBoundaryCondition : ParallelObject {
<a name="line98"> 98: </a><strong><font color="#FF0000"> protected:</font></strong>
<a name="line100">100: </a><strong><font color="#FF0000"> std:</font></strong>:string _labelName;
<a name="line101">101: </a> int _marker;
<a name="line103">103: </a><strong><font color="#FF0000"> public:</font></strong>
<a name="line104">104: </a> GeneralBoundaryCondition(<A href="../../docs/manualpages/Sys/MPI_Comm.html#MPI_Comm">MPI_Comm</A> comm, const int debug = 0) : ParallelObject(comm, debug) {};
<a name="line105">105: </a> virtual ~GeneralBoundaryCondition() {};
<a name="line106">106: </a><strong><font color="#FF0000"> public:</font></strong>
<a name="line107">107: </a> virtual const std::string& getLabelName() const {<font color="#4169E1">return</font> this->_labelName;};
<a name="line108">108: </a> virtual void setLabelName(const std::string& name) {this->_labelName = name;};
<a name="line109">109: </a> virtual int getMarker() const {<font color="#4169E1">return</font> this->_marker;};
<a name="line110">110: </a> virtual void setMarker(const int marker) {this->_marker = marker;};
<a name="line111">111: </a>
<a name="line112">112: </a><strong><font color="#FF0000"> public:</font></strong>
<a name="line114">114: </a> virtual double integrateDual(unsigned int dof) {
<a name="line115">115: </a> //when implementing this one should have some notion of what the dof number is built into the BC; this would constitute having some cell or something known
<a name="line116">116: </a> //by the object such that that cell can be set and integrated within.
<a name="line117">117: </a> throw Exception(<font color="#666666">"GeneralBoundaryCondition->integrateDual: Nonimplemented base-class version called."</font>);
<a name="line118">118: </a> <font color="#4169E1">return</font> 3.;
<a name="line119">119: </a> };
<a name="line120">120: </a>
<a name="line121">121: </a> virtual void setReorder(int * reorder) {
<a name="line122">122: </a> throw Exception(<font color="#666666">"GeneralBoundaryCondition->setReorder(): Unimplemented base class version called."</font>);
<a name="line123">123: </a> }
<a name="line125">125: </a> virtual const int * getReorder() {
<a name="line126">126: </a> throw Exception(<font color="#666666">"GeneralBoundaryCondition->getReorder(): Unimplemented base class version called."</font>);
<a name="line127">127: </a> <font color="#4169E1">return</font> <A href="../../docs/manualpages/Sys/PETSC_NULL.html#PETSC_NULL">PETSC_NULL</A>;
<a name="line128">128: </a> }
<a name="line130">130: </a> };
<a name="line131">131: </a>
<a name="line132">132: </a> <font color="#B22222">/*</font>
<a name="line133">133: </a><font color="#B22222"> Include at least counts of all the part of the triple, as well as all the information for the cell.</font>
<a name="line134">134: </a><font color="#B22222"> */</font>
<a name="line136">136: </a><font color="#A020F0">#if 0</font>
<a name="line138">138: </a> class GeneralFiniteElement : public ParallelObject {
<a name="line139">139: </a><strong><font color="#FF0000"> private:</font></strong>
<a name="line140">140: </a><strong><font color="#FF0000"> public:</font></strong>
<a name="line141">141: </a> virtual double integrateDual(unsigned int dof) {
<a name="line142">142: </a> //evaluate a degree of freedom
<a name="line143">143: </a> <font color="#4169E1">return</font> 0.;
<a name="line144">144: </a> }
<a name="line145">145: </a> virtual int closureIndex(unsigned int dof) {
<a name="line146">146: </a> <font color="#4169E1">return</font> 0;
<a name="line147">147: </a> }
<a name="line148">148: </a> virtual int dataIndex(unsigned int dof) {
<a name="line149">149: </a> <font color="#4169E1">return</font> 0;
<a name="line150">150: </a> }
<a name="line151">151: </a> };
<a name="line153">153: </a><font color="#A020F0">#endif</font>
<a name="line155">155: </a> //we almost, ALMOST need an overall view of a local reference topology <font color="#4169E1">for</font> this kind of stuff (and the boundary conditions).
<a name="line157">157: </a> class GeneralIntegral : public ParallelObject {
<a name="line158">158: </a><strong><font color="#FF0000"> public:</font></strong>
<a name="line159">159: </a> <font color="#4169E1">typedef</font> std::string name_type;
<a name="line160">160: </a><strong><font color="#FF0000"> private:</font></strong>
<a name="line161">161: </a> //the integral should only apply to the labeled points in some way, probably over the closure(support(point));
<a name="line164">164: </a> //the integrals will have some set of cells or cell-like objects they act on; this includes potentially internal faces.
<a name="line165">165: </a> //But, <font color="#4169E1">for</font> cell integrals these should be set to <font color="#666666">"height"</font> and <font color="#666666">"0"</font>
<a name="line167">167: </a> name_type _label_name;
<a name="line168">168: </a> int _label_marker; //We could use this <font color="#4169E1">if</font> there's only a certain label and marker that the given integral applies to
<a name="line170">170: </a> int _num_coefficients; //<font color="#4169E1">for</font> the linear forms
<a name="line172">172: </a> int _space_dimension; //the number of DoFs we're dealing with here.
<a name="line173">173: </a> int _tensor_rank; //the tensor rank; it BETTER be one or two.
<a name="line174">174: </a> int _topological_dimension; //the topological dimension of the given mesh item -- tells us <font color="#4169E1">if</font> it's a cell or facet integral
<a name="line176">176: </a> int * _closure2data; //<font color="#4169E1">if</font> there is some API-level data storage, this maps the unknowns <font color="#4169E1">for</font> the WHOLE CLOSURE onto the unknowns <font color="#4169E1">for</font> the API
<a name="line178">178: </a><strong><font color="#FF0000"> public:</font></strong>
<a name="line179">179: </a>
<a name="line180">180: </a> GeneralIntegral (<A href="../../docs/manualpages/Sys/MPI_Comm.html#MPI_Comm">MPI_Comm</A> comm, int debug = 0) : ParallelObject(comm, debug) {
<a name="line181">181: </a> _tensor_rank = 0;
<a name="line182">182: </a> _space_dimension = 0;
<a name="line183">183: </a> _topological_dimension = 0;
<a name="line184">184: </a> _label_marker = 0;
<a name="line185">185: </a> }
<a name="line187">187: </a> GeneralIntegral (<A href="../../docs/manualpages/Sys/MPI_Comm.html#MPI_Comm">MPI_Comm</A> comm, name_type labelname, int labelmarker, int nCoefficients = 0, int debug = 0) : ParallelObject(comm, debug) {
<a name="line188">188: </a> _num_coefficients = nCoefficients;
<a name="line189">189: </a> _label_name = labelname;
<a name="line190">190: </a> _label_marker = labelmarker;
<a name="line191">191: </a> }
<a name="line193">193: </a> virtual ~GeneralIntegral () {};
<a name="line196">196: </a> int getNumCoefficients() {
<a name="line197">197: </a> <font color="#4169E1">return</font> _num_coefficients;
<a name="line198">198: </a> }
<a name="line200">200: </a> void setNumCoefficients(int nc) {
<a name="line201">201: </a> _num_coefficients = nc;
<a name="line202">202: </a> }
<a name="line205">205: </a> name_type getLabelName() {
<a name="line206">206: </a> <font color="#4169E1">return</font> _label_name;
<a name="line207">207: </a> }
<a name="line209">209: </a> int getLabelMarker() {
<a name="line210">210: </a> <font color="#4169E1">return</font> _label_marker;
<a name="line211">211: </a> }
<a name="line213">213: </a> void setLabelName(name_type newName) {
<a name="line214">214: </a> _label_name = newName;
<a name="line215">215: </a> }
<a name="line217">217: </a> void setLabelMarker(int newMarker) {
<a name="line218">218: </a> _label_marker = newMarker;
<a name="line219">219: </a> }
<a name="line220">220: </a>
<a name="line222">222: </a> virtual void setSpaceDimension(int dim) {
<a name="line223">223: </a> _space_dimension = dim;
<a name="line224">224: </a> }
<a name="line225">225: </a>
<a name="line226">226: </a> virtual int getSpaceDimension() {
<a name="line227">227: </a> <font color="#4169E1">return</font> _space_dimension;
<a name="line228">228: </a> }
<a name="line230">230: </a> virtual void setTensorRank(int rank) {
<a name="line231">231: </a> _tensor_rank = rank;
<a name="line232">232: </a> }
<a name="line233">233: </a>
<a name="line234">234: </a> virtual int getTensorRank() {
<a name="line235">235: </a> <font color="#4169E1">return</font> _tensor_rank;
<a name="line236">236: </a> }
<a name="line238">238: </a>
<a name="line239">239: </a>
<a name="line240">240: </a> virtual const int * getReorder() {
<a name="line241">241: </a> <font color="#4169E1">return</font> _closure2data;
<a name="line242">242: </a> }
<a name="line244">244: </a> virtual void setReorder(int * reorder) {
<a name="line245">245: </a> _closure2data = reorder;
<a name="line246">246: </a> }
<a name="line248">248: </a> //use the UFC lingo here
<a name="line249">249: </a> //have some notion of the cell initialized and in-state in the eventual implementation.
<a name="line250">250: </a> virtual void tabulateTensor(double * tensor, const double * coefficients = <A href="../../docs/manualpages/Sys/PETSC_NULL.html#PETSC_NULL">PETSC_NULL</A>) {
<a name="line251">251: </a> throw Exception(<font color="#666666">"GeneralIntegral->tabulateTensor: Nonimplemented Base class version called."</font>);
<a name="line252">252: </a> <font color="#4169E1">return</font>;
<a name="line253">253: </a> }
<a name="line254">254: </a> };
<a name="line256">256: </a> class GeneralDiscretization : ParallelObject { //this should largely resemble the old form of the discretizations, only with specifics of evaluation to FIAT removed.
<a name="line257">257: </a> <font color="#4169E1">typedef</font> std::map<std::string, Obj<GeneralBoundaryCondition> > boundaryConditions_type;
<a name="line258">258: </a><strong><font color="#FF0000"> protected:</font></strong>
<a name="line259">259: </a> boundaryConditions_type _boundaryConditions;
<a name="line260">260: </a> Obj<GeneralBoundaryCondition> _exactSolution;
<a name="line261">261: </a><strong><font color="#FF0000"> std:</font></strong>:map<int,int> _dim2dof; //not good enough <font color="#4169E1">for</font> tensor product assembly.... however we can generalize this into some sort of <font color="#666666">"getClosureItemDofs"</font> or something per cell
<a name="line262">262: </a><strong><font color="#FF0000"> std:</font></strong>:map<int,int> _dim2class;
<a name="line263">263: </a> int _quadSize;
<a name="line264">264: </a> int _basisSize;
<a name="line265">265: </a> const int * _indices;
<a name="line266">266: </a><strong><font color="#FF0000"> std:</font></strong>:map<int, const int *> _exclusionIndices;
<a name="line267">267: </a> const int * _closure2data; //local index reordering
<a name="line269">269: </a><strong><font color="#FF0000"> public:</font></strong>
<a name="line271">271: </a> <font color="#4169E1">typedef</font> std::set<std::string> names_type;
<a name="line273">273: </a> GeneralDiscretization(<A href="../../docs/manualpages/Sys/MPI_Comm.html#MPI_Comm">MPI_Comm</A> comm, const int debug = 0) : ParallelObject(comm, debug), _quadSize(0), _basisSize(0), _indices(NULL) {};
<a name="line274">274: </a> virtual ~GeneralDiscretization() {
<a name="line275">275: </a> <font color="#4169E1">if</font> (this->_indices) {delete [] this->_indices;}
<a name="line276">276: </a> <font color="#4169E1">for</font>(std::map<int, const int *>::iterator i_iter = _exclusionIndices.begin(); i_iter != _exclusionIndices.end(); ++i_iter) {
<a name="line277">277: </a> delete [] i_iter->second;
<a name="line278">278: </a> }
<a name="line279">279: </a> <font color="#4169E1">if</font> (_closure2data) {
<a name="line280">280: </a> delete _closure2data;
<a name="line281">281: </a> }
<a name="line282">282: </a> };
<a name="line283">283: </a><strong><font color="#FF0000"> public:</font></strong>
<a name="line284">284: </a> virtual const bool hasBoundaryCondition() {<font color="#4169E1">return</font> (this->_boundaryConditions.find(<font color="#666666">"</font><font color="#4169E1">default</font>") != this->_boundaryConditions.end());};
<a name="line285">285: </a> virtual Obj<GeneralBoundaryCondition> getBoundaryCondition() {<font color="#4169E1">return</font> this->getBoundaryCondition(<font color="#666666">"</font><font color="#4169E1">default</font>");};
<a name="line286">286: </a> virtual void setBoundaryCondition(const Obj<GeneralBoundaryCondition>& boundaryCondition) {this->setBoundaryCondition(<font color="#666666">"</font><font color="#4169E1">default</font>", boundaryCondition);};
<a name="line287">287: </a> virtual Obj<GeneralBoundaryCondition> getBoundaryCondition(const std::string& name) {<font color="#4169E1">return</font> this->_boundaryConditions[name];};
<a name="line288">288: </a> virtual void setBoundaryCondition(const std::string& name, const Obj<GeneralBoundaryCondition>& boundaryCondition) {this->_boundaryConditions[name] = boundaryCondition;};
<a name="line289">289: </a> virtual names_type getBoundaryConditions() const {
<a name="line290">290: </a> Obj<names_type> names = names_type();
<a name="line291">291: </a> <font color="#4169E1">for</font>(boundaryConditions_type::const_iterator d_iter = this->_boundaryConditions.begin(); d_iter != this->_boundaryConditions.end(); ++d_iter) {
<a name="line292">292: </a> names->insert(d_iter->first);
<a name="line293">293: </a> }
<a name="line294">294: </a> <font color="#4169E1">return</font> names;
<a name="line295">295: </a> };
<a name="line297">297: </a> //eh?
<a name="line298">298: </a> //virtual const Obj<BoundaryCondition>& getExactSolution() {<font color="#4169E1">return</font> this->_exactSolution;};
<a name="line299">299: </a> //virtual void setExactSolution(const Obj<GeneralBoundaryCondition>& exactSolution) {this->_exactSolution = exactSolution;};
<a name="line300">300: </a> virtual const int getQuadratureSize() {<font color="#4169E1">return</font> this->_quadSize;};
<a name="line301">301: </a> virtual void setQuadratureSize(const int size) {this->_quadSize = size;};
<a name="line302">302: </a> virtual const int getBasisSize() {<font color="#4169E1">return</font> this->_basisSize;};
<a name="line303">303: </a> virtual void setBasisSize(const int size) {this->_basisSize = size;};
<a name="line305">305: </a> //eh, until they get this together in UFC keep these around.
<a name="line307">307: </a> virtual int getNumDof(const int dim) {<font color="#4169E1">return</font> this->_dim2dof[dim];};
<a name="line308">308: </a> virtual void setNumDof(const int dim, const int numDof) {this->_dim2dof[dim] = numDof;};
<a name="line309">309: </a> virtual int getDofClass(const int dim) {<font color="#4169E1">return</font> this->_dim2class[dim];};
<a name="line310">310: </a> virtual void setDofClass(const int dim, const int dofClass) {this->_dim2class[dim] = dofClass;};
<a name="line311">311: </a><strong><font color="#FF0000"> public:</font></strong>
<a name="line313">313: </a> <font color="#B22222">/*</font>
<a name="line314">314: </a><font color="#B22222"> </font>
<a name="line315">315: </a><font color="#B22222"> Functions for interacting with external libraries for handling finite element assembly that might have different cell layout.</font>
<a name="line316">316: </a><font color="#B22222"> </font>
<a name="line317">317: </a><font color="#B22222"> */</font>
<a name="line319">319: </a> virtual void createReorder() {
<a name="line320">320: </a> throw Exception(<font color="#666666">"GeneralDiscretization->createReorderings: Unimplemented base function"</font>);
<a name="line321">321: </a> <font color="#4169E1">return</font>;
<a name="line322">322: </a> }
<a name="line324">324: </a> virtual const int * getReorder() {
<a name="line325">325: </a> <font color="#4169E1">return</font> _closure2data;
<a name="line326">326: </a> }
<a name="line328">328: </a> virtual void setReorder(int * reorder) {
<a name="line329">329: </a> _closure2data = reorder;
<a name="line330">330: </a> }
<a name="line332">332: </a> //Yeah... not messing with this part.
<a name="line334">334: </a> virtual const int *getIndices() {<font color="#4169E1">return</font> this->_indices;};
<a name="line335">335: </a> virtual const int *getIndices(const int marker) {
<a name="line337">337: </a> <font color="#4169E1">if</font> (!marker) <font color="#4169E1">return</font> this->getIndices();
<a name="line338">338: </a> <font color="#4169E1">return</font> this->_exclusionIndices[marker];
<a name="line339">339: </a> };
<a name="line340">340: </a> virtual void setIndices(const int *indices) {this->_indices = indices;};
<a name="line341">341: </a> virtual void setIndices(const int *indices, const int marker) {
<a name="line342">342: </a> <font color="#4169E1">if</font> (!marker) this->_indices = indices;
<a name="line343">343: </a> this->_exclusionIndices[marker] = indices;
<a name="line344">344: </a> };
<a name="line346">346: </a> //<font color="#4169E1">return</font> the size of the space
<a name="line347">347: </a> virtual int size() {
<a name="line348">348: </a> throw Exception(<font color="#666666">"GeneralDiscretization->size(): Nonimplemented base class function called."</font>);
<a name="line349">349: </a> <font color="#4169E1">return</font> 0;
<a name="line350">350: </a> }
<a name="line351">351: </a> virtual double evaluateRHS(int dof) {
<a name="line352">352: </a> throw Exception(<font color="#666666">"GeneralDiscretization->evaluateRHS: Nonimplemented base class function called."</font>);
<a name="line353">353: </a> }
<a name="line354">354: </a> };
<a name="line356">356: </a> //The GenericFormSubProblem shown here should basically contain the whole problem as it does the discretization-like setup, which might <font color="#4169E1">break</font>
<a name="line357">357: </a> //<font color="#4169E1">if</font> you define multiple ones right now. Set the multiple different spaces using different discretizations.
<a name="line359">359: </a> class GenericFormSubProblem : SubProblem { //takes information from some abstract notion of a problem and sets up the thing.
<a name="line360">360: </a><strong><font color="#FF0000"> public:</font></strong>
<a name="line361">361: </a> <font color="#4169E1">typedef</font> std::map<std::string, Obj<GeneralDiscretization> > discretizations_type;
<a name="line362">362: </a> <font color="#4169E1">typedef</font> std::map<std::string, Obj<GeneralIntegral> > integral_type;
<a name="line363">363: </a> <font color="#4169E1">typedef</font> std::set<std::string> names_type;
<a name="line365">365: </a> GenericFormSubProblem(<A href="../../docs/manualpages/Sys/MPI_Comm.html#MPI_Comm">MPI_Comm</A> comm, int debug = 1) : SubProblem(comm, debug) {};
<a name="line367">367: </a> ~GenericFormSubProblem(){};
<a name="line369">369: </a><strong><font color="#FF0000"> private:</font></strong>
<a name="line370">370: </a>
<a name="line371">371: </a> name_type _solutionSectionName;
<a name="line372">372: </a> name_type _forcingSectionName;
<a name="line373">373: </a> discretizations_type _discretizations;
<a name="line374">374: </a> integral_type _integrals;
<a name="line375">375: </a> Obj<GeneralBoundaryCondition> _exactSolution; //evaluates a function over all unknowns on the form containing an exact solution. Per discretization later.
<a name="line376">376: </a> int * _closure2data; //a mapping from closure indices to data indices <font color="#4169E1">for</font> the overall element
<a name="line379">379: </a> //helper functions, stolen directly from Mesh.hh with slight modifications to remove FIAT dependence and instead use stuff from GeneralDiscretization
<a name="line381">381: </a><strong><font color="#FF0000"> public:</font></strong>
<a name="line382">382: </a>
<a name="line383">383: </a> const Obj<GeneralDiscretization>& getDiscretization() {<font color="#4169E1">return</font> this->getDiscretization(<font color="#666666">"</font><font color="#4169E1">default</font>");};
<a name="line384">384: </a> const Obj<GeneralDiscretization>& getDiscretization(const std::string& name) {<font color="#4169E1">return</font> this->_discretizations[name];};
<a name="line385">385: </a>
<a name="line386">386: </a> void setDiscretization(const Obj<GeneralDiscretization>& disc) {this->setDiscretization(<font color="#666666">"</font><font color="#4169E1">default</font>", disc);};
<a name="line387">387: </a> void setDiscretization(const std::string& name, const Obj<GeneralDiscretization>& disc) {this->_discretizations[name] = disc;};
<a name="line389">389: </a> const Obj<GeneralIntegral>& getIntegral() {<font color="#4169E1">return</font> this->getIntegral(<font color="#666666">"</font><font color="#4169E1">default</font>");};
<a name="line390">390: </a> const Obj<GeneralIntegral>& getIntegral(const std::string& name) {<font color="#4169E1">return</font> this->_integrals[name];};
<a name="line392">392: </a> void setIntegral(const Obj<GeneralIntegral>& integral) {this->setIntegral(<font color="#666666">"</font><font color="#4169E1">default</font>", integral);};
<a name="line393">393: </a> void setIntegral(const std::string& name, const Obj<GeneralIntegral> integral) {this->_integrals[name] = integral;};
<a name="line395">395: </a> //FAIL! this won't be used.
<a name="line396">396: </a> void setExactSolution(Obj<GeneralBoundaryCondition> exactsol) {
<a name="line397">397: </a> _exactSolution = exactsol;
<a name="line398">398: </a> }
<a name="line400">400: </a> Obj<GeneralBoundaryCondition> getExactSolution(){<font color="#4169E1">return</font> _exactSolution;};
<a name="line402">402: </a> Obj<names_type> getDiscretizations() const {
<a name="line403">403: </a> Obj<names_type> names = names_type();
<a name="line404">404: </a>
<a name="line405">405: </a> <font color="#4169E1">for</font>(discretizations_type::const_iterator d_iter = this->_discretizations.begin(); d_iter != this->_discretizations.end(); ++d_iter) {
<a name="line406">406: </a> names->insert(d_iter->first);
<a name="line407">407: </a> }
<a name="line408">408: </a> <font color="#4169E1">return</font> names;
<a name="line409">409: </a> };
<a name="line411">411: </a> Obj<names_type> getIntegrals() const {
<a name="line412">412: </a> Obj<names_type> names = names_type();
<a name="line413">413: </a> <font color="#4169E1">for</font> (integral_type::const_iterator i_iter = this->_integrals.begin(); i_iter != this->_integrals.end(); ++i_iter) {
<a name="line414">414: </a> names->insert(i_iter->first);
<a name="line415">415: </a> }
<a name="line416">416: </a> <font color="#4169E1">return</font> names;
<a name="line417">417: </a> }
<a name="line419">419: </a> //TODO: Implement a cell interface class towards flexible handling of reordering between various parts of this thing.
<a name="line421">421: </a> virtual void setCell(Obj<PETSC_MESH_TYPE> mesh, PETSC_MESH_TYPE::point_type c) const { //implementations should set some state of the derived type to the present cell
<a name="line422">422: </a> throw Exception(<font color="#666666">"Using the unimplemented base class version of setCell in GeneralDiscretization."</font>);
<a name="line423">423: </a> <font color="#4169E1">return</font>;
<a name="line424">424: </a> };
<a name="line426">426: </a> virtual int localSpaceDimension() {
<a name="line427">427: </a> throw Exception(<font color="#666666">"GeneralDiscretization->localSpaceDimension(): using the unimplemented base class version."</font>);
<a name="line428">428: </a> <font color="#4169E1">return</font> 0;
<a name="line429">429: </a> }
<a name="line430">430: </a>
<a name="line431">431: </a> <font color="#B22222">/*</font>
<a name="line432">432: </a><font color="#B22222"> Functions handling the creation and application of reordering from element libraries and sieve.</font>
<a name="line433">433: </a><font color="#B22222"> */</font>
<a name="line435">435: </a> virtual void createReorder() {
<a name="line436">436: </a> throw Exception(<font color="#666666">"GeneralFormSubProblem->buildOrderings(): nonimplemented base function"</font>);
<a name="line437">437: </a> <font color="#4169E1">return</font>;
<a name="line438">438: </a> }
<a name="line440">440: </a> virtual const int * getReorder() {
<a name="line441">441: </a> <font color="#4169E1">return</font> _closure2data;
<a name="line442">442: </a> }
<a name="line444">444: </a> virtual void setReorder(int * order) {
<a name="line445">445: </a> _closure2data = order;
<a name="line446">446: </a> }
<a name="line448">448: </a> <font color="#B22222">/*</font>
<a name="line449">449: </a><font color="#B22222"> Functions handling the mesh data layout from the overall subproblem</font>
<a name="line450">450: </a><font color="#B22222"> */</font>
<a name="line452">452: </a> int setFiberDimensions(const Obj<PETSC_MESH_TYPE> mesh, const Obj<PETSC_MESH_TYPE::real_section_type> s, const Obj<names_type>& discs, names_type& bcLabels) {
<a name="line453">453: </a> const int debug = this->debug();
<a name="line454">454: </a> int maxDof = 0;
<a name="line455">455: </a>
<a name="line456">456: </a> <font color="#4169E1">for</font>(names_type::const_iterator f_iter = discs->begin(); f_iter != discs->end(); ++f_iter) {
<a name="line457">457: </a> s->addSpace();
<a name="line458">458: </a> }
<a name="line459">459: </a> <font color="#4169E1">for</font>(int d = 0; d <= mesh->getDimension(); ++d) {
<a name="line460">460: </a> int numDof = 0;
<a name="line461">461: </a> int f = 0;
<a name="line462">462: </a>
<a name="line463">463: </a> <font color="#4169E1">for</font>(names_type::const_iterator f_iter = discs->begin(); f_iter != discs->end(); ++f_iter, ++f) {
<a name="line464">464: </a> const Obj<GeneralDiscretization>& disc = this->getDiscretization(*f_iter);
<a name="line465">465: </a> const int sDof = disc->getNumDof(d);
<a name="line466">466: </a>
<a name="line467">467: </a> numDof += sDof;
<a name="line468">468: </a> <font color="#4169E1">if</font> (sDof) s->setFiberDimension(mesh->depthStratum(d), sDof, f);
<a name="line469">469: </a> }
<a name="line470">470: </a> <font color="#4169E1">if</font> (numDof) s->setFiberDimension(mesh->depthStratum(d), numDof);
<a name="line471">471: </a> maxDof = std::max(maxDof, numDof);
<a name="line472">472: </a> }
<a name="line473">473: </a> // Process exclusions
<a name="line474">474: </a> <font color="#4169E1">typedef</font> ISieveVisitor::PointRetriever<PETSC_MESH_TYPE::sieve_type> Visitor;
<a name="line475">475: </a> int f = 0;
<a name="line476">476: </a>
<a name="line477">477: </a> <font color="#4169E1">for</font>(names_type::const_iterator f_iter = discs->begin(); f_iter != discs->end(); ++f_iter, ++f) {
<a name="line478">478: </a> const Obj<GeneralDiscretization>& disc = this->getDiscretization(*f_iter);
<a name="line479">479: </a><strong><font color="#FF0000"> std:</font></strong>:string labelName = <font color="#666666">"exclude-"</font>+*f_iter;
<a name="line480">480: </a><strong><font color="#FF0000"> std:</font></strong>:set<PETSC_MESH_TYPE::point_type> seen;
<a name="line481">481: </a> Visitor pV((int) pow(mesh->getSieve()->getMaxConeSize(), mesh->depth()), true);
<a name="line482">482: </a>
<a name="line483">483: </a> <font color="#4169E1">if</font> (mesh->hasLabel(labelName)) {
<a name="line484">484: </a> const Obj<PETSC_MESH_TYPE::label_type>& label = mesh->getLabel(labelName);
<a name="line485">485: </a> const Obj<PETSC_MESH_TYPE::label_sequence>& exclusion = mesh->getLabelStratum(labelName, 1);
<a name="line486">486: </a> const PETSC_MESH_TYPE::label_sequence::iterator end = exclusion->end();
<a name="line487">487: </a> <font color="#4169E1">if</font> (debug > 1) {label->view(labelName.c_str());}
<a name="line488">488: </a>
<a name="line489">489: </a> <font color="#4169E1">for</font>(PETSC_MESH_TYPE::label_sequence::iterator e_iter = exclusion->begin(); e_iter != end; ++e_iter) {
<a name="line490">490: </a> ISieveTraversal<PETSC_MESH_TYPE::sieve_type>::orientedClosure(*mesh->getSieve(), *e_iter, pV);
<a name="line491">491: </a> const Visitor::point_type *oPoints = pV.getPoints();
<a name="line492">492: </a> const int oSize = pV.getSize();
<a name="line493">493: </a>
<a name="line494">494: </a> <font color="#4169E1">for</font>(int cl = 0; cl < oSize; ++cl) {
<a name="line495">495: </a> <font color="#4169E1">if</font> (seen.find(oPoints[cl]) != seen.end()) <font color="#4169E1">continue</font>;
<a name="line496">496: </a> <font color="#4169E1">if</font> (mesh->getValue(label, oPoints[cl]) == 1) {
<a name="line497">497: </a> seen.insert(oPoints[cl]);
<a name="line498">498: </a> s->setFiberDimension(oPoints[cl], 0, f);
<a name="line499">499: </a> s->addFiberDimension(oPoints[cl], -disc->getNumDof(mesh->depth(oPoints[cl])));
<a name="line500">500: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" point: "</font> << oPoints[cl] << <font color="#666666">" dim: "</font> << disc->getNumDof(mesh->depth(oPoints[cl])) << std::endl;}
<a name="line501">501: </a> }
<a name="line502">502: </a> }
<a name="line503">503: </a> pV.clear();
<a name="line504">504: </a> }
<a name="line505">505: </a> }
<a name="line506">506: </a> }
<a name="line507">507: </a> // Process constraints
<a name="line508">508: </a> f = 0;
<a name="line509">509: </a> <font color="#4169E1">for</font>(std::set<std::string>::const_iterator f_iter = discs->begin(); f_iter != discs->end(); ++f_iter, ++f) {
<a name="line510">510: </a> const Obj<GeneralDiscretization>& disc = this->getDiscretization(*f_iter);
<a name="line511">511: </a> const Obj<std::set<std::string> > bcs = disc->getBoundaryConditions();
<a name="line512">512: </a><strong><font color="#FF0000"> std:</font></strong>:string excludeName = <font color="#666666">"exclude-"</font>+*f_iter;
<a name="line513">513: </a>
<a name="line514">514: </a> <font color="#4169E1">for</font>(std::set<std::string>::const_iterator bc_iter = bcs->begin(); bc_iter != bcs->end(); ++bc_iter) {
<a name="line515">515: </a> const Obj<GeneralBoundaryCondition>& bc = disc->getBoundaryCondition(*bc_iter);
<a name="line516">516: </a> const Obj<PETSC_MESH_TYPE::label_sequence>& boundary = mesh->getLabelStratum(bc->getLabelName(), bc->getMarker());
<a name="line517">517: </a>
<a name="line518">518: </a> bcLabels.insert(bc->getLabelName());
<a name="line519">519: </a> <font color="#4169E1">if</font> (mesh->hasLabel(excludeName)) {
<a name="line520">520: </a> const Obj<PETSC_MESH_TYPE::label_type>& label = mesh->getLabel(excludeName);
<a name="line521">521: </a>
<a name="line522">522: </a> <font color="#4169E1">for</font>(PETSC_MESH_TYPE::label_sequence::iterator e_iter = boundary->begin(); e_iter != boundary->end(); ++e_iter) {
<a name="line523">523: </a> <font color="#4169E1">if</font> (!mesh->getValue(label, *e_iter)) {
<a name="line524">524: </a> const int numDof = disc->getNumDof(mesh->depth(*e_iter));
<a name="line525">525: </a>
<a name="line526">526: </a> <font color="#4169E1">if</font> (numDof) s->addConstraintDimension(*e_iter, numDof);
<a name="line527">527: </a> <font color="#4169E1">if</font> (numDof) s->setConstraintDimension(*e_iter, numDof, f);
<a name="line528">528: </a> }
<a name="line529">529: </a> }
<a name="line530">530: </a> } <font color="#4169E1">else</font> {
<a name="line531">531: </a> <font color="#4169E1">for</font>(PETSC_MESH_TYPE::label_sequence::iterator e_iter = boundary->begin(); e_iter != boundary->end(); ++e_iter) {
<a name="line532">532: </a> const int numDof = disc->getNumDof(mesh->depth(*e_iter));
<a name="line533">533: </a>
<a name="line534">534: </a> <font color="#4169E1">if</font> (numDof) s->addConstraintDimension(*e_iter, numDof);
<a name="line535">535: </a> <font color="#4169E1">if</font> (numDof) s->setConstraintDimension(*e_iter, numDof, f);
<a name="line536">536: </a> }
<a name="line537">537: </a> }
<a name="line538">538: </a> }
<a name="line539">539: </a> }
<a name="line540">540: </a> <font color="#4169E1">return</font> maxDof;
<a name="line541">541: </a> };
<a name="line542">542: </a> void calculateIndices(Obj<PETSC_MESH_TYPE> mesh) {
<a name="line543">543: </a> <font color="#4169E1">typedef</font> ISieveVisitor::PointRetriever<PETSC_MESH_TYPE::sieve_type> Visitor;
<a name="line544">544: </a> // Should have an iterator over the whole tree
<a name="line545">545: </a> Obj<names_type> discs = this->getDiscretizations();
<a name="line546">546: </a> const int debug = this->debug();
<a name="line547">547: </a><strong><font color="#FF0000"> std:</font></strong>:map<std::string, std::pair<int, int*> > indices;
<a name="line548">548: </a>
<a name="line549">549: </a> <font color="#4169E1">for</font>(names_type::const_iterator d_iter = discs->begin(); d_iter != discs->end(); ++d_iter) {
<a name="line550">550: </a> const Obj<GeneralDiscretization>& disc = this->getDiscretization(*d_iter);
<a name="line551">551: </a> indices[*d_iter] = std::pair<int, int*>(0, new int[disc->size()]); //size isn't a function of the mesh it's a function of the local function space
<a name="line552">552: </a> disc->setIndices(indices[*d_iter].second);
<a name="line553">553: </a> }
<a name="line554">554: </a> const Obj<PETSC_MESH_TYPE::label_sequence>& cells = mesh->heightStratum(0);
<a name="line555">555: </a> Visitor pV((int) pow(mesh->getSieve()->getMaxConeSize(), mesh->depth())+1, true);
<a name="line556">556: </a> ISieveTraversal<PETSC_MESH_TYPE::sieve_type>::orientedClosure(*mesh->getSieve(), *cells->begin(), pV);
<a name="line557">557: </a> const Visitor::point_type *oPoints = pV.getPoints();
<a name="line558">558: </a> const int oSize = pV.getSize();
<a name="line559">559: </a> int offset = 0;
<a name="line560">560: </a>
<a name="line561">561: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">"Closure for first element"</font> << std::endl;}
<a name="line562">562: </a> <font color="#4169E1">for</font>(int cl = 0; cl < oSize; ++cl) {
<a name="line563">563: </a> const int dim = mesh->depth(oPoints[cl]);
<a name="line564">564: </a>
<a name="line565">565: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" point "</font> << oPoints[cl] << <font color="#666666">" depth "</font> << dim << std::endl;}
<a name="line566">566: </a> <font color="#4169E1">for</font>(names_type::const_iterator d_iter = discs->begin(); d_iter != discs->end(); ++d_iter) {
<a name="line567">567: </a> const Obj<GeneralDiscretization>& disc = this->getDiscretization(*d_iter);
<a name="line568">568: </a> const int num = disc->getNumDof(dim);
<a name="line569">569: </a>
<a name="line570">570: </a> //<font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" disc "</font> << disc->getName() << <font color="#666666">" numDof "</font> << num << std::endl;}
<a name="line571">571: </a> <font color="#4169E1">for</font>(int o = 0; o < num; ++o) {
<a name="line572">572: </a> indices[*d_iter].second[indices[*d_iter].first++] = offset++;
<a name="line573">573: </a> }
<a name="line574">574: </a> }
<a name="line575">575: </a> }
<a name="line576">576: </a> pV.clear();
<a name="line577">577: </a> <font color="#4169E1">if</font> (debug > 1) {
<a name="line578">578: </a> <font color="#4169E1">for</font>(names_type::const_iterator d_iter = discs->begin(); d_iter != discs->end(); ++d_iter) {
<a name="line579">579: </a> //const Obj<GeneralDiscretization>& disc = this->getDiscretization(*d_iter);
<a name="line580">580: </a>
<a name="line581">581: </a> //std::cout << <font color="#666666">"Discretization "</font> << disc->getName() << <font color="#666666">" indices:"</font>;
<a name="line582">582: </a> <font color="#4169E1">for</font>(int i = 0; i < indices[*d_iter].first; ++i) {
<a name="line583">583: </a><strong><font color="#FF0000"> std:</font></strong>:cout << <font color="#666666">" "</font> << indices[*d_iter].second[i];
<a name="line584">584: </a> }
<a name="line585">585: </a><strong><font color="#FF0000"> std:</font></strong>:cout << std::endl;
<a name="line586">586: </a> }
<a name="line587">587: </a> }
<a name="line588">588: </a> };
<a name="line590">590: </a> void calculateIndicesExcluded(const Obj<PETSC_MESH_TYPE> mesh, const Obj<PETSC_MESH_TYPE::real_section_type>& s, const Obj<names_type>& discs) {
<a name="line591">591: </a> <font color="#4169E1">typedef</font> ISieveVisitor::PointRetriever<PETSC_MESH_TYPE::sieve_type> Visitor;
<a name="line592">592: </a> <font color="#4169E1">typedef</font> std::map<std::string, std::pair<int, indexSet> > indices_type;
<a name="line593">593: </a> const Obj<PETSC_MESH_TYPE::label_type>& indexLabel = mesh->createLabel(<font color="#666666">"cellExclusion"</font>);
<a name="line594">594: </a> const int debug = this->debug();
<a name="line595">595: </a> int marker = 0;
<a name="line596">596: </a><strong><font color="#FF0000"> std:</font></strong>:map<indices_type, int> indexMap;
<a name="line597">597: </a> indices_type indices;
<a name="line598">598: </a> Visitor pV((int) pow(mesh->getSieve()->getMaxConeSize(), mesh->depth())+1, true);
<a name="line599">599: </a>
<a name="line600">600: </a> <font color="#4169E1">for</font>(names_type::const_iterator d_iter = discs->begin(); d_iter != discs->end(); ++d_iter) {
<a name="line601">601: </a> const Obj<GeneralDiscretization>& disc = this->getDiscretization(*d_iter);
<a name="line602">602: </a> const int size = disc->size();
<a name="line603">603: </a>
<a name="line604">604: </a> indices[*d_iter].second.resize(size);
<a name="line605">605: </a> }
<a name="line606">606: </a> const names_type::const_iterator dBegin = discs->begin();
<a name="line607">607: </a> const names_type::const_iterator dEnd = discs->end();
<a name="line608">608: </a><strong><font color="#FF0000"> std:</font></strong>:set<PETSC_MESH_TYPE::point_type> seen;
<a name="line609">609: </a> int f = 0;
<a name="line610">610: </a>
<a name="line611">611: </a> <font color="#4169E1">for</font>(names_type::const_iterator f_iter = dBegin; f_iter != dEnd; ++f_iter, ++f) {
<a name="line612">612: </a><strong><font color="#FF0000"> std:</font></strong>:string labelName = <font color="#666666">"exclude-"</font>+*f_iter;
<a name="line613">613: </a>
<a name="line614">614: </a> <font color="#4169E1">if</font> (mesh->hasLabel(labelName)) {
<a name="line615">615: </a> const Obj<PETSC_MESH_TYPE::label_sequence>& exclusion = mesh->getLabelStratum(labelName, 1);
<a name="line616">616: </a> const PETSC_MESH_TYPE::label_sequence::iterator end = exclusion->end();
<a name="line617">617: </a>
<a name="line618">618: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">"Processing exclusion "</font> << labelName << std::endl;}
<a name="line619">619: </a> <font color="#4169E1">for</font>(PETSC_MESH_TYPE::label_sequence::iterator e_iter = exclusion->begin(); e_iter != end; ++e_iter) {
<a name="line620">620: </a> <font color="#4169E1">if</font> (mesh->height(*e_iter)) <font color="#4169E1">continue</font>;
<a name="line621">621: </a> ISieveTraversal<PETSC_MESH_TYPE::sieve_type>::orientedClosure(*mesh->getSieve(), *e_iter, pV);
<a name="line622">622: </a> const Visitor::point_type *oPoints = pV.getPoints();
<a name="line623">623: </a> const int oSize = pV.getSize();
<a name="line624">624: </a> int offset = 0;
<a name="line625">625: </a>
<a name="line626">626: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" Closure for cell "</font> << *e_iter << std::endl;}
<a name="line627">627: </a> <font color="#4169E1">for</font>(int cl = 0; cl < oSize; ++cl) {
<a name="line628">628: </a> int g = 0;
<a name="line629">629: </a>
<a name="line630">630: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" point "</font> << oPoints[cl] << std::endl;}
<a name="line631">631: </a> <font color="#4169E1">for</font>(names_type::const_iterator g_iter = dBegin; g_iter != dEnd; ++g_iter, ++g) {
<a name="line632">632: </a> const int fDim = s->getFiberDimension(oPoints[cl], g);
<a name="line633">633: </a>
<a name="line634">634: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" disc "</font> << *g_iter << <font color="#666666">" numDof "</font> << fDim << std::endl;}
<a name="line635">635: </a> <font color="#4169E1">for</font>(int d = 0; d < fDim; ++d) {
<a name="line636">636: </a> indices[*g_iter].second[indices[*g_iter].first++] = offset++;
<a name="line637">637: </a> }
<a name="line638">638: </a> }
<a name="line639">639: </a> }
<a name="line640">640: </a> pV.clear();
<a name="line641">641: </a> const std::map<indices_type, int>::iterator entry = indexMap.find(indices);
<a name="line642">642: </a>
<a name="line643">643: </a> <font color="#4169E1">if</font> (debug > 1) {
<a name="line644">644: </a> <font color="#4169E1">for</font>(std::map<indices_type, int>::iterator i_iter = indexMap.begin(); i_iter != indexMap.end(); ++i_iter) {
<a name="line645">645: </a> <font color="#4169E1">for</font>(names_type::const_iterator g_iter = discs->begin(); g_iter != discs->end(); ++g_iter) {
<a name="line646">646: </a><strong><font color="#FF0000"> std:</font></strong>:cout << <font color="#666666">"Discretization ("</font> << i_iter->second << <font color="#666666">") "</font> << *g_iter << <font color="#666666">" indices:"</font>;
<a name="line647">647: </a> <font color="#4169E1">for</font>(int i = 0; i < ((indices_type) i_iter->first)[*g_iter].first; ++i) {
<a name="line648">648: </a><strong><font color="#FF0000"> std:</font></strong>:cout << <font color="#666666">" "</font> << ((indices_type) i_iter->first)[*g_iter].second[i];
<a name="line649">649: </a> }
<a name="line650">650: </a><strong><font color="#FF0000"> std:</font></strong>:cout << std::endl;
<a name="line651">651: </a> }
<a name="line652">652: </a><strong><font color="#FF0000"> std:</font></strong>:cout << <font color="#666666">"Comparison: "</font> << (indices == i_iter->first) << std::endl;
<a name="line653">653: </a> }
<a name="line654">654: </a> <font color="#4169E1">for</font>(names_type::const_iterator g_iter = discs->begin(); g_iter != discs->end(); ++g_iter) {
<a name="line655">655: </a><strong><font color="#FF0000"> std:</font></strong>:cout << <font color="#666666">"Discretization "</font> << *g_iter << <font color="#666666">" indices:"</font>;
<a name="line656">656: </a> <font color="#4169E1">for</font>(int i = 0; i < indices[*g_iter].first; ++i) {
<a name="line657">657: </a><strong><font color="#FF0000"> std:</font></strong>:cout << <font color="#666666">" "</font> << indices[*g_iter].second[i];
<a name="line658">658: </a> }
<a name="line659">659: </a><strong><font color="#FF0000"> std:</font></strong>:cout << std::endl;
<a name="line660">660: </a> }
<a name="line661">661: </a> }
<a name="line662">662: </a> <font color="#4169E1">if</font> (entry != indexMap.end()) {
<a name="line663">663: </a> mesh->setValue(indexLabel, *e_iter, entry->second);
<a name="line664">664: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" Found existing indices with marker "</font> << entry->second << std::endl;}
<a name="line665">665: </a> } <font color="#4169E1">else</font> {
<a name="line666">666: </a> indexMap[indices] = ++marker;
<a name="line667">667: </a> mesh->setValue(indexLabel, *e_iter, marker);
<a name="line668">668: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" Created new indices with marker "</font> << marker << std::endl;}
<a name="line669">669: </a> }
<a name="line670">670: </a> <font color="#4169E1">for</font>(names_type::const_iterator g_iter = discs->begin(); g_iter != discs->end(); ++g_iter) {
<a name="line671">671: </a> indices[*g_iter].first = 0;
<a name="line672">672: </a> <font color="#4169E1">for</font>(unsigned int i = 0; i < indices[*g_iter].second.size(); ++i) indices[*g_iter].second[i] = 0;
<a name="line673">673: </a> }
<a name="line674">674: </a> }
<a name="line675">675: </a> }
<a name="line676">676: </a> }
<a name="line677">677: </a> <font color="#4169E1">if</font> (debug > 1) {indexLabel->view(<font color="#666666">"cellExclusion"</font>);}
<a name="line678">678: </a> <font color="#4169E1">for</font>(std::map<indices_type, int>::iterator i_iter = indexMap.begin(); i_iter != indexMap.end(); ++i_iter) {
<a name="line679">679: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">"Setting indices for marker "</font> << i_iter->second << std::endl;}
<a name="line680">680: </a> <font color="#4169E1">for</font>(names_type::const_iterator g_iter = discs->begin(); g_iter != discs->end(); ++g_iter) {
<a name="line681">681: </a> const Obj<GeneralDiscretization>& disc = this->getDiscretization(*g_iter);
<a name="line682">682: </a> const indexSet indSet = ((indices_type) i_iter->first)[*g_iter].second;
<a name="line683">683: </a> const int size = indSet.size();
<a name="line684">684: </a> int *_indices = new int[size];
<a name="line685">685: </a>
<a name="line686">686: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" field "</font> << *g_iter << std::endl;}
<a name="line687">687: </a> <font color="#4169E1">for</font>(int i = 0; i < size; ++i) {
<a name="line688">688: </a> _indices[i] = indSet[i];
<a name="line689">689: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" indices["</font><<i<<<font color="#666666">"] = "</font> << _indices[i] << std::endl;}
<a name="line690">690: </a> }
<a name="line691">691: </a> disc->setIndices(_indices, i_iter->second);
<a name="line692">692: </a> }
<a name="line693">693: </a> }
<a name="line694">694: </a> };
<a name="line695">695: </a><strong><font color="#FF0000"> public:</font></strong>
<a name="line696">696: </a> void setupField(const Obj<PETSC_MESH_TYPE> mesh, const Obj<PETSC_MESH_TYPE::real_section_type>& s, const int cellMarker = 2, const bool noUpdate = false, const bool setAll = false) {
<a name="line697">697: </a> <font color="#4169E1">typedef</font> ISieveVisitor::PointRetriever<PETSC_MESH_TYPE::sieve_type> Visitor;
<a name="line698">698: </a> const Obj<names_type>& discs = this->getDiscretizations();
<a name="line699">699: </a> const int debug = s->debug();
<a name="line700">700: </a> names_type bcLabels;
<a name="line701">701: </a>
<a name="line702">702: </a> s->setChart(mesh->getSieve()->getChart());
<a name="line703">703: </a> int maxDof = this->setFiberDimensions(mesh, s, discs, bcLabels);
<a name="line704">704: </a> this->calculateIndices(mesh);
<a name="line705">705: </a> this->calculateIndicesExcluded(mesh, s, discs);
<a name="line706">706: </a> this->createReorder();
<a name="line707">707: </a> mesh->allocate(s);
<a name="line708">708: </a> s->defaultConstraintDof();
<a name="line709">709: </a> const Obj<PETSC_MESH_TYPE::label_type>& cellExclusion = mesh->getLabel(<font color="#666666">"cellExclusion"</font>);
<a name="line710">710: </a>
<a name="line711">711: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">"Setting boundary values to "</font> << std::endl;}
<a name="line712">712: </a> <font color="#4169E1">for</font>(names_type::const_iterator n_iter = bcLabels.begin(); n_iter != bcLabels.end(); ++n_iter) {
<a name="line713">713: </a> Obj<PETSC_MESH_TYPE::label_sequence> boundaryCells = mesh->getLabelStratum(*n_iter, cellMarker);
<a name="line714">714: </a> <font color="#4169E1">if</font> (setAll) boundaryCells = mesh->heightStratum(0);
<a name="line715">715: </a> //const Obj<PETSC_MESH_TYPE::real_section_type>& coordinates = mesh->getRealSection(<font color="#666666">"coordinates"</font>);
<a name="line716">716: </a> const Obj<names_type>& discs = this->getDiscretizations();
<a name="line717">717: </a> const PETSC_MESH_TYPE::point_type firstCell = *boundaryCells->begin();
<a name="line718">718: </a> const int numFields = discs->size();
<a name="line719">719: </a><strong><font color="#FF0000"> PETSC_MESH_TYPE:</font></strong>:real_section_type::value_type *values = new PETSC_MESH_TYPE::real_section_type::value_type[mesh->sizeWithBC(s, firstCell)];
<a name="line720">720: </a> int *dofs = new int[maxDof];
<a name="line721">721: </a> int *v = new int[numFields];
<a name="line722">722: </a> Visitor pV((int) pow(mesh->getSieve()->getMaxConeSize(), mesh->depth())+1, true);
<a name="line723">723: </a>
<a name="line724">724: </a> <font color="#4169E1">for</font>(PETSC_MESH_TYPE::label_sequence::iterator c_iter = boundaryCells->begin(); c_iter != boundaryCells->end(); ++c_iter) {
<a name="line725">725: </a> ISieveTraversal<PETSC_MESH_TYPE::sieve_type>::orientedClosure(*mesh->getSieve(), *c_iter, pV);
<a name="line726">726: </a> const Visitor::point_type *oPoints = pV.getPoints();
<a name="line727">727: </a> const int oSize = pV.getSize();
<a name="line728">728: </a>
<a name="line729">729: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" Boundary cell "</font> << *c_iter << std::endl;}
<a name="line730">730: </a> //mesh->computeElementGeometry(coordinates, *c_iter, v0, J, <A href="../../docs/manualpages/Sys/PETSC_NULL.html#PETSC_NULL">PETSC_NULL</A>, detJ);
<a name="line731">731: </a> this->setCell(mesh, *c_iter);
<a name="line732">732: </a> <font color="#4169E1">for</font>(int f = 0; f < numFields; ++f) v[f] = 0;
<a name="line733">733: </a> <font color="#4169E1">for</font>(int cl = 0; cl < oSize; ++cl) {
<a name="line734">734: </a> //<font color="#4169E1">if</font> (*c_iter == 0) std::cout << oPoints[cl] << std::endl;
<a name="line735">735: </a> const int cDim = s->getConstraintDimension(oPoints[cl]);
<a name="line736">736: </a> int off = 0;
<a name="line737">737: </a> int f = 0;
<a name="line738">738: </a> int i = -1;
<a name="line739">739: </a>
<a name="line740">740: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" point "</font> << oPoints[cl] << std::endl;}
<a name="line741">741: </a> <font color="#4169E1">if</font> (cDim || setAll) {
<a name="line742">742: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" constrained excMarker: "</font> << mesh->getValue(cellExclusion, *c_iter) << std::endl;}
<a name="line743">743: </a> <font color="#4169E1">for</font>(names_type::const_iterator f_iter = discs->begin(); f_iter != discs->end(); ++f_iter, ++f) {
<a name="line744">744: </a> const Obj<GeneralDiscretization>& disc = this->getDiscretization(*f_iter);
<a name="line745">745: </a> const Obj<names_type> bcs = disc->getBoundaryConditions();
<a name="line746">746: </a> const int fDim = s->getFiberDimension(oPoints[cl], f);//disc->getNumDof(this->depth(oPoints[cl]));
<a name="line747">747: </a> const int *indices = disc->getIndices(mesh->getValue(cellExclusion, *c_iter));
<a name="line748">748: </a> int b = 0;
<a name="line749">749: </a>
<a name="line750">750: </a> <font color="#4169E1">for</font>(names_type::const_iterator bc_iter = bcs->begin(); bc_iter != bcs->end(); ++bc_iter, ++b) {
<a name="line751">751: </a> const Obj<GeneralBoundaryCondition>& bc = disc->getBoundaryCondition(*bc_iter);
<a name="line752">752: </a> const int value = mesh->getValue(mesh->getLabel(bc->getLabelName()), oPoints[cl]);
<a name="line753">753: </a> <font color="#4169E1">if</font> (b > 0) v[f] -= fDim;
<a name="line754">754: </a> <font color="#4169E1">if</font> (value == bc->getMarker()) {
<a name="line755">755: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" field "</font> << *f_iter << <font color="#666666">" marker "</font> << value << std::endl;}
<a name="line756">756: </a> <font color="#4169E1">for</font>(int d = 0; d < fDim; ++d, ++v[f]) {
<a name="line757">757: </a> dofs[++i] = off+d;
<a name="line758">758: </a> //<font color="#4169E1">if</font> (!noUpdate) values[indices[v[f]]] = (*bc->getDualIntegrator())(v0, J, v[f], bc->getFunction());
<a name="line759">759: </a> <font color="#4169E1">if</font> (!noUpdate) {
<a name="line760">760: </a> values[indices[v[f]]] = bc->integrateDual(v[f]);
<a name="line761">761: </a> }
<a name="line762">762: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" setting values["</font><<indices[v[f]]<<<font color="#666666">"] = "</font> << values[indices[v[f]]] << std::endl;}
<a name="line763">763: </a> }
<a name="line764">764: </a> // Allow only one condition per point
<a name="line765">765: </a> ++b;
<a name="line766">766: </a> <font color="#4169E1">break</font>;
<a name="line767">767: </a> } <font color="#4169E1">else</font> {
<a name="line768">768: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" field "</font> << *f_iter << std::endl;}
<a name="line769">769: </a> <font color="#4169E1">for</font>(int d = 0; d < fDim; ++d, ++v[f]) {
<a name="line770">770: </a> <font color="#4169E1">if</font> (!setAll) {
<a name="line771">771: </a> values[indices[v[f]]] = 0.0;
<a name="line772">772: </a> } <font color="#4169E1">else</font> {
<a name="line773">773: </a> //TODO: <font color="#4169E1">do</font> strides of the rank of the unknown space; we need a natural way of handling vectors in a single discretization.
<a name="line774">774: </a> values[indices[v[f]]] = bc->integrateDual(v[f]);
<a name="line775">775: </a> }
<a name="line776">776: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" setting values["</font><<indices[v[f]]<<<font color="#666666">"] = "</font> << values[indices[v[f]]] << std::endl;}
<a name="line777">777: </a> }
<a name="line778">778: </a> }
<a name="line779">779: </a> }
<a name="line780">780: </a> <font color="#4169E1">if</font> (b == 0) {
<a name="line781">781: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" field "</font> << *f_iter << std::endl;}
<a name="line782">782: </a> <font color="#4169E1">for</font>(int d = 0; d < fDim; ++d, ++v[f]) {
<a name="line783">783: </a> values[indices[v[f]]] = 0.0;
<a name="line784">784: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" setting values["</font><<indices[v[f]]<<<font color="#666666">"] = "</font> << values[indices[v[f]]] << std::endl;}
<a name="line785">785: </a> }
<a name="line786">786: </a> }
<a name="line787">787: </a> off += fDim;
<a name="line788">788: </a> }
<a name="line789">789: </a> <font color="#4169E1">if</font> (i != cDim-1) {throw ALE::Exception(<font color="#666666">"Invalid constraint initialization"</font>);}
<a name="line790">790: </a> s->setConstraintDof(oPoints[cl], dofs);
<a name="line791">791: </a> } <font color="#4169E1">else</font> {
<a name="line792">792: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" unconstrained"</font> << std::endl;}
<a name="line793">793: </a> <font color="#4169E1">for</font>(names_type::const_iterator f_iter = discs->begin(); f_iter != discs->end(); ++f_iter, ++f) {
<a name="line794">794: </a> const Obj<GeneralDiscretization>& disc = this->getDiscretization(*f_iter);
<a name="line795">795: </a> const int fDim = s->getFiberDimension(oPoints[cl], f);//disc->getNumDof(this->depth(oPoints[cl]));
<a name="line796">796: </a> const int *indices = disc->getIndices(mesh->getValue(cellExclusion, *c_iter));
<a name="line797">797: </a>
<a name="line798">798: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" field "</font> << *f_iter << std::endl;}
<a name="line799">799: </a> <font color="#4169E1">for</font>(int d = 0; d < fDim; ++d, ++v[f]) {
<a name="line800">800: </a> values[indices[v[f]]] = 0.0;
<a name="line801">801: </a> <font color="#4169E1">if</font> (debug > 1) {std::cout << <font color="#666666">" setting values["</font><<indices[v[f]]<<<font color="#666666">"] = "</font> << values[indices[v[f]]] << std::endl;}
<a name="line802">802: </a> }
<a name="line803">803: </a> }
<a name="line804">804: </a> }
<a name="line805">805: </a> }
<a name="line806">806: </a> <font color="#4169E1">if</font> (debug > 1) {
<a name="line807">807: </a> <font color="#4169E1">for</font>(int f = 0; f < numFields; ++f) v[f] = 0;
<a name="line808">808: </a> <font color="#4169E1">for</font>(int cl = 0; cl < oSize; ++cl) {
<a name="line809">809: </a> int f = 0;
<a name="line810">810: </a> <font color="#4169E1">for</font>(names_type::const_iterator f_iter = discs->begin(); f_iter != discs->end(); ++f_iter, ++f) {
<a name="line811">811: </a> const Obj<GeneralDiscretization>& disc = this->getDiscretization(*f_iter);
<a name="line812">812: </a> const int fDim = s->getFiberDimension(oPoints[cl], f);
<a name="line813">813: </a> const int *indices = disc->getIndices(mesh->getValue(cellExclusion, *c_iter));
<a name="line814">814: </a>
<a name="line815">815: </a> <font color="#4169E1">for</font>(int d = 0; d < fDim; ++d, ++v[f]) {
<a name="line816">816: </a><strong><font color="#FF0000"> std:</font></strong>:cout << <font color="#666666">" "</font><<*f_iter<<<font color="#666666">"-value["</font><<indices[v[f]]<<<font color="#666666">"] "</font> << values[indices[v[f]]] << std::endl;
<a name="line817">817: </a> }
<a name="line818">818: </a> }
<a name="line819">819: </a> }
<a name="line820">820: </a> }
<a name="line821">821: </a> <font color="#4169E1">if</font> (!noUpdate) {
<a name="line822">822: </a> mesh->updateAll(s, *c_iter, values);
<a name="line823">823: </a> }
<a name="line824">824: </a> pV.clear();
<a name="line825">825: </a> }
<a name="line826">826: </a> delete [] dofs;
<a name="line827">827: </a> delete [] values;
<a name="line828">828: </a> }
<a name="line829">829: </a> <font color="#4169E1">if</font> (debug > 1) {s->view(<font color="#666666">""</font>);}
<a name="line830">830: </a> };
<a name="line831">831: </a> };
<a name="line832">832: </a> <font color="#B22222">/*</font>
<a name="line834">834: </a><font color="#B22222"> Jacobian and RHS assembly functions to pass to <A href="../../docs/manualpages/DMMG/DMMG.html#DMMG">DMMG</A> which depend on a GenericFormSubProblem rather than on some options.</font>
<a name="line835">835: </a><font color="#B22222"> </font>
<a name="line837">837: </a><font color="#B22222"> */</font>
<a name="line842">842: </a> <A href="../../docs/manualpages/Sys/PetscErrorCode.html#PetscErrorCode">PetscErrorCode</A> RHS_FEMProblem(::Mesh mesh, SectionReal X, SectionReal section, void * ctx) {
<a name="line843">843: </a> GenericFormSubProblem * subproblem = (GenericFormSubProblem *)ctx;
<a name="line844">844: </a> Obj<PETSC_MESH_TYPE> m;
<a name="line846">846: </a>
<a name="line848">848: </a> <A href="../../docs/manualpages/Mesh/MeshGetMesh.html#MeshGetMesh">MeshGetMesh</A>(mesh, m);
<a name="line849">849: </a> <A href="../../docs/manualpages/Mesh/SectionRealZero.html#SectionRealZero">SectionRealZero</A>(section);
<a name="line850">850: </a> Obj<PETSC_MESH_TYPE::real_section_type> s;
<a name="line851">851: </a> <A href="../../docs/manualpages/Mesh/SectionRealGetSection.html#SectionRealGetSection">SectionRealGetSection</A>(section, s);
<a name="line852">852: </a> // Loop over cells
<a name="line853">853: </a> //loop over integrals;
<a name="line854">854: </a>
<a name="line855">855: </a><strong><font color="#FF0000"> GenericFormSubProblem:</font></strong>:names_type integral_names = subproblem->getIntegrals();
<a name="line856">856: </a><strong><font color="#FF0000"> GenericFormSubProblem:</font></strong>:names_type::const_iterator n_iter = integral_names.begin();
<a name="line857">857: </a><strong><font color="#FF0000"> GenericFormSubProblem:</font></strong>:names_type::const_iterator n_iter_end = integral_names.end();
<a name="line858">858: </a> //const Obj<PETSC_MESH_TYPE::order_type>& order = m->getFactory()->getGlobalOrder(m, <font color="#666666">"</font><font color="#4169E1">default</font>", s);
<a name="line859">859: </a> <font color="#4169E1">while</font> (n_iter != n_iter_end) {
<a name="line860">860: </a> Obj<GeneralIntegral> cur_integral = subproblem->getIntegral(*n_iter);
<a name="line861">861: </a> //get the integral's topological objects.
<a name="line862">862: </a><strong><font color="#FF0000"> std:</font></strong>:string cur_marker_name = cur_integral->getLabelName();
<a name="line863">863: </a> int cur_marker_num = cur_integral->getLabelMarker();
<a name="line864">864: </a> int cur_rank = cur_integral->getTensorRank();
<a name="line865">865: </a> int cur_dimension = cur_integral->getSpaceDimension();
<a name="line866">866: </a> Obj<PETSC_MESH_TYPE::label_sequence> integral_cells = m->getLabelStratum(cur_marker_name, cur_marker_num);
<a name="line867">867: </a><strong><font color="#FF0000"> PETSC_MESH_TYPE:</font></strong>:label_sequence::iterator ic_iter = integral_cells->begin();
<a name="line868">868: </a><strong><font color="#FF0000"> PETSC_MESH_TYPE:</font></strong>:label_sequence::iterator ic_iter_end = integral_cells->end();
<a name="line869">869: </a> <font color="#4169E1">if</font> (cur_rank == 1) {
<a name="line870">870: </a> <A href="../../docs/manualpages/Sys/PetscScalar.html#PetscScalar">PetscScalar</A> * values;
<a name="line871">871: </a> <A href="../../docs/manualpages/Sys/PetscMalloc.html#PetscMalloc">PetscMalloc</A>(cur_dimension*<font color="#4169E1">sizeof</font>(<A href="../../docs/manualpages/Sys/PetscScalar.html#PetscScalar">PetscScalar</A>), &values);
<a name="line872">872: </a> <A href="../../docs/manualpages/Sys/PetscScalar.html#PetscScalar">PetscScalar</A> * elemVec;
<a name="line873">873: </a> <A href="../../docs/manualpages/Sys/PetscMalloc.html#PetscMalloc">PetscMalloc</A>(cur_dimension*<font color="#4169E1">sizeof</font>(<A href="../../docs/manualpages/Sys/PetscScalar.html#PetscScalar">PetscScalar</A>), &elemVec);
<a name="line874">874: </a> Obj<GenericFormSubProblem::names_type> discs = subproblem->getDiscretizations();
<a name="line875">875: </a> //loop over cells
<a name="line876">876: </a> <font color="#4169E1">while</font> (ic_iter != ic_iter_end) {
<a name="line877">877: </a> subproblem->setCell(m, *ic_iter);
<a name="line878">878: </a> //loop over discretizations
<a name="line879">879: </a><strong><font color="#FF0000"> GenericFormSubProblem:</font></strong>:names_type::iterator d_iter = discs->begin();
<a name="line880">880: </a><strong><font color="#FF0000"> GenericFormSubProblem:</font></strong>:names_type::iterator d_iter_end = discs->end();
<a name="line881">881: </a> <font color="#4169E1">while</font> (d_iter != d_iter_end) {
<a name="line882">882: </a> Obj<GeneralDiscretization> disc = subproblem->getDiscretization(*d_iter);
<a name="line883">883: </a> //evaluate the RHS at each index point
<a name="line884">884: </a> <font color="#4169E1">for</font> (int i = 0; i < disc->size(); i++) {
<a name="line885">885: </a> values[disc->getIndices()[i]] = -1.*disc->evaluateRHS(i);
<a name="line886">886: </a> }
<a name="line887">887: </a> d_iter++;
<a name="line888">888: </a> }
<a name="line889">889: </a> cur_integral->tabulateTensor(elemVec, values);
<a name="line890">890: </a> SectionRealUpdateAdd(section, *ic_iter, elemVec);
<a name="line891">891: </a> ic_iter++;
<a name="line892">892: </a> }
<a name="line893">893: </a> <A href="../../docs/manualpages/Mesh/SectionRealGetSection.html#SectionRealGetSection">SectionRealGetSection</A>(section, s);
<a name="line894">894: </a> } <font color="#4169E1">else</font> <font color="#4169E1">if</font> (cur_rank == 2) {
<a name="line895">895: </a> //cancel out BCs <font color="#4169E1">if</font> necessary... this doesn't require any knowledge of the discretization form (<font color="#4169E1">if</font> handled right).
<a name="line896">896: </a> <A href="../../docs/manualpages/Sys/PetscScalar.html#PetscScalar">PetscScalar</A> * full_tensor;
<a name="line897">897: </a> <A href="../../docs/manualpages/Sys/PetscMalloc.html#PetscMalloc">PetscMalloc</A>(cur_dimension*cur_dimension*<font color="#4169E1">sizeof</font>(<A href="../../docs/manualpages/Sys/PetscScalar.html#PetscScalar">PetscScalar</A>), &full_tensor);
<a name="line898">898: </a> <A href="../../docs/manualpages/Sys/PetscScalar.html#PetscScalar">PetscScalar</A> * elemVec;
<a name="line899">899: </a> <A href="../../docs/manualpages/Sys/PetscMalloc.html#PetscMalloc">PetscMalloc</A>(cur_dimension*<font color="#4169E1">sizeof</font>(<A href="../../docs/manualpages/Sys/PetscScalar.html#PetscScalar">PetscScalar</A>), &elemVec);
<a name="line900">900: </a> <font color="#4169E1">while</font> (ic_iter != ic_iter_end) {
<a name="line901">901: </a> subproblem->setCell(m, *ic_iter);
<a name="line902">902: </a> cur_integral->tabulateTensor(full_tensor);
<a name="line903">903: </a> //create the linear contribution from the BCs
<a name="line904">904: </a> <A href="../../docs/manualpages/Sys/PetscScalar.html#PetscScalar">PetscScalar</A> * xValues;
<a name="line905">905: </a> <A href="../../docs/manualpages/Mesh/SectionRealRestrict.html#SectionRealRestrict">SectionRealRestrict</A>(X, *ic_iter, &xValues); //get the coefficients -- BUG: setCell restricts as well; static
<a name="line906">906: </a> <font color="#4169E1">for</font>(int f = 0; f < cur_dimension; f++) {
<a name="line907">907: </a> elemVec[f] = 0.;
<a name="line908">908: </a> <font color="#4169E1">for</font>(int g = 0; g < cur_dimension; g++) {
<a name="line909">909: </a> elemVec[f] += full_tensor[f*cur_dimension+g]*xValues[g];
<a name="line910">910: </a> }
<a name="line911">911: </a> }
<a name="line912">912: </a> SectionRealUpdateAdd(section, *ic_iter, elemVec);
<a name="line913">913: </a> ic_iter++;
<a name="line914">914: </a> }
<a name="line915">915: </a> //delete full_tensor;
<a name="line916">916: </a> //delete elemVec;
<a name="line917">917: </a> } <font color="#4169E1">else</font> {
<a name="line918">918: </a> throw Exception(<font color="#666666">"RHS_FEMProblem: Unsupported tensor rank"</font>);
<a name="line919">919: </a> }
<a name="line920">920: </a> n_iter++;
<a name="line921">921: </a> <A href="../../docs/manualpages/Mesh/SectionRealGetSection.html#SectionRealGetSection">SectionRealGetSection</A>(section, s);
<a name="line922">922: </a> }
<a name="line923">923: </a> // Exchange neighbors
<a name="line924">924: </a> <A href="../../docs/manualpages/Mesh/SectionRealComplete.html#SectionRealComplete">SectionRealComplete</A>(section);
<a name="line925">925: </a> // Subtract the constant
<a name="line926">926: </a> <font color="#4169E1">if</font> (m->hasRealSection(<font color="#666666">"constant"</font>)) {
<a name="line927">927: </a> const Obj<PETSC_MESH_TYPE::real_section_type>& constant = m->getRealSection(<font color="#666666">"constant"</font>);
<a name="line928">928: </a> Obj<PETSC_MESH_TYPE::real_section_type> s;
<a name="line929">929: </a>
<a name="line930">930: </a> <A href="../../docs/manualpages/Mesh/SectionRealGetSection.html#SectionRealGetSection">SectionRealGetSection</A>(section, s);
<a name="line931">931: </a> s->axpy(-1.0, constant);
<a name="line932">932: </a> }
<a name="line933">933: </a> <A href="../../docs/manualpages/Sys/PetscTruth.html#PetscTruth">PetscTruth</A> flag;
<a name="line934">934: </a> <A href="../../docs/manualpages/Sys/PetscOptionsHasName.html#PetscOptionsHasName">PetscOptionsHasName</A>(<A href="../../docs/manualpages/Sys/PETSC_NULL.html#PETSC_NULL">PETSC_NULL</A>, <font color="#666666">"-vec_view"</font>, &flag);
<a name="line935">935: </a> <font color="#4169E1">if</font> (flag) {
<a name="line936">936: </a> <A href="../../docs/manualpages/Mesh/SectionRealGetSection.html#SectionRealGetSection">SectionRealGetSection</A>(section, s);
<a name="line937">937: </a> s->view(<font color="#666666">"RHS"</font>);
<a name="line938">938: </a> }
<a name="line939">939: </a> <font color="#4169E1">return</font>(0);
<a name="line940">940: </a> }
<a name="line945">945: </a> <A href="../../docs/manualpages/Sys/PetscErrorCode.html#PetscErrorCode">PetscErrorCode</A> Jac_FEMProblem(::Mesh mesh, SectionReal section, <A href="../../docs/manualpages/Mat/Mat.html#Mat">Mat</A> A, void * ctx) {
<a name="line947">947: </a> GenericFormSubProblem * subproblem = (GenericFormSubProblem *)ctx;
<a name="line948">948: </a> Obj<PETSC_MESH_TYPE::real_section_type> s;
<a name="line949">949: </a> Obj<PETSC_MESH_TYPE> m;
<a name="line951">951: </a> <A href="../../docs/manualpages/Mat/MatZeroEntries.html#MatZeroEntries">MatZeroEntries</A>(A);
<a name="line952">952: </a> <A href="../../docs/manualpages/Mesh/MeshGetMesh.html#MeshGetMesh">MeshGetMesh</A>(mesh, m);
<a name="line953">953: </a> <A href="../../docs/manualpages/Mesh/SectionRealGetSection.html#SectionRealGetSection">SectionRealGetSection</A>(section, s);
<a name="line954">954: </a> //loop over integrals; <font color="#4169E1">for</font> now.
<a name="line955">955: </a><strong><font color="#FF0000"> GenericFormSubProblem:</font></strong>:names_type integral_names = subproblem->getIntegrals();
<a name="line956">956: </a><strong><font color="#FF0000"> GenericFormSubProblem:</font></strong>:names_type::iterator n_iter = integral_names.begin();
<a name="line957">957: </a><strong><font color="#FF0000"> GenericFormSubProblem:</font></strong>:names_type::iterator n_iter_end = integral_names.end();
<a name="line958">958: </a> const Obj<PETSC_MESH_TYPE::order_type>& order = m->getFactory()->getGlobalOrder(m, <font color="#666666">"</font><font color="#4169E1">default</font>", s);
<a name="line959">959: </a> <font color="#4169E1">while</font> (n_iter != n_iter_end) {
<a name="line960">960: </a> Obj<GeneralIntegral> cur_integral = subproblem->getIntegral(*n_iter);
<a name="line961">961: </a> //get the integral's topological objects.
<a name="line962">962: </a><strong><font color="#FF0000"> std:</font></strong>:string cur_marker_name = cur_integral->getLabelName();
<a name="line963">963: </a> int cur_marker_num = cur_integral->getLabelMarker();
<a name="line964">964: </a> int cur_rank = cur_integral->getTensorRank();
<a name="line965">965: </a> int cur_dimension = cur_integral->getSpaceDimension();
<a name="line966">966: </a> //GOOD LORD >:(
<a name="line967">967: </a> m->setMaxDof(subproblem->localSpaceDimension());
<a name="line969">969: </a> //divide here; ignore integral ranks that aren't 2 in the jacobian construction.
<a name="line970">970: </a> <font color="#4169E1">if</font> (cur_rank == 2) {
<a name="line971">971: </a> Obj<PETSC_MESH_TYPE::label_sequence> integral_cells = m->getLabelStratum(cur_marker_name, cur_marker_num);
<a name="line972">972: </a><strong><font color="#FF0000"> PETSC_MESH_TYPE:</font></strong>:label_sequence::iterator ic_iter = integral_cells->begin();
<a name="line973">973: </a><strong><font color="#FF0000"> PETSC_MESH_TYPE:</font></strong>:label_sequence::iterator ic_iter_end = integral_cells->end();
<a name="line974">974: </a> <A href="../../docs/manualpages/Sys/PetscScalar.html#PetscScalar">PetscScalar</A> * tensor;
<a name="line975">975: </a> <A href="../../docs/manualpages/Sys/PetscMalloc.html#PetscMalloc">PetscMalloc</A>(cur_dimension*cur_dimension*<font color="#4169E1">sizeof</font>(<A href="../../docs/manualpages/Sys/PetscScalar.html#PetscScalar">PetscScalar</A>), &tensor);
<a name="line976">976: </a> <font color="#4169E1">while</font> (ic_iter != ic_iter_end) {
<a name="line977">977: </a> subproblem->setCell(m, *ic_iter);
<a name="line978">978: </a> cur_integral->tabulateTensor(tensor);
<a name="line979">979: </a> updateOperator(A, m, s, order, *ic_iter, tensor, <A href="../../docs/manualpages/Sys/ADD_VALUES.html#ADD_VALUES">ADD_VALUES</A>);
<a name="line980">980: </a> ic_iter++;
<a name="line981">981: </a> }
<a name="line982">982: </a> }
<a name="line983">983: </a> n_iter++;
<a name="line984">984: </a> }
<a name="line985">985: </a> <A href="../../docs/manualpages/Mat/MatAssemblyBegin.html#MatAssemblyBegin">MatAssemblyBegin</A>(A, MAT_FINAL_ASSEMBLY);
<a name="line986">986: </a> <A href="../../docs/manualpages/Mat/MatAssemblyEnd.html#MatAssemblyEnd">MatAssemblyEnd</A>(A, MAT_FINAL_ASSEMBLY);
<a name="line987">987: </a> //<A href="../../docs/manualpages/Mat/MatView.html#MatView">MatView</A>(A, <A href="../../docs/manualpages/Viewer/PETSC_VIEWER_STDOUT_SELF.html#PETSC_VIEWER_STDOUT_SELF">PETSC_VIEWER_STDOUT_SELF</A>);
<a name="line988">988: </a> <font color="#4169E1">return</font>(0);
<a name="line989">989: </a> }
<a name="line994">994: </a> <A href="../../docs/manualpages/Sys/PetscErrorCode.html#PetscErrorCode">PetscErrorCode</A> SubProblemView(SectionReal section, std::string name, <A href="../../docs/manualpages/Viewer/PetscViewer.html#PetscViewer">PetscViewer</A> viewer, int firstField = 0, int lastField = 0) {
<a name="line995">995: </a> //<font color="#666666">"vectorize"</font> takes the first n discretizations and writes them out as a vector
<a name="line997">997: </a>
<a name="line999">999: </a> Obj<PETSC_MESH_TYPE> m;
<a name="line1000">1000: </a> Obj<PETSC_MESH_TYPE::real_section_type> field;
<a name="line1001">1001: </a> <A href="../../docs/manualpages/Mesh/SectionRealGetBundle.html#SectionRealGetBundle">SectionRealGetBundle</A>(section, m);
<a name="line1002">1002: </a> <A href="../../docs/manualpages/Mesh/SectionRealGetSection.html#SectionRealGetSection">SectionRealGetSection</A>(section, field);
<a name="line1003">1003: </a> const ALE::Obj<PETSC_MESH_TYPE::numbering_type>& numbering = m->getFactory()->getNumbering(m, 0);
<a name="line1004">1004: </a> <A href="../../docs/manualpages/Viewer/PetscViewerASCIIPrintf.html#PetscViewerASCIIPrintf">PetscViewerASCIIPrintf</A>(viewer, <font color="#666666">"POINT_DATA %d\n"</font>, numbering->getGlobalSize());
<a name="line1005">1005: </a>
<a name="line1006">1006: </a> <font color="#4169E1">if</font> (lastField - firstField > 0) {
<a name="line1007">1007: </a> <A href="../../docs/manualpages/Viewer/PetscViewerASCIIPrintf.html#PetscViewerASCIIPrintf">PetscViewerASCIIPrintf</A>(viewer, <font color="#666666">"VECTORS %s double\n"</font>, name.c_str());
<a name="line1008">1008: </a>
<a name="line1009">1009: </a> } <font color="#4169E1">else</font> {
<a name="line1010">1010: </a> <font color="#4169E1">if</font> (name == <font color="#666666">""</font>) {
<a name="line1011">1011: </a> <A href="../../docs/manualpages/Viewer/PetscViewerASCIIPrintf.html#PetscViewerASCIIPrintf">PetscViewerASCIIPrintf</A>(viewer, <font color="#666666">"SCALARS Unknown double %d\n"</font>, 1);
<a name="line1012">1012: </a> } <font color="#4169E1">else</font> {
<a name="line1013">1013: </a> <A href="../../docs/manualpages/Viewer/PetscViewerASCIIPrintf.html#PetscViewerASCIIPrintf">PetscViewerASCIIPrintf</A>(viewer, <font color="#666666">"SCALARS %s double %d\n"</font>, name.c_str(), 1);
<a name="line1014">1014: </a> }
<a name="line1015">1015: </a> <A href="../../docs/manualpages/Viewer/PetscViewerASCIIPrintf.html#PetscViewerASCIIPrintf">PetscViewerASCIIPrintf</A>(viewer, <font color="#666666">"LOOKUP_TABLE default\n"</font>);
<a name="line1016">1016: </a> }
<a name="line1017">1017: </a> <font color="#4169E1">typedef</font> PETSC_MESH_TYPE::real_section_type::value_type value_type;
<a name="line1018">1018: </a> const Obj<PETSC_MESH_TYPE::real_section_type::chart_type>& chart = field->getChart();
<a name="line1019">1019: </a> const MPI_Datatype mpiType = ALE::New::ParallelFactory<value_type>::singleton(field->debug())->getMPIType();
<a name="line1020">1020: </a> int enforceDim;
<a name="line1021">1021: </a> int fiberDim = lastField - firstField + 1;
<a name="line1022">1022: </a> <font color="#4169E1">if</font> (lastField - firstField > 0) {
<a name="line1023">1023: </a> enforceDim = 3; //we need at least three vector components to be written out
<a name="line1024">1024: </a> } <font color="#4169E1">else</font> {
<a name="line1025">1025: </a> enforceDim = 0;
<a name="line1026">1026: </a> }
<a name="line1027">1027: </a> <font color="#4169E1">if</font> (field->commRank() == 0) {
<a name="line1028">1028: </a> <font color="#4169E1">for</font>(PETSC_MESH_TYPE::real_section_type::chart_type::const_iterator p_iter = chart->begin(); p_iter != chart->end(); ++p_iter) {
<a name="line1029">1029: </a> <font color="#4169E1">if</font> (!numbering->hasPoint(*p_iter)) <font color="#4169E1">continue</font>;
<a name="line1030">1030: </a> const value_type *array = field->restrictPoint(*p_iter);
<a name="line1031">1031: </a> const int& dim = field->getFiberDimension(*p_iter);
<a name="line1032">1032: </a> ostringstream line;
<a name="line1033">1033: </a>
<a name="line1034">1034: </a> // Perhaps there should be a flag <font color="#4169E1">for</font> excluding boundary values
<a name="line1035">1035: </a> <font color="#4169E1">if</font> (dim != 0) {
<a name="line1036">1036: </a> <font color="#4169E1">for</font>(int d = firstField; d <= lastField; d++) {
<a name="line1037">1037: </a> <font color="#4169E1">if</font> (d > 0) {
<a name="line1038">1038: </a> line << <font color="#666666">" "</font>;
<a name="line1039">1039: </a> }
<a name="line1040">1040: </a> line << array[d];
<a name="line1041">1041: </a> }
<a name="line1042">1042: </a> <font color="#4169E1">for</font>(int d = fiberDim; d < enforceDim; d++) {
<a name="line1043">1043: </a> line << <font color="#666666">" 0.0"</font>;
<a name="line1044">1044: </a> }
<a name="line1045">1045: </a> line << std::endl;
<a name="line1046">1046: </a> <A href="../../docs/manualpages/Viewer/PetscViewerASCIIPrintf.html#PetscViewerASCIIPrintf">PetscViewerASCIIPrintf</A>(viewer, <font color="#666666">"%s"</font>, line.str().c_str());
<a name="line1047">1047: </a> }
<a name="line1048">1048: </a> }
<a name="line1049">1049: </a> <font color="#4169E1">for</font>(int p = 1; p < field->commSize(); p++) {
<a name="line1050">1050: </a> value_type *remoteValues;
<a name="line1051">1051: </a> int numLocalElementsAndFiberDim[2];
<a name="line1052">1052: </a> int size;
<a name="line1053">1053: </a> MPI_Status status;
<a name="line1054">1054: </a>
<a name="line1055">1055: </a> <A href="http://www.mcs.anl.gov/mpi/www/www3/MPI_Recv.html#MPI_Recv">MPI_Recv</A>(numLocalElementsAndFiberDim, 2, MPI_INT, p, 1, field->comm(), &status);
<a name="line1056">1056: </a> size = numLocalElementsAndFiberDim[0]*numLocalElementsAndFiberDim[1];
<a name="line1057">1057: </a> <A href="../../docs/manualpages/Sys/PetscMalloc.html#PetscMalloc">PetscMalloc</A>(size * <font color="#4169E1">sizeof</font>(value_type), &remoteValues);
<a name="line1058">1058: </a> <A href="http://www.mcs.anl.gov/mpi/www/www3/MPI_Recv.html#MPI_Recv">MPI_Recv</A>(remoteValues, size, mpiType, p, 1, field->comm(), &status);
<a name="line1059">1059: </a>
<a name="line1060">1060: </a> <font color="#4169E1">for</font>(int e = 0; e < numLocalElementsAndFiberDim[0]; e++) {
<a name="line1061">1061: </a> <font color="#4169E1">for</font>(int d = 0; d < fiberDim; d++) {
<a name="line1062">1062: </a> <font color="#4169E1">if</font> (mpiType == MPI_INT) {
<a name="line1063">1063: </a> <A href="../../docs/manualpages/Viewer/PetscViewerASCIIPrintf.html#PetscViewerASCIIPrintf">PetscViewerASCIIPrintf</A>(viewer, <font color="#666666">"%d"</font>, remoteValues[e*numLocalElementsAndFiberDim[1]+d]);
<a name="line1064">1064: </a> } <font color="#4169E1">else</font> {
<a name="line1065">1065: </a> <A href="../../docs/manualpages/Viewer/PetscViewerASCIIPrintf.html#PetscViewerASCIIPrintf">PetscViewerASCIIPrintf</A>(viewer, <font color="#666666">"%G"</font>, remoteValues[e*numLocalElementsAndFiberDim[1]+d]);
<a name="line1066">1066: </a> }
<a name="line1067">1067: </a> }
<a name="line1068">1068: </a> <font color="#4169E1">for</font>(int d = fiberDim; d < enforceDim; d++) {
<a name="line1069">1069: </a> <A href="../../docs/manualpages/Viewer/PetscViewerASCIIPrintf.html#PetscViewerASCIIPrintf">PetscViewerASCIIPrintf</A>(viewer, <font color="#666666">" 0.0"</font>);
<a name="line1070">1070: </a> }
<a name="line1071">1071: </a> <A href="../../docs/manualpages/Viewer/PetscViewerASCIIPrintf.html#PetscViewerASCIIPrintf">PetscViewerASCIIPrintf</A>(viewer, <font color="#666666">"\n"</font>);
<a name="line1072">1072: </a> }
<a name="line1073">1073: </a> <A href="../../docs/manualpages/Sys/PetscFree.html#PetscFree">PetscFree</A>(remoteValues);
<a name="line1074">1074: </a> }
<a name="line1075">1075: </a> } <font color="#4169E1">else</font> {
<a name="line1076">1076: </a> value_type *localValues;
<a name="line1077">1077: </a> int numLocalElements = numbering->getLocalSize();
<a name="line1078">1078: </a> const int size = numLocalElements*fiberDim;
<a name="line1079">1079: </a> int k = 0;
<a name="line1080">1080: </a>
<a name="line1081">1081: </a> <A href="../../docs/manualpages/Sys/PetscMalloc.html#PetscMalloc">PetscMalloc</A>(size * <font color="#4169E1">sizeof</font>(value_type), &localValues);
<a name="line1082">1082: </a> <font color="#4169E1">for</font>(PETSC_MESH_TYPE::real_section_type::chart_type::const_iterator p_iter = chart->begin(); p_iter != chart->end(); ++p_iter) {
<a name="line1083">1083: </a> <font color="#4169E1">if</font> (!numbering->hasPoint(*p_iter)) <font color="#4169E1">continue</font>;
<a name="line1084">1084: </a> <font color="#4169E1">if</font> (numbering->isLocal(*p_iter)) {
<a name="line1085">1085: </a> const value_type *array = field->restrictPoint(*p_iter);
<a name="line1086">1086: </a> //const int& dim = field->getFiberDimension(*p_iter);
<a name="line1087">1087: </a>
<a name="line1088">1088: </a> <font color="#4169E1">for</font>(int i = firstField; i <= lastField; ++i) {
<a name="line1089">1089: </a> localValues[k++] = array[i];
<a name="line1090">1090: </a> }
<a name="line1091">1091: </a> }
<a name="line1092">1092: </a> }
<a name="line1093">1093: </a> <font color="#4169E1">if</font> (k != size) {
<a name="line1094">1094: </a> <A href="../../docs/manualpages/Sys/SETERRQ2.html#SETERRQ2">SETERRQ2</A>(PETSC_ERR_PLIB, <font color="#666666">"Invalid number of values to send for field, %d should be %d"</font>, k, size);
<a name="line1095">1095: </a> }
<a name="line1096">1096: </a> int numLocalElementsAndFiberDim[2] = {numLocalElements, fiberDim};
<a name="line1097">1097: </a> <A href="http://www.mcs.anl.gov/mpi/www/www3/MPI_Send.html#MPI_Send">MPI_Send</A>(numLocalElementsAndFiberDim, 2, MPI_INT, 0, 1, field->comm());
<a name="line1098">1098: </a> <A href="http://www.mcs.anl.gov/mpi/www/www3/MPI_Send.html#MPI_Send">MPI_Send</A>(localValues, size, mpiType, 0, 1, field->comm());
<a name="line1099">1099: </a> <A href="../../docs/manualpages/Sys/PetscFree.html#PetscFree">PetscFree</A>(localValues);
<a name="line1100">1100: </a> }
<a name="line1101">1101: </a> <font color="#4169E1">return</font>(0);
<a name="line1102">1102: </a> }
<a name="line1103">1103: </a> } //namespace Problem
<a name="line1104">1104: </a>} //namespace ALE
<a name="line1106">1106: </a><font color="#A020F0">#endif</font>
</pre>
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