xref: /petsc/include/petscdmplex.h (revision 60dd46ca9875962950ab5c8a8f4d94fdb4c0f129) 
1 /*
2   DMPlex, for parallel unstructured distributed mesh problems.
3 */
4 #if !defined(PETSCDMPLEX_H)
5 #define PETSCDMPLEX_H
6 
7 #include <petscsection.h>
8 #include <petscdm.h>
9 #include <petscdmplextypes.h>
10 #include <petscdt.h>
11 #include <petscfe.h>
12 #include <petscfv.h>
13 #include <petscsftypes.h>
14 #include <petscdmfield.h>
15 
16 PETSC_EXTERN PetscClassId PETSCPARTITIONER_CLASSID;
17 
18 /*J
19   PetscPartitionerType - String with the name of a PETSc graph partitioner
20 
21   Level: beginner
22 
23 .seealso: PetscPartitionerSetType(), PetscPartitioner
24 J*/
25 typedef const char *PetscPartitionerType;
26 #define PETSCPARTITIONERCHACO    "chaco"
27 #define PETSCPARTITIONERPARMETIS "parmetis"
28 #define PETSCPARTITIONERPTSCOTCH "ptscotch"
29 #define PETSCPARTITIONERSHELL    "shell"
30 #define PETSCPARTITIONERSIMPLE   "simple"
31 #define PETSCPARTITIONERGATHER   "gather"
32 #define PETSCPARTITIONERMATPARTITIONING "matpartitioning"
33 
34 PETSC_EXTERN PetscFunctionList PetscPartitionerList;
35 PETSC_EXTERN PetscErrorCode PetscPartitionerCreate(MPI_Comm, PetscPartitioner *);
36 PETSC_EXTERN PetscErrorCode PetscPartitionerDestroy(PetscPartitioner *);
37 PETSC_EXTERN PetscErrorCode PetscPartitionerSetType(PetscPartitioner, PetscPartitionerType);
38 PETSC_EXTERN PetscErrorCode PetscPartitionerGetType(PetscPartitioner, PetscPartitionerType *);
39 PETSC_EXTERN PetscErrorCode PetscPartitionerSetUp(PetscPartitioner);
40 PETSC_EXTERN PetscErrorCode PetscPartitionerSetFromOptions(PetscPartitioner);
41 PETSC_EXTERN PetscErrorCode PetscPartitionerViewFromOptions(PetscPartitioner,PetscObject,const char[]);
42 PETSC_EXTERN PetscErrorCode PetscPartitionerView(PetscPartitioner, PetscViewer);
43 PETSC_EXTERN PetscErrorCode PetscPartitionerRegister(const char [], PetscErrorCode (*)(PetscPartitioner));
44 PETSC_EXTERN PetscErrorCode PetscPartitionerRegisterDestroy(void);
45 
46 PETSC_EXTERN PetscErrorCode PetscPartitionerPartition(PetscPartitioner, DM, PetscSection, IS *);
47 
48 PETSC_EXTERN PetscErrorCode PetscPartitionerShellSetPartition(PetscPartitioner, PetscInt, const PetscInt[], const PetscInt[]);
49 PETSC_EXTERN PetscErrorCode PetscPartitionerShellSetRandom(PetscPartitioner, PetscBool);
50 PETSC_EXTERN PetscErrorCode PetscPartitionerShellGetRandom(PetscPartitioner, PetscBool *);
51 
52 PETSC_EXTERN PetscErrorCode PetscPartitionerMatPartitioningGetMatPartitioning(PetscPartitioner part, MatPartitioning *mp);
53 
54 PETSC_EXTERN PetscErrorCode DMPlexCreate(MPI_Comm, DM*);
55 PETSC_EXTERN PetscErrorCode DMPlexCreateCohesiveSubmesh(DM, PetscBool, const char [], PetscInt, DM *);
56 PETSC_EXTERN PetscErrorCode DMPlexCreateFromCellList(MPI_Comm, PetscInt, PetscInt, PetscInt, PetscInt, PetscBool, const int[], PetscInt, const double[], DM*);
57 PETSC_EXTERN PetscErrorCode DMPlexCreateFromCellListParallel(MPI_Comm, PetscInt, PetscInt, PetscInt, PetscInt, PetscBool, const int[], PetscInt, const PetscReal[], PetscSF *, DM *);
58 PETSC_EXTERN PetscErrorCode DMPlexCreateFromDAG(DM, PetscInt, const PetscInt [], const PetscInt [], const PetscInt [], const PetscInt [], const PetscScalar []);
59 PETSC_EXTERN PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm, PetscInt, PetscBool, DM*);
60 PETSC_EXTERN PetscErrorCode DMPlexSetOptionsPrefix(DM, const char []);
61 PETSC_EXTERN PetscErrorCode DMPlexGetChart(DM, PetscInt *, PetscInt *);
62 PETSC_EXTERN PetscErrorCode DMPlexSetChart(DM, PetscInt, PetscInt);
63 PETSC_EXTERN PetscErrorCode DMPlexGetConeSize(DM, PetscInt, PetscInt *);
64 PETSC_EXTERN PetscErrorCode DMPlexSetConeSize(DM, PetscInt, PetscInt);
65 PETSC_EXTERN PetscErrorCode DMPlexAddConeSize(DM, PetscInt, PetscInt);
66 PETSC_EXTERN PetscErrorCode DMPlexGetCone(DM, PetscInt, const PetscInt *[]);
67 PETSC_EXTERN PetscErrorCode DMPlexGetConeTuple(DM, IS, PetscSection *, IS *);
68 PETSC_EXTERN PetscErrorCode DMPlexGetConeRecursive(DM, IS, PetscInt *, IS *[], PetscSection *[]);
69 PETSC_EXTERN PetscErrorCode DMPlexRestoreConeRecursive(DM, IS, PetscInt *, IS *[], PetscSection *[]);
70 PETSC_EXTERN PetscErrorCode DMPlexGetConeRecursiveVertices(DM, IS, IS *);
71 PETSC_EXTERN PetscErrorCode DMPlexSetCone(DM, PetscInt, const PetscInt[]);
72 PETSC_EXTERN PetscErrorCode DMPlexInsertCone(DM, PetscInt, PetscInt, PetscInt);
73 PETSC_EXTERN PetscErrorCode DMPlexInsertConeOrientation(DM, PetscInt, PetscInt, PetscInt);
74 PETSC_EXTERN PetscErrorCode DMPlexGetConeOrientation(DM, PetscInt, const PetscInt *[]);
75 PETSC_EXTERN PetscErrorCode DMPlexSetConeOrientation(DM, PetscInt, const PetscInt[]);
76 PETSC_EXTERN PetscErrorCode DMPlexGetSupportSize(DM, PetscInt, PetscInt *);
77 PETSC_EXTERN PetscErrorCode DMPlexSetSupportSize(DM, PetscInt, PetscInt);
78 PETSC_EXTERN PetscErrorCode DMPlexGetSupport(DM, PetscInt, const PetscInt *[]);
79 PETSC_EXTERN PetscErrorCode DMPlexSetSupport(DM, PetscInt, const PetscInt[]);
80 PETSC_EXTERN PetscErrorCode DMPlexInsertSupport(DM, PetscInt, PetscInt, PetscInt);
81 PETSC_EXTERN PetscErrorCode DMPlexGetConeSection(DM, PetscSection *);
82 PETSC_EXTERN PetscErrorCode DMPlexGetSupportSection(DM, PetscSection *);
83 PETSC_EXTERN PetscErrorCode DMPlexGetCones(DM, PetscInt *[]);
84 PETSC_EXTERN PetscErrorCode DMPlexGetConeOrientations(DM, PetscInt *[]);
85 PETSC_EXTERN PetscErrorCode DMPlexGetMaxSizes(DM, PetscInt *, PetscInt *);
86 PETSC_EXTERN PetscErrorCode DMPlexSymmetrize(DM);
87 PETSC_EXTERN PetscErrorCode DMPlexStratify(DM);
88 PETSC_EXTERN PetscErrorCode DMPlexEqual(DM,DM,PetscBool*);
89 PETSC_EXTERN PetscErrorCode DMPlexReverseCell(DM, PetscInt);
90 PETSC_EXTERN PetscErrorCode DMPlexOrientCell(DM,PetscInt,PetscInt,const PetscInt[]);
91 PETSC_EXTERN PetscErrorCode DMPlexCompareOrientations(DM, PetscInt, PetscInt, const PetscInt [], PetscInt *, PetscBool *);
92 PETSC_EXTERN PetscErrorCode DMPlexOrient(DM);
93 PETSC_EXTERN PetscErrorCode DMPlexPreallocateOperator(DM, PetscInt, PetscInt[], PetscInt[], PetscInt[], PetscInt[], Mat, PetscBool);
94 PETSC_EXTERN PetscErrorCode DMPlexGetPointLocal(DM,PetscInt,PetscInt*,PetscInt*);
95 PETSC_EXTERN PetscErrorCode DMPlexPointLocalRead(DM,PetscInt,const PetscScalar*,void*);
96 PETSC_EXTERN PetscErrorCode DMPlexPointLocalRef(DM,PetscInt,PetscScalar*,void*);
97 PETSC_EXTERN PetscErrorCode DMPlexGetPointLocalField(DM,PetscInt,PetscInt,PetscInt*,PetscInt*);
98 PETSC_EXTERN PetscErrorCode DMPlexPointLocalFieldRef(DM,PetscInt,PetscInt,PetscScalar*,void*);
99 PETSC_EXTERN PetscErrorCode DMPlexPointLocalFieldRead(DM,PetscInt,PetscInt,const PetscScalar*,void*);
100 PETSC_EXTERN PetscErrorCode DMPlexGetPointGlobal(DM,PetscInt,PetscInt*,PetscInt*);
101 PETSC_EXTERN PetscErrorCode DMPlexPointGlobalRead(DM,PetscInt,const PetscScalar*,const void*);
102 PETSC_EXTERN PetscErrorCode DMPlexPointGlobalRef(DM,PetscInt,PetscScalar*,void*);
103 PETSC_EXTERN PetscErrorCode DMPlexGetPointGlobalField(DM,PetscInt,PetscInt,PetscInt*,PetscInt*);
104 PETSC_EXTERN PetscErrorCode DMPlexPointGlobalFieldRef(DM,PetscInt,PetscInt,PetscScalar*,void*);
105 PETSC_EXTERN PetscErrorCode DMPlexPointGlobalFieldRead(DM,PetscInt,PetscInt,const PetscScalar*, void*);
106 
107 /* Topological interpolation */
108 PETSC_EXTERN const char * const DMPlexInterpolatedFlags[];
109 typedef enum {
110   DMPLEX_INTERPOLATED_INVALID = -1,
111   DMPLEX_INTERPOLATED_NONE = 0,
112   DMPLEX_INTERPOLATED_PARTIAL,
113   DMPLEX_INTERPOLATED_MIXED,
114   DMPLEX_INTERPOLATED_FULL
115 } DMPlexInterpolatedFlag;
116 PETSC_EXTERN PetscErrorCode DMPlexInterpolate(DM, DM *);
117 PETSC_EXTERN PetscErrorCode DMPlexUninterpolate(DM, DM *);
118 PETSC_EXTERN PetscErrorCode DMPlexInterpolatePointSF(DM, PetscSF);
119 PETSC_EXTERN PetscErrorCode DMPlexIsInterpolated(DM, DMPlexInterpolatedFlag *);
120 PETSC_EXTERN PetscErrorCode DMPlexIsInterpolatedCollective(DM, DMPlexInterpolatedFlag *);
121 
122 PETSC_EXTERN PetscErrorCode DMPlexFilter(DM, DMLabel, PetscInt, DM *);
123 PETSC_EXTERN PetscErrorCode DMPlexGetCellNumbering(DM, IS *);
124 PETSC_EXTERN PetscErrorCode DMPlexGetVertexNumbering(DM, IS *);
125 PETSC_EXTERN PetscErrorCode DMPlexCreatePointNumbering(DM, IS *);
126 PETSC_EXTERN PetscErrorCode DMPlexCreateRankField(DM, Vec *);
127 PETSC_EXTERN PetscErrorCode DMPlexCreateLabelField(DM, DMLabel, Vec *);
128 
129 PETSC_EXTERN PetscErrorCode DMPlexGetDepth(DM, PetscInt *);
130 PETSC_EXTERN PetscErrorCode DMPlexGetDepthLabel(DM, DMLabel *);
131 PETSC_EXTERN PetscErrorCode DMPlexGetDepthStratum(DM, PetscInt, PetscInt *, PetscInt *);
132 PETSC_EXTERN PetscErrorCode DMPlexGetHeightStratum(DM, PetscInt, PetscInt *, PetscInt *);
133 
134 /* Topological Operations */
135 PETSC_EXTERN PetscErrorCode DMPlexGetMeet(DM, PetscInt, const PetscInt [], PetscInt *, const PetscInt **);
136 PETSC_EXTERN PetscErrorCode DMPlexGetFullMeet(DM, PetscInt, const PetscInt [], PetscInt *, const PetscInt **);
137 PETSC_EXTERN PetscErrorCode DMPlexRestoreMeet(DM, PetscInt, const PetscInt [], PetscInt *, const PetscInt **);
138 PETSC_EXTERN PetscErrorCode DMPlexGetJoin(DM, PetscInt, const PetscInt [], PetscInt *, const PetscInt **);
139 PETSC_EXTERN PetscErrorCode DMPlexGetFullJoin(DM, PetscInt, const PetscInt [], PetscInt *, const PetscInt **);
140 PETSC_EXTERN PetscErrorCode DMPlexRestoreJoin(DM, PetscInt, const PetscInt [], PetscInt *, const PetscInt **);
141 PETSC_EXTERN PetscErrorCode DMPlexGetTransitiveClosure(DM, PetscInt, PetscBool, PetscInt *, PetscInt *[]);
142 PETSC_EXTERN PetscErrorCode DMPlexRestoreTransitiveClosure(DM, PetscInt, PetscBool, PetscInt *, PetscInt *[]);
143 
144 /* Mesh Generation */
145 PETSC_EXTERN PetscErrorCode DMPlexGenerate(DM, const char [], PetscBool , DM *);
146 PETSC_EXTERN PetscErrorCode DMPlexGenerateRegister(const char[],PetscErrorCode (*)(DM,PetscBool,DM*),PetscErrorCode (*)(DM,double*,DM*),PetscInt);
147 PETSC_EXTERN PetscErrorCode DMPlexGenerateRegisterAll(void);
148 PETSC_EXTERN PetscErrorCode DMPlexGenerateRegisterDestroy(void);
149 PETSC_EXTERN PetscErrorCode DMPlexCopyCoordinates(DM, DM);
150 PETSC_EXTERN PetscErrorCode DMPlexCreateDoublet(MPI_Comm, PetscInt, PetscBool, PetscBool, PetscBool, PetscReal, DM *);
151 PETSC_EXTERN PetscErrorCode DMPlexCreateSquareBoundary(DM, const PetscReal [], const PetscReal [], const PetscInt []);
152 PETSC_EXTERN PetscErrorCode DMPlexCreateCubeBoundary(DM, const PetscReal [], const PetscReal [], const PetscInt []);
153 PETSC_EXTERN PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm, PetscInt, PetscBool, const PetscInt[], const PetscReal[], const PetscReal[], const DMBoundaryType[], PetscBool, DM *);
154 PETSC_EXTERN PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm, PetscInt, PetscBool, DM *);
155 PETSC_EXTERN PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm, PetscInt, DMBoundaryType, DM *);
156 PETSC_EXTERN PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm, PetscInt, PetscBool, DM *);
157 PETSC_EXTERN PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm, const PetscInt[], const PetscReal[], const PetscReal[], const DMBoundaryType[], PetscBool, PetscBool, DM *);
158 PETSC_EXTERN PetscErrorCode DMPlexExtrude(DM, PetscInt, PetscReal, PetscBool, PetscBool, DM *);
159 PETSC_EXTERN PetscErrorCode DMPlexCreateConeSection(DM, PetscSection *);
160 PETSC_EXTERN PetscErrorCode DMPlexInvertCell(PetscInt, PetscInt, int []);
161 
162 PETSC_EXTERN PetscErrorCode DMPlexCheckSymmetry(DM);
163 PETSC_EXTERN PetscErrorCode DMPlexCheckSkeleton(DM, PetscInt);
164 PETSC_EXTERN PetscErrorCode DMPlexCheckFaces(DM, PetscInt);
165 PETSC_EXTERN PetscErrorCode DMPlexCheckGeometry(DM);
166 PETSC_EXTERN PetscErrorCode DMPlexCheckPointSF(DM);
167 PETSC_EXTERN PetscErrorCode DMPlexCheckConesConformOnInterfaces(DM);
168 PETSC_EXTERN PetscErrorCode DMPlexCheckCellShape(DM, PetscBool, PetscReal);
169 
170 PETSC_EXTERN PetscErrorCode DMPlexTriangleSetOptions(DM, const char *);
171 PETSC_EXTERN PetscErrorCode DMPlexTetgenSetOptions(DM, const char *);
172 
173 PETSC_EXTERN PetscErrorCode DMPlexCreateFromFile(MPI_Comm, const char[], PetscBool, DM *);
174 PETSC_EXTERN PetscErrorCode DMPlexCreateExodus(MPI_Comm, PetscInt, PetscBool, DM *);
175 PETSC_EXTERN PetscErrorCode DMPlexCreateExodusFromFile(MPI_Comm, const char [], PetscBool, DM *);
176 PETSC_EXTERN PetscErrorCode DMPlexCreateCGNS(MPI_Comm, PetscInt, PetscBool, DM *);
177 PETSC_EXTERN PetscErrorCode DMPlexCreateCGNSFromFile(MPI_Comm, const char[], PetscBool, DM *);
178 PETSC_EXTERN PetscErrorCode DMPlexCreateGmsh(MPI_Comm, PetscViewer, PetscBool, DM *);
179 PETSC_EXTERN PetscErrorCode DMPlexCreateGmshFromFile(MPI_Comm, const char [], PetscBool, DM *);
180 PETSC_EXTERN PetscErrorCode DMPlexCreateFluent(MPI_Comm, PetscViewer, PetscBool, DM *);
181 PETSC_EXTERN PetscErrorCode DMPlexCreateFluentFromFile(MPI_Comm, const char [], PetscBool, DM *);
182 PETSC_EXTERN PetscErrorCode DMPlexCreateMedFromFile(MPI_Comm, const char [], PetscBool, DM *);
183 PETSC_EXTERN PetscErrorCode DMPlexCreatePLYFromFile(MPI_Comm, const char [], PetscBool, DM *);
184 
185 /* Mesh Partitioning and Distribution */
186 PETSC_EXTERN PetscErrorCode DMPlexCreateNeighborCSR(DM, PetscInt, PetscInt *, PetscInt **, PetscInt **);
187 PETSC_EXTERN PetscErrorCode DMPlexGetPartitioner(DM, PetscPartitioner *);
188 PETSC_EXTERN PetscErrorCode DMPlexSetPartitioner(DM, PetscPartitioner);
189 PETSC_EXTERN PetscErrorCode DMPlexCreatePartition(DM, const char[], PetscInt, PetscBool, PetscSection *, IS *, PetscSection *, IS *);
190 PETSC_EXTERN PetscErrorCode DMPlexCreatePartitionerGraph(DM, PetscInt, PetscInt *, PetscInt **, PetscInt **, IS *);
191 PETSC_EXTERN PetscErrorCode DMPlexCreatePartitionClosure(DM, PetscSection, IS, PetscSection *, IS *);
192 PETSC_EXTERN PetscErrorCode DMPlexPartitionLabelInvert(DM, DMLabel, PetscSF, DMLabel);
193 PETSC_EXTERN PetscErrorCode DMPlexPartitionLabelClosure(DM, DMLabel);
194 PETSC_EXTERN PetscErrorCode DMPlexPartitionLabelAdjacency(DM, DMLabel);
195 PETSC_EXTERN PetscErrorCode DMPlexPartitionLabelPropagate(DM, DMLabel);
196 PETSC_EXTERN PetscErrorCode DMPlexPartitionLabelCreateSF(DM, DMLabel, PetscSF *);
197 PETSC_EXTERN PetscErrorCode DMPlexSetPartitionBalance(DM, PetscBool);
198 PETSC_EXTERN PetscErrorCode DMPlexGetPartitionBalance(DM, PetscBool *);
199 PETSC_EXTERN PetscErrorCode DMPlexIsDistributed(DM, PetscBool *);
200 PETSC_EXTERN PetscErrorCode DMPlexDistribute(DM, PetscInt, PetscSF*, DM*);
201 PETSC_EXTERN PetscErrorCode DMPlexDistributeOverlap(DM, PetscInt, PetscSF *, DM *);
202 PETSC_EXTERN PetscErrorCode DMPlexGetOverlap(DM, PetscInt *);
203 PETSC_EXTERN PetscErrorCode DMPlexDistributeField(DM,PetscSF,PetscSection,Vec,PetscSection,Vec);
204 PETSC_EXTERN PetscErrorCode DMPlexDistributeFieldIS(DM, PetscSF, PetscSection, IS, PetscSection, IS *);
205 PETSC_EXTERN PetscErrorCode DMPlexDistributeData(DM,PetscSF,PetscSection,MPI_Datatype,void*,PetscSection,void**);
206 PETSC_EXTERN PetscErrorCode DMPlexRebalanceSharedPoints(DM, PetscInt, PetscBool, PetscBool, PetscBool*);
207 PETSC_EXTERN PetscErrorCode DMPlexMigrate(DM, PetscSF, DM);
208 PETSC_EXTERN PetscErrorCode DMPlexGetGatherDM(DM, PetscSF*, DM*);
209 PETSC_EXTERN PetscErrorCode DMPlexGetRedundantDM(DM, PetscSF*, DM*);
210 PETSC_EXTERN PetscErrorCode DMPlexSetAdjacencyUser(DM, PetscErrorCode (*)(DM,PetscInt,PetscInt*,PetscInt[],void*),void*);
211 PETSC_EXTERN PetscErrorCode DMPlexGetAdjacencyUser(DM, PetscErrorCode (**)(DM,PetscInt,PetscInt*,PetscInt[],void*),void**);
212 PETSC_EXTERN PetscErrorCode DMPlexSetAdjacencyUseCone(DM,PetscBool);
213 PETSC_EXTERN PetscErrorCode DMPlexGetAdjacencyUseCone(DM,PetscBool*);
214 PETSC_EXTERN PetscErrorCode DMPlexSetAdjacencyUseClosure(DM,PetscBool);
215 PETSC_EXTERN PetscErrorCode DMPlexGetAdjacencyUseClosure(DM,PetscBool*);
216 PETSC_EXTERN PetscErrorCode DMPlexSetAdjacencyUseAnchors(DM,PetscBool);
217 PETSC_EXTERN PetscErrorCode DMPlexGetAdjacencyUseAnchors(DM,PetscBool*);
218 PETSC_EXTERN PetscErrorCode DMPlexGetAdjacency(DM, PetscInt, PetscInt *, PetscInt *[]);
219 PETSC_EXTERN PetscErrorCode DMPlexSetMigrationSF(DM, PetscSF);
220 PETSC_EXTERN PetscErrorCode DMPlexGetMigrationSF(DM, PetscSF *);
221 
222 PETSC_EXTERN PetscErrorCode DMPlexGetOrdering(DM, MatOrderingType, DMLabel, IS *);
223 PETSC_EXTERN PetscErrorCode DMPlexPermute(DM, IS, DM *);
224 
225 PETSC_EXTERN PetscErrorCode DMPlexCreateProcessSF(DM, PetscSF, IS *, PetscSF *);
226 PETSC_EXTERN PetscErrorCode DMPlexCreateTwoSidedProcessSF(DM, PetscSF, PetscSection, IS, PetscSection, IS, IS *, PetscSF *);
227 PETSC_EXTERN PetscErrorCode DMPlexDistributeOwnership(DM, PetscSection, IS *, PetscSection, IS *);
228 PETSC_EXTERN PetscErrorCode DMPlexCreateOverlapLabel(DM, PetscInt, PetscSection, IS, PetscSection, IS, DMLabel *);
229 PETSC_EXTERN PetscErrorCode DMPlexCreateOverlapMigrationSF(DM, PetscSF, PetscSF *);
230 PETSC_EXTERN PetscErrorCode DMPlexStratifyMigrationSF(DM, PetscSF, PetscSF *);
231 
232 /* Submesh Support */
233 PETSC_EXTERN PetscErrorCode DMPlexCreateSubmesh(DM, DMLabel, PetscInt, PetscBool, DM*);
234 PETSC_EXTERN PetscErrorCode DMPlexCreateHybridMesh(DM, DMLabel, DMLabel, DMLabel *, DMLabel *, DM *, DM *);
235 PETSC_EXTERN PetscErrorCode DMPlexGetSubpointMap(DM, DMLabel*);
236 PETSC_EXTERN PetscErrorCode DMPlexSetSubpointMap(DM, DMLabel);
237 PETSC_EXTERN PetscErrorCode DMPlexCreateSubpointIS(DM, IS *);
238 PETSC_EXTERN PetscErrorCode DMPlexGetSubpoint(DM, PetscInt, PetscInt *);
239 PETSC_EXTERN PetscErrorCode DMPlexGetAuxiliaryPoint(DM, DM, PetscInt, PetscInt *);
240 
241 PETSC_EXTERN PetscErrorCode DMPlexLabelComplete(DM, DMLabel);
242 PETSC_EXTERN PetscErrorCode DMPlexLabelCohesiveComplete(DM, DMLabel, DMLabel, PetscBool, DM);
243 PETSC_EXTERN PetscErrorCode DMPlexLabelAddCells(DM, DMLabel);
244 PETSC_EXTERN PetscErrorCode DMPlexLabelClearCells(DM, DMLabel);
245 
246 PETSC_EXTERN PetscErrorCode DMPlexGetRefinementLimit(DM, PetscReal *);
247 PETSC_EXTERN PetscErrorCode DMPlexSetRefinementLimit(DM, PetscReal);
248 PETSC_EXTERN PetscErrorCode DMPlexGetRefinementUniform(DM, PetscBool *);
249 PETSC_EXTERN PetscErrorCode DMPlexSetRefinementUniform(DM, PetscBool);
250 PETSC_EXTERN PetscErrorCode DMPlexGetRefinementFunction(DM, PetscErrorCode (**)(const PetscReal [], PetscReal *));
251 PETSC_EXTERN PetscErrorCode DMPlexSetRefinementFunction(DM, PetscErrorCode (*)(const PetscReal [], PetscReal *));
252 PETSC_EXTERN PetscErrorCode DMPlexCreateCoarsePointIS(DM, IS *);
253 PETSC_EXTERN PetscErrorCode DMPlexGetRegularRefinement(DM, PetscBool *);
254 PETSC_EXTERN PetscErrorCode DMPlexSetRegularRefinement(DM, PetscBool);
255 PETSC_EXTERN PetscErrorCode DMPlexRefineSimplexToTensor(DM, DM*);
256 
257 /* Support for cell-vertex meshes */
258 PETSC_EXTERN PetscErrorCode DMPlexGetNumFaceVertices(DM, PetscInt, PetscInt, PetscInt *);
259 PETSC_EXTERN PetscErrorCode DMPlexGetOrientedFace(DM, PetscInt, PetscInt, const PetscInt [], PetscInt, PetscInt [], PetscInt [], PetscInt [], PetscBool *);
260 
261 /* Geometry Support */
262 PETSC_EXTERN PetscErrorCode DMPlexGetMinRadius(DM, PetscReal *);
263 PETSC_EXTERN PetscErrorCode DMPlexSetMinRadius(DM, PetscReal);
264 PETSC_EXTERN PetscErrorCode DMPlexComputeProjection2Dto1D(PetscScalar[], PetscReal[]);
265 PETSC_EXTERN PetscErrorCode DMPlexComputeProjection3Dto1D(PetscScalar[], PetscReal[]);
266 PETSC_EXTERN PetscErrorCode DMPlexComputeProjection3Dto2D(PetscInt, PetscScalar[], PetscReal[]);
267 
268 /* Point Location */
269 typedef struct _PetscGridHash *PetscGridHash;
270 PETSC_EXTERN PetscErrorCode PetscGridHashCreate(MPI_Comm, PetscInt, const PetscScalar[], PetscGridHash *);
271 PETSC_EXTERN PetscErrorCode PetscGridHashEnlarge(PetscGridHash, const PetscScalar []);
272 PETSC_EXTERN PetscErrorCode PetscGridHashSetGrid(PetscGridHash, const PetscInt [], const PetscReal []);
273 PETSC_EXTERN PetscErrorCode PetscGridHashGetEnclosingBox(PetscGridHash, PetscInt, const PetscScalar [], PetscInt [], PetscInt []);
274 PETSC_EXTERN PetscErrorCode PetscGridHashDestroy(PetscGridHash *);
275 PETSC_EXTERN PetscErrorCode DMPlexFindVertices(DM, PetscInt, const PetscReal [], PetscReal, PetscInt []);
276 
277 /* FVM Support */
278 PETSC_EXTERN PetscErrorCode DMPlexComputeCellGeometryFVM(DM, PetscInt, PetscReal *, PetscReal [], PetscReal []);
279 PETSC_EXTERN PetscErrorCode DMPlexComputeGeometryFVM(DM, Vec *, Vec *);
280 PETSC_EXTERN PetscErrorCode DMPlexComputeGradientFVM(DM, PetscFV, Vec, Vec, DM *);
281 PETSC_EXTERN PetscErrorCode DMPlexGetDataFVM(DM, PetscFV, Vec *, Vec *, DM *);
282 
283 /* FEM Support */
284 PETSC_EXTERN PetscErrorCode DMPlexComputeGeometryFEM(DM, Vec *);
285 PETSC_EXTERN PetscErrorCode DMPlexInsertBoundaryValues(DM, PetscBool, Vec, PetscReal, Vec, Vec, Vec);
286 PETSC_EXTERN PetscErrorCode DMPlexInsertBoundaryValuesEssential(DM, PetscReal, PetscInt, PetscInt, const PetscInt[], DMLabel, PetscInt, const PetscInt[],
287                                                                 PetscErrorCode (*)(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar *, void *), void *, Vec );
288 PETSC_EXTERN PetscErrorCode DMPlexInsertBoundaryValuesEssentialField(DM, PetscReal, Vec, PetscInt, PetscInt, const PetscInt[], DMLabel, PetscInt, const PetscInt [],
289                                                                      void (*)(PetscInt, PetscInt, PetscInt,
290                                                                               const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
291                                                                               const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
292                                                                               PetscReal, const PetscReal[], PetscInt, const PetscScalar[],
293                                                                               PetscScalar[]),
294                                                                      void *, Vec);
295 PETSC_EXTERN PetscErrorCode DMPlexInsertBoundaryValuesRiemann(DM, PetscReal, Vec, Vec, Vec, PetscInt, PetscInt, const PetscInt[], DMLabel, PetscInt, const PetscInt [],
296                                                               PetscErrorCode (*)(PetscReal,const PetscReal*,const PetscReal*,const PetscScalar*,PetscScalar*,void*), void *, Vec);
297 PETSC_EXTERN PetscErrorCode DMPlexMarkBoundaryFaces(DM, PetscInt, DMLabel);
298 
299 PETSC_EXTERN PetscErrorCode DMPlexCreateSection(DM, DMLabel [], const PetscInt [], const PetscInt [], PetscInt, const PetscInt [], const IS [], const IS [], IS, PetscSection *);
300 PETSC_EXTERN PetscErrorCode DMPlexGetSubdomainSection(DM, PetscSection*);
301 
302 PETSC_EXTERN PetscErrorCode DMPlexComputeCellGeometryAffineFEM(DM, PetscInt, PetscReal *, PetscReal *, PetscReal *, PetscReal *);
303 PETSC_EXTERN PetscErrorCode DMPlexComputeCellGeometryFEM(DM, PetscInt, PetscQuadrature, PetscReal *, PetscReal *, PetscReal *, PetscReal *);
304 PETSC_EXTERN PetscErrorCode DMPlexCoordinatesToReference(DM, PetscInt, PetscInt, const PetscReal [], PetscReal[]);
305 PETSC_EXTERN PetscErrorCode DMPlexReferenceToCoordinates(DM, PetscInt, PetscInt, const PetscReal [], PetscReal[]);
306 PETSC_EXTERN PetscErrorCode DMPlexShearGeometry(DM, DMDirection, PetscReal[]);
307 PETSC_EXTERN PetscErrorCode DMPlexRemapGeometry(DM, PetscReal,
308                                                 void (*)(PetscInt, PetscInt, PetscInt,
309                                                          const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
310                                                          const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
311                                                          PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]));
312 
313 PETSC_EXTERN PetscErrorCode DMPlexVecGetClosure(DM, PetscSection, Vec, PetscInt, PetscInt *, PetscScalar *[]);
314 PETSC_EXTERN PetscErrorCode DMPlexVecRestoreClosure(DM, PetscSection, Vec, PetscInt, PetscInt *, PetscScalar *[]);
315 PETSC_EXTERN PetscErrorCode DMPlexVecSetClosure(DM, PetscSection, Vec, PetscInt, const PetscScalar[], InsertMode);
316 PETSC_EXTERN PetscErrorCode DMPlexMatSetClosure(DM, PetscSection, PetscSection, Mat, PetscInt, const PetscScalar[], InsertMode);
317 PETSC_EXTERN PetscErrorCode DMPlexGetClosureIndices(DM, PetscSection, PetscSection, PetscInt, PetscInt *, PetscInt **, PetscInt *);
318 PETSC_EXTERN PetscErrorCode DMPlexRestoreClosureIndices(DM, PetscSection, PetscSection, PetscInt, PetscInt *, PetscInt **,PetscInt *);
319 PETSC_EXTERN PetscErrorCode DMPlexMatSetClosureRefined(DM, PetscSection, PetscSection, DM, PetscSection, PetscSection, Mat, PetscInt, const PetscScalar[], InsertMode);
320 PETSC_EXTERN PetscErrorCode DMPlexMatGetClosureIndicesRefined(DM, PetscSection, PetscSection, DM, PetscSection, PetscSection, PetscInt, PetscInt[], PetscInt[]);
321 PETSC_EXTERN PetscErrorCode DMPlexCreateClosureIndex(DM, PetscSection);
322 PETSC_EXTERN PetscErrorCode DMPlexSetClosurePermutationTensor(DM, PetscInt, PetscSection);
323 
324 PETSC_EXTERN PetscErrorCode DMPlexConstructGhostCells(DM, const char [], PetscInt *, DM *);
325 PETSC_EXTERN PetscErrorCode DMPlexConstructCohesiveCells(DM, DMLabel, DMLabel, DM *);
326 
327 PETSC_EXTERN PetscErrorCode DMPlexGetHybridBounds(DM, PetscInt *, PetscInt *, PetscInt *, PetscInt *);
328 PETSC_EXTERN PetscErrorCode DMPlexSetHybridBounds(DM, PetscInt, PetscInt, PetscInt, PetscInt);
329 PETSC_EXTERN PetscErrorCode DMPlexGetVTKCellHeight(DM, PetscInt *);
330 PETSC_EXTERN PetscErrorCode DMPlexSetVTKCellHeight(DM, PetscInt);
331 PETSC_EXTERN PetscErrorCode DMPlexVTKWriteAll(PetscObject, PetscViewer);
332 PETSC_EXTERN PetscErrorCode DMPlexGetGhostCellStratum(DM, PetscInt *, PetscInt *);
333 PETSC_EXTERN PetscErrorCode DMPlexSetGhostCellStratum(DM, PetscInt, PetscInt);
334 PETSC_EXTERN PetscErrorCode DMPlexGetInteriorCellStratum(DM, PetscInt *, PetscInt *);
335 
336 PETSC_EXTERN PetscErrorCode DMPlexGetCellFields(DM, IS, Vec, Vec, Vec, PetscScalar **, PetscScalar **, PetscScalar **);
337 PETSC_EXTERN PetscErrorCode DMPlexRestoreCellFields(DM, IS, Vec, Vec, Vec, PetscScalar **, PetscScalar **, PetscScalar **);
338 PETSC_EXTERN PetscErrorCode DMPlexGetFaceFields(DM, PetscInt, PetscInt, Vec, Vec, Vec, Vec, Vec, PetscInt *, PetscScalar **, PetscScalar **);
339 PETSC_EXTERN PetscErrorCode DMPlexRestoreFaceFields(DM, PetscInt, PetscInt, Vec, Vec, Vec, Vec, Vec, PetscInt *, PetscScalar **, PetscScalar **);
340 PETSC_EXTERN PetscErrorCode DMPlexGetFaceGeometry(DM, PetscInt, PetscInt, Vec, Vec, PetscInt *, PetscFVFaceGeom **, PetscReal **);
341 PETSC_EXTERN PetscErrorCode DMPlexRestoreFaceGeometry(DM, PetscInt, PetscInt, Vec, Vec, PetscInt *, PetscFVFaceGeom **, PetscReal **);
342 
343 PETSC_EXTERN PetscErrorCode DMPlexGetScale(DM, PetscUnit, PetscReal *);
344 PETSC_EXTERN PetscErrorCode DMPlexSetScale(DM, PetscUnit, PetscReal);
345 
346 typedef struct {
347   DM    dm;
348   Vec   u; /* The base vector for the Jacobian action J(u) x */
349   Mat   J; /* Preconditioner for testing */
350   void *user;
351 } JacActionCtx;
352 
353 PETSC_EXTERN PetscErrorCode DMPlexInsertBoundaryValuesFEM(DM, Vec);
354 PETSC_EXTERN PetscErrorCode DMPlexSetMaxProjectionHeight(DM, PetscInt);
355 PETSC_EXTERN PetscErrorCode DMPlexGetMaxProjectionHeight(DM, PetscInt*);
356 PETSC_EXTERN PetscErrorCode DMPlexProjectFieldLocal(DM, Vec,
357                                                     void (**)(PetscInt, PetscInt, PetscInt,
358                                                               const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
359                                                               const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
360                                                               PetscReal, const PetscReal [], PetscScalar []), InsertMode, Vec);
361 PETSC_EXTERN PetscErrorCode DMPlexComputeL2DiffLocal(DM, PetscReal, PetscErrorCode (**)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **, Vec, PetscReal *);
362 PETSC_EXTERN PetscErrorCode DMPlexComputeL2FieldDiff(DM, PetscReal, PetscErrorCode (**)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **, Vec, PetscReal[]);
363 PETSC_EXTERN PetscErrorCode DMPlexComputeL2DiffVec(DM, PetscReal, PetscErrorCode (**)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **, Vec, Vec);
364 PETSC_EXTERN PetscErrorCode DMPlexComputeCellwiseIntegralFEM(DM, Vec, Vec, void *);
365 PETSC_EXTERN PetscErrorCode DMPlexComputeIntegralFEM(DM, Vec, PetscScalar *, void *);
366 PETSC_EXTERN PetscErrorCode DMPlexComputeBdIntegral(DM, Vec, DMLabel, PetscInt, const PetscInt[],
367                                                     void (*)(PetscInt, PetscInt, PetscInt,
368                                                              const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
369                                                              const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
370                                                              PetscReal, const PetscReal[], const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]),
371                                                     PetscScalar *, void *);
372 PETSC_EXTERN PetscErrorCode DMPlexComputeInterpolatorNested(DM, DM, Mat, void *);
373 PETSC_EXTERN PetscErrorCode DMPlexComputeInterpolatorGeneral(DM, DM, Mat, void *);
374 PETSC_EXTERN PetscErrorCode DMPlexComputeGradientClementInterpolant(DM, Vec, Vec);
375 PETSC_EXTERN PetscErrorCode DMPlexComputeInjectorFEM(DM, DM, VecScatter *, void *);
376 PETSC_EXTERN PetscErrorCode DMPlexComputeMassMatrixNested(DM, DM, Mat, void *);
377 PETSC_EXTERN PetscErrorCode DMPlexComputeMassMatrixGeneral(DM, DM, Mat, void *);
378 
379 PETSC_EXTERN PetscErrorCode DMPlexCreateRigidBody(DM, MatNullSpace *);
380 PETSC_EXTERN PetscErrorCode DMPlexCreateRigidBodies(DM, PetscInt, DMLabel, const PetscInt[], const PetscInt[], MatNullSpace *);
381 
382 PETSC_EXTERN PetscErrorCode DMPlexSetSNESLocalFEM(DM,void *,void *,void *);
383 PETSC_EXTERN PetscErrorCode DMPlexSNESComputeBoundaryFEM(DM, Vec, void *);
384 PETSC_EXTERN PetscErrorCode DMPlexSNESComputeResidualFEM(DM, Vec, Vec, void *);
385 PETSC_EXTERN PetscErrorCode DMPlexSNESComputeJacobianFEM(DM, Vec, Mat, Mat, void *);
386 PETSC_EXTERN PetscErrorCode DMPlexComputeJacobianAction(DM, IS, PetscReal, PetscReal, Vec, Vec, Vec, Vec, void *);
387 PETSC_EXTERN PetscErrorCode DMPlexComputeBdResidualSingle(DM, PetscReal, DMLabel, PetscInt, const PetscInt[], PetscInt, Vec, Vec, Vec);
388 PETSC_EXTERN PetscErrorCode DMPlexComputeBdJacobianSingle(DM, PetscReal, DMLabel, PetscInt, const PetscInt[], PetscInt, Vec, Vec, PetscReal, Mat, Mat);
389 
390 PETSC_EXTERN PetscErrorCode DMPlexTSComputeBoundary(DM, PetscReal, Vec, Vec, void *);
391 PETSC_EXTERN PetscErrorCode DMPlexTSComputeRHSFunctionFVM(DM, PetscReal, Vec, Vec, void *);
392 PETSC_EXTERN PetscErrorCode DMPlexTSComputeIFunctionFEM(DM, PetscReal, Vec, Vec, Vec, void *);
393 PETSC_EXTERN PetscErrorCode DMPlexTSComputeIJacobianFEM(DM, PetscReal, Vec, Vec, PetscReal, Mat, Mat, void *);
394 
395 PETSC_EXTERN PetscErrorCode DMPlexComputeRHSFunctionFVM(DM, PetscReal, Vec, Vec, void *);
396 PETSC_EXTERN PetscErrorCode DMPlexReconstructGradientsFVM(DM,Vec,Vec);
397 
398 /* anchors */
399 PETSC_EXTERN PetscErrorCode DMPlexGetAnchors(DM, PetscSection*, IS*);
400 PETSC_EXTERN PetscErrorCode DMPlexSetAnchors(DM, PetscSection, IS);
401 /* tree */
402 PETSC_EXTERN PetscErrorCode DMPlexSetReferenceTree(DM, DM);
403 PETSC_EXTERN PetscErrorCode DMPlexGetReferenceTree(DM, DM*);
404 PETSC_EXTERN PetscErrorCode DMPlexReferenceTreeGetChildSymmetry(DM, PetscInt, PetscInt, PetscInt, PetscInt, PetscInt, PetscInt *, PetscInt *);
405 PETSC_EXTERN PetscErrorCode DMPlexCreateDefaultReferenceTree(MPI_Comm, PetscInt, PetscBool, DM*);
406 PETSC_EXTERN PetscErrorCode DMPlexSetTree(DM, PetscSection, PetscInt [], PetscInt []);
407 PETSC_EXTERN PetscErrorCode DMPlexGetTree(DM, PetscSection *, PetscInt *[], PetscInt *[], PetscSection *, PetscInt *[]);
408 PETSC_EXTERN PetscErrorCode DMPlexGetTreeParent(DM, PetscInt, PetscInt *, PetscInt *);
409 PETSC_EXTERN PetscErrorCode DMPlexGetTreeChildren(DM, PetscInt, PetscInt *, const PetscInt *[]);
410 PETSC_EXTERN PetscErrorCode DMPlexTreeRefineCell(DM, PetscInt, DM *);
411 PETSC_EXTERN PetscErrorCode DMPlexComputeInjectorReferenceTree(DM, Mat *);
412 PETSC_EXTERN PetscErrorCode DMPlexTransferVecTree(DM,Vec,DM,Vec,PetscSF,PetscSF,PetscInt *,PetscInt *,PetscBool,PetscReal);
413 
414 /* natural order */
415 PETSC_EXTERN PetscErrorCode DMPlexCreateGlobalToNaturalSF(DM, PetscSection, PetscSF, PetscSF *);
416 PETSC_EXTERN PetscErrorCode DMPlexSetGlobalToNaturalSF(DM, PetscSF);
417 PETSC_EXTERN PetscErrorCode DMPlexGetGlobalToNaturalSF(DM, PetscSF *);
418 PETSC_EXTERN PetscErrorCode DMPlexGlobalToNaturalBegin(DM, Vec, Vec);
419 PETSC_EXTERN PetscErrorCode DMPlexGlobalToNaturalEnd(DM, Vec, Vec);
420 PETSC_EXTERN PetscErrorCode DMPlexNaturalToGlobalBegin(DM, Vec, Vec);
421 PETSC_EXTERN PetscErrorCode DMPlexNaturalToGlobalEnd(DM, Vec, Vec);
422 
423 /* mesh adaptation */
424 PETSC_EXTERN PetscErrorCode DMPlexAdapt(DM, Vec, const char [], DM *);
425 
426 PETSC_EXTERN PetscErrorCode DMPlexGlobalToLocalBasis(DM, Vec);
427 PETSC_EXTERN PetscErrorCode DMPlexLocalToGlobalBasis(DM, Vec);
428 PETSC_EXTERN PetscErrorCode DMPlexCreateBasisRotation(DM, PetscReal, PetscReal, PetscReal);
429 #endif
430