xref: /petsc/include/petscdmplex.h (revision 137cd93a843fbc4563fa3623d36faae7208dd63c) 
1552f7358SJed Brown /*
2552f7358SJed Brown   DMPlex, for parallel unstructured distributed mesh problems.
3552f7358SJed Brown */
4552f7358SJed Brown #if !defined(__PETSCDMPLEX_H)
5552f7358SJed Brown #define __PETSCDMPLEX_H
6552f7358SJed Brown 
7552f7358SJed Brown #include <petscdm.h>
8a0845e3aSMatthew G. Knepley #include <petscdt.h>
9a0845e3aSMatthew G. Knepley #include <petscfe.h>
100bacfa0aSMatthew G. Knepley #include <petscfv.h>
11799f573fSMatthew G. Knepley #include <petscsftypes.h>
12552f7358SJed Brown 
1377623264SMatthew G. Knepley PETSC_EXTERN PetscClassId PETSCPARTITIONER_CLASSID;
1477623264SMatthew G. Knepley 
1577623264SMatthew G. Knepley /*J
1677623264SMatthew G. Knepley   PetscPartitionerType - String with the name of a PETSc graph partitioner
1777623264SMatthew G. Knepley 
1877623264SMatthew G. Knepley   Level: beginner
1977623264SMatthew G. Knepley 
2077623264SMatthew G. Knepley .seealso: PetscPartitionerSetType(), PetscPartitioner
2177623264SMatthew G. Knepley J*/
2277623264SMatthew G. Knepley typedef const char *PetscPartitionerType;
2377623264SMatthew G. Knepley #define PETSCPARTITIONERCHACO    "chaco"
2477623264SMatthew G. Knepley #define PETSCPARTITIONERPARMETIS "parmetis"
25*137cd93aSLisandro Dalcin #define PETSCPARTITIONERPTSCOTCH "ptscotch"
2677623264SMatthew G. Knepley #define PETSCPARTITIONERSHELL    "shell"
27555a9cf8SMatthew G. Knepley #define PETSCPARTITIONERSIMPLE   "simple"
286462276dSToby Isaac #define PETSCPARTITIONERGATHER   "gather"
2977623264SMatthew G. Knepley 
3077623264SMatthew G. Knepley PETSC_EXTERN PetscFunctionList PetscPartitionerList;
3177623264SMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscPartitionerCreate(MPI_Comm, PetscPartitioner *);
3277623264SMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscPartitionerDestroy(PetscPartitioner *);
3377623264SMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscPartitionerSetType(PetscPartitioner, PetscPartitionerType);
3477623264SMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscPartitionerGetType(PetscPartitioner, PetscPartitionerType *);
3577623264SMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscPartitionerSetUp(PetscPartitioner);
3677623264SMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscPartitionerSetFromOptions(PetscPartitioner);
378aec7d55SBarry Smith PETSC_STATIC_INLINE PetscErrorCode PetscPartitionerViewFromOptions(PetscPartitioner A,PetscObject B,const char name[]) {return PetscObjectViewFromOptions((PetscObject)A,B,name);}
3877623264SMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscPartitionerView(PetscPartitioner, PetscViewer);
3977623264SMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscPartitionerRegister(const char [], PetscErrorCode (*)(PetscPartitioner));
4077623264SMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscPartitionerRegisterDestroy(void);
4177623264SMatthew G. Knepley 
42f8987ae8SMichael Lange PETSC_EXTERN PetscErrorCode PetscPartitionerPartition(PetscPartitioner, DM, PetscSection, IS *);
4377623264SMatthew G. Knepley 
445680f57bSMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscPartitionerShellSetPartition(PetscPartitioner, PetscInt, const PetscInt[], const PetscInt[]);
45df8115dbSMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscPartitionerShellSetRandom(PetscPartitioner, PetscBool);
46df8115dbSMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscPartitionerShellGetRandom(PetscPartitioner, PetscBool *);
4777623264SMatthew G. Knepley 
48552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexCreate(MPI_Comm, DM*);
4927c04023SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateCohesiveSubmesh(DM, PetscBool, const char [], PetscInt, DM *);
500fde5641SMatthew G Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateFromCellList(MPI_Comm, PetscInt, PetscInt, PetscInt, PetscInt, PetscBool, const int[], PetscInt, const double[], DM*);
51fba955ccSBarry Smith PETSC_EXTERN PetscErrorCode DMPlexCreateFromCellListParallel(MPI_Comm, PetscInt, PetscInt, PetscInt, PetscInt, PetscBool, const int[], PetscInt, const PetscReal[], PetscSF *, DM *);
5206bbee04SMatthew G Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateFromDAG(DM, PetscInt, const PetscInt [], const PetscInt [], const PetscInt [], const PetscInt [], const PetscScalar []);
538415267dSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm, PetscInt, PetscBool, DM*);
54a9074c1eSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexSetOptionsPrefix(DM, const char []);
55552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetChart(DM, PetscInt *, PetscInt *);
56552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexSetChart(DM, PetscInt, PetscInt);
57552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetConeSize(DM, PetscInt, PetscInt *);
58552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexSetConeSize(DM, PetscInt, PetscInt);
59feb68dd6SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexAddConeSize(DM, PetscInt, PetscInt);
60552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetCone(DM, PetscInt, const PetscInt *[]);
61552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexSetCone(DM, PetscInt, const PetscInt[]);
629f074e33SMatthew G Knepley PETSC_EXTERN PetscErrorCode DMPlexInsertCone(DM, PetscInt, PetscInt, PetscInt);
6377c88f5bSMatthew G Knepley PETSC_EXTERN PetscErrorCode DMPlexInsertConeOrientation(DM, PetscInt, PetscInt, PetscInt);
64552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetConeOrientation(DM, PetscInt, const PetscInt *[]);
65552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexSetConeOrientation(DM, PetscInt, const PetscInt[]);
66552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetSupportSize(DM, PetscInt, PetscInt *);
67552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexSetSupportSize(DM, PetscInt, PetscInt);
68552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetSupport(DM, PetscInt, const PetscInt *[]);
69552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexSetSupport(DM, PetscInt, const PetscInt[]);
70552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexInsertSupport(DM, PetscInt, PetscInt, PetscInt);
71552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetConeSection(DM, PetscSection *);
728cb4d582SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetSupportSection(DM, PetscSection *);
73552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetCones(DM, PetscInt *[]);
74552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetConeOrientations(DM, PetscInt *[]);
75552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetMaxSizes(DM, PetscInt *, PetscInt *);
76552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexSymmetrize(DM);
77552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexStratify(DM);
784e3744c5SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexEqual(DM,DM,PetscBool*);
79cb11e54dSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexReverseCell(DM, PetscInt);
80d27a0f52SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexOrient(DM);
8175d3a19aSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexInterpolate(DM, DM *);
824e3744c5SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexUninterpolate(DM, DM *);
83e101f074SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexPreallocateOperator(DM, PetscInt, PetscInt[], PetscInt[], PetscInt[], PetscInt[], Mat, PetscBool);
84552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetPointLocal(DM,PetscInt,PetscInt*,PetscInt*);
85081a2d76SSatish Balay PETSC_EXTERN PetscErrorCode DMPlexPointLocalRead(DM,PetscInt,const PetscScalar*,void*);
86a89cf0ddSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexPointLocalRef(DM,PetscInt,PetscScalar*,void*);
87a89cf0ddSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetPointLocalField(DM,PetscInt,PetscInt,PetscInt*,PetscInt*);
88a89cf0ddSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexPointLocalFieldRef(DM,PetscInt,PetscInt,PetscScalar*,void*);
89081a2d76SSatish Balay PETSC_EXTERN PetscErrorCode DMPlexPointLocalFieldRead(DM,PetscInt,PetscInt,const PetscScalar*,void*);
90552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetPointGlobal(DM,PetscInt,PetscInt*,PetscInt*);
91552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexPointGlobalRead(DM,PetscInt,const PetscScalar*,const void*);
92a89cf0ddSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexPointGlobalRef(DM,PetscInt,PetscScalar*,void*);
93a89cf0ddSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetPointGlobalField(DM,PetscInt,PetscInt,PetscInt*,PetscInt*);
94a89cf0ddSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexPointGlobalFieldRef(DM,PetscInt,PetscInt,PetscScalar*,void*);
95081a2d76SSatish Balay PETSC_EXTERN PetscErrorCode DMPlexPointGlobalFieldRead(DM,PetscInt,PetscInt,const PetscScalar*, void*);
96552f7358SJed Brown 
978b51c812SSatish Balay PETSC_EXTERN PetscErrorCode DMPlexFilter(DM, DMLabel, PetscInt, DM *);
98552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetCellNumbering(DM, IS *);
99552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetVertexNumbering(DM, IS *);
100ef48cebcSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreatePointNumbering(DM, IS *);
10108a22f4bSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateRankField(DM, Vec *);
102552f7358SJed Brown 
10375d3a19aSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetDepth(DM, PetscInt *);
1043ded2ed9SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetDepthLabel(DM, DMLabel *);
10575d3a19aSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetDepthStratum(DM, PetscInt, PetscInt *, PetscInt *);
10675d3a19aSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetHeightStratum(DM, PetscInt, PetscInt *, PetscInt *);
10775d3a19aSMatthew G. Knepley 
10875d3a19aSMatthew G. Knepley /* Topological Operations */
109552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetMeet(DM, PetscInt, const PetscInt [], PetscInt *, const PetscInt **);
110552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetFullMeet(DM, PetscInt, const PetscInt [], PetscInt *, const PetscInt **);
111552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexRestoreMeet(DM, PetscInt, const PetscInt [], PetscInt *, const PetscInt **);
112552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetJoin(DM, PetscInt, const PetscInt [], PetscInt *, const PetscInt **);
113552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetFullJoin(DM, PetscInt, const PetscInt [], PetscInt *, const PetscInt **);
114552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexRestoreJoin(DM, PetscInt, const PetscInt [], PetscInt *, const PetscInt **);
115552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetTransitiveClosure(DM, PetscInt, PetscBool, PetscInt *, PetscInt *[]);
116552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexRestoreTransitiveClosure(DM, PetscInt, PetscBool, PetscInt *, PetscInt *[]);
117552f7358SJed Brown 
11875d3a19aSMatthew G. Knepley /* Mesh Generation */
119552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGenerate(DM, const char [], PetscBool , DM *);
120930319cbSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCopyCoordinates(DM, DM);
1211df5d5c5SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateDoublet(MPI_Comm, PetscInt, PetscBool, PetscBool, PetscBool, PetscReal, DM *);
12226492d91SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateSquareBoundary(DM, const PetscReal [], const PetscReal [], const PetscInt []);
123552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexCreateCubeBoundary(DM, const PetscReal [], const PetscReal [], const PetscInt []);
124ad6ef69fSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm, PetscInt, PetscInt, PetscBool, DM *);
125bff4a2f0SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateHexBoxMesh(MPI_Comm, PetscInt, const PetscInt[], DMBoundaryType, DMBoundaryType, DMBoundaryType, DM *);
12665a81367SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm, PetscInt, PetscBool, DM *);
127dbc1dc17SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm, PetscInt, DMBoundaryType, DM *);
12824119c2aSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm, PetscInt, PetscBool, DM *);
129552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexCreateConeSection(DM, PetscSection *);
130459e96c1SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexInvertCell(PetscInt, PetscInt, int []);
131ca8062c8SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCheckSymmetry(DM);
13258723a97SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCheckSkeleton(DM, PetscBool, PetscInt);
1339bf0dad6SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCheckFaces(DM, PetscBool, PetscInt);
13475d3a19aSMatthew G. Knepley 
135d9deefdfSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexTriangleSetOptions(DM, const char *);
136776fd405SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexTetgenSetOptions(DM, const char *);
137d9deefdfSMatthew G. Knepley 
138d6218766SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateFromFile(MPI_Comm, const char[], PetscBool, DM *);
139d6218766SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateExodus(MPI_Comm, PetscInt, PetscBool, DM *);
140d6218766SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateExodusFromFile(MPI_Comm, const char [], PetscBool, DM *);
141d6218766SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateCGNS(MPI_Comm, PetscInt, PetscBool, DM *);
142d6218766SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateCGNSFromFile(MPI_Comm, const char[], PetscBool, DM *);
143d6218766SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateGmsh(MPI_Comm, PetscViewer, PetscBool, DM *);
144d6218766SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateGmshFromFile(MPI_Comm, const char [], PetscBool, DM *);
145d6218766SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateFluent(MPI_Comm, PetscViewer, PetscBool, DM *);
146d6218766SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateFluentFromFile(MPI_Comm, const char [], PetscBool, DM *);
147d6218766SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateMedFromFile(MPI_Comm, const char [], PetscBool, DM *);
148f2801cd6SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreatePLYFromFile(MPI_Comm, const char [], PetscBool, DM *);
149d6218766SMatthew G. Knepley 
15075d3a19aSMatthew G. Knepley /* Mesh Partitioning and Distribution */
151552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexCreateNeighborCSR(DM, PetscInt, PetscInt *, PetscInt **, PetscInt **);
1525680f57bSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetPartitioner(DM, PetscPartitioner *);
15371bb2955SLawrence Mitchell PETSC_EXTERN PetscErrorCode DMPlexSetPartitioner(DM, PetscPartitioner);
154ac17c9edSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreatePartition(DM, const char[], PetscInt, PetscBool, PetscSection *, IS *, PetscSection *, IS *);
1553fa7752dSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexCreatePartitionerGraph(DM, PetscInt, PetscInt *, PetscInt **, PetscInt **, IS *);
156552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexCreatePartitionClosure(DM, PetscSection, IS, PetscSection *, IS *);
1571fd9873aSMichael Lange PETSC_EXTERN PetscErrorCode DMPlexPartitionLabelInvert(DM, DMLabel, PetscSF, DMLabel);
1585abbe4feSMichael Lange PETSC_EXTERN PetscErrorCode DMPlexPartitionLabelClosure(DM, DMLabel);
15924d039d7SMichael Lange PETSC_EXTERN PetscErrorCode DMPlexPartitionLabelAdjacency(DM, DMLabel);
160be200f8dSMichael Lange PETSC_EXTERN PetscErrorCode DMPlexPartitionLabelPropagate(DM, DMLabel);
161aa3148a8SMichael Lange PETSC_EXTERN PetscErrorCode DMPlexPartitionLabelCreateSF(DM, DMLabel, PetscSF *);
16280cf41d5SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexDistribute(DM, PetscInt, PetscSF*, DM*);
163b9f40539SMichael Lange PETSC_EXTERN PetscErrorCode DMPlexDistributeOverlap(DM, PetscInt, PetscSF *, DM *);
164552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexDistributeField(DM,PetscSF,PetscSection,Vec,PetscSection,Vec);
165b0a623aaSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexDistributeFieldIS(DM, PetscSF, PetscSection, IS, PetscSection, IS *);
166552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexDistributeData(DM,PetscSF,PetscSection,MPI_Datatype,void*,PetscSection,void**);
16745800214SMichael Lange PETSC_EXTERN PetscErrorCode DMPlexMigrate(DM, PetscSF, DM);
1686462276dSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexGetRedundantDM(DM, DM*);
1693c1f0c11SLawrence Mitchell PETSC_EXTERN PetscErrorCode DMPlexSetAdjacencyUser(DM, PetscErrorCode (*)(DM,PetscInt,PetscInt*,PetscInt[],void*),void*);
1703c1f0c11SLawrence Mitchell PETSC_EXTERN PetscErrorCode DMPlexGetAdjacencyUser(DM, PetscErrorCode (**)(DM,PetscInt,PetscInt*,PetscInt[],void*),void**);
17170034214SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexSetAdjacencyUseCone(DM,PetscBool);
17270034214SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetAdjacencyUseCone(DM,PetscBool*);
17370034214SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexSetAdjacencyUseClosure(DM,PetscBool);
17470034214SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetAdjacencyUseClosure(DM,PetscBool*);
175a17985deSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexSetAdjacencyUseAnchors(DM,PetscBool);
176a17985deSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexGetAdjacencyUseAnchors(DM,PetscBool*);
17770034214SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetAdjacency(DM, PetscInt, PetscInt *, PetscInt *[]);
17875d3a19aSMatthew G. Knepley 
179c99f2573SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetOrdering(DM, MatOrderingType, DMLabel, IS *);
180f5cedc29SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexPermute(DM, IS, DM *);
181f5cedc29SMatthew G. Knepley 
182b0a623aaSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateProcessSF(DM, PetscSF, IS *, PetscSF *);
183b0a623aaSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateTwoSidedProcessSF(DM, PetscSF, PetscSection, IS, PetscSection, IS, IS *, PetscSF *);
184b0a623aaSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexDistributeOwnership(DM, PetscSection, IS *, PetscSection, IS *);
185a9f1d5b2SMichael Lange PETSC_EXTERN PetscErrorCode DMPlexCreateOverlap(DM, PetscInt, PetscSection, IS, PetscSection, IS, DMLabel *);
18646f9b1c3SMichael Lange PETSC_EXTERN PetscErrorCode DMPlexCreateOverlapMigrationSF(DM, PetscSF, PetscSF *);
18745800214SMichael Lange PETSC_EXTERN PetscErrorCode DMPlexStratifyMigrationSF(DM, PetscSF, PetscSF *);
188b0a623aaSMatthew G. Knepley 
18975d3a19aSMatthew G. Knepley /* Submesh Support */
1903cf72582SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateSubmesh(DM, DMLabel, PetscInt, DM*);
1913cf72582SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateHybridMesh(DM, DMLabel, DMLabel *, DM *);
192552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetSubpointMap(DM, DMLabel*);
193552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexSetSubpointMap(DM, DMLabel);
194552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexCreateSubpointIS(DM, IS *);
195552f7358SJed Brown 
1962be2b188SMatthew G Knepley PETSC_EXTERN PetscErrorCode DMPlexLabelComplete(DM, DMLabel);
1970f66a230SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexLabelCohesiveComplete(DM, DMLabel, DMLabel, PetscBool, DM);
1986cf0e42fSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexLabelAddCells(DM, DMLabel);
199f402d5e4SToby Isaac PETSC_EXTERN PetscErrorCode DMPlexLabelClearCells(DM, DMLabel);
200552f7358SJed Brown 
20175d3a19aSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetRefinementLimit(DM, PetscReal *);
20275d3a19aSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexSetRefinementLimit(DM, PetscReal);
20375d3a19aSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetRefinementUniform(DM, PetscBool *);
20475d3a19aSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexSetRefinementUniform(DM, PetscBool);
2051e4cba6aSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetRefinementFunction(DM, PetscErrorCode (**)(const PetscReal [], PetscReal *));
2061e4cba6aSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexSetRefinementFunction(DM, PetscErrorCode (*)(const PetscReal [], PetscReal *));
2072389894bSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateCoarsePointIS(DM, IS *);
2080aef6b92SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetRegularRefinement(DM, PetscBool *);
2090aef6b92SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexSetRegularRefinement(DM, PetscBool);
210e5337592SStefano Zampini PETSC_EXTERN PetscErrorCode DMPlexRefineSimplexToTensor(DM, DM*);
211552f7358SJed Brown 
21218ad9376SMatthew G. Knepley /* Support for cell-vertex meshes */
21318ad9376SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetNumFaceVertices(DM, PetscInt, PetscInt, PetscInt *);
214f5d69827SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetOrientedFace(DM, PetscInt, PetscInt, const PetscInt [], PetscInt, PetscInt [], PetscInt [], PetscInt [], PetscBool *);
21518ad9376SMatthew G. Knepley 
2160f0bf202SMatthew G. Knepley /* Geometry Support */
2170f0bf202SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGetMinRadius(DM, PetscReal *);
2180f0bf202SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexSetMinRadius(DM, PetscReal);
219741bfc07SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexComputeProjection2Dto1D(PetscScalar[], PetscReal[]);
220741bfc07SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexComputeProjection3Dto1D(PetscScalar[], PetscReal[]);
221741bfc07SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexComputeProjection3Dto2D(PetscInt, PetscScalar[], PetscReal[]);
2220f0bf202SMatthew G. Knepley 
223c4eade1cSMatthew G. Knepley /* Point Location */
224c4eade1cSMatthew G. Knepley typedef struct _PetscGridHash *PetscGridHash;
225c4eade1cSMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscGridHashCreate(MPI_Comm, PetscInt, const PetscScalar[], PetscGridHash *);
226c4eade1cSMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscGridHashEnlarge(PetscGridHash, const PetscScalar []);
227c4eade1cSMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscGridHashSetGrid(PetscGridHash, const PetscInt [], const PetscReal []);
2281c6dfc3eSMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscGridHashGetEnclosingBox(PetscGridHash, PetscInt, const PetscScalar [], PetscInt [], PetscInt []);
229c4eade1cSMatthew G. Knepley PETSC_EXTERN PetscErrorCode PetscGridHashDestroy(PetscGridHash *);
230c4eade1cSMatthew G. Knepley 
231834e62ceSMatthew G. Knepley /* FVM Support */
232cc08537eSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexComputeCellGeometryFVM(DM, PetscInt, PetscReal *, PetscReal [], PetscReal []);
2330f0bf202SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexComputeGeometryFVM(DM, Vec *, Vec *);
234856ac710SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexComputeGradientFVM(DM, PetscFV, Vec, Vec, DM *);
235b27d5b9eSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexGetDataFVM(DM, PetscFV, Vec *, Vec *, DM *);
236834e62ceSMatthew G. Knepley 
237552f7358SJed Brown /* FEM Support */
238bdd6f66aSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexInsertBoundaryValues(DM, PetscBool, Vec, PetscReal, Vec, Vec, Vec);
2391c531cf8SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexInsertBoundaryValuesEssential(DM, PetscReal, PetscInt, PetscInt, const PetscInt[], DMLabel, PetscInt, const PetscInt[],
240b278463cSMatthew G. Knepley                                                                 PetscErrorCode (*)(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar *, void *), void *, Vec );
2411c531cf8SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexInsertBoundaryValuesEssentialField(DM, PetscReal, Vec, PetscInt, PetscInt, const PetscInt[], DMLabel, PetscInt, const PetscInt [],
242b278463cSMatthew G. Knepley                                                                      void (*)(PetscInt, PetscInt, PetscInt,
243b278463cSMatthew G. Knepley                                                                               const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
244b278463cSMatthew G. Knepley                                                                               const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
245191494d9SMatthew G. Knepley                                                                               PetscReal, const PetscReal[], PetscInt, const PetscScalar[],
246b278463cSMatthew G. Knepley                                                                               PetscScalar[]),
247b278463cSMatthew G. Knepley                                                                      void *, Vec);
2481c531cf8SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexInsertBoundaryValuesRiemann(DM, PetscReal, Vec, Vec, Vec, PetscInt, PetscInt, const PetscInt[], DMLabel, PetscInt, const PetscInt [],
249b278463cSMatthew G. Knepley                                                               PetscErrorCode (*)(PetscReal,const PetscReal*,const PetscReal*,const PetscScalar*,PetscScalar*,void*), void *, Vec);
250a6ba4734SToby Isaac PETSC_EXTERN PetscErrorCode DMPlexMarkBoundaryFaces(DM, DMLabel);
251d7ddef95SMatthew G. Knepley 
252ab1d0545SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateSection(DM, PetscInt, PetscInt, const PetscInt [], const PetscInt [], PetscInt, const PetscInt [], const IS [], const IS [], IS, PetscSection *);
253be36d101SStefano Zampini PETSC_EXTERN PetscErrorCode DMPlexGetSubdomainSection(DM, PetscSection*);
25475d3a19aSMatthew G. Knepley 
2558e0841e0SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexComputeCellGeometryAffineFEM(DM, PetscInt, PetscReal *, PetscReal *, PetscReal *, PetscReal *);
256dfccc68fSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexComputeCellGeometryFEM(DM, PetscInt, PetscQuadrature, PetscReal *, PetscReal *, PetscReal *, PetscReal *);
257c0d900a5SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexComputeGeometryFEM(DM, Vec *);
258d6143a4eSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexCoordinatesToReference(DM, PetscInt, PetscInt, const PetscReal [], PetscReal[]);
2599d150b73SToby Isaac PETSC_EXTERN PetscErrorCode DMPlexReferenceToCoordinates(DM, PetscInt, PetscInt, const PetscReal [], PetscReal[]);
260d6143a4eSToby Isaac 
2617c1f9639SMatthew G Knepley PETSC_EXTERN PetscErrorCode DMPlexVecGetClosure(DM, PetscSection, Vec, PetscInt, PetscInt *, PetscScalar *[]);
2627c1f9639SMatthew G Knepley PETSC_EXTERN PetscErrorCode DMPlexVecRestoreClosure(DM, PetscSection, Vec, PetscInt, PetscInt *, PetscScalar *[]);
263552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexVecSetClosure(DM, PetscSection, Vec, PetscInt, const PetscScalar[], InsertMode);
2647c1f9639SMatthew G Knepley PETSC_EXTERN PetscErrorCode DMPlexMatSetClosure(DM, PetscSection, PetscSection, Mat, PetscInt, const PetscScalar[], InsertMode);
2656ecaa68aSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexGetClosureIndices(DM, PetscSection, PetscSection, PetscInt, PetscInt *, PetscInt **, PetscInt *);
26646bdb399SToby Isaac PETSC_EXTERN PetscErrorCode DMPlexRestoreClosureIndices(DM, PetscSection, PetscSection, PetscInt, PetscInt *, PetscInt **,PetscInt *);
2670405ed22SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexMatSetClosureRefined(DM, PetscSection, PetscSection, DM, PetscSection, PetscSection, Mat, PetscInt, const PetscScalar[], InsertMode);
2687c927364SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexMatGetClosureIndicesRefined(DM, PetscSection, PetscSection, DM, PetscSection, PetscSection, PetscInt, PetscInt[], PetscInt[]);
269ee72d991SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateClosureIndex(DM, PetscSection);
2703194fc30SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateSpectralClosurePermutation(DM, PetscSection);
271552f7358SJed Brown 
272552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexConstructGhostCells(DM, const char [], PetscInt *, DM *);
273a89082eeSMatthew G Knepley PETSC_EXTERN PetscErrorCode DMPlexConstructCohesiveCells(DM, DMLabel, DM *);
274552f7358SJed Brown 
275770b213bSMatthew G Knepley PETSC_EXTERN PetscErrorCode DMPlexGetHybridBounds(DM, PetscInt *, PetscInt *, PetscInt *, PetscInt *);
276770b213bSMatthew G Knepley PETSC_EXTERN PetscErrorCode DMPlexSetHybridBounds(DM, PetscInt, PetscInt, PetscInt, PetscInt);
277552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetVTKCellHeight(DM, PetscInt *);
278552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexSetVTKCellHeight(DM, PetscInt);
279552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexVTKWriteAll(PetscObject, PetscViewer);
280552f7358SJed Brown 
281552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexGetScale(DM, PetscUnit, PetscReal *);
282552f7358SJed Brown PETSC_EXTERN PetscErrorCode DMPlexSetScale(DM, PetscUnit, PetscReal);
283552f7358SJed Brown 
284552f7358SJed Brown typedef struct {
285552f7358SJed Brown   DM    dm;
286552f7358SJed Brown   Vec   u; /* The base vector for the Jacbobian action J(u) x */
287552f7358SJed Brown   Mat   J; /* Preconditioner for testing */
288552f7358SJed Brown   void *user;
289552f7358SJed Brown } JacActionCtx;
290552f7358SJed Brown 
2913351dd3dSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexInsertBoundaryValuesFEM(DM, Vec);
292b29cfa1cSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexSetMaxProjectionHeight(DM, PetscInt);
293b29cfa1cSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexGetMaxProjectionHeight(DM, PetscInt*);
294e29c0834SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexProjectFieldLocal(DM, Vec,
295e29c0834SMatthew G. Knepley                                                     void (**)(PetscInt, PetscInt, PetscInt,
296e29c0834SMatthew G. Knepley                                                               const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
297e29c0834SMatthew G. Knepley                                                               const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[],
298e29c0834SMatthew G. Knepley                                                               PetscReal, const PetscReal [], PetscScalar []), InsertMode, Vec);
2990163fd50SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexComputeL2FieldDiff(DM, PetscReal, PetscErrorCode (**)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **, Vec, PetscReal[]);
3000163fd50SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexComputeL2DiffVec(DM, PetscReal, PetscErrorCode (**)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *), void **, Vec, Vec);
3010f2d7e86SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexComputeIntegralFEM(DM, Vec, PetscReal *, void *);
30268132eb9SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexComputeInterpolatorNested(DM, DM, Mat, void *);
30368132eb9SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexComputeInterpolatorGeneral(DM, DM, Mat, void *);
3047c927364SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexComputeInjectorFEM(DM, DM, VecScatter *, void *);
3051c41a8caSMatthew G. Knepley 
306026175e5SToby Isaac PETSC_EXTERN PetscErrorCode DMPlexCreateRigidBody(DM, MatNullSpace *);
307026175e5SToby Isaac 
3089f520fc2SToby Isaac PETSC_EXTERN PetscErrorCode DMPlexSetSNESLocalFEM(DM,void *,void *,void *);
309bdd6f66aSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexSNESComputeBoundaryFEM(DM, Vec, void *);
3100f2d7e86SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexSNESComputeResidualFEM(DM, Vec, Vec, void *);
3110f2d7e86SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexSNESComputeJacobianFEM(DM, Vec, Mat, Mat, void *);
312a925c78cSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexSNESComputeJacobianActionFEM(DM, Vec, Vec, Vec, void *);
3130f2d7e86SMatthew G. Knepley 
314ef68eab9SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexTSComputeBoundary(DM, PetscReal, Vec, Vec, void *);
315924a1b8fSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexTSComputeRHSFunctionFVM(DM, PetscReal, Vec, Vec, void *);
316adbe6fbbSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexTSComputeIFunctionFEM(DM, PetscReal, Vec, Vec, Vec, void *);
317756a1f44SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexTSComputeIJacobianFEM(DM, PetscReal, Vec, Vec, PetscReal, Mat, Mat, void *);
318adbe6fbbSMatthew G. Knepley 
3191c41a8caSMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexComputeRHSFunctionFVM(DM, PetscReal, Vec, Vec, void *);
3205d16530eSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexReconstructGradientsFVM(DM,Vec,Vec);
321a68b90caSToby Isaac 
322a17985deSToby Isaac /* anchors */
323a17985deSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexGetAnchors(DM, PetscSection*, IS*);
324a17985deSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexSetAnchors(DM, PetscSection, IS);
325d6a7ad0dSToby Isaac /* tree */
326d6a7ad0dSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexSetReferenceTree(DM, DM);
327d6a7ad0dSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexGetReferenceTree(DM, DM*);
328dcbd3bf7SToby Isaac PETSC_EXTERN PetscErrorCode DMPlexReferenceTreeGetChildSymmetry(DM, PetscInt, PetscInt, PetscInt, PetscInt, PetscInt, PetscInt *, PetscInt *);
329da43764aSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexCreateDefaultReferenceTree(MPI_Comm, PetscInt, PetscBool, DM*);
330b2f41788SToby Isaac PETSC_EXTERN PetscErrorCode DMPlexSetTree(DM, PetscSection, PetscInt [], PetscInt []);
331b2f41788SToby Isaac PETSC_EXTERN PetscErrorCode DMPlexGetTree(DM, PetscSection *, PetscInt *[], PetscInt *[], PetscSection *, PetscInt *[]);
332d961a43aSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexGetTreeParent(DM, PetscInt, PetscInt *, PetscInt *);
333d961a43aSToby Isaac PETSC_EXTERN PetscErrorCode DMPlexGetTreeChildren(DM, PetscInt, PetscInt *, const PetscInt *[]);
3346f5f1567SToby Isaac PETSC_EXTERN PetscErrorCode DMPlexTreeRefineCell(DM, PetscInt, DM *);
3353b490a17SToby Isaac PETSC_EXTERN PetscErrorCode DMPlexComputeInjectorReferenceTree(DM, Mat *);
336bbcf1e96SToby Isaac PETSC_EXTERN PetscErrorCode DMPlexTransferVecTree(DM,Vec,DM,Vec,PetscSF,PetscSF,PetscInt *,PetscInt *,PetscBool,PetscReal);
337fa534816SMatthew G. Knepley 
338fa534816SMatthew G. Knepley /* natural order */
339fa534816SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexCreateGlobalToNaturalSF(DM, PetscSection, PetscSF, PetscSF *);
340fa534816SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGlobalToNaturalBegin(DM, Vec, Vec);
341fa534816SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexGlobalToNaturalEnd(DM, Vec, Vec);
342fa534816SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexNaturalToGlobalBegin(DM, Vec, Vec);
343fa534816SMatthew G. Knepley PETSC_EXTERN PetscErrorCode DMPlexNaturalToGlobalEnd(DM, Vec, Vec);
3440bbe5d31Sbarral 
3450bbe5d31Sbarral /* mesh adaptation */
3460f7e110dSbarral PETSC_EXTERN PetscErrorCode DMPlexAdapt(DM, Vec, const char [], DM *);
347552f7358SJed Brown #endif
348