Actual source code: dmpleximpl.h
petsc-master 2020-01-22
1: #if !defined(_PLEXIMPL_H)
2: #define _PLEXIMPL_H
4: #include <petscmat.h>
5: #include <petscdmplex.h>
6: #include <petscbt.h>
7: #include <petscsf.h>
8: #include <petsc/private/dmimpl.h>
10: PETSC_EXTERN PetscLogEvent DMPLEX_Interpolate;
11: PETSC_EXTERN PetscLogEvent DMPLEX_Partition;
12: PETSC_EXTERN PetscLogEvent DMPLEX_PartSelf;
13: PETSC_EXTERN PetscLogEvent DMPLEX_PartLabelInvert;
14: PETSC_EXTERN PetscLogEvent DMPLEX_PartLabelCreateSF;
15: PETSC_EXTERN PetscLogEvent DMPLEX_PartStratSF;
16: PETSC_EXTERN PetscLogEvent DMPLEX_CreatePointSF;
17: PETSC_EXTERN PetscLogEvent DMPLEX_Distribute;
18: PETSC_EXTERN PetscLogEvent DMPLEX_DistributeCones;
19: PETSC_EXTERN PetscLogEvent DMPLEX_DistributeLabels;
20: PETSC_EXTERN PetscLogEvent DMPLEX_DistributeSF;
21: PETSC_EXTERN PetscLogEvent DMPLEX_DistributeOverlap;
22: PETSC_EXTERN PetscLogEvent DMPLEX_DistributeField;
23: PETSC_EXTERN PetscLogEvent DMPLEX_DistributeData;
24: PETSC_EXTERN PetscLogEvent DMPLEX_Migrate;
25: PETSC_EXTERN PetscLogEvent DMPLEX_InterpolateSF;
26: PETSC_EXTERN PetscLogEvent DMPLEX_GlobalToNaturalBegin;
27: PETSC_EXTERN PetscLogEvent DMPLEX_GlobalToNaturalEnd;
28: PETSC_EXTERN PetscLogEvent DMPLEX_NaturalToGlobalBegin;
29: PETSC_EXTERN PetscLogEvent DMPLEX_NaturalToGlobalEnd;
30: PETSC_EXTERN PetscLogEvent DMPLEX_Stratify;
31: PETSC_EXTERN PetscLogEvent DMPLEX_Symmetrize;
32: PETSC_EXTERN PetscLogEvent DMPLEX_Preallocate;
33: PETSC_EXTERN PetscLogEvent DMPLEX_ResidualFEM;
34: PETSC_EXTERN PetscLogEvent DMPLEX_JacobianFEM;
35: PETSC_EXTERN PetscLogEvent DMPLEX_InterpolatorFEM;
36: PETSC_EXTERN PetscLogEvent DMPLEX_InjectorFEM;
37: PETSC_EXTERN PetscLogEvent DMPLEX_IntegralFEM;
38: PETSC_EXTERN PetscLogEvent DMPLEX_CreateGmsh;
39: PETSC_EXTERN PetscLogEvent DMPLEX_RebalanceSharedPoints;
40: PETSC_EXTERN PetscLogEvent DMPLEX_CreateFromFile;
41: PETSC_EXTERN PetscLogEvent DMPLEX_CreateFromCellList;
42: PETSC_EXTERN PetscLogEvent DMPLEX_CreateFromCellList_Coordinates;
44: PETSC_EXTERN PetscBool PetscPartitionerRegisterAllCalled;
45: PETSC_EXTERN PetscErrorCode PetscPartitionerRegisterAll(void);
47: PETSC_EXTERN const char * const CellRefiners[];
48: typedef enum {REFINER_NOOP = 0,
49: REFINER_SIMPLEX_1D,
50: REFINER_SIMPLEX_2D,
51: REFINER_HYBRID_SIMPLEX_2D,
52: REFINER_SIMPLEX_TO_HEX_2D,
53: REFINER_HYBRID_SIMPLEX_TO_HEX_2D,
54: REFINER_HEX_2D,
55: REFINER_HYBRID_HEX_2D,
56: REFINER_SIMPLEX_3D,
57: REFINER_HYBRID_SIMPLEX_3D,
58: REFINER_SIMPLEX_TO_HEX_3D,
59: REFINER_HYBRID_SIMPLEX_TO_HEX_3D,
60: REFINER_HEX_3D,
61: REFINER_HYBRID_HEX_3D} CellRefiner;
63: typedef struct _PetscPartitionerOps *PetscPartitionerOps;
64: struct _PetscPartitionerOps {
65: PetscErrorCode (*setfromoptions)(PetscOptionItems*,PetscPartitioner);
66: PetscErrorCode (*setup)(PetscPartitioner);
67: PetscErrorCode (*view)(PetscPartitioner,PetscViewer);
68: PetscErrorCode (*destroy)(PetscPartitioner);
69: PetscErrorCode (*partition)(PetscPartitioner, PetscInt, PetscInt, PetscInt[], PetscInt[], PetscSection, PetscSection, PetscSection, IS *);
70: };
72: struct _p_PetscPartitioner {
73: PETSCHEADER(struct _PetscPartitionerOps);
74: void *data; /* Implementation object */
75: PetscInt height; /* Height of points to partition into non-overlapping subsets */
76: PetscInt edgeCut; /* The number of edge cut by the partition */
77: PetscReal balance; /* The maximum partition size divided by the minimum size */
78: PetscViewer viewer;
79: PetscViewer viewerGraph;
80: PetscBool viewGraph;
81: PetscBool noGraph; /* if true, the partitioner does not need the connectivity graph, only the number of local vertices */
82: PetscBool usevwgt; /* if true, the partitioner looks at the local section vertSection to weight the vertices of the graph */
83: };
85: typedef struct {
86: PetscInt dummy;
87: } PetscPartitioner_Chaco;
89: typedef struct {
90: MPI_Comm pcomm;
91: PetscInt ptype;
92: PetscReal imbalanceRatio;
93: PetscInt debugFlag;
94: PetscInt randomSeed;
95: } PetscPartitioner_ParMetis;
97: typedef struct {
98: MPI_Comm pcomm;
99: PetscInt strategy;
100: PetscReal imbalance;
101: } PetscPartitioner_PTScotch;
103: static const char *const
104: PTScotchStrategyList[] = {
105: "DEFAULT",
106: "QUALITY",
107: "SPEED",
108: "BALANCE",
109: "SAFETY",
110: "SCALABILITY",
111: "RECURSIVE",
112: "REMAP"
113: };
115: typedef struct {
116: PetscSection section; /* Sizes for each partition */
117: IS partition; /* Points in each partition */
118: PetscBool random; /* Flag for a random partition */
119: } PetscPartitioner_Shell;
121: typedef struct {
122: PetscInt dummy;
123: } PetscPartitioner_Simple;
125: typedef struct {
126: PetscInt dummy;
127: } PetscPartitioner_Gather;
129: /* Utility struct to store the contents of a Fluent file in memory */
130: typedef struct {
131: int index; /* Type of section */
132: unsigned int zoneID;
133: unsigned int first;
134: unsigned int last;
135: int type;
136: int nd; /* Either ND or element-type */
137: void *data;
138: } FluentSection;
140: struct _PetscGridHash {
141: PetscInt dim;
142: PetscReal lower[3]; /* The lower-left corner */
143: PetscReal upper[3]; /* The upper-right corner */
144: PetscReal extent[3]; /* The box size */
145: PetscReal h[3]; /* The subbox size */
146: PetscInt n[3]; /* The number of subboxes */
147: PetscSection cellSection; /* Offsets for cells in each subbox*/
148: IS cells; /* List of cells in each subbox */
149: DMLabel cellsSparse; /* Sparse storage for cell map */
150: };
152: /* Point Numbering in Plex:
154: Points are numbered contiguously by stratum. Strate are organized as follows:
156: First Stratum: Cells [height 0]
157: Second Stratum: Vertices [depth 0]
158: Third Stratum: Faces [height 1]
159: Fourth Stratum: Edges [depth 1]
161: We do this so that the numbering of a cell-vertex mesh does not change after interpolation. Within a given stratum,
162: we allow additional segregation of points. When hybrid, or prismatic, points are present, the first hybrid point in
163: a stratum is indicated by hybridPointMax[depth]. In addition, we allow ghost cells to be defined for use in finite
164: volume methods, and these do not have full cones. These cells occur after any hybrid cells, and this division is
165: indicated by ghostCellStart.
166: */
167: typedef struct {
168: PetscInt refct;
170: PetscSection coneSection; /* Layout of cones (inedges for DAG) */
171: PetscInt maxConeSize; /* Cached for fast lookup */
172: PetscInt *cones; /* Cone for each point */
173: PetscInt *coneOrientations; /* Orientation of each cone point, means cone traveral should start on point 'o', and if negative start on -(o+1) and go in reverse */
174: PetscSection supportSection; /* Layout of cones (inedges for DAG) */
175: PetscInt maxSupportSize; /* Cached for fast lookup */
176: PetscInt *supports; /* Cone for each point */
177: PetscBool refinementUniform; /* Flag for uniform cell refinement */
178: PetscReal refinementLimit; /* Maximum volume for refined cell */
179: PetscErrorCode (*refinementFunc)(const PetscReal [], PetscReal *); /* Function giving the maximum volume for refined cell */
180: PetscInt hybridPointMax[8]; /* Allow segregation of some points, each dimension has a divider (used in VTK output and refinement) */
181: PetscInt overlap; /* Overlap of the partitions as passed to DMPlexDistribute() or DMPlexDistributeOverlap() */
182: PetscInt ghostCellStart; /* The first ghost cell (for FV BC) or -1 */
183: DMPlexInterpolatedFlag interpolated;
184: DMPlexInterpolatedFlag interpolatedCollective;
186: PetscInt *facesTmp; /* Work space for faces operation */
188: /* Hierarchy */
189: PetscBool regularRefinement; /* This flag signals that we are a regular refinement of coarseMesh */
191: /* Generation */
192: char *tetgenOpts;
193: char *triangleOpts;
194: PetscPartitioner partitioner;
195: PetscBool partitionBalance; /* Evenly divide partition overlap when distributing */
196: PetscBool remeshBd;
198: /* Submesh */
199: DMLabel subpointMap; /* Label each original mesh point in the submesh with its depth, subpoint are the implicit numbering */
201: /* Labels and numbering */
202: PetscObjectState depthState; /* State of depth label, so that we can determine if a user changes it */
203: PetscObjectState celltypeState; /* State of celltype label, so that we can determine if a user changes it */
204: IS globalVertexNumbers;
205: IS globalCellNumbers;
207: /* Constraints */
208: PetscSection anchorSection; /* maps constrained points to anchor points */
209: IS anchorIS; /* anchors indexed by the above section */
210: PetscErrorCode (*createanchors)(DM); /* automatically compute anchors (probably from tree constraints) */
211: PetscErrorCode (*computeanchormatrix)(DM,PetscSection,PetscSection,Mat);
213: /* Tree: automatically construct constraints for hierarchically non-conforming meshes */
214: PetscSection parentSection; /* dof == 1 if point has parent */
215: PetscInt *parents; /* point to parent */
216: PetscInt *childIDs; /* point to child ID */
217: PetscSection childSection; /* inverse of parent section */
218: PetscInt *children; /* point to children */
219: DM referenceTree; /* reference tree to which child ID's refer */
220: PetscErrorCode (*getchildsymmetry)(DM,PetscInt,PetscInt,PetscInt,PetscInt,PetscInt,PetscInt*,PetscInt*);
222: /* MATIS support */
223: PetscSection subdomainSection;
225: /* Adjacency */
226: PetscBool useAnchors; /* Replace constrained points with their anchors in adjacency lists */
227: PetscErrorCode (*useradjacency)(DM,PetscInt,PetscInt*,PetscInt[],void*); /* User callback for adjacency */
228: void *useradjacencyctx; /* User context for callback */
230: /* Projection */
231: PetscInt maxProjectionHeight; /* maximum height of cells used in DMPlexProject functions */
233: /* Output */
234: PetscInt vtkCellHeight; /* The height of cells for output, default is 0 */
235: PetscReal scale[NUM_PETSC_UNITS]; /* The scale for each SI unit */
237: /* Geometry */
238: PetscReal minradius; /* Minimum distance from cell centroid to face */
239: PetscBool useHashLocation; /* Use grid hashing for point location */
240: PetscGridHash lbox; /* Local box for searching */
242: /* Debugging */
243: PetscBool printSetValues;
244: PetscInt printFEM;
245: PetscInt printL2;
246: PetscReal printTol;
247: } DM_Plex;
249: PETSC_EXTERN PetscErrorCode DMPlexVTKWriteAll_VTU(DM,PetscViewer);
250: PETSC_EXTERN PetscErrorCode VecView_Plex_Local(Vec,PetscViewer);
251: PETSC_EXTERN PetscErrorCode VecView_Plex_Native(Vec,PetscViewer);
252: PETSC_EXTERN PetscErrorCode VecView_Plex(Vec,PetscViewer);
253: PETSC_EXTERN PetscErrorCode VecLoad_Plex_Local(Vec,PetscViewer);
254: PETSC_EXTERN PetscErrorCode VecLoad_Plex_Native(Vec,PetscViewer);
255: PETSC_EXTERN PetscErrorCode VecLoad_Plex(Vec,PetscViewer);
256: PETSC_INTERN PetscErrorCode DMPlexGetFieldType_Internal(DM, PetscSection, PetscInt, PetscInt *, PetscInt *, PetscViewerVTKFieldType *);
257: PETSC_INTERN PetscErrorCode DMPlexView_GLVis(DM,PetscViewer);
258: PETSC_INTERN PetscErrorCode DMSetUpGLVisViewer_Plex(PetscObject,PetscViewer);
259: #if defined(PETSC_HAVE_HDF5)
260: PETSC_EXTERN PetscErrorCode VecView_Plex_Local_HDF5(Vec, PetscViewer);
261: PETSC_EXTERN PetscErrorCode VecView_Plex_HDF5(Vec, PetscViewer);
262: PETSC_EXTERN PetscErrorCode VecLoad_Plex_HDF5(Vec, PetscViewer);
263: PETSC_EXTERN PetscErrorCode VecView_Plex_HDF5_Native(Vec, PetscViewer);
264: PETSC_EXTERN PetscErrorCode VecLoad_Plex_HDF5_Native(Vec, PetscViewer);
265: PETSC_EXTERN PetscErrorCode DMPlexView_HDF5(DM, PetscViewer);
266: PETSC_EXTERN PetscErrorCode DMPlexLoad_HDF5(DM, PetscViewer);
267: #endif
269: PETSC_INTERN PetscErrorCode DMPlexClosurePoints_Private(DM,PetscInt,const PetscInt[],IS*);
270: PETSC_INTERN PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *, DM);
271: PETSC_INTERN PetscErrorCode DMCoarsen_Plex(DM, MPI_Comm, DM *);
272: PETSC_INTERN PetscErrorCode DMCoarsenHierarchy_Plex(DM, PetscInt, DM []);
273: PETSC_INTERN PetscErrorCode DMRefine_Plex(DM, MPI_Comm, DM *);
274: PETSC_INTERN PetscErrorCode DMRefineHierarchy_Plex(DM, PetscInt, DM []);
275: PETSC_INTERN PetscErrorCode DMAdaptLabel_Plex(DM, DMLabel, DM *);
276: PETSC_INTERN PetscErrorCode DMAdaptMetric_Plex(DM, Vec, DMLabel, DM *);
277: PETSC_INTERN PetscErrorCode DMPlexInsertBoundaryValues_Plex(DM, PetscBool, Vec, PetscReal, Vec, Vec, Vec);
278: PETSC_INTERN PetscErrorCode DMProjectFunctionLocal_Plex(DM,PetscReal,PetscErrorCode(**)(PetscInt,PetscReal,const PetscReal[],PetscInt,PetscScalar *,void *),void **,InsertMode,Vec);
279: PETSC_INTERN PetscErrorCode DMProjectFunctionLabelLocal_Plex(DM,PetscReal,DMLabel,PetscInt,const PetscInt[],PetscInt,const PetscInt[],PetscErrorCode(**)(PetscInt,PetscReal,const PetscReal[],PetscInt,PetscScalar *,void *),void **,InsertMode,Vec);
280: PETSC_INTERN PetscErrorCode DMProjectFieldLocal_Plex(DM,PetscReal,Vec,void (**)(PetscInt,PetscInt,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[],const PetscScalar[],const PetscScalar[],const PetscInt[],const PetscInt[],const PetscScalar[],const PetscScalar[],const PetscScalar[],PetscReal,const PetscReal[],PetscInt,const PetscScalar[],PetscScalar[]),InsertMode,Vec);
281: PETSC_INTERN PetscErrorCode DMProjectFieldLabelLocal_Plex(DM,PetscReal,DMLabel,PetscInt,const PetscInt[],PetscInt,const PetscInt[],Vec,void (**)(PetscInt,PetscInt,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[],const PetscScalar[],const PetscScalar[],const PetscInt[],const PetscInt[],const PetscScalar[],const PetscScalar[],const PetscScalar[],PetscReal,const PetscReal[],PetscInt,const PetscScalar[],PetscScalar[]),InsertMode,Vec);
282: PETSC_INTERN PetscErrorCode DMComputeL2Diff_Plex(DM,PetscReal,PetscErrorCode(**)(PetscInt,PetscReal,const PetscReal[],PetscInt,PetscScalar *,void *),void **,Vec,PetscReal *);
283: PETSC_INTERN PetscErrorCode DMComputeL2GradientDiff_Plex(DM,PetscReal,PetscErrorCode(**)(PetscInt,PetscReal,const PetscReal[], const PetscReal[],PetscInt,PetscScalar *,void *),void **,Vec,const PetscReal [],PetscReal *);
284: PETSC_INTERN PetscErrorCode DMComputeL2FieldDiff_Plex(DM,PetscReal,PetscErrorCode(**)(PetscInt,PetscReal,const PetscReal[],PetscInt,PetscScalar *,void *),void **,Vec,PetscReal *);
285: PETSC_INTERN PetscErrorCode DMLocatePoints_Plex(DM, Vec, DMPointLocationType, PetscSF);
287: PETSC_INTERN PetscErrorCode DMPlexBuildFromCellList_Internal(DM, PetscInt, PetscInt, PetscInt, PetscInt, const int[], PetscBool);
288: PETSC_INTERN PetscErrorCode DMPlexBuildFromCellList_Parallel_Internal(DM, PetscInt, PetscInt, PetscInt, PetscInt, const int[], PetscBool, PetscSF *);
289: PETSC_INTERN PetscErrorCode DMPlexBuildCoordinates_Internal(DM, PetscInt, PetscInt, PetscInt, const double[]);
290: PETSC_INTERN PetscErrorCode DMPlexBuildCoordinates_Parallel_Internal(DM, PetscInt, PetscInt, PetscInt, PetscSF, const PetscReal[]);
291: PETSC_INTERN PetscErrorCode DMPlexLoadLabels_HDF5_Internal(DM, PetscViewer);
292: PETSC_INTERN PetscErrorCode DMPlexView_HDF5_Internal(DM, PetscViewer);
293: PETSC_INTERN PetscErrorCode DMPlexLoad_HDF5_Internal(DM, PetscViewer);
294: PETSC_INTERN PetscErrorCode DMPlexLoad_HDF5_Xdmf_Internal(DM, PetscViewer);
295: PETSC_INTERN PetscErrorCode VecView_Plex_HDF5_Internal(Vec, PetscViewer);
296: PETSC_INTERN PetscErrorCode VecView_Plex_HDF5_Native_Internal(Vec, PetscViewer);
297: PETSC_INTERN PetscErrorCode VecView_Plex_Local_HDF5_Internal(Vec, PetscViewer);
298: PETSC_INTERN PetscErrorCode VecLoad_Plex_HDF5_Internal(Vec, PetscViewer);
299: PETSC_INTERN PetscErrorCode VecLoad_Plex_HDF5_Native_Internal(Vec, PetscViewer);
300: /* TODO Make these INTERN */
301: PETSC_EXTERN PetscErrorCode DMPlexView_ExodusII_Internal(DM, int, PetscInt);
302: PETSC_EXTERN PetscErrorCode VecViewPlex_ExodusII_Nodal_Internal(Vec, int, int);
303: PETSC_EXTERN PetscErrorCode VecLoadPlex_ExodusII_Nodal_Internal(Vec, int, int);
304: PETSC_EXTERN PetscErrorCode VecViewPlex_ExodusII_Zonal_Internal(Vec, int, int);
305: PETSC_EXTERN PetscErrorCode VecLoadPlex_ExodusII_Zonal_Internal(Vec, int, int);
306: PETSC_INTERN PetscErrorCode DMPlexVTKGetCellType_Internal(DM,PetscInt,PetscInt,PetscInt*);
307: PETSC_INTERN PetscErrorCode DMPlexGetAdjacency_Internal(DM,PetscInt,PetscBool,PetscBool,PetscBool,PetscInt*,PetscInt*[]);
308: PETSC_INTERN PetscErrorCode DMPlexGetFaces_Internal(DM,PetscInt,PetscInt*,PetscInt*,const PetscInt*[]);
309: PETSC_INTERN PetscErrorCode DMPlexGetRawFaces_Internal(DM,DMPolytopeType,const PetscInt[], PetscInt*,PetscInt*,const PetscInt*[]);
310: PETSC_INTERN PetscErrorCode DMPlexRestoreFaces_Internal(DM,PetscInt,PetscInt*,PetscInt*,const PetscInt*[]);
311: PETSC_INTERN PetscErrorCode DMPlexRefineUniform_Internal(DM,CellRefiner,DM*);
312: PETSC_INTERN PetscErrorCode DMPlexGetCellRefiner_Internal(DM,CellRefiner*);
313: PETSC_INTERN PetscErrorCode CellRefinerGetAffineTransforms_Internal(CellRefiner, PetscInt *, PetscReal *[], PetscReal *[], PetscReal *[]);
314: PETSC_INTERN PetscErrorCode CellRefinerGetAffineFaceTransforms_Internal(CellRefiner, PetscInt *, PetscReal *[], PetscReal *[], PetscReal *[], PetscReal *[]);
315: PETSC_INTERN PetscErrorCode CellRefinerRestoreAffineTransforms_Internal(CellRefiner, PetscInt *, PetscReal *[], PetscReal *[], PetscReal *[]);
316: PETSC_INTERN PetscErrorCode CellRefinerInCellTest_Internal(CellRefiner, const PetscReal[], PetscBool *);
317: PETSC_INTERN PetscErrorCode DMPlexInvertCell_Internal(PetscInt, PetscInt, PetscInt[]);
318: PETSC_INTERN PetscErrorCode DMPlexVecSetFieldClosure_Internal(DM, PetscSection, Vec, PetscBool[], PetscInt, PetscInt, const PetscInt[], const PetscScalar[], InsertMode);
319: PETSC_INTERN PetscErrorCode DMPlexProjectConstraints_Internal(DM, Vec, Vec);
320: PETSC_EXTERN PetscErrorCode DMPlexCreateReferenceTree_SetTree(DM, PetscSection, PetscInt[], PetscInt[]);
321: PETSC_EXTERN PetscErrorCode DMPlexCreateReferenceTree_Union(DM,DM,const char *,DM*);
322: PETSC_EXTERN PetscErrorCode DMPlexComputeInterpolatorTree(DM,DM,PetscSF,PetscInt *,Mat);
323: PETSC_EXTERN PetscErrorCode DMPlexComputeInjectorTree(DM,DM,PetscSF,PetscInt *,Mat);
324: PETSC_EXTERN PetscErrorCode DMPlexAnchorsModifyMat(DM,PetscSection,PetscInt,PetscInt,const PetscInt[],const PetscInt ***,const PetscScalar[],PetscInt*,PetscInt*,PetscInt*[],PetscScalar*[],PetscInt[],PetscBool);
325: PETSC_EXTERN PetscErrorCode indicesPoint_private(PetscSection,PetscInt,PetscInt,PetscInt *,PetscBool,PetscInt,PetscInt []);
326: PETSC_EXTERN PetscErrorCode indicesPointFields_private(PetscSection,PetscInt,PetscInt,PetscInt [],PetscBool,PetscInt,PetscInt []);
327: PETSC_INTERN PetscErrorCode DMPlexLocatePoint_Internal(DM,PetscInt,const PetscScalar [],PetscInt,PetscInt *);
328: /* these two are PETSC_EXTERN just because of src/dm/impls/plex/examples/tests/ex18.c */
329: PETSC_EXTERN PetscErrorCode DMPlexOrientCell_Internal(DM,PetscInt,PetscInt,PetscBool);
330: PETSC_EXTERN PetscErrorCode DMPlexOrientInterface_Internal(DM);
332: /* Applications may use this function */
333: PETSC_EXTERN PetscErrorCode DMPlexCreateNumbering_Plex(DM, PetscInt, PetscInt, PetscInt, PetscInt *, PetscSF, IS *);
335: PETSC_INTERN PetscErrorCode DMPlexCreateCellNumbering_Internal(DM, PetscBool, IS *);
336: PETSC_INTERN PetscErrorCode DMPlexCreateVertexNumbering_Internal(DM, PetscBool, IS *);
337: PETSC_INTERN PetscErrorCode DMPlexRefine_Internal(DM, DMLabel, DM *);
338: PETSC_INTERN PetscErrorCode DMPlexCoarsen_Internal(DM, DMLabel, DM *);
339: PETSC_INTERN PetscErrorCode DMCreateMatrix_Plex(DM, Mat*);
341: PETSC_INTERN PetscErrorCode DMPlexGetOverlap_Plex(DM, PetscInt *);
343: /* invert dihedral symmetry: return a^-1,
344: * using the representation described in
345: * DMPlexGetConeOrientation() */
346: PETSC_STATIC_INLINE PetscInt DihedralInvert(PetscInt N, PetscInt a)
347: {
348: return (a <= 0) ? a : (N - a);
349: }
351: /* invert dihedral symmetry: return b * a,
352: * using the representation described in
353: * DMPlexGetConeOrientation() */
354: PETSC_STATIC_INLINE PetscInt DihedralCompose(PetscInt N, PetscInt a, PetscInt b)
355: {
356: if (!N) return 0;
357: return (a >= 0) ?
358: ((b >= 0) ? ((a + b) % N) : -(((a - b - 1) % N) + 1)) :
359: ((b >= 0) ? -(((N - b - a - 1) % N) + 1) : ((N + b - a) % N));
360: }
362: /* swap dihedral symmetries: return b * a^-1,
363: * using the representation described in
364: * DMPlexGetConeOrientation() */
365: PETSC_STATIC_INLINE PetscInt DihedralSwap(PetscInt N, PetscInt a, PetscInt b)
366: {
367: return DihedralCompose(N,DihedralInvert(N,a),b);
368: }
370: PETSC_EXTERN PetscErrorCode DMPlexComputeResidual_Internal(DM, IS , PetscReal, Vec, Vec, PetscReal, Vec, void *);
371: PETSC_EXTERN PetscErrorCode DMPlexComputeJacobian_Internal(DM, IS, PetscReal, PetscReal, Vec, Vec, Mat, Mat, void *);
372: PETSC_EXTERN PetscErrorCode DMPlexReconstructGradients_Internal(DM, PetscFV, PetscInt, PetscInt, Vec, Vec, Vec, Vec);
374: /* Matvec with A in row-major storage, x and y can be aliased */
375: PETSC_STATIC_INLINE void DMPlex_Mult2D_Internal(const PetscScalar A[], PetscInt ldx, const PetscScalar x[], PetscScalar y[])
376: {
377: PetscScalar z[2];
378: z[0] = x[0]; z[1] = x[ldx];
379: y[0] = A[0]*z[0] + A[1]*z[1];
380: y[ldx] = A[2]*z[0] + A[3]*z[1];
381: (void)PetscLogFlops(6.0);
382: }
383: PETSC_STATIC_INLINE void DMPlex_Mult3D_Internal(const PetscScalar A[], PetscInt ldx, const PetscScalar x[], PetscScalar y[])
384: {
385: PetscScalar z[3];
386: z[0] = x[0]; z[1] = x[ldx]; z[2] = x[ldx*2];
387: y[0] = A[0]*z[0] + A[1]*z[1] + A[2]*z[2];
388: y[ldx] = A[3]*z[0] + A[4]*z[1] + A[5]*z[2];
389: y[ldx*2] = A[6]*z[0] + A[7]*z[1] + A[8]*z[2];
390: (void)PetscLogFlops(15.0);
391: }
392: PETSC_STATIC_INLINE void DMPlex_MultTranspose2D_Internal(const PetscScalar A[], PetscInt ldx, const PetscScalar x[], PetscScalar y[])
393: {
394: PetscScalar z[2];
395: z[0] = x[0]; z[1] = x[ldx];
396: y[0] = A[0]*z[0] + A[2]*z[1];
397: y[ldx] = A[1]*z[0] + A[3]*z[1];
398: (void)PetscLogFlops(6.0);
399: }
400: PETSC_STATIC_INLINE void DMPlex_MultTranspose3D_Internal(const PetscScalar A[], PetscInt ldx, const PetscScalar x[], PetscScalar y[])
401: {
402: PetscScalar z[3];
403: z[0] = x[0]; z[1] = x[ldx]; z[2] = x[ldx*2];
404: y[0] = A[0]*z[0] + A[3]*z[1] + A[6]*z[2];
405: y[ldx] = A[1]*z[0] + A[4]*z[1] + A[7]*z[2];
406: y[ldx*2] = A[2]*z[0] + A[5]*z[1] + A[8]*z[2];
407: (void)PetscLogFlops(15.0);
408: }
409: PETSC_STATIC_INLINE void DMPlex_Mult2DReal_Internal(const PetscReal A[], PetscInt ldx, const PetscScalar x[], PetscScalar y[])
410: {
411: PetscScalar z[2];
412: z[0] = x[0]; z[1] = x[ldx];
413: y[0] = A[0]*z[0] + A[1]*z[1];
414: y[ldx] = A[2]*z[0] + A[3]*z[1];
415: (void)PetscLogFlops(6.0);
416: }
417: PETSC_STATIC_INLINE void DMPlex_Mult3DReal_Internal(const PetscReal A[], PetscInt ldx, const PetscScalar x[], PetscScalar y[])
418: {
419: PetscScalar z[3];
420: z[0] = x[0]; z[1] = x[ldx]; z[2] = x[ldx*2];
421: y[0] = A[0]*z[0] + A[1]*z[1] + A[2]*z[2];
422: y[ldx] = A[3]*z[0] + A[4]*z[1] + A[5]*z[2];
423: y[ldx*2] = A[6]*z[0] + A[7]*z[1] + A[8]*z[2];
424: (void)PetscLogFlops(15.0);
425: }
426: PETSC_STATIC_INLINE void DMPlex_MultTranspose2DReal_Internal(const PetscReal A[], PetscInt ldx, const PetscScalar x[], PetscScalar y[])
427: {
428: PetscScalar z[2];
429: z[0] = x[0]; z[1] = x[ldx];
430: y[0] = A[0]*z[0] + A[2]*z[1];
431: y[ldx] = A[1]*z[0] + A[3]*z[1];
432: (void)PetscLogFlops(6.0);
433: }
434: PETSC_STATIC_INLINE void DMPlex_MultTranspose3DReal_Internal(const PetscReal A[], PetscInt ldx, const PetscScalar x[], PetscScalar y[])
435: {
436: PetscScalar z[3];
437: z[0] = x[0]; z[1] = x[ldx]; z[2] = x[ldx*2];
438: y[0] = A[0]*z[0] + A[3]*z[1] + A[6]*z[2];
439: y[ldx] = A[1]*z[0] + A[4]*z[1] + A[7]*z[2];
440: y[ldx*2] = A[2]*z[0] + A[5]*z[1] + A[8]*z[2];
441: (void)PetscLogFlops(15.0);
442: }
444: PETSC_STATIC_INLINE void DMPlex_MatMult2D_Internal(const PetscScalar A[], PetscInt n, PetscInt ldb, const PetscScalar B[], PetscScalar C[])
445: {
446: PetscInt j;
447: for (j = 0; j < n; ++j) {
448: PetscScalar z[2];
449: z[0] = B[0+j]; z[1] = B[1*ldb+j];
450: DMPlex_Mult2D_Internal(A, 1, z, z);
451: C[0+j] = z[0]; C[1*ldb+j] = z[1];
452: }
453: (void)PetscLogFlops(8.0*n);
454: }
455: PETSC_STATIC_INLINE void DMPlex_MatMult3D_Internal(const PetscScalar A[], PetscInt n, PetscInt ldb, const PetscScalar B[], PetscScalar C[])
456: {
457: PetscInt j;
458: for (j = 0; j < n; ++j) {
459: PetscScalar z[3];
460: z[0] = B[0+j]; z[1] = B[1*ldb+j]; z[2] = B[2*ldb+j];
461: DMPlex_Mult3D_Internal(A, 1, z, z);
462: C[0+j] = z[0]; C[1*ldb+j] = z[1]; C[2*ldb+j] = z[2];
463: }
464: (void)PetscLogFlops(8.0*n);
465: }
466: PETSC_STATIC_INLINE void DMPlex_MatMultTranspose2D_Internal(const PetscScalar A[], PetscInt n, PetscInt ldb, const PetscScalar B[], PetscScalar C[])
467: {
468: PetscInt j;
469: for (j = 0; j < n; ++j) {
470: PetscScalar z[2];
471: z[0] = B[0+j]; z[1] = B[1*ldb+j];
472: DMPlex_MultTranspose2D_Internal(A, 1, z, z);
473: C[0+j] = z[0]; C[1*ldb+j] = z[1];
474: }
475: (void)PetscLogFlops(8.0*n);
476: }
477: PETSC_STATIC_INLINE void DMPlex_MatMultTranspose3D_Internal(const PetscScalar A[], PetscInt n, PetscInt ldb, const PetscScalar B[], PetscScalar C[])
478: {
479: PetscInt j;
480: for (j = 0; j < n; ++j) {
481: PetscScalar z[3];
482: z[0] = B[0+j]; z[1] = B[1*ldb+j]; z[2] = B[2*ldb+j];
483: DMPlex_MultTranspose3D_Internal(A, 1, z, z);
484: C[0+j] = z[0]; C[1*ldb+j] = z[1]; C[2*ldb+j] = z[2];
485: }
486: (void)PetscLogFlops(8.0*n);
487: }
489: PETSC_STATIC_INLINE void DMPlex_MatMultLeft2D_Internal(const PetscScalar A[], PetscInt m, PetscInt ldb, const PetscScalar B[], PetscScalar C[])
490: {
491: PetscInt j;
492: for (j = 0; j < m; ++j) {
493: DMPlex_MultTranspose2D_Internal(A, 1, &B[j*ldb], &C[j*ldb]);
494: }
495: (void)PetscLogFlops(8.0*m);
496: }
497: PETSC_STATIC_INLINE void DMPlex_MatMultLeft3D_Internal(const PetscScalar A[], PetscInt m, PetscInt ldb, const PetscScalar B[], PetscScalar C[])
498: {
499: PetscInt j;
500: for (j = 0; j < m; ++j) {
501: DMPlex_MultTranspose3D_Internal(A, 1, &B[j*ldb], &C[j*ldb]);
502: }
503: (void)PetscLogFlops(8.0*m);
504: }
505: PETSC_STATIC_INLINE void DMPlex_MatMultTransposeLeft2D_Internal(const PetscScalar A[], PetscInt m, PetscInt ldb, const PetscScalar B[], PetscScalar C[])
506: {
507: PetscInt j;
508: for (j = 0; j < m; ++j) {
509: DMPlex_Mult2D_Internal(A, 1, &B[j*ldb], &C[j*ldb]);
510: }
511: (void)PetscLogFlops(8.0*m);
512: }
513: PETSC_STATIC_INLINE void DMPlex_MatMultTransposeLeft3D_Internal(const PetscScalar A[], PetscInt m, PetscInt ldb, const PetscScalar B[], PetscScalar C[])
514: {
515: PetscInt j;
516: for (j = 0; j < m; ++j) {
517: DMPlex_Mult3D_Internal(A, 1, &B[j*ldb], &C[j*ldb]);
518: }
519: (void)PetscLogFlops(8.0*m);
520: }
522: PETSC_STATIC_INLINE void DMPlex_Transpose2D_Internal(PetscScalar A[])
523: {
524: PetscScalar tmp;
525: tmp = A[1]; A[1] = A[2]; A[2] = tmp;
526: }
527: PETSC_STATIC_INLINE void DMPlex_Transpose3D_Internal(PetscScalar A[])
528: {
529: PetscScalar tmp;
530: tmp = A[1]; A[1] = A[3]; A[3] = tmp;
531: tmp = A[2]; A[2] = A[6]; A[6] = tmp;
532: tmp = A[5]; A[5] = A[7]; A[7] = tmp;
533: }
535: PETSC_STATIC_INLINE void DMPlex_Invert2D_Internal(PetscReal invJ[], PetscReal J[], PetscReal detJ)
536: {
537: const PetscReal invDet = 1.0/detJ;
539: invJ[0] = invDet*J[3];
540: invJ[1] = -invDet*J[1];
541: invJ[2] = -invDet*J[2];
542: invJ[3] = invDet*J[0];
543: (void)PetscLogFlops(5.0);
544: }
546: PETSC_STATIC_INLINE void DMPlex_Invert3D_Internal(PetscReal invJ[], PetscReal J[], PetscReal detJ)
547: {
548: const PetscReal invDet = 1.0/detJ;
550: invJ[0*3+0] = invDet*(J[1*3+1]*J[2*3+2] - J[1*3+2]*J[2*3+1]);
551: invJ[0*3+1] = invDet*(J[0*3+2]*J[2*3+1] - J[0*3+1]*J[2*3+2]);
552: invJ[0*3+2] = invDet*(J[0*3+1]*J[1*3+2] - J[0*3+2]*J[1*3+1]);
553: invJ[1*3+0] = invDet*(J[1*3+2]*J[2*3+0] - J[1*3+0]*J[2*3+2]);
554: invJ[1*3+1] = invDet*(J[0*3+0]*J[2*3+2] - J[0*3+2]*J[2*3+0]);
555: invJ[1*3+2] = invDet*(J[0*3+2]*J[1*3+0] - J[0*3+0]*J[1*3+2]);
556: invJ[2*3+0] = invDet*(J[1*3+0]*J[2*3+1] - J[1*3+1]*J[2*3+0]);
557: invJ[2*3+1] = invDet*(J[0*3+1]*J[2*3+0] - J[0*3+0]*J[2*3+1]);
558: invJ[2*3+2] = invDet*(J[0*3+0]*J[1*3+1] - J[0*3+1]*J[1*3+0]);
559: (void)PetscLogFlops(37.0);
560: }
562: PETSC_STATIC_INLINE void DMPlex_Det2D_Internal(PetscReal *detJ, const PetscReal J[])
563: {
564: *detJ = J[0]*J[3] - J[1]*J[2];
565: (void)PetscLogFlops(3.0);
566: }
568: PETSC_STATIC_INLINE void DMPlex_Det3D_Internal(PetscReal *detJ, const PetscReal J[])
569: {
570: *detJ = (J[0*3+0]*(J[1*3+1]*J[2*3+2] - J[1*3+2]*J[2*3+1]) +
571: J[0*3+1]*(J[1*3+2]*J[2*3+0] - J[1*3+0]*J[2*3+2]) +
572: J[0*3+2]*(J[1*3+0]*J[2*3+1] - J[1*3+1]*J[2*3+0]));
573: (void)PetscLogFlops(12.0);
574: }
576: PETSC_STATIC_INLINE void DMPlex_Det2D_Scalar_Internal(PetscReal *detJ, const PetscScalar J[])
577: {
578: *detJ = PetscRealPart(J[0])*PetscRealPart(J[3]) - PetscRealPart(J[1])*PetscRealPart(J[2]);
579: (void)PetscLogFlops(3.0);
580: }
582: PETSC_STATIC_INLINE void DMPlex_Det3D_Scalar_Internal(PetscReal *detJ, const PetscScalar J[])
583: {
584: *detJ = (PetscRealPart(J[0*3+0])*(PetscRealPart(J[1*3+1])*PetscRealPart(J[2*3+2]) - PetscRealPart(J[1*3+2])*PetscRealPart(J[2*3+1])) +
585: PetscRealPart(J[0*3+1])*(PetscRealPart(J[1*3+2])*PetscRealPart(J[2*3+0]) - PetscRealPart(J[1*3+0])*PetscRealPart(J[2*3+2])) +
586: PetscRealPart(J[0*3+2])*(PetscRealPart(J[1*3+0])*PetscRealPart(J[2*3+1]) - PetscRealPart(J[1*3+1])*PetscRealPart(J[2*3+0])));
587: (void)PetscLogFlops(12.0);
588: }
590: PETSC_STATIC_INLINE void DMPlex_WaxpyD_Internal(PetscInt dim, PetscReal a, const PetscReal *x, const PetscReal *y, PetscReal *w) {PetscInt d; for (d = 0; d < dim; ++d) w[d] = a*x[d] + y[d];}
592: PETSC_STATIC_INLINE PetscReal DMPlex_DotD_Internal(PetscInt dim, const PetscScalar *x, const PetscReal *y) {PetscReal sum = 0.0; PetscInt d; for (d = 0; d < dim; ++d) sum += PetscRealPart(x[d])*y[d]; return sum;}
594: PETSC_STATIC_INLINE PetscReal DMPlex_DotRealD_Internal(PetscInt dim, const PetscReal *x, const PetscReal *y) {PetscReal sum = 0.0; PetscInt d; for (d = 0; d < dim; ++d) sum += x[d]*y[d]; return sum;}
596: PETSC_STATIC_INLINE PetscReal DMPlex_NormD_Internal(PetscInt dim, const PetscReal *x) {PetscReal sum = 0.0; PetscInt d; for (d = 0; d < dim; ++d) sum += x[d]*x[d]; return PetscSqrtReal(sum);}
598: PETSC_STATIC_INLINE PetscErrorCode DMPlexFixFaceOrientations_Translate_Private(PetscInt ornt, PetscInt *start, PetscBool *reverse)
599: {
601: *reverse = (ornt < 0) ? PETSC_TRUE : PETSC_FALSE;
602: *start = *reverse ? -(ornt+1) : ornt;
603: return(0);
604: }
606: PETSC_STATIC_INLINE PetscErrorCode DMPlexFixFaceOrientations_Combine_Private(PetscInt coneSize, PetscInt origStart, PetscBool origReverse, PetscInt rotateStart, PetscBool rotateReverse, PetscInt *newStart, PetscBool *newReverse)
607: {
609: *newReverse = (origReverse == rotateReverse) ? PETSC_FALSE : PETSC_TRUE;
610: *newStart = rotateReverse ? (coneSize + rotateStart - origStart) : (coneSize + origStart - rotateStart);
611: *newStart %= coneSize;
612: return(0);
613: }
615: PETSC_STATIC_INLINE PetscErrorCode DMPlexFixFaceOrientations_TranslateBack_Private(PetscInt coneSize, PetscInt start, PetscBool reverse, PetscInt *ornt)
616: {
618: if (coneSize < 3) {
619: /* edges just get flipped if start == 1 regardless direction */
620: *ornt = start ? -2 : 0;
621: } else {
622: *ornt = reverse ? -(start+1) : start;
623: }
624: return(0);
625: }
627: PETSC_STATIC_INLINE PetscErrorCode DMPlexFixFaceOrientations_Permute_Private(PetscInt n, const PetscInt arr[], PetscInt start, PetscBool reverse, PetscInt newarr[])
628: {
629: PetscInt i;
632: if (reverse) {for (i=0; i<n; i++) newarr[i] = arr[(n+start-i)%n];}
633: else {for (i=0; i<n; i++) newarr[i] = arr[(start+i)%n];}
634: return(0);
635: }
637: PETSC_INTERN PetscErrorCode DMPlexGetPointDualSpaceFEM(DM,PetscInt,PetscInt,PetscDualSpace *);
638: PETSC_INTERN PetscErrorCode DMPlexGetIndicesPoint_Internal(PetscSection,PetscInt,PetscInt,PetscInt *,PetscBool,const PetscInt[],const PetscInt[],PetscInt[]);
639: PETSC_INTERN PetscErrorCode DMPlexGetIndicesPointFields_Internal(PetscSection,PetscInt,PetscInt,PetscInt[],PetscBool,const PetscInt***,PetscInt,const PetscInt[],PetscInt[]);
640: PETSC_INTERN PetscErrorCode DMPlexGetCompressedClosure(DM, PetscSection, PetscInt, PetscInt *, PetscInt **, PetscSection *, IS *, const PetscInt **);
641: PETSC_INTERN PetscErrorCode DMPlexRestoreCompressedClosure(DM, PetscSection, PetscInt, PetscInt *, PetscInt **, PetscSection *, IS *, const PetscInt **);
643: PETSC_EXTERN PetscErrorCode DMSNESGetFEGeom(DMField, IS, PetscQuadrature, PetscBool, PetscFEGeom **);
644: PETSC_EXTERN PetscErrorCode DMSNESRestoreFEGeom(DMField, IS, PetscQuadrature, PetscBool, PetscFEGeom **);
645: PETSC_EXTERN PetscErrorCode DMPlexComputeResidual_Patch_Internal(DM, PetscSection, IS, PetscReal, Vec, Vec, Vec, void *);
646: PETSC_EXTERN PetscErrorCode DMPlexComputeJacobian_Patch_Internal(DM, PetscSection, PetscSection, IS, PetscReal, PetscReal, Vec, Vec, Mat, Mat, void *);
647: PETSC_INTERN PetscErrorCode DMCreateSubDomainDM_Plex(DM,DMLabel,PetscInt,IS*,DM*);
648: PETSC_INTERN PetscErrorCode DMPlexBasisTransformPoint_Internal(DM, DM, Vec, PetscInt, PetscBool[], PetscBool, PetscScalar *);
649: PETSC_EXTERN PetscErrorCode DMPlexBasisTransformPointTensor_Internal(DM, DM, Vec, PetscInt, PetscBool, PetscInt, PetscScalar *);
650: PETSC_INTERN PetscErrorCode DMPlexBasisTransformApplyReal_Internal(DM, const PetscReal[], PetscBool, PetscInt, const PetscReal *, PetscReal *, void *);
651: PETSC_INTERN PetscErrorCode DMPlexBasisTransformApply_Internal(DM, const PetscReal[], PetscBool, PetscInt, const PetscScalar *, PetscScalar *, void *);
652: PETSC_INTERN PetscErrorCode DMCreateNeumannOverlap_Plex(DM, IS*, Mat*, PetscErrorCode (**)(Mat, PetscReal, Vec, Vec, PetscReal, IS, void*), void **);
654: #endif /* _PLEXIMPL_H */