xref: /petsc/src/dm/impls/plex/plexfem.c (revision 0483ade4e28a7dc56238618f7a207d5848f2b8ef) 
1 #include <petsc-private/dmpleximpl.h>   /*I      "petscdmplex.h"   I*/
2 
3 #include <petscfe.h>
4 
5 #undef __FUNCT__
6 #define __FUNCT__ "DMPlexGetScale"
7 PetscErrorCode DMPlexGetScale(DM dm, PetscUnit unit, PetscReal *scale)
8 {
9   DM_Plex *mesh = (DM_Plex*) dm->data;
10 
11   PetscFunctionBegin;
12   PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
13   PetscValidPointer(scale, 3);
14   *scale = mesh->scale[unit];
15   PetscFunctionReturn(0);
16 }
17 
18 #undef __FUNCT__
19 #define __FUNCT__ "DMPlexSetScale"
20 PetscErrorCode DMPlexSetScale(DM dm, PetscUnit unit, PetscReal scale)
21 {
22   DM_Plex *mesh = (DM_Plex*) dm->data;
23 
24   PetscFunctionBegin;
25   PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
26   mesh->scale[unit] = scale;
27   PetscFunctionReturn(0);
28 }
29 
30 PETSC_STATIC_INLINE PetscInt epsilon(PetscInt i, PetscInt j, PetscInt k)
31 {
32   switch (i) {
33   case 0:
34     switch (j) {
35     case 0: return 0;
36     case 1:
37       switch (k) {
38       case 0: return 0;
39       case 1: return 0;
40       case 2: return 1;
41       }
42     case 2:
43       switch (k) {
44       case 0: return 0;
45       case 1: return -1;
46       case 2: return 0;
47       }
48     }
49   case 1:
50     switch (j) {
51     case 0:
52       switch (k) {
53       case 0: return 0;
54       case 1: return 0;
55       case 2: return -1;
56       }
57     case 1: return 0;
58     case 2:
59       switch (k) {
60       case 0: return 1;
61       case 1: return 0;
62       case 2: return 0;
63       }
64     }
65   case 2:
66     switch (j) {
67     case 0:
68       switch (k) {
69       case 0: return 0;
70       case 1: return 1;
71       case 2: return 0;
72       }
73     case 1:
74       switch (k) {
75       case 0: return -1;
76       case 1: return 0;
77       case 2: return 0;
78       }
79     case 2: return 0;
80     }
81   }
82   return 0;
83 }
84 
85 #undef __FUNCT__
86 #define __FUNCT__ "DMPlexCreateRigidBody"
87 /*@C
88   DMPlexCreateRigidBody - create rigid body modes from coordinates
89 
90   Collective on DM
91 
92   Input Arguments:
93 + dm - the DM
94 . section - the local section associated with the rigid field, or NULL for the default section
95 - globalSection - the global section associated with the rigid field, or NULL for the default section
96 
97   Output Argument:
98 . sp - the null space
99 
100   Note: This is necessary to take account of Dirichlet conditions on the displacements
101 
102   Level: advanced
103 
104 .seealso: MatNullSpaceCreate()
105 @*/
106 PetscErrorCode DMPlexCreateRigidBody(DM dm, PetscSection section, PetscSection globalSection, MatNullSpace *sp)
107 {
108   MPI_Comm       comm;
109   Vec            coordinates, localMode, mode[6];
110   PetscSection   coordSection;
111   PetscScalar   *coords;
112   PetscInt       dim, vStart, vEnd, v, n, m, d, i, j;
113   PetscErrorCode ierr;
114 
115   PetscFunctionBegin;
116   ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
117   ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
118   if (dim == 1) {
119     ierr = MatNullSpaceCreate(comm, PETSC_TRUE, 0, NULL, sp);CHKERRQ(ierr);
120     PetscFunctionReturn(0);
121   }
122   if (!section)       {ierr = DMGetDefaultSection(dm, &section);CHKERRQ(ierr);}
123   if (!globalSection) {ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr);}
124   ierr = PetscSectionGetConstrainedStorageSize(globalSection, &n);CHKERRQ(ierr);
125   ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
126   ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
127   ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
128   m    = (dim*(dim+1))/2;
129   ierr = VecCreate(comm, &mode[0]);CHKERRQ(ierr);
130   ierr = VecSetSizes(mode[0], n, PETSC_DETERMINE);CHKERRQ(ierr);
131   ierr = VecSetUp(mode[0]);CHKERRQ(ierr);
132   for (i = 1; i < m; ++i) {ierr = VecDuplicate(mode[0], &mode[i]);CHKERRQ(ierr);}
133   /* Assume P1 */
134   ierr = DMGetLocalVector(dm, &localMode);CHKERRQ(ierr);
135   for (d = 0; d < dim; ++d) {
136     PetscScalar values[3] = {0.0, 0.0, 0.0};
137 
138     values[d] = 1.0;
139     ierr      = VecSet(localMode, 0.0);CHKERRQ(ierr);
140     for (v = vStart; v < vEnd; ++v) {
141       ierr = DMPlexVecSetClosure(dm, section, localMode, v, values, INSERT_VALUES);CHKERRQ(ierr);
142     }
143     ierr = DMLocalToGlobalBegin(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr);
144     ierr = DMLocalToGlobalEnd(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr);
145   }
146   ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
147   for (d = dim; d < dim*(dim+1)/2; ++d) {
148     PetscInt i, j, k = dim > 2 ? d - dim : d;
149 
150     ierr = VecSet(localMode, 0.0);CHKERRQ(ierr);
151     for (v = vStart; v < vEnd; ++v) {
152       PetscScalar values[3] = {0.0, 0.0, 0.0};
153       PetscInt    off;
154 
155       ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
156       for (i = 0; i < dim; ++i) {
157         for (j = 0; j < dim; ++j) {
158           values[j] += epsilon(i, j, k)*PetscRealPart(coords[off+i]);
159         }
160       }
161       ierr = DMPlexVecSetClosure(dm, section, localMode, v, values, INSERT_VALUES);CHKERRQ(ierr);
162     }
163     ierr = DMLocalToGlobalBegin(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr);
164     ierr = DMLocalToGlobalEnd(dm, localMode, INSERT_VALUES, mode[d]);CHKERRQ(ierr);
165   }
166   ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
167   ierr = DMRestoreLocalVector(dm, &localMode);CHKERRQ(ierr);
168   for (i = 0; i < dim; ++i) {ierr = VecNormalize(mode[i], NULL);CHKERRQ(ierr);}
169   /* Orthonormalize system */
170   for (i = dim; i < m; ++i) {
171     PetscScalar dots[6];
172 
173     ierr = VecMDot(mode[i], i, mode, dots);CHKERRQ(ierr);
174     for (j = 0; j < i; ++j) dots[j] *= -1.0;
175     ierr = VecMAXPY(mode[i], i, dots, mode);CHKERRQ(ierr);
176     ierr = VecNormalize(mode[i], NULL);CHKERRQ(ierr);
177   }
178   ierr = MatNullSpaceCreate(comm, PETSC_FALSE, m, mode, sp);CHKERRQ(ierr);
179   for (i = 0; i< m; ++i) {ierr = VecDestroy(&mode[i]);CHKERRQ(ierr);}
180   PetscFunctionReturn(0);
181 }
182 
183 #undef __FUNCT__
184 #define __FUNCT__ "DMPlexProjectFunctionLocal"
185 PetscErrorCode DMPlexProjectFunctionLocal(DM dm, PetscInt numComp, void (**funcs)(const PetscReal [], PetscScalar *), InsertMode mode, Vec localX)
186 {
187   Vec            coordinates;
188   PetscSection   section, cSection;
189   PetscInt       dim, vStart, vEnd, v, c, d;
190   PetscScalar   *values, *cArray;
191   PetscReal     *coords;
192   PetscErrorCode ierr;
193 
194   PetscFunctionBegin;
195   ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
196   ierr = DMGetDefaultSection(dm, &section);CHKERRQ(ierr);
197   ierr = DMPlexGetCoordinateSection(dm, &cSection);CHKERRQ(ierr);
198   ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
199   ierr = PetscMalloc(numComp * sizeof(PetscScalar), &values);CHKERRQ(ierr);
200   ierr = VecGetArray(coordinates, &cArray);CHKERRQ(ierr);
201   ierr = PetscSectionGetDof(cSection, vStart, &dim);CHKERRQ(ierr);
202   ierr = PetscMalloc(dim * sizeof(PetscReal),&coords);CHKERRQ(ierr);
203   for (v = vStart; v < vEnd; ++v) {
204     PetscInt dof, off;
205 
206     ierr = PetscSectionGetDof(cSection, v, &dof);CHKERRQ(ierr);
207     ierr = PetscSectionGetOffset(cSection, v, &off);CHKERRQ(ierr);
208     if (dof > dim) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Cannot have more coordinates %d then dimensions %d", dof, dim);
209     for (d = 0; d < dof; ++d) coords[d] = PetscRealPart(cArray[off+d]);
210     for (c = 0; c < numComp; ++c) (*funcs[c])(coords, &values[c]);
211     ierr = VecSetValuesSection(localX, section, v, values, mode);CHKERRQ(ierr);
212   }
213   ierr = VecRestoreArray(coordinates, &cArray);CHKERRQ(ierr);
214   /* Temporary, must be replaced by a projection on the finite element basis */
215   {
216     PetscInt eStart = 0, eEnd = 0, e, depth;
217 
218     ierr = DMPlexGetLabelSize(dm, "depth", &depth);CHKERRQ(ierr);
219     --depth;
220     if (depth > 1) {ierr = DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd);CHKERRQ(ierr);}
221     for (e = eStart; e < eEnd; ++e) {
222       const PetscInt *cone = NULL;
223       PetscInt        coneSize, d;
224       PetscScalar    *coordsA, *coordsB;
225 
226       ierr = DMPlexGetConeSize(dm, e, &coneSize);CHKERRQ(ierr);
227       ierr = DMPlexGetCone(dm, e, &cone);CHKERRQ(ierr);
228       if (coneSize != 2) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_SIZ, "Cone size %d for point %d should be 2", coneSize, e);
229       ierr = VecGetValuesSection(coordinates, cSection, cone[0], &coordsA);CHKERRQ(ierr);
230       ierr = VecGetValuesSection(coordinates, cSection, cone[1], &coordsB);CHKERRQ(ierr);
231       for (d = 0; d < dim; ++d) {
232         coords[d] = 0.5*(PetscRealPart(coordsA[d]) + PetscRealPart(coordsB[d]));
233       }
234       for (c = 0; c < numComp; ++c) (*funcs[c])(coords, &values[c]);
235       ierr = VecSetValuesSection(localX, section, e, values, mode);CHKERRQ(ierr);
236     }
237   }
238 
239   ierr = PetscFree(coords);CHKERRQ(ierr);
240   ierr = PetscFree(values);CHKERRQ(ierr);
241 #if 0
242   const PetscInt localDof = this->_mesh->sizeWithBC(s, *cells->begin());
243   PetscReal      detJ;
244 
245   ierr = PetscMalloc(localDof * sizeof(PetscScalar), &values);CHKERRQ(ierr);
246   ierr = PetscMalloc2(dim,PetscReal,&v0,dim*dim,PetscReal,&J);CHKERRQ(ierr);
247   ALE::ISieveVisitor::PointRetriever<PETSC_MESH_TYPE::sieve_type> pV(PetscPowInt(this->_mesh->getSieve()->getMaxConeSize(),dim+1), true);
248 
249   for (PetscInt c = cStart; c < cEnd; ++c) {
250     ALE::ISieveTraversal<PETSC_MESH_TYPE::sieve_type>::orientedClosure(*this->_mesh->getSieve(), c, pV);
251     const PETSC_MESH_TYPE::point_type *oPoints = pV.getPoints();
252     const int                          oSize   = pV.getSize();
253     int                                v       = 0;
254 
255     ierr = DMPlexComputeCellGeometry(dm, c, v0, J, NULL, &detJ);CHKERRQ(ierr);
256     for (PetscInt cl = 0; cl < oSize; ++cl) {
257       const PetscInt fDim;
258 
259       ierr = PetscSectionGetDof(oPoints[cl], &fDim);CHKERRQ(ierr);
260       if (pointDim) {
261         for (PetscInt d = 0; d < fDim; ++d, ++v) {
262           values[v] = (*this->_options.integrate)(v0, J, v, initFunc);
263         }
264       }
265     }
266     ierr = DMPlexVecSetClosure(dm, NULL, localX, c, values);CHKERRQ(ierr);
267     pV.clear();
268   }
269   ierr = PetscFree2(v0,J);CHKERRQ(ierr);
270   ierr = PetscFree(values);CHKERRQ(ierr);
271 #endif
272   PetscFunctionReturn(0);
273 }
274 
275 #undef __FUNCT__
276 #define __FUNCT__ "DMPlexProjectFunction"
277 /*@C
278   DMPlexProjectFunction - This projects the given function into the function space provided.
279 
280   Input Parameters:
281 + dm      - The DM
282 . numComp - The number of components (functions)
283 . funcs   - The coordinate functions to evaluate
284 - mode    - The insertion mode for values
285 
286   Output Parameter:
287 . X - vector
288 
289   Level: developer
290 
291   Note:
292   This currently just calls the function with the coordinates of each vertex and edge midpoint, and stores the result in a vector.
293   We will eventually fix it.
294 
295 .seealso: DMPlexComputeL2Diff()
296 @*/
297 PetscErrorCode DMPlexProjectFunction(DM dm, PetscInt numComp, void (**funcs)(const PetscReal [], PetscScalar *), InsertMode mode, Vec X)
298 {
299   Vec            localX;
300   PetscErrorCode ierr;
301 
302   PetscFunctionBegin;
303   ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr);
304   ierr = DMPlexProjectFunctionLocal(dm, numComp, funcs, mode, localX);CHKERRQ(ierr);
305   ierr = DMLocalToGlobalBegin(dm, localX, mode, X);CHKERRQ(ierr);
306   ierr = DMLocalToGlobalEnd(dm, localX, mode, X);CHKERRQ(ierr);
307   ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr);
308   PetscFunctionReturn(0);
309 }
310 
311 #undef __FUNCT__
312 #define __FUNCT__ "DMPlexComputeL2Diff"
313 /*@C
314   DMPlexComputeL2Diff - This function computes the L_2 difference between a function u and an FEM interpolant solution u_h.
315 
316   Input Parameters:
317 + dm    - The DM
318 . quad  - The PetscQuadrature object for each field
319 . funcs - The functions to evaluate for each field component
320 - X     - The coefficient vector u_h
321 
322   Output Parameter:
323 . diff - The diff ||u - u_h||_2
324 
325   Level: developer
326 
327 .seealso: DMPlexProjectFunction()
328 @*/
329 PetscErrorCode DMPlexComputeL2Diff(DM dm, PetscQuadrature quad[], void (**funcs)(const PetscReal [], PetscScalar *), Vec X, PetscReal *diff)
330 {
331   const PetscInt debug = 0;
332   PetscSection   section;
333   Vec            localX;
334   PetscReal     *coords, *v0, *J, *invJ, detJ;
335   PetscReal      localDiff = 0.0;
336   PetscInt       dim, numFields, numComponents = 0, cStart, cEnd, c, field, fieldOffset, comp;
337   PetscErrorCode ierr;
338 
339   PetscFunctionBegin;
340   ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
341   ierr = DMGetDefaultSection(dm, &section);CHKERRQ(ierr);
342   ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr);
343   ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr);
344   ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr);
345   ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, localX);CHKERRQ(ierr);
346   for (field = 0; field < numFields; ++field) {
347     numComponents += quad[field].numComponents;
348   }
349   ierr = DMPlexProjectFunctionLocal(dm, numComponents, funcs, INSERT_BC_VALUES, localX);CHKERRQ(ierr);
350   ierr = PetscMalloc4(dim,PetscReal,&coords,dim,PetscReal,&v0,dim*dim,PetscReal,&J,dim*dim,PetscReal,&invJ);CHKERRQ(ierr);
351   ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
352   for (c = cStart; c < cEnd; ++c) {
353     PetscScalar *x;
354     PetscReal    elemDiff = 0.0;
355 
356     ierr = DMPlexComputeCellGeometry(dm, c, v0, J, invJ, &detJ);CHKERRQ(ierr);
357     if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c);
358     ierr = DMPlexVecGetClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr);
359 
360     for (field = 0, comp = 0, fieldOffset = 0; field < numFields; ++field) {
361       const PetscInt   numQuadPoints = quad[field].numQuadPoints;
362       const PetscReal *quadPoints    = quad[field].quadPoints;
363       const PetscReal *quadWeights   = quad[field].quadWeights;
364       const PetscInt   numBasisFuncs = quad[field].numBasisFuncs;
365       const PetscInt   numBasisComps = quad[field].numComponents;
366       const PetscReal *basis         = quad[field].basis;
367       PetscInt         q, d, e, fc, f;
368 
369       if (debug) {
370         char title[1024];
371         ierr = PetscSNPrintf(title, 1023, "Solution for Field %d", field);CHKERRQ(ierr);
372         ierr = DMPrintCellVector(c, title, numBasisFuncs*numBasisComps, &x[fieldOffset]);CHKERRQ(ierr);
373       }
374       for (q = 0; q < numQuadPoints; ++q) {
375         for (d = 0; d < dim; d++) {
376           coords[d] = v0[d];
377           for (e = 0; e < dim; e++) {
378             coords[d] += J[d*dim+e]*(quadPoints[q*dim+e] + 1.0);
379           }
380         }
381         for (fc = 0; fc < numBasisComps; ++fc) {
382           PetscScalar funcVal;
383           PetscScalar interpolant = 0.0;
384 
385           (*funcs[comp+fc])(coords, &funcVal);
386           for (f = 0; f < numBasisFuncs; ++f) {
387             const PetscInt fidx = f*numBasisComps+fc;
388             interpolant += x[fieldOffset+fidx]*basis[q*numBasisFuncs*numBasisComps+fidx];
389           }
390           if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, "    elem %d field %d diff %g\n", c, field, PetscSqr(PetscRealPart(interpolant - funcVal))*quadWeights[q]*detJ);CHKERRQ(ierr);}
391           elemDiff += PetscSqr(PetscRealPart(interpolant - funcVal))*quadWeights[q]*detJ;
392         }
393       }
394       comp        += numBasisComps;
395       fieldOffset += numBasisFuncs*numBasisComps;
396     }
397     ierr = DMPlexVecRestoreClosure(dm, NULL, localX, c, NULL, &x);CHKERRQ(ierr);
398     if (debug) {ierr = PetscPrintf(PETSC_COMM_SELF, "  elem %d diff %g\n", c, elemDiff);CHKERRQ(ierr);}
399     localDiff += elemDiff;
400   }
401   ierr  = PetscFree4(coords,v0,J,invJ);CHKERRQ(ierr);
402   ierr  = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr);
403   ierr  = MPI_Allreduce(&localDiff, diff, 1, MPIU_REAL, MPI_SUM, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr);
404   *diff = PetscSqrtReal(*diff);
405   PetscFunctionReturn(0);
406 }
407 
408 #if 0
409 
410 #undef __FUNCT__
411 #define __FUNCT__ "DMPlexComputeResidualFEM"
412 PetscErrorCode DMPlexComputeResidualFEM(DM dm, Vec X, Vec F, void *user)
413 {
414   DM_Plex         *mesh   = (DM_Plex*) dm->data;
415   PetscFEM        *fem    = (PetscFEM*) &((DM*) user)[1];
416   PetscQuadrature *quad   = fem->quad;
417   PetscQuadrature *quadBd = fem->quadBd;
418   PetscSection     section;
419   PetscReal       *v0, *n, *J, *invJ, *detJ;
420   PetscScalar     *elemVec, *u;
421   PetscInt         dim, numFields, field, numBatchesTmp = 1, numCells, cStart, cEnd, c;
422   PetscInt         cellDof, numComponents;
423   PetscBool        has;
424   PetscErrorCode   ierr;
425 
426   PetscFunctionBegin;
427   if (has && quadBd) {
428     DMLabel         label;
429     IS              pointIS;
430     const PetscInt *points;
431     PetscInt        numPoints, p;
432 
433     ierr = DMPlexGetLabel(dm, "boundary", &label);CHKERRQ(ierr);
434     ierr = DMLabelGetStratumSize(label, 1, &numPoints);CHKERRQ(ierr);
435     ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr);
436     ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr);
437     for (field = 0, cellDof = 0, numComponents = 0; field < numFields; ++field) {
438       cellDof       += quadBd[field].numBasisFuncs*quadBd[field].numComponents;
439       numComponents += quadBd[field].numComponents;
440     }
441     ierr = PetscMalloc7(numPoints*cellDof,PetscScalar,&u,numPoints*dim,PetscReal,&v0,numPoints*dim,PetscReal,&n,numPoints*dim*dim,PetscReal,&J,numPoints*dim*dim,PetscReal,&invJ,numPoints,PetscReal,&detJ,numPoints*cellDof,PetscScalar,&elemVec);CHKERRQ(ierr);
442     for (p = 0; p < numPoints; ++p) {
443       const PetscInt point = points[p];
444       PetscScalar   *x;
445       PetscInt       i;
446 
447       /* TODO: Add normal determination here */
448       ierr = DMPlexComputeCellGeometry(dm, point, &v0[p*dim], &J[p*dim*dim], &invJ[p*dim*dim], &detJ[p]);CHKERRQ(ierr);
449       if (detJ[p] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", detJ[p], point);
450       ierr = DMPlexVecGetClosure(dm, NULL, X, point, NULL, &x);CHKERRQ(ierr);
451 
452       for (i = 0; i < cellDof; ++i) u[p*cellDof+i] = x[i];
453       ierr = DMPlexVecRestoreClosure(dm, NULL, X, point, NULL, &x);CHKERRQ(ierr);
454     }
455     for (field = 0; field < numFields; ++field) {
456       const PetscInt numQuadPoints = quadBd[field].numQuadPoints;
457       const PetscInt numBasisFuncs = quadBd[field].numBasisFuncs;
458       void           (*f0)(const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscReal[], PetscScalar[]) = fem->f0BdFuncs[field];
459       void           (*f1)(const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscReal[], PetscScalar[]) = fem->f1BdFuncs[field];
460       /* Conforming batches */
461       PetscInt blockSize  = numBasisFuncs*numQuadPoints;
462       PetscInt numBlocks  = 1;
463       PetscInt batchSize  = numBlocks * blockSize;
464       PetscInt numBatches = numBatchesTmp;
465       PetscInt numChunks  = numPoints / (numBatches*batchSize);
466       /* Remainder */
467       PetscInt numRemainder = numPoints % (numBatches * batchSize);
468       PetscInt offset       = numPoints - numRemainder;
469 
470       ierr = (*mesh->integrateBdResidualFEM)(numChunks*numBatches*batchSize, numFields, field, quadBd, u, v0, n, J, invJ, detJ, f0, f1, elemVec);CHKERRQ(ierr);
471       ierr = (*mesh->integrateBdResidualFEM)(numRemainder, numFields, field, quadBd, &u[offset*cellDof], &v0[offset*dim], &n[offset*dim], &J[offset*dim*dim], &invJ[offset*dim*dim], &detJ[offset],
472                                              f0, f1, &elemVec[offset*cellDof]);CHKERRQ(ierr);
473     }
474     for (p = 0; p < numPoints; ++p) {
475       const PetscInt point = points[p];
476 
477       if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "Residual", cellDof, &elemVec[p*cellDof]);CHKERRQ(ierr);}
478       ierr = DMPlexVecSetClosure(dm, NULL, F, point, &elemVec[p*cellDof], ADD_VALUES);CHKERRQ(ierr);
479     }
480     ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr);
481     ierr = ISDestroy(&pointIS);CHKERRQ(ierr);
482     ierr = PetscFree7(u,v0,n,J,invJ,detJ,elemVec);CHKERRQ(ierr);
483   }
484   PetscFunctionReturn(0);
485 }
486 
487 #else
488 
489 #undef __FUNCT__
490 #define __FUNCT__ "DMPlexComputeResidualFEM"
491 /*@
492   DMPlexComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user
493 
494   Input Parameters:
495 + dm - The mesh
496 . X  - Local input vector
497 - user - The user context
498 
499   Output Parameter:
500 . F  - Local output vector
501 
502   Note:
503   The second member of the user context must be an FEMContext.
504 
505   We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator,
506   like a GPU, or vectorize on a multicore machine.
507 
508   Level: developer
509 
510 .seealso: DMPlexComputeJacobianActionFEM()
511 @*/
512 PetscErrorCode DMPlexComputeResidualFEM(DM dm, Vec X, Vec F, void *user)
513 {
514   DM_Plex          *mesh = (DM_Plex*) dm->data;
515   PetscFEM         *fem  = (PetscFEM*) &((DM*) user)[1];
516   PetscFE          *fe   = fem->fe;
517   const char       *name = "Residual";
518   PetscQuadrature   q;
519   PetscCellGeometry geom;
520   PetscSection      section;
521   PetscReal        *v0, *J, *invJ, *detJ;
522   PetscScalar      *elemVec, *u;
523   PetscInt          dim, numFields, f, numCells, cStart, cEnd, c;
524   PetscInt          cellDof = 0, numComponents = 0;
525   PetscErrorCode    ierr;
526 
527   PetscFunctionBegin;
528   ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr);
529   ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
530   ierr = DMGetDefaultSection(dm, &section);CHKERRQ(ierr);
531   ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr);
532   ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
533   numCells = cEnd - cStart;
534   for (f = 0; f < numFields; ++f) {
535     PetscInt Nb, Nc;
536 
537     ierr = PetscFEGetDimension(fe[f], &Nb);CHKERRQ(ierr);
538     ierr = PetscFEGetNumComponents(fe[f], &Nc);CHKERRQ(ierr);
539     cellDof       += Nb*Nc;
540     numComponents += Nc;
541   }
542   ierr = DMPlexProjectFunctionLocal(dm, numComponents, fem->bcFuncs, INSERT_BC_VALUES, X);CHKERRQ(ierr);
543   ierr = VecSet(F, 0.0);CHKERRQ(ierr);
544   ierr = PetscMalloc6(numCells*cellDof,PetscScalar,&u,numCells*dim,PetscReal,&v0,numCells*dim*dim,PetscReal,&J,numCells*dim*dim,PetscReal,&invJ,numCells,PetscReal,&detJ,numCells*cellDof,PetscScalar,&elemVec);CHKERRQ(ierr);
545   for (c = cStart; c < cEnd; ++c) {
546     PetscScalar *x = NULL;
547     PetscInt     i;
548 
549     ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr);
550     if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c);
551     ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr);
552     for (i = 0; i < cellDof; ++i) u[c*cellDof+i] = x[i];
553     ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr);
554   }
555   for (f = 0; f < numFields; ++f) {
556     void   (*f0)(const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscScalar[], const PetscScalar[], PetscScalar[]) = fem->f0Funcs[f];
557     void   (*f1)(const PetscScalar[], const PetscScalar[], const PetscReal[], const PetscScalar[], const PetscScalar[], PetscScalar[]) = fem->f1Funcs[f];
558     PetscInt Nb;
559     /* Conforming batches */
560     PetscInt numBlocks  = 1;
561     PetscInt numBatches = 1;
562     PetscInt numChunks, Ne, blockSize, batchSize;
563     /* Remainder */
564     PetscInt Nr, offset;
565 
566     ierr = PetscFEGetQuadrature(fe[f], &q);CHKERRQ(ierr);
567     ierr = PetscFEGetDimension(fe[f], &Nb);CHKERRQ(ierr);
568     blockSize = Nb*q.numQuadPoints;
569     batchSize = numBlocks * blockSize;
570     numChunks = numCells / (numBatches*batchSize);
571     Ne        = numChunks*numBatches*batchSize;
572     Nr        = numCells % (numBatches*batchSize);
573     offset    = numCells - Nr;
574     geom.v0   = v0;
575     geom.J    = J;
576     geom.invJ = invJ;
577     geom.detJ = detJ;
578     ierr = PetscFEIntegrateResidual(fe[f], Ne, numFields, fe, f, geom, u, f0, f1, elemVec);CHKERRQ(ierr);
579     geom.v0   = &v0[offset*dim];
580     geom.J    = &J[offset*dim*dim];
581     geom.invJ = &invJ[offset*dim*dim];
582     geom.detJ = &detJ[offset];
583     ierr = PetscFEIntegrateResidual(fe[f], Nr, numFields, fe, f, geom, &u[offset*cellDof], f0, f1, &elemVec[offset*cellDof]);CHKERRQ(ierr);
584   }
585   for (c = cStart; c < cEnd; ++c) {
586     if (mesh->printFEM > 1) {ierr = DMPrintCellVector(c, name, cellDof, &elemVec[c*cellDof]);CHKERRQ(ierr);}
587     ierr = DMPlexVecSetClosure(dm, section, F, c, &elemVec[c*cellDof], ADD_VALUES);CHKERRQ(ierr);
588   }
589   ierr = PetscFree6(u,v0,J,invJ,detJ,elemVec);CHKERRQ(ierr);
590   if (mesh->printFEM) {ierr = DMPrintLocalVec(dm, name, F);CHKERRQ(ierr);}
591   ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr);
592   PetscFunctionReturn(0);
593 }
594 
595 #endif
596 
597 #undef __FUNCT__
598 #define __FUNCT__ "DMPlexComputeJacobianActionFEM"
599 /*@C
600   DMPlexComputeJacobianActionFEM - Form the local action of Jacobian J(u) on the local input X using pointwise functions specified by the user
601 
602   Input Parameters:
603 + dm - The mesh
604 . J  - The Jacobian shell matrix
605 . X  - Local input vector
606 - user - The user context
607 
608   Output Parameter:
609 . F  - Local output vector
610 
611   Note:
612   The second member of the user context must be an FEMContext.
613 
614   We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator,
615   like a GPU, or vectorize on a multicore machine.
616 
617   Level: developer
618 
619 .seealso: DMPlexComputeResidualFEM()
620 @*/
621 PetscErrorCode DMPlexComputeJacobianActionFEM(DM dm, Mat Jac, Vec X, Vec F, void *user)
622 {
623   DM_Plex          *mesh = (DM_Plex*) dm->data;
624   PetscFEM         *fem  = (PetscFEM*) &((DM*) user)[1];
625   PetscFE          *fe   = fem->fe;
626   PetscQuadrature   quad;
627   PetscCellGeometry geom;
628   PetscSection      section;
629   JacActionCtx     *jctx;
630   PetscReal        *v0, *J, *invJ, *detJ;
631   PetscScalar      *elemVec, *u, *a;
632   PetscInt          dim, numFields, field, numCells, cStart, cEnd, c;
633   PetscInt          cellDof = 0;
634   PetscErrorCode    ierr;
635 
636   PetscFunctionBegin;
637   /* ierr = PetscLogEventBegin(DMPLEX_JacobianActionFEM,dm,0,0,0);CHKERRQ(ierr); */
638   ierr = MatShellGetContext(Jac, &jctx);CHKERRQ(ierr);
639   ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
640   ierr = DMGetDefaultSection(dm, &section);CHKERRQ(ierr);
641   ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr);
642   ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
643   numCells = cEnd - cStart;
644   for (field = 0; field < numFields; ++field) {
645     PetscInt Nb, Nc;
646 
647     ierr = PetscFEGetDimension(fe[field], &Nb);CHKERRQ(ierr);
648     ierr = PetscFEGetNumComponents(fe[field], &Nc);CHKERRQ(ierr);
649     cellDof += Nb*Nc;
650   }
651   ierr = VecSet(F, 0.0);CHKERRQ(ierr);
652   ierr = PetscMalloc7(numCells*cellDof,PetscScalar,&u,numCells*cellDof,PetscScalar,&a,numCells*dim,PetscReal,&v0,numCells*dim*dim,PetscReal,&J,numCells*dim*dim,PetscReal,&invJ,numCells,PetscReal,&detJ,numCells*cellDof,PetscScalar,&elemVec);CHKERRQ(ierr);
653   for (c = cStart; c < cEnd; ++c) {
654     PetscScalar *x;
655     PetscInt     i;
656 
657     ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr);
658     if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c);
659     ierr = DMPlexVecGetClosure(dm, NULL, jctx->u, c, NULL, &x);CHKERRQ(ierr);
660     for (i = 0; i < cellDof; ++i) u[c*cellDof+i] = x[i];
661     ierr = DMPlexVecRestoreClosure(dm, NULL, jctx->u, c, NULL, &x);CHKERRQ(ierr);
662     ierr = DMPlexVecGetClosure(dm, NULL, X, c, NULL, &x);CHKERRQ(ierr);
663     for (i = 0; i < cellDof; ++i) a[c*cellDof+i] = x[i];
664     ierr = DMPlexVecRestoreClosure(dm, NULL, X, c, NULL, &x);CHKERRQ(ierr);
665   }
666   for (field = 0; field < numFields; ++field) {
667     PetscInt Nb;
668     /* Conforming batches */
669     PetscInt numBlocks  = 1;
670     PetscInt numBatches = 1;
671     PetscInt numChunks, Ne, blockSize, batchSize;
672     /* Remainder */
673     PetscInt Nr, offset;
674 
675     ierr = PetscFEGetQuadrature(fe[field], &quad);CHKERRQ(ierr);
676     ierr = PetscFEGetDimension(fe[field], &Nb);CHKERRQ(ierr);
677     blockSize = Nb*quad.numQuadPoints;
678     batchSize = numBlocks * blockSize;
679     numChunks = numCells / (numBatches*batchSize);
680     Ne        = numChunks*numBatches*batchSize;
681     Nr        = numCells % (numBatches*batchSize);
682     offset    = numCells - Nr;
683     geom.v0   = v0;
684     geom.J    = J;
685     geom.invJ = invJ;
686     geom.detJ = detJ;
687     ierr = PetscFEIntegrateJacobianAction(fe[field], Ne, numFields, fe, field, geom, u, a, fem->g0Funcs, fem->g1Funcs, fem->g2Funcs, fem->g3Funcs, elemVec);CHKERRQ(ierr);
688     geom.v0   = &v0[offset*dim];
689     geom.J    = &J[offset*dim*dim];
690     geom.invJ = &invJ[offset*dim*dim];
691     geom.detJ = &detJ[offset];
692     ierr = PetscFEIntegrateJacobianAction(fe[field], Nr, numFields, fe, field, geom, &u[offset*cellDof], &a[offset*cellDof],
693                                           fem->g0Funcs, fem->g1Funcs, fem->g2Funcs, fem->g3Funcs, &elemVec[offset*cellDof]);CHKERRQ(ierr);
694   }
695   for (c = cStart; c < cEnd; ++c) {
696     if (mesh->printFEM > 1) {ierr = DMPrintCellVector(c, "Jacobian Action", cellDof, &elemVec[c*cellDof]);CHKERRQ(ierr);}
697     ierr = DMPlexVecSetClosure(dm, NULL, F, c, &elemVec[c*cellDof], ADD_VALUES);CHKERRQ(ierr);
698   }
699   ierr = PetscFree7(u,a,v0,J,invJ,detJ,elemVec);CHKERRQ(ierr);
700   if (mesh->printFEM) {
701     PetscMPIInt rank, numProcs;
702     PetscInt    p;
703 
704     ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr);
705     ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &numProcs);CHKERRQ(ierr);
706     ierr = PetscPrintf(PetscObjectComm((PetscObject)dm), "Jacobian Action:\n");CHKERRQ(ierr);
707     for (p = 0; p < numProcs; ++p) {
708       if (p == rank) {ierr = VecView(F, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
709       ierr = PetscBarrier((PetscObject) dm);CHKERRQ(ierr);
710     }
711   }
712   /* ierr = PetscLogEventEnd(DMPLEX_JacobianActionFEM,dm,0,0,0);CHKERRQ(ierr); */
713   PetscFunctionReturn(0);
714 }
715 
716 #undef __FUNCT__
717 #define __FUNCT__ "DMPlexComputeJacobianFEM"
718 /*@
719   DMPlexComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user.
720 
721   Input Parameters:
722 + dm - The mesh
723 . X  - Local input vector
724 - user - The user context
725 
726   Output Parameter:
727 . Jac  - Jacobian matrix
728 
729   Note:
730   The second member of the user context must be an FEMContext.
731 
732   We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator,
733   like a GPU, or vectorize on a multicore machine.
734 
735   Level: developer
736 
737 .seealso: FormFunctionLocal()
738 @*/
739 PetscErrorCode DMPlexComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP, MatStructure *str,void *user)
740 {
741   DM_Plex          *mesh = (DM_Plex*) dm->data;
742   PetscFEM         *fem  = (PetscFEM*) &((DM*) user)[1];
743   PetscFE          *fe   = fem->fe;
744   const char       *name = "Jacobian";
745   PetscQuadrature   quad;
746   PetscCellGeometry geom;
747   PetscSection      section, globalSection;
748   PetscReal        *v0, *J, *invJ, *detJ;
749   PetscScalar      *elemMat, *u;
750   PetscInt          dim, numFields, f, fieldI, fieldJ, numCells, cStart, cEnd, c;
751   PetscInt          cellDof = 0, numComponents = 0;
752   PetscBool         isShell;
753   PetscErrorCode    ierr;
754 
755   PetscFunctionBegin;
756   ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr);
757   ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
758   ierr = DMGetDefaultSection(dm, &section);CHKERRQ(ierr);
759   ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr);
760   ierr = PetscSectionGetNumFields(section, &numFields);CHKERRQ(ierr);
761   ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
762   numCells = cEnd - cStart;
763   for (f = 0; f < numFields; ++f) {
764     PetscInt Nb, Nc;
765 
766     ierr = PetscFEGetDimension(fe[f], &Nb);CHKERRQ(ierr);
767     ierr = PetscFEGetNumComponents(fe[f], &Nc);CHKERRQ(ierr);
768     cellDof       += Nb*Nc;
769     numComponents += Nc;
770   }
771   ierr = DMPlexProjectFunctionLocal(dm, numComponents, fem->bcFuncs, INSERT_BC_VALUES, X);CHKERRQ(ierr);
772   ierr = MatZeroEntries(JacP);CHKERRQ(ierr);
773   ierr = PetscMalloc6(numCells*cellDof,PetscScalar,&u,numCells*dim,PetscReal,&v0,numCells*dim*dim,PetscReal,&J,numCells*dim*dim,PetscReal,&invJ,numCells,PetscReal,&detJ,numCells*cellDof*cellDof,PetscScalar,&elemMat);CHKERRQ(ierr);
774   for (c = cStart; c < cEnd; ++c) {
775     PetscScalar *x;
776     PetscInt     i;
777 
778     ierr = DMPlexComputeCellGeometry(dm, c, &v0[c*dim], &J[c*dim*dim], &invJ[c*dim*dim], &detJ[c]);CHKERRQ(ierr);
779     if (detJ[c] <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ[c], c);
780     ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr);
781     for (i = 0; i < cellDof; ++i) u[c*cellDof+i] = x[i];
782     ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr);
783   }
784   ierr = PetscMemzero(elemMat, numCells*cellDof*cellDof * sizeof(PetscScalar));CHKERRQ(ierr);
785   for (fieldI = 0; fieldI < numFields; ++fieldI) {
786     PetscInt Nb;
787     ierr = PetscFEGetQuadrature(fe[fieldI], &quad);CHKERRQ(ierr);
788     ierr = PetscFEGetDimension(fe[fieldI], &Nb);CHKERRQ(ierr);
789     for (fieldJ = 0; fieldJ < numFields; ++fieldJ) {
790       void   (*g0)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->g0Funcs[fieldI*numFields+fieldJ];
791       void   (*g1)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->g1Funcs[fieldI*numFields+fieldJ];
792       void   (*g2)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->g2Funcs[fieldI*numFields+fieldJ];
793       void   (*g3)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal[], PetscScalar[]) = fem->g3Funcs[fieldI*numFields+fieldJ];
794       /* Conforming batches */
795       PetscInt numBlocks  = 1;
796       PetscInt numBatches = 1;
797       PetscInt numChunks, Ne, blockSize, batchSize;
798       /* Remainder */
799       PetscInt Nr, offset;
800 
801       blockSize = Nb*quad.numQuadPoints;
802       batchSize = numBlocks * blockSize;
803       numChunks = numCells / (numBatches*batchSize);
804       Ne        = numChunks*numBatches*batchSize;
805       Nr        = numCells % (numBatches*batchSize);
806       offset    = numCells - Nr;
807       geom.v0   = v0;
808       geom.J    = J;
809       geom.invJ = invJ;
810       geom.detJ = detJ;
811       ierr = PetscFEIntegrateJacobian(fe[fieldI], Ne, numFields, fe, fieldI, fieldJ, geom, u, g0, g1, g2, g3, elemMat);CHKERRQ(ierr);
812       geom.v0   = &v0[offset*dim];
813       geom.J    = &J[offset*dim*dim];
814       geom.invJ = &invJ[offset*dim*dim];
815       geom.detJ = &detJ[offset];
816       ierr = PetscFEIntegrateJacobian(fe[fieldI], Nr, numFields, fe, fieldI, fieldJ, geom, &u[offset*cellDof], g0, g1, g2, g3, &elemMat[offset*cellDof*cellDof]);CHKERRQ(ierr);
817     }
818   }
819   for (c = cStart; c < cEnd; ++c) {
820     if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, cellDof, cellDof, &elemMat[c*cellDof*cellDof]);CHKERRQ(ierr);}
821     ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, c, &elemMat[c*cellDof*cellDof], ADD_VALUES);CHKERRQ(ierr);
822   }
823   ierr = PetscFree6(u,v0,J,invJ,detJ,elemMat);CHKERRQ(ierr);
824   ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
825   ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
826   if (mesh->printFEM) {
827     ierr = PetscPrintf(PETSC_COMM_WORLD, "%s:\n", name);CHKERRQ(ierr);
828     ierr = MatChop(JacP, 1.0e-10);CHKERRQ(ierr);
829     ierr = MatView(JacP, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
830   }
831   ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr);
832   ierr = PetscObjectTypeCompare((PetscObject) Jac, MATSHELL, &isShell);CHKERRQ(ierr);
833   if (isShell) {
834     JacActionCtx *jctx;
835 
836     ierr = MatShellGetContext(Jac, &jctx);CHKERRQ(ierr);
837     ierr = VecCopy(X, jctx->u);CHKERRQ(ierr);
838   }
839   *str = SAME_NONZERO_PATTERN;
840   PetscFunctionReturn(0);
841 }
842