Actual source code: ex77.c

petsc-main 2021-04-20
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  1: static char help[] = "Nonlinear elasticity problem in 3d with simplicial finite elements.\n\
  2: We solve a nonlinear elasticity problem, modelled as an incompressible Neo-Hookean solid, \n\
  3:  with pressure loading in a rectangular domain, using a parallel unstructured mesh (DMPLEX) to discretize it.\n\n\n";

  5: /*
  6: Nonlinear elasticity problem, which we discretize using the finite
  7: element method on an unstructured mesh. This uses both Dirichlet boundary conditions (fixed faces)
  8: and nonlinear Neumann boundary conditions (pressure loading).
  9: The Lagrangian density (modulo boundary conditions) for this problem is given by
 10: \begin{equation}
 11:   \frac{\mu}{2} (\mathrm{Tr}{C}-3) + J p + \frac{\kappa}{2} (J-1).
 12: \end{equation}

 14: Discretization:

 16: We use PetscFE to generate a tabulation of the finite element basis functions
 17: at quadrature points. We can currently generate an arbitrary order Lagrange
 18: element.

 20: Field Data:

 22:   DMPLEX data is organized by point, and the closure operation just stacks up the
 23: data from each sieve point in the closure. Thus, for a P_2-P_1 Stokes element, we
 24: have

 26:   cl{e} = {f e_0 e_1 e_2 v_0 v_1 v_2}
 27:   x     = [u_{e_0} v_{e_0} u_{e_1} v_{e_1} u_{e_2} v_{e_2} u_{v_0} v_{v_0} p_{v_0} u_{v_1} v_{v_1} p_{v_1} u_{v_2} v_{v_2} p_{v_2}]

 29: The problem here is that we would like to loop over each field separately for
 30: integration. Therefore, the closure visitor in DMPlexVecGetClosure() reorders
 31: the data so that each field is contiguous

 33:   x'    = [u_{e_0} v_{e_0} u_{e_1} v_{e_1} u_{e_2} v_{e_2} u_{v_0} v_{v_0} u_{v_1} v_{v_1} u_{v_2} v_{v_2} p_{v_0} p_{v_1} p_{v_2}]

 35: Likewise, DMPlexVecSetClosure() takes data partitioned by field, and correctly
 36: puts it into the Sieve ordering.

 38: */

 40: #include <petscdmplex.h>
 41: #include <petscsnes.h>
 42: #include <petscds.h>

 44: typedef enum {RUN_FULL, RUN_TEST} RunType;

 46: typedef struct {
 47:   PetscInt      debug;             /* The debugging level */
 48:   RunType       runType;           /* Whether to run tests, or solve the full problem */
 49:   PetscLogEvent createMeshEvent;
 50:   PetscBool     showInitial, showSolution;
 51:   /* Domain and mesh definition */
 52:   PetscInt      dim;               /* The topological mesh dimension */
 53:   PetscBool     interpolate;       /* Generate intermediate mesh elements */
 54:   PetscBool     simplex;           /* Use simplices or tensor product cells */
 55:   PetscReal     refinementLimit;   /* The largest allowable cell volume */
 56:   PetscBool     testPartition;     /* Use a fixed partitioning for testing */
 57:   PetscReal     mu;                /* The shear modulus */
 58:   PetscReal     p_wall;            /* The wall pressure */
 59: } AppCtx;

 61: #if 0
 62: PETSC_STATIC_INLINE void Det2D(PetscReal *detJ, const PetscReal J[])
 63: {
 64:   *detJ = J[0]*J[3] - J[1]*J[2];
 65: }
 66: #endif

 68: PETSC_STATIC_INLINE void Det3D(PetscReal *detJ, const PetscScalar J[])
 69: {
 70:   *detJ = PetscRealPart(J[0*3+0]*(J[1*3+1]*J[2*3+2] - J[1*3+2]*J[2*3+1]) +
 71:                         J[0*3+1]*(J[1*3+2]*J[2*3+0] - J[1*3+0]*J[2*3+2]) +
 72:                         J[0*3+2]*(J[1*3+0]*J[2*3+1] - J[1*3+1]*J[2*3+0]));
 73: }

 75: #if 0
 76: PETSC_STATIC_INLINE void Cof2D(PetscReal C[], const PetscReal A[])
 77: {
 78:   C[0] =  A[3];
 79:   C[1] = -A[2];
 80:   C[2] = -A[1];
 81:   C[3] =  A[0];
 82: }
 83: #endif

 85: PETSC_STATIC_INLINE void Cof3D(PetscReal C[], const PetscScalar A[])
 86: {
 87:   C[0*3+0] = PetscRealPart(A[1*3+1]*A[2*3+2] - A[1*3+2]*A[2*3+1]);
 88:   C[0*3+1] = PetscRealPart(A[1*3+2]*A[2*3+0] - A[1*3+0]*A[2*3+2]);
 89:   C[0*3+2] = PetscRealPart(A[1*3+0]*A[2*3+1] - A[1*3+1]*A[2*3+0]);
 90:   C[1*3+0] = PetscRealPart(A[0*3+2]*A[2*3+1] - A[0*3+1]*A[2*3+2]);
 91:   C[1*3+1] = PetscRealPart(A[0*3+0]*A[2*3+2] - A[0*3+2]*A[2*3+0]);
 92:   C[1*3+2] = PetscRealPart(A[0*3+1]*A[2*3+0] - A[0*3+0]*A[2*3+1]);
 93:   C[2*3+0] = PetscRealPart(A[0*3+1]*A[1*3+2] - A[0*3+2]*A[1*3+1]);
 94:   C[2*3+1] = PetscRealPart(A[0*3+2]*A[1*3+0] - A[0*3+0]*A[1*3+2]);
 95:   C[2*3+2] = PetscRealPart(A[0*3+0]*A[1*3+1] - A[0*3+1]*A[1*3+0]);
 96: }

 98: PetscErrorCode zero_scalar(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx)
 99: {
100:   u[0] = 0.0;
101:   return 0;
102: }

104: PetscErrorCode zero_vector(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx)
105: {
106:   const PetscInt Ncomp = dim;

108:   PetscInt       comp;
109:   for (comp = 0; comp < Ncomp; ++comp) u[comp] = 0.0;
110:   return 0;
111: }

113: PetscErrorCode coordinates(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx)
114: {
115:   const PetscInt Ncomp = dim;

117:   PetscInt       comp;
118:   for (comp = 0; comp < Ncomp; ++comp) u[comp] = x[comp];
119:   return 0;
120: }

122: PetscErrorCode elasticityMaterial(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx)
123: {
124:   AppCtx *user = (AppCtx *) ctx;
125:   u[0] = user->mu;
126:   return 0;
127: }

129: PetscErrorCode wallPressure(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx)
130: {
131:   AppCtx *user = (AppCtx *) ctx;
132:   u[0] = user->p_wall;
133:   return 0;
134: }

136: void f1_u_3d(PetscInt dim, PetscInt Nf, PetscInt NfAux,
137:           const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
138:           const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
139:           PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f1[])
140: {
141:   const PetscInt  Ncomp = dim;
142:   const PetscReal mu = PetscRealPart(a[0]), kappa = 3.0;
143:   PetscReal       cofu_x[9/*Ncomp*dim*/], detu_x, p = PetscRealPart(u[Ncomp]);
144:   PetscInt        comp, d;

146:   Cof3D(cofu_x, u_x);
147:   Det3D(&detu_x, u_x);
148:   p += kappa * (detu_x - 1.0);

150:   /* f1 is the first Piola-Kirchhoff tensor */
151:   for (comp = 0; comp < Ncomp; ++comp) {
152:     for (d = 0; d < dim; ++d) {
153:       f1[comp*dim+d] = mu * u_x[comp*dim+d] + p * cofu_x[comp*dim+d];
154:     }
155:   }
156: }

158: void g3_uu_3d(PetscInt dim, PetscInt Nf, PetscInt NfAux,
159:           const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
160:           const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
161:           PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g3[])
162: {
163:   const PetscInt  Ncomp = dim;
164:   const PetscReal mu = PetscRealPart(a[0]), kappa = 3.0;
165:   PetscReal       cofu_x[9/*Ncomp*dim*/], detu_x, pp, pm, p = PetscRealPart(u[Ncomp]);
166:   PetscInt        compI, compJ, d1, d2;

168:   Cof3D(cofu_x, u_x);
169:   Det3D(&detu_x, u_x);
170:   p += kappa * (detu_x - 1.0);
171:   pp = p/detu_x + kappa;
172:   pm = p/detu_x;

174:   /* g3 is the first elasticity tensor, i.e. A_i^I_j^J = S^{IJ} g_{ij} + C^{KILJ} F^k_K F^l_L g_{kj} g_{li} */
175:   for (compI = 0; compI < Ncomp; ++compI) {
176:     for (compJ = 0; compJ < Ncomp; ++compJ) {
177:       const PetscReal G = (compI == compJ) ? 1.0 : 0.0;

179:       for (d1 = 0; d1 < dim; ++d1) {
180:         for (d2 = 0; d2 < dim; ++d2) {
181:           const PetscReal g = (d1 == d2) ? 1.0 : 0.0;

183:           g3[((compI*Ncomp+compJ)*dim+d1)*dim+d2] = g * G * mu + pp * cofu_x[compI*dim+d1] * cofu_x[compJ*dim+d2] - pm * cofu_x[compI*dim+d2] * cofu_x[compJ*dim+d1];
184:         }
185:       }
186:     }
187:   }
188: }

190: void f0_bd_u_3d(PetscInt dim, PetscInt Nf, PetscInt NfAux,
191:     const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
192:     const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
193:     PetscReal t, const PetscReal x[], const PetscReal n[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[])
194: {
195:   const PetscInt    Ncomp = dim;
196:   const PetscScalar p = a[aOff[1]];
197:   PetscReal         cofu_x[9/*Ncomp*dim*/];
198:   PetscInt          comp, d;

200:   Cof3D(cofu_x, u_x);
201:   for (comp = 0; comp < Ncomp; ++comp) {
202:     for (d = 0, f0[comp] = 0.0; d < dim; ++d) f0[comp] += cofu_x[comp*dim+d] * n[d];
203:     f0[comp] *= p;
204:   }
205: }

207: void g1_bd_uu_3d(PetscInt dim, PetscInt Nf, PetscInt NfAux,
208:     const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
209:     const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
210:     PetscReal t, PetscReal u_tShift, const PetscReal x[], const PetscReal n[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g1[])
211: {
212:   const PetscInt Ncomp = dim;
213:   PetscScalar    p = a[aOff[1]];
214:   PetscReal      cofu_x[9/*Ncomp*dim*/], m[3/*Ncomp*/], detu_x;
215:   PetscInt       comp, compI, compJ, d;

217:   Cof3D(cofu_x, u_x);
218:   Det3D(&detu_x, u_x);
219:   p /= detu_x;

221:   for (comp = 0; comp < Ncomp; ++comp) for (d = 0, m[comp] = 0.0; d < dim; ++d) m[comp] += cofu_x[comp*dim+d] * n[d];
222:   for (compI = 0; compI < Ncomp; ++compI) {
223:     for (compJ = 0; compJ < Ncomp; ++compJ) {
224:       for (d = 0; d < dim; ++d) {
225:         g1[(compI*Ncomp+compJ)*dim+d] = p * (m[compI] * cofu_x[compJ*dim+d] - cofu_x[compI*dim+d] * m[compJ]);
226:       }
227:     }
228:   }
229: }

231: void f0_p_3d(PetscInt dim, PetscInt Nf, PetscInt NfAux,
232:           const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
233:           const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
234:           PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[])
235: {
236:   PetscReal detu_x;
237:   Det3D(&detu_x, u_x);
238:   f0[0] = detu_x - 1.0;
239: }

241: void g1_pu_3d(PetscInt dim, PetscInt Nf, PetscInt NfAux,
242:            const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
243:            const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
244:            PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g1[])
245: {
246:   PetscReal cofu_x[9/*Ncomp*dim*/];
247:   PetscInt  compI, d;

249:   Cof3D(cofu_x, u_x);
250:   for (compI = 0; compI < dim; ++compI)
251:     for (d = 0; d < dim; ++d) g1[compI*dim+d] = cofu_x[compI*dim+d];
252: }

254: void g2_up_3d(PetscInt dim, PetscInt Nf, PetscInt NfAux,
255:            const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[],
256:            const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[],
257:            PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g2[])
258: {
259:   PetscReal cofu_x[9/*Ncomp*dim*/];
260:   PetscInt  compI, d;

262:   Cof3D(cofu_x, u_x);
263:   for (compI = 0; compI < dim; ++compI)
264:     for (d = 0; d < dim; ++d) g2[compI*dim+d] = cofu_x[compI*dim+d];
265: }

267: PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options)
268: {
269:   const char    *runTypes[2] = {"full", "test"};
270:   PetscInt       run;

274:   options->debug           = 0;
275:   options->runType         = RUN_FULL;
276:   options->dim             = 3;
277:   options->interpolate     = PETSC_FALSE;
278:   options->simplex         = PETSC_TRUE;
279:   options->refinementLimit = 0.0;
280:   options->mu              = 1.0;
281:   options->p_wall          = 0.4;
282:   options->testPartition   = PETSC_FALSE;
283:   options->showInitial     = PETSC_FALSE;
284:   options->showSolution    = PETSC_TRUE;

286:   PetscOptionsBegin(comm, "", "Nonlinear elasticity problem options", "DMPLEX");
287:   PetscOptionsInt("-debug", "The debugging level", "ex77.c", options->debug, &options->debug, NULL);
288:   run  = options->runType;
289:   PetscOptionsEList("-run_type", "The run type", "ex77.c", runTypes, 2, runTypes[options->runType], &run, NULL);

291:   options->runType = (RunType) run;

293:   PetscOptionsInt("-dim", "The topological mesh dimension", "ex77.c", options->dim, &options->dim, NULL);
294:   PetscOptionsBool("-interpolate", "Generate intermediate mesh elements", "ex77.c", options->interpolate, &options->interpolate, NULL);
295:   PetscOptionsBool("-simplex", "Use simplices or tensor product cells", "ex77.c", options->simplex, &options->simplex, NULL);
296:   PetscOptionsReal("-refinement_limit", "The largest allowable cell volume", "ex77.c", options->refinementLimit, &options->refinementLimit, NULL);
297:   PetscOptionsBool("-test_partition", "Use a fixed partition for testing", "ex77.c", options->testPartition, &options->testPartition, NULL);
298:   PetscOptionsReal("-shear_modulus", "The shear modulus", "ex77.c", options->mu, &options->mu, NULL);
299:   PetscOptionsReal("-wall_pressure", "The wall pressure", "ex77.c", options->p_wall, &options->p_wall, NULL);

301:   PetscOptionsBool("-show_initial", "Output the initial guess for verification", "ex77.c", options->showInitial, &options->showInitial, NULL);
302:   PetscOptionsBool("-show_solution", "Output the solution for verification", "ex77.c", options->showSolution, &options->showSolution, NULL);
303:   PetscOptionsEnd();

305:   PetscLogEventRegister("CreateMesh", DM_CLASSID, &options->createMeshEvent);
306:   return(0);
307: }

309: PetscErrorCode DMVecViewLocal(DM dm, Vec v, PetscViewer viewer)
310: {
311:   Vec            lv;
312:   PetscInt       p;
313:   PetscMPIInt    rank, size;

317:   MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);
318:   MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size);
319:   DMGetLocalVector(dm, &lv);
320:   DMGlobalToLocalBegin(dm, v, INSERT_VALUES, lv);
321:   DMGlobalToLocalEnd(dm, v, INSERT_VALUES, lv);
322:   PetscPrintf(PETSC_COMM_WORLD, "Local function\n");
323:   for (p = 0; p < size; ++p) {
324:     if (p == rank) {VecView(lv, PETSC_VIEWER_STDOUT_SELF);}
325:     PetscBarrier((PetscObject) dm);
326:   }
327:   DMRestoreLocalVector(dm, &lv);
328:   return(0);
329: }

331: PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
332: {
333:   PetscInt       dim             = user->dim;
334:   PetscBool      interpolate     = user->interpolate;
335:   PetscReal      refinementLimit = user->refinementLimit;
336:   const PetscInt cells[3]        = {3, 3, 3};

340:   PetscLogEventBegin(user->createMeshEvent,0,0,0,0);
341:   DMPlexCreateBoxMesh(comm, dim, user->simplex, user->simplex ? NULL : cells, NULL, NULL, NULL, interpolate, dm);
342:   /* Label the faces (bit of a hack here, until it is properly implemented for simplices) */
343:   {
344:     DM              cdm;
345:     DMLabel         label;
346:     IS              is;
347:     PetscInt        d, dim = user->dim, b, f, Nf;
348:     const PetscInt *faces;
349:     PetscInt        csize;
350:     PetscScalar    *coords = NULL;
351:     PetscSection    cs;
352:     Vec             coordinates ;

354:     DMCreateLabel(*dm, "boundary");
355:     DMGetLabel(*dm, "boundary", &label);
356:     DMPlexMarkBoundaryFaces(*dm, 1, label);
357:     DMGetStratumIS(*dm, "boundary", 1,  &is);
358:     if (is) {
359:       PetscReal faceCoord;
360:       PetscInt  v;

362:       ISGetLocalSize(is, &Nf);
363:       ISGetIndices(is, &faces);

365:       DMGetCoordinatesLocal(*dm, &coordinates);
366:       DMGetCoordinateDM(*dm, &cdm);
367:       DMGetLocalSection(cdm, &cs);

369:       /* Check for each boundary face if any component of its centroid is either 0.0 or 1.0 */
370:       for (f = 0; f < Nf; ++f) {
371:         DMPlexVecGetClosure(cdm, cs, coordinates, faces[f], &csize, &coords);
372:         /* Calculate mean coordinate vector */
373:         for (d = 0; d < dim; ++d) {
374:           const PetscInt Nv = csize/dim;
375:           faceCoord = 0.0;
376:           for (v = 0; v < Nv; ++v) faceCoord += PetscRealPart(coords[v*dim+d]);
377:           faceCoord /= Nv;
378:           for (b = 0; b < 2; ++b) {
379:             if (PetscAbs(faceCoord - b*1.0) < PETSC_SMALL) {
380:               DMSetLabelValue(*dm, "Faces", faces[f], d*2+b+1);
381:             }
382:           }
383:         }
384:         DMPlexVecRestoreClosure(cdm, cs, coordinates, faces[f], &csize, &coords);
385:       }
386:       ISRestoreIndices(is, &faces);
387:     }
388:     ISDestroy(&is);
389:   }
390:   {
391:     DM refinedMesh     = NULL;
392:     DM distributedMesh = NULL;
393:     PetscPartitioner part;

395:     DMPlexGetPartitioner(*dm, &part);

397:     /* Refine mesh using a volume constraint */
398:     DMPlexSetRefinementLimit(*dm, refinementLimit);
399:     if (user->simplex) {DMRefine(*dm, comm, &refinedMesh);}
400:     if (refinedMesh) {
401:       DMDestroy(dm);
402:       *dm  = refinedMesh;
403:     }
404:     /* Setup test partitioning */
405:     if (user->testPartition) {
406:       PetscInt         triSizes_n2[2]       = {4, 4};
407:       PetscInt         triPoints_n2[8]      = {3, 5, 6, 7, 0, 1, 2, 4};
408:       PetscInt         triSizes_n3[3]       = {2, 3, 3};
409:       PetscInt         triPoints_n3[8]      = {3, 5, 1, 6, 7, 0, 2, 4};
410:       PetscInt         triSizes_n5[5]       = {1, 2, 2, 1, 2};
411:       PetscInt         triPoints_n5[8]      = {3, 5, 6, 4, 7, 0, 1, 2};
412:       PetscInt         triSizes_ref_n2[2]   = {8, 8};
413:       PetscInt         triPoints_ref_n2[16] = {1, 5, 6, 7, 10, 11, 14, 15, 0, 2, 3, 4, 8, 9, 12, 13};
414:       PetscInt         triSizes_ref_n3[3]   = {5, 6, 5};
415:       PetscInt         triPoints_ref_n3[16] = {1, 7, 10, 14, 15, 2, 6, 8, 11, 12, 13, 0, 3, 4, 5, 9};
416:       PetscInt         triSizes_ref_n5[5]   = {3, 4, 3, 3, 3};
417:       PetscInt         triPoints_ref_n5[16] = {1, 7, 10, 2, 11, 13, 14, 5, 6, 15, 0, 8, 9, 3, 4, 12};
418:       PetscInt         tetSizes_n2[2]       = {3, 3};
419:       PetscInt         tetPoints_n2[6]      = {1, 2, 3, 0, 4, 5};
420:       const PetscInt  *sizes = NULL;
421:       const PetscInt  *points = NULL;
422:       PetscInt         cEnd;
423:       PetscMPIInt      rank, size;

425:       MPI_Comm_rank(comm, &rank);
426:       MPI_Comm_size(comm, &size);
427:       DMPlexGetHeightStratum(*dm, 0, NULL, &cEnd);
428:       if (!rank) {
429:         if (dim == 2 && user->simplex && size == 2 && cEnd == 8) {
430:            sizes = triSizes_n2; points = triPoints_n2;
431:         } else if (dim == 2 && user->simplex && size == 3 && cEnd == 8) {
432:           sizes = triSizes_n3; points = triPoints_n3;
433:         } else if (dim == 2 && user->simplex && size == 5 && cEnd == 8) {
434:           sizes = triSizes_n5; points = triPoints_n5;
435:         } else if (dim == 2 && user->simplex && size == 2 && cEnd == 16) {
436:            sizes = triSizes_ref_n2; points = triPoints_ref_n2;
437:         } else if (dim == 2 && user->simplex && size == 3 && cEnd == 16) {
438:           sizes = triSizes_ref_n3; points = triPoints_ref_n3;
439:         } else if (dim == 2 && user->simplex && size == 5 && cEnd == 16) {
440:           sizes = triSizes_ref_n5; points = triPoints_ref_n5;
441:         } else if (dim == 3 && user->simplex && size == 2 && cEnd == 6) {
442:           sizes = tetSizes_n2; points = tetPoints_n2;
443:         } else SETERRQ(comm, PETSC_ERR_ARG_WRONG, "No stored partition matching run parameters");
444:       }
445:       PetscPartitionerSetType(part, PETSCPARTITIONERSHELL);
446:       PetscPartitionerShellSetPartition(part, size, sizes, points);
447:     } else {
448:       PetscPartitionerSetFromOptions(part);
449:     }
450:     /* Distribute mesh over processes */
451:     DMPlexDistribute(*dm, 0, NULL, &distributedMesh);
452:     if (distributedMesh) {
453:       DMDestroy(dm);
454:       *dm  = distributedMesh;
455:     }
456:   }
457:   DMSetFromOptions(*dm);
458:   DMViewFromOptions(*dm, NULL, "-dm_view");

460:   PetscLogEventEnd(user->createMeshEvent,0,0,0,0);
461:   return(0);
462: }

464: PetscErrorCode SetupProblem(DM dm, PetscInt dim, AppCtx *user)
465: {
466:   PetscDS        ds;
467:   PetscWeakForm  wf;
468:   DMLabel        label;
469:   PetscInt       bd;

473:   DMGetDS(dm, &ds);
474:   PetscDSSetResidual(ds, 0, NULL, f1_u_3d);
475:   PetscDSSetResidual(ds, 1, f0_p_3d, NULL);
476:   PetscDSSetJacobian(ds, 0, 0, NULL, NULL,  NULL,  g3_uu_3d);
477:   PetscDSSetJacobian(ds, 0, 1, NULL, NULL,  g2_up_3d, NULL);
478:   PetscDSSetJacobian(ds, 1, 0, NULL, g1_pu_3d, NULL,  NULL);

480:   DMGetLabel(dm, "Faces", &label);
481:   DMAddBoundary(dm, DM_BC_NATURAL, "pressure", label, 0, NULL, 0, 0, NULL, NULL, NULL, user, &bd);
482:   PetscDSGetBoundary(ds, bd, &wf, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL);
483:   PetscWeakFormSetIndexBdResidual(wf, label, 1, 0, 0, f0_bd_u_3d, 0, NULL);
484:   PetscWeakFormSetIndexBdJacobian(wf, label, 1, 0, 0, 0, NULL, 0, g1_bd_uu_3d, 0, NULL, 0, NULL);

486:   DMAddBoundary(dm, DM_BC_ESSENTIAL, "fixed", label, 0, NULL, 0, 0, NULL, (void (*)(void)) coordinates, NULL, user, NULL);
487:   return(0);
488: }

490: PetscErrorCode SetupMaterial(DM dm, DM dmAux, AppCtx *user)
491: {
492:   PetscErrorCode (*matFuncs[2])(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar u[], void *ctx) = {elasticityMaterial, wallPressure};
493:   Vec            A;
494:   void          *ctxs[2];

498:   ctxs[0] = user; ctxs[1] = user;
499:   DMCreateLocalVector(dmAux, &A);
500:   DMProjectFunctionLocal(dmAux, 0.0, matFuncs, ctxs, INSERT_ALL_VALUES, A);
501:   DMSetAuxiliaryVec(dm, NULL, 0, A);
502:   VecDestroy(&A);
503:   return(0);
504: }

506: PetscErrorCode SetupNearNullSpace(DM dm, AppCtx *user)
507: {
508:   /* Set up the near null space (a.k.a. rigid body modes) that will be used by the multigrid preconditioner */
509:   DM             subdm;
510:   MatNullSpace   nearNullSpace;
511:   PetscInt       fields = 0;
512:   PetscObject    deformation;

516:   DMCreateSubDM(dm, 1, &fields, NULL, &subdm);
517:   DMPlexCreateRigidBody(subdm, 0, &nearNullSpace);
518:   DMGetField(dm, 0, NULL, &deformation);
519:   PetscObjectCompose(deformation, "nearnullspace", (PetscObject) nearNullSpace);
520:   DMDestroy(&subdm);
521:   MatNullSpaceDestroy(&nearNullSpace);
522:   return(0);
523: }

525: static PetscErrorCode SetupAuxDM(DM dm, PetscInt NfAux, PetscFE feAux[], AppCtx *user)
526: {
527:   DM             dmAux, coordDM;
528:   PetscInt       f;

532:   /* MUST call DMGetCoordinateDM() in order to get p4est setup if present */
533:   DMGetCoordinateDM(dm, &coordDM);
534:   if (!feAux) return(0);
535:   DMClone(dm, &dmAux);
536:   DMSetCoordinateDM(dmAux, coordDM);
537:   for (f = 0; f < NfAux; ++f) {DMSetField(dmAux, f, NULL, (PetscObject) feAux[f]);}
538:   DMCreateDS(dmAux);
539:   SetupMaterial(dm, dmAux, user);
540:   DMDestroy(&dmAux);
541:   return(0);
542: }

544: PetscErrorCode SetupDiscretization(DM dm, AppCtx *user)
545: {
546:   DM              cdm   = dm;
547:   const PetscInt  dim   = user->dim;
548:   const PetscBool simplex = user->simplex;
549:   PetscFE         fe[2], feAux[2];
550:   MPI_Comm        comm;
551:   PetscErrorCode  ierr;

554:   PetscObjectGetComm((PetscObject) dm, &comm);
555:   /* Create finite element */
556:   PetscFECreateDefault(comm, dim, dim, simplex, "def_", PETSC_DEFAULT, &fe[0]);
557:   PetscObjectSetName((PetscObject) fe[0], "deformation");
558:   PetscFECreateDefault(comm, dim, 1, simplex, "pres_", PETSC_DEFAULT, &fe[1]);
559:   PetscFECopyQuadrature(fe[0], fe[1]);

561:   PetscObjectSetName((PetscObject) fe[1], "pressure");

563:   PetscFECreateDefault(comm, dim, 1, simplex, "elastMat_", PETSC_DEFAULT, &feAux[0]);
564:   PetscObjectSetName((PetscObject) feAux[0], "elasticityMaterial");
565:   PetscFECopyQuadrature(fe[0], feAux[0]);
566:   /* It is not yet possible to define a field on a submesh (e.g. a boundary), so we will use a normal finite element */
567:   PetscFECreateDefault(comm, dim, 1, simplex, "wall_pres_", PETSC_DEFAULT, &feAux[1]);
568:   PetscObjectSetName((PetscObject) feAux[1], "wall_pressure");
569:   PetscFECopyQuadrature(fe[0], feAux[1]);

571:   /* Set discretization and boundary conditions for each mesh */
572:   DMSetField(dm, 0, NULL, (PetscObject) fe[0]);
573:   DMSetField(dm, 1, NULL, (PetscObject) fe[1]);
574:   DMCreateDS(dm);
575:   SetupProblem(dm, dim, user);
576:   while (cdm) {
577:     SetupAuxDM(cdm, 2, feAux, user);
578:     DMCopyDisc(dm, cdm);
579:     DMGetCoarseDM(cdm, &cdm);
580:   }
581:   PetscFEDestroy(&fe[0]);
582:   PetscFEDestroy(&fe[1]);
583:   PetscFEDestroy(&feAux[0]);
584:   PetscFEDestroy(&feAux[1]);
585:   return(0);
586: }


589: int main(int argc, char **argv)
590: {
591:   SNES           snes;                 /* nonlinear solver */
592:   DM             dm;                   /* problem definition */
593:   Vec            u,r;                  /* solution, residual vectors */
594:   Mat            A,J;                  /* Jacobian matrix */
595:   AppCtx         user;                 /* user-defined work context */
596:   PetscInt       its;                  /* iterations for convergence */

599:   PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
600:   ProcessOptions(PETSC_COMM_WORLD, &user);
601:   SNESCreate(PETSC_COMM_WORLD, &snes);
602:   CreateMesh(PETSC_COMM_WORLD, &user, &dm);
603:   SNESSetDM(snes, dm);
604:   DMSetApplicationContext(dm, &user);

606:   SetupDiscretization(dm, &user);
607:   DMPlexCreateClosureIndex(dm, NULL);
608:   SetupNearNullSpace(dm, &user);

610:   DMCreateGlobalVector(dm, &u);
611:   VecDuplicate(u, &r);

613:   DMSetMatType(dm,MATAIJ);
614:   DMCreateMatrix(dm, &J);
615:   A = J;

617:   DMPlexSetSNESLocalFEM(dm,&user,&user,&user);
618:   SNESSetJacobian(snes, A, J, NULL, NULL);

620:   SNESSetFromOptions(snes);

622:   {
623:     PetscErrorCode (*initialGuess[2])(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void* ctx);
624:     initialGuess[0] = coordinates; initialGuess[1] = zero_scalar;
625:     DMProjectFunction(dm, 0.0, initialGuess, NULL, INSERT_VALUES, u);
626:   }
627:   if (user.showInitial) {DMVecViewLocal(dm, u, PETSC_VIEWER_STDOUT_SELF);}

629:   if (user.runType == RUN_FULL) {
630:     if (user.debug) {
631:       PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");
632:       VecView(u, PETSC_VIEWER_STDOUT_WORLD);
633:     }
634:     SNESSolve(snes, NULL, u);
635:     SNESGetIterationNumber(snes, &its);
636:     PetscPrintf(PETSC_COMM_WORLD, "Number of SNES iterations = %D\n", its);
637:     if (user.showSolution) {
638:       PetscPrintf(PETSC_COMM_WORLD, "Solution\n");
639:       VecChop(u, 3.0e-9);
640:       VecView(u, PETSC_VIEWER_STDOUT_WORLD);
641:     }
642:   } else {
643:     PetscReal res = 0.0;

645:     /* Check initial guess */
646:     PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");
647:     VecView(u, PETSC_VIEWER_STDOUT_WORLD);
648:     /* Check residual */
649:     SNESComputeFunction(snes, u, r);
650:     PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");
651:     VecChop(r, 1.0e-10);
652:     VecView(r, PETSC_VIEWER_STDOUT_WORLD);
653:     VecNorm(r, NORM_2, &res);
654:     PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", (double)res);
655:     /* Check Jacobian */
656:     {
657:       Vec b;

659:       SNESComputeJacobian(snes, u, A, A);
660:       VecDuplicate(u, &b);
661:       VecSet(r, 0.0);
662:       SNESComputeFunction(snes, r, b);
663:       MatMult(A, u, r);
664:       VecAXPY(r, 1.0, b);
665:       VecDestroy(&b);
666:       PetscPrintf(PETSC_COMM_WORLD, "Au - b = Au + F(0)\n");
667:       VecChop(r, 1.0e-10);
668:       VecView(r, PETSC_VIEWER_STDOUT_WORLD);
669:       VecNorm(r, NORM_2, &res);
670:       PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", (double)res);
671:     }
672:   }
673:   VecViewFromOptions(u, NULL, "-sol_vec_view");

675:   if (A != J) {MatDestroy(&A);}
676:   MatDestroy(&J);
677:   VecDestroy(&u);
678:   VecDestroy(&r);
679:   SNESDestroy(&snes);
680:   DMDestroy(&dm);
681:   PetscFinalize();
682:   return ierr;
683: }

685: /*TEST

687:   build:
688:     requires: !complex

690:   test:
691:     suffix: 0
692:     requires: ctetgen !single
693:     args: -run_type full -dim 3 -dm_refine 2 -interpolate 1 -bc_fixed 1 -bc_pressure 2 -wall_pressure 0.4 -def_petscspace_degree 2 -pres_petscspace_degree 1 -elastMat_petscspace_degree 0 -wall_pres_petscspace_degree 0 -snes_rtol 1e-05 -ksp_type fgmres -ksp_rtol 1e-10 -pc_type fieldsplit -pc_fieldsplit_type schur -pc_fieldsplit_schur_factorization_type upper -fieldsplit_deformation_ksp_type preonly -fieldsplit_deformation_pc_type lu -fieldsplit_pressure_ksp_rtol 1e-10 -fieldsplit_pressure_pc_type jacobi -snes_monitor_short -ksp_monitor_short -snes_converged_reason -ksp_converged_reason -show_solution 0

695:   test:
696:     suffix: 1
697:     requires: ctetgen superlu_dist
698:     nsize: 2
699:     args: -run_type full -dim 3 -dm_refine 0 -interpolate 1 -test_partition -bc_fixed 1 -bc_pressure 2 -wall_pressure 0.4 -def_petscspace_degree 2 -pres_petscspace_degree 1 -elastMat_petscspace_degree 0 -wall_pres_petscspace_degree 0 -snes_rtol 1e-05 -ksp_type fgmres -ksp_rtol 1e-10 -pc_type fieldsplit -pc_fieldsplit_type schur -pc_fieldsplit_schur_factorization_type upper -fieldsplit_deformation_ksp_type preonly -fieldsplit_deformation_pc_type lu -fieldsplit_pressure_ksp_rtol 1e-10 -fieldsplit_pressure_pc_type jacobi -snes_monitor_short -ksp_monitor_short -snes_converged_reason -ksp_converged_reason -show_solution 0
700:     timeoutfactor: 2

702:   test:
703:     suffix: 2
704:     requires: ctetgen !single
705:     args: -run_type full -dim 3 -dm_refine 2 -interpolate 1 -bc_fixed 3,4,5,6 -bc_pressure 2 -wall_pressure 1.0 -def_petscspace_degree 2 -pres_petscspace_degree 1 -elastMat_petscspace_degree 0 -wall_pres_petscspace_degree 0 -snes_rtol 1e-05 -ksp_type fgmres -ksp_rtol 1e-10 -pc_type fieldsplit -pc_fieldsplit_type schur -pc_fieldsplit_schur_factorization_type upper -fieldsplit_deformation_ksp_type preonly -fieldsplit_deformation_pc_type lu -fieldsplit_pressure_ksp_rtol 1e-10 -fieldsplit_pressure_pc_type jacobi -snes_monitor_short -ksp_monitor_short -snes_converged_reason -ksp_converged_reason -show_solution 0

707:   test:
708:     requires: ctetgen superlu_dist
709:     suffix: 4
710:     nsize: 2
711:     args: -run_type full -dim 3 -dm_refine 0 -interpolate 1 -test_partition -bc_fixed 1 -bc_pressure 2 -wall_pressure 0.4 -def_petscspace_degree 2 -pres_petscspace_degree 1 -elastMat_petscspace_degree 0 -wall_pres_petscspace_degree 0 -snes_rtol 1e-05 -ksp_type fgmres -ksp_rtol 1e-10 -pc_type fieldsplit -pc_fieldsplit_type schur -pc_fieldsplit_schur_factorization_type upper -fieldsplit_deformation_ksp_type preonly -fieldsplit_deformation_pc_type lu -fieldsplit_pressure_ksp_rtol 1e-10 -fieldsplit_pressure_pc_type jacobi -snes_monitor_short -ksp_monitor_short -snes_converged_reason -ksp_converged_reason -show_solution 0
712:     output_file: output/ex77_1.out

714:   test:
715:     requires: ctetgen !single
716:     suffix: 3
717:     args: -run_type full -dim 3 -dm_refine 2 -interpolate 1 -bc_fixed 3,4,5,6 -bc_pressure 2 -wall_pressure 1.0 -def_petscspace_degree 2 -pres_petscspace_degree 1 -elastMat_petscspace_degree 0 -wall_pres_petscspace_degree 0 -snes_rtol 1e-05 -ksp_type fgmres -ksp_rtol 1e-10 -pc_type fieldsplit -pc_fieldsplit_type schur -pc_fieldsplit_schur_factorization_type upper -fieldsplit_deformation_ksp_type preonly -fieldsplit_deformation_pc_type lu -fieldsplit_pressure_ksp_rtol 1e-10 -fieldsplit_pressure_pc_type jacobi -snes_monitor_short -ksp_monitor_short -snes_converged_reason -ksp_converged_reason -show_solution 0
718:     output_file: output/ex77_2.out

720:   #TODO: this example deadlocks for me when using ParMETIS
721:   test:
722:     requires: ctetgen superlu_dist !single
723:     suffix: 2_par
724:     nsize: 4
725:     args: -run_type full -dim 3 -dm_refine 2 -interpolate 1 -bc_fixed 3,4,5,6 -bc_pressure 2 -wall_pressure 1.0 -def_petscspace_degree 2 -pres_petscspace_degree 1 -elastMat_petscspace_degree 0 -wall_pres_petscspace_degree 0 -snes_rtol 1e-05 -ksp_type fgmres -ksp_rtol 1e-10 -pc_type fieldsplit -pc_fieldsplit_type schur -pc_fieldsplit_schur_factorization_type upper -fieldsplit_deformation_ksp_type preonly -fieldsplit_deformation_pc_type lu -fieldsplit_pressure_ksp_rtol 1e-10 -fieldsplit_pressure_pc_type jacobi -snes_monitor_short -ksp_monitor_short -snes_converged_reason -ksp_converged_reason -show_solution 0 -petscpartitioner_type simple
726:     output_file: output/ex77_2.out

728: TEST*/