1 static char help[] = "Tests for cell geometry\n\n"; 2 3 #include <petscdmplex.h> 4 5 typedef enum {RUN_REFERENCE, RUN_HEX_CURVED, RUN_FILE, RUN_DISPLAY} RunType; 6 7 typedef struct { 8 DM dm; 9 RunType runType; /* Type of mesh to use */ 10 PetscBool transform; /* Use random coordinate transformations */ 11 /* Data for input meshes */ 12 PetscReal *v0, *J, *invJ, *detJ; /* FEM data */ 13 PetscReal *centroid, *normal, *vol; /* FVM data */ 14 } AppCtx; 15 16 static PetscErrorCode ReadMesh(MPI_Comm comm, AppCtx *user, DM *dm) 17 { 18 PetscFunctionBegin; 19 PetscCall(DMCreate(comm, dm)); 20 PetscCall(DMSetType(*dm, DMPLEX)); 21 PetscCall(DMSetFromOptions(*dm)); 22 PetscCall(DMSetApplicationContext(*dm, user)); 23 PetscCall(PetscObjectSetName((PetscObject) *dm, "Input Mesh")); 24 PetscCall(DMViewFromOptions(*dm, NULL, "-dm_view")); 25 PetscFunctionReturn(0); 26 } 27 28 static PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options) 29 { 30 const char *runTypes[4] = {"reference", "hex_curved", "file", "display"}; 31 PetscInt run; 32 33 PetscFunctionBeginUser; 34 options->runType = RUN_REFERENCE; 35 options->transform = PETSC_FALSE; 36 37 PetscOptionsBegin(comm, "", "Geometry Test Options", "DMPLEX"); 38 run = options->runType; 39 PetscCall(PetscOptionsEList("-run_type", "The run type", "ex8.c", runTypes, 3, runTypes[options->runType], &run, NULL)); 40 options->runType = (RunType) run; 41 PetscCall(PetscOptionsBool("-transform", "Use random transforms", "ex8.c", options->transform, &options->transform, NULL)); 42 43 if (options->runType == RUN_FILE) { 44 PetscInt dim, cStart, cEnd, numCells, n; 45 PetscBool flg, feFlg; 46 47 PetscCall(ReadMesh(PETSC_COMM_WORLD, options, &options->dm)); 48 PetscCall(DMGetDimension(options->dm, &dim)); 49 PetscCall(DMPlexGetHeightStratum(options->dm, 0, &cStart, &cEnd)); 50 numCells = cEnd-cStart; 51 PetscCall(PetscMalloc4(numCells*dim, &options->v0, numCells*dim*dim, &options->J, numCells*dim*dim, &options->invJ, numCells, &options->detJ)); 52 PetscCall(PetscMalloc1(numCells*dim, &options->centroid)); 53 PetscCall(PetscMalloc1(numCells*dim, &options->normal)); 54 PetscCall(PetscMalloc1(numCells, &options->vol)); 55 n = numCells*dim; 56 PetscCall(PetscOptionsRealArray("-v0", "Input v0 for each cell", "ex8.c", options->v0, &n, &feFlg)); 57 PetscCheck(!feFlg || n == numCells*dim, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Invalid size of v0 %" PetscInt_FMT " should be %" PetscInt_FMT, n, numCells*dim); 58 n = numCells*dim*dim; 59 PetscCall(PetscOptionsRealArray("-J", "Input Jacobian for each cell", "ex8.c", options->J, &n, &flg)); 60 PetscCheck(!flg || n == numCells*dim*dim, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Invalid size of J %" PetscInt_FMT " should be %" PetscInt_FMT, n, numCells*dim*dim); 61 n = numCells*dim*dim; 62 PetscCall(PetscOptionsRealArray("-invJ", "Input inverse Jacobian for each cell", "ex8.c", options->invJ, &n, &flg)); 63 PetscCheck(!flg || n == numCells*dim*dim, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Invalid size of invJ %" PetscInt_FMT " should be %" PetscInt_FMT, n, numCells*dim*dim); 64 n = numCells; 65 PetscCall(PetscOptionsRealArray("-detJ", "Input Jacobian determinant for each cell", "ex8.c", options->detJ, &n, &flg)); 66 PetscCheck(!flg || n == numCells, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Invalid size of detJ %" PetscInt_FMT " should be %" PetscInt_FMT, n, numCells); 67 n = numCells*dim; 68 if (!feFlg) { 69 PetscCall(PetscFree4(options->v0, options->J, options->invJ, options->detJ)); 70 options->v0 = options->J = options->invJ = options->detJ = NULL; 71 } 72 PetscCall(PetscOptionsRealArray("-centroid", "Input centroid for each cell", "ex8.c", options->centroid, &n, &flg)); 73 PetscCheck(!flg || n == numCells*dim, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Invalid size of centroid %" PetscInt_FMT " should be %" PetscInt_FMT, n, numCells*dim); 74 if (!flg) { 75 PetscCall(PetscFree(options->centroid)); 76 options->centroid = NULL; 77 } 78 n = numCells*dim; 79 PetscCall(PetscOptionsRealArray("-normal", "Input normal for each cell", "ex8.c", options->normal, &n, &flg)); 80 PetscCheck(!flg || n == numCells*dim, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Invalid size of normal %" PetscInt_FMT " should be %" PetscInt_FMT, n, numCells*dim); 81 if (!flg) { 82 PetscCall(PetscFree(options->normal)); 83 options->normal = NULL; 84 } 85 n = numCells; 86 PetscCall(PetscOptionsRealArray("-vol", "Input volume for each cell", "ex8.c", options->vol, &n, &flg)); 87 PetscCheck(!flg || n == numCells, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Invalid size of vol %" PetscInt_FMT " should be %" PetscInt_FMT, n, numCells); 88 if (!flg) { 89 PetscCall(PetscFree(options->vol)); 90 options->vol = NULL; 91 } 92 } else if (options->runType == RUN_DISPLAY) { 93 PetscCall(ReadMesh(PETSC_COMM_WORLD, options, &options->dm)); 94 } 95 PetscOptionsEnd(); 96 97 if (options->transform) PetscCall(PetscPrintf(comm, "Using random transforms\n")); 98 PetscFunctionReturn(0); 99 } 100 101 static PetscErrorCode ChangeCoordinates(DM dm, PetscInt spaceDim, PetscScalar vertexCoords[]) 102 { 103 PetscSection coordSection; 104 Vec coordinates; 105 PetscScalar *coords; 106 PetscInt vStart, vEnd, v, d, coordSize; 107 108 PetscFunctionBegin; 109 PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd)); 110 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 111 PetscCall(PetscSectionSetNumFields(coordSection, 1)); 112 PetscCall(PetscSectionSetFieldComponents(coordSection, 0, spaceDim)); 113 PetscCall(PetscSectionSetChart(coordSection, vStart, vEnd)); 114 for (v = vStart; v < vEnd; ++v) { 115 PetscCall(PetscSectionSetDof(coordSection, v, spaceDim)); 116 PetscCall(PetscSectionSetFieldDof(coordSection, v, 0, spaceDim)); 117 } 118 PetscCall(PetscSectionSetUp(coordSection)); 119 PetscCall(PetscSectionGetStorageSize(coordSection, &coordSize)); 120 PetscCall(VecCreate(PETSC_COMM_SELF, &coordinates)); 121 PetscCall(PetscObjectSetName((PetscObject) coordinates, "coordinates")); 122 PetscCall(VecSetSizes(coordinates, coordSize, PETSC_DETERMINE)); 123 PetscCall(VecSetFromOptions(coordinates)); 124 PetscCall(VecGetArray(coordinates, &coords)); 125 for (v = vStart; v < vEnd; ++v) { 126 PetscInt off; 127 128 PetscCall(PetscSectionGetOffset(coordSection, v, &off)); 129 for (d = 0; d < spaceDim; ++d) { 130 coords[off+d] = vertexCoords[(v-vStart)*spaceDim+d]; 131 } 132 } 133 PetscCall(VecRestoreArray(coordinates, &coords)); 134 PetscCall(DMSetCoordinateDim(dm, spaceDim)); 135 PetscCall(DMSetCoordinatesLocal(dm, coordinates)); 136 PetscCall(VecDestroy(&coordinates)); 137 PetscCall(DMViewFromOptions(dm, NULL, "-dm_view")); 138 PetscFunctionReturn(0); 139 } 140 141 #define RelativeError(a,b) PetscAbs(a-b)/(1.0+PetscMax(PetscAbs(a),PetscAbs(b))) 142 143 static PetscErrorCode CheckFEMGeometry(DM dm, PetscInt cell, PetscInt spaceDim, PetscReal v0Ex[], PetscReal JEx[], PetscReal invJEx[], PetscReal detJEx) 144 { 145 PetscReal v0[3], J[9], invJ[9], detJ; 146 PetscInt d, i, j; 147 148 PetscFunctionBegin; 149 PetscCall(DMPlexComputeCellGeometryFEM(dm, cell, NULL, v0, J, invJ, &detJ)); 150 for (d = 0; d < spaceDim; ++d) { 151 if (v0[d] != v0Ex[d]) { 152 switch (spaceDim) { 153 case 2: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid v0 (%g, %g) != (%g, %g)", (double)v0[0], (double)v0[1], (double)v0Ex[0], (double)v0Ex[1]); 154 case 3: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid v0 (%g, %g, %g) != (%g, %g, %g)", (double)v0[0], (double)v0[1], (double)v0[2], (double)v0Ex[0], (double)v0Ex[1], (double)v0Ex[2]); 155 default: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid space dimension %" PetscInt_FMT, spaceDim); 156 } 157 } 158 } 159 for (i = 0; i < spaceDim; ++i) { 160 for (j = 0; j < spaceDim; ++j) { 161 PetscCheck(RelativeError(J[i*spaceDim+j], JEx[i*spaceDim+j]) < 10*PETSC_SMALL, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid J[%" PetscInt_FMT ",%" PetscInt_FMT "]: %g != %g", i, j, (double)J[i*spaceDim+j], (double)JEx[i*spaceDim+j]); 162 PetscCheck(RelativeError(invJ[i*spaceDim+j], invJEx[i*spaceDim+j]) < 10*PETSC_SMALL, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid invJ[%" PetscInt_FMT ",%" PetscInt_FMT "]: %g != %g", i, j, (double)invJ[i*spaceDim+j], (double)invJEx[i*spaceDim+j]); 163 } 164 } 165 PetscCheck(RelativeError(detJ, detJEx) < 10*PETSC_SMALL, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid |J| = %g != %g diff %g", (double)detJ, (double)detJEx,(double)(detJ - detJEx)); 166 PetscFunctionReturn(0); 167 } 168 169 static PetscErrorCode CheckFVMGeometry(DM dm, PetscInt cell, PetscInt spaceDim, PetscReal centroidEx[], PetscReal normalEx[], PetscReal volEx) 170 { 171 PetscReal tol = PetscMax(10*PETSC_SMALL, 1e-10); 172 PetscReal centroid[3], normal[3], vol; 173 PetscInt d; 174 175 PetscFunctionBegin; 176 PetscCall(DMPlexComputeCellGeometryFVM(dm, cell, volEx? &vol : NULL, centroidEx? centroid : NULL, normalEx? normal : NULL)); 177 for (d = 0; d < spaceDim; ++d) { 178 if (centroidEx) 179 PetscCheck(RelativeError(centroid[d], centroidEx[d]) < tol, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Cell %" PetscInt_FMT ", Invalid centroid[%" PetscInt_FMT "]: %g != %g diff %g", cell, d, (double)centroid[d], (double)centroidEx[d],(double)(centroid[d]-centroidEx[d])); 180 if (normalEx) 181 PetscCheck(RelativeError(normal[d], normalEx[d]) < tol, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Cell %" PetscInt_FMT ", Invalid normal[%" PetscInt_FMT "]: %g != %g", cell, d, (double) normal[d], (double) normalEx[d]); 182 } 183 if (volEx) 184 PetscCheck(RelativeError(volEx, vol) < tol, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Cell %" PetscInt_FMT ", Invalid volume = %g != %g diff %g", cell, (double)vol, (double)volEx,(double)(vol - volEx)); 185 PetscFunctionReturn(0); 186 } 187 188 static PetscErrorCode CheckGaussLaw(DM dm, PetscInt cell) 189 { 190 DMPolytopeType ct; 191 PetscReal tol = PetscMax(10*PETSC_SMALL, 1e-10); 192 PetscReal normal[3], integral[3] = {0., 0., 0.}, area; 193 const PetscInt *cone, *ornt; 194 PetscInt coneSize, f, dim, cdim, d; 195 196 PetscFunctionBegin; 197 PetscCall(DMGetDimension(dm, &dim)); 198 PetscCall(DMGetCoordinateDim(dm, &cdim)); 199 if (dim != cdim) PetscFunctionReturn(0); 200 PetscCall(DMPlexGetCellType(dm, cell, &ct)); 201 if (ct == DM_POLYTOPE_TRI_PRISM_TENSOR) PetscFunctionReturn(0); 202 PetscCall(DMPlexGetConeSize(dm, cell, &coneSize)); 203 PetscCall(DMPlexGetCone(dm, cell, &cone)); 204 PetscCall(DMPlexGetConeOrientation(dm, cell, &ornt)); 205 for (f = 0; f < coneSize; ++f) { 206 const PetscInt sgn = dim == 1? (f == 0 ? -1 : 1) : (ornt[f] < 0 ? -1 : 1); 207 208 PetscCall(DMPlexComputeCellGeometryFVM(dm, cone[f], &area, NULL, normal)); 209 for (d = 0; d < cdim; ++d) integral[d] += sgn*area*normal[d]; 210 } 211 for (d = 0; d < cdim; ++d) PetscCheck(PetscAbsReal(integral[d]) < tol, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Cell %" PetscInt_FMT " Surface integral for component %" PetscInt_FMT ": %g != 0. as it should be for a constant field", cell, d, (double) integral[d]); 212 PetscFunctionReturn(0); 213 } 214 215 static PetscErrorCode CheckCell(DM dm, PetscInt cell, PetscBool transform, PetscReal v0Ex[], PetscReal JEx[], PetscReal invJEx[], PetscReal detJEx, PetscReal centroidEx[], PetscReal normalEx[], PetscReal volEx, PetscReal faceCentroidEx[], PetscReal faceNormalEx[], PetscReal faceVolEx[]) 216 { 217 const PetscInt *cone; 218 PetscInt coneSize, c; 219 PetscInt dim, depth, cdim; 220 221 PetscFunctionBegin; 222 PetscCall(DMPlexGetDepth(dm, &depth)); 223 PetscCall(DMGetDimension(dm, &dim)); 224 PetscCall(DMGetCoordinateDim(dm, &cdim)); 225 if (v0Ex) PetscCall(CheckFEMGeometry(dm, cell, cdim, v0Ex, JEx, invJEx, detJEx)); 226 if (dim == depth && centroidEx) { 227 PetscCall(CheckFVMGeometry(dm, cell, cdim, centroidEx, normalEx, volEx)); 228 PetscCall(CheckGaussLaw(dm, cell)); 229 if (faceCentroidEx) { 230 PetscCall(DMPlexGetConeSize(dm, cell, &coneSize)); 231 PetscCall(DMPlexGetCone(dm, cell, &cone)); 232 for (c = 0; c < coneSize; ++c) { 233 PetscCall(CheckFVMGeometry(dm, cone[c], dim, &faceCentroidEx[c*dim], &faceNormalEx[c*dim], faceVolEx[c])); 234 } 235 } 236 } 237 if (transform) { 238 Vec coordinates; 239 PetscSection coordSection; 240 PetscScalar *coords = NULL, *origCoords, *newCoords; 241 PetscReal *v0ExT, *JExT, *invJExT, detJExT=0, *centroidExT, *normalExT, volExT=0; 242 PetscReal *faceCentroidExT, *faceNormalExT, faceVolExT; 243 PetscRandom r, ang, ang2; 244 PetscInt coordSize, numCorners, t; 245 246 PetscCall(DMGetCoordinatesLocal(dm, &coordinates)); 247 PetscCall(DMGetCoordinateSection(dm, &coordSection)); 248 PetscCall(DMPlexVecGetClosure(dm, coordSection, coordinates, cell, &coordSize, &coords)); 249 PetscCall(PetscMalloc2(coordSize, &origCoords, coordSize, &newCoords)); 250 PetscCall(PetscMalloc5(cdim, &v0ExT, cdim*cdim, &JExT, cdim*cdim, &invJExT, cdim, ¢roidExT, cdim, &normalExT)); 251 PetscCall(PetscMalloc2(cdim, &faceCentroidExT, cdim, &faceNormalExT)); 252 for (c = 0; c < coordSize; ++c) origCoords[c] = coords[c]; 253 PetscCall(DMPlexVecRestoreClosure(dm, coordSection, coordinates, cell, &coordSize, &coords)); 254 numCorners = coordSize/cdim; 255 256 PetscCall(PetscRandomCreate(PETSC_COMM_SELF, &r)); 257 PetscCall(PetscRandomSetFromOptions(r)); 258 PetscCall(PetscRandomSetInterval(r, 0.0, 10.0)); 259 PetscCall(PetscRandomCreate(PETSC_COMM_SELF, &ang)); 260 PetscCall(PetscRandomSetFromOptions(ang)); 261 PetscCall(PetscRandomSetInterval(ang, 0.0, 2*PETSC_PI)); 262 PetscCall(PetscRandomCreate(PETSC_COMM_SELF, &ang2)); 263 PetscCall(PetscRandomSetFromOptions(ang2)); 264 PetscCall(PetscRandomSetInterval(ang2, 0.0, PETSC_PI)); 265 for (t = 0; t < 1; ++t) { 266 PetscScalar trans[3]; 267 PetscReal R[9], rot[3], rotM[9]; 268 PetscReal scale, phi, theta, psi = 0.0, norm; 269 PetscInt d, e, f, p; 270 271 for (c = 0; c < coordSize; ++c) newCoords[c] = origCoords[c]; 272 PetscCall(PetscRandomGetValueReal(r, &scale)); 273 PetscCall(PetscRandomGetValueReal(ang, &phi)); 274 PetscCall(PetscRandomGetValueReal(ang2, &theta)); 275 for (d = 0; d < cdim; ++d) { 276 PetscCall(PetscRandomGetValue(r, &trans[d])); 277 } 278 switch (cdim) { 279 case 2: 280 R[0] = PetscCosReal(phi); R[1] = -PetscSinReal(phi); 281 R[2] = PetscSinReal(phi); R[3] = PetscCosReal(phi); 282 break; 283 case 3: 284 { 285 const PetscReal ct = PetscCosReal(theta), st = PetscSinReal(theta); 286 const PetscReal cp = PetscCosReal(phi), sp = PetscSinReal(phi); 287 const PetscReal cs = PetscCosReal(psi), ss = PetscSinReal(psi); 288 R[0] = ct*cs; R[1] = sp*st*cs - cp*ss; R[2] = sp*ss + cp*st*cs; 289 R[3] = ct*ss; R[4] = cp*cs + sp*st*ss; R[5] = cp*st*ss - sp*cs; 290 R[6] = -st; R[7] = sp*ct; R[8] = cp*ct; 291 break; 292 } 293 default: SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Invalid coordinate dimension %" PetscInt_FMT, cdim); 294 } 295 if (v0Ex) { 296 detJExT = detJEx; 297 for (d = 0; d < cdim; ++d) { 298 v0ExT[d] = v0Ex[d]; 299 for (e = 0; e < cdim; ++e) { 300 JExT[d*cdim+e] = JEx[d*cdim+e]; 301 invJExT[d*cdim+e] = invJEx[d*cdim+e]; 302 } 303 } 304 for (d = 0; d < cdim; ++d) { 305 v0ExT[d] *= scale; 306 v0ExT[d] += PetscRealPart(trans[d]); 307 /* Only scale dimensions in the manifold */ 308 for (e = 0; e < dim; ++e) { 309 JExT[d*cdim+e] *= scale; 310 invJExT[d*cdim+e] /= scale; 311 } 312 if (d < dim) detJExT *= scale; 313 } 314 /* Do scaling and translation before rotation, so that we can leave out the normal dimension for lower dimensional manifolds */ 315 for (d = 0; d < cdim; ++d) { 316 for (e = 0, rot[d] = 0.0; e < cdim; ++e) { 317 rot[d] += R[d*cdim+e] * v0ExT[e]; 318 } 319 } 320 for (d = 0; d < cdim; ++d) v0ExT[d] = rot[d]; 321 for (d = 0; d < cdim; ++d) { 322 for (e = 0; e < cdim; ++e) { 323 for (f = 0, rotM[d*cdim+e] = 0.0; f < cdim; ++f) { 324 rotM[d*cdim+e] += R[d*cdim+f] * JExT[f*cdim+e]; 325 } 326 } 327 } 328 for (d = 0; d < cdim; ++d) { 329 for (e = 0; e < cdim; ++e) { 330 JExT[d*cdim+e] = rotM[d*cdim+e]; 331 } 332 } 333 for (d = 0; d < cdim; ++d) { 334 for (e = 0; e < cdim; ++e) { 335 for (f = 0, rotM[d*cdim+e] = 0.0; f < cdim; ++f) { 336 rotM[d*cdim+e] += invJExT[d*cdim+f] * R[e*cdim+f]; 337 } 338 } 339 } 340 for (d = 0; d < cdim; ++d) { 341 for (e = 0; e < cdim; ++e) { 342 invJExT[d*cdim+e] = rotM[d*cdim+e]; 343 } 344 } 345 } 346 if (centroidEx) { 347 volExT = volEx; 348 for (d = 0; d < cdim; ++d) { 349 centroidExT[d] = centroidEx[d]; 350 normalExT[d] = normalEx[d]; 351 } 352 for (d = 0; d < cdim; ++d) { 353 centroidExT[d] *= scale; 354 centroidExT[d] += PetscRealPart(trans[d]); 355 normalExT[d] /= scale; 356 /* Only scale dimensions in the manifold */ 357 if (d < dim) volExT *= scale; 358 } 359 /* Do scaling and translation before rotation, so that we can leave out the normal dimension for lower dimensional manifolds */ 360 for (d = 0; d < cdim; ++d) { 361 for (e = 0, rot[d] = 0.0; e < cdim; ++e) { 362 rot[d] += R[d*cdim+e] * centroidExT[e]; 363 } 364 } 365 for (d = 0; d < cdim; ++d) centroidExT[d] = rot[d]; 366 for (d = 0; d < cdim; ++d) { 367 for (e = 0, rot[d] = 0.0; e < cdim; ++e) { 368 rot[d] += R[d*cdim+e] * normalExT[e]; 369 } 370 } 371 for (d = 0; d < cdim; ++d) normalExT[d] = rot[d]; 372 for (d = 0, norm = 0.0; d < cdim; ++d) norm += PetscSqr(normalExT[d]); 373 norm = PetscSqrtReal(norm); 374 if (norm != 0.) for (d = 0; d < cdim; ++d) normalExT[d] /= norm; 375 } 376 for (d = 0; d < cdim; ++d) { 377 for (p = 0; p < numCorners; ++p) { 378 newCoords[p*cdim+d] *= scale; 379 newCoords[p*cdim+d] += trans[d]; 380 } 381 } 382 for (p = 0; p < numCorners; ++p) { 383 for (d = 0; d < cdim; ++d) { 384 for (e = 0, rot[d] = 0.0; e < cdim; ++e) { 385 rot[d] += R[d*cdim+e] * PetscRealPart(newCoords[p*cdim+e]); 386 } 387 } 388 for (d = 0; d < cdim; ++d) newCoords[p*cdim+d] = rot[d]; 389 } 390 391 PetscCall(ChangeCoordinates(dm, cdim, newCoords)); 392 if (v0Ex) PetscCall(CheckFEMGeometry(dm, 0, cdim, v0ExT, JExT, invJExT, detJExT)); 393 if (dim == depth && centroidEx) { 394 PetscCall(CheckFVMGeometry(dm, cell, cdim, centroidExT, normalExT, volExT)); 395 PetscCall(CheckGaussLaw(dm, cell)); 396 if (faceCentroidEx) { 397 PetscCall(DMPlexGetConeSize(dm, cell, &coneSize)); 398 PetscCall(DMPlexGetCone(dm, cell, &cone)); 399 for (c = 0; c < coneSize; ++c) { 400 PetscInt off = c*cdim; 401 402 faceVolExT = faceVolEx[c]; 403 for (d = 0; d < cdim; ++d) { 404 faceCentroidExT[d] = faceCentroidEx[off+d]; 405 faceNormalExT[d] = faceNormalEx[off+d]; 406 } 407 for (d = 0; d < cdim; ++d) { 408 faceCentroidExT[d] *= scale; 409 faceCentroidExT[d] += PetscRealPart(trans[d]); 410 faceNormalExT[d] /= scale; 411 /* Only scale dimensions in the manifold */ 412 if (d < dim-1) { 413 faceVolExT *= scale; 414 } 415 } 416 for (d = 0; d < cdim; ++d) { 417 for (e = 0, rot[d] = 0.0; e < cdim; ++e) { 418 rot[d] += R[d*cdim+e] * faceCentroidExT[e]; 419 } 420 } 421 for (d = 0; d < cdim; ++d) faceCentroidExT[d] = rot[d]; 422 for (d = 0; d < cdim; ++d) { 423 for (e = 0, rot[d] = 0.0; e < cdim; ++e) { 424 rot[d] += R[d*cdim+e] * faceNormalExT[e]; 425 } 426 } 427 for (d = 0; d < cdim; ++d) faceNormalExT[d] = rot[d]; 428 for (d = 0, norm = 0.0; d < cdim; ++d) norm += PetscSqr(faceNormalExT[d]); 429 norm = PetscSqrtReal(norm); 430 for (d = 0; d < cdim; ++d) faceNormalExT[d] /= norm; 431 432 PetscCall(CheckFVMGeometry(dm, cone[c], cdim, faceCentroidExT, faceNormalExT, faceVolExT)); 433 } 434 } 435 } 436 } 437 PetscCall(PetscRandomDestroy(&r)); 438 PetscCall(PetscRandomDestroy(&ang)); 439 PetscCall(PetscRandomDestroy(&ang2)); 440 PetscCall(PetscFree2(origCoords, newCoords)); 441 PetscCall(PetscFree5(v0ExT, JExT, invJExT, centroidExT, normalExT)); 442 PetscCall(PetscFree2(faceCentroidExT, faceNormalExT)); 443 } 444 PetscFunctionReturn(0); 445 } 446 447 static PetscErrorCode TestTriangle(MPI_Comm comm, PetscBool transform) 448 { 449 DM dm; 450 451 PetscFunctionBegin; 452 PetscCall(DMPlexCreateReferenceCell(comm, DM_POLYTOPE_TRIANGLE, &dm)); 453 PetscCall(DMViewFromOptions(dm, NULL, "-dm_view")); 454 /* Check reference geometry: determinant is scaled by reference volume (2.0) */ 455 { 456 PetscReal v0Ex[2] = {-1.0, -1.0}; 457 PetscReal JEx[4] = {1.0, 0.0, 0.0, 1.0}; 458 PetscReal invJEx[4] = {1.0, 0.0, 0.0, 1.0}; 459 PetscReal detJEx = 1.0; 460 PetscReal centroidEx[2] = {-((PetscReal)1.)/((PetscReal)3.), -((PetscReal)1.)/((PetscReal)3.)}; 461 PetscReal normalEx[2] = {0.0, 0.0}; 462 PetscReal volEx = 2.0; 463 464 PetscCall(CheckCell(dm, 0, transform, v0Ex, JEx, invJEx, detJEx, centroidEx, normalEx, volEx, NULL, NULL, NULL)); 465 } 466 /* Move to 3D: Check reference geometry: determinant is scaled by reference volume (2.0) */ 467 { 468 PetscScalar vertexCoords[9] = {-1.0, -1.0, 0.0, 1.0, -1.0, 0.0, -1.0, 1.0, 0.0}; 469 PetscReal v0Ex[3] = {-1.0, -1.0, 0.0}; 470 PetscReal JEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 471 PetscReal invJEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 472 PetscReal detJEx = 1.0; 473 PetscReal centroidEx[3] = {-((PetscReal)1.)/((PetscReal)3.), -((PetscReal)1.)/((PetscReal)3.), 0.0}; 474 PetscReal normalEx[3] = {0.0, 0.0, 1.0}; 475 PetscReal volEx = 2.0; 476 477 PetscCall(ChangeCoordinates(dm, 3, vertexCoords)); 478 PetscCall(CheckCell(dm, 0, transform, v0Ex, JEx, invJEx, detJEx, centroidEx, normalEx, volEx, NULL, NULL, NULL)); 479 } 480 /* Cleanup */ 481 PetscCall(DMDestroy(&dm)); 482 PetscFunctionReturn(0); 483 } 484 485 static PetscErrorCode TestQuadrilateral(MPI_Comm comm, PetscBool transform) 486 { 487 DM dm; 488 489 PetscFunctionBegin; 490 PetscCall(DMPlexCreateReferenceCell(comm, DM_POLYTOPE_QUADRILATERAL, &dm)); 491 PetscCall(DMViewFromOptions(dm, NULL, "-dm_view")); 492 /* Check reference geometry: determinant is scaled by reference volume (2.0) */ 493 { 494 PetscReal v0Ex[2] = {-1.0, -1.0}; 495 PetscReal JEx[4] = {1.0, 0.0, 0.0, 1.0}; 496 PetscReal invJEx[4] = {1.0, 0.0, 0.0, 1.0}; 497 PetscReal detJEx = 1.0; 498 PetscReal centroidEx[2] = {0.0, 0.0}; 499 PetscReal normalEx[2] = {0.0, 0.0}; 500 PetscReal volEx = 4.0; 501 502 PetscCall(CheckCell(dm, 0, transform, v0Ex, JEx, invJEx, detJEx, centroidEx, normalEx, volEx, NULL, NULL, NULL)); 503 } 504 /* Move to 3D: Check reference geometry: determinant is scaled by reference volume (4.0) */ 505 { 506 PetscScalar vertexCoords[12] = {-1.0, -1.0, 0.0, 1.0, -1.0, 0.0, 1.0, 1.0, 0.0, -1.0, 1.0, 0.0}; 507 PetscReal v0Ex[3] = {-1.0, -1.0, 0.0}; 508 PetscReal JEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 509 PetscReal invJEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 510 PetscReal detJEx = 1.0; 511 PetscReal centroidEx[3] = {0.0, 0.0, 0.0}; 512 PetscReal normalEx[3] = {0.0, 0.0, 1.0}; 513 PetscReal volEx = 4.0; 514 515 PetscCall(ChangeCoordinates(dm, 3, vertexCoords)); 516 PetscCall(CheckCell(dm, 0, transform, v0Ex, JEx, invJEx, detJEx, centroidEx, normalEx, volEx, NULL, NULL, NULL)); 517 } 518 /* Cleanup */ 519 PetscCall(DMDestroy(&dm)); 520 PetscFunctionReturn(0); 521 } 522 523 static PetscErrorCode TestTetrahedron(MPI_Comm comm, PetscBool transform) 524 { 525 DM dm; 526 527 PetscFunctionBegin; 528 PetscCall(DMPlexCreateReferenceCell(comm, DM_POLYTOPE_TETRAHEDRON, &dm)); 529 PetscCall(DMViewFromOptions(dm, NULL, "-dm_view")); 530 /* Check reference geometry: determinant is scaled by reference volume (4/3) */ 531 { 532 PetscReal v0Ex[3] = {-1.0, -1.0, -1.0}; 533 PetscReal JEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 534 PetscReal invJEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 535 PetscReal detJEx = 1.0; 536 PetscReal centroidEx[3] = {-0.5, -0.5, -0.5}; 537 PetscReal normalEx[3] = {0.0, 0.0, 0.0}; 538 PetscReal volEx = (PetscReal)4.0/(PetscReal)3.0; 539 540 PetscCall(CheckCell(dm, 0, transform, v0Ex, JEx, invJEx, detJEx, centroidEx, normalEx, volEx, NULL, NULL, NULL)); 541 } 542 /* Cleanup */ 543 PetscCall(DMDestroy(&dm)); 544 PetscFunctionReturn(0); 545 } 546 547 static PetscErrorCode TestHexahedron(MPI_Comm comm, PetscBool transform) 548 { 549 DM dm; 550 551 PetscFunctionBegin; 552 PetscCall(DMPlexCreateReferenceCell(comm, DM_POLYTOPE_HEXAHEDRON, &dm)); 553 PetscCall(DMViewFromOptions(dm, NULL, "-dm_view")); 554 /* Check reference geometry: determinant is scaled by reference volume 8.0 */ 555 { 556 PetscReal v0Ex[3] = {-1.0, -1.0, -1.0}; 557 PetscReal JEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 558 PetscReal invJEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 559 PetscReal detJEx = 1.0; 560 PetscReal centroidEx[3] = {0.0, 0.0, 0.0}; 561 PetscReal normalEx[3] = {0.0, 0.0, 0.0}; 562 PetscReal volEx = 8.0; 563 564 PetscCall(CheckCell(dm, 0, transform, v0Ex, JEx, invJEx, detJEx, centroidEx, normalEx, volEx, NULL, NULL, NULL)); 565 } 566 /* Cleanup */ 567 PetscCall(DMDestroy(&dm)); 568 PetscFunctionReturn(0); 569 } 570 571 static PetscErrorCode TestHexahedronCurved(MPI_Comm comm) 572 { 573 DM dm; 574 PetscScalar coords[24] = {-1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, -1.0, 575 -1.0, -1.0, 1.1, 1.0, -1.0, 1.0, 1.0, 1.0, 1.1, -1.0, 1.0, 1.0}; 576 577 PetscFunctionBegin; 578 PetscCall(DMPlexCreateReferenceCell(comm, DM_POLYTOPE_HEXAHEDRON, &dm)); 579 PetscCall(ChangeCoordinates(dm, 3, coords)); 580 PetscCall(DMViewFromOptions(dm, NULL, "-dm_view")); 581 { 582 PetscReal centroidEx[3] = {0.0, 0.0, 0.016803278688524603}; 583 PetscReal normalEx[3] = {0.0, 0.0, 0.0}; 584 PetscReal volEx = 8.1333333333333346; 585 586 PetscCall(CheckCell(dm, 0, PETSC_FALSE, NULL, NULL, NULL, 0.0, centroidEx, normalEx, volEx, NULL, NULL, NULL)); 587 } 588 PetscCall(DMDestroy(&dm)); 589 PetscFunctionReturn(0); 590 } 591 592 /* This wedge is a tensor product cell, rather than a normal wedge */ 593 static PetscErrorCode TestWedge(MPI_Comm comm, PetscBool transform) 594 { 595 DM dm; 596 597 PetscFunctionBegin; 598 PetscCall(DMPlexCreateReferenceCell(comm, DM_POLYTOPE_TRI_PRISM_TENSOR, &dm)); 599 PetscCall(DMViewFromOptions(dm, NULL, "-dm_view")); 600 /* Check reference geometry: determinant is scaled by reference volume 4.0 */ 601 { 602 #if 0 603 /* FEM geometry is not functional for wedges */ 604 PetscReal v0Ex[3] = {-1.0, -1.0, -1.0}; 605 PetscReal JEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 606 PetscReal invJEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 607 PetscReal detJEx = 1.0; 608 #endif 609 610 { 611 PetscReal centroidEx[3] = {-((PetscReal)1.)/((PetscReal)3.), -((PetscReal)1.)/((PetscReal)3.), 0.0}; 612 PetscReal normalEx[3] = {0.0, 0.0, 0.0}; 613 PetscReal volEx = 4.0; 614 PetscReal faceVolEx[5] = {2.0, 2.0, 4.0, PETSC_SQRT2*4.0, 4.0}; 615 PetscReal faceNormalEx[15] = {0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, -1.0, 0.0, PETSC_SQRT2/2.0, PETSC_SQRT2/2.0, 0.0, -1.0, 0.0, 0.0}; 616 PetscReal faceCentroidEx[15] = {-((PetscReal)1.)/((PetscReal)3.), -((PetscReal)1.)/((PetscReal)3.), -1.0, 617 -((PetscReal)1.)/((PetscReal)3.), -((PetscReal)1.)/((PetscReal)3.), 1.0, 618 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0}; 619 620 PetscCall(CheckCell(dm, 0, transform, NULL, NULL, NULL, 0.0, centroidEx, normalEx, volEx, faceCentroidEx, faceNormalEx, faceVolEx)); 621 } 622 } 623 /* Cleanup */ 624 PetscCall(DMDestroy(&dm)); 625 PetscFunctionReturn(0); 626 } 627 628 int main(int argc, char **argv) 629 { 630 AppCtx user; 631 632 PetscFunctionBeginUser; 633 PetscCall(PetscInitialize(&argc, &argv, NULL,help)); 634 PetscCall(ProcessOptions(PETSC_COMM_WORLD, &user)); 635 if (user.runType == RUN_REFERENCE) { 636 PetscCall(TestTriangle(PETSC_COMM_SELF, user.transform)); 637 PetscCall(TestQuadrilateral(PETSC_COMM_SELF, user.transform)); 638 PetscCall(TestTetrahedron(PETSC_COMM_SELF, user.transform)); 639 PetscCall(TestHexahedron(PETSC_COMM_SELF, user.transform)); 640 PetscCall(TestWedge(PETSC_COMM_SELF, user.transform)); 641 } else if (user.runType == RUN_HEX_CURVED) { 642 PetscCall(TestHexahedronCurved(PETSC_COMM_SELF)); 643 } else if (user.runType == RUN_FILE) { 644 PetscInt dim, cStart, cEnd, c; 645 646 PetscCall(DMGetDimension(user.dm, &dim)); 647 PetscCall(DMPlexGetHeightStratum(user.dm, 0, &cStart, &cEnd)); 648 for (c = 0; c < cEnd-cStart; ++c) { 649 PetscReal *v0 = user.v0 ? &user.v0[c*dim] : NULL; 650 PetscReal *J = user.J ? &user.J[c*dim*dim] : NULL; 651 PetscReal *invJ = user.invJ ? &user.invJ[c*dim*dim] : NULL; 652 PetscReal detJ = user.detJ ? user.detJ[c] : 0.0; 653 PetscReal *centroid = user.centroid ? &user.centroid[c*dim] : NULL; 654 PetscReal *normal = user.normal ? &user.normal[c*dim] : NULL; 655 PetscReal vol = user.vol ? user.vol[c] : 0.0; 656 657 PetscCall(CheckCell(user.dm, c+cStart, PETSC_FALSE, v0, J, invJ, detJ, centroid, normal, vol, NULL, NULL, NULL)); 658 } 659 PetscCall(PetscFree4(user.v0,user.J,user.invJ,user.detJ)); 660 PetscCall(PetscFree(user.centroid)); 661 PetscCall(PetscFree(user.normal)); 662 PetscCall(PetscFree(user.vol)); 663 PetscCall(DMDestroy(&user.dm)); 664 } else if (user.runType == RUN_DISPLAY) { 665 DM gdm, dmCell; 666 Vec cellgeom, facegeom; 667 const PetscScalar *cgeom; 668 PetscInt dim, d, cStart, cEnd, cEndInterior, c; 669 670 PetscCall(DMGetCoordinateDim(user.dm, &dim)); 671 PetscCall(DMPlexConstructGhostCells(user.dm, NULL, NULL, &gdm)); 672 if (gdm) { 673 PetscCall(DMDestroy(&user.dm)); 674 user.dm = gdm; 675 } 676 PetscCall(DMPlexComputeGeometryFVM(user.dm, &cellgeom, &facegeom)); 677 PetscCall(DMPlexGetHeightStratum(user.dm, 0, &cStart, &cEnd)); 678 PetscCall(DMPlexGetGhostCellStratum(user.dm, &cEndInterior, NULL)); 679 if (cEndInterior >= 0) cEnd = cEndInterior; 680 PetscCall(VecGetDM(cellgeom, &dmCell)); 681 PetscCall(VecGetArrayRead(cellgeom, &cgeom)); 682 for (c = 0; c < cEnd-cStart; ++c) { 683 PetscFVCellGeom *cg; 684 685 PetscCall(DMPlexPointLocalRead(dmCell, c, cgeom, &cg)); 686 PetscCall(PetscPrintf(PETSC_COMM_SELF, "Cell %4" PetscInt_FMT ": Centroid (", c)); 687 for (d = 0; d < dim; ++d) { 688 if (d > 0) PetscCall(PetscPrintf(PETSC_COMM_SELF, ", ")); 689 PetscCall(PetscPrintf(PETSC_COMM_SELF, "%12.2g", (double)cg->centroid[d])); 690 } 691 PetscCall(PetscPrintf(PETSC_COMM_SELF, ") Vol %12.2g\n", (double)cg->volume)); 692 } 693 PetscCall(VecRestoreArrayRead(cellgeom, &cgeom)); 694 PetscCall(VecDestroy(&cellgeom)); 695 PetscCall(VecDestroy(&facegeom)); 696 PetscCall(DMDestroy(&user.dm)); 697 } 698 PetscCall(PetscFinalize()); 699 return 0; 700 } 701 702 /*TEST 703 704 test: 705 suffix: 1 706 args: -dm_view ascii::ascii_info_detail 707 test: 708 suffix: 2 709 args: -run_type hex_curved 710 test: 711 suffix: 3 712 args: -transform 713 test: 714 suffix: 4 715 requires: exodusii 716 args: -run_type file -dm_plex_filename ${wPETSC_DIR}/share/petsc/datafiles/meshes/simpleblock-100.exo -dm_view ascii::ascii_info_detail -v0 -1.5,-0.5,0.5,-0.5,-0.5,0.5,0.5,-0.5,0.5 -J 0.0,0.0,0.5,0.0,0.5,0.0,-0.5,0.0,0.0,0.0,0.0,0.5,0.0,0.5,0.0,-0.5,0.0,0.0,0.0,0.0,0.5,0.0,0.5,0.0,-0.5,0.0,0.0 -invJ 0.0,0.0,-2.0,0.0,2.0,0.0,2.0,0.0,0.0,0.0,0.0,-2.0,0.0,2.0,0.0,2.0,0.0,0.0,0.0,0.0,-2.0,0.0,2.0,0.0,2.0,0.0,0.0 -detJ 0.125,0.125,0.125 -centroid -1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0 -normal 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0 -vol 1.0,1.0,1.0 717 test: 718 suffix: 5 719 args: -run_type file -dm_plex_dim 3 -dm_plex_simplex 0 -dm_plex_box_faces 3,1,1 -dm_plex_box_lower -1.5,-0.5,-0.5 -dm_plex_box_upper 1.5,0.5,0.5 -dm_view ascii::ascii_info_detail -centroid -1.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0 -normal 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0 -vol 1.0,1.0,1.0 720 test: 721 suffix: 6 722 args: -run_type file -dm_plex_dim 1 -dm_plex_simplex 0 -dm_plex_box_faces 3 -dm_plex_box_lower -1.5 -dm_plex_box_upper 1.5 -dm_view ascii::ascii_info_detail -centroid -1.0,0.0,1.0 -vol 1.0,1.0,1.0 723 TEST*/ 724