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 PetscErrorCode ierr; 19 20 PetscFunctionBegin; 21 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 22 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 23 ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); 24 ierr = DMSetApplicationContext(*dm, user);CHKERRQ(ierr); 25 ierr = PetscObjectSetName((PetscObject) *dm, "Input Mesh");CHKERRQ(ierr); 26 ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); 27 PetscFunctionReturn(0); 28 } 29 30 static PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options) 31 { 32 const char *runTypes[4] = {"reference", "hex_curved", "file", "display"}; 33 PetscInt run; 34 PetscErrorCode ierr; 35 36 PetscFunctionBeginUser; 37 options->runType = RUN_REFERENCE; 38 options->transform = PETSC_FALSE; 39 40 ierr = PetscOptionsBegin(comm, "", "Geometry Test Options", "DMPLEX");CHKERRQ(ierr); 41 run = options->runType; 42 ierr = PetscOptionsEList("-run_type", "The run type", "ex8.c", runTypes, 3, runTypes[options->runType], &run, NULL);CHKERRQ(ierr); 43 options->runType = (RunType) run; 44 ierr = PetscOptionsBool("-transform", "Use random transforms", "ex8.c", options->transform, &options->transform, NULL);CHKERRQ(ierr); 45 46 if (options->runType == RUN_FILE) { 47 PetscInt dim, cStart, cEnd, numCells, n; 48 PetscBool flg, feFlg, fvFlg; 49 50 ierr = ReadMesh(PETSC_COMM_WORLD, options, &options->dm);CHKERRQ(ierr); 51 ierr = DMGetDimension(options->dm, &dim);CHKERRQ(ierr); 52 ierr = DMPlexGetHeightStratum(options->dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 53 numCells = cEnd-cStart; 54 ierr = PetscMalloc4(numCells*dim, &options->v0, numCells*dim*dim, &options->J, numCells*dim*dim, &options->invJ, numCells, &options->detJ);CHKERRQ(ierr); 55 ierr = PetscMalloc3(numCells*dim, &options->centroid, numCells*dim, &options->normal, numCells, &options->vol);CHKERRQ(ierr); 56 n = numCells*dim; 57 ierr = PetscOptionsRealArray("-v0", "Input v0 for each cell", "ex8.c", options->v0, &n, &feFlg);CHKERRQ(ierr); 58 if (feFlg && n != numCells*dim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Invalid size of v0 %D should be %D", n, numCells*dim); 59 n = numCells*dim*dim; 60 ierr = PetscOptionsRealArray("-J", "Input Jacobian for each cell", "ex8.c", options->J, &n, &flg);CHKERRQ(ierr); 61 if (flg && n != numCells*dim*dim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Invalid size of J %D should be %D", n, numCells*dim*dim); 62 n = numCells*dim*dim; 63 ierr = PetscOptionsRealArray("-invJ", "Input inverse Jacobian for each cell", "ex8.c", options->invJ, &n, &flg);CHKERRQ(ierr); 64 if (flg && n != numCells*dim*dim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Invalid size of invJ %D should be %D", n, numCells*dim*dim); 65 n = numCells; 66 ierr = PetscOptionsRealArray("-detJ", "Input Jacobian determinant for each cell", "ex8.c", options->detJ, &n, &flg);CHKERRQ(ierr); 67 if (flg && n != numCells) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Invalid size of detJ %D should be %D", n, numCells); 68 n = numCells*dim; 69 if (!feFlg) { 70 ierr = PetscFree4(options->v0, options->J, options->invJ, options->detJ);CHKERRQ(ierr); 71 options->v0 = options->J = options->invJ = options->detJ = NULL; 72 } 73 ierr = PetscOptionsRealArray("-centroid", "Input centroid for each cell", "ex8.c", options->centroid, &n, &fvFlg);CHKERRQ(ierr); 74 if (fvFlg && n != numCells*dim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Invalid size of centroid %D should be %D", n, numCells*dim); 75 n = numCells*dim; 76 ierr = PetscOptionsRealArray("-normal", "Input normal for each cell", "ex8.c", options->normal, &n, &flg);CHKERRQ(ierr); 77 if (flg && n != numCells*dim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Invalid size of normal %D should be %D", n, numCells*dim); 78 n = numCells; 79 ierr = PetscOptionsRealArray("-vol", "Input volume for each cell", "ex8.c", options->vol, &n, &flg);CHKERRQ(ierr); 80 if (flg && n != numCells) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Invalid size of vol %D should be %D", n, numCells); 81 if (!fvFlg) { 82 ierr = PetscFree3(options->centroid, options->normal, options->vol);CHKERRQ(ierr); 83 options->centroid = options->normal = options->vol = NULL; 84 } 85 } else if (options->runType == RUN_DISPLAY) { 86 ierr = ReadMesh(PETSC_COMM_WORLD, options, &options->dm);CHKERRQ(ierr); 87 } 88 ierr = PetscOptionsEnd();CHKERRQ(ierr); 89 90 if (options->transform) {ierr = PetscPrintf(comm, "Using random transforms\n");CHKERRQ(ierr);} 91 PetscFunctionReturn(0); 92 } 93 94 static PetscErrorCode ChangeCoordinates(DM dm, PetscInt spaceDim, PetscScalar vertexCoords[]) 95 { 96 PetscSection coordSection; 97 Vec coordinates; 98 PetscScalar *coords; 99 PetscInt vStart, vEnd, v, d, coordSize; 100 PetscErrorCode ierr; 101 102 PetscFunctionBegin; 103 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 104 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 105 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 106 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 107 ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr); 108 for (v = vStart; v < vEnd; ++v) { 109 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 110 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 111 } 112 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 113 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 114 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 115 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 116 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 117 ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr); 118 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 119 for (v = vStart; v < vEnd; ++v) { 120 PetscInt off; 121 122 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 123 for (d = 0; d < spaceDim; ++d) { 124 coords[off+d] = vertexCoords[(v-vStart)*spaceDim+d]; 125 } 126 } 127 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 128 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 129 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 130 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 131 ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr); 132 PetscFunctionReturn(0); 133 } 134 135 #define RelativeError(a,b) PetscAbs(a-b)/(1.0+PetscMax(PetscAbs(a),PetscAbs(b))) 136 137 static PetscErrorCode CheckFEMGeometry(DM dm, PetscInt cell, PetscInt spaceDim, PetscReal v0Ex[], PetscReal JEx[], PetscReal invJEx[], PetscReal detJEx) 138 { 139 PetscReal v0[3], J[9], invJ[9], detJ; 140 PetscInt d, i, j; 141 PetscErrorCode ierr; 142 143 PetscFunctionBegin; 144 ierr = DMPlexComputeCellGeometryFEM(dm, cell, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 145 for (d = 0; d < spaceDim; ++d) { 146 if (v0[d] != v0Ex[d]) { 147 switch (spaceDim) { 148 case 2: SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid v0 (%g, %g) != (%g, %g)", (double)v0[0], (double)v0[1], (double)v0Ex[0], (double)v0Ex[1]); 149 case 3: SETERRQ6(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]); 150 default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid space dimension %D", spaceDim); 151 } 152 } 153 } 154 for (i = 0; i < spaceDim; ++i) { 155 for (j = 0; j < spaceDim; ++j) { 156 if (RelativeError(J[i*spaceDim+j],JEx[i*spaceDim+j]) > 10*PETSC_SMALL) SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid J[%D,%D]: %g != %g", i, j, (double)J[i*spaceDim+j], (double)JEx[i*spaceDim+j]); 157 if (RelativeError(invJ[i*spaceDim+j],invJEx[i*spaceDim+j]) > 10*PETSC_SMALL) SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid invJ[%D,%D]: %g != %g", i, j, (double)invJ[i*spaceDim+j], (double)invJEx[i*spaceDim+j]); 158 } 159 } 160 if (RelativeError(detJ,detJEx) > 10*PETSC_SMALL) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid |J| = %g != %g diff %g", (double)detJ, (double)detJEx,(double)(detJ - detJEx)); 161 PetscFunctionReturn(0); 162 } 163 164 static PetscErrorCode CheckFVMGeometry(DM dm, PetscInt cell, PetscInt spaceDim, PetscReal centroidEx[], PetscReal normalEx[], PetscReal volEx) 165 { 166 PetscReal tol = PetscMax(10*PETSC_SMALL, 1e-10); 167 PetscReal centroid[3], normal[3], vol; 168 PetscInt d; 169 PetscErrorCode ierr; 170 171 PetscFunctionBegin; 172 ierr = DMPlexComputeCellGeometryFVM(dm, cell, &vol, centroid, normal);CHKERRQ(ierr); 173 for (d = 0; d < spaceDim; ++d) { 174 if (RelativeError(centroid[d],centroidEx[d]) > tol) SETERRQ5(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Cell %D, Invalid centroid[%D]: %g != %g diff %g", cell, d, (double)centroid[d], (double)centroidEx[d],(double)(centroid[d]-centroidEx[d])); 175 if (RelativeError(normal[d],normalEx[d]) > tol) SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Cell %D, Invalid normal[%D]: %g != %g", cell, d, (double)normal[d], (double)normalEx[d]); 176 } 177 if (RelativeError(volEx,vol) > tol) SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Cell %D, Invalid volume = %g != %g diff %g", cell, (double)vol, (double)volEx,(double)(vol - volEx)); 178 PetscFunctionReturn(0); 179 } 180 181 static PetscErrorCode CheckGaussLaw(DM dm, PetscInt cell) 182 { 183 DMPolytopeType ct; 184 PetscReal tol = PetscMax(10*PETSC_SMALL, 1e-10); 185 PetscReal normal[3], integral[3] = {0., 0., 0.}, area; 186 const PetscInt *cone, *ornt; 187 PetscInt coneSize, f, dim, cdim, d; 188 PetscErrorCode ierr; 189 190 PetscFunctionBegin; 191 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 192 ierr = DMGetCoordinateDim(dm, &cdim);CHKERRQ(ierr); 193 if (dim != cdim) PetscFunctionReturn(0); 194 ierr = DMPlexGetCellType(dm, cell, &ct);CHKERRQ(ierr); 195 if (ct == DM_POLYTOPE_TRI_PRISM_TENSOR) PetscFunctionReturn(0); 196 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 197 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 198 ierr = DMPlexGetConeOrientation(dm, cell, &ornt);CHKERRQ(ierr); 199 for (f = 0; f < coneSize; ++f) { 200 const PetscInt sgn = ornt[f] < 0 ? -1 : 1; 201 202 ierr = DMPlexComputeCellGeometryFVM(dm, cone[f], &area, NULL, normal);CHKERRQ(ierr); 203 for (d = 0; d < cdim; ++d) integral[d] += sgn*area*normal[d]; 204 } 205 for (d = 0; d < cdim; ++d) if (PetscAbsReal(integral[d]) > tol) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Cell %D Surface integral for component %D: %g != 0. as it should be for a constant field", cell, d, (double) integral[d]); 206 PetscFunctionReturn(0); 207 } 208 209 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[]) 210 { 211 const PetscInt *cone; 212 PetscInt coneSize, c; 213 PetscInt dim, depth, cdim; 214 PetscErrorCode ierr; 215 216 PetscFunctionBegin; 217 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 218 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 219 ierr = DMGetCoordinateDim(dm, &cdim);CHKERRQ(ierr); 220 if (v0Ex) { 221 ierr = CheckFEMGeometry(dm, cell, cdim, v0Ex, JEx, invJEx, detJEx);CHKERRQ(ierr); 222 } 223 if (dim == depth && centroidEx) { 224 ierr = CheckFVMGeometry(dm, cell, cdim, centroidEx, normalEx, volEx);CHKERRQ(ierr); 225 ierr = CheckGaussLaw(dm, cell);CHKERRQ(ierr); 226 if (faceCentroidEx) { 227 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 228 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 229 for (c = 0; c < coneSize; ++c) { 230 ierr = CheckFVMGeometry(dm, cone[c], dim, &faceCentroidEx[c*dim], &faceNormalEx[c*dim], faceVolEx[c]);CHKERRQ(ierr); 231 } 232 } 233 } 234 if (transform) { 235 Vec coordinates; 236 PetscSection coordSection; 237 PetscScalar *coords = NULL, *origCoords, *newCoords; 238 PetscReal *v0ExT, *JExT, *invJExT, detJExT=0, *centroidExT, *normalExT, volExT=0; 239 PetscReal *faceCentroidExT, *faceNormalExT, faceVolExT; 240 PetscRandom r, ang, ang2; 241 PetscInt coordSize, numCorners, t; 242 243 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 244 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 245 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 246 ierr = PetscMalloc2(coordSize, &origCoords, coordSize, &newCoords);CHKERRQ(ierr); 247 ierr = PetscMalloc5(cdim, &v0ExT, cdim*cdim, &JExT, cdim*cdim, &invJExT, cdim, ¢roidExT, cdim, &normalExT);CHKERRQ(ierr); 248 ierr = PetscMalloc2(cdim, &faceCentroidExT, cdim, &faceNormalExT);CHKERRQ(ierr); 249 for (c = 0; c < coordSize; ++c) origCoords[c] = coords[c]; 250 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 251 numCorners = coordSize/cdim; 252 253 ierr = PetscRandomCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 254 ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr); 255 ierr = PetscRandomSetInterval(r, 0.0, 10.0);CHKERRQ(ierr); 256 ierr = PetscRandomCreate(PETSC_COMM_SELF, &ang);CHKERRQ(ierr); 257 ierr = PetscRandomSetFromOptions(ang);CHKERRQ(ierr); 258 ierr = PetscRandomSetInterval(ang, 0.0, 2*PETSC_PI);CHKERRQ(ierr); 259 ierr = PetscRandomCreate(PETSC_COMM_SELF, &ang2);CHKERRQ(ierr); 260 ierr = PetscRandomSetFromOptions(ang2);CHKERRQ(ierr); 261 ierr = PetscRandomSetInterval(ang2, 0.0, PETSC_PI);CHKERRQ(ierr); 262 for (t = 0; t < 1; ++t) { 263 PetscScalar trans[3]; 264 PetscReal R[9], rot[3], rotM[9]; 265 PetscReal scale, phi, theta, psi = 0.0, norm; 266 PetscInt d, e, f, p; 267 268 for (c = 0; c < coordSize; ++c) newCoords[c] = origCoords[c]; 269 ierr = PetscRandomGetValueReal(r, &scale);CHKERRQ(ierr); 270 ierr = PetscRandomGetValueReal(ang, &phi);CHKERRQ(ierr); 271 ierr = PetscRandomGetValueReal(ang2, &theta);CHKERRQ(ierr); 272 for (d = 0; d < cdim; ++d) { 273 ierr = PetscRandomGetValue(r, &trans[d]);CHKERRQ(ierr); 274 } 275 switch (cdim) { 276 case 2: 277 R[0] = PetscCosReal(phi); R[1] = -PetscSinReal(phi); 278 R[2] = PetscSinReal(phi); R[3] = PetscCosReal(phi); 279 break; 280 case 3: 281 { 282 const PetscReal ct = PetscCosReal(theta), st = PetscSinReal(theta); 283 const PetscReal cp = PetscCosReal(phi), sp = PetscSinReal(phi); 284 const PetscReal cs = PetscCosReal(psi), ss = PetscSinReal(psi); 285 R[0] = ct*cs; R[1] = sp*st*cs - cp*ss; R[2] = sp*ss + cp*st*cs; 286 R[3] = ct*ss; R[4] = cp*cs + sp*st*ss; R[5] = cp*st*ss - sp*cs; 287 R[6] = -st; R[7] = sp*ct; R[8] = cp*ct; 288 break; 289 } 290 default: SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Invalid coordinate dimension %D", cdim); 291 } 292 if (v0Ex) { 293 detJExT = detJEx; 294 for (d = 0; d < cdim; ++d) { 295 v0ExT[d] = v0Ex[d]; 296 for (e = 0; e < cdim; ++e) { 297 JExT[d*cdim+e] = JEx[d*cdim+e]; 298 invJExT[d*cdim+e] = invJEx[d*cdim+e]; 299 } 300 } 301 for (d = 0; d < cdim; ++d) { 302 v0ExT[d] *= scale; 303 v0ExT[d] += PetscRealPart(trans[d]); 304 /* Only scale dimensions in the manifold */ 305 for (e = 0; e < dim; ++e) { 306 JExT[d*cdim+e] *= scale; 307 invJExT[d*cdim+e] /= scale; 308 } 309 if (d < dim) detJExT *= scale; 310 } 311 /* Do scaling and translation before rotation, so that we can leave out the normal dimension for lower dimensional manifolds */ 312 for (d = 0; d < cdim; ++d) { 313 for (e = 0, rot[d] = 0.0; e < cdim; ++e) { 314 rot[d] += R[d*cdim+e] * v0ExT[e]; 315 } 316 } 317 for (d = 0; d < cdim; ++d) v0ExT[d] = rot[d]; 318 for (d = 0; d < cdim; ++d) { 319 for (e = 0; e < cdim; ++e) { 320 for (f = 0, rotM[d*cdim+e] = 0.0; f < cdim; ++f) { 321 rotM[d*cdim+e] += R[d*cdim+f] * JExT[f*cdim+e]; 322 } 323 } 324 } 325 for (d = 0; d < cdim; ++d) { 326 for (e = 0; e < cdim; ++e) { 327 JExT[d*cdim+e] = rotM[d*cdim+e]; 328 } 329 } 330 for (d = 0; d < cdim; ++d) { 331 for (e = 0; e < cdim; ++e) { 332 for (f = 0, rotM[d*cdim+e] = 0.0; f < cdim; ++f) { 333 rotM[d*cdim+e] += invJExT[d*cdim+f] * R[e*cdim+f]; 334 } 335 } 336 } 337 for (d = 0; d < cdim; ++d) { 338 for (e = 0; e < cdim; ++e) { 339 invJExT[d*cdim+e] = rotM[d*cdim+e]; 340 } 341 } 342 } 343 if (centroidEx) { 344 volExT = volEx; 345 for (d = 0; d < cdim; ++d) { 346 centroidExT[d] = centroidEx[d]; 347 normalExT[d] = normalEx[d]; 348 } 349 for (d = 0; d < cdim; ++d) { 350 centroidExT[d] *= scale; 351 centroidExT[d] += PetscRealPart(trans[d]); 352 normalExT[d] /= scale; 353 /* Only scale dimensions in the manifold */ 354 if (d < dim) volExT *= scale; 355 } 356 /* Do scaling and translation before rotation, so that we can leave out the normal dimension for lower dimensional manifolds */ 357 for (d = 0; d < cdim; ++d) { 358 for (e = 0, rot[d] = 0.0; e < cdim; ++e) { 359 rot[d] += R[d*cdim+e] * centroidExT[e]; 360 } 361 } 362 for (d = 0; d < cdim; ++d) centroidExT[d] = rot[d]; 363 for (d = 0; d < cdim; ++d) { 364 for (e = 0, rot[d] = 0.0; e < cdim; ++e) { 365 rot[d] += R[d*cdim+e] * normalExT[e]; 366 } 367 } 368 for (d = 0; d < cdim; ++d) normalExT[d] = rot[d]; 369 for (d = 0, norm = 0.0; d < cdim; ++d) norm += PetscSqr(normalExT[d]); 370 norm = PetscSqrtReal(norm); 371 for (d = 0; d < cdim; ++d) normalExT[d] /= norm; 372 } 373 for (d = 0; d < cdim; ++d) { 374 for (p = 0; p < numCorners; ++p) { 375 newCoords[p*cdim+d] *= scale; 376 newCoords[p*cdim+d] += trans[d]; 377 } 378 } 379 for (p = 0; p < numCorners; ++p) { 380 for (d = 0; d < cdim; ++d) { 381 for (e = 0, rot[d] = 0.0; e < cdim; ++e) { 382 rot[d] += R[d*cdim+e] * PetscRealPart(newCoords[p*cdim+e]); 383 } 384 } 385 for (d = 0; d < cdim; ++d) newCoords[p*cdim+d] = rot[d]; 386 } 387 388 ierr = ChangeCoordinates(dm, cdim, newCoords);CHKERRQ(ierr); 389 if (v0Ex) { 390 ierr = CheckFEMGeometry(dm, 0, cdim, v0ExT, JExT, invJExT, detJExT);CHKERRQ(ierr); 391 } 392 if (dim == depth && centroidEx) { 393 ierr = CheckFVMGeometry(dm, cell, cdim, centroidExT, normalExT, volExT);CHKERRQ(ierr); 394 ierr = CheckGaussLaw(dm, cell);CHKERRQ(ierr); 395 if (faceCentroidEx) { 396 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 397 ierr = DMPlexGetCone(dm, cell, &cone);CHKERRQ(ierr); 398 for (c = 0; c < coneSize; ++c) { 399 PetscInt off = c*cdim; 400 401 faceVolExT = faceVolEx[c]; 402 for (d = 0; d < cdim; ++d) { 403 faceCentroidExT[d] = faceCentroidEx[off+d]; 404 faceNormalExT[d] = faceNormalEx[off+d]; 405 } 406 for (d = 0; d < cdim; ++d) { 407 faceCentroidExT[d] *= scale; 408 faceCentroidExT[d] += PetscRealPart(trans[d]); 409 faceNormalExT[d] /= scale; 410 /* Only scale dimensions in the manifold */ 411 if (d < dim-1) { 412 faceVolExT *= scale; 413 } 414 } 415 for (d = 0; d < cdim; ++d) { 416 for (e = 0, rot[d] = 0.0; e < cdim; ++e) { 417 rot[d] += R[d*cdim+e] * faceCentroidExT[e]; 418 } 419 } 420 for (d = 0; d < cdim; ++d) faceCentroidExT[d] = rot[d]; 421 for (d = 0; d < cdim; ++d) { 422 for (e = 0, rot[d] = 0.0; e < cdim; ++e) { 423 rot[d] += R[d*cdim+e] * faceNormalExT[e]; 424 } 425 } 426 for (d = 0; d < cdim; ++d) faceNormalExT[d] = rot[d]; 427 for (d = 0, norm = 0.0; d < cdim; ++d) norm += PetscSqr(faceNormalExT[d]); 428 norm = PetscSqrtReal(norm); 429 for (d = 0; d < cdim; ++d) faceNormalExT[d] /= norm; 430 431 ierr = CheckFVMGeometry(dm, cone[c], cdim, faceCentroidExT, faceNormalExT, faceVolExT);CHKERRQ(ierr); 432 } 433 } 434 } 435 } 436 ierr = PetscRandomDestroy(&r);CHKERRQ(ierr); 437 ierr = PetscRandomDestroy(&ang);CHKERRQ(ierr); 438 ierr = PetscRandomDestroy(&ang2);CHKERRQ(ierr); 439 ierr = PetscFree2(origCoords, newCoords);CHKERRQ(ierr); 440 ierr = PetscFree5(v0ExT, JExT, invJExT, centroidExT, normalExT);CHKERRQ(ierr); 441 ierr = PetscFree2(faceCentroidExT, faceNormalExT);CHKERRQ(ierr); 442 } 443 PetscFunctionReturn(0); 444 } 445 446 static PetscErrorCode TestTriangle(MPI_Comm comm, PetscBool transform) 447 { 448 DM dm; 449 PetscErrorCode ierr; 450 451 PetscFunctionBegin; 452 ierr = DMPlexCreateReferenceCell(comm, DM_POLYTOPE_TRIANGLE, &dm);CHKERRQ(ierr); 453 ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr); 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 ierr = CheckCell(dm, 0, transform, v0Ex, JEx, invJEx, detJEx, centroidEx, normalEx, volEx, NULL, NULL, NULL);CHKERRQ(ierr); 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 ierr = ChangeCoordinates(dm, 3, vertexCoords);CHKERRQ(ierr); 478 ierr = CheckCell(dm, 0, transform, v0Ex, JEx, invJEx, detJEx, centroidEx, normalEx, volEx, NULL, NULL, NULL);CHKERRQ(ierr); 479 } 480 /* Cleanup */ 481 ierr = DMDestroy(&dm);CHKERRQ(ierr); 482 PetscFunctionReturn(0); 483 } 484 485 static PetscErrorCode TestQuadrilateral(MPI_Comm comm, PetscBool transform) 486 { 487 DM dm; 488 PetscErrorCode ierr; 489 490 PetscFunctionBegin; 491 ierr = DMPlexCreateReferenceCell(comm, DM_POLYTOPE_QUADRILATERAL, &dm);CHKERRQ(ierr); 492 ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr); 493 /* Check reference geometry: determinant is scaled by reference volume (2.0) */ 494 { 495 PetscReal v0Ex[2] = {-1.0, -1.0}; 496 PetscReal JEx[4] = {1.0, 0.0, 0.0, 1.0}; 497 PetscReal invJEx[4] = {1.0, 0.0, 0.0, 1.0}; 498 PetscReal detJEx = 1.0; 499 PetscReal centroidEx[2] = {0.0, 0.0}; 500 PetscReal normalEx[2] = {0.0, 0.0}; 501 PetscReal volEx = 4.0; 502 503 ierr = CheckCell(dm, 0, transform, v0Ex, JEx, invJEx, detJEx, centroidEx, normalEx, volEx, NULL, NULL, NULL);CHKERRQ(ierr); 504 } 505 /* Move to 3D: Check reference geometry: determinant is scaled by reference volume (4.0) */ 506 { 507 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}; 508 PetscReal v0Ex[3] = {-1.0, -1.0, 0.0}; 509 PetscReal JEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 510 PetscReal invJEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 511 PetscReal detJEx = 1.0; 512 PetscReal centroidEx[3] = {0.0, 0.0, 0.0}; 513 PetscReal normalEx[3] = {0.0, 0.0, 1.0}; 514 PetscReal volEx = 4.0; 515 516 ierr = ChangeCoordinates(dm, 3, vertexCoords);CHKERRQ(ierr); 517 ierr = CheckCell(dm, 0, transform, v0Ex, JEx, invJEx, detJEx, centroidEx, normalEx, volEx, NULL, NULL, NULL);CHKERRQ(ierr); 518 } 519 /* Cleanup */ 520 ierr = DMDestroy(&dm);CHKERRQ(ierr); 521 PetscFunctionReturn(0); 522 } 523 524 static PetscErrorCode TestTetrahedron(MPI_Comm comm, PetscBool transform) 525 { 526 DM dm; 527 PetscErrorCode ierr; 528 529 PetscFunctionBegin; 530 ierr = DMPlexCreateReferenceCell(comm, DM_POLYTOPE_TETRAHEDRON, &dm);CHKERRQ(ierr); 531 ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr); 532 /* Check reference geometry: determinant is scaled by reference volume (4/3) */ 533 { 534 PetscReal v0Ex[3] = {-1.0, -1.0, -1.0}; 535 PetscReal JEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 536 PetscReal invJEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 537 PetscReal detJEx = 1.0; 538 PetscReal centroidEx[3] = {-0.5, -0.5, -0.5}; 539 PetscReal normalEx[3] = {0.0, 0.0, 0.0}; 540 PetscReal volEx = (PetscReal)4.0/(PetscReal)3.0; 541 542 ierr = CheckCell(dm, 0, transform, v0Ex, JEx, invJEx, detJEx, centroidEx, normalEx, volEx, NULL, NULL, NULL);CHKERRQ(ierr); 543 } 544 /* Cleanup */ 545 ierr = DMDestroy(&dm);CHKERRQ(ierr); 546 PetscFunctionReturn(0); 547 } 548 549 static PetscErrorCode TestHexahedron(MPI_Comm comm, PetscBool transform) 550 { 551 DM dm; 552 PetscErrorCode ierr; 553 554 PetscFunctionBegin; 555 ierr = DMPlexCreateReferenceCell(comm, DM_POLYTOPE_HEXAHEDRON, &dm);CHKERRQ(ierr); 556 ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr); 557 /* Check reference geometry: determinant is scaled by reference volume 8.0 */ 558 { 559 PetscReal v0Ex[3] = {-1.0, -1.0, -1.0}; 560 PetscReal JEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 561 PetscReal invJEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 562 PetscReal detJEx = 1.0; 563 PetscReal centroidEx[3] = {0.0, 0.0, 0.0}; 564 PetscReal normalEx[3] = {0.0, 0.0, 0.0}; 565 PetscReal volEx = 8.0; 566 567 ierr = CheckCell(dm, 0, transform, v0Ex, JEx, invJEx, detJEx, centroidEx, normalEx, volEx, NULL, NULL, NULL);CHKERRQ(ierr); 568 } 569 /* Cleanup */ 570 ierr = DMDestroy(&dm);CHKERRQ(ierr); 571 PetscFunctionReturn(0); 572 } 573 574 static PetscErrorCode TestHexahedronCurved(MPI_Comm comm) 575 { 576 DM dm; 577 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, 578 -1.0, -1.0, 1.1, 1.0, -1.0, 1.0, 1.0, 1.0, 1.1, -1.0, 1.0, 1.0}; 579 PetscErrorCode ierr; 580 581 PetscFunctionBegin; 582 ierr = DMPlexCreateReferenceCell(comm, DM_POLYTOPE_HEXAHEDRON, &dm);CHKERRQ(ierr); 583 ierr = ChangeCoordinates(dm, 3, coords);CHKERRQ(ierr); 584 ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr); 585 { 586 PetscReal centroidEx[3] = {0.0, 0.0, 0.016803278688524603}; 587 PetscReal normalEx[3] = {0.0, 0.0, 0.0}; 588 PetscReal volEx = 8.1333333333333346; 589 590 ierr = CheckCell(dm, 0, PETSC_FALSE, NULL, NULL, NULL, 0.0, centroidEx, normalEx, volEx, NULL, NULL, NULL);CHKERRQ(ierr); 591 } 592 ierr = DMDestroy(&dm);CHKERRQ(ierr); 593 PetscFunctionReturn(0); 594 } 595 596 /* This wedge is a tensor product cell, rather than a normal wedge */ 597 static PetscErrorCode TestWedge(MPI_Comm comm, PetscBool transform) 598 { 599 DM dm; 600 PetscErrorCode ierr; 601 602 PetscFunctionBegin; 603 ierr = DMPlexCreateReferenceCell(comm, DM_POLYTOPE_TRI_PRISM_TENSOR, &dm);CHKERRQ(ierr); 604 ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr); 605 /* Check reference geometry: determinant is scaled by reference volume 4.0 */ 606 { 607 #if 0 608 /* FEM geometry is not functional for wedges */ 609 PetscReal v0Ex[3] = {-1.0, -1.0, -1.0}; 610 PetscReal JEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 611 PetscReal invJEx[9] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0}; 612 PetscReal detJEx = 1.0; 613 #endif 614 615 { 616 PetscReal centroidEx[3] = {-((PetscReal)1.)/((PetscReal)3.), -((PetscReal)1.)/((PetscReal)3.), 0.0}; 617 PetscReal normalEx[3] = {0.0, 0.0, 0.0}; 618 PetscReal volEx = 4.0; 619 PetscReal faceVolEx[5] = {2.0, 2.0, 4.0, PETSC_SQRT2*4.0, 4.0}; 620 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}; 621 PetscReal faceCentroidEx[15] = {-((PetscReal)1.)/((PetscReal)3.), -((PetscReal)1.)/((PetscReal)3.), -1.0, 622 -((PetscReal)1.)/((PetscReal)3.), -((PetscReal)1.)/((PetscReal)3.), 1.0, 623 0.0, -1.0, 0.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0}; 624 625 ierr = CheckCell(dm, 0, transform, NULL, NULL, NULL, 0.0, centroidEx, normalEx, volEx, faceCentroidEx, faceNormalEx, faceVolEx);CHKERRQ(ierr); 626 } 627 } 628 /* Cleanup */ 629 ierr = DMDestroy(&dm);CHKERRQ(ierr); 630 PetscFunctionReturn(0); 631 } 632 633 int main(int argc, char **argv) 634 { 635 AppCtx user; 636 PetscErrorCode ierr; 637 638 ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; 639 ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); 640 if (user.runType == RUN_REFERENCE) { 641 ierr = TestTriangle(PETSC_COMM_SELF, user.transform);CHKERRQ(ierr); 642 ierr = TestQuadrilateral(PETSC_COMM_SELF, user.transform);CHKERRQ(ierr); 643 ierr = TestTetrahedron(PETSC_COMM_SELF, user.transform);CHKERRQ(ierr); 644 ierr = TestHexahedron(PETSC_COMM_SELF, user.transform);CHKERRQ(ierr); 645 ierr = TestWedge(PETSC_COMM_SELF, user.transform);CHKERRQ(ierr); 646 } else if (user.runType == RUN_HEX_CURVED) { 647 ierr = TestHexahedronCurved(PETSC_COMM_SELF);CHKERRQ(ierr); 648 } else if (user.runType == RUN_FILE) { 649 PetscInt dim, cStart, cEnd, c; 650 651 ierr = DMGetDimension(user.dm, &dim);CHKERRQ(ierr); 652 ierr = DMPlexGetHeightStratum(user.dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 653 for (c = 0; c < cEnd-cStart; ++c) { 654 PetscReal *v0 = user.v0 ? &user.v0[c*dim] : NULL; 655 PetscReal *J = user.J ? &user.J[c*dim*dim] : NULL; 656 PetscReal *invJ = user.invJ ? &user.invJ[c*dim*dim] : NULL; 657 PetscReal detJ = user.detJ ? user.detJ[c] : 0.0; 658 PetscReal *centroid = user.centroid ? &user.centroid[c*dim] : NULL; 659 PetscReal *normal = user.normal ? &user.normal[c*dim] : NULL; 660 PetscReal vol = user.vol ? user.vol[c] : 0.0; 661 662 ierr = CheckCell(user.dm, c+cStart, PETSC_FALSE, v0, J, invJ, detJ, centroid, normal, vol, NULL, NULL, NULL);CHKERRQ(ierr); 663 } 664 ierr = PetscFree4(user.v0,user.J,user.invJ,user.detJ);CHKERRQ(ierr); 665 ierr = PetscFree3(user.centroid,user.normal,user.vol);CHKERRQ(ierr); 666 ierr = DMDestroy(&user.dm);CHKERRQ(ierr); 667 } else if (user.runType == RUN_DISPLAY) { 668 DM gdm, dmCell; 669 Vec cellgeom, facegeom; 670 const PetscScalar *cgeom; 671 PetscInt dim, d, cStart, cEnd, cEndInterior, c; 672 673 ierr = DMGetCoordinateDim(user.dm, &dim);CHKERRQ(ierr); 674 ierr = DMPlexConstructGhostCells(user.dm, NULL, NULL, &gdm);CHKERRQ(ierr); 675 if (gdm) { 676 ierr = DMDestroy(&user.dm);CHKERRQ(ierr); 677 user.dm = gdm; 678 } 679 ierr = DMPlexComputeGeometryFVM(user.dm, &cellgeom, &facegeom);CHKERRQ(ierr); 680 ierr = DMPlexGetHeightStratum(user.dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 681 ierr = DMPlexGetGhostCellStratum(user.dm, &cEndInterior, NULL);CHKERRQ(ierr); 682 if (cEndInterior >= 0) cEnd = cEndInterior; 683 ierr = VecGetDM(cellgeom, &dmCell);CHKERRQ(ierr); 684 ierr = VecGetArrayRead(cellgeom, &cgeom);CHKERRQ(ierr); 685 for (c = 0; c < cEnd-cStart; ++c) { 686 PetscFVCellGeom *cg; 687 688 ierr = DMPlexPointLocalRead(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 689 ierr = PetscPrintf(PETSC_COMM_SELF, "Cell %4D: Centroid (", c);CHKERRQ(ierr); 690 for (d = 0; d < dim; ++d) { 691 if (d > 0) {ierr = PetscPrintf(PETSC_COMM_SELF, ", ");CHKERRQ(ierr);} 692 ierr = PetscPrintf(PETSC_COMM_SELF, "%12.2g", cg->centroid[d]);CHKERRQ(ierr); 693 } 694 ierr = PetscPrintf(PETSC_COMM_SELF, ") Vol %12.2g\n", cg->volume);CHKERRQ(ierr); 695 } 696 ierr = VecRestoreArrayRead(cellgeom, &cgeom);CHKERRQ(ierr); 697 ierr = VecDestroy(&cellgeom);CHKERRQ(ierr); 698 ierr = VecDestroy(&facegeom);CHKERRQ(ierr); 699 ierr = DMDestroy(&user.dm);CHKERRQ(ierr); 700 } 701 ierr = PetscFinalize(); 702 return ierr; 703 } 704 705 /*TEST 706 707 test: 708 suffix: 1 709 args: -dm_view ascii::ascii_info_detail 710 test: 711 suffix: 2 712 args: -run_type hex_curved 713 test: 714 suffix: 3 715 args: -transform 716 test: 717 suffix: 4 718 requires: exodusii 719 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 1.0,1.0,1.0 720 test: 721 suffix: 5 722 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 1.0,1.0,1.0 723 724 TEST*/ 725