#include /*I "petscdmplex.h" I*/ #undef __FUNCT__ #define __FUNCT__ "DMPlexLocatePoint_Simplex_2D_Internal" static PetscErrorCode DMPlexLocatePoint_Simplex_2D_Internal(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) { const PetscInt embedDim = 2; PetscReal x = PetscRealPart(point[0]); PetscReal y = PetscRealPart(point[1]); PetscReal v0[2], J[4], invJ[4], detJ; PetscReal xi, eta; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexComputeCellGeometry(dm, c, v0, J, invJ, &detJ);CHKERRQ(ierr); xi = invJ[0*embedDim+0]*(x - v0[0]) + invJ[0*embedDim+1]*(y - v0[1]); eta = invJ[1*embedDim+0]*(x - v0[0]) + invJ[1*embedDim+1]*(y - v0[1]); if ((xi >= 0.0) && (eta >= 0.0) && (xi + eta <= 2.0)) *cell = c; else *cell = -1; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexLocatePoint_General_2D_Internal" static PetscErrorCode DMPlexLocatePoint_General_2D_Internal(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) { PetscSection coordSection; Vec coordsLocal; PetscScalar *coords; const PetscInt faces[8] = {0, 1, 1, 2, 2, 3, 3, 0}; PetscReal x = PetscRealPart(point[0]); PetscReal y = PetscRealPart(point[1]); PetscInt crossings = 0, f; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, coordSection, coordsLocal, c, NULL, &coords);CHKERRQ(ierr); for (f = 0; f < 4; ++f) { PetscReal x_i = PetscRealPart(coords[faces[2*f+0]*2+0]); PetscReal y_i = PetscRealPart(coords[faces[2*f+0]*2+1]); PetscReal x_j = PetscRealPart(coords[faces[2*f+1]*2+0]); PetscReal y_j = PetscRealPart(coords[faces[2*f+1]*2+1]); PetscReal slope = (y_j - y_i) / (x_j - x_i); PetscBool cond1 = (x_i <= x) && (x < x_j) ? PETSC_TRUE : PETSC_FALSE; PetscBool cond2 = (x_j <= x) && (x < x_i) ? PETSC_TRUE : PETSC_FALSE; PetscBool above = (y < slope * (x - x_i) + y_i) ? PETSC_TRUE : PETSC_FALSE; if ((cond1 || cond2) && above) ++crossings; } if (crossings % 2) *cell = c; else *cell = -1; ierr = DMPlexVecRestoreClosure(dm, coordSection, coordsLocal, c, NULL, &coords);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexLocatePoint_Simplex_3D_Internal" static PetscErrorCode DMPlexLocatePoint_Simplex_3D_Internal(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) { const PetscInt embedDim = 3; PetscReal v0[3], J[9], invJ[9], detJ; PetscReal x = PetscRealPart(point[0]); PetscReal y = PetscRealPart(point[1]); PetscReal z = PetscRealPart(point[2]); PetscReal xi, eta, zeta; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexComputeCellGeometry(dm, c, v0, J, invJ, &detJ);CHKERRQ(ierr); xi = invJ[0*embedDim+0]*(x - v0[0]) + invJ[0*embedDim+1]*(y - v0[1]) + invJ[0*embedDim+2]*(z - v0[2]); eta = invJ[1*embedDim+0]*(x - v0[0]) + invJ[1*embedDim+1]*(y - v0[1]) + invJ[1*embedDim+2]*(z - v0[2]); zeta = invJ[2*embedDim+0]*(x - v0[0]) + invJ[2*embedDim+1]*(y - v0[1]) + invJ[2*embedDim+2]*(z - v0[2]); if ((xi >= 0.0) && (eta >= 0.0) && (zeta >= 0.0) && (xi + eta + zeta <= 2.0)) *cell = c; else *cell = -1; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexLocatePoint_General_3D_Internal" static PetscErrorCode DMPlexLocatePoint_General_3D_Internal(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) { PetscSection coordSection; Vec coordsLocal; PetscScalar *coords; const PetscInt faces[24] = {0, 1, 2, 3, 5, 4, 7, 6, 1, 0, 4, 5, 3, 2, 6, 7, 1, 5, 6, 2, 0, 3, 7, 4}; PetscBool found = PETSC_TRUE; PetscInt f; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, coordSection, coordsLocal, c, NULL, &coords);CHKERRQ(ierr); for (f = 0; f < 6; ++f) { /* Check the point is under plane */ /* Get face normal */ PetscReal v_i[3]; PetscReal v_j[3]; PetscReal normal[3]; PetscReal pp[3]; PetscReal dot; v_i[0] = PetscRealPart(coords[faces[f*4+3]*3+0]-coords[faces[f*4+0]*3+0]); v_i[1] = PetscRealPart(coords[faces[f*4+3]*3+1]-coords[faces[f*4+0]*3+1]); v_i[2] = PetscRealPart(coords[faces[f*4+3]*3+2]-coords[faces[f*4+0]*3+2]); v_j[0] = PetscRealPart(coords[faces[f*4+1]*3+0]-coords[faces[f*4+0]*3+0]); v_j[1] = PetscRealPart(coords[faces[f*4+1]*3+1]-coords[faces[f*4+0]*3+1]); v_j[2] = PetscRealPart(coords[faces[f*4+1]*3+2]-coords[faces[f*4+0]*3+2]); normal[0] = v_i[1]*v_j[2] - v_i[2]*v_j[1]; normal[1] = v_i[2]*v_j[0] - v_i[0]*v_j[2]; normal[2] = v_i[0]*v_j[1] - v_i[1]*v_j[0]; pp[0] = PetscRealPart(coords[faces[f*4+0]*3+0] - point[0]); pp[1] = PetscRealPart(coords[faces[f*4+0]*3+1] - point[1]); pp[2] = PetscRealPart(coords[faces[f*4+0]*3+2] - point[2]); dot = normal[0]*pp[0] + normal[1]*pp[1] + normal[2]*pp[2]; /* Check that projected point is in face (2D location problem) */ if (dot < 0.0) { found = PETSC_FALSE; break; } } if (found) *cell = c; else *cell = -1; ierr = DMPlexVecRestoreClosure(dm, coordSection, coordsLocal, c, NULL, &coords);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMLocatePoints_Plex" /* Need to implement using the guess */ PetscErrorCode DMLocatePoints_Plex(DM dm, Vec v, IS *cellIS) { PetscInt cell = -1 /*, guess = -1*/; PetscInt bs, numPoints, p; PetscInt dim, cStart, cEnd, cMax, c, coneSize; PetscInt *cells; PetscScalar *a; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); if (cMax >= 0) cEnd = PetscMin(cEnd, cMax); ierr = VecGetLocalSize(v, &numPoints);CHKERRQ(ierr); ierr = VecGetBlockSize(v, &bs);CHKERRQ(ierr); ierr = VecGetArray(v, &a);CHKERRQ(ierr); if (bs != dim) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Block size for point vector %d must be the mesh coordinate dimension %d", bs, dim); numPoints /= bs; ierr = PetscMalloc(numPoints * sizeof(PetscInt), &cells);CHKERRQ(ierr); for (p = 0; p < numPoints; ++p) { const PetscScalar *point = &a[p*bs]; switch (dim) { case 2: for (c = cStart; c < cEnd; ++c) { ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); switch (coneSize) { case 3: ierr = DMPlexLocatePoint_Simplex_2D_Internal(dm, point, c, &cell);CHKERRQ(ierr); break; case 4: ierr = DMPlexLocatePoint_General_2D_Internal(dm, point, c, &cell);CHKERRQ(ierr); break; default: SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No point location for cell with cone size %d", coneSize); } if (cell >= 0) break; } break; case 3: for (c = cStart; c < cEnd; ++c) { ierr = DMPlexGetConeSize(dm, c, &coneSize);CHKERRQ(ierr); switch (coneSize) { case 4: ierr = DMPlexLocatePoint_Simplex_3D_Internal(dm, point, c, &cell);CHKERRQ(ierr); break; case 8: ierr = DMPlexLocatePoint_General_3D_Internal(dm, point, c, &cell);CHKERRQ(ierr); break; default: SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No point location for cell with cone size %d", coneSize); } if (cell >= 0) break; } break; default: SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No point location for mesh dimension %d", dim); } cells[p] = cell; } ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); ierr = ISCreateGeneral(PETSC_COMM_SELF, numPoints, cells, PETSC_OWN_POINTER, cellIS);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeProjection2Dto1D_Internal" /* DMPlexComputeProjection2Dto1D_Internal - Rewrite coordinates to be the 1D projection of the 2D */ static PetscErrorCode DMPlexComputeProjection2Dto1D_Internal(PetscScalar coords[], PetscReal R[]) { const PetscReal x = PetscRealPart(coords[2] - coords[0]); const PetscReal y = PetscRealPart(coords[3] - coords[1]); const PetscReal r = sqrt(x*x + y*y), c = x/r, s = y/r; PetscFunctionBegin; R[0] = c; R[1] = s; R[2] = -s; R[3] = c; coords[0] = 0.0; coords[1] = r; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeProjection3Dto2D_Internal" /* DMPlexComputeProjection3Dto2D_Internal - Rewrite coordinates to be the 2D projection of the 3D */ static PetscErrorCode DMPlexComputeProjection3Dto2D_Internal(PetscInt coordSize, PetscScalar coords[], PetscReal R[]) { PetscReal x1[3], x2[3], n[3], norm; PetscReal x1p[3], x2p[3], xnp[3]; PetscReal sqrtz, alpha; const PetscInt dim = 3; PetscInt d, e, p; PetscFunctionBegin; /* 0) Calculate normal vector */ for (d = 0; d < dim; ++d) { x1[d] = PetscRealPart(coords[1*dim+d] - coords[0*dim+d]); x2[d] = PetscRealPart(coords[2*dim+d] - coords[0*dim+d]); } n[0] = x1[1]*x2[2] - x1[2]*x2[1]; n[1] = x1[2]*x2[0] - x1[0]*x2[2]; n[2] = x1[0]*x2[1] - x1[1]*x2[0]; norm = sqrt(n[0]*n[0] + n[1]*n[1] + n[2]*n[2]); n[0] /= norm; n[1] /= norm; n[2] /= norm; /* 1) Take the normal vector and rotate until it is \hat z Let the normal vector be and alpha = 1/sqrt(1 - nz^2), then R = / alpha nx nz alpha ny nz -1/alpha \ | -alpha ny alpha nx 0 | \ nx ny nz / will rotate the normal vector to \hat z */ sqrtz = sqrt(1.0 - n[2]*n[2]); /* Check for n = z */ if (sqrtz < 1.0e-10) { if (n[2] < 0.0) { if (coordSize > 9) { coords[2] = PetscRealPart(coords[3*dim+0] - coords[0*dim+0]); coords[3] = PetscRealPart(coords[3*dim+0] - coords[0*dim+0]); coords[4] = x2[0]; coords[5] = x2[1]; coords[6] = x1[0]; coords[7] = x1[1]; } else { coords[2] = x2[0]; coords[3] = x2[1]; coords[4] = x1[0]; coords[5] = x1[1]; } R[0] = 1.0; R[1] = 0.0; R[2] = 0.0; R[3] = 0.0; R[4] = 1.0; R[5] = 0.0; R[6] = 0.0; R[7] = 0.0; R[8] = -1.0; } else { for (p = 3; p < coordSize/3; ++p) { coords[p*2+0] = PetscRealPart(coords[p*dim+0] - coords[0*dim+0]); coords[p*2+1] = PetscRealPart(coords[p*dim+1] - coords[0*dim+1]); } coords[2] = x1[0]; coords[3] = x1[1]; coords[4] = x2[0]; coords[5] = x2[1]; R[0] = 1.0; R[1] = 0.0; R[2] = 0.0; R[3] = 0.0; R[4] = 1.0; R[5] = 0.0; R[6] = 0.0; R[7] = 0.0; R[8] = 1.0; } coords[0] = 0.0; coords[1] = 0.0; PetscFunctionReturn(0); } alpha = 1.0/sqrtz; R[0] = alpha*n[0]*n[2]; R[1] = alpha*n[1]*n[2]; R[2] = -sqrtz; R[3] = -alpha*n[1]; R[4] = alpha*n[0]; R[5] = 0.0; R[6] = n[0]; R[7] = n[1]; R[8] = n[2]; for (d = 0; d < dim; ++d) { x1p[d] = 0.0; x2p[d] = 0.0; for (e = 0; e < dim; ++e) { x1p[d] += R[d*dim+e]*x1[e]; x2p[d] += R[d*dim+e]*x2[e]; } } if (PetscAbsReal(x1p[2]) > 1.0e-9) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid rotation calculated"); if (PetscAbsReal(x2p[2]) > 1.0e-9) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid rotation calculated"); /* 2) Project to (x, y) */ for (p = 3; p < coordSize/3; ++p) { for (d = 0; d < dim; ++d) { xnp[d] = 0.0; for (e = 0; e < dim; ++e) { xnp[d] += R[d*dim+e]*PetscRealPart(coords[p*dim+e] - coords[0*dim+e]); } if (d < dim-1) coords[p*2+d] = xnp[d]; } } coords[0] = 0.0; coords[1] = 0.0; coords[2] = x1p[0]; coords[3] = x1p[1]; coords[4] = x2p[0]; coords[5] = x2p[1]; /* Output R^T which rotates \hat z to the input normal */ for (d = 0; d < dim; ++d) { for (e = d+1; e < dim; ++e) { PetscReal tmp; tmp = R[d*dim+e]; R[d*dim+e] = R[e*dim+d]; R[e*dim+d] = tmp; } } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "Invert2D_Internal" PETSC_STATIC_INLINE void Invert2D_Internal(PetscReal invJ[], PetscReal J[], PetscReal detJ) { const PetscReal invDet = 1.0/detJ; invJ[0] = invDet*J[3]; invJ[1] = -invDet*J[1]; invJ[2] = -invDet*J[2]; invJ[3] = invDet*J[0]; PetscLogFlops(5.0); } #undef __FUNCT__ #define __FUNCT__ "Invert3D_Internal" PETSC_STATIC_INLINE void Invert3D_Internal(PetscReal invJ[], PetscReal J[], PetscReal detJ) { const PetscReal invDet = 1.0/detJ; invJ[0*3+0] = invDet*(J[1*3+1]*J[2*3+2] - J[1*3+2]*J[2*3+1]); invJ[0*3+1] = invDet*(J[0*3+2]*J[2*3+1] - J[0*3+1]*J[2*3+2]); invJ[0*3+2] = invDet*(J[0*3+1]*J[1*3+2] - J[0*3+2]*J[1*3+1]); invJ[1*3+0] = invDet*(J[1*3+2]*J[2*3+0] - J[1*3+0]*J[2*3+2]); invJ[1*3+1] = invDet*(J[0*3+0]*J[2*3+2] - J[0*3+2]*J[2*3+0]); invJ[1*3+2] = invDet*(J[0*3+2]*J[1*3+0] - J[0*3+0]*J[1*3+2]); invJ[2*3+0] = invDet*(J[1*3+0]*J[2*3+1] - J[1*3+1]*J[2*3+0]); invJ[2*3+1] = invDet*(J[0*3+1]*J[2*3+0] - J[0*3+0]*J[2*3+1]); invJ[2*3+2] = invDet*(J[0*3+0]*J[1*3+1] - J[0*3+1]*J[1*3+0]); PetscLogFlops(37.0); } #undef __FUNCT__ #define __FUNCT__ "Det2D_Internal" PETSC_STATIC_INLINE void Det2D_Internal(PetscReal *detJ, PetscReal J[]) { *detJ = J[0]*J[3] - J[1]*J[2]; PetscLogFlops(3.0); } #undef __FUNCT__ #define __FUNCT__ "Det3D_Internal" PETSC_STATIC_INLINE void Det3D_Internal(PetscReal *detJ, PetscReal J[]) { *detJ = (J[0*3+0]*(J[1*3+1]*J[2*3+2] - J[1*3+2]*J[2*3+1]) + J[0*3+1]*(J[1*3+2]*J[2*3+0] - J[1*3+0]*J[2*3+2]) + J[0*3+2]*(J[1*3+0]*J[2*3+1] - J[1*3+1]*J[2*3+0])); PetscLogFlops(12.0); } #undef __FUNCT__ #define __FUNCT__ "Volume_Triangle_Internal" PETSC_STATIC_INLINE void Volume_Triangle_Internal(PetscReal *vol, PetscReal coords[]) { /* Signed volume is 1/2 the determinant | 1 1 1 | | x0 x1 x2 | | y0 y1 y2 | but if x0,y0 is the origin, we have | x1 x2 | | y1 y2 | */ const PetscReal x1 = coords[2] - coords[0], y1 = coords[3] - coords[1]; const PetscReal x2 = coords[4] - coords[0], y2 = coords[5] - coords[1]; PetscReal M[4], detM; M[0] = x1; M[1] = x2; M[2] = y1; M[3] = y2; Det2D_Internal(&detM, M); *vol = 0.5*detM; PetscLogFlops(5.0); } #undef __FUNCT__ #define __FUNCT__ "Volume_Triangle_Origin_Internal" PETSC_STATIC_INLINE void Volume_Triangle_Origin_Internal(PetscReal *vol, PetscReal coords[]) { Det2D_Internal(vol, coords); *vol *= 0.5; } #undef __FUNCT__ #define __FUNCT__ "Volume_Tetrahedron_Internal" PETSC_STATIC_INLINE void Volume_Tetrahedron_Internal(PetscReal *vol, PetscReal coords[]) { /* Signed volume is 1/6th of the determinant | 1 1 1 1 | | x0 x1 x2 x3 | | y0 y1 y2 y3 | | z0 z1 z2 z3 | but if x0,y0,z0 is the origin, we have | x1 x2 x3 | | y1 y2 y3 | | z1 z2 z3 | */ const PetscReal x1 = coords[3] - coords[0], y1 = coords[4] - coords[1], z1 = coords[5] - coords[2]; const PetscReal x2 = coords[6] - coords[0], y2 = coords[7] - coords[1], z2 = coords[8] - coords[2]; const PetscReal x3 = coords[9] - coords[0], y3 = coords[10] - coords[1], z3 = coords[11] - coords[2]; PetscReal M[9], detM; M[0] = x1; M[1] = x2; M[2] = x3; M[3] = y1; M[4] = y2; M[5] = y3; M[6] = z1; M[7] = z2; M[8] = z3; Det3D_Internal(&detM, M); *vol = -0.16666666666666666666666*detM; PetscLogFlops(10.0); } #undef __FUNCT__ #define __FUNCT__ "Volume_Tetrahedron_Origin_Internal" PETSC_STATIC_INLINE void Volume_Tetrahedron_Origin_Internal(PetscReal *vol, PetscReal coords[]) { Det3D_Internal(vol, coords); *vol *= -0.16666666666666666666666; } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeLineGeometry_Internal" static PetscErrorCode DMPlexComputeLineGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) { PetscSection coordSection; Vec coordinates; PetscScalar *coords; PetscInt numCoords, d; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); *detJ = 0.0; if (numCoords == 4) { const PetscInt dim = 2; PetscReal R[4], J0; if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} ierr = DMPlexComputeProjection2Dto1D_Internal(coords, R);CHKERRQ(ierr); if (J) { J0 = 0.5*PetscRealPart(coords[1]); J[0] = R[0]*J0; J[1] = R[1]; J[2] = R[2]*J0; J[3] = R[3]; Det2D_Internal(detJ, J); } if (invJ) {Invert2D_Internal(invJ, J, *detJ);} } else if (numCoords == 2) { const PetscInt dim = 1; if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} if (J) { J[0] = 0.5*(PetscRealPart(coords[1]) - PetscRealPart(coords[0])); *detJ = J[0]; PetscLogFlops(2.0); } if (invJ) {invJ[0] = 1.0/J[0]; PetscLogFlops(1.0);} } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of coordinates for this segment is %d != 2", numCoords); ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeTriangleGeometry_Internal" static PetscErrorCode DMPlexComputeTriangleGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) { PetscSection coordSection; Vec coordinates; PetscScalar *coords; PetscInt numCoords, d, f, g; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); *detJ = 0.0; if (numCoords == 9) { const PetscInt dim = 3; PetscReal R[9], J0[9] = {1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0}; if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} ierr = DMPlexComputeProjection3Dto2D_Internal(numCoords, coords, R);CHKERRQ(ierr); if (J) { const PetscInt pdim = 2; for (d = 0; d < pdim; d++) { for (f = 0; f < pdim; f++) { J0[d*dim+f] = 0.5*(PetscRealPart(coords[(f+1)*pdim+d]) - PetscRealPart(coords[0*pdim+d])); } } PetscLogFlops(8.0); Det3D_Internal(detJ, J0); for (d = 0; d < dim; d++) { for (f = 0; f < dim; f++) { J[d*dim+f] = 0.0; for (g = 0; g < dim; g++) { J[d*dim+f] += R[d*dim+g]*J0[g*dim+f]; } } } PetscLogFlops(18.0); } if (invJ) {Invert3D_Internal(invJ, J, *detJ);} } else if (numCoords == 6) { const PetscInt dim = 2; if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} if (J) { for (d = 0; d < dim; d++) { for (f = 0; f < dim; f++) { J[d*dim+f] = 0.5*(PetscRealPart(coords[(f+1)*dim+d]) - PetscRealPart(coords[0*dim+d])); } } PetscLogFlops(8.0); Det2D_Internal(detJ, J); } if (invJ) {Invert2D_Internal(invJ, J, *detJ);} } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of coordinates for this triangle is %d != 6", numCoords); ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeRectangleGeometry_Internal" static PetscErrorCode DMPlexComputeRectangleGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) { PetscSection coordSection; Vec coordinates; PetscScalar *coords; PetscInt numCoords, d, f, g; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); *detJ = 0.0; if (numCoords == 12) { const PetscInt dim = 3; PetscReal R[9], J0[9] = {1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0}; if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} ierr = DMPlexComputeProjection3Dto2D_Internal(numCoords, coords, R);CHKERRQ(ierr); if (J) { const PetscInt pdim = 2; for (d = 0; d < pdim; d++) { J0[d*dim+0] = 0.5*(PetscRealPart(coords[1*pdim+d]) - PetscRealPart(coords[0*pdim+d])); J0[d*dim+1] = 0.5*(PetscRealPart(coords[3*pdim+d]) - PetscRealPart(coords[0*pdim+d])); } PetscLogFlops(8.0); Det3D_Internal(detJ, J0); for (d = 0; d < dim; d++) { for (f = 0; f < dim; f++) { J[d*dim+f] = 0.0; for (g = 0; g < dim; g++) { J[d*dim+f] += R[d*dim+g]*J0[g*dim+f]; } } } PetscLogFlops(18.0); } if (invJ) {Invert3D_Internal(invJ, J, *detJ);} } else if (numCoords == 8) { const PetscInt dim = 2; if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} if (J) { for (d = 0; d < dim; d++) { J[d*dim+0] = 0.5*(PetscRealPart(coords[1*dim+d]) - PetscRealPart(coords[0*dim+d])); J[d*dim+1] = 0.5*(PetscRealPart(coords[3*dim+d]) - PetscRealPart(coords[0*dim+d])); } PetscLogFlops(8.0); Det2D_Internal(detJ, J); } if (invJ) {Invert2D_Internal(invJ, J, *detJ);} } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of coordinates for this quadrilateral is %d != 6", numCoords); ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeTetrahedronGeometry_Internal" static PetscErrorCode DMPlexComputeTetrahedronGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) { PetscSection coordSection; Vec coordinates; PetscScalar *coords; const PetscInt dim = 3; PetscInt d; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); *detJ = 0.0; if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} if (J) { for (d = 0; d < dim; d++) { /* I orient with outward face normals */ J[d*dim+0] = 0.5*(PetscRealPart(coords[2*dim+d]) - PetscRealPart(coords[0*dim+d])); J[d*dim+1] = 0.5*(PetscRealPart(coords[1*dim+d]) - PetscRealPart(coords[0*dim+d])); J[d*dim+2] = 0.5*(PetscRealPart(coords[3*dim+d]) - PetscRealPart(coords[0*dim+d])); } PetscLogFlops(18.0); Det3D_Internal(detJ, J); } if (invJ) {Invert3D_Internal(invJ, J, *detJ);} ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeHexahedronGeometry_Internal" static PetscErrorCode DMPlexComputeHexahedronGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) { PetscSection coordSection; Vec coordinates; PetscScalar *coords; const PetscInt dim = 3; PetscInt d; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); *detJ = 0.0; if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} if (J) { for (d = 0; d < dim; d++) { J[d*dim+0] = 0.5*(PetscRealPart(coords[3*dim+d]) - PetscRealPart(coords[0*dim+d])); J[d*dim+1] = 0.5*(PetscRealPart(coords[1*dim+d]) - PetscRealPart(coords[0*dim+d])); J[d*dim+2] = 0.5*(PetscRealPart(coords[4*dim+d]) - PetscRealPart(coords[0*dim+d])); } PetscLogFlops(18.0); Det3D_Internal(detJ, J); } if (invJ) {Invert3D_Internal(invJ, J, *detJ);} ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeCellGeometry" /*@C DMPlexComputeCellGeometry - Compute the Jacobian, inverse Jacobian, and Jacobian determinant for a given cell Collective on DM Input Arguments: + dm - the DM - cell - the cell Output Arguments: + v0 - the translation part of this affine transform . J - the Jacobian of the transform from the reference element . invJ - the inverse of the Jacobian - detJ - the Jacobian determinant Level: advanced Fortran Notes: Since it returns arrays, this routine is only available in Fortran 90, and you must include petsc.h90 in your code. .seealso: DMPlexGetCoordinateSection(), DMPlexGetCoordinateVec() @*/ PetscErrorCode DMPlexComputeCellGeometry(DM dm, PetscInt cell, PetscReal *v0, PetscReal *J, PetscReal *invJ, PetscReal *detJ) { PetscInt depth, dim, coneSize; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); if (depth == 1) { ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); switch (dim) { case 1: ierr = DMPlexComputeLineGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); break; case 2: switch (coneSize) { case 3: ierr = DMPlexComputeTriangleGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); break; case 4: ierr = DMPlexComputeRectangleGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); break; default: SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported number of vertices %D in cell %D for element geometry computation", coneSize, cell); } break; case 3: switch (coneSize) { case 4: ierr = DMPlexComputeTetrahedronGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); break; case 8: ierr = DMPlexComputeHexahedronGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); break; default: SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported number of vertices %D in cell %D for element geometry computation", coneSize, cell); } break; default: SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension %D for element geometry computation", dim); } } else { /* We need to keep a pointer to the depth label */ ierr = DMPlexGetLabelValue(dm, "depth", cell, &dim);CHKERRQ(ierr); /* Cone size is now the number of faces */ switch (dim) { case 1: ierr = DMPlexComputeLineGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); break; case 2: switch (coneSize) { case 3: ierr = DMPlexComputeTriangleGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); break; case 4: ierr = DMPlexComputeRectangleGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); break; default: SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported number of vertices %D in cell %D for element geometry computation", coneSize, cell); } break; case 3: switch (coneSize) { case 4: ierr = DMPlexComputeTetrahedronGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); break; case 6: ierr = DMPlexComputeHexahedronGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); break; default: SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported number of vertices %D in cell %D for element geometry computation", coneSize, cell); } break; default: SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension %D for element geometry computation", dim); } } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeGeometryFVM_1D_Internal" static PetscErrorCode DMPlexComputeGeometryFVM_1D_Internal(DM dm, PetscInt dim, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) { PetscSection coordSection; Vec coordinates; PetscScalar *coords; PetscInt coordSize; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); if (dim != 2) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "We only support 2D edges right now"); if (centroid) { centroid[0] = 0.5*PetscRealPart(coords[0] + coords[dim+0]); centroid[1] = 0.5*PetscRealPart(coords[1] + coords[dim+1]); } if (normal) { normal[0] = PetscRealPart(coords[1] - coords[dim+1]); normal[1] = -PetscRealPart(coords[0] - coords[dim+0]); } if (vol) { *vol = sqrt(PetscSqr(PetscRealPart(coords[0] - coords[dim+0])) + PetscSqr(PetscRealPart(coords[1] - coords[dim+1]))); } ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeGeometryFVM_2D_Internal" /* Centroid_i = (\sum_n A_n Cn_i ) / A */ static PetscErrorCode DMPlexComputeGeometryFVM_2D_Internal(DM dm, PetscInt dim, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) { PetscSection coordSection; Vec coordinates; PetscScalar *coords = NULL; PetscReal vsum = 0.0, csum[3] = {0.0, 0.0, 0.0}, vtmp, ctmp[4], v0[3], R[9]; PetscInt tdim = 2, coordSize, numCorners, p, d, e; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetConeSize(dm, cell, &numCorners);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); dim = coordSize/numCorners; if (normal) { if (dim > 2) { const PetscReal x0 = PetscRealPart(coords[dim+0] - coords[0]), x1 = PetscRealPart(coords[dim*2+0] - coords[0]); const PetscReal y0 = PetscRealPart(coords[dim+1] - coords[1]), y1 = PetscRealPart(coords[dim*2+1] - coords[1]); const PetscReal z0 = PetscRealPart(coords[dim+2] - coords[2]), z1 = PetscRealPart(coords[dim*2+2] - coords[2]); PetscReal norm; v0[0] = PetscRealPart(coords[0]); v0[1] = PetscRealPart(coords[1]); v0[2] = PetscRealPart(coords[2]); normal[0] = y0*z1 - z0*y1; normal[1] = z0*x1 - x0*z1; normal[2] = x0*y1 - y0*x1; norm = sqrt(normal[0]*normal[0] + normal[1]*normal[1] + normal[2]*normal[2]); normal[0] /= norm; normal[1] /= norm; normal[2] /= norm; } else { for (d = 0; d < dim; ++d) normal[d] = 0.0; } } if (dim == 3) {ierr = DMPlexComputeProjection3Dto2D_Internal(coordSize, coords, R);CHKERRQ(ierr);} for (p = 0; p < numCorners; ++p) { /* Need to do this copy to get types right */ for (d = 0; d < tdim; ++d) { ctmp[d] = PetscRealPart(coords[p*tdim+d]); ctmp[tdim+d] = PetscRealPart(coords[((p+1)%numCorners)*tdim+d]); } Volume_Triangle_Origin_Internal(&vtmp, ctmp); vsum += vtmp; for (d = 0; d < tdim; ++d) { csum[d] += (ctmp[d] + ctmp[tdim+d])*vtmp; } } for (d = 0; d < tdim; ++d) { csum[d] /= (tdim+1)*vsum; } ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); if (vol) *vol = PetscAbsReal(vsum); if (centroid) { if (dim > 2) { for (d = 0; d < dim; ++d) { centroid[d] = v0[d]; for (e = 0; e < dim; ++e) { centroid[d] += R[d*dim+e]*csum[e]; } } } else for (d = 0; d < dim; ++d) centroid[d] = csum[d]; } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeGeometryFVM_3D_Internal" /* Centroid_i = (\sum_n V_n Cn_i ) / V */ static PetscErrorCode DMPlexComputeGeometryFVM_3D_Internal(DM dm, PetscInt dim, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) { PetscSection coordSection; Vec coordinates; PetscScalar *coords = NULL; PetscReal vsum = 0.0, vtmp, coordsTmp[3*3]; const PetscInt *faces; PetscInt numFaces, f, coordSize, numCorners, p, d; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); if (centroid) for (d = 0; d < dim; ++d) centroid[d] = 0.0; ierr = DMPlexGetConeSize(dm, cell, &numFaces);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr); for (f = 0; f < numFaces; ++f) { ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, faces[f], &coordSize, &coords);CHKERRQ(ierr); numCorners = coordSize/dim; switch (numCorners) { case 3: for (d = 0; d < dim; ++d) { coordsTmp[0*dim+d] = PetscRealPart(coords[0*dim+d]); coordsTmp[1*dim+d] = PetscRealPart(coords[1*dim+d]); coordsTmp[2*dim+d] = PetscRealPart(coords[2*dim+d]); } Volume_Tetrahedron_Origin_Internal(&vtmp, coordsTmp); vsum += vtmp; if (centroid) { for (d = 0; d < dim; ++d) { for (p = 0; p < 3; ++p) centroid[d] += coordsTmp[p*dim+d]*vtmp; } } break; case 4: /* DO FOR PYRAMID */ /* First tet */ for (d = 0; d < dim; ++d) { coordsTmp[0*dim+d] = PetscRealPart(coords[0*dim+d]); coordsTmp[1*dim+d] = PetscRealPart(coords[1*dim+d]); coordsTmp[2*dim+d] = PetscRealPart(coords[3*dim+d]); } Volume_Tetrahedron_Origin_Internal(&vtmp, coordsTmp); vsum += vtmp; if (centroid) { for (d = 0; d < dim; ++d) { for (p = 0; p < 3; ++p) centroid[d] += coordsTmp[p*dim+d]*vtmp; } } /* Second tet */ for (d = 0; d < dim; ++d) { coordsTmp[0*dim+d] = PetscRealPart(coords[1*dim+d]); coordsTmp[1*dim+d] = PetscRealPart(coords[2*dim+d]); coordsTmp[2*dim+d] = PetscRealPart(coords[3*dim+d]); } Volume_Tetrahedron_Origin_Internal(&vtmp, coordsTmp); vsum += vtmp; if (centroid) { for (d = 0; d < dim; ++d) { for (p = 0; p < 3; ++p) centroid[d] += coordsTmp[p*dim+d]*vtmp; } } break; default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Cannot handle faces with %d vertices", numCorners); } ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); } if (vol) *vol = PetscAbsReal(vsum); if (normal) for (d = 0; d < dim; ++d) normal[d] = 0.0; if (centroid) for (d = 0; d < dim; ++d) centroid[d] /= (vsum*4); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "DMPlexComputeCellGeometryFVM" /*@C DMPlexComputeCellGeometryFVM - Compute the volume for a given cell Collective on DM Input Arguments: + dm - the DM - cell - the cell Output Arguments: + volume - the cell volume . centroid - the cell centroid - normal - the cell normal, if appropriate Level: advanced Fortran Notes: Since it returns arrays, this routine is only available in Fortran 90, and you must include petsc.h90 in your code. .seealso: DMPlexGetCoordinateSection(), DMPlexGetCoordinateVec() @*/ PetscErrorCode DMPlexComputeCellGeometryFVM(DM dm, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) { PetscInt depth, dim; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); if (depth != dim) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh must be interpolated"); /* We need to keep a pointer to the depth label */ ierr = DMPlexGetLabelValue(dm, "depth", cell, &depth);CHKERRQ(ierr); /* Cone size is now the number of faces */ switch (depth) { case 1: ierr = DMPlexComputeGeometryFVM_1D_Internal(dm, dim, cell, vol, centroid, normal);CHKERRQ(ierr); break; case 2: ierr = DMPlexComputeGeometryFVM_2D_Internal(dm, dim, cell, vol, centroid, normal);CHKERRQ(ierr); break; case 3: ierr = DMPlexComputeGeometryFVM_3D_Internal(dm, dim, cell, vol, centroid, normal);CHKERRQ(ierr); break; default: SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension %D for element geometry computation", dim); } PetscFunctionReturn(0); }