/usr/lib/petscdir/3.4.2/include/sieve/DMBuilder.hh is in libpetsc3.4.2-dev 3.4.2.dfsg1-8.1+b1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#define included_ALE_DMBuilder_hh
#ifndef included_ALE_Mesh_hh
#include <sieve/Mesh.hh>
#endif
#include <petscdmmesh.hh>
namespace ALE {
class DMBuilder {
public:
#undef __FUNCT__
#define __FUNCT__ "createBasketMesh"
static PetscErrorCode createBasketMesh(MPI_Comm comm, const int dim, const bool structured, const bool interpolate, const int debug, DM *dm) {
typedef PETSC_MESH_TYPE::real_section_type::value_type real;
PetscErrorCode ierr;
PetscFunctionBegin;
if (structured) {
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP, "Structured grids cannot handle boundary meshes");
} else {
typedef ALE::Mesh<PetscInt,PetscScalar> FlexMesh;
typedef PETSC_MESH_TYPE::point_type point_type;
DM boundary;
ierr = DMCreate(comm, &boundary);CHKERRQ(ierr);
ierr = DMSetType(boundary, DMMESH);CHKERRQ(ierr);
Obj<PETSC_MESH_TYPE> meshBd = new PETSC_MESH_TYPE(comm, dim-1, debug);
Obj<PETSC_MESH_TYPE::sieve_type> sieve = new PETSC_MESH_TYPE::sieve_type(comm, debug);
std::map<point_type,point_type> renumbering;
Obj<FlexMesh> mB;
meshBd->setSieve(sieve);
if (dim == 2) {
real lower[2] = {0.0, 0.0};
real upper[2] = {1.0, 1.0};
int edges = 2;
mB = ALE::MeshBuilder<FlexMesh>::createSquareBoundary(comm, lower, upper, edges, debug);
} else if (dim == 3) {
real lower[3] = {0.0, 0.0, 0.0};
real upper[3] = {1.0, 1.0, 1.0};
int faces[3] = {3, 3, 3};
mB = ALE::MeshBuilder<FlexMesh>::createCubeBoundary(comm, lower, upper, faces, debug);
} else {
SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP, "Dimension not supported: %d", dim);
}
ALE::ISieveConverter::convertMesh(*mB, *meshBd, renumbering, false);
ierr = DMMeshSetMesh(boundary, meshBd);CHKERRQ(ierr);
*dm = boundary;
}
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "createBoxMesh"
static PetscErrorCode createBoxMesh(MPI_Comm comm, const int dim, const bool structured, const bool interpolate, const int debug, DM *dm) {
typedef PETSC_MESH_TYPE::real_section_type::value_type real;
PetscErrorCode ierr;
PetscFunctionBegin;
if (structured) {
DM da;
const PetscInt dof = 1;
const PetscInt pd = PETSC_DECIDE;
if (dim == 2) {
ierr = DMDACreate2d(comm, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE, DMDA_STENCIL_BOX, -3, -3, pd, pd, dof, 1, NULL, NULL, &da);CHKERRQ(ierr);
} else if (dim == 3) {
ierr = DMDACreate3d(comm, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE, DMDA_STENCIL_BOX, -3, -3, -3, pd, pd, pd, dof, 1, NULL, NULL, NULL, &da);CHKERRQ(ierr);
} else {
SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP, "Dimension not supported: %d", dim);
}
ierr = DMDASetUniformCoordinates(da, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0);CHKERRQ(ierr);
*dm = da;
} else {
typedef ALE::Mesh<PetscInt,PetscScalar> FlexMesh;
typedef PETSC_MESH_TYPE::point_type point_type;
DM mesh;
DM boundary;
ierr = DMCreate(comm, &boundary);CHKERRQ(ierr);
ierr = DMSetType(boundary, DMMESH);CHKERRQ(ierr);
Obj<PETSC_MESH_TYPE> meshBd = new PETSC_MESH_TYPE(comm, dim-1, debug);
Obj<PETSC_MESH_TYPE::sieve_type> sieve = new PETSC_MESH_TYPE::sieve_type(comm, debug);
std::map<point_type,point_type> renumbering;
Obj<FlexMesh> mB;
meshBd->setSieve(sieve);
if (dim == 2) {
real lower[2] = {0.0, 0.0};
real upper[2] = {1.0, 1.0};
int edges[2] = {2, 2};
mB = ALE::MeshBuilder<FlexMesh>::createSquareBoundary(comm, lower, upper, edges, debug);
} else if (dim == 3) {
real lower[3] = {0.0, 0.0, 0.0};
real upper[3] = {1.0, 1.0, 1.0};
int faces[3] = {3, 3, 3};
mB = ALE::MeshBuilder<FlexMesh>::createCubeBoundary(comm, lower, upper, faces, debug);
} else {
SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP, "Dimension not supported: %d", dim);
}
ALE::ISieveConverter::convertMesh(*mB, *meshBd, renumbering, false);
ierr = DMMeshSetMesh(boundary, meshBd);CHKERRQ(ierr);
ierr = DMMeshGenerate(boundary, (PetscBool) interpolate, &mesh);CHKERRQ(ierr);
ierr = DMDestroy(&boundary);CHKERRQ(ierr);
*dm = mesh;
}
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "createReentrantBoxMesh"
static PetscErrorCode createReentrantBoxMesh(MPI_Comm comm, const int dim, const bool interpolate, const int debug, DM *dm) {
typedef ALE::Mesh<PetscInt,PetscScalar> FlexMesh;
typedef PETSC_MESH_TYPE::point_type point_type;
typedef PETSC_MESH_TYPE::real_section_type::value_type real;
DM mesh;
DM boundary;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMCreate(comm, &boundary);CHKERRQ(ierr);
ierr = DMSetType(boundary, DMMESH);CHKERRQ(ierr);
Obj<PETSC_MESH_TYPE> meshBd = new PETSC_MESH_TYPE(comm, dim-1, debug);
Obj<PETSC_MESH_TYPE::sieve_type> sieve = new PETSC_MESH_TYPE::sieve_type(comm, debug);
std::map<point_type,point_type> renumbering;
Obj<FlexMesh> mB;
meshBd->setSieve(sieve);
if (dim == 2) {
real lower[2] = {-1.0, -1.0};
real upper[2] = {1.0, 1.0};
real offset[2] = {0.5, 0.5};
mB = ALE::MeshBuilder<FlexMesh>::createReentrantBoundary(comm, lower, upper, offset, debug);
} else if (dim == 3) {
real lower[3] = {-1.0, -1.0, -1.0};
real upper[3] = { 1.0, 1.0, 1.0};
real offset[3] = { 0.5, 0.5, 0.5};
mB = ALE::MeshBuilder<FlexMesh>::createFicheraCornerBoundary(comm, lower, upper, offset, debug);
} else {
SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP, "Dimension not supported: %d", dim);
}
ALE::ISieveConverter::convertMesh(*mB, *meshBd, renumbering, false);
ierr = DMMeshSetMesh(boundary, meshBd);CHKERRQ(ierr);
ierr = DMMeshGenerate(boundary, (PetscBool) interpolate, &mesh);CHKERRQ(ierr);
ierr = DMDestroy(&boundary);CHKERRQ(ierr);
*dm = mesh;
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "createSphericalMesh"
static PetscErrorCode createSphericalMesh(MPI_Comm comm, const int dim, const bool interpolate, const int debug, DM *dm) {
typedef ALE::Mesh<PetscInt,PetscScalar> FlexMesh;
typedef PETSC_MESH_TYPE::point_type point_type;
DM mesh;
DM boundary;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMCreate(comm, &boundary);CHKERRQ(ierr);
ierr = DMSetType(boundary, DMMESH);CHKERRQ(ierr);
Obj<PETSC_MESH_TYPE> meshBd = new PETSC_MESH_TYPE(comm, dim-1, debug);
Obj<PETSC_MESH_TYPE::sieve_type> sieve = new PETSC_MESH_TYPE::sieve_type(comm, debug);
std::map<point_type,point_type> renumbering;
Obj<FlexMesh> mB;
meshBd->setSieve(sieve);
if (dim == 2) {
mB = ALE::MeshBuilder<FlexMesh>::createCircularReentrantBoundary(comm, 100, 1.0, 1.0, debug);
} else {
SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP, "Dimension not supported: %d", dim);
}
ALE::ISieveConverter::convertMesh(*mB, *meshBd, renumbering, false);
ierr = DMMeshSetMesh(boundary, meshBd);CHKERRQ(ierr);
ierr = DMMeshGenerate(boundary, (PetscBool) interpolate, &mesh);CHKERRQ(ierr);
ierr = DMDestroy(&boundary);CHKERRQ(ierr);
*dm = mesh;
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "createReentrantSphericalMesh"
static PetscErrorCode createReentrantSphericalMesh(MPI_Comm comm, const int dim, const bool interpolate, const int debug, DM *dm) {
typedef ALE::Mesh<PetscInt,PetscScalar> FlexMesh;
typedef PETSC_MESH_TYPE::point_type point_type;
DM mesh;
DM boundary;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMCreate(comm, &boundary);CHKERRQ(ierr);
ierr = DMSetType(boundary, DMMESH);CHKERRQ(ierr);
Obj<PETSC_MESH_TYPE> meshBd = new PETSC_MESH_TYPE(comm, dim-1, debug);
Obj<PETSC_MESH_TYPE::sieve_type> sieve = new PETSC_MESH_TYPE::sieve_type(comm, debug);
std::map<point_type,point_type> renumbering;
Obj<FlexMesh> mB;
meshBd->setSieve(sieve);
if (dim == 2) {
mB = ALE::MeshBuilder<FlexMesh>::createCircularReentrantBoundary(comm, 100, 1.0, 0.9, debug);
} else {
SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP, "Dimension not supported: %d", dim);
}
ALE::ISieveConverter::convertMesh(*mB, *meshBd, renumbering, false);
ierr = DMMeshSetMesh(boundary, meshBd);CHKERRQ(ierr);
ierr = DMMeshGenerate(boundary, (PetscBool) interpolate, &mesh);CHKERRQ(ierr);
ierr = DMDestroy(&boundary);CHKERRQ(ierr);
*dm = mesh;
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "MeshRefineSingularity"
static PetscErrorCode MeshRefineSingularity(DM mesh, double * singularity, double factor, DM *refinedMesh) {
typedef PETSC_MESH_TYPE::real_section_type::value_type real;
ALE::Obj<PETSC_MESH_TYPE> oldMesh;
double oldLimit;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMMeshGetMesh(mesh, oldMesh);CHKERRQ(ierr);
ierr = DMCreate(oldMesh->comm(), refinedMesh);CHKERRQ(ierr);
ierr = DMSetType(*refinedMesh, DMMESH);CHKERRQ(ierr);
int dim = oldMesh->getDimension();
oldLimit = oldMesh->getMaxVolume();
//double oldLimInv = 1./oldLimit;
real curLimit, tmpLimit;
real minLimit = oldLimit/16384.; //arbitrary;
const ALE::Obj<PETSC_MESH_TYPE::real_section_type>& coordinates = oldMesh->getRealSection("coordinates");
const ALE::Obj<PETSC_MESH_TYPE::real_section_type>& volume_limits = oldMesh->getRealSection("volume_limits");
volume_limits->setFiberDimension(oldMesh->heightStratum(0), 1);
oldMesh->allocate(volume_limits);
const ALE::Obj<PETSC_MESH_TYPE::label_sequence>& cells = oldMesh->heightStratum(0);
PETSC_MESH_TYPE::label_sequence::iterator c_iter = cells->begin();
PETSC_MESH_TYPE::label_sequence::iterator c_iter_end = cells->end();
real centerCoords[dim];
while (c_iter != c_iter_end) {
const real * coords = oldMesh->restrictClosure(coordinates, *c_iter);
for (int i = 0; i < dim; i++) {
centerCoords[i] = 0;
for (int j = 0; j < dim+1; j++) {
centerCoords[i] += coords[j*dim+i];
}
centerCoords[i] = centerCoords[i]/(dim+1);
}
real dist = 0.;
for (int i = 0; i < dim; i++) {
dist += (centerCoords[i] - singularity[i])*(centerCoords[i] - singularity[i]);
}
if (dist > 0.) {
dist = sqrt(dist);
real mu = pow(dist, factor);
//PetscPrintf(oldMesh->comm(), "%f\n", mu);
tmpLimit = oldLimit*pow(mu, dim);
if (tmpLimit > minLimit) {
curLimit = tmpLimit;
} else curLimit = minLimit;
} else curLimit = minLimit;
//PetscPrintf(oldMesh->comm(), "%f, %f\n", dist, tmpLimit);
volume_limits->updatePoint(*c_iter, &curLimit);
c_iter++;
}
#ifdef PETSC_OPT_SIEVE
ALE::Obj<PETSC_MESH_TYPE> newMesh = ALE::Generator<PETSC_MESH_TYPE>::refineMeshV(oldMesh, volume_limits, true);
#else
ALE::Obj<PETSC_MESH_TYPE> newMesh = ALE::Generator<PETSC_MESH_TYPE>::refineMesh(oldMesh, volume_limits, true);
#endif
ierr = DMMeshSetMesh(*refinedMesh, newMesh);CHKERRQ(ierr);
const ALE::Obj<PETSC_MESH_TYPE::real_section_type>& s = newMesh->getRealSection("default");
const Obj<std::set<std::string> >& discs = oldMesh->getDiscretizations();
for(std::set<std::string>::const_iterator f_iter = discs->begin(); f_iter != discs->end(); ++f_iter) {
newMesh->setDiscretization(*f_iter, oldMesh->getDiscretization(*f_iter));
}
newMesh->setupField(s);
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "MeshRefineSingularity_Fichera"
static PetscErrorCode MeshRefineSingularity_Fichera(DM mesh, double * singularity, double factor, DM *refinedMesh) {
typedef PETSC_MESH_TYPE::real_section_type::value_type real;
ALE::Obj<PETSC_MESH_TYPE> oldMesh;
real oldLimit;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMMeshGetMesh(mesh, oldMesh);CHKERRQ(ierr);
ierr = DMCreate(oldMesh->comm(), refinedMesh);CHKERRQ(ierr);
ierr = DMSetType(*refinedMesh, DMMESH);CHKERRQ(ierr);
int dim = oldMesh->getDimension();
oldLimit = oldMesh->getMaxVolume();
//double oldLimInv = 1./oldLimit;
real curLimit, tmpLimit;
real minLimit = oldLimit/16384.; //arbitrary;
const ALE::Obj<PETSC_MESH_TYPE::real_section_type>& coordinates = oldMesh->getRealSection("coordinates");
const ALE::Obj<PETSC_MESH_TYPE::real_section_type>& volume_limits = oldMesh->getRealSection("volume_limits");
volume_limits->setFiberDimension(oldMesh->heightStratum(0), 1);
oldMesh->allocate(volume_limits);
const ALE::Obj<PETSC_MESH_TYPE::label_sequence>& cells = oldMesh->heightStratum(0);
PETSC_MESH_TYPE::label_sequence::iterator c_iter = cells->begin();
PETSC_MESH_TYPE::label_sequence::iterator c_iter_end = cells->end();
real centerCoords[dim];
while (c_iter != c_iter_end) {
const real *coords = oldMesh->restrictClosure(coordinates, *c_iter);
for (int i = 0; i < dim; i++) {
centerCoords[i] = 0;
for (int j = 0; j < dim+1; j++) {
centerCoords[i] += coords[j*dim+i];
}
centerCoords[i] = centerCoords[i]/(dim+1);
//PetscPrintf(oldMesh->comm(), "%f, ", centerCoords[i]);
}
//PetscPrintf(oldMesh->comm(), "\n");
real dist = 0.;
real cornerdist = 0.;
//HERE'S THE DIFFERENCE: if centercoords is less than the singularity coordinate for each direction, include that direction in the distance
/*
for (int i = 0; i < dim; i++) {
if (centerCoords[i] <= singularity[i]) {
dist += (centerCoords[i] - singularity[i])*(centerCoords[i] - singularity[i]);
}
}
*/
//determine: the per-dimension distance: cases
for (int i = 0; i < dim; i++) {
cornerdist = 0.;
if (centerCoords[i] > singularity[i]) {
for (int j = 0; j < dim; j++) {
if (j != i) cornerdist += (centerCoords[j] - singularity[j])*(centerCoords[j] - singularity[j]);
}
if (cornerdist < dist || dist == 0.) dist = cornerdist;
}
}
//patch up AROUND the corner by minimizing between the distance from the relevant axis and the singular vertex
real singdist = 0.;
for (int i = 0; i < dim; i++) {
singdist += (centerCoords[i] - singularity[i])*(centerCoords[i] - singularity[i]);
}
if (singdist < dist || dist == 0.) dist = singdist;
if (dist > 0.) {
dist = sqrt(dist);
real mu = pow(dist, factor);
//PetscPrintf(oldMesh->comm(), "%f, %f\n", mu, dist);
tmpLimit = oldLimit*pow(mu, dim);
if (tmpLimit > minLimit) {
curLimit = tmpLimit;
} else curLimit = minLimit;
} else curLimit = minLimit;
//PetscPrintf(oldMesh->comm(), "%f, %f\n", dist, tmpLimit);
volume_limits->updatePoint(*c_iter, &curLimit);
c_iter++;
}
#ifdef PETSC_OPT_SIEVE
ALE::Obj<PETSC_MESH_TYPE> newMesh = ALE::Generator<PETSC_MESH_TYPE>::refineMeshV(oldMesh, volume_limits, true);
#else
ALE::Obj<PETSC_MESH_TYPE> newMesh = ALE::Generator<PETSC_MESH_TYPE>::refineMesh(oldMesh, volume_limits, true);
#endif
ierr = DMMeshSetMesh(*refinedMesh, newMesh);CHKERRQ(ierr);
const ALE::Obj<PETSC_MESH_TYPE::real_section_type>& s = newMesh->getRealSection("default");
const Obj<std::set<std::string> >& discs = oldMesh->getDiscretizations();
for(std::set<std::string>::const_iterator f_iter = discs->begin(); f_iter != discs->end(); ++f_iter) {
newMesh->setDiscretization(*f_iter, oldMesh->getDiscretization(*f_iter));
}
newMesh->setupField(s);
// PetscPrintf(newMesh->comm(), "refined\n");
PetscFunctionReturn(0);
};
};
}
#endif
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