/usr/lib/petscdir/3.1/include/sieve/problem/Ex_UFC.hh is in libpetsc3.1-dev 3.1.dfsg-11ubuntu1.
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#define included_ALE_Problem_Bratu_hh
#include <DMBuilder.hh>
#include <petscmesh_viewers.hh>
#include <petscdmmg.h>
#include <UFCProblem.hh>
namespace ALE {
namespace Problem {
typedef enum {RUN_FULL, RUN_TEST, RUN_MESH} RunType;
typedef enum {NEUMANN, DIRICHLET} BCType;
typedef enum {POISSON, VECTORPOISSON, STOKES, MIXEDPOISSON} UFCFormType;
typedef enum {ASSEMBLY_FULL, ASSEMBLY_STORED, ASSEMBLY_CALCULATED} AssemblyType;
typedef union {SectionReal section; Vec vec;} ExactSolType;
typedef struct {
PetscInt debug; // The debugging level
RunType run; // The run type
PetscInt dim; // The topological mesh dimension
PetscTruth reentrantMesh; // Generate a reentrant mesh?
PetscTruth circularMesh; // Generate a circular mesh?
PetscTruth refineSingularity; // Generate an a priori graded mesh for the poisson problem
PetscTruth generateMesh; // Generate the unstructure mesh
PetscTruth interpolate; // Generate intermediate mesh elements
PetscReal refinementLimit; // The largest allowable cell volume
char baseFilename[2048]; // The base filename for mesh files
char partitioner[2048]; // The graph partitioner
ufc::function * func; // The function to project -- should be the WHOLE RANK of the object
BCType bcType; // The type of boundary conditions
ufc::function * exactFunc; // The exact solution function
ExactSolType exactSol; // The discrete exact solution
ExactSolType error; // The discrete cell-wise error
AssemblyType operatorAssembly; // The type of operator assembly
//double (*integrate)(const double *, const double *, const int, double (*)(const double *)); // Basis functional application
double reentrant_angle; // The angle for the reentrant corner.
UFCFormType form_type; // The form to solve
} Ex_UFCOptions;
namespace UFCFunctions {
class coordinates : public ufc::function {
int _dim;
int nevaluations;
public:
coordinates(int dim) {
_dim = dim;
nevaluations = 0;
}
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
if (nevaluations < 6) {
values[0] = coordinates[_dim];
} else {
values[0] = -10.;
}
}
};
class zero_scalar : public ufc::function {
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
values[0] = 0.;
}
};
class zero_vector : public ufc::function {
private:
int _order;
public:
zero_vector(int ord) : ufc::function() {
_order = ord;
};
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
for (int i = 0; i < _order; i++) values[i] = 0.;
}
};
class constant_scalar : public ufc::function {
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
values[0] = -4.0;
}
};
class constant_vector : public ufc::function {
private:
int _order;
double _constant;
public:
constant_vector(int ord, double constant) : ufc::function() {
_order = ord;
_constant = constant;
}
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
for (int i = 0; i < _order; i++) values[i] = _constant;
}
};
class nonlinear_2d_scalar : public ufc::function {
public:
double lambda;
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
// PetscScalar nonlinear_2d(const double x[]) {
values[0] = -4.0 - lambda*PetscExpScalar(coordinates[0]*coordinates[0] + coordinates[1]*coordinates[1]);
}
};
class singularity_2d_scalar : public ufc::function {
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
//PetscScalar singularity_2d(const double x[]) {
values[0] = 0.;
}
};
class singularity_exact_2d_scalar : public ufc::function {
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
//PetscScalar singularity_exact_2d(const double x[]) {
double r = sqrt(coordinates[0]*coordinates[0] + coordinates[1]*coordinates[1]);
double theta;
if (r == 0.) {
values[0] = 0.;
return;
} else theta = asin(coordinates[1]/r);
if (coordinates[0] < 0) {
theta = 2*M_PI - theta;
}
values[0] = pow(r, 2./3.)*sin((2./3.)*theta);
}
};
class singularity_3d_exact_scalar : public ufc::function {
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
//PetscScalar singularity_exact_3d(const double x[]) {
values[0] = sin(coordinates[0] + coordinates[1] + coordinates[2]);
}
};
class singularity_3d_scalar : public ufc::function {
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
//PetscScalar singularity_3d(const double x[]) {
values[0] = (3)*sin(coordinates[0] + coordinates[1] + coordinates[2]);
}
};
class linear_2d_scalar : public ufc::function {
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
//PetscScalar linear_2d(const double x[]) {
values[0] = -6.0*(coordinates[0] - 0.5) - 6.0*(coordinates[1] - 0.5);
}
};
class quadratic_2d_scalar : public ufc::function {
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
//PetscScalar quadratic_2d(const double x[]) {
values[0] = coordinates[0]*coordinates[0] + coordinates[1]*coordinates[1];
}
};
class quadratic_vector : public ufc::function {
private:
int _embed_dim;
int _vector_dim;
double _factor;
public:
quadratic_vector (int embed_dim, int vector_dim, double factor = 1.) : ufc::function() {
_embed_dim = embed_dim;
_vector_dim = vector_dim;
_factor = factor;
}
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
//PetscScalar quadratic_2d(const double x[]) {
for (int i = 0; i < _vector_dim; i++) {
values[i] = 0.;
for (int j = 0; j < _embed_dim; j++) {
values[i] += _factor*coordinates[j]*coordinates[j];
}
}
}
};
class cubic_2d_scalar : public ufc::function {
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
//PetscScalar cubic_2d(const double x[]) {
values[0] = coordinates[0]*coordinates[0]*coordinates[0] - 1.5*coordinates[0]*coordinates[0]
+ coordinates[1]*coordinates[1]*coordinates[1] - 1.5*coordinates[1]*coordinates[1] + 0.5;
}
};
class nonlinear_3d_scalar : public ufc::function {
public:
double lambda;
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) {
//PetscScalar nonlinear_3d(const double x[]) {
values[0] = -4.0 - lambda*PetscExpScalar((2.0/3.0)*(coordinates[0]*coordinates[0] + coordinates[1]*coordinates[1] + coordinates[2]*coordinates[2]));
}
};
class linear_3d_scalar : public ufc::function {
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) {
//PetscScalar linear_3d(const double x[]) {
values[0] = -6.0*(coordinates[0] - 0.5) - 6.0*(coordinates[1] - 0.5) - 6.0*(coordinates[2] - 0.5);
}
};
class quadratic_3d_scalar : public ufc::function {
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) {
//PetscScalar quadratic_3d(const double x[]) {
values[0] = (2.0/3.0)*(coordinates[0]*coordinates[0] + coordinates[1]*coordinates[1] + coordinates[2]*coordinates[2]);
}
};
class cubic_3d_scalar : public ufc::function {
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) {
//PetscScalar cubic_3d(const double x[]) {
values[0] = coordinates[0]*coordinates[0]*coordinates[0] - 1.5*coordinates[0]*coordinates[0]
+ coordinates[1]*coordinates[1]*coordinates[1] - 1.5*coordinates[1]*coordinates[1]
+ coordinates[2]*coordinates[2]*coordinates[2] - 1.5*coordinates[2]*coordinates[2] + 0.75;
}
};
class cosx_scalar : public ufc::function {
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) {
//PetscScalar cos_x(const double x[]) {
values[0] = cos(2.0*PETSC_PI*coordinates[0]);
}
};
class lid_driven : public ufc::function {
private:
int _dim;
int _topdim;
double _topcoord;
int _flowdirectiondim;
int _curdim;
double _velocity;
public:
lid_driven(int dim, double velocity, double topcoord) : ufc::function() {
_dim = dim;
_velocity = velocity;
_topcoord = topcoord;
}
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
if (coordinates[1] >= _topcoord) {
if (_dim == 2) {
values[0] = 4*(coordinates[0] - 1.)*coordinates[0]*_velocity;
} else if (_dim == 3) {
values[0] = 16*(coordinates[0] - 1.)*coordinates[0]*(coordinates[2] - 1.)*coordinates[2]*_velocity;
}
} else {
values[0] = 0.;
}
}
};
void pinion_pressure(Obj<PETSC_MESH_TYPE> m, int pinned_dimension, double coord_thresh, std::string marker_name, int marker_num) {
//mark a single vertex on the marker label with "marker_num"; we probably don't want to use "marker" due to the possibility of relabeling a boundary vertex
const Obj<PETSC_MESH_TYPE::label_type> & marker = m->createLabel(marker_name);
//first vertex -- nei! don't pin the lid!
int dim = m->getDimension();
//int depth = m->depth();
//ALE::ISieveVisitor::PointRetriever<PETSC_MESH_TYPE::sieve_type> pV((int) pow(m->getSieve()->getMaxConeSize(), m->depth())+1, true);
const Obj<PETSC_MESH_TYPE::label_sequence>& cells = m->heightStratum(0);
const Obj<PETSC_MESH_TYPE::real_section_type>& coordinates = m->getRealSection("coordinates");
PETSC_MESH_TYPE::label_sequence::iterator c_iter = cells->begin();
PETSC_MESH_TYPE::label_sequence::iterator c_iter_end = cells->end();
ALE::ISieveVisitor::PointRetriever<PETSC_MESH_TYPE::sieve_type> pV((int) pow(m->getSieve()->getMaxConeSize(), m->depth())+1, true);
while (c_iter != c_iter_end) {
ALE::ISieveTraversal<PETSC_MESH_TYPE::sieve_type>::orientedClosure(*m->getSieve(), *c_iter, pV);
const PETSC_MESH_TYPE::point_type *oPoints = pV.getPoints();
const int oSize = pV.getSize();
for (int i = 0; i < oSize; i++) {
if (m->depth(oPoints[i]) == 0) {
const double * coords = coordinates->restrictPoint(oPoints[i]);
if (fabs(coords[0] - 0.5) < 0.01 && fabs(coords[1] - 0.5) < 0.01 && dim == 2) {
m->setValue(marker, oPoints[i], marker_num);
m->setValue(marker, *c_iter, marker_num + 1);
PetscPrintf(m->comm(), "pinned %d\n", oPoints[i]);
} else if (fabs(coords[0] - 0.5) < 0.1 && fabs(coords[1] - 0.5) < 0.1 && fabs(coords[2] - 0.5) < 0.1 && dim == 3) {
m->setValue(marker, oPoints[i], marker_num);
m->setValue(marker, *c_iter, marker_num + 1);
}
}
}
pV.clear();
c_iter++;
}
marker->view(marker_name.c_str());
}
void mark_frictionless(Obj<PETSC_MESH_TYPE> m, int constrained_dim, double lowcoord, double highcoord, std::string marker_name, int marker_num) {
//mark a single vertex on the marker label with "marker_num"; we probably don't want to use "marker" due to the possibility of relabeling a boundary vertex
const Obj<PETSC_MESH_TYPE::label_type> & marker = m->createLabel(marker_name);
int dim = m->getDimension();
//int depth = m->depth();
//ALE::ISieveVisitor::PointRetriever<PETSC_MESH_TYPE::sieve_type> pV((int) pow(m->getSieve()->getMaxConeSize(), m->depth())+1, true);
const Obj<PETSC_MESH_TYPE::label_sequence>& cells = m->heightStratum(0); //cells with unknowns on the topological boundary
const Obj<PETSC_MESH_TYPE::real_section_type>& coordinates = m->getRealSection("coordinates");
PETSC_MESH_TYPE::label_sequence::iterator c_iter = cells->begin();
PETSC_MESH_TYPE::label_sequence::iterator c_iter_end = cells->end();
ALE::ISieveVisitor::PointRetriever<PETSC_MESH_TYPE::sieve_type> pV((int) pow(m->getSieve()->getMaxConeSize(), m->depth())+1, true);
while (c_iter != c_iter_end) {
ALE::ISieveTraversal<PETSC_MESH_TYPE::sieve_type>::orientedClosure(*m->getSieve(), *c_iter, pV);
const PETSC_MESH_TYPE::point_type *oPoints = pV.getPoints();
const int oSize = pV.getSize();
for (int i = 0; i < oSize; i++) {
PETSC_MESH_TYPE::point_type p = oPoints[i];
if (m->getValue(m->getLabel("marker"), p) == 1) {
const double * coords = m->restrictClosure(coordinates, p);
//if any aren't at the threshhold don't constrain
bool flag = true;
for (int d = 0; d < m->depth(p)+1; d++) {
if (coords[d*dim+constrained_dim] <= lowcoord || coords[d*dim+constrained_dim] >= highcoord) {
//m->setValue(marker, p, marker_num);
//m->setValue(marker, *c_iter, marker_num+1);
} else {
flag = false;
}
if (flag) {
m->setValue(marker, p, marker_num);
m->setValue(marker, *c_iter, marker_num+1);
}
}
}
}
pV.clear();
c_iter++;
}
marker->view(marker_name.c_str());
}
};
class Ex_UFC : ALE::ParallelObject {
public:
protected:
Ex_UFCOptions _options;
DM _dm;
Obj<PETSC_MESH_TYPE> _mesh;
DMMG *_dmmg;
UFCHook *_ufchook; // Basic interface to the UFC object
GenericFormSubProblem * _subproblem; // Problem interface object.
public:
Ex_UFC(MPI_Comm comm, const int debug = 0) : ALE::ParallelObject(comm, debug) {
PetscErrorCode ierr = this->processOptions(comm, &this->_options);CHKERRXX(ierr);
this->_dm = PETSC_NULL;
this->_dmmg = PETSC_NULL;
this->_subproblem = PETSC_NULL;
this->_ufchook = PETSC_NULL;
// this->_options.form_type = POISSON;
};
~Ex_UFC() {
PetscErrorCode ierr;
if (this->_dmmg) {ierr = DMMGDestroy(this->_dmmg);CHKERRXX(ierr);}
//ierr = this->destroyExactSolution(this->_options.exactSol);CHKERRXX(ierr);
//ierr = this->destroyExactSolution(this->_options.error);CHKERRXX(ierr);
ierr = this->destroyMesh();CHKERRXX(ierr);
};
public:
#undef __FUNCT__
#define __FUNCT__ "Ex_UFCProcessOptions"
PetscErrorCode processOptions(MPI_Comm comm, Ex_UFCOptions *options) {
const char *runTypes[3] = {"full", "test", "mesh"};
const char *bcTypes[2] = {"neumann", "dirichlet"};
const char *asTypes[4] = {"full", "stored", "calculated"};
const char *fTypes[4] = {"poisson", "vectorpoisson", "stokes", "mixedpoisson"};
ostringstream filename;
PetscInt run, bc, as, f;
PetscErrorCode ierr;
PetscFunctionBegin;
options->debug = 0;
options->run = RUN_FULL;
options->form_type = POISSON;
options->dim = 2;
options->generateMesh = PETSC_TRUE;
options->interpolate = PETSC_TRUE;
options->refinementLimit = 0.0;
options->bcType = DIRICHLET;
options->operatorAssembly = ASSEMBLY_FULL;
options->reentrantMesh = PETSC_FALSE;
options->circularMesh = PETSC_FALSE;
options->refineSingularity= PETSC_FALSE;
ierr = PetscOptionsBegin(comm, "", "UFC Example Problem Options", "DMMG");CHKERRQ(ierr);
ierr = PetscOptionsInt("-debug", "The debugging level", "bratu.cxx", options->debug, &options->debug, PETSC_NULL);CHKERRQ(ierr);
run = options->run;
ierr = PetscOptionsEList("-form", "The form type", "ex_ufc.cxx", fTypes, 3, fTypes[options->form_type], &f, PETSC_NULL);CHKERRQ(ierr);
options->form_type = (UFCFormType) f;
ierr = PetscOptionsEList("-run", "The run type", "ex_ufc.cxx", runTypes, 3, runTypes[options->run], &run, PETSC_NULL);CHKERRQ(ierr);
options->run = (RunType) run;
ierr = PetscOptionsInt("-dim", "The topological mesh dimension", "bratu.cxx", options->dim, &options->dim, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsTruth("-reentrant", "Make a reentrant-corner mesh", "bratu.cxx", options->reentrantMesh, &options->reentrantMesh, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsTruth("-circular_mesh", "Make a reentrant-corner mesh", "bratu.cxx", options->circularMesh, &options->circularMesh, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsTruth("-singularity", "Refine the mesh around a singularity with a priori poisson error estimation", "bratu.cxx", options->refineSingularity, &options->refineSingularity, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsTruth("-generate", "Generate the unstructured mesh", "bratu.cxx", options->generateMesh, &options->generateMesh, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsTruth("-interpolate", "Generate intermediate mesh elements", "bratu.cxx", options->interpolate, &options->interpolate, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsReal("-refinement_limit", "The largest allowable cell volume", "bratu.cxx", options->refinementLimit, &options->refinementLimit, PETSC_NULL);CHKERRQ(ierr);
filename << "data/bratu_" << options->dim <<"d";
ierr = PetscStrcpy(options->baseFilename, filename.str().c_str());CHKERRQ(ierr);
ierr = PetscOptionsString("-base_filename", "The base filename for mesh files", "bratu.cxx", options->baseFilename, options->baseFilename, 2048, PETSC_NULL);CHKERRQ(ierr);
ierr = PetscStrcpy(options->partitioner, "chaco");CHKERRQ(ierr);
ierr = PetscOptionsString("-partitioner", "The graph partitioner", "pflotran.cxx", options->partitioner, options->partitioner, 2048, PETSC_NULL);CHKERRQ(ierr);
bc = options->bcType;
ierr = PetscOptionsEList("-bc_type","Type of boundary condition","bratu.cxx",bcTypes,2,bcTypes[options->bcType],&bc,PETSC_NULL);CHKERRQ(ierr);
options->bcType = (BCType) bc;
as = options->operatorAssembly;
ierr = PetscOptionsEList("-assembly_type","Type of operator assembly","bratu.cxx",asTypes,3,asTypes[options->operatorAssembly],&as,PETSC_NULL);CHKERRQ(ierr);
options->operatorAssembly = (AssemblyType) as;
ierr = PetscOptionsEnd();
this->setDebug(options->debug);
PetscFunctionReturn(0);
};
public: // Accessors
Ex_UFCOptions *getOptions() {return &this->_options;};
int dim() const {return this->_options.dim;};
bool interpolated() const {return this->_options.interpolate;};
void interpolated(const bool i) {this->_options.interpolate = (PetscTruth) i;};
BCType bcType() const {return this->_options.bcType;};
UFCHook * ufcHook() const {return this->_ufchook;};
void ufcHook(UFCHook * uh) {this->_ufchook = uh;};
void bcType(const BCType bc) {this->_options.bcType = bc;};
AssemblyType opAssembly() const {return this->_options.operatorAssembly;};
UFCFormType FormType() const {return this->_options.form_type;};
void FormType(const UFCFormType f) {this->_options.form_type = f;};
void opAssembly(const AssemblyType at) {this->_options.operatorAssembly = at;};
DM getDM() const {return this->_dm;};
DMMG *getDMMG() const {return this->_dmmg;};
ALE::Problem::ExactSolType exactSolution() const {return this->_options.exactSol;};
public: // Mesh
#undef __FUNCT__
#define __FUNCT__ "CreateMesh"
PetscErrorCode createMesh() {
PetscTruth view;
PetscErrorCode ierr;
PetscFunctionBegin;
if (_options.circularMesh) {
if (_options.reentrantMesh) {
_options.reentrant_angle = .9;
ierr = ALE::DMBuilder::createReentrantSphericalMesh(comm(), dim(), interpolated(), debug(), &this->_dm);CHKERRQ(ierr);
} else {
ierr = ALE::DMBuilder::createSphericalMesh(comm(), dim(), interpolated(), debug(), &this->_dm);CHKERRQ(ierr);
}
} else {
if (_options.reentrantMesh) {
_options.reentrant_angle = .75;
ierr = ALE::DMBuilder::createReentrantBoxMesh(comm(), dim(), interpolated(), debug(), &this->_dm);CHKERRQ(ierr);
} else {
ierr = ALE::DMBuilder::createBoxMesh(comm(), dim(), PETSC_FALSE, interpolated(), debug(), &this->_dm);CHKERRQ(ierr);
}
}
ierr = refineMesh();CHKERRQ(ierr);
if (this->commSize() > 1) {
::Mesh parallelMesh;
ierr = MeshDistribute((::Mesh) this->_dm, _options.partitioner, ¶llelMesh);CHKERRQ(ierr);
ierr = MeshDestroy((::Mesh) this->_dm);CHKERRQ(ierr);
this->_dm = (DM) parallelMesh;
}
ierr = MeshGetMesh((::Mesh) this->_dm, this->_mesh);CHKERRQ(ierr);
if (bcType() == DIRICHLET) {
this->_mesh->markBoundaryCells("marker");
}
ierr = PetscOptionsHasName(PETSC_NULL, "-mesh_view_vtk", &view);CHKERRQ(ierr);
if (view) {
PetscViewer viewer;
ierr = PetscViewerCreate(this->comm(), &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSC_VIEWER_ASCII);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "bratu.vtk");CHKERRQ(ierr);
ierr = MeshView((::Mesh) this->_dm, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);
}
ierr = PetscOptionsHasName(PETSC_NULL, "-mesh_view", &view);CHKERRQ(ierr);
if (view) {this->_mesh->view("Mesh");}
ierr = PetscOptionsHasName(PETSC_NULL, "-mesh_view_simple", &view);CHKERRQ(ierr);
if (view) {ierr = MeshView((::Mesh) this->_dm, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);}
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "RefineMesh"
PetscErrorCode refineMesh() {
PetscErrorCode ierr;
PetscFunctionBegin;
if (_options.refinementLimit > 0.0) {
::Mesh refinedMesh;
ierr = MeshRefine((::Mesh) this->_dm, _options.refinementLimit, (PetscTruth) interpolated(), &refinedMesh);CHKERRQ(ierr);
ierr = MeshDestroy((::Mesh) this->_dm);CHKERRQ(ierr);
this->_dm = (DM) refinedMesh;
ierr = MeshGetMesh((::Mesh) this->_dm, this->_mesh);CHKERRQ(ierr);
if (_options.refineSingularity) {
::Mesh refinedMesh2;
double singularity[3] = {0.0, 0.0, 0.0};
if (dim() == 2) {
ierr = ALE::DMBuilder::MeshRefineSingularity((::Mesh) this->_dm, singularity, _options.reentrant_angle, &refinedMesh2);CHKERRQ(ierr);
} else if (dim() == 3) {
ierr = ALE::DMBuilder::MeshRefineSingularity_Fichera((::Mesh) this->_dm, singularity, 0.75, &refinedMesh2);CHKERRQ(ierr);
}
ierr = MeshDestroy((::Mesh) this->_dm);CHKERRQ(ierr);
this->_dm = (DM) refinedMesh2;
ierr = MeshGetMesh((::Mesh) this->_dm, this->_mesh);CHKERRQ(ierr);
#ifndef PETSC_OPT_SIEVE
ierr = MeshIDBoundary((::Mesh) this->_dm);CHKERRQ(ierr);
#endif
}
}
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "DestroyMesh"
PetscErrorCode destroyMesh() {
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MeshDestroy((::Mesh) this->_dm);CHKERRQ(ierr);
PetscFunctionReturn(0);
};
#include "../examples/tutorials/bratu_2d.h"
#include "../examples/tutorials/bratu_3d.h"
#include "../examples/tutorials/vector_poisson_2d.h"
#include "../examples/tutorials/vector_poisson_3d.h"
#include "../examples/tutorials/stokes_2d.h"
#include "../examples/tutorials/stokes_3d.h"
public:
#undef __FUNCT__
#define __FUNCT__ "CreateProblem"
PetscErrorCode createProblem() {
PetscErrorCode ierr;
PetscFunctionBegin;
//first step; set up a UFCDiscretization object for each element or subelement in the form, depending on what kind of form we're using.
if (dim() == 2) {
if (FormType() == POISSON) {
//PetscPrintf(_mesh->comm(), "setting up the laplacian dirichlet problem.\n");
_ufchook = new UFCHook(new bratu_2dBilinearForm(), new bratu_2dLinearForm());
//PetscPrintf(_mesh->comm(), "created the UFC hook.");
_subproblem = new UFCFormSubProblem(_mesh->comm(), _ufchook->_cell, _ufchook->_b_finite_element);
//PetscPrintf(_mesh->comm(), "created the subproblem\n");
//set up the unknown discretization.
Obj<UFCDiscretization> disc = new UFCDiscretization(_mesh->comm(), _ufchook->_b_finite_element, _ufchook->_cell);
disc->setNumDof(0, 1);
disc->setNumDof(1, 1);
disc->setNumDof(2, 0);
//PetscPrintf(_mesh->comm(), "set up the discretization numdofs\n");
Obj<UFCCellIntegral> jac_integral = new UFCCellIntegral(_mesh->comm(), _ufchook->_b_cell_integrals[0], _ufchook->_cell, "height", 0, 2, 6);
Obj<UFCCellIntegral> rhs_integral = new UFCCellIntegral(_mesh->comm(), _ufchook->_l_cell_integrals[0], _ufchook->_cell, "height", 0, 1, 6, 1);
if (bcType() == DIRICHLET) {
Obj<UFCBoundaryCondition> bc;
if (_options.reentrantMesh) {
disc->setRHSFunction(new UFCFunctions::constant_vector(1, 0.));
bc = UFCBoundaryCondition(_mesh->comm(), new UFCFunctions::singularity_exact_2d_scalar(), new UFCFunctions::singularity_exact_2d_scalar(), _ufchook->_b_finite_element, _ufchook->_cell, "marker", 1);
} else {
disc->setRHSFunction(new UFCFunctions::constant_vector(1, -4.));
bc = UFCBoundaryCondition(_mesh->comm(), new UFCFunctions::quadratic_2d_scalar(), new UFCFunctions::quadratic_2d_scalar(), _ufchook->_b_finite_element, _ufchook->_cell, "marker", 1);
}
PetscPrintf(_mesh->comm(), "set up the discretization BCs\n");
disc->setBoundaryCondition(bc);
}
_subproblem->setDiscretization(disc);
_subproblem->setIntegral("jac_integral", jac_integral);
_subproblem->setIntegral("rhs_integral", rhs_integral);
} else if (FormType() == VECTORPOISSON) {
_ufchook = new UFCHook(new vector_poisson_2dBilinearForm(), new vector_poisson_2dLinearForm());
_subproblem = new UFCFormSubProblem(_mesh->comm(), _ufchook->_cell, _ufchook->_b_finite_element);
//do it as one discretization for now.
//TODO rewrite evaluate_rhs to take into account vectors; it should just zero everything now.
Obj<UFCDiscretization> disc_x = new UFCDiscretization(_mesh->comm(), _ufchook->_b_sub_finite_elements[0], _ufchook->_cell);
disc_x->setNumDof(0, 1);
disc_x->setNumDof(1, 0);
disc_x->setNumDof(2, 0);
disc_x->setRHSFunction(new UFCFunctions::constant_vector(1, -4.));
Obj<UFCDiscretization> disc_y = new UFCDiscretization(_mesh->comm(), _ufchook->_b_sub_finite_elements[1], _ufchook->_cell);
disc_y->setNumDof(0, 1);
disc_y->setNumDof(1, 0);
disc_y->setNumDof(2, 0);
disc_y->setRHSFunction(new UFCFunctions::constant_vector(1, -4.));
Obj<UFCCellIntegral> jac_integral = new UFCCellIntegral(_mesh->comm(), _ufchook->_b_cell_integrals[0], _ufchook->_cell, "height", 0, 2, 6);
Obj<UFCCellIntegral> rhs_integral = new UFCCellIntegral(_mesh->comm(), _ufchook->_l_cell_integrals[0], _ufchook->_cell, "height", 0, 1, 6, 1);
_subproblem->setIntegral("jac_integral", jac_integral);
_subproblem->setIntegral("rhs_integral", rhs_integral);
if (bcType() == DIRICHLET) {
Obj<UFCBoundaryCondition> bc_x = UFCBoundaryCondition(_mesh->comm(), new UFCFunctions::quadratic_vector(2, 1), new UFCFunctions::quadratic_vector(2, 1), _ufchook->_b_sub_finite_elements[0], _ufchook->_cell, "marker", 1);
Obj<UFCBoundaryCondition> bc_y = UFCBoundaryCondition(_mesh->comm(), new UFCFunctions::quadratic_vector(2, 1), new UFCFunctions::quadratic_vector(2, 1), _ufchook->_b_sub_finite_elements[1], _ufchook->_cell, "marker", 1);
disc_x->setBoundaryCondition(bc_x);
disc_y->setBoundaryCondition(bc_y);
}
_subproblem->setDiscretization("1", disc_x);
_subproblem->setDiscretization("2", disc_y);
} else if (FormType() == STOKES) {
_ufchook = new UFCHook(new stokes_2dBilinearForm(), new stokes_2dLinearForm());
_subproblem = new UFCFormSubProblem(_mesh->comm(), _ufchook->_cell, _ufchook->_b_finite_element);
Obj<UFCDiscretization> vx = new UFCDiscretization(_mesh->comm(), new stokes_2dBilinearForm_finite_element_0_0_0(), _ufchook->_cell);
vx->setNumDof(0, 1);
vx->setNumDof(1, 1);
vx->setNumDof(2, 0);
//vx->setRHSFunction(new UFCFunctions::lid_driven(1, 0.93, 0, 0, 0.0));
vx->setRHSFunction(new UFCFunctions::constant_vector(1, 0.0)); //0 bulk force
Obj<UFCDiscretization> vy = new UFCDiscretization(_mesh->comm(), new stokes_2dBilinearForm_finite_element_0_0_1(), _ufchook->_cell);
vy->setNumDof(0, 1);
vy->setNumDof(1, 1);
vy->setNumDof(2, 0);
//vy->setRHSFunction(new UFCFunctions::lid_driven(1, 0.93, 0, 1, 0.0));
vy->setRHSFunction(new UFCFunctions::constant_vector(1, 0.0)); //0 bulk force
Obj<UFCDiscretization> w = new UFCDiscretization(_mesh->comm(), new stokes_2dBilinearForm_finite_element_0_1(), _ufchook->_cell);
w->setNumDof(0, 1);
w->setNumDof(1, 0);
w->setNumDof(2, 0);
w->setRHSFunction(new UFCFunctions::constant_vector(1, 0.0)); //0 divergence??
Obj<UFCCellIntegral> jac_integral = new UFCCellIntegral(_mesh->comm(), _ufchook->_b_cell_integrals[0], _ufchook->_cell, "height", 0, 2, 15);
Obj<UFCCellIntegral> rhs_integral = new UFCCellIntegral(_mesh->comm(), _ufchook->_l_cell_integrals[0], _ufchook->_cell, "height", 0, 1, 15, 1);
_subproblem->setIntegral("jac_integral", jac_integral);
_subproblem->setIntegral("rhs_integral", rhs_integral);
if (bcType() == DIRICHLET) {
//UFCFunctions::mark_frictionless(_mesh, 1, 0., 1., "ly", 1);
UFCFunctions::pinion_pressure(_mesh, 1, 0.01, std::string("w"), 1);
Obj<UFCBoundaryCondition> lx = new UFCBoundaryCondition(_mesh->comm(), new UFCFunctions::lid_driven(2, 1., 0.99), new UFCFunctions::constant_vector(1, 0.), vx->getFiniteElement(), _ufchook->_cell, "marker", 1);
Obj<UFCBoundaryCondition> ly = new UFCBoundaryCondition(_mesh->comm(), new UFCFunctions::constant_vector(1, 0.), new UFCFunctions::constant_vector(1, 0.), vy->getFiniteElement(), _ufchook->_cell, "marker", 1);
Obj<UFCBoundaryCondition> wp = new UFCBoundaryCondition(_mesh->comm(), new UFCFunctions::constant_vector(1, 0.), new UFCFunctions::constant_vector(1, 0.), w->getFiniteElement(), _ufchook->_cell, "w", 1);
vx->setBoundaryCondition("lx", lx);
vy->setBoundaryCondition("ly", ly);
w->setBoundaryCondition("w", wp);
}
_subproblem->setDiscretization("vx", vx);
_subproblem->setDiscretization("vy", vy);
_subproblem->setDiscretization("w", w);
}
} else if (dim() == 3) {
if (FormType() == POISSON) {
_ufchook = new UFCHook(new bratu_3dBilinearForm(), new bratu_3dLinearForm());
_subproblem = new UFCFormSubProblem(_mesh->comm(), _ufchook->_cell, _ufchook->_b_finite_element);
Obj<UFCDiscretization> disc = new UFCDiscretization(_mesh->comm(), _ufchook->_b_finite_element, _ufchook->_cell);
//second order
Obj<UFCCellIntegral> jac_integral = new UFCCellIntegral(_mesh->comm(), _ufchook->_b_cell_integrals[0], _ufchook->_cell, "height", 0, 2, 10);
Obj<UFCCellIntegral> rhs_integral = new UFCCellIntegral(_mesh->comm(), _ufchook->_l_cell_integrals[0], _ufchook->_cell, "height", 0, 1, 10, 1);
disc->setRHSFunction(new UFCFunctions::constant_scalar);
disc->setNumDof(0, 1);
disc->setNumDof(1, 1);
disc->setNumDof(2, 0);
disc->setNumDof(3, 0);
if (bcType() == DIRICHLET) {
Obj<UFCBoundaryCondition> bc = UFCBoundaryCondition(_mesh->comm(), new UFCFunctions::quadratic_vector(3, 1), new UFCFunctions::quadratic_vector(3, 1), _ufchook->_b_finite_element, _ufchook->_cell, "marker", 1);
disc->setBoundaryCondition(bc);
}
_subproblem->setDiscretization(disc);
_subproblem->setIntegral("jac_integral", jac_integral);
_subproblem->setIntegral("rhs_integral", rhs_integral);
} else if (FormType() == VECTORPOISSON) {
_ufchook = new UFCHook(new vector_poisson_3dBilinearForm(), new vector_poisson_3dLinearForm());
_subproblem = new UFCFormSubProblem(_mesh->comm(), _ufchook->_cell, _ufchook->_b_finite_element);
//do it as one discretization for now.
//TODO rewrite evaluate_rhs to take into account vectors; it should just zero everything now.
Obj<UFCDiscretization> disc_x = new UFCDiscretization(_mesh->comm(), _ufchook->_b_sub_finite_elements[0], _ufchook->_cell);
disc_x->setNumDof(0, 1);
disc_x->setNumDof(1, 1);
disc_x->setNumDof(2, 0);
disc_x->setNumDof(3, 0);
disc_x->setRHSFunction(new UFCFunctions::constant_vector(1, -4.));
Obj<UFCDiscretization> disc_y = new UFCDiscretization(_mesh->comm(), _ufchook->_b_sub_finite_elements[1], _ufchook->_cell);
disc_y->setNumDof(0, 1);
disc_y->setNumDof(1, 1);
disc_y->setNumDof(2, 0);
disc_y->setNumDof(3, 0);
disc_y->setRHSFunction(new UFCFunctions::constant_vector(1, -4.));
Obj<UFCDiscretization> disc_z = new UFCDiscretization(_mesh->comm(), _ufchook->_b_sub_finite_elements[2], _ufchook->_cell);
disc_z->setNumDof(0, 1);
disc_z->setNumDof(1, 1);
disc_z->setNumDof(2, 0);
disc_z->setNumDof(3, 0);
disc_z->setRHSFunction(new UFCFunctions::constant_vector(1, -4.));
Obj<UFCCellIntegral> jac_integral = new UFCCellIntegral(_mesh->comm(), _ufchook->_b_cell_integrals[0], _ufchook->_cell, "height", 0, 2, 30);
Obj<UFCCellIntegral> rhs_integral = new UFCCellIntegral(_mesh->comm(), _ufchook->_l_cell_integrals[0], _ufchook->_cell, "height", 0, 1, 30, 1);
_subproblem->setIntegral("jac_integral", jac_integral);
_subproblem->setIntegral("rhs_integral", rhs_integral);
if (bcType() == DIRICHLET) {
Obj<UFCBoundaryCondition> bc_x = UFCBoundaryCondition(_mesh->comm(), new UFCFunctions::quadratic_vector(3, 1, 1.), new UFCFunctions::coordinates(0), _ufchook->_b_sub_finite_elements[0], _ufchook->_cell, "marker", 1);
Obj<UFCBoundaryCondition> bc_y = UFCBoundaryCondition(_mesh->comm(), new UFCFunctions::quadratic_vector(3, 1, 1.), new UFCFunctions::coordinates(1), _ufchook->_b_sub_finite_elements[1], _ufchook->_cell, "marker", 1);
Obj<UFCBoundaryCondition> bc_z = UFCBoundaryCondition(_mesh->comm(), new UFCFunctions::quadratic_vector(3, 1, 1.), new UFCFunctions::coordinates(2), _ufchook->_b_sub_finite_elements[1], _ufchook->_cell, "marker", 1);
disc_x->setBoundaryCondition(bc_x);
disc_y->setBoundaryCondition(bc_y);
disc_z->setBoundaryCondition(bc_z);
}
_subproblem->setDiscretization("ux", disc_x);
_subproblem->setDiscretization("uy", disc_y);
_subproblem->setDiscretization("uz", disc_z);
} else if (FormType() == STOKES) {
_ufchook = new UFCHook(new stokes_3dBilinearForm(), new stokes_3dLinearForm());
_subproblem = new UFCFormSubProblem(_mesh->comm(), _ufchook->_cell, _ufchook->_b_finite_element);
Obj<UFCDiscretization> vx = new UFCDiscretization(_mesh->comm(), new stokes_3dBilinearForm_finite_element_0_0_0(), _ufchook->_cell);
vx->setNumDof(0, 1);
vx->setNumDof(1, 1);
vx->setNumDof(2, 0);
vx->setNumDof(3, 0);
vx->setRHSFunction(new UFCFunctions::constant_vector(1, 0.0)); //0 bulk force
Obj<UFCDiscretization> vy = new UFCDiscretization(_mesh->comm(), new stokes_3dBilinearForm_finite_element_0_0_1(), _ufchook->_cell);
vy->setNumDof(0, 1);
vy->setNumDof(1, 1);
vy->setNumDof(2, 0);
vy->setNumDof(3, 0);
vy->setRHSFunction(new UFCFunctions::constant_vector(1, 0.0)); //0 bulk force
Obj<UFCDiscretization> vz = new UFCDiscretization(_mesh->comm(), new stokes_3dBilinearForm_finite_element_0_0_2(), _ufchook->_cell);
vz->setNumDof(0, 1);
vz->setNumDof(1, 1);
vz->setNumDof(2, 0);
vz->setNumDof(3, 0);
vz->setRHSFunction(new UFCFunctions::constant_vector(1, 0.0)); //0 bulk force
Obj<UFCDiscretization> w = new UFCDiscretization(_mesh->comm(), new stokes_3dBilinearForm_finite_element_0_1(), _ufchook->_cell);
w->setNumDof(0, 1);
w->setNumDof(1, 0);
w->setNumDof(2, 0);
w->setNumDof(3, 0);
w->setRHSFunction(new UFCFunctions::constant_vector(1, 0.0)); //0 divergence??
Obj<UFCCellIntegral> jac_integral = new UFCCellIntegral(_mesh->comm(), _ufchook->_b_cell_integrals[0], _ufchook->_cell, "height", 0, 2, 34);
Obj<UFCCellIntegral> rhs_integral = new UFCCellIntegral(_mesh->comm(), _ufchook->_l_cell_integrals[0], _ufchook->_cell, "height", 0, 1, 34, 1);
_subproblem->setIntegral("jac_integral", jac_integral);
_subproblem->setIntegral("rhs_integral", rhs_integral);
if (bcType() == DIRICHLET) {
UFCFunctions::pinion_pressure(_mesh, 1, 0.01, "w", 1);
Obj<UFCBoundaryCondition> lx = new UFCBoundaryCondition(_mesh->comm(), new UFCFunctions::lid_driven(3, 10., 0.99), new UFCFunctions::constant_vector(1, 0.), vx->getFiniteElement(), _ufchook->_cell, "marker", 1);
Obj<UFCBoundaryCondition> ly = new UFCBoundaryCondition(_mesh->comm(), new UFCFunctions::constant_vector(1, 0.), new UFCFunctions::constant_vector(1, 0.), vy->getFiniteElement(), _ufchook->_cell, "marker", 1);
Obj<UFCBoundaryCondition> lz = new UFCBoundaryCondition(_mesh->comm(), new UFCFunctions::constant_vector(1, 0.), new UFCFunctions::constant_vector(1, 0.), vz->getFiniteElement(), _ufchook->_cell, "marker", 1);
Obj<UFCBoundaryCondition> wp = new UFCBoundaryCondition(_mesh->comm(), new UFCFunctions::constant_vector(1, 0.), new UFCFunctions::constant_vector(1, 0.), w->getFiniteElement(), _ufchook->_cell, "w", 1);
vx->setBoundaryCondition("lx", lx);
vy->setBoundaryCondition("ly", ly);
vz->setBoundaryCondition("lz", lz);
w->setBoundaryCondition("w", wp);
}
_subproblem->setDiscretization("vx", vx);
_subproblem->setDiscretization("vy", vy);
_subproblem->setDiscretization("vz", vz);
_subproblem->setDiscretization("w", w);
}
}
PetscPrintf(_mesh->comm(), "done setting up the problem\n");
const ALE::Obj<PETSC_MESH_TYPE::real_section_type>& s = this->_mesh->getRealSection("default");
s->setDebug(debug());
_subproblem->setupField(this->_mesh, s);
PetscTruth flag;
ierr = PetscOptionsHasName(PETSC_NULL, "-vec_view", &flag);CHKERRQ(ierr);
if (flag) {s->view("Exact Solution");}
ierr = PetscOptionsHasName(PETSC_NULL, "-mesh_view", &flag);CHKERRQ(ierr);
if (flag) {_mesh->view("setup mesh");}
PetscFunctionReturn(0);
};
public:
//Note to self: the exact solution function should include all discretizations in it and therefore go over the TOTAL fiberdimension of the form
//later do it per-discretization for easier mixed and otherwise problems.
#undef __FUNCT__
#define __FUNCT__ "CreateExactSolution"
PetscErrorCode createExactSolution() {
PetscTruth flag;
PetscErrorCode ierr;
PetscFunctionBegin;
::Mesh mesh = (::Mesh) this->_dm;
ierr = MeshGetSectionReal(mesh, "exactSolution", &this->_options.exactSol.section);CHKERRQ(ierr);
const Obj<PETSC_MESH_TYPE::real_section_type>& s = this->_mesh->getRealSection("exactSolution");
//this->_mesh->setupField(s);
this->_subproblem->setupField(this->_mesh, s, 2, false, true);
ierr = PetscOptionsHasName(PETSC_NULL, "-vec_view", &flag);CHKERRQ(ierr);
if (flag) {s->view("Exact Solution");}
ierr = PetscOptionsHasName(PETSC_NULL, "-vec_view_vtk", &flag);CHKERRQ(ierr);
if (flag) {
PetscViewer viewer;
ierr = PetscViewerCreate(this->comm(), &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSC_VIEWER_ASCII);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "exact_sol.vtk");CHKERRQ(ierr);
ierr = MeshView((::Mesh) this->_dm, viewer);CHKERRQ(ierr);
ierr = SectionRealView(exactSolution().section, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);
}
ierr = MeshGetSectionReal(mesh, "error", &this->_options.error.section);CHKERRQ(ierr);
const Obj<PETSC_MESH_TYPE::real_section_type>& e = this->_mesh->getRealSection("error");
e->setChart(PETSC_MESH_TYPE::real_section_type::chart_type(*this->_mesh->heightStratum(0)));
e->setFiberDimension(this->_mesh->heightStratum(0), 1);
this->_mesh->allocate(e);
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "DestroyExactSolution"
PetscErrorCode destroyExactSolution(ALE::Problem::ExactSolType sol) {
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = SectionRealDestroy(sol.section);CHKERRQ(ierr);
PetscFunctionReturn(0);
};
public:
#undef __FUNCT__
#define __FUNCT__ "CreateSolver"
PetscErrorCode createSolver() {
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMMGCreate(this->comm(), 1, this->_subproblem, &this->_dmmg);CHKERRQ(ierr);
ierr = DMMGSetDM(this->_dmmg, this->_dm);CHKERRQ(ierr);
if (opAssembly() == ALE::Problem::ASSEMBLY_FULL) {
//PetscPrintf(MPI_COMM_WORLD, "setting local.\n");
ierr = DMMGSetSNESLocal(this->_dmmg, ALE::Problem::RHS_FEMProblem, ALE::Problem::Jac_FEMProblem, 0, 0);CHKERRQ(ierr);
#if 0
} else if (opAssembly() == ALE::Problem::ASSEMBLY_CALCULATED) {
ierr = DMMGSetMatType(this->_dmmg, MATSHELL);CHKERRQ(ierr);
ierr = DMMGSetSNESLocal(this->_dmmg, ALE::Problem::UFCFunctions::Rhs_Unstructured, ALE::Problem::UFCFunctions::Jac_Unstructured_Calculated, 0, 0);CHKERRQ(ierr);
} else if (opAssembly() == ALE::Problem::ASSEMBLY_STORED) {
ierr = DMMGSetMatType(this->_dmmg, MATSHELL);CHKERRQ(ierr);
ierr = DMMGSetSNESLocal(this->_dmmg, ALE::Problem::UFCFunctions::Rhs_Unstructured, ALE::Problem::UFCFunctions::Jac_Unstructured_Stored, 0, 0);CHKERRQ(ierr);
#endif
} else {
SETERRQ1(PETSC_ERR_ARG_WRONG, "Assembly type not supported: %d", opAssembly());
}
ierr = DMMGSetFromOptions(this->_dmmg);CHKERRQ(ierr);
if (bcType() == ALE::Problem::NEUMANN) {
// With Neumann conditions, we tell DMMG that constants are in the null space of the operator
ierr = DMMGSetNullSpace(this->_dmmg, PETSC_TRUE, 0, PETSC_NULL);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "Ex_UFCSolve"
PetscErrorCode solve() {
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMMGSolve(this->_dmmg);CHKERRQ(ierr);
// Report on solve
SNES snes = DMMGGetSNES(this->_dmmg);
PetscInt its;
PetscTruth flag;
SNESConvergedReason reason;
ierr = SNESGetIterationNumber(snes, &its);CHKERRQ(ierr);
ierr = SNESGetConvergedReason(snes, &reason);CHKERRQ(ierr);
ierr = PetscPrintf(comm(), "Number of nonlinear iterations = %D\n", its);CHKERRQ(ierr);
ierr = PetscPrintf(comm(), "Reason for solver termination: %s\n", SNESConvergedReasons[reason]);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL, "-vec_view", &flag);CHKERRQ(ierr);
if (flag) {ierr = VecView(DMMGGetx(this->_dmmg), PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);}
ierr = PetscOptionsHasName(PETSC_NULL, "-vec_view_draw", &flag);CHKERRQ(ierr);
if (flag && dim() == 2) {ierr = VecView(DMMGGetx(this->_dmmg), PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);}
const Obj<PETSC_MESH_TYPE::real_section_type>& sol = this->_mesh->getRealSection("default");
SectionReal solution;
double error;
ierr = MeshGetSectionReal((::Mesh) this->_dm, "default", &solution);CHKERRQ(ierr);
ierr = SectionRealToVec(solution, (::Mesh) this->_dm, SCATTER_REVERSE, DMMGGetx(this->_dmmg));CHKERRQ(ierr);
ierr = this->calculateError(solution, &error);CHKERRQ(ierr);
ierr = PetscPrintf(comm(), "Total error: %g\n", error);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL, "-vec_view_vtk", &flag);CHKERRQ(ierr);
if (flag) {
PetscViewer viewer;
ierr = PetscViewerCreate(comm(), &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSC_VIEWER_ASCII);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "sol.vtk");CHKERRQ(ierr);
ierr = MeshView((::Mesh) this->_dm, viewer);CHKERRQ(ierr);
if (FormType() == POISSON) {
ierr = SectionRealView(solution, viewer);CHKERRQ(ierr);
} else {
ierr = ALE::Problem::SubProblemView(solution, "velocity", viewer, 0, dim()-1);
if (FormType() == STOKES) {
//ierr = ALE::Problem::SubProblemView(solution, "pressure", viewer, dim(), dim());
}
}
ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);
ierr = PetscViewerCreate(comm(), &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSC_VIEWER_ASCII);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "error.vtk");CHKERRQ(ierr);
ierr = MeshView((::Mesh) this->_dm, viewer);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK_CELL);CHKERRQ(ierr);
ierr = SectionRealView(this->_options.error.section, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL, "-vec_view", &flag);CHKERRQ(ierr);
if (flag) {sol->view("Solution");}
ierr = PetscOptionsHasName(PETSC_NULL, "-hierarchy_vtk", &flag);CHKERRQ(ierr);
if (flag) {
double offset[3] = {2.0, 0.0, 0.25};
PetscViewer viewer;
ierr = PetscViewerCreate(comm(), &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSC_VIEWER_ASCII);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "mesh_hierarchy.vtk");CHKERRQ(ierr);
ierr = PetscOptionsReal("-hierarchy_vtk", PETSC_NULL, "bratu.cxx", *offset, offset, PETSC_NULL);CHKERRQ(ierr);
ierr = VTKViewer::writeHeader(viewer);CHKERRQ(ierr);
ierr = VTKViewer::writeHierarchyVertices(this->_dmmg, viewer, offset);CHKERRQ(ierr);
ierr = VTKViewer::writeHierarchyElements(this->_dmmg, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);
}
ierr = SectionRealDestroy(solution);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
};
public:
#undef __FUNCT__
#define __FUNCT__ "CalculateError"
PetscErrorCode calculateError(SectionReal X, double *error) {
//PetscScalar (*func)(const double *) = this->_options.exactFunc;
PetscErrorCode ierr;
PetscFunctionBegin;
//const int dim = this->_mesh->getDimension();
double localError = 0.0;
// Loop over cells
const Obj<PETSC_MESH_TYPE::label_sequence>& cells = this->_mesh->heightStratum(0);
for(PETSC_MESH_TYPE::label_sequence::iterator c_iter = cells->begin(); c_iter != cells->end(); ++c_iter) {
PetscScalar *x;
//double elemError = 0.0;
//this->_mesh->computeElementGeometry(coordinates, *c_iter, v0, J, invJ, detJ);
if (debug()) {
//std::cout << "Element " << *c_iter << " v0: (" << v0[0]<<","<<v0[1]<<")" << "J " << J[0]<<","<<J[1]<<","<<J[2]<<","<<J[3] << " detJ " << detJ << std::endl;
}
ierr = SectionRealRestrict(X, *c_iter, &x);CHKERRQ(ierr);
// Loop over quadrature points
/*TODO rewrite with form
for(int q = 0; q < numQuadPoints; ++q) {
for(int d = 0; d < dim; d++) {
coords[d] = v0[d];
for(int e = 0; e < dim; e++) {
coords[d] += J[d*dim+e]*(quadPoints[q*dim+e] + 1.0);
}
if (debug()) {std::cout << "q: "<<q<<" coords["<<d<<"] " << coords[d] << std::endl;}
}
const PetscScalar funcVal = (*func)(coords);
if (debug()) {std::cout << "q: "<<q<<" funcVal " << funcVal << std::endl;}
double interpolant = 0.0;
for(int f = 0; f < numBasisFuncs; ++f) {
interpolant += x[f]*basis[q*numBasisFuncs+f];
}
if (debug()) {std::cout << "q: "<<q<<" interpolant " << interpolant << std::endl;}
elemError += (interpolant - funcVal)*(interpolant - funcVal)*quadWeights[q];
if (debug()) {std::cout << "q: "<<q<<" elemError " << elemError << std::endl;}
}
if (debug()) {
std::cout << "Element " << *c_iter << " error: " << elemError << std::endl;
}
ierr = SectionRealUpdateAdd(this->_options.error.section, *c_iter, &elemError);CHKERRQ(ierr);
localError += elemError;
*/
}
ierr = MPI_Allreduce(&localError, error, 1, MPI_DOUBLE, MPI_SUM, comm());CHKERRQ(ierr);
//ierr = PetscFree4(coords,v0,J,invJ);CHKERRQ(ierr);
*error = sqrt(*error);
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "CheckError"
PetscErrorCode checkError(ALE::Problem::ExactSolType sol) {
const char *name;
PetscScalar norm;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = this->calculateError(sol.section, &norm);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject) sol.section, &name);CHKERRQ(ierr);
PetscPrintf(comm(), "Error for trial solution %s: %g\n", name, norm);
PetscFunctionReturn(0);
};
#undef __FUNCT__
#define __FUNCT__ "CheckResidual"
PetscErrorCode checkResidual(ALE::Problem::ExactSolType sol) {
const char *name;
PetscScalar norm;
PetscTruth flag;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscOptionsHasName(PETSC_NULL, "-vec_view", &flag);CHKERRQ(ierr);
::Mesh mesh = (::Mesh) this->_dm;
SectionReal residual;
ierr = SectionRealDuplicate(sol.section, &residual);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) residual, "residual");CHKERRQ(ierr);
ierr = ALE::Problem::RHS_FEMProblem(mesh, sol.section, residual, this->_subproblem);CHKERRQ(ierr);
if (flag) {ierr = SectionRealView(residual, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);}
ierr = SectionRealNorm(residual, mesh, NORM_2, &norm);CHKERRQ(ierr);
ierr = SectionRealDestroy(residual);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject) sol.section, &name);CHKERRQ(ierr);
PetscPrintf(comm(), "Residual for trial solution %s: %g\n", name, norm);
PetscFunctionReturn(0);
};
};
}
}
#endif
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