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Commit 4a0bdb2f authored by Thomas Witkowski's avatar Thomas Witkowski
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Work on pdd and some other small code refactorings.

parent a27257cd
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Showing with 324 additions and 444 deletions
AMDiS/src/AMDiS_fwd.h
View file @ 4a0bdb2f
......@@ -52,6 +52,7 @@ namespace AMDiS {
class ITL_BasePreconditioner;
class LeafDataPeriodic;
class LevelAdmin;
class Line;
class MacroElement;
class MacroInfo;
class Marker;
......@@ -80,9 +81,13 @@ namespace AMDiS {
class RCNeighbourList;
class RefinementManager;
class RobinBC;
class SubElInfo;
class SurfaceOperator;
class SMIAdapter;
class SystemVector;
class Tetrahedron;
class TraverseStack;
class Triangle;
class VertexInfo;
class VertexVector;
......
AMDiS/src/DOFMatrix.cc
View file @ 4a0bdb2f
......@@ -222,6 +222,17 @@ namespace AMDiS {
DegreeOfFreedom col = colIndices[j];
double entry = elMat[i][j];
/*
if (MPI::COMM_WORLD.Get_rank() == 0 && (row >= 156 || col >= 156))
std::cout << "PROB 0: " << row << " " << col << std::endl;
if (MPI::COMM_WORLD.Get_rank() == 1 && (row >= 151 || col >= 151))
std::cout << "PROB 1: " << row << " " << col << std::endl;
if (MPI::COMM_WORLD.Get_rank() == 2 && (row >= 146 || col >= 146))
std::cout << "PROB 2: " << row << " " << col << std::endl;
if (MPI::COMM_WORLD.Get_rank() == 3 && (row >= 153 || col >= 153))
std::cout << "PROB 3: " << row << " " << col << std::endl;
*/
if (add)
ins[row][col] += sign * entry;
else
......
AMDiS/src/ParallelDomainProblem.cc
View file @ 4a0bdb2f
......@@ -88,11 +88,9 @@ namespace AMDiS {
// === Global refinements. ===
// refinementManager->globalRefine(mesh, 1);
refinementManager->globalRefine(mesh, 12);
// updateLocalGlobalNumbering(nRankDOFs, nOverallDOFs);
// exit(0);
updateLocalGlobalNumbering(nRankDOFs, nOverallDOFs);
// === Create petsc matrix. ===
......@@ -155,6 +153,8 @@ namespace AMDiS {
void ParallelDomainProblemBase::solvePetscMatrix(DOFVector<double> *vec)
{
clock_t t = clock();
KSP ksp;
PC pc;
......@@ -220,7 +220,9 @@ namespace AMDiS {
}
for (int i = 0; i < static_cast<int>(sendBuffers.size()); i++)
delete [] sendBuffers[i];
delete [] sendBuffers[i];
std::cout << "SOLUTION = " << TIME_USED(t,clock()) << std::endl;
}
......@@ -513,8 +515,8 @@ namespace AMDiS {
sendIt = sendNewDofs.begin();
sendIt != sendNewDofs.end();
++sendIt, i++) {
int nSendDOFs = sendIt->second.size() * 2;
sendBuffers[i] = new int[nSendDOFs];
int nSendDofs = sendIt->second.size() * 2;
sendBuffers[i] = new int[nSendDofs];
int c = 0;
for (std::map<const DegreeOfFreedom*, DegreeOfFreedom>::iterator
dofIt = sendIt->second.begin();
......@@ -526,7 +528,7 @@ namespace AMDiS {
sendDofs[sendIt->first].push_back(dofIt->first);
}
mpiComm.Isend(sendBuffers[i], nSendDOFs, MPI_INT, sendIt->first, 0);
mpiComm.Isend(sendBuffers[i], nSendDofs, MPI_INT, sendIt->first, 0);
}
i = 0;
......@@ -602,32 +604,6 @@ namespace AMDiS {
delete [] recvBuffers[i];
}
#if 1
// === Create local information from sendDofs and recvDofs
for (std::map<int, std::vector<const DegreeOfFreedom*> >::iterator
it = sendDofs.begin();
it != sendDofs.end();
++it)
for (std::vector<const DegreeOfFreedom*>::iterator dofIt = it->second.begin();
dofIt != it->second.end();
dofIt++) {
// std::cout << "AND SET S " << (*dofIt)[0] << " = " << mapGlobalLocalDOFs[(*dofIt)[0]] << std::endl;
// const_cast<DegreeOfFreedom*>(*dofIt)[0] = mapGlobalLocalDOFs[(*dofIt)[0]];
}
for (std::map<int, std::vector<const DegreeOfFreedom*> >::iterator
it = recvDofs.begin();
it != recvDofs.end();
++it)
for (std::vector<const DegreeOfFreedom*>::iterator dofIt = it->second.begin();
dofIt != it->second.end();
dofIt++) {
// std::cout << "AND SET R " << (*dofIt)[0] << " = " << mapGlobalLocalDOFs[(*dofIt)[0]] << std::endl;
// const_cast<DegreeOfFreedom*>(*dofIt)[0] = mapGlobalLocalDOFs[(*dofIt)[0]];
}
#endif
}
......@@ -656,8 +632,8 @@ namespace AMDiS {
// === Traverse on interior boundaries and move all not ranked owned DOFs from ===
// === rankDOFs to boundaryDOFs ===
std::map<int, std::vector<const DegreeOfFreedom*> > sendNewDOFs;
std::map<int, std::vector<const DegreeOfFreedom*> > recvNewDOFs;
std::map<int, std::vector<const DegreeOfFreedom*> > sendNewDofs = sendDofs;
std::map<int, std::vector<const DegreeOfFreedom*> > recvNewDofs = recvDofs;
for (std::map<int, std::vector<AtomicBoundary> >::iterator it =
myIntBoundary.boundary.begin();
......@@ -699,7 +675,7 @@ namespace AMDiS {
boundDOFs);
for (int i = 0; i < static_cast<int>(boundDOFs.size()); i++) {
newBoundaryDOFs[boundDOFs[i]] = mpiRank;
sendNewDOFs[it->first].push_back(boundDOFs[i]);
sendNewDofs[it->first].push_back(boundDOFs[i]);
}
}
}
......@@ -748,7 +724,7 @@ namespace AMDiS {
for (int i = 0; i < static_cast<int>(boundDOFs.size()); i++) {
rankDOFs.erase(boundDOFs[i]);
newBoundaryDOFs[boundDOFs[i]] = it->first;
recvNewDOFs[it->first].push_back(boundDOFs[i]);
recvNewDofs[it->first].push_back(boundDOFs[i]);
}
}
......@@ -787,13 +763,72 @@ namespace AMDiS {
// === Send new DOF indices. ===
for (int rank = 0; rank < mpiSize; rank++) {
if (rank == mpiRank)
continue;
std::vector<int*> sendBuffers(sendNewDofs.size());
std::vector<int*> recvBuffers(recvNewDofs.size());
i = 0;
for (std::map<int, std::vector<const DegreeOfFreedom*> >::iterator
sendIt = sendNewDofs.begin();
sendIt != sendNewDofs.end();
++sendIt, i++) {
int nSendDofs = sendIt->second.size();
sendBuffers[i] = new int[nSendDofs];
int c = 0;
for (std::vector<const DegreeOfFreedom*>::iterator dofIt = sendIt->second.begin();
dofIt != sendIt->second.end();
++dofIt)
sendBuffers[i][c++] = (*dofIt)[0] + rstart;
mpiComm.Isend(sendBuffers[i], nSendDofs, MPI_INT, sendIt->first, 0);
}
i = 0;
for (std::map<int, std::vector<const DegreeOfFreedom*> >::iterator
recvIt = recvNewDofs.begin();
recvIt != recvNewDofs.end(); ++recvIt, i++) {
int nRecvDofs = recvIt->second.size();
recvBuffers[i] = new int[nRecvDofs];
mpiComm.Irecv(recvBuffers[i], nRecvDofs, MPI_INT, recvIt->first, 0);
}
mpiComm.Barrier();
i = 0;
for (std::map<int, std::vector<const DegreeOfFreedom*> >::iterator
sendIt = sendNewDofs.begin();
sendIt != sendNewDofs.end();
++sendIt)
delete [] sendBuffers[i++];
i = 0;
int newDofIndex = nRankDOFs;
for (std::map<int, std::vector<const DegreeOfFreedom*> >::iterator
recvIt = recvNewDofs.begin();
recvIt != recvNewDofs.end(); ++recvIt) {
int j = 0;
for (std::vector<const DegreeOfFreedom*>::iterator dofIt = recvIt->second.begin();
dofIt != recvIt->second.end();
++dofIt) {
const_cast<DegreeOfFreedom*>(*dofIt)[0] = newDofIndex;
// if (mpiRank == 1)
// std::cout << "SET TO " << newDofIndex << std::endl;
mapLocalGlobalDOFs[newDofIndex] = recvBuffers[i][j];
mapGlobalLocalDOFs[recvBuffers[i][j]] = newDofIndex;
isRankDOF[newDofIndex] = false;
newDofIndex++;
j++;
}
delete [] recvBuffers[i++];
}
// === Update list of dofs that must be communicated for solution exchange. ===
sendDofs = sendNewDofs;
recvDofs = recvNewDofs;
}
......
AMDiS/src/Recovery.h
View file @ 4a0bdb2f
......@@ -31,10 +31,6 @@
using namespace std;
using namespace AMDiS;
// ============================================================================
// ===== class Monomial =======================================================
// ============================================================================
class Monomial : public
BinaryAbstractFunction<double, WorldVector<double>, WorldVector<double> >
{
......@@ -46,9 +42,9 @@ public:
exponent(expon)
{
degree_ = exponent[0];
for (int i=1; i<exponent.size(); i++)
for (int i = 1; i<exponent.size(); i++)
degree_ += exponent[i];
};
}
virtual ~Monomial() {};
......@@ -60,39 +56,40 @@ public:
result *= pow(y[i] - z[i], exponent[i]);
return result;
};
}
private:
WorldVector<int> exponent;
};
// ============================================================================
// ===== class RecoveryStructure ==============================================
// ============================================================================
class RecoveryStructure
{
public: // construtor, destructor
// constructor
RecoveryStructure() :
coords(NULL),
A(NULL), rec_uh(NULL), rec_grdUh(NULL),
A(NULL),
rec_uh(NULL),
rec_grdUh(NULL),
neighbors(NULL)
{};
{}
// Destructor?
~RecoveryStructure()
{
clear();
};
RecoveryStructure(const RecoveryStructure& rhs) :
coords(NULL),
A(NULL), rec_uh(NULL), rec_grdUh(NULL),
neighbors(NULL) {
}
RecoveryStructure(const RecoveryStructure& rhs)
: coords(NULL),
A(NULL),
rec_uh(NULL),
rec_grdUh(NULL),
neighbors(NULL)
{
*this=rhs;
};
}
RecoveryStructure& operator=(const RecoveryStructure& rhs);
......
AMDiS/src/RecoveryEstimator.h
View file @ 4a0bdb2f
......@@ -27,161 +27,120 @@
namespace AMDiS {
// ============================================================================
// ===== class RecoveryEstimator ============================================
// ============================================================================
/** \brief
* Error estimator using the recovery gradient of the finite element solution.
*/
/// Error estimator using the recovery gradient of the finite element solution.
class RecoveryEstimator : public Estimator
{
public:
/** \brief
* Creator class.
*/
/// Creator class.
class Creator : public EstimatorCreator
{
public:
Creator() : EstimatorCreator(), uh(NULL) {};
Creator()
: EstimatorCreator(),
uh(NULL)
{}
virtual ~Creator() {};
virtual ~Creator() {}
inline void setSolution(DOFVector<double> *uh_)
{
uh = uh_;
};
}
/** \brief
* Returns a new Estimator object.
*/
/// Returns a new Estimator object.
Estimator* create()
{
return new RecoveryEstimator(name, uh, row);
};
}
protected:
DOFVector<double> *uh;
};
/** \brief
* constructor
*/
/// constructor
RecoveryEstimator(std::string name, DOFVector<double> *uh, int r = -1);
/** \brief
* destructor.
*/
virtual ~RecoveryEstimator() {};
/// destructor.
virtual ~RecoveryEstimator() {}
/** \brief
* implements \ref Estimator::estimate().
*/
/// implements \ref Estimator::estimate().
virtual double estimate(double timestep = 0.0);
/*----- Setting functions -----*/
// Sets uh.
/// Sets uh.
inline void setUh(DOFVector<double> *uh)
{
uh_ = uh;
};
}
// Sets f.
/// Sets f.
inline void setFct(AbstractFunction<double, WorldVector<double> > *fct)
{
f_vec = fct;
};
}
///
inline void setFct(AbstractFunction<double, double> *fct)
{
f_scal = fct;
};
}
// Sets auxiliar vector.
/// Sets auxiliar vector.
inline void setAuxVec(DOFVector<double> *uh)
{
aux_vec = uh;
};
}
/*----- Getting functions -----*/
// Gets recovery gradient.
/// Gets recovery gradient.
inline DOFVector<WorldVector<double> >* getRecGrd()
{
return rec_grd;
};
}
// Gets higher-order recovery solution.
/// Gets higher-order recovery solution.
inline DOFVector<double>* getRecUh()
{
return rec_uh;
};
}
protected: // protected members
/** \brief
* finite element solution
*/
protected:
/// finite element solution
DOFVector<double> *uh_;
/** \brief
* absolute or relative error?
*/
/// absolute or relative error?
int relative_;
/** \brief
* constant for scaling the estimator
*/
/// constant for scaling the estimator
double C;
/** \brief
* recovery method
*/
/// recovery method
int method;
/** \brief
* Working finite element space
*/
/// Working finite element space
const FiniteElemSpace *feSpace;
/** \brief
* Degree of corresponding basic functions
*/
/// Degree of corresponding basic functions
int degree;
/** \brief
* Basis functions for recovery vector.
*/
/// Basis functions for recovery vector.
const BasisFunction *rec_basFcts;
/** \brief
* Recovery gradient
*/
/// Recovery gradient
DOFVector<WorldVector<double> > *rec_grd;
/** \brief
* Higher-order recovery solution
*/
/// Higher-order recovery solution
DOFVector<double> *rec_uh;
/** \brief
* Diffusion coefficient (for flux recovery)
*/
/// Diffusion coefficient (for flux recovery)
AbstractFunction<double, WorldVector<double> > *f_vec;
AbstractFunction<double, double> *f_scal;
/** \brief
* auxiliar vector
*/
/// auxiliar vector
DOFVector<double> *aux_vec;
/** \brief
* Recovery structure.
*/
/// Recovery structure.
Recovery *rec_struct;
};
......
AMDiS/src/RefinementManager.h
View file @ 4a0bdb2f
......@@ -24,19 +24,10 @@
#include "Global.h"
#include "Flag.h"
#include "AMDiS_fwd.h"
namespace AMDiS {
class Element;
class Line;
class Triangle;
class Tetrahedron;
class Mesh;
class ElInfo;
class TraverseStack;
class RCNeighbourList;
/** \ingroup Adaption
* \brief
* Base class of RefinementManager1d, RefinementManager2d, RefinementManager3d.
......@@ -60,7 +51,8 @@ namespace AMDiS {
* Generates new coordinates on curved boundaries. Can be overriden by
* sub classes if used.
*/
virtual void setNewCoords() {
virtual void setNewCoords()
{
FUNCNAME("RefinementManager::setNewCoords");
ERROR_EXIT("called for base class!\n");
}
......@@ -78,11 +70,13 @@ namespace AMDiS {
Flag globalRefine(Mesh *aMesh, int mark);
/// Set \ref newCoords
inline void newCoord(bool nc) {
inline void newCoord(bool nc)
{
newCoords = nc;
}
inline bool newCoord() {
inline bool newCoord()
{
return newCoords;
}
......@@ -90,21 +84,25 @@ namespace AMDiS {
* Implements the refinement of el_info->el. Can be overriden by sub
* classes if used.
*/
virtual ElInfo* refineFunction(ElInfo* ) {
virtual ElInfo* refineFunction(ElInfo*)
{
FUNCNAME("RefinementManager::refineFunction()");
ERROR_EXIT("called for base class!\n");
return NULL;
}
inline void setMesh(Mesh *m) {
inline void setMesh(Mesh *m)
{
mesh = m;
}
inline void setStack(TraverseStack *s) {
inline void setStack(TraverseStack *s)
{
stack = s;
}
inline TraverseStack *getStack() {
inline TraverseStack *getStack()
{
return stack;
}
......
AMDiS/src/RefinementManager1d.h
View file @ 4a0bdb2f
......@@ -31,37 +31,25 @@ namespace AMDiS {
class RefinementManager1d : public RefinementManager
{
public:
/** \brief
* Calls base class constructor.
*/
/// Calls base class constructor.
RefinementManager1d()
: RefinementManager()
{};
{}
/** \brief
* destructor
*/
virtual ~RefinementManager1d() {};
/// destructor
virtual ~RefinementManager1d() {}
/** \brief
* Implements RefinementManager::refineMesh.
*/
/// Implements RefinementManager::refineMesh.
Flag refineMesh(Mesh *aMesh);
/** \brief
* Implements RefinementManager::setNewCoords
*/
/// Implements RefinementManager::setNewCoords
void setNewCoords();
protected:
/** \brief
* Used by refineMesh while mesh traversal
*/
/// Used by refineMesh while mesh