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Commit c096fbb7 authored by Thomas Witkowski's avatar Thomas Witkowski
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Work on pdd

parent deafc91a
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Showing with 223 additions and 117 deletions
AMDiS/src/DOFMatrix.cc
View file @ c096fbb7
......@@ -14,7 +14,6 @@
#include "BoundaryCondition.h"
#include "BoundaryManager.h"
#include "Assembler.h"
#include "Utilities.h"
namespace AMDiS {
......
AMDiS/src/ParallelDomainProblem.cc
View file @ c096fbb7
......@@ -276,6 +276,10 @@ namespace AMDiS {
void ParallelDomainProblemBase::createInteriorBoundaryInfo(std::vector<const DegreeOfFreedom*>& rankDOFs,
std::map<const DegreeOfFreedom*, int>& boundaryDOFs)
{
FUNCNAME("ParallelDomainProblemBase::createInteriorBoundaryInfo()");
// === First, create all the information about the interior boundaries. ===
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL | Mesh::FILL_NEIGH);
while (elInfo) {
......@@ -323,20 +327,86 @@ namespace AMDiS {
/// === And add the part of the interior boundary. ===
AtomicBoundary& bound =
interiorBoundary.getNewAtomicBoundary(ranksBoundary ? mpiRank :
partitionVec[elInfo->getNeighbour(i)->getIndex()]);
(ranksBoundary ?
myIntBoundary.getNewAtomicBoundary(partitionVec[elInfo->getNeighbour(i)->getIndex()]) :
otherIntBoundary.getNewAtomicBoundary(partitionVec[elInfo->getNeighbour(i)->getIndex()]));
bound.rankObject.el = element;
bound.rankObject.subObjAtBoundary = EDGE;
bound.rankObject.ithObjAtBoundary = i;
bound.neighbourObject.el = elInfo->getNeighbour(i);
bound.neighbourObject.subObjAtBoundary = EDGE;
bound.neighbourObject.ithObjAtBoundary = -1;
std::cout << "ADD IN " << mpiRank << ": " << element->getIndex() << " " << elInfo->getNeighbour(i)->getIndex() << std::endl;
}
}
}
elInfo = stack.traverseNext(elInfo);
}
// === Once we have this information, we must care about their order. Eventually ===
// === all the boundaries have to be in the same order on both ranks (because ===
// === each boundary is shared by exactly two ranks). ===
std::vector<int*> sendBuffers;
std::vector<int*> recvBuffers;
for (std::map<int, std::vector<AtomicBoundary> >::iterator rankIt = myIntBoundary.boundary.begin();
rankIt != myIntBoundary.boundary.end();
++rankIt) {
int* buffer = new int[rankIt->second.size()];
for (int i = 0; i < static_cast<int>(rankIt->second.size()); i++)
buffer[i] = (rankIt->second)[i].rankObject.el->getIndex();
sendBuffers.push_back(buffer);
mpiComm.Isend(buffer, rankIt->second.size(), MPI_INT, rankIt->first, 0);
}
for (std::map<int, std::vector<AtomicBoundary> >::iterator rankIt = otherIntBoundary.boundary.begin();
rankIt != otherIntBoundary.boundary.end();
++rankIt) {
int *buffer = new int[rankIt->second.size()];
recvBuffers.push_back(buffer);
mpiComm.Irecv(buffer, rankIt->second.size(), MPI_INT, rankIt->first, 0);
}
mpiComm.Barrier();
int i = 0;
for (std::map<int, std::vector<AtomicBoundary> >::iterator rankIt = otherIntBoundary.boundary.begin();
rankIt != otherIntBoundary.boundary.end();
++rankIt) {
// === We have received from rank "rankIt->first" the ordered list of element ===
// === indices. We now have to sort the corresponding list in this rank to ===
// === get the same order. ===
for (int j = 0; j < static_cast<int>(rankIt->second.size()); j++) {
// If the expected object is not at place, search for it.
if ((rankIt->second)[j].neighbourObject.el->getIndex() != recvBuffers[i][j]) {
int k = j + 1;
for (; k < static_cast<int>(rankIt->second.size()); k++)
if ((rankIt->second)[k].neighbourObject.el->getIndex() == recvBuffers[i][j])
break;
// The element must always be found, because the list is just in another order.
TEST_EXIT(k < rankIt->second.size())("Should never happen!\n");
// Swap the current with the found element.
AtomicBoundary tmpBound = (rankIt->second)[k];
(rankIt->second)[k] = (rankIt->second)[j];
(rankIt->second)[j] = tmpBound;
}
}
delete [] recvBuffers[i++];
}
for (int i = 0; i < static_cast<int>(sendBuffers.size()); i++)
delete [] sendBuffers[i];
}
......@@ -527,8 +597,10 @@ namespace AMDiS {
void ParallelDomainProblemBase::updateLocalGlobalNumbering(int& nRankDOFs,
int& nOverallDOFs)
{
FUNCNAME("ParallelDomainProblemBase::updateLocalGlobalNumbering()");
std::set<const DegreeOfFreedom*> rankDOFs;
std::set<const DegreeOfFreedom*> boundaryDOFs;
std::map<const DegreeOfFreedom*, int> boundaryDOFs;
/// === Get all DOFs in ranks partition. ===
......@@ -545,20 +617,105 @@ namespace AMDiS {
}
// === Traverse on interior boundaries and move all not ranked owned DOFs from
// rankDOFs to boundaryDOFs === //
// === Traverse on interior boundaries and move all not ranked owned DOFs from ===
// === rankDOFs to boundaryDOFs ===
for (std::map<int, std::vector<AtomicBoundary> >::iterator it =
interiorBoundary.boundary.begin();
it != interiorBoundary.boundary.end();
myIntBoundary.boundary.begin();
it != myIntBoundary.boundary.end();
++it) {
for (int i = 0; i < it->second.size(); i++) {
for (std::vector<AtomicBoundary>::iterator boundIt = it->second.begin();
boundIt != it->second.end();
++boundIt) {
const DegreeOfFreedom *dof1 = NULL;
const DegreeOfFreedom *dof2 = NULL;
switch (boundIt->rankObject.ithObjAtBoundary) {
case 0:
dof1 = boundIt->rankObject.el->getDOF(1);
dof2 = boundIt->rankObject.el->getDOF(2);
break;
case 1:
dof1 = boundIt->rankObject.el->getDOF(0);
dof2 = boundIt->rankObject.el->getDOF(2);
break;
case 2:
dof1 = boundIt->rankObject.el->getDOF(0);
dof2 = boundIt->rankObject.el->getDOF(1);
break;
default:
ERROR_EXIT("Should never happen!\n");
}
std::vector<const DegreeOfFreedom*> boundDOFs;
addAllDOFs(boundIt->rankObject.el, boundIt->rankObject.ithObjAtBoundary,
boundDOFs);
}
}
}
void ParallelDomainProblemBase::addAllDOFs(Element *el, int ithEdge,
std::vector<const DegreeOfFreedom*>& dofs,
bool addVertices)
{
FUNCNAME("ParallelDomainProblemBase::addAllDOFs()");
const DegreeOfFreedom* boundDOF1 = NULL;
const DegreeOfFreedom* boundDOF2 = NULL;
if (addVertices) {
switch (ithEdge) {
case 0:
boundDOF1 = el->getDOF(1);
boundDOF2 = el->getDOF(2);
break;
case 1:
boundDOF1 = el->getDOF(0);
boundDOF2 = el->getDOF(2);
break;
case 2:
boundDOF1 = el->getDOF(0);
boundDOF2 = el->getDOF(1);
break;
default:
ERROR_EXIT("Should never happen!\n");
}
dofs.push_back(boundDOF1);
}
switch (ithEdge) {
case 0:
if (el->getSecondChild() && el->getSecondChild()->getFirstChild()) {
addAllDOFs(el->getSecondChild()->getFirstChild(), 0, dofs, false);
dofs.push_back(el->getSecondChild()->getFirstChild()->getDOF(2));
addAllDOFs(el->getSecondChild()->getSecondChild(), 1, dofs, false);
}
break;
case 1:
if (el->getFirstChild() && el->getFirstChild()->getFirstChild()) {
addAllDOFs(el->getFirstChild()->getFirstChild(), 0, dofs, false);
dofs.push_back(el->getFirstChild()->getFirstChild()->getDOF(2));
addAllDOFs(el->getFirstChild()->getSecondChild(), 1, dofs, false);
}
break;
case 2:
if (el->getFirstChild()) {
addAllDOFs(el->getFirstChild(), 0, dofs, false);
dofs.push_back(el->getFirstChild()->getDOF(2));
addAllDOFs(el->getSecondChild(), 1, dofs, false);
}
break;
default:
ERROR_EXIT("Should never happen!\n");
}
if (addVertices)
dofs.push_back(boundDOF2);
}
void ParallelDomainProblemBase::createDOFMemberInfo(
std::map<const DegreeOfFreedom*, std::set<int> >& partitionDOFs,
std::vector<const DegreeOfFreedom*>& rankDOFs,
......
AMDiS/src/ParallelDomainProblem.h
View file @ c096fbb7
......@@ -137,9 +137,15 @@ namespace AMDiS {
void updateLocalGlobalNumbering(int& nRankDOFs, int& nOverallDOFs);
void addAllDOFs(Element *el, int ithEdge,
std::vector<const DegreeOfFreedom*>& dofs,
bool addVertices = true);
/** \brief
* This function traverses the whole mesh, i.e. before it is really partitioned,
* and collects information about which DOF corresponds to which rank.
* and collects information about which DOF corresponds to which rank. Can only
* be used, if \ref partitionVec is set correctly. This is only the case, when
* the macro mesh is partitioned.
*
* @param[out] partionDOFs Stores to each DOF pointer the set of ranks the DOF is
* part of.
......@@ -215,10 +221,20 @@ namespace AMDiS {
int nRankDOFs;
/** \brief
* Defines the interioir boundaries of the domain that result from partitioning
* the whole mesh.
* Defines the interior boundaries of the domain that result from partitioning
* the whole mesh. Contains only the boundaries, which are owned by the rank, i.e.,
* the object gives for every neighbour rank i the boundaries this rank owns and
* shares with rank i.
*/
InteriorBoundary myIntBoundary;
/** \brief
* Defines the interior boundaries of the domain that result from partitioning
* the whole mesh. Contains only the boundaries, which are not owned by the rank,
* i.e., the object gives for every neighbour rank i the boundaries that are
* owned by rank i and are shared with this rank.
*/
InteriorBoundary interiorBoundary;
InteriorBoundary otherIntBoundary;
/** \brief
* This map contains for each rank the list of dofs the current rank must send
......
AMDiS/src/UmfPackSolver.h
View file @ c096fbb7
......@@ -51,7 +51,8 @@ namespace AMDiS {
/** \brief
* Returns a new UmfPackSolver object.
*/
OEMSolver* create() {
OEMSolver* create()
{
return new UmfPackSolver(this->name);
}
};
......@@ -67,7 +68,11 @@ namespace AMDiS {
}
/// Destructor
~UmfPackSolver() { if (solver) delete solver;}
~UmfPackSolver()
{
if (solver)
delete solver;
}
/// Solves the system directly
int solveSystem(const DOFMatrix::base_matrix_type& A,
......
AMDiS/src/Utilities.h deleted 100644 → 0
View file @ deafc91a
// ============================================================================
// == ==
// == AMDiS - Adaptive multidimensional simulations ==
// == ==
// ============================================================================
// == ==
// == crystal growth group ==
// == ==
// == Stiftung caesar ==
// == Ludwig-Erhard-Allee 2 ==
// == 53175 Bonn ==
// == germany ==
// == ==
// ============================================================================
// == ==
// == http://www.caesar.de/cg/AMDiS ==
// == ==
// ============================================================================
/** \file Utilities.h */
#ifndef AMDIS_UTILITIES_H
#define AMDIS_UTILITIES_H
#include <vector>
#include <algorithm>
template <typename T>
std::vector<T> inline invert_reorder(const std::vector<T>& v)
{
T my_max= *std::max_element(v.begin(), v.end()) + 1;
std::vector<T> u(my_max, T(-1));
for (int i= 0; i < v.size(); i++)
if (v[i] >= 0) {
assert(u[v[i]] == -1); // check double insertion
u[v[i]]= T(i);
}
assert(find(u.begin(), u.end(), T(-1)) == u.end()); // check if all entries are set
return u;
}
#endif // AMDIS_UTILITIES_H
AMDiS/src/ValueWriter.h
View file @ c096fbb7
......@@ -29,18 +29,10 @@
#include "Flag.h"
#include "Mesh.h"
#include "DataCollector.h"
#include "AMDiS_fwd.h"
namespace AMDiS {
class DOFAdmin;
class ElInfo;
template<typename T> class DOFVector;
// ============================================================================
// ===== class ValueWriter ====================================================
// ============================================================================
/** \ingroup Output
* \brief
* ValueWriter is a static class which writes the values of a DOFVector
......@@ -53,9 +45,7 @@ namespace AMDiS {
class ValueWriter
{
public:
/** \brief
* Writes DOFVector values to values->feSpace->mesh.
*/
/// Writes DOFVector values to values->feSpace->mesh.
static void writeValues(DataCollector *dc,
const std::string filename,
double time = 0.0,
......@@ -64,34 +54,22 @@ namespace AMDiS {
bool (*writeElem)(ElInfo*) = NULL);
protected:
/** \brief
* File to which the values should be written
*/
/// File to which the values should be written
static FILE *valueFile;
/** \brief
* Global interpolation point indexing
*/
/// Global interpolation point indexing
static DOFVector<int> *interpPointInd;
/** \brief
* list of coords for each dof
*/
/// list of coords for each dof
static DOFVector< std::list<WorldVector<double> > > *dofCoords;
/** \brief
* DOFAdmin of values
*/
/// DOFAdmin of values
static const DOFAdmin *admin;
/** \brief
* Pointer to have a global access to values
*/
/// Pointer to have a global access to values
static DOFVector<double> *valueVec;
/** \brief
* Total number of interpolation points.
*/
/// Total number of interpolation points.
static int ni;
};
......
AMDiS/src/VertexInfo.h
View file @ c096fbb7
......@@ -26,35 +26,27 @@
namespace AMDiS {
/** \brief
* Stores coordinates and output index for one vertex.
*/
/// Stores coordinates and output index for one vertex.
class VertexInfo
{
public:
/** \brief
* Coordinates for this vertex.
*/
/// Coordinates for this vertex.
WorldVector<double> coords;
/** \brief
* Index for the output file.
*/
/// Index for the output file.
int outputIndex;
/** \brief
* Used to check, whether coords are already stored for a given dof.
*/
bool operator==(const WorldVector<double>& c) {
/// Used to check, whether coords are already stored for a given dof.
bool operator==(const WorldVector<double>& c)
{
return (c == coords);
};
}
/** \brief
* Used to check, whether coords are already stored for a given dof.
*/
bool operator!=(const WorldVector<double>& c) {
/// Used to check, whether coords are already stored for a given dof.
bool operator!=(const WorldVector<double>& c)
{
return (c != coords);
};
}
};
}
......
AMDiS/src/VertexVector.h
View file @ c096fbb7
......@@ -21,24 +21,27 @@ namespace AMDiS {
~VertexVector();
const DOFAdmin *getAdmin() { return admin; };
const DOFAdmin *getAdmin()
{
return admin;
}
void resize(int size) {
int i, oldSize = static_cast<int>(vec.size());
void resize(int size)
{
int oldSize = static_cast<int>(vec.size());
vec.resize(size);
for(i = oldSize; i < size; i++) {
for (int i = oldSize; i < size; i++)
vec[i] = i;
}
}
void set(DegreeOfFreedom val);
void compressDOFContainer(int size, std::vector<DegreeOfFreedom> &newDOF) {
void compressDOFContainer(int size, std::vector<DegreeOfFreedom> &newDOF)
{
DOFContainer::compressDOFContainer(size, newDOF);
int totalSize = getAdmin()->getSize();
for(int i = size; i < totalSize; i++) {
for(int i = size; i < totalSize; i++)
vec[i] = i;
}
}
protected:
......
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