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Commit 9c5daa06 authored by Thomas Witkowski's avatar Thomas Witkowski
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* Some more or less important changes

parent edb60cbf
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Showing with 449 additions and 458 deletions
AMDiS/bin/Makefile.am
View file @ 9c5daa06
......@@ -19,7 +19,8 @@ if USE_PARALLEL_AMDIS
$(PARALLEL_DIR)/ParallelDomainProblem.h $(PARALLEL_DIR)/ParallelDomainProblem.cc \
$(PARALLEL_DIR)/ParMetisPartitioner.h $(PARALLEL_DIR)/ParMetisPartitioner.cc \
$(PARALLEL_DIR)/PartitionElementData.h
PARALLEL_INCLUDES = -I$(MPI_DIR)/include -I$(PARMETIS_DIR)
PARALLEL_INCLUDES = -I/work/home7/witkowsk/local/include \
-I$(MPI_DIR)/include -I$(PARMETIS_DIR)
else
PARALLEL_AMDIS_SOURCES =
PARALLEL_INCLUDES =
......@@ -27,6 +28,10 @@ endif
libamdis_la_CXXFLAGS =
if USE_PARALLEL_AMDIS
libamdis_la_CXXFLAGS += -DHAVE_PARALLEL_AMDIS=1
endif
if ENABLE_UMFPACK
libamdis_la_CXXFLAGS += -DHAVE_UMFPACK=1
AMDIS_INCLUDES += -I$(LIB_DIR)/UFconfig \
......
AMDiS/bin/Makefile.in
View file @ 9c5daa06
......@@ -36,17 +36,18 @@ PRE_UNINSTALL = :
POST_UNINSTALL = :
build_triplet = @build@
host_triplet = @host@
@ENABLE_UMFPACK_TRUE@am__append_1 = -DHAVE_UMFPACK=1
@ENABLE_UMFPACK_TRUE@am__append_2 = -I$(LIB_DIR)/UFconfig \
@USE_PARALLEL_AMDIS_TRUE@am__append_1 = -DHAVE_PARALLEL_AMDIS=1
@ENABLE_UMFPACK_TRUE@am__append_2 = -DHAVE_UMFPACK=1
@ENABLE_UMFPACK_TRUE@am__append_3 = -I$(LIB_DIR)/UFconfig \
@ENABLE_UMFPACK_TRUE@ -I$(LIB_DIR)/AMD/Include \
@ENABLE_UMFPACK_TRUE@ -I$(LIB_DIR)/UMFPACK/Include
@ENABLE_MKL_TRUE@am__append_3 = -DHAVE_MKL=1 -I${MKL_INC}
@ENABLE_DUNE_TRUE@am__append_4 = -DHAVE_DUNE=1
@ENABLE_DUNE_TRUE@am__append_5 = -I$(DUNE_DIR)
@ENABLE_BOOST_TRUE@am__append_6 = -DHAVE_BOOST=1
@AMDIS_DEBUG_TRUE@am__append_7 = -g -O0 -Wall -DDEBUG=1 $(OPENMP_FLAG) -ftemplate-depth-30 $(INCLUDES) #-pedantic
@AMDIS_DEBUG_FALSE@am__append_8 = -O2 -Wall -DDEBUG=0 $(OPENMP_FLAG) -ftemplate-depth-30 $(INCLUDES) #-pedantic
@ENABLE_MKL_TRUE@am__append_4 = -DHAVE_MKL=1 -I${MKL_INC}
@ENABLE_DUNE_TRUE@am__append_5 = -DHAVE_DUNE=1
@ENABLE_DUNE_TRUE@am__append_6 = -I$(DUNE_DIR)
@ENABLE_BOOST_TRUE@am__append_7 = -DHAVE_BOOST=1
@AMDIS_DEBUG_TRUE@am__append_8 = -g -O0 -Wall -DDEBUG=1 $(OPENMP_FLAG) -ftemplate-depth-30 $(INCLUDES) #-pedantic
@AMDIS_DEBUG_FALSE@am__append_9 = -O2 -Wall -DDEBUG=0 $(OPENMP_FLAG) -ftemplate-depth-30 $(INCLUDES) #-pedantic
subdir = bin
DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
......@@ -484,7 +485,7 @@ SOURCE_DIR = ../src
LIB_DIR = ../lib
PARALLEL_DIR = $(SOURCE_DIR)
PARMETIS_DIR = ../lib/ParMetis-3.1
AMDIS_INCLUDES = -I$(SOURCE_DIR) $(am__append_2) $(am__append_5)
AMDIS_INCLUDES = -I$(SOURCE_DIR) $(am__append_3) $(am__append_6)
@USE_PARALLEL_AMDIS_FALSE@PARALLEL_AMDIS_SOURCES =
@USE_PARALLEL_AMDIS_TRUE@PARALLEL_AMDIS_SOURCES = \
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/ConditionalEstimator.h $(PARALLEL_DIR)/ConditionalEstimator.cc \
......@@ -498,9 +499,12 @@ AMDIS_INCLUDES = -I$(SOURCE_DIR) $(am__append_2) $(am__append_5)
@USE_PARALLEL_AMDIS_TRUE@ $(PARALLEL_DIR)/PartitionElementData.h
@USE_PARALLEL_AMDIS_FALSE@PARALLEL_INCLUDES =
@USE_PARALLEL_AMDIS_TRUE@PARALLEL_INCLUDES = -I$(MPI_DIR)/include -I$(PARMETIS_DIR)
libamdis_la_CXXFLAGS = $(am__append_1) $(am__append_3) $(am__append_4) \
$(am__append_6) $(am__append_7) $(am__append_8)
@USE_PARALLEL_AMDIS_TRUE@PARALLEL_INCLUDES = -I/work/home7/witkowsk/local/include \
@USE_PARALLEL_AMDIS_TRUE@ -I$(MPI_DIR)/include -I$(PARMETIS_DIR)
libamdis_la_CXXFLAGS = $(am__append_1) $(am__append_2) $(am__append_4) \
$(am__append_5) $(am__append_7) $(am__append_8) \
$(am__append_9)
INCLUDES = $(AMDIS_INCLUDES) $(PARALLEL_INCLUDES)
libamdis_la_SOURCES = \
$(PARALLEL_AMDIS_SOURCES) \
......
AMDiS/libtool
View file @ 9c5daa06
......@@ -44,7 +44,7 @@ available_tags=" CXX F77"
# ### BEGIN LIBTOOL CONFIG
# Libtool was configured on host p2s148:
# Libtool was configured on host p2s256:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
......@@ -6760,7 +6760,7 @@ build_old_libs=`case $build_libtool_libs in yes) $echo no;; *) $echo yes;; esac`
# End:
# ### BEGIN LIBTOOL TAG CONFIG: CXX
# Libtool was configured on host p2s148:
# Libtool was configured on host p2s256:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
......@@ -7065,7 +7065,7 @@ include_expsyms=""
# ### BEGIN LIBTOOL TAG CONFIG: F77
# Libtool was configured on host p2s148:
# Libtool was configured on host p2s256:
# Shell to use when invoking shell scripts.
SHELL="/bin/sh"
......
AMDiS/src/AdaptStationary.h
View file @ 9c5daa06
......@@ -55,27 +55,19 @@ namespace AMDiS {
public:
MEMORY_MANAGED(AdaptStationary);
/** \brief
* Creates a AdaptStationary object with given name.
*/
/// Creates a AdaptStationary object with given name.
AdaptStationary(const std::string &name,
ProblemIterationInterface *prob,
AdaptInfo *info);
/** \brief
* Destructor
*/
/// Destructor
virtual ~AdaptStationary() {}
/** \brief
* Implementation of AdaptBase::adapt()
*/
/// Implementation of AdaptBase::adapt()
virtual int adapt();
protected:
/** \brief
* Initialisation
*/
/// Initialisation
void initialize();
};
......
AMDiS/src/DOFMatrix.cc
View file @ 9c5daa06
......@@ -47,6 +47,10 @@ namespace AMDiS {
colFESpace->getBasisFcts()->getNumber());
applyDBCs.clear();
#ifdef HAVE_PARALLEL_AMDIS
applicationOrdering = NULL;
#endif
}
DOFMatrix::DOFMatrix(const DOFMatrix& rhs)
......
AMDiS/src/DOFMatrix.h
View file @ 9c5daa06
......@@ -30,6 +30,7 @@
#include <set>
#include <memory>
#include <list>
#include "Global.h"
#include "Flag.h"
#include "RCNeighbourList.h"
......@@ -40,6 +41,10 @@
#include "Boundary.h"
#include "Serializable.h"
#ifdef HAVE_PARALLEL_AMDIS
#include "petscao.h"
#endif
namespace AMDiS {
// ============================================================================
......@@ -420,23 +425,17 @@ namespace AMDiS {
return rowFESpace;
}
/** \brief
* Returns const \ref colFESpace
*/
/// Returns const \ref colFESpace
const FiniteElemSpace* getColFESpace() const {
return colFESpace;
}
/** \brief
* Returns const \ref rowFESpace
*/
/// Returns const \ref rowFESpace
const FiniteElemSpace* getFESpace() const {
return rowFESpace;
}
/** \brief
* Returns number of rows (\ref matrix.size())
*/
/// Returns number of rows (\ref matrix.size())
inline int getSize() const {
return matrix.size();
}
......@@ -455,58 +454,44 @@ namespace AMDiS {
*/
int getNumCols() const;
/** \brief
* Returns \ref name
*/
/// Returns \ref name
inline const std::string& getName() const {
return name;
}
/** \brief
* Resizes \ref matrix to n rows
*/
/// Resizes \ref matrix to n rows
inline void resize(int n) {
TEST_EXIT_DBG(n >= 0)("Can't resize DOFMatrix to negative size\n");
matrix.resize(n);
}
/** \brief
* Returns \ref matrix[i] which is the i-th row
*/
/// Returns \ref matrix[i] which is the i-th row
inline const std::vector<MatEntry>& operator[](int i) const {
TEST_EXIT_DBG((i >= 0) && (i < (static_cast<int>(matrix.size()))))
("Illegal matrix index %d.\n",i);
return matrix[i];
}
/** \brief
* Returns \ref matrix[i] which is the i-th row
*/
/// Returns \ref matrix[i] which is the i-th row
inline std::vector<MatEntry>& operator[](int i) {
TEST_EXIT_DBG((i >= 0) && (i < (static_cast<int>(matrix.size()))))
("Illegal vector index %d.\n", i);
return matrix[i];
}
/** \brief
* Access to \ref matrix[a][b].entry
*/
/// Access to \ref matrix[a][b].entry
inline double physAcc(DegreeOfFreedom a, DegreeOfFreedom b) const {
return matrix[a][b].entry;
}
/** \brief
* Access to \ref matrix[a][b].col
*/
/// Access to \ref matrix[a][b].col
inline DegreeOfFreedom physToLogIndex(DegreeOfFreedom a,
DegreeOfFreedom b) const
{
return matrix[a][b].col;
}
/** \brief
* Returns physical column index of logical index b in row a
*/
/// Returns physical column index of logical index b in row a
inline DegreeOfFreedom logToPhysIndex(DegreeOfFreedom a, DegreeOfFreedom b) const
{
int size = static_cast<int>(matrix[a].size());
......@@ -517,19 +502,13 @@ namespace AMDiS {
return -1;
}
/** \brief
* Returns value at logical indices a,b
*/
/// Returns value at logical indices a,b
double logAcc(DegreeOfFreedom a, DegreeOfFreedom b) const;
/** \brief
* Changes col at logical indices a,b to c
*/
/// Changes col at logical indices a,b to c
void changeColOfEntry(DegreeOfFreedom a, DegreeOfFreedom b, DegreeOfFreedom c);
/** \brief
* Changes col of \ref matrix[a][b] to c
*/
/// Changes col of \ref matrix[a][b] to c
inline void changePhysColOfEntry(DegreeOfFreedom a,
DegreeOfFreedom b,
DegreeOfFreedom c)
......@@ -565,24 +544,16 @@ namespace AMDiS {
void removeRowsWithDBC(std::set<int> *rows);
/** \brief
* Prints \ref matrix to stdout
*/
/// Prints \ref matrix to stdout
void print() const;
/** \brief
* Prints a row of \ref matrix to stdout
*/
/// Prints a row of \ref matrix to stdout
void printRow(int i) const;
/** \brief
* Removes all matrix entries
*/
/// Removes all matrix entries
void clear();
/** \brief
* Test whether \ref matrix is symmetric. Exits if not.
*/
/// Test whether \ref matrix is symmetric. Exits if not.
void test();
bool symmetric();
......@@ -612,9 +583,7 @@ namespace AMDiS {
}
void createPictureFile(const char* filename, int dim);
// ===== Serializable implementation =====
void serialize(std::ostream &out)
{
unsigned int matrixSize = matrix.size();
......@@ -640,13 +609,15 @@ namespace AMDiS {
}
}
///
int memsize();
protected:
/** \brief
* Used by updateMatrix
*/
//static int assembleFct(ElInfo *el_info);
#ifdef HAVE_PARALLEL_AMDIS
/// Sets the petsc application ordering object to map dof indices.
void useApplicationOrdering(AO *ao) {
applicationOrdering = ao;
}
#endif
protected:
/** \brief
......@@ -661,19 +632,13 @@ namespace AMDiS {
*/
const FiniteElemSpace *colFESpace;
/** \brief
* Name of the DOFMatrix
*/
/// Name of the DOFMatrix
std::string name;
/** \brief
* Sparse matrix stored in an STL vector of MatrixRow objects
*/
/// Sparse matrix stored in an STL vector of MatrixRow objects
std::vector<MatrixRow> matrix;
/** \brief
* Used while mesh traversal
*/
/// Used while mesh traversal
static DOFMatrix *traversePtr;
/** \brief
......@@ -688,28 +653,26 @@ namespace AMDiS {
*/
std::vector<double*> operatorFactor;
/** \brief
*
*/
///
std::vector<double*> operatorEstFactor;
/** \brief
*
*/
///
BoundaryManager *boundaryManager;
/** \brief
*
*/
///
bool coupleMatrix;
/** \brief
* Temporary variable used in assemble()
*/
/// Temporary variable used in assemble()
ElementMatrix *elementMatrix;
///
std::set<int> applyDBCs;
#ifdef HAVE_PARALLEL_AMDIS
/// Petsc application ordering to map dof indices.
AO *applicationOrdering;
#endif
friend class DOFAdmin;
friend class DOFVector<double>;
friend class DOFVector<unsigned char>;
......@@ -718,7 +681,8 @@ namespace AMDiS {
};
inline DegreeOfFreedom logToPhysIndex(DOFMatrix *m, DegreeOfFreedom a, DegreeOfFreedom b)
inline DegreeOfFreedom logToPhysIndex(DOFMatrix *m,
DegreeOfFreedom a, DegreeOfFreedom b)
{
return m->logToPhysIndex(a, b);
}
......@@ -729,16 +693,11 @@ namespace AMDiS {
double max(std::vector<MatEntry> *row);
/** \brief
* Addes two matrices. The result matrix is overwritten.
*/
/// Addes two matrices. The result matrix is overwritten.
void addDOFMatrix(DOFMatrix *result, const DOFMatrix *a, const DOFMatrix *b);
/** \brief
* Addes matrix a to matrix result.
*/
/// Addes matrix a to matrix result.
void addDOFMatrix(DOFMatrix *result, const DOFMatrix *a);
}
#endif // AMDIS_DOFMATRIX_H
AMDiS/src/DOFVector.h
View file @ 9c5daa06
......@@ -26,6 +26,10 @@
// ===== includes ============================================================
// ===========================================================================
#include <vector>
#include <memory>
#include <list>
#include "FixVec.h"
#include "Global.h"
#include "Flag.h"
......@@ -39,9 +43,10 @@
#include "Serializable.h"
#include "DOFMatrix.h"
#include "BasisFunction.h"
#include <vector>
#include <memory>
#include <list>
#ifdef HAVE_PARALLEL_AMDIS
#include "petscao.h"
#endif
namespace AMDiS {
......@@ -584,24 +589,16 @@ namespace AMDiS {
*/
T max() const;
/** \brief
* Returns absolute maximum of DOFVector
*/
/// Returns absolute maximum of DOFVector
T absMax() const;
/** \brief
* Used by interpol while mesh traversal
*/
/// Used by interpol while mesh traversal
static int interpolFct(ElInfo* elinfo);
/** \brief
* Prints \ref vec to stdout
*/
/// Prints \ref vec to stdout
void print() const;
/** \brief
*
*/
///
int calcMemoryUsage() const;
/** \brief
......@@ -612,8 +609,6 @@ namespace AMDiS {
void interpol(DOFVector<T> *v, double factor);
// ===== Serializable implementation =====
void serialize(std::ostream &out) {
unsigned int size = vec.size();
out.write(reinterpret_cast<const char*>(&size), sizeof(unsigned int));
......@@ -635,6 +630,13 @@ namespace AMDiS {
getRecoveryGradient(DOFVector<WorldVector<T> >*) const;
#ifdef HAVE_PARALLEL_AMDIS
/// Sets the petsc application ordering object to map dof indices.
void useApplicationOrdering(AO *ao) {
applicationOrdering = ao;
}
#endif
protected:
/** \brief
* Used by Int while mesh traversal
......@@ -662,45 +664,34 @@ namespace AMDiS {
static int DoubleWell_fct(ElInfo* elinfo);
protected:
/** \brief
* Name of this DOFVector
*/
/// Name of this DOFVector
std::string name;
/** \brief
* FiniteElemSpace of the vector
*/
/// FiniteElemSpace of the vector
const FiniteElemSpace *feSpace;
/** \brief
* Data container
*/
/// Data container
std::vector<T> vec;
/** \brief
* Specifies what operation should be performed after coarsening
*/
/// Specifies what operation should be performed after coarsening
CoarsenOperation coarsenOperation;
/** \brief
* Used by \ref interpol
*/
/// Used by \ref interpol
AbstractFunction<T, WorldVector<double> > *interFct;
/** \brief
* Used for mesh traversal
*/
/// Used for mesh traversal
static DOFVector<T> *traverseVector;
#ifdef HAVE_PARALLEL_AMDIS
/// Petsc application ordering to map dof indices.
AO *applicationOrdering;
#endif
protected:
/** \brief
* Used while calculating vector norms
*/
/// Used while calculating vector norms
static FastQuadrature *quad_fast;
/** \brief
* Stores the last calculated vector norm
*/
/// Stores the last calculated vector norm
static double norm;
};
......@@ -744,9 +735,7 @@ namespace AMDiS {
feSpace->getAdmin()->addDOFContainer(this);
}
/** \brief
* Deregisters itself at DOFAdmin.
*/
/// Deregisters itself at DOFAdmin.
~DOFVectorDOF() {
feSpace->getAdmin()->removeDOFContainer(this);
}
......@@ -759,16 +748,12 @@ namespace AMDiS {
return DOFVector<DegreeOfFreedom>::operator[](i);
}
/** \brief
* Implements DOFIndexedBase::getSize()
*/
/// Implements DOFIndexedBase::getSize()
int getSize() const {
return DOFVector<DegreeOfFreedom>::getSize();
}
/** \brief
* Implements DOFIndexedBase::resize()
*/
/// Implements DOFIndexedBase::resize()
void resize(int size) {
DOFVector<DegreeOfFreedom>::resize(size);
}
......
AMDiS/src/DOFVector.hh
View file @ 9c5daa06
......@@ -66,6 +66,10 @@ namespace AMDiS {
coarsenOperation(NO_OPERATION)
{
init(f, n);
#ifdef HAVE_PARALLEL_AMDIS
applicationOrdering = NULL;
#endif
}
template<typename T>
......
AMDiS/src/Element.cc
View file @ 9c5daa06
......@@ -41,7 +41,6 @@ namespace AMDiS {
newCoord = NULL;
elementData = NULL;
mark = 0;
hidden = false;
if (mesh) {
setDOFPtrs();
......@@ -139,7 +138,6 @@ namespace AMDiS {
el->mesh = mesh;
el->index = index;
el->mark = mark;
el->hidden = hidden;
if (newCoord) {
WorldVector<double> *nc = NEW WorldVector<double>();
*nc = *newCoord;
......@@ -422,9 +420,6 @@ namespace AMDiS {
// write mark
out.write(reinterpret_cast<const char*>(&mark), sizeof(signed char));
// write hidden flag
out.write(reinterpret_cast<const char*>(&hidden), sizeof(hidden));
// write newCoord
if (newCoord) {
out << "WorldVector\n";
......@@ -506,9 +501,6 @@ namespace AMDiS {
// read mark
in.read(reinterpret_cast<char*>(&mark), sizeof(signed char));
// read hidden
in.read(reinterpret_cast<char*>(&hidden), sizeof(bool));
// read newCoord
in >> typeName;
in.get();
......
AMDiS/src/Element.h
View file @ 9c5daa06
......@@ -230,16 +230,6 @@ namespace AMDiS {
return newCoord;