diff --git a/AMDiS/bin/Makefile.am b/AMDiS/bin/Makefile.am
index c650107263f7e31f7ab407b318baa8de2b9234cc..6b3303d4e07391d3893724ae7fe1ebbacae3f73e 100644
--- a/AMDiS/bin/Makefile.am
+++ b/AMDiS/bin/Makefile.am
@@ -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 \
diff --git a/AMDiS/bin/Makefile.in b/AMDiS/bin/Makefile.in
index 3c77cd69ebc7bf1843f5297a72da10bf7c27e7bf..623d04b026aed80e68662a65fcd298850219bd7b 100644
--- a/AMDiS/bin/Makefile.in
+++ b/AMDiS/bin/Makefile.in
@@ -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) \
diff --git a/AMDiS/libtool b/AMDiS/libtool
index c1ffc52dc2a18e9aea6a1c54bd62b799a57e937c..fcd0e2f7c8e2ddac64e11b952c5570c79e95b93b 100755
--- a/AMDiS/libtool
+++ b/AMDiS/libtool
@@ -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"
diff --git a/AMDiS/src/AdaptStationary.h b/AMDiS/src/AdaptStationary.h
index 0c30c6dbed973d1a09f5df52ae40e157f19ed58c..8bf24778ebf2fd9590ebb905b49e122b6637c213 100644
--- a/AMDiS/src/AdaptStationary.h
+++ b/AMDiS/src/AdaptStationary.h
@@ -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();
};
diff --git a/AMDiS/src/DOFMatrix.cc b/AMDiS/src/DOFMatrix.cc
index 8138d34ab9ae0a21b07743bcc7de5af8b7aec4de..98c48edc5d1325eb23f4c451bfa5297fd52211d5 100644
--- a/AMDiS/src/DOFMatrix.cc
+++ b/AMDiS/src/DOFMatrix.cc
@@ -47,6 +47,10 @@ namespace AMDiS {
colFESpace->getBasisFcts()->getNumber());
applyDBCs.clear();
+
+#ifdef HAVE_PARALLEL_AMDIS
+ applicationOrdering = NULL;
+#endif
}
DOFMatrix::DOFMatrix(const DOFMatrix& rhs)
diff --git a/AMDiS/src/DOFMatrix.h b/AMDiS/src/DOFMatrix.h
index da73d1dec1678d3e23b546845e3343a3d91c9f69..49d5ea3c53b823b4de7d7cb95ca1a432240c3342 100644
--- a/AMDiS/src/DOFMatrix.h
+++ b/AMDiS/src/DOFMatrix.h
@@ -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
diff --git a/AMDiS/src/DOFVector.h b/AMDiS/src/DOFVector.h
index 5b1ae2cee1ec9b3dd024a49a99ed6f2e64139aef..ebd581b0edb1bebb80c51afb4853fae5e220f048 100644
--- a/AMDiS/src/DOFVector.h
+++ b/AMDiS/src/DOFVector.h
@@ -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);
}
diff --git a/AMDiS/src/DOFVector.hh b/AMDiS/src/DOFVector.hh
index 8c29fab6fbbad835d47e18efa9c38584e6a7c847..d476dd76feb56f23e7aae43f31ae27e00a9edaee 100644
--- a/AMDiS/src/DOFVector.hh
+++ b/AMDiS/src/DOFVector.hh
@@ -66,6 +66,10 @@ namespace AMDiS {
coarsenOperation(NO_OPERATION)
{
init(f, n);
+
+#ifdef HAVE_PARALLEL_AMDIS
+ applicationOrdering = NULL;
+#endif
}
template<typename T>
diff --git a/AMDiS/src/Element.cc b/AMDiS/src/Element.cc
index 57d5e53ff299e75003f68726254714db7b604fd7..c8ac2cb33abafa45ed22fe7fef91cd467592bcbd 100644
--- a/AMDiS/src/Element.cc
+++ b/AMDiS/src/Element.cc
@@ -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();
diff --git a/AMDiS/src/Element.h b/AMDiS/src/Element.h
index c2bf1d84cf01631f7093a9b35f61bcf1c0828170..8e9700c0677881099d854949d523d23f33439df2 100644
--- a/AMDiS/src/Element.h
+++ b/AMDiS/src/Element.h
@@ -230,16 +230,6 @@ namespace AMDiS {
return newCoord;
}
- /// Returns \ref hidden, i.e., if the element is visible for mesh traverses.
- inline bool isHidden() {
- return hidden;
- }
-
- /// Sets \ref hidden, i.e., wether the element is hidden for mesh traverses or not.
- inline void setHidden(bool b) {
- hidden = b;
- }
-
/** \} */
// ===== setting methods ======================================================
@@ -529,12 +519,6 @@ namespace AMDiS {
/// Pointer to Element's leaf data
ElementData* elementData;
- /* \brief
- * If true, this element (and therefor also all it's children) is hidden for
- * all mesh traverses. If the value is set to false, it may be traversed.
- */
- bool hidden;
-
/** \brief
* This map is used for deletion of all DOFs of all elements of a mesh. Once
* a DOF-vector (all DOFS at a node, edge, etc.) is deleted, its address is
diff --git a/AMDiS/src/MacroElement.cc b/AMDiS/src/MacroElement.cc
index 561189177cc2c0d1904b000cbabe37ea3546417e..2e1fe7883a38f909f33deb436400933cc9450471 100644
--- a/AMDiS/src/MacroElement.cc
+++ b/AMDiS/src/MacroElement.cc
@@ -26,9 +26,8 @@ namespace AMDiS {
MacroElement::~MacroElement()
{
- if (element) {
+ if (element)
DELETE element;
- }
}
MacroElement& MacroElement::operator=(const MacroElement &el)
diff --git a/AMDiS/src/MacroReader.cc b/AMDiS/src/MacroReader.cc
index b01b5e4399d41e7b8e9cbc10ffba06b6fa3bcaa6..2409b0ecfd262a915b3fa1c970d61b52d056de91 100644
--- a/AMDiS/src/MacroReader.cc
+++ b/AMDiS/src/MacroReader.cc
@@ -1100,26 +1100,8 @@ namespace AMDiS {
/*********************************************************************/
n_neigh = 1;
- // static int faceOfEdge[6][2] = { {2, 3},
- // {1, 3},
- // {1, 2},
- // {0, 3},
- // {0, 2},
- // {0, 1} };
-
- // bool periodicEdge;
- // if(periodic[faceOfEdge[k][0]] || periodic[faceOfEdge[k][1]]) {
- // periodicEdge = true;
- // } else {
- // periodicEdge = false;
- // }
-
if (newEdge(mesh, (*(mel+i)), k, &n_neigh/*, periodicEdge*/)) {
- // if(periodicEdge) {
- // mesh->incrementNumberOfEdges(2);
- // } else {
mesh->incrementNumberOfEdges(1);
- // }
max_n_neigh = max(max_n_neigh, n_neigh);
}
}
diff --git a/AMDiS/src/Mesh.cc b/AMDiS/src/Mesh.cc
index 44f81033db6a367fa40615fc6a5752b0a52ae8a8..d3b380b750f0d57b412e132edf1619819c2c0710 100644
--- a/AMDiS/src/Mesh.cc
+++ b/AMDiS/src/Mesh.cc
@@ -262,9 +262,51 @@ namespace AMDiS {
}
}
- void Mesh::addMacroElement(MacroElement* m) {
- macroElements.push_back(m);
- m->setIndex(macroElements.size());
+ void Mesh::addMacroElement(MacroElement* me)
+ {
+ macroElements.push_back(me);
+ me->setIndex(macroElements.size());
+ }
+
+ void Mesh::removeMacroElement(MacroElement* me)
+ {
+ FUNCNAME("Mesh::removeMacroElement()");
+
+ TEST_EXIT(dim == 2)("Not yet implemented!\n");
+
+ bool found = false;
+
+ // Remove the macro element from mesh's list of all macro elements.
+ for (std::deque<MacroElement*>::iterator it = macroElements.begin();
+ it != macroElements.end();
+ ++it) {
+ if (*it == me) {
+ macroElements.erase(it, it + 1);
+ found = true;
+ break;
+ }
+ }
+
+ TEST_EXIT(found)("Cannot find MacroElement that should be removed!\n");
+
+ // Go through all neighbours of the macro element and remove this macro element
+ // to be neighbour of some other macro element.
+ for (int i = 0; i < dim; i++) {
+ if (me->getNeighbour(i)) {
+ for (int j = 0; j < dim; j++) {
+ if (me->getNeighbour(i)->getNeighbour(j) == me) {
+ me->getNeighbour(i)->setNeighbour(j, NULL);
+ }
+ }
+ } else {
+ // There is no neighbour at this edge, so we have to decrease the number
+ // of edges in the mesh.
+ nEdges--;
+ }
+ }
+
+ nLeaves--;
+ nElements--;
}
int Mesh::traverse(int level, Flag flag, int (*el_fct)(ElInfo*))
@@ -496,7 +538,7 @@ namespace AMDiS {
FUNCNAME("Mesh::freeDOF()");
TEST_EXIT_DBG(position >= CENTER && position <= FACE)
- ("unknown position %d\n",position);
+ ("unknown position %d\n", position);
int ndof = nDOF[position];
if (ndof) {
@@ -512,7 +554,7 @@ namespace AMDiS {
}
TEST_EXIT_DBG(ndof <= MAX_DOF)
- ("ndof too big: ndof=%d, MAX_DOF=%d\n",ndof,MAX_DOF);
+ ("ndof too big: ndof=%d, MAX_DOF=%d\n", ndof, MAX_DOF);
for (int i = 0; i < static_cast<int>(admin.size()); i++) {
DOFAdmin *localAdmin = admin[i];
@@ -571,8 +613,6 @@ namespace AMDiS {
};
}
-
-
bool Mesh::findElInfoAtPoint(const WorldVector<double>& xy,
ElInfo *el_info,
DimVec<double>& bary,
@@ -937,10 +977,10 @@ namespace AMDiS {
node.deserialize(in);
// read admins
- int i, size;
+ int size;
in.read(reinterpret_cast<char*>(&size), sizeof(int));
admin.resize(size, NULL);
- for (i = 0; i < size; i++) {
+ for (int i = 0; i < size; i++) {
if (!admin[i]) {
admin[i] = NEW DOFAdmin(this);
}
@@ -952,13 +992,13 @@ namespace AMDiS {
std::vector< std::vector<int> > neighbourIndices(size);
- for (i = 0; i < static_cast<int>(macroElements.size()); i++) {
+ for (int i = 0; i < static_cast<int>(macroElements.size()); i++) {
if (macroElements[i]) {
DELETE macroElements[i];
}
}
macroElements.resize(size);
- for(i = 0; i < size; i++) {
+ for (int i = 0; i < size; i++) {
macroElements[i] = NEW MacroElement(dim);
macroElements[i]->writeNeighboursTo(&(neighbourIndices[i]));
macroElements[i]->deserialize(in);
@@ -971,9 +1011,9 @@ namespace AMDiS {
in.read(reinterpret_cast<char*>(&initialized), sizeof(bool));
// set neighbour pointer in macro elements
- int j, neighs = getGeo(NEIGH);
- for(i = 0; i < static_cast<int>(macroElements.size()); i++) {
- for(j = 0; j < neighs; j++) {
+ int neighs = getGeo(NEIGH);
+ for (int i = 0; i < static_cast<int>(macroElements.size()); i++) {
+ for (int j = 0; j < neighs; j++) {
int index = neighbourIndices[i][j];
if(index != -1) {
macroElements[i]->setNeighbour(j, macroElements[index]);
@@ -986,7 +1026,7 @@ namespace AMDiS {
// set mesh pointer in elements
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(this, -1, CALL_EVERY_EL_PREORDER);
- while(elInfo) {
+ while (elInfo) {
elInfo->getElement()->setMesh(this);
elInfo = stack.traverseNext(elInfo);
}
@@ -1057,8 +1097,7 @@ namespace AMDiS {
void Mesh::clearMacroFileInfo()
{
- macroFileInfo->clear(getNumberOfEdges(),
- getNumberOfVertices());
+ macroFileInfo->clear(nEdges, nVertices);
DELETE macroFileInfo;
macroFileInfo = NULL;
}
diff --git a/AMDiS/src/Mesh.h b/AMDiS/src/Mesh.h
index d107be226e2014ac1785367cd4a224c46011a286..d9d87abca22f904a2b9ee5f88887310d7afc9d8c 100644
--- a/AMDiS/src/Mesh.h
+++ b/AMDiS/src/Mesh.h
@@ -414,6 +414,13 @@ namespace AMDiS {
/// Adds a macro element to the mesh
void addMacroElement(MacroElement* me);
+ /* \brief
+ * Removes a macro element from the mesh. This works only for the case, that
+ * there are no global or local refinements, i.e., all macro elements have no
+ * children.
+ */
+ void removeMacroElement(MacroElement* me);
+
/// Frees the array of DOF pointers (see \ref createDOFPtrs)
void freeDOFPtrs(DegreeOfFreedom **ptrs);
diff --git a/AMDiS/src/ParallelDomainProblem.cc b/AMDiS/src/ParallelDomainProblem.cc
index 7ccc6de1833b6e58fb7fb7961c9229a8a441ebc2..ac9b5573d9353f4dd9465edb5896156a9438d413 100644
--- a/AMDiS/src/ParallelDomainProblem.cc
+++ b/AMDiS/src/ParallelDomainProblem.cc
@@ -12,10 +12,13 @@
namespace AMDiS {
ParallelDomainProblemBase::ParallelDomainProblemBase(const std::string& name,
- ProblemIterationInterface *iterationIF,
- ProblemTimeInterface *timeIF,
+ ProblemIterationInterface *iIF,
+ ProblemTimeInterface *tIF,
Mesh *m)
- : mesh(m)
+ : iterationIF(iIF),
+ timeIF(tIF),
+ mesh(m),
+ nRankDOFs(0)
{
mpiRank = MPI::COMM_WORLD.Get_rank();
mpiSize = MPI::COMM_WORLD.Get_size();
@@ -23,6 +26,11 @@ namespace AMDiS {
partitioner = new ParMetisPartitioner(mesh, &mpiComm);
}
+ Flag ParallelDomainProblemBase::oneIteration(AdaptInfo *adaptInfo, Flag toDo)
+ {
+ return iterationIF->oneIteration(adaptInfo, toDo);
+ }
+
void ParallelDomainProblemBase::initParallelization(AdaptInfo *adaptInfo)
{
if (mpiSize <= 1)
@@ -35,29 +43,99 @@ namespace AMDiS {
// and now partition the mesh
partitionMesh(adaptInfo);
+ std::vector<int> rankDofs;
+ std::map<int, std::set<int> > partitionDofs;
TraverseStack stack;
ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
int nLeaves = 0;
while (elInfo) {
Element *element = elInfo->getElement();
+
+ // Hidde elements which are not part of ranks partition.
PartitionElementData *partitionData =
dynamic_cast<PartitionElementData*>
(element->getElementData(PARTITION_ED));
if (partitionData->getPartitionStatus() != IN) {
- element->setHidden(true);
} else {
- nLeaves++;
}
-
+
+ // Determine to each dof the partition(s) it corresponds to.
+ for (int i = 0; i < 3; i++)
+ partitionDofs[element->getDOF(i, 0)].insert(partitionVec[element->getIndex()]);
+
elInfo = stack.traverseNext(elInfo);
}
- mesh->setNumberOfLeaves(nLeaves);
+
+ for (std::map<int, std::set<int> >::iterator it = partitionDofs.begin();
+ it != partitionDofs.end();
+ ++it) {
+ for (std::set<int>::iterator itpart1 = it->second.begin();
+ itpart1 != it->second.end();
+ ++itpart1) {
+ if (*itpart1 == mpiRank) {
+ if (it->second.size() == 1) {
+ rankDofs.push_back(it->first);
+ } else {
+ bool insert = true;
+ for (std::set<int>::iterator itpart2 = it->second.begin();
+ itpart2 != it->second.end();
+ ++itpart2) {
+ if (*itpart2 > mpiRank) {
+ insert = false;
+ break;
+ }
+ }
+ if (insert) {
+ rankDofs.push_back(it->first);
+ }
+ }
+ }
+ }
+ }
+
+ bool removed = false;
+ do {
+ removed = false;
+ for (std::deque<MacroElement*>::iterator it = mesh->firstMacroElement();
+ it != mesh->endOfMacroElements();
+ ++it) {
+ PartitionElementData *partitionData =
+ dynamic_cast<PartitionElementData*>
+ ((*it)->getElement()->getElementData(PARTITION_ED));
+ if (partitionData->getPartitionStatus() != IN) {
+ mesh->removeMacroElement(*it);
+ removed = true;
+ break;
+ }
+ }
+ } while (removed);
+
+ int *gOrder = (int*)(malloc(sizeof(int) * rankDofs.size()));
+ int *lOrder = (int*)(malloc(sizeof(int) * rankDofs.size()));
+
+ for (std::vector<int>::iterator it = rankDofs.begin();
+ it != rankDofs.end(); ++it) {
+ gOrder[nRankDOFs++] = *it;
+ }
+
+ int rstart = 0;
+ MPI_Scan(&nRankDOFs, &rstart, 1, MPI_INT, MPI_SUM, PETSC_COMM_WORLD);
+
+ for (int i = 0; i < nRankDOFs; i++) {
+ lOrder[i] = rstart - nRankDOFs + i;
+ }
+
+ AOCreateBasic(PETSC_COMM_WORLD, nRankDOFs, gOrder, lOrder, &applicationOrdering);
+
+ free(gOrder);
+ free(lOrder);
}
void ParallelDomainProblemBase::exitParallelization(AdaptInfo *adaptInfo)
{
+ AODestroy(applicationOrdering);
}
double ParallelDomainProblemBase::setElemWeights(AdaptInfo *adaptInfo)
diff --git a/AMDiS/src/ParallelDomainProblem.h b/AMDiS/src/ParallelDomainProblem.h
index 40903a96e0bc3fc09079a485c2693f03e4ce20d7..77995799be3cb5ffeb6ba5f31af4c3eed3356440 100644
--- a/AMDiS/src/ParallelDomainProblem.h
+++ b/AMDiS/src/ParallelDomainProblem.h
@@ -28,6 +28,7 @@
#include "ProblemTimeInterface.h"
#include "ProblemIterationInterface.h"
#include "AdaptInfo.h"
+#include "petscao.h"
#include "mpi.h"
namespace AMDiS {
@@ -67,7 +68,15 @@ namespace AMDiS {
virtual void transferInitialSolution(AdaptInfo *adaptInfo) {}
- virtual Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo = FULL_ITERATION) {}
+ virtual void beginIteration(AdaptInfo *adaptInfo) {
+ iterationIF->beginIteration(adaptInfo);
+ }
+
+ virtual Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo = FULL_ITERATION);
+
+ virtual void endIteration(AdaptInfo *adaptInfo) {
+ iterationIF->endIteration(adaptInfo);
+ }
virtual int getNumProblems() {}
@@ -75,6 +84,16 @@ namespace AMDiS {
return name;
}
+ /// Returns pointer to \ref applicationOrdering.
+ AO* getApplicationOrdering() {
+ return &applicationOrdering;
+ }
+
+ /// Returns \ref nRankDOFs, the number of DOFs in the rank mesh.
+ int getNumberRankDOFs() {
+ return nRankDOFs;
+ }
+
virtual ProblemStatBase *getProblem(int number = 0) {}
virtual void serialize(std::ostream&) {}
@@ -82,6 +101,12 @@ namespace AMDiS {
virtual void deserialize(std::istream&) {}
protected:
+ ///
+ ProblemIterationInterface *iterationIF;
+
+ ///
+ ProblemTimeInterface *timeIF;
+
/// The rank of the current process.
int mpiRank;
@@ -121,6 +146,12 @@ namespace AMDiS {
* of the parition it corresponds to is stored.
*/
std::map<int, int> oldPartitionVec;
+
+ /// Petsc application ordering
+ AO applicationOrdering;
+
+ /// Number of DOFs in the rank mesh.
+ int nRankDOFs;
};
class ParallelDomainProblemScal : public ParallelDomainProblemBase
diff --git a/AMDiS/src/ProblemIterationInterface.h b/AMDiS/src/ProblemIterationInterface.h
index 742f9be822480e6a385396c30f6fbe58f7e543f6..f3a2c538739104583c1ec0c77638aef4f775b781 100644
--- a/AMDiS/src/ProblemIterationInterface.h
+++ b/AMDiS/src/ProblemIterationInterface.h
@@ -55,10 +55,8 @@ namespace AMDiS {
public:
virtual ~ProblemIterationInterface() {};
- /** \brief
- * Called before each adaption loop iteration.
- */
- virtual void beginIteration(AdaptInfo *adaptInfo) {};
+ /// Called before each adaption loop iteration.
+ virtual void beginIteration(AdaptInfo *adaptInfo) {}
/** \brief
* Determines the execution order of the single adaption steps. If adapt is
@@ -67,14 +65,10 @@ namespace AMDiS {
*/
virtual Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo = FULL_ITERATION) = 0;
- /** \brief
- * Called after each adaption loop iteration.
- */
- virtual void endIteration(AdaptInfo *adaptInfo) {};
+ /// Called after each adaption loop iteration.
+ virtual void endIteration(AdaptInfo *adaptInfo) {}
- /** \brief
- * Returns number of managed problems
- */
+ /// Returns number of managed problems
virtual int getNumProblems() = 0;
/** \brief
@@ -83,24 +77,18 @@ namespace AMDiS {
*/
virtual ProblemStatBase *getProblem(int number = 0) = 0;
- /** \brief
- * Returns the problem with the given name.
- */
- virtual ProblemStatBase *getProblem(const std::string& name) { return NULL; };
+ /// Returns the problem with the given name.
+ virtual ProblemStatBase *getProblem(const std::string& name) {
+ return NULL;
+ }
- /** \brief
- * Returns the name of the problem.
- */
+ /// Returns the name of the problem.
virtual const std::string& getName() = 0;
- /** \brief
- * Function that serializes the problem plus information about the iteration.
- */
+ /// Function that serializes the problem plus information about the iteration.
virtual void serialize(std::ostream &out) = 0;
- /** \brief
- * Function that deserializes the problem plus information about the iteration.
- */
+ /// Function that deserializes the problem plus information about the iteration.
virtual void deserialize(std::istream &in) = 0;
};
diff --git a/AMDiS/src/ProblemScal.cc b/AMDiS/src/ProblemScal.cc
index b9fb370f3790c0b462026472e578c76f4abb2725..ba622f8d0a3d6af11f78ef142a727fa6c1bc438a 100644
--- a/AMDiS/src/ProblemScal.cc
+++ b/AMDiS/src/ProblemScal.cc
@@ -147,6 +147,17 @@ namespace AMDiS {
rhs->getBoundaryManager()->addBoundaryCondition(periodic);
}
+#ifdef HAVE_PARALLEL_AMDIS
+ void ProblemScal::useApplicationOrdering(AO *ao, int nDofs)
+ {
+ applicationOrdering = ao;
+ nRankDOFs = nDofs;
+ systemMatrix->useApplicationOrdering(ao);
+ rhs->useApplicationOrdering(ao);
+ }
+#endif
+
+
void ProblemScal::createMesh()
{
TEST_EXIT(Parameters::initialized())("parameters not initialized\n");
@@ -169,16 +180,16 @@ namespace AMDiS {
switch (dim) {
case 1:
- coarseningManager_ = NEW CoarseningManager1d();
- refinementManager_ = NEW RefinementManager1d();
+ coarseningManager = NEW CoarseningManager1d();
+ refinementManager = NEW RefinementManager1d();
break;
case 2:
- coarseningManager_ = NEW CoarseningManager2d();
- refinementManager_ = NEW RefinementManager2d();
+ coarseningManager = NEW CoarseningManager2d();
+ refinementManager = NEW RefinementManager2d();
break;
case 3:
- coarseningManager_ = NEW CoarseningManager3d();
- refinementManager_ = NEW RefinementManager3d();
+ coarseningManager = NEW CoarseningManager3d();
+ refinementManager = NEW RefinementManager3d();
break;
default:
ERROR_EXIT("invalid dim!\n");
@@ -189,8 +200,8 @@ namespace AMDiS {
void ProblemScal::setMeshFromProblemVec(ProblemVec* pv, int i)
{
mesh = pv->getMesh(i);
- coarseningManager_ = pv->getCoarseningManager(i);
- refinementManager_ = pv->getRefinementManager(i);
+ coarseningManager = pv->getCoarseningManager(i);
+ refinementManager = pv->getRefinementManager(i);
}
@@ -207,14 +218,14 @@ namespace AMDiS {
Flag ProblemScal::refineMesh(AdaptInfo *adaptInfo)
{
- return refinementManager_->refineMesh(mesh);
+ return refinementManager->refineMesh(mesh);
}
Flag ProblemScal::coarsenMesh(AdaptInfo *adaptInfo)
{
if (adaptInfo->isCoarseningAllowed(0)) {
- return coarseningManager_->coarsenMesh(mesh);
+ return coarseningManager->coarsenMesh(mesh);
} else {
WARNING("coarsening not allowed\n");
return 0;
@@ -273,8 +284,8 @@ namespace AMDiS {
adoptFlag.isSet(INIT_FE_SPACE))) {
TEST_EXIT(!mesh)("mesh already created\n");
mesh = adoptProblem->getMesh();
- refinementManager_ = adoptProblem->refinementManager_;
- coarseningManager_ = adoptProblem->coarseningManager_;
+ refinementManager = adoptProblem->refinementManager;
+ coarseningManager = adoptProblem->coarseningManager;
}
}
@@ -285,10 +296,12 @@ namespace AMDiS {
if (feSpace_) {
WARNING("feSpace already created\n");
} else {
- if (initFlag.isSet(INIT_FE_SPACE) || (initFlag.isSet(INIT_SYSTEM) && !adoptFlag.isSet(INIT_FE_SPACE))) {
+ if (initFlag.isSet(INIT_FE_SPACE) ||
+ (initFlag.isSet(INIT_SYSTEM) && !adoptFlag.isSet(INIT_FE_SPACE))) {
createFESpace();
}
- if (adoptProblem && (adoptFlag.isSet(INIT_FE_SPACE) || adoptFlag.isSet(INIT_SYSTEM))) {
+ if (adoptProblem &&
+ (adoptFlag.isSet(INIT_FE_SPACE) || adoptFlag.isSet(INIT_SYSTEM))) {
TEST_EXIT(!feSpace_)("feSpace already created");
feSpace_ = dynamic_cast<ProblemScal*>(adoptProblem)->getFESpace();
}
@@ -412,7 +425,7 @@ namespace AMDiS {
if (initFlag.isSet(INIT_GLOBAL_REFINES)) {
int globalRefinements = 0;
GET_PARAMETER(0, mesh->getName() + "->global refinements", "%d", &globalRefinements);
- refinementManager_->globalRefine(mesh, globalRefinements);
+ refinementManager->globalRefine(mesh, globalRefinements);
}
}
}
@@ -576,7 +589,11 @@ namespace AMDiS {
mesh->dofCompress();
MSG("%d DOFs for %s\n",
+#ifdef HAVE_PARALLEL_AMDIS
+ nRankDOFs,
+#else
feSpace_->getAdmin()->getUsedSize(),
+#endif
feSpace_->getName().c_str());
Flag assembleFlag =
@@ -603,20 +620,20 @@ namespace AMDiS {
ElInfo *elInfo = stack.traverseFirst(mesh, -1, assembleFlag);
while (elInfo) {
- if (useGetBound) {
- bound = GET_MEMORY(BoundaryType, feSpace_->getBasisFcts()->getNumber());
- feSpace_->getBasisFcts()->getBound(elInfo, bound);
- } else {
- bound = NULL;
- }
-
- systemMatrix->assemble(1.0, elInfo, bound);
- rhs->assemble(1.0, elInfo, bound);
-
- if (useGetBound) {
- FREE_MEMORY(bound, BoundaryType, feSpace_->getBasisFcts()->getNumber());
- }
-
+ if (useGetBound) {
+ bound = GET_MEMORY(BoundaryType, feSpace_->getBasisFcts()->getNumber());
+ feSpace_->getBasisFcts()->getBound(elInfo, bound);
+ } else {
+ bound = NULL;
+ }
+
+ systemMatrix->assemble(1.0, elInfo, bound);
+ rhs->assemble(1.0, elInfo, bound);
+
+ if (useGetBound) {
+ FREE_MEMORY(bound, BoundaryType, feSpace_->getBasisFcts()->getNumber());
+ }
+
if (systemMatrix->getBoundaryManager())
systemMatrix->getBoundaryManager()->fillBoundaryConditions(elInfo, systemMatrix);
if (rhs->getBoundaryManager())
diff --git a/AMDiS/src/ProblemScal.h b/AMDiS/src/ProblemScal.h
index 6cecdf75f6b48a8d9a6a827643901b861935c485..f574fdbf474b41397cb16523aded7342ba4004b8 100644
--- a/AMDiS/src/ProblemScal.h
+++ b/AMDiS/src/ProblemScal.h
@@ -22,6 +22,8 @@
#ifndef AMDIS_PROBLEMSCAL_H
#define AMDIS_PROBLEMSCAL_H
+#include <list>
+
#include "Global.h"
#include "ProblemStatBase.h"
#include "MemoryManager.h"
@@ -30,7 +32,10 @@
#include "Boundary.h"
#include "StandardProblemIteration.h"
#include "ProblemVec.h"
-#include <list>
+
+#ifdef HAVE_PARALLEL_AMDIS
+#include "petscao.h"
+#endif
namespace AMDiS {
@@ -58,7 +63,7 @@ namespace AMDiS {
ProblemScal(const std::string &nameStr,
ProblemIterationInterface *problemIteration = NULL)
: StandardProblemIteration(this),
- name(nameStr),
+ name(nameStr),
feSpace_(NULL),
mesh(NULL),
marker(NULL),
@@ -71,56 +76,42 @@ namespace AMDiS {
leftPrecon(NULL),
rightPrecon(NULL),
useGetBound(true),
- refinementManager_(NULL),
- coarseningManager_(NULL),
+ refinementManager(NULL),
+ coarseningManager(NULL),
+#ifdef HAVE_PARALLEL_AMDIS
+ applicationOrdering(NULL),
+ nRankDOFs(0),
+#endif
info_(10)
{}
- /** \brief
- * Destructor
- */
+ /// Destructor
virtual ~ProblemScal();
- /** \brief
- * Initialisation of the problem.
- */
+ /// Initialisation of the problem.
virtual void initialize(Flag initFlag,
ProblemScal *adoptProblem = NULL,
Flag adoptFlag = INIT_NOTHING);
- /** \brief
- * Used in \ref initialize().
- */
+ /// Used in \ref initialize().
virtual void createMesh();
- /** \brief
- * Used in \ref initialize().
- */
+ /// Used in \ref initialize().
virtual void createFESpace();
- /** \brief
- * Used in \ref initialize().
- */
+ /// Used in \ref initialize().
virtual void createMatricesAndVectors();
- /** \brief
- * Used in \ref initialize().
- */
+ /// Used in \ref initialize().
virtual void createSolver();
- /** \brief
- * Used in \ref initialize().
- */
+ /// Used in \ref initialize().
virtual void createEstimator();
- /** \brief
- * Used in \ref initialize().
- */
+ /// Used in \ref initialize().
virtual void createMarker();
- /** \brief
- * Used in \ref initialize().
- */
+ /// Used in \ref initialize().
virtual void createFileWriter();
/** \brief
@@ -173,16 +164,12 @@ namespace AMDiS {
bool assembleMatrix = true,
bool assembleVector = true);
- /** \brief
- * Returns number of managed problems
- */
+ /// Returns number of managed problems
virtual int getNumProblems() {
return 1;
}
- /** \brief
- * Implementation of ProblemStatBase::getNumComponents()
- */
+ /// Implementation of ProblemStatBase::getNumComponents()
virtual int getNumComponents() {
return 1;
}
@@ -195,61 +182,50 @@ namespace AMDiS {
return this;
}
- /** \brief
- * Writes output files.
- */
+ /// Writes output files.
void writeFiles(AdaptInfo *adaptInfo, bool force);
- /** \brief
- * Interpolates fct to \ref solution.
- */
- void
- interpolInitialSolution(AbstractFunction<double, WorldVector<double> > *fct);
+ /// Interpolates fct to \ref solution.
+ void interpolInitialSolution(AbstractFunction<double, WorldVector<double> > *fct);
/// Adds an Operator to \ref systemMatrix.
void addMatrixOperator(Operator *op,
- double *factor = NULL,
- double *estFactor = NULL);
+ double *factor = NULL, double *estFactor = NULL);
/// Adds an Operator to \ref rhs.
void addVectorOperator(Operator *op,
- double *factor = NULL,
- double *estFactor = NULL);
+ double *factor = NULL, double *estFactor = NULL);
- /** \brief
- * Adds dirichlet boundary conditions.
- */
+ /// Adds dirichlet boundary conditions.
virtual void addDirichletBC(BoundaryType type,
AbstractFunction<double, WorldVector<double> >* b);
- /** \brief
- * Adds dirichlet boundary conditions.
- */
+ /// Adds dirichlet boundary conditions.
virtual void addDirichletBC(BoundaryType type,
DOFVector<double> *vec);
- /** \brief
- * Adds robin boundary conditions.
- */
+ /// Adds robin boundary conditions.
virtual void addRobinBC(BoundaryType type,
AbstractFunction<double, WorldVector<double> > *n,
AbstractFunction<double, WorldVector<double> > *r);
- /** \brief
- * Adds robin boundary conditions.
- */
+ /// Adds robin boundary conditions.
virtual void addRobinBC(BoundaryType type,
DOFVector<double> *n,
DOFVector<double> *r);
- /** \brief
- * Adds Neumann boundary conditions.
- */
+ /// Adds Neumann boundary conditions.
virtual void addNeumannBC(BoundaryType type,
AbstractFunction<double, WorldVector<double> > *n);
+ /// Adds periodic boundary conditions.
virtual void addPeriodicBC(BoundaryType type);
+
+#ifdef HAVE_PARALLEL_AMDIS
+ /// Sets the petsc application ordering object to map dof indices.
+ void useApplicationOrdering(AO *ao, int nDofs);
+#endif
// ===== getting-methods ======================================================
@@ -257,53 +233,39 @@ namespace AMDiS {
* \{
*/
- /** \brief
- * Returns \ref solution.
- */
+ /// Returns \ref solution.
inline DOFVector<double>* getSolution() {
return solution;
}
- /** \brief
- * Returns \ref rhs.
- */
+ /// Returns \ref rhs.
inline DOFVector<double>* getRHS() {
return rhs;
}
- /** \brief
- * Returns \ref systemMatrix.
- */
+ /// Returns \ref systemMatrix.
inline DOFMatrix *getSystemMatrix() {
return systemMatrix;
}
- /** \brief
- * Returns \ref mesh
- */
+ /// Returns \ref mesh
inline Mesh* getMesh() {
return mesh;
}
- /** \brief
- * Returns \ref feSpace_.
- */
+ /// Returns \ref feSpace_.
inline FiniteElemSpace* getFESpace() {
return feSpace_;
}
- /** \brief
- * Returns \ref estimator_.
- */
+ /// Returns \ref estimator_.
inline Estimator* getEstimator() {
return estimator;
}
- /** \brief
- * Returns \ref refinementManager_.
- */
+ /// Returns \ref refinementManager.
inline RefinementManager* getRefinementManager() {
- return refinementManager_;
+ return refinementManager;
}
/// Returns \ref solver.
@@ -338,7 +300,7 @@ namespace AMDiS {
///
inline CoarseningManager *getCoarseningManager() {
- return coarseningManager_;
+ return coarseningManager;
}
/** \} */
@@ -349,47 +311,35 @@ namespace AMDiS {
* \{
*/
- /** \brief
- * Sets \ref mesh
- */
+ /// Sets \ref mesh
void setMeshFromProblemVec(ProblemVec* pv, int i = 0);
- /** \brief
- * Sets \ref feSpace_.
- */
+ /// Sets \ref feSpace_.
inline void setFESpace(FiniteElemSpace* fe) {
feSpace_ = fe;
}
- /** \brief
- * Sets \ref estimator_.
- */
+ /// Sets \ref estimator_.
inline void setEstimator(Estimator* est) {
estimator = est;
}
- /** \brief
- * Sets \ref solver.
- */
+ /// Sets \ref solver.
inline void setSolver(OEMSolver<DOFVector<double> >* sol) {
solver = sol;
}
- /** \brief
- * Sets \ref leftPrecon.
- */
+ /// Sets \ref leftPrecon.
inline void setLeftPrecon(Preconditioner<DOFVector<double> > *p) {
leftPrecon = p;
}
- /** \brief
- * Sets \ref rightPrecon.
- */
+ /// Sets \ref rightPrecon.
inline void setRightPrecon(Preconditioner<DOFVector<double> > *p) {
rightPrecon = p;
}
-
+ /// Sets \ref marker.
inline void setMarker(Marker *m) {
marker = m;
}
@@ -398,16 +348,10 @@ namespace AMDiS {
void writeResidualMesh(AdaptInfo *adaptInfo, const std::string name);
- // ===== Serializable implementation =====
-
- /** \brief
- * serialization
- */
+ /// serialization
virtual void serialize(std::ostream &out);
- /** \brief
- * deserialization
- */
+ /// deserialization
virtual void deserialize(std::istream &in);
std::vector<FileWriterInterface*> getFileWriterList() {
@@ -462,17 +406,26 @@ namespace AMDiS {
* If new refinement algorithms should be realized, one has to override
* RefinementManager and give one instance of it to AdaptStationary.
*/
- RefinementManager *refinementManager_;
+ RefinementManager *refinementManager;
/** \brief
* All actions of mesh coarsening are performed by coarseningManager.
* If new coarsening algorithms should be realized, one has to override
* CoarseningManager and give one instance of it to AdaptStationary.
*/
- CoarseningManager *coarseningManager_;
+ CoarseningManager *coarseningManager;
+#ifdef HAVE_PARALLEL_AMDIS
+ /// Petsc application ordering to map dof indices.
+ AO *applicationOrdering;
+
+ /// Number of DOFs in the rank partition.
+ int nRankDOFs;
+#endif
+
/// Info level.
int info_;
+
};
}
diff --git a/AMDiS/src/RefinementManager.h b/AMDiS/src/RefinementManager.h
index 23a9e843db2aebc5a3fb68156fa7757719c81ba9..69fab8829ea750c708cf451657397bbe8dde6d10 100644
--- a/AMDiS/src/RefinementManager.h
+++ b/AMDiS/src/RefinementManager.h
@@ -22,19 +22,11 @@
#ifndef AMDIS_REFINEMENTMANAGER_H
#define AMDIS_REFINEMENTMANAGER_H
-// ============================================================================
-// ===== includes =============================================================
-// ============================================================================
-
#include "Global.h"
#include "Flag.h"
namespace AMDiS {
- // ============================================================================
- // ===== forward declarations =================================================
- // ============================================================================
-
class Element;
class Line;
class Triangle;
@@ -44,9 +36,6 @@ namespace AMDiS {
class TraverseStack;
class RCNeighbourList;
- // ============================================================================
- // ===== class RefinementManager ==============================================
- // ============================================================================
/** \ingroup Adaption
* \brief
@@ -57,18 +46,15 @@ namespace AMDiS {
class RefinementManager
{
public:
- /** \brief
- * Constructs a RefinementManager which belongs to aMesh
- */
+ /// Constructs a RefinementManager which belongs to aMesh
RefinementManager()
- : mesh(NULL), newCoords(false),
+ : mesh(NULL),
+ newCoords(false),
stack(NULL)
- {};
+ {}
- /** \brief
- * destructor
- */
- virtual ~RefinementManager() {};
+ /// Destructor
+ virtual ~RefinementManager() {}
/** \brief
* Generates new coordinates on curved boundaries. Can be overriden by
@@ -77,7 +63,7 @@ namespace AMDiS {
virtual void setNewCoords() {
FUNCNAME("RefinementManager::setNewCoords");
ERROR_EXIT("called for base class!\n");
- };
+ }
/** \brief
* Fulfills the refinement for all positive marked elements of the mesh.
@@ -88,21 +74,17 @@ namespace AMDiS {
*/
virtual Flag refineMesh(Mesh *aMesh);
- /** \brief
- * All elements of the mesh will be refined.
- */
+ /// All elements of the mesh will be refined.
Flag globalRefine(Mesh *aMesh, int mark);
- /** \brief
- * set \ref newCoords
- */
+ /// Set \ref newCoords
inline void newCoord(bool nc) {
newCoords = nc;
- };
+ }
inline bool newCoord() {
return newCoords;
- };
+ }
/** \brief
* Implements the refinement of el_info->el. Can be overriden by sub
@@ -112,51 +94,39 @@ namespace AMDiS {
FUNCNAME("RefinementManager::refineFunction()");
ERROR_EXIT("called for base class!\n");
return NULL;
- };
+ }
inline void setMesh(Mesh *m) {
mesh = m;
- };
+ }
inline void setStack(TraverseStack *s) {
stack = s;
- };
+ }
inline TraverseStack *getStack() {
return stack;
- };
+ }
protected:
- /** \brief
- * Used by \ref globalRefine
- */
+ /// Used by \ref globalRefine
static int globalRefineFct(ElInfo* elinfo);
protected:
- /** \brief
- * The Mesh to be refined
- */
+ /// The Mesh to be refined
Mesh *mesh;
- /** \brief
- * Number of new vertices on a boundary edge
- */
+ /// Number of new vertices on a boundary edge
bool newCoords;
- /** \brief
- * Still more refinement to do?
- */
+ /// Still more refinement to do?
static bool doMoreRecursiveRefine;
- /** \brief
- * number of DOFVectors which must be interpolated during refinement
- */
+ /// Number of DOFVectors which must be interpolated during refinement
static int callRefineInterpol;
- /** \brief
- * Used for non recursive traversal
- */
+ /// Used for non recursive traversal
TraverseStack* stack;
/** \brief
@@ -165,9 +135,7 @@ namespace AMDiS {
*/
static RefinementManager* traversePtr;
- /** \brief
- * Used by globalRefine to remember the given mark value
- */
+ /// Used by globalRefine to remember the given mark value
static int globalMark;
};
diff --git a/AMDiS/src/RefinementManager2d.h b/AMDiS/src/RefinementManager2d.h
index fd36e4187df3f4879a323c246ca536f24ec94353..ab541dfcb658c1d14b6f287ce51f7cfdc940cbc0 100644
--- a/AMDiS/src/RefinementManager2d.h
+++ b/AMDiS/src/RefinementManager2d.h
@@ -26,10 +26,6 @@
namespace AMDiS {
- // ============================================================================
- // ===== class RefinementManager2d ============================================
- // ============================================================================
-
/** \ingroup Adaption
* \brief
* Implements a RefinementManager for 2-dimensional meshes.
@@ -39,27 +35,19 @@ namespace AMDiS {
public:
MEMORY_MANAGED(RefinementManager2d);
- /** \brief
- * Calls base class constructor.
- */
+ /// Calls base class constructor.
RefinementManager2d()
: RefinementManager()
- {};
+ {}
- /** \brief
- * destructor
- */
- virtual ~RefinementManager2d() {};
+ /// Destructor
+ virtual ~RefinementManager2d() {}
protected:
- /** \brief
- * Used by \ref setNewCoords
- */
+ /// Used by \ref setNewCoords
static int newCoordsFct(ElInfo *el_info);
- /** \brief
- * Implements RefinementManager::setNewCoords
- */
+ /// Implements RefinementManager::setNewCoords
void setNewCoords();
/** \brief
@@ -73,20 +61,14 @@ namespace AMDiS {
int getRefinePatch(ElInfo **el_info, DegreeOfFreedom *edge[2], int dir,
RCNeighbourList* refineList, int *n_neigh);
- /** \brief
- * Refines all elements in the patch.
- */
+ /// Refines all elements in the patch.
DegreeOfFreedom refinePatch(DegreeOfFreedom *edge[2], RCNeighbourList* refineList,
int n_neigh, bool bound);
- /** \brief
- * Implements RefinementManager::refineFunction.
- */
+ /// Implements RefinementManager::refineFunction.
ElInfo* refineFunction(ElInfo* el_info);
- /** \brief
- * Refines one Triangle.
- */
+ /// Refines one Triangle.
void bisectTriangle(Triangle *el, DegreeOfFreedom* newDofs[3]);
};
diff --git a/AMDiS/src/Traverse.cc b/AMDiS/src/Traverse.cc
index 40b7e74e16304a79bc3f4826a369f076195c5212..b767e0aed517a06cc872de19ac7f8bb91ecbaabc 100644
--- a/AMDiS/src/Traverse.cc
+++ b/AMDiS/src/Traverse.cc
@@ -132,11 +132,10 @@ namespace AMDiS {
if (stack_used == 0) { /* first call */
currentMacro = traverse_mesh->firstMacroElement();
- // Search for the first macro element that corresponds to the current thread
- // and that is not hidden. So increment as long as one of this conditions does
- // not hold and the current macro element is not the last one.
- while (((*currentMacro)->getIndex() % maxThreads_ != myThreadId_ ||
- (*currentMacro)->getElement()->isHidden()) &&
+ // Search for the first macro element that corresponds to the current thread.
+ // So increment as long as one of this condition does not hold and the
+ // current macro element is not the last one.
+ while ((*currentMacro)->getIndex() % maxThreads_ != myThreadId_ &&
currentMacro != traverse_mesh->endOfMacroElements()) {
currentMacro++;
}
@@ -166,13 +165,12 @@ namespace AMDiS {
/* goto next macro element */
if (stack_used < 1) {
- // Again, search for the next macro element that corresponds to the current
- // thread and that is not hidden.
+ // Again, search for the next macro element that corresponds to the
+ // current thread.
do {
currentMacro++;
- } while (currentMacro != traverse_mesh->endOfMacroElements() &&
- ((*currentMacro)->getIndex() % maxThreads_ != myThreadId_ ||
- (*currentMacro)->getElement()->isHidden()));
+ } while (currentMacro != traverse_mesh->endOfMacroElements() &&
+ (*currentMacro)->getIndex() % maxThreads_ != myThreadId_);
if (currentMacro == traverse_mesh->endOfMacroElements()) {
return NULL;
@@ -198,49 +196,14 @@ namespace AMDiS {
int visitedChildren = info_stack[stack_used];
if (visitedChildren == 0) {
- // No children of this element have been visited.
-
- if (el->getFirstChild()->isHidden()) {
- // The first child is hidden, so omit it.
- info_stack[stack_used]++;
- visitedChildren++;
-
- // And check the second child.
- if (el->getSecondChild()->isHidden()) {
- // Also the second child is hidden, so omit it too and start the
- // traverse procedure again to go up into the stack.
-
- info_stack[stack_used]++;
-
- return traverseLeafElement();
- } else {
- // Only the first child is hidden, so go down on the second one.
- el = const_cast<Element*>(el->getSecondChild());
- }
- } else {
- // The first child is not hidden, so go down on it.
- el = const_cast<Element*>(el->getFirstChild());
- }
-
+ el = const_cast<Element*>(el->getFirstChild());
} else {
- // The first child has been visited before, so check the second one.
- if (el->getSecondChild()->isHidden()) {
- // The second one is hidden, so omit it and start the traverse
- // procedure again to go up into the stack;
- info_stack[stack_used]++;
-
- return traverseLeafElement();
- } else {
- // The secod child is not hidden, so go down on it.
- el = const_cast<Element*>(el->getSecondChild());
- }
+ el = const_cast<Element*>(el->getSecondChild());
}
-
info_stack[stack_used]++;
elinfo_stack[stack_used + 1]->fillElInfo(visitedChildren,
elinfo_stack[stack_used]);
- info_stack[stack_used + 1] = 0;
stack_used++;
TEST_EXIT_DBG(stack_used < stack_size)