diff --git a/AMDiS/AMDISUse.cmake b/AMDiS/AMDISUse.cmake
index 371737d71e0bc9a2b7be930606c364e0f281ed1e..fd46490db00595f2c15fdfd5ee6568097c4facc5 100644
--- a/AMDiS/AMDISUse.cmake
+++ b/AMDiS/AMDISUse.cmake
@@ -14,11 +14,17 @@ if(AMDIS_HAS_PARALLEL_DOMAIN)
list(APPEND AMDIS_LIBRARIES ${PETSC_LIBRARY_SYS} ${PETSC_LIBRARIES})
list(APPEND AMDIS_INCLUDE_DIRS ${PETSC_INCLUDES})
else()
- message(FATAL_ERROR "Could nit find PETSc!")
+ message(FATAL_ERROR "Could not find PETSc!")
endif(PETSC_FOUND)
elseif(AMDIS_HAS_PARALLEL_DOMAIN STREQUAL "PMTL")
find_package(MTL REQUIRED)
list(APPEND AMDIS_LIBRARIES ${MTL_LIBRARIES})
+ find_library(PARMETIS_LIB parmetis)
+ if(PARMETIS_LIB)
+ list(APPEND AMDIS_LIBRARIES ${PARMETIS_LIB})
+ else(PARMETIS_LIB)
+ message(ERROR "could not find the parmetis libraries needed by amdis")
+ endif(PARMETIS_LIB)
endif()
endif(AMDIS_HAS_PARALLEL_DOMAIN)
diff --git a/AMDiS/src/AdaptInstationary.cc b/AMDiS/src/AdaptInstationary.cc
index 81bd2712c5ced2bbf7ebdb82e40c489b434907d0..2cef837795c42efc5818b5af42f0d9ae46041716 100644
--- a/AMDiS/src/AdaptInstationary.cc
+++ b/AMDiS/src/AdaptInstationary.cc
@@ -19,8 +19,10 @@
#if HAVE_PARALLEL_DOMAIN_AMDIS
#include "parallel/MeshDistributor.h"
+#ifndef HAVE_PARALLEL_MTL4
#include <petsc.h>
#endif
+#endif
namespace AMDiS {
diff --git a/AMDiS/src/AdaptStationary.cc b/AMDiS/src/AdaptStationary.cc
index d02b92688427a5be77c08f6c3de070143d4b1e00..d6a817c20d3d4715fdb7dc30bcd0dde2c5ffd3cc 100644
--- a/AMDiS/src/AdaptStationary.cc
+++ b/AMDiS/src/AdaptStationary.cc
@@ -18,8 +18,10 @@
#if HAVE_PARALLEL_DOMAIN_AMDIS
#include "parallel/MeshDistributor.h"
+#ifndef HAVE_PARALLEL_MTL4
#include <petsc.h>
#endif
+#endif
namespace AMDiS {
diff --git a/AMDiS/src/DOFVector.cc b/AMDiS/src/DOFVector.cc
index 0d390f634738ca4c3cfe656e6888dacb3ade5c37..a7283f19d4e33ab2f221534e68099f183e3d1846 100644
--- a/AMDiS/src/DOFVector.cc
+++ b/AMDiS/src/DOFVector.cc
@@ -68,7 +68,7 @@ namespace AMDiS {
template<>
- const double& DOFVector<double>::evalAtPoint(WorldVector<double> &p, ElInfo *oldElInfo, double* values) const
+ const double DOFVector<double>::evalAtPoint(WorldVector<double> &p, ElInfo *oldElInfo, double* values) const
{
FUNCNAME("DOFVector<double>::evalAtCoords()");
@@ -114,7 +114,7 @@ namespace AMDiS {
template<>
- const WorldVector<double>& DOFVector<WorldVector<double> >::evalAtPoint(WorldVector<double> &p, ElInfo *oldElInfo, WorldVector<double>* values) const
+ const WorldVector<double> DOFVector<WorldVector<double> >::evalAtPoint(WorldVector<double> &p, ElInfo *oldElInfo, WorldVector<double>* values) const
{
FUNCNAME("DOFVector<double>::evalAtCoords()");
diff --git a/AMDiS/src/DOFVector.h b/AMDiS/src/DOFVector.h
index e8e28eb3627a5ea1323a868f7244f53c665eb688..0a4f38a56a778daf4292a13af2c5fd0281f02cf3 100644
--- a/AMDiS/src/DOFVector.h
+++ b/AMDiS/src/DOFVector.h
@@ -542,7 +542,7 @@ namespace AMDiS {
/// eval DOFVector at given point p. If oldElInfo != NULL the search for the element, where p is inside,
/// starts from oldElInfo.
- const T& evalAtPoint(WorldVector<double> &p, ElInfo *oldElInfo = NULL, T* value = NULL) const;
+ const T evalAtPoint(WorldVector<double> &p, ElInfo *oldElInfo = NULL, T* value = NULL) const;
/// Writes the data of the DOFVector to an output stream.
void serialize(std::ostream &out)
@@ -582,8 +582,8 @@ namespace AMDiS {
};
- template<>
- const double& DOFVector<double>::evalAtPoint(WorldVector<double> &p, ElInfo *oldElInfo, double* value) const;
+ /*template<>
+ const double DOFVector<double>::evalAtPoint(WorldVector<double> &p, ElInfo *oldElInfo, double* value) const;
template<>
const WorldVector<double>& DOFVector<WorldVector<double> >::evalAtPoint(WorldVector<double> &p, ElInfo *oldElInfo, WorldVector<double>* value) const;
@@ -592,7 +592,7 @@ namespace AMDiS {
void DOFVector<double>::refineInterpol(RCNeighbourList&, int);
template<>
- void DOFVector<double>::coarseRestrict(RCNeighbourList&, int);
+ void DOFVector<double>::coarseRestrict(RCNeighbourList&, int); */
inline double min(const DOFVector<double>& v)
{
diff --git a/AMDiS/src/MTL4Solver.h b/AMDiS/src/MTL4Solver.h
index c48b98087c235db2612ff236929a06036429b4a5..7632c2bc1dbe68339ece299208634dcaa43849b7 100644
--- a/AMDiS/src/MTL4Solver.h
+++ b/AMDiS/src/MTL4Solver.h
@@ -55,7 +55,7 @@ namespace AMDiS {
error = worker.solve(matrix ,mtl_x, mtl_b);
- mtl::dense_vector<typename MTLMatrix::value_type> r(mtl_b);
+ MTLVector r(mtl_b);
r -= matrix * mtl_x;
double residual = two_norm(r);
MSG("MTL4Solver: ||b-Ax||= %e\n", residual);
diff --git a/AMDiS/src/ProblemImplicit.cc b/AMDiS/src/ProblemImplicit.cc
index 8069b5451d984223ada1e0bd9602ead9a6d2a0b3..5677e6d636012b4fa07df9c64e7b759d0514291f 100644
--- a/AMDiS/src/ProblemImplicit.cc
+++ b/AMDiS/src/ProblemImplicit.cc
@@ -12,14 +12,15 @@
#include "ProblemImplicit.h"
#include "MathFunctions.h"
-
+#include "io/ArhReader.h"
using namespace std;
namespace AMDiS {
- void ProblemImplicitBase::readDofVec(std::istream& in, DOFVector<double>* vec,
+ void ProblemImplicit::readDofVec(const std::string& filename, DOFVector<double>* vec,
Mesh* mesh)
{
+#if 0
long size = mesh->getNumberOfVertices();
TEST_EXIT(vec->getSize()>=size)("dofvector smaller than vertex data vector\n");
@@ -34,13 +35,15 @@ namespace AMDiS {
in >> buf;
(*vec)[i] = atof(buf.c_str());
}
+#endif
+ ArhReader::read(filename, vec->getFeSpace()->getMesh(), vec);
}
- void ProblemImplicitBase::readR(std::istream& inStream, double eps,
+ void ProblemImplicit::readR(const std::string& inStream, double eps,
Mesh* mesh, int implMesh , int comp)
{
- FUNCNAME("ProblemImplicitBase::readR()");
+ FUNCNAME("ProblemImplicit::readR()");
DOFVector<double>* r = getSignedDistance(implMesh, comp);
DOFVector<double>* phi1 = getPhi1(implMesh, comp);
@@ -67,7 +70,7 @@ namespace AMDiS {
}
- void ProblemImplicitBase::readPhi1(istream& inStream, double eps,
+ void ProblemImplicit::readPhi1(const std::string& inStream, double eps,
Mesh* mesh, int implMesh, int comp)
{
DOFVector<double>* r = getSignedDistance(implMesh, comp);
@@ -95,7 +98,7 @@ namespace AMDiS {
}
- void ProblemImplicitBase::readPhi2(istream& inStream, double eps,
+ void ProblemImplicit::readPhi2(const std::string& inStream, double eps,
Mesh* mesh, int implMesh, int comp)
{
DOFVector<double>* r = getSignedDistance(implMesh, comp);
@@ -122,21 +125,27 @@ namespace AMDiS {
}
- std::string ProblemImplicitBase::getDofFilename(std::string path, int implMesh)
+ std::string ProblemImplicit::getDofFilename(std::string path, int implMesh)
{
+ FUNCNAME("ProblemImplicit::getDofFilename()");
std::string suffix = "[" +
boost::lexical_cast< std::string >(implMesh) +
"]";
std::string dofFilename("");
Parameters::get(path + "dof file" + suffix, dofFilename);
- if (implMesh == 0 && dofFilename.length() == 0)
+ TEST_EXIT(dofFilename.length() == 0)("dof file was changed to \"arh file\" and reads an arh file now");
+ Parameters::get(path + "arh file" + suffix, dofFilename);
+ if (implMesh == 0 && dofFilename.length() == 0) {
Parameters::get(path + "dof file", dofFilename);
+ TEST_EXIT(dofFilename.length() == 0)("dof file was changed to \"arh file\" and reads an arh file now");
+ Parameters::get(path + "arh file", dofFilename);
+ }
return dofFilename;
}
- double ProblemImplicitBase::getEpsilon(std::string path, int implMesh)
+ double ProblemImplicit::getEpsilon(std::string path, int implMesh)
{
std::string suffix = "[" +
boost::lexical_cast< std::string >(implMesh) +
@@ -150,7 +159,7 @@ namespace AMDiS {
}
- int ProblemImplicitBase::getType(std::string path, int implMesh)
+ int ProblemImplicit::getType(std::string path, int implMesh)
{
std::string suffix = "[" +
boost::lexical_cast< std::string >(implMesh) +
@@ -215,17 +224,16 @@ namespace AMDiS {
{
FUNCNAME("ProblemImplicit::createImplicitMesh()");
- if (!isImplicitMesh(p))
- return false;
std::string path = name + "->implicit mesh["
+ boost::lexical_cast< std::string >(p) + "]->";
int nImplMeshes(0);
Parameters::get(path + "nr meshes", nImplMeshes);
-
- r[p].resize(nImplMeshes);
- phi1[p].resize(nImplMeshes);
- phi2[p].resize(nImplMeshes);
- levelSet[p].resize(nImplMeshes);
+ if (nImplMeshes == 0)
+ return false;
+ r[p].resize(nImplMeshes, NULL);
+ phi1[p].resize(nImplMeshes, NULL);
+ phi2[p].resize(nImplMeshes, NULL);
+ levelSet[p].resize(nImplMeshes, NULL);
for ( int i = 0; i < nImplMeshes ; ++i ) {
(r[p])[i] = new DOFVector< double >(getFeSpace(p), "r");
@@ -256,21 +264,19 @@ namespace AMDiS {
TEST_EXIT(meshes[comp] != NULL)("the mesh was not created\n");
- std::ifstream inStream(dofFilename.c_str());
switch (serType) {
case 0:
- readR(inStream, eps, meshes[comp], implMesh, comp);
+ readR(dofFilename, eps, meshes[comp], implMesh, comp);
break;
case 1:
- readPhi1(inStream, eps, meshes[comp], implMesh, comp);
+ readPhi1(dofFilename, eps, meshes[comp], implMesh, comp);
break;
case 2:
- readPhi2(inStream, eps, meshes[comp], implMesh, comp);
+ readPhi2(dofFilename, eps, meshes[comp], implMesh, comp);
break;
default:
WARNING("unknown implicit mesh type\n");
}
- inStream.close();
return true;
}
@@ -279,8 +285,8 @@ namespace AMDiS {
{
FUNCNAME("ProblemImplicit::createMesh()");
- ProblemStatSeq::createMesh();
-
+ ProblemStat::createMesh();
+#if 0
implMesh.resize(meshes.size());
for (unsigned int i = 0 ; i < meshes.size() ; ++i ) {
std::string path = name + "->implicit mesh[" +
@@ -298,7 +304,8 @@ namespace AMDiS {
inStream.close();
} else
implMesh[i] = false;
- }
+ }
+#endif
}
@@ -308,7 +315,27 @@ namespace AMDiS {
{
FUNCNAME("ProblemImplicit::initialize()");
- ProblemStatSeq::initialize(initFlag);
- createImplicitMesh();
+ ProblemStat::initialize(initFlag);
+ if ( initFlag.isSet(INIT_IMPLICIT_MESH) )
+ createImplicitMesh();
+ }
+
+ ProblemImplicit::~ProblemImplicit()
+ {
+ for ( unsigned int p(0); p < meshes.size(); ++p ) {
+ for ( unsigned int i = 0; i < r[p].size() ; ++i )
+ if ( r[p][i] != NULL)
+ delete r[p][i];
+ for ( unsigned int i(0); i < phi1[p].size(); ++i )
+ if ( phi1[p][i] != NULL)
+ delete phi1[p][i];
+ for ( unsigned int i(0); i < phi2[p].size(); ++i )
+ if ( phi2[p][i] != NULL)
+ delete phi2[p][i];
+ for ( unsigned int i(0); i < levelSet[p].size(); ++i )
+ if ( levelSet[p][i] != NULL)
+ delete levelSet[p][i];
+ }
+
}
}
diff --git a/AMDiS/src/ProblemImplicit.h b/AMDiS/src/ProblemImplicit.h
index 377fad7d8faf240a3608c5aa7ddae827cca5b6f7..cd8acc5abd8137849b94a362f07be31924d5f242 100644
--- a/AMDiS/src/ProblemImplicit.h
+++ b/AMDiS/src/ProblemImplicit.h
@@ -23,81 +23,69 @@
#ifndef AMDIS_PROBLEM_IMPLICIT_H
#define AMDIS_PROBLEM_IMPLICIT_H
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+#ifdef HAVE_PARALLEL_MTL4
+#include "parallel/Mtl4Solver.h"
+#else
+#include "parallel/PetscProblemStat.h"
+#endif
+#else
#include "ProblemStat.h"
-
+#endif
namespace AMDiS {
using namespace std;
+ const Flag INIT_IMPLICIT_MESH = 0X2000L;
- class ProblemImplicitBase
- {
- public:
- virtual ~ProblemImplicitBase() {}
-
- virtual bool createImplicitMesh() = 0;
-
- virtual DOFVector<double>* getSignedDistance(unsigned int im = 0,
- unsigned int m = 0) = 0;
-
- virtual DOFVector<double>* getPhi1(unsigned int im = 0,
- unsigned int m = 0) = 0;
-
- virtual DOFVector<double>* getPhi2(unsigned int im = 0,
- unsigned int m = 0) = 0;
-
- virtual DOFVector<double>* getLevelset(unsigned int im = 0,
- unsigned int m = 0) = 0;
-
- protected:
- void readDofVec(istream& , DOFVector<double>* , Mesh*);
-
- void readR(istream&, double, Mesh*, int implMesh = 0, int comp = 0);
-
- void readPhi1(istream&, double, Mesh*, int implMesh = 0, int comp = 0);
-
- void readPhi2(istream&, double, Mesh*, int implMesh = 0, int comp = 0);
-
- string getDofFilename(string path, int implMesh = 0);
-
- double getEpsilon(string path, int implMesh = 0);
-
- int getType(string path, int implMesh = 0);
-
- virtual bool isImplicitMesh(int comp = 0) = 0;
- };
-
-
- class ProblemImplicit : public ProblemStatSeq,
- public ProblemImplicitBase
+ class ProblemImplicit : public ProblemStat
{
public:
ProblemImplicit(string name,
ProblemIterationInterface* problem = NULL)
- : ProblemStatSeq(name, problem),
+ : ProblemStat(name, problem),
r(0),
phi1(0),
phi2(0),
- levelSet(0),
- implMesh(0)
+ levelSet(0)
{}
- virtual void createMesh();
+ virtual ~ProblemImplicit();
- virtual bool createImplicitMesh();
+ virtual void createMesh();
virtual void initialize(Flag initFlag,
ProblemStatSeq* adoptProblem = NULL,
Flag adoptFlag = INIT_NOTHING);
- DOFVector<double>* getSignedDistance(unsigned int im = 0, unsigned int m = 0);
+ bool createImplicitMesh();
- DOFVector<double>* getPhi1(unsigned int im = 0, unsigned int m = 0);
+ DOFVector<double>* getSignedDistance(unsigned int im = 0,
+ unsigned int m = 0) ;
- DOFVector<double>* getPhi2(unsigned int im = 0, unsigned int m = 0);
+ DOFVector<double>* getPhi1(unsigned int im = 0,
+ unsigned int m = 0) ;
+
+ DOFVector<double>* getPhi2(unsigned int im = 0,
+ unsigned int m = 0) ;
+
+ DOFVector<double>* getLevelset(unsigned int im = 0,
+ unsigned int m = 0) ;
- DOFVector<double>* getLevelset(unsigned int im = 0, unsigned int m = 0);
-
protected:
+ void readDofVec(const std::string& , DOFVector<double>* , Mesh*);
+
+ void readR(const std::string&, double, Mesh*, int implMesh = 0, int comp = 0);
+
+ void readPhi1(const std::string&, double, Mesh*, int implMesh = 0, int comp = 0);
+
+ void readPhi2(const std::string&, double, Mesh*, int implMesh = 0, int comp = 0);
+
+ string getDofFilename(string path, int implMesh = 0);
+
+ double getEpsilon(string path, int implMesh = 0);
+
+ int getType(string path, int implMesh = 0);
+
bool createImplicitMesh(int p);
bool createImplicitMesh(string, int, int);
@@ -115,12 +103,8 @@ namespace AMDiS {
/// (levelSet(x): x \in \Omega: 1, x \not \in Omega: -1, x \in \Gamma: 0)
vector< vector<DOFVector<double>*> > levelSet;
- vector<bool> implMesh;
-
- bool isImplicitMesh(int comp = 0)
- {
- return implMesh[comp];
- }
};
+
+
}
#endif
diff --git a/AMDiS/src/nonlin/NonLinSolver.h b/AMDiS/src/nonlin/NonLinSolver.h
index f865c6f9398f94a9a20f903baef21d97d80f0aa0..bb1d8b306d020d6aded233f37e22dcd357a12603 100644
--- a/AMDiS/src/nonlin/NonLinSolver.h
+++ b/AMDiS/src/nonlin/NonLinSolver.h
@@ -33,8 +33,12 @@
#include "ProblemStat.h"
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+#ifdef HAVE_PARALLEL_MTL4
+#include "parallel/Mtl4Solver.h"
+#else
#include "parallel/PetscProblemStat.h"
#endif
+#endif
namespace AMDiS {
diff --git a/AMDiS/src/nonlin/ProblemNonLin.h b/AMDiS/src/nonlin/ProblemNonLin.h
index f4a55d596ba9cd03c2d5eb685e2e88d761099f6e..0158d4cb6c8970561f8b8dfebf32ab96651a5ee8 100644
--- a/AMDiS/src/nonlin/ProblemNonLin.h
+++ b/AMDiS/src/nonlin/ProblemNonLin.h
@@ -30,8 +30,12 @@
#include "MatrixVector.h"
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+#ifdef HAVE_PARALLEL_MTL4
+#include "parallel/Mtl4Solver.h"
+#else
#include "parallel/PetscProblemStat.h"
#endif
+#endif
namespace AMDiS {