diff --git a/AMDiS/libtool b/AMDiS/libtool
index ace48e58891430cbcc2eae0fee1709dd2bac898f..80535d8da2bd29747389d924ce2317d5403a05f2 100755
--- a/AMDiS/libtool
+++ b/AMDiS/libtool
@@ -82,13 +82,13 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="gcc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+CC="gcc"
# Is the compiler the GNU C compiler?
with_gcc=yes
@@ -171,7 +171,7 @@ dlopen_self=unknown
dlopen_self_static=unknown
# Compiler flag to prevent dynamic linking.
-link_static_flag=""
+link_static_flag="-static"
# Compiler flag to turn off builtin functions.
no_builtin_flag=" -fno-builtin"
@@ -6798,13 +6798,13 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="gcc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicxx"
+CC="g++"
# Is the compiler the GNU C compiler?
with_gcc=yes
@@ -6887,7 +6887,7 @@ dlopen_self=unknown
dlopen_self_static=unknown
# Compiler flag to prevent dynamic linking.
-link_static_flag=""
+link_static_flag="-static"
# Compiler flag to turn off builtin functions.
no_builtin_flag=" -fno-builtin"
@@ -6954,11 +6954,11 @@ predeps=""
# Dependencies to place after the objects being linked to create a
# shared library.
-postdeps="-lmpi_cxx -lmpi -lopen-rte -lopen-pal -libverbs -lrt -lnuma -ldl -lnsl -lutil -ldl -lstdc++ -lm -lgcc_s -lpthread -lc -lgcc_s"
+postdeps="-lstdc++ -lm -lgcc_s -lc -lgcc_s"
# The library search path used internally by the compiler when linking
# a shared library.
-compiler_lib_search_path="-L/usr/lib64 -L/licsoft/libraries/openmpi/1.2.6/64bit/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2 -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/fastfs/wir/local/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../.."
+compiler_lib_search_path="-L/usr/lib64/gcc/x86_64-suse-linux/4.1.2 -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/fastfs/wir/local/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../.."
# Method to check whether dependent libraries are shared objects.
deplibs_check_method="pass_all"
@@ -7103,7 +7103,7 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="/licsoft/libraries/openmpi/1.2.6/64bit/bin/mpicc"
+LTCC="gcc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
diff --git a/AMDiS/src/io/ArhReader.cc b/AMDiS/src/io/ArhReader.cc
index 465750ef76b25d02fac43de78b608fe40fdf1114..b6131839fa313f0946482c387afd771cccd64633 100644
--- a/AMDiS/src/io/ArhReader.cc
+++ b/AMDiS/src/io/ArhReader.cc
@@ -24,27 +24,35 @@ namespace AMDiS {
using namespace std;
- void ArhReader::read(std::string filename, Mesh *mesh)
+ void ArhReader::read(string filename, Mesh *mesh,
+ DOFVector<double>* vec0,
+ DOFVector<double>* vec1,
+ DOFVector<double>* vec2)
{
- std::vector<DOFVector<double>*> vecs(0);
- ArhReader::read(filename, mesh, vecs);
- }
+ vector<DOFVector<double>*> vecs(0);
+ if (vec0 != NULL)
+ vecs.push_back(vec0);
+ if (vec1 != NULL)
+ vecs.push_back(vec1);
+ if (vec2 != NULL)
+ vecs.push_back(vec2);
-
- void ArhReader::read(std::string filename, Mesh *mesh, DOFVector<double>* vec)
- {
- std::vector<DOFVector<double>*> vecs(1);
- vecs[0] = vec;
-
ArhReader::read(filename, mesh, vecs);
}
void ArhReader::read(string filename, Mesh *mesh,
- std::vector<DOFVector<double>*> vecs)
+ vector<DOFVector<double>*> vecs)
{
FUNCNAME("ArhReader::read()");
+ // === Get set of all macro elements in mesh. ===
+ std::set<int> macroInMesh;
+ for (std::deque<MacroElement*>::iterator it = mesh->getMacroElements().begin();
+ it != mesh->getMacroElements().end(); ++it)
+ macroInMesh.insert((*it)->getIndex());
+
+
RefinementManager *refManager = NULL;
switch (mesh->getDim()) {
case 2:
@@ -88,7 +96,8 @@ namespace AMDiS {
MeshStructure elementStructure;
elementStructure.init(structureCode, codeSize);
- elementStructure.fitMeshToStructure(mesh, refManager, false, elIndex);
+ if (macroInMesh.count(elIndex) == 1)
+ elementStructure.fitMeshToStructure(mesh, refManager, false, elIndex);
uint32_t nValuesPerVector = 0;
file.read(reinterpret_cast<char*>(&nValuesPerVector), 4);
@@ -96,7 +105,8 @@ namespace AMDiS {
for (unsigned int j = 0; j < nValueVectors; j++) {
vector<double> values(nValuesPerVector);
file.read(reinterpret_cast<char*>(&(values[0])), 8 * nValuesPerVector);
- setDofValues(elIndex, mesh, values, vecs[j]);
+ if (macroInMesh.count(elIndex) == 1)
+ setDofValues(elIndex, mesh, values, vecs[j]);
}
}
@@ -107,7 +117,7 @@ namespace AMDiS {
void ArhReader::setDofValues(int macroElIndex, Mesh *mesh,
- std::vector<double>& values, DOFVector<double>* vec)
+ vector<double>& values, DOFVector<double>* vec)
{
FUNCNAME("ArhReader::setDofValues()");
diff --git a/AMDiS/src/io/ArhReader.h b/AMDiS/src/io/ArhReader.h
index 15a895474e7916fca71663ac779a042b4b26fe73..7c57b454ac938a021212790e5f098780a396c77f 100644
--- a/AMDiS/src/io/ArhReader.h
+++ b/AMDiS/src/io/ArhReader.h
@@ -30,9 +30,10 @@ namespace AMDiS {
class ArhReader
{
public:
- static void read(std::string filename, Mesh *mesh);
-
- static void read(std::string filename, Mesh *mesh, DOFVector<double>* vec);
+ static void read(std::string filename, Mesh *mesh,
+ DOFVector<double>* vec0 = NULL,
+ DOFVector<double>* vec1 = NULL,
+ DOFVector<double>* vec2 = NULL);
static void read(std::string filename, Mesh *mesh,
std::vector<DOFVector<double>*> vecs);
diff --git a/AMDiS/src/io/ArhWriter.cc b/AMDiS/src/io/ArhWriter.cc
index 196f685f4eb9711ff239615e8fe2711d17b9c435..236dd3d296f98968c2dc6e963ac37311c959f116 100644
--- a/AMDiS/src/io/ArhWriter.cc
+++ b/AMDiS/src/io/ArhWriter.cc
@@ -24,24 +24,25 @@ namespace AMDiS {
using namespace std;
- void ArhWriter::write(string filename, Mesh *mesh)
+ void ArhWriter::write(string filename, Mesh *mesh,
+ DOFVector<double>* vec0,
+ DOFVector<double>* vec1,
+ DOFVector<double>* vec2)
{
- std::vector<DOFVector<double>*> vecs(0);
- ArhWriter::write(filename, mesh, vecs);
- }
-
-
- void ArhWriter::write(std::string filename, Mesh *mesh, DOFVector<double>* vec)
- {
- std::vector<DOFVector<double>*> vecs(1);
- vecs[0] = vec;
+ vector<DOFVector<double>*> vecs(0);
+ if (vec0 != NULL)
+ vecs.push_back(vec0);
+ if (vec1 != NULL)
+ vecs.push_back(vec1);
+ if (vec2 != NULL)
+ vecs.push_back(vec2);
ArhWriter::write(filename, mesh, vecs);
}
- void ArhWriter::write(std::string filename, Mesh *mesh,
- std::vector<DOFVector<double>*> vecs)
+ void ArhWriter::write(string filename, Mesh *mesh,
+ vector<DOFVector<double>*> vecs)
{
FUNCNAME("ArhWriter::write()");
@@ -69,7 +70,7 @@ namespace AMDiS {
file.write(reinterpret_cast<char*>(&nAllValues), 4);
MeshStructure elementStructure;
- std::vector<std::vector<double> > values(vecs.size());
+ vector<vector<double> > values(vecs.size());
int32_t macroElIndex = -1;
elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
@@ -111,9 +112,9 @@ namespace AMDiS {
}
- void ArhWriter::writeMacroElement(std::ofstream &file,
+ void ArhWriter::writeMacroElement(ofstream &file,
MeshStructure &code,
- std::vector<std::vector<double> >& values,
+ vector<vector<double> >& values,
int32_t elIndex)
{
file.write(reinterpret_cast<char*>(&elIndex), 4);
diff --git a/AMDiS/src/io/ArhWriter.h b/AMDiS/src/io/ArhWriter.h
index 67ca01c2a670a6960013cf47e64ce763877c0379..4c2939b73c915d63727ea1dfe9a78ab8f5f048c6 100644
--- a/AMDiS/src/io/ArhWriter.h
+++ b/AMDiS/src/io/ArhWriter.h
@@ -33,9 +33,10 @@ namespace AMDiS {
class ArhWriter
{
public:
- static void write(std::string filename, Mesh *mesh);
-
- static void write(std::string filename, Mesh *mesh, DOFVector<double>* vec);
+ static void write(std::string filename, Mesh *mesh,
+ DOFVector<double>* vec0 = NULL,
+ DOFVector<double>* vec1 = NULL,
+ DOFVector<double>* vec2 = NULL);
static void write(std::string filename, Mesh *mesh,
std::vector<DOFVector<double>*> vecs);