diff --git a/AMDiS/libtool b/AMDiS/libtool
index 10b5aa1c338e90d57869a52c6b277086fbe72364..3b6673371f6b9a9c8f45abefeac61e4c5b70b66e 100755
--- a/AMDiS/libtool
+++ b/AMDiS/libtool
@@ -82,13 +82,13 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="/usr/lib/openmpi/1.2.7-gcc//bin/mpicc"
+LTCC="gcc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="/usr/lib/openmpi/1.2.7-gcc//bin/mpicc"
+CC="gcc"
# Is the compiler the GNU C compiler?
with_gcc=yes
@@ -174,7 +174,7 @@ 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"
@@ -6801,13 +6801,13 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="/usr/lib/openmpi/1.2.7-gcc//bin/mpicc"
+LTCC="gcc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
# A language-specific compiler.
-CC="/usr/lib/openmpi/1.2.7-gcc//bin/mpiCC"
+CC="g++"
# Is the compiler the GNU C compiler?
with_gcc=yes
@@ -6893,7 +6893,7 @@ 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"
@@ -6960,11 +6960,11 @@ predeps=""
# Dependencies to place after the objects being linked to create a
# shared library.
-postdeps="-lmpi_cxx -lmpi -lopen-rte -lopen-pal -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=`echo "-L/usr/lib/openmpi/1.2.7-gcc/lib -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2/../../.." | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
+compiler_lib_search_path=`echo "-L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -L/usr/lib/gcc/i386-redhat-linux/4.1.2/../../.." | $SED -e "s@${gcc_dir}@\${gcc_dir}@g;s@${gcc_ver}@\${gcc_ver}@g"`
# Method to check whether dependent libraries are shared objects.
deplibs_check_method="pass_all"
@@ -7109,7 +7109,7 @@ AR="ar"
AR_FLAGS="cru"
# A C compiler.
-LTCC="/usr/lib/openmpi/1.2.7-gcc//bin/mpicc"
+LTCC="gcc"
# LTCC compiler flags.
LTCFLAGS="-g -O2"
diff --git a/AMDiS/src/ElInfo2d.cc b/AMDiS/src/ElInfo2d.cc
index fbd38c3f29d6d0617b304566119bb1e3d7216e9b..a486147b186847d9038e09894b145e3c84af3ea6 100644
--- a/AMDiS/src/ElInfo2d.cc
+++ b/AMDiS/src/ElInfo2d.cc
@@ -79,7 +79,7 @@ namespace AMDiS {
int edgeNo = oppVertex_[i] = mel->getOppVertex(i);
- if (nb->getFirstChild() && (edgeNo != 2)) {
+ if (nb->getFirstChild() && edgeNo != 2) {
// Search for the next neighbour. In many cases, the neighbour element
// may be refinemed in a way, such that there is no new vertex on the
@@ -113,6 +113,7 @@ namespace AMDiS {
// -------
//
// nb el
+ //
// That means, the edge 0 of the same level neighbour is the common
// edge, i.e., the direct neighbour is the second child of the same
// level neighbour.
@@ -178,10 +179,21 @@ namespace AMDiS {
break;
case 2:
+ if (*(macroNeighbour->getElement()->getDOF(2)) == *(element_->getDOF(0))) {
+ neighbourCoord_[i][0] = macroNeighbour->coord[2];
+ neighbourCoord_[i][1] = macroNeighbour->coord[1];
+ } else if (*(macroNeighbour->getElement()->getDOF(2)) == *(element_->getDOF(1))) {
+ neighbourCoord_[i][0] = macroNeighbour->coord[0];
+ neighbourCoord_[i][1] = macroNeighbour->coord[2];
+ } else {
+ ERROR_EXIT("Should not happen!\n");
+ }
+
// I've deleted here some code, be I think that this case is not
// possible. If an error occurs in this line, please check AMDiS
// revision <= 476 at the same position.
- ERROR_EXIT("Should not happen!\n");
+ // ERROR_EXIT("Should not happen!\n");
+
break;
default:
diff --git a/AMDiS/src/Element.cc b/AMDiS/src/Element.cc
index a3f77696e758bec87ab889cf7e6688aa5c0b0ab3..6934a84c6825f8d6f31858602b4bf6467f8480a4 100644
--- a/AMDiS/src/Element.cc
+++ b/AMDiS/src/Element.cc
@@ -156,14 +156,16 @@ namespace AMDiS {
if (ndof > 0) {
for (int i = 0; i < mesh->getGeo(position); i++) {
if (dof[j] != NULL) {
- if (Mesh::serializedDOFs[dof[j][0]] == NULL) {
+ std::pair<DegreeOfFreedom, int> idx = std::make_pair(dof[j][0], pos);
+
+ if (Mesh::serializedDOFs[idx] == NULL) {
el->dof[j] = new DegreeOfFreedom[ndof];
for (int k = 0; k < ndof; k++)
el->dof[j][k] = dof[j][k];
- Mesh::serializedDOFs[dof[j][0]] = el->dof[j];
+ Mesh::serializedDOFs[idx] = el->dof[j];
} else {
- el->dof[j] = Mesh::serializedDOFs[dof[j][0]];
+ el->dof[j] = Mesh::serializedDOFs[idx];
}
} else {
el->dof[j] = NULL;
@@ -175,12 +177,10 @@ namespace AMDiS {
/* =========== And clone the children ============= */
- if (child[0]) {
+ if (child[0])
el->child[0] = child[0]->cloneWithDOFs();
- }
- if (child[1]) {
+ if (child[1])
el->child[1] = child[1]->cloneWithDOFs();
- }
return el;
}
@@ -264,7 +264,7 @@ namespace AMDiS {
int edges = mesh->getGeo(EDGE);
int faces = mesh->getGeo(FACE);
- if ((nd = admin->getNumberOfDOFs(VERTEX))) {
+ if (nd = admin->getNumberOfDOFs(VERTEX)) {
nd0 = admin->getNumberOfPreDOFs(VERTEX);
n0 = admin->getMesh()->getNode(VERTEX);
for (i = 0; i < vertices; i++) {
@@ -273,7 +273,7 @@ namespace AMDiS {
}
if (mesh->getDim() > 1) {
- if ((nd = admin->getNumberOfDOFs(EDGE))) {
+ if (nd = admin->getNumberOfDOFs(EDGE)) {
nd0 = admin->getNumberOfPreDOFs(EDGE);
n0 = admin->getMesh()->getNode(EDGE);
for (i = 0; i < edges; i++) {
@@ -283,7 +283,7 @@ namespace AMDiS {
}
if (mesh->getDim() == 3) {
- if ((nd = admin->getNumberOfDOFs(FACE))) {
+ if (nd = admin->getNumberOfDOFs(FACE)) {
nd0 = admin->getNumberOfPreDOFs(FACE);
n0 = admin->getMesh()->getNode(FACE);
for (i = 0; i < faces; i++) {
@@ -292,10 +292,11 @@ namespace AMDiS {
}
}
- if ((nd = admin->getNumberOfDOFs(CENTER))) {
+ if (nd = admin->getNumberOfDOFs(CENTER)) {
nd0 = admin->getNumberOfPreDOFs(CENTER);
n0 = admin->getMesh()->getNode(CENTER);
- i = 0; /* only one center */
+ // only one center
+ i = 0;
CHANGE_DOFS_2(this);
}
}
@@ -389,18 +390,26 @@ namespace AMDiS {
if (ndof > 0) {
for (int i = 0; i < mesh->getGeo(position); i++) {
if (dof[j] != NULL) {
- if (Mesh::serializedDOFs[dof[j][0]] == NULL) {
- Mesh::serializedDOFs[dof[j][0]] = dof[j];
+ // Create index to check if the dofs were already written.
+ std::pair<DegreeOfFreedom, int> idx = std::make_pair(dof[j][0], pos);
+
+ if (Mesh::serializedDOFs[idx] == NULL) {
+ Mesh::serializedDOFs[idx] = dof[j];
out.write(reinterpret_cast<const char*>(&ndof), sizeof(int));
- out.write(reinterpret_cast<const char*>(dof[j]), ndof * sizeof(DegreeOfFreedom));
+ out.write(reinterpret_cast<const char*>(&pos), sizeof(int));
+ out.write(reinterpret_cast<const char*>(dof[j]),
+ ndof * sizeof(DegreeOfFreedom));
} else {
int minusOne = -1;
out.write(reinterpret_cast<const char*>(&minusOne), sizeof(int));
- out.write(reinterpret_cast<const char*>(&(dof[j][0])), sizeof(DegreeOfFreedom));
+ out.write(reinterpret_cast<const char*>(&pos), sizeof(int));
+ out.write(reinterpret_cast<const char*>(&(dof[j][0])),
+ sizeof(DegreeOfFreedom));
}
} else {
int zero = 0;
out.write(reinterpret_cast<const char*>(&zero), sizeof(int));
+ out.write(reinterpret_cast<const char*>(&pos), sizeof(int));
}
j++;
}
@@ -466,32 +475,35 @@ namespace AMDiS {
dof = new DegreeOfFreedom*[nodes];
- // std::cout << "-- n = " << nodes << std::endl;
-
for (int i = 0; i < nodes; i++) {
- int nDofs;
+ int nDofs, pos;
in.read(reinterpret_cast<char*>(&nDofs), sizeof(int));
-
- // std::cout << "d = " << nDofs << std::endl;
+ in.read(reinterpret_cast<char*>(&pos), sizeof(int));
if (nDofs) {
if (nDofs != -1) {
dof[i] = new DegreeOfFreedom[nDofs];
in.read(reinterpret_cast<char*>(dof[i]), nDofs * sizeof(DegreeOfFreedom));
- if (Mesh::serializedDOFs[dof[i][0]] != NULL) {
- DegreeOfFreedom *dofPtr = Mesh::serializedDOFs[dof[i][0]];
+
+ // Create index to check if the dofs were alread read from file.
+ std::pair<DegreeOfFreedom, int> idx = std::make_pair(dof[i][0], pos);
+
+ if (Mesh::serializedDOFs[idx] != NULL) {
+ DegreeOfFreedom *dofPtr = Mesh::serializedDOFs[idx];
delete [] dof[i];
dof[i] = dofPtr;
} else {
- Mesh::serializedDOFs[dof[i][0]] = dof[i];
+ Mesh::serializedDOFs[idx] = dof[i];
}
+
} else {
DegreeOfFreedom index;
in.read(reinterpret_cast<char*>(&index), sizeof(DegreeOfFreedom));
- TEST_EXIT(Mesh::serializedDOFs.find(index) != Mesh::serializedDOFs.end())
+
+ std::pair<DegreeOfFreedom, int> idx = std::make_pair(index, pos);
+ TEST_EXIT(Mesh::serializedDOFs.find(idx) != Mesh::serializedDOFs.end())
("This should never happen!\n");
- dof[i] = Mesh::serializedDOFs[index];
- // std::cout << "i = " << index << " " << Mesh::serializedDOFs[index] << " " << Mesh::serializedDOFs[index][0] << std::endl;
+ dof[i] = Mesh::serializedDOFs[idx];
}
} else {
dof[i] = NULL;
@@ -501,8 +513,6 @@ namespace AMDiS {
// read index
in.read(reinterpret_cast<char*>(&index), sizeof(int));
- // std::cout << "index = " << index << std::endl;
-
// read mark
in.read(reinterpret_cast<char*>(&mark), sizeof(signed char));
@@ -527,11 +537,11 @@ namespace AMDiS {
if (typeName != "NULL") {
elementData = CreatorMap<ElementData>::getCreator(typeName)->create();
- if (elementData) {
+
+ if (elementData)
elementData->deserialize(in);
- } else {
- ERROR_EXIT("unexpected type name\n");
- }
+ else
+ ERROR_EXIT("unexpected type name\n");
} else {
elementData = NULL;
}
@@ -544,9 +554,8 @@ namespace AMDiS {
result += sizeof(Element);
result += mesh->getNumberOfNodes() * sizeof(DegreeOfFreedom*);
- if (child[0]) {
- result += child[0]->calcMemoryUsage() + child[1]->calcMemoryUsage();
- }
+ if (child[0])
+ result += child[0]->calcMemoryUsage() + child[1]->calcMemoryUsage();
return result;
}
diff --git a/AMDiS/src/Mesh.cc b/AMDiS/src/Mesh.cc
index ac4f86fdc9c9fb06b9419b4c0a804e805d032701..3e75bcad1fd0a3989810ff29d9d64df96a1f1ff0 100644
--- a/AMDiS/src/Mesh.cc
+++ b/AMDiS/src/Mesh.cc
@@ -66,7 +66,7 @@ namespace AMDiS {
Mesh* Mesh::traversePtr = NULL;
std::vector<DegreeOfFreedom> Mesh::dof_used;
const int Mesh::MAX_DOF = 100;
- std::map<DegreeOfFreedom, DegreeOfFreedom*> Mesh::serializedDOFs;
+ std::map<std::pair<DegreeOfFreedom, int>, DegreeOfFreedom*> Mesh::serializedDOFs;
struct delmem {
DegreeOfFreedom* ptr;
@@ -894,6 +894,39 @@ namespace AMDiS {
return found;
}
+ bool Mesh::getDofIndexCoords(DegreeOfFreedom dof,
+ const FiniteElemSpace* feSpace,
+ WorldVector<double>& coords)
+ {
+ DimVec<double>* baryCoords;
+ bool found = false;
+ TraverseStack stack;
+ Vector<DegreeOfFreedom> dofVec(feSpace->getBasisFcts()->getNumber());
+
+ ElInfo *elInfo = stack.traverseFirst(this, -1,
+ Mesh::CALL_LEAF_EL | Mesh::FILL_COORDS);
+ while (elInfo) {
+ feSpace->getBasisFcts()->getLocalIndicesVec(elInfo->getElement(),
+ feSpace->getAdmin(),
+ &dofVec);
+ for (int i = 0; i < feSpace->getBasisFcts()->getNumber(); i++) {
+ if (dofVec[i] == dof) {
+ baryCoords = feSpace->getBasisFcts()->getCoords(i);
+ elInfo->coordToWorld(*baryCoords, coords);
+ found = true;
+ break;
+ }
+ }
+
+ if (found)
+ break;
+
+ elInfo = stack.traverseNext(elInfo);
+ }
+
+ return found;
+ }
+
void Mesh::setDiameter(const WorldVector<double>& w)
{
diam = w;
diff --git a/AMDiS/src/Mesh.h b/AMDiS/src/Mesh.h
index 8905e5f9923bdd0bf1967a2d89eda878562e6718..68dc9399b33a528190cb191de9bd53cf75bef158 100644
--- a/AMDiS/src/Mesh.h
+++ b/AMDiS/src/Mesh.h
@@ -502,6 +502,9 @@ namespace AMDiS {
const FiniteElemSpace* feSpace,
WorldVector<double>& coords);
+ bool getDofIndexCoords(DegreeOfFreedom dof,
+ const FiniteElemSpace* feSpace,
+ WorldVector<double>& coords);
/// Returns FILL_ANY_?D
inline static const Flag& getFillAnyFlag(int dim)
@@ -749,8 +752,17 @@ namespace AMDiS {
/// Used by check functions
static std::vector<DegreeOfFreedom> dof_used;
- ///
- static std::map<DegreeOfFreedom, DegreeOfFreedom*> serializedDOFs;
+ /** \brief
+ * This map is used for serialization and deserialization of mesh elements.
+ * During the serialization process, all elements are visited and their dof indices
+ * are written to the file. If a dof index at a position, i.e. vertex, line or face,
+ * was written to file, the combination of dof index and position is inserted to
+ * this map. That ensures that the same dof at the same position, but being part of
+ * another element, is not written twice to the file.
+ * When a state should be deserialized, the information can be used to construct
+ * exactly the same dof structure.
+ */
+ static std::map<std::pair<DegreeOfFreedom, int>, DegreeOfFreedom*> serializedDOFs;
/** \brief
* Used while mesh refinement. To create new elements