From 5e754b0400a79e507a786d38f2bbdbdc6d4d099f Mon Sep 17 00:00:00 2001
From: Thomas Witkowski <thomas.witkowski@gmx.de>
Date: Wed, 18 Apr 2012 05:18:17 +0000
Subject: [PATCH] Fixed problem for compiling AMDiS in sequentiel mode.
---
AMDiS/CMakeLists.txt | 3 +-
AMDiS/src/BoundaryObject.cc | 138 +++++++++++++++++++++++++
AMDiS/src/BoundaryObject.h | 127 +++++++++++++++++++++++
AMDiS/src/Line.h | 2 +-
AMDiS/src/MeshStructure.h | 30 +++---
AMDiS/src/parallel/InteriorBoundary.cc | 136 ++----------------------
AMDiS/src/parallel/InteriorBoundary.h | 93 +----------------
7 files changed, 296 insertions(+), 233 deletions(-)
create mode 100644 AMDiS/src/BoundaryObject.cc
create mode 100644 AMDiS/src/BoundaryObject.h
diff --git a/AMDiS/CMakeLists.txt b/AMDiS/CMakeLists.txt
index 718c38ee..971e990c 100644
--- a/AMDiS/CMakeLists.txt
+++ b/AMDiS/CMakeLists.txt
@@ -70,6 +70,7 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
${SOURCE_DIR}/BasisFunction.cc
${SOURCE_DIR}/Boundary.cc
${SOURCE_DIR}/BoundaryManager.cc
+ ${SOURCE_DIR}/BoundaryObject.cc
${SOURCE_DIR}/Cholesky.cc
${SOURCE_DIR}/CoarseningManager.cc
${SOURCE_DIR}/CoarseningManager1d.cc
@@ -166,7 +167,6 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
${SOURCE_DIR}/io/VtkWriter.cc
${SOURCE_DIR}/io/VtkVectorWriter.cc
${SOURCE_DIR}/nonlin/ProblemNonLin.cc
- ${SOURCE_DIR}/parallel/InteriorBoundary.cc
${SOURCE_DIR}/time/RosenbrockAdaptInstationary.cc
${SOURCE_DIR}/time/RosenbrockMethod.cc
${SOURCE_DIR}/time/RosenbrockStationary.cc
@@ -225,6 +225,7 @@ if(ENABLE_PARALLEL_DOMAIN)
${SOURCE_DIR}/parallel/DofComm.cc
${SOURCE_DIR}/parallel/CheckerPartitioner.cc
${SOURCE_DIR}/parallel/ElementObjectDatabase.cc
+ ${SOURCE_DIR}/parallel/InteriorBoundary.cc
${SOURCE_DIR}/parallel/MeshDistributor.cc
${SOURCE_DIR}/parallel/MeshLevelData.cc
${SOURCE_DIR}/parallel/MeshManipulation.cc
diff --git a/AMDiS/src/BoundaryObject.cc b/AMDiS/src/BoundaryObject.cc
new file mode 100644
index 00000000..435fc002
--- /dev/null
+++ b/AMDiS/src/BoundaryObject.cc
@@ -0,0 +1,138 @@
+//
+// Software License for AMDiS
+//
+// Copyright (c) 2010 Dresden University of Technology
+// All rights reserved.
+// Authors: Simon Vey, Thomas Witkowski et al.
+//
+// This file is part of AMDiS
+//
+// See also license.opensource.txt in the distribution.
+
+
+#include "BoundaryObject.h"
+#include "Mesh.h"
+#include "FiniteElemSpace.h"
+#include "BasisFunction.h"
+
+namespace AMDiS {
+
+ BoundaryObject::BoundaryObject()
+ : elType(0),
+ reverseMode(false),
+ excludedSubstructures(0)
+ {}
+
+
+ BoundaryObject::BoundaryObject(Element *e,
+ int eType,
+ GeoIndex sObj,
+ int iObj,
+ bool rMode)
+ : el(e),
+ elIndex(e->getIndex()),
+ elType(eType),
+ subObj(sObj),
+ ithObj(iObj),
+ reverseMode(rMode),
+ excludedSubstructures(0)
+ {}
+
+
+ bool BoundaryObject::computeReverseMode(BoundaryObject &obj0,
+ BoundaryObject &obj1,
+ const FiniteElemSpace *feSpace,
+ BoundaryType boundary)
+ {
+ FUNCNAME("BoundaryObject::computeReverseMode()");
+
+ bool reverseMode = false;
+
+ switch (feSpace->getMesh()->getDim()) {
+ case 2:
+ reverseMode = true;
+ break;
+
+ case 3:
+ TEST_EXIT_DBG(obj1.elType == 0)
+ ("Only 3D macro elements with level 0 are supported. This element has level %d!\n",
+ obj1.elType);
+
+
+ if (obj0.subObj == EDGE) {
+ int el0_v0 = obj0.el->getVertexOfEdge(obj0.ithObj, 0);
+ int el0_v1 = obj0.el->getVertexOfEdge(obj0.ithObj, 1);
+ int el1_v0 = obj0.el->getVertexOfEdge(obj1.ithObj, 0);
+ int el1_v1 = obj0.el->getVertexOfEdge(obj1.ithObj, 1);
+
+ const BasisFunction *basFcts = feSpace->getBasisFcts();
+ int nBasFcts = basFcts->getNumber();
+ std::vector<DegreeOfFreedom> localDofs0(nBasFcts), localDofs1(nBasFcts);
+ basFcts->getLocalIndices(obj0.el, feSpace->getAdmin(), localDofs0);
+ basFcts->getLocalIndices(obj1.el, feSpace->getAdmin(), localDofs1);
+
+ Mesh *mesh = feSpace->getMesh();
+
+ if (mesh->isPeriodicAssociation(boundary) == false) {
+ TEST_EXIT_DBG(localDofs0[el0_v0] == localDofs1[el1_v0] ||
+ localDofs0[el0_v0] == localDofs1[el1_v1])
+ ("This should not happen!\n");
+ TEST_EXIT_DBG(localDofs0[el0_v1] == localDofs1[el1_v0] ||
+ localDofs0[el0_v1] == localDofs1[el1_v1])
+ ("This should not happen!\n");
+
+ if (localDofs0[el0_v0] != localDofs1[el1_v0])
+ reverseMode = true;
+ } else {
+ if (mesh->associated(localDofs0[el0_v0], localDofs1[el1_v0]) == false)
+ reverseMode = true;
+ }
+ }
+
+ if (obj0.subObj == FACE && obj0.ithObj != 1) {
+ const BasisFunction *basFcts = feSpace->getBasisFcts();
+ int nBasFcts = basFcts->getNumber();
+ std::vector<DegreeOfFreedom> localDofs0(nBasFcts), localDofs1(nBasFcts);
+ basFcts->getLocalIndices(obj0.el, feSpace->getAdmin(), localDofs0);
+ basFcts->getLocalIndices(obj1.el, feSpace->getAdmin(), localDofs1);
+
+ if (obj0.ithObj == 2 || obj0.ithObj == 3)
+ reverseMode = (localDofs0[0] != localDofs1[0]);
+
+ if (obj0.ithObj == 0)
+ reverseMode = (localDofs0[1] != localDofs1[1]);
+ }
+ break;
+
+ default:
+ ERROR_EXIT("This should not happen!\n");
+ }
+
+ return reverseMode;
+ }
+
+
+ bool BoundaryObject::operator==(const BoundaryObject& other) const
+ {
+ return (other.elIndex == elIndex &&
+ other.subObj == subObj &&
+ other.ithObj == ithObj);
+ }
+
+
+ bool BoundaryObject::operator!=(const BoundaryObject& other) const
+ {
+ return (other.elIndex != elIndex ||
+ other.subObj != subObj ||
+ other.ithObj != ithObj);
+ }
+
+
+ bool AtomicBoundary::operator==(const AtomicBoundary& other) const
+ {
+ return (rankObj == other.rankObj &&
+ neighObj == other.neighObj &&
+ type == other.type);
+ }
+
+}
diff --git a/AMDiS/src/BoundaryObject.h b/AMDiS/src/BoundaryObject.h
new file mode 100644
index 00000000..11d7ceda
--- /dev/null
+++ b/AMDiS/src/BoundaryObject.h
@@ -0,0 +1,127 @@
+// ============================================================================
+// == ==
+// == AMDiS - Adaptive multidimensional simulations ==
+// == ==
+// == http://www.amdis-fem.org ==
+// == ==
+// ============================================================================
+//
+// Software License for AMDiS
+//
+// Copyright (c) 2010 Dresden University of Technology
+// All rights reserved.
+// Authors: Simon Vey, Thomas Witkowski et al.
+//
+// This file is part of AMDiS
+//
+// See also license.opensource.txt in the distribution.
+
+
+
+/** \file BoundaryObject.h */
+
+#ifndef AMDIS_BOUNDARY_OBJECT_H
+#define AMDIS_BOUNDARY_OBJECT_H
+
+#include <vector>
+
+#include "MacroElement.h"
+#include "Element.h"
+#include "Boundary.h"
+
+namespace AMDiS {
+
+ using namespace std;
+
+ typedef vector<pair<GeoIndex, int> > ExcludeList;
+
+ /// Defines the geometrical objects that forms the boundary;
+ struct BoundaryObject {
+
+ BoundaryObject();
+
+ BoundaryObject(Element *e,
+ int eType,
+ GeoIndex sObj,
+ int iObj,
+ bool rMode = false);
+
+ static bool computeReverseMode(BoundaryObject &obj0,
+ BoundaryObject &obj1,
+ const FiniteElemSpace *feSpace,
+ BoundaryType boundary);
+
+ bool operator==(const BoundaryObject& other) const;
+
+ bool operator!=(const BoundaryObject& other) const;
+
+ /// The macro element to which the boundary element corresponds to.
+ Element* el;
+
+ /// Index of the macro element.
+ int elIndex;
+
+ /// Element type index, only used in 3d.
+ int elType;
+
+ /** \brief
+ * Defines the geometrical object at the boundary. It must be "a part" of the
+ * macro element \ref el, i.e., either 1 (a vertex), 2 (an edge) or 3
+ * (a face).
+ */
+ GeoIndex subObj;
+
+ /** \brief
+ * Defines which of vertex, edge or face of the macro element is part of the
+ * boundary.
+ *
+ * Example: If the macro element is a triangle, than \ref subObj may be either
+ * 1 (vertex) or 2 (edge). Assume its the last one. So this variable defines
+ * which of the three possible edges of the triangle is at the interior
+ * boundary.
+ */
+ int ithObj;
+
+ bool reverseMode;
+
+ /** \brief
+ * In many situations it may be necessary to exclude some parts of the
+ * element to be part of the boundary. In 3d, when a face is part of the
+ * boundary, an edge or an vertex may be exludeded. In 2d only vertices may
+ * be exluded to be part of an edge boundary. This list contains pairs of
+ * exludeded structures. The first component of every pair denotes if it is
+ * a vertex or an edge, and the second component denotes the local index of
+ * the structure.
+ */
+ ExcludeList excludedSubstructures;
+ };
+
+
+
+ /** \brief
+ * Defines one atomic part of the boundary, i.e., two boundary objects where
+ * the boundary goes through.
+ */
+ struct AtomicBoundary {
+ AtomicBoundary()
+ : type(INTERIOR)
+ {}
+
+ bool operator==(const AtomicBoundary& other) const;
+
+ /// The rank's part of the boundary.
+ BoundaryObject rankObj;
+
+ /// The object on the other side of the boundary.
+ BoundaryObject neighObj;
+
+ /// Integer flag that is used to distinguish between different types of
+ /// boundaries. Till now it is used only for periodic boundaries, which are
+ /// also handles as interior boundaries.
+ BoundaryType type;
+ };
+
+
+}
+
+#endif
diff --git a/AMDiS/src/Line.h b/AMDiS/src/Line.h
index 661db9f7..484024a6 100644
--- a/AMDiS/src/Line.h
+++ b/AMDiS/src/Line.h
@@ -24,7 +24,7 @@
#define AMDIS_LINE_H
#include "Element.h"
-#include "parallel/InteriorBoundary.h"
+#include "BoundaryObject.h"
namespace AMDiS {
diff --git a/AMDiS/src/MeshStructure.h b/AMDiS/src/MeshStructure.h
index c9b86f3e..77593db4 100644
--- a/AMDiS/src/MeshStructure.h
+++ b/AMDiS/src/MeshStructure.h
@@ -28,7 +28,7 @@
#include "AMDiS_fwd.h"
#include "Global.h"
-#include "parallel/InteriorBoundary.h"
+#include "BoundaryObject.h"
namespace AMDiS {
@@ -46,6 +46,7 @@ namespace AMDiS {
void clear();
+
/** \brief
* Creates a mesh structure code from a mesh object by traversing it in
* preorder.
@@ -96,10 +97,8 @@ namespace AMDiS {
return (currentCode & 1) == 0;
}
- /** \brief
- * Merges a mesh structure code with its own mesh structure code. The result
- * overwrites the own mesh structure code.
- */
+ /// Merges a mesh structure code with its own mesh structure code. The result
+ /// overwrites the own mesh structure code.
void merge(MeshStructure *struc)
{
MeshStructure temp(*this);
@@ -109,14 +108,14 @@ namespace AMDiS {
/** \brief
* Fits a given mesh to the mesh structure code.
*
- * \param debugMode In debugMode, the whole mesh is fitted to the mesh structure
- * code. Otherwise, the mesh is fitted only on the partition
- * of the current process.
+ * \param debugMode In debugMode, the whole mesh is fitted to the mesh
+ * structure code. Otherwise, the mesh is fitted only on
+ * the partition of the current process.
* \param macroElIndex If the mesh structure code represents only one macro
* element, this can be denoted here by its index. In this
- * case, only the corresponding macro element will be fitted
- * to the code. Otherwise, this variable is negative and the
- * whole mesh will be adapted.
+ * case, only the corresponding macro element will be
+ * fitted to the code. Otherwise, this variable is
+ * negative and the whole mesh will be adapted.
*/
void fitMeshToStructure(Mesh *mesh,
RefinementManager *manager,
@@ -187,7 +186,11 @@ namespace AMDiS {
/// Insert a new element to the structure code. Is used by the init function.
void insertElement(bool isLeaf);
- void addAlongSide(Element *el, GeoIndex subObj, int ithObj, int elType, bool reverseOrder);
+ void addAlongSide(Element *el,
+ GeoIndex subObj,
+ int ithObj,
+ int elType,
+ bool reverseOrder);
/// Merges two mesh structure codes to one structure code.
void merge(MeshStructure *structure1,
@@ -208,7 +211,8 @@ namespace AMDiS {
int nElements;
- /// If true, some output is printed to screen during mesh structure code generation.
+ /// If true, some output is printed to screen during mesh structure
+ /// code generation.
bool debugMode;
static const int structureSize;
diff --git a/AMDiS/src/parallel/InteriorBoundary.cc b/AMDiS/src/parallel/InteriorBoundary.cc
index bd776e17..f3e694a4 100644
--- a/AMDiS/src/parallel/InteriorBoundary.cc
+++ b/AMDiS/src/parallel/InteriorBoundary.cc
@@ -10,7 +10,7 @@
// See also license.opensource.txt in the distribution.
-#include "InteriorBoundary.h"
+#include "parallel/InteriorBoundary.h"
#include "FiniteElemSpace.h"
#include "BasisFunction.h"
#include "Serializer.h"
@@ -18,125 +18,6 @@
namespace AMDiS {
- BoundaryObject::BoundaryObject()
- : elType(0),
- reverseMode(false),
- excludedSubstructures(0)
- {}
-
-
- BoundaryObject::BoundaryObject(Element *e,
- int eType,
- GeoIndex sObj,
- int iObj,
- bool rMode)
- : el(e),
- elIndex(e->getIndex()),
- elType(eType),
- subObj(sObj),
- ithObj(iObj),
- reverseMode(rMode),
- excludedSubstructures(0)
- {}
-
-
- bool BoundaryObject::computeReverseMode(BoundaryObject &obj0,
- BoundaryObject &obj1,
- const FiniteElemSpace *feSpace,
- BoundaryType boundary)
- {
- FUNCNAME("BoundaryObject::computeReverseMode()");
-
- bool reverseMode = false;
-
- switch (feSpace->getMesh()->getDim()) {
- case 2:
- reverseMode = true;
- break;
-
- case 3:
- TEST_EXIT_DBG(obj1.elType == 0)
- ("Only 3D macro elements with level 0 are supported. This element has level %d!\n",
- obj1.elType);
-
-
- if (obj0.subObj == EDGE) {
- int el0_v0 = obj0.el->getVertexOfEdge(obj0.ithObj, 0);
- int el0_v1 = obj0.el->getVertexOfEdge(obj0.ithObj, 1);
- int el1_v0 = obj0.el->getVertexOfEdge(obj1.ithObj, 0);
- int el1_v1 = obj0.el->getVertexOfEdge(obj1.ithObj, 1);
-
- const BasisFunction *basFcts = feSpace->getBasisFcts();
- int nBasFcts = basFcts->getNumber();
- std::vector<DegreeOfFreedom> localDofs0(nBasFcts), localDofs1(nBasFcts);
- basFcts->getLocalIndices(obj0.el, feSpace->getAdmin(), localDofs0);
- basFcts->getLocalIndices(obj1.el, feSpace->getAdmin(), localDofs1);
-
- Mesh *mesh = feSpace->getMesh();
-
- if (mesh->isPeriodicAssociation(boundary) == false) {
- TEST_EXIT_DBG(localDofs0[el0_v0] == localDofs1[el1_v0] ||
- localDofs0[el0_v0] == localDofs1[el1_v1])
- ("This should not happen!\n");
- TEST_EXIT_DBG(localDofs0[el0_v1] == localDofs1[el1_v0] ||
- localDofs0[el0_v1] == localDofs1[el1_v1])
- ("This should not happen!\n");
-
- if (localDofs0[el0_v0] != localDofs1[el1_v0])
- reverseMode = true;
- } else {
- if (mesh->associated(localDofs0[el0_v0], localDofs1[el1_v0]) == false)
- reverseMode = true;
- }
- }
-
- if (obj0.subObj == FACE && obj0.ithObj != 1) {
- const BasisFunction *basFcts = feSpace->getBasisFcts();
- int nBasFcts = basFcts->getNumber();
- std::vector<DegreeOfFreedom> localDofs0(nBasFcts), localDofs1(nBasFcts);
- basFcts->getLocalIndices(obj0.el, feSpace->getAdmin(), localDofs0);
- basFcts->getLocalIndices(obj1.el, feSpace->getAdmin(), localDofs1);
-
- if (obj0.ithObj == 2 || obj0.ithObj == 3)
- reverseMode = (localDofs0[0] != localDofs1[0]);
-
- if (obj0.ithObj == 0)
- reverseMode = (localDofs0[1] != localDofs1[1]);
- }
- break;
-
- default:
- ERROR_EXIT("This should not happen!\n");
- }
-
- return reverseMode;
- }
-
-
- bool BoundaryObject::operator==(const BoundaryObject& other) const
- {
- return (other.elIndex == elIndex &&
- other.subObj == subObj &&
- other.ithObj == ithObj);
- }
-
-
- bool BoundaryObject::operator!=(const BoundaryObject& other) const
- {
- return (other.elIndex != elIndex ||
- other.subObj != subObj ||
- other.ithObj != ithObj);
- }
-
-
- bool AtomicBoundary::operator==(const AtomicBoundary& other) const
- {
- return (rankObj == other.rankObj &&
- neighObj == other.neighObj &&
- type == other.type);
- }
-
-
AtomicBoundary& InteriorBoundary::getNewAtomic(int rank)
{
boundary[rank].resize(boundary[rank].size() + 1);
@@ -176,7 +57,8 @@ namespace AMDiS {
int mSize = boundary.size();
SerUtil::serialize(out, mSize);
- for (RankToBoundMap::iterator it = boundary.begin(); it != boundary.end(); ++it) {
+ for (RankToBoundMap::iterator it = boundary.begin();
+ it != boundary.end(); ++it) {
int rank = it->first;
int boundSize = it->second.size();
SerUtil::serialize(out, rank);
@@ -246,9 +128,9 @@ namespace AMDiS {
bound.rankObj.el = elIndexMap[bound.rankObj.elIndex];
- // For the case of periodic interior boundaries, a rank may have an boundary
- // with itself. In this case, also the pointer to the neighbour object must
- // be set correctly.
+ // For the case of periodic interior boundaries, a rank may have an
+ // boundary with itself. In this case, also the pointer to the neighbour
+ // object must be set correctly.
if (elIndexMap.count(bound.neighObj.elIndex))
bound.neighObj.el = elIndexMap[bound.neighObj.elIndex];
else
@@ -258,7 +140,8 @@ namespace AMDiS {
}
- void InteriorBoundary::serializeExcludeList(std::ostream &out, ExcludeList &list)
+ void InteriorBoundary::serializeExcludeList(std::ostream &out,
+ ExcludeList &list)
{
int size = list.size();
SerUtil::serialize(out, size);
@@ -269,7 +152,8 @@ namespace AMDiS {
}
- void InteriorBoundary::deserializeExcludeList(std::istream &in, ExcludeList &list)
+ void InteriorBoundary::deserializeExcludeList(std::istream &in,
+ ExcludeList &list)
{
int size = 0;
SerUtil::deserialize(in, size);
diff --git a/AMDiS/src/parallel/InteriorBoundary.h b/AMDiS/src/parallel/InteriorBoundary.h
index dc04842f..2bf154f3 100644
--- a/AMDiS/src/parallel/InteriorBoundary.h
+++ b/AMDiS/src/parallel/InteriorBoundary.h
@@ -27,104 +27,13 @@
#include <map>
#include "AMDiS_fwd.h"
-#include "MacroElement.h"
-#include "Element.h"
-#include "Boundary.h"
+#include "BoundaryObject.h"
#include "parallel/MeshLevelData.h"
namespace AMDiS {
using namespace std;
- typedef vector<pair<GeoIndex, int> > ExcludeList;
-
- /// Defines the geometrical objects that forms the boundary;
- struct BoundaryObject {
-
- BoundaryObject();
-
- BoundaryObject(Element *e,
- int eType,
- GeoIndex sObj,
- int iObj,
- bool rMode = false);
-
- static bool computeReverseMode(BoundaryObject &obj0,
- BoundaryObject &obj1,
- const FiniteElemSpace *feSpace,
- BoundaryType boundary);
-
- bool operator==(const BoundaryObject& other) const;
-
- bool operator!=(const BoundaryObject& other) const;
-
- /// The macro element to which the boundary element corresponds to.
- Element* el;
-
- /// Index of the macro element.
- int elIndex;
-
- /// Element type index, only used in 3d.
- int elType;
-
- /** \brief
- * Defines the geometrical object at the boundary. It must be "a part" of the
- * macro element \ref el, i.e., either 1 (a vertex), 2 (an edge) or 3 (a face).
- */
- GeoIndex subObj;
-
- /** \brief
- * Defines which of vertex, edge or face of the macro element is part of the
- * boundary.
- *
- * Example: If the macro element is a triangle, than \ref subObj may be either
- * 1 (vertex) or 2 (edge). Assume its the last one. So this variable defines
- * which of the three possible edges of the triangle is at the interior
- * boundary.
- */
- int ithObj;
-
- bool reverseMode;
-
- /** \brief
- * In many situations it may be necessary to exclude some parts of the
- * element to be part of the boundary. In 3d, when a face is part of the
- * boundary, an edge or an vertex may be exludeded. In 2d only vertices may
- * be exluded to be part of an edge boundary. This list contains pairs of
- * exludeded structures. The first component of every pair denotes if it is
- * a vertex or an edge, and the second component denotes the local index of
- * the structure.
- */
- ExcludeList excludedSubstructures;
- };
-
-
-
- /** \brief
- * Defines one atomic part of the boundary, i.e., two boundary objects where the
- * boundary goes through.
- */
- struct AtomicBoundary {
- AtomicBoundary()
- : type(INTERIOR)
- {}
-
- bool operator==(const AtomicBoundary& other) const;
-
- /// The rank's part of the boundary.
- BoundaryObject rankObj;
-
- /// The object on the other side of the boundary.
- BoundaryObject neighObj;
-
- /// Integer flag that is used to distinguish between different types of
- /// boundaries. Till now it is used only for periodic boundaries, which are also
- /// handles as interior boundaries.
- BoundaryType type;
- };
-
-
-
/** \brief
* Defines the interior boundary, i.e. a bound within the domain. It is used for
* the classical domain decomposition parallelization.
--
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