From dfd9bc02caa0e69930f3c434bf84c78e036fc5e2 Mon Sep 17 00:00:00 2001
From: Siqi Ling <lsq0473@gmail.com>
Date: Mon, 8 Jun 2015 12:30:44 +0000
Subject: [PATCH] merge parallel multimesh branch to the trunk
---
AMDiS/src/AMDiS_fwd.h | 4 +
AMDiS/src/Assembler.cc | 189 +-
AMDiS/src/BoundaryObject.cc | 2 +
AMDiS/src/CoarseningManager3d.cc | 3 +-
AMDiS/src/CouplingIterationInterface.h | 2 +-
AMDiS/src/CouplingProblemStat.h | 399 +-
AMDiS/src/CouplingTimeInterface.h | 2 +-
AMDiS/src/DOFMatrix.h | 10 +
AMDiS/src/Debug.cc | 63 +-
AMDiS/src/Debug.h | 6 +
AMDiS/src/ElInfo2d.cc | 2 +-
AMDiS/src/Element.cc | 8 +-
AMDiS/src/Lagrange.cc | 1 -
AMDiS/src/Mesh.cc | 71 +-
AMDiS/src/Mesh.h | 5 +
AMDiS/src/MeshStructure.cc | 34 +-
AMDiS/src/MeshStructure.h | 14 +-
AMDiS/src/ProblemStat.cc | 73 +-
AMDiS/src/ProblemStat.h | 21 +-
AMDiS/src/RefinementManager3d.cc | 22 +-
AMDiS/src/RefinementManager3d.h | 5 +-
AMDiS/src/StandardProblemIteration.h | 2 +-
AMDiS/src/est/Estimator.cc | 12 +-
AMDiS/src/est/ResidualEstimator.cc | 35 +-
AMDiS/src/io/FileWriter.cc | 4 +-
AMDiS/src/io/FileWriter.hh | 1 +
AMDiS/src/io/detail/VtkWriter.cc | 21 +-
AMDiS/src/io/detail/VtkWriter.h | 6 +-
AMDiS/src/parallel/DofComm.cc | 61 +-
AMDiS/src/parallel/DofComm.h | 20 +-
AMDiS/src/parallel/ElementObjectDatabase.cc | 224 +-
AMDiS/src/parallel/ElementObjectDatabase.h | 51 +-
AMDiS/src/parallel/InteriorBoundary.cc | 35 +-
AMDiS/src/parallel/InteriorBoundary.h | 15 +
AMDiS/src/parallel/MatrixNnzStructure.cc | 20 +-
AMDiS/src/parallel/MatrixNnzStructure.h | 4 +
AMDiS/src/parallel/MeshDistributor.cc | 1216 +--
AMDiS/src/parallel/MeshDistributor.h | 135 +-
AMDiS/src/parallel/MeshManipulation.cc | 14 +-
AMDiS/src/parallel/MeshManipulation.h | 4 +
.../src/parallel/ParallelCoarseSpaceSolver.cc | 11 +-
AMDiS/src/parallel/ParallelDebug.cc | 338 +-
AMDiS/src/parallel/ParallelDebug.h | 19 +-
AMDiS/src/parallel/ParallelDofMapping.cc | 116 +-
AMDiS/src/parallel/ParallelDofMapping.h | 111 +-
AMDiS/src/parallel/ParallelProblemStat.cc | 13 +-
AMDiS/src/parallel/ParallelSolver.cc | 6 +-
AMDiS/src/parallel/ParallelTypes.h | 4 +
AMDiS/src/parallel/PetscSolverFeti.cc | 12 +-
AMDiS/src/parallel/PetscSolverGlobalMatrix.cc | 5 +-
AMDiS/src/parallel/PetscSolverSchur.cc | 11 +-
AMDiS/src/utility/to_string.hpp | 41 +
extensions/ProblemStatMassConserve.h | 13 +-
extensions/ProblemStatMassConserve_mm.h | 123 +
extensions/Refinement.h | 26 +-
extensions/Refinement_Level.h | 1 +
.../base_problems/CouplingBaseProblem.h | 17 +-
.../base_problems/CouplingBaseProblem2.h | 49 +-
.../CouplingBaseProblem2_cxx11.h | 201 +-
.../NavierStokes_TH_MultiPhase.hh | 1 +
extensions/demo/multimesh/CMakeLists.txt | 33 +
.../init/cahnHilliard_navierStokes.dat.2d | 126 +
.../multimesh/init/dend002.dat.2d.m.bicg.2p | 138 +
.../multimesh/init/heat.dat.2d.m_1015_1010 | 85 +
.../demo/multimesh/init/heat.dat.2d.s_16_16 | 76 +
.../demo/multimesh/macro/macro.square.2d | 47 +
.../macro/macro.square.2d.666466.tmp | 236 +
.../macro/macro.square.2d.685642.tmp | 236 +
.../demo/multimesh/macro/macro_corner_1x1.2d | 24 +
.../macro/macro_corner_1x1.2d.736102.tmp | 6708 +++++++++++++++++
.../macro/macro_corner_1x1.2d.801668.tmp | 6708 +++++++++++++++++
.../macro/macro_corner_1x1.2d.991261.tmp | 6708 +++++++++++++++++
extensions/demo/multimesh/src/Anisotropy.h | 175 +
.../demo/multimesh/src/CahnHilliard_mm.h | 127 +
.../demo/multimesh/src/CahnHilliard_mm.hh | 222 +
.../demo/multimesh/src/MyProblemInstat.cc | 158 +
.../demo/multimesh/src/MyProblemInstat.h | 96 +
extensions/demo/multimesh/src/Refinement.cc | 184 +
extensions/demo/multimesh/src/Refinement.h | 39 +
.../src/cahnHilliard_navierStokes.cc | 187 +
.../src/cahnHilliard_navierStokes_mm.cc | 186 +
extensions/demo/multimesh/src/dendrites.cc | 234 +
.../demo/multimesh/src/diffuseDomain.cc | 340 +
.../init/cahnHilliard_navierStokes.dat.2d | 8 +-
84 files changed, 25635 insertions(+), 1380 deletions(-)
create mode 100644 AMDiS/src/utility/to_string.hpp
create mode 100644 extensions/ProblemStatMassConserve_mm.h
create mode 100644 extensions/demo/multimesh/CMakeLists.txt
create mode 100644 extensions/demo/multimesh/init/cahnHilliard_navierStokes.dat.2d
create mode 100644 extensions/demo/multimesh/init/dend002.dat.2d.m.bicg.2p
create mode 100644 extensions/demo/multimesh/init/heat.dat.2d.m_1015_1010
create mode 100644 extensions/demo/multimesh/init/heat.dat.2d.s_16_16
create mode 100644 extensions/demo/multimesh/macro/macro.square.2d
create mode 100644 extensions/demo/multimesh/macro/macro.square.2d.666466.tmp
create mode 100644 extensions/demo/multimesh/macro/macro.square.2d.685642.tmp
create mode 100644 extensions/demo/multimesh/macro/macro_corner_1x1.2d
create mode 100644 extensions/demo/multimesh/macro/macro_corner_1x1.2d.736102.tmp
create mode 100644 extensions/demo/multimesh/macro/macro_corner_1x1.2d.801668.tmp
create mode 100644 extensions/demo/multimesh/macro/macro_corner_1x1.2d.991261.tmp
create mode 100644 extensions/demo/multimesh/src/Anisotropy.h
create mode 100644 extensions/demo/multimesh/src/CahnHilliard_mm.h
create mode 100644 extensions/demo/multimesh/src/CahnHilliard_mm.hh
create mode 100644 extensions/demo/multimesh/src/MyProblemInstat.cc
create mode 100644 extensions/demo/multimesh/src/MyProblemInstat.h
create mode 100644 extensions/demo/multimesh/src/Refinement.cc
create mode 100644 extensions/demo/multimesh/src/Refinement.h
create mode 100644 extensions/demo/multimesh/src/cahnHilliard_navierStokes.cc
create mode 100644 extensions/demo/multimesh/src/cahnHilliard_navierStokes_mm.cc
create mode 100644 extensions/demo/multimesh/src/dendrites.cc
create mode 100644 extensions/demo/multimesh/src/diffuseDomain.cc
diff --git a/AMDiS/src/AMDiS_fwd.h b/AMDiS/src/AMDiS_fwd.h
index ecbe2de4..3c030371 100644
--- a/AMDiS/src/AMDiS_fwd.h
+++ b/AMDiS/src/AMDiS_fwd.h
@@ -163,6 +163,10 @@ namespace AMDiS {
template<typename T> class WorldVector;
template<typename T> class WorldMatrix;
template<typename T> class VectorOfFixVecs;
+
+ namespace detail {
+ template <class P> class CouplingProblemStat;
+ }
typedef mtl::dense2D<double> ElementMatrix;
diff --git a/AMDiS/src/Assembler.cc b/AMDiS/src/Assembler.cc
index b73de0b3..4e0941a7 100644
--- a/AMDiS/src/Assembler.cc
+++ b/AMDiS/src/Assembler.cc
@@ -53,7 +53,6 @@ namespace AMDiS {
Assembler::~Assembler()
{}
-
void Assembler::calculateElementMatrix(const ElInfo *elInfo,
ElementMatrix& userMat,
double factor)
@@ -64,19 +63,22 @@ namespace AMDiS {
Element *el = elInfo->getElement();
if (el != lastMatEl || !operat->isOptimized()) {
- initElement(elInfo, elInfo);
+ initElement(elInfo);
if (rememberElMat)
set_to_zero(elementMatrix);
lastMatEl = el;
} else {
+ // Only possible in single mesh case when one operator
+ // is used more than twice?
if (rememberElMat) {
- userMat += factor * elementMatrix;
+ if (&userMat != &elementMatrix)
+ userMat += factor * elementMatrix;
return;
}
}
-
+
ElementMatrix& mat = rememberElMat ? elementMatrix : userMat;
if (secondOrderAssembler)
@@ -91,8 +93,7 @@ namespace AMDiS {
if (rememberElMat && &userMat != &elementMatrix)
userMat += factor * elementMatrix;
}
-
-
+
void Assembler::calculateElementMatrix(const ElInfo *rowElInfo,
const ElInfo *colElInfo,
const ElInfo *smallElInfo,
@@ -101,115 +102,68 @@ namespace AMDiS {
ElementMatrix& userMat,
double factor)
{
- if (remember && (factor != 1.0 || operat->uhOld))
- rememberElMat = true;
-
- Element *el = smallElInfo->getElement();
+ Element *el = smallElInfo->getElement();
+ // initElement and calculateElementMatrix always need to be
+ // recalculated since the smaller ElInfo can be different
lastVecEl = lastMatEl = NULL;
if ((el != lastMatEl && el != lastVecEl) || !operat->isOptimized())
initElement(smallElInfo, largeElInfo);
- if (el != lastMatEl || !operat->isOptimized()) {
- if (rememberElMat)
- set_to_zero(elementMatrix);
+ if (el != lastMatEl || !operat->isOptimized())
lastMatEl = el;
- } else {
- if (rememberElMat) {
+ else {
+ ERROR_EXIT("Never reached because lastVecEl = lastMatEl = NULL;\n");
+ if (&userMat != &elementMatrix)
userMat += factor * elementMatrix;
- return;
- }
+ return;
}
-
- ElementMatrix& mat = rememberElMat ? elementMatrix : userMat;
-
- if (secondOrderAssembler) {
- // calculate element matrices always on smallest element
- secondOrderAssembler->calculateElementMatrix(smallElInfo, mat);
- // smallElInfo stores refinement-relation to largeElInfo
- ElementMatrix &m =
- smallElInfo->getSubElemGradCoordsMat(rowFeSpace->getBasisFcts()->getDegree()); // muste be moved to next if-else block when generalized for multiple polynomial degrees
-
- if (!rowColFeSpaceEqual) {
- if (smallElInfo == colElInfo)
- tmpMat = m * mat;
- else
- tmpMat = mat * trans(m);
-
- mat = tmpMat;
- }
- }
+ // In multimesh case, elementMatrix is always be recalculated, because each time we
+ // need to do transformation here.
+ set_to_zero(elementMatrix);
+
+ ElementMatrix& mat = elementMatrix;
- if (firstOrderAssemblerGrdPsi) {
+ if (secondOrderAssembler)
+ secondOrderAssembler->calculateElementMatrix(smallElInfo, mat);
+ if (firstOrderAssemblerGrdPsi)
firstOrderAssemblerGrdPsi->calculateElementMatrix(smallElInfo, mat);
-
- if (!rowColFeSpaceEqual) {
- if (largeElInfo == rowElInfo) {
- ElementMatrix &m =
- smallElInfo->getSubElemGradCoordsMat(rowFeSpace->getBasisFcts()->getDegree());
-
- tmpMat = m * mat;
- } else {
- ElementMatrix &m =
- smallElInfo->getSubElemCoordsMat(rowFeSpace->getBasisFcts()->getDegree());
-
- tmpMat = mat * trans(m);
- }
-
- mat = tmpMat;
- }
- }
-
- if (firstOrderAssemblerGrdPhi) {
+ if (firstOrderAssemblerGrdPhi)
firstOrderAssemblerGrdPhi->calculateElementMatrix(smallElInfo, mat);
-
- if (!rowColFeSpaceEqual) {
- if (largeElInfo == colElInfo) {
- ElementMatrix &m =
- smallElInfo->getSubElemGradCoordsMat(rowFeSpace->getBasisFcts()->getDegree());
-
- tmpMat = mat * trans(m);
- } else {
- ElementMatrix &m =
- smallElInfo->getSubElemCoordsMat(rowFeSpace->getBasisFcts()->getDegree());
-
- tmpMat = m * mat;
- }
-
- mat = tmpMat;
- }
- }
-
- if (zeroOrderAssembler) {
+ if (zeroOrderAssembler)
zeroOrderAssembler->calculateElementMatrix(smallElInfo, mat);
+
+
- if (!rowColFeSpaceEqual) {
- ElementMatrix &m =
- smallElInfo->getSubElemCoordsMat(rowFeSpace->getBasisFcts()->getDegree());
-
- if (smallElInfo == colElInfo)
- tmpMat = m * mat;
- else
- tmpMat = mat * trans(m);
-
- mat = tmpMat;
- }
- }
+ ElementMatrix &m =
+ smallElInfo->getSubElemCoordsMat(rowFeSpace->getBasisFcts()->getDegree());
- if (rememberElMat && &userMat != &elementMatrix)
- userMat += factor * elementMatrix;
+ if (!rowColFeSpaceEqual) {
+ if (smallElInfo == colElInfo)
+ tmpMat = m * mat;
+ else
+ tmpMat = mat * trans(m);
+
+ mat = tmpMat;
+ } else if (smallElInfo == colElInfo) {
+ tmpMat = m * mat * trans(m);
+ mat = tmpMat;
+ }
+
+ // This is for the call in matVecAssemble
+ if (&userMat != &elementMatrix)
+ userMat += factor * elementMatrix;
}
-
void Assembler::calculateElementVector(const ElInfo *elInfo,
ElementVector& userVec,
double factor)
{
if (remember && factor != 1.0)
rememberElVec = true;
-
+
Element *el = elInfo->getElement();
if ((el != lastMatEl && el != lastVecEl) || !operat->isOptimized())
@@ -221,6 +175,8 @@ namespace AMDiS {
lastVecEl = el;
} else {
+ // Only possible in single mesh case when one operator
+ // is used more than twice at dof vector?
if (rememberElVec) {
userVec += factor * elementVector;
return;
@@ -246,7 +202,6 @@ namespace AMDiS {
userVec += factor * elementVector;
}
-
void Assembler::calculateElementVector(const ElInfo *mainElInfo,
const ElInfo *auxElInfo,
const ElInfo *smallElInfo,
@@ -256,36 +211,33 @@ namespace AMDiS {
{
FUNCNAME("Assembler::calculateElementVector()");
- if (remember && factor != 1.0)
- rememberElVec = true;
-
Element *el = mainElInfo->getElement();
+ // initElement and calculateElementVector always need to be
+ // recalculated since the smaller ElInfo can be different
+ lastVecEl = lastMatEl = NULL;
if ((el != lastMatEl && el != lastVecEl) || !operat->isOptimized())
initElement(smallElInfo, largeElInfo);
-
- if (el != lastVecEl || !operat->isOptimized()) {
- if (rememberElVec)
- set_to_zero(elementVector);
-
+
+ if (el != lastVecEl || !operat->isOptimized())
lastVecEl = el;
- } else {
- if (rememberElVec) {
- userVec += factor * elementVector;
- return;
- }
+ else {
+ ERROR_EXIT("Never reached because lastVecEl = lastMatEl = NULL;\n");
+ userVec += factor * elementVector;
+ return;
}
- ElementVector& vec = rememberElVec ? elementVector : userVec;
+
+ set_to_zero(elementVector);
+ ElementVector& vec = elementVector;
if (operat->uhOld && remember) {
+
if (smallElInfo->getLevel() == largeElInfo->getLevel())
matVecAssemble(auxElInfo, vec);
- else
+ else
matVecAssemble(mainElInfo, auxElInfo, smallElInfo, largeElInfo, vec);
- if (rememberElVec)
- userVec += factor * elementVector;
-
+ userVec += factor * elementVector;
return;
}
@@ -306,13 +258,12 @@ namespace AMDiS {
}
}
- if (rememberElVec)
- userVec += factor * elementVector;
+ userVec += factor * elementVector;
}
-
void Assembler::matVecAssemble(const ElInfo *elInfo, ElementVector& vec)
{
+
Element *el = elInfo->getElement();
ElementVector uhOldLoc(operat->uhOld->getFeSpace() == rowFeSpace ?
nRow : nCol);
@@ -323,7 +274,8 @@ namespace AMDiS {
calculateElementMatrix(elInfo, elementMatrix);
}
- vec += elementMatrix*uhOldLoc;
+
+ vec += elementMatrix * uhOldLoc;
}
@@ -331,7 +283,7 @@ namespace AMDiS {
const ElInfo *smallElInfo, const ElInfo *largeElInfo,
ElementVector& vec)
{
- FUNCNAME("Assembler::matVecAssemble()");
+ FUNCNAME("Assembler::matVecAssemble()");
TEST_EXIT(rowFeSpace->getBasisFcts() == colFeSpace->getBasisFcts())
("Works only for equal basis functions for different components!\n");
@@ -343,7 +295,7 @@ namespace AMDiS {
usedEl = mainElInfo->getElement();
else
ERROR("Mesh is incorrect.\n");
-
+
const BasisFunction *basFcts = rowFeSpace->getBasisFcts();
int nBasFcts = basFcts->getNumber();
ElementVector uhOldLoc(nBasFcts);
@@ -353,10 +305,11 @@ namespace AMDiS {
if (mainElInfo->getElement() != lastMatEl) {
set_to_zero(elementMatrix);
calculateElementMatrix(mainElInfo, auxElInfo, smallElInfo, largeElInfo,
- rowFeSpace == operat->uhOld->getFeSpace(), elementMatrix);
+ rowFeSpace == operat->uhOld->getFeSpace(), elementMatrix);
}
vec += elementMatrix * uhOldLoc;
+
}
@@ -472,4 +425,4 @@ namespace AMDiS {
checkQuadratures();
}
-}
+}
\ No newline at end of file
diff --git a/AMDiS/src/BoundaryObject.cc b/AMDiS/src/BoundaryObject.cc
index 6478af25..f7b4393b 100644
--- a/AMDiS/src/BoundaryObject.cc
+++ b/AMDiS/src/BoundaryObject.cc
@@ -56,6 +56,8 @@ namespace AMDiS {
FUNCNAME("BoundaryObject::computeReverseMode()");
bool reverseMode = false;
+
+ TEST_EXIT_DBG(obj0.el && obj1.el)("BoundaryObject without element pointer.\n");
switch (feSpace->getMesh()->getDim()) {
case 2:
diff --git a/AMDiS/src/CoarseningManager3d.cc b/AMDiS/src/CoarseningManager3d.cc
index 85ce619c..4b56e6f8 100644
--- a/AMDiS/src/CoarseningManager3d.cc
+++ b/AMDiS/src/CoarseningManager3d.cc
@@ -99,7 +99,7 @@ namespace AMDiS {
#if HAVE_PARALLEL_DOMAIN_AMDIS
vector<FixRefinementPatch::EdgeInEl> refineEdges;
- FixRefinementPatch::getOtherEl(stack, refineEdges);
+ FixRefinementPatch::getOtherEl(mesh, stack, refineEdges);
// === If the refinement edge must be fixed, add also the other part of this ===
// === edge to the refinement patch. ===
@@ -110,6 +110,7 @@ namespace AMDiS {
return;
Element *otherEl = refineEdges[0].first;
+ TEST_EXIT_DBG(otherEl->getMesh() == mesh)("Something is wrong.\n");
TraverseStack stack2;
ElInfo *elInfo2 =
diff --git a/AMDiS/src/CouplingIterationInterface.h b/AMDiS/src/CouplingIterationInterface.h
index b19eb44d..d65c608f 100644
--- a/AMDiS/src/CouplingIterationInterface.h
+++ b/AMDiS/src/CouplingIterationInterface.h
@@ -40,7 +40,7 @@ namespace AMDiS {
* problem-list, that is filled by addProblem. Alternatively one can a access
* each problem by an unique name.
*/
- class CouplingIterationInterface : public ProblemIterationInterface
+ class CouplingIterationInterface : public virtual ProblemIterationInterface
{
public:
virtual ~CouplingIterationInterface() {}
diff --git a/AMDiS/src/CouplingProblemStat.h b/AMDiS/src/CouplingProblemStat.h
index 0c69f06f..c2b3d81f 100644
--- a/AMDiS/src/CouplingProblemStat.h
+++ b/AMDiS/src/CouplingProblemStat.h
@@ -31,7 +31,7 @@
#include "AMDiS_fwd.h"
#include "ProblemStat.h"
#include "Initfile.h"
-#include <boost/lexical_cast.hpp>
+#include "utility/to_string.hpp"
namespace AMDiS {
@@ -43,21 +43,26 @@ namespace AMDiS {
* computations.
*/
template<typename ProblemStatType>
- class CouplingProblemStat
+ class CouplingProblemStat : public ProblemStatSeq
{
+ protected:
+ typedef ProblemStatSeq super;
+
+ using super::nComponents;
+ using super::meshes;
+ using super::nMeshes;
+ using super::feSpaces;
+ using super::name;
+ using super::refinementManager;
+ using super::coarseningManager;
+
public:
/// Constructor
CouplingProblemStat(std::string name_)
- : name(name_),
- nComponents(0),
- nMeshes(0),
- refinementManager(NULL),
- coarseningManager(NULL)
+ : super(name_),
+ dim(-1)
{}
- /// Destructor
- virtual ~CouplingProblemStat() {}
-
/// add problem by number
virtual void addProblem(ProblemStatType* prob)
{
@@ -71,112 +76,193 @@ namespace AMDiS {
Flag adoptFlag = INIT_NOTHING)
{ FUNCNAME("CouplingProblemStat::initialize()");
- // create one refinement-/coarseningmanager for all problems
- if (refinementManager != NULL && coarseningManager != NULL) {
- WARNING("refinement-/coarseningmanager already created\n");
- } else {
- if (!adoptProblem)
- createRefCoarseManager();
- else {
- refinementManager = adoptProblem->getRefinementManager();
- coarseningManager = adoptProblem->getCoarseningManager();
- }
+ super::initialize(initFlag - INIT_MESH);
+
+ const Flag DEFAULT_INIT = (INIT_FE_SPACE | INIT_MESH | CREATE_MESH | INIT_SYSTEM | INIT_SOLVER | INIT_ESTIMATOR | INIT_MARKER | INIT_FILEWRITER);
+ for (size_t p = 0; p < problems.size(); ++p) {
+ problems[p]->initialize(initFlag - DEFAULT_INIT);
}
-
- if (refinementManager == NULL || coarseningManager == NULL)
- WARNING("no refinement-/coarseningmanager created\n");
- // create Meshes and FeSpaces
+ for (size_t i = 0; i < meshes.size(); i++) {
+ int globalRefinements = 0;
+
+ // If AMDiS is compiled for parallel computations, the global refinements are
+ // ignored here. Later, each rank will add the global refinements to its
+ // private mesh.
+ #ifndef HAVE_PARALLEL_DOMAIN_AMDIS
+ Parameters::get(meshes[i]->getName() + "->global refinements",
+ globalRefinements);
+ #endif
+ bool initMesh = initFlag.isSet(INIT_MESH);
+ // Initialize the meshes if there is no serialization file.
+ if (initMesh && meshes[i] && !(meshes[i]->isInitialized())) {
+ meshes[i]->initialize();
+ refinementManager->globalRefine(meshes[i], globalRefinements);
+ }
+ }
+ }
+
+
+ /// Used in \ref initialize().
+ virtual void createMesh() override
+ {
// all problems must have the same dimension (?)
- int dim = 0;
+ dim = 0;
Parameters::get(name + "->dim", dim);
TEST_EXIT(dim)("No problem dimension specified for \"%s->dim\"!\n",
name.c_str());
- std::map<std::string, Mesh*> meshByName;
+ std::map<std::pair<std::string, int>, Mesh*> meshByName; // (name, refSet) --> Mesh*
+ typedef std::map<std::pair<std::string, int>, Mesh*>::iterator MeshIterator;
+
std::vector<std::set<Mesh*> > meshesForProblems(problems.size());
- std::map<std::pair<Mesh*, int>, FiniteElemSpace*> feSpaceMap;
+
for (size_t i = 0; i < problems.size(); ++i) {
TEST_EXIT(problems[i])("problem[%d] does not exist!\n",i);
- for (size_t j = 0; j < problems[i]->getNumComponents(); j++) {
- // mesh
-
+
+ int nComponents = problems[i]->getNumComponents();
+
+ int nAddComponents = 0;
+ Parameters::get(problems[i]->getName() + "->additional components", nAddComponents);
+
+ problems[i]->componentMeshes.resize(nComponents + nAddComponents);
+
+ for (size_t j = 0; j < nComponents + nAddComponents; j++) {
+ // name of the mesh
std::string meshName("");
Parameters::get(problems[i]->getName() + "->mesh", meshName);
TEST_EXIT(meshName != "")("No mesh name specified for \"%s->mesh\"!\n",
problems[i]->getName().c_str());
-
- if (meshByName.find(meshName) == meshByName.end()) {
+
+ // dimension of the mesh
+ int mesh_dim = 0;
+ Parameters::get(problems[i]->getName() + "->dim", mesh_dim);
+ TEST_EXIT(dim == mesh_dim)("Mesh-dimension must be the same for all problems!\n");
+
+ // refinement set (optional)
+ int refSet = 0;
+ Parameters::get(problems[i]->getName() + "->refinement set[" + to_string(j) + "]", refSet);
+
+ // create a new Mesh only if not already created for other problem
+ Mesh* componentMesh;
+ MeshIterator meshIt = meshByName.find(std::make_pair(meshName, refSet));
+ if (meshIt == meshByName.end()) {
Mesh *newMesh = new Mesh(meshName, dim);
- meshByName[meshName] = newMesh;
meshes.push_back(newMesh);
- meshesForProblems[i].insert(newMesh);
+ meshByName[std::make_pair(meshName, refSet)] = newMesh;
+ componentMesh = newMesh;
nMeshes++;
- } else
- meshesForProblems[i].insert(meshByName[meshName]);
+ } else {
+ componentMesh = meshIt->second;
+ }
+ problems[i]->componentMeshes[j] = componentMesh;
+ }
+
+ // copy unqiue set of meshes to problem[i]->meshes
+ std::set<Mesh*> uniqueMeshes;
+ for (size_t j = 0; j < problems[i]->componentMeshes.size(); ++j)
+ uniqueMeshes.insert(problems[i]->componentMeshes[j]);
+ problems[i]->meshes.clear();
+ problems[i]->meshes.insert(problems[i]->meshes.begin(), uniqueMeshes.begin(), uniqueMeshes.end());
+ }
+ }
- problems[i]->setComponentMesh(j, meshByName[meshName]);
+ /// Used in \ref initialize().
+ virtual void createFeSpace(DOFAdmin *admin) override
+ {
+ std::vector<std::set<FiniteElemSpace const*> > feSpacesForProblems(problems.size());
+ std::map<std::pair<Mesh*, std::string>, FiniteElemSpace*> feSpaceMap;
+
+ for (size_t p = 0; p < problems.size(); ++p) {
+ TEST_EXIT(problems[p])("problem[%d] does not exist!\n",p);
+
+ int nComponents = problems[p]->getNumComponents();
+
+ int nAddComponents = 0;
+ Parameters::get(problems[p]->getName() + "->additional components", nAddComponents);
+ problems[p]->componentSpaces.resize(nComponents + nAddComponents, NULL);
+ problems[p]->traverseInfo.resize(nComponents);
+
+ for (size_t i = 0; i < nComponents + nAddComponents; i++) {
+
+ std::string componentString = "[" + to_string(i) + "]";
+
+ std::string feSpaceName = "";
+ std::string initFileStr = problems[p]->getName() + "->feSpace" + componentString;
+ Parameters::get(initFileStr, feSpaceName);
+
+ // synonym for "feSpace"
+ if (feSpaceName.size() == 0) {
+ initFileStr = problems[p]->getName() + "->finite element space" + componentString;
+ Parameters::get(initFileStr, feSpaceName);
+ }
+
+ // for backward compatibility also accept the old syntax
+ if (feSpaceName.size() == 0) {
+ int degree = 1;
+ initFileStr = problems[p]->getName() + "->polynomial degree" + componentString;
+ Parameters::get(initFileStr, degree);
+ TEST_EXIT(degree > 0)
+ ("Poynomial degree in component %d must be larger than zero!\n", i);
+
+ feSpaceName = "Lagrange" + to_string(degree);
+ }
+
+ if (feSpaceName.size() == 0)
+ feSpaceName = "Lagrange1";
+
+ if (feSpaceMap[std::make_pair(problems[p]->componentMeshes[i], feSpaceName)] == NULL) {
+ BasisFunctionCreator *basisFctCreator =
+ dynamic_cast<BasisFunctionCreator*>(CreatorMap<BasisFunction>::getCreator(feSpaceName, initFileStr));
+ TEST_EXIT(basisFctCreator)
+ ("No valid basisfunction type found in parameter \"%s\"\n", initFileStr.c_str());
+ basisFctCreator->setDim(dim);
- // feSpace
- int degree = 1;
- Parameters::get(problems[i]->getName() + "->polynomial degree[" +
- boost::lexical_cast<std::string>(j) + "]", degree);
-
- if (feSpaceMap[std::pair<Mesh*, int>(meshByName[meshName], degree)] == NULL) {
- std::stringstream s;
- s << problems[i]->getName() << "->feSpace[" << j << "]";
-
FiniteElemSpace *newFeSpace =
- FiniteElemSpace::provideFeSpace(NULL, Lagrange::getLagrange(dim, degree),
- meshByName[meshName], s.str());
- feSpaceMap[std::pair<Mesh*, int>(meshByName[meshName], degree)] = newFeSpace;
+ FiniteElemSpace::provideFeSpace(admin, basisFctCreator->create(),
+ problems[p]->componentMeshes[i],
+ "FeSpace" + componentString + " (" + feSpaceName + ")");
+
+ feSpaceMap[std::make_pair(problems[p]->componentMeshes[i], feSpaceName)] = newFeSpace;
feSpaces.push_back(newFeSpace);
}
-
- // problems[i]->setComponentSpace(j, feSpaceMap[std::pair<Mesh*, int>(meshByName[meshName], degree)]);
+ problems[p]->componentSpaces[i] = feSpaceMap[std::make_pair(problems[p]->componentMeshes[i], feSpaceName)];
+ }
+
+ // copy unqiue set of meshes to problem[p]->meshes
+ std::set<FiniteElemSpace const*> uniqueFeSpaces;
+ for (size_t i = 0; i < problems[p]->componentSpaces.size(); ++i)
+ uniqueFeSpaces.insert(problems[p]->componentSpaces[i]);
+ problems[p]->feSpaces.clear();
+ problems[p]->feSpaces.insert(problems[p]->feSpaces.begin(), uniqueFeSpaces.begin(), uniqueFeSpaces.end());
+
+ // create traverseInfo
+ for (int i = 0; i < nComponents; i++) {
+ for (int j = 0; j < nComponents; j++)
+ problems[p]->traverseInfo.getMatrix(i, j).setFeSpace(problems[p]->componentSpaces[i], problems[p]->componentSpaces[j]);
+
+ problems[p]->traverseInfo.getVector(i).setFeSpace(problems[p]->componentSpaces[i]);
}
}
- for (size_t i = 0; i < problems.size(); i++) {
- std::vector<Mesh*> problemMeshes(meshesForProblems[i].begin(), meshesForProblems[i].end());
- problems[i]->setMeshes(problemMeshes);
- problems[i]->setRefinementManager(refinementManager);
- problems[i]->setCoarseningManager(coarseningManager);
- problems[i]->initialize(INIT_ALL - INIT_MESH);
- }
-
+ // create dof admin for vertex dofs if neccessary
for (size_t i = 0; i < meshes.size(); i++) {
- int globalRefinements = 0;
-
- // If AMDiS is compiled for parallel computations, the global refinements are
- // ignored here. Later, each rank will add the global refinements to its
- // private mesh.
- #ifndef HAVE_PARALLEL_DOMAIN_AMDIS
- Parameters::get(meshes[i]->getName() + "->global refinements",
- globalRefinements);
- #endif
-
- bool initMesh = initFlag.isSet(INIT_MESH);
-
- // Initialize the meshes if there is no serialization file.
- if (initMesh && meshes[i] && !(meshes[i]->isInitialized())) {
- meshes[i]->initialize();
- refinementManager->globalRefine(meshes[i], globalRefinements);
+ if (meshes[i]->getNumberOfDofs(VERTEX) == 0) {
+ DimVec<int> ln_dof(meshes[i]->getDim(), DEFAULT_VALUE, 0);
+ ln_dof[VERTEX] = 1;
+ meshes[i]->createDOFAdmin("vertex dofs", ln_dof);
}
}
}
- void createRefCoarseManager()
+ /// Used in \ref initialize().
+ virtual void createRefCoarseManager() override
{
FUNCNAME("CouplingProblemStat::createRefCoarseManager()");
-
- int dim = 0;
- Parameters::get(name + "->dim", dim);
- TEST_EXIT(dim)("No problem dimension specified for \"%s->dim\"!\n",
- name.c_str());
+ assert( dim > 0);
switch (dim) {
case 1:
@@ -194,20 +280,65 @@ namespace AMDiS {
default:
ERROR_EXIT("invalid dim!\n");
}
+
+ for (size_t p = 0; p < problems.size(); p++) {
+ problems[p]->setRefinementManager(refinementManager);
+ problems[p]->setCoarseningManager(coarseningManager);
+ }
+ }
+
+ /// Used in \ref initialize().
+ virtual void createMatricesAndVectors() override
+ {
+ for (size_t p = 0; p < problems.size(); ++p) {
+ assert( problems[p] );
+ problems[p]->createMatricesAndVectors();
+ }
+ }
+
+ /// Used in \ref initialize().
+ virtual void createSolver() override
+ {
+ for (size_t p = 0; p < problems.size(); ++p) {
+ assert( problems[p] );
+ problems[p]->createSolver();
+ }
}
+ /// Used in \ref initialize().
+ virtual void createEstimator() override
+ {
+ for (size_t p = 0; p < problems.size(); ++p) {
+ assert( problems[p] );
+ problems[p]->createEstimator();
+ }
+ }
+
+ /// Used in \ref initialize().
+ virtual void createMarker() override
+ {
+ for (size_t p = 0; p < problems.size(); ++p) {
+ assert( problems[p] );
+ problems[p]->createMarker();
+ }
+ }
+
+ /// Used in \ref initialize().
+ virtual void createFileWriter() override
+ {
+ for (size_t p = 0; p < problems.size(); ++p) {
+ assert( problems[p] );
+ problems[p]->createFileWriter();
+ }
+ }
+
+
/// Returns number of managed problems
virtual int getNumProblems()
{
return problems.size();
}
- /// Implementation of ProblemStatBase::getNumComponents()
- virtual int getNumComponents()
- {
- return nComponents;
- }
-
/** \brief
* Returns the problem with the given number. If only one problem
* is managed by this master problem, the number hasn't to be given.
@@ -223,64 +354,48 @@ namespace AMDiS {
return meshes[number];
}
- /// Returns \ref meshes
- inline std::vector<Mesh*> getMeshes()
- {
- return meshes;
- }
-
- /// Returns \ref refinementManager.
- inline RefinementManager* getRefinementManager(int comp = 0)
- {
- return refinementManager;
- }
-
- /// Returns \ref refinementManager.
- inline CoarseningManager* getCoarseningManager(int comp = 0)
- {
- return coarseningManager;
- }
-
- /// Returns the name of the problem
- inline virtual std::string getName()
- {
- return name;
- }
+ using super::getNumComponents;
+ using super::getRefinementManager;
+ using super::getCoarseningManager;
+ using super::getName;
protected:
- /// Name of this problem.
- std::string name;
-
- /// Number of problem components
- int nComponents;
-
- /** \brief
- * Number of problem meshes. If all components are defined on the same mesh,
- * this number is 1. Otherwise, this variable is the number of different meshes
- * within the problem.
- */
- int nMeshes;
-
- /// FE spaces of this problem.
- std::vector<FiniteElemSpace*> feSpaces;
-
- /// Meshes of this problem.
- std::vector<Mesh*> meshes;
-
- /** \brief
- * All actions of mesh refinement are performed by refinementManager.
- * If new refinement algorithms should be realized, one has to override
- * RefinementManager and give one instance of it to AdaptStationary.
- */
- 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;
+// /// Name of this problem.
+// std::string name;
+//
+// /// Number of problem components
+// int nComponents;
+
+ /// unqiue mesh-dimension for all problems
+ int dim;
+
+// /** \brief
+// * Number of problem meshes. If all components are defined on the same mesh,
+// * this number is 1. Otherwise, this variable is the number of different meshes
+// * within the problem.
+// */
+// int nMeshes;
+
+// /// FE spaces of this problem.
+// std::vector<FiniteElemSpace*> feSpaces;
+//
+// /// Meshes of this problem.
+// std::vector<Mesh*> meshes;
+
+// /** \brief
+// * All actions of mesh refinement are performed by refinementManager.
+// * If new refinement algorithms should be realized, one has to override
+// * RefinementManager and give one instance of it to AdaptStationary.
+// */
+// 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;
std::vector<ProblemStatType*> problems;
};
diff --git a/AMDiS/src/CouplingTimeInterface.h b/AMDiS/src/CouplingTimeInterface.h
index fe3187d7..be62c3ea 100644
--- a/AMDiS/src/CouplingTimeInterface.h
+++ b/AMDiS/src/CouplingTimeInterface.h
@@ -36,7 +36,7 @@ namespace AMDiS {
*
* \brief
*/
- class CouplingTimeInterface : public ProblemTimeInterface
+ class CouplingTimeInterface : public virtual ProblemTimeInterface
{
public:
void addTimeInterface(ProblemTimeInterface *interface)
diff --git a/AMDiS/src/DOFMatrix.h b/AMDiS/src/DOFMatrix.h
index f28f1f29..0a36a5a4 100644
--- a/AMDiS/src/DOFMatrix.h
+++ b/AMDiS/src/DOFMatrix.h
@@ -344,6 +344,16 @@ namespace AMDiS {
{
return nnzPerRow;
}
+
+ std::vector<DegreeOfFreedom>& getRowIndices()
+ {
+ return rowIndices;
+ }
+
+ std::vector<DegreeOfFreedom>& getColIndices()
+ {
+ return colIndices;
+ }
/// Writes the matrix to an output stream.
void serialize(std::ostream &out);
diff --git a/AMDiS/src/Debug.cc b/AMDiS/src/Debug.cc
index 85f3bf1d..dd6ebc7f 100644
--- a/AMDiS/src/Debug.cc
+++ b/AMDiS/src/Debug.cc
@@ -71,7 +71,7 @@ namespace AMDiS {
io::VtkWriter::writeFile(tmp, filename + lexical_cast<std::string>(myRank) + ".vtu",
io::VtkWriter::ASCII,
false,
- false);
+ false);
}
}
#endif
@@ -751,8 +751,7 @@ namespace AMDiS {
elInfo = stack.traverseNext(elInfo);
}
}
-
-
+
void testSortedDofs(Mesh *mesh, ElementIdxToDofs &elMap)
{
FUNCNAME("debug::dbgTestElementMap()");
@@ -797,6 +796,64 @@ namespace AMDiS {
}
+ void createNodeCoords(Mesh *mesh, ElementIdxToCoords& coords)
+ {
+ TraverseStack stack;
+ ElInfo *elInfo =
+ stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL | Mesh::FILL_COORDS);
+
+ while (elInfo) {
+ coords.insert(std::make_pair(elInfo->getElement()->getIndex(), elInfo->getCoords()));
+
+ elInfo = stack.traverseNext(elInfo);
+ }
+ }
+
+ void testNodeCoords(Mesh* mesh, ElementIdxToCoords& coords)
+ {
+ FUNCNAME("debug::testNodeCoords()");
+
+ int dim = mesh->getDim();
+
+ TraverseStack stack;
+ ElInfo *elInfo =
+ stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL | Mesh::FILL_COORDS);
+
+ while (elInfo) {
+ Element *el = elInfo->getElement();
+
+ FixVec<WorldVector<double>, VERTEX> elCoords = elInfo->getCoords();
+
+ for (size_t i = 0; i < (size_t)(size(elCoords)); i++)
+ for (size_t j = 0; j < (size_t)(mesh->getDim()); j++)
+ if(elCoords[i][j] != coords[el->getIndex()][i][j]) {
+
+ MSG("[DBG] Wrong coordnate on element = %d, vertex index = %d\n!", el->getIndex(), i);
+
+ switch (dim) {
+ case 2:
+ std::cout << "[DBG]: one coord is: ";
+ std::cout << "(" << elCoords[i][0] << ", " << elCoords[i][1]<< ") ";
+ std::cout << "another is: ";
+ std::cout << "(" << coords[el->getIndex()][i][0] << ", " << coords[el->getIndex()][i][1] << ")\n";
+ break;
+ case 3:
+ std::cout << "[DBG]: one coord is: ";
+ std::cout << "(" << elCoords[i][0] << ", " << elCoords[i][1]<< ", " << elCoords[i][2] << ") ";
+ std::cout << "another is: ";
+ std::cout << "(" << coords[el->getIndex()][i][0] << ", " << coords[el->getIndex()][i][1]
+ << ". " << coords[el->getIndex()][i][2] << ")\n";
+ break;
+ default:
+ ERROR_EXIT("What is this?\n");
+ }
+ ERROR_EXIT("Mesh vertex coords don't match!\n");
+ }
+
+ elInfo = stack.traverseNext(elInfo);
+ }
+ }
+
void sortDofs(const DegreeOfFreedom* dof0,
const DegreeOfFreedom* dof1,
const DegreeOfFreedom* dof2,
diff --git a/AMDiS/src/Debug.h b/AMDiS/src/Debug.h
index 51da6683..248c2f03 100644
--- a/AMDiS/src/Debug.h
+++ b/AMDiS/src/Debug.h
@@ -28,6 +28,7 @@
#include <set>
#include "AMDiS_fwd.h"
#include "Global.h"
+#include "FixVec.h"
namespace AMDiS {
@@ -41,6 +42,7 @@ namespace AMDiS {
};
typedef std::map<int, DofContainer> ElementIdxToDofs;
+ typedef std::map<int, FixVec<WorldVector<double>, VERTEX> > ElementIdxToCoords;
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
void writeLocalElementDofs(int rank,
@@ -185,6 +187,10 @@ namespace AMDiS {
void exportDofVectorByCoords(const DOFVector<double>* vec,
std::string filename);
+ void createNodeCoords(Mesh *mesh, ElementIdxToCoords& coords);
+
+ void testNodeCoords(Mesh* mesh, ElementIdxToCoords& coords);
+
/** \brief
* Traverse a mesh and store for each element all its vertex DOFs in local sorted
* order (by values).
diff --git a/AMDiS/src/ElInfo2d.cc b/AMDiS/src/ElInfo2d.cc
index 99b9ccf6..92054469 100644
--- a/AMDiS/src/ElInfo2d.cc
+++ b/AMDiS/src/ElInfo2d.cc
@@ -875,4 +875,4 @@ namespace AMDiS {
{
return getSubElemCoordsMat(degree);
}
-}
+}
\ No newline at end of file
diff --git a/AMDiS/src/Element.cc b/AMDiS/src/Element.cc
index ca37629e..a169d20c 100644
--- a/AMDiS/src/Element.cc
+++ b/AMDiS/src/Element.cc
@@ -67,6 +67,11 @@ namespace AMDiS {
elementData->deleteDecorated();
delete elementData;
}
+
+// if (dof) {
+// delete [] dof;
+// dof = NULL;
+// }
}
@@ -146,7 +151,8 @@ namespace AMDiS {
if (dof[j]) {
if (deletedDOFs.count(dof[j]) == 0) {
deletedDOFs[dof[j]] = true;
- delete [] dof[j];
+// delete [] dof[j];
+ mesh->freeDof(dof[j], position);
}
}
j++;
diff --git a/AMDiS/src/Lagrange.cc b/AMDiS/src/Lagrange.cc
index 283c32be..e1d273bd 100644
--- a/AMDiS/src/Lagrange.cc
+++ b/AMDiS/src/Lagrange.cc
@@ -1963,7 +1963,6 @@ namespace AMDiS {
RCNeighbourList* list,
int n, BasisFunction* basFct)
{
- FUNCNAME_DBG("Lagrange::refineInter4_3d");
if (n < 1)
return;
diff --git a/AMDiS/src/Mesh.cc b/AMDiS/src/Mesh.cc
index 31796081..41e7be70 100644
--- a/AMDiS/src/Mesh.cc
+++ b/AMDiS/src/Mesh.cc
@@ -89,6 +89,7 @@ namespace AMDiS {
vector<DegreeOfFreedom> Mesh::dof_used;
const int Mesh::MAX_DOF = 100;
map<pair<DegreeOfFreedom, int>, DegreeOfFreedom*> Mesh::serializedDOFs;
+ std::set<string> Mesh::refinedMeshNames;
Mesh::Mesh(string aName, int dimension)
: name(aName),
@@ -236,7 +237,7 @@ namespace AMDiS {
// for the vector index the corresponding element is stored in.
// 3. Get this element from macroElements, and set it as the i-th
// neighbour for the current element.
- if((*it)->getNeighbour(i)!=NULL) {
+ if ((*it)->getNeighbour(i)!=NULL) {
macroElements[insertCounter]->
setNeighbour(i, macroElements[mapIndex[(*it)->getNeighbour(i)->getIndex()]]);
}
@@ -275,6 +276,50 @@ namespace AMDiS {
me->setIndex(macroElements.size());
}
+ void Mesh::removeAllMacroElements()
+ {
+ // Delete all the dofs
+ Element::deletedDOFs.clear();
+ for (deque<MacroElement*>::const_iterator it = macroElements.begin();
+ it != macroElements.end(); ++it) {
+ (*it)->getElement()->deleteElementDOFs();
+ }
+ Element::deletedDOFs.clear();
+
+ // Set all neighbors null
+ for (deque<MacroElement*>::const_iterator macroIt = macroElements.begin();
+ macroIt != macroElements.end(); ++macroIt) {
+
+ for (int i = 0; i < getGeo(NEIGH); i++)
+ (*macroIt)->setNeighbour(i, NULL);
+
+ Element *mel = (*macroIt)->getElement();
+ // Delete element hierarchie
+ if (!(mel->isLeaf())) {
+ delete mel->getChild(0);
+ delete mel->getChild(1);
+
+ mel->child[0] = NULL;
+ mel->child[1] = NULL;
+
+ mel->setElementData(elementDataPrototype->clone());
+ }
+ }
+
+ macroElements.clear();
+ nLeaves = 0;
+ nElements = 0;
+ nVertices = 0;
+
+ for (size_t i = 0; i < admin.size(); i++)
+ {
+ TEST_EXIT_DBG(admin[i]->getUsedSize() == admin[i]->getHoleCount())
+ ("All macro elements has been removed. But not all dofs are cleaned. (UsedSize = %d, HoleCount = %d)\n",
+ admin[i]->getUsedSize(), admin[i]->getHoleCount());
+
+ admin[i]->reset();
+ }
+ }
void Mesh::removeMacroElements(std::set<MacroElement*>& delMacros,
vector<const FiniteElemSpace*>& feSpaces)
@@ -577,6 +622,7 @@ namespace AMDiS {
return;
delete [] ptrs;
+ ptrs = NULL;
}
@@ -1259,7 +1305,7 @@ namespace AMDiS {
Parameters::get("parallel->repartitioning->strategy", strategy);
- if(strategy && !preserveMacroFileInfo) {
+ if (strategy && !preserveMacroFileInfo) {
MSG("Preserve macroFileInfo.\n");
preserveMacroFileInfo = true;
}
@@ -1410,7 +1456,7 @@ namespace AMDiS {
RefinementManager *refManager;
if (dim == 2)
refManager = new RefinementManager2d();
- else if(dim == 3)
+ else if (dim == 3)
refManager = new RefinementManager3d();
else
{
@@ -1439,15 +1485,20 @@ namespace AMDiS {
// === We have refined the mesh, so reduce the number of global refinements. ===
- int globalRefinements = 0;
- Parameters::get(name + "->global refinements", globalRefinements);
+ // This is avoid to minus parallel prerefinement multiple times
+ if (refinedMeshNames.count(name + "->global refinements") == 0) {
+ refinedMeshNames.insert(name + "->global refinements");
+
+ int globalRefinements = 0;
+ Parameters::get(name + "->global refinements", globalRefinements);
- if (globalRefinements < nParallelPreRefinements)
- globalRefinements = 0;
- else
- globalRefinements -= nParallelPreRefinements;
+ if (globalRefinements < nParallelPreRefinements)
+ globalRefinements = 0;
+ else
+ globalRefinements -= nParallelPreRefinements;
- Parameters::set(name + "->global refinements", globalRefinements);
+ Parameters::set(name + "->global refinements", globalRefinements);
+ }
// === Print a note to the screen that another mesh file will be used. ===
diff --git a/AMDiS/src/Mesh.h b/AMDiS/src/Mesh.h
index 9df196c5..e40e79d1 100644
--- a/AMDiS/src/Mesh.h
+++ b/AMDiS/src/Mesh.h
@@ -405,6 +405,8 @@ namespace AMDiS {
/// elements have no children.
void removeMacroElements(std::set<MacroElement*>& macros,
std::vector<const FiniteElemSpace*>& feSpaces);
+
+ void removeAllMacroElements();
/// Frees the array of DOF pointers (see \ref createDofPtrs)
void freeDofPtrs(DegreeOfFreedom **ptrs);
@@ -494,6 +496,7 @@ namespace AMDiS {
* @param[out] coords DOF vector that stores the coordinates to each DOF.
*/
void getDofIndexCoords(DOFVector<WorldVector<double> >& coords);
+
/** \brief
* Traverse the mesh and get all DOFs in this mesh for a given FE space.
@@ -817,6 +820,8 @@ namespace AMDiS {
/// Used by check functions
static std::vector<DegreeOfFreedom> dof_used;
+
+ static std::set<std::string> refinedMeshNames;
/// This map is used for serialization and deserialization of mesh elements.
/// During the serialization process, all elements are visited and their
diff --git a/AMDiS/src/MeshStructure.cc b/AMDiS/src/MeshStructure.cc
index e5523539..b6b0b78f 100644
--- a/AMDiS/src/MeshStructure.cc
+++ b/AMDiS/src/MeshStructure.cc
@@ -90,12 +90,12 @@ namespace AMDiS {
}
- void MeshStructure::init(BoundaryObject &bound)
+ void MeshStructure::init(BoundaryObject &bound, Element* element)
{
FUNCNAME("MeshStructure::init()");
- Element *el = bound.el;
-
+ Element* el = (element == NULL) ? bound.el : element;
+
TEST_EXIT_DBG(el)("No element!\n");
clear();
@@ -454,7 +454,8 @@ namespace AMDiS {
void MeshStructure::getMeshStructureValues(int macroElIndex,
const DOFVector<double>* vec,
- std::vector<double>& values)
+ std::vector<double>& values,
+ bool withElIndex)
{
FUNCNAME_DBG("MeshStructure::getMeshStructureValues()");
@@ -465,10 +466,10 @@ namespace AMDiS {
int nVertexPreDofs = feSpace->getAdmin()->getNumberOfPreDofs(VERTEX);
bool feSpaceHasNonVertexDofs = (feSpace->getBasisFcts()->getDegree() > 1);
values.clear();
-#if (DEBUG != 0)
+
// In debug mode we add the macro element index to the value code.
- values.push_back(static_cast<double>(macroElIndex));
-#endif
+ if (withElIndex)
+ values.push_back(static_cast<double>(macroElIndex));
ElementDofIterator elDofIter(feSpace);
TraverseStack stack;
@@ -507,7 +508,8 @@ namespace AMDiS {
void MeshStructure::setMeshStructureValues(int macroElIndex,
DOFVector<double>* vec,
- const std::vector<double>& values)
+ const std::vector<double>& values,
+ bool withElIndex)
{
FUNCNAME_DBG("MeshStructure::setMeshStructureValues()");
@@ -518,12 +520,13 @@ namespace AMDiS {
bool feSpaceHasNonVertexDofs = (feSpace->getBasisFcts()->getDegree() > 1);
int nVertexPreDofs = feSpace->getAdmin()->getNumberOfPreDofs(VERTEX);
unsigned int counter = 0;
-#if (DEBUG != 0)
- TEST_EXIT(static_cast<int>(values[0]) == macroElIndex)
- ("Value structure code was created for macro element index %d, but should be set to macro element index %d\n",
- static_cast<int>(values[0]), macroElIndex);
- counter++;
-#endif
+
+ if (withElIndex) {
+ TEST_EXIT(static_cast<int>(values[0]) == macroElIndex)
+ ("Value structure code was created for macro element index %d, but should be set to macro element index %d\n",
+ static_cast<int>(values[0]), macroElIndex);
+ counter++;
+ }
TEST_EXIT_DBG(static_cast<int>(values.size()) >= mesh->getGeo(VERTEX))
("Should not happen!\n");
@@ -562,7 +565,8 @@ namespace AMDiS {
elInfo = stack.traverseNext(elInfo);
}
- TEST_EXIT_DBG(values.size() == counter)("Should not happen!\n");
+ TEST_EXIT_DBG(values.size() == counter)
+ ("Should not happen! values size %d, counter %d\n", values.size(), counter);
}
}
diff --git a/AMDiS/src/MeshStructure.h b/AMDiS/src/MeshStructure.h
index d8ab6efd..bfc211c9 100644
--- a/AMDiS/src/MeshStructure.h
+++ b/AMDiS/src/MeshStructure.h
@@ -32,6 +32,12 @@
#include "Global.h"
#include "BoundaryObject.h"
+#if (DEBUG != 0)
+#define WITH_ELINDEX true
+#else
+#define WITH_ELINDEX false
+#endif
+
namespace AMDiS {
class MeshStructure
@@ -60,7 +66,7 @@ namespace AMDiS {
*/
void init(Mesh *mesh, int macroElIndex = -1);
- void init(BoundaryObject &bound);
+ void init(BoundaryObject &bound, Element* mesh = NULL);
void init(const std::vector<uint64_t>& initCode, int n)
{
@@ -169,7 +175,8 @@ namespace AMDiS {
*/
void getMeshStructureValues(int macroElIndex,
const DOFVector<double>* vec,
- std::vector<double>& values);
+ std::vector<double>& values,
+ bool withElIndex = WITH_ELINDEX);
/** \brief
@@ -182,7 +189,8 @@ namespace AMDiS {
*/
void setMeshStructureValues(int macroElIndex,
DOFVector<double>* vec,
- const std::vector<double>& values);
+ const std::vector<double>& values,
+ bool withElIndex = WITH_ELINDEX);
/// Insert a new element to the structure code. Is used by the init function.
void insertElement(bool isLeaf);
diff --git a/AMDiS/src/ProblemStat.cc b/AMDiS/src/ProblemStat.cc
index ab2145b5..2e455797 100644
--- a/AMDiS/src/ProblemStat.cc
+++ b/AMDiS/src/ProblemStat.cc
@@ -59,6 +59,7 @@ namespace AMDiS {
: StandardProblemIteration(this),
name(nameStr),
nComponents(-1),
+ nAddComponents(0),
nMeshes(0),
traverseInfo(0),
solver(NULL),
@@ -77,8 +78,11 @@ namespace AMDiS {
buildTime(0.0)
{
Parameters::get(name + "->components", nComponents);
+ Parameters::get(name + "->additional components", nAddComponents);
TEST_EXIT(nComponents > 0)("No value set for parameter \"%s->components\"!\n",
name.c_str());
+ TEST_EXIT(nAddComponents >= 0)("Wrong parameter \"%s->additional components\"!\n",
+ name.c_str());
estimator.resize(nComponents, NULL);
marker.resize(nComponents, NULL);
@@ -121,6 +125,10 @@ namespace AMDiS {
if (solution)
delete solution;
solution = NULL;
+
+ if (solver)
+ delete solver;
+ solver = NULL;
if (systemMatrix) {
for (int i = 0; i < nComponents; i++)
@@ -152,8 +160,7 @@ namespace AMDiS {
marker[i] = NULL;
}
}
-
-
+
void ProblemStatSeq::initialize(Flag initFlag,
ProblemStatSeq *adoptProblem,
Flag adoptFlag)
@@ -175,7 +182,9 @@ namespace AMDiS {
adoptFlag.isSet(INIT_FE_SPACE))) {
meshes = adoptProblem->getMeshes();
componentMeshes = adoptProblem->componentMeshes;
-
+
+ TEST_EXIT(adoptProblem->getNumAddComponents() + nAddComponents > 0)
+ ("Not yet implemented.\n");
// If the adopt problem has fewer components than this problem, but only one
// mesh for all component, than scal up the componentMeshes array.
if (adoptProblem->getNumComponents() < nComponents) {
@@ -225,6 +234,9 @@ namespace AMDiS {
feSpaces = adoptProblem->getFeSpaces();
componentSpaces = adoptProblem->componentSpaces;
traverseInfo = adoptProblem->traverseInfo;
+
+ TEST_EXIT(adoptProblem->getNumAddComponents() + nAddComponents > 0)
+ ("Not yet implemented.\n");
// If the adopt problem has fewer components than this problem, but only one
// fe space for all component, than scal up the componentSpaces array.
@@ -376,8 +388,7 @@ namespace AMDiS {
void ProblemStatSeq::createMesh()
{
FUNCNAME("ProblemStat::createMesh()");
-
- componentMeshes.resize(nComponents);
+
map<int, Mesh*> meshForRefinementSet;
string meshName("");
@@ -389,8 +400,10 @@ namespace AMDiS {
Parameters::get(name + "->dim", dim);
TEST_EXIT(dim)("No problem dimension specified for \"%s->dim\"!\n",
name.c_str());
+
+ componentMeshes.resize(nComponents + nAddComponents);
- for (int i = 0; i < nComponents; i++) {
+ for (int i = 0; i < nComponents + nAddComponents; i++) {
int refSet = -1;
Parameters::get(name + "->refinement set[" + lexical_cast<string>(i) + "]",
refSet);
@@ -445,11 +458,14 @@ namespace AMDiS {
Parameters::get(name + "->dim", dim);
TEST_EXIT(dim != -1)("no problem dimension specified!\n");
- componentSpaces.resize(nComponents, NULL);
+ componentSpaces.resize(nComponents + nAddComponents, NULL);
traverseInfo.resize(nComponents);
- for (int i = 0; i < nComponents; i++) {
- TEST_EXIT(componentSpaces[i] == NULL)("feSpace already created\n");
+ for (int i = 0; i < nComponents + nAddComponents; i++) {
+ if (componentSpaces[i] != NULL) {
+ WARNING("feSpace already created\n");
+ continue;
+ }
string componentString = "[" + boost::lexical_cast<string>(i) + "]";
string feSpaceName = "";
@@ -791,7 +807,7 @@ namespace AMDiS {
int nMeshes = static_cast<int>(meshes.size());
Flag refineFlag = 0;
for (int i = 0; i < nMeshes; i++)
- if (adaptInfo->isRefinementAllowed(i))
+ if (i >= nComponents || adaptInfo->isRefinementAllowed(i))
refineFlag |= refinementManager->refineMesh(meshes[i]);
return refineFlag;
@@ -803,7 +819,7 @@ namespace AMDiS {
int nMeshes = static_cast<int>(meshes.size());
Flag coarsenFlag = 0;
for (int i = 0; i < nMeshes; i++)
- if (adaptInfo->isCoarseningAllowed(i))
+ if (i >= nComponents || adaptInfo->isCoarseningAllowed(i))
coarsenFlag |= coarseningManager->coarsenMesh(meshes[i]);
return coarsenFlag;
@@ -828,10 +844,6 @@ namespace AMDiS {
FUNCNAME("ProblemStat::buildAfterCoarsen()");
if (dualMeshTraverseRequired()) {
-#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
- ERROR_EXIT("Dual mesh assemble does not work in parallel code!\n");
-#endif
-
dualAssemble(adaptInfo, flag, asmMatrix, asmVector);
return;
}
@@ -1004,11 +1016,17 @@ namespace AMDiS {
FUNCNAME("ProblemStat::dualAssemble()");
TEST_EXIT(asmVector)("Not yet implemented!\n");
+
+ Timer t;
for (unsigned int i = 0; i < meshes.size(); i++)
meshes[i]->dofCompress();
-
- Timer t;
+
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ MPI::COMM_WORLD.Barrier();
+ INFO(info, 8)("dof compression needed %.5f seconds\n", t.elapsed());
+#endif
+ t.reset();
Flag assembleFlag =
flag |
@@ -1122,12 +1140,12 @@ namespace AMDiS {
dualTraverse.setFillSubElemMat(true, basisFcts);
bool cont = dualTraverse.traverseFirst(meshes[0], meshes[1], -1, -1,
assembleFlag, assembleFlag, dualElInfo);
-
+
while (cont) {
bool newEl0 = (dualElInfo.rowElInfo->getElement()->getIndex() != oldElIndex0);
bool newEl1 = (dualElInfo.colElInfo->getElement()->getIndex() != oldElIndex1);
oldElIndex0 = dualElInfo.rowElInfo->getElement()->getIndex();
- oldElIndex1 = dualElInfo.colElInfo->getElement()->getIndex();
+ oldElIndex1 = dualElInfo.colElInfo->getElement()->getIndex();
for (int i = 0; i < nComponents; i++) {
for (int j = 0; j < nComponents; j++) {
@@ -1151,9 +1169,11 @@ namespace AMDiS {
if (matrix)
matrix->assemble(1.0, elInfo, bound);
+
if (i == j)
rhs->getDOFVector(i)->assemble(1.0, elInfo, bound);
+
}
ElInfo *mainElInfo, *auxElInfo;
@@ -1171,11 +1191,11 @@ namespace AMDiS {
if (traverseInfo.difAuxSpace(i) && i == j)
rhs->getDOFVector(i)->assemble2(1.0, mainElInfo, auxElInfo,
dualElInfo.smallElInfo,
- dualElInfo.largeElInfo, bound);
+ dualElInfo.largeElInfo, bound);
if (traverseInfo.difAuxSpace(i, j) && matrix)
matrix->assemble2(1.0, mainElInfo, auxElInfo,
- dualElInfo.smallElInfo, dualElInfo.largeElInfo, bound);
+ dualElInfo.smallElInfo, dualElInfo.largeElInfo, bound);
if (matrix && matrix->getBoundaryManager())
matrix->getBoundaryManager()->fillBoundaryConditions(mainElInfo, matrix);
@@ -1206,16 +1226,17 @@ namespace AMDiS {
matrix->getBoundaryManager()->fillBoundaryConditions(rowElInfo, matrix);
}
- if (i == j)
+ if (i == j) {
+ ERROR_EXIT("In which case can this routine be reached??\n");
rhs->getDOFVector(i)->assemble(1.0, rowElInfo, bound);
- }
+ }
+ }
}
}
cont = dualTraverse.traverseNext(dualElInfo);
}
-
for (int i = 0; i < nComponents; i++) {
for (int j = 0; j < nComponents; j++) {
DOFMatrix *matrix = (asmMatrix ? (*systemMatrix)[i][j] : NULL);
@@ -1241,10 +1262,14 @@ namespace AMDiS {
solverMatrix.setMatrix(*systemMatrix);
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ MPI::COMM_WORLD.Barrier();
+#endif
INFO(info, 8)("fillin of assembled matrix: %d\n", nnz);
INFO(info, 8)("buildAfterCoarsen needed %.5f seconds\n",
t.elapsed());
+ buildTime = t.elapsed();
}
diff --git a/AMDiS/src/ProblemStat.h b/AMDiS/src/ProblemStat.h
index 03544cbc..f5492819 100644
--- a/AMDiS/src/ProblemStat.h
+++ b/AMDiS/src/ProblemStat.h
@@ -164,6 +164,11 @@ namespace AMDiS {
{
return nComponents;
}
+
+ virtual int getNumAddComponents()
+ {
+ return nAddComponents;
+ }
/// Returns the problem with the given number. If only one problem
/// is managed by this master problem, the number hasn't to be given.
@@ -327,7 +332,7 @@ namespace AMDiS {
{
FUNCNAME("ProblemStatSeq::getFeSpace()");
TEST_EXIT(comp < static_cast<int>(componentSpaces.size()) && comp >= 0)
- ("invalid component number\n");
+ ("invalid component number: %d\n", comp);
return componentSpaces[comp];
}
@@ -435,11 +440,16 @@ namespace AMDiS {
feSpaces[comp] = feSpace;
}
+ void setFeSpaces(std::vector<FiniteElemSpace const*> feSpaces_)
+ {
+ feSpaces = feSpaces_;
+ }
+
void setComponentSpace(int comp, const FiniteElemSpace *feSpace)
{
if (static_cast<int>(componentSpaces.size()) < nComponents)
componentSpaces.resize(nComponents);
- TEST_EXIT(comp >= 0 && comp < nComponents)
+ TEST_EXIT(comp >= 0 && comp < nComponents + nAddComponents)
("Component number not in feasable range!");
componentSpaces[comp] = feSpace;
@@ -515,7 +525,7 @@ namespace AMDiS {
{
if (static_cast<int>(componentMeshes.size()) < nComponents)
componentMeshes.resize(nComponents);
- TEST_EXIT(comp >= 0 && comp < nComponents)
+ TEST_EXIT(comp >= 0 && comp < nComponents + nAddComponents)
("Component number not in feasable range!");
componentMeshes[comp] = mesh;
@@ -570,6 +580,9 @@ namespace AMDiS {
/// Number of problem components
int nComponents;
+
+ /// Number of additional components
+ int nAddComponents;
/// Stores the names for all components. Is used for naming the solution
/// vectors, \ref solution.
@@ -677,6 +690,8 @@ namespace AMDiS {
double solutionTime;
double buildTime;
+
+ template <class> friend class detail::CouplingProblemStat;
};
#ifndef HAVE_PARALLEL_DOMAIN_AMDIS
diff --git a/AMDiS/src/RefinementManager3d.cc b/AMDiS/src/RefinementManager3d.cc
index 15a099e0..176b173d 100644
--- a/AMDiS/src/RefinementManager3d.cc
+++ b/AMDiS/src/RefinementManager3d.cc
@@ -40,7 +40,7 @@ using namespace std;
namespace AMDiS {
- FixRefinementPatch::ConnectedEdges FixRefinementPatch::connectedEdges(0);
+ map<Mesh*, FixRefinementPatch::ConnectedEdges> FixRefinementPatch::connectedEdges;
void RefinementManager3d::bisectTetrahedron(RCNeighbourList& refineList,
int index,
@@ -631,7 +631,9 @@ namespace AMDiS {
ElInfo* RefinementManager3d::refineFunction(ElInfo* elInfo)
{
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
FUNCNAME_DBG("RefinementManager3d::refineFunction()");
+#endif
Element *el = elInfo->getElement();
@@ -666,7 +668,7 @@ namespace AMDiS {
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
vector<FixRefinementPatch::EdgeInEl> refineEdges;
- FixRefinementPatch::getOtherEl(stack, refineEdges);
+ FixRefinementPatch::getOtherEl(mesh, stack, refineEdges);
// if (refineEdges.size()) {
// MSG("FIX REFINEMENT PATH ON ELEMENT %d %d: %d additional edges\n",
// elInfo->getElement()->getIndex(),
@@ -827,12 +829,13 @@ namespace AMDiS {
}
- void FixRefinementPatch::getOtherEl(TraverseStack *stack,
+ void FixRefinementPatch::getOtherEl(Mesh* mesh,
+ TraverseStack *stack,
vector<EdgeInEl>& refineEdges)
{
FUNCNAME_DBG("FixRefinementPatch::getOtherEl()");
- if (!FixRefinementPatch::connectedEdges.empty()) {
+ if (!FixRefinementPatch::connectedEdges[mesh].empty()) {
// === Get stack of current traverse. ===
vector<ElInfo*> elInfos;
vector<int> infos;
@@ -840,6 +843,8 @@ namespace AMDiS {
int checkIndex = stackUsed;
int localEdgeNo = 0;
ElInfo *elInfo = elInfos[stackUsed];
+
+ TEST_EXIT_DBG(elInfo->getMesh() == mesh)("Something is wrong.\n");
// === Calculate the refinement edge number on the macro element level. ===
@@ -880,11 +885,12 @@ namespace AMDiS {
refineEdges.clear();
- for (int i = 0; i < static_cast<int>(connectedEdges.size()); i++) {
- if (connectedEdges[i].first.first->getIndex() == macroElIndex &&
- connectedEdges[i].first.second == localEdgeNo) {
+ for (int i = 0; i < static_cast<int>(connectedEdges[mesh].size()); i++) {
+ TEST_EXIT_DBG(connectedEdges[mesh][i].first.first->getMesh() == mesh)("Something is wrong.\n");
+ if (connectedEdges[mesh][i].first.first->getIndex() == macroElIndex &&
+ connectedEdges[mesh][i].first.second == localEdgeNo) {
// We have found that this edge must be fixed.
- refineEdges.push_back(connectedEdges[i].second);
+ refineEdges.push_back(connectedEdges[mesh][i].second);
}
}
}
diff --git a/AMDiS/src/RefinementManager3d.h b/AMDiS/src/RefinementManager3d.h
index fe73a153..28993428 100644
--- a/AMDiS/src/RefinementManager3d.h
+++ b/AMDiS/src/RefinementManager3d.h
@@ -86,9 +86,10 @@ namespace AMDiS {
typedef std::pair<EdgeInEl, EdgeInEl> EdgesMap;
typedef std::vector<EdgesMap> ConnectedEdges;
- static ConnectedEdges connectedEdges;
+ static std::map<Mesh*, ConnectedEdges> connectedEdges;
- static void getOtherEl(TraverseStack *stack,
+ static void getOtherEl(Mesh* mesh,
+ TraverseStack *stack,
std::vector<EdgeInEl> &refineEdges);
};
diff --git a/AMDiS/src/StandardProblemIteration.h b/AMDiS/src/StandardProblemIteration.h
index 3ae5226f..f30d04e0 100644
--- a/AMDiS/src/StandardProblemIteration.h
+++ b/AMDiS/src/StandardProblemIteration.h
@@ -31,7 +31,7 @@
namespace AMDiS {
/// A master problem for a single non coupled problem.
- class StandardProblemIteration : public ProblemIterationInterface
+ class StandardProblemIteration : public virtual ProblemIterationInterface
{
public:
/// constructor
diff --git a/AMDiS/src/est/Estimator.cc b/AMDiS/src/est/Estimator.cc
index c723a2d3..f5cb5807 100644
--- a/AMDiS/src/est/Estimator.cc
+++ b/AMDiS/src/est/Estimator.cc
@@ -39,10 +39,12 @@ namespace AMDiS {
double Estimator::estimate(double ts)
- { FUNCNAME("Estimator::estimate()");
+ {
+// FUNCNAME("Estimator::estimate()");
+
bool dualTraverse = false;
-
+/*
for (unsigned int i = 0; i < matrix.size(); i++) {
TEST_EXIT(traverseInfo.getStatus(row, i) != SingleComponentInfo::DIF_SPACES_WITH_DIF_AUX)
("Not yet implemented!\n");
@@ -73,10 +75,10 @@ namespace AMDiS {
auxFeSpace->getBasisFcts()->getDegree())
("Mh, do you really want to do this? Think about it ...\n");
}
-
+*/
-// mesh = uh[row == -1 ? 0 : row]->getFeSpace()->getMesh();
-// auxMesh = NULL;
+ mesh = uh[row == -1 ? 0 : row]->getFeSpace()->getMesh();
+ auxMesh = NULL;
init(ts);
diff --git a/AMDiS/src/est/ResidualEstimator.cc b/AMDiS/src/est/ResidualEstimator.cc
index 3838d795..e0533247 100644
--- a/AMDiS/src/est/ResidualEstimator.cc
+++ b/AMDiS/src/est/ResidualEstimator.cc
@@ -165,7 +165,7 @@ namespace AMDiS {
secondOrderTerms[system] = secondOrderTerms[system] || (*it)->secondOrderTerms();
}
}
-
+
#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
initParallel();
#endif
@@ -180,7 +180,15 @@ namespace AMDiS {
if (C1 == 0.0)
return;
- DOFVector<WorldVector<double> > coords(uh[0]->getFeSpace(), "tmp");
+ size_t comp = 0;
+ for(; comp < uh.size(); comp++)
+ if(uh[comp]->getFeSpace()->getMesh() == mesh)
+ break;
+
+ TEST_EXIT_DBG(comp < uh.size())("No mesh in the solution is found?.\n");
+ TEST_EXIT_DBG(*(uh[comp]->getFeSpace()->getAdmin()) == mesh->getDofAdmin(0))("The admin is not the first one in the mesh.\n");
+
+ DOFVector<WorldVector<double> > coords(uh[comp]->getFeSpace(), "tmp");
mesh->getDofIndexCoords(coords);
Parallel::InteriorBoundary &intBoundary =
@@ -210,14 +218,16 @@ namespace AMDiS {
if (bObj.subObj == VERTEX)
continue;
+ bObj.el = intBoundary.getElementPtr(bObj.elIndex, mesh);
+ TEST_EXIT_DBG(bObj.el)("No element found in the map.\n");
bObj.el->getSubBoundary(bObj, subBound);
}
-
+
if (subBound.size() == 0)
continue;
WorldVector<int> faceIndices;
-
+
for (unsigned int i = 0; i < subBound.size(); i++) {
Element *el = subBound[i].el;
int oppV = subBound[i].ithObj;
@@ -229,7 +239,8 @@ namespace AMDiS {
double detNeigh = abs(elInfo->calcGrdLambda(*lambdaNeigh));
stdMpiDet.getSendData(it->first).push_back(detNeigh);
-
+
+
for (int system = 0; system < nSystems; system++) {
if (matrix[system] == NULL || secondOrderTerms[system] == false)
continue;
@@ -250,7 +261,7 @@ namespace AMDiS {
}
stdMpiDet.recv(it->first);
- stdMpiGrdUh.recv(it->first);
+ stdMpiGrdUh.recv(it->first);
}
stdMpiDet.updateSendDataSize();
@@ -258,7 +269,7 @@ namespace AMDiS {
stdMpiDet.startCommunication();
stdMpiGrdUh.startCommunication();
-
+
for (Parallel::RankToBoundMap::iterator it = allBounds.begin();
it != allBounds.end(); ++it) {
vector<BoundaryObject> subBound;
@@ -268,18 +279,22 @@ namespace AMDiS {
if (bObj.subObj == VERTEX)
continue;
+ bObj.el = intBoundary.getElementPtr(bObj.elIndex, mesh);
+ TEST_EXIT(bObj.el)("No element found in the map.\n");
bObj.el->getSubBoundary(bObj, subBound);
}
if (subBound.size() == 0)
continue;
-
+
+ // Highly possible mesh is not correct, for example: hanging node, if the following error occurs
// Highly possible mesh is not correct, for example: hanging node
TEST_EXIT_DBG(subBound.size() == stdMpiDet.getRecvData(it->first).size())
- ("Should not happen: %d %d from rank %d\n", subBound.size(), stdMpiDet.getRecvData(it->first).size(), it->first);
+ ("Should not happen: rank %d from rank %d should recv %d (recv %d)\n",
+ MPI::COMM_WORLD.Get_rank(), it->first, subBound.size(), stdMpiDet.getRecvData(it->first).size());
TEST_EXIT_DBG(subBound.size() == stdMpiGrdUh.getRecvData(it->first).size())
- ("Should not happen!\n");
+ ("Should not happen!\n");
for (unsigned int i = 0; i < subBound.size(); i++) {
elBoundDet[subBound[i]] = stdMpiDet.getRecvData(it->first)[i];
diff --git a/AMDiS/src/io/FileWriter.cc b/AMDiS/src/io/FileWriter.cc
index 67a6b4aa..cff618c9 100644
--- a/AMDiS/src/io/FileWriter.cc
+++ b/AMDiS/src/io/FileWriter.cc
@@ -155,7 +155,6 @@ namespace AMDiS
// vector<string> componentNames;
// for (unsigned int i = 0; i < dataCollectors.size(); i++)
// componentNames.push_back(dataCollectors[i]->getValues()->getName());
-
VtkWriter::detail::writeParallelFile(paraFilename + paraviewParallelFileExt,
MPI::COMM_WORLD.Get_size(),
filename,
@@ -163,7 +162,8 @@ namespace AMDiS
solutionNames,
VtkWriter::Vtuformat(paraViewMode),
(paraViewPrecision == 1),
- writeParaViewVectorFormat);
+ writeParaViewVectorFormat,
+ createSubDir > 0);
}
#endif
diff --git a/AMDiS/src/io/FileWriter.hh b/AMDiS/src/io/FileWriter.hh
index 1a98bf8d..ef9db694 100644
--- a/AMDiS/src/io/FileWriter.hh
+++ b/AMDiS/src/io/FileWriter.hh
@@ -263,3 +263,4 @@ namespace AMDiS
} // end namespace AMDiS
#endif
+
diff --git a/AMDiS/src/io/detail/VtkWriter.cc b/AMDiS/src/io/detail/VtkWriter.cc
index 1c049431..1d834f7a 100644
--- a/AMDiS/src/io/detail/VtkWriter.cc
+++ b/AMDiS/src/io/detail/VtkWriter.cc
@@ -207,15 +207,16 @@ namespace AMDiS { namespace io {
const vector<string> &componentNames,
::AMDiS::io::VtkWriter::Vtuformat format,
bool highPrecision,
- bool writeAsVector
+ bool writeAsVector,
+ bool createSubDir
)
{
using boost::lexical_cast;
vector< string > fileNames(nRanks);
- for (int i = 0; i < nRanks; i++) {
+ for (int i = 0; i < nRanks; i++)
fileNames[i] = fnPrefix + "-p" + lexical_cast<string>(i) + "-" + fnPostfix;
- }
- writeParallelFile(name, nRanks, fileNames, componentNames, format, highPrecision, writeAsVector);
+
+ writeParallelFile(name, nRanks, fileNames, componentNames, format, highPrecision, writeAsVector, createSubDir);
}
void writeParallelFile(string name, int nRanks,
@@ -223,11 +224,11 @@ namespace AMDiS { namespace io {
const vector<string> &componentNames,
::AMDiS::io::VtkWriter::Vtuformat format,
bool highPrecision,
- bool writeAsVector
+ bool writeAsVector,
+ bool createSubDir
)
{
FUNCNAME("writeParallelFile()");
-
using boost::lexical_cast;
#ifndef HAVE_COMPRESSION
@@ -296,9 +297,11 @@ namespace AMDiS { namespace io {
for (int i = 0; i < nRanks; i++) {
boost::filesystem::path filepath(subNames[i]);
- file << " <Piece Source=\""
- << boost::filesystem::basename(filepath)
- << boost::filesystem::extension(filepath) << "\"/>\n";
+ file << " <Piece Source=\"";
+ if (createSubDir)
+ file << "./data/";
+ file << boost::filesystem::basename(filepath)
+ << boost::filesystem::extension(filepath) << "\"/>\n";
}
file << " </PUnstructuredGrid>\n";
diff --git a/AMDiS/src/io/detail/VtkWriter.h b/AMDiS/src/io/detail/VtkWriter.h
index c01844c8..d65ebbf8 100644
--- a/AMDiS/src/io/detail/VtkWriter.h
+++ b/AMDiS/src/io/detail/VtkWriter.h
@@ -295,7 +295,8 @@ namespace AMDiS { namespace io {
const std::vector<std::string> &componentNames,
::AMDiS::io::VtkWriter::Vtuformat format = ::AMDiS::io::VtkWriter::ASCII,
bool highPrecision = false,
- bool writeAsVector = false
+ bool writeAsVector = false,
+ bool createSubDir = false
);
/// Writes a pvtu file which contains the links to the rank files in @subNames
@@ -304,7 +305,8 @@ namespace AMDiS { namespace io {
const std::vector<std::string> &componentNames,
::AMDiS::io::VtkWriter::Vtuformat format = ::AMDiS::io::VtkWriter::ASCII,
bool highPrecision = false,
- bool writeAsVector = false
+ bool writeAsVector = false,
+ bool createSubDir = false
);
/// Writes the connectivity for the case dim = 2 and degree = 2 to an output file.
diff --git a/AMDiS/src/parallel/DofComm.cc b/AMDiS/src/parallel/DofComm.cc
index 550adde7..2ce3c704 100644
--- a/AMDiS/src/parallel/DofComm.cc
+++ b/AMDiS/src/parallel/DofComm.cc
@@ -34,40 +34,58 @@ namespace AMDiS { namespace Parallel {
void DofComm::init(vector<const FiniteElemSpace*> &fe)
{
- FUNCNAME("DofComm::init()");
-
feSpaces = fe;
+ mesh = feSpaces[0]->getMesh();
sendDofs.clear();
recvDofs.clear();
periodicDofs.clear();
}
-
- void DofComm::create(InteriorBoundary &boundary)
+ void DofComm::create(Mesh* mesh, InteriorBoundary &boundary)
{
FUNCNAME("DofComm::create()");
+ TEST_EXIT(mesh == this->mesh) ("No equal mesh.\n");
- createContainer(boundary.getOwn(), sendDofs);
- createContainer(boundary.getOther(), recvDofs);
+ sendDofs.clear();
+ recvDofs.clear();
+ periodicDofs.clear();
+
+ createContainer(mesh, boundary, boundary.getOwn(), sendDofs);
+ createContainer(mesh, boundary, boundary.getOther(), recvDofs);
+
+#if (DEBUG != 0)
+ {
+ std::set<DegreeOfFreedom> sds;
+ for (DofComm::Iterator it(sendDofs, feSpaces[0]);
+ !it.end(); it.nextRank())
+ for (; !it.endDofIter(); it.nextDof())
+ sds.insert(it.getDofIndex());
+
+ for (DofComm::Iterator it2(recvDofs, feSpaces[0]);
+ !it2.end(); it2.nextRank())
+ for (; !it2.endDofIter(); it2.nextDof())
+ TEST_EXIT(!sds.count(it2.getDofIndex()))("Send and recv have same dofs.\n");
+ }
+#endif
}
- void DofComm::createContainer(RankToBoundMap &boundary,
+
+ void DofComm::createContainer(Mesh* mesh,
+ InteriorBoundary &boundary,
+ RankToBoundMap &rankToBoundMap,
DataType &data)
{
- FUNCNAME("DofComm::createContainer()");
-
// === Fill data. ===
for (unsigned int i = 0; i < feSpaces.size(); i++)
- for (InteriorBoundary::iterator it(boundary); !it.end(); ++it)
- it->rankObj.el->getAllDofs(feSpaces[i], it->rankObj,
- data[it.getRank()][feSpaces[i]]);
-
+ for (InteriorBoundary::iterator it(rankToBoundMap); !it.end(); ++it)
+ boundary.getElementPtr(it->rankObj.elIndex, mesh)
+ ->getAllDofs(feSpaces[i], it->rankObj, data[it.getRank()][feSpaces[i]]);
// === Remove empty data containers. ===
-
+
DataIter dit = data.begin();
while (dit != data.end()) {
FeMapIter it = dit->second.begin();
@@ -100,8 +118,6 @@ namespace AMDiS { namespace Parallel {
const FiniteElemSpace *feSpace,
bool countDouble)
{
- FUNCNAME("DofComm::getNumberDofs()");
-
DofContainerSet dofSet;
DofContainer dofVec;
@@ -127,8 +143,6 @@ namespace AMDiS { namespace Parallel {
int DofComm::getDegree(const FiniteElemSpace *feSpace,
const DegreeOfFreedom *dof)
{
- FUNCNAME("DofComm::getDegree()");
-
int degree = 0;
for (map<int, FeMapType>::iterator it = sendDofs.begin();
@@ -151,7 +165,7 @@ namespace AMDiS { namespace Parallel {
bool DofComm::Iterator::setNextFeMap()
{
- FUNCNAME("DofComm::Iterator::setNextFeMap()");
+ FUNCNAME_DBG("DofComm::Iterator::setNextFeMap()");
if (dataIter != data.end()) {
TEST_EXIT_DBG(dataIter->second.size())("Should not happen!\n");
@@ -182,21 +196,16 @@ namespace AMDiS { namespace Parallel {
void MultiLevelDofComm::init(MeshLevelData &levelData,
vector<const FiniteElemSpace*> &fe)
{
- FUNCNAME("MultiLevelDofComm::init()");
-
int nLevel = levelData.getNumberOfLevels();
for (int level = 0; level < nLevel; level++)
levelDofComm[level].init(fe);
}
-
- void MultiLevelDofComm::create(MultiLevelInteriorBoundary &boundary)
+ void MultiLevelDofComm::create(Mesh* mesh, MultiLevelInteriorBoundary &boundary)
{
- FUNCNAME("MultiLevelDofComm::create()");
-
for (map<int, DofComm>::iterator it = levelDofComm.begin();
it != levelDofComm.end(); ++it)
- it->second.create(boundary[it->first]);
+ it->second.create(mesh, boundary[it->first]);
}
} }
diff --git a/AMDiS/src/parallel/DofComm.h b/AMDiS/src/parallel/DofComm.h
index 40e290ef..c5fb2aff 100644
--- a/AMDiS/src/parallel/DofComm.h
+++ b/AMDiS/src/parallel/DofComm.h
@@ -46,7 +46,12 @@ namespace AMDiS { namespace Parallel {
void init(std::vector<const FiniteElemSpace*> &fe);
- void create(InteriorBoundary &boundary);
+ void create(Mesh* mesh, InteriorBoundary &boundary);
+
+ Mesh* getMesh()
+ {
+ return mesh;
+ }
DataType& getSendDofs()
{
@@ -74,7 +79,9 @@ namespace AMDiS { namespace Parallel {
const DegreeOfFreedom *dof);
protected:
- void createContainer(RankToBoundMap &boundary,
+ void createContainer(Mesh* mesh,
+ InteriorBoundary& boundary,
+ RankToBoundMap& rankToBoundMap,
DataType &data);
protected:
@@ -95,6 +102,8 @@ namespace AMDiS { namespace Parallel {
std::vector<const FiniteElemSpace*> feSpaces;
+ Mesh* mesh;
+
friend class Iterator;
public:
@@ -243,10 +252,11 @@ namespace AMDiS { namespace Parallel {
class MultiLevelDofComm {
public:
- void init(MeshLevelData &levelData,
- std::vector<const FiniteElemSpace*> &fe);
+ void init(MeshLevelData &levelData,
+ std::vector<const FiniteElemSpace*> &fe);
- void create(MultiLevelInteriorBoundary &boundary);
+ void create(Mesh* mesh, MultiLevelInteriorBoundary &boundary);
+
inline DofComm& operator[](int level)
{
diff --git a/AMDiS/src/parallel/ElementObjectDatabase.cc b/AMDiS/src/parallel/ElementObjectDatabase.cc
index 238aabbb..85fa644b 100644
--- a/AMDiS/src/parallel/ElementObjectDatabase.cc
+++ b/AMDiS/src/parallel/ElementObjectDatabase.cc
@@ -22,12 +22,24 @@
#include "VertexVector.h"
#include "parallel/ElementObjectDatabase.h"
#include "parallel/MeshLevelData.h"
+#include <fstream>
#include "Serializer.h"
using namespace std;
namespace AMDiS { namespace Parallel {
+
+ void ElementObjectDatabase::init(vector<Mesh*>& meshes_,
+ map<Mesh*, vector<const FiniteElemSpace*> >& meshToFeSpaces)
+ {
+ meshes = meshes_;
+ for(size_t i = 0; i < meshes.size(); i++)
+ feSpaces.push_back(meshToFeSpaces[meshes[i]][0]);
+
+ macroMesh = meshes[0];
+ feSpace = meshToFeSpaces[macroMesh][0];
+ }
void ElementObjectData::serialize(std::ostream &out) const
{
@@ -45,40 +57,50 @@ namespace AMDiS { namespace Parallel {
void ElementObjectDatabase::create(map<int, int>& rankMap, MeshLevelData& ld)
{
- FUNCNAME("ElementObjectDatabase::create()");
+ FUNCNAME_DBG("ElementObjectDatabase::create()");
macroElementRankMap = &rankMap;
levelData = &ld;
-
// === Reset temporary data ===
tmpVertexElements.clear();
tmpEdgeElements.clear();
tmpFaceElements.clear();
-
// === Fills macro element data structures. ===
TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(mesh, -1,
- Mesh::CALL_LEAF_EL |
- Mesh::FILL_NEIGH |
- Mesh::FILL_BOUND);
- while (elInfo) {
- TEST_EXIT_DBG(elInfo->getLevel() == 0)("Should not happen!\n");
-
- Element *el = elInfo->getElement();
- macroElIndexMap.insert(make_pair(el->getIndex(), el));
- macroElIndexTypeMap.insert(make_pair(el->getIndex(), elInfo->getType()));
-
- // Add all sub object of the element to the variable elObjDb.
- addElement(elInfo);
-
- elInfo = stack.traverseNext(elInfo);
- }
-
+ ElInfo* elInfo = NULL;
+
+ for(size_t i = 0; i < meshes.size(); i++) {
+
+ elInfo = stack.traverseFirst(meshes[i], -1,
+ Mesh::CALL_LEAF_EL |
+ Mesh::FILL_NEIGH |
+ Mesh::FILL_BOUND);
+ while (elInfo) {
+ TEST_EXIT_DBG(elInfo->getLevel() == 0)("Should not happen!\n");
+
+ Element *el = elInfo->getElement();
+
+ // Macro data info is stored once.
+ if (i == 0) {
+ macroElIndexTypeMap.insert(make_pair(el->getIndex(), elInfo->getType()));
+
+ // Add all sub object of the element to the variable elObjDb.
+ addElement(el);
+
+ addElementPeriodicBoundary(elInfo);
+ }
+ // Element pointer has to be stored for each mesh one copy.
+ macroElIndexMap[el->getIndex()][meshes[i]] = el;
+
+ elInfo = stack.traverseNext(elInfo);
+ }
+ }
+
// === Move temporary data to original one ===
for (map<DegreeOfFreedom, vector<ElementObjectData> >::iterator it = tmpVertexElements.begin();
@@ -96,38 +118,33 @@ namespace AMDiS { namespace Parallel {
faceElements[it->first] = it->second;
tmpFaceElements.clear();
-
-
// Handle periodic boudaries
createPeriodicData();
// Create data about the reverse modes of neighbouring elements.
createReverseModeData();
}
-
-
- void ElementObjectDatabase::createMacroElementInfo(vector<MacroElement*> &mel)
+
+ void ElementObjectDatabase::createMacroElementInfo(std::map<Mesh*, std::vector<MacroElement*> >& mel)
{
macroElIndexMap.clear();
macroElIndexTypeMap.clear();
-
- for (vector<MacroElement*>::iterator it = mel.begin();
- it != mel.end(); ++it) {
- macroElIndexMap.insert(make_pair((*it)->getIndex(), (*it)->getElement()));
- macroElIndexTypeMap.insert(make_pair((*it)->getIndex(), (*it)->getElType()));
+
+ std::map<Mesh*, std::vector<MacroElement*> >::iterator iter = mel.begin();
+ while(iter != mel.end()) {
+ Mesh* mesh = iter->first;
+ for (vector<MacroElement*>::iterator it = iter->second.begin();
+ it != iter->second.end(); it++) {
+ macroElIndexMap[(*it)->getIndex()][mesh] = (*it)->getElement();
+ if(iter == mel.begin())
+ macroElIndexTypeMap.insert(make_pair((*it)->getIndex(), (*it)->getElType()));
+ }
+ iter++;
}
}
-
- void ElementObjectDatabase::addElement(ElInfo *elInfo)
+ void ElementObjectDatabase::addElement(Element *el)
{
- FUNCNAME("ElementObjectDatabase::addElement()");
-
- TEST_EXIT_DBG(mesh)("Mesh not set!\n");
-
- Element *el = elInfo->getElement();
-
-
// === First, add all element objects to the database. ===
for (int i = 0; i < el->getGeo(VERTEX); i++)
@@ -138,14 +155,20 @@ namespace AMDiS { namespace Parallel {
for (int i = 0; i < el->getGeo(FACE); i++)
addFace(el, i);
+ }
+
+ void ElementObjectDatabase::addElementPeriodicBoundary(ElInfo* elInfo)
+ {
+ FUNCNAME("ElementObjectDatabase::addElementPeriodicBoundary()");
+ TEST_EXIT_DBG(macroMesh)("Mesh not set!\n");
- // === Get periodic boundary information. ===
+ Element *el = elInfo->getElement();
- switch (mesh->getDim()) {
+ switch (macroMesh->getDim()) {
case 2:
for (int i = 0; i < el->getGeo(EDGE); i++) {
- if (mesh->isPeriodicAssociation(elInfo->getBoundary(EDGE, i))) {
+ if (macroMesh->isPeriodicAssociation(elInfo->getBoundary(EDGE, i))) {
// The current element's i-th edge is periodic.
Element *neigh = elInfo->getNeighbour(i);
@@ -161,9 +184,9 @@ namespace AMDiS { namespace Parallel {
// Add both vertices of the edge to be periodic.
DegreeOfFreedom mappedDof0 =
- mesh->getPeriodicAssociations(boundaryType)[edge0.first];
+ macroMesh->getPeriodicAssociations(boundaryType)[edge0.first];
DegreeOfFreedom mappedDof1 =
- mesh->getPeriodicAssociations(boundaryType)[edge0.second];
+ macroMesh->getPeriodicAssociations(boundaryType)[edge0.second];
periodicVertices[make_pair(edge0.first, mappedDof0)] = boundaryType;
periodicVertices[make_pair(edge0.second, mappedDof1)] = boundaryType;
@@ -174,7 +197,7 @@ namespace AMDiS { namespace Parallel {
break;
case 3:
for (int i = 0; i < el->getGeo(FACE); i++) {
- if (mesh->isPeriodicAssociation(elInfo->getBoundary(FACE, i))) {
+ if (macroMesh->isPeriodicAssociation(elInfo->getBoundary(FACE, i))) {
// The current element's i-th face is periodic.
Element *neigh = elInfo->getNeighbour(i);
@@ -189,11 +212,11 @@ namespace AMDiS { namespace Parallel {
/// Add all three vertices of the face to be periodic.
DegreeOfFreedom mappedDof0 =
- mesh->getPeriodicAssociations(boundaryType)[face0.get<0>()];
+ macroMesh->getPeriodicAssociations(boundaryType)[face0.get<0>()];
DegreeOfFreedom mappedDof1 =
- mesh->getPeriodicAssociations(boundaryType)[face0.get<1>()];
+ macroMesh->getPeriodicAssociations(boundaryType)[face0.get<1>()];
DegreeOfFreedom mappedDof2 =
- mesh->getPeriodicAssociations(boundaryType)[face0.get<2>()];
+ macroMesh->getPeriodicAssociations(boundaryType)[face0.get<2>()];
periodicVertices[make_pair(face0.get<0>(), mappedDof0)] = boundaryType;
periodicVertices[make_pair(face0.get<1>(), mappedDof1)] = boundaryType;
@@ -204,11 +227,11 @@ namespace AMDiS { namespace Parallel {
periodicDofAssoc[face0.get<2>()].insert(boundaryType);
TEST_EXIT_DBG(face0.get<0>() ==
- mesh->getPeriodicAssociations(boundaryType)[face1.get<0>()] &&
+ macroMesh->getPeriodicAssociations(boundaryType)[face1.get<0>()] &&
face0.get<1>() ==
- mesh->getPeriodicAssociations(boundaryType)[face1.get<1>()] &&
+ macroMesh->getPeriodicAssociations(boundaryType)[face1.get<1>()] &&
face0.get<2>() ==
- mesh->getPeriodicAssociations(boundaryType)[face1.get<2>()])
+ macroMesh->getPeriodicAssociations(boundaryType)[face1.get<2>()])
("Should not happen!\n");
// Create all three edges of the element and add them to be periodic.
@@ -231,7 +254,8 @@ namespace AMDiS { namespace Parallel {
break;
default:
ERROR_EXIT("Should not happen!\n");
- }
+ }
+
}
@@ -248,8 +272,6 @@ namespace AMDiS { namespace Parallel {
void ElementObjectDatabase::addEdge(Element *el, int ith)
{
- FUNCNAME("ElementObjectDatabase::addEdge()");
-
DofEdge edge = el->getEdge(ith);
int elIndex = el->getIndex();
ElementObjectData elObj(elIndex, ith);
@@ -272,9 +294,9 @@ namespace AMDiS { namespace Parallel {
void ElementObjectDatabase::createPeriodicData()
{
- FUNCNAME("ElementObjectDatabase::createPeriodicData()");
+ FUNCNAME_DBG("ElementObjectDatabase::createPeriodicData()");
- TEST_EXIT_DBG(mesh)("Mesh not set!\n");
+ TEST_EXIT_DBG(macroMesh)("Mesh not set!\n");
// === Return, if there are no periodic vertices, i.e., there are no ===
// === periodic boundaries in the mesh. ===
@@ -285,8 +307,8 @@ namespace AMDiS { namespace Parallel {
// === Calculate smallest periodic boundary ID in mesh. ===
smallestPeriodicBcType = 0;
- for (map<BoundaryType, VertexVector*>::iterator it = mesh->getPeriodicAssociations().begin();
- it != mesh->getPeriodicAssociations().end(); ++it)
+ for (map<BoundaryType, VertexVector*>::iterator it = macroMesh->getPeriodicAssociations().begin();
+ it != macroMesh->getPeriodicAssociations().end(); ++it)
smallestPeriodicBcType = std::min(smallestPeriodicBcType, it->first);
// === Get all vertex DOFs that have multiple periodic associations. ===
@@ -299,8 +321,8 @@ namespace AMDiS { namespace Parallel {
vector<DegreeOfFreedom> multPeriodicDof2, multPeriodicDof3;
for (map<DegreeOfFreedom, std::set<BoundaryType> >::iterator it = periodicDofAssoc.begin();
it != periodicDofAssoc.end(); ++it) {
- TEST_EXIT_DBG((mesh->getDim() == 2 && it->second.size() <= 2) ||
- (mesh->getDim() == 3 && it->second.size() <= 3))
+ TEST_EXIT_DBG((macroMesh->getDim() == 2 && it->second.size() <= 2) ||
+ (macroMesh->getDim() == 3 && it->second.size() <= 3))
("Should not happen!\n");
if (it->second.size() == 2)
@@ -309,14 +331,14 @@ namespace AMDiS { namespace Parallel {
multPeriodicDof3.push_back(it->first);
}
- if (mesh->getDim() == 2) {
+ if (macroMesh->getDim() == 2) {
TEST_EXIT_DBG(multPeriodicDof2.size() == 0 ||
multPeriodicDof2.size() == 4)
("Should not happen (%d)!\n", multPeriodicDof2.size());
TEST_EXIT_DBG(multPeriodicDof3.size() == 0)("Should not happen!\n");
}
- if (mesh->getDim() == 3) {
+ if (macroMesh->getDim() == 3) {
TEST_EXIT_DBG(multPeriodicDof3.size() == 0 ||
multPeriodicDof3.size() == 8)
("Should not happen (%d)!\n", multPeriodicDof3.size());
@@ -401,7 +423,7 @@ namespace AMDiS { namespace Parallel {
for (map<DofEdge, std::set<DofEdge> >::iterator it = periodicEdgeAssoc.begin();
it != periodicEdgeAssoc.end(); ++it) {
if (it->second.size() > 1) {
- TEST_EXIT_DBG(mesh->getDim() == 3)("Should not happen!\n");
+ TEST_EXIT_DBG(macroMesh->getDim() == 3)("Should not happen!\n");
TEST_EXIT_DBG(it->second.size() == 2)("Should not happen!\n");
DofEdge edge0 = it->first;
@@ -462,31 +484,31 @@ namespace AMDiS { namespace Parallel {
#endif
}
-
BoundaryType ElementObjectDatabase::getNewBoundaryType()
{
- FUNCNAME("ElementObjectDatabase::getNewBoundaryType()");
+ FUNCNAME_DBG("ElementObjectDatabase::getNewBoundaryType()");
BoundaryType newPeriodicBoundaryType = 0;
- for (map<BoundaryType, VertexVector*>::iterator it = mesh->getPeriodicAssociations().begin();
- it != mesh->getPeriodicAssociations().end(); ++it)
+ for (map<BoundaryType, VertexVector*>::iterator it = macroMesh->getPeriodicAssociations().begin();
+ it != macroMesh->getPeriodicAssociations().end(); ++it)
newPeriodicBoundaryType = std::min(newPeriodicBoundaryType, it->first);
TEST_EXIT_DBG(newPeriodicBoundaryType < 0)("Should not happen!\n");
newPeriodicBoundaryType--;
- mesh->getPeriodicAssociations()[newPeriodicBoundaryType] =
- new VertexVector(feSpace->getAdmin(), "");
-
+ for(size_t i = 0; i < meshes.size(); i++) {
+ meshes[i]->getPeriodicAssociations()[newPeriodicBoundaryType] =
+ new VertexVector(feSpaces[i]->getAdmin(), "");
+ }
+
return newPeriodicBoundaryType;
}
-
-
+
BoundaryType
ElementObjectDatabase::provideConnectedPeriodicBoundary(BoundaryType b0,
BoundaryType b1)
{
- FUNCNAME("ElementObjectDatabase::provideConnectedPeriodicBoundary()");
+ FUNCNAME_DBG("ElementObjectDatabase::provideConnectedPeriodicBoundary()");
std::pair<BoundaryType, BoundaryType> bConn =
(b0 <= b1 ? make_pair(b0, b1) : make_pair(b1, b0));
@@ -494,25 +516,27 @@ namespace AMDiS { namespace Parallel {
if (bConnMap.count(bConn) == 0) {
BoundaryType newPeriodicBoundaryType = getNewBoundaryType();
- VertexVector &vecB0 = mesh->getPeriodicAssociations(b0);
- VertexVector &vecB1 = mesh->getPeriodicAssociations(b1);
- VertexVector &vecC = mesh->getPeriodicAssociations(newPeriodicBoundaryType);
+ for(size_t i = 0; i < meshes.size(); i++) {
+
+ VertexVector &vecB0 = meshes[i]->getPeriodicAssociations(b0);
+ VertexVector &vecB1 = meshes[i]->getPeriodicAssociations(b1);
+ VertexVector &vecC = meshes[i]->getPeriodicAssociations(newPeriodicBoundaryType);
- DOFIteratorBase it(const_cast<DOFAdmin*>(feSpace->getAdmin()), USED_DOFS);
+ DOFIteratorBase it(const_cast<DOFAdmin*>(feSpaces[i]->getAdmin()), USED_DOFS);
- for (it.reset(); !it.end(); ++it) {
- if (!it.isDofFree()) {
- TEST_EXIT_DBG(vecB1[vecB0[it.getDOFIndex()]] == vecB0[vecB1[it.getDOFIndex()]])
- ("Should not happen!\n");
+ for (it.reset(); !it.end(); ++it) {
+ if (!it.isDofFree()) {
+ TEST_EXIT_DBG(vecB1[vecB0[it.getDOFIndex()]] == vecB0[vecB1[it.getDOFIndex()]])
+ ("Should not happen!\n");
- vecC[it.getDOFIndex()] = vecB1[vecB0[it.getDOFIndex()]];
+ vecC[it.getDOFIndex()] = vecB1[vecB0[it.getDOFIndex()]];
+ }
}
}
bConnMap[bConn] = newPeriodicBoundaryType;
}
-
-
+
return bConnMap[bConn];
}
@@ -560,8 +584,6 @@ namespace AMDiS { namespace Parallel {
void ElementObjectDatabase::clear()
{
- FUNCNAME("ElementObjectDatabase::clear()");
-
vertexElements.clear();
edgeElements.clear();
faceElements.clear();
@@ -592,11 +614,11 @@ namespace AMDiS { namespace Parallel {
void ElementObjectDatabase::createReverseModeData()
{
- FUNCNAME("ElementObjectDatabase::createReverseModeData()");
+ FUNCNAME_DBG("ElementObjectDatabase::createReverseModeData()");
// === In 2D, all reverse modes are always true! ===
- if (mesh->getDim() == 2)
+ if (macroMesh->getDim() == 2)
return;
@@ -608,12 +630,12 @@ namespace AMDiS { namespace Parallel {
vector<ElementObjectData>& els = edgeIt->second;
for (unsigned int i = 0; i < els.size(); i++) {
- BoundaryObject obj0(macroElIndexMap[els[i].elIndex],
+ BoundaryObject obj0(macroElIndexMap[els[i].elIndex][macroMesh],
macroElIndexTypeMap[els[i].elIndex],
EDGE, els[i].ithObject);
for (unsigned int j = i + 1; j < els.size(); j++) {
- BoundaryObject obj1(macroElIndexMap[els[j].elIndex],
+ BoundaryObject obj1(macroElIndexMap[els[j].elIndex][macroMesh],
macroElIndexTypeMap[els[j].elIndex],
EDGE, els[j].ithObject);
@@ -633,12 +655,12 @@ namespace AMDiS { namespace Parallel {
vector<ElementObjectData>& els = faceIt->second;
for (unsigned int i = 0; i < els.size(); i++) {
- BoundaryObject obj0(macroElIndexMap[els[i].elIndex],
+ BoundaryObject obj0(macroElIndexMap[els[i].elIndex][macroMesh],
macroElIndexTypeMap[els[i].elIndex],
FACE, els[i].ithObject);
for (unsigned int j = i + 1; j < els.size(); j++) {
- BoundaryObject obj1(macroElIndexMap[els[j].elIndex],
+ BoundaryObject obj1(macroElIndexMap[els[j].elIndex][macroMesh],
macroElIndexTypeMap[els[j].elIndex],
FACE, els[j].ithObject);
@@ -661,12 +683,12 @@ namespace AMDiS { namespace Parallel {
vector<ElementObjectData> &edges1 = edgeElements[edgeIt->first.second];
for (unsigned int i = 0; i < edges0.size(); i++) {
- BoundaryObject obj0(macroElIndexMap[edges0[i].elIndex],
+ BoundaryObject obj0(macroElIndexMap[edges0[i].elIndex][macroMesh],
macroElIndexTypeMap[edges0[i].elIndex],
EDGE, edges0[i].ithObject);
for (unsigned int j = 0; j < edges1.size(); j++) {
- BoundaryObject obj1(macroElIndexMap[edges1[j].elIndex],
+ BoundaryObject obj1(macroElIndexMap[edges1[j].elIndex][macroMesh],
macroElIndexTypeMap[edges1[j].elIndex],
EDGE, edges1[j].ithObject);
@@ -686,12 +708,12 @@ namespace AMDiS { namespace Parallel {
vector<ElementObjectData> &faces0 = faceElements[faceIt->first.first];
vector<ElementObjectData> &faces1 = faceElements[faceIt->first.second];
- TEST_EXIT_DBG(faces0.size() == faces1.size() == 1)("Should not happen!\n");
+ TEST_EXIT_DBG((faces0.size() == 1) && (faces1.size() == 1))("Should not happen!\n");
- BoundaryObject obj0(macroElIndexMap[faces0[0].elIndex],
+ BoundaryObject obj0(macroElIndexMap[faces0[0].elIndex][macroMesh],
macroElIndexTypeMap[faces0[0].elIndex],
FACE, faces0[0].ithObject);
- BoundaryObject obj1(macroElIndexMap[faces1[0].elIndex],
+ BoundaryObject obj1(macroElIndexMap[faces1[0].elIndex][macroMesh],
macroElIndexTypeMap[faces1[0].elIndex],
FACE, faces1[0].ithObject);
@@ -751,7 +773,7 @@ namespace AMDiS { namespace Parallel {
int ElementObjectDatabase::getOwner(vector<ElementObjectData>& objData,
int level)
{
- FUNCNAME("ElementObjectDatabase::getOwner()");
+ FUNCNAME_DBG("ElementObjectDatabase::getOwner()");
int owner = -1;
@@ -826,8 +848,6 @@ namespace AMDiS { namespace Parallel {
void ElementObjectDatabase::serialize(ostream &out)
{
- FUNCNAME("ElementObjectDatabase::serialize()");
-
int nSize = vertexElements.size();
SerUtil::serialize(out, nSize);
for (flat_map<DegreeOfFreedom, vector<ElementObjectData> >::iterator it = vertexElements.begin();
@@ -946,8 +966,6 @@ namespace AMDiS { namespace Parallel {
void ElementObjectDatabase::deserialize(istream &in)
{
- FUNCNAME("ElementObjectDatabase::deserialize()");
-
int nSize;
SerUtil::deserialize(in, nSize);
vertexElements.clear();
@@ -1142,7 +1160,7 @@ namespace AMDiS { namespace Parallel {
}
}
-
+ //TODO: 047 not yet reimplemented.
unsigned long ElementObjectDatabase::calculateMemoryUsage()
{
FUNCNAME("ElementObjectDatabase::calculateMemoryUsage()");
diff --git a/AMDiS/src/parallel/ElementObjectDatabase.h b/AMDiS/src/parallel/ElementObjectDatabase.h
index 2e5fed1b..f2355ab8 100644
--- a/AMDiS/src/parallel/ElementObjectDatabase.h
+++ b/AMDiS/src/parallel/ElementObjectDatabase.h
@@ -38,6 +38,7 @@
//#include "Serializer.h"
#include "FiniteElemSpace.h"
#include "Mesh.h"
+#include "parallel/ParallelTypes.h"
namespace AMDiS { namespace Parallel {
@@ -102,21 +103,18 @@ namespace AMDiS { namespace Parallel {
public:
ElementObjectDatabase()
: feSpace(NULL),
- mesh(NULL),
+ macroMesh(NULL),
iterGeoPos(CENTER),
macroElementRankMap(NULL),
levelData(NULL)
{}
-
- void setFeSpace(const FiniteElemSpace *fe)
- {
- feSpace = fe;
- mesh = feSpace->getMesh();
- }
+
+ void init(std::vector<Mesh*>&,
+ std::map<Mesh*, std::vector<const FiniteElemSpace*> >&);
Mesh* getMesh()
{
- return mesh;
+ return macroMesh;
}
/*
@@ -126,7 +124,7 @@ namespace AMDiS { namespace Parallel {
void create(std::map<int, int>& macroElementRankMap,
MeshLevelData& levelData);
- void createMacroElementInfo(std::vector<MacroElement*> &mel);
+ void createMacroElementInfo(std::map<Mesh*, std::vector<MacroElement*> >& mel);
/// Create for a filled object database the membership information for all
/// element objects. An object is owned by a rank, if the rank has the
@@ -405,7 +403,7 @@ namespace AMDiS { namespace Parallel {
inline bool getEdgeReverseMode(ElementObjectData &obj0,
ElementObjectData &obj1)
{
- if (mesh->getDim() == 2)
+ if (macroMesh->getDim() == 2)
return true;
if (edgeReverseMode.empty())
@@ -437,9 +435,17 @@ namespace AMDiS { namespace Parallel {
return (t >= smallestPeriodicBcType);
}
- inline Element* getElementPtr(int index)
+ inline Element* getElementPtr(int index, Mesh* mesh)
{
- return macroElIndexMap[index];
+ FUNCNAME_DBG("ElementObjectDatabase::getElementPtr()");
+ TEST_EXIT_DBG(macroElIndexMap[index][mesh])
+ ("No element pointer in macroElIndex map. Something is wrong.\n");
+ return macroElIndexMap[index][mesh];
+ }
+
+ inline MacroElIndexMap& getElIndexMap()
+ {
+ return macroElIndexMap;
}
inline int getElementType(int index)
@@ -469,9 +475,11 @@ namespace AMDiS { namespace Parallel {
* periodic boundary, all information about subobjects of the element on
* this boundary are collected.
*
- * \param[in] elInfo ElInfo object of the element.
+ * \param[in] Element the element.
*/
- void addElement(ElInfo *elInfo);
+ void addElement(Element* el);
+
+ void addElementPeriodicBoundary(ElInfo* elInfo);
/// Adds the i-th DOF vertex of an element to the object database.
void addVertex(Element *el, int ith);
@@ -515,9 +523,14 @@ namespace AMDiS { namespace Parallel {
private:
const FiniteElemSpace* feSpace;
- /// The mesh that is used to store all its element information in
- /// the database.
- Mesh *mesh;
+ /// The macro mesh that is used to store all its element information in the database.
+ Mesh *macroMesh;
+
+ /// Used to get mesh or element pointers. meshes[0] is always equal to \ref macroMesh
+ std::vector<Mesh*> meshes;
+
+ /// Corresponding FE spaces of meshes.
+ std::vector<const FiniteElemSpace*> feSpaces;
/// Maps to each vertex DOF all element objects that represent this vertex.
@@ -608,12 +621,14 @@ namespace AMDiS { namespace Parallel {
std::map<int, int> *macroElementRankMap;
/// Maps to each macro element index a pointer to the corresponding element.
- flat_map<int, Element*> macroElIndexMap;
+ MacroElIndexMap macroElIndexMap;
/// Maps to each macro element index the type of this element.
flat_map<int, int> macroElIndexTypeMap;
MeshLevelData* levelData;
+
+ friend class ParallelDebug;
};
} }
diff --git a/AMDiS/src/parallel/InteriorBoundary.cc b/AMDiS/src/parallel/InteriorBoundary.cc
index bfdfc94d..4eb43ec0 100644
--- a/AMDiS/src/parallel/InteriorBoundary.cc
+++ b/AMDiS/src/parallel/InteriorBoundary.cc
@@ -31,17 +31,17 @@ namespace AMDiS { namespace Parallel {
using namespace std;
-
void InteriorBoundary::create(MeshLevelData &levelData,
int level,
ElementObjectDatabase &elObjDb)
{
- FUNCNAME("InteriorBoundary::clear()");
+ FUNCNAME("InteriorBoundary::create()");
own.clear();
other.clear();
periodic.clear();
+ macroElIndexMap = elObjDb.getElIndexMap();
Mesh *mesh = elObjDb.getMesh();
TEST_EXIT_DBG(mesh)("Should not happen!\n");
TEST_EXIT_DBG(level < levelData.getNumberOfLevels())
@@ -96,17 +96,16 @@ namespace AMDiS { namespace Parallel {
AtomicBoundary bound;
bound.maxLevel = elObjDb.getIterateMaxLevel();
- bound.rankObj.el = elObjDb.getElementPtr(rankBoundEl.elIndex);
bound.rankObj.elIndex = rankBoundEl.elIndex;
bound.rankObj.elType = elObjDb.getElementType(rankBoundEl.elIndex);
bound.rankObj.subObj = geoIndex;
bound.rankObj.ithObj = rankBoundEl.ithObject;
-
if (geoIndex == FACE) {
for (int edgeNo = 0; edgeNo < 3; edgeNo++) {
+ Element* el = elObjDb.getElementPtr(bound.rankObj.elIndex, mesh);
int edgeOfFace =
- bound.rankObj.el->getEdgeOfFace(bound.rankObj.ithObj, edgeNo);
+ el->getEdgeOfFace(bound.rankObj.ithObj, edgeNo);
bound.rankObj.excludedSubstructures.push_back(make_pair(EDGE, edgeOfFace));
}
@@ -122,7 +121,6 @@ namespace AMDiS { namespace Parallel {
if (!levelData.rankInLevel(it2->first, level))
continue;
- bound.neighObj.el = elObjDb.getElementPtr(it2->second.elIndex);
bound.neighObj.elIndex = it2->second.elIndex;
bound.neighObj.elType = elObjDb.getElementType(it2->second.elIndex);
bound.neighObj.subObj = geoIndex;
@@ -147,7 +145,6 @@ namespace AMDiS { namespace Parallel {
ElementObjectData& ownerBoundEl = objData[owner];
- bound.neighObj.el = elObjDb.getElementPtr(ownerBoundEl.elIndex);
bound.neighObj.elIndex = ownerBoundEl.elIndex;
bound.neighObj.elType = -1;
bound.neighObj.subObj = geoIndex;
@@ -168,7 +165,6 @@ namespace AMDiS { namespace Parallel {
}
}
-
// === Create periodic boundary data structure. ===
int removePeriodicBoundary = 0;
@@ -190,13 +186,11 @@ namespace AMDiS { namespace Parallel {
ElementObjectData& perDofEl1 = elIt->second;
AtomicBoundary bound;
- bound.rankObj.el = elObjDb.getElementPtr(perDofEl0.elIndex);
bound.rankObj.elIndex = perDofEl0.elIndex;
bound.rankObj.elType = elObjDb.getElementType(perDofEl0.elIndex);
bound.rankObj.subObj = VERTEX;
bound.rankObj.ithObj = perDofEl0.ithObject;
- bound.neighObj.el = elObjDb.getElementPtr(perDofEl1.elIndex);
bound.neighObj.elIndex = perDofEl1.elIndex;
bound.neighObj.elType = elObjDb.getElementType(perDofEl1.elIndex);
bound.neighObj.subObj = VERTEX;
@@ -250,7 +244,6 @@ namespace AMDiS { namespace Parallel {
b = bound;
} else {
ElementObjectData& ownerBoundEl = objData[owner];
- bound.neighObj.el = elObjDb.getElementPtr(ownerBoundEl.elIndex);
bound.neighObj.elIndex = ownerBoundEl.elIndex;
bound.neighObj.elType = -1;
bound.neighObj.ithObj = ownerBoundEl.ithObject;
@@ -286,13 +279,11 @@ namespace AMDiS { namespace Parallel {
ElementObjectData& perEdgeEl1 = elIt->second;
AtomicBoundary bound;
- bound.rankObj.el = elObjDb.getElementPtr(perEdgeEl0.elIndex);
bound.rankObj.elIndex = perEdgeEl0.elIndex;
bound.rankObj.elType = elObjDb.getElementType(perEdgeEl0.elIndex);
bound.rankObj.subObj = EDGE;
bound.rankObj.ithObj = perEdgeEl0.ithObject;
- bound.neighObj.el = elObjDb.getElementPtr(perEdgeEl1.elIndex);
bound.neighObj.elIndex = perEdgeEl1.elIndex;
bound.neighObj.elType = elObjDb.getElementType(perEdgeEl1.elIndex);
bound.neighObj.subObj = EDGE;
@@ -326,7 +317,6 @@ namespace AMDiS { namespace Parallel {
b = bound;
ElementObjectData& ownerBoundEl = objData[owner];
- b.neighObj.el = elObjDb.getElementPtr(ownerBoundEl.elIndex);
b.neighObj.elIndex = ownerBoundEl.elIndex;
b.neighObj.elType = -1;
b.neighObj.ithObj = ownerBoundEl.ithObject;
@@ -371,13 +361,11 @@ namespace AMDiS { namespace Parallel {
ElementObjectData& perFaceEl1 = elIt->second;
AtomicBoundary bound;
- bound.rankObj.el = elObjDb.getElementPtr(perFaceEl0.elIndex);
bound.rankObj.elIndex = perFaceEl0.elIndex;
bound.rankObj.elType = elObjDb.getElementType(perFaceEl0.elIndex);
bound.rankObj.subObj = FACE;
bound.rankObj.ithObj = perFaceEl0.ithObject;
- bound.neighObj.el = elObjDb.getElementPtr(perFaceEl1.elIndex);
bound.neighObj.elIndex = perFaceEl1.elIndex;
bound.neighObj.elType = elObjDb.getElementType(perFaceEl1.elIndex);
bound.neighObj.subObj = FACE;
@@ -405,7 +393,6 @@ namespace AMDiS { namespace Parallel {
b = bound;
ElementObjectData& ownerBoundEl = objData[owner];
- b.neighObj.el = elObjDb.getElementPtr(ownerBoundEl.elIndex);
b.neighObj.elIndex = ownerBoundEl.elIndex;
b.neighObj.elType = -1;
b.neighObj.ithObj = ownerBoundEl.ithObject;
@@ -579,8 +566,6 @@ namespace AMDiS { namespace Parallel {
void InteriorBoundary::serialize(ostream &out,
RankToBoundMap& boundary)
{
- FUNCNAME("InteriorBoundary::serialize()");
-
int mSize = boundary.size();
SerUtil::serialize(out, mSize);
for (RankToBoundMap::iterator it = boundary.begin();
@@ -627,7 +612,7 @@ namespace AMDiS { namespace Parallel {
RankToBoundMap& boundary,
map<int, Element*> &elIndexMap)
{
- FUNCNAME("InteriorBoundary::deserialize()");
+ FUNCNAME_DBG("InteriorBoundary::deserialize()");
int mSize = 0;
SerUtil::deserialize(in, mSize);
@@ -707,8 +692,6 @@ namespace AMDiS { namespace Parallel {
AtomicBoundary& InteriorBoundary::getNewOwn(int rank)
{
- FUNCNAME("InteriorBoundary::getNewOwn()");
-
int size = own[rank].size();
own[rank].resize(size + 1);
return own[rank][size];
@@ -717,8 +700,6 @@ namespace AMDiS { namespace Parallel {
AtomicBoundary& InteriorBoundary::getNewOther(int rank)
{
- FUNCNAME("InteriorBoundary::getNewOther()");
-
int size = other[rank].size();
other[rank].resize(size + 1);
return other[rank][size];
@@ -765,8 +746,6 @@ namespace AMDiS { namespace Parallel {
bool InteriorBoundary::removeOwn(BoundaryObject& bound)
{
- FUNCNAME("InteriorBoundary::removeOwn()");
-
bool removed = false;
for (map<int, vector<AtomicBoundary> >::iterator it = own.begin();
@@ -787,8 +766,6 @@ namespace AMDiS { namespace Parallel {
bool InteriorBoundary::removeOther(BoundaryObject& bound)
{
- FUNCNAME("InteriorBoundary::removeOther()");
-
bool removed = false;
for (map<int, vector<AtomicBoundary> >::iterator it = other.begin();
@@ -841,8 +818,6 @@ namespace AMDiS { namespace Parallel {
void MultiLevelInteriorBoundary::create(MeshLevelData &levelData,
ElementObjectDatabase &elObjDb)
{
- FUNCNAME(" MultLevelInteriorBoundary::create()");
-
levelIntBound.clear();
int nLevel = levelData.getNumberOfLevels();
diff --git a/AMDiS/src/parallel/InteriorBoundary.h b/AMDiS/src/parallel/InteriorBoundary.h
index ce9b03f8..2df6d68b 100644
--- a/AMDiS/src/parallel/InteriorBoundary.h
+++ b/AMDiS/src/parallel/InteriorBoundary.h
@@ -48,6 +48,19 @@ namespace AMDiS { namespace Parallel {
{
return own;
}
+
+ inline MacroElIndexMap& getElIndexMap()
+ {
+ return macroElIndexMap;
+ }
+
+ inline Element* getElementPtr(int index, Mesh* mesh)
+ {
+ FUNCNAME_DBG("ElementObjectDatabase::getElementPtr()");
+ TEST_EXIT_DBG(macroElIndexMap[index][mesh])
+ ("No element pointer in macroElIndex map. Something is wrong.\n");
+ return macroElIndexMap[index][mesh];
+ }
RankToBoundMap& getOther()
{
@@ -126,6 +139,8 @@ namespace AMDiS { namespace Parallel {
private:
RankToBoundMap own, other, periodic;
+
+ MacroElIndexMap macroElIndexMap;
friend class ParallelDebug;
diff --git a/AMDiS/src/parallel/MatrixNnzStructure.cc b/AMDiS/src/parallel/MatrixNnzStructure.cc
index a4ee9eb8..fa388647 100644
--- a/AMDiS/src/parallel/MatrixNnzStructure.cc
+++ b/AMDiS/src/parallel/MatrixNnzStructure.cc
@@ -48,7 +48,6 @@ namespace AMDiS { namespace Parallel {
}
}
-
void MatrixNnzStructure::create(Matrix<DOFMatrix*> &mat,
ParallelDofMapping &rowDofMap,
ParallelDofMapping &colDofMap,
@@ -58,11 +57,14 @@ namespace AMDiS { namespace Parallel {
{
FUNCNAME("MatrixNnzStructure::create()");
- int nRankRows = rowDofMap.getRankDofs(); // Number of DOFs owned by rank.
- int rankStartRowIndex = rowDofMap.getStartDofs(); // Smallest global index of a DOF owned by the rank.
+ int nRankRows = rowDofMap.getRankDofs(); // Number of DOFs owned by rank.
+
+ int rankStartRowIndex = rowDofMap.getStartDofs(); // Smallest global index of a DOF owned by the rank.
int nRankCols = colDofMap.getRankDofs();
+
int nOverallCols = colDofMap.getOverallDofs(); // Number of global DOFs (this value is thus the same on all ranks).
+
int rankStartColIndex = colDofMap.getStartDofs();
create(nRankRows, (!localMatrix ? nRankRows : -1));
@@ -98,7 +100,7 @@ namespace AMDiS { namespace Parallel {
TEST_EXIT_DBG(feSpace)("No FE space found!\n");
- for (DofComm::Iterator it(rowDofMap.getDofComm().getRecvDofs(), feSpace);
+ for (DofComm::Iterator it(rowDofMap.getDofComm(feSpace).getRecvDofs(), feSpace);
!it.end(); it.nextRank()) {
sendMatrixEntry[it.getRank()].resize(0);
@@ -115,7 +117,7 @@ namespace AMDiS { namespace Parallel {
if (mat[i][j])
feSpace = mat[i][j]->getRowFeSpace();
- for (DofComm::Iterator it(rowDofMap.getDofComm().getSendDofs(), feSpace);
+ for (DofComm::Iterator it(rowDofMap.getDofComm(feSpace).getSendDofs(), feSpace);
!it.end(); it.nextRank())
recvFromRank.insert(it.getRank());
}
@@ -151,15 +153,15 @@ namespace AMDiS { namespace Parallel {
// === Iterate on all DOFs of the row mapping. ===
- DofMap::iterator rowIt = rowDofMap[rowComp].begin();
+ DofMap::iterator rowIt = rowDofMap[rowComp].begin(); // row dofmap DOFIt
DofMap::iterator rowEndIt = rowDofMap[rowComp].end();
for (; rowIt != rowEndIt; ++rowIt) {
// Go to the corresponding matrix row (note, both the mapping and the
// matrix rows are stored in increasing order).
- while (cursor.value() != rowIt->first)
+ while (cursor.value() != rowIt->first)
++cursor;
- size_t _row = cursor.value();
+ size_t _row = cursor.value(); // DegreeOfFreedom
// The corresponding global matrix row index of the current row DOF.
int petscRowIdx = 0;
@@ -190,7 +192,7 @@ namespace AMDiS { namespace Parallel {
if (localMatrix == false)
localPetscRowIdx -= rankStartRowIndex;
- TEST_EXIT_DBG(localPetscRowIdx >= 0 && localPetscRowIdx < nRankRows)
+ TEST_EXIT(localPetscRowIdx >= 0 && localPetscRowIdx < nRankRows)
("Should not happen! \n Debug info: DOF = %d globalRowIndx = %d petscRowIdx = %d localPetscRowIdx = %d rStart = %d compontens = %d from %d nRankRows = %d\n",
_row,
rowDofMap[rowComp][_row].global,
diff --git a/AMDiS/src/parallel/MatrixNnzStructure.h b/AMDiS/src/parallel/MatrixNnzStructure.h
index 0bf3ef7e..589de906 100644
--- a/AMDiS/src/parallel/MatrixNnzStructure.h
+++ b/AMDiS/src/parallel/MatrixNnzStructure.h
@@ -62,8 +62,12 @@ namespace AMDiS { namespace Parallel {
void create(int nRows0, int nRows1 = -1);
public:
+ // Array containing the number of nonzeros in the various rows of the DIAGONAL
+ // portion of the local submatrix (possibly different for each row)
int *dnnz;
+ // Array containing the number of nonzeros in the various rows of the OFF-DIAGONAL
+ // portion of the local submatrix (possibly different for each row)
int *onnz;
};
diff --git a/AMDiS/src/parallel/MeshDistributor.cc b/AMDiS/src/parallel/MeshDistributor.cc
index eda979bf..39ca8816 100644
--- a/AMDiS/src/parallel/MeshDistributor.cc
+++ b/AMDiS/src/parallel/MeshDistributor.cc
@@ -86,7 +86,7 @@ namespace AMDiS { namespace Parallel {
: problemStat(0),
initialized(false),
name("parallel"),
- mesh(NULL),
+ macroMesh(NULL),
refineManager(NULL),
partitioner(NULL),
initialPartitioner(NULL),
@@ -100,7 +100,6 @@ namespace AMDiS { namespace Parallel {
repartitioningCounter(0),
repartitioningFailed(0),
debugOutputDir(""),
- lastMeshChangeIndex(0),
createBoundaryDofFlag(0),
boundaryDofInfo(1),
meshAdaptivity(true),
@@ -214,12 +213,13 @@ namespace AMDiS { namespace Parallel {
("Parallelization does not work with only one process!\n");
TEST_EXIT(feSpaces.size() > 0)
("No FE space has been defined for the mesh distributor!\n");
- TEST_EXIT(mesh)("No mesh has been defined for the mesh distributor!\n");
+ TEST_EXIT(meshes.size() > 0)("No mesh has been defined for the mesh distributor!\n");
// === Sort FE spaces with respect to the degree of the basis ===
// === functions. Use stuiped bubble sort for this. ===
+ //TODO Maybe unnecessary anymore
bool doNext = false;
do {
doNext = false;
@@ -234,9 +234,51 @@ namespace AMDiS { namespace Parallel {
}
} while (doNext);
- elObjDb.setFeSpace(feSpaces[0]);
-
+ // Sort FE spaces seperately for each mesh.
+ map<Mesh*, vector<const FiniteElemSpace*> >::iterator iter = meshToFeSpaces.begin();
+ while(iter != meshToFeSpaces.end()) {
+ vector<const FiniteElemSpace*>& spaces = iter->second;
+
+ bool doNext = false;
+ do {
+ doNext = false;
+ for (size_t i = 0; i < spaces.size() - 1; i++) {
+ if (spaces[i]->getBasisFcts()->getDegree() >
+ spaces[i + 1]->getBasisFcts()->getDegree()) {
+ const FiniteElemSpace *tmp = spaces[i + 1];
+ spaces[i + 1] = spaces[i];
+ spaces[i] = tmp;
+ doNext = true;
+ }
+ }
+ } while (doNext);
+ ++iter;
+ }
+
+ // Test, if the mesh is the macro mesh only! Paritioning of the mesh is
+ // supported only for macro meshes, so it will not work yet if the mesh is
+ // already refined in some way.
+ testForMacroMesh();
+
+#if (DEBUG != 0)
+ // Check whether meshes come from the same macro mesh. The way is to compare
+ // the node coords of each macro element in the meshes.
+ debug::ElementIdxToCoords macroCoords;
+ debug::createNodeCoords(macroMesh, macroCoords);
+
+ for (size_t i = 1; i < meshes.size(); i++) {
+ debug::testNodeCoords(meshes[i], macroCoords);
+ }
+#endif
+
+ // Initialize dof communicators which have been created in addProblemStat.
+ for (size_t i = 0; i < meshes.size(); i++)
+ dofComms[meshes[i]].init(levelData, meshToFeSpaces[meshes[i]]);
+
+ // Initialize element object DB
+ elObjDb.init(meshes, meshToFeSpaces);
+
// If the problem has been already read from a file, we need only to set
// isRankDofs to all matrices and rhs vector and to remove periodic
// boundary conditions (if there are some).
@@ -247,7 +289,7 @@ namespace AMDiS { namespace Parallel {
elObjDb.createMacroElementInfo(allMacroElements);
- updateLocalGlobalNumbering();
+ updateDofRelatedStruct();
elObjDb.setData(partitionMap, levelData);
@@ -268,8 +310,10 @@ namespace AMDiS { namespace Parallel {
#if (DEBUG != 0)
- debug::ElementIdxToDofs elMap;
- debug::createSortedDofs(mesh, elMap);
+ std::vector<debug::ElementIdxToDofs> elMap(meshes.size());
+ for (size_t i = 0; i < meshes.size(); i++) {
+ debug::createSortedDofs(meshes[i], elMap[i]);
+ }
#endif
if (mpiRank == 0) {
@@ -281,84 +325,94 @@ namespace AMDiS { namespace Parallel {
Parameters::get("parallel->debug->write mesh partitioning", writePartMesh);
if (writePartMesh > 0) {
- debug::writeElementIndexMesh(mesh , debugOutputDir + "elementIndex");
+ debug::writeElementIndexMesh(macroMesh , debugOutputDir + "elementIndex");
ParallelDebug::writePartitioning(*this, debugOutputDir + "part");
}
}
// Create interior boundary information.
createInteriorBoundary(true);
-
-
+
// === Remove neighbourhood relations due to periodic bounday conditions. ===
-
- for (deque<MacroElement*>::iterator it = mesh->firstMacroElement();
- it != mesh->endOfMacroElements(); ++it) {
- for (int i = 0; i < mesh->getGeo(NEIGH); i++) {
- if ((*it)->getNeighbour(i) &&
- mesh->isPeriodicAssociation((*it)->getBoundary(i))) {
-
- int neighIndex = (*it)->getNeighbour(i)->getIndex();
-
- (*it)->getNeighbour(i)->setNeighbour((*it)->getOppVertex(i), NULL);
- (*it)->setNeighbour(i, NULL);
- (*it)->setBoundary(i, 0);
-
- macroElementNeighbours[(*it)->getIndex()][i] = -1;
- macroElementNeighbours[neighIndex][(*it)->getOppVertex(i)] = -1;
+
+ for (size_t i = 0; i < meshes.size(); i++) {
+ for (deque<MacroElement*>::iterator it = meshes[i]->firstMacroElement();
+ it != meshes[i]->endOfMacroElements(); ++it) {
+ for (int j = 0; j < macroMesh->getGeo(NEIGH); j++) {
+ if ((*it)->getNeighbour(j) &&
+ meshes[i]->isPeriodicAssociation((*it)->getBoundary(j))) {
+
+ int neighIndex = (*it)->getNeighbour(j)->getIndex();
+
+ (*it)->getNeighbour(j)->setNeighbour((*it)->getOppVertex(j), NULL);
+ (*it)->setNeighbour(j, NULL);
+ (*it)->setBoundary(j, 0);
+
+ if (i == 0) {
+ macroElementNeighbours[(*it)->getIndex()][j] = -1;
+ macroElementNeighbours[neighIndex][(*it)->getOppVertex(j)] = -1;
+ }
+ }
}
}
}
-
- for (vector<MacroElement*>::iterator it = allMacroElements.begin();
- it != allMacroElements.end(); ++it) {
- for (int i = 0; i < mesh->getGeo(NEIGH); i++) {
- if ((*it)->getNeighbour(i) &&
+
+ for (map<Mesh*, std::vector<MacroElement*> >::iterator iter = allMacroElements.begin();
+ iter != allMacroElements.end(); iter++) {
+ Mesh* mesh = iter->first;
+ vector<MacroElement*>& allMacros = iter->second;
+
+ for (vector<MacroElement*>::iterator it = allMacros.begin();
+ it != allMacros.end(); ++it) {
+ for (int i = 0; i < macroMesh->getGeo(NEIGH); i++) {
+ if ((*it)->getNeighbour(i) &&
mesh->isPeriodicAssociation((*it)->getBoundary(i))) {
-
- int neighIndex = (*it)->getNeighbour(i)->getIndex();
-
- (*it)->getNeighbour(i)->setNeighbour((*it)->getOppVertex(i), NULL);
- (*it)->setNeighbour(i, NULL);
- (*it)->setBoundary(i, 0);
-
- macroElementNeighbours[(*it)->getIndex()][i] = -1;
- macroElementNeighbours[neighIndex][(*it)->getOppVertex(i)] = -1;
-
+
+ int neighIndex = (*it)->getNeighbour(i)->getIndex();
+
+ (*it)->getNeighbour(i)->setNeighbour((*it)->getOppVertex(i), NULL);
+ (*it)->setNeighbour(i, NULL);
+ (*it)->setBoundary(i, 0);
+
+ if (i == 0) {
+ macroElementNeighbours[(*it)->getIndex()][i] = -1;
+ macroElementNeighbours[neighIndex][(*it)->getOppVertex(i)] = -1;
+ }
+ }
}
}
}
// === Remove all macro elements that are not part of the rank partition. ===
-
+
removeMacroElements();
-
+
// === Create new global and local DOF numbering. ===
-
-
+
// We have to remove the VertexVectors, which contain periodic assoiciations,
// because they are not valid anymore after some macro elements have been
// removed and the corresponding DOFs were deleted.
- for (map<BoundaryType, VertexVector*>::iterator it = mesh->getPeriodicAssociations().begin();
- it != mesh->getPeriodicAssociations().end(); ++it)
- const_cast<DOFAdmin&>(mesh->getDofAdmin(0)).removeDOFContainer(dynamic_cast<DOFContainer*>(it->second));
+ for (size_t i = 0; i < meshes.size(); i++)
+ for (map<BoundaryType, VertexVector*>::iterator it = meshes[i]->getPeriodicAssociations().begin();
+ it != meshes[i]->getPeriodicAssociations().end(); ++it)
+ const_cast<DOFAdmin&>(meshes[i]->getDofAdmin(0)).removeDOFContainer(dynamic_cast<DOFContainer*>(it->second));
- updateLocalGlobalNumbering();
+ updateDofRelatedStruct();
// === In 3D we have to fix the mesh to allow local refinements. ===
fix3dMeshRefinement();
-
// === If in debug mode, make some tests. ===
#if (DEBUG != 0)
MSG("AMDiS runs in debug mode, so make some test ...\n");
ParallelDebug::testAllElements(*this);
- debug::testSortedDofs(mesh, elMap);
+ for (size_t i = 0; i < meshes.size(); i++)
+ debug::testSortedDofs(meshes[i], elMap[i]);
ParallelDebug::testInteriorBoundary(*this);
ParallelDebug::followBoundary(*this);
@@ -375,50 +429,56 @@ namespace AMDiS { namespace Parallel {
#endif
// === Global refinements. ===
-
- int globalRefinement = 0;
- Parameters::get(mesh->getName() + "->global refinements", globalRefinement);
-
- if (globalRefinement > 0) {
- bool doRefineInter = true;
- Parameters::get(mesh->getName() + "->refinement interpol", doRefineInter);
- std::map<DOFVector<double>*, RefineCoarsenOperation> rememberOp;
- if (!doRefineInter) {
- // no refinement during initial global refinement
- for (int iadmin = 0; iadmin < mesh->getNumberOfDOFAdmin(); iadmin++) {
- std::list<DOFIndexedBase*>::iterator it;
- DOFAdmin* admin = const_cast<DOFAdmin*>(&mesh->getDofAdmin(iadmin));
- std::list<DOFIndexedBase*>::iterator end = admin->endDOFIndexed();
- for (it = admin->beginDOFIndexed(); it != end; it++) {
- DOFVector<double>* vec = dynamic_cast<DOFVector<double>*>(*it);
- if (vec) {
- rememberOp[vec] = vec->getRefineOperation();
- vec->setRefineOperation(NO_OPERATION);
+ bool oneMeshRefined = false;
+ for (size_t i = 0; i < meshes.size(); i++) {
+
+ int globalRefinement = 0;
+ Parameters::get(meshes[i]->getName() + "->global refinements", globalRefinement);
+
+ if (globalRefinement > 0) {
+ oneMeshRefined = true;
+ bool doRefineInter = true;
+ Parameters::get(meshes[i]->getName() + "->refinement interpol", doRefineInter);
+ std::map<DOFVector<double>*, RefineCoarsenOperation> rememberOp;
+ if (!doRefineInter) {
+ // No refinement during initial global refinement
+ for (int iadmin = 0; iadmin < meshes[i]->getNumberOfDOFAdmin(); iadmin++) {
+ std::list<DOFIndexedBase*>::iterator it;
+ DOFAdmin* admin = const_cast<DOFAdmin*>(&meshes[i]->getDofAdmin(iadmin));
+ std::list<DOFIndexedBase*>::iterator end = admin->endDOFIndexed();
+ for (it = admin->beginDOFIndexed(); it != end; it++) {
+ DOFVector<double>* vec = dynamic_cast<DOFVector<double>*>(*it);
+ if (vec) {
+ rememberOp[vec] = vec->getRefineOperation();
+ vec->setRefineOperation(NO_OPERATION);
+ }
}
}
}
- }
- refineManager->globalRefine(mesh, globalRefinement);
- if (!doRefineInter) {
- // no refinement during initial global refinement
- for (int iadmin = 0; iadmin < mesh->getNumberOfDOFAdmin(); iadmin++) {
- std::list<DOFIndexedBase*>::iterator it;
- DOFAdmin* admin = const_cast<DOFAdmin*>(&mesh->getDofAdmin(iadmin));
- std::list<DOFIndexedBase*>::iterator end = admin->endDOFIndexed();
- for (it = admin->beginDOFIndexed(); it != end; it++) {
- DOFVector<double>* vec = dynamic_cast<DOFVector<double>*>(*it);
- if (vec)
- vec->setRefineOperation(rememberOp[vec]);
+ refineManager->globalRefine(meshes[i], globalRefinement);
+ if (!doRefineInter) {
+ // No refinement during initial global refinement
+ for (int iadmin = 0; iadmin < meshes[i]->getNumberOfDOFAdmin(); iadmin++) {
+ std::list<DOFIndexedBase*>::iterator it;
+ DOFAdmin* admin = const_cast<DOFAdmin*>(&meshes[i]->getDofAdmin(iadmin));
+ std::list<DOFIndexedBase*>::iterator end = admin->endDOFIndexed();
+ for (it = admin->beginDOFIndexed(); it != end; it++) {
+ DOFVector<double>* vec = dynamic_cast<DOFVector<double>*>(*it);
+ if (vec)
+ vec->setRefineOperation(rememberOp[vec]);
+ }
}
}
- }
- updateLocalGlobalNumbering();
+ updateDofRelatedStruct(meshes[i]);
#if (DEBUG != 0)
- ParallelDebug::testPeriodicBoundary(*this);
+ ParallelDebug::testPeriodicBoundary(*this);
#endif
+ }
}
-
+ if (oneMeshRefined)
+ updateLocalGlobalNumbering();
+
// And delete some data, we there is no mesh adaptivty.
if (!meshAdaptivity)
elObjDb.clear();
@@ -432,24 +492,19 @@ namespace AMDiS { namespace Parallel {
{
FUNCNAME("MeshDistributor::createInitialPartitioning()");
- // Test, if the mesh is the macro mesh only! Paritioning of the mesh is
- // supported only for macro meshes, so it will not work yet if the mesh is
- // already refined in some way.
- testForMacroMesh();
-
// For later mesh repartitioning, we need to store some information about
// the macro mesh.
createMacroElementInfo();
- // create an initial partitioning of the mesh
+ // Create an initial partitioning of the mesh
bool useInitialPartitioning =
initialPartitioner->createInitialPartitioning();
- // set the element weights, which are 1 at the very first begin
+ // Set the element weights, which are 1 at the very first begin
setInitialElementWeights();
if (!useInitialPartitioning) {
- // and now partition the mesh
+ // And now partition the mesh
bool partitioningSucceed =
initialPartitioner->partition(elemWeights, INITIAL);
TEST_EXIT(partitioningSucceed)("Initial partitioning does not work!\n");
@@ -470,7 +525,7 @@ namespace AMDiS { namespace Parallel {
elemWeights.clear();
string filename = "";
- Parameters::get(mesh->getName() + "->macro weights", filename);
+ Parameters::get(macroMesh->getName() + "->macro weights", filename);
if (filename != "") {
MSG("Read macro weights from %s\n", filename.c_str());
@@ -506,7 +561,7 @@ namespace AMDiS { namespace Parallel {
}
TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
+ ElInfo *elInfo = stack.traverseFirst(macroMesh, -1, Mesh::CALL_LEAF_EL);
while (elInfo) {
elemWeights[elInfo->getElement()->getIndex()] = 1.0;
elInfo = stack.traverseNext(elInfo);
@@ -523,37 +578,49 @@ namespace AMDiS { namespace Parallel {
// === Add all FE spaces from stationary problem. ===
-
+
vector<const FiniteElemSpace*> newFeSpaces = probStat->getFeSpaces();
- for (int i = 0; i < static_cast<int>(newFeSpaces.size()); i++)
+
+ for (size_t i = 0; i < newFeSpaces.size(); i++)
if (find(feSpaces.begin(), feSpaces.end(), newFeSpaces[i]) ==
feSpaces.end())
+ {
+ // Find new fespace, then add mesh if it's new
+ Mesh* mesh = newFeSpaces[i]->getMesh();
+ if (find(meshes.begin(), meshes.end(), mesh) == meshes.end()) {
+ TEST_EXIT(meshes.size() < 2)
+ ("Currently max two meshes supported on parallel mode.\n");
+
+ meshes.push_back(mesh);
+ dofComms[mesh] = MultiLevelDofComm();
+ lastMeshChangeIndexs[mesh] = 0;
+ }
+
feSpaces.push_back(newFeSpaces[i]);
+ meshToFeSpaces[mesh].push_back(newFeSpaces[i]);
+ }
- // === Add mesh of stationary problem and create a corresponding ===
- // === refinement manager object. ===
-
- if (mesh != NULL) {
- TEST_EXIT(mesh == probStat->getMesh())
- ("Does not yet support for different meshes! %s\n", probStat->getMesh()->getName().c_str());
- } else {
- mesh = probStat->getMesh();
- }
+ // === Set the first mesh to be the macro mesh and pass it to partitioner. ===
+ // === Create a corresponding refinement manager object. ===
- switch (mesh->getDim()) {
- case 2:
- refineManager = new RefinementManager2d();
- break;
- case 3:
- refineManager = new RefinementManager3d();
- break;
- default:
- ERROR_EXIT("This should not happen for dim = %d!\n", mesh->getDim());
+ if (problemStat.empty()) {
+ macroMesh = meshes[0];
+
+ switch (macroMesh->getDim()) {
+ case 2:
+ refineManager = new RefinementManager2d();
+ break;
+ case 3:
+ refineManager = new RefinementManager3d();
+ break;
+ default:
+ ERROR_EXIT("This should not happen for dim = %d!\n", macroMesh->getDim());
+ }
+
+ partitioner->setMesh(macroMesh);
+ initialPartitioner->setMesh(macroMesh);
}
- partitioner->setMesh(mesh);
- initialPartitioner->setMesh(mesh);
-
// === Check whether the stationary problem should be serialized. ===
@@ -639,8 +706,6 @@ namespace AMDiS { namespace Parallel {
void MeshDistributor::addProblemStatGlobal(ProblemStatSeq *probStat)
{
- FUNCNAME("MeshDistributor::addProblemStatGlobal()");
-
if (globalMeshDistributor == NULL)
globalMeshDistributor = new MeshDistributor();
@@ -678,30 +743,33 @@ namespace AMDiS { namespace Parallel {
{
FUNCNAME("MeshDistributor::testForMacroMesh()");
- int nMacroElements = 0;
+ for (size_t i = 0; i < meshes.size(); i++) {
+
+ int nMacroElements = 0;
- TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
- while (elInfo) {
- TEST_EXIT(elInfo->getLevel() == 0)
- ("Mesh is already refined! This does not work with parallelization!\n");
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(meshes[i], -1, Mesh::CALL_LEAF_EL);
+ while (elInfo) {
+ TEST_EXIT(elInfo->getLevel() == 0)
+ ("Mesh is already refined! This does not work with parallelization!\n");
- TEST_EXIT(elInfo->getType() == 0)
- ("Only macro elements with level 0 are supported!\n");
-
- nMacroElements++;
+ TEST_EXIT(elInfo->getType() == 0)
+ ("Only macro elements with level 0 are supported!\n");
+
+ nMacroElements++;
- elInfo = stack.traverseNext(elInfo);
- }
+ elInfo = stack.traverseNext(elInfo);
+ }
- TEST_EXIT(nMacroElements >= MPI::COMM_WORLD.Get_size())
- ("The mesh has less macro elements than number of mpi processes!\n");
+ TEST_EXIT(nMacroElements >= MPI::COMM_WORLD.Get_size())
+ ("The mesh has less macro elements than number of mpi processes!\n");
+ }
}
void MeshDistributor::synchVector(SystemVector &vec)
{
- FUNCNAME("MeshDistributor::synchVector()");
+ FUNCNAME_DBG("MeshDistributor::synchVector()");
int nLevels = levelData.getNumberOfLevels();
for (int level = nLevels - 1; level >= 0; level--) {
@@ -709,54 +777,80 @@ namespace AMDiS { namespace Parallel {
if (mpiComm == MPI::COMM_SELF)
continue;
-
- StdMpi<vector<double> > stdMpi(mpiComm);
-
- for (DofComm::Iterator it(dofComm[level].getSendDofs());
- !it.end(); it.nextRank()) {
- vector<double> dofs;
+
+ vector<Mesh*> sysMeshes;
+
+ // std::set of mesh pointer cannot be used for parallel
+ for (size_t i = 0; i < meshes.size(); i++)
+ for (int j = 0; j < vec.getSize(); j++)
+ if (meshes[i] == vec.getFeSpace(j)->getMesh()) {
+ sysMeshes.push_back(meshes[i]);
+ break;
+ }
+
+ TEST_EXIT_DBG(sysMeshes.size() <= 2)
+ ("This really should not happen.\n");
+
+ vector<Mesh*>::iterator meshIt = sysMeshes.begin();
+ while(meshIt != sysMeshes.end())
+ {
+ StdMpi<vector<double> > stdMpi(mpiComm);
- for (int i = 0; i < vec.getSize(); i++) {
- DOFVector<double> &dofVec = *(vec.getDOFVector(i));
- for (it.beginDofIter(vec.getFeSpace(i)); !it.endDofIter(); it.nextDof())
- dofs.push_back(dofVec[it.getDofIndex()]);
+ MultiLevelDofComm& dofComm = dofComms[*meshIt];
+
+ for (DofComm::Iterator it(dofComm[level].getSendDofs());
+ !it.end(); it.nextRank()) {
+ vector<double> dofs;
+
+ for (int j = 0; j < vec.getSize(); j++) {
+ if (vec.getFeSpace(j)->getMesh() != *meshIt)
+ continue;
+
+ DOFVector<double> &dofVec = *(vec.getDOFVector(j));
+ for (it.beginDofIter(vec.getFeSpace(j)); !it.endDofIter(); it.nextDof())
+ dofs.push_back(dofVec[it.getDofIndex()]);
+ }
+
+ int rank = it.getRank();
+ // if (level > 0)
+ // rank = levelData.mapRank(rank, 0, level);
+ stdMpi.send(rank, dofs);
}
- int rank = it.getRank();
- // if (level > 0)
- // rank = levelData.mapRank(rank, 0, level);
- stdMpi.send(rank, dofs);
- }
-
- for (DofComm::Iterator it(dofComm[level].getRecvDofs());
- !it.end(); it.nextRank()) {
- int rank = it.getRank();
- // if (level > 0)
- // rank = levelData.mapRank(rank, 0, level);
- stdMpi.recv(rank);
- }
-
- stdMpi.startCommunication();
-
- for (DofComm::Iterator it(dofComm[level].getRecvDofs());
- !it.end(); it.nextRank()) {
- int rank = it.getRank();
- // if (level > 0)
- // rank = levelData.mapRank(rank, 0, level);
+ for (DofComm::Iterator it(dofComm[level].getRecvDofs());
+ !it.end(); it.nextRank()) {
+ int rank = it.getRank();
+ // if (level > 0)
+ // rank = levelData.mapRank(rank, 0, level);
+ stdMpi.recv(rank);
+ }
- int counter = 0;
- vector<double> &recvData = stdMpi.getRecvData(rank);
+ stdMpi.startCommunication();
- for (int i = 0; i < vec.getSize(); i++) {
- DOFVector<double> &dofVec = *(vec.getDOFVector(i));
+ for (DofComm::Iterator it(dofComm[level].getRecvDofs());
+ !it.end(); it.nextRank()) {
+ int rank = it.getRank();
+ // if (level > 0)
+ // rank = levelData.mapRank(rank, 0, level);
- for (it.beginDofIter(vec.getFeSpace(i)); !it.endDofIter(); it.nextDof()) {
- TEST_EXIT_DBG(counter < recvData.size())
- ("Recv data from rank %d has only %d entries!\n", rank, recvData.size());
- dofVec[it.getDofIndex()] = recvData[counter++];
+ size_t counter = 0;
+ vector<double> &recvData = stdMpi.getRecvData(rank);
+
+ for (int j = 0; j < vec.getSize(); j++) {
+ if (vec.getFeSpace(j)->getMesh() != *meshIt)
+ continue;
+
+ DOFVector<double> &dofVec = *(vec.getDOFVector(j));
+
+ for (it.beginDofIter(vec.getFeSpace(j)); !it.endDofIter(); it.nextDof()) {
+ TEST_EXIT_DBG(counter < recvData.size())
+ ("Recv data from rank %d has only %d entries!\n", rank, recvData.size());
+ dofVec[it.getDofIndex()] = recvData[counter++];
+ }
}
}
- }
+ meshIt++;
+ } // End while
}
}
@@ -765,7 +859,7 @@ namespace AMDiS { namespace Parallel {
{
FUNCNAME("MeshDistributor::fix3dMeshRefinement()");
- if (mesh->getDim() != 3)
+ if (macroMesh->getDim() != 3)
return;
Timer t;
@@ -777,9 +871,9 @@ namespace AMDiS { namespace Parallel {
std::set<int> rankMacroEls;
TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL);
+ ElInfo *elInfo = stack.traverseFirst(macroMesh, 0, Mesh::CALL_EL_LEVEL);
while (elInfo) {
- for (int i = 0; i < mesh->getGeo(EDGE); i++) {
+ for (int i = 0; i < macroMesh->getGeo(EDGE); i++) {
ElementObjectData elData(elInfo->getElement()->getIndex(), i);
DofEdge e = elObjDb.getEdgeLocalMap(elData);
allEdges.insert(e);
@@ -832,44 +926,48 @@ namespace AMDiS { namespace Parallel {
// neighbours of each other, but can not reach any other element of the
// other index sets by neighbourhood relations.
vector<std::set<int> > disconnectedEls;
- helpToFix(allEls, edgeNoInEl, disconnectedEls);
+ helpToFix(allEls, disconnectedEls);
// Fix the edges
for (int dc0 = 0; dc0 < static_cast<int>(disconnectedEls.size()); dc0++) {
for (int dc1 = 0; dc1 < static_cast<int>(disconnectedEls.size()); dc1++) {
if (dc0 == dc1)
continue;
-
- int elIdx = *(disconnectedEls[dc1].begin());
- pair<Element*, int> edge0 =
- make_pair(elObjDb.getElementPtr(elIdx), edgeNoInEl[elIdx]);
-
- for (std::set<int>::iterator elIt = disconnectedEls[dc0].begin();
- elIt != disconnectedEls[dc0].end(); ++elIt) {
- pair<Element*, int> edge1 =
- make_pair(elObjDb.getElementPtr(*elIt), edgeNoInEl[*elIt]);
-#if (DEBUG != 0)
- DofEdge dofEdge0 = edge0.first->getEdge(edge0.second);
- DofEdge dofEdge1 = edge1.first->getEdge(edge1.second);
+ for (size_t i = 0; i < meshes.size(); i++) {
- WorldVector<double> c0, c1;
- mesh->getDofIndexCoords(dofEdge0.first, feSpaces[0], c0);
- mesh->getDofIndexCoords(dofEdge0.second, feSpaces[0], c1);
+ int elIdx = *(disconnectedEls[dc1].begin());
- // MSG("FOUND EDGE %d/%d <-> %d/%d\n",
- // edge0.first->getIndex(), edge0.second,
- // edge1.first->getIndex(), edge1.second);
+ pair<Element*, int> edge0 =
+ make_pair(elObjDb.getElementPtr(elIdx, meshes[i]), edgeNoInEl[elIdx]);
- // MSG("FOUND EDGE: %d %d with coords %f %f %f %f %f %f\n",
- // dofEdge0.first, dofEdge0.second,
- // c0[0], c0[1], c0[2],
- // c1[0], c1[1], c1[2]);
-
- TEST_EXIT_DBG(dofEdge0 == dofEdge1)("Should noth happen!\n");
+ for (std::set<int>::iterator elIt = disconnectedEls[dc0].begin();
+ elIt != disconnectedEls[dc0].end(); ++elIt) {
+ pair<Element*, int> edge1 =
+ make_pair(elObjDb.getElementPtr(*elIt, meshes[i]), edgeNoInEl[*elIt]);
+
+#if (DEBUG != 0)
+ DofEdge dofEdge0 = edge0.first->getEdge(edge0.second);
+ DofEdge dofEdge1 = edge1.first->getEdge(edge1.second);
+
+ WorldVector<double> c0, c1;
+ meshes[i]->getDofIndexCoords(dofEdge0.first, meshToFeSpaces[meshes[i]][0], c0);
+ meshes[i]->getDofIndexCoords(dofEdge0.second, meshToFeSpaces[meshes[i]][0], c1);
+
+ // MSG("FOUND EDGE %d/%d <-> %d/%d\n",
+ // edge0.first->getIndex(), edge0.second,
+ // edge1.first->getIndex(), edge1.second);
+
+ // MSG("FOUND EDGE: %d %d with coords %f %f %f %f %f %f\n",
+ // dofEdge0.first, dofEdge0.second,
+ // c0[0], c0[1], c0[2],
+ // c1[0], c1[1], c1[2]);
+
+ TEST_EXIT_DBG(dofEdge0 == dofEdge1)("Should noth happen!\n");
#endif
- FixRefinementPatch::connectedEdges.push_back(make_pair(edge1, edge0));
+ FixRefinementPatch::connectedEdges[meshes[i]].push_back(make_pair(edge1, edge0));
+ }
}
}
}
@@ -881,7 +979,6 @@ namespace AMDiS { namespace Parallel {
void MeshDistributor::helpToFix(std::set<int> &elems,
- map<int, int> &edgeNoInEl,
vector<std::set<int> > &disconnectedEls)
{
std::set<int> firstElem;
@@ -893,7 +990,7 @@ namespace AMDiS { namespace Parallel {
do {
found = false;
for (std::set<int>::iterator elIt = firstElem.begin(); elIt != firstElem.end(); ++elIt) {
- for (int i = 0; i < mesh->getGeo(NEIGH); i++) {
+ for (int i = 0; i < macroMesh->getGeo(NEIGH); i++) {
int neighEl = macroElementNeighbours[*elIt][i];
if (neighEl != -1 && otherElems.count(neighEl)) {
firstElem.insert(neighEl);
@@ -909,7 +1006,7 @@ namespace AMDiS { namespace Parallel {
disconnectedEls.push_back(firstElem);
if (otherElems.size())
- helpToFix(otherElems, edgeNoInEl, disconnectedEls);
+ helpToFix(otherElems, disconnectedEls);
}
@@ -933,19 +1030,22 @@ namespace AMDiS { namespace Parallel {
void MeshDistributor::removePeriodicBoundaryConditions()
{
// Remove periodic boundaries in boundary manager on matrices and vectors.
- for (unsigned int i = 0; i < problemStat.size(); i++)
+ for (size_t i = 0; i < problemStat.size(); i++)
removePeriodicBoundaryConditions(problemStat[i]);
// Remove periodic boundaries on elements in mesh.
- TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_EVERY_EL_PREORDER);
- while (elInfo) {
- elInfo->getElement()->deleteElementData(PERIODIC);
- elInfo = stack.traverseNext(elInfo);
- }
+ for (size_t i = 0; i < meshes.size(); i++) {
+
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(meshes[i], -1, Mesh::CALL_EVERY_EL_PREORDER);
+ while (elInfo) {
+ elInfo->getElement()->deleteElementData(PERIODIC);
+ elInfo = stack.traverseNext(elInfo);
+ }
- // Remove periodic vertex associations
- mesh->getPeriodicAssociations().clear();
+ // Remove periodic vertex associations
+ meshes[i]->getPeriodicAssociations().clear();
+ }
}
@@ -1122,12 +1222,19 @@ namespace AMDiS { namespace Parallel {
Parameters::get("parallel->debug->skip check mesh change", skip);
// === If mesh has not been changed on all ranks, return. ===
-
- int recvAllValues = 0;
- int sendValue = static_cast<int>(mesh->getChangeIndex() != lastMeshChangeIndex);
- mpiComm.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);
+ vector<int> meshAllValues(meshes.size(), 0);
+
+ for (size_t i = 0; i < meshes.size(); i++) {
+#if (DEBUG != 0)
+ MSG("mesh[%d] change index = %d, stored last index = %d.\n",
+ i, meshes[i]->getChangeIndex(), lastMeshChangeIndexs[meshes[i]]);
+#endif
+ int sendValue =
+ static_cast<int>(meshes[i]->getChangeIndex() != lastMeshChangeIndexs[meshes[i]]);
+ mpiComm.Allreduce(&sendValue, &meshAllValues[i], 1, MPI_INT, MPI_SUM);
+ }
- if (recvAllValues == 0)
+ if (meshAllValues.size() == count(meshAllValues.begin(), meshAllValues.end(), 0))
return;
TEST_EXIT(levelData.getNumberOfLevels() == 1)
@@ -1136,70 +1243,79 @@ namespace AMDiS { namespace Parallel {
// === At least one rank mesh has been changed, so the boundaries must be ===
// === adapted to the new mesh structure. ===
- if (skip == 0) {
- int iterationCounter = 0;
-
+ if (skip != 0) {
+ for (size_t i = 0; i < meshes.size(); i++)
+ if (meshAllValues[i] != 0)
+ updateDofRelatedStruct(meshes[i]);
+ } else {
// To check the interior boundaries, the ownership of the boundaries is not
// important. Therefore, we add all boundaries to one boundary container.
RankToBoundMap allBound;
for (InteriorBoundary::iterator it(intBoundary[0].getOwn()); !it.end(); ++it)
- if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) ||
- (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
+ if ((macroMesh->getDim() == 2 && it->rankObj.subObj == EDGE) ||
+ (macroMesh->getDim() == 3 && it->rankObj.subObj == FACE))
allBound[it.getRank()].push_back(*it);
for (InteriorBoundary::iterator it(intBoundary[0].getOther());
!it.end(); ++it)
- if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) ||
- (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
+ if ((macroMesh->getDim() == 2 && it->rankObj.subObj == EDGE) ||
+ (macroMesh->getDim() == 3 && it->rankObj.subObj == FACE))
allBound[it.getRank()].push_back(*it);
for (InteriorBoundary::iterator it(intBoundary[0].getPeriodic());
!it.end(); ++it)
if (it.getRank() != mpiRank)
- if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) ||
- (mesh->getDim() == 3 && it->rankObj.subObj == FACE))
+ if ((macroMesh->getDim() == 2 && it->rankObj.subObj == EDGE) ||
+ (macroMesh->getDim() == 3 && it->rankObj.subObj == FACE))
allBound[it.getRank()].push_back(*it);
- do {
- bool meshChanged = false;
+ for (size_t i = 0; i < meshes.size(); i++) {
+ if (meshAllValues[i] == 0)
+ continue;
+
+ int iterationCounter = 0;
+ do {
+ bool meshChanged = false;
// === Check the boundaries and adapt mesh if necessary. ===
#if (DEBUG != 0)
- MSG("Run checkAndAdaptBoundary ...\n");
+ MSG("Run checkAndAdaptBoundary for mesh[%d]...\n", i);
#endif
// Check for periodic boundaries within rank's subdomain.
- for (InteriorBoundary::iterator it(intBoundary[0].getPeriodic());
- !it.end(); ++it) {
- if (it.getRank() == mpiRank) {
- if ((mesh->getDim() == 2 && it->rankObj.subObj == EDGE) ||
- (mesh->getDim() == 3 && it->rankObj.subObj == FACE)) {
- MeshStructure elCode;
- elCode.init(it->rankObj);
-
- MeshManipulation mm(mesh);
- meshChanged |= mm.fitElementToMeshCode(elCode, it->neighObj);
+ for (InteriorBoundary::iterator it(intBoundary[0].getPeriodic());
+ !it.end(); ++it) {
+ if (it.getRank() == mpiRank) {
+ if ((macroMesh->getDim() == 2 && it->rankObj.subObj == EDGE) ||
+ (macroMesh->getDim() == 3 && it->rankObj.subObj == FACE)) {
+ MeshStructure elCode;
+ elCode.init(it->rankObj, elObjDb.getElementPtr(it->rankObj.elIndex, meshes[i]));
+
+ MeshManipulation mm(meshes[i]);
+ it->neighObj.el = elObjDb.getElementPtr(it->neighObj.elIndex, meshes[i]);
+ meshChanged |= mm.fitElementToMeshCode(elCode, it->neighObj);
+ }
}
}
- }
- meshChanged |= checkAndAdaptBoundary(allBound);
-
+ meshChanged |= checkAndAdaptBoundary(allBound, meshes[i]);
+
- // === Check on all ranks if at least one rank's mesh has changed. ===
-
- int sendValue = static_cast<int>(meshChanged);
- recvAllValues = 0;
- mpiComm.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);
+ // === Check on all ranks if at least one rank's mesh has changed. ===
+
+ int sendValue = static_cast<int>(meshChanged);
+ meshAllValues[i] = 0;
+ mpiComm.Allreduce(&sendValue, &meshAllValues[i], 1, MPI_INT, MPI_SUM);
+
+ MSG("Mesh changed on %d ranks!\n", meshAllValues[i]);
+ iterationCounter++;
+ } while (meshAllValues[i] != 0);
- MSG("Mesh changed on %d ranks!\n", recvAllValues);
- iterationCounter++;
- } while (recvAllValues != 0);
-
- MSG("Number of iteration to adapt mesh: %d\n", iterationCounter);
+ MSG("Number of iteration to adapt mesh: %d\n", iterationCounter);
+ updateDofRelatedStruct(meshes[i]);
+ }
}
-
mpiComm.Barrier();
MSG("Parallel mesh adaption needed %.5f seconds\n", t.elapsed());
@@ -1253,7 +1369,11 @@ namespace AMDiS { namespace Parallel {
int mpiSize = mpiComm.Get_size();
vector<int> nDofsInRank(mpiSize);
- int nDofs = mesh->getDofAdmin(0).getUsedDofs();
+ int nDofs = 0;
+
+ for (size_t i = 0; i < meshes.size(); i++)
+ nDofs += meshes[i]->getDofAdmin(0).getUsedDofs();
+
mpiComm.Gather(&nDofs, 1, MPI_INT, &(nDofsInRank[0]), 1, MPI_INT, 0);
if (mpiRank == 0) {
@@ -1299,7 +1419,7 @@ namespace AMDiS { namespace Parallel {
}
- bool MeshDistributor::checkAndAdaptBoundary(RankToBoundMap &allBound)
+ bool MeshDistributor::checkAndAdaptBoundary(RankToBoundMap &allBound, Mesh* mesh)
{
FUNCNAME_DBG("MeshDistributor::checkAndAdaptBoundary()");
@@ -1312,7 +1432,7 @@ namespace AMDiS { namespace Parallel {
for (vector<AtomicBoundary>::iterator boundIt = it->second.begin();
boundIt != it->second.end(); ++boundIt) {
MeshStructure elCode;
- elCode.init(boundIt->rankObj);
+ elCode.init(boundIt->rankObj, elObjDb.getElementPtr(boundIt->rankObj.elIndex, mesh));
sendCodes[it->first].push_back(elCode);
}
}
@@ -1330,7 +1450,6 @@ namespace AMDiS { namespace Parallel {
bool meshChanged = false;
-// int cCounter = 0;
for (RankToBoundMap::iterator it = allBound.begin();
it != allBound.end(); ++it) {
@@ -1341,7 +1460,7 @@ namespace AMDiS { namespace Parallel {
boundIt != it->second.end(); ++boundIt, i++) {
MeshStructure elCode;
- elCode.init(boundIt->rankObj);
+ elCode.init(boundIt->rankObj, elObjDb.getElementPtr(boundIt->rankObj.elIndex, mesh));
#if (DEBUG != 0)
ParallelDebug::followBoundary(mesh, *boundIt, elCode);
@@ -1355,7 +1474,9 @@ namespace AMDiS { namespace Parallel {
TEST_EXIT_DBG(refineManager)("Refinement manager is not set correctly!\n");
MeshManipulation mm(mesh);
+ boundIt->rankObj.el = elObjDb.getElementPtr(boundIt->rankObj.elIndex, mesh);
meshChanged |= mm.fitElementToMeshCode(recvCodes[i], boundIt->rankObj);
+ boundIt->rankObj.el = NULL;
}
}
}
@@ -1473,11 +1594,13 @@ namespace AMDiS { namespace Parallel {
elemWeights.clear();
{
- TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
- while (elInfo) {
- elemWeights[elInfo->getMacroElement()->getIndex()]++;
- elInfo = stack.traverseNext(elInfo);
+ for (size_t i = 0; i < meshes.size(); i++) {
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(meshes[i], -1, Mesh::CALL_LEAF_EL);
+ while (elInfo) {
+ elemWeights[elInfo->getMacroElement()->getIndex()]++;
+ elInfo = stack.traverseNext(elInfo);
+ }
}
}
@@ -1510,7 +1633,8 @@ namespace AMDiS { namespace Parallel {
Timer t;
#if (DEBUG != 0)
- ParallelDebug::testDoubleDofs(mesh);
+ for (size_t i = 0; i < meshes.size(); i++)
+ ParallelDebug::testDoubleDofs(meshes[i]);
int writePartMesh = 1;
#else
int writePartMesh = 0;
@@ -1540,7 +1664,7 @@ namespace AMDiS { namespace Parallel {
partitioner->partition(elemWeights, ADAPTIVE_REPART);
if (!partitioningSucceed) {
mpiComm.Barrier();
- repartitioningFailed = repartitioningWaitAfterFail;;
+ repartitioningFailed = repartitioningWaitAfterFail;
MSG("Mesh partitioner created empty partition!\n");
MSG("Mesh repartitioning needed %.5f seconds\n", t.elapsed());
return false;
@@ -1561,7 +1685,7 @@ namespace AMDiS { namespace Parallel {
}
}
- TEST_EXIT_DBG(!(partitioner->getSendElements().size() == mesh->getMacroElements().size() &&
+ TEST_EXIT_DBG(!(partitioner->getSendElements().size() == macroMesh->getMacroElements().size() &&
partitioner->getRecvElements().size() == 0))
("Partition is empty, should not happen!\n");
@@ -1571,19 +1695,18 @@ namespace AMDiS { namespace Parallel {
switch (strategy)
{
case 0:
- quickRepartition();
+ // Always starts from meshes[0], the macro mesh
+ for (size_t i = 0; i < meshes.size(); i++)
+ quickRepartition(meshes[i]);
break;
case 1:
- fullRepartition();
+ for (size_t i = 0; i < meshes.size(); i++)
+ fullRepartition(meshes[i]);
break;
default:
ERROR_EXIT("Unknown repartition strategy = %d!\n", strategy);
}
-
- partitioner->createPartitionMap(partitionMap);
-
- createInteriorBoundary(false);
-
+ // This is done outside repartition, don't forget!
updateLocalGlobalNumbering();
@@ -1594,7 +1717,8 @@ namespace AMDiS { namespace Parallel {
repartitioningCounter,
feSpaces[0]);
ParallelDebug::testAllElements(*this);
- ParallelDebug::testDoubleDofs(mesh);
+ for (size_t i = 0; i < meshes.size(); i++)
+ ParallelDebug::testDoubleDofs(meshes[i]);
ParallelDebug::testInteriorBoundary(*this);
ParallelDebug::testPeriodicBoundary(*this);
@@ -1607,12 +1731,12 @@ namespace AMDiS { namespace Parallel {
return true;
}
- void MeshDistributor::quickRepartition()
+ void MeshDistributor::quickRepartition(Mesh* mesh)
{
FUNCNAME("MeshDistributor::quickRepartition()");
#if (DEBUG != 0)
- MSG("Run quickRepartition ...\n");
+ MSG("... Run quickRepartition ...\n");
#endif
MPI::Intracomm &mpiComm = MPI::COMM_WORLD;
@@ -1620,15 +1744,15 @@ namespace AMDiS { namespace Parallel {
// === macro elements. ===
map<int, MacroElement*> elIndexMap;
- for (vector<MacroElement*>::iterator it = allMacroElements.begin();
- it != allMacroElements.end(); ++it)
+ for (vector<MacroElement*>::iterator it = allMacroElements[mesh].begin();
+ it != allMacroElements[mesh].end(); ++it)
elIndexMap[(*it)->getIndex()] = *it;
// === Create set of all new macro elements this rank will receive from ===
// === other ranks. ===
- std::set<MacroElement*> newMacroEl;
+ vector<MacroElement*> newMacroEl;
for (map<int, vector<int> >::iterator it = partitioner->getRecvElements().begin();
it != partitioner->getRecvElements().end(); ++it) {
for (vector<int>::iterator elIt = it->second.begin();
@@ -1636,12 +1760,16 @@ namespace AMDiS { namespace Parallel {
TEST_EXIT_DBG(elIndexMap.count(*elIt) == 1)
("Could not find macro element %d\n", *elIt);
- newMacroEl.insert(elIndexMap[*elIt]);
+ TEST_EXIT_DBG(find(newMacroEl.begin(), newMacroEl.end(),
+ elIndexMap[*elIt]) == newMacroEl.end())
+ ("The mesh received the same macro element %d twice! Something is wrong...\n", *elIt);
+
+ newMacroEl.push_back(elIndexMap[*elIt]);
}
}
std::set<MacroElement*> allMacroEl;
- for (std::set<MacroElement*>::iterator it = newMacroEl.begin();
+ for (vector<MacroElement*>::iterator it = newMacroEl.begin();
it != newMacroEl.end(); ++it)
allMacroEl.insert(*it);
@@ -1651,7 +1779,7 @@ namespace AMDiS { namespace Parallel {
// === Add new macro elements to mesh. ===
- for (std::set<MacroElement*>::iterator it = newMacroEl.begin();
+ for (vector<MacroElement*>::iterator it = newMacroEl.begin();
it != newMacroEl.end(); ++it) {
MacroElement *mel = *it;
@@ -1673,6 +1801,9 @@ namespace AMDiS { namespace Parallel {
map<int, MeshCodeVec> sendCodes;
map<int, vector<vector<double> > > sendValues;
+
+ TEST_EXIT(interchangeVectors.size() > 0)
+ ("There are no interchange vectors defined!\n");
for (map<int, vector<int> >::iterator it = partitioner->getSendElements().begin();
it != partitioner->getSendElements().end(); ++it) {
@@ -1682,11 +1813,17 @@ namespace AMDiS { namespace Parallel {
elCode.init(mesh, *elIt);
sendCodes[it->first].push_back(elCode);
- for (unsigned int i = 0; i < interchangeVectors.size(); i++) {
+ for (size_t i = 0; i < interchangeVectors.size(); i++) {
+ //only the vectors defined on the corresponding mesh
+ if (interchangeVectors[i]->getFeSpace()->getMesh() != mesh)
+ continue;
+
vector<double> valVec;
elCode.getMeshStructureValues(*elIt, interchangeVectors[i], valVec);
sendValues[it->first].push_back(valVec);
}
+ TEST_EXIT_DBG(!sendValues[it->first].empty())
+ ("There is no DOFVector defined on this mesh.\n");
}
}
@@ -1697,9 +1834,6 @@ namespace AMDiS { namespace Parallel {
stdMpi.recv(it->first);
stdMpi.startCommunication();
- TEST_EXIT(interchangeVectors.size() > 0)
- ("There are no interchange vectors defined!\n");
-
StdMpi<vector<vector<double> > > stdMpi2(mpiComm, true);
stdMpi2.send(sendValues);
for (map<int, vector<int> >::iterator it = partitioner->getRecvElements().begin();
@@ -1771,51 +1905,58 @@ namespace AMDiS { namespace Parallel {
// Note that also if there are no macros to be deleted, this function will
// update the number of elements, vertices, etc. of the mesh.
- mesh->removeMacroElements(deleteMacroElements, feSpaces);
+ mesh->removeMacroElements(deleteMacroElements, meshToFeSpaces[mesh]);
// === Remove double DOFs. ===
MeshManipulation meshManipulation(mesh);
- meshManipulation.deleteDoubleDofs(feSpaces, newMacroEl, elObjDb);
-
+ meshManipulation.deleteDoubleDofs(meshToFeSpaces[mesh], newMacroEl, elObjDb);
mesh->dofCompress();
-
-// partitioner->createPartitionMap(partitionMap);
-//
-//
-// createInteriorBoundary(false);
-//
-// updateLocalGlobalNumbering();
// === After mesh adaption, set values of interchange vectors. ===
for (map<int, vector<int> >::iterator it = partitioner->getRecvElements().begin();
it != partitioner->getRecvElements().end(); ++it) {
+
MeshCodeVec &recvCodes = stdMpi.getRecvData()[it->first];
vector<vector<double> > &recvValues = stdMpi2.getRecvData()[it->first];
+
int i = 0, j = 0;
for (vector<int>::iterator elIt = it->second.begin();
elIt != it->second.end(); ++elIt) {
- for (unsigned int k = 0; k < interchangeVectors.size(); k++)
+
+ for (size_t k = 0; k < interchangeVectors.size(); k++) {
+ if (interchangeVectors[k]->getFeSpace()->getMesh() != mesh)
+ continue;
+
recvCodes[i].setMeshStructureValues(*elIt,
interchangeVectors[k],
recvValues[j++]);
+ }
i++;
}
}
- // In 3D we have to make some test, if the resulting mesh is valid.
- fix3dMeshRefinement();
+ if (mesh == macroMesh) {
+ // In 3D we have to make some test, if the resulting mesh is valid.
+ fix3dMeshRefinement();
+ // PartitionMap is needed for createInteriorBoundary
+ partitioner->createPartitionMap(partitionMap);
+ // InteriorBoundary is needed for updateDofRelatedStruct
+ createInteriorBoundary(false);
+ }
+ updateDofRelatedStruct(mesh);
+
}
- void MeshDistributor::fullRepartition()
+ void MeshDistributor::fullRepartition(Mesh* mesh)
{
FUNCNAME("MeshDistributor::fullRepartition()");
#if (DEBUG != 0)
- MSG("Run fullRepartition ...\n");
+ MSG("... Run fullRepartition ...\n");
#endif
TEST_EXIT(interchangeVectors.size() > 0)
@@ -1826,18 +1967,17 @@ namespace AMDiS { namespace Parallel {
MPI::Intracomm &mpiComm = MPI::COMM_WORLD;
-#if DEBUG != 0
+#if (DEBUG != 0)
int nOldLeaves = mesh->getNumberOfLeaves();
- int nAllOldLeaves = 0;
- mpiComm.Allreduce(&nOldLeaves, &nAllOldLeaves, 1, MPI_INT, MPI_SUM);
+ mpi::globalAdd(mpiComm, nOldLeaves);
#endif
// === Create map that maps macro element indices to pointers to the ===
// === macro elements. ===
map<int, MacroElement*> elIndexMap;
- for (vector<MacroElement*>::iterator it = allMacroElements.begin();
- it != allMacroElements.end(); ++it)
+ for (vector<MacroElement*>::iterator it = allMacroElements[mesh].begin();
+ it != allMacroElements[mesh].end(); ++it)
elIndexMap[(*it)->getIndex()] = *it;
@@ -1877,6 +2017,9 @@ namespace AMDiS { namespace Parallel {
elCode.init(mesh, macroId);
for (size_t i = 0; i < interchangeVectors.size(); i++) {
+ if (interchangeVectors[i]->getFeSpace()->getMesh() != mesh)
+ continue;
+
vector<double> valVec;
elCode.getMeshStructureValues(macroId, interchangeVectors[i], valVec);
elValue.push_back(valVec);
@@ -1887,16 +2030,15 @@ namespace AMDiS { namespace Parallel {
}
// === Rebuild all macros in order to clean and renumber the dofs. ===
-
- // Remove domain meshes, not optimized.
- mesh->removeMacroElements(allMacroEl, feSpaces);
+
+ mesh->removeAllMacroElements();
TEST_EXIT_DBG(!mesh->getNumberOfMacros())
("Still %d macros remain?\n", mesh->getNumberOfMacros());
// Add all macros again.
- for (vector<MacroElement*>::iterator it = allMacroElements.begin();
- it != allMacroElements.end(); ++it) {
+ for (vector<MacroElement*>::iterator it = allMacroElements[mesh].begin();
+ it != allMacroElements[mesh].end(); ++it) {
MacroElement *mel = *it;
int elIndex = mel->getIndex();
@@ -1931,8 +2073,8 @@ namespace AMDiS { namespace Parallel {
}
// New dof indices for all macro elements.
- io::MacroReader::restoreMacroDofs(*(mesh->getMacroFileInfo()));
-
+ io::MacroReader::restoreMacroDofs(*(mesh->getMacroFileInfo()), 0);
+
// === Update the current mesh partition. ===
for (map<int, vector<int> >::iterator it = partitioner->getSendElements().begin();
@@ -1958,17 +2100,19 @@ namespace AMDiS { namespace Parallel {
std::set<MacroElement*> deleteMacroElements;
- for (vector<MacroElement*>::iterator it = allMacroElements.begin();
- it != allMacroElements.end(); ++it)
+ for (vector<MacroElement*>::iterator it = allMacroElements[mesh].begin();
+ it != allMacroElements[mesh].end(); ++it)
if (allMacroEl.find(*it) == allMacroEl.end())
deleteMacroElements.insert(*it);
-
+
// Note that also if there are no macros to be deleted, this function will
// update the number of elements, vertices, etc. of the mesh.
- mesh->removeMacroElements(deleteMacroElements, feSpaces);
+ mesh->removeMacroElements(deleteMacroElements, meshToFeSpaces[mesh]);
mesh->dofCompress();
- fix3dMeshRefinement();
-
+ // In fullRepartition, we need to call fix3d here instead of in the end.
+ if (mesh == macroMesh)
+ fix3dMeshRefinement();
+
// === Adapte all domain macro elements. ===
// Send and receive mesh structure codes.
@@ -2020,15 +2164,10 @@ namespace AMDiS { namespace Parallel {
TEST_EXIT_DBG(allMacroEl.find(elIndexMap[*elIt]) != allMacroEl.end())
("Received a macro element[%d] which doesn't belong to the domain. Something wrong.\n", *elIt);
-// MSG("%d-\n", *elIt);
-//
-// TEST_EXIT_DBG(elIndexMap[*elIt]->getElement()->isLeaf())
-// ("Macro %d already refined before applying mesh structure code?\n", *elIt);
recvCodes[i++].fitMeshToStructure(mesh, refineManager, false, *elIt);
}
}
-
// === After mesh adaption, set values of interchange vectors. ===
@@ -2039,19 +2178,20 @@ namespace AMDiS { namespace Parallel {
TEST_EXIT_DBG(domainMacroCodes.count(macroId))
("Reserved macro element[%d] has no stored structure data. Something wrong.\n", macroId);
-
-// MSG("%d-\n", *macroId);
-//
-// TEST_EXIT_DBG(elIndexMap[macroId]->getElement()->isLeaf())
-// ("Macro %d already refined before applying mesh structure code?\n", macroId);
+
domainMacroCodes[macroId].fitMeshToStructure(mesh, refineManager, false, macroId);
-
+
+ int j = 0;
for (size_t i = 0; i < interchangeVectors.size(); i++) {
+ if (interchangeVectors[i]->getFeSpace()->getMesh() != mesh)
+ continue;
+
domainMacroCodes[macroId].setMeshStructureValues(macroId,
interchangeVectors[i],
- domainMacroValues[macroId][i]);
-#if DEBUG != 0
+ domainMacroValues[macroId][j++]);
+
+#if (DEBUG != 0)
MeshStructure code;
code.init(mesh, macroId);
TEST_EXIT(code.getCode() == domainMacroCodes[macroId].getCode())
@@ -2067,21 +2207,30 @@ namespace AMDiS { namespace Parallel {
int i = 0, j = 0;
for (vector<int>::iterator elIt = it->second.begin();
elIt != it->second.end(); ++elIt) {
- for (unsigned int k = 0; k < interchangeVectors.size(); k++)
+ for (size_t k = 0; k < interchangeVectors.size(); k++) {
+ if (interchangeVectors[k]->getFeSpace()->getMesh() != mesh)
+ continue;
+
recvCodes[i].setMeshStructureValues(*elIt,
interchangeVectors[k],
recvValues[j++]);
+ }
i++;
}
}
-#if DEBUG != 0
+ if (mesh == macroMesh) {
+ partitioner->createPartitionMap(partitionMap);
+ createInteriorBoundary(false);
+ }
+ updateDofRelatedStruct(mesh);
+
+#if (DEBUG != 0)
int nNewLeaves = mesh->getNumberOfLeaves();
- int nAllNewLeaves = 0;
- mpiComm.Allreduce(&nNewLeaves, &nAllNewLeaves, 1, MPI_INT, MPI_SUM);
+ mpi::globalAdd(mpiComm, nNewLeaves);
- TEST_EXIT(nAllOldLeaves == nAllNewLeaves)
- ("Overall number of leaves change from %d to %d\n", nAllOldLeaves, nAllNewLeaves);
+ TEST_EXIT(nOldLeaves == nNewLeaves)
+ ("Overall number of leaves change from %d to %d\n", nOldLeaves, nNewLeaves);
#endif
}
@@ -2094,9 +2243,15 @@ namespace AMDiS { namespace Parallel {
elObjDb.create(partitionMap, levelData);
elObjDb.updateRankData();
+#if (DEBUG != 0)
+ if (mpiRank == 0)
+ ParallelDebug::writePeriodicElObjInfo(*this, debugOutputDir);
+#endif
// === If requested, calculate and print memory usage of element ===
// === object database. ===
+
+ //TODO To be reimplemented
if (printMemoryUsage && firstCall) {
unsigned long memsize = elObjDb.calculateMemoryUsage();
MSG("Memory usage of element object database = %5.f KByte\n",
@@ -2111,14 +2266,13 @@ namespace AMDiS { namespace Parallel {
if (firstCall) {
int tmpSend = static_cast<int>(intBoundary[0].hasPeriodic());
- int tmpRecv = 0;
- MPI::COMM_WORLD.Allreduce(&tmpSend, &tmpRecv, 1, MPI_INT, MPI_MAX);
- hasPeriodicBoundary = static_cast<bool>(tmpRecv);
+ mpi::globalAdd(MPI::COMM_WORLD, tmpSend);
+ hasPeriodicBoundary = static_cast<bool>(tmpSend);
}
}
- void MeshDistributor::createBoundaryDofs()
+ void MeshDistributor::createBoundaryDofs(Mesh* mesh)
{
FUNCNAME("MeshDistributor::createBoundaryDofs()");
@@ -2126,14 +2280,19 @@ namespace AMDiS { namespace Parallel {
if (printTimings)
t = new Timer();
- // === Create DOF communicator. ===
-
- dofComm.init(levelData, feSpaces);
- dofComm.create(intBoundary);
-
-
- // === If requested, create more information on communication DOFs. ===
+ // === Create all DOF communicators, if mesh is NULL. ===
+ // === Otherwise create only special one. ===
+ if (!mesh) {
+ std::map<Mesh*, MultiLevelDofComm>::iterator it = dofComms.begin();
+ for (; it != dofComms.end(); it++)
+ it->second.create(it->first, intBoundary);
+ } else {
+ TEST_EXIT_DBG(dofComms.find(mesh) != dofComms.end())("No such mesh.\n");
+ dofComms[mesh].create(mesh, intBoundary);
+ }
+ // === If requested, create more information on communication DOFs. ===
+
if (createBoundaryDofFlag.isSet(BOUNDARY_SUBOBJ_SORTED)) {
int nLevels = levelData.getNumberOfLevels();
@@ -2154,7 +2313,9 @@ namespace AMDiS { namespace Parallel {
!it.end(); ++it) {
if (it->rankObj.subObj == geo) {
DofContainer dofs;
- it->rankObj.el->getAllDofs(feSpace, it->rankObj, dofs);
+
+ intBoundary[level].getElementPtr(it->rankObj.elIndex, feSpace->getMesh())
+ ->getAllDofs(feSpace, it->rankObj, dofs);
if (createBoundaryDofFlag.isSet(BOUNDARY_FILL_INFO_SEND_DOFS))
boundaryDofInfo[level][feSpace].
@@ -2169,7 +2330,9 @@ namespace AMDiS { namespace Parallel {
!it.end(); ++it) {
if (it->rankObj.subObj == geo) {
DofContainer dofs;
- it->rankObj.el->getAllDofs(feSpace, it->rankObj, dofs);
+
+ intBoundary[level].getElementPtr(it->rankObj.elIndex, feSpace->getMesh())
+ ->getAllDofs(feSpace, it->rankObj, dofs);
if (createBoundaryDofFlag.isSet(BOUNDARY_FILL_INFO_RECV_DOFS))
boundaryDofInfo[level][feSpace].
@@ -2190,19 +2353,30 @@ namespace AMDiS { namespace Parallel {
void MeshDistributor::removeMacroElements()
{
- std::set<MacroElement*> macrosToRemove;
- for (deque<MacroElement*>::iterator it = mesh->firstMacroElement();
- it != mesh->endOfMacroElements(); ++it)
- if (partitioner->getElementInRank()[(*it)->getIndex()] == false)
- macrosToRemove.insert(*it);
+ for (size_t i = 0; i < meshes.size(); i++) {
+ std::set<MacroElement*> macrosToRemove;
+ for (deque<MacroElement*>::iterator it = meshes[i]->firstMacroElement();
+ it != meshes[i]->endOfMacroElements(); ++it)
+ if (partitioner->getElementInRank()[(*it)->getIndex()] == false)
+ macrosToRemove.insert(*it);
- mesh->removeMacroElements(macrosToRemove, feSpaces);
+ meshes[i]->removeMacroElements(macrosToRemove, meshToFeSpaces[meshes[i]]);
+ }
+ }
+
+ void MeshDistributor::updateDofRelatedStruct()
+ {
+ for (size_t i = 0; i < meshes.size(); i++)
+ updateDofRelatedStruct(meshes[i]);
+
+ updateLocalGlobalNumbering();
}
-
- void MeshDistributor::updateLocalGlobalNumbering()
+ void MeshDistributor::updateDofRelatedStruct(Mesh* mesh)
{
- FUNCNAME("MeshDistributor::updateLocalGlobalNumbering()");
+ FUNCNAME("MeshDistributor::updateDofRelatedStruct()");
+
+ TEST_EXIT(mesh)("No mesh.\n");
Timer t;
@@ -2214,28 +2388,15 @@ namespace AMDiS { namespace Parallel {
#endif
// === Update DOF communicator objects. ===
-
- createBoundaryDofs();
+ createBoundaryDofs(mesh);
// === Update all registered DOF mapping objects. ===
-
- updateParallelDofMappings();
-
-
- // === Create periodic DOF maps, if there are periodic boundaries. ===
-
- if (hasPeriodicBoundary) {
- createPeriodicMap();
-
- for (int i = 0; i < static_cast<int>(dofMaps.size()); i++)
- dofMaps[i]->updateMatIndex();
- }
+ updateDofsToDofMapping(mesh);
// === Update DOF admins due to new number of DOFs. ===
-
- lastMeshChangeIndex = mesh->getChangeIndex();
+ lastMeshChangeIndexs[mesh] = mesh->getChangeIndex();
#if (DEBUG != 0)
@@ -2243,91 +2404,148 @@ namespace AMDiS { namespace Parallel {
stringstream ss;
ss << debugOutputDir << "elementMaps." << fileNumber ;
- //write local Element Maps to csv file
+ // Write local Element Maps to csv file
ParallelDebug::writeCsvElementMap(feSpaces[0],
*(dofMaps[0]),
ss.str(), "csv");
fileNumber++;
- ParallelDebug::testDofContainerCommunication(*this);
-
- MSG("------------- Debug information -------------\n");
- MSG("| number of levels: %d\n", levelData.getNumberOfLevels());
- MSG("| number of FE spaces: %d\n", feSpaces.size());
-
-
- for (int i = 0; i < static_cast<int>(dofMaps.size()); i++) {
- vector<const FiniteElemSpace*>& dofMapSpaces = dofMaps[i]->getFeSpaces();
-
- for (int j = 0; j < static_cast<int>(dofMapSpaces.size()); j++) {
- const FiniteElemSpace *feSpace = dofMapSpaces[j];
- MSG("| FE space = %d (pointer adr %p):\n", j, feSpace);
- MSG("| nRankDofs = %d\n", (*(dofMaps[i]))[feSpace].nRankDofs);
- MSG("| nOverallDofs = %d\n", (*(dofMaps[i]))[feSpace].nOverallDofs);
- MSG("| rStartDofs = %d\n", (*(dofMaps[i]))[feSpace].rStartDofs);
- }
- }
+ ParallelDebug::testDofContainerCommunication(*this, mesh);
// debug::writeElementIndexMesh(mesh, debugOutputDir + "elementIndex-" +
// lexical_cast<string>(mpiRank) + ".vtu");
- ParallelDebug::writeDebugFile(feSpaces[feSpaces.size() - 1],
- *(dofMaps[0]),
- debugOutputDir + "mpi-dbg", "dat");
debug::testSortedDofs(mesh, elMap);
int test = 0;
Parameters::get("parallel->remove periodic boundary", test);
- if (test == 0) {
- ParallelDebug::testCommonDofs(*this, true);
- ParallelDebug::testGlobalIndexByCoords(*this);
- }
+ if (test == 0)
+ ParallelDebug::testCommonDofs(*this, mesh, true);
+#endif
+
+ MPI::COMM_WORLD.Barrier();
+ MSG("Update parallel data structures needed %.5f seconds\n", t.elapsed());
+ }
+
+ void MeshDistributor::updateLocalGlobalNumbering()
+ {
+ FUNCNAME("MeshDistributor::updateLocalGlobalNumbering()");
+
+ Timer t;
+#if (DEBUG != 0)
+ bool printInfo = true;
#else
+ bool printInfo = false;
+#endif
+ Parameters::get("parallel->print dofmap info", printInfo);
+
+ for (size_t i = 0; i < dofMaps.size(); i++) {
+ dofMaps[i]->update();
+ if (printInfo)
+ dofMaps[i]->printInfo();
+ }
+
+ // === Create periodic DOF maps, if there are periodic boundaries. ===
- for (int i = 0; i < static_cast<int>(dofMaps.size()); i++) {
- vector<const FiniteElemSpace*>& dofMapSpaces = dofMaps[i]->getFeSpaces();
+ if (hasPeriodicBoundary) {
+ createPeriodicMap();
- for (int j = 0; j < static_cast<int>(dofMapSpaces.size()); j++)
- MSG("FE space %d: nRankDofs = %d nOverallDofs = %d\n", j,
- (*(dofMaps[i]))[feSpaces[j]].nRankDofs,
- (*(dofMaps[i]))[feSpaces[j]].nOverallDofs);
+ for (size_t i = 0; i < dofMaps.size(); i++)
+ dofMaps[i]->updateMatIndex();
}
- int tmp = 0;
- Parameters::get(name + "->write parallel debug file", tmp);
- if (tmp)
- ParallelDebug::writeDebugFile(feSpaces[feSpaces.size() - 1],
- *(dofMaps[0]),
- debugOutputDir + "mpi-dbg", "dat");
-#endif
+ if (printInfo) {
+ int test = 0;
+ Parameters::get("parallel->remove periodic boundary", test);
+
+ MSG("------------- Debug information -------------\n");
+ for (size_t k = 0; k < meshes.size(); k++) {
+ Mesh* mesh = meshes[k];
+
+ MSG("| mesh pointer adr: %p\n", mesh);
+ MSG("| number of levels: %d\n", levelData.getNumberOfLevels());
+ MSG("| number of FE spaces: %d\n", meshToFeSpaces[mesh].size());
+
+
+ for (size_t i = 0; i < dofMaps.size(); i++) {
+ vector<const FiniteElemSpace*> dofMapSpaces = dofMaps[i]->getFeSpaces(mesh);
+
+ if (dofMapSpaces.empty())
+ continue;
+
+ for (size_t j = 0; j < dofMapSpaces.size(); j++) {
+ const FiniteElemSpace *feSpace = dofMapSpaces[j];
+ MSG("| FE space = %d (pointer adr %p):\n", j, feSpace);
+ MSG("| nRankDofs = %d\n", (*(dofMaps[i]))[feSpace].nRankDofs);
+ MSG("| nOverallDofs = %d\n", (*(dofMaps[i]))[feSpace].nOverallDofs);
+ MSG("| rStartDofs = %d\n", (*(dofMaps[i]))[feSpace].rStartDofs);
+ }
+ }
+
+// ParallelDebug::writeDebugFile(meshToFeSpaces[mesh][meshToFeSpaces[mesh].size() - 1],
+// *(dofMaps[0]),
+// debugOutputDir + "mpi-dbg", "dat");
+
+ if (test == 0)
+ ParallelDebug::testGlobalIndexByCoords(*this, mesh);
+ }
+
+ } else {
+
+// int tmp = 0;
+// Parameters::get(name + "->write parallel debug file", tmp);
+
+ for (size_t k = 0; k < meshes.size(); k++) {
+ Mesh* mesh = meshes[k];
+
+ for (size_t i = 0; i < dofMaps.size(); i++) {
+
+ vector<const FiniteElemSpace*> dofMapSpaces = dofMaps[i]->getFeSpaces(mesh);
+
+ if (dofMapSpaces.empty())
+ continue;
+
+ for (size_t j = 0; j < dofMapSpaces.size(); j++)
+ MSG("FE space %d (mesh ptr %p): nRankDofs = %d nOverallDofs = %d\n", j, dofMapSpaces[j]->getMesh(),
+ (*(dofMaps[i]))[dofMapSpaces[j]].nRankDofs,
+ (*(dofMaps[i]))[dofMapSpaces[j]].nOverallDofs);
+ }
+
+// Write debug file for each mesh and each dofmap?
+// if (tmp)
+// ParallelDebug::writeDebugFile(meshToFeSpaces[mesh][meshToFeSpaces[mesh].size() - 1],
+// *(dofMaps[0]),
+// debugOutputDir + "mpi-dbg", "dat");
+ }
+ }
- MSG("Rebuild of parallel data structures needed %.5f seconds\n", t.elapsed());
+ MPI::COMM_WORLD.Barrier();
+ MSG("Update dof mapping needed %.5f seconds\n", t.elapsed());
}
- void MeshDistributor::updateParallelDofMappings()
+ void MeshDistributor::updateDofsToDofMapping(Mesh* mesh)
{
- FUNCNAME("MeshDistributor::updateParallelDofMappings()");
+ FUNCNAME("MeshDistributor::updateDofsToDofMapping()");
Timer *t = NULL;
if (printTimings)
t = new Timer();
TEST_EXIT(dofMaps.size())("No DOF mapping defined!\n");
-
- for (int i = 0; i < static_cast<int>(dofMaps.size()); i++) {
- vector<const FiniteElemSpace*>& dofMapSpaces = dofMaps[i]->getFeSpaces();
+
+ for (size_t i = 0; i < dofMaps.size(); i++) {
+ vector<const FiniteElemSpace*> dofMapSpaces = dofMaps[i]->getFeSpaces(mesh);
- dofMaps[i]->clear();
-
- for (int j = 0; j < static_cast<int>(dofMapSpaces.size()); j++)
- updateLocalGlobalNumbering(*(dofMaps[i]), dofMapSpaces[j]);
+ if (dofMapSpaces.empty())
+ continue;
+
+ dofMaps[i]->clear(mesh);
+
+ for (size_t j = 0; j < dofMapSpaces.size(); j++)
+ updateDofsToDofMapping(*(dofMaps[i]), dofMapSpaces[j]);
- dofMaps[i]->update();
-#if (DEBUG != 0)
- dofMaps[i]->printInfo();
-#endif
}
if (printTimings && t) {
@@ -2337,10 +2555,12 @@ namespace AMDiS { namespace Parallel {
}
- void MeshDistributor::updateLocalGlobalNumbering(ParallelDofMapping &dofMap,
+ void MeshDistributor::updateDofsToDofMapping(ParallelDofMapping &dofMap,
const FiniteElemSpace *feSpace)
{
- DofComm &dcom = dofMap.getDofComm();
+
+ DofComm &dcom = dofMap[feSpace].getDofComm();
+ Mesh* mesh = feSpace->getMesh();
// === Get all DOFs in ranks partition. ===
@@ -2387,7 +2607,7 @@ namespace AMDiS { namespace Parallel {
// MPI::COMM_WORLD.Barrier(); [TODO: CHANGE BECAUSE NOT ALL RANKS HAVE PERIODIC MAP!!!]
double first = MPI::Wtime();
- for (unsigned int i = 0; i < feSpaces.size(); i++)
+ for (size_t i = 0; i < feSpaces.size(); i++)
createPeriodicMap(feSpaces[i]);
// MPI::COMM_WORLD.Barrier();
@@ -2400,9 +2620,19 @@ namespace AMDiS { namespace Parallel {
FUNCNAME("MeshDistributor::createPeriodicMap()");
TEST_EXIT(dofMaps.size())("No DOF mapping defined!\n");
-
- DofComm::DataType &periodicDofs = dofComm[0].getPeriodicDofs();
- ComponentDofMap &dofMap = (*(dofMaps[0]))[feSpace];
+
+ ParallelDofMapping* parDofMap = NULL;
+ for (size_t i = 0; i < dofMaps.size(); i++)
+ if (dofMaps[i]->hasFeSpace(feSpace)) {
+ parDofMap = dofMaps[i];
+ break;
+ }
+
+ TEST_EXIT_DBG(parDofMap)("FE space not found in parallel dof map.\n");
+ ComponentDofMap &dofMap = (*parDofMap)[feSpace];
+ Mesh* mesh = feSpace->getMesh();
+ DofComm::DataType &periodicDofs = dofComms[mesh][0].getPeriodicDofs();
+
StdMpi<vector<int> > stdMpi(MPI::COMM_WORLD, false);
@@ -2420,15 +2650,15 @@ namespace AMDiS { namespace Parallel {
TEST_EXIT_DBG(it->second.size() % 2 == 0)("Should not happen!\n");
- for (unsigned int i = 0; i < it->second.size(); i++) {
+ for (size_t i = 0; i < it->second.size(); i++) {
AtomicBoundary &bound = it->second[i];
-
- TEST_EXIT_DBG(bound.rankObj.el)("No rank object!\n");
- TEST_EXIT_DBG(bound.neighObj.el)("No neigh object!\n");
-
+
DofContainer dofs0, dofs1;
- bound.rankObj.el->getAllDofs(feSpace, bound.rankObj, dofs0);
- bound.neighObj.el->getAllDofs(feSpace, bound.neighObj, dofs1);
+
+ intBoundary[0].getElementPtr(bound.rankObj.elIndex, mesh)
+ ->getAllDofs(feSpace, bound.rankObj, dofs0);
+ intBoundary[0].getElementPtr(bound.neighObj.elIndex, mesh)
+ ->getAllDofs(feSpace, bound.neighObj, dofs1);
TEST_EXIT_DBG(dofs0.size() == dofs1.size())
("Number of DOFs does not fit together: %d %d\n",
@@ -2436,7 +2666,7 @@ namespace AMDiS { namespace Parallel {
BoundaryType type = bound.type;
- for (unsigned int j = 0; j < dofs0.size(); j++) {
+ for (size_t j = 0; j < dofs0.size(); j++) {
DegreeOfFreedom globalDof0 = dofMap[*(dofs0[j])].global;
DegreeOfFreedom globalDof1 = dofMap[*(dofs1[j])].global;
@@ -2454,7 +2684,8 @@ namespace AMDiS { namespace Parallel {
boundIt != it->second.end(); ++boundIt) {
int nDofs = dofs.size();
- boundIt->rankObj.el->getAllDofs(feSpace, boundIt->rankObj, dofs);
+ intBoundary[0].getElementPtr(boundIt->rankObj.elIndex, mesh)
+ ->getAllDofs(feSpace, boundIt->rankObj, dofs);
for (unsigned int i = 0; i < (dofs.size() - nDofs); i++)
rankToDofType[it->first].push_back(boundIt->type);
@@ -2519,9 +2750,10 @@ namespace AMDiS { namespace Parallel {
continue;
DofContainer dofs;
- boundIt->rankObj.el->getAllDofs(feSpace, boundIt->rankObj, dofs);
+ intBoundary[0].getElementPtr(boundIt->rankObj.elIndex, mesh)
+ ->getAllDofs(feSpace, boundIt->rankObj, dofs);
- for (unsigned int i = 0; i < dofs.size(); i++) {
+ for (size_t i = 0; i < dofs.size(); i++) {
DegreeOfFreedom globalDof = dofMap[*dofs[i]].global;
std::set<BoundaryType>& assoc =
@@ -2553,44 +2785,49 @@ namespace AMDiS { namespace Parallel {
void MeshDistributor::createMacroElementInfo()
{
- FUNCNAME("MeshDistributor::createMacroElementInfo()");
-
- for (deque<MacroElement*>::iterator it = mesh->firstMacroElement();
- it != mesh->endOfMacroElements(); ++it) {
-
- allMacroElements.push_back(*it);
-
+ // Store neighbours info.
+ for (deque<MacroElement*>::iterator it = macroMesh->firstMacroElement();
+ it != macroMesh->endOfMacroElements(); ++it) {
+
int elIndex = (*it)->getIndex();
+
+ macroElementNeighbours[elIndex].resize(macroMesh->getGeo(NEIGH));
+ for (int i = 0; i < macroMesh->getGeo(NEIGH); i++)
+ macroElementNeighbours[elIndex][i] =
+ (*it)->getNeighbour(i) ? (*it)->getNeighbour(i)->getIndex() : -1;
+ }
- macroElementNeighbours[elIndex].resize(mesh->getGeo(NEIGH));
- for (int i = 0; i < mesh->getGeo(NEIGH); i++)
- macroElementNeighbours[elIndex][i] =
- (*it)->getNeighbour(i) ? (*it)->getNeighbour(i)->getIndex() : -1;
- }
+ // Store macro elements
+ for (size_t i = 0; i < meshes.size(); i++)
+ for (deque<MacroElement*>::iterator it = meshes[i]->firstMacroElement();
+ it != meshes[i]->endOfMacroElements(); ++it)
+ allMacroElements[meshes[i]].push_back(*it);
+
}
-
void MeshDistributor::updateMacroElementInfo()
{
- deque<MacroElement*>& meshMacros = mesh->getMacroElements();
-
- for (unsigned int i = 0; i < allMacroElements.size(); i++) {
- for (deque<MacroElement*>::iterator it = meshMacros.begin();
+ for (size_t i = 0; i < meshes.size(); i++) {
+ deque<MacroElement*>& meshMacros = meshes[i]->getMacroElements();
+
+ vector<MacroElement*>& allMacros = allMacroElements[meshes[i]];
+
+ for (size_t j = 0; j < allMacros.size(); j++) {
+ for (deque<MacroElement*>::iterator it = meshMacros.begin();
it != meshMacros.end(); ++it) {
- if ((*it)->getIndex() == allMacroElements[i]->getIndex() &&
- *it != allMacroElements[i]) {
- delete allMacroElements[i];
- allMacroElements[i] = *it;
+ if ((*it)->getIndex() == allMacros[j]->getIndex() &&
+ *it != allMacros[j]) {
+ delete allMacros[j];
+ allMacros[j] = *it;
+ }
}
}
}
}
-
+ //TODO To be changed if necessary
void MeshDistributor::serialize(ostream &out)
{
- FUNCNAME("MeshDistributor::serialize()");
-
checkMeshChange(false);
partitioner->serialize(out);
@@ -2608,8 +2845,8 @@ namespace AMDiS { namespace Parallel {
int nSize = allMacroElements.size();
SerUtil::serialize(out, nSize);
- for (int i = 0; i < nSize; i++)
- allMacroElements[i]->serialize(out);
+// for (int i = 0; i < nSize; i++)
+// allMacroElements[i]->serialize(out);
SerUtil::serialize(out, nMeshChangesAfterLastRepartitioning);
SerUtil::serialize(out, repartitioningCounter);
@@ -2617,10 +2854,9 @@ namespace AMDiS { namespace Parallel {
}
+ //TODO To be changed if necessary
void MeshDistributor::deserialize(istream &in)
{
- FUNCNAME("MeshDistributor::deserialize()");
-
partitioner->deserialize(in);
SerUtil::deserialize(in, elemWeights);
@@ -2631,7 +2867,7 @@ namespace AMDiS { namespace Parallel {
for (unsigned int i = 0; i < feSpaces.size(); i++) {
ElementDofIterator elDofIter(feSpaces[i]);
TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL);
+ ElInfo *elInfo = stack.traverseFirst(meshes[0], -1, Mesh::CALL_LEAF_EL);
while (elInfo) {
elDofIter.reset(elInfo->getElement());
do {
@@ -2644,7 +2880,7 @@ namespace AMDiS { namespace Parallel {
elObjDb.deserialize(in);
- intBoundary.deserialize(in, mesh);
+ intBoundary.deserialize(in, meshes[0]);
// === Deerialieze FE space dependent data ===
@@ -2652,15 +2888,15 @@ namespace AMDiS { namespace Parallel {
int nSize = 0;
SerUtil::deserialize(in, nSize);
- allMacroElements.resize(nSize);
- for (int i = 0; i < nSize; i++) {
- // We do not need the neighbour indices, but must still read them.
- vector<int> indices;
- allMacroElements[i] = new MacroElement(mesh->getDim());
- allMacroElements[i]->writeNeighboursTo(&indices);
- allMacroElements[i]->deserialize(in);
- allMacroElements[i]->getElement()->setMesh(mesh);
- }
+// allMacroElements.resize(nSize);
+// for (int i = 0; i < nSize; i++) {
+// // We do not need the neighbour indices, but must still read them.
+// vector<int> indices;
+// allMacroElements[i] = new MacroElement(mesh->getDim());
+// allMacroElements[i]->writeNeighboursTo(&indices);
+// allMacroElements[i]->deserialize(in);
+// allMacroElements[i]->getElement()->setMesh(mesh);
+// }
SerUtil::deserialize(in, nMeshChangesAfterLastRepartitioning);
SerUtil::deserialize(in, repartitioningCounter);
diff --git a/AMDiS/src/parallel/MeshDistributor.h b/AMDiS/src/parallel/MeshDistributor.h
index fcff9718..efad03e2 100644
--- a/AMDiS/src/parallel/MeshDistributor.h
+++ b/AMDiS/src/parallel/MeshDistributor.h
@@ -115,7 +115,7 @@ namespace AMDiS { namespace Parallel {
void removeInterchangeVector(SystemVector* vec);
/** \brief
- * This function checks if the mesh has changed on at least on rank. In
+ * This function checks if the mesh has changed on at least one rank. In
* this case, the interior boundaries are adapted on all ranks such that
* they fit together on all ranks. Furthermore the function
* \ref updateLocalGlobalNumbering() is called to update the DOF numberings
@@ -134,9 +134,6 @@ namespace AMDiS { namespace Parallel {
/// ranks.
bool repartitionMesh();
- void quickRepartition();
-
- void fullRepartition();
void getImbalanceFactor(double &imbalance,
int &minDofs,
@@ -159,9 +156,19 @@ namespace AMDiS { namespace Parallel {
return name;
}
- inline Mesh* getMesh()
+ inline Mesh* getMacroMesh()
+ {
+ return macroMesh;
+ }
+
+ inline Mesh* getMesh(int i = 0)
{
- return mesh;
+ return meshes[i];
+ }
+
+ inline int getNumberOfMeshes()
+ {
+ return meshes.size();
}
/// Returns the periodic mapping handler, \ref periodicMap.
@@ -174,6 +181,16 @@ namespace AMDiS { namespace Parallel {
{
return dofComm[level];
}
+
+ DofComm& getDofComm(Mesh* mesh, int level)
+ {
+ return dofComms[mesh][level];
+ }
+
+ std::map<Mesh*, MultiLevelDofComm>& getDofComms()
+ {
+ return dofComms;
+ }
InteriorBoundary& getIntBoundary(int level)
{
@@ -182,7 +199,16 @@ namespace AMDiS { namespace Parallel {
inline long getLastMeshChangeIndex()
{
- return lastMeshChangeIndex;
+ int overallMeshChangeIndex = 0;
+ for(size_t i = 0; i < meshes.size(); i++) {
+ overallMeshChangeIndex += lastMeshChangeIndexs[meshes[i]];
+ }
+ return overallMeshChangeIndex;
+ }
+
+ inline long getLastMeshChangeIndex(Mesh* m)
+ {
+ return lastMeshChangeIndexs[m];
}
inline int getMpiRank()
@@ -271,10 +297,42 @@ namespace AMDiS { namespace Parallel {
/// DOFVector, but instead sends all values of all DOFVectors all at once.
void synchVector(SystemVector &vec);
+ /// Works quite similar to the function \ref synchVector, but instead the
+ /// values of subdomain vectors are add along the boundaries.
template<typename T>
void synchAddVector(DOFVector<T> &vec)
{
- synchVector(vec, functors::add_assign<T>());
+ const FiniteElemSpace *fe = vec.getFeSpace();
+
+ int nLevels = levelData.getNumberOfLevels();
+ for (int level = nLevels - 1; level >= 0; level--) {
+ StdMpi<std::vector<T> > stdMpi(levelData.getMpiComm(level));
+
+ for (DofComm::Iterator it(dofComm[level].getRecvDofs(), fe);
+ !it.end(); it.nextRank()) {
+ std::vector<T> dofs;
+ dofs.reserve(it.getDofs().size());
+
+ for (; !it.endDofIter(); it.nextDof())
+ dofs.push_back(vec[it.getDofIndex()]);
+
+ stdMpi.send(it.getRank(), dofs);
+ }
+
+ for (DofComm::Iterator it(dofComm[level].getSendDofs());
+ !it.end(); it.nextRank())
+ stdMpi.recv(it.getRank());
+
+ stdMpi.startCommunication();
+
+ for (DofComm::Iterator it(dofComm[level].getSendDofs(), fe);
+ !it.end(); it.nextRank())
+ for (; !it.endDofIter(); it.nextDof())
+ vec[it.getDofIndex()] +=
+ stdMpi.getRecvData(it.getRank())[it.getDofCounter()];
+ }
+
+ synchVector(vec);
}
/// In 3D, a subdomain may not be a valid AMDiS mesh if it contains two
@@ -288,8 +346,6 @@ namespace AMDiS { namespace Parallel {
/** \brief Is used only within \ref fix3dMeshRefinement.
*
* \param[in] elems Set of macro element indices.
- * \param[in] edgeNoInEl Maps from each element index in elems to a
- * local edge number.
* \param[out] disconnectedEls On output, this vector contains sets of
* element indices. The union is equal to elems.
* Each set contains all element indices, which
@@ -298,7 +354,6 @@ namespace AMDiS { namespace Parallel {
* cannot be reached via neigbourhood relation.
*/
void helpToFix(std::set<int> &elems,
- std::map<int, int> &edgeNoInEl,
std::vector<std::set<int> > &disconnectedEls);
void setBoundaryDofRequirement(Flag flag)
@@ -334,16 +389,16 @@ namespace AMDiS { namespace Parallel {
{
return levelData;
}
-
- /// Updates all registered parallel DOF mappings, see \ref dofMaps.
- void updateParallelDofMappings();
+
+ /// Update dof communicators, boundary dof info and the parallel dof mappings.
+ /// If it is called for all meshes, \ref updateLocalGlobalNumbering is automatically
+ /// called inside. If it is used for each mesh seperately, please don't forget to
+ /// add \ref updateLocalGlobalNumbering to update the global matrix index.
+ void updateDofRelatedStruct();
+
+ void updateDofRelatedStruct(Mesh* mesh);
void updateLocalGlobalNumbering();
-
- /// Updates the local and global DOF numbering after the mesh has been
- /// changed.
- void updateLocalGlobalNumbering(ParallelDofMapping &dmap,
- const FiniteElemSpace *feSpace);
/// set variable \ref repartitioningAllowed
void setRepartitioningAllowed(bool allowed)
@@ -357,6 +412,18 @@ namespace AMDiS { namespace Parallel {
}
protected:
+ /// Rebuild only part of the mesh domain, which is necessary
+ void quickRepartition(Mesh* mesh);
+
+ /// Rebuild whole mesh domain
+ void fullRepartition(Mesh* mesh);
+
+ /// Updates all registered parallel DOF mappings, see \ref dofMaps.
+ void updateDofsToDofMapping(Mesh* mesh = NULL);
+
+ /// Updates the DOF after the mesh has been changed, see \ref dofMaps.
+ void updateDofsToDofMapping(ParallelDofMapping &dmap,
+ const FiniteElemSpace *feSpace);
/// Checks if repartition is needed.
bool isRepartitionNecessary();
@@ -380,7 +447,7 @@ namespace AMDiS { namespace Parallel {
void createInteriorBoundary(bool firstCall);
///
- void createBoundaryDofs();
+ void createBoundaryDofs(Mesh* mesh = NULL);
/// Removes all macro elements from the mesh that are not part of ranks
/// partition.
@@ -415,12 +482,13 @@ namespace AMDiS { namespace Parallel {
*
* \param[in] allBound Defines a map from rank to interior boundaries
* which should be checked.
+ * \param[in] mesh The mesh the interior boundaries belong to.
*
* \return If the mesh has been changed by this function, it returns
* true. Otherwise, it returns false, i.e., the given interior
* boundaries fit together on both sides.
*/
- bool checkAndAdaptBoundary(RankToBoundMap &allBound);
+ bool checkAndAdaptBoundary(RankToBoundMap &allBound, Mesh* mesh);
/// Removes all periodic boundary condition information from all matrices and
/// vectors of all stationary problems and from the mesh itself.
@@ -507,10 +575,16 @@ namespace AMDiS { namespace Parallel {
/// Set of all different FE spaces.
std::vector<const FiniteElemSpace*> feSpaces;
- /// Pointer to the only mesh. Note that we do not yet support multi mesh
- /// method, thus even if we consider coupled problems, all problems must
- /// be defined on the same mesh.
- Mesh *mesh;
+ /// Always equal to meshes[0] which is used as macro
+ /// mesh. For example, passed to \ref meshPartitioner.
+ Mesh *macroMesh;
+
+ /// Meshes to be managed for parallelization. Currently only two meshes
+ /// are allowed since multi mesh method is limited to two meshes.
+ std::vector<Mesh*> meshes;
+
+ /// Stores the map of meshes and the corresponding FE spaces defined on them
+ MeshToFeSpaces meshToFeSpaces;
/// A refinement manager that should be used on the mesh. It is used to
/// refine elements at interior boundaries in order to fit together with
@@ -543,8 +617,11 @@ namespace AMDiS { namespace Parallel {
/// partitioning the whole mesh.
MultiLevelInteriorBoundary intBoundary;
- /// Dof communicator object
+ /// Dof communicator object // TODO: to be deleted
MultiLevelDofComm dofComm;
+
+ /// Dof communicator objects for each mesh
+ std::map<Mesh*, MultiLevelDofComm> dofComms;
PeriodicMap periodicMap;
@@ -592,7 +669,7 @@ namespace AMDiS { namespace Parallel {
/// Stores the mesh change index. This is used to recognize changes in the
/// mesh structure (e.g. through refinement or coarsening managers).
- long lastMeshChangeIndex;
+ std::map<Mesh*, long> lastMeshChangeIndexs;
/// Stores for all macro elements of the original macro mesh the
/// neighbourhood information based on element indices. Thus, each macro
@@ -602,7 +679,9 @@ namespace AMDiS { namespace Parallel {
/// Store all macro elements of the overall mesh, i.e., before the
/// mesh is redistributed for the first time.
- std::vector<MacroElement*> allMacroElements;
+ /// Store all macro elements of the overall mesh, i.e., before the
+ /// mesh is redistributed for the first time.
+ std::map<Mesh*, std::vector<MacroElement*> > allMacroElements;
Flag createBoundaryDofFlag;
diff --git a/AMDiS/src/parallel/MeshManipulation.cc b/AMDiS/src/parallel/MeshManipulation.cc
index d10676dc..91facf8a 100644
--- a/AMDiS/src/parallel/MeshManipulation.cc
+++ b/AMDiS/src/parallel/MeshManipulation.cc
@@ -53,6 +53,14 @@ namespace AMDiS { namespace Parallel {
delete refineManager;
}
+ void MeshManipulation::deleteDoubleDofs(std::vector<const FiniteElemSpace*>& feSpaces,
+ std::vector<MacroElement*>& newMacroEl,
+ ElementObjectDatabase &elObjDb)
+ {
+ std::set<MacroElement*> newMacroElSet(newMacroEl.begin(), newMacroEl.end());
+ deleteDoubleDofs(feSpaces, newMacroElSet, elObjDb);
+ }
+
void MeshManipulation::deleteDoubleDofs(vector<const FiniteElemSpace*>& feSpaces,
std::set<MacroElement*>& newMacroEl,
@@ -90,7 +98,6 @@ namespace AMDiS { namespace Parallel {
elInfo = stack.traverseNext(elInfo);
}
-
#if (DEBUG != 0)
DOFVector<WorldVector<double> > coords(feSpace, "dofCorrds");
feSpace->getMesh()->getDofIndexCoords(coords);
@@ -153,6 +160,8 @@ namespace AMDiS { namespace Parallel {
Element *el0 = (*it)->getElement();
Element *el1 = macroIndexMap[elIt->elIndex]->getElement();
+ TEST_EXIT_DBG(el0->getMesh() == el1->getMesh())("Mesh is different.\n");
+
bool reverseMode = elObjDb.getEdgeReverseMode(elObj, *elIt);
BoundaryObject b0(el0, 0, EDGE, i, reverseMode);
@@ -163,6 +172,7 @@ namespace AMDiS { namespace Parallel {
el0->getAllDofs(feSpace, b0, dofs0, true, &dofGeoIndex0);
el1->getAllDofs(feSpace, b1, dofs1, true, &dofGeoIndex1);
+
#if (DEBUG != 0)
if (feSpaces.size())
debug::testDofsByCoords(coords, dofs0, dofs1);
@@ -170,7 +180,6 @@ namespace AMDiS { namespace Parallel {
TEST_EXIT_DBG(dofs0.size() == dofs1.size())
("Should not happen!\n");
#endif
-
for (unsigned int i = 0; i < dofs0.size(); i++) {
mapDelDofs[dofs0[i]] = dofs1[i];
dofPosIndex[dofs0[i]] = dofGeoIndex0[i];
@@ -234,7 +243,6 @@ namespace AMDiS { namespace Parallel {
}
}
}
-
macrosProcessed.insert((*it)->getIndex());
}
diff --git a/AMDiS/src/parallel/MeshManipulation.h b/AMDiS/src/parallel/MeshManipulation.h
index 037ad608..172785ef 100644
--- a/AMDiS/src/parallel/MeshManipulation.h
+++ b/AMDiS/src/parallel/MeshManipulation.h
@@ -42,6 +42,10 @@ namespace AMDiS { namespace Parallel {
void deleteDoubleDofs(std::vector<const FiniteElemSpace*>& feSpaces,
std::set<MacroElement*>& newMacroEl,
ElementObjectDatabase &elObj);
+
+ void deleteDoubleDofs(std::vector<const FiniteElemSpace*>& feSpaces,
+ std::vector<MacroElement*>& newMacroEl,
+ ElementObjectDatabase &elObjDb);
/** \brief
* Starts the procedure to fit a given edge/face of a macro element with a
diff --git a/AMDiS/src/parallel/ParallelCoarseSpaceSolver.cc b/AMDiS/src/parallel/ParallelCoarseSpaceSolver.cc
index e372bd84..d4276767 100644
--- a/AMDiS/src/parallel/ParallelCoarseSpaceSolver.cc
+++ b/AMDiS/src/parallel/ParallelCoarseSpaceSolver.cc
@@ -50,6 +50,7 @@ namespace AMDiS { namespace Parallel {
TEST_EXIT(meshDistributor)("No mesh distributor object defined!\n");
domainComm = meshDistributor->getMpiComm(meshLevel);
+
if (meshLevel >= 1)
coarseSpaceComm = meshDistributor->getMpiComm(meshLevel - 1);
@@ -140,14 +141,14 @@ namespace AMDiS { namespace Parallel {
bool localMatrix = (domainComm == MPI::COMM_SELF);
if (checkMeshChange()) {
- int nMat = uniqueCoarseMap.size() + 1;
+ int nMat = uniqueCoarseMap.size() + 1; // Not multilevel should always be 1
nnz.resize(nMat);
for (int i = 0; i < nMat; i++) {
nnz[i].resize(nMat);
for (int j = 0; j < nMat; j++)
nnz[i][j].clear();
}
-
+
nnz[0][0].create(seqMat, *interiorMap,
(coarseSpaceMap.size() == 0 ? &(meshDistributor->getPeriodicMap()) : NULL),
meshDistributor->getElementObjectDb(),
@@ -157,7 +158,7 @@ namespace AMDiS { namespace Parallel {
for (int j = 0; j < nMat; j++) {
if (i == 0 && j == 0)
continue;
-
+
ParallelDofMapping &rowMap =
(i == 0 ? *interiorMap : *(uniqueCoarseMap[i - 1]));
ParallelDofMapping &colMap =
@@ -172,7 +173,6 @@ namespace AMDiS { namespace Parallel {
// === Create PETSc matrices and PETSc vectors with the computed ===
// === nnz data structure. ===
-
int nRankInteriorRows = interiorMap->getRankDofs();
int nOverallInteriorRows = interiorMap->getOverallDofs();
@@ -197,7 +197,7 @@ namespace AMDiS { namespace Parallel {
300, PETSC_NULL, 300, PETSC_NULL, &mat[0][0]);
}
}
-
+
MatSetOption(mat[0][0], MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);
if (meshLevel == 0) {
@@ -216,7 +216,6 @@ namespace AMDiS { namespace Parallel {
&vecRhs[0]);
}
-
int nCoarseMap = uniqueCoarseMap.size();
for (int i = 0; i < nCoarseMap; i++) {
ParallelDofMapping* cMap = uniqueCoarseMap[i];
diff --git a/AMDiS/src/parallel/ParallelDebug.cc b/AMDiS/src/parallel/ParallelDebug.cc
index 14fe0d5b..fa4a30e7 100644
--- a/AMDiS/src/parallel/ParallelDebug.cc
+++ b/AMDiS/src/parallel/ParallelDebug.cc
@@ -181,7 +181,7 @@ namespace AMDiS { namespace Parallel {
perMap.periodicDofAssociations[feSpace].begin();
it != perMap.periodicDofAssociations[feSpace].end(); ++it) {
WorldVector<double> c;
- pdb.mesh->getDofIndexCoords(it->first, pdb.feSpaces[0], c);
+ pdb.macroMesh->getDofIndexCoords(it->first, pdb.feSpaces[0], c);
}
@@ -292,7 +292,7 @@ namespace AMDiS { namespace Parallel {
for (unsigned int i = 0; i < dofs.size(); i++) {
WorldVector<double> c;
- pdb.mesh->getDofIndexCoords(*(dofs[i]), feSpace, c);
+ pdb.macroMesh->getDofIndexCoords(*(dofs[i]), feSpace, c);
sendCoords[it->first].push_back(c);
rankToDofType[it->first].push_back(boundIt->type);
}
@@ -321,7 +321,7 @@ namespace AMDiS { namespace Parallel {
int nEqual = 0;
- for (int j = 0; j < pdb.mesh->getDim(); j++)
+ for (int j = 0; j < pdb.macroMesh->getDim(); j++)
if (c0[j] == c1[j])
nEqual++;
@@ -329,9 +329,9 @@ namespace AMDiS { namespace Parallel {
MSG("[DBG] %d-ith periodic DOF in boundary between ranks %d <-> %d is not correct!\n",
i, mpiRank, it->first);
MSG("[DBG] Coords on rank %d: %f %f %f\n",
- mpiRank, c0[0], c0[1], (pdb.mesh->getDim() == 3 ? c0[2] : 0.0));
+ mpiRank, c0[0], c0[1], (pdb.macroMesh->getDim() == 3 ? c0[2] : 0.0));
MSG("[DBG] Coords on rank %d: %f %f %f\n",
- it->first, c1[0], c1[1], (pdb.mesh->getDim() == 3 ? c1[2] : 0.0));
+ it->first, c1[0], c1[1], (pdb.macroMesh->getDim() == 3 ? c1[2] : 0.0));
foundError = 1;
}
@@ -343,13 +343,16 @@ namespace AMDiS { namespace Parallel {
}
- void ParallelDebug::testCommonDofs(MeshDistributor &pdb, bool printCoords)
+ // Test if the coordinates of recv and send dofs in dofcomm are matched
+ void ParallelDebug::testCommonDofs(MeshDistributor &pdb, Mesh* mesh, bool printCoords)
{
FUNCNAME("ParallelDebug::testCommonDofs()");
Timer t;
// Get FE space with basis functions of the highest degree
- const FiniteElemSpace *feSpace = pdb.feSpaces[pdb.feSpaces.size() - 1];
+ const FiniteElemSpace *feSpace =
+ pdb.meshToFeSpaces[mesh][pdb.meshToFeSpaces[mesh].size() - 1];
+ MultiLevelDofComm& dofComm = pdb.dofComms[mesh];
int testCommonDofs = 1;
Parameters::get("dbg->test common dofs", testCommonDofs);
@@ -387,14 +390,14 @@ namespace AMDiS { namespace Parallel {
RankToCoords recvCoords;
DOFVector<WorldVector<double> > coords(feSpace, "dofCorrds");
- pdb.mesh->getDofIndexCoords(coords);
+ mesh->getDofIndexCoords(coords);
- for (DofComm::Iterator it(pdb.dofComm[level].getSendDofs(), feSpace);
+ for (DofComm::Iterator it(dofComm[level].getSendDofs(), feSpace);
!it.end(); it.nextRank())
for (; !it.endDofIter(); it.nextDof())
sendCoords[it.getRank()].push_back(coords[it.getDofIndex()]);
- for (DofComm::Iterator it(pdb.dofComm[level].getRecvDofs(), feSpace);
+ for (DofComm::Iterator it(dofComm[level].getRecvDofs(), feSpace);
!it.end(); it.nextRank())
for (; !it.endDofIter(); it.nextDof())
recvCoords[it.getRank()].push_back(coords[it.getDofIndex()]);
@@ -487,7 +490,7 @@ namespace AMDiS { namespace Parallel {
MSG("%s\n", oss.str().c_str());
debug::printInfoByDof(feSpace,
- *(pdb.dofComm[level].getRecvDofs()[it->first][feSpace][i]));
+ *(dofComm[level].getRecvDofs()[it->first][feSpace][i]));
}
ERROR("Wrong DOFs in rank %d!\n", mpiRank);
foundError = 1;
@@ -501,83 +504,102 @@ namespace AMDiS { namespace Parallel {
MSG("Test common dofs needed %.5f seconds\n", t.elapsed());
}
-
- void ParallelDebug::testGlobalIndexByCoords(MeshDistributor &pdb)
+ // Test dofmap dofs with same global index have same coords
+ void ParallelDebug::testGlobalIndexByCoords(MeshDistributor &pdb, Mesh* mesh)
{
FUNCNAME("ParallelDebug::testGlobalIndexByCoords()");
// Get FE space with basis functions of the highest degree
- const FiniteElemSpace *feSpace = pdb.feSpaces[pdb.feSpaces.size() - 1];
-
- DOFVector<WorldVector<double> > coords(feSpace, "tmp");
- pdb.mesh->getDofIndexCoords(coords);
-
- int nLevels = pdb.levelData.getNumberOfLevels();
- for (int level = 0; level < nLevels; level++) {
- MPI::Intracomm &mpiComm = pdb.levelData.getMpiComm(level);
- if (mpiComm == MPI::COMM_SELF)
- continue;
-
-// int mpiRank = mpiComm.Get_rank();
-// int mpiSize = mpiComm.Get_size();
-
- typedef map<int, WorldVector<double> > CoordsIndexMap;
- CoordsIndexMap coordsToIndex;
+ MultiLevelDofComm& dofComm = pdb.dofComms[mesh];
+
+ for (size_t i = 0; i < pdb.dofMaps.size(); i++) {
+ vector<const FiniteElemSpace*> dofMapSpaces = pdb.dofMaps[i]->getFeSpaces(mesh);
- DOFIterator<WorldVector<double> > it(&coords, USED_DOFS);
- for (it.reset(); !it.end(); ++it) {
- int idx = (*(pdb.dofMaps[level]))[feSpace][it.getDOFIndex()].global;
- coordsToIndex[idx] = *it;
-// MSG(" CHECK FOR DOF %d/%d AT COORDS %f %f %f\n",
-// it.getDOFIndex(),
-// coordsToIndex[(*it)],
-// (*it)[0], (*it)[1], (pdb.mesh->getDim() == 3 ? (*it)[2] : 0.0));
- }
+ if(dofMapSpaces.empty())
+ continue;
- StdMpi<CoordsIndexMap> stdMpi(mpiComm, true);
- for (DofComm::Iterator it(pdb.dofComm[level].getSendDofs(), feSpace);
- !it.end(); it.nextRank())
- stdMpi.send(it.getRank(), coordsToIndex);
- for (DofComm::Iterator it(pdb.dofComm[level].getRecvDofs(), feSpace);
- !it.end(); it.nextRank())
- stdMpi.recv(it.getRank());
+ const FiniteElemSpace *feSpace = NULL;
+ ParallelDofMapping* dfmap = pdb.dofMaps[i];
- stdMpi.startCommunication();
+ size_t j = pdb.meshToFeSpaces[mesh].size() - 1;
+ for( ; j >= 0; j--)
+ if(find(dofMapSpaces.begin(), dofMapSpaces.end(), pdb.meshToFeSpaces[mesh][j])
+ != dofMapSpaces.end())
+ break;
+ feSpace = pdb.meshToFeSpaces[mesh][j];
- int foundError = 0;
- for (DofComm::Iterator it(pdb.dofComm[level].getRecvDofs(), feSpace);
- !it.end(); it.nextRank()) {
- CoordsIndexMap& otherCoords = stdMpi.getRecvData(it.getRank());
+ TEST_EXIT(dfmap || feSpace)("Something is wrong.\n");
- for (; !it.endDofIter(); it.nextDof()) {
- WorldVector<double> recvCoords = coords[it.getDofIndex()];
- int idx = (*(pdb.dofMaps[level]))[feSpace][it.getDofIndex()].global;
-
- TEST_EXIT_DBG(otherCoords.count(idx))("Global index not found in neighbour partition\n");
-
- WorldVector<double> diff = otherCoords[idx] - recvCoords;
- double dist = sqrt(diff*diff);
- if (dist > DBL_TOL) {
- stringstream oss;
- oss.precision(5);
- oss << "DOF at coords ";
- for (int i = 0; i < Global::getGeo(WORLD); i++)
- oss << recvCoords[i] << " ";
- oss << " do not fit together on rank "
- << mpiComm.Get_rank() << " (global index: "
- << it.getDofIndex() << ") and on rank "
- << it.getRank() << " "
- << " - LEVEL " << level;
-
- MSG("[DBG] %s\n", oss.str().c_str());
+ DOFVector<WorldVector<double> > coords(feSpace, "tmp");
+ mesh->getDofIndexCoords(coords);
+
+ int nLevels = pdb.levelData.getNumberOfLevels();
+ for (int level = 0; level < nLevels; level++) {
+ MPI::Intracomm &mpiComm = pdb.levelData.getMpiComm(level);
+ if (mpiComm == MPI::COMM_SELF)
+ continue;
+
+ // int mpiRank = mpiComm.Get_rank();
+ // int mpiSize = mpiComm.Get_size();
+
+ typedef map<int, WorldVector<double> > CoordsIndexMap;
+ CoordsIndexMap coordsToIndex;
+
+ DOFIterator<WorldVector<double> > it(&coords, USED_DOFS);
+ for (it.reset(); !it.end(); ++it) {
+ int idx = (*dfmap)[feSpace][it.getDOFIndex()].global;
+ coordsToIndex[idx] = *it;
+ // MSG(" CHECK FOR DOF %d/%d AT COORDS %f %f %f\n",
+ // it.getDOFIndex(),
+ // coordsToIndex[(*it)],
+ // (*it)[0], (*it)[1], (pdb.mesh->getDim() == 3 ? (*it)[2] : 0.0));
+ }
+
+ StdMpi<CoordsIndexMap> stdMpi(mpiComm, true);
+ for (DofComm::Iterator it(dofComm[level].getSendDofs(), feSpace);
+ !it.end(); it.nextRank())
+ stdMpi.send(it.getRank(), coordsToIndex);
+ for (DofComm::Iterator it(dofComm[level].getRecvDofs(), feSpace);
+ !it.end(); it.nextRank())
+ stdMpi.recv(it.getRank());
+
+ stdMpi.startCommunication();
+
+ int foundError = 0;
+ for (DofComm::Iterator it(dofComm[level].getRecvDofs(), feSpace);
+ !it.end(); it.nextRank()) {
+ CoordsIndexMap& otherCoords = stdMpi.getRecvData(it.getRank());
+
+ for (; !it.endDofIter(); it.nextDof()) {
+ WorldVector<double> recvCoords = coords[it.getDofIndex()];
+ int idx = (*dfmap)[feSpace][it.getDofIndex()].global;
- foundError = 1;
+ TEST_EXIT_DBG(otherCoords.count(idx))("Global index not found in neighbour partition\n");
+
+ WorldVector<double> diff = otherCoords[idx] - recvCoords;
+ double dist = sqrt(diff*diff);
+ if (dist > DBL_TOL) {
+ stringstream oss;
+ oss.precision(5);
+ oss << "DOF at coords ";
+ for (int i = 0; i < Global::getGeo(WORLD); i++)
+ oss << recvCoords[i] << " ";
+ oss << " do not fit together on rank "
+ << mpiComm.Get_rank() << " (global index: "
+ << it.getDofIndex() << ") and on rank "
+ << it.getRank() << " "
+ << " - LEVEL " << level;
+
+ MSG("[DBG] %s\n", oss.str().c_str());
+
+ foundError = 1;
+ }
}
}
- }
- mpi::globalAdd(foundError);
- TEST_EXIT(foundError == 0)("Error found on at least on rank!\n");
+ mpi::globalAdd(foundError);
+ TEST_EXIT(foundError == 0)("Error found on at least on rank!\n");
+ }
}
}
@@ -585,13 +607,15 @@ namespace AMDiS { namespace Parallel {
void ParallelDebug::testAllElements(MeshDistributor &pdb)
{
FUNCNAME("ParallelDebug::testAllElements()");
+
+ TEST_EXIT(pdb.macroMesh) ("No macro mesh in mesh distributor.\n");
std::set<int> macroElements;
int minElementIndex = numeric_limits<int>::max();
int maxElementIndex = numeric_limits<int>::min();
TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(pdb.mesh, 0, Mesh::CALL_EL_LEVEL);
+ ElInfo *elInfo = stack.traverseFirst(pdb.macroMesh, 0, Mesh::CALL_EL_LEVEL);
while (elInfo) {
int elIndex = elInfo->getElement()->getIndex();
minElementIndex = std::min(minElementIndex, elIndex);
@@ -599,7 +623,7 @@ namespace AMDiS { namespace Parallel {
macroElements.insert(elInfo->getElement()->getIndex());
elInfo = stack.traverseNext(elInfo);
}
-
+
MPI::Intracomm mpiComm = MPI::COMM_WORLD;
@@ -619,14 +643,14 @@ namespace AMDiS { namespace Parallel {
}
if (recvId > 1) {
- ERROR_EXIT("Element %d is member of more than pne partition!\n", i);
+ ERROR_EXIT("Element %d is member of more than pne partition!\n", i);
}
}
}
}
-
- void ParallelDebug::testDofContainerCommunication(MeshDistributor &pdb)
+ // Test dofcomm whether send and recv dofs match
+ void ParallelDebug::testDofContainerCommunication(MeshDistributor &pdb, Mesh* mesh)
{
FUNCNAME("ParallelDebug::testDofContainerCommunication()");
@@ -635,24 +659,26 @@ namespace AMDiS { namespace Parallel {
typedef map<int, map<const FiniteElemSpace*, DofContainer> >::iterator it_type;
MPI::Intracomm &mpiComm = pdb.levelData.getMpiComm(0);
+ MultiLevelDofComm& dofComm = pdb.dofComms[mesh];
+
map<int, int> sendNumber;
- for (it_type it = pdb.dofComm[0].getSendDofs().begin();
- it != pdb.dofComm[0].getSendDofs().end(); ++it)
+ for (it_type it = dofComm[0].getSendDofs().begin();
+ it != dofComm[0].getSendDofs().end(); ++it)
for (map<const FiniteElemSpace*, DofContainer>::iterator dcIt = it->second.begin();
dcIt != it->second.end(); ++dcIt)
sendNumber[it->first] += dcIt->second.size();
map<int, int> recvNumber;
- for (it_type it = pdb.dofComm[0].getRecvDofs().begin();
- it != pdb.dofComm[0].getRecvDofs().end(); ++it)
+ for (it_type it = dofComm[0].getRecvDofs().begin();
+ it != dofComm[0].getRecvDofs().end(); ++it)
for (map<const FiniteElemSpace*, DofContainer>::iterator dcIt = it->second.begin();
dcIt != it->second.end(); ++dcIt)
recvNumber[it->first] += dcIt->second.size();
StdMpi<int> stdMpi(mpiComm);
stdMpi.send(sendNumber);
- for (it_type it = pdb.dofComm[0].getRecvDofs().begin();
- it != pdb.dofComm[0].getRecvDofs().end(); ++it)
+ for (it_type it = dofComm[0].getRecvDofs().begin();
+ it != dofComm[0].getRecvDofs().end(); ++it)
stdMpi.recv(it->first);
stdMpi.startCommunication();
@@ -666,12 +692,24 @@ namespace AMDiS { namespace Parallel {
foundError = 1;
}
}
+
+ std::set<DegreeOfFreedom> sendDofs;
+ for (DofComm::Iterator it(dofComm[0].getSendDofs(), pdb.meshToFeSpaces[mesh][0]);
+ !it.end(); it.nextRank())
+ for (; !it.endDofIter(); it.nextDof())
+ sendDofs.insert(it.getDofIndex());
+
+ for (DofComm::Iterator it2(dofComm[0].getRecvDofs(), pdb.meshToFeSpaces[mesh][0]);
+ !it2.end(); it2.nextRank())
+ for (; !it2.endDofIter(); it2.nextDof())
+ TEST_EXIT(!sendDofs.count(it2.getDofIndex()))
+ ("Send and recv dof contaniners share same dof %d.\n", it2.getDofIndex());
mpi::globalAdd(foundError);
TEST_EXIT(foundError == 0)("Error found on at least one rank!\n");
}
-
+ // Test whether one domain has two dofs with same coordinates
void ParallelDebug::testDoubleDofs(Mesh *mesh)
{
FUNCNAME("ParallelDebug::testDoubleDofs()");
@@ -763,7 +801,7 @@ namespace AMDiS { namespace Parallel {
dofit != rankDofs.end(); ++dofit) {
cout << " " << **dofit << endl;
WorldVector<double> coords;
- pdb.mesh->getDofIndexCoords(*dofit, pdb.feSpaces[0], coords);
+ pdb.macroMesh->getDofIndexCoords(*dofit, pdb.feSpaces[0], coords);
coords.print();
}
@@ -772,7 +810,7 @@ namespace AMDiS { namespace Parallel {
dofit != rankAllDofs.end(); ++dofit) {
cout << " " << **dofit << endl;
WorldVector<double> coords;
- pdb.mesh->getDofIndexCoords(*dofit, pdb.feSpaces[0], coords);
+ pdb.macroMesh->getDofIndexCoords(*dofit, pdb.feSpaces[0], coords);
coords.print();
}
}
@@ -816,14 +854,29 @@ namespace AMDiS { namespace Parallel {
it->neighObj.elIndex, it->neighObj.subObj, it->neighObj.ithObj);
}
}
-
+
+ void ParallelDebug::writeDebugFile(MeshToFeSpaces& meshToFeSpaces,
+ ParallelDofMapping &dofMap,
+ string debugOutputDir)
+ {
+ int i = 0;
+ MeshToFeSpaces::iterator it = meshToFeSpaces.begin();
+ while(it != meshToFeSpaces.end()) {
+ string prefix = debugOutputDir + "mpi-dbg-mesh" + boost::lexical_cast<string>(i);
+ writeDebugFile(it->second[it->second.size() - 1],
+ dofMap, prefix, "dat");
+ it++;
+ i++;
+ }
+
+ }
void ParallelDebug::writeDebugFile(const FiniteElemSpace *feSpace,
ParallelDofMapping &dofMap,
string prefix,
string postfix)
{
- FUNCNAME("ParallelDebug::writeCoordsFile()");
+ FUNCNAME("ParallelDebug::writeDebugFile()");
Mesh *mesh = feSpace->getMesh();
@@ -890,7 +943,7 @@ namespace AMDiS { namespace Parallel {
map<int, double> vec;
TraverseStack stack;
- ElInfo *elInfo = stack.traverseFirst(pdb.mesh, -1, Mesh::CALL_LEAF_EL);
+ ElInfo *elInfo = stack.traverseFirst(pdb.macroMesh, -1, Mesh::CALL_LEAF_EL);
while (elInfo) {
int index = elInfo->getMacroElement()->getIndex();
@@ -898,7 +951,7 @@ namespace AMDiS { namespace Parallel {
elInfo = stack.traverseNext(elInfo);
}
- io::ElementFileWriter::writeFile(vec, pdb.mesh, filename);
+ io::ElementFileWriter::writeFile(vec, pdb.macroMesh, filename);
}
@@ -1116,4 +1169,103 @@ namespace AMDiS { namespace Parallel {
}
}
+
+ void ParallelDebug::writeDofMap(ParallelDofMapping &dofMap, int component, string filename, string postfix)
+ {
+ filename += boost::lexical_cast<std::string>(MPI::COMM_WORLD.Get_rank());
+ filename = filename + "." + postfix;
+
+ ofstream file;
+ file.open(filename.c_str(), ios::out | ios::trunc);
+
+ DofToMatIndex::MapType& data = dofMap.getMatData(component);
+
+ DofToMatIndex::MapType::iterator it = data.begin();
+
+ file << &dofMap << "\n";
+ file << dofMap[component].nRankDofs << "\n";
+
+ //
+// for (DofComm::Iterator it(dofComm->getRecvDofs(), feSpace);
+// !it.end(); it.nextRank()) {
+// int rank = it.getRank();
+// // if (meshLevel > 0)
+// // rank = levelData->mapRank(rank, 0, meshLevel);
+//
+// int i = 0;
+// for (; !it.endDofIter(); it.nextDof())
+// if (nonRankDofs.count(it.getDofIndex()))
+// dofMap[it.getDofIndex()].global = stdMpi.getRecvData(rank)[i++];
+// }
+ //
+
+ while (it != data.end()) {
+ if (dofMap.isMatIndexFromGlobal())
+ file << it->first << " " << it->second << "\n";
+ else
+ file << it->first << " " << it->second << "\n";
+ it++;
+ }
+ file.close();
+ }
+
+ void ParallelDebug::writePeriodicElObjInfo(MeshDistributor &pdb, string debugOutputDir)
+ {
+ string filename = debugOutputDir + "periodic-info.dat";
+ ofstream file;
+ file.open(filename.c_str());
+
+ ElementObjectDatabase& elObjDb = pdb.getElementObjectDb();
+
+ file << "periodicVertices:\n";
+ for (PerBoundMap<DegreeOfFreedom>::iterator it = elObjDb.periodicVertices.begin();
+ it != elObjDb.periodicVertices.end(); it++) {
+ file << it->first.first << ", " << it->first.second
+ << " : " << it->second << endl;
+ }
+ file << "periodicEdges:\n";
+ for (PerBoundMap<DofEdge>::iterator it = elObjDb.periodicEdges.begin();
+ it != elObjDb.periodicEdges.end(); it++) {
+ file << it->first.first.first << " " << it->first.first.second << ", "
+ << it->first.second.first << " " << it->first.second.second << " : "
+ << it->second << endl;
+ }
+ file << "periodicFaces:\n";
+ for (PerBoundMap<DofFace>::iterator it = elObjDb.periodicFaces.begin();
+ it != elObjDb.periodicFaces.end(); it++) {
+ file << it->first.first.get<0>() << it->first.first.get<1>()
+ << it->first.first.get<2>() << ", "
+ << it->first.second.get<0>() << it->first.second.get<1>()
+ << it->first.second.get<2>() << " : "
+ << it->second << endl;
+ }
+ file << "periodicDofAssoc:\n";
+ {std::map<DegreeOfFreedom, std::set<BoundaryType> >::iterator it;
+ for (it = elObjDb.periodicDofAssoc.begin();
+ it != elObjDb.periodicDofAssoc.end(); it++) {
+ file << it->first << endl;
+ for(std::set<BoundaryType>::iterator it2 = it->second.begin(); it2 != it->second.end(); it2++)
+ file << *it2 << " ";
+ file << endl;
+ }}
+ file << "periodicEdgeAssoc:\n";
+ {std::map<DofEdge, std::set<DofEdge> >::iterator it;
+ for (it = elObjDb.periodicEdgeAssoc.begin();
+ it != elObjDb.periodicEdgeAssoc.end(); it++) {
+ file << it->first.first << " " << it->first.second << endl;
+ for(std::set<DofEdge>::iterator it2 = it->second.begin(); it2 != it->second.end(); it2++)
+ file << "(" << (*it2).first << ", " << (*it2).second << ") ";
+ file << endl;
+ }}
+ file.close();
+ }
+
+ void ParallelDebug::writeInterchangeVector(MeshDistributor &pdb, string debugOutputDir)
+ {
+ for (size_t i = 0; i < pdb.interchangeVectors.size(); i++) {
+ string filename = debugOutputDir + "-int" + boost::lexical_cast<string>(i) + ".vtu";
+ io::VtkWriter::writeFile(pdb.interchangeVectors[i], filename);
+ }
+ }
+
} } // end namespaces
diff --git a/AMDiS/src/parallel/ParallelDebug.h b/AMDiS/src/parallel/ParallelDebug.h
index e8e3a83d..fc893904 100644
--- a/AMDiS/src/parallel/ParallelDebug.h
+++ b/AMDiS/src/parallel/ParallelDebug.h
@@ -76,7 +76,7 @@ namespace AMDiS
* \param[in] printCoords If true, the coords of all common dofs are
* printed to the screen.
*/
- static void testCommonDofs(MeshDistributor &pdb, bool printCoords = false);
+ static void testCommonDofs(MeshDistributor &pdb, Mesh* mesh, bool printCoords = false);
/** \brief
* This function is used for debugging only. It checks if on all ranks DOFs
@@ -86,7 +86,7 @@ namespace AMDiS
*
* \param[in] pdb Parallel problem definition used for debugging.
*/
- static void testGlobalIndexByCoords(MeshDistributor &pdb);
+ static void testGlobalIndexByCoords(MeshDistributor &pdb, Mesh* mesh);
/** \brief
* Tests if all elements in the macro mesh are memeber of exactly one rank.
@@ -101,7 +101,7 @@ namespace AMDiS
*
* \param[in] pdb Parallel problem definition used for debugging.
*/
- static void testDofContainerCommunication(MeshDistributor &pdb);
+ static void testDofContainerCommunication(MeshDistributor &pdb, Mesh* mesh);
/// Tests if there are multiple DOFs in mesh with the same coords.
static void testDoubleDofs(Mesh *mesh);
@@ -161,6 +161,10 @@ namespace AMDiS
ParallelDofMapping &dofMap,
std::string prefix,
std::string postfix);
+
+ static void writeDebugFile(MeshToFeSpaces& meshToFeSpaces,
+ ParallelDofMapping &dofMap,
+ std::string debugOutputDir);
/** \brief
* This functions create a Paraview file with the macro mesh where the
@@ -199,6 +203,15 @@ namespace AMDiS
ParallelDofMapping &dofMap,
std::string prefix,
std::string postfix);
+
+ static void writeDofMap(ParallelDofMapping &dofMap,
+ int component,
+ std::string filename,
+ std::string postfix);
+
+ static void writePeriodicElObjInfo(MeshDistributor &pdb, std::string debugOutputDir);
+
+ static void writeInterchangeVector(MeshDistributor &pdb, std::string debugOutputDir);
};
} // end namespace Parallel
} // end namespace AMDiS
diff --git a/AMDiS/src/parallel/ParallelDofMapping.cc b/AMDiS/src/parallel/ParallelDofMapping.cc
index 6ae8be43..60ef2d80 100644
--- a/AMDiS/src/parallel/ParallelDofMapping.cc
+++ b/AMDiS/src/parallel/ParallelDofMapping.cc
@@ -29,8 +29,6 @@ namespace AMDiS { namespace Parallel {
void DofToMatIndex::getReverse(int rowIndex, int &component, int &dofIndex) const
{
- FUNCNAME("DofToMatIndex::getReverse()");
-
for (map<int, boost::container::flat_map<DegreeOfFreedom, int> >::const_iterator it0 = data.begin();
it0 != data.end(); ++it0)
for (boost::container::flat_map<DegreeOfFreedom, int>::const_iterator it1 = it0->second.begin();
@@ -70,8 +68,6 @@ namespace AMDiS { namespace Parallel {
void ComponentDofMap::update()
{
- FUNCNAME("ComponentDofMap::update()");
-
// === Compute local indices for all rank owned DOFs. ===
for (DofMap::iterator it = dofMap.begin(); it != dofMap.end(); ++it)
@@ -95,8 +91,6 @@ namespace AMDiS { namespace Parallel {
void ComponentDofMap::computeGlobalMapping()
{
- FUNCNAME("ComponentDofMap::computeGlobalMapping()");
-
for (DofMap::iterator it = dofMap.begin(); it != dofMap.end(); ++it)
it->second.global = it->second.local + rStartDofs;
}
@@ -104,7 +98,7 @@ namespace AMDiS { namespace Parallel {
void ComponentDofMap::computeNonLocalIndices()
{
- FUNCNAME("ComponentDofMap::computeNonLocalIndices()");
+ FUNCNAME_DBG("ComponentDofMap::computeNonLocalIndices()");
TEST_EXIT_DBG(dofComm)("No DOF communicator defined!\n");
@@ -116,14 +110,18 @@ namespace AMDiS { namespace Parallel {
for (DofComm::Iterator it(dofComm->getSendDofs(), feSpace);
!it.end(); it.nextRank()) {
int rank = it.getRank();
+
// if (meshLevel > 0)
// rank = levelData->mapRank(rank, 0, meshLevel);
- for (; !it.endDofIter(); it.nextDof())
+ for (; !it.endDofIter(); it.nextDof()) {
+ TEST_EXIT_DBG(dofMap.count(it.getDofIndex()))
+ ("DOF index not in the dofmap. Something is wrong.\n");
if (dofMap.count(it.getDofIndex()) &&
!nonRankDofs.count(it.getDofIndex()))
stdMpi.getSendData(rank).
push_back(dofMap[it.getDofIndex()].global);
+ }
}
stdMpi.updateSendDataSize();
@@ -165,19 +163,24 @@ namespace AMDiS { namespace Parallel {
// rank = levelData->mapRank(rank, 0, meshLevel);
int i = 0;
- for (; !it.endDofIter(); it.nextDof())
+ for (; !it.endDofIter(); it.nextDof()) {
+ TEST_EXIT_DBG(nonRankDofs.count(it.getDofIndex()))("Something is wrong.\n");
+
if (nonRankDofs.count(it.getDofIndex()))
dofMap[it.getDofIndex()].global = stdMpi.getRecvData(rank)[i++];
+ }
}
+
}
void FeSpaceData::init(vector<const FiniteElemSpace*> &f0,
vector<const FiniteElemSpace*> &f1,
bool globalMapping)
- {
+ {
componentSpaces = f0;
feSpaces = f1;
+
for (vector<const FiniteElemSpace*>::iterator it = feSpaces.begin();
it != feSpaces.end(); ++it) {
if (componentData.count(*it))
@@ -185,7 +188,8 @@ namespace AMDiS { namespace Parallel {
else
componentData.insert(make_pair(*it, ComponentDofMap()));
- componentData[*it].setFeSpace(*it);
+ componentData[*it].setFeSpace(*it);
+ componentData[*it].setMesh((*it)->getMesh());
componentData[*it].setGlobalMapping(globalMapping);
}
}
@@ -205,6 +209,7 @@ namespace AMDiS { namespace Parallel {
componentData.insert(make_pair(component, ComponentDofMap()));
componentData[component].setFeSpace(componentSpaces[component]);
+ componentData[component].setMesh(componentSpaces[component]->getMesh());
componentData[component].setGlobalMapping(globalMapping);
}
}
@@ -212,8 +217,7 @@ namespace AMDiS { namespace Parallel {
ParallelDofMapping::ParallelDofMapping(DofMappingMode mode,
bool matIndexFromGlobal)
- : dofComm(NULL),
- globalMapping(true),
+ : globalMapping(true),
needMatIndexFromGlobal(matIndexFromGlobal),
nRankDofs(1),
nLocalDofs(1),
@@ -236,12 +240,10 @@ namespace AMDiS { namespace Parallel {
rStartDofs = -1;
}
-
void ParallelDofMapping::init(vector<const FiniteElemSpace*> &fe,
vector<const FiniteElemSpace*> &uniqueFe,
bool b)
{
- FUNCNAME("ParallelDofMapping::init()");
globalMapping = b;
componentSpaces = fe;
@@ -249,20 +251,27 @@ namespace AMDiS { namespace Parallel {
data->init(fe, uniqueFe, globalMapping);
}
-
-
- void ParallelDofMapping::clear()
+
+ void ParallelDofMapping::clear(Mesh* mesh)
{
- FUNCNAME("ParallelDofMapping::clear()");
- for (ComponentIterator &it = data->getIteratorData(); !it.end(); it.next())
- it->clear();
+ for (ComponentIterator &it = data->getIteratorData(); !it.end(); it.next())
+ if (!mesh || it->getMesh() == mesh)
+ it->clear();
nRankDofs = -1;
nLocalDofs = -1;
nOverallDofs = -1;
rStartDofs = -1;
- dofToMatIndex.clear();
+
+ if (!mesh)
+ dofToMatIndex.clear();
+ else
+ for (unsigned int component = 0; component < componentSpaces.size();
+ component++) {
+ if (mesh == (*data)[component].getMesh())
+ dofToMatIndex.clear(component);
+ }
}
@@ -273,24 +282,24 @@ namespace AMDiS { namespace Parallel {
for (ComponentIterator &it = data->getIteratorData(); !it.end(); it.next())
it->setMpiComm(m);
}
-
-
- void ParallelDofMapping::setDofComm(DofComm &dc)
+
+
+ void ParallelDofMapping::setDofComms(std::map<Mesh*, MultiLevelDofComm>& dofComms, int level)
{
- FUNCNAME("ParallelDofMapping::setDofComm()");
-
- dofComm = &dc;
-
- // Add the DOF communicator also to all FE space DOF mappings.
- for (ComponentIterator &it = data->getIteratorData(); !it.end(); it.next())
- it->setDofComm(dc);
+ FUNCNAME("ParallelDofMapping::setDofComms()");
+
+ for (ComponentIterator &it = data->getIteratorData(); !it.end(); it.next()) {
+
+ TEST_EXIT(dofComms.find(const_cast<Mesh*>(it->getMesh())) != dofComms.end())
+ ("DofComm and ParallelDofMapping not match.\n");
+
+ it->setDofComm(dofComms[const_cast<Mesh*>(it->getMesh())][level]);
+ }
}
int ParallelDofMapping::computeRankDofs()
{
- FUNCNAME("ParallelDofMapping::computeRankDofs()");
-
int result = 0;
for (ComponentIterator &it = data->getIteratorComponent(); !it.end(); it.next())
result += it->nRankDofs;
@@ -301,8 +310,6 @@ namespace AMDiS { namespace Parallel {
int ParallelDofMapping::computeLocalDofs()
{
- FUNCNAME("ParallelDofMapping::computeLocalDofs()");
-
int result = 0;
for (ComponentIterator &it = data->getIteratorComponent(); !it.end(); it.next())
result += it->nLocalDofs;
@@ -313,8 +320,6 @@ namespace AMDiS { namespace Parallel {
int ParallelDofMapping::computeOverallDofs()
{
- FUNCNAME("ParallelDofMapping::computeOverallDofs()");
-
int result = 0;
for (ComponentIterator &it = data->getIteratorComponent(); !it.end(); it.next())
result += it->nOverallDofs;
@@ -325,46 +330,38 @@ namespace AMDiS { namespace Parallel {
int ParallelDofMapping::computeStartDofs()
{
- FUNCNAME("ParallelDofMapping::computeStartDofs()");
-
int result = 0;
for (ComponentIterator &it = data->getIteratorComponent(); !it.end(); it.next())
result += it->rStartDofs;
return result;
}
-
-
- void ParallelDofMapping::update()
+
+ void ParallelDofMapping::update(Mesh* mesh)
{
- FUNCNAME("ParallelDofMapping::update()");
-
// First, update all FE space DOF mappings.
for (ComponentIterator &it = data->getIteratorData(); !it.end(); it.next())
- it->update();
-
+ if (!mesh || it->getMesh() == mesh)
+ it->update();
+
// Compute all numbers from this mappings.
nRankDofs = computeRankDofs();
nLocalDofs = computeLocalDofs();
nOverallDofs = computeOverallDofs();
rStartDofs = computeStartDofs();
-
// And finally, compute the matrix indices.
computeMatIndex(needMatIndexFromGlobal);
}
-
void ParallelDofMapping::updateMatIndex()
{
- FUNCNAME("ParallelDofMapping::updateMatIndex()");
-
computeMatIndex(needMatIndexFromGlobal);
}
void ParallelDofMapping::computeMatIndex(bool globalIndex)
{
- FUNCNAME("ParallelDofMapping::computeMatIndex()");
+ FUNCNAME_DBG("ParallelDofMapping::computeMatIndex()");
dofToMatIndex.clear();
@@ -377,7 +374,7 @@ namespace AMDiS { namespace Parallel {
for (unsigned int component = 0; component < componentSpaces.size();
component++) {
-
+
// Traverse all DOFs of the FE space and create for all rank owned DOFs
// a matrix index.
DofMap& dofMap = (*data)[component].getMap();
@@ -390,7 +387,6 @@ namespace AMDiS { namespace Parallel {
dofToMatIndex.add(component, it->first, globalMatIndex);
}
}
-
// Increase the offset for the next FE space by the number of DOFs owned
// by the rank in the current FE space.
offset += (*data)[component].nRankDofs;
@@ -399,8 +395,10 @@ namespace AMDiS { namespace Parallel {
if (!globalMapping)
continue;
+
+ DofComm* dofComm = &((*data)[component].getDofComm());
TEST_EXIT_DBG(dofComm != NULL)("No communicator given!\n");
-
+
// === Communicate the matrix indices for all DOFs that are on some ===
// === interior boundaries. ===
@@ -410,6 +408,9 @@ namespace AMDiS { namespace Parallel {
vector<DegreeOfFreedom> sendGlobalDofs;
for (; !it.endDofIter(); it.nextDof()) {
+ TEST_EXIT_DBG((*data)[component].isRankDof(it.getDofIndex()))
+ ("Send dof %d is not a rank dof\n", it.getDofIndex());
+
if (dofMap.count(it.getDofIndex())) {
if (globalIndex)
sendGlobalDofs.push_back(dofToMatIndex.get(component,
@@ -453,7 +454,6 @@ namespace AMDiS { namespace Parallel {
}
}
-
// === Communicate DOFs on periodic boundaries. ===
stdMpi.clear();
@@ -490,7 +490,7 @@ namespace AMDiS { namespace Parallel {
// if (meshLevel > 0)
// rank = levelData->mapRank(rank, 0, meshLevel);
- int counter = 0;
+ size_t counter = 0;
for (; !it.endDofIter(); it.nextDof()) {
if (dofMap.count(it.getDofIndex())) {
@@ -519,7 +519,7 @@ namespace AMDiS { namespace Parallel {
int firstComponent,
int nComponents)
{
- FUNCNAME("ParallelDofMapping::createIndexSet()");
+ FUNCNAME_DBG("ParallelDofMapping::createIndexSet()");
int firstRankDof = -1;
ComponentDofMap &compMap = (*data)[firstComponent];
diff --git a/AMDiS/src/parallel/ParallelDofMapping.h b/AMDiS/src/parallel/ParallelDofMapping.h
index 443b3eb1..398f9930 100644
--- a/AMDiS/src/parallel/ParallelDofMapping.h
+++ b/AMDiS/src/parallel/ParallelDofMapping.h
@@ -62,6 +62,11 @@ namespace AMDiS { namespace Parallel {
{
data.clear();
}
+
+ inline void clear(int component)
+ {
+ data[component].clear();
+ }
/** Add a new mapping for a given DOF.
*
@@ -228,6 +233,25 @@ namespace AMDiS { namespace Parallel {
{
return dofMap;
}
+
+ const FiniteElemSpace* getFeSpace() const
+ {
+ return feSpace;
+ }
+
+ const Mesh* getMesh() const
+ {
+ return mesh;
+ }
+
+ DofComm& getDofComm()
+ {
+ FUNCNAME("ComponentDofMap::getDofComm()");
+
+ TEST_EXIT_DBG(dofComm)("No DOF communicator object defined!\n");
+
+ return *dofComm;
+ }
DofMap::iterator begin()
{
@@ -247,6 +271,11 @@ namespace AMDiS { namespace Parallel {
{
feSpace = fe;
}
+
+ void setMesh(Mesh* mesh_)
+ {
+ mesh = mesh_;
+ }
/// Informs the mapping whether a global index must be computed.
void setGlobalMapping(bool b)
@@ -282,6 +311,8 @@ namespace AMDiS { namespace Parallel {
/// The FE space this mapping belongs to. This is used only the get the
/// correct DOF communicator in \ref dofComm.
const FiniteElemSpace *feSpace;
+
+ const Mesh* mesh;
/// Mapping data from DOF indices to local and global indices.
DofMap dofMap;
@@ -320,6 +351,7 @@ namespace AMDiS { namespace Parallel {
class ComponentDataInterface
{
public:
+ virtual ~ComponentDataInterface() {};
/// Access via component number
virtual ComponentDofMap& operator[](int compNumber) = 0;
@@ -653,6 +685,13 @@ namespace AMDiS { namespace Parallel {
*/
ParallelDofMapping(DofMappingMode mode,
bool matIndexFromGlobal = false);
+
+ ~ParallelDofMapping()
+ {
+ if (data)
+ delete data;
+ data = NULL;
+ }
/** \brief
* Initialize the parallel DOF mapping.
@@ -686,20 +725,17 @@ namespace AMDiS { namespace Parallel {
}
/// Clear all data.
- void clear();
+ void clear(Mesh* mesh = NULL);
/// Set the DOF communicator objects that are required to exchange information
/// about DOFs that are on interior boundaries.
- void setDofComm(DofComm &dofComm);
+
+ void setDofComms(std::map<Mesh*, MultiLevelDofComm>& dofComms, int level);
/// Returns the DOF communicator.
- DofComm& getDofComm()
+ DofComm& getDofComm(const FiniteElemSpace* feSpace)
{
- FUNCNAME("ParallelDofMapping::getDofComm()");
-
- TEST_EXIT_DBG(dofComm)("No DOF communicator object defined!\n");
-
- return *dofComm;
+ return (*data)[feSpace].getDofComm();
}
inline bool isMatIndexFromGlobal()
@@ -739,6 +775,14 @@ namespace AMDiS { namespace Parallel {
return nRankDofs;
}
+
+ inline int getRankDofs(int component) const
+ {
+ int nDofs = (*data)[component].nRankDofs;
+ TEST_EXIT_DBG(nDofs >= 0)("Should not happen!\n");
+
+ return nDofs;
+ }
/// Returns \ref nLocalDofs, thus the number of DOFs in ranks subdomain.
inline int getLocalDofs() const
@@ -747,7 +791,15 @@ namespace AMDiS { namespace Parallel {
return nLocalDofs;
}
+
+ inline int getLocalDofs(int component) const
+ {
+ int nDofs = (*data)[component].nLocalDofs;
+ TEST_EXIT_DBG(nDofs >= 0)("Should not happen!\n");
+ return nDofs;
+ }
+
/// Returns \ref nOverallDofs, thus the number of all DOFs in this mapping.
inline int getOverallDofs() const
{
@@ -755,6 +807,14 @@ namespace AMDiS { namespace Parallel {
return nOverallDofs;
}
+
+ inline int getOverallDofs(int component) const
+ {
+ int nDofs = (*data)[component].nOverallDofs;
+ TEST_EXIT_DBG(nDofs >= 0)("Should not happen!\n");
+
+ return nDofs;
+ }
/// Returns \ref rStartDofs, thus the smallest global index of a DOF that is
/// owned by the rank.
@@ -764,13 +824,26 @@ namespace AMDiS { namespace Parallel {
return rStartDofs;
}
+
+ inline int getStartDofs(int component) const
+ {
+ int nDofs = (*data)[component].rStartDofs;
+ TEST_EXIT_DBG(nDofs >= 0)("Should not happen!\n");
+
+ return nDofs;
+ }
/// Update the mapping.
- void update();
+ void update(Mesh* mesh = NULL);
/// Updates only the DOF to matrix index mapping
void updateMatIndex();
+ inline DofToMatIndex::MapType& getMatData(int component)
+ {
+ return dofToMatIndex.getData(component);
+ }
+
/// Returns the global matrix index of a given DOF for a given
/// component number.
inline int getMatIndex(int ithComponent, DegreeOfFreedom d) const
@@ -793,9 +866,22 @@ namespace AMDiS { namespace Parallel {
}
/// Returns the set of unique FE spaces.
- inline std::vector<const FiniteElemSpace*>& getFeSpaces()
+ std::vector<const FiniteElemSpace*> getFeSpaces(Mesh* mesh = NULL)
{
- return feSpaces;
+ if (!mesh)
+ return feSpaces;
+
+ std::vector<const FiniteElemSpace*> thisMeshSpaces;
+ for (size_t i = 0; i < feSpaces.size(); i++)
+ if (feSpaces[i]->getMesh() == mesh)
+ thisMeshSpaces.push_back(feSpaces[i]);
+ return thisMeshSpaces;
+ }
+
+ bool hasFeSpace(const FiniteElemSpace* feSpace)
+ {
+ return (std::find(feSpaces.begin(), feSpaces.end(), feSpace)
+ != feSpaces.end());
}
// Writes all data of this object to an output stream.
@@ -839,9 +925,6 @@ namespace AMDiS { namespace Parallel {
private:
MPI::Intracomm mpiComm;
- /// DOF communicator for all DOFs on interior boundaries.
- DofComm *dofComm;
-
/// Is true if there are DOFs in at least one subdomain that are not owned
/// by the rank. If the value is false, each rank contains only DOFs that
/// are also owned by this rank.
diff --git a/AMDiS/src/parallel/ParallelProblemStat.cc b/AMDiS/src/parallel/ParallelProblemStat.cc
index 5353dc28..f6236949 100644
--- a/AMDiS/src/parallel/ParallelProblemStat.cc
+++ b/AMDiS/src/parallel/ParallelProblemStat.cc
@@ -66,6 +66,7 @@ namespace AMDiS { namespace Parallel {
Flag adoptFlag)
{
FUNCNAME("ParallelProblemStat::initialize()");
+ MSG("ParallelProblemStat::initialize()\n");
MSG("Initialization phase 0 needed %.5f seconds\n",
MPI::Wtime() - initTimeStamp);
@@ -81,7 +82,17 @@ namespace AMDiS { namespace Parallel {
("ParallelProblem loaded, but no ParallelSolver selected! This does not fit together.\n");
parallelSolver->setMeshDistributor(meshDistributor, 0);
- parallelSolver->init(getComponentSpaces(), getFeSpaces());
+
+ // For the additional component with extra mesh and fespace, we don't need to put them
+ // into the parallel system.
+ std::vector<const FiniteElemSpace*> tmpFeSpaces, tmpComponentSpaces(getComponentSpaces().begin(),
+ getComponentSpaces().begin() + getNumComponents());
+
+ for (int i = 0; i < tmpComponentSpaces.size(); i++)
+ if (std::find(tmpFeSpaces.begin(), tmpFeSpaces.end(), tmpComponentSpaces[i]) == tmpFeSpaces.end())
+ tmpFeSpaces.push_back(tmpComponentSpaces[i]);
+
+ parallelSolver->init(tmpComponentSpaces, tmpFeSpaces);
}
diff --git a/AMDiS/src/parallel/ParallelSolver.cc b/AMDiS/src/parallel/ParallelSolver.cc
index 11b318d9..887f52c7 100644
--- a/AMDiS/src/parallel/ParallelSolver.cc
+++ b/AMDiS/src/parallel/ParallelSolver.cc
@@ -41,7 +41,6 @@ namespace AMDiS { namespace Parallel {
meshDistributor->removeDofMap(dofMap);
}
-
void ParallelSolver::init(std::vector<const FiniteElemSpace*> &fe0,
std::vector<const FiniteElemSpace*> &fe1,
bool createGlobalMapping)
@@ -61,7 +60,10 @@ namespace AMDiS { namespace Parallel {
dofMap.init(componentSpaces, feSpaces);
dofMap.setMpiComm(levelData.getMpiComm(meshLevel));
- dofMap.setDofComm(meshDistributor->getDofComm(meshLevel));
+
+ // The meshes and fespaces of the dofmap come from the main problem.
+ // The meshes and feSpaces of dofcomms may come from diff problems.
+ dofMap.setDofComms(meshDistributor->getDofComms(), meshLevel);
dofMap.clear();
meshDistributor->registerDofMap(dofMap);
}
diff --git a/AMDiS/src/parallel/ParallelTypes.h b/AMDiS/src/parallel/ParallelTypes.h
index eafd48e8..82395d46 100644
--- a/AMDiS/src/parallel/ParallelTypes.h
+++ b/AMDiS/src/parallel/ParallelTypes.h
@@ -78,6 +78,10 @@ namespace AMDiS { namespace Parallel {
typedef std::vector<MeshStructure> MeshCodeVec;
typedef std::map<int, std::vector<AtomicBoundary> > RankToBoundMap;
+
+ typedef boost::container::flat_map<int, boost::container::flat_map<Mesh*, Element*> > MacroElIndexMap;
+
+ typedef std::map<Mesh*, std::vector<const FiniteElemSpace*> > MeshToFeSpaces;
} } // end namespaces
#endif
diff --git a/AMDiS/src/parallel/PetscSolverFeti.cc b/AMDiS/src/parallel/PetscSolverFeti.cc
index a77a9221..e3b52fbe 100644
--- a/AMDiS/src/parallel/PetscSolverFeti.cc
+++ b/AMDiS/src/parallel/PetscSolverFeti.cc
@@ -135,7 +135,7 @@ namespace AMDiS { namespace Parallel {
levelData.getMpiComm(meshLevel + 1) != MPI::COMM_SELF) {
dofMapSubDomain.init(componentSpaces, feSpaces);
dofMapSubDomain.setMpiComm(levelData.getMpiComm(meshLevel + 1));
- dofMapSubDomain.setDofComm(meshDistributor->getDofComm(meshLevel + 1));
+ dofMapSubDomain.setDofComms(meshDistributor->getDofComms(), meshLevel + 1);
dofMapSubDomain.clear();
meshDistributor->registerDofMap(dofMapSubDomain);
}
@@ -228,8 +228,8 @@ namespace AMDiS { namespace Parallel {
if (fetiPreconditioner == FETI_DIRICHLET)
interiorDofMap.clear();
- primalDofMap.setDofComm(meshDistributor->getDofComm(meshLevel));
- lagrangeMap.setDofComm(meshDistributor->getDofComm(meshLevel));
+ primalDofMap.setDofComms(meshDistributor->getDofComms(), meshLevel);
+ lagrangeMap.setDofComms(meshDistributor->getDofComms(), meshLevel);
primalDofMap.setMpiComm(levelData.getMpiComm(meshLevel));
dualDofMap.setMpiComm(levelData.getMpiComm(meshLevel));
@@ -238,11 +238,11 @@ namespace AMDiS { namespace Parallel {
if (fetiPreconditioner == FETI_DIRICHLET)
interiorDofMap.setMpiComm(levelData.getMpiComm(meshLevel + 1));
- localDofMap.setDofComm(meshDistributor->getDofComm(meshLevel + 1));
+ localDofMap.setDofComms(meshDistributor->getDofComms(), meshLevel + 1);
if (stokesMode) {
interfaceDofMap.clear();
- interfaceDofMap.setDofComm(meshDistributor->getDofComm(meshLevel));
+ interfaceDofMap.setDofComms(meshDistributor->getDofComms(), meshLevel);
interfaceDofMap.setMpiComm(levelData.getMpiComm(0));
}
@@ -1537,7 +1537,7 @@ namespace AMDiS { namespace Parallel {
massMapping =
new ParallelDofMapping(COMPONENT_WISE, true);
massMapping->init(pressureFeSpace, pressureFeSpace);
- massMapping->setDofComm(meshDistributor->getDofComm(meshLevel));
+ massMapping->setDofComms(meshDistributor->getDofComms(), meshLevel);
massMapping->setMpiComm(meshDistributor->getMeshLevelData().getMpiComm(0));
}
(*massMapping)[0] = interfaceDofMap[pressureComponent];
diff --git a/AMDiS/src/parallel/PetscSolverGlobalMatrix.cc b/AMDiS/src/parallel/PetscSolverGlobalMatrix.cc
index dbb2bfa5..7c29a966 100644
--- a/AMDiS/src/parallel/PetscSolverGlobalMatrix.cc
+++ b/AMDiS/src/parallel/PetscSolverGlobalMatrix.cc
@@ -186,7 +186,7 @@ namespace AMDiS { namespace Parallel {
FUNCNAME_DBG("PetscSolverGlobalMatrix::fillPetscMatrixWithCoarseSpace()");
TEST_EXIT_DBG(interiorMap)("No interiorMap! Should not happen!\n");
- TEST_EXIT_DBG(coarseSpaceMap.size() == seqMat->getSize())
+ TEST_EXIT_DBG(coarseSpaceMap.size() == (size_t)seqMat->getSize())
("Wrong sizes %d %d\n", coarseSpaceMap.size(), seqMat->getSize());
// === Prepare traverse of sequentially created matrices. ===
@@ -875,8 +875,7 @@ namespace AMDiS { namespace Parallel {
// Get PETSc's mat index of the row DOF.
int index = 0;
if (interiorMap->isMatIndexFromGlobal())
- index =
- interiorMap->getMatIndex(rowComp, globalRowDof) + rStartInterior;
+ index = interiorMap->getMatIndex(rowComp, globalRowDof) + rStartInterior;
else
index =
interiorMap->getMatIndex(rowComp, dof) + rStartInterior;
diff --git a/AMDiS/src/parallel/PetscSolverSchur.cc b/AMDiS/src/parallel/PetscSolverSchur.cc
index 0713cc8f..9092ff50 100644
--- a/AMDiS/src/parallel/PetscSolverSchur.cc
+++ b/AMDiS/src/parallel/PetscSolverSchur.cc
@@ -35,6 +35,7 @@ namespace AMDiS { namespace Parallel {
TEST_EXIT_DBG(interiorMap)("No parallel DOF map defined!\n");
const FiniteElemSpace *feSpace = componentSpaces[0];
+ Mesh* mesh = feSpace->getMesh();
// typedef map<int, DofContainer> RankToDofContainer;
#if 0
typedef map<DegreeOfFreedom, bool> DofIndexToBool;
@@ -42,7 +43,7 @@ namespace AMDiS { namespace Parallel {
boundaryDofs.clear();
std::set<DegreeOfFreedom> boundaryLocalDofs;
- for (DofComm::Iterator it(meshDistributor->getDofComm(0).getSendDofs(), feSpace);
+ for (DofComm::Iterator it(meshDistributor->getDofComm(mesh, 0).getSendDofs(), feSpace);
!it.end(); it.nextRank())
for (; !it.endDofIter(); it.nextDof()) {
boundaryLocalDofs.insert(it.getDofIndex());
@@ -104,7 +105,7 @@ namespace AMDiS { namespace Parallel {
std::set<DegreeOfFreedom> otherBoundaryLocalDofs;
- for (DofComm::Iterator it(meshDistributor->getDofComm(0).getRecvDofs(), feSpace);
+ for (DofComm::Iterator it(meshDistributor->getDofComm(mesh, 0).getRecvDofs(), feSpace);
!it.end(); it.nextRank())
for (; !it.endDofIter(); it.nextDof())
otherBoundaryLocalDofs.insert(it.getDofIndex());
@@ -140,7 +141,7 @@ namespace AMDiS { namespace Parallel {
StdMpi<vector<DegreeOfFreedom> > stdMpi(domainComm);
- for (DofComm::Iterator it(meshDistributor->getDofComm(0).getSendDofs(), feSpace);
+ for (DofComm::Iterator it(meshDistributor->getDofComm(mesh, 0).getSendDofs(), feSpace);
!it.end(); it.nextRank()) {
stdMpi.getSendData(it.getRank()).resize(0);
stdMpi.getSendData(it.getRank()).reserve(it.getDofs().size());
@@ -157,13 +158,13 @@ namespace AMDiS { namespace Parallel {
stdMpi.updateSendDataSize();
- for (DofComm::Iterator it(meshDistributor->getDofComm(0).getRecvDofs(), feSpace);
+ for (DofComm::Iterator it(meshDistributor->getDofComm(mesh, 0).getRecvDofs(), feSpace);
!it.end(); it.nextRank())
stdMpi.recv(it.getRank());
stdMpi.startCommunication();
- for (DofComm::Iterator it(meshDistributor->getDofComm(0).getRecvDofs(), feSpace);
+ for (DofComm::Iterator it(meshDistributor->getDofComm(mesh, 0).getRecvDofs(), feSpace);
!it.end(); it.nextRank())
for (; !it.endDofIter(); it.nextDof()) {
int globalRecvDof = (*interiorMap)[feSpace][it.getDofIndex()].global;
diff --git a/AMDiS/src/utility/to_string.hpp b/AMDiS/src/utility/to_string.hpp
new file mode 100644
index 00000000..a60baf20
--- /dev/null
+++ b/AMDiS/src/utility/to_string.hpp
@@ -0,0 +1,41 @@
+/******************************************************************************
+ *
+ * AMDiS - Adaptive multidimensional simulations
+ *
+ * Copyright (C) 2013 Dresden University of Technology. All Rights Reserved.
+ * Web: https://fusionforge.zih.tu-dresden.de/projects/amdis
+ *
+ * Authors:
+ * Simon Vey, Thomas Witkowski, Andreas Naumann, Simon Praetorius, et al.
+ *
+ * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+ * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ *
+ *
+ * This file is part of AMDiS
+ *
+ * See also license.opensource.txt in the distribution.
+ *
+ ******************************************************************************/
+
+
+
+/** \file to_string.hpp */
+
+#ifndef AMDIS_UTILITY_TO_STRING_HPP
+#define AMDIS_UTILITY_TO_STRING_HPP
+
+#include <string>
+#include <boost/lexical_cast.hpp>
+
+namespace AMDiS {
+
+ template <class T>
+ inline std::string to_string(const T& value)
+ {
+ return boost::lexical_cast<std::string>(value);
+ }
+
+} // end namspace AMDiS
+
+#endif // AMDIS_UTILITY_TO_STRING_HPP
diff --git a/extensions/ProblemStatMassConserve.h b/extensions/ProblemStatMassConserve.h
index 37a20de5..24def0d5 100644
--- a/extensions/ProblemStatMassConserve.h
+++ b/extensions/ProblemStatMassConserve.h
@@ -42,9 +42,9 @@ struct ProblemStatMassConserve : public ExtendedProblemStat, public StandardRefi
prob2(NULL),
comp(0)
{
-#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
- TEST_EXIT(false)("Multi-Mesh approach does not work in parallel mode for the moment. Need to be implemented!\n");
-#endif
+// #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+// TEST_EXIT(false)("Multi-Mesh approach does not work in parallel mode for the moment. Need to be implemented!\n");
+// #endif
Parameters::get(name_ + "->mass conservation component", comp);
@@ -213,9 +213,10 @@ struct ProblemStatMassConserve : public ExtendedProblemStat, public StandardRefi
bool storeMatrixData = false)
{
SolverMatrix<Matrix<DOFMatrix*> > solverMatrix_;
- Matrix<DOFMatrix*> mat(1,1);
- mat[0][0] = prob2->getSystemMatrix(0,0);
- solverMatrix_.setMatrix(mat);
+// Matrix<DOFMatrix*> mat(1,1);
+// mat[0][0] = prob2->getSystemMatrix(0,0);
+// solverMatrix_.setMatrix(mat);
+ solverMatrix_.setMatrix(*(prob2->getSystemMatrix()));
std::vector<const FiniteElemSpace*> feSpaces0;
feSpaces0.push_back(prob2->getFeSpace(0));
diff --git a/extensions/ProblemStatMassConserve_mm.h b/extensions/ProblemStatMassConserve_mm.h
new file mode 100644
index 00000000..c1792b1c
--- /dev/null
+++ b/extensions/ProblemStatMassConserve_mm.h
@@ -0,0 +1,123 @@
+/******************************************************************************
+ *
+ * Mass-conserving ProblemStat for AMDiS
+ *
+ * Copyright (C) 2013 Dresden University of Technology. All Rights Reserved.
+ * Web: https://fusionforge.zih.tu-dresden.de/projects/amdis/trunk/extensions
+ *
+ * Author: Simon Praetorius
+ *
+ * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+ * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ *
+ *
+ * See also license.opensource.txt in the distribution.
+ *
+ ******************************************************************************/
+
+/** \file ProblemStatMassConserve_mm.h */
+
+
+#ifndef AMDIS_EXTENSIONS_PROBLEM_STAT_MASS_CONSERVE_MULTI_MESH
+#define AMDIS_EXTENSIONS_PROBLEM_STAT_MASS_CONSERVE_MULTI_MESH
+
+#include "ExtendedProblemStat.h"
+#include "Refinement.h"
+#include <boost/lexical_cast.hpp>
+
+namespace AMDiS {
+
+/// Implementation of ProblemStat to allow for the conservation of mass of one
+/// solution component, i.e. project the old-solution to the new mesh so that
+/// the scalar-product is conserved: \f$ (u^*, v) = (u^\text{old}, v) \f$, where \f$ u^*,v \f$ live on the
+/// new mesh and \f$ u^\text{old} \f$ lives on the old mesh.
+struct ProblemStatMassConserve : public ExtendedProblemStat, public StandardRefineOperation
+{
+ ProblemStatMassConserve(std::string name_)
+ : ExtendedProblemStat(name_),
+ initialMeshAdoption(false),
+ comp(-1),
+ old_solution(NULL)
+ {
+ Parameters::get(name_ + "->mass conservation component", comp);
+ assert( comp >= 0 );
+
+ Parameters::get(name_ + "->additional components", nAddComponents);
+ nAddComponents++;
+ Parameters::set(name_ + "->additional components", nAddComponents);
+
+ comp_old = nComponents - 1 + nAddComponents;
+
+ int degree = 1;
+ Parameters::get(name_ + "->polynomial degree[" + boost::lexical_cast<std::string>(comp) + "]", degree);
+ Parameters::set(name_ + "->polynomial degree[" + boost::lexical_cast<std::string>(comp_old) + "]", degree);
+
+ int refSet = 123;
+ Parameters::set(name_ + "->refinement set[" + boost::lexical_cast<std::string>(comp_old) + "]", refSet);
+ }
+
+ ~ProblemStatMassConserve()
+ {
+ if (old_solution) {
+ delete old_solution; old_solution = NULL;
+ }
+ }
+
+ virtual void initialize(Flag initFlag,
+ ProblemStatSeq *adoptProblem = NULL,
+ Flag adoptFlag = INIT_NOTHING) override
+ {
+ ExtendedProblemStat::initialize(initFlag, adoptProblem, adoptFlag);
+ old_solution = new DOFVector<double>(getFeSpace(comp_old), "old-solution");
+ }
+
+ void buildAfterCoarsen(AdaptInfo *adaptInfo, Flag flag,
+ bool assembleMatrix = true,
+ bool assembleVector = true) override
+ { FUNCNAME("ProblemStatMassConserve_mm::buildAfterCoarsen()");
+
+ if (!initialMeshAdoption) {
+ fitMeshes(comp, comp_old);
+ old_solution->interpol(getSolution(comp));
+ initialMeshAdoption = true;
+ }
+ ExtendedProblemStat::buildAfterCoarsen(adaptInfo, flag, assembleMatrix, assembleVector);
+ }
+
+ /// copy solution to old_solution after regular solve
+ void solve(AdaptInfo *adaptInfo,
+ bool createMatrixData = true,
+ bool storeMatrixData = false) override
+ { FUNCNAME("ProblemStatMassConserve_mm::solve()");
+
+ ExtendedProblemStat::solve(adaptInfo, createMatrixData, storeMatrixData);
+
+ fitMeshes(comp, comp_old);
+ old_solution->interpol(getSolution(comp));
+ }
+
+ DOFVector<double>* getOldSolution(int comp0 = 0) { assert( comp0 == comp ); return old_solution; }
+
+protected:
+ void fitMeshes(int comp1, int comp2)
+ {
+ MeshStructure meshStructure2;
+ meshStructure2.init(getMesh(comp1));
+ getCoarseningManager()->globalCoarsen(getMesh(comp2), -2);
+ meshStructure2.fitMeshToStructure(getMesh(comp2), getRefinementManager());
+ }
+
+private:
+ /// true if initial-solution/-mesh is copied to temporary problem
+ bool initialMeshAdoption;
+
+ /// component the should be copnserved
+ int comp;
+ int comp_old;
+
+ DOFVector<double>* old_solution;
+};
+
+}
+
+#endif // PROBLEM_STAT_MASS_CONSERVE
\ No newline at end of file
diff --git a/extensions/Refinement.h b/extensions/Refinement.h
index 9765182b..9069e5b4 100644
--- a/extensions/Refinement.h
+++ b/extensions/Refinement.h
@@ -70,7 +70,7 @@ public:
virtual ~RefinementLevel()
{
- finalize();
+// finalize();
delete coarseningManager;
delete refinementManager;
@@ -98,7 +98,7 @@ public:
refineOperation = refineOperation_;
}
- void refine(bool onlyRefine= false)
+ void refine(bool onlyRefine= false, bool meshRepartation = false)
{
FUNCNAME("RefinementLevel::refine()");
@@ -122,6 +122,11 @@ public:
calcMeshSizes(minH, maxH, minLevel, maxLevel, false);
int nr = mesh->getNumberOfVertices();
meshChanged = meshChanged && oldOldNr!=nr && oldNr!=nr;
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ int sendValue = static_cast<int>(meshChanged);
+ Parallel::mpi::globalAdd(MPI::COMM_WORLD, sendValue);
+ meshChanged = static_cast<bool>(sendValue);
+#endif
if (meshChanged) {
MSG("(local) mesh sizes: [%f, %f], Vs: %d, ELs: %d\n",
minH, maxH, nr, mesh->getNumberOfElements());
@@ -131,14 +136,17 @@ public:
oldOldNr = oldNr;
oldNr = nr;
}
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ Parallel::MeshDistributor::globalMeshDistributor->checkMeshChange(meshRepartation);
+#endif
calcMeshSizes(minH, maxH, minLevel, maxLevel, true);
MSG("Final (global) mesh: [%f, %f], Vs: %d, ELs: %d, Level: [%d, %d]\n",
minH, maxH, mesh->getNumberOfVertices(), mesh->getNumberOfElements(), minLevel, maxLevel);
}
- void refine(int numRefinements_, bool onlyRefine= false) {
+ void refine(int numRefinements_, bool onlyRefine= false, bool repartation = false) {
numRefinements = numRefinements_;
- refine(onlyRefine);
+ refine(onlyRefine, repartation);
numRefinements = numRefinements0;
}
@@ -318,7 +326,7 @@ public:
virtual ~RefinementLocal()
{
- finalize();
+// finalize();
delete coarseningManager;
delete refinementManager;
@@ -377,6 +385,11 @@ public:
calcMeshSizes(minH, maxH, minLevel, maxLevel, false);
int nr = mesh->getNumberOfVertices();
meshChanged = meshChanged && oldOldNr!=nr && oldNr!=nr;
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ int sendValue = static_cast<int>(meshChanged);
+ Parallel::mpi::globalAdd(MPI::COMM_WORLD, sendValue);
+ meshChanged = static_cast<bool>(sendValue);
+#endif
if (meshChanged) {
MSG("(local) mesh sizes: [%f, %f], Vs: %d, ELs: %d\n",
minH, maxH, nr, mesh->getNumberOfElements());
@@ -386,6 +399,9 @@ public:
oldOldNr = oldNr;
oldNr = nr;
}
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ Parallel::MeshDistributor::globalMeshDistributor->checkMeshChange();
+#endif
calcMeshSizes(minH, maxH, minLevel, maxLevel, true);
MSG("Final (global) mesh: [%f, %f], Vs: %d, ELs: %d, Level: [%d, %d]\n",
minH, maxH, mesh->getNumberOfVertices(), mesh->getNumberOfElements(), minLevel, maxLevel);
diff --git a/extensions/Refinement_Level.h b/extensions/Refinement_Level.h
index 7dabe69e..5753d5ad 100644
--- a/extensions/Refinement_Level.h
+++ b/extensions/Refinement_Level.h
@@ -20,6 +20,7 @@
#define EXTENSIONS_REFINEMENT_LEVEL_PHASEFIELD_H
#include "ElementFunction.h"
+#include "Refinement.h"
namespace AMDiS { namespace extensions {
diff --git a/extensions/base_problems/CouplingBaseProblem.h b/extensions/base_problems/CouplingBaseProblem.h
index 653fe3e9..d12de90a 100644
--- a/extensions/base_problems/CouplingBaseProblem.h
+++ b/extensions/base_problems/CouplingBaseProblem.h
@@ -42,23 +42,12 @@ public:
if (prob3_) baseProblems.push_back(prob3_);
if (prob4_) baseProblems.push_back(prob4_);
}
-
- CouplingBaseProblem(std::string name_,
- std::vector<BaseProblemType*> probs_)
- : CProblemStat(name_), name(name_)
- {
- dow = Global::getGeo(WORLD);
- TEST_EXIT(probs_.size()>1)("You should have at least one base problem!\n");
- for ( int i = 0 ; i < probs_.size() ; ++i )
- if ( probs_[i] )
- baseProblems.push_back( probs_[i] );
- }
~CouplingBaseProblem() { }
- virtual void initialize(Flag initFlag,
- ProblemStatSeq *adoptProblem = NULL,
- Flag adoptFlag = INIT_NOTHING) override
+ void initialize(Flag initFlag,
+ ProblemStatSeq *adoptProblem = NULL,
+ Flag adoptFlag = INIT_NOTHING) override
{
for (size_t i = 0; i < baseProblems.size(); i++) {
for (size_t j = 0; j < baseProblems[i]->getNumProblems(); j++)
diff --git a/extensions/base_problems/CouplingBaseProblem2.h b/extensions/base_problems/CouplingBaseProblem2.h
index df2c140a..55b27b01 100644
--- a/extensions/base_problems/CouplingBaseProblem2.h
+++ b/extensions/base_problems/CouplingBaseProblem2.h
@@ -23,7 +23,9 @@
#include "GenericLoops.h"
+#ifndef MAX_NUM_COUPLED_PROBLEMS
#define MAX_NUM_COUPLED_PROBLEMS 10
+#endif
namespace AMDiS { namespace base_problems {
@@ -100,8 +102,8 @@ namespace detail {
template<class ProblemType=ProblemStat,
BOOST_PP_ENUM_PARAMS_WITH_A_DEFAULT(MAX_NUM_COUPLED_PROBLEMS, class BaseProblemType, void) >
class CouplingBaseProblem : public CouplingIterationInterface,
- public CouplingTimeInterface,
- public AMDiS::detail::CouplingProblemStat<ProblemType>
+ public CouplingTimeInterface,
+ public AMDiS::detail::CouplingProblemStat<ProblemType>
{
public:
typedef AMDiS::detail::CouplingProblemStat<ProblemType> CProblemStat;
@@ -128,7 +130,9 @@ public:
template<BOOST_PP_ENUM(BOOST_PP_INC(n), BASEPROBLEM_TYPES, BaseProblemType)> \
CouplingBaseProblem(std::string name_, \
BOOST_PP_REPEAT_ ## z(BOOST_PP_INC(n), BASEPROBLEM_ARGS2, nil) ) \
- : CProblemStat(name_),\
+ : ProblemIterationInterface(),\
+ ProblemTimeInterface(),\
+ CProblemStat(name_),\
baseProblems( BOOST_PP_ENUM_PARAMS_Z(z, BOOST_PP_INC(n), *prob) ), name(name_) \
{ dow = Global::getGeo(WORLD); } \
/****************************************************************************/
@@ -139,8 +143,8 @@ public:
~CouplingBaseProblem() { }
virtual void initialize(Flag initFlag,
- ProblemStatSeq *adoptProblem = NULL,
- Flag adoptFlag = INIT_NOTHING) override
+ ProblemStatSeq *adoptProblem = NULL,
+ Flag adoptFlag = INIT_NOTHING) override
{
using namespace AMDiS::extensions;
tools::FOR_EACH< detail::AddProblem >::loop2(*this, baseProblems);
@@ -225,6 +229,41 @@ public:
else
throw(std::runtime_error("problem with given name '" + name_ + "' does not exist"));
}
+
+ // final overriders for some functions...
+
+ virtual void serialize(std::ostream &out) {};
+ virtual void deserialize(std::istream &in) {};
+
+ // using CouplingIterationInterface::beginIteration
+ virtual void beginIteration(AdaptInfo *adaptInfo) override
+ {
+ CouplingIterationInterface::beginIteration(adaptInfo);
+ }
+
+ // using CouplingIterationInterface::oneIteration
+ virtual Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo) override
+ {
+ return CouplingIterationInterface::oneIteration(adaptInfo,toDo);
+ }
+
+ // using CouplingIterationInterface::endIteration
+ virtual void endIteration(AdaptInfo *adaptInfo) override
+ {
+ CouplingIterationInterface::endIteration(adaptInfo);
+ }
+
+ // using CProblemStat::getNumProblems
+ virtual int getNumProblems() override
+ {
+ return CProblemStat::getNumProblems();
+ }
+
+ // using CProblemStat::getProblem
+ virtual ProblemType *getProblem(int number = 0) override
+ {
+ return CProblemStat::getProblem(number);
+ }
protected:
BaseProblemsTupleType baseProblems;
diff --git a/extensions/base_problems/CouplingBaseProblem2_cxx11.h b/extensions/base_problems/CouplingBaseProblem2_cxx11.h
index 748fce8b..d28e6937 100644
--- a/extensions/base_problems/CouplingBaseProblem2_cxx11.h
+++ b/extensions/base_problems/CouplingBaseProblem2_cxx11.h
@@ -17,84 +17,86 @@
namespace AMDiS {
-namespace detail {
-
- /// for generic loops this struct can be passed
- struct AddProblem {
- template<typename CouplingProblemStatType, typename BaseProblemType>
- static void call(CouplingProblemStatType& couplingProblemStat, BaseProblemType& baseProblem) {
- for (size_t j = 0; j < baseProblem.getNumProblems(); j++)
- couplingProblemStat.addProblem(baseProblem.getProblem(j));
- }
- };
-
- /// for generic loops this struct can be passed
- struct AddTimeInterface {
- template<typename CouplingProblemStatType, typename BaseProblemType>
- static void call(CouplingProblemStatType& couplingProblemStat, BaseProblemType& baseProblem) {
- couplingProblemStat.addTimeInterface(&baseProblem);
- }
- };
+namespace extensions {
+
+ namespace detail {
- /// for generic loops this struct can be passed
- struct AddIterationInterface {
- template<typename CouplingProblemStatType, typename BaseProblemType>
- static void call(CouplingProblemStatType& couplingProblemStat, BaseProblemType& baseProblem) {
- couplingProblemStat.addIterationInterface(&baseProblem);
- }
- };
+ /// for generic loops this struct can be passed
+ struct AddProblem {
+ template<typename CouplingProblemStatType, typename BaseProblemType>
+ static void call(CouplingProblemStatType& couplingProblemStat, BaseProblemType& baseProblem) {
+ for (size_t j = 0; j < baseProblem.getNumProblems(); j++)
+ couplingProblemStat.addProblem(baseProblem.getProblem(j));
+ }
+ };
+
+ /// for generic loops this struct can be passed
+ struct AddTimeInterface {
+ template<typename CouplingProblemStatType, typename BaseProblemType>
+ static void call(CouplingProblemStatType& couplingProblemStat, BaseProblemType& baseProblem) {
+ couplingProblemStat.addTimeInterface(&baseProblem);
+ }
+ };
+
+ /// for generic loops this struct can be passed
+ struct AddIterationInterface {
+ template<typename CouplingProblemStatType, typename BaseProblemType>
+ static void call(CouplingProblemStatType& couplingProblemStat, BaseProblemType& baseProblem) {
+ couplingProblemStat.addIterationInterface(&baseProblem);
+ }
+ };
+
+ /// Functor for generic loops. Method initData() is called for each element in a sequence.
+ struct InitData {
+ template<typename BaseProblemType>
+ static void call(BaseProblemType& baseProblem) { baseProblem.initData(); }
+ };
+
+ /// Functor for generic loops. Method initData() is called for each element in a sequence.
+ struct FinalizeData {
+ template<typename BaseProblemType>
+ static void call(BaseProblemType& baseProblem) { baseProblem.finalizeData(); }
+ };
+
+ /// Functor for generic loops. Method fillOperators() is called for each element in a sequence.
+ struct FillOperators {
+ template<typename BaseProblemType>
+ static void call(BaseProblemType& baseProblem) { baseProblem.fillOperators(); }
+ };
+
+ /// Functor for generic loops. Method fillBoundaryConditions() is called for each element in a sequence.
+ struct FillBoundaryConditions {
+ template<typename BaseProblemType>
+ static void call(BaseProblemType& baseProblem) { baseProblem.fillBoundaryConditions(); }
+ };
- /// Functor for generic loops. Method initData() is called for each element in a sequence.
- struct InitData {
- template<typename BaseProblemType>
- static void call(BaseProblemType& baseProblem) { baseProblem.initData(); }
- };
- /// Functor for generic loops. Method initData() is called for each element in a sequence.
- struct FinalizeData {
- template<typename BaseProblemType>
- static void call(BaseProblemType& baseProblem) { baseProblem.finalizeData(); }
- };
+ struct FindProblem {
+ template<typename BaseProblemType, typename ProblemType>
+ static void call(BaseProblemType& baseProblem, const std::string& name, ProblemType& prob) {
+ if (baseProblem.getName() == name)
+ prob = baseProblem.getProblem();
+ }
+ };
- /// Functor for generic loops. Method fillOperators() is called for each element in a sequence.
- struct FillOperators {
- template<typename BaseProblemType>
- static void call(BaseProblemType& baseProblem) { baseProblem.fillOperators(); }
- };
+ struct FindBaseProblem {
+ template<typename BaseProblemType, typename ProblemType>
+ static void call(BaseProblemType& baseProblem, const std::string& name, ProblemType*& prob) {
+ typedef typename boost::mpl::if_<typename boost::is_same<BaseProblemType, ProblemType>::type,
+ boost::mpl::bool_<true>,
+ boost::mpl::bool_<false> >::type assign;
+ call(baseProblem, name, prob, assign());
+ }
+ template<typename BaseProblemType, typename ProblemType>
+ static void call(BaseProblemType& baseProblem, const std::string& name, ProblemType*& prob, boost::mpl::bool_<true>) {
+ if (baseProblem.getName() == name)
+ prob = &baseProblem;
+ }
+ template<typename BaseProblemType, typename ProblemType>
+ static void call(BaseProblemType& baseProblem, const std::string& name, ProblemType*& prob, boost::mpl::bool_<false>) {}
+ };
- /// Functor for generic loops. Method fillBoundaryConditions() is called for each element in a sequence.
- struct FillBoundaryConditions {
- template<typename BaseProblemType>
- static void call(BaseProblemType& baseProblem) { baseProblem.fillBoundaryConditions(); }
- };
-
-
- struct FindProblem {
- template<typename BaseProblemType, typename ProblemType>
- static void call(BaseProblemType& baseProblem, const std::string& name, ProblemType& prob) {
- if (baseProblem.getName() == name)
- prob = baseProblem.getProblem();
- }
- };
-
- struct FindBaseProblem {
- template<typename BaseProblemType, typename ProblemType>
- static void call(BaseProblemType& baseProblem, const std::string& name, ProblemType*& prob) {
- typedef typename boost::mpl::if_<typename boost::is_same<BaseProblemType, ProblemType>::type,
- boost::mpl::bool_<true>,
- boost::mpl::bool_<false> >::type assign;
- call(baseProblem, name, prob, assign());
- }
- template<typename BaseProblemType, typename ProblemType>
- static void call(BaseProblemType& baseProblem, const std::string& name, ProblemType*& prob, boost::mpl::bool_<true>) {
- if (baseProblem.getName() == name)
- prob = &baseProblem;
- }
- template<typename BaseProblemType, typename ProblemType>
- static void call(BaseProblemType& baseProblem, const std::string& name, ProblemType*& prob, boost::mpl::bool_<false>) {}
- };
-
-} // end namespace detail
+ } // end namespace detail
/**
* \ingroup Problem
@@ -103,16 +105,18 @@ namespace detail {
*/
template<typename ProblemType=ProblemStat, typename... BaseProblemTypes >
class CouplingBaseProblem : public CouplingIterationInterface,
- public CouplingTimeInterface,
- public detail::CouplingProblemStat<ProblemType>
+ public CouplingTimeInterface,
+ public AMDiS::detail::CouplingProblemStat<ProblemType>
{
public:
- typedef detail::CouplingProblemStat<ProblemType> CProblemStat;
+ typedef AMDiS::detail::CouplingProblemStat<ProblemType> CProblemStat;
typedef std::tuple<BaseProblemTypes&...> BaseProblemsTupleType;
template<typename... BaseProblemTypes_>
CouplingBaseProblem(std::string name_, BaseProblemTypes_&&... baseProblems_)
- : CProblemStat(name_),
+ : ProblemIterationInterface(), // virtual base class constructor
+ ProblemTimeInterface(), // virtual base class constructor
+ CProblemStat(name_),
baseProblems(baseProblems_...),
name(name_)
{
@@ -131,8 +135,8 @@ public:
* method.
**/
virtual void initialize(Flag initFlag,
- ProblemStatSeq *adoptProblem = NULL,
- Flag adoptFlag = INIT_NOTHING) override
+ ProblemStatSeq *adoptProblem = NULL,
+ Flag adoptFlag = INIT_NOTHING) override
{
tools::FOR_EACH< detail::AddProblem >::loop2(*this, baseProblems);
tools::FOR_EACH< detail::AddIterationInterface >::loop2(*this, baseProblems);
@@ -217,7 +221,42 @@ public:
else
throw(std::runtime_error("problem with given name '" + name_ + "' does not exist"));
}
-
+
+ // final overriders for some functions...
+
+ virtual void serialize(std::ostream &out) {};
+ virtual void deserialize(std::istream &in) {};
+
+ // using CouplingIterationInterface::beginIteration
+ virtual void beginIteration(AdaptInfo *adaptInfo) override
+ {
+ CouplingIterationInterface::beginIteration(adaptInfo);
+ }
+
+ // using CouplingIterationInterface::oneIteration
+ virtual Flag oneIteration(AdaptInfo *adaptInfo, Flag toDo) override
+ {
+ return CouplingIterationInterface::oneIteration(adaptInfo,toDo);
+ }
+
+ // using CouplingIterationInterface::endIteration
+ virtual void endIteration(AdaptInfo *adaptInfo) override
+ {
+ CouplingIterationInterface::endIteration(adaptInfo);
+ }
+
+ // using CProblemStat::getNumProblems
+ virtual int getNumProblems() override
+ {
+ return CProblemStat::getNumProblems();
+ }
+
+ // using CProblemStat::getProblem
+ virtual ProblemType *getProblem(int number = 0) override
+ {
+ return CProblemStat::getProblem(number);
+ }
+
protected:
BaseProblemsTupleType baseProblems;
@@ -227,6 +266,8 @@ protected:
std::string name;
};
+} // end namespace extensions
+
} // end namespace AMDiS
#endif // COUPLING_BASE_PROBLEM_H
diff --git a/extensions/base_problems/NavierStokes_TH_MultiPhase.hh b/extensions/base_problems/NavierStokes_TH_MultiPhase.hh
index 62c0dec9..b536b888 100644
--- a/extensions/base_problems/NavierStokes_TH_MultiPhase.hh
+++ b/extensions/base_problems/NavierStokes_TH_MultiPhase.hh
@@ -242,3 +242,4 @@ void NavierStokes_TH_MultiPhase<P>::addLaplaceTerm(int i)
} // end namespace detail
} }
+
diff --git a/extensions/demo/multimesh/CMakeLists.txt b/extensions/demo/multimesh/CMakeLists.txt
new file mode 100644
index 00000000..74786f7e
--- /dev/null
+++ b/extensions/demo/multimesh/CMakeLists.txt
@@ -0,0 +1,33 @@
+project("dendrites_karma")
+cmake_minimum_required(VERSION 2.8)
+
+find_package(AMDIS REQUIRED)
+
+if(AMDIS_FOUND)
+ message("amdis was found\n")
+ include(${AMDIS_USE_FILE})
+ SET(BASIS_LIBS ${AMDIS_LIBRARIES})
+endif(AMDIS_FOUND)
+
+
+set(dendrites ./src/dendrites.cc
+ ./src/MyProblemInstat.cc
+ ./src/Refinement.cc)
+
+set(diffuse ./src/diffuseDomain.cc)
+
+set(chns src/cahnHilliard_navierStokes.cc)
+
+
+add_executable("dendrites" ${dendrites})
+target_link_libraries("dendrites" ${BASIS_LIBS})
+
+add_executable("diffuse" ${diffuse})
+target_link_libraries("diffuse" ${BASIS_LIBS})
+
+add_executable("chns" ${chns})
+target_link_libraries("chns" ${BASIS_LIBS})
+
+
+add_executable("chns_mm" src/cahnHilliard_navierStokes_mm.cc)
+target_link_libraries("chns_mm" ${BASIS_LIBS})
\ No newline at end of file
diff --git a/extensions/demo/multimesh/init/cahnHilliard_navierStokes.dat.2d b/extensions/demo/multimesh/init/cahnHilliard_navierStokes.dat.2d
new file mode 100644
index 00000000..7c1ba3db
--- /dev/null
+++ b/extensions/demo/multimesh/init/cahnHilliard_navierStokes.dat.2d
@@ -0,0 +1,126 @@
+dimension of world: 2
+
+parallel->repartitioning: 0
+parallel->repartitioning->strategy: 1 % 0..quick, 1..full
+
+% =================== MESH ================================
+mesh_name: mesh
+mesh->macro file name: ./macro/macro.square.2d
+mesh->global refinements: 0
+
+mesh->refinement->level in outer domain: 3
+mesh->refinement->level in inner domain: 3
+mesh->refinement->level on interface: 10
+mesh->refinement->initial level: 7
+mesh->check: 0
+
+% ============== USER-PARAMETER ==========================
+ch->epsilon: 0.01
+ch->gamma: 1
+ch->double-well type: 0
+
+ch->initial interface: 2
+ch->ellipse->a: 0.3
+ch->ellipse->b: 0.5
+
+ns->viscosity: 1
+ns->density: 1
+
+ns->theta: 0.5
+%ns->force: [0.0, -1.0] % gravitational force
+
+ns->laplace operator: 0
+% type of laplace operator:
+% 0... div(nu*grad(u)),
+% 1... div(0.5*nu*(grad(u)+grad(u)^T))
+
+ns->non-linear term: 2
+% type of non-linear term:
+% 0... u^old*grad(u_i^old),
+% 1... u'*grad(u_i^old),
+% 2... u^old*grad(u'_i)
+% 3... (1)+(2)-(0)
+
+
+
+ch->space->mass conservation component: 0
+
+% =========== OUTPUT ==============================================
+prefix: _restrict3
+ch->space->output->filename: ./output/ch${prefix}_
+
+ns->velocity->output->filename: ./output/velocity${prefix}_
+ns->space->output[2]->filename: ./output/pressure${prefix}_
+
+% ==================== TIMESTEPS ===============================
+adapt->timestep: 1.e-2
+adapt->max timestep: 1e+10
+adapt->min timestep: 1e-10
+adapt->start time: 0.0
+adapt->end time: 3 %1.e-2
+
+% ============= PROBLEM-SPACES - CH =============================
+ch->space->components: 2
+ch->space->polynomial degree[0]: 3
+ch->space->polynomial degree[1]: 3
+
+ch->space->dim: 2
+ch->space->mesh: mesh
+
+% ============= PROBLEM-SPACES - NS ===========================
+ns->space->components: 3
+ns->space->polynomial degree[0]: 2
+ns->space->polynomial degree[1]: 2
+ns->space->polynomial degree[2]: 1
+
+ns->space->dim: 2
+ns->space->mesh: mesh
+
+% ============= PROBLEM-SPACES - CHNS ===========================
+chns->components: 5
+chns->dim: 2
+chns->mesh: mesh
+
+% ================== SOLVER - CH ================================
+ch->space->solver: direct
+%ch->space->solver->backend: mtl
+ch->space->solver->petsc prefix: ch
+ch->space->solver->symmetric strategy: 0
+ch->space->solver->store symbolic: 0
+ch->space->solver->tolerance: 1.e-8
+ch->space->solver->info: 1
+
+% ================== SOLVER - NS ================================
+ns->space->solver: direct
+%ns->space->solver->backend: mtl
+ns->space->solver->petsc prefix: ns
+ns->space->solver->symmetric strategy: 0
+ns->space->solver->store symbolic: 0
+ns->space->solver->tolerance: 1.e-8
+ns->space->solver->info: 1
+
+% =================== OUTPUT - CH ===============================
+ch->space->output->ParaView animation: 1
+ch->space->output->ParaView format: 1
+ch->space->output->write every i-th timestep: 1
+ch->space->output->append index: 1
+ch->space->output->index length: 9
+ch->space->output->index decimals: 7
+
+% =================== OUTPUT - NS ===============================
+ns->velocity->output->ParaView animation: 1
+ns->velocity->output->ParaView vector format: 1
+ns->velocity->output->write vector as 3d vector: 1
+ns->velocity->output->write every i-th timestep: 10
+ns->velocity->output->append index: 1
+ns->velocity->output->index length: 9
+ns->velocity->output->index decimals: 7
+
+ns->space->output[2]->ParaView animation: 1
+ns->space->output[2]->ParaView format: 1
+ns->space->output[2]->write every i-th timestep: 10
+ns->space->output[2]->append index: 1
+ns->space->output[2]->index length: 9
+ns->space->output[2]->index decimals: 7
+
+
diff --git a/extensions/demo/multimesh/init/dend002.dat.2d.m.bicg.2p b/extensions/demo/multimesh/init/dend002.dat.2d.m.bicg.2p
new file mode 100644
index 00000000..6f86f2b8
--- /dev/null
+++ b/extensions/demo/multimesh/init/dend002.dat.2d.m.bicg.2p
@@ -0,0 +1,138 @@
+dimension of world: 2
+
+
+parallel->repartitioning: 1
+parallel->repartitioning->strategy: 1 % 0..quick, 1..full
+parallel->pre refine: 8
+
+
+dendrites->write arh file: 1
+dendrites->write phi arh: ./output/phi800.arh
+dendrites->write rho arh: ./output/rho800.arh
+
+%dendrites->read arh file: ./output/dend.arh
+%dendrites->read phi arh: ./output/phi.arh
+%dendrites->read rho arh: ./output/rho.arh
+
+
+
+dendritesMesh->macro file name: ./macro/macro_corner_1x1.2d
+dendritesMesh->global refinements: 10
+
+dendritesMesh->scal x: 1000
+dendritesMesh->scal y: 1000
+
+
+dendrites->space->dim: 2
+
+dendrites->space->polynomial degree[0]: 1
+dendrites->space->polynomial degree[1]: 1
+
+dendrites->space->mesh: dendritesMesh
+dendrites->space->components: 2
+
+dendrites->space->refinement set[0]: 0
+dendrites->space->refinement set[1]: 1
+
+
+dendrites->space->solver: bicgstab
+%dendrites->space->solver: umfpack
+dendrites->space->solver->ell: 4
+dendrites->space->solver->max iteration: 1000
+dendrites->space->solver->tolerance: 1.e-8
+dendrites->space->solver->info: 5
+dendrites->space->solver->left precon: no
+dendrites->space->solver->right precon: no
+
+dendrites->space->estimator[0]: residual
+dendrites->space->estimator[0]->C0: 0.0
+dendrites->space->estimator[0]->C1: 1.0
+dendrites->space->estimator[0]->C2: 0.0
+dendrites->space->estimator[0]->C3: 0.0
+
+dendrites->space->estimator[1]: residual
+dendrites->space->estimator[1]->C0: 0.0
+dendrites->space->estimator[1]->C1: 1.0
+dendrites->space->estimator[1]->C2: 0.0
+dendrites->space->estimator[1]->C3: 0.0
+
+dendrites->adapt[0]->tolerance: 0.5
+dendrites->adapt[0]->info: 8
+dendrites->adapt[0]->coarsen allowed: 1
+
+dendrites->adapt[1]->tolerance: 0.25
+dendrites->adapt[1]->info: 8
+dendrites->adapt[1]->coarsen allowed: 1
+
+
+dendrites->adapt->timestep: 1.0
+dendrites->adapt->max timestep: 1.0
+dendrites->adapt->end time: 800.0
+dendrites->adapt->start time: 0.0
+
+dendrites->adapt->strategy: 0 % 0=explicit, 1=implicit
+dendrites->adapt->max iteration: 1
+
+dendrites->initial->marker[0]->strategy: 0 % 0=none, 1=GR, 2=MS, 3=ES, 4=GERS
+dendrites->initial->marker[1]->strategy: 0 % 0=none, 1=GR, 2=MS, 3=ES, 4=GERS
+
+dendrites->initial->adapt->max iteration: 1
+dendrites->initial->adapt->info: 8
+
+dendrites->space->marker[0]->strategy: 3 % 0=none, 1=GR, 2=MS, 3=ES, 4=GERS
+dendrites->space->marker[0]->ESTheta: 0.8
+dendrites->space->marker[0]->ESThetaC: 0.2
+dendrites->space->marker[0]->info: 8
+dendrites->space->marker[0]->min refinement level: 10
+
+dendrites->space->marker[1]->strategy: 3 % 0=none, 1=GR, 2=MS, 3=ES, 4=GERS
+dendrites->space->marker[1]->ESTheta: 0.8
+dendrites->space->marker[1]->ESThetaC: 0.2
+dendrites->space->marker[1]->info: 8
+dendrites->space->marker[1]->min refinement level: 10
+
+dendrites->space->output[0]->filename: ./output/002/phi2
+dendrites->space->output[0]->ParaView format: 1
+dendrites->space->output[0]->ParaView mode: 2
+dendrites->space->output[0]->ParaView create subdirectory: 1
+dendrites->space->output[0]->ParaView animation: 1
+dendrites->space->output[0]->write every i-th timestep: 25
+dendrites->space->output[0]->append index: 1
+dendrites->space->output[0]->index length: 8
+dendrites->space->output[0]->index decimals: 2
+
+dendrites->space->output[1]->filename: ./output/002/rho2
+dendrites->space->output[1]->ParaView format: 1
+dendrites->space->output[1]->ParaView mode: 2
+dendrites->space->output[1]->ParaView create subdirectory: 1
+dendrites->space->output[1]->ParaView animation: 1
+dendrites->space->output[1]->write every i-th timestep: 25
+dendrites->space->output[1]->append index: 1
+dendrites->space->output[1]->index length: 8
+dendrites->space->output[1]->index decimals: 2
+
+dendrites->space->output->write every i-th timestep: 25
+
+dendrites->space->output->write serialization: 0
+dendrites->space->output->serialization filename: ./output/002/dendrites.ser
+
+dendrites->space->input->read serialization: 0
+dendrites->space->input->serialization filename: ./output/002/dendrites.ser
+
+
+% === INTERFACE PARAMETER ===
+
+dendrites->radius: 3.00 % radius of initial island
+
+dendrites->h init interface: 0.1
+dendrites->h interface: 0.1
+dendrites->ref interface: 0
+
+% === MODEL PARAMETER ===
+
+dendrites->karma model->D: 1.00
+dendrites->karma model->gamma: 0.05
+dendrites->karma model->rho initial: 0.65
+
+
+parallel->output->serialization filename: ./output/002/parallel.ser
diff --git a/extensions/demo/multimesh/init/heat.dat.2d.m_1015_1010 b/extensions/demo/multimesh/init/heat.dat.2d.m_1015_1010
new file mode 100644
index 00000000..9b1f0edf
--- /dev/null
+++ b/extensions/demo/multimesh/init/heat.dat.2d.m_1015_1010
@@ -0,0 +1,85 @@
+dimension of world: 2
+
+parallel->repartitioning: 1
+parallel->repartitioning->strategy: 1 % 0..quick, 1..full
+parallel->repartitioning->imbalance: 0.05 % =5%
+
+
+mesh->macro file name: ./macro/macro.square.2d
+
+% phase
+mesh->max refinement level: 30
+mesh->update refinement level: 30
+mesh->refinement->level in inner domain: 10
+mesh->refinement->level in outer domain: 10
+mesh->refinement->level on interface: 15
+mesh->refinement->initial level: 0
+mesh->refinement->interface width: 0.03
+
+% heat
+mesh2->max refinement level: 30
+mesh2->update refinement level: 30
+mesh2->refinement->level in inner domain: 10 %
+mesh2->refinement->level in outer domain: 10 %
+mesh2->refinement->level on interface: 10
+mesh2->refinement->initial level: 0
+mesh2->refinement->interface width: 0.03
+
+%mesh->refinement->global heat refine: 3
+
+mesh->scale mesh: 1
+mesh->dimension: [2, 2]
+
+radius: 3.5
+center: [2,2]
+epsilon: 0.1
+
+
+heat->mesh: mesh
+heat->dim: 2
+heat->components: 1
+heat->additional components: 1
+heat->polynomial degree[0]: 1
+heat->polynomial degree[1]: 1
+heat->refinement set[0]: 0
+heat->refinement set[1]: 1
+
+heat->solver: cg
+heat->solver->max iteration: 10000
+heat->solver->tolerance: 1.e-8
+heat->solver->info: 2
+heat->solver->left precon: no
+heat->solver->right precon: no
+
+% heat->estimator[0]: residual
+% heat->estimator[0]->C0: 0.0
+% heat->estimator[0]->C1: 1.0
+% heat->estimator[0]->C2: 0.0
+% heat->estimator[0]->C3: 0.0
+
+adapt[0]->tolerance: 0.05
+adapt[0]->time tolerance: 0.05
+
+adapt->strategy: 0 % 0=explicit, 1=implicit
+adapt->max iteration: 100
+
+adapt[0]->coarsen allowed: 1
+adapt[0]->refine bisections: 2
+adapt[0]->coarsen bisections: 2
+
+heat->marker[0]->strategy: 0 % 0=none, 1=GR, 2=MS, 3=ES, 4=GERS
+heat->marker[0]->MSGamma: 0.5
+heat->marker[0]->MSGammaC: 0.1
+
+% ==================== TIMESTEPS ===============================
+adapt->timestep: 1
+adapt->start time: 0
+adapt->end time: 3
+
+heat->output->filename: ./output/heat_m_
+heat->output->ParaView animation: 1
+heat->output->ParaView format: 1
+heat->output->write every i-th timestep: 1
+heat->output->append index: 1
+heat->output->index length: 9
+heat->output->index decimals: 7
diff --git a/extensions/demo/multimesh/init/heat.dat.2d.s_16_16 b/extensions/demo/multimesh/init/heat.dat.2d.s_16_16
new file mode 100644
index 00000000..4d9fc84f
--- /dev/null
+++ b/extensions/demo/multimesh/init/heat.dat.2d.s_16_16
@@ -0,0 +1,76 @@
+dimension of world: 2
+
+parallel->repartitioning: 1
+parallel->repartition ith change: 5
+parallel->repartitioning->strategy: 0 % 0..quick, 1..full
+parallel->repartitioning->imbalance: 0.1 % =10%
+
+
+mesh->macro file name: ./macro/macro.square.2d
+
+
+mesh->max refinement level: 30
+mesh->update refinement level: 30
+mesh->refinement->level in inner domain: 16
+mesh->refinement->level in outer domain: 16
+mesh->refinement->level on interface: 16
+mesh->refinement->initial level: 0
+mesh->refinement->interface width: 0.03
+
+mesh->scale mesh: 1
+mesh->dimension: [2, 2]
+
+radius: 3.5
+center: [2,2]
+epsilon: 0.1
+
+
+heat->mesh: mesh
+heat->dim: 2
+heat->components: 1
+heat->additional components: 1
+heat->polynomial degree[0]: 1
+heat->polynomial degree[1]: 1
+%heat->refinement set[0]: 0
+%heat->refinement set[1]: 0
+
+heat->solver: cg
+heat->solver->max iteration: 10000
+heat->solver->tolerance: 1.e-8
+heat->solver->info: 2
+heat->solver->left precon: no
+heat->solver->right precon: no
+
+%heat->estimator[0]: residual
+%heat->estimator[0]->C0: 0.0
+%heat->estimator[0]->C1: 1.0
+%heat->estimator[0]->C2: 0.0
+%heat->estimator[0]->C3: 0.0
+
+adapt[0]->tolerance: 0.05
+adapt[0]->time tolerance: 0.05
+
+adapt->strategy: 0 % 0=explicit, 1=implicit
+adapt->max iteration: 100
+
+adapt[0]->coarsen allowed: 1
+adapt[0]->refine bisections: 2
+adapt[0]->coarsen bisections: 2
+
+heat->marker[0]->strategy: 0 % 0=none, 1=GR, 2=MS, 3=ES, 4=GERS
+heat->marker[0]->MSGamma: 0.5
+heat->marker[0]->MSGammaC: 0.1
+
+% ==================== TIMESTEPS ===============================
+adapt->timestep: 1
+adapt->start time: 0
+adapt->end time: 3
+
+heat->output->filename: ./output/heat_s_
+heat->output->ParaView animation: 1
+heat->output->ParaView format: 1
+heat->output->write every i-th timestep: 1
+heat->output->append index: 1
+heat->output->index length: 9
+heat->output->index decimals: 7
+
diff --git a/extensions/demo/multimesh/macro/macro.square.2d b/extensions/demo/multimesh/macro/macro.square.2d
new file mode 100644
index 00000000..7d310bfb
--- /dev/null
+++ b/extensions/demo/multimesh/macro/macro.square.2d
@@ -0,0 +1,47 @@
+DIM: 2
+DIM_OF_WORLD: 2
+
+number of elements: 8
+number of vertices: 9
+
+vertex coordinates:
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+element boundaries:
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+element neighbours:
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diff --git a/extensions/demo/multimesh/macro/macro.square.2d.666466.tmp b/extensions/demo/multimesh/macro/macro.square.2d.666466.tmp
new file mode 100644
index 00000000..17c80569
--- /dev/null
+++ b/extensions/demo/multimesh/macro/macro.square.2d.666466.tmp
@@ -0,0 +1,236 @@
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+
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diff --git a/extensions/demo/multimesh/macro/macro.square.2d.685642.tmp b/extensions/demo/multimesh/macro/macro.square.2d.685642.tmp
new file mode 100644
index 00000000..287a9815
--- /dev/null
+++ b/extensions/demo/multimesh/macro/macro.square.2d.685642.tmp
@@ -0,0 +1,236 @@
+DIM: 2
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+
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+vertex coordinates:
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diff --git a/extensions/demo/multimesh/macro/macro_corner_1x1.2d b/extensions/demo/multimesh/macro/macro_corner_1x1.2d
new file mode 100644
index 00000000..1e525f90
--- /dev/null
+++ b/extensions/demo/multimesh/macro/macro_corner_1x1.2d
@@ -0,0 +1,24 @@
+DIM: 2
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+
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+
+vertex coordinates:
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+element boundaries:
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diff --git a/extensions/demo/multimesh/macro/macro_corner_1x1.2d.736102.tmp b/extensions/demo/multimesh/macro/macro_corner_1x1.2d.736102.tmp
new file mode 100644
index 00000000..f152f950
--- /dev/null
+++ b/extensions/demo/multimesh/macro/macro_corner_1x1.2d.736102.tmp
@@ -0,0 +1,6708 @@
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diff --git a/extensions/demo/multimesh/macro/macro_corner_1x1.2d.801668.tmp b/extensions/demo/multimesh/macro/macro_corner_1x1.2d.801668.tmp
new file mode 100644
index 00000000..f152f950
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diff --git a/extensions/demo/multimesh/macro/macro_corner_1x1.2d.991261.tmp b/extensions/demo/multimesh/macro/macro_corner_1x1.2d.991261.tmp
new file mode 100644
index 00000000..f152f950
--- /dev/null
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diff --git a/extensions/demo/multimesh/src/Anisotropy.h b/extensions/demo/multimesh/src/Anisotropy.h
new file mode 100644
index 00000000..82ce4fc8
--- /dev/null
+++ b/extensions/demo/multimesh/src/Anisotropy.h
@@ -0,0 +1,175 @@
+#include "AMDiS.h"
+
+inline double pow2(const double &v)
+{
+ return v * v;
+}
+
+inline double pow4(const double &v)
+{
+ return v * v * v * v;
+}
+
+// === Anisotropy functions for 2D ===
+
+class Aniso2d_Square : public AbstractFunction<double, WorldVector<double> >
+{
+public:
+ Aniso2d_Square(double g)
+ : AbstractFunction<double, WorldVector<double> >(2),
+ gamma(g),
+ anisoReg(1e-6)
+ {
+ eps2 = 1.0 - 3.0 * gamma;
+ eps4 = 4.0 * gamma / (1.0 - 3.0 * gamma);
+ }
+
+ double operator()(const WorldVector<double>& n) const
+ {
+ double eta = eps2 *
+ (1.0 + eps4 * (pow4(n[0]) + pow4(n[1])) / (pow4(norm(&n)) + anisoReg));
+
+ return eta * eta;
+ }
+
+private:
+ double gamma;
+
+ double anisoReg;
+
+ double eps2, eps4;
+};
+
+
+class Aniso2d_Laplace : public AbstractFunction<WorldMatrix<double>, WorldVector<double> >
+{
+public:
+ Aniso2d_Laplace(double g)
+ : AbstractFunction<WorldMatrix<double>, WorldVector<double> >(2),
+ gamma(g),
+ anisoReg(1e-6)
+ {
+ eps2 = 1.0 - 3.0 * gamma;
+ eps4 = 4.0 * gamma / (1.0 - 3.0 * gamma);
+ }
+
+ WorldMatrix<double> operator()(const WorldVector<double>& n) const
+ {
+ WorldMatrix<double> result;
+ result.set(0.0);
+
+ double d = (pow4(n[0]) + pow4(n[1])) / (pow4(norm(&n)) + anisoReg);
+ double normSquare = pow2(norm(&n)) + anisoReg;
+ double eta = eps2 * (1 + eps4 * d);
+
+ result[0][0] =
+ eta * (eta + 16.0 * gamma * (pow2(n[0]) / normSquare - d));
+
+ result[1][1] =
+ eta * (eta + 16.0 * gamma * (pow2(n[1]) / normSquare - d));
+
+ return result;
+ }
+
+private:
+ double gamma;
+
+ double anisoReg;
+
+ double eps2, eps4;
+};
+
+
+// === Anisotropy functions for 3D ===
+
+class Aniso3d_Square : public AbstractFunction<double, WorldVector<double> >
+{
+public:
+ Aniso3d_Square(double g)
+ : AbstractFunction<double, WorldVector<double> >(2),
+ gamma(g),
+ anisoReg(1e-6)
+ {
+ eps2 = 1.0 - 3.0 * gamma;
+ eps4 = 4.0 * gamma / (1.0 - 3.0 * gamma);
+ }
+
+ double operator()(const WorldVector<double>& n) const
+ {
+ double eta = eps2 *
+ (1.0 + eps4 * (pow4(n[0]) + pow4(n[1]) + pow4(n[2])) / (pow4(norm(&n)) + anisoReg));
+
+ return eta * eta;
+ }
+
+private:
+ double gamma;
+
+ double anisoReg;
+
+ double eps2, eps4;
+};
+
+
+class Aniso3d_Laplace : public AbstractFunction<WorldMatrix<double>, WorldVector<double> >
+{
+public:
+ Aniso3d_Laplace(double g)
+ : AbstractFunction<WorldMatrix<double>, WorldVector<double> >(2),
+ gamma(g),
+ anisoReg(1e-6)
+ {
+ eps2 = 1.0 - 3.0 * gamma;
+ eps4 = 4.0 * gamma / (1.0 - 3.0 * gamma);
+ }
+
+ WorldMatrix<double> operator()(const WorldVector<double>& n) const
+ {
+ WorldMatrix<double> &result = const_cast<WorldMatrix<double>&>(tmpWorldMat);
+ result.set(0.0);
+
+ double d = (pow4(n[0]) + pow4(n[1]) + pow4(n[2])) / (pow4(norm(&n)) + anisoReg);
+ double normSquare = pow2(norm(&n)) + anisoReg;
+ double eta = eps2 * (1 + eps4 * d);
+
+ result[0][0] =
+ eta * (eta + 16.0 * gamma * (pow2(n[0]) / normSquare - d));
+
+ result[1][1] =
+ eta * (eta + 16.0 * gamma * (pow2(n[1]) / normSquare - d));
+
+ result[2][2] =
+ eta * (eta + 16.0 * gamma * (pow2(n[2]) / normSquare - d));
+
+ return result;
+ }
+
+private:
+ WorldMatrix<double> tmpWorldMat;
+
+ double gamma;
+
+ double anisoReg;
+
+ double eps2, eps4;
+};
+
+
+class NullFct : public AbstractFunction<WorldVector<double>, WorldMatrix<double> >
+{
+public:
+
+ NullFct()
+ : AbstractFunction<WorldVector<double>, WorldMatrix<double> >(1)
+ {
+ result.set(0.0);
+ }
+
+ WorldVector<double> operator()(const WorldMatrix<double>& n) const
+ {
+ return result;
+ }
+
+private:
+ WorldVector<double> result;
+};
diff --git a/extensions/demo/multimesh/src/CahnHilliard_mm.h b/extensions/demo/multimesh/src/CahnHilliard_mm.h
new file mode 100644
index 00000000..ab4f6072
--- /dev/null
+++ b/extensions/demo/multimesh/src/CahnHilliard_mm.h
@@ -0,0 +1,127 @@
+/******************************************************************************
+ *
+ * Extension of AMDiS - Adaptive multidimensional simulations
+ *
+ * Copyright (C) 2013 Dresden University of Technology. All Rights Reserved.
+ * Web: https://fusionforge.zih.tu-dresden.de/projects/amdis
+ *
+ * Authors: Simon Praetorius et al.
+ *
+ * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+ * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ *
+ *
+ * See also license.opensource.txt in the distribution.
+ *
+ ******************************************************************************/
+
+#ifndef CAHN_HILLIARD_H
+#define CAHN_HILLIARD_H
+
+#include "AMDiS.h"
+#include "BaseProblem.h"
+#include "ProblemStatMassConserve_mm.h"
+#include "chns.h"
+#include "operations/functors.hpp"
+
+namespace AMDiS { namespace base_problems {
+
+namespace detail {
+
+ struct c_; // name for the concentration component
+
+ class CahnHilliard_mm : public BaseProblem<ProblemStatMassConserve>
+ {
+ public: // definition of types
+
+ typedef BaseProblem<ProblemStatMassConserve> super;
+ typedef CahnHilliard_mm self;
+ using super::prob;
+
+ public: // public methods
+
+ CahnHilliard_mm(const std::string &name_);
+ ~CahnHilliard_mm() {};
+
+ void solveInitialProblem(AMDiS::AdaptInfo *adaptInfo) override;
+
+ double getEpsilon() { return eps; }
+ int getDoubleWellType() { return doubleWell; }
+
+ void fillOperators() override;
+ void fillBoundaryConditions() override {}
+
+ void finalizeData() override;
+
+ protected: // protected variables
+
+ bool useMobility;
+ bool useReinit;
+
+ unsigned dim;
+
+ int doubleWell;
+
+ double gamma;
+ double eps;
+ double minusEps;
+ double epsInv;
+ double minusEpsInv;
+ double epsSqr;
+ double minusEpsSqr;
+ };
+
+
+ class MobilityCH0_mm : public FunctorBase //: public AbstractFunction<double,double>
+ {
+ public:
+ MobilityCH0_mm(double gamma_=1.0) :
+ gamma(gamma_),
+ delta(1.e-6) { }
+
+ typedef double result_type;
+ int getDegree(int d0) const { return d0 * 4; }
+
+ double operator()(const double &ch) const
+ {
+ double phase = std::max(0.0, std::min(1.0, ch));
+ double mobility = 0.25*sqr(phase)*sqr(phase-1.0);
+ return gamma * std::max(mobility, delta);
+ }
+
+ protected:
+ double gamma;
+ double delta;
+ };
+
+ class MobilityCH1_mm : public FunctorBase // : public AbstractFunction<double,double>
+ {
+ public:
+ MobilityCH1_mm(double gamma_=1.0) :
+ gamma(gamma_),
+ delta(1.e-6) { }
+
+ typedef double result_type;
+ int getDegree(int d0) const { return d0 * 4; }
+
+ double operator()(const double &ch) const
+ {
+ double phase = std::max(-1.0, std::min(1.0, ch));
+ double mobility = 0.25*sqr(sqr(phase)-1.0);
+ return gamma * std::max(mobility, delta);
+ }
+
+ protected:
+ double gamma;
+ double delta;
+ };
+
+} // end namespace detail
+
+typedef detail::CahnHilliard_mm CahnHilliard_mm;
+
+} }
+
+#include "CahnHilliard_mm.hh"
+
+#endif // CAHN_HILLIARD_H
diff --git a/extensions/demo/multimesh/src/CahnHilliard_mm.hh b/extensions/demo/multimesh/src/CahnHilliard_mm.hh
new file mode 100644
index 00000000..978ce3f6
--- /dev/null
+++ b/extensions/demo/multimesh/src/CahnHilliard_mm.hh
@@ -0,0 +1,222 @@
+/******************************************************************************
+ *
+ * Extension of AMDiS - Adaptive multidimensional simulations
+ *
+ * Copyright (C) 2013 Dresden University of Technology. All Rights Reserved.
+ * Web: https://fusionforge.zih.tu-dresden.de/projects/amdis
+ *
+ * Authors: Simon Praetorius et al.
+ *
+ * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+ * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ *
+ *
+ * See also license.opensource.txt in the distribution.
+ *
+ ******************************************************************************/
+
+
+#include "SignedDistFunctors.h"
+#include "PhaseFieldConvert.h"
+
+#include "HL_SignedDistTraverse.h"
+#include "Recovery.h"
+#include "GenericOperatorTerm.h"
+
+namespace AMDiS { namespace base_problems {
+
+namespace detail {
+
+
+CahnHilliard_mm::CahnHilliard_mm(const std::string &name_) :
+ super(name_),
+ useMobility(false),
+ useReinit(false),
+ doubleWell(0),
+ gamma(1.0),
+ eps(0.1),
+ minusEps(-0.1),
+ epsInv(10.0),
+ minusEpsInv(-10.0),
+ epsSqr(0.01),
+ minusEpsSqr(-0.01)
+{
+ // parameters for CH
+ Parameters::get(name_ + "->use mobility", useMobility); // mobility
+ Parameters::get(name_ + "->gamma", gamma); // mobility
+ Parameters::get(name_ + "->epsilon", eps); // interface width
+
+ // type of double well: 0= [0,1], 1= [-1,1]
+ Parameters::get(name_ + "->double-well type", doubleWell);
+
+ Parameters::get(name_ + "->use reinit", useReinit);
+
+ // transformation of the parameters
+ minusEps = -eps;
+ epsInv = 1.0/eps;
+ minusEpsInv = -epsInv;
+ epsSqr = sqr(eps);
+ minusEpsSqr = -epsSqr;
+}
+
+
+
+void CahnHilliard_mm::solveInitialProblem(AdaptInfo *adaptInfo)
+{
+ using namespace AMDiS::extensions;
+ Flag initFlag = self::initDataFromFile(adaptInfo);
+
+ if (!initFlag.isSet(DATA_ADOPTED)) {
+ int initialInterface = 0;
+ Initfile::get(self::name + "->initial interface", initialInterface);
+ double initialEps = eps;
+ Initfile::get(self::name + "->initial epsilon", initialEps);
+
+ if (initialInterface == 0) {
+ /// horizontale Linie
+ double a= 0.0, dir= -1.0;
+ Initfile::get(self::name + "->line->pos", a);
+ Initfile::get(self::name + "->line->direction", dir);
+ prob->getSolution()->getDOFVector(0)->interpol(new Plane(a, dir));
+ }
+ else if (initialInterface == 1) {
+ /// schraege Linie
+ double theta = m_pi/4.0;
+ prob->getSolution()->getDOFVector(0)->interpol(new PlaneRotation(0.0, theta, 1.0));
+ transformDOFInterpolation(prob->getSolution()->getDOFVector(0),new PlaneRotation(0.0, -theta, -1.0), new AMDiS::Min<double>);
+ }
+ else if (initialInterface == 2) {
+ /// Ellipse
+ double a= 1.0, b= 1.0;
+ Initfile::get(self::name + "->ellipse->a", a);
+ Initfile::get(self::name + "->ellipse->b", b);
+ prob->getSolution()->getDOFVector(0)->interpol(new Ellipse(a,b));
+ }
+ else if (initialInterface == 3) {
+ /// zwei horizontale Linien
+ double a= 0.75, b= 0.375;
+ Initfile::get(self::name + "->lines->pos1", a);
+ Initfile::get(self::name + "->lines->pos2", b);
+ prob->getSolution()->getDOFVector(0)->interpol(new Plane(a, -1.0));
+ transformDOFInterpolation(prob->getSolution()->getDOFVector(0),new Plane(b, 1.0), new AMDiS::Max<double>);
+ }
+ else if (initialInterface == 4) {
+ /// Kreis
+ double radius= 1.0;
+ Initfile::get(self::name + "->kreis->radius", radius);
+ prob->getSolution()->getDOFVector(0)->interpol(new Circle(radius));
+ } else if (initialInterface == 5) {
+ /// Rechteck
+ double width = 0.5;
+ double height = 0.3;
+ WorldVector<double> center; center.set(0.5);
+ Initfile::get(self::name + "->rectangle->width", width);
+ Initfile::get(self::name + "->rectangle->height", height);
+ Initfile::get(self::name + "->rectangle->center", center);
+ prob->getSolution()->getDOFVector(0)->interpol(new Rectangle(width, height, center));
+ }
+
+ if (useReinit) {
+ FiniteElemSpace* feSpace = FiniteElemSpace::provideFeSpace(
+ const_cast<DOFAdmin*>(self::getMesh()->getVertexAdmin()),
+ Lagrange::getLagrange(self::getMesh()->getDim(), 1),
+ self::getMesh(),
+ "P1");
+ DOFVector<double> tmp(feSpace, "tmp");
+ tmp.interpol(prob->getSolution()->getDOFVector(0));
+
+ HL_SignedDistTraverse reinit("reinit", self::getMesh()->getDim());
+ reinit.calcSignedDistFct(adaptInfo, &tmp);
+
+#ifndef HAVE_PARALLEL_DOMAIN_AMDIS
+ Recovery recovery(L2_NORM, 1);
+ recovery.recoveryUh(&tmp, *prob->getSolution()->getDOFVector(0));
+#else
+ prob->getSolution()->getDOFVector(0)->interpol(&tmp);
+#endif
+ }
+
+
+ /// create phase-field from signed-dist-function
+ if (doubleWell == 0) {
+ forEachDOF(prob->getSolution()->getDOFVector(0),
+ new SignedDistToPhaseField(initialEps));
+ } else {
+ forEachDOF(prob->getSolution()->getDOFVector(0),
+ new SignedDistToCh(initialEps));
+ }
+ }
+}
+
+
+void CahnHilliard_mm::fillOperators()
+{
+ const FiniteElemSpace* feSpace0 = prob->getFeSpace(0);
+ const FiniteElemSpace* feSpace1 = prob->getFeSpace(1);
+
+ DOFVector<double>* c = prob->getSolution()->getDOFVector(0);
+// DOFVector<double>* mu = prob->getSolution()->getDOFVector(1);
+
+ // -nabla*(grad(c))
+ Operator *opChL = new Operator(feSpace0, feSpace0);
+ addSOT(opChL, 1.0);
+
+ // div(M(c)grad(mu)), with M(c)=gamma/4*(c^2-1)^2
+ Operator *opChLM = new Operator(feSpace1, feSpace1);
+ if (useMobility) {
+ if (doubleWell == 0)
+ addSOT(opChLM, function_(MobilityCH0_mm(gamma), valueOf(c)) );
+ else
+ addSOT(opChLM, function_(MobilityCH1_mm(gamma), valueOf(c)) );
+ } else
+ addSOT(opChLM, gamma );
+
+ // -2*c_old^3 + 3/2*c_old^2
+ Operator *opChWExpl = new Operator(feSpace0, feSpace0);
+ Operator *opChWImpl = new Operator(feSpace0, feSpace0);
+ if (doubleWell == 0) {
+ addZOT(opChWExpl, -2.0*pow<3>(valueOf(c)) + 1.5*pow<2>(valueOf(c)));
+ addZOT(opChWImpl, -3.0*pow<2>(valueOf(c)) + 3.0*valueOf(c) - 0.5);
+ } else {
+ addZOT(opChWExpl, -2.0*pow<3>(valueOf(c)));
+ addZOT(opChWImpl, -3.0*pow<2>(valueOf(c)) + 1.0);
+ }
+
+
+ // mu + eps^2*laplace(c) + c - 3*(c_old^2)*c = -2*c_old^3 [+ BC]
+ // ----------------------------------------------------------------------
+ prob->addMatrixOperator(*opChWImpl, 0, 0); /// < -3*phi*c*c_old^2 , psi >
+ prob->addMatrixOperator(*opChL, 0, 0, &minusEpsSqr, &minusEpsSqr); /// < -eps^2*phi*grad(c) , grad(psi) >
+ // . . . vectorOperators . . . . . . . . . . . . . . .
+ prob->addVectorOperator(*opChWExpl, 0); /// < -2*phi*c_old^3 , psi >
+
+ Operator *opM01new = new Operator(feSpace0, feSpace1);
+ addZOT(opM01new, 1.0);
+ prob->addMatrixOperator(*opM01new, 0, 1); /// < phi*mu , psi >
+
+ // dt(c) = laplace(mu) - u*grad(c)
+ // -----------------------------------
+ Operator *opM10new = new Operator(feSpace1, feSpace0);
+ addZOT(opM10new, 1.0);
+ prob->addMatrixOperator(*opM10new, 1, 0, self::getInvTau(), self::getInvTau()); /// < phi*c/tau , psi >
+ prob->addMatrixOperator(*opChLM, 1, 1); /// < phi*grad(mu) , grad(psi) >
+ // . . . vectorOperators . . . . . . . . . . . . . . .
+ Operator *opChMold = new Operator(feSpace1, feSpace0);
+ addZOT(opChMold, 1.0); opChMold->setUhOld(prob->getOldSolution(0));
+// addZOT(opChMold, valueOf(prob->getSolution(0)));
+ prob->addVectorOperator(*opChMold, 1, self::getInvTau(), self::getInvTau()); /// < phi*c^old/tau , psi >
+}
+
+
+
+void CahnHilliard_mm::finalizeData()
+{
+// self::setAssembleMatrixOnlyOnce_butTimestepChange(0,1);
+// self::setAssembleMatrixOnlyOnce_butTimestepChange(1,0);
+// if (!useMobility)
+// self::setAssembleMatrixOnlyOnce_butTimestepChange(1,1);
+}
+
+} // end namespace detail
+
+} }
diff --git a/extensions/demo/multimesh/src/MyProblemInstat.cc b/extensions/demo/multimesh/src/MyProblemInstat.cc
new file mode 100644
index 00000000..7f13a648
--- /dev/null
+++ b/extensions/demo/multimesh/src/MyProblemInstat.cc
@@ -0,0 +1,158 @@
+#include "AMDiS.h"
+#include "MyProblemInstat.h"
+#include "Refinement.h"
+
+using namespace AMDiS;
+
+void MyProblemInstat::solveInitialProblem(AdaptInfo *adaptInfo)
+{
+ FUNCNAME("MyProblemInstat::solveInitialProblem()");
+
+
+ string phiArh = "", rhoArh = ""; int nProc;
+ Parameters::get("dendrites->read phi arh", phiArh);
+ Parameters::get("dendrites->read rho arh", rhoArh);
+ Parameters::get("dendrites->number of processors", nProc);
+
+ if (phiArh != "" && rhoArh != "") {
+
+ io::Arh2Reader::readFile(phiArh.c_str(),
+ problemStat->getSolution(0), NULL, NULL, true, nProc);
+ io::Arh2Reader::readFile(rhoArh.c_str(),
+ problemStat->getSolution(1), NULL, NULL, true, nProc);
+
+ oldSolution->getDOFVector(0)->copy(*(problemStat->getSolution()->getDOFVector(0)));
+ oldSolution->getDOFVector(1)->copy(*(problemStat->getSolution()->getDOFVector(1)));
+
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ Parallel::MeshDistributor::globalMeshDistributor->checkMeshChange(false);
+#endif
+ return;
+ }
+
+ if (serial <= 0) {
+
+ double r = 0.0;
+ Parameters::get("dendrites->radius", r);
+
+ AbstractFunction<double, WorldVector<double> > *signedDistFct = new Circle(r);
+ AbstractFunction<double, WorldVector<double> > *initialPhaseField =
+ new InitialPhaseField(signedDistFct);
+
+ Refinement refinePhi(problemStat->getSolution()->getDOFVector(0),
+ initialPhaseField,
+ problemStat->getRefinementManager(0),
+ problemStat->getCoarseningManager(0));
+ refinePhi.refine(hInitInterface);
+
+ if (problemStat->getMesh(0) != problemStat->getMesh(1)) {
+ Refinement refineRho(problemStat->getSolution()->getDOFVector(1),
+ initialPhaseField,
+ problemStat->getRefinementManager(1),
+ problemStat->getCoarseningManager(1));
+ refineRho.refine(hInitInterface);
+ }
+
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ Parallel::MeshDistributor::globalMeshDistributor->checkMeshChange(false);
+#endif
+ problemStat->getSolution()->getDOFVector(1)->set(-rhoInitial);
+
+ delete signedDistFct;
+ delete initialPhaseField;
+ }
+
+ problemStat->getMesh(0)->dofCompress();
+ problemStat->getMesh(1)->dofCompress();
+}
+
+
+void MyProblemInstat::closeTimestep(AdaptInfo *adaptInfo)
+{
+ FUNCNAME("MyProblemInstat::closeTimestep()");
+
+ ProblemInstat::closeTimestep(adaptInfo);
+
+ if (refInterface) {
+ Refinement refinePhi(problemStat->getSolution()->getDOFVector(0),
+ NULL,
+ problemStat->getRefinementManager(0),
+ problemStat->getCoarseningManager(0));
+ refinePhi.refine(hInterface);
+
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ Parallel::MeshDistributor::globalMeshDistributor->checkMeshChange(false);
+#endif
+ }
+
+ if (problemStat->getMesh(0)->getDim() == 3)
+ return;
+
+#ifndef HAVE_PARALLEL_DOMAIN_AMDIS
+
+ /*
+ mtl::dense_vector<double> localVec(problemStat->getFeSpace(0)->getBasisFcts()->getNumber());
+ DOFVector<double> *phi = problemStat->getSolution()->getDOFVector(0);
+
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(problemStat->getMesh(0), -1,
+ Mesh::CALL_LEAF_EL |
+ Mesh::FILL_COORDS);
+ while (elInfo) {
+ std::vector<int> zeroCoords(0);
+
+ for (int i = 0; i < 3; i++)
+ if (elInfo->getCoord(i)[1] == 0.0)
+ zeroCoords.push_back(i);
+
+ if (zeroCoords.size() == 2) {
+ phi->getLocalVector(elInfo->getElement(), localVec);
+
+ if (sign(localVec[zeroCoords[0]]) != sign(localVec[zeroCoords[1]])) {
+ if (elInfo->getCoord(zeroCoords[0])[0] > elInfo->getCoord(zeroCoords[1])[0])
+ std::swap(zeroCoords[0], zeroCoords[1]);
+
+ TEST_EXIT(localVec[zeroCoords[0]] > 0.0)("Error 1\n");
+ TEST_EXIT(localVec[zeroCoords[1]] < 0.0)("Error 2\n");
+
+ double m = (localVec[zeroCoords[0]] - localVec[zeroCoords[1]]) /
+ (elInfo->getCoord(zeroCoords[1])[0] - elInfo->getCoord(zeroCoords[0])[0]);
+ double xZero =
+ elInfo->getCoord(zeroCoords[0])[0] + (localVec[zeroCoords[0]] / m);
+
+ MSG("Tip-x position at t = %f : %f\n", adaptInfo->getTime(), xZero);
+ }
+ }
+
+ zeroCoords.clear();
+
+ for (int i = 0; i < 3; i++)
+ if (elInfo->getCoord(i)[0] == 0.0)
+ zeroCoords.push_back(i);
+
+ if (zeroCoords.size() == 2) {
+ phi->getLocalVector(elInfo->getElement(), localVec);
+
+ if (sign(localVec[zeroCoords[0]]) != sign(localVec[zeroCoords[1]])) {
+ if (elInfo->getCoord(zeroCoords[0])[1] > elInfo->getCoord(zeroCoords[1])[1])
+ std::swap(zeroCoords[0], zeroCoords[1]);
+
+ TEST_EXIT(localVec[zeroCoords[0]] > 0.0)("Error 1\n");
+ TEST_EXIT(localVec[zeroCoords[1]] < 0.0)("Error 2\n");
+
+ double m = (localVec[zeroCoords[0]] - localVec[zeroCoords[1]]) /
+ (elInfo->getCoord(zeroCoords[1])[1] - elInfo->getCoord(zeroCoords[0])[1]);
+ double yZero =
+ elInfo->getCoord(zeroCoords[0])[1] + (localVec[zeroCoords[0]] / m);
+
+ MSG("Tip-y position at t = %f : %f\n", adaptInfo->getTime(), yZero);
+ }
+ }
+
+ elInfo = stack.traverseNext(elInfo);
+ }
+ */
+
+#endif
+
+}
diff --git a/extensions/demo/multimesh/src/MyProblemInstat.h b/extensions/demo/multimesh/src/MyProblemInstat.h
new file mode 100644
index 00000000..b85aadad
--- /dev/null
+++ b/extensions/demo/multimesh/src/MyProblemInstat.h
@@ -0,0 +1,96 @@
+#include "AMDiS.h"
+
+using namespace AMDiS;
+
+class Circle : public AbstractFunction<double, WorldVector<double> >
+{
+public:
+ Circle(double radius_, WorldVector<double> midPoint_)
+ : radius(radius_),
+ midPoint(midPoint_)
+ {}
+
+ Circle(double radius_)
+ : radius(radius_)
+ {
+ midPoint.set(0.0);
+ }
+
+ double operator()(const WorldVector<double>& x) const
+ {
+ double result = 0.0;
+ for (int k = 0; k < x.getSize(); k++)
+ result += sqr(x[k] - midPoint[k]);
+
+ result = sqrt(result) - radius;
+ return result;
+ };
+private:
+ double radius;
+ WorldVector<double> midPoint;
+};
+
+
+class InitialPhaseField : public AbstractFunction<double, WorldVector<double> >
+{
+public:
+ InitialPhaseField(AbstractFunction<double,WorldVector<double> > *dist_)
+ : dist(dist_)
+ {}
+
+ double operator()(const WorldVector<double> &x) const
+ {
+ return -tanh((*dist)(x) / sqrt(2.0));
+ }
+
+private:
+ AbstractFunction<double,WorldVector<double> > *dist;
+};
+
+
+class MyProblemInstat : public ProblemInstat
+{
+public:
+ MyProblemInstat(std::string name, ProblemStat &probStat)
+ : ProblemInstat(name, probStat),
+ hInitInterface(0.0),
+ hInterface(0.0),
+ refInterface(0),
+ rhoInitial(0.0),
+ serial(0)
+ {
+ FUNCNAME("MyProblemInstat::MyProblemInstat()");
+
+ Parameters::get("dendrites->h init interface", hInitInterface);
+ Parameters::get("dendrites->h interface", hInterface);
+ Parameters::get("dendrites->ref interface", refInterface);
+ Parameters::get("dendrites->karma model->rho initial", rhoInitial);
+ Parameters::get("dendrites->space->input->read serialization", serial);
+
+ TEST_EXIT(rhoInitial > 0.0)("Initial rho must be greater than 0!\n");
+ }
+
+ void solveInitialProblem(AdaptInfo *adaptInfo);
+
+ void closeTimestep(AdaptInfo *adaptInfo);
+
+private:
+ inline int sign(double value)
+ {
+ return (value < 0.0 ? 1 : 0);
+ }
+
+private:
+ /// Minimal length of each edge of all elements in the phase field transition;
+ double hInitInterface;
+
+ double hInterface;
+
+ /// If non zero, do not use estimator and marking strategy, but instead the interface
+ /// refinement algorithm on the solution vector.
+ int refInterface;
+
+ double rhoInitial;
+
+ int serial;
+};
diff --git a/extensions/demo/multimesh/src/Refinement.cc b/extensions/demo/multimesh/src/Refinement.cc
new file mode 100644
index 00000000..ffd6a57f
--- /dev/null
+++ b/extensions/demo/multimesh/src/Refinement.cc
@@ -0,0 +1,184 @@
+#include <limits>
+#include "Refinement.h"
+
+using namespace std;
+using namespace AMDiS;
+
+
+Refinement::Refinement(DOFVector<double> *phasefield_,
+ AbstractFunction<double, WorldVector<double> > *phasefieldFct_,
+ RefinementManager *refinementManager_,
+ CoarseningManager *coarseningManager_)
+ : phasefield(phasefield_),
+ phasefieldFct(phasefieldFct_),
+ refinementManager(refinementManager_),
+ coarseningManager(coarseningManager_),
+ info_(0)
+{
+ feSpace = phasefield->getFeSpace();
+ mesh = feSpace->getMesh();
+}
+
+
+Refinement::~Refinement()
+{
+}
+
+
+void Refinement::refine(double h)
+{
+ FUNCNAME("Refinement::refine()");
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ MPI::COMM_WORLD.Barrier();
+ double first = MPI::Wtime();
+ double m0 = 0.0, m1 = 0.0;
+#endif
+ // build mesh for phasefield-function
+ bool meshChanged=true;
+ Flag markFlag;
+ double minH = 0.0, maxH = 1.0, oldMinH = 100.0, oldMaxH = 0.0;
+
+ int i = 0;
+ while (meshChanged || minH != oldMinH || maxH != oldMaxH) {
+ oldMinH = minH;
+ oldMaxH = maxH;
+
+ if (phasefieldFct != NULL)
+ phasefield->interpol(phasefieldFct);
+
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ double t0 = MPI::Wtime();
+ markElements(markFlag, h);
+ m0 += MPI::Wtime() - t0;
+
+ t0 = MPI::Wtime();
+ meshChanged = refineMesh(markFlag);
+ m1 += MPI::Wtime() - t0;
+
+#else
+ markElements(markFlag, h);
+ meshChanged = refineMesh(markFlag);
+#endif
+
+ calcMeshSizes(minH, maxH);
+
+ if (meshChanged || minH != oldMinH || maxH != oldMaxH) {
+ int nr = phasefield->getUsedSize();
+ MSG("%d Mesh sizes: [%f, %f], DOFs: %d, ELs: %d\n", i++,
+ minH, maxH, nr, mesh->getNumberOfLeaves());
+ }
+ }
+
+ if (phasefieldFct != NULL)
+ phasefield->interpol(phasefieldFct);
+
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ Parallel::mpi::globalMax(m0);
+ Parallel::mpi::globalMax(m1);
+
+ MPI::COMM_WORLD.Barrier();
+ MSG("Local mesh refinement (phase field) needed %.5f seconds [ %.5f %.5f ]\n", MPI::Wtime() - first, m0, m1);
+#endif
+}
+
+
+void Refinement::calcMeshSizes(double &minH, double &maxH)
+{
+ int dim = mesh->getDim();
+ FixVec<WorldVector<double>, VERTEX> coords(dim, NO_INIT);
+
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL | Mesh::FILL_COORDS);
+ minH=1e15; maxH=0.0;
+ while (elInfo) {
+ coords = elInfo->getCoords();
+ double h = 0.0;
+ for (int i = 0; i < coords.getSize(); i++)
+ for(int j = i + 1; j < coords.getSize(); j++)
+ if (i != j)
+ h = std::max(h, norm(coords[i] - coords[j]));
+ minH = std::min(h, minH);
+ maxH = std::max(h, maxH);
+ elInfo = stack.traverseNext(elInfo);
+ }
+}
+
+
+void Refinement::markElements(Flag &markFlag, double hInterface)
+{
+ DOFVector<double> *vec = phasefield;
+ const DOFAdmin* admin = feSpace->getAdmin();
+ const BasisFunction *basFcts = feSpace->getBasisFcts();
+
+ int dim = mesh->getDim();
+ int numBasFcts = basFcts->getNumber();
+
+ std::vector<DegreeOfFreedom> localIndices(numBasFcts);
+ FixVec<WorldVector<double>, VERTEX> coords(dim, NO_INIT);
+
+ bool elMarkRefine=false, elMarkCoarsen=false;
+
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(mesh, -1, Mesh::CALL_LEAF_EL | Mesh::FILL_COORDS);
+ while (elInfo) {
+ Element *el = elInfo->getElement();
+ basFcts->getLocalIndices(el, admin, localIndices);
+ // for every vertex
+ double smax = -1e12, smin = 1e12;
+ coords = elInfo->getCoords();
+ for (int i = 0; i < numBasFcts; i++) {
+ // search for coords of this vertex in the coord-list of this dof
+ smin = std::min(smin, (*vec)[localIndices[i]]);
+ smax = std::max(smax, (*vec)[localIndices[i]]);
+ }
+
+ if (smin < 0.1 && smax > -0.1) {
+ double h = 0.0;
+ for (int i = 0; i < coords.getSize(); i++)
+ for (int j = i + 1; j < coords.getSize(); j++)
+ h = std::max(h, norm(coords[i] - coords[j]));
+
+ if (h > hInterface) {
+ elMarkRefine = true;
+ elInfo->getElement()->setMark(1);
+ }
+ } else {
+ if (smax - smin > 0.2) {
+ elMarkRefine = true;
+ elInfo->getElement()->setMark(1);
+ }
+ if (smax -smin < 0.1) {
+ elMarkCoarsen = true;
+ elInfo->getElement()->setMark(-1);
+ }
+ }
+
+ elInfo = stack.traverseNext(elInfo);
+ }
+
+ markFlag = 0;
+ if (elMarkRefine)
+ markFlag = 1;
+ if (elMarkCoarsen)
+ markFlag |= 2;
+}
+
+
+bool Refinement::refineMesh(Flag markFlag)
+{
+ FUNCNAME("Refinement::refineMesh()");
+
+ int oldSize = phasefield->getUsedSize();
+ if (markFlag.isSet(1))
+ refinementManager->refineMesh(mesh);
+ if (markFlag.isSet(2))
+ coarseningManager->coarsenMesh(mesh);
+ if (markFlag.isSet(1) || markFlag.isSet(2)) {
+ int newSize = phasefield->getUsedSize();
+ if (oldSize != newSize)
+ return true;
+ INFO(info_,1)(">> InterfaceRefinement refined DOFs: %d\n",newSize);
+ }
+ return false;
+}
+
diff --git a/extensions/demo/multimesh/src/Refinement.h b/extensions/demo/multimesh/src/Refinement.h
new file mode 100644
index 00000000..8d0b6845
--- /dev/null
+++ b/extensions/demo/multimesh/src/Refinement.h
@@ -0,0 +1,39 @@
+/** \file Refinement.h */
+
+#ifndef REFINEMENT_PHASEFIELD_H
+#define REFINEMENT_PHASEFIELD_H
+
+#include "AMDiS.h"
+
+using namespace std;
+using namespace AMDiS;
+
+/* define instationary problem */
+class Refinement
+{
+public:
+ Refinement(DOFVector<double> *phasefield, AbstractFunction<double, WorldVector<double> > *phasefieldFct, RefinementManager *refinementManager, CoarseningManager *coarseningManager);
+ ~Refinement();
+
+ void refine(double h);
+
+ void calcMeshSizes(double &minH, double &maxH);
+ void markElements(Flag &markFlag, double hInterface);
+ bool refineMesh(Flag markFlag);
+
+protected:
+ inline double norm(const WorldVector<double> &x)
+ {
+ return sqrt(x * x);
+ }
+
+protected:
+ AbstractFunction<double, WorldVector<double> > *phasefieldFct;
+ DOFVector<double> *phasefield;
+ const FiniteElemSpace *feSpace;
+ Mesh *mesh;
+ RefinementManager *refinementManager;
+ CoarseningManager *coarseningManager;
+ int info_;
+};
+#endif // REFINEMENT_PHASEFIELD_H
diff --git a/extensions/demo/multimesh/src/cahnHilliard_navierStokes.cc b/extensions/demo/multimesh/src/cahnHilliard_navierStokes.cc
new file mode 100644
index 00000000..f36d323f
--- /dev/null
+++ b/extensions/demo/multimesh/src/cahnHilliard_navierStokes.cc
@@ -0,0 +1,187 @@
+/******************************************************************************
+ *
+ * Extension of AMDiS - Adaptive multidimensional simulations
+ *
+ * Copyright (C) 2013 Dresden University of Technology. All Rights Reserved.
+ * Web: https://fusionforge.zih.tu-dresden.de/projects/amdis
+ *
+ * Authors: Simon Praetorius et al.
+ *
+ * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+ * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ *
+ *
+ * See also license.opensource.txt in the distribution.
+ *
+ ******************************************************************************/
+
+#include "AMDiS.h"
+#if __cplusplus > 199711L
+ #include "CouplingBaseProblem2_cxx11.h"
+#else
+ #include "CouplingBaseProblem2.h"
+#endif
+#include "CahnHilliard.h"
+// #include "ProblemStatMassConserve2.h" // using COARSE_RESTRICT
+#include "ProblemStatMassConserve.h" // using multi mesh
+#include "NavierStokes_TaylorHood.h"
+#include "Refinement.h"
+#include "MeshFunction_Level.h"
+
+using namespace AMDiS;
+
+typedef base_problems::detail::CahnHilliard<ProblemStatMassConserve> CHType;
+typedef NavierStokes_TaylorHood NSType;
+
+class CahnHilliardNavierStokes : public CouplingBaseProblem< ProblemStat, CHType, NSType >
+{
+public: // typedefs
+
+ typedef CouplingBaseProblem< ProblemStat, CHType, NSType > super;
+
+public: // methods
+
+ /// Constructor
+ CahnHilliardNavierStokes(std::string name,
+ CHType &chProb_,
+ NSType &nsProb_)
+ : super(name, chProb_, nsProb_),
+ chProb(&chProb_),
+ nsProb(&nsProb_),
+ refFunction(NULL),
+ refinement(NULL),
+ minus1(-1.0)
+ { }
+
+ /// Destructor
+ ~CahnHilliardNavierStokes()
+ {
+ if (refFunction) { delete refFunction; refFunction = NULL; }
+ if (refinement) { delete refinement; refinement = NULL; }
+ }
+
+ /// Called before first adaption loop
+ virtual void initData()
+ {
+ refFunction = new PhaseFieldRefinement(chProb->getMesh());
+ refinement = new RefinementLevelDOF(chProb->getFeSpace(0),
+ refFunction,
+ chProb->getSolution()->getDOFVector(0));
+ }
+
+ /// Set initial condition and perform initial refinement
+ virtual void solveInitialProblem(AdaptInfo *adaptInfo)
+ {
+ // initial refinement
+ refinement->refine(0);
+
+ // refine until interfaces is resolved
+ for (int i = 0; i < 5; ++i) {
+ chProb->solveInitialProblem(adaptInfo);
+ refinement->refine(5);
+ }
+
+ super::solveInitialProblem(adaptInfo);
+
+ std::string prefix = "";
+ Parameters::get("prefix", prefix);
+
+ double c = chProb->getSolution()->getDOFVector(0)->Int();
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ if (MPI::COMM_WORLD.Get_rank() == 0)
+#endif
+ {
+ std::ofstream out(("concentration" + prefix + ".dat").c_str(), ios_base::out);
+ out.setf(std::ios::scientific, std::ios::floatfield );
+ out.precision(16);
+ out << c << "\n";
+ }
+ // activate mass-conservative coarsening
+ refinement->setRefineOperation(adaptInfo, chProb->getProblem());
+ }
+
+ /// Called at the end of each timestep.
+ virtual void closeTimestep(AdaptInfo *adaptInfo)
+ {
+ super::closeTimestep(adaptInfo);
+
+ std::string prefix = "";
+ Parameters::get("prefix", prefix);
+
+ double c = chProb->getSolution()->getDOFVector(0)->Int();
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ if (MPI::COMM_WORLD.Get_rank() == 0)
+#endif
+ {
+ std::ofstream out(("concentration" + prefix + ".dat").c_str(), ios_base::app);
+ out.setf(std::ios::scientific, std::ios::floatfield );
+ out.precision(16);
+ out << c << "\n";
+ }
+
+ refinement->refine(1);
+ // checkMeshChange
+ }
+
+ virtual void fillCouplingOperators()
+ {
+ double M0 = 1.0;
+ Parameters::get(name + "->M0",M0);
+
+ DOFVector<double>* c = chProb->getSolution()->getDOFVector(0);
+ DOFVector<double>* mu = chProb->getSolution()->getDOFVector(1);
+
+ // < grad(mu) * c , theta >
+ for (size_t i = 0; i < dow; i++) {
+ Operator *opCGradMu = new Operator(nsProb->getFeSpace(i),
+ chProb->getFeSpace(0));
+ addZOT(opCGradMu, M0 * valueOf(mu) * derivativeOf(c, i) );
+ nsProb->getProblem(0)->addVectorOperator(opCGradMu, i);
+ }
+
+ // < - u * c , grad(theta) >
+ for (size_t i = 0; i < dow; i++) {
+ Operator *opUGradC = new Operator(chProb->getFeSpace(1),
+ chProb->getFeSpace(0));
+ addFOT(opUGradC, -valueOf(nsProb->getSolution()->getDOFVector(i)), i, GRD_PSI );
+ chProb->getProblem()->addMatrixOperator(opUGradC, 1, 0);
+ }
+ }
+
+protected: // variables
+
+ CHType *chProb;
+ NSType *nsProb;
+ PhaseFieldRefinement* refFunction;
+ RefinementLevelDOF *refinement;
+
+ double minus1;
+ double concentration;
+};
+
+
+int main(int argc, char** argv)
+{ FUNCNAME("main");
+
+ AMDiS::init(argc, argv);
+ Timer t;
+
+ CHType chProb("ch");
+ NSType nsProb("ns");
+
+ CahnHilliardNavierStokes chns("chns", chProb, nsProb);
+ chns.initialize(INIT_ALL);
+ chns.initTimeInterface();
+
+ // Adapt-Infos
+ AdaptInfo adaptInfo("adapt", chns.getNumComponents());
+ AdaptInstationary adaptInstat("adapt", chns, adaptInfo, chns, adaptInfo);
+
+ int error_code = adaptInstat.adapt();
+
+ MSG("elapsed time= %d sec\n", t.elapsed());
+ AMDiS::finalize();
+
+ return error_code;
+}
+
diff --git a/extensions/demo/multimesh/src/cahnHilliard_navierStokes_mm.cc b/extensions/demo/multimesh/src/cahnHilliard_navierStokes_mm.cc
new file mode 100644
index 00000000..e9399e4e
--- /dev/null
+++ b/extensions/demo/multimesh/src/cahnHilliard_navierStokes_mm.cc
@@ -0,0 +1,186 @@
+/******************************************************************************
+ *
+ * Extension of AMDiS - Adaptive multidimensional simulations
+ *
+ * Copyright (C) 2013 Dresden University of Technology. All Rights Reserved.
+ * Web: https://fusionforge.zih.tu-dresden.de/projects/amdis
+ *
+ * Authors: Simon Praetorius et al.
+ *
+ * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
+ * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ *
+ *
+ * See also license.opensource.txt in the distribution.
+ *
+ ******************************************************************************/
+
+#include "AMDiS.h"
+#if __cplusplus > 199711L
+ #include "CouplingBaseProblem2_cxx11.h"
+#else
+ #include "CouplingBaseProblem2.h"
+#endif
+#include "CahnHilliard_mm.h"
+#include "ProblemStatMassConserve_mm.h" // using multi mesh
+#include "NavierStokes_TaylorHood.h"
+#include "Refinement.h"
+#include "MeshFunction_Level.h"
+
+using namespace AMDiS;
+
+typedef base_problems::CahnHilliard_mm CHType;
+typedef NavierStokes_TaylorHood NSType;
+
+class CahnHilliardNavierStokes : public CouplingBaseProblem< ProblemStat, CHType, NSType >
+{
+public: // typedefs
+
+ typedef CouplingBaseProblem< ProblemStat, CHType, NSType > super;
+
+public: // methods
+
+ /// Constructor
+ CahnHilliardNavierStokes(std::string name,
+ CHType &chProb_,
+ NSType &nsProb_)
+ : super(name, chProb_, nsProb_),
+ chProb(&chProb_),
+ nsProb(&nsProb_),
+ refFunction(NULL),
+ refinement(NULL),
+ minus1(-1.0)
+ { }
+
+ /// Destructor
+ ~CahnHilliardNavierStokes()
+ {
+ if (refFunction) { delete refFunction; refFunction = NULL; }
+ if (refinement) { delete refinement; refinement = NULL; }
+ }
+
+ /// Called before first adaption loop
+ virtual void initData()
+ {
+ refFunction = new PhaseFieldRefinement(chProb->getMesh());
+ refinement = new RefinementLevelDOF(chProb->getFeSpace(0),
+ refFunction,
+ chProb->getSolution()->getDOFVector(0));
+ }
+
+ /// Set initial condition and perform initial refinement
+ virtual void solveInitialProblem(AdaptInfo *adaptInfo)
+ {
+ // initial refinement
+ refinement->refine(0);
+
+ // refine until interfaces is resolved
+ for (int i = 0; i < 5; ++i) {
+ chProb->solveInitialProblem(adaptInfo);
+ refinement->refine(5);
+ }
+
+ super::solveInitialProblem(adaptInfo);
+
+ std::string prefix = "";
+ Parameters::get("prefix", prefix);
+
+ double c = chProb->getSolution()->getDOFVector(0)->Int();
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ if (MPI::COMM_WORLD.Get_rank() == 0)
+#endif
+ {
+ std::ofstream out(("concentration" + prefix + ".dat").c_str(), ios_base::out);
+ out.setf(std::ios::scientific, std::ios::floatfield );
+ out.precision(16);
+ out << c << "\n";
+ }
+ // activate mass-conservative coarsening
+ refinement->setRefineOperation(adaptInfo, chProb->getProblem());
+ }
+
+ /// Called at the end of each timestep.
+ virtual void closeTimestep(AdaptInfo *adaptInfo)
+ {
+ super::closeTimestep(adaptInfo);
+
+ std::string prefix = "";
+ Parameters::get("prefix", prefix);
+
+ double c = chProb->getSolution()->getDOFVector(0)->Int();
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ if (MPI::COMM_WORLD.Get_rank() == 0)
+#endif
+ {
+ std::ofstream out(("concentration" + prefix + ".dat").c_str(), ios_base::app);
+ out.setf(std::ios::scientific, std::ios::floatfield );
+ out.precision(16);
+ out << c << "\n";
+ }
+
+ refinement->refine(1);
+ // checkMeshChange
+ }
+
+ virtual void fillCouplingOperators()
+ {
+ double M0 = 1.0;
+ Parameters::get(name + "->M0",M0);
+
+ DOFVector<double>* c = chProb->getSolution()->getDOFVector(0);
+ DOFVector<double>* mu = chProb->getSolution()->getDOFVector(1);
+
+ // < grad(mu) * c , theta >
+ for (size_t i = 0; i < dow; i++) {
+ Operator *opCGradMu = new Operator(nsProb->getFeSpace(i),
+ chProb->getFeSpace(0));
+ addZOT(opCGradMu, M0 * valueOf(mu) * derivativeOf(c, i) );
+ nsProb->getProblem(0)->addVectorOperator(opCGradMu, i);
+ }
+
+ // < - u * c , grad(theta) >
+ for (size_t i = 0; i < dow; i++) {
+ Operator *opUGradC = new Operator(chProb->getFeSpace(1),
+ chProb->getFeSpace(0));
+ addFOT(opUGradC, -valueOf(nsProb->getSolution()->getDOFVector(i)), i, GRD_PSI );
+ chProb->getProblem()->addMatrixOperator(opUGradC, 1, 0);
+ }
+ }
+
+protected: // variables
+
+ CHType *chProb;
+ NSType *nsProb;
+ PhaseFieldRefinement* refFunction;
+ RefinementLevelDOF *refinement;
+
+ double minus1;
+ double concentration;
+};
+
+
+int main(int argc, char** argv)
+{ FUNCNAME("main");
+
+ AMDiS::init(argc, argv);
+ Timer t;
+
+ CHType chProb("ch");
+ NSType nsProb("ns");
+
+ CahnHilliardNavierStokes chns("chns", chProb, nsProb);
+ chns.initialize(INIT_ALL);
+ chns.initTimeInterface();
+
+ // Adapt-Infos
+ AdaptInfo adaptInfo("adapt", chns.getNumComponents());
+ AdaptInstationary adaptInstat("adapt", chns, adaptInfo, chns, adaptInfo);
+
+ int error_code = adaptInstat.adapt();
+
+ MSG("elapsed time= %d sec\n", t.elapsed());
+ AMDiS::finalize();
+
+ return error_code;
+}
+
diff --git a/extensions/demo/multimesh/src/dendrites.cc b/extensions/demo/multimesh/src/dendrites.cc
new file mode 100644
index 00000000..fe753b94
--- /dev/null
+++ b/extensions/demo/multimesh/src/dendrites.cc
@@ -0,0 +1,234 @@
+#include "AMDiS.h"
+#include "MyProblemInstat.h"
+#include "Anisotropy.h"
+
+using namespace AMDiS;
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+using namespace AMDiS::Parallel;
+#endif
+using namespace AMDiS::io;
+
+class DoublewellExpl : public AbstractFunction<double, double>
+{
+public:
+ DoublewellExpl()
+ : AbstractFunction<double, double>(3)
+ {}
+
+ double operator()(const double& u) const
+ {
+ return 2.0 * u * u * u;
+ }
+};
+
+class DoublewellImpl : public AbstractFunction<double, double>
+{
+public:
+ DoublewellImpl()
+ : AbstractFunction<double, double>(2)
+ {}
+
+ double operator()(const double& u) const
+ {
+ return 3.0 * u * u - 1.0;
+ }
+};
+
+class Karma : public AbstractFunction<double, double>
+{
+public:
+ Karma()
+ : AbstractFunction<double, double>(4)
+ {}
+
+ double operator()(const double& u) const
+ {
+ return pow((1.0 - u * u), 2.0);
+ }
+};
+
+using namespace std;
+typedef vector<vector<double> > DataVec;
+
+void scalMesh(Mesh *mesh, double scalFactorX, double scalFactorY, double scalFactorZ)
+{
+ for (std::deque<MacroElement*>::iterator it = mesh->firstMacroElement();
+ it != mesh->endOfMacroElements(); ++it) {
+ for (int i = 0; i < mesh->getGeo(VERTEX); i++) {
+ WorldVector<double> &x = (*it)->getCoord(i);
+
+ if (scalFactorX != 0.0)
+ x[0] *= scalFactorX;
+
+ if (scalFactorY != 0.0)
+ x[1] *= scalFactorY;
+
+ if (scalFactorZ != 0.0)
+ x[2] *= scalFactorZ;
+ }
+ }
+}
+
+
+int main(int argc, char** argv)
+{
+ FUNCNAME("main");
+
+ Timer t;
+
+ AMDiS::init(argc, argv);
+
+ ProblemStat dendSpace("dendrites->space");
+ dendSpace.initialize(INIT_ALL);
+
+ MyProblemInstat probInstat("dendrites", dendSpace);
+ probInstat.initialize(INIT_ALL);
+
+ // create adapt info
+ AdaptInfo adaptInfo("dendrites->adapt", dendSpace.getNumComponents());
+
+ // create initial adapt info
+ AdaptInfo adaptInfoInitial("dendrites->initial->adapt", dendSpace.getNumComponents());
+
+ // create instationary adapt
+ AdaptInstationary adaptInstat("dendrites->adapt",
+ dendSpace,
+ adaptInfo,
+ probInstat,
+ adaptInfoInitial);
+
+ // === Scal mesh ===
+
+ double scalFactorX = 0.0;
+ Parameters::get("dendritesMesh->scal x", scalFactorX);
+
+ double scalFactorY = 0.0;
+ Parameters::get("dendritesMesh->scal y", scalFactorY);
+
+ double scalFactorZ = 0.0;
+ Parameters::get("dendritesMesh->scal z", scalFactorZ);
+
+ if (!dendSpace.isDeserialized()) {
+ if (scalFactorX != 0.0 || scalFactorY != 0.0 || scalFactorZ != 0.0) {
+ scalMesh(dendSpace.getMesh(0), scalFactorX, scalFactorY, scalFactorZ);
+
+ if (dendSpace.getMesh(0) != dendSpace.getMesh(1))
+ scalMesh(dendSpace.getMesh(1), scalFactorX, scalFactorY, scalFactorZ);
+
+ if (scalFactorZ == 0.0)
+ MSG("Mesh scaled with %f x %f\n", scalFactorX, scalFactorY);
+ else
+ MSG("Mesh scaled with %f x %f x %f\n", scalFactorX, scalFactorY, scalFactorZ);
+ }
+ }
+
+
+
+ double thermalDif = 0.0;
+ Parameters::get("dendrites->karma model->D", thermalDif);
+
+ double a2 = 0.6267;
+ double lambda = thermalDif / a2;
+
+ double gamma = 0.0;
+ Parameters::get("dendrites->karma model->gamma", gamma);
+
+ double rhoInitial = 0.0;
+ Parameters::get("dendrites->karma model->rho initial", rhoInitial);
+
+ MSG("Karma model parameters:\n");
+ MSG(" D = %f\n", thermalDif);
+ MSG(" gamma = %f\n", gamma);
+ MSG(" Delta = %f\n", rhoInitial);
+ MSG("\n");
+
+ DOFVector<double> *oldPhi = probInstat.getOldSolution()->getDOFVector(0);
+
+ AbstractFunction<double, WorldVector<double> > *anisoSquare;
+ AbstractFunction<WorldMatrix<double>, WorldVector<double> > *anisoLaplace;
+
+ switch (dendSpace.getMesh(0)->getDim()) {
+ case 2:
+ anisoSquare = new Aniso2d_Square(gamma);
+ anisoLaplace = new Aniso2d_Laplace(gamma);
+ break;
+ case 3:
+ anisoSquare = new Aniso3d_Square(gamma);
+ anisoLaplace = new Aniso3d_Laplace(gamma);
+ break;
+ default:
+ ERROR_EXIT("This should not happen!\n");
+ }
+
+ NullFct nullFct;
+
+ ///
+
+ Operator opPhiTau(dendSpace.getFeSpace(0), dendSpace.getFeSpace(0));
+ opPhiTau.addZeroOrderTerm(new FctGradient_ZOT(oldPhi, anisoSquare));
+ opPhiTau.setUhOld(probInstat.getOldSolution()->getDOFVector(0));
+ dendSpace.addMatrixOperator(opPhiTau, 0, 0, probInstat.getInvTau(), probInstat.getInvTau());
+ dendSpace.addVectorOperator(opPhiTau, 0, probInstat.getInvTau(), probInstat.getInvTau());
+
+ Operator opDoublewellImpl(dendSpace.getFeSpace(0), dendSpace.getFeSpace(0));
+ opDoublewellImpl.addZeroOrderTerm(new VecAtQP_ZOT(oldPhi, new DoublewellImpl));
+ dendSpace.addMatrixOperator(opDoublewellImpl, 0, 0);
+
+ Operator opDoublewellExpl(dendSpace.getFeSpace(0));
+ opDoublewellExpl.addZeroOrderTerm(new VecAtQP_ZOT(oldPhi, new DoublewellExpl));
+ dendSpace.addVectorOperator(opDoublewellExpl, 0);
+
+ Operator opKarmaFct(dendSpace.getFeSpace(0), dendSpace.getFeSpace(1));
+ opKarmaFct.addZeroOrderTerm(new VecAtQP_ZOT(oldPhi, new Karma));
+ dendSpace.addMatrixOperator(opKarmaFct, 0, 1, &lambda, &lambda);
+
+ Operator opAnisoLaplace(dendSpace.getFeSpace(0), dendSpace.getFeSpace(0));
+ opAnisoLaplace.addSecondOrderTerm(new MatrixGradient_SOT(oldPhi, anisoLaplace, &nullFct));
+ dendSpace.addMatrixOperator(opAnisoLaplace, 0, 0);
+
+
+ ///
+
+ Operator opLaplace(dendSpace.getFeSpace(1), dendSpace.getFeSpace(1));
+ opLaplace.addSecondOrderTerm(new Simple_SOT(&thermalDif));
+ dendSpace.addMatrixOperator(opLaplace, 1, 1);
+
+ Operator opUTau(dendSpace.getFeSpace(1), dendSpace.getFeSpace(1));
+ opUTau.addZeroOrderTerm(new Simple_ZOT);
+ opUTau.setUhOld(probInstat.getOldSolution()->getDOFVector(1));
+ dendSpace.addMatrixOperator(opUTau, 1, 1, probInstat.getInvTau(), probInstat.getInvTau());
+ dendSpace.addVectorOperator(opUTau, 1, probInstat.getInvTau(), probInstat.getInvTau());
+
+
+ Operator opPhiUTau(dendSpace.getFeSpace(1), dendSpace.getFeSpace(0));
+ opPhiUTau.addZeroOrderTerm(new Simple_ZOT(-0.5));
+ opPhiUTau.setUhOld(probInstat.getOldSolution()->getDOFVector(0));
+ dendSpace.addMatrixOperator(opPhiUTau, 1, 0, probInstat.getInvTau(), probInstat.getInvTau());
+ dendSpace.addVectorOperator(opPhiUTau, 1, probInstat.getInvTau(), probInstat.getInvTau());
+
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ MeshDistributor::globalMeshDistributor->addInterchangeVector(probInstat.getOldSolution());
+ MeshDistributor::globalMeshDistributor->addInterchangeVector(dendSpace.getSolution());
+#endif
+
+ // ===== start adaption loop =====
+ int errorCode = adaptInstat.adapt();
+
+
+ printf("whole process needs %.5f seconds\n", t.elapsed());
+
+
+ bool isWrite = false; string phiname, rhoname;
+ Parameters::get("dendrites->write arh file", isWrite);
+ Parameters::get("dendrites->write phi arh", phiname);
+ Parameters::get("dendrites->write rho arh", rhoname);
+
+ if (isWrite) {
+ io::Arh2Writer::writeFile(dendSpace.getSolution(0), phiname.c_str());
+ io::Arh2Writer::writeFile(dendSpace.getSolution(1), rhoname.c_str());
+ }
+
+ AMDiS::finalize();
+
+ return errorCode;
+}
diff --git a/extensions/demo/multimesh/src/diffuseDomain.cc b/extensions/demo/multimesh/src/diffuseDomain.cc
new file mode 100644
index 00000000..ba67e18f
--- /dev/null
+++ b/extensions/demo/multimesh/src/diffuseDomain.cc
@@ -0,0 +1,340 @@
+#include "AMDiS.h"
+#include <fstream>
+#include "Refinement.h"
+#include "Refinement_Level.h"
+#include "SignedDistFunctors.h"
+#include "Helpers.h"
+#include "PhaseFieldConvert.h"
+#include "GenericOperatorTerm.h"
+#include "ExtendedProblemStat.h"
+
+
+#define USE_UH_OLD 1
+
+
+using namespace AMDiS;
+
+
+class MySignedDistRefinement : public SignedDistRefinement
+{
+public:
+ MySignedDistRefinement(Mesh* mesh_) : SignedDistRefinement(mesh_)
+ {
+ Parameters::get("mesh2->refinement->level in inner domain",lInner);
+ Parameters::get("mesh2->refinement->level in outer domain",lOuter);
+ Parameters::get("mesh2->refinement->level on interface",lInterface);
+
+ lInterface-= mesh->getMacroElementLevel();
+ lInner-= mesh->getMacroElementLevel();
+ lOuter-= mesh->getMacroElementLevel();
+
+ int local_globalSize = 10;
+ Parameters::get("mesh2->refinement->initial level", local_globalSize);
+ globalSize = local_globalSize;
+
+ Parameters::get("mesh2->refinement->interface width",interfaceWidth);
+ Parameters::get("mesh2->refinement->fade out width",fadeOutWidth);
+ Parameters::get("mesh2->refinement->sign in inner domain",signInInnerDomain);
+ };
+};
+
+
+/// Dirichlet boundary function
+class G : public AbstractFunction<double, WorldVector<double> >,
+ public TimedObject
+{
+public:
+ /// Implementation of AbstractFunction::operator().
+
+ double operator()(const WorldVector<double>& x) const
+ {
+ return 1.0;
+ }
+};
+
+
+
+/// RHS function
+class F : public AbstractFunction<double, WorldVector<double> >,
+ public TimedObject
+{
+public:
+ F(int degree) : AbstractFunction<double, WorldVector<double> >(degree) {}
+
+ /// Implementation of AbstractFunction::operator().
+ double operator()(const WorldVector<double>& x) const
+ {
+ return 1.0;
+ }
+};
+
+struct DDProblemInstat : ProblemInstat
+{
+ DDProblemInstat(std::string name, ProblemStat& prob)
+ : ProblemInstat(name, prob),
+ radius(1.0),
+ epsilon(0.1),
+ maxLevel(15),
+ temperRefment(NULL),
+ temperRefFct(NULL),
+ c(radius, center),
+ ic(radius, center)
+ {
+ Parameters::get("radius", radius);
+ Parameters::get("epsilon", epsilon);
+ center.set(0.0);
+ Parameters::get("center", center);
+ Parameters::get("mesh->max refinement level", maxLevel);
+ }
+
+ ~DDProblemInstat()
+ {
+ if (phase)
+ delete phase;
+ phase = NULL;
+
+ if (phaseRefFct)
+ delete phaseRefFct;
+ phaseRefFct = NULL;
+
+ if (phaseRefment)
+ delete phaseRefment;
+ phaseRefment = NULL;
+
+ if (temperRefFct)
+ delete temperRefFct;
+ temperRefFct = NULL;
+
+ if (temperRefment)
+ delete temperRefment;
+ temperRefment = NULL;
+ }
+
+ void initialize(Flag initFlag,
+ ProblemInstat *adoptProblem = NULL,
+ Flag adoptFlag = INIT_NOTHING) override
+ {
+ problemStat->initialize(initFlag);
+
+ ProblemInstat::initialize(INIT_NOTHING);
+
+ phase = new DOFVector<double>(problemStat->getFeSpace(1), "phase2");
+ phaseRefFct = new SignedDistRefinement(problemStat->getMesh(1));
+ phaseRefment = new RefinementLevelCoords2(problemStat->getFeSpace(1),
+ phaseRefFct, &c);
+
+ if (problemStat->getMeshes().size() == 2) {
+ temperRefFct = new MySignedDistRefinement(problemStat->getMesh(0));
+ temperRefment = new RefinementLevelCoords2(problemStat->getFeSpace(0),
+ temperRefFct, &c);
+ }
+ }
+
+
+
+ void solveInitialProblem(AdaptInfo *adaptInfo) override
+ {
+ FUNCNAME("DDProblemInstat::solveInitialProblem");
+ Timer t;
+
+ SignedDistFctToPhaseField* p =
+ new SignedDistFctToPhaseField(epsilon, &ic, 3.0);
+
+ phaseRefment->refine(maxLevel);
+ phase->interpol(p);
+// phase->interpol(new One());
+ *phase << valueOf(phase) + 1.e-5;
+
+
+ if (problemStat->getMeshes().size() == 2) {
+ temperRefment->refine(maxLevel, false, true); // when not use marker and estimator
+
+// int refLevel = 0;
+// Parameters::get("mesh->refinement->global heat refine", refLevel);
+// MSG("refLevel is %d\n", refLevel);
+// problemStat->getRefinementManager()->globalRefine(problemStat->getMesh(0), refLevel);
+ }
+
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ MPI::COMM_WORLD.Barrier();
+#endif
+ MSG("mesh refinement and interpolation need %.5f seconds\n", t.elapsed());
+
+ delete p;
+ }
+
+
+ DOFVector<double>* getPhase() { return phase; }
+
+ double getEpsilon() { return epsilon; }
+
+
+protected:
+
+ double radius;
+ double epsilon;
+ int maxLevel;
+
+ WorldVector<double> center;
+
+ SignedDistRefinement* phaseRefFct;
+ SignedDistRefinement* temperRefFct;
+
+ RefinementLevelCoords2* phaseRefment;
+ RefinementLevelCoords2* temperRefment;
+
+ Circle c;
+ InverseCircle ic;
+
+ DOFVector<double>* phase;
+
+};
+
+
+
+// ===========================================================================
+
+// ===== main program ========================================================
+
+// ===========================================================================
+
+
+int main(int argc, char* argv[])
+{
+ FUNCNAME("main");
+
+ AMDiS::init(argc, argv);
+
+ // ===== create and init the scalar problem =====
+
+ ProblemStat heatSpace("heat");
+
+ DDProblemInstat instat("heat", heatSpace);
+
+ instat.initialize(INIT_ALL);
+
+ // === create adapt info ===
+
+ AdaptInfo adaptInfo("adapt", heatSpace.getNumComponents());
+
+ // create instationary adapt
+
+ AdaptInstationary adaptInstat("adapt",heatSpace,adaptInfo,instat,adaptInfo);
+
+
+ // scale the mesh to a given size
+
+ bool scaleMesh = false;
+
+ Initfile::get("mesh->scale mesh",scaleMesh);
+
+ if (scaleMesh) {
+ WorldVector<double> scale; scale.set(1.0);
+ Initfile::get("mesh->dimension",scale);
+ for (int i = 0; i < heatSpace.getMeshes().size(); i++)
+ Helpers::scaleMesh(heatSpace.getMesh(i), scale);
+ }
+
+ bool operatorOpt = true;
+ Initfile::get("optimized operator", operatorOpt);
+
+
+ // ===== create rhs functions =====
+
+
+ int degree = heatSpace.getFeSpace()->getBasisFcts()->getDegree();
+ F *rhsFct = new F(degree);
+ rhsFct->setTimePtr(adaptInfo.getTimePtr());
+
+
+ // ===== create operators =====
+
+
+ // create laplace
+ Operator A(heatSpace.getFeSpace());
+ addSOT(A, valueOf(instat.getPhase()));
+ heatSpace.addMatrixOperator(A, 0, 0);
+
+
+ // create zero order operator
+ Operator C(heatSpace.getFeSpace());
+ addZOT(C, valueOf(instat.getPhase()));
+ heatSpace.addMatrixOperator(C, 0, 0, instat.getInvTau(), instat.getInvTau());
+
+
+#if USE_UH_OLD
+
+ Operator C2(heatSpace.getFeSpace());
+ C2.setUhOld(heatSpace.getSolution(0));
+ addZOT(C2, valueOf(instat.getPhase()));
+ heatSpace.addVectorOperator(C2, 0, instat.getInvTau(), instat.getInvTau());
+
+#else
+
+ Operator C2(heatSpace.getFeSpace());
+ addZOT(C2, valueOf(heatSpace.getSolution(0)) * valueOf(instat.getPhase()));
+ heatSpace.addVectorOperator(C2, 0, instat.getInvTau(), instat.getInvTau());
+
+#endif
+
+ Operator DBC(heatSpace.getFeSpace());
+ addZOT(DBC, (36.0 / instat.getEpsilon()) * (1.0 - valueOf(instat.getPhase())));
+ heatSpace.addMatrixOperator(DBC, 0, 0);
+
+
+ // create RHS operator
+ Operator F(heatSpace.getFeSpace());
+ addZOT(F, valueOf(instat.getPhase()) * eval(rhsFct));
+ heatSpace.addVectorOperator(F, 0);
+
+ if (A.getNeedDualTraverse())
+ MSG("A need dual traversal.\n");
+ if (C.getNeedDualTraverse())
+ MSG("C need dual traversal.\n");
+ if (C2.getNeedDualTraverse())
+ MSG("C2 need dual traversal.\n");
+ if (DBC.getNeedDualTraverse())
+ MSG("DBC need dual traversal.\n");
+ if (F.getNeedDualTraverse())
+ MSG("F need dual traversal.\n");
+
+
+ if (!operatorOpt) {
+ A.useOptimizedAssembler(false);
+ C.useOptimizedAssembler(false);
+ C2.useOptimizedAssembler(false);
+ DBC.useOptimizedAssembler(false);
+ F.useOptimizedAssembler(false);
+ }
+
+
+
+ // ===== create boundary functions =====
+
+ G *boundaryFct = new G;
+// boundaryFct->setTimePtr(instat.getTime());
+
+ heatSpace.addDirichletBC(1, 0, 0, boundaryFct);
+
+ heatSpace.addDirichletBC(3, 0, 0, boundaryFct);
+
+
+#ifdef HAVE_PARALLEL_DOMAIN_AMDIS
+ MPI::COMM_WORLD.Barrier();
+#endif
+
+ Timer t;
+ // ===== start adaption loop =====
+
+ adaptInstat.adapt();
+
+ printf("whole process needs %.5f seconds\n", t.elapsed());
+
+ delete rhsFct;rhsFct=NULL;
+ delete boundaryFct;boundaryFct=NULL;
+
+ AMDiS::finalize();
+}
+
+
+
diff --git a/extensions/demo/other/init/cahnHilliard_navierStokes.dat.2d b/extensions/demo/other/init/cahnHilliard_navierStokes.dat.2d
index 6f428c97..b80b775a 100644
--- a/extensions/demo/other/init/cahnHilliard_navierStokes.dat.2d
+++ b/extensions/demo/other/init/cahnHilliard_navierStokes.dat.2d
@@ -58,8 +58,8 @@ adapt->end time: 100.0
% ============= PROBLEM-SPACES - CH =============================
ch->space->components: 2
-ch->space->polynomial degree[0]: 3
-ch->space->polynomial degree[1]: 3
+ch->space->polynomial degree[0]: 1
+ch->space->polynomial degree[1]: 1
ch->space->dim: 2
ch->space->mesh: mesh
@@ -80,7 +80,7 @@ chns->mesh: mesh
% ================== SOLVER - CH ================================
ch->space->solver: direct
-ch->space->solver->backend: mtl
+%ch->space->solver->backend: mtl
ch->space->solver->petsc prefix: ch
ch->space->solver->symmetric strategy: 0
ch->space->solver->store symbolic: 0
@@ -89,7 +89,7 @@ ch->space->solver->info: 1
% ================== SOLVER - NS ================================
ns->space->solver: direct
-ns->space->solver->backend: mtl
+%ns->space->solver->backend: mtl
ns->space->solver->petsc prefix: ns
ns->space->solver->symmetric strategy: 0
ns->space->solver->store symbolic: 0
--
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