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Commit 9c44b131 authored by Praetorius, Simon's avatar Praetorius, Simon
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merge of branches/expr to trunk

parent a091668f
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AMDiS/AMDISConfig.cmake.in
View file @ 9c44b131
......@@ -59,12 +59,12 @@ unset(_AMDIS_LIB CACHE)
# Boost libraries
# ---------------
set(AMDIS_HAS_PARALLEL_DOMAIN @ENABLE_PARALLEL_DOMAIN@)
set(AMDIS_NEED_COMPRESSION @ENABLE_COMPRESSIN@)
set(AMDIS_NEED_COMPRESSION @ENABLE_COMPRESSION@)
set(BOOST_LIBS_REQUIRED system iostreams filesystem program_options date_time)
if(AMDIS_NEED_COMPRESSION)
if(WIN32 AND AMDIS_NEED_COMPRESSION)
list(APPEND BOOST_LIBS_REQUIRED zlib bzip2)
endif(AMDIS_NEED_COMPRESSION)
endif(WIN32 AND AMDIS_NEED_COMPRESSION)
set(BOOST_VERSION "1.42")
if(AMDIS_HAS_PARALLEL_DOMAIN)
......
AMDiS/CMakeLists.txt
View file @ 9c44b131
......@@ -56,6 +56,8 @@ option(ENABLE_OUTPUT "AMDiS output printing, disable only for debugging!" true)
mark_as_advanced(ENABLE_OUTPUT)
mark_as_advanced(ENABLE_BDDCML)
mark_as_advanced(USE_PETSC_DEV)
find_package(Boost 1.44 REQUIRED)
......@@ -81,6 +83,7 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
${SOURCE_DIR}/Boundary.cc
${SOURCE_DIR}/BoundaryManager.cc
${SOURCE_DIR}/BoundaryObject.cc
${SOURCE_DIR}/Bubble.cc
${SOURCE_DIR}/Cholesky.cc
${SOURCE_DIR}/CoarseningManager.cc
${SOURCE_DIR}/CoarseningManager1d.cc
......@@ -125,7 +128,7 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
${SOURCE_DIR}/OperatorTerm.cc
${SOURCE_DIR}/Parametric.cc
${SOURCE_DIR}/PeriodicBC.cc
${SOURCE_DIR}/ProblemImplicit.cc
#${SOURCE_DIR}/ProblemImplicit.cc
${SOURCE_DIR}/ProblemInstat.cc
${SOURCE_DIR}/ProblemInterpol.cc
${SOURCE_DIR}/ProblemStat.cc
......@@ -342,7 +345,7 @@ endif(ENABLE_UMFPACK)
if(ENABLE_HYPRE)
include(FindHYPRE.cmake)
include(HYPREConfig.cmake)
message("have hypre: ${HAVE_HYPRE}")
if (HAVE_HYPRE)
if (NOT MPI_FOUND)
......@@ -437,13 +440,15 @@ if(ENABLE_EXTENSIONS)
if(ENABLE_SEQ_PETSC)
list(APPEND EXTENSIONS_SRC
${EXTENSIONS_DIR}/preconditioner/PetscPreconPfc.cc
${EXTENSIONS_DIR}/preconditioner/PetscPreconPfcDiag.cc
${EXTENSIONS_DIR}/preconditioner/PetscPreconCahnHilliard.cc)
endif(ENABLE_SEQ_PETSC)
if(ENABLE_PARALLEL_DOMAIN)
list(APPEND EXTENSIONS_SRC
# ${EXTENSIONS_DIR}/preconditioner/PetscSolverNavierStokes2.cc
${EXTENSIONS_DIR}/preconditioner/PetscSolverPfc.cc)
${EXTENSIONS_DIR}/preconditioner/PetscSolverPfc.cc
${EXTENSIONS_DIR}/preconditioner/PetscSolverPfc_diag.cc)
endif(ENABLE_PARALLEL_DOMAIN)
list(APPEND COMPILEFLAGS "-DHAVE_EXTENSIONS=1")
......@@ -502,7 +507,7 @@ if(ENABLE_EXTENSIONS)
if(ENABLE_BASE_PROBLEMS)
SET(BASE_PROBLEMS_SRC
# ${EXTENSIONS_DIR}/base_problems/CahnHilliard.cc
${EXTENSIONS_DIR}/base_problems/CahnHilliard.cc
${EXTENSIONS_DIR}/base_problems/CahnHilliard_RB.cc
${EXTENSIONS_DIR}/base_problems/CahnHilliardNavierStokes.cc
# ${EXTENSIONS_DIR}/base_problems/DiffuseDomainFsi.cc
......@@ -511,13 +516,15 @@ if(ENABLE_EXTENSIONS)
# ${EXTENSIONS_DIR}/base_problems/NavierStokes_Chorin.cc
${EXTENSIONS_DIR}/base_problems/NavierStokesCahnHilliard.cc
${EXTENSIONS_DIR}/base_problems/NavierStokesPhase_TaylorHood.cc
# ${EXTENSIONS_DIR}/base_problems/NavierStokes_TaylorHood.cc
${EXTENSIONS_DIR}/base_problems/NavierStokes_TaylorHood.cc
${EXTENSIONS_DIR}/base_problems/NavierStokes_TaylorHood_RB.cc
# ${EXTENSIONS_DIR}/base_problems/NavierStokes_TH_MultiPhase.cc
${EXTENSIONS_DIR}/base_problems/NavierStokes_TH_MultiPhase.cc
${EXTENSIONS_DIR}/base_problems/NavierStokes_TH_MultiPhase_RB.cc
${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal.cc
${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_Phase.cc
${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_RB.cc)
${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_RB.cc
${EXTENSIONS_DIR}/base_problems/PolarizationField.cc
${EXTENSIONS_DIR}/base_problems/QuasiCrystal.cc)
list(APPEND COMPILEFLAGS "-DHAVE_BASE_PROBLEMS=1")
list(APPEND AMDIS_INCLUDE_DIRS ${EXTENSIONS_DIR}/base_problems)
if(WIN32)
......@@ -647,11 +654,21 @@ INSTALL(FILES ${HEADERS}
DESTINATION include/amdis/est/)
list(APPEND deb_add_dirs "include/amdis/est")
FILE(GLOB HEADERS "${SOURCE_DIR}/expressions/*.h")
FILE(GLOB HEADERS "${SOURCE_DIR}/expressions/*.h*")
INSTALL(FILES ${HEADERS}
DESTINATION include/amdis/expressions/)
list(APPEND deb_add_dirs "include/amdis/expressions")
FILE(GLOB HEADERS "${SOURCE_DIR}/operations/*.h*")
INSTALL(FILES ${HEADERS}
DESTINATION include/amdis/operations/)
list(APPEND deb_add_dirs "include/amdis/operations")
FILE(GLOB HEADERS "${SOURCE_DIR}/traits/*.h*")
INSTALL(FILES ${HEADERS}
DESTINATION include/amdis/traits/)
list(APPEND deb_add_dirs "include/amdis/traits")
FILE(GLOB HEADERS "${SOURCE_DIR}/time/*.h")
INSTALL(FILES ${HEADERS}
DESTINATION include/amdis/time/)
......
AMDiS/src/AMDiS.h
View file @ 9c44b131
......@@ -37,6 +37,7 @@
#include "Boundary.h"
#include "BoundaryCondition.h"
#include "BoundaryManager.h"
#include "Bubble.h"
#include "CoarseningManager.h"
#include "CoarseningManager1d.h"
#include "CoarseningManager2d.h"
......@@ -73,7 +74,7 @@
#include "Line.h"
#include "MacroElement.h"
#include "Marker.h"
#include "MathFunctions.h"
// #include "MathFunctions.h"
#include "MatrixVector.h"
#include "Mesh.h"
#include "MeshStructure.h"
......@@ -85,7 +86,7 @@
#include "ProblemStat.h"
#include "ProblemInstat.h"
#include "ProblemTimeInterface.h"
#include "ProblemImplicit.h"
// #include "ProblemImplicit.h"
#include "ProblemInterpol.h"
#include "ProblemStatBase.h"
#include "SecondOrderTerm.h"
......@@ -106,6 +107,7 @@
#include "TimedObject.h"
#include "TransformDOF.h"
#include "Traverse.h"
#include "Traits.h"
#include "Triangle.h"
#include "VertexVector.h"
#include "ZeroOrderTerm.h"
......@@ -153,7 +155,7 @@
#include "parallel/ParallelProblemStat.h"
#if HAVE_PARALLEL_MTL4
#include "parallel/PMTL4Solver.h"
// #include "parallel/PMTL4Solver.h"
#else
#include "parallel/PetscSolver.h"
#include "parallel/PetscSolverNavierStokes.h"
......
AMDiS/src/AMDiS_fwd.h
View file @ 9c44b131
......@@ -104,7 +104,7 @@ namespace AMDiS {
class ElementFileWriter;
class GNUPlotWriter;
class MacroReader;
class MacroWriter;
struct MacroWriter;
class PngWriter;
class PovrayWriter;
class Spreadsheet;
......
AMDiS/src/AdaptInfo.h
View file @ 9c44b131
......@@ -57,6 +57,7 @@ namespace AMDiS {
fac_sum(1.0),
spaceTolerance(0.0),
timeTolerance(0.0),
timeRelativeTolerance(0.0),
timeErrLow(0.0),
coarsenAllowed(0),
refinementAllowed(1),
......@@ -65,6 +66,7 @@ namespace AMDiS {
{
Parameters::get(prefix + "->tolerance", spaceTolerance);
Parameters::get(prefix + "->time tolerance", timeTolerance);
Parameters::get(prefix + "->time relative tolerance", timeRelativeTolerance);
Parameters::get(prefix + "->coarsen allowed", coarsenAllowed);
Parameters::get(prefix + "->refinement allowed", refinementAllowed);
Parameters::get(prefix + "->refine bisections", refineBisections);
......@@ -72,6 +74,8 @@ namespace AMDiS {
Parameters::get(prefix + "->sum factor", fac_sum);
Parameters::get(prefix + "->max factor", fac_max);
if (timeTolerance == 0.0 && timeRelativeTolerance == 0.0)
timeTolerance = 1.0;
timeErrLow = timeTolerance * 0.3;
}
......@@ -95,6 +99,9 @@ namespace AMDiS {
/// Time tolerance.
double timeTolerance;
/// Relative time tolerance
double timeRelativeTolerance;
/// Lower bound for the time error.
double timeErrLow;
......@@ -143,6 +150,7 @@ namespace AMDiS {
maxSolverIterations(0),
solverTolerance(1e-8),
solverResidual(0.0),
globalTimeTolerance(1.0),
scalContents(size),
deserialized(false),
rosenbrockMode(false)
......@@ -175,6 +183,7 @@ namespace AMDiS {
Parameters::get(name + "->min timestep", minTimestep);
Parameters::get(name + "->max timestep", maxTimestep);
Parameters::get(name + "->number of timesteps", nTimesteps);
Parameters::get(name + "->time tolerance", globalTimeTolerance);
}
/// Resets all variables to zero (or something equivalent)
......@@ -481,6 +490,12 @@ namespace AMDiS {
return scalContents[index]->timeTolerance;
}
/// Returns \ref timeRelativeTolerance.
inline double getTimeRelativeTolerance(int index)
{
return scalContents[index]->timeRelativeTolerance;
}
/// Sets \ref time
inline double setTime(double t)
{
......@@ -690,6 +705,18 @@ namespace AMDiS {
{
return solverResidual;
}
inline void setGlobalTimeTolerance(double tol)
{
globalTimeTolerance = tol;
}
inline double getGlobalTimeTolerance()
{
return globalTimeTolerance;
}
/// Returns true, if the adaptive procedure was deserialized from a file.
bool isDeserialized() const
......@@ -796,6 +823,9 @@ namespace AMDiS {
///
double solverResidual;
/// tolerance for the overall time error
double globalTimeTolerance;
/// Scalar adapt infos.
std::vector<ScalContent*> scalContents;
......
AMDiS/src/AdaptInstationary.cc
View file @ 9c44b131
......@@ -162,12 +162,6 @@ namespace AMDiS {
problemIteration->oneIteration(adaptInfo, FULL_ITERATION);
problemIteration->endIteration(adaptInfo);
adaptInfo->setLastProcessedTimestep(adaptInfo->getTimestep());
if (dbgMode) {
std::cout << "=== ADAPT INFO DEBUG MODE ===\n";
std::cout << "=== explicitTimeStrategy() ===\n";
adaptInfo->printTimeErrorLowInfo();
}
}
......@@ -207,15 +201,24 @@ namespace AMDiS {
// === Space iterations. ===
do {
problemIteration->beginIteration(adaptInfo);
if (dbgMode) {
std::cout << "=== ADAPT INFO DEBUG MODE ===\n";
std::cout << "=== in implicitTimeStrategy() ===\n";
std::cout << "=== space/time iteration "<< adaptInfo->getSpaceIteration()
<<" : "<< adaptInfo->getTimestepIteration() <<" ===\n";
adaptInfo->printTimeErrorLowInfo();
}
if (problemIteration->oneIteration(adaptInfo, FULL_ITERATION)) {
if (dbgMode) {
std::cout << "=== ADAPT INFO DEBUG MODE ===\n";
std::cout << "=== in implicitTimeStrategy() ===\n";
std::cout << "=== space/time iteration "<< adaptInfo->getSpaceIteration()
<<" : "<< adaptInfo->getTimestepIteration() <<" ===\n";
adaptInfo->printTimeErrorLowInfo();
}
Flag adapted = problemIteration->oneIteration(adaptInfo, FULL_ITERATION);
#if HAVE_PARALLEL_DOMAIN_AMDIS
int recvAllValues = 0;
int isAdapted = static_cast<bool>(adapted);
MPI::COMM_WORLD.Allreduce(&isAdapted, &recvAllValues, 1, MPI_INT, MPI_SUM);
if (recvAllValues) {
#else
if (adapted) {
#endif
if (!fixedTimestep &&
!adaptInfo->timeToleranceReached() &&
!(adaptInfo->getTimestep() <= adaptInfo->getMinTimestep())) {
......@@ -244,7 +247,6 @@ namespace AMDiS {
adaptInfo->setLastProcessedTimestep(adaptInfo->getTimestep());
// After successful iteration/timestep the timestep will be changed according
// adaption rules for next timestep.
// First, check for increase of timestep
......
AMDiS/src/AdaptStationary.cc
View file @ 9c44b131
......@@ -99,7 +99,7 @@ namespace AMDiS {
void AdaptStationary::initialize()
{
{
Parameters::get(name + "->info", info);
}
......
AMDiS/src/BasisFunction.cc
View file @ 9c44b131
......@@ -25,6 +25,7 @@
#include "DOFVector.h"
#include "BasisFunction.h"
#include "Lagrange.h"
#include "Bubble.h"
namespace AMDiS {
......
AMDiS/src/BasisFunction.h
View file @ 9c44b131
......@@ -27,6 +27,7 @@
#include <string>
#include "AMDiS_fwd.h"
#include "CreatorInterface.h"
#include "Global.h"
#include "Boundary.h"
#include "MatrixVector.h"
......@@ -311,6 +312,12 @@ namespace AMDiS {
const ElementVector& uh,
WorldMatrix<double>* val) const;
/**
* override this method, if the base of your finite element space is not
* nodal
*/
virtual bool isNodal() const = 0;
protected:
/// Textual description
std::string name;
......@@ -339,6 +346,26 @@ namespace AMDiS {
/// Vector of second derivatives
std::vector<D2BasFctType*> *d2Phi;
};
/**
* \brief
* Interface for creators of concrete BasisFunctions.
*/
class BasisFunctionCreator : public CreatorInterface<BasisFunction>
{
public:
virtual ~BasisFunctionCreator() {}
/// Sets \ref problem
void setDim(int dim_)
{
dim = dim_;
}
protected:
/// dimension of the mesh
int dim;
};
}
#include "BasisFunction.hh"
......
AMDiS/src/Bubble.cc 0 → 100644
View file @ 9c44b131
This diff is collapsed.
AMDiS/src/Bubble.h 0 → 100644
View file @ 9c44b131
/******************************************************************************
*
* 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.
*
******************************************************************************/
// Created by Roman Weissflog & Philipp Schulz
/** \file Bubble.h */
#ifndef AMDIS_BUBBLE_H
#define AMDIS_BUBBLE_H
#include <list>
#include <boost/numeric/mtl/mtl.hpp>
#include "AbstractFunction.h"
#include "BasisFunction.h"
#include "FixVec.h"
namespace AMDiS {
/** \ingroup FEMSpace
* \brief
* Lagrange basis functions plus Bubble function. Sub class of BasisFunction
*/
class Bubble : public BasisFunction
{
public:
/// Creator class used in the BasisFunctionCreatorMap.
class Creator : public BasisFunctionCreator
{
public:
virtual ~Creator() {}
/// Returns a new Lagrange object.
BasisFunction* create()
{
return getBubble(this->dim, this->dim + 1); // has to be generalized in later versions of bubble functions
}
};
protected:
/// Constructs lagrange/bubble basis functions with the given dim and degree.
/// Constructor is protected to avoid multiple instantiation of identical
/// basis functions. Use \ref getBubble instead.
Bubble(int dim_, int degree_);
/** \brief
* destructor
*/
virtual ~Bubble();
public:
/// Returns a pointer to lagrange and bubble basis functions with the given dim and
/// degree. Multiple instantiation of identical basis functions is avoided
/// by rembering once created basis functions in \ref allBasFcts.
static Bubble* getBubble(int dim, int degree);
/// Implements BasisFunction::interpol
void interpol(const ElInfo *, int, const int *,
AbstractFunction<double, WorldVector<double> >*,
mtl::dense_vector<double>&) const override;
/// Implements BasisFunction::interpol
void interpol(const ElInfo *, int,
const int *b_no,
AbstractFunction<WorldVector<double>, WorldVector<double> >*,
mtl::dense_vector<WorldVector<double> >&) const override;
/// Returns the barycentric coordinates of the i-th basis function.
DimVec<double> *getCoords(int i) const override;
/// Implements BasisFunction::getBound
void getBound(const ElInfo*, BoundaryType *) const override;
/** \brief
* Calculates the local vertex indices which are involved in evaluating
* the nodeIndex-th DOF at the positionIndex-th part of type position
* (VERTEX/EDGE/FACE/CENTER). nodeIndex determines the permutation
* of the involved vertices. So in 1d for lagrange4 there are two DOFs at
* the CENTER (which is an edge in this case). Then vertices[0] = {0, 1} and
* vertices[1] = {1, 0}. This allows to use the same local basis function
* for all DOFs at the same position.
*/
static void setVertices(int dim, int degree,
GeoIndex position, int positionIndex, int nodeIndex,
int** vertices);
/// Implements BasisFunction::refineInter
inline void refineInter(DOFIndexed<double> *drv, RCNeighbourList* list, int n) override
{
if (refineInter_fct)
(*refineInter_fct)(drv, list, n, this);
}
/// Implements BasisFunction::coarseRestrict
inline void coarseRestr(DOFIndexed<double> *drv, RCNeighbourList* list, int n) override
{
if (coarseRestr_fct)
(*coarseRestr_fct)(drv, list, n, this);
}
/// Implements BasisFunction::coarseInter
inline void coarseInter(DOFIndexed<double> *drv, RCNeighbourList* list, int n) override
{
if (coarseInter_fct)
(*coarseInter_fct)(drv, list, n, this);
}
/// Implements BasisFunction::getLocalIndices().
void getLocalIndices(const Element *el,
const DOFAdmin *admin,
std::vector<DegreeOfFreedom> &dofs) const override;
/// Implements BasisFunction::getLocalDofPtrVec()
/// Returns an vector filled with all DOFs per position
void getLocalDofPtrVec(const Element *el,
const DOFAdmin *admin,
std::vector<const DegreeOfFreedom*>& vec) const override;
/// Implements BasisFunction::l2ScpFctBas
void l2ScpFctBas(Quadrature* q,
AbstractFunction<double, WorldVector<double> >* f,
DOFVector<double>* fh) override;
/// Implements BasisFunction::l2ScpFctBas
void l2ScpFctBas(Quadrature* q,
AbstractFunction<WorldVector<double>, WorldVector<double> >* f,
DOFVector<WorldVector<double> >* fh) override;
static void clear();
/// Implements BasisFunction::isnodal
bool isNodal() const override
{
return false;
}
protected:
/// sets the barycentric coordinates (stored in \ref bary) of the local
/// basis functions.
void setBary();
/// Implements BasisFunction::setNDOF
void setNDOF() override;
/// Sets used function pointers
void setFunctionPointer();
/// Used by \ref getVec
int* orderOfPositionIndices(const Element* el,
GeoIndex position,
int positionIndex) const override;
private:
/// barycentric coordinates of the locations of all basis functions
std::vector<DimVec<double>* > *bary;
/** \name static dim-degree-arrays
* \{
*/
static std::vector<DimVec<double>* > baryDimDegree;
static DimVec<int>* ndofDimDegree;
static int nBasFctsDimDegree;
static std::vector<BasFctType*> phifunc;
static std::vector<GrdBasFctType*> grdPhifunc;
static std::vector<D2BasFctType*> D2Phifunc;
/** \} */
/// List of all used BasisFunctions in the whole program. Avoids duplicate
/// instantiation of identical BasisFunctions.
static Bubble* Singleton;
protected:
/// Pointer to the used refineInter function
void (*refineInter_fct)(DOFIndexed<double> *, RCNeighbourList*, int, BasisFunction*);
static void refineInter2_1d(DOFIndexed<double> *, RCNeighbourList*, int,
BasisFunction*);
static void refineInter3_2d(DOFIndexed<double> *, RCNeighbourList*, int,
BasisFunction*);
static void refineInter4_3d(DOFIndexed<double> *, RCNeighbourList*, int,
BasisFunction*);
/// Pointer to the used coarseRestr function
void (*coarseRestr_fct)(DOFIndexed<double> *, RCNeighbourList*, int, BasisFunction*);
static void coarseRestr2_1d(DOFIndexed<double> *, RCNeighbourList*, int,
BasisFunction*);
static void coarseRestr3_2d(DOFIndexed<double> *, RCNeighbourList*, int,
BasisFunction*);
static void coarseRestr4_3d(DOFIndexed<double> *, RCNeighbourList*, int,
BasisFunction*);
/// Pointer to the used coarseInter function
void (*coarseInter_fct)(DOFIndexed<double> *, RCNeighbourList*, int, BasisFunction*);
static void coarseInter2_1d(DOFIndexed<double> *, RCNeighbourList*, int,
BasisFunction*);
static void coarseInter3_2d(DOFIndexed<double> *, RCNeighbourList*, int,
BasisFunction*);
static void coarseInter4_3d(DOFIndexed<double> *, RCNeighbourList*, int,
BasisFunction*);
/// AbstractFunction which implements lagrange/bubble basis functions
class Phi : public BasFctType
{
public:
/// Constructs the local lagrange/bubble basis function for the given position,
/// positionIndex and nodeIndex. owner_ is a pointer to the Bubble
/// object this basis function belongs to.
Phi(Bubble* owner, GeoIndex position, int positionIndex, int nodeIndex);
/// Destructor
virtual ~Phi();
private:
/// vertices needed for evaluation of this function
int* vertices;
/// Pointer to the evaluating function
double (*func)(const DimVec<double>& lambda, int* vert);
/// Returns \ref func(lambda, vertices)
inline double operator()(const DimVec<double>& lambda) const override
{
return func(lambda, vertices);