merge of branches/expr to trunk

AMDiS/AMDISConfig.cmake.in

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -99,7 +99,7 @@ namespace AMDiS {
 
 
   void AdaptStationary::initialize()
-  {  
+  {
     Parameters::get(name + "->info", info);
   }
 

AMDiS/src/BasisFunction.cc

@@ -25,6 +25,7 @@
 #include "DOFVector.h"
 #include "BasisFunction.h"
 #include "Lagrange.h"
+#include "Bubble.h"
 
 namespace AMDiS {
 

AMDiS/src/BasisFunction.h

@@ -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.h

+/******************************************************************************
+ *
+ * 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,