merge of trunk with arhfile2 branch: 'using namespace' removed from header...

merge of trunk with arhfile2 branch: 'using namespace' removed from header files, file readers/writer moved to subnamespace AMDiS::io, test for arh2writer added

AMDiS/AMDISConfig.cmake.in

@@ -55,14 +55,28 @@ else()
 endif()
 unset(_AMDIS_LIB CACHE)
 
+
 # Boost libraries
 # ---------------
+set(AMDIS_HAS_PARALLEL_DOMAIN @ENABLE_PARALLEL_DOMAIN@)
+set(AMDIS_NEED_COMPRESSION @ENABLE_COMPRESSIN@)
+
+set(BOOST_LIBS_REQUIRED system iostreams filesystem program_options date_time)
+if(AMDIS_NEED_COMPRESSION)
+  list(APPEND BOOST_LIBS_REQUIRED zlib bzip2)
+endif(AMDIS_NEED_COMPRESSION)
+
+set(BOOST_VERSION "1.42")
+if(AMDIS_HAS_PARALLEL_DOMAIN)
+  set(BOOST_VERSION "1.48")
+endif(AMDIS_HAS_PARALLEL_DOMAIN)
+
 if(WIN32)
   set(Boost_USE_STATIC_LIBS ON)
-  find_package(Boost 1.42 REQUIRED system iostreams filesystem program_options date_time zlib bzip2)
+  find_package(Boost ${BOOST_VERSION} REQUIRED ${BOOST_LIBS_REQUIRED})
 else()
   set(Boost_USE_STATIC_LIBS OFF)
-  find_package(Boost 1.42 REQUIRED system iostreams filesystem program_options date_time)
+  find_package(Boost ${BOOST_VERSION} REQUIRED ${BOOST_LIBS_REQUIRED})
 endif()
 if(Boost_FOUND)
   list(APPEND AMDIS_LIBRARIES ${Boost_LIBRARIES})
@@ -81,11 +95,10 @@ list(APPEND AMDIS_INCLUDE_DIRS ${AMDIS_INCLUDE_DIR}/muparser)
 # ------------------------------------------------------------------
 
 set(AMDIS_NEED_ZOLTAN @ENABLE_ZOLTAN@)
-set(AMDIS_HAS_PARALLEL_DOMAIN @ENABLE_PARALLEL_DOMAIN@)
 set(AMDIS_OPENMP @ENABLE_OPENMP@)
 set(AMDIS_NEED_UMFPACK @ENABLE_UMFPACK@)
 set(AMDIS_NEED_HYPRE @ENABLE_HYPRE@)
-set(AMDIS_NEED_PETSC @ENABLE_PETSC@)
+set(AMDIS_NEED_SEQ_PETSC @ENABLE_SEQ_PETSC@)
 set(AMDIS_NEED_PNG @ENABLE_PNG@)
 set(AMDIS_NEED_BDDCML @ENABLE_BDDCML@)
 set(AMDIS_NEED_MKL @ENABLE_MKL@)

AMDiS/CMakeLists.txt

@@ -41,13 +41,14 @@ endif()
 SET(ENABLE_PARALLEL_DOMAIN "OFF" CACHE STRING "use parallel domain decomposition. please set to one of: PMTL, PETSC, OFF" )
 option(USE_PETSC_DEV false)
 option(ENABLE_ZOLTAN false)
-option(ENABLE_PETSC "Use sequential PETSc solvers" false)
+option(ENABLE_SEQ_PETSC "Use sequential PETSc solvers" false)
 option(ENABLE_UMFPACK "Use of UMFPACK solver" false)
 option(ENABLE_HYPRE "Use HYPRE AMG solver" false)
 option(ENABLE_PNG "use png reader/writer" false)
 option(ENABLE_BDDCML "Use of BDDCML library" false)
 option(ENABLE_EXTENSIONS "Use extensions" false)
 option(ENABLE_OPENMP "Use OpenMP" false)
+option(ENABLE_COMPRESSION "Use output compression" false)
 option(ENABLE_OUTPUT "AMDiS output printing, disable only for debugging!" true)
 
 
@@ -160,7 +161,11 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
 	      ${SOURCE_DIR}/est/ResidualEstimator.cc
 	      ${SOURCE_DIR}/est/SimpleResidualEstimator.cc
 	      ${SOURCE_DIR}/io/ArhReader.cc
-	      ${SOURCE_DIR}/io/ArhWriter.cc
+	      ${SOURCE_DIR}/io/detail/ArhReader.cc
+              ${SOURCE_DIR}/io/Arh2Reader.cc
+              ${SOURCE_DIR}/io/detail/Arh2Reader.cc
+	      ${SOURCE_DIR}/io/detail/ArhWriter.cc
+              ${SOURCE_DIR}/io/detail/Arh2Writer.cc
 	      ${SOURCE_DIR}/io/DofWriter.cc
 	      ${SOURCE_DIR}/io/ElementFileWriter.cc
 	      ${SOURCE_DIR}/io/FileWriter.cc
@@ -176,6 +181,7 @@ SET(AMDIS_SRC ${SOURCE_DIR}/AdaptBase.cc
 	      ${SOURCE_DIR}/io/ValueWriter.cc
 	      ${SOURCE_DIR}/io/VtkWriter.cc
 	      ${SOURCE_DIR}/io/VtkVectorWriter.cc
+              ${SOURCE_DIR}/io/detail/VtkWriter.cc
 	      ${SOURCE_DIR}/nonlin/ProblemNonLin.cc
 	      ${SOURCE_DIR}/solver/SolverMatrix.cc
 	      ${SOURCE_DIR}/time/RosenbrockAdaptInstationary.cc
@@ -257,7 +263,7 @@ if(ENABLE_PARALLEL_DOMAIN)
 		set(PETSC_EXECUTABLE_RUNS ON)
 		find_package(PETSc REQUIRED)
 		include_directories(${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
-		list(APPEND COMPILEFLAGS "-DHAVE_PARALLEL_PETSC")
+		list(APPEND COMPILEFLAGS "-DHAVE_PARALLEL_PETSC" "-DPETSC_VERSION=${PETSC_VERSION}")
 		list(APPEND AMDIS_INCLUDE_DIRS ${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
 		list(APPEND PARALLEL_DOMAIN_AMDIS_SRC 
 			${SOURCE_DIR}/parallel/MatrixNnzStructure.cc
@@ -297,7 +303,7 @@ if(ENABLE_PARALLEL_DOMAIN)
 endif(ENABLE_PARALLEL_DOMAIN)
 
 
-if(ENABLE_PETSC)
+if(ENABLE_SEQ_PETSC)
   find_package(MPI REQUIRED)
   if(MPI_FOUND)
     list(APPEND COMPILEFLAGS "${MPI_COMPILE_FLAGS}")
@@ -309,12 +315,12 @@ if(ENABLE_PETSC)
   find_package(PETSc REQUIRED)
   include_directories(${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
   list(APPEND AMDIS_INCLUDE_DIRS ${PETSC_DIR}/include ${PETSC_DIR}/${PETSC_ARCH}/include)
-  list(APPEND COMPILEFLAGS "-DHAVE_PETSC" "-DPETSC_VERSION=${PETSC_VERSION}")
+  list(APPEND COMPILEFLAGS "-DHAVE_SEQ_PETSC" "-DPETSC_VERSION=${PETSC_VERSION}")
   
   list(APPEND AMDIS_SRC   
 	${SOURCE_DIR}/solver/PetscSolver.cc
 	${SOURCE_DIR}/solver/PetscTypes.cc)
-endif(ENABLE_PETSC)
+endif(ENABLE_SEQ_PETSC)
 
 if(ENABLE_UMFPACK)
 	find_file(UMFPACK_H umfpack.h
@@ -362,6 +368,9 @@ if(ENABLE_PNG)
 	endif()
 endif(ENABLE_PNG)
 
+if(ENABLE_COMPRESSION)
+  list(APPEND COMPILEFLAGS "-DHAVE_COMPRESSION=1")
+endif(ENABLE_COMPRESSION)
 
 if(NOT ENABLE_OUTPUT)
        message(WARNING "AMDiS cout output disabled!")
@@ -421,11 +430,11 @@ if(ENABLE_EXTENSIONS)
 	      ${EXTENSIONS_DIR}/preconditioner/PhaseFieldCrystal_.cc
 	      ${EXTENSIONS_DIR}/preconditioner/CahnHilliard_.cc)
 	      
-      if(ENABLE_PETSC)
+      if(ENABLE_SEQ_PETSC)
 	list(APPEND EXTENSIONS_SRC
 	      ${EXTENSIONS_DIR}/preconditioner/PetscPreconPfc.cc
 	      ${EXTENSIONS_DIR}/preconditioner/PetscPreconCahnHilliard.cc)
-      endif(ENABLE_PETSC)
+      endif(ENABLE_SEQ_PETSC)
       
       if(ENABLE_PARALLEL_DOMAIN)
 	list(APPEND EXTENSIONS_SRC
@@ -651,6 +660,11 @@ FILE(GLOB HEADERS "${SOURCE_DIR}/io/*.hh")
 INSTALL(FILES ${HEADERS}
 	DESTINATION include/amdis/io)
 	
+FILE(GLOB HEADERS "${SOURCE_DIR}/io/detail/*h")
+INSTALL(FILES ${HEADERS}
+        DESTINATION include/amdis/io/detail)
+list(APPEND deb_add_dirs "include/amdis/io/detail")        
+
 FILE(GLOB HEADERS "${REINIT_SOURCE_DIR}/*.h")
 INSTALL(FILES ${HEADERS}
 	DESTINATION include/amdis/reinit)

AMDiS/src/AMDiS.cc

@@ -36,7 +36,7 @@ namespace AMDiS {
 
   void init(int argc, char **argv, std::string initFileName)
   {
-#if defined(HAVE_PARALLEL_DOMAIN_AMDIS) || defined(HAVE_PETSC)
+#if defined(HAVE_PARALLEL_DOMAIN_AMDIS) || defined(HAVE_SEQ_PETSC)
   #ifdef HAVE_PARALLEL_MTL4
     mtl_environment = new mtl::par::environment(argc, argv);
   #else
@@ -142,12 +142,10 @@ namespace AMDiS {
   #ifdef HAVE_PARALLEL_MTL4
     if (mtl_environment)
       delete mtl_environment;
-  #else
-    PetscFinalize();
   #endif
 #endif
     
-#ifdef HAVE_PETSC
+#if (defined HAVE_SEQ_PETSC) || (defined HAVE_PARALLEL_PETSC)
     PetscFinalize();
 #endif
     

AMDiS/src/AMDiS.h

@@ -113,7 +113,9 @@
 #include "est/Estimator.h"
 
 #include "io/ArhReader.h"
+#include "io/Arh2Reader.h"
 #include "io/ArhWriter.h"
+#include "io/Arh2Writer.h"
 #include "io/DataCollector.h"
 #include "io/FileWriter.h"
 #include "io/GNUPlotWriter.h"
@@ -126,6 +128,11 @@
 #include "io/ValueWriter.h"
 #include "io/VtkWriter.h"
 #include "io/VtkVectorWriter.h"
+#ifdef HAVE_EXTENSIONS
+#include "io/VtkReader.h"
+#endif
+#include "io/Reader.h"
+#include "io/Writer.h"
 
 #include "nonlin/ProblemNonLin.h"
 #include "nonlin/NonLinSolver.h"

AMDiS/src/AMDiS_fwd.h

@@ -100,6 +100,16 @@ namespace AMDiS {
   class VertexInfo;
   class VertexVector;
   
+  namespace io {
+    class ElementFileWriter;
+    class GNUPlotWriter;
+    class MacroReader;
+    class MacroWriter;
+    class PngWriter;
+    class PovrayWriter;
+    class Spreadsheet;
+  }
+
 #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
   namespace Parallel {
     class ElementObjectDatabase;

AMDiS/src/AdaptBase.h

@@ -31,14 +31,12 @@
 
 namespace AMDiS {
 
-  using namespace std;
-
   /// Interface for adaption loops.
   class AdaptBase
   {
   public:
     /// Constructor
-    AdaptBase(string sname,
+    AdaptBase(std::string sname,
 	      ProblemIterationInterface *problemIteration_,
 	      AdaptInfo *adapt,
 	      ProblemTimeInterface *problemTime_ = nullptr,
@@ -60,7 +58,7 @@ namespace AMDiS {
     virtual int adapt() = 0;
 
     /// Returns \ref name
-    inline string getName() const 
+    inline std::string getName() const 
     { 
       return name; 
     }
@@ -103,7 +101,7 @@ namespace AMDiS {
 
   protected:
     /// Name of the adaption loop
-    string name;
+    std::string name;
 
     /// Problem iteration interface
     ProblemIterationInterface *problemIteration;

AMDiS/src/AdaptInstationary.cc

@@ -33,6 +33,8 @@
 #endif
 #endif
 
+using namespace std;
+
 namespace AMDiS {
 
   AdaptInstationary::AdaptInstationary(std::string name,

AMDiS/src/AdaptInstationary.h

@@ -35,8 +35,6 @@
 
 namespace AMDiS {
 
-  using namespace std;
-
   /** \ingroup Adaption  
    * \brief
    * AdaptInstationary implements the adaptive procdure for time dependent 
@@ -48,21 +46,21 @@ namespace AMDiS {
   public:
     /// Creates a AdaptInstationary object with the given name for the time 
     /// dependent problem problemInstat. TODO: Make obsolete!
-    AdaptInstationary(string name, 
+    AdaptInstationary(std::string name, 
 		      ProblemIterationInterface *problemStat,
 		      AdaptInfo *info,
 		      ProblemTimeInterface *problemInstat,
 		      AdaptInfo *initialInfo,
-                      time_t initialTimestampSet = 0);
+                      std::time_t initialTimestampSet = 0);
 
     /// Creates a AdaptInstationary object with the given name for the time 
     /// dependent problem problemInstat.
-    AdaptInstationary(string name, 
+    AdaptInstationary(std::string name, 
 		      ProblemIterationInterface &problemStat,
 		      AdaptInfo &info,
 		      ProblemTimeInterface &problemInstat,
 		      AdaptInfo &initialInfo,
-                      time_t initialTimestampSet = 0);
+                      std::time_t initialTimestampSet = 0);
 
     /** \brief
      * This funciton is used only to avoid double code in both constructors. If the
@@ -73,7 +71,7 @@ namespace AMDiS {
     void initConstructor(ProblemIterationInterface *problemStat,  
 			 AdaptInfo *info,
 			 AdaptInfo *initialInfo,
-			 time_t initialTimestampSet);
+			 std::time_t initialTimestampSet);
 
     /// Destructor
     virtual ~AdaptInstationary() {}
@@ -94,10 +92,10 @@ namespace AMDiS {
     int adapt() override;
 
     /// Serialization
-    virtual void serialize(ostream &out);
+    virtual void serialize(std::ostream &out);
 
     /// deserialization
-    virtual void deserialize(istream &in);
+    virtual void deserialize(std::istream &in);
 
 
   protected:
@@ -113,7 +111,7 @@ namespace AMDiS {
     virtual void oneTimestep();
 
     /// Initialisation of this AdaptInstationary object
-    void initialize(string aName);
+    void initialize(std::string aName);
 
     /// Implements the explit time strategy. Used by \ref oneTimestep().
     virtual void explicitTimeStrategy();
@@ -160,18 +158,18 @@ namespace AMDiS {
     int queueRuntime;
 
     /// Name of the file used to automatically serialize the problem.
-    string queueSerializationFilename;
+    std::string queueSerializationFilename;
 
     /// Timestamp at the beginning of all calculations. It is used to calculate the 
     /// overall runtime of the problem.
-    time_t initialTimestamp;
+    std::time_t initialTimestamp;
 
     /// Timestamp at the beginning of the last timestep iteration. Is is used to 
     /// calculate the runtime of the last timestep.
-    time_t iterationTimestamp;
+    std::time_t iterationTimestamp;
 
     /// Stores the runtime (in seconds) of some last timestep iterations.
-    queue<int> lastIterationsDuration;
+    std::queue<int> lastIterationsDuration;
 
     /// In debug mode, the adapt loop will print information about timestep decreasing 
     /// and increasing.

AMDiS/src/AdaptStationary.h

@@ -40,8 +40,6 @@
 
 namespace AMDiS {
 
-  using namespace std;
-
   /** \ingroup Adaption 
    * \brief
    * AdaptStationary contains information about the adaptive procedure and the
@@ -51,12 +49,12 @@ namespace AMDiS {
   {
   public:
     /// Creates a AdaptStationary object with given name. TODO: Make obsolete!
-    AdaptStationary(string name,
+    AdaptStationary(std::string name,
 		    ProblemIterationInterface *prob,
 		    AdaptInfo *info);
 
     /// Creates a AdaptStationary object with given name.
-    AdaptStationary(string name,
+    AdaptStationary(std::string name,
 		    ProblemIterationInterface &prob,
 		    AdaptInfo &info);
 

AMDiS/src/BasisFunction.h

@@ -34,8 +34,6 @@
 
 namespace AMDiS {
 
-  using namespace std;
-
   /// Function interface for evaluating basis functions.
   class BasFctType
   {
@@ -91,7 +89,7 @@ namespace AMDiS {
   {  
   protected:
     /// Creates a BasisFunction object of given dim and degree 
-    BasisFunction(string name, int dim, int degree);
+    BasisFunction(std::string name, int dim, int degree);
 
     /// destructor
     virtual ~BasisFunction();
@@ -145,7 +143,7 @@ namespace AMDiS {
     }
 
     /// Returns \ref name of BasisFunction
-    inline string getName() const 
+    inline std::string getName() const 
     { 
       return name; 
     }
@@ -271,13 +269,13 @@ namespace AMDiS {
     /// Returns local dof indices of the element for the given fe space.
     virtual void getLocalIndices(const Element *el,
 				 const DOFAdmin *admin,
-				 vector<DegreeOfFreedom> &indices) const
+				 std::vector<DegreeOfFreedom> &indices) const
     {}
 
     ///
     virtual void getLocalDofPtrVec(const Element *el, 
 				   const DOFAdmin *admin,
-				   vector<const DegreeOfFreedom*>& vec) const
+				   std::vector<const DegreeOfFreedom*>& vec) const
     {}
 
 
@@ -315,7 +313,7 @@ namespace AMDiS {
 
   protected:
     /// Textual description
-    string name;     
+    std::string name;     
 
     /// Number of basisfunctions on one Element                 
     int nBasFcts;
@@ -333,13 +331,13 @@ namespace AMDiS {
     DimVec<int> *nDOF;
 
     /// Vector of the local functions
-    vector<BasFctType*> *phi;
+    std::vector<BasFctType*> *phi;
 
     /// Vector of gradients
-    vector<GrdBasFctType*> *grdPhi;
+    std::vector<GrdBasFctType*> *grdPhi;
 
     /// Vector of second derivatives
-    vector<D2BasFctType*> *d2Phi;
+    std::vector<D2BasFctType*> *d2Phi;
   };
 
 }

AMDiS/src/BoundaryObject.h

@@ -33,9 +33,7 @@
 
 namespace AMDiS {
 
-  using namespace std;
-
-  typedef vector<pair<GeoIndex, int> > ExcludeList;
+  typedef std::vector<std::pair<GeoIndex, int> > ExcludeList;
 
   /// Defines the geometrical objects that forms the boundary;
   struct BoundaryObject {

AMDiS/src/CoarseningManager3d.cc

@@ -30,6 +30,8 @@
 #include "DOFIndexed.h"
 #include "Debug.h"
 
+using namespace std;
+
 namespace AMDiS {
 
   void CoarseningManager3d::coarsenFunction(ElInfo *elInfo)

AMDiS/src/Collection.h

@@ -24,19 +24,18 @@
 #include "MTL4Types.h"
 
 namespace AMDiS {
-  template< typename T >
+  template<typename T>
   struct Collection {};
 
-  using namespace MTLTypes;
-  template< >
-    struct Collection< MTLMatrix > {
-      typedef mtl::matrix::inserter< MTLMatrix > Inserter;
+  template<>
+    struct Collection< MTLTypes::MTLMatrix > {
+      typedef mtl::matrix::inserter< MTLTypes::MTLMatrix > Inserter;
     };
 
-  template< >
-    struct Collection< MTLVector > {
-      typedef mtl::vector::inserter< MTLVector > Inserter;
-      typedef MTLMatrix PreconditionMatrix;
+  template<>
+    struct Collection< MTLTypes::MTLVector > {
+      typedef mtl::vector::inserter< MTLTypes::MTLVector > Inserter;
+      typedef MTLTypes::MTLMatrix PreconditionMatrix;
     };
 }
 #endif

AMDiS/src/CouplingProblemStat.h

@@ -35,19 +35,19 @@
 
 namespace AMDiS {
 
-  using namespace std;
-
+  namespace detail
+  {
 
     /** \brief
     * This class defines a coupled stationary problem definition in sequential
     * computations. 
     */
     template<typename ProblemStatType>
-  class CouplingProblemStatImpl
+    class CouplingProblemStat
     {
     public:
       /// Constructor
-    CouplingProblemStatImpl(std::string name_)
+      CouplingProblemStat(std::string name_)
 	: name(name_),
 	  nComponents(0),
 	  nMeshes(0),
@@ -56,7 +56,7 @@ namespace AMDiS {
       {}
 
       /// Destructor
-    virtual ~CouplingProblemStatImpl() {}
+      virtual ~CouplingProblemStat() {}
 
       /// add problem by number
       virtual void addProblem(ProblemStatType* prob)
@@ -96,14 +96,14 @@ namespace AMDiS {
 		      name.c_str());
 
 	std::map<std::string, Mesh*> meshByName;
-      std::vector< std::set<Mesh*> > meshesForProblems(problems.size());
+	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
 
-	  string meshName("");
+	    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());
@@ -123,26 +123,26 @@ namespace AMDiS {
 	    // feSpace
 	    int degree = 1;
 	    Parameters::get(problems[i]->getName() + "->polynomial degree[" + 
-                          boost::lexical_cast<string>(j) + "]", degree);
+			    boost::lexical_cast<std::string>(j) + "]", degree);
 
-          if (feSpaceMap[pair<Mesh*, int>(meshByName[meshName], degree)] == nullptr) {
-            stringstream s;
+	    if (feSpaceMap[std::pair<Mesh*, int>(meshByName[meshName], degree)] == nullptr) {
+	      std::stringstream s;
 	      s << problems[i]->getName() << "->feSpace[" << j << "]";
       
 	      FiniteElemSpace *newFeSpace = 
 		FiniteElemSpace::provideFeSpace(nullptr, Lagrange::getLagrange(dim, degree),
 						meshByName[meshName], s.str());
-            feSpaceMap[pair<Mesh*, int>(meshByName[meshName], degree)] = newFeSpace;
+	      feSpaceMap[std::pair<Mesh*, int>(meshByName[meshName], degree)] = newFeSpace;
 	      feSpaces.push_back(newFeSpace);
 	    }
       
-//           problems[i]->setComponentSpace(j, feSpaceMap[pair<Mesh*, int>(meshByName[meshName], degree)]);
+  //           problems[i]->setComponentSpace(j, feSpaceMap[std::pair<Mesh*, int>(meshByName[meshName], degree)]);
 
 	  }
 	}
 
 	for (size_t i = 0; i < problems.size(); i++) {
-        vector<Mesh*> problemMeshes(meshesForProblems[i].begin(), meshesForProblems[i].end());
+	  std::vector<Mesh*> problemMeshes(meshesForProblems[i].begin(), meshesForProblems[i].end());
 	  problems[i]->setMeshes(problemMeshes);
 	  problems[i]->setRefinementManager(refinementManager);
 	  problems[i]->setCoarseningManager(coarseningManager);
@@ -155,10 +155,10 @@ namespace AMDiS {
 	  // 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
+  #ifndef HAVE_PARALLEL_DOMAIN_AMDIS
 	  Parameters::get(meshes[i]->getName() + "->global refinements",
 			  globalRefinements);
-#endif
+  #endif
 
 	  bool initMesh = initFlag.isSet(INIT_MESH);
 
@@ -225,7 +225,7 @@ namespace AMDiS {
       }
 
       /// Returns \ref meshes
-    inline vector<Mesh*> getMeshes() 
+      inline std::vector<Mesh*> getMeshes() 
       {
 	return meshes; 
       }
@@ -243,7 +243,7 @@ namespace AMDiS {
       }
 
       /// Returns the name of the problem
-    inline virtual string getName() 
+      inline virtual std::string getName() 
       { 
 	return name; 
       }
@@ -251,7 +251,7 @@ namespace AMDiS {
     protected:
       
       /// Name of this problem.
-    string name;
+      std::string name;
 
       /// Number of problem components
       int nComponents;
@@ -264,10 +264,10 @@ namespace AMDiS {
       int nMeshes;
 
       /// FE spaces of this problem.
-    vector<FiniteElemSpace*> feSpaces;
+      std::vector<FiniteElemSpace*> feSpaces;
 
       /// Meshes of this problem.
-    vector<Mesh*> meshes;
+      std::vector<Mesh*> meshes;
 
       /** \brief
       * All actions of mesh refinement are performed by refinementManager.
@@ -283,11 +283,13 @@ namespace AMDiS {
       */
       CoarseningManager *coarseningManager;
 
-    vector<ProblemStatType*> problems;
+      std::vector<ProblemStatType*> problems;
     };