some corrections in CMakeLists

AMDiS/AMDISConfig.cmake.in

@@ -64,6 +64,8 @@ set(AMDIS_NEED_UMFPACK @ENABLE_UMFPACK@)
 set(AMDIS_NEED_PNG @ENABLE_PNG@)
 set(AMDIS_NEED_BDDCML @ENABLE_BDDCML@)
 set(AMDIS_NEED_MKL @ENABLE_MKL@)
+set(AMDIS_NEED_EXTENSIONS @ENABLE_EXTENSIONS@)
+set(AMDIS_NEED_BASE_PROBLEMS @ENABLE_BASE_PROBLEMS@)
 set(AMDIS_USE_FILE ${AMDIS_DIR}/AMDISUse.cmake)
 set(AMDIS_COMPILEFLAGS "@COMPILEFLAGS@")
 set(AMDIS_VERSION @CurrentRevision@)
@@ -161,6 +163,18 @@ if(AMDIS_NEED_BDDCML)
 	list(APPEND AMDIS_LIBRARIES ${AMDIS_BDDCML_LINK_LIST})
 endif(AMDIS_NEED_BDDCML)
 
+if(AMDIS_NEED_EXTENSIONS)
+	list(APPEND AMDIS_INCLUDE_DIRS ${AMDIS_INCLUDE_DIR}/extensions)
+	list(APPEND AMDIS_INCLUDE_DIRS ${AMDIS_INCLUDE_DIR}/extensions/time)
+	list(APPEND AMDIS_INCLUDE_DIRS ${AMDIS_INCLUDE_DIR}/extensions/nanoflann)
+	list(APPEND AMDIS_INCLUDE_DIRS ${AMDIS_INCLUDE_DIR}/extensions/pugixml/src)
+	list(APPEND AMDIS_LIBRARIES ${AMDIS_LIBRARY_DIR}/libextensions.so)
+endif(AMDIS_NEED_EXTENSIONS)
+
+if(AMDIS_NEED_BASE_PROBLEMS)
+	list(APPEND AMDIS_INCLUDE_DIRS ${AMDIS_INCLUDE_DIR}/base_problems)
+	list(APPEND AMDIS_LIBRARIES ${AMDIS_LIBRARY_DIR}/libbase_problems.so)
+endif(AMDIS_NEED_BASE_PROBLEMS)
 
 #add directories for reinit
 list(APPEND AMDIS_INCLUDE_DIRS ${AMDIS_INCLUDE_DIR}/reinit)

AMDiS/CMakeLists.txt

@@ -42,6 +42,7 @@ option(ENABLE_ZOLTAN false)
 option(ENABLE_UMFPACK "Use of UMFPACK solver" false)
 option(ENABLE_PNG "use png reader/writer" false)
 option(ENABLE_BDDCML "Use of BDDCML library" false)
+option(ENABLE_EXTENSIONS "Use extensions" false)
 
 find_package(Boost 1.42 REQUIRED)
 if(Boost_FOUND)
@@ -336,42 +337,100 @@ endif(ENABLE_BDDCML)
 
 
 if(ENABLE_EXTENSIONS)
+  option(ENABLE_BASE_PROBLEMS "Use base_problems" false)
   find_path(EXTENSIONS_DIR NAMES ${SOURCE_DIR}/../../extensions/Helpers.h DOC "Path to AMDiS extensions.")
   if (EXTENSIONS_DIR)
     if (NOT EXISTS ${EXTENSIONS_DIR}/Helpers.h OR NOT EXISTS ${EXTENSIONS_DIR}/base_problems/BaseProblem.h)
       message(FATAL_ERROR "Wrong extensions directory! Directory must contain the 'Helpers.h' and the subdirectory 'base_problems'")
     else()
   
-    SET(EXTENSIONS_SRC
-	    ${EXTENSIONS_DIR}/Helpers.cc
-	    ${EXTENSIONS_DIR}/BackgroundMesh.cc
-	    ${EXTENSIONS_DIR}/GeometryTools.cc
-	    ${EXTENSIONS_DIR}/POperators.cc
-	    ${EXTENSIONS_DIR}/time/ExtendedRosenbrockStationary.cc
-	    ${EXTENSIONS_DIR}/pugixml/src/pugixml.cpp)
-  list(APPEND COMPILEFLAGS "-DHAVE_EXTENSIONS=1")
-
-
-  if(ENABLE_BASE_PROBLEMS)
-      SET(BASE_PROBLEMS_SRC
-	      ${EXTENSIONS_DIR}/base_problems/CahnHilliard.cc
-# 	      ${EXTENSIONS_DIR}/base_problems/DiffuseDomainFsi.cc
-	      ${EXTENSIONS_DIR}/base_problems/LinearElasticity.cc
-	      ${EXTENSIONS_DIR}/base_problems/LinearElasticityPhase.cc
-# 	      ${EXTENSIONS_DIR}/base_problems/NavierStokes_Chorin.cc
-# 	      ${EXTENSIONS_DIR}/base_problems/NavierStokesPhase_Chorin.cc
-	      ${EXTENSIONS_DIR}/base_problems/NavierStokesPhase_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_RB.cc
-	      ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_Base.cc
-# 	      ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal.cc
-	      ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_Phase.cc
-	      ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_RB.cc)
-    list(APPEND COMPILEFLAGS "-DHAVE_BASE_PROBLEMS=1")
+      SET(EXTENSIONS_SRC
+	      ${EXTENSIONS_DIR}/Helpers.cc
+	      ${EXTENSIONS_DIR}/BackgroundMesh.cc
+	      ${EXTENSIONS_DIR}/GeometryTools.cc
+	      ${EXTENSIONS_DIR}/POperators.cc
+	      ${EXTENSIONS_DIR}/time/ExtendedRosenbrockStationary.cc
+	      ${EXTENSIONS_DIR}/pugixml/src/pugixml.cpp)
+      list(APPEND COMPILEFLAGS "-DHAVE_EXTENSIONS=1")
+      list(APPEND AMDIS_INCLUDE_DIRS ${EXTENSIONS_DIR})
+      list(APPEND AMDIS_INCLUDE_DIRS ${EXTENSIONS_DIR}/time)
+      list(APPEND AMDIS_INCLUDE_DIRS ${EXTENSIONS_DIR}/nanoflann)
+      list(APPEND AMDIS_INCLUDE_DIRS ${EXTENSIONS_DIR}/pugixml/src)
+      add_library(extensions SHARED ${EXTENSIONS_SRC})
+      list(APPEND AMDIS_LIBS extensions)
+
+      FILE(GLOB HEADERS "${EXTENSIONS_DIR}/*.h")
+      INSTALL(FILES ${HEADERS}
+	      DESTINATION include/amdis/extensions/)
+      FILE(GLOB HEADERS "${EXTENSIONS_DIR}/*.hh")
+      INSTALL(FILES ${HEADERS}
+	      DESTINATION include/amdis/extensions/)
+
+      list(APPEND deb_add_dirs "include/amdis/extensions")
+
+      FILE(GLOB HEADERS "${EXTENSIONS_DIR}/time/*.h")
+      INSTALL(FILES ${HEADERS}
+	      DESTINATION include/amdis/extensions/time/)
+      FILE(GLOB HEADERS "${EXTENSIONS_DIR}/time/*.hh")
+      INSTALL(FILES ${HEADERS}
+	      DESTINATION include/amdis/extensions/time/)
+
+      list(APPEND deb_add_dirs "include/amdis/extensions/time")
+
+      FILE(GLOB HEADERS "${EXTENSIONS_DIR}/nanoflann/*.hpp")
+      INSTALL(FILES ${HEADERS}
+	      DESTINATION include/amdis/extensions/nanoflann/)
+
+      list(APPEND deb_add_dirs "include/amdis/extensions/nanoflann")
+
+      FILE(GLOB HEADERS "${EXTENSIONS_DIR}/pugixml/src/*.hpp")
+      INSTALL(FILES ${HEADERS}
+	      DESTINATION include/amdis/extensions/pugixml/)
+
+      list(APPEND deb_add_dirs "include/amdis/extensions/pugixml")
+
+      install(TARGETS extensions
+	      LIBRARY DESTINATION lib/amdis/ )
+
+# === baseProblems ====================================================================
+      
+      if(ENABLE_BASE_PROBLEMS)
+	  SET(BASE_PROBLEMS_SRC
+		  ${EXTENSIONS_DIR}/base_problems/CahnHilliard.cc
+    # 	      ${EXTENSIONS_DIR}/base_problems/DiffuseDomainFsi.cc
+		  ${EXTENSIONS_DIR}/base_problems/LinearElasticity.cc
+		  ${EXTENSIONS_DIR}/base_problems/LinearElasticityPhase.cc
+    # 	      ${EXTENSIONS_DIR}/base_problems/NavierStokes_Chorin.cc
+    # 	      ${EXTENSIONS_DIR}/base_problems/NavierStokesPhase_Chorin.cc
+		  ${EXTENSIONS_DIR}/base_problems/NavierStokesPhase_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_RB.cc
+		  ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_Base.cc
+    # 	      ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal.cc
+# 		  ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_Phase.cc
+		  ${EXTENSIONS_DIR}/base_problems/PhaseFieldCrystal_RB.cc)
+	list(APPEND COMPILEFLAGS "-DHAVE_BASE_PROBLEMS=1")
+	list(APPEND AMDIS_INCLUDE_DIRS ${EXTENSIONS_DIR}/base_problems)
+	add_library(base_problems SHARED ${BASE_PROBLEMS_SRC})
+	list(APPEND AMDIS_LIBS base_problems)
+
+	FILE(GLOB HEADERS "${EXTENSIONS_DIR}/base_problems/*.h")
+	INSTALL(FILES ${HEADERS}
+		DESTINATION include/amdis/base_problems/)
+	FILE(GLOB HEADERS "${EXTENSIONS_DIR}/base_problems/*.hh")
+	INSTALL(FILES ${HEADERS}
+		DESTINATION include/amdis/base_problems/)
+
+	list(APPEND deb_add_dirs "include/amdis/base_problems")
+
+	install(TARGETS base_problems
+		LIBRARY DESTINATION lib/amdis/ )
     
-  endif(ENABLE_BASE_PROBLEMS)
+      endif(ENABLE_BASE_PROBLEMS)
+    endif()
+  endif()
 endif(ENABLE_EXTENSIONS)
 
 
@@ -401,13 +460,6 @@ list(APPEND AMDIS_INCLUDE_DIRS ${MTL_INCLUDE_DIR})
 #include_directories(${MTL_INCLUDE_DIR})
 list(APPEND AMDIS_INCLUDE_DIRS ${SOURCE_DIR})
 
-if(ENABLE_EXTENSIONS)
-  list(APPEND AMDIS_INCLUDE_DIRS ${EXTENSIONS_DIR})
-  if(ENABLE_BASE_PROBLEMS)
-    list(APPEND AMDIS_INCLUDE_DIRS ${EXTENSIONS_DIR}/base_problems)
-  endif(ENABLE_BASE_PROBLEMS)
-endif(ENABLE_EXTENSIONS)
-
 #include_directories(${SOURCE_DIR})
 include_directories(${AMDIS_INCLUDE_DIRS})
 
@@ -416,22 +468,9 @@ add_library(compositeFEM SHARED ${COMPOSITE_FEM_SRC})
 add_library(reinit SHARED ${REINIT_SRC})
 add_library(muparser SHARED ${MUPARSER_SRC})
 
-if(ENABLE_EXTENSIONS)
-  add_library(extensions SHARED ${EXTENSIONS_SRC})
-  if(ENABLE_BASE_PROBLEMS)
-    add_library(base_problems SHARED ${BASE_PROBLEMS_SRC})
-  endif(ENABLE_BASE_PROBLEMS)
-endif(ENABLE_EXTENSIONS)
-
 #target_link_libraries(compositeFEM amdis)
 #target_link_libraries(reinit amdis)
 list(APPEND AMDIS_LIBS amdis ${Boost_LIBRARIES})
-if(ENABLE_EXTENSIONS)
-  list(APPEND AMDIS_LIBS extensions)
-  if(ENABLE_BASE_PROBLEMS)
-    list(APPEND AMDIS_LIBS base_problems)
-  endif(ENABLE_BASE_PROBLEMS)
-endif(ENABLE_EXTENSIONS)
 
 if(WIN32)
 	list(APPEND COMPILEFLAGS "-D_SCL_SECURE_NO_WARNINGS" "-D_CRT_SECURE_NO_WARNINGS")
@@ -489,52 +528,6 @@ FILE(GLOB HEADERS "${SOURCE_DIR}/io/*.hh")
 INSTALL(FILES ${HEADERS}
 	DESTINATION include/amdis/io)
 
-# ========== (begin) extensions ==========================
-if (ENABLE_EXTENSIONS)
-  FILE(GLOB HEADERS "${EXTENSIONS_DIR}/*.h")
-  INSTALL(FILES ${HEADERS}
-	  DESTINATION include/amdis/extensions/)
-  FILE(GLOB HEADERS "${EXTENSIONS_DIR}/*.hh")
-  INSTALL(FILES ${HEADERS}
-	  DESTINATION include/amdis/extensions/)
-  
-  list(APPEND deb_add_dirs "include/amdis/extensions")
-
-  FILE(GLOB HEADERS "${EXTENSIONS_DIR}/time/*.h")
-  INSTALL(FILES ${HEADERS}
-	  DESTINATION include/amdis/extensions/time/)
-  FILE(GLOB HEADERS "${EXTENSIONS_DIR}/time/*.hh")
-  INSTALL(FILES ${HEADERS}
-	  DESTINATION include/amdis/extensions/time/)
-  
-  list(APPEND deb_add_dirs "include/amdis/extensions/time")
-
-  FILE(GLOB HEADERS "${EXTENSIONS_DIR}/nanoflann/*.hpp")
-  INSTALL(FILES ${HEADERS}
-	  DESTINATION include/amdis/extensions/nanoflann/)
-
-  list(APPEND deb_add_dirs "include/amdis/extensions/nanoflann")
-
-  FILE(GLOB HEADERS "${EXTENSIONS_DIR}/pugixml/src/*.hpp")
-  INSTALL(FILES ${HEADERS}
-	  DESTINATION include/amdis/extensions/pugixml/)
-
-  list(APPEND deb_add_dirs "include/amdis/extensions/pugixml")
-  
-  if(ENABLE_BASE_PROBLEMS)
-    FILE(GLOB HEADERS "${EXTENSIONS_DIR}/base_problems/*.h")
-    INSTALL(FILES ${HEADERS}
-	    DESTINATION include/amdis/base_problems/)
-    FILE(GLOB HEADERS "${EXTENSIONS_DIR}/base_problems/*.hh")
-    INSTALL(FILES ${HEADERS}
-	    DESTINATION include/amdis/base_problems/)
-
-    list(APPEND deb_add_dirs "include/amdis/base_problems")
-    
-  endif(ENABLE_BASE_PROBLEMS)
-endif(ENABLE_EXTENSIONS)
-# ========== (end) extensions ==========================
-
 FILE(GLOB HEADERS "${REINIT_SOURCE_DIR}/*.h")
 INSTALL(FILES ${HEADERS}
 	DESTINATION include/amdis/reinit)
@@ -554,17 +547,6 @@ list(APPEND deb_add_dirs "lib/amdis")
 install(TARGETS amdis compositeFEM reinit muparser
 	LIBRARY DESTINATION lib/amdis/ )
 
-if (ENABLE_EXTENSIONS)
-  list(APPEND deb_add_dirs "lib/amdis/extensions")
-  install(TARGETS extensions
-	  LIBRARY DESTINATION lib/amdis/extensions/ )
-  if(ENABLE_BASE_PROBLEMS)
-    list(APPEND deb_add_dirs "lib/amdis/extensions/base_problems")
-    install(TARGETS base_problems
-	    LIBRARY DESTINATION lib/amdis/base_problems/ )
-  endif(ENABLE_BASE_PROBLEMS)
-endif(ENABLE_EXTENSIONS)
-
 configure_file(${AMDIS_SOURCE_DIR}/AMDISConfig.cmake.in
 		${AMDIS_BINARY_DIR}/AMDISConfig.cmake
 		@ONLY

extensions/base_problems/BaseProblem.h

@@ -6,6 +6,7 @@
 #include "AMDiS.h"
 #include "time/RosenbrockStationary.h"
 #include "CouplingTimeInterface.h"
+#include "VtuReader.h"
 
 using namespace AMDiS;
 
@@ -41,7 +42,7 @@ public:
     fillBoundaryConditions();
   };
 
-  /// read solution DOFVectors from .arh or .dat files
+  /// read solution DOFVectors from .arh, .dat or .vtu files
   virtual Flag initDataFromFile(AdaptInfo *adaptInfo);
 
   /// calls \ref initDataFromFile

extensions/base_problems/BaseProblem.hh

@@ -39,28 +39,28 @@ Flag BaseProblem<ProblemType>::initDataFromFile(AdaptInfo *adaptInfo)
   Initfile::get(name + "->read data from file", readDataFromFile, 2);
   if (!readDataFromFile)
     return initFlag;
-  
-  Initfile::get(name + "->read arh files", readArhFiles, 2);
-  Initfile::get(name + "->read dat files", readDatFiles, 2);
-  if (readArhFiles && readDatFiles) {
-    WARNING("You can not read data from both formats, .arh and .dat! The .arh-format is selected.\n");
-  }
 
-  std::string data_file="", phase_file="";
+  std::string readFormat = "arh";
+  Initfile::get(name + "->read format", readFormat, 2);
+  if (readFormat != "arh" && readFormat != "dat" && readFormat != "vtu") {
+    WARNING("You can not read data from formats other than .arh, .dat or .vtu! The .arh-format is selected.\n");
+  }
 
   // read data and mesh from arh-files/dat-files
   MSG("read data from file...\n");
-  if (readArhFiles) {
-    Initfile::get(name + "->data file", data_file);
-    if (data_file.size() == 0) return initFlag;
-    if (!file_exists(data_file))
-      throw(std::runtime_error("The file '" + data_file + "' does not exist!"));
+  if (readFormat == "arh") {
+    std::string filename = "";
+    Initfile::get(name + "->value file", filename);
+    if (filename.size() == 0) return initFlag;
+    if (!file_exists(filename))
+      throw(std::runtime_error("The file '" + filename + "' does not exist!"));
     
     std::vector<DOFVector<double>*> solutions;
     for (size_t i = 0; i < prob->getNumComponents(); i++)
       solutions.push_back(prob->getSolution()->getDOFVector(i));
-    ArhReader::read(data_file, prob->getMesh(), solutions);
-  } else if(readDatFiles) {
+    ArhReader::read(filename, prob->getMesh(), solutions);
+  }
+  else if (readFormat == "dat") {
     bool preserveMacroFileInfo = false;
     Parameters::get(prob->getMesh()->getName() + "->preserve macroFileInfo", preserveMacroFileInfo);
     if (prob->getMesh()->getMacroFileInfo() == NULL || !preserveMacroFileInfo)
@@ -73,8 +73,40 @@ Flag BaseProblem<ProblemType>::initDataFromFile(AdaptInfo *adaptInfo)
 	throw(std::runtime_error("The file '" + filename + "'does not exist!"));
       ValueReader::readValue(filename,prob->getMesh(),prob->getSolution()->getDOFVector(i),prob->getMesh()->getMacroFileInfo());
     }
-  } else
-    throw(std::runtime_error("Parameter 'read data from file' set to 'true', but no input format specified!"));
+  }
+  else if (readFormat == "vtu") {
+    std::vector<std::string> filenames;
+    Initfile::get(name + "->value file", filenames);
+    if (filenames.size() == 0)
+      return initFlag;
+    int arh_idx = -1, vtu_idx = -1;
+    for (size_t i = 0; i < filenames.size(); i++) {
+      if (!file_exists(filenames[i]))
+	throw(std::runtime_error("The file '" + filenames[i] + "' does not exist!"));
+      if (filenames[i].find(".vtu") != std::string::npos)
+	vtu_idx = i;
+      else if (filenames[i].find(".arh") != std::string::npos)
+	arh_idx = i;
+      else
+	throw(std::runtime_error("The file '" + filenames[i] + "' must have the extension .arh or .vtu!"));
+    }
+    if (arh_idx >= 0) {
+      ArhReader::read(filenames[arh_idx], prob->getMesh());
+    }
+    if (vtu_idx >= 0) {
+      std::vector<DOFVector<double>*> solutions;
+      std::vector<std::string> names;
+      for (size_t i = 0; i < prob->getNumComponents(); i++) {
+	solutions.push_back(prob->getSolution()->getDOFVector(i));
+	names.push_back(prob->getComponentName(i));
+      }
+      VtuReader::readValue(filenames[vtu_idx], prob->getMesh(), solutions, names);
+    } else
+      throw(std::runtime_error("You have to specify a .vtu file!"));
+  }
+  else {
+    throw(std::runtime_error("Parameter 'read data from file' set to 'true', but no parameter 'read format' specified!"));
+  }
   
   initFlag.setFlag(DATA_ADOPTED);
   initFlag.setFlag(MESH_ADOPTED);