And moved Reinit library to src and updated makefiles.

AMDiS/Reinit/Makefile

-SHELL = /bin/sh
-COMPILE = g++
-DEFS = -DPACKAGE=\"AMDiS\" -DVERSION=\"0.1\" -DHAVE_DLFCN_H=1 
-DEBUG = 0
-AMDIS_DIR = ../
-
-INCLUDES = -I./src -I$(AMDIS_DIR)/src -I$(AMDIS_DIR)/compositeFEM/src -I$(AMDIS_DIR)/lib/mtl4
-
-ifeq ($(strip $(DEBUG)), 0)
-       CPPFLAGS = -O2
-else
-       CPPFLAGS = -g -O0
-endif
-CPPFLAGS +=  -ftemplate-depth-40
-
-VPATH = .:$(AMDIS_DIR)/Reinit/src
-
-LIBOFILES = \
-BoundaryElementDist.o \
-BoundaryElementNormalDist.o \
-BoundaryElementLevelSetDist.o \
-BoundaryElementTopDist.o \
-BoundaryElementEdgeDist.o \
-ElementLevelSet.o \
-ElementUpdate_2d.o \
-ElementUpdate_3d.o \
-HL_SignedDist.o \
-HL_SignedDistTraverse.o \
-VelocityExt.o \
-VelocityExtFromVelocityField.o \
-NormEps.o 
-
-all: libreinit.a
-
-# statische Bibliothek
-libreinit.a: $(LIBOFILES)
-	rm -f lib/libreinit.a
-	ar cq lib/libreinit.a $(LIBOFILES)
-
-.cc.o: $*.cc
-	$(COMPILE) $(DEFS) $(INCLUDES) $(CPPFLAGS) -c -o $*.o $<
-
-clean: 
-	-rm -rf *.o

AMDiS/Reinit/src/HL_SignedDistLevels.h

-// ============================================================================
-// ==                                                                        ==
-// == AMDiS - Adaptive multidimensional simulations                          ==
-// ==                                                                        ==
-// ==  http://www.amdis-fem.org                                              ==
-// ==                                                                        ==
-// ============================================================================
-//
-// Software License for AMDiS
-//
-// Copyright (c) 2010 Dresden University of Technology 
-// All rights reserved.
-// Authors: Simon Vey, Thomas Witkowski et al.
-//
-// This file is part of AMDiS
-//
-// See also license.opensource.txt in the distribution.
-
-
-
-
-#ifndef HL_SIGNEDDISTLEVELS
-#define HL_SIGNEDDISTLEVELS
-
-#include <queue>
-#include <vector>
-#include <time.h>
-#include "ElInfo.h"
-#include "FixVec.h"
-#include "Traverse.h"
-#include "ElementLevelSet.h"
-#include "BoundaryElementDist.h"
-#include "ElementUpdate.h"
-#include "ElementUpdate_2d.h"
-#include "ElementUpdate_3d.h"
-#include "HL_SignedDist.h"
-#include "VelocityExt.h"
-#include "SMIAdapter.h"
-#include "smi.h"
-
-using namespace AMDiS;
-
-typedef struct
-{
-  int ElNum;
-  int VertNum;
-} Vert_Struct;
-
-class HL_SignedDistLevels : public HL_SignedDist
-{
-public:
-  HL_SignedDistLevels(const char *name_, 
-		      int dim_,
-		      bool doVelocityExt = false,
-		      Flag velExtType_ = VEL_EXT)
-    : HL_SignedDist(name_, dim_, doVelocityExt, velExtType_),
-      smiAdapter(NULL)
-  {
-    FUNCNAME("HL_SignedDistLevels::HL_SignedDistLevels()");
-
-    // ===== Read parameters from init file. =====
-    GET_PARAMETER(0, name + "->tolerance", "%f", &tol);
-    GET_PARAMETER(0, name + "->count_how_often_saved_in_list", "%d", &count_in_list);
-    GET_PARAMETER(0, name + "->save_in_list->the ..th", "%d", &print_in_list);
-    GET_PARAMETER(0, name + "->save_in_list->after the ..th traversing of the list", "%d", &print_in_list_2);
-    GET_PARAMETER(0, name + "->print_level", "%d", &chosen_level);
-    GET_PARAMETER(0, name + "->print_level_yes_no", "%d", &print_level);
-
-    TEST_EXIT(tol > 0)("illegal tolerance !\n");
-  }
-
- protected:
-  /**
-   * Initializes the boundary: calculation of the distance of boundary 
-   * vertices to the interface. 
-   * Interface is given by \ref lS_DOF and result is stored in 
-   * \ref sD_DOF.
-   */
-  void initializeBoundary();
-
-  /**
-   * function for transvering Mesh to SMi an Adding the quantities
-   **/
-  void Mesh_to_SMI_and_quantity ();
-
-  /**
-   * function for creating the first list, in which elementnumber of 
-   * boundary-elements are saved
-   */
-  void createFirstList(const int elStatus, 
-		       const int *elVertStatusVec, 
-		       int ElNum, 
-		       const int NumVertIntPoints);
-
-  /**
-   * Calculates the distance function and stores result in sD_DOF.
-   * Requirement: The boundary values are already set in \ref sD_DOF.
-   */
-  void HL_updateIteration();
-
-  /**
-   * function for traversing the list "List_Element"
-   * returns 1 if min one element is set in the new list
-   * returns 0 if no element is set in the new list
-   */ 
-  int traverseListElement();
-
-  /**
-   * function for creating all levels higher than 1 an saving pairs of 
-   * elements and node in the right list
-   **/
-  void createLevels ();
- 
-  /**
-   * function collects the next neighbours, creates an according list 
-   * and saves the pair in it
-   * returns true if one or more neighbours exist and false if not
-   **/
-  bool collectNeighbours_setLevels (const int Element,
-				    const int currentIndex,
-				    bool *elementInNewListSet);
-
-  /**
-   * function for traversing the list of list, named "Level_"
-   **/ 
-  void traversingListLevel_ ( DOFVector<double> *boundVal_DOF );
- 
-  /**
-   * calls the next neighbours and puts them into the right list
-   * returns true if an element had to be saved in an lower level 
-   * than the current index
-   * this means the loop over all lists Level_[i] has to be repaeated again
-   * "Vert" is a local node
-   **/
-  bool search_and_include_comb(int ElNum, 
-			       int Vert, 
-			       int *nodeIndices, 
-			       const int Index);
-
-  /**
-   * checking whether the element "ElNum_in" has to be included into 
-   * the second list
-   * if yes it will be included
-   * returns true if the level of the element is smaler than he current index
-   * returns false if the level is greater thean the current index
-   * "Vert_1_in" and "Vert_2_in" are localvertizes
-   */ 
-  bool includeIntoList (int ElNum_in, 
-			int VertNum_1_in, 
-			int VertNum_2_in, 
-			const int Index);
- 
-  /**
-   * gets the neighbour according to the node "VertNum_in" and two of 
-   * its nodes (in local koordinates)
-   * returns "false" if the called neighbour exists and "true" if not
-   * Vert_Up_in is given in global coordinates, the other points are 
-   * given in local coordinates
-   */ 
-  bool getNextNeighbour (const int ElNum_in, 
-			 const int Vert_Up_in, 
-			 const int VertNum_in, 
-			 int &ElNum_out, 
-			 int &VertNum_1_out, 
-			 int &VertNum_2_out);
-
-  /**
-   * function needed in the function "traversingListELVert"
-   **/
-  int getNext_node_l_r (int elem_l_r_in,
-			int neighbour_l_r_in, 
-			int node_l_r_in, 
-			const int Vert);
-
-  //==================================
-  void print_quantity_5 (int cntr);
-
-  /**
-   * function for printinq the quantity 6
-   * attention: we need at least read_transaction in smi for calling 
-   * this function
-   **/
-  void print_quantity_6 ();
-  //====================================
-
- protected:
-  /**
-   * Tolerance for Hopf-Lax update iteration loop.
-   */
-  double tol;
-
-  /**
-   * is needed for transfering the mesh to SMI
-   */
-  SMIAdapter *smiAdapter;
-
-  /**
-   * in this list boundary-elements are saved;
-   * is needed for creating the list "List_El_Vert"
-   */
-  queue<int> List_Element;
-  
-  /**
-   * in this list structs filled with element-number and vertex-number 
-   * are saved;
-   * is needed for traversing the mesh efficiently
-   */
-  queue<Vert_Struct> Level;
-  
-  queue<Vert_Struct> helpLevel;
-  
-  queue<Vert_Struct> List_El_Vert;       //Listen noch einmal kontrollieren!
-  
-  /**
-   * in this vector the lists of different levels are saved
-   **/
-  vector<queue<Vert_Struct> > Level_;
-
-  /**
-   * 0 ->do not count updates
-   * 1 ->count updates
-   **/ 
-  int count_updates; 
-
-  /**
-   * 1 -> it will be count how often a node is saved in the second list
-   * 0 ->it will not be count
-   **/ 
-  int count_in_list; 
-
-  int print_in_list;
-  int print_in_list_2;
-  
-  /**
-   * level which will be printed in a file
-   **/
-  int chosen_level;
-  
-  /**
-   * 1->a special level will be printed in a file
-   * 0->no level is printed in a file
-   **/
-  int print_level;
-};
-
-#endif  // HL_SIGNEDDISTLEVELS

AMDiS/src/Makefile.am

-lib_LTLIBRARIES = libamdis.la libcompositeFEM.la
+lib_LTLIBRARIES = libamdis.la libcompositeFEM.la libreinit.la
 
 LIB_DIR = ../lib
 PARALLEL_DIR = $(SOURCE_DIR)
@@ -249,6 +249,21 @@ parallel/ParMetisPartitioner.h \
 parallel/PetscSolver.h \
 parallel/StdMpi.h \
 parallel/ZoltanPartitioner.h \
+reinit/BoundaryElementDist.h \
+reinit/BoundaryElementEdgeDist.h \
+reinit/BoundaryElementLevelSetDist.h \
+reinit/BoundaryElementNormalDist.h \
+reinit/BoundaryElementTopDist.h \
+reinit/ElementLevelSet.h \
+reinit/ElementUpdate.h \
+reinit/ElementUpdate_2d.h \
+reinit/ElementUpdate_3d.h \
+reinit/HL_SignedDist.h \
+reinit/HL_SignedDistBornemann.h \
+reinit/HL_SignedDistTraverse.h \
+reinit/NormEps.h \
+reinit/VelocityExt.h \
+reinit/VelocityExtFromVelocityField.h \
 time/RosenbrockAdaptInstationary.h \
 time/RosenbrockStationary.h \
 time/RosenbrockMethod.h 
@@ -377,3 +392,19 @@ compositeFEM/LevelSetAdaptMesh.cc \
 compositeFEM/PenaltyOperator.cc \
 compositeFEM/SubElementAssembler.cc \
 compositeFEM/SubPolytope.cc
+
+libreinit_la_CXXFLAGS = $(libamdis_la_CXXFLAGS)
+libreinit_la_SOURCES = \
+reinit/BoundaryElementDist.cc \
+reinit/BoundaryElementEdgeDist.cc \
+reinit/BoundaryElementLevelSetDist.cc \
+reinit/BoundaryElementNormalDist.cc \
+reinit/BoundaryElementTopDist.cc \
+reinit/ElementLevelSet.cc \
+reinit/ElementUpdate_2d.cc \
+reinit/ElementUpdate_3d.cc \
+reinit/HL_SignedDist.cc \
+reinit/HL_SignedDistTraverse.cc \
+reinit/NormEps.cc \
+reinit/VelocityExt.cc \
+reinit/VelocityExtFromVelocityField.cc
\ No newline at end of file