From cc386fc3193cbfc2eb942f82277f339a01147315 Mon Sep 17 00:00:00 2001
From: Hauke Rabbel <rabbel@ipfdd.de>
Date: Wed, 9 Mar 2016 17:26:28 +0100
Subject: [PATCH 01/11] Added convenience interface Ingredients::synchronize()

The idea behind this is to make the code more readable, because
otherwise the more cryptic syntax Ingredients::synchronize(IngredientsType&)
had to be used. The latter is still available in case it is needed.
---
 include/LeMonADE/core/Ingredients.h | 31 +++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/include/LeMonADE/core/Ingredients.h b/include/LeMonADE/core/Ingredients.h
index 286949f..aa01e8a 100644
--- a/include/LeMonADE/core/Ingredients.h
+++ b/include/LeMonADE/core/Ingredients.h
@@ -203,6 +203,37 @@ template <class Config> class Ingredients: public Config::context_type
 		return molecules;
 	}
 
+	/**
+	 * @brief Synchronizes the Features and establishing consistency in the system.
+	 *
+	 * @details This function only calls the function 
+	 * context_type::synchronize(Ingredients&) with itsself as argument. Thus
+	 * it causes all features to subsequently call their synchonize routines.
+	 * Calling this function on an instance ( "ingredients.synchronize();" )
+	 * is equivalent to calling  "ingredients.synchonize(ingredients));"
+	 */
+	void synchronize()
+	{
+		context_type::synchronize(*this);
+	}
+	
+	/**
+	 * @brief Synchronizes the Features and establishing consistency in the system.
+	 *
+	 * @details This function only calls the function 
+	 * context_type::synchronize(Ingredients& ing). Thus it causes all features 
+	 * to subsequently call their synchonize routines with the same argument.
+	 * This function allows to synchronize one instance of Ingredients with
+	 * another instance.
+	 *
+	 * @param ingredients A reference to the Ingredients instance to synchronize with
+	 */
+	template<class IngredientsType>
+	void synchronize(IngredientsType& ing)
+	{
+		context_type::synchronize(ing);
+	}
+	
 	/**
 	 * @brief Export the relevant functionality of all meta-information and molecules
 	 * for reading bfm-files.

From 2b14ae6348b18d59133be15aafe07816661501f8 Mon Sep 17 00:00:00 2001
From: Hauke Rabbel <rabbel@ipfdd.de>
Date: Fri, 1 Apr 2016 17:12:50 +0200
Subject: [PATCH 02/11] added basic test for Ingredients::synchronize() and
 Ingredients::synchronize(const Ingredients&) to validate the newly added
 convenience interface Ingredience::synchronize()

---
 tests/core/TestIngredients.cpp | 171 +++++++++++++++++++++++++++++++++
 1 file changed, 171 insertions(+)

diff --git a/tests/core/TestIngredients.cpp b/tests/core/TestIngredients.cpp
index 1586ca2..d320075 100644
--- a/tests/core/TestIngredients.cpp
+++ b/tests/core/TestIngredients.cpp
@@ -42,6 +42,7 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 #include <LeMonADE/core/Molecules.h>
 #include <LeMonADE/feature/FeatureBondset.h>
 #include <LeMonADE/feature/FeatureBox.h>
+#include <LeMonADE/feature/FeatureExcludedVolume.h>
 #include <LeMonADE/utility/Vector3D.h>
 #include <LeMonADE/core/ConfigureSystem.h>
 
@@ -98,3 +99,173 @@ TEST(IngredientsTest, printMetaData){
 			
 }
 
+
+TEST(IngredientsTest, synchronize_noargument){
+	typedef LOKI_TYPELIST_2(FeatureBox, FeatureBondset<>) Features1;
+	typedef ConfigureSystem<VectorInt3,Features1,3> Config1;
+	typedef Ingredients < Config1> MyIngredients1;
+	
+	typedef LOKI_TYPELIST_3(FeatureBox, FeatureBondset<>,FeatureExcludedVolume<>) Features2;
+	typedef ConfigureSystem<VectorInt3,Features1,3> Config2;
+	typedef Ingredients < Config2> MyIngredients2;
+	
+	
+	MyIngredients1 ingredients1;
+	MyIngredients2 ingredients2;
+
+	//exception from FeatureBox is exspected, as box size is not set
+	EXPECT_THROW(ingredients1.synchronize(),std::runtime_error);	
+	EXPECT_THROW(ingredients2.synchronize(),std::runtime_error);	
+	
+	ingredients1.setBoxX(10);
+	ingredients1.setBoxY(10);
+	ingredients1.setBoxZ(10);
+	ingredients1.setPeriodicX(true);
+	ingredients1.setPeriodicY(true);
+	
+	ingredients2.setBoxX(10);
+	ingredients2.setBoxY(10);
+	ingredients2.setBoxZ(10);
+	ingredients2.setPeriodicX(true);
+	ingredients2.setPeriodicY(false);
+	
+	//exception from FeatureBox is exspected, as periodicity not fully set
+	EXPECT_THROW(ingredients1.synchronize(),std::runtime_error);	
+	EXPECT_THROW(ingredients2.synchronize(),std::runtime_error);	
+	
+	ingredients1.setPeriodicZ(false);
+	ingredients2.setPeriodicZ(false);
+	
+	//now add the bondset and some particles so that effect of synchronize
+	//can be checked
+	ingredients1.modifyBondset().addBFMclassicBondset();
+	ingredients2.modifyBondset().addBFMclassicBondset();
+	
+	ingredients1.modifyMolecules().addMonomer(1,1,1);
+	ingredients1.modifyMolecules().addMonomer(1,4,6);
+	ingredients1.modifyMolecules().addMonomer(7,7,1);
+	//this one violates excluded volume, but excluded volume feauture is not used
+	ingredients1.modifyMolecules().addMonomer(7,8,2);
+	//in ingredients1 this one is ok, but in ingredients2 it will violate box dimensions
+	ingredients1.modifyMolecules().addMonomer(3,9,2);
+	
+	ingredients2.modifyMolecules().addMonomer(1,1,1);
+	ingredients2.modifyMolecules().addMonomer(1,4,6);
+	ingredients2.modifyMolecules().addMonomer(7,7,1);
+	//this one violates excluded volume
+	ingredients2.modifyMolecules().addMonomer(7,8,2);
+	//this one violates box dimensions due to periodicity
+	ingredients2.modifyMolecules().addMonomer(3,9,2);
+	
+	//now make some invalid bonds
+	ingredients1.modifyMolecules().connect(0,1);
+	ingredients2.modifyMolecules().connect(0,1);
+	
+	
+	//again, try to synchronize. 
+	EXPECT_THROW(ingredients1.synchronize(),std::runtime_error);
+	EXPECT_THROW(ingredients2.synchronize(),std::runtime_error);
+	
+	//change position of monomer 1, so that bond is valid.
+	ingredients1.modifyMolecules()[1].setZ(1);
+	ingredients2.modifyMolecules()[1].setZ(1);
+	
+	//again, try to synchronize. ingredients1 should work now 
+	EXPECT_NO_THROW(ingredients1.synchronize());
+	EXPECT_THROW(ingredients2.synchronize(),std::runtime_error);
+	
+	//now change the conflicting particle coordinate for excluded volume 
+	//and synchronize again..still fails due to periodicit
+	ingredients2.modifyMolecules()[3].setY(5);
+	EXPECT_THROW(ingredients2.synchronize(),std::runtime_error);
+	
+	//now change the conflicting particle coordinate for periodicity 
+	//and synchronize again..should work now
+	ingredients2.modifyMolecules()[4].setY(5);
+	EXPECT_NO_THROW(ingredients2.synchronize());
+}
+
+TEST(IngredientsTest, synchronize_withargument){
+	typedef LOKI_TYPELIST_2(FeatureBox, FeatureBondset<>) Features1;
+	typedef ConfigureSystem<VectorInt3,Features1,3> Config1;
+	typedef Ingredients < Config1> MyIngredients1;
+	
+	typedef LOKI_TYPELIST_3(FeatureBox, FeatureBondset<>,FeatureExcludedVolume<>) Features2;
+	typedef ConfigureSystem<VectorInt3,Features1,3> Config2;
+	typedef Ingredients < Config2> MyIngredients2;
+	
+	
+	MyIngredients1 ingredients1;
+	MyIngredients2 ingredients2;
+
+	//exception from FeatureBox is exspected, as box size is not set
+	EXPECT_THROW(ingredients1.synchronize(ingredients1),std::runtime_error);	
+	EXPECT_THROW(ingredients2.synchronize(ingredients2),std::runtime_error);	
+	
+	ingredients1.setBoxX(10);
+	ingredients1.setBoxY(10);
+	ingredients1.setBoxZ(10);
+	ingredients1.setPeriodicX(true);
+	ingredients1.setPeriodicY(true);
+	
+	ingredients2.setBoxX(10);
+	ingredients2.setBoxY(10);
+	ingredients2.setBoxZ(10);
+	ingredients2.setPeriodicX(true);
+	ingredients2.setPeriodicY(false);
+	
+	//exception from FeatureBox is exspected, as periodicity not fully set
+	EXPECT_THROW(ingredients1.synchronize(ingredients1),std::runtime_error);	
+	EXPECT_THROW(ingredients2.synchronize(ingredients2),std::runtime_error);	
+	
+	ingredients1.setPeriodicZ(false);
+	ingredients2.setPeriodicZ(false);
+	
+	//now add the bondset and some particles so that effect of synchronize
+	//can be checked
+	ingredients1.modifyBondset().addBFMclassicBondset();
+	ingredients2.modifyBondset().addBFMclassicBondset();
+	
+	ingredients1.modifyMolecules().addMonomer(1,1,1);
+	ingredients1.modifyMolecules().addMonomer(1,4,6);
+	ingredients1.modifyMolecules().addMonomer(7,7,1);
+	//this one violates excluded volume, but excluded volume feauture is not used
+	ingredients1.modifyMolecules().addMonomer(7,8,2);
+	//in ingredients1 this one is ok, but in ingredients2 it will violate box dimensions
+	ingredients1.modifyMolecules().addMonomer(3,9,2);
+	
+	ingredients2.modifyMolecules().addMonomer(1,1,1);
+	ingredients2.modifyMolecules().addMonomer(1,4,6);
+	ingredients2.modifyMolecules().addMonomer(7,7,1);
+	//this one violates excluded volume
+	ingredients2.modifyMolecules().addMonomer(7,8,2);
+	//this one violates box dimensions due to periodicity
+	ingredients2.modifyMolecules().addMonomer(3,9,2);
+	
+	//now make some invalid bonds
+	ingredients1.modifyMolecules().connect(0,1);
+	ingredients2.modifyMolecules().connect(0,1);
+	
+	
+	//again, try to synchronize. 
+	EXPECT_THROW(ingredients1.synchronize(ingredients1),std::runtime_error);
+	EXPECT_THROW(ingredients2.synchronize(ingredients2),std::runtime_error);
+	
+	//change position of monomer 1, so that bond is valid.
+	ingredients1.modifyMolecules()[1].setZ(1);
+	ingredients2.modifyMolecules()[1].setZ(1);
+	
+	//again, try to synchronize. ingredients1 should work now 
+	EXPECT_NO_THROW(ingredients1.synchronize(ingredients1));
+	EXPECT_THROW(ingredients2.synchronize(ingredients2),std::runtime_error);
+	
+	//now change the conflicting particle coordinate for excluded volume 
+	//and synchronize again..still fails due to periodicity
+	ingredients2.modifyMolecules()[3].setY(5);
+	EXPECT_THROW(ingredients2.synchronize(ingredients2),std::runtime_error);
+	
+	//now change the conflicting particle coordinate for periodicity 
+	//and synchronize again..should work now
+	ingredients2.modifyMolecules()[4].setY(5);
+	EXPECT_NO_THROW(ingredients2.synchronize(ingredients2));
+}

From 2159f94a2907b4f2546fb5b5047446b684b6d8c5 Mon Sep 17 00:00:00 2001
From: Hauke Rabbel <rabbel@ipfdd.de>
Date: Mon, 4 Apr 2016 13:35:39 +0200
Subject: [PATCH 03/11] Changed updaters UpdaterReadBfmFile and
 UpdaterSynchronize, so that they use the new interface
 Ingredients::synchronize() instead of Ingredients::synchronize(Ingredients&)

---
 include/LeMonADE/updater/UpdaterReadBfmFile.h | 7 +++----
 include/LeMonADE/updater/UpdaterSynchronize.h | 2 +-
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/include/LeMonADE/updater/UpdaterReadBfmFile.h b/include/LeMonADE/updater/UpdaterReadBfmFile.h
index b8f6750..35a2274 100644
--- a/include/LeMonADE/updater/UpdaterReadBfmFile.h
+++ b/include/LeMonADE/updater/UpdaterReadBfmFile.h
@@ -102,9 +102,8 @@ class UpdaterReadBfmFile: public AbstractUpdater
 		}
 		else
 			throw std::runtime_error("ReadBFMFile::init()...read type must have value READ_LAST_CONFIG_SAVE(0), READ_LAST_CONFIG_FAST(1), or READ_STEPWISE(2)\n");
-
-
-		ingredients.synchronize(ingredients);
+		
+		ingredients.synchronize();
   };
 
 
@@ -145,7 +144,7 @@ class UpdaterReadBfmFile: public AbstractUpdater
 		throw std::runtime_error("ReadBFMFile::execute()...read type must have value READ_LAST_CONFIG_SAVE(0), READ_LAST_CONFIG_FAST(1), or READ_STEPWISE(2)\n");
 		
 		  
-	ingredients.synchronize(ingredients); 
+	ingredients.synchronize(); 
 	return retVal;	  
   }
 
diff --git a/include/LeMonADE/updater/UpdaterSynchronize.h b/include/LeMonADE/updater/UpdaterSynchronize.h
index af1136c..d9375f5 100644
--- a/include/LeMonADE/updater/UpdaterSynchronize.h
+++ b/include/LeMonADE/updater/UpdaterSynchronize.h
@@ -69,7 +69,7 @@ template< class T > class UpdaterSynchronize: public IngredientsUpdater < T >
 template<class T >
 bool UpdaterSynchronize<T>::execute()
 {
-	this->getIngredients().synchronize( this->getIngredients() );
+	this->getIngredients().synchronize();
 	return true;
 }
 

From 567cf43e3ca33a29b398c32f13cb7373c721719f Mon Sep 17 00:00:00 2001
From: Hauke Rabbel <rabbel@ipfdd.de>
Date: Tue, 5 Apr 2016 09:20:47 +0200
Subject: [PATCH 04/11] Added compile flags for build types Debug and Release
 (Default) in top level CMakeLists.txt

---
 CMakeLists.txt | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index a8e17c7..d635415 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -41,9 +41,18 @@ SET (APPLICATION_ID "${APPLICATION_VENDOR_ID}.${PROJECT_NAME}")
 
 
 #
-# Debugging Options
+# Compile options
 #
-SET (CMAKE_VERBOSE_MAKEFILE 0) # Use 1 for debugging, 0 for release
+IF(NOT CMAKE_BUILD_TYPE)
+SET (CMAKE_BUILD_TYPE "Release") #default build type is Release
+SET (CMAKE_VERBOSE_MAKEFILE 0) 
+ENDIF(NOT CMAKE_BUILD_TYPE)
+
+SET (CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -msse2 -mssse3 -fexpensive-optimizations ")
+SET (CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} -O3 -msse2 -mssse3 -fexpensive-optimizations ")
+
+SET (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -Wall -g -DDEBUG ")
+SET (CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0 -Wall -g -DDEBUG ")
 
 #
 # Project Output Paths

From e281a31d565a7b67f7bd015f1cb3549a5897c110 Mon Sep 17 00:00:00 2001
From: Hauke Rabbel <rabbel@ipfdd.de>
Date: Tue, 5 Apr 2016 11:11:26 +0200
Subject: [PATCH 05/11] *Bugfix in Molecules copy constructor:

Removed static cast to reference of derived class,
because it causes undefined behaviour. This occured in
particular, when using different compiler optimizations.
Aditionally, the cast was pointless anyways.
The same change was applied to Molecules assignment operator.

*Improved errormessages from Molecules::connect(...)
*Added Test for Molecules assignment operator
---
 include/LeMonADE/core/Molecules.h | 104 ++++++++++--------------------
 tests/core/TestMolecules.cpp      |  39 ++++++++++-
 2 files changed, 72 insertions(+), 71 deletions(-)

diff --git a/include/LeMonADE/core/Molecules.h b/include/LeMonADE/core/Molecules.h
index 7247db1..45b9c15 100644
--- a/include/LeMonADE/core/Molecules.h
+++ b/include/LeMonADE/core/Molecules.h
@@ -94,12 +94,7 @@ template < class Vertex, uint max_connectivity = 7, class Edge = int > class Mol
   
   //! Conversion constructor
   template < class V, uint m, class E> Molecules (const Molecules<V,m,E>& src);
-  
-  Molecules (const Molecules<Vertex,max_connectivity, Edge>& src);
-
-  //template < class V, uint m, class E >
-  //Molecules<Vertex,max_connectivity, Edge>& operator=  (const Molecules<V,m,E>& src);
-
+ 
   Molecules<Vertex,max_connectivity, Edge>& operator=  (const Molecules<Vertex,max_connectivity, Edge>& src);
 
   Molecules<Vertex,max_connectivity, Edge>& operator+=  (const Molecules<Vertex,max_connectivity, Edge>& src);
@@ -305,8 +300,8 @@ template < class Vertex, uint max_connectivity = 7, class Edge = int > class Mol
 /*****************************************************************************/
 
 /**
- * Copy one object of Molecules into another, i.e. copies vertex,
- * connectivity and age information.
+ * Copys and Converts one type of Molecules object into another, i.e. copies vertex,
+ * connectivity and age information, and does type-conversion
  *
  * @param src A reference to another graph to copy from.
  * @tparam m Maximum allowed connectivity of the source graph
@@ -314,70 +309,37 @@ template < class Vertex, uint max_connectivity = 7, class Edge = int > class Mol
  * @tparam E Edge type of the source graph
  */
 template < class Vertex, uint max_connectivity, class Edge>
-Molecules<Vertex,max_connectivity, Edge>::Molecules (const Molecules<Vertex,max_connectivity,Edge>& src)
+template < class V, uint m, class E >
+Molecules<Vertex,max_connectivity, Edge>::Molecules (const Molecules<V,m,E>& src)
 {
-  
+	
 	clear();
 	vertices.resize(src.size());
 	
 	for ( uint i = 0 ; i < vertices.size(); ++i) {
-		//copy all vertices.
-		this->vertices[i]=static_cast<const typename Molecules<Vertex,max_connectivity, Edge>::internal_vertex_type&>(src[i]);
-		
-		///@todo rethink: this copy should not be necessary because we are also copying the topology, or?
-		
-		//copy the edges, too
-		uint32_t nNeighbours=src.getNumLinks(i);//vertices[i].getNumLinks();
 		
-		for(uint j=0; j<nNeighbours;++j){
-			// copy connections and edges contents
-			connect(i, src.getNeighborIdx(i,j), src.getLinkInfo(i,src.getNeighborIdx(i,j)));
+		//this initializes a new vertex, all connectivity information is lost
+		this->vertices[i]=src[i];		
+		//copy the connectivity and edges, too
+		uint32_t nNeighbours=src.getNumLinks(i);
+		try{
+			for(uint j=0; j<nNeighbours;++j){
+				connect(i, src.getNeighborIdx(i,j), src.getLinkInfo(i,src.getNeighborIdx(i,j)));
+			}
 		}
+		catch(std::runtime_error& e){
+			std::stringstream errormessage;
+			errormessage<<"Error when copying connectivity information in "
+			<<"Molecules copy constructor.\n Original error:\n"
+			<<e.what();
+			
+			throw std::runtime_error(errormessage.str());
+		}
+		
 	}
 	
 	this->myAge = src.getAge();
-}
-
-
-
-/**
- * Copys and Converts one type of Molecules object into another, i.e. copies vertex,
- * connectivity and age information, and does type-conversion
- * 
- * @todo testing!!!
- *
- * @param src A reference to another graph to copy from.
- * @tparam m Maximum allowed connectivity of the source graph
- * @tparam V Vertex type of the source graph
- * @tparam E Edge type of the source graph
- */
-template < class Vertex, uint max_connectivity, class Edge>
-template < class V, uint m, class E >
-Molecules<Vertex,max_connectivity, Edge>::Molecules (const Molecules<V,m,E>& src)
-{
-  
-	clear();
-	vertices.resize(src.size());
-
-	for ( uint i = 0 ; i < vertices.size(); ++i) {
-	    //copy all vertices.
-	    this->vertices[i]=static_cast<const typename Molecules<Vertex,max_connectivity, Edge>::internal_vertex_type&>(src[i]);
-
-	    ///@todo rethink: this copy should not be necessary because we are also copying the topology, or?
-
-
-	    //copy the edges, too
-	    uint32_t nNeighbours=src.getNumLinks(i);//vertices[i].getNumLinks();
-
-	    for(uint j=0; j<nNeighbours;++j){
-		  // copy connections and edges contents
-		  connect(i, src.getNeighborIdx(i,j), src.getLinkInfo(i,src.getNeighborIdx(i,j)));
-	    }
-
-	  }
-
-	  this->myAge = src.getAge();
-
+	
 }
   
 /**
@@ -398,12 +360,12 @@ Molecules<Vertex,max_connectivity, Edge>& Molecules<Vertex, max_connectivity, Ed
 	
 	for ( uint i = 0 ; i < vertices.size(); ++i) {
 		//copy all vertices.
-		this->vertices[i]=static_cast<const typename Molecules<Vertex,max_connectivity, Edge>::internal_vertex_type&>(src[i]);
+		//this does not copy the connectivity info, but it is copied 
+		//in the loop below
+		this->vertices[i]=src[i];
 		
-		///@todo rethink: this copy should not be necessary because we are also copying the topology, or?
-		
-		//copy the edges, too
-		uint32_t nNeighbours=src.getNumLinks(i);//vertices[i].getNumLinks();
+		//copy the connectivity and edges, too
+		uint32_t nNeighbours=src.getNumLinks(i);
 		
 		for(uint j=0; j<nNeighbours;++j){
 			// copy connections and edges contents
@@ -487,7 +449,7 @@ void Molecules <Vertex,max_connectivity,Edge>::connect(uint32_t a, uint32_t b, c
       vertices.at(a).connect(b);
       vertices.at(b).connect(a);
     }
-    //catch error due to non-existent indices here
+    //method vertices.at(int) might throw out_of_range exception.
     catch(std::out_of_range& exception){
     	std::stringstream messagestream;
       messagestream<<"Molecules::connect(int a, int b): a="<<a<<" and b="<<b<<std::endl;
@@ -503,10 +465,12 @@ void Molecules <Vertex,max_connectivity,Edge>::connect(uint32_t a, uint32_t b, c
       //re-throw exception
       throw std::range_error(messagestream.str());
     }
-    //catch other errormessages here (only type string)
-    catch(std::string& errormessage){
+    //catch other errormessages here. we normally use runtime_error
+    catch(std::runtime_error& e){
       std::stringstream messagestream;
+      messagestream<<"Molecules::connect(int a, int b): a="<<a<<" and b="<<b<<std::endl;
       messagestream<<"Indices were: a="<<a<<" ,b="<<b<<std::endl;
+      messagestream<<e.what();
       //re-throw exception
       throw std::runtime_error(messagestream.str());
     }
diff --git a/tests/core/TestMolecules.cpp b/tests/core/TestMolecules.cpp
index c4b5c61..a2e7fe7 100644
--- a/tests/core/TestMolecules.cpp
+++ b/tests/core/TestMolecules.cpp
@@ -245,7 +245,7 @@ TEST_F(MoleculesTest, Constructors){
   //this should throw an exception, because the max connectivity of molecules1 
   //is too high
   EXPECT_ANY_THROW( (Molecules<VectorInt3, 2> (molecules1)) );
-  
+
   //create new objects from molecules1
   Molecules<VectorInt3> molecules2(molecules1);
   Molecules<VectorInt3, 8> molecules3(molecules2);
@@ -261,6 +261,43 @@ TEST_F(MoleculesTest, Constructors){
   EXPECT_EQ(molecules2.getLinkInfo(0,4),molecules3.getLinkInfo(0,4));
 }
 
+TEST_F(MoleculesTest, AssignmentOperator){
+  
+  //setup of a molecules object first
+  Molecules <VectorInt3> molecules1;
+  
+  molecules1.resize(10);
+  molecules1.connect(0,1);
+  molecules1.connect(0,2);
+  molecules1.connect(0,3);
+  molecules1.connect(0,4,2);
+  molecules1[1].setAllCoordinates(2,3,4);
+  
+  //copy to molecules object of same type, and with higher max
+  //connectivity...should both work
+  Molecules<VectorInt3> molecules2;
+  molecules2=molecules1;
+  Molecules<VectorInt3, 8> molecules3;
+  molecules3=molecules2;
+  
+  //check if everything was copied correctly
+  EXPECT_EQ(7,molecules2.getMaxConnectivity());
+  EXPECT_EQ(8,molecules3.getMaxConnectivity());
+  EXPECT_EQ(10,molecules2.size());
+  EXPECT_EQ(10,molecules3.size());
+  EXPECT_EQ(molecules1[1],molecules2[1]);
+  EXPECT_EQ(molecules2[1],molecules3[1]);
+  EXPECT_EQ(molecules1.getLinkInfo(0,4),molecules2.getLinkInfo(0,4));
+  EXPECT_EQ(molecules2.getLinkInfo(0,4),molecules3.getLinkInfo(0,4));
+  
+  
+  //now try to assign to molecules object with too low max connectivity
+  //this should throw an exception
+  Molecules<VectorInt3, 2> molecules4;
+  EXPECT_ANY_THROW( molecules4=molecules1) ;
+  
+}
+
 TEST_F(MoleculesTest,Clear){
   MyIngredients ingredients;
 

From 3bc1d44688e80ed52406d47624da7caae7cd0e99 Mon Sep 17 00:00:00 2001
From: Hauke Rabbel <rabbel@ipfdd.de>
Date: Mon, 11 Apr 2016 14:09:41 +0200
Subject: [PATCH 06/11] *Added output about compiler flags depending on build
 type to CMakeLists.txt *Added information about build type option to Readme
 *Added build type option to configure script

---
 CMakeLists.txt | 33 +++++++++++++++++++++++++++------
 README.md      |  8 ++++++--
 configure      | 22 ++++++++++++++++------
 3 files changed, 49 insertions(+), 14 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index d635415..bb89e15 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -43,16 +43,37 @@ SET (APPLICATION_ID "${APPLICATION_VENDOR_ID}.${PROJECT_NAME}")
 #
 # Compile options
 #
-IF(NOT CMAKE_BUILD_TYPE)
-SET (CMAKE_BUILD_TYPE "Release") #default build type is Release
-SET (CMAKE_VERBOSE_MAKEFILE 0) 
-ENDIF(NOT CMAKE_BUILD_TYPE)
 
+#define possible flags
 SET (CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -msse2 -mssse3 -fexpensive-optimizations ")
 SET (CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} -O3 -msse2 -mssse3 -fexpensive-optimizations ")
 
-SET (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -Wall -g -DDEBUG ")
-SET (CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0 -Wall -g -DDEBUG ")
+SET (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -Wall -DDEBUG ")
+SET (CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0 -Wall -DDEBUG ")
+
+#define value of CMAKE_BUILD_TYPE depending on input
+IF(NOT CMAKE_BUILD_TYPE)
+SET (CMAKE_BUILD_TYPE "Release") #default build type is Release
+ELSEIF(CMAKE_BUILD_TYPE STREQUAL "Release")
+SET (CMAKE_BUILD_TYPE "Release") 
+ELSEIF(CMAKE_BUILD_TYPE STREQUAL "Debug")
+SET (CMAKE_BUILD_TYPE "Debug") 
+ELSE(NOT CMAKE_BUILD_TYPE)
+MESSAGE(FATAL_ERROR "Invalid build type ${CMAKE_BUILD_TYPE} specified.")
+ENDIF(NOT CMAKE_BUILD_TYPE)
+
+#output depending on build type
+IF(CMAKE_BUILD_TYPE STREQUAL "Release")
+SET (CMAKE_VERBOSE_MAKEFILE 0)
+MESSAGE("Build type is ${CMAKE_BUILD_TYPE}")
+MESSAGE("USING CXX COMPILER FLAGS ${CMAKE_CXX_FLAGS_RELEASE}")
+MESSAGE("USING C COMPILER FLAGS ${CMAKE_C_FLAGS_RELEASE}")
+ELSEIF(CMAKE_BUILD_TYPE STREQUAL "Debug")
+SET (CMAKE_VERBOSE_MAKEFILE 1)
+MESSAGE("Build type is ${CMAKE_BUILD_TYPE}")
+MESSAGE("USING CXX COMPILER FLAGS ${CMAKE_CXX_FLAGS_DEBUG}")
+MESSAGE("USING C COMPILER FLAGS ${CMAKE_C_FLAGS_DEBUG}")
+ENDIF(CMAKE_BUILD_TYPE STREQUAL "Release")
 
 #
 # Project Output Paths
diff --git a/README.md b/README.md
index 8db4420..fef1fd7 100644
--- a/README.md
+++ b/README.md
@@ -51,11 +51,15 @@ template metaprogramming in C++.
     # installs the library and headers
     sudo make install #only if you want to install the software after build
 ````
-* If you also want to compile and run the tests, there is a third option, which can be
+* If you also want to compile and run the tests, there is another option, which can be
   passed to either the configure script (first build method), or to cmake (second build method)
   This option is -DLEMONADE_TESTS=ON . You need internet access, because the process will
   download the googletest library
-
+* Another option that can be passed is -DCMAKE_BUILD_TYPE=Release/Debug. The default value 
+  is Release, which uses compiler flags for optimization. If the option "Debug" is chosen,
+  no compiler optimizations are used, compiler warnings are enabled by -Wall, and 
+  debugging information is compiled into the binary with -g. Other flags then "Release",
+  or "Debug" are not allowed and will lead to termination and an error message by cmake.
 
 ## Getting Started
 
diff --git a/configure b/configure
index 691c5b5..8a47e88 100755
--- a/configure
+++ b/configure
@@ -7,16 +7,19 @@ function usage
     echo "-DINSTALLDIR_LEMONADE=/path/to/install/LeMonADE/"
     echo "-DBUILDDIR=/path/to/build/LeMonADE/"
     echo "-DLEMONADE_TESTS=ON/OFF"
+    echo "-DCMAKE_BUILD_TYPE=Release/Debug"
     echo "default build directory is ./build"
     echo "default install directory is /usr/local"
     echo "default option for tests is OFF"
+    echo "default option for build type is Release"
 }
 
 #default values for build directory and install prefix
 PWD_PATH=$(pwd)
 BUILDDIR="build"
-INSTALLDIR_OPTION="-DINSTALLDIR_LEMONADE=/usr/local"
-TEST_ARGUMENT="-DLEMONADE_TESTS=OFF"
+#INSTALLDIR_OPTION="-DINSTALLDIR_LEMONADE=/usr/local"
+#TEST_ARGUMENT="-DLEMONADE_TESTS=OFF"
+CMAKE_ARGUMENTS=""
 
 #parse command line arguments
 for arg in "$@"; do
@@ -27,7 +30,7 @@ for arg in "$@"; do
             ;;
             
 	-DINSTALLDIR_LEMONADE=*)	       	
-			INSTALLDIR_ARGUMENT=${arg}
+			CMAKE_ARGUMENTS+=${arg}" "
 			INSTALLDIR=${arg#*=}
 			echo "Install directory set to "$INSTALLDIR
 			;;
@@ -38,10 +41,16 @@ for arg in "$@"; do
 			;;
 
 	-DLEMONADE_TESTS=*)
-			TEST_ARGUMENT=${arg}
+			CMAKE_ARGUMENTS+=${arg}" "
 			TESTOPTION=${arg#*=}
 			echo "Compiling tests set to "$TESTOPTION
 			;;
+			
+	-DCMAKE_BUILD_TYPE=*)
+			CMAKE_ARGUMENTS+=${arg}" "
+			BUILDOPTION=${arg#*=}
+			echo "Build type set to "$BUILDOPTION
+			;;
 
 	* )                     		
 			echo "unknown parameter"
@@ -58,8 +67,9 @@ if [ ! -d $BUILDDIR ]; then
     mkdir -p $BUILDDIR
 fi
 
+echo "Arguments passed to cmake are "${CMAKE_ARGUMENTS}
 
-(cd $BUILDDIR >/dev/null 2>&1 && cmake $INSTALLDIR_ARGUMENT $TEST_ARGUMENT $PWD_PATH)
+(cd $BUILDDIR >/dev/null 2>&1 && cmake $CMAKE_ARGUMENTS $PWD_PATH)
 
 ########### set up the wrapper makefile ##################
 
@@ -77,7 +87,7 @@ all: ./${BUILDDIR}/Makefile
 .PHONY: all
 
 ./${BUILDDIR}/Makefile:
-	@ (cd ${BUILDDIR} >/dev/null 2>&1 && cmake ${INSTALLDIR_ARGUMENT} ${PWD_PATH})
+	@ (cd ${BUILDDIR} >/dev/null 2>&1 && cmake ${CMAKE_ARGUMENTS} ${PWD_PATH})
 
 clean:
 	@- \$(MAKE) --silent -C ${BUILDDIR} clean || true

From 812917e2a12a90ceb0353828c17bc31ded2167d5 Mon Sep 17 00:00:00 2001
From: Hauke Rabbel <rabbel@ipfdd.de>
Date: Mon, 11 Apr 2016 14:29:45 +0200
Subject: [PATCH 07/11] Added test for copy constructor of molecules to
 FeatureAttributes

---
 tests/feature/TestFeatureAttributes.cpp | 38 +++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/tests/feature/TestFeatureAttributes.cpp b/tests/feature/TestFeatureAttributes.cpp
index 2150564..1fa48a8 100644
--- a/tests/feature/TestFeatureAttributes.cpp
+++ b/tests/feature/TestFeatureAttributes.cpp
@@ -184,3 +184,41 @@ TEST_F(FeatureAttributesTest,ReadAttributesClass)
   
   
 }
+
+TEST_F(FeatureAttributesTest,CopyConstructor)
+{
+	typedef MyIngredients::molecules_type MyMolecules;
+	MyMolecules molecules1;
+	
+	//check if attributes are copied corriectly by copy constructor
+	molecules1.resize(5);
+	molecules1[0].setAttributeTag(1);
+	molecules1[1].setAttributeTag(2);
+	molecules1[2].setAttributeTag(3);
+	molecules1[3].setAttributeTag(4);
+	molecules1[4].setAttributeTag(5);
+	//create new objects from molecules1
+	
+	typedef ConfigureSystem<VectorInt3,Features,8> Config8;
+	typedef Ingredients<Config8> MyIngredients8;
+	typedef MyIngredients8::molecules_type MyMolecules8;
+	MyMolecules molecules2(molecules1);
+	MyMolecules8 molecules3(molecules2);
+	
+	EXPECT_EQ(molecules1[0].getAttributeTag(),molecules2[0].getAttributeTag());
+	EXPECT_EQ(molecules1[0].getAttributeTag(),molecules3[0].getAttributeTag());
+	
+	EXPECT_EQ(molecules1[1].getAttributeTag(),molecules2[1].getAttributeTag());
+	EXPECT_EQ(molecules1[1].getAttributeTag(),molecules3[1].getAttributeTag());
+	
+	EXPECT_EQ(molecules1[2].getAttributeTag(),molecules2[2].getAttributeTag());
+	EXPECT_EQ(molecules1[2].getAttributeTag(),molecules3[2].getAttributeTag());
+	
+	EXPECT_EQ(molecules1[3].getAttributeTag(),molecules2[3].getAttributeTag());
+	EXPECT_EQ(molecules1[3].getAttributeTag(),molecules3[3].getAttributeTag());
+	
+	EXPECT_EQ(molecules1[4].getAttributeTag(),molecules2[4].getAttributeTag());
+	EXPECT_EQ(molecules1[4].getAttributeTag(),molecules3[4].getAttributeTag());
+	
+}
+

From 0fc64c94063310aadaf4bc2be39935159855e7c1 Mon Sep 17 00:00:00 2001
From: Hauke Rabbel <rabbel@ipfdd.de>
Date: Wed, 13 Apr 2016 14:14:44 +0200
Subject: [PATCH 08/11] Removed header Lemonade.h and its usage.

---
 include/LeMonADE/LeMonADE.h                   | 65 -------------------
 .../analyzer/AnalyzerRadiusOfGyration.h       |  4 +-
 projects/SimpleSimulator/main.cpp             | 11 ++--
 3 files changed, 9 insertions(+), 71 deletions(-)
 delete mode 100644 include/LeMonADE/LeMonADE.h

diff --git a/include/LeMonADE/LeMonADE.h b/include/LeMonADE/LeMonADE.h
deleted file mode 100644
index 8519dbb..0000000
--- a/include/LeMonADE/LeMonADE.h
+++ /dev/null
@@ -1,65 +0,0 @@
-/*--------------------------------------------------------------------------------
-    ooo      L   attice-based  |
-  o\.|./o    e   xtensible     | LeMonADE: An Open Source Implementation of the
- o\.\|/./o   Mon te-Carlo      |           Bond-Fluctuation-Model for Polymers
-oo---0---oo  A   lgorithm and  |
- o/./|\.\o   D   evelopment    | Copyright (C) 2013-2015 by 
-  o/.|.\o    E   nvironment    | LeMonADE Principal Developers (see AUTHORS)
-    ooo                        | 
-----------------------------------------------------------------------------------
-
-This file is part of LeMonADE.
-
-LeMonADE is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-LeMonADE is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
-
---------------------------------------------------------------------------------*/
-
-#ifndef LEMONADE_LEMONADE_H
-#define LEMONADE_LEMONADE_H
-
-#include <LeMonADE/core/Ingredients.h>
-#include <LeMonADE/core/ConfigureSystem.h>
-#include <LeMonADE/utility/Vector3D.h>
-#include <LeMonADE/feature/FeatureBondset.h>
-#include <LeMonADE/feature/FeatureBox.h>
-#include <LeMonADE/feature/FeatureAttributes.h>
-#include <LeMonADE/feature/FeatureMoleculesIO.h>
-#include <LeMonADE/analyzer/AnalyzerWriteBfmFile.h>
-#include <LeMonADE/updater/UpdaterReadBfmFile.h>
-#include <LeMonADE/io/FileImport.h>
-#include <LeMonADE/utility/DepthIterator.h>
-#include <LeMonADE/utility/MonomerGroup.h>
-#include <LeMonADE/utility/TaskManager.h>
-#include <LeMonADE/core/MoleculesRead.h>
-#include <LeMonADE/utility/DistanceCalculation.h>
-#include <LeMonADE/utility/NumericFunctions.h>
-#include <LeMonADE/utility/NumericTools.h>
-#include <LeMonADE/Version.h>
-
-/**
- * @file
- *
- * @namespace LeMonADE
- *
- * @brief The namespace <b>LeMonADe</b> of the Monte-Carlo-Algorithm-project
- *
- * @details The name is an abbreviation of
- * * <b>L</b>attice-based <b>e</b>xtensible <b>Mon</b>te-Carlo <b>A</b>lgorithm and <b>D</b>evelopment <b>E</b>nvironment"
- * 
- * @todo do we use the namespace?
- **/
-using namespace Lemonade;
-
-#endif
-
diff --git a/include/LeMonADE/analyzer/AnalyzerRadiusOfGyration.h b/include/LeMonADE/analyzer/AnalyzerRadiusOfGyration.h
index c655c97..4ab36ff 100644
--- a/include/LeMonADE/analyzer/AnalyzerRadiusOfGyration.h
+++ b/include/LeMonADE/analyzer/AnalyzerRadiusOfGyration.h
@@ -30,12 +30,12 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 
 #include <string>
 
-#include <LeMonADE/LeMonADE.h>
+#include <LeMonADE/utility/Vector3D.h>
 #include <LeMonADE/analyzer/AbstractAnalyzer.h>
 #include <LeMonADE/utility/NumericTools.h>
 #include <LeMonADE/utility/NumericFunctions.h>
 #include <LeMonADE/utility/ResultFormattingTools.h>
-#include <LeMonADE/utility/Vector3D.h>
+#include <LeMonADE/utility/MonomerGroup.h>
 
 
 /************************************************************************
diff --git a/projects/SimpleSimulator/main.cpp b/projects/SimpleSimulator/main.cpp
index 73158ff..6d2a0f3 100644
--- a/projects/SimpleSimulator/main.cpp
+++ b/projects/SimpleSimulator/main.cpp
@@ -2,13 +2,16 @@
 
 #include <cstring>
 
-#include <LeMonADE/LeMonADE.h>
 #include <LeMonADE/utility/RandomNumberGenerators.h>
-#include <LeMonADE/updater/UpdaterSimpleSimulator.h>
+#include <LeMonADE/core/ConfigureSystem.h>
+#include <LeMonADE/core/Ingredients.h>
+#include <LeMonADE/feature/FeatureMoleculesIO.h>
+#include <LeMonADE/feature/FeatureAttributes.h>
 #include <LeMonADE/feature/FeatureExcludedVolume.h>
 #include <LeMonADE/feature/FeatureFixedMonomers.h>
-
-
+#include <LeMonADE/utility/TaskManager.h>
+#include <LeMonADE/updater/UpdaterReadBfmFile.h>
+#include <LeMonADE/updater/UpdaterSimpleSimulator.h>
 
 int main(int argc, char* argv[])
 {

From 804d00d6b98e2146c8e57d035e7e4a38051cf4f2 Mon Sep 17 00:00:00 2001
From: Hauke Rabbel <rabbel@ipfdd.de>
Date: Wed, 13 Apr 2016 14:39:18 +0200
Subject: [PATCH 09/11] removed use of header Lemonade.h also in tests.

---
 tests/core/TestCopyOperator.cpp                | 6 +++++-
 tests/feature/TestExcludedVolume.cpp           | 4 +++-
 tests/feature/TestFeatureLattice.cpp           | 3 ++-
 tests/feature/TestFeatureLatticePowerOfTwo.cpp | 3 ++-
 4 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/tests/core/TestCopyOperator.cpp b/tests/core/TestCopyOperator.cpp
index ffcadbb..b3bc534 100644
--- a/tests/core/TestCopyOperator.cpp
+++ b/tests/core/TestCopyOperator.cpp
@@ -35,8 +35,12 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 /*****************************************************************************/
 
 #include "gtest/gtest.h"
+#include<stdint.h>
 
-#include <LeMonADE/LeMonADE.h>
+#include <LeMonADE/core/ConfigureSystem.h>
+#include <LeMonADE/core/Ingredients.h>
+#include <LeMonADE/feature/FeatureMoleculesIO.h>
+#include <LeMonADE/feature/FeatureAttributes.h>
 #include <LeMonADE/feature/FeatureExcludedVolume.h>
 #include <LeMonADE/updater/moves/MoveLocalSc.h>
 
diff --git a/tests/feature/TestExcludedVolume.cpp b/tests/feature/TestExcludedVolume.cpp
index 4ae4ad8..f6b338b 100644
--- a/tests/feature/TestExcludedVolume.cpp
+++ b/tests/feature/TestExcludedVolume.cpp
@@ -27,7 +27,9 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 
 #include "gtest/gtest.h"
 
-#include <LeMonADE/LeMonADE.h>
+#include <LeMonADE/core/ConfigureSystem.h>
+#include <LeMonADE/core/Ingredients.h>
+#include <LeMonADE/feature/FeatureBondset.h>
 #include <LeMonADE/feature/FeatureExcludedVolume.h>
 
 using namespace std;
diff --git a/tests/feature/TestFeatureLattice.cpp b/tests/feature/TestFeatureLattice.cpp
index d274b45..6ba5196 100644
--- a/tests/feature/TestFeatureLattice.cpp
+++ b/tests/feature/TestFeatureLattice.cpp
@@ -27,7 +27,8 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 
 #include "gtest/gtest.h"
 
-#include <LeMonADE/LeMonADE.h>
+#include <LeMonADE/core/ConfigureSystem.h>
+#include <LeMonADE/core/Ingredients.h>
 #include <LeMonADE/feature/FeatureLattice.h>
 
 /*****************************************************************************/
diff --git a/tests/feature/TestFeatureLatticePowerOfTwo.cpp b/tests/feature/TestFeatureLatticePowerOfTwo.cpp
index 02cf748..1521239 100644
--- a/tests/feature/TestFeatureLatticePowerOfTwo.cpp
+++ b/tests/feature/TestFeatureLatticePowerOfTwo.cpp
@@ -27,7 +27,8 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 
 #include "gtest/gtest.h"
 
-#include <LeMonADE/LeMonADE.h>
+#include <LeMonADE/core/ConfigureSystem.h>
+#include <LeMonADE/core/Ingredients.h>
 #include <LeMonADE/feature/FeatureLatticePowerOfTwo.h>
 
 using namespace std;

From 762bdcd906644d139bf7e1147a9ae40a49dc69fe Mon Sep 17 00:00:00 2001
From: Martin Wengenmayr <martin.wengenmayr@mailbox.tu-dresden.de>
Date: Fri, 29 Apr 2016 14:30:43 +0200
Subject: [PATCH 10/11] Bugfix 1.1.1 (#29)

* Fixed copy-paste error in include guard for AmalyzerWriteBfmFileSubgroup

* changed the version number according to last fix in AnalyzerWriteBfmFileSubgroup
---
 CMakeLists.txt                                           | 2 +-
 include/LeMonADE/analyzer/AnalyzerWriteBfmFileSubGroup.h | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index bb89e15..829294b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -34,7 +34,7 @@ SET (APPLICATION_CODENAME "${PROJECT_NAME}")
 SET (APPLICATION_COPYRIGHT_YEARS "2015")
 SET (APPLICATION_VERSION_MAJOR 1)
 SET (APPLICATION_VERSION_MINOR 1)
-SET (APPLICATION_VERSION_PATCH 0)
+SET (APPLICATION_VERSION_PATCH 1)
 SET (APPLICATION_VERSION_TYPE SNAPSHOT)
 SET (APPLICATION_VERSION_STRING "${APPLICATION_VERSION_MAJOR}.${APPLICATION_VERSION_MINOR}.${APPLICATION_VERSION_PATCH}-${APPLICATION_VERSION_TYPE}")
 SET (APPLICATION_ID "${APPLICATION_VENDOR_ID}.${PROJECT_NAME}")
diff --git a/include/LeMonADE/analyzer/AnalyzerWriteBfmFileSubGroup.h b/include/LeMonADE/analyzer/AnalyzerWriteBfmFileSubGroup.h
index 075b654..080b2ca 100644
--- a/include/LeMonADE/analyzer/AnalyzerWriteBfmFileSubGroup.h
+++ b/include/LeMonADE/analyzer/AnalyzerWriteBfmFileSubGroup.h
@@ -26,7 +26,7 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 --------------------------------------------------------------------------------*/
 
 #ifndef LEMONADE_ANALYZER_ANALYZERWRITEBFMFILESUBGROUP_H
-#ifndef LEMONADE_ANALYZER_ANALYZERWRITEBFMFILESUBGROUP_H
+#define LEMONADE_ANALYZER_ANALYZERWRITEBFMFILESUBGROUP_H
 
 #include <set>
 #include <map>

From 3521480db332620b53a0a02ee91449533318564b Mon Sep 17 00:00:00 2001
From: Ron Dockhorn <nordocky@gmail.com>
Date: Fri, 29 Apr 2016 14:33:14 +0200
Subject: [PATCH 11/11] Release 1.1.2

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 829294b..78e8d5e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -34,7 +34,7 @@ SET (APPLICATION_CODENAME "${PROJECT_NAME}")
 SET (APPLICATION_COPYRIGHT_YEARS "2015")
 SET (APPLICATION_VERSION_MAJOR 1)
 SET (APPLICATION_VERSION_MINOR 1)
-SET (APPLICATION_VERSION_PATCH 1)
+SET (APPLICATION_VERSION_PATCH 2)
 SET (APPLICATION_VERSION_TYPE SNAPSHOT)
 SET (APPLICATION_VERSION_STRING "${APPLICATION_VERSION_MAJOR}.${APPLICATION_VERSION_MINOR}.${APPLICATION_VERSION_PATCH}-${APPLICATION_VERSION_TYPE}")
 SET (APPLICATION_ID "${APPLICATION_VENDOR_ID}.${PROJECT_NAME}")