Merge branch 'release-1.1.2'

CMakeLists.txt

@@ -34,16 +34,46 @@ 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}")
 
 
 #
-# Debugging Options
-#
-SET (CMAKE_VERBOSE_MAKEFILE 0) # Use 1 for debugging, 0 for release
+# Compile options
+#
+
+#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 "${CMAKE_CXX_FLAGS_DEBUG} -O0 -Wall -DDEBUG ")
+SET (CMAKE_C_FLAGS_DEBUG "${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

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
 

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

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>
 
 
 /************************************************************************

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.