Merge pull request #119 from Bondoki/master

Patch LeMonADE Version 2.2.0

CMakeLists.txt

@@ -3,7 +3,7 @@
 #   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   D   evelopment    | Copyright (C) 2013-2020 by
 #   o/.|.\o    E   nvironment    | LeMonADE Principal Developers (see AUTHORS)
 #     ooo                        |
 # ---------------------------------------------------------------------------------
@@ -31,25 +31,22 @@ CMAKE_MINIMUM_REQUIRED (VERSION 2.6.2)
 PROJECT (LeMonADE)
 SET (APPLICATION_NAME "LeMonADE")
 SET (APPLICATION_CODENAME "${PROJECT_NAME}")
-SET (APPLICATION_COPYRIGHT_YEARS "2019")
-SET (APPLICATION_VERSION_MAJOR 2)
-SET (APPLICATION_VERSION_MINOR 1)
-SET (APPLICATION_VERSION_PATCH 0)
-SET (APPLICATION_VERSION_TYPE SNAPSHOT)
-SET (APPLICATION_VERSION_STRING "${APPLICATION_VERSION_MAJOR}.${APPLICATION_VERSION_MINOR}.${APPLICATION_VERSION_PATCH}-${APPLICATION_VERSION_TYPE}")
-SET (APPLICATION_ID "${APPLICATION_VENDOR_ID}.${PROJECT_NAME}")
+SET (APPLICATION_COPYRIGHT_YEARS "2013-2020")
+SET (APPLICATION_VERSION_MAJOR "2")
+SET (APPLICATION_VERSION_MINOR "2")
+SET (APPLICATION_VERSION_PATCH "0")
 
 
 #
 # Compile options
 #
 
 #define possible flags
-SET (CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -msse2 -mssse3 -std=c++11 -fexpensive-optimizations ")
-SET (CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} -O3 -msse2 -mssse3 -std=c++11 -fexpensive-optimizations ")
+SET (CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -msse2 -mssse3 -std=c++11 -fexpensive-optimizations -Wno-error=narrowing")
+SET (CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} -O3 -msse2 -mssse3 -std=c++11 -fexpensive-optimizations -Wno-error=narrowing")
 
-SET (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -std=c++11 -Wall -Wextra -DDEBUG ")
-SET (CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0 -std=c++11 -Wall -Wextra -DDEBUG ")
+SET (CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -std=c++11 -Wall -Wextra -DDEBUG -Wno-error=narrowing")
+SET (CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -O0 -std=c++11 -Wall -Wextra -DDEBUG -Wno-error=narrowing")
 
 #define value of CMAKE_BUILD_TYPE depending on input
 IF(NOT CMAKE_BUILD_TYPE)
@@ -84,14 +81,22 @@ SET (LIBRARY_OUTPUT_PATH "${CMAKE_BINARY_DIR}/lib")
 SET (LEMONADE_INCLUDE_DIR "${LEMONADE_DIR}/include")
 SET (LEMONADE_LIBRARY_DIR ${LIBRARY_OUTPUT_PATH})
 
+#
+# Configure and replace Version.h with updated cmake info
+#
+SET (APPLICATION_VERSION_TYPE "${CMAKE_BUILD_TYPE}")
+SET (APPLICATION_VERSION_STRING "${APPLICATION_VERSION_MAJOR}.${APPLICATION_VERSION_MINOR}.${APPLICATION_VERSION_PATCH}-(C)${APPLICATION_COPYRIGHT_YEARS}-${APPLICATION_VERSION_TYPE}")
+SET (APPLICATION_ID "${APPLICATION_NAME}.${PROJECT_NAME}")
+configure_file( ${LEMONADE_DIR}/include/LeMonADE/Version.h.in ${LEMONADE_DIR}/include/LeMonADE/Version.h @ONLY)
+
+
 #
 # Project Search Paths
 #
 LIST (APPEND CMAKE_PREFIX_PATH "${LEMONADE_DIR}")
 INCLUDE_DIRECTORIES("${LEMONADE_DIR}/include")
 
 
-
 #
 # add Build Targets
 #

include/LeMonADE/Version.h

@@ -3,7 +3,7 @@
   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   D   evelopment    | Copyright (C) 2013-2020 by
   o/.|.\o    E   nvironment    | LeMonADE Principal Developers (see AUTHORS)
     ooo                        |
 ----------------------------------------------------------------------------------
@@ -25,9 +25,44 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 
 --------------------------------------------------------------------------------*/
 
+/*
+ * AUTO-GENERATION WARNING:
+ *     "Version.h" has been automatically generated from "Version.h.in".
+ *     DO NOT edit "Version.h", as any changes will be automatically discarded.
+ */
+
+
 #ifndef LEMONADE_VERSION_H
 #define LEMONADE_VERSION_H
 
-const double LEMONADE_VERSION = 2.0;
+#define APPLICATION_NAME               "LeMonADE"
+#define APPLICATION_CODENAME           "LeMonADE"
+#define APPLICATION_COPYRIGHT_YEARS    "2013-2020"
+#define APPLICATION_VERSION_MAJOR      2
+#define APPLICATION_VERSION_MINOR      2
+#define APPLICATION_VERSION_PATCH      0
+#define APPLICATION_VERSION_TYPE       "Release"
+#define APPLICATION_VERSION_STRING     "2.2.0-(C)2013-2020-Release"
+#define APPLICATION_ID                 "LeMonADE.LeMonADE"
+
+#ifndef APPLICATION_VERSION_MAJOR
+#   define APPLICATION_VERSION_MAJOR 0
+#endif
+
+#ifndef APPLICATION_VERSION_MINOR
+#   define APPLICATION_VERSION_MINOR 0
+#endif
+
+#ifndef APPLICATION_VERSION_PATCH
+#   define APPLICATION_VERSION_PATCH 0
+#endif
+
+#ifndef APPLICATION_VERSION_TYPE
+#   define APPLICATION_VERSION_TYPE "RELEASE"
+#endif
+
+#define APPLICATION_VERSION_MAJOR_MINOR      2.2
+
+const double LEMONADE_VERSION = APPLICATION_VERSION_MAJOR_MINOR;
 
 #endif

include/LeMonADE/Version.h.in

@@ -0,0 +1,68 @@
+/*--------------------------------------------------------------------------------
+    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) 2013-2020 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/>.
+
+--------------------------------------------------------------------------------*/
+
+/*
+ * AUTO-GENERATION WARNING:
+ *     "Version.h" has been automatically generated from "Version.h.in".
+ *     DO NOT edit "Version.h", as any changes will be automatically discarded.
+ */
+
+
+#ifndef LEMONADE_VERSION_H
+#define LEMONADE_VERSION_H
+
+#cmakedefine APPLICATION_NAME               "@APPLICATION_NAME@"
+#cmakedefine APPLICATION_CODENAME           "@APPLICATION_CODENAME@"
+#cmakedefine APPLICATION_COPYRIGHT_YEARS    "@APPLICATION_COPYRIGHT_YEARS@"
+#define APPLICATION_VERSION_MAJOR      @APPLICATION_VERSION_MAJOR@
+#define APPLICATION_VERSION_MINOR      @APPLICATION_VERSION_MINOR@
+#define APPLICATION_VERSION_PATCH      @APPLICATION_VERSION_PATCH@
+#cmakedefine APPLICATION_VERSION_TYPE       "@APPLICATION_VERSION_TYPE@"
+#cmakedefine APPLICATION_VERSION_STRING     "@APPLICATION_VERSION_STRING@"
+#cmakedefine APPLICATION_ID                 "@APPLICATION_ID@"
+
+#ifndef APPLICATION_VERSION_MAJOR
+#   define APPLICATION_VERSION_MAJOR 0
+#endif
+
+#ifndef APPLICATION_VERSION_MINOR
+#   define APPLICATION_VERSION_MINOR 0
+#endif
+
+#ifndef APPLICATION_VERSION_PATCH
+#   define APPLICATION_VERSION_PATCH 0
+#endif
+
+#ifndef APPLICATION_VERSION_TYPE
+#   define APPLICATION_VERSION_TYPE "RELEASE"
+#endif
+
+#define APPLICATION_VERSION_MAJOR_MINOR      @APPLICATION_VERSION_MAJOR@.@APPLICATION_VERSION_MINOR@
+
+const double LEMONADE_VERSION = APPLICATION_VERSION_MAJOR_MINOR;
+
+#endif

include/LeMonADE/feature/FeatureWall.h

@@ -68,7 +68,7 @@ class Wall
     }
 
     //! setter function for the base vector of the wall
-    VectorInt3 setBase(uint32_t baseX_, uint32_t baseY_, uint32_t baseZ_) {
+    void setBase(uint32_t baseX_, uint32_t baseY_, uint32_t baseZ_) {
         base.setAllCoordinates(baseX_,baseY_,baseZ_);
     }
 
@@ -78,7 +78,7 @@ class Wall
     }
 
     //! setter function for the normal vector of the wall
-    VectorInt3 setNormal(uint32_t norX_, uint32_t norY_, uint32_t norZ_) {
+    void setNormal(uint32_t norX_, uint32_t norY_, uint32_t norZ_) {
       VectorInt3 test(norX_, norY_, norZ_);
       if(test==VectorInt3(1,0,0) || test==VectorInt3(0,1,0) || test==VectorInt3(0,0,1) ){
         normal.setAllCoordinates(norX_,norY_,norZ_);

include/LeMonADE/utility/AttributeTags.h

@@ -102,7 +102,7 @@ class MonomerLabel
   /**
   * @brief assignment operator
   */
-  MonomerLabel& operator= ( const MonomerLabel &Label )
+  void operator= ( const MonomerLabel &Label )
   { 
     chainID = Label.chainID;
     nLabels = Label.nLabels;
@@ -132,17 +132,17 @@ class MonomerLabel
   //! set the chain ID the Label belongs to 
   void     setchainID(const uint32_t chainID_){chainID=chainID_ ;}
   //! get the chain ID the Label belongs to
-  const uint32_t& getchainID(		       ) const { return chainID  ;}
+  const uint32_t getchainID(		       ) const { return chainID  ;}
 
   //! set the number of labels sitting on the monomer 
   void     setnLabels(const uint32_t nLabels_){nLabels=nLabels_ ;}
   //! get the number of labels sitting on the monomer 
-  const uint32_t& getnLabels(		       ) const { return nLabels  ;}
+  const uint32_t getnLabels(		       ) const { return nLabels  ;}
 
   //! set the ID of the label(s) on the monomer
   void     setlabelID(const uint32_t labelID_){labelID=labelID_ ;}
   //! get the ID of the label(s) on the monomer
-  const uint32_t& getlabelID(		       ) const { return labelID  ;}
+  const uint32_t getlabelID(		       ) const { return labelID  ;}
 
   //! set the chain ID, number of labels and label id 
   void     setAll(const uint32_t chainID_,const uint32_t nLabels_,const uint32_t labelID_)

projects/SimpleSimulator/main.cpp

@@ -12,6 +12,7 @@
 #include <LeMonADE/utility/TaskManager.h>
 #include <LeMonADE/updater/UpdaterReadBfmFile.h>
 #include <LeMonADE/updater/UpdaterSimpleSimulator.h>
+#include <LeMonADE/Version.h>
 
 int main(int argc, char* argv[])
 {
@@ -46,6 +47,22 @@ int main(int argc, char* argv[])
 		if(argc==5) outfile=argv[4];
 		else outfile=argv[1];
 	}
+
+	std::cout << APPLICATION_NAME " is free software: you can redistribute it and/or modify" << std::endl
+              << "it under the terms of the GNU General Public License as published by" << std::endl
+              << "the Free Software Foundation, either version 3 of the License, or" << std::endl
+              << "(at your option) any later version." << std::endl
+              << APPLICATION_NAME " is distributed in the hope that it will be useful," << std::endl
+              << "but WITHOUT ANY WARRANTY; without even the implied warranty of" << std::endl
+              << "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the" << std::endl
+              << "GNU General Public License for more details." << std::endl
+              << "You should have received a copy of the GNU General Public License" << std::endl
+              << "along with " << APPLICATION_NAME << ". If not, see <http://www.gnu.org/licenses/>." << std::endl << std::endl;
+
+    	std::cout << APPLICATION_NAME << " " << APPLICATION_VERSION_STRING << std::endl
+              << "Copyright (C) " << APPLICATION_COPYRIGHT_YEARS << std::endl
+              << "LeMonADE Version " <<  LEMONADE_VERSION << std::endl << std::endl;
+
 
 	//seed the globally available random number generators
 	RandomNumberGenerators rng;

tests/core/TestIngredients.cpp

@@ -48,7 +48,26 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 
 using namespace std;
 
-TEST(IngredientsTest, Constructors){
+class IngredientsTest: public ::testing::Test{
+
+public:
+  //redirect cout output
+  virtual void SetUp(){
+    originalBuffer=cout.rdbuf();
+    cout.rdbuf(tempStream.rdbuf());
+  };
+
+  //restore original output
+  virtual void TearDown(){
+    cout.rdbuf(originalBuffer);
+  };
+
+  private:
+    std::streambuf* originalBuffer;
+    std::ostringstream tempStream;
+};
+
+TEST_F(IngredientsTest, Constructors){
 
 	typedef LOKI_TYPELIST_2(FeatureBox, FeatureBondset<>) Features;
 	typedef ConfigureSystem<VectorInt3,Features,3> Config;
@@ -61,7 +80,7 @@ TEST(IngredientsTest, Constructors){
 	EXPECT_STREQ("new_lemonade" ,ingredientsWithOutName.getName().c_str());
 }
 
-TEST(IngredientsTest, GetterAndSetter){
+TEST_F(IngredientsTest, GetterAndSetter){
 
 		typedef LOKI_TYPELIST_2(FeatureBox, FeatureBondset<>) Features;
 		typedef ConfigureSystem<VectorInt3,Features,3> Config;
@@ -82,7 +101,7 @@ TEST(IngredientsTest, GetterAndSetter){
 
 }
 
-TEST(IngredientsTest, printMetaData){
+TEST_F(IngredientsTest, printMetaData){
 	typedef LOKI_TYPELIST_2(FeatureBox, FeatureBondset<>) Features;
 	typedef ConfigureSystem<VectorInt3,Features,3> Config;
 	typedef Ingredients < Config> MyIngredients;
@@ -100,7 +119,7 @@ TEST(IngredientsTest, printMetaData){
 }
 
 
-TEST(IngredientsTest, synchronize_noargument){
+TEST_F(IngredientsTest, synchronize_noargument){
 	typedef LOKI_TYPELIST_2(FeatureBox, FeatureBondset<>) Features1;
 	typedef ConfigureSystem<VectorInt3,Features1,3> Config1;
 	typedef Ingredients < Config1> MyIngredients1;
@@ -185,7 +204,7 @@ TEST(IngredientsTest, synchronize_noargument){
 	EXPECT_NO_THROW(ingredients2.synchronize());
 }
 
-TEST(IngredientsTest, synchronize_withargument){
+TEST_F(IngredientsTest, synchronize_withargument){
 	typedef LOKI_TYPELIST_2(FeatureBox, FeatureBondset<>) Features1;
 	typedef ConfigureSystem<VectorInt3,Features1,3> Config1;
 	typedef Ingredients < Config1> MyIngredients1;

tests/feature/TestFeatureAttributes.cpp

@@ -80,9 +80,9 @@ class FeatureAttributesTest: public ::testing::Test{
     cout.rdbuf(originalBuffer);
   };
 
-private:
-  std::streambuf* originalBuffer;
-  std::ostringstream tempStream;
+  private:
+    std::streambuf* originalBuffer;
+    std::ostringstream tempStream;
 };
 
 TEST_F(FeatureAttributesTest,MonomerAttributeTag)
@@ -248,16 +248,19 @@ TEST_F(FeatureAttributesTest,MonomerLabel)
   typedef MyIngredientsTags::molecules_type MyMolecules1;
   MyMolecules1 molecules9;
 
-  //check if attributes are copied corriectly by copy constructor
+  //check if attributes are copied correctly by copy constructor
   molecules9.resize(3);
+
   //if it runs throught then there is no error in the assign constructor
   molecules9[0].setAttributeTag(MonomerLabel(1,23,45));
+
   EXPECT_EQ( molecules9[0].getAttributeTag().getchainID(), 1);
   EXPECT_EQ( molecules9[0].getAttributeTag().getnLabels(),23);
   EXPECT_EQ( molecules9[0].getAttributeTag().getlabelID(),45);
+
   molecules9[1].setAttributeTag(MonomerLabel(3,2,4));
 
-  //negative falues do not make much sense
+  //negative values do not make much sense
   EXPECT_THROW(molecules9[2].setAttributeTag(MonomerLabel(12,5,-1)), std::runtime_error);
   EXPECT_THROW(molecules9[2].setAttributeTag(MonomerLabel(12,-5,1)), std::runtime_error);
   EXPECT_THROW(molecules9[2].setAttributeTag(MonomerLabel(-12,5,1)), std::runtime_error);
@@ -307,7 +310,6 @@ TEST_F(FeatureAttributesTest,ReadAttributesClassForMonomerLabels)
   stream5<<"\n1-5:c\n";
   EXPECT_THROW(read.execute(),std::runtime_error);
 
-
 }
 
 

tests/feature/TestFeatureWall.cpp

@@ -92,6 +92,7 @@ TEST(TestFeatureWall,Moves)
 
     //build wall in y-z-plane at x=2 -> x=1 should be forbidden
     Wall wall1;
+
     wall1.setBase(2,0,0);
     // check forbidden nomal vector: must be a unit vector! P(1,0,0)
     EXPECT_ANY_THROW(wall1.setNormal(2,0,0));