Merge branch 'Release-2.2.2'

CHANGELOG.md

@@ -6,7 +6,7 @@
 * only documentation of principal version changes in CHANGELOG
 
 LeMonADE 1.0
-* bare copy of LeMonADE library from ITP (Leibniz-Institute for Polymer Research IPF) with basic functinonalities
+* bare copy of LeMonADE library from ITP (Leibniz-Institute of Polymer Research Dresden IPF) with basic functionalities
 
 LeMonADE 2.0
 * adding abstract system setup Updater: UpdaterAbstractCreate
@@ -25,3 +25,7 @@ LeMonADE 2.2
 * add analyzers for the calculation of the mean-square displacement
 * add various features and moves to enable reactive and reversible bonds
 
+LeMonADE 2.2.2
+* HotFix for default R250 values
+* ColdFix for implementation of RNG Mersenne Twister 
+* ColdFix for ResultFormattingTools

CMakeLists.txt

@@ -31,10 +31,10 @@ CMAKE_MINIMUM_REQUIRED (VERSION 2.6.2)
 PROJECT (LeMonADE)
 SET (APPLICATION_NAME "LeMonADE")
 SET (APPLICATION_CODENAME "${PROJECT_NAME}")
-SET (APPLICATION_COPYRIGHT_YEARS "2013-2020")
+SET (APPLICATION_COPYRIGHT_YEARS "2013-2021")
 SET (APPLICATION_VERSION_MAJOR "2")
 SET (APPLICATION_VERSION_MINOR "2")
-SET (APPLICATION_VERSION_PATCH "1")
+SET (APPLICATION_VERSION_PATCH "2")
 
 
 #

README.md

@@ -103,6 +103,8 @@ Find the information about active developers, former contributors, and people wh
 ## References
 
 This library has been used in the following publications (without guarantee for completeness)
+* *"Multimolecular Structure Formation with Linear Dendritic Copolymers"*; M. Wengenmayr, R. Dockhorn, J.-U. Sommer; [Macromolecules XX, XXXX-XXXX (2021)](https://doi.org/10.1021/acs.macromol.1c00226)
+* *"Analysis of the Gel Point of Polymer Model Networks by Computer Simulations"*; M. Lang, T. Müller; [Macromolecules 53, 498-512 (2020)](https://doi.org/10.1021/acs.macromol.9b02217)
 * *"Polyolefins Formed by Chain Walking Catalysis—A Matter of Branching Density Only?"*; R. Dockhorn, L. Plüschke, M. Geisler, J. Zessin, P. Lindner, R. Mundil, J. Merna, J.-U. Sommer, A. Lederer; [J. Am. Chem. Soc. 141, 15586–15596 (2019)](https://pubs.acs.org/doi/10.1021/jacs.9b06785)
 * *"Tendomers – force sensitive bis-rotaxanes with jump-like deformation behavior"*; T. Müller, J.-U. Sommer, M. Lang; [Soft Matter, 15, 3671-3679  (2019)](https://doi.org/10.1039/C9SM00292H)
 * *"Dendrimers in Solution of Linear Polymers: Crowding Effects"*; M. Wengenmayr, R. Dockhorn, J.-U. Sommer; [Macromolecules 52, 2616–2626 (2019)](https://doi.org/10.1021/acs.macromol.9b00010)

include/LeMonADE/Version.h

@@ -37,12 +37,12 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 
 #define APPLICATION_NAME               "LeMonADE"
 #define APPLICATION_CODENAME           "LeMonADE"
-#define APPLICATION_COPYRIGHT_YEARS    "2013-2020"
+#define APPLICATION_COPYRIGHT_YEARS    "2013-2021"
 #define APPLICATION_VERSION_MAJOR      2
 #define APPLICATION_VERSION_MINOR      2
-#define APPLICATION_VERSION_PATCH      1
+#define APPLICATION_VERSION_PATCH      2
 #define APPLICATION_VERSION_TYPE       "Release"
-#define APPLICATION_VERSION_STRING     "2.2.1-(C)2013-2020-Release"
+#define APPLICATION_VERSION_STRING     "2.2.2-(C)2013-2021-Release"
 #define APPLICATION_ID                 "LeMonADE.LeMonADE"
 
 #ifndef APPLICATION_VERSION_MAJOR

include/LeMonADE/analyzer/AnalyzerAbstractDump.h

@@ -15,8 +15,6 @@
 #include <LeMonADE/analyzer/AbstractAnalyzer.h>
 #include <LeMonADE/utility/Vector3D.h>
 #include <LeMonADE/utility/ResultFormattingTools.h>
-#include <LeMonADE/utility/MonomerGroup.h>
-#include <LeMonADE/utility/DistanceCalculation.h>
 
 /*************************************************************************
  * definition of AnalyzerAbstractDump class
@@ -98,8 +96,12 @@ template < class IngredientsType , class T > class AnalyzerAbstractDump : public
 	uint32_t getNumberOfColumns(){ return NColumns; }
 	//! set the buffer size for dumping data 
 	void setBufferSize(uint32_t bufferSize_){ bufferSize=bufferSize_;}
-        //! get the buffer size
-        uint32_t getBufferSize(){return bufferSize;}
+	//! get the buffer size
+	uint32_t getBufferSize(){return bufferSize;}
+	//! get the variable isFirstFileDump 
+	bool getIsFirstFileDump() const { return isFirstFileDump; }  
+	//! reset the variable isFirstFileDump to false (could be used if the filename changes in between data dumpings)
+	void resetIsFirstFileDump() {isFirstFileDump=true;}
 };
 
 /*************************************************************************

include/LeMonADE/analyzer/AnalyzerWriteBfmFile.h

@@ -134,6 +134,11 @@ class AnalyzerWriteBfmFile: public AbstractAnalyzer
    *
    **/
   virtual void cleanup(){};
+protected: 
+
+  //! set the name of the file for output which only works for the overwrite case 
+  void setFilename(std::string filename){_filename=filename;}
+
 private:
   //! Write Writes that only need to be in the header
   void writeHeader();

include/LeMonADE/core/Molecules.h

@@ -133,7 +133,7 @@ template < class Vertex, uint max_connectivity = 7, class Edge = int > class Mol
    *
    * @return The actual time in the graph.
    */
-  const uint64_t 	getAge() const 			{return myAge;}
+  uint64_t 	getAge() const 			{return myAge;}
 
 
   /**

include/LeMonADE/feature/FeatureBondset.h

@@ -223,17 +223,15 @@ class FeatureBondset : public Feature
   template<class IngredientsType,class MoveLabelType>
   bool checkMove(const IngredientsType& ingredients, const MoveLabelBase<MoveLabelType>& move) const
   {
-
-	  //get the number of bond partners of the particle to be moved
-          int32_t MonID=move.getIndex()+move.getDir();
-	  if ( MonID == -1 ) return false;
-	  uint32_t ID=move.getConnectedLabel();
-          const typename IngredientsType::molecules_type& molecules=ingredients.getMolecules();
-	  if (ID == 0 ) return true; 
-	  ID--;
-          auto bond(molecules[MonID].getVector3D()-molecules[ID].getVector3D());
-	  if (!bondset.isValidStrongCheck( bond ) ) return false; 
-      if ( bond.getLength()>3.) return false; // otherwise I could get xtraps 
+      //get the number of bond partners of the particle to be moved
+      int32_t MonID=move.getIndex()+move.getDir();
+      if ( MonID == -1 ) return false;
+      uint32_t ID=move.getConnectedLabel();
+      const typename IngredientsType::molecules_type& molecules=ingredients.getMolecules();
+      if (ID == 0 ) return true; 
+      ID--;
+      auto bond(molecules[MonID].getVector3D()-molecules[ID].getVector3D());
+      if (!bondset.isValidStrongCheck( bond ) ) return false; 
       return true;
   }
 

include/LeMonADE/feature/FeatureLabel.h

@@ -55,7 +55,7 @@ class MonomerLabel
 	MonomerLabel():label(0){}
 
 	//! is labeled 
-	const uint32_t getLabel() const {return label;}
+	uint32_t getLabel() const {return label;}
 	//! set label on/off
 	void setLabel(uint32_t label_){ label=label_;}