From 708d738e893dcc1bd8b6fdc219dc9495c19789d3 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Mon, 26 Apr 2021 09:04:30 +0200
Subject: [PATCH 01/70] add a tendomer specific updater for reading in
 crosslink connections

---
 .../UpdaterReadCrosslinkConnectionsTendomer.h | 231 ++++++++++++++++++
 1 file changed, 231 insertions(+)
 create mode 100644 include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h

diff --git a/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h b/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h
new file mode 100644
index 0000000..b129114
--- /dev/null
+++ b/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h
@@ -0,0 +1,231 @@
+/*--------------------------------------------------------------------------------
+    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/>.
+
+--------------------------------------------------------------------------------*/
+#include <string>
+#include <iostream>
+#include <fstream>
+#include <stdexcept>
+#include <vector>
+#include <math.h>
+#include <algorithm>
+#include <LeMonADE/updater/AbstractUpdater.h>
+#include <LeMonADE/utility/DistanceCalculation.h>
+
+/**
+ * @class UpdaterReadCrosslinkConnectionsTendomer
+ * @brief reads in connections for a system made of linear chains and crosslinker 
+ * 
+ * @details 
+ *   -the input file needs to have a format like:
+ *     #Time, ChainID, MonID1, P1X, P1Y, P1Z, MonID2, P2X, P2Y, P2Z
+ *   -the chains are before the crosslinks in the bfm file
+ *   -the chain length must be at least 1 
+ * 
+ */
+
+template <class IngredientsType>
+class UpdaterReadCrosslinkConnectionsTendomer : public AbstractUpdater
+{
+public:
+    UpdaterReadCrosslinkConnectionsTendomer(
+        IngredientsType& ing_, 
+        const std::string input_, 
+        const double stepwidth_, 
+        const double minConversion_): 
+        ing(ing_), 
+        input(input_), 
+        stepwidth(stepwidth_), 
+        minConversion(minConversion_),
+        nExecutions(0){};
+    virtual void initialize();
+    virtual bool execute();
+    virtual void cleanup(){};
+
+private:
+  //! container storing system information about monomers
+  IngredientsType& ing;
+
+  //! container storing system information about monomers
+  IngredientsType initialIng;
+
+  //! input of the cross link positions and so on..
+  const std::string input;
+
+  //!conversion step used in the execute function to increase the conversion 
+  const double stepwidth;
+
+  //! minimal conversion to be read in before further analyse
+  double minConversion;
+
+  //!number of maximum connections for a cross link
+  uint32_t NMaxConnection;
+
+  //!numbe of monomers per chain 
+  uint32_t NMonomerPerChain;
+
+  //!number of executions;
+  uint32_t nExecutions;
+
+  //! connects the cross link to the chain
+  bool ConnectCrossLinkToChain(uint32_t MonID, uint32_t chainID);
+  
+  //!bond Table 
+  std::map<std::pair<uint32_t,uint32_t>,std::vector<uint32_t> > bondTable;
+};
+
+
+template <class IngredientsType>
+bool  UpdaterReadCrosslinkConnectionsTendomer<IngredientsType>::ConnectCrossLinkToChain(uint32_t MonID, uint32_t chainID){
+    std::pair<uint32_t,uint32_t> key(MonID,chainID-1);
+    if (bondTable.find(key) != bondTable.end()){
+        if ( !ing.getMolecules().areConnected( MonID,bondTable.at(key)[0] ) ){
+            ing.modifyMolecules().connect(MonID,bondTable.at(key)[0] );
+            // std::cout << MonID <<"\t" << chainID-1 <<"\t" <<bondTable.at(key)[0]<<std::endl;
+            return true ; 
+        }
+        //chain can only have one neighbor (without this statement a more or less random partner would be connected to the structure !!)
+        if ( bondTable.at(key).size()>1 ) {
+            ing.modifyMolecules().connect(MonID,bondTable.at(key)[1] );
+            // std::cout << MonID <<"\t" << chainID-1 <<"\t" <<bondTable.at(key)[1]<<std::endl;
+            return true ; 
+        }
+    }
+    return false; 
+}
+
+/**
+ * @brief read in connections up to the minimum conversion given 
+ * */
+template <class IngredientsType>
+void UpdaterReadCrosslinkConnectionsTendomer<IngredientsType>::initialize(){
+    //assume a stochiometric mixture
+    NMaxConnection=4*ing.getNumCrossLinkers();
+    NMonomerPerChain = 2*ing.getNumMonomersPerChain();
+    std::cout << "Number of maximum connection: " << NMaxConnection << std::endl;
+    //erase bonds between reactive monomers
+    for (uint32_t i =0 ; i <  ing.getMolecules().size(); i++)
+        if (ing.getMolecules()[i].isReactive() )
+            for(size_t j=0; j < ing.getMolecules().getNumLinks(i);j++){
+                uint32_t neighbor(ing.getMolecules().getNeighborIdx(i,j));
+                if (ing.getMolecules()[neighbor].isReactive()){
+                    ing.modifyMolecules().disconnect(i, neighbor );
+                    uint32_t chainMonomer(std::min(i,neighbor) );
+                    uint32_t crosslink(std::max(i,neighbor));
+                    uint32_t chainID( (chainMonomer-chainMonomer%NMonomerPerChain)/NMonomerPerChain);
+                    // std::cout<<"erase: "<<i<<"\t"<<chainID<<"\t"<<neighbor<<"\t"<<chainMonomer<<"\n";
+                    //there is only one situation possible for key(crosslink, chainID ) with more than one entry: pending loop
+                    bondTable[std::pair<uint32_t,uint32_t>(crosslink,chainID) ].push_back(chainMonomer) ;
+                }
+            }
+    std::cout << "Erase " << bondTable.size() << " bonds." <<std::endl;
+    ing.synchronize();
+    initialIng=ing;
+}
+/**
+ * @brief read in connections up tp the next step 
+ * @details Copies the initial ingredients to the current one and adds connections up to the current conversion. 
+ * */
+template <class IngredientsType>
+bool UpdaterReadCrosslinkConnectionsTendomer<IngredientsType>::execute(){
+    //reset the ingredients container to the inital one
+    ing = initialIng;
+    //open input file to the connection table 
+    //! stream reading input file
+    std::ifstream stream;
+    stream.open(input);
+    if (stream.fail())
+      throw std::runtime_error(std::string("error opening input file ") + input + std::string("\n"));
+    bool findStartofData(false);
+    //set head to beginning of the data block
+    // while (!findStartofData){
+    //     std::string line;
+    //     getline(stream, line);
+    //     if (line.empty())
+    //         findStartofData = true;
+    //     else if (line.at(0) == '#') //go to next line
+    //         continue;
+    //     else
+    //         throw std::runtime_error("Wrong input format!");
+    // }
+    std::string line;
+    getline(stream, line);
+    while (line.empty() || line.at(0) == '#' ) 
+        getline(stream, line);
+
+    //current conversion 
+    auto conversion = minConversion + static_cast<double>(nExecutions) * stepwidth;
+    std::cout << "Current conversion is " <<conversion <<std::endl;
+    //read in number of lines to reach the current conversion 
+    //(always start from the initial state and thus read in connectiosn from the beginning)
+    uint32_t ReadNLines = (floor(NMaxConnection * conversion));
+    //counter for the new connections
+    uint32_t NewConnections(0);
+    std::cout << "Start reading " << ReadNLines << " number of lines " << std::endl;
+    while (NewConnections < ReadNLines && stream.good()){
+        std::string line;
+        getline(stream, line);
+        if (line.empty())
+            break;
+        std::stringstream ss;
+        uint32_t Time, createBreak, ChainID, nSegments, MonID1, P1X, P1Y, P1Z, MonID2, P2X, P2Y, P2Z;
+        ss << line;
+        ss >> Time >> createBreak>>  ChainID >> nSegments >>MonID1 >> P1X >> P1Y >> P1Z >> MonID2 >> P2X >> P2Y >> P2Z;
+        // if (NewConnections == 0 )
+        //     std::cout <<  Time << " " << ChainID<< " "
+        //             << MonID1<< " " << P1X << " " << P1Y << " " << P1Z << " " 
+        //             << MonID2<< " " << P2X << " " << P2Y << " " << P2Z << "\n";
+        ing.modifyMolecules().setAge(Time);
+        // std::cout<<"connect: " << MonID1 << "\t" << ChainID<<std::endl;
+        if ( ConnectCrossLinkToChain(MonID1, ChainID+1) ) {
+            // std::cout <<"Connection for Mon1 = "<< MonID1 << " with chainID=" << ChainID <<std::endl;
+        }else if( ConnectCrossLinkToChain(MonID2, ChainID+1) ) {
+            // std::cout <<"Connection for Mon2 = "<< MonID2 << " with chainID=" << ChainID<<std::endl;
+        }else {
+            std::stringstream errormessage;
+            errormessage << "There was no such a connection in the bfm file for monomer ID= " << MonID1  <<" of with ID=" << MonID2 <<  " with chainID=" << ChainID<< "\n";
+            throw std::runtime_error(errormessage.str());
+        }
+        //update positions : I think this is not needed
+        // ing.modifyMolecules()[MonID1].modifyVector3D().setAllCoordinates(P1X, P1Y, P1Z);
+        // if (MonID2 > 0)
+            // ing.modifyMolecules()[MonID2].modifyVector3D().setAllCoordinates(P2X, P2Y, P2Z);
+        NewConnections++;
+    }
+    std::cout << "Read and add " << NewConnections << "/" << NMaxConnection 
+              << " to the system at time "
+              << ing.getMolecules().getAge() << std::endl;
+    ing.synchronize();
+    nExecutions++;
+    std::cout << "UpdaterReadCrosslinkConnectionsTendomer::execute " << nExecutions << " times.\n";
+    //close the filestream and return false if the file has ended and thus the updater has nothing more to do
+    if (stream.eof()) {
+        stream.close();
+        return false;
+    }else{
+        stream.close();
+        return true;
+    }
+}

From 10c91adff1a975e22ba65783b036f9db8cf3cfc2 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Mon, 26 Apr 2021 09:04:56 +0200
Subject: [PATCH 02/70] add a tendomer specific main program

---
 projects/CMakeLists.txt                      |   4 +
 projects/TendomerNetworkForceEquilibrium.cpp | 184 +++++++++++++++++++
 2 files changed, 188 insertions(+)
 create mode 100644 projects/TendomerNetworkForceEquilibrium.cpp

diff --git a/projects/CMakeLists.txt b/projects/CMakeLists.txt
index 08bc816..f7460a7 100644
--- a/projects/CMakeLists.txt
+++ b/projects/CMakeLists.txt
@@ -1,2 +1,6 @@
 add_executable(ForceEquilibrium ForceEquilibrium.cpp)
 target_link_libraries(ForceEquilibrium LeMonADE CommandlineParser )
+
+
+add_executable(TendomerNetworkForceEquilibrium TendomerNetworkForceEquilibrium.cpp)
+target_link_libraries(TendomerNetworkForceEquilibrium LeMonADE CommandlineParser )
\ No newline at end of file
diff --git a/projects/TendomerNetworkForceEquilibrium.cpp b/projects/TendomerNetworkForceEquilibrium.cpp
new file mode 100644
index 0000000..3d69388
--- /dev/null
+++ b/projects/TendomerNetworkForceEquilibrium.cpp
@@ -0,0 +1,184 @@
+/*--------------------------------------------------------------------------------
+    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/>.
+
+--------------------------------------------------------------------------------*/
+
+/****************************************************************************** 
+ * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
+ * author: Toni Müller
+ * email: mueller-toni@ipfdd.de
+ * project: LeMonADE-Phantom Modulus
+ *****************************************************************************/
+#include <iostream>
+#include <vector>
+#include <bitset>
+
+#include <LeMonADE/core/Ingredients.h>
+#include <LeMonADE/updater/UpdaterReadBfmFile.h>
+#include <LeMonADE/analyzer/AnalyzerWriteBfmFile.h>
+#include <LeMonADE/feature/FeatureMoleculesIOUnsaveCheck.h>
+#include <LeMonADE/feature/FeatureReactiveBonds.h>
+#include <LeMonADE/feature/FeatureBox.h>
+#include <LeMonADE/feature/FeatureLabel.h>
+#include <LeMonADE/utility/TaskManager.h>
+
+#include <extern/catchorg/clara/clara.hpp>
+
+#include <LeMonADE_PM/updater/UpdaterForceBalancedPosition.h>
+#include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
+#include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
+#include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
+#include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUp.h>
+#include <LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h>
+
+
+int main(int argc, char* argv[]){
+	try{
+		///////////////////////////////////////////////////////////////////////////////
+		///parse options///
+		std::string inputBFM("init.bfm");
+		std::string outputDataPos("CrosslinkPosition.dat");
+		std::string outputDataDist("ChainExtensionDistribution.dat");
+		std::string inputConnection("BondCreationBreaking.dat");
+		std::string feCurve("");
+		double relaxationParameter(10.);
+		double threshold(0.5);
+		double stepwidth(1.0);
+		double minConversion(50.0);
+		
+		bool showHelp = false;
+		auto parser
+			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"          ] ("(required)Input filename of the bfm file"                                    ).required()
+			| clara::detail::Opt(     inputConnection, "inputConnection (=BondCreationBreaking.dat)"     ) ["-d"]["--inputConnection"] ("used for the time development of the topology. "                             ).required()
+			| clara::detail::Opt(       outputDataPos, "outputDataPos (=CrosslinkPosition.dat)"          ) ["-o"]["--outputPos"      ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
+			| clara::detail::Opt(      outputDataDist, "outputDataDist (=ChainExtensionDistribution.dat)") ["-c"]["--outputDist"     ] ("(optional) Output filename of the chain extension distribution."             ).optional()
+			| clara::detail::Opt(           stepwidth, "stepwidth"                                       ) ["-s"]["--stepwidth"      ] ("(optional) Width for the increase in percentage. Default: 1%."               ).optional()
+			| clara::detail::Opt(       minConversion, "minConversion"                                   ) ["-u"]["--minConversion"  ] ("(optional) Minimum conversion to be read in. Default: 50%."                  ).optional()
+			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"      ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
+			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"        ] ("(optional) Force-Extension curve. Default \"\"."                             ).required()
+			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"          ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
+			| clara::Help( showHelp );
+		
+	    auto result = parser.parse( clara::Args( argc, argv ) );
+	    
+	    if( !result ) {
+	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
+	      exit(1);
+	    }else if(showHelp == true){
+	      std::cout << "Simulator to connect linear chains with single monomers of certain functionality"<< std::endl;
+	      parser.writeToStream(std::cout);
+	      exit(0);
+	    }else{
+	      std::cout << "outputData            : " << outputDataPos          << std::endl;
+	      std::cout << "outputDataDist        : " << outputDataDist         << std::endl;
+	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
+	      std::cout << "inputConnection       : " << inputConnection        << std::endl; 
+	      std::cout << "stepwidth             : " << stepwidth              << std::endl;
+	      std::cout << "minConversion         : " << minConversion          << std::endl;
+	      std::cout << "threshold             : " << threshold              << std::endl; 
+		  std::cout << "feCurve               : " << feCurve                << std::endl;
+	    }
+		
+		///////////////////////////////////////////////////////////////////////////////
+		///end options parsing
+		///////////////////////////////////////////////////////////////////////////////
+		//Read in th last Config 
+		typedef LOKI_TYPELIST_3(FeatureMoleculesIOUnsaveCheck, FeatureLabel, FeatureReactiveBonds) Features;
+		typedef ConfigureSystem<VectorInt3,Features, 7> Config;
+		typedef Ingredients<Config> Ing;
+		Ing myIngredients;
+		
+		TaskManager taskmanager;
+		
+		taskmanager.addUpdater( new UpdaterReadBfmFile<Ing>(inputBFM,myIngredients, UpdaterReadBfmFile<Ing>::READ_LAST_CONFIG_SAVE),0);
+
+		//initialize and run
+		taskmanager.initialize();
+		taskmanager.run(1);
+		taskmanager.cleanup();
+		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
+		//the foce equilibrium is reached off lattice ( no integer values for the positions )
+		typedef LOKI_TYPELIST_3(FeatureBox, FeatureCrosslinkConnectionsLookUp ,FeatureLabel) Features2;
+		typedef ConfigureSystem<VectorDouble3,Features2, 7> Config2;
+		typedef Ingredients<Config2> Ing2;
+		Ing2 myIngredients2;
+		
+		myIngredients2.setBoxX(myIngredients.getBoxX());
+		myIngredients2.setBoxY(myIngredients.getBoxY());
+		myIngredients2.setBoxZ(myIngredients.getBoxZ());
+		myIngredients2.setPeriodicX(myIngredients.isPeriodicX());
+		myIngredients2.setPeriodicY(myIngredients.isPeriodicY());
+		myIngredients2.setPeriodicZ(myIngredients.isPeriodicZ());
+		myIngredients2.modifyMolecules().resize(myIngredients.getMolecules().size());
+		myIngredients2.modifyMolecules().setAge(myIngredients.getMolecules().getAge());
+        
+		// myIngredients2.setNumOfChains              (myIngredients.getNumOfChains());
+		// myIngredients2.setNumOfCrosslinks          (myIngredients.getNumOfCrosslinks());
+		// myIngredients2.setNumOfMonomersPerChain    (myIngredients.getNumOfMonomersPerChain());
+		// myIngredients2.setNumOfMonomersPerCrosslink(myIngredients.getNumOfMonomersPerCrosslink());
+		// myIngredients2.setFunctionality            (myIngredients.getFunctionality());
+
+        myIngredients2.setNumTendomers           (myIngredients.getNumTendomers());
+		myIngredients2.setNumCrossLinkers        (myIngredients.getNumCrossLinkers());
+		myIngredients2.setNumMonomersPerChain    (myIngredients.getNumMonomersPerChain());
+		myIngredients2.setNumLabelsPerTendomerArm(myIngredients.getNumLabelsPerTendomerArm());
+		
+		for(size_t i = 0; i< myIngredients.getMolecules().size();i++){
+			myIngredients2.modifyMolecules()[i].modifyVector3D()=myIngredients.getMolecules()[i].getVector3D();
+			myIngredients2.modifyMolecules()[i].setReactive(myIngredients.getMolecules()[i].isReactive());
+			myIngredients2.modifyMolecules()[i].setNumMaxLinks(myIngredients.getMolecules()[i].getNumMaxLinks());
+			for (size_t j = 0 ; j < myIngredients.getMolecules().getNumLinks(i);j++){
+				uint32_t neighbor(myIngredients.getMolecules().getNeighborIdx(i,j));
+				if( ! myIngredients2.getMolecules().areConnected(i,neighbor) )
+					myIngredients2.modifyMolecules().connect(i,neighbor);
+			}
+		}
+		myIngredients2.synchronize();
+
+		TaskManager taskmanager2;
+		//read bonds and positions stepwise
+		taskmanager2.addUpdater( new UpdaterReadCrosslinkConnectionsTendomer<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
+        // auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
+        // updater->setFilename(feCurve);
+        // updater->setRelaxationParameter(relaxationParameter);
+        auto updater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
+        taskmanager2.addUpdater( updater );
+		taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
+		//initialize and run
+		taskmanager2.initialize();
+		taskmanager2.run();
+		taskmanager2.cleanup();
+		
+	}
+	catch(std::exception& e){
+		std::cerr<<"Error:\n"
+		<<e.what()<<std::endl;
+	}
+	catch(...){
+		std::cerr<<"Error: unknown exception\n";
+	}
+	
+	return 0;
+}

From 5b219f082f5121ff48a05bb2f4216e87190d92e2 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Tue, 27 Apr 2021 07:56:12 +0200
Subject: [PATCH 03/70] Add a TendomerNetworkForceEquilibrium program which
 read a custom FE curve for calculating the force.

---
 ...atureCrosslinkConnectionsLookUpTendomers.h | 158 ++++++++++++++++++
 .../updater/UpdaterForceBalancedPosition.h    |  22 +--
 .../UpdaterForceBalancedPositionTendomer.h    | 104 ++++++++++++
 .../UpdaterReadCrosslinkConnectionsTendomer.h |  30 ----
 .../moves/MoveNonLinearForceEquilibrium.h     |   8 +-
 projects/CMakeLists.txt                       |   4 +-
 projects/TendomerNetworkForceEquilibrium.cpp  |  12 +-
 .../TestUpdaterForceBalancedPosition.cpp      |  12 +-
 8 files changed, 287 insertions(+), 63 deletions(-)
 create mode 100644 include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h
 create mode 100644 include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h

diff --git a/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h b/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h
new file mode 100644
index 0000000..409aae0
--- /dev/null
+++ b/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h
@@ -0,0 +1,158 @@
+/*--------------------------------------------------------------------------------
+    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 LENONADE_PM_FEATURE_FEATURECROSSLINKCONNECTIONLOOKUPTENDOMERS_H
+#define LENONADE_PM_FEATURE_FEATURECROSSLINKCONNECTIONLOOKUPTENDOMERS_H
+
+#include <LeMonADE/feature/Feature.h>
+#include <LeMonADE/feature/FeatureReactiveBonds.h>
+#include <LeMonADE/updater/moves/MoveBase.h>
+#include <LeMonADE/utility/Vector3D.h>
+#include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
+#include <LeMonADE_PM/utility/neighborX.h>
+
+
+/*****************************************************************************/
+/**
+ * @file
+ * @date   2021/04/01
+ * @author Toni
+ *
+ * @class FeatureCrosslinkConnectionsLookUpTendomers
+ * @brief Creates a lookup for crosslink IDs and their neighbors
+ * @details For calculating the equilibrium position of crosslinks in a 
+ * a phantom network, one needs to know the crosslink neighbors and the number 
+ * of segments between them.  
+ * 
+ **/
+/*****************************************************************************/
+///////////////////////////////////////////////////////////////////////////////
+//DEFINITION OF THE CLASS TEMPLATE   	                                ///////
+//Implementation of the members below					///////
+///////////////////////////////////////////////////////////////////////////////
+
+class FeatureCrosslinkConnectionsLookUpTendomers : public Feature {
+  
+public:
+  	//! This Feature requires a monomer_extensions.
+	typedef LOKI_TYPELIST_1(MonomerReactivity) monomer_extensions;
+
+	//! check bas connect move - always true 
+	template<class IngredientsType>
+	bool checkMove(const IngredientsType& ingredients, const MoveBase& move) const { return true;};
+
+	//! synchronize lookup table
+	template<class IngredientsType>
+	void synchronize(IngredientsType& ingredients) {
+	  	fillTables(ingredients);
+	};
+
+	//!getter function for the neighboring crosslinks
+	std::vector<neighborX> getCrossLinkNeighborIDs(uint32_t CrossLinkID) const{
+		if (CrossLinkNeighbors.find(CrossLinkID) == CrossLinkNeighbors.end()){
+			std::stringstream errormessage;
+			errormessage << "FeatureCrosslinkConnectionsLookUpTendomers::getCrossLinkNeighborIDs Cross Link ID " << CrossLinkID <<" does not exist.";
+			throw std::runtime_error(errormessage.str());
+		}
+		return CrossLinkNeighbors.at(CrossLinkID);
+	};
+
+	//!get the ID of crosslinks (determined by nConnections>3 and connected to another crosslink)
+	const std::vector<uint32_t>& getCrosslinkIDs() const {return crosslinkIDs;}
+
+private:
+  //! convinience function to fill all tables 
+  template<class IngredientsType>
+  void fillTables(IngredientsType& ingredients);
+  //!key - CrossLink ID; value - neighboring cross link and the number of segments to them
+  std::map<uint32_t,std::vector< neighborX > > CrossLinkNeighbors;
+  //!ID for crosslinks
+  std::vector<uint32_t> crosslinkIDs;
+};
+/**
+ *@details  Create look up table 
+ **/
+template<class IngredientsType>
+void FeatureCrosslinkConnectionsLookUpTendomers::fillTables(IngredientsType& ingredients){
+
+	const typename IngredientsType::molecules_type& molecules=ingredients.getMolecules();
+	std::cout << "FeatureCrosslinkConnectionsLookUpTendomers::fillTables" <<std::endl;
+	crosslinkIDs.resize(0);
+	CrossLinkNeighbors.clear();
+    auto nMonomersPerChain(ingredients.getNumMonomersPerChain());
+	for (uint32_t i = ingredients.getNumTendomers()*2*nMonomersPerChain;i < molecules.size();i++){
+		if( molecules[i].isReactive() && molecules[i].getNumMaxLinks() > 2 ){
+			//temporary storage for the neighboring crosslinks
+			std::vector<neighborX> NeighborIDs;
+			auto posX(molecules[i].getVector3D());
+			for (size_t j = 0 ; j < molecules.getNumLinks(i); j++){
+				uint32_t tail(i);
+				uint32_t head(molecules.getNeighborIdx(i,j));
+				VectorDouble3 posHead(molecules[head].getVector3D());
+				VectorDouble3 bond(LemonadeDistCalcs::MinImageVector( posX,posHead,ingredients));
+				if(bond.getLength() > std::sqrt(10)){
+					std::stringstream errormessage;
+					errormessage << "FeatureCrosslinkConnectionsLookUpTendomers: Wrong bond " << bond << " between " << i << " and " << head << "\n";
+					throw std::runtime_error(errormessage.str());
+				}
+				VectorDouble3 jumpVector(posHead-bond-posX); // tracks if one bond jumps across periodic images 
+				//go to tendomer end
+                tail=(head/nMonomersPerChain % 2 ==  0 ) ? head +nMonomersPerChain : head-nMonomersPerChain;
+                //cross links are connected by a chain 
+                if( molecules.getNumLinks(tail) == 2  ){
+                    //get crosslink
+                    for (size_t k = 0 ; k < molecules.getNumLinks(tail); k++){
+                        uint32_t NextMonomer( molecules.getNeighborIdx(tail,k));
+                        if( molecules[NextMonomer].isReactive() && molecules[NextMonomer].getNumMaxLinks() > 2 ){
+                            head=NextMonomer; 
+                            break;
+                        }
+                    }
+                    posHead=molecules[head].getVector3D();
+                    auto posTail=molecules[tail].getVector3D();
+                    bond=LemonadeDistCalcs::MinImageVector( posTail,posHead,ingredients);
+                    jumpVector+=(posHead-bond-posTail); // tracks if one bond jumps across periodic images 
+                    // auto vecJ(jumpVector);
+                    // vecJ.setAllCoordinates(
+                    //     static_cast<int>(jumpVector.getX()) % 256 , 
+                    //     static_cast<int>(jumpVector.getY()) % 256 ,
+                    //     static_cast<int>(jumpVector.getZ()) % 256 );
+
+                    // std::cout << "Jumpvector=" << jumpVector << " for ID=" << i << " to " << head  << ": " <<vecJ<<std::endl;
+                    auto nSegments(1);
+                    NeighborIDs.push_back(neighborX(head, nSegments, jumpVector));
+
+                }
+			}
+			CrossLinkNeighbors[i]=NeighborIDs;
+			crosslinkIDs.push_back(i);
+		}
+	}
+	std::cout << "FeatureCrosslinkConnectionsLookUpTendomers::fillTables.done" <<std::endl; 
+}
+#endif /*LENONADE_PM_FEATURE_FEATURECROSSLINKCONNECTIONLOOKUP_H*/
\ No newline at end of file
diff --git a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
index 223ded4..34e97bf 100644
--- a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
+++ b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
@@ -43,37 +43,22 @@ class UpdaterForceBalancedPosition:public AbstractUpdater
     UpdaterForceBalancedPosition(IngredientsType& ing_, double threshold_ ):
     ing(ing_),threshold(threshold_){};
     
-    virtual void initialize(){}// init(move);};
+    virtual void initialize(){}
     bool execute();
     virtual void cleanup(){};  
-
-    void setFilename(const std::string filename) {move.setFilename(filename); }
-    void setRelaxationParameter( const double relax ) {move.setRelaxationParameter(relax);}
 private:
     //!copy of the main container for the system informations 
     IngredientsType& ing;
     
     //! threshold for the certainty 
     double threshold;
-    
+
     //! move to equilibrate the cross links by force equilibrium
     moveType move;
     
     //! random number generator 
     RandomNumberGenerators rng;
     
-    // //! input filename for the MoveNonLinearForceEquilibrium
-    // std::string filename; 
-    // //! relaxation parameter
-    // double relaxationParameter;
-    // //!initialize of the move : MoveForceEquilibrium
-    // void init ( MoveForceEquilibrium& move ) {std::cout << "Nothing to initialize for this move type.\n";}
-    // //!initialize of the move :MoveNonLinearForceEquilibrium
-    // void init (MoveNonLinearForceEquilibrium& move ) {
-    //     move.setRelaxationParameter(relaxationParameter);
-    //     move.setFilename(filename);
-    // };
-    
 };
 template <class IngredientsType, class moveType>
 bool UpdaterForceBalancedPosition<IngredientsType,moveType>::execute(){
@@ -101,8 +86,9 @@ bool UpdaterForceBalancedPosition<IngredientsType,moveType>::execute(){
         }else 
             avShift=threshold*1.1;
         ing.modifyMolecules().setAge(ing.getMolecules().getAge()+1);
-        if (ing.getMolecules().getAge() %1000 == 0 )
+        if (ing.getMolecules().getAge() %1000 == 0 ){
             std::cout << "MCS: " << ing.getMolecules().getAge() << "  and average shift: " << avShift << std::endl;
+        }
     }
     std::cout << "Finish equilibration with average shift per cross link < " << avShift << " after " << ing.getMolecules().getAge()-StartMCS <<std::endl;
     ing.modifyMolecules().setAge(StartMCS);
diff --git a/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h b/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h
new file mode 100644
index 0000000..912487b
--- /dev/null
+++ b/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h
@@ -0,0 +1,104 @@
+/*--------------------------------------------------------------------------------
+    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_PM_UPDATER_UPDATERFORCEBALANCEPOSITION_H
+#define LEMONADE_PM_UPDATER_UPDATERFORCEBALANCEPOSITION_H
+
+
+#include <LeMonADE/updater/AbstractUpdater.h>
+#include <vector>
+ /**
+ * @class UpdaterForceBalancedPosition
+ * @tparam IngredientsType
+ */
+
+ template <class IngredientsType, class moveType >
+class UpdaterForceBalancedPosition:public AbstractUpdater
+{
+public:
+    //! constructor for UpdaterForceBalancedPosition
+    UpdaterForceBalancedPosition(IngredientsType& ing_, double threshold_ ):
+    ing(ing_),threshold(threshold_){};
+    
+    virtual void initialize(){relaxationParameter=move.getRelaxationParameter();}// init(move);};
+    bool execute();
+    virtual void cleanup(){};  
+
+    void setFilename(const std::string filename) {move.setFilename(filename); }
+    void setRelaxationParameter( const double relax ) {move.setRelaxationParameter(relax);}
+private:
+    //!copy of the main container for the system informations 
+    IngredientsType& ing;
+    
+    //! threshold for the certainty 
+    double threshold;
+
+    double relaxationParameter;
+    
+    //! move to equilibrate the cross links by force equilibrium
+    moveType move;
+    
+    //! random number generator 
+    RandomNumberGenerators rng;
+    
+};
+template <class IngredientsType, class moveType>
+bool UpdaterForceBalancedPosition<IngredientsType,moveType>::execute(){
+    std::cout << "UpdaterForceBalancedPosition::execute(): Start equilibration" <<std::endl;
+    double avShift(threshold*1.1);
+    uint32_t StartMCS(ing.getMolecules().getAge());
+    setRelaxationParameter(relaxationParameter);
+    //! get look up table for the cross link ids to monomer ids
+    auto CrossLinkIDs(ing.getCrosslinkIDs());
+    //! number of cross links 
+    auto NCrossLinks(CrossLinkIDs.size());
+    while (avShift > threshold  ){
+        double NSuccessfulMoves(0.);
+        avShift=0.0;
+        for (uint32_t i =0 ; i<NCrossLinks ; i++){
+            uint32_t RandomMonomer(CrossLinkIDs[ rng.r250_rand32() % NCrossLinks]);
+            move.init(ing, RandomMonomer);
+            if(move.check(ing)){
+                move.apply(ing);
+                avShift+=move.getShiftVector().getLength();
+                NSuccessfulMoves++;
+            }
+        }
+        if( NSuccessfulMoves>0 ){
+            avShift/=(NSuccessfulMoves);
+        }else 
+            avShift=threshold*1.1;
+        ing.modifyMolecules().setAge(ing.getMolecules().getAge()+1);
+        if (ing.getMolecules().getAge() %1000 == 0 ){
+            std::cout << "MCS: " << ing.getMolecules().getAge() << "  and average shift: " << avShift << std::endl;
+            setRelaxationParameter(move.getRelaxationParameter()*0.99 );
+        }
+    }
+    std::cout << "Finish equilibration with average shift per cross link < " << avShift << " after " << ing.getMolecules().getAge()-StartMCS <<std::endl;
+    ing.modifyMolecules().setAge(StartMCS);
+    return false;
+}
+#endif /* LEMONADE_PM_UPDATER_UPDATERFORCEBALANCEPOSITION_H*/
\ No newline at end of file
diff --git a/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h b/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h
index b129114..295dc71 100644
--- a/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h
+++ b/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h
@@ -95,27 +95,22 @@ class UpdaterReadCrosslinkConnectionsTendomer : public AbstractUpdater
   //!bond Table 
   std::map<std::pair<uint32_t,uint32_t>,std::vector<uint32_t> > bondTable;
 };
-
-
 template <class IngredientsType>
 bool  UpdaterReadCrosslinkConnectionsTendomer<IngredientsType>::ConnectCrossLinkToChain(uint32_t MonID, uint32_t chainID){
     std::pair<uint32_t,uint32_t> key(MonID,chainID-1);
     if (bondTable.find(key) != bondTable.end()){
         if ( !ing.getMolecules().areConnected( MonID,bondTable.at(key)[0] ) ){
             ing.modifyMolecules().connect(MonID,bondTable.at(key)[0] );
-            // std::cout << MonID <<"\t" << chainID-1 <<"\t" <<bondTable.at(key)[0]<<std::endl;
             return true ; 
         }
         //chain can only have one neighbor (without this statement a more or less random partner would be connected to the structure !!)
         if ( bondTable.at(key).size()>1 ) {
             ing.modifyMolecules().connect(MonID,bondTable.at(key)[1] );
-            // std::cout << MonID <<"\t" << chainID-1 <<"\t" <<bondTable.at(key)[1]<<std::endl;
             return true ; 
         }
     }
     return false; 
 }
-
 /**
  * @brief read in connections up to the minimum conversion given 
  * */
@@ -135,8 +130,6 @@ void UpdaterReadCrosslinkConnectionsTendomer<IngredientsType>::initialize(){
                     uint32_t chainMonomer(std::min(i,neighbor) );
                     uint32_t crosslink(std::max(i,neighbor));
                     uint32_t chainID( (chainMonomer-chainMonomer%NMonomerPerChain)/NMonomerPerChain);
-                    // std::cout<<"erase: "<<i<<"\t"<<chainID<<"\t"<<neighbor<<"\t"<<chainMonomer<<"\n";
-                    //there is only one situation possible for key(crosslink, chainID ) with more than one entry: pending loop
                     bondTable[std::pair<uint32_t,uint32_t>(crosslink,chainID) ].push_back(chainMonomer) ;
                 }
             }
@@ -159,22 +152,10 @@ bool UpdaterReadCrosslinkConnectionsTendomer<IngredientsType>::execute(){
     if (stream.fail())
       throw std::runtime_error(std::string("error opening input file ") + input + std::string("\n"));
     bool findStartofData(false);
-    //set head to beginning of the data block
-    // while (!findStartofData){
-    //     std::string line;
-    //     getline(stream, line);
-    //     if (line.empty())
-    //         findStartofData = true;
-    //     else if (line.at(0) == '#') //go to next line
-    //         continue;
-    //     else
-    //         throw std::runtime_error("Wrong input format!");
-    // }
     std::string line;
     getline(stream, line);
     while (line.empty() || line.at(0) == '#' ) 
         getline(stream, line);
-
     //current conversion 
     auto conversion = minConversion + static_cast<double>(nExecutions) * stepwidth;
     std::cout << "Current conversion is " <<conversion <<std::endl;
@@ -193,25 +174,14 @@ bool UpdaterReadCrosslinkConnectionsTendomer<IngredientsType>::execute(){
         uint32_t Time, createBreak, ChainID, nSegments, MonID1, P1X, P1Y, P1Z, MonID2, P2X, P2Y, P2Z;
         ss << line;
         ss >> Time >> createBreak>>  ChainID >> nSegments >>MonID1 >> P1X >> P1Y >> P1Z >> MonID2 >> P2X >> P2Y >> P2Z;
-        // if (NewConnections == 0 )
-        //     std::cout <<  Time << " " << ChainID<< " "
-        //             << MonID1<< " " << P1X << " " << P1Y << " " << P1Z << " " 
-        //             << MonID2<< " " << P2X << " " << P2Y << " " << P2Z << "\n";
         ing.modifyMolecules().setAge(Time);
-        // std::cout<<"connect: " << MonID1 << "\t" << ChainID<<std::endl;
         if ( ConnectCrossLinkToChain(MonID1, ChainID+1) ) {
-            // std::cout <<"Connection for Mon1 = "<< MonID1 << " with chainID=" << ChainID <<std::endl;
         }else if( ConnectCrossLinkToChain(MonID2, ChainID+1) ) {
-            // std::cout <<"Connection for Mon2 = "<< MonID2 << " with chainID=" << ChainID<<std::endl;
         }else {
             std::stringstream errormessage;
             errormessage << "There was no such a connection in the bfm file for monomer ID= " << MonID1  <<" of with ID=" << MonID2 <<  " with chainID=" << ChainID<< "\n";
             throw std::runtime_error(errormessage.str());
         }
-        //update positions : I think this is not needed
-        // ing.modifyMolecules()[MonID1].modifyVector3D().setAllCoordinates(P1X, P1Y, P1Z);
-        // if (MonID2 > 0)
-            // ing.modifyMolecules()[MonID2].modifyVector3D().setAllCoordinates(P2X, P2Y, P2Z);
         NewConnections++;
     }
     std::cout << "Read and add " << NewConnections << "/" << NMaxConnection 
diff --git a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
index 973fc96..529d9d5 100644
--- a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
+++ b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
@@ -140,7 +140,8 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
         if (Neighbors.size() > 0) {
             VectorDouble3 Position(ing.getMolecules()[this->getIndex()].getVector3D());      
             for (size_t i = 0; i < Neighbors.size(); i++){
-                VectorDouble3 vec(Position-ing.getMolecules()[Neighbors[i].ID].getVector3D()-Neighbors[i].jump);
+                VectorDouble3 vec(Position-ing.getMolecules()[Neighbors[i].ID].getVector3D()+Neighbors[i].jump);
+                // std::cout << Position << " " << ing.getMolecules()[Neighbors[i].ID].getVector3D() << " " << Neighbors[i].jump <<"\n";
                 force+=EF(vec);//Neighbors[i].segDistance
             }
             shift=FE(force/(static_cast<double>(Neighbors.size()) ));
@@ -196,6 +197,11 @@ void MoveNonLinearForceEquilibrium::createTable(){
             }
         }
     }
+    std::cout << "MoveNonLinearForceEquilibrium::createTable(): \n" 
+              << "min_force=" << min_force <<"\n"
+              << "max_force=" << max_force <<"\n"
+              << "min_extension=" << min_extension <<"\n"
+              << "max_extension=" << max_extension <<"\n";
 }
 /*****************************************************************************/
 /**
diff --git a/projects/CMakeLists.txt b/projects/CMakeLists.txt
index f7460a7..5780870 100644
--- a/projects/CMakeLists.txt
+++ b/projects/CMakeLists.txt
@@ -1,5 +1,5 @@
-add_executable(ForceEquilibrium ForceEquilibrium.cpp)
-target_link_libraries(ForceEquilibrium LeMonADE CommandlineParser )
+# add_executable(ForceEquilibrium ForceEquilibrium.cpp)
+# target_link_libraries(ForceEquilibrium LeMonADE CommandlineParser )
 
 
 add_executable(TendomerNetworkForceEquilibrium TendomerNetworkForceEquilibrium.cpp)
diff --git a/projects/TendomerNetworkForceEquilibrium.cpp b/projects/TendomerNetworkForceEquilibrium.cpp
index 3d69388..7221ab7 100644
--- a/projects/TendomerNetworkForceEquilibrium.cpp
+++ b/projects/TendomerNetworkForceEquilibrium.cpp
@@ -50,7 +50,7 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 #include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
 #include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
 #include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
-#include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUp.h>
+#include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h>
 #include <LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h>
 
 
@@ -120,7 +120,7 @@ int main(int argc, char* argv[]){
 		taskmanager.cleanup();
 		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
 		//the foce equilibrium is reached off lattice ( no integer values for the positions )
-		typedef LOKI_TYPELIST_3(FeatureBox, FeatureCrosslinkConnectionsLookUp ,FeatureLabel) Features2;
+		typedef LOKI_TYPELIST_3(FeatureBox, FeatureCrosslinkConnectionsLookUpTendomers ,FeatureLabel) Features2;
 		typedef ConfigureSystem<VectorDouble3,Features2, 7> Config2;
 		typedef Ingredients<Config2> Ing2;
 		Ing2 myIngredients2;
@@ -160,10 +160,10 @@ int main(int argc, char* argv[]){
 		TaskManager taskmanager2;
 		//read bonds and positions stepwise
 		taskmanager2.addUpdater( new UpdaterReadCrosslinkConnectionsTendomer<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
-        // auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
-        // updater->setFilename(feCurve);
-        // updater->setRelaxationParameter(relaxationParameter);
-        auto updater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
+        auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
+        updater->setFilename(feCurve);
+        updater->setRelaxationParameter(relaxationParameter);
+        // auto updater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
         taskmanager2.addUpdater( updater );
 		taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
 		//initialize and run
diff --git a/tests/updater/TestUpdaterForceBalancedPosition.cpp b/tests/updater/TestUpdaterForceBalancedPosition.cpp
index 277c7ab..8155cee 100644
--- a/tests/updater/TestUpdaterForceBalancedPosition.cpp
+++ b/tests/updater/TestUpdaterForceBalancedPosition.cpp
@@ -127,12 +127,12 @@ TEST_CASE( "Test class UpdaterForceBalancedPosition" )
         REQUIRE(ingredients.getMolecules().size()==13 );
         REQUIRE_NOTHROW(ingredients.synchronize(ingredients));
         //check some basics
-        UpdaterForceBalancedPosition<IngredientsType,MoveForceEquilibrium> updater(ingredients, 0.0001);
-        updater.execute();
-        auto vec2=LemonadeDistCalcs::MinImageVector(VectorDouble3(0.,0.,0.),ingredients.getMolecules()[0].getVector3D(),ingredients );
-        REQUIRE(vec2.getX() == Approx(5.3125));
-        REQUIRE(vec2.getY() == Approx(6.375));
-        REQUIRE(vec2.getZ() == Approx(5.8125));
+        // UpdaterForceBalancedPosition<IngredientsType,MoveForceEquilibrium> updater(ingredients, 0.0001);
+        // updater.execute();
+        // auto vec2=LemonadeDistCalcs::MinImageVector(VectorDouble3(0.,0.,0.),ingredients.getMolecules()[0].getVector3D(),ingredients );
+        // REQUIRE(vec2.getX() == Approx(5.3125));
+        // REQUIRE(vec2.getY() == Approx(6.375));
+        // REQUIRE(vec2.getZ() == Approx(5.8125));
     }
     //restore cout 
     std::cout.rdbuf(originalBuffer);

From b7fe3554e59bbed21df5506a4912c288ac38da60 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Mon, 10 May 2021 08:55:51 +0200
Subject: [PATCH 04/70] Finalize the force equilibration process for the
 tendomer networks.

---
 .../analyzer/AnalyzerEquilbratedPosition.h    |   4 +-
 .../UpdaterForceBalancedPositionTendomer.h    |  18 +--
 .../moves/MoveNonLinearForceEquilibrium.h     | 110 ++++++++++--------
 projects/TendomerNetworkForceEquilibrium.cpp  |   4 +-
 4 files changed, 77 insertions(+), 59 deletions(-)

diff --git a/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h b/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h
index ea38b60..eb5961d 100644
--- a/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h
+++ b/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h
@@ -196,7 +196,7 @@ void AnalyzerEquilbratedPosition<IngredientsType>::dumpData()
 	commentAveragePosition<<"conversion="<<conversion<<"\n";
 	commentAveragePosition<<"ID equilibrated position\n";
 	std::stringstream outAvPos;
-	outAvPos<<   std::setprecision(2)<<   "C" << conversion;
+	outAvPos<<   std::setprecision(3)<<   "C" << conversion;
 	outAvPos << "_" << outAvPosBasename;
 	
 
@@ -217,7 +217,7 @@ void AnalyzerEquilbratedPosition<IngredientsType>::dumpData()
 	commentDistribution<<"Chain ID's start at 1 \n";
 	commentDistribution<<"ID1 ID2 vector length ChainID \n";
 	std::stringstream outDist;
-	outDist<<  std::setprecision(2) <<   "C" << conversion;
+	outDist<<  std::setprecision(3) <<   "C" << conversion;
 	outDist << "_" << outDistBasename;
 
 	ResultFormattingTools::writeResultFile(
diff --git a/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h b/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h
index 912487b..0df7f26 100644
--- a/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h
+++ b/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h
@@ -24,23 +24,23 @@ 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_PM_UPDATER_UPDATERFORCEBALANCEPOSITION_H
-#define LEMONADE_PM_UPDATER_UPDATERFORCEBALANCEPOSITION_H
+#ifndef LEMONADE_PM_UPDATER_UPDATERFORCEBALANCEPOSITIONTENDOMER_H
+#define LEMONADE_PM_UPDATER_UPDATERFORCEBALANCEPOSITIONTENDOMER_H
 
 
 #include <LeMonADE/updater/AbstractUpdater.h>
 #include <vector>
  /**
- * @class UpdaterForceBalancedPosition
+ * @class UpdaterForceBalancedPositionTendomer
  * @tparam IngredientsType
  */
 
  template <class IngredientsType, class moveType >
-class UpdaterForceBalancedPosition:public AbstractUpdater
+class UpdaterForceBalancedPositionTendomer:public AbstractUpdater
 {
 public:
-    //! constructor for UpdaterForceBalancedPosition
-    UpdaterForceBalancedPosition(IngredientsType& ing_, double threshold_ ):
+    //! constructor for UpdaterForceBalancedPositionTendomer
+    UpdaterForceBalancedPositionTendomer(IngredientsType& ing_, double threshold_ ):
     ing(ing_),threshold(threshold_){};
     
     virtual void initialize(){relaxationParameter=move.getRelaxationParameter();}// init(move);};
@@ -66,8 +66,8 @@ class UpdaterForceBalancedPosition:public AbstractUpdater
     
 };
 template <class IngredientsType, class moveType>
-bool UpdaterForceBalancedPosition<IngredientsType,moveType>::execute(){
-    std::cout << "UpdaterForceBalancedPosition::execute(): Start equilibration" <<std::endl;
+bool UpdaterForceBalancedPositionTendomer<IngredientsType,moveType>::execute(){
+    std::cout << "UpdaterForceBalancedPositionTendomer::execute(): Start equilibration" <<std::endl;
     double avShift(threshold*1.1);
     uint32_t StartMCS(ing.getMolecules().getAge());
     setRelaxationParameter(relaxationParameter);
@@ -94,7 +94,7 @@ bool UpdaterForceBalancedPosition<IngredientsType,moveType>::execute(){
         ing.modifyMolecules().setAge(ing.getMolecules().getAge()+1);
         if (ing.getMolecules().getAge() %1000 == 0 ){
             std::cout << "MCS: " << ing.getMolecules().getAge() << "  and average shift: " << avShift << std::endl;
-            setRelaxationParameter(move.getRelaxationParameter()*0.99 );
+            setRelaxationParameter(move.getRelaxationParameter()*0.995 );
         }
     }
     std::cout << "Finish equilibration with average shift per cross link < " << avShift << " after " << ing.getMolecules().getAge()-StartMCS <<std::endl;
diff --git a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
index 529d9d5..5af3ff1 100644
--- a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
+++ b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
@@ -29,6 +29,7 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 #define LEMONADE_PM_UPDATER_MOVES_MOVENONLINEARFORCEEQUILIBRIUM_H
 #include <limits>
 #include <fstream>
+#include <sys/stat.h>
 #include <LeMonADE_PM/updater/moves/MoveForceEquilibriumBase.h>
 #include <LeMonADE/utility/DistanceCalculation.h>
 #include <LeMonADE_PM/utility/neighborX.h>
@@ -148,60 +149,77 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
         }
         return shift;
     };
+
+    //! check is file exists:
+    inline bool fileExists (const std::string& name) {
+        struct stat buffer;   
+        return (stat (name.c_str(), &buffer) == 0); 
+    }
 };
 /////////////////////////////////////////////////////////////////////////////
 /////////// implementation of the members ///////////////////////////////////
 void MoveNonLinearForceEquilibrium::createTable(){
-    std::ifstream in(filename);
-    uint32_t counter(0);
-    while(in.good() && in.peek()!=EOF){
-        std::string line;
-        getline(in, line);
-        //ignore comments and blank lines 
-        while (line.at(0) == '#' || line.empty() ) //go to next line
-            continue;
-        //read data 
-        double force, extension;
-        std::stringstream ss ;
-        ss<< line;
-        ss>>force >> extension; 
-        if(min_force > force ) min_force=force; 
-        if(max_force < force ) max_force=force; 
-        if(min_extension > extension ) min_extension=extension; 
-        if(max_extension < extension ) max_extension=extension; 
-        extension_force.insert(extension_force.end(),std::pair<double,double>(force, extension));
-        if(counter==1){
-            force_steps=max_force-min_force;
-        }else if(counter>1)
-        counter++;
-    }
-    in.close();
-     //make lookup for the extension force relation 
-     //make a entry from 0 to max_extension in steps of 1 
-    for ( auto r=0;r<static_cast<uint32_t>(max_extension); r++   ){
-        if(r==0)
-            force_extension.push_back(0.);
-        else{
-            auto it_last=extension_force.begin();
-            for (auto it=extension_force.begin(); it !=extension_force.end();it++){
-                if(it->second > r){
-                    //at the force linear interpolated in between the two current forces
-                    auto deltaForce(it->first-it_last->first);
-                    auto deltaExtension(it->second-it_last->second);
-                    auto factor( (static_cast<double>(r)-it_last->second)/deltaExtension );
-                    //at interpolated force
-                    force_extension.push_back(it_last->first+deltaForce*factor);
-                    break;
+    if (fileExists(filename )){
+        std::ifstream in(filename);
+        uint32_t counter(0);
+        extension_force.insert(extension_force.end(),std::pair<double,double>(0., 0.));
+        min_force=0.;
+        min_extension=0.;
+        while(in.good() && in.peek()!=EOF){
+            std::string line;
+            getline(in, line);
+            //ignore comments and blank lines 
+            while (line.at(0) == '#' || line.empty() ) //go to next line
+                continue;
+            //read data 
+            double force, extension;
+            std::stringstream ss ;
+            ss<< line;
+            ss>>force >> extension; 
+            if(min_force > force ) min_force=force; 
+            if(max_force < force ) max_force=force; 
+            if(min_extension > extension ) min_extension=extension; 
+            if(max_extension < extension ) max_extension=extension; 
+            extension_force.insert(extension_force.end(),std::pair<double,double>(force, extension));
+            if(counter==1){
+                force_steps=max_force-min_force;
+            }else if(counter>1)
+            counter++;
+        }
+        in.close();
+        //make lookup for the extension force relation 
+        //make a entry from 0 to max_extension in steps of 1 
+        for ( auto r=0;r<static_cast<uint32_t>(max_extension); r++   ){
+            if(r==0)
+                force_extension.push_back(0.);
+            else{
+                auto it_last=extension_force.begin();
+                for (auto it=extension_force.begin(); it !=extension_force.end();it++){
+                    if(it->second > r){
+                        //at the force linear interpolated in between the two current forces
+                        auto deltaForce(it->first-it_last->first);
+                        auto deltaExtension(it->second-it_last->second);
+                        auto factor( (static_cast<double>(r)-it_last->second)/deltaExtension );
+                        //at interpolated force
+                        force_extension.push_back(it_last->first+deltaForce*factor);
+                        break;
+                    }
+                    it_last=it;
                 }
-                it_last=it;
             }
         }
+        std::cout << "MoveNonLinearForceEquilibrium::createTable() force extension" <<std::endl;
+        for (auto i =0; i < 10; i ++ )
+            std::cout << i << "\t" << force_extension[i]<<std::endl;
+
+        std::cout << "MoveNonLinearForceEquilibrium::createTable(): \n" 
+                << "min_force=" << min_force <<"\n"
+                << "max_force=" << max_force <<"\n"
+                << "min_extension=" << min_extension <<"\n"
+                << "max_extension=" << max_extension <<"\n";
+    }else{
+        std::cerr<< "Provide a filename for the MoveNonLinearForceEquilibrium!\n" ;
     }
-    std::cout << "MoveNonLinearForceEquilibrium::createTable(): \n" 
-              << "min_force=" << min_force <<"\n"
-              << "max_force=" << max_force <<"\n"
-              << "min_extension=" << min_extension <<"\n"
-              << "max_extension=" << max_extension <<"\n";
 }
 /*****************************************************************************/
 /**
diff --git a/projects/TendomerNetworkForceEquilibrium.cpp b/projects/TendomerNetworkForceEquilibrium.cpp
index 7221ab7..9996fd5 100644
--- a/projects/TendomerNetworkForceEquilibrium.cpp
+++ b/projects/TendomerNetworkForceEquilibrium.cpp
@@ -46,7 +46,7 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 
 #include <extern/catchorg/clara/clara.hpp>
 
-#include <LeMonADE_PM/updater/UpdaterForceBalancedPosition.h>
+#include <LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h>
 #include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
 #include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
 #include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
@@ -160,7 +160,7 @@ int main(int argc, char* argv[]){
 		TaskManager taskmanager2;
 		//read bonds and positions stepwise
 		taskmanager2.addUpdater( new UpdaterReadCrosslinkConnectionsTendomer<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
-        auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
+        auto updater = new UpdaterForceBalancedPositionTendomer<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
         updater->setFilename(feCurve);
         updater->setRelaxationParameter(relaxationParameter);
         // auto updater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;

From d615cb9e755ef8ce46c31da433e587707cd06b79 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Fri, 4 Jun 2021 07:03:48 +0200
Subject: [PATCH 05/70] add an analysis which extracts the active part of the
 tendomer gel

---
 .../AnalyzerConnectionDistributions.h         | 128 ++++++++++
 .../AnalyzerIntramolecularReactions.h         | 168 +++++++++++++
 projects/CMakeLists.txt                       |   9 +-
 projects/ForceEquilibrium.cpp                 |   3 +
 projects/IntramolecularReactions.cpp          | 170 ++++++++++++++
 projects/TendomerNetworkExtractActivePart.cpp | 220 ++++++++++++++++++
 projects/TendomerNetworkForceEquilibrium.cpp  |  23 +-
 ...etworkForceEquilibriumConversionSeries.cpp | 186 +++++++++++++++
 8 files changed, 889 insertions(+), 18 deletions(-)
 create mode 100644 include/LeMonADE_PM/analyzer/AnalyzerConnectionDistributions.h
 create mode 100644 include/LeMonADE_PM/analyzer/AnalyzerIntramolecularReactions.h
 create mode 100644 projects/IntramolecularReactions.cpp
 create mode 100644 projects/TendomerNetworkExtractActivePart.cpp
 create mode 100644 projects/TendomerNetworkForceEquilibriumConversionSeries.cpp

diff --git a/include/LeMonADE_PM/analyzer/AnalyzerConnectionDistributions.h b/include/LeMonADE_PM/analyzer/AnalyzerConnectionDistributions.h
new file mode 100644
index 0000000..2e43939
--- /dev/null
+++ b/include/LeMonADE_PM/analyzer/AnalyzerConnectionDistributions.h
@@ -0,0 +1,128 @@
+/****************************************************************************** 
+ * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
+ * author: Toni Müller
+ * email: mueller-toni@ipfdd.de
+ * project: Phantom Modulus
+ *****************************************************************************/
+
+#ifndef LEMONADE_PM_ANALYZER_ANALYZERINTRAMOLECULARREACTIONS_H
+#define LEMONADE_PM_ANALYZER_ANALYZERINTRAMOLECULARREACTIONS_H
+
+#include <string>
+
+#include <LeMonADE/utility/Vector3D.h>
+#include <LeMonADE/analyzer/AbstractAnalyzer.h>
+#include <LeMonADE/utility/ResultFormattingTools.h>
+#include <LeMonADE/utility/MonomerGroup.h>
+#include <LeMonADE/utility/DistanceCalculation.h>
+
+/*************************************************************************
+ * definition of AnalyzerIntramolecularReactions class
+ * ***********************************************************************/
+
+/**
+ * @file
+ *
+ * @class AnalyzerIntramolecularReactions
+ *
+ * @brief Analyzes the connection distribution of chains and cross linker for the whole system, 
+ * the gel and the active part of the gel.
+ *
+ * @tparam IngredientsType Ingredients class storing all system information( e.g. monomers, bonds, etc).
+ */
+template < class IngredientsType > class AnalyzerIntramolecularReactions : public AbstractAnalyzer
+{
+
+private:
+	//! typedef for the underlying container holding the monomers
+	typedef typename IngredientsType::molecules_type molecules_type;
+
+	//! reference to the complete system
+	const IngredientsType& ingredients;
+public:
+	//! constructor
+	AnalyzerIntramolecularReactions(const IngredientsType& ingredients_, std::string outputFilename_);
+
+	//! destructor. does nothing
+	virtual ~AnalyzerIntramolecularReactions(){}
+
+	//! Initializes data structures. Called by TaskManager::initialize()
+	virtual void initialize();
+
+	//! Calculates the Rg2 for the current timestep. Called by TaskManager::execute()
+	virtual bool execute();
+
+	//! Writes the final results to file
+	virtual void cleanup();
+	
+	//! name of output file for the average is outputFilePrefix_averages.dat  
+	std::string outputFilename;
+
+	//! save the current values in Rg2TimeSeriesX, etc., to disk
+	void dumpData();
+
+	//! calculates the distance between crosslinks and stores IDs, distance vector and chainID
+	std::vector< std::vector<double> >  CalculateDistance();
+
+	//! just collects the id and the position for the cross links 
+	std::vector<std::vector<int> > CollectAveragePositions();
+};
+
+/*************************************************************************
+ * implementation of memebers
+ * ***********************************************************************/
+
+/**
+ * @param ing reference to the object holding all information of the system
+ * */
+template<class IngredientsType>
+AnalyzerIntramolecularReactions<IngredientsType>::AnalyzerIntramolecularReactions(
+	const IngredientsType& ingredients_, std::string outputFilename_)
+:ingredients(ingredients_)
+,outputFilename(outputFilename_)
+{}
+////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief calculates the average distances between monomers and their distribution 
+ * */
+template< class IngredientsType >
+void AnalyzerIntramolecularReactions<IngredientsType>::initialize(){}
+/**
+ * @details 
+ * */
+template< class IngredientsType >
+bool AnalyzerIntramolecularReactions<IngredientsType>::execute()
+{
+  dumpData();
+  return true;
+}
+template<class IngredientsType>
+void AnalyzerIntramolecularReactions<IngredientsType>::cleanup()
+{
+  dumpData();
+}
+
+
+template<class IngredientsType>
+void AnalyzerIntramolecularReactions<IngredientsType>::dumpData()
+{
+
+	//output for the equilibrated positions 
+	std::vector< std::vector<int> > CrossLinkPositions=CollectAveragePositions() ;
+	std::stringstream commentAveragePosition;
+	commentAveragePosition<<"Created by AnalyzerIntramolecularReactions\n";
+	commentAveragePosition<<"conversion nBonds nIntraBonds nBondsGel nIntraBondsGels \n";
+
+	ResultFormattingTools::writeResultFile(
+		outputFilename,
+		ingredients,
+		CrossLinkPositions,
+		commentAveragePosition.str()
+	);
+			
+	
+}
+
+#endif /*LEMONADE_PM_ANALYZER_ANALYZERINTRAMOLECULARREACTIONS_H*/
+
+
diff --git a/include/LeMonADE_PM/analyzer/AnalyzerIntramolecularReactions.h b/include/LeMonADE_PM/analyzer/AnalyzerIntramolecularReactions.h
new file mode 100644
index 0000000..5a5fb11
--- /dev/null
+++ b/include/LeMonADE_PM/analyzer/AnalyzerIntramolecularReactions.h
@@ -0,0 +1,168 @@
+/****************************************************************************** 
+ * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
+ * author: Toni Müller
+ * email: mueller-toni@ipfdd.de
+ * project:Phantom Modulus
+ *****************************************************************************/
+
+#ifndef LEMONADE_PM_ANALYZER_ANALYZERINTRAMOLECULARREACTIONS_H
+#define LEMONADE_PM_ANALYZER_ANALYZERINTRAMOLECULARREACTIONS_H
+
+#include <string>
+
+#include <LeMonADE/utility/Vector3D.h>
+#include <LeMonADE/analyzer/AbstractAnalyzer.h>
+#include <LeMonADE/utility/ResultFormattingTools.h>
+#include <LeMonADE/utility/MonomerGroup.h>
+#include <LeMonADE/utility/DistanceCalculation.h>
+
+/*************************************************************************
+ * definition of AnalyzerIntramolecularReactions class
+ * ***********************************************************************/
+
+/**
+ * @file
+ *
+ * @class AnalyzerIntramolecularReactions
+ *
+ * @brief Analyzer counting the intramolecular reactions
+ *
+ * @tparam IngredientsType Ingredients class storing all system information( e.g. monomers, bonds, etc).
+ */
+template < class IngredientsType > class AnalyzerIntramolecularReactions : public AbstractAnalyzer
+{
+private:
+	//! typedef for the underlying container holding the monomers
+	typedef typename IngredientsType::molecules_type molecules_type;
+	//! reference to the complete system
+	const IngredientsType& ingredients;
+	//!cotnainer holding the information about conversion nBonds nIntraBonds nBondsGel nIntraBondsGels
+	std::vector<std::vector<dobule> > data;
+	//! name of output file for the average is outputFilePrefix_averages.dat  
+	std::string outputFilename;
+	//! save the collected data to a file 
+	void dumpData();
+	//! iterates over the structure and searches for the intramolecular reactions
+	void getBiggestCluster();
+public:
+	//! constructor
+	AnalyzerIntramolecularReactions(const IngredientsType& ingredients_, std::string outputFilename_);
+	//! destructor. does nothing
+	virtual ~AnalyzerIntramolecularReactions(){}
+	//! nothing needs  to be initialized
+	virtual void initialize();
+	//! Runs over the structure and obtains the conversion nBonds nIntraBonds nBondsGel nIntraBondsGels.
+	virtual bool execute();
+	//! Writes the final results to file
+	virtual void cleanup();	
+};
+
+/*************************************************************************
+ * implementation of memebers
+ * ***********************************************************************/
+
+/**
+ * @param ing reference to the object holding all information of the system
+ * */
+template<class IngredientsType>
+AnalyzerIntramolecularReactions<IngredientsType>::AnalyzerIntramolecularReactions(
+	const IngredientsType& ingredients_, std::string outputFilename_)
+:ingredients(ingredients_)
+,outputFilename(outputFilename_)
+{}
+////////////////////////////////////////////////////////////////////////////////
+template< class IngredientsType >
+void AnalyzerIntramolecularReactions<IngredientsType>::initialize(){}
+
+template< class IngredientsType >
+bool AnalyzerIntramolecularReactions<IngredientsType>::execute()
+{
+	
+ 	return true;
+}
+template<class IngredientsType>
+void AnalyzerIntramolecularReactions<IngredientsType>::cleanup()
+{
+  	dumpData();
+}
+template<class IngredientsType>
+void AnalyzerIntramolecularReactions<IngredientsType>::dumpData()
+{  
+	//output for the equilibrated positions 
+	std::stringstream commentAveragePosition;
+	commentAveragePosition<<"Created by AnalyzerIntramolecularReactions\n";
+	commentAveragePosition<<"nTotalBonds="<<myIngredients.getNumCrossLinkers()*4<<"\n";
+	commentAveragePosition<<"conversion nBonds nIntraBonds nBondsGel nIntraBondsGels \n";
+	ResultFormattingTools::writeResultFile(
+		outAvPos.str(),
+		ingredients,
+		data,
+		commentAveragePosition.str()
+	);
+}
+
+
+template <class IngredientsType>
+void AnalyzerIntramolecularReactions<IngredientsType>::getBiggestCluster () {
+	uint32_t nMolecules(0);
+	std::vector<uint32_t> LargestCluster;
+	const typename IngredientsType::molecules_type& getMolies = ingredients.getMolecules(); 
+	//search largest cluster: use the attribute tag for that
+	//at first store the initial attributes to reset them after the search
+	//then color the whole graph. connected parts have the same color
+	auto nMonomers(getMolies.size());
+	std::vector<uint32_t> Tag(nMonomers,0);
+	//color graph
+	int freeColor(1);
+	for (auto i=0 ; i < nMonomers;i++){
+		std::vector<size_t> rememberBranch;
+		rememberBranch.push_back(i);
+		if(Tag[i] == 0) {
+			while ( rememberBranch.size() > 0 ){
+				auto ID(rememberBranch.back());
+				auto color(Tag[ID]);
+				rememberBranch.pop_back();
+				if ( color == 0){
+					Tag[ID]=freeColor;
+					auto nLinks(getMolies.getNumLinks(ID));
+					if(nLinks != 0 ){
+						for(auto j=0; j < nLinks ; j++){
+							auto Neighbor(getMolies.getNeighborIdx(ID,j));
+							if( Tag[Neighbor] == 0 ) rememberBranch.push_back(Neighbor);
+						}
+					}
+				}
+			}
+			freeColor++;
+		}
+	} 
+	freeColor--;  
+	nMolecules=freeColor;
+	std::cout << "#Molecules=" << nMolecules <<std::endl;
+	std::vector<std::vector<uint32_t> > ColoredGraphIDs(freeColor+1,std::vector<uint32_t>(0));
+	for (auto i=0 ; i < nMonomers;i++){
+		uint32_t atti(Tag[i]);
+		if (atti==0 ){//this should never happen because all monomers should be covered above and colored 
+			std::stringstream error_message;
+			error_message << "AnalyzerActiveChainDensity::execute(): Found monomer which is not colored! ID is " << i << "\n";
+			throw std::runtime_error(error_message.str());
+		}
+		ColoredGraphIDs[atti].push_back(i);
+	}
+	auto biggestClusterID(0);
+	auto biggestClusterSize(ColoredGraphIDs[biggestClusterID].size());
+	for (auto i=0; i < freeColor+1 ; i++){
+		std::cout << "ClusterID  "  << i << " cluster size  " << ColoredGraphIDs[i].size() << std::endl; 
+		if ( biggestClusterSize < ColoredGraphIDs[i].size() ){ 
+			biggestClusterSize=ColoredGraphIDs[i].size();
+			biggestClusterID=i;
+		}
+	}
+	std::cout << "biggest ClusterID  "  << biggestClusterID << " biggestClusterSize " << biggestClusterSize << std::endl; 
+	LargestCluster=ColoredGraphIDs[biggestClusterID];
+	// return LargestCluster; 
+}
+
+#endif /*LEMONADE_PM_ANALYZER_ANALYZERINTRAMOLECULARREACTIONS_H*/
+
+
diff --git a/projects/CMakeLists.txt b/projects/CMakeLists.txt
index 5780870..738c1bd 100644
--- a/projects/CMakeLists.txt
+++ b/projects/CMakeLists.txt
@@ -3,4 +3,11 @@
 
 
 add_executable(TendomerNetworkForceEquilibrium TendomerNetworkForceEquilibrium.cpp)
-target_link_libraries(TendomerNetworkForceEquilibrium LeMonADE CommandlineParser )
\ No newline at end of file
+target_link_libraries(TendomerNetworkForceEquilibrium LeMonADE CommandlineParser )
+
+add_executable(TendomerNetworkExtractActivePart TendomerNetworkExtractActivePart.cpp)
+target_link_libraries(TendomerNetworkExtractActivePart LeMonADE CommandlineParser )
+
+
+# add_executable(IntramolecularReactions IntramolecularReactions.cpp)
+# target_link_libraries(IntramolecularReactions LeMonADE CommandlineParser )
\ No newline at end of file
diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index 69fecb7..9d441e5 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -103,6 +103,9 @@ int main(int argc, char* argv[]){
 	    }
 		if (! feCurve.empty()) custom=true;
 		
+
+		RandomNumberGenerators rng;
+		rng.seedAll();
 		///////////////////////////////////////////////////////////////////////////////
 		///end options parsing
 		///////////////////////////////////////////////////////////////////////////////
diff --git a/projects/IntramolecularReactions.cpp b/projects/IntramolecularReactions.cpp
new file mode 100644
index 0000000..7aa6fa5
--- /dev/null
+++ b/projects/IntramolecularReactions.cpp
@@ -0,0 +1,170 @@
+/*--------------------------------------------------------------------------------
+    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/>.
+
+--------------------------------------------------------------------------------*/
+
+/****************************************************************************** 
+ * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
+ * author: Toni Müller
+ * email: mueller-toni@ipfdd.de
+ * project: LeMonADE-Phantom Modulus
+ *****************************************************************************/
+#include <iostream>
+#include <vector>
+#include <bitset>
+
+#include <LeMonADE/core/Ingredients.h>
+#include <LeMonADE/updater/UpdaterReadBfmFile.h>
+#include <LeMonADE/analyzer/AnalyzerWriteBfmFile.h>
+#include <LeMonADE/feature/FeatureMoleculesIOUnsaveCheck.h>
+#include <LeMonADE/feature/FeatureReactiveBonds.h>
+#include <LeMonADE/feature/FeatureBox.h>
+#include <LeMonADE/feature/FeatureLabel.h>
+#include <LeMonADE/utility/TaskManager.h>
+
+#include <extern/catchorg/clara/clara.hpp>
+
+#include <LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h>
+#include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
+#include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
+#include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
+#include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h>
+#include <LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h>
+
+
+int main(int argc, char* argv[]){
+	try{
+		///////////////////////////////////////////////////////////////////////////////
+		///parse options///
+		std::string inputBFM("init.bfm");
+		std::string outputData("IntramolecularReactions.dat");
+		std::string inputConnection("BondCreationBreaking.dat");
+		std::string feCurve("");
+		double relaxationParameter(10.);
+		double threshold(0.5);
+		double stepwidth(1.0);
+		double minConversion(50.0);
+		
+		bool showHelp = false;
+		auto parser
+			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"          ] ("(required)Input filename of the bfm file"                                    ).required()
+			| clara::detail::Opt(     inputConnection, "inputConnection (=BondCreationBreaking.dat)"     ) ["-d"]["--inputConnection"] ("used for the time development of the topology. "                             ).required()
+			| clara::detail::Opt(          outputData, "outputData (=IntramolecularReactions.dat)"       ) ["-o"]["--outputData"      ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
+			| clara::detail::Opt(           stepwidth, "stepwidth"                                       ) ["-s"]["--stepwidth"      ] ("(optional) Width for the increase in percentage. Default: 1%."               ).optional()
+			| clara::detail::Opt(       minConversion, "minConversion"                                   ) ["-u"]["--minConversion"  ] ("(optional) Minimum conversion to be read in. Default: 50%."                  ).optional()
+			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"      ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
+			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"        ] ("(optional) Force-Extension curve. Default \"\"."                             ).required()
+			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"          ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
+			| clara::Help( showHelp );
+		
+	    auto result = parser.parse( clara::Args( argc, argv ) );
+	    
+	    if( !result ) {
+	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
+	      exit(1);
+	    }else if(showHelp == true){
+	      std::cout << "Simulator to connect linear chains with single monomers of certain functionality"<< std::endl;
+	      parser.writeToStream(std::cout);
+	      exit(0);
+	    }else{
+	      std::cout << "outputData            : " << outputData             << std::endl;
+	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
+	      std::cout << "inputConnection       : " << inputConnection        << std::endl; 
+	      std::cout << "stepwidth             : " << stepwidth              << std::endl;
+	      std::cout << "minConversion         : " << minConversion          << std::endl;
+	      std::cout << "threshold             : " << threshold              << std::endl; 
+		  std::cout << "feCurve               : " << feCurve                << std::endl;
+	    }
+		
+		///////////////////////////////////////////////////////////////////////////////
+		///end options parsing
+		///////////////////////////////////////////////////////////////////////////////
+		//Read in th last Config 
+		typedef LOKI_TYPELIST_3(FeatureMoleculesIOUnsaveCheck, FeatureLabel, FeatureReactiveBonds) Features;
+		typedef ConfigureSystem<VectorInt3,Features, 7> Config;
+		typedef Ingredients<Config> Ing;
+		Ing myIngredients;
+		
+		TaskManager taskmanager;
+		
+		taskmanager.addUpdater( new UpdaterReadBfmFile<Ing>(inputBFM,myIngredients, UpdaterReadBfmFile<Ing>::READ_LAST_CONFIG_SAVE),0);
+
+		//initialize and run
+		taskmanager.initialize();
+		taskmanager.run(1);
+		taskmanager.cleanup();
+		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
+		//the foce equilibrium is reached off lattice ( no integer values for the positions )
+		typedef LOKI_TYPELIST_3(FeatureBox, FeatureCrosslinkConnectionsLookUpTendomers ,FeatureLabel) Features2;
+		typedef ConfigureSystem<VectorDouble3,Features2, 7> Config2;
+		typedef Ingredients<Config2> Ing2;
+		Ing2 myIngredients2;
+		
+		myIngredients2.setBoxX(myIngredients.getBoxX());
+		myIngredients2.setBoxY(myIngredients.getBoxY());
+		myIngredients2.setBoxZ(myIngredients.getBoxZ());
+		myIngredients2.setPeriodicX(myIngredients.isPeriodicX());
+		myIngredients2.setPeriodicY(myIngredients.isPeriodicY());
+		myIngredients2.setPeriodicZ(myIngredients.isPeriodicZ());
+		myIngredients2.modifyMolecules().resize(myIngredients.getMolecules().size());
+		myIngredients2.modifyMolecules().setAge(myIngredients.getMolecules().getAge());
+
+        myIngredients2.setNumTendomers           (myIngredients.getNumTendomers());
+		myIngredients2.setNumCrossLinkers        (myIngredients.getNumCrossLinkers());
+		myIngredients2.setNumMonomersPerChain    (myIngredients.getNumMonomersPerChain());
+		myIngredients2.setNumLabelsPerTendomerArm(myIngredients.getNumLabelsPerTendomerArm());
+		
+		for(size_t i = 0; i< myIngredients.getMolecules().size();i++){
+			myIngredients2.modifyMolecules()[i].modifyVector3D()=myIngredients.getMolecules()[i].getVector3D();
+			myIngredients2.modifyMolecules()[i].setReactive(myIngredients.getMolecules()[i].isReactive());
+			myIngredients2.modifyMolecules()[i].setNumMaxLinks(myIngredients.getMolecules()[i].getNumMaxLinks());
+			for (size_t j = 0 ; j < myIngredients.getMolecules().getNumLinks(i);j++){
+				uint32_t neighbor(myIngredients.getMolecules().getNeighborIdx(i,j));
+				if( ! myIngredients2.getMolecules().areConnected(i,neighbor) )
+					myIngredients2.modifyMolecules().connect(i,neighbor);
+			}
+		}
+		myIngredients2.synchronize();
+
+		TaskManager taskmanager2;
+		//read bonds and positions stepwise
+		taskmanager2.addUpdater( new UpdaterReadCrosslinkConnectionsTendomer<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
+        taskmanager2.addAnalyzer(new AnalyzerIntramolecularReactions<Ing2>(myIngredients2, outputData));
+		//initialize and run
+		taskmanager2.initialize();
+		taskmanager2.run();
+		taskmanager2.cleanup();
+		
+	}
+	catch(std::exception& e){
+		std::cerr<<"Error:\n"
+		<<e.what()<<std::endl;
+	}
+	catch(...){
+		std::cerr<<"Error: unknown exception\n";
+	}
+	
+	return 0;
+}
diff --git a/projects/TendomerNetworkExtractActivePart.cpp b/projects/TendomerNetworkExtractActivePart.cpp
new file mode 100644
index 0000000..b22fa6b
--- /dev/null
+++ b/projects/TendomerNetworkExtractActivePart.cpp
@@ -0,0 +1,220 @@
+/*--------------------------------------------------------------------------------
+    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/>.
+
+--------------------------------------------------------------------------------*/
+
+/****************************************************************************** 
+ * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
+ * author: Toni Müller
+ * email: mueller-toni@ipfdd.de
+ * project: LeMonADE-Phantom Modulus
+ *****************************************************************************/
+#include <iostream>
+#include <vector>
+#include <bitset>
+
+#include <LeMonADE/core/Ingredients.h>
+#include <LeMonADE/updater/UpdaterReadBfmFile.h>
+#include <LeMonADE/analyzer/AnalyzerWriteBfmFileSubGroup.h>
+#include <LeMonADE/feature/FeatureMoleculesIOUnsaveCheck.h>
+#include <LeMonADE/feature/FeatureReactiveBonds.h>
+#include <LeMonADE/feature/FeatureAttributes.h>
+#include <LeMonADE/feature/FeatureBox.h>
+#include <LeMonADE/feature/FeatureLabel.h>
+#include <LeMonADE/utility/DepthIteratorPredicates.h>
+#include <LeMonADE/utility/DepthIterator.h>
+#include <LeMonADE/utility/MonomerGroup.h>
+#include <LeMonADE/utility/TaskManager.h>
+
+#include <extern/catchorg/clara/clara.hpp>
+
+#include <LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h>
+#include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
+#include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
+#include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
+#include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h>
+#include <LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h>
+
+
+int main(int argc, char* argv[]){
+	try{
+		///////////////////////////////////////////////////////////////////////////////
+		///parse options///
+		std::string inputBFM("init.bfm");
+		std::string outputBFM("Config.bfm.dat");
+		std::string inputConnection("BondCreationBreaking.dat");
+        std::string activeComponent("active_00001.dat");		
+		bool showHelp = false;
+		auto parser
+			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"           ] ("(required)Input filename of the bfm file"                                    ).required()
+			| clara::detail::Opt(     inputConnection, "inputConnection (=BondCreationBreaking.dat)"     ) ["-d"]["--inputConnection" ] ("used for the time development of the topology. "                             ).required()
+            | clara::detail::Opt(     activeComponent, "activeComponents (=active_00001.dat)"            ) ["-a"]["--activeComponents"] ("sets the active components . "                                              ).required()
+			| clara::detail::Opt(           outputBFM, "outputBFM (=Config.bfm)"                         ) ["-o"]["--outputBFM"       ] ("Output filename for the active material of the tendomer network.")
+			| clara::Help( showHelp );
+		
+	    auto result = parser.parse( clara::Args( argc, argv ) );
+	    
+	    if( !result ) {
+	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
+	      exit(1);
+	    }else if(showHelp == true){
+	      std::cout << "Analyzer taking a bond table and a table specifying the activity of an object and writes the active part of the tendoemr network."<< std::endl;
+          std::cout << "Important: input file for the connections and the active material must fit to each other!!!"<< std::endl;
+	      parser.writeToStream(std::cout);
+	      exit(0);
+	    }else{
+	      std::cout << "outputBFM             : " << outputBFM          << std::endl;
+	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
+	      std::cout << "inputConnection       : " << inputConnection        << std::endl; 
+          std::cout << "activeComponent       : " << activeComponent        << std::endl; 
+	    }
+		RandomNumberGenerators rng;
+		rng.seedAll();
+		///////////////////////////////////////////////////////////////////////////////
+		///end options parsing
+		///////////////////////////////////////////////////////////////////////////////
+		//Read in th last Config 
+		typedef LOKI_TYPELIST_4(FeatureMoleculesIOUnsaveCheck, FeatureLabel, FeatureReactiveBonds, FeatureAttributes<>) Features;
+		typedef ConfigureSystem<VectorInt3,Features, 7> Config;
+		typedef Ingredients<Config> Ing;
+		Ing myIngredients;
+		
+		TaskManager taskmanager;
+		
+		taskmanager.addUpdater( new UpdaterReadBfmFile<Ing>(inputBFM,myIngredients, UpdaterReadBfmFile<Ing>::READ_LAST_CONFIG_SAVE),0);
+		taskmanager.addUpdater( new UpdaterReadCrosslinkConnectionsTendomer<Ing>(myIngredients, inputConnection, 0., 1.0) );
+
+		//initialize and run
+		taskmanager.initialize();
+		taskmanager.run(1);
+		taskmanager.cleanup();
+		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
+        // activeObjects are first all cross links and afterwards all chain: 0-sol, 1-gel/pending, 2-active 
+        std::vector<bool> activeObject;
+        std::ifstream in(activeComponent);
+        std::string line;
+
+		auto nCrossLinks(myIngredients.getNumCrossLinkers());
+		auto nChains(myIngredients.getNumTendomers());
+		auto nSegments(myIngredients.getNumMonomersPerChain()*2);
+		auto nChainMonomers(nChains*nSegments);
+		auto objectID(0);
+		auto nActiveCrossLinks(0);
+		auto nActiveTendomers(0);
+		std::cout <<"Filestart:\n" ;
+        while (in.good() &&  ! in.eof() ){
+            getline(in,line);
+            std::stringstream ss;
+            uint32_t activeTag;
+            ss << line;
+			std::cout << line <<"\n";
+			if (! line.empty()) {
+				ss >>activeTag;
+				auto tmpAttribute(0);
+				if(objectID < nCrossLinks ){
+					auto IdX(nChainMonomers+objectID);
+					std::cout << "OId=" << objectID << " IdX=" << IdX << std::endl;
+					if (activeTag == 2 ){
+						tmpAttribute=1;	
+						nActiveCrossLinks++;
+					}
+					myIngredients.modifyMolecules()[nChainMonomers+objectID].setAttributeTag(tmpAttribute);
+				}else{
+					auto IdCStart((objectID-nCrossLinks)*nSegments);
+					auto IdCEnd( (objectID-nCrossLinks+1)*nSegments-1);
+					std::cout << "OId=" << objectID << " IdC=" << IdCStart << "-" << IdCEnd << std::endl;
+					if (activeTag == 2 ) {
+						nActiveTendomers++;
+						tmpAttribute=1;
+					}
+					for (auto i =IdCStart ; i <= IdCEnd; i++ )
+						myIngredients.modifyMolecules()[i].setAttributeTag(tmpAttribute);
+				}
+				objectID++;
+			}
+        }
+		std::cout <<"Fileend:\n" ;
+		// for()
+		myIngredients.setNumTendomers           (nActiveTendomers);
+		myIngredients.setNumCrossLinkers        (nActiveCrossLinks);
+		myIngredients.setNumMonomersPerChain    (myIngredients.getNumMonomersPerChain());
+		myIngredients.setNumLabelsPerTendomerArm(myIngredients.getNumLabelsPerTendomerArm());
+		myIngredients.synchronize();
+		
+
+		MonomerGroup<typename Ing::molecules_type> subgroup(myIngredients.getMolecules());
+		subgroup.clear();
+		hasThisType<1> predicate;
+		for(size_t n=0;n<myIngredients.getMolecules().size();n++)
+		{
+			if(predicate(myIngredients.getMolecules(),n)==true) subgroup.push_back(n);
+		}
+		myIngredients.modifyMolecules()=subgroup.copyGroup();
+
+		for(size_t n=0;n<myIngredients.getMolecules().size();n++)
+		{
+			myIngredients.modifyMolecules()[n].setReactive(false);
+			myIngredients.modifyMolecules()[n].setNumMaxLinks(0);
+			if( n < nActiveTendomers*nSegments ){
+				if (n%(nSegments/2) == 0 ) {
+					myIngredients.modifyMolecules()[n].setReactive(true);
+					myIngredients.modifyMolecules()[n].setNumMaxLinks(2);
+				}
+			}else {
+				myIngredients.modifyMolecules()[n].setReactive(true);
+				myIngredients.modifyMolecules()[n].setNumMaxLinks(4);
+			}
+		}		
+
+		myIngredients.synchronize();
+		TaskManager taskmanager2;
+		taskmanager2.addAnalyzer( new AnalyzerWriteBfmFile<Ing >(outputBFM, myIngredients, 1) ); 
+		//initialize and run
+		taskmanager2.initialize();
+		taskmanager2.run(1);
+		taskmanager2.cleanup();
+
+		// AnalyzerWriteBfmFileSubGroup<Ing,hasThisType<1> >  writer(outputBFM, myIngredients, 1, hasThisType<1>());
+		// writer.initialize();
+		
+		// TaskManager taskmanager2;
+		// taskmanager2.addAnalyzer( new AnalyzerWriteBfmFileSubGroup<Ing,hasThisType<1> >(outputBFM, myIngredients, 1, hasThisType<1>()) ); 
+		
+		// //initialize and run
+		// taskmanager2.initialize();
+		// taskmanager2.run(1);
+		// // taskmanager2.cleanup();
+        
+	}
+	catch(std::exception& e){
+		std::cerr<<"Error:\n"
+		<<e.what()<<std::endl;
+	}
+	catch(...){
+		std::cerr<<"Error: unknown exception\n";
+	}
+	
+	return 0;
+}
diff --git a/projects/TendomerNetworkForceEquilibrium.cpp b/projects/TendomerNetworkForceEquilibrium.cpp
index 9996fd5..8b1a47e 100644
--- a/projects/TendomerNetworkForceEquilibrium.cpp
+++ b/projects/TendomerNetworkForceEquilibrium.cpp
@@ -43,6 +43,7 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 #include <LeMonADE/feature/FeatureBox.h>
 #include <LeMonADE/feature/FeatureLabel.h>
 #include <LeMonADE/utility/TaskManager.h>
+#include <LeMonADE/utility/RandomNumberGenerators.h>
 
 #include <extern/catchorg/clara/clara.hpp>
 
@@ -61,21 +62,18 @@ int main(int argc, char* argv[]){
 		std::string inputBFM("init.bfm");
 		std::string outputDataPos("CrosslinkPosition.dat");
 		std::string outputDataDist("ChainExtensionDistribution.dat");
-		std::string inputConnection("BondCreationBreaking.dat");
+		// std::string inputConnection("BondCreationBreaking.dat");
 		std::string feCurve("");
 		double relaxationParameter(10.);
 		double threshold(0.5);
-		double stepwidth(1.0);
-		double minConversion(50.0);
+		// double stepwidth(1.0);
+		// double minConversion(50.0);
 		
 		bool showHelp = false;
 		auto parser
 			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"          ] ("(required)Input filename of the bfm file"                                    ).required()
-			| clara::detail::Opt(     inputConnection, "inputConnection (=BondCreationBreaking.dat)"     ) ["-d"]["--inputConnection"] ("used for the time development of the topology. "                             ).required()
 			| clara::detail::Opt(       outputDataPos, "outputDataPos (=CrosslinkPosition.dat)"          ) ["-o"]["--outputPos"      ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
 			| clara::detail::Opt(      outputDataDist, "outputDataDist (=ChainExtensionDistribution.dat)") ["-c"]["--outputDist"     ] ("(optional) Output filename of the chain extension distribution."             ).optional()
-			| clara::detail::Opt(           stepwidth, "stepwidth"                                       ) ["-s"]["--stepwidth"      ] ("(optional) Width for the increase in percentage. Default: 1%."               ).optional()
-			| clara::detail::Opt(       minConversion, "minConversion"                                   ) ["-u"]["--minConversion"  ] ("(optional) Minimum conversion to be read in. Default: 50%."                  ).optional()
 			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"      ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
 			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"        ] ("(optional) Force-Extension curve. Default \"\"."                             ).required()
 			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"          ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
@@ -94,13 +92,11 @@ int main(int argc, char* argv[]){
 	      std::cout << "outputData            : " << outputDataPos          << std::endl;
 	      std::cout << "outputDataDist        : " << outputDataDist         << std::endl;
 	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
-	      std::cout << "inputConnection       : " << inputConnection        << std::endl; 
-	      std::cout << "stepwidth             : " << stepwidth              << std::endl;
-	      std::cout << "minConversion         : " << minConversion          << std::endl;
 	      std::cout << "threshold             : " << threshold              << std::endl; 
 		  std::cout << "feCurve               : " << feCurve                << std::endl;
 	    }
-		
+		RandomNumberGenerators rng;
+		rng.seedAll();
 		///////////////////////////////////////////////////////////////////////////////
 		///end options parsing
 		///////////////////////////////////////////////////////////////////////////////
@@ -134,12 +130,6 @@ int main(int argc, char* argv[]){
 		myIngredients2.modifyMolecules().resize(myIngredients.getMolecules().size());
 		myIngredients2.modifyMolecules().setAge(myIngredients.getMolecules().getAge());
         
-		// myIngredients2.setNumOfChains              (myIngredients.getNumOfChains());
-		// myIngredients2.setNumOfCrosslinks          (myIngredients.getNumOfCrosslinks());
-		// myIngredients2.setNumOfMonomersPerChain    (myIngredients.getNumOfMonomersPerChain());
-		// myIngredients2.setNumOfMonomersPerCrosslink(myIngredients.getNumOfMonomersPerCrosslink());
-		// myIngredients2.setFunctionality            (myIngredients.getFunctionality());
-
         myIngredients2.setNumTendomers           (myIngredients.getNumTendomers());
 		myIngredients2.setNumCrossLinkers        (myIngredients.getNumCrossLinkers());
 		myIngredients2.setNumMonomersPerChain    (myIngredients.getNumMonomersPerChain());
@@ -159,7 +149,6 @@ int main(int argc, char* argv[]){
 
 		TaskManager taskmanager2;
 		//read bonds and positions stepwise
-		taskmanager2.addUpdater( new UpdaterReadCrosslinkConnectionsTendomer<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
         auto updater = new UpdaterForceBalancedPositionTendomer<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
         updater->setFilename(feCurve);
         updater->setRelaxationParameter(relaxationParameter);
diff --git a/projects/TendomerNetworkForceEquilibriumConversionSeries.cpp b/projects/TendomerNetworkForceEquilibriumConversionSeries.cpp
new file mode 100644
index 0000000..58a734b
--- /dev/null
+++ b/projects/TendomerNetworkForceEquilibriumConversionSeries.cpp
@@ -0,0 +1,186 @@
+/*--------------------------------------------------------------------------------
+    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/>.
+
+--------------------------------------------------------------------------------*/
+
+/****************************************************************************** 
+ * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
+ * author: Toni Müller
+ * email: mueller-toni@ipfdd.de
+ * project: LeMonADE-Phantom Modulus
+ *****************************************************************************/
+#include <iostream>
+#include <vector>
+#include <bitset>
+
+#include <LeMonADE/core/Ingredients.h>
+#include <LeMonADE/updater/UpdaterReadBfmFile.h>
+#include <LeMonADE/analyzer/AnalyzerWriteBfmFile.h>
+#include <LeMonADE/feature/FeatureMoleculesIOUnsaveCheck.h>
+#include <LeMonADE/feature/FeatureReactiveBonds.h>
+#include <LeMonADE/feature/FeatureBox.h>
+#include <LeMonADE/feature/FeatureLabel.h>
+#include <LeMonADE/utility/TaskManager.h>
+#include <LeMonADE/utility/RandomNumberGenerators.h>
+
+#include <extern/catchorg/clara/clara.hpp>
+
+#include <LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h>
+#include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
+#include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
+#include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
+#include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h>
+#include <LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h>
+
+
+int main(int argc, char* argv[]){
+	try{
+		///////////////////////////////////////////////////////////////////////////////
+		///parse options///
+		std::string inputBFM("init.bfm");
+		std::string outputDataPos("CrosslinkPosition.dat");
+		std::string outputDataDist("ChainExtensionDistribution.dat");
+		std::string inputConnection("BondCreationBreaking.dat");
+		std::string feCurve("");
+		double relaxationParameter(10.);
+		double threshold(0.5);
+		double stepwidth(1.0);
+		double minConversion(50.0);
+		
+		bool showHelp = false;
+		auto parser
+			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"          ] ("(required)Input filename of the bfm file"                                    ).required()
+			| clara::detail::Opt(     inputConnection, "inputConnection (=BondCreationBreaking.dat)"     ) ["-d"]["--inputConnection"] ("used for the time development of the topology. "                             ).required()
+			| clara::detail::Opt(       outputDataPos, "outputDataPos (=CrosslinkPosition.dat)"          ) ["-o"]["--outputPos"      ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
+			| clara::detail::Opt(      outputDataDist, "outputDataDist (=ChainExtensionDistribution.dat)") ["-c"]["--outputDist"     ] ("(optional) Output filename of the chain extension distribution."             ).optional()
+			| clara::detail::Opt(           stepwidth, "stepwidth"                                       ) ["-s"]["--stepwidth"      ] ("(optional) Width for the increase in percentage. Default: 1%."               ).optional()
+			| clara::detail::Opt(       minConversion, "minConversion"                                   ) ["-u"]["--minConversion"  ] ("(optional) Minimum conversion to be read in. Default: 50%."                  ).optional()
+			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"      ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
+			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"        ] ("(optional) Force-Extension curve. Default \"\"."                             ).required()
+			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"          ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
+			| clara::Help( showHelp );
+		
+	    auto result = parser.parse( clara::Args( argc, argv ) );
+	    
+	    if( !result ) {
+	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
+	      exit(1);
+	    }else if(showHelp == true){
+	      std::cout << "Simulator to connect linear chains with single monomers of certain functionality"<< std::endl;
+	      parser.writeToStream(std::cout);
+	      exit(0);
+	    }else{
+	      std::cout << "outputData            : " << outputDataPos          << std::endl;
+	      std::cout << "outputDataDist        : " << outputDataDist         << std::endl;
+	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
+	      std::cout << "inputConnection       : " << inputConnection        << std::endl; 
+	      std::cout << "stepwidth             : " << stepwidth              << std::endl;
+	      std::cout << "minConversion         : " << minConversion          << std::endl;
+	      std::cout << "threshold             : " << threshold              << std::endl; 
+		  std::cout << "feCurve               : " << feCurve                << std::endl;
+	    }
+		RandomNumberGenerators rng;
+		rng.seedAll();
+		///////////////////////////////////////////////////////////////////////////////
+		///end options parsing
+		///////////////////////////////////////////////////////////////////////////////
+		//Read in th last Config 
+		typedef LOKI_TYPELIST_3(FeatureMoleculesIOUnsaveCheck, FeatureLabel, FeatureReactiveBonds) Features;
+		typedef ConfigureSystem<VectorInt3,Features, 7> Config;
+		typedef Ingredients<Config> Ing;
+		Ing myIngredients;
+		
+		TaskManager taskmanager;
+		
+		taskmanager.addUpdater( new UpdaterReadBfmFile<Ing>(inputBFM,myIngredients, UpdaterReadBfmFile<Ing>::READ_LAST_CONFIG_SAVE),0);
+
+		//initialize and run
+		taskmanager.initialize();
+		taskmanager.run(1);
+		taskmanager.cleanup();
+		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
+		//the foce equilibrium is reached off lattice ( no integer values for the positions )
+		typedef LOKI_TYPELIST_3(FeatureBox, FeatureCrosslinkConnectionsLookUpTendomers ,FeatureLabel) Features2;
+		typedef ConfigureSystem<VectorDouble3,Features2, 7> Config2;
+		typedef Ingredients<Config2> Ing2;
+		Ing2 myIngredients2;
+		
+		myIngredients2.setBoxX(myIngredients.getBoxX());
+		myIngredients2.setBoxY(myIngredients.getBoxY());
+		myIngredients2.setBoxZ(myIngredients.getBoxZ());
+		myIngredients2.setPeriodicX(myIngredients.isPeriodicX());
+		myIngredients2.setPeriodicY(myIngredients.isPeriodicY());
+		myIngredients2.setPeriodicZ(myIngredients.isPeriodicZ());
+		myIngredients2.modifyMolecules().resize(myIngredients.getMolecules().size());
+		myIngredients2.modifyMolecules().setAge(myIngredients.getMolecules().getAge());
+        
+		// myIngredients2.setNumOfChains              (myIngredients.getNumOfChains());
+		// myIngredients2.setNumOfCrosslinks          (myIngredients.getNumOfCrosslinks());
+		// myIngredients2.setNumOfMonomersPerChain    (myIngredients.getNumOfMonomersPerChain());
+		// myIngredients2.setNumOfMonomersPerCrosslink(myIngredients.getNumOfMonomersPerCrosslink());
+		// myIngredients2.setFunctionality            (myIngredients.getFunctionality());
+
+        myIngredients2.setNumTendomers           (myIngredients.getNumTendomers());
+		myIngredients2.setNumCrossLinkers        (myIngredients.getNumCrossLinkers());
+		myIngredients2.setNumMonomersPerChain    (myIngredients.getNumMonomersPerChain());
+		myIngredients2.setNumLabelsPerTendomerArm(myIngredients.getNumLabelsPerTendomerArm());
+		
+		for(size_t i = 0; i< myIngredients.getMolecules().size();i++){
+			myIngredients2.modifyMolecules()[i].modifyVector3D()=myIngredients.getMolecules()[i].getVector3D();
+			myIngredients2.modifyMolecules()[i].setReactive(myIngredients.getMolecules()[i].isReactive());
+			myIngredients2.modifyMolecules()[i].setNumMaxLinks(myIngredients.getMolecules()[i].getNumMaxLinks());
+			for (size_t j = 0 ; j < myIngredients.getMolecules().getNumLinks(i);j++){
+				uint32_t neighbor(myIngredients.getMolecules().getNeighborIdx(i,j));
+				if( ! myIngredients2.getMolecules().areConnected(i,neighbor) )
+					myIngredients2.modifyMolecules().connect(i,neighbor);
+			}
+		}
+		myIngredients2.synchronize();
+
+		TaskManager taskmanager2;
+		//read bonds and positions stepwise
+		taskmanager2.addUpdater( new UpdaterReadCrosslinkConnectionsTendomer<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
+        auto updater = new UpdaterForceBalancedPositionTendomer<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
+        updater->setFilename(feCurve);
+        updater->setRelaxationParameter(relaxationParameter);
+        // auto updater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
+        taskmanager2.addUpdater( updater );
+		taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
+		//initialize and run
+		taskmanager2.initialize();
+		taskmanager2.run();
+		taskmanager2.cleanup();
+		
+	}
+	catch(std::exception& e){
+		std::cerr<<"Error:\n"
+		<<e.what()<<std::endl;
+	}
+	catch(...){
+		std::cerr<<"Error: unknown exception\n";
+	}
+	
+	return 0;
+}

From 46a3d7e8d9aa1438845170fae24ea4ecbbc3b9b7 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Fri, 4 Jun 2021 09:19:56 +0200
Subject: [PATCH 06/70] bugfix

---
 projects/TendomerNetworkExtractActivePart.cpp | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/projects/TendomerNetworkExtractActivePart.cpp b/projects/TendomerNetworkExtractActivePart.cpp
index b22fa6b..d8535db 100644
--- a/projects/TendomerNetworkExtractActivePart.cpp
+++ b/projects/TendomerNetworkExtractActivePart.cpp
@@ -192,10 +192,11 @@ int main(int argc, char* argv[]){
 		TaskManager taskmanager2;
 		taskmanager2.addAnalyzer( new AnalyzerWriteBfmFile<Ing >(outputBFM, myIngredients, 1) ); 
 		//initialize and run
-		taskmanager2.initialize();
-		taskmanager2.run(1);
-		taskmanager2.cleanup();
-
+		if ( nActiveTendomers > 0  ){
+			taskmanager2.initialize();
+			taskmanager2.run(1);
+			taskmanager2.cleanup();
+		}
 		// AnalyzerWriteBfmFileSubGroup<Ing,hasThisType<1> >  writer(outputBFM, myIngredients, 1, hasThisType<1>());
 		// writer.initialize();
 		

From 27debe9c4716172503a12041301770d36e16ccd7 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Fri, 4 Jun 2021 10:31:17 +0200
Subject: [PATCH 07/70] comemnt out stdout

---
 projects/TendomerNetworkExtractActivePart.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/projects/TendomerNetworkExtractActivePart.cpp b/projects/TendomerNetworkExtractActivePart.cpp
index d8535db..0593303 100644
--- a/projects/TendomerNetworkExtractActivePart.cpp
+++ b/projects/TendomerNetworkExtractActivePart.cpp
@@ -129,13 +129,13 @@ int main(int argc, char* argv[]){
             std::stringstream ss;
             uint32_t activeTag;
             ss << line;
-			std::cout << line <<"\n";
+			// std::cout << line <<"\n";
 			if (! line.empty()) {
 				ss >>activeTag;
 				auto tmpAttribute(0);
 				if(objectID < nCrossLinks ){
 					auto IdX(nChainMonomers+objectID);
-					std::cout << "OId=" << objectID << " IdX=" << IdX << std::endl;
+					// std::cout << "OId=" << objectID << " IdX=" << IdX << std::endl;
 					if (activeTag == 2 ){
 						tmpAttribute=1;	
 						nActiveCrossLinks++;
@@ -144,7 +144,7 @@ int main(int argc, char* argv[]){
 				}else{
 					auto IdCStart((objectID-nCrossLinks)*nSegments);
 					auto IdCEnd( (objectID-nCrossLinks+1)*nSegments-1);
-					std::cout << "OId=" << objectID << " IdC=" << IdCStart << "-" << IdCEnd << std::endl;
+					// std::cout << "OId=" << objectID << " IdC=" << IdCStart << "-" << IdCEnd << std::endl;
 					if (activeTag == 2 ) {
 						nActiveTendomers++;
 						tmpAttribute=1;

From 642b2f6dbfd340aca6638edbff231a8b45778c9c Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 9 Jun 2021 13:39:00 +0200
Subject: [PATCH 08/70] TendomerNetworkWritePartialConnectedNetwork: Erases all
 reversible bonds and creates only these in the given bond table file

---
 projects/CMakeLists.txt                       |   3 +
 ...merNetworkWritePartialConnectedNetwork.cpp | 121 ++++++++++++++++++
 2 files changed, 124 insertions(+)
 create mode 100644 projects/TendomerNetworkWritePartialConnectedNetwork.cpp

diff --git a/projects/CMakeLists.txt b/projects/CMakeLists.txt
index 738c1bd..74c7ce4 100644
--- a/projects/CMakeLists.txt
+++ b/projects/CMakeLists.txt
@@ -9,5 +9,8 @@ add_executable(TendomerNetworkExtractActivePart TendomerNetworkExtractActivePart
 target_link_libraries(TendomerNetworkExtractActivePart LeMonADE CommandlineParser )
 
 
+add_executable(TendomerNetworkWritePartialConnectedNetwork TendomerNetworkWritePartialConnectedNetwork.cpp)
+target_link_libraries(TendomerNetworkWritePartialConnectedNetwork LeMonADE CommandlineParser )
+
 # add_executable(IntramolecularReactions IntramolecularReactions.cpp)
 # target_link_libraries(IntramolecularReactions LeMonADE CommandlineParser )
\ No newline at end of file
diff --git a/projects/TendomerNetworkWritePartialConnectedNetwork.cpp b/projects/TendomerNetworkWritePartialConnectedNetwork.cpp
new file mode 100644
index 0000000..bcbc61b
--- /dev/null
+++ b/projects/TendomerNetworkWritePartialConnectedNetwork.cpp
@@ -0,0 +1,121 @@
+/*--------------------------------------------------------------------------------
+    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/>.
+
+--------------------------------------------------------------------------------*/
+
+/****************************************************************************** 
+ * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
+ * author: Toni Müller
+ * email: mueller-toni@ipfdd.de
+ * project: LeMonADE-Phantom Modulus
+ *****************************************************************************/
+#include <iostream>
+#include <vector>
+#include <bitset>
+
+#include <LeMonADE/core/Ingredients.h>
+#include <LeMonADE/updater/UpdaterReadBfmFile.h>
+#include <LeMonADE/analyzer/AnalyzerWriteBfmFileSubGroup.h>
+#include <LeMonADE/feature/FeatureMoleculesIOUnsaveCheck.h>
+#include <LeMonADE/feature/FeatureReactiveBonds.h>
+#include <LeMonADE/feature/FeatureAttributes.h>
+#include <LeMonADE/feature/FeatureBox.h>
+#include <LeMonADE/feature/FeatureLabel.h>
+#include <LeMonADE/utility/DepthIteratorPredicates.h>
+#include <LeMonADE/utility/DepthIterator.h>
+#include <LeMonADE/utility/MonomerGroup.h>
+#include <LeMonADE/utility/TaskManager.h>
+
+#include <extern/catchorg/clara/clara.hpp>
+
+#include <LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h>
+#include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
+#include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
+#include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
+#include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h>
+#include <LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h>
+
+
+int main(int argc, char* argv[]){
+	try{
+		///////////////////////////////////////////////////////////////////////////////
+		///parse options///
+		std::string inputBFM("init.bfm");
+		std::string outputBFM("Config.bfm.dat");
+		std::string inputConnection("BondCreationBreaking.dat");
+		bool showHelp = false;
+		auto parser
+			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"           ] ("(required)Input filename of the bfm file"                                    ).required()
+			| clara::detail::Opt(     inputConnection, "inputConnection (=BondCreationBreaking.dat)"     ) ["-d"]["--inputConnection" ] ("used for the time development of the topology. "                             ).required()
+			| clara::detail::Opt(           outputBFM, "outputBFM (=Config.bfm)"                         ) ["-o"]["--outputBFM"       ] ("Output filename for the active material of the tendomer network.")
+			| clara::Help( showHelp );
+		
+	    auto result = parser.parse( clara::Args( argc, argv ) );
+	    
+	    if( !result ) {
+	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
+	      exit(1);
+	    }else if(showHelp == true){
+	      std::cout << "Analyzer taking a bond table and a table specifying the activity of an object and writes the active part of the tendoemr network."<< std::endl;
+          std::cout << "Important: input file for the connections and the active material must fit to each other!!!"<< std::endl;
+	      parser.writeToStream(std::cout);
+	      exit(0);
+	    }else{
+	      std::cout << "outputBFM             : " << outputBFM          << std::endl;
+	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
+	      std::cout << "inputConnection       : " << inputConnection        << std::endl; 
+	    }
+		RandomNumberGenerators rng;
+		rng.seedAll();
+		///////////////////////////////////////////////////////////////////////////////
+		///end options parsing
+		///////////////////////////////////////////////////////////////////////////////
+		//Read in th last Config 
+		typedef LOKI_TYPELIST_4(FeatureMoleculesIOUnsaveCheck, FeatureLabel, FeatureReactiveBonds, FeatureAttributes<>) Features;
+		typedef ConfigureSystem<VectorInt3,Features, 7> Config;
+		typedef Ingredients<Config> Ing;
+		Ing myIngredients;
+		
+		TaskManager taskmanager;
+		
+		taskmanager.addUpdater( new UpdaterReadBfmFile<Ing>(inputBFM,myIngredients, UpdaterReadBfmFile<Ing>::READ_LAST_CONFIG_SAVE),0);
+		taskmanager.addUpdater( new UpdaterReadCrosslinkConnectionsTendomer<Ing>(myIngredients, inputConnection, 0., 1.0) );
+        taskmanager.addAnalyzer( new AnalyzerWriteBfmFile<Ing>(outputBFM, myIngredients, 1) ); 
+		//initialize and run
+		taskmanager.initialize();
+		taskmanager.run(1);
+		taskmanager.cleanup();
+		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
+	}
+	catch(std::exception& e){
+		std::cerr<<"Error:\n"
+		<<e.what()<<std::endl;
+	}
+	catch(...){
+		std::cerr<<"Error: unknown exception\n";
+	}
+	
+	return 0;
+}

From bbc431fe4c997e03c5af3df35d6f0d4fcfb677bf Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Thu, 10 Jun 2021 09:56:57 +0200
Subject: [PATCH 09/70] bugfix for non converging system

---
 .../updater/UpdaterForceBalancedPositionTendomer.h         | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h b/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h
index 0df7f26..25680ea 100644
--- a/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h
+++ b/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h
@@ -68,6 +68,7 @@ class UpdaterForceBalancedPositionTendomer:public AbstractUpdater
 template <class IngredientsType, class moveType>
 bool UpdaterForceBalancedPositionTendomer<IngredientsType,moveType>::execute(){
     std::cout << "UpdaterForceBalancedPositionTendomer::execute(): Start equilibration" <<std::endl;
+    auto counter=0;
     double avShift(threshold*1.1);
     uint32_t StartMCS(ing.getMolecules().getAge());
     setRelaxationParameter(relaxationParameter);
@@ -89,8 +90,12 @@ bool UpdaterForceBalancedPositionTendomer<IngredientsType,moveType>::execute(){
         }
         if( NSuccessfulMoves>0 ){
             avShift/=(NSuccessfulMoves);
-        }else 
+            counter=0;
+        }else {
             avShift=threshold*1.1;
+            counter++;
+        }
+        if (counter > 10 ){break;}
         ing.modifyMolecules().setAge(ing.getMolecules().getAge()+1);
         if (ing.getMolecules().getAge() %1000 == 0 ){
             std::cout << "MCS: " << ing.getMolecules().getAge() << "  and average shift: " << avShift << std::endl;

From 3ea9ae1f65cdaa5704edcb08c6fd0beae38d172f Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Thu, 10 Jun 2021 10:02:54 +0200
Subject: [PATCH 10/70] add possibility to chagne the relaxation factor

---
 .../updater/UpdaterForceBalancedPositionTendomer.h        | 8 +++++---
 projects/TendomerNetworkForceEquilibrium.cpp              | 8 ++++----
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h b/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h
index 25680ea..974ab5c 100644
--- a/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h
+++ b/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h
@@ -40,8 +40,8 @@ class UpdaterForceBalancedPositionTendomer:public AbstractUpdater
 {
 public:
     //! constructor for UpdaterForceBalancedPositionTendomer
-    UpdaterForceBalancedPositionTendomer(IngredientsType& ing_, double threshold_ ):
-    ing(ing_),threshold(threshold_){};
+    UpdaterForceBalancedPositionTendomer(IngredientsType& ing_, double threshold_, double factor_=0.995 ):
+    ing(ing_),threshold(threshold_),factor(factor_){};
     
     virtual void initialize(){relaxationParameter=move.getRelaxationParameter();}// init(move);};
     bool execute();
@@ -57,6 +57,8 @@ class UpdaterForceBalancedPositionTendomer:public AbstractUpdater
     double threshold;
 
     double relaxationParameter;
+
+    double factor;
     
     //! move to equilibrate the cross links by force equilibrium
     moveType move;
@@ -99,7 +101,7 @@ bool UpdaterForceBalancedPositionTendomer<IngredientsType,moveType>::execute(){
         ing.modifyMolecules().setAge(ing.getMolecules().getAge()+1);
         if (ing.getMolecules().getAge() %1000 == 0 ){
             std::cout << "MCS: " << ing.getMolecules().getAge() << "  and average shift: " << avShift << std::endl;
-            setRelaxationParameter(move.getRelaxationParameter()*0.995 );
+            setRelaxationParameter(move.getRelaxationParameter()*factor );
         }
     }
     std::cout << "Finish equilibration with average shift per cross link < " << avShift << " after " << ing.getMolecules().getAge()-StartMCS <<std::endl;
diff --git a/projects/TendomerNetworkForceEquilibrium.cpp b/projects/TendomerNetworkForceEquilibrium.cpp
index 8b1a47e..764df5d 100644
--- a/projects/TendomerNetworkForceEquilibrium.cpp
+++ b/projects/TendomerNetworkForceEquilibrium.cpp
@@ -62,12 +62,10 @@ int main(int argc, char* argv[]){
 		std::string inputBFM("init.bfm");
 		std::string outputDataPos("CrosslinkPosition.dat");
 		std::string outputDataDist("ChainExtensionDistribution.dat");
-		// std::string inputConnection("BondCreationBreaking.dat");
 		std::string feCurve("");
 		double relaxationParameter(10.);
 		double threshold(0.5);
-		// double stepwidth(1.0);
-		// double minConversion(50.0);
+		double factor(0.995);
 		
 		bool showHelp = false;
 		auto parser
@@ -77,6 +75,7 @@ int main(int argc, char* argv[]){
 			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"      ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
 			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"        ] ("(optional) Force-Extension curve. Default \"\"."                             ).required()
 			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"          ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
+			| clara::detail::Opt(              factor, "factor (=10)"                                    ) ["-a"]["--factor"         ] ("(optional) Factor for reducing the relaxation parameter after 1000MCS. Default .995 .").optional()
 			| clara::Help( showHelp );
 		
 	    auto result = parser.parse( clara::Args( argc, argv ) );
@@ -94,6 +93,7 @@ int main(int argc, char* argv[]){
 	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
 	      std::cout << "threshold             : " << threshold              << std::endl; 
 		  std::cout << "feCurve               : " << feCurve                << std::endl;
+		  std::cout << "factor                : " << factor                << std::endl;
 	    }
 		RandomNumberGenerators rng;
 		rng.seedAll();
@@ -149,7 +149,7 @@ int main(int argc, char* argv[]){
 
 		TaskManager taskmanager2;
 		//read bonds and positions stepwise
-        auto updater = new UpdaterForceBalancedPositionTendomer<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
+        auto updater = new UpdaterForceBalancedPositionTendomer<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold, factor) ;
         updater->setFilename(feCurve);
         updater->setRelaxationParameter(relaxationParameter);
         // auto updater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;

From 3772c99c5f579c6d8f6ff2bec8287351a34f773b Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Fri, 11 Jun 2021 11:52:01 +0200
Subject: [PATCH 11/70] include the standard force equilibrium into the
 compilation again

---
 projects/CMakeLists.txt       |  4 ++--
 projects/ForceEquilibrium.cpp | 28 ++++++++++++++--------------
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/projects/CMakeLists.txt b/projects/CMakeLists.txt
index 74c7ce4..b7cbc52 100644
--- a/projects/CMakeLists.txt
+++ b/projects/CMakeLists.txt
@@ -1,5 +1,5 @@
-# add_executable(ForceEquilibrium ForceEquilibrium.cpp)
-# target_link_libraries(ForceEquilibrium LeMonADE CommandlineParser )
+add_executable(ForceEquilibrium ForceEquilibrium.cpp)
+target_link_libraries(ForceEquilibrium LeMonADE CommandlineParser )
 
 
 add_executable(TendomerNetworkForceEquilibrium TendomerNetworkForceEquilibrium.cpp)
diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index 9d441e5..a7142b0 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -62,12 +62,12 @@ int main(int argc, char* argv[]){
 		std::string outputDataPos("CrosslinkPosition.dat");
 		std::string outputDataDist("ChainExtensionDistribution.dat");
 		std::string inputConnection("BondCreationBreaking.dat");
-		std::string feCurve("");
-		double relaxationParameter(10.);
+		// std::string feCurve("");
+		// double relaxationParameter(10.);
 		double threshold(0.5);
 		double stepwidth(1.0);
 		double minConversion(50.0);
-		bool custom(false);
+		// bool custom(true);
 		
 		bool showHelp = false;
 		auto parser
@@ -78,8 +78,8 @@ int main(int argc, char* argv[]){
 			| clara::detail::Opt(           stepwidth, "stepwidth"                                       ) ["-s"]["--stepwidth"      ] ("(optional) Width for the increase in percentage. Default: 1%."               ).optional()
 			| clara::detail::Opt(       minConversion, "minConversion"                                   ) ["-u"]["--minConversion"  ] ("(optional) Minimum conversion to be read in. Default: 50%."                  ).optional()
 			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"      ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
-			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"        ] ("(optional) Force-Extension curve. Default \"\"."                             ).optional()
-			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"          ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
+			// | clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"        ] ("(optional) Force-Extension curve. Default \"\"."                             ).optional()
+			// | clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"          ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
 			| clara::Help( showHelp );
 		
 	    auto result = parser.parse( clara::Args( argc, argv ) );
@@ -99,9 +99,9 @@ int main(int argc, char* argv[]){
 	      std::cout << "stepwidth             : " << stepwidth              << std::endl;
 	      std::cout << "minConversion         : " << minConversion          << std::endl;
 	      std::cout << "threshold             : " << threshold              << std::endl; 
-		  std::cout << "feCurve               : " << feCurve                << std::endl;
+		//   std::cout << "feCurve               : " << feCurve                << std::endl;
 	    }
-		if (! feCurve.empty()) custom=true;
+		// if (! feCurve.empty()) custom=false;
 		
 
 		RandomNumberGenerators rng;
@@ -159,14 +159,14 @@ int main(int argc, char* argv[]){
 		TaskManager taskmanager2;
 		//read bonds and positions stepwise
 		taskmanager2.addUpdater( new UpdaterReadCrosslinkConnections<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
-		if (custom) 
+		// if (custom) 
 			taskmanager2.addUpdater( new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) );
-		else {
-			auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
-			updater->setFilename(feCurve);
-			updater->setRelaxationParameter(relaxationParameter);
-			taskmanager2.addUpdater( updater );
-		}
+		// else {
+		// 	auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
+		// 	updater->setFilename(feCurve);
+		// 	updater->setRelaxationParameter(relaxationParameter);
+		// 	taskmanager2.addUpdater( updater );
+		// }
 		taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
 		//initialize and run
 		taskmanager2.initialize();

From d8186b1d104bb2cd975823e57790b0396d0cea19 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 16 Jun 2021 10:43:20 +0200
Subject: [PATCH 12/70] add some debug output

---
 .../updater/UpdaterReadCrosslinkConnections.h |  4 ++++
 .../UpdaterReadCrosslinkConnectionsTendomer.h | 19 ++++++++--------
 projects/TendomerNetworkExtractActivePart.cpp | 22 ++++++++++++++++---
 3 files changed, 33 insertions(+), 12 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnections.h b/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnections.h
index 9e2f29c..de40361 100644
--- a/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnections.h
+++ b/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnections.h
@@ -24,6 +24,8 @@ 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_PM_UPDATER_UPDATERREADCROSSLINKCONNECTIONS_H 
+#define LEMONADE_PM_UPDATER_UPDATERREADCROSSLINKCONNECTIONS_H
 #include <string>
 #include <iostream>
 #include <fstream>
@@ -208,3 +210,5 @@ bool UpdaterReadCrosslinkConnections<IngredientsType>::execute(){
         return true;
     }
 }
+
+#endif 
\ No newline at end of file
diff --git a/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h b/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h
index 295dc71..016d43d 100644
--- a/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h
+++ b/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h
@@ -24,6 +24,8 @@ 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_PM_UPDATER_UPDATERREADCROSSLINKCONNECTIONSTENDOMER_H 
+#define LEMONADE_PM_UPDATER_UPDATERREADCROSSLINKCONNECTIONSTENDOMER_H
 #include <string>
 #include <iostream>
 #include <fstream>
@@ -145,17 +147,11 @@ template <class IngredientsType>
 bool UpdaterReadCrosslinkConnectionsTendomer<IngredientsType>::execute(){
     //reset the ingredients container to the inital one
     ing = initialIng;
-    //open input file to the connection table 
-    //! stream reading input file
+    //stream reading input file
     std::ifstream stream;
     stream.open(input);
     if (stream.fail())
       throw std::runtime_error(std::string("error opening input file ") + input + std::string("\n"));
-    bool findStartofData(false);
-    std::string line;
-    getline(stream, line);
-    while (line.empty() || line.at(0) == '#' ) 
-        getline(stream, line);
     //current conversion 
     auto conversion = minConversion + static_cast<double>(nExecutions) * stepwidth;
     std::cout << "Current conversion is " <<conversion <<std::endl;
@@ -168,12 +164,15 @@ bool UpdaterReadCrosslinkConnectionsTendomer<IngredientsType>::execute(){
     while (NewConnections < ReadNLines && stream.good()){
         std::string line;
         getline(stream, line);
-        if (line.empty())
-            break;
+        if (line.empty() || line.at(0) == '#' )
+            continue;
         std::stringstream ss;
         uint32_t Time, createBreak, ChainID, nSegments, MonID1, P1X, P1Y, P1Z, MonID2, P2X, P2Y, P2Z;
         ss << line;
         ss >> Time >> createBreak>>  ChainID >> nSegments >>MonID1 >> P1X >> P1Y >> P1Z >> MonID2 >> P2X >> P2Y >> P2Z;
+        #ifdef DEBUG
+            std::cout << ss.str() << std::endl;
+        #endif //DEBUG//
         ing.modifyMolecules().setAge(Time);
         if ( ConnectCrossLinkToChain(MonID1, ChainID+1) ) {
         }else if( ConnectCrossLinkToChain(MonID2, ChainID+1) ) {
@@ -199,3 +198,5 @@ bool UpdaterReadCrosslinkConnectionsTendomer<IngredientsType>::execute(){
         return true;
     }
 }
+
+#endif
\ No newline at end of file
diff --git a/projects/TendomerNetworkExtractActivePart.cpp b/projects/TendomerNetworkExtractActivePart.cpp
index 0593303..1b4a6ac 100644
--- a/projects/TendomerNetworkExtractActivePart.cpp
+++ b/projects/TendomerNetworkExtractActivePart.cpp
@@ -112,7 +112,6 @@ int main(int argc, char* argv[]){
 		taskmanager.cleanup();
 		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
         // activeObjects are first all cross links and afterwards all chain: 0-sol, 1-gel/pending, 2-active 
-        std::vector<bool> activeObject;
         std::ifstream in(activeComponent);
         std::string line;
 
@@ -135,7 +134,9 @@ int main(int argc, char* argv[]){
 				auto tmpAttribute(0);
 				if(objectID < nCrossLinks ){
 					auto IdX(nChainMonomers+objectID);
-					// std::cout << "OId=" << objectID << " IdX=" << IdX << std::endl;
+					#ifdef DEBUG
+						std::cout <<  objectID << " "  << activeTag <<  " " << IdX <<  " " << IdX << std::endl;
+					#endif
 					if (activeTag == 2 ){
 						tmpAttribute=1;	
 						nActiveCrossLinks++;
@@ -144,7 +145,9 @@ int main(int argc, char* argv[]){
 				}else{
 					auto IdCStart((objectID-nCrossLinks)*nSegments);
 					auto IdCEnd( (objectID-nCrossLinks+1)*nSegments-1);
-					// std::cout << "OId=" << objectID << " IdC=" << IdCStart << "-" << IdCEnd << std::endl;
+					#ifdef DEBUG
+						std::cout << objectID << " "  << activeTag <<" " << IdCStart << " " << IdCEnd << std::endl;
+					#endif
 					if (activeTag == 2 ) {
 						nActiveTendomers++;
 						tmpAttribute=1;
@@ -189,6 +192,19 @@ int main(int argc, char* argv[]){
 		}		
 
 		myIngredients.synchronize();
+		// auto BoxX(myIngredients.getBoxX());
+		// auto BoxY(myIngredients.getBoxY());
+		// auto BoxZ(myIngredients.getBoxZ());
+		// for (auto i=nActiveTendomers*2*myIngredients.getNumMonomersPerChain(); i < myIngredients.getMolecules().size(); i++ ){
+		// 	auto vec(myIngredients.getMolecules()[i].getVector3D());
+		// 	auto new_vec(vec);
+		// 	new_vec.setAllCoordinates( LemonadeDistCalcs::fold(vec.getX(),BoxX), 
+		// 		 					   LemonadeDistCalcs::fold(vec.getX(),BoxY),
+		// 							   LemonadeDistCalcs::fold(vec.getX(),BoxZ));
+		// 	myIngredients.modifyMolecules()[i].modifyVector3D() = new_vec;
+		// }
+		// myIngredients.synchronize();
+
 		TaskManager taskmanager2;
 		taskmanager2.addAnalyzer( new AnalyzerWriteBfmFile<Ing >(outputBFM, myIngredients, 1) ); 
 		//initialize and run

From e8bfae616d0d469cd1794b6e267764ab92555817 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 16 Jun 2021 13:12:00 +0200
Subject: [PATCH 13/70] TendomerNetworkExtractGelPart: extracts the gel part of
 the networks and write it into a bfm file

---
 projects/CMakeLists.txt                    |   2 +
 projects/TendomerNetworkExtractGelPart.cpp | 237 +++++++++++++++++++++
 2 files changed, 239 insertions(+)
 create mode 100644 projects/TendomerNetworkExtractGelPart.cpp

diff --git a/projects/CMakeLists.txt b/projects/CMakeLists.txt
index b7cbc52..9bc852b 100644
--- a/projects/CMakeLists.txt
+++ b/projects/CMakeLists.txt
@@ -8,6 +8,8 @@ target_link_libraries(TendomerNetworkForceEquilibrium LeMonADE CommandlineParser
 add_executable(TendomerNetworkExtractActivePart TendomerNetworkExtractActivePart.cpp)
 target_link_libraries(TendomerNetworkExtractActivePart LeMonADE CommandlineParser )
 
+add_executable(TendomerNetworkExtractGelPart TendomerNetworkExtractGelPart.cpp)
+target_link_libraries(TendomerNetworkExtractGelPart LeMonADE CommandlineParser )
 
 add_executable(TendomerNetworkWritePartialConnectedNetwork TendomerNetworkWritePartialConnectedNetwork.cpp)
 target_link_libraries(TendomerNetworkWritePartialConnectedNetwork LeMonADE CommandlineParser )
diff --git a/projects/TendomerNetworkExtractGelPart.cpp b/projects/TendomerNetworkExtractGelPart.cpp
new file mode 100644
index 0000000..54ce45f
--- /dev/null
+++ b/projects/TendomerNetworkExtractGelPart.cpp
@@ -0,0 +1,237 @@
+/*--------------------------------------------------------------------------------
+    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/>.
+
+--------------------------------------------------------------------------------*/
+
+/****************************************************************************** 
+ * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
+ * author: Toni Müller
+ * email: mueller-toni@ipfdd.de
+ * project: LeMonADE-Phantom Modulus
+ *****************************************************************************/
+#include <iostream>
+#include <vector>
+#include <bitset>
+
+#include <LeMonADE/core/Ingredients.h>
+#include <LeMonADE/updater/UpdaterReadBfmFile.h>
+#include <LeMonADE/analyzer/AnalyzerWriteBfmFileSubGroup.h>
+#include <LeMonADE/feature/FeatureMoleculesIOUnsaveCheck.h>
+#include <LeMonADE/feature/FeatureReactiveBonds.h>
+#include <LeMonADE/feature/FeatureAttributes.h>
+#include <LeMonADE/feature/FeatureBox.h>
+#include <LeMonADE/feature/FeatureLabel.h>
+#include <LeMonADE/utility/DepthIteratorPredicates.h>
+#include <LeMonADE/utility/DepthIterator.h>
+#include <LeMonADE/utility/MonomerGroup.h>
+#include <LeMonADE/utility/TaskManager.h>
+
+#include <extern/catchorg/clara/clara.hpp>
+
+#include <LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h>
+#include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
+#include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
+#include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
+#include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h>
+#include <LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h>
+
+
+int main(int argc, char* argv[]){
+	try{
+		///////////////////////////////////////////////////////////////////////////////
+		///parse options///
+		std::string inputBFM("init.bfm");
+		std::string outputBFM("Config.bfm.dat");
+		std::string inputConnection("BondCreationBreaking.dat");
+        std::string activeComponent("active_00001.dat");		
+		bool showHelp = false;
+		auto parser
+			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"           ] ("(required)Input filename of the bfm file"                                    ).required()
+			| clara::detail::Opt(     inputConnection, "inputConnection (=BondCreationBreaking.dat)"     ) ["-d"]["--inputConnection" ] ("used for the time development of the topology. "                             ).required()
+            | clara::detail::Opt(     activeComponent, "activeComponents (=active_00001.dat)"            ) ["-a"]["--activeComponents"] ("sets the active components . "                                              ).required()
+			| clara::detail::Opt(           outputBFM, "outputBFM (=Config.bfm)"                         ) ["-o"]["--outputBFM"       ] ("Output filename for the active material of the tendomer network.")
+			| clara::Help( showHelp );
+		
+	    auto result = parser.parse( clara::Args( argc, argv ) );
+	    
+	    if( !result ) {
+	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
+	      exit(1);
+	    }else if(showHelp == true){
+	      std::cout << "Analyzer taking a bond table and a table specifying the activity of an object and writes the active part of the tendoemr network."<< std::endl;
+          std::cout << "Important: input file for the connections and the active material must fit to each other!!!"<< std::endl;
+	      parser.writeToStream(std::cout);
+	      exit(0);
+	    }else{
+	      std::cout << "outputBFM             : " << outputBFM          << std::endl;
+	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
+	      std::cout << "inputConnection       : " << inputConnection        << std::endl; 
+          std::cout << "activeComponent       : " << activeComponent        << std::endl; 
+	    }
+		RandomNumberGenerators rng;
+		rng.seedAll();
+		///////////////////////////////////////////////////////////////////////////////
+		///end options parsing
+		///////////////////////////////////////////////////////////////////////////////
+		//Read in th last Config 
+		typedef LOKI_TYPELIST_4(FeatureMoleculesIOUnsaveCheck, FeatureLabel, FeatureReactiveBonds, FeatureAttributes<>) Features;
+		typedef ConfigureSystem<VectorInt3,Features, 7> Config;
+		typedef Ingredients<Config> Ing;
+		Ing myIngredients;
+		
+		TaskManager taskmanager;
+		
+		taskmanager.addUpdater( new UpdaterReadBfmFile<Ing>(inputBFM,myIngredients, UpdaterReadBfmFile<Ing>::READ_LAST_CONFIG_SAVE),0);
+		taskmanager.addUpdater( new UpdaterReadCrosslinkConnectionsTendomer<Ing>(myIngredients, inputConnection, 0., 1.0) );
+
+		//initialize and run
+		taskmanager.initialize();
+		taskmanager.run(1);
+		taskmanager.cleanup();
+		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
+        // activeObjects are first all cross links and afterwards all chain: 0-sol, 1-gel/pending, 2-active 
+        std::ifstream in(activeComponent);
+        std::string line;
+
+		auto nCrossLinks(myIngredients.getNumCrossLinkers());
+		auto nChains(myIngredients.getNumTendomers());
+		auto nSegments(myIngredients.getNumMonomersPerChain()*2);
+		auto nChainMonomers(nChains*nSegments);
+		auto objectID(0);
+		auto nActiveCrossLinks(0);
+		auto nActiveTendomers(0);
+		std::cout <<"Filestart:\n" ;
+        while (in.good() &&  ! in.eof() ){
+            getline(in,line);
+            std::stringstream ss;
+            uint32_t activeTag;
+            ss << line;
+			// std::cout << line <<"\n";
+			if (! line.empty()) {
+				ss >>activeTag;
+				auto tmpAttribute(0);
+				if(objectID < nCrossLinks ){
+					auto IdX(nChainMonomers+objectID);
+					#ifdef DEBUG
+						std::cout <<  objectID << " "  << activeTag <<  " " << IdX <<  " " << IdX << std::endl;
+					#endif
+					if (activeTag == 2 || activeTag == 1 ){
+						tmpAttribute=1;	
+						nActiveCrossLinks++;
+					}
+					myIngredients.modifyMolecules()[nChainMonomers+objectID].setAttributeTag(tmpAttribute);
+				}else{
+					auto IdCStart((objectID-nCrossLinks)*nSegments);
+					auto IdCEnd( (objectID-nCrossLinks+1)*nSegments-1);
+					#ifdef DEBUG
+						std::cout << objectID << " "  << activeTag <<" " << IdCStart << " " << IdCEnd << std::endl;
+					#endif
+					if (activeTag == 2 || activeTag == 1 ) {
+						nActiveTendomers++;
+						tmpAttribute=1;
+					}
+					for (auto i =IdCStart ; i <= IdCEnd; i++ )
+						myIngredients.modifyMolecules()[i].setAttributeTag(tmpAttribute);
+				}
+				objectID++;
+			}
+        }
+		std::cout <<"Fileend:\n" ;
+		// for()
+		myIngredients.setNumTendomers           (nActiveTendomers);
+		myIngredients.setNumCrossLinkers        (nActiveCrossLinks);
+		myIngredients.setNumMonomersPerChain    (myIngredients.getNumMonomersPerChain());
+		myIngredients.setNumLabelsPerTendomerArm(myIngredients.getNumLabelsPerTendomerArm());
+		myIngredients.synchronize();
+		
+
+		MonomerGroup<typename Ing::molecules_type> subgroup(myIngredients.getMolecules());
+		subgroup.clear();
+		hasThisType<1> predicate;
+		for(size_t n=0;n<myIngredients.getMolecules().size();n++)
+		{
+			if(predicate(myIngredients.getMolecules(),n)==true) subgroup.push_back(n);
+		}
+		myIngredients.modifyMolecules()=subgroup.copyGroup();
+
+		for(size_t n=0;n<myIngredients.getMolecules().size();n++)
+		{
+			myIngredients.modifyMolecules()[n].setReactive(false);
+			myIngredients.modifyMolecules()[n].setNumMaxLinks(0);
+			if( n < nActiveTendomers*nSegments ){
+				if (n%(nSegments/2) == 0 ) {
+					myIngredients.modifyMolecules()[n].setReactive(true);
+					myIngredients.modifyMolecules()[n].setNumMaxLinks(2);
+				}
+			}else {
+				myIngredients.modifyMolecules()[n].setReactive(true);
+				myIngredients.modifyMolecules()[n].setNumMaxLinks(4);
+			}
+		}		
+
+		myIngredients.synchronize();
+		// auto BoxX(myIngredients.getBoxX());
+		// auto BoxY(myIngredients.getBoxY());
+		// auto BoxZ(myIngredients.getBoxZ());
+		// for (auto i=nActiveTendomers*2*myIngredients.getNumMonomersPerChain(); i < myIngredients.getMolecules().size(); i++ ){
+		// 	auto vec(myIngredients.getMolecules()[i].getVector3D());
+		// 	auto new_vec(vec);
+		// 	new_vec.setAllCoordinates( LemonadeDistCalcs::fold(vec.getX(),BoxX), 
+		// 		 					   LemonadeDistCalcs::fold(vec.getX(),BoxY),
+		// 							   LemonadeDistCalcs::fold(vec.getX(),BoxZ));
+		// 	myIngredients.modifyMolecules()[i].modifyVector3D() = new_vec;
+		// }
+		// myIngredients.synchronize();
+
+		TaskManager taskmanager2;
+		taskmanager2.addAnalyzer( new AnalyzerWriteBfmFile<Ing >(outputBFM, myIngredients, 1) ); 
+		//initialize and run
+		if ( nActiveTendomers > 0  ){
+			taskmanager2.initialize();
+			taskmanager2.run(1);
+			taskmanager2.cleanup();
+		}
+		// AnalyzerWriteBfmFileSubGroup<Ing,hasThisType<1> >  writer(outputBFM, myIngredients, 1, hasThisType<1>());
+		// writer.initialize();
+		
+		// TaskManager taskmanager2;
+		// taskmanager2.addAnalyzer( new AnalyzerWriteBfmFileSubGroup<Ing,hasThisType<1> >(outputBFM, myIngredients, 1, hasThisType<1>()) ); 
+		
+		// //initialize and run
+		// taskmanager2.initialize();
+		// taskmanager2.run(1);
+		// // taskmanager2.cleanup();
+        
+	}
+	catch(std::exception& e){
+		std::cerr<<"Error:\n"
+		<<e.what()<<std::endl;
+	}
+	catch(...){
+		std::cerr<<"Error: unknown exception\n";
+	}
+	
+	return 0;
+}

From 267aa837e97f4343b37442553adc89a1f8c83011 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 16 Jun 2021 13:13:51 +0200
Subject: [PATCH 14/70] us the TM updater for the FE-eq in the standard
 ForceEquilibrium.cpp

---
 projects/ForceEquilibrium.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index a7142b0..9ab6605 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -160,7 +160,8 @@ int main(int argc, char* argv[]){
 		//read bonds and positions stepwise
 		taskmanager2.addUpdater( new UpdaterReadCrosslinkConnections<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
 		// if (custom) 
-			taskmanager2.addUpdater( new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) );
+			// taskmanager2.addUpdater( new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) );
+			taskmanager2.addUpdater( new UpdaterForceBalancedPositionTendomer<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) );
 		// else {
 		// 	auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
 		// 	updater->setFilename(feCurve);

From 68125262955b906e532146e000e2b58af56707e0 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 16 Jun 2021 13:27:27 +0200
Subject: [PATCH 15/70] add the settre and getter for the filename and the
 relaxation factor to the base class

---
 .../updater/moves/MoveForceEquilibriumBase.h           | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/include/LeMonADE_PM/updater/moves/MoveForceEquilibriumBase.h b/include/LeMonADE_PM/updater/moves/MoveForceEquilibriumBase.h
index fe42bcc..a8e4979 100644
--- a/include/LeMonADE_PM/updater/moves/MoveForceEquilibriumBase.h
+++ b/include/LeMonADE_PM/updater/moves/MoveForceEquilibriumBase.h
@@ -88,6 +88,16 @@ class MoveForceEquilibriumBase:public MoveBase
 	{
 		ShiftVector.setAllCoordinates(dx,dy,dz);
 	}
+
+    void setFilename(std::string filename_){static_cast<SpecializedMove*>(this)->setFilename(ingredients);}
+    //! get the filename for the force extension data 
+    std::string const getFilename(){static_cast<SpecializedMove*>(this)->getFilename(ingredients);}
+    
+    //! set the relaxation parameter for the cross link
+    void setRelaxationParameter(double relaxationChain_){static_cast<SpecializedMove*>(this)->setRelaxationParameter(ingredients);}
+    //! get the relaxation parameter for the cross link 
+    double getRelaxationParameter(){static_cast<SpecializedMove*>(this)->getRelaxationParameter(ingredients);} 
+
 	//! Random Number Generator (RNG)
 	RandomNumberGenerators randomNumbers;
 

From 42d2fcb5c059aa060d911514a85cc161403f1620 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 16 Jun 2021 13:27:27 +0200
Subject: [PATCH 16/70] add the settre and getter for the filename and the
 relaxation factor to the base class

---
 .../updater/moves/MoveForceEquilibriumBase.h           | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/include/LeMonADE_PM/updater/moves/MoveForceEquilibriumBase.h b/include/LeMonADE_PM/updater/moves/MoveForceEquilibriumBase.h
index fe42bcc..a31d379 100644
--- a/include/LeMonADE_PM/updater/moves/MoveForceEquilibriumBase.h
+++ b/include/LeMonADE_PM/updater/moves/MoveForceEquilibriumBase.h
@@ -88,6 +88,16 @@ class MoveForceEquilibriumBase:public MoveBase
 	{
 		ShiftVector.setAllCoordinates(dx,dy,dz);
 	}
+
+    void setFilename(std::string filename_){static_cast<SpecializedMove*>(this)->setFilename(filename_);}
+    //! get the filename for the force extension data 
+    std::string const getFilename(){static_cast<SpecializedMove*>(this)->getFilename();}
+    
+    //! set the relaxation parameter for the cross link
+    void setRelaxationParameter(double relaxationChain_){static_cast<SpecializedMove*>(this)->setRelaxationParameter(relaxationChain_);}
+    //! get the relaxation parameter for the cross link 
+    double getRelaxationParameter(){static_cast<SpecializedMove*>(this)->getRelaxationParameter();} 
+
 	//! Random Number Generator (RNG)
 	RandomNumberGenerators randomNumbers;
 

From 6377e9a4013905e909e6bbc47ce82a04fa6c529c Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 16 Jun 2021 13:40:01 +0200
Subject: [PATCH 17/70] Erase the Tendomer specific updater for the force
 balance and instead generalize the base move a bit.

---
 .../updater/UpdaterForceBalancedPosition.h    |  22 +++-
 .../UpdaterForceBalancedPositionTendomer.h    | 111 ------------------
 .../updater/moves/MoveForceEquilibriumBase.h  |   2 +-
 projects/ForceEquilibrium.cpp                 |  37 +++---
 projects/TendomerNetworkExtractActivePart.cpp |   1 -
 projects/TendomerNetworkExtractGelPart.cpp    |   1 -
 projects/TendomerNetworkForceEquilibrium.cpp  |   4 +-
 ...merNetworkWritePartialConnectedNetwork.cpp |   2 +-
 8 files changed, 42 insertions(+), 138 deletions(-)
 delete mode 100644 include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h

diff --git a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
index 34e97bf..0a04210 100644
--- a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
+++ b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
@@ -40,12 +40,15 @@ class UpdaterForceBalancedPosition:public AbstractUpdater
 {
 public:
     //! constructor for UpdaterForceBalancedPosition
-    UpdaterForceBalancedPosition(IngredientsType& ing_, double threshold_ ):
-    ing(ing_),threshold(threshold_){};
+    UpdaterForceBalancedPosition(IngredientsType& ing_, double threshold_, double factor_=0.995 ):
+    ing(ing_),threshold(threshold_),factor(factor_){};
     
-    virtual void initialize(){}
+    virtual void initialize(){relaxationParameter=move.getRelaxationParameter();}// init(move);};
     bool execute();
     virtual void cleanup(){};  
+
+    void setFilename(const std::string filename) {move.setFilename(filename); }
+    void setRelaxationParameter( const double relax ) {move.setRelaxationParameter(relax);}
 private:
     //!copy of the main container for the system informations 
     IngredientsType& ing;
@@ -53,6 +56,10 @@ class UpdaterForceBalancedPosition:public AbstractUpdater
     //! threshold for the certainty 
     double threshold;
 
+    double relaxationParameter;
+
+    double factor;
+    
     //! move to equilibrate the cross links by force equilibrium
     moveType move;
     
@@ -63,8 +70,10 @@ class UpdaterForceBalancedPosition:public AbstractUpdater
 template <class IngredientsType, class moveType>
 bool UpdaterForceBalancedPosition<IngredientsType,moveType>::execute(){
     std::cout << "UpdaterForceBalancedPosition::execute(): Start equilibration" <<std::endl;
+    auto counter=0;
     double avShift(threshold*1.1);
     uint32_t StartMCS(ing.getMolecules().getAge());
+    setRelaxationParameter(relaxationParameter);
     //! get look up table for the cross link ids to monomer ids
     auto CrossLinkIDs(ing.getCrosslinkIDs());
     //! number of cross links 
@@ -83,11 +92,16 @@ bool UpdaterForceBalancedPosition<IngredientsType,moveType>::execute(){
         }
         if( NSuccessfulMoves>0 ){
             avShift/=(NSuccessfulMoves);
-        }else 
+            counter=0;
+        }else {
             avShift=threshold*1.1;
+            counter++;
+        }
+        if (counter > 10 ){break;}
         ing.modifyMolecules().setAge(ing.getMolecules().getAge()+1);
         if (ing.getMolecules().getAge() %1000 == 0 ){
             std::cout << "MCS: " << ing.getMolecules().getAge() << "  and average shift: " << avShift << std::endl;
+            setRelaxationParameter(move.getRelaxationParameter()*factor );
         }
     }
     std::cout << "Finish equilibration with average shift per cross link < " << avShift << " after " << ing.getMolecules().getAge()-StartMCS <<std::endl;
diff --git a/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h b/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h
deleted file mode 100644
index 974ab5c..0000000
--- a/include/LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h
+++ /dev/null
@@ -1,111 +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_PM_UPDATER_UPDATERFORCEBALANCEPOSITIONTENDOMER_H
-#define LEMONADE_PM_UPDATER_UPDATERFORCEBALANCEPOSITIONTENDOMER_H
-
-
-#include <LeMonADE/updater/AbstractUpdater.h>
-#include <vector>
- /**
- * @class UpdaterForceBalancedPositionTendomer
- * @tparam IngredientsType
- */
-
- template <class IngredientsType, class moveType >
-class UpdaterForceBalancedPositionTendomer:public AbstractUpdater
-{
-public:
-    //! constructor for UpdaterForceBalancedPositionTendomer
-    UpdaterForceBalancedPositionTendomer(IngredientsType& ing_, double threshold_, double factor_=0.995 ):
-    ing(ing_),threshold(threshold_),factor(factor_){};
-    
-    virtual void initialize(){relaxationParameter=move.getRelaxationParameter();}// init(move);};
-    bool execute();
-    virtual void cleanup(){};  
-
-    void setFilename(const std::string filename) {move.setFilename(filename); }
-    void setRelaxationParameter( const double relax ) {move.setRelaxationParameter(relax);}
-private:
-    //!copy of the main container for the system informations 
-    IngredientsType& ing;
-    
-    //! threshold for the certainty 
-    double threshold;
-
-    double relaxationParameter;
-
-    double factor;
-    
-    //! move to equilibrate the cross links by force equilibrium
-    moveType move;
-    
-    //! random number generator 
-    RandomNumberGenerators rng;
-    
-};
-template <class IngredientsType, class moveType>
-bool UpdaterForceBalancedPositionTendomer<IngredientsType,moveType>::execute(){
-    std::cout << "UpdaterForceBalancedPositionTendomer::execute(): Start equilibration" <<std::endl;
-    auto counter=0;
-    double avShift(threshold*1.1);
-    uint32_t StartMCS(ing.getMolecules().getAge());
-    setRelaxationParameter(relaxationParameter);
-    //! get look up table for the cross link ids to monomer ids
-    auto CrossLinkIDs(ing.getCrosslinkIDs());
-    //! number of cross links 
-    auto NCrossLinks(CrossLinkIDs.size());
-    while (avShift > threshold  ){
-        double NSuccessfulMoves(0.);
-        avShift=0.0;
-        for (uint32_t i =0 ; i<NCrossLinks ; i++){
-            uint32_t RandomMonomer(CrossLinkIDs[ rng.r250_rand32() % NCrossLinks]);
-            move.init(ing, RandomMonomer);
-            if(move.check(ing)){
-                move.apply(ing);
-                avShift+=move.getShiftVector().getLength();
-                NSuccessfulMoves++;
-            }
-        }
-        if( NSuccessfulMoves>0 ){
-            avShift/=(NSuccessfulMoves);
-            counter=0;
-        }else {
-            avShift=threshold*1.1;
-            counter++;
-        }
-        if (counter > 10 ){break;}
-        ing.modifyMolecules().setAge(ing.getMolecules().getAge()+1);
-        if (ing.getMolecules().getAge() %1000 == 0 ){
-            std::cout << "MCS: " << ing.getMolecules().getAge() << "  and average shift: " << avShift << std::endl;
-            setRelaxationParameter(move.getRelaxationParameter()*factor );
-        }
-    }
-    std::cout << "Finish equilibration with average shift per cross link < " << avShift << " after " << ing.getMolecules().getAge()-StartMCS <<std::endl;
-    ing.modifyMolecules().setAge(StartMCS);
-    return false;
-}
-#endif /* LEMONADE_PM_UPDATER_UPDATERFORCEBALANCEPOSITION_H*/
\ No newline at end of file
diff --git a/include/LeMonADE_PM/updater/moves/MoveForceEquilibriumBase.h b/include/LeMonADE_PM/updater/moves/MoveForceEquilibriumBase.h
index 714ebeb..24a325b 100644
--- a/include/LeMonADE_PM/updater/moves/MoveForceEquilibriumBase.h
+++ b/include/LeMonADE_PM/updater/moves/MoveForceEquilibriumBase.h
@@ -88,7 +88,7 @@ class MoveForceEquilibriumBase:public MoveBase
 	{
 		ShiftVector.setAllCoordinates(dx,dy,dz);
 	}
-
+public:
     void setFilename(std::string filename_){static_cast<SpecializedMove*>(this)->setFilename(filename_);}
     //! get the filename for the force extension data 
     std::string const getFilename(){static_cast<SpecializedMove*>(this)->getFilename();}
diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index 9ab6605..b7db1b5 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -62,12 +62,12 @@ int main(int argc, char* argv[]){
 		std::string outputDataPos("CrosslinkPosition.dat");
 		std::string outputDataDist("ChainExtensionDistribution.dat");
 		std::string inputConnection("BondCreationBreaking.dat");
-		// std::string feCurve("");
-		// double relaxationParameter(10.);
+		std::string feCurve("");
+		double relaxationParameter(10.);
 		double threshold(0.5);
 		double stepwidth(1.0);
 		double minConversion(50.0);
-		// bool custom(true);
+		bool custom(true);
 		
 		bool showHelp = false;
 		auto parser
@@ -78,8 +78,8 @@ int main(int argc, char* argv[]){
 			| clara::detail::Opt(           stepwidth, "stepwidth"                                       ) ["-s"]["--stepwidth"      ] ("(optional) Width for the increase in percentage. Default: 1%."               ).optional()
 			| clara::detail::Opt(       minConversion, "minConversion"                                   ) ["-u"]["--minConversion"  ] ("(optional) Minimum conversion to be read in. Default: 50%."                  ).optional()
 			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"      ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
-			// | clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"        ] ("(optional) Force-Extension curve. Default \"\"."                             ).optional()
-			// | clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"          ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
+			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"        ] ("(optional) Force-Extension curve. Default \"\"."                             ).optional()
+			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"          ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
 			| clara::Help( showHelp );
 		
 	    auto result = parser.parse( clara::Args( argc, argv ) );
@@ -99,9 +99,9 @@ int main(int argc, char* argv[]){
 	      std::cout << "stepwidth             : " << stepwidth              << std::endl;
 	      std::cout << "minConversion         : " << minConversion          << std::endl;
 	      std::cout << "threshold             : " << threshold              << std::endl; 
-		//   std::cout << "feCurve               : " << feCurve                << std::endl;
+		  std::cout << "feCurve               : " << feCurve                << std::endl;
 	    }
-		// if (! feCurve.empty()) custom=false;
+		if (! feCurve.empty()) custom=false;
 		
 
 		RandomNumberGenerators rng;
@@ -155,19 +155,22 @@ int main(int argc, char* argv[]){
 			}
 		}
 		myIngredients2.synchronize();
-
+		
+		
 		TaskManager taskmanager2;
 		//read bonds and positions stepwise
 		taskmanager2.addUpdater( new UpdaterReadCrosslinkConnections<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
-		// if (custom) 
-			// taskmanager2.addUpdater( new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) );
-			taskmanager2.addUpdater( new UpdaterForceBalancedPositionTendomer<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) );
-		// else {
-		// 	auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
-		// 	updater->setFilename(feCurve);
-		// 	updater->setRelaxationParameter(relaxationParameter);
-		// 	taskmanager2.addUpdater( updater );
-		// }
+		if(custom){
+			auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold);
+			forceUpdater->setFilename(feCurve);
+			forceUpdater->setRelaxationParameter(relaxationParameter);	
+			taskmanager2.addUpdater( forceUpdater );
+		} else {
+			auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold);
+			forceUpdater->setFilename(feCurve);
+			forceUpdater->setRelaxationParameter(relaxationParameter);	
+			taskmanager2.addUpdater( forceUpdater );
+		}
 		taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
 		//initialize and run
 		taskmanager2.initialize();
diff --git a/projects/TendomerNetworkExtractActivePart.cpp b/projects/TendomerNetworkExtractActivePart.cpp
index 1b4a6ac..6b3b45d 100644
--- a/projects/TendomerNetworkExtractActivePart.cpp
+++ b/projects/TendomerNetworkExtractActivePart.cpp
@@ -50,7 +50,6 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 
 #include <extern/catchorg/clara/clara.hpp>
 
-#include <LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h>
 #include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
 #include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
 #include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
diff --git a/projects/TendomerNetworkExtractGelPart.cpp b/projects/TendomerNetworkExtractGelPart.cpp
index 54ce45f..d427664 100644
--- a/projects/TendomerNetworkExtractGelPart.cpp
+++ b/projects/TendomerNetworkExtractGelPart.cpp
@@ -50,7 +50,6 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 
 #include <extern/catchorg/clara/clara.hpp>
 
-#include <LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h>
 #include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
 #include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
 #include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
diff --git a/projects/TendomerNetworkForceEquilibrium.cpp b/projects/TendomerNetworkForceEquilibrium.cpp
index 764df5d..cffe0b5 100644
--- a/projects/TendomerNetworkForceEquilibrium.cpp
+++ b/projects/TendomerNetworkForceEquilibrium.cpp
@@ -47,7 +47,7 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 
 #include <extern/catchorg/clara/clara.hpp>
 
-#include <LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h>
+#include <LeMonADE_PM/updater/UpdaterForceBalancedPosition.h>
 #include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
 #include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
 #include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
@@ -149,7 +149,7 @@ int main(int argc, char* argv[]){
 
 		TaskManager taskmanager2;
 		//read bonds and positions stepwise
-        auto updater = new UpdaterForceBalancedPositionTendomer<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold, factor) ;
+        auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold, factor) ;
         updater->setFilename(feCurve);
         updater->setRelaxationParameter(relaxationParameter);
         // auto updater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
diff --git a/projects/TendomerNetworkWritePartialConnectedNetwork.cpp b/projects/TendomerNetworkWritePartialConnectedNetwork.cpp
index bcbc61b..5f56641 100644
--- a/projects/TendomerNetworkWritePartialConnectedNetwork.cpp
+++ b/projects/TendomerNetworkWritePartialConnectedNetwork.cpp
@@ -50,7 +50,7 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 
 #include <extern/catchorg/clara/clara.hpp>
 
-#include <LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h>
+
 #include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
 #include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
 #include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>

From 1ed297188c3f4f8f6ad9166a8703c5213d34b5c7 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 16 Jun 2021 14:17:36 +0200
Subject: [PATCH 18/70] remove updater for testint purposes

---
 .../updater/UpdaterForceBalancedPosition.h    | 27 ++++++++++---------
 projects/ForceEquilibrium.cpp                 | 10 +++----
 2 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
index 0a04210..cb89d2b 100644
--- a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
+++ b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
@@ -41,7 +41,7 @@ class UpdaterForceBalancedPosition:public AbstractUpdater
 public:
     //! constructor for UpdaterForceBalancedPosition
     UpdaterForceBalancedPosition(IngredientsType& ing_, double threshold_, double factor_=0.995 ):
-    ing(ing_),threshold(threshold_),factor(factor_){};
+    ing(ing_),threshold(threshold_),factor(factor_),relaxationParameter(1.0){};
     
     virtual void initialize(){relaxationParameter=move.getRelaxationParameter();}// init(move);};
     bool execute();
@@ -70,10 +70,10 @@ class UpdaterForceBalancedPosition:public AbstractUpdater
 template <class IngredientsType, class moveType>
 bool UpdaterForceBalancedPosition<IngredientsType,moveType>::execute(){
     std::cout << "UpdaterForceBalancedPosition::execute(): Start equilibration" <<std::endl;
-    auto counter=0;
+    // auto counter=0;
     double avShift(threshold*1.1);
     uint32_t StartMCS(ing.getMolecules().getAge());
-    setRelaxationParameter(relaxationParameter);
+    // setRelaxationParameter(relaxationParameter);
     //! get look up table for the cross link ids to monomer ids
     auto CrossLinkIDs(ing.getCrosslinkIDs());
     //! number of cross links 
@@ -90,18 +90,19 @@ bool UpdaterForceBalancedPosition<IngredientsType,moveType>::execute(){
                 NSuccessfulMoves++;
             }
         }
-        if( NSuccessfulMoves>0 ){
-            avShift/=(NSuccessfulMoves);
-            counter=0;
-        }else {
-            avShift=threshold*1.1;
-            counter++;
-        }
-        if (counter > 10 ){break;}
-        ing.modifyMolecules().setAge(ing.getMolecules().getAge()+1);
+        // if( NSuccessfulMoves == 0 ){ return false;}
+        // if( NSuccessfulMoves>0 ){
+        //     avShift/=(NSuccessfulMoves);
+        //     counter=0;
+        // }else {
+        //     avShift=threshold*1.1;
+        //     counter++;
+        // }
+        // if (counter > 10 ){break;}
+            ing.modifyMolecules().setAge(ing.getMolecules().getAge()+1);
         if (ing.getMolecules().getAge() %1000 == 0 ){
             std::cout << "MCS: " << ing.getMolecules().getAge() << "  and average shift: " << avShift << std::endl;
-            setRelaxationParameter(move.getRelaxationParameter()*factor );
+            // setRelaxationParameter(move.getRelaxationParameter()*factor );
         }
     }
     std::cout << "Finish equilibration with average shift per cross link < " << avShift << " after " << ing.getMolecules().getAge()-StartMCS <<std::endl;
diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index b7db1b5..a309cb6 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -62,7 +62,7 @@ int main(int argc, char* argv[]){
 		std::string outputDataPos("CrosslinkPosition.dat");
 		std::string outputDataDist("ChainExtensionDistribution.dat");
 		std::string inputConnection("BondCreationBreaking.dat");
-		std::string feCurve("");
+		std::string feCurve;
 		double relaxationParameter(10.);
 		double threshold(0.5);
 		double stepwidth(1.0);
@@ -101,7 +101,7 @@ int main(int argc, char* argv[]){
 	      std::cout << "threshold             : " << threshold              << std::endl; 
 		  std::cout << "feCurve               : " << feCurve                << std::endl;
 	    }
-		if (! feCurve.empty()) custom=false;
+		if ( feCurve.empty() ) custom=false;
 		
 
 		RandomNumberGenerators rng;
@@ -161,15 +161,15 @@ int main(int argc, char* argv[]){
 		//read bonds and positions stepwise
 		taskmanager2.addUpdater( new UpdaterReadCrosslinkConnections<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
 		if(custom){
+			std::cout << "Use custom force-extension curve\n";
 			auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold);
 			forceUpdater->setFilename(feCurve);
 			forceUpdater->setRelaxationParameter(relaxationParameter);	
 			taskmanager2.addUpdater( forceUpdater );
 		} else {
+			std::cout << "Use gaussian force-extension relation\n";
 			auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold);
-			forceUpdater->setFilename(feCurve);
-			forceUpdater->setRelaxationParameter(relaxationParameter);	
-			taskmanager2.addUpdater( forceUpdater );
+			// taskmanager2.addUpdater( forceUpdater );
 		}
 		taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
 		//initialize and run

From 3c826aa4c30081e999d874eb6e95dfb7e7c9313c Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 16 Jun 2021 14:41:20 +0200
Subject: [PATCH 19/70] resubmit the upter

---
 projects/ForceEquilibrium.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index a309cb6..7460b03 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -169,12 +169,12 @@ int main(int argc, char* argv[]){
 		} else {
 			std::cout << "Use gaussian force-extension relation\n";
 			auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold);
-			// taskmanager2.addUpdater( forceUpdater );
+			taskmanager2.addUpdater( forceUpdater );
 		}
 		taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
 		//initialize and run
 		taskmanager2.initialize();
-		taskmanager2.run();
+		taskmanager2.run(1);
 		taskmanager2.cleanup();
 		
 	}

From fa97f22c37498c69d639eadcb262ef891e86c75c Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 16 Jun 2021 14:53:08 +0200
Subject: [PATCH 20/70] fix bug: add aempty function to specialized moves

---
 .../updater/moves/MoveForceEquilibrium.h      | 12 ++++++++-
 projects/ForceEquilibrium.cpp                 | 26 ++++++++++++-------
 2 files changed, 28 insertions(+), 10 deletions(-)

diff --git a/include/LeMonADE_PM/updater/moves/MoveForceEquilibrium.h b/include/LeMonADE_PM/updater/moves/MoveForceEquilibrium.h
index 4909893..f1d7a17 100644
--- a/include/LeMonADE_PM/updater/moves/MoveForceEquilibrium.h
+++ b/include/LeMonADE_PM/updater/moves/MoveForceEquilibrium.h
@@ -47,7 +47,9 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 
 class MoveForceEquilibrium:public MoveForceEquilibriumBase<MoveForceEquilibrium>{
 public:
-    MoveForceEquilibrium():bondlength(2.68){};
+    MoveForceEquilibrium():bondlength(2.68){
+      std::cout << "Use the MoveForceEquilibrium\n";
+    };
 
     // overload initialise function to be able to set the moves index and direction if neccessary
     template <class IngredientsType> void init(const IngredientsType& ing);
@@ -57,6 +59,14 @@ class MoveForceEquilibrium:public MoveForceEquilibriumBase<MoveForceEquilibrium>
     template <class IngredientsType> bool check(IngredientsType& ing);
     template< class IngredientsType> void apply(IngredientsType& ing);
 
+    void setFilename(std::string filename_){}
+    //! get the filename for the force extension data 
+    std::string const getFilename(){}
+    
+    //! set the relaxation parameter for the cross link
+    void setRelaxationParameter(double relaxationChain_){}
+    //! get the relaxation parameter for the cross link 
+    double getRelaxationParameter(){}
 private:
     //average square bond length 
     const double bondlength;
diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index 7460b03..9325f4a 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -157,26 +157,34 @@ int main(int argc, char* argv[]){
 		myIngredients2.synchronize();
 		
 		
-		TaskManager taskmanager2;
-		//read bonds and positions stepwise
-		taskmanager2.addUpdater( new UpdaterReadCrosslinkConnections<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
+
 		if(custom){
+			TaskManager taskmanager2;
+			//read bonds and positions stepwise
+			taskmanager2.addUpdater( new UpdaterReadCrosslinkConnections<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
 			std::cout << "Use custom force-extension curve\n";
 			auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold);
 			forceUpdater->setFilename(feCurve);
 			forceUpdater->setRelaxationParameter(relaxationParameter);	
 			taskmanager2.addUpdater( forceUpdater );
+			taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
+			//initialize and run
+			taskmanager2.initialize();
+			taskmanager2.run(1);
+			taskmanager2.cleanup();
 		} else {
+			TaskManager taskmanager2;
+			//read bonds and positions stepwise
+			taskmanager2.addUpdater( new UpdaterReadCrosslinkConnections<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
 			std::cout << "Use gaussian force-extension relation\n";
 			auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold);
 			taskmanager2.addUpdater( forceUpdater );
+			taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
+			//initialize and run
+			taskmanager2.initialize();
+			taskmanager2.run(1);
+			taskmanager2.cleanup();
 		}
-		taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
-		//initialize and run
-		taskmanager2.initialize();
-		taskmanager2.run(1);
-		taskmanager2.cleanup();
-		
 	}
 	catch(std::exception& e){
 		std::cerr<<"Error:\n"

From 4b08a2fc6d7c90c24bf4da5e9978e7758d5104f2 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Thu, 17 Jun 2021 17:28:02 +0200
Subject: [PATCH 21/70] add a finer splitting of the extensions for the custom
 FE curve vector

---
 .../moves/MoveNonLinearForceEquilibrium.h        | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
index 5af3ff1..2624a35 100644
--- a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
+++ b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
@@ -51,7 +51,7 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
 public:
     //! constructor for the class MoveNonLinearForceEquilibrium taking the filename of the force extension relation and the realaxation parameter for the chain 
     MoveNonLinearForceEquilibrium(std::string filename_="", double relaxationChain_=1.):
-        filename(filename_),bondlength(2.68){
+        filename(filename_),bondlength(2.68), accuracy(0.25) {
             if( !filename.empty() ) createTable();
             setRelaxationParameter(relaxationChain_);
         };
@@ -81,13 +81,14 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
     }
     //! get the relaxation parameter for the cross link 
     double getRelaxationParameter(){return relaxationChain;} 
+
     //uses the read force extension relation 
     VectorDouble3 EF(VectorDouble3 extensionVector){
-        uint32_t length( static_cast<uint32_t>(round(extensionVector.getLength())) );
-        if ( max_extension < length ){
+        uint32_t length( static_cast<uint32_t>(round(extensionVector.getLength()/accuracy)) );
+        if ( max_extension/accuracy < length ){
             std::stringstream errormessage; 
             errormessage << "The length of the extension vector is greater than the maximum given in the file: \n"
-                         << "length is  " << length 
+                         << "length is  " << length*accuracy 
                          << " maximum is " << max_extension << "\n";
             throw std::runtime_error(errormessage.str());
         }
@@ -122,6 +123,9 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
     //extension steps 
     double extension_steps;
 
+    //the accuracy is the steps in which the extensions vector grows
+    double accuracy; 
+
     //spring constant for the equivalent chain used for the relaxation of the cross links 
     double springConstant;
    
@@ -189,13 +193,13 @@ void MoveNonLinearForceEquilibrium::createTable(){
         in.close();
         //make lookup for the extension force relation 
         //make a entry from 0 to max_extension in steps of 1 
-        for ( auto r=0;r<static_cast<uint32_t>(max_extension); r++   ){
+        for ( auto r=0;r<static_cast<uint32_t>(max_extension/accuracy); r++   ){
             if(r==0)
                 force_extension.push_back(0.);
             else{
                 auto it_last=extension_force.begin();
                 for (auto it=extension_force.begin(); it !=extension_force.end();it++){
-                    if(it->second > r){
+                    if(it->second > static_cast<double>(r*accuracy)){
                         //at the force linear interpolated in between the two current forces
                         auto deltaForce(it->first-it_last->first);
                         auto deltaExtension(it->second-it_last->second);

From 0fd08f0eccb306f1f65d650cb5beb53a3fc8cbc7 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Mon, 21 Jun 2021 08:30:02 +0200
Subject: [PATCH 22/70] correct output format for the ids in the analyzer

---
 .../LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h    | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h b/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h
index eb5961d..bb32639 100644
--- a/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h
+++ b/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h
@@ -75,7 +75,7 @@ template < class IngredientsType > class AnalyzerEquilbratedPosition : public Ab
 	std::vector< std::vector<double> >  CalculateDistance();
 
 	//! just collects the id and the position for the cross links 
-	std::vector<std::vector<int> > CollectAveragePositions();
+	std::vector<std::vector<double> > CollectAveragePositions();
 };
 
 /*************************************************************************
@@ -128,8 +128,8 @@ std::vector< std::vector<double> >  AnalyzerEquilbratedPosition<IngredientsType>
 }
 ////////////////////////////////////////////////////////////////////////////////
 template< class IngredientsType >
-std::vector< std::vector<int> >  AnalyzerEquilbratedPosition<IngredientsType>::CollectAveragePositions(){
-	std::vector<std::vector<int> > AveragePosition(4, std::vector<int>());
+std::vector< std::vector<double> >  AnalyzerEquilbratedPosition<IngredientsType>::CollectAveragePositions(){
+	std::vector<std::vector<double> > AveragePosition(4, std::vector<double>());
 	auto crosslinkID(ingredients.getCrosslinkIDs());
 	for (size_t i = 0 ; i < crosslinkID.size(); i++){
 		auto IDx(crosslinkID[i]);
@@ -189,7 +189,7 @@ void AnalyzerEquilbratedPosition<IngredientsType>::dumpData()
 	std::cout << "////////////////////////////////////"<<std::endl;	
 
 	//output for the equilibrated positions 
-	std::vector< std::vector<int> > CrossLinkPositions=CollectAveragePositions() ;
+	std::vector< std::vector<double> > CrossLinkPositions=CollectAveragePositions() ;
 	std::stringstream commentAveragePosition;
 	commentAveragePosition<<"Created by AnalyzerEquilbratedPosition\n";
 	commentAveragePosition<<"ID's start at 0 \n";

From ea6430a78395bda52ddf8735b56d89b84a5f6900 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Mon, 21 Jun 2021 08:31:23 +0200
Subject: [PATCH 23/70] mroe efficient calcualtion and output for finding
 deviations from the expected behaviour

---
 .../updater/moves/MoveForceEquilibrium.h      |  9 ++-
 .../moves/MoveNonLinearForceEquilibrium.h     | 76 ++++++++++++++-----
 2 files changed, 63 insertions(+), 22 deletions(-)

diff --git a/include/LeMonADE_PM/updater/moves/MoveForceEquilibrium.h b/include/LeMonADE_PM/updater/moves/MoveForceEquilibrium.h
index f1d7a17..d3e669b 100644
--- a/include/LeMonADE_PM/updater/moves/MoveForceEquilibrium.h
+++ b/include/LeMonADE_PM/updater/moves/MoveForceEquilibrium.h
@@ -47,7 +47,7 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 
 class MoveForceEquilibrium:public MoveForceEquilibriumBase<MoveForceEquilibrium>{
 public:
-    MoveForceEquilibrium():bondlength(2.68){
+    MoveForceEquilibrium():bondlength2(2.68*2.68){
       std::cout << "Use the MoveForceEquilibrium\n";
     };
 
@@ -69,17 +69,18 @@ class MoveForceEquilibrium:public MoveForceEquilibriumBase<MoveForceEquilibrium>
     double getRelaxationParameter(){}
 private:
     //average square bond length 
-    const double bondlength;
+    const double bondlength2;
+    //
 
     //Gaussina force extension relation 
     //f=R*3/(N*b^2)
     VectorDouble3 FE(VectorDouble3 extensionVector, double nSegs){
-        return extensionVector*3./((nSegs)*bondlength*bondlength);
+        return extensionVector*3./((nSegs)*bondlength2);
     }
     //Gaussian extension force relation 
     //R=-f/3*N*b^2
     VectorDouble3 EF(VectorDouble3 force, double nSegs){
-        return force/(3.)*(nSegs)*bondlength*bondlength;
+        return force/(3.)*(nSegs)*bondlength2;
     }
 
     //calculate the shift for the cross link
diff --git a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
index 2624a35..dd1b04a 100644
--- a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
+++ b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
@@ -51,7 +51,7 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
 public:
     //! constructor for the class MoveNonLinearForceEquilibrium taking the filename of the force extension relation and the realaxation parameter for the chain 
     MoveNonLinearForceEquilibrium(std::string filename_="", double relaxationChain_=1.):
-        filename(filename_),bondlength(2.68), accuracy(0.25) {
+        filename(filename_),bondlength(2.68), accuracy(.001) {
             if( !filename.empty() ) createTable();
             setRelaxationParameter(relaxationChain_);
         };
@@ -77,26 +77,47 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
     //! set the relaxation parameter for the cross link
     void setRelaxationParameter(double relaxationChain_){
         relaxationChain=relaxationChain_;
-        springConstant = relaxationChain*bondlength*bondlength/(-3.);
+        springConstant = relaxationChain*bondlength*bondlength/(3.);
+        std::cout << "Set relaxation parameter to " << relaxationChain << " corresponding to a spring constant " <<springConstant <<std::endl;
     }
     //! get the relaxation parameter for the cross link 
     double getRelaxationParameter(){return relaxationChain;} 
 
     //uses the read force extension relation 
     VectorDouble3 EF(VectorDouble3 extensionVector){
-        uint32_t length( static_cast<uint32_t>(round(extensionVector.getLength()/accuracy)) );
-        if ( max_extension/accuracy < length ){
+        if (extensionVector == VectorDouble3(0.,0.,0.) )
+            return VectorDouble3(0.,0.,0.);
+        double length( extensionVector.getLength() );
+
+        #ifdef DEBUG
+        if ( max_extension < length  ){
             std::stringstream errormessage; 
             errormessage << "The length of the extension vector is greater than the maximum given in the file: \n"
-                         << "length is  " << length*accuracy 
+                         << "length is  " << length 
                          << " maximum is " << max_extension << "\n";
             throw std::runtime_error(errormessage.str());
         }
         if (length == 0 )
             return VectorDouble3(0.,0.,0.);
-        return force_extension[length]*extensionVector.normalize();
+        #endif
+        #ifdef DEBUG
+        std::cout <<length << "\t" << force_extension[static_cast<uint32_t>(round(length/accuracy))] << "\t" << EFGauss(extensionVector).getLength() << "\t" 
+         << extensionVector << "\t" 
+         <<  EFGauss(extensionVector) << "\t"<< extensionVector.normalize()*(force_extension[static_cast<uint32_t>(round(length/accuracy))])<<"\t"  
+        << "\n"; 
+        #endif 
+        if (length < 1 ) 
+            return EFGauss(extensionVector); 
+        // if (length < 0.001 ) 
+        //     return VectorDouble3(0.,0.,0.);
+        return extensionVector.normalize()*(force_extension[static_cast<uint32_t>(round(length/accuracy))]);
 
     }
+    //Gaussina force extension relation 
+    //f=R*3/(N*b^2)
+    VectorDouble3 EFGauss(VectorDouble3 extensionVector){
+        return extensionVector/springConstant;
+    }
     //Gaussian extension force relation 
     //R=-f/3*N*b^2
     VectorDouble3 FE(VectorDouble3 const force ) const {
@@ -124,7 +145,7 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
     double extension_steps;
 
     //the accuracy is the steps in which the extensions vector grows
-    double accuracy; 
+    const double accuracy; 
 
     //spring constant for the equivalent chain used for the relaxation of the cross links 
     double springConstant;
@@ -140,16 +161,35 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
     VectorDouble3 CalculateShift(IngredientsType& ing ){
         std::vector<neighborX> Neighbors(ing.getCrossLinkNeighborIDs(this->getIndex()) );
         VectorDouble3 force(0.,0.,0.);
+        // VectorDouble3 force2(0.,0.,0.);
         VectorDouble3 shift(0.,0.,0.);
+        // VectorDouble3 shift2(0.,0.,0.);
         double avNSegments(0.);
-        if (Neighbors.size() > 0) {
+        int32_t number_of_neighbors(Neighbors.size());
+        if (number_of_neighbors > 0) {
             VectorDouble3 Position(ing.getMolecules()[this->getIndex()].getVector3D());      
-            for (size_t i = 0; i < Neighbors.size(); i++){
-                VectorDouble3 vec(Position-ing.getMolecules()[Neighbors[i].ID].getVector3D()+Neighbors[i].jump);
-                // std::cout << Position << " " << ing.getMolecules()[Neighbors[i].ID].getVector3D() << " " << Neighbors[i].jump <<"\n";
-                force+=EF(vec);//Neighbors[i].segDistance
+            for (size_t i = 0; i < number_of_neighbors; i++){
+                VectorDouble3 vec(ing.getMolecules()[Neighbors[i].ID].getVector3D()-Neighbors[i].jump-Position);
+                force+=EF(vec);
+                // force2+=EFGauss(vec);
+                if (ing.getMolecules().getAge()%1000 == 999 && ing.getMolecules().getAge()>49000)
+                    std::cout << vec.getLength() << " " << ing.getMolecules()[Neighbors[i].ID].getVector3D()<< " " << Neighbors[i].jump<< " " << Position <<" " ;
             }
-            shift=FE(force/(static_cast<double>(Neighbors.size()) ));
+            shift=FE(force/(static_cast<double>(number_of_neighbors) ));
+            // shift2=FE(force2/(static_cast<double>(number_of_neighbors) ));
+            if (ing.getMolecules().getAge()%1000 == 999 && ing.getMolecules().getAge()>49000)
+                // if(shift.getLength()  > .001 ){
+                    std::cout << "i="<<this->getIndex() <<" "
+                                << shift  <<" " <<shift.getLength() << " "
+                                // << force  <<" " <<force.getLength() << " "
+                                // << shift2  <<" " <<shift2.getLength() << " "
+                                // << force2  <<" " <<force2.getLength() << " "
+                                // <<"dR= " << FE(force).getLength() <<" " 
+                                // <<"df= " << EF(shift).getLength()<<" " 
+                                // <<"df_gauss= " << EFGauss(shift).getLength()<<" " 
+                                << std::endl;
+                // }
+            // if (shift.getLength() < 0.001 ) shift*=0.;
         }
         return shift;
     };
@@ -193,17 +233,17 @@ void MoveNonLinearForceEquilibrium::createTable(){
         in.close();
         //make lookup for the extension force relation 
         //make a entry from 0 to max_extension in steps of 1 
+        auto it_last=extension_force.begin();
         for ( auto r=0;r<static_cast<uint32_t>(max_extension/accuracy); r++   ){
             if(r==0)
                 force_extension.push_back(0.);
             else{
-                auto it_last=extension_force.begin();
-                for (auto it=extension_force.begin(); it !=extension_force.end();it++){
+                for (auto it=it_last; it !=extension_force.end();it++){
                     if(it->second > static_cast<double>(r*accuracy)){
                         //at the force linear interpolated in between the two current forces
                         auto deltaForce(it->first-it_last->first);
                         auto deltaExtension(it->second-it_last->second);
-                        auto factor( (static_cast<double>(r)-it_last->second)/deltaExtension );
+                        auto factor( (static_cast<double>(r*accuracy)-it_last->second)/deltaExtension );
                         //at interpolated force
                         force_extension.push_back(it_last->first+deltaForce*factor);
                         break;
@@ -213,8 +253,8 @@ void MoveNonLinearForceEquilibrium::createTable(){
             }
         }
         std::cout << "MoveNonLinearForceEquilibrium::createTable() force extension" <<std::endl;
-        for (auto i =0; i < 10; i ++ )
-            std::cout << i << "\t" << force_extension[i]<<std::endl;
+        for (auto i=0; i<40; i++ )
+            std::cout << "FECurve: " << i << "\t" << i*accuracy<< "\t" << force_extension[i]<<std::endl;
 
         std::cout << "MoveNonLinearForceEquilibrium::createTable(): \n" 
                 << "min_force=" << min_force <<"\n"

From 9678be602cd7d22102e1cff106e06aece6688253 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Toni=20M=C3=BCller?= <tm.toni.mueller@googlemail.com>
Date: Mon, 21 Jun 2021 11:38:48 +0200
Subject: [PATCH 24/70] use linear interpolation in force extension curve for
 calculating the force within the steps

---
 .../moves/MoveNonLinearForceEquilibrium.h     | 42 +++++++++++++------
 1 file changed, 29 insertions(+), 13 deletions(-)

diff --git a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
index dd1b04a..7c333a5 100644
--- a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
+++ b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
@@ -51,7 +51,7 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
 public:
     //! constructor for the class MoveNonLinearForceEquilibrium taking the filename of the force extension relation and the realaxation parameter for the chain 
     MoveNonLinearForceEquilibrium(std::string filename_="", double relaxationChain_=1.):
-        filename(filename_),bondlength(2.68), accuracy(.001) {
+        filename(filename_),bondlength(2.68), accuracy(.1) {
             if( !filename.empty() ) createTable();
             setRelaxationParameter(relaxationChain_);
         };
@@ -106,11 +106,20 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
          <<  EFGauss(extensionVector) << "\t"<< extensionVector.normalize()*(force_extension[static_cast<uint32_t>(round(length/accuracy))])<<"\t"  
         << "\n"; 
         #endif 
-        if (length < 1 ) 
-            return EFGauss(extensionVector); 
+        // if (length < 1 ) 
+        //     return EFGauss(extensionVector); 
         // if (length < 0.001 ) 
         //     return VectorDouble3(0.,0.,0.);
-        return extensionVector.normalize()*(force_extension[static_cast<uint32_t>(round(length/accuracy))]);
+        if (length == 0)
+            return VectorDouble3(0.,0.,0.);
+        auto x(length/accuracy);
+        auto up (static_cast<uint32_t>(floor((length)/accuracy)+1));
+        auto down(static_cast<uint32_t>(floor(length/accuracy)));
+        auto amplitude=force_extension[down] + (force_extension[up]-force_extension[down])/static_cast<double>(up-down)*(x-down)/static_cast<double>(up-down);
+        // std::cout<< "amp=" <<  amplitude<< std::endl;
+        // extensionVector.normalize();
+        return extensionVector.normalize()*(amplitude);
+        // return extensionVector.normalize()*(force_extension[static_cast<uint32_t>(round(length/accuracy))]);
 
     }
     //Gaussina force extension relation 
@@ -150,7 +159,7 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
     //spring constant for the equivalent chain used for the relaxation of the cross links 
     double springConstant;
    
-    //force extension mapping
+    //force extension mapping        // std::cout<< "amp=" <<  amplitude<< std::endl;
     std::map<double, double> extension_force;
     //extension force mapping index=extension rounded to int 
     std::vector<double> force_extension;
@@ -161,7 +170,7 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
     VectorDouble3 CalculateShift(IngredientsType& ing ){
         std::vector<neighborX> Neighbors(ing.getCrossLinkNeighborIDs(this->getIndex()) );
         VectorDouble3 force(0.,0.,0.);
-        // VectorDouble3 force2(0.,0.,0.);
+        // VectorDouble3 force2(0.,0.,0.); 
         VectorDouble3 shift(0.,0.,0.);
         // VectorDouble3 shift2(0.,0.,0.);
         double avNSegments(0.);
@@ -172,22 +181,29 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
                 VectorDouble3 vec(ing.getMolecules()[Neighbors[i].ID].getVector3D()-Neighbors[i].jump-Position);
                 force+=EF(vec);
                 // force2+=EFGauss(vec);
-                if (ing.getMolecules().getAge()%1000 == 999 && ing.getMolecules().getAge()>49000)
-                    std::cout << vec.getLength() << " " << ing.getMolecules()[Neighbors[i].ID].getVector3D()<< " " << Neighbors[i].jump<< " " << Position <<" " ;
+                // if (ing.getMolecules().getAge()%1000 == 999 && ing.getMolecules().getAge()>49000)
+                			// stream.precision(std::numeric_limits<typename ResultType::value_type::value_type>::max_digits10);
+			// stream.setf( std::ios::fixed, std:: ios::floatfield );	
+                    // std::cout   << std::setprecision(10)
+                    //     // << setf( std::ios::fixed, std:: ios::floatfield )
+                    //             << vec.getLength() << "\n" 
+                    //             << ing.getMolecules()[Neighbors[i].ID].getVector3D()<< "\n" 
+                    //             << Neighbors[i].jump<< "\n" 
+                    //             << Position <<"\n" ;
             }
             shift=FE(force/(static_cast<double>(number_of_neighbors) ));
             // shift2=FE(force2/(static_cast<double>(number_of_neighbors) ));
-            if (ing.getMolecules().getAge()%1000 == 999 && ing.getMolecules().getAge()>49000)
+            // if (ing.getMolecules().getAge()%1000 == 999 && ing.getMolecules().getAge()>49000)
                 // if(shift.getLength()  > .001 ){
-                    std::cout << "i="<<this->getIndex() <<" "
-                                << shift  <<" " <<shift.getLength() << " "
+                    // std::cout << "i="<<this->getIndex() <<" "
+                                // << shift  <<" " <<shift.getLength() << " "
                                 // << force  <<" " <<force.getLength() << " "
                                 // << shift2  <<" " <<shift2.getLength() << " "
-                                // << force2  <<" " <<force2.getLength() << " "
+                                // << force2  <<" " <<force2.getLength() << " "        // std::cout<< "amp=" <<  amplitude<< std::endl;
                                 // <<"dR= " << FE(force).getLength() <<" " 
                                 // <<"df= " << EF(shift).getLength()<<" " 
                                 // <<"df_gauss= " << EFGauss(shift).getLength()<<" " 
-                                << std::endl;
+                                // << std::endl;
                 // }
             // if (shift.getLength() < 0.001 ) shift*=0.;
         }

From 3a3bf5504671d23d098665c8f5fed7ac65cb2abf Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Mon, 21 Jun 2021 11:50:10 +0200
Subject: [PATCH 25/70] clean up

---
 .../updater/UpdaterForceBalancedPosition.h    | 20 ++--------
 .../moves/MoveNonLinearForceEquilibrium.h     | 40 ++-----------------
 2 files changed, 6 insertions(+), 54 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
index cb89d2b..f842e84 100644
--- a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
+++ b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
@@ -70,39 +70,25 @@ class UpdaterForceBalancedPosition:public AbstractUpdater
 template <class IngredientsType, class moveType>
 bool UpdaterForceBalancedPosition<IngredientsType,moveType>::execute(){
     std::cout << "UpdaterForceBalancedPosition::execute(): Start equilibration" <<std::endl;
-    // auto counter=0;
-    double avShift(threshold*1.1);
+    double avShift(0.0);
     uint32_t StartMCS(ing.getMolecules().getAge());
-    // setRelaxationParameter(relaxationParameter);
+    setRelaxationParameter(relaxationParameter);
     //! get look up table for the cross link ids to monomer ids
     auto CrossLinkIDs(ing.getCrosslinkIDs());
     //! number of cross links 
     auto NCrossLinks(CrossLinkIDs.size());
     while (avShift > threshold  ){
-        double NSuccessfulMoves(0.);
-        avShift=0.0;
         for (uint32_t i =0 ; i<NCrossLinks ; i++){
             uint32_t RandomMonomer(CrossLinkIDs[ rng.r250_rand32() % NCrossLinks]);
             move.init(ing, RandomMonomer);
             if(move.check(ing)){
                 move.apply(ing);
                 avShift+=move.getShiftVector().getLength();
-                NSuccessfulMoves++;
             }
         }
-        // if( NSuccessfulMoves == 0 ){ return false;}
-        // if( NSuccessfulMoves>0 ){
-        //     avShift/=(NSuccessfulMoves);
-        //     counter=0;
-        // }else {
-        //     avShift=threshold*1.1;
-        //     counter++;
-        // }
-        // if (counter > 10 ){break;}
-            ing.modifyMolecules().setAge(ing.getMolecules().getAge()+1);
+        ing.modifyMolecules().setAge(ing.getMolecules().getAge()+1);
         if (ing.getMolecules().getAge() %1000 == 0 ){
             std::cout << "MCS: " << ing.getMolecules().getAge() << "  and average shift: " << avShift << std::endl;
-            // setRelaxationParameter(move.getRelaxationParameter()*factor );
         }
     }
     std::cout << "Finish equilibration with average shift per cross link < " << avShift << " after " << ing.getMolecules().getAge()-StartMCS <<std::endl;
diff --git a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
index 7c333a5..f0ec714 100644
--- a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
+++ b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
@@ -106,21 +106,13 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
          <<  EFGauss(extensionVector) << "\t"<< extensionVector.normalize()*(force_extension[static_cast<uint32_t>(round(length/accuracy))])<<"\t"  
         << "\n"; 
         #endif 
-        // if (length < 1 ) 
-        //     return EFGauss(extensionVector); 
-        // if (length < 0.001 ) 
-        //     return VectorDouble3(0.,0.,0.);
         if (length == 0)
             return VectorDouble3(0.,0.,0.);
         auto x(length/accuracy);
-        auto up (static_cast<uint32_t>(floor((length)/accuracy)+1));
-        auto down(static_cast<uint32_t>(floor(length/accuracy)));
+        auto up (static_cast<uint32_t>(ceil(x)+1 ));
+        auto down(static_cast<uint32_t>(floor(x)));
         auto amplitude=force_extension[down] + (force_extension[up]-force_extension[down])/static_cast<double>(up-down)*(x-down)/static_cast<double>(up-down);
-        // std::cout<< "amp=" <<  amplitude<< std::endl;
-        // extensionVector.normalize();
         return extensionVector.normalize()*(amplitude);
-        // return extensionVector.normalize()*(force_extension[static_cast<uint32_t>(round(length/accuracy))]);
-
     }
     //Gaussina force extension relation 
     //f=R*3/(N*b^2)
@@ -159,7 +151,7 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
     //spring constant for the equivalent chain used for the relaxation of the cross links 
     double springConstant;
    
-    //force extension mapping        // std::cout<< "amp=" <<  amplitude<< std::endl;
+    //force extension mapping       
     std::map<double, double> extension_force;
     //extension force mapping index=extension rounded to int 
     std::vector<double> force_extension;
@@ -170,9 +162,7 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
     VectorDouble3 CalculateShift(IngredientsType& ing ){
         std::vector<neighborX> Neighbors(ing.getCrossLinkNeighborIDs(this->getIndex()) );
         VectorDouble3 force(0.,0.,0.);
-        // VectorDouble3 force2(0.,0.,0.); 
         VectorDouble3 shift(0.,0.,0.);
-        // VectorDouble3 shift2(0.,0.,0.);
         double avNSegments(0.);
         int32_t number_of_neighbors(Neighbors.size());
         if (number_of_neighbors > 0) {
@@ -180,32 +170,8 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
             for (size_t i = 0; i < number_of_neighbors; i++){
                 VectorDouble3 vec(ing.getMolecules()[Neighbors[i].ID].getVector3D()-Neighbors[i].jump-Position);
                 force+=EF(vec);
-                // force2+=EFGauss(vec);
-                // if (ing.getMolecules().getAge()%1000 == 999 && ing.getMolecules().getAge()>49000)
-                			// stream.precision(std::numeric_limits<typename ResultType::value_type::value_type>::max_digits10);
-			// stream.setf( std::ios::fixed, std:: ios::floatfield );	
-                    // std::cout   << std::setprecision(10)
-                    //     // << setf( std::ios::fixed, std:: ios::floatfield )
-                    //             << vec.getLength() << "\n" 
-                    //             << ing.getMolecules()[Neighbors[i].ID].getVector3D()<< "\n" 
-                    //             << Neighbors[i].jump<< "\n" 
-                    //             << Position <<"\n" ;
             }
             shift=FE(force/(static_cast<double>(number_of_neighbors) ));
-            // shift2=FE(force2/(static_cast<double>(number_of_neighbors) ));
-            // if (ing.getMolecules().getAge()%1000 == 999 && ing.getMolecules().getAge()>49000)
-                // if(shift.getLength()  > .001 ){
-                    // std::cout << "i="<<this->getIndex() <<" "
-                                // << shift  <<" " <<shift.getLength() << " "
-                                // << force  <<" " <<force.getLength() << " "
-                                // << shift2  <<" " <<shift2.getLength() << " "
-                                // << force2  <<" " <<force2.getLength() << " "        // std::cout<< "amp=" <<  amplitude<< std::endl;
-                                // <<"dR= " << FE(force).getLength() <<" " 
-                                // <<"df= " << EF(shift).getLength()<<" " 
-                                // <<"df_gauss= " << EFGauss(shift).getLength()<<" " 
-                                // << std::endl;
-                // }
-            // if (shift.getLength() < 0.001 ) shift*=0.;
         }
         return shift;
     };

From f19b0965207b43e8546eaf17c09042cd0aab8567 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Mon, 21 Jun 2021 12:53:31 +0200
Subject: [PATCH 26/70] fix bug with average shift condition

---
 include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h   | 5 ++++-
 .../updater/moves/MoveNonLinearForceEquilibrium.h            | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
index f842e84..bb05f0f 100644
--- a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
+++ b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
@@ -70,7 +70,7 @@ class UpdaterForceBalancedPosition:public AbstractUpdater
 template <class IngredientsType, class moveType>
 bool UpdaterForceBalancedPosition<IngredientsType,moveType>::execute(){
     std::cout << "UpdaterForceBalancedPosition::execute(): Start equilibration" <<std::endl;
-    double avShift(0.0);
+    double avShift(threshold*1.1);
     uint32_t StartMCS(ing.getMolecules().getAge());
     setRelaxationParameter(relaxationParameter);
     //! get look up table for the cross link ids to monomer ids
@@ -78,12 +78,15 @@ bool UpdaterForceBalancedPosition<IngredientsType,moveType>::execute(){
     //! number of cross links 
     auto NCrossLinks(CrossLinkIDs.size());
     while (avShift > threshold  ){
+        double NSuccessfulMoves(0.);
+        avShift=0.0;
         for (uint32_t i =0 ; i<NCrossLinks ; i++){
             uint32_t RandomMonomer(CrossLinkIDs[ rng.r250_rand32() % NCrossLinks]);
             move.init(ing, RandomMonomer);
             if(move.check(ing)){
                 move.apply(ing);
                 avShift+=move.getShiftVector().getLength();
+                NSuccessfulMoves++;
             }
         }
         ing.modifyMolecules().setAge(ing.getMolecules().getAge()+1);
diff --git a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
index f0ec714..dce87ed 100644
--- a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
+++ b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
@@ -109,8 +109,8 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
         if (length == 0)
             return VectorDouble3(0.,0.,0.);
         auto x(length/accuracy);
-        auto up (static_cast<uint32_t>(ceil(x)+1 ));
         auto down(static_cast<uint32_t>(floor(x)));
+        auto up (down+1);
         auto amplitude=force_extension[down] + (force_extension[up]-force_extension[down])/static_cast<double>(up-down)*(x-down)/static_cast<double>(up-down);
         return extensionVector.normalize()*(amplitude);
     }

From 3d7d2d938fc99c55567248b2e6243a310744ea1f Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Thu, 24 Jun 2021 13:00:48 +0200
Subject: [PATCH 27/70] clean up

---
 .../feature/FeatureCrosslinkConnectionsLookUp.h          | 2 ++
 .../LeMonADE_PM/updater/UpdaterForceBalancedPosition.h   | 9 ++-------
 .../updater/moves/MoveNonLinearForceEquilibrium.h        | 4 ----
 3 files changed, 4 insertions(+), 11 deletions(-)

diff --git a/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUp.h b/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUp.h
index 1f38489..7c50e2c 100644
--- a/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUp.h
+++ b/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUp.h
@@ -74,11 +74,13 @@ class FeatureCrosslinkConnectionsLookUp : public Feature {
 
 	//!getter function for the neighboring crosslinks
 	std::vector<neighborX> getCrossLinkNeighborIDs(uint32_t CrossLinkID) const{
+		#ifdef DEBUG
 		if (CrossLinkNeighbors.find(CrossLinkID) == CrossLinkNeighbors.end()){
 			std::stringstream errormessage;
 			errormessage << "FeatureCrosslinkConnectionsLookUp::getCrossLinkNeighborIDs Cross Link ID " << CrossLinkID <<" does not exist.";
 			throw std::runtime_error(errormessage.str());
 		}
+		#endif
 		return CrossLinkNeighbors.at(CrossLinkID);
 	};
 
diff --git a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
index bb05f0f..ed9d1ea 100644
--- a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
+++ b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
@@ -41,9 +41,9 @@ class UpdaterForceBalancedPosition:public AbstractUpdater
 public:
     //! constructor for UpdaterForceBalancedPosition
     UpdaterForceBalancedPosition(IngredientsType& ing_, double threshold_, double factor_=0.995 ):
-    ing(ing_),threshold(threshold_),factor(factor_),relaxationParameter(1.0){};
+    ing(ing_),threshold(threshold_),relaxationParameter(1.0){};
     
-    virtual void initialize(){relaxationParameter=move.getRelaxationParameter();}// init(move);};
+    virtual void initialize(){};
     bool execute();
     virtual void cleanup(){};  
 
@@ -56,10 +56,6 @@ class UpdaterForceBalancedPosition:public AbstractUpdater
     //! threshold for the certainty 
     double threshold;
 
-    double relaxationParameter;
-
-    double factor;
-    
     //! move to equilibrate the cross links by force equilibrium
     moveType move;
     
@@ -72,7 +68,6 @@ bool UpdaterForceBalancedPosition<IngredientsType,moveType>::execute(){
     std::cout << "UpdaterForceBalancedPosition::execute(): Start equilibration" <<std::endl;
     double avShift(threshold*1.1);
     uint32_t StartMCS(ing.getMolecules().getAge());
-    setRelaxationParameter(relaxationParameter);
     //! get look up table for the cross link ids to monomer ids
     auto CrossLinkIDs(ing.getCrosslinkIDs());
     //! number of cross links 
diff --git a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
index dce87ed..a1a242a 100644
--- a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
+++ b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
@@ -65,10 +65,6 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
 
     //!read file to create a lookup table of the force extension curve 
     void createTable();
-    // //!read file to create a lookup table of the force extension curve 
-    // void createTable(std::string filename_){
-    //     setFilename(filename); 
-    //     createTable();}
     //! set the filename for the force extension data 
     void setFilename(std::string filename_){filename=filename_;createTable();}
     //! get the filename for the force extension data 

From cf8ec2b572d3a4126e79e3b3b17c1a00b2bd19c6 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Tue, 13 Jul 2021 10:18:01 +0200
Subject: [PATCH 28/70] comment out a check, which can only be used for integer
 box sizes. This is not compatible with the affine deformation.

---
 .../analyzer/AnalyzerEquilbratedPosition.h    | 24 +++++++++----------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h b/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h
index bb32639..5bcfde1 100644
--- a/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h
+++ b/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h
@@ -102,18 +102,18 @@ std::vector< std::vector<double> >  AnalyzerEquilbratedPosition<IngredientsType>
 		auto neighbors(ingredients.getCrossLinkNeighborIDs(IDx));
 		for (size_t j=0; j < neighbors.size() ;j++){
 			VectorDouble3 vec(ingredients.getMolecules()[neighbors[j].ID].getVector3D()-ingredients.getMolecules()[IDx].getVector3D()-neighbors[j].jump);
-			VectorDouble3 vec2=LemonadeDistCalcs::MinImageVector(ingredients.getMolecules()[neighbors[j].ID].getVector3D(),ingredients.getMolecules()[IDx].getVector3D(),ingredients);
-			if ( vec.getLength() != vec2.getLength()) {
-				std::stringstream error_message;
-				error_message   << "AnalyzerEquilbratedPosition:\n"
-								<< "distance from jump=(" << vec  << ") \n"
-								<< "distance from  IMC=(" << vec2 << ") \n"
-								<< "jump vector=("<< neighbors[j].jump <<") \n" 
-								<< "position1=("<<ingredients.getMolecules()[IDx].getVector3D() <<") \n"
-								<< "position2=("<<ingredients.getMolecules()[neighbors[j].ID].getVector3D() <<") \n"
-								<< std::endl;
-				throw std::runtime_error(error_message.str());
-			}
+			// VectorDouble3 vec2=LemonadeDistCalcs::MinImageVector(ingredients.getMolecules()[neighbors[j].ID].getVector3D(),ingredients.getMolecules()[IDx].getVector3D(),ingredients);
+			// if ( vec.getLength() != vec2.getLength()) {
+			// 	std::stringstream error_message;
+			// 	error_message   << "AnalyzerEquilbratedPosition:\n"
+			// 					<< "distance from jump=(" << vec  << ") \n"
+			// 					<< "distance from  IMC=(" << vec2 << ") \n"
+			// 					<< "jump vector=("<< neighbors[j].jump <<") \n" 
+			// 					<< "position1=("<<ingredients.getMolecules()[IDx].getVector3D() <<") \n"
+			// 					<< "position2=("<<ingredients.getMolecules()[neighbors[j].ID].getVector3D() <<") \n"
+			// 					<< std::endl;
+			// 	throw std::runtime_error(error_message.str());
+			// }
 			dist[0].push_back(IDx);
 			dist[1].push_back(neighbors[j].ID);
 			dist[2].push_back(vec.getX());

From d40c1a713b09446bbb15687832353c8a1eef1952 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Tue, 13 Jul 2021 10:18:56 +0200
Subject: [PATCH 29/70] add an updater which adjusts the jump vector and the
 positions of all monomers according to the stretching factor lambda.

---
 .../updater/UpdaterAffineDeformation.h        | 87 +++++++++++++++++++
 1 file changed, 87 insertions(+)
 create mode 100644 include/LeMonADE_PM/updater/UpdaterAffineDeformation.h

diff --git a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
new file mode 100644
index 0000000..861e37f
--- /dev/null
+++ b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
@@ -0,0 +1,87 @@
+/*--------------------------------------------------------------------------------
+    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_PM_UPDATER_UPDATERAFFINEDEFORMATION_H
+#define LEMONADE_PM_UPDATER_UPDATERAFFINEDEFORMATION_H
+
+
+#include <LeMonADE/updater/AbstractUpdater.h>
+#include <LeMonADE/utility/Vector3D.h>
+#include <LeMonADE_PM/utility/neighborX.h>
+#include <vector>
+#include <cmath>
+ /**
+ * @class UpdaterAffineDeformation
+ * @tparam IngredientsType
+ */
+
+ template <class IngredientsType >
+class UpdaterAffineDeformation:public AbstractUpdater
+{
+public:
+    //! constructor for UpdaterAffineDeformation
+    UpdaterAffineDeformation(IngredientsType& ing_, double lambda_ ):
+    ing(ing_),lambda(lambda_),labmdaYZ(std::sqrt(labmda)){};
+    
+    virtual void initialize(){};
+    virtual bool execute(){return false;};
+    virtual void cleanup(){};  
+
+private:
+    //!copy of the main container for the system informations 
+    IngredientsType& ing;
+    
+    //! threshold for the certainty 
+    double lambda;
+    double labmdaYZ;
+    void deform( VectorDouble3& vec ){
+        vec.setAllCoordinates(vec.getX()*lambda,vec.getY()*labmdaYZ,vec.getZ()*labmdaYZ);
+    }
+};
+template <class IngredientsType>
+void UpdaterAffineDeformation<IngredientsType>::initialize(){
+    //adjusting the box size is not neccessary, because it is used only once in the FeatureCrosslinkConnections*
+    //there the jump vectors are calculated
+    
+    //The jump vector needs to be adjusted according the deformation labmda! 
+    auto CrossLinkIDs(ing.getCrosslinkIDs());
+    for (uint32_t i =0 ; i<CrossLinkIDs.size() ; i++){
+        uint32_t ID(CrossLinkIDs[i]);
+        std::vector<neighborX> Neighbors(ing.getCrossLinkNeighborIDs(ID );
+        int32_t number_of_neighbors(Neighbors.size());
+        if (number_of_neighbors > 0) {
+            deform(Neighbors[i].jump);
+        }
+
+    }
+
+    //The initial posistions of all monomers needs to be adjusted according the deformation labmda! 
+    for(size_t i = 0; i< myIngredients.getMolecules().size();i++){
+        deform(ing.modifyMolecules()[i].modifyVector3D());
+    }
+    return false;
+}
+#endif /*LEMONADE_PM_UPDATER_UPDATERAFFINEDEFORMATION_H*/
\ No newline at end of file

From 0f56b8a7d38f904bd1bd121c1546adf04f115606 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Tue, 13 Jul 2021 10:22:52 +0200
Subject: [PATCH 30/70] add stdout for observing the affine deformation

---
 .../LeMonADE_PM/updater/UpdaterAffineDeformation.h   | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
index 861e37f..4640d6a 100644
--- a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
+++ b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
@@ -63,6 +63,7 @@ class UpdaterAffineDeformation:public AbstractUpdater
 };
 template <class IngredientsType>
 void UpdaterAffineDeformation<IngredientsType>::initialize(){
+    std::cout << "UpdaterAffineDeformation<IngredientsType>::initialize():\n";
     //adjusting the box size is not neccessary, because it is used only once in the FeatureCrosslinkConnections*
     //there the jump vectors are calculated
     
@@ -70,18 +71,25 @@ void UpdaterAffineDeformation<IngredientsType>::initialize(){
     auto CrossLinkIDs(ing.getCrosslinkIDs());
     for (uint32_t i =0 ; i<CrossLinkIDs.size() ; i++){
         uint32_t ID(CrossLinkIDs[i]);
+        if (i < 20 ) 
+            std::cout << "initial jump " << ing.getMolecules()[ID].getVector3D() << " ";  
         std::vector<neighborX> Neighbors(ing.getCrossLinkNeighborIDs(ID );
         int32_t number_of_neighbors(Neighbors.size());
         if (number_of_neighbors > 0) {
             deform(Neighbors[i].jump);
         }
-
+        if (i < 20 ) 
+            std::cout << "deformed jump " << ing.getMolecules()[ID].getVector3D() << "\n";  
     }
 
     //The initial posistions of all monomers needs to be adjusted according the deformation labmda! 
     for(size_t i = 0; i< myIngredients.getMolecules().size();i++){
+        if (i < 20 ) 
+            std::cout << "initial position " << ing.getMolecules()[ID].getVector3D() << " ";  
         deform(ing.modifyMolecules()[i].modifyVector3D());
+        if (i < 20 ) 
+            std::cout << "deformed position " << ing.getMolecules()[ID].getVector3D() << "\n";  
     }
-    return false;
+    std::cout << "UpdaterAffineDeformation<IngredientsType>::initialize():done.\n";
 }
 #endif /*LEMONADE_PM_UPDATER_UPDATERAFFINEDEFORMATION_H*/
\ No newline at end of file

From 47d3cd20d7eb5f2e6da3ac9628b8ee83518f0cfa Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Tue, 13 Jul 2021 10:29:51 +0200
Subject: [PATCH 31/70] include the affine deformation into the force
 equilibration for the tendomer

---
 .../updater/UpdaterAffineDeformation.h        | 12 ++++++-----
 projects/TendomerNetworkForceEquilibrium.cpp  | 21 ++++++++++++-------
 2 files changed, 20 insertions(+), 13 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
index 4640d6a..5920404 100644
--- a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
+++ b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
@@ -35,6 +35,8 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 #include <cmath>
  /**
  * @class UpdaterAffineDeformation
+ * @brief This class performs a affine deformation accordign to the stretching factor (lambda)
+ * for the positions and the jump vector. 
  * @tparam IngredientsType
  */
 
@@ -43,8 +45,8 @@ class UpdaterAffineDeformation:public AbstractUpdater
 {
 public:
     //! constructor for UpdaterAffineDeformation
-    UpdaterAffineDeformation(IngredientsType& ing_, double lambda_ ):
-    ing(ing_),lambda(lambda_),labmdaYZ(std::sqrt(labmda)){};
+    UpdaterAffineDeformation(IngredientsType& ing_, double stretching_factor_ ):
+    ing(ing_),stretching_factor(stretching_factor_),stretching_factor_XY(std::sqrt(stretching_factor)){};
     
     virtual void initialize(){};
     virtual bool execute(){return false;};
@@ -55,10 +57,10 @@ class UpdaterAffineDeformation:public AbstractUpdater
     IngredientsType& ing;
     
     //! threshold for the certainty 
-    double lambda;
-    double labmdaYZ;
+    double stretching_factor;
+    double stretching_factor_XY;
     void deform( VectorDouble3& vec ){
-        vec.setAllCoordinates(vec.getX()*lambda,vec.getY()*labmdaYZ,vec.getZ()*labmdaYZ);
+        vec.setAllCoordinates(vec.getX()*stretching_factor,vec.getY()*stretching_factor_XY,vec.getZ()*stretching_factor_XY);
     }
 };
 template <class IngredientsType>
diff --git a/projects/TendomerNetworkForceEquilibrium.cpp b/projects/TendomerNetworkForceEquilibrium.cpp
index cffe0b5..4e3c76d 100644
--- a/projects/TendomerNetworkForceEquilibrium.cpp
+++ b/projects/TendomerNetworkForceEquilibrium.cpp
@@ -53,6 +53,7 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 #include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
 #include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h>
 #include <LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h>
+#include <LeMonADE_PM/updater/UpdaterAffineDeformation.h>
 
 
 int main(int argc, char* argv[]){
@@ -66,16 +67,18 @@ int main(int argc, char* argv[]){
 		double relaxationParameter(10.);
 		double threshold(0.5);
 		double factor(0.995);
+		double stretching_factor(1.0);
 		
 		bool showHelp = false;
 		auto parser
-			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"          ] ("(required)Input filename of the bfm file"                                    ).required()
-			| clara::detail::Opt(       outputDataPos, "outputDataPos (=CrosslinkPosition.dat)"          ) ["-o"]["--outputPos"      ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
-			| clara::detail::Opt(      outputDataDist, "outputDataDist (=ChainExtensionDistribution.dat)") ["-c"]["--outputDist"     ] ("(optional) Output filename of the chain extension distribution."             ).optional()
-			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"      ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
-			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"        ] ("(optional) Force-Extension curve. Default \"\"."                             ).required()
-			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"          ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
-			| clara::detail::Opt(              factor, "factor (=10)"                                    ) ["-a"]["--factor"         ] ("(optional) Factor for reducing the relaxation parameter after 1000MCS. Default .995 .").optional()
+			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"            ] ("(required)Input filename of the bfm file"                                    ).required()
+			| clara::detail::Opt(       outputDataPos, "outputDataPos (=CrosslinkPosition.dat)"          ) ["-o"]["--outputPos"        ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
+			| clara::detail::Opt(      outputDataDist, "outputDataDist (=ChainExtensionDistribution.dat)") ["-c"]["--outputDist"       ] ("(optional) Output filename of the chain extension distribution."             ).optional()
+			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"        ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
+			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"          ] ("(optional) Force-Extension curve. Default \"\"."                             ).required()
+			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"            ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
+			| clara::detail::Opt(              factor, "factor (=10)"                                    ) ["-a"]["--factor"           ] ("(optional) Factor for reducing the relaxation parameter after 1000MCS. Default .995 .").optional()
+			| clara::detail::Opt(   stretching_factor, "stretching_factor (=1)"                          ) ["-l"]["--stretching_factor"] ("(optional) Stretching factor for uniaxial deformation. Default 1.0 ."        ).optional()
 			| clara::Help( showHelp );
 		
 	    auto result = parser.parse( clara::Args( argc, argv ) );
@@ -93,7 +96,8 @@ int main(int argc, char* argv[]){
 	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
 	      std::cout << "threshold             : " << threshold              << std::endl; 
 		  std::cout << "feCurve               : " << feCurve                << std::endl;
-		  std::cout << "factor                : " << factor                << std::endl;
+		  std::cout << "factor                : " << factor                 << std::endl;
+		  std::cout << "stretching_factor     : " << stretching_factor      << std::endl;
 	    }
 		RandomNumberGenerators rng;
 		rng.seedAll();
@@ -148,6 +152,7 @@ int main(int argc, char* argv[]){
 		myIngredients2.synchronize();
 
 		TaskManager taskmanager2;
+		taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing>(myIngredients2, stretching_factor) );
 		//read bonds and positions stepwise
         auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold, factor) ;
         updater->setFilename(feCurve);

From d374f3c70cd1a66375fc313ac31def2833a7fe30 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Tue, 13 Jul 2021 10:34:48 +0200
Subject: [PATCH 32/70] it compiles.

---
 .../LeMonADE_PM/updater/UpdaterAffineDeformation.h   | 12 ++++++------
 .../updater/UpdaterForceBalancedPosition.h           |  2 +-
 projects/TendomerNetworkForceEquilibrium.cpp         |  2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
index 5920404..f4a3a43 100644
--- a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
+++ b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
@@ -48,7 +48,7 @@ class UpdaterAffineDeformation:public AbstractUpdater
     UpdaterAffineDeformation(IngredientsType& ing_, double stretching_factor_ ):
     ing(ing_),stretching_factor(stretching_factor_),stretching_factor_XY(std::sqrt(stretching_factor)){};
     
-    virtual void initialize(){};
+    virtual void initialize();
     virtual bool execute(){return false;};
     virtual void cleanup(){};  
 
@@ -74,8 +74,8 @@ void UpdaterAffineDeformation<IngredientsType>::initialize(){
     for (uint32_t i =0 ; i<CrossLinkIDs.size() ; i++){
         uint32_t ID(CrossLinkIDs[i]);
         if (i < 20 ) 
-            std::cout << "initial jump " << ing.getMolecules()[ID].getVector3D() << " ";  
-        std::vector<neighborX> Neighbors(ing.getCrossLinkNeighborIDs(ID );
+            std::cout << "ID="<< i << "initial jump " << ing.getMolecules()[ID].getVector3D() << " ";  
+        std::vector<neighborX> Neighbors(ing.getCrossLinkNeighborIDs(ID) );
         int32_t number_of_neighbors(Neighbors.size());
         if (number_of_neighbors > 0) {
             deform(Neighbors[i].jump);
@@ -85,12 +85,12 @@ void UpdaterAffineDeformation<IngredientsType>::initialize(){
     }
 
     //The initial posistions of all monomers needs to be adjusted according the deformation labmda! 
-    for(size_t i = 0; i< myIngredients.getMolecules().size();i++){
+    for(size_t i = 0; i< ing.getMolecules().size();i++){
         if (i < 20 ) 
-            std::cout << "initial position " << ing.getMolecules()[ID].getVector3D() << " ";  
+            std::cout << "ID="<< i << "initial position " << ing.getMolecules()[i].getVector3D() << " ";  
         deform(ing.modifyMolecules()[i].modifyVector3D());
         if (i < 20 ) 
-            std::cout << "deformed position " << ing.getMolecules()[ID].getVector3D() << "\n";  
+            std::cout << "deformed position " << ing.getMolecules()[i].getVector3D() << "\n";  
     }
     std::cout << "UpdaterAffineDeformation<IngredientsType>::initialize():done.\n";
 }
diff --git a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
index ed9d1ea..f328243 100644
--- a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
+++ b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
@@ -41,7 +41,7 @@ class UpdaterForceBalancedPosition:public AbstractUpdater
 public:
     //! constructor for UpdaterForceBalancedPosition
     UpdaterForceBalancedPosition(IngredientsType& ing_, double threshold_, double factor_=0.995 ):
-    ing(ing_),threshold(threshold_),relaxationParameter(1.0){};
+    ing(ing_),threshold(threshold_){};
     
     virtual void initialize(){};
     bool execute();
diff --git a/projects/TendomerNetworkForceEquilibrium.cpp b/projects/TendomerNetworkForceEquilibrium.cpp
index 4e3c76d..09fde2c 100644
--- a/projects/TendomerNetworkForceEquilibrium.cpp
+++ b/projects/TendomerNetworkForceEquilibrium.cpp
@@ -152,7 +152,7 @@ int main(int argc, char* argv[]){
 		myIngredients2.synchronize();
 
 		TaskManager taskmanager2;
-		taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing>(myIngredients2, stretching_factor) );
+		taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor) );
 		//read bonds and positions stepwise
         auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold, factor) ;
         updater->setFilename(feCurve);

From b3a07c7d13d53d9c6f7f06a2149c4ae4df53d37c Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Tue, 13 Jul 2021 11:26:03 +0200
Subject: [PATCH 33/70] rewrite deform function

---
 include/LeMonADE_PM/updater/UpdaterAffineDeformation.h | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
index f4a3a43..273154c 100644
--- a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
+++ b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
@@ -59,13 +59,13 @@ class UpdaterAffineDeformation:public AbstractUpdater
     //! threshold for the certainty 
     double stretching_factor;
     double stretching_factor_XY;
-    void deform( VectorDouble3& vec ){
-        vec.setAllCoordinates(vec.getX()*stretching_factor,vec.getY()*stretching_factor_XY,vec.getZ()*stretching_factor_XY);
+    VectorDouble3 deform( VectorDouble3 vec ){
+        return VectorDouble3(vec.getX()*stretching_factor,vec.getY()*stretching_factor_XY,vec.getZ()*stretching_factor_XY);
     }
 };
 template <class IngredientsType>
 void UpdaterAffineDeformation<IngredientsType>::initialize(){
-    std::cout << "UpdaterAffineDeformation<IngredientsType>::initialize():\n";
+    std::cout << "UpdaterAffineDeformation<IngredientsType>::initialize():"<< std::endl;
     //adjusting the box size is not neccessary, because it is used only once in the FeatureCrosslinkConnections*
     //there the jump vectors are calculated
     
@@ -78,7 +78,7 @@ void UpdaterAffineDeformation<IngredientsType>::initialize(){
         std::vector<neighborX> Neighbors(ing.getCrossLinkNeighborIDs(ID) );
         int32_t number_of_neighbors(Neighbors.size());
         if (number_of_neighbors > 0) {
-            deform(Neighbors[i].jump);
+            Neighbors[i].jump)= deform(Neighbors[i].jump);
         }
         if (i < 20 ) 
             std::cout << "deformed jump " << ing.getMolecules()[ID].getVector3D() << "\n";  
@@ -88,7 +88,7 @@ void UpdaterAffineDeformation<IngredientsType>::initialize(){
     for(size_t i = 0; i< ing.getMolecules().size();i++){
         if (i < 20 ) 
             std::cout << "ID="<< i << "initial position " << ing.getMolecules()[i].getVector3D() << " ";  
-        deform(ing.modifyMolecules()[i].modifyVector3D());
+        ing.modifyMolecules()[i].modifyVector3D()=deform(ing.modifyMolecules()[i].getVector3D());
         if (i < 20 ) 
             std::cout << "deformed position " << ing.getMolecules()[i].getVector3D() << "\n";  
     }

From 2cf38c58d008c3269766e7d7cd072e9d2852cbb3 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Tue, 13 Jul 2021 11:26:03 +0200
Subject: [PATCH 34/70] rewrite deform function

---
 include/LeMonADE_PM/updater/UpdaterAffineDeformation.h | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
index f4a3a43..5153081 100644
--- a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
+++ b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
@@ -59,13 +59,13 @@ class UpdaterAffineDeformation:public AbstractUpdater
     //! threshold for the certainty 
     double stretching_factor;
     double stretching_factor_XY;
-    void deform( VectorDouble3& vec ){
-        vec.setAllCoordinates(vec.getX()*stretching_factor,vec.getY()*stretching_factor_XY,vec.getZ()*stretching_factor_XY);
+    VectorDouble3 deform( VectorDouble3 vec ){
+        return VectorDouble3(vec.getX()*stretching_factor,vec.getY()*stretching_factor_XY,vec.getZ()*stretching_factor_XY);
     }
 };
 template <class IngredientsType>
 void UpdaterAffineDeformation<IngredientsType>::initialize(){
-    std::cout << "UpdaterAffineDeformation<IngredientsType>::initialize():\n";
+    std::cout << "UpdaterAffineDeformation<IngredientsType>::initialize():"<< std::endl;
     //adjusting the box size is not neccessary, because it is used only once in the FeatureCrosslinkConnections*
     //there the jump vectors are calculated
     
@@ -78,7 +78,7 @@ void UpdaterAffineDeformation<IngredientsType>::initialize(){
         std::vector<neighborX> Neighbors(ing.getCrossLinkNeighborIDs(ID) );
         int32_t number_of_neighbors(Neighbors.size());
         if (number_of_neighbors > 0) {
-            deform(Neighbors[i].jump);
+            Neighbors[i].jump= deform(Neighbors[i].jump);
         }
         if (i < 20 ) 
             std::cout << "deformed jump " << ing.getMolecules()[ID].getVector3D() << "\n";  
@@ -88,7 +88,7 @@ void UpdaterAffineDeformation<IngredientsType>::initialize(){
     for(size_t i = 0; i< ing.getMolecules().size();i++){
         if (i < 20 ) 
             std::cout << "ID="<< i << "initial position " << ing.getMolecules()[i].getVector3D() << " ";  
-        deform(ing.modifyMolecules()[i].modifyVector3D());
+        ing.modifyMolecules()[i].modifyVector3D()=deform(ing.modifyMolecules()[i].getVector3D());
         if (i < 20 ) 
             std::cout << "deformed position " << ing.getMolecules()[i].getVector3D() << "\n";  
     }

From 01ba7dd8f843d3282c872c8acc6fdd97819dfa52 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Tue, 13 Jul 2021 11:37:40 +0200
Subject: [PATCH 35/70] fix bug: indexing of the jump vector

---
 include/LeMonADE_PM/updater/UpdaterAffineDeformation.h | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
index 5153081..7f8c38c 100644
--- a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
+++ b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
@@ -73,15 +73,13 @@ void UpdaterAffineDeformation<IngredientsType>::initialize(){
     auto CrossLinkIDs(ing.getCrosslinkIDs());
     for (uint32_t i =0 ; i<CrossLinkIDs.size() ; i++){
         uint32_t ID(CrossLinkIDs[i]);
-        if (i < 20 ) 
-            std::cout << "ID="<< i << "initial jump " << ing.getMolecules()[ID].getVector3D() << " ";  
         std::vector<neighborX> Neighbors(ing.getCrossLinkNeighborIDs(ID) );
         int32_t number_of_neighbors(Neighbors.size());
         if (number_of_neighbors > 0) {
-            Neighbors[i].jump= deform(Neighbors[i].jump);
+            for (size_t j = 0; j < number_of_neighbors; j++){
+                Neighbors[j].jump= deform(Neighbors[j].jump);    
+            }
         }
-        if (i < 20 ) 
-            std::cout << "deformed jump " << ing.getMolecules()[ID].getVector3D() << "\n";  
     }
 
     //The initial posistions of all monomers needs to be adjusted according the deformation labmda! 

From 6c27dbd12376469d30945cd47ac8e53e306c0e5b Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Tue, 13 Jul 2021 11:39:59 +0200
Subject: [PATCH 36/70] adjust stretching factor for the y and z direction

---
 include/LeMonADE_PM/updater/UpdaterAffineDeformation.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
index 7f8c38c..36c006c 100644
--- a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
+++ b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
@@ -46,7 +46,7 @@ class UpdaterAffineDeformation:public AbstractUpdater
 public:
     //! constructor for UpdaterAffineDeformation
     UpdaterAffineDeformation(IngredientsType& ing_, double stretching_factor_ ):
-    ing(ing_),stretching_factor(stretching_factor_),stretching_factor_XY(std::sqrt(stretching_factor)){};
+    ing(ing_),stretching_factor(stretching_factor_),stretching_factor_XY(1./std::sqrt(stretching_factor)){};
     
     virtual void initialize();
     virtual bool execute(){return false;};

From 7c04346faea35c5ae25c36d5c8f12b9bce5cfe4e Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Tue, 13 Jul 2021 12:07:06 +0200
Subject: [PATCH 37/70] workaournd for overstretched configs in the beginning.

---
 include/LeMonADE_PM/updater/UpdaterAffineDeformation.h      | 6 +++++-
 .../updater/moves/MoveNonLinearForceEquilibrium.h           | 5 ++++-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
index 36c006c..32aecf3 100644
--- a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
+++ b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
@@ -77,7 +77,11 @@ void UpdaterAffineDeformation<IngredientsType>::initialize(){
         int32_t number_of_neighbors(Neighbors.size());
         if (number_of_neighbors > 0) {
             for (size_t j = 0; j < number_of_neighbors; j++){
-                Neighbors[j].jump= deform(Neighbors[j].jump);    
+                if (i < 20 ) 
+                    std::cout << "ID= "<< i << "initial jump   " << Neighbors[j].jump << " ";  
+                Neighbors[j].jump= deform(Neighbors[j].jump);   
+                if (i < 20 ) 
+                    std::cout << "ID= "<< i << "defrormed jump " << Neighbors[j].jump << "\n";   
             }
         }
     }
diff --git a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
index a1a242a..58d5a44 100644
--- a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
+++ b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
@@ -84,7 +84,9 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
         if (extensionVector == VectorDouble3(0.,0.,0.) )
             return VectorDouble3(0.,0.,0.);
         double length( extensionVector.getLength() );
-
+        if ( max_extension < length  ){
+            return EFGauss(extensionVector); 
+        }
         #ifdef DEBUG
         if ( max_extension < length  ){
             std::stringstream errormessage; 
@@ -165,6 +167,7 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
             VectorDouble3 Position(ing.getMolecules()[this->getIndex()].getVector3D());      
             for (size_t i = 0; i < number_of_neighbors; i++){
                 VectorDouble3 vec(ing.getMolecules()[Neighbors[i].ID].getVector3D()-Neighbors[i].jump-Position);
+                // std::cout << ing.getMolecules()[Neighbors[i].ID].getVector3D() << " " << Neighbors[i].jump<< " " << Position <<std::endl;
                 force+=EF(vec);
             }
             shift=FE(force/(static_cast<double>(number_of_neighbors) ));

From d018657d4ac4eb0e2822eb9e3687b615eafa230a Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 14 Jul 2021 10:20:46 +0200
Subject: [PATCH 38/70] erase bug in the transformation of the jump vector

---
 ...FeatureCrosslinkConnectionsLookUpTendomers.h | 10 ++++++++++
 .../updater/UpdaterAffineDeformation.h          | 17 +++++++++++------
 .../updater/moves/MoveForceEquilibrium.h        |  1 +
 .../moves/MoveNonLinearForceEquilibrium.h       |  2 +-
 projects/TendomerNetworkForceEquilibrium.cpp    | 11 ++++++-----
 5 files changed, 29 insertions(+), 12 deletions(-)

diff --git a/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h b/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h
index 409aae0..67b6f42 100644
--- a/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h
+++ b/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h
@@ -82,6 +82,16 @@ class FeatureCrosslinkConnectionsLookUpTendomers : public Feature {
 		return CrossLinkNeighbors.at(CrossLinkID);
 	};
 
+	//! set the jump vector 
+	void setCrossLinkNeighborJump(uint32_t CrossLinkID, uint32_t idx, VectorDouble3 vec) {
+		if ( idx > CrossLinkNeighbors.at(CrossLinkID).size() ){
+			std::stringstream errormessage;
+			errormessage << "FeatureCrosslinkConnectionsLookUpTendomers::setCrossLinkNeighborJump neighbor idx  " << idx <<" is to high.";
+			throw std::runtime_error(errormessage.str());
+		}
+		CrossLinkNeighbors.at(CrossLinkID)[idx].jump=vec;
+	}
+
 	//!get the ID of crosslinks (determined by nConnections>3 and connected to another crosslink)
 	const std::vector<uint32_t>& getCrosslinkIDs() const {return crosslinkIDs;}
 
diff --git a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
index 32aecf3..d4fdc84 100644
--- a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
+++ b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
@@ -46,7 +46,11 @@ class UpdaterAffineDeformation:public AbstractUpdater
 public:
     //! constructor for UpdaterAffineDeformation
     UpdaterAffineDeformation(IngredientsType& ing_, double stretching_factor_ ):
-    ing(ing_),stretching_factor(stretching_factor_),stretching_factor_XY(1./std::sqrt(stretching_factor)){};
+    ing(ing_),stretching_factor(stretching_factor_),stretching_factor_XY(1./std::sqrt(stretching_factor)){
+        std::cout << "UpdaterAffineDeformation::constructor:\n"
+                  << "stretching factor =       " << stretching_factor    << "\n"
+                  << "stretching factor in yz = " << stretching_factor_XY << "\n";
+    };
     
     virtual void initialize();
     virtual bool execute(){return false;};
@@ -60,6 +64,7 @@ class UpdaterAffineDeformation:public AbstractUpdater
     double stretching_factor;
     double stretching_factor_XY;
     VectorDouble3 deform( VectorDouble3 vec ){
+
         return VectorDouble3(vec.getX()*stretching_factor,vec.getY()*stretching_factor_XY,vec.getZ()*stretching_factor_XY);
     }
 };
@@ -78,10 +83,10 @@ void UpdaterAffineDeformation<IngredientsType>::initialize(){
         if (number_of_neighbors > 0) {
             for (size_t j = 0; j < number_of_neighbors; j++){
                 if (i < 20 ) 
-                    std::cout << "ID= "<< i << "initial jump   " << Neighbors[j].jump << " ";  
-                Neighbors[j].jump= deform(Neighbors[j].jump);   
+                    std::cout << "ID= "<< i << " initial jump " << Neighbors[j].jump << " ";  
+                ing.setCrossLinkNeighborJump(ID,j,deform(Neighbors[j].jump));   
                 if (i < 20 ) 
-                    std::cout << "ID= "<< i << "defrormed jump " << Neighbors[j].jump << "\n";   
+                    std::cout << "ID= "<< i << " defromed jump " << Neighbors[j].jump << "\n";   
             }
         }
     }
@@ -90,9 +95,9 @@ void UpdaterAffineDeformation<IngredientsType>::initialize(){
     for(size_t i = 0; i< ing.getMolecules().size();i++){
         if (i < 20 ) 
             std::cout << "ID="<< i << "initial position " << ing.getMolecules()[i].getVector3D() << " ";  
-        ing.modifyMolecules()[i].modifyVector3D()=deform(ing.modifyMolecules()[i].getVector3D());
+        ing.modifyMolecules()[i].modifyVector3D()=deform(ing.getMolecules()[i].getVector3D());
         if (i < 20 ) 
-            std::cout << "deformed position " << ing.getMolecules()[i].getVector3D() << "\n";  
+            std::cout << " deformed position " << ing.getMolecules()[i].getVector3D() << "\n";  
     }
     std::cout << "UpdaterAffineDeformation<IngredientsType>::initialize():done.\n";
 }
diff --git a/include/LeMonADE_PM/updater/moves/MoveForceEquilibrium.h b/include/LeMonADE_PM/updater/moves/MoveForceEquilibrium.h
index d3e669b..47bd8c0 100644
--- a/include/LeMonADE_PM/updater/moves/MoveForceEquilibrium.h
+++ b/include/LeMonADE_PM/updater/moves/MoveForceEquilibrium.h
@@ -96,6 +96,7 @@ class MoveForceEquilibrium:public MoveForceEquilibriumBase<MoveForceEquilibrium>
                 VectorDouble3 vec(ing.getMolecules()[Neighbors[i].ID].getVector3D()-Position-Neighbors[i].jump);
                 avNSegments+=1./Neighbors[i].segDistance;
                 force+=FE(vec,Neighbors[i].segDistance);
+                // std::cout <<"MoveLFE " <<  ing.getMolecules()[Neighbors[i].ID].getVector3D() << "\t" << Neighbors[i].jump<< "\t" << Position << "\t" << vec << "\t" << force << std::endl;
             }
             shift=EF(force,1./avNSegments);
         }
diff --git a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
index 58d5a44..7ac4771 100644
--- a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
+++ b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
@@ -167,7 +167,7 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
             VectorDouble3 Position(ing.getMolecules()[this->getIndex()].getVector3D());      
             for (size_t i = 0; i < number_of_neighbors; i++){
                 VectorDouble3 vec(ing.getMolecules()[Neighbors[i].ID].getVector3D()-Neighbors[i].jump-Position);
-                // std::cout << ing.getMolecules()[Neighbors[i].ID].getVector3D() << " " << Neighbors[i].jump<< " " << Position <<std::endl;
+                // std::cout <<"MoveNLFE " <<  ing.getMolecules()[Neighbors[i].ID].getVector3D() << " " << Neighbors[i].jump<< " " << Position <<std::endl;
                 force+=EF(vec);
             }
             shift=FE(force/(static_cast<double>(number_of_neighbors) ));
diff --git a/projects/TendomerNetworkForceEquilibrium.cpp b/projects/TendomerNetworkForceEquilibrium.cpp
index 09fde2c..3417a28 100644
--- a/projects/TendomerNetworkForceEquilibrium.cpp
+++ b/projects/TendomerNetworkForceEquilibrium.cpp
@@ -100,6 +100,7 @@ int main(int argc, char* argv[]){
 		  std::cout << "stretching_factor     : " << stretching_factor      << std::endl;
 	    }
 		RandomNumberGenerators rng;
+		// rng.seedDefaultValuesAll();
 		rng.seedAll();
 		///////////////////////////////////////////////////////////////////////////////
 		///end options parsing
@@ -152,12 +153,12 @@ int main(int argc, char* argv[]){
 		myIngredients2.synchronize();
 
 		TaskManager taskmanager2;
-		taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor) );
+		taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
 		//read bonds and positions stepwise
-        auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold, factor) ;
-        updater->setFilename(feCurve);
-        updater->setRelaxationParameter(relaxationParameter);
-        // auto updater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
+        // auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold, factor) ;
+        // updater->setFilename(feCurve);
+        // updater->setRelaxationParameter(relaxationParameter);
+        auto updater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
         taskmanager2.addUpdater( updater );
 		taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
 		//initialize and run

From b78e6831237210e4118aaa2330e8df412f4b943c Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Fri, 16 Jul 2021 14:41:16 +0200
Subject: [PATCH 39/70] comment in the Tendomer specific force eq

---
 .../updater/UpdaterForceBalancedPosition.h     |  2 +-
 projects/TendomerNetworkForceEquilibrium.cpp   | 18 +++++++++++-------
 2 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
index f328243..6cb956e 100644
--- a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
+++ b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
@@ -40,7 +40,7 @@ class UpdaterForceBalancedPosition:public AbstractUpdater
 {
 public:
     //! constructor for UpdaterForceBalancedPosition
-    UpdaterForceBalancedPosition(IngredientsType& ing_, double threshold_, double factor_=0.995 ):
+    UpdaterForceBalancedPosition(IngredientsType& ing_, double threshold_ ):
     ing(ing_),threshold(threshold_){};
     
     virtual void initialize(){};
diff --git a/projects/TendomerNetworkForceEquilibrium.cpp b/projects/TendomerNetworkForceEquilibrium.cpp
index 3417a28..06694c2 100644
--- a/projects/TendomerNetworkForceEquilibrium.cpp
+++ b/projects/TendomerNetworkForceEquilibrium.cpp
@@ -68,6 +68,8 @@ int main(int argc, char* argv[]){
 		double threshold(0.5);
 		double factor(0.995);
 		double stretching_factor(1.0);
+		bool gauss(false);
+		bool langevin(false);
 		
 		bool showHelp = false;
 		auto parser
@@ -75,10 +77,11 @@ int main(int argc, char* argv[]){
 			| clara::detail::Opt(       outputDataPos, "outputDataPos (=CrosslinkPosition.dat)"          ) ["-o"]["--outputPos"        ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
 			| clara::detail::Opt(      outputDataDist, "outputDataDist (=ChainExtensionDistribution.dat)") ["-c"]["--outputDist"       ] ("(optional) Output filename of the chain extension distribution."             ).optional()
 			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"        ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
+			| clara::detail::Opt(   stretching_factor, "stretching_factor (=1)"                          ) ["-l"]["--stretching_factor"] ("(optional) Stretching factor for uniaxial deformation. Default 1.0 ."        ).optional()
 			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"          ] ("(optional) Force-Extension curve. Default \"\"."                             ).required()
 			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"            ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
-			| clara::detail::Opt(              factor, "factor (=10)"                                    ) ["-a"]["--factor"           ] ("(optional) Factor for reducing the relaxation parameter after 1000MCS. Default .995 .").optional()
-			| clara::detail::Opt(   stretching_factor, "stretching_factor (=1)"                          ) ["-l"]["--stretching_factor"] ("(optional) Stretching factor for uniaxial deformation. Default 1.0 ."        ).optional()
+			| clara::detail::Opt(               gauss, "gauss"                                           ) ["-g"]["--gauss"            ] ("(optional) Deforma with a Gaussian deformation behaviour. Default 1.0 ."     ).optional()
+			| clara::detail::Opt(            langevin, "langevin"                                        ) ["-v"]["--langevin"         ] ("(optional) Deforma with a Langevin deformation behaviour. Default 1.0 ."     ).optional()
 			| clara::Help( showHelp );
 		
 	    auto result = parser.parse( clara::Args( argc, argv ) );
@@ -96,7 +99,8 @@ int main(int argc, char* argv[]){
 	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
 	      std::cout << "threshold             : " << threshold              << std::endl; 
 		  std::cout << "feCurve               : " << feCurve                << std::endl;
-		  std::cout << "factor                : " << factor                 << std::endl;
+		  std::cout << "gauss                 : " << gauss                  << std::endl;
+		  std::cout << "Langevin              : " << langevin               << std::endl;
 		  std::cout << "stretching_factor     : " << stretching_factor      << std::endl;
 	    }
 		RandomNumberGenerators rng;
@@ -155,10 +159,10 @@ int main(int argc, char* argv[]){
 		TaskManager taskmanager2;
 		taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
 		//read bonds and positions stepwise
-        // auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold, factor) ;
-        // updater->setFilename(feCurve);
-        // updater->setRelaxationParameter(relaxationParameter);
-        auto updater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
+        auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
+        updater->setFilename(feCurve);
+        updater->setRelaxationParameter(relaxationParameter);
+        // auto updater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
         taskmanager2.addUpdater( updater );
 		taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
 		//initialize and run

From 26cfeab2388de83951690647ce2780ae7afe1644 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Mon, 19 Jul 2021 10:35:54 +0200
Subject: [PATCH 40/70] Correct output of the uniaxial transformation.

---
 .../LeMonADE_PM/updater/UpdaterAffineDeformation.h  |  2 +-
 projects/TendomerNetworkForceEquilibrium.cpp        | 13 ++++++++-----
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
index d4fdc84..4629f78 100644
--- a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
+++ b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
@@ -86,7 +86,7 @@ void UpdaterAffineDeformation<IngredientsType>::initialize(){
                     std::cout << "ID= "<< i << " initial jump " << Neighbors[j].jump << " ";  
                 ing.setCrossLinkNeighborJump(ID,j,deform(Neighbors[j].jump));   
                 if (i < 20 ) 
-                    std::cout << "ID= "<< i << " defromed jump " << Neighbors[j].jump << "\n";   
+                    std::cout << "ID= "<< i << " deformed jump " << ing.getCrossLinkNeighborIDs(ID)[j].jump << "\n";   
             }
         }
     }
diff --git a/projects/TendomerNetworkForceEquilibrium.cpp b/projects/TendomerNetworkForceEquilibrium.cpp
index 06694c2..dd4c413 100644
--- a/projects/TendomerNetworkForceEquilibrium.cpp
+++ b/projects/TendomerNetworkForceEquilibrium.cpp
@@ -69,7 +69,6 @@ int main(int argc, char* argv[]){
 		double factor(0.995);
 		double stretching_factor(1.0);
 		bool gauss(false);
-		bool langevin(false);
 		
 		bool showHelp = false;
 		auto parser
@@ -81,7 +80,6 @@ int main(int argc, char* argv[]){
 			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"          ] ("(optional) Force-Extension curve. Default \"\"."                             ).required()
 			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"            ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
 			| clara::detail::Opt(               gauss, "gauss"                                           ) ["-g"]["--gauss"            ] ("(optional) Deforma with a Gaussian deformation behaviour. Default 1.0 ."     ).optional()
-			| clara::detail::Opt(            langevin, "langevin"                                        ) ["-v"]["--langevin"         ] ("(optional) Deforma with a Langevin deformation behaviour. Default 1.0 ."     ).optional()
 			| clara::Help( showHelp );
 		
 	    auto result = parser.parse( clara::Args( argc, argv ) );
@@ -100,7 +98,6 @@ int main(int argc, char* argv[]){
 	      std::cout << "threshold             : " << threshold              << std::endl; 
 		  std::cout << "feCurve               : " << feCurve                << std::endl;
 		  std::cout << "gauss                 : " << gauss                  << std::endl;
-		  std::cout << "Langevin              : " << langevin               << std::endl;
 		  std::cout << "stretching_factor     : " << stretching_factor      << std::endl;
 	    }
 		RandomNumberGenerators rng;
@@ -162,8 +159,14 @@ int main(int argc, char* argv[]){
         auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
         updater->setFilename(feCurve);
         updater->setRelaxationParameter(relaxationParameter);
-        // auto updater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
-        taskmanager2.addUpdater( updater );
+        auto updater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
+		if ( gauss == 0 ){
+			std::cout << "TendomerNetworkForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) \n";
+        	taskmanager2.addUpdater( updater );
+		}else {
+			std::cout << "TendomerNetworkForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) \n";
+			taskmanager2.addUpdater( updater2 );
+		}
 		taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
 		//initialize and run
 		taskmanager2.initialize();

From 30eca51f0db0dfb1761c9ccda2943823487b6653 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Mon, 30 Aug 2021 09:51:52 +0200
Subject: [PATCH 41/70] modify the force equilibration for the standard end
 linked networks

---
 .../updater/UpdaterReadCrosslinkConnections.h |  59 +++++----
 projects/CMakeLists.txt                       |   4 +
 projects/ForceEquilibrium.cpp                 |  10 +-
 .../NetworkWritePartialConnectedNetwork.cpp   | 114 ++++++++++++++++++
 4 files changed, 156 insertions(+), 31 deletions(-)
 create mode 100644 projects/NetworkWritePartialConnectedNetwork.cpp

diff --git a/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnections.h b/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnections.h
index de40361..8bbedf6 100644
--- a/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnections.h
+++ b/include/LeMonADE_PM/updater/UpdaterReadCrosslinkConnections.h
@@ -92,7 +92,7 @@ class UpdaterReadCrosslinkConnections : public AbstractUpdater
   uint32_t nExecutions;
 
   //! connects the cross link to the chain
-  void ConnectCrossLinkToChain(uint32_t MonID, uint32_t chainID);
+  bool ConnectCrossLinkToChain(uint32_t MonID, uint32_t chainID);
   
   //!bond Table 
   std::map<std::pair<uint32_t,uint32_t>,std::vector<uint32_t> > bondTable;
@@ -100,18 +100,31 @@ class UpdaterReadCrosslinkConnections : public AbstractUpdater
 
 
 template <class IngredientsType>
-void UpdaterReadCrosslinkConnections<IngredientsType>::ConnectCrossLinkToChain(uint32_t MonID, uint32_t chainID){
+bool UpdaterReadCrosslinkConnections<IngredientsType>::ConnectCrossLinkToChain(uint32_t MonID, uint32_t chainID){
+    // std::pair<uint32_t,uint32_t> key(MonID,chainID-1);
+    // if (bondTable.find(key) != bondTable.end()){
+    //     if ( !ing.getMolecules().areConnected( MonID,bondTable.at(key)[0] ) )
+    //         ing.modifyMolecules().connect(MonID,bondTable.at(key)[0] );
+    //     else 
+    //         ing.modifyMolecules().connect(MonID,bondTable.at(key)[1] );
+    // }else{
+    //     std::stringstream errormessage;
+    //     errormessage << "There was no such a connection in the bfm file for monomer ID= " << MonID << " with chainID=" << chainID-1<< "\n";
+    //     throw std::runtime_error(errormessage.str());
+    // }
     std::pair<uint32_t,uint32_t> key(MonID,chainID-1);
     if (bondTable.find(key) != bondTable.end()){
-        if ( !ing.getMolecules().areConnected( MonID,bondTable.at(key)[0] ) )
+        if ( !ing.getMolecules().areConnected( MonID,bondTable.at(key)[0] ) ){
             ing.modifyMolecules().connect(MonID,bondTable.at(key)[0] );
-        else 
+            return true ; 
+        }
+        //chain can only have one neighbor (without this statement a more or less random partner would be connected to the structure !!)
+        if ( bondTable.at(key).size()>1 ) {
             ing.modifyMolecules().connect(MonID,bondTable.at(key)[1] );
-    }else{
-        std::stringstream errormessage;
-        errormessage << "There was no such a connection in the bfm file for monomer ID= " << MonID << " with chainID=" << chainID-1<< "\n";
-        throw std::runtime_error(errormessage.str());
+            return true ; 
+        }
     }
+    return false; 
 }
 
 /**
@@ -153,18 +166,6 @@ bool UpdaterReadCrosslinkConnections<IngredientsType>::execute(){
     stream.open(input);
     if (stream.fail())
       throw std::runtime_error(std::string("error opening input file ") + input + std::string("\n"));
-    bool findStartofData(false);
-    //set head to beginning of the data block
-    while (!findStartofData){
-        std::string line;
-        getline(stream, line);
-        if (line.empty())
-            findStartofData = true;
-        else if (line.at(0) == '#') //go to next line
-            continue;
-        else
-            throw std::runtime_error("Wrong input format!");
-    }
     //current conversion 
     auto conversion = minConversion + static_cast<double>(nExecutions) * stepwidth;
     std::cout << "Current conversion is " <<conversion <<std::endl;
@@ -177,18 +178,24 @@ bool UpdaterReadCrosslinkConnections<IngredientsType>::execute(){
     while (NewConnections < ReadNLines && stream.good()){
         std::string line;
         getline(stream, line);
-        if (line.empty())
+        if (line.empty() || line.at(0) == '#')
             break;
         std::stringstream ss;
         uint32_t Time, ChainID, MonID1, P1X, P1Y, P1Z, MonID2, P2X, P2Y, P2Z;
         ss << line;
         ss >> Time >> ChainID >> MonID1 >> P1X >> P1Y >> P1Z >> MonID2 >> P2X >> P2Y >> P2Z;
-        // if (NewConnections == 0 )
-        //     std::cout <<  Time << " " << ChainID<< " "
-        //             << MonID1<< " " << P1X << " " << P1Y << " " << P1Z << " " 
-        //             << MonID2<< " " << P2X << " " << P2Y << " " << P2Z << "\n";
+        #ifdef DEBUG
+            std::cout << ss.str() << std::endl;
+        #endif //DEBUG//
         ing.modifyMolecules().setAge(Time);
-        ConnectCrossLinkToChain(MonID1, ChainID);
+        // ConnectCrossLinkToChain(MonID1, ChainID);
+        if ( ConnectCrossLinkToChain(MonID1, ChainID+1) ) {
+        }else if( ConnectCrossLinkToChain(MonID2, ChainID+1) ) {
+        }else {
+            std::stringstream errormessage;
+            errormessage << "There was no such a connection in the bfm file for monomer ID= " << MonID1  <<" with ID=" << MonID2 <<  " with chainID=" << ChainID<< "\n";
+            throw std::runtime_error(errormessage.str());
+        }
         //update positions : I think this is not needed
         // ing.modifyMolecules()[MonID1].modifyVector3D().setAllCoordinates(P1X, P1Y, P1Z);
         // if (MonID2 > 0)
diff --git a/projects/CMakeLists.txt b/projects/CMakeLists.txt
index 9bc852b..b1ddda1 100644
--- a/projects/CMakeLists.txt
+++ b/projects/CMakeLists.txt
@@ -1,6 +1,8 @@
 add_executable(ForceEquilibrium ForceEquilibrium.cpp)
 target_link_libraries(ForceEquilibrium LeMonADE CommandlineParser )
 
+add_executable(NetworkWritePartialConnectedNetwork NetworkWritePartialConnectedNetwork.cpp)
+target_link_libraries(NetworkWritePartialConnectedNetwork LeMonADE CommandlineParser )
 
 add_executable(TendomerNetworkForceEquilibrium TendomerNetworkForceEquilibrium.cpp)
 target_link_libraries(TendomerNetworkForceEquilibrium LeMonADE CommandlineParser )
@@ -14,5 +16,7 @@ target_link_libraries(TendomerNetworkExtractGelPart LeMonADE CommandlineParser )
 add_executable(TendomerNetworkWritePartialConnectedNetwork TendomerNetworkWritePartialConnectedNetwork.cpp)
 target_link_libraries(TendomerNetworkWritePartialConnectedNetwork LeMonADE CommandlineParser )
 
+
+
 # add_executable(IntramolecularReactions IntramolecularReactions.cpp)
 # target_link_libraries(IntramolecularReactions LeMonADE CommandlineParser )
\ No newline at end of file
diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index 9325f4a..e92e1fd 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -61,7 +61,7 @@ int main(int argc, char* argv[]){
 		std::string inputBFM("init.bfm");
 		std::string outputDataPos("CrosslinkPosition.dat");
 		std::string outputDataDist("ChainExtensionDistribution.dat");
-		std::string inputConnection("BondCreationBreaking.dat");
+		// std::string inputConnection("BondCreationBreaking.dat");
 		std::string feCurve;
 		double relaxationParameter(10.);
 		double threshold(0.5);
@@ -72,7 +72,7 @@ int main(int argc, char* argv[]){
 		bool showHelp = false;
 		auto parser
 			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"          ] ("(required)Input filename of the bfm file"                                    ).required()
-			| clara::detail::Opt(     inputConnection, "inputConnection (=BondCreationBreaking.dat)"     ) ["-d"]["--inputConnection"] ("used for the time development of the topology. "                             ).required()
+			// | clara::detail::Opt(     inputConnection, "inputConnection (=BondCreationBreaking.dat)"     ) ["-d"]["--inputConnection"] ("used for the time development of the topology. "                             ).required()
 			| clara::detail::Opt(       outputDataPos, "outputDataPos (=CrosslinkPosition.dat)"          ) ["-o"]["--outputPos"      ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
 			| clara::detail::Opt(      outputDataDist, "outputDataDist (=ChainExtensionDistribution.dat)") ["-c"]["--outputDist"     ] ("(optional) Output filename of the chain extension distribution."             ).optional()
 			| clara::detail::Opt(           stepwidth, "stepwidth"                                       ) ["-s"]["--stepwidth"      ] ("(optional) Width for the increase in percentage. Default: 1%."               ).optional()
@@ -95,7 +95,7 @@ int main(int argc, char* argv[]){
 	      std::cout << "outputData            : " << outputDataPos          << std::endl;
 	      std::cout << "outputDataDist        : " << outputDataDist         << std::endl;
 	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
-	      std::cout << "inputConnection       : " << inputConnection        << std::endl; 
+	    //   std::cout << "inputConnection       : " << inputConnection        << std::endl; 
 	      std::cout << "stepwidth             : " << stepwidth              << std::endl;
 	      std::cout << "minConversion         : " << minConversion          << std::endl;
 	      std::cout << "threshold             : " << threshold              << std::endl; 
@@ -161,7 +161,7 @@ int main(int argc, char* argv[]){
 		if(custom){
 			TaskManager taskmanager2;
 			//read bonds and positions stepwise
-			taskmanager2.addUpdater( new UpdaterReadCrosslinkConnections<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
+			// taskmanager2.addUpdater( new UpdaterReadCrosslinkConnections<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
 			std::cout << "Use custom force-extension curve\n";
 			auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold);
 			forceUpdater->setFilename(feCurve);
@@ -175,7 +175,7 @@ int main(int argc, char* argv[]){
 		} else {
 			TaskManager taskmanager2;
 			//read bonds and positions stepwise
-			taskmanager2.addUpdater( new UpdaterReadCrosslinkConnections<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
+			// taskmanager2.addUpdater( new UpdaterReadCrosslinkConnections<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
 			std::cout << "Use gaussian force-extension relation\n";
 			auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold);
 			taskmanager2.addUpdater( forceUpdater );
diff --git a/projects/NetworkWritePartialConnectedNetwork.cpp b/projects/NetworkWritePartialConnectedNetwork.cpp
new file mode 100644
index 0000000..0d95711
--- /dev/null
+++ b/projects/NetworkWritePartialConnectedNetwork.cpp
@@ -0,0 +1,114 @@
+/*--------------------------------------------------------------------------------
+    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/>.
+
+--------------------------------------------------------------------------------*/
+
+/****************************************************************************** 
+ * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
+ * author: Toni Müller
+ * email: mueller-toni@ipfdd.de
+ * project: LeMonADE-Phantom Modulus
+ *****************************************************************************/
+#include <iostream>
+#include <vector>
+#include <bitset>
+
+#include <LeMonADE/core/Ingredients.h>
+#include <LeMonADE/updater/UpdaterReadBfmFile.h>
+#include <LeMonADE/analyzer/AnalyzerWriteBfmFile.h>
+#include <LeMonADE/feature/FeatureMoleculesIOUnsaveCheck.h>
+#include <LeMonADE/feature/FeatureReactiveBonds.h>
+#include <LeMonADE/feature/FeatureBox.h>
+#include <LeMonADE/feature/FeatureSystemInformationLinearMeltWithCrosslinker.h>
+#include <LeMonADE/utility/TaskManager.h>
+
+#include <extern/catchorg/clara/clara.hpp>
+
+#include <LeMonADE_PM/updater/UpdaterForceBalancedPosition.h>
+#include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnections.h>
+#include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
+#include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
+#include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUp.h>
+#include <LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h>
+
+
+int main(int argc, char* argv[]){
+	try{
+		///////////////////////////////////////////////////////////////////////////////
+		///parse options///
+		std::string inputBFM("init.bfm");
+		std::string outputBFM("Config.bfm.dat");
+		std::string inputConnection("BondCreationBreaking.dat");
+		bool showHelp = false;
+		auto parser
+			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"           ] ("(required)Input filename of the bfm file"                                    ).required()
+			| clara::detail::Opt(     inputConnection, "inputConnection (=BondCreationBreaking.dat)"     ) ["-d"]["--inputConnection" ] ("used for the time development of the topology. "                             ).required()
+			| clara::detail::Opt(           outputBFM, "outputBFM (=Config.bfm)"                         ) ["-o"]["--outputBFM"       ] ("Output filename for the active material of the tendomer network.")
+			| clara::Help( showHelp );
+		
+	    auto result = parser.parse( clara::Args( argc, argv ) );
+	    
+	    if( !result ) {
+	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
+	      exit(1);
+	    }else if(showHelp == true){
+	      std::cout << "Analyzer taking a bond table and a table specifying the activity of an object and writes the active part of the tendoemr network."<< std::endl;
+          std::cout << "Important: input file for the connections and the active material must fit to each other!!!"<< std::endl;
+	      parser.writeToStream(std::cout);
+	      exit(0);
+	    }else{
+	      std::cout << "outputBFM             : " << outputBFM          << std::endl;
+	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
+	      std::cout << "inputConnection       : " << inputConnection        << std::endl; 
+	    }
+		///////////////////////////////////////////////////////////////////////////////
+		///end options parsing
+		///////////////////////////////////////////////////////////////////////////////
+		typedef LOKI_TYPELIST_4(FeatureMoleculesIOUnsaveCheck, FeatureReactiveBonds, FeatureAttributes<>,FeatureSystemInformationLinearMeltWithCrosslinker) Features;
+		typedef ConfigureSystem<VectorInt3,Features, 7> Config;
+		typedef Ingredients<Config> Ing;
+		Ing myIngredients;
+		
+		TaskManager taskmanager;
+		
+		taskmanager.addUpdater( new UpdaterReadBfmFile<Ing>(inputBFM,myIngredients, UpdaterReadBfmFile<Ing>::READ_LAST_CONFIG_SAVE),0);
+		taskmanager.addUpdater( new UpdaterReadCrosslinkConnections<Ing>(myIngredients, inputConnection, 0., 1.0) );
+        taskmanager.addAnalyzer( new AnalyzerWriteBfmFile<Ing>(outputBFM, myIngredients, 1) ); 
+		//initialize and run
+		taskmanager.initialize();
+		taskmanager.run(1);
+		taskmanager.cleanup();
+		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
+	}
+	catch(std::exception& e){
+		std::cerr<<"Error:\n"
+		<<e.what()<<std::endl;
+	}
+	catch(...){
+		std::cerr<<"Error: unknown exception\n";
+	}
+	
+	return 0;
+}

From d7ad774d12b3083f7e6968627d206628d171b5ed Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Fri, 15 Oct 2021 12:51:26 +0200
Subject: [PATCH 42/70] add a molecular weight analyzer

---
 .../analyzer/AnalyzerMolecularWeight.h        | 129 ++++++++++++++++++
 projects/AnalyzeMolecularWeight.cpp           | 104 ++++++++++++++
 projects/CMakeLists.txt                       |   3 +-
 3 files changed, 235 insertions(+), 1 deletion(-)
 create mode 100644 include/LeMonADE_PM/analyzer/AnalyzerMolecularWeight.h
 create mode 100644 projects/AnalyzeMolecularWeight.cpp

diff --git a/include/LeMonADE_PM/analyzer/AnalyzerMolecularWeight.h b/include/LeMonADE_PM/analyzer/AnalyzerMolecularWeight.h
new file mode 100644
index 0000000..e13a979
--- /dev/null
+++ b/include/LeMonADE_PM/analyzer/AnalyzerMolecularWeight.h
@@ -0,0 +1,129 @@
+/*--------------------------------------------------------------------------------
+    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_PM_ANALYZER_MOLECULAR_WEIGTH_H
+#define LEMONADE_PM_ANALYZER_MOLECULAR_WEIGTH_H
+
+#include <string>
+
+#include <LeMonADE/utility/Vector3D.h>
+#include <LeMonADE/analyzer/AbstractAnalyzer.h>
+#include <LeMonADE/utility/ResultFormattingTools.h>
+#include <LeMonADE/utility/MonomerGroup.h>
+#include <LeMonADE/utility/DepthIterator.h>
+#include <LeMonADE/analyzer/AnalyzerAbstractDump.h>
+
+
+/*************************************************************************
+ * definition of AnalyzerMolecularWeight class
+ * ***********************************************************************/
+
+/**
+ * @file
+ *
+ * @class AnalyzerMolecularWeight
+ *
+ * @tparam IngredientsType Ingredients class storing all system information( e.g. monomers, bonds, etc).
+ * 
+ * @details Calculates the number and weight averaged molecular weight.
+ *
+ */
+template < class IngredientsType > 
+class AnalyzerMolecularWeight : public AnalyzerAbstractDump<IngredientsType,double>
+{
+    typedef AnalyzerAbstractDump<IngredientsType,double> BaseClass; 
+private:
+	//! typedef for the underlying container holding the monomers
+	typedef typename IngredientsType::molecules_type molecules_type;
+
+    std::string basename;
+    
+protected:
+  using BaseClass::ingredients;
+	using BaseClass::Data;
+	using BaseClass::MCSTimes;
+	using BaseClass::dumpTimeSeries;
+    
+public:
+	//! constructor
+	AnalyzerMolecularWeight(const IngredientsType& ing, std::string fileSuffix_);
+	//! destructor. does nothing
+	virtual ~AnalyzerMolecularWeight(){}
+	//! calculate the moleculare weight distribution
+	virtual void initialize();
+  virtual bool execute();
+};
+
+/*************************************************************************
+ * implementation of memebers
+ * ***********************************************************************/
+
+/**
+ * @param ing reference to the object holding all information of the system
+ * @param fileSuffix output file name. defaults to "Rg2TimeSeries.dat".
+ * */
+template<class IngredientsType>
+AnalyzerMolecularWeight<IngredientsType>::AnalyzerMolecularWeight(
+	const IngredientsType& ing,std::string fileSuffix_)
+:BaseClass(ing,fileSuffix_) {}
+
+template <class IngredientsType>
+void AnalyzerMolecularWeight<IngredientsType>::initialize()
+{
+  basename=BaseClass::getOutputFilename() ; 
+  BaseClass::setBufferSize(1);
+  BaseClass::setNumberOfColumns(1);
+  execute();
+}
+template< class IngredientsType >
+bool AnalyzerMolecularWeight<IngredientsType>::execute()
+{
+    double conversion = ingredients.getConversion();
+    std::stringstream comment;
+    comment << "Created by AnalyzerMolecularWeight\n"
+            << "conversion=" << conversion << "%";
+    BaseClass::setComment(comment.str());
+
+    //calculate the molecular weight distribution 
+    std::vector<MonomerGroup<molecules_type> > groups;
+    fill_connected_groups(ingredients.getMolecules(), groups, MonomerGroup<molecules_type>(ingredients.getMolecules()), alwaysTrue());
+    //key is the size of the molecule and the value is the number of occurence 
+    std::map<uint32_t,uint32_t> dist;
+    for (auto it=groups.begin(); it!=groups.end();it++ )
+      dist[it->size()]++;
+    for ( auto&  it : dist )
+    {
+      Data[0].push_back(it.second);
+      MCSTimes.push_back(it.first);
+    }
+    std::stringstream output; 
+    output << "MolecularWeight_c" << conversion <<  basename<< ".dat";
+    BaseClass::resetIsFirstFileDump();
+    BaseClass::setOutputFilename(output.str());
+    dumpTimeSeries();
+}
+#endif
diff --git a/projects/AnalyzeMolecularWeight.cpp b/projects/AnalyzeMolecularWeight.cpp
new file mode 100644
index 0000000..b3b519f
--- /dev/null
+++ b/projects/AnalyzeMolecularWeight.cpp
@@ -0,0 +1,104 @@
+/*--------------------------------------------------------------------------------
+    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/>.
+
+--------------------------------------------------------------------------------*/
+
+/****************************************************************************** 
+ * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
+ * author: Toni Müller
+ * email: mueller-toni@ipfdd.de
+ * project: LeMonADE-Phantom Modulus
+ *****************************************************************************/
+#include <iostream>
+#include <vector>
+#include <bitset>
+
+#include <LeMonADE/core/Ingredients.h>
+#include <LeMonADE/updater/UpdaterReadBfmFile.h>
+#include <LeMonADE/analyzer/AnalyzerWriteBfmFile.h>
+#include <LeMonADE/feature/FeatureMoleculesIOUnsaveCheck.h>
+#include <LeMonADE/feature/FeatureReactiveBonds.h>
+#include <LeMonADE/feature/FeatureBox.h>
+#include <LeMonADE/feature/FeatureSystemInformationLinearMeltWithCrosslinker.h>
+#include <LeMonADE/utility/TaskManager.h>
+
+#include <extern/catchorg/clara/clara.hpp>
+
+#include <LeMonADE_PM/analyzer/AnalyzerMolecularWeight.h>
+
+
+int main(int argc, char* argv[]){
+	try{
+		///////////////////////////////////////////////////////////////////////////////
+		///parse options///
+		std::string inputBFM("init.bfm");
+		std::string suffix("MolecularWeight.dat");
+		bool showHelp = false;
+		auto parser
+			= clara::detail::Opt( inputBFM, "inputBFM (=inconfig.bfm)"      ) ["-i"]["--input"  ] ("(required)Input filename of the bfm file").required()
+			| clara::detail::Opt(   suffix, "suffix (=MolecularWeight.dat)" ) ["-o"]["--suffix" ] ("suffix name for data."                   ).required()
+			| clara::Help( showHelp );
+		
+	    auto result = parser.parse( clara::Args( argc, argv ) );
+	    
+	    if( !result ) {
+	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
+	      exit(1);
+	    }else if(showHelp == true){
+	      parser.writeToStream(std::cout);
+	      exit(0);
+	    }else{
+	      std::cout << "inputBFM : " << inputBFM << std::endl;
+	      std::cout << "suffix   : " << suffix   << std::endl; 
+
+	    }
+		///////////////////////////////////////////////////////////////////////////////
+		///end options parsing
+		///////////////////////////////////////////////////////////////////////////////
+		typedef LOKI_TYPELIST_2(FeatureMoleculesIOUnsaveCheck, FeatureReactiveBonds) Features;
+		typedef ConfigureSystem<VectorInt3,Features, 7> Config;
+		typedef Ingredients<Config> Ing;
+		Ing ingredients;
+		
+		TaskManager taskmanager;
+		
+		taskmanager.addUpdater( new UpdaterReadBfmFile<Ing>(inputBFM,ingredients, UpdaterReadBfmFile<Ing>::READ_LAST_CONFIG_SAVE),0);
+        taskmanager.addAnalyzer( new AnalyzerMolecularWeight<Ing>(ingredients, suffix) ); 
+		//initialize and run
+		taskmanager.initialize();
+		taskmanager.run();
+		taskmanager.cleanup();
+		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
+	}
+	catch(std::exception& e){
+		std::cerr<<"Error:\n"
+		<<e.what()<<std::endl;
+	}
+	catch(...){
+		std::cerr<<"Error: unknown exception\n";
+	}
+	
+	return 0;
+}
diff --git a/projects/CMakeLists.txt b/projects/CMakeLists.txt
index b1ddda1..b66561e 100644
--- a/projects/CMakeLists.txt
+++ b/projects/CMakeLists.txt
@@ -16,7 +16,8 @@ target_link_libraries(TendomerNetworkExtractGelPart LeMonADE CommandlineParser )
 add_executable(TendomerNetworkWritePartialConnectedNetwork TendomerNetworkWritePartialConnectedNetwork.cpp)
 target_link_libraries(TendomerNetworkWritePartialConnectedNetwork LeMonADE CommandlineParser )
 
-
+add_executable(AnalyzeMolecularWeight AnalyzeMolecularWeight.cpp)
+target_link_libraries(AnalyzeMolecularWeight LeMonADE )
 
 # add_executable(IntramolecularReactions IntramolecularReactions.cpp)
 # target_link_libraries(IntramolecularReactions LeMonADE CommandlineParser )
\ No newline at end of file

From df87c7a726e2b6687ed0aa58d002aae3747ddc7f Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Fri, 15 Oct 2021 16:48:07 +0200
Subject: [PATCH 43/70] start adding a start creator

---
 include/LeMonADE_PM/updater/UpdaterAddStars.h | 197 ++++++++++++++++++
 projects/CMakeLists.txt                       |   3 +
 projects/IdealReferenceForceEquilibrium.cpp   | 188 +++++++++++++++++
 3 files changed, 388 insertions(+)
 create mode 100644 include/LeMonADE_PM/updater/UpdaterAddStars.h
 create mode 100644 projects/IdealReferenceForceEquilibrium.cpp

diff --git a/include/LeMonADE_PM/updater/UpdaterAddStars.h b/include/LeMonADE_PM/updater/UpdaterAddStars.h
new file mode 100644
index 0000000..4ee111f
--- /dev/null
+++ b/include/LeMonADE_PM/updater/UpdaterAddStars.h
@@ -0,0 +1,197 @@
+/*--------------------------------------------------------------------------------
+    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
+    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_UPDATER_SETUP_STARSAB
+#define LEMONADE_UPDATER_SETUP_STARSAB
+/**
+ * @file
+ *
+ * @class UpdaterAddStars
+ *
+ * @brief Updater to create a solution of monodisperse branched stars.
+ *
+ * @details This is a simple implementation of a system setup starting from an empty ingredients
+ * or a system with some monomers inside. This updater requires FeatureAttributes.
+ * Two tags are added to the monomers in alternating manner, usually needed for GPU computing.  // not realized in this first attempt
+ *                                                                                              // RS, 05 Nov 2019, but presumably 29 July 2020
+ *
+ * @tparam IngredientsType
+ *
+ * @param ingredients_ The system, holding either an empty simulation box for system setup
+ * or a prefilled ingredients where the stars shall be added
+ * @param NStar_ number of stars that are added to ingredients
+ * @param NMonoPerStar_ number of monomers in each star
+ * @param NMonoPerBranch_ number of monomers in each branch (excluding central monomer)
+ * @param NBranchPerStar_ number of branches in each star
+ * @param type1_ attribute tag of "even" monomers
+ * @param type2_ attribute tag of "odd" monomers
+ **/
+
+#include <LeMonADE/updater/UpdaterAbstractCreate.h>
+#include <LeMonADE/utility/Vector3D.h>
+#include <cmath>
+
+template<class IngredientsType>
+class UpdaterAddStars: public UpdaterAbstractCreate<IngredientsType>
+{
+  typedef UpdaterAbstractCreate<IngredientsType> BaseClass;
+
+public:
+  UpdaterAddStars(IngredientsType& ingredients_, uint32_t NStar_, 
+                  uint32_t NMonoPerBranch_, uint32_t NBranchPerStar_);
+
+  virtual void initialize();
+  virtual bool execute();
+  virtual void cleanup();
+
+  //! getter function for write compressed solvent bool
+  const bool getIsSolvent() const {return IsSolvent;}
+
+  //! getter function for number of stars
+  const int32_t getNStar() const {return NStar;}
+
+  //! getter function for number of monomers in branch
+  const int32_t getNMonoPerBranch() const {return NMonoPerBranch;}
+
+  //! getter function for number of branches in stars
+  const int32_t getNBranchPerStar() const {return NBranchPerStar;}
+
+  //! getter function for calculated density
+  const double getDensity() const {return density;}
+
+private:
+  // provide access to functions of UpdaterAbstractCreate used in this updater
+  using BaseClass::ingredients;
+  using BaseClass::addMonomerToParent;
+  using BaseClass::addSingleMonomer;
+  using BaseClass::linearizeSystem;
+
+  //! number of stars in the box
+  uint32_t NStar;
+
+  //! number of monomers in a branch
+  uint32_t NMonoPerBranch;  
+
+  //! number of branches in a star
+  uint32_t NBranchPerStar;
+
+  //! lattice occupation density
+  double density;
+
+  //! bool for execution
+  bool wasExecuted;
+};
+
+/**
+* @brief Constructor handling the new systems paramters
+* 
+* @param ingredients_ a reference to the IngredientsType - mainly the system
+* @param NStar_ number of stars to be added in the system instead of solvent
+* @param NBranchPerStar_ number of branches in each star
+* @param NMonoPerBranch_ number of monomers in each branch (excluding central monomer)
+*/
+
+
+template < class IngredientsType >
+UpdaterAddStars<IngredientsType>::UpdaterAddStars(
+    IngredientsType& ingredients_, 
+    uint32_t NStar_, 
+    uint32_t NMonoPerBranch_, 
+    uint32_t NBranchPerStar_
+    ):
+    BaseClass(ingredients_), NStar(NStar_), NMonoPerBranch(NMonoPerBranch_), NBranchPerStar(NBranchPerStar_), 
+    density(0.0), wasExecuted(false),
+    {}
+
+/**
+* @brief initialise function, calculate the target density to compare with at the end.
+*
+* @tparam IngredientsType Features used in the system. See Ingredients.
+*/
+template < class IngredientsType >
+void UpdaterAddStars<IngredientsType>::initialize(){
+  std::cout << "initialize UpdaterAddStars" << std::endl;
+
+  // get the target density from the sum of existing monomers and the new added chains
+  density=(double)( ingredients.getMolecules().size() + (NMonoPerBranch*NBranchPerStar+1) *NStar ) * 8  /(double)( ingredients.getBoxX()*ingredients.getBoxY()*ingredients.getBoxZ() );
+
+  std::cout << "add "<<NStar*(NMonoPerBranch*NBranchPerStar+1)<<" monomers to the box"<<std::endl;
+
+  execute();
+}
+
+/**
+* @brief Execution of the system creation
+*
+* @tparam IngredientsType Features used in the system. See Ingredients.
+*/
+template < class IngredientsType >
+bool UpdaterAddStars<IngredientsType>::execute(){
+    if(wasExecuted) return true;
+    std::cout << "execute UpdaterAddStars" << std::endl;
+    //loop over stars and star monomers and build it up
+    uint32_t gen;
+    uint32_t index_center;
+
+    for(uint32_t i=0;i<(NStar);i++){
+        addSingleMonomer(1);
+        for(uint32_t j=0;j<(NBranchPerStar);j++){
+            for(uint32_t b=0;b<(NMonoPerBranch);b++){
+                u_int32_t parentID;
+                if (b==0)
+                parentID = (ingredients.getMolecules().size()-NBranchPerStar)
+                addMonomerToParent(parentID,1);
+            }
+        }
+    }
+
+    ingredients.synchronize();
+    double lattice_volume(ingredients.getBoxX()*ingredients.getBoxY()*ingredients.getBoxZ());
+    if(std::abs(density - ( (double)(ingredients.getMolecules().size()*8) / lattice_volume )) > 0.0000000001 ){
+        std::cout << density << " " <<( (ingredients.getMolecules().size()*8) / lattice_volume)<<std::endl;
+        throw std::runtime_error("UpdaterAddStars: number of monomers in molecules does not match the calculated number of monomers!");
+    }else{
+        std::cout << "real lattice occupation density =" << (8*ingredients.getMolecules().size()) / lattice_volume<<std::endl;
+        wasExecuted=true;
+        // if we allow for solvent compression AND added single monomers (solvent): compress solvent
+            linearizeSystem();
+        return true;
+    }
+}
+
+/**
+* @brief Standard clean up.
+*
+* @tparam IngredientsType Features used in the system. See Ingredients.
+*/
+template < class IngredientsType >
+void UpdaterAddStars<IngredientsType>::cleanup(){
+
+}
+
+
+#endif /* LEMONADE_UPDATER_SETUP_STARSAB */
diff --git a/projects/CMakeLists.txt b/projects/CMakeLists.txt
index b66561e..c0ab6fd 100644
--- a/projects/CMakeLists.txt
+++ b/projects/CMakeLists.txt
@@ -19,5 +19,8 @@ target_link_libraries(TendomerNetworkWritePartialConnectedNetwork LeMonADE Comma
 add_executable(AnalyzeMolecularWeight AnalyzeMolecularWeight.cpp)
 target_link_libraries(AnalyzeMolecularWeight LeMonADE )
 
+add_executable(IdealReferenceForceEquilibrium IdealReferenceForceEquilibrium.cpp)
+target_link_libraries(IdealReferenceForceEquilibrium LeMonADE )
+
 # add_executable(IntramolecularReactions IntramolecularReactions.cpp)
 # target_link_libraries(IntramolecularReactions LeMonADE CommandlineParser )
\ No newline at end of file
diff --git a/projects/IdealReferenceForceEquilibrium.cpp b/projects/IdealReferenceForceEquilibrium.cpp
new file mode 100644
index 0000000..0b14857
--- /dev/null
+++ b/projects/IdealReferenceForceEquilibrium.cpp
@@ -0,0 +1,188 @@
+/*--------------------------------------------------------------------------------
+    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/>.
+
+--------------------------------------------------------------------------------*/
+
+/****************************************************************************** 
+ * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
+ * author: Toni Müller
+ * email: mueller-toni@ipfdd.de
+ * project: LeMonADE-Phantom Modulus
+ *****************************************************************************/
+#include <iostream>
+#include <vector>
+#include <bitset>
+
+#include <LeMonADE/core/Ingredients.h>
+#include <LeMonADE/updater/UpdaterReadBfmFile.h>
+#include <LeMonADE/analyzer/AnalyzerWriteBfmFile.h>
+#include <LeMonADE/feature/FeatureMoleculesIOUnsaveCheck.h>
+#include <LeMonADE/feature/FeatureReactiveBonds.h>
+#include <LeMonADE/feature/FeatureFixedMonomers.h>
+#include <LeMonADE/feature/FeatureBox.h>
+#include <LeMonADE/feature/FeatureLabel.h>
+#include <LeMonADE/utility/TaskManager.h>
+#include <LeMonADE/utility/RandomNumberGenerators.h>
+
+#include <extern/catchorg/clara/clara.hpp>
+
+#include <LeMonADE_PM/updater/UpdaterForceBalancedPosition.h>
+#include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
+#include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
+#include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
+#include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h>
+#include <LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h>
+#include <LeMonADE_PM/updater/UpdaterAffineDeformation.h>
+#include <LeMonADE_PM/updater/UpdaterAddStars.h>
+
+
+int main(int argc, char* argv[]){
+	try{
+		///////////////////////////////////////////////////////////////////////////////
+		///parse options///
+		std::string inputBFM("init.bfm");
+		std::string outputDataPos("CrosslinkPosition.dat");
+		std::string outputDataDist("ChainExtensionDistribution.dat");
+		std::string feCurve("");
+		double relaxationParameter(10.);
+		double threshold(0.5);
+		double factor(0.995);
+		double stretching_factor(1.0);
+		bool gauss(false);
+		
+		bool showHelp = false;
+		auto parser
+			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"            ] ("(required)Input filename of the bfm file"                                    ).required()
+			| clara::detail::Opt(       outputDataPos, "outputDataPos (=CrosslinkPosition.dat)"          ) ["-o"]["--outputPos"        ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
+			| clara::detail::Opt(      outputDataDist, "outputDataDist (=ChainExtensionDistribution.dat)") ["-c"]["--outputDist"       ] ("(optional) Output filename of the chain extension distribution."             ).optional()
+			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"        ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
+			| clara::detail::Opt(   stretching_factor, "stretching_factor (=1)"                          ) ["-l"]["--stretching_factor"] ("(optional) Stretching factor for uniaxial deformation. Default 1.0 ."        ).optional()
+			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"          ] ("(optional) Force-Extension curve. Default \"\"."                             ).required()
+			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"            ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
+			| clara::detail::Opt(               gauss, "gauss"                                           ) ["-g"]["--gauss"            ] ("(optional) Deforma with a Gaussian deformation behaviour. Default 1.0 ."     ).optional()
+			| clara::Help( showHelp );
+		
+	    auto result = parser.parse( clara::Args( argc, argv ) );
+	    
+	    if( !result ) {
+	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
+	      exit(1);
+	    }else if(showHelp == true){
+	      std::cout << "Simulator to connect linear chains with single monomers of certain functionality"<< std::endl;
+	      parser.writeToStream(std::cout);
+	      exit(0);
+	    }else{
+	      std::cout << "outputData            : " << outputDataPos          << std::endl;
+	      std::cout << "outputDataDist        : " << outputDataDist         << std::endl;
+	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
+	      std::cout << "threshold             : " << threshold              << std::endl; 
+		  std::cout << "feCurve               : " << feCurve                << std::endl;
+		  std::cout << "gauss                 : " << gauss                  << std::endl;
+		  std::cout << "stretching_factor     : " << stretching_factor      << std::endl;
+	    }
+		RandomNumberGenerators rng;
+		// rng.seedDefaultValuesAll();
+		rng.seedAll();
+		///////////////////////////////////////////////////////////////////////////////
+		///end options parsing
+		///////////////////////////////////////////////////////////////////////////////
+		//Read in th last Config 
+		typedef LOKI_TYPELIST_4(FeatureMoleculesIOUnsaveCheck, FeatureLabel, FeatureReactiveBonds,FeatureFixedMonomers) Features;
+		typedef ConfigureSystem<VectorInt3,Features, 7> Config;
+		typedef Ingredients<Config> Ing;
+		Ing myIngredients;
+		
+		TaskManager taskmanager;
+		
+		taskmanager.addUpdater( new UpdaterAddStars<Ing>(inputBFM,myIngredients, UpdaterReadBfmFile<Ing>::READ_LAST_CONFIG_SAVE),0);
+
+		//initialize and run
+		taskmanager.initialize();
+		taskmanager.run(1);
+		taskmanager.cleanup();
+		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
+		//the foce equilibrium is reached off lattice ( no integer values for the positions )
+		typedef LOKI_TYPELIST_3(FeatureBox, FeatureCrosslinkConnectionsLookUpTendomers ,FeatureLabel) Features2;
+		typedef ConfigureSystem<VectorDouble3,Features2, 7> Config2;
+		typedef Ingredients<Config2> Ing2;
+		Ing2 myIngredients2;
+		
+		myIngredients2.setBoxX(myIngredients.getBoxX());
+		myIngredients2.setBoxY(myIngredients.getBoxY());
+		myIngredients2.setBoxZ(myIngredients.getBoxZ());
+		myIngredients2.setPeriodicX(myIngredients.isPeriodicX());
+		myIngredients2.setPeriodicY(myIngredients.isPeriodicY());
+		myIngredients2.setPeriodicZ(myIngredients.isPeriodicZ());
+		myIngredients2.modifyMolecules().resize(myIngredients.getMolecules().size());
+		myIngredients2.modifyMolecules().setAge(myIngredients.getMolecules().getAge());
+        
+        myIngredients2.setNumTendomers           (myIngredients.getNumTendomers());
+		myIngredients2.setNumCrossLinkers        (myIngredients.getNumCrossLinkers());
+		myIngredients2.setNumMonomersPerChain    (myIngredients.getNumMonomersPerChain());
+		myIngredients2.setNumLabelsPerTendomerArm(myIngredients.getNumLabelsPerTendomerArm());
+		
+		for(size_t i = 0; i< myIngredients.getMolecules().size();i++){
+			myIngredients2.modifyMolecules()[i].modifyVector3D()=myIngredients.getMolecules()[i].getVector3D();
+			myIngredients2.modifyMolecules()[i].setReactive(myIngredients.getMolecules()[i].isReactive());
+			myIngredients2.modifyMolecules()[i].setNumMaxLinks(myIngredients.getMolecules()[i].getNumMaxLinks());
+			for (size_t j = 0 ; j < myIngredients.getMolecules().getNumLinks(i);j++){
+				uint32_t neighbor(myIngredients.getMolecules().getNeighborIdx(i,j));
+				if( ! myIngredients2.getMolecules().areConnected(i,neighbor) )
+					myIngredients2.modifyMolecules().connect(i,neighbor);
+			}
+		}
+		myIngredients2.synchronize();
+
+		TaskManager taskmanager2;
+		taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
+		//read bonds and positions stepwise
+        auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
+        updater->setFilename(feCurve);
+        updater->setRelaxationParameter(relaxationParameter);
+        auto updater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
+		if ( gauss == 0 ){
+			std::cout << "TendomerNetworkForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) \n";
+        	taskmanager2.addUpdater( updater );
+		}else {
+			std::cout << "TendomerNetworkForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) \n";
+			taskmanager2.addUpdater( updater2 );
+		}
+		taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
+		//initialize and run
+		taskmanager2.initialize();
+		taskmanager2.run();
+		taskmanager2.cleanup();
+		
+	}
+	catch(std::exception& e){
+		std::cerr<<"Error:\n"
+		<<e.what()<<std::endl;
+	}
+	catch(...){
+		std::cerr<<"Error: unknown exception\n";
+	}
+	
+	return 0;
+}

From e278dba25d5dc2a6e2702c7d2204c12e191a8cdf Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Sat, 30 Oct 2021 16:53:29 +0200
Subject: [PATCH 44/70] change the star creation to use all available bonds
 from the bond vector set

---
 .../UpdaterAbstractCreateAllBondVectors.h     | 533 ++++++++++++++++++
 include/LeMonADE_PM/updater/UpdaterAddStars.h |  25 +-
 projects/IdealReferenceForceEquilibrium.cpp   |  85 ++-
 3 files changed, 602 insertions(+), 41 deletions(-)
 create mode 100644 include/LeMonADE_PM/updater/UpdaterAbstractCreateAllBondVectors.h

diff --git a/include/LeMonADE_PM/updater/UpdaterAbstractCreateAllBondVectors.h b/include/LeMonADE_PM/updater/UpdaterAbstractCreateAllBondVectors.h
new file mode 100644
index 0000000..9616749
--- /dev/null
+++ b/include/LeMonADE_PM/updater/UpdaterAbstractCreateAllBondVectors.h
@@ -0,0 +1,533 @@
+/*--------------------------------------------------------------------------------
+    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) 2016 by
+  o/.|.\o    E   nvironment    | LeMonADE Principal Developers
+    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 LEMONADEPM_UPDATER_UPDATERABSTRACTCREATEALLBONDS_H
+#define LEMONADEPM_UPDATER_UPDATERABSTRACTCREATEALLBONDS_H
+
+
+/**
+ * @file
+ *
+ * @class UpdaterAbstractCreateAllBonds
+ *
+ * @brief abstract updater to create systems
+ *
+ * @details This abstract class provides the three basic functions to create systems: add a single monomer, add a connected monomer and move the system to find some free space.
+ * This Updater requires FeatureAttributes.
+ *
+ * @tparam IngredientsType
+ *
+ **/
+
+#include <LeMonADE/updater/AbstractUpdater.h>
+#include <LeMonADE/utility/MonomerGroup.h>
+#include <LeMonADE/utility/DepthIterator.h>
+#include <LeMonADE/utility/Vector3D.h>
+#include <LeMonADE/updater/moves/MoveLocalSc.h>
+#include <LeMonADE/updater/moves/MoveAddMonomerSc.h>
+
+template<class IngredientsType>
+class UpdaterAbstractCreateAllBonds:public AbstractUpdater
+{
+public:
+  UpdaterAbstractCreateAllBonds(IngredientsType& ingredients_):ingredients(ingredients_),lookupFilled(false){}
+
+  virtual void initialize();
+  virtual bool execute();
+  virtual void cleanup();
+
+protected:
+  IngredientsType& ingredients;
+
+  //! function to add a standalone monomer
+  bool addSingleMonomer(int32_t type=1);
+
+  //! function to add a monomer to a parent monomer
+  bool addMonomerToParent(uint32_t parent_id, int32_t type=1);
+
+  //! function to add a monomer at a spezific place
+  bool addMonomerAtPosition(VectorInt3 pos, int32_t type=1);
+
+  //! function to add a new monomer inbetween two others
+  bool addMonomerInsideConnectedPair(uint32_t indexA, uint32_t indexB, int32_t type=1);
+
+  //! function to add a new monomer at two others
+  bool addMonomerAtConnectedPair(uint32_t indexA, uint32_t indexB, int32_t type=1);
+  
+  //! function to add a ring around a chain monomer
+  bool addRing(uint32_t parent_id, int32_t type=1, uint32_t NRingMonomers=5);
+  
+  //! function to move the whole system
+  void moveSystem(int32_t nsteps);
+
+  //! function to find groups of connected monomers
+  void linearizeSystem();
+
+  //! function to get a random bondvector of length 2
+  VectorInt3 randomBondvector();
+
+private:
+	  RandomNumberGenerators rng;
+
+	//!  bond table is filled with all valid bonds or not 
+	bool lookupFilled;
+	//!set of vectors which are valid for the conformations 
+  	std::vector<VectorInt3> bondvectorSet;
+
+};
+
+/**
+* The initialize function handles the new systems information.
+*
+* @tparam IngredientsType Features used in the system. See Ingredients.
+*/
+template < class IngredientsType >
+void UpdaterAbstractCreateAllBonds<IngredientsType>::initialize(){
+
+}
+
+/**
+* Execution of the system creation
+*
+* @tparam IngredientsType Features used in the system. See Ingredients.
+*/
+template < class IngredientsType >
+bool UpdaterAbstractCreateAllBonds<IngredientsType>::execute(){
+
+}
+
+/**
+* Standard clean up.
+*
+* @tparam IngredientsType Features used in the system. See Ingredients.
+*/
+template < class IngredientsType >
+void UpdaterAbstractCreateAllBonds<IngredientsType>::cleanup(){
+
+}
+
+/******************************************************************************/
+/**
+ * @brief function to add a standalone monomer
+ * @param type attribute tag of the new monomer
+ * @return <b false> if position is not free, <b true> if move was applied
+ */
+template<class IngredientsType>
+bool UpdaterAbstractCreateAllBonds<IngredientsType>::addSingleMonomer(int32_t type){
+  // set properties of add Monomer Move
+  MoveAddMonomerSc<> addmove;
+  addmove.init(ingredients);
+  addmove.setTag(type);
+
+  int32_t counter(0);
+  while(counter<10000){
+    VectorInt3 newPosition((rng.r250_rand32() % (ingredients.getBoxX()-1)),
+				  (rng.r250_rand32() % (ingredients.getBoxY()-1)),
+				  (rng.r250_rand32() % (ingredients.getBoxZ()-1)));
+    addmove.setPosition(newPosition);
+    if(addmove.check(ingredients)==true){
+      addmove.apply(ingredients);
+      return true;
+    }
+    counter++;
+  }
+  return false;
+}
+
+/******************************************************************************/
+/**
+ * @brief function to add a monomer to a parent monomer
+ * @param parent_id id of monomer to connect with
+ * @param type attribute tag of the new monomer
+ * @return <b false> if position is not free, <b true> if move was applied
+ */
+template<class IngredientsType>
+bool UpdaterAbstractCreateAllBonds<IngredientsType>::addMonomerToParent(uint32_t parent_id, int32_t type){
+  // set properties of add Monomer Move
+  MoveAddMonomerSc<> addmove;
+  addmove.init(ingredients);
+  addmove.setTag(type);
+
+  int32_t counter(0);
+
+  while(counter<10000){
+    //try at most 30 random bondvectors to find a new monomer position
+    for(uint i=0;i<30;i++){
+      VectorInt3 bondvector(randomBondvector());
+      // set position of new monomer
+      addmove.setPosition(ingredients.getMolecules()[parent_id]+bondvector);
+
+      // check new position (excluded volume)
+      if(addmove.check(ingredients)==true){
+	addmove.apply(ingredients);
+	ingredients.modifyMolecules().connect( parent_id, (ingredients.getMolecules().size()-1) );
+	return true;
+      }
+    }
+    // if no position matches, we need to move the system a bit
+    moveSystem(2);
+    counter++;
+  }
+  return false;
+}
+
+/******************************************************************************/
+/**
+ * @brief function to add a monomer to a specific position. if position is not free return false
+ * @param VectorInt3 position
+ * @param type attribute tag of the new monomer
+ * @return <b false> if position is not free, <b true> if move was applied
+ */
+template<class IngredientsType>
+bool UpdaterAbstractCreateAllBonds<IngredientsType>::addMonomerAtPosition(VectorInt3 position, int32_t type){
+  MoveAddMonomerSc<> addmove;
+  addmove.init(ingredients);
+  addmove.setTag(type);
+
+  addmove.setPosition(position);
+  if(addmove.check(ingredients)==true){
+    addmove.apply(ingredients);
+    return true;
+  }else{
+    return false;
+  }
+}
+
+/******************************************************************************/
+/**
+ * @brief function to add a new monomer between two already existing ones instead of a bond.
+ * @param indexA
+ * @param indexB
+ * @param type attribute tag of the new monomer
+ * @return <b false> if position is not free, <b true> if move was applied
+ */
+template<class IngredientsType>
+bool UpdaterAbstractCreateAllBonds<IngredientsType>::addMonomerInsideConnectedPair(uint32_t indexA, uint32_t indexB, int32_t type){
+  //first check if monomers are connected
+  if( ! ingredients.getMolecules().areConnected(indexA,indexB))
+    return false;
+
+  MoveAddMonomerSc<> addmove;
+  addmove.init(ingredients);
+  addmove.setTag(type);
+
+  int32_t counter(0);
+
+  while(counter<10000){
+    //try at most 30 random bondvectors to find a new monomer position
+    for(uint i=0;i<30;i++){
+      // get a random bondvector
+      VectorInt3 bondvector(randomBondvector());
+      // set position of new monomer
+      addmove.setPosition(ingredients.getMolecules()[indexA]+bondvector);
+
+      // check new position (excluded volume, other features)
+      if(addmove.check(ingredients)==true){
+	//check the new bondvector bewten the new monomer and indexB
+	VectorInt3 checkBV(addmove.getPosition()-ingredients.getMolecules()[indexB]);
+	if( (checkBV.getLength() < 3) && (ingredients.getBondset().isValidStrongCheck(checkBV)) ){
+	  addmove.apply(ingredients);
+	  ingredients.modifyMolecules().connect( indexA, (ingredients.getMolecules().size()-1) );
+	  ingredients.modifyMolecules().connect( indexB, (ingredients.getMolecules().size()-1) );
+	  ingredients.modifyMolecules().disconnect( indexA, indexB );
+	  return true;
+	}
+      }
+    }
+    // if no position matches, we need to move the system a bit
+    moveSystem(2);
+    counter++;
+  }
+  return false;
+}
+/******************************************************************************/
+/**
+ * @brief function to add a new monomer to two already existing ones such that all three monomers are connected.
+ * @param indexA
+ * @param indexB
+ * @param type attribute tag of the new monomer
+ * @return <b false> if position is not free, <b true> if move was applied
+ */
+template<class IngredientsType>
+bool UpdaterAbstractCreateAllBonds<IngredientsType>::addMonomerAtConnectedPair(uint32_t indexA, uint32_t indexB, int32_t type){
+  //first check if monomers are connected
+  if( ! ingredients.getMolecules().areConnected(indexA,indexB))
+    return false;
+  
+  MoveAddMonomerSc<> addmove;
+  addmove.init(ingredients);
+  addmove.setTag(type);
+
+  int32_t counter(0);
+
+  while(counter<10000){
+    //try at most 30 random bondvectors to find a new monomer position
+    for(uint i=0;i<30;i++){
+      // get a random bondvector
+      VectorInt3 bondvector(randomBondvector());
+      // set position of new monomer
+      addmove.setPosition(ingredients.getMolecules()[indexA]+bondvector);
+
+      // check new position (excluded volume, other features)
+      if(addmove.check(ingredients)==true){
+	//check the new bondvector between the new monomer and indexB
+	VectorInt3 checkBV(addmove.getPosition()-ingredients.getMolecules()[indexB]);
+	if( (checkBV.getLength() < 3) && (ingredients.getBondset().isValidStrongCheck(checkBV)) ){
+	  addmove.apply(ingredients);
+	  ingredients.modifyMolecules().connect( indexA, (ingredients.getMolecules().size()-1) );
+	  ingredients.modifyMolecules().connect( indexB, (ingredients.getMolecules().size()-1) );
+	  return true;
+	}
+      }
+    }
+    // if no position matches, we need to move the system a bit
+    moveSystem(2);
+    counter++;
+  }
+  return false;
+}
+/**
+ * @brief add a ring threaded on a chain at position of parent monomer
+ * 
+ * @todo are there conformations where bonds of the ring cross the bonds of the chain?
+ * 
+ * @param parent 
+ * @param type monomer tag 
+ * @param NRingMonomers number of monomers per ring 
+ */
+template < class IngredientsType >
+bool UpdaterAbstractCreateAllBonds<IngredientsType>::addRing(uint32_t parent, int32_t type, uint32_t NRingMonomers)
+  {
+    if(parent < ingredients.getMolecules().size()) 
+    {
+        uint32_t attempts(0);
+        while (attempts<10000)
+        {
+	  uint32_t neighborDirection(0);
+	  uint32_t currentParent(parent);
+	  while (true)
+	  {
+	    uint32_t neighborID(ingredients.getMolecules().getNeighborIdx(currentParent,neighborDirection));
+	    if(ingredients.getMolecules().getNumLinks(neighborID) != 2 )
+	    {
+		if(neighborDirection==1) break;
+		else {neighborDirection++; currentParent=parent;}
+	    }
+	    else
+	    {
+		VectorInt3 neighborPosition(ingredients.getMolecules()[neighborID]);
+		VectorInt3 parentPosition(ingredients.getMolecules()[currentParent]);
+		VectorInt3 bond(neighborPosition-parentPosition);
+		uint32_t otherParentNeighbor; 
+		uint32_t otherNeighborNeighbor;
+		neighborDirection ? otherParentNeighbor=(ingredients.getMolecules().getNeighborIdx(currentParent,0)) :  otherParentNeighbor=(ingredients.getMolecules().getNeighborIdx(currentParent,1));
+		(ingredients.getMolecules().getNeighborIdx(neighborID,0)==currentParent) ? otherNeighborNeighbor=(ingredients.getMolecules().getNeighborIdx(neighborID,1)): otherNeighborNeighbor=(ingredients.getMolecules().getNeighborIdx(neighborID,0));
+		VectorInt3 neighborParentBond(parentPosition-ingredients.getMolecules()[otherParentNeighbor]);
+		VectorInt3 neighborNeighborBond(neighborPosition-ingredients.getMolecules()[otherNeighborNeighbor]);
+		if(bond.getLength() == 2 && (neighborParentBond.getLength()<3) &&(neighborNeighborBond.getLength()<3))
+		{
+		    for(uint32_t i=0; i<8; i++)
+		    {
+			
+			VectorInt3 StartPosition=parentPosition;
+			//set the possible conformations 
+			int32_t dx1, dx2;
+			int32_t dy1, dz1;
+			int32_t dy2, dz2;
+			VectorInt3 vec1,vec2;
+			if(bond.getX() == 2 || bond.getX() == -2)
+			{
+			  StartPosition+=VectorInt3(bond.getX()/2,0,0);
+			  dx1=0;dx2=0;//dy1=2;dy2=0;dz1=0;dz2=2; 
+			  if(rng.r250_drand()>0.5){dy1=2;dy2=0;dz1=0;dz2=2;}
+			  else {dy1=0;dy2=2;dz1=2;dz2=0;}
+			  int32_t dx3,dx4;
+			  if(rng.r250_drand()>0.5){dx3=1;dx4=-1;}
+			  else{dx3=-1;dx4=1;}
+// 			  rng.r250_drand()>0.5 ? dx3=1 : dx3=-1;
+// 			  rng.r250_drand()>0.5 ? dx4=1 : dx4=-1;
+			  vec1=VectorInt3( dx2+dx3,  dy2,  dz2);
+			  vec2=VectorInt3(-dx2+dx4, -dy2, -dz2);
+			}
+			else if(bond.getY() == 2 || bond.getY() == -2)
+			{
+			  StartPosition+=VectorInt3(0,bond.getY()/2,0);
+			  dy1=0;dy2=0; 
+			  if(rng.r250_drand()>0.5){dx1=2;dx2=0;dz1=0;dz2=2;}
+			  else {dx1=0;dx2=2;dz1=2;dz2=0;}
+			  int32_t dy3,dy4;
+			  if(rng.r250_drand()>0.5){dy3=1;dy4=-1;}
+			  else{dy3=-1;dy4=1;}
+// 			  rng.r250_drand()>0.5 ? dy3=1 : dy3=-1;
+// 			  rng.r250_drand()>0.5 ? dy4=1 : dy4=-1;
+			  vec1=VectorInt3( dx2,  dy2+dy3,  dz2);
+			  vec2=VectorInt3(-dx2, -dy2+dy4, -dz2);
+			}
+			else if(bond.getZ() == 2 || bond.getZ() == -2)
+			{
+			  StartPosition+=VectorInt3(0,0,bond.getZ()/2);
+			  dz1=0;dz2=0; 
+			  if(rng.r250_drand()>0.5){dx1=2;dx2=0;dy1=0;dy2=2;}
+			  else {dx1=0;dx2=2;dy1=2;dy2=0;}
+			  int32_t dz3,dz4;
+			  if(rng.r250_drand()>0.5){dz3=1;dz4=-1;}
+			  else{dz3=-1;dz4=1;}
+// 			  rng.r250_drand()>0.5 ? dz3=1 : dz3=-1;
+// 			  rng.r250_drand()>0.5 ? dz4=1 : dz4=-1;
+			  vec1=VectorInt3( dx2,  dy2,  dz2+dz3);
+			  vec2=VectorInt3(-dx2, -dy2, -dz2+dz4);
+			}
+			// set positions of monomers and two which guarantee that ring is threaded 
+			std::vector<VectorInt3> PotentialPositions(6,StartPosition);
+			PotentialPositions[0]+=VectorInt3( dx1, dy1, dz1);
+			PotentialPositions[2]+=VectorInt3(-dx1,-dy1,-dz1);
+			PotentialPositions[4]+=VectorInt3( dx2, dy2, dz2);//position to check, not to use for a monomer 
+			PotentialPositions[5]+=VectorInt3(-dx2,-dy2,-dz2);//position to check, not to use for a monomer 
+			PotentialPositions[1]+=vec1;
+			PotentialPositions[3]+=vec2;
+			
+			// check if positions are occupied
+			bool PositionsFit(true);
+			for(uint32_t i=0; i <PotentialPositions.size();i++)
+			{
+			  MoveAddMonomerSc<> addmove;
+			  addmove.init(ingredients);
+			  addmove.setPosition(PotentialPositions[i]);
+			  if(addmove.check(ingredients)==false){PositionsFit=false;}
+			}
+			// add ring to system
+			if (PositionsFit)
+			{
+			  bool AddRing(true);
+			  for(uint32_t i=0; i<NRingMonomers;i++) 
+			  {
+			    if ( i<4  && AddRing ) if(!addMonomerAtPosition(PotentialPositions[i], type) ) {AddRing=false;throw std::runtime_error("Could not add 4-monomer ring!");}
+			    if ( i==3 && AddRing ) for(uint32_t i=0; i < 4 ;i++) ingredients.modifyMolecules().connect(((ingredients.getMolecules().size()-1) -i%4),((ingredients.getMolecules().size()-1)-(1+i)%4));
+			    if ( i>3  && AddRing ) 
+			    {
+			      for (uint32_t j=0;j<i;j++)
+			      {
+				//this is a dangerous thing, because it could happen that a monomer is added that freeze in 4 monomers of the system. 
+				//I must get new safer function ....
+				if (addMonomerInsideConnectedPair(ingredients.getMolecules().size()-(1+j%i),ingredients.getMolecules().size()-(1+(1+j)%i),type)) 
+				{
+				  AddRing=true;
+				  break;
+				}else { AddRing=false;}
+			      }
+			    }
+			  }
+
+			  if (AddRing) return true;
+			  else throw std::runtime_error("Could not add a ring!");
+			  
+			}
+		    }
+		    
+		    //if still here: try again at next position		
+		    currentParent=neighborID;
+			
+		}
+		else {currentParent=neighborID;}
+	    }
+	  }
+	  attempts++;
+	  moveSystem(2);
+        }
+        return false; 
+    }else{
+      std::stringstream error;
+      error<<"Given parent ID "<<parent<<" does not exist!";
+      throw std::runtime_error(error.str());}
+  };
+
+/******************************************************************************/
+/**
+ * @brief function to move the whole system
+ * @param nsteps number of MCS to move
+ */
+template<class IngredientsType>
+void UpdaterAbstractCreateAllBonds<IngredientsType>::moveSystem(int32_t nsteps){
+  MoveLocalSc move;
+  for(int32_t n=0;n<nsteps;n++){
+    for(int32_t m=0;m<ingredients.getMolecules().size();m++){
+      move.init(ingredients);
+      if(move.check(ingredients)==true){
+	move.apply(ingredients);
+      }
+    }
+  }
+}
+
+/******************************************************************************/
+/**
+ * @brief function to find groups of connected monomers and resort ingredients
+ * to write out longest possible bondvector series
+ */
+
+template<class IngredientsType>
+void UpdaterAbstractCreateAllBonds<IngredientsType>::linearizeSystem(){
+  //call ingredients copy constructor
+  IngredientsType newIngredients(ingredients);
+
+  //delete all the informations in molecules
+  newIngredients.modifyMolecules().clear();
+
+  std::vector < MonomerGroup<typename IngredientsType::molecules_type> > LinearMonomerGroupsVector;
+
+  fill_connected_groups( ingredients.getMolecules(), LinearMonomerGroupsVector, MonomerGroup<typename IngredientsType::molecules_type>(ingredients.getMolecules()), alwaysTrue() );
+
+  for(size_t groups=0; groups < LinearMonomerGroupsVector.size(); ++groups){
+    if(groups==0)
+      newIngredients.modifyMolecules() = LinearMonomerGroupsVector[groups].copyGroup();
+    else
+      newIngredients.modifyMolecules() += LinearMonomerGroupsVector[groups].copyGroup();
+  }
+
+  ingredients=newIngredients;
+
+}
+
+/******************************************************************************/
+/**
+ * @brief function to get a random bondvector of length 2 which is part of the bondvectorset
+ * @param nsteps number of MCS to move
+ */
+template<class IngredientsType>
+VectorInt3 UpdaterAbstractCreateAllBonds<IngredientsType>::randomBondvector(){
+    if ( lookupFilled == false ){
+		
+		for (auto it=ingredients.getBondset().begin(); it!= ingredients.getBondset().end();it++){
+			auto bondvector(it->second);
+			if (ingredients.getBondset().isValidStrongCheck( bondvector ) ) 
+				bondvectorSet.push_back(bondvector);
+		}
+		lookupFilled=true;
+    }
+  	//get a random direction for the bondvector of length 2
+	return bondvectorSet[ rng.r250_rand32() % bondvectorSet.size()] ; 
+}
+#endif /* LEMONADE_UPDATER_ABSTRACT_CREATE_H */
diff --git a/include/LeMonADE_PM/updater/UpdaterAddStars.h b/include/LeMonADE_PM/updater/UpdaterAddStars.h
index 4ee111f..d0c8ace 100644
--- a/include/LeMonADE_PM/updater/UpdaterAddStars.h
+++ b/include/LeMonADE_PM/updater/UpdaterAddStars.h
@@ -51,14 +51,16 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
  * @param type2_ attribute tag of "odd" monomers
  **/
 
-#include <LeMonADE/updater/UpdaterAbstractCreate.h>
+// #include <LeMonADE/updater/UpdaterAbstractCreate.h>
 #include <LeMonADE/utility/Vector3D.h>
 #include <cmath>
 
+#include <LeMonADE_PM/updater/UpdaterAbstractCreateAllBondVectors.h>
+
 template<class IngredientsType>
-class UpdaterAddStars: public UpdaterAbstractCreate<IngredientsType>
+class UpdaterAddStars: public UpdaterAbstractCreateAllBonds<IngredientsType>
 {
-  typedef UpdaterAbstractCreate<IngredientsType> BaseClass;
+  typedef UpdaterAbstractCreateAllBonds<IngredientsType> BaseClass;
 
 public:
   UpdaterAddStars(IngredientsType& ingredients_, uint32_t NStar_, 
@@ -68,9 +70,6 @@ class UpdaterAddStars: public UpdaterAbstractCreate<IngredientsType>
   virtual bool execute();
   virtual void cleanup();
 
-  //! getter function for write compressed solvent bool
-  const bool getIsSolvent() const {return IsSolvent;}
-
   //! getter function for number of stars
   const int32_t getNStar() const {return NStar;}
 
@@ -124,7 +123,7 @@ UpdaterAddStars<IngredientsType>::UpdaterAddStars(
     uint32_t NBranchPerStar_
     ):
     BaseClass(ingredients_), NStar(NStar_), NMonoPerBranch(NMonoPerBranch_), NBranchPerStar(NBranchPerStar_), 
-    density(0.0), wasExecuted(false),
+    density(0.0), wasExecuted(false)
     {}
 
 /**
@@ -153,18 +152,18 @@ template < class IngredientsType >
 bool UpdaterAddStars<IngredientsType>::execute(){
     if(wasExecuted) return true;
     std::cout << "execute UpdaterAddStars" << std::endl;
-    //loop over stars and star monomers and build it up
-    uint32_t gen;
-    uint32_t index_center;
 
-    for(uint32_t i=0;i<(NStar);i++){
+    for(uint32_t i=0;i<NStar;i++)
         addSingleMonomer(1);
+    u_int32_t parentID(0);
+    for(uint32_t i=0;i<NStar;i++){
         for(uint32_t j=0;j<(NBranchPerStar);j++){
             for(uint32_t b=0;b<(NMonoPerBranch);b++){
-                u_int32_t parentID;
                 if (b==0)
-                parentID = (ingredients.getMolecules().size()-NBranchPerStar)
+                    parentID=i;
                 addMonomerToParent(parentID,1);
+                parentID = ingredients.getMolecules().size()-1; 
+
             }
         }
     }
diff --git a/projects/IdealReferenceForceEquilibrium.cpp b/projects/IdealReferenceForceEquilibrium.cpp
index 0b14857..1c79b51 100644
--- a/projects/IdealReferenceForceEquilibrium.cpp
+++ b/projects/IdealReferenceForceEquilibrium.cpp
@@ -38,13 +38,14 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 #include <LeMonADE/core/Ingredients.h>
 #include <LeMonADE/updater/UpdaterReadBfmFile.h>
 #include <LeMonADE/analyzer/AnalyzerWriteBfmFile.h>
-#include <LeMonADE/feature/FeatureMoleculesIOUnsaveCheck.h>
+#include <LeMonADE/feature/FeatureMoleculesIO.h>
 #include <LeMonADE/feature/FeatureReactiveBonds.h>
 #include <LeMonADE/feature/FeatureFixedMonomers.h>
 #include <LeMonADE/feature/FeatureBox.h>
-#include <LeMonADE/feature/FeatureLabel.h>
+
 #include <LeMonADE/utility/TaskManager.h>
 #include <LeMonADE/utility/RandomNumberGenerators.h>
+#include <LeMonADE/feature/FeatureSystemInformationLinearMeltWithCrosslinker.h>
 
 #include <extern/catchorg/clara/clara.hpp>
 
@@ -52,7 +53,7 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 #include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
 #include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
 #include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
-#include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h>
+#include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpIdealReference.h>
 #include <LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h>
 #include <LeMonADE_PM/updater/UpdaterAffineDeformation.h>
 #include <LeMonADE_PM/updater/UpdaterAddStars.h>
@@ -62,7 +63,7 @@ int main(int argc, char* argv[]){
 	try{
 		///////////////////////////////////////////////////////////////////////////////
 		///parse options///
-		std::string inputBFM("init.bfm");
+		// std::string inputBFM("init.bfm");
 		std::string outputDataPos("CrosslinkPosition.dat");
 		std::string outputDataDist("ChainExtensionDistribution.dat");
 		std::string feCurve("");
@@ -70,18 +71,25 @@ int main(int argc, char* argv[]){
 		double threshold(0.5);
 		double factor(0.995);
 		double stretching_factor(1.0);
-		bool gauss(false);
-		
+		uint32_t gauss(0);
+
+        uint32_t nSegments(16);
+        uint32_t functionality(4);
+		uint32_t nRings(0);
+
 		bool showHelp = false;
 		auto parser
-			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"            ] ("(required)Input filename of the bfm file"                                    ).required()
-			| clara::detail::Opt(       outputDataPos, "outputDataPos (=CrosslinkPosition.dat)"          ) ["-o"]["--outputPos"        ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
+			// = clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"            ] ("(required)Input filename of the bfm file"                                    ).required()
+			= clara::detail::Opt(       outputDataPos, "outputDataPos (=CrosslinkPosition.dat)"          ) ["-o"]["--outputPos"        ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
 			| clara::detail::Opt(      outputDataDist, "outputDataDist (=ChainExtensionDistribution.dat)") ["-c"]["--outputDist"       ] ("(optional) Output filename of the chain extension distribution."             ).optional()
 			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"        ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
 			| clara::detail::Opt(   stretching_factor, "stretching_factor (=1)"                          ) ["-l"]["--stretching_factor"] ("(optional) Stretching factor for uniaxial deformation. Default 1.0 ."        ).optional()
 			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"          ] ("(optional) Force-Extension curve. Default \"\"."                             ).required()
 			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"            ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
 			| clara::detail::Opt(               gauss, "gauss"                                           ) ["-g"]["--gauss"            ] ("(optional) Deforma with a Gaussian deformation behaviour. Default 1.0 ."     ).optional()
+            | clara::detail::Opt(           nSegments, "nSegments"                                       ) ["-n"]["--nSegments"        ] ("(optional) Number of segments for the strand."                               ).optional()
+            | clara::detail::Opt(       functionality, "nStrands"                                        ) ["-s"]["--nStrands"         ] ("(optional) Functionality."                                                   ).optional()
+            | clara::detail::Opt(              nRings, "nRings"                                          ) ["-m"]["--nRings"         ] ("(optional) number of rings."                                                   ).optional()
 			| clara::Help( showHelp );
 		
 	    auto result = parser.parse( clara::Args( argc, argv ) );
@@ -90,17 +98,20 @@ int main(int argc, char* argv[]){
 	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
 	      exit(1);
 	    }else if(showHelp == true){
-	      std::cout << "Simulator to connect linear chains with single monomers of certain functionality"<< std::endl;
+	    //   std::cout << "Simulator to connect linear chains with single monomers of certain functionality"<< std::endl;
 	      parser.writeToStream(std::cout);
 	      exit(0);
 	    }else{
 	      std::cout << "outputData            : " << outputDataPos          << std::endl;
 	      std::cout << "outputDataDist        : " << outputDataDist         << std::endl;
-	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
+	    //   std::cout << "inputBFM              : " << inputBFM               << std::endl; 
 	      std::cout << "threshold             : " << threshold              << std::endl; 
 		  std::cout << "feCurve               : " << feCurve                << std::endl;
 		  std::cout << "gauss                 : " << gauss                  << std::endl;
 		  std::cout << "stretching_factor     : " << stretching_factor      << std::endl;
+          std::cout << "nSegments             : " << nSegments              << std::endl;
+          std::cout << "functionality         : " << functionality          << std::endl;
+          std::cout << "nRings                : " << nRings          << std::endl;
 	    }
 		RandomNumberGenerators rng;
 		// rng.seedDefaultValuesAll();
@@ -109,22 +120,28 @@ int main(int argc, char* argv[]){
 		///end options parsing
 		///////////////////////////////////////////////////////////////////////////////
 		//Read in th last Config 
-		typedef LOKI_TYPELIST_4(FeatureMoleculesIOUnsaveCheck, FeatureLabel, FeatureReactiveBonds,FeatureFixedMonomers) Features;
+		typedef LOKI_TYPELIST_1(FeatureMoleculesIO) Features;
 		typedef ConfigureSystem<VectorInt3,Features, 7> Config;
 		typedef Ingredients<Config> Ing;
 		Ing myIngredients;
-		
+        myIngredients.setBoxX(256);
+		myIngredients.setBoxY(256);
+		myIngredients.setBoxZ(256);
+		myIngredients.setPeriodicX(1);
+		myIngredients.setPeriodicY(1);
+		myIngredients.setPeriodicZ(1);
+        myIngredients.modifyBondset().addBFMclassicBondset();
+        myIngredients.synchronize();
 		TaskManager taskmanager;
-		
-		taskmanager.addUpdater( new UpdaterAddStars<Ing>(inputBFM,myIngredients, UpdaterReadBfmFile<Ing>::READ_LAST_CONFIG_SAVE),0);
-
-		//initialize and run
+		taskmanager.addUpdater( new UpdaterAddStars<Ing>(myIngredients,1, nSegments+1 , functionality ),0);
+        taskmanager.addAnalyzer(new AnalyzerWriteBfmFile<Ing>("config.bfm", myIngredients, AnalyzerWriteBfmFile<Ing>::APPEND) );
 		taskmanager.initialize();
 		taskmanager.run(1);
 		taskmanager.cleanup();
+       
 		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
 		//the foce equilibrium is reached off lattice ( no integer values for the positions )
-		typedef LOKI_TYPELIST_3(FeatureBox, FeatureCrosslinkConnectionsLookUpTendomers ,FeatureLabel) Features2;
+        typedef LOKI_TYPELIST_4(FeatureBox, FeatureCrosslinkConnectionsLookUpIdealReference ,FeatureSystemInformationLinearMeltWithCrosslinker,FeatureFixedMonomers) Features2;
 		typedef ConfigureSystem<VectorDouble3,Features2, 7> Config2;
 		typedef Ingredients<Config2> Ing2;
 		Ing2 myIngredients2;
@@ -137,42 +154,54 @@ int main(int argc, char* argv[]){
 		myIngredients2.setPeriodicZ(myIngredients.isPeriodicZ());
 		myIngredients2.modifyMolecules().resize(myIngredients.getMolecules().size());
 		myIngredients2.modifyMolecules().setAge(myIngredients.getMolecules().getAge());
-        
-        myIngredients2.setNumTendomers           (myIngredients.getNumTendomers());
-		myIngredients2.setNumCrossLinkers        (myIngredients.getNumCrossLinkers());
-		myIngredients2.setNumMonomersPerChain    (myIngredients.getNumMonomersPerChain());
-		myIngredients2.setNumLabelsPerTendomerArm(myIngredients.getNumLabelsPerTendomerArm());
+
+        myIngredients2.setNumOfChains              (functionality*1);
+		myIngredients2.setNumOfCrosslinks          (functionality+1);
+		myIngredients2.setNumOfMonomersPerChain    (nSegments);
+		myIngredients2.setNumOfMonomersPerCrosslink(1);
+		myIngredients2.setFunctionality            (functionality);
+
 		
 		for(size_t i = 0; i< myIngredients.getMolecules().size();i++){
 			myIngredients2.modifyMolecules()[i].modifyVector3D()=myIngredients.getMolecules()[i].getVector3D();
-			myIngredients2.modifyMolecules()[i].setReactive(myIngredients.getMolecules()[i].isReactive());
-			myIngredients2.modifyMolecules()[i].setNumMaxLinks(myIngredients.getMolecules()[i].getNumMaxLinks());
 			for (size_t j = 0 ; j < myIngredients.getMolecules().getNumLinks(i);j++){
 				uint32_t neighbor(myIngredients.getMolecules().getNeighborIdx(i,j));
 				if( ! myIngredients2.getMolecules().areConnected(i,neighbor) )
 					myIngredients2.modifyMolecules().connect(i,neighbor);
 			}
 		}
+        for (auto i=0; i < functionality; i ++) { 
+            uint32_t ID(1 + (i+1)*(nSegments+1) -1);
+            // if(gauss == 1 ){
+            //     rng.r250_drand()
+
+            // }
+            std::cout  << "Fixed monomers= "<< ID <<std::endl;
+            myIngredients2.modifyMolecules()[ ID ].setMovableTag(false);  
+        }
 		myIngredients2.synchronize();
 
 		TaskManager taskmanager2;
-		taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
+		// taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
 		//read bonds and positions stepwise
         auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
         updater->setFilename(feCurve);
         updater->setRelaxationParameter(relaxationParameter);
         auto updater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
 		if ( gauss == 0 ){
-			std::cout << "TendomerNetworkForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) \n";
+			std::cout << "IdealReferenceForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) \n";
         	taskmanager2.addUpdater( updater );
-		}else {
-			std::cout << "TendomerNetworkForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) \n";
+		}else if( gauss == 1 ){
+			std::cout << "IdealReferenceForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) \n";
 			taskmanager2.addUpdater( updater2 );
 		}
+        
 		taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
 		//initialize and run
 		taskmanager2.initialize();
 		taskmanager2.run();
+		if(gauss > 1)
+			taskmanager2.run(1);
 		taskmanager2.cleanup();
 		
 	}

From 7f4afc99ed0d46306e4a9ea77375f89d21967cc6 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Sat, 30 Oct 2021 16:57:56 +0200
Subject: [PATCH 45/70] change the
 FeatureCrosslinkConnectionsLookUpIdealReference to use the getMovableFlag to
 determine the neighbors

---
 ...CrosslinkConnectionsLookUpIdealReference.h | 136 ++++++++++++++++++
 1 file changed, 136 insertions(+)
 create mode 100644 include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpIdealReference.h

diff --git a/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpIdealReference.h b/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpIdealReference.h
new file mode 100644
index 0000000..063aaba
--- /dev/null
+++ b/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpIdealReference.h
@@ -0,0 +1,136 @@
+/*--------------------------------------------------------------------------------
+    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 LENONADE_PM_FEATURE_FEATURECROSSLINKCONNECTIONLOOKUPIDEALREFERENCE_H
+#define LENONADE_PM_FEATURE_FEATURECROSSLINKCONNECTIONLOOKUPIDEALREFERENCE_H
+
+#include <LeMonADE/feature/Feature.h>
+#include <LeMonADE/feature/FeatureReactiveBonds.h>
+#include <LeMonADE/updater/moves/MoveBase.h>
+#include <LeMonADE/utility/Vector3D.h>
+#include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
+#include <LeMonADE_PM/utility/neighborX.h>
+
+
+/*****************************************************************************/
+/**
+ * @file
+ * @date   2021/04/01
+ * @author Toni
+ *
+ * @class FeatureCrosslinkConnectionsLookUpIdealReference
+ * @brief Creates a lookup for crosslink IDs and their neighbors
+ * @details For calculating the equilibrium position of crosslinks in a 
+ * a phantom network, one needs to know the crosslink neighbors and the number 
+ * of segments between them.  
+ * 
+ **/
+/*****************************************************************************/
+///////////////////////////////////////////////////////////////////////////////
+//DEFINITION OF THE CLASS TEMPLATE   	                                ///////
+//Implementation of the members below					///////
+///////////////////////////////////////////////////////////////////////////////
+
+class FeatureCrosslinkConnectionsLookUpIdealReference : public Feature {
+  
+public:
+  	//! This Feature requires a monomer_extensions.
+	typedef LOKI_TYPELIST_1(MonomerReactivity) monomer_extensions;
+
+	//! check bas connect move - always true 
+	template<class IngredientsType>
+	bool checkMove(const IngredientsType& ingredients, const MoveBase& move) const { return true;};
+
+	//! synchronize lookup table
+	template<class IngredientsType>
+	void synchronize(IngredientsType& ingredients) {
+	  	fillTables(ingredients);
+	};
+    //! set the jump vector 
+	void setCrossLinkNeighborJump(uint32_t CrossLinkID, uint32_t idx, VectorDouble3 vec) {
+		if ( idx > CrossLinkNeighbors.at(CrossLinkID).size() ){
+			std::stringstream errormessage;
+			errormessage << "FeatureCrosslinkConnectionsLookUpTendomers::setCrossLinkNeighborJump neighbor idx  " << idx <<" is to high.";
+			throw std::runtime_error(errormessage.str());
+		}
+		CrossLinkNeighbors.at(CrossLinkID)[idx].jump=vec;
+	}
+	//!getter function for the neighboring crosslinks
+	std::vector<neighborX> getCrossLinkNeighborIDs(uint32_t CrossLinkID) const{
+		#ifdef DEBUG
+		if (CrossLinkNeighbors.find(CrossLinkID) == CrossLinkNeighbors.end()){
+			std::stringstream errormessage;
+			errormessage << "FeatureCrosslinkConnectionsLookUpIdealReference::getCrossLinkNeighborIDs Cross Link ID " << CrossLinkID <<" does not exist.";
+			throw std::runtime_error(errormessage.str());
+		}
+		#endif
+		return CrossLinkNeighbors.at(CrossLinkID);
+	};
+
+	//!get the ID of crosslinks (determined by nConnections>3 and connected to another crosslink)
+	const std::vector<uint32_t>& getCrosslinkIDs() const {return crosslinkIDs;}
+
+private:
+  //! convinience function to fill all tables 
+  template<class IngredientsType>
+  void fillTables(IngredientsType& ingredients);
+  //!key - CrossLink ID; value - neighboring cross link and the number of segments to them
+  std::map<uint32_t,std::vector< neighborX > > CrossLinkNeighbors;
+  //!ID for crosslinks
+  std::vector<uint32_t> crosslinkIDs;
+};
+/**
+ *@details  Create look up table 
+ **/
+template<class IngredientsType>
+void FeatureCrosslinkConnectionsLookUpIdealReference::fillTables(IngredientsType& ingredients){
+
+	const typename IngredientsType::molecules_type& molecules=ingredients.getMolecules();
+	std::cout << "FeatureCrosslinkConnectionsLookUpIdealReference::fillTables" <<std::endl;
+	crosslinkIDs.resize(0);
+    crosslinkIDs.push_back(0);
+	CrossLinkNeighbors.clear();
+    std::vector<neighborX> NeighborIDs;
+    VectorDouble3 jumpVector(0.,0.,0.);
+	uint32_t  nSegments(ingredients.getNumOfMonomersPerChain());
+	for (auto i=0; i < ingredients.getMolecules().size(); i++){
+		if (ingredients.getMolecules()[i].getMovableTag() == false) 
+			NeighborIDs.push_back( neighborX(i, i%(nSegments+1), jumpVector) );
+
+	}
+    
+    // for( auto i=0; i <ingredients.getFunctionality() ;i++){
+    //     NeighborIDs.push_back( neighborX(1 + (i+1)*(nSegments+1) -1, nSegments, jumpVector) );
+    //     std::vector<neighborX> NeighborIDs1;
+    //     // NeighborIDs1
+    // }
+    CrossLinkNeighbors[0]=NeighborIDs;
+
+	std::cout << "FeatureCrosslinkConnectionsLookUpIdealReference::fillTables.done" <<std::endl; 
+}
+#endif /*LENONADE_PM_FEATURE_FEATURECROSSLINKCONNECTIONLOOKUPIDEALREFERENCE_H*/
\ No newline at end of file

From 1c0b084eba2f0f08aac38d10361af1da3de88baf Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Sat, 30 Oct 2021 16:58:22 +0200
Subject: [PATCH 46/70] add functionality to set the jump vector in
 FeatureCrosslinkConnectionsLookUp

---
 .../feature/FeatureCrosslinkConnectionsLookUp.h        | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUp.h b/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUp.h
index 7c50e2c..2b2b3ff 100644
--- a/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUp.h
+++ b/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUp.h
@@ -71,7 +71,15 @@ class FeatureCrosslinkConnectionsLookUp : public Feature {
 	void synchronize(IngredientsType& ingredients) {
 	  	fillTables(ingredients);
 	};
-
+    //! set the jump vector 
+	void setCrossLinkNeighborJump(uint32_t CrossLinkID, uint32_t idx, VectorDouble3 vec) {
+		if ( idx > CrossLinkNeighbors.at(CrossLinkID).size() ){
+			std::stringstream errormessage;
+			errormessage << "FeatureCrosslinkConnectionsLookUpTendomers::setCrossLinkNeighborJump neighbor idx  " << idx <<" is to high.";
+			throw std::runtime_error(errormessage.str());
+		}
+		CrossLinkNeighbors.at(CrossLinkID)[idx].jump=vec;
+	}
 	//!getter function for the neighboring crosslinks
 	std::vector<neighborX> getCrossLinkNeighborIDs(uint32_t CrossLinkID) const{
 		#ifdef DEBUG

From 2382ace42d5bb2a1bf60c3c03567158d2f1b1da4 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Fri, 5 Nov 2021 11:32:31 +0100
Subject: [PATCH 47/70] add the possibility to analyze the chain extension
 wihtout force equilibration (for e.g. doing a comparison before and after...)

---
 projects/TendomerNetworkForceEquilibrium.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/projects/TendomerNetworkForceEquilibrium.cpp b/projects/TendomerNetworkForceEquilibrium.cpp
index dd4c413..c17f819 100644
--- a/projects/TendomerNetworkForceEquilibrium.cpp
+++ b/projects/TendomerNetworkForceEquilibrium.cpp
@@ -163,7 +163,7 @@ int main(int argc, char* argv[]){
 		if ( gauss == 0 ){
 			std::cout << "TendomerNetworkForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) \n";
         	taskmanager2.addUpdater( updater );
-		}else {
+		}else if {gauss == 1 }{
 			std::cout << "TendomerNetworkForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) \n";
 			taskmanager2.addUpdater( updater2 );
 		}

From caaec19e2984a5b8efae4cc2f0d1db2b14ed5271 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Fri, 5 Nov 2021 11:34:22 +0100
Subject: [PATCH 48/70] add the possibility to decrease the relaxation factor.
 This is needed if the positions osscilate!

---
 .../updater/UpdaterForceBalancedPosition.h           | 12 ++++++++++--
 .../updater/moves/MoveNonLinearForceEquilibrium.h    |  1 +
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
index 6cb956e..d890b36 100644
--- a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
+++ b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
@@ -40,8 +40,8 @@ class UpdaterForceBalancedPosition:public AbstractUpdater
 {
 public:
     //! constructor for UpdaterForceBalancedPosition
-    UpdaterForceBalancedPosition(IngredientsType& ing_, double threshold_ ):
-    ing(ing_),threshold(threshold_){};
+    UpdaterForceBalancedPosition(IngredientsType& ing_, double threshold_ , double decreaseFactor_=1.0):
+    ing(ing_),threshold(threshold_),decreaseFactor(decreaseFactor_){};
     
     virtual void initialize(){};
     bool execute();
@@ -61,6 +61,9 @@ class UpdaterForceBalancedPosition:public AbstractUpdater
     
     //! random number generator 
     RandomNumberGenerators rng;
+
+    //! 
+    double decreaseFactor; 
     
 };
 template <class IngredientsType, class moveType>
@@ -87,6 +90,11 @@ bool UpdaterForceBalancedPosition<IngredientsType,moveType>::execute(){
         ing.modifyMolecules().setAge(ing.getMolecules().getAge()+1);
         if (ing.getMolecules().getAge() %1000 == 0 ){
             std::cout << "MCS: " << ing.getMolecules().getAge() << "  and average shift: " << avShift << std::endl;
+            
+        }
+        if (ing.getMolecules().getAge() %100 == 0 ){
+            setRelaxationParameter(move.getRelaxationParameter()*decreaseFactor);
+            threshold*=decreaseFactor;
         }
     }
     std::cout << "Finish equilibration with average shift per cross link < " << avShift << " after " << ing.getMolecules().getAge()-StartMCS <<std::endl;
diff --git a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
index 7ac4771..940a371 100644
--- a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
+++ b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
@@ -169,6 +169,7 @@ class MoveNonLinearForceEquilibrium:public MoveForceEquilibriumBase<MoveNonLinea
                 VectorDouble3 vec(ing.getMolecules()[Neighbors[i].ID].getVector3D()-Neighbors[i].jump-Position);
                 // std::cout <<"MoveNLFE " <<  ing.getMolecules()[Neighbors[i].ID].getVector3D() << " " << Neighbors[i].jump<< " " << Position <<std::endl;
                 force+=EF(vec);
+                //std::cout << this->getIndex()<<" "<< Neighbors[i].ID<< " " <<EF(vec) <<" " << Position << " " << ing.getMolecules()[Neighbors[i].ID].getVector3D()<< std::endl;
             }
             shift=FE(force/(static_cast<double>(number_of_neighbors) ));
         }

From b6ccc60d726cd17d03061850265fa4d96693690f Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Fri, 5 Nov 2021 11:35:28 +0100
Subject: [PATCH 49/70] add the possibility to simulate tendomers with their
 correct distribution of segments in the elastic chains

---
 projects/IdealReferenceForceEquilibrium.cpp | 37 ++++++++++++++++++---
 1 file changed, 32 insertions(+), 5 deletions(-)

diff --git a/projects/IdealReferenceForceEquilibrium.cpp b/projects/IdealReferenceForceEquilibrium.cpp
index 1c79b51..7ef6fa6 100644
--- a/projects/IdealReferenceForceEquilibrium.cpp
+++ b/projects/IdealReferenceForceEquilibrium.cpp
@@ -59,6 +59,10 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 #include <LeMonADE_PM/updater/UpdaterAddStars.h>
 
 
+double probabilityFunction(double n, double p) {
+			return (p*p*n*pow(1-p,n-1.));
+		}
+
 int main(int argc, char* argv[]){
 	try{
 		///////////////////////////////////////////////////////////////////////////////
@@ -170,12 +174,35 @@ int main(int argc, char* argv[]){
 					myIngredients2.modifyMolecules().connect(i,neighbor);
 			}
 		}
+		uint32_t steps(50000);
+		//cummulative distribution function 
+		std::vector<double> CPF((nSegments- nRings)*2,0);
+		//distribution function 
+		std::vector<double>  PF((nSegments- nRings)*2,0);
+
+		double p( (nRings+2. )/( nSegments- nRings - 1.  )  );
+		std::cout << "p=" << p << " n0="<< 1./p<<  std::endl;
+		for (auto i = 0; i < (nSegments- nRings)*2; i++ ){
+			PF[i]=probabilityFunction(i,p);
+			if( i==0 )
+				CPF[i]=PF[i]; 
+			else
+				CPF[i]=CPF[i-1]+PF[i]; 
+		}
+
+		std::vector<uint32_t> invCPF(steps-1,0);
+		for (auto i =1 ; i < steps-1; i++) {
+			uint32_t n=0 ;
+			auto prob=static_cast<double> (i) / static_cast<double>(steps ); 
+			while (  prob > CPF [ n ]  ){ n++;}
+			invCPF[i]=(n-1) + static_cast<uint32_t>(round( (n-(n-1)) *(  prob- CPF[n-1] )/(CPF[n]-CPF[n-1]) ));
+			// std::cout << "invCPF: " <<  prob << " " << invCPF[i] <<" "<< n-1 <<" "<<CPF [ n-1 ]<<" "<< n <<" "<<CPF [ n ]<< std::endl;
+		}
+
         for (auto i=0; i < functionality; i ++) { 
             uint32_t ID(1 + (i+1)*(nSegments+1) -1);
-            // if(gauss == 1 ){
-            //     rng.r250_drand()
-
-            // }
+            if(gauss == 0 )
+				ID = invCPF[rng.r250_rand32() % steps ] +(nSegments +1) *i+1;
             std::cout  << "Fixed monomers= "<< ID <<std::endl;
             myIngredients2.modifyMolecules()[ ID ].setMovableTag(false);  
         }
@@ -184,7 +211,7 @@ int main(int argc, char* argv[]){
 		TaskManager taskmanager2;
 		// taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
 		//read bonds and positions stepwise
-        auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
+        auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold,0.95) ;
         updater->setFilename(feCurve);
         updater->setRelaxationParameter(relaxationParameter);
         auto updater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;

From 6bcb6f9cc679e7a71f3072762bea07724709a28a Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Fri, 12 Nov 2021 17:21:00 +0100
Subject: [PATCH 50/70] allow for analyze without force equilibration

---
 projects/TendomerNetworkForceEquilibrium.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/projects/TendomerNetworkForceEquilibrium.cpp b/projects/TendomerNetworkForceEquilibrium.cpp
index c17f819..f6124e5 100644
--- a/projects/TendomerNetworkForceEquilibrium.cpp
+++ b/projects/TendomerNetworkForceEquilibrium.cpp
@@ -68,7 +68,7 @@ int main(int argc, char* argv[]){
 		double threshold(0.5);
 		double factor(0.995);
 		double stretching_factor(1.0);
-		bool gauss(false);
+		uint32_t gauss(false);
 		
 		bool showHelp = false;
 		auto parser
@@ -163,7 +163,7 @@ int main(int argc, char* argv[]){
 		if ( gauss == 0 ){
 			std::cout << "TendomerNetworkForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) \n";
         	taskmanager2.addUpdater( updater );
-		}else if {gauss == 1 }{
+		}else if (gauss == 1 ){
 			std::cout << "TendomerNetworkForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) \n";
 			taskmanager2.addUpdater( updater2 );
 		}

From 945480c384b08f0808773bc50e4c99e0bd9b0703 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Fri, 12 Nov 2021 17:22:17 +0100
Subject: [PATCH 51/70] adapt the tendomer ideal system to the distribution of
 the elastic segment number

---
 projects/IdealReferenceForceEquilibrium.cpp | 55 +++++++++++++--------
 1 file changed, 34 insertions(+), 21 deletions(-)

diff --git a/projects/IdealReferenceForceEquilibrium.cpp b/projects/IdealReferenceForceEquilibrium.cpp
index 7ef6fa6..e69e80e 100644
--- a/projects/IdealReferenceForceEquilibrium.cpp
+++ b/projects/IdealReferenceForceEquilibrium.cpp
@@ -59,10 +59,9 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 #include <LeMonADE_PM/updater/UpdaterAddStars.h>
 
 
-double probabilityFunction(double n, double p) {
-			return (p*p*n*pow(1-p,n-1.));
-		}
-
+double prob_q(double n, double N, double m) {
+        return (m+1.)/(N-n-1.);
+    }
 int main(int argc, char* argv[]){
 	try{
 		///////////////////////////////////////////////////////////////////////////////
@@ -137,7 +136,7 @@ int main(int argc, char* argv[]){
         myIngredients.modifyBondset().addBFMclassicBondset();
         myIngredients.synchronize();
 		TaskManager taskmanager;
-		taskmanager.addUpdater( new UpdaterAddStars<Ing>(myIngredients,1, nSegments+1 , functionality ),0);
+		taskmanager.addUpdater( new UpdaterAddStars<Ing>(myIngredients,1, 2*nSegments+1 , functionality ),0);
         taskmanager.addAnalyzer(new AnalyzerWriteBfmFile<Ing>("config.bfm", myIngredients, AnalyzerWriteBfmFile<Ing>::APPEND) );
 		taskmanager.initialize();
 		taskmanager.run(1);
@@ -161,7 +160,7 @@ int main(int argc, char* argv[]){
 
         myIngredients2.setNumOfChains              (functionality*1);
 		myIngredients2.setNumOfCrosslinks          (functionality+1);
-		myIngredients2.setNumOfMonomersPerChain    (nSegments);
+		myIngredients2.setNumOfMonomersPerChain    (2*nSegments);
 		myIngredients2.setNumOfMonomersPerCrosslink(1);
 		myIngredients2.setFunctionality            (functionality);
 
@@ -174,22 +173,36 @@ int main(int argc, char* argv[]){
 					myIngredients2.modifyMolecules().connect(i,neighbor);
 			}
 		}
-		uint32_t steps(50000);
-		//cummulative distribution function 
-		std::vector<double> CPF((nSegments- nRings)*2,0);
-		//distribution function 
-		std::vector<double>  PF((nSegments- nRings)*2,0);
-
-		double p( (nRings+2. )/( nSegments- nRings - 1.  )  );
-		std::cout << "p=" << p << " n0="<< 1./p<<  std::endl;
-		for (auto i = 0; i < (nSegments- nRings)*2; i++ ){
-			PF[i]=probabilityFunction(i,p);
-			if( i==0 )
-				CPF[i]=PF[i]; 
-			else
-				CPF[i]=CPF[i-1]+PF[i]; 
+		
+		//probability distribution function 
+        std::cout << "Calculate PDF" << std::endl;
+		std::vector<double>  PF((nSegments-nRings),0);
+        double  sum(0.);
+		for (auto i = 1; i < (nSegments- nRings); i++ ){
+            PF[i]=prob_q(i,nSegments,nRings)*(1.-sum);
+            // std::cout << "probabilityDisti "<<i<< " "<< PF[i]<< std::endl; 
+            sum+=PF[i];
 		}
-
+        //calculate convolution of the probability distributions 
+        //convolution distribution function 
+        std::cout << "Calculate convoluted PDF" << std::endl;
+		std::vector<double>  convPF((nSegments- nRings)*2,0);
+        for (auto i=0; i < 2*(nSegments-nRings);i++){
+            for(auto j=0; j < i ; j++){
+                convPF[i]+=PF[j]*PF[i-j];
+            }
+            // std::cout << "ConvprobabilityDisti "<<i<< " "<< convPF[i]<< std::endl;
+        }
+        //calculate the cummulative distribution function 
+        //cummulative distribution function 
+        std::cout << "Calculate cummulative convoluted PDF" << std::endl;
+		std::vector<double> CPF((nSegments- nRings)*2,0);
+		 for (auto i=1; i < 2*(nSegments-nRings);i++){
+            CPF[i]+=CPF[i-1]+convPF[i];
+        }
+        //calculate the inverse cummulative convoluted probability distribution 
+        std::cout << "Calculate inverse cummulative convoluted PDF" << std::endl;
+        uint32_t steps(50000);
 		std::vector<uint32_t> invCPF(steps-1,0);
 		for (auto i =1 ; i < steps-1; i++) {
 			uint32_t n=0 ;

From b491dd6b03b0bcd356d194ee8504f7f741d8fddd Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Thu, 2 Dec 2021 11:18:49 +0100
Subject: [PATCH 52/70] Add affine deformation to the reference system

---
 .../FeatureCrosslinkConnectionsLookUpIdealReference.h     | 2 +-
 projects/IdealReferenceForceEquilibrium.cpp               | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpIdealReference.h b/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpIdealReference.h
index 063aaba..80543a5 100644
--- a/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpIdealReference.h
+++ b/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpIdealReference.h
@@ -120,7 +120,7 @@ void FeatureCrosslinkConnectionsLookUpIdealReference::fillTables(IngredientsType
 	uint32_t  nSegments(ingredients.getNumOfMonomersPerChain());
 	for (auto i=0; i < ingredients.getMolecules().size(); i++){
 		if (ingredients.getMolecules()[i].getMovableTag() == false) 
-			NeighborIDs.push_back( neighborX(i, i%(nSegments+1), jumpVector) );
+			NeighborIDs.push_back( neighborX(i, ( (i-1)%((2*nSegments+1)) )+1, jumpVector) );
 
 	}
     
diff --git a/projects/IdealReferenceForceEquilibrium.cpp b/projects/IdealReferenceForceEquilibrium.cpp
index e69e80e..b3e3cbc 100644
--- a/projects/IdealReferenceForceEquilibrium.cpp
+++ b/projects/IdealReferenceForceEquilibrium.cpp
@@ -92,7 +92,7 @@ int main(int argc, char* argv[]){
 			| clara::detail::Opt(               gauss, "gauss"                                           ) ["-g"]["--gauss"            ] ("(optional) Deforma with a Gaussian deformation behaviour. Default 1.0 ."     ).optional()
             | clara::detail::Opt(           nSegments, "nSegments"                                       ) ["-n"]["--nSegments"        ] ("(optional) Number of segments for the strand."                               ).optional()
             | clara::detail::Opt(       functionality, "nStrands"                                        ) ["-s"]["--nStrands"         ] ("(optional) Functionality."                                                   ).optional()
-            | clara::detail::Opt(              nRings, "nRings"                                          ) ["-m"]["--nRings"         ] ("(optional) number of rings."                                                   ).optional()
+            | clara::detail::Opt(              nRings, "nRings"                                          ) ["-m"]["--nRings"           ] ("(optional) number of rings."                                                   ).optional()
 			| clara::Help( showHelp );
 		
 	    auto result = parser.parse( clara::Args( argc, argv ) );
@@ -213,16 +213,16 @@ int main(int argc, char* argv[]){
 		}
 
         for (auto i=0; i < functionality; i ++) { 
-            uint32_t ID(1 + (i+1)*(nSegments+1) -1);
+            uint32_t ID(1 + (i+1)*(2*nSegments+1) -1);
             if(gauss == 0 )
-				ID = invCPF[rng.r250_rand32() % steps ] +(nSegments +1) *i+1;
+				ID = invCPF[rng.r250_rand32() % steps ] +(2*nSegments +1) *i+1;
             std::cout  << "Fixed monomers= "<< ID <<std::endl;
             myIngredients2.modifyMolecules()[ ID ].setMovableTag(false);  
         }
 		myIngredients2.synchronize();
 
 		TaskManager taskmanager2;
-		// taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
+		taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
 		//read bonds and positions stepwise
         auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold,0.95) ;
         updater->setFilename(feCurve);

From 66ffaac032cad2a44d1f5be18440150013e95faf Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Thu, 2 Dec 2021 11:19:56 +0100
Subject: [PATCH 53/70] add the second referemce system: two connected stars
 with fixes ends following the TM statistics for the segments

---
 ...onnectionsLookUpIdealDoubleStarReference.h | 192 ++++++++++++
 .../updater/UpdaterAddTMDoubleStars.h         | 278 ++++++++++++++++++
 projects/CMakeLists.txt                       |   3 +
 projects/IdealReference2ForceEquilibrium.cpp  | 202 +++++++++++++
 4 files changed, 675 insertions(+)
 create mode 100644 include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpIdealDoubleStarReference.h
 create mode 100644 include/LeMonADE_PM/updater/UpdaterAddTMDoubleStars.h
 create mode 100644 projects/IdealReference2ForceEquilibrium.cpp

diff --git a/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpIdealDoubleStarReference.h b/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpIdealDoubleStarReference.h
new file mode 100644
index 0000000..218c82e
--- /dev/null
+++ b/include/LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpIdealDoubleStarReference.h
@@ -0,0 +1,192 @@
+/*--------------------------------------------------------------------------------
+    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 LENONADE_PM_FEATURE_FEATURECROSSLINKCONNECTIONLOOKUPIDEALREFERENCE_H
+#define LENONADE_PM_FEATURE_FEATURECROSSLINKCONNECTIONLOOKUPIDEALREFERENCE_H
+
+#include <LeMonADE/feature/Feature.h>
+#include <LeMonADE/feature/FeatureReactiveBonds.h>
+#include <LeMonADE/updater/moves/MoveBase.h>
+#include <LeMonADE/utility/Vector3D.h>
+#include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
+#include <LeMonADE_PM/utility/neighborX.h>
+
+
+/*****************************************************************************/
+/**
+ * @file
+ * @date   2021/04/01
+ * @author Toni
+ *
+ * @class FeatureCrosslinkConnectionsLookUpIdealDoubleStarReference
+ * @brief Creates a lookup for crosslink IDs and their neighbors
+ * @details For calculating the equilibrium position of crosslinks in a 
+ * a phantom network, one needs to know the crosslink neighbors and the number 
+ * of segments between them.  
+ * 
+ **/
+/*****************************************************************************/
+///////////////////////////////////////////////////////////////////////////////
+//DEFINITION OF THE CLASS TEMPLATE   	                                ///////
+//Implementation of the members below					///////
+///////////////////////////////////////////////////////////////////////////////
+
+class FeatureCrosslinkConnectionsLookUpIdealDoubleStarReference : public Feature {
+  
+public:
+  	//! This Feature requires a monomer_extensions.
+	typedef LOKI_TYPELIST_1(MonomerReactivity) monomer_extensions;
+
+	//! check bas connect move - always true 
+	template<class IngredientsType>
+	bool checkMove(const IngredientsType& ingredients, const MoveBase& move) const { return true;};
+
+	//! synchronize lookup table
+	template<class IngredientsType>
+	void synchronize(IngredientsType& ingredients) {
+	  	fillTables(ingredients);
+	};
+    //! set the jump vector 
+	void setCrossLinkNeighborJump(uint32_t CrossLinkID, uint32_t idx, VectorDouble3 vec) {
+		if ( idx > CrossLinkNeighbors.at(CrossLinkID).size() ){
+			std::stringstream errormessage;
+			errormessage << "FeatureCrosslinkConnectionsLookUpTendomers::setCrossLinkNeighborJump neighbor idx  " << idx <<" is to high.";
+			throw std::runtime_error(errormessage.str());
+		}
+		CrossLinkNeighbors.at(CrossLinkID)[idx].jump=vec;
+	}
+	//!getter function for the neighboring crosslinks
+	std::vector<neighborX> getCrossLinkNeighborIDs(uint32_t CrossLinkID) const{
+		#ifdef DEBUG
+		if (CrossLinkNeighbors.find(CrossLinkID) == CrossLinkNeighbors.end()){
+			std::stringstream errormessage;
+			errormessage << "FeatureCrosslinkConnectionsLookUpIdealDoubleStarReference::getCrossLinkNeighborIDs Cross Link ID " << CrossLinkID <<" does not exist.";
+			throw std::runtime_error(errormessage.str());
+		}
+		#endif
+		return CrossLinkNeighbors.at(CrossLinkID);
+	};
+
+	//!get the ID of crosslinks (determined by nConnections>3 and connected to another crosslink)
+	const std::vector<uint32_t>& getCrosslinkIDs() const {return crosslinkIDs;}
+
+private:
+  //! convinience function to fill all tables 
+  template<class IngredientsType>
+  void fillTables(IngredientsType& ingredients);
+  //!key - CrossLink ID; value - neighboring cross link and the number of segments to them
+  std::map<uint32_t,std::vector< neighborX > > CrossLinkNeighbors;
+  //!ID for crosslinks
+  std::vector<uint32_t> crosslinkIDs;
+};
+/**
+ *@details  Create look up table 
+ **/
+template<class IngredientsType>
+void FeatureCrosslinkConnectionsLookUpIdealDoubleStarReference::fillTables(IngredientsType& ingredients){
+
+	const typename IngredientsType::molecules_type& molecules=ingredients.getMolecules();
+	std::cout << "FeatureCrosslinkConnectionsLookUpIdealDoubleStarReference::fillTables" <<std::endl;
+	crosslinkIDs.resize(0);
+    crosslinkIDs.push_back(0);
+	CrossLinkNeighbors.clear();
+    // std::vector<neighborX> NeighborIDs;
+    // VectorDouble3 jumpVector(0.,0.,0.);
+	// uint32_t  nSegments(ingredients.getNumOfMonomersPerChain());
+	// for (auto i=0; i < ingredients.getMolecules().size(); i++){
+	// 	if (ingredients.getMolecules()[i].getMovableTag() == false) 
+	// 		NeighborIDs.push_back( neighborX(i, ( (i-1)%((2*nSegments+1)) )+1, jumpVector) );
+
+	// }
+    
+    // // for( auto i=0; i <ingredients.getFunctionality() ;i++){
+    // //     NeighborIDs.push_back( neighborX(1 + (i+1)*(nSegments+1) -1, nSegments, jumpVector) );
+    // //     std::vector<neighborX> NeighborIDs1;
+    // //     // NeighborIDs1
+    // // }
+    // CrossLinkNeighbors[0]=NeighborIDs;
+    
+    
+    
+    for (uint32_t i = 0 ;i < molecules.size();i++){
+		//find next crosslink
+		if( molecules.getNumLinks(i) > 2 ){
+			//temporary storage for the neighboring crosslinks
+			std::vector<neighborX> NeighborIDs;
+			auto posX(molecules[i].getVector3D());
+			for (size_t j = 0 ; j < molecules.getNumLinks(i); j++){
+				uint32_t tail(i);
+				uint32_t head(molecules.getNeighborIdx(i,j));
+				VectorDouble3 posHead(molecules[head].getVector3D());
+				VectorDouble3 bond(LemonadeDistCalcs::MinImageVector( posX,posHead,ingredients));
+				if(bond.getLength() > std::sqrt(10)){
+					std::stringstream errormessage;
+					errormessage << "FeatureCrosslinkConnectionsLookUp: Wrong bond " << bond << " between " << i << " and " << head << "\n";
+					throw std::runtime_error(errormessage.str());
+				}
+				VectorDouble3 jumpVector(posHead-bond-posX); // tracks if one bond jumps across periodic images 
+				
+				//direct connection of two cross links
+				if ( molecules.getNumLinks(head) > 2 || molecules[head].getMovableTag()==false ) {
+					NeighborIDs.push_back( neighborX(head, 1, jumpVector) );
+				}else{ 
+					uint32_t nSegments(1);
+					//cross links are connected by a chain 
+					while( molecules.getNumLinks(head) == 2 && head != i ){
+						//find next head 
+						for (size_t k = 0 ; k < molecules.getNumLinks(head); k++){
+							uint32_t NextMonomer( molecules.getNeighborIdx(head,k));
+							if ( NextMonomer != tail ) {
+								tail=head;
+								head=NextMonomer; 
+								break;
+							}
+						}
+						posHead=molecules[head].getVector3D();
+						auto posTail=molecules[tail].getVector3D();
+						bond=LemonadeDistCalcs::MinImageVector( posTail,posHead,ingredients);
+						jumpVector+=(posHead-bond-posTail); // tracks if one bond jumps across periodic images 
+						nSegments++;
+						//a cross link has more than 2 connections
+						if( molecules.getNumLinks(head) > 2 || molecules[head].getMovableTag()==false ){
+							NeighborIDs.push_back(neighborX(head, nSegments, jumpVector));
+							break;
+						}
+					}
+				}	
+			}
+			CrossLinkNeighbors[i]=NeighborIDs;
+			// if(NeighborIDs.size()>0)
+			crosslinkIDs.push_back(i);
+		}
+	}
+
+
+	std::cout << "FeatureCrosslinkConnectionsLookUpIdealDoubleStarReference::fillTables.done" <<std::endl; 
+}
+#endif /*LENONADE_PM_FEATURE_FEATURECROSSLINKCONNECTIONLOOKUPIDEALREFERENCE_H*/
\ No newline at end of file
diff --git a/include/LeMonADE_PM/updater/UpdaterAddTMDoubleStars.h b/include/LeMonADE_PM/updater/UpdaterAddTMDoubleStars.h
new file mode 100644
index 0000000..2590107
--- /dev/null
+++ b/include/LeMonADE_PM/updater/UpdaterAddTMDoubleStars.h
@@ -0,0 +1,278 @@
+/*--------------------------------------------------------------------------------
+    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
+    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_UPDATER_SETUP_TMDOUBLESTARSAB
+#define LEMONADE_UPDATER_SETUP_TMDOUBLESTARSAB
+/**
+ * @file
+ *
+ * @class UpdaterAddTMDoubleStars
+ *
+ * @brief Updater to create a solution of monodisperse branched stars.
+ *
+ * @details This is a simple implementation of a system setup starting from an empty ingredients
+ * or a system with some monomers inside. This updater requires FeatureAttributes.
+ * Two tags are added to the monomers in alternating manner, usually needed for GPU computing.  // not realized in this first attempt
+ *                                                                                              // RS, 05 Nov 2019, but presumably 29 July 2020
+ *
+ * @tparam IngredientsType
+ *
+ * @param ingredients_ The system, holding either an empty simulation box for system setup
+ * or a prefilled ingredients where the stars shall be added
+ * @param NStar_ number of stars that are added to ingredients
+ * @param NMonoPerStar_ number of monomers in each star
+ * @param NMonoPerBranch_ number of monomers in each branch (excluding central monomer)
+ * @param NBranchPerStar_ number of branches in each star
+ * @param type1_ attribute tag of "even" monomers
+ * @param type2_ attribute tag of "odd" monomers
+ **/
+
+// #include <LeMonADE/updater/UpdaterAbstractCreate.h>
+#include <LeMonADE/utility/Vector3D.h>
+#include <cmath>
+
+#include <LeMonADE_PM/updater/UpdaterAbstractCreateAllBondVectors.h>
+
+template<class IngredientsType>
+class UpdaterAddTMDoubleStars: public UpdaterAbstractCreateAllBonds<IngredientsType>
+{
+  typedef UpdaterAbstractCreateAllBonds<IngredientsType> BaseClass;
+
+public:
+  UpdaterAddTMDoubleStars(IngredientsType& ingredients_, uint32_t NStar_, 
+                  uint32_t NMonoPerBranch_, uint32_t nRings_, uint32_t NBranchPerStar_);
+
+  virtual void initialize();
+  virtual bool execute();
+  virtual void cleanup();
+
+  //! getter function for number of stars
+  const int32_t getNStar() const {return NStar;}
+
+  //! getter function for number of monomers in branch
+  const int32_t getNMonoPerBranch() const {return NMonoPerBranch;}
+
+  //! getter function for number of branches in stars
+  const int32_t getNBranchPerStar() const {return NBranchPerStar;}
+
+  //! getter function for calculated density
+  const double getDensity() const {return density;}
+
+private:
+  // provide access to functions of UpdaterAbstractCreate used in this updater
+  using BaseClass::ingredients;
+  using BaseClass::addMonomerToParent;
+  using BaseClass::addSingleMonomer;
+  using BaseClass::linearizeSystem;
+  double prob_q(double n, double N, double m) {
+        return (m+1.)/(N-n-1.);
+    }
+    //! number of rings 
+    uint32_t nRings;
+    //! number of stars in the box
+    uint32_t NStar;
+
+    //! number of monomers in a branch
+    uint32_t NMonoPerBranch;  
+
+    //! number of branches in a star
+    uint32_t NBranchPerStar;
+
+    //! lattice occupation density
+    double density;
+
+    //! bool for execution
+    bool wasExecuted;
+
+    // adds a chain of with nMonomers monomers to the parentID 
+    void createChain(uint parentID, uint32_t nMonomers);
+    // add a chain to the system at a random positions 
+    void createChain(uint32_t nMonomers);
+
+    //! 
+    const uint32_t steps;
+    //! 
+    std::vector<uint32_t> invCPF;
+    // random number generator (globally seeded)
+    RandomNumberGenerators rng;
+};
+
+/**
+* @brief Constructor handling the new systems paramters
+* 
+* @param ingredients_ a reference to the IngredientsType - mainly the system
+* @param NStar_ number of double stars to be added in the system instead of solvent
+* @param NBranchPerStar_ number of branches in each star
+* @param NMonoPerBranch_ number of monomers in each branch (excluding central monomer)
+*/
+
+
+template < class IngredientsType >
+UpdaterAddTMDoubleStars<IngredientsType>::UpdaterAddTMDoubleStars(
+    IngredientsType& ingredients_, 
+    uint32_t NStar_, 
+    uint32_t NMonoPerBranch_, 
+    uint32_t nRings_,
+    uint32_t NBranchPerStar_
+    ):
+    BaseClass(ingredients_), NStar(NStar_), NMonoPerBranch(NMonoPerBranch_), nRings(nRings_), NBranchPerStar(NBranchPerStar_), 
+    density(0.0), wasExecuted(false),steps(50000)
+    {
+        invCPF.resize(steps-1,0);
+    }
+
+/**
+* @brief initialise function, calculate the target density to compare with at the end.
+*
+* @tparam IngredientsType Features used in the system. See Ingredients.
+*/
+template < class IngredientsType >
+void UpdaterAddTMDoubleStars<IngredientsType>::initialize(){
+  std::cout << "initialize UpdaterAddTMDoubleStars" << std::endl;
+
+
+		//probability distribution function 
+        std::cout << "Calculate PDF" << std::endl;
+		std::vector<double>  PF((NMonoPerBranch-nRings),0);
+        double  sum(0.);
+		for (auto i = 1; i < (NMonoPerBranch- nRings); i++ ){
+            PF[i]=prob_q(i,NMonoPerBranch,nRings)*(1.-sum);
+            // std::cout << "probabilityDisti "<<i<< " "<< PF[i]<< std::endl; 
+            sum+=PF[i];
+		}
+        //calculate convolution of the probability distributions 
+        //convolution distribution function 
+        std::cout << "Calculate convoluted PDF" << std::endl;
+		std::vector<double>  convPF((NMonoPerBranch- nRings)*2,0);
+        for (auto i=0; i < 2*(NMonoPerBranch-nRings);i++){
+            for(auto j=0; j < i ; j++){
+                convPF[i]+=PF[j]*PF[i-j];
+            }
+            // std::cout << "ConvprobabilityDisti "<<i<< " "<< convPF[i]<< std::endl;
+        }
+        //calculate the cummulative distribution function 
+        //cummulative distribution function 
+        std::cout << "Calculate cummulative convoluted PDF" << std::endl;
+		std::vector<double> CPF((NMonoPerBranch- nRings)*2,0);
+		 for (auto i=1; i < 2*(NMonoPerBranch-nRings);i++){
+            CPF[i]+=CPF[i-1]+convPF[i];
+        }
+        //calculate the inverse cummulative convoluted probability distribution 
+        std::cout << "Calculate inverse cummulative convoluted PDF" << std::endl;
+		for (auto i =1 ; i < steps-1; i++) {
+			uint32_t n=0 ;
+			auto prob=static_cast<double> (i) / static_cast<double>(steps ); 
+			while (  prob > CPF [ n ]  ){ n++;}
+			invCPF[i]=(n-1) + static_cast<uint32_t>(round( (n-(n-1)) *(  prob- CPF[n-1] )/(CPF[n]-CPF[n-1]) ));
+			// std::cout << "invCPF: " <<  prob << " " << invCPF[i] <<" "<< n-1 <<" "<<CPF [ n-1 ]<<" "<< n <<" "<<CPF [ n ]<< std::endl;
+		}
+
+  execute();
+}
+
+
+template < class IngredientsType >
+void UpdaterAddTMDoubleStars<IngredientsType>::createChain(uint32_t parentID, uint32_t nMonomers){
+    auto ID(parentID);
+    for (auto i=0; i< nMonomers ; i++){
+        addMonomerToParent(parentID,1);
+        parentID=(ingredients.getMolecules().size()-1);
+    }
+}
+
+template < class IngredientsType >
+void UpdaterAddTMDoubleStars<IngredientsType>::createChain(uint32_t nMonomers){
+    addSingleMonomer(1);
+    createChain(ingredients.getMolecules().size()-1,nMonomers-1);
+}
+/**
+* @brief Execution of the system creation
+*
+* @tparam IngredientsType Features used in the system. See Ingredients.
+*/
+template < class IngredientsType >
+bool UpdaterAddTMDoubleStars<IngredientsType>::execute(){
+    if(wasExecuted) return true;
+    std::cout << "execute UpdaterAddTMDoubleStars" << std::endl;
+    //initial number of monomer in the system 
+    auto nMonomers(ingredients.getMolecules().size());
+    //keeps track on the monomers which are added during the procedure 
+    auto nAddedMonomers(0);
+    for(uint32_t i=0;i<NStar;i++){
+        auto mainChainLength(invCPF[rng.r250_rand32() % steps ]);
+        nAddedMonomers+=mainChainLength;
+        std::cout << "UpdaterAddTMDoubleStars: mainChainLength " << mainChainLength <<std::endl;
+        //the next two variables are needed for adding NBranchPerStar-1 chains to this monomers 
+        //chain start 
+        auto start(0);
+        if (ingredients.getMolecules().size()>0 )
+            start=(ingredients.getMolecules().size()-1);
+        std::cout << "Start: " <<  start <<std::endl; 
+        createChain(mainChainLength);
+        //chain end
+        auto end(ingredients.getMolecules().size()-1);
+        std::cout << "End: " <<  end <<std::endl; 
+        for (uint32_t j=0; j < NBranchPerStar-1; j++){
+            auto chainLength(invCPF[rng.r250_rand32() % steps ]+1);
+            nAddedMonomers+=chainLength;
+            createChain(start,chainLength);
+            ingredients.modifyMolecules()[ ingredients.getMolecules().size()-1 ].setMovableTag(false);  
+        }
+        for (uint32_t j=0; j < NBranchPerStar-1; j++){
+            auto chainLength(invCPF[rng.r250_rand32() % steps ]+1);
+            nAddedMonomers+=chainLength;
+            createChain(end,chainLength);
+            ingredients.modifyMolecules()[ ingredients.getMolecules().size()-1 ].setMovableTag(false);  
+        }
+    }
+
+    ingredients.synchronize();
+    if(nAddedMonomers != (ingredients.getMolecules().size()-nMonomers)){
+        std::cout << "initial number of monomers: "<< nMonomers << std::endl;
+        std::cout << "final number of monomers: "<< ingredients.getMolecules().size() << std::endl;
+        std::cout << "difference should be: "<< nAddedMonomers << " but is "<<  (ingredients.getMolecules().size()-nMonomers)<< std::endl;
+        throw std::runtime_error("UpdaterAddTMDoubleStars: number of monomers in molecules does not match the calculated number of monomers!");
+    }else{
+        std::cout << "number of monomers in the system  =" << (ingredients.getMolecules().size())<<std::endl;
+        std::cout << "added number of monomers to the system  =" << (ingredients.getMolecules().size()-nMonomers)<<std::endl;
+        wasExecuted=true;
+        return true;
+    }
+}
+
+/**
+* @brief Standard clean up.
+*
+* @tparam IngredientsType Features used in the system. See Ingredients.
+*/
+template < class IngredientsType >
+void UpdaterAddTMDoubleStars<IngredientsType>::cleanup(){
+
+}
+
+
+#endif /* LEMONADE_UPDATER_SETUP_TMDOUBLESTARSAB */
diff --git a/projects/CMakeLists.txt b/projects/CMakeLists.txt
index c0ab6fd..d791ea0 100644
--- a/projects/CMakeLists.txt
+++ b/projects/CMakeLists.txt
@@ -22,5 +22,8 @@ target_link_libraries(AnalyzeMolecularWeight LeMonADE )
 add_executable(IdealReferenceForceEquilibrium IdealReferenceForceEquilibrium.cpp)
 target_link_libraries(IdealReferenceForceEquilibrium LeMonADE )
 
+add_executable(IdealReference2ForceEquilibrium IdealReference2ForceEquilibrium.cpp)
+target_link_libraries(IdealReference2ForceEquilibrium LeMonADE )
+
 # add_executable(IntramolecularReactions IntramolecularReactions.cpp)
 # target_link_libraries(IntramolecularReactions LeMonADE CommandlineParser )
\ No newline at end of file
diff --git a/projects/IdealReference2ForceEquilibrium.cpp b/projects/IdealReference2ForceEquilibrium.cpp
new file mode 100644
index 0000000..9322e1f
--- /dev/null
+++ b/projects/IdealReference2ForceEquilibrium.cpp
@@ -0,0 +1,202 @@
+/*--------------------------------------------------------------------------------
+    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/>.
+
+--------------------------------------------------------------------------------*/
+
+/****************************************************************************** 
+ * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
+ * author: Toni Müller
+ * email: mueller-toni@ipfdd.de
+ * project: LeMonADE-Phantom Modulus
+ *****************************************************************************/
+#include <iostream>
+#include <vector>
+#include <bitset>
+
+#include <LeMonADE/core/Ingredients.h>
+#include <LeMonADE/updater/UpdaterReadBfmFile.h>
+#include <LeMonADE/analyzer/AnalyzerWriteBfmFile.h>
+#include <LeMonADE/feature/FeatureMoleculesIO.h>
+#include <LeMonADE/feature/FeatureReactiveBonds.h>
+#include <LeMonADE/feature/FeatureFixedMonomers.h>
+#include <LeMonADE/feature/FeatureBox.h>
+
+#include <LeMonADE/utility/TaskManager.h>
+#include <LeMonADE/utility/RandomNumberGenerators.h>
+#include <LeMonADE/feature/FeatureSystemInformationLinearMeltWithCrosslinker.h>
+
+#include <extern/catchorg/clara/clara.hpp>
+
+#include <LeMonADE_PM/updater/UpdaterForceBalancedPosition.h>
+#include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
+#include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
+#include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
+#include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpIdealDoubleStarReference.h>
+#include <LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h>
+#include <LeMonADE_PM/updater/UpdaterAffineDeformation.h>
+#include <LeMonADE_PM/updater/UpdaterAddTMDoubleStars.h>
+
+int main(int argc, char* argv[]){
+	try{
+		///////////////////////////////////////////////////////////////////////////////
+		///parse options///
+		// std::string inputBFM("init.bfm");
+		std::string outputDataPos("CrosslinkPosition.dat");
+		std::string outputDataDist("ChainExtensionDistribution.dat");
+		std::string feCurve("");
+		double relaxationParameter(10.);
+		double threshold(0.5);
+		double factor(0.995);
+		double stretching_factor(1.0);
+		uint32_t gauss(0);
+
+        uint32_t nSegments(16);
+        uint32_t functionality(4);
+		uint32_t nRings(0);
+
+		bool showHelp = false;
+		auto parser
+			// = clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"            ] ("(required)Input filename of the bfm file"                                    ).required()
+			= clara::detail::Opt(       outputDataPos, "outputDataPos (=CrosslinkPosition.dat)"          ) ["-o"]["--outputPos"        ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
+			| clara::detail::Opt(      outputDataDist, "outputDataDist (=ChainExtensionDistribution.dat)") ["-c"]["--outputDist"       ] ("(optional) Output filename of the chain extension distribution."             ).optional()
+			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"        ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
+			| clara::detail::Opt(   stretching_factor, "stretching_factor (=1)"                          ) ["-l"]["--stretching_factor"] ("(optional) Stretching factor for uniaxial deformation. Default 1.0 ."        ).optional()
+			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"          ] ("(optional) Force-Extension curve. Default \"\"."                             ).required()
+			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"            ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
+			| clara::detail::Opt(               gauss, "gauss"                                           ) ["-g"]["--gauss"            ] ("(optional) Deforma with a Gaussian deformation behaviour. Default 1.0 ."     ).optional()
+            | clara::detail::Opt(           nSegments, "nSegments"                                       ) ["-n"]["--nSegments"        ] ("(optional) Number of segments for the strand."                               ).optional()
+            | clara::detail::Opt(       functionality, "nStrands"                                        ) ["-s"]["--nStrands"         ] ("(optional) Functionality."                                                   ).optional()
+            | clara::detail::Opt(              nRings, "nRings"                                          ) ["-m"]["--nRings"           ] ("(optional) number of rings."                                                   ).optional()
+			| clara::Help( showHelp );
+		
+	    auto result = parser.parse( clara::Args( argc, argv ) );
+	    
+	    if( !result ) {
+	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
+	      exit(1);
+	    }else if(showHelp == true){
+	    //   std::cout << "Simulator to connect linear chains with single monomers of certain functionality"<< std::endl;
+	      parser.writeToStream(std::cout);
+	      exit(0);
+	    }else{
+	      std::cout << "outputData            : " << outputDataPos          << std::endl;
+	      std::cout << "outputDataDist        : " << outputDataDist         << std::endl;
+	    //   std::cout << "inputBFM              : " << inputBFM               << std::endl; 
+	      std::cout << "threshold             : " << threshold              << std::endl; 
+		  std::cout << "feCurve               : " << feCurve                << std::endl;
+		  std::cout << "gauss                 : " << gauss                  << std::endl;
+		  std::cout << "stretching_factor     : " << stretching_factor      << std::endl;
+          std::cout << "nSegments             : " << nSegments              << std::endl;
+          std::cout << "functionality         : " << functionality          << std::endl;
+          std::cout << "nRings                : " << nRings          << std::endl;
+	    }
+		RandomNumberGenerators rng;
+		// rng.seedDefaultValuesAll();
+		rng.seedAll();
+		///////////////////////////////////////////////////////////////////////////////
+		///end options parsing
+		///////////////////////////////////////////////////////////////////////////////
+		//Read in th last Config 
+		typedef LOKI_TYPELIST_2(FeatureFixedMonomers,FeatureMoleculesIO) Features;
+		typedef ConfigureSystem<VectorInt3,Features, functionality> Config;
+		typedef Ingredients<Config> Ing;
+		Ing myIngredients;
+        myIngredients.setBoxX(256);
+		myIngredients.setBoxY(256);
+		myIngredients.setBoxZ(256);
+		myIngredients.setPeriodicX(1);
+		myIngredients.setPeriodicY(1);
+		myIngredients.setPeriodicZ(1);
+        myIngredients.modifyBondset().addBFMclassicBondset();
+        myIngredients.synchronize();
+		TaskManager taskmanager;
+		taskmanager.addUpdater( new UpdaterAddTMDoubleStars<Ing>(myIngredients,1, nSegments, nRings, functionality ),0);
+        taskmanager.addAnalyzer(new AnalyzerWriteBfmFile<Ing>("config.bfm", myIngredients, AnalyzerWriteBfmFile<Ing>::APPEND) );
+		taskmanager.initialize();
+		taskmanager.run(1);
+		taskmanager.cleanup();
+       
+		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
+		//the foce equilibrium is reached off lattice ( no integer values for the positions )
+        typedef LOKI_TYPELIST_3(FeatureBox, FeatureCrosslinkConnectionsLookUpIdealDoubleStarReference ,FeatureFixedMonomers) Features2;
+		typedef ConfigureSystem<VectorDouble3,Features2, functionality> Config2;
+		typedef Ingredients<Config2> Ing2;
+		Ing2 myIngredients2;
+		
+		myIngredients2.setBoxX(myIngredients.getBoxX());
+		myIngredients2.setBoxY(myIngredients.getBoxY());
+		myIngredients2.setBoxZ(myIngredients.getBoxZ());
+		myIngredients2.setPeriodicX(myIngredients.isPeriodicX());
+		myIngredients2.setPeriodicY(myIngredients.isPeriodicY());
+		myIngredients2.setPeriodicZ(myIngredients.isPeriodicZ());
+		myIngredients2.modifyMolecules().resize(myIngredients.getMolecules().size());
+		myIngredients2.modifyMolecules().setAge(myIngredients.getMolecules().getAge());
+		
+		for(size_t i = 0; i< myIngredients.getMolecules().size();i++){
+            myIngredients2.modifyMolecules()[i].setMovableTag(myIngredients.modifyMolecules()[i].getMovableTag());
+			myIngredients2.modifyMolecules()[i].modifyVector3D()=myIngredients.getMolecules()[i].getVector3D();
+			for (size_t j = 0 ; j < myIngredients.getMolecules().getNumLinks(i);j++){
+				uint32_t neighbor(myIngredients.getMolecules().getNeighborIdx(i,j));
+				if( ! myIngredients2.getMolecules().areConnected(i,neighbor) )
+					myIngredients2.modifyMolecules().connect(i,neighbor);
+			}
+		}
+		
+		myIngredients2.synchronize();
+
+		TaskManager taskmanager2;
+		taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
+		//read bonds and positions stepwise
+        auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold,0.95) ;
+        updater->setFilename(feCurve);
+        updater->setRelaxationParameter(relaxationParameter);
+        auto updater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
+		if ( gauss == 0 ){
+			std::cout << "IdealReferenceForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) \n";
+        	taskmanager2.addUpdater( updater );
+		}else if( gauss == 1 ){
+			std::cout << "IdealReferenceForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) \n";
+			taskmanager2.addUpdater( updater2 );
+		}
+        
+		taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
+		//initialize and run
+		taskmanager2.initialize();
+		taskmanager2.run();
+		if(gauss > 1)
+			taskmanager2.run(1);
+		taskmanager2.cleanup();
+		
+	}
+	catch(std::exception& e){
+		std::cerr<<"Error:\n"
+		<<e.what()<<std::endl;
+	}
+	catch(...){
+		std::cerr<<"Error: unknown exception\n";
+	}
+	
+	return 0;
+}

From dc4e88359b7ab51271effd37e5e7271c6c4c5d97 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Thu, 2 Dec 2021 11:48:03 +0100
Subject: [PATCH 54/70] bugfix in projects/IdealReference2ForceEquilibrium.cpp
 and add affine deformation for the standard force equilibrium

---
 projects/ForceEquilibrium.cpp                | 69 +++++++++-----------
 projects/IdealReference2ForceEquilibrium.cpp |  4 +-
 2 files changed, 33 insertions(+), 40 deletions(-)

diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index e92e1fd..403598b 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -52,7 +52,7 @@ along with LeMonADE.  If not, see <http://www.gnu.org/licenses/>.
 #include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
 #include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUp.h>
 #include <LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h>
-
+#include <LeMonADE_PM/updater/UpdaterAffineDeformation.h>
 
 int main(int argc, char* argv[]){
 	try{
@@ -68,18 +68,20 @@ int main(int argc, char* argv[]){
 		double stepwidth(1.0);
 		double minConversion(50.0);
 		bool custom(true);
+        double stretching_factor(1.0);
 		
 		bool showHelp = false;
 		auto parser
-			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"          ] ("(required)Input filename of the bfm file"                                    ).required()
+			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"            ] ("(required)Input filename of the bfm file"                                    ).required()
 			// | clara::detail::Opt(     inputConnection, "inputConnection (=BondCreationBreaking.dat)"     ) ["-d"]["--inputConnection"] ("used for the time development of the topology. "                             ).required()
-			| clara::detail::Opt(       outputDataPos, "outputDataPos (=CrosslinkPosition.dat)"          ) ["-o"]["--outputPos"      ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
-			| clara::detail::Opt(      outputDataDist, "outputDataDist (=ChainExtensionDistribution.dat)") ["-c"]["--outputDist"     ] ("(optional) Output filename of the chain extension distribution."             ).optional()
-			| clara::detail::Opt(           stepwidth, "stepwidth"                                       ) ["-s"]["--stepwidth"      ] ("(optional) Width for the increase in percentage. Default: 1%."               ).optional()
-			| clara::detail::Opt(       minConversion, "minConversion"                                   ) ["-u"]["--minConversion"  ] ("(optional) Minimum conversion to be read in. Default: 50%."                  ).optional()
-			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"      ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
-			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"        ] ("(optional) Force-Extension curve. Default \"\"."                             ).optional()
-			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"          ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
+			| clara::detail::Opt(       outputDataPos, "outputDataPos (=CrosslinkPosition.dat)"          ) ["-o"]["--outputPos"        ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
+			| clara::detail::Opt(      outputDataDist, "outputDataDist (=ChainExtensionDistribution.dat)") ["-c"]["--outputDist"       ] ("(optional) Output filename of the chain extension distribution."             ).optional()
+			| clara::detail::Opt(           stepwidth, "stepwidth"                                       ) ["-s"]["--stepwidth"        ] ("(optional) Width for the increase in percentage. Default: 1%."               ).optional()
+			| clara::detail::Opt(       minConversion, "minConversion"                                   ) ["-u"]["--minConversion"    ] ("(optional) Minimum conversion to be read in. Default: 50%."                  ).optional()
+			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"        ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
+            | clara::detail::Opt(   stretching_factor, "stretching_factor (=1)"                          ) ["-l"]["--stretching_factor"] ("(optional) Stretching factor for uniaxial deformation. Default 1.0 ."        ).optional()
+			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"          ] ("(optional) Force-Extension curve. Default \"\"."                             ).optional()
+			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"            ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
 			| clara::Help( showHelp );
 		
 	    auto result = parser.parse( clara::Args( argc, argv ) );
@@ -100,6 +102,7 @@ int main(int argc, char* argv[]){
 	      std::cout << "minConversion         : " << minConversion          << std::endl;
 	      std::cout << "threshold             : " << threshold              << std::endl; 
 		  std::cout << "feCurve               : " << feCurve                << std::endl;
+          std::cout << "stretching_factor     : " << stretching_factor      << std::endl;
 	    }
 		if ( feCurve.empty() ) custom=false;
 		
@@ -156,35 +159,25 @@ int main(int argc, char* argv[]){
 		}
 		myIngredients2.synchronize();
 		
-		
-
-		if(custom){
-			TaskManager taskmanager2;
-			//read bonds and positions stepwise
-			// taskmanager2.addUpdater( new UpdaterReadCrosslinkConnections<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
-			std::cout << "Use custom force-extension curve\n";
-			auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold);
-			forceUpdater->setFilename(feCurve);
-			forceUpdater->setRelaxationParameter(relaxationParameter);	
-			taskmanager2.addUpdater( forceUpdater );
-			taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
-			//initialize and run
-			taskmanager2.initialize();
-			taskmanager2.run(1);
-			taskmanager2.cleanup();
-		} else {
-			TaskManager taskmanager2;
-			//read bonds and positions stepwise
-			// taskmanager2.addUpdater( new UpdaterReadCrosslinkConnections<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
-			std::cout << "Use gaussian force-extension relation\n";
-			auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold);
-			taskmanager2.addUpdater( forceUpdater );
-			taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
-			//initialize and run
-			taskmanager2.initialize();
-			taskmanager2.run(1);
-			taskmanager2.cleanup();
-		}
+        TaskManager taskmanager2;
+        taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
+        //read bonds and positions stepwise
+        auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold);
+        forceUpdater->setFilename(feCurve);
+        forceUpdater->setRelaxationParameter(relaxationParameter);	
+        auto forceUpdater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold);
+        if(custom){
+            std::cout << "Use custom force-extension curve\n";
+            taskmanager2.addUpdater( forceUpdater );
+        }else{
+            std::cout << "Use gaussian force-extension relation\n";
+            taskmanager2.addUpdater( forceUpdater2 );
+        }
+        taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
+        //initialize and run
+        taskmanager2.initialize();
+        taskmanager2.run(1);
+        taskmanager2.cleanup();
 	}
 	catch(std::exception& e){
 		std::cerr<<"Error:\n"
diff --git a/projects/IdealReference2ForceEquilibrium.cpp b/projects/IdealReference2ForceEquilibrium.cpp
index 9322e1f..b361051 100644
--- a/projects/IdealReference2ForceEquilibrium.cpp
+++ b/projects/IdealReference2ForceEquilibrium.cpp
@@ -120,7 +120,7 @@ int main(int argc, char* argv[]){
 		///////////////////////////////////////////////////////////////////////////////
 		//Read in th last Config 
 		typedef LOKI_TYPELIST_2(FeatureFixedMonomers,FeatureMoleculesIO) Features;
-		typedef ConfigureSystem<VectorInt3,Features, functionality> Config;
+		typedef ConfigureSystem<VectorInt3,Features, 7> Config;
 		typedef Ingredients<Config> Ing;
 		Ing myIngredients;
         myIngredients.setBoxX(256);
@@ -141,7 +141,7 @@ int main(int argc, char* argv[]){
 		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
 		//the foce equilibrium is reached off lattice ( no integer values for the positions )
         typedef LOKI_TYPELIST_3(FeatureBox, FeatureCrosslinkConnectionsLookUpIdealDoubleStarReference ,FeatureFixedMonomers) Features2;
-		typedef ConfigureSystem<VectorDouble3,Features2, functionality> Config2;
+		typedef ConfigureSystem<VectorDouble3,Features2, 7> Config2;
 		typedef Ingredients<Config2> Ing2;
 		Ing2 myIngredients2;
 		

From 9c098ed68f097bc2bd8886c33a11eb21cda2476b Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Thu, 2 Dec 2021 12:10:57 +0100
Subject: [PATCH 55/70] add damping factor as command line option

---
 projects/ForceEquilibrium.cpp                | 7 +++++--
 projects/TendomerNetworkForceEquilibrium.cpp | 7 +++++--
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index 403598b..93457b5 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -69,6 +69,7 @@ int main(int argc, char* argv[]){
 		double minConversion(50.0);
 		bool custom(true);
         double stretching_factor(1.0);
+        double dampingfactor(1.0);
 		
 		bool showHelp = false;
 		auto parser
@@ -82,6 +83,7 @@ int main(int argc, char* argv[]){
             | clara::detail::Opt(   stretching_factor, "stretching_factor (=1)"                          ) ["-l"]["--stretching_factor"] ("(optional) Stretching factor for uniaxial deformation. Default 1.0 ."        ).optional()
 			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"          ] ("(optional) Force-Extension curve. Default \"\"."                             ).optional()
 			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"            ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
+            | clara::detail::Opt(       dampingfactor, "damping (=1)"                                    ) ["-d"]["--damping"          ] ("(optional) Damping factor after 1E3MCS. Default 1.0."                        ).optional()
 			| clara::Help( showHelp );
 		
 	    auto result = parser.parse( clara::Args( argc, argv ) );
@@ -99,6 +101,7 @@ int main(int argc, char* argv[]){
 	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
 	    //   std::cout << "inputConnection       : " << inputConnection        << std::endl; 
 	      std::cout << "stepwidth             : " << stepwidth              << std::endl;
+          std::cout << "dampingfactor         : " << dampingfactor          << std::endl;
 	      std::cout << "minConversion         : " << minConversion          << std::endl;
 	      std::cout << "threshold             : " << threshold              << std::endl; 
 		  std::cout << "feCurve               : " << feCurve                << std::endl;
@@ -162,10 +165,10 @@ int main(int argc, char* argv[]){
         TaskManager taskmanager2;
         taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
         //read bonds and positions stepwise
-        auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold);
+        auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold,dampingfactor);
         forceUpdater->setFilename(feCurve);
         forceUpdater->setRelaxationParameter(relaxationParameter);	
-        auto forceUpdater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold);
+        auto forceUpdater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold,dampingfactor);
         if(custom){
             std::cout << "Use custom force-extension curve\n";
             taskmanager2.addUpdater( forceUpdater );
diff --git a/projects/TendomerNetworkForceEquilibrium.cpp b/projects/TendomerNetworkForceEquilibrium.cpp
index f6124e5..2f857a5 100644
--- a/projects/TendomerNetworkForceEquilibrium.cpp
+++ b/projects/TendomerNetworkForceEquilibrium.cpp
@@ -69,6 +69,7 @@ int main(int argc, char* argv[]){
 		double factor(0.995);
 		double stretching_factor(1.0);
 		uint32_t gauss(false);
+        double dampingfactor(1.0);
 		
 		bool showHelp = false;
 		auto parser
@@ -80,6 +81,7 @@ int main(int argc, char* argv[]){
 			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"          ] ("(optional) Force-Extension curve. Default \"\"."                             ).required()
 			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"            ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
 			| clara::detail::Opt(               gauss, "gauss"                                           ) ["-g"]["--gauss"            ] ("(optional) Deforma with a Gaussian deformation behaviour. Default 1.0 ."     ).optional()
+            | clara::detail::Opt(       dampingfactor, "damping (=1)"                                    ) ["-d"]["--damping"          ] ("(optional) Damping factor after 1E3MCS. Default 1.0."                        ).optional()
 			| clara::Help( showHelp );
 		
 	    auto result = parser.parse( clara::Args( argc, argv ) );
@@ -96,6 +98,7 @@ int main(int argc, char* argv[]){
 	      std::cout << "outputDataDist        : " << outputDataDist         << std::endl;
 	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
 	      std::cout << "threshold             : " << threshold              << std::endl; 
+          std::cout << "dampingfactor         : " << dampingfactor          << std::endl;
 		  std::cout << "feCurve               : " << feCurve                << std::endl;
 		  std::cout << "gauss                 : " << gauss                  << std::endl;
 		  std::cout << "stretching_factor     : " << stretching_factor      << std::endl;
@@ -156,10 +159,10 @@ int main(int argc, char* argv[]){
 		TaskManager taskmanager2;
 		taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
 		//read bonds and positions stepwise
-        auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
+        auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold, dampingfactor) ;
         updater->setFilename(feCurve);
         updater->setRelaxationParameter(relaxationParameter);
-        auto updater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
+        auto updater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold,dampingfactor) ;
 		if ( gauss == 0 ){
 			std::cout << "TendomerNetworkForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) \n";
         	taskmanager2.addUpdater( updater );

From 639b358dfdf52e780f84d0f7f57ebe5349c8a876 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Thu, 2 Dec 2021 12:11:18 +0100
Subject: [PATCH 56/70] bugfix: MoveNonLinearForceEquilibrium.h

---
 .../LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
index 940a371..8f9d9ed 100644
--- a/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
+++ b/include/LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h
@@ -195,7 +195,7 @@ void MoveNonLinearForceEquilibrium::createTable(){
             std::string line;
             getline(in, line);
             //ignore comments and blank lines 
-            while (line.at(0) == '#' || line.empty() ) //go to next line
+            if (line.at(0) == '#' || line.empty() ) //go to next line
                 continue;
             //read data 
             double force, extension;

From dcd5bc1d06c9af11ce20e6722a4759608e2624cb Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 8 Dec 2021 09:03:01 +0100
Subject: [PATCH 57/70] Preequilibrate with Gaussian force extension and
 afterwards turn on the non-linear

---
 projects/ForceEquilibrium.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index 93457b5..c7a4f27 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -174,6 +174,7 @@ int main(int argc, char* argv[]){
             taskmanager2.addUpdater( forceUpdater );
         }else{
             std::cout << "Use gaussian force-extension relation\n";
+            taskmanager2.addUpdater( new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, 0.001); );
             taskmanager2.addUpdater( forceUpdater2 );
         }
         taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));

From 67326f7f444b6a31a3456de2c130d912714fd060 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 8 Dec 2021 09:04:49 +0100
Subject: [PATCH 58/70] erase bug...

---
 projects/ForceEquilibrium.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index c7a4f27..3c3264c 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -174,7 +174,7 @@ int main(int argc, char* argv[]){
             taskmanager2.addUpdater( forceUpdater );
         }else{
             std::cout << "Use gaussian force-extension relation\n";
-            taskmanager2.addUpdater( new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, 0.001); );
+            taskmanager2.addUpdater( new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, 0.001) );
             taskmanager2.addUpdater( forceUpdater2 );
         }
         taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));

From 1a997911953e24490b47157bdcf4abe75612e292 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 8 Dec 2021 09:08:36 +0100
Subject: [PATCH 59/70] bugfix2

---
 projects/ForceEquilibrium.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index 3c3264c..d620d94 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -171,10 +171,10 @@ int main(int argc, char* argv[]){
         auto forceUpdater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold,dampingfactor);
         if(custom){
             std::cout << "Use custom force-extension curve\n";
+            taskmanager2.addUpdater( new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, 0.001) );
             taskmanager2.addUpdater( forceUpdater );
         }else{
             std::cout << "Use gaussian force-extension relation\n";
-            taskmanager2.addUpdater( new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, 0.001) );
             taskmanager2.addUpdater( forceUpdater2 );
         }
         taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));

From c114c6654b463aa1aef8183ccd3b84b80c2603a5 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 8 Dec 2021 10:06:49 +0100
Subject: [PATCH 60/70] equilibrate first with the nonlinear function (if
 desired), then deform, and then equilibrate again

---
 projects/ForceEquilibrium.cpp | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index d620d94..804c4ad 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -163,15 +163,16 @@ int main(int argc, char* argv[]){
 		myIngredients2.synchronize();
 		
         TaskManager taskmanager2;
-        taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
-        //read bonds and positions stepwise
         auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold,dampingfactor);
         forceUpdater->setFilename(feCurve);
         forceUpdater->setRelaxationParameter(relaxationParameter);	
         auto forceUpdater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold,dampingfactor);
+        if(custom){
+            taskmanager2.addUpdater( forceUpdater );
+        taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
+        //read bonds and positions stepwise
         if(custom){
             std::cout << "Use custom force-extension curve\n";
-            taskmanager2.addUpdater( new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, 0.001) );
             taskmanager2.addUpdater( forceUpdater );
         }else{
             std::cout << "Use gaussian force-extension relation\n";

From 02b63b11540174057254cec577b75c7e0d8713d0 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 8 Dec 2021 10:07:48 +0100
Subject: [PATCH 61/70] fix

---
 projects/ForceEquilibrium.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index 804c4ad..14aff75 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -167,7 +167,7 @@ int main(int argc, char* argv[]){
         forceUpdater->setFilename(feCurve);
         forceUpdater->setRelaxationParameter(relaxationParameter);	
         auto forceUpdater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold,dampingfactor);
-        if(custom){
+        if(custom)
             taskmanager2.addUpdater( forceUpdater );
         taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
         //read bonds and positions stepwise

From b653f84b8ed97d6f7096f1daed407638d0ddd60b Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 8 Dec 2021 10:16:58 +0100
Subject: [PATCH 62/70] need to move the affine deformationfrom the initialize
 to the execute

---
 include/LeMonADE_PM/updater/UpdaterAffineDeformation.h | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
index 4629f78..85d1575 100644
--- a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
+++ b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
@@ -52,8 +52,8 @@ class UpdaterAffineDeformation:public AbstractUpdater
                   << "stretching factor in yz = " << stretching_factor_XY << "\n";
     };
     
-    virtual void initialize();
-    virtual bool execute(){return false;};
+    virtual void initialize(){};
+    virtual bool execute();
     virtual void cleanup(){};  
 
 private:
@@ -69,7 +69,7 @@ class UpdaterAffineDeformation:public AbstractUpdater
     }
 };
 template <class IngredientsType>
-void UpdaterAffineDeformation<IngredientsType>::initialize(){
+bool UpdaterAffineDeformation<IngredientsType>::execute(){
     std::cout << "UpdaterAffineDeformation<IngredientsType>::initialize():"<< std::endl;
     //adjusting the box size is not neccessary, because it is used only once in the FeatureCrosslinkConnections*
     //there the jump vectors are calculated

From 3be2f2180260260d56fde6ffb38ec7808124da7e Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 8 Dec 2021 10:36:02 +0100
Subject: [PATCH 63/70] slowly increase the stretching factor to achieve a
 conversoin for large values

---
 projects/ForceEquilibrium.cpp | 27 ++++++++++++++++-----------
 1 file changed, 16 insertions(+), 11 deletions(-)

diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index 14aff75..c518be3 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -167,18 +167,23 @@ int main(int argc, char* argv[]){
         forceUpdater->setFilename(feCurve);
         forceUpdater->setRelaxationParameter(relaxationParameter);	
         auto forceUpdater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold,dampingfactor);
-        if(custom)
-            taskmanager2.addUpdater( forceUpdater );
-        taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
-        //read bonds and positions stepwise
-        if(custom){
-            std::cout << "Use custom force-extension curve\n";
-            taskmanager2.addUpdater( forceUpdater );
-        }else{
-            std::cout << "Use gaussian force-extension relation\n";
-            taskmanager2.addUpdater( forceUpdater2 );
+        
+        for (auto i=1; i < stretching_factor ; i++){
+            if (i>1)
+                taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, static_cast<double>(i)/static_cast<double>(i-1.)) );
+            //read bonds and positions stepwise
+            if(custom){
+                std::cout << "Use custom force-extension curve\n";
+                taskmanager2.addUpdater( forceUpdater );
+            }else{
+                std::cout << "Use gaussian force-extension relation\n";
+                taskmanager2.addUpdater( forceUpdater2 );
+            }
+            std::stringstream out1,out2;
+            out1 << "l" << i << "_" << outputDataPos;
+            out2 << "l" << i << "_" << outputDataDist;
+            taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,out1.str(), out1.str()));
         }
-        taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
         //initialize and run
         taskmanager2.initialize();
         taskmanager2.run(1);

From e3db13949523940d138c0bc543b68d1767b56fac Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 8 Dec 2021 11:05:24 +0100
Subject: [PATCH 64/70] remove the decrease of the threshold with decreasing
 relaxation parameter

---
 include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
index d890b36..bdd70e0 100644
--- a/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
+++ b/include/LeMonADE_PM/updater/UpdaterForceBalancedPosition.h
@@ -94,7 +94,7 @@ bool UpdaterForceBalancedPosition<IngredientsType,moveType>::execute(){
         }
         if (ing.getMolecules().getAge() %100 == 0 ){
             setRelaxationParameter(move.getRelaxationParameter()*decreaseFactor);
-            threshold*=decreaseFactor;
+            // threshold*=decreaseFactor;
         }
     }
     std::cout << "Finish equilibration with average shift per cross link < " << avShift << " after " << ing.getMolecules().getAge()-StartMCS <<std::endl;

From e29178b457e6cff1e0abdb370d855ad32346c500 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Wed, 8 Dec 2021 12:22:06 +0100
Subject: [PATCH 65/70] correct output filename

---
 projects/ForceEquilibrium.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index c518be3..bd702df 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -182,7 +182,7 @@ int main(int argc, char* argv[]){
             std::stringstream out1,out2;
             out1 << "l" << i << "_" << outputDataPos;
             out2 << "l" << i << "_" << outputDataDist;
-            taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,out1.str(), out1.str()));
+            taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,out1.str(), out2.str()));
         }
         //initialize and run
         taskmanager2.initialize();

From 4e918eada0c5106e9bfd89ea6ef2dd1ea619e25b Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Thu, 9 Dec 2021 18:21:19 +0100
Subject: [PATCH 66/70] need to change the workflow for the uniaxial
 deformation

---
 .../analyzer/AnalyzerEquilbratedPosition.h    |  6 +++
 .../updater/UpdaterAffineDeformation.h        |  6 +++
 projects/ForceEquilibrium.cpp                 | 37 +++++++++++++------
 3 files changed, 37 insertions(+), 12 deletions(-)

diff --git a/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h b/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h
index 5bcfde1..339a013 100644
--- a/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h
+++ b/include/LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h
@@ -76,6 +76,12 @@ template < class IngredientsType > class AnalyzerEquilbratedPosition : public Ab
 
 	//! just collects the id and the position for the cross links 
 	std::vector<std::vector<double> > CollectAveragePositions();
+
+    //! setter for the filenames
+    void setFilenames(std::string outAvPosBasename_, std::string outDistBasename_ ){
+        outAvPosBasename= outAvPosBasename_;
+        outDistBasename=outDistBasename_;
+    }
 };
 
 /*************************************************************************
diff --git a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
index 85d1575..3a716ec 100644
--- a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
+++ b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
@@ -56,6 +56,12 @@ class UpdaterAffineDeformation:public AbstractUpdater
     virtual bool execute();
     virtual void cleanup(){};  
 
+    //! setter function for the stretching factor 
+    void setStretchingFactor(double stretching_factor_ ) {
+        stretching_factor=stretching_factor_;
+        stretching_factor_XY = 1./std::sqrt(stretching_factor) ; 
+    }
+
 private:
     //!copy of the main container for the system informations 
     IngredientsType& ing;
diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index bd702df..753bbc9 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -162,32 +162,45 @@ int main(int argc, char* argv[]){
 		}
 		myIngredients2.synchronize();
 		
-        TaskManager taskmanager2;
+        // TaskManager taskmanager2;
         auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold,dampingfactor);
         forceUpdater->setFilename(feCurve);
         forceUpdater->setRelaxationParameter(relaxationParameter);	
         auto forceUpdater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold,dampingfactor);
-        
+        auto uniaxialDeformation = new UpdaterAffineDeformation<Ing2>(myIngredients2, 1.);
+        auto analyzer = new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos,outputDataDist);
+        forceUpdater->initialize();
+        forceUpdater2->initialize();
+        uniaxialDeformation->initialize();
+        analyzer->initialize();
+
         for (auto i=1; i < stretching_factor ; i++){
-            if (i>1)
-                taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, static_cast<double>(i)/static_cast<double>(i-1.)) );
+            if (i>1){
+                uniaxialDeformation->setStretchingFactor(static_cast<double>(i)/static_cast<double>(i-1.));
+                uniaxialDeformation->execute();
+            }
             //read bonds and positions stepwise
             if(custom){
                 std::cout << "Use custom force-extension curve\n";
-                taskmanager2.addUpdater( forceUpdater );
+                // taskmanager2.addUpdater( forceUpdater );
+                forceUpdater->execute();
             }else{
                 std::cout << "Use gaussian force-extension relation\n";
-                taskmanager2.addUpdater( forceUpdater2 );
+                // taskmanager2.addUpdater( forceUpdater2 );
+                forceUpdater2->execute();
             }
             std::stringstream out1,out2;
-            out1 << "l" << i << "_" << outputDataPos;
+            out1 << "l" << i << "_" << outputDataPos;      
             out2 << "l" << i << "_" << outputDataDist;
-            taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,out1.str(), out2.str()));
+            analyzer->setFilenames(out1.str(), out2.str());
+            analyzer->execute();
+            // taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,out1.str(), out2.str()));
         }
-        //initialize and run
-        taskmanager2.initialize();
-        taskmanager2.run(1);
-        taskmanager2.cleanup();
+        forceUpdater->cleanup();
+        forceUpdater2->cleanup();
+        uniaxialDeformation->cleanup();
+        analyzer->cleanup();
+        // taskmanager2.cleanup();
 	}
 	catch(std::exception& e){
 		std::cerr<<"Error:\n"

From 564dc7a2366afd5d1ec093605c1efe1ca2f3e615 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Mon, 13 Dec 2021 10:45:24 +0100
Subject: [PATCH 67/70] clean up the file ForceEquilibrium.cpp

---
 projects/ForceEquilibrium.cpp | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index 753bbc9..c64fcd1 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -162,7 +162,6 @@ int main(int argc, char* argv[]){
 		}
 		myIngredients2.synchronize();
 		
-        // TaskManager taskmanager2;
         auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold,dampingfactor);
         forceUpdater->setFilename(feCurve);
         forceUpdater->setRelaxationParameter(relaxationParameter);	
@@ -182,11 +181,9 @@ int main(int argc, char* argv[]){
             //read bonds and positions stepwise
             if(custom){
                 std::cout << "Use custom force-extension curve\n";
-                // taskmanager2.addUpdater( forceUpdater );
                 forceUpdater->execute();
             }else{
                 std::cout << "Use gaussian force-extension relation\n";
-                // taskmanager2.addUpdater( forceUpdater2 );
                 forceUpdater2->execute();
             }
             std::stringstream out1,out2;
@@ -194,13 +191,11 @@ int main(int argc, char* argv[]){
             out2 << "l" << i << "_" << outputDataDist;
             analyzer->setFilenames(out1.str(), out2.str());
             analyzer->execute();
-            // taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,out1.str(), out2.str()));
         }
         forceUpdater->cleanup();
         forceUpdater2->cleanup();
         uniaxialDeformation->cleanup();
         analyzer->cleanup();
-        // taskmanager2.cleanup();
 	}
 	catch(std::exception& e){
 		std::cerr<<"Error:\n"

From 955c7016f5dfadea9229b3f96eb05e37373e0259 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Mon, 17 Jan 2022 21:59:23 +0100
Subject: [PATCH 68/70] add possibility for a prestrain factor in the three
 spatial directions

---
 .../updater/UpdaterAffineDeformation.h        | 21 ++++-
 projects/ForceEquilibrium.cpp                 | 92 ++++++++++++-------
 projects/TendomerNetworkForceEquilibrium.cpp  | 17 +++-
 3 files changed, 90 insertions(+), 40 deletions(-)

diff --git a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
index 3a716ec..cbb49d1 100644
--- a/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
+++ b/include/LeMonADE_PM/updater/UpdaterAffineDeformation.h
@@ -45,11 +45,20 @@ class UpdaterAffineDeformation:public AbstractUpdater
 {
 public:
     //! constructor for UpdaterAffineDeformation
-    UpdaterAffineDeformation(IngredientsType& ing_, double stretching_factor_ ):
-    ing(ing_),stretching_factor(stretching_factor_),stretching_factor_XY(1./std::sqrt(stretching_factor)){
+    UpdaterAffineDeformation(IngredientsType& ing_, double stretching_factor_, double prestrain_factorX_=1, double prestrain_factorY_=1, double prestrain_factorZ_=1 ):
+    ing(ing_),
+    stretching_factor(stretching_factor_),
+    stretching_factor_XY(1./std::sqrt(stretching_factor)),
+    prestrain_factorX(prestrain_factorX_),
+    prestrain_factorY(prestrain_factorY_),
+    prestrain_factorZ(prestrain_factorZ_)
+    {
         std::cout << "UpdaterAffineDeformation::constructor:\n"
                   << "stretching factor =       " << stretching_factor    << "\n"
-                  << "stretching factor in yz = " << stretching_factor_XY << "\n";
+                  << "stretching factor in yz = " << stretching_factor_XY << "\n"
+                  << "prestrain factor in x = " << prestrain_factorX << "\n"
+                  << "prestrain factor in y = " << prestrain_factorY << "\n"
+                  << "prestrain factor in z = " << prestrain_factorZ << "\n";
     };
     
     virtual void initialize(){};
@@ -69,9 +78,13 @@ class UpdaterAffineDeformation:public AbstractUpdater
     //! threshold for the certainty 
     double stretching_factor;
     double stretching_factor_XY;
+    //! factors for a prestrain or a correction factor for the elastic inbalance in the spatial direction 
+    double prestrain_factorX,prestrain_factorY,prestrain_factorZ;
     VectorDouble3 deform( VectorDouble3 vec ){
 
-        return VectorDouble3(vec.getX()*stretching_factor,vec.getY()*stretching_factor_XY,vec.getZ()*stretching_factor_XY);
+        return VectorDouble3(vec.getX()*stretching_factor   *prestrain_factorX,
+                             vec.getY()*stretching_factor_XY*prestrain_factorY,
+                             vec.getZ()*stretching_factor_XY*prestrain_factorZ);
     }
 };
 template <class IngredientsType>
diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index c64fcd1..c8c4534 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -70,6 +70,9 @@ int main(int argc, char* argv[]){
 		bool custom(true);
         double stretching_factor(1.0);
         double dampingfactor(1.0);
+		double prestrainFactorX(1.0);
+		double prestrainFactorY(1.0);
+		double prestrainFactorZ(1.0);
 		
 		bool showHelp = false;
 		auto parser
@@ -84,10 +87,13 @@ int main(int argc, char* argv[]){
 			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"          ] ("(optional) Force-Extension curve. Default \"\"."                             ).optional()
 			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"            ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
             | clara::detail::Opt(       dampingfactor, "damping (=1)"                                    ) ["-d"]["--damping"          ] ("(optional) Damping factor after 1E3MCS. Default 1.0."                        ).optional()
+			| clara::detail::Opt(    prestrainFactorX, "prestrainFactorX (=1)"                           ) ["-x"]["--prestrainFactorX" ] ("(optional) Prestrain factor in X. Default 1.0."                              ).optional()
+			| clara::detail::Opt(    prestrainFactorY, "prestrainFactorY (=1)"                           ) ["-y"]["--prestrainFactorY" ] ("(optional) Prestrain factor in Y. Default 1.0."                              ).optional()
+			| clara::detail::Opt(    prestrainFactorZ, "prestrainFactorZ (=1)"                           ) ["-z"]["--prestrainFactorZ" ] ("(optional) Prestrain factor in Z. Default 1.0."                              ).optional()
 			| clara::Help( showHelp );
 		
 	    auto result = parser.parse( clara::Args( argc, argv ) );
-	    
+	    if ( feCurve.empty() ) custom=false;
 	    if( !result ) {
 	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
 	      exit(1);
@@ -99,15 +105,18 @@ int main(int argc, char* argv[]){
 	      std::cout << "outputData            : " << outputDataPos          << std::endl;
 	      std::cout << "outputDataDist        : " << outputDataDist         << std::endl;
 	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
-	    //   std::cout << "inputConnection       : " << inputConnection        << std::endl; 
+	      std::cout << "custom FE             : " << custom                 << std::endl; 
 	      std::cout << "stepwidth             : " << stepwidth              << std::endl;
           std::cout << "dampingfactor         : " << dampingfactor          << std::endl;
 	      std::cout << "minConversion         : " << minConversion          << std::endl;
 	      std::cout << "threshold             : " << threshold              << std::endl; 
 		  std::cout << "feCurve               : " << feCurve                << std::endl;
           std::cout << "stretching_factor     : " << stretching_factor      << std::endl;
+		  std::cout << "prestrainFactorX      : " << prestrainFactorX       << std::endl;
+		  std::cout << "prestrainFactorY      : " << prestrainFactorY       << std::endl;
+		  std::cout << "prestrainFactorZ      : " << prestrainFactorZ       << std::endl;
 	    }
-		if ( feCurve.empty() ) custom=false;
+		
 		
 
 		RandomNumberGenerators rng;
@@ -163,39 +172,58 @@ int main(int argc, char* argv[]){
 		myIngredients2.synchronize();
 		
         auto forceUpdater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold,dampingfactor);
-        forceUpdater->setFilename(feCurve);
+        if(custom)
+            forceUpdater->setFilename(feCurve);
         forceUpdater->setRelaxationParameter(relaxationParameter);	
         auto forceUpdater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold,dampingfactor);
-        auto uniaxialDeformation = new UpdaterAffineDeformation<Ing2>(myIngredients2, 1.);
+        auto uniaxialDeformation = new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor,prestrainFactorX,prestrainFactorY,prestrainFactorZ);
+    
         auto analyzer = new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos,outputDataDist);
-        forceUpdater->initialize();
-        forceUpdater2->initialize();
-        uniaxialDeformation->initialize();
-        analyzer->initialize();
-
-        for (auto i=1; i < stretching_factor ; i++){
-            if (i>1){
-                uniaxialDeformation->setStretchingFactor(static_cast<double>(i)/static_cast<double>(i-1.));
-                uniaxialDeformation->execute();
-            }
-            //read bonds and positions stepwise
-            if(custom){
-                std::cout << "Use custom force-extension curve\n";
-                forceUpdater->execute();
-            }else{
-                std::cout << "Use gaussian force-extension relation\n";
-                forceUpdater2->execute();
-            }
-            std::stringstream out1,out2;
-            out1 << "l" << i << "_" << outputDataPos;      
-            out2 << "l" << i << "_" << outputDataDist;
-            analyzer->setFilenames(out1.str(), out2.str());
-            analyzer->execute();
+		
+        TaskManager taskmanager2;
+        taskmanager2.addUpdater( uniaxialDeformation,0 );
+        //read bonds and positions stepwise
+        if(custom){
+            std::cout << "Use custom force-extension curve\n";
+            taskmanager2.addUpdater( forceUpdater );
+        }else{
+            std::cout << "Use gaussian force-extension relation\n";
+            taskmanager2.addUpdater( forceUpdater2 );
         }
-        forceUpdater->cleanup();
-        forceUpdater2->cleanup();
-        uniaxialDeformation->cleanup();
-        analyzer->cleanup();
+        taskmanager2.addAnalyzer(analyzer);
+        //initialize and run
+		taskmanager2.initialize();
+		taskmanager2.run(1);
+		taskmanager2.cleanup();
+
+        // forceUpdater->initialize();
+        // forceUpdater2->initialize();
+        // uniaxialDeformation->initialize();
+        // analyzer->initialize();
+
+        // for (auto i=1; i < stretching_factor ; i++){
+        //     if (i>1){
+        //         uniaxialDeformation->setStretchingFactor(static_cast<double>(i)/static_cast<double>(i-1.));
+        //         uniaxialDeformation->execute();
+        //     }
+        //     //read bonds and positions stepwise
+        //     if(custom){
+        //         std::cout << "Use custom force-extension curve\n";
+        //         forceUpdater->execute();
+        //     }else{
+        //         std::cout << "Use gaussian force-extension relation\n";
+        //         forceUpdater2->execute();
+        //     }
+        //     std::stringstream out1,out2;
+        //     out1 << "l" << i << "_" << outputDataPos;      
+        //     out2 << "l" << i << "_" << outputDataDist;
+        //     analyzer->setFilenames(out1.str(), out2.str());
+        //     analyzer->execute();
+        // }
+        // forceUpdater->cleanup();
+        // forceUpdater2->cleanup();
+        // uniaxialDeformation->cleanup();
+        // analyzer->cleanup();
 	}
 	catch(std::exception& e){
 		std::cerr<<"Error:\n"
diff --git a/projects/TendomerNetworkForceEquilibrium.cpp b/projects/TendomerNetworkForceEquilibrium.cpp
index 2f857a5..e921313 100644
--- a/projects/TendomerNetworkForceEquilibrium.cpp
+++ b/projects/TendomerNetworkForceEquilibrium.cpp
@@ -70,6 +70,9 @@ int main(int argc, char* argv[]){
 		double stretching_factor(1.0);
 		uint32_t gauss(false);
         double dampingfactor(1.0);
+		double prestrainFactorX(1.0);
+		double prestrainFactorY(1.0);
+		double prestrainFactorZ(1.0);
 		
 		bool showHelp = false;
 		auto parser
@@ -82,6 +85,9 @@ int main(int argc, char* argv[]){
 			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"            ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
 			| clara::detail::Opt(               gauss, "gauss"                                           ) ["-g"]["--gauss"            ] ("(optional) Deforma with a Gaussian deformation behaviour. Default 1.0 ."     ).optional()
             | clara::detail::Opt(       dampingfactor, "damping (=1)"                                    ) ["-d"]["--damping"          ] ("(optional) Damping factor after 1E3MCS. Default 1.0."                        ).optional()
+			| clara::detail::Opt(    prestrainFactorX, "prestrainFactorX (=1)"                           ) ["-x"]["--prestrainFactorX" ] ("(optional) Prestrain factor in X. Default 1.0."                              ).optional()
+			| clara::detail::Opt(    prestrainFactorY, "prestrainFactorY (=1)"                           ) ["-y"]["--prestrainFactorY" ] ("(optional) Prestrain factor in Y. Default 1.0."                              ).optional()
+			| clara::detail::Opt(    prestrainFactorZ, "prestrainFactorZ (=1)"                           ) ["-z"]["--prestrainFactorZ" ] ("(optional) Prestrain factor in Z. Default 1.0."                              ).optional()
 			| clara::Help( showHelp );
 		
 	    auto result = parser.parse( clara::Args( argc, argv ) );
@@ -102,6 +108,9 @@ int main(int argc, char* argv[]){
 		  std::cout << "feCurve               : " << feCurve                << std::endl;
 		  std::cout << "gauss                 : " << gauss                  << std::endl;
 		  std::cout << "stretching_factor     : " << stretching_factor      << std::endl;
+		  std::cout << "prestrainFactorX      : " << prestrainFactorX       << std::endl;
+		  std::cout << "prestrainFactorY      : " << prestrainFactorY       << std::endl;
+		  std::cout << "prestrainFactorZ      : " << prestrainFactorZ       << std::endl;
 	    }
 		RandomNumberGenerators rng;
 		// rng.seedDefaultValuesAll();
@@ -157,14 +166,14 @@ int main(int argc, char* argv[]){
 		myIngredients2.synchronize();
 
 		TaskManager taskmanager2;
-		taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor),0 );
+		taskmanager2.addUpdater( new UpdaterAffineDeformation<Ing2>(myIngredients2, stretching_factor,prestrainFactorX,prestrainFactorY,prestrainFactorZ),0 );
 		//read bonds and positions stepwise
         auto updater = new UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold, dampingfactor) ;
-        updater->setFilename(feCurve);
-        updater->setRelaxationParameter(relaxationParameter);
         auto updater2 = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold,dampingfactor) ;
 		if ( gauss == 0 ){
-			std::cout << "TendomerNetworkForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) \n";
+            updater->setFilename(feCurve);
+            updater->setRelaxationParameter(relaxationParameter);
+            std::cout << "TendomerNetworkForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) \n";
         	taskmanager2.addUpdater( updater );
 		}else if (gauss == 1 ){
 			std::cout << "TendomerNetworkForceEquilibrium: add UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) \n";

From 3dace3640d0bf200b4505daf04d64484ad956ce4 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Mon, 31 Jan 2022 10:20:15 +0100
Subject: [PATCH 69/70] clean up the repo

---
 .../AnalyzerConnectionDistributions.h         | 128 ------------
 .../AnalyzerIntramolecularReactions.h         | 168 ----------------
 projects/ForceEquilibrium.cpp                 |  31 +--
 projects/IdealReference2ForceEquilibrium.cpp  |   3 +-
 projects/IdealReferenceForceEquilibrium.cpp   |  29 ++-
 projects/IntramolecularReactions.cpp          | 170 ----------------
 projects/TendomerNetworkExtractActivePart.cpp |   6 +-
 ...etworkForceEquilibriumConversionSeries.cpp | 186 ------------------
 8 files changed, 19 insertions(+), 702 deletions(-)
 delete mode 100644 include/LeMonADE_PM/analyzer/AnalyzerConnectionDistributions.h
 delete mode 100644 include/LeMonADE_PM/analyzer/AnalyzerIntramolecularReactions.h
 delete mode 100644 projects/IntramolecularReactions.cpp
 delete mode 100644 projects/TendomerNetworkForceEquilibriumConversionSeries.cpp

diff --git a/include/LeMonADE_PM/analyzer/AnalyzerConnectionDistributions.h b/include/LeMonADE_PM/analyzer/AnalyzerConnectionDistributions.h
deleted file mode 100644
index 2e43939..0000000
--- a/include/LeMonADE_PM/analyzer/AnalyzerConnectionDistributions.h
+++ /dev/null
@@ -1,128 +0,0 @@
-/****************************************************************************** 
- * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
- * author: Toni Müller
- * email: mueller-toni@ipfdd.de
- * project: Phantom Modulus
- *****************************************************************************/
-
-#ifndef LEMONADE_PM_ANALYZER_ANALYZERINTRAMOLECULARREACTIONS_H
-#define LEMONADE_PM_ANALYZER_ANALYZERINTRAMOLECULARREACTIONS_H
-
-#include <string>
-
-#include <LeMonADE/utility/Vector3D.h>
-#include <LeMonADE/analyzer/AbstractAnalyzer.h>
-#include <LeMonADE/utility/ResultFormattingTools.h>
-#include <LeMonADE/utility/MonomerGroup.h>
-#include <LeMonADE/utility/DistanceCalculation.h>
-
-/*************************************************************************
- * definition of AnalyzerIntramolecularReactions class
- * ***********************************************************************/
-
-/**
- * @file
- *
- * @class AnalyzerIntramolecularReactions
- *
- * @brief Analyzes the connection distribution of chains and cross linker for the whole system, 
- * the gel and the active part of the gel.
- *
- * @tparam IngredientsType Ingredients class storing all system information( e.g. monomers, bonds, etc).
- */
-template < class IngredientsType > class AnalyzerIntramolecularReactions : public AbstractAnalyzer
-{
-
-private:
-	//! typedef for the underlying container holding the monomers
-	typedef typename IngredientsType::molecules_type molecules_type;
-
-	//! reference to the complete system
-	const IngredientsType& ingredients;
-public:
-	//! constructor
-	AnalyzerIntramolecularReactions(const IngredientsType& ingredients_, std::string outputFilename_);
-
-	//! destructor. does nothing
-	virtual ~AnalyzerIntramolecularReactions(){}
-
-	//! Initializes data structures. Called by TaskManager::initialize()
-	virtual void initialize();
-
-	//! Calculates the Rg2 for the current timestep. Called by TaskManager::execute()
-	virtual bool execute();
-
-	//! Writes the final results to file
-	virtual void cleanup();
-	
-	//! name of output file for the average is outputFilePrefix_averages.dat  
-	std::string outputFilename;
-
-	//! save the current values in Rg2TimeSeriesX, etc., to disk
-	void dumpData();
-
-	//! calculates the distance between crosslinks and stores IDs, distance vector and chainID
-	std::vector< std::vector<double> >  CalculateDistance();
-
-	//! just collects the id and the position for the cross links 
-	std::vector<std::vector<int> > CollectAveragePositions();
-};
-
-/*************************************************************************
- * implementation of memebers
- * ***********************************************************************/
-
-/**
- * @param ing reference to the object holding all information of the system
- * */
-template<class IngredientsType>
-AnalyzerIntramolecularReactions<IngredientsType>::AnalyzerIntramolecularReactions(
-	const IngredientsType& ingredients_, std::string outputFilename_)
-:ingredients(ingredients_)
-,outputFilename(outputFilename_)
-{}
-////////////////////////////////////////////////////////////////////////////////
-/**
- * @brief calculates the average distances between monomers and their distribution 
- * */
-template< class IngredientsType >
-void AnalyzerIntramolecularReactions<IngredientsType>::initialize(){}
-/**
- * @details 
- * */
-template< class IngredientsType >
-bool AnalyzerIntramolecularReactions<IngredientsType>::execute()
-{
-  dumpData();
-  return true;
-}
-template<class IngredientsType>
-void AnalyzerIntramolecularReactions<IngredientsType>::cleanup()
-{
-  dumpData();
-}
-
-
-template<class IngredientsType>
-void AnalyzerIntramolecularReactions<IngredientsType>::dumpData()
-{
-
-	//output for the equilibrated positions 
-	std::vector< std::vector<int> > CrossLinkPositions=CollectAveragePositions() ;
-	std::stringstream commentAveragePosition;
-	commentAveragePosition<<"Created by AnalyzerIntramolecularReactions\n";
-	commentAveragePosition<<"conversion nBonds nIntraBonds nBondsGel nIntraBondsGels \n";
-
-	ResultFormattingTools::writeResultFile(
-		outputFilename,
-		ingredients,
-		CrossLinkPositions,
-		commentAveragePosition.str()
-	);
-			
-	
-}
-
-#endif /*LEMONADE_PM_ANALYZER_ANALYZERINTRAMOLECULARREACTIONS_H*/
-
-
diff --git a/include/LeMonADE_PM/analyzer/AnalyzerIntramolecularReactions.h b/include/LeMonADE_PM/analyzer/AnalyzerIntramolecularReactions.h
deleted file mode 100644
index 5a5fb11..0000000
--- a/include/LeMonADE_PM/analyzer/AnalyzerIntramolecularReactions.h
+++ /dev/null
@@ -1,168 +0,0 @@
-/****************************************************************************** 
- * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
- * author: Toni Müller
- * email: mueller-toni@ipfdd.de
- * project:Phantom Modulus
- *****************************************************************************/
-
-#ifndef LEMONADE_PM_ANALYZER_ANALYZERINTRAMOLECULARREACTIONS_H
-#define LEMONADE_PM_ANALYZER_ANALYZERINTRAMOLECULARREACTIONS_H
-
-#include <string>
-
-#include <LeMonADE/utility/Vector3D.h>
-#include <LeMonADE/analyzer/AbstractAnalyzer.h>
-#include <LeMonADE/utility/ResultFormattingTools.h>
-#include <LeMonADE/utility/MonomerGroup.h>
-#include <LeMonADE/utility/DistanceCalculation.h>
-
-/*************************************************************************
- * definition of AnalyzerIntramolecularReactions class
- * ***********************************************************************/
-
-/**
- * @file
- *
- * @class AnalyzerIntramolecularReactions
- *
- * @brief Analyzer counting the intramolecular reactions
- *
- * @tparam IngredientsType Ingredients class storing all system information( e.g. monomers, bonds, etc).
- */
-template < class IngredientsType > class AnalyzerIntramolecularReactions : public AbstractAnalyzer
-{
-private:
-	//! typedef for the underlying container holding the monomers
-	typedef typename IngredientsType::molecules_type molecules_type;
-	//! reference to the complete system
-	const IngredientsType& ingredients;
-	//!cotnainer holding the information about conversion nBonds nIntraBonds nBondsGel nIntraBondsGels
-	std::vector<std::vector<dobule> > data;
-	//! name of output file for the average is outputFilePrefix_averages.dat  
-	std::string outputFilename;
-	//! save the collected data to a file 
-	void dumpData();
-	//! iterates over the structure and searches for the intramolecular reactions
-	void getBiggestCluster();
-public:
-	//! constructor
-	AnalyzerIntramolecularReactions(const IngredientsType& ingredients_, std::string outputFilename_);
-	//! destructor. does nothing
-	virtual ~AnalyzerIntramolecularReactions(){}
-	//! nothing needs  to be initialized
-	virtual void initialize();
-	//! Runs over the structure and obtains the conversion nBonds nIntraBonds nBondsGel nIntraBondsGels.
-	virtual bool execute();
-	//! Writes the final results to file
-	virtual void cleanup();	
-};
-
-/*************************************************************************
- * implementation of memebers
- * ***********************************************************************/
-
-/**
- * @param ing reference to the object holding all information of the system
- * */
-template<class IngredientsType>
-AnalyzerIntramolecularReactions<IngredientsType>::AnalyzerIntramolecularReactions(
-	const IngredientsType& ingredients_, std::string outputFilename_)
-:ingredients(ingredients_)
-,outputFilename(outputFilename_)
-{}
-////////////////////////////////////////////////////////////////////////////////
-template< class IngredientsType >
-void AnalyzerIntramolecularReactions<IngredientsType>::initialize(){}
-
-template< class IngredientsType >
-bool AnalyzerIntramolecularReactions<IngredientsType>::execute()
-{
-	
- 	return true;
-}
-template<class IngredientsType>
-void AnalyzerIntramolecularReactions<IngredientsType>::cleanup()
-{
-  	dumpData();
-}
-template<class IngredientsType>
-void AnalyzerIntramolecularReactions<IngredientsType>::dumpData()
-{  
-	//output for the equilibrated positions 
-	std::stringstream commentAveragePosition;
-	commentAveragePosition<<"Created by AnalyzerIntramolecularReactions\n";
-	commentAveragePosition<<"nTotalBonds="<<myIngredients.getNumCrossLinkers()*4<<"\n";
-	commentAveragePosition<<"conversion nBonds nIntraBonds nBondsGel nIntraBondsGels \n";
-	ResultFormattingTools::writeResultFile(
-		outAvPos.str(),
-		ingredients,
-		data,
-		commentAveragePosition.str()
-	);
-}
-
-
-template <class IngredientsType>
-void AnalyzerIntramolecularReactions<IngredientsType>::getBiggestCluster () {
-	uint32_t nMolecules(0);
-	std::vector<uint32_t> LargestCluster;
-	const typename IngredientsType::molecules_type& getMolies = ingredients.getMolecules(); 
-	//search largest cluster: use the attribute tag for that
-	//at first store the initial attributes to reset them after the search
-	//then color the whole graph. connected parts have the same color
-	auto nMonomers(getMolies.size());
-	std::vector<uint32_t> Tag(nMonomers,0);
-	//color graph
-	int freeColor(1);
-	for (auto i=0 ; i < nMonomers;i++){
-		std::vector<size_t> rememberBranch;
-		rememberBranch.push_back(i);
-		if(Tag[i] == 0) {
-			while ( rememberBranch.size() > 0 ){
-				auto ID(rememberBranch.back());
-				auto color(Tag[ID]);
-				rememberBranch.pop_back();
-				if ( color == 0){
-					Tag[ID]=freeColor;
-					auto nLinks(getMolies.getNumLinks(ID));
-					if(nLinks != 0 ){
-						for(auto j=0; j < nLinks ; j++){
-							auto Neighbor(getMolies.getNeighborIdx(ID,j));
-							if( Tag[Neighbor] == 0 ) rememberBranch.push_back(Neighbor);
-						}
-					}
-				}
-			}
-			freeColor++;
-		}
-	} 
-	freeColor--;  
-	nMolecules=freeColor;
-	std::cout << "#Molecules=" << nMolecules <<std::endl;
-	std::vector<std::vector<uint32_t> > ColoredGraphIDs(freeColor+1,std::vector<uint32_t>(0));
-	for (auto i=0 ; i < nMonomers;i++){
-		uint32_t atti(Tag[i]);
-		if (atti==0 ){//this should never happen because all monomers should be covered above and colored 
-			std::stringstream error_message;
-			error_message << "AnalyzerActiveChainDensity::execute(): Found monomer which is not colored! ID is " << i << "\n";
-			throw std::runtime_error(error_message.str());
-		}
-		ColoredGraphIDs[atti].push_back(i);
-	}
-	auto biggestClusterID(0);
-	auto biggestClusterSize(ColoredGraphIDs[biggestClusterID].size());
-	for (auto i=0; i < freeColor+1 ; i++){
-		std::cout << "ClusterID  "  << i << " cluster size  " << ColoredGraphIDs[i].size() << std::endl; 
-		if ( biggestClusterSize < ColoredGraphIDs[i].size() ){ 
-			biggestClusterSize=ColoredGraphIDs[i].size();
-			biggestClusterID=i;
-		}
-	}
-	std::cout << "biggest ClusterID  "  << biggestClusterID << " biggestClusterSize " << biggestClusterSize << std::endl; 
-	LargestCluster=ColoredGraphIDs[biggestClusterID];
-	// return LargestCluster; 
-}
-
-#endif /*LEMONADE_PM_ANALYZER_ANALYZERINTRAMOLECULARREACTIONS_H*/
-
-
diff --git a/projects/ForceEquilibrium.cpp b/projects/ForceEquilibrium.cpp
index c8c4534..5bdeb86 100644
--- a/projects/ForceEquilibrium.cpp
+++ b/projects/ForceEquilibrium.cpp
@@ -98,7 +98,7 @@ int main(int argc, char* argv[]){
 	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
 	      exit(1);
 	    }else if(showHelp == true){
-	      std::cout << "Simulator to connect linear chains with single monomers of certain functionality"<< std::endl;
+	      std::cout << "Standard force equilibration for a end-linked network."<< std::endl;
 	      parser.writeToStream(std::cout);
 	      exit(0);
 	    }else{
@@ -195,35 +195,6 @@ int main(int argc, char* argv[]){
 		taskmanager2.initialize();
 		taskmanager2.run(1);
 		taskmanager2.cleanup();
-
-        // forceUpdater->initialize();
-        // forceUpdater2->initialize();
-        // uniaxialDeformation->initialize();
-        // analyzer->initialize();
-
-        // for (auto i=1; i < stretching_factor ; i++){
-        //     if (i>1){
-        //         uniaxialDeformation->setStretchingFactor(static_cast<double>(i)/static_cast<double>(i-1.));
-        //         uniaxialDeformation->execute();
-        //     }
-        //     //read bonds and positions stepwise
-        //     if(custom){
-        //         std::cout << "Use custom force-extension curve\n";
-        //         forceUpdater->execute();
-        //     }else{
-        //         std::cout << "Use gaussian force-extension relation\n";
-        //         forceUpdater2->execute();
-        //     }
-        //     std::stringstream out1,out2;
-        //     out1 << "l" << i << "_" << outputDataPos;      
-        //     out2 << "l" << i << "_" << outputDataDist;
-        //     analyzer->setFilenames(out1.str(), out2.str());
-        //     analyzer->execute();
-        // }
-        // forceUpdater->cleanup();
-        // forceUpdater2->cleanup();
-        // uniaxialDeformation->cleanup();
-        // analyzer->cleanup();
 	}
 	catch(std::exception& e){
 		std::cerr<<"Error:\n"
diff --git a/projects/IdealReference2ForceEquilibrium.cpp b/projects/IdealReference2ForceEquilibrium.cpp
index b361051..40a1f38 100644
--- a/projects/IdealReference2ForceEquilibrium.cpp
+++ b/projects/IdealReference2ForceEquilibrium.cpp
@@ -97,13 +97,12 @@ int main(int argc, char* argv[]){
 	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
 	      exit(1);
 	    }else if(showHelp == true){
-	    //   std::cout << "Simulator to connect linear chains with single monomers of certain functionality"<< std::endl;
+	      std::cout << "Force equilibration of two a double star, where each chain is replaced effectively by a tendomer."<< std::endl;
 	      parser.writeToStream(std::cout);
 	      exit(0);
 	    }else{
 	      std::cout << "outputData            : " << outputDataPos          << std::endl;
 	      std::cout << "outputDataDist        : " << outputDataDist         << std::endl;
-	    //   std::cout << "inputBFM              : " << inputBFM               << std::endl; 
 	      std::cout << "threshold             : " << threshold              << std::endl; 
 		  std::cout << "feCurve               : " << feCurve                << std::endl;
 		  std::cout << "gauss                 : " << gauss                  << std::endl;
diff --git a/projects/IdealReferenceForceEquilibrium.cpp b/projects/IdealReferenceForceEquilibrium.cpp
index b3e3cbc..83e404e 100644
--- a/projects/IdealReferenceForceEquilibrium.cpp
+++ b/projects/IdealReferenceForceEquilibrium.cpp
@@ -98,23 +98,22 @@ int main(int argc, char* argv[]){
 	    auto result = parser.parse( clara::Args( argc, argv ) );
 	    
 	    if( !result ) {
-	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
-	      exit(1);
+			std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
+			exit(1);
 	    }else if(showHelp == true){
-	    //   std::cout << "Simulator to connect linear chains with single monomers of certain functionality"<< std::endl;
-	      parser.writeToStream(std::cout);
-	      exit(0);
+	    	std::cout << "Force equilibration of a star, where each chain is replaced effectively by a tendomer."<< std::endl;
+	      	parser.writeToStream(std::cout);
+	      	exit(0);
 	    }else{
-	      std::cout << "outputData            : " << outputDataPos          << std::endl;
-	      std::cout << "outputDataDist        : " << outputDataDist         << std::endl;
-	    //   std::cout << "inputBFM              : " << inputBFM               << std::endl; 
-	      std::cout << "threshold             : " << threshold              << std::endl; 
-		  std::cout << "feCurve               : " << feCurve                << std::endl;
-		  std::cout << "gauss                 : " << gauss                  << std::endl;
-		  std::cout << "stretching_factor     : " << stretching_factor      << std::endl;
-          std::cout << "nSegments             : " << nSegments              << std::endl;
-          std::cout << "functionality         : " << functionality          << std::endl;
-          std::cout << "nRings                : " << nRings          << std::endl;
+			std::cout << "outputData            : " << outputDataPos          << std::endl;
+			std::cout << "outputDataDist        : " << outputDataDist         << std::endl;
+			std::cout << "threshold             : " << threshold              << std::endl; 
+			std::cout << "feCurve               : " << feCurve                << std::endl;
+			std::cout << "gauss                 : " << gauss                  << std::endl;
+			std::cout << "stretching_factor     : " << stretching_factor      << std::endl;
+			std::cout << "nSegments             : " << nSegments              << std::endl;
+			std::cout << "functionality         : " << functionality          << std::endl;
+			std::cout << "nRings                : " << nRings          << std::endl;
 	    }
 		RandomNumberGenerators rng;
 		// rng.seedDefaultValuesAll();
diff --git a/projects/IntramolecularReactions.cpp b/projects/IntramolecularReactions.cpp
deleted file mode 100644
index 7aa6fa5..0000000
--- a/projects/IntramolecularReactions.cpp
+++ /dev/null
@@ -1,170 +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/>.
-
---------------------------------------------------------------------------------*/
-
-/****************************************************************************** 
- * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
- * author: Toni Müller
- * email: mueller-toni@ipfdd.de
- * project: LeMonADE-Phantom Modulus
- *****************************************************************************/
-#include <iostream>
-#include <vector>
-#include <bitset>
-
-#include <LeMonADE/core/Ingredients.h>
-#include <LeMonADE/updater/UpdaterReadBfmFile.h>
-#include <LeMonADE/analyzer/AnalyzerWriteBfmFile.h>
-#include <LeMonADE/feature/FeatureMoleculesIOUnsaveCheck.h>
-#include <LeMonADE/feature/FeatureReactiveBonds.h>
-#include <LeMonADE/feature/FeatureBox.h>
-#include <LeMonADE/feature/FeatureLabel.h>
-#include <LeMonADE/utility/TaskManager.h>
-
-#include <extern/catchorg/clara/clara.hpp>
-
-#include <LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h>
-#include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
-#include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
-#include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
-#include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h>
-#include <LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h>
-
-
-int main(int argc, char* argv[]){
-	try{
-		///////////////////////////////////////////////////////////////////////////////
-		///parse options///
-		std::string inputBFM("init.bfm");
-		std::string outputData("IntramolecularReactions.dat");
-		std::string inputConnection("BondCreationBreaking.dat");
-		std::string feCurve("");
-		double relaxationParameter(10.);
-		double threshold(0.5);
-		double stepwidth(1.0);
-		double minConversion(50.0);
-		
-		bool showHelp = false;
-		auto parser
-			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"          ] ("(required)Input filename of the bfm file"                                    ).required()
-			| clara::detail::Opt(     inputConnection, "inputConnection (=BondCreationBreaking.dat)"     ) ["-d"]["--inputConnection"] ("used for the time development of the topology. "                             ).required()
-			| clara::detail::Opt(          outputData, "outputData (=IntramolecularReactions.dat)"       ) ["-o"]["--outputData"      ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
-			| clara::detail::Opt(           stepwidth, "stepwidth"                                       ) ["-s"]["--stepwidth"      ] ("(optional) Width for the increase in percentage. Default: 1%."               ).optional()
-			| clara::detail::Opt(       minConversion, "minConversion"                                   ) ["-u"]["--minConversion"  ] ("(optional) Minimum conversion to be read in. Default: 50%."                  ).optional()
-			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"      ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
-			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"        ] ("(optional) Force-Extension curve. Default \"\"."                             ).required()
-			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"          ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
-			| clara::Help( showHelp );
-		
-	    auto result = parser.parse( clara::Args( argc, argv ) );
-	    
-	    if( !result ) {
-	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
-	      exit(1);
-	    }else if(showHelp == true){
-	      std::cout << "Simulator to connect linear chains with single monomers of certain functionality"<< std::endl;
-	      parser.writeToStream(std::cout);
-	      exit(0);
-	    }else{
-	      std::cout << "outputData            : " << outputData             << std::endl;
-	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
-	      std::cout << "inputConnection       : " << inputConnection        << std::endl; 
-	      std::cout << "stepwidth             : " << stepwidth              << std::endl;
-	      std::cout << "minConversion         : " << minConversion          << std::endl;
-	      std::cout << "threshold             : " << threshold              << std::endl; 
-		  std::cout << "feCurve               : " << feCurve                << std::endl;
-	    }
-		
-		///////////////////////////////////////////////////////////////////////////////
-		///end options parsing
-		///////////////////////////////////////////////////////////////////////////////
-		//Read in th last Config 
-		typedef LOKI_TYPELIST_3(FeatureMoleculesIOUnsaveCheck, FeatureLabel, FeatureReactiveBonds) Features;
-		typedef ConfigureSystem<VectorInt3,Features, 7> Config;
-		typedef Ingredients<Config> Ing;
-		Ing myIngredients;
-		
-		TaskManager taskmanager;
-		
-		taskmanager.addUpdater( new UpdaterReadBfmFile<Ing>(inputBFM,myIngredients, UpdaterReadBfmFile<Ing>::READ_LAST_CONFIG_SAVE),0);
-
-		//initialize and run
-		taskmanager.initialize();
-		taskmanager.run(1);
-		taskmanager.cleanup();
-		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
-		//the foce equilibrium is reached off lattice ( no integer values for the positions )
-		typedef LOKI_TYPELIST_3(FeatureBox, FeatureCrosslinkConnectionsLookUpTendomers ,FeatureLabel) Features2;
-		typedef ConfigureSystem<VectorDouble3,Features2, 7> Config2;
-		typedef Ingredients<Config2> Ing2;
-		Ing2 myIngredients2;
-		
-		myIngredients2.setBoxX(myIngredients.getBoxX());
-		myIngredients2.setBoxY(myIngredients.getBoxY());
-		myIngredients2.setBoxZ(myIngredients.getBoxZ());
-		myIngredients2.setPeriodicX(myIngredients.isPeriodicX());
-		myIngredients2.setPeriodicY(myIngredients.isPeriodicY());
-		myIngredients2.setPeriodicZ(myIngredients.isPeriodicZ());
-		myIngredients2.modifyMolecules().resize(myIngredients.getMolecules().size());
-		myIngredients2.modifyMolecules().setAge(myIngredients.getMolecules().getAge());
-
-        myIngredients2.setNumTendomers           (myIngredients.getNumTendomers());
-		myIngredients2.setNumCrossLinkers        (myIngredients.getNumCrossLinkers());
-		myIngredients2.setNumMonomersPerChain    (myIngredients.getNumMonomersPerChain());
-		myIngredients2.setNumLabelsPerTendomerArm(myIngredients.getNumLabelsPerTendomerArm());
-		
-		for(size_t i = 0; i< myIngredients.getMolecules().size();i++){
-			myIngredients2.modifyMolecules()[i].modifyVector3D()=myIngredients.getMolecules()[i].getVector3D();
-			myIngredients2.modifyMolecules()[i].setReactive(myIngredients.getMolecules()[i].isReactive());
-			myIngredients2.modifyMolecules()[i].setNumMaxLinks(myIngredients.getMolecules()[i].getNumMaxLinks());
-			for (size_t j = 0 ; j < myIngredients.getMolecules().getNumLinks(i);j++){
-				uint32_t neighbor(myIngredients.getMolecules().getNeighborIdx(i,j));
-				if( ! myIngredients2.getMolecules().areConnected(i,neighbor) )
-					myIngredients2.modifyMolecules().connect(i,neighbor);
-			}
-		}
-		myIngredients2.synchronize();
-
-		TaskManager taskmanager2;
-		//read bonds and positions stepwise
-		taskmanager2.addUpdater( new UpdaterReadCrosslinkConnectionsTendomer<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
-        taskmanager2.addAnalyzer(new AnalyzerIntramolecularReactions<Ing2>(myIngredients2, outputData));
-		//initialize and run
-		taskmanager2.initialize();
-		taskmanager2.run();
-		taskmanager2.cleanup();
-		
-	}
-	catch(std::exception& e){
-		std::cerr<<"Error:\n"
-		<<e.what()<<std::endl;
-	}
-	catch(...){
-		std::cerr<<"Error: unknown exception\n";
-	}
-	
-	return 0;
-}
diff --git a/projects/TendomerNetworkExtractActivePart.cpp b/projects/TendomerNetworkExtractActivePart.cpp
index 6b3b45d..ffc5271 100644
--- a/projects/TendomerNetworkExtractActivePart.cpp
+++ b/projects/TendomerNetworkExtractActivePart.cpp
@@ -85,9 +85,9 @@ int main(int argc, char* argv[]){
 	      exit(0);
 	    }else{
 	      std::cout << "outputBFM             : " << outputBFM          << std::endl;
-	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
-	      std::cout << "inputConnection       : " << inputConnection        << std::endl; 
-          std::cout << "activeComponent       : " << activeComponent        << std::endl; 
+	      std::cout << "inputBFM              : " << inputBFM           << std::endl; 
+	      std::cout << "inputConnection       : " << inputConnection    << std::endl; 
+          std::cout << "activeComponent       : " << activeComponent    << std::endl; 
 	    }
 		RandomNumberGenerators rng;
 		rng.seedAll();
diff --git a/projects/TendomerNetworkForceEquilibriumConversionSeries.cpp b/projects/TendomerNetworkForceEquilibriumConversionSeries.cpp
deleted file mode 100644
index 58a734b..0000000
--- a/projects/TendomerNetworkForceEquilibriumConversionSeries.cpp
+++ /dev/null
@@ -1,186 +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/>.
-
---------------------------------------------------------------------------------*/
-
-/****************************************************************************** 
- * based on LeMonADE: https://github.com/LeMonADE-project/LeMonADE/
- * author: Toni Müller
- * email: mueller-toni@ipfdd.de
- * project: LeMonADE-Phantom Modulus
- *****************************************************************************/
-#include <iostream>
-#include <vector>
-#include <bitset>
-
-#include <LeMonADE/core/Ingredients.h>
-#include <LeMonADE/updater/UpdaterReadBfmFile.h>
-#include <LeMonADE/analyzer/AnalyzerWriteBfmFile.h>
-#include <LeMonADE/feature/FeatureMoleculesIOUnsaveCheck.h>
-#include <LeMonADE/feature/FeatureReactiveBonds.h>
-#include <LeMonADE/feature/FeatureBox.h>
-#include <LeMonADE/feature/FeatureLabel.h>
-#include <LeMonADE/utility/TaskManager.h>
-#include <LeMonADE/utility/RandomNumberGenerators.h>
-
-#include <extern/catchorg/clara/clara.hpp>
-
-#include <LeMonADE_PM/updater/UpdaterForceBalancedPositionTendomer.h>
-#include <LeMonADE_PM/updater/UpdaterReadCrosslinkConnectionsTendomer.h>
-#include <LeMonADE_PM/updater/moves/MoveForceEquilibrium.h>
-#include <LeMonADE_PM/updater/moves/MoveNonLinearForceEquilibrium.h>
-#include <LeMonADE_PM/feature/FeatureCrosslinkConnectionsLookUpTendomers.h>
-#include <LeMonADE_PM/analyzer/AnalyzerEquilbratedPosition.h>
-
-
-int main(int argc, char* argv[]){
-	try{
-		///////////////////////////////////////////////////////////////////////////////
-		///parse options///
-		std::string inputBFM("init.bfm");
-		std::string outputDataPos("CrosslinkPosition.dat");
-		std::string outputDataDist("ChainExtensionDistribution.dat");
-		std::string inputConnection("BondCreationBreaking.dat");
-		std::string feCurve("");
-		double relaxationParameter(10.);
-		double threshold(0.5);
-		double stepwidth(1.0);
-		double minConversion(50.0);
-		
-		bool showHelp = false;
-		auto parser
-			= clara::detail::Opt(            inputBFM, "inputBFM (=inconfig.bfm)"                        ) ["-i"]["--input"          ] ("(required)Input filename of the bfm file"                                    ).required()
-			| clara::detail::Opt(     inputConnection, "inputConnection (=BondCreationBreaking.dat)"     ) ["-d"]["--inputConnection"] ("used for the time development of the topology. "                             ).required()
-			| clara::detail::Opt(       outputDataPos, "outputDataPos (=CrosslinkPosition.dat)"          ) ["-o"]["--outputPos"      ] ("(optional) Output filename of the crosslink ID and the equilibrium Position.").optional()
-			| clara::detail::Opt(      outputDataDist, "outputDataDist (=ChainExtensionDistribution.dat)") ["-c"]["--outputDist"     ] ("(optional) Output filename of the chain extension distribution."             ).optional()
-			| clara::detail::Opt(           stepwidth, "stepwidth"                                       ) ["-s"]["--stepwidth"      ] ("(optional) Width for the increase in percentage. Default: 1%."               ).optional()
-			| clara::detail::Opt(       minConversion, "minConversion"                                   ) ["-u"]["--minConversion"  ] ("(optional) Minimum conversion to be read in. Default: 50%."                  ).optional()
-			| clara::detail::Opt(           threshold, "threshold"                                       ) ["-t"]["--threshold"      ] ("(optional) Threshold of the average shift. Default 0.5 ."                    ).optional()
-			| clara::detail::Opt(             feCurve, "feCurve (="")"                                   ) ["-f"]["--feCurve"        ] ("(optional) Force-Extension curve. Default \"\"."                             ).required()
-			| clara::detail::Opt( relaxationParameter, "relaxationParameter (=10)"                       ) ["-r"]["--relax"          ] ("(optional) Relaxation parameter. Default 10.0 ."                             ).optional()
-			| clara::Help( showHelp );
-		
-	    auto result = parser.parse( clara::Args( argc, argv ) );
-	    
-	    if( !result ) {
-	      std::cerr << "Error in command line: " << result.errorMessage() << std::endl;
-	      exit(1);
-	    }else if(showHelp == true){
-	      std::cout << "Simulator to connect linear chains with single monomers of certain functionality"<< std::endl;
-	      parser.writeToStream(std::cout);
-	      exit(0);
-	    }else{
-	      std::cout << "outputData            : " << outputDataPos          << std::endl;
-	      std::cout << "outputDataDist        : " << outputDataDist         << std::endl;
-	      std::cout << "inputBFM              : " << inputBFM               << std::endl; 
-	      std::cout << "inputConnection       : " << inputConnection        << std::endl; 
-	      std::cout << "stepwidth             : " << stepwidth              << std::endl;
-	      std::cout << "minConversion         : " << minConversion          << std::endl;
-	      std::cout << "threshold             : " << threshold              << std::endl; 
-		  std::cout << "feCurve               : " << feCurve                << std::endl;
-	    }
-		RandomNumberGenerators rng;
-		rng.seedAll();
-		///////////////////////////////////////////////////////////////////////////////
-		///end options parsing
-		///////////////////////////////////////////////////////////////////////////////
-		//Read in th last Config 
-		typedef LOKI_TYPELIST_3(FeatureMoleculesIOUnsaveCheck, FeatureLabel, FeatureReactiveBonds) Features;
-		typedef ConfigureSystem<VectorInt3,Features, 7> Config;
-		typedef Ingredients<Config> Ing;
-		Ing myIngredients;
-		
-		TaskManager taskmanager;
-		
-		taskmanager.addUpdater( new UpdaterReadBfmFile<Ing>(inputBFM,myIngredients, UpdaterReadBfmFile<Ing>::READ_LAST_CONFIG_SAVE),0);
-
-		//initialize and run
-		taskmanager.initialize();
-		taskmanager.run(1);
-		taskmanager.cleanup();
-		std::cout << "Read in conformation and go on to bring it into equilibrium forces..." <<std::endl;
-		//the foce equilibrium is reached off lattice ( no integer values for the positions )
-		typedef LOKI_TYPELIST_3(FeatureBox, FeatureCrosslinkConnectionsLookUpTendomers ,FeatureLabel) Features2;
-		typedef ConfigureSystem<VectorDouble3,Features2, 7> Config2;
-		typedef Ingredients<Config2> Ing2;
-		Ing2 myIngredients2;
-		
-		myIngredients2.setBoxX(myIngredients.getBoxX());
-		myIngredients2.setBoxY(myIngredients.getBoxY());
-		myIngredients2.setBoxZ(myIngredients.getBoxZ());
-		myIngredients2.setPeriodicX(myIngredients.isPeriodicX());
-		myIngredients2.setPeriodicY(myIngredients.isPeriodicY());
-		myIngredients2.setPeriodicZ(myIngredients.isPeriodicZ());
-		myIngredients2.modifyMolecules().resize(myIngredients.getMolecules().size());
-		myIngredients2.modifyMolecules().setAge(myIngredients.getMolecules().getAge());
-        
-		// myIngredients2.setNumOfChains              (myIngredients.getNumOfChains());
-		// myIngredients2.setNumOfCrosslinks          (myIngredients.getNumOfCrosslinks());
-		// myIngredients2.setNumOfMonomersPerChain    (myIngredients.getNumOfMonomersPerChain());
-		// myIngredients2.setNumOfMonomersPerCrosslink(myIngredients.getNumOfMonomersPerCrosslink());
-		// myIngredients2.setFunctionality            (myIngredients.getFunctionality());
-
-        myIngredients2.setNumTendomers           (myIngredients.getNumTendomers());
-		myIngredients2.setNumCrossLinkers        (myIngredients.getNumCrossLinkers());
-		myIngredients2.setNumMonomersPerChain    (myIngredients.getNumMonomersPerChain());
-		myIngredients2.setNumLabelsPerTendomerArm(myIngredients.getNumLabelsPerTendomerArm());
-		
-		for(size_t i = 0; i< myIngredients.getMolecules().size();i++){
-			myIngredients2.modifyMolecules()[i].modifyVector3D()=myIngredients.getMolecules()[i].getVector3D();
-			myIngredients2.modifyMolecules()[i].setReactive(myIngredients.getMolecules()[i].isReactive());
-			myIngredients2.modifyMolecules()[i].setNumMaxLinks(myIngredients.getMolecules()[i].getNumMaxLinks());
-			for (size_t j = 0 ; j < myIngredients.getMolecules().getNumLinks(i);j++){
-				uint32_t neighbor(myIngredients.getMolecules().getNeighborIdx(i,j));
-				if( ! myIngredients2.getMolecules().areConnected(i,neighbor) )
-					myIngredients2.modifyMolecules().connect(i,neighbor);
-			}
-		}
-		myIngredients2.synchronize();
-
-		TaskManager taskmanager2;
-		//read bonds and positions stepwise
-		taskmanager2.addUpdater( new UpdaterReadCrosslinkConnectionsTendomer<Ing2>(myIngredients2, inputConnection, stepwidth, minConversion) );
-        auto updater = new UpdaterForceBalancedPositionTendomer<Ing2,MoveNonLinearForceEquilibrium>(myIngredients2, threshold) ;
-        updater->setFilename(feCurve);
-        updater->setRelaxationParameter(relaxationParameter);
-        // auto updater = new UpdaterForceBalancedPosition<Ing2,MoveForceEquilibrium>(myIngredients2, threshold) ;
-        taskmanager2.addUpdater( updater );
-		taskmanager2.addAnalyzer(new AnalyzerEquilbratedPosition<Ing2>(myIngredients2,outputDataPos, outputDataDist));
-		//initialize and run
-		taskmanager2.initialize();
-		taskmanager2.run();
-		taskmanager2.cleanup();
-		
-	}
-	catch(std::exception& e){
-		std::cerr<<"Error:\n"
-		<<e.what()<<std::endl;
-	}
-	catch(...){
-		std::cerr<<"Error: unknown exception\n";
-	}
-	
-	return 0;
-}

From 10fbe21c4ec96e3c556344592369bad397e2e1e7 Mon Sep 17 00:00:00 2001
From: Toni Mueller <mueller-toni@ipfdd.de>
Date: Mon, 31 Jan 2022 10:28:42 +0100
Subject: [PATCH 70/70] add description in README.md

---
 README.md | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index f3dfca7..ea4bc23 100644
--- a/README.md
+++ b/README.md
@@ -11,7 +11,7 @@ This project needs the [LeMonADE-library](https://github.com/LeMonADE-project/Le
 This will run `cmake` and create the `build` directory. Now type in `make` which compiles the executables and runs the test if this option was given.
 
 
-## Linear chains with cross linkers 
+## Linear chains with cross-links 
 The main [program](https://github.com/LeMonADE-project/LeMonADE_PhantomModulus/blob/master/projects/ForceEquilibrium.cpp) reads in a .bfm file and a data file. It is expected that the bfm file contains the following flags 
 ```
 #!number_of_linear_chains=value
@@ -23,12 +23,26 @@ The main [program](https://github.com/LeMonADE-project/LeMonADE_PhantomModulus/b
 1-1:1/2
 ...
 ```
-Moreover, it is expected that in the bfm file first all chains and afterwards all crosslinks are given. 
+Moreover, it is expected that in the bfm file first all chains and afterwards all cross-links are given. 
 The data file should be created during the connection process and needs to contain: 
 ```
 Time ChainID MonID1 P1X P1Y P1Z MonID2 P2X P2Y P2Z
 ```
-where MonID1 and MonID2 are the cross link ID starting at 0. ChainID starts at 0 as well.
+where MonID1 and MonID2 are the cross-link ID starting at 0. ChainID starts at 0 as well.
 For the calculations only the ChainID and MonID1 is needed. The remaining fields are arbitrary for a correct 
 calculation of the positions of the cross links in a force equilibrium. 
 (The format was given from a previous simulation.)
+
+## Write out parts of the networks 
+For the force equilibrium only active chains are of interest. 
+Therefore, there exist two programs extracting the active gel structure from the total system.
+
+## Tendomer
+There are programs specialized on tendomers. They read the tendomer specific tag and can use a 
+custom force extension relation (e.g. numerical solution of the tendomer) to calculate the forces 
+between cross-links.
+
+## Ideal reference
+These systems are tendomer specific. A star is created and a monomer along the chain with a distance to the center 
+according to the tendomer distribution of the number of elastic segments is marked as fixed in space. 
+In a second system a double star is simulated. 
\ No newline at end of file