Restart ffs

Examples/User/ForwardFlux/GROMACS/ADP/Template_Input.json

@@ -34,6 +34,7 @@
 			"nInterfaces" : 5,
 			"computeInitialFlux" : true,
 			"N0Target" : 100,
+			"NLastSuccessful": 100,
 			"outputDirectoryName" : "FFSoutput",
 			"saveTrajectories" : true
 		}

Examples/User/ForwardFlux/LAMMPS/ADP/Template_Input.json

@@ -33,6 +33,7 @@
 			"nInterfaces" : 5,
 			"computeInitialFlux" : true,
 			"N0Target" : 100,
+			"NLastSuccessful": 100,
 			"outputDirectoryName" : "FFSoutput",
 			"saveTrajectories" : true
 		}

Examples/User/ForwardFlux/LAMMPS/Langevin/Template_Input.json

@@ -17,6 +17,7 @@
 			"interfaces" : [],
 			"nInterfaces" : 5,
 			"N0Target" : 100,
+			"NLastSuccessful": 100,
 			"computeInitialFlux" : true,
 			"outputDirectoryName" : "FFSoutput",
 			"saveTrajectories" : true

schema/Methods/forwardflux.method.json

@@ -24,6 +24,10 @@
 			"type" : "integer",
 			"minimum" : 1
 		},
+		"NLastSuccessful" : {
+			"type" : "integer",
+			"minimum" : 1
+		},
 		"trials" : {
 			"type" : "array",
 			"minItems" : 1,

src/Methods/DirectForwardFlux.cpp

@@ -58,7 +58,7 @@ namespace SSAGES
 		// Else check the FFS interfaces
 		else
 		{
-			CheckForInterfaceCrossings(snapshot, cvmanager);
+			CheckForInterfaceCrossings(snapshot, cvmanager); 
 			//FluxBruteForce(snapshot,cvs);
 		}
 		// Other modes?
@@ -287,18 +287,27 @@ namespace SSAGES
 		unsigned int npicks = _M[0];
 		std::vector<unsigned int> picks;
 		picks.resize(npicks);
+
+		// if the initial flux has already been realized or
+		// we've got more than _N0Target configurations for zero surface 		
+		if (_current_interface == 0)
+			_N[_current_interface]=_N0Target;
+
+		//if the calculation starts from a non-zero surface (for restart)
+		if (_N[_current_interface] == 0)
+			_N[_current_interface]=_NLastSuccessful;
 
 		if(IsMasterRank(world_))
 		{
-			std::uniform_int_distribution<int> distribution(0,_N[0]-1);
+			std::uniform_int_distribution<int> distribution(0,_N[_current_interface]-1);
 		  	for (unsigned int i=0; i < npicks ; i++)
 				picks[i] = distribution(_generator);
 		}
 		MPI_Bcast(picks.data(),npicks,MPI_UNSIGNED,0,world_);
 
 		//set correct attempt index if a given ID is picked twice
 		std::vector<unsigned int> attempt_count;
-		attempt_count.resize(_N[0],0);
+		attempt_count.resize(_N[_current_interface],0);
 
 		//each proc adds to the queue
 		for (unsigned int i=0; i < npicks ; i++)

src/Methods/DirectForwardFlux.h

@@ -58,10 +58,10 @@ namespace SSAGES
 		DirectForwardFlux(const MPI_Comm& world,
 		                  const MPI_Comm& comm, 
 		                  double ninterfaces, std::vector<double> interfaces,
-		                  unsigned int N0Target, std::vector<unsigned int> M,
+		                  unsigned int N0Target, unsigned int NLastSuccessful, std::vector<unsigned int> M,
 		                  bool initialFluxFlag, bool saveTrajectories, 
 		                  unsigned int currentInterface, std::string output_directory, unsigned int frequency)
-		: ForwardFlux(world, comm, ninterfaces, interfaces, N0Target, M, 
+		: ForwardFlux(world, comm, ninterfaces, interfaces, N0Target, NLastSuccessful, M, 
 		              initialFluxFlag, saveTrajectories, currentInterface, output_directory, frequency) {}
 
 		//! Post-integration hook.

src/Methods/ForwardFlux.cpp

@@ -658,6 +658,7 @@ namespace SSAGES
 			throw BuildException({"The size of \"interfaces\" and \"trials\" must be equal to \"nInterfaces\". See documentation for more information"});
 
 		auto N0Target = json.get("N0Target", 1).asInt();
+		auto NLastSuccessful = json.get("NLastSuccessful", 1).asInt();
 		auto initialFluxFlag = json.get("computeInitialFlux", true).asBool();
 		auto saveTrajectories = json.get("saveTrajectories", true).asBool();
 		auto currentInterface = json.get("currentInterface", 0).asInt();
@@ -673,7 +674,7 @@ namespace SSAGES
 
 		if(flavor == "DirectForwardFlux")
 		{
-			return new DirectForwardFlux(world, comm, ninterfaces, interfaces, N0Target, M, initialFluxFlag, saveTrajectories, currentInterface, output_directory, freq);            	
+			return new DirectForwardFlux(world, comm, ninterfaces, interfaces, N0Target, NLastSuccessful, M, initialFluxFlag, saveTrajectories, currentInterface, output_directory, freq);            	
 		}
 		else 
 		{

src/Methods/ForwardFlux.h

@@ -101,6 +101,9 @@ namespace SSAGES
         //! Number of configurations to store at lambda0, target
         unsigned int _N0Target;
 
+        //! Number of configurations stored at last achived interface, for restart
+        unsigned int _NLastSuccessful;
+
         //! Flux of trajectories out of state A. Denoted PhiA0 over h_A in Allen2009.
         double _fluxA0;
 
@@ -272,6 +275,7 @@ namespace SSAGES
 		 * \param ninterfaces Number of interfaces.
 		 * \param interfaces Vector of interfaces.
 		 * \param N0Target Required number of initial configurations.
+         * \param NLastSuccessful The number of stored configurations at last achieved interface.
 		 * \param M Vector of trials.
 		 * \param initialFluxFlag Flag for first step of this method.
 		 * \param saveTrajectories Flag to save flux trajectories.
@@ -284,10 +288,10 @@ namespace SSAGES
 		ForwardFlux(const MPI_Comm& world,
 		            const MPI_Comm& comm, 
 		            double ninterfaces, std::vector<double> interfaces,
-		            unsigned int N0Target, std::vector<unsigned int> M,
+		            unsigned int N0Target, unsigned int NLastSuccessful, std::vector<unsigned int> M,
 		            bool initialFluxFlag, bool saveTrajectories,
 		            unsigned int currentInterface, std::string output_directory, unsigned int frequency) : 
-		 Method(frequency, world, comm), _ninterfaces(ninterfaces), _interfaces(interfaces), _N0Target(N0Target), 
+		 Method(frequency, world, comm), _ninterfaces(ninterfaces), _interfaces(interfaces), _N0Target(N0Target), _NLastSuccessful(NLastSuccessful),
 		 _M(M), _initialFluxFlag(initialFluxFlag), _saveTrajectories(saveTrajectories), _current_interface(currentInterface),
 		 _output_directory(output_directory), _generator(1), iteration_(0) 
 		{
@@ -349,17 +353,23 @@ namespace SSAGES
 				std::cerr << "\n";
 				MPI_Abort(world_, EXIT_FAILURE);
 			}
-
+        
 			// This is to generate an artificial Lambda0ConfigLibrary, Hadi's code does this for real
 			// THIS SHOULD BE SOMEWHERE ELSE!!! 
+
+			if (!_initialFluxFlag)
+			{
+                _N0Target = NLastSuccessful;
+			}
+
 			Lambda0ConfigLibrary.resize(_N0Target);
 			std::normal_distribution<double> distribution(0,1);
 			for (unsigned int i = 0; i < _N0Target ; i++)
 			{
-				Lambda0ConfigLibrary[i].l = 0;
+				Lambda0ConfigLibrary[i].l = _current_interface;
 				Lambda0ConfigLibrary[i].n = i;
 				Lambda0ConfigLibrary[i].a = 0;
-				Lambda0ConfigLibrary[i].lprev = 0;
+				Lambda0ConfigLibrary[i].lprev = _current_interface;
 				Lambda0ConfigLibrary[i].nprev = i;
 				Lambda0ConfigLibrary[i].aprev = 0;
 				//FFSConfigID ffsconfig = Lambda0ConfigLibrary[i];