Reintroduced time stochasticity as gaelle was using, this time as a XML parameter

addons/PhysiBoSS/src/maboss_intracellular.cpp

@@ -24,6 +24,7 @@ MaBoSSIntracellular::MaBoSSIntracellular(MaBoSSIntracellular* copy)
 	discrete_time = copy->discrete_time;
 	time_tick = copy->time_tick;
 	scaling = copy->scaling;
+	time_stochasticity = copy->time_stochasticity;
 	initial_values = copy->initial_values;
 	mutations = copy->mutations;
 	parameters = copy->parameters;
@@ -36,6 +37,7 @@ MaBoSSIntracellular::MaBoSSIntracellular(MaBoSSIntracellular* copy)
 		maboss.set_update_time_step(copy->time_step);
 		maboss.set_discrete_time(copy->discrete_time, copy->time_tick);
 		maboss.set_scaling(copy->scaling);
+		maboss.set_time_stochasticity(copy->time_stochasticity);
 		maboss.restart_node_values();
 		//maboss.set_state(copy->maboss.get_maboss_state());
 		//std::cout << get_state();
@@ -72,6 +74,7 @@ MaBoSSIntracellular::MaBoSSIntracellular(std::vector<char>& buffer, int& len_buf
 
 	MPI_Unpack(&buffer[0], len_buffer, &position, &(this->time_tick), 1, MPI_DOUBLE, MPI_COMM_WORLD);
 	MPI_Unpack(&buffer[0], len_buffer, &position, &(this->scaling),  1, MPI_DOUBLE, MPI_COMM_WORLD);
+	MPI_Unpack(&buffer[0], len_buffer, &position, &(this->time_stochasticity),  1, MPI_DOUBLE, MPI_COMM_WORLD);
 
 
 	this->maboss.init_maboss(this->bnd_filename, this->cfg_filename);
@@ -180,6 +183,10 @@ void MaBoSSIntracellular::pack(std::vector<char>& buffer, int& len_buffer, int&
 	buffer.resize(len_buffer);
 	MPI_Pack(&(this->scaling), 1, MPI_DOUBLE, &buffer[0], len_buffer, &position, MPI_COMM_WORLD);
 
+	len_buffer = position + sizeof(double);		
+	buffer.resize(len_buffer);
+	MPI_Pack(&(this->time_stochasticity), 1, MPI_DOUBLE, &buffer[0], len_buffer, &position, MPI_COMM_WORLD);
+
 	// Mutations
 	len_buffer = position + sizeof(int);		
 	buffer.resize(len_buffer);
@@ -373,6 +380,13 @@ void MaBoSSIntracellular::initialize_intracellular_from_pugixml(pugi::xml_node&
 		scaling = PhysiCell::xml_get_my_double_value( node_scaling );
 		maboss.set_scaling(scaling);
 	}
+	
+	pugi::xml_node node_time_stochasticity = node.child( "time_stochasticity" ); 
+	if( node_time_stochasticity )
+	{ 
+		time_stochasticity = PhysiCell::xml_get_my_double_value( node_time_stochasticity );
+		maboss.set_time_stochasticity(time_stochasticity);
+	}
 }
 
 MaBoSSIntracellular* getMaBoSSModel(PhysiCell::Phenotype& phenotype) {

addons/PhysiBoSS/src/maboss_intracellular.h

@@ -24,6 +24,7 @@ class MaBoSSIntracellular : public PhysiCell::Intracellular {
 	bool discrete_time = false;
 	double time_tick = 0.5;
 	double scaling = 1.0;
+	double time_stochasticity = 0.0;
 	
 	std::map<std::string, double> initial_values;
 	std::map<std::string, double> mutations;

addons/PhysiBoSS/src/maboss_network.h

@@ -34,7 +34,7 @@ class MaBoSSNetwork
 		
 		/** \brief Real time to update, after applying noise */
 		double time_to_update;
-
+		double time_stochasticity = 0;
 		double scaling = 1.0;
 		
 		/** \brief Initial value probabilities, by node */
@@ -46,7 +46,7 @@ class MaBoSSNetwork
 		std::map< std::string, Node*> nodesByName;
 		std::map< std::string, const Symbol*> parametersByName;
 	
-		inline void set_time_to_update(){this->time_to_update = this->get_update_time_step();}
+		inline void set_time_to_update(){this->time_to_update = ( 1 + (PhysiCell::UniformRandom()*2-1)*time_stochasticity ) * this->get_update_time_step();}
 
 	
 	public:
@@ -128,7 +128,7 @@ class MaBoSSNetwork
 		
 		/** \brief Get time to update*/
 		inline double get_time_to_update() {return this->time_to_update;}
-		inline void set_time_to_update(double time) { this->time_to_update = time; }
+		inline void set_time_to_update(double time) { this->time_to_update = ( 1 + (PhysiCell::UniformRandom()*2-1)*time_stochasticity ) *  time; }
 		
 		/** \brief Change simulation mode */
 		inline void set_discrete_time(bool discrete_time, double time_tick) { 
@@ -136,7 +136,7 @@ class MaBoSSNetwork
 		}
 
 		inline void set_scaling(double scaling) { this->scaling = scaling; }
-		
+		inline void set_time_stochasticity(double t_stochasticity) { this->time_stochasticity = t_stochasticity; }
 		/** 
 		 * \brief Print current state of all the nodes of the network 
 		 * \param node_values Boolean vector mapping a boolean network