Natural Convection Example

spatialpy/Solver.py

@@ -500,22 +500,22 @@ def __create_propensity_file(self, file_name=None):
                 outstr += "};"
                 input_constants += outstr + "\n"
 
-                outstr = "static double input_data_fn[{0}] = ".format(len(self.model.listOfDataFunctions)*ncells)
-                outstr += "{"
-                for ndf, df in enumerate(self.model.listOfDataFunctions):
-                    for i in range(ncells):
-                        if i > 0 and ndf==0:
-                            outstr += ','
-                        c = self.model.domain.coordinates()
-                        outstr += str(df.map( [c[i,0],c[i,1],c[i,2]] ))
-                outstr += "};"
-                input_constants += outstr + "\n"
+                if len(self.model.listOfDataFunctions)>0:
+                    outstr = "static double input_data_fn[{0}] = ".format(len(self.model.listOfDataFunctions)*ncells)
+                    outstr += "{"
+                    for ndf, df in enumerate(self.model.listOfDataFunctions):
+                        for i in range(ncells):
+                            if i > 0 and ndf==0:
+                                outstr += ','
+                            c = self.model.domain.coordinates()
+                            outstr += str(df.map( [c[i,0],c[i,1],c[i,2]] ))
+                    outstr += "};"
+                    input_constants += outstr + "\n"
             else:
                 input_constants += "static int input_N_dense[0] = {};\n"
                 input_constants += "static size_t input_irN[0] = {};\n"
                 input_constants += "static size_t input_jcN[0] = {};\n"
                 input_constants += "static int input_prN[0] = {};\n"
-                input_constants += "static double input_data_fn[0] = {};\n"
 
             G = self.model._create_dependency_graph()
             outstr = "static size_t input_irG[{0}] = ".format(len(G.indices))

spatialpy/ssa_sdpd-c-simulation-engine/include/NRMConstant_v5.hpp

@@ -58,8 +58,6 @@ namespace Spatialpy{
         double previousFiringTime; //keep the time of the last reaction that fired (from last call of selectReaction)
 
         //these two could be combined
-        //std::vector<firingTimeT> nextFiringTime;//for each reaction channel
-        //std::vector<std::pair<int,int> > binIndexAndPositionInBin;//for each reaction channel
         std::unordered_map<reactionIndexT,firingTimeT> nextFiringTime;
         std::unordered_map<reactionIndexT,std::pair<int,int> > binIndexAndPositionInBin; //for each reaction channel
 

spatialpy/ssa_sdpd-c-simulation-engine/include/particle.hpp

@@ -41,8 +41,8 @@ namespace Spatialpy{
     struct EventNode;
 
     struct Particle{
-        Particle(ParticleSystem *sys, unsigned int id=0, double x=0, double y=0, double z=0,
-                    int type=0, double nu=0.01, double mass=1, double c=0,
+        Particle(ParticleSystem *sys, unsigned int id=0, double xl=0, double yl=0,
+                    double zl=0, int type=0, double nu=0.01, double mass=1, double c=0,
                     double rho=1, int solidTag=0);
         ParticleSystem *sys;
         unsigned int id;
@@ -53,10 +53,10 @@ namespace Spatialpy{
         double x[3];
         double v[3];
         double vt[3];
-        double mass;
-        double rho;
         double nu;
+        double mass;
         double c;
+        double rho;
         int solidTag;
         double bvf_phi;
         double normal[3];
@@ -68,10 +68,8 @@ namespace Spatialpy{
         //std::shared_ptr<double[]> data_fn;
         // chem_rxn_system
         unsigned int*xx; // populaion of discrete/stochastic species
-        double *C;
-        double *Q;
-        //std::shared_ptr<double[]> C;  // concentration of chem species
-        //std::shared_ptr<double[]> Q;  // flux of chem species
+        double *C; // concentration of chem species
+        double *Q; // flux of chem species
         // below here for simulation
         std::vector<NeighborNode> neighbors;
 

spatialpy/ssa_sdpd-c-simulation-engine/include/particle_system.hpp

@@ -82,7 +82,6 @@ namespace Spatialpy{
         char boundary_conditions[3];
         bool static_domain;
         size_t num_types;
-        size_t num_data_fn;
 
         ChemRxnFun* chem_rxn_rhs_functions;
         size_t num_chem_species;
@@ -91,6 +90,7 @@ namespace Spatialpy{
         PropensityFun* stoch_rxn_propensity_functions;
         size_t num_stoch_species;
         size_t num_stoch_rxns;
+        size_t num_data_fn;
 
         const char * const* species_names;