Finish converting C files to C++

spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/build/Makefile

@@ -1,4 +1,5 @@
-CC = g++
+CC = gcc
+C++ = g++
 CFLAGS = -c -std=c++14 -Wall -O3
 SIMFLAGS = -l. -std=c++14 -Wall -O3
 LFLAGS = -pthread -lm
@@ -22,14 +23,14 @@ CORE: $(OBJ)
 #	make -d -f $(ROOTINC_ESC)/external/ANN/src/Makefile.spatialpy ROOTINC=$(ROOTINC_ESC)
 
 main.o:
-	$(CC) -c $(GPROFFLAG) $(GDB_FLAG) -o main.o $(MODEL) $(INCDIRPARAMS) $(CFLAGS)
+	$(C++) -c $(GPROFFLAG) $(GDB_FLAG) -o main.o $(MODEL) $(INCDIRPARAMS) $(CFLAGS)
 
 %.o: $(ROOT)/src/%.cpp
-	$(CC) -c $(GPROFFLAG) $(GDB_FLAG) -o $@ "$<" $(INCDIRPARAMS) $(CFLAGS)
+	$(C++) -c $(GPROFFLAG) $(GDB_FLAG) -o $@ "$<" $(INCDIRPARAMS) $(CFLAGS)
 
 %.o: $(ROOT)/src/%.c
 	$(CC) -c $(GPROFFLAG) $(GDB_FLAG) -o $@ "$<" $(INCDIRPARAMS) $(CFLAGS)
 
 ssa_sdpd: main.o 
-	$(CC) $(GPROFFLAG) $(GDB_FLAG) -o ssa_sdpd $(addprefix $(COREDIR)/,$(OBJ))  main.o $(addprefix $(COREDIR)/,$(ANNOBJECTS)) $(LFLAGS)
+	$(C++) $(GPROFFLAG) $(GDB_FLAG) -o ssa_sdpd $(addprefix $(COREDIR)/,$(OBJ))  main.o $(addprefix $(COREDIR)/,$(ANNOBJECTS)) $(LFLAGS)
 

spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.h → spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.hpp

@@ -28,6 +28,6 @@ See the file LICENSE.txt for details.
 
 #include "particle_system.hpp"
 
-void read_lammps_input_file(const char*filename, ParticleSystem*system);
+void read_lammps_input_file(const char*filename, Spatialpy::ParticleSystem*system);
 
 #endif //read_lammps_input_file_h

spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/propensity_file_template.cpp

@@ -26,7 +26,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include <time.h>
 #include <unistd.h>
 
-#include "count_cores.h"
+#include "count_cores.hpp"
 #include "particle_system.hpp"
 #include "propensities.hpp"
 #include "simulate.hpp"

spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.c → spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp

@@ -27,7 +27,7 @@ See the file LICENSE.txt for details.
 #include <stdlib.h>
 #include <string.h>
 
-#include "output.h"
+#include "output.hpp"
 #include "particle_system.hpp"
 
 namespace Spatialpy{

spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.c → spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.cpp

@@ -25,7 +25,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 #include <errno.h>
 
-#include "pthread_barrier.h"
+#include "pthread_barrier.hpp"
 
 #ifdef __APPLE__
 

spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.c → spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.cpp

@@ -26,10 +26,10 @@ See the file LICENSE.txt for details.
 #include <stdio.h>
 #include <stdlib.h>
 
-#include "read_lammps_input_file.h"
+#include "read_lammps_input_file.hpp"
 
 
-void read_lammps_input_file(const char*filename, ParticleSystem*system){
+void read_lammps_input_file(const char*filename, Spatialpy::ParticleSystem*system){
     char* s;
     FILE* fp = fopen(filename, "r");
     if(fp == NULL){
@@ -73,7 +73,7 @@ void read_lammps_input_file(const char*filename, ParticleSystem*system){
     s=fgets(buffer,1024,fp);
     //printf("Is this 'Masses': '%s'\n",buffer);
     s=fgets(buffer,1024,fp);
-    double *masses_of_types = malloc(sizeof(double)*ntypes);
+    double *masses_of_types = (double*) std::malloc(sizeof(double)*ntypes);
     int i,j;
     double tmp_d;
     for(i=0;i<ntypes;i++){
@@ -89,7 +89,7 @@ void read_lammps_input_file(const char*filename, ParticleSystem*system){
     s=fgets(buffer,1024,fp);
     int id,type,is_solid;
     double rho,x,y,z;
-    Particle*me;
+    Spatialpy::Particle*me;
     for(i=0;i<natoms;i++){
         s=fgets(buffer,1024,fp);
         r = sscanf(buffer, "%d 0 %d %lf %lf %lf %lf %d",&id,&type,&rho,&x,&y,&z,&is_solid);

spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate.cpp

@@ -22,10 +22,10 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include <stdlib.h>
 #include <unistd.h>
 
-#include "model.h"
-#include "output.h"
+#include "model.hpp"
+#include "output.hpp"
 #include "particle_system.hpp"
-#include "pthread_barrier.h"
+#include "pthread_barrier.hpp"
 #include "simulate.hpp"
 #include "simulate_rdme.hpp"
 

spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp

@@ -28,7 +28,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include <string.h>
 
 //#include "binheap.h"
-#include "output.h"
+#include "output.hpp"
 #include "particle_system.hpp"
 #include "propensities.hpp"
 #include "simulate_rdme.hpp"

spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.c → spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.cpp

@@ -32,12 +32,12 @@ See the file LICENSE.txt for details.
 
 // Include ANN KD Tree
 #include "ANN/ANN.h"
-#include "model.h"
-#include "output.h"
+#include "model.hpp"
+#include "output.hpp"
 #include "particle_system.hpp"
 #include "simulate.hpp"
 #include "simulate_rdme.hpp"
-#include "pthread_barrier.h"
+#include "pthread_barrier.hpp"
 
 namespace Spatialpy{
     struct arg {

spatialpy/solvers/solver.py

@@ -460,7 +460,7 @@ def compile(self, debug=False, profile=False):
         # Match except word characters \w = ([a-zA-Z0-9_]) and \_ = _ replace with ''
         propfilename = re.sub(r'[^\w\_]', '', self.model_name)
         self.propfilename = f"{propfilename}_generated_model"
-        self.prop_file_name = os.path.join(self.build_dir, f'{self.propfilename}.c')
+        self.prop_file_name = os.path.join(self.build_dir, f'{self.propfilename}.cpp')
 
         if self.debug_level >= 1:
             print(f"Compiling Solver.  Build dir: {self.build_dir}")