diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/build/Makefile b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/build/Makefile
index 0d61c901..f5c9d0d5 100644
--- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/build/Makefile
+++ b/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)
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/count_cores.h b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/count_cores.hpp
similarity index 100%
rename from spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/count_cores.h
rename to spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/count_cores.hpp
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/model.h b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/model.hpp
similarity index 100%
rename from spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/model.h
rename to spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/model.hpp
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/output.h b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/output.hpp
similarity index 100%
rename from spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/output.h
rename to spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/output.hpp
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/pthread_barrier.h b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/pthread_barrier.hpp
similarity index 100%
rename from spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/pthread_barrier.h
rename to spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/pthread_barrier.hpp
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.h b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.hpp
similarity index 93%
rename from spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.h
rename to spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.hpp
index 18581750..cfd9001e 100644
--- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/read_lammps_input_file.h
+++ b/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
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/propensity_file_template.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/propensity_file_template.cpp
index d523f72d..8b1e80e7 100644
--- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/propensity_file_template.cpp
+++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/propensity_file_template.cpp
@@ -26,7 +26,7 @@ along with this program. If not, see .
#include
#include
-#include "count_cores.h"
+#include "count_cores.hpp"
#include "particle_system.hpp"
#include "propensities.hpp"
#include "simulate.hpp"
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.c b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.cpp
similarity index 100%
rename from spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.c
rename to spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/count_cores.cpp
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.c b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.cpp
similarity index 100%
rename from spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.c
rename to spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.cpp
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.c b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp
similarity index 99%
rename from spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.c
rename to spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp
index 023f64ae..a37b75e1 100644
--- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.c
+++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp
@@ -27,7 +27,7 @@ See the file LICENSE.txt for details.
#include
#include
-#include "output.h"
+#include "output.hpp"
#include "particle_system.hpp"
namespace Spatialpy{
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.c b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.cpp
similarity index 98%
rename from spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.c
rename to spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.cpp
index b3573437..254ee855 100644
--- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.c
+++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/pthread_barrier.cpp
@@ -25,7 +25,7 @@ along with this program. If not, see .
#include
-#include "pthread_barrier.h"
+#include "pthread_barrier.hpp"
#ifdef __APPLE__
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.c b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.cpp
similarity index 94%
rename from spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.c
rename to spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.cpp
index 638e77c1..6a4ed8ee 100644
--- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/read_lammps_input_file.c
+++ b/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
#include
-#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.
#include
#include
-#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"
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp
index 1f88ae1d..351b97b3 100644
--- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp
+++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp
@@ -28,7 +28,7 @@ along with this program. If not, see .
#include
//#include "binheap.h"
-#include "output.h"
+#include "output.hpp"
#include "particle_system.hpp"
#include "propensities.hpp"
#include "simulate_rdme.hpp"
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.c b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.cpp
similarity index 99%
rename from spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.c
rename to spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.cpp
index de60e34b..0c6227ca 100644
--- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.c
+++ b/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 {
diff --git a/spatialpy/solvers/solver.py b/spatialpy/solvers/solver.py
index 0b4cc337..6936f86e 100644
--- a/spatialpy/solvers/solver.py
+++ b/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}")