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}")