From f6f2ab4d13c1a9821e2cd8f3fdb45ae6268cf087 Mon Sep 17 00:00:00 2001
From: Josh C <jcooper6@unca.edu>
Date: Sun, 18 Dec 2022 14:42:28 -0500
Subject: [PATCH 1/2] Changed all .c files to .cpp and .h files to .hpp

---
 .../include/{count_cores.h => count_cores.hpp}                    | 0
 .../ssa_sdpd-c-simulation-engine/include/{model.h => model.hpp}   | 0
 .../ssa_sdpd-c-simulation-engine/include/{output.h => output.hpp} | 0
 .../include/{pthread_barrier.h => pthread_barrier.hpp}            | 0
 .../{read_lammps_input_file.h => read_lammps_input_file.hpp}      | 0
 .../src/{count_cores.c => count_cores.cpp}                        | 0
 .../ssa_sdpd-c-simulation-engine/src/{model.c => model.cpp}       | 0
 .../ssa_sdpd-c-simulation-engine/src/{output.c => output.cpp}     | 0
 .../src/{pthread_barrier.c => pthread_barrier.cpp}                | 0
 .../src/{read_lammps_input_file.c => read_lammps_input_file.cpp}  | 0
 .../src/{simulate_threads.c => simulate_threads.cpp}              | 0
 11 files changed, 0 insertions(+), 0 deletions(-)
 rename spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/{count_cores.h => count_cores.hpp} (100%)
 rename spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/{model.h => model.hpp} (100%)
 rename spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/{output.h => output.hpp} (100%)
 rename spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/{pthread_barrier.h => pthread_barrier.hpp} (100%)
 rename spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/include/{read_lammps_input_file.h => read_lammps_input_file.hpp} (100%)
 rename spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/{count_cores.c => count_cores.cpp} (100%)
 rename spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/{model.c => model.cpp} (100%)
 rename spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/{output.c => output.cpp} (100%)
 rename spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/{pthread_barrier.c => pthread_barrier.cpp} (100%)
 rename spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/{read_lammps_input_file.c => read_lammps_input_file.cpp} (100%)
 rename spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/{simulate_threads.c => simulate_threads.cpp} (100%)

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 100%
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
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 100%
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
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 100%
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
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 100%
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
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 100%
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

From 3d0ce89a0b759ea446d45f86a18ec20daa41b757 Mon Sep 17 00:00:00 2001
From: Josh C <jcooper6@unca.edu>
Date: Sun, 18 Dec 2022 15:35:59 -0500
Subject: [PATCH 2/2] Update files to reference .cpp files, fix Makefile

---
 .../c_base/ssa_sdpd-c-simulation-engine/build/Makefile   | 9 +++++----
 .../include/read_lammps_input_file.hpp                   | 2 +-
 .../propensity_file_template.cpp                         | 2 +-
 .../c_base/ssa_sdpd-c-simulation-engine/src/output.cpp   | 2 +-
 .../ssa_sdpd-c-simulation-engine/src/pthread_barrier.cpp | 2 +-
 .../src/read_lammps_input_file.cpp                       | 8 ++++----
 .../c_base/ssa_sdpd-c-simulation-engine/src/simulate.cpp | 6 +++---
 .../ssa_sdpd-c-simulation-engine/src/simulate_rdme.cpp   | 2 +-
 .../src/simulate_threads.cpp                             | 6 +++---
 spatialpy/solvers/solver.py                              | 2 +-
 10 files changed, 21 insertions(+), 20 deletions(-)

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/read_lammps_input_file.hpp b/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.hpp
+++ 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 <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"
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/output.cpp b/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.cpp
+++ 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 <stdlib.h>
 #include <string.h>
 
-#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.cpp b/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.cpp
+++ 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 <http://www.gnu.org/licenses/>.
 
 #include <errno.h>
 
-#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.cpp b/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.cpp
+++ 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 <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);
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate.cpp b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate.cpp
index 48db2fb2..f8bc80ee 100644
--- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate.cpp
+++ b/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"
 
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 <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"
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/simulate_threads.cpp b/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.cpp
+++ 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}")