basic binding working

.gitmodules

@@ -0,0 +1,8 @@
+[submodule "extern/pybind11"]
+	path = extern/pybind11
+	url = ../../pybind/pybind11
+	branch = stable
+[submodule "extern/eigen"]
+	path = extern/eigen
+	url = ../../libigl/eigen
+	branch = master

Makefile

@@ -13,29 +13,40 @@ CC                    = g++
 CPP_COMPILER_OPTIONS += -c -g3 -ggdb -fopenmp -Wno-deprecated -Wunused-variable -DMUPARSER 
 CPP_LINKER_OPTIONS   += -g3 -ggdb -fopenmp  
 
+INC_PYTHON            = $(shell python3.8-config --cflags)
+LIB_PYTHON            = $(shell python3.8-config --ldflags)
+PYTHON_NAME           = bin/wield$(shell python3.8-config --extension-suffix)
+
 ifdef EMACS
 PREFIX                = $(shell pwd)/
 endif
 EXCLUDE               = $(PREFIX)/src/MainOld.cpp
 SRC_MAIN              = $(filter-out $(EXCLUDE), $(shell find ./src/ -name '*.cc'))
-EXE 		      = $(subst ./src/,./bin/, $(SRC_MAIN:.cc=))
-SRC		      = $(filter-out $(EXCLUDE), $(shell find ./src/ -name '*.cpp'))
+EXE 		      = bin/wield
+SRC		      = $(filter-out $(EXCLUDE), $(shell find ./src/ -mindepth 2 -name  '*.cpp'))
 HDR		      = $(filter-out $(EXCLUDE), $(shell find ./inc/ ./src/ -name '*.h'))
 OBJ 		      = $(subst ./src/,./obj/, $(SRC:.cpp=.o)) 
 OBJ_MAIN              = $(subst ./src/,./obj/, $(SRC_MAIN:.cc=.o))
-INC 		      = -I./src \
+INC 		      = -O3 -I./src \
 		        -I./inc \
-		        $(INC_EXT)
-LIB		      = $(LIB_EXT) -lmuparser
+			-I./extern/eigen/
+LIB		      = $(LIB_EXT) -lmuparser $(LIB_PYTHON) -lpython3.8
+
 
 .SECONDARY: $(OBJ) $(OBJ_MAIN)
 
-all: make_directories $(EXE)
+all: make_directories $(EXE) $(PYTHON_NAME)
 	@echo $(B_ON)$(FG_GREEN)"###"
 	@echo "### DONE" 
 	@echo "###"$(RESET)	
 
-$(PREFIX)bin/%: ./obj/%.o $(OBJ) 
+$(PYTHON_NAME): ./src/python.cpp $(OBJ)
+	@echo $(B_ON)$(FG_BLUE)"###"
+	@echo "### LINKING $@" 
+	@echo "###"$(RESET)
+	$(CC) $(INC) -I./extern/pybind11/include/ -O3 -Wall -shared -std=c++11 -fPIC $(INC_PYTHON) src/python.cpp -o $@
+
+bin/wield: ./obj/wield.o $(OBJ) 
 	@echo $(B_ON)$(FG_BLUE)"###"
 	@echo "### LINKING $@" 
 	@echo "###"$(RESET)

src/Integrator/wieldSurface.h

@@ -82,6 +82,20 @@ double Surface(Wield::Series::FourierSeries<Mollifier> C1,
   return real(w12);
 }
 
+//double SurfaceGaussDirac(//Wield::Series::FourierSeries<Wield::Series::GaussDirac> C1,
+//						 //Eigen::Matrix3d R1,
+//						 //Wield::Series::FourierSeries<Wield::Series::GaussDirac> C2,
+//						 //Eigen::Matrix3d R2,
+//						 double epsilon,
+//						 double tolerance
+//	)
+//{
+//	std::cout << "made it inside..." << std::endl;
+//	return 0.0;
+//	//Surface(C1,R1,C2,R2,epsilon,tolerance);
+//}
+
+
 template<class Mollifier>
 double Surface(Wield::Series::FourierSeries<Mollifier> C1,
 	       Eigen::Matrix3d R1,

src/Series/wieldFourierSeries.h

@@ -30,7 +30,6 @@ class FourierSeries
 	// {
 	//   return exp(-sigma*sigma*(x*x + y*y + z*z)/4.) / sqrt(8*pi*pi*pi);
 	// }
-
 	FourierSeries(const FourierSeries<Mollifier> &copy) : order(copy.order),
 														  alphaX(copy.alphaX),
 														  alphaY(copy.alphaY),
@@ -101,6 +100,24 @@ class FourierSeries
 			WIELD_PROGRESS_COMPLETE("Computing CSL");
 	}
 
+	FourierSeries(int _order,
+				  double _alphaX,
+				  double _alphaY,
+				  double _alphaZ,
+				  double _sigma,
+				  std::vector<double> X,
+				  std::vector<double> Y,
+				  std::vector<double> Z,
+				  int numThreads = 1,
+				  int verbose = false
+		) :FourierSeries(_order,_alphaX,_alphaY,_alphaZ,Mollifier(_sigma),X,Y,Z,numThreads,verbose)
+	{}
+
+	FourierSeries() : phiHat(0)
+	{
+	}
+
+
 	std::complex<double> &operator()(signed int i, signed int j, signed int k)
 	{
 		return C[(2 * order - 1) * (2 * order - 1) * (order + i - 1) + (2 * order - 1) * (order + j - 1) + (order + k - 1)];

src/Utils/wieldEigen.h

@@ -9,9 +9,9 @@
 #define eigen_assert(A) if (!(A)){ WIELD_EXCEPTION_NEW("Eigen Exception: the conditional (" << #A << ") failed");}
 //#define eigen_assert(A) if (!(A)){ cout << "Problem here"<< endl;}
 
-#include "eigen3/Eigen/Core"
-#include "eigen3/Eigen/Geometry"
-#include "eigen3/Eigen/LU"
+#include "Eigen/Core"
+#include "Eigen/Geometry"
+#include "Eigen/LU"
 
 #define Success Success_tmp
 #undef  Success_tmp

src/python.cpp

@@ -0,0 +1,76 @@
+#include <iostream>
+// #include <fstream>
+// #include <vector>
+// #include <fstream>
+// #include <stdexcept>
+// #include <csignal>
+// 
+// #include "tclap/CmdLine.h"
+// #include "TCLAP/IgnoreArg.h"
+// 
+// #include "Main/wieldEnergy1D.h"
+// #include "Main/wieldEnergy2D.h"
+// #include "Main/wieldCSL.h"
+// #include "Main/wieldEnergyOffset.h"
+// #include "Main/wieldBlenderVoxelData.h"
+// #include "Main/wieldVisualizeOR.h"
+// #include "Main/wieldEnergySurfaceSphere.h"
+// #include "Main/wieldEnergyInterface1D.h"
+// #include "Main/wieldEnergyOR1D.h"
+// #include "Main/wieldFacet2D.h"
+// #include "Utils/wieldExceptions.h"
+// #include "Utils/wieldProgress.h"
+// 
+
+#include "Reader/Reader.h"
+#include "Series/wieldGaussDirac.h"
+#include "Series/wieldFourierSeries.h"
+#include "Integrator/wieldSurface.h"
+
+#include "pybind11/pybind11.h"
+#include "pybind11/stl.h"
+#include "pybind11/eigen.h"
+
+double add(double i, double j) {
+    return i + j;
+}
+
+
+double SurfaceGaussDirac(Wield::Series::FourierSeries<Wield::Series::GaussDirac> C1,
+						 Eigen::Matrix3d R1,
+						 Wield::Series::FourierSeries<Wield::Series::GaussDirac> C2,
+						 Eigen::Matrix3d R2,
+						 double epsilon,
+						 double tolerance)
+{
+	return Wield::Integrator::Surface(C1,R1,C2,R2,epsilon,tolerance);
+}
+
+//PYBIND11_MODULE(wield, m) {
+//    m.doc() = "pybind11 example plugin"; // optional module docstring
+//
+//    m.def("add", &add, "A function that adds two numbers");
+//}
+
+//Wield::Integrator::Surface<Wield::Series::GaussDirac>;
+//int null()
+//{
+//	&createMatrixFromAngle;
+//	Wield::Integrator::Surface<Wield::Series::GaussDirac>;
+//}
+
+PYBIND11_MODULE(wield,m) {
+
+	pybind11::class_<Wield::Series::FourierSeries<Wield::Series::GaussDirac>>(m,"Crystal")
+		.def(pybind11::init<
+			 const int, const double, const double, const double,
+			 const double, std::vector<double>, std::vector<double>,std::vector<double>,
+			 int, int >());
+
+	m.def("Surface",&SurfaceGaussDirac,"Surface integrate");
+	//m.def("Surface",&add,"Surface integrate");
+	m.def("createMatrixFromAngle",&createMatrixFromAngle,"Surface integrate");
+
+}
+
+