adds cmake

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "pybind11"]
+	path = pybind11
+	url = https://github.com/pybind/pybind11.git

CMakeLists.txt

@@ -0,0 +1,22 @@
+cmake_minimum_required(VERSION 3.1)
+
+project(single_e)
+
+# boost
+find_package(Boost REQUIRED)
+
+# python
+find_package(PythonLibs REQUIRED)
+
+# Pybind11
+add_subdirectory(pybind11)
+
+pybind11_add_module(single_e single_e.cpp)
+
+target_link_libraries(single_e PRIVATE "${Boost_LIBRARIES}")
+target_include_directories(single_e PRIVATE ${Boost_INCLUDE_DIR} ${PYTHON_INCLUDE_DIRS})
+
+add_custom_command(
+    TARGET single_e POST_BUILD VERBATIM
+    COMMAND ${CMAKE_COMMAND} -E copy "$<TARGET_FILE:single_e>" "${CMAKE_SOURCE_DIR}/isolver.so"
+)

model1.py

@@ -20,4 +20,12 @@
 
 
 
+E_0, T_0,I_0 = x.characteristic_val()
+exp_data = np.loadtxt('HypD_9Hz_cv_current',skiprows=19)
+exp_t = exp_data[:,0]/T_0
+exp_I = exp_data[:,1]/I_0
+
+plt.plot(exp_t,exp_I,label='data')
+plt.plot(time,output,label='sim')
+plt.show()
 

python_wrapper.py

@@ -48,7 +48,7 @@ def non_dim_capacative(self,parameters):
 		self.E_reverse=self.E_reverse/self.E_0
 		self.dE=self.dE/self.E_0
 		return parameters
-	
+
 
 	def times(self):
 		final_time=(self.E_reverse-self.E_start)*2
@@ -57,14 +57,14 @@ def simulate(self, parameters, time):
 		#Parameters 1-4= Cdl, Cdl1, Cdl2, Cdl3, omega
 		output=isolver.I_tot_solver(parameters[0], parameters[1], parameters[2], parameters[3], parameters[4],self.v, self.alpha, self.E_start, self.E_reverse, self.dE, self.Ru, self.E0_mean, self.k0_mean, self.E0_sigma, 1)
 		output=np.array(output)
-		final_time=(self.E_reverse-self.E_start)*2
-		time=np.linspace(0,final_time,len(output), dtype='double')
-		plt.plot(time,output)
-		plt.xlabel('time')
-		plt.ylabel('Itot')
-		plt.show()
+		##final_time=(self.E_reverse-self.E_start)*2
+		##time=np.linspace(0,final_time,len(output), dtype='double')
+		##plt.plot(time,output)
+		##plt.xlabel('time')
+		##plt.ylabel('Itot')
+		##plt.show()
 		return output
-	
-	
+
+