ftir et epitaxie corrigées

.idea/misc.xml

 <?xml version="1.0" encoding="UTF-8"?>
 <project version="4">
-  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.9 (eam-vcsel)" project-jdk-type="Python SDK" />
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.8 (eam-vcsel)" project-jdk-type="Python SDK" />
 </project>
\ No newline at end of file

calculation.py

@@ -62,9 +62,9 @@ def zandberg_electromagnetic_amplitude(electric_field=0., wavelength=1e-6):
 
 
 
-def ftir_reflectivity(filename='eam_2'):
+def ftir_reflectivity(filename='eam_2', document_folder=True, linux=True):
     # import data
-    wavelength, r = vtx.import_vertex_70_data(filename)
+    wavelength, r = vtx.import_vertex_70_data(filename, document_folder=document_folder, linux=linux)
 
     # smooth the curve (I know it is cheating but ftir currently is out of service, so data is disgusting)
     bspl = splrep(wavelength, r, s=4.5)
@@ -72,7 +72,7 @@ def ftir_reflectivity(filename='eam_2'):
 
     #  correct data
     r_max = np.max(r)
-    r = r * 0.99 / r_max
+    r = r * 0.96 / r_max
 
     # plot
     plt.plot_reflectivity(wavelength, r)

epitaxy.py

@@ -159,6 +159,80 @@ def reflectivity_from_growth_speed_1x2(bypass_dbr=True, delta_speed=0.1, start_w
 
 
 
+def reflectivity_from_growth_speed_1x1(bypass_dbr=True, delta_speed=0.1, start_wavelength=700e-9, stop_wavelength=1000e-9, electric_field=0., n_points=200):
+    # reflectivity computation parameters
+    wavelength = np.linspace(start_wavelength, stop_wavelength, num=n_points)
+    r = np.zeros(len(wavelength))
+
+    # epitaxy structure parameters
+    speed_array = np.array([1.05, 1.10])
+    v_al5 = 900 * speed_array
+
+    cell_list = [v_al5]
+    cell_names = ['v_al5']
+
+    # figure parameters
+    # create a figure
+    fig = make_subplots(rows=1, cols=1,
+                        subplot_titles=(cell_names[0]))
+
+    for i in tqdm(range(len(cell_list))):
+        for j in range(len(cell_list[i])):
+            argument = {cell_names[i]: cell_list[i][j]}
+
+            sl = sls.structure_eam(bypass_dbr=bypass_dbr,
+                                   **argument,
+                                   v_ga6=100.*0.95,
+                                   v_ga11=850.*0.95)
+
+            for k in range(len(wavelength)):
+                sl = op.algaas_super_lattice_refractive_index(sl, electric_field, wavelength[k])
+
+                n = sl['refractive_index'].to_numpy(dtype=np.complex128)
+                d = sl['thickness'].to_numpy(dtype=np.complex128)
+
+                r[k] = op.reflection(n, d, wavelength[k])
+
+            # add the traces
+            fig.add_trace(
+                go.Scatter(
+                    x=wavelength,
+                    y=r,
+                    name=cell_names[i] +' = ' +str(cell_list[i][j]) +' um/h'),
+                row=row_num(i),
+                col=col_num(i),
+            )
+
+            # create axis objects
+            fig.update_layout(
+                xaxis=dict(
+                    title='wavelength [m]'
+                ),
+                yaxis=dict(
+                    title='reflectivity [1]',
+                    titlefont=dict(
+                        color='#1f77b4'
+                    ),
+                    tickfont=dict(
+                        color='#1f77b4'
+                    )
+                )
+            )
+
+
+    # update layout properties
+    fig.update_layout(
+        title_text='reflectivity as a function of wavelength',
+        width=1600,
+    )
+
+
+    # show the figure
+    fig.show()
+
+
+
+
 def row_num(x):
     if x>=2:
         return 2