Add some wavelength-dependent effects

AreaPlot.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-#Author: Craig Lage, NYU; 
+#Author: Craig Lage, NYU;
 #Date: 16-Nov-15
 
 #This program plots the pixel area plots from the Poisson CCD solver
@@ -77,7 +77,7 @@ def ReadAreaFile(filename, nx, ny):
         j = int(items[1])
         area[i,j] = float(items[2])
     return area
-                 
+
 
 #****************MAIN PROGRAM*****************
 
@@ -98,7 +98,7 @@ def ReadAreaFile(filename, nx, ny):
 NyCenter = 4
 Area_0 = 100.0
 
-filename = outputfiledir + '/' + outputfilebase +'_%d_Area'%step
+filename = outputfiledir + '/' + outputfilebase +'_%d_Area'%step+'.dat'
 
 area = ReadAreaFile(filename, Nx, Ny)
 
@@ -183,7 +183,7 @@ def ReadAreaFile(filename, nx, ny):
 for i in range(Nx+1):
     plot([10.0 + 10.0 * i, 10.0 + 10.0 * i], [10.0, 100.0], color = 'black')
 for j in range(Ny+1):
-    plot([10.0, 100.0], [10.0 + 10.0 * j, 10.0 + 10.0 * j], color = 'black') 
+    plot([10.0, 100.0], [10.0 + 10.0 * j, 10.0 + 10.0 * j], color = 'black')
 for i in range(Nx):
     for j in range(Ny):
         if i == NxCenter and j == NyCenter:

AreaPlot_Corr.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-#Author: Craig Lage, NYU; 
+#Author: Craig Lage, NYU;
 #Date: 16-Nov-15
 
 #This program plots the pixel area plots from the Poisson CCD solver
@@ -77,7 +77,7 @@ def ReadAreaFile(filename, nx, ny):
         j = int(items[1])
         area[i,j] = float(items[2])
     return area
-                 
+
 
 #****************MAIN PROGRAM*****************
 
@@ -98,7 +98,7 @@ def ReadAreaFile(filename, nx, ny):
 NyCenter = 4
 Area_0 = 100.0
 
-filename = outputfiledir + '/' + outputfilebase +'_%d_Area'%step
+filename = outputfiledir + '/' + outputfilebase +'_%d_Area'%step+'.dat'
 
 area = ReadAreaFile(filename, Nx, Ny)
 
@@ -183,7 +183,7 @@ def ReadAreaFile(filename, nx, ny):
 for i in range(Nx+1):
     plot([10.0 + 10.0 * i, 10.0 + 10.0 * i], [10.0, 100.0], color = 'black')
 for j in range(Ny+1):
-    plot([10.0, 100.0], [10.0 + 10.0 * j, 10.0 + 10.0 * j], color = 'black') 
+    plot([10.0, 100.0], [10.0 + 10.0 * j, 10.0 + 10.0 * j], color = 'black')
 for i in range(Nx):
     for j in range(Ny):
         if i == NxCenter and j == NyCenter:

AreaTrend.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-#Author: Craig Lage, NYU; 
+#Author: Craig Lage, NYU;
 #Date: 16-Nov-15
 
 #This program plots the pixel area plots from the Poisson CCD solver
@@ -77,7 +77,7 @@ def ReadAreaFile(filename, nx, ny):
         j = int(items[1])
         area[i,j] = float(items[2])
     return area
-                 
+
 
 #****************MAIN PROGRAM*****************
 dirs = ["data/run1","data/run2","data/run3","data/run4","data/run6"]
@@ -99,7 +99,7 @@ def ReadAreaFile(filename, nx, ny):
     NyCenter = int((ConfigData["FilledPixelCoords_0_0"][1] - ConfigData["PixelBoundaryLowerLeft"][1]) / ConfigData["PixelSize"])
     NumElec = ConfigData["CollectedCharge_0_0"]
 
-    filename = outputfiledir + '/' + outputfilebase +'_0_Area'
+    filename = outputfiledir + '/' + outputfilebase +'_0_Area' + '.dat'
 
     area = ReadAreaFile(filename, Nx, Ny)
 

ChargeDistribution.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-#Author: Craig Lage, NYU; 
+#Author: Craig Lage, NYU;
 #Date: 26-Jan-15
 
 #This program plots the Poisson equation solutions from the C++ Poisson solver
@@ -12,13 +12,13 @@
 #****************SUBROUTINES*****************
 class Array3dHDF5Elec(object):
     def __init__(self, dir, filebase, n):
-        elecfile = dir+'/'+filebase+'_'+str(n)+'_Elec'
+        elecfile = dir+'/'+filebase+'_'+str(n)+'_Elec' + '.hdf5'
         hdfelec = h5py.File(elecfile,'r')
         Dimension = hdfelec[hdfelec.items()[0][0]].attrs[u'Dimension']
         self.nx=Dimension[0]
         self.ny=Dimension[1]
         self.nz=Dimension[2]
-        
+
         Lower_Left = hdfelec[hdfelec.items()[0][0]].attrs[u'Lower_Left']
         self.xmin=Lower_Left[0]
         self.ymin=Lower_Left[1]
@@ -28,11 +28,11 @@ def __init__(self, dir, filebase, n):
         self.xmax=Upper_Right[0]
         self.ymax=Upper_Right[1]
         self.zmax=100.0
-        
+
         self.dx=(self.xmax-self.xmin)/self.nx
         self.dy=(self.ymax-self.ymin)/self.ny
         self.dzp=(self.zmax-self.zmin)/(ConfigData["Nx"] * ConfigData["ScaleFactor"] + 1)
-        
+
         self.x=linspace(self.xmin+self.dx/2,self.xmax-self.dx/2,self.nx)
         self.y=linspace(self.ymin+self.dy/2,self.ymax-self.dy/2,self.ny)
         self.zp=linspace(self.zmin+self.dzp/2,self.zmax-self.dzp/2,(ConfigData["Nx"] * ConfigData["ScaleFactor"] + 1))[0:16*ConfigData["ScaleFactor"]]
@@ -140,7 +140,7 @@ def ReadConfigFile(filename):
 # This holds all of the data
 ScaleFactor = ConfigData["ScaleFactor"]
 GridsPerPixel = ConfigData["GridsPerPixel"]
-dat = Array3dHDF5Elec(outputfiledir, outputfilebase, run) 
+dat = Array3dHDF5Elec(outputfiledir, outputfilebase, run)
 
 nxx = dat.nx - 1
 nyy = dat.ny - 1
@@ -228,9 +228,3 @@ def ReadConfigFile(filename):
 ax3.imshow(log10(fliplr(plotarray)), interpolation = 'nearest')
 savefig(outputfiledir+"/plots/ChargeDistribution_%d.pdf"%run)
 close(fig)
-
-
-
-
-
-

ChargeDistribution_XYZDist.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-#Author: Craig Lage, NYU; 
+#Author: Craig Lage, NYU;
 #Date: 26-Jan-15
 
 #This program plots the Poisson equation solutions from the C++ Poisson solver
@@ -12,13 +12,13 @@
 #****************SUBROUTINES*****************
 class Array3dHDF5Elec(object):
     def __init__(self, dir, filebase, n):
-        elecfile = dir+'/'+filebase+'_'+str(n)+'_Elec'
+        elecfile = dir+'/'+filebase+'_'+str(n)+'_Elec' + '.hdf5'
         hdfelec = h5py.File(elecfile,'r')
         Dimension = hdfelec[hdfelec.items()[0][0]].attrs[u'Dimension']
         self.nx=Dimension[0]
         self.ny=Dimension[1]
         self.nz=Dimension[2]
-        
+
         Lower_Left = hdfelec[hdfelec.items()[0][0]].attrs[u'Lower_Left']
         self.xmin=Lower_Left[0]
         self.ymin=Lower_Left[1]
@@ -28,11 +28,11 @@ def __init__(self, dir, filebase, n):
         self.xmax=Upper_Right[0]
         self.ymax=Upper_Right[1]
         self.zmax=100.0
-        
+
         self.dx=(self.xmax-self.xmin)/self.nx
         self.dy=(self.ymax-self.ymin)/self.ny
         self.dzp=(self.zmax-self.zmin)/(ConfigData["Nx"] * ConfigData["ScaleFactor"] + 1)
-        
+
         self.x=linspace(self.xmin+self.dx/2,self.xmax-self.dx/2,self.nx)
         self.y=linspace(self.ymin+self.dy/2,self.ymax-self.dy/2,self.ny)
         self.zp=linspace(self.zmin+self.dzp/2,self.zmax-self.dzp/2,(ConfigData["Nx"] * ConfigData["ScaleFactor"] + 1))[0:16*ConfigData["ScaleFactor"]]
@@ -140,7 +140,7 @@ def ReadConfigFile(filename):
 # This holds all of the data
 ScaleFactor = ConfigData["ScaleFactor"]
 GridsPerPixel = ConfigData["GridsPerPixel"]
-dat = Array3dHDF5Elec(outputfiledir, outputfilebase, run) 
+dat = Array3dHDF5Elec(outputfiledir, outputfilebase, run)
 
 nxx = dat.nx - 1
 nyy = dat.ny - 1
@@ -257,9 +257,3 @@ def ReadConfigFile(filename):
 ax6.set_ylabel("Charge Density")
 savefig(outputfiledir+"/plots/ChargeDistribution_XYZ_%d.pdf"%run)
 close(fig)
-
-
-
-
-
-

ChargeDistribution_XYZDist_N.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-#Author: Craig Lage, NYU; 
+#Author: Craig Lage, NYU;
 #Date: 26-Jan-15
 
 #This program plots the Poisson equation solutions from the C++ Poisson solver
@@ -12,15 +12,15 @@
 #****************SUBROUTINES*****************
 class Array3dHDF5Elec(object):
     def __init__(self, dir, filebase, n):
-        elecfile = dir+'/'+filebase+'_'+str(n)+'_Elec'
+        elecfile = dir+'/'+filebase+'_'+str(n)+'_Elec' + '.hdf5'
         hdfelec = h5py.File(elecfile,'r')
-        holefile = dir+'/'+filebase+'_'+str(n)+'_Hole'
+        holefile = dir+'/'+filebase+'_'+str(n)+'_Hole' + '.hdf5'
         hdfhole = h5py.File(holefile,'r')
         Dimension = hdfelec[hdfelec.items()[0][0]].attrs[u'Dimension']
         self.nx=Dimension[0]
         self.ny=Dimension[1]
         self.nz=Dimension[2]
-        
+
         Lower_Left = hdfelec[hdfelec.items()[0][0]].attrs[u'Lower_Left']
         self.xmin=Lower_Left[0]
         self.ymin=Lower_Left[1]
@@ -30,11 +30,11 @@ def __init__(self, dir, filebase, n):
         self.xmax=Upper_Right[0]
         self.ymax=Upper_Right[1]
         self.zmax=100.0
-        
+
         self.dx=(self.xmax-self.xmin)/self.nx
         self.dy=(self.ymax-self.ymin)/self.ny
         self.dzp=(self.zmax-self.zmin)/(ConfigData["Nx"] * ConfigData["ScaleFactor"] + 1)
-        
+
         self.x=linspace(self.xmin+self.dx/2,self.xmax-self.dx/2,self.nx)
         self.y=linspace(self.ymin+self.dy/2,self.ymax-self.dy/2,self.ny)
         self.zp=linspace(self.zmin+self.dzp/2,self.zmax-self.dzp/2,(ConfigData["Nx"] * ConfigData["ScaleFactor"] + 1))[0:32*ConfigData["ScaleFactor"]]
@@ -74,7 +74,7 @@ def ZIndex(z):
         self.Channelkmin = ZIndex(ConfigData["GateOxide"] * EPSILON_SI / EPSILON_OX)
 
         self.elec=array(hdfelec[hdfelec.items()[0][0]])
-        self.hole=array(hdfhole[hdfhole.items()[0][0]])        
+        self.hole=array(hdfhole[hdfhole.items()[0][0]])
 
 def ReadConfigFile(filename):
     # This reads the config file for the necessary settings
@@ -143,7 +143,7 @@ def ReadConfigFile(filename):
 # This holds all of the data
 ScaleFactor = ConfigData["ScaleFactor"]
 GridsPerPixel = ConfigData["GridsPerPixel"]
-dat = Array3dHDF5Elec(outputfiledir, outputfilebase, run) 
+dat = Array3dHDF5Elec(outputfiledir, outputfilebase, run)
 
 nxx = dat.nx - 1
 nyy = dat.ny - 1
@@ -186,7 +186,7 @@ def ReadConfigFile(filename):
 
     if i == 1:
         nxcenter += ScaleFactor * GridsPerPixel / 2
-        nycenter += ScaleFactor * GridsPerPixel / 2        
+        nycenter += ScaleFactor * GridsPerPixel / 2
 
     fig = figure(figsize = (12,12))
     suptitle("%s Charge Distribution"%carriers[i], fontsize = 36)
@@ -265,20 +265,14 @@ def ReadConfigFile(filename):
         ax6.plot(dat.z[:],plotarray, label = '(X,Y) = (%.2f,%.2f)'%(dat.x[nxcenter],dat.y[nycenter]))
     if i == 1:
         plotarray = log10(plotdata[nxcenter,nycenter,:]+0.01)
-        ax6.plot(dat.z[:],plotarray, label = '(X,Y) = (%.2f,%.2f)'%(dat.x[nxcenter],dat.y[nycenter]))        
-        nycenter -= ScaleFactor * GridsPerPixel / 2        
+        ax6.plot(dat.z[:],plotarray, label = '(X,Y) = (%.2f,%.2f)'%(dat.x[nxcenter],dat.y[nycenter]))
+        nycenter -= ScaleFactor * GridsPerPixel / 2
         plotarray = log10(plotdata[nxcenter,nycenter,:]+0.01)
-        ax6.plot(dat.z[:],plotarray, label = '(X,Y) = (%.2f,%.2f)'%(dat.x[nxcenter],dat.y[nycenter]))        
+        ax6.plot(dat.z[:],plotarray, label = '(X,Y) = (%.2f,%.2f)'%(dat.x[nxcenter],dat.y[nycenter]))
         legend(bbox_to_anchor=(1.05, 0.5), loc=2, fontsize = 9)
     ax6.set_ylabel("Log Charge Density")
     ax6.set_xlim(ax6.get_xlim()[::-1])
     ax6.set_xticks([0.0,1.0,2.0])
     ax6.set_xlabel("Z ( Microns)")
     savefig(outputfiledir+"/plots/%sDistribution_XYZ_%d.pdf"%(carriers[i],run))
     close(fig)
-
-
-
-
-
-