changes since UIUC move

David Mayerich
1 parent c2b9aa35
Showing 26 changed files with 117 additions and 113 deletions Show diff stats
CMakeLists.txt
FindMatplotlib.cmake
FindPyQt4.cmake
README.md
cube27.pos
cyl3000fvp5.pos
cylslab3000.pos
etaGold.txt
etaSilver.txt
etaSilverAnalytic.txt
etaSilverPalik.txt
mpidefs-parallel.f90
mpidefs-serial.f90
msinput.inp
mstm-generic-main-v2.2.f90
mstm-gui.py
mstm-intrinsics.f90
mstm-main-v2.2.f90
mstm-manual-2011-v2.2.pdf
mstm-modules-v2.2.f90
@@ -42,6 +42,7 @@ class GuiWindow(QtGui.QMainWindow):
 		self.ui.spinRadius.setValue(self.params.a)
  
 	def getParams(self):
+		#get the parameters from the GUI and store them in the params structure
 		self.params.minLambda = self.ui.spinStartLambda.value()
 		self.params.maxLambda = self.ui.spinEndLambda.value()
 		self.params.snapshotLambda = self.ui.spinNearFieldLambda.value()
@@ -276,15 +277,11 @@ def RunSimulation(spectralSim = True):
 		parameters['real_ref_index_scale_factor'] = n.real
 		parameters['imag_ref_index_scale_factor'] = n.imag
 		parameters['length_scale_factor'] = (2.0 * 3.14159)/l
+		#parameters['length_scale_factor'] = 1.0/l
 		parameters['scattering_plane_angle_deg'] = gamma;
 		parameters['near_field_output_data'] = 0
 		#parameters['number_spheres'] = 1
  
-		#a = parameters.a;
-		#d = parameters.d;
-		#parameters.clearSpheres()
-		#parameters.addSphere(a, -(d + 2*a)/2, 0, 0)
-		#parameters.addSphere(a, (d + 2*a)/2, 0, 0)
  
 		#save the scripted input file
 		parameters.saveFile(l, 'scriptParams.inp')
@@ -303,8 +300,8 @@ def RunSimulation(spectralSim = True):
 		if parameters['calculate_near_field']:
 			results.parseNearField('nf-temp.dat')
  
-		#get the scattering amplitude matrix
-		results.calcScatteringAmp()
+			#get the scattering amplitude matrix
+			results.calcScatteringAmp()
  
  
 		#update the progress bar
@@ -3,49 +3,49 @@ from pylab import *
  
 class SimParserClass:
  
-    simResults = dict()
-    
-    sxNearField = 0
-    syNearField = 0
-    intersectedNearField = 0
-    
-    #near field data
-    gridNearField = []
-    maxNearField = []
-    
-    #the stokes matrix is read from the output
-    stokesMatrix = []
-    scatAmpMatrix = []
-    
+	simResults = dict()
+	
+	sxNearField = 0
+	syNearField = 0
+	intersectedNearField = 0
+	
+	#near field data
+	gridNearField = []
+	maxNearField = []
+	
+	#the stokes matrix is read from the output
+	stokesMatrix = []
+	scatAmpMatrix = []
+	
  
-    def __init__(self, parameters):
-        
-        self.params = parameters;
-        
-        self.simResults['lambda'] = list()      
+	def __init__(self, parameters):
+		
+		self.params = parameters;
+		
+		self.simResults['lambda'] = list()      
  
-        self.simResults['extinction_unpolarized'] = list()
-        self.simResults['extinction_parallel'] = list()
-        self.simResults['extinction_perpendicular'] = list()
-        self.simResults['extinction_total'] = list()
-        self.simResults['detector_field'] = list()
-        
-        self.gridNearField = []
-        self.maxNearField = []
-        
-        
-    def parseSimFile(self, l, fileName):
-        self.simResults['lambda'].append(l)
-        inFile = open(fileName, 'r')
+		self.simResults['extinction_unpolarized'] = list()
+		self.simResults['extinction_parallel'] = list()
+		self.simResults['extinction_perpendicular'] = list()
+		self.simResults['extinction_total'] = list()
+		self.simResults['detector_field'] = list()
+		
+		self.gridNearField = []
+		self.maxNearField = []
+		
+		
+	def parseSimFile(self, l, fileName):
+		self.simResults['lambda'].append(l)
+		inFile = open(fileName, 'r')
  
-        
-        while True:
-            
-            line = inFile.readline().strip()
+		
+		while True:
+			
+			line = inFile.readline().strip()
  
 			#if the simulation is for a single plane wave
-            if int(self.params['fixed_or_random_orientation']) == 0:
-                if line == 'scattering matrix elements':
+			if int(self.params['fixed_or_random_orientation']) == 0:
+				if line == 'scattering matrix elements':
 					#empty the stokes matrix
 					self.stokesMatrix = []
 					inFile.readline()
@@ -53,53 +53,54 @@ class SimParserClass:
 						values = map(float, inFile.readline().strip().split())
 						self.stokesMatrix.append(values)
 					break;
-                elif line == 'unpolarized total ext, abs, scat efficiencies, w.r.t. xv, and asym. parm':
-                    values = inFile.readline().strip().split(' ')
-                    self.simResults['extinction_unpolarized'].append(values[0])
-                elif line == 'parallel total ext, abs, scat efficiencies':
-                    values = inFile.readline().strip().split(' ')
-                    self.simResults['extinction_parallel'].append(values[0])
-                elif line == 'perpendicular total ext, abs, scat efficiencies':
-                    values = inFile.readline().strip().split(' ')
-                    self.simResults['extinction_perpendicular'].append(values[0])
-                
-            #if the simulation is for random orientations
-            else:
-                if line == 'scattering matrix elements':
-                    break
-                elif line == 'total ext, abs, scat efficiencies, w.r.t. xv, and asym. parm':
-                    values = inFile.readline().strip().split(' ')
-                    self.simResults['extinction_total'].append(values[0])
-                    
-    def parseNearField(self, fileName):
-        
-        inFile = open(fileName, 'r')
-        
-        #get the size of the near field grid
-        line = inFile.readline().strip()
-        self.sxNearField, self.syNearField = map(int, line.split())
-        
-        #get the number of spheres that are intersected
-        line = inFile.readline().strip()
-        self.intersectedNearField = int(line)
-        
-        #process intersections here-----------
-        
+				elif line == 'unpolarized total ext, abs, scat efficiencies, w.r.t. xv, and asym. parm':
+					values = inFile.readline().strip().split(' ')
+					self.simResults['extinction_unpolarized'].append(values[0])
+				elif line == 'parallel total ext, abs, scat efficiencies':
+					values = inFile.readline().strip().split(' ')
+					self.simResults['extinction_parallel'].append(values[0])
+				elif line == 'perpendicular total ext, abs, scat efficiencies':
+					values = inFile.readline().strip().split(' ')
+					self.simResults['extinction_perpendicular'].append(values[0])
+				
+			#if the simulation is for random orientations
+			else:
+				if line == 'scattering matrix elements':
+					break
+				elif line == 'total ext, abs, scat efficiencies, w.r.t. xv, and asym. parm':
+					values = inFile.readline().strip().split(' ')
+					self.simResults['extinction_total'].append(values[0])
+					
+	def parseNearField(self, fileName):
+		
+		inFile = open(fileName, 'r')
+		
+		#get the size of the near field grid
+		line = inFile.readline().strip()
+		self.sxNearField, self.syNearField = map(int, line.split())
+		
+		#get the number of spheres that are intersected
+		line = inFile.readline().strip()
+		self.intersectedNearField = int(line)
+		
+		#process intersections here-----------
+		
  
-        #get the field values
-        self.gridNearField = []
-        for y in range(self.syNearField):
-            self.gridNearField.append([])
-            for x in range(self.sxNearField):
-                line = inFile.readline().strip()
-                values = map(float, line.split())
-                self.gridNearField[y].append(values[2])
-                
-        E = array(self.gridNearField)
-        self.maxNearField.append(abs(E).max())
-        
-    #calculate and return the scattering amplitude matrix
-    def calcScatteringAmp(self):
+		#get the field values
+		self.gridNearField = []
+		for y in range(self.syNearField):
+			self.gridNearField.append([])
+			for x in range(self.sxNearField):
+				line = inFile.readline().strip()
+				values = map(float, line.split())
+				self.gridNearField[y].append(values[2])
+				
+		E = array(self.gridNearField)
+		#the enhancement is E^4 (so (E^2)^2)
+		self.maxNearField.append(pow(abs(E).max(), 2))
+		
+	#calculate and return the scattering amplitude matrix
+	def calcScatteringAmp(self):
 		#compute the number of entries in the stokes matrix
 		nEntries = len(self.stokesMatrix)
  
@@ -122,29 +123,35 @@ class SimParserClass:
 		E = [S[0], S[2]]
 		self.simResults['detector_field'].append(E)
 		print(E)
-               
+			
  
-    def saveFile(self, fileName):
-        outFile = open(fileName, 'w')
-        outFile.write(str(self))
-        outFile.close()
+	def saveFile(self, fileName):
+		outFile = open(fileName, 'w')
+		outFile.write(str(self))
+		outFile.close()
  
-    def __getitem__(self, key):
-        return self.simResults[key];
+	def __getitem__(self, key):
+		return self.simResults[key];
  
-    def __str__(self):
-        result = '';
+	def __str__(self):
+		result = '';
  
-        for i in range(len(self.simResults['lambda'])):
-            result += str(self.simResults['lambda'][i])
-            result += '\t' + str(self.simResults['extinction_unpolarized'][i])
-            result += '\t' + str(self.simResults['extinction_parallel'][i])
-            result += '\t' + str(self.simResults['extinction_perpendicular'][i])
-            result += '\t' + str(self.simResults['detector_field'][i][0]) + '\t' + str(self.simResults['detector_field'][i][1])
-            
-            #parse the near field if it is included in the simulation
-            #if int(parameters['calculate_near_field']) == 1:
-            #    result += '\t' + str(maxNearField)
-                
-            result += '\n'
-        return result
+		for i in range(len(self.simResults['lambda'])):
+			result += str(self.simResults['lambda'][i])
+			if int(self.params['fixed_or_random_orientation']) == 0:
+				result += '\t' + str(self.simResults['extinction_unpolarized'][i])
+				result += '\t' + str(self.simResults['extinction_parallel'][i])
+				result += '\t' + str(self.simResults['extinction_perpendicular'][i])
+			else:
+				result += '\t' + str(self.simResults['extinction_total'][i])
+				
+			#result += '\t' + str(self.simResults['detector_field'][i][0]) + '\t' + str(self.simResults['detector_field'][i][1])
+				
+			
+			
+			#parse the near field if it is included in the simulation
+			#if int(parameters['calculate_near_field']) == 1:
+			#    result += '\t' + str(maxNearField)
+				
+			result += '\n'
+		return result