Merge branch 'develop'

giadarol · giadarol · commit dd0a95748a72 · 2016-02-26T16:23:43.000+01:00
diff --git a/MP_system.py b/MP_system.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                                          
-#                   PyECLOUD Version 4.37                     
+#                   PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/PyEC4PyHT.py b/PyEC4PyHT.py
@@ -8,7 +8,7 @@
 #     
 #     This file is part of the code:
 #                                                                                          
-#                   PyECLOUD Version 4.37                     
+#                   PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
@@ -86,7 +86,7 @@ def __init__(self, L_ecloud, slicer, Dt_ref, pyecl_input_folder='./', flag_clean
 				slice_by_slice_mode=False, **kwargs):
 		
 		
-		print 'PyECLOUD Version 4.37'
+		print 'PyECLOUD Version 5.0.1'
 		print 'PyHEADTAIL module'
 		print 'Initializing ecloud from folder: '+pyecl_input_folder
 		self.slicer = slicer
@@ -421,11 +421,6 @@ def _reinitialize(self):
 		self.MP_e.nel_mp[:self.init_N_mp] = self.init_nel
 		self.MP_e.N_mp = self.init_N_mp
 		
-		MP_e = self.MP_e
-		dynamics = self.dynamics
-		impact_man = self.impact_man
-		spacech_ele = self.spacech_ele
-
 		if self.save_ele_distributions_last_track:
 			self.rho_ele_last_track = []
 
diff --git a/beam_and_timing.py b/beam_and_timing.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                                          
-#                   PyECLOUD Version 4.37                     
+#                   PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/buildup_simulation.py b/buildup_simulation.py
@@ -9,7 +9,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                   
+#		           PyECLOUD Version 5.0.1                   
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
@@ -59,7 +59,7 @@
 class BuildupSimulation(object):
 	def __init__(self, pyecl_input_folder='./', **kwargs):
 
-		print 'PyECLOUD Version 4.37'
+		print 'PyECLOUD Version 5.0.1'
 		beamtim,MP_e, dynamics,impact_man, pyeclsaver, \
 				gas_ion_flag, resgasion, t_ion, \
 				spacech_ele,t_sc_ON, photoem_flag, phemiss,\
diff --git a/change_version_number.py b/change_version_number.py
@@ -9,7 +9,7 @@
         with open(filename) as fid:
             content=fid.read()
         if 'giovanni.iadarola@cern.ch' in content:
-            content=content.replace('PyECLOUD Version 4.37', 'PyECLOUD Version 4.37')
+            content=content.replace('PyECLOUD Version 5.0.1', 'PyECLOUD Version 5.0.1')
             with open(filename,'w') as fid:
                 fid.write(content)
         
diff --git a/doc/reference/reference.pdf b/doc/reference/reference.pdf
diff --git a/doc/reference/src/reference.tex b/doc/reference/src/reference.tex
@@ -446,7 +446,7 @@ \subsection{Simulation parameters}
 \end{enumerate}\\ \hline
 \multicolumn{2}{p{.97\textwidth}}{
 When flag\_bunched\_beam = 1 the following parameters must be provided:}\\ \hline
-\textbf{sigmaz}&	[m] Bunch length (1 $\sigma$). \\ \hline
+\textbf{sigmaz}&	[m] Bunch length (1$\sigma$). \\ \hline
 \textbf{t\_offs}&	[s] Delay in the longitudinal profile (n.b. if t\_offs=0 only half of the first bunch is simulated).\\ \hline
 \textbf{filling\_pattern\_file}&	Name of a file providing the intensities of the different bunches (zeros for empty slots). 
 The data can be provided also in form of a python list with no need to provide an input file, e.g. filling\_pattern\_file=4*(72*[1.]+8*[0.]).\\ \hline
diff --git a/dynamics_Boris_f2py.py b/dynamics_Boris_f2py.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                     
+#		           PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/dynamics_Boris_multipole.py b/dynamics_Boris_multipole.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                                           
-#                          PyECLOUD Version 4.37                   
+#                          PyECLOUD Version 5.0.1                   
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/dynamics_dipole.py b/dynamics_dipole.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                     
+#		           PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/dynamics_strong_B_generalized.py b/dynamics_strong_B_generalized.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                     
+#		           PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/gas_ionization_class.py b/gas_ionization_class.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                     
+#		           PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/gen_photoemission_class.py b/gen_photoemission_class.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                   
+#		           PyECLOUD Version 5.0.1                   
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/geom_impact_ellip.py b/geom_impact_ellip.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37               
+#		           PyECLOUD Version 5.0.1               
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/geom_impact_poly.py b/geom_impact_poly.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                                          
-#                   PyECLOUD Version 4.37                   
+#                   PyECLOUD Version 5.0.1                   
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/geom_impact_poly_fast_impact.py b/geom_impact_poly_fast_impact.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                                          
-#                   PyECLOUD Version 4.37                   
+#                   PyECLOUD Version 5.0.1                   
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/geom_impact_rect_fast_impact.py b/geom_impact_rect_fast_impact.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                                          
-#                   PyECLOUD Version 4.37                   
+#                   PyECLOUD Version 5.0.1                   
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/impact_management_class.py b/impact_management_class.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                     
+#		           PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/init.py b/init.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                      
+#		           PyECLOUD Version 5.0.1                      
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/main.py b/main.py
@@ -9,7 +9,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                   
+#		           PyECLOUD Version 5.0.1                   
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/proc_video3.py b/proc_video3.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                  
+#		           PyECLOUD Version 5.0.1                  
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/pyecloud_saver.py b/pyecloud_saver.py
@@ -8,7 +8,7 @@
 #     
 #     This file is part of the code:
 #                                                                                          
-#                   PyECLOUD Version 4.37                     
+#                   PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
@@ -68,7 +68,7 @@ def __init__(self, logfile_path):
 		self.logfile_path = logfile_path
 		print 'Starting pyecloud_saver init.'
 		flog=open(self.logfile_path,'w')
-		flog.write('PyECLOUD Version 4.37\n')
+		flog.write('PyECLOUD Version 5.0.1\n')
 		timestr = time.strftime("%d %b %Y %H:%M:%S", time.localtime())
 		flog.write('Simulation started on %s\n'%timestr)
 		flog.close()
diff --git a/sec_emission.py b/sec_emission.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                     
+#		           PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/sec_emission_model_ECLOUD.py b/sec_emission_model_ECLOUD.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                     
+#		           PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/sec_emission_model_ECLOUD_nunif.py b/sec_emission_model_ECLOUD_nunif.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                     
+#		           PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/sec_emission_model_accurate_low_ene.py b/sec_emission_model_accurate_low_ene.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                     
+#		           PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/sec_emission_model_cos_low_ener.py b/sec_emission_model_cos_low_ener.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                     
+#		           PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/sec_emission_model_flat_low_ener.py b/sec_emission_model_flat_low_ener.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                     
+#		           PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/sincc_cosincc_cubsincc.py b/sincc_cosincc_cubsincc.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                      		            
-#		           PyECLOUD Version 4.37                      
+#		           PyECLOUD Version 5.0.1                      
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/space_charge_class.py b/space_charge_class.py
@@ -8,7 +8,7 @@
 #     This file is part of the code:
 #                                                                      		    
 # 
-#		           PyECLOUD Version 4.37                     
+#		           PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/space_charge_class_SW_old.py b/space_charge_class_SW_old.py
@@ -8,7 +8,7 @@
 #     This file is part of the code:
 #                                                                      		    
 # 
-#		           PyECLOUD Version 4.37                     
+#		           PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/test_StrongB_generalized.py b/test_StrongB_generalized.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                                          
-#                   PyECLOUD Version 4.37                     
+#                   PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 
diff --git a/test_StrongB_generalized_2.py b/test_StrongB_generalized_2.py
@@ -7,7 +7,7 @@
 #     
 #     This file is part of the code:
 #                                                                                          
-#                   PyECLOUD Version 4.37                     
+#                   PyECLOUD Version 5.0.1                     
 #                  
 #                                                                       
 #     Author and contact:   Giovanni IADAROLA 

Original file line number	Diff line number	Diff line change
`@@ -7,7 +7,7 @@`
`7`	`7`	`#`
`8`	`8`	`# This file is part of the code:`
`9`	`9`	`#`
`10`		`-# PyECLOUD Version 4.37`
	`10`	`+# PyECLOUD Version 5.0.1`
`11`	`11`	`#`
`12`	`12`	`#`
`13`	`13`	`# Author and contact: Giovanni IADAROLA`
Original file line number	Diff line number	Diff line change
`@@ -8,7 +8,7 @@`
`8`	`8`	`#`
`9`	`9`	`# This file is part of the code:`
`10`	`10`	`#`
`11`		`-# PyECLOUD Version 4.37`
	`11`	`+# PyECLOUD Version 5.0.1`
`12`	`12`	`#`
`13`	`13`	`#`
`14`	`14`	`# Author and contact: Giovanni IADAROLA`
`@@ -86,7 +86,7 @@ def __init__(self, L_ecloud, slicer, Dt_ref, pyecl_input_folder='./', flag_clean`
`86`	`86`	`slice_by_slice_mode=False, **kwargs):`
`87`	`87`
`88`	`88`
`89`		`- print 'PyECLOUD Version 4.37'`
	`89`	`+ print 'PyECLOUD Version 5.0.1'`
`90`	`90`	`print 'PyHEADTAIL module'`
`91`	`91`	`print 'Initializing ecloud from folder: '+pyecl_input_folder`
`92`	`92`	`self.slicer = slicer`
`@@ -421,11 +421,6 @@ def _reinitialize(self):`
`421`	`421`	`self.MP_e.nel_mp[:self.init_N_mp] = self.init_nel`
`422`	`422`	`self.MP_e.N_mp = self.init_N_mp`
`423`	`423`
`424`		`- MP_e = self.MP_e`
`425`		`- dynamics = self.dynamics`
`426`		`- impact_man = self.impact_man`
`427`		`- spacech_ele = self.spacech_ele`
`428`		`-`
`429`	`424`	`if self.save_ele_distributions_last_track:`
`430`	`425`	`self.rho_ele_last_track = []`
`431`	`426`
Original file line number	Diff line number	Diff line change
`@@ -9,7 +9,7 @@`
`9`	`9`	`#`
`10`	`10`	`# This file is part of the code:`
`11`	`11`	`#`
`12`		`-# PyECLOUD Version 4.37`
	`12`	`+# PyECLOUD Version 5.0.1`
`13`	`13`	`#`
`14`	`14`	`#`
`15`	`15`	`# Author and contact: Giovanni IADAROLA`
`@@ -59,7 +59,7 @@`
`59`	`59`	`class BuildupSimulation(object):`
`60`	`60`	`def __init__(self, pyecl_input_folder='./', **kwargs):`
`61`	`61`
`62`		`- print 'PyECLOUD Version 4.37'`
	`62`	`+ print 'PyECLOUD Version 5.0.1'`
`63`	`63`	`beamtim,MP_e, dynamics,impact_man, pyeclsaver, \`
`64`	`64`	`gas_ion_flag, resgasion, t_ion, \`
`65`	`65`	`spacech_ele,t_sc_ON, photoem_flag, phemiss,\`