Merge branch 'develop'

PyCOMPLETE · Oct 27, 2017 · 2bb0ba8 · 2bb0ba8
2 parents 26ac39e + d336880
commit 2bb0ba8
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Showing 45 changed files with 1,032 additions and 1,170 deletions.
diff --git a/MP_system.py b/MP_system.py
@@ -7,7 +7,7 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 6.6.0
+#                   PyECLOUD Version 6.7.0
 #
 #
 #     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 6.6.0
+#                   PyECLOUD Version 6.7.0
 #
 #
 #     Author and contact:   Giovanni IADAROLA
@@ -67,7 +67,7 @@ class Ecloud(object):
     def __init__(self, L_ecloud, slicer, Dt_ref, pyecl_input_folder='./', flag_clean_slices=False,
                  slice_by_slice_mode=False, space_charge_obj=None, MP_e_mass=m_e, MP_e_charge=-e, **kwargs):
 
-        print 'PyECLOUD Version 6.6.0'
+        print 'PyECLOUD Version 6.7.0'
 
         # These git commands return the hash and the branch of the specified git directory.
         path_to_git = os.path.dirname(os.path.abspath(__file__)) +'/.git'

diff --git a/PyEC4PyHT_fastion.py b/PyEC4PyHT_fastion.py
@@ -8,7 +8,7 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 6.6.0
+#                   PyECLOUD Version 6.7.0
 #
 #
 #     Author and contact:   Giovanni IADAROLA

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 6.6.0
+#                   PyECLOUD Version 6.7.0
 #
 #
 #     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 6.6.0
+#                   PyECLOUD Version 6.7.0
 #
 #
 #     Author and contact:   Giovanni IADAROLA
@@ -59,7 +59,7 @@
 class BuildupSimulation(object):
     def __init__(self, pyecl_input_folder='./', **kwargs):
 
-        print 'PyECLOUD Version 6.6.0'
+        print 'PyECLOUD Version 6.7.0'
         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 '[email protected]' in content:
-            content=content.replace('PyECLOUD Version 6.6.0', 'PyECLOUD Version 6.6.0')
+            content=content.replace('PyECLOUD Version 6.7.0', 'PyECLOUD Version 6.7.0')
             with open(filename,'w') as fid:
                 fid.write(content)
 

diff --git a/default_input_parameters.py b/default_input_parameters.py
@@ -1,5 +1,8 @@
 from scipy.constants import m_p
 
+# To be safe, only use immutable python types as default values in the parameters_dict.
+# This most importantly excludes python lists. Tuples may be used in their place.
+
 parameters_dict = {
     'simulation_parameters': {
         'mandatory': {
@@ -96,6 +99,8 @@
             'x_aper': None,
             'y_aper': None,
             'filename_chm': None,
+            'filename_chm_photoem': None,
+            'flag_counter_clockwise_chamb': None,
 
             # Tracking and magnetic field
             'track_method': 'StrongBdip',
@@ -271,4 +276,3 @@
     parameters_dict['combined_simulations_secondaryEmission_machine_parameters']['mandatory'].update(parameters_dict[key]['mandatory'])
     parameters_dict['combined_simulations_secondaryEmission_machine_parameters']['optional'].update(parameters_dict[key]['optional'])
 
-
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
@@ -8,7 +8,8 @@
 
 \usepackage{placeins}
 
-\usepackage{hyperref}
+\usepackage[hidelinks]{hyperref}
+\usepackage{url}
 
 
 \usepackage[english]{babel}
@@ -37,6 +38,9 @@
 
 \definecolor{Gray}{gray}{0.90}
 
+
+
+
 \begin{document}
 
 
@@ -285,8 +289,12 @@ \subsection{Simulation parameters}
 \multicolumn{2}{p{.97\textwidth}}{When chamb\_type = `ellip' or  'rect' the following input variables must be provided:} \\ \hline
 \textbf{x\_aper, y\_aper} & Horizontal and vertical semi-apertures of the transverse chamber profile.  \\ \hline
 \multicolumn{2}{p{.97\textwidth}}{When chamb\_type = `polyg' the following input variable must be provided:} \\ \hline
-\textbf{filename\_chm} & Name of file containing horizontal and vertical vertexes of the chamber profile.  \\ \hline
+\textbf{filename\_chm} & Name of file containing horizontal and vertical vertexes of the chamber profile. \\\hline
+\textbf{filename\_chm\_photoem} & Name of file containing horizontal and vertical vertexes of the chamber profile that is used for the photoemission mode 'per\_segment'.
+    The chamber file must also contain the cumulative distribution function of the emission probability for each segment.
+    The vertexes of this chamber must lie on the edges of the main chamber.\\ \hline
     \textbf{flag\_assume\_convex} & [optional] Default: True \\\hline
+    \textbf{flag\_counter\_clockwise\_chamb} & [optional] Default: True. Only needed for the photoemission model 'per\_segment'. It specifies the order in which the vertexes are defined. \\\hline
 \end{longtable}
 
 
@@ -382,7 +390,7 @@ \subsection{Simulation parameters}
 \multicolumn{2}{p{.97\textwidth}}{\textbf{Photoemission parameters} (if generation by photoemission is not desired, the following parameters can be omitted).}
 \\ \hline
 \textbf{photoem\_flag} & (optional -- default=0) \newline
-    (0 $\Rightarrow$ Off, 1 $\Rightarrow$ On, 2 or 'from\_file' $\Rightarrow$ From file) Enables primary electron generation by photoemission.
+    (0 $\Rightarrow$ Off, 1 $\Rightarrow$ traditional, 2 or 'from\_file' $\Rightarrow$ From file, 3 or 'per\_segment' $\Rightarrow$ Part of chamber definition) Enables primary electron generation by photoemission.
 \\ \hline
 \textbf{k\_pe\_st} & [m$^{-1}$] Number of photoelectrons to be generated per proton and per unit length.
 \\ \hline
@@ -429,7 +437,9 @@ \subsection{Simulation parameters}
     \multicolumn{2}{p{.97\textwidth}}{\textbf{The coordinates of all generated photoelectrons is specified from a file}}
     \\
     \hline
-    \textbf{inv\_CDF\_all\_photoem\_file} & See inv\_CDF\_refl\_photoem\_file, but for all photons. If it is set to 'unif\_no\_file', the photoelectron generation is uniform over the whole surface.
+    \textbf{inv\_CDF\_all\_photoem\_file} & See inv\_CDF\_refl\_photoem\_file, but for all photons.
+    If it is set to 'unif\_no\_file', the photoelectron generation is uniform over the whole surface.
+    Example scripts to generate a file with the correct format can be found in the folder \url{PyECLOUD/other/photoemission\_angular\_distribution}.
 \end{longtable}
 
 

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 6.6.0
+#                   PyECLOUD Version 6.7.0
 #
 #
 #     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 6.6.0
+#                          PyECLOUD Version 6.7.0
 #
 #
 #     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 6.6.0
+#                   PyECLOUD Version 6.7.0
 #
 #
 #     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 6.6.0
+#                   PyECLOUD Version 6.7.0
 #
 #
 #     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 6.6.0
+#                   PyECLOUD Version 6.7.0
 #
 #
 #     Author and contact:   Giovanni IADAROLA