Merge branch 'develop'

PyCOMPLETE · Feb 15, 2018 · 70c3b85 · 70c3b85
2 parents 2bb0ba8 + 2dc9d66
commit 70c3b85
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diff --git a/change_version_number.py → 002_change_version_number.py b/change_version_number.py → 002_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 6.7.0', 'PyECLOUD Version 6.7.0')
+            content=content.replace('PyECLOUD Version 6.7.1', 'PyECLOUD Version 6.7.1')
             with open(filename,'w') as fid:
                 fid.write(content)
 

diff --git a/003_change_preamble.py b/003_change_preamble.py
@@ -0,0 +1,113 @@
+raise ValueError("Not to be used to change the version!\nComment this line to change preamble.")
+
+
+import os
+
+before_preamble = 0
+in_preamble = 1
+after_preamble = 2
+
+
+id_preamble_begin = '#-Begin-preamble----'
+id_preamble_end = '#-End-preamble--------'
+
+preamble_new = """#-Begin-preamble-------------------------------------------------------
+#
+#                           CERN
+#
+#     European Organization for Nuclear Research
+#
+#
+#     This file is part of the code:
+#
+#                   PyECLOUD Version 6.7.1
+#
+#
+#     Main author:          Giovanni IADAROLA
+#                           BE-ABP Group
+#                           CERN
+#                           CH-1211 GENEVA 23
+#                           SWITZERLAND
+#                           giovanni.iadarola@cern.ch
+#
+#     Contributors:         Eleanora Belli
+#                           Philipp Dijkstal
+#                           Lotta Mether
+#                           Annalisa Romano
+#                           Giovanni Rumolo
+#
+#
+#     Copyright  CERN,  Geneva  2011  -  Copyright  and  any   other
+#     appropriate  legal  protection  of  this  computer program and
+#     associated documentation reserved  in  all  countries  of  the
+#     world.
+#
+#     Organizations collaborating with CERN may receive this program
+#     and documentation freely and without charge.
+#
+#     CERN undertakes no obligation  for  the  maintenance  of  this
+#     program,  nor responsibility for its correctness,  and accepts
+#     no liability whatsoever resulting from its use.
+#
+#     Program  and documentation are provided solely for the use  of
+#     the organization to which they are distributed.
+#
+#     This program  may  not  be  copied  or  otherwise  distributed
+#     without  permission. This message must be retained on this and
+#     any other authorized copies.
+#
+#     The material cannot be sold. CERN should be  given  credit  in
+#     all references.
+#
+#-End-preamble---------------------------------------------------------"""
+
+new_preamble_lines = preamble_new.split('\n')
+
+
+
+for dirpath, _, filenames in os.walk('.'):
+    full_paths = [os.path.join(dirpath, x) for x in filenames]
+
+    python_files = [x for x in full_paths if x.endswith('.py')]
+    for path in python_files:
+
+        if os.path.abspath(path) == os.path.abspath(__file__):
+            continue
+
+        with open(path, 'r') as f:
+            content = f.read()
+
+        if new_preamble_lines[0] not in content:
+            continue
+
+        print(path)
+
+        lines = content.split('\n')
+
+        prev_line = None
+        new_lines = []
+        status = before_preamble
+
+        for line in lines:
+            if status == before_preamble:
+                if id_preamble_begin in line:
+                    status = in_preamble
+                    new_lines.extend(new_preamble_lines)
+            elif status == in_preamble:
+                if id_preamble_end in prev_line:
+                    status = after_preamble
+            elif status == after_preamble:
+                pass
+
+
+            if status != in_preamble:
+                new_lines.append(line)
+
+            prev_line = line
+
+        new_lines = [x+'\n' for ctr, x in enumerate(new_lines) if ctr+1 != len(new_lines)]
+
+        with open(path, 'w') as f:
+            f.writelines(new_lines)
+        print('Modified %s' % path)
+
diff --git a/MP_system.py b/MP_system.py
@@ -1,4 +1,4 @@
-#----------------------------------------------------------------------
+#-Begin-preamble-------------------------------------------------------
 #
 #                           CERN
 #
@@ -7,23 +7,21 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 6.7.0
+#                   PyECLOUD Version 6.7.1
 #
 #
-#     Author and contact:   Giovanni IADAROLA
+#     Main author:          Giovanni IADAROLA
 #                           BE-ABP Group
 #                           CERN
 #                           CH-1211 GENEVA 23
 #                           SWITZERLAND
 #                           giovanni.iadarola@cern.ch
 #
-#                contact:   Giovanni RUMOLO
-#                           BE-ABP Group
-#                           CERN
-#                           CH-1211 GENEVA 23
-#                           SWITZERLAND
-#                           giovanni.rumolo@cern.ch
-#
+#     Contributors:         Eleanora Belli
+#                           Philipp Dijkstal
+#                           Lotta Mether
+#                           Annalisa Romano
+#                           Giovanni Rumolo
 #
 #
 #     Copyright  CERN,  Geneva  2011  -  Copyright  and  any   other
@@ -47,7 +45,8 @@
 #
 #     The material cannot be sold. CERN should be  given  credit  in
 #     all references.
-#----------------------------------------------------------------------
+#
+#-End-preamble---------------------------------------------------------
 
 import numpy as np
 from numpy.random import rand

diff --git a/PyEC4PyHT.py b/PyEC4PyHT.py
@@ -1,5 +1,4 @@
-#----------------------------------------------------------------------
-#----------------------------------------------------------------------
+#-Begin-preamble-------------------------------------------------------
 #
 #                           CERN
 #
@@ -8,23 +7,21 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 6.7.0
+#                   PyECLOUD Version 6.7.1
 #
 #
-#     Author and contact:   Giovanni IADAROLA
+#     Main author:          Giovanni IADAROLA
 #                           BE-ABP Group
 #                           CERN
 #                           CH-1211 GENEVA 23
 #                           SWITZERLAND
 #                           giovanni.iadarola@cern.ch
 #
-#                contact:   Giovanni RUMOLO
-#                           BE-ABP Group
-#                           CERN
-#                           CH-1211 GENEVA 23
-#                           SWITZERLAND
-#                           giovanni.rumolo@cern.ch
-#
+#     Contributors:         Eleanora Belli
+#                           Philipp Dijkstal
+#                           Lotta Mether
+#                           Annalisa Romano
+#                           Giovanni Rumolo
 #
 #
 #     Copyright  CERN,  Geneva  2011  -  Copyright  and  any   other
@@ -48,7 +45,8 @@
 #
 #     The material cannot be sold. CERN should be  given  credit  in
 #     all references.
-#----------------------------------------------------------------------
+#
+#-End-preamble---------------------------------------------------------
 
 import os
 import subprocess
@@ -67,7 +65,7 @@ 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 6.7.0'
+        print 'PyECLOUD Version 6.7.1'
 
         # 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
@@ -1,5 +1,4 @@
-#----------------------------------------------------------------------
-#----------------------------------------------------------------------
+#-Begin-preamble-------------------------------------------------------
 #
 #                           CERN
 #
@@ -8,23 +7,21 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 6.7.0
+#                   PyECLOUD Version 6.7.1
 #
 #
-#     Author and contact:   Giovanni IADAROLA
+#     Main author:          Giovanni IADAROLA
 #                           BE-ABP Group
 #                           CERN
 #                           CH-1211 GENEVA 23
 #                           SWITZERLAND
 #                           giovanni.iadarola@cern.ch
 #
-#                contact:   Giovanni RUMOLO
-#                           BE-ABP Group
-#                           CERN
-#                           CH-1211 GENEVA 23
-#                           SWITZERLAND
-#                           giovanni.rumolo@cern.ch
-#
+#     Contributors:         Eleanora Belli
+#                           Philipp Dijkstal
+#                           Lotta Mether
+#                           Annalisa Romano
+#                           Giovanni Rumolo
 #
 #
 #     Copyright  CERN,  Geneva  2011  -  Copyright  and  any   other
@@ -48,7 +45,8 @@
 #
 #     The material cannot be sold. CERN should be  given  credit  in
 #     all references.
-#----------------------------------------------------------------------
+#
+#-End-preamble---------------------------------------------------------
 
 import numpy as np
 from scipy.constants import c, e

diff --git a/beam_and_timing.py b/beam_and_timing.py
@@ -1,4 +1,4 @@
-#----------------------------------------------------------------------
+#-Begin-preamble-------------------------------------------------------
 #
 #                           CERN
 #
@@ -7,23 +7,21 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 6.7.0
+#                   PyECLOUD Version 6.7.1
 #
 #
-#     Author and contact:   Giovanni IADAROLA
+#     Main author:          Giovanni IADAROLA
 #                           BE-ABP Group
 #                           CERN
 #                           CH-1211 GENEVA 23
 #                           SWITZERLAND
 #                           giovanni.iadarola@cern.ch
 #
-#                contact:   Giovanni RUMOLO
-#                           BE-ABP Group
-#                           CERN
-#                           CH-1211 GENEVA 23
-#                           SWITZERLAND
-#                           giovanni.rumolo@cern.ch
-#
+#     Contributors:         Eleanora Belli
+#                           Philipp Dijkstal
+#                           Lotta Mether
+#                           Annalisa Romano
+#                           Giovanni Rumolo
 #
 #
 #     Copyright  CERN,  Geneva  2011  -  Copyright  and  any   other
@@ -47,7 +45,8 @@
 #
 #     The material cannot be sold. CERN should be  given  credit  in
 #     all references.
-#----------------------------------------------------------------------
+#
+#-End-preamble---------------------------------------------------------
 
 
 import numpy as np

diff --git a/buildup_simulation.py b/buildup_simulation.py
@@ -1,6 +1,6 @@
 #!/afs/cern.ch/project/uslarp/opt/lxplus64/Python-2.7.2/bin/python
 
-#----------------------------------------------------------------------
+#-Begin-preamble-------------------------------------------------------
 #
 #                           CERN
 #
@@ -9,23 +9,21 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 6.7.0
+#                   PyECLOUD Version 6.7.1
 #
 #
-#     Author and contact:   Giovanni IADAROLA
+#     Main author:          Giovanni IADAROLA
 #                           BE-ABP Group
 #                           CERN
 #                           CH-1211 GENEVA 23
 #                           SWITZERLAND
 #                           giovanni.iadarola@cern.ch
 #
-#                contact:   Giovanni RUMOLO
-#                           BE-ABP Group
-#                           CERN
-#                           CH-1211 GENEVA 23
-#                           SWITZERLAND
-#                           giovanni.rumolo@cern.ch
-#
+#     Contributors:         Eleanora Belli
+#                           Philipp Dijkstal
+#                           Lotta Mether
+#                           Annalisa Romano
+#                           Giovanni Rumolo
 #
 #
 #     Copyright  CERN,  Geneva  2011  -  Copyright  and  any   other
@@ -49,7 +47,8 @@
 #
 #     The material cannot be sold. CERN should be  given  credit  in
 #     all references.
-#----------------------------------------------------------------------
+#
+#-End-preamble---------------------------------------------------------
 
 
 import init as init
@@ -59,7 +58,7 @@
 class BuildupSimulation(object):
     def __init__(self, pyecl_input_folder='./', **kwargs):
 
-        print 'PyECLOUD Version 6.7.0'
+        print 'PyECLOUD Version 6.7.1'
         beamtim,MP_e, dynamics,impact_man, pyeclsaver, \
                 gas_ion_flag, resgasion, t_ion, \
                 spacech_ele,t_sc_ON, photoem_flag, phemiss,\

diff --git a/default_input_parameters.py b/default_input_parameters.py
@@ -4,6 +4,7 @@
 # This most importantly excludes python lists. Tuples may be used in their place.
 
 parameters_dict = {
+    'superparameters':{'pi'}, #are allowed anywhere and can be repeated (for backwards compatibility)
     'simulation_parameters': {
         'mandatory': {
 

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
@@ -390,7 +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 $\Rightarrow$ traditional, 2 or 'from\_file' $\Rightarrow$ From file, 3 or 'per\_segment' $\Rightarrow$ Part of chamber definition) Enables primary electron generation by photoemission.
+    (0 $\Rightarrow$ Off, 1 $\Rightarrow$ traditional, 2 or 'from\_file' $\Rightarrow$ Angular distribution 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