Merge branch 'develop'

PyCOMPLETE · Feb 11, 2019 · 048cf62 · 048cf62
2 parents 2344b4a + 4d7e1e4
commit 048cf62
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Showing 46 changed files with 1,304 additions and 137 deletions.
diff --git a/002_change_version_number.py b/002_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 7.6.0', 'PyECLOUD Version 7.6.0')
+            content = content.replace('PyECLOUD Version 7.6.1', 'PyECLOUD Version 7.6.1')
             with open(filename, 'w') as fid:
                 fid.write(content)
 

diff --git a/003_change_preamble.py b/003_change_preamble.py
@@ -20,7 +20,7 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          Giovanni IADAROLA

diff --git a/MP_system.py b/MP_system.py
@@ -7,7 +7,7 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          Giovanni IADAROLA

diff --git a/PyEC4PyHT.py b/PyEC4PyHT.py
@@ -7,7 +7,7 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          Giovanni IADAROLA
@@ -104,7 +104,7 @@ def __init__(self, L_ecloud, slicer, Dt_ref, pyecl_input_folder='./', flag_clean
                  beam_monitor=None, verbose=False, save_pyecl_outp_as=None,
                  **kwargs):
 
-        print 'PyECLOUD Version 7.6.0'
+        print 'PyECLOUD Version 7.6.1'
 
         # 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'
@@ -247,6 +247,8 @@ def track(self, beam):
         slices = beam.get_slices(self.slicer)
 
         for i in xrange(slices.n_slices - 1, -1, -1):
+            if self.verbose:
+                print('Slice %d/%d'%(i, slices.n_slices))
 
             # select particles in the slice
             ix = slices.particle_indices_of_slice(i)

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 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          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 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          Giovanni IADAROLA
@@ -62,7 +62,7 @@ class BuildupSimulation(object):
     def __init__(self, pyecl_input_folder='./', skip_beam=False, skip_spacech_ele=False,
                  skip_pyeclsaver=False, ignore_kwargs=[], spacech_ele=None, **kwargs):
 
-        print 'PyECLOUD Version 7.6.0'
+        print 'PyECLOUD Version 7.6.1'
         beamtim, spacech_ele, t_sc_ON, flag_presence_sec_beams, sec_beams_list, \
             config_dict, flag_multiple_clouds, cloud_list, checkpoint_folder = init.read_input_files_and_init_components(\
                 pyecl_input_folder=pyecl_input_folder,
@@ -257,8 +257,6 @@ def sim_time_step(self, beamtim_obj=None, Dt_substep_custom=None, N_sub_steps_cu
 
     def load_state(self, filename_simulation_state, force_disable_save_simulation_state=True, filen_main_outp='Pyecltest_restarted', load_from_folder='./'):  # , reset_pyeclsaver = True):
 
-        print 'Reloading state from file: %s...' % filename_simulation_state
-
         with open(load_from_folder + filename_simulation_state, 'rb') as fid:
             dict_state = cPickle.load(fid)
 
@@ -292,7 +290,7 @@ def load_state(self, filename_simulation_state, force_disable_save_simulation_st
         return dict_state
 
     def load_checkpoint(self, filename_simulation_checkpoint, load_from_folder='./'):
-        print 'Realoading from checkpoint: %s...' % (load_from_folder + filename_simulation_checkpoint)
+        print('Reloading from checkpoint: %s...' % (load_from_folder + filename_simulation_checkpoint))
 
         i_checkp = int(filename_simulation_checkpoint.split('.pkl')[0].split('_')[-1])
         dict_state = self.load_state(filename_simulation_checkpoint, force_disable_save_simulation_state=False, filen_main_outp=None, load_from_folder=load_from_folder)

diff --git a/cloud_manager.py b/cloud_manager.py
@@ -7,7 +7,7 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Author and contact:   Giovanni IADAROLA

diff --git a/default_input_parameters.py b/default_input_parameters.py
@@ -100,7 +100,9 @@
             'dec_fact_out': 1,
 
             # Where to put this?
-            't_ion': -1
+            't_ion': -1,
+
+            'extract_sey': True,
         },
     },
     'machine_parameters': {

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 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          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 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          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 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          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 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          Giovanni IADAROLA

diff --git a/electron_emission.py b/electron_emission.py
@@ -7,7 +7,7 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          Giovanni IADAROLA
@@ -74,6 +74,8 @@ def sec_energy_hilleret_model2(switch_no_increase_energy, Ngen, sigmafit, mufit,
 
     elif switch_no_increase_energy == 1:
 
+        raise ValueError('This part of the code is not supported anymore!')
+
         en_eV = np.zeros_like(En_impact_eV, dtype=float)
 
         flag_low_energy = En_impact_eV < thresh_low_energy
@@ -167,7 +169,7 @@ def get_angle_dist_func(string):
 "photoelectron_angle_distribution = 'cosine_3D'"
 and in the secondary emission input file:
 "secondary_angle_distribution = 'cosine_3D'"
-For more info, see presentation by P. Dijkstal on the angle of emission 
+For more info, see presentation by P. Dijkstal on the angle of emission
 of generated electrons (https://indico.cern.ch/event/673160/).
 """)
         time.sleep(3)
@@ -259,5 +261,3 @@ def get_energy_distribution_func(energy_distribution, e_pe_sigma, e_pe_max):
         raise ValueError('Energy distribution %s is invalid!' % energy_distribution)
 
     return get_energy(e_pe_sigma, e_pe_max)
-
-
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 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          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 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          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 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          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 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          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 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          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 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          Giovanni IADAROLA

diff --git a/h000_find_and_modify_preamble.py b/h000_find_and_modify_preamble.py
@@ -16,7 +16,7 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          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 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          Giovanni IADAROLA
@@ -229,7 +229,7 @@ def backtrack_and_second_emiss(self, old_pos, MP_e):
                 nel_emit_tot_events, event_type, event_info,\
                     nel_replace, x_replace, y_replace, z_replace, vx_replace, vy_replace, vz_replace, i_seg_replace,\
                     nel_new_MPs, x_new_MPs, y_new_MPs, z_new_MPs, vx_new_MPs, vy_new_MPs, vz_new_MPs, i_seg_new_MPs =\
-                    self.sey_mod.impacts_on_surface(
+                    sey_mod.impacts_on_surface(
                         MP_e.mass, nel_impact, x_impact, y_impact, z_impact,
                         vx_impact, vy_impact, vz_impact, Norm_x, Norm_y, i_found,
                         v_impact_n, E_impact_eV, costheta_impact, nel_mp_th, flag_seg
@@ -277,11 +277,13 @@ def backtrack_and_second_emiss(self, old_pos, MP_e):
 
     def extract_sey_curves(self, n_rep, E_impact_eV_test, cos_theta_test, charge, mass):
 
-        del_true_mat = np.zeros((len(cos_theta_test), len(E_impact_eV_test)))
-        del_elast_mat = np.zeros((len(cos_theta_test), len(E_impact_eV_test)))
+        deltas = {}
+        for etype in self.sey_mod.event_types.keys():
+            etype_name = self.sey_mod.event_types[etype]
+            deltas[etype_name] = np.zeros((len(cos_theta_test), len(E_impact_eV_test)))
         print('Extracting SEY curves...')
         for i_ct, ct in enumerate(cos_theta_test):
-            print('%d/%d'%(i_ct + 1, len(cos_theta_test)))
+            print('%d/%d' % (i_ct + 1, len(cos_theta_test)))
             for i_ene, Ene in enumerate(E_impact_eV_test):
 
                 # nel_emit, flag_elast, flag_truesec = sey_mod.SEY_process(nel_impact=np.ones(n_rep),
@@ -307,10 +309,13 @@ def extract_sey_curves(self, n_rep, E_impact_eV_test, cos_theta_test, charge, ma
                         costheta_impact=ct * np.ones_like(nel_impact),
                         nel_mp_th=1,
                         flag_seg=True)
-                del_tot = (np.sum(nel_replace) + np.sum(nel_new_MPs)) / n_rep
-                del_true_mat[i_ct, i_ene] = del_tot * float(np.sum(event_type)) / float(n_rep)
-                del_elast_mat[i_ct, i_ene] = del_tot * float(np.sum(~event_type)) / float(n_rep)
-        print('Done extracting SEY curves.')
 
-        return del_true_mat, del_elast_mat
+                for etype in self.sey_mod.event_types.keys():
+                    etype_name = self.sey_mod.event_types[etype]
+                    thisdelta = deltas[etype_name]
+                    thisdelta[i_ct, i_ene] = np.sum(nel_emit_tot_events[event_type == etype]) / np.sum(nel_impact)
+                    deltas[etype_name] = thisdelta
+
+        print('Done extracting SEY curves.')
 
+        return deltas
diff --git a/init.py b/init.py
@@ -7,7 +7,7 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          Giovanni IADAROLA
@@ -413,7 +413,7 @@ def read_input_files_and_init_components(pyecl_input_folder='./', skip_beam=Fals
                                        flag_cos_angle_hist=thiscloud.flag_cos_angle_hist, cos_angle_width=thiscloud.cos_angle_width,
                                        flag_multiple_clouds=flag_multiple_clouds, cloud_name=thiscloud.cloud_name, flag_last_cloud=flag_last_cloud,
                                        checkpoint_DT=cc.checkpoint_DT, checkpoint_folder=cc.checkpoint_folder, copy_main_outp_folder=cc.copy_main_outp_folder,
-                                       copy_main_outp_DT=cc.copy_main_outp_DT)
+                                       copy_main_outp_DT=cc.copy_main_outp_DT, extract_sey=cc.extract_sey)
             print('pyeclsaver saves to file: %s' % pyeclsaver.filen_main_outp)
 
         # Init electron tracker

diff --git a/main.py b/main.py
@@ -9,7 +9,7 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 7.6.0
+#                   PyECLOUD Version 7.6.1
 #
 #
 #     Main author:          Giovanni IADAROLA