Merge branch 'develop'

PyCOMPLETE · Jun 11, 2018 · 7affa66 · 7affa66
2 parents b48e140 + 5099ddc
commit 7affa66
Show file tree

Hide file tree

Showing 55 changed files with 409 additions and 58 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 7.2.0', 'PyECLOUD Version 7.2.0')
+            content=content.replace('PyECLOUD Version 7.3.0', 'PyECLOUD Version 7.3.0')
             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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     Main author:          Giovanni IADAROLA
@@ -84,7 +84,7 @@ def __init__(self, L_ecloud, slicer, Dt_ref, pyecl_input_folder='./', flag_clean
                  beam_monitor=None, verbose=False,
                  **kwargs):
 
-        print 'PyECLOUD Version 7.2.0'
+        print 'PyECLOUD Version 7.3.0'
 
         # 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'
@@ -155,7 +155,7 @@ def __init__(self, L_ecloud, slicer, Dt_ref, pyecl_input_folder='./', flag_clean
 
         self.N_tracks = 0
 
-        self.cloudsim.spacech_ele.flag_decimate = False
+        #self.cloudsim.spacech_ele.flag_decimate = False
 
 
 
@@ -310,16 +310,21 @@ def _track_single_slice(self, beam, ix, dz):
         dummybeamtim.tt_curr = self.cloudsim.t_sc_ON + 1. # In order to have the PIC activated
         dummybeamtim.lam_t_curr = np.mean(beam.particlenumber_per_mp/dz)*len(ix)
         dummybeamtim.Dt = dt
+        dummybeamtim.Dt_curr = dt
         dummybeamtim.sigmax = np.std(beam.x[ix]) 
         dummybeamtim.sigmay = np.std(beam.y[ix])
         dummybeamtim.x_beam_pos = np.mean(beam.x[ix])+self.x_beam_offset
         dummybeamtim.y_beam_pos = np.mean(beam.y[ix])+self.y_beam_offset
         dummybeamtim.flag_new_bunch_pass = False
 
+        # Force space charge recomputation (to be switched between bunches in multibunch mode)
+        force_recompute_space_charge = True
+
         # Perform cloud simulation step
         self.cloudsim.sim_time_step(beamtim_obj=dummybeamtim, 
                 Dt_substep_custom=Dt_substep, N_sub_steps_custom=N_sub_steps, 
-                kick_mode_for_beam_field=self.kick_mode_for_beam_field)
+                kick_mode_for_beam_field=self.kick_mode_for_beam_field,
+                force_recompute_space_charge=force_recompute_space_charge)
 
 
         # Build MP_system-like object with beam coordinates

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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     Main author:          Giovanni IADAROLA
@@ -94,6 +94,8 @@ def __init__(self,flag_bunched_beam, fact_beam, coast_dens, beam_charge, beam_fi
         if chamb.is_outside(np.array([x_beam_pos]),np.array([y_beam_pos])):
             raise ValueError('The beam is outside the chamber!')
 
+        flag_unif_Dt = True
+
         if flag_bunched_beam:
             print 'Start beam profile generation.'
 
@@ -130,11 +132,23 @@ def __init__(self,flag_bunched_beam, fact_beam, coast_dens, beam_charge, beam_fi
             lam_t_array=bunch_train4(t, b_spac,t_offs,ppb_vect,sigmaz_vect);
             print 'Done beam profile generation.'
         else:
+            print 'Loading beam profile from file:'
+            print beam_long_prof_file
+
             dict_lam=sio.loadmat(beam_long_prof_file)
             t=np.squeeze(dict_lam['t'].real)
             lam_t_array=np.squeeze(dict_lam['lam_t_array'].real)
             t_inter=t[-1]
-            Dt=t[1]-t[0]
+
+            Dt_vect = np.diff(t)
+            if (np.max(np.abs(Dt_vect))-np.mean(np.abs(Dt_vect))) > 1e-4*np.mean(np.abs(Dt_vect)):
+                flag_unif_Dt = False
+            else:
+                print 'Beam profile loaded from file.'
+                print 'Uniform time step detected.'
+                print 'The time step Dt provided in simulation_parameters.input will be ignored.'
+                Dt=t[1]-t[0]
+                print 'Time step set to Dt = %.3e s.'%Dt
 
         if flag_secodary_beam:
             if len(t)!=len(t_primary_beam):
@@ -284,7 +298,8 @@ def __init__(self,flag_bunched_beam, fact_beam, coast_dens, beam_charge, beam_fi
 
 
         else:
-            print 'Loading beam field map from file'
+            print 'Loading beam field map from file:'
+            print beam_field_file
             dict_beam=sio.loadmat(beam_field_file)
 
             Ex_beam=np.squeeze(dict_beam['Ex'].real)
@@ -316,6 +331,11 @@ def __init__(self,flag_bunched_beam, fact_beam, coast_dens, beam_charge, beam_fi
             self.xx_beam=xx_beam
             self.yy_beam=yy_beam
 
+        if not(flag_unif_Dt):
+            print 'Cloud simulation in non-uniform Dt mode.'
+            print 'Dt provided in input will be used only as reference for savings and substeps.'
+
+        self.flag_unif_Dt=flag_unif_Dt
         self.Nt=Nt
         self.b_spac=b_spac
         self.lam_t_array=lam_t_array
@@ -343,6 +363,7 @@ def __init__(self,flag_bunched_beam, fact_beam, coast_dens, beam_charge, beam_fi
     def next_time_step(self):
         self.ii_curr+=1
         self.tt_curr=self.t[self.ii_curr]
+        self.Dt_curr=self.t[self.ii_curr+1]-self.t[self.ii_curr]
         self.lam_t_curr=self.lam_t_array[self.ii_curr]
         self.pass_numb=int(np.floor(self.tt_curr/self.b_spac));
         self.flag_new_bunch_pass=(self.pass_numb>self._pass_numb_old)
@@ -352,7 +373,7 @@ def next_time_step(self):
 
 
     def end_simulation(self):
-        return ((self.ii_curr+1)>=self.Nt)
+        return ((self.ii_curr+2)>=self.Nt) # I need the last point to compute Dt
 
     def get_beam_eletric_field(self, MP_e):
 

diff --git a/buildup_simulation.py b/buildup_simulation.py
@@ -9,7 +9,7 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     Main author:          Giovanni IADAROLA
@@ -60,7 +60,7 @@ 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 7.2.0'
+        print 'PyECLOUD Version 7.3.0'
         beamtim, spacech_ele, t_sc_ON, flag_presence_sec_beams, sec_beams_list, \
         config_dict, flag_multiple_clouds, cloud_list = init.read_input_files_and_init_components(\
                                                     pyecl_input_folder=pyecl_input_folder, 
@@ -112,7 +112,8 @@ def run(self, t_end_sim = None):
 
 
 
-    def sim_time_step(self, beamtim_obj=None, Dt_substep_custom=None, N_sub_steps_custom=None, kick_mode_for_beam_field=False):
+    def sim_time_step(self, beamtim_obj=None, Dt_substep_custom=None, N_sub_steps_custom=None, kick_mode_for_beam_field=False,
+                      force_recompute_space_charge=False):
 
         if beamtim_obj is not None:
             beamtim = beamtim_obj
@@ -128,6 +129,7 @@ def sim_time_step(self, beamtim_obj=None, Dt_substep_custom=None, N_sub_steps_cu
 
         flag_recompute_space_charge = spacech_ele.check_for_recomputation(t_curr=beamtim.tt_curr)
 
+
         # Loop over clouds: gather fields, move, generate new MPs
         for i_cloud, cloud in enumerate(cloud_list):
             MP_e = cloud.MP_e
@@ -170,9 +172,19 @@ def sim_time_step(self, beamtim_obj=None, Dt_substep_custom=None, N_sub_steps_cu
             old_pos=MP_e.get_positions()
 
             ## Motion
-            if Dt_substep_custom is None and N_sub_steps_custom is None:
+            if Dt_substep_custom is None and N_sub_steps_custom is None and beamtim.flag_unif_Dt:
+                # Standard simulation mode
                 MP_e = dynamics.step(MP_e, Ex_n, Ey_n)
+            elif Dt_substep_custom is None and N_sub_steps_custom is None and not(beamtim.flag_unif_Dt):
+                # Dt from non-uniform beam profile
+                if self.config_dict['track_method'] not in ['Boris', 'BorisMultipole']:
+                    raise ValueError("""track_method should be 'Boris' or 'BorisMultipole' to use custom substeps!""")
+                Dt_substep_target = cloud.dynamics.Dt/cloud.dynamics.N_sub_steps
+                N_substeps_curr = np.round(beamtim.Dt_curr/Dt_substep_target)
+                Dt_substep_curr = beamtim.Dt_curr/N_substeps_curr
+                MP_e = dynamics.stepcustomDt(MP_e, Ex_n, Ey_n, Dt_substep=Dt_substep_curr, N_sub_steps=N_substeps_curr)
             else:
+                # Custom steps and substeps provided as arguments of sim_time_step
                 if self.config_dict['track_method'] not in ['Boris', 'BorisMultipole']:
                     raise ValueError("""track_method should be 'Boris' or 'BorisMultipole' to use custom substeps!""")
                 MP_e = dynamics.stepcustomDt(MP_e, Ex_n, Ey_n, Dt_substep=Dt_substep_custom, N_sub_steps=N_sub_steps_custom)
@@ -182,11 +194,11 @@ def sim_time_step(self, beamtim_obj=None, Dt_substep_custom=None, N_sub_steps_cu
 
             ## Gas ionization (main and secondary beams)
             if(beamtim.tt_curr<t_ion and gas_ion_flag==1):
-                MP_e = resgasion.generate(MP_e, beamtim.lam_t_curr, beamtim.Dt, beamtim.sigmax, beamtim.sigmay,
+                MP_e = resgasion.generate(MP_e, beamtim.lam_t_curr, beamtim.Dt_curr, beamtim.sigmax, beamtim.sigmay,
                                           x_beam_pos = beamtim.x_beam_pos, y_beam_pos = beamtim.y_beam_pos)
                 if flag_presence_sec_beams:
                     for sec_beam in sec_beams_list:
-                        MP_e = resgasion.generate(MP_e, sec_beam.lam_t_curr, sec_beam.Dt, sec_beam.sigmax, sec_beam.sigmay,
+                        MP_e = resgasion.generate(MP_e, sec_beam.lam_t_curr, sec_beam.Dt_curr, sec_beam.sigmax, sec_beam.sigmay,
                                                   x_beam_pos = sec_beam.x_beam_pos, y_beam_pos = sec_beam.y_beam_pos)
 
             ## Photoemission (main and secondary beams)
@@ -195,10 +207,10 @@ def sim_time_step(self, beamtim_obj=None, Dt_substep_custom=None, N_sub_steps_cu
                 if flag_presence_sec_beams:
                     for sec_beam in sec_beams_list:
                         lam_curr_phem += sec_beam.lam_t_curr
-                phemiss.generate(MP_e, lam_curr_phem, beamtim.Dt)
+                phemiss.generate(MP_e, lam_curr_phem, beamtim.Dt_curr)
 
             # Compute space charge field
-            if (beamtim.tt_curr>t_sc_ON) and flag_recompute_space_charge:
+            if ((beamtim.tt_curr>t_sc_ON) and flag_recompute_space_charge) or force_recompute_space_charge:
                 flag_reset = cloud is cloud_list[0] # The first cloud resets the distribution
                 flag_solve = cloud is cloud_list[-1] # The last cloud computes the fields
                 spacech_ele.recompute_spchg_efield(MP_e, flag_solve=flag_solve, flag_reset=flag_reset)

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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     Main author:          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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     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 7.2.0
+#                   PyECLOUD Version 7.3.0
 #
 #
 #     Main author:          Giovanni IADAROLA