Merge remote-tracking branch 'kparasch/ecloud' into release/0.21.5

test_data/pyecloud_pinch/Pinch_creation/.gitignore

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+*.h5
+*.mat
+MP_state*
+*.txt

test_data/pyecloud_pinch/Pinch_creation/000_buildup.py

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+from PyECLOUD.buildup_simulation import BuildupSimulation
+
+sim = BuildupSimulation()
+sim.run()

test_data/pyecloud_pinch/Pinch_creation/001_pinch.py

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+import json
+import scipy.io
+from scipy.constants import c,e
+import matplotlib.pyplot as plt
+import numpy as np
+# from cmcrameri import cm
+from rich.progress import Progress
+import glob
+import os
+
+import sys
+import filemanager as exfm
+
+from PyECLOUD.buildup_simulation import BuildupSimulation
+import argparse
+
+if os.path.exists("Pinch.h5"):
+    os.remove("Pinch.h5")
+
+zeta_max = 0.2
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--ecloud", nargs="?", type=str, default="ecloud.q3r1.ir1.0")
+args = parser.parse_args()
+
+ecloud = args.ecloud
+
+mod_factor = 1
+
+out_pinch = f"Pinch.h5"
+
+mp_states = []
+mp_state_files = ["MP_state_0"]
+for name in mp_state_files:
+    mp_system = scipy.io.loadmat(name)
+    mp_system['nel_mp'] = mp_system['nel_mp']/len(mp_state_files)
+    mp_states.append(mp_system)
+
+t_min = 2.5e-9 - zeta_max / c
+t_max = 2.5e-9 + zeta_max / c
+t_end_sim = t_max + 0.02 / c
+total_N_particles = sum([mp_system["N_mp"][0][0] for mp_system in mp_states])
+total_N_particles *= 2 #put more particles to max allowed
+total_N_particles += 10000 #put more particles to max allowed
+
+PyPICmode = 'ShortleyWeller_WithTelescopicGrids'
+target_grid = {'x_min_target' : -12e-3, 'x_max_target' : 12e-3,
+               'y_min_target' : -5e-3, 'y_max_target' : 5e-3,
+               'Dh_target' : 1.e-4}
+f_telescope = 0.5
+N_nodes_discard = 10
+N_min_Dh_main = 50
+
+sim = BuildupSimulation(extract_sey=False, N_mp_max=total_N_particles, PyPICmode=PyPICmode,
+                        target_grid=target_grid, f_telescope=f_telescope,
+                        N_nodes_discard=N_nodes_discard, N_min_Dh_main=N_min_Dh_main,
+                        init_unif_edens_flag=0, Dt_sc=None)
+
+sim = BuildupSimulation(extract_sey=False, N_mp_max=total_N_particles,
+                        init_unif_edens_flag=0, Dt_sc=None)
+
+
+sim.cloud_list[0].MP_e.init_from_dict(mp_states[0])
+sim.cloud_list[0].MP_e.nel_mp_ref *= len(mp_states)
+prev_mp = sim.cloud_list[0].MP_e.N_mp
+for mp_system in mp_states[1:]:
+    sim.cloud_list[0].MP_e.add_from_file(mp_system)
+    now_mp = sim.cloud_list[0].MP_e.N_mp
+    print(now_mp, mp_system["N_mp"][0][0], now_mp - prev_mp)
+    prev_mp = now_mp
+
+N_mp = sim.cloud_list[0].MP_e.N_mp
+max_nel_mp = np.max(sim.cloud_list[0].MP_e.nel_mp[:N_mp])
+sim.cloud_list[0].MP_e.nel_mp_split = 3*(max_nel_mp)
+
+print(sim.cloud_list[0].MP_e.nel_mp_split)
+
+print("Start timestep iter")
+
+## simulation
+def time_step(sim, t_end_sim=None):
+    beamtim = sim.beamtim
+    if t_end_sim is not None and beamtim.tt_curr is not None:
+        if beamtim.tt_curr >= t_end_sim:
+            print("Reached user defined t_end_sim --> Ending simulation")
+            return 1
+
+    beamtim.next_time_step()
+
+    if sim.flag_presence_sec_beams:
+        for sec_beam in sim.sec_beams_list:
+            sec_beam.next_time_step()
+
+    sim.sim_time_step(force_reinterp_fields_at_substeps=True, skip_MP_cleaning=True, skip_MP_regen=True)
+
+    if beamtim.flag_new_bunch_pass:
+        print(
+            "**** Done pass_numb = %d/%d\n"
+            % (beamtim.pass_numb, beamtim.N_pass_tot)
+        )
+    return 0
+
+
+
+xg = sim.spacech_ele.xg
+yg = sim.spacech_ele.yg
+zg = []
+
+ii = 0
+jj = 0
+
+with Progress() as progress:
+    task = progress.add_task("PyECLOUD tracking", total=t_end_sim)
+
+    while not time_step(sim, t_end_sim=t_end_sim):
+#        print(sim.cloud_list[0].MP_e.N_mp/total_N_particles)
+        ii += 1
+        tt = sim.beamtim.tt_curr
+        progress.update(task, completed=tt)
+        if tt > t_min and tt < t_max:
+            if ii%mod_factor == 0.:
+#                print(jj, ii, -c*(tt-2.5e-9))
+                zg.append(-c*(tt-2.5e-9))
+                exfm.dict_to_h5({'phi' : sim.spacech_ele.phi, 'rho' : sim.spacech_ele.rho}, out_pinch, group='slices/slice%d'%jj, readwrite_opts='a')
+                jj += 1
+
+grid_dict = {"xg" : np.array(xg),
+             "yg" : np.array(yg),
+             "zg" : np.array(zg),
+}
+exfm.dict_to_h5(grid_dict, out_pinch, group='grid', readwrite_opts='a')

test_data/pyecloud_pinch/Pinch_creation/beam.beam

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+# BEAM PARAMETERS
+energy_eV = 0.450000e+12
+nemittx = 2.00e-6
+nemitty = 2.00e-6   #m
+Dp_p = 0
+
+
+# x_beam_pos = 0
+# y_beam_pos = 0
+
+beam_field_file = 'computeFD'
+Dh_beam_field=1.0e-4
+Nx = None
+Ny = None
+nimag = None
+#save_beam_field_file_as = 'beam1field.mat'
+
+
+b_spac   = 25e-9     #s (to be specified also if you load the profile from file - 
+                     #   it is used as period for clean and save)
+fact_beam = 1.200000e+11
+
+
+
+flag_bunched_beam = 1 # 1: bunched beam 0:load profile from file  
+
+# to be filled in case of bunched beam
+sigmaz = 9.000000e-02
+t_offs = 2.5e-9
+filling_pattern_file = 1*(48*[1.]+7*[0.])
+#filling_pattern_file = 2*(3*(48*[1.]+7*[0.])+32*[0.]) + [0.]
+
+beam_long_prof_file = -1

test_data/pyecloud_pinch/Pinch_creation/filemanager.py

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+### Adapted from https://github.com/PyECLOUD/myfilemanager.py
+
+import h5py
+import numpy
+
+class obj_from_dict:
+    def __init__(self, mydict):
+        for key in mydict.keys():
+            setattr(self, key, mydict[key])
+
+def h5_to_dict(filename, group=None):
+    fid = h5py.File(filename, 'r')
+    if group == None :
+        grp = fid 
+    else:
+        grp = fid[group]
+    mydict={}
+    for key in grp.keys():
+        mydict[key] = grp[key][()]
+    return mydict
+
+def h5_to_obj(filename, group=None):
+    return obj_from_dict(h5_to_dict(filename, group=group))
+
+def overwrite(dict_save, filename, group=None, verbose=False):
+    with h5py.File(filename, 'a') as fid:
+        if group == None :
+            grp = fid 
+        else:
+            grp = fid[group]
+
+        for kk in dict_save.keys():
+            if verbose: print('Overwriting '+kk)
+            grp[kk][...] = dict_save[kk]
+
+def dict_to_h5(dict_save, filename, compression_opts=4, group=None, readwrite_opts='w', verbose=False):
+    with h5py.File(filename, readwrite_opts) as fid:
+        if group == None :
+            grp = fid 
+        else:
+            grp = fid.create_group(group)
+
+        for kk in dict_save.keys():
+            if verbose: print('Writing '+kk)
+            if isinstance(dict_save[kk], numpy.ndarray):
+                dset = grp.create_dataset(kk, shape=dict_save[kk].shape, dtype=dict_save[kk].dtype, compression='gzip', compression_opts=compression_opts)
+                dset[...] = dict_save[kk]
+            else:
+                grp[kk] = dict_save[kk]
+
+def print_h5(filename):
+    def print_this(x,y): print(x,y)
+    with h5py.File(filename,'r') as fid:
+        fid.visititems(print_this)

test_data/pyecloud_pinch/Pinch_creation/machine_parameters.input

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+# MACHINE PARAMETERS
+
+# Choose chamb_type='ellip'/ 'polyg'
+chamb_type = 'polyg_cython'
+# flag_assume_convex = False
+
+x_aper = 2.300000e-02
+y_aper = 1.800000e-02
+
+#For polygonal chamber
+filename_chm = 'LHC_chm_ver.mat'
+
+# Choose track_method= 'StrongBdip' / 'StrongBgen'/ 'Boris'
+track_method= 'BorisMultipole'
+# N_sub_steps = 5
+
+B_multip = [0., 12.1]
+B_skew = [0., 0.]
+
+betafx = 80.
+betafy = 80.
+
+# gas ionization parameters
+gas_ion_flag = 0
+P_nTorr=12.;
+sigma_ion_MBarn=2.;
+Temp_K=300.;
+unif_frac=0.1
+E_init_ion=0.1;   #in eV
+
+# photoemission parameters
+photoem_flag = 0
+inv_CDF_refl_photoem_file = 'unif_no_file'
+k_pe_st=0.0001233
+refl_frac=1.
+alimit=10.*pi/180.
+e_pe_sigma=5. #in eV
+e_pe_max=7.   #in eV  
+x0_refl=0. #no effect since uniform seeding
+y0_refl=0. #no effect since uniform seeding
+out_radius = .1
+phem_resc_fac=0.995
+
+
+# initial uniform electron density
+init_unif_edens_flag=1
+init_unif_edens=1e8
+E_init_unif_edens = 1.
+# init_unif_flag=1
+# Nel_init_unif=1e8
+# E_init_unif = 1.

test_data/pyecloud_pinch/Pinch_creation/secondary_emission_parameters.input

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+# secondary emission model
+Emax = 332.;
+del_max = 1.50000
+R0 = 0.7
+switch_model=0
+
+# hilleret model for sec. emission
+E_th = 35.;
+sigmafit =1.0828;
+mufit = 1.6636;
+
+switch_no_increase_energy = 0
+thresh_low_energy = -1
+
+scrub_en_th = 20.#eV
+secondary_angle_distribution = 'cosine_3D'

test_data/pyecloud_pinch/Pinch_creation/simulation_parameters.input

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+# SIMULATION PARAMETERS
+
+machine_param_file='machine_parameters.input'
+secondary_emission_parameters_file='secondary_emission_parameters.input'
+beam_parameters_file='beam.beam' 
+
+#secondary_beams_file_list = ['beam2.beam']
+#additional_clouds_file_list = ['electrons2.cloud']
+
+logfile_path = 'logfile.txt'
+progress_path = 'progress.txt'
+stopfile = 'progress.stop'
+
+Dt = 25.000000e-12
+t_end=1e-9;       #s (no effect if log. profile is imported from file)
+
+import numpy as np
+dec_fact_out = int(np.round(5 * 25e-12/Dt))
+# save_mat_every = 6
+
+lam_th=1.e2        #e-/m
+Dx_hist=1.e-3      #m
+r_center=2.e-3     #m
+
+
+Dt_En_hist = 25e-9 #s
+Nbin_En_hist= 100
+En_hist_max= 1000.  #eV
+
+t_ion=100.;        #s
+
+N_mp_max=200000;   #size of allocated vectors 
+
+#Regen parameters
+
+N_mp_regen=400000;
+N_mp_regen_low=5000;
+N_mp_after_regen=10000;
+t_ON_regen_low=0.
+fact_split=1.5;
+fact_clean=1e-4;
+nel_mp_ref_0=1e8*3.14*0.055**2/10000/2.
+regen_hist_cut = 1.e-4
+
+N_mp_soft_regen = 100000
+N_mp_after_soft_regen = 40000
+
+
+# Number of bins
+Nx_regen=51;#it must be odd!
+Ny_regen=51;#it must be odd!
+Nvx_regen=51;#it must be odd!
+Nvy_regen=101;#it must be odd!
+Nvz_regen=51;#it must be odd!
+
+#Sp_ch params
+Dt_sc = 0.3e-9
+Dh_sc = 0.2e-3
+# Dt_sc# = 0.5e-9
+# Dh_sc# = 0.1e-3
+t_sc_ON=0e-9;		#s
+sparse_solver = 'klu'
+
+#save_mp_state_time_file =  -1 
+#save_mp_state_time_file = np.arange(88,136,1)*25e-9 # 1x48 bunches
+save_mp_state_time_file = np.arange(44,46,1)*25e-9 # 
+
+flag_hist_impact_seg = 1
+
+flag_movie = 0             #1/0
+flag_sc_movie = 0             #1/0
+
+flag_verbose_file = False
+flag_verbose_stdout = False
+flag_detailed_MP_info = 0
+dec_fac_secbeam_prof=dec_fact_out
+
+el_density_probes = [{'x' : 3.578528e-07, 'y': 6.051342e-03, 'r_obs': 1e-3},{'x' : -1.186982e-06, 'y': -0.006264070337426034, 'r_obs': 1e-3}]
+#	[\
+#	{'x' : .007, 'y': .004, 'r_obs': 1e-3},\
+#	{'x' : .007, 'y': -.004, 'r_obs': 1e-3}]