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@giadarol
giadarol committed Apr 30, 2018
2 parents 7a223ef + 9414535 commit b48e140
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Showing 47 changed files with 1,024 additions and 909 deletions.
2 changes: 1 addition & 1 deletion 002_change_version_number.py
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Expand Up @@ -9,7 +9,7 @@
with open(filename) as fid:
content=fid.read()
if '[email protected]' in content:
content=content.replace('PyECLOUD Version 7.1.2', 'PyECLOUD Version 7.1.2')
content=content.replace('PyECLOUD Version 7.2.0', 'PyECLOUD Version 7.2.0')
with open(filename,'w') as fid:
fid.write(content)

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2 changes: 1 addition & 1 deletion 003_change_preamble.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@
#
# This file is part of the code:
#
# PyECLOUD Version 7.1.2
# PyECLOUD Version 7.2.0
#
#
# Main author: Giovanni IADAROLA
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19 changes: 18 additions & 1 deletion MP_system.py
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Expand Up @@ -7,7 +7,7 @@
#
# This file is part of the code:
#
# PyECLOUD Version 7.1.2
# PyECLOUD Version 7.2.0
#
#
# Main author: Giovanni IADAROLA
Expand Down Expand Up @@ -524,3 +524,20 @@ def add_from_file(self, filename_MPs):

self.N_mp=int(self.N_mp+Nint_new_MP);

def extract_dict(self):
dict_MP = {
'x_mp':self.x_mp[:self.N_mp].copy(),
'y_mp':self.y_mp[:self.N_mp].copy(),
'z_mp':self.z_mp[:self.N_mp].copy(),
'vx_mp':self.vx_mp[:self.N_mp].copy(),
'vy_mp':self.vy_mp[:self.N_mp].copy(),
'vy_mp':self.vz_mp[:self.N_mp].copy(),
'nel_mp':self.nel_mp[:self.N_mp].copy(),
'N_mp':self.N_mp,
}
return dict_MP

def init_from_dict(self, dict_MP):
self.N_mp = 0
self.add_from_file(dict_MP)

205 changes: 98 additions & 107 deletions PyEC4PyHT.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
#
# This file is part of the code:
#
# PyECLOUD Version 7.1.2
# PyECLOUD Version 7.2.0
#
#
# Main author: Giovanni IADAROLA
Expand Down Expand Up @@ -50,22 +50,41 @@

import os
import subprocess
import time

import numpy as np
from scipy.constants import c, e, m_e

import myloadmat_to_obj as mlm
import init
import buildup_simulation as bsim

class MP_light(object):
class Empty(object):
pass

class DummyBeamTim(object):
def __init__(self, PyPIC_state):
self.PyPIC_state = PyPIC_state

def get_beam_eletric_field(self, MP_e):
if (MP_e.N_mp>0):
## compute beam electric field
Ex_n_beam, Ey_n_beam = self.PyPIC_state.gather(MP_e.x_mp[0:MP_e.N_mp],MP_e.y_mp[0:MP_e.N_mp])
else:
Ex_n_beam=0.
Ey_n_beam=0.
return Ex_n_beam, Ey_n_beam


extra_allowed_kwargs = {'x_beam_offset', 'y_beam_offset', 'probes_position'}

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, **kwargs):
slice_by_slice_mode=False, space_charge_obj=None, kick_mode_for_beam_field=False,
beam_monitor=None, verbose=False,
**kwargs):

print 'PyECLOUD Version 7.1.2'
print 'PyECLOUD Version 7.2.0'

# 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'
Expand Down Expand Up @@ -94,27 +113,15 @@ def __init__(self, L_ecloud, slicer, Dt_ref, pyecl_input_folder='./', flag_clean
self.pyecl_input_folder = pyecl_input_folder
self.kwargs = kwargs

(
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, skip_beam=True,
skip_pyeclsaver=True, skip_spacech_ele=(space_charge_obj is not None),
ignore_kwargs=extra_allowed_kwargs, **kwargs)

cc = mlm.obj_from_dict(config_dict)

if space_charge_obj is not None:
spacech_ele = space_charge_obj

if cc.track_method == 'Boris':
self.cloudsim = bsim.BuildupSimulation(
pyecl_input_folder=pyecl_input_folder, skip_beam=True,
spacech_ele=space_charge_obj,
skip_pyeclsaver=True, ignore_kwargs=extra_allowed_kwargs, **kwargs)


if self.cloudsim.config_dict['track_method'] == 'Boris':
pass
elif cc.track_method == 'BorisMultipole':
elif self.cloudsim.config_dict['track_method'] == 'BorisMultipole':
pass
else:
raise ValueError("""track_method should be 'Boris' or 'BorisMultipole' - others are not implemented in the PyEC4PyHT module""")
Expand All @@ -126,6 +133,7 @@ def __init__(self, L_ecloud, slicer, Dt_ref, pyecl_input_folder='./', flag_clean
if 'y_beam_offset' in kwargs:
self.y_beam_offset = kwargs['y_beam_offset']


# initialize proton density probes
self.save_ele_field_probes = False
self.x_probes = -1
Expand All @@ -147,30 +155,13 @@ def __init__(self, L_ecloud, slicer, Dt_ref, pyecl_input_folder='./', flag_clean

self.N_tracks = 0

spacech_ele.flag_decimate = False
self.cloudsim.spacech_ele.flag_decimate = False



if self.cloudsim.flag_multiple_clouds:
raise ValueError('Multiple clouds not yet tested in PyEC4PyHT!')

if flag_multiple_clouds:
raise ValueError('Multiple clouds not yet implemented in PyEC4PyHT!')
else:
cloud = cloud_list[0]

MP_e = cloud.MP_e
dynamics = cloud.dynamics
impact_man = cloud.impact_man
pyeclsaver = cloud.pyeclsaver
gas_ion_flag = cloud.gas_ion_flag
resgasion = cloud.resgasion
t_ion = cloud.t_ion
photoem_flag = cloud.photoem_flag
phemiss = cloud.phemiss

self.MP_e = MP_e
self.dynamics = dynamics
self.impact_man = impact_man
self.spacech_ele = spacech_ele

self.gas_ion_flag = gas_ion_flag
self.resgasion = resgasion

self.save_ele_distributions_last_track = False
self.save_ele_potential_and_field = False
Expand All @@ -182,30 +173,35 @@ def __init__(self, L_ecloud, slicer, Dt_ref, pyecl_input_folder='./', flag_clean

self.track_only_first_time = False

self.init_x = self.MP_e.x_mp[:self.MP_e.N_mp].copy()
self.init_y = self.MP_e.y_mp[:self.MP_e.N_mp].copy()
self.init_z = self.MP_e.z_mp[:self.MP_e.N_mp].copy()
self.init_vx = self.MP_e.vx_mp[:self.MP_e.N_mp].copy()
self.init_vy = self.MP_e.vy_mp[:self.MP_e.N_mp].copy()
self.init_vz = self.MP_e.vz_mp[:self.MP_e.N_mp].copy()
self.init_nel = self.MP_e.nel_mp[:self.MP_e.N_mp].copy()
self.init_N_mp = self.MP_e.N_mp
self.initial_MP_e_clouds = [cl.MP_e.extract_dict() for cl in self.cloudsim.cloud_list]

self.flag_clean_slices = flag_clean_slices

self.beam_PyPIC_state = self.cloudsim.spacech_ele.PyPICobj.get_state_object()

self.slice_by_slice_mode = slice_by_slice_mode
if self.slice_by_slice_mode:
self.track = self._track_in_single_slice_mode
self.finalize_and_reinitialize = self._finalize_and_reinitialize

self.spacech_ele = self.cloudsim.spacech_ele # For backwards compatibility

self.kick_mode_for_beam_field = kick_mode_for_beam_field
self.beam_monitor = beam_monitor

self.verbose = verbose

# @profile
def track(self, beam):

if self.track_only_first_time:
if self.N_tracks>0:
print 'Warning: Track skipped because track_only_first_time is True.'
return


if self.verbose:
start_time = time.mktime(time.localtime())

self._reinitialize()

if hasattr(beam.particlenumber_per_mp, '__iter__'):
Expand All @@ -225,8 +221,17 @@ def track(self, beam):
dz = (slices.z_bins[i + 1] - slices.z_bins[i])

self._track_single_slice(beam, ix, dz)


# Used by Lotta to debug fastion mode
if self.beam_monitor is not None:
self.beam_monitor.dump(beam)

self._finalize()

if self.verbose:
stop_time = time.mktime(time.localtime())
print 'Done track %d in %.1f s'%(self.N_tracks, stop_time-start_time)

self.N_tracks+=1

Expand All @@ -252,15 +257,7 @@ def replace_with_recorded_field_map(self, delete_ecloud_data=True):

if delete_ecloud_data:
self.spacech_ele=None
self.Mp_e = None
self.init_nel = None
self.init_vx = None
self.init_vy = None
self.init_vz = None
self.init_x = None
self.init_y = None
self.init_z = None

self.cloudsim=None

else:
print 'Warning: efieldmap already exists. I do nothing.'
Expand All @@ -284,10 +281,8 @@ def track_once_and_replace_with_recorded_field_map(self, bunch, delete_ecloud_da

def _track_single_slice(self, beam, ix, dz):

MP_e = self.MP_e
dynamics = self.dynamics
impact_man = self.impact_man
spacech_ele = self.spacech_ele

spacech_ele = self.cloudsim.spacech_ele

dt = dz / (beam.beta * c)

Expand All @@ -300,47 +295,48 @@ def _track_single_slice(self, beam, ix, dz):
Dt_substep = dt/N_sub_steps
#print Dt_substep, N_sub_steps, dt


# beam field
MP_p = MP_light()
self.beam_PyPIC_state.scatter(
x_mp = beam.x[ix]+self.x_beam_offset,
y_mp = beam.y[ix]+self.y_beam_offset,
nel_mp = beam.x[ix]*0.+beam.particlenumber_per_mp/dz,
charge = beam.charge)
self.cloudsim.spacech_ele.PyPICobj.solve_states([self.beam_PyPIC_state])

#build dummy beamtim object
dummybeamtim = DummyBeamTim(self.beam_PyPIC_state)

# OK for single bunch, to be modified for multibunch:
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.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

# 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)


# Build MP_system-like object with beam coordinates
MP_p = Empty()
MP_p.x_mp = beam.x[ix]+self.x_beam_offset
MP_p.y_mp = beam.y[ix]+self.y_beam_offset
MP_p.nel_mp = beam.x[ix]*0.+beam.particlenumber_per_mp/dz#they have to become cylinders
MP_p.N_mp = len(beam.x[ix])
MP_p.charge = beam.charge
#compute beam field (it assumes electrons!)
spacech_ele.recompute_spchg_efield(MP_p)
#scatter to electrons
Ex_n_beam, Ey_n_beam = spacech_ele.get_sc_eletric_field(MP_e)


## compute electron field map
spacech_ele.recompute_spchg_efield(MP_e)

## compute electron field on electrons
Ex_sc_n, Ey_sc_n = spacech_ele.get_sc_eletric_field(MP_e)

## compute electron field on beam particles
## compute cloud field on beam particles
Ex_sc_p, Ey_sc_p = spacech_ele.get_sc_eletric_field(MP_p)

## Total electric field on electrons
Ex_n=Ex_sc_n+Ex_n_beam
Ey_n=Ey_sc_n+Ey_n_beam

## save position before motion step
old_pos=MP_e.get_positions()

## motion electrons
MP_e = dynamics.stepcustomDt(MP_e, Ex_n,Ey_n, Dt_substep=Dt_substep, N_sub_steps=N_sub_steps)

## impacts: backtracking and secondary emission
MP_e = impact_man.backtrack_and_second_emiss(old_pos, MP_e)

## kick beam particles
fact_kick = beam.charge/(beam.mass*beam.beta*beam.beta*beam.gamma*c*c)*self.L_ecloud
beam.xp[ix]+=fact_kick*Ex_sc_p
beam.yp[ix]+=fact_kick*Ey_sc_p

## Diagnostics
if self.save_ele_distributions_last_track:
self.rho_ele_last_track.append(spacech_ele.rho.copy())
#print 'Here'
Expand All @@ -367,7 +363,7 @@ def _track_single_slice(self, beam, ix, dz):
self.N_MP_last_track.append(MP_e.N_mp)

if self.save_ele_field_probes:
MP_probes = MP_light()
MP_probes = Empty()
MP_probes.x_mp = self.x_probes
MP_probes.y_mp = self.y_probes
MP_probes.nel_mp = self.x_probes*0.+1. #fictitious charge of 1 C
Expand All @@ -379,14 +375,9 @@ def _track_single_slice(self, beam, ix, dz):

def _reinitialize(self):

self.MP_e.x_mp[:self.init_N_mp] = self.init_x #it is a mutation and not a binding (and we have tested it :-))
self.MP_e.y_mp[:self.init_N_mp] = self.init_y
self.MP_e.z_mp[:self.init_N_mp] = self.init_z
self.MP_e.vx_mp[:self.init_N_mp] = self.init_vx
self.MP_e.vy_mp[:self.init_N_mp] = self.init_vy
self.MP_e.vz_mp[:self.init_N_mp] = self.init_vz
self.MP_e.nel_mp[:self.init_N_mp] = self.init_nel
self.MP_e.N_mp = self.init_N_mp

for cloud, initdict in zip(self.cloudsim.cloud_list, self.initial_MP_e_clouds):
cloud.MP_e.init_from_dict(initdict)

if self.save_ele_distributions_last_track:
self.rho_ele_last_track = []
Expand Down
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