Merge branch 'develop' into python3_master

PyCOMPLETE · Dec 13, 2019 · 08c5cec · 08c5cec
2 parents 0d30755 + f4a83b0
commit 08c5cec
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diff --git a/000_run_simulation.py b/000_run_simulation.py
@@ -1,10 +1,4 @@
-import sys, os
-BIN = os.path.expanduser("../")
-sys.path.append(BIN)
-
-
 from PyECLOUD.buildup_simulation import BuildupSimulation
 
-
 sim = BuildupSimulation()
 sim.run()
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 'giovanni.iadarola@cern.ch' in content:
-            content = content.replace('PyECLOUD Version 8.3.0', 'PyECLOUD Version 8.3.0')
+            content = content.replace('PyECLOUD Version 8.4.0', 'PyECLOUD Version 8.4.0')
             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 8.3.0
+#                   PyECLOUD Version 8.4.0
 #
 #
 #     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 8.3.0
+#                   PyECLOUD Version 8.4.0
 #
 #
 #     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 8.3.0
+#                   PyECLOUD Version 8.4.0
 #
 #
 #     Main author:          Giovanni IADAROLA
@@ -66,6 +66,8 @@ class Empty(object):
 
 
 class DummyBeamTim(object):
+    """Dummy beam-timing class to interface with buildup simulation"""
+
     def __init__(self, PyPIC_state):
         self.PyPIC_state = PyPIC_state
 
@@ -100,6 +102,8 @@ def get_beam_eletric_field(self, MP_e):
 
 class Ecloud(object):
     def generate_twin_ecloud_with_shared_space_charge(self):
+        """Generate an identical Ecloud objet with shared space-charge member."""
+
         if hasattr(self, "efieldmap"):
             raise ValueError(
                 "Ecloud has been replaced with field map. I cannot generate a twin ecloud!"
@@ -136,8 +140,105 @@ def __init__(
         force_interp_at_substeps_interacting_slices=False,
         **kwargs
     ):
+        """
+        Construct an e-cloud object that can be inserted in a PyHEADTAIL machine
+
+        Parameters
+        ---------
+
+        L_ecloud : m
+            Length of the e-cloud interaction
+
+        slicer :
+            PyHEADTAIL slicer object, used to define slices for e-cloud insteraction.
+            Needs to be provided only if slice_by_slice_mode is False.
+
+        Dt_ref : s
+            Target duration of the sub-steps perfomed in each slice.
+
+        pyecl_input_folder : path
+            Folder containing the PyECLOUD input files defining the e-cloud.
+
+        flag_clean_slices : {True, False}
+            If True, slicing is redone before the e-cloud interation.
+            This flag has no effect is slice_by_slice_mode is True.
+
+        slice_by_slice_mode : {True, False}
+
+            - If False, the e-cloud receives a full bunch, slicing is done interally,
+              the cloud is automatically re-initialized after each interaction.
+            - If True, the e-cloud receives one slice at a time (the slice object
+              should have metadata in a member called slice_info. The reinitialization
+              of the cloud is done based on the meta-data or esplicitly by the user.
+
+        space_charge_obj :
+
+            - If None a space-charge object (Particle In Cell) is constructed for
+              the e-cloud
+            - If not None the provided space-charge objeci is used
+
+        kick_mode_for_beam_field : {True, False}
+            If True, the force of the beam on the electrons is applied as a
+            discrete kick (used mainly for fast beam-ion simulations).
+
+        beam_monitor :
+            PyHEADTAIL beam-monitor, used sometimes for debug purposes.
+
+        verbose : {True, False}
+
+        save_pyecl_outp_as : path
+            File in which cloud evolution is stored.
+
+        force_reinterp_at_substeps_interacting_slices : {True, False}
+            Fields from beams and clouds are re-interpolated at each subsstep.
+
+        x_beam_offset : m
+            Horizontal position of the PyHEADTAIL reference trajectoy in
+            the PyECLOUD referece system.
+
+        y_beam_offset: m
+            Vertical position of the PyHEADTAIL reference trajectoy in
+            the PyECLOUD referece system.
+
+        probes_position : dict
+            Positions at which electron density and field can be measured.
+
+        enable_kick_x :
+            Enable horizontal kick from the cloud on the beam.
+
+        enable_kick_y :
+            Enable vertical kick from the cloud on the beam.
+
+        **kwargs :
+            Any input parameter of PyECLOUD can be passes as a keyword arguments.
+            Parameters definded in the input files are overridden by those passas as
+            keyword arguments.
+
+        Additional information
+        ----------------------
+        After building the object, the following members can be set to true to record
+        additional information (which is then attached as a member to the ecloud object
+        itself. After setting any of these ot true the [ecloud]._reinitialize
+        function needs to be called to prepare the data storage, which also resets cloud
+        state.
+
+        [ecloud].save_ele_distributions_last_track
+        [ecloud].save_ele_potential_and_field
+        [ecloud].save_ele_potential
+        [ecloud].save_ele_field
+        [ecloud].save_ele_MP_position
+        [ecloud].save_ele_MP_velocity
+        [ecloud].save_ele_MP_size
+
+        [ecloud].save_beam_distributions_last_track
+        [ecloud].save_beam_potential_and_field
+        [ecloud].save_beam_potential
+        [ecloud].save_beam_field
+
+
+        """
 
-        print("PyECLOUD Version 8.3.0")
+        print("PyECLOUD Version 8.4.0")
 
         # 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"
@@ -264,6 +365,7 @@ def __init__(
 
         self.slice_by_slice_mode = slice_by_slice_mode
         if self.slice_by_slice_mode:
+            assert(slicer is None)
             self.track = self._track_in_single_slice_mode
             self.finalize_and_reinitialize = self._finalize_and_reinitialize
 

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 8.3.0
+#                   PyECLOUD Version 8.4.0
 #
 #
 #     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 8.3.0
+#                   PyECLOUD Version 8.4.0
 #
 #
 #     Main author:          Giovanni IADAROLA
@@ -71,7 +71,7 @@ def __init__(
         **kwargs
     ):
 
-        print("PyECLOUD Version 8.3.0")
+        print("PyECLOUD Version 8.4.0")
         (
             beamtim,
             spacech_ele,

diff --git a/cloud_manager.py b/cloud_manager.py
@@ -7,7 +7,7 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 8.3.0
+#                   PyECLOUD Version 8.4.0
 #
 #
 #     Author and contact:   Giovanni IADAROLA

diff --git a/cross_ionization.py b/cross_ionization.py
@@ -7,7 +7,7 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 8.3.0
+#                   PyECLOUD Version 8.4.0
 #
 #
 #     Main author:          Giovanni IADAROLA

diff --git a/default_input_parameters.py b/default_input_parameters.py
@@ -149,9 +149,9 @@
             'B_map_file': None,
             'Bz_map_file': None, # documented?
             'fact_Bmap': 1.,
-            'B0x': 0.,
-            'B0y': 0.,
-            'B0z': 0.,
+            'B0x': None,
+            'B0y': None,
+            'B0z': None,
             'B_zero_thrhld': None,
             'N_sub_steps': 1,
             'B_multip': [],

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
@@ -416,6 +416,9 @@ \subsection{Simulation parameters}
     \\ \hline
     \textbf{B\_skew} & The skew parameters can be included through B\_skew. For a skew quadrupole with a gradient of 12 T/m, set B\_multip to [0.,0.] and B\_skew to [0.,12.].
     B\_skew specifies $b'_n =\frac{\partial^n B_x}{\partial x^n}$ and defaults to {\it None}. \\ \hline
+    \textbf{B0x, B0y, B0z} & (optional -- default = 0) \newline
+    [T] Uniform magnetic fields added to the map.
+    \\ \hline
 \end{longtable}
 
 

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 8.3.0
+#                   PyECLOUD Version 8.4.0
 #
 #
 #     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 8.3.0
+#                   PyECLOUD Version 8.4.0
 #
 #
 #     Main author:          Giovanni IADAROLA
@@ -57,7 +57,8 @@
 
 class pusher_Boris_multipole():
 
-    def __init__(self, Dt, N_sub_steps=1, B_multip=None, B_skew=None):
+    def __init__(self, Dt, N_sub_steps=1, B_multip=None, B_skew=None,
+        B0x=None, B0y=None, B0z=None):
 
         self.N_sub_steps = N_sub_steps
         self.Dt = Dt
@@ -79,40 +80,47 @@ def __init__(self, Dt, N_sub_steps=1, B_multip=None, B_skew=None):
         else:
             self.B_field_skew = np.array(B_skew, dtype=float) / factorial
 
+        self.B0x = B0x
+        self.B0y = B0y
+        self.B0z = B0z
         print("Tracker: Boris multipole")
 
         print("N_subst_init=%d" % self.N_sub_steps)
 
     #@profile
-    def step(self, MP_e, Ex_n, Ey_n, Ez_n=0., Bx_n=np.asarray([0.]), By_n=np.asarray([0.]), Bz_n=np.asarray([0.])):
-
-        if (Bx_n == np.asarray([0.])).all() and (By_n == np.asarray([0.])).all() and (Bz_n == np.asarray([0.])).all():
-            custom_B = 0
-        else:
-            custom_B = 1
-
-        if MP_e.N_mp > 0:
-
-            xn1 = MP_e.x_mp[0:MP_e.N_mp]
-            yn1 = MP_e.y_mp[0:MP_e.N_mp]
-            zn1 = MP_e.z_mp[0:MP_e.N_mp]
-            vxn1 = MP_e.vx_mp[0:MP_e.N_mp]
-            vyn1 = MP_e.vy_mp[0:MP_e.N_mp]
-            vzn1 = MP_e.vz_mp[0:MP_e.N_mp]
-            if Ez_n != 0.:
-                raise ValueError('Oooops! Not implemented....')
+    def step(self, MP_e, Ex_n, Ey_n, Ez_n=0., Bx_n=None, By_n=None, Bz_n=None):
+        MP_e = self.stepcustomDt(MP_e, Ex_n, Ey_n, Ez_n,
+            Bx_n, By_n, Bz_n,
+            Dt_substep=self.Dtt, N_sub_steps=self.N_sub_steps)
+        return MP_e
 
-            boris_step_multipole(self.N_sub_steps, self.Dtt, self.B_field, self.B_field_skew,
-                                 xn1, yn1, zn1, vxn1, vyn1, vzn1,
-                                 Ex_n, Ey_n, Bx_n, By_n, Bz_n, custom_B, MP_e.charge, MP_e.mass)
+    def stepcustomDt(self, MP_e, Ex_n, Ey_n, Ez_n=0.,
+        Bx_n=None, By_n=None, Bz_n=None,
+        Dt_substep=None, N_sub_steps=None):
 
-        return MP_e
+        custom_B = 0
+        Bx_arr = np.zeros(MP_e.N_mp)
+        By_arr = np.zeros(MP_e.N_mp)
+        Bz_arr = np.zeros(MP_e.N_mp)
 
-    def stepcustomDt(self, MP_e, Ex_n, Ey_n, Ez_n=0., Bx_n=np.asarray([0.]), By_n=np.asarray([0.]), Bz_n=np.asarray([0.]), Dt_substep=None, N_sub_steps=None):
+        if self.B0x is not None:
+            Bx_arr += self.B0x
+            custom_B = 1
+        if self.B0y is not None:
+            By_arr += self.B0y
+            custom_B = 1
+        if self.B0z is not None:
+            Bz_arr += self.B0z
+            custom_B = 1
 
-        if (Bx_n == np.asarray([0.])).all() and (By_n == np.asarray([0.])).all() and (Bz_n == np.asarray([0.])).all():
-            custom_B = 0
-        else:
+        if Bx_n is not None:
+            Bx_arr += Bx_n
+            custom_B = 1
+        if By_n is not None:
+            By_arr += By_n
+            custom_B = 1
+        if Bz_n is not None:
+            Bz_arr += Bz_n
             custom_B = 1
 
         if MP_e.N_mp > 0:
@@ -128,7 +136,7 @@ def stepcustomDt(self, MP_e, Ex_n, Ey_n, Ez_n=0., Bx_n=np.asarray([0.]), By_n=np
                 raise ValueError('Oooops! Not implemented....')
 
             boris_step_multipole(N_sub_steps, Dt_substep, self.B_field, self.B_field_skew,
-                                 xn1, yn1, zn1, vxn1, vyn1, vzn1,
-                                 Ex_n, Ey_n, Bx_n, By_n, Bz_n, custom_B, MP_e.charge, MP_e.mass)
+                         xn1, yn1, zn1, vxn1, vyn1, vzn1,
+                         Ex_n, Ey_n, Bx_arr, By_arr, Bz_arr, custom_B, MP_e.charge, MP_e.mass)
 
         return MP_e
diff --git a/dynamics_dipole.py b/dynamics_dipole.py
@@ -7,7 +7,7 @@
 #
 #     This file is part of the code:
 #
-#                   PyECLOUD Version 8.3.0
+#                   PyECLOUD Version 8.4.0
 #
 #
 #     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 8.3.0
+#                   PyECLOUD Version 8.4.0
 #
 #
 #     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 8.3.0
+#                   PyECLOUD Version 8.4.0
 #
 #
 #     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 8.3.0
+#                   PyECLOUD Version 8.4.0
 #
 #
 #     Main author:          Giovanni IADAROLA