Update Particle Container to Pure SoA (#3850)

* Update Particle Container to Pure SoA

Transition particle containers to pure SoA layouts.

* Python: Pure SoA Particle

* Update Particle Container to Pure SoA

Transition particle containers to pure SoA layouts.

* Python: Pure SoA Particle

* fix a couple of places where we underflow the particle idcpu

* fixed bad merge

* fix bad merge again

* Update Particle Container to Pure SoA

Transition particle containers to pure SoA layouts.

* Python: Pure SoA Particle

* skip positions for pure SoA plotfiles

* Update Particle Container to Pure SoA

Transition particle containers to pure SoA layouts.

Co-authored-by: Andrew Myers <atmyers@lbl.gov>

* Python: Pure SoA Particle

* correctly account for positions in restart

---------

Co-authored-by: Andrew Myers <atmyers2@gmail.com>
Co-authored-by: Andrew Myers <atmyers@lbl.gov>

Author: ax3l

Docs/source/usage/workflows/python_extend.rst

@@ -252,7 +252,8 @@ Particles can be added to the simulation at specific positions and with specific
 .. autoclass:: pywarpx.particle_containers.ParticleContainerWrapper
    :members:
 
-The ``get_particle_structs()`` and ``get_particle_arrays()`` functions are called
+The ``get_particle_real_arrays()``, ``get_particle_int_arrays()`` and
+``get_particle_idcpu_arrays()`` functions are called
 by several utility functions of the form ``get_particle_{comp_name}`` where
 ``comp_name`` is one of ``x``, ``y``, ``z``, ``r``, ``theta``, ``id``, ``cpu``,
 ``weight``, ``ux``, ``uy`` or ``uz``.

Examples/Tests/particle_data_python/PICMI_inputs_2d.py

@@ -153,10 +153,10 @@ def add_particles():
 ##########################
 
 assert (elec_wrapper.nps == 270 / (2 - args.unique))
-assert (elec_wrapper.particle_container.get_comp_index('w') == 0)
-assert (elec_wrapper.particle_container.get_comp_index('newPid') == 4)
+assert (elec_wrapper.particle_container.get_comp_index('w') == 2)
+assert (elec_wrapper.particle_container.get_comp_index('newPid') == 6)
 
-new_pid_vals = elec_wrapper.get_particle_arrays('newPid', 0)
+new_pid_vals = elec_wrapper.get_particle_real_arrays('newPid', 0)
 for vals in new_pid_vals:
     assert np.allclose(vals, 5)
 

Examples/Tests/particle_data_python/PICMI_inputs_prev_pos_2d.py

@@ -120,12 +120,12 @@
 elec_count = elec_wrapper.nps
 
 # check that the runtime attributes have the right indices
-assert (elec_wrapper.particle_container.get_comp_index('prev_x') == 4)
-assert (elec_wrapper.particle_container.get_comp_index('prev_z') == 5)
+assert (elec_wrapper.particle_container.get_comp_index('prev_x') == 6)
+assert (elec_wrapper.particle_container.get_comp_index('prev_z') == 7)
 
 # sanity check that the prev_z values are reasonable and
 # that the correct number of values are returned
-prev_z_vals = elec_wrapper.get_particle_arrays('prev_z', 0)
+prev_z_vals = elec_wrapper.get_particle_real_arrays('prev_z', 0)
 running_count = 0
 
 for z_vals in prev_z_vals:

Examples/Tests/restart/PICMI_inputs_runtime_component_analyze.py

@@ -158,10 +158,10 @@ def add_particles():
 ##########################
 
 assert electron_wrapper.nps == 90
-assert electron_wrapper.particle_container.get_comp_index("w") == 0
-assert electron_wrapper.particle_container.get_comp_index("newPid") == 4
+assert electron_wrapper.particle_container.get_comp_index("w") == 2
+assert electron_wrapper.particle_container.get_comp_index("newPid") == 6
 
-new_pid_vals = electron_wrapper.get_particle_arrays("newPid", 0)
+new_pid_vals = electron_wrapper.get_particle_real_arrays("newPid", 0)
 for vals in new_pid_vals:
     assert np.allclose(vals, 5)