Change _libwarpx.py functions to LibWarpX class methods (#2696)

* Initial attempt at moving function into LibWarpX

* Bugfix - undefined structs in get_particle_theta

This is untested, identified by IDE/visual inspection only

* Unify newlines

* Delete libwarpx.clight (duplicated picmi.py)

See picmi.constants.c

* Change function descriptive comment to docstring

Also remove extra newline in __init__ beginning.

* Replace pywarpx/_libwarpx calls appropriately

* Fix atexit register of finalize function

* Reorder WarpX.py imports for pre-commit

* Use picmi.Simulation.extension = libwarpx alias

This will hopefully preempt user script changes if we restructure things
to allow multiple WarpX runs to be done within a single Python script.

* Fix libwarpx ref in WarpX.getProbLo/getProbHi

* Update get_particle_boundary_buffer doc reference

3 files changed, 21 insertions, 24 deletions

diff --git a/Examples/Modules/ParticleBoundaryProcess/PICMI_inputs_reflection.py b/Examples/Modules/ParticleBoundaryProcess/PICMI_inputs_reflection.py
index c9903ad22..d7d023ef6 100755
--- a/Examples/Modules/ParticleBoundaryProcess/PICMI_inputs_reflection.py
+++ b/Examples/Modules/ParticleBoundaryProcess/PICMI_inputs_reflection.py
@@ -2,7 +2,6 @@
 #
 # --- Input file to test particle reflection off an absorbing boundary
 
-import pywarpx
 from pywarpx import picmi
 
 constants = picmi.constants
@@ -115,20 +114,20 @@ sim.step(max_steps)
 # buffer functions as intended
 ################################################
 
-n = pywarpx.get_particle_boundary_buffer_size("electrons", 'z_hi')
+n = sim.extension.get_particle_boundary_buffer_size("electrons", 'z_hi')
 print("Number of electrons in upper buffer:", n)
 assert n == 63
 
-n = pywarpx.get_particle_boundary_buffer_size("electrons", 'z_lo')
+n = sim.extension.get_particle_boundary_buffer_size("electrons", 'z_lo')
 print("Number of electrons in lower buffer:", n)
 assert n == 67
 
-scraped_steps = pywarpx.get_particle_boundary_buffer("electrons", 'z_hi', 'step_scraped', 0)
+scraped_steps = sim.extension.get_particle_boundary_buffer("electrons", 'z_hi', 'step_scraped', 0)
 for arr in scraped_steps:
     # print(arr)
     assert all(arr == 4)
 
-scraped_steps = pywarpx.get_particle_boundary_buffer("electrons", 'z_lo', 'step_scraped', 0)
+scraped_steps = sim.extension.get_particle_boundary_buffer("electrons", 'z_lo', 'step_scraped', 0)
 for arr in scraped_steps:
     # print(arr)
     assert all(arr == 8)
diff --git a/Examples/Modules/ParticleBoundaryScrape/PICMI_inputs_scrape.py b/Examples/Modules/ParticleBoundaryScrape/PICMI_inputs_scrape.py
index 90f526e4b..8009da0cc 100755
--- a/Examples/Modules/ParticleBoundaryScrape/PICMI_inputs_scrape.py
+++ b/Examples/Modules/ParticleBoundaryScrape/PICMI_inputs_scrape.py
@@ -3,7 +3,6 @@
 # --- Input file to test the particle scraper and the Python wrappers
 # --- to access the buffer of scraped particles.
 
-import pywarpx
 from pywarpx import picmi
 
 ##########################
@@ -117,25 +116,25 @@ sim.step(max_steps)
 
 from mpi4py import MPI as mpi
 
-my_id = pywarpx.getMyProc()
+my_id = sim.extension.getMyProc()
 
-n = pywarpx.get_particle_boundary_buffer_size("electrons", 'eb')
+n = sim.extension.get_particle_boundary_buffer_size("electrons", 'eb')
 print(f"Number of electrons in buffer (proc #{my_id}): {n}")
 assert n == 612
 
-scraped_steps = pywarpx.get_particle_boundary_buffer("electrons", 'eb', 'step_scraped', 0)
+scraped_steps = sim.extension.get_particle_boundary_buffer("electrons", 'eb', 'step_scraped', 0)
 for arr in scraped_steps:
     assert all(arr > 40)
 
-weights = pywarpx.get_particle_boundary_buffer("electrons", 'eb', 'w', 0)
+weights = sim.extension.get_particle_boundary_buffer("electrons", 'eb', 'w', 0)
 n = sum(len(arr) for arr in weights)
 print(f"Number of electrons in this proc's buffer (proc #{my_id}): {n}")
 n_sum =  mpi.COMM_WORLD.allreduce(n, op=mpi.SUM)
 assert n_sum == 612
 
 # clear the particle buffer
-pywarpx.clearParticleBoundaryBuffer()
+sim.extension.clearParticleBoundaryBuffer()
 # confirm that the buffer was cleared
-n = pywarpx.get_particle_boundary_buffer_size("electrons", 'eb')
+n = sim.extension.get_particle_boundary_buffer_size("electrons", 'eb')
 print(f"Number of electrons in buffer (proc #{my_id}): {n}")
 assert n == 0
diff --git a/Examples/Modules/embedded_boundary_python_API/PICMI_inputs_EB_API.py b/Examples/Modules/embedded_boundary_python_API/PICMI_inputs_EB_API.py
index 6dea197d3..4619defe1 100755
--- a/Examples/Modules/embedded_boundary_python_API/PICMI_inputs_EB_API.py
+++ b/Examples/Modules/embedded_boundary_python_API/PICMI_inputs_EB_API.py
@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
 import numpy as np
-import pywarpx
 from pywarpx import fields, picmi
 
 max_steps = 1
@@ -84,10 +83,10 @@ sim.initialize_inputs()
 
 sim.step(1)
 
-print("======== Testing pywarpx.get_mesh_edge_lengths =========")
+print("======== Testing sim.extension.get_mesh_edge_lengths =========")
 
-ly_slice_x = np.array(pywarpx.get_mesh_edge_lengths(0,1,include_ghosts=False)[0])[int(nx/2),:,:]
-lz_slice_x = np.array(pywarpx.get_mesh_edge_lengths(0,2,include_ghosts=False)[0])[int(nx/2),:,:]
+ly_slice_x = np.array(sim.extension.get_mesh_edge_lengths(0,1,include_ghosts=False)[0])[int(nx/2),:,:]
+lz_slice_x = np.array(sim.extension.get_mesh_edge_lengths(0,2,include_ghosts=False)[0])[int(nx/2),:,:]
 
 n_edge_y_lo = int((ny - 30)/2)
 n_edge_y_hi = int(ny - (ny - 30)/2)
@@ -105,8 +104,8 @@ print("Perimeter of the middle x-slice:", perimeter_slice_x)
 assert np.isclose(perimeter_slice_x, perimeter_slice_x_true, rtol=1e-05, atol=1e-08)
 
 
-lx_slice_y = np.array(pywarpx.get_mesh_edge_lengths(0,0,include_ghosts=False)[0])[:,int(ny/2),:]
-lz_slice_y = np.array(pywarpx.get_mesh_edge_lengths(0,2,include_ghosts=False)[0])[:,int(ny/2),:]
+lx_slice_y = np.array(sim.extension.get_mesh_edge_lengths(0,0,include_ghosts=False)[0])[:,int(ny/2),:]
+lz_slice_y = np.array(sim.extension.get_mesh_edge_lengths(0,2,include_ghosts=False)[0])[:,int(ny/2),:]
 
 n_edge_x_lo = int((nx - 30)/2)
 n_edge_x_hi = int(nx - (nx - 30)/2)
@@ -125,8 +124,8 @@ print("Perimeter of the middle y-slice:", perimeter_slice_y)
 assert np.isclose(perimeter_slice_y, perimeter_slice_y_true, rtol=1e-05, atol=1e-08)
 
 
-lx_slice_z = np.array(pywarpx.get_mesh_edge_lengths(0,0,include_ghosts=False)[0])[:,:,int(nz/2)]
-ly_slice_z = np.array(pywarpx.get_mesh_edge_lengths(0,1,include_ghosts=False)[0])[:,:,int(nz/2)]
+lx_slice_z = np.array(sim.extension.get_mesh_edge_lengths(0,0,include_ghosts=False)[0])[:,:,int(nz/2)]
+ly_slice_z = np.array(sim.extension.get_mesh_edge_lengths(0,1,include_ghosts=False)[0])[:,:,int(nz/2)]
 
 n_edge_x_lo = int((nx - 30)/2)
 n_edge_x_hi = int(nx - (nx - 30)/2)
@@ -143,9 +142,9 @@ perimeter_slice_z_true = L_cavity*4
 print("Perimeter of the middle z-slice:", perimeter_slice_z)
 assert np.isclose(perimeter_slice_z, perimeter_slice_z_true, rtol=1e-05, atol=1e-08)
 
-print("======== Testing pywarpx.get_mesh_face_areas =========")
+print("======== Testing sim.extension.get_mesh_face_areas =========")
 
-Sx_slice = np.sum(np.array(pywarpx.get_mesh_face_areas(0,0,include_ghosts=False)[0])[int(nx/2),:,:])
+Sx_slice = np.sum(np.array(sim.extension.get_mesh_face_areas(0,0,include_ghosts=False)[0])[int(nx/2),:,:])
 dx = (xmax-xmin)/nx
 Ax = dx*dx
 Sx_slice_true = L_cavity*L_cavity - 2*Ax
@@ -153,7 +152,7 @@ print("Area of the middle x-slice:", Sx_slice)
 assert np.isclose(Sx_slice, Sx_slice_true, rtol=1e-05, atol=1e-08)
 
 
-Sy_slice = np.sum(np.array(pywarpx.get_mesh_face_areas(0,1,include_ghosts=False)[0])[:,int(ny/2),:])
+Sy_slice = np.sum(np.array(sim.extension.get_mesh_face_areas(0,1,include_ghosts=False)[0])[:,int(ny/2),:])
 dy = (ymax-ymin)/ny
 Ay = dy*dy
 Sy_slice_true = L_cavity*L_cavity - 2*Ay
@@ -161,7 +160,7 @@ print("Area of the middle y-slice:", Sx_slice)
 assert np.isclose(Sy_slice, Sy_slice_true, rtol=1e-05, atol=1e-08)
 
 
-Sz_slice = np.sum(np.array(pywarpx.get_mesh_face_areas(0,2,include_ghosts=False)[0])[:,:,int(nz/2)])
+Sz_slice = np.sum(np.array(sim.extension.get_mesh_face_areas(0,2,include_ghosts=False)[0])[:,:,int(nz/2)])
 dz = (zmax-zmin)/nz
 Az = dz*dz
 Sz_slice_true = L_cavity*L_cavity - 2*Az