From e08767c1211754d3d771cf39f8587d7528fe19ef Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Mon, 20 Dec 2021 17:55:58 -0800
Subject: [PATCH 01/22] Add PICMI Script for 2D Case

---
 .../laser_acceleration/PICMI_inputs_2d.py     | 148 ++++++++++++++++++
 1 file changed, 148 insertions(+)
 create mode 100755 Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
new file mode 100755
index 00000000000..fdc1ed5f682
--- /dev/null
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
@@ -0,0 +1,148 @@
+from pywarpx import picmi
+
+# Physical constants
+c = picmi.constants.c
+q_e = picmi.constants.q_e
+
+# Number of time steps
+max_steps = 1000
+
+# Number of cells
+nx = 64
+nz = 512
+
+# Physical domain
+xmin = -30e-06
+xmax =  30e-06
+zmin = -56e-06
+zmax =  12e-06
+
+# Domain decomposition
+max_grid_size = 64
+blocking_factor = 32
+
+# Create grid
+grid = picmi.Cartesian2DGrid(
+    number_of_cells = [nx, nz],
+    lower_bound = [xmin, zmin],
+    upper_bound = [xmax, zmax],
+    lower_boundary_conditions = ['open', 'open'],
+    upper_boundary_conditions = ['open', 'open'],
+    lower_boundary_conditions_particles = ['absorbing', 'absorbing'],
+    upper_boundary_conditions_particles = ['absorbing', 'absorbing'],
+    moving_window_velocity = [0., c],
+    warpx_max_grid_size = max_grid_size,
+    warpx_blocking_factor = blocking_factor)
+
+# Particles: plasma electrons
+plasma_density = 2e23
+plasma_xmin = -20e-06
+plasma_ymin = None
+plasma_zmin = 10e-06
+plasma_xmax = 20e-06
+plasma_ymax = None
+plasma_zmax = None
+uniform_distribution = picmi.UniformDistribution(
+    density = plasma_density,
+    lower_bound = [plasma_xmin, plasma_ymin, plasma_zmin],
+    upper_bound = [plasma_xmax, plasma_ymax, plasma_zmax],
+    fill_in = True)
+electrons = picmi.Species(
+    particle_type = 'electron',
+    name = 'electrons',
+    initial_distribution = uniform_distribution)
+
+# Particles: beam electrons
+q_tot = 1e-12
+x_m = 0.
+y_m = 0.
+z_m = -28e-06
+x_rms = 0.5e-06
+y_rms = 0.5e-06
+z_rms = 0.5e-06
+ux_m = 0.
+uy_m = 0.
+uz_m = 500.
+ux_th = 2.
+uy_th = 2.
+uz_th = 50.
+gaussian_bunch_distribution = picmi.GaussianBunchDistribution(
+    n_physical_particles = q_tot / q_e,
+    rms_bunch_size = [x_rms, y_rms, z_rms],
+    rms_velocity = [c*ux_th, c*uy_th, c*uz_th],
+    centroid_position = [x_m, y_m, z_m],
+    centroid_velocity = [c*ux_m, c*uy_m, c*uz_m])
+beam = picmi.Species(
+    particle_type = 'electron',
+    name = 'beam',
+    initial_distribution = gaussian_bunch_distribution)
+
+# Laser
+e_max = 16e12
+position_z = 9e-06
+profile_t_peak = 30.e-15
+profile_focal_distance = 100e-06
+laser = picmi.GaussianLaser(
+    wavelength = 0.8e-06,
+    waist = 5e-06,
+    duration = 15e-15,
+    focal_position = [0, 0, profile_focal_distance + position_z],
+    centroid_position = [0, 0, position_z - c*profile_t_peak],
+    propagation_direction = [0, 0, 1],
+    polarization_direction = [0, 1, 0],
+    E0 = e_max,
+    fill_in = False)
+laser_antenna = picmi.LaserAntenna(
+    position = [0., 0., position_z],
+    normal_vector = [0, 0, 1])
+
+# Electromagnetic solver
+solver = picmi.ElectromagneticSolver(
+    grid = grid,
+    method = 'Yee',
+    cfl = 1.,
+    divE_cleaning = 0)
+
+# Diagnostics
+diag_field_list = ["B", "E", "J", "rho"]
+field_diag = picmi.FieldDiagnostic(
+    name = 'diag1',
+    grid = grid,
+    period = 200,
+    data_list = diag_field_list)
+
+# Set up simulation
+sim = picmi.Simulation(
+    solver = solver,
+    max_steps = max_steps,
+    verbose = 1,
+    particle_shape = 'cubic',
+    warpx_use_filter = 1)
+
+# Add plasma electrons
+sim.add_species(
+    electrons,
+    layout = picmi.GriddedLayout(grid = grid, n_macroparticle_per_cell = [1, 1, 1]))
+
+# Add beam electrons
+sim.add_species(
+    beam,
+    layout = picmi.PseudoRandomLayout(grid = grid, n_macroparticles = 100))
+
+# Add laser
+sim.add_laser(
+    laser,
+    injection_method = laser_antenna)
+
+# Add diagnostics
+sim.add_diagnostic(field_diag)
+
+# Write input file that can be used to run with the compiled version
+sim.write_input_file(file_name = 'inputs_2d_picmi')
+
+# Initialize inputs and WarpX instance
+sim.initialize_inputs()
+sim.initialize_warpx()
+
+# Advance simulation until last time step
+sim.step(max_steps)

From ba41e8d306c00a301d6e9a08daafa85261ec9975 Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Tue, 21 Dec 2021 11:48:32 -0800
Subject: [PATCH 02/22] Add PICMI Script for 3D Case

---
 .../laser_acceleration/PICMI_inputs_3d.py     | 121 ++++++++++++++++++
 1 file changed, 121 insertions(+)
 create mode 100755 Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
new file mode 100755
index 00000000000..617ea98792e
--- /dev/null
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
@@ -0,0 +1,121 @@
+from pywarpx import picmi
+
+# Physical constants
+c = picmi.constants.c
+q_e = picmi.constants.q_e
+
+# Number of time steps
+max_steps = 1000
+
+# Number of cells
+nx = 64
+ny = 64
+nz = 512
+
+# Physical domain
+xmin = -30e-06
+xmax =  30e-06
+ymin = -30e-06
+ymax =  30e-06
+zmin = -56e-06
+zmax =  12e-06
+
+# Domain decomposition
+max_grid_size = 64
+blocking_factor = 32
+
+# Create grid
+grid = picmi.Cartesian3DGrid(
+    number_of_cells = [nx, ny, nz],
+    lower_bound = [xmin, ymin, zmin],
+    upper_bound = [xmax, ymax, zmax],
+    lower_boundary_conditions = ['periodic', 'periodic', 'dirichlet'],
+    upper_boundary_conditions = ['periodic', 'periodic', 'dirichlet'],
+    lower_boundary_conditions_particles = ['periodic', 'periodic', 'absorbing'],
+    upper_boundary_conditions_particles = ['periodic', 'periodic', 'absorbing'],
+    moving_window_velocity = [0., 0., c],
+    warpx_max_grid_size = max_grid_size,
+    warpx_blocking_factor = blocking_factor)
+
+# Particles: plasma electrons
+plasma_density = 2e23
+plasma_xmin = -20e-06
+plasma_ymin = -20e-06
+plasma_zmin = 10e-06
+plasma_xmax = 20e-06
+plasma_ymax = 20e-06
+plasma_zmax = None
+uniform_distribution = picmi.UniformDistribution(
+    density = plasma_density,
+    lower_bound = [plasma_xmin, plasma_ymin, plasma_zmin],
+    upper_bound = [plasma_xmax, plasma_ymax, plasma_zmax],
+    fill_in = True)
+electrons = picmi.Species(
+    particle_type = 'electron',
+    name = 'electrons',
+    initial_distribution = uniform_distribution)
+
+# Laser
+e_max = 16e12
+position_z = 9e-06
+profile_t_peak = 30.e-15
+profile_focal_distance = 100e-06
+laser = picmi.GaussianLaser(
+    wavelength = 0.8e-06,
+    waist = 5e-06,
+    duration = 15e-15,
+    focal_position = [0, 0, profile_focal_distance + position_z],
+    centroid_position = [0, 0, position_z - c*profile_t_peak],
+    propagation_direction = [0, 0, 1],
+    polarization_direction = [0, 1, 0],
+    E0 = e_max,
+    fill_in = False)
+laser_antenna = picmi.LaserAntenna(
+    position = [0., 0., position_z],
+    normal_vector = [0, 0, 1])
+
+# Electromagnetic solver
+solver = picmi.ElectromagneticSolver(
+    grid = grid,
+    method = 'Yee',
+    cfl = 1.,
+    divE_cleaning = 0)
+
+# Diagnostics
+diag_field_list = ["B", "E", "J", "rho"]
+field_diag = picmi.FieldDiagnostic(
+    name = 'diag1',
+    grid = grid,
+    period = 1000,
+    data_list = diag_field_list)
+
+# Set up simulation
+sim = picmi.Simulation(
+    solver = solver,
+    max_steps = max_steps,
+    verbose = 1,
+    particle_shape = 'cubic',
+    warpx_use_filter = 1)
+
+# Add plasma electrons
+sim.add_species(
+    electrons,
+    layout = picmi.GriddedLayout(grid = grid, n_macroparticle_per_cell = [1, 1, 1]))
+
+# Add laser
+sim.add_laser(
+    laser,
+    injection_method = laser_antenna)
+
+# Add diagnostics
+sim.add_diagnostic(field_diag)
+
+# Write input file that can be used to run with the compiled version
+sim.write_input_file(file_name = 'inputs_3d_picmi')
+
+# Initialize inputs and WarpX instance
+sim.initialize_inputs()
+sim.initialize_warpx()
+
+# Advance simulation until last time step
+sim.step(max_steps)

From 24f486ce26bd10f3082df1f7548349b161d89b3d Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Tue, 21 Dec 2021 11:50:23 -0800
Subject: [PATCH 03/22] Cleaning

---
 .../Physics_applications/laser_acceleration/PICMI_inputs_2d.py  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
index fdc1ed5f682..7786d4f8684 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
@@ -108,7 +108,7 @@
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
-    period = 200,
+    period = 1000,
     data_list = diag_field_list)
 
 # Set up simulation

From 2e66abb527c740876b55b97762ffbf34e41b9870 Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Tue, 21 Dec 2021 14:03:56 -0800
Subject: [PATCH 04/22] Add PICMI Script for 1D Case

---
 .../laser_acceleration/PICMI_inputs_1d.py     | 115 ++++++++++++++++++
 1 file changed, 115 insertions(+)
 create mode 100755 Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
new file mode 100755
index 00000000000..49ab37aa8b0
--- /dev/null
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
@@ -0,0 +1,115 @@
+from pywarpx import picmi
+
+# Physical constants
+c = picmi.constants.c
+q_e = picmi.constants.q_e
+
+# Number of time steps
+max_steps = 1000
+
+# Number of cells
+nz = 512
+
+# Physical domain
+zmin = -56e-06
+zmax =  12e-06
+
+# Domain decomposition
+max_grid_size = 64
+blocking_factor = 32
+
+# Create grid
+grid = picmi.Cartesian1DGrid(
+    number_of_cells = [nz],
+    lower_bound = [zmin],
+    upper_bound = [zmax],
+    lower_boundary_conditions = ['dirichlet'],
+    upper_boundary_conditions = ['dirichlet'],
+    lower_boundary_conditions_particles = ['absorbing'],
+    upper_boundary_conditions_particles = ['absorbing'],
+    moving_window_velocity = [0., 0., c],
+    warpx_max_grid_size = max_grid_size,
+    warpx_blocking_factor = blocking_factor)
+
+# Particles: plasma electrons
+plasma_density = 2e23
+plasma_xmin = None
+plasma_ymin = None
+plasma_zmin = 10e-06
+plasma_xmax = None
+plasma_ymax = None
+plasma_zmax = None
+uniform_distribution = picmi.UniformDistribution(
+    density = plasma_density,
+    lower_bound = [plasma_xmin, plasma_ymin, plasma_zmin],
+    upper_bound = [plasma_xmax, plasma_ymax, plasma_zmax],
+    fill_in = True)
+electrons = picmi.Species(
+    particle_type = 'electron',
+    name = 'electrons',
+    initial_distribution = uniform_distribution)
+
+# Laser
+e_max = 16e12
+position_z = 9e-06
+profile_t_peak = 30.e-15
+profile_focal_distance = 100e-06
+laser = picmi.GaussianLaser(
+    wavelength = 0.8e-06,
+    waist = 5e-06,
+    duration = 15e-15,
+    focal_position = [0, 0, profile_focal_distance + position_z],
+    centroid_position = [0, 0, position_z - c*profile_t_peak],
+    propagation_direction = [0, 0, 1],
+    polarization_direction = [0, 1, 0],
+    E0 = e_max,
+    fill_in = False)
+laser_antenna = picmi.LaserAntenna(
+    position = [0., 0., position_z],
+    normal_vector = [0, 0, 1])
+
+# Electromagnetic solver
+solver = picmi.ElectromagneticSolver(
+    grid = grid,
+    method = 'Yee',
+    cfl = 0.9,
+    divE_cleaning = 0)
+
+# Diagnostics
+diag_field_list = ["B", "E", "J", "rho"]
+field_diag = picmi.FieldDiagnostic(
+    name = 'diag1',
+    grid = grid,
+    period = 1000,
+    data_list = diag_field_list)
+
+# Set up simulation
+sim = picmi.Simulation(
+    solver = solver,
+    max_steps = max_steps,
+    verbose = 1,
+    particle_shape = 'cubic',
+    warpx_use_filter = 1)
+
+# Add plasma electrons
+sim.add_species(
+    electrons,
+    layout = picmi.GriddedLayout(grid = grid, n_macroparticle_per_cell = [10]))
+
+# Add laser
+sim.add_laser(
+    laser,
+    injection_method = laser_antenna)
+
+# Add diagnostics
+sim.add_diagnostic(field_diag)
+
+# Write input file that can be used to run with the compiled version
+sim.write_input_file(file_name = 'inputs_1d_picmi')
+
+# Initialize inputs and WarpX instance
+sim.initialize_inputs()
+sim.initialize_warpx()
+
+# Advance simulation until last time step
+sim.step(max_steps)

From 86298a92595cfc553204a909a53ddd8c1feab9e1 Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Tue, 21 Dec 2021 14:55:21 -0800
Subject: [PATCH 05/22] Add PICMI Script for RZ Case

---
 .../laser_acceleration/PICMI_inputs_rz.py     | 149 ++++++++++++++++++
 1 file changed, 149 insertions(+)
 create mode 100755 Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py
new file mode 100755
index 00000000000..75cb9047cc2
--- /dev/null
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py
@@ -0,0 +1,149 @@
+from pywarpx import picmi
+
+# Physical constants
+c = picmi.constants.c
+q_e = picmi.constants.q_e
+
+# Number of time steps
+max_steps = 1000
+
+# Number of cells
+nr = 64
+nz = 512
+
+# Physical domain
+rmin =  0
+rmax =  30e-06
+zmin = -56e-06
+zmax =  12e-06
+
+# Domain decomposition
+max_grid_size = 64
+blocking_factor = 32
+
+# Create grid
+grid = picmi.CylindricalGrid(
+    number_of_cells = [nr, nz],
+    n_azimuthal_modes = 2,
+    lower_bound = [rmin, zmin],
+    upper_bound = [rmax, zmax],
+    lower_boundary_conditions = ['none', 'dirichlet'],
+    upper_boundary_conditions = ['dirichlet', 'dirichlet'],
+    lower_boundary_conditions_particles = ['absorbing', 'absorbing'],
+    upper_boundary_conditions_particles = ['absorbing', 'absorbing'],
+    moving_window_zvelocity = c,
+    warpx_max_grid_size = max_grid_size,
+    warpx_blocking_factor = blocking_factor)
+
+# Particles: plasma electrons
+plasma_density = 2e23
+plasma_xmin = -20e-06
+plasma_ymin = None
+plasma_zmin = 10e-06
+plasma_xmax = 20e-06
+plasma_ymax = None
+plasma_zmax = None
+uniform_distribution = picmi.UniformDistribution(
+    density = plasma_density,
+    lower_bound = [plasma_xmin, plasma_ymin, plasma_zmin],
+    upper_bound = [plasma_xmax, plasma_ymax, plasma_zmax],
+    fill_in = True)
+electrons = picmi.Species(
+    particle_type = 'electron',
+    name = 'electrons',
+    initial_distribution = uniform_distribution)
+
+# Particles: beam electrons
+q_tot = 1e-12
+x_m = 0.
+y_m = 0.
+z_m = -28e-06
+x_rms = 0.5e-06
+y_rms = 0.5e-06
+z_rms = 0.5e-06
+ux_m = 0.
+uy_m = 0.
+uz_m = 500.
+ux_th = 2.
+uy_th = 2.
+uz_th = 50.
+gaussian_bunch_distribution = picmi.GaussianBunchDistribution(
+    n_physical_particles = q_tot / q_e,
+    rms_bunch_size = [x_rms, y_rms, z_rms],
+    rms_velocity = [c*ux_th, c*uy_th, c*uz_th],
+    centroid_position = [x_m, y_m, z_m],
+    centroid_velocity = [c*ux_m, c*uy_m, c*uz_m])
+beam = picmi.Species(
+    particle_type = 'electron',
+    name = 'beam',
+    initial_distribution = gaussian_bunch_distribution)
+
+# Laser
+e_max = 16e12
+position_z = 9e-06
+profile_t_peak = 30.e-15
+profile_focal_distance = 100e-06
+laser = picmi.GaussianLaser(
+    wavelength = 0.8e-06,
+    waist = 5e-06,
+    duration = 15e-15,
+    focal_position = [0, 0, profile_focal_distance + position_z],
+    centroid_position = [0, 0, position_z - c*profile_t_peak],
+    propagation_direction = [0, 0, 1],
+    polarization_direction = [0, 1, 0],
+    E0 = e_max,
+    fill_in = False)
+laser_antenna = picmi.LaserAntenna(
+    position = [0., 0., position_z],
+    normal_vector = [0, 0, 1])
+
+# Electromagnetic solver
+solver = picmi.ElectromagneticSolver(
+    grid = grid,
+    method = 'Yee',
+    cfl = 1.,
+    divE_cleaning = 0)
+
+# Diagnostics
+diag_field_list = ["B", "E", "J", "rho"]
+field_diag = picmi.FieldDiagnostic(
+    name = 'diag1',
+    grid = grid,
+    period = 1000,
+    data_list = diag_field_list)
+
+# Set up simulation
+sim = picmi.Simulation(
+    solver = solver,
+    max_steps = max_steps,
+    verbose = 1,
+    particle_shape = 'cubic',
+    warpx_use_filter = 1)
+
+# Add plasma electrons
+sim.add_species(
+    electrons,
+    layout = picmi.GriddedLayout(grid = grid, n_macroparticle_per_cell = [1, 4, 1]))
+
+# Add beam electrons
+sim.add_species(
+    beam,
+    layout = picmi.PseudoRandomLayout(grid = grid, n_macroparticles = 100))
+
+# Add laser
+sim.add_laser(
+    laser,
+    injection_method = laser_antenna)
+
+# Add diagnostics
+sim.add_diagnostic(field_diag)
+
+# Write input file that can be used to run with the compiled version
+sim.write_input_file(file_name = 'inputs_rz_picmi')
+
+# Initialize inputs and WarpX instance
+sim.initialize_inputs()
+sim.initialize_warpx()
+
+# Advance simulation until last time step
+sim.step(max_steps)

From 901f78f40a9f49df8d2f1c54850a64acebfd353f Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Wed, 22 Dec 2021 10:22:41 -0800
Subject: [PATCH 06/22] Remove Old PICMI Script

---
 .../PICMI_inputs_laser_acceleration.py        | 146 ------------------
 1 file changed, 146 deletions(-)
 delete mode 100755 Examples/Physics_applications/laser_acceleration/PICMI_inputs_laser_acceleration.py

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_laser_acceleration.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_laser_acceleration.py
deleted file mode 100755
index 7e75e14de26..00000000000
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_laser_acceleration.py
+++ /dev/null
@@ -1,146 +0,0 @@
-#!/usr/bin/env python3
-#
-import numpy as np
-from pywarpx import picmi
-#from warp import picmi
-
-constants = picmi.constants
-
-##########################
-# physics parameters
-##########################
-
-# --- laser
-
-laser_a0              = 4.        # Normalized potential vector
-laser_wavelength      = 8e-07     # Wavelength of the laser (in meters)
-laser_waist           = 5e-06     # Waist of the laser (in meters)
-laser_duration        = 15e-15    # Duration of the laser (in seconds)
-laser_polarization    = 0.        # Polarization angle (in rad)
-laser_injection_loc   = 9.e-6     # Position of injection (in meters, along z)
-laser_focal_distance  = 100.e-6   # Focal distance from the injection (in meters)
-laser_t_peak          = 30.e-15   # The time at which the laser reaches its peak
-                                  #   at the antenna injection location (in seconds)
-# --- plasma
-
-plasma_density = 1.e24
-plasma_min     = [-20.e-6, -20.e-6,  0.0e-6]
-plasma_max     = [ 20.e-6,  20.e-6,  1.e-3]
-
-
-##########################
-# numerics parameters
-##########################
-
-# --- Nb time steps
-
-max_steps = 10
-
-# --- grid
-
-nx = 64
-ny = 64
-nz = 480
-
-xmin = 1.5*plasma_min[0]
-xmax = 1.5*plasma_max[0]
-ymin = 1.5*plasma_min[1]
-ymax = 1.5*plasma_max[1]
-zmin = -56.e-6
-zmax = 12.e-6
-
-moving_window_velocity = [0., 0., constants.c]
-
-number_per_cell_each_dim = [2, 2, 1]
-
-##########################
-# physics components
-##########################
-
-# --- laser
-
-laser = picmi.GaussianLaser(wavelength            = laser_wavelength,
-                            waist                 = laser_waist,
-                            duration              = laser_duration,
-                            focal_position        = [0., 0., laser_focal_distance + laser_injection_loc],
-                            centroid_position     = [0., 0., laser_injection_loc - constants.c*laser_t_peak],
-                            polarization_direction = [np.cos(laser_polarization), np.sin(laser_polarization), 0.],
-                            propagation_direction = [0,0,1],
-                            E0 = laser_a0*2.*np.pi*constants.m_e*constants.c**2/(constants.q_e*laser_wavelength)) # Maximum amplitude of the laser field (in V/m)
-
-laser_antenna = picmi.LaserAntenna(position = [0., 0., laser_injection_loc],  # This point is on the laser plane
-                                   normal_vector = [0., 0., 1.])  # The plane normal direction
-
-# --- plasma
-
-uniform_plasma = picmi.UniformDistribution(density     = plasma_density,
-                                           lower_bound = plasma_min,
-                                           upper_bound = plasma_max,
-                                           fill_in     = True)
-
-electrons = picmi.Species(particle_type = 'electron',
-                          name = 'electrons',
-                          initial_distribution = uniform_plasma)
-
-
-##########################
-# numerics components
-##########################
-
-grid = picmi.Cartesian3DGrid(number_of_cells = [nx, ny, nz],
-                             lower_bound = [xmin, ymin, zmin],
-                             upper_bound = [xmax, ymax, zmax],
-                             lower_boundary_conditions = ['periodic', 'periodic', 'open'],
-                             upper_boundary_conditions = ['periodic', 'periodic', 'open'],
-                             lower_boundary_conditions_particles = ['periodic', 'periodic', 'absorbing'],
-                             upper_boundary_conditions_particles = ['periodic', 'periodic', 'absorbing'],
-                             moving_window_velocity = moving_window_velocity,
-                             warpx_max_grid_size=32)
-
-solver = picmi.ElectromagneticSolver(grid=grid, method='CKC', cfl=1.)
-
-
-##########################
-# diagnostics
-##########################
-
-diag_field_list = ["rho", "E", "B", "J"]
-field_diag1 = picmi.FieldDiagnostic(name = 'diag1',
-                                    grid = grid,
-                                    period = 10,
-                                    write_dir = '.',
-                                    warpx_file_prefix = 'Python_LaserAccelerationMR_plt',
-                                    data_list = diag_field_list)
-
-part_diag1 = picmi.ParticleDiagnostic(name = 'diag1',
-                                      period = 10,
-                                      species = [electrons],
-                                      data_list = ['ux', 'uy', 'uz', 'weighting'])
-
-##########################
-# simulation setup
-##########################
-
-sim = picmi.Simulation(solver = solver,
-                       max_steps = max_steps,
-                       verbose = 1,
-                       warpx_current_deposition_algo = 'esirkepov',
-                       warpx_use_filter = 0)
-
-sim.add_species(electrons, layout=picmi.GriddedLayout(grid=grid, n_macroparticle_per_cell=number_per_cell_each_dim))
-
-sim.add_laser(laser, injection_method=laser_antenna)
-
-sim.add_diagnostic(field_diag1)
-sim.add_diagnostic(part_diag1)
-
-##########################
-# simulation run
-##########################
-
-# write_inputs will create an inputs file that can be used to run
-# with the compiled version.
-#sim.write_input_file(file_name = 'inputs_from_PICMI')
-
-# Alternatively, sim.step will run WarpX, controlling it from Python
-sim.step(max_steps)

From 379372c480c5a0ffe0135c897990f2b124fb9198 Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Wed, 22 Dec 2021 10:52:51 -0800
Subject: [PATCH 07/22] Remove Old Test Python_LaserAccelerationMR

---
 Regression/WarpX-tests.ini | 18 ------------------
 1 file changed, 18 deletions(-)

diff --git a/Regression/WarpX-tests.ini b/Regression/WarpX-tests.ini
index a74dbdca8ca..116eeb8fc3b 100644
--- a/Regression/WarpX-tests.ini
+++ b/Regression/WarpX-tests.ini
@@ -1657,24 +1657,6 @@ compareParticles = 1
 particleTypes = electrons beam
 analysisRoutine = Examples/analysis_default_regression.py
 
-[Python_LaserAccelerationMR]
-buildDir = .
-inputFile = Examples/Physics_applications/laser_acceleration/PICMI_inputs_laser_acceleration.py
-runtime_params =
-customRunCmd = python3 PICMI_inputs_laser_acceleration.py
-dim = 3
-addToCompileString = USE_PYTHON_MAIN=TRUE
-restartTest = 0
-useMPI = 1
-numprocs = 2
-useOMP = 1
-numthreads = 1
-compileTest = 0
-doVis = 0
-compareParticles = 1
-particleTypes = electrons
-analysisRoutine = Examples/analysis_default_regression.py
-
 [Python_Langmuir_2d]
 buildDir = .
 inputFile = Examples/Tests/Langmuir/PICMI_inputs_langmuir2d.py

From 692ef1a6d7b6732f5bad0f8b7546ee82a6dc7f3d Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Wed, 22 Dec 2021 12:10:06 -0800
Subject: [PATCH 08/22] inputs_3d: Move Inputs From runtime_params

---
 .../Physics_applications/laser_acceleration/inputs_3d     | 8 +++++---
 Regression/WarpX-tests.ini                                | 4 ++--
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/Examples/Physics_applications/laser_acceleration/inputs_3d b/Examples/Physics_applications/laser_acceleration/inputs_3d
index 492f5dd8a94..4429b98396c 100644
--- a/Examples/Physics_applications/laser_acceleration/inputs_3d
+++ b/Examples/Physics_applications/laser_acceleration/inputs_3d
@@ -1,8 +1,8 @@
 #################################
 ####### GENERAL PARAMETERS ######
 #################################
-max_step = 1000
-amr.n_cell =  64  64  512
+max_step = 100           # for production, run for longer time, e.g. max_step = 1000
+amr.n_cell = 32 32 256   # for production, run with finer mesh, e.g. amr.n_cell = 64 64 512
 amr.max_grid_size = 64   # maximum size of each AMReX box, used to decompose the domain
 amr.blocking_factor = 32 # minimum size of each AMReX box, used to decompose the domain
 geometry.dims = 3
@@ -28,6 +28,8 @@ warpx.cfl = 1. # if 1., the time step is set to its CFL limit
 warpx.do_moving_window = 1
 warpx.moving_window_dir = z # Only z is supported for the moment
 warpx.moving_window_v = 1.0 # units of speed of light
+warpx.do_dynamic_scheduling = 0 # for production, set this to 1 (default)
+warpx.serialize_ics = 1         # for production, set this to 0 (default)
 
 # Order of particle shape factors
 algo.particle_shape = 3
@@ -45,7 +47,7 @@ electrons.xmin = -20.e-6
 electrons.xmax =  20.e-6
 electrons.ymin = -20.e-6
 electrons.ymax =  20.e-6
-electrons.zmin =  10.e-6
+electrons.zmin =  0
 electrons.profile = constant
 electrons.density = 2.e23  # number of electrons per m^3
 electrons.momentum_distribution_type = "at_rest"
diff --git a/Regression/WarpX-tests.ini b/Regression/WarpX-tests.ini
index 116eeb8fc3b..59980228d78 100644
--- a/Regression/WarpX-tests.ini
+++ b/Regression/WarpX-tests.ini
@@ -877,7 +877,7 @@ analysisRoutine = Examples/Modules/laser_injection/analysis_1d.py
 [LaserAcceleration]
 buildDir = .
 inputFile = Examples/Physics_applications/laser_acceleration/inputs_3d
-runtime_params = warpx.do_dynamic_scheduling=0 amr.n_cell=32 32 256 max_step=100 electrons.zmin=0.e-6 warpx.serialize_ics=1
+runtime_params =
 dim = 3
 addToCompileString =
 restartTest = 0
@@ -911,7 +911,7 @@ analysisRoutine = Examples/analysis_default_regression.py
 [LaserAcceleration_single_precision_comms]
 buildDir = .
 inputFile = Examples/Physics_applications/laser_acceleration/inputs_3d
-runtime_params = warpx.do_dynamic_scheduling=0 amr.n_cell=32 32 256 max_step=100 electrons.zmin=0.e-6 warpx.serialize_ics=1 warpx.do_single_precision_comms=1
+runtime_params = warpx.do_single_precision_comms=1
 dim = 3
 addToCompileString =
 restartTest = 0

From 6db8d6333b2fda0960b3dbe021902517b4570fca Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Wed, 22 Dec 2021 13:16:08 -0800
Subject: [PATCH 09/22] inputs_2d: Move Inputs From runtime_params

---
 .../Physics_applications/laser_acceleration/inputs_2d    | 9 +++++----
 Regression/WarpX-tests.ini                               | 4 ++--
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/Examples/Physics_applications/laser_acceleration/inputs_2d b/Examples/Physics_applications/laser_acceleration/inputs_2d
index 88ab197ce72..52b613c5617 100644
--- a/Examples/Physics_applications/laser_acceleration/inputs_2d
+++ b/Examples/Physics_applications/laser_acceleration/inputs_2d
@@ -1,16 +1,16 @@
 #################################
 ####### GENERAL PARAMETERS ######
 #################################
-max_step = 1000
+max_step = 200 # for production, run for longer time, e.g. max_step = 1000
 amr.n_cell =  64  512
 amr.max_grid_size = 64   # maximum size of each AMReX box, used to decompose the domain
 amr.blocking_factor = 32 # minimum size of each AMReX box, used to decompose the domain
 geometry.dims = 2
 geometry.prob_lo     = -30.e-6   -56.e-6    # physical domain
 geometry.prob_hi     =  30.e-6    12.e-6
-amr.max_level = 0 # Maximum level in hierarchy (1 might be unstable, >1 is not supported)
-# warpx.fine_tag_lo = -5.e-6   -35.e-6
-# warpx.fine_tag_hi =  5.e-6   -25.e-6
+amr.max_level = 1 # Maximum level in hierarchy (1 might be unstable, >1 is not supported)
+warpx.fine_tag_lo = -5.e-6   -35.e-6
+warpx.fine_tag_hi =  5.e-6   -25.e-6
 
 #################################
 ####### Boundary condition ######
@@ -28,6 +28,7 @@ warpx.cfl = 1. # if 1., the time step is set to its CFL limit
 warpx.do_moving_window = 1
 warpx.moving_window_dir = z # Only z is supported for the moment
 warpx.moving_window_v = 1.0 # units of speed of light
+warpx.serialize_ics = 1 # for production, set this to 0 (default)
 
 # Order of particle shape factors
 algo.particle_shape = 3
diff --git a/Regression/WarpX-tests.ini b/Regression/WarpX-tests.ini
index 59980228d78..e6f5292a707 100644
--- a/Regression/WarpX-tests.ini
+++ b/Regression/WarpX-tests.ini
@@ -944,7 +944,7 @@ analysisRoutine = Examples/analysis_default_regression.py
 [LaserAccelerationMR]
 buildDir = .
 inputFile = Examples/Physics_applications/laser_acceleration/inputs_2d
-runtime_params = amr.max_level=1 max_step=200 warpx.serialize_ics=1 warpx.fine_tag_lo=-5.e-6 -35.e-6 warpx.fine_tag_hi=5.e-6 -25.e-6
+runtime_params =
 dim = 2
 addToCompileString =
 restartTest = 0
@@ -961,7 +961,7 @@ analysisRoutine = Examples/analysis_default_regression.py
 [RefinedInjection]
 buildDir = .
 inputFile = Examples/Physics_applications/laser_acceleration/inputs_2d
-runtime_params = amr.max_level=1 max_step=200 warpx.serialize_ics=1 warpx.fine_tag_lo=-5.e-6 -35.e-6 warpx.fine_tag_hi=5.e-6 -25.e-6 warpx.refine_plasma=1
+runtime_params = warpx.refine_plasma=1
 dim = 2
 addToCompileString =
 restartTest = 0

From 0ceab68f08b853cc63b1c8131593eb0139e48acd Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Wed, 22 Dec 2021 13:38:23 -0800
Subject: [PATCH 10/22] Update PICMI Script for 2D Case

---
 .../laser_acceleration/PICMI_inputs_2d.py            | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
index 7786d4f8684..bd356215a68 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
@@ -5,7 +5,7 @@
 q_e = picmi.constants.q_e
 
 # Number of time steps
-max_steps = 1000
+max_steps = 200
 
 # Number of cells
 nx = 64
@@ -16,6 +16,10 @@
 xmax =  30e-06
 zmin = -56e-06
 zmax =  12e-06
+xmin_refined = -5e-06
+xmax_refined =  5e-06
+zmin_refined = -35e-06
+zmax_refined = -25e-06
 
 # Domain decomposition
 max_grid_size = 64
@@ -32,7 +36,8 @@
     upper_boundary_conditions_particles = ['absorbing', 'absorbing'],
     moving_window_velocity = [0., c],
     warpx_max_grid_size = max_grid_size,
-    warpx_blocking_factor = blocking_factor)
+    warpx_blocking_factor = blocking_factor,
+    refined_regions = [[1, [xmin_refined, zmin_refined], [xmax_refined, zmax_refined]]])
 
 # Particles: plasma electrons
 plasma_density = 2e23
@@ -117,7 +122,8 @@
     max_steps = max_steps,
     verbose = 1,
     particle_shape = 'cubic',
-    warpx_use_filter = 1)
+    warpx_use_filter = 1,
+    warpx_serialize_ics = 1)
 
 # Add plasma electrons
 sim.add_species(

From 0dc1d0c31963a745df90dba250b194b5c8734640 Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Wed, 22 Dec 2021 13:41:29 -0800
Subject: [PATCH 11/22] Update PICMI Script for 3D Case

---
 .../laser_acceleration/PICMI_inputs_3d.py          | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
index 617ea98792e..2d9be34f85a 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
@@ -5,12 +5,12 @@
 q_e = picmi.constants.q_e
 
 # Number of time steps
-max_steps = 1000
+max_steps = 100
 
 # Number of cells
-nx = 64
-ny = 64
-nz = 512
+nx = 32
+ny = 32
+nz = 256
 
 # Physical domain
 xmin = -30e-06
@@ -41,7 +41,7 @@
 plasma_density = 2e23
 plasma_xmin = -20e-06
 plasma_ymin = -20e-06
-plasma_zmin = 10e-06
+plasma_zmin = 0
 plasma_xmax = 20e-06
 plasma_ymax = 20e-06
 plasma_zmax = None
@@ -95,7 +95,9 @@
     max_steps = max_steps,
     verbose = 1,
     particle_shape = 'cubic',
-    warpx_use_filter = 1)
+    warpx_use_filter = 1,
+    warpx_serialize_ics = 1,
+    warpx_do_dynamic_scheduling = 0)
 
 # Add plasma electrons
 sim.add_species(

From 04e8362bf751dc2d8ffaf232be2d256710f44029 Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Wed, 22 Dec 2021 13:48:07 -0800
Subject: [PATCH 12/22] inputs_1d: Move Inputs From runtime_params

---
 Examples/Physics_applications/laser_acceleration/inputs_1d | 6 ++++--
 Regression/WarpX-tests.ini                                 | 2 +-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/Examples/Physics_applications/laser_acceleration/inputs_1d b/Examples/Physics_applications/laser_acceleration/inputs_1d
index f58c7375fc5..9e88ca7db66 100644
--- a/Examples/Physics_applications/laser_acceleration/inputs_1d
+++ b/Examples/Physics_applications/laser_acceleration/inputs_1d
@@ -1,8 +1,8 @@
 #################################
 ####### GENERAL PARAMETERS ######
 #################################
-max_step = 1000
-amr.n_cell =  512
+max_step = 100
+amr.n_cell =  256
 amr.max_grid_size = 64   # maximum size of each AMReX box, used to decompose the domain
 amr.blocking_factor = 32 # minimum size of each AMReX box, used to decompose the domain
 geometry.dims = 1
@@ -26,6 +26,8 @@ warpx.cfl = 0.9 # if 1., the time step is set to its CFL limit
 warpx.do_moving_window = 1
 warpx.moving_window_dir = z # Only z is supported for the moment
 warpx.moving_window_v = 1.0 # units of speed of light
+warpx.do_dynamic_scheduling = 0
+warpx.serialize_ics = 1
 
 # Order of particle shape factors
 algo.particle_shape = 3
diff --git a/Regression/WarpX-tests.ini b/Regression/WarpX-tests.ini
index e6f5292a707..cfb2a438f42 100644
--- a/Regression/WarpX-tests.ini
+++ b/Regression/WarpX-tests.ini
@@ -894,7 +894,7 @@ analysisRoutine = Examples/analysis_default_regression.py
 [LaserAcceleration_1d]
 buildDir = .
 inputFile = Examples/Physics_applications/laser_acceleration/inputs_1d
-runtime_params = warpx.do_dynamic_scheduling=0 amr.n_cell=256 max_step=100 electrons.zmin=10.e-6 warpx.serialize_ics=1
+runtime_params =
 dim = 1
 addToCompileString =
 restartTest = 0

From f413939b99516ffe1889ceefa1f4a85b0c992754 Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Wed, 22 Dec 2021 14:03:20 -0800
Subject: [PATCH 13/22] inputs_2d_rz: Move Inputs From runtime_params

---
 Examples/Physics_applications/laser_acceleration/inputs_2d_rz | 4 +++-
 Regression/WarpX-tests.ini                                    | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/Examples/Physics_applications/laser_acceleration/inputs_2d_rz b/Examples/Physics_applications/laser_acceleration/inputs_2d_rz
index 5647e9e22c6..f5746620b57 100644
--- a/Examples/Physics_applications/laser_acceleration/inputs_2d_rz
+++ b/Examples/Physics_applications/laser_acceleration/inputs_2d_rz
@@ -1,7 +1,7 @@
 #################################
 ####### GENERAL PARAMETERS ######
 #################################
-max_step = 1000
+max_step = 10
 amr.n_cell =  64  512
 amr.max_grid_size = 64   # maximum size of each AMReX box, used to decompose the domain
 amr.blocking_factor = 32 # minimum size of each AMReX box, used to decompose the domain
@@ -86,3 +86,5 @@ diag1.intervals = 200
 diag1.diag_type = Full
 diag1.fields_to_plot = Ex Ey Ez Bx By Bz jx jy jz rho
 diag1.dump_rz_modes = 1
+diag1.electrons.variables = w ux uy uz
+diag1.beam.variables = w ux uy uz
diff --git a/Regression/WarpX-tests.ini b/Regression/WarpX-tests.ini
index cfb2a438f42..73d6e80e7ad 100644
--- a/Regression/WarpX-tests.ini
+++ b/Regression/WarpX-tests.ini
@@ -1643,7 +1643,7 @@ analysisRoutine = Examples/analysis_default_regression.py
 [LaserAccelerationRZ]
 buildDir = .
 inputFile = Examples/Physics_applications/laser_acceleration/inputs_2d_rz
-runtime_params = diag1.electrons.variables=w ux uy uz diag1.beam.variables=w ux uy uz max_step=10
+runtime_params =
 dim = 2
 addToCompileString = USE_RZ=TRUE
 restartTest = 0

From cb861a2e3237c3f1416e1f10169af131aaf335e8 Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Wed, 22 Dec 2021 14:04:27 -0800
Subject: [PATCH 14/22] Rename inputs_2d_rz as inputs_rz

---
 .../laser_acceleration/{inputs_2d_rz => inputs_rz}              | 0
 Regression/WarpX-tests.ini                                      | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename Examples/Physics_applications/laser_acceleration/{inputs_2d_rz => inputs_rz} (100%)

diff --git a/Examples/Physics_applications/laser_acceleration/inputs_2d_rz b/Examples/Physics_applications/laser_acceleration/inputs_rz
similarity index 100%
rename from Examples/Physics_applications/laser_acceleration/inputs_2d_rz
rename to Examples/Physics_applications/laser_acceleration/inputs_rz
diff --git a/Regression/WarpX-tests.ini b/Regression/WarpX-tests.ini
index 73d6e80e7ad..0650c2e7369 100644
--- a/Regression/WarpX-tests.ini
+++ b/Regression/WarpX-tests.ini
@@ -1642,7 +1642,7 @@ analysisRoutine = Examples/analysis_default_regression.py
 
 [LaserAccelerationRZ]
 buildDir = .
-inputFile = Examples/Physics_applications/laser_acceleration/inputs_2d_rz
+inputFile = Examples/Physics_applications/laser_acceleration/inputs_rz
 runtime_params =
 dim = 2
 addToCompileString = USE_RZ=TRUE

From 58365342f4ef672b65b9135649034bd3dfbc8178 Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Wed, 22 Dec 2021 14:05:24 -0800
Subject: [PATCH 15/22] Update PICMI Script for 1D Case

---
 .../laser_acceleration/PICMI_inputs_1d.py                 | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
index 49ab37aa8b0..314d876c8f2 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
@@ -5,10 +5,10 @@
 q_e = picmi.constants.q_e
 
 # Number of time steps
-max_steps = 1000
+max_steps = 100
 
 # Number of cells
-nz = 512
+nz = 256
 
 # Physical domain
 zmin = -56e-06
@@ -89,7 +89,9 @@
     max_steps = max_steps,
     verbose = 1,
     particle_shape = 'cubic',
-    warpx_use_filter = 1)
+    warpx_use_filter = 1,
+    warpx_serialize_ics = 1,
+    warpx_do_dynamic_scheduling = 0)
 
 # Add plasma electrons
 sim.add_species(

From f81541fa1acda198effedbd44206e38d3f8519d6 Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Wed, 22 Dec 2021 14:11:59 -0800
Subject: [PATCH 16/22] Update PICMI Script for RZ Case

---
 .../laser_acceleration/PICMI_inputs_rz.py             | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py
index 75cb9047cc2..1b510c0a93d 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py
@@ -5,7 +5,7 @@
 q_e = picmi.constants.q_e
 
 # Number of time steps
-max_steps = 1000
+max_steps = 10
 
 # Number of cells
 nr = 64
@@ -109,8 +109,14 @@
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
-    period = 1000,
+    period = 10,
     data_list = diag_field_list)
+diag_particle_list = ["weighting", "momentum"]
+particle_diag = picmi.ParticleDiagnostic(
+    name = 'diag1',
+    period = 10,
+    species = [electrons, beam],
+    data_list = diag_particle_list)
 
 # Set up simulation
 sim = picmi.Simulation(
@@ -137,6 +143,7 @@
 
 # Add diagnostics
 sim.add_diagnostic(field_diag)
+sim.add_diagnostic(particle_diag)
 
 # Write input file that can be used to run with the compiled version
 sim.write_input_file(file_name = 'inputs_rz_picmi')

From 3abaf2096e4e5601116b9761b6778244f71dcbf4 Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Wed, 22 Dec 2021 14:12:41 -0800
Subject: [PATCH 17/22] inputs_rz: Fix Diagnostic Interval

---
 Examples/Physics_applications/laser_acceleration/inputs_rz | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Examples/Physics_applications/laser_acceleration/inputs_rz b/Examples/Physics_applications/laser_acceleration/inputs_rz
index f5746620b57..b76c40a51b4 100644
--- a/Examples/Physics_applications/laser_acceleration/inputs_rz
+++ b/Examples/Physics_applications/laser_acceleration/inputs_rz
@@ -82,7 +82,7 @@ laser1.wavelength = 0.8e-6               # The wavelength of the laser (in m)
 
 # Diagnostics
 diagnostics.diags_names = diag1
-diag1.intervals = 200
+diag1.intervals = 10
 diag1.diag_type = Full
 diag1.fields_to_plot = Ex Ey Ez Bx By Bz jx jy jz rho
 diag1.dump_rz_modes = 1

From a188bf16fba7117c4f052d4b6e527368c7894350 Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Wed, 22 Dec 2021 14:14:37 -0800
Subject: [PATCH 18/22] Fix Diagnostic Interval For All Inputs

---
 .../Physics_applications/laser_acceleration/PICMI_inputs_1d.py  | 2 +-
 .../Physics_applications/laser_acceleration/PICMI_inputs_2d.py  | 2 +-
 .../Physics_applications/laser_acceleration/PICMI_inputs_3d.py  | 2 +-
 Examples/Physics_applications/laser_acceleration/inputs_1d      | 2 +-
 Examples/Physics_applications/laser_acceleration/inputs_3d      | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
index 314d876c8f2..f04854e9eb8 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
@@ -80,7 +80,7 @@
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
-    period = 1000,
+    period = 100,
     data_list = diag_field_list)
 
 # Set up simulation
diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
index bd356215a68..9f290d66d6a 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
@@ -113,7 +113,7 @@
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
-    period = 1000,
+    period = 200,
     data_list = diag_field_list)
 
 # Set up simulation
diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
index 2d9be34f85a..e52b4695696 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
@@ -86,7 +86,7 @@
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
-    period = 1000,
+    period = 100,
     data_list = diag_field_list)
 
 # Set up simulation
diff --git a/Examples/Physics_applications/laser_acceleration/inputs_1d b/Examples/Physics_applications/laser_acceleration/inputs_1d
index 9e88ca7db66..6d37fb48ccd 100644
--- a/Examples/Physics_applications/laser_acceleration/inputs_1d
+++ b/Examples/Physics_applications/laser_acceleration/inputs_1d
@@ -63,6 +63,6 @@ laser1.wavelength = 0.8e-6               # The wavelength of the laser (in m)
 
 # Diagnostics
 diagnostics.diags_names = diag1
-diag1.intervals = 200
+diag1.intervals = 100
 diag1.diag_type = Full
 diag1.fields_to_plot = Ex Ey Ez Bx By Bz jx jy jz rho
diff --git a/Examples/Physics_applications/laser_acceleration/inputs_3d b/Examples/Physics_applications/laser_acceleration/inputs_3d
index 4429b98396c..dea1d2ccb47 100644
--- a/Examples/Physics_applications/laser_acceleration/inputs_3d
+++ b/Examples/Physics_applications/laser_acceleration/inputs_3d
@@ -70,6 +70,6 @@ laser1.wavelength = 0.8e-6               # The wavelength of the laser (in m)
 
 # Diagnostics
 diagnostics.diags_names = diag1
-diag1.intervals = 1000
+diag1.intervals = 100
 diag1.diag_type = Full
 diag1.fields_to_plot = Ex Ey Ez Bx By Bz jx jy jz rho

From af5ce49ae5b907317eed347ea06a616a44a9db27 Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Wed, 22 Dec 2021 15:25:58 -0800
Subject: [PATCH 19/22] Add New Test For Each PICMI Script

---
 .../laser_acceleration/PICMI_inputs_1d.py     |  6 +-
 .../laser_acceleration/PICMI_inputs_2d.py     |  6 +-
 .../laser_acceleration/PICMI_inputs_3d.py     |  6 +-
 .../laser_acceleration/PICMI_inputs_rz.py     | 12 ++--
 .../Python_LaserAcceleration.json             | 25 +++++++
 .../Python_LaserAccelerationMR.json           | 61 ++++++++++------
 .../Python_LaserAccelerationRZ.json           | 66 +++++++++++++++++
 .../Python_LaserAcceleration_1d.json          | 23 ++++++
 Regression/WarpX-tests.ini                    | 72 +++++++++++++++++++
 9 files changed, 247 insertions(+), 30 deletions(-)
 create mode 100644 Regression/Checksum/benchmarks_json/Python_LaserAcceleration.json
 create mode 100644 Regression/Checksum/benchmarks_json/Python_LaserAccelerationRZ.json
 create mode 100644 Regression/Checksum/benchmarks_json/Python_LaserAcceleration_1d.json

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
index f04854e9eb8..7136cdb077c 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
@@ -76,12 +76,14 @@
     divE_cleaning = 0)
 
 # Diagnostics
-diag_field_list = ["B", "E", "J", "rho"]
+diag_field_list = ['B', 'E', 'J', 'rho']
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
     period = 100,
-    data_list = diag_field_list)
+    data_list = diag_field_list,
+    write_dir = '.',
+    warpx_file_prefix = 'Python_LaserAcceleration_1d_plt')
 
 # Set up simulation
 sim = picmi.Simulation(
diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
index 9f290d66d6a..022bc15d3e3 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
@@ -109,12 +109,14 @@
     divE_cleaning = 0)
 
 # Diagnostics
-diag_field_list = ["B", "E", "J", "rho"]
+diag_field_list = ['B', 'E', 'J', 'rho']
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
     period = 200,
-    data_list = diag_field_list)
+    data_list = diag_field_list,
+    write_dir = '.',
+    warpx_file_prefix = 'Python_LaserAccelerationMR_plt')
 
 # Set up simulation
 sim = picmi.Simulation(
diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
index e52b4695696..91f5615a562 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
@@ -82,12 +82,14 @@
     divE_cleaning = 0)
 
 # Diagnostics
-diag_field_list = ["B", "E", "J", "rho"]
+diag_field_list = ['B', 'E', 'J', 'rho']
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
     period = 100,
-    data_list = diag_field_list)
+    data_list = diag_field_list,
+    write_dir = '.',
+    warpx_file_prefix = 'Python_LaserAcceleration_plt')
 
 # Set up simulation
 sim = picmi.Simulation(
diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py
index 1b510c0a93d..2b6fe820c94 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py
@@ -105,18 +105,22 @@
     divE_cleaning = 0)
 
 # Diagnostics
-diag_field_list = ["B", "E", "J", "rho"]
+diag_field_list = ['B', 'E', 'J', 'rho']
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
     period = 10,
-    data_list = diag_field_list)
-diag_particle_list = ["weighting", "momentum"]
+    data_list = diag_field_list,
+    write_dir = '.',
+    warpx_file_prefix = 'Python_LaserAccelerationRZ_plt')
+diag_particle_list = ['weighting', 'momentum']
 particle_diag = picmi.ParticleDiagnostic(
     name = 'diag1',
     period = 10,
     species = [electrons, beam],
-    data_list = diag_particle_list)
+    data_list = diag_particle_list,
+    write_dir = '.',
+    warpx_file_prefix = 'Python_LaserAccelerationRZ_plt')
 
 # Set up simulation
 sim = picmi.Simulation(
diff --git a/Regression/Checksum/benchmarks_json/Python_LaserAcceleration.json b/Regression/Checksum/benchmarks_json/Python_LaserAcceleration.json
new file mode 100644
index 00000000000..401dc1a96e5
--- /dev/null
+++ b/Regression/Checksum/benchmarks_json/Python_LaserAcceleration.json
@@ -0,0 +1,25 @@
+{
+  "electrons": {
+    "particle_cpu": 69212.0,
+    "particle_id": 2655287162.0,
+    "particle_momentum_x": 1.79212316501518e-20,
+    "particle_momentum_y": 7.225819832716737e-20,
+    "particle_momentum_z": 4.231725460519779e-20,
+    "particle_position_x": 0.7139122621161638,
+    "particle_position_y": 0.7150340887578206,
+    "particle_position_z": 1.317577060864619,
+    "particle_weight": 12926557617.187498
+  },
+  "lev=0": {
+    "Bx": 5863879.027613791,
+    "By": 2411.49823974812,
+    "Bz": 116025.4367923822,
+    "Ex": 6267728226590.701,
+    "Ey": 1670763224821434.0,
+    "Ez": 104345981838458.8,
+    "jx": 555687757148559.1,
+    "jy": 1595895515963762.0,
+    "jz": 1045266123023548.0,
+    "rho": 2211742630.95043
+  }
+}
\ No newline at end of file
diff --git a/Regression/Checksum/benchmarks_json/Python_LaserAccelerationMR.json b/Regression/Checksum/benchmarks_json/Python_LaserAccelerationMR.json
index f00d487d106..cfee789f139 100644
--- a/Regression/Checksum/benchmarks_json/Python_LaserAccelerationMR.json
+++ b/Regression/Checksum/benchmarks_json/Python_LaserAccelerationMR.json
@@ -1,25 +1,46 @@
 {
+  "beam": {
+    "particle_cpu": 0.0,
+    "particle_id": 5050.0,
+    "particle_momentum_x": 4.561019131383119e-20,
+    "particle_momentum_y": 4.149842919134552e-20,
+    "particle_momentum_z": 1.364708476750903e-17,
+    "particle_position_x": 4.652770082118157e-05,
+    "particle_position_y": 0.001484501913502292,
+    "particle_weight": 12483018148921.525
+  },
   "electrons": {
-    "particle_cpu": 695224.0,
-    "particle_id": 290501119140.0,
-    "particle_momentum_x": 2.36755772669732e-19,
-    "particle_momentum_y": 1.9290614212841715e-21,
-    "particle_momentum_z": 1.8938349865018830e-20,
-    "particle_position_x": 7.0065548820957835,
-    "particle_position_y": 7.006554897199218,
-    "particle_position_z": 4.600065455619851,
-    "particle_weight": 21640883789.062504
+    "particle_cpu": 4788.0,
+    "particle_id": 13694226.0,
+    "particle_momentum_x": 4.2751178407573573e-20,
+    "particle_momentum_y": 1.9580305087551049e-19,
+    "particle_momentum_z": 8.913655221012198e-20,
+    "particle_position_x": 0.04741929968294934,
+    "particle_position_y": 0.08483137297620588,
+    "particle_weight": 119232421874999.98
   },
   "lev=0": {
-    "Bx": 2.0570940778040221,
-    "By": 2449254.9647385371,
-    "Bz": 71239.03439068704,
-    "Ex": 752773908979237.0,
-    "Ey": 1907341714160.9873,
-    "Ez": 28672358913898.098,
-    "jx": 1.9287740799385943e+18,
-    "jy": 69804336095097.0,
-    "jz": 742686844234635.5,
-    "rho": 27910721385.365227
+    "Bx": 24121595.02471585,
+    "By": 78232.13397859206,
+    "Bz": 601058.5314543134,
+    "Ex": 22865766698494.82,
+    "Ey": 6508549201873332.0,
+    "Ez": 32072534017950.55,
+    "jx": 1130516319665756.0,
+    "jy": 2.325136305137274e+18,
+    "jz": 6769519391624705.0,
+    "rho": 152898720.2638083
+  },
+  "lev=1": {
+    "Bx": 53303280.78531405,
+    "By": 213761.8564937196,
+    "Bz": 1321618.978929098,
+    "Ex": 47856565901964.84,
+    "Ey": 1.455101409934242e+16,
+    "Ez": 65304559419893.03,
+    "jx": 46169274324016.0,
+    "jy": 9.274837523569297e+18,
+    "jz": 1.926277235505425e+16,
+    "rho": 67304284.98422323
   }
-}
+}
\ No newline at end of file
diff --git a/Regression/Checksum/benchmarks_json/Python_LaserAccelerationRZ.json b/Regression/Checksum/benchmarks_json/Python_LaserAccelerationRZ.json
new file mode 100644
index 00000000000..8007cf2dd4d
--- /dev/null
+++ b/Regression/Checksum/benchmarks_json/Python_LaserAccelerationRZ.json
@@ -0,0 +1,66 @@
+{
+  "beam": {
+    "particle_cpu": 0.0,
+    "particle_id": 5050.0,
+    "particle_momentum_x": 3.87997644296733e-20,
+    "particle_momentum_y": 5.078338417986405e-20,
+    "particle_momentum_z": 1.350360018411703e-17,
+    "particle_position_x": 6.242147159505209e-05,
+    "particle_position_y": 0.002676436329644457,
+    "particle_theta": 151.408043244598,
+    "particle_weight": 6241509.074460764
+  },
+  "electrons": {
+    "particle_cpu": 4128.0,
+    "particle_id": 10445216.0,
+    "particle_momentum_x": 2.114384362557539e-24,
+    "particle_momentum_y": 3.9172628978456397e-22,
+    "particle_momentum_z": 1.2567935092687156e-23,
+    "particle_position_x": 0.04160250004822599,
+    "particle_position_y": 0.047891250425121774,
+    "particle_theta": 7325.124728188977,
+    "particle_weight": 813672305.532158
+  },
+  "lev=0": {
+    "Bx": 101913.9132182723,
+    "By": 1330.818599062426,
+    "Bz": 4514.781857725756,
+    "Ex": 246731098537.3218,
+    "Ey": 37825184509557.35,
+    "Ez": 590251477994.7521,
+    "jx": 1353405747591.269,
+    "jy": 2.147722453194553e+17,
+    "jz": 1863310088559710.0,
+    "rho": 38912415.75698389,
+    "Br_0_real": 0.2137064585155872,
+    "Br_1_imag": 172.2988890744096,
+    "Br_1_real": 101913.9323749251,
+    "Btheta_0_real": 1326.759151241743,
+    "Btheta_1_imag": 103543.8641160633,
+    "Btheta_1_real": 225.3854904799976,
+    "Bz_0_real": 0.2910069650253564,
+    "Bz_1_imag": 0.8113703469857545,
+    "Bz_1_real": 4514.731146319417,
+    "Er_0_real": 235160954221.997,
+    "Er_1_imag": 38566923642693.89,
+    "Er_1_real": 71516895156.89052,
+    "Etheta_0_real": 78758938.63585563,
+    "Etheta_1_imag": 59697352935.93607,
+    "Etheta_1_real": 37825159479125.69,
+    "Ez_0_real": 563243350549.5107,
+    "Ez_1_imag": 1442184351135.906,
+    "Ez_1_real": 39851376061.69563,
+    "Jr_0_real": 955171862749.2391,
+    "Jr_1_imag": 2.267085398348701e+17,
+    "Jr_1_real": 1672099718770.67,
+    "Jtheta_0_real": 355427737499.2148,
+    "Jtheta_1_imag": 911714777272.9283,
+    "Jtheta_1_real": 2.147722332337163e+17,
+    "Jz_0_real": 1745718246376104.0,
+    "Jz_1_imag": 499465565312123.3,
+    "Jz_1_real": 532424954910440.6,
+    "rho_0_real": 38503729.9081786,
+    "rho_1_imag": 20910554.24239848,
+    "rho_1_real": 1806820.209899142
+  }
+}
\ No newline at end of file
diff --git a/Regression/Checksum/benchmarks_json/Python_LaserAcceleration_1d.json b/Regression/Checksum/benchmarks_json/Python_LaserAcceleration_1d.json
new file mode 100644
index 00000000000..12f6f0c8189
--- /dev/null
+++ b/Regression/Checksum/benchmarks_json/Python_LaserAcceleration_1d.json
@@ -0,0 +1,23 @@
+{
+  "electrons": {
+    "particle_cpu": 0.0,
+    "particle_id": 0.0,
+    "particle_momentum_x": 0.0,
+    "particle_momentum_y": 0.0,
+    "particle_momentum_z": 0.0,
+    "particle_position_x": 0.0,
+    "particle_weight": 0.0
+  },
+  "lev=0": {
+    "Bx": 178016.7504669478,
+    "By": 0.0,
+    "Bz": 0.0,
+    "Ex": 0.0,
+    "Ey": 40878227583310.83,
+    "Ez": 568254685.6950157,
+    "jx": 0.0,
+    "jy": 30442928969125.46,
+    "jz": 1108530282155.6707,
+    "rho": 3127749.1976868743
+  }
+}
\ No newline at end of file
diff --git a/Regression/WarpX-tests.ini b/Regression/WarpX-tests.ini
index 0650c2e7369..b42e78459f5 100644
--- a/Regression/WarpX-tests.ini
+++ b/Regression/WarpX-tests.ini
@@ -891,6 +891,24 @@ compareParticles = 1
 particleTypes = electrons
 analysisRoutine = Examples/analysis_default_regression.py
 
+[Python_LaserAcceleration]
+buildDir = .
+inputFile = Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
+runtime_params =
+customRunCmd = python3 PICMI_inputs_3d.py
+dim = 3
+addToCompileString = USE_PYTHON_MAIN=TRUE
+restartTest = 0
+useMPI = 1
+numprocs = 2
+useOMP = 1
+numthreads = 1
+compileTest = 0
+doVis = 0
+compareParticles = 1
+particleTypes = electrons
+analysisRoutine = Examples/analysis_default_regression.py
+
 [LaserAcceleration_1d]
 buildDir = .
 inputFile = Examples/Physics_applications/laser_acceleration/inputs_1d
@@ -908,6 +926,24 @@ compareParticles = 1
 particleTypes = electrons
 analysisRoutine = Examples/analysis_default_regression.py
 
+[Python_LaserAcceleration_1d]
+buildDir = .
+inputFile = Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
+runtime_params =
+customRunCmd = python3 PICMI_inputs_1d.py
+dim = 1
+addToCompileString = USE_PYTHON_MAIN=TRUE
+restartTest = 0
+useMPI = 1
+numprocs = 2
+useOMP = 1
+numthreads = 1
+compileTest = 0
+doVis = 0
+compareParticles = 1
+particleTypes = electrons
+analysisRoutine = Examples/analysis_default_regression.py
+
 [LaserAcceleration_single_precision_comms]
 buildDir = .
 inputFile = Examples/Physics_applications/laser_acceleration/inputs_3d
@@ -958,6 +994,24 @@ compareParticles = 1
 particleTypes = electrons beam
 analysisRoutine = Examples/analysis_default_regression.py
 
+[Python_LaserAccelerationMR]
+buildDir = .
+inputFile = Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
+runtime_params =
+customRunCmd = python3 PICMI_inputs_2d.py
+dim = 2
+addToCompileString = USE_PYTHON_MAIN=TRUE
+restartTest = 0
+useMPI = 1
+numprocs = 2
+useOMP = 1
+numthreads = 1
+compileTest = 0
+doVis = 0
+compareParticles = 1
+particleTypes = electrons beam
+analysisRoutine = Examples/analysis_default_regression.py
+
 [RefinedInjection]
 buildDir = .
 inputFile = Examples/Physics_applications/laser_acceleration/inputs_2d
@@ -1657,6 +1711,24 @@ compareParticles = 1
 particleTypes = electrons beam
 analysisRoutine = Examples/analysis_default_regression.py
 
+[Python_LaserAccelerationRZ]
+buildDir = .
+inputFile = Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py
+runtime_params =
+customRunCmd = python3 PICMI_inputs_rz.py
+dim = 2
+addToCompileString = USE_RZ=TRUE USE_PYTHON_MAIN=TRUE
+restartTest = 0
+useMPI = 1
+numprocs = 2
+useOMP = 1
+numthreads = 1
+compileTest = 0
+doVis = 0
+compareParticles = 1
+particleTypes = electrons beam
+analysisRoutine = Examples/analysis_default_regression.py
+
 [Python_Langmuir_2d]
 buildDir = .
 inputFile = Examples/Tests/Langmuir/PICMI_inputs_langmuir2d.py

From f042610cbad37f9b09cf44436aac2b754732af2d Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Wed, 22 Dec 2021 16:21:35 -0800
Subject: [PATCH 20/22] Remove Old PICMI Script From Workflow yml Files

---
 .github/workflows/intel.yml    | 2 +-
 .github/workflows/macos.yml    | 2 +-
 .github/workflows/ubuntu.yml   | 2 +-
 Docs/source/usage/examples.rst | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/intel.yml b/.github/workflows/intel.yml
index 793eceaf996..ce5ac80db0d 100644
--- a/.github/workflows/intel.yml
+++ b/.github/workflows/intel.yml
@@ -93,7 +93,7 @@ jobs:
         source /opt/intel/oneapi/setvars.sh
         set -e
         export OMP_NUM_THREADS=2
-        Examples/Physics_applications/laser_acceleration/PICMI_inputs_laser_acceleration.py
+        Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
 
   build_dpcc:
     name: oneAPI DPC++ SP
diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
index d6896853d65..a8e1fdc2ac0 100644
--- a/.github/workflows/macos.yml
+++ b/.github/workflows/macos.yml
@@ -56,4 +56,4 @@ jobs:
     - name: run pywarpx
       run: |
         export OMP_NUM_THREADS=1
-        mpirun -n 2 Examples/Physics_applications/laser_acceleration/PICMI_inputs_laser_acceleration.py
+        mpirun -n 2 Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
diff --git a/.github/workflows/ubuntu.yml b/.github/workflows/ubuntu.yml
index d640f1bc7e4..a6c06396137 100644
--- a/.github/workflows/ubuntu.yml
+++ b/.github/workflows/ubuntu.yml
@@ -82,4 +82,4 @@ jobs:
     - name: run pywarpx
       run: |
         export OMP_NUM_THREADS=1
-        mpirun -n 2 Examples/Physics_applications/laser_acceleration/PICMI_inputs_laser_acceleration.py
+        mpirun -n 2 Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
diff --git a/Docs/source/usage/examples.rst b/Docs/source/usage/examples.rst
index 3fe62a5c46a..43d02dad1f5 100644
--- a/Docs/source/usage/examples.rst
+++ b/Docs/source/usage/examples.rst
@@ -38,7 +38,7 @@ AMReX ``inputs``:
 
 PICMI files:
 
-* :download:`Without mesh refinement<../../../Examples/Physics_applications/laser_acceleration/PICMI_inputs_laser_acceleration.py>`
+* :download:`Without mesh refinement<../../../Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py>`
 
 Plasma mirror
 -------------

From d37cfdcd26c4678ce8dee310cdd35a16c627a038 Mon Sep 17 00:00:00 2001
From: Edoardo Zoni <ezoni@lbl.gov>
Date: Thu, 23 Dec 2021 08:31:23 -0800
Subject: [PATCH 21/22] Dump RZ Modes for RZ Case

---
 .../Physics_applications/laser_acceleration/PICMI_inputs_rz.py   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py
index 2b6fe820c94..79ef33b1280 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py
@@ -111,6 +111,7 @@
     grid = grid,
     period = 10,
     data_list = diag_field_list,
+    warpx_dump_rz_modes = 1,
     write_dir = '.',
     warpx_file_prefix = 'Python_LaserAccelerationRZ_plt')
 diag_particle_list = ['weighting', 'momentum']

From 2c3ddab377855a3f16238f2f3ec90d48f75c3ef7 Mon Sep 17 00:00:00 2001
From: Axel Huebl <axel.huebl@plasma.ninja>
Date: Mon, 3 Jan 2022 06:44:44 -0800
Subject: [PATCH 22/22] LWFA PICMI: Add Shellbang

Add missing shellbang lines.
---
 .../Physics_applications/laser_acceleration/PICMI_inputs_1d.py  | 2 ++
 .../Physics_applications/laser_acceleration/PICMI_inputs_2d.py  | 2 ++
 .../Physics_applications/laser_acceleration/PICMI_inputs_3d.py  | 2 ++
 .../Physics_applications/laser_acceleration/PICMI_inputs_rz.py  | 2 ++
 4 files changed, 8 insertions(+)

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
index 7136cdb077c..3a4a7d6b53a 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 from pywarpx import picmi
 
 # Physical constants
diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
index 022bc15d3e3..c2d0ebb4656 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 from pywarpx import picmi
 
 # Physical constants
diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
index 91f5615a562..3e6e70e0831 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 from pywarpx import picmi
 
 # Physical constants
diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py
index 79ef33b1280..1f43a0b8893 100755
--- a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py
+++ b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_rz.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 from pywarpx import picmi
 
 # Physical constants