Clean up input files for tests with MCC (#2552)

* Added embedded_circle test

* Add embedded_circle test files

* Removed diag files

* removed PICMI input file

* Update to use default regression analysis

* Added line breaks for spacing

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* Added description

* Added Ar and Xe to pre-defined particle types

* added Boltzmann's constant to pre-defined constants and cleaned up the MCC CI test input

* Added Boltzmann's constant to warpx parser

* cleaned up embedded circle CI test input

* Remove duplicate entry.

Co-authored-by: kzhu-ME <kevin.zhu@modernelectron.com>
Co-authored-by: Kevin Z. Zhu <86268612+KZhu-ME@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

7 files changed, 71 insertions, 82 deletions

diff --git a/Docs/source/usage/parameters.rst b/Docs/source/usage/parameters.rst
index 46ae26d5b..4c7829d4c 100644
--- a/Docs/source/usage/parameters.rst
+++ b/Docs/source/usage/parameters.rst
@@ -453,8 +453,8 @@ m_u      unified atomic mass unit (Dalton)
 epsilon0 vacuum permittivity
 mu0      vacuum permeability
 clight   speed of light
+kb       Boltzmann's constant (J/K)
 pi       math constant pi
-kb       Boltzmann constant (J/K)
 ======== ===================
 
 See ``Source/Utils/WarpXConst.H`` for the values.
diff --git a/Examples/Physics_applications/capacitive_discharge/PICMI_inputs_2d.py b/Examples/Physics_applications/capacitive_discharge/PICMI_inputs_2d.py
index b9bc0bb3d..171e410b4 100644
--- a/Examples/Physics_applications/capacitive_discharge/PICMI_inputs_2d.py
+++ b/Examples/Physics_applications/capacitive_discharge/PICMI_inputs_2d.py
@@ -23,7 +23,7 @@ D_CA = 0.067 # m
 N_INERT = 9.64e20 # m^-3
 T_INERT = 300.0 # K
 
-FREQ = 13.56e6 # MHz
+FREQ = 13.56e6 # Hz
 
 VOLTAGE = 450.0
 
@@ -292,6 +292,7 @@ mcc_ions = picmi.MCCCollisions(
 
 grid = picmi.Cartesian2DGrid(
     number_of_cells = [nx, ny],
+    warpx_max_grid_size=128,
     lower_bound = [xmin, ymin],
     upper_bound = [xmax, ymax],
     bc_xmin = 'dirichlet',
diff --git a/Examples/Physics_applications/capacitive_discharge/analysis.py b/Examples/Physics_applications/capacitive_discharge/analysis.py
index 22d1c725a..1563438bd 100755
--- a/Examples/Physics_applications/capacitive_discharge/analysis.py
+++ b/Examples/Physics_applications/capacitive_discharge/analysis.py
@@ -14,5 +14,5 @@ import checksumAPI
 
 my_check = checksumAPI.evaluate_checksum(
     'background_mcc', 'Python_background_mcc_plt00050',
-    do_particles=True, rtol=7.5e-2
+    do_particles=True, rtol=2.5e-3
 )
diff --git a/Examples/Physics_applications/capacitive_discharge/inputs_2d b/Examples/Physics_applications/capacitive_discharge/inputs_2d
index 5d7194c46..9917d8248 100644
--- a/Examples/Physics_applications/capacitive_discharge/inputs_2d
+++ b/Examples/Physics_applications/capacitive_discharge/inputs_2d
@@ -1,9 +1,15 @@
 # Input file for MCC testing. This runs an eighth of a voltage input period
 # of the first benchmark case of Turner et al. (2013).
 
+my_constants.Ngas = 9.64e+20 # m^-3
+my_constants.Tgas = 300 # K
+my_constants.Nplasma = 2.56e14 # m^-3
+my_constants.freq = 13.56e6 # Hz
+my_constants.Mion = 6.67e-27 # kg
+
 max_step = 50
 warpx.verbose = 0
-warpx.const_dt = 1.8436578171091445e-10
+warpx.const_dt = 1.0/(400*freq)
 warpx.do_electrostatic = labframe
 warpx.self_fields_required_precision = 1e-06
 warpx.use_filter = 0
@@ -18,56 +24,44 @@ geometry.prob_hi = 0.067 0.0041875
 
 boundary.field_lo = pec periodic
 boundary.field_hi = pec periodic
-boundary.potential_hi_x = 450.0*sin(2*pi*13.56e6*t)
+boundary.potential_hi_x = 450.0*sin(2*pi*freq*t)
 
 # Order of particle shape factors
 algo.particle_shape = 1
 
 particles.species_names = electrons he_ions
-electrons.mass = m_e
-electrons.charge = -q_e
+electrons.species_type = electron
 electrons.injection_style = nuniformpercell
 electrons.initialize_self_fields = 0
 electrons.num_particles_per_cell_each_dim = 32 16
 electrons.profile = constant
-electrons.density = 2.56e14
-electrons.momentum_distribution_type = gaussian
-electrons.ux_m = 0.0
-electrons.uy_m = 0.0
-electrons.uz_m = 0.0
-electrons.ux_th = 0.0022492462021094224
-electrons.uy_th = 0.0022492462021094224
-electrons.uz_th = 0.0022492462021094224
+electrons.density = Nplasma
+electrons.momentum_distribution_type = maxwell_boltzmann
+electrons.theta = (kb*30000/(m_e*clight^2))
 
-he_ions.mass = 6.67e-27
+he_ions.species_type = helium
 he_ions.charge = q_e
 he_ions.injection_style = nuniformpercell
 he_ions.initialize_self_fields = 0
 he_ions.num_particles_per_cell_each_dim = 32 16
 he_ions.profile = constant
-he_ions.density = 2.56e14
-he_ions.momentum_distribution_type = gaussian
-he_ions.ux_m = 0.0
-he_ions.uy_m = 0.0
-he_ions.uz_m = 0.0
-he_ions.ux_th = 2.6332116917541573e-06
-he_ions.uy_th = 2.6332116917541573e-06
-he_ions.uz_th = 2.6332116917541573e-06
+he_ions.density = Nplasma
+he_ions.momentum_distribution_type = maxwell_boltzmann
+he_ions.theta = (kb*Tgas/(Mion*clight^2))
 
 collisions.collision_names = coll_elec coll_ion
 coll_ion.type = background_mcc
 coll_ion.species = he_ions
-coll_ion.background_density = 9.64e+20
-coll_ion.background_temperature = 300
+coll_ion.background_density = Ngas
+coll_ion.background_temperature = Tgas
 coll_ion.scattering_processes = elastic back
 coll_ion.elastic_cross_section = ../../../../warpx-data/MCC_cross_sections/He/ion_scattering.dat
 coll_ion.back_cross_section = ../../../../warpx-data/MCC_cross_sections/He/ion_back_scatter.dat
 
 coll_elec.type = background_mcc
 coll_elec.species = electrons
-coll_elec.background_density = 9.64e+20
-coll_elec.background_temperature = 300
-coll_elec.background_mass = 6.67e-27
+coll_elec.background_density = Ngas
+coll_elec.background_temperature = Tgas
 coll_elec.scattering_processes = elastic excitation1 excitation2 ionization
 coll_elec.elastic_cross_section = ../../../../warpx-data/MCC_cross_sections/He/electron_scattering.dat
 coll_elec.excitation1_energy = 19.82
diff --git a/Examples/Tests/embedded_circle/inputs_2d b/Examples/Tests/embedded_circle/inputs_2d
index c7ce62194..b1362ad94 100644
--- a/Examples/Tests/embedded_circle/inputs_2d
+++ b/Examples/Tests/embedded_circle/inputs_2d
@@ -1,5 +1,5 @@
 # This is a 2D electrostatic simulation containing a circle embedded boundary at
-# the center of the grid domain, pre -seeded with equal density of argon ions
+# the center of the grid domain, pre-seeded with equal density of argon ions
 # and electrons.
 
 max_step = 11
@@ -28,24 +28,19 @@ boundary.particle_hi = absorbing periodic
 algo.particle_shape = 1
 
 particles.species_names = electrons ar_ions
-electrons.mass = m_e
-electrons.charge = -q_e
+electrons.species_type = electron
 electrons.injection_style = nuniformpercell
 electrons.initialize_self_fields = 1
 electrons.num_particles_per_cell_each_dim = 2 2
 electrons.density = 10.2e16
-electrons.momentum_distribution_type = gaussian
 electrons.profile = constant
-electrons.ux_m = 0.0
-electrons.uy_m = 0.0
-electrons.uz_m = 0.0
-electrons.ux_th = 0.0022492462021094224
-electrons.uy_th = 0.0022492462021094224
-electrons.uz_th = 0.0022492462021094224
+electrons.momentum_distribution_type = maxwell_boltzmann
+electrons.theta = (kb*30000/(m_e*clight^2))
 electrons.save_particles_at_zlo = 1
 electrons.save_particles_at_zhi = 1
 electrons.save_particles_at_eb = 1
-ar_ions.mass = 6.633520326333601e-26
+
+ar_ions.species_type = argon
 ar_ions.charge = q_e
 ar_ions.injection_style = nuniformpercell
 ar_ions.initialize_self_fields = 1
@@ -66,9 +61,8 @@ ar_ions.save_particles_at_eb = 1
 collisions.collision_names = coll_electrons coll_ar_ions
 coll_electrons.type = background_mcc
 coll_electrons.species = electrons
-coll_electrons.background_density = 2.1458888524486985e+23
-coll_electrons.background_temperature = 450.00000000000006
-coll_electrons.background_mass = 6.633520326333601e-26
+coll_electrons.background_density = 2.15e+23
+coll_electrons.background_temperature = 450
 coll_electrons.scattering_processes = excitation1 elastic ionization
 coll_electrons.excitation1_cross_section = ../../../../warpx-data/MCC_cross_sections/Ar/excitation_1.dat
 coll_electrons.excitation1_energy = 11.5
@@ -78,8 +72,8 @@ coll_electrons.ionization_energy = 15.7596112
 coll_electrons.ionization_species = ar_ions
 coll_ar_ions.type = background_mcc
 coll_ar_ions.species = ar_ions
-coll_ar_ions.background_density = 2.1458888524486985e+23
-coll_ar_ions.background_temperature = 450.00000000000006
+coll_ar_ions.background_density = 2.15e+23
+coll_ar_ions.background_temperature = 450
 coll_ar_ions.scattering_processes = back elastic charge_exchange
 coll_ar_ions.back_cross_section = ../../../../warpx-data/MCC_cross_sections/Ar/ion_back_scatter.dat
 coll_ar_ions.elastic_cross_section = ../../../../warpx-data/MCC_cross_sections/Ar/ion_scattering.dat
diff --git a/Regression/Checksum/benchmarks_json/background_mcc.json b/Regression/Checksum/benchmarks_json/background_mcc.json
index ea6d2e54e..c6a60bb7a 100644
--- a/Regression/Checksum/benchmarks_json/background_mcc.json
+++ b/Regression/Checksum/benchmarks_json/background_mcc.json
@@ -1,26 +1,26 @@
 {
   "electrons": {
-    "particle_cpu": 190617.0,
-    "particle_id": 58601432186.0,
-    "particle_momentum_x": 1.008747465656768e-18,
-    "particle_momentum_y": 2.799754668819323e-19,
-    "particle_momentum_z": 2.792680383829936e-19,
-    "particle_position_x": 17149.64926526631,
-    "particle_position_y": 940.0852322133724,
-    "particle_weight": 61513602111.81641
+    "particle_cpu": 190805.0,
+    "particle_id": 58572159554.0,
+    "particle_momentum_x": 1.0096555379894353e-18,
+    "particle_momentum_y": 2.792308861947816e-19,
+    "particle_momentum_z": 2.7912608371353956e-19,
+    "particle_position_x": 17158.992965684767,
+    "particle_position_y": 941.2938975939338,
+    "particle_weight": 61532370208.74024
   },
   "he_ions": {
-    "particle_cpu": 262683.0,
-    "particle_id": 206652536825.0,
-    "particle_momentum_x": 2.843447398515225e-18,
-    "particle_momentum_y": 2.206898408374442e-18,
-    "particle_momentum_z": 2.20679498286358e-18,
-    "particle_position_x": 17598.68900871454,
-    "particle_position_y": 1099.660397150414,
-    "particle_weight": 71950444915.7715
+    "particle_cpu": 262726.0,
+    "particle_id": 206636597294.0,
+    "particle_momentum_x": 2.8337541918025354e-18,
+    "particle_momentum_y": 2.194599746445289e-18,
+    "particle_momentum_z": 2.1971043484994987e-18,
+    "particle_position_x": 17599.236953657848,
+    "particle_position_y": 1099.5894721489742,
+    "particle_weight": 71945924133.3008
   },
   "lev=0": {
-    "rho_electrons": 0.03589657270088979,
-    "rho_he_ions": 0.04191032436797355
+    "rho_electrons": 0.03590777765584312,
+    "rho_he_ions": 0.041907813459370793
   }
 }
\ No newline at end of file
diff --git a/Regression/Checksum/benchmarks_json/embedded_circle.json b/Regression/Checksum/benchmarks_json/embedded_circle.json
index d1857cad5..deb770777 100644
--- a/Regression/Checksum/benchmarks_json/embedded_circle.json
+++ b/Regression/Checksum/benchmarks_json/embedded_circle.json
@@ -1,27 +1,27 @@
 {
   "ar_ions": {
-    "particle_cpu": 31740.0,
-    "particle_id": 3219770578.0,
-    "particle_momentum_x": 2.661332598290843e-18,
-    "particle_momentum_y": 2.6484537197836753e-18,
-    "particle_momentum_z": 2.6446763485694346e-18,
-    "particle_position_x": 3.174118714858889,
-    "particle_position_y": 3.174074331596828,
-    "particle_weight": 988031616.2109375
+    "particle_cpu": 31744.0,
+    "particle_id": 3220043046.0,
+    "particle_momentum_x": 2.673023392216285e-18,
+    "particle_momentum_y": 2.6733267061000188e-18,
+    "particle_momentum_z": 2.667060599749979e-18,
+    "particle_position_x": 3.1743018682048367,
+    "particle_position_y": 3.1742959462007088,
+    "particle_weight": 988093872.0703125
   },
   "electrons": {
-    "particle_cpu": 30737.0,
-    "particle_id": 1041042475.0,
-    "particle_momentum_x": 3.014851468379113e-20,
-    "particle_momentum_y": 3.016132024233842e-20,
-    "particle_momentum_z": 3.0169481587733156e-20,
-    "particle_position_x": 3.0760407489559514,
-    "particle_position_y": 3.072305059445631,
-    "particle_weight": 956794738.7695312
+    "particle_cpu": 30724.0,
+    "particle_id": 1040144086.0,
+    "particle_momentum_x": 2.991377867057318e-20,
+    "particle_momentum_y": 3.014091741533624e-20,
+    "particle_momentum_z": 3.022811783218703e-20,
+    "particle_position_x": 3.0722092755241888,
+    "particle_position_y": 3.072232836690298,
+    "particle_weight": 956467895.5078125
   },
   "lev=0": {
-    "phi": 56888.72655917703,
-    "rho_ar_ions": 257.78992245244984,
-    "rho_electrons": 250.2854445348176
+    "phi": 56898.52308944405,
+    "rho_ar_ions": 257.80642870099507,
+    "rho_electrons": 250.17704417223325
   }
 }
\ No newline at end of file