Add interspecies collision in main sheath simulation

post-process/PythonScripts/geometryXVx/sheath/plot_conservation_energy

@@ -16,6 +16,7 @@ from gysdata import DiskStore
 from plot_utils import plot_field1d, plot_field2d
 from math_utils import compute_moment, differentiate
 from geometryXVx.utils import compute_krook_sink_constant, compute_krook_sink_adaptive, compute_kinetic_source
+from geometryXVx.utils import compute_collinter_energy_exchange, compute_temperature
 
 
 if __name__ == '__main__':
@@ -47,14 +48,16 @@ if __name__ == '__main__':
     particle_flux = compute_moment(fdistribu, 'v_x', moment_order=1)
     momentum_flux = compute_moment(fdistribu, 'v_x', moment_order=2)
     energy_flux = compute_moment(fdistribu, 'v_x', moment_order=3)
+    temperature = compute_temperature(density, particle_flux, momentum_flux)
 
     momentum_flux = momentum_flux.chunk({'time': len(momentum_flux['time'])})
     dmomentum_flux_dt = differentiate(momentum_flux, 'time')
     grad_flux_over_m = differentiate(energy_flux, 'x') / np.sqrt(mass)
     force_term = 2*particle_flux*charge/np.sqrt(mass)*electric_field
     energy_source = compute_moment(compute_krook_sink_constant(ds), 'v_x', moment_order=2) \
             + compute_moment(compute_krook_sink_adaptive(ds, density), 'v_x', moment_order=2) \
-            + compute_moment(compute_kinetic_source(ds), 'v_x', moment_order=2)
+            + compute_moment(compute_kinetic_source(ds), 'v_x', moment_order=2) \
+            + 2*compute_collinter_energy_exchange(ds, density, temperature)
     error = dmomentum_flux_dt + grad_flux_over_m - energy_source - force_term
 
     time_diag = fdistribu.coords['time'].values[args.itime]

post-process/PythonScripts/geometryXVx/sheath/plot_conservation_momentum

@@ -17,6 +17,7 @@ from gysdata import DiskStore
 from plot_utils import plot_field1d, plot_field2d
 from math_utils import compute_moment, differentiate
 from geometryXVx.utils import compute_krook_sink_constant, compute_krook_sink_adaptive, compute_kinetic_source
+from geometryXVx.utils import compute_collinter_momentum_exchange, compute_temperature
 
 
 if __name__ == '__main__':
@@ -47,14 +48,16 @@ if __name__ == '__main__':
     density = compute_moment(fdistribu, 'v_x', moment_order=0)
     particle_flux = compute_moment(fdistribu, 'v_x', moment_order=1)
     momentum_flux = compute_moment(fdistribu, 'v_x', moment_order=2)
+    temperature = compute_temperature(density, particle_flux, momentum_flux)
 
     particle_flux = particle_flux.chunk({'time': len(particle_flux['time'])})
     dgamma_dt = differentiate(particle_flux, 'time')
     grad_flux_over_m = differentiate(momentum_flux, 'x') / np.sqrt(mass)
     force_term = density*charge/np.sqrt(mass)*electric_field
     momentum_source = compute_moment(compute_krook_sink_constant(ds), 'v_x', moment_order=1) \
             + compute_moment(compute_krook_sink_adaptive(ds, density), 'v_x', moment_order=1) \
-            + compute_moment(compute_kinetic_source(ds), 'v_x', moment_order=1)
+            + compute_moment(compute_kinetic_source(ds), 'v_x', moment_order=1) \
+            + compute_collinter_momentum_exchange(ds, density, particle_flux/density, temperature)
     error = dgamma_dt + grad_flux_over_m - momentum_source - force_term
 
     time_diag = fdistribu.coords['time'].values[args.itime]

post-process/PythonScripts/geometryXVx/utils.py

@@ -4,6 +4,7 @@
 """
 
 import os
+import numpy as np
 import yaml
 import xarray as xr
 
@@ -86,3 +87,70 @@ def compute_kinetic_source(diskstore):
         print('Info: no kinetic source in simulation:', e)
         return xr.zeros_like(diskstore['fdistribu'])
 
+
+def compute_collinter_collision_frequency(diskstore, density, temperature):
+    '''Computes the interspecies collision frequency
+    '''
+
+    charges = diskstore['fdistribu_charges']
+    masses = diskstore['fdistribu_masses']
+    charges_pow4 = charges**4
+    collfreq_onespec = diskstore['collinter_nustar0'] * charges_pow4 \
+        * np.sqrt(masses.sel(species='electrons')/masses) \
+        / diskstore['Lx'] * density / np.power(temperature, 1.5)
+
+    density_flipped = density.copy()
+    density_flipped.coords['species'] = density.coords['species'][::-1]
+    density_ratio = density/density_flipped
+
+    temperature_flipped = temperature.copy()
+    temperature_flipped.coords['species'] = temperature.coords['species'][::-1]
+    temperature_ratio = temperature/temperature_flipped
+
+    charges_ratio = charges/charges.values[::-1]
+    masses_ratio = masses/masses.values[::-1]
+
+    collfreq_bothspecies = collfreq_onespec * np.sqrt(2.) / (charges_ratio * charges_ratio) \
+        * (1. + masses_ratio) / density_ratio \
+        / np.power(1. + masses_ratio/temperature_ratio, 1.5)
+
+    return collfreq_bothspecies
+
+
+def compute_collinter_momentum_exchange(diskstore, density, fluid_velocity, temperature):
+    '''Computes the interspecies collision operator expression of the 
+    momentum exchange term
+    '''
+    try:
+        collfreq = compute_collinter_collision_frequency(diskstore, density, temperature)
+        masses = diskstore['fdistribu_masses']
+        masses_ratio = masses/masses.values[::-1]
+        fluid_velocity_flipped = fluid_velocity.copy()
+        fluid_velocity_flipped.coords['species'] = fluid_velocity_flipped.coords['species'][::-1]
+        momentum_term = -collfreq*density * (fluid_velocity - np.sqrt(masses_ratio) \
+                                    * fluid_velocity_flipped)
+        return momentum_term
+    except KeyError as e:
+        print('Info: no inter_species collisions in simulation:', e)
+        return xr.zeros_like(diskstore['electrostatic_potential'])
+
+
+def compute_collinter_energy_exchange(diskstore, density, temperature):
+    '''Computes the interspecies collision operator expression of the 
+    energy exchange term
+    '''
+    try:
+        temperature_flipped = temperature.copy()
+        temperature_flipped.coords['species'] = temperature_flipped.coords['species'][::-1]
+
+        masses = diskstore['fdistribu_masses']
+        masses_flipped = masses.copy()
+        masses_flipped.coords['species'] = masses_flipped.coords['species'][::-1]
+        ma_on_ma_mb = masses/(masses + masses_flipped)
+        collfreq = compute_collinter_collision_frequency(diskstore, density, temperature)
+
+        return -3*collfreq*density*ma_on_ma_mb*(temperature - temperature_flipped)
+
+    except KeyError as e:
+        print('Info: no inter_species collisions in simulation:', e)
+        return xr.zeros_like(diskstore['electrostatic_potential'])

post-process/PythonScripts/gysdata/data_structure_sheath.yaml

@@ -37,6 +37,14 @@ fdistribu_eq:
   dimensions: [ *speciesd , *vxd ]
   path: { file: 'VOICEXX_initstate.h5', dataset: 'fdistribu_eq' }
 
+collinter_nustar0:
+  dimensions: [ ]
+  path: { file: 'VOICEXX_initstate.h5', dataset: 'collinter_nustar0' }
+
+Lx:
+  dimensions: [ ]
+  path: { file: 'VOICEXX_initstate.h5', dataset: 'Lx' }
+
 krook_sink_constant_amplitude:
   dimensions: [ ]
   path: { file: 'VOICEXX_initstate.h5', dataset: 'krook_sink_constant_amplitude' }

simulations/geometryXVx/sheath/pdi_out.yml.hpp

@@ -9,6 +9,7 @@ constexpr char const* const PDI_CFG = R"PDI_CFG(
   time_saved : double
   nbstep_diag: int
   iter_saved : int
+  Lx : double
   MeshX_extents: { type: array, subtype: int64, size: 1 }
   MeshX:
     type: array
@@ -36,6 +37,7 @@ constexpr char const* const PDI_CFG = R"PDI_CFG(
     subtype: double
     size: [ '$fdistribu_eq_extents[0]', '$fdistribu_eq_extents[1]' ]
   collintra_nustar0 : double
+  collinter_nustar0 : double
 
   krook_sink_adaptive_extent : double
   krook_sink_adaptive_stiffness : double
@@ -118,8 +120,10 @@ constexpr char const* const PDI_CFG = R"PDI_CFG(
         - Nvx
         - MeshX
         - MeshVx
+        - Lx
         - nbstep_diag
         - collintra_nustar0
+        - collinter_nustar0
         - Nkinspecies
         - fdistribu_charges
         - fdistribu_masses

simulations/geometryXVx/sheath/sheath.cpp

@@ -332,6 +332,7 @@ int main(int argc, char** argv)
     ddc::expose_to_pdi("Nvx", vx_size.value());
     ddc::expose_to_pdi("MeshX", meshX_coord);
     ddc::expose_to_pdi("MeshVx", meshVx_coord);
+    ddc::expose_to_pdi("Lx", ddcHelper::total_interval_length(gridx));
     ddc::expose_to_pdi("nbstep_diag", nbstep_diag);
     ddc::expose_to_pdi("Nkinspecies", nb_kinspecies.value());
     ddc::expose_to_pdi("fdistribu_charges", ddc::discrete_space<IDimSp>().charges()[dom_kinsp]);

simulations/geometryXVx/sheath/sheath.yaml.hpp

@@ -46,7 +46,7 @@ constexpr char const* const params_yaml = R"PARAMS_CFG(Mesh:
   temperature: 1.
 
 CollisionsInfo:
-  enable_inter: false
+  enable_inter: true
   nustar0: 0.1
 
 Algorithm: