Index

_

_MAX_FILTER_PASSES (in module jaxincell) (in module jaxincell._filters) _repeat_filter() (in module jaxincell) (in module jaxincell._filters)

_shift_with_bc_1d() (in module jaxincell) (in module jaxincell._filters) _simulation() (jaxincell._simulation.Simulation method) (jaxincell.Simulation method)

A

ALL_DOMAIN_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._domain_parameters) ALL_ELECTRON_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) ALL_EXTERNAL_FIELD_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._external_field_parameters) ALL_ION_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions)

ALL_SOLVER_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._solver_parameters) ALL_SOURCE_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._source_parameters) ALL_SPECIES_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) assemble_output() (jaxincell._simulation.Simulation method) (jaxincell.Simulation method)

B

binomial_filter_3point() (in module jaxincell) (in module jaxincell._filters) boltzmann_constant (in module jaxincell) (in module jaxincell._constants) boris_step() (in module jaxincell) Boris_step() (in module jaxincell._algorithms) boris_step() (in module jaxincell._particles) boris_step_relativistic() (in module jaxincell) (in module jaxincell._particles) build_domain() (jaxincell._simulation.Simulation method) (jaxincell.Simulation method) build_domain_hash() (in module jaxincell._parameters) (in module jaxincell._parameters._domain_parameters) build_domain_state() (in module jaxincell._state_initialization)

build_external_field_hash() (in module jaxincell._parameters) (in module jaxincell._parameters._external_field_parameters) build_hash_values() (jaxincell._simulation.Simulation method) (jaxincell.Simulation method) build_parameter_hash() (in module jaxincell._parameters._utils) build_runtime_flat_parameter_routes() (in module jaxincell._routing) build_runtime_parameter_sections() (in module jaxincell._routing) build_runtime_species_label_routes() (in module jaxincell._routing) build_solver_hash() (in module jaxincell._parameters) (in module jaxincell._parameters._solver_parameters) build_source_hash() (in module jaxincell._parameters) (in module jaxincell._parameters._source_parameters) build_species_hash() (in module jaxincell._parameters) (in module jaxincell._parameters._species_parameters)

C

calculate_charge_density() (in module jaxincell) charge_density_BCs() (in module jaxincell) classify_and_sort_input_parameters() (jaxincell._simulation.Simulation method) (jaxincell.Simulation method) clean_and_initialize_domain_parameters() (in module jaxincell._parameters) (in module jaxincell._parameters._domain_parameters) clean_and_initialize_external_field_parameters() (in module jaxincell._parameters) (in module jaxincell._parameters._external_field_parameters) clean_and_initialize_parameters() (jaxincell._simulation.Simulation method) (jaxincell.Simulation method) clean_and_initialize_solver_parameters() (in module jaxincell._parameters) (in module jaxincell._parameters._solver_parameters) clean_and_initialize_source_parameters() (in module jaxincell._parameters) (in module jaxincell._parameters._source_parameters) clean_and_initialize_species_parameters() (in module jaxincell._parameters) (in module jaxincell._parameters._species_parameters)

clean_runtime_input_parameters() (in module jaxincell._routing) (jaxincell._simulation.Simulation method) (jaxincell.Simulation method) CN_step() (in module jaxincell._algorithms) coerce_species_initial_phase_space_parameters() (in module jaxincell._parameters) (in module jaxincell._parameters._species_parameters) curlB() (in module jaxincell) (in module jaxincell._fields) curlE() (in module jaxincell) (in module jaxincell._fields) current_density() (in module jaxincell) current_density_periodic_CN() (in module jaxincell) current_domain_state() (jaxincell._simulation.Simulation method) (jaxincell.Simulation method)

D

DEFAULT_ELECTRON_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) DEFAULT_INITIAL_ELECTRON_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) DEFAULT_INITIAL_ION_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) DEFAULT_ION_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) diagnostics() (in module jaxincell) (in module jaxincell._diagnostics) DIFFERENTIABLE_DOMAIN_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._domain_parameters) DIFFERENTIABLE_ELECTRON_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions)

DIFFERENTIABLE_EXTERNAL_FIELD_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._external_field_parameters) DIFFERENTIABLE_INPUT_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._sections) DIFFERENTIABLE_ION_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) DIFFERENTIABLE_SOLVER_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._solver_parameters) DIFFERENTIABLE_SOURCE_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._source_parameters) DIFFERENTIABLE_SPECIES_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) domain_parameters (jaxincell._simulation.Simulation property) (jaxincell.Simulation property)

E

E_from_Gauss_1D_Cartesian() (in module jaxincell) (in module jaxincell._fields) E_from_Gauss_1D_FFT() (in module jaxincell) (in module jaxincell._fields) E_from_Poisson_1D_FFT() (in module jaxincell) (in module jaxincell._fields)

elementary_charge (in module jaxincell) (in module jaxincell._constants) epsilon_0 (in module jaxincell) (in module jaxincell._constants) external_field_parameters (jaxincell._simulation.Simulation property) (jaxincell.Simulation property)

F

field_update() (in module jaxincell) (in module jaxincell._fields) field_update1() (in module jaxincell) (in module jaxincell._fields) field_update2() (in module jaxincell) (in module jaxincell._fields) fields_to_particles_grid() (in module jaxincell) (in module jaxincell._particles)

fields_to_particles_periodic_CN() (in module jaxincell) (in module jaxincell._particles) filter_scalar_field() (in module jaxincell) (in module jaxincell._filters) filter_vector_field() (in module jaxincell) (in module jaxincell._filters) FLAT_DIFFERENTIABLE_INPUT_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._sections)

G

get_S2_weights_and_indices_periodic_CN() (in module jaxincell)

I

initialize_field_state() (in module jaxincell._state_initialization) initialize_fields() (jaxincell._simulation.Simulation method) (jaxincell.Simulation method) initialize_particle_state() (in module jaxincell._state_initialization) initialize_particles() (jaxincell._simulation.Simulation method) (jaxincell.Simulation method)

initialize_species_phase_space() (in module jaxincell._state_initialization) input_parameters (jaxincell._simulation.Simulation property) (jaxincell.Simulation property) iter_species_parameter_groups() (in module jaxincell._routing)

J

jaxincell module jaxincell.__main__ module jaxincell._algorithms module jaxincell._boundary_conditions module jaxincell._constants module jaxincell._diagnostics module jaxincell._fields module jaxincell._filters module jaxincell._parameters module jaxincell._parameters._domain_parameters module jaxincell._parameters._external_field_parameters module

jaxincell._parameters._sections module jaxincell._parameters._solver_parameters module jaxincell._parameters._source_parameters module jaxincell._parameters._species_definitions module jaxincell._parameters._species_parameters module jaxincell._parameters._utils module jaxincell._particles module jaxincell._plot module jaxincell._routing module jaxincell._simulation module jaxincell._state_initialization module

L

load_parameters() (in module jaxincell) (in module jaxincell._simulation)

M

main() (in module jaxincell.__main__) make_particles_from_state() (in module jaxincell._state_initialization) mass_electron (in module jaxincell) (in module jaxincell._constants) mass_proton (in module jaxincell) (in module jaxincell._constants) merge_parameter_trees() (in module jaxincell._routing) module jaxincell jaxincell.__main__ jaxincell._algorithms jaxincell._boundary_conditions jaxincell._constants jaxincell._diagnostics jaxincell._fields jaxincell._filters jaxincell._parameters jaxincell._parameters._domain_parameters jaxincell._parameters._external_field_parameters jaxincell._parameters._sections jaxincell._parameters._solver_parameters jaxincell._parameters._source_parameters jaxincell._parameters._species_definitions jaxincell._parameters._species_parameters jaxincell._parameters._utils jaxincell._particles jaxincell._plot jaxincell._routing jaxincell._simulation jaxincell._state_initialization

mu_0 (in module jaxincell) (in module jaxincell._constants)

O

overlay_parameter_defaults() (in module jaxincell._parameters._utils)

P

PARAMETER_SECTION_KEYS (in module jaxincell._parameters) (in module jaxincell._parameters._sections) PARAMETER_SECTIONS (in module jaxincell._parameters) (in module jaxincell._parameters._sections)

plot() (in module jaxincell) (in module jaxincell._plot) print_simulation_information() (in module jaxincell._state_initialization) put_parameter_path() (in module jaxincell._routing)

R

reinitialize_simulation_state() (jaxincell._simulation.Simulation method) (jaxincell.Simulation method) resolve_species_references() (in module jaxincell._parameters) (in module jaxincell._parameters._species_parameters) rotation() (in module jaxincell) (in module jaxincell._particles)

route_flat_initial_parameters() (in module jaxincell._routing) route_nested_initial_species_parameters() (in module jaxincell._routing) run() (jaxincell._simulation.Simulation method) (jaxincell.Simulation method)

S

set_BC_particles() (in module jaxincell) (in module jaxincell._boundary_conditions) set_BC_positions() (in module jaxincell) (in module jaxincell._boundary_conditions) set_BC_single_particle() (in module jaxincell) (in module jaxincell._boundary_conditions) set_BC_single_particle_positions() (in module jaxincell) (in module jaxincell._boundary_conditions) set_parameter_section() (jaxincell._simulation.Simulation method) (jaxincell.Simulation method) Simulation (class in jaxincell) (class in jaxincell._simulation) simulation() (jaxincell._simulation.Simulation method) (jaxincell.Simulation method) single_particle_charge_density() (in module jaxincell) solver_parameters (jaxincell._simulation.Simulation property) (jaxincell.Simulation property) source_parameters (jaxincell._simulation.Simulation property) (jaxincell.Simulation property)

SPECIES_AXES (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) SPECIES_CANONICAL_PREFIXES (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) SPECIES_DEFAULT_LABELS (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) SPECIES_DEFAULT_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) SPECIES_DIFFERENTIABLE_KEYS (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) SPECIES_INITIAL_DEFAULT_PARAMETERS (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) SPECIES_PARAMETER_KEYS (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) species_parameters (jaxincell._simulation.Simulation property) (jaxincell.Simulation property) SPECIES_TYPES (in module jaxincell._parameters) (in module jaxincell._parameters._species_definitions) speed_of_light (in module jaxincell) (in module jaxincell._constants)