NEOPAX._species¶

Attributes¶

`JOULE_PER_EV`
`JOULE_PER_KEV`
`EV_PER_JOULE`
`STATE_DENSITY_TO_PHYSICAL`
`STATE_TEMPERATURE_TO_EV`
`COULOMB_LOG_MODEL_DEFAULT`
`COULOMB_LOG_MODEL_NTSS_LEGACY`
`COULOMB_LOG_MODEL_FIRST_PRINCIPLES`

Classes¶

Species

JAX-compatible species container for arbitrary number of species.

Functions¶

`get_Thermodynamical_Forces_A1`(q, n, T, dndr, dTdr, Er)
`get_Thermodynamical_Forces_A2`(T, dTdr)
`get_Thermodynamical_Forces_A3`(Er)
`_species_flatten`(s)
`_species_unflatten`(aux_data, children)
`collisionality`(→ float)	Collisionality of species_a against all species.
`collisionality_local`(→ float)	Collisionality of species_a against all species using local profiles at one radius.
`collisionality_ntss_like`(→ float)	NTSSfusion-like thermal-speed effective collision frequency cnue(vth).
`collisionality_ntss_like_local`(→ float)	Local NTSSfusion-like thermal-speed effective collision frequency cnue(vth).
`_electron_index`(→ int)
`zeff`(→ float)	Effective charge Zeff = sum_i n_i Z_i^2 / n_e using ion species only.
`zeff_local`(→ float)	Local effective charge Zeff = sum_i n_i Z_i^2 / n_e using ion species only.
`collisionality_ntss_zeff`(→ float)	Legacy NTSSfusion-like simplified electron collisionality using Zeff.
`collisionality_ntss_zeff_local`(→ float)	Local legacy NTSSfusion-like simplified electron collisionality using Zeff.
`nuD_ab`(→ float)	Pairwise pitch-angle scattering frequency for species a against species b.
`nuD_ab_local`(→ float)	Pairwise pitch-angle scattering frequency using local profiles at one radius.
`gamma_ab`(→ float)	Prefactor for pairwise collisionality.
`gamma_ab_local`(→ float)	Prefactor for pairwise collisionality using local profiles at one radius.
`nupar_ab`(→ float)	Parallel collisionality.
`coulomb_logarithm`(→ float)	Coulomb logarithm for collisions between species a and b.
`coulomb_logarithm_local`(→ float)	Coulomb logarithm using local profiles at one radius.
`_coulomb_logarithm_default`(→ float)
`_coulomb_logarithm_default_local`(→ float)
`coulomb_logarithm_ntss_legacy`(→ float)	Legacy NTSS/TC_DKES piecewise Coulomb logarithm.
`coulomb_logarithm_ntss_legacy_local`(→ float)	Local legacy NTSS/TC_DKES piecewise Coulomb logarithm.
`coulomb_logarithm_first_principles`(→ float)	Coulomb logarithm from impact parameters.
`coulomb_logarithm_first_principles_local`(→ float)	Local Coulomb logarithm from impact parameters.
`tau_ab_ntss_like`(→ float)	NTSSfusion-like test-particle collision time tau(a,b).
`tau_ab_ntss_like_local`(→ float)	Local NTSSfusion-like test-particle collision time tau(a,b).
`ntss_collision_kernel`(→ float)	Velocity kernel used by NTSSfusion for effective collisionality.
`ntss_collision_kernel_thermal`(→ float)	NTSSfusion kernel evaluated at vn=1 (thermal speed of test species).
`ntss_collision_kernel_thermal_local`(→ float)	Local NTSSfusion kernel evaluated at vn=1 (thermal speed of test species).
`impact_parameter`(→ float)	Impact parameters for classical Coulomb collision.
`impact_parameter_local`(→ float)	Local impact parameters for classical Coulomb collision.
`impact_parameter_perp`(→ float)	Distance of the closest approach for a 90° Coulomb collision.
`impact_parameter_perp_local`(→ float)	Local distance of the closest approach for a 90 degree Coulomb collision.
`debroglie_length`(→ float)	Thermal DeBroglie wavelength.
`debroglie_length_local`(→ float)	Local thermal DeBroglie wavelength.
`debye_length`(→ float)	Scale length for charge screening.
`debye_length_local`(→ float)	Local scale length for charge screening.
`chandrasekhar`(→ jax.Array)	Chandrasekhar function.
`_dchandrasekhar`(x)
`get_species_idx`(→ int)	Return the index of a species by name from a tuple of species names.

Module Contents¶

NEOPAX._species.JOULE_PER_EV¶

NEOPAX._species.JOULE_PER_KEV¶

NEOPAX._species.EV_PER_JOULE¶

NEOPAX._species.STATE_DENSITY_TO_PHYSICAL = 1e+20¶

NEOPAX._species.STATE_TEMPERATURE_TO_EV = 1000.0¶

NEOPAX._species.COULOMB_LOG_MODEL_DEFAULT = 0¶

NEOPAX._species.COULOMB_LOG_MODEL_NTSS_LEGACY = 1¶

NEOPAX._species.COULOMB_LOG_MODEL_FIRST_PRINCIPLES = 2¶

NEOPAX._species.get_Thermodynamical_Forces_A1(q, n, T, dndr, dTdr, Er)¶

NEOPAX._species.get_Thermodynamical_Forces_A2(T, dTdr)¶

NEOPAX._species.get_Thermodynamical_Forces_A3(Er)¶

class NEOPAX._species.Species¶

JAX-compatible species container for arbitrary number of species. All fields are JAX arrays for differentiability and vmap support.

number_species: int¶

species_indices: jaxtyping.Array¶

mass_mp: jaxtyping.Float[jaxtyping.Array, ...]¶

charge_qp: jaxtyping.Float[jaxtyping.Array, ...]¶

names: tuple[str, Ellipsis] = ()¶

is_frozen: jaxtyping.Array = None¶

property charge¶

property mass¶

property species_idx: dict¶: Return a mapping from species name to index.

property ion_indices: tuple¶: Return a tuple of all species indices except the electron (‘e’).

NEOPAX._species._species_flatten(s)¶

NEOPAX._species._species_unflatten(aux_data, children)¶

NEOPAX._species.collisionality(species_a: int, species: Species, v: float, r_index: int, density, temperature, v_thermal, coulomb_log_model: int = COULOMB_LOG_MODEL_DEFAULT) → float¶: Collisionality of species_a against all species.

NEOPAX._species.collisionality_local(species_a: int, species: Species, v: float, density_local, temperature_local, v_thermal_local, coulomb_log_model: int = COULOMB_LOG_MODEL_DEFAULT) → float¶: Collisionality of species_a against all species using local profiles at one radius.

NEOPAX._species.collisionality_ntss_like(species_a: int, species: Species, v: float, r_index: int, density, temperature, v_thermal) → float¶: NTSSfusion-like thermal-speed effective collision frequency cnue(vth).

NEOPAX._species.collisionality_ntss_like_local(species_a: int, species: Species, v: float, density_local, temperature_local, v_thermal_local) → float¶: Local NTSSfusion-like thermal-speed effective collision frequency cnue(vth).

NEOPAX._species._electron_index(species: Species) → int¶

NEOPAX._species.zeff(species: Species, density, r_index: int) → float¶: Effective charge Zeff = sum_i n_i Z_i^2 / n_e using ion species only.

NEOPAX._species.zeff_local(species: Species, density_local) → float¶: Local effective charge Zeff = sum_i n_i Z_i^2 / n_e using ion species only.

NEOPAX._species.collisionality_ntss_zeff(species_a: int, species: Species, v: float, r_index: int, density, temperature, v_thermal) → float¶

Legacy NTSSfusion-like simplified electron collisionality using Zeff.

For electrons this follows the compact electron + Zeff form used in the legacy DKES path. For ions we keep the explicit multispecies sum.

NEOPAX._species.collisionality_ntss_zeff_local(species_a: int, species: Species, v: float, density_local, temperature_local, v_thermal_local) → float¶: Local legacy NTSSfusion-like simplified electron collisionality using Zeff.

NEOPAX._species.nuD_ab(species: Species, species_a: int, species_b: int, v: float, r_index: int, density, temperature, v_thermal, coulomb_log_model: int = COULOMB_LOG_MODEL_DEFAULT) → float¶: Pairwise pitch-angle scattering frequency for species a against species b.

NEOPAX._species.nuD_ab_local(species: Species, species_a: int, species_b: int, v: float, density_local, temperature_local, v_thermal_local, coulomb_log_model: int = COULOMB_LOG_MODEL_DEFAULT) → float¶: Pairwise pitch-angle scattering frequency using local profiles at one radius.

NEOPAX._species.gamma_ab(species: Species, species_a: int, species_b: int, v: float, r_index: int, temperature, density, v_thermal, coulomb_log_model: int = COULOMB_LOG_MODEL_DEFAULT) → float¶: Prefactor for pairwise collisionality.

NEOPAX._species.gamma_ab_local(species: Species, species_a: int, species_b: int, temperature_local, density_local, v_thermal_local, coulomb_log_model: int = COULOMB_LOG_MODEL_DEFAULT) → float¶: Prefactor for pairwise collisionality using local profiles at one radius.

NEOPAX._species.nupar_ab(species: Species, species_a: int, species_b: int, v: float, r_index: int, density, temperature, v_thermal) → float¶: Parallel collisionality.

NEOPAX._species.coulomb_logarithm(species: Species, species_a: int, species_b: int, r_index: int, temperature, density, v_thermal, coulomb_log_model: int = COULOMB_LOG_MODEL_DEFAULT) → float¶: Coulomb logarithm for collisions between species a and b.

NEOPAX._species.coulomb_logarithm_local(species: Species, species_a: int, species_b: int, temperature_local, density_local, v_thermal_local, coulomb_log_model: int = COULOMB_LOG_MODEL_DEFAULT) → float¶: Coulomb logarithm using local profiles at one radius.

NEOPAX._species._coulomb_logarithm_default(temperature, density, r_index: int) → float¶

NEOPAX._species._coulomb_logarithm_default_local(temperature_local, density_local) → float¶

NEOPAX._species.coulomb_logarithm_ntss_legacy(temperature, density, r_index: int) → float¶: Legacy NTSS/TC_DKES piecewise Coulomb logarithm.

NEOPAX._species.coulomb_logarithm_ntss_legacy_local(temperature_local, density_local) → float¶: Local legacy NTSS/TC_DKES piecewise Coulomb logarithm.

NEOPAX._species.coulomb_logarithm_first_principles(species: Species, species_a: int, species_b: int, r_index: int, density, temperature, v_thermal) → float¶: Coulomb logarithm from impact parameters.

NEOPAX._species.coulomb_logarithm_first_principles_local(species: Species, species_a: int, species_b: int, density_local, temperature_local, v_thermal_local) → float¶: Local Coulomb logarithm from impact parameters.

NEOPAX._species.tau_ab_ntss_like(species: Species, species_a: int, species_b: int, r_index: int, density, temperature, v_thermal) → float¶: NTSSfusion-like test-particle collision time tau(a,b).

NEOPAX._species.tau_ab_ntss_like_local(species: Species, species_a: int, species_b: int, density_local, temperature_local, v_thermal_local) → float¶: Local NTSSfusion-like test-particle collision time tau(a,b).

NEOPAX._species.ntss_collision_kernel(species: Species, species_a: int, species_b: int, v: float, v_thermal_b) → float¶: Velocity kernel used by NTSSfusion for effective collisionality.

NEOPAX._species.ntss_collision_kernel_thermal(species: Species, species_a: int, species_b: int, r_index: int, temperature) → float¶: NTSSfusion kernel evaluated at vn=1 (thermal speed of test species).

NEOPAX._species.ntss_collision_kernel_thermal_local(species: Species, species_a: int, species_b: int, temperature_local) → float¶: Local NTSSfusion kernel evaluated at vn=1 (thermal speed of test species).

NEOPAX._species.impact_parameter(species: Species, species_a: int, species_b: int, r_index: int, density, temperature, v_thermal) → float¶: Impact parameters for classical Coulomb collision.

NEOPAX._species.impact_parameter_local(species: Species, species_a: int, species_b: int, density_local, temperature_local, v_thermal_local) → float¶: Local impact parameters for classical Coulomb collision.

NEOPAX._species.impact_parameter_perp(species: Species, species_a: int, species_b: int, r_index: int, v_thermal) → float¶: Distance of the closest approach for a 90° Coulomb collision.

NEOPAX._species.impact_parameter_perp_local(species: Species, species_a: int, species_b: int, v_thermal_local) → float¶: Local distance of the closest approach for a 90 degree Coulomb collision.

NEOPAX._species.debroglie_length(species: Species, species_a: int, species_b: int, r_index: int, v_thermal) → float¶: Thermal DeBroglie wavelength.

NEOPAX._species.debroglie_length_local(species: Species, species_a: int, species_b: int, v_thermal_local) → float¶: Local thermal DeBroglie wavelength.

NEOPAX._species.debye_length(species: Species, r_index: int, density, temperature) → float¶: Scale length for charge screening.

NEOPAX._species.debye_length_local(species: Species, density_local, temperature_local) → float¶: Local scale length for charge screening.

NEOPAX._species.chandrasekhar(x: jax.Array) → jax.Array¶: Chandrasekhar function.

NEOPAX._species._dchandrasekhar(x)¶

NEOPAX._species.get_species_idx(name: str, names: tuple[str, Ellipsis]) → int¶: Return the index of a species by name from a tuple of species names.