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Remove re-export aliases from combined.py and update runtime_params callers. #2333

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Remove re-export aliases from combined.py and update runtime_params callers. #2333

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64 changes: 0 additions & 64 deletions docs/configuration.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -1469,58 +1469,6 @@ transport model.
Width of HWHM Gaussian smoothing kernel operating on transport model outputs.
If using the ``QLKNN_7_11`` transport model, the default is set to 0.1.

``smooth_everywhere`` (bool [default = False])
Smooth across entire radial domain regardless of inner and outer patches.

``apply_inner_patch`` (**time-varying-scalar** [default = False])
If ``True``, set a patch for inner core transport coefficients below
``rho_inner``. Typically used as an ad-hoc measure for MHD (e.g. sawteeth) or
EM (e.g. KBM) transport in the inner-core. If using a
`CombinedTransportModel`, ensure that the inner patch is only set on the
global model rather than its component models to avoid conflicts.

``D_e_inner`` (**time-varying-scalar** [default = 0.2])
Particle diffusivity value for inner transport patch.

``V_e_inner`` (**time-varying-scalar** [default = 0.0])
Particle convection value for inner transport patch.

``chi_i_inner`` (**time-varying-scalar** [default = 1.0])
Ion heat conduction value for inner transport patch.

``chi_e_inner`` (**time-varying-scalar** [default = 1.0])
Electron heat conduction value for inner transport patch.

``rho_inner`` (**time-varying-scalar** [default = 0.3])
:math:`\hat{\rho}` below which inner patch is applied.
Note that ``rho_inner`` and ``rho_outer`` must have the same interpolation
mode to simplify the validation test ``rho_inner < rho_outer`` at all times.

``apply_outer_patch`` (**time-varying-scalar** [default = False])
If ``True``, set a patch for outer core transport coefficients above
``rho_outer``. Useful for the L-mode near-edge region where models like
QLKNN10D are not applicable. Only used if ``set_pedestal==False``.
If using a `CombinedTransportModel`, ensure that the outer patch is
only set on the global model rather than its component models to avoid
conflicts.

``D_e_outer`` (**time-varying-scalar** [default = 0.2])
Particle diffusivity value for outer transport patch.

``V_e_outer`` (**time-varying-scalar** [default = 0.0])
Particle convection value for outer transport patch.

``chi_i_outer`` (**time-varying-scalar** [default = 1.0])
Ion heat conduction value for outer transport patch.

``chi_e_outer`` (**time-varying-scalar** [default = 1.0])
Electron heat conduction value for outer transport patch.

``rho_outer`` (**time-varying-scalar** [default = 0.9])
:math:`\hat{\rho}` above which outer patch is applied.
Note that ``rho_inner`` and ``rho_outer`` must have the same interpolation
mode to simplify the validation test ``rho_inner < rho_outer`` at all times.

``fast_ion_stabilization`` (**time-varying-scalar** [default = False])
If ``True``, apply a fast ion stabilization correction to the :math:`R/L_{Ti}`
input of quasilinear transport models (QLKNN, TGLFNN, QuaLiKiz). The fast ion
Expand Down Expand Up @@ -3003,18 +2951,6 @@ CHEASE geometry), is shown below. The configuration file is also available in
},
'transport': {
'model_name': 'qlknn',
'apply_inner_patch': True,
'D_e_inner': 0.25,
'V_e_inner': 0.0,
'chi_i_inner': 1.5,
'chi_e_inner': 1.5,
'rho_inner': 0.3,
'apply_outer_patch': True,
'D_e_outer': 0.1,
'V_e_outer': 0.0,
'chi_i_outer': 2.0,
'chi_e_outer': 2.0,
'rho_outer': 0.9,
'chi_min': 0.05,
'chi_max': 100,
'D_e_min': 0.05,
Expand Down
2 changes: 1 addition & 1 deletion torax/_src/config/runtime_params.py
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Expand Up @@ -86,7 +86,7 @@ class RuntimeParams:
profile_conditions: profile_conditions.RuntimeParams
solver: solver_params.RuntimeParams
sources: Mapping[str, sources_params.RuntimeParams]
transport: transport_model_params.RuntimeParams
transport: transport_model_params.CombinedRuntimeParams
time_step_calculator: time_step_calculator_runtime_params.RuntimeParams


Expand Down
4 changes: 2 additions & 2 deletions torax/_src/models.py
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Expand Up @@ -22,7 +22,7 @@
from torax._src.pedestal_model import pedestal_model as pedestal_model_lib
from torax._src.sources import source_models as source_models_lib
from torax._src.time_step_calculator.time_step_calculator import TimeStepCalculator
from torax._src.transport_model import transport_model as transport_model_lib
from torax._src.transport_model import combined as combined_lib


@dataclasses.dataclass(frozen=True, eq=False)
Expand All @@ -36,7 +36,7 @@ class Models(static_dataclass.StaticDataclass):
"""

source_models: source_models_lib.SourceModels
transport_model: transport_model_lib.TransportModel
transport_model: combined_lib.CombinedTransportModel
pedestal_model: pedestal_model_lib.PedestalModel
neoclassical_models: neoclassical_models_lib.NeoclassicalModels
mhd_models: mhd_model_lib.MHDModels
Expand Down
91 changes: 48 additions & 43 deletions torax/_src/transport_model/combined.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,15 +17,16 @@
A class for combining transport models.
"""

# pylint: disable=invalid-name

import dataclasses
from typing import Callable, Sequence, Tuple
import chex
from typing import Callable, Sequence
import jax
import jax.numpy as jnp
from torax._src import array_typing
from torax._src import constants
from torax._src import jax_utils
from torax._src import state
from torax._src import static_dataclass
from torax._src.config import runtime_params as runtime_params_lib
from torax._src.geometry import geometry
from torax._src.pedestal_model import pedestal_model_output as pedestal_model_output_lib
Expand All @@ -37,27 +38,8 @@
MIN_SMOOTHING_WIDTH = 1e-5


@chex.dataclass
class SmoothingZoneParams:
rho_min: array_typing.FloatScalar
rho_max: array_typing.FloatScalar
smoothing_width: array_typing.FloatScalar


@jax.tree_util.register_dataclass
@dataclasses.dataclass(frozen=True)
class RuntimeParams(transport_runtime_params_lib.RuntimeParams):
"""Runtime parameters for the CombinedTransportModel."""

transport_model_params: Tuple[transport_runtime_params_lib.RuntimeParams, ...]
pedestal_transport_model_params: Tuple[
transport_runtime_params_lib.RuntimeParams, ...
]
smoothing_zones: Tuple[SmoothingZoneParams, ...]


@dataclasses.dataclass(frozen=True, eq=False)
class CombinedTransportModel(transport_model_lib.TransportModel):
class CombinedTransportModel(static_dataclass.StaticDataclass):
"""Combines coefficients from a tuple of transport models."""

transport_models: tuple[transport_model_lib.TransportModel, ...]
Expand All @@ -82,23 +64,12 @@ def __call__(
core_profiles,
pedestal_model_output,
)

# In contrast to the base TransportModel, we do not apply domain restriction
# or output masking (enabled/disabled channels) as these are handled at the
# component model level in call_implementation here.

# Apply min/max clipping
transport_coeffs = self._apply_clipping(
transport_runtime_params,
transport_coeffs,
)

# In contrast to the base TransportModel, we do not apply patches, as these
# should be handled by instantiating constant component models instead.
# However, the rho_inner and rho_outer arguments are currently required
# in the case where the inner/outer region are to be excluded from
# smoothing.

transport_coeffs = self._smooth_coeffs(
runtime_params,
geo,
Expand All @@ -110,7 +81,7 @@ def __call__(

def call_implementation(
self,
transport_runtime_params: transport_runtime_params_lib.RuntimeParams,
transport_runtime_params: transport_runtime_params_lib.CombinedRuntimeParams,
runtime_params: runtime_params_lib.RuntimeParams,
geo: geometry.Geometry,
core_profiles: state.CoreProfiles,
Expand All @@ -120,7 +91,8 @@ def call_implementation(

Args:
transport_runtime_params: Input runtime parameters for this transport
model. Can change without triggering a JAX recompilation.
model (expected to be an instance of CombinedRuntimeParams at runtime).
Can change without triggering a JAX recompilation.
runtime_params: Runtime parameters for the simulation at the current time.
geo: Geometry of the torus at the current time.
core_profiles: Core plasma profiles.
Expand All @@ -129,9 +101,6 @@ def call_implementation(
Returns:
coeffs: The transport coefficients
"""
# Required for pytype
assert isinstance(transport_runtime_params, RuntimeParams)

core_coeffs = self._combine(
self.transport_models,
transport_runtime_params.transport_model_params,
Expand Down Expand Up @@ -255,6 +224,41 @@ def _combine(

return transport_model_lib.TurbulentTransport(**accumulators)

def _apply_clipping(
self,
transport_runtime_params: transport_runtime_params_lib.CombinedRuntimeParams,
transport_coeffs: transport_model_lib.TurbulentTransport,
) -> transport_model_lib.TurbulentTransport:
"""Applies min/max clipping to transport coefficients for PDE stability."""
chi_face_ion = jnp.clip(
transport_coeffs.chi_face_ion,
transport_runtime_params.chi_min,
transport_runtime_params.chi_max,
)
chi_face_el = jnp.clip(
transport_coeffs.chi_face_el,
transport_runtime_params.chi_min,
transport_runtime_params.chi_max,
)
d_face_el = jnp.clip(
transport_coeffs.d_face_el,
transport_runtime_params.D_e_min,
transport_runtime_params.D_e_max,
)
v_face_el = jnp.clip(
transport_coeffs.v_face_el,
transport_runtime_params.V_e_min,
transport_runtime_params.V_e_max,
)

return dataclasses.replace(
transport_coeffs,
chi_face_ion=chi_face_ion,
chi_face_el=chi_face_el,
d_face_el=d_face_el,
v_face_el=v_face_el,
)

def _smooth_coeffs(
self,
runtime_params: runtime_params_lib.RuntimeParams,
Expand All @@ -263,7 +267,6 @@ def _smooth_coeffs(
pedestal_model_output: pedestal_model_output_lib.PedestalModelOutput,
) -> transport_model_lib.TurbulentTransport:
"""Gaussian smoothing of turbulent transport coefficients."""
assert isinstance(runtime_params.transport, RuntimeParams)
smoothing_matrix = _build_smoothing_matrix(
runtime_params.transport,
runtime_params,
Expand All @@ -280,7 +283,7 @@ def smooth_single_coeff(coeff):
lambda: jnp.dot(smoothing_matrix, coeff),
)

return jax.tree_util.tree_map(smooth_single_coeff, transport_coeffs)
return jax.tree.map(smooth_single_coeff, transport_coeffs)


def _add_optional(
Expand All @@ -305,14 +308,16 @@ def _pedestal_domain_mask(


def _build_smoothing_matrix(
transport_runtime_params: RuntimeParams,
transport_runtime_params: (
transport_runtime_params_lib.CombinedRuntimeParams
),
runtime_params: runtime_params_lib.RuntimeParams,
geo: geometry.Geometry,
pedestal_model_output: pedestal_model_output_lib.PedestalModelOutput,
) -> jax.Array:
"""Builds a smoothing matrix for the combined transport model."""
# To reduce the range of the convolution, weights under lower_cutoff are
# clipped to zero
# clipped to zero.
lower_cutoff = 0.01
# used for eps, small number to avoid divisions by zero for sigma = 0
consts = constants.CONSTANTS
Expand Down
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