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Implement average charge state equilibria.
Electron temperature dependent. Uses a polynomial fit for a selection of common impurities based on Mavrin 2018, including heavy impurities. * Adds a new routine to calculate average impurity charge state for an IonMixture. * Modifies the DynamicIonMixture dataclass to hold a separate Z_override attribute instead of calculating the average itself. This is used in the charge state calculation function. * Updates core_profile_setters to calculate and return the Zimp/Zi profiles according to the new routines * Better separation of ne and ion density + charge state setting * Updates Qualikiz to use the new Zimp/Zi arrays * Adds average Zimp to default output plots * Updates boundary condition calculations to calculate boundary Zimp according to the boundary temperature. * New sim integration test with tungsten added. * Some sim tests which did not have a Z_override now have spatially varying Zimp, which leads to small O(1e-4) changes. The small impact is because the default impurity is Neon. Small <5% runtime increase. This was ascertained to not be due to the (jitted) charge state calculations themselves, but due to surrounding code in non-jitted functions in the sim loop which call the charge state calculations. This will be rectified in an upcoming PR. ~10% compilation time increase due to added dependency of nimp and zimp on electron temperature. PiperOrigin-RevId: 717475094
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| # Copyright 2024 DeepMind Technologies Limited | ||
| # | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
|
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| """Routines for calculating impurity charge states.""" | ||
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|
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| from typing import Final, Mapping, Sequence | ||
| import immutabledict | ||
| from jax import numpy as jnp | ||
| import numpy as np | ||
| from torax import array_typing | ||
| from torax import constants | ||
| from torax.config import plasma_composition | ||
|
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||
| # Polynomial fit coefficients from A. A. Mavrin (2018): | ||
| # Improved fits of coronal radiative cooling rates for high-temperature plasmas, | ||
| # Radiation Effects and Defects in Solids, 173:5-6, 388-398, | ||
| # DOI: 10.1080/10420150.2018.1462361 | ||
| _MAVRIN_Z_COEFFS: Final[Mapping[str, array_typing.ArrayFloat]] = ( | ||
| immutabledict.immutabledict({ | ||
| 'C': np.array([ # Carbon | ||
| [5.8588e00, -1.7632e00, -7.3521e00, -1.2217e01, -7.2007e00], | ||
| [6.0000e00, 0.0000e00, 0.0000e00, 0.0000e00, 0.0000e00], | ||
| ]), | ||
| 'N': np.array([ # Nitrogen | ||
| [6.9728e00, 1.5668e-01, 1.8861e00, 3.3818e00, 0.0000e00], | ||
| [7.0000e00, 0.0000e00, 0.0000e00, 0.0000e00, 0.0000e00], | ||
| ]), | ||
| 'O': np.array([ # Oxygen | ||
| [4.0451e00, -2.2093e01, -3.8664e01, -1.8560e01, 0.0000e00], | ||
| [7.9878e00, 8.0180e-02, -3.7050e-02, -4.6261e-01, -4.3092e00], | ||
| [8.0000e00, 0.0000e00, 0.0000e00, 0.0000e00, 0.0000e00], | ||
| ]), | ||
| 'Ne': np.array([ # Neon | ||
| [8.9737e00, -1.3242e01, -5.3631e01, -6.4696e01, -2.5303e01], | ||
| [9.9532e00, 2.1413e-01, -8.0723e-01, 3.6868e00, -7.0678e00], | ||
| [1.0000e01, 0.0000e00, 0.0000e00, 0.0000e00, 0.0000e00], | ||
| ]), | ||
| 'Ar': np.array([ # Argon | ||
| [1.3171e01, -2.0781e01, -4.3776e01, -1.1595e01, 6.8717e00], | ||
| [1.5986e01, 1.1413e00, 2.5023e00, 1.8455e00, -4.8830e-02], | ||
| [1.4948e01, 7.9986e00, -8.0048e00, 3.5667e00, -5.9213e-01], | ||
| ]), | ||
| 'Kr': np.array([ # Krypton | ||
| [7.7040e01, 3.0638e02, 5.6890e02, 4.6320e02, 1.3630e02], | ||
| [2.4728e01, 1.5186e00, 1.5744e01, 6.8446e01, -1.0279e02], | ||
| [2.5368e01, 2.3443e01, -2.5703e01, 1.3215e01, -2.4682e00], | ||
| ]), | ||
| 'Xe': np.array([ # Xenon | ||
| [3.0532e02, 1.3973e03, 2.5189e03, 1.9967e03, 5.8178e02], | ||
| [3.2616e01, 1.6271e01, -4.8384e01, -2.9061e01, 8.6824e01], | ||
| [4.8066e01, -1.7259e02, 6.6739e02, -9.0008e02, 4.0756e02], | ||
| [-5.7527e01, 2.4056e02, -1.9931e02, 7.3261e01, -1.0019e01], | ||
| ]), | ||
| 'W': np.array([ # Tungsten | ||
| [2.6703e01, 1.6518e01, 2.1027e01, 3.4582e01, 1.6823e01], | ||
| [3.6902e01, -7.9611e01, 2.5532e02, -1.0577e01, -2.5887e02], | ||
| [6.3795e01, -1.0011e02, 1.5985e02, -8.4207e01, 1.5119e01], | ||
| ]), | ||
| }) | ||
| ) | ||
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| # Temperature boundaries in keV, separating the rows for the fit coefficients. | ||
| _TEMPERATURE_INTERVALS: Final[Mapping[str, array_typing.ArrayFloat]] = ( | ||
| immutabledict.immutabledict({ | ||
| 'C': np.array([0.7]), | ||
| 'N': np.array([0.7]), | ||
| 'O': np.array([0.3, 1.5]), | ||
| 'Ne': np.array([0.5, 2.0]), | ||
| 'Ar': np.array([0.6, 3.0]), | ||
| 'Kr': np.array([0.447, 4.117]), | ||
| 'Xe': np.array([0.3, 1.5, 8.0]), | ||
| 'W': np.array([1.5, 4.0]), | ||
| }) | ||
| ) | ||
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| # pylint: disable=invalid-name | ||
| def calculate_average_charge_state_single_species( | ||
| Te: array_typing.ArrayFloat, | ||
| ion_symbol: str, | ||
| ) -> array_typing.ArrayFloat: | ||
| """Calculates the average charge state of an impurity based on the Marvin 2018 polynomial fit. | ||
| The polynomial fit range is 0.1-100 keV, which is well within the typical | ||
| bounds of core tokamak modelling. For safety, inputs are clipped to avoid | ||
| extrapolation outside this range. | ||
| Args: | ||
| Te: Electron temperature [keV]. | ||
| ion_symbol: Species to calculate average charge state for. | ||
| Returns: | ||
| Z: Average charge state [amu]. | ||
| """ | ||
|
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||
| if ion_symbol not in constants.ION_SYMBOLS: | ||
| raise ValueError( | ||
| f'Invalid ion symbol: {ion_symbol}. Allowed symbols are :' | ||
| f' {constants.ION_SYMBOLS}' | ||
| ) | ||
| # Return the Z value for light ions that are fully ionized for T > 0.1 keV. | ||
| if ion_symbol not in _MAVRIN_Z_COEFFS: | ||
| return jnp.ones_like(Te) * constants.ION_PROPERTIES_DICT[ion_symbol].Z | ||
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| # Avoid extrapolating fitted polynomial out of bounds. | ||
| Te_allowed_range = (0.1, 100.0) | ||
| Te = jnp.clip(Te, *Te_allowed_range) | ||
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| # Gather coefficients for each temperature | ||
| interval_indices = jnp.searchsorted(_TEMPERATURE_INTERVALS[ion_symbol], Te) | ||
| Zavg_coeffs_in_range = jnp.take( | ||
| _MAVRIN_Z_COEFFS[ion_symbol], interval_indices, axis=0 | ||
| ).transpose() | ||
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| def _calculate_in_range(X, coeffs): | ||
| """Return Mavrin 2018 Zavg polynomial.""" | ||
| A0, A1, A2, A3, A4 = coeffs | ||
| return A0 + A1 * X + A2 * X**2 + A3 * X**3 + A4 * X**4 | ||
|
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| X = jnp.log10(Te) | ||
| Zavg = _calculate_in_range(X, Zavg_coeffs_in_range) | ||
|
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| return Zavg | ||
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| def get_average_charge_state( | ||
| ion_symbols: Sequence[str], | ||
| ion_mixture: plasma_composition.DynamicIonMixture, | ||
| Te: array_typing.ArrayFloat, | ||
| ) -> array_typing.ArrayFloat: | ||
| """Calculates or prescribes average impurity charge state profile (JAX-compatible). | ||
| Args: | ||
| ion_symbols: Species to calculate average charge state for. | ||
| ion_mixture: DynamicIonMixture object containing impurity information. The | ||
| index of the ion_mixture.fractions array corresponds to the index of the | ||
| ion_symbols array. | ||
| Te: Electron temperature [keV]. Can be any sized array, e.g. on cell grid, | ||
| face grid, or a single scalar. | ||
| Returns: | ||
| avg_Z: Average charge state profile [amu]. | ||
| The shape of avg_Z is the same as Te. | ||
| """ | ||
|
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| if ion_mixture.Z_override is not None: | ||
| return jnp.ones_like(Te) * ion_mixture.Z_override | ||
|
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| avg_Z = jnp.zeros_like(Te) | ||
| for ion_symbol, fraction in zip(ion_symbols, ion_mixture.fractions): | ||
| avg_Z += fraction * calculate_average_charge_state_single_species( | ||
| Te, ion_symbol | ||
| ) | ||
|
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| return avg_Z |
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