PySDM 3.0.0rc22__tar.gz → 3.0.0rc23__tar.gz

{pysdm-3.0.0rc22 → pysdm-3.0.0rc23}/.github/workflows/tests.yml

@@ -126,7 +126,7 @@ jobs:
             test-suite: "unit_tests/!(dynamics)"
       fail-fast: true
     runs-on: ${{ matrix.platform }}
-    timeout-minutes: ${{ startsWith(matrix.platform, 'ubuntu-') && 25 || 40 }}
+    timeout-minutes: ${{ startsWith(matrix.platform, 'ubuntu-') && 30 || 40 }}
     steps:
       - uses: actions/checkout@v4.1.6
         with:
@@ -239,7 +239,7 @@ jobs:
             test-suite: "multi-process_e"
       fail-fast: true
     runs-on: ${{ matrix.platform }}
-    timeout-minutes: 30
+    timeout-minutes: ${{ startsWith(matrix.platform, 'windows-') && 35 || 30 }}
     steps:
       - name: Debug contexts
         run: |

{pysdm-3.0.0rc22/pysdm.egg-info → pysdm-3.0.0rc23}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pysdm
-Version: 3.0.0rc22
+Version: 3.0.0rc23
 Summary: Pythonic particle-based (super-droplet) warm-rain/aqueous-chemistry cloud microphysics package with box, parcel & 1D/2D prescribed-flow examples in Python, Julia and Matlab
 Author-email: "https://github.com/open-atmos/PySDM/graphs/contributors" <sylwester.arabas@agh.edu.pl>
 License-Expression: GPL-3.0-only
@@ -60,7 +60,8 @@ Dynamic: requires-dist
 [![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://github.com/open-atmos/PySDM/graphs/commit-activity)
 [![OpenHub](https://www.openhub.net/p/atmos-cloud-sim-uj-PySDM/widgets/project_thin_badge?format=gif)](https://www.openhub.net/p/atmos-cloud-sim-uj-PySDM)
 [![status](https://joss.theoj.org/papers/62cad07440b941f73f57d187df1aa6e9/status.svg)](https://joss.theoj.org/papers/62cad07440b941f73f57d187df1aa6e9)
-[![DOI](https://zenodo.org/badge/199064632.svg)](https://zenodo.org/badge/latestdoi/199064632)    
+[![DOI](https://zenodo.org/badge/199064632.svg)](https://zenodo.org/badge/latestdoi/199064632)
+[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/open-atmos/PySDM)    
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 [![PL Funding](https://img.shields.io/static/v1?label=PL%20Funding%20by&color=d21132&message=NCN&logoWidth=25&logo=image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABQAAAANCAYAAACpUE5eAAAABmJLR0QA/wD/AP+gvaeTAAAAKUlEQVQ4jWP8////fwYqAiZqGjZqIHUAy4dJS6lqIOMdEZvRZDPcDQQAb3cIaY1Sbi4AAAAASUVORK5CYII=)](https://www.ncn.gov.pl/?language=en)
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{pysdm-3.0.0rc22 → pysdm-3.0.0rc23}/PySDM/attributes/isotopes/__init__.py

@@ -3,4 +3,4 @@ isotopic fractionation related attributes
 """
 
 from .moles import Moles1H, Moles16O, MolesLightWater
-from ..isotopes import delta
+from ..isotopes import delta, bolin_numbers

pysdm-3.0.0rc23/PySDM/attributes/isotopes/bolin_numbers.py

@@ -0,0 +1,64 @@
+"""
+Derived droplet attribute representing the Bolin number for heavy
+water isotopologues (D, 17O, 18O substitutions).
+
+The Bolin number is a dimensionless coefficient relating the
+heavy-isotope mole tendency to the bulk liquid-water mass tendency
+during phase change.
+Registered for all isotopes listed in ``HEAVY_ISOTOPES``.
+"""
+
+from PySDM.attributes.impl import DerivedAttribute, register_attribute
+from PySDM.dynamics.isotopic_fractionation import HEAVY_ISOTOPES
+
+
+class BolinNumberImpl(DerivedAttribute):
+    """Backend-evaluated Bolin number for a selected heavy isotopologue."""
+
+    def __init__(self, builder, *, heavy_isotope: str):
+        """
+        Parameters
+        ----------
+        builder
+            Attribute builder instance.
+        heavy_isotope : str
+            Heavy isotopologue identifier (entry of ``HEAVY_ISOTOPES``).
+        """
+        self.moles_heavy = builder.get_attribute(f"moles_{heavy_isotope}")
+        self.moles_light = builder.get_attribute("moles light water")
+        self.cell_id = builder.get_attribute("cell id")
+        self.molality_in_dry_air = builder.particulator.environment[
+            f"molality {heavy_isotope} in dry air"
+        ]
+        super().__init__(
+            builder,
+            name="Bolin number for " + heavy_isotope,
+            dependencies=(self.moles_heavy, self.moles_light, self.cell_id),
+        )
+
+    def recalculate(self):
+        """Recomputes the Bolin number using backend implementation."""
+        self.particulator.backend.bolin_number(
+            output=self.data,
+            cell_id=self.cell_id.data,
+            relative_humidity=self.particulator.environment["RH"],
+            temperature=self.particulator.environment["T"],
+            density_dry_air=self.particulator.environment["dry_air_density"],
+            moles_light_molecule=self.moles_light.data,
+            moles_heavy=self.moles_heavy.data,
+            molality_in_dry_air=self.molality_in_dry_air,
+        )
+
+
+def make_bolin_number_factory(heavy_isotope: str):
+    """Returns an attribute factory for the given heavy isotopologue."""
+
+    def _factory(builder):
+        """Instantiates ``BolinNumberImpl`` for the provided builder."""
+        return BolinNumberImpl(builder, heavy_isotope=heavy_isotope)
+
+    return _factory
+
+
+for iso in HEAVY_ISOTOPES:
+    register_attribute(name=f"Bolin number for {iso}")(make_bolin_number_factory(iso))

pysdm-3.0.0rc23/PySDM/backends/impl_numba/methods/isotope_methods.py

@@ -0,0 +1,203 @@
+"""
+CPU implementation of isotope-relates backend methods
+"""
+
+from functools import cached_property
+
+import numba
+
+from PySDM.backends.impl_common.backend_methods import BackendMethods
+
+
+class IsotopeMethods(BackendMethods):
+    """
+    CPU backend methods for droplet isotope processing.
+
+    Provides Numba-accelerated kernels for:
+    - isotopic ratio to delta conversion,
+    - Bolin number evaluation,
+    - heavy-isotope fractionation during condensation/evaporation.
+    """
+
+    @cached_property
+    def _isotopic_delta_body(self):
+        """Numba kernel to convert isotopic ratios to delta values."""
+        ff = self.formulae_flattened
+
+        @numba.njit(**self.default_jit_flags)
+        def body(output, ratio, reference_ratio):
+            for i in numba.prange(output.shape[0]):  # pylint: disable=not-an-iterable
+                output[i] = ff.trivia__isotopic_ratio_2_delta(ratio[i], reference_ratio)
+
+        return body
+
+    def isotopic_delta(self, output, ratio, reference_ratio):
+        """Compute isotopic delta for droplets."""
+        self._isotopic_delta_body(output.data, ratio.data, reference_ratio)
+
+    @cached_property
+    def _isotopic_fractionation_body(self):
+        """
+        Kernel updating heavy-isotope content during phase change.
+
+        Computes the heavy-isotope mass change per droplet using the Bolin
+        number (Bo) and the instantaneous heavy-to-total mass ratio:
+
+            dm_heavy = (dm_total / Bo) * (m_heavy / m_total)
+            dn_heavy = dm_heavy / M_heavy
+
+        Updates:
+        - moles_heavy_molecule per droplet,
+        - molality of heavy isotope in dry air.
+        """
+
+        @numba.njit(**{**self.default_jit_flags, **{"parallel": False}})
+        def body(
+            *,
+            cell_id,
+            cell_volume,
+            multiplicity,
+            dm_total,
+            signed_water_mass,
+            dry_air_density,
+            molar_mass_heavy_molecule,
+            moles_heavy_molecule,
+            bolin_number,
+            molality_in_dry_air,
+        ):
+            for sd_id in range(multiplicity.shape[0]):
+                mass_ratio_heavy_to_total = (
+                    moles_heavy_molecule[sd_id] * molar_mass_heavy_molecule
+                ) / signed_water_mass[sd_id]
+                if bolin_number[sd_id] == 0:
+                    dm_heavy = 0
+                else:
+                    dm_heavy = (
+                        dm_total[sd_id]
+                        / bolin_number[sd_id]
+                        * mass_ratio_heavy_to_total
+                    )
+                dn_heavy_molecule = dm_heavy / molar_mass_heavy_molecule
+                moles_heavy_molecule[sd_id] += dn_heavy_molecule
+                mass_of_dry_air = (
+                    dry_air_density[cell_id[sd_id]] * cell_volume[cell_id[sd_id]]
+                )
+                molality_in_dry_air[cell_id[sd_id]] -= (
+                    dn_heavy_molecule * multiplicity[sd_id] / mass_of_dry_air
+                )
+
+        return body
+
+    def isotopic_fractionation(
+        self,
+        *,
+        cell_id,
+        cell_volume,
+        multiplicity,
+        dm_total,
+        signed_water_mass,
+        dry_air_density,
+        molar_mass_heavy_molecule,
+        moles_heavy_molecule,
+        bolin_number,
+        molality_in_dry_air,
+    ):  # pylint: disable=too-many-positional-arguments
+        """Update heavy-isotope composition during droplet growth/evaporation."""
+        self._isotopic_fractionation_body(
+            cell_id=cell_id.data,
+            cell_volume=cell_volume.data,
+            multiplicity=multiplicity.data,
+            dm_total=dm_total.data,
+            signed_water_mass=signed_water_mass.data,
+            dry_air_density=dry_air_density.data,
+            molar_mass_heavy_molecule=molar_mass_heavy_molecule,
+            moles_heavy_molecule=moles_heavy_molecule.data,
+            bolin_number=bolin_number.data,
+            molality_in_dry_air=molality_in_dry_air.data,
+        )
+
+    @cached_property
+    def _bolin_number_body(self):
+        """
+        Kernel computing the Bolin number per droplet.
+
+        Calculates the isotope relaxation timescale ratio (Bolin number)
+        based on droplet composition, ambient temperature, relative humidity,
+        and water vapor properties:
+
+            Bo = tau_heavy / tau_bulk
+
+        Updates the output array with per-droplet Bolin numbers.
+        """
+        ff = self.formulae_flattened
+
+        @numba.njit(**{**self.default_jit_flags, **{"parallel": False}})
+        def body(
+            *,
+            output,
+            cell_id,
+            relative_humidity,
+            temperature,
+            density_dry_air,
+            moles_light_molecule,
+            moles_heavy,
+            molality_in_dry_air,
+        ):  # pylint: disable=too-many-locals
+            for i in numba.prange(output.shape[0]):  # pylint: disable=not-an-iterable
+                T = temperature[cell_id[i]]
+                pvs_water = ff.saturation_vapour_pressure__pvs_water(T)
+                moles_heavy_atom = moles_heavy[i]
+                moles_light_isotope = moles_light_molecule[i]  # TODO #1787
+                conc_vap_total = (
+                    pvs_water * relative_humidity[cell_id[i]] / ff.constants.R_str / T
+                )
+                rho_v = pvs_water / T / ff.constants.Rv
+
+                isotopic_fraction = ff.trivia__isotopic_fraction(
+                    molality_in_dry_air=molality_in_dry_air[cell_id[i]],
+                    density_dry_air=density_dry_air[cell_id[i]],
+                    total_vap_concentration=conc_vap_total,
+                )
+                D_ratio_heavy_to_light = (
+                    ff.isotope_diffusivity_ratios__ratio_2H_heavy_to_light(T)
+                )
+                output[i] = ff.isotope_relaxation_timescale__bolin_number(
+                    D_ratio_heavy_to_light=D_ratio_heavy_to_light,
+                    alpha=ff.isotope_equilibrium_fractionation_factors__alpha_l_2H(T),
+                    D_light=ff.constants.D0,
+                    Fk=ff.drop_growth__Fk(
+                        T=T, K=ff.constants.K0, lv=ff.constants.l_tri
+                    ),
+                    R_vap=ff.trivia__isotopic_ratio_assuming_single_heavy_isotope(
+                        isotopic_fraction
+                    ),
+                    R_liq=moles_heavy_atom / moles_light_isotope,
+                    relative_humidity=relative_humidity[cell_id[i]],
+                    rho_v=rho_v,
+                )
+
+        return body
+
+    def bolin_number(
+        self,
+        *,
+        output,
+        cell_id,
+        relative_humidity,
+        temperature,
+        density_dry_air,
+        moles_light_molecule,
+        moles_heavy,
+        molality_in_dry_air,
+    ):
+        """Bolin number per droplet"""
+        self._bolin_number_body(
+            output=output.data,
+            cell_id=cell_id.data,
+            relative_humidity=relative_humidity.data,
+            temperature=temperature.data,
+            density_dry_air=density_dry_air.data,
+            moles_light_molecule=moles_light_molecule.data,
+            moles_heavy=moles_heavy.data,
+            molality_in_dry_air=molality_in_dry_air.data,
+        )

pysdm-3.0.0rc23/PySDM/backends/impl_thrust_rtc/methods/isotope_methods.py

@@ -0,0 +1,100 @@
+"""
+GPU implementation of isotope-relates backend methods
+"""
+
+from functools import cached_property
+
+from PySDM.backends.impl_thrust_rtc.conf import NICE_THRUST_FLAGS
+from PySDM.backends.impl_thrust_rtc.nice_thrust import nice_thrust
+
+from ..conf import trtc
+from ..methods.thrust_rtc_backend_methods import ThrustRTCBackendMethods
+
+
+class IsotopeMethods(ThrustRTCBackendMethods):
+    @cached_property
+    def __isotopic_delta(self):
+        return trtc.For(
+            param_names=("output", "ratio", "reference_ratio"),
+            name_iter="i",
+            body=f"""
+            output[i] = {self.formulae.trivia.isotopic_ratio_2_delta.c_inline(
+                ratio="ratio[i]",
+                reference_ratio="reference_ratio"
+            )};
+            """.replace("real_type", self._get_c_type()),
+        )
+
+    @nice_thrust(**NICE_THRUST_FLAGS)
+    def isotopic_delta(self, output, ratio, reference_ratio):
+        self.__isotopic_delta.launch_n(
+            n=output.shape[0],
+            args=(output.data, ratio.data, self._get_floating_point(reference_ratio)),
+        )
+
+    @cached_property
+    def __isotopic_fractionation(self):
+        return trtc.For(
+            param_names=(
+                "cell_id",
+                "cell_volume",
+                "multiplicity",
+                "dm_total",
+                "signed_water_mass",
+                "dry_air_density",
+                "molar_mass_heavy_molecule",
+                "moles_heavy_molecule",
+                "bolin_number",
+                "molality_in_dry_air",
+            ),
+            name_iter="i",
+            body="""
+            auto cid = cell_id[i];
+
+            real_type mass_ratio = (moles_heavy_molecule[i] * molar_mass_heavy_molecule) / signed_water_mass[i];
+
+            real_type dm_heavy = 0;
+
+            if (bolin_number[i] != 0) {
+                dm_heavy = dm_total[i] / bolin_number[i] * mass_ratio;
+            }
+
+            real_type dn_heavy = dm_heavy / molar_mass_heavy_molecule;
+
+            moles_heavy_molecule[i] += dn_heavy;
+
+            real_type mass_of_dry_air = dry_air_density[cid] * cell_volume[cid];
+
+            atomicAdd((real_type*) &molality_in_dry_air[cid], -dn_heavy * multiplicity[i] / mass_of_dry_air);
+            """.replace("real_type", self._get_c_type()),
+        )
+
+    @nice_thrust(**NICE_THRUST_FLAGS)
+    def isotopic_fractionation(
+        self,
+        cell_id,
+        cell_volume,
+        multiplicity,
+        dm_total,
+        signed_water_mass,
+        dry_air_density,
+        molar_mass_heavy_molecule,
+        moles_heavy_molecule,
+        bolin_number,
+        molality_in_dry_air,
+    ):  # pylint: disable=too-many-positional-arguments
+        self.__isotopic_fractionation.launch_n(
+            n=len(multiplicity),
+            args=(
+                cell_id.data,
+                cell_volume.data,
+                multiplicity.data,
+                dm_total.data,
+                signed_water_mass.data,
+                dry_air_density.data,
+                self._get_floating_point(molar_mass_heavy_molecule),
+                moles_heavy_molecule.data,
+                bolin_number.data,
+                molality_in_dry_air.data,
+            ),
+        )

{pysdm-3.0.0rc22 → pysdm-3.0.0rc23}/PySDM/dynamics/isotopic_fractionation.py

@@ -37,7 +37,12 @@ class IsotopicFractionation:
 
         builder.request_attribute("diffusional growth mass change")
         for isotope in self.isotopes:
+            if isotope not in HEAVY_ISOTOPES:
+                raise AssertionError(
+                    f"Isotopic fractionation not implemented for {isotope}"
+                )
             builder.request_attribute(f"moles_{isotope}")
+            builder.request_attribute(f"Bolin number for {isotope}")
 
     def __call__(self):
         self.particulator.isotopic_fractionation(self.isotopes)

{pysdm-3.0.0rc22 → pysdm-3.0.0rc23}/PySDM/particulator.py

@@ -449,8 +449,27 @@ class Particulator:  # pylint: disable=too-many-public-methods,too-many-instance
             )
 
     def isotopic_fractionation(self, heavy_isotopes: tuple):
-        self.backend.isotopic_fractionation()
         for isotope in heavy_isotopes:
+            self.backend.isotopic_fractionation(
+                cell_id=self.attributes["cell id"],
+                cell_volume=self.environment.mesh.dv,
+                multiplicity=self.attributes["multiplicity"],
+                dm_total=self.attributes["diffusional growth mass change"],
+                signed_water_mass=self.attributes["signed water mass"],
+                dry_air_density=self.environment["dry_air_density"],
+                molar_mass_heavy_molecule=getattr(
+                    self.formulae.constants,
+                    {
+                        "2H": "M_2H_1H_16O",
+                        "3H": "M_3H_1H_16O",
+                        "17O": "M_1H2_17O",
+                        "18O": "M_1H2_18O",
+                    }[isotope],
+                ),
+                moles_heavy_molecule=self.attributes[f"moles_{isotope}"],  # TODO #1787
+                molality_in_dry_air=self.environment[f"molality {isotope} in dry air"],
+                bolin_number=self.attributes[f"Bolin number for {isotope}"],
+            )
             self.attributes.mark_updated(f"moles_{isotope}")
 
     def seeding(

pysdm-3.0.0rc23/PySDM/physics/isotope_ratio_evolution/gedzelman_and_arnold_1994.py

@@ -0,0 +1,22 @@
+"""
+saturation when no change in isotopic ratio
+in liquid eq 22 and in vapour eq 23
+in [Gedzelman & Arnold 1994](https://doi.org/10.1029/93JD03518)
+"""
+
+
+# pylint: disable=too-few-public-methods
+class GedzelmanAndArnold1994:
+    def __init__(self, _):
+        pass
+
+    # pylint: disable=too-many-arguments
+    @staticmethod
+    def saturation_for_zero_dR_condition(
+        _, diff_rat_light_to_heavy, iso_ratio_x, iso_ratio_r, iso_ratio_v, b, alpha_w
+    ):
+        return (diff_rat_light_to_heavy * iso_ratio_x - iso_ratio_r / alpha_w) / (
+            diff_rat_light_to_heavy * iso_ratio_x
+            - (1 + b) * iso_ratio_v
+            + b * iso_ratio_r / alpha_w
+        )

pysdm-3.0.0rc23/PySDM/physics/isotope_relaxation_timescale/zaba_et_al.py

@@ -0,0 +1,49 @@
+"""isotope e-folding timescale based on Fick's first law and Fourier's law"""
+
+
+class ZabaEtAl:  # pylint: disable=too-few-public-methods
+    def __init__(self, _):
+        pass
+
+    @staticmethod
+    def tau(
+        const, *, rho_s, radius, D_iso, D, S, R_liq, alpha, R_vap, Fk
+    ):  # pylint: disable=unused-argument
+        """relative growth of heavy isotope as a function of mass"""
+        return 1 / (
+            3
+            * rho_s
+            / radius**2
+            / const.rho_w
+            / alpha
+            * D_iso
+            * (S * (alpha * R_vap / R_liq - 1) + (S - 1) / (1 + D * Fk))
+        )
+
+    @staticmethod
+    def bolin_number(
+        D_ratio_heavy_to_light,
+        alpha,
+        D_light,
+        Fk,
+        R_vap,
+        R_liq,
+        relative_humidity,
+        rho_v,
+    ):  # pylint: disable=too-many-arguments,too-many-positional-arguments
+        # TODO #1809 Numba can't compile when * in bolin_number
+        """Heavy to total isotopic-timescales ratio (tau_heavy/tau_total).
+
+        Returns:
+            tau_heavy/tau_total = (relative total mass change)/(relative heavy mass change)
+        """
+        return (
+            alpha
+            * (1 - relative_humidity)
+            / D_ratio_heavy_to_light
+            / (
+                (1 + rho_v * D_light * Fk)
+                * relative_humidity
+                * (1 - alpha * R_vap / R_liq)
+            )
+        )

{pysdm-3.0.0rc22 → pysdm-3.0.0rc23}/README.md

@@ -10,7 +10,8 @@
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