PySDM 2.110__tar.gz → 2.111__tar.gz

{pysdm-2.110 → pysdm-2.111}/.github/workflows/pdoc.yml

@@ -26,13 +26,11 @@ jobs:
       - uses: actions/setup-python@v5.0.0
         with:
           python-version: "3.12"
-      - run: |
-          pip install pdoc nbformat gitpython
-          pip install -e .
-          pip install -e examples
+      - run: pip install pdoc nbformat gitpython
+      - run: pip install -e .
+      - run: pip install -e examples
+      - run: python -We docs/generate_html.py . .
 
-          python -We docs/generate_html.py . .
-        
       - if: ${{ github.ref == 'refs/heads/main' && matrix.platform == 'ubuntu-latest' }}
         uses: JamesIves/github-pages-deploy-action@4.1.1
         with:

{pysdm-2.110/pysdm.egg-info → pysdm-2.111}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pysdm
-Version: 2.110
+Version: 2.111
 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
 Home-page: https://github.com/open-atmos/PySDM
 Author: https://github.com/open-atmos/PySDM/graphs/contributors

{pysdm-2.110 → pysdm-2.111}/PySDM/formulae.py

@@ -49,6 +49,7 @@ class Formulae:  # pylint: disable=too-few-public-methods,too-many-instance-attr
         heterogeneous_ice_nucleation_rate: str = "Null",
         fragmentation_function: str = "AlwaysN",
         isotope_equilibrium_fractionation_factors: str = "Null",
+        isotope_kinetic_fractionation_factors: str = "Null",
         isotope_meteoric_water_line: str = "Null",
         isotope_ratio_evolution: str = "Null",
         isotope_diffusivity_ratios: str = "Null",
@@ -88,6 +89,9 @@ class Formulae:  # pylint: disable=too-few-public-methods,too-many-instance-attr
         self.isotope_equilibrium_fractionation_factors = (
             isotope_equilibrium_fractionation_factors
         )
+        self.isotope_kinetic_fractionation_factors = (
+            isotope_kinetic_fractionation_factors
+        )
         self.isotope_meteoric_water_line = isotope_meteoric_water_line
         self.isotope_ratio_evolution = isotope_ratio_evolution
         self.isotope_diffusivity_ratios = isotope_diffusivity_ratios

{pysdm-2.110 → pysdm-2.111}/PySDM/particulator.py

@@ -506,7 +506,7 @@ class Particulator:  # pylint: disable=too-many-public-methods,too-many-instance
             predicted_dry_potential_temperature=self.environment.get_predicted("thd"),
         )
         self.attributes.mark_updated("signed water mass")
-        # TODO #1389 - should we update here?
+        # TODO #1524 - should we update here?
         # self.update_TpRH(only_if_not_last='VapourDepositionOnIce')
 
     def immersion_freezing_time_dependent(

{pysdm-2.110 → pysdm-2.111}/PySDM/physics/__init__.py

@@ -31,6 +31,7 @@ from . import (
     hygroscopicity,
     impl,
     isotope_equilibrium_fractionation_factors,
+    isotope_kinetic_fractionation_factors,
     isotope_meteoric_water_line,
     isotope_ratio_evolution,
     isotope_diffusivity_ratios,

pysdm-2.111/PySDM/physics/isotope_kinetic_fractionation_factors/__init__.py

@@ -0,0 +1,7 @@
+"""
+kinetic fractionation factors for water isotopologues
+"""
+
+from PySDM.impl.null_physics_class import Null
+from .jouzel_and_merlivat_1984 import JouzelAndMerlivat1984
+from .craig_gordon import CraigGordon

pysdm-2.111/PySDM/physics/isotope_kinetic_fractionation_factors/craig_gordon.py

@@ -0,0 +1,17 @@
+"""
+kinetic fractionation factor in the framework of the Craig-Gordon model
+as given in eq. 1.5 in
+[Rozanski_et_al_2001 (UNESCO, ed. Mook)
+](https://web.archive.org/web/20160322221332/https://hydrology.nl/images/docs/ihp/Mook_III.pdf)
+and as used in [Pierchala et al. 2022](https://doi.org/10.1016/j.gca.2022.01.020)
+"""
+
+
+class CraigGordon:  # pylint: disable=too-few-public-methods
+    def __init__(self, _):
+        pass
+
+    @staticmethod
+    def alpha_kinetic(*, relative_humidity, turbulence_parameter_n, delta_diff, theta):
+        """delta_diff = 1 - heavy_to_light_diffusivity_ratio"""
+        return 1 + theta * turbulence_parameter_n * delta_diff * (1 - relative_humidity)

pysdm-2.111/PySDM/physics/isotope_kinetic_fractionation_factors/jouzel_and_merlivat_1984.py

@@ -0,0 +1,21 @@
+"""
+kinetic fractionation factor from [Jouzel & Merlivat 1984](https://doi.org/10.1029/JD089iD07p11749)
+(as eq. 3e for n=1 in [Stewart 1975](https://doi.org/10.1029/JC080i009p01133))
+"""
+
+
+class JouzelAndMerlivat1984:  # pylint: disable=too-few-public-methods
+    def __init__(self, _):
+        pass
+
+    @staticmethod
+    def alpha_kinetic(
+        alpha_equilibrium, relative_humidity, heavy_to_light_diffusivity_ratio
+    ):
+        """eq. (11) or eq. (14)"""
+        return relative_humidity / (
+            alpha_equilibrium
+            / heavy_to_light_diffusivity_ratio
+            * (relative_humidity - 1)
+            + 1
+        )

{pysdm-2.110 → pysdm-2.111}/PySDM/physics/particle_shape_and_density/mixed_phase_spheres.py

@@ -47,6 +47,6 @@ class MixedPhaseSpheres:
     @staticmethod
     def dm_dt(const, r, r_dr_dt):
         """
-        note: no ice phase support here yet! TODO #1389
+        note: no ice phase support here yet! TODO #1524
         """
         return 4 * const.PI * const.rho_w * r * r_dr_dt

{pysdm-2.110 → pysdm-2.111}/docs/bibliography.json

@@ -198,7 +198,8 @@
       "examples/PySDM_examples/Pierchala_et_al_2022/fig_3.ipynb",
       "examples/PySDM_examples/Pierchala_et_al_2022/fig_4.ipynb",
       "examples/PySDM_examples/Pierchala_et_al_2022/__init__.py",
-      "examples/PySDM_examples/Pierchala_et_al_2022/commons.py"
+      "examples/PySDM_examples/Pierchala_et_al_2022/commons.py",
+      "PySDM/physics/isotope_kinetic_fractionation_factors/craig_gordon.py"
     ],
     "label": "Pierchala et al. 2022 (Geochim. Cosmochim. Acta 322)",
     "title": "Quantification the diffusion-induced fractionation of <sup>1</sup>H<sub>2</sub><sup>17</sup>O isotopologue in air accompanying the process of water evaporation"
@@ -572,7 +573,8 @@
   },
   "https://doi.org/10.1029/JC080i009p01133": {
     "usages": [
-      "PySDM/physics/isotope_diffusivity_ratios/stewart_1975.py"
+      "PySDM/physics/isotope_diffusivity_ratios/stewart_1975.py",
+      "PySDM/physics/isotope_kinetic_fractionation_factors/jouzel_and_merlivat_1984.py"
     ],
     "label": "Stewart 1975 (J. Geophys. Res. Oceans 80)",
     "title": "Stable isotope fractionation due to evaporation and isotopic exchange of falling waterdrops: Applications to atmospheric processes and evaporation of lakes"
@@ -811,5 +813,27 @@
     ],
     "title": "The Growth of Cloud Drops in Uniformly Cooled Air",
     "label": "Howell 1949 (J. Atmos. Sci.)"
+  },
+  "https://doi.org/10.1029/JD089iD07p11749": {
+    "usages": [
+      "PySDM/physics/isotope_kinetic_fractionation_factors/jouzel_and_merlivat_1984.py",
+      "tests/unit_tests/physics/test_isotope_kinetic_fractionation_factors.py"
+    ],
+    "title": "Deuterium and oxygen 18 in precipitation: Modeling of the isotopic effects during snow formation",
+    "label": "Jouzel & Merlivat 1984 (J. Geophys. Res. Atmos. 89)"
+  },
+  "https://web.archive.org/web/20160322221332/https://hydrology.nl/images/docs/ihp/Mook_III.pdf": {
+    "usages": [
+      "PySDM/physics/isotope_kinetic_fractionation_factors/craig_gordon.py"
+    ],
+    "title": "Environmental isotopes in the hydrological cycle - Principles and applications: Vol III Surface water",
+    "label": "Rozanski_et_al_2001 (UNESCO, ed. Mook)"
+  },
+  "https://web.archive.org/web/20200729203147/https://nucleus.iaea.org/rpst/documents/VSMOW_SLAP.pdf": {
+    "usages": [
+      "PySDM/physics/constants_defaults.py"
+    ],
+    "title": "IAEA Reference Sheet for International Measurement Standards: VSMOW & SLAP",
+    "label": "IAEA 2006"
   }
 }

{pysdm-2.110 → pysdm-2.111}/docs/generate_html.py

@@ -68,6 +68,7 @@ def check_urls(urls_from_json):
                 r"\b(https://digitallibrary\.un\.org/record/(?:[0-9])+)\b",
                 r"\b(http://mi\.mathnet\.ru/dan(?:[0-9])+)\b",
                 r"\b(https://archive.org/details/(?:[0-9a-z_\.-])+)\b",
+                r"\b(https://web.archive.org/web/(?:[0-9])+/https://(?:[0-9a-zA-Z_\.-/])+)\b",
             ):
                 urls = re.findall(pattern, text)
                 if urls:

{pysdm-2.110 → pysdm-2.111}/examples/PySDM_examples/Abade_and_Albuquerque_2024/simulation.py

@@ -57,7 +57,7 @@ class Simulation(BasicSimulation):
         )
         del attributes["volume"]
 
-        # TODO #1389
+        # TODO #1524
         if settings.enable_immersion_freezing:
             attributes["freezing temperature"] = np.full(
                 shape=(settings.n_sd,), fill_value=250