PySDM 2.46__tar.gz → 2.47__tar.gz

{PySDM-2.46 → PySDM-2.47}/.github/workflows/cancel.yml

@@ -8,7 +8,7 @@ jobs:
   cancel:
     runs-on: ubuntu-latest
     steps:
-    - uses: styfle/cancel-workflow-action@0.9.1
+    - uses: styfle/cancel-workflow-action@0.12.1
       with:
         all_but_latest: true
         workflow_id: ${{ github.event.workflow.id }}

{PySDM-2.46 → PySDM-2.47}/.github/workflows/joss.yml

@@ -12,7 +12,7 @@ jobs:
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4.1.1
       - name: TeX and PDF
         uses: docker://openjournals/paperdraft:latest
         with:
@@ -21,7 +21,7 @@ jobs:
           GIT_SHA: $GITHUB_SHA
           JOURNAL: joss
       - name: Upload
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v4.3.1
         with:
           name: paper
           path: paper/

{PySDM-2.46 → PySDM-2.47}/.github/workflows/joss_paper.yml

@@ -16,10 +16,10 @@ jobs:
   python:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v1
+      - uses: actions/checkout@v4.1.1
+      - uses: actions/setup-python@v5.0.0
         with:
-          python-version: 3.9
+          python-version: 3.11
       - run: pip install -e .[tests]
       - run: pip install pytest-codeblocks pytest
 

{PySDM-2.46 → PySDM-2.47}/.github/workflows/readme_snippets.yml

@@ -16,8 +16,8 @@ jobs:
   python:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v1
+      - uses: actions/checkout@v4.1.1
+      - uses: actions/setup-python@v5.0.0
         with:
           python-version: 3.9
       - run: pip install -e .[tests]
@@ -39,14 +39,14 @@ jobs:
   julia:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v1
+      - uses: actions/checkout@v4.1.1
+      - uses: actions/setup-python@v5.0.0
         with:
           python-version: 3.9
       - run: pip install -e .
       - run: pip install pytest-codeblocks pytest
       - run: python -c "import pytest_codeblocks; code=pytest_codeblocks.extract_from_file('README.md'); f=open('readme.jl', 'w'); f.writelines(block.code for block in code if block.syntax=='Julia'); f.close()"
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v1.9.6
       - run: cat -n readme.jl
       - run: julia readme.jl
       - run: sed -i 's/CPU/GPU/g' readme.jl
@@ -55,22 +55,22 @@ jobs:
   matlab:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v1
+      - uses: actions/checkout@v4.1.1
+      - uses: actions/setup-python@v5.0.0
         with:
           python-version: 3.8
       - run: pip install -e .
       - run: pip install pytest-codeblocks pytest
       - run: python -c "import pytest_codeblocks; code=pytest_codeblocks.extract_from_file('README.md'); f=open('readme.m', 'w'); f.writelines(block.code for block in code if block.syntax=='Matlab'); f.close()"
       - run: cat -n readme.m
-      - uses: matlab-actions/setup-matlab@v0
+      - uses: matlab-actions/setup-matlab@v2.1.0
         with:
           release: R2021a
-      - uses: matlab-actions/run-command@v0
+      - uses: matlab-actions/run-command@v2.1.0
         with:
           command: readme
       - run: sed -i 's/CPU/GPU/g' readme.m
-      - uses: matlab-actions/run-command@v0
+      - uses: matlab-actions/run-command@v2.1.0
         with:
           command: readme
 

{PySDM-2.46 → PySDM-2.47}/.github/workflows/stale.yml

@@ -18,7 +18,7 @@ jobs:
       pull-requests: write
 
     steps:
-    - uses: actions/stale@v9
+    - uses: actions/stale@v9.0.0
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         stale-issue-message: 'Stale issue message'

{PySDM-2.46 → PySDM-2.47}/.github/workflows/tests+artifacts+pypi.yml

@@ -18,8 +18,8 @@ jobs:
   precommit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v1
+      - uses: actions/checkout@v4.1.1
+      - uses: actions/setup-python@v5.0.0
         with:
           python-version: 3.8
       - run: |
@@ -49,7 +49,7 @@ jobs:
         pip install pytest-cov
         pytest --durations=10 -We tests/unit_tests --cov-report=xml --cov=PySDM
     - if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v4.1.0
       with:
         fail_ci_if_error: true
         verbose: true
@@ -60,11 +60,11 @@ jobs:
         platform: [ubuntu-latest, macos-latest, windows-latest]
     runs-on: ${{ matrix.platform }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4.1.1
         with:
           submodules: recursive
           persist-credentials: false
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5.0.0
         with:
           python-version: 3.9
       - run: |
@@ -83,12 +83,12 @@ jobs:
   pylint:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4.1.1
       with:
         submodules: recursive
         fetch-depth: 0 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5.0.0
       with:
         python-version: 3.9
     - name: Install dependencies
@@ -113,7 +113,7 @@ jobs:
   zenodo_json:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4.1.1
       - uses: notiz-dev/github-action-json-property@release
         with: 
           path: '.zenodo.json'
@@ -131,13 +131,13 @@ jobs:
             python-version: "3.8"
       fail-fast: false
     runs-on: ${{ matrix.platform }}
-    timeout-minutes: 90
+    timeout-minutes: 100
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4.1.1
         with:
           submodules: recursive
           fetch-depth: 0
-      - uses: actions/setup-python@v1
+      - uses: actions/setup-python@v5.0.0
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -183,11 +183,11 @@ jobs:
       fail-fast: false
     runs-on: ${{ matrix.platform }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4.1.1
         with:
           submodules: recursive
           fetch-depth: 0
-      - uses: actions/setup-python@v1
+      - uses: actions/setup-python@v5.0.0
         with:
           python-version: ${{ matrix.python-version }}
       - run: |
@@ -220,7 +220,7 @@ jobs:
   devops:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4.1.1
         with:
           submodules: recursive
           fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
@@ -236,11 +236,11 @@ jobs:
       fail-fast: false
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4.1.1
         with:
           submodules: recursive
           fetch-depth: 0  # https://github.com/pypa/setuptools_scm/issues/480
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5.0.0
         with:
           python-version: "3.11"
 
@@ -253,7 +253,7 @@ jobs:
           exit `fgrep -i warning build.log | grep -v impl_numba/warnings.py | grep -v "no previously-included files matching" | wc -l`
           twine check --strict dist/*
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           path: ${{ matrix.packages-dir}}/dist
           name: dist
@@ -266,10 +266,10 @@ jobs:
     runs-on: ${{ matrix.platform }}
     needs: [package]
     steps:
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v5.0.0
         with:
           python-version: ${{ matrix.python-version }}
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v3
         with:
           name: dist
           path: dist     
@@ -283,7 +283,7 @@ jobs:
     permissions:
       id-token: write
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v3
         with:
           name: dist
           path: dist     

{PySDM-2.46 → PySDM-2.47}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.46
+Version: 2.47
 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-2.46 → PySDM-2.47}/PySDM/attributes/impl/mapper.py

@@ -29,6 +29,7 @@ from PySDM.attributes.physics import (
     Volume,
     WaterMass,
     WetToCriticalVolumeRatio,
+    ReynoldsNumber,
 )
 from PySDM.attributes.physics.critical_supersaturation import CriticalSupersaturation
 from PySDM.attributes.physics.dry_volume import (
@@ -45,6 +46,7 @@ from PySDM.attributes.physics.relative_fall_velocity import RelativeFallMomentum
 from PySDM.dynamics.impl.chemistry_utils import AQUEOUS_COMPOUNDS
 from PySDM.dynamics.isotopic_fractionation import HEAVY_ISOTOPES
 from PySDM.physics.surface_tension import Constant
+from PySDM.physics.ventilation import Neglect
 
 attributes = {
     "multiplicity": lambda _, __: Multiplicities,
@@ -116,6 +118,11 @@ attributes = {
     "moles_1H": lambda _, __: Moles1H,
     "moles_16O": lambda _, __: Moles16O,
     "moles light water": lambda _, __: MolesLightWater,
+    "Reynolds number": lambda _, formulae: (
+        make_dummy_attribute_factory("Reynolds number")
+        if formulae.ventilation.__name__ == Neglect.__name__
+        else ReynoldsNumber
+    ),
 }
 
 

{PySDM-2.46 → PySDM-2.47}/PySDM/attributes/physics/__init__.py

@@ -16,3 +16,4 @@ from .relative_fall_velocity import RelativeFallMomentum, RelativeFallVelocity
 from .temperature import Temperature
 from .terminal_velocity import TerminalVelocity
 from .volume import Volume
+from .reynolds_number import ReynoldsNumber

PySDM-2.47/PySDM/attributes/physics/reynolds_number.py

@@ -0,0 +1,27 @@
+"""
+particle Reynolds number
+"""
+
+from ..impl.derived_attribute import DerivedAttribute
+
+
+class ReynoldsNumber(DerivedAttribute):
+    def __init__(self, builder):
+        self.radius = builder.get_attribute("radius")
+        self.velocity_wrt_air = builder.get_attribute("relative fall velocity")
+        self.cell_id = builder.get_attribute("cell id")
+        super().__init__(
+            builder,
+            name="Reynolds number",
+            dependencies=(self.radius, self.velocity_wrt_air, self.cell_id),
+        )
+
+    def recalculate(self):
+        self.particulator.backend.reynolds_number(
+            output=self.data,
+            cell_id=self.cell_id.get(),
+            dynamic_viscosity=self.particulator.environment["air dynamic viscosity"],
+            density=self.particulator.environment["air density"],
+            radius=self.radius.data,
+            velocity_wrt_air=self.velocity_wrt_air.data,
+        )

{PySDM-2.46 → PySDM-2.47}/PySDM/backends/impl_numba/methods/condensation_methods.py

@@ -20,7 +20,15 @@ _Counters = namedtuple(
 )
 _Attributes = namedtuple(
     typename="_Attributes",
-    field_names=("water_mass", "v_cr", "multiplicity", "vdry", "kappa", "f_org"),
+    field_names=(
+        "water_mass",
+        "v_cr",
+        "multiplicity",
+        "vdry",
+        "kappa",
+        "f_org",
+        "reynolds_number",
+    ),
 )
 _CellData = namedtuple(
     typename="_CellData",
@@ -32,6 +40,8 @@ _CellData = namedtuple(
         "prhod",
         "pthd",
         "predicted_water_vapour_mixing_ratio",
+        "air_density",
+        "air_dynamic_viscosity",
     ),
 )
 _RelativeTolerances = namedtuple(
@@ -56,6 +66,7 @@ class CondensationMethods(BackendMethods):
                 vdry=kwargs["vdry"].data,
                 kappa=kwargs["kappa"].data,
                 f_org=kwargs["f_org"].data,
+                reynolds_number=kwargs["reynolds_number"].data,
             ),
             idx=kwargs["idx"].data,
             cell_data=_CellData(
@@ -68,6 +79,8 @@ class CondensationMethods(BackendMethods):
                 predicted_water_vapour_mixing_ratio=(
                     kwargs["predicted_water_vapour_mixing_ratio"].data
                 ),
+                air_density=kwargs["air_density"].data,
+                air_dynamic_viscosity=kwargs["air_dynamic_viscosity"].data,
             ),
             rtols=_RelativeTolerances(
                 x=kwargs["rtol_x"],
@@ -154,6 +167,8 @@ class CondensationMethods(BackendMethods):
                         / 2
                         * cell_data.dv_mean
                     ),
+                    air_density=cell_data.air_density[cell_id],
+                    air_dynamic_viscosity=cell_data.air_dynamic_viscosity[cell_id],
                     rtols=rtols,
                     timestep=timestep,
                     n_substeps=counters.n_substeps[cell_id],
@@ -249,6 +264,8 @@ class CondensationMethods(BackendMethods):
             d_water_vapour_mixing_ratio__dt_predicted,
             drhod_dt,
             m_d,
+            air_density,
+            air_dynamic_viscosity,
             rtol_x,
             timestep,
             n_substeps,
@@ -277,7 +294,13 @@ class CondensationMethods(BackendMethods):
                 pvs = formulae.saturation_vapour_pressure__pvs_Celsius(
                     T - formulae.constants.T0
                 )
+                DTp = formulae.diffusion_thermics__D(T, p)
                 RH = pv / pvs
+                Sc = formulae.trivia__air_schmidt_number(
+                    dynamic_viscosity=air_dynamic_viscosity,
+                    diffusivity=DTp,
+                    density=air_density,
+                )
                 (
                     ml_new,
                     success_within_substep,
@@ -291,10 +314,11 @@ class CondensationMethods(BackendMethods):
                     T,
                     p,
                     RH,
+                    Sc,
                     cell_idx,
                     lv,
                     pvs,
-                    formulae.diffusion_thermics__D(T, p),
+                    DTp,
                     formulae.diffusion_thermics__K(T, p),
                     rtol_x,
                 )
@@ -353,8 +377,20 @@ class CondensationMethods(BackendMethods):
         RH_rtol,
     ):
         @numba.njit(**jit_flags)
-        def minfun(  # pylint: disable=too-many-arguments
-            x_new, x_old, timestep, kappa, f_org, rd3, temperature, RH, lv, pvs, D, K
+        def minfun(  # pylint: disable=too-many-arguments,too-many-locals
+            x_new,
+            x_old,
+            timestep,
+            kappa,
+            f_org,
+            rd3,
+            temperature,
+            RH,
+            lv,
+            pvs,
+            D,
+            K,
+            ventilation_factor,
         ):
             volume = formulae.condensation_coordinate__volume(x_new)
             RH_eq = formulae.hygroscopicity__RH_eq(
@@ -367,7 +403,14 @@ class CondensationMethods(BackendMethods):
                 ),
             )
             r_dr_dt = formulae.drop_growth__r_dr_dt(
-                RH_eq, temperature, RH, lv, pvs, D, K
+                RH_eq,
+                temperature,
+                RH,
+                lv,
+                pvs,
+                D,
+                K,
+                ventilation_factor,
             )
             return (
                 x_old
@@ -383,6 +426,7 @@ class CondensationMethods(BackendMethods):
             T,
             p,
             RH,
+            Sc,
             cell_idx,
             lv,
             pvs,
@@ -420,6 +464,12 @@ class CondensationMethods(BackendMethods):
                 ):
                     Dr = formulae.diffusion_kinetics__D(DTp, r_old, lambdaD)
                     Kr = formulae.diffusion_kinetics__K(KTp, r_old, lambdaK)
+                    ventilation_factor = formulae.ventilation__ventilation_coefficient(
+                        sqrt_re_times_cbrt_sc=formulae.trivia__sqrt_re_times_cbrt_sc(
+                            Re=attributes.reynolds_number[drop],
+                            Sc=Sc,
+                        )
+                    )
                     args = (
                         x_old,
                         timestep,
@@ -432,9 +482,17 @@ class CondensationMethods(BackendMethods):
                         pvs,
                         Dr,
                         Kr,
+                        ventilation_factor,
                     )
                     r_dr_dt_old = formulae.drop_growth__r_dr_dt(
-                        RH_eq, T, RH, lv, pvs, Dr, Kr
+                        RH_eq,
+                        T,
+                        RH,
+                        lv,
+                        pvs,
+                        Dr,
+                        Kr,
+                        ventilation_factor,
                     )
                     dx_old = timestep * formulae.condensation_coordinate__dx_dt(
                         x_old, r_dr_dt_old
@@ -601,6 +659,8 @@ class CondensationMethods(BackendMethods):
             d_water_vapour_mixing_ratio__dt,
             drhod_dt,
             m_d,
+            air_density,
+            air_dynamic_viscosity,
             rtols,
             timestep,
             n_substeps,
@@ -615,6 +675,8 @@ class CondensationMethods(BackendMethods):
                 d_water_vapour_mixing_ratio__dt,
                 drhod_dt,
                 m_d,
+                air_density,
+                air_dynamic_viscosity,
                 rtols.x,
             )
             success = True

{PySDM-2.46 → PySDM-2.47}/PySDM/backends/impl_numba/methods/physics_methods.py

@@ -2,6 +2,8 @@
 CPU implementation of backend methods wrapping basic physics formulae
 """
 
+from functools import cached_property
+
 import numba
 from numba import prange
 
@@ -125,3 +127,70 @@ class PhysicsMethods(BackendMethods):
 
     def mass_of_water_volume(self, mass, volume):
         self.mass_of_volume_body(mass.data, volume.data)
+
+    @cached_property
+    def __air_density_body(self):
+        formulae = self.formulae.flatten
+
+        @numba.njit(**{**conf.JIT_FLAGS, "fastmath": formulae.fastmath})
+        def body(output, rhod, water_vapour_mixing_ratio):
+            for i in numba.prange(output.shape[0]):  # pylint: disable=not-an-iterable
+                output[i] = (
+                    formulae.state_variable_triplet__rho_of_rhod_and_water_vapour_mixing_ratio(
+                        rhod[i], water_vapour_mixing_ratio[i]
+                    )
+                )
+
+        return body
+
+    def air_density(self, *, output, rhod, water_vapour_mixing_ratio):
+        self.__air_density_body(output.data, rhod.data, water_vapour_mixing_ratio.data)
+
+    @cached_property
+    def __air_dynamic_viscosity_body(self):
+        formulae = self.formulae.flatten
+
+        @numba.njit(**{**conf.JIT_FLAGS, "fastmath": formulae.fastmath})
+        def body(output, temperature):
+            for i in numba.prange(output.shape[0]):  # pylint: disable=not-an-iterable
+                output[i] = formulae.air_dynamic_viscosity__eta_air(temperature[i])
+
+        return body
+
+    def air_dynamic_viscosity(self, *, output, temperature):
+        self.__air_dynamic_viscosity_body(output.data, temperature.data)
+
+    @cached_property
+    def __reynolds_number_body(self):
+        formulae = self.formulae.flatten
+
+        @numba.njit(**{**conf.JIT_FLAGS, "fastmath": formulae.fastmath})
+        def body(  # pylint: disable=too-many-arguments
+            output,
+            cell_id,
+            air_dynamic_viscosity,
+            air_density,
+            radius,
+            velocity_wrt_air,
+        ):
+            for i in numba.prange(output.shape[0]):  # pylint: disable=not-an-iterable
+                output[i] = formulae.particle_shape_and_density__reynolds_number(
+                    radius=radius[i],
+                    velocity_wrt_air=velocity_wrt_air[i],
+                    dynamic_viscosity=air_dynamic_viscosity[cell_id[i]],
+                    density=air_density[cell_id[i]],
+                )
+
+        return body
+
+    def reynolds_number(
+        self, *, output, cell_id, dynamic_viscosity, density, radius, velocity_wrt_air
+    ):
+        self.__reynolds_number_body(
+            output.data,
+            cell_id.data,
+            dynamic_viscosity.data,
+            density.data,
+            radius.data,
+            velocity_wrt_air.data,
+        )