PyPI - PySDM - Versions diffs - 3.0.0rc30__tar.gz → 3.0.0rc32__tar.gz - Mend

Files changed (1041) hide show

{pysdm-3.0.0rc30 → pysdm-3.0.0rc32}/docs/markdown/pysdm_landing.md RENAMED Viewed

@@ -155,8 +155,7 @@ ParticleVolumeVersusRadiusLogarithmSpectrum = pyimport("PySDM.products").Particl
 radius_bins_edges = 10 .^ range(log10(10*si.um), log10(5e3*si.um), length=32)
 env = Box(dt=1 * si.s, dv=1e6 * si.m^3)
-builder = Builder(n_sd=n_sd, backend=CPU(), environment=env)
-builder.add_dynamic(Coalescence(collision_kernel=Golovin(b=1.5e3 / si.s)))
+builder = Builder(n_sd=n_sd, backend=CPU(), environment=env, dynamics=(Coalescence(collision_kernel=Golovin(b=1.5e3 / si.s)),))
 products = [ParticleVolumeVersusRadiusLogarithmSpectrum(radius_bins_edges=radius_bins_edges, name="dv/dlnr")]
 particulator = builder.build(attributes, products)
 ```
@@ -175,8 +174,7 @@ ParticleVolumeVersusRadiusLogarithmSpectrum = py.importlib.import_module('PySDM.
 radius_bins_edges = logspace(log10(10 * si.um), log10(5e3 * si.um), 32);
 env = Box(pyargs('dt', 1 * si.s, 'dv', 1e6 * si.m ^ 3));
-builder = Builder(pyargs('n_sd', int32(n_sd), 'backend', CPU(), 'environment', env));
-builder.add_dynamic(Coalescence(pyargs('collision_kernel', Golovin(1.5e3 / si.s))));
+builder = Builder(pyargs('n_sd', int32(n_sd), 'backend', CPU(), 'environment', env, 'dynamics', py.tuple({Coalescence(pyargs('collision_kernel', Golovin(1.5e3 / si.s)))})));
 products = py.list({ ParticleVolumeVersusRadiusLogarithmSpectrum(pyargs( ...
   'radius_bins_edges', py.numpy.array(radius_bins_edges), ...
   'name', 'dv/dlnr' ...
@@ -199,8 +197,7 @@ from PySDM.products import ParticleVolumeVersusRadiusLogarithmSpectrum
 radius_bins_edges = np.logspace(np.log10(10 * si.um), np.log10(5e3 * si.um), num=32)
 env = Box(dt=1 * si.s, dv=1e6 * si.m ** 3)
-builder = Builder(n_sd=n_sd, backend=CPU(), environment=env)
-builder.add_dynamic(Coalescence(collision_kernel=Golovin(b=1.5e3 / si.s)))
+builder = Builder(n_sd=n_sd, backend=CPU(), environment=env, dynamics=(Coalescence(collision_kernel=Golovin(b=1.5e3 / si.s)),))
 products = [ParticleVolumeVersusRadiusLogarithmSpectrum(radius_bins_edges=radius_bins_edges, name='dv/dlnr')]
 particulator = builder.build(attributes, products)
 ```
@@ -302,12 +299,11 @@ The resultant plot (generated with the Python code) looks as follows:
 The component submodules used to create this simulation are visualized below:
 ```mermaid
  graph
-    COAL[":Coalescence"] --->|passed as arg to| BUILDER_ADD_DYN(["Builder.add_dynamic()"])
+    COAL[":Coalescence"] --->|passed as arg to| BUILDER_INIT(["Builder.__init__()"])
     BUILDER_INSTANCE["builder :Builder"] -...-|has a method| BUILDER_BUILD(["Builder.build()"])
     ATTRIBUTES[attributes: dict] -->|passed as arg to| BUILDER_BUILD
     N_SD["n_sd :int"] ---->|passed as arg to| BUILDER_INIT
     BUILDER_INIT(["Builder.__init__()"]) --->|instantiates| BUILDER_INSTANCE
-    BUILDER_INSTANCE -..-|has a method| BUILDER_ADD_DYN(["Builder.add_dynamic()"])
     ENV_INIT(["Box.__init__()"]) -->|instantiates| ENV
     DT[dt :float] -->|passed as arg to| ENV_INIT
     DV[dv :float] -->|passed as arg to| ENV_INIT
@@ -340,7 +336,6 @@ The component submodules used to create this simulation are visualized below:
     click COAL "https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision.html#Coalescence"
     click BUILDER_INSTANCE "https://open-atmos.github.io/PySDM/PySDM/builder.html"
     click BUILDER_INIT "https://open-atmos.github.io/PySDM/PySDM/builder.html"
-    click BUILDER_ADD_DYN "https://open-atmos.github.io/PySDM/PySDM/builder.html"
     click ENV_INIT "https://open-atmos.github.io/PySDM/PySDM/environments.html"
     click ENV "https://open-atmos.github.io/PySDM/PySDM/environments.html"
     click KERNEL_INIT "https://open-atmos.github.io/PySDM/PySDM/dynamics/collisions/collision_kernels.html"
@@ -410,9 +405,10 @@ output_points = 40
 n_sd = 256
 formulae = Formulae()
-builder = Builder(backend=CPU(formulae), n_sd=n_sd, environment=env)
-builder.add_dynamic(AmbientThermodynamics())
-builder.add_dynamic(Condensation())
+builder = Builder(backend=CPU(formulae), n_sd=n_sd, environment=env, dynamics=(
+    AmbientThermodynamics(),
+    Condensation(),
+))
 r_dry, specific_concentration = spectral_sampling.Logarithmic(spectrum).sample_deterministic(n_sd)
 v_dry = formulae.trivia.volume(radius=r_dry)
@@ -491,9 +487,12 @@ output_points = 40;
 n_sd = 256;
 formulae = Formulae();
-builder = Builder(pyargs('backend', CPU(formulae), 'n_sd', int32(n_sd), 'environment', env));
-builder.add_dynamic(AmbientThermodynamics());
-builder.add_dynamic(Condensation());
+builder = Builder(pyargs( ...
+    'backend', CPU(formulae), ...
+     'n_sd', int32(n_sd), ...
+      'environment', env, ...
+      'dynamics', py.tuple({AmbientThermodynamics(), Condensation()}) ...
+));
 tmp = spectral_sampling.Logarithmic(spectrum).sample_deterministic(int32(n_sd));
 r_dry = tmp{1};
@@ -592,9 +591,10 @@ output_points = 40
 n_sd = 256
 formulae = Formulae()
-builder = Builder(backend=CPU(formulae), n_sd=n_sd, environment=env)
-builder.add_dynamic(AmbientThermodynamics())
-builder.add_dynamic(Condensation())
+builder = Builder(backend=CPU(formulae), n_sd=n_sd, environment=env, dynamics=(
+    AmbientThermodynamics(),
+    Condensation(),
+))
 r_dry, specific_concentration = spectral_sampling.Logarithmic(spectrum).sample_deterministic(n_sd)
 v_dry = formulae.trivia.volume(radius=r_dry)

@@ -18,7 +18,7 @@ jobs:
       pull-requests: write
     steps:
-    - uses: actions/stale@v10.2.0
+    - uses: actions/stale@v10.3.0
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         stale-issue-message: 'Stale issue message'

@@ -185,7 +185,7 @@ jobs:
             test-suite: "tests/smoke_tests/parcel_d"
       fail-fast: true
     runs-on: ${{ matrix.platform }}
-    timeout-minutes: ${{ startsWith(matrix.platform, 'windows-') && 35 || 22 }}
+    timeout-minutes: ${{ startsWith(matrix.platform, 'windows-') && 35 || 25 }}
     steps:
       - uses: actions/checkout@v4.1.6
         with:
@@ -212,7 +212,8 @@ jobs:
         python-version: ["3.12"]
         test-suite:
           - "isotopes_chemistry_extraterrestrial"
-          - "coagulation_freezing"
+          - "homogeneous_freezing"
+          - "coagulation_immersion_freezing"
           - "condensation_a"
           - "condensation_b"
           - "condensation_c"
@@ -237,7 +238,12 @@ jobs:
             test-suite: "multi-process_d"
           - platform: "macos-14"
             test-suite: "multi-process_e"
-      fail-fast: true
+          # TODO #1870
+          - platform: "ubuntu-24.04"
+            test-suite: "homogeneous_freezing"
+          - platform: "windows-latest"
+            test-suite: "homogeneous_freezing"
+      fail-fast: false
     runs-on: ${{ matrix.platform }}
     timeout-minutes: ${{ startsWith(matrix.platform, 'windows-') && 35 || 30 }}
     steps:
@@ -288,7 +294,7 @@ jobs:
           python -m pytest ${{ env.pytest_options }} tests/examples_tests/test_tests_completeness.py
       - run: |
           python -m pip install pytest-timeout
-          python -m pytest ${{ env.pytest_options }} --basetemp=/tmp/pytest --timeout_method=thread --timeout=${{ startsWith(matrix.platform, 'windows-') && 1000 || 900 }} tests/examples_tests/test_run* --suite ${{ matrix.test-suite }}
+          python -m pytest ${{ env.pytest_options }} --basetemp=/tmp/pytest --timeout_method=thread --timeout=${{ startsWith(matrix.platform, 'windows-') && 1200 || 900 }} tests/examples_tests/test_run* --suite ${{ matrix.test-suite }}
       - if: ( ! startsWith(matrix.platform, 'windows-') ) && contains(matrix.test-suite, env.anim_test-suite) && matrix.python-version == env.anim_python-version
         run: |

@@ -76,11 +76,11 @@ jobs:
         with:
           release: R2024b
           cache: true
-      - uses: matlab-actions/run-command@v3.1.1
+      - uses: matlab-actions/run-command@v3.1.2
         with:
           command: tutorial_code
       - run: sed -i -e 's/CPU/GPU/g' tutorial_code.m
-      - uses: matlab-actions/run-command@v3.1.1
+      - uses: matlab-actions/run-command@v3.1.2
         with:
           command: tutorial_code

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pysdm
-Version: 3.0.0rc30
+Version: 3.0.0rc32
 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

@@ -83,7 +83,7 @@ def _condensation(
         RH_max=RH_max.data,
         success=success.data,
     )
-    particulator.attributes.mark_updated("water mass")
+    particulator.attributes.mark_updated("signed water mass")
 @lru_cache()

@@ -17,7 +17,7 @@ from PySDM.physics.particle_shape_and_density import LiquidSpheres, MixedPhaseSp
 class Builder:
-    def __init__(self, n_sd, backend, environment=None):
+    def __init__(self, n_sd, backend, environment=None, dynamics=None):
         assert not inspect.isclass(backend)
         self.formulae = backend.formulae
         self.particulator = Particulator(n_sd, backend)
@@ -26,11 +26,14 @@ class Builder:
         self.aerosol_radius_threshold = 0
         self.condensation_params = None
         self.particulator.environment = environment.instantiate(builder=self)
+        if dynamics is not None:
+            for dynamic in dynamics:
+                self._register_dynamic(dynamic)
     def _set_condensation_parameters(self, **kwargs):
         self.condensation_params = kwargs
-    def add_dynamic(self, dynamic):
+    def _register_dynamic(self, dynamic):
         assert self.particulator.environment is not None
         key = inspect.getmro(type(dynamic))[-2].__name__
         assert key not in self.particulator.dynamics

@@ -573,6 +573,7 @@ class Particulator:  # pylint: disable=too-many-public-methods,too-many-instance
             temperature=self.environment["T"],
             relative_humidity_ice=self.environment["RH_ice"],
         )
+        self.attributes.mark_updated("signed water mass")
     def homogeneous_freezing_threshold(self):
         self.backend.homogeneous_freezing_threshold(
@@ -583,6 +584,7 @@ class Particulator:  # pylint: disable=too-many-public-methods,too-many-instance
             temperature=self.environment["T"],
             relative_humidity_ice=self.environment["RH_ice"],
         )
+        self.attributes.mark_updated("signed water mass")
     def thaw_instantaneous(self):
         self.backend.thaw_instantaneous(
@@ -592,3 +594,4 @@ class Particulator:  # pylint: disable=too-many-public-methods,too-many-instance
             cell=self.attributes["cell id"],
             temperature=self.environment["T"],
         )
+        self.attributes.mark_updated("signed water mass")

@@ -356,6 +356,16 @@ KOOP_MURRAY_C5 = -1.71736e-4 / si.K**5
 KOOP_MURRAY_C6 = -7.46953e-7 / si.K**6
 """ 〃 """
+KOOP_MURRAY_DAW_C0 = -273.111686
+""" homogeneous ice nucleation rate for pure water droplets adapted
+for DAW ([Spichtinger et al. 2023](https://doi.org/10.5194/acp-23-2035-2023)) """
+KOOP_MURRAY_DAW_C1 = 1689.25134
+""" 〃 """
+KOOP_MURRAY_DAW_C2 = -2449.65042
+""" 〃 """
+KOOP_MURRAY_DAW_UNIT = 1 / si.m**3 / si.s
+""" 〃 """
 J_HET = np.nan
 J_HOM = np.nan
 """ constant ice nucleation rates """

@@ -7,3 +7,4 @@ from .null import Null
 from .koop import Koop2000
 from .koop_corr import Koop_Correction
 from .koop_murray import KoopMurray2016
+from .koop_murray_dwa_adaption import KoopMurray2016_DWA

@@ -0,0 +1,34 @@
+"""
+Koop and Murray homogeneous nucleation rate parameterization for pure water droplets
+adapted for water activity formulation
+ ([Spichtinger et al. 2023](https://doi.org/10.5194/acp-23-2035-2023))
+"""
+import numpy as np
+class KoopMurray2016_DWA:
+    def __init__(self, const):
+        pass
+    @staticmethod
+    def d_a_w_ice_within_range(const, da_w_ice):
+        return da_w_ice >= const.KOOP_MIN_DA_W_ICE
+    @staticmethod
+    def d_a_w_ice_maximum(const, da_w_ice):
+        return np.where(
+            da_w_ice > const.KOOP_MAX_DA_W_ICE, const.KOOP_MAX_DA_W_ICE, da_w_ice
+        )
+    @staticmethod
+    def j_hom(const, T, da_w_ice):  # pylint: disable=unused-argument
+        return (
+            10
+            ** (
+                const.KOOP_MURRAY_DAW_C0
+                + const.KOOP_MURRAY_DAW_C1 * da_w_ice
+                + const.KOOP_MURRAY_DAW_C2 * da_w_ice**2.0
+            )
+            * const.KOOP_MURRAY_DAW_UNIT
+        )

@@ -948,6 +948,7 @@
       "PySDM/physics/constants_defaults.py",
       "PySDM/physics/diffusion_ice_capacity/columnar.py",
       "PySDM/physics/homogeneous_ice_nucleation_rate/koop_corr.py",
+      "PySDM/physics/homogeneous_ice_nucleation_rate/koop_murray_dwa_adaption.py",
       "examples/PySDM_examples/Spichtinger_et_al_2023/__init__.py",
       "examples/PySDM_examples/Spichtinger_et_al_2023/data/reference_bulk.py",
       "examples/PySDM_examples/Spichtinger_et_al_2023/fig_B1.ipynb",
@@ -1014,14 +1015,22 @@
     "label": "Bartman 2020 (MSc thesis)",
     "title": "PySDM v1.0: Pythonic particle-based cloud microphysics package"
   },
-    "https://web.archive.org/web/20220629123450/https://web.gps.caltech.edu/~als/research-articles/other_stuff/hayes-2004-3.pdf" : {
+  "https://web.archive.org/web/20220629123450/https://web.gps.caltech.edu/~als/research-articles/other_stuff/hayes-2004-3.pdf" : {
     "usages": [
       "tests/unit_tests/physics/test_constants.py"
     ],
     "label": "Hayes 2004",
     "title": "An Introduction to Isotopic Calculations"
   },
-  "https://doi.org/10.1175/1520-0469%281974%29031%3C1040%3ASTTDCE%3E2.0.CO%3B2" : {
+  "https://doi.org/10.1039/c003297b": {
+    "usages": [
+      "examples/PySDM_examples/Murray_et_al_2010/fig_3.ipynb",
+      "examples/PySDM_examples/Murray_et_al_2010/__init__.py"
+    ],
+    "title": "Kinetics of the homogeneous freezing of water",
+    "label": "Murray et al. 2010 (Phys. Chem. Chem. Phys. 12)"
+  },
+  "https://doi.org/10.1175/1520-0469%281974%29031%3C1040%3ASTTDCE%3E2.0.CO%3B2": {
     "usages": [
       "PySDM/dynamics/collisions/collision_kernels/long1974.py",
       "examples/PySDM_examples/Long_1974/__init__.py",

PySDM 3.0.0rc30__tar.gz → 3.0.0rc32__tar.gz

PySDM 3.0.0rc30tar.gz → 3.0.0rc32tar.gz