PySDM-examples 3.0.0rc28__tar.gz → 3.0.0rc30__tar.gz

{pysdm_examples-3.0.0rc28 → pysdm_examples-3.0.0rc30}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pysdm-examples
-Version: 3.0.0rc28
+Version: 3.0.0rc30
 Summary: PySDM usage examples reproducing results from literature and depicting how to use PySDM from Python Jupyter notebooks
 Home-page: https://github.com/open-atmos/PySDM
 Author: https://github.com/open-atmos/PySDM/graphs/contributors
@@ -23,6 +23,7 @@ Requires-Dist: vtk
 Requires-Dist: pyrcel
 Requires-Dist: pyvinecopulib
 Requires-Dist: networkx
+Requires-Dist: PyVista
 Provides-Extra: ci-version-pins
 Requires-Dist: PySDM[CI_version_pins]; extra == "ci-version-pins"
 Requires-Dist: PyMPDATA==1.7.1; extra == "ci-version-pins"
@@ -35,7 +36,7 @@ Requires-Dist: seaborn==0.13.2; extra == "ci-version-pins"
 Requires-Dist: numdifftools==0.9.42; extra == "ci-version-pins"
 Requires-Dist: vtk==9.6.1; extra == "ci-version-pins"
 Requires-Dist: pyrcel==1.3.4; extra == "ci-version-pins"
-Requires-Dist: pyvinecopulib==0.7.3; extra == "ci-version-pins"
+Requires-Dist: pyvinecopulib==0.7.6; extra == "ci-version-pins"
 Dynamic: author
 Dynamic: author-email
 Dynamic: description

pysdm_examples-3.0.0rc30/PySDM_examples/Arabas_and_Pawlowska_2011/__init__.py

@@ -0,0 +1,14 @@
+# pylint: disable=invalid-name
+"""
+condensation example using parcel environment based on
+[Arabas Pawlowska 2011 (GMD)](https://doi.org/10.5194/gmd-4-15-2011)
+
+fig_1.ipynb:
+.. include:: ./fig_1.ipynb.badges.md
+
+fig_2.ipynb:
+.. include:: ./fig_2.ipynb.badges.md
+"""
+
+from .simulation import Simulation
+from .settings import Settings

pysdm_examples-3.0.0rc30/PySDM_examples/Arabas_and_Pawlowska_2011/settings.py

@@ -0,0 +1,66 @@
+from PySDM import Formulae
+from PySDM.physics import si
+from PySDM.initialisation.spectra import Lognormal, Sum
+
+
+class Settings:
+    def __init__(self):
+        self.dt = 0.25 * si.s
+        self.mass_of_dry_air = 1000 * si.kg
+        self.p0 = 1000 * si.hPa
+        self.RH0 = 0.99 * si.dimensionless
+        self.T0 = 280 * si.K
+        self.w = 0.25 * si.m / si.s
+
+        self.initial_air_density = 1.245 * si.kg / si.m**3
+
+        self.output_interval = 4
+        self.output_points = 250
+        self.n_sd = 1024
+
+        self.formulae = Formulae()
+
+        self.cloud_range = (1 * si.um, 25 * si.um)
+
+        self.kappa_sea_salt = 1.28 * si.dimensionless
+        self.kappa_sulphate = 0.61 * si.dimensionless
+
+        sea_salt_spectrum = Sum(
+            (
+                Lognormal(
+                    norm_factor=51.1 / si.cm**3,
+                    m_mode=0.10 * si.um,
+                    s_geom=1.90,
+                ),
+                Lognormal(
+                    norm_factor=2.21 / si.cm**3,
+                    m_mode=1.00 * si.um,
+                    s_geom=2.00,
+                ),
+                Lognormal(
+                    norm_factor=1e-5 / si.cm**3,
+                    m_mode=6.00 * si.um,
+                    s_geom=3.00,
+                ),
+            )
+        )
+
+        sulphate_spectrum = Lognormal(
+            norm_factor=100 / si.cm**3,
+            m_mode=0.08 * si.um,
+            s_geom=1.45,
+        )
+
+        self.total_aerosol_concentration = (
+            sea_salt_spectrum.norm_factor + sulphate_spectrum.norm_factor
+        )
+
+        self.aerosol_modes_by_kappa = {
+            self.kappa_sea_salt: sea_salt_spectrum,
+            self.kappa_sulphate: sulphate_spectrum,
+        }
+
+        self.aerosol_mode_names = (
+            "sea salt",
+            "sulphate",
+        )

pysdm_examples-3.0.0rc30/PySDM_examples/Arabas_and_Pawlowska_2011/simulation.py

@@ -0,0 +1,156 @@
+import numpy as np
+
+from PySDM_examples.utils.basic_simulation import BasicSimulation
+
+from PySDM import Builder, products
+from PySDM.backends import CPU
+from PySDM.dynamics import AmbientThermodynamics, Condensation
+from PySDM.environments import Parcel
+from PySDM.initialisation import discretise_multiplicities
+from PySDM.initialisation.hygroscopic_equilibrium import equilibrate_wet_radii
+from PySDM.initialisation.sampling import spectral_sampling
+
+
+class Simulation(BasicSimulation):
+    def __init__(
+        self,
+        settings,
+        product_list=None,
+    ):
+        self.settings = settings
+
+        environment = Parcel(
+            dt=settings.dt,
+            mass_of_dry_air=settings.mass_of_dry_air,
+            p0=settings.p0,
+            initial_relative_humidity=settings.RH0,
+            T0=settings.T0,
+            w=settings.w,
+        )
+
+        builder = Builder(
+            backend=CPU(settings.formulae),
+            n_sd=settings.n_sd,
+            environment=environment,
+        )
+
+        builder.add_dynamic(AmbientThermodynamics())
+        builder.add_dynamic(Condensation())
+
+        builder.request_attribute("radius")
+
+        self.builder = builder
+
+        attributes, self.mode_id = self._make_attributes()
+
+        if product_list is None:
+            product_list = (
+                products.AmbientRelativeHumidity(name="RH"),
+                products.Time(name="time"),
+                products.AmbientTemperature(name="T"),
+            )
+
+        particulator = builder.build(
+            attributes=attributes,
+            products=product_list,
+        )
+
+        super().__init__(
+            particulator=particulator,
+            output_attributes=["radius"],
+        )
+
+    def _make_attributes(self):
+        settings = self.settings
+        formulae = settings.formulae
+        environment = self.builder.particulator.environment
+
+        parcel_volume = environment.mass_of_dry_air / settings.initial_air_density
+
+        n_components = len(settings.aerosol_modes_by_kappa)
+
+        if settings.n_sd % n_components != 0:
+            raise ValueError(
+                f"settings.n_sd={settings.n_sd} must be divisible by "
+                f"n_components={n_components}"
+            )
+
+        n_sd_per_component = settings.n_sd // n_components
+
+        dry_volume_parts = []
+        kappa_vdry_parts = []
+        multiplicity_parts = []
+        mode_id_parts = []
+
+        for component_id, (kappa, spectrum) in enumerate(
+            settings.aerosol_modes_by_kappa.items()
+        ):
+            r_dry, concentration = spectral_sampling.Logarithmic(
+                spectrum=spectrum
+            ).sample_deterministic(n_sd_per_component)
+
+            v_dry = formulae.trivia.volume(radius=r_dry)
+
+            dry_volume_parts.append(v_dry)
+            kappa_vdry_parts.append(kappa * v_dry)
+
+            multiplicity_parts.append(
+                discretise_multiplicities(concentration * parcel_volume)
+            )
+
+            mode_id_parts.append(
+                np.full(n_sd_per_component, component_id, dtype=np.int64)
+            )
+
+        dry_volume = np.concatenate(dry_volume_parts)
+        kappa_times_dry_volume = np.concatenate(kappa_vdry_parts)
+        multiplicity = np.concatenate(multiplicity_parts)
+        mode_id = np.concatenate(mode_id_parts)
+
+        r_wet = equilibrate_wet_radii(
+            r_dry=formulae.trivia.radius(volume=dry_volume),
+            environment=environment,
+            kappa_times_dry_volume=kappa_times_dry_volume,
+        )
+
+        attributes = {
+            "multiplicity": multiplicity,
+            "dry volume": dry_volume,
+            "kappa times dry volume": kappa_times_dry_volume,
+            "volume": formulae.trivia.volume(radius=r_wet),
+        }
+
+        self._sanity_check_attributes(attributes, mode_id, parcel_volume)
+
+        return attributes, mode_id
+
+    def _sanity_check_attributes(self, attributes, mode_id, volume):
+        for attribute in attributes.values():
+            assert attribute.shape[0] == self.settings.n_sd
+
+        assert mode_id.shape[0] == self.settings.n_sd
+
+        assert np.all(attributes["multiplicity"] > 0)
+        assert np.all(attributes["dry volume"] > 0)
+        assert np.all(attributes["volume"] >= attributes["dry volume"])
+
+        kappa_eff = attributes["kappa times dry volume"] / attributes["dry volume"]
+
+        for component_id, kappa in enumerate(
+            self.settings.aerosol_modes_by_kappa.keys()
+        ):
+            mask = mode_id == component_id
+            assert np.any(mask)
+            assert np.allclose(kappa_eff[mask], kappa)
+
+        np.testing.assert_allclose(
+            np.sum(attributes["multiplicity"]) / volume,
+            self.settings.total_aerosol_concentration,
+            rtol=1e-2,
+        )
+
+    def run(self):
+        return self._run(
+            nt=self.settings.output_interval * self.settings.output_points,
+            steps_per_output_interval=self.settings.output_interval,
+        )

{pysdm_examples-3.0.0rc28 → pysdm_examples-3.0.0rc30}/PySDM_examples/Grabowski_and_Pawlowska_2023/settings.py

@@ -55,21 +55,26 @@ class Settings:
             },
         }[aerosol]
 
-        const = self.formulae.constants
         self.vertical_velocity = vertical_velocity
         self.initial_pressure = initial_pressure
         self.initial_temperature = initial_temperature
-        pv0 = (
-            initial_relative_humidity
-            * self.formulae.saturation_vapour_pressure.pvs_water(initial_temperature)
-        )
-        self.initial_vapour_mixing_ratio = const.eps * pv0 / (initial_pressure - pv0)
+        self.initial_relative_humidity = initial_relative_humidity
         self.t_max = displacement / vertical_velocity
         self.timestep = dt
         self.output_interval = self.timestep
         self.rtol_thd = rtol_thd
         self.rtol_x = rtol_x
 
+        self.initial_vapour_mixing_ratio = (
+            self.formulae.trivia.water_vapour_mixing_ratio(
+                self.initial_pressure,
+                self.initial_relative_humidity,
+                self.formulae.saturation_vapour_pressure.pvs_water(
+                    self.initial_temperature
+                ),
+            )
+        )
+
     @property
     def initial_air_density(self):
         const = self.formulae.constants

{pysdm_examples-3.0.0rc28 → pysdm_examples-3.0.0rc30}/PySDM_examples/Grabowski_and_Pawlowska_2023/simulation.py

@@ -26,7 +26,7 @@ class Simulation(BasicSimulation):
             environment=Parcel(
                 dt=settings.timestep,
                 p0=settings.initial_pressure,
-                initial_water_vapour_mixing_ratio=settings.initial_vapour_mixing_ratio,
+                initial_relative_humidity=settings.initial_relative_humidity,
                 T0=settings.initial_temperature,
                 w=settings.vertical_velocity,
                 mass_of_dry_air=44 * si.kg,

{pysdm_examples-3.0.0rc28 → pysdm_examples-3.0.0rc30}/PySDM_examples/Jensen_and_Nugent_2017/simulation.py

@@ -28,24 +28,20 @@ class Simulation(BasicSimulation):
         gccn: bool = False,
         gravitational_coalsecence: bool = False,
     ):
-        const = settings.formulae.constants
-        pvs_water = settings.formulae.saturation_vapour_pressure.pvs_water
-        initial_water_vapour_mixing_ratio = const.eps / (
-            settings.p0 / settings.RH0 / pvs_water(settings.T0) - 1
-        )
 
         n_gccn = np.count_nonzero(table_3.NA) if gccn else 0
 
         builder = Builder(
             n_sd=N_SD_NON_GCCN + n_gccn,
             backend=CPU(
-                formulae=settings.formulae, override_jit_flags={"parallel": False}
+                formulae=settings.formulae,
+                override_jit_flags={"parallel": False},
             ),
             environment=Parcel(
                 dt=settings.dt,
                 mass_of_dry_air=666 * si.kg,
                 p0=settings.p0,
-                initial_water_vapour_mixing_ratio=initial_water_vapour_mixing_ratio,
+                initial_relative_humidity=settings.RH0,
                 T0=settings.T0,
                 w=settings.vertical_velocity,
                 z0=settings.z0,
@@ -77,7 +73,12 @@ class Simulation(BasicSimulation):
             )  # TODO #1266: check which temp, pres, RH assumed in the paper for NA???
 
         pd0 = settings.formulae.trivia.p_d(
-            settings.p0, initial_water_vapour_mixing_ratio
+            settings.p0,
+            settings.formulae.trivia.water_vapour_mixing_ratio(
+                settings.p0,
+                settings.RH0,
+                settings.formulae.saturation_vapour_pressure.pvs_water(settings.T0),
+            ),
         )
         rhod0 = settings.formulae.state_variable_triplet.rhod_of_pd_T(pd0, settings.T0)
 

{pysdm_examples-3.0.0rc28 → pysdm_examples-3.0.0rc30}/PySDM_examples/Pyrcel/simulation.py

@@ -15,11 +15,13 @@ class Simulation(BasicSimulation):
     def __init__(
         self,
         settings,
+        *,
         products=None,
         scipy_solver=False,
         rtol_thd=1e-10,
         rtol_x=1e-10,
         mass_of_dry_air=44 * si.kg,
+        additional_attributes=None,
     ):
         n_sd = sum(settings.n_sd_per_mode)
         builder = Builder(
@@ -36,6 +38,9 @@ class Simulation(BasicSimulation):
                 mass_of_dry_air=mass_of_dry_air,
             ),
         )
+        if additional_attributes is not None:
+            for attribute in additional_attributes:
+                builder.request_attribute(attribute)
         builder.add_dynamic(AmbientThermodynamics())
         builder.add_dynamic(Condensation(rtol_thd=rtol_thd, rtol_x=rtol_x))
 
@@ -74,7 +79,9 @@ class Simulation(BasicSimulation):
             scipy_ode_condensation_solver.patch_particulator(self.particulator)
 
         self.output_attributes = {
-            "volume": tuple([] for _ in range(self.particulator.n_sd))
+            attr: tuple([] for _ in range(self.particulator.n_sd))
+            for attr in ["volume"]
+            + (list(additional_attributes) if additional_attributes is not None else [])
         }
         self.settings = settings
 

{pysdm_examples-3.0.0rc28 → pysdm_examples-3.0.0rc30}/PySDM_examples/Strzabala_2025_BEng/__init__.py

@@ -4,5 +4,5 @@ ParaView visualisation of a parcel-model example based on the test case from
 [Pyrcel package docs](https://pyrcel.readthedocs.io/)
 
 paraview_parcel_model.ipynb:
-.. include:: ./paraview.ipynb.badges.md
+.. include:: ./pyvista_animation.ipynb.badges.md
 """

{pysdm_examples-3.0.0rc28 → pysdm_examples-3.0.0rc30}/PySDM_examples/Yang_et_al_2018/simulation.py

@@ -26,13 +26,7 @@ class Simulation:
             dt=dt_output / self.n_substeps,
             mass_of_dry_air=settings.mass_of_dry_air,
             p0=settings.p0,
-            initial_water_vapour_mixing_ratio=self.formulae.constants.eps
-            / (
-                settings.p0
-                / settings.RH0
-                / self.formulae.saturation_vapour_pressure.pvs_water(settings.T0)
-                - 1
-            ),
+            initial_relative_humidity=settings.RH0,
             T0=settings.T0,
             w=settings.w,
             z0=settings.z0,

{pysdm_examples-3.0.0rc28 → pysdm_examples-3.0.0rc30}/PySDM_examples/utils/basic_simulation.py

@@ -2,8 +2,11 @@ import numpy as np
 
 
 class BasicSimulation:
-    def __init__(self, particulator):
+    def __init__(self, particulator, output_attributes=None):
+        for k in output_attributes or []:
+            assert k in particulator.attributes
         self.particulator = particulator
+        self.output_attributes = output_attributes
 
     def _save(self, output):
         for k, v in self.particulator.products.items():
@@ -11,11 +14,15 @@ class BasicSimulation:
             if isinstance(value, np.ndarray) and value.shape[0] == 1:
                 value = value[0]
             output[k].append(value)
+        for k in self.output_attributes or []:
+            value = self.particulator.attributes[k].to_ndarray()
+            output[k].append(value)
 
     def _run(self, nt, steps_per_output_interval):
         output = {k: [] for k in self.particulator.products}
+        output |= {k: [] for k in self.output_attributes or []}
         self._save(output)
         for _ in range(0, nt + 1, steps_per_output_interval):
             self.particulator.run(steps=steps_per_output_interval)
             self._save(output)
-        return output
+        return {k: np.asarray(v) for k, v in output.items()}

{pysdm_examples-3.0.0rc28 → pysdm_examples-3.0.0rc30}/pysdm_examples.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pysdm-examples
-Version: 3.0.0rc28
+Version: 3.0.0rc30
 Summary: PySDM usage examples reproducing results from literature and depicting how to use PySDM from Python Jupyter notebooks
 Home-page: https://github.com/open-atmos/PySDM
 Author: https://github.com/open-atmos/PySDM/graphs/contributors
@@ -23,6 +23,7 @@ Requires-Dist: vtk
 Requires-Dist: pyrcel
 Requires-Dist: pyvinecopulib
 Requires-Dist: networkx
+Requires-Dist: PyVista
 Provides-Extra: ci-version-pins
 Requires-Dist: PySDM[CI_version_pins]; extra == "ci-version-pins"
 Requires-Dist: PyMPDATA==1.7.1; extra == "ci-version-pins"
@@ -35,7 +36,7 @@ Requires-Dist: seaborn==0.13.2; extra == "ci-version-pins"
 Requires-Dist: numdifftools==0.9.42; extra == "ci-version-pins"
 Requires-Dist: vtk==9.6.1; extra == "ci-version-pins"
 Requires-Dist: pyrcel==1.3.4; extra == "ci-version-pins"
-Requires-Dist: pyvinecopulib==0.7.3; extra == "ci-version-pins"
+Requires-Dist: pyvinecopulib==0.7.6; extra == "ci-version-pins"
 Dynamic: author
 Dynamic: author-email
 Dynamic: description

{pysdm_examples-3.0.0rc28 → pysdm_examples-3.0.0rc30}/pysdm_examples.egg-info/SOURCES.txt

@@ -16,6 +16,9 @@ PySDM_examples/Alpert_and_Knopf_2016/simulation.py
 PySDM_examples/Alpert_and_Knopf_2016/table.py
 PySDM_examples/Alpert_and_Knopf_2016/table_1.py
 PySDM_examples/Alpert_and_Knopf_2016/table_2.py
+PySDM_examples/Arabas_and_Pawlowska_2011/__init__.py
+PySDM_examples/Arabas_and_Pawlowska_2011/settings.py
+PySDM_examples/Arabas_and_Pawlowska_2011/simulation.py
 PySDM_examples/Arabas_and_Shima_2017/__init__.py
 PySDM_examples/Arabas_and_Shima_2017/example.py
 PySDM_examples/Arabas_and_Shima_2017/settings.py
@@ -132,7 +135,6 @@ PySDM_examples/Srivastava_1982/settings.py
 PySDM_examples/Srivastava_1982/simulation.py
 PySDM_examples/Stewart_1975/__init__.py
 PySDM_examples/Strzabala_2025_BEng/__init__.py
-PySDM_examples/Strzabala_2025_BEng/paraview_parcel_model.py
 PySDM_examples/Toon_et_al_1980/__init__.py
 PySDM_examples/Van_Hook_1968/__init__.py
 PySDM_examples/Ware_et_al_2025/__init__.py

{pysdm_examples-3.0.0rc28 → pysdm_examples-3.0.0rc30}/pysdm_examples.egg-info/requires.txt

@@ -11,6 +11,7 @@ vtk
 pyrcel
 pyvinecopulib
 networkx
+PyVista
 
 [CI_version_pins]
 PySDM[CI_version_pins]
@@ -24,4 +25,4 @@ seaborn==0.13.2
 numdifftools==0.9.42
 vtk==9.6.1
 pyrcel==1.3.4
-pyvinecopulib==0.7.3
+pyvinecopulib==0.7.6

{pysdm_examples-3.0.0rc28 → pysdm_examples-3.0.0rc30}/setup.py

@@ -36,6 +36,7 @@ setup(
         "pyrcel",
         "pyvinecopulib",
         "networkx",
+        "PyVista",
     ],
     extras_require={
         "CI_version_pins": [
@@ -50,7 +51,7 @@ setup(
             "numdifftools==0.9.42",
             "vtk==9.6.1",
             "pyrcel==1.3.4",
-            "pyvinecopulib==0.7.3",
+            "pyvinecopulib==0.7.6",
         ]
     },
     author="https://github.com/open-atmos/PySDM/graphs/contributors",