PySDM-examples 3.0.0rc30__tar.gz → 3.0.0rc32__tar.gz

{pysdm_examples-3.0.0rc30 → pysdm_examples-3.0.0rc32}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pysdm-examples
-Version: 3.0.0rc30
+Version: 3.0.0rc32
 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
@@ -34,7 +34,7 @@ Requires-Dist: joblib==1.5.3; extra == "ci-version-pins"
 Requires-Dist: ipywidgets==8.1.7; extra == "ci-version-pins"
 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: vtk==9.6.2; extra == "ci-version-pins"
 Requires-Dist: pyrcel==1.3.4; extra == "ci-version-pins"
 Requires-Dist: pyvinecopulib==0.7.6; extra == "ci-version-pins"
 Dynamic: author

{pysdm_examples-3.0.0rc30 → pysdm_examples-3.0.0rc32}/PySDM_examples/Abade_and_Albuquerque_2024/simulation.py

@@ -22,6 +22,24 @@ from PySDM.environments import Parcel
 
 class Simulation(BasicSimulation):
     def __init__(self, settings):
+
+        dynamics = [
+            AmbientThermodynamics(),
+            Condensation(),
+        ]
+
+        if settings.enable_immersion_freezing:
+            dynamics.append(
+                Freezing(
+                    immersion_freezing=(
+                        "singular" if settings.singular else "time-dependent"
+                    )
+                )
+            )
+
+        if settings.enable_vapour_deposition_on_ice:
+            dynamics.append(VapourDepositionOnIce(adaptive=True))
+
         builder = Builder(
             backend=settings.backend,
             n_sd=settings.n_sd,
@@ -34,20 +52,8 @@ class Simulation(BasicSimulation):
                 w=settings.updraft,
                 mixed_phase=True,
             ),
+            dynamics=dynamics,
         )
-        builder.add_dynamic(AmbientThermodynamics())
-        builder.add_dynamic(Condensation())
-
-        if settings.enable_immersion_freezing:
-            builder.add_dynamic(
-                Freezing(
-                    immersion_freezing=(
-                        "singular" if settings.singular else "time-dependent"
-                    )
-                )
-            )
-        if settings.enable_vapour_deposition_on_ice:
-            builder.add_dynamic(VapourDepositionOnIce(adaptive=True))
 
         r_dry, n_in_dv = ConstantMultiplicity(
             settings.soluble_aerosol

{pysdm_examples-3.0.0rc30 → pysdm_examples-3.0.0rc32}/PySDM_examples/Abdul_Razzak_Ghan_2000/run_ARG_parcel.py

@@ -52,9 +52,12 @@ def run_parcel(
     )
     n_sd = n_sd_per_mode * len(aerosol.modes)
 
-    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()],
+    )
     builder.request_attribute("critical saturation")
 
     attributes = {

{pysdm_examples-3.0.0rc30 → pysdm_examples-3.0.0rc32}/PySDM_examples/Alpert_and_Knopf_2016/simulation.py

@@ -218,8 +218,8 @@ def simulation(
         n_sd=n_sd,
         backend=CPU(formulae=formulae),
         environment=Box(dt=time_step, dv=volume),
+        dynamics=[Freezing(immersion_freezing="time-dependent")],
     )
-    builder.add_dynamic(Freezing(immersion_freezing="time-dependent"))
     builder.request_attribute("volume")
 
     if hasattr(spectrum, "s_geom") and spectrum.s_geom == 1:

{pysdm_examples-3.0.0rc30 → pysdm_examples-3.0.0rc32}/PySDM_examples/Arabas_and_Pawlowska_2011/simulation.py

@@ -32,11 +32,12 @@ class Simulation(BasicSimulation):
             backend=CPU(settings.formulae),
             n_sd=settings.n_sd,
             environment=environment,
+            dynamics=(
+                AmbientThermodynamics(),
+                Condensation(),
+            ),
         )
 
-        builder.add_dynamic(AmbientThermodynamics())
-        builder.add_dynamic(Condensation())
-
         builder.request_attribute("radius")
 
         self.builder = builder

{pysdm_examples-3.0.0rc30 → pysdm_examples-3.0.0rc32}/PySDM_examples/Arabas_and_Shima_2017/simulation.py

@@ -36,16 +36,16 @@ class Simulation:
                 T0=settings.T0,
                 w=settings.w,
             ),
+            dynamics=[
+                AmbientThermodynamics(),
+                Condensation(
+                    rtol_x=settings.rtol_x,
+                    rtol_thd=settings.rtol_thd,
+                    dt_cond_range=settings.dt_cond_range,
+                ),
+            ],
         )
 
-        builder.add_dynamic(AmbientThermodynamics())
-        builder.add_dynamic(
-            Condensation(
-                rtol_x=settings.rtol_x,
-                rtol_thd=settings.rtol_thd,
-                dt_cond_range=settings.dt_cond_range,
-            )
-        )
         attributes = {}
         r_dry = np.array([settings.r_dry])
         attributes["dry volume"] = settings.formulae.trivia.volume(radius=r_dry)

{pysdm_examples-3.0.0rc30 → pysdm_examples-3.0.0rc32}/PySDM_examples/Arabas_et_al_2025/make_particulator.py

@@ -65,16 +65,18 @@ def make_particulator(
         thaw_flag = None
     attributes["multiplicity"] *= total_particle_number
 
-    builder = Builder(n_sd=n_sd, backend=backend, environment=Box(dt, volume))
+    builder = Builder(
+        n_sd=n_sd,
+        backend=backend,
+        environment=Box(dt, volume),
+        dynamics=[Freezing(immersion_freezing=immersion_freezing_flag, thaw=thaw_flag)],
+    )
 
     env = builder.particulator.environment
     env["T"] = initial_temperature
     env["RH"] = A_VALUE_LARGER_THAN_ONE
     env["rhod"] = 1.0
 
-    builder.add_dynamic(
-        Freezing(immersion_freezing=immersion_freezing_flag, thaw=thaw_flag)
-    )
     builder.request_attribute("volume")
 
     return builder.build(

{pysdm_examples-3.0.0rc30 → pysdm_examples-3.0.0rc32}/PySDM_examples/Bieli_et_al_2022/simulation.py

@@ -8,25 +8,24 @@ from PySDM.initialisation.sampling.spectral_sampling import ConstantMultiplicity
 
 def make_core(settings, coal_eff):
     backend = CPU
-
+    collision = Collision(
+        collision_kernel=settings.kernel,
+        coalescence_efficiency=coal_eff,
+        breakup_efficiency=settings.break_eff,
+        fragmentation_function=settings.fragmentation,
+        adaptive=settings.adaptive,
+    )
     builder = Builder(
         n_sd=settings.n_sd,
         backend=backend(settings.formulae),
         environment=Box(dv=settings.dv, dt=settings.dt),
+        dynamics=[collision],
     )
     builder.particulator.environment["rhod"] = 1.0
     attributes = {}
     attributes["volume"], attributes["multiplicity"] = ConstantMultiplicity(
         settings.spectrum
     ).sample_deterministic(settings.n_sd)
-    collision = Collision(
-        collision_kernel=settings.kernel,
-        coalescence_efficiency=coal_eff,
-        breakup_efficiency=settings.break_eff,
-        fragmentation_function=settings.fragmentation,
-        adaptive=settings.adaptive,
-    )
-    builder.add_dynamic(collision)
     common_args = {
         "attr": "volume",
         "attr_unit": "m^3",

{pysdm_examples-3.0.0rc30 → pysdm_examples-3.0.0rc32}/PySDM_examples/Grabowski_and_Pawlowska_2023/simulation.py

@@ -31,10 +31,10 @@ class Simulation(BasicSimulation):
                 w=settings.vertical_velocity,
                 mass_of_dry_air=44 * si.kg,
             ),
-        )
-        builder.add_dynamic(AmbientThermodynamics())
-        builder.add_dynamic(
-            Condensation(rtol_thd=settings.rtol_thd, rtol_x=settings.rtol_x)
+            dynamics=(
+                AmbientThermodynamics(),
+                Condensation(rtol_thd=settings.rtol_thd, rtol_x=settings.rtol_x),
+            ),
         )
         for attribute in (
             "critical saturation",

{pysdm_examples-3.0.0rc30 → pysdm_examples-3.0.0rc32}/PySDM_examples/Jensen_and_Nugent_2017/simulation.py

@@ -46,19 +46,22 @@ class Simulation(BasicSimulation):
                 w=settings.vertical_velocity,
                 z0=settings.z0,
             ),
+            dynamics=[
+                # TODO #1266: order matters here, but error message is not saying it!
+                AmbientThermodynamics(),
+                Condensation(),
+            ]
+            + (
+                []
+                if not gravitational_coalsecence
+                else [Coalescence(collision_kernel=Geometric())]
+            ),
         )
 
         additional_derived_attributes = ("radius", "equilibrium saturation")
         for additional_derived_attribute in additional_derived_attributes:
             builder.request_attribute(additional_derived_attribute)
 
-        builder.add_dynamic(
-            AmbientThermodynamics()
-        )  # TODO #1266: order matters here, but error message is not saying it!
-        builder.add_dynamic(Condensation())
-        if gravitational_coalsecence:
-            builder.add_dynamic(Coalescence(collision_kernel=Geometric()))
-
         self.r_dry, n_in_unit_volume = Logarithmic(
             spectrum=settings.dry_radii_spectrum,
         ).sample_deterministic(builder.particulator.n_sd - n_gccn)

{pysdm_examples-3.0.0rc30 → pysdm_examples-3.0.0rc32}/PySDM_examples/Kreidenweis_et_al_2003/simulation.py

@@ -25,6 +25,17 @@ class Simulation(BasicSimulation):
                 T0=settings.T0,
                 w=settings.w,
             ),
+            dynamics=(
+                AmbientThermodynamics(),
+                Condensation(),
+                AqueousChemistry(
+                    environment_mole_fractions=settings.ENVIRONMENT_MOLE_FRACTIONS,
+                    system_type=settings.system_type,
+                    n_substep=settings.n_substep,
+                    dry_rho=settings.DRY_RHO,
+                    dry_molar_mass=settings.dry_molar_mass,
+                ),
+            ),
         )
 
         attributes = builder.particulator.environment.init_attributes(
@@ -38,18 +49,6 @@ class Simulation(BasicSimulation):
             **settings.starting_amounts,
         }
 
-        builder.add_dynamic(AmbientThermodynamics())
-        builder.add_dynamic(Condensation())
-        builder.add_dynamic(
-            AqueousChemistry(
-                environment_mole_fractions=settings.ENVIRONMENT_MOLE_FRACTIONS,
-                system_type=settings.system_type,
-                n_substep=settings.n_substep,
-                dry_rho=settings.DRY_RHO,
-                dry_molar_mass=settings.dry_molar_mass,
-            )
-        )
-
         products = products or (
             PySDM_products.AmbientRelativeHumidity(name="RH", unit="%"),
             PySDM_products.WaterMixingRatio(

{pysdm_examples-3.0.0rc30 → pysdm_examples-3.0.0rc32}/PySDM_examples/Long_1974/simulation.py

@@ -15,19 +15,20 @@ class Simulation(BasicSimulation):
             n_sd=settings.n_sd,
             backend=CPU(),
             environment=Box(dv=settings.dv, dt=settings.dt),
+            dynamics=(
+                Coalescence(
+                    collision_kernel=settings.kernel,
+                    coalescence_efficiency=settings.coal_eff,
+                    adaptive=settings.adaptive,
+                ),
+            ),
         )
         builder.particulator.environment["rhod"] = settings.rhod
         attributes = {}
         attributes["volume"], attributes["multiplicity"] = ConstantMultiplicity(
             settings.spectrum
         ).sample_deterministic(settings.n_sd)
-        builder.add_dynamic(
-            Coalescence(
-                collision_kernel=settings.kernel,
-                coalescence_efficiency=settings.coal_eff,
-                adaptive=settings.adaptive,
-            )
-        )
+
         products = (
             ParticleVolumeVersusRadiusLogarithmSpectrum(
                 radius_bins_edges=settings.radius_bins_edges, name="dv/dlnr"

{pysdm_examples-3.0.0rc30 → pysdm_examples-3.0.0rc32}/PySDM_examples/Lowe_et_al_2019/simulation.py

@@ -24,6 +24,7 @@ class Simulation(BasicSimulation):
                 T0=settings.T0,
                 w=settings.w,
             ),
+            dynamics=(AmbientThermodynamics(), Condensation()),
         )
 
         attributes = {
@@ -73,9 +74,6 @@ class Simulation(BasicSimulation):
         if settings.model == "Constant":
             del attributes["dry volume organic"]
 
-        builder.add_dynamic(AmbientThermodynamics())
-        builder.add_dynamic(Condensation())
-
         products = products or (
             PySDM_products.ParcelDisplacement(name="z"),
             PySDM_products.Time(name="t"),

pysdm_examples-3.0.0rc32/PySDM_examples/Luettmer_homogeneous_freezing/__init__.py

@@ -0,0 +1,17 @@
+"""
+Homogeneous freezing example
+
+.. include:: ./fig_1_2_3.ipynb
+.. include:: ./fig_4_5_6_S3_S4.ipynb
+.. include:: ./fig_S1_S2.ipynb
+.. include:: ./simple_homogenous_freezing_example.ipynb
+"""
+
+from .settings import Settings
+from .simulation import Simulation
+from .plot import (
+    plot_thermodynamics_and_bulk,
+    plot_freezing_temperatures_histogram,
+    plot_freezing_temperatures_histogram_allinone,
+    plot_freezing_temperatures_2d_histogram_seaborn,
+)

pysdm_examples-3.0.0rc32/PySDM_examples/Luettmer_homogeneous_freezing/commons.py

@@ -0,0 +1,91 @@
+"""commons for homogeneous freezing notebooks"""
+
+from PySDM_examples.Luettmer_homogeneous_freezing.settings import Settings
+from PySDM_examples.Luettmer_homogeneous_freezing.simulation import Simulation
+from PySDM import Formulae
+from PySDM.physics.constants import si
+from PySDM.backends import CPU
+
+formulae = Formulae(
+    particle_shape_and_density="MixedPhaseSpheres",
+)
+
+
+def run_simulations(setting):
+
+    simulation = {
+        "settings": setting,
+        "ensemble_member_outputs": [],
+    }
+    for _ in range(setting["number_of_ensemble_runs"]):
+        model_setup = Settings(**simulation["settings"])
+        model_setup.formulae.seed += 1
+        model = Simulation(model_setup)
+        simulation["ensemble_member_outputs"].append(model.run())
+
+    return simulation
+
+
+def hom_pure_droplet_freezing_backend():
+    cmn = {"override_jit_flags": {"parallel": False}}
+    backends = {
+        "threshold": CPU(
+            formulae=Formulae(
+                particle_shape_and_density="MixedPhaseSpheres",
+                homogeneous_ice_nucleation_rate="Null",
+                saturation_vapour_pressure="MurphyKoop2005",
+            ),
+            **cmn,
+        ),
+        "KoopMurray2016": CPU(
+            formulae=Formulae(
+                particle_shape_and_density="MixedPhaseSpheres",
+                homogeneous_ice_nucleation_rate="KoopMurray2016",
+                saturation_vapour_pressure="MurphyKoop2005",
+            ),
+            **cmn,
+        ),
+        "Spichtinger2023": CPU(
+            formulae=Formulae(
+                particle_shape_and_density="MixedPhaseSpheres",
+                homogeneous_ice_nucleation_rate="Koop_Correction",
+                saturation_vapour_pressure="MurphyKoop2005",
+            ),
+            **cmn,
+        ),
+        "Koop2000": CPU(
+            formulae=Formulae(
+                particle_shape_and_density="MixedPhaseSpheres",
+                homogeneous_ice_nucleation_rate="Koop2000",
+                saturation_vapour_pressure="MurphyKoop2005",
+            ),
+            **cmn,
+        ),
+        "KoopMurray2016_DWA": CPU(
+            formulae=Formulae(
+                particle_shape_and_density="MixedPhaseSpheres",
+                homogeneous_ice_nucleation_rate="KoopMurray2016_DWA",
+                saturation_vapour_pressure="MurphyKoop2005",
+            ),
+            **cmn,
+        ),
+    }
+    return backends
+
+
+def hom_pure_droplet_freezing_standard_setup():
+    standard = {
+        "n_sd": int(1e3),
+        "w_updraft": 1.0 * si.meter / si.second,
+        "T0": 245 * si.kelvin,
+        "dz": 1.0 * si.meter,
+        "n_ccn": 750 / si.cm**3,
+        "r_ccn": 15 * si.nanometer,
+        "type_droplet_distribution": "monodisperse",
+        "RH_0": 0.995,
+        "p0": 500 * si.hectopascals,
+        "deposition_enable": True,
+        "number_of_ensemble_runs": 1,
+        "silent": True,
+    }
+    return standard