PySDM 2.99__tar.gz → 2.100__tar.gz

{pysdm-2.99 → pysdm-2.100}/.pre-commit-config.yaml

@@ -4,7 +4,7 @@ default_stages: [commit]
 
 repos:
   - repo: https://github.com/psf/black
-    rev: 24.1.0
+    rev: 25.1.0
     hooks:
       - id: black
 
@@ -14,7 +14,7 @@ repos:
 #      - id: isort
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer

{pysdm-2.99 → pysdm-2.100}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.99
+Version: 2.100
 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-2.99 → pysdm-2.100}/PySDM/attributes/impl/attribute_registry.py

@@ -1,4 +1,4 @@
-""" definition of decorator used to register PySDM attribute classes """
+"""definition of decorator used to register PySDM attribute classes"""
 
 import warnings
 

{pysdm-2.99 → pysdm-2.100}/PySDM/attributes/impl/dummy_attribute.py

@@ -1,5 +1,5 @@
-""" logic around `PySDM.attributes.impl.dummy_attribute.DummyAttribute` - parent class
-for do-nothing attributes """
+"""logic around `PySDM.attributes.impl.dummy_attribute.DummyAttribute` - parent class
+for do-nothing attributes"""
 
 import numpy as np
 

pysdm-2.100/PySDM/backends/impl_common/__init__.py

@@ -0,0 +1 @@
+"""common code for all backends"""

pysdm-2.100/PySDM/backends/impl_numba/__init__.py

@@ -0,0 +1 @@
+"""the guts of the CPU backend"""

{pysdm-2.99 → pysdm-2.100}/PySDM/backends/impl_numba/methods/__init__.py

@@ -1,4 +1,4 @@
-""" method classes of the CPU backend """
+"""method classes of the CPU backend"""
 
 from .chemistry_methods import ChemistryMethods
 from .collisions_methods import CollisionsMethods

{pysdm-2.99 → pysdm-2.100}/PySDM/backends/impl_numba/methods/seeding_methods.py

@@ -1,4 +1,4 @@
-""" CPU implementation of backend methods for particle injections """
+"""CPU implementation of backend methods for particle injections"""
 
 from functools import cached_property
 

pysdm-2.100/PySDM/backends/impl_numba/test_helpers/__init__.py

@@ -0,0 +1 @@
+"""logic intended to be used in tests only including the SciPy-based condensation solver"""

pysdm-2.100/PySDM/backends/impl_thrust_rtc/__init__.py

@@ -0,0 +1 @@
+"""the guts of the GPU backend"""

pysdm-2.100/PySDM/backends/impl_thrust_rtc/methods/__init__.py

@@ -0,0 +1 @@
+"""method classes of the GPU backend"""

{pysdm-2.99 → pysdm-2.100}/PySDM/dynamics/collisions/coalescence_efficiencies/constEc.py

@@ -1,4 +1,4 @@
-""" constant value """
+"""constant value"""
 
 
 class ConstEc:

pysdm-2.100/PySDM/dynamics/collisions/collision_kernels/impl/__init__.py

@@ -0,0 +1 @@
+"""common code for implementing collision kernels"""

{pysdm-2.99 → pysdm-2.100}/PySDM/dynamics/collisions/collision_kernels/impl/gravitational.py

@@ -1,4 +1,4 @@
-""" common parent class for gravitational collision kernels """
+"""common parent class for gravitational collision kernels"""
 
 
 class Gravitational:  # pylint: disable=too-few-public-methods

{pysdm-2.99 → pysdm-2.100}/PySDM/dynamics/collisions/collision_kernels/impl/parameterized.py

@@ -1,4 +1,4 @@
-""" common parent class for collision kernels specified using Berry's parameterization """
+"""common parent class for collision kernels specified using Berry's parameterization"""
 
 from PySDM.physics import constants as const
 

pysdm-2.100/PySDM/dynamics/impl/__init__.py

@@ -0,0 +1,3 @@
+"""stuff not intended to be imported from user code"""
+
+from .register_dynamic import register_dynamic

{pysdm-2.99 → pysdm-2.100}/PySDM/dynamics/impl/register_dynamic.py

@@ -1,5 +1,5 @@
-""" decorator for dynamics classes
-ensuring that their instances can be re-used with multiple builders """
+"""decorator for dynamics classes
+ensuring that their instances can be re-used with multiple builders"""
 
 from copy import deepcopy
 

{pysdm-2.99 → pysdm-2.100}/PySDM/dynamics/seeding.py

@@ -1,6 +1,6 @@
-""" particle injection handling, requires initalising a simulation with
+"""particle injection handling, requires initalising a simulation with
 enough particles flagged with NaN multiplicity (translated to zeros
-at multiplicity discretisation """
+at multiplicity discretisation"""
 
 from collections.abc import Sized
 

{pysdm-2.99 → pysdm-2.100}/PySDM/environments/impl/__init__.py

@@ -1,3 +1,3 @@
-""" common internals not intended to be imported from user code """
+"""common internals not intended to be imported from user code"""
 
 from PySDM.environments.impl.register_environment import register_environment

{pysdm-2.99 → pysdm-2.100}/PySDM/environments/impl/register_environment.py

@@ -1,5 +1,5 @@
-""" decorator for environment classes
-ensuring that their instances can be re-used with multiple builders """
+"""decorator for environment classes
+ensuring that their instances can be re-used with multiple builders"""
 
 from copy import deepcopy
 

{pysdm-2.99 → pysdm-2.100}/PySDM/environments/parcel.py

@@ -30,7 +30,7 @@ class Parcel(Moist):  # pylint: disable=too-many-instance-attributes
         mixed_phase=False,
         variables: Optional[List[str]] = None,
     ):
-        variables = (variables or []) + ["rhod", "z", "t"]
+        variables = (variables or []) + ["rhod", "z"]
         super().__init__(dt, Mesh.mesh_0d(), variables, mixed_phase=mixed_phase)
 
         self.p0 = p0
@@ -38,44 +38,34 @@ class Parcel(Moist):  # pylint: disable=too-many-instance-attributes
         self.T0 = T0
         self.z0 = z0
         self.mass_of_dry_air = mass_of_dry_air
-
         self.w = w if callable(w) else lambda _: w
-
-        self.formulae = None
         self.delta_liquid_water_mixing_ratio = np.nan
-        self.params = None
 
     @property
     def dv(self):
         rhod_mean = (self.get_predicted("rhod")[0] + self["rhod"][0]) / 2
-        return self.formulae.trivia.volume_of_density_mass(
+        return self.particulator.formulae.trivia.volume_of_density_mass(
             rhod_mean, self.mass_of_dry_air
         )
 
     def register(self, builder):
-        self.formulae = builder.particulator.formulae
-        pd0 = self.formulae.trivia.p_d(self.p0, self.initial_water_vapour_mixing_ratio)
-        rhod0 = self.formulae.state_variable_triplet.rhod_of_pd_T(pd0, self.T0)
-        self.mesh.dv = self.formulae.trivia.volume_of_density_mass(
+        formulae = builder.particulator.formulae
+        pd0 = formulae.trivia.p_d(self.p0, self.initial_water_vapour_mixing_ratio)
+        rhod0 = formulae.state_variable_triplet.rhod_of_pd_T(pd0, self.T0)
+        self.mesh.dv = formulae.trivia.volume_of_density_mass(
             rhod0, self.mass_of_dry_air
         )
 
         Moist.register(self, builder)
 
-        params = (
-            self.initial_water_vapour_mixing_ratio,
-            self.formulae.trivia.th_std(pd0, self.T0),
-            rhod0,
-            self.z0,
-            0,
-        )
-        self["water_vapour_mixing_ratio"][:] = params[0]
-        self["thd"][:] = params[1]
-        self["rhod"][:] = params[2]
-        self["z"][:] = params[3]
-        self["t"][:] = params[4]
+        self["water_vapour_mixing_ratio"][:] = self.initial_water_vapour_mixing_ratio
+        self["thd"][:] = formulae.trivia.th_std(pd0, self.T0)
+        self["rhod"][:] = rhod0
+        self["z"][:] = self.z0
 
-        self._tmp["water_vapour_mixing_ratio"][:] = params[0]
+        self._tmp["water_vapour_mixing_ratio"][
+            :
+        ] = self.initial_water_vapour_mixing_ratio
         self.sync_parcel_vars()
         Moist.sync(self)
         self.notify()
@@ -94,7 +84,7 @@ class Parcel(Moist):  # pylint: disable=too-many-instance-attributes
             n_in_dv = np.array([n_in_dv])
 
         attributes = {}
-        dry_volume = self.formulae.trivia.volume(radius=r_dry)
+        dry_volume = self.particulator.formulae.trivia.volume(radius=r_dry)
         attributes["kappa times dry volume"] = dry_volume * kappa
         attributes["multiplicity"] = n_in_dv
         r_wet = equilibrate_wet_radii(
@@ -103,43 +93,44 @@ class Parcel(Moist):  # pylint: disable=too-many-instance-attributes
             kappa_times_dry_volume=attributes["kappa times dry volume"],
             rtol=rtol,
         )
-        attributes["volume"] = self.formulae.trivia.volume(radius=r_wet)
+        attributes["volume"] = self.particulator.formulae.trivia.volume(radius=r_wet)
         if include_dry_volume_in_attribute:
             attributes["dry volume"] = dry_volume
         return attributes
 
     def advance_parcel_vars(self):
+        """compute new values of displacement, dry-air density and volume,
+        and write them to self._tmp and self.mesh.dv"""
         dt = self.particulator.dt
+        formulae = self.particulator.formulae
         T = self["T"][0]
         p = self["p"][0]
-        t = self["t"][0]
 
-        dz_dt = self.w(t + dt / 2)  # "mid-point"
+        dz_dt = self.w((self.particulator.n_steps + 1 / 2) * dt)  # "mid-point"
         water_vapour_mixing_ratio = (
             self["water_vapour_mixing_ratio"][0]
             - self.delta_liquid_water_mixing_ratio / 2
         )
 
-        # derivate evaluated at p_old, T_old, mixrat_mid, w_mid
-        drho_dz = self.formulae.hydrostatics.drho_dz(
-            g=self.formulae.constants.g_std,
+        # derivative evaluated at p_old, T_old, mixrat_mid, w_mid
+        drho_dz = formulae.hydrostatics.drho_dz(
+            g=formulae.constants.g_std,
             p=p,
             T=T,
             water_vapour_mixing_ratio=water_vapour_mixing_ratio,
-            lv=self.formulae.latent_heat.lv(T),
+            lv=formulae.latent_heat.lv(T),
             d_liquid_water_mixing_ratio__dz=(
                 self.delta_liquid_water_mixing_ratio / dz_dt / dt
             ),
         )
-        drhod_dz = drho_dz
+        drhod_dz = drho_dz  # TODO #407
 
-        self.particulator.backend.explicit_euler(self._tmp["t"], dt, 1)
         self.particulator.backend.explicit_euler(self._tmp["z"], dt, dz_dt)
         self.particulator.backend.explicit_euler(
             self._tmp["rhod"], dt, dz_dt * drhod_dz
         )
 
-        self.mesh.dv = self.formulae.trivia.volume_of_density_mass(
+        self.mesh.dv = formulae.trivia.volume_of_density_mass(
             (self._tmp["rhod"][0] + self["rhod"][0]) / 2, self.mass_of_dry_air
         )
 

{pysdm-2.99 → pysdm-2.100}/PySDM/exporters/netcdf_exporter.py

@@ -1,5 +1,5 @@
-""" netCDF exporter implemented using
- [SciPy.io.netcdf_file](https://docs.scipy.org/doc/scipy/reference/tutorial/io.html#netcdf)
+"""netCDF exporter implemented using
+[SciPy.io.netcdf_file](https://docs.scipy.org/doc/scipy/reference/tutorial/io.html#netcdf)
 """
 
 import numpy as np

pysdm-2.100/PySDM/impl/__init__.py

@@ -0,0 +1 @@
+"""stuff not intended to be used from user code"""

pysdm-2.100/PySDM/initialisation/impl/__init__.py

@@ -0,0 +1,2 @@
+"""commons (incl. `PySDM.initialisation.impl.spectrum.Spectrum` base class)
+not intended to be imported from user code"""

pysdm-2.100/PySDM/initialisation/sampling/__init__.py

@@ -0,0 +1 @@
+"""particle attribute sampling logic"""

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/air_dynamic_viscosity/__init__.py

@@ -1,3 +1,3 @@
-""" air dynamic viscosity formulae """
+"""air dynamic viscosity formulae"""
 
 from .zografos_et_al_1987 import ZografosEtAl1987

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/bulk_phase_partitioning/__init__.py

@@ -1,4 +1,4 @@
-""" phase partitioning formulae for bulk description of cloud water """
+"""phase partitioning formulae for bulk description of cloud water"""
 
 from PySDM.impl.null_physics_class import Null
 from .kaul_et_al_2015 import KaulEtAl2015

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/impl/fake_unit_registry.py

@@ -1,7 +1,7 @@
-""" logic around `PySDM.physics.impl.fake_unit_registry.FakeUnitRegistry` - PySDM mock of Pint's
- [UnitRegistry](https://pint.readthedocs.io/en/stable/developers_reference.html#pint.UnitRegistry),
- with the genuine Pint class used only within unit tests through the
- `PySDM.physics.dimensional_analysis.DimensionalAnalysis` context manager
+"""logic around `PySDM.physics.impl.fake_unit_registry.FakeUnitRegistry` - PySDM mock of Pint's
+[UnitRegistry](https://pint.readthedocs.io/en/stable/developers_reference.html#pint.UnitRegistry),
+with the genuine Pint class used only within unit tests through the
+`PySDM.physics.dimensional_analysis.DimensionalAnalysis` context manager
 """
 
 

pysdm-2.100/PySDM/physics/impl/flag.py

@@ -0,0 +1,6 @@
+"""flag disabling `PySDM.physics.impl.fake_unit_registry.FakeUnitRegistry` within
+`PySDM.physics.dimensional_analysis.DimensionalAnalysis`
+context manager
+"""
+
+DIMENSIONAL_ANALYSIS = False

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/isotope_diffusivity_ratios/__init__.py

@@ -1,4 +1,4 @@
-""" heavy-to-light diffusivity ratios for water molecules """
+"""heavy-to-light diffusivity ratios for water molecules"""
 
 from PySDM.impl.null_physics_class import Null
 from .grahams_law import GrahamsLaw

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/isotope_diffusivity_ratios/grahams_law.py

@@ -1,5 +1,5 @@
-""" [Graham's law](https://en.wikipedia.org/wiki/Graham%27s_law)
-    see also eq. (21) in [Horita et al. 2008](https://doi.org/10.1080/10256010801887174)
+"""[Graham's law](https://en.wikipedia.org/wiki/Graham%27s_law)
+see also eq. (21) in [Horita et al. 2008](https://doi.org/10.1080/10256010801887174)
 """
 
 

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/isotope_equilibrium_fractionation_factors/__init__.py

@@ -1,5 +1,5 @@
-""" factors describing partitioning of water isotopologues under thermodynamic
-phase equilibrium, defined as ratios alpha of isotopic ratios R """
+"""factors describing partitioning of water isotopologues under thermodynamic
+phase equilibrium, defined as ratios alpha of isotopic ratios R"""
 
 from PySDM.impl.null_physics_class import Null
 from .barkan_and_luz_2005 import BarkanAndLuz2005

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/isotope_meteoric_water_line/__init__.py

@@ -1,4 +1,4 @@
-""" definitions of meteoric water line parameters
+"""definitions of meteoric water line parameters
 and definitions of the excess quantities"""
 
 from PySDM.impl.null_physics_class import Null

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/isotope_meteoric_water_line/picciotto_et_al_1960.py

@@ -1,7 +1,7 @@
-""" based on [Picciotto et al. 1960](https://doi.org/10.1038/187857a0)
- where delta(2H)= slope_coeff * delta(18O) + intercept_coeff formulae is given
- with swapped 2H and 18O in a paper
- """
+"""based on [Picciotto et al. 1960](https://doi.org/10.1038/187857a0)
+where delta(2H)= slope_coeff * delta(18O) + intercept_coeff formulae is given
+with swapped 2H and 18O in a paper
+"""
 
 
 class PicciottoEtAl1960:  # pylint: disable=too-few-public-methods

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/isotope_ratio_evolution/__init__.py

@@ -1,4 +1,4 @@
-""" isotope-ratio evolution formulae (incl. Rayleigh distillation) """
+"""isotope-ratio evolution formulae (incl. Rayleigh distillation)"""
 
 from PySDM.impl.null_physics_class import Null
 from .merlivat_and_jouzel_1979 import MerlivatAndJouzel1979

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/isotope_ratio_evolution/rayleigh_distillation.py

@@ -1,4 +1,4 @@
-""" Fractional distillation assuming continuous removal under equilibrium """
+"""Fractional distillation assuming continuous removal under equilibrium"""
 
 
 class RayleighDistillation:  # pylint:disable=too-few-public-methods

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/isotope_relaxation_timescale/bolin_1958.py

@@ -1,5 +1,5 @@
-""" Timescale derived for tritium with assumption of zero ambient concentration - see text above
-    Table 1 [Bolin 1958](https://digitallibrary.un.org/record/3892725) """
+"""Timescale derived for tritium with assumption of zero ambient concentration - see text above
+Table 1 [Bolin 1958](https://digitallibrary.un.org/record/3892725)"""
 
 import numpy as np
 

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/isotope_relaxation_timescale/miyake_et_al_1968.py

@@ -1,4 +1,4 @@
-""" eq. 28 in [Miyake et al. 1968](https://doi.org/10.2467/mripapers1950.19.2_243) """
+"""eq. 28 in [Miyake et al. 1968](https://doi.org/10.2467/mripapers1950.19.2_243)"""
 
 
 class MiyakeEtAl1968:  # pylint: disable=too-few-public-methods

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/isotope_temperature_inference/picciotto_et_al_1960.py

@@ -1,5 +1,5 @@
-""" based on [Picciotto et al. 1960](https://doi.org/10.1038/187857a0)
- where delta(T)=-(a*T + b) formulae given, here cast as T(delta)=(-delta-b)/a """
+"""based on [Picciotto et al. 1960](https://doi.org/10.1038/187857a0)
+where delta(T)=-(a*T + b) formulae given, here cast as T(delta)=(-delta-b)/a"""
 
 
 class PicciottoEtAl1960:  # pylint: disable=too-few-public-methods

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/terminal_velocity/__init__.py

@@ -1,4 +1,4 @@
-""" terminal velocity formulae """
+"""terminal velocity formulae"""
 
 from .rogers_yau import RogersYau
 from .gunn_kinzer_1949 import GunnKinzer1949

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/terminal_velocity/gunn_kinzer_1949.py

@@ -1,4 +1,4 @@
-""" [Gunn & Kinzer 1949](https://doi.org/10.1175/1520-0469(1949)006%3C0243:TTVOFF%3E2.0.CO;2) """
+"""[Gunn & Kinzer 1949](https://doi.org/10.1175/1520-0469(1949)006%3C0243:TTVOFF%3E2.0.CO;2)"""
 
 
 class GunnKinzer1949:  # pylint: disable=too-few-public-methods

{pysdm-2.99 → pysdm-2.100}/PySDM/physics/terminal_velocity/power_series.py

@@ -1,4 +1,4 @@
-""" power-series formulation """
+"""power-series formulation"""
 
 
 class PowerSeries:  # pylint: disable=too-few-public-methods

{pysdm-2.99 → pysdm-2.100}/PySDM/products/impl/__init__.py

@@ -1,4 +1,4 @@
-""" commons, not intended to be imported from user code """
+"""commons, not intended to be imported from user code"""
 
 from PySDM.products.impl.moist_environment_product import MoistEnvironmentProduct
 from PySDM.products.impl.moment_product import MomentProduct

{pysdm-2.99 → pysdm-2.100}/PySDM/products/impl/moment_product.py

@@ -1,4 +1,4 @@
-""" common code for products computing statistical moments (e.g., effective radius, acidity) """
+"""common code for products computing statistical moments (e.g., effective radius, acidity)"""
 
 from abc import ABC
 

{pysdm-2.99 → pysdm-2.100}/PySDM/products/impl/register_product.py

@@ -1,5 +1,5 @@
-""" decorator for product classes
-ensuring that their instances can be re-used with multiple builders """
+"""decorator for product classes
+ensuring that their instances can be re-used with multiple builders"""
 
 from copy import deepcopy
 

{pysdm-2.99 → pysdm-2.100}/PySDM/products/optical/__init__.py

@@ -1,4 +1,4 @@
-""" cloud optical properties """
+"""cloud optical properties"""
 
 from .cloud_optical_depth import CloudOpticalDepth
 from .cloud_albedo import CloudAlbedo

{pysdm-2.99 → pysdm-2.100}/PySDM/products/parcel/__init__.py

@@ -1,4 +1,4 @@
-""" products specific to the parcel environment """
+"""products specific to the parcel environment"""
 
 from .cloud_water_path import ParcelLiquidWaterPath
 from .parcel_displacement import ParcelDisplacement

{pysdm-2.99 → pysdm-2.100}/PySDM/products/size_spectral/__init__.py

@@ -1,4 +1,4 @@
-""" products expressing particle size-spectral quantities """
+"""products expressing particle size-spectral quantities"""
 
 from .arbitrary_moment import (
     RadiusFirstMoment,

{pysdm-2.99 → pysdm-2.100}/PySDM.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: PySDM
-Version: 2.99
+Version: 2.100
 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-2.99 → pysdm-2.100}/examples/PySDM_examples/Arabas_et_al_2023/commons.py

@@ -1,4 +1,4 @@
-""" ABIFM and INAS parameters and other constants """
+"""ABIFM and INAS parameters and other constants"""
 
 from PySDM import Formulae
 from PySDM.physics import si

{pysdm-2.99 → pysdm-2.100}/examples/PySDM_examples/Pierchala_et_al_2022/commons.py

@@ -1,5 +1,5 @@
-""" common data for use in the
-  [Pierchala et al. 2022](https://doi.org/10.1016/j.gca.2022.01.020) example
+"""common data for use in the
+[Pierchala et al. 2022](https://doi.org/10.1016/j.gca.2022.01.020) example
 """
 
 from PySDM.physics import constants_defaults as const