PySDM-examples 2.121__tar.gz → 2.122__tar.gz

{pysdm_examples-2.121 → pysdm_examples-2.122}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pysdm-examples
-Version: 2.121
+Version: 2.122
 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
@@ -75,12 +75,12 @@ The 2D prescribed-flow framework used here can be traced back to the work of
     and dry-air potential temperature.
   In PySDM-examples, the Eulerian advection is handled using the <a href="https://doi.org/10.21105/joss.03896">PyMPDATA</a> Numba-based
     implementation of the <a href="https://doi.org/10.1002/fld.1071">MPDATA numerical scheme of Smolarkiewicz (e.g., 2006)</a>.
-  An animation depicting PySDM simulation capturing <mark>aerosol collisional processing</mark> by warm rain is shown below:
-
-<video controls style="width:100%">
-  <source src="https://github.com/open-atmos/PySDM/releases/download/tip/docs_intro_animation_ubuntu-24.04.mp4" type="video/mp4">
-  Your browser does not support the video tag.
-</video>
+  An animation depicting PySDM simulation capturing <mark>aerosol collisional processing</mark> by warm rain is shown below
+  (<a href="https://github.com/open-atmos/PySDM/blob/main/examples/PySDM_examples/_HOWTOs/paraview_hello_world.ipynb">see
+  the Paraview hello-world HOWTO Jupyter notbook for code generating the simulation and visualisation</a>):
+<center>
+  <img src="https://github.com/open-atmos/PySDM/releases/download/tip/docs_intro_animation_ubuntu-24.04.gif" style="width:80%" />
+</center>
 
 Example notebooks:
 - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Arabas_et_al_2015.html">Arabas_et_al_2015</a>

{pysdm_examples-2.121 → pysdm_examples-2.122}/PySDM_examples/Arabas_et_al_2015/example.py

@@ -1,6 +1,6 @@
 from open_atmos_jupyter_utils import TemporaryFile
 from PySDM_examples.Arabas_et_al_2015 import Settings, SpinUp
-from PySDM_examples.Szumowski_et_al_1998 import Simulation, Storage
+from PySDM_examples.utils.kinematic_2d import Simulation, Storage
 from PySDM_examples.utils import DummyController
 
 from PySDM import Formulae

{pysdm_examples-2.121 → pysdm_examples-2.122}/PySDM_examples/Arabas_et_al_2015/example_benchmark.py

@@ -2,7 +2,7 @@ import importlib
 
 from matplotlib import pyplot as plt
 from PySDM_examples.Arabas_et_al_2015 import Settings
-from PySDM_examples.Szumowski_et_al_1998 import Simulation, Storage
+from PySDM_examples.utils.kinematic_2d import Simulation, Storage
 
 import PySDM.backends.impl_numba.conf
 from PySDM import Formulae

{pysdm_examples-2.121 → pysdm_examples-2.122}/PySDM_examples/Morrison_and_Grabowski_2007/__init__.py

@@ -3,10 +3,6 @@
 prescribed-flow simulation settings data from
 [Morrison & Grabowski 2007 (JAS)](https://doi.org/10.1175/JAS3980)
 
-fig_2.ipynb:
-.. include:: ./fig_2.ipynb.badges.md
-
-fig_3.ipynb:
-.. include:: ./fig_3.ipynb.badges.md
+fig_1.ipynb:
+.. include:: ./fig_1.ipynb.badges.md
 """
-from .cumulus import Cumulus

pysdm_examples-2.122/PySDM_examples/utils/kinematic_2d/__init__.py

@@ -0,0 +1,19 @@
+# pylint: disable=invalid-name
+"""
+The 2D prescribed-flow framework used here can be traced back to the work
+of [Kessler 1969 (section 3C)](https://doi.org/10.1007/978-1-935704-36-2_1), can be found also in
+[Szumowski et al. 1998 (Atmos. Res.)](https://doi.org/10.1016/S0169-8095(97)00082-3).
+
+The setup mimics a stratiform cloud deck and features periodic horizontal boundary condition
+and vanishing flow at vertical boundaries.
+It was introduced in [Morrison & Grabowski 2007](https://doi.org/10.1175/JAS3980) and later adopted
+for particle-based simulations in [Arabas et al. 2015](https://doi.org/10.5194/gmd-8-1677-2015)
+It uses a non-devergent single-eddy flow field resulting in an updraft-downdraft pair in the domain.
+The flow field advects two scalar fields in an Eulerian way: water vapour mixing ratio
+and dry-air potential temperature.
+"""
+
+from .gui_settings import GUISettings
+from .mpdata_2d import MPDATA_2D
+from .simulation import Simulation
+from .storage import Storage

{pysdm_examples-2.121/PySDM_examples/Szumowski_et_al_1998 → pysdm_examples-2.122/PySDM_examples/utils/kinematic_2d}/gui.py

@@ -2,8 +2,10 @@ import os
 import sys
 
 from open_atmos_jupyter_utils import TemporaryFile
-from PySDM_examples.Szumowski_et_al_1998.gui_controller import GUIController
-from PySDM_examples.Szumowski_et_al_1998.gui_viewer import GUIViewer
+from PySDM_examples.utils.kinematic_2d.gui_controller import (
+    GUIController,
+)
+from PySDM_examples.utils.kinematic_2d.gui_viewer import GUIViewer
 from PySDM_examples.utils.widgets import HTML, Tab, VBox, display
 
 from PySDM.exporters import NetCDFExporter

{pysdm_examples-2.121/PySDM_examples/Szumowski_et_al_1998 → pysdm_examples-2.122/PySDM_examples/utils/kinematic_2d}/gui_viewer.py

@@ -3,7 +3,7 @@ import warnings
 import numpy as np
 from matplotlib import pyplot, rcParams
 from open_atmos_jupyter_utils import save_and_make_link
-from PySDM_examples.Szumowski_et_al_1998.plots import (
+from PySDM_examples.utils.kinematic_2d.plots import (
     _ImagePlot,
     _SpectrumPlot,
     _TemperaturePlot,

{pysdm_examples-2.121/PySDM_examples/Szumowski_et_al_1998 → pysdm_examples-2.122/PySDM_examples/utils/kinematic_2d}/mpdata_2d.py

@@ -5,7 +5,7 @@ from threading import Thread
 import numpy as np
 from PyMPDATA import Options, ScalarField, Solver, Stepper, VectorField
 from PyMPDATA.boundary_conditions import Periodic
-from PySDM_examples.Szumowski_et_al_1998.fields import (
+from PySDM_examples.utils.kinematic_2d.fields import (
     nondivergent_vector_field_2d,
     x_vec_coord,
     z_vec_coord,

{pysdm_examples-2.121/PySDM_examples/Szumowski_et_al_1998 → pysdm_examples-2.122/PySDM_examples/utils/kinematic_2d}/simulation.py

@@ -1,8 +1,8 @@
 import numpy as np
-from PySDM_examples.Szumowski_et_al_1998.make_default_product_collection import (
+from PySDM_examples.utils.kinematic_2d.make_default_product_collection import (
     make_default_product_collection,
 )
-from PySDM_examples.Szumowski_et_al_1998.mpdata_2d import MPDATA_2D
+from PySDM_examples.utils.kinematic_2d.mpdata_2d import MPDATA_2D
 from PySDM_examples.utils import DummyController
 
 from PySDM.backends import CPU

{pysdm_examples-2.121 → pysdm_examples-2.122}/docs/pysdm_examples_landing.md

@@ -39,12 +39,12 @@ The 2D prescribed-flow framework used here can be traced back to the work of
     and dry-air potential temperature.
   In PySDM-examples, the Eulerian advection is handled using the <a href="https://doi.org/10.21105/joss.03896">PyMPDATA</a> Numba-based
     implementation of the <a href="https://doi.org/10.1002/fld.1071">MPDATA numerical scheme of Smolarkiewicz (e.g., 2006)</a>.
-  An animation depicting PySDM simulation capturing <mark>aerosol collisional processing</mark> by warm rain is shown below:
-
-<video controls style="width:100%">
-  <source src="https://github.com/open-atmos/PySDM/releases/download/tip/docs_intro_animation_ubuntu-24.04.mp4" type="video/mp4">
-  Your browser does not support the video tag.
-</video>
+  An animation depicting PySDM simulation capturing <mark>aerosol collisional processing</mark> by warm rain is shown below
+  (<a href="https://github.com/open-atmos/PySDM/blob/main/examples/PySDM_examples/_HOWTOs/paraview_hello_world.ipynb">see
+  the Paraview hello-world HOWTO Jupyter notbook for code generating the simulation and visualisation</a>):
+<center>
+  <img src="https://github.com/open-atmos/PySDM/releases/download/tip/docs_intro_animation_ubuntu-24.04.gif" style="width:80%" />
+</center>
 
 Example notebooks:
 - `PySDM_examples.Arabas_et_al_2015`

{pysdm_examples-2.121 → pysdm_examples-2.122}/pyproject.toml

@@ -4,4 +4,4 @@ local_scheme = "no-local-version"
 version_scheme = "post-release"
 
 [build-system]
-requires = ['setuptools==80.7.1', 'setuptools-scm==8.3.1']
+requires = ['setuptools==80.8.0', 'setuptools-scm==8.3.1']

{pysdm_examples-2.121 → pysdm_examples-2.122}/pysdm_examples.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pysdm-examples
-Version: 2.121
+Version: 2.122
 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
@@ -75,12 +75,12 @@ The 2D prescribed-flow framework used here can be traced back to the work of
     and dry-air potential temperature.
   In PySDM-examples, the Eulerian advection is handled using the <a href="https://doi.org/10.21105/joss.03896">PyMPDATA</a> Numba-based
     implementation of the <a href="https://doi.org/10.1002/fld.1071">MPDATA numerical scheme of Smolarkiewicz (e.g., 2006)</a>.
-  An animation depicting PySDM simulation capturing <mark>aerosol collisional processing</mark> by warm rain is shown below:
-
-<video controls style="width:100%">
-  <source src="https://github.com/open-atmos/PySDM/releases/download/tip/docs_intro_animation_ubuntu-24.04.mp4" type="video/mp4">
-  Your browser does not support the video tag.
-</video>
+  An animation depicting PySDM simulation capturing <mark>aerosol collisional processing</mark> by warm rain is shown below
+  (<a href="https://github.com/open-atmos/PySDM/blob/main/examples/PySDM_examples/_HOWTOs/paraview_hello_world.ipynb">see
+  the Paraview hello-world HOWTO Jupyter notbook for code generating the simulation and visualisation</a>):
+<center>
+  <img src="https://github.com/open-atmos/PySDM/releases/download/tip/docs_intro_animation_ubuntu-24.04.gif" style="width:80%" />
+</center>
 
 Example notebooks:
 - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Arabas_et_al_2015.html">Arabas_et_al_2015</a>

{pysdm_examples-2.121 → pysdm_examples-2.122}/pysdm_examples.egg-info/SOURCES.txt

@@ -85,7 +85,6 @@ PySDM_examples/Merlivat_and_Nief_1967/__init__.py
 PySDM_examples/Miyake_et_al_1968/__init__.py
 PySDM_examples/Morrison_and_Grabowski_2007/__init__.py
 PySDM_examples/Morrison_and_Grabowski_2007/common.py
-PySDM_examples/Morrison_and_Grabowski_2007/cumulus.py
 PySDM_examples/Morrison_and_Grabowski_2007/strato_cumulus.py
 PySDM_examples/Niedermeier_et_al_2014/__init__.py
 PySDM_examples/Niedermeier_et_al_2014/settings.py
@@ -121,18 +120,6 @@ PySDM_examples/Srivastava_1982/example.py
 PySDM_examples/Srivastava_1982/settings.py
 PySDM_examples/Srivastava_1982/simulation.py
 PySDM_examples/Stewart_1975/__init__.py
-PySDM_examples/Szumowski_et_al_1998/__init__.py
-PySDM_examples/Szumowski_et_al_1998/fields.py
-PySDM_examples/Szumowski_et_al_1998/gui.py
-PySDM_examples/Szumowski_et_al_1998/gui_controller.py
-PySDM_examples/Szumowski_et_al_1998/gui_settings.py
-PySDM_examples/Szumowski_et_al_1998/gui_viewer.py
-PySDM_examples/Szumowski_et_al_1998/make_default_product_collection.py
-PySDM_examples/Szumowski_et_al_1998/mpdata_2d.py
-PySDM_examples/Szumowski_et_al_1998/plots.py
-PySDM_examples/Szumowski_et_al_1998/simulation.py
-PySDM_examples/Szumowski_et_al_1998/sounding.py
-PySDM_examples/Szumowski_et_al_1998/storage.py
 PySDM_examples/Toon_et_al_1980/__init__.py
 PySDM_examples/Van_Hook_1968/__init__.py
 PySDM_examples/Yang_et_al_2018/__init__.py
@@ -161,6 +148,17 @@ PySDM_examples/utils/dummy_controller.py
 PySDM_examples/utils/progbar_controller.py
 PySDM_examples/utils/pvanim.py
 PySDM_examples/utils/read_vtk_1d.py
+PySDM_examples/utils/kinematic_2d/__init__.py
+PySDM_examples/utils/kinematic_2d/fields.py
+PySDM_examples/utils/kinematic_2d/gui.py
+PySDM_examples/utils/kinematic_2d/gui_controller.py
+PySDM_examples/utils/kinematic_2d/gui_settings.py
+PySDM_examples/utils/kinematic_2d/gui_viewer.py
+PySDM_examples/utils/kinematic_2d/make_default_product_collection.py
+PySDM_examples/utils/kinematic_2d/mpdata_2d.py
+PySDM_examples/utils/kinematic_2d/plots.py
+PySDM_examples/utils/kinematic_2d/simulation.py
+PySDM_examples/utils/kinematic_2d/storage.py
 PySDM_examples/utils/widgets/__init__.py
 PySDM_examples/utils/widgets/freezer.py
 PySDM_examples/utils/widgets/progbar_updater.py

pysdm_examples-2.121/PySDM_examples/Morrison_and_Grabowski_2007/cumulus.py

@@ -1,136 +0,0 @@
-import numpy as np
-from PySDM_examples.Morrison_and_Grabowski_2007.common import Common
-from PySDM_examples.Szumowski_et_al_1998 import sounding
-from scipy.integrate import solve_ivp
-from scipy.interpolate import interp1d
-
-from PySDM.physics import si
-
-
-class Cumulus(Common):
-    def __init__(self, formulae):
-        super().__init__(formulae)
-        self.size = (9 * si.km, 2.7 * si.km)
-        self.hx = 1.8 * si.km
-        self.x0 = 3.6 * si.km
-        self.xc = self.size[0] / 2
-        self.dz = 50 * si.m
-        self.grid = tuple(s / self.dz for s in self.size)
-        for g in self.grid:
-            assert int(g) == g
-        self.grid = tuple(int(g) for g in self.grid)
-        self.dt = 1 * si.s
-        self.simulation_time = 60 * si.min
-
-        self.__init_profiles()
-
-    def __init_profiles(self):
-        z_of_p = self.__z_of_p()
-        T_of_z = interp1d(z_of_p, sounding.temperature)
-        p_of_z = interp1d(z_of_p, sounding.pressure)
-        q_of_z = interp1d(z_of_p, sounding.mixing_ratio)
-
-        z_points_scalar = np.linspace(
-            self.dz / 2, self.size[-1] - self.dz / 2, num=self.grid[-1], endpoint=True
-        )
-        z_points_both = np.linspace(
-            0, self.size[-1], num=2 * self.grid[-1] + 1, endpoint=True
-        )
-        rhod_of_z = self.__rhod_of_z(T_of_z, p_of_z, q_of_z, z_of_p, z_points_both)
-        self.rhod = interp1d(z_points_both / self.size[-1], rhod_of_z)
-        self.initial_water_vapour_mixing_ratio = q_of_z(z_points_scalar)
-        self.th_std0 = self.formulae.trivia.th_std(
-            p_of_z(z_points_scalar), T_of_z(z_points_scalar)
-        )
-
-    def rhod_of_zZ(self, zZ):
-        return self.rhod(zZ)
-
-    def __rhod_of_z(self, T_of_z, p_of_z, q_of_z, z_of_p, z_points):
-        def drhod_dz(z, _):
-            lv = self.formulae.latent_heat_vapourisation.lv(T_of_z(z))
-            return self.formulae.hydrostatics.drho_dz(
-                p_of_z(z), T_of_z(z), q_of_z(z), lv
-            )
-
-        theta_std0 = self.formulae.trivia.th_std(
-            sounding.pressure[0], sounding.temperature[0]
-        )
-        rhod0 = self.formulae.state_variable_triplet.rho_d(
-            sounding.pressure[0], sounding.mixing_ratio[0], theta_std0
-        )
-        rhod_solution = solve_ivp(
-            fun=drhod_dz,
-            t_span=(0, np.amax(z_of_p)),
-            y0=np.asarray((rhod0,)),
-            t_eval=z_points,
-        )
-        assert rhod_solution.success
-        return rhod_solution.y[0]
-
-    def __z_of_p(self):
-        T_virt_of_p = interp1d(
-            sounding.pressure,
-            sounding.temperature
-            * (1 + sounding.mixing_ratio / self.formulae.constants.eps)
-            / (1 + sounding.mixing_ratio),
-        )
-
-        def dz_dp(p, _):
-            return (
-                -self.formulae.constants.Rd
-                * T_virt_of_p(p)
-                / self.formulae.constants.g_std
-                / p
-            )
-
-        z_of_p = solve_ivp(
-            fun=dz_dp,
-            t_span=(max(sounding.pressure), min(sounding.pressure)),
-            y0=np.asarray((0,)),
-            t_eval=sounding.pressure,
-        )
-        assert z_of_p.success
-        return z_of_p.y[0]
-
-    @staticmethod
-    def z0(z):
-        return np.where(z <= 1.7 * si.km, 0, 0.7 * si.km)
-
-    @staticmethod
-    def hz(z):
-        return np.where(z <= 1.7 * si.km, 3.4 * si.km, 2.0 * si.km)
-
-    def alpha(self, x):
-        return np.where(abs(x - self.xc) <= 0.9 * si.km, 1, 0)
-
-    @staticmethod
-    def beta(x):
-        return np.where(x <= 5.4 * si.km, 1, -1)
-
-    @staticmethod
-    def A1(t):
-        if t <= 900 * si.s:
-            return 5.73e2
-        if t <= 1500 * si.s:
-            return 5.73e2 + 2.02e3 * (1 + np.cos(np.pi * ((t - 900) / 600 + 1)))
-        return 1.15e3 + 1.72e3 * (1 + np.cos(np.pi * ((min(t, 2400) - 1500) / 900 + 1)))
-
-    @staticmethod
-    def A2(t):
-        if t <= 300 * si.s:
-            return 0
-        if t <= 1500 * si.s:
-            return 6e2 * (1 + np.cos(np.pi * ((t - 300) / 600 - 1)))
-        return 5e2 * (1 + np.cos(np.pi * ((min(2400, t) - 1500) / 900 - 1)))
-
-    # see Appendix (page 2859)
-    def stream_function(self, xX, zZ, t):
-        x = xX * self.size[0]
-        z = zZ * self.size[-1]
-        return (
-            -self.A1(t)
-            * np.cos(self.alpha(x) * np.pi * (x - self.x0) / self.hx)
-            * np.sin(self.beta(x) * np.pi * (z - self.z0(z)) / self.hz(z))
-            + self.A2(t) / 2 * zZ**2
-        )

pysdm_examples-2.121/PySDM_examples/Szumowski_et_al_1998/__init__.py

@@ -1,9 +0,0 @@
-# pylint: disable=invalid-name
-"""
-2D GUI-equipped prescribed-flow warm-rain case based on
-[Szumowski et al. 1998 (Atmos. Res.)](https://doi.org/10.1016/S0169-8095(97)00082-3)
-"""
-from .gui_settings import GUISettings
-from .mpdata_2d import MPDATA_2D
-from .simulation import Simulation
-from .storage import Storage

pysdm_examples-2.121/PySDM_examples/Szumowski_et_al_1998/sounding.py

@@ -1,93 +0,0 @@
-import numpy as np
-
-from PySDM.physics import constants as const
-from PySDM.physics import si
-
-pressure = (
-    np.array(
-        (
-            1014,
-            1010,
-            1000,
-            990,
-            975,
-            960,
-            950,
-            925,
-            900,
-            875,
-            850,
-            825,
-            800,
-            790,
-            775,
-            765,
-            755,
-            745,
-            730,
-            715,
-            700,
-        )
-    )
-    * si.hPa
-)
-
-temperature = (
-    np.array(
-        (
-            25.2,
-            24.8,
-            23.6,
-            22.5,
-            21.8,
-            20.5,
-            19.9,
-            18.2,
-            16.8,
-            14.8,
-            13.3,
-            11.9,
-            11.0,
-            11.3,
-            10.9,
-            11.2,
-            10.2,
-            11.0,
-            11.2,
-            10.0,
-            8.8,
-        )
-    )
-    * si.kelvin
-    + const.T0
-)
-
-mixing_ratio = (
-    np.array(
-        (
-            14.5,
-            14.5,
-            14.5,
-            14.0,
-            13.7,
-            13.9,
-            13.9,
-            10.3,
-            10.3,
-            10.0,
-            9.9,
-            8.9,
-            7.9,
-            4.0,
-            2.3,
-            1.2,
-            1.2,
-            0.9,
-            0.6,
-            2.0,
-            1.6,
-        )
-    )
-    * si.g
-    / si.kg
-)