PySDM-examples 3.0.0rc34__tar.gz → 3.0.0rc36__tar.gz

{pysdm_examples-3.0.0rc34/pysdm_examples.egg-info → pysdm_examples-3.0.0rc36}/PKG-INFO

@@ -1,11 +1,9 @@
 Metadata-Version: 2.4
 Name: pysdm-examples
-Version: 3.0.0rc34
+Version: 3.0.0rc36
 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
-Author-email: sylwester.arabas@agh.edu.pl
-License: GPL-3.0
+Author-email: "https://github.com/open-atmos/PySDM/graphs/contributors" <sylwester.arabas@agh.edu.pl>
+License-Expression: GPL-3.0-only
 Project-URL: Tracker, https://github.com/open-atmos/PySDM/issues
 Project-URL: Documentation, https://open-atmos.github.io/PySDM/PySDM_examples
 Project-URL: Source, https://github.com/open-atmos/PySDM/tree/main/examples
@@ -24,6 +22,8 @@ Requires-Dist: pyrcel
 Requires-Dist: pyvinecopulib
 Requires-Dist: networkx
 Requires-Dist: PyVista
+Requires-Dist: cmcrameri
+Requires-Dist: cmap
 Provides-Extra: ci-version-pins
 Requires-Dist: PySDM[CI_version_pins]; extra == "ci-version-pins"
 Requires-Dist: PyMPDATA==1.7.3; extra == "ci-version-pins"
@@ -35,18 +35,12 @@ 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==9.6.2; extra == "ci-version-pins"
-Requires-Dist: pyrcel==1.3.4; extra == "ci-version-pins"
+Requires-Dist: pyrcel==1.3.5; extra == "ci-version-pins"
 Requires-Dist: pyvinecopulib==0.7.6; extra == "ci-version-pins"
-Dynamic: author
-Dynamic: author-email
+Requires-Dist: cmcrameri==1.9; extra == "ci-version-pins"
+Requires-Dist: cmap==0.7.2; extra == "ci-version-pins"
 Dynamic: description
 Dynamic: description-content-type
-Dynamic: home-page
-Dynamic: license
-Dynamic: project-url
-Dynamic: provides-extra
-Dynamic: requires-dist
-Dynamic: summary
 
 # Introduction
 

{pysdm_examples-3.0.0rc34 → pysdm_examples-3.0.0rc36}/PySDM_examples/Arabas_et_al_2015/example_benchmark.py

@@ -54,7 +54,7 @@ def main():
         for sd in n_sd:
             settings.n_sd_per_gridbox = sd
             storage = Storage()
-            simulation = Simulation(settings, storage, None, backend)
+            simulation = Simulation(settings, storage, None, backend())
             simulation.reinit(products=[WallTime()])
             simulation.run()
             times[key].append(storage.load("wall time")[-1])

pysdm_examples-3.0.0rc36/PySDM_examples/Ware_et_al_2025/__init__.py

@@ -0,0 +1,22 @@
+"""
+SDM adaptivity example based on
+[Ware et al. 2025 (arXiv)](https://doi.org/10.48550/arXiv.2509.05536)
+
+fig_1.ipynb:
+.. include:: ./fig_1.ipynb.badges.md
+
+fig_3_4.ipynb:
+.. include:: ./fig_3_4.ipynb.badges.md
+
+fig_5.ipynb:
+.. include:: ./fig_5.ipynb.badges.md
+
+fig_6_7_8.ipynb:
+.. include:: ./fig_6_7_8.ipynb.badges.md
+
+fig_A1.ipynb:
+.. include:: ./fig_A1.ipynb.badges.md
+
+"""
+
+# pylint: disable=invalid-name

pysdm_examples-3.0.0rc36/PySDM_examples/Ware_et_al_2025/example.py

@@ -0,0 +1,252 @@
+from typing import Optional
+from packaging import version
+
+import numpy as np
+import matplotlib
+from matplotlib import pyplot
+from open_atmos_jupyter_utils import show_plot
+
+from PySDM.builder import Builder
+from PySDM.dynamics import Coalescence
+from PySDM.environments import Box
+from PySDM.products import (
+    ParticleVolumeVersusRadiusLogarithmSpectrum,
+    WallTime,
+    CollisionRateDeficitPerGridbox,
+)
+
+from PySDM import Formulae
+from PySDM.dynamics.collisions.collision_kernels import Golovin
+from PySDM.initialisation import spectra
+from PySDM.physics import si
+
+_matplotlib_version_3_3_3 = version.parse("3.3.0")
+_matplotlib_version_actual = version.parse(matplotlib.__version__)
+
+
+def error_measure(y, y_true, x):
+    # The length of each bin on a logarithmic scale.
+    dlnr = np.gradient(np.log(x))
+
+    F = np.cumsum(y * dlnr)
+    CDF_Golovin = np.cumsum(y_true * dlnr)
+
+    return np.trapz(np.abs(CDF_Golovin - F), np.log(x))
+
+
+class Settings:
+    def __init__(self: int, steps: Optional[list] = None):
+        steps = steps or [0, 1200, 2400, 3600]
+        self.formulae = Formulae()
+        self.n_sd = 2**13
+        self.n_part = 2**23 / si.metre**3
+        self.X0 = self.formulae.trivia.volume(radius=30.531 * si.micrometres)
+        self.dv = 1e6 * si.metres**3
+        self.norm_factor = self.n_part * self.dv
+        self.rho = 1000 * si.kilogram / si.metre**3
+        self.dt = 1 * si.seconds
+        self.adaptive = False
+        self.steps = steps
+        self.kernel = Golovin(b=1.5e3 / si.second)
+        self.spectrum = spectra.Exponential(norm_factor=self.norm_factor, scale=self.X0)
+        self.radius_bins_edges = np.logspace(
+            np.log10(10 * si.um), np.log10(5e3 * si.um), num=128, endpoint=True
+        )
+
+    @property
+    def output_steps(self):
+        return [int(step / self.dt) for step in self.steps]
+
+
+class SpectrumColors:
+    def __init__(self, begining="#2cbdfe", end="#b317b1"):
+        self.b = begining
+        self.e = end
+
+    def __call__(self, value: float):
+        bR, bG, bB = int(self.b[1:3], 16), int(self.b[3:5], 16), int(self.b[5:7], 16)
+        eR, eG, eB = int(self.e[1:3], 16), int(self.e[3:5], 16), int(self.e[5:7], 16)
+        R = bR + int((eR - bR) * value)
+        G = bG + int((eG - bG) * value)
+        B = bB + int((eB - bB) * value)
+        result = f"#{hex(R)[2:4]}{hex(G)[2:4]}{hex(B)[2:4]}"
+        return result
+
+
+class SpectrumPlotter:
+    def __init__(self, settings, title=None, grid=True, legend=True, log_base=10):
+        self.settings = settings
+        self.format = "pdf"
+        self.colors = SpectrumColors()
+        self.smooth = False
+        self.smooth_scope = 2
+        self.legend = legend
+        self.grid = grid
+        self.title = title
+        self.xlabel = "particle radius [µm]"
+        self.ylabel = "dm/dlnr [g/m^3/(unit dr/r)]"
+        self.log_base = log_base
+        self._ax = None
+        self.finished = False
+
+    @property
+    def ax(self):
+        return self._ax or pyplot.gca()
+
+    @ax.setter
+    def ax(self, value):
+        self._ax = value
+
+    def finish(self):
+        if self.finished:
+            return
+        self.finished = True
+        if self.grid:
+            self.ax.grid()
+
+        base_arg = {
+            "base"
+            + (
+                "x" if _matplotlib_version_actual < _matplotlib_version_3_3_3 else ""
+            ): self.log_base
+        }
+        if self.title is not None:
+            self.ax.set_title(self.title)
+        self.ax.set_xscale("log", **base_arg)
+        self.ax.set_xlabel(self.xlabel)
+        self.ax.set_ylabel(self.ylabel)
+        if self.legend:
+            self.ax.legend()
+
+    def show(self):
+        self.finish()
+        pyplot.tight_layout()
+        show_plot()
+
+    def save(self, file):
+        self.finish()
+        pyplot.savefig(file, format=self.format)
+
+    def plot(
+        self, spectrum, t, label=None, color=None, title=None, add_error_to_label=False
+    ):
+        error = self.plot_analytic_solution(self.settings, t, spectrum, title)
+        if label is not None and add_error_to_label:
+            label += f" error={error:.4g}"
+        self.plot_data(self.settings, t, spectrum, label, color)
+        return error
+
+    def plot_analytic_solution(self, settings, t, spectrum, title):
+        if t == 0:
+            analytic_solution = settings.spectrum.size_distribution
+        else:
+
+            def analytic_solution(x):
+                return settings.norm_factor * settings.kernel.analytic_solution(
+                    x=x, t=t, x_0=settings.X0, N_0=settings.n_part
+                )
+
+        volume_bins_edges = self.settings.formulae.trivia.volume(
+            settings.radius_bins_edges
+        )
+        dm = np.diff(volume_bins_edges)
+        dr = np.diff(settings.radius_bins_edges)
+
+        pdf_m_x = volume_bins_edges[:-1] + dm / 2
+        pdf_m_y = analytic_solution(pdf_m_x)
+
+        pdf_r_x = settings.radius_bins_edges[:-1] + dr / 2
+        pdf_r_y = pdf_m_y * dm / dr * pdf_r_x
+
+        x = pdf_r_x * si.metres / si.micrometres
+        y_true = (
+            pdf_r_y
+            * self.settings.formulae.trivia.volume(radius=pdf_r_x)
+            * settings.rho
+            / settings.dv
+            * si.kilograms
+            / si.grams
+        )
+
+        self.ax.plot(x, y_true, color="black")
+
+        if spectrum is not None:
+            y = spectrum * si.kilograms / si.grams
+            error = error_measure(y, y_true, x)
+            self.title = (
+                title or f"error measure: {error:.2f}"
+            )  # TODO #327 relative error
+            return error
+        return None
+
+    def plot_data(self, settings, t, spectrum, label, color):
+        if self.smooth:
+            scope = self.smooth_scope
+            if t != 0:
+                new = np.copy(spectrum)
+                for _ in range(2):
+                    for i in range(scope, len(spectrum) - scope):
+                        new[i] = np.mean(spectrum[i - scope : i + scope + 1])
+                    scope = 1
+                    for i in range(scope, len(spectrum) - scope):
+                        spectrum[i] = np.mean(new[i - scope : i + scope + 1])
+
+            x = settings.radius_bins_edges[:-scope]
+            dx = np.diff(x)
+            self.ax.plot(
+                (x[:-1] + dx / 2) * si.metres / si.micrometres,
+                spectrum[:-scope] * si.kilograms / si.grams,
+                label=label or f"t = {t}s",
+                color=color
+                or self.colors(t / (self.settings.output_steps[-1] * self.settings.dt)),
+            )
+        else:
+            self.ax.step(
+                settings.radius_bins_edges[:-1] * si.metres / si.micrometres,
+                spectrum * si.kilograms / si.grams,
+                where="post",
+                label=label or f"t = {t}s",
+                color=color
+                or self.colors(t / (self.settings.output_steps[-1] * self.settings.dt)),
+            )
+
+
+def run(settings, backend, observers=(), sampling_method="deterministic"):
+    builder = Builder(
+        n_sd=settings.n_sd,
+        backend=backend,
+        environment=Box(dv=settings.dv, dt=settings.dt),
+        dynamics=(
+            Coalescence(collision_kernel=settings.kernel, adaptive=settings.adaptive),
+        ),
+    )
+    builder.particulator.environment["rhod"] = 1.0
+    attributes = {}
+    sampling = settings.sampling
+    attributes["volume"], attributes["multiplicity"] = getattr(
+        sampling, f"sample_{sampling_method}"
+    )(settings.n_sd, backend=backend)
+    products = (
+        ParticleVolumeVersusRadiusLogarithmSpectrum(
+            settings.radius_bins_edges, name="dv/dlnr"
+        ),
+        WallTime(),
+        CollisionRateDeficitPerGridbox(name="deficit"),
+    )
+    particulator = builder.build(attributes, products)
+
+    for observer in observers:
+        particulator.observers.append(observer)
+
+    vals = {}
+    deficit = 0
+    particulator.products["wall time"].reset()
+    for step in settings.output_steps:
+        particulator.run(step - particulator.n_steps)
+        vals[step] = particulator.products["dv/dlnr"].get()[0]
+        vals[step][:] *= settings.rho
+        deficit += particulator.products["deficit"].get()
+    deficit = deficit / len(settings.output_steps)
+
+    exec_time = particulator.products["wall time"].get()
+    return vals, exec_time, deficit

{pysdm_examples-3.0.0rc34 → pysdm_examples-3.0.0rc36}/PySDM_examples/utils/kinematic_2d/simulation.py

@@ -21,11 +21,11 @@ from PySDM.initialisation.sampling import spatial_sampling
 
 
 class Simulation:
-    def __init__(self, settings, storage, SpinUp, backend_class=CPU):
+    def __init__(self, settings, storage, SpinUp, backend=None):
         self.settings = settings
         self.storage = storage
         self.particulator = None
-        self.backend_class = backend_class
+        self.backend = backend or CPU(settings.formulae)
         self.SpinUp = SpinUp
 
     @property
@@ -34,7 +34,7 @@ class Simulation:
 
     def reinit(self, products=None):
         formulae = self.settings.formulae
-        backend = self.backend_class(formulae=formulae)
+        backend = self.backend
         environment = Kinematic2D(
             dt=self.settings.dt,
             grid=self.settings.grid,

pysdm_examples-3.0.0rc36/pyproject.toml

@@ -0,0 +1,61 @@
+[tool.setuptools_scm]
+root = ".."
+local_scheme = "no-local-version"
+version_scheme = "post-release"
+
+[build-system]
+requires = ['setuptools==82.0.1', 'setuptools-scm==9.2.2']
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+include = ["PySDM_examples", "PySDM_examples*"]
+
+[project]
+name = "pysdm-examples"
+description = "PySDM usage examples reproducing results from literature and depicting how to use PySDM from Python Jupyter notebooks"
+license = "GPL-3.0-only"
+authors = [
+    {name = "https://github.com/open-atmos/PySDM/graphs/contributors", email = "sylwester.arabas@agh.edu.pl"}
+]
+dynamic = ["version", "readme"]
+dependencies = [
+    "PySDM",
+    "PyMPDATA",
+    "open-atmos-jupyter-utils",
+    "pystrict",
+    "matplotlib",
+    "joblib",
+    "ipywidgets",
+    "seaborn",
+    "numdifftools",
+    "vtk",
+    "pyrcel",
+    "pyvinecopulib",
+    "networkx",
+    "PyVista",
+    "cmcrameri",
+    "cmap",
+]
+
+[project.optional-dependencies]
+CI_version_pins = [
+    "PySDM[CI_version_pins]",
+    "PyMPDATA==1.7.3",
+    "open-atmos-jupyter-utils==1.5.0",
+    "pystrict==1.3",
+    "matplotlib!=3.9.1",
+    "joblib==1.5.3",
+    "ipywidgets==8.1.7",
+    "seaborn==0.13.2",
+    "numdifftools==0.9.42",
+    "vtk==9.6.2",
+    "pyrcel==1.3.5",
+    "pyvinecopulib==0.7.6",
+    "cmcrameri==1.9",
+    "cmap==0.7.2",
+]
+
+[project.urls]
+Tracker = "https://github.com/open-atmos/PySDM/issues"
+Documentation = "https://open-atmos.github.io/PySDM/PySDM_examples"
+Source = "https://github.com/open-atmos/PySDM/tree/main/examples"

{pysdm_examples-3.0.0rc34 → pysdm_examples-3.0.0rc36/pysdm_examples.egg-info}/PKG-INFO

@@ -1,11 +1,9 @@
 Metadata-Version: 2.4
 Name: pysdm-examples
-Version: 3.0.0rc34
+Version: 3.0.0rc36
 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
-Author-email: sylwester.arabas@agh.edu.pl
-License: GPL-3.0
+Author-email: "https://github.com/open-atmos/PySDM/graphs/contributors" <sylwester.arabas@agh.edu.pl>
+License-Expression: GPL-3.0-only
 Project-URL: Tracker, https://github.com/open-atmos/PySDM/issues
 Project-URL: Documentation, https://open-atmos.github.io/PySDM/PySDM_examples
 Project-URL: Source, https://github.com/open-atmos/PySDM/tree/main/examples
@@ -24,6 +22,8 @@ Requires-Dist: pyrcel
 Requires-Dist: pyvinecopulib
 Requires-Dist: networkx
 Requires-Dist: PyVista
+Requires-Dist: cmcrameri
+Requires-Dist: cmap
 Provides-Extra: ci-version-pins
 Requires-Dist: PySDM[CI_version_pins]; extra == "ci-version-pins"
 Requires-Dist: PyMPDATA==1.7.3; extra == "ci-version-pins"
@@ -35,18 +35,12 @@ 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==9.6.2; extra == "ci-version-pins"
-Requires-Dist: pyrcel==1.3.4; extra == "ci-version-pins"
+Requires-Dist: pyrcel==1.3.5; extra == "ci-version-pins"
 Requires-Dist: pyvinecopulib==0.7.6; extra == "ci-version-pins"
-Dynamic: author
-Dynamic: author-email
+Requires-Dist: cmcrameri==1.9; extra == "ci-version-pins"
+Requires-Dist: cmap==0.7.2; extra == "ci-version-pins"
 Dynamic: description
 Dynamic: description-content-type
-Dynamic: home-page
-Dynamic: license
-Dynamic: project-url
-Dynamic: provides-extra
-Dynamic: requires-dist
-Dynamic: summary
 
 # Introduction
 

{pysdm_examples-3.0.0rc34 → pysdm_examples-3.0.0rc36}/pysdm_examples.egg-info/SOURCES.txt

@@ -145,6 +145,7 @@ PySDM_examples/Strzabala_2025_BEng/__init__.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/Ware_et_al_2025/example.py
 PySDM_examples/Yang_et_al_2018/__init__.py
 PySDM_examples/Yang_et_al_2018/settings.py
 PySDM_examples/Yang_et_al_2018/simulation.py

{pysdm_examples-3.0.0rc34 → pysdm_examples-3.0.0rc36}/pysdm_examples.egg-info/requires.txt

@@ -12,6 +12,8 @@ pyrcel
 pyvinecopulib
 networkx
 PyVista
+cmcrameri
+cmap
 
 [CI_version_pins]
 PySDM[CI_version_pins]
@@ -24,5 +26,7 @@ ipywidgets==8.1.7
 seaborn==0.13.2
 numdifftools==0.9.42
 vtk==9.6.2
-pyrcel==1.3.4
+pyrcel==1.3.5
 pyvinecopulib==0.7.6
+cmcrameri==1.9
+cmap==0.7.2

pysdm_examples-3.0.0rc36/setup.py

@@ -0,0 +1,21 @@
+import re
+
+from setuptools import setup
+
+
+def get_long_description():
+    """returns contents of the pdoc landing site with pdoc links converted into URLs"""
+    with open("docs/pysdm_examples_landing.md", "r", encoding="utf8") as file:
+        pdoc_links = re.compile(
+            r"(`)([\w\d_-]*).([\w\d_-]*)(`)", re.MULTILINE | re.UNICODE
+        )
+        return pdoc_links.sub(
+            r'<a href="https://open-atmos.github.io/PySDM/\2/\3.html">\3</a>',
+            file.read(),
+        )
+
+
+setup(
+    long_description=get_long_description(),
+    long_description_content_type="text/markdown",
+)

pysdm_examples-3.0.0rc34/PySDM_examples/Ware_et_al_2025/__init__.py

@@ -1,10 +0,0 @@
-"""
-SDM adaptivity example based on
-[Ware et al. 2025 (arXiv)](https://doi.org/10.48550/arXiv.2509.05536)
-
-fig_A1.ipynb:
-.. include:: ./fig_A1.ipynb.badges.md
-
-"""
-
-# pylint: disable=invalid-name

pysdm_examples-3.0.0rc34/pyproject.toml

@@ -1,7 +0,0 @@
-[tool.setuptools_scm]
-root = ".."
-local_scheme = "no-local-version"
-version_scheme = "post-release"
-
-[build-system]
-requires = ['setuptools==82.0.1', 'setuptools-scm==9.2.2']

pysdm_examples-3.0.0rc34/setup.py

@@ -1,69 +0,0 @@
-import os
-import re
-
-from setuptools import find_packages, setup
-
-
-def get_long_description():
-    """returns contents of the pdoc landing site with pdoc links converted into URLs"""
-    with open("docs/pysdm_examples_landing.md", "r", encoding="utf8") as file:
-        pdoc_links = re.compile(
-            r"(`)([\w\d_-]*).([\w\d_-]*)(`)", re.MULTILINE | re.UNICODE
-        )
-        return pdoc_links.sub(
-            r'<a href="https://open-atmos.github.io/PySDM/\2/\3.html">\3</a>',
-            file.read(),
-        )
-
-
-CI = "CI" in os.environ
-
-setup(
-    name="pysdm-examples",
-    description="PySDM usage examples reproducing results from literature "
-    "and depicting how to use PySDM from Python Jupyter notebooks",
-    install_requires=[
-        "PySDM",
-        "PyMPDATA",
-        "open-atmos-jupyter-utils",
-        "pystrict",
-        "matplotlib",
-        "joblib",
-        "ipywidgets",
-        "seaborn",
-        "numdifftools",
-        "vtk",
-        "pyrcel",
-        "pyvinecopulib",
-        "networkx",
-        "PyVista",
-    ],
-    extras_require={
-        "CI_version_pins": [
-            "PySDM[CI_version_pins]",
-            "PyMPDATA==1.7.3",
-            "open-atmos-jupyter-utils==1.5.0",
-            "pystrict==1.3",
-            "matplotlib!=3.9.1",
-            "joblib==1.5.3",
-            "ipywidgets==8.1.7",
-            "seaborn==0.13.2",
-            "numdifftools==0.9.42",
-            "vtk==9.6.2",
-            "pyrcel==1.3.4",
-            "pyvinecopulib==0.7.6",
-        ]
-    },
-    author="https://github.com/open-atmos/PySDM/graphs/contributors",
-    author_email="sylwester.arabas@agh.edu.pl",
-    long_description=get_long_description(),
-    long_description_content_type="text/markdown",
-    url="https://github.com/open-atmos/PySDM",
-    license="GPL-3.0",
-    packages=find_packages(include=["PySDM_examples", "PySDM_examples.*"]),
-    project_urls={
-        "Tracker": "https://github.com/open-atmos/PySDM/issues",
-        "Documentation": "https://open-atmos.github.io/PySDM/PySDM_examples",
-        "Source": "https://github.com/open-atmos/PySDM/tree/main/examples",
-    },
-)