PySDM-examples 3.0.0rc43__tar.gz → 3.0.2__tar.gz

{pysdm_examples-3.0.0rc43 → pysdm_examples-3.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pysdm-examples
-Version: 3.0.0rc43
+Version: 3.0.2
 Summary: PySDM usage examples reproducing results from literature and depicting how to use PySDM from Python Jupyter notebooks
 Author-email: "https://github.com/open-atmos/PySDM/graphs/contributors" <sylwester.arabas@agh.edu.pl>
 License-Expression: GPL-3.0-only
@@ -39,6 +39,7 @@ Requires-Dist: pyrcel==2.0.0; extra == "ci-version-pins"
 Requires-Dist: pyvinecopulib==1.0.0; extra == "ci-version-pins"
 Requires-Dist: cmcrameri==1.10; extra == "ci-version-pins"
 Requires-Dist: cmap==0.7.2; extra == "ci-version-pins"
+Requires-Dist: netCDF4==1.7.4; extra == "ci-version-pins"
 Dynamic: description
 Dynamic: description-content-type
 
@@ -84,17 +85,14 @@ The 2D prescribed-flow framework used here can be traced back to the work of
   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
-  (<a href="https://github.com/open-atmos/PySDM/blob/main/examples/PySDM_examples/_HOWTOs/paraview_hello_world.ipynb">see
+  (<a href="https://github.com/open-atmos/PySDM/blob/main/examples/PySDM_examples/tutorials/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>
-  - in-notebook GUI for setting up, running and interactively visualising the 2D kinematic simulations (with an option to export raw data to <mark>VTK</mark> and <mark>netCDF</mark> files, as well as to save plots to SVG or PDF):
-  - "hello world" notebook depicting how to automate using Python the process of loading data and creating animations in <mark>Paraview</mark>
-- <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Arabas_et_al_2025.html">Arabas_et_al_2025</a>: adaptation of the 2D kinematic setup for studying <mark>glaciation</mark> of the cloud deck by <mark>immersion freezing</mark>
+- `PySDM_examples.featured.Arabas_et_al_2025`: adaptation of the 2D kinematic setup for studying <mark>glaciation</mark> of the cloud deck by <mark>immersion freezing</mark>
 
 ## 1D kinematic environment (prescribed-flow, single-column)
 
@@ -106,19 +104,10 @@ As in the 2D kinematic framework above, the Eulerian advection is handled by
   <a href="https://open-atmos.github.io/PyMPDATA/">PyMPDATA</a>.
 
 Example notebooks:
-- <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Shipway_and_Hill_2012.html">Shipway_and_Hill_2012</a>: reproducing figures from the <a href="https://doi.org/10.1002/qj.1913">Shipway & Hill 2012</a> paper;
-- <a href="https://open-atmos.github.io/PySDM/PySDM_examples/deJong_Mackay_et_al_2023.html">deJong_Mackay_et_al_2023</a>: reproducing figures from the <a href="https://doi.org/10.5194/gmd-16-4193-2023">de Jong et al. 2023</a> paper where the single-column
+- `PySDM_examples.featured.Shipway_and_Hill_2012`: reproducing figures from the <a href="https://doi.org/10.1002/qj.1913">Shipway & Hill 2012</a> paper;
+- `PySDM_examples.featured.deJong_Mackay_et_al_2023`: reproducing figures from the <a href="https://doi.org/10.5194/gmd-16-4193-2023">de Jong et al. 2023</a> paper where the single-column
    framework was used to exemplify operation of the <mark>Monte-Carlo collisional breakup scheme</mark> in PySDM (scheme introduced in that paper).
 
-## OD/1D iterative parcel/column environment mimicking removal of precipitation
-
-This framework uses a parcel model with removal of precipitation for analysis,
-iterative equilibration, the isotopic composition of the water vapour and
-rain water in a column of air (no Eulerian transport, only iterative passage of a parcel through the column).
-
-<a href="https://open-atmos.github.io/PySDM/PySDM_examples/Rozanski_and_Sonntag_1982.html">Rozanski_and_Sonntag_1982</a>: bulk microphysics example (i.e. single super droplet) with
-deuterium and heavy-oxygen <mark>water isotopologues</mark> featured.
-
 ## 0D parcel environment
 
 The parcel framework implemented in PySDM uses a hydrostatic profile and adiabatic mass and energy conservation
@@ -126,19 +115,17 @@ The parcel framework implemented in PySDM uses a hydrostatic profile and adiabat
 
 Example notebooks include:
 - condensation only
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Arabas_and_Shima_2017.html">Arabas_and_Shima_2017</a>: monodisperse particle spectrum, activation/deactivation cycle
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Yang_et_al_2018.html">Yang_et_al_2018</a>: polydisperse particle spectrum, activation/deactivation cycles
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Abdul_Razzak_Ghan_2000.html">Abdul_Razzak_Ghan_2000</a>: polydisperse activation, comparison against <mark>GCM parameterisation</mark>
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Pyrcel.html">Pyrcel</a>: polydisperse activation, mimicking example test case from <mark>Pyrcel</mark> documentation
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Strzabala_2025_BEng.html">Strzabala_2025_BEng</a>: ParaView visualisation example
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Lowe_et_al_2019.html">Lowe_et_al_2019</a>: externally mixed polydisperse size spectrum with <mark>surface-active organics</mark> case
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Grabowski_and_Pawlowska_2023.html">Grabowski_and_Pawlowska_2023</a>: polydisperse activation, focus on <mark>ripening</mark>
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Jensen_and_Nugent_2017.html">Jensen_and_Nugent_2017</a>: polydisperse activation featuring <mark>giant CCN</mark>
+  - `PySDM_examples.featured.Arabas_and_Shima_2017`: monodisperse particle spectrum, activation/deactivation cycle
+  - `PySDM_examples.featured.Yang_et_al_2018`: polydisperse particle spectrum, activation/deactivation cycles
+  - `PySDM_examples.featured.Abdul_Razzak_Ghan_2000`: polydisperse activation, comparison against <mark>GCM parameterisation</mark>
+  - `PySDM_examples.featured.pyrcel_docs_testcase`: polydisperse activation, mimicking example test case from <mark>Pyrcel</mark> documentation
+  - `PySDM_examples.featured.Lowe_et_al_2019`: externally mixed polydisperse size spectrum with <mark>surface-active organics</mark> case
+  - `PySDM_examples.featured.Grabowski_and_Pawlowska_2023`: polydisperse activation, focus on <mark>ripening</mark>
+  - `PySDM_examples.featured.Jensen_and_Nugent_2017`: polydisperse activation featuring <mark>giant CCN</mark>
 - condensation and aqueous-chemistry
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Kreidenweis_et_al_2003.html">Kreidenweis_et_al_2003</a>: <mark>Hoppel gap</mark> simulation setup (i.e. depiction of evolution of aerosol mass spectrum from a monomodal to bimodal due to aqueous‐phase SO2 oxidation)
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Jaruga_and_Pawlowska_2018.html">Jaruga_and_Pawlowska_2018</a>: exploration of numerical convergence using the above Hoppel-gap simulation setup
+  - `PySDM_examples.featured.Kreidenweis_et_al_2003`: <mark>Hoppel gap</mark> simulation setup (i.e. depiction of evolution of aerosol mass spectrum from a monomodal to bimodal due to aqueous‐phase SO2 oxidation)
+  - `PySDM_examples.sandbox.Jaruga_and_Pawlowska_2018`: exploration of numerical convergence using the above Hoppel-gap simulation setup
 - freezing
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Spichtinger_et_al_2023.html">Spichtinger_et_al_2023</a>: <mark>homogeneous freezing</mark> and ice growth (<mark>Wegener-Bergeron-Findeisen process</mark>)
 
 The parcel environment is also featured in the <a href="https://open-atmos.github.io/PySDM/PySDM.html#tutorials">PySDM tutorials</a>.
 
@@ -153,33 +140,32 @@ The box environment is void of any spatial or thermodynamic context, it constitu
 Example notebooks include:
 
 - coalescence only:
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Shima_et_al_2009.html">Shima_et_al_2009</a>: using <mark>Golovin additive kernel</mark> for comparison against analytic solution, featuring interactive in-notebook interface for selecting simulation parameters
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Berry_1967.html">Berry_1967</a>: examples using geometric, hydrodynamic and electric-field collision kernels
+  - `PySDM_examples.featured.Shima_et_al_2009`: using <mark>Golovin additive kernel</mark> for comparison against analytic solution, featuring interactive in-notebook interface for selecting simulation parameters
+  - `PySDM_examples.featured.Berry_1967`: examples using geometric, hydrodynamic and electric-field collision kernels
 - coalescence and breakup:
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Bieli_et_al_2022.html">Bieli_et_al_2022</a>: evolution of moments under collisional growth and breakage
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/deJong_Mackay_et_al_2023.html">deJong_Mackay_et_al_2023</a>: validation of the breakup scheme against analytical solutions from <a href="https://doi.org/10.1175/1520-0469(1982)039%3C1317:ASMOPC%3E2.0.CO;2">Srivastava 1982</a>
+  - `PySDM_examples.featured.Bieli_et_al_2022`: evolution of moments under collisional growth and breakage
+  - `PySDM_examples.featured.deJong_Mackay_et_al_2023`: validation of the breakup scheme against analytical solutions from <a href="https://doi.org/10.1175/1520-0469(1982)039%3C1317:ASMOPC%3E2.0.CO;2">Srivastava 1982</a>
 - immersion freezing only:
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Alpert_and_Knopf_2016.html">Alpert_and_Knopf_2016</a>: stochastic immersion freezing with monodisperse vs. lognormal immersed surface areas
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Arabas_et_al_2025.html">Arabas_et_al_2025</a>: comparison of time-dependent and singular immersion freezing schemes
+  - `PySDM_examples.featured.Alpert_and_Knopf_2016`: stochastic immersion freezing with monodisperse vs. lognormal immersed surface areas
+  - `PySDM_examples.featured.Arabas_et_al_2025`: comparison of time-dependent and singular immersion freezing schemes
 
 The box environment is also featured in the <a href="https://open-atmos.github.io/PySDM/PySDM.html#tutorials">PySDM tutorials</a>.
 
 ## examples depicting isotope-related formulae (without any simulation context)
 - <mark>equilibrium isotopic fractionation</mark> formulae:
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Lamb_et_al_2017.html">Lamb_et_al_2017</a>
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Bolot_et_al_2013.html">Bolot_et_al_2013</a>
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Merlivat_and_Nief_1967.html">Merlivat_and_Nief_1967</a>
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Van_Hook_1968.html">Van_Hook_1968</a>
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Graf_et_al_2019.html">Graf_et_al_2019</a>
+  - `PySDM_examples.misc.Lamb_et_al_2017`
+  - `PySDM_examples.misc.Bolot_et_al_2013`
+  - `PySDM_examples.misc.Merlivat_and_Nief_1967`
+  - `PySDM_examples.misc.Van_Hook_1968`
 - <mark>Rayleigh fractionation</mark>:
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Pierchala_et_al_2022.html">Pierchala_et_al_2022</a>: reproducing model plots for a <mark>triple-isotope</mark> lab study, including <mark>kinetic fractionation</mark>
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Gonfiantini_1986.html">Gonfiantini_1986</a>: flat-surface evaporation at different humidities for D and <sup>18</sup>O
+  - `PySDM_examples.featured.Pierchala_et_al_2022`: reproducing model plots for a <mark>triple-isotope</mark> lab study, including <mark>kinetic fractionation</mark>
+  - `PySDM_examples.misc.Gonfiantini_1986`: flat-surface evaporation at different humidities for D and <sup>18</sup>O
 - isotopic relaxation timescale:
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Miyake_et_al_1968.html">Miyake_et_al_1968</a>: incl. comparison of different <mark>ventilation</mark> parameterisations
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Bolin_1958.html">Bolin_1958</a>
+  - `PySDM_examples.misc.Miyake_et_al_1968`: incl. comparison of different <mark>ventilation</mark> parameterisations
+  - `PySDM_examples.misc.Bolin_1958`
 - below-cloud <mark>kinetic fractionation</mark>:
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Gedzelman_and_Arnold_1994.html">Gedzelman_and_Arnold_1994</a>
+  - `PySDM_examples.misc.Gedzelman_and_Arnold_1994`
 
 ## examples depicting extraterrestrial clouds (formulae-only, no simulations yet)
 - Titan (methane clouds):
-  - <a href="https://open-atmos.github.io/PySDM/PySDM_examples/Toon_et_al_1980.html">Toon_et_al_1980</a>
+  - `PySDM_examples.misc.Toon_et_al_1980`

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Abdul_Razzak_Ghan_2000/run_ARG_parcel.py

@@ -1,7 +1,10 @@
 from collections import namedtuple
 
 import numpy as np
-from PySDM_examples.Abdul_Razzak_Ghan_2000.aerosol import CONSTANTS_ARG, AerosolARG
+from PySDM_examples.featured.Abdul_Razzak_Ghan_2000.aerosol import (
+    CONSTANTS_ARG,
+    AerosolARG,
+)
 
 from PySDM import Particulator, Formulae
 from PySDM import products as PySDM_products
@@ -97,7 +100,7 @@ def run_parcel(
     }
 
     for _ in range(n_steps):
-        particulator.run(steps=1)
+        particulator.advance(n_steps=1)
         for product in particulator.products.values():
             value = product.get()
             output[product.name].append(value[0])

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Alpert_and_Knopf_2016/simulation.py

@@ -256,7 +256,7 @@ def simulation(
         if cooling_rate != 0:
             env["T"] -= np.full((1,), cooling_rate * time_step / 2)
             env["a_w_ice"] = svp.pvs_ice(env["T"][0]) / svp.pvs_water(env["T"][0])
-        particulator.run(0 if i == 0 else 1)
+        particulator.advance(0 if i == 0 else 1)
         if cooling_rate != 0:
             env["T"] -= np.full((1,), cooling_rate * time_step / 2)
 

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Alpert_and_Knopf_2016/table_1.py

@@ -1,4 +1,4 @@
-from PySDM_examples.Alpert_and_Knopf_2016.table import Table
+from PySDM_examples.featured.Alpert_and_Knopf_2016.table import Table
 
 from PySDM.initialisation.spectra import Lognormal, TopHat
 from PySDM.physics import si

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Alpert_and_Knopf_2016/table_2.py

@@ -1,4 +1,4 @@
-from PySDM_examples.Alpert_and_Knopf_2016.table import Table
+from PySDM_examples.featured.Alpert_and_Knopf_2016.table import Table
 
 from PySDM.initialisation.spectra import Lognormal
 from PySDM.physics import si

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Arabas_and_Shima_2017/__init__.py

@@ -6,4 +6,7 @@ fig_5.ipynb:
 .. include:: ./fig_5.ipynb.badges.md
 """
 
+from .simulation import Simulation
+from .settings import Settings
+
 # pylint: disable=invalid-name

pysdm_examples-3.0.2/PySDM_examples/featured/Arabas_and_Shima_2017/example.py

@@ -0,0 +1,11 @@
+from PySDM_examples.featured.Arabas_and_Shima_2017.settings import setups
+from PySDM_examples.featured.Arabas_and_Shima_2017.simulation import Simulation
+
+
+def main():
+    for settings in setups:
+        Simulation(settings).run()
+
+
+if __name__ == "__main__":
+    main()

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Arabas_and_Shima_2017/simulation.py

@@ -100,7 +100,7 @@ class Simulation:
 
         self.save(output)
         for _ in range(self.n_output):
-            self.particulator.run(self.n_substeps)
+            self.particulator.advance(self.n_substeps)
             self.save(output)
 
         return output

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Arabas_et_al_2025/__init__.py

@@ -2,26 +2,21 @@
 box-model and 2D prescribed-flow immersion-freezing examples based on
 [Arabas et al. 2025](https://doi.org/10.1029/2024MS004770)
 
-aida.ipynb:
-.. include:: ./aida.ipynb.badges.md
-
-copula_hello.ipynb:
-.. include:: ./copula_hello.ipynb.badges.md
-
 fig_2.ipynb:
 .. include:: ./fig_2.ipynb.badges.md
 
-figs_10_and_11_and_animations.ipynb:
-.. include:: ./figs_10_and_11_and_animations.ipynb.badges.md
-
 fig_A2.ipynb:
 .. include:: ./fig_A2.ipynb.badges.md
 
+
 figs_3_and_7_and_8.ipynb:
 .. include:: ./figs_3_and_7_and_8.ipynb.badges.md
 
 figs_5_and_6.ipynb:
 .. include:: ./figs_5_and_6.ipynb.badges.md
+
+figs_10_and_11_and_animations.ipynb:
+.. include:: ./figs_10_and_11_and_animations.ipynb.badges.md
 """
 
 from .make_particulator import make_particulator

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Arabas_et_al_2025/plots.py

@@ -1,8 +1,8 @@
 import matplotlib
 import numpy as np
 from matplotlib import pyplot
-from PySDM_examples.Arabas_et_al_2025.curved_text import CurvedText
-from PySDM_examples.Arabas_et_al_2025.frozen_fraction import FrozenFraction
+from PySDM_examples.featured.Arabas_et_al_2025.curved_text import CurvedText
+from PySDM_examples.featured.Arabas_et_al_2025.frozen_fraction import FrozenFraction
 
 from PySDM.physics import si
 

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Arabas_et_al_2025/run_simulation.py

@@ -18,7 +18,7 @@ def run_simulation(particulator, temperature_profile, n_steps):
                 particulator.environment,
                 T=temperature_profile((step - 0.5) * particulator.dt),
             )
-            particulator.run(step - particulator.n_steps)
+            particulator.advance(step - particulator.n_steps)
             update_thermo(
                 particulator.environment, T=temperature_profile(step * particulator.dt)
             )

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Berry_1967/example.py

@@ -1,9 +1,9 @@
 import os
 
 import numpy as np
-from PySDM_examples.Berry_1967.settings import Settings
-from PySDM_examples.Berry_1967.spectrum_plotter import SpectrumPlotter
-from PySDM_examples.Shima_et_al_2009.example import run
+from PySDM_examples.featured.Berry_1967.settings import Settings
+from PySDM_examples.featured.Berry_1967.spectrum_plotter import SpectrumPlotter
+from PySDM_examples.featured.Shima_et_al_2009.example import run
 
 from PySDM.dynamics.collisions.collision_kernels import (
     Electric,

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Berry_1967/spectrum_plotter.py

@@ -1,6 +1,6 @@
 from matplotlib import pyplot
 from open_atmos_jupyter_utils import show_plot
-from PySDM_examples.Shima_et_al_2009.spectrum_plotter import (
+from PySDM_examples.featured.Shima_et_al_2009.spectrum_plotter import (
     SpectrumPlotter as SuperSpectrumPlotter,
 )
 

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Bieli_et_al_2022/__init__.py

@@ -1,8 +1,8 @@
-"""
-collision-only box-model example from [Bieli et al. 2022](https://doi.org/10.1029/2022MS002994)
-
-make_fig_3.ipynb:
-.. include:: ./make_fig_3.ipynb.badges.md
-"""
-
-# pylint: disable=invalid-name
+"""
+collision-only box-model example from [Bieli et al. 2022](https://doi.org/10.1029/2022MS002994)
+
+fig_3a.ipynb:
+.. include:: ./fig_3a.ipynb.badges.md
+"""
+
+# pylint: disable=invalid-name

pysdm_examples-3.0.2/PySDM_examples/featured/Grabowski_and_Pawlowska_2023/__init__.py

@@ -0,0 +1,23 @@
+# pylint: disable=invalid-name
+"""
+ripening-focused parcel-model example based on
+[Grabowski & Pawlowska 2023 (GRL)](https://doi.org/10.1029/2022GL101917)
+
+fig_1.ipynb:
+.. include:: ./fig_1.ipynb.badges.md
+
+fig_2.ipynb:
+.. include:: ./fig_2.ipynb.badges.md
+
+fig_3.ipynb:
+.. include:: ./fig_3.ipynb.badges.md
+
+fig_4.ipynb:
+.. include:: ./fig_4.ipynb.badges.md
+
+fig_ripening_rate.ipynb:
+.. include:: ./fig_ripening_rate.ipynb.badges.md
+"""
+
+from .settings import Settings
+from .simulation import Simulation

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Jensen_and_Nugent_2017/__init__.py

@@ -1,3 +1,4 @@
+# pylint: disable=invalid-name
 """
 Fig_1.ipynb:
 .. include:: ./Fig_1.ipynb.badges.md

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Jensen_and_Nugent_2017/simulation.py

@@ -1,7 +1,7 @@
 import numpy as np
 from PySDM_examples.utils import BasicSimulation
-from PySDM_examples.Jensen_and_Nugent_2017.settings import Settings
-from PySDM_examples.Jensen_and_Nugent_2017 import table_3
+from PySDM_examples.featured.Jensen_and_Nugent_2017.settings import Settings
+from PySDM_examples.featured.Jensen_and_Nugent_2017 import table_3
 from PySDM import Particulator
 from PySDM.physics import si
 from PySDM.backends import CPU

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Long_1974/__init__.py

@@ -2,6 +2,9 @@
 """
 piecewise collision-coalescence example from
 [Long 1974 (JAS)](https://doi.org/10.1175/1520-0469%281974%29031%3C1040%3ASTTDCE%3E2.0.CO%3B2)
+
+figs_10_11_13_14.ipynb:
+.. include:: ./figs_10_11_13_14.ipynb.badges.md
 """
 
 from .settings import Settings

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Lowe_et_al_2019/settings.py

@@ -1,7 +1,7 @@
 from functools import lru_cache
 
 import numpy as np
-from PySDM_examples.Lowe_et_al_2019.constants_def import LOWE_CONSTS
+from PySDM_examples.featured.Lowe_et_al_2019.constants_def import LOWE_CONSTS
 from pystrict import strict
 
 from PySDM import Formulae

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Lowe_et_al_2019/simulation.py

@@ -135,7 +135,7 @@ class Simulation(BasicSimulation):
     def run(self):
         output = {k: [] for k in self.particulator.products}
         for step in self.settings.output_steps:
-            self.particulator.run(step - self.particulator.n_steps)
+            self.particulator.advance(step - self.particulator.n_steps)
             self._save_scalars(output)
         self._save_final_timestep_products(output)
         return output

pysdm_examples-3.0.2/PySDM_examples/featured/Luettmer_et_al_2026/__init__.py

@@ -0,0 +1,25 @@
+# pylint: disable=invalid-name
+"""
+Homogeneous freezing example
+
+fig_1_2_3.ipynb:
+.. include:: ./fig_1_2_3.ipynb.badges.md
+
+fig_4_5_6_S3_S4.ipynb:
+.. include:: ./fig_4_5_6_S3_S4.ipynb.badges.md
+
+fig_S1_S2.ipynb:
+.. include:: ./fig_S1_S2.ipynb.badges.md
+
+simple_homogenous_freezing_example.ipynb:
+.. include:: ./simple_homogenous_freezing_example.ipynb.badges.md
+"""
+
+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-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Luettmer_et_al_2026/commons.py

@@ -1,7 +1,7 @@
 """commons for homogeneous freezing notebooks"""
 
-from PySDM_examples.Luettmer_et_al_2026.settings import Settings
-from PySDM_examples.Luettmer_et_al_2026.simulation import Simulation
+from PySDM_examples.featured.Luettmer_et_al_2026.settings import Settings
+from PySDM_examples.featured.Luettmer_et_al_2026.simulation import Simulation
 from PySDM import Formulae
 from PySDM.physics.constants import si
 from PySDM.backends import CPU

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Luettmer_et_al_2026/simulation.py

@@ -170,7 +170,7 @@ class Simulation:
 
         while True:
 
-            self.particulator.run(self.n_substeps)
+            self.particulator.advance(self.n_substeps)
             self.save(output)
 
             w_cr_v_ratio = self.particulator.attributes[

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Shima_et_al_2009/example.py

@@ -2,8 +2,8 @@ import os
 from typing import Optional
 
 import numpy as np
-from PySDM_examples.Shima_et_al_2009.settings import Settings
-from PySDM_examples.Shima_et_al_2009.spectrum_plotter import SpectrumPlotter
+from PySDM_examples.featured.Shima_et_al_2009.settings import Settings
+from PySDM_examples.featured.Shima_et_al_2009.spectrum_plotter import SpectrumPlotter
 
 from PySDM.backends import CPU
 from PySDM import Particulator
@@ -46,7 +46,7 @@ def run(settings, backend=CPU, observers=()):
     vals = {}
     particulator.products["wall time"].reset()
     for step in settings.output_steps:
-        particulator.run(step - particulator.n_steps)
+        particulator.advance(step - particulator.n_steps)
         vals[step] = particulator.products["dv/dlnr"].get()[0]
         vals[step][:] *= settings.rho
 

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Shima_et_al_2009/example_timing.py

@@ -1,7 +1,7 @@
 import os
 
 from matplotlib import pyplot as plt
-from PySDM_examples.Shima_et_al_2009.settings import Settings
+from PySDM_examples.featured.Shima_et_al_2009.settings import Settings
 
 from PySDM.backends import Numba, ThrustRTC
 from PySDM import Particulator
@@ -18,7 +18,7 @@ def run(settings, backend):
     attributes["volume"], attributes["multiplicity"] = sampling.sample_deterministic(
         settings.n_sd
     )
-    particles = Particulator(
+    particulator = Particulator(
         n_sd=settings.n_sd,
         environment=env,
         dynamics=(Coalescence(collision_kernel=settings.kernel),),
@@ -29,8 +29,8 @@ def run(settings, backend):
     states = {}
     last_wall_time = None
     for step in settings.output_steps:
-        particles.run(step - particles.n_steps)
-        last_wall_time = particles.products["wall time"].get()
+        particulator.advance(step - particulator.n_steps)
+        last_wall_time = particulator.products["wall time"].get()
 
     return states, last_wall_time
 

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Shima_et_al_2009/spectrum_plotter.py

@@ -3,7 +3,7 @@ import numpy as np
 from matplotlib import pyplot
 from open_atmos_jupyter_utils import show_plot
 from packaging import version
-from PySDM_examples.Shima_et_al_2009.error_measure import error_measure
+from PySDM_examples.featured.Shima_et_al_2009.error_measure import error_measure
 
 from PySDM.physics.constants import si
 
@@ -57,18 +57,11 @@ class SpectrumPlotter:
             ): self.log_base
         }
         if self.title is not None:
-            try:
-                self.ax.title(self.title)
-            except TypeError:
-                self.ax.set_title(self.title)
-        try:
-            self.ax.xscale("log", **base_arg)
-            self.ax.xlabel(self.xlabel)
-            self.ax.ylabel(self.ylabel)
-        except AttributeError:
-            self.ax.set_xscale("log", **base_arg)
-            self.ax.set_xlabel(self.xlabel)
-            self.ax.set_ylabel(self.ylabel)
+            self.ax.title(self.title)
+        self.ax.xscale("log", **base_arg)
+        self.ax.xlabel(self.xlabel)
+        self.ax.ylabel(self.ylabel)
+
         if self.legend:
             self.ax.legend()
 

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Shima_et_al_2009/tutorial_example.py

@@ -43,7 +43,7 @@ def run(settings, observers=()):
     vals = {}
     particulator.products["wall time"].reset()
     for step in settings.output_steps:
-        particulator.run(step - particulator.n_steps)
+        particulator.advance(step - particulator.n_steps)
         vals[step] = particulator.products["dv/dlnr"].get()[0]
         vals[step][:] *= settings.rho
 

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Shipway_and_Hill_2012/simulation.py

@@ -2,7 +2,7 @@ from collections import namedtuple
 from typing import List, Any
 
 import numpy as np
-from PySDM_examples.Shipway_and_Hill_2012.mpdata_1d import MPDATA_1D
+from PySDM_examples.featured.Shipway_and_Hill_2012.mpdata_1d import MPDATA_1D
 
 import PySDM.products as PySDM_products
 from PySDM import Particulator
@@ -267,7 +267,7 @@ class Simulation:
                 self.particulator.dynamics["Displacement"].upload_courant_field(
                     (mpdata.advector / self.g_factor_vec,)
                 )
-            self.particulator.run(steps=1)
+            self.particulator.advance(n_steps=1)
             self.save(step + 1)
 
         Outputs = namedtuple("Outputs", "products attributes")

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Srivastava_1982/example.py

@@ -2,9 +2,12 @@ from collections import namedtuple
 
 import numpy as np
 from matplotlib import pyplot
-from PySDM_examples.Srivastava_1982.equations import Equations, EquationsHelpers
-from PySDM_examples.Srivastava_1982.settings import SimProducts
-from PySDM_examples.Srivastava_1982.simulation import Simulation
+from PySDM_examples.featured.Srivastava_1982.equations import (
+    Equations,
+    EquationsHelpers,
+)
+from PySDM_examples.featured.Srivastava_1982.settings import SimProducts
+from PySDM_examples.featured.Srivastava_1982.simulation import Simulation
 
 from PySDM.dynamics import Collision
 from PySDM.dynamics.collisions.breakup_efficiencies import ConstEb

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Srivastava_1982/simulation.py

@@ -1,5 +1,5 @@
 import numpy as np
-from PySDM_examples.Srivastava_1982.settings import SimProducts
+from PySDM_examples.featured.Srivastava_1982.settings import SimProducts
 
 from PySDM import Particulator, Formulae
 from PySDM.environments import Box
@@ -70,7 +70,7 @@ class Simulation:
 
                 for step in range(len(x)):
                     if step != 0:
-                        particulator.run(steps=1)
+                        particulator.advance(n_steps=1)
                     for prod in self.settings.prods:
                         (self.simulation_res[n_sd][prod][seed][step],) = (
                             particulator.products[prod].get()

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Ware_et_al_2025/example.py

@@ -243,7 +243,7 @@ def run(settings, backend, observers=(), sampling_method="deterministic"):
     deficit = 0
     particulator.products["wall time"].reset()
     for step in settings.output_steps:
-        particulator.run(step - particulator.n_steps)
+        particulator.advance(step - particulator.n_steps)
         vals[step] = particulator.products["dv/dlnr"].get()[0]
         vals[step][:] *= settings.rho
         deficit += particulator.products["deficit"].get()

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Yang_et_al_2018/settings.py

@@ -1,7 +1,7 @@
 import numpy as np
 from pystrict import strict
 
-from PySDM_examples import Jensen_and_Nugent_2017
+from PySDM_examples.featured import Jensen_and_Nugent_2017
 
 from PySDM.backends import CPU
 from PySDM.dynamics import condensation

{pysdm_examples-3.0.0rc43/PySDM_examples → pysdm_examples-3.0.2/PySDM_examples/featured}/Yang_et_al_2018/simulation.py

@@ -116,7 +116,7 @@ class Simulation:
 
         self.save(output)
         for _ in range(self.n_steps):
-            self.particulator.run(self.n_substeps)
+            self.particulator.advance(self.n_substeps)
             self.save(output)
         for k, v in output.items():
             output[k] = np.asarray(v)