PySDM-examples 2.78__py3-none-any.whl → 2.80__py3-none-any.whl

PySDM_examples/Abade_and_Albuquerque_2024/__init__.py

@@ -2,6 +2,9 @@
 """
 mixed-phase example using parcel environment based on
 [Abade & Albuquerque 2024 (QJRMS)](https://doi.org/10.1002/qj.4775)
+
+fig_2.ipynb:
+.. include:: ./fig_2.ipynb.badges.md
 """
 
 from .simulation import Simulation

PySDM_examples/Abdul_Razzak_Ghan_2000/__init__.py

@@ -2,4 +2,10 @@
 """
 condensation example using parcel environment based on
 [Abdul-Razzak & Ghan 2000 (JGR)](https://doi.org/10.1029/1999JD901161)
+
+figs1-5.ipynb:
+.. include:: ./figs1-5.ipynb.badges.md
+
+fig_4_kinetic_limitations.ipynb:
+.. include:: ./fig_4_kinetic_limitations.ipynb.badges.md
 """

PySDM_examples/Alpert_and_Knopf_2016/__init__.py

@@ -1,6 +1,21 @@
 """
 box-environment example based on
 [Alpert & Knopf 2016 (Atmos. Chem. Phys. 16)](https://doi.org/10.5194/acp-16-2083-2016)
+
+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_5.ipynb:
+.. include:: ./fig_5.ipynb.badges.md
 """
 
 # pylint: disable=invalid-name

PySDM_examples/Arabas_and_Shima_2017/__init__.py

@@ -1,6 +1,9 @@
 """
 condensation-evaportaion parcel example based on
 [Arabas and Shima 2017 (Nonlin. Processes Geophys. 24)](https://doi.org/10.5194/npg-24-535-2017)
+
+fig_5.ipynb:
+.. include:: ./fig_5.ipynb.badges.md
 """
 
 # pylint: disable=invalid-name

PySDM_examples/Arabas_et_al_2015/__init__.py

@@ -2,6 +2,12 @@
 """
 2D prescribed-flow case extended with Paraview visualisation with spin-up logic from
 [Arabas et al. 2015](http://doi.org/10.5194/gmd-8-1677-2015)
+
+gui.ipynb:
+.. include:: ./gui.ipynb.badges.md
+
+paraview_hello_world.ipynb:
+.. include:: ./paraview_hello_world.ipynb.badges.md
 """
 from .settings import Settings
 from .spin_up import SpinUp

PySDM_examples/Arabas_et_al_2015/spin_up.py

@@ -1,4 +1,4 @@
-from PySDM.dynamics import Collision, Displacement, Freezing
+from PySDM.dynamics import Collision, Displacement
 
 
 class SpinUp:
@@ -8,13 +8,11 @@ class SpinUp:
         self.particulator = particulator
         self.set(Collision, "enable", False)
         self.set(Displacement, "enable_sedimentation", False)
-        self.set(Freezing, "enable", False)
 
     def notify(self):
         if self.particulator.n_steps == self.spin_up_steps:
             self.set(Collision, "enable", True)
             self.set(Displacement, "enable_sedimentation", True)
-            self.set(Freezing, "enable", True)
 
     def set(self, dynamic, attr, value):
         key = dynamic.__name__

PySDM_examples/Arabas_et_al_2023/__init__.py

@@ -1,6 +1,27 @@
 """
 box-model and 2D prescribed-flow immersion-freezing examples based on
 [Arabas et al. 2023](https://arxiv.org/abs/2308.05015)
+
+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
+
+fig_11.ipynb:
+.. include:: ./figs_10_and_11_and_animations.ipynb
+
+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
 """
 
 from .make_particulator import make_particulator

PySDM_examples/Arabas_et_al_2023/commons.py

@@ -13,7 +13,7 @@ FREEZING_CONSTANTS = {
     "illite": {"ABIFM_M": 54.48, "ABIFM_C": -10.67},
 }
 
-COOLING_RATES = (3.75 * si.K / si.min, 0.75 * si.K / si.min, 0.15 * si.K / si.min)
+COOLING_RATES = (-3.75 * si.K / si.min, -0.75 * si.K / si.min, -0.15 * si.K / si.min)
 
 BEST_FIT_LN_S_GEOM = 0.25
 

PySDM_examples/Arabas_et_al_2023/make_particulator.py

@@ -37,7 +37,7 @@ def make_particulator(
         "particle_shape_and_density": "MixedPhaseSpheres",
     }
     formulae = Formulae(**formulae_ctor_args)
-    backend = CPU(formulae)
+    backend = CPU(formulae, override_jit_flags={"parallel": False})
 
     sampling = SpectroGlacialSampling(
         freezing_temperature_spectrum=formulae.freezing_temperature_spectrum,

PySDM_examples/Arabas_et_al_2023/plots.py

@@ -103,14 +103,14 @@ def make_freezing_spec_plot(
             _ = CurvedText(
                 x=T.squeeze(),
                 y=qi.squeeze(),
-                text=f"                      {multiplier}x median A",
+                text=f"                      {multiplier}x median S",
                 va="bottom",
                 color="black",
                 axes=prim,
             )
     title = f"$σ_g$=exp({np.log(surf_spec.s_geom):.3g})"
     if cooling_rate_K_min is not None:
-        title += f", cooling rate: {cooling_rate_K_min} K/min"
+        title += f", c={cooling_rate_K_min} K/min"
     prim.set_title(title)
     # prim.set_ylabel('ice water content [$g/m^3$]')
     prim.set_yticks([])

PySDM_examples/Bartman_et_al_2021/__init__.py

@@ -1,4 +1,13 @@
 # pylint: disable=invalid-name
 """
 condensation and coalescence adaptivity examples
+
+demo.ipynb:
+.. include:: ./demo.ipynb.badges.md
+
+demo_fig2.ipynb:
+.. include:: ./demo_fig2.ipynb.badges.md
+
+demo_fig3.ipynb:
+.. include:: ./demo_fig3.ipynb.badges.md
 """

PySDM_examples/Berry_1967/__init__.py

@@ -1,6 +1,9 @@
 """
 box-model coalescence-only example based on
 [Berry 1967 (J. Atmos. Sci. 24)](https://doi.org/10.1175/1520-0469(1967)024%3C0688:CDGBC%3E2.0.CO;2)
+
+figs_5_8_10.ipynb:
+.. include:: ./figs_5_8_10.ipynb.badges.md
 """
 
 # pylint: disable=invalid-name

PySDM_examples/Bieli_et_al_2022/__init__.py

@@ -1,5 +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

PySDM_examples/Bolot_et_al_2013/__init__.py

@@ -1,6 +1,9 @@
 """
 figures from Bolot et al. 2013 (Atmos. Chem. Phys. 13)
 https://doi.org/10.5194/acp-13-7903-2013
+
+fig_1.ipynb:
+.. include:: ./fig_1.ipynb.badges.md
 """
 
 # pylint: disable=invalid-name

PySDM_examples/Bulenok_2023_MasterThesis/__init__.py

@@ -2,4 +2,7 @@
 """
 Box-model coalescence-breakup performance benchmark from
 [Bulenok 2023 MSc thesis](https://www.ap.uj.edu.pl/diplomas/166879)
+
+performance_comparison_Srivastava_Setup.ipynb:
+.. include:: ./performance_comparison_Srivastava_Setup.ipynb.badges.md
 """

PySDM_examples/Gedzelman_and_Arnold_1994/__init__.py

@@ -3,4 +3,7 @@
 Formulae-only example depicting changes in drop and ambient vapour isotopic composition
 upon evaporation of rain in subsaturated environment based on
 [Gedzelman and Arnold 1994](https://doi.org/10.1029/93JD03518)
+
+fig_2.ipynb:
+.. include:: ./fig_2.ipynb.badges.md
 """

PySDM_examples/Grabowski_and_Pawlowska_2023/__init__.py

@@ -2,6 +2,21 @@
 """
 ripening-focused parcel-model example based on
 [Grabowski & Pawlowska 2023 (GRL)](https://doi.org/10.1029/2022GL101917)
+
+figure_1.ipynb:
+.. include:: ./figure_1.ipynb.badges.md
+
+figure_2.ipynb:
+.. include:: ./figure_2.ipynb.badges.md
+
+figure_3.ipynb:
+.. include:: ./figure_3.ipynb.badges.md
+
+figure_4.ipynb:
+.. include:: ./figure_4.ipynb.badges.md
+
+figure_ripening_rate.ipynb:
+.. include:: ./figure_ripening_rate.ipynb.badges.md
 """
 from .settings import Settings
 from .simulation import Simulation

PySDM_examples/Graf_et_al_2019/__init__.py

@@ -2,4 +2,10 @@
 """
 Parcel-model Condensation,Isotope example
 [Graf.et.al 2019](https://doi.org/10.5194/acp-19-747-2019)
+
+figure_4.ipynb:
+.. include:: ./figure_4.ipynb.badges.md
+
+Table_1.ipynb:
+.. include:: ./Table_1.ipynb.badges.md
 """

PySDM_examples/Jaruga_and_Pawlowska_2018/__init__.py

@@ -2,4 +2,10 @@
 """
 aqueous-chemistry parcel-model example based on
 [Jaruga & Pawlowska 2018 (GMD)](https://doi.org/10.5194/gmd-11-3623-2018)
+
+fig_2.ipynb:
+.. include:: ./fig_2.ipynb.badges.md
+
+fig_3.ipynb:
+.. include:: ./fig_3.ipynb.badges.md
 """

PySDM_examples/Jensen_and_Nugent_2017/__init__.py

@@ -1,2 +1,22 @@
+"""
+Fig_1.ipynb:
+.. include:: ./Fig_1.ipynb.badges.md
+
+Fig_3_and_Tab_4_upper_rows.ipynb:
+.. include:: ./Fig_3_and_Tab_4_upper_rows.ipynb.badges.md
+
+Fig_4_and_7_and_Tab_4_bottom_rows.ipynb:
+.. include:: ./Fig_4_and_7_and_Tab_4_bottom_rows.ipynb.badges.md
+
+Fig_5.ipynb:
+.. include:: ./Fig_5.ipynb.badges.md
+
+Fig_6.ipynb:
+.. include:: ./Fig_6.ipynb.badges.md
+
+Fig_8.ipynb:
+.. include:: ./Fig_8.ipynb.badges.md
+"""
+
 from .settings import Settings
 from .simulation import Simulation

PySDM_examples/Kreidenweis_et_al_2003/__init__.py

@@ -2,6 +2,9 @@
 """
 aqueous-phase chemistry parcel-model example from
 [Kreidenweis et al. 2003 (JGR)](https://doi.org/10.1029/2002JD002697)
+
+fig_1.ipynb:
+.. include:: ./fig_1.ipynb.badges.md
 """
 from .settings import Settings
 from .simulation import Simulation

PySDM_examples/Lamb_et_al_2017/__init__.py

@@ -2,4 +2,7 @@
 """
 Formulae-only example depicting equilibrium isotopic fractionation over ice based on
 [Lamb et al. 2017](https://doi.org/10.1073/pnas.1618374114)
+
+fig_4.ipynb:
+.. include:: ./fig_4.ipynb.badges.md
 """

PySDM_examples/Lowe_et_al_2019/__init__.py

@@ -2,6 +2,18 @@
 """
 parcel-model example focused on surfactants based on
 [Lowe et al. 2019 (Nature Comm.)](https://doi.org/10.1038/s41467-019-12982-0)
+
+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_s2.ipynb:
+.. include:: ./fig_s2.ipynb.badges.md
 """
 from .settings import Settings
 from .simulation import Simulation

PySDM_examples/Merlivat_and_Nief_1967/__init__.py

@@ -1,6 +1,9 @@
 """
 figure from Merlivat and Nief 1967 (Tellus)
 https://doi.org/10.3402/tellusa.v19i1.9756
+
+fig_2.ipynb:
+.. include:: ./fig_2.ipynb.badges.md
 """
 
 # pylint: disable=invalid-name

PySDM_examples/Miyake_et_al_1968/__init__.py

@@ -2,4 +2,7 @@
 """
 isotopic adjustment time plot following
 [Friedman et al. 1962 (JGR)](https://doi.org/10.1029/JZ067i007p02761)
+
+fig_19.ipynb:
+.. include:: ./fig_19.ipynb.badges.md
 """

PySDM_examples/Morrison_and_Grabowski_2007/__init__.py

@@ -2,5 +2,11 @@
 """
 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
 """
 from .cumulus import Cumulus

PySDM_examples/Niedermeier_et_al_2014/__init__.py

@@ -1,4 +1,9 @@
-""" based on [Niedermeier et al. 2014](https://doi.org/10.1002/2013GL058684) """
+"""
+based on [Niedermeier et al. 2014](https://doi.org/10.1002/2013GL058684)
+
+fig_2.ipynb:
+.. include:: ./fig_2.ipynb.badges.md
+"""
 
 from .settings import Settings
 from .simulation import Simulation

PySDM_examples/Pierchala_et_al_2022/__init__.py

@@ -1,6 +1,12 @@
 """
 based on Pierchala et al. 2022 (Geochim. Cosmochim. Acta)
 https://doi.org/10.1016/j.gca.2022.01.020
+
+fig_3.ipynb:
+.. include:: ./fig_3.ipynb.badges.md
+
+fig_4.ipynb:
+.. include:: ./fig_4.ipynb.badges.md
 """
 
 # pylint: disable=invalid-name

PySDM_examples/Pyrcel/__init__.py

@@ -2,6 +2,9 @@
 """
 parcel-model example based on the test case from
 [Pyrcel package docs](https://pyrcel.readthedocs.io/)
+
+example_basic_run.ipynb:
+.. include:: ./example_basic_run.ipynb.badges.md
 """
 from .settings import Settings
 from .simulation import Simulation

PySDM_examples/Rozanski_and_Sonntag_1982/__init__.py

@@ -1,6 +1,9 @@
 """
 based on Rozanski and Sonntag 1982 (Tellus)
 https://doi.org/10.3402/tellusa.v34i2.10795
+
+figs_4_5_6.ipynb:
+.. include:: ./figs_4_5_6.ipynb.badges.md
 """
 
 # pylint: disable=invalid-name

PySDM_examples/Shima_et_al_2009/__init__.py

@@ -2,4 +2,7 @@
 """
 box-model coalescence-only example featuring Golovin analytic solution following setup from
 [Shima et al. 2009](https://doi.org/10.1002/qj.441)
+
+fig_2.ipynb:
+.. include:: ./fig_2.ipynb.badges.md
 """

PySDM_examples/Shipway_and_Hill_2012/__init__.py

@@ -2,6 +2,9 @@
 """
 single-column prescribed-flow constant-temperature example from
 [Shipway & Hill 2012](https://doi.org/10.1002/qj.1913)
+
+fig_1.ipynb:
+.. include:: ./fig_1.ipynb.badges.md
 """
 from .plot import plot
 from .settings import Settings

PySDM_examples/Singer_Ward/__init__.py

@@ -1 +1,9 @@
+"""
+kohler.ipynb:
+.. include:: ./kohler.ipynb.badges.md
+
+MWE_joss_paper.ipynb:
+.. include:: ./MWE_joss_paper.ipynb.badges.md
+"""
+
 # pylint: disable=invalid-name

PySDM_examples/Srivastava_1982/__init__.py

@@ -1,6 +1,9 @@
 """
 box-model examples feat. analytic solution for breakup from
 [Srivastava 1982 (JAS)](https://doi.org/10.1175/1520-0469(1982)039%3C1317:ASMOPC%3E2.0.CO;2)
+
+figures.ipynb:
+.. include:: ./figures.ipynb.badges.md
 """
 
 from .equations import Equations, EquationsHelpers

PySDM_examples/Szumowski_et_al_1998/simulation.py

@@ -197,9 +197,14 @@ class Simulation:
                         attributes[name][copy] = array * (
                             1 - self.settings.freezing_inp_frac
                         )
-                    elif len(array.shape) > 1:
-                        attributes[name][:, orig] = array
-                        attributes[name][:, copy] = array
+                    elif len(array.shape) > 1:  # particle positions
+                        # TODO #599: seed
+                        for dim, _ in enumerate(array.shape):
+                            # only to make particles not shadow each other in visualisations
+                            attributes[name][dim, orig] = array[dim, :]
+                            attributes[name][dim, copy] = np.random.permutation(
+                                array[dim, :]
+                            )
                     else:
                         attributes[name][orig] = array
                         attributes[name][copy] = array

PySDM_examples/Van_Hook_1968/__init__.py

@@ -1,6 +1,9 @@
 """
 figure from Van Hook 1968 (J. Phys. Chem.)
 https://doi.org/10.1021/j100850a028
+
+fig_1.ipynb:
+.. include:: ./fig_1.ipynb.badges.md
 """
 
 # pylint: disable=invalid-name

PySDM_examples/Yang_et_al_2018/__init__.py

@@ -2,6 +2,9 @@
 """
 parcel-model condensation-evaporation example based on
 [Yang et al. 2018 (ACP)](https://doi.org/10.5194/acp-18-7313-2018)
+
+fig_2.ipynb:
+.. include:: ./fig_2.ipynb.badges.md
 """
 from .settings import Settings
 from .simulation import Simulation

PySDM_examples/__init__.py

@@ -1,6 +1,5 @@
 """
-PySDM_examples package includes common Python modules used in PySDM smoke tests
-and in example notebooks (but the package wheels do not include the notebooks)
+.. include:: ../docs/pysdm_examples_landing.md
 """
 
 from importlib.metadata import PackageNotFoundError, version

PySDM_examples/deJong_Azimi/__init__.py

@@ -1,6 +1,12 @@
 """
 box- and single-column coalescence-focused examples used to test new
 moment-based microphysics in (Cloudy.jl)[https://github.com/CliMA/Cloudy.jl]
+
+box.ipynb:
+.. include:: ./box.ipynb.badges.md
+
+rainshaft.ipynb:
+.. include:: ./rainshaft.ipynb.badges.md
 """
 
 # pylint: disable=invalid-name

PySDM_examples/deJong_Mackay_et_al_2023/__init__.py

@@ -1,6 +1,18 @@
 """
 box- and single-column breakup-focused examples from
 [de Jong et al. 2023](https://doi.org/10.5194/gmd-16-4193-2023)
+
+fig_9.ipynb:
+.. include:: ./fig_9.ipynb.badges.md
+
+figs_3_4_5.ipynb:
+.. include:: ./figs_3_4_5.ipynb.badges.md
+
+figs_6_7_8.ipynb:
+.. include:: ./figs_6_7_8.ipynb.badges.md
+
+figs_10_11_12_13.ipynb:
+.. include:: ./figs_10_11_12_13.ipynb.badges.md
 """
 
 # pylint: disable=invalid-name

PySDM_examples/seeding/__init__.py

@@ -1,2 +1,10 @@
+"""
+hello_world.ipynb:
+.. include:: ./hello_world.ipynb.badges.md
+
+seeding_no_collisions.ipynb:
+.. include:: ./seeding_no_collisions.ipynb.badges.md
+"""
+
 from .settings import Settings
 from .simulation import Simulation