PySDM-examples 2.79__tar.gz → 2.80__tar.gz

{PySDM-examples-2.79 → PySDM-examples-2.80}/MANIFEST.in

@@ -1,2 +1,3 @@
 global-exclude *.ipynb
 global-exclude *.csv
+include docs/*.md

PySDM-examples-2.80/PKG-INFO

@@ -0,0 +1,140 @@
+Metadata-Version: 2.1
+Name: PySDM-examples
+Version: 2.80
+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
+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
+Description: # Introduction
+        
+        <img align="left" src="https://raw.githubusercontent.com/open-atmos/PySDM/main/.github/pysdm_logo.svg" width=150 height=219 alt="pysdm logo" style="padding-right:1em">
+        
+        PySDM examples are engineered as Jupyter Python notebooks supported by auxiliary Python commons
+          that constitute a separate <mark>PySDM-examples</mark> Python package which is also
+          <a href="https://pypi.org/p/PySDM-examples">available at PyPI</a>.
+        The examples have additional dependencies listed in
+          <a href="https://github.com/open-atmos/PySDM/blob/main/examples/setup.py">PySDM-examples package setup.py file</a>.
+        Running the example Jupyter notebooks requires the <mark>PySDM-examples</mark> package to be pip-installed.
+        For installation instructions see [project docs homepage](https://open-atmos.github.io/PySDM).
+        Note that the Jupyter notebooks themselves are not included in the package wheels, but are included
+          in the source .tar.gz file on PyPI, and are conveninently browsable on GitHub.
+        All notebooks feature header cells with badges enabling single-click execution on
+          <a href="https://colab.research.google.com/">Google Colab</a> and on
+          <a href="https://mybinder.org/">mybinder.org</a>.
+        The examples package is also used in the PySDM test suite.
+        
+        # Example gallery
+        
+        The examples are named referring to the journal paper they aim to reproduce simulations from
+        (or sometimes just where the inspiration originated from).
+        The list below groups all examples by the dimensionality and type of the employed modelling framework
+        ("environment" in PySDM nomenclature, which can be: <mark>box</mark>, <mark>parcel</mark>,
+        <mark>single-column</mark>, <mark>2D prescribed flow</mark>), and by the set of physical processes simulated
+        (<mark>condensation</mark>, collisional <mark>coagulation</mark> and <mark>breakup</mark>,
+        <mark>drop freezing</mark>, <mark>isotopic fractionation</mark>, <mark>aqueous chemistry</mark>,
+        <mark>seeding</mark>, ...).
+        
+        ## 2D kinematic environment (prescribed-flow) mimicking Sc deck
+        
+        The 2D prescribed-flow framework used here can be traced back to the work of
+          <a href="https://doi.org/10.1007/978-1-935704-36-2_1">Kessler 1969 (section 3C)</a>.
+          The setup employed in PySDM-examples, which mimics a stratiform cloud deck and features periodic horizontal boundary condition
+            and vanishing flow at vertical boundaries, was introduced in <a href="https://doi.org/10.1175/JAS3980">Morrison and Grabowski (2007)</a>
+            and later adopted for particle-based simulations in <a href="https://doi.org/10.5194/gmd-8-1677-2015">Arabas et al. (2015)</a>.
+          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.
+          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:
+        
+        ![animation](https://github.com/open-atmos/PySDM/wiki/files/kinematic_2D_example.gif)
+        
+        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_2023.html">Arabas_et_al_2023</a>: 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)
+        
+        The single-column PySDM environment is a reimplementation of the <mark>Met Office KiD framework</mark>
+          introduced in <a href="https://doi.org/10.1002/qj.1913">Shipway & Hill 2012</a>.
+        The framework features a single Eulerian-transported field of water vapour mixing ratio
+          (vertical profile of potential temperature is fixed).
+        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
+           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
+          to drive evolution of thermodynamic state and microphysical properties of particles.
+        
+        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/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>
+        - 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
+        
+        The parcel environment is also featured in the <a href="https://open-atmos.github.io/PySDM/PySDM.html#tutorials">PySDM tutorials</a>.
+        
+        ## 0D box environment
+        
+        The box environment is void of any spatial or thermodynamic context, it constitutes the most basic framework.
+        
+        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
+        - 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>
+        - 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_2023.html">Arabas_et_al_2023</a>: 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>
+        - <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>
+        - 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
+        - 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>
+        
+Platform: UNKNOWN
+Description-Content-Type: text/markdown
+Provides-Extra: tests

{PySDM-examples-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.80/PySDM_examples/Arabas_et_al_2023/__init__.py

@@ -0,0 +1,29 @@
+"""
+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
+from .plots import make_freezing_spec_plot, make_pdf_plot, make_temperature_plot
+from .run_simulation import run_simulation

{PySDM-examples-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.80/PySDM_examples/Bartman_et_al_2021/__init__.py

@@ -0,0 +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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.80/PySDM_examples/Grabowski_and_Pawlowska_2023/__init__.py

@@ -0,0 +1,22 @@
+# pylint: disable=invalid-name
+"""
+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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.80/PySDM_examples/Jensen_and_Nugent_2017/__init__.py

@@ -0,0 +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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.80/PySDM_examples/Niedermeier_et_al_2014/__init__.py

@@ -0,0 +1,9 @@
+"""
+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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.80/PySDM_examples/Singer_Ward/__init__.py

@@ -0,0 +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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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-2.79 → PySDM-examples-2.80}/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