PySDM-examples 2.80__tar.gz → 2.81__tar.gz

pysdm_examples-2.81/PKG-INFO

@@ -0,0 +1,151 @@
+Metadata-Version: 2.1
+Name: PySDM-examples
+Version: 2.81
+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-Content-Type: text/markdown
+Requires-Dist: PySDM
+Requires-Dist: PyMPDATA
+Requires-Dist: open-atmos-jupyter-utils
+Requires-Dist: pystrict
+Requires-Dist: matplotlib
+Requires-Dist: joblib
+Requires-Dist: ipywidgets
+Requires-Dist: seaborn
+Requires-Dist: numdifftools
+Requires-Dist: vtk
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: nbconvert; extra == "tests"
+
+# 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>

{PySDM-examples-2.80 → pysdm_examples-2.81}/PySDM_examples/Kreidenweis_et_al_2003/simulation.py

@@ -114,7 +114,7 @@ class Simulation(BasicSimulation):
                 key="S_VI",
                 dry_radius_bins_edges=settings.dry_radius_bins_edges,
                 name="dm_S_VI/dlog_10(dry diameter)",
-                unit='ug / m^3"',
+                unit="ug / m^3",
             ),
         )
 

{PySDM-examples-2.80 → pysdm_examples-2.81}/PySDM_examples/Srivastava_1982/simulation.py

@@ -70,7 +70,7 @@ class Simulation:
                     if step != 0:
                         particulator.run(steps=1)
                     for prod in self.settings.prods:
-                        self.simulation_res[n_sd][prod][seed][step] = (
+                        (self.simulation_res[n_sd][prod][seed][step],) = (
                             particulator.products[prod].get()
                         )
 

{PySDM-examples-2.80 → pysdm_examples-2.81}/PySDM_examples/deJong_Azimi/simulation_0D.py

@@ -48,9 +48,9 @@ def run_box(settings, backend_class=CPU):
     for i, step in enumerate(settings.steps):
         particulator.run(step - particulator.n_steps)
         y[i] = particulator.products["dv/dlnr"].get()[0]
-        mom[i, 0] = particulator.products["M0"].get()
-        mom[i, 1] = particulator.products["M1"].get()
-        mom[i, 2] = particulator.products["M2"].get()
+        (mom[i, 0],) = particulator.products["M0"].get()
+        (mom[i, 1],) = particulator.products["M1"].get()
+        (mom[i, 2],) = particulator.products["M2"].get()
 
     return namedtuple("_", ("radius_bins_left_edges", "dv_dlnr", "moments"))(
         radius_bins_left_edges=settings.radius_bins_edges[:-1], dv_dlnr=y, moments=mom

{PySDM-examples-2.80 → pysdm_examples-2.81}/PySDM_examples/deJong_Mackay_et_al_2023/simulation_0D.py

@@ -79,11 +79,11 @@ def run_box_breakup(
         core.run(step - core.n_steps)
         y[i] = core.products["dv/dlnr"].get()[0]
         if return_nv:
-            y2[i] = core.products["N(v)"].get()[0]
-        rates[i, 0] = core.products["cr"].get()
-        rates[i, 1] = core.products["crd"].get()
-        rates[i, 2] = core.products["cor"].get()
-        rates[i, 3] = core.products["br"].get()
+            (y2[i],) = core.products["N(v)"].get()
+        (rates[i, 0],) = core.products["cr"].get()
+        (rates[i, 1],) = core.products["crd"].get()
+        (rates[i, 2],) = core.products["cor"].get()
+        (rates[i, 3],) = core.products["br"].get()
 
     x = (settings.radius_bins_edges[:-1] / si.micrometres,)[0]
 
@@ -124,10 +124,10 @@ def run_box_NObreakup(settings, steps=None, backend_class=CPU):
     # run
     for i, step in enumerate(steps):
         core.run(step - core.n_steps)
-        y[i] = core.products["dv/dlnr"].get()[0]
-        rates[i, 0] = core.products["cr"].get()
-        rates[i, 1] = core.products["crd"].get()
-        rates[i, 2] = core.products["cor"].get()
+        (y[i],) = core.products["dv/dlnr"].get()
+        (rates[i, 0],) = core.products["cr"].get()
+        (rates[i, 1],) = core.products["crd"].get()
+        (rates[i, 2],) = core.products["cor"].get()
 
     x = (settings.radius_bins_edges[:-1] / si.micrometres,)[0]
 

{PySDM-examples-2.80 → pysdm_examples-2.81}/PySDM_examples/seeding/simulation.py

@@ -90,7 +90,10 @@ class Simulation:
                 data[data == 0] = np.nan
                 attr.append(data)
             for key, prod in output["products"].items():
-                prod.append(float(self.particulator.products[key].get()))
+                value = self.particulator.products[key].get()
+                if not isinstance(value, float):
+                    (value,) = value
+                prod.append(float(value))
         for out in ("attributes", "products"):
             for key, val in output[out].items():
                 output[out][key] = np.array(val)

pysdm_examples-2.81/PySDM_examples.egg-info/PKG-INFO

@@ -0,0 +1,151 @@
+Metadata-Version: 2.1
+Name: PySDM-examples
+Version: 2.81
+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-Content-Type: text/markdown
+Requires-Dist: PySDM
+Requires-Dist: PyMPDATA
+Requires-Dist: open-atmos-jupyter-utils
+Requires-Dist: pystrict
+Requires-Dist: matplotlib
+Requires-Dist: joblib
+Requires-Dist: ipywidgets
+Requires-Dist: seaborn
+Requires-Dist: numdifftools
+Requires-Dist: vtk
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: nbconvert; extra == "tests"
+
+# 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>

pysdm_examples-2.81/pyproject.toml

@@ -0,0 +1,5 @@
+[tool.setuptools_scm]
+root = ".."
+
+[build-system]
+requires = ['setuptools==75.3.0', 'setuptools-scm==8.1.0']

{PySDM-examples-2.80 → pysdm_examples-2.81}/setup.py

@@ -26,7 +26,6 @@ setup(
     use_scm_version={
         "local_scheme": lambda _: "",
         "version_scheme": "post-release",
-        "root": "..",
     },
     install_requires=[
         "PySDM",

PySDM-examples-2.80/PKG-INFO

@@ -1,140 +0,0 @@
-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