Add "Flexible Microphysics" option, based on Cloudy.jl #333

edejong-caltech · 2024-02-22T21:38:29Z

Purpose

Creates a flexible many-moment microphysics option based on the computational framework of Cloudy.jl.

To-do

Make Cloudy dependency an extension
Add physical default parameters (see Cloudy.jl issue )
Test condensation in parcel model
Refactor the sedimentation to return a moment_weighted terminal velocity

Next steps:

Test coalescence in box model (maybe)
Test condensation + coalescence + sedimentation in (KiD or CliMA Atmos single column)

Content

Link existing dynamics in a new module
Write unit tests for new Cloudy dynamics

Note: GPU and performance tests are not and will not be included in the initial integration.

I have read and checked the items on the review checklist.

…ysics.jl into ej/add_cloudy

…into ej/add_cloudy

…ysics.jl into ej/add_cloudy

…into ej/add_cloudy

codecov · 2024-03-11T21:31:27Z

Codecov Report

Attention: Patch coverage is 0% with 30 lines in your changes are missing coverage. Please review.

Project coverage is 96.16%. Comparing base (d38910d) to head (699496d).
Report is 2 commits behind head on main.

Files	Patch %	Lines
ext/CloudyExt.jl	0.00%	30 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #333      +/-   ##
==========================================
- Coverage   98.11%   96.16%   -1.95%     
==========================================
  Files          35       36       +1     
  Lines        1165     1225      +60     
==========================================
+ Hits         1143     1178      +35     
- Misses         22       47      +25

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

trontrytel · 2024-03-11T23:18:38Z

docs/src/MicrophysicsFlexible.md

@@ -0,0 +1,39 @@
+# Microphysics Flexible
+


You should also add the docs page you are creating to the docs make file. Maybe somewhere here:

CloudMicrophysics.jl/docs/make.jl

Line 41 in e2e1a54

"Non-equilibrium cloud formation" => "MicrophysicsNonEq.md",

trontrytel · 2024-03-11T23:23:01Z

docs/src/MicrophysicsFlexible.md

+
+The `MicrophysicsFlexible.jl` module relies on the extension defined in `ext/CloudyExt.jl`, based on a flexible N-moment microphysics scheme built in the external package `Cloudy.jl`. This option currently handles warm-rain processes including coalescence, condensation/evaporation, and sedimentation (terminal velocity). Unlike typical moment-based schemes which distinguish between categories such as rain and cloud, and which determine rates of conversion between categories (the canonical autoconversion, accretion, and self-collection), this option gives the user the flexibility to define as many or as few moments as they please, with these coalescence-based processes being solved directly without relying on conversion rates. Likewise, the rate of condensation/evaporation is defined through the rate of diffusion of water vapor to/from the surface of droplets defined by the subdistributions which underpin the method. The user has not only the flexibility to specify the number of moments (and therefore the complexity/accuracy) to use, but also the assumed size distributions corresponding to these moments. For instance, one might define a 5-moment implementation using an Exponential mode for smaller cloud droplets, plus a Gamma mode for larger rain droplets. Or, more creatively, perhaps a 12-moment implementation comprised of four Gamma modes.
+
+Options for dynamics and size distributions are under continuous development in the `Cloudy.jl` package, thus only the default and suggested use cases are described in detail here.


Maybe it would be good to add a link to Cloudy documentation, paper or repo somewhere? Especially since w don't want to explain the details of how the collisions or condensation are handled

trontrytel · 2024-03-11T23:31:09Z

docs/src/MicrophysicsFlexible.md

+|---------------------|------------------------------------------|----------------------------|
+| ``pdists``          | Vector of subdistributions corresponding | ``[Exponential, Gamma]``   |
+|                     | to the moments                           |                            |
+| ``mom``             | Prognostic moments, in the same order as | ``[0, 0, 0, 0, 0]``        |


Does it mean that by default I have two distributions - one Exponential and one Gamma? Which sizes do they refer to? And why by default do I have the 0 moment 5 times? (It probably just shows I should read Cloudy docs...

Actually these have changed, and the Cloudy docs aren't helpful... I"ll try to make it more self explanatory

trontrytel · 2024-03-11T23:35:25Z

src/MicrophysicsFlexible.jl

+    weighted_vt(clinfo)
+
+ - `clinfo` - kwarg structure containing pdists, moments, and coalescence parameters
+Returns the integrated fall speeds corresponding to the rate of change of prognostic moments


Would it be correct to say moment-weighted terminal velocities?

trontrytel · 2024-03-11T23:38:47Z

docs/src/MicrophysicsFlexible.md

+| ``KernelFunc``      | Form of the coalescence kernel function  | ``LongKernelFunction``     |
+| ``mass_thresholds`` | Particle size thresholds for coalescence | ``[10.0, Inf]``            |
+|                     | integration                              |                            |
+| ``kernel order``    | Polynomial order for the approx. kernel  | ``1``                      |


The CLSetup has more fields than what the table shows? Are they not meant to be changed by the user?

Correct, unless the user really knows what they're doing ;)

trontrytel · 2024-03-11T23:43:31Z

test/microphysicsflexible_tests.jl

+        TT.@test length(clinfo.mom) == 5
+        TT.@test length(clinfo.NProgMoms) == 2
+
+        # Test coalescence


Should the mass be conserved in this approach when doing collisions? Could we test that?

Yes, but these tests are already covered in Cloudy.jl so I think it would be redundant here

These tests are only to check that the new features/structs that are created in CM.jl work. But, if you think it would be useful to create some redundant tests, I can absolutely do so! Let's open an issue if so.

It's fine. Lets add as many tests as is necessary to test that Cloudy can be used in CM.

trontrytel · 2024-03-12T00:15:04Z

parcel/Example_NMoment_condensation.jl

+"""
+    ODE problem definitions
+"""
+function parcel_model_cloudy(dY, Y, p, t)


I'll think about how to unify the OG parcel model with the Cloudy parcel model. But it's ok to have two separate ones for now. My only concern is that we won't see anywhere if this example stops working. So you could add the plot to the docs somewhere (then the docs will break if things break). Or move it to tests.

Let's address in this in a future PR, where I will also add a box model test case and such "smoke tests". I'll open an issue.

…into ej/add_cloudy

edejong-caltech added 2 commits February 22, 2024 13:16

Add preliminary cloudy condensation + coalescence, with unit tests

e05dfdf

Add sedimentation

3552686

trontrytel added enhancement New feature or request work-in-progress labels Feb 24, 2024

edejong-caltech added 12 commits February 28, 2024 11:05

Merge branch 'ej/add_cloudy' of https://github.com/CliMA/CloudMicroph…

dc76710

…ysics.jl into ej/add_cloudy

Merge branch 'main' of https://github.com/CliMA/CloudMicrophysics.jl …

2946f92

…into ej/add_cloudy

Make cloudy deps an extension instead

742c7eb

Add docs

69b5f01

Add condensation-only parcel model example for Cloudy

8a9841e

Add compat entry for Cloudy

299095e

Merge branch 'ej/add_cloudy' of https://github.com/CliMA/CloudMicroph…

71afaa1

…ysics.jl into ej/add_cloudy

Merge branch 'main' of https://github.com/CliMA/CloudMicrophysics.jl …

344bb68

…into ej/add_cloudy

Update Cloudy version #

0bb5ce0

Rename sedimentation + fix condensation tests

8886486

Put units into SI

67979fd

Julia Formatter

0db2f2e

edejong-caltech marked this pull request as ready for review March 11, 2024 21:15

edejong-caltech requested review from trontrytel and sajjadazimi March 11, 2024 21:15

Add normalization factors

e9b7671

trontrytel added needs review and removed work-in-progress labels Mar 11, 2024

trontrytel reviewed Mar 11, 2024

View reviewed changes

trontrytel reviewed Mar 12, 2024

View reviewed changes

trontrytel approved these changes Mar 12, 2024

View reviewed changes

trontrytel added Approved 🍀 and removed needs review labels Mar 12, 2024

sajjadazimi approved these changes Mar 12, 2024

View reviewed changes

edejong-caltech added 2 commits March 12, 2024 17:47

Fix documentation errors

bd821e2

Merge branch 'main' of https://github.com/CliMA/CloudMicrophysics.jl …

699496d

…into ej/add_cloudy

edejong-caltech merged commit 3fcd6ef into main Mar 13, 2024
8 of 10 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Add "Flexible Microphysics" option, based on Cloudy.jl #333

Add "Flexible Microphysics" option, based on Cloudy.jl #333

edejong-caltech commented Feb 22, 2024 •

edited

Loading

codecov bot commented Mar 11, 2024 •

edited

Loading

trontrytel Mar 11, 2024

edejong-caltech Mar 13, 2024

trontrytel Mar 11, 2024 •

edited

Loading

edejong-caltech Mar 13, 2024

trontrytel Mar 11, 2024

edejong-caltech Mar 13, 2024

trontrytel Mar 11, 2024

edejong-caltech Mar 13, 2024

trontrytel Mar 11, 2024

edejong-caltech Mar 13, 2024

trontrytel Mar 11, 2024

edejong-caltech Mar 13, 2024

edejong-caltech Mar 13, 2024

trontrytel Mar 13, 2024

trontrytel Mar 12, 2024

edejong-caltech Mar 13, 2024


		The `MicrophysicsFlexible.jl` module relies on the extension defined in `ext/CloudyExt.jl`, based on a flexible N-moment microphysics scheme built in the external package `Cloudy.jl`. This option currently handles warm-rain processes including coalescence, condensation/evaporation, and sedimentation (terminal velocity). Unlike typical moment-based schemes which distinguish between categories such as rain and cloud, and which determine rates of conversion between categories (the canonical autoconversion, accretion, and self-collection), this option gives the user the flexibility to define as many or as few moments as they please, with these coalescence-based processes being solved directly without relying on conversion rates. Likewise, the rate of condensation/evaporation is defined through the rate of diffusion of water vapor to/from the surface of droplets defined by the subdistributions which underpin the method. The user has not only the flexibility to specify the number of moments (and therefore the complexity/accuracy) to use, but also the assumed size distributions corresponding to these moments. For instance, one might define a 5-moment implementation using an Exponential mode for smaller cloud droplets, plus a Gamma mode for larger rain droplets. Or, more creatively, perhaps a 12-moment implementation comprised of four Gamma modes.

		Options for dynamics and size distributions are under continuous development in the `Cloudy.jl` package, thus only the default and suggested use cases are described in detail here.

Add "Flexible Microphysics" option, based on Cloudy.jl #333

Add "Flexible Microphysics" option, based on Cloudy.jl #333

Conversation

edejong-caltech commented Feb 22, 2024 • edited Loading

Purpose

To-do

Next steps:

Content

codecov bot commented Mar 11, 2024 • edited Loading

Codecov Report

Choose a reason for hiding this comment

Choose a reason for hiding this comment

trontrytel Mar 11, 2024 • edited Loading

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

edejong-caltech commented Feb 22, 2024 •

edited

Loading

codecov bot commented Mar 11, 2024 •

edited

Loading

trontrytel Mar 11, 2024 •

edited

Loading