Bettina-ayse #221

jbathmann · 2023-01-31T19:42:08Z

This PR contains a first implementation of the soil water content modification for bettina called BETTINA-AYSE. For details see ODD protocol by heinermann/janosch.

Benchmark files are provided.

Tasks

Example simulations by reviewers (@ChrisWudel ?)
Code review (@mcwimm ?)
Consistency checks with low water saturations (@jvollhueter ?)
Update tag documentation for new tags (@jbathmann !)

ChrisWudel · 2023-02-06T07:54:09Z

Hi, I would like to do some simulations. How did you imagine the example simulations there is probably a lack of comparative data for growth, as I don't have any available at the moment.

mcwimm · 2023-02-06T08:02:44Z

Hi, I would like to do some simulations. How did you imagine the example simulations there is probably a lack of comparative data for growth, as I don't have any available at the moment.

test data are provided in the benchmark folder (https://github.com/pymanga/pyMANGA/pull/221/files)

ChrisWudel · 2023-02-06T11:51:14Z

So, I have tested the "SoilWaterContent_CI.xml", "SoilWaterContent.xml" and "test_Benchmarks_CI.py" on Windows, and they work without any problems.
I will also carry out a test to see whether meaningful results are produced; I will contact Janosch about this.

mcwimm

Code looks 👍 Although I did not understand everything at the first attempt. Can we chat about it later today?

TreeModelLib/GrowthAndDeathDynamics/SimpleBettina/SimpleBettina.py

TreeModelLib/BelowgroundCompetition/SoilWaterContent/__init__.py

TreeModelLib/BelowgroundCompetition/SoilWaterContent/SoilWaterContent.py

jbathmann · 2023-02-14T10:29:51Z

@ChrisWudel Thank you for running the model!

jbathmann · 2023-02-14T10:53:01Z

Documentation added. YAPF used.

Benchmarks/ExampleSetups/ExmouthGulf/python_script.py

Benchmarks/ExampleSetups/ExmouthGulf/python_source.py

Benchmarks/ExampleSetups/OGSExampleSetup/python_source.py

Benchmarks/ModuleBenchmarks/BelowgroundCompetition/OGSLargeScale3D/python_script.py

Benchmarks/manual_Benchmarks.py

TreeModelLib/BelowgroundCompetition/SoilWaterContent/SoilWaterContent.py

mcwimm · 2023-02-18T13:05:27Z

TreeModelLib/BelowgroundCompetition/SoilWaterContent/SoilWaterContent.py

+        ## Measure for pore-size distribution
+        self._n = float(args.find("n").text)
+        ## Suction pressure [hPa]
+        self._psi_matrix = float(args.find("psi_matrix").text)


So far, we always changed everything to SI also if this differs from the ODD, see for example SimpleBettina.
I would prefer to do everything is SI units to be consistent.

TreeModelLib/BelowgroundCompetition/SoilWaterContent/SoilWaterContent.py

TreeModelLib/GrowthAndDeathDynamics/Mortality/Random/Random.py

TreeModelLib/GrowthAndDeathDynamics/Mortality/RandomGrowth/RandomGrowth.py

...aProject/tree_dynamics/belowground_competition/SoilWaterContent/soil_properties/s_omega_r.md

...aProject/tree_dynamics/belowground_competition/SoilWaterContent/soil_properties/s_omega_s.md

mcwimm · 2023-04-17T12:34:47Z

TreeModelLib/BelowgroundCompetition/SoilWaterContent/SoilWaterContent.py

+        ## Maximal soil water content [m**3]
+        self._max_soil_water_content = (
+            self._omega_r + (self._omega_s - self._omega_r) / ((
+                1 + (-self._alpha * self._psi_matrix / 100)**self._n)**(


Why "/100"?

mcwimm · 2023-05-04T13:14:52Z

TreeModelLib/BelowgroundCompetition/SoilWaterContent/SoilWaterContent.py

+        exponent = 1 / (1 - 1 / self._n)
+        self._psi_matrix = - (
+            base ** exponent - 1) ** (1 / self._n) / self._alpha
+        self._psi_matrix[np.where(self._psi_matrix < -7860000)] = -7860000


Comment Janosch: Theoretical value representing very low water content (expon. pF-curve returns infinite big value)

Co-authored-by: mcwimm <48250781+mcwimm@users.noreply.github.com>

jbathmann requested review from mcwimm and ChrisWudel January 31, 2023 19:42

mcwimm reviewed Feb 6, 2023

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mcwimm mentioned this pull request Feb 18, 2023

New structure #219

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pymanga force-pushed the bettina_ayse branch from b6ff824 to c307d98 Compare February 28, 2023 12:15

jbathmann commented Feb 28, 2023

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mcwimm force-pushed the bettina_ayse branch 2 times, most recently from 70ae2a0 to eb0f706 Compare August 21, 2024 14:54

jbathmann added 12 commits August 22, 2024 16:04

[TML/BC/SWC] Files added

b8ea05f

Restructuring of Bettina in order to assess relevant information

6cf3a24

[TML/BC/SWC] Load of precipitation data based on config file

e7300aa

[TML/SWC] Integrate precipitation added

de47a21

[TML/SWC] comments an datatyping

5c339e8

[TML/SWC] precipitation arrays. Units -> SI

b70db9a

[TML/SWC] add precipitation amount to patch

edcc425

[TML/SWC] update of matrix potential for each patch

5f8f9be

[TML/SWC] Getter for bg_resources according to bettina model

e1dcbd0

[TML/SWC] code style

da1aeea

[TML/BC] Implementation of tree resource uptake

df24054

[TML/SWC] Comments

3cfa1fe

jbathmann and others added 14 commits August 22, 2024 16:04

[TML/SWC] Benchmarks added

06e2d38

[TML] comments+corrections as suggested in PR review

004ffd5

Apply suggestions from code review

e9026e0

Co-authored-by: mcwimm <48250781+mcwimm@users.noreply.github.com>

[TML/SWC] apply suggestions from mcwimm

85d4dba

[Doc] Documentation of SWC files added

6aace08

python tag generation

07066d8

Apply suggestions from code review

459ed6c

Co-authored-by: mcwimm <48250781+mcwimm@users.noreply.github.com>

[Tag generation]

07f0d07

[TML/SWC] hPA -> PA

a8ef74b

tmp

5a4fbef

[RL] update to v3.1.0 structure

23aba85

[PML+RL] simplification of code

5966a3e

[benchmark] update benchmarks

7b5f18a

[PML] rename _resources to _factor

65966e7

mcwimm force-pushed the bettina_ayse branch from b3d4b5c to 65966e7 Compare August 22, 2024 14:05

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Bettina-ayse #221

Bettina-ayse #221

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Bettina-ayse #221

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Bettina-ayse #221

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