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Fixes to methane Tech Note#2091

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samsrabin merged 6 commits into
ESCOMP:masterfrom
samsrabin:tech-note-methane-fixes
Sep 19, 2023
Merged

Fixes to methane Tech Note#2091
samsrabin merged 6 commits into
ESCOMP:masterfrom
samsrabin:tech-note-methane-fixes

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@samsrabin samsrabin commented Aug 9, 2023 •
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Description of changes

Various minor fixes to the methane section of the Tech Note:

  • Added missing citation links
  • Added missing equation references
  • Corrected superscript syntax
  • Corrected units in a table
  • Corrected use of $\phi$ to $\varphi$

Equation references still missing:

  • "The gaseous concentration is calculated with Henry’s law as described in equation ."
  • "… with the same representation as Equation but with the gas diffusivity of oxygen."
  • "The solution to equation is solved in several sequential steps: …"

Specific notes

Contributors other than yourself, if any: @jinmuluo

CTSM Issues Fixed: Item 3 in #1990.

Are answers expected to change (and if so in what way)? No

Any User Interface Changes (namelist or namelist defaults changes)? No

Testing performed, if any: Rendered HTML looks good.

@samsrabin samsrabin added tag: simple bfb documentation additions or edits to user-facing documentation or its infrastructure PR status: ready PR: this is ready to merge in, with all tests satisfactory and reviews complete next this should get some attention in the next week or two. Normally each Thursday SE meeting. and removed PR status: ready PR: this is ready to merge in, with all tests satisfactory and reviews complete labels Aug 9, 2023
@samsrabin samsrabin marked this pull request as draft August 9, 2023 19:56
@samsrabin samsrabin self-assigned this Aug 17, 2023
@wwieder

wwieder commented Aug 22, 2023

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@samsrabin I think that:

  1. the gaseous concentration is calculated with Henry’s law as described in equation (2.25.7), since C_{e} is the expected equilibrium gaseous partial pressure.
  2. O2 can also diffuse in from the atmosphere to the soil layer via the reverse of the same pathway, with the same representation as Equation (2.25.8) but with the gas diffusivity of oxygen because A is the diffusive transport (of CH4) through aerenchyma.

@samsrabin

samsrabin commented Aug 23, 2023

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Thanks, @wwieder!

@samsrabin samsrabin added the PR status: ready PR: this is ready to merge in, with all tests satisfactory and reviews complete label Sep 6, 2023
@samsrabin samsrabin marked this pull request as ready for review September 6, 2023 16:54
@samsrabin samsrabin mentioned this pull request Sep 6, 2023
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@samsrabin samsrabin removed the next this should get some attention in the next week or two. Normally each Thursday SE meeting. label Sep 7, 2023
@samsrabin samsrabin mentioned this pull request Sep 14, 2023
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@samsrabin samsrabin requested a review from wwieder September 14, 2023 17:10
wwieder
wwieder approved these changes Sep 14, 2023
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Thanks for making these updates, @samsrabin

Comment thread doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst

+----------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------+
| :math:`{D}_{0}` (m\ :sup:`2` s\ :sup:`-1`) | CH\ :sub:`4` | O\ :sub:`2` |
| :math:`{D}_{0}` (cm\ :sup:`2` s\ :sup:`-1`) | CH\ :sub:`4` | O\ :sub:`2` |

@wwieder wwieder Sep 14, 2023

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I'm assuming you checked these units with the code?

@samsrabin samsrabin Sep 14, 2023

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Yep! The constants are set here, where the correct units are given in the comment:
https://github.com/samsrabin/CTSM/blob/7ae1372c0c39747ba71ae399cd2c5964e72f917d/src/main/clm_varcon.F90#L244-L247

When they're used, they're multiplied by 1e-4 to convert D0 from cm2/s to m2/s:
https://github.com/samsrabin/CTSM/blob/7ae1372c0c39747ba71ae399cd2c5964e72f917d/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90#L400

However, it looks like the table is missing a digit. Will add.

Comment thread doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst
Comment thread doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst
samsrabin added a commit that referenced this pull request Sep 19, 2023
@samsrabin
Merge 5 bit-for-bit pull requests:
2e2434d 
* Add system and unit tests for making fsurdat with all crops everywhere (#2081)
* Rework master_list* files etc. (#2087)
* Fixes to methane Tech Note (#2091)
* Add is_doy_in_interval() function (#2158)
* Avoid using subprocess.run() in FSURDATMODIFYCTSM (#2125)

Closes issues:
* Add unit test for making fsurdat with all crops everywhere (#2079)
* Rework master_list_(no)?fates.rst? (#2083)
* conda run -n can fail if a conda environment is already active (#2109)
* conda fails to load for SystemTests (#2111)
@samsrabin samsrabin merged commit 08e64d0 into ESCOMP:master Sep 19, 2023
samsrabin added a commit to samsrabin/CTSM that referenced this pull request Sep 19, 2023
@samsrabin
Merge tag 'ctsm5.1.dev142' into newcropcals-rxsowwindow
8537757 
b4b changes to Python scripts, history lists, tech note, and clm_time_manager.

* Add system and unit tests for making fsurdat with all crops everywhere (ESCOMP#2081)
* Rework master_list* files etc. (ESCOMP#2087)
* Fixes to methane Tech Note (ESCOMP#2091)
* Add is_doy_in_interval() function (ESCOMP#2158)
* Avoid using subprocess.run() in FSURDATMODIFYCTSM (ESCOMP#2125)

Closes issues:
* Add unit test for making fsurdat with all crops everywhere (ESCOMP#2079)
* Rework master_list_(no)?fates.rst? (ESCOMP#2083)
* conda run -n can fail if a conda environment is already active (ESCOMP#2109)
* conda fails to load for SystemTests (ESCOMP#2111)
samsrabin added a commit to samsrabin/CTSM that referenced this pull request Sep 20, 2023
@samsrabin
Merge tag 'ctsm5.1.dev142' into newcropcals-rxsowwindow
ff687dc 
b4b changes to Python scripts, history lists, tech note, and clm_time_manager.

* Add system and unit tests for making fsurdat with all crops everywhere (ESCOMP#2081)
* Rework master_list* files etc. (ESCOMP#2087)
* Fixes to methane Tech Note (ESCOMP#2091)
* Add is_doy_in_interval() function (ESCOMP#2158)
* Avoid using subprocess.run() in FSURDATMODIFYCTSM (ESCOMP#2125)

Closes issues:
* Add unit test for making fsurdat with all crops everywhere (ESCOMP#2079)
* Rework master_list_(no)?fates.rst? (ESCOMP#2083)
* conda run -n can fail if a conda environment is already active (ESCOMP#2109)
* conda fails to load for SystemTests (ESCOMP#2111)
samsrabin added a commit to samsrabin/CTSM that referenced this pull request Sep 21, 2023
@samsrabin
Merge tag 'ctsm5.1.dev142' into newcropcals-rxsowwindow
1382c5d 
b4b changes to Python scripts, history lists, tech note, and clm_time_manager.

* Add system and unit tests for making fsurdat with all crops everywhere (ESCOMP#2081)
* Rework master_list* files etc. (ESCOMP#2087)
* Fixes to methane Tech Note (ESCOMP#2091)
* Add is_doy_in_interval() function (ESCOMP#2158)
* Avoid using subprocess.run() in FSURDATMODIFYCTSM (ESCOMP#2125)

Closes issues:
* Add unit test for making fsurdat with all crops everywhere (ESCOMP#2079)
* Rework master_list_(no)?fates.rst? (ESCOMP#2083)
* conda run -n can fail if a conda environment is already active (ESCOMP#2109)
* conda fails to load for SystemTests (ESCOMP#2111)
samsrabin added a commit to samsrabin/CTSM that referenced this pull request Sep 27, 2023
@samsrabin
Merge tag 'ctsm5.1.dev142' into hist-anomalies
1e1b604 
b4b changes to Python scripts, history lists, tech note, and clm_time_manager.

* Add system and unit tests for making fsurdat with all crops everywhere (ESCOMP#2081)
* Rework master_list* files etc. (ESCOMP#2087)
* Fixes to methane Tech Note (ESCOMP#2091)
* Add is_doy_in_interval() function (ESCOMP#2158)
* Avoid using subprocess.run() in FSURDATMODIFYCTSM (ESCOMP#2125)

Closes issues:
* Add unit test for making fsurdat with all crops everywhere (ESCOMP#2079)
* Rework master_list_(no)?fates.rst? (ESCOMP#2083)
* conda run -n can fail if a conda environment is already active (ESCOMP#2109)
* conda fails to load for SystemTests (ESCOMP#2111)
samsrabin added a commit to samsrabin/CTSM that referenced this pull request Oct 2, 2023
@samsrabin
Merge tag 'ctsm5.1.dev142' into tillage
d43c617 
b4b changes to Python scripts, history lists, tech note, and clm_time_manager.

* Add system and unit tests for making fsurdat with all crops everywhere (ESCOMP#2081)
* Rework master_list* files etc. (ESCOMP#2087)
* Fixes to methane Tech Note (ESCOMP#2091)
* Add is_doy_in_interval() function (ESCOMP#2158)
* Avoid using subprocess.run() in FSURDATMODIFYCTSM (ESCOMP#2125)

Closes issues:
* Add unit test for making fsurdat with all crops everywhere (ESCOMP#2079)
* Rework master_list_(no)?fates.rst? (ESCOMP#2083)
* conda run -n can fail if a conda environment is already active (ESCOMP#2109)
* conda fails to load for SystemTests (ESCOMP#2111)
samsrabin added a commit to samsrabin/CTSM that referenced this pull request Oct 3, 2023
@samsrabin
Merge tag 'ctsm5.1.dev142' into tillage-and-residues3
0d36638 
b4b changes to Python scripts, history lists, tech note, and clm_time_manager.

* Add system and unit tests for making fsurdat with all crops everywhere (ESCOMP#2081)
* Rework master_list* files etc. (ESCOMP#2087)
* Fixes to methane Tech Note (ESCOMP#2091)
* Add is_doy_in_interval() function (ESCOMP#2158)
* Avoid using subprocess.run() in FSURDATMODIFYCTSM (ESCOMP#2125)

Closes issues:
* Add unit test for making fsurdat with all crops everywhere (ESCOMP#2079)
* Rework master_list_(no)?fates.rst? (ESCOMP#2083)
* conda run -n can fail if a conda environment is already active (ESCOMP#2109)
* conda fails to load for SystemTests (ESCOMP#2111)
samsrabin added a commit to samsrabin/CTSM that referenced this pull request Oct 4, 2023
@samsrabin
Merge tag 'ctsm5.1.dev142' into hillslope_hydrology-ssr
595d95d 
b4b changes to Python scripts, history lists, tech note, and clm_time_manager.

* Add system and unit tests for making fsurdat with all crops everywhere (ESCOMP#2081)
* Rework master_list* files etc. (ESCOMP#2087)
* Fixes to methane Tech Note (ESCOMP#2091)
* Add is_doy_in_interval() function (ESCOMP#2158)
* Avoid using subprocess.run() in FSURDATMODIFYCTSM (ESCOMP#2125)

Closes issues:
* Add unit test for making fsurdat with all crops everywhere (ESCOMP#2079)
* Rework master_list_(no)?fates.rst? (ESCOMP#2083)
* conda run -n can fail if a conda environment is already active (ESCOMP#2109)
* conda fails to load for SystemTests (ESCOMP#2111)
samsrabin added a commit to samsrabin/CTSM that referenced this pull request Oct 5, 2023
@samsrabin
Merge tag 'ctsm5.1.dev142' into soil-gas-diffusivity-bugfix
d369f8d 
b4b changes to Python scripts, history lists, tech note, and clm_time_manager.

* Add system and unit tests for making fsurdat with all crops everywhere (ESCOMP#2081)
* Rework master_list* files etc. (ESCOMP#2087)
* Fixes to methane Tech Note (ESCOMP#2091)
* Add is_doy_in_interval() function (ESCOMP#2158)
* Avoid using subprocess.run() in FSURDATMODIFYCTSM (ESCOMP#2125)

Closes issues:
* Add unit test for making fsurdat with all crops everywhere (ESCOMP#2079)
* Rework master_list_(no)?fates.rst? (ESCOMP#2083)
* conda run -n can fail if a conda environment is already active (ESCOMP#2109)
* conda fails to load for SystemTests (ESCOMP#2111)
samsrabin added a commit to samsrabin/CTSM that referenced this pull request Dec 23, 2023
@samsrabin
Merge tag 'ctsm5.1.dev142' into tillage-mike-merge142
19c4790 
b4b changes to Python scripts, history lists, tech note, and clm_time_manager.

* Add system and unit tests for making fsurdat with all crops everywhere (ESCOMP#2081)
* Rework master_list* files etc. (ESCOMP#2087)
* Fixes to methane Tech Note (ESCOMP#2091)
* Add is_doy_in_interval() function (ESCOMP#2158)
* Avoid using subprocess.run() in FSURDATMODIFYCTSM (ESCOMP#2125)

Closes issues:
* Add unit test for making fsurdat with all crops everywhere (ESCOMP#2079)
* Rework master_list_(no)?fates.rst? (ESCOMP#2083)
* conda run -n can fail if a conda environment is already active (ESCOMP#2109)
* conda fails to load for SystemTests (ESCOMP#2111)

# Conflicts:
#	src/biogeochem/CNBalanceCheckMod.F90
#	src/biogeochem/CNCIsoFluxMod.F90
#	src/biogeochem/CNDriverMod.F90
#	src/biogeochem/CNPhenologyMod.F90
#	src/biogeochem/CNProductsMod.F90
#	src/biogeochem/CNVegCarbonFluxType.F90
#	src/biogeochem/CNVegNitrogenFluxType.F90
#	src/biogeochem/EDBGCDynMod.F90
#	src/main/clm_initializeMod.F90
#	src/main/controlMod.F90
#	src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90
samsrabin added a commit to samsrabin/CTSM that referenced this pull request Dec 23, 2023
@samsrabin
Merge tag 'ctsm5.1.dev142' into tillage-mike-merge142
9cdc75a 
b4b changes to Python scripts, history lists, tech note, and clm_time_manager.

* Add system and unit tests for making fsurdat with all crops everywhere (ESCOMP#2081)
* Rework master_list* files etc. (ESCOMP#2087)
* Fixes to methane Tech Note (ESCOMP#2091)
* Add is_doy_in_interval() function (ESCOMP#2158)
* Avoid using subprocess.run() in FSURDATMODIFYCTSM (ESCOMP#2125)

Closes issues:
* Add unit test for making fsurdat with all crops everywhere (ESCOMP#2079)
* Rework master_list_(no)?fates.rst? (ESCOMP#2083)
* conda run -n can fail if a conda environment is already active (ESCOMP#2109)
* conda fails to load for SystemTests (ESCOMP#2111)
@samsrabin samsrabin added simple b4b bit-for-bit labels Aug 8, 2024
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