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Wombatmid docs#94

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pearseb wants to merge 60 commits intomainfrom
wombatmid-docs
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Wombatmid docs#94
pearseb wants to merge 60 commits intomainfrom
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@pearseb pearseb commented Mar 18, 2026

Very large additions here to the WOMBAT-mid documentation. Note sure how many words and equations but a lot... Sorry Dougie. Maybe best to just look at whether things are rendered or not and over time we can iron out whatever mistakes I have unintentionally included.

Pearse

@pearseb pearseb requested a review from dougiesquire March 18, 2026 03:14
@pearseb pearseb self-assigned this Mar 18, 2026
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pearseb commented Mar 23, 2026

@dougiesquire
These docs are finally ready for some review at some point. Like we talked about, maybe just check that the tracer tendencies are actually the same as what we have in the model.

But, this isn't pressing. We can get to this later before I publish the paper about WOMBAT-mid.

pearseb and others added 26 commits March 26, 2026 10:29
@pearseb @dougiesquire
Create WOMBATmid_update_from_source.md
373bd6b 
Created new documentation file for WOMBAT-mid
@pearseb @dougiesquire
Made first additions to WOMBAT-mid
2b40273 
Covered light and nutrient limitations.
@pearseb @dougiesquire
Revise WOMBATmid update_from_source documentation
05d4e25 
Additions to the description of phytoplankton growth limitations by iron and silicic acid.
@pearseb @dougiesquire
Updated:
45f7ee3 
* Chlorophyll growth
* Light limitation
* Realised growth rate of phytoplankton
@pearseb @dougiesquire
Updates to WOMBAT-mid documentation Steps 1-7. Steps 8-20 still required
0f3d68b
@pearseb @dougiesquire
Iron chemistry and silicic acid uptake completed
be16218
@pearseb @dougiesquire
Completed steps 10 - 23. Large additions here.
4458e9e
@pearseb @dougiesquire
small corrections. Seeing if the pages render properly on html.
3377cbc
@pearseb @dougiesquire
Trying \leftarrow rather than ← in my markdown for rendering pur…
9640473 
…poses
@pearseb @dougiesquire
Trying \mathrm{} for inline $Si(OH)_{4}$ rendering
865ef64
@pearseb @dougiesquire
Okay, now trying the Si(OH)<sub>4</sub> outside of math equations
7c04bf4
@pearseb @dougiesquire
Testing \mathrm{} within inline equations for silicic acid
da5d523
@pearseb @dougiesquire
New test of equations to get rendering to work
8a48ef9
@pearseb @dougiesquire
New test for rendering
a2bce6f
@pearseb @dougiesquire
new test for rendering
e341138
@pearseb @dougiesquire
New test for rendering
cda36a5
@pearseb @dougiesquire
Changing the chemical formula of Si(OH)4 to H4SiO4
ed1c487
@pearseb @dougiesquire
Corrected all instances of NH4, N2O, NO3 and O2 to use the <sub>x</su…
5caface 
…b> diction and also corrected all Si(OH)_{4} to use H4SiO4 in equations, which appears to render properly
@pearseb @dougiesquire
Fix of $N_{2}$O that caused rendering of all equations beyond it to f…
83b2afb 
…ail (I think)
@dougiesquire
Reorganise WOMBATmid docs
59e7796 
Combine update_from_source and update_from_bottom docs

Add WOMBATmid docs to model description
@pearseb @dougiesquire
Trying \begin{align} for equations
efaf004
@pearseb @dougiesquire
Pushing for the hell of it
11c675e
@pearseb @dougiesquire
Testing \begin{align}
818ddaa
@pearseb @dougiesquire
Added \begin{align} thorughout. Checking effect on tracer tendency ca…
922b3f3 
…lculations
@pearseb @dougiesquire
Test of align
501e475
@pearseb @dougiesquire
Trying \aligned
4cad294
pearseb added 29 commits March 26, 2026 10:30
@pearseb @dougiesquire
Adding <br> to the end of - statements under where
2d90353
@pearseb @dougiesquire
added <br> to all where statements
22a0806
@pearseb @dougiesquire
Made all where statements in italics and trying to correct tracer ten…
2a41c04 
…dencies
@pearseb @dougiesquire
Issues with no3 tracer tendencies equation
b9b64b6
@pearseb @dougiesquire
Replaced all &larr; and &rarr; with \leftarrow and \rightarrow
849ec84
@pearseb @dougiesquire
Trying a new format for the tracer tendencies
8004c0b
@pearseb @dougiesquire
Test
f2b080e
@pearseb @dougiesquire
test
46ea6a5
@pearseb @dougiesquire
Testing aligned for tracer tendencies
1ff316a
@pearseb @dougiesquire
New test in tracer tendencies
20e0b36
@pearseb @dougiesquire
New test
6e8e63e
@pearseb @dougiesquire
trying & on different side of = sign
f22a9cc
@pearseb @dougiesquire
Trying wihtout \left( and \right)
0b8803d
@pearseb @dougiesquire
Okay, the \left( and \right) parentheses appears to be the big issue
15d32a3
@pearseb @dougiesquire
Trying $$ around \align
85eeb91
@pearseb @dougiesquire
Playing now with tracer tendencies line breaks for readability
7a39cbb
@pearseb @dougiesquire
Making sure that & only follows a //
67d6b4a
@pearseb @dougiesquire
New test of tracer tendencies rendering
a032b0c
@pearseb @dougiesquire
Iron tracer tendency
60975c3
@pearseb @dougiesquire
Finished the tracer tendencies
d188ead
@pearseb @dougiesquire
All equations should render now
9e9a13f
@pearseb @dougiesquire
Corrected some equations without \\
028d355
@pearseb @dougiesquire
Correction to equations
6c4ce64
@pearseb @dougiesquire
Cleaning up the equations
656f817
@pearseb @dougiesquire
Correcting the equations
48b79b1
@pearseb @dougiesquire
Added \quad to the RHS of all equations
c38520d
@pearseb @dougiesquire
Altered N2O production by ammonia oxidizers
61d5464
@pearseb @dougiesquire
Edits to the new N2o production from AOA
52a8b37
@pearseb @dougiesquire
Small error
88e9539
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