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Since 0d76de1 GLM v3.1 doesn't recognize my phytoplankton namelist file (neither NML nor CSV) when starting a simulation. I did test this on Windows 10 Home and macOS Catalina. I always get

         aed2_phytoplankton initialization
 Unknown file type "aed2/aed2_phyto_pars.csv"
STOP Error reading namelist phyto_data

Thanks!

Initialising "AED2" external module:
init_var_aed2_models : nwq = 15 nwqben = 1
spatial AED2 var initialisation from file:
../External/AED2/resuspension_map.csv
set_env_aed2_models : linking to host environment vars
Successful.

Log successfully initialised variables to screen and report unused columns.

move outside of IF so computes if no CO2

DIAG_VAR or DIAG_VAR_S for Psed_POC? ... check

Also, add new diagnostic for POM vvel; to help GLEON MMOM group

It seems that all the provided parameterizations for k600 are rather valid for oceans, open lakes or estuaries. I was wondering why no formula for more sheltered lakes was included (for example Cole & Caraco, 1998). In my experience, gas exchange is underestimated in lakes if there is no lower limit for gas exchange in no-wind conditions and Cole & Caraco, 1998 seems to perform well in such cases.

I've posted this on the AEMON forum as well, but thought I'd put it up here too:
When I try to run aed modules beyond tracer and noncohesive, I'm getting seg faults, although if I take those modules out, I can (sometimes) run a few more modules. This issue is occurring on multiple systems:
I have GLM 3.0.1 running on a Unix cluster, and Ubuntu in Windows subsystem for Linux, and 3.0.0 on a Mac. The two Unix versions are just running the package installed from apt-get, which provides glm built with gcc 7.4.0, and libaed version 1.3.1 built with gfortran 8.3.0. The mac is running the downloaded package from the AED website, and provides glm built with gcc 4.2.1 and libaed2 version 1.3.0 built with gfortran 8.3.0.
I have also re-built GLM from source using AED_tools on Ubuntu, which bumped it to 3.0.2, but didn’t affect the issue.

Here's some more detail about what runs and what doesn't (I've been primarily testing with Kinneret, but I'm getting the same issues with my lake as well):

Runs
Tracer and noncohesive
Oxygen alone (sometimes have to try a few times if it failed previously)
Oxygen, carbon, silica
Oxygen, carbon, silica, nitrogen (Mac and cluster ONLY, and sometimes have to try a few times, never runs on Ubuntu in WSL)
Fails
Tracer, noncohesive, and oxygen
Tracer and oxygen
Noncohesive and oxygen
Oxygen, carbon, silica, nitrogen (always fails on Ubuntu in WSL, sometimes on Mac and Unix cluster)
Adding phosphorus to O, C, S, and N breaks, but not with a seg fault, (it needs noncohesive)
Flipping tracer or noncohesive to after o2 fails, but not with a seg fault (they need to be first)

My fortran is far too weak to start figuring out where the modules are stomping on each other, but hopefully the above lists of combinations help narrow it down. There was a suggestion on AEMON to compile with Intel, so I'll work on giving that a shot.

Hi,

If simCH4ebb is true (or undefined) in the config file, I get a segfault in my Simstrat-AED2 model. I found out that it is related to the following warning during compilation of AED2:

src/aed2_carbon.F90:715:0:

   _DIAG_VAR_S_(data%id_atm_ch4_ebb) = ebb_flux * (1-data%ch4_bub_disf1) * secs_per_day

Warning: 'ebb_flux' may be used uninitialized in this function [-Wmaybe-uninitialized]

Hi everyone,

I have concerns about the transfer of organic matter within the lake I want to model. I added in my inflow non-zero values of OGM_doc, OGM_don and OGM_dop but when I plot the evolution of nitrates, phosphates or chlorophyll the chronicles are identical, with or without inflow. The only parameter that changes (and this is logical) is the three components of the DOM. However in the equations of NO3 or PO4 the DOM appears so I don't understand why the transformation is not done.

Thanks for your help,

Alexis

methane oxidation
nitrification
Fe oxidation
Sulfide oxidation

In my aed2.nml file I have
simDryDeposition = .TRUE.
atm_pip_dd = 0.004
simWetDeposition = .TRUE.
atm_frp_conc = 1.8
but in the resulting .nc file the value of PHS_atm_dip_flux is all zeros. If I change the 0.004 and 1.8 to 0.0 and 0.0 the results change, suggesting that atmospheric deposition is being accounted for, but the diagnostic variable is not being reported.
I also find that OGM_sed_dop is all zeros, though OGM_sed_pop is not. Is it possible there is a bug in the calculation of these?

Currently running GLM 3.0.0 with AED2 1.3.0 and tested this on a Mac and a Windows machine. It seems that the settling configuration in the aed2_mobility subroutines is not functioning as intended. Changing the settling configuration won't affect the model outcome, as it seems that GLM is always using the DEFAULT CASE with vvel = data%w_pom and vvel_cpom = data%w_cpom (instead of for instance Stoke's Law).

My guess is that the keywords from aed2.h aren't read in properly, as AED2 doesn't recognize the settling/migration keyword.

There is a bug in the carbon module on line 278:
data%id_depth= aed2_locate_global('layer_ht')

It should be 'depth' instead of 'layer_ht'!

The current version assigns the layer height to the depth array (instead of depth).

Kinneret upper sed zone starts at 20m, and WQ NaNs if lake starts below this

Need to pass velocity as env variable to allow velocity to be used in gas exchange for N2O and CH4