Variable Mapping update - Future scenarios data Thomas Kleinen MPI-ESM

assigned to @k204212

changed the description

mentioned in merge request !1 (merged)

@m300020 Please have a look at the suggested changes: Link You can give review comments or answer here in this issue, as you prefer.

I was looking for suitable CF standard_names in https://cfconventions.org/Data/cf-standard-names/current/build/cf-standard-name-table.html but in some cases I had to come up with something. Since most of these variables did not exist in CMIP6 I also "invented" the shortnames. Feel free to suggest alternatives. Please have a close look at the units, cell_methods and dimensions if they are properly defined (eg. "mean where land", or just "mean" for the cell_methods).

In general, for which of these variables it is a "net flux" rather than just a "flux"?

termiteCH4 - methane emissions from termites: The standard_name surface_net_upward_mass_flux_of_methane_due_to_emission_from_termites does not exist so far. One could select something more general like surface_upward_mass_flux_of_methane_due_to_emission_from_biological_production which exists as surface_upward_mass_flux_of_methane_due_to_emission_from_wetland_biological_production.
herbivoreCH4 - Methane emissions from Herbivores: same comment as above
fVegFireCH4 - Methane emissions from Fires (forest plus vegetation): Found standard_name biomass_burning_carbon_flux and adapted this. The out_name is taken from fVegFire, being the same variable for CO2. This CMIP6 variable has the standard_name surface_upward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_emission_from_vegetation_in_fires. Idk if we should rather adapt that one?
wetlandCH4 - Methane emissions from Wetlands: used the CMIP6 variable wetlandCH4, I altered however the comment and replaced "NH4" by "CH4" which was probably a typo?!
wetlandFrac - Wetland area percentage: used CMIP6 variable wetlandFrac
fSoilCH4 - Methane uptake by soil: There was no comment in the excel sheet, should we add more information in the comment attribute? I set a yet non-existent standard_name surface_net_upward_mass_flux_of_methane_due_to_soil_uptake.
emich4 - Methane emissions: no specific comment
lightning nox: Not to be submitted? Or am I mistaken?
ch4brdn - Atmospheric Methane burden: "atmospheric burden" seems to be usually reported in moles or kg. But we can leave it as defined in the excel sheet.
ch4 - Mass fraction of CH4 in air: no specific comment
Mass fraction of decayed CH4 in air: Not to be submitted
lossch4 - Atmospheric Methane decay rate: Adapted standard_name as tendency_of_atmosphere_mass_content_of_methane_due_to_chemical_destruction. standard_name exists with "mole_content" rather than "mass_content". It does not have a vertical axis (just time,lat,lon)?

Hi Martin,

1+2) termiteCH4 -- I guess "surface_upward_mass_flux_of_methane_due_to_emission_from_termites" it is (without "net"), as this needs to be relatively specific. The same goes for the herbivoreCH4. 3) fVegFireCH4 -- I am sorry, what exactly is your question? I think we should base it on the "surface_upward_mass_flux_of_carbon_dioxide_expressed_as_carbon_due_to_emission_from_fires", so that would make it "surface_upward_mass_flux_of_methane_due_to_emission_from_fires" (without the "expressed as carbon"). Frankly I am unsure about the exact meaning of "biomass burning", as sometimes this seems to mean only human-made fires, but sometimes it seems to mean all fires, i.e. natural AND human-made. We avoid this issue by simply using "fires". 4+5) perfect! And yes, I am sure NH4 was a typo. 6) Comment could be: "Removal of CH4 by oxidation in dry soils." 7) emich4 -- do we need a specific comment? I am also wondering about "realm aerosol", I would have assumed it to be "atmos" or "atmosChem". The same goes for "lossCH4". 8) I think we should have on lightning NOx variable. What we don't need is the atmospheric NOx content. 9) Yes, the burden is mostly reported as mass -- but the it's usually for the entire atmosphere, not spatially explicit. For the spatial field, it makes more sense to report it per unit area, I think. 12) We have the lossch4 also on atmospheric levels, so we COULD also provide a vertical dimension. I don't think it would add much information, though.

Hi @m300020 please have another look at the changes: LINK

I adjusted the standard_names according to your suggestions. We also added the lightning NOx variable (8). Concerning variable (7) emich4, you can decide whether you want to add a more specific comment than the current one "Methane emitted from the surface, prescribed emissions from e.g. geological and anthropogenic sources. Positive flux direction upwards.".

Hallo Martin,

das sieht so weit alles sehr gut aus.

Für emich4, sollte es eher so aussehen: "Prescribed methane emissions from the surface, from e.g. geological and anthropogenic sources. Positive flux direction upwards."

Das ist inhaltlich gleich, aber da prescribed emission vorne steht, wird schneller klar, was es sein soll.

Gruß, Thomas

assigned to @m300020 and unassigned @k204212

To be confirmed by @m300020 in process of submitting new standard names for CMOR

1. Methane Emissions from Termites

Term surface_upward_mass_flux_of_methane_due_to_emission_from_termites

Description Methane emitted from the surface, generated by termites. Positive direction upwards.

Units Kg m-2 s-1

CMOR name termiteCH4

2. Methane Emissions from Herbivores

Term surface_upward_mass_flux_of_methane_due_to_emission_from_herbivores

Description Methane emitted from the surface, generated by herbivorous mammals. Positive direction upwards.

Units Kg m-2 s-1

CMOR name herbivoreCH4

3. Methane Emissions from fires

Term surface_upward_mass_flux_of_methane_due_to_emission_from_fires

Description Methane emitted from the surface, generated by biomass burning (fires). Positive direction upwards.

Units Kg m-2 s-1

CMOR name firesCH4

4. Methane Uptake by the soil

Term surface_upward_flux_of_methane_due_to_soil_uptake

Description Removal of CH4 by oxidation in dry soils. Upward flux of methane (CH4) from soil uptake. Positive direction upwards.

Units Kg m-2 s-1

CMOR name fsoilCH4

5. atmospheric Methane decay rate Using the already existing below description

Term tendency_of_mole_concentration_of_methane_due_to_chemical_gross_destruction

Description mass of CH4 destroyed in the atmosphere by chemical reaction with OH

Units Kg m-2 s-1

CMOR name lossCH4

Looks really good so far -- I don't see anything wrong at the moment. :-)

Proposal submitted at CF discussion forum: (https://github.com/cf-convention/discuss/issues/162)

The below proposed variables are a part of MPI-ESM model development within the German paleo-climate initiative, Project PalMod (www.palmod.de)

Proposer's name Swati Gehlot, DKRZ, Hamburg Date 2022-07-05

Methane Emissions from Termites Term surface_upward_mass_flux_of_methane_due_to_emission_from_termites

Description The surface called "surface" means the lower boundary of the atmosphere. "Upward" indicates a vector component which is positive when directed upward (negative downward). In accordance with common usage in geophysical disciplines, "flux" implies per unit area, called "flux density" in physics. The chemical formula for methane is CH4. The mass is the total mass of the molecules. The specification of a physical process by the phrase "due_to_" process means that the quantity named is a single term in a sum of terms which together compose the general quantity named by omitting the phrase. "Emission" means emission from a primary source located anywhere within the atmosphere, including at the lower boundary (i.e. the surface of the earth). "Emission" is a process entirely distinct from "re-emission" which is used in some standard names. Termites belong to any of a group of cellulose-eating insects, the social system of which shows remarkable parallels with those of ants and bees, although it has evolved independently. The precise conditions under which termites produce and consume methane can vary between models.

Units kg m-2 s-1 CMOR name termiteCH4 Related standard names: surface_upward_mass_flux_of_methane_due_to_emission_from_wetland_biological_production

Methane Emissions from Herbivore Mammals Term surface_upward_mass_flux_of_methane_due_to_emission_from_herbivore_mammals

Description The surface called "surface" means the lower boundary of the atmosphere. "Upward" indicates a vector component which is positive when directed upward (negative downward). In accordance with common usage in geophysical disciplines, "flux" implies per unit area, called "flux density" in physics. The chemical formula for methane is CH4. The mass is the total mass of the molecules. The specification of a physical process by the phrase "due_to_" process means that the quantity named is a single term in a sum of terms which together compose the general quantity named by omitting the phrase. "Emission" means emission from a primary source located anywhere within the atmosphere, including at the lower boundary (i.e. the surface of the earth). "Emission" is a process entirely distinct from "re-emission" which is used in some standard names. Herbivores are animals that feed on vegetation. Mammals are any vertebrates within the class Mammalia. Examples of large herbivore mammals include cows, elks, and buffalos. These animals eat grass, tree bark, aquatic vegetation, and shrubby growth. Herbivores can also be medium-sized animals such as sheep and goats, which eat shrubby vegetation and grasses. Small herbivores include rabbits, chipmunks, squirrels, and mice. The precise conditions under which herbivore mammals produce and consume methane can vary between models.

Units kg m-2 s-1 CMOR name herbivoreCH4 Related standard names: surface_upward_mass_flux_of_methane_due_to_emission_from_wetland_biological_production

Methane Emissions from Fires Term surface_upward_mass_flux_of_methane_due_to_emission_from_fires

Description Methane emitted from the surface, generated by biomass burning (fires). Positive direction upwards. The surface called "surface" means the lower boundary of the atmosphere. "Upward" indicates a vector component which is positive when directed upward (negative downward). In accordance with common usage in geophysical disciplines, "flux" implies per unit area, called "flux density" in physics. The chemical formula for methane is CH4. The mass is the total mass of the molecules. The specification of a physical process by the phrase "due_to_" process means that the quantity named is a single term in a sum of terms which together compose the general quantity named by omitting the phrase. "Emission" means emission from a primary source located anywhere within the atmosphere, including at the lower boundary (i.e. the surface of the earth). "Emission" is a process entirely distinct from "re-emission" which is used in some standard names. The term "fires" means all biomass fires, whether naturally occurring or ignited by humans. The precise conditions under which fires produce and consume methane can vary between models.

Units kg m-2 s-1 CMOR name firesCH4 Related standard names: surface_upward_mass_flux_of_nitrogen_compounds_expressed_as_nitrogen_due_to_emission_from_fires

Methane Uptake by Non-Wetland Soils Term surface_downward_mass_flux_of_methane_due_to_non_wetland_soil_biological_consumption

Description The surface called "surface" means the lower boundary of the atmosphere. "Downward" indicates a vector component which is positive when directed downward (negative upward). In accordance with common usage in geophysical disciplines, "flux" implies per unit area, called "flux density" in physics. The chemical formula for methane is CH4. The mass is the total mass of the molecules. The specification of a physical process by the phrase "due_to_" process means that the quantity named is a single term in a sum of terms which together compose the general quantity named by omitting the phrase. Non-wetland soils are all soils except for wetlands. Wetlands are areas where water covers the soil, or is present either at or near the surface of the soil all year or for varying periods of time during the year, including during the growing season. The precise conditions under which non-wetland soils produce and consume methane can vary between models.

Units kg m-2 s-1 CMOR name fsoilCH4 Related standard names: surface_downward_mass_flux_of_methane_due_to_wetland_biological_consumption

Update variable mapping for methane variables. @m300020 please have a look and provide your feedback on the same.

surface_upward_mass_flux_of_methane_due_to_emission_from_termites - do we need a vertsum expression for averaging over 11 tiles here? The excel sheet states that it is sum of all tiles however, the GRIB codes list 11 tiles for this variable (code 154). @m300020 can you please confirm?
surface_upward_mass_flux_of_methane_due_to_emission_from_herbivore_mammals - the code does not exist in jsbach_methane_codes (/work/bk1192/from_Mistral/bk1192/WG2/WP2.3/future_scenarios_2021/GRIB_codes/pmt0550_20RN_SSP585_r2_jsbach_methane.codes)
surface_upward_mass_flux_of_methane_due_to_emission_from_fires - please confirm that the variable code is 151 (not to be confused with code 24 ECHAM6)
surface_net_upward_mass_flux_of_methane_due_to_emission_from_wetland_biological_processes - the code does not exist in jsbach_methane_codes (/work/bk1192/from_Mistral/bk1192/WG2/WP2.3/future_scenarios_2021/GRIB_codes/pmt0550_20RN_SSP585_r2_jsbach_methane.codes)
methane (CH4) decay rate in the atmosphere - please confirm which code does the variable represents out of the below:

code 41 31 ch4_dec_mass 0.00 1.00 decayed CH4 mass (avg) [kg(CH4) m-2 s-1]

or

code 45 1 ch4_dec_mass_tot_acc 0.00 1.00 decayed CH4 mass total (avg) [kg(CH4) m-2 s-1]

Termites: Yes, this needs a vertsum. While we do have tile-level output, it doesn't make sense to distribute it, as the total is much more meaningful.
Herbivores: This output doesn't exist in this particular experiment, but other experiments (deglaciation) have it.
Fires: Yes, this is code 151 in the jsbach methane file.
Wetlands: this is code # 125, needs a vertsum, too.
Decay rate: Sorry, this is more complicated, it's not directly contained in the output. It's in the echam6_ch4 file, code 8 divided by code 45.

Please be advised that the methane fluxes will likely need a sign flip (multiply with -1), as they are defined positive downwards in the jsbach_methane file.

Dear Thomas (@m300020),

for testing purposes I CMORized 100 years of your transient-deglaciation...-methane simulation (pmt0531a 6000-6099, corresponding to years 2000-2099 on the absolute time axis, running from 1-23900, leaving out the first 1000 years as spinup). I activated only a few variables for the first test, amongst them are your CH4 variables. You can find the output here: /work/bk1192/k204212/palmod_TK/transient-deglaciation-prescribed-glac1d-methane_r1i1p1f1-CR/archive/PalMod2 Please have a look and report if your variables look as expected.

I would have a few more questions regarding your simulations:

regarding Herbivores: that would be box_CH4_out_herbivore_acc in the jsbach_methane stream? However also in /work/bk1192/from_Mistral/bk1192/WG2/WP2.3/transient_deglaciation_2020 this variable does not exist.
the jsbach initial files (containing glac, slm, cover type etc) for your simulations cannot be found under /work/mh0110/m211003/mpiesm-1.2.00p1/experiments/ as it is the case for Maries simulations. Can you point me to the correct location please?
I would need the branch dates for all the SSP* simulations, I assume they all branched from pmt0531d?

Do you want to set different references as attribute in the CMORized files than Marie?

REFERENCES="Kapsch, M.-L., Mikolajewicz, U., Ziemen, F., & Schannwell, C. (2022). Ocean response in transient simulations of the last deglaciation dominated by underlying ice-sheet reconstruction and method of meltwater distribution. Geophysical Research Letters, 49, e2021GL096767. https://doi.org/10.1029/2021GL096767\nMPI-ESM: Mauritsen, T. et al. (2019), Developments in the MPI‐M Earth System Model version 1.2 (MPI‐ESM1.2) and Its Response to Increasing CO2, J. Adv. Model. Earth Syst.,11, 998-1038, doi:10.1029/2018MS001400,\nMueller, W.A. et al. (2018): A high‐resolution version of the Max Planck Institute Earth System Model MPI‐ESM1.2‐HR. J. Adv. Model. EarthSyst.,10,1383–1413, doi:10.1029/2017MS001217"

Which physics_version should we use with respect to Maries model version? She used 3 different model versions:

VARIANT_INFO="Predecessor model version to p2. p2 contains a range of bug fixes and an updated model tuning: 
it comprises the introduction of a brine plume parameterization in MPI-OM and a modification of sea-ice lead closure parameters, 
improvement of the automated topography generation scripts (e.g. baroclinic exchange in shallow fjords), and a replacement 
of the direct use of topographic roughness in ECHAM6 by a parameterized treatment like the one in the standard ECHAM6 model. 
Tuning parameters are taken from Mauritsen and Roeckner (2020) and comprise the surface value of the critical humidity profile 
for cloud formation (crs), the threshold between cloud water and ice (csecfrl) and the fall speed of cloud ice (cvtfall). 
Additionally, a mean volcanic aerosol forcing was taken into account. For details see Supporting Information of Kapsch et al., 2022."

VARIANT_INFO="Equivalent to p2 but with a different model tuning. 
For details see Supporting Information of Kapsch et al., 2022."

If you used a different version in terms of tuning etc. we would have to set a new physics version as well (p4 then)

Along with above question, we can define a VARIANT_INFO attribute, holding information about what would be special about this specific simulation with respect to other realisations. Since you have only one realisation for each of your experiments, we should explain the differences to Maries physics version, if there are.

Kind regards, Martin

Hi Martin,

apologies -- I was on holiday and didn't get around to replying before.

I'm sorry, but I don't quite understand the time axis you are using for the processed files. I assume CMOR can't do a "real" time axis -- my personal files have time running from negative 23000 to zero, but I do know that some netcdf tools don't like negative years.

Initial files are here: /work/bm1030/from_Mistral/bm1030/m300020/mpiesm-palmod_tk_r10081/experiments/pmt0531_XX/restart/topo
SSP simulations did branch from pmt0531_d, year 5600 (= 1550 CE), but only years after 1850 CE are actually provided, the 300 years in between are just about identical to pmt0531_d
REFERENCES="Kleinen, T., Mikolajewicz, U. and Brovkin, V. (2020). Terrestrial methane emissions from the Last Glacial Maximum to the preindustrial period. Climate of the Past, 16(2):575–595. doi: 10.5194/cp-16-575-2020.\nKleinen, T., Gromov, S., Steil, B. and Brovkin, V. (2021). Atmospheric methane underestimated in future climate projections. Environmental Research Letters, 16(9):094006. doi: 10.1088/1748-9326/ac1814.\nKapsch, M.-L., Mikolajewicz, U., Ziemen, F., & Schannwell, C. (2022). Ocean response in transient simulations of the last deglaciation dominated by underlying ice-sheet reconstruction and method of meltwater distribution. Geophysical Research Letters, 49, e2021GL096767. https://doi.org/10.1029/2021GL096767\nMPI-ESM: Mauritsen, T. et al. (2019), Developments in the MPI‐M Earth System Model version 1.2 (MPI‐ESM1.2) and Its Response to Increasing CO2, J. Adv. Model. Earth Syst.,11, 998-1038, doi:10.1029/2018MS001400,\nMueller, W.A. et al. (2018): A high‐resolution version of the Max Planck Institute Earth System Model MPI‐ESM1.2‐HR. J. Adv. Model. EarthSyst.,10,1383–1413, doi:10.1029/2017MS001217"
physics_version should be identical with Maries warmest experiment -- in the Paper that's Variant 1. Model code is -- with the exception of the methane bits -- identical to that one.
VARIANT_INFO might contain something like "with full methane cycle"?
With regard to the Herbivores: That isn't (yet) in the experiment you have, but we have re-run the methane parts of the deglaciation experiment, which then includes methane. I'll have that output ready for you next week, you can then simply exchange the echam6_ch4 and the jsbach_methane files.
The output looks very good, though there is one exception: emilnox. Emilnox is in the original data with units kg/s, i.e. kg per grid-cell, but in the processed output it's kg/m2/s. The latter makes more sense, but it requires division by grid-cell area for the original data file.

Thanks! Thomas

@m300020 where are the initial files located for the SSP simulations? They cannot be found under /work/bm1030/from_Mistral/bm1030/m300020/mpiesm-palmod_tk_r10081/experiments/.

@k204212 Initial files can be found here: /work/bm1030/from_Mistral/bm1030/m300020/mpiesm-palmod_tk_r10186_megan_next/experiments/<experiment_id>/restart/topo

with experiment_id one of: pmt0550_20RN_SSP119_r2, pmt0550_20RN_SSP126_r2, pmt0550_20RN_SSP245_r2, pmt0550_20RN_SSP370_r2 or pmt0550_20RN_SSP585_r2

Best, Thomas

@m300020 I produced again test-output for the CH4-Variables at /work/bk1192/k204212/palmod_TK/transient-deglaciation-prescribed-glac1d-methane_r1i1p1f1-CR/archive/cmor_2001-2100 - this time all should be available

I have one question regarding the herbivoreCH4: It is provided on 11 tiles in units mol(CH4) m-2 (gridarea) s-1. So my approach was to use the following recipe (integrate over the tiles and multiply with molar mass to get kg m-2 s-1): vertsum(var172)*16.04*1e-3 of *_jsbach_methane_mm_* code 172 / name box_CH4_out_herbivore_acc - Is that correct?

Please also have a look at the global attributes if they are correct (references, variant_info, source_id, source, ...). In the other thread, Bo suggested to use MPI-ESM1-2-CR-CH4 as source_id instead of MPI-ESM1-2-CR-CHEM. Do you want to follow her suggestion or leave it at -CHEM? I don't mind either option.

If you are happy with the global attributes and your CH4 variables, I would try to produce test-data for all possible variables (i.e. your CH4 variables and all variables yet produced for Marie), and then you could simply tell me which variables you find are yet missing, and which of the produced variables can be omitted in the full standardisation. (Alternatively you can provide me with a full list of the variables you want to publish).

Hi Martin,

thanks a bunch for processing this -- I'm really glad to see it. It is mostly correct, too. :-) The herbivore CH4 is nearly right, it is just missing a sign flip -- it now shows negative values for emissions to the atmosphere, those should be positive, so a multiplication with -1 is necessary. However, lossCH4 looks funny. I fear I screwed up there -- I gave you the formula to determine the lifetime of methane there, not the destruction rate, here: #2 (comment 108439)

So I apologize, for the destruction rate (lossch4) it's code 45.

MPI-ESM1-2-CR-CH4 is great, I like it better than CHEM.

With regard to the global attributes, however, I am wondering whether something got mixed up in the conversion. These look like Marie's attributes, especially the source id of MPI-ESM1-2-CR. Or did I overlook something?

@m300020 I produced now all possible variables for a 100yr period for the transient simulation as I did for SSP119. Additionally to the variables that have been produced for SSP119, the herbivoreCH4 variable could get produced: /work/bk1192/k204212/palmod_TK/transient-deglaciation-prescribed-glac1d-methane_r1i1p1f1-CR/archive/cmor_1-100

I fixed the sign-flip for herbivoreCH4 and the formula for lossCH4. I am sorry I mixed up the configuration for the global attributes with Maries in the previous processing, but that is fixed now as well. As for the SSP119 simulation, the references attribute will have to be replaced manually with NCOs because of a CMOR limitation of only supporting strings up to 1024 characters length.

Hi,

I looked at the output. Looks very good. The only thing I noticed in the metadata was the experiment name: ":experiment = "transient deglaciation with GLAC-1D ice sheets, methane preliminary" ;" I think we can remove the "methane preliminary" from that. Output values also seem quite all right. So from my point of view the only issue remaining are the missing C-cycle variables...

@m300020 removing the methane preliminary would make the experiment title the same as for Maries experiment without the methane cycle. If methane preliminary is not correct, maybe you can rephrase the experiment title in some way so that it is clear how it differs from Maries transient simulation with glac1d ice sheets.

@k204212 I see, that makes a lot of sense. What I don't like is the "preliminary", so maybe we can substitute "with methane cycle" for "methane preliminary"? What do you think?

Ok, I will alter the experiment title in this way.

Variable Mapping update - Future scenarios data Thomas Kleinen MPI-ESM

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