ESM2025-N-cycle

This page is dedicated to the ESM2025 project (Earth System Models - European Project), especially for the N-cycle modelling. On this topic are working Marion Gehlen, Juliette Lathière, Didier Hauglustaine, Nicolas Vuichard and Karine Laurent.

Working Documents

• Notebooks :
  • (22/04/20) 2 different notebooks are useful : Data_viewer and Analyse_3_sflx_NAT_dyn
    1. Data_viewer: To easily see a dataset. Interactive mode in order to change different variable at different time.
    2. Analyse_3_sflx_NAT_dyn: The 3 datasets (transcom, bouwman, piscidee=Pisces+orchidee) are loaded. Difference are computed (with Bouwman as a reference). Plots are made per month with same scale. Then, a seasonal analysis is done, calculating means/min/max of each dataset per month/year/season.
  • (22/05/23) compare three inventories by total emissions and repatition.
    3. Budget_inventories: Using the output of Incasflx with the three inventories, different sums/computations/plots given percentages and charts per land and ocean, plots per latitude bands, per hemisphere of these emissions...
  • (22/06/15) notebooks to construct charts from CEDS emissions --supplementary data mainly--
    4. CEDS_charts_supllementary_data_N2O and Charts_N2O_CEDS : Notebooks to reconstruct charts in the article of McDuffie? 'A global anthropogenic emission inventory of atmospheric pollutants' (same notebooks exist with NH3 charts). It uses the emissions of N2O distributed per category (Agriculture, Energy, Industrial, Transportation, Residential, Commercial, Other, Solvents production and application, Waste, International Shipping)
  • (22/08/04) 2 notebooks created: in relation with CEDS emissions.
    5. work_on_data_to_complete_sectors_with_unknows_categories : Notebook in order to better understand repartition of subcategories that are not in CEDS emissions files and grouped in sectors.
    6. Transform_2000nc_from1970_to1999_via_CEDScsv : To reconstruct geographical emissions from 1970 to 1999 from 2000's emissions and with a ratio computed thanks to csv's data. Need to use obelix' script home/users/klaurent/CEDS_transform/nco_transform_1970_1999_ncfiles.sh after this notebook (delete _FillValue mainly).

• Emissions files :
  1. Bouwman : 360x180, created in 1999, Flux of agr waste burning, biofuel, biomass burning, deforestation, excreta, fossil fuel, industry, ocean, aquatic, soil
  2. Transcom : 360x180, created in 2015, total flux of N₂O from OCN, PISCES and EDGAR, ACTUAL PERIOD
  3. Pisces (N2Oflx_OClim_CNRM-ESM2-1_piControl_r1i1p1f2_gn_185001-234912.nc), 362x294 (irregular grid), created in 2018, total flux of N2O for ocean
  4. Orchidee (ORCHIDEE_SH1_fN2O.nc), 720x360, created in 2022, total flux of N2O for land surfaces
  5. CEDS emissions from McDuffie/Hoesly?

• Bouwman Inventory :
  1. 846 N₂O emission measurements in agricultural fields and 99 measurements for NO emissions
  2. The data set includes literature reference; location of the Measurement; climate; soil type, texture, organic C content, N content, drainage, and pH; residues left in the field; crop; fertilizer type; N application rate; method and timing of fertilizer application; NH₄+ application rate (for organic fertilizers), N₂O/NO emission/denitrification (expressed as total over the measurement period, as % of N rate, and as % of N rate accounting for control); measurement technique; length of measurement period; frequency of the measurements; and additional information, such as year/season of measurement, information on soil, crop or fertilizer management, specific characteristics of the fertilizer used, and specific weather events important for explaining the measured emissions.
  3. global gridded (1°x1° resolution) data bases of soil type, soil texture, NDVI (vegetation indices) and climate.
  4. global emission thus calculated is 6.8 Tg N₂O-N y-1. The tropics (± 30° of the equator) contribute 5.4 Tg N₂O-N y-1 and the emission from extra-tropical regions (poleward of 30°) is 1.4 Tg N₂O-N y-1 .

• Transcom Inventory :
  1. "Emissions from natural soils (6–7 TgN yr −1 ) account for 60–70 % of global N2O emissions (Syakila and Kroeze, 2011; Zaehle et al., 2011). The remaining 30–40 % of emissions is from oceans (4.5 TgN yr −1 )"
  2. Five different inversion frameworks (chemistry transport model) : MOZART4 (2.5° × 1.88°), ACMt42167 (2.8° × 2.8°), TM3 (5.0° × 3.75°), TM5 (6.0° × 4.0°), LMDZ4 (3.75° × 2.5°).
  3. Data set from Orchidee O-CN, Pisces, edgar-4.1, gfed-2 and from different category (terrestrial biosphere, ocean, waste water, solid waste, solvents, fuel prod, ground transport, industry combustion, residential and other combustion, shipping, biomass burning)

• Values of N₂O emissions per inventory :

(MtN/yr)	Ocean	Land	Total	(MtN2O/yr)	Ocean	Land	Total
Bouwman	3.595	7.531	11.126	xxx	5.650	11.835	17.485
Transcom	4.222	10.573	14.795	xxx	6.634	16.614	23.248
Piscidee	3.962	7.107	11.069	xxx	6.226	11.168	17.394

• Comparison between Incasflx outputs and masks on NetCDF files:

	- Output INCASFLX -			- Notebook computing (FracMask?) -			- Notebook computing (0/1 Mask) -
(MtN2O/yr)	Ocean	Land	Ratio O/L	Ocean	Land	Ratio O/L	Ocean	Land	Ratio O/L
Bouwman	5.6505	11.835	0.478	6.58	10.945	0.6012	5.973	11.552	0.517
	32.3%	67.7%		37.6%	62.4%		34.1%	65.9%
Transcom	6.634	16.614	0.399	8.879	14.421	0.616	8.118	15.184	0.535
	28.5%	71.5%		38.1%	61.9%		34.8%	65.2%
Piscidee	6.226	11.168	0.557	6.651	10.782	0.617	6.095	11.339	0.538
	35.8%	64.2%		38.2%	61.8%		34.9%	65.1%

General remarks: Variable for Bouwman = fn2o_oce & fn2o_soil. Land emissions > Ocean emissions. Ocean emissions ~ 6 Mt/yr. Land emissions -> differences because of different period (pre-industrial & nowadays). Per line, Ocean+Land are equal independently of the calculation made.

• CEDS emissions for N₂O (and NH₃):

Meeting Reports

On Wednesday, 24th August

In person with Didier and Nicolas. PDF support [see attached file].

Resume of august simulations and work.

• Transformation of CEDS emissions: from 1970 to 1999, use of netCDF file 2000 with a factor per sector to create netcdf emissions. Notebooks Transform_2000nc_from1970_to1999_via_CEDScsv.ipynb and work_on_data_to_complete_sectors_with_unknows_categories.ipynb
• 2 simulations: L39.v03 as a base (pre-industrial, constrained to 285ppm), then pi_piscideeL (free, pre industrial, 40 years).

Results seem good regarding vertical pressure profile, total loss N₂O, pattern of emissions. Need to investigate more and continue.

TO DO

• Make graph of pressure for those two simulations,
• Continue piscideeL 5 years and compute mean of loss,
• Resume differences between former simulations,
• Re-create netCDF files with only manure_management (and not soil_emissions) for agricultural sector.

On Tuesday, 12th July

In person with Didier.

Discussion of simulations and set-up to make.

Check N₂O loss in 1999 for v03 simulation (to be continued) and create pi_piscideeL run from it to turn 40 years (1980-2020, L means libre/free/not rescaled at 285 ppm).

Explanation of how to create ncfiles from 1970 to 1999 from 2000's geographical repartition and ratio computed with total emissions per sector (csv file). Once done, adapt ciclad's code to transform them on Incasflx 144x142 grid.

On Monday, 11th July

In person with Didier, Nicolas and Juliette.

Conversation on Workshop N₂O source in Toulouse (6-8 July) : very interesting to see different communities (observation, inversion, modellers)

First result with a decreasing total emission (from 285 ppm to 280 ppm in 20 years) : seems to be promising.

Reflection on what is needed in order to move to coupled system. Remembrance of deadlines and expectations for ESM2025 project. Land emission per year ok, Nicolas will ask to Sarah or Laurent to have same emission for ocean. After that, work with Thibault Lurton and/or Anne Cozic to adapt code.

How to reconstruct anthropologic N₂O emission between 1850 and 1970 ? Try to find some proxy (population or chemical species that exists during this period)

TO DO

• Reconstruct N₂O emission with CEDS inventory with rescaling year by year (height with total budget and spatial with year 2000)
• When all is fixed, simulation from 1970 to 2015 in order to see if the model is coherent or not (with a rescaling at ~300ppm : CMIP6).
• Find information on Japanese model (the one of Prabir Patra)
• Get more information on Pisces simulation (does it use flag or many change in order to have it? Is it possible to have emissions per year from pre-industrial to present time?)

Next

• Computation of loss rate
• Coupled model (with Anne and Thibaut)

On Wednesday, 29th June

In person with Didier and Juliette + in visio with Marion.

Explanation of the remapping problem with pisces' file. The common CDO functions doesn't work (not conservative + white columns or column with outliers).

Solution : See Germain if he has some same files (grid 294x362 and not 292x292) + in correspondence with O. Marti for a better interpolation. work in progress

TO DO

• Understand and find a solution to the remapping problem.
• Send an e-mail to Sarah Berthet, in charge of different projects on N₂O : could be seen during the N₂O workshop in Toulouse (from 6th to 8th July).
• Simulations in 39 layers with invariants outputs in two different configurations.
• On profile picture, try to invert axis + use logarithm scale.
• Check availabilities for next meetings.

+ Meeting with Ddiier

• See different scripts to compute the N₂O-loss and N₂O-burden.
• Show what and how to change Incasflx files in order to use a irregular grid as input (avoiding the remapping problem).

On Wednesday, 15th June

In person with Nicolas and Didier.

Waiting for the first result with the 39-layers configuration.

After the General Assembly of ESM2025, pisces emissions seems to be too high... In fact, there was a problem of units conversion (mostly because of a misunderstanding of input units (mol N rather than mol N₂O).

Nicolas asked if lightning is implemented because it seems to have an total emission between 0.5 and 2 Tg/Nyr?.

Some works will be presented during the N₂O workshop in Toulouse from July, 6th to 8th.

To DO

• Analyse the vertical profile when the 39-layers configuration of one year is done.
• + See Didier for the next steps.
• Re-compute the calculation with the good value of pisces emissions.

On Wednesday, 1st June

In person with Nicolas, Juliette, Didier. Special guest : Anne.

Special demands to Anne :

• Passage from 79 layers to 39 : is it easy and feasible ? Seems to change some configuration's files (oxidants for example).
• svn for INCA ok, if need to change orchidee's sources, ask to Nicolas (but no need for this moment).
• Make some time series for long run test (feasible with the training course),
• Add output variables that would be computing into the code (have to see Anne when it will be time).

Show results on Bouwman (with aqua and soil flux): slight difference again. Using mask 0/1 (and not fractional one) is better.

Show on-going result of CEDS inventory (from McDuffie?): problem with units, needs to calculate annual mean to correspond to article's images.

To DO

• Finish charts of CEDS inventory. Notebooks used: CEDS_charts_supplementary_data_N2O.ipynb and Charts_N2O_CEDS.ipynb.
• Schedule a meeting with Didier when 39 layers' configuration is ready.
• Make simulation with oce and soil flux for Bouwman (not with aqua !!).

On Wednesday, 18th May

In person with Juliette, Didier, Nicolas.

• Notebook Budget_inventories : total budget of N₂O emissions (in tables), differences found between outputs INCASFLX and calculations in notebook (with mask, area and change units), different charts (by latitude, by land/ocean part, with histograms...)

Using the mask with fraction:

FracMask?	- Output INCASFLX -			- Notebook computing -
(Mt/yr)	Ocean	Land	Ratio O/L	Ocean	Land	Ratio O/L
Bouwman	5.650486	11.83547	0.478	13.967	16.726	0.835
	32.3%	67.7%		45.5%	54.5%
Transcom	6.634	16.614	0.399	8.879	14.421	0.616
	28.5%	71.5%		38.1%	61.9%
Piscidee	6.432	7.107	0.905	6.579	6.989	0.941
	47.5%	52.5%		48.5%	51.5%

Using the mask with 0/1 values:

0/1 Mask	- Output INCASFLX -			- Notebook computing -
(Mt/yr)	Ocean	Land	Ratio O/L	Ocean	Land	Ratio O/L
Bouwman	5.650486	11.83547	0.478	12.797	17.899	0.714
	32.3%	67.7%		41.7%	58.3%
Transcom	6.634	16.614	0.399	8.118	15.184	0.535
	28.5%	71.5%		34.8%	65.2%
Piscidee	6.432	7.107	0.905	6.174	7.395	0.834
	47.5%	52.5%		45.5%	54.5%

Those differences can be explained by the different power that may exist between marine or continental fluxes at coasts notably. With mask, these two fluxes have the same importance so it changes total flux.

Values per latitudes:

(Tg/yr)	90-30S	30S-0	0-30N	30-90N	Total
Bouwman	5.728	7.115	9.948	8.392	31.183
Trancsom	2.714	7.432	8.762	4.857	23.765
Piscidee	1.736	4.413	4.392	3.302	13.843

Calcul file by file: From Transcom (orchidee+pisces) : (no mask + not output of sflx) -> correspond to values of table 2 thompson part 1.

	- Output INCASFLX -			- Notebook computing -
(Mt/yr)	Ocean	Land	Ratio O/L	Ocean	Land	Ratio O/L
Transcom	6.634174	16.61481	0.399293	4.23125	10.59692	0.399291

Transcom is not a pre-industrial inventory, it's actual. So, it's better to work with piscidee inventory.

To DO

• Modify Bouwman run to take only 'oce' and 'soil' variables -> relaunch notebook to compare if it's better,
• Continue modification in INCA's code.

On Friday, 13th May

Informal with Didier.

Preparation to change INCA's code in Irene.

• Modify inca.card to take new NAT files and BBG from ciclad.
• Modify mksflx_p2p.F90 to put flx_n2o_ant to zero and add aflux terms.
• Modify sflx_inti.F90 to take into account BBG emissions.
• Modify set_ub_vals.F90 to rescale N₂O flux (with parallel part and constant N₂O flux at 285 ppb)

Launch different runs in order to check each step.

Next

• Change ANT in ciclad,
• Put flx_n2o_ant to 0,
• Erase the rescaling,
• Add N2O loss as an output...

On Wednesday, 4th May

In person with Juliette and Marion.

• Presentation of the Wiki page.
• Presentation of the two notebooks.
• Discussion on the different conceptions used in ocean and land communities (different grids, different units in the flux (mol/m2/s vs kg/m2/s)...).

On Analyse_3_sflx_NAT_dyn.ipynb, discussions on visualization with scale, calculation of the full emission on earth per year or per month.

To DO

• Make an analysis per month, per hemisphere, in order to get the total flux emissions for each inventory.
• Take information on where the inventories come from (especially Bouwman and Transcom).
• Draw tables which resume datas used, total emissions, models used in files...
• Compare native grid and regular grid for pisces.
• Compare values of each file used with outputs of INCASFLX.
• Compare total emissions on ocean and land with literature (ciais, ippc) and Bouwman and Trancsom inventories.

On Wednesday, 20th April

In person with Nicolas.

Discussion on:

• New page on Wiki/igcmg (this one !)
• Explanation of the created notebooks (Data_viewer and Analyse_3_sflx_NAT_dyn)
  • Data_viewer : interactive ok but add choices/texts...
  • Analyse_3_sflx_NAT_dyn : change the seasonal analysis made.
• Test with Nicolas' network to know about access to my notebooks.
• Speak about dods/orchidee to avoid downloading images on wiki.

Now, focus on N2O with long living time, but after, we can test on other compounds.

To DO

• Change colorbar with mean+/-std, add some texts on Notebooks and add units on charts
• Erase rescaling in Bouwman to have a better comparison
• Analyse the 3 datasets in a different way : global tables with sum per year, per region, per type (ocean/land) (watch out units)
• Give "procedure" and access to notebooks to all
• Compare with Auburn data (and Tian 2020)
• Look at Mendeley (or Zottero) for bibliography

Nicolas: Paths to have regional masks (from Transcom)

On Wednesday, 6th April

In Visio with Nicolas, Juliette, Didier, Marion.

Mainly, this meeting was to talk a bit more about the project and the work I(=Karine) can make before the training session (April 14th & 15th).

Discussion on:

• the first result made with INCAFLX and 3 different inventories,
• the planning we can set up (which kind of simulation...)
• the impact of N2O on chemistry (if everything is coupled),
• the certainty (or uncertainty) of inventories used (to determine an appropriate scaling),
• the work of Pierre for aquatic emissions (importance of river emissions),

Planning : Run simulation without chemistry and no rescaling, first for pre-industrial, then until now to see/understand the correction we can make on both period (a different correction for each period).

=> This have to be detailed and confirmed

Maybe run only 10 years to know where are sinks, determine some lifetime/seasonal cycle in order to calculate the scaling we may use.

Suggestions to work with the GES branch for the code (branch for coupled model with CO₂ , CH₄ and N₂O)

Meeting every 2 weeks same day, same time (ie, Wednesday at 10:00)

To DO

• Ask for writing a Wiki page on IGCMG
• Log on JupyterHub?
• Make an "experiment plan" for future simulations
• Analyse the results that I've already (seasonal analyses, comparison between inventories with Bouwman as a reference, recap origin/grid resolution...)
• Show the aquatic variable of Bouwman (and maybe some others)

Didier : emissions file for pre-industrial fires to be send to Karine

Bibliography