A Hitchhikers Guide to the Black Arts (of Earth system modelling)
Contents
1. a ws oO D w wo ojo 1 o o 1 oy ojo N w N N D O1O 0 0 0 0 0 c0 o H fo N O I oO on oO OY oO Pp ce N Ke oO on oO D oO OY oO js H wo pan O ws ojo N ojo Ba ojo N C O 0 0 0 0 c0 o0 f a Re o N n fo uo oO N oO N D w oO N io fo w io w oO oO 9 GO CO N on oO N oO fo ws O N w D oO Pp oO oO w fo uo oO N Oo oO sl Ww oj o OV w oj o A e a w N oj o N wW ojlo Jj ojo j e o eS Ko Ss wo D oO D Xe D Ko is wo Ss GENIE 1 grid worjh2 configuration Light blue numbers are the i co ordinates Green numbers are the co ordinates The depth of the ocean at any location is indicated by its k value a number between 1 and 16 with 16 being the surface layer of the ocean and 1 the maximum possible depth anywhere Numbers gt 90 91 92 93 94 and shaded grey are land and specify the direction of run off Location 22 33 08 is highlighted in yellow You can follow the progress of the dye and hence diagnose the properties of ocean circulation in the model by plotting vertical and or horizontal slices that go through or near the cell location in which you inject the dye tracer 3D netCDF file You can also plot the overturning circulation from the 2D netCDF file vari2. bg_par_ocn_force_scale_val_48 0 0 The first line simply tells GENIE to ignore the complicated way of specifying forcings Section 4 in the User Manual The second line points GENIE to a set of files that define what geochemical property is going to be altered plus information about how the forcing changes with time if at all These two lines you do not need to worry about any further here There are three lines bg_par_force_point_i 20 that specify the location in the ocean of the geochemical forcing is going to be applied The point sources are specified in i j k coordinates which in this case is 22 33 08 For the ocean model resolution we are using the grid is 36x36x16 longitude i is counted from left to right 1 to 36 latitude j is counted from bottom to top 1 to 36 level depth k is counted from downwards top to bottom 16 down to 1 Thus 22 33 08 is a release of tracer in the North Atlantic a little south of Greenland and intermediate depth level 8 out of 16 Refer to the Figure for grid information Finally there is a scaling parameter og_par_ocn_force_scale_val_48 which specifies the magnitude of the flux to be applied in units of mol yr You are going to run a brief experiment in which you will be injecting a conservative dye tracer in the ocean BIOGEM has two tracers defined for this purpose blue and red Open the user config file exp6_color
3. released at depth e g variable ocn_colr Changes in tracer inventory with time can be tracked in the time series file biogem_series_ocn_colr res Spend a little while altering the flux og_par_ocn_force_scale_val_48 and or location bg_par_force_point_i bg_par_force_point_j bg_par_force_point_k of tracer input Note how you can use conservative tracers to help diagnose and better understand the circulation of the ocean 10 09 08 94 94 94 94 94 onl gil oil L 91 omi 1 16 09 L 05 02 02 03 04 05 04 04 07 07 07 92 99 os 93 93 OS 12 03 01 OL 02 02 01 09 94 m m j Da a 93 93 91 12 93 91 06 05 05 L 09 0S 03 1 12 05 03 06 03 03 01 01 03 02 04 03 03 02 01 02 01 02 01 03 01 02 01 01 01 02 01 04 02 05 03 08 04 97 05 1 91 05 91 04 1 91 03 91 03 1 91 03 1 09 02 1 06 02 04 02 02 02 01 01 01 01 01 01 04 03 04 03 04 02 94 94 Oo N A O O o A ie N A O oO WO A Ko K Ww oO w oO K oO io Pp oO N OC oO oO of co clolo oj o 9 9 9 9 9 9 9 o9 a Ool o 9 9 9 0 CO OF CO CO 9 2 CO OO OO oO OO 0 0 0 0 0 aro a w w w ojojo NINI N oO N I w SS on oO Ww j 4 N ojojoj ojlojojlojo Balar oG OG Ga o a Ss f e e A U ojo Ae W ojo w oO fo NI N ojo oe E OO OO OO O O a D oO D oO D w D
4. UoB Earth system modelling workshop 26 27 August 2009 SESSION 2a Atlantic meridional overturning circulation stability and global warming A Hitchhikers Guide to the Black Arts of Earth system modelling SESSION 2a Atlantic meridional overturning circulation stability and global warming Stuff to keep in mind e Nothing at all keep your mind completely empty and let the wonderful truths of the GENIE 1 model permeate your entire being Background reading Rahmstorf et al 2006 In Encyclopedia of QuaternarySciences Edited by S A Elias Elsevier Amsterdam Provides the background to the Atlantic Meridional Overturning Circulation or Thermohaline Ocean Circulation and its hypothesized hysteresis loop Hargreaves J C J D Annan N R Edwards R Marsh An efficient climate forecasting method using an intermediate complexity Earth System Model and the ensemble Kalman filter Climate Dynamics Volume 23 Issue 7 8 Dec 2004 Pages 745 760 Marsh R A Yool T M Lenton M Y Gulamali N R Edwards J G Shepherd M Krznaric S Newhouse S J Cox Bistability of the thermohaline circulation identified through comprehensive 2 parameter sweeps of an efficient climate model Climate Dynamics Volume 23 Issue 7 8 Dec 2004 Pages 761 777 9 0 9 1 9 2 UoB Earth system modelling workshop 26 27 August 2009 SESSION 2a Atlantic meridional overturning circulation stability and globa
5. able phys_opsi global overturning streamfunction phys_opsi overturning in he Atlantic The progress of the dye plume can also be easily followed in the BIOGEM 2D netCDF file by viewing the water column integrated tracer inventory variable See Sabine et al 2004 for the use of water column integrals in this case in the context of the distribution of anthropogenic CO uptake and storage You can also select an additional blue dye tracer To do this you will need to edit the file configure_forcings_ocn dat which can be found in the genie_forcings pyyyyz_Fred 9 3 9 4 UoB Earth system modelling workshop 26 27 August 2009 SESSION 2a Atlantic meridional overturning circulation stability and global warming directory This directory contains the basic specification of the forcing such as which tracer whether the forcing should be restoring to a prescribed value or a flux etc see user manual On line 54 in configure_forcings_ocn dat the f in column 04 needs to be set to t i e as per for RED numerical color tracer on the line above You will also have to create a file specifying the time dependent information for the forcing For the red tracer this file is already present and called biogem_force_flux_ocn_colr_sig dat Copy this file e g by transferring to the local machine and rename to biogem_force_flux_ocn_colb_sig dat before transferring back again The co
6. ed dye tracer In the user config file the lines bg_par_atm_force_scale_val_3 1000 0 bg_par_atm_force_scale_val_4 27 0 scale the CO flux and its 5 C isotopic signature respectively The scaling values are given to you for a CO release of 1000 PgC yr current emissions are about 8 PgC yr 1 at 27 o typical of fossil fuel carbon Altering the value assigned to bg_par_atm_force_scale_val_3 in the user config file gives immediate control over emissions rate You can also adjust the emissions to have a time varying rate by editing the file biogem_force_flux_atm_pCO2_sig dat which can be found in the directory genie_forcings pyyyyz_FpC02_Fp13co2 The format of this file is START OF DATA 0 0 8 3333e 013 1 0 8 3333e 013 1 0 0 0 999999 9 0 0 UoB Earth system modelling workshop 26 27 August 2009 SESSION 2a Atlantic meridional overturning circulation stability and global warming END OF DATA and defines a total emission of 1000 PgC 8 333 10 mol CO2 over the first 1 year of the model experiment Year 999999 9 has no special meaning and is simply just a number way in the future Between the start and end tags the data is in 2 columns the first contains a series of tie points for defining the timing of changes in emissions and the 2 contains the flux information in units of mol yr Note that at each time step of the model the CO flux is interpolated bet
7. er input beyond which the AMOC rapidly decreases in strength How important is the precise location of the freshwater input i e try tipping it in somewhere else Units the freshwater forcing is implemented as negative salinity just to really screw with your mind The units are PSU yr Which sort of does not mean much to me either A value of bg_par_ocn_force_scale_val_2 of 34 9 would be equivalent to taking all the salt out of 1 kg of freshwater since the mean global salinity is 34 9 PSU Or equivalently since the ocean volume is fixed the ocean model uses the rigid lid approximation assumption 34 9 is equivalent to adding I kg of freshwater to a surface box So a value of bg_par_ocn_force_scale_val_2 of 3 49x10 3 49E04 would be a flux of 1 m yr 1000 kg m of freshwater So in the example above bg_par_ocn_force_scale_val_2 1 0E18 the freshwater flux is 1 0x10 3 49 x10 2 8653 x10 m yr The literature invariably gives freshwater fluxes in units of SV 10 m s So in the example the freshwater flux is 9 0797 x10 m s 365 2524 x3600 31557600 s yr Or 0 9 Sv Read the literature but generally fluxes of not much less than 0 05 Sv and to quite specific places have to be applied in models in order to induce a collapse of the AMOC 10 10 1 10 2 UoB Earth system modelling workshop 26 27 August 2009 SESSION 2a Atlantic meridional overturning ci
8. eriments with differing fluxes of freshwater into the ocean The new user config file is called exp7_hosing The default i j location of the flux input is the same but now the injection is to the surface level k 16 of the ocean Note that the forcing of the salinity tracer is negative freshwater negative salinity compared to sea water See below for some exciting units discussion To orientate you in freshwater forcing space bg_par_ocn_force_scale_val_2 1 0E18 should be sufficient to make stuff happen To run the model for 101 years using a pre industrial re start UoB Earth system modelling workshop 26 27 August 2009 SESSION 2a Atlantic meridional overturning circulation stability and global warming CoO oo 11 years should be long enough to see a collapse start to occur but you might want to run the model for longer e g 51 years to save the time year 50 annual average state The most obvious property of the Earth system to follow is the Atlantic overturning strength biogem_series_misc_opsi res The AMOC stream function in the fields_biogem_2d nc 2 D time slice netCDF results file field pnys_opsia is also illustrative You can also try and identify the salinity anomaly due to freshwater input in the salinity tracer field 3D netCDF file There are also important impacts on surface air temperatures field atm_temp in fields_biogem_2d nc Note the importance of the AMOC in transpor
9. injection and edit the namelist parameter controlling the flux of red dye to read bg_par_ocn_force_scale_val_48 1 0E12 which specifies a flux of 1 0x10 mol yr Remove the snowball configured GENIE executable program from genie genie main type make cleanall and return to the home directory The experimental design is a little different from the previous modern simulation in that a new base config genie_eb_go_gs_ac_bg_itfclsd_161_JH is being used this specifies a higher resolution ocean model with 16 levels in the vertical hence the 161 short for 16 levels don t get the one 1 and el 1 mixed up it is almost impossible to distinguish them on the computer terminal screen The iftclsd is short for Indonesian through flow closed while JH is the person s initials I created the base config originally for Also now included is seasonality of solar insolation Run the model for 101 years using a new pre industrial spin up that is provided as a re start oupkicolorinjection 101 genie nti modern Melee PHF UoB Earth system modelling workshop 26 27 August 2009 SESSION 2a Atlantic meridional overturning circulation stability and global warming View the results the impact on the Red tracer distributions in NetCDF time slice files For instance the 2 D NetCDF file fields_biogem_2d nc has fields of bottom water properties which facilitate tracking the dispersal of tracers
10. l warming Geochemical forcing of GENIE poking the climate beast Wally Broecker The BIOGEM ocean biogeochemistry module in GENIE provides a framework for applying time and spatially variable forcings of the Earth system fluxes or restored to boundary conditions that can be prescribed for any gas dissolved substance or particulate and including temperature and salinity Examples include freshwater input a negative salinity flux forcing of the North Atlantic to alter ocean circulation fossil fuel CO emissions to the atmosphere a CO gas flux forcing or aeolian iron supply to the surface ocean based on a 2 D detrital dust flux forcing field Section 4 in the User Manual describes the original and most flexible provision for applying time dependent forcings However a simpler way is provided of applying forcings in GENIE compared to the gobbledygook in the User Manual and geochemical fluxes or boundary conditions can be specified in just a few additional lines in the user config file if the forcing has a simple spatial pattern e g fluxes applied equally to the entire ocean to the entire surface or to a single location in the ocean View the user config file exp6_colorinjection You will see the following new lines under the heading FORCINGS bg_ctrl_force_oldformat false bg_par_fordir_name genie_forcings pyyyyz_Fred bg_par_force_point_i 22 bg_par_force_point_j 33 bg_par_force_point_k 8
11. lb bit is a mnemonic for the blue color tracer The mnemonics and index numbers for the various tracers in GENIE are listed in the genie user manual namelists document see the mygenie webpage Finally you need to add the line to the user config file bg_par_ocn_force_scale_val_49 1 0E12 You have now added a new forcing of the model It actually is not very exciting because the two tracers are being added in identical positions set by the 3 namelist paramneters bg_par_force_point_i 22 bg_par_force_point_j 33 bg_par_force_point_k 8 This way of configuring forcings is a little restrictive and is designed mostly for forcings that can be applied as a Single point source or uniformly to the ocean surface or atmosphere The full and most flexible way of configuring and applying forcings is detailed in the user manual However you can set independent locations for the red and blue dyes by editing the default i j k locations in configure_forcings_ocn dat columns 7 8 and 9 An interesting honest and illustrative exercise is too use the dye tracer either one to pick out the path taken by Mediterranean Intermediate Water Despite the low resolution of the GENIE 1 ocean circulation model component and the highly restricted representation of the Mediterranean the model does predict a salty Mediterranean as a consequence of P E in this basin and its catchments being negative and this water makes its
12. ow important is the time scale or shape of the emissions trajectory For total emissions above this where in the ocean does the surface first become under saturated These are questions that are addressed with simple CO release experiments in ocean carbon cycle models and everyone seems to get a GRL paper out of it each and every time No names mentioned
13. rculation stability and global warming Exploring the consequences of fossil fuel CO2 emissions For the next experiment s you can chuck CO into the atmosphere just for the hell of it As much as you want Apparently humans are actually doing this now Imagine that The user config for GENIE 1 exp8_co2emissions is provided and configured with climate being responsive to COQ i e it takes account of CO climate feedbacks as well as a rate of calcification in the surface ocean that is responsive to pH i e it takes into account CO gt calcification feedbacks which will additionally interact with climate see Ridgwell et al 2007b Anything could happen The only difference from the user config files provided previously is the addition of a prescribed release of CO to the atmosphere which by default is set for 1000 PgC over an interval of a single year Releasing CO just over a single year is obviously rather unrealistic but represents a useful idealized experiment for assessing the time scale s of fossil fuel CO uptake by the ocean The number of tracers has also been increased and an ocean carbon cycle selected so you will have to do a make cleanall before proceeding Run the experiment for 101 years starting from the re start used previously i e exia_cosemlseinoe 101 gonde sitet mciern Aelovelo _Sem0r and view the run time output particularly atmospheric CO2 ocean surface temperature SST sea ice e
14. ting heat to NE American and NW Europe the file the Day After Tomorrow was not entirely inaccurate in this particular respect Be aware of the possibility of climate impacts far from the location of fresh water forcing Look out for any significant looking impacts on atmospheric COs sea ice extent etc To more easily assess some of these impacts you will need to create an anomaly difference map in Panoply 1 First open a dataset e g atm_temp surface air temperature in the 2D netCDF file 2 From the upper LH corner of the Dataset Browser window from the drop down menu select the name of the plot you have just created atm_temp in field_biogem_2D 3 Again from the upper LH corner of the Dataset Browser window now click on the Combine Plot icon 4 You now have a plot window that is displaying a difference map By default it is showing you the difference between two identical in time slices The two different slices are labeled Array 1 LH side and Array 2 RH side Keep one array Array 1 fixed to the initial year 1 centered on 0 5 and vary the year in the second array Array 2 Note that you can select in Panoply whether Array 1 Array 2 is plotted or Array 2 Array 1 or various proportional or relative differences QUESTIONS What is the largest freshwater flux that can be sustained without collapsing the AMOC say to below 5 or 1 Sv strength Is there a threshold tipping point of freshwat
15. way out in the subsurface into the Atlantic Simply specify a dye injection somewhere in the Mediterranean be careful with the restricted depth of the Mediterranean if you inject too deeply into the crust then you will not see anything refer to the figure for the depth level k number of the maximum depth of the water column in each location and it is better to inject it relatively close to the opening of the gateway Run for 101 years Then 1 View the dye tagged plume of Mediterranean Intermediate Water by plotting a lat lon slice from the 3D netCDF file This will give you the depth of the plume How does this compare with salinity observations salinity observations and appropriate global datasets can be found on the web with a little patience You can also view the water column integrated distribution 2D netCDF 2 Try viewing the plume via a lat depth slice Refer to the figure to determine the i value up the Atlantic that will just graze the edge of what passes for Spain at this low model resolution Which direction does it head after exiting the Mediterranean Is this realistic Instead of adding a dye tracer you could add fresh water to assess the sensitivity of the Atlantic Meridional Overturning Circulation AMOC to collapse You will be carrying a classic hosing experiment i e in the model as if you were directing a garden hose of tap water at the North Atlantic and running a series of model exp
16. ween the time points The purpose of the 0 0 8 3333e 013 120 8 43333e 013 1 0 0 0 bit is thus to effect a sharp turn off of the flux at the end of first year To extend the period of emissions for example 0 0 8 3333e 013 10 0 8 3333e 013 10 0 0 0 would give you 1000 PgC yr over 10 years In contrast 0 0 8 3333e 013 10 0 0 0 would result in a linear ramp down of flux from 8 3333e 016 mol yr at the start of year 0 0 to zero at the start of year 10 0 a total emission of 1000x10x0 5 5000 PgC over 10 years See the User Manual for further details on the construction and use of forcings of the GENIE model By editing and saving the flux and or timing information you can exert fine control on the CO emissions trajectory and total fossil fuel burn For instance the IPCC SRES scenarios of possible future CO emissions can be reconstructed and their implications tested in GENIE Play with different CO releases and note their impact on climate and ocean biogeochemistry Much more realistic and appropriate to our current global experimenting is a lower rate order of 10 or 20 PgC yr released over a longer interval of order 100 years How much CO emissions does it take to significantly collapse the AMOC and over what time scale Or alternatively what is the atmospheric pCO threshold What is the maximum total CO release that can be made without inducing aragonite saturation anywhere H
17. xtent and Atlantic Meridional Overturning AMO strength Viewing the time series results file biogem_series_fexport_CaCO3 res will show how global carbonate production responds to the ensuing ocean acidification which itself is recorded in the file biogem_series_misc_SSpH res Note how atmospheric CO starts to decay away after the first year as fossil fuel CO is progressively taken up by the ocean In the 3 D netCDF time slice file ocean pH is a particularly relevant field to consider together with calcite and aragonite saturation note that ocean surface waters in which aragonite becomes under saturated Q lt 1 0 is regarded as a critical threshold for organisms making aragonite shells and skeletons and spells TROUBLE for some poor calcifying marine organism somewhere Also temperature is particularly relevant to future global change as well as sea ice extent and whatever else takes your fancy Also try creating difference maps in Panoply to assess the geographical characteristics of ocean acidification impacts Ideally one would run a parallel experiment identical except for zero CO release being specified to act as a control for the calculation of the differences A difference map for the water column integral of DIC 2D netCDF file for instance reveals where fossil fuel CO is preferentially taken up by the ocean You can easily modify the experimental design to release more less CO as you did for the r
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