Configuring a run with more aerosol diagnostics in (NorESM2)

In both the default CAM5-aerosol packages (MAM3,MAM7) and the Oslo-aerosol packages, the budget terms can be taken out using a variable in the namelist :

&phys_ctl_nl
history_aerosol = .true.
/

Two more diagnostics are useful:

Enable estimates multiple calls to radiation which are necessary for effective radiative forcing estimates

Enable diagnostics for AEROCOM

To enable this, take the file cam/src/physics/cam_oslo$ vim preprocessorDefinitions.h and copy it to your SourceMods/src.cam folder

Change both preprocessor definitions to true

#define AEROCOM
#define AEROFFL

The AEROCOM-token turns on diagnostics needed for AEROCOM The AEROFFL-token tells the model to do additional radiation-diagnostics for aerosol indirect effect

Fields produced in monthly average files when running with budgets activated

Running with budgets activated will produce the following terms in the monthly output files:

Output variable name	Meaning	Comment
SF{Tracer}	Emissions from surface
GS_{Tracer}	gas phase chemistry	3D-emissions and gas phase washout included in this term
AQ_{Tracer}	aquous chemistry
{Tracer}_Mixnuc1	Activation in clouds and evaporation of cloud droplets
{Tracer}_DDF	Dry deposition flux (aerosol tracers)
{Tracer}_SFWET	Wet deposition flux (aerosol tracers)
{Tracer}_condtend	loss/production in condensation/nuclation	(CAM-Oslo only)
{Tracer}_coagTend	loss/production in coagulation	(CAM-Oslo only)
DF_{Tracer}	dry deposition flux (gas tracers)	output with history_aerosol with CAM-Oslo only
WD_A_{Tracer}	wet deposititon flux (gas tracers)	output with history_aerosol with CAM-Oslo only
{Tracer}_CLXF	3D-emissions (“external forcing”)	output with history_aerosol with CAM-Oslo only
{Tracer}_clcoagTend	loss of tracer due to coagulation with cloud droplets	output with history_aerosol with CAM-Oslo only

Note: Since 3D-emissions and and gas washout rates are included in the term GS_{Tracer} in the mozart chemistry solver, the individual terms can be found like this (example for SO2):

ncap2 -O -s GS_ONLY_SO2=GS_SO2-WD_A_SO2-SO2_CLXF infile.nc outfile.nc

More info on SO2 budgets (see /models/atm/cam/tools/diagnostics/ncl/ModIvsModII/ for scripts with info on all tracers):

GS_SO2 contains the SO2 budget terms for all that goes on in the chemistry-routine, which is
1) Gas phase chemistry, 2) Wet deposition, and 3) 3D-emissions.
Gas phase chemistry is both production from DMS (GS_DMS) and loss through OH (GL_OH)
For calculations of net loss, e.g. used to calculate SO2 life-times, we're interested in the
loss through OH from the chemistry-term (GL_OH).
GS_SO2 = GL_OH + SO2_CLXF - WD_A_SO2 - GS_DMS*64/62
or
GL_OH = GS_SO2 - SO2_CLXF + WD_A_SO2 + GS_DMS*64/62

Estimating chemical loss w.r.t. S (instead of SO2 or DMS), for comparison with CAM4-Oslo numbers:
net chemial loss gas phase = (GS_SO2/1.998 - SO2_CLXF + WD_A_SO2)/1.998 + GS_DMS/1.938
net chemical loss = net chemial loss gas phase + AQ_SO2/1.998

Finally, total net loss (used to calculate life-time = -load/(net loss), where load = cb_SO2/1.998):
net loss =
- WD_A_SO2/1.998 ;wet deposition in kg/m2/sec (positive in output file)
- DF_SO2/1.998 ;dry deposition in kg/m2/sec (positive in output file)
+ AQ_SO2/1.998 ;wet phase production of SO4 in kg/m2/ses (negative in output file)
+ (GS_SO2 - SO2_CLXF + WD_A_SO2)/1.998 + GS_DMS/1.938 ; net chemical loss gas phase

Looking at the aerosol budgets (CAM-Oslo only)

Go to the directory models/atm/cam/tools/diagnostics/ncl/budgets

Change the filename to use in the file budgets.ncl (“myFileName” around line 18). Should be for example yearly average of month-avg file in a run with budgets

Run the script budgets.sh to create a pdf-file (output.pdf)

Making ncl plots of often used aerosol and cloud fields, including ERFs, for two model versions (CAM-Oslo only)

Make a local copy (on Linux) of the directory models/atm/cam/tools/diagnostics/ncl/ModIvsModII

Then, in ModIvsModII.csh (note: read the header info):

- edit model info for the first model (shown to the left in the plots), modelI = CAM4-Oslo or CAM5-Oslo

- give the paths of the model data (PD and PI, run with #define AEROCOM & AEROFFL) for Model I (CAM4-Oslo or CAM5-Oslo) and Model II (CAM5-Oslo)

- choose desired plot format (plotf=ps, eps, pdf or png)

Run the script: ./ModIvsModII.csh

Edit general model info in ModIvsModII.htm, and manually also cut and paste the mass budget numbers from the script output into this file

Place all plots and htm files on the same directory

Open ModIvsModII.htm in your browser: hyper-links to all plots are found in this file

Preparing output for AEROCOM

To prepare output for aerocom, use the script located at models/atm/cam/tools/aerocom/ in the svn repository.

The script requires <ModelName>_<ExperimentName> and <Period> as input.

The script creates files named like

“aerocom3_<ModelName>_<ExperimentName>_<VariableName>_<VerticalCoordinateType>_<Period>_<Frequency>.nc”

<ModelName> ⇒ eg NorESM-CAM53
<ExperimentName> ⇒ svn{RevisionNumber}_YYMMDD{initials}_Freetext
<VariableName> ⇒ aerocom variable names
<VerticalCoordinateType> ⇒ “Surface”, “Column”, “ModelLevel”, “SurfaceAtStations”, “ModelLevelAtStations”
<Period> ⇒ eg “2008”, “2010”, “9999”
<Frequency> ⇒ “timeinvariant”,”hourly”, “daily”, “monthly”, “sat1000”, “sat1330”, “sat2200”, “sat0130”

Note that VerticalCoordinateType is dependent on the variable!! It is not a question about “vertical coordinate type used in model simulations”!

The script copies files on norstore into /projects/NS2345K/CAM-Oslo/DO_AEROCOM/<ModelName>_<ExperimentName>/renamed/