===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 : 

<file>
&phys_ctl_nl
history_aerosol = .true.
/
</file>

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

<file>
#define AEROCOM
#define AEROFFL
</file>

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): 
<file>
ncap2 -O -s GS_ONLY_SO2=GS_SO2-WD_A_SO2-SO2_CLXF infile.nc outfile.nc
</file>

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
  * Assuming that you have produced output data from 4 simulations: two different model versions, each with PD and PI emissions, and all run with #define AEROCOM & AEROFFL:   
  * 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 modelI = CAM5-Oslo ?
  * - provide paths and partial file names of the model data (PD and PI) for Model I (CAM4-Oslo or CAM5-Oslo) and Model II (must be CAM5-Oslo)
  * - choose desired plot format (plotf=ps, eps, pdf or png)
  * Run the script: ./ModIvsModII.csh
  * Furthermore, to display the plots in an organized form by use of a web browser (only possible if the chosen plot format is png):    
  * - download htm template files from ftp://ftp.met.no/projects/noresmatm/upload/NorESM2Diagnostics/ModIvsModII/htm-templates/
  * - edit general model info (only) in ModIvsModII.htm, and manually cut and paste the mass budget numbers from the script output into this file 
  * - copy all png (plots) and htm files to the desired output (common) directory
  * - open ModIvsModII.htm in your browser: hyper-links to all other htm files, including plots, are found here
  * Example: ftp://ftp.met.no/projects/noresmatm/upload/NorESM2Diagnostics/ModIvsModII/revision610inclSOA-Nudged_1984-12to1985-11_vs_CAM4-Oslo/ModIvsModII.htm

===Preparing output for AEROCOM analysis===

To prepare output so that it is processed automatically by the aerocom tools, use the script located at **models/atm/cam/tools/aerocom/** in the svn repository. The script prepares files such that the idl aerocom tools prepare plots for the aerocom webinterface:
[[http://aerocom.met.no/cgi-bin/aerocom/surfobs_annualrs.pl?PROJECT=NorESM&MODELLIST=NorESM&FULL=explicit&INFO=nohover&PERFORMANCE=ind&YEARFILTER=ALLYEARS&PSFILTER=ALLVARS&Type0=ZONALOBS&Ref0=AERONETSun&Run0=CAM53-Oslo_r773bNudge_151215AG_PD_DMS_733b&Parameter0=OD550_AER&Station0=WORLD&Year0=an9999&Period0=mALLYEAR | URL link to NorESM on AeroCom webinterface]]

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

<Period>: for a climatological average and run choose 9999 , for nudged simulations choose the year of the meteorology

<ModelName>_<ExperimentName>: is the dataset identifier under which the plots appear on the AeroCom webinterface \\ 
of the form NorESM-CAM5_svn{RevisionNumber}_YYMMDD{initials}_Freetext. \\
Example: "NorESM-CAM5_svn1094_151201AG_CMIP6endelig" \\
Initials AG: Alf Grini, AK: Alf Kirkevåg, DO: Dirk Olivie...

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/**