Model Diagnostic Tools

NorESM Diagnostic Packages

Please, refer to GUIDE_ReadME_first and the ReadME files in each of the Model Components Diagnostic Tools (Packages) locations below for more details.

Usage: nohup [your work directory path]/[amwg/ice_diag]_template.csh >& out &
Purpose: Model solution validation, evaluation, and analysis
compared to observations and reference model simulation.
Description: Automated diagnostic packages for each of the NorESM model components (atmosphere, sea ice, land, ocean)
based on the NCAR CESM diagnostics packages.
Written in NCL, NCO and C-Shell. Output is in the form of: .ps or .png plots and web-pages.
The packages are installed and stored in 4 locations; please use them on Cruncher or Grunch when possible:
On cruncher.uio.no/norstore.uio.no in:
/projects/NS2345K/diagnostics/Packages
On grunch.bccs.uib.no/hexagon.bccs.uib.no in:
/work-common/shared/noresm/diagnostics/Packages
On vilje.hpc.ntnu.no in:
/work/shared/noresm/diagnostics/Packages
There are 6 diagnostic tools CAM_DIAG (ready for use), CICE_DIAG (ready for use), CLM_DIAG (in testing),
POP_DIAG (in testing), MICOM_DIAG (in development) and CVDP_DIAG (the new NCAR Climate Package, in testing)
Currently only the CAM (AMWG) and the CICE packages are ported and ready to use.
You will find for each of those c-shell macroscript *_template.csh.[machine]
Copy it in your working directory, change the paths and file names in the user-defined part of it and run.

Report any problems or suggestions to Detelina Ivanova: detelina.ivanova@nersc.no

MICOM Diagnostic Package (NEW 2015.04.23)

First version of MICOM diagnostic package is available on grunch/norstore/hexagon/vilje. Please find more details here.

SVN Repository for NorESM Diagnostic Packages (NEW 2015.04.23)

The NorESM Diagnostic Packages can be downloaded via svn using the command:

svn export svn://noresg.norstore.no/NoresmDiagnosticPackages

A web-viewer is available at https://webserver1.norstore.uio.no:8443/websvn/wsvn/NORESG-diagpacks (user: guestuser, passw: friendly).

Aerosol and Chemistry, Clouds and Forcing Diagnostics

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 :

Configuring a run with more aerosol diagnostics in (NorESM2)

&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

Tracer Budget terms

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)

NCL Model Version Comparison package (Alf K)

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

Automatic 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: 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/

Other tools

ESMVALtool http://www.geosci-model-dev-discuss.net/8/7541/2015/gmdd-8-7541-2015-discussion.html

cis tools http://www.cistools.net

JASMIN http://www.jasmin.ac.uk/services/jasmin-analysis-platform/