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If you need POP2 (e.g. compset B), enter cpan, key in: install Switch, then exit cpan.

cp /n/home05/pchan/spcam2_0-cesm1_1_1/scripts/create_new_build.sh ~/  #please copy a newer version after May 2018 (the CentOS7 update)

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The above figure is adapted from http://wwwwww2.cesm.ucar.edu/events/tutorials/2016/practical1-bertini.pdf p.48.

There is no need to copy the CESM download folder. (for CESM1, which someone already downloaded for you)

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Naming conventions of nc files: http://wwwwww2.cesm.ucar.edu/models/cesm1.1/filename_conventions_cesm.html

*.h* files are history files. Similar for r (restart), i (initial), d (diagnostic).

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How namelists are built in CESM?

$RUNDIR/*_in are namelists directly read by Fortran program. They are recommended NOT to be edited directly, but instead, indirectly through user_nl_* and env_*.xml. The processes of indirectly creating namelists are as follows:

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• preview_namelists 
  • calls Buildconf/$comp.buildnml.csh
  • copies *_in to CaseDocs/

• Buildconf/$comp.buildnml.csh 
  • call $CCSMROOT/models/**/bld/build-namelist, which create namelist Buildconf/*conf/*_in
  • copy *_in to $RUNDIR (overwrite)

• build-namelist 
  • takes “infile” from user_nl_*
  • writes out Buildconf/*conf/*_in and Buildconf/*.input_data_list

When job is submitted:

• $CASE.submit submits $CASE.run
• $CASE.run calls preview_namelists
• Same things happen again.

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How to modify namelists in CESM?

If possible, always use user_nl_* and env_*.xml.

E.g. Change the path to an input data file: ./xmlchange SSTICE_DATA_FILENAME=/path/to/new_sst.nc (this can also be listed as a line in user_nl_cam).

E.g. To customize CAM output, edit user_nl_cam according to userguide, and master field list: v1.1.1, v1.2.2.

If impossible, manually change $RUNDIR/*_in, and disable copying (overwriting) in Buildconf/$comp.buildnml.csh

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1. grep -Ev '^\s*$|^\s*!' user_nl_*
   can display all non-empty uncommented lines in user_nl_*

2. ./preview_namelists can update namelists (and input_data_list)

3. grep '' Buildconf/*.input_data_list
   can list out all input data.
   

4. DIN_LOC_ROOT=`./xmlquery -valonly -silent DIN_LOC_ROOT`
   ./check_input_data -inputdata $DIN_LOC_ROOT -check
   can check input data

5. Section &seq_infodata_inparm in drv_in can be checked in $RUNDIR/cpl.log.$LID

6. Always compare default namelist and new namelist

7. Sometimes, user_nl_* are not interpreted literally. E.g. specifying prescribed_ozone_file could remove lines for prescribed_ozone_cycle_yr, prescribed_ozone_name, etc.

8. Never edit namelist in CaseDocs/ or Buildconf/, they are overwritten every time and NOT read by Fortran program.

References:

http://jules-lsm.github.io/vn4.2/namelists/intro.html

http://www.lahey.com/docs/lfpro73help/f95arnameliststmt.htm

http://www.codezone.co.uk/fortran/namelist.shtml

http://www.cesm.ucar.edu/models/cesm1.1/cesm/doc/usersguide/c1128.html

http://www.cesm.ucar.edu/events/tutorials/2016/practical4-hannay.pdf

Compset

Compset is a short form for "component set", which specifies component models, forcing scenarios and physics options for those models.

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List all available compset by ~pchan/spcam2_0-cesm1_1_1/scripts/create_newcase -list, or browse http://wwwwww2.cesm.ucar.edu/models/cesm1.1/cesm/doc/modelnl/compsets.html

You can view technical details about compset in README.case under case root directory, after you have created a case with that compset.

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Details coming

SourceMod related

http://wwwwww2.cgd.ucar.edu/cms/bundy/cam_interface.pdf

Technical Note (283 pp.): http://wwwwww2.cesm.ucar.edu/models/cesm1.1/cam/docs/description/cam5_desc.pdf

http://wwwwww2.cgd.ucar.edu/cms/eaton/cam/atm_desdoc/node2.html#SECTION00024000000000000000

Reference Manual: http://wwwwww2.cesm.ucar.edu/models/cesm1.2/cam/docs/rm5_3/rm.html#subcol_intro

Userguide?: http://wwwwww2.cesm.ucar.edu/models/cesm1.0/cam/docs/ug5_1_1/ug.pdf

CAM uses dry static energy as prognostic variable (instead of temperature). Detailed discretization is implemented in geopotential.F90:geopotential_dse, and described in 4.11.5 in cam4_desc.pdf.

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Unconfirmed: aquaplanet - src.aquap do not take effect.

References

http://wwwwww2.cesm.ucar.edu/events/tutorials/2016/coursework.html (look for practical sessions)

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