Case_Instruction

1. git clone model
git clone https://github.com/email-clm/clm-microbe.git clm-microbe 

if you want to clone an older vesion
git clone https://github.com/email-clm/clm-microbe.git clm-microbe
cd clm-microbe
git reset --hard 5d87124 (head on May 16th, 2017, could be head of any other commits)

2. Create a new case
./create_newcase --case test --mach peony --compset I1850CLM45CN --res CLM_USRDAT -compiler gnu

The case name can include path, then the case will be created to other directory
The machine name should be your local machine name, but the configuration should be set up in the machine files
The compset could be many different combination, refer to http://www.cesm.ucar.edu/models/cesm1.2/cesm/doc/modelnl/compsets.html
The resolution can be user defined (CLM_USRDAT) or other pre-defined, http://www.cesm.ucar.edu/models/cesm1.1/cesm/doc/modelnl/grid.html
The compiler should be gnu for peony machine, it might be changed if the real compiler on the machine is changed.

3. edit env_build.xml
L37, change user account to your own account
L70, append "-microbe on"

4. edit env_run.xml
L19, change the path to your own directory
L56 ndays -> nyears
L59, change the number for the exact duratin of simulation
L70, optional (for expert only), for restarting points
L79, optional (for expert only), for resubmission
L288 & 290, if using different machines, it might needs modifications
L299, default is true, change to false if you do not want to archive
L302, optional (for expert only)
L328, CLM1PT
L337, starting year of the meteorological data
L339, ending year of the meterological data
L357, -mask navy
L369, on
L372, 1x1pt_US-Brw, it needs to be consistent with the real data (/inputdata in the folder)
L425, change the CO2 concentration as appropriate
L430, 433, 436, 439, mask file should be consistent with the L372 (for exmpert only)

5. Namelist
user_nl_clm
&clm_inparm
hist_mfilt = 365
hist_nhtfrq = -24
 fsurdat = '/storage/projects/inputdata/lnd/clm2/surfdata_map/surfdata_1x1pt_NGEE_US-Brw_I20TRCLM45CN_simyr1850.nc'
 fpftcon = '/storage/xxu/cases/SJ_CN_ad_spinup/pft-physiology.c130801.Sanjiang_CN-SJ1_I1850CLM45CN.nc'
 stream_fldfilename_ndep = '/storage/projects/inputdata/lnd/clm2/ndepdata/fndep_clm_hist_simyr1849-2006_1.9x2.5_c100428.nc'
/

Create surface and dynamic PFT file if needed.
NUMLON, order of cell along longitudal direction # notice the resolution of the spatial data when determining these numbers
NUMLAT, order of cell along latidual direction # notice the resolution of the spatial data when determining these numbers

ncks -d lsmlon,NUMLON,NUMLON -d lsmlat,NUMLAT, NUMLAT /storage/projects/inputdata/lnd/clm2/surfdata/surfdata_360x720cru_simyr1850_c130415.nc surfdata_1x1pt_%case%_simyr1850.nc
ncks -d lsmlon,267,267 -d lsmlat,275,275 /storage/projects/inputdata/lnd/clm2/surfdata/surfdata_360x720cru_simyr1850_c130415.nc surfdata_1x1pt_Sanjiang_CN-SJ1_I1850CLM45CN_simyr1850.nc
for Sanjiang station (N 47.51, E 133.5)

dyn file
ncks -d lsmlon,267,267 -d lsmlat,275,275 /storage/projects/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_0.5x0.5_simyr1850-2010.nc surfdata.pftdyn_1x1pt_%case%_simry1850-2010.nc
ncks -d lsmlon,267,267 -d lsmlat,275,275 /storage/projects/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_0.5x0.5_simyr1850-2010.nc surfdata.pftdyn_1x1pt_Sanjiang_CN-SJ1_simry1850-2010.nc

user_nl_datm

6. get data or parameter ready
copy microbepar_in file to your run directory

7. case setup
In the case folder, launch ./cesm_setup

8. build case
In the case folder, ./casename.build

9. run case
In the case folder, ./casename.run


other useful information: 
Getting your Mac ready for netCDF
http://mazamascience.com/WorkingWithData/?p=1474

CESM: Building CESM 1.2 on Mac OSX
http://hannahlab.org/cesm-building-cesm-1-2-on-mac-osx/
https://github.com/fmyuan/E3SM/wiki/ALM-on-Mac-OSX:-environments,-building,-and-running