CESM Research Tools: CLM4.5 in CESM1.2.0 User's Guide Documentation
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Spinning up the CLM4.5 biogeochemistry (CLMBGC spinup)

To get the CLM4.5-BGC model to a steady state, you first run it from arbitrary initial conditions using the "accelerated decomposition spinup" (-bgc_spinup on in CLM configure) mode for 1000 simulation years. After this you branch from this mode in the "final spinup" (-bgc_spinup off in CLM configure), and run for (at least 200+ simulation years).

Spinup of CLM4.5-BGC

45_AD_SPINUP

For the first step of running 1000+ years in "-bgc_spinup on" mode, you will setup a case, and then edit the values in env_build.xml and env_run.xml so that the right configuration is turned on and the simulation is setup to run for the required length of simulation time. So do the following:

Example 4-3. Example AD_SPINUP Simulation for CLM4.5-BGC

> cd scripts
> ./create_newcase -case BGC_spinup -res f19_g16 -compset I1850CRUCLM45BGC -mach yellowstone_intel
> cd BGC_spinup
# Append "-spinup on" to CLM_BLDNML_OPTS
> ./xmlchange CLM_BLDNML_OPTS="-bgc_spinup on" -append
# The following sets CLM_FORCE_COLDSTART to "on", and run-type to startup (you could also use an editor)
> ./xmlchange CLM_FORCE_COLDSTART=on,RUN_TYPE=startup
# Make the output history files only annual, by adding the following to the user_nl_clm namelist
> echo 'hist_nhtfrq = -8760' >> user_nl_clm
# Now setup
> ./cesm_setup -case
# Now build
> ./BGC_spinup.build
# The following sets RESUBMIT to 30 times in env_run.xml (you could also use an editor)
# The following sets STOP_DATE,STOP_N and STOP_OPTION to Jan/1/1001, 20, "nyears" in env_run.xml (you could also use an editor)
> ./xmlchange RESUBMIT=20,STOP_N=50,STOP_OPTION=nyears,STOP_DATE=10010101
# Now run normally
> ./BGC_spinup.submit

Note: This same procedure works for CLM4.5-CN as well, you can typically shorten the spinup time from 1000 years to 600 though.

Afterwards save the last restart file from this simulation to use in the next step.

Final spinup for CLM4.5-BGC

Next save the last restart file from this step and use it as the "finidat" file to use for one more spinup for at least 200+ years in normal mode. So do the following:

Example 4-4. Example Final CLMBGC Spinup Simulation for CLM4.5-BGC

> cd scripts
> ./create_newcase -case BGC_finalspinup -res f19_g16 -compset I1850CRUCLM45BGC -mach yellowstone_intel
> cd BGC_finalspinup
# Now, Copy the last CLM restart file from the earlier case into your run directory
> cp /ptmp/$LOGIN/archive/BGC_spinup/rest/BGC_spinup.clm*.r*.1002-01-01-00000.nc \
/glade/scratch/$LOGIN/CN_finalspinup
# Set the runtype to startup
> ./xmlchange RUN_TYPE=startup
# And copy the rpointer files for datm and drv from the earlier case
> cp /glade/scratch/$LOGIN/archive/BGC_spinup/rest/rpointer.atm /ptmp/$LOGIN/CN_finalspinup
> cp /glade/scratch/$LOGIN/archive/BGC_spinup/rest/rpointer.drv /ptmp/$LOGIN/CN_finalspinup
# Set the finidat file to the last restart file saved in previous step
> echo ' finidat = "BGC_spinup.clm2.r.1002-01-01-00000.nc"' > user_nl_clm
# Now setup
> ./cesm_setup
> Now build
> ./BGC_finalspinup.build
# The following sets RESUBMIT to 4 times in env_run.xml (you could also use an editor)
# The following sets STOP_N and STOP_OPTION to 50 and "nyears" in env_run.xml (you could also use an editor)
> ./xmlchange RESUBMIT=4,STOP_OPTION=nyears,STOP_N=50
> Now run as normal
> ./BGC_finalspinup.submit

To assess if the model is spunup plot trends of CLMBGC variables of interest. If you see a trend, you may need to run the simulation longer. Finally save the restart file from the end of this simulation to use as an "finidat" file for future simulations.

Note: This same final spinup procedure works for CLM4.5-CN as well, you can typically shorten the spinup time from 200 years to 50 though.

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