remove doc that is now in rst files

README.md

@@ -1,115 +1,8 @@
-# ctsm-dev
-dev version of Community Terrestrial Systems Model (includes the Community Land Model of CESM)
+# ctsm-docs
 
-## out of the box run on abel
-CLONE from GitHub (run only first time, or to update clm/ctsm version), in home folder
+Local documentation for the Community Terrestrial Systems Model (includes the Community Land Model of CESM).
 
-    git clone -b release-clm5.0 https://github.com/NordicESMhub/ctsm.git
+Look at https://ctsm-docs.readthedocs.io/en/latest/
 
-LOAD necessary modules in .bashrc (only first time)
-
-    emacs .bashrc & 
-add these three modules 
-
-    module load python2/2.7.10
-    module load cesm
-    module load git
-
-save and close
-
-CHECK loaded modules
-
-    module list
-
-Create your own branches before continuing, in ~/ctsm AND in ~ctsm/cime. Do this for FATES or any other modules in addition.
-
-    git branch <username_clm5.0.12>   # useful for remembering version, name according to function e.g. username_cime_clm5.0.12 and username_fates_clm5.0.12
-    git checkout  <username_clm5.0.12>
-    git branch # to verify that you are on the branch you just created
-
-
-LOAD externals of CTSM (FATES and so on; only necessary first time), in folder ~/ctsm. If you are updating FATES go here first: (https://github.com/NordicESMhub/ctsm-dev/blob/master/Updating_FATES.md)
-
-    ./manage_externals/checkout_externals
-
-NB! Fates is not automatically checked out with the latest version (as it is still under development), and this has to be done manually. 
-Follow https://github.com/NordicESMhub/ctsm-dev/blob/master/Updating_FATES (based on https://github.uio.no/huit/clm5.0_notes/issues/26 and https://github.com/ESCOMP/ctsm/wiki/Protocols-on-updating-FATES-within-CTSM)
-
-
-### Set inputdata for all your cases
-(only first time)
-
-    cd ~/ctsm/cime/scripts
-    ./link_dirtree $CESM_DATA /work/users/$USER/inputdata
-
-### Set your Notur project account
-
-
-NB! this example is connected to project nn2806k (for your own project, change the project code. To see available projects and resources, use cost -p):
-
-     export CESM_ACCOUNT=nn2806k
-
-### create new case
-
-navigate to ~/ctsm/cime/scripts/
-
-we try two new cases
-
-./query_config --compsets (to see available compsets --> choose I... for clm compsets)
-./query_config --grids (to see available resolutions)
-
-1) global (fates must be updated before use)
-
-        ./create_newcase --case ../../../ctsm_cases/fates_f19_g17 --compset 2000_DATM%GSWP3v1_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV --res f19_g17 --machine abel --run-unsupported --project $CESM_ACCOUNT
-
-or other example without fates
-
-        ./create_newcase --case ~/cases/I2000Clm50BgcCruGs  --compset I2000Clm50BgcCruGs   --res f19_g17 --machine abel --run-unsupported --project geofag
-
-
-2) single cell (out of the box for brazil)
-
-        ./create_newcase --case ~/cases/brazil_I1PtClm50SpGs --compset I1PtClm50SpGs  --res  1x1_brazil --machine abel --run-unsupported --project geofag
-
-or other compset
-
-         ./create_newcase --case ~/cases/brazil_I2000Clm50BgcCruGs --compset I2000Clm50BgcCruGs  --res  1x1_brazil --machine abel --run-unsupported --project geofag
-
-
-
-### set up new case
-navigate to the case directory, e.g. ~/ctsm_cases/fates_f19_g17
-
-1) check the configuration
-
-./xmlquery --l #(--l list --f file) 
-
-eg 
-
-        ./xmlquery STOP_OPTION
-2) Change configuration
-
-        ./xmlchange STOP_OPTION=ndays #(nyears, nmonths)
-        ./xmlchange STOP_N=5 #(then 5 days)
-        ./xmlchange NTASKS=1 #(number of CPU's, can be increased if excitation error)
-or edit the xml files is another way to change these parameters
-
-3) 
-
-           ./case.setup  #(--reset)
-        
-4) edit user_nl_clm   
-add this below
-
-        hist_mfilt=5 #(number of output files)
-        hist_nhtfrq=-24 #(means daily outputs)
-
-### case build
-
-    (./case.build --clean)
-    ./case.build
-### run case
-
-    ./case.submit