fill in information from pervious repo

get.rst

@@ -12,14 +12,54 @@ NordicESMhub maintains a CTSM repository with all the configuration files for ru
 
 If you machine is not in the list and would like we support it, please contact us.
 
+How to get CTSM
+++++++++++++++++
+CLONE from GitHub (run only first time, or to update clm/ctsm version), in home folder
+
+::
+
+    git clone -b release-clm5.0 https://github.com/NordicESMhub/ctsm.git
+
+LOAD necessary modules in .bashrc (only first time)
+
+::
+
+    emacs .bashrc & 
+
+On abel, add these three modules 
+
+::
+
+    module load python2/2.7.10
+    module load cesm
+    module load git
+		        
+save and close
+
+CHECK loaded modules
+
+::
+
+    module list
+
+
 How to get a specific branch
 +++++++++++++++++++++++++++++
 
+
 Which branch do I run?
 ++++++++++++++++++++++
 
 
 Get CTSM for modifying the source code
 -----------------------------------------
 
+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
+
 When you need to do your own development.

run.rst

@@ -1,22 +1,116 @@
 Run CTSM 
 ========
 
+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
+
 Run your very first CTSM case
 ------------------------------
 
-This should be example without fates
+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
+        
+
+navigate to ~/ctsm/cime/scripts/
+
+::
+
+   ./create_newcase --case ~/cases/I2000Clm50BgcCruGs  --compset I2000Clm50BgcCruGs   --res f19_g17 --machine abel --run-unsupported --project geofag
+
+
+navigate to ~/cases/I2000Clm50BgcCruGs
+
+
+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) setup case
+~~~~~~~~~~~~~~
+
+::
+
+    ./case.setup  #(--reset)
+        
+4) edit user_nl_clm   
+~~~~~~~~~~~~~~~~~~~~
+
+add this below
+
+::
+
+	hist_mfilt=5 #(number of output files)
+	hist_nhtfrq=-24 #(means daily outputs)
+
+5) case build
+~~~~~~~~~~~~~~
+
+::    
+
+    (./case.build --clean)
+    ./case.build
+
+6) run case
+~~~~~~~~~~~~~~
+
+::
+
+    ./case.submit 
+
+	
 Run fates
 -----------
 
+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)
+
+::
+
+   ./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
+    
 Run a single cell case  
 -----------------------
 
 Out of the box
 +++++++++++++++
 
+::
+
+  ./create_newcase --case ~/cases/brazil_I1PtClm50SpGs --compset I1PtClm50SpGs  --res  1x1_brazil --machine abel --run-unsupported --project geofag
+
 Customized
 +++++++++++
 
+::
+
+   ./create_newcase --case ~/cases/brazil_I2000Clm50BgcCruGs --compset I2000Clm50BgcCruGs  --res  1x1_brazil --machine abel --run-unsupported --project geofag
+
 - Step-1: Tutorial_creating_surface_data_for_single_point.md
 - Step-2: For atmospheric forcing README_Single point (own atm forcing and surface data) (include scripts)

setup.rst

@@ -27,8 +27,17 @@ This will return something like:
 In the example above, two projects can be used (geofag and nn1000k). Then make sure you choose the right project when running CTSM.
 
 
+
 Inputdata
 ----------
 
+(only first time)
+
+::
+
+    cd ~/ctsm/cime/scripts
+    ./link_dirtree $CESM_DATA /work/users/$USER/inputdata
+
+
 Machines
 ---------