Changes between Version 18 and Version 19 of Documentation/UserGuide/FLUXNETValidation

Timestamp:

2019-12-20T17:06:16+01:00 (3 years ago)

Author:

mmcgrath

Comment:

Documentation for running FLUXNET comparisions with a clean SVN install and CAN

Documentation/UserGuide/FLUXNETValidation

@@ -183 +183 @@
 SECHIBA_reset_time=y
 SPLIT_DT=1
-SPINUP_PERIOD='${TIME_YEAR}'
 SPINUP_ANALYTIC=y
 NBUFF=0
@@ -228 +227 @@
 }}}
 
+Note that we did not copy SPINUP_PERIOD.  This is because it uses a variable that is evaluated during the execution of Job_ENSEMBLE, and therefore we let the script copy the value onto the end of the run.def.
+
 Note that many of the Nitrogen variables above were also in PARAM/orchidee.def!  Remove the following from PARAM/orchidee.def:  
 
@@ -263 +264 @@
 ATM_CO2 = _AUTO_: DEFAULT = 350.
 }}}
+
+For FLUXNET jobs, we generally impose vegetation at the site.  While this is set in fluxnet.card in the UserChoices, this doesn't seem to get passed to the run.def in the spinup unless we also place it in the run.def.
+
+{{{
+IMPOSE_VEG=y
+}}}
+
 
 The addition of the orchidee.def and orchidee_pft.def required adding them to the [ParametersFiles] in SPINUP/SUBJOBS/OOL_SEC_STO/COMP/orchidee_ol.card, so that libIGCM copies the new files to the PARAM directory of the running code.  It also required changes to the driver, to select from the correct orchidee_pft.def file.  To fix this, I simply copied OOL_SEC_STO_FG2/COMP/orchidee_ol.* to SPINUP/SUBJOB/OOL_SEC_STO/COMP/.  
@@ -285 +293 @@
 Make sure this matches with the fluxnet.card that you copied at the beginning!
 
-The script expects any variables in the NameSitesParam keyword of fluxnet.card to be present in PARAM/run.def.  SECHIBA_VEGMAX is currently in PARAM/orchidee_pft.def_*.  So, depending on what you have present in SPINUP/SUBJOB/OOL_SEC_STO/COMP/orchidee_ol.card for DefSuffix, you need to move the following lines to PARAM/run.def from PARAM/orchidee_pft.def_DefSuffix, removing the lines in PARAM/orchidee_pft.def_DefSuffix.  The the specific case of 28 PFTs that we are using here:
+The script adds any variables in the NameSitesParam keyword of fluxnet.card in the PARAM/run.def.  SECHIBA_VEGMAX is currently in PARAM/orchidee_pft.def_*.  So, depending on what you have present in SPINUP/SUBJOB/OOL_SEC_STO/COMP/orchidee_ol.card for DefSuffix, you need to remove the following lines in PARAM/orchidee_pft.def_DefSuffix, and the Job_ENSEMBLE script will add them to the end of the run.def as it copies it around.  The specific case of 28 PFTs that we are using here:
 
 {{{
 emacs PARAM/orchidee_pft.def_28pft.1ac &
-emacs PARAM/run.def
-(move the following lines from orchidee_pft to run.def...location in the run.def should not matter)
+
+(remove the following)
 SECHIBA_VEGMAX__01=0.0357142857143
 SECHIBA_VEGMAX__02=0.0357142857143
@@ -354 +362 @@
 
 CRUP=n
-ok_stomate=y
 ok_newhydrol=y
 impose_veg=y
@@ -362 +369 @@
 }}}
 
-Some additional variables which need to be in run.def and not orchidee.def (anything with _AUTO_ or _AUTOBLOCKER_ after it):
+Some additional variables which need to be in run.def and not orchidee.def (anything with _AUTO_ or _AUTOBLOCKER_ after it, since the .card files look to run.def to change these values, and they don't look into the included files):
 
 {{{
@@ -370 +377 @@
 (make sure the following are in run.def and not in orchidee.def)
 
-STOMATE_IMPOSE_CN = _AUTO_
 SECHIBA_restart_in = _AUTOBLOCKER_
 STOMATE_RESTART_FILEIN = _AUTOBLOCKER_
@@ -383 +389 @@
 STOMATE_OK_STOMATE = _AUTOBLOCKER_ 
 NINPUT_UPDATE = _AUTO_
+STOMATE_IMPOSE_CN = _AUTO_
+
+(remove the following from orchidee.def)
+impose_veg=n
+
+(make sure the following to PARAM/run.def.  Also make sure it is all capitals!)
+IMPOSE_VEG=y
 
 (now copy the files)
 cp PARAM/*def ../SPINUP/SUBJOB/OOL_SEC_STO/PARAM/
 }}}
-Notice that SPINUP_PERIOD and SPINUP_ANALYTIC had to be deleted from orchidee.def, but we already had them in run.def since we copied them from fluxnet.card.
-
-Note that we can not use the analytical spinup at the present.  In order to use the analytical spinup, we need to make sure CyclicBegin and CyclicEnd appear in the ${}/STOI/config.card, as ${}/STOI/COMP/stomate.card checks for these values.  I have not yet figured out how to do that.
-
-Some variables appear in fluxnet.card, but they are also special variables having an AUTO value in orchidee.def (that we moved to param.def).  Therefore, remove the following lines from FLUXNET/fluxnet.card and PARAM/run.def (if they exist).  We remove the _AUTO_ value of SPINUP_PERIOD since we attempt to calculate that in an automatic way using
-a different variable in Job_ENSEMBLE, as opposed to in SPINUP/COMP/spinup.driver.
+
+Note that we can not use the analytical spinup at the present (the value is changed in the next step).  In order to use the analytical spinup, we need to make sure CyclicBegin and CyclicEnd appear in the ${}/STOI/config.card, as ${}/STOI/COMP/stomate.card checks for these values.  I have not yet figured out how to do that.
+
+Some variables appear in fluxnet.card, but they are also special variables having an AUTO value in orchidee.def (that we moved to param.def).  Therefore, remove the following lines from FLUXNET/fluxnet.card and PARAM/run.def (if they exist).  We remove the _AUTO_ value of SPINUP_PERIOD since we attempt to calculate that in an automatic way using a different variable in Job_ENSEMBLE, as opposed to in SPINUP/COMP/spinup.driver.
 {{{
 NINPUT_UPDATE=0Y