Merge pull request #1 from NGEET/master

update my fork with master

.gitattributes

@@ -0,0 +1,28 @@
+# -----------------------------------------------------------------------------------------------------
+# Repo-wide git configuration file
+#
+# This file overrides the configurations specified below for all git users that have cloned this repo.
+# This is primarily being implemented to allow users to develop code with any operating system (OS)
+# preferred and mitigates potential problems with end of line (eol) character differences.
+# -----------------------------------------------------------------------------------------------------
+
+## Set the default end of line behavior (i.e. normalization to `lf` upon commit) for all files git recognizes as text
+* text=auto
+
+# Note that the above *only* applies to newly commited files.  If the file previously existed with a `crlf` end of file
+# and was checked out to local, then git will not change the eol character during check-in (i.e. commit).  For 
+# windows users they will see a warning like this:
+# warning: CRLF will be replaced by LF in functional_unit_testing/allometry/drive_allomtests.py.
+# The file will have its original line endings in your working directory
+
+## Explicitly declare to git which files should be normalized (i.e. treated as text files)
+*.cdl text
+*.F90 text
+*.F90_in text
+*.py text
+*.sh text
+*.txt text
+*.xml text
+
+## Declare to git which file types are binary files and should not have end of line modified
+*.mod binary

.gitignore

@@ -48,4 +48,6 @@ Thumbs.db
 
 
 # Old Files
-*~
+*~
+# Editor specific setting files
+*.vscode

CONTRIBUTING.md

@@ -21,6 +21,10 @@ Those who wish to contribute code to FATES must have those changes integrated th
 * It is best to create an issue to describe the work you are undertaking prior to starting.  This helps the community sync with your efforts, prevents duplication of efforts, and science is not done in a vaccuum!
 * Expect peers to interact, help, discuss and eventually approve your submission (pull-request)
 
+## Joining Discussions and Meetings
+
+In addition to the github discussions, we hold a roughly biweekly call, which covers both scientific and technical issues related to FATES. We use a google group to organize, schedule, and discuss these calls.  Emails to the list are moderated and we try to be pretty ruthless about preventing anything other than this topic from appearing on it.  To join, apply to the group here: https://groups.google.com/forum/#!forum/fates_model
+
 ## Things to Remember
 
 * Make commits in logical units (i.e. group changes)

LICENSE.txt

@@ -1,6 +1,6 @@
 Functionally Assembled Terrestrial Ecosystem Simulator (“FATES”)
 
-Copyright (c) 2016-2018, The Regents of the University of California, through Lawrence
+Copyright (c) 2016-2020, The Regents of the University of California, through Lawrence
 Berkeley National Laboratory, University Corporation for Atmospheric Research, Los Alamos
 National Security, LLC (LANS), as operator of Los Alamos National Laboratory (LANL), and
 President and Fellows of Harvard College. All rights reserved.

biogeochem/EDCanopyStructureMod.F90

@@ -14,10 +14,12 @@ module EDCanopyStructureMod
   use EDPftvarcon           , only : EDPftvarcon_inst
   use FatesAllometryMod     , only : carea_allom
   use EDCohortDynamicsMod   , only : copy_cohort, terminate_cohorts, fuse_cohorts
-  use EDCohortDynamicsMod   , only : InitPRTCohort
+  use EDCohortDynamicsMod   , only : InitPRTObject
+  use EDCohortDynamicsMod   , only : InitPRTBoundaryConditions
+  use EDCohortDynamicsMod   , only : SendCohortToLitter
   use FatesAllometryMod     , only : tree_lai
   use FatesAllometryMod     , only : tree_sai
-  use EDtypesMod            , only : ed_site_type, ed_patch_type, ed_cohort_type, ncwd
+  use EDtypesMod            , only : ed_site_type, ed_patch_type, ed_cohort_type
   use EDTypesMod            , only : nclmax
   use EDTypesMod            , only : nlevleaf
   use EDtypesMod            , only : AREA
@@ -117,9 +119,7 @@ subroutine canopy_structure( currentSite , bc_in )
       ! !USES:
 
       use EDParamsMod, only : ED_val_comp_excln
-      use EDtypesMod , only : ncwd
       use EDTypesMod , only : min_patch_area
-      use EDTypesMod , only : val_check_ed_vars
       use FatesInterfaceMod, only : bc_in_type
       !
       ! !ARGUMENTS    
@@ -193,7 +193,7 @@ subroutine canopy_structure( currentSite , bc_in )
 
             ! Its possible that before we even enter this scheme
             ! some cohort numbers are very low.  Terminate them.
-            call terminate_cohorts(currentSite, currentPatch, 1)
+            call terminate_cohorts(currentSite, currentPatch, 1, 12)
 
             ! Calculate how many layers we have in this canopy
             ! This also checks the understory to see if its crown 
@@ -206,12 +206,12 @@ subroutine canopy_structure( currentSite , bc_in )
 
             ! After demotions, we may then again have cohorts that are very very
             ! very sparse, remove them
-            call terminate_cohorts(currentSite, currentPatch, 1)
+            call terminate_cohorts(currentSite, currentPatch, 1,13)
 
             call fuse_cohorts(currentSite, currentPatch, bc_in)
 
             ! Remove cohorts for various other reasons
-            call terminate_cohorts(currentSite, currentPatch, 2)
+            call terminate_cohorts(currentSite, currentPatch, 2,13)
 
 
             ! ---------------------------------------------------------------------------------------
@@ -230,12 +230,12 @@ subroutine canopy_structure( currentSite , bc_in )
                end do
 
                ! Remove cohorts that are incredibly sparse
-               call terminate_cohorts(currentSite, currentPatch, 1)
+               call terminate_cohorts(currentSite, currentPatch, 1,14)
 
                call fuse_cohorts(currentSite, currentPatch, bc_in)
 
                ! Remove cohorts for various other reasons
-               call terminate_cohorts(currentSite, currentPatch, 2)
+               call terminate_cohorts(currentSite, currentPatch, 2,14)
 
             end if
 
@@ -331,7 +331,6 @@ end subroutine canopy_structure
    subroutine DemoteFromLayer(currentSite,currentPatch,i_lyr)
 
       use EDParamsMod, only : ED_val_comp_excln
-      use EDtypesMod , only : ncwd
       use SFParamsMod, only : SF_val_CWD_frac
 
       ! !ARGUMENTS
@@ -658,11 +657,17 @@ subroutine DemoteFromLayer(currentSite,currentPatch,i_lyr)
 
                   allocate(copyc)
 
-                  call InitPRTCohort(copyc)
+                  ! Initialize the PARTEH object and point to the
+                  ! correct boundary condition fields
+                  copyc%prt => null()
+                  call InitPRTObject(copyc%prt)
+                  call InitPRTBoundaryConditions(copyc)
+
                   if( hlm_use_planthydro.eq.itrue ) then
                      call InitHydrCohort(currentSite,copyc)
                   endif
-		  call copy_cohort(currentCohort, copyc)
+
+                  call copy_cohort(currentCohort, copyc)
 
                   newarea = currentCohort%c_area - cc_loss
                   copyc%n = currentCohort%n*newarea/currentCohort%c_area 
@@ -708,50 +713,10 @@ subroutine DemoteFromLayer(currentSite,currentPatch,i_lyr)
 
                if(currentCohort%canopy_layer>nclmax )then 
 
-                  ! put the litter from the terminated cohorts into the fragmenting pools
-                  do i_cwd=1,ncwd
-
-                     currentPatch%CWD_AG(i_cwd)  = currentPatch%CWD_AG(i_cwd) + &
-                          (struct_c + sapw_c ) * &
-                          EDPftvarcon_inst%allom_agb_frac(currentCohort%pft) * &
-                          SF_val_CWD_frac(i_cwd)*currentCohort%n/currentPatch%area  
-
-                     currentPatch%CWD_BG(i_cwd)  = currentPatch%CWD_BG(i_cwd) + &
-                          (struct_c + sapw_c) * & 
-                          (1.0_r8-EDPftvarcon_inst%allom_agb_frac(currentCohort%pft)) * &
-                          SF_val_CWD_frac(i_cwd)*currentCohort%n/currentPatch%area !litter flux per m2.
-
-                  enddo
-
-                  currentPatch%leaf_litter(currentCohort%pft)  = &
-                       currentPatch%leaf_litter(currentCohort%pft) + &
-                       leaf_c * currentCohort%n/currentPatch%area ! leaf litter flux per m2.
-
-                  currentPatch%root_litter(currentCohort%pft)  = &
-                       currentPatch%root_litter(currentCohort%pft) + &
-                       (fnrt_c + store_c) * currentCohort%n/currentPatch%area
-
-                  ! keep track of the above fluxes at the site level as a 
-                  ! CWD/litter input flux (in kg / site-m2 / yr)
-                  do i_cwd=1,ncwd
-                     currentSite%CWD_AG_diagnostic_input_carbonflux(i_cwd) = &
-                          currentSite%CWD_AG_diagnostic_input_carbonflux(i_cwd) &
-                          + currentCohort%n * (struct_c + sapw_c) * & 
-                          SF_val_CWD_frac(i_cwd) * EDPftvarcon_inst%allom_agb_frac(currentCohort%pft) &
-                          * hlm_days_per_year / AREA
-                     currentSite%CWD_BG_diagnostic_input_carbonflux(i_cwd) = &
-                          currentSite%CWD_BG_diagnostic_input_carbonflux(i_cwd) &
-                          + currentCohort%n * (struct_c + sapw_c) * & 
-                          SF_val_CWD_frac(i_cwd) * (1.0_r8 -  &
-                          EDPftvarcon_inst%allom_agb_frac(currentCohort%pft)) * hlm_days_per_year / AREA
-                  enddo
-
-                  currentSite%leaf_litter_diagnostic_input_carbonflux(currentCohort%pft) = &
-                       currentSite%leaf_litter_diagnostic_input_carbonflux(currentCohort%pft) +  &
-                       currentCohort%n * leaf_c * hlm_days_per_year  / AREA
-                  currentSite%root_litter_diagnostic_input_carbonflux(currentCohort%pft) = &
-                       currentSite%root_litter_diagnostic_input_carbonflux(currentCohort%pft) + &
-                       currentCohort%n * (fnrt_c  + store_c) * hlm_days_per_year  / AREA
+                  ! put the litter from the terminated cohorts 
+                  ! straight into the fragmenting pools
+                  call SendCohortToLitter(currentSite,currentPatch, &
+                       currentCohort,currentCohort%n)
 
                   currentCohort%n            = 0.0_r8
                   currentCohort%c_area       = 0.0_r8
@@ -1145,7 +1110,12 @@ subroutine PromoteIntoLayer(currentSite,currentPatch,i_lyr)
 
                      allocate(copyc)
 
-                     call InitPRTCohort(copyc)
+                     ! Initialize the PARTEH object and point to the
+                     ! correct boundary condition fields
+                     copyc%prt => null()
+                     call InitPRTObject(copyc%prt)
+                     call InitPRTBoundaryConditions(copyc)
+
                      if( hlm_use_planthydro.eq.itrue ) then
                         call InitHydrCohort(CurrentSite,copyc)
                      endif
@@ -1287,8 +1257,6 @@ subroutine canopy_summarization( nsites, sites, bc_in )
 
     use FatesInterfaceMod    , only : bc_in_type
     use EDPatchDynamicsMod   , only : set_patchno
-    use FatesAllometryMod    , only : set_root_fraction
-    use FatesAllometryMod    , only : i_hydro_rootprof_context
     use FatesSizeAgeTypeIndicesMod, only : sizetype_class_index
     use EDtypesMod           , only : area
     use EDPftvarcon          , only : EDPftvarcon_inst
@@ -1330,18 +1298,6 @@ subroutine canopy_summarization( nsites, sites, bc_in )
 
        do while(associated(currentPatch))
 
-          ! Calculate rooting depth fractions for the patch x pft
-          ! Note that we are calling for the root fractions in the hydrologic context.
-          ! See explanation in FatesAllometryMod.  In other locations, this
-          ! function is called to return the profile of biomass as used for litter
-
-          do ft = 1, numpft
-             call set_root_fraction(currentPatch%rootfr_ft(ft,1:bc_in(s)%nlevsoil), ft, &
-                  bc_in(s)%zi_sisl,lowerb=lbound(bc_in(s)%zi_sisl,1), &
-                  icontext=i_hydro_rootprof_context)
-          end do
-
-
           !zero cohort-summed variables. 
           currentPatch%total_canopy_area = 0.0_r8
           currentPatch%total_tree_area = 0.0_r8