Merge pull request #2 from glemieux/cross_grid_glemieux

Update to `sci.1.57.2_api.23.0.0` and add distance utilities

README.md

@@ -1,18 +1,23 @@
-# FATES
+
+![FATES_logo](.github/images/logo_fates_small.png)
 ------------------------------
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3825473.svg)](https://doi.org/10.5281/zenodo.3825473)
 
 This repository holds the Functionally Assembled Terrestrial Ecosystem Simulator (FATES).  FATES is a numerical terrestrial ecosystem model. Its development and support is primarily supported by the Department of Energy's Office of Science, through the Next Generation Ecosystem Experiment - Tropics ([NGEE-T](https://ngee-tropics.lbl.gov/)) project.
 
-For more information on the FATES model, see our [wiki](https://github.com/NGEET/fates/wiki) and [technical documentation](https://fates-docs.readthedocs.io/en/latest/index.html).
+For more information on the FATES model, see our [User's Guide](https://fates-users-guide.readthedocs.io/en/latest/) and [technical documentation](https://fates-docs.readthedocs.io/en/latest/index.html).
 
 
 ## Important Guides:
 ------------------------------
 
+[User's Guide](https://fates-users-guide.readthedocs.io/en/latest/)
+
 [How to Contribute](https://github.com/NGEET/fates/blob/master/CONTRIBUTING.md)
 
-[List of Unsupported or Broken Features](https://github.com/NGEET/fates/wiki/Current-Unsupported-or-Broken-Features)
+[Table of FATES and Host Land Model API compatability](https://fates-users-guide.readthedocs.io/en/latest/user/Table-of-FATES-API-and-HLM-STATUS.html)
+
+[List of Unsupported or Broken Features](https://fates-users-guide.readthedocs.io/en/latest/user/Current-Unsupported-or-Broken-Features.html)
 
 [Code of Conduct](https://github.com/NGEET/fates/blob/master/CODE_OF_CONDUCT.md)
 
@@ -27,8 +32,6 @@ FATES has support to be run via the Energy Exascale Earth System Model (E3SM), t
 https://github.com/E3SM-Project/E3SM
 
 https://github.com/ESCOMP/cesm
-https://github.com/ESCOMP/ctsm
-
 
 ## Important Note About Host-Models and Compatible Branches:
 ------------------------------------------------------------

biogeochem/EDLoggingMortalityMod.F90

@@ -40,6 +40,7 @@ module EDLoggingMortalityMod
    use EDParamsMod       , only : logging_mechanical_frac 
    use EDParamsMod       , only : logging_coll_under_frac 
    use EDParamsMod       , only : logging_dbhmax_infra
+   use FatesInterfaceTypesMod , only : bc_in_type
    use FatesInterfaceTypesMod , only : hlm_current_year
    use FatesInterfaceTypesMod , only : hlm_current_month
    use FatesInterfaceTypesMod , only : hlm_current_day
@@ -72,7 +73,8 @@ module EDLoggingMortalityMod
    logical, protected :: logging_time   ! If true, logging should be 
                                         ! performed during the current time-step
 
-
+   logical, parameter :: debug = .false.
+
    ! harvest litter localization specifies how much of the litter from a falling
    ! tree lands within the newly generated patch, and how much lands outside of 
    ! the new patch, and thus in the original patch.  By setting this to zero,
@@ -257,7 +259,7 @@ subroutine LoggingMortality_frac( pft_i, dbh, canopy_layer, lmort_direct, &
 
          ! transfer of area to secondary land is based on overall area affected, not just logged crown area
          ! l_degrad accounts for the affected area between logged crowns
-         if(int(prt_params%woody(pft_i)) == 1)then ! only set logging rates for trees
+         if(prt_params%woody(pft_i) == itrue)then ! only set logging rates for trees
 
             ! direct logging rates, based on dbh min and max criteria
             if (dbh >= logging_dbhmin .and. .not. &
@@ -394,7 +396,7 @@ end subroutine get_harvest_rate_area
 
    ! ============================================================================
 
-   subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site_areadis)
+   subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site_areadis, bc_in)
 
       ! -------------------------------------------------------------------------------------------
       !
@@ -440,6 +442,8 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
       type(ed_patch_type) , intent(inout), target  :: currentPatch
       type(ed_patch_type) , intent(inout), target  :: newPatch
       real(r8)            , intent(in)             :: patch_site_areadis
+      type(bc_in_type)    , intent(in)             :: bc_in
+
 
       !LOCAL VARIABLES:
       type(ed_cohort_type), pointer      :: currentCohort
@@ -539,7 +543,7 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
                ! plants that were impacted. Thus, no direct dead can occur
                ! here, and indirect are impacts.
 
-               if(int(prt_params%woody(pft)) == itrue) then
+               if(prt_params%woody(pft) == itrue) then
                   direct_dead   = 0.0_r8
                   indirect_dead = logging_coll_under_frac * &
                        (1._r8-currentPatch%fract_ldist_not_harvested) * currentCohort%n * &
@@ -567,7 +571,9 @@ subroutine logging_litter_fluxes(currentSite, currentPatch, newPatch, patch_site
             ! derived from the current patch, so we need to multiply by patch_areadis/np%area
             ! ----------------------------------------------------------------------------------------
 
-            call set_root_fraction(currentSite%rootfrac_scr, pft, currentSite%zi_soil)
+            call set_root_fraction(currentSite%rootfrac_scr, pft, &
+                 currentSite%zi_soil, &
+                 bc_in%max_rooting_depth_index_col)
 
             ag_wood = (direct_dead+indirect_dead) * (struct_m + sapw_m ) * &
                   prt_params%allom_agb_frac(currentCohort%pft)

biogeochem/EDMortalityFunctionsMod.F90

@@ -6,6 +6,8 @@ module EDMortalityFunctionsMod
 
    use FatesConstantsMod     , only : r8 => fates_r8
    use FatesGlobals          , only : fates_log
+   use FatesGlobals          , only : endrun => fates_endrun
+   use FatesGlobals          , only : fates_log
    use EDPftvarcon           , only : EDPftvarcon_inst
    use EDTypesMod            , only : ed_cohort_type
    use EDTypesMod            , only : ed_site_type
@@ -19,14 +21,18 @@ module EDMortalityFunctionsMod
    use FatesInterfaceTypesMod     , only : hlm_use_planthydro
    use EDLoggingMortalityMod , only : LoggingMortality_frac
    use EDParamsMod           , only : fates_mortality_disturbance_fraction
-   use FatesInterfaceTypesMod     , only : bc_in_type
 
    use PRTGenericMod,          only : all_carbon_elements
    use PRTGenericMod,          only : store_organ
-
+   use shr_log_mod           , only : errMsg => shr_log_errMsg
+
    implicit none
    private
 
+
+   logical, parameter :: debug = .false.
+   character(len=*), parameter, private :: sourcefile = &
+        __FILE__
 
    public :: mortality_rates
    public :: Mortality_Derivative
@@ -62,7 +68,6 @@ subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort,smort,asmor
     real(r8),intent(out) :: smort  ! size dependent senescence term
     real(r8),intent(out) :: asmort ! age dependent senescence term 
 
-    integer  :: ifp
     real(r8) :: frac  ! relativised stored carbohydrate
     real(r8) :: leaf_c_target      ! target leaf biomass kgC
     real(r8) :: store_c
@@ -165,6 +170,7 @@ subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort,smort,asmor
     else
        write(fates_log(),*) 'dbh problem in mortality_rates', &
             cohort_in%dbh,cohort_in%pft,cohort_in%n,cohort_in%canopy_layer
+       call endrun(msg=errMsg(sourcefile, __LINE__))
     endif
     !-------------------------------------------------------------------------------- 
     !    Mortality due to cold and freezing stress (frmort), based on ED2 and:           
@@ -173,8 +179,8 @@ subroutine mortality_rates( cohort_in,bc_in,cmort,hmort,bmort,frmort,smort,asmor
     !           Eastern US carbon sink.  Glob. Change Biol., 12, 2370-2390,              
     !           doi: 10.1111/j.1365-2486.2006.01254.x                                    
 
-    ifp = cohort_in%patchptr%patchno
-    temp_in_C = bc_in%t_veg24_pa(ifp) - tfrz
+    temp_in_C = cohort_in%patchptr%tveg24%GetMean() - tfrz
+
     temp_dep_fraction  = max(0.0_r8, min(1.0_r8, 1.0_r8 - (temp_in_C - &
                          EDPftvarcon_inst%freezetol(cohort_in%pft))/frost_mort_buffer) )
     frmort    = EDPftvarcon_inst%mort_scalar_coldstress(cohort_in%pft) * temp_dep_fraction