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Moved contents of ed_driver to the clm_fates interface
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Merge branch 'rgknox-eddriver-clean'

ed_driver performed a variety of operations. Along with calling the
main ED dynamics routines, it also performed timing calculations and
the mapping and prepping of FATES/ED state variables into CLM
compliant formats for boundary conditions and IO (vi
clm_ed_inst%ed_clm_link). These commits migrate the latter functions
to live in the clm_fates interface, where CLM calls are appropriate
and the mapping functions and calls are supposed to live.

changes were also added to the udata% timing structure, which was
updated in ed_driver. Two notable changes are the migration of the
n_sub global to be included with the udata%, and removing
udata%cohort_index from regulating the cohort_fusion process. We have
found that udata%cohort_index is not threadsafe (along with the rest
of that structure), and an alternative means using
.not.associated(currentcohort, nextcohort) was implemented instead to
avoid self fusion.

Note: These changes were also built off of PR #59, if those changes
aren't up to snuff, this branch needs to update first.

Fixes: n/a

User interface changes?: No

Code review: rgknox

Test suite: ed - lawrencium-lr2 intel; yellowstone gnu, intel, pgi
Test baseline: 1aaba89
Test namelist changes: none
Test answer changes: b4b

Test summary: pass except for expected fails - #14 f19 f09 restart,
and #43 gnu f10 restart
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@bandre-ucar
bandre-ucar committed May 20, 2016
2 parents 1aaba89 + dc7a6fb commit 94118a5
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Showing 6 changed files with 100 additions and 117 deletions.
21 changes: 13 additions & 8 deletions components/clm/src/ED/biogeochem/EDCohortDynamicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -68,8 +68,8 @@ subroutine create_cohort(patchptr, pft, nn, hite, dbh, &
!----------------------------------------------------------------------

allocate(new_cohort)
udata%cohort_number = udata%cohort_number + 1 !give each cohort a unique number for checking cohort fusing routine.
udata%cohort_number = udata%cohort_number + 1 !give each cohort a unique number for checking cohort fusing routine.

call nan_cohort(new_cohort) ! Make everything in the cohort not-a-number
call zero_cohort(new_cohort) ! Zero things that need to be zeroed.

Expand Down Expand Up @@ -613,7 +613,6 @@ subroutine fuse_cohorts(patchptr)
iterate = 1
fusion_took_place = 0
currentPatch => patchptr
! maxcohorts = currentPatch%NCL_p * numCohortsPerPatch
maxcohorts = numCohortsPerPatch

!---------------------------------------------------------------------!
Expand All @@ -624,8 +623,13 @@ subroutine fuse_cohorts(patchptr)

currentCohort => currentPatch%tallest

!CHANGED FROM C VERSION loop from tallest to smallest, fusing if they are similar
do while (currentCohort%indexnumber /= currentPatch%shortest%indexnumber)
! The following logic continues the loop while the current cohort is not the shortest cohort
! if they point to the same target (ie equivalence), then the loop ends.
! This loop is different than the simple "continue while associated" loop in that
! it omits the last cohort (because it has already been compared by that point)

do while ( .not.associated(currentCohort,currentPatch%shortest) )

nextc => currentPatch%tallest

do while (associated(nextc))
Expand All @@ -636,7 +640,8 @@ subroutine fuse_cohorts(patchptr)

if (diff < dynamic_fusion_tolerance) then

if (currentCohort%indexnumber /= nextc%indexnumber) then
! Don't fuse a cohort with itself!
if (.not.associated(currentCohort,nextc) ) then

if (currentCohort%pft == nextc%pft) then

Expand Down Expand Up @@ -982,8 +987,8 @@ subroutine copy_cohort( currentCohort,copyc )
n => copyc

udata%cohort_number = udata%cohort_number + 1
n%indexnumber = udata%cohort_number

n%indexnumber = udata%cohort_number
! VEGETATION STRUCTURE
n%pft = o%pft
n%n = o%n
Expand Down
12 changes: 6 additions & 6 deletions components/clm/src/ED/biogeochem/EDPhysiologyMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ module EDPhysiologyMod
use EDCohortDynamicsMod , only : create_cohort, fuse_cohorts, sort_cohorts
use EDPhenologyType , only : ed_phenology_type
use EDTypesMod , only : dg_sf, dinc_ed, external_recruitment
use EDTypesMod , only : ncwd, nlevcan_ed, n_sub, numpft_ed, senes
use EDTypesMod , only : ncwd, nlevcan_ed, numpft_ed, senes
use EDTypesMod , only : ed_site_type, ed_patch_type, ed_cohort_type

implicit none
Expand Down Expand Up @@ -250,7 +250,7 @@ subroutine phenology( currentSite, ed_phenology_inst, temperature_inst, watersta
use EDTypesMod, only : udata
!
! !ARGUMENTS:
type(ed_site_type) , intent(inout), pointer:: currentSite
type(ed_site_type) , intent(inout), target :: currentSite
type(ed_phenology_type) , intent(in) :: ed_phenology_inst
type(temperature_type) , intent(in) :: temperature_inst
type(waterstate_type) , intent(in) :: waterstate_inst
Expand Down Expand Up @@ -504,7 +504,7 @@ subroutine phenology_leafonoff(currentSite)
! !USES:
!
! !ARGUMENTS:
type(ed_site_type), intent(inout), pointer:: currentSite
type(ed_site_type), intent(inout), target :: currentSite
!
! !LOCAL VARIABLES:
type(ed_patch_type) , pointer :: currentPatch
Expand Down Expand Up @@ -771,9 +771,9 @@ subroutine Growth_Derivatives( currentCohort)
! NPP
if ( DEBUG ) write(iulog,*) 'EDphys 716 ',currentCohort%npp_acc

currentCohort%npp = currentCohort%npp_acc * N_SUB !Link to CLM. convert from kgC/indiv/day into kgC/indiv/year
currentCohort%gpp = currentCohort%gpp_acc * N_SUB !Link to CLM. convert from kgC/indiv/day into kgC/indiv/year
currentCohort%resp = currentCohort%resp_acc * N_SUB !Link to CLM. convert from kgC/indiv/day into kgC/indiv/year
currentCohort%npp = currentCohort%npp_acc * udata%n_sub !Link to CLM. convert from kgC/indiv/day into kgC/indiv/year
currentCohort%gpp = currentCohort%gpp_acc * udata%n_sub !Link to CLM. convert from kgC/indiv/day into kgC/indiv/year
currentCohort%resp = currentCohort%resp_acc * udata%n_sub !Link to CLM. convert from kgC/indiv/day into kgC/indiv/year

currentSite%flux_in = currentSite%flux_in + currentCohort%npp_acc * currentCohort%n

Expand Down
97 changes: 10 additions & 87 deletions components/clm/src/ED/main/EDMainMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ module EDMainMod
! ============================================================================

use shr_kind_mod , only : r8 => shr_kind_r8
use spmdMod , only : masterproc

use decompMod , only : bounds_type
use clm_varctl , only : iulog
use atm2lndType , only : atm2lnd_type
Expand All @@ -16,7 +16,7 @@ module EDMainMod
use EDPatchDynamicsMod , only : disturbance_rates, fuse_patches, spawn_patches, terminate_patches
use EDPhysiologyMod , only : canopy_derivs, non_canopy_derivs, phenology, recruitment, trim_canopy
use SFMainMod , only : fire_model
use EDtypesMod , only : ncwd, n_sub, numpft_ed, udata
use EDtypesMod , only : ncwd, numpft_ed, udata
use EDtypesMod , only : ed_site_type, ed_patch_type, ed_cohort_type
use EDPhenologyType , only : ed_phenology_type
use EDCLMLinkMod , only : ed_clm_type
Expand All @@ -26,11 +26,11 @@ module EDMainMod

!
! !PUBLIC MEMBER FUNCTIONS:
public :: ed_driver
public :: ed_ecosystem_dynamics
public :: ed_update_site
!
! !PRIVATE MEMBER FUNCTIONS:
private :: ed_ecosystem_dynamics

private :: ed_integrate_state_variables
private :: ed_total_balance_check

Expand All @@ -41,83 +41,6 @@ module EDMainMod

contains

!-----------------------------------------------------------------------
subroutine ed_driver( bounds, ed_allsites_inst, ed_clm_inst, ed_phenology_inst, &
atm2lnd_inst, soilstate_inst, temperature_inst, waterstate_inst, canopystate_inst)
!
! !DESCRIPTION:
! Main ed model routine containing gridcell loop
!
! !USES:
use clm_time_manager , only : get_days_per_year, get_curr_date
use clm_time_manager , only : get_ref_date, timemgr_datediff
use CanopySTateType , only : canopystate_type
!
! !ARGUMENTS:
type(bounds_type) , intent(in) :: bounds
type(ed_site_type) , intent(inout), target :: ed_allsites_inst( bounds%begg: )
type(ed_clm_type) , intent(inout) :: ed_clm_inst
type(ed_phenology_type) , intent(inout) :: ed_phenology_inst
type(atm2lnd_type) , intent(in) :: atm2lnd_inst
type(soilstate_type) , intent(in) :: soilstate_inst
type(temperature_type) , intent(in) :: temperature_inst
type(waterstate_type) , intent(inout) :: waterstate_inst
type(canopystate_type) , intent(inout) :: canopystate_inst
!
! !LOCAL VARIABLES:
type(ed_site_type), pointer :: currentSite
real(r8) :: dayDiff ! day of run
integer :: dayDiffInt ! integer of day of run
integer :: g ! gridcell
integer :: yr ! year (0, ...)
integer :: mon ! month (1, ..., 12)
integer :: day ! day of month (1, ..., 31)
integer :: sec ! seconds of the day
integer :: ncdate ! current date
integer :: nbdate ! base date (reference date)
!-----------------------------------------------------------------------

call ed_clm_inst%SetValues( bounds, 0._r8 )

! timing statements.
n_sub = get_days_per_year()
udata%deltat = 1.0_r8/n_sub !for working out age of patches in years
if(udata%time_period == 0)then
udata%time_period = n_sub
endif

call get_curr_date(yr, mon, day, sec)
ncdate = yr*10000 + mon*100 + day
call get_ref_date(yr, mon, day, sec)
nbdate = yr*10000 + mon*100 + day

call timemgr_datediff(nbdate, 0, ncdate, sec, dayDiff)

dayDiffInt = floor(dayDiff)
udata%time_period = mod( dayDiffInt , n_sub )

! where most things happen
do g = bounds%begg,bounds%endg
if (ed_allsites_inst(g)%istheresoil) then
currentSite => ed_allsites_inst(g)
call ed_ecosystem_dynamics(currentSite, &
ed_clm_inst, ed_phenology_inst, atm2lnd_inst, &
soilstate_inst, temperature_inst, waterstate_inst)

call ed_update_site( ed_allsites_inst(g))
endif
enddo

! link to CLM structures
call ed_clm_inst%ed_clm_link( bounds, ed_allsites_inst(bounds%begg:bounds%endg), &
ed_phenology_inst, waterstate_inst, canopystate_inst)

if (masterproc) then
write(iulog, *) 'clm: leaving ED model', bounds%begg, bounds%endg, dayDiffInt
end if

end subroutine ed_driver

!-------------------------------------------------------------------------------!
subroutine ed_ecosystem_dynamics(currentSite, &
ed_clm_inst, ed_phenology_inst, atm2lnd_inst, &
Expand All @@ -127,7 +50,7 @@ subroutine ed_ecosystem_dynamics(currentSite, &
! Core of ed model, calling all subsequent vegetation dynamics routines
!
! !ARGUMENTS:
type(ed_site_type) , intent(inout), pointer :: currentSite
type(ed_site_type) , intent(inout), target :: currentSite
type(ed_phenology_type) , intent(in) :: ed_phenology_inst
type(ed_clm_type) , intent(in) :: ed_clm_inst
type(atm2lnd_type) , intent(in) :: atm2lnd_inst
Expand Down Expand Up @@ -221,10 +144,10 @@ subroutine ed_integrate_state_variables(currentSite, soilstate_inst, temperature
! !USES:
!
! !ARGUMENTS:
type(ed_site_type) , intent(in) :: currentSite
type(soilstate_type) , intent(in) :: soilstate_inst
type(temperature_type) , intent(in) :: temperature_inst
type(waterstate_type) , intent(in) :: waterstate_inst
type(ed_site_type) , intent(in) :: currentSite
type(soilstate_type) , intent(in) :: soilstate_inst
type(temperature_type) , intent(in) :: temperature_inst
type(waterstate_type) , intent(in) :: waterstate_inst
!
! !LOCAL VARIABLES:
type(ed_patch_type) , pointer :: currentPatch
Expand Down Expand Up @@ -418,7 +341,7 @@ subroutine ed_update_site( currentSite )
enddo

! FIX(RF,032414). This needs to be monthly, not annual
if((udata%time_period == N_SUB-1))then
if((udata%time_period == udata%n_sub-1))then
write(iulog,*) 'calling trim canopy'
call trim_canopy(currentSite)
endif
Expand Down
4 changes: 0 additions & 4 deletions components/clm/src/ED/main/EDRestVectorMod.F90
View file
Original file line number Diff line number Diff line change
Expand Up @@ -634,7 +634,6 @@ subroutine getVectors( this, bounds, ed_allsites_inst )
! !USES:
use clm_time_manager , only : get_nstep
use EDCLMLinkMod , only : ed_clm_type
use EDInitMod , only : ed_init_sites
use EDMainMod , only : ed_update_site
!
! !ARGUMENTS:
Expand Down Expand Up @@ -662,9 +661,6 @@ subroutine getVectors( this, bounds, ed_allsites_inst )
end if
end do

! call ed_clm_inst%ed_clm_link( bounds, ed_allsites_inst(bounds%begg:bounds%endg), &
! ed_phenology_inst, waterstate_inst, canopystate_inst)

if (this%DEBUG) then
call this%printIoInfoLL ( bounds, ed_allsites_inst(bounds%begg:bounds%endg) )
call this%printDataInfoLL ( bounds, ed_allsites_inst(bounds%begg:bounds%endg) )
Expand Down
8 changes: 5 additions & 3 deletions components/clm/src/ED/main/EDTypesMod.F90
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ module EDTypesMod

! MODEL PARAMETERS
real(r8) :: timestep_secs ! subdaily timestep in seconds (e.g. 1800 or 3600)
integer :: n_sub ! num of substeps in year

real(r8), parameter :: AREA = 10000.0_r8 ! Notional area of simulated forest m2
integer doy

Expand Down Expand Up @@ -438,13 +438,15 @@ module EDTypesMod
!************************************

type userdata
integer :: cohort_number ! Counts up the number of cohorts which have been made.
integer :: cohort_number ! Counts up the number of cohorts which have been made.
integer :: n_sub ! num of substeps in year
real(r8) :: deltat ! fraction of year used for each timestep (1/N_SUB)
integer :: time_period ! Within year timestep (1:N_SUB) day of year
integer :: restart_year ! Which year of simulation are we starting in?
end type userdata

type(userdata), public, target :: udata

type(userdata), public, target :: udata ! THIS WAS NOT THREADSAFE
!-------------------------------------------------------------------------------------!

public :: ed_hist_scpfmaps
Expand Down
75 changes: 66 additions & 9 deletions components/clm/src/utils/clmfates_interfaceMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -45,16 +45,17 @@ module CLMFatesInterfaceMod
use SolarAbsorbedType , only : solarabs_type
use clm_time_manager , only : is_restart
use ncdio_pio , only : file_desc_t

use clm_time_manager , only : get_days_per_year, get_curr_date
use clm_time_manager , only : get_ref_date, timemgr_datediff
use spmdMod , only : masterproc

! Used FATES Modules
use FatesInterfaceMod , only : fates_interface_type
use EDCLMLinkMod , only : ed_clm_type
use EDPhenologyType , only : ed_phenology_type

use EDMainMod , only : ed_driver


use EDTypesMod , only : udata
use EDMainMod , only : ed_ecosystem_dynamics
use EDMainMod , only : ed_update_site

implicit none

Expand Down Expand Up @@ -192,6 +193,19 @@ subroutine dynamics_driv(this, nc, bounds_clump, &
integer , intent(in) :: nc
type(waterstate_type) , intent(inout) :: waterstate_inst
type(canopystate_type) , intent(inout) :: canopystate_inst

! !LOCAL VARIABLES:
real(r8) :: dayDiff ! day of run
integer :: dayDiffInt ! integer of day of run
integer :: g ! gridcell
integer :: yr ! year (0, ...)
integer :: mon ! month (1, ..., 12)
integer :: day ! day of month (1, ..., 31)
integer :: sec ! seconds of the day
integer :: ncdate ! current date
integer :: nbdate ! base date (reference date)
!-----------------------------------------------------------------------


! ---------------------------------------------------------------------------------
! INTERF-TODO: REMOVE ED_DRIVER ARGUMENTS OF CLM STUCTURED TYPES AND
Expand All @@ -204,13 +218,56 @@ subroutine dynamics_driv(this, nc, bounds_clump, &
! this%fates(nc)%fatesbc)
! ---------------------------------------------------------------------------------


call this%fates2hlm_inst%SetValues( bounds_clump, 0._r8 )

! timing statements.
udata%n_sub = get_days_per_year()
udata%deltat = 1.0_r8/dble(udata%n_sub) !for working out age of patches in years
if(udata%time_period == 0)then
udata%time_period = udata%n_sub
endif

call get_curr_date(yr, mon, day, sec)
ncdate = yr*10000 + mon*100 + day
call get_ref_date(yr, mon, day, sec)
nbdate = yr*10000 + mon*100 + day

call timemgr_datediff(nbdate, 0, ncdate, sec, dayDiff)

dayDiffInt = floor(dayDiff)
udata%time_period = mod( dayDiffInt , udata%n_sub )

call ed_driver( bounds_clump, &

! TODO-INTEF: PROCEDURE FOR CONVERTING CLM/ALM FIELDS TO MODEL BOUNDARY
! CONDITIONS. IE.


! where most things happen
do g = bounds_clump%begg,bounds_clump%endg
if (this%fates(nc)%sites(g)%istheresoil) then
call ed_ecosystem_dynamics(this%fates(nc)%sites(g), &
this%fates2hlm_inst, &
this%phen_inst, atm2lnd_inst, &
soilstate_inst, temperature_inst, waterstate_inst)

call ed_update_site(this%fates(nc)%sites(g))
endif
enddo

! link to CLM/ALM structures
call this%fates2hlm_inst%ed_clm_link( bounds_clump, &
this%fates(nc)%sites(bounds_clump%begg:bounds_clump%endg), &
this%fates2hlm_inst, &
this%phen_inst, &
atm2lnd_inst, soilstate_inst, temperature_inst, &
waterstate_inst, canopystate_inst)
waterstate_inst, &
canopystate_inst)


if (masterproc) then
write(iulog, *) 'clm: leaving ED model', bounds_clump%begg, &
bounds_clump%endg, dayDiffInt
end if


return
end subroutine dynamics_driv
Expand Down

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