-
Notifications
You must be signed in to change notification settings - Fork 92
/
Copy pathEDMainMod.F90
1169 lines (926 loc) · 51.2 KB
/
EDMainMod.F90
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
module EDMainMod
! ===========================================================================
! Main ED module.
! ============================================================================
use shr_kind_mod , only : r8 => shr_kind_r8
use FatesGlobals , only : fates_log
use FatesInterfaceTypesMod , only : hlm_freq_day
use FatesInterfaceTypesMod , only : hlm_day_of_year
use FatesInterfaceTypesMod , only : hlm_days_per_year
use FatesInterfaceTypesMod , only : hlm_current_year
use FatesInterfaceTypesMod , only : hlm_current_month
use FatesInterfaceTypesMod , only : hlm_current_day
use FatesInterfaceTypesMod , only : hlm_use_planthydro
use FatesInterfaceTypesMod , only : hlm_parteh_mode
use FatesInterfaceTypesMod , only : hlm_use_cohort_age_tracking
use FatesInterfaceTypesMod , only : hlm_reference_date
use FatesInterfaceTypesMod , only : hlm_use_ed_prescribed_phys
use FatesInterfaceTypesMod , only : hlm_use_tree_damage
use FatesInterfaceTypesMod , only : hlm_use_ed_st3
use FatesInterfaceTypesMod , only : hlm_use_sp
use FatesInterfaceTypesMod , only : bc_in_type
use FatesInterfaceTypesMod , only : bc_out_type
use FatesInterfaceTypesMod , only : hlm_masterproc
use FatesInterfaceTypesMod , only : numpft
use FatesInterfaceTypesMod , only : hlm_use_nocomp
use PRTGenericMod , only : prt_carbon_allom_hyp
use PRTGenericMod , only : prt_cnp_flex_allom_hyp
use PRTGenericMod , only : nitrogen_element
use PRTGenericMod , only : phosphorus_element
use EDCohortDynamicsMod , only : terminate_cohorts
use EDCohortDynamicsMod , only : fuse_cohorts
use EDCohortDynamicsMod , only : EvaluateAndCorrectDBH
use EDCohortDynamicsMod , only : DamageRecovery
use EDPatchDynamicsMod , only : disturbance_rates
use EDPatchDynamicsMod , only : fuse_patches
use EDPatchDynamicsMod , only : spawn_patches
use EDPatchDynamicsMod , only : terminate_patches
use EDPhysiologyMod , only : phenology
use EDPhysiologyMod , only : satellite_phenology
use EDPhysiologyMod , only : recruitment
use EDPhysiologyMod , only : trim_canopy
use EDPhysiologyMod , only : SeedUpdate
use EDPhysiologyMod , only : ZeroAllocationRates
use EDPhysiologyMod , only : ZeroLitterFluxes
use EDPhysiologyMod , only : PreDisturbanceLitterFluxes
use EDPhysiologyMod , only : PreDisturbanceIntegrateLitter
use EDPhysiologyMod , only : UpdateRecruitL2FR
use EDPhysiologyMod , only : UpdateRecruitStoich
use EDPhysiologyMod , only : SetRecruitL2FR
use EDPhysiologyMod , only : GenerateDamageAndLitterFluxes
use FatesSoilBGCFluxMod , only : FluxIntoLitterPools
use FatesSoilBGCFluxMod , only : EffluxIntoLitterPools
use FatesSoilBGCFluxMod , only : PrepNutrientAquisitionBCs
use FatesSoilBGCFluxMod , only : PrepCH4BCs
use SFMainMod , only : DailyFireModel
use FatesSizeAgeTypeIndicesMod, only : get_age_class_index
use FatesSizeAgeTypeIndicesMod, only : coagetype_class_index
use FatesLitterMod , only : litter_type
use FatesLitterMod , only : ncwd
use EDtypesMod , only : ed_site_type
use EDTypesMod , only : set_patchno
use FatesPatchMod , only : fates_patch_type
use FatesCohortMod , only : fates_cohort_type
use EDTypesMod , only : AREA
use EDTypesMod , only : site_massbal_type
use PRTGenericMod , only : num_elements
use PRTGenericMod , only : element_list
use PRTGenericMod , only : element_pos
use EDTypesMod , only : phen_dstat_moiston
use EDTypesMod , only : phen_dstat_timeon
use FatesConstantsMod , only : itrue,ifalse
use FatesConstantsMod , only : primaryland, secondaryland
use FatesConstantsMod , only : n_landuse_cats
use FatesConstantsMod , only : nearzero
use FatesConstantsMod , only : m2_per_ha
use FatesConstantsMod , only : sec_per_day
use FatesConstantsMod , only : nocomp_bareground
use FatesPlantHydraulicsMod , only : do_growthrecruiteffects
use FatesPlantHydraulicsMod , only : UpdateSizeDepPlantHydProps
use FatesPlantHydraulicsMod , only : UpdateSizeDepPlantHydStates
use FatesPlantHydraulicsMod , only : InitPlantHydStates
use FatesPlantHydraulicsMod , only : UpdateSizeDepRhizHydProps
use FatesPlantHydraulicsMod , only : AccumulateMortalityWaterStorage
use FatesAllometryMod , only : h_allom
use EDLoggingMortalityMod , only : IsItLoggingTime
use EDLoggingMortalityMod , only : get_harvestable_carbon
use DamageMainMod , only : IsItDamageTime
use FatesGlobals , only : endrun => fates_endrun
use ChecksBalancesMod , only : SiteMassStock
use ChecksBalancesMod , only : CheckIntegratedMassPools
use EDMortalityFunctionsMod , only : Mortality_Derivative
use EDTypesMod , only : AREA_INV
use PRTGenericMod, only : carbon12_element
use PRTGenericMod, only : leaf_organ
use PRTGenericMod, only : fnrt_organ
use PRTGenericMod, only : sapw_organ
use PRTGenericMod, only : store_organ
use PRTGenericMod, only : repro_organ
use PRTGenericMod, only : struct_organ
use PRTLossFluxesMod, only : PRTMaintTurnover
use PRTParametersMod , only : prt_params
use EDPftvarcon, only : EDPftvarcon_inst
use FatesHistoryInterfaceMod, only : fates_hist
use FatesLandUseChangeMod, only: FatesGrazing
! CIME Globals
use shr_log_mod , only : errMsg => shr_log_errMsg
use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
implicit none
private
!
! !PUBLIC MEMBER FUNCTIONS:
public :: ed_ecosystem_dynamics
public :: ed_update_site
!
! !PRIVATE MEMBER FUNCTIONS:
private :: ed_integrate_state_variables
private :: TotalBalanceCheck
private :: bypass_dynamics
logical :: debug = .false.
integer, parameter :: final_check_id = -1
character(len=*), parameter, private :: sourcefile = &
__FILE__
!
! 10/30/09: Created by Rosie Fisher
!-----------------------------------------------------------------------
contains
!-------------------------------------------------------------------------------!
subroutine ed_ecosystem_dynamics(currentSite, bc_in, bc_out)
!
! !DESCRIPTION:
! Core of ed model, calling all subsequent vegetation dynamics routines
!
! !ARGUMENTS:
type(ed_site_type) , intent(inout), target :: currentSite
type(bc_in_type) , intent(in) :: bc_in
type(bc_out_type) , intent(inout) :: bc_out
!
! !LOCAL VARIABLES:
type(fates_patch_type), pointer :: currentPatch
integer :: el ! Loop counter for variables
integer :: do_patch_dynamics ! for some modes, we turn off patch dynamics
!-----------------------------------------------------------------------
if (debug .and.( hlm_masterproc==itrue)) write(fates_log(),'(A,I4,A,I2.2,A,I2.2)') 'FATES Dynamics: ',&
hlm_current_year,'-',hlm_current_month,'-',hlm_current_day
! Consider moving this towards the end, because some of these
! are being integrated over the short time-step
do el = 1,num_elements
call currentSite%mass_balance(el)%ZeroMassBalFlux()
end do
call currentSite%flux_diags%ZeroFluxDiags()
! Call a routine that simply identifies if logging should occur
! This is limited to a global event until more structured event handling is enabled
call IsItLoggingTime(hlm_masterproc,currentSite)
! Call a routine that identifies if damage should occur
call IsItDamageTime(hlm_masterproc)
!**************************************************************************
! Fire, growth, biogeochemistry.
!**************************************************************************
!FIX(SPM,032414) take this out. On startup these values are all zero and on restart it
!zeros out values read in the restart file
! Zero turnover rates and growth diagnostics
call ZeroAllocationRates(currentSite)
! Zero fluxes in and out of litter pools
call ZeroLitterFluxes(currentSite)
! Zero mass balance
call TotalBalanceCheck(currentSite, 0)
! We do not allow phenology while in ST3 mode either, it is hypothetically
! possible to allow this, but we have not plugged in the litter fluxes
! of flushing or turning over leaves for non-dynamics runs
if (hlm_use_ed_st3.eq.ifalse)then
if(hlm_use_sp.eq.ifalse) then
call phenology(currentSite, bc_in )
else
call satellite_phenology(currentSite, bc_in )
end if ! SP phenology
end if
if (hlm_use_ed_st3.eq.ifalse.and.hlm_use_sp.eq.ifalse) then ! Bypass if ST3
! Check that the site doesn't consist solely of a single bareground patch.
! If so, skip the fire model. Since the bareground patch should be the
! oldest patch per set_patchno, we check that the youngest patch isn't zero.
! If there are multiple patches on the site, the bareground patch is avoided
! at the level of the fire_model subroutines.
if (currentSite%youngest_patch%nocomp_pft_label .ne. nocomp_bareground)then
call DailyFireModel(currentSite, bc_in)
end if
! Calculate disturbance and mortality based on previous timestep vegetation.
! disturbance_rates calls logging mortality and other mortalities, Yi Xu
call disturbance_rates(currentSite, bc_in)
! Integrate state variables from annual rates to daily timestep
call ed_integrate_state_variables(currentSite, bc_in, bc_out )
! at this point in the call sequence, if flag to transition_landuse_from_off_to_on was set, unset it as it is no longer needed
if(currentSite%transition_landuse_from_off_to_on) then
currentSite%transition_landuse_from_off_to_on = .false.
endif
else
! ed_intergrate_state_variables is where the new cohort flag
! is set. This flag designates wether a cohort has
! experienced a day, and therefore has been populated with non-nonsense
! values. If we aren't entering that sequence, we need to set the flag
! Make sure cohorts are marked as non-recruits
call bypass_dynamics(currentSite,bc_out)
end if
!******************************************************************************
! Reproduction, Recruitment and Cohort Dynamics : controls cohort organization
!******************************************************************************
if(hlm_use_ed_st3.eq.ifalse.and.hlm_use_sp.eq.ifalse) then
currentPatch => currentSite%oldest_patch
do while (associated(currentPatch))
! adds small cohort of each PFT
call recruitment(currentSite, currentPatch, bc_in)
!YL --------------
! call recruitment(currentSite, currentPatch, bc_in, bc_out)
currentPatch => currentPatch%younger
enddo
call TotalBalanceCheck(currentSite,1)
currentPatch => currentSite%oldest_patch
do while (associated(currentPatch))
! puts cohorts in right order
call currentPatch%SortCohorts()
! kills cohorts that are too few
call terminate_cohorts(currentSite, currentPatch, 1, 10, bc_in )
! fuses similar cohorts
call fuse_cohorts(currentSite,currentPatch, bc_in )
! kills cohorts for various other reasons
call terminate_cohorts(currentSite, currentPatch, 2, 10, bc_in )
currentPatch => currentPatch%younger
enddo
end if
call TotalBalanceCheck(currentSite,2)
!*********************************************************************************
! Patch dynamics sub-routines: fusion, new patch creation (spwaning), termination.
!*********************************************************************************
! turn off patch dynamics if SP or ST3 modes in use
do_patch_dynamics = itrue
if(hlm_use_ed_st3.eq.itrue .or. &
hlm_use_sp.eq.itrue)then
do_patch_dynamics = ifalse
end if
! make new patches from disturbed land
if (do_patch_dynamics.eq.itrue ) then
call spawn_patches(currentSite, bc_in)
call TotalBalanceCheck(currentSite,3)
! fuse on the spawned patches.
call fuse_patches(currentSite, bc_in )
! If using BC FATES hydraulics, update the rhizosphere geometry
! based on the new cohort-patch structure
! 'rhizosphere geometry' (column-level root biomass + rootfr --> root length
! density --> node radii and volumes)
if( (hlm_use_planthydro.eq.itrue) .and. do_growthrecruiteffects) then
call UpdateSizeDepRhizHydProps(currentSite, bc_in)
!! call UpdateSizeDepRhizHydStates(currentSite, bc_in) ! keeping if re-implemented (RGK 12-2021)
end if
! SP has changes in leaf carbon but we don't expect them to be in balance.
call TotalBalanceCheck(currentSite,4)
! kill patches that are too small
call terminate_patches(currentSite, bc_in)
end if
! Final instantaneous mass balance check
call TotalBalanceCheck(currentSite,5)
end subroutine ed_ecosystem_dynamics
!-------------------------------------------------------------------------------!
subroutine ed_integrate_state_variables(currentSite, bc_in, bc_out )
!
! !DESCRIPTION:
! FIX(SPM,032414) refactor so everything goes through interface
!
! !USES:
use FatesInterfaceTypesMod, only : hlm_num_lu_harvest_cats
use PRTGenericMod , only : leaf_organ
use PRTGenericMod , only : repro_organ
use PRTGenericMod , only : sapw_organ
use PRTGenericMod , only : struct_organ
use PRTGenericMod , only : store_organ
use PRTGenericMod , only : fnrt_organ
use FatesInterfaceTypesMod, only : hlm_use_cohort_age_tracking
use FatesConstantsMod, only : itrue
use FatesConstantsMod , only : nearzero
use EDCanopyStructureMod , only : canopy_structure
! !ARGUMENTS:
type(ed_site_type) , intent(inout) :: currentSite
type(bc_in_type) , intent(in) :: bc_in
type(bc_out_type) , intent(inout) :: bc_out
!
! !LOCAL VARIABLES:
type(site_massbal_type), pointer :: site_cmass
type(fates_patch_type) , pointer :: currentPatch
type(fates_cohort_type) , pointer :: currentCohort
type(fates_cohort_type) , pointer :: nc
type(fates_cohort_type) , pointer :: storesmallcohort
type(fates_cohort_type) , pointer :: storebigcohort
integer :: snull
integer :: tnull
integer :: c ! Counter for litter size class
integer :: ft ! Counter for PFT
integer :: io_si ! global site index for history writing
integer :: iscpf ! index for the size-class x pft multiplexed bins
integer :: el ! Counter for element type (c,n,p,etc)
real(r8) :: cohort_biomass_store ! remembers the biomass in the cohort for balance checking
real(r8) :: dbh_old ! dbh of plant before daily PRT [cm]
real(r8) :: height_old ! height of plant before daily PRT [m]
logical :: is_drought ! logical for if the plant (site) is in a drought state
real(r8) :: delta_dbh ! correction for dbh
real(r8) :: delta_height ! correction for height
real(r8) :: mean_temp
logical :: newly_recovered ! If the current loop is dealing with a newly created cohort, which
! was created because it is a clone of the previous cohort in
! a lowered damage state. This cohort should bypass several calculations
! because it inherited them (such as daily carbon balance)
real(r8) :: target_leaf_c
real(r8) :: current_fates_landuse_state_vector(n_landuse_cats)
real(r8) :: harvestable_forest_c(hlm_num_lu_harvest_cats)
integer :: harvest_tag(hlm_num_lu_harvest_cats)
real(r8) :: n_old
real(r8) :: n_recover
real(r8) :: sapw_c
real(r8) :: leaf_c
real(r8) :: fnrt_c
real(r8) :: struct_c
real(r8) :: repro_c
real(r8) :: total_c
real(r8) :: store_c
real(r8) :: cc_leaf_c
real(r8) :: cc_fnrt_c
real(r8) :: cc_struct_c
real(r8) :: cc_repro_c
real(r8) :: cc_store_c
real(r8) :: cc_sapw_c
real(r8) :: sapw_c0
real(r8) :: leaf_c0
real(r8) :: fnrt_c0
real(r8) :: struct_c0
real(r8) :: repro_c0
real(r8) :: store_c0
real(r8) :: total_c0
real(r8) :: nc_carbon
real(r8) :: cc_carbon
integer,parameter :: leaf_c_id = 1
!-----------------------------------------------------------------------
current_fates_landuse_state_vector = currentSite%get_current_landuse_statevector()
! Clear site GPP and AR passing to HLM
bc_out%gpp_site = 0._r8
bc_out%ar_site = 0._r8
! Patch level biomass are required for C-based harvest
call get_harvestable_carbon(currentSite, bc_in%site_area, bc_in%hlm_harvest_catnames, harvestable_forest_c)
! Set a pointer to this sites carbon12 mass balance
site_cmass => currentSite%mass_balance(element_pos(carbon12_element))
! This call updates the assessment of the total stoichiometry
! for a new recruit, based on its PFT and the L2FR of
! a new recruit. This is called here, because it is
! prior to the growth sequence, where reproductive
! tissues are allocated
call UpdateRecruitStoich(currentSite)
currentPatch => currentSite%oldest_patch
do while(associated(currentPatch))
currentPatch%age = currentPatch%age + hlm_freq_day
! FIX(SPM,032414) valgrind 'Conditional jump or move depends on uninitialised value'
if( currentPatch%age < 0._r8 )then
write(fates_log(),*) 'negative patch age?',currentPatch%age, &
currentPatch%patchno,currentPatch%area
call endrun(msg=errMsg(sourcefile, __LINE__))
endif
! add age increment to secondary forest patches as well
if (currentPatch%land_use_label .ne. primaryland) then
currentPatch%age_since_anthro_disturbance = &
currentPatch%age_since_anthro_disturbance + hlm_freq_day
endif
! check to see if the patch has moved to the next age class
currentPatch%age_class = get_age_class_index(currentPatch%age)
! Within this loop, we may be creating new cohorts, which
! are copies of pre-existing cohorts with reduced damage classes.
! If that is true, we want to bypass some of the things in
! this loop (such as calculation of npp, etc) because they
! are derived from the donor and have been modified accordingly
newly_recovered = .false.
currentCohort => currentPatch%shortest
do while(associated(currentCohort))
ft = currentCohort%pft
! Some cohorts are created and inserted to the list while
! the loop is going. These are pointed to the "taller" position
! of current, and then inherit properties of their donor (current)
! we don't need to repeat things before allocation for these
! newly_recovered cohorts
if_not_newlyrecovered: if(.not.newly_recovered) then
! Calculate the mortality derivatives
mean_temp = currentPatch%tveg24%GetMean()
call Mortality_Derivative(currentSite, currentCohort, bc_in, &
currentPatch%btran_ft, mean_temp, &
currentPatch%land_use_label, &
currentPatch%age_since_anthro_disturbance, current_fates_landuse_state_vector, &
harvestable_forest_c, harvest_tag)
! -----------------------------------------------------------------------------
! Apply Plant Allocation and Reactive Transport
! -----------------------------------------------------------------------------
! -----------------------------------------------------------------------------
! Identify the net carbon gain for this dynamics interval
! Set the available carbon pool, identify allocation portions, and
! decrement the available carbon pool to zero.
! -----------------------------------------------------------------------------
if (hlm_use_ed_prescribed_phys .eq. itrue) then
if (currentCohort%canopy_layer .eq. 1) then
currentCohort%npp_acc = EDPftvarcon_inst%prescribed_npp_canopy(ft) &
* currentCohort%c_area / currentCohort%n / hlm_days_per_year
else
currentCohort%npp_acc = EDPftvarcon_inst%prescribed_npp_understory(ft) &
* currentCohort%c_area / currentCohort%n / hlm_days_per_year
endif
! We don't explicitly define a respiration rate for prescribe phys
! but we do need to pass mass balance. So we say it is zero respiration
currentCohort%gpp_acc = currentCohort%npp_acc
currentCohort%resp_m_acc = 0._r8
end if
! -----------------------------------------------------------------------------
! Save NPP/GPP/R in these "hold" style variables. These variables
! persist after this routine is complete, and used in I/O diagnostics.
! Whereas the _acc style variables are zero'd because they are key
! accumulation state variables.
!
! convert from kgC/indiv/day into kgC/indiv/year
! <x>_acc_hold is remembered until the next dynamics step (used for I/O)
! <x>_acc will be reset soon and will be accumulated on the next leaf
! photosynthesis step
! -----------------------------------------------------------------------------
currentCohort%gpp_acc_hold = currentCohort%gpp_acc * real(hlm_days_per_year,r8)
currentCohort%resp_m_acc_hold = currentCohort%resp_m_acc * real(hlm_days_per_year,r8)
! at this point we have the info we need to calculate growth respiration
! as a "tax" on the difference between daily GPP and daily maintenance respiration
if (hlm_use_ed_prescribed_phys .eq. ifalse) then
currentCohort%resp_g_acc_hold = prt_params%grperc(ft) * &
max(0._r8,(currentCohort%gpp_acc - currentCohort%resp_m_acc)) * real(hlm_days_per_year,r8)
else
! set growth respiration to zero in prescribed physiology mode,
! that way the npp_acc vars will be set to the nominal gpp values set above.
currentCohort%resp_g_acc_hold = 0._r8
endif
! calculate the npp as the difference between gpp and autotrophic respiration
! (NPP is also updated if there is any excess respiration from nutrient limitations)
currentCohort%npp_acc = currentCohort%gpp_acc - &
(currentCohort%resp_m_acc + currentCohort%resp_g_acc_hold/real(hlm_days_per_year,r8))
currentCohort%npp_acc_hold = currentCohort%gpp_acc_hold - &
(currentCohort%resp_m_acc_hold + currentCohort%resp_g_acc_hold)
! allow herbivores to graze
call FatesGrazing(currentCohort%prt, ft, currentPatch%land_use_label, currentCohort%height)
! Conduct Maintenance Turnover (parteh)
if(debug) call currentCohort%prt%CheckMassConservation(ft,3)
if(any(currentSite%dstatus(ft) == [phen_dstat_moiston,phen_dstat_timeon])) then
is_drought = .false.
else
is_drought = .true.
end if
call PRTMaintTurnover(currentCohort%prt,ft, currentCohort%canopy_layer,is_drought)
! -----------------------------------------------------------------------------------
! Call the routine that advances leaves in age.
! This will move a portion of the leaf mass in each
! age bin, to the next bin. This will not handle movement
! of mass from the oldest bin into the litter pool, that is something else.
! -----------------------------------------------------------------------------------
call currentCohort%prt%AgeLeaves(ft,currentCohort%canopy_layer, sec_per_day)
! Plants can acquire N from 3 sources (excluding re-absorption),
! the source doesn't affect how its allocated (yet), so they
! are combined into daily_n_gain, which is the value used in the following
! allocation scheme
currentCohort%daily_n_gain = currentCohort%daily_nh4_uptake + &
currentCohort%daily_no3_uptake + currentCohort%sym_nfix_daily
currentCohort%resp_excess_hold = 0._r8
end if if_not_newlyrecovered
! If the current diameter of a plant is somehow less than what is consistent
! with what is allometrically consistent with the stuctural biomass, then
! correct the dbh to match.
call EvaluateAndCorrectDBH(currentCohort,delta_dbh,delta_height)
! We want to save these values for the newly recovered cohort as well
height_old = currentCohort%height
dbh_old = currentCohort%dbh
! -----------------------------------------------------------------------------
! Growth and Allocation (PARTEH)
! -----------------------------------------------------------------------------
! We split the allocation into phases (currently for all hypotheses)
! In phase 1, allocation, we address prioritized allocation that should
! only happen once per day, this is only allocation that does not grow stature.
! In phase 2, allocation , we address allocation that can be performed
! as many times as necessary. This is allocation that does not contain stature
! growth. This is separate from phase 1, because some recovering plants
! will have new allocation targets that need to be updated after they change status.
! In Phase 3, we assume that the plant has reached its targets, and any
! left-over resources are used to grow the stature of the plant
if(.not.newly_recovered)then
call currentCohort%prt%DailyPRT(phase=1)
end if
call currentCohort%prt%DailyPRT(phase=2)
if((.not.newly_recovered) .and. (hlm_use_tree_damage .eq. itrue) ) then
! The loop order is shortest to tallest
! The recovered cohort (ie one with larger targets)
! is newly created in DamageRecovery(), and
! is inserted into the next position, following the
! original and current (unrecovered) cohort.
! we pass it back here in case the pointer is
! needed for diagnostics
call DamageRecovery(currentSite,currentPatch,currentCohort,newly_recovered)
else
newly_recovered = .false.
end if
call currentCohort%prt%DailyPRT(phase=3)
! If nutrients are limiting growth, and carbon continues
! to accumulate beyond the plant's storage capacity, then
! it will burn carbon as what we call "excess respiration"
! We must subtract this term from NPP. We do not need to subtract it from
! currentCohort%npp_acc, it has already been removed from this in
! the daily growth code (PARTEH).
currentCohort%npp_acc_hold = currentCohort%npp_acc_hold - currentCohort%resp_excess_hold
! Passing gpp_acc_hold to HLM
bc_out%gpp_site = bc_out%gpp_site + currentCohort%gpp_acc_hold * &
AREA_INV * currentCohort%n / hlm_days_per_year / sec_per_day
bc_out%ar_site = bc_out%ar_site + (currentCohort%resp_m_acc_hold + &
currentCohort%resp_g_acc_hold + currentCohort%resp_excess_hold) * &
AREA_INV * currentCohort%n / hlm_days_per_year / sec_per_day
! Update the mass balance tracking for the daily nutrient uptake flux
! Then zero out the daily uptakes, they have been used
! -----------------------------------------------------------------------------
call EffluxIntoLitterPools(currentSite, currentPatch, currentCohort, bc_in )
if(element_pos(nitrogen_element)>0) then
! Mass balance for N uptake
currentSite%mass_balance(element_pos(nitrogen_element))%net_root_uptake = &
currentSite%mass_balance(element_pos(nitrogen_element))%net_root_uptake + &
(currentCohort%daily_n_gain-currentCohort%daily_n_efflux)*currentCohort%n
end if
if(element_pos(phosphorus_element)>0) then
! Mass balance for P uptake
currentSite%mass_balance(element_pos(phosphorus_element))%net_root_uptake = &
currentSite%mass_balance(element_pos(phosphorus_element))%net_root_uptake + &
(currentCohort%daily_p_gain-currentCohort%daily_p_efflux)*currentCohort%n
end if
! mass balance for C efflux (if any)
currentSite%mass_balance(element_pos(carbon12_element))%net_root_uptake = &
currentSite%mass_balance(element_pos(carbon12_element))%net_root_uptake - &
currentCohort%daily_c_efflux*currentCohort%n
! Save NPP diagnostic for flux accounting [kg/m2/day]
currentSite%flux_diags%npp = currentSite%flux_diags%npp + &
currentCohort%npp_acc_hold/hlm_days_per_year * currentCohort%n * area_inv
! And simultaneously add the input fluxes to mass balance accounting
site_cmass%gpp_acc = site_cmass%gpp_acc + &
currentCohort%gpp_acc * currentCohort%n
site_cmass%aresp_acc = site_cmass%aresp_acc + &
currentCohort%resp_m_acc*currentCohort%n + &
(currentCohort%resp_g_acc_hold+currentCohort%resp_excess_hold) * &
currentCohort%n/real( hlm_days_per_year,r8)
call currentCohort%prt%CheckMassConservation(ft,5)
! Update the leaf biophysical rates based on proportion of leaf
! mass in the different leaf age classes. Following growth
! and turnover, these proportions won't change again. This
! routine is also called following fusion
call currentCohort%UpdateCohortBioPhysRates()
! This cohort has grown, it is no longer "new"
currentCohort%isnew = .false.
! Update the plant height (if it has grown)
call h_allom(currentCohort%dbh,ft,currentCohort%height)
currentCohort%dhdt = (currentCohort%height-height_old)/hlm_freq_day
currentCohort%ddbhdt = (currentCohort%dbh-dbh_old)/hlm_freq_day
! Carbon assimilate has been spent at this point
! and can now be safely zero'd
currentCohort%npp_acc = 0.0_r8
currentCohort%gpp_acc = 0.0_r8
currentCohort%resp_m_acc = 0.0_r8
! BOC...update tree 'hydraulic geometry'
! (size --> heights of elements --> hydraulic path lengths -->
! maximum node-to-node conductances)
if( (hlm_use_planthydro.eq.itrue) .and. do_growthrecruiteffects) then
call UpdateSizeDepPlantHydProps(currentSite,currentCohort, bc_in)
call UpdateSizeDepPlantHydStates(currentSite,currentCohort)
end if
! if we are in age-dependent mortality mode
if (hlm_use_cohort_age_tracking .eq. itrue) then
! update cohort age
currentCohort%coage = currentCohort%coage + hlm_freq_day
if(currentCohort%coage < 0.0_r8)then
write(fates_log(),*) 'negative cohort age?',currentCohort%coage
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
! update cohort age class and age x pft class
call coagetype_class_index(currentCohort%coage, currentCohort%pft, &
currentCohort%coage_class,currentCohort%coage_by_pft_class)
end if
currentCohort => currentCohort%taller
end do
currentPatch => currentPatch%younger
end do
! We keep a record of the L2FRs of plants
! that are near the recruit size, for different
! pfts and canopy layer. We use this mean to
! set the L2FRs of newly recruited plants
call UpdateRecruitL2FR(currentSite)
! Update history diagnostics related to Nutrients (if any)
! -----------------------------------------------------------------------------
select case(hlm_parteh_mode)
case (prt_cnp_flex_allom_hyp)
call fates_hist%update_history_nutrflux(currentSite)
end select
! When plants die, the water goes with them. This effects
! the water balance.
if( hlm_use_planthydro == itrue ) then
currentPatch => currentSite%youngest_patch
do while(associated(currentPatch))
currentCohort => currentPatch%shortest
do while(associated(currentCohort))
call AccumulateMortalityWaterStorage(currentSite,currentCohort,&
-1.0_r8 * currentCohort%dndt * hlm_freq_day)
currentCohort => currentCohort%taller
end do
currentPatch => currentPatch%older
end do
end if
! With growth and mortality rates now calculated we can determine the seed rain
! fluxes. However, because this is potentially a cross-patch mixing model
! we will calculate this as a group
call SeedUpdate(currentSite)
! Calculate all other litter fluxes
! -----------------------------------------------------------------------------------
currentPatch => currentSite%youngest_patch
do while(associated(currentPatch))
call GenerateDamageAndLitterFluxes( currentSite, currentPatch, bc_in)
call PreDisturbanceLitterFluxes( currentSite, currentPatch, bc_in)
call PreDisturbanceIntegrateLitter(currentPatch )
currentPatch => currentPatch%older
enddo
! RGK: This call is unecessary for CLM coupling. I believe we
! can remove it completely if/when this call is added in ELM to
! subroutine UpdateLitterFluxes(this,bounds_clump) in elmfates_interfaceMod.F90
call FluxIntoLitterPools(currentsite, bc_in, bc_out)
! Update cohort number.
! This needs to happen after the CWD_input and seed_input calculations as they
! assume the pre-mortality currentCohort%n.
currentPatch => currentSite%youngest_patch
do while(associated(currentPatch))
currentCohort => currentPatch%shortest
do while(associated(currentCohort))
currentCohort%n = max(0._r8,currentCohort%n + currentCohort%dndt * hlm_freq_day )
currentCohort%sym_nfix_daily = 0._r8
currentCohort => currentCohort%taller
enddo
currentPatch => currentPatch%older
enddo
return
end subroutine ed_integrate_state_variables
!-------------------------------------------------------------------------------!
subroutine ed_update_site( currentSite, bc_in, bc_out, is_restarting )
!
! !DESCRIPTION:
! Calls routines to consolidate the ED growth process.
! Canopy Structure to assign canopy layers to cohorts
! Canopy Spread to figure out the size of tree crowns
! Trim_canopy to figure out the target leaf biomass.
! Extra recruitment to fill empty patches.
!
! !USES:
use EDCanopyStructureMod , only : canopy_spread, canopy_structure
!
! !ARGUMENTS:
type(ed_site_type) , intent(inout), target :: currentSite
type(bc_in_type) , intent(in) :: bc_in
type(bc_out_type) , intent(inout) :: bc_out
logical,intent(in) :: is_restarting ! is this called during restart read?
!
! !LOCAL VARIABLES:
type (fates_patch_type) , pointer :: currentPatch
!-----------------------------------------------------------------------
! check patch order (set second argument to true)
if (debug) then
call set_patchno(currentSite,.true.,1)
end if
if(hlm_use_sp.eq.ifalse .and. (.not.is_restarting))then
call canopy_spread(currentSite)
end if
call TotalBalanceCheck(currentSite,6)
if(hlm_use_sp.eq.ifalse .and. (.not.is_restarting) )then
call canopy_structure(currentSite, bc_in)
endif
call TotalBalanceCheck(currentSite,final_check_id)
! Update recruit L2FRs based on new canopy position
call SetRecruitL2FR(currentSite)
currentSite%area_by_age(:) = 0._r8
currentPatch => currentSite%oldest_patch
do while(associated(currentPatch))
if(.not.is_restarting)then
call terminate_cohorts(currentSite, currentPatch, 1, 11, bc_in)
call terminate_cohorts(currentSite, currentPatch, 2, 11, bc_in)
end if
! This cohort count is used in the photosynthesis loop
call currentPatch%CountCohorts()
! Update the total area of by patch age class array
currentSite%area_by_age(currentPatch%age_class) = &
currentSite%area_by_age(currentPatch%age_class) + currentPatch%area
currentPatch => currentPatch%younger
enddo
! Check to see if the time integrated fluxes match the state
! Dont call this if we are restarting, it will double count the flux
if(.not.is_restarting)then
call CheckIntegratedMassPools(currentSite)
end if
! The HLMs need to know about nutrient demand, and/or
! root mass and affinities
call PrepNutrientAquisitionBCs(currentSite,bc_in,bc_out)
! The HLM methane module needs information about
! rooting mass, distributions, respiration rates and NPP
call PrepCH4BCs(currentSite,bc_in,bc_out)
! FIX(RF,032414). This needs to be monthly, not annual
! If this is the second to last day of the year, then perform trimming
if( hlm_day_of_year == hlm_days_per_year-1 .and. (.not.is_restarting)) then
if(hlm_use_sp.eq.ifalse)then
call trim_canopy(currentSite)
endif
endif
end subroutine ed_update_site
!-------------------------------------------------------------------------------!
subroutine TotalBalanceCheck (currentSite, call_index )
!
! !DESCRIPTION:
! This routine looks at the mass flux in and out of the FATES and compares it to
! the change in total stocks (states).
! Fluxes in are NPP. Fluxes out are decay of CWD and litter into SOM pools.
!
! !ARGUMENTS:
type(ed_site_type) , intent(inout) :: currentSite
integer , intent(in) :: call_index
!
! !LOCAL VARIABLES:
type(site_massbal_type),pointer :: site_mass
real(r8) :: biomass_stock ! total biomass in Kg/site
real(r8) :: litter_stock ! total litter in Kg/site
real(r8) :: seed_stock ! total seed mass in Kg/site
real(r8) :: total_stock ! total ED carbon in Kg/site
real(r8) :: change_in_stock ! Change since last time we set ed_allsites_inst%old_stock in this routine. KgC/site
real(r8) :: error ! How much carbon did we gain or lose (should be zero!)
real(r8) :: error_frac ! Error as a fraction of total biomass
real(r8) :: net_flux ! Difference between recorded fluxes in and out. KgC/site
real(r8) :: flux_in ! mass flux into fates control volume
real(r8) :: flux_out ! mass flux out of fates control volume
real(r8) :: leaf_m ! Mass in leaf tissues kg
real(r8) :: fnrt_m ! "" fine root
real(r8) :: sapw_m ! "" sapwood
real(r8) :: store_m ! "" storage
real(r8) :: struct_m ! "" structure
real(r8) :: repro_m ! "" reproduction
integer :: el ! loop counter for element types
! nb. There is no time associated with these variables
! because this routine can be called between any two
! arbitrary points in code, even if no time has passed.
! Also, the carbon pools are per site/gridcell, so that
! we can account for the changing areas of patches.
type(fates_patch_type) , pointer :: currentPatch
type(fates_cohort_type) , pointer :: currentCohort
type(litter_type), pointer :: litt
logical, parameter :: print_cohorts = .true. ! Set to true if you want
! to print cohort data
! upon fail (lots of text)
!-----------------------------------------------------------------------
if(hlm_use_sp.eq.ifalse)then
change_in_stock = 0.0_r8
! Loop through the number of elements in the system
do el = 1, num_elements
site_mass => currentSite%mass_balance(el)
call SiteMassStock(currentSite,el,total_stock,biomass_stock,litter_stock,seed_stock)
change_in_stock = total_stock - site_mass%old_stock
flux_in = site_mass%seed_in + &
site_mass%net_root_uptake + &
site_mass%gpp_acc + &
site_mass%flux_generic_in + &
site_mass%patch_resize_err
flux_out = sum(site_mass%wood_product_harvest(:)) + &
sum(site_mass%wood_product_landusechange(:)) + &
site_mass%burn_flux_to_atm + &
site_mass%seed_out + &
site_mass%flux_generic_out + &
site_mass%frag_out + &
site_mass%aresp_acc + &
site_mass%herbivory_flux_out
net_flux = flux_in - flux_out
error = abs(net_flux - change_in_stock)
if(change_in_stock>0.0)then
error_frac = error/abs(total_stock)
else
error_frac = 0.0_r8
end if
if ( error_frac > 10e-6_r8 .or. (error /= error) ) then
write(fates_log(),*) 'mass balance error detected'
write(fates_log(),*) 'element type (see PRTGenericMod.F90): ',element_list(el)
write(fates_log(),*) 'error fraction relative to biomass stock: ',error_frac