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trcini_pisces.F90 @ 13891

Last change on this file since 13891 was 12377, checked in by acc, 4 years ago

The big one. Merging all 2019 developments from the option 1 branch back onto the trunk.

This changeset reproduces 2019/dev_r11943_MERGE_2019 on the trunk using a 2-URL merge
onto a working copy of the trunk. I.e.:

svn merge --ignore-ancestry \

svn+ssh://acc@forge.ipsl.jussieu.fr/ipsl/forge/projets/nemo/svn/NEMO/trunk \
svn+ssh://acc@forge.ipsl.jussieu.fr/ipsl/forge/projets/nemo/svn/NEMO/branches/2019/dev_r11943_MERGE_2019 ./

The --ignore-ancestry flag avoids problems that may otherwise arise from the fact that
the merge history been trunk and branch may have been applied in a different order but
care has been taken before this step to ensure that all applicable fixes and updates
are present in the merge branch.

The trunk state just before this step has been branched to releases/release-4.0-HEAD
and that branch has been immediately tagged as releases/release-4.0.2. Any fixes
or additions in response to tickets on 4.0, 4.0.1 or 4.0.2 should be done on
releases/release-4.0-HEAD. From now on future 'point' releases (e.g. 4.0.2) will
remain unchanged with periodic releases as needs demand. Note release-4.0-HEAD is a
transitional naming convention. Future full releases, say 4.2, will have a release-4.2
branch which fulfills this role and the first point release (e.g. 4.2.0) will be made
immediately following the release branch creation.

2020 developments can be started from any trunk revision later than this one.

Property svn:keywords set to Id

File size: 16.5 KB

Rev	Line
[935]	1	MODULE trcini_pisces
	2	!!======================================================================
	3	!! * MODULE trcini_pisces *
	4	!! TOP : initialisation of the PISCES biochemical model
	5	!!======================================================================
	6	!! History : - ! 1988-07 (E. Maier-Reiner) Original code
	7	!! - ! 1999-10 (O. Aumont, C. Le Quere)
	8	!! - ! 2002 (O. Aumont) PISCES
	9	!! 1.0 ! 2005-03 (O. Aumont, A. El Moussaoui) F90
	10	!! 2.0 ! 2007-12 (C. Ethe, G. Madec) from trcini.pisces.h90
[3680]	11	!! 3.5 ! 2012-05 (C. Ethe) Merge PISCES-LOBSTER
[935]	12	!!----------------------------------------------------------------------
	13	!! trc_ini_pisces : PISCES biochemical model initialisation
	14	!!----------------------------------------------------------------------
[7646]	15	USE par_trc ! TOP parameters
[3294]	16	USE oce_trc ! shared variables between ocean and passive tracers
	17	USE trc ! passive tracers common variables
[7646]	18	USE trcnam_pisces ! PISCES namelist
[3294]	19	USE sms_pisces ! PISCES Source Minus Sink variables
[10222]	20	USE sedini ! SEDIMENTS initialization routine
[935]	21
	22	IMPLICIT NONE
	23	PRIVATE
	24
	25	PUBLIC trc_ini_pisces ! called by trcini.F90 module
	26
	27	!!----------------------------------------------------------------------
[10067]	28	!! NEMO/TOP 4.0 , NEMO Consortium (2018)
[1146]	29	!! $Id$
[10068]	30	!! Software governed by the CeCILL license (see ./LICENSE)
[935]	31	!!----------------------------------------------------------------------
	32	CONTAINS
	33
[12377]	34	SUBROUTINE trc_ini_pisces( Kmm )
[935]	35	!!----------------------------------------------------------------------
	36	!! * ROUTINE trc_ini_pisces *
	37	!!
	38	!! ** Purpose : Initialisation of the PISCES biochemical model
	39	!!----------------------------------------------------------------------
[12377]	40	INTEGER, INTENT(in) :: Kmm ! time level indices
[7646]	41	!
	42	CALL trc_nam_pisces
	43	!
[12377]	44	IF( ln_p4z .OR. ln_p5z ) THEN ; CALL p4z_ini( Kmm ) ! PISCES
	45	ELSE ; CALL p2z_ini( Kmm ) ! LOBSTER
[3680]	46	ENDIF
	47
	48	END SUBROUTINE trc_ini_pisces
	49
[9169]	50
[12377]	51	SUBROUTINE p4z_ini( Kmm )
[3680]	52	!!----------------------------------------------------------------------
	53	!! * ROUTINE p4z_ini *
	54	!!
	55	!! ** Purpose : Initialisation of the PISCES biochemical model
	56	!!----------------------------------------------------------------------
	57	USE p4zsms ! Main P4Z routine
	58	USE p4zche ! Chemical model
	59	USE p4zsink ! vertical flux of particulate matter due to sinking
	60	USE p4zopt ! optical model
[12377]	61	USE p4zbc ! Boundary conditions
[3680]	62	USE p4zfechem ! Iron chemistry
	63	USE p4zrem ! Remineralisation of organic matter
	64	USE p4zflx ! Gas exchange
[10227]	65	USE p4zlim ! Co-limitations of differents nutrients
[3680]	66	USE p4zprod ! Growth rate of the 2 phyto groups
	67	USE p4zmicro ! Sources and sinks of microzooplankton
	68	USE p4zmeso ! Sources and sinks of mesozooplankton
	69	USE p4zmort ! Mortality terms for phytoplankton
	70	USE p4zlys ! Calcite saturation
[5385]	71	USE p4zsed ! Sedimentation & burial
[7646]	72	USE p4zpoc ! Remineralization of organic particles
	73	USE p4zligand ! Remineralization of organic ligands
[10227]	74	USE p5zlim ! Co-limitations of differents nutrients
[7646]	75	USE p5zprod ! Growth rate of the 2 phyto groups
	76	USE p5zmicro ! Sources and sinks of microzooplankton
	77	USE p5zmeso ! Sources and sinks of mesozooplankton
	78	USE p5zmort ! Mortality terms for phytoplankton
[3680]	79	!
[12377]	80	INTEGER, INTENT(in) :: Kmm ! time level indices
[9169]	81	REAL(wp), SAVE :: sco2 = 2.312e-3_wp
	82	REAL(wp), SAVE :: alka0 = 2.426e-3_wp
	83	REAL(wp), SAVE :: oxyg0 = 177.6e-6_wp
	84	REAL(wp), SAVE :: po4 = 2.165e-6_wp
	85	REAL(wp), SAVE :: bioma0 = 1.000e-8_wp
	86	REAL(wp), SAVE :: silic1 = 91.51e-6_wp
	87	REAL(wp), SAVE :: no3 = 30.9e-6_wp * 7.625_wp
[3680]	88	!
[7646]	89	INTEGER :: ji, jj, jk, jn, ierr
[3294]	90	REAL(wp) :: zcaralk, zbicarb, zco3
	91	REAL(wp) :: ztmas, ztmas1
[7646]	92	CHARACTER(len = 20) :: cltra
[3294]	93	!!----------------------------------------------------------------------
[9169]	94	!
[7646]	95	IF(lwp) THEN
	96	WRITE(numout,*)
	97	IF( ln_p4z ) THEN
[9169]	98	WRITE(numout,*) 'p4z_ini : PISCES biochemical model initialisation'
	99	WRITE(numout,*) '~~~~~~~'
[7646]	100	ELSE
[9169]	101	WRITE(numout,*) 'p5z_ini : PISCES biochemical model initialisation'
	102	WRITE(numout,*) '~~~~~~~ With variable stoichiometry'
[7646]	103	ENDIF
	104	ENDIF
	105	!
	106	! Allocate PISCES arrays
[3680]	107	ierr = sms_pisces_alloc()
	108	ierr = ierr + p4z_che_alloc()
	109	ierr = ierr + p4z_sink_alloc()
	110	ierr = ierr + p4z_opt_alloc()
	111	ierr = ierr + p4z_flx_alloc()
[5385]	112	ierr = ierr + p4z_sed_alloc()
[10362]	113	ierr = ierr + p4z_lim_alloc()
[7646]	114	IF( ln_p4z ) THEN
	115	ierr = ierr + p4z_prod_alloc()
	116	ELSE
	117	ierr = ierr + p5z_lim_alloc()
	118	ierr = ierr + p5z_prod_alloc()
	119	ENDIF
[10362]	120	ierr = ierr + p4z_rem_alloc()
[3680]	121	!
[10425]	122	CALL mpp_sum( 'trcini_pisces', ierr )
[3680]	123	IF( ierr /= 0 ) CALL ctl_stop( 'STOP', 'pisces_alloc: unable to allocate PISCES arrays' )
	124	!
[4996]	125	ryyss = nyear_len(1) * rday ! number of seconds per year
	126	r1_ryyss = 1. / ryyss
	127	!
[2715]	128
[7646]	129	! assign an index in trc arrays for each prognostic variables
	130	DO jn = 1, jptra
	131	cltra = ctrcnm(jn)
	132	IF( cltra == 'DIC' ) jpdic = jn !: dissolved inoganic carbon concentration
	133	IF( cltra == 'Alkalini' ) jptal = jn !: total alkalinity
	134	IF( cltra == 'O2' ) jpoxy = jn !: oxygen carbon concentration
	135	IF( cltra == 'CaCO3' ) jpcal = jn !: calcite concentration
	136	IF( cltra == 'PO4' ) jppo4 = jn !: phosphate concentration
	137	IF( cltra == 'POC' ) jppoc = jn !: small particulate organic phosphate concentration
	138	IF( cltra == 'Si' ) jpsil = jn !: silicate concentration
	139	IF( cltra == 'PHY' ) jpphy = jn !: phytoplancton concentration
	140	IF( cltra == 'ZOO' ) jpzoo = jn !: zooplancton concentration
	141	IF( cltra == 'DOC' ) jpdoc = jn !: dissolved organic carbon concentration
	142	IF( cltra == 'PHY2' ) jpdia = jn !: Diatoms Concentration
	143	IF( cltra == 'ZOO2' ) jpmes = jn !: Mesozooplankton Concentration
	144	IF( cltra == 'DSi' ) jpdsi = jn !: Diatoms Silicate Concentration
	145	IF( cltra == 'Fer' ) jpfer = jn !: Iron Concentration
	146	IF( cltra == 'BFe' ) jpbfe = jn !: Big iron particles Concentration
	147	IF( cltra == 'GOC' ) jpgoc = jn !: Big particulate organic phosphate concentration
	148	IF( cltra == 'SFe' ) jpsfe = jn !: Small iron particles Concentration
	149	IF( cltra == 'DFe' ) jpdfe = jn !: Diatoms iron Concentration
	150	IF( cltra == 'GSi' ) jpgsi = jn !: (big) Silicate Concentration
	151	IF( cltra == 'NFe' ) jpnfe = jn !: Nano iron Concentration
	152	IF( cltra == 'NCHL' ) jpnch = jn !: Nano Chlorophyll Concentration
	153	IF( cltra == 'DCHL' ) jpdch = jn !: Diatoms Chlorophyll Concentration
	154	IF( cltra == 'NO3' ) jpno3 = jn !: Nitrates Concentration
	155	IF( cltra == 'NH4' ) jpnh4 = jn !: Ammonium Concentration
	156	IF( cltra == 'DON' ) jpdon = jn !: Dissolved organic N Concentration
	157	IF( cltra == 'DOP' ) jpdop = jn !: Dissolved organic P Concentration
	158	IF( cltra == 'PON' ) jppon = jn !: Small Nitrogen particle Concentration
	159	IF( cltra == 'POP' ) jppop = jn !: Small Phosphorus particle Concentration
	160	IF( cltra == 'GON' ) jpgon = jn !: Big Nitrogen particles Concentration
	161	IF( cltra == 'GOP' ) jpgop = jn !: Big Phosphorus Concentration
	162	IF( cltra == 'PHYN' ) jpnph = jn !: Nanophytoplankton N biomass
	163	IF( cltra == 'PHYP' ) jppph = jn !: Nanophytoplankton P biomass
	164	IF( cltra == 'DIAN' ) jpndi = jn !: Diatoms N biomass
	165	IF( cltra == 'DIAP' ) jppdi = jn !: Diatoms P biomass
	166	IF( cltra == 'PIC' ) jppic = jn !: Picophytoplankton C biomass
	167	IF( cltra == 'PICN' ) jpnpi = jn !: Picophytoplankton N biomass
	168	IF( cltra == 'PICP' ) jpppi = jn !: Picophytoplankton P biomass
[10362]	169	IF( cltra == 'PCHL' ) jppch = jn !: Diatoms Chlorophyll Concentration
[7646]	170	IF( cltra == 'PFe' ) jppfe = jn !: Picophytoplankton Fe biomass
	171	IF( cltra == 'LGW' ) jplgw = jn !: Weak ligands
[9169]	172	END DO
[7646]	173
[3680]	174	CALL p4z_sms_init ! Maint routine
[9169]	175	!
[935]	176
	177	! Set biological ratios
	178	! ---------------------
[3294]	179	rno3 = 16._wp / 122._wp
	180	po4r = 1._wp / 122._wp
	181	o2nit = 32._wp / 122._wp
[6325]	182	o2ut = 133._wp / 122._wp
	183	rdenit = ( ( o2ut + o2nit ) * 0.80 - rno3 - rno3 * 0.60 ) / rno3
[3294]	184	rdenita = 3._wp / 5._wp
[7646]	185	IF( ln_p5z ) THEN
	186	no3rat3 = no3rat3 / rno3
	187	po4rat3 = po4rat3 / po4r
	188	ENDIF
[935]	189
[1007]	190	! Initialization of tracer concentration in case of no restart
	191	!--------------------------------------------------------------
[7646]	192	IF( .NOT.ln_rsttr ) THEN
[12377]	193	tr(:,:,:,jpdic,Kmm) = sco2
	194	tr(:,:,:,jpdoc,Kmm) = bioma0
	195	tr(:,:,:,jptal,Kmm) = alka0
	196	tr(:,:,:,jpoxy,Kmm) = oxyg0
	197	tr(:,:,:,jpcal,Kmm) = bioma0
	198	tr(:,:,:,jppo4,Kmm) = po4 / po4r
	199	tr(:,:,:,jppoc,Kmm) = bioma0
	200	tr(:,:,:,jpgoc,Kmm) = bioma0
	201	tr(:,:,:,jpbfe,Kmm) = bioma0 * 5.e-6
	202	tr(:,:,:,jpsil,Kmm) = silic1
	203	tr(:,:,:,jpdsi,Kmm) = bioma0 * 0.15
	204	tr(:,:,:,jpgsi,Kmm) = bioma0 * 5.e-6
	205	tr(:,:,:,jpphy,Kmm) = bioma0
	206	tr(:,:,:,jpdia,Kmm) = bioma0
	207	tr(:,:,:,jpzoo,Kmm) = bioma0
	208	tr(:,:,:,jpmes,Kmm) = bioma0
	209	tr(:,:,:,jpfer,Kmm) = 0.6E-9
	210	tr(:,:,:,jpsfe,Kmm) = bioma0 * 5.e-6
	211	tr(:,:,:,jpdfe,Kmm) = bioma0 * 5.e-6
	212	tr(:,:,:,jpnfe,Kmm) = bioma0 * 5.e-6
	213	tr(:,:,:,jpnch,Kmm) = bioma0 * 12. / 55.
	214	tr(:,:,:,jpdch,Kmm) = bioma0 * 12. / 55.
	215	tr(:,:,:,jpno3,Kmm) = no3
	216	tr(:,:,:,jpnh4,Kmm) = bioma0
[7753]	217	IF( ln_ligand) THEN
[12377]	218	tr(:,:,:,jplgw,Kmm) = 0.6E-9
[7753]	219	ENDIF
	220	IF( ln_p5z ) THEN
[12377]	221	tr(:,:,:,jpdon,Kmm) = bioma0
	222	tr(:,:,:,jpdop,Kmm) = bioma0
	223	tr(:,:,:,jppon,Kmm) = bioma0
	224	tr(:,:,:,jppop,Kmm) = bioma0
	225	tr(:,:,:,jpgon,Kmm) = bioma0
	226	tr(:,:,:,jpgop,Kmm) = bioma0
	227	tr(:,:,:,jpnph,Kmm) = bioma0
	228	tr(:,:,:,jppph,Kmm) = bioma0
	229	tr(:,:,:,jppic,Kmm) = bioma0
	230	tr(:,:,:,jpnpi,Kmm) = bioma0
	231	tr(:,:,:,jpppi,Kmm) = bioma0
	232	tr(:,:,:,jpndi,Kmm) = bioma0
	233	tr(:,:,:,jppdi,Kmm) = bioma0
	234	tr(:,:,:,jppfe,Kmm) = bioma0 * 5.e-6
	235	tr(:,:,:,jppch,Kmm) = bioma0 * 12. / 55.
[7753]	236	ENDIF
[1287]	237	! initialize the half saturation constant for silicate
	238	! ----------------------------------------------------
[7753]	239	xksi(:,:) = 2.e-6
	240	xksimax(:,:) = xksi(:,:)
[10362]	241	IF( ln_p5z ) THEN
	242	sized(:,:,:) = 1.0
	243	sizen(:,:,:) = 1.0
	244	sized(:,:,:) = 1.0
	245	ENDIF
[3294]	246	END IF
	247
	248
[7646]	249	CALL p4z_sink_init ! vertical flux of particulate organic matter
	250	CALL p4z_opt_init ! Optic: PAR in the water column
	251	IF( ln_p4z ) THEN
	252	CALL p4z_lim_init ! co-limitations by the various nutrients
	253	CALL p4z_prod_init ! phytoplankton growth rate over the global ocean.
	254	ELSE
	255	CALL p5z_lim_init ! co-limitations by the various nutrients
	256	CALL p5z_prod_init ! phytoplankton growth rate over the global ocean.
	257	ENDIF
[12377]	258	CALL p4z_bc_init( Kmm ) ! boundary conditions
[7646]	259	CALL p4z_fechem_init ! Iron chemistry
	260	CALL p4z_rem_init ! remineralisation
	261	CALL p4z_poc_init ! remineralisation of organic particles
	262	IF( ln_ligand ) &
	263	& CALL p4z_ligand_init ! remineralisation of organic ligands
[3294]	264
[7646]	265	IF( ln_p4z ) THEN
	266	CALL p4z_mort_init ! phytoplankton mortality
	267	CALL p4z_micro_init ! microzooplankton
	268	CALL p4z_meso_init ! mesozooplankton
	269	ELSE
	270	CALL p5z_mort_init ! phytoplankton mortality
	271	CALL p5z_micro_init ! microzooplankton
	272	CALL p5z_meso_init ! mesozooplankton
	273	ENDIF
	274	CALL p4z_lys_init ! calcite saturation
	275	IF( .NOT.l_co2cpl ) &
	276	& CALL p4z_flx_init ! gas exchange
	277
[10222]	278	! Initialization of the sediment model
[12377]	279	IF( ln_sediment) &
	280	& CALL sed_init ! Initialization of the sediment model
[10222]	281
[12377]	282	CALL p4z_sed_init ! loss of organic matter in the sediments
	283
[3294]	284	IF(lwp) WRITE(numout,*)
[9169]	285	IF(lwp) WRITE(numout,*) ' ==>>> Initialization of PISCES tracers done'
[3294]	286	IF(lwp) WRITE(numout,*)
[935]	287	!
[3680]	288	END SUBROUTINE p4z_ini
[2715]	289
[9169]	290
[12377]	291	SUBROUTINE p2z_ini( Kmm )
[2528]	292	!!----------------------------------------------------------------------
[3680]	293	!! * ROUTINE p2z_ini *
[2528]	294	!!
[3680]	295	!! ** Purpose : Initialisation of the LOBSTER biochemical model
[2528]	296	!!----------------------------------------------------------------------
[2715]	297	!
[3680]	298	USE p2zopt
	299	USE p2zexp
	300	USE p2zbio
	301	USE p2zsed
	302	!
[12377]	303	INTEGER, INTENT(in) :: Kmm ! time level indices
[7646]	304	INTEGER :: ji, jj, jk, jn, ierr
	305	CHARACTER(len = 10) :: cltra
[2715]	306	!!----------------------------------------------------------------------
[3680]	307
	308	IF(lwp) WRITE(numout,*)
	309	IF(lwp) WRITE(numout,*) ' p2z_ini : LOBSTER biochemical model initialisation'
[9169]	310	IF(lwp) WRITE(numout,*) ' ~~~~~~~'
[3680]	311
	312	ierr = sms_pisces_alloc()
	313	ierr = ierr + p2z_exp_alloc()
[2715]	314	!
[10425]	315	CALL mpp_sum( 'trcini_pisces', ierr )
[3680]	316	IF( ierr /= 0 ) CALL ctl_stop( 'STOP', 'p2z_ini: unable to allocate LOBSTER arrays' )
	317
[7646]	318	DO jn = 1, jptra
	319	cltra = ctrcnm(jn)
	320	IF( cltra == 'DET' ) jpdet = jn !: detritus [mmoleN/m3]
	321	IF( cltra == 'ZOO' ) jpzoo = jn !: zooplancton concentration [mmoleN/m3]
	322	IF( cltra == 'PHY' ) jpphy = jn !: phytoplancton concentration [mmoleN/m3]
	323	IF( cltra == 'NO3' ) jpno3 = jn !: nitrate concentration [mmoleN/m3]
	324	IF( cltra == 'NH4' ) jpnh4 = jn !: ammonium concentration [mmoleN/m3]
	325	IF( cltra == 'DOM' ) jpdom = jn !: dissolved organic matter [mmoleN/m3]
	326	ENDDO
	327
	328	jpkb = 10 ! last level where depth less than 200 m
	329	DO jk = jpkm1, 1, -1
	330	IF( gdept_1d(jk) > 200. ) jpkb = jk
	331	END DO
	332	IF (lwp) WRITE(numout,*)
	333	IF (lwp) WRITE(numout,*) ' first vertical layers where biology is active (200m depth ) ', jpkb
	334	IF (lwp) WRITE(numout,*)
	335	jpkbm1 = jpkb - 1
	336	!
	337
	338
[3680]	339	! LOBSTER initialisation for GYRE : init NO3=f(density) by asklod AS Kremeur 2005-07
	340	! ----------------------
	341	IF( .NOT. ln_rsttr ) THEN ! in case of no restart
[12377]	342	tr(:,:,:,jpdet,Kmm) = 0.1 * tmask(:,:,:)
	343	tr(:,:,:,jpzoo,Kmm) = 0.1 * tmask(:,:,:)
	344	tr(:,:,:,jpnh4,Kmm) = 0.1 * tmask(:,:,:)
	345	tr(:,:,:,jpphy,Kmm) = 0.1 * tmask(:,:,:)
	346	tr(:,:,:,jpdom,Kmm) = 1.0 * tmask(:,:,:)
	347	WHERE( rhd(:,:,:) <= 24.5e-3 ) ; tr(:,:,:,jpno3,Kmm) = 2._wp * tmask(:,:,:)
	348	ELSE WHERE ; tr(:,:,:,jpno3,Kmm) = ( 15.55 * ( rhd(:,:,:) * 1000. ) - 380.11 ) * tmask(:,:,:)
[3680]	349	END WHERE
	350	ENDIF
[12377]	351	! ! Namelist read
	352	CALL p2z_opt_init ! Optics parameters
	353	CALL p2z_sed_init ! sedimentation
	354	CALL p2z_bio_init ! biology
	355	CALL p2z_exp_init( Kmm ) ! export
[2715]	356	!
[3680]	357	IF(lwp) WRITE(numout,*)
[9169]	358	IF(lwp) WRITE(numout,*) ' ==>>> Initialization of LOBSTER tracers done'
[3680]	359	IF(lwp) WRITE(numout,*)
	360	!
	361	END SUBROUTINE p2z_ini
[935]	362
	363	!!======================================================================
	364	END MODULE trcini_pisces

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