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p4zrem.F90 in NEMO/trunk/src/TOP/PISCES/P4Z – NEMO

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source: NEMO/trunk/src/TOP/PISCES/P4Z/p4zrem.F90 @ 10222

Last change on this file since 10222 was 10222, checked in by aumont, 5 years ago
update of the sediment module + enhancement, bug correction in PISCES generating O2 negative values
Property svn:keywords set to `Id`
File size: 17.9 KB

Rev	Line
[3443]	1	MODULE p4zrem
	2	!!======================================================================
	3	!! * MODULE p4zrem *
	4	!! TOP : PISCES Compute remineralization/dissolution of organic compounds
	5	!!=========================================================================
	6	!! History : 1.0 ! 2004 (O. Aumont) Original code
	7	!! 2.0 ! 2007-12 (C. Ethe, G. Madec) F90
	8	!! 3.4 ! 2011-06 (O. Aumont, C. Ethe) Quota model for iron
	9	!!----------------------------------------------------------------------
	10	!! p4z_rem : Compute remineralization/dissolution of organic compounds
	11	!! p4z_rem_init : Initialisation of parameters for remineralisation
	12	!! p4z_rem_alloc : Allocate remineralisation variables
	13	!!----------------------------------------------------------------------
	14	USE oce_trc ! shared variables between ocean and passive tracers
	15	USE trc ! passive tracers common variables
	16	USE sms_pisces ! PISCES Source Minus Sink variables
	17	USE p4zche ! chemical model
	18	USE p4zprod ! Growth rate of the 2 phyto groups
[9570]	19	USE p4zice
[3443]	20	USE prtctl_trc ! print control for debugging
	21	USE iom ! I/O manager
	22
	23
	24	IMPLICIT NONE
	25	PRIVATE
	26
	27	PUBLIC p4z_rem ! called in p4zbio.F90
	28	PUBLIC p4z_rem_init ! called in trcsms_pisces.F90
	29	PUBLIC p4z_rem_alloc
	30
[9169]	31	REAL(wp), PUBLIC :: xremikc !: remineralisation rate of DOC
	32	REAL(wp), PUBLIC :: xremikn !: remineralisation rate of DON
	33	REAL(wp), PUBLIC :: xremikp !: remineralisation rate of DOP
	34	REAL(wp), PUBLIC :: xremik !: remineralisation rate of POC
	35	REAL(wp), PUBLIC :: nitrif !: NH4 nitrification rate
	36	REAL(wp), PUBLIC :: xsirem !: remineralisation rate of POC
	37	REAL(wp), PUBLIC :: xsiremlab !: fast remineralisation rate of POC
	38	REAL(wp), PUBLIC :: xsilab !: fraction of labile biogenic silica
	39	REAL(wp), PUBLIC :: feratb !: Fe/C quota in bacteria
	40	REAL(wp), PUBLIC :: xkferb !: Half-saturation constant for bacteria Fe/C
[3443]	41
[9169]	42	REAL(wp), PUBLIC, ALLOCATABLE, SAVE, DIMENSION(:,:,:) :: denitr !: denitrification array
[3443]	43
	44	!!----------------------------------------------------------------------
[10067]	45	!! NEMO/TOP 4.0 , NEMO Consortium (2018)
[10069]	46	!! $Id$
[10068]	47	!! Software governed by the CeCILL license (see ./LICENSE)
[3443]	48	!!----------------------------------------------------------------------
	49	CONTAINS
	50
[5385]	51	SUBROUTINE p4z_rem( kt, knt )
[3443]	52	!!---------------------------------------------------------------------
	53	!! * ROUTINE p4z_rem *
	54	!!
	55	!! ** Purpose : Compute remineralization/scavenging of organic compounds
	56	!!
	57	!! ** Method : - ???
	58	!!---------------------------------------------------------------------
[5385]	59	INTEGER, INTENT(in) :: kt, knt ! ocean time step
[3443]	60	!
	61	INTEGER :: ji, jj, jk
[7646]	62	REAL(wp) :: zremik, zremikc, zremikn, zremikp, zsiremin, zfact
[3446]	63	REAL(wp) :: zsatur, zsatur2, znusil, znusil2, zdep, zdepmin, zfactdep
[7646]	64	REAL(wp) :: zbactfer, zolimit, zonitr, zrfact2
[8533]	65	REAL(wp) :: zammonic, zoxyrem
[7646]	66	REAL(wp) :: zosil, ztem, zdenitnh4, zolimic, zolimin, zolimip, zdenitrn, zdenitrp
[3443]	67	CHARACTER (len=25) :: charout
[9125]	68	REAL(wp), DIMENSION(jpi,jpj ) :: ztempbac
	69	REAL(wp), DIMENSION(jpi,jpj,jpk) :: zdepbac, zolimi, zdepprod, zfacsi, zfacsib
	70	REAL(wp), ALLOCATABLE, DIMENSION(:,:,:) :: zw3d
[3443]	71	!!---------------------------------------------------------------------
	72	!
[9124]	73	IF( ln_timing ) CALL timing_start('p4z_rem')
[3443]	74	!
[9125]	75	! Initialisation of arrys
[7753]	76	zdepprod(:,:,:) = 1._wp
	77	ztempbac(:,:) = 0._wp
	78	zfacsib(:,:,:) = xsilab / ( 1.0 - xsilab )
	79	zfacsi(:,:,:) = xsilab
[3443]	80
	81	! Computation of the mean phytoplankton concentration as
	82	! a crude estimate of the bacterial biomass
	83	! this parameterization has been deduced from a model version
	84	! that was modeling explicitely bacteria
	85	! -------------------------------------------------------
	86	DO jk = 1, jpkm1
	87	DO jj = 1, jpj
	88	DO ji = 1, jpi
	89	zdep = MAX( hmld(ji,jj), heup(ji,jj) )
[6140]	90	IF( gdept_n(ji,jj,jk) < zdep ) THEN
[5385]	91	zdepbac(ji,jj,jk) = MIN( 0.7 * ( trb(ji,jj,jk,jpzoo) + 2.* trb(ji,jj,jk,jpmes) ), 4.e-6 )
[3443]	92	ztempbac(ji,jj) = zdepbac(ji,jj,jk)
	93	ELSE
[6140]	94	zdepmin = MIN( 1., zdep / gdept_n(ji,jj,jk) )
[3446]	95	zdepbac (ji,jj,jk) = zdepmin*0.683 ztempbac(ji,jj)
	96	zdepprod(ji,jj,jk) = zdepmin**0.273
[3443]	97	ENDIF
	98	END DO
	99	END DO
	100	END DO
	101
[7646]	102	IF( ln_p4z ) THEN
	103	DO jk = 1, jpkm1
	104	DO jj = 1, jpj
	105	DO ji = 1, jpi
	106	! DOC ammonification. Depends on depth, phytoplankton biomass
	107	! and a limitation term which is supposed to be a parameterization of the bacterial activity.
	108	zremik = xremik * xstep / 1.e-6 * xlimbac(ji,jj,jk) * zdepbac(ji,jj,jk)
	109	zremik = MAX( zremik, 2.74e-4 * xstep )
	110	! Ammonification in oxic waters with oxygen consumption
	111	! -----------------------------------------------------
	112	zolimit = zremik * ( 1.- nitrfac(ji,jj,jk) ) * trb(ji,jj,jk,jpdoc)
	113	zolimi(ji,jj,jk) = MIN( ( trb(ji,jj,jk,jpoxy) - rtrn ) / o2ut, zolimit )
	114	! Ammonification in suboxic waters with denitrification
	115	! -------------------------------------------------------
[8533]	116	zammonic = zremik * nitrfac(ji,jj,jk) * trb(ji,jj,jk,jpdoc)
	117	denitr(ji,jj,jk) = zammonic * ( 1. - nitrfac2(ji,jj,jk) )
[10222]	118	denitr(ji,jj,jk) = MIN( ( trb(ji,jj,jk,jpno3) - rtrn ) / rdenit, denitr(ji,jj,jk) )
	119	zoxyrem = zammonic - denitr(ji,jj,jk)
[7646]	120	!
	121	zolimi (ji,jj,jk) = MAX( 0.e0, zolimi (ji,jj,jk) )
	122	denitr (ji,jj,jk) = MAX( 0.e0, denitr (ji,jj,jk) )
[8533]	123	zoxyrem = MAX( 0.e0, zoxyrem )
	124
[7646]	125	!
[8533]	126	tra(ji,jj,jk,jppo4) = tra(ji,jj,jk,jppo4) + zolimi (ji,jj,jk) + denitr(ji,jj,jk) + zoxyrem
	127	tra(ji,jj,jk,jpnh4) = tra(ji,jj,jk,jpnh4) + zolimi (ji,jj,jk) + denitr(ji,jj,jk) + zoxyrem
[7646]	128	tra(ji,jj,jk,jpno3) = tra(ji,jj,jk,jpno3) - denitr (ji,jj,jk) * rdenit
[8533]	129	tra(ji,jj,jk,jpdoc) = tra(ji,jj,jk,jpdoc) - zolimi (ji,jj,jk) - denitr(ji,jj,jk) - zoxyrem
[7646]	130	tra(ji,jj,jk,jpoxy) = tra(ji,jj,jk,jpoxy) - zolimi (ji,jj,jk) * o2ut
[8533]	131	tra(ji,jj,jk,jpdic) = tra(ji,jj,jk,jpdic) + zolimi (ji,jj,jk) + denitr(ji,jj,jk) + zoxyrem
	132	tra(ji,jj,jk,jptal) = tra(ji,jj,jk,jptal) + rno3 * ( zolimi(ji,jj,jk) + zoxyrem &
[7646]	133	& + ( rdenit + 1.) * denitr(ji,jj,jk) )
	134	END DO
[3443]	135	END DO
	136	END DO
[7646]	137	ELSE
	138	DO jk = 1, jpkm1
	139	DO jj = 1, jpj
	140	DO ji = 1, jpi
	141	! DOC ammonification. Depends on depth, phytoplankton biomass
	142	! and a limitation term which is supposed to be a parameterization of the bacterial activity.
	143	! -----------------------------------------------------------------
	144	zremik = xstep / 1.e-6 * MAX(0.01, xlimbac(ji,jj,jk)) * zdepbac(ji,jj,jk)
	145	zremik = MAX( zremik, 2.74e-4 * xstep / xremikc )
[3443]	146
[7646]	147	zremikc = xremikc * zremik
	148	zremikn = xremikn / xremikc
	149	zremikp = xremikp / xremikc
[3443]	150
[7646]	151	! Ammonification in oxic waters with oxygen consumption
	152	! -----------------------------------------------------
	153	zolimit = zremikc * ( 1.- nitrfac(ji,jj,jk) ) * trb(ji,jj,jk,jpdoc)
	154	zolimic = MAX( 0.e0, MIN( ( trb(ji,jj,jk,jpoxy) - rtrn ) / o2ut, zolimit ) )
	155	zolimi(ji,jj,jk) = zolimic
	156	zolimin = zremikn * zolimic * trb(ji,jj,jk,jpdon) / ( trb(ji,jj,jk,jpdoc) + rtrn )
	157	zolimip = zremikp * zolimic * trb(ji,jj,jk,jpdop) / ( trb(ji,jj,jk,jpdoc) + rtrn )
	158
	159	! Ammonification in suboxic waters with denitrification
	160	! -------------------------------------------------------
	161	zolimit = zremikc * nitrfac(ji,jj,jk) * trb(ji,jj,jk,jpdoc)
	162	denitr(ji,jj,jk) = MIN( ( trb(ji,jj,jk,jpno3) - rtrn ) / rdenit, zolimit )
	163	denitr(ji,jj,jk) = MAX( 0.e0, denitr(ji,jj,jk) )
	164	zdenitrn = zremikn * denitr(ji,jj,jk) * trb(ji,jj,jk,jpdon) / ( trb(ji,jj,jk,jpdoc) + rtrn )
	165	zdenitrp = zremikp * denitr(ji,jj,jk) * trb(ji,jj,jk,jpdop) / ( trb(ji,jj,jk,jpdoc) + rtrn )
	166
	167	tra(ji,jj,jk,jppo4) = tra(ji,jj,jk,jppo4) + zolimip + zdenitrp
	168	tra(ji,jj,jk,jpnh4) = tra(ji,jj,jk,jpnh4) + zolimin + zdenitrn
	169	tra(ji,jj,jk,jpno3) = tra(ji,jj,jk,jpno3) - denitr(ji,jj,jk) * rdenit
	170	tra(ji,jj,jk,jpdoc) = tra(ji,jj,jk,jpdoc) - zolimic - denitr(ji,jj,jk)
	171	tra(ji,jj,jk,jpdon) = tra(ji,jj,jk,jpdon) - zolimin - zdenitrn
	172	tra(ji,jj,jk,jpdop) = tra(ji,jj,jk,jpdop) - zolimip - zdenitrp
	173	tra(ji,jj,jk,jpoxy) = tra(ji,jj,jk,jpoxy) - zolimic * o2ut
	174	tra(ji,jj,jk,jpdic) = tra(ji,jj,jk,jpdic) + zolimic + denitr(ji,jj,jk)
	175	tra(ji,jj,jk,jptal) = tra(ji,jj,jk,jptal) + rno3 * ( zolimin + ( rdenit + 1.) * zdenitrn )
	176	END DO
	177	END DO
	178	END DO
	179	!
	180	ENDIF
	181
	182
[3443]	183	DO jk = 1, jpkm1
	184	DO jj = 1, jpj
	185	DO ji = 1, jpi
	186	! NH4 nitrification to NO3. Ceased for oxygen concentrations
	187	! below 2 umol/L. Inhibited at strong light
	188	! ----------------------------------------------------------
[7646]	189	zonitr = nitrif * xstep * trb(ji,jj,jk,jpnh4) * ( 1.- nitrfac(ji,jj,jk) ) &
	190	& / ( 1.+ emoy(ji,jj,jk) ) * ( 1. + fr_i(ji,jj) * emoy(ji,jj,jk) )
	191	zdenitnh4 = nitrif * xstep * trb(ji,jj,jk,jpnh4) * nitrfac(ji,jj,jk)
[10222]	192	zdenitnh4 = MIN( ( trb(ji,jj,jk,jpno3) - rtrn ) / rdenita, zdenitnh4 )
[3443]	193	! Update of the tracers trends
	194	! ----------------------------
[7646]	195	tra(ji,jj,jk,jpnh4) = tra(ji,jj,jk,jpnh4) - zonitr - zdenitnh4
	196	tra(ji,jj,jk,jpno3) = tra(ji,jj,jk,jpno3) + zonitr - rdenita * zdenitnh4
[3443]	197	tra(ji,jj,jk,jpoxy) = tra(ji,jj,jk,jpoxy) - o2nit * zonitr
[7646]	198	tra(ji,jj,jk,jptal) = tra(ji,jj,jk,jptal) - 2 * rno3 * zonitr + rno3 * ( rdenita - 1. ) * zdenitnh4
[3443]	199	END DO
	200	END DO
	201	END DO
	202
[7753]	203	IF(ln_ctl) THEN ! print mean trends (used for debugging)
	204	WRITE(charout, FMT="('rem1')")
	205	CALL prt_ctl_trc_info(charout)
	206	CALL prt_ctl_trc(tab4d=tra, mask=tmask, clinfo=ctrcnm)
	207	ENDIF
[3443]	208
	209	DO jk = 1, jpkm1
	210	DO jj = 1, jpj
	211	DO ji = 1, jpi
	212
	213	! Bacterial uptake of iron. No iron is available in DOC. So
	214	! Bacteries are obliged to take up iron from the water. Some
	215	! studies (especially at Papa) have shown this uptake to be significant
	216	! ----------------------------------------------------------
[7646]	217	zbactfer = feratb * rfact2 * prmax(ji,jj,jk) * xlimbacl(ji,jj,jk) &
	218	& * trb(ji,jj,jk,jpfer) / ( xkferb + trb(ji,jj,jk,jpfer) ) &
[3446]	219	& * zdepprod(ji,jj,jk) * zdepbac(ji,jj,jk)
[3443]	220	tra(ji,jj,jk,jpfer) = tra(ji,jj,jk,jpfer) - zbactfer*0.16
	221	tra(ji,jj,jk,jpsfe) = tra(ji,jj,jk,jpsfe) + zbactfer*0.12
	222	tra(ji,jj,jk,jpbfe) = tra(ji,jj,jk,jpbfe) + zbactfer*0.04
	223	END DO
	224	END DO
	225	END DO
	226
[7753]	227	IF(ln_ctl) THEN ! print mean trends (used for debugging)
	228	WRITE(charout, FMT="('rem2')")
	229	CALL prt_ctl_trc_info(charout)
	230	CALL prt_ctl_trc(tab4d=tra, mask=tmask, clinfo=ctrcnm)
	231	ENDIF
[3443]	232
[7646]	233	! Initialization of the array which contains the labile fraction
	234	! of bSi. Set to a constant in the upper ocean
	235	! ---------------------------------------------------------------
[3443]	236
	237	DO jk = 1, jpkm1
	238	DO jj = 1, jpj
	239	DO ji = 1, jpi
[7646]	240	zdep = MAX( hmld(ji,jj), heup_01(ji,jj) )
	241	zsatur = MAX( rtrn, ( sio3eq(ji,jj,jk) - trb(ji,jj,jk,jpsil) ) / ( sio3eq(ji,jj,jk) + rtrn ) )
	242	zsatur2 = ( 1. + tsn(ji,jj,jk,jp_tem) / 400.)**37
	243	znusil = 0.225 * ( 1. + tsn(ji,jj,jk,jp_tem) / 15.) * zsatur + 0.775 * zsatur2 * zsatur**9.25
[3443]	244	! Remineralization rate of BSi depedant on T and saturation
	245	! ---------------------------------------------------------
[7646]	246	IF ( gdept_n(ji,jj,jk) > zdep ) THEN
	247	zfacsib(ji,jj,jk) = zfacsib(ji,jj,jk-1) * EXP( -0.5 * ( xsiremlab - xsirem ) &
	248	& * znusil * e3t_n(ji,jj,jk) / wsbio4(ji,jj,jk) )
	249	zfacsi(ji,jj,jk) = zfacsib(ji,jj,jk) / ( 1.0 + zfacsib(ji,jj,jk) )
	250	zfacsib(ji,jj,jk) = zfacsib(ji,jj,jk) * EXP( -0.5 * ( xsiremlab - xsirem ) &
	251	& * znusil * e3t_n(ji,jj,jk) / wsbio4(ji,jj,jk) )
	252	ENDIF
	253	zsiremin = ( xsiremlab * zfacsi(ji,jj,jk) + xsirem * ( 1. - zfacsi(ji,jj,jk) ) ) * xstep * znusil
[5385]	254	zosil = zsiremin * trb(ji,jj,jk,jpgsi)
[3443]	255	!
	256	tra(ji,jj,jk,jpgsi) = tra(ji,jj,jk,jpgsi) - zosil
	257	tra(ji,jj,jk,jpsil) = tra(ji,jj,jk,jpsil) + zosil
	258	!
	259	END DO
	260	END DO
	261	END DO
	262
	263	IF(ln_ctl) THEN ! print mean trends (used for debugging)
[7646]	264	WRITE(charout, FMT="('rem3')")
[3443]	265	CALL prt_ctl_trc_info(charout)
	266	CALL prt_ctl_trc(tab4d=tra, mask=tmask, clinfo=ctrcnm)
[7753]	267	ENDIF
[3443]	268
[5385]	269	IF( knt == nrdttrc ) THEN
[9125]	270	ALLOCATE( zw3d(jpi,jpj,jpk) )
[7753]	271	zfact = 1.e+3 * rfact2r ! conversion from mol/l/kt to mol/m3/s
	272	!
	273	IF( iom_use( "REMIN" ) ) THEN
	274	zw3d(:,:,:) = zolimi(:,:,:) * tmask(:,:,:) * zfact ! Remineralisation rate
	275	CALL iom_put( "REMIN" , zw3d )
	276	ENDIF
	277	IF( iom_use( "DENIT" ) ) THEN
	278	zw3d(:,:,:) = denitr(:,:,:) * rdenit * rno3 * tmask(:,:,:) * zfact ! Denitrification
	279	CALL iom_put( "DENIT" , zw3d )
	280	ENDIF
	281	!
[9125]	282	DEALLOCATE( zw3d )
[7753]	283	ENDIF
[3443]	284	!
[9124]	285	IF( ln_timing ) CALL timing_stop('p4z_rem')
[3443]	286	!
	287	END SUBROUTINE p4z_rem
	288
	289
	290	SUBROUTINE p4z_rem_init
	291	!!----------------------------------------------------------------------
	292	!! * ROUTINE p4z_rem_init *
	293	!!
	294	!! ** Purpose : Initialization of remineralization parameters
	295	!!
	296	!! ** Method : Read the nampisrem namelist and check the parameters
	297	!! called at the first timestep
	298	!!
	299	!! ** input : Namelist nampisrem
	300	!!
	301	!!----------------------------------------------------------------------
[7646]	302	NAMELIST/nampisrem/ xremik, nitrif, xsirem, xsiremlab, xsilab, feratb, xkferb, &
	303	& xremikc, xremikn, xremikp
[4147]	304	INTEGER :: ios ! Local integer output status for namelist read
[9124]	305	!!----------------------------------------------------------------------
[9169]	306	!
	307	IF(lwp) THEN
	308	WRITE(numout,*)
	309	WRITE(numout,*) 'p4z_rem_init : Initialization of remineralization parameters'
	310	WRITE(numout,*) '~~~~~~~~~~~~'
	311	ENDIF
	312	!
[4147]	313	REWIND( numnatp_ref ) ! Namelist nampisrem in reference namelist : Pisces remineralization
	314	READ ( numnatp_ref, nampisrem, IOSTAT = ios, ERR = 901)
[9169]	315	901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'nampisrem in reference namelist', lwp )
[4147]	316	REWIND( numnatp_cfg ) ! Namelist nampisrem in configuration namelist : Pisces remineralization
	317	READ ( numnatp_cfg, nampisrem, IOSTAT = ios, ERR = 902 )
[9169]	318	902 IF( ios > 0 ) CALL ctl_nam ( ios , 'nampisrem in configuration namelist', lwp )
	319	IF(lwm) WRITE( numonp, nampisrem )
[4147]	320
[3443]	321	IF(lwp) THEN ! control print
[9169]	322	WRITE(numout,*) ' Namelist parameters for remineralization, nampisrem'
[7646]	323	IF( ln_p4z ) THEN
[9169]	324	WRITE(numout,*) ' remineralization rate of DOC xremik =', xremik
[7646]	325	ELSE
[9169]	326	WRITE(numout,*) ' remineralization rate of DOC xremikc =', xremikc
	327	WRITE(numout,*) ' remineralization rate of DON xremikn =', xremikn
	328	WRITE(numout,*) ' remineralization rate of DOP xremikp =', xremikp
[7646]	329	ENDIF
[9169]	330	WRITE(numout,*) ' remineralization rate of Si xsirem =', xsirem
	331	WRITE(numout,*) ' fast remineralization rate of Si xsiremlab =', xsiremlab
	332	WRITE(numout,*) ' fraction of labile biogenic silica xsilab =', xsilab
	333	WRITE(numout,*) ' NH4 nitrification rate nitrif =', nitrif
	334	WRITE(numout,*) ' Bacterial Fe/C ratio feratb =', feratb
	335	WRITE(numout,*) ' Half-saturation constant for bact. Fe/C xkferb =', xkferb
[3443]	336	ENDIF
	337	!
[9169]	338	denitr(:,:,:) = 0._wp
[3443]	339	!
	340	END SUBROUTINE p4z_rem_init
	341
	342
	343	INTEGER FUNCTION p4z_rem_alloc()
	344	!!----------------------------------------------------------------------
	345	!! * ROUTINE p4z_rem_alloc *
	346	!!----------------------------------------------------------------------
[7646]	347	ALLOCATE( denitr(jpi,jpj,jpk), STAT=p4z_rem_alloc )
[3443]	348	!
	349	IF( p4z_rem_alloc /= 0 ) CALL ctl_warn('p4z_rem_alloc: failed to allocate arrays')
	350	!
	351	END FUNCTION p4z_rem_alloc
	352
	353	!!======================================================================
	354	END MODULE p4zrem

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