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nemogcm.F90 in NEMO/trunk/src/OCE – NEMO

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source: NEMO/trunk/src/OCE/nemogcm.F90 @ 14125

Last change on this file since 14125 was 14118, checked in by techene, 3 years ago
#2385 bug fixes for qco
Property svn:keywords set to `Id`
File size: 32.6 KB

Rev	Line
[2496]	1	MODULE nemogcm
[2442]	2	!!======================================================================
[2496]	3	!! * MODULE nemogcm *
	4	!! Ocean system : NEMO GCM (ocean dynamics, on-line tracers, biochemistry and sea-ice)
[2442]	5	!!======================================================================
[1593]	6	!! History : OPA ! 1990-10 (C. Levy, G. Madec) Original code
	7	!! 7.0 ! 1991-11 (M. Imbard, C. Levy, G. Madec)
[3764]	8	!! 7.1 ! 1993-03 (M. Imbard, C. Levy, G. Madec, O. Marti, M. Guyon, A. Lazar,
	9	!! P. Delecluse, C. Perigaud, G. Caniaux, B. Colot, C. Maes) release 7.1
[1593]	10	!! - ! 1992-06 (L.Terray) coupling implementation
[3764]	11	!! - ! 1993-11 (M.A. Filiberti) IGLOO sea-ice
	12	!! 8.0 ! 1996-03 (M. Imbard, C. Levy, G. Madec, O. Marti, M. Guyon, A. Lazar,
[2104]	13	!! P. Delecluse, L.Terray, M.A. Filiberti, J. Vialar, A.M. Treguier, M. Levy) release 8.0
[1593]	14	!! 8.1 ! 1997-06 (M. Imbard, G. Madec)
[9656]	15	!! 8.2 ! 1999-11 (M. Imbard, H. Goosse) sea-ice model
[3764]	16	!! ! 1999-12 (V. Thierry, A-M. Treguier, M. Imbard, M-A. Foujols) OPEN-MP
[1593]	17	!! ! 2000-07 (J-M Molines, M. Imbard) Open Boundary Conditions (CLIPPER)
	18	!! NEMO 1.0 ! 2002-08 (G. Madec) F90: Free form and modules
	19	!! - ! 2004-06 (R. Redler, NEC CCRLE, Germany) add OASIS[3/4] coupled interfaces
	20	!! - ! 2004-08 (C. Talandier) New trends organization
	21	!! - ! 2005-06 (C. Ethe) Add the 1D configuration possibility
	22	!! - ! 2005-11 (V. Garnier) Surface pressure gradient organization
	23	!! - ! 2006-03 (L. Debreu, C. Mazauric) Agrif implementation
	24	!! - ! 2006-04 (G. Madec, R. Benshila) Step reorganization
	25	!! - ! 2007-07 (J. Chanut, A. Sellar) Unstructured open boundaries (BDY)
	26	!! 3.2 ! 2009-08 (S. Masson) open/write in the listing file in mpp
[3764]	27	!! 3.3 ! 2010-05 (K. Mogensen, A. Weaver, M. Martin, D. Lea) Assimilation interface
[2236]	28	!! - ! 2010-10 (C. Ethe, G. Madec) reorganisation of initialisation phase
[3294]	29	!! 3.3.1! 2011-01 (A. R. Porter, STFC Daresbury) dynamical allocation
[5836]	30	!! - ! 2011-11 (C. Harris) decomposition changes for running with CICE
[14072]	31	!! 3.6 ! 2012-05 (C. Calone, J. Simeon, G. Madec, C. Ethe) Add grid coarsening
[5836]	32	!! - ! 2014-12 (G. Madec) remove KPP scheme and cross-land advection (cla)
[7646]	33	!! 4.0 ! 2016-10 (G. Madec, S. Flavoni) domain configuration / user defined interface
[1593]	34	!!----------------------------------------------------------------------
[3]	35
	36	!!----------------------------------------------------------------------
[6140]	37	!! nemo_gcm : solve ocean dynamics, tracer, biogeochemistry and/or sea-ice
	38	!! nemo_init : initialization of the NEMO system
	39	!! nemo_ctl : initialisation of the contol print
	40	!! nemo_closefile: close remaining open files
	41	!! nemo_alloc : dynamical allocation
[3]	42	!!----------------------------------------------------------------------
[6140]	43	USE step_oce ! module used in the ocean time stepping module (step.F90)
[14053]	44	!
[7646]	45	USE phycst ! physical constant (par_cst routine)
	46	USE domain ! domain initialization (dom_init & dom_cfg routines)
[14053]	47	USE wet_dry ! Wetting and drying setting (wad_init routine)
	48	USE usrdef_nam ! user defined configuration namelist
	49	USE tide_mod, ONLY : tide_init ! tidal components initialization (tide_init routine)
	50	USE bdyini , ONLY : bdy_init ! open boundary cond. setting (bdy_init routine)
[6140]	51	USE istate ! initial state setting (istate_init routine)
	52	USE trdini ! dyn/tra trends initialization (trd_init routine)
[14086]	53	USE asminc ! assimilation increments
	54	USE asmbkg ! writing out state trajectory
	55	USE diadct ! sections transports (dia_dct_init routine)
	56	USE diaobs ! Observation diagnostics (dia_obs_init routine)
	57	USE diacfl ! CFL diagnostics (dia_cfl_init routine)
	58	USE diamlr ! IOM context management for multiple-linear-regression analysis
	59	USE isfstp ! ice shelf (isf_stp_init routine)
[6140]	60	USE icbini ! handle bergs, initialisation
[14053]	61	USE icbstp , ONLY : icb_end ! handle bergs, close iceberg files
[6140]	62	USE cpl_oasis3 ! OASIS3 coupling
[14053]	63	USE dyndmp ! Momentum damping (C1D only)
	64	USE step_diu ! diurnal bulk SST timestepping (called from here if run offline)
	65	USE crsini ! initialise grid coarsening utility
	66	USE dia25h , ONLY : dia_25h_init ! 25h mean output (initialisation)
[6140]	67	USE c1d ! 1D configuration
	68	USE step_c1d ! Time stepping loop for the 1D configuration
[1594]	69	#if defined key_top
[6140]	70	USE trcini ! passive tracer initialisation
[1594]	71	#endif
[7646]	72	#if defined key_nemocice_decomp
	73	USE ice_domain_size, only: nx_global, ny_global
	74	#endif
[14053]	75	#if defined key_qco
	76	USE stpmlf ! NEMO time-stepping (stp_MLF routine)
	77	#else
	78	USE step ! NEMO time-stepping (stp routine)
	79	#endif
[7646]	80	!
[6140]	81	USE lib_mpp ! distributed memory computing
[7646]	82	USE mppini ! shared/distributed memory setting (mpp_init routine)
[14072]	83	USE lbcnfd , ONLY : isendto, nsndto ! Setup of north fold exchanges
[7646]	84	USE lib_fortran ! Fortran utilities (allows no signed zero when 'key_nosignedzero' defined)
[14086]	85	#if defined key_iomput
	86	USE xios ! xIOserver
	87	#endif
	88	#if defined key_agrif
	89	USE agrif_all_update ! Master Agrif update
	90	USE agrif_oce_update
	91	#endif
	92	USE halo_mng
[268]	93
[2715]	94	IMPLICIT NONE
[3]	95	PRIVATE
	96
[2496]	97	PUBLIC nemo_gcm ! called by model.F90
	98	PUBLIC nemo_init ! needed by AGRIF
[3764]	99	PUBLIC nemo_alloc ! needed by TAM
[467]	100
[2498]	101	CHARACTER(lc) :: cform_aaa="( /, 'AAAAAAAA', / ) " ! flag for output listing
[1593]	102
[10425]	103	#if defined key_mpp_mpi
[11536]	104	! need MPI_Wtime
[10425]	105	INCLUDE 'mpif.h'
	106	#endif
	107
[3]	108	!!----------------------------------------------------------------------
[9570]	109	!! NEMO/OCE 4.0 , NEMO Consortium (2018)
[2392]	110	!! $Id$
[10068]	111	!! Software governed by the CeCILL license (see ./LICENSE)
[3]	112	!!----------------------------------------------------------------------
	113	CONTAINS
	114
[2496]	115	SUBROUTINE nemo_gcm
[3]	116	!!----------------------------------------------------------------------
[2496]	117	!! * ROUTINE nemo_gcm *
[3]	118	!!
[3764]	119	!! ** Purpose : NEMO solves the primitive equations on an orthogonal
[1593]	120	!! curvilinear mesh on the sphere.
[3]	121	!!
	122	!! ** Method : - model general initialization
	123	!! - launch the time-stepping (stp routine)
[1593]	124	!! - finalize the run by closing files and communications
[3]	125	!!
[2715]	126	!! References : Madec, Delecluse, Imbard, and Levy, 1997: internal report, IPSL.
[1593]	127	!! Madec, 2008, internal report, IPSL.
[3]	128	!!----------------------------------------------------------------------
[7646]	129	INTEGER :: istp ! time step index
[11536]	130	REAL(wp):: zstptiming ! elapsed time for 1 time step
[389]	131	!!----------------------------------------------------------------------
[2382]	132	!
[392]	133	#if defined key_agrif
[1593]	134	CALL Agrif_Init_Grids() ! AGRIF: set the meshes
[389]	135	#endif
[1593]	136	! !-----------------------!
[2496]	137	CALL nemo_init !== Initialisations ==!
[1593]	138	! !-----------------------!
[2715]	139	#if defined key_agrif
[12377]	140	Kbb_a = Nbb; Kmm_a = Nnn; Krhs_a = Nrhs ! agrif_oce module copies of time level indices
[13216]	141	CALL Agrif_Declare_Var ! " " " " " DYN/TRA
[2715]	142	# if defined key_top
[3680]	143	CALL Agrif_Declare_Var_top ! " " " " " TOP
[2715]	144	# endif
	145	#endif
[682]	146	! check that all process are still there... If some process have an error,
	147	! they will never enter in step and other processes will wait until the end of the cpu time!
[10425]	148	CALL mpp_max( 'nemogcm', nstop )
[682]	149
[1593]	150	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	151
	152	! !-----------------------!
	153	! !== time stepping ==!
	154	! !-----------------------!
[12489]	155	!
	156	! !== set the model time-step ==!
	157	!
[900]	158	istp = nit000
[9210]	159	!
[2236]	160	#if defined key_c1d
[9210]	161	DO WHILE ( istp <= nitend .AND. nstop == 0 ) !== C1D time-stepping ==!
	162	CALL stp_c1d( istp )
	163	istp = istp + 1
	164	END DO
[2236]	165	#else
[9210]	166	!
	167	# if defined key_agrif
	168	! !== AGRIF time-stepping ==!
	169	CALL Agrif_Regrid()
[9213]	170	!
[9780]	171	! Recursive update from highest nested level to lowest:
[12377]	172	Kbb_a = Nbb; Kmm_a = Nnn; Krhs_a = Nrhs ! agrif_oce module copies of time level indices
[9780]	173	CALL Agrif_step_child_adj(Agrif_Update_All)
[14086]	174	CALL Agrif_step_child_adj(Agrif_Check_parent_bat)
[9780]	175	!
[9210]	176	DO WHILE( istp <= nitend .AND. nstop == 0 )
[14053]	177	# if defined key_qco
[13237]	178	CALL stp_MLF
[14053]	179	# else
[9210]	180	CALL stp
[14053]	181	# endif
[9210]	182	istp = istp + 1
	183	END DO
	184	!
	185	# else
	186	!
	187	IF( .NOT.ln_diurnal_only ) THEN !== Standard time-stepping ==!
	188	!
	189	DO WHILE( istp <= nitend .AND. nstop == 0 )
[14053]	190	!
[10425]	191	ncom_stp = istp
[11536]	192	IF( ln_timing ) THEN
	193	zstptiming = MPI_Wtime()
	194	IF ( istp == ( nit000 + 1 ) ) elapsed_time = zstptiming
	195	IF ( istp == nitend ) elapsed_time = zstptiming - elapsed_time
	196	ENDIF
[14053]	197	!
	198	# if defined key_qco
[13237]	199	CALL stp_MLF ( istp )
[14053]	200	# else
[14072]	201	CALL stp ( istp )
[14053]	202	# endif
[389]	203	istp = istp + 1
[14053]	204	!
[11536]	205	IF( lwp .AND. ln_timing ) WRITE(numtime,*) 'timing step ', istp-1, ' : ', MPI_Wtime() - zstptiming
[14053]	206	!
[389]	207	END DO
[9210]	208	!
	209	ELSE !== diurnal SST time-steeping only ==!
	210	!
	211	DO WHILE( istp <= nitend .AND. nstop == 0 )
[14072]	212	CALL stp_diurnal( istp ) ! time step only the diurnal SST
[9210]	213	istp = istp + 1
	214	END DO
	215	!
	216	ENDIF
	217	!
	218	# endif
	219	!
[2236]	220	#endif
[9210]	221	!
[6140]	222	IF( ln_diaobs ) CALL dia_obs_wri
[3609]	223	!
	224	IF( ln_icebergs ) CALL icb_end( nitend )
[3764]	225
[1593]	226	! !------------------------!
	227	! !== finalize the run ==!
	228	! !------------------------!
[7646]	229	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
[1593]	230	!
[7646]	231	IF( nstop /= 0 .AND. lwp ) THEN ! error print
[11536]	232	WRITE(ctmp1,*) ' ==>>> nemo_gcm: a total of ', nstop, ' errors have been found'
[12933]	233	IF( ngrdstop > 0 ) THEN
	234	WRITE(ctmp9,'(i2)') ngrdstop
[13011]	235	WRITE(ctmp2,*) ' E R R O R detected in Agrif grid '//TRIM(ctmp9)
	236	WRITE(ctmp3,) ' Look for "E R R O R" messages in all existing '//TRIM(ctmp9)//'_ocean_output files'
	237	CALL ctl_stop( ' ', ctmp1, ' ', ctmp2, ' ', ctmp3 )
[12933]	238	ELSE
[13011]	239	WRITE(ctmp2,) ' Look for "E R R O R" messages in all existing ocean_output files'
	240	CALL ctl_stop( ' ', ctmp1, ' ', ctmp2 )
[12933]	241	ENDIF
[389]	242	ENDIF
[1593]	243	!
[9124]	244	IF( ln_timing ) CALL timing_finalize
[3294]	245	!
[2496]	246	CALL nemo_closefile
[4990]	247	!
[3769]	248	#if defined key_iomput
[9210]	249	CALL xios_finalize ! end mpp communications with xios
	250	IF( lk_oasis ) CALL cpl_finalize ! end coupling and mpp communications with OASIS
[532]	251	#else
[9210]	252	IF ( lk_oasis ) THEN ; CALL cpl_finalize ! end coupling and mpp communications with OASIS
[13011]	253	ELSEIF( lk_mpp ) THEN ; CALL mppstop ! end mpp communications
[4990]	254	ENDIF
[532]	255	#endif
[900]	256	!
[10436]	257	IF(lwm) THEN
	258	IF( nstop == 0 ) THEN ; STOP 0
[11536]	259	ELSE ; STOP 123
[10436]	260	ENDIF
[10425]	261	ENDIF
	262	!
[2496]	263	END SUBROUTINE nemo_gcm
[389]	264
	265
[2496]	266	SUBROUTINE nemo_init
[389]	267	!!----------------------------------------------------------------------
[2496]	268	!! * ROUTINE nemo_init *
[389]	269	!!
[2496]	270	!! ** Purpose : initialization of the NEMO GCM
[389]	271	!!----------------------------------------------------------------------
[11536]	272	INTEGER :: ios, ilocal_comm ! local integers
[9213]	273	!!
[14053]	274	NAMELIST/namctl/ sn_cfctl, ln_timing, ln_diacfl, nn_isplt, nn_jsplt , nn_ictls, &
	275	& nn_ictle, nn_jctls , nn_jctle
[9213]	276	NAMELIST/namcfg/ ln_read_cfg, cn_domcfg, ln_closea, ln_write_cfg, cn_domcfg_out, ln_use_jattr
[3]	277	!!----------------------------------------------------------------------
[1593]	278	!
[5407]	279	cxios_context = 'nemo'
[2496]	280	!
[11536]	281	! !-------------------------------------------------!
	282	! ! set communicator & select the local rank !
	283	! ! must be done as soon as possible to get narea !
	284	! !-------------------------------------------------!
[1593]	285	!
[1412]	286	#if defined key_iomput
[2200]	287	IF( Agrif_Root() ) THEN
[5407]	288	IF( lk_oasis ) THEN
[7646]	289	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
[11536]	290	CALL xios_initialize( "not used" , local_comm =ilocal_comm ) ! send nemo communicator to xios
[4990]	291	ELSE
[11536]	292	CALL xios_initialize( "for_xios_mpi_id", return_comm=ilocal_comm ) ! nemo local communicator given by xios
[4990]	293	ENDIF
[2200]	294	ENDIF
[11536]	295	CALL mpp_start( ilocal_comm )
[532]	296	#else
[5407]	297	IF( lk_oasis ) THEN
[4990]	298	IF( Agrif_Root() ) THEN
[7646]	299	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
[4990]	300	ENDIF
[11536]	301	CALL mpp_start( ilocal_comm )
[4990]	302	ELSE
[11536]	303	CALL mpp_start( )
[2236]	304	ENDIF
[532]	305	#endif
[11536]	306	!
	307	narea = mpprank + 1 ! mpprank: the rank of proc (0 --> mppsize -1 )
	308	lwm = (narea == 1) ! control of output namelists
	309	!
	310	! !---------------------------------------------------------------!
	311	! ! Open output files, reference and configuration namelist files !
	312	! !---------------------------------------------------------------!
	313	!
	314	! open ocean.output as soon as possible to get all output prints (including errors messages)
	315	IF( lwm ) CALL ctl_opn( numout, 'ocean.output', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, -1, .FALSE. )
	316	! open reference and configuration namelist files
[12377]	317	CALL load_nml( numnam_ref, 'namelist_ref', -1, lwm )
	318	CALL load_nml( numnam_cfg, 'namelist_cfg', -1, lwm )
[11536]	319	IF( lwm ) CALL ctl_opn( numond, 'output.namelist.dyn', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, -1, .FALSE. )
	320	! open /dev/null file to be able to supress output write easily
[12641]	321	IF( Agrif_Root() ) THEN
[11536]	322	CALL ctl_opn( numnul, '/dev/null', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, -1, .FALSE. )
[12641]	323	#ifdef key_agrif
	324	ELSE
[14072]	325	numnul = Agrif_Parent(numnul)
[12641]	326	#endif
	327	ENDIF
[11536]	328	! !--------------------!
[12377]	329	! ! Open listing units ! -> need sn_cfctl from namctl to define lwp
[11536]	330	! !--------------------!
	331	!
	332	READ ( numnam_ref, namctl, IOSTAT = ios, ERR = 901 )
	333	901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in reference namelist' )
	334	READ ( numnam_cfg, namctl, IOSTAT = ios, ERR = 902 )
	335	902 IF( ios > 0 ) CALL ctl_nam ( ios , 'namctl in configuration namelist' )
	336	!
[12377]	337	! finalize the definition of namctl variables
[12933]	338	IF( narea < sn_cfctl%procmin .OR. narea > sn_cfctl%procmax .OR. MOD( narea - sn_cfctl%procmin, sn_cfctl%procincr ) /= 0 ) &
	339	& CALL nemo_set_cfctl( sn_cfctl, .FALSE. )
[11536]	340	!
[12377]	341	lwp = (narea == 1) .OR. sn_cfctl%l_oceout ! control of all listing output print
	342	!
[11536]	343	IF(lwp) THEN ! open listing units
[1593]	344	!
[14053]	345	IF( .NOT.lwm ) & ! alreay opened for narea == 1
[11536]	346	& CALL ctl_opn( numout, 'ocean.output', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, -1, .FALSE., narea )
[1593]	347	!
[1579]	348	WRITE(numout,*)
[11536]	349	WRITE(numout,*) ' CNRS - NERC - Met OFFICE - MERCATOR-ocean - CMCC'
[1593]	350	WRITE(numout,*) ' NEMO team'
[1579]	351	WRITE(numout,*) ' Ocean General Circulation Model'
[14053]	352	WRITE(numout,*) ' NEMO version 4.0 (2020) '
[1579]	353	WRITE(numout,*)
[10510]	354	WRITE(numout,*) " ._ ._ ._ ._ ._ "
	355	WRITE(numout,*) " _.-._)`\_.-._)`\_.-._)`\_.-._)`\_.-._)`\_ "
[1579]	356	WRITE(numout,*)
[10510]	357	WRITE(numout,*) " o _, _, "
	358	WRITE(numout,*) " o .' ( .-' / "
	359	WRITE(numout,*) " o _/..._'. .' / "
	360	WRITE(numout,*) " ( o .-'` ` '-./ _.' "
	361	WRITE(numout,*) " ) ( o) ;= <_ ( "
	362	WRITE(numout,*) " ( '-.,\\__ __.-;`\ '. ) "
	363	WRITE(numout,*) " ) ) \) \|`\ \) '. \ ( ( "
	364	WRITE(numout,*) " ( ( \_/ '-._\ ) ) "
[10583]	365	WRITE(numout,*) " ) ) jgs ` ( ( "
[10510]	366	WRITE(numout,*) " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ "
	367	WRITE(numout,*)
[14053]	368	!
	369	WRITE(numout,cform_aaa) ! Flag AAAAAAA
	370	!
	371	! ! Control print of the working precision
	372	WRITE(numout,*)
	373	IF( wp == dp ) THEN ; WRITE(numout,*) "par_kind : wp = Working precision = dp = double-precision"
	374	ELSE ; WRITE(numout,*) "par_kind : wp = Working precision = sp = single-precision"
[13226]	375	ENDIF
[14053]	376	WRITE(numout,) "~~~~~~~~ ***************"
	377	WRITE(numout,*)
[1593]	378	!
[473]	379	ENDIF
[10425]	380	!
[11536]	381	IF(lwm) WRITE( numond, namctl )
	382	!
	383	! !------------------------------------!
	384	! ! Set global domain size parameters !
	385	! !------------------------------------!
	386	!
	387	READ ( numnam_ref, namcfg, IOSTAT = ios, ERR = 903 )
	388	903 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in reference namelist' )
	389	READ ( numnam_cfg, namcfg, IOSTAT = ios, ERR = 904 )
[14072]	390	904 IF( ios > 0 ) CALL ctl_nam ( ios , 'namcfg in configuration namelist' )
[11536]	391	!
	392	IF( ln_read_cfg ) THEN ! Read sizes in domain configuration file
[13286]	393	CALL domain_cfg ( cn_cfg, nn_cfg, Ni0glo, Nj0glo, jpkglo, jperio )
[11536]	394	ELSE ! user-defined namelist
[13286]	395	CALL usr_def_nam( cn_cfg, nn_cfg, Ni0glo, Nj0glo, jpkglo, jperio )
[11536]	396	ENDIF
	397	!
	398	IF(lwm) WRITE( numond, namcfg )
	399	!
	400	! !-----------------------------------------!
	401	! ! mpp parameters and domain decomposition !
	402	! !-----------------------------------------!
	403	CALL mpp_init
[2715]	404
[13286]	405	CALL halo_mng_init()
[7646]	406	! Now we know the dimensions of the grid and numout has been set: we can allocate arrays
[2715]	407	CALL nemo_alloc()
	408
[12377]	409	! Initialise time level indices
[14053]	410	Nbb = 1 ; Nnn = 2 ; Naa = 3 ; Nrhs = Naa
[13216]	411	#if defined key_agrif
[14053]	412	Kbb_a = Nbb ; Kmm_a = Nnn ; Krhs_a = Nrhs ! agrif_oce module copies of time level indices
[14072]	413	#endif
[2496]	414	! !-------------------------------!
	415	! ! NEMO general initialization !
	416	! !-------------------------------!
[473]	417
[14053]	418	CALL nemo_ctl ! Control prints of namctl and namcfg
[2382]	419	!
[9213]	420	! ! General initialization
	421	IF( ln_timing ) CALL timing_init ! timing
	422	IF( ln_timing ) CALL timing_start( 'nemo_init')
[3294]	423	!
[9367]	424	CALL phy_cst ! Physical constants
	425	CALL eos_init ! Equation of state
	426	IF( lk_c1d ) CALL c1d_init ! 1D column configuration
	427	CALL wad_init ! Wetting and drying options
[13216]	428
	429	#if defined key_agrif
	430	CALL Agrif_Declare_Var_ini ! " " " " " DOM
	431	#endif
[14053]	432	CALL dom_init( Nbb, Nnn, Naa ) ! Domain
[14072]	433	IF( ln_crs ) CALL crs_init( Nnn ) ! coarsened grid: domain initialization
[12377]	434	IF( sn_cfctl%l_prtctl ) &
	435	& CALL prt_ctl_init ! Print control
[14072]	436
[12377]	437	CALL diurnal_sst_bulk_init ! diurnal sst
[14072]	438	IF( ln_diurnal ) CALL diurnal_sst_coolskin_init ! cool skin
	439	!
[12377]	440	IF( ln_diurnal_only ) THEN ! diurnal only: a subset of the initialisation routines
	441	CALL istate_init( Nbb, Nnn, Naa ) ! ocean initial state (Dynamics and tracers)
	442	CALL sbc_init( Nbb, Nnn, Naa ) ! Forcings : surface module
	443	CALL tra_qsr_init ! penetrative solar radiation qsr
	444	IF( ln_diaobs ) THEN ! Observation & model comparison
	445	CALL dia_obs_init( Nnn ) ! Initialize observational data
	446	CALL dia_obs( nit000 - 1, Nnn ) ! Observation operator for restart
[14072]	447	ENDIF
[12377]	448	IF( lk_asminc ) CALL asm_inc_init( Nbb, Nnn, Nrhs ) ! Assimilation increments
[9213]	449	!
	450	RETURN ! end of initialization
[6140]	451	ENDIF
[12377]	452	!
[13216]	453
[12377]	454	CALL istate_init( Nbb, Nnn, Naa ) ! ocean initial state (Dynamics and tracers)
[3651]	455
[14072]	456	! ! external forcing
[12377]	457	CALL tide_init ! tidal harmonics
	458	CALL sbc_init( Nbb, Nnn, Naa ) ! surface boundary conditions (including sea-ice)
	459	CALL bdy_init ! Open boundaries initialisation
[9019]	460
[5836]	461	! ! Ocean physics
[12377]	462	CALL zdf_phy_init( Nnn ) ! Vertical physics
[14072]	463
[2082]	464	! ! Lateral physics
[9019]	465	CALL ldf_tra_init ! Lateral ocean tracer physics
[13558]	466	CALL ldf_eiv_init ! eddy induced velocity param. must be done after ldf_tra_init
[9019]	467	CALL ldf_dyn_init ! Lateral ocean momentum physics
[2082]	468
[9019]	469	! ! Active tracers
	470	IF( ln_traqsr ) CALL tra_qsr_init ! penetrative solar radiation qsr
	471	CALL tra_bbc_init ! bottom heat flux
[10350]	472	CALL tra_bbl_init ! advective (and/or diffusive) bottom boundary layer scheme
[9019]	473	CALL tra_dmp_init ! internal tracer damping
	474	CALL tra_adv_init ! horizontal & vertical advection
	475	CALL tra_ldf_init ! lateral mixing
[2027]	476
[9019]	477	! ! Dynamics
[12377]	478	IF( lk_c1d ) CALL dyn_dmp_init ! internal momentum damping
	479	CALL dyn_adv_init ! advection (vector or flux form)
	480	CALL dyn_vor_init ! vorticity term including Coriolis
	481	CALL dyn_ldf_init ! lateral mixing
	482	CALL dyn_hpg_init( Nnn ) ! horizontal gradient of Hydrostatic pressure
	483	CALL dyn_spg_init ! surface pressure gradient
[3764]	484
[14032]	485	! ! Icebergs
	486	CALL icb_init( rn_Dt, nit000) ! initialise icebergs instance
	487
	488	! ice shelf
	489	CALL isf_init( Nbb, Nnn, Naa )
[5836]	490	#if defined key_top
	491	! ! Passive tracers
[12377]	492	CALL trc_init( Nbb, Nnn, Naa )
[5836]	493	#endif
[9019]	494	IF( l_ldfslp ) CALL ldf_slp_init ! slope of lateral mixing
[5836]	495
	496	! ! Misc. options
[9019]	497	CALL sto_par_init ! Stochastic parametrization
	498	IF( ln_sto_eos ) CALL sto_pts_init ! RRandom T/S fluctuations
[14072]	499
[5836]	500	! ! Diagnostics
[12377]	501	CALL flo_init( Nnn ) ! drifting Floats
[9019]	502	IF( ln_diacfl ) CALL dia_cfl_init ! Initialise CFL diagnostics
[11536]	503	CALL dia_dct_init ! Sections tranports
[12377]	504	CALL dia_hsb_init( Nnn ) ! heat content, salt content and volume budgets
	505	CALL trd_init( Nnn ) ! Mixed-layer/Vorticity/Integral constraints trends
	506	CALL dia_obs_init( Nnn ) ! Initialize observational data
	507	CALL dia_25h_init( Nbb ) ! 25h mean outputs
	508	CALL dia_detide_init ! Weights computation for daily detiding of model diagnostics
	509	IF( ln_diaobs ) CALL dia_obs( nit000-1, Nnn ) ! Observation operator for restart
	510	CALL dia_mlr_init ! Initialisation of IOM context management for multiple-linear-regression analysis
[6140]	511
[9019]	512	! ! Assimilation increments
[12377]	513	IF( lk_asminc ) CALL asm_inc_init( Nbb, Nnn, Nrhs ) ! Initialize assimilation increments
[1593]	514	!
[9213]	515	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	516	!
	517	IF( ln_timing ) CALL timing_stop( 'nemo_init')
	518	!
[2496]	519	END SUBROUTINE nemo_init
[467]	520
	521
[2496]	522	SUBROUTINE nemo_ctl
[467]	523	!!----------------------------------------------------------------------
[2496]	524	!! * ROUTINE nemo_ctl *
[467]	525	!!
[3764]	526	!! ** Purpose : control print setting
[467]	527	!!
[11536]	528	!! ** Method : - print namctl and namcfg information and check some consistencies
[467]	529	!!----------------------------------------------------------------------
[2442]	530	!
[2496]	531	IF(lwp) THEN ! control print
[531]	532	WRITE(numout,*)
[7646]	533	WRITE(numout,*) 'nemo_ctl: Control prints'
[9213]	534	WRITE(numout,*) '~~~~~~~~'
[1593]	535	WRITE(numout,*) ' Namelist namctl'
[10570]	536	WRITE(numout,*) ' sn_cfctl%l_runstat = ', sn_cfctl%l_runstat
	537	WRITE(numout,*) ' sn_cfctl%l_trcstat = ', sn_cfctl%l_trcstat
	538	WRITE(numout,*) ' sn_cfctl%l_oceout = ', sn_cfctl%l_oceout
	539	WRITE(numout,*) ' sn_cfctl%l_layout = ', sn_cfctl%l_layout
[12377]	540	WRITE(numout,*) ' sn_cfctl%l_prtctl = ', sn_cfctl%l_prtctl
	541	WRITE(numout,*) ' sn_cfctl%l_prttrc = ', sn_cfctl%l_prttrc
	542	WRITE(numout,*) ' sn_cfctl%l_oasout = ', sn_cfctl%l_oasout
[14072]	543	WRITE(numout,*) ' sn_cfctl%procmin = ', sn_cfctl%procmin
	544	WRITE(numout,*) ' sn_cfctl%procmax = ', sn_cfctl%procmax
	545	WRITE(numout,*) ' sn_cfctl%procincr = ', sn_cfctl%procincr
	546	WRITE(numout,*) ' sn_cfctl%ptimincr = ', sn_cfctl%ptimincr
[9019]	547	WRITE(numout,*) ' timing by routine ln_timing = ', ln_timing
	548	WRITE(numout,*) ' CFL diagnostics ln_diacfl = ', ln_diacfl
[531]	549	ENDIF
[2442]	550	!
[13286]	551	IF( .NOT.ln_read_cfg ) ln_closea = .false. ! dealing possible only with a domcfg file
[4147]	552	IF(lwp) THEN ! control print
	553	WRITE(numout,*)
	554	WRITE(numout,*) ' Namelist namcfg'
[7646]	555	WRITE(numout,*) ' read domain configuration file ln_read_cfg = ', ln_read_cfg
	556	WRITE(numout,*) ' filename to be read cn_domcfg = ', TRIM(cn_domcfg)
[9213]	557	WRITE(numout,*) ' keep closed seas in the domain (if exist) ln_closea = ', ln_closea
	558	WRITE(numout,*) ' create a configuration definition file ln_write_cfg = ', ln_write_cfg
[7646]	559	WRITE(numout,*) ' filename to be written cn_domcfg_out = ', TRIM(cn_domcfg_out)
	560	WRITE(numout,*) ' use file attribute if exists as i/p j-start ln_use_jattr = ', ln_use_jattr
[4147]	561	ENDIF
[9213]	562	!
	563	IF( 1._wp /= SIGN(1._wp,-0._wp) ) CALL ctl_stop( 'nemo_ctl: The intrinsec SIGN function follows f2003 standard.', &
[10425]	564	& 'Compile with key_nosignedzero enabled:', &
	565	& '--> add -Dkey_nosignedzero to the definition of %CPP in your arch file' )
[3764]	566	!
[9023]	567	#if defined key_agrif
[9124]	568	IF( ln_timing ) CALL ctl_stop( 'AGRIF not implemented with ln_timing = true')
[9023]	569	#endif
	570	!
[2496]	571	END SUBROUTINE nemo_ctl
[467]	572
	573
[2496]	574	SUBROUTINE nemo_closefile
[467]	575	!!----------------------------------------------------------------------
[2496]	576	!! * ROUTINE nemo_closefile *
[467]	577	!!
	578	!! ** Purpose : Close the files
	579	!!----------------------------------------------------------------------
[1593]	580	!
	581	IF( lk_mpp ) CALL mppsync
	582	!
[1685]	583	CALL iom_close ! close all input/output files managed by iom_*
[1593]	584	!
[4147]	585	IF( numstp /= -1 ) CLOSE( numstp ) ! time-step file
[9019]	586	IF( numrun /= -1 ) CLOSE( numrun ) ! run statistics file
[4624]	587	IF( lwm.AND.numond /= -1 ) CLOSE( numond ) ! oce output namelist
	588	IF( lwm.AND.numoni /= -1 ) CLOSE( numoni ) ! ice output namelist
[4147]	589	IF( numevo_ice /= -1 ) CLOSE( numevo_ice ) ! ice variables (temp. evolution)
	590	IF( numout /= 6 ) CLOSE( numout ) ! standard model output file
	591	IF( numdct_vol /= -1 ) CLOSE( numdct_vol ) ! volume transports
	592	IF( numdct_heat /= -1 ) CLOSE( numdct_heat ) ! heat transports
	593	IF( numdct_salt /= -1 ) CLOSE( numdct_salt ) ! salt transports
[1593]	594	!
[2442]	595	numout = 6 ! redefine numout in case it is used after this point...
	596	!
[2496]	597	END SUBROUTINE nemo_closefile
[467]	598
[2715]	599
	600	SUBROUTINE nemo_alloc
	601	!!----------------------------------------------------------------------
	602	!! * ROUTINE nemo_alloc *
	603	!!
	604	!! ** Purpose : Allocate all the dynamic arrays of the OPA modules
	605	!!
	606	!! ** Method :
	607	!!----------------------------------------------------------------------
[9213]	608	USE diawri , ONLY : dia_wri_alloc
	609	USE dom_oce , ONLY : dom_oce_alloc
	610	USE trc_oce , ONLY : trc_oce_alloc
	611	USE bdy_oce , ONLY : bdy_oce_alloc
[2715]	612	!
	613	INTEGER :: ierr
	614	!!----------------------------------------------------------------------
	615	!
[14072]	616	ierr = oce_alloc () ! ocean
[9213]	617	ierr = ierr + dia_wri_alloc()
	618	ierr = ierr + dom_oce_alloc() ! ocean domain
	619	ierr = ierr + zdf_oce_alloc() ! ocean vertical physics
	620	ierr = ierr + trc_oce_alloc() ! shared TRC / TRA arrays
	621	ierr = ierr + bdy_oce_alloc() ! bdy masks (incl. initialization)
[2715]	622	!
[10425]	623	CALL mpp_sum( 'nemogcm', ierr )
[9213]	624	IF( ierr /= 0 ) CALL ctl_stop( 'STOP', 'nemo_alloc: unable to allocate standard ocean arrays' )
[2715]	625	!
	626	END SUBROUTINE nemo_alloc
	627
[14072]	628
[12933]	629	SUBROUTINE nemo_set_cfctl(sn_cfctl, setto )
[10570]	630	!!----------------------------------------------------------------------
	631	!! * ROUTINE nemo_set_cfctl *
	632	!!
	633	!! ** Purpose : Set elements of the output control structure to setto.
	634	!!
	635	!! ** Method : Note this routine can be used to switch on/off some
[12933]	636	!! types of output for selected areas.
[10570]	637	!!----------------------------------------------------------------------
[12933]	638	TYPE(sn_ctl), INTENT(inout) :: sn_cfctl
	639	LOGICAL , INTENT(in ) :: setto
[10570]	640	!!----------------------------------------------------------------------
[12933]	641	sn_cfctl%l_runstat = setto
	642	sn_cfctl%l_trcstat = setto
[10570]	643	sn_cfctl%l_oceout = setto
	644	sn_cfctl%l_layout = setto
[12377]	645	sn_cfctl%l_prtctl = setto
	646	sn_cfctl%l_prttrc = setto
	647	sn_cfctl%l_oasout = setto
[10570]	648	END SUBROUTINE nemo_set_cfctl
	649
[3]	650	!!======================================================================
[2496]	651	END MODULE nemogcm

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