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nemogcm.F90 in NEMO/branches/2020/dev_r12377_KERNEL-06_techene_e3/src/OCE – NEMO

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source: NEMO/branches/2020/dev_r12377_KERNEL-06_techene_e3/src/OCE/nemogcm.F90 @ 12732

Last change on this file since 12732 was 12732, checked in by techene, 4 years ago
some cleaning and proper module/routine name, mini bug introduced and corrected in sbcice_cice
Property svn:keywords set to `Id`
File size: 36.4 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
[12482]	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)
[7646]	44	USE phycst ! physical constant (par_cst routine)
	45	USE domain ! domain initialization (dom_init & dom_cfg routines)
[9161]	46	USE closea ! treatment of closed seas (for ln_closea)
[7646]	47	USE usrdef_nam ! user defined configuration
[12377]	48	USE tide_mod, ONLY : tide_init ! tidal components initialization (tide_init routine)
[9019]	49	USE bdy_oce, ONLY : ln_bdy
[6140]	50	USE bdyini ! open boundary cond. setting (bdy_init routine)
	51	USE istate ! initial state setting (istate_init routine)
	52	USE ldfdyn ! lateral viscosity setting (ldfdyn_init routine)
	53	USE ldftra ! lateral diffusivity setting (ldftra_init routine)
	54	USE trdini ! dyn/tra trends initialization (trd_init routine)
[12482]	55	USE asminc ! assimilation increments
[6140]	56	USE asmbkg ! writing out state trajectory
	57	USE diaptr ! poleward transports (dia_ptr_init routine)
	58	USE diadct ! sections transports (dia_dct_init routine)
	59	USE diaobs ! Observation diagnostics (dia_obs_init routine)
	60	USE diacfl ! CFL diagnostics (dia_cfl_init routine)
[12377]	61	USE diamlr ! IOM context management for multiple-linear-regression analysis
[12724]	62	#if defined key_qco
[12732]	63	USE stepMLF ! NEMO time-stepping (stp_MLF routine)
[12724]	64	#else
	65	USE step ! NEMO time-stepping (stp routine)
	66	#endif
[12377]	67	USE isfstp ! ice shelf (isf_stp_init routine)
[6140]	68	USE icbini ! handle bergs, initialisation
	69	USE icbstp ! handle bergs, calving, themodynamics and transport
	70	USE cpl_oasis3 ! OASIS3 coupling
	71	USE c1d ! 1D configuration
	72	USE step_c1d ! Time stepping loop for the 1D configuration
	73	USE dyndmp ! Momentum damping
	74	USE stopar ! Stochastic param.: ???
	75	USE stopts ! Stochastic param.: ???
[12377]	76	USE diu_layers ! diurnal bulk SST and coolskin
[7646]	77	USE step_diu ! diurnal bulk SST timestepping (called from here if run offline)
	78	USE crsini ! initialise grid coarsening utility
[12214]	79	USE dia25h ! 25h mean output
[12377]	80	USE diadetide ! Weights computation for daily detiding of model diagnostics
[7646]	81	USE sbc_oce , ONLY : lk_oasis
	82	USE wet_dry ! Wetting and drying setting (wad_init routine)
[1594]	83	#if defined key_top
[6140]	84	USE trcini ! passive tracer initialisation
[1594]	85	#endif
[7646]	86	#if defined key_nemocice_decomp
	87	USE ice_domain_size, only: nx_global, ny_global
	88	#endif
	89	!
[12724]	90	USE in_out_manager ! I/O manager
[6140]	91	USE lib_mpp ! distributed memory computing
[7646]	92	USE mppini ! shared/distributed memory setting (mpp_init routine)
[12482]	93	USE lbcnfd , ONLY : isendto, nsndto, nfsloop, nfeloop ! Setup of north fold exchanges
[7646]	94	USE lib_fortran ! Fortran utilities (allows no signed zero when 'key_nosignedzero' defined)
[1412]	95	#if defined key_iomput
[6140]	96	USE xios ! xIOserver
[1359]	97	#endif
[9780]	98	#if defined key_agrif
	99	USE agrif_all_update ! Master Agrif update
	100	#endif
[268]	101
[2715]	102	IMPLICIT NONE
[3]	103	PRIVATE
	104
[2496]	105	PUBLIC nemo_gcm ! called by model.F90
	106	PUBLIC nemo_init ! needed by AGRIF
[3764]	107	PUBLIC nemo_alloc ! needed by TAM
[467]	108
[2498]	109	CHARACTER(lc) :: cform_aaa="( /, 'AAAAAAAA', / ) " ! flag for output listing
[1593]	110
[10425]	111	#if defined key_mpp_mpi
[11536]	112	! need MPI_Wtime
[10425]	113	INCLUDE 'mpif.h'
	114	#endif
	115
[3]	116	!!----------------------------------------------------------------------
[9570]	117	!! NEMO/OCE 4.0 , NEMO Consortium (2018)
[2392]	118	!! $Id$
[10068]	119	!! Software governed by the CeCILL license (see ./LICENSE)
[3]	120	!!----------------------------------------------------------------------
	121	CONTAINS
	122
[2496]	123	SUBROUTINE nemo_gcm
[3]	124	!!----------------------------------------------------------------------
[2496]	125	!! * ROUTINE nemo_gcm *
[3]	126	!!
[3764]	127	!! ** Purpose : NEMO solves the primitive equations on an orthogonal
[1593]	128	!! curvilinear mesh on the sphere.
[3]	129	!!
	130	!! ** Method : - model general initialization
[12732]	131	!! - launch the time-stepping (stp routine)
[1593]	132	!! - finalize the run by closing files and communications
[3]	133	!!
[2715]	134	!! References : Madec, Delecluse, Imbard, and Levy, 1997: internal report, IPSL.
[1593]	135	!! Madec, 2008, internal report, IPSL.
[3]	136	!!----------------------------------------------------------------------
[7646]	137	INTEGER :: istp ! time step index
[11536]	138	REAL(wp):: zstptiming ! elapsed time for 1 time step
[389]	139	!!----------------------------------------------------------------------
[2382]	140	!
[392]	141	#if defined key_agrif
[1593]	142	CALL Agrif_Init_Grids() ! AGRIF: set the meshes
[389]	143	#endif
[1593]	144	! !-----------------------!
[2496]	145	CALL nemo_init !== Initialisations ==!
[1593]	146	! !-----------------------!
[2715]	147	#if defined key_agrif
[12377]	148	Kbb_a = Nbb; Kmm_a = Nnn; Krhs_a = Nrhs ! agrif_oce module copies of time level indices
[3680]	149	CALL Agrif_Declare_Var_dom ! AGRIF: set the meshes for DOM
[12482]	150	CALL Agrif_Declare_Var ! " " " " " DYN/TRA
[2715]	151	# if defined key_top
[3680]	152	CALL Agrif_Declare_Var_top ! " " " " " TOP
[2715]	153	# endif
[9570]	154	# if defined key_si3
[9611]	155	CALL Agrif_Declare_Var_ice ! " " " " " Sea ice
[7646]	156	# endif
[2715]	157	#endif
[682]	158	! check that all process are still there... If some process have an error,
	159	! they will never enter in step and other processes will wait until the end of the cpu time!
[10425]	160	CALL mpp_max( 'nemogcm', nstop )
[682]	161
[1593]	162	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	163
	164	! !-----------------------!
	165	! !== time stepping ==!
	166	! !-----------------------!
[12724]	167	!
	168	! !== set the model time-step ==!
	169	!
[900]	170	istp = nit000
[9210]	171	!
[2236]	172	#if defined key_c1d
[9210]	173	DO WHILE ( istp <= nitend .AND. nstop == 0 ) !== C1D time-stepping ==!
	174	CALL stp_c1d( istp )
	175	istp = istp + 1
	176	END DO
[2236]	177	#else
[9210]	178	!
	179	# if defined key_agrif
	180	! !== AGRIF time-stepping ==!
	181	CALL Agrif_Regrid()
[9213]	182	!
[9780]	183	! Recursive update from highest nested level to lowest:
[12377]	184	Kbb_a = Nbb; Kmm_a = Nnn; Krhs_a = Nrhs ! agrif_oce module copies of time level indices
[9780]	185	CALL Agrif_step_child_adj(Agrif_Update_All)
	186	!
[9210]	187	DO WHILE( istp <= nitend .AND. nstop == 0 )
[12724]	188	#if defined key_qco
[12732]	189	CALL stp_MLF
[12724]	190	#else
	191	CALL stp
	192	#endif
[9210]	193	istp = istp + 1
	194	END DO
	195	!
	196	IF( .NOT. Agrif_Root() ) THEN
	197	CALL Agrif_ParentGrid_To_ChildGrid()
	198	IF( ln_diaobs ) CALL dia_obs_wri
	199	IF( ln_timing ) CALL timing_finalize
	200	CALL Agrif_ChildGrid_To_ParentGrid()
	201	ENDIF
	202	!
	203	# else
	204	!
	205	IF( .NOT.ln_diurnal_only ) THEN !== Standard time-stepping ==!
	206	!
	207	DO WHILE( istp <= nitend .AND. nstop == 0 )
[11536]	208
[10425]	209	ncom_stp = istp
[11536]	210	IF( ln_timing ) THEN
	211	zstptiming = MPI_Wtime()
	212	IF ( istp == ( nit000 + 1 ) ) elapsed_time = zstptiming
	213	IF ( istp == nitend ) elapsed_time = zstptiming - elapsed_time
	214	ENDIF
[12482]	215
[12724]	216	#if defined key_qco
[12732]	217	CALL stp_MLF ( istp )
[12724]	218	#else
	219	CALL stp ( istp )
	220	#endif
[389]	221	istp = istp + 1
[11536]	222
	223	IF( lwp .AND. ln_timing ) WRITE(numtime,*) 'timing step ', istp-1, ' : ', MPI_Wtime() - zstptiming
	224
[389]	225	END DO
[9210]	226	!
	227	ELSE !== diurnal SST time-steeping only ==!
	228	!
	229	DO WHILE( istp <= nitend .AND. nstop == 0 )
[12482]	230	CALL stp_diurnal( istp ) ! time step only the diurnal SST
[9210]	231	istp = istp + 1
	232	END DO
	233	!
	234	ENDIF
	235	!
	236	# endif
	237	!
[2236]	238	#endif
[9210]	239	!
[6140]	240	IF( ln_diaobs ) CALL dia_obs_wri
[3609]	241	!
	242	IF( ln_icebergs ) CALL icb_end( nitend )
[3764]	243
[1593]	244	! !------------------------!
	245	! !== finalize the run ==!
	246	! !------------------------!
[7646]	247	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
[1593]	248	!
[7646]	249	IF( nstop /= 0 .AND. lwp ) THEN ! error print
[11536]	250	WRITE(ctmp1,*) ' ==>>> nemo_gcm: a total of ', nstop, ' errors have been found'
	251	CALL ctl_stop( ctmp1 )
[389]	252	ENDIF
[1593]	253	!
[9124]	254	IF( ln_timing ) CALL timing_finalize
[3294]	255	!
[2496]	256	CALL nemo_closefile
[4990]	257	!
[3769]	258	#if defined key_iomput
[9210]	259	CALL xios_finalize ! end mpp communications with xios
	260	IF( lk_oasis ) CALL cpl_finalize ! end coupling and mpp communications with OASIS
[532]	261	#else
[9210]	262	IF ( lk_oasis ) THEN ; CALL cpl_finalize ! end coupling and mpp communications with OASIS
[11536]	263	ELSEIF( lk_mpp ) THEN ; CALL mppstop ! end mpp communications
[4990]	264	ENDIF
[532]	265	#endif
[900]	266	!
[10436]	267	IF(lwm) THEN
	268	IF( nstop == 0 ) THEN ; STOP 0
[11536]	269	ELSE ; STOP 123
[10436]	270	ENDIF
[10425]	271	ENDIF
	272	!
[2496]	273	END SUBROUTINE nemo_gcm
[389]	274
	275
[2496]	276	SUBROUTINE nemo_init
[389]	277	!!----------------------------------------------------------------------
[2496]	278	!! * ROUTINE nemo_init *
[389]	279	!!
[2496]	280	!! ** Purpose : initialization of the NEMO GCM
[389]	281	!!----------------------------------------------------------------------
[11536]	282	INTEGER :: ios, ilocal_comm ! local integers
[9213]	283	!!
[12377]	284	NAMELIST/namctl/ sn_cfctl, nn_print, nn_ictls, nn_ictle, &
[10570]	285	& nn_isplt , nn_jsplt, nn_jctls, nn_jctle, &
[9019]	286	& ln_timing, ln_diacfl
[9213]	287	NAMELIST/namcfg/ ln_read_cfg, cn_domcfg, ln_closea, ln_write_cfg, cn_domcfg_out, ln_use_jattr
[3]	288	!!----------------------------------------------------------------------
[1593]	289	!
[5407]	290	cxios_context = 'nemo'
[2496]	291	!
[11536]	292	! !-------------------------------------------------!
	293	! ! set communicator & select the local rank !
	294	! ! must be done as soon as possible to get narea !
	295	! !-------------------------------------------------!
[1593]	296	!
[1412]	297	#if defined key_iomput
[2200]	298	IF( Agrif_Root() ) THEN
[5407]	299	IF( lk_oasis ) THEN
[7646]	300	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
[11536]	301	CALL xios_initialize( "not used" , local_comm =ilocal_comm ) ! send nemo communicator to xios
[4990]	302	ELSE
[11536]	303	CALL xios_initialize( "for_xios_mpi_id", return_comm=ilocal_comm ) ! nemo local communicator given by xios
[4990]	304	ENDIF
[2200]	305	ENDIF
[11536]	306	CALL mpp_start( ilocal_comm )
[532]	307	#else
[5407]	308	IF( lk_oasis ) THEN
[4990]	309	IF( Agrif_Root() ) THEN
[7646]	310	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
[4990]	311	ENDIF
[11536]	312	CALL mpp_start( ilocal_comm )
[4990]	313	ELSE
[11536]	314	CALL mpp_start( )
[2236]	315	ENDIF
[532]	316	#endif
[11536]	317	!
	318	narea = mpprank + 1 ! mpprank: the rank of proc (0 --> mppsize -1 )
	319	lwm = (narea == 1) ! control of output namelists
	320	!
	321	! !---------------------------------------------------------------!
	322	! ! Open output files, reference and configuration namelist files !
	323	! !---------------------------------------------------------------!
	324	!
	325	! open ocean.output as soon as possible to get all output prints (including errors messages)
	326	IF( lwm ) CALL ctl_opn( numout, 'ocean.output', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, -1, .FALSE. )
	327	! open reference and configuration namelist files
[12377]	328	CALL load_nml( numnam_ref, 'namelist_ref', -1, lwm )
	329	CALL load_nml( numnam_cfg, 'namelist_cfg', -1, lwm )
[11536]	330	IF( lwm ) CALL ctl_opn( numond, 'output.namelist.dyn', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, -1, .FALSE. )
	331	! open /dev/null file to be able to supress output write easily
[12724]	332	IF( Agrif_Root() ) THEN
[11536]	333	CALL ctl_opn( numnul, '/dev/null', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, -1, .FALSE. )
[12724]	334	#ifdef key_agrif
	335	ELSE
	336	numnul = Agrif_Parent(numnul)
	337	#endif
	338	ENDIF
[11536]	339	! !--------------------!
[12377]	340	! ! Open listing units ! -> need sn_cfctl from namctl to define lwp
[11536]	341	! !--------------------!
	342	!
	343	READ ( numnam_ref, namctl, IOSTAT = ios, ERR = 901 )
	344	901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in reference namelist' )
	345	READ ( numnam_cfg, namctl, IOSTAT = ios, ERR = 902 )
	346	902 IF( ios > 0 ) CALL ctl_nam ( ios , 'namctl in configuration namelist' )
	347	!
[12377]	348	! finalize the definition of namctl variables
	349	IF( sn_cfctl%l_allon ) THEN
	350	! Turn on all options.
	351	CALL nemo_set_cfctl( sn_cfctl, .TRUE., .TRUE. )
	352	! Ensure all processors are active
	353	sn_cfctl%procmin = 0 ; sn_cfctl%procmax = 1000000 ; sn_cfctl%procincr = 1
	354	ELSEIF( sn_cfctl%l_config ) THEN
	355	! Activate finer control of report outputs
	356	! optionally switch off output from selected areas (note this only
	357	! applies to output which does not involve global communications)
	358	IF( ( narea < sn_cfctl%procmin .OR. narea > sn_cfctl%procmax ) .OR. &
	359	& ( MOD( narea - sn_cfctl%procmin, sn_cfctl%procincr ) /= 0 ) ) &
	360	& CALL nemo_set_cfctl( sn_cfctl, .FALSE., .FALSE. )
	361	ELSE
	362	! turn off all options.
	363	CALL nemo_set_cfctl( sn_cfctl, .FALSE., .TRUE. )
	364	ENDIF
[11536]	365	!
[12377]	366	lwp = (narea == 1) .OR. sn_cfctl%l_oceout ! control of all listing output print
	367	!
[11536]	368	IF(lwp) THEN ! open listing units
[1593]	369	!
[11536]	370	IF( .NOT. lwm ) & ! alreay opened for narea == 1
	371	& CALL ctl_opn( numout, 'ocean.output', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, -1, .FALSE., narea )
[1593]	372	!
[1579]	373	WRITE(numout,*)
[11536]	374	WRITE(numout,*) ' CNRS - NERC - Met OFFICE - MERCATOR-ocean - CMCC'
[1593]	375	WRITE(numout,*) ' NEMO team'
[1579]	376	WRITE(numout,*) ' Ocean General Circulation Model'
[10510]	377	WRITE(numout,*) ' NEMO version 4.0 (2019) '
[1579]	378	WRITE(numout,*)
[10510]	379	WRITE(numout,*) " ._ ._ ._ ._ ._ "
	380	WRITE(numout,*) " _.-._)`\_.-._)`\_.-._)`\_.-._)`\_.-._)`\_ "
[1579]	381	WRITE(numout,*)
[10510]	382	WRITE(numout,*) " o _, _, "
	383	WRITE(numout,*) " o .' ( .-' / "
	384	WRITE(numout,*) " o _/..._'. .' / "
	385	WRITE(numout,*) " ( o .-'` ` '-./ _.' "
	386	WRITE(numout,*) " ) ( o) ;= <_ ( "
	387	WRITE(numout,*) " ( '-.,\\__ __.-;`\ '. ) "
	388	WRITE(numout,*) " ) ) \) \|`\ \) '. \ ( ( "
	389	WRITE(numout,*) " ( ( \_/ '-._\ ) ) "
[10583]	390	WRITE(numout,*) " ) ) jgs ` ( ( "
[10510]	391	WRITE(numout,*) " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ "
	392	WRITE(numout,*)
[1593]	393	!
[7646]	394	WRITE(numout,cform_aaa) ! Flag AAAAAAA
	395	!
[473]	396	ENDIF
[10425]	397	!
[11536]	398	IF(lwm) WRITE( numond, namctl )
	399	!
	400	! !------------------------------------!
	401	! ! Set global domain size parameters !
	402	! !------------------------------------!
	403	!
	404	READ ( numnam_ref, namcfg, IOSTAT = ios, ERR = 903 )
	405	903 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in reference namelist' )
	406	READ ( numnam_cfg, namcfg, IOSTAT = ios, ERR = 904 )
[12482]	407	904 IF( ios > 0 ) CALL ctl_nam ( ios , 'namcfg in configuration namelist' )
[11536]	408	!
	409	IF( ln_read_cfg ) THEN ! Read sizes in domain configuration file
	410	CALL domain_cfg ( cn_cfg, nn_cfg, jpiglo, jpjglo, jpkglo, jperio )
	411	ELSE ! user-defined namelist
	412	CALL usr_def_nam( cn_cfg, nn_cfg, jpiglo, jpjglo, jpkglo, jperio )
	413	ENDIF
	414	!
	415	IF(lwm) WRITE( numond, namcfg )
	416	!
	417	! !-----------------------------------------!
	418	! ! mpp parameters and domain decomposition !
	419	! !-----------------------------------------!
	420	CALL mpp_init
[2715]	421
[7646]	422	! Now we know the dimensions of the grid and numout has been set: we can allocate arrays
[2715]	423	CALL nemo_alloc()
	424
[12377]	425	! Initialise time level indices
	426	Nbb = 1; Nnn = 2; Naa = 3; Nrhs = Naa
	427
[2496]	428	! !-------------------------------!
	429	! ! NEMO general initialization !
	430	! !-------------------------------!
[473]	431
[7646]	432	CALL nemo_ctl ! Control prints
[2382]	433	!
[9213]	434	! ! General initialization
	435	IF( ln_timing ) CALL timing_init ! timing
	436	IF( ln_timing ) CALL timing_start( 'nemo_init')
[3294]	437	!
[9367]	438	CALL phy_cst ! Physical constants
	439	CALL eos_init ! Equation of state
	440	IF( lk_c1d ) CALL c1d_init ! 1D column configuration
	441	CALL wad_init ! Wetting and drying options
[12377]	442	CALL dom_init( Nbb, Nnn, Naa, "OPA") ! Domain
[12482]	443	IF( ln_crs ) CALL crs_init( Nnn ) ! coarsened grid: domain initialization
[12377]	444	IF( sn_cfctl%l_prtctl ) &
	445	& CALL prt_ctl_init ! Print control
[12482]	446
[12377]	447	CALL diurnal_sst_bulk_init ! diurnal sst
[12482]	448	IF( ln_diurnal ) CALL diurnal_sst_coolskin_init ! cool skin
	449	!
[12377]	450	IF( ln_diurnal_only ) THEN ! diurnal only: a subset of the initialisation routines
	451	CALL istate_init( Nbb, Nnn, Naa ) ! ocean initial state (Dynamics and tracers)
	452	CALL sbc_init( Nbb, Nnn, Naa ) ! Forcings : surface module
	453	CALL tra_qsr_init ! penetrative solar radiation qsr
	454	IF( ln_diaobs ) THEN ! Observation & model comparison
	455	CALL dia_obs_init( Nnn ) ! Initialize observational data
	456	CALL dia_obs( nit000 - 1, Nnn ) ! Observation operator for restart
[12482]	457	ENDIF
[12377]	458	IF( lk_asminc ) CALL asm_inc_init( Nbb, Nnn, Nrhs ) ! Assimilation increments
[9213]	459	!
	460	RETURN ! end of initialization
[6140]	461	ENDIF
[12377]	462	!
[12482]	463
[12377]	464	CALL istate_init( Nbb, Nnn, Naa ) ! ocean initial state (Dynamics and tracers)
[3651]	465
[12482]	466	! ! external forcing
[12377]	467	CALL tide_init ! tidal harmonics
	468	CALL sbc_init( Nbb, Nnn, Naa ) ! surface boundary conditions (including sea-ice)
	469	CALL bdy_init ! Open boundaries initialisation
[9019]	470
[5836]	471	! ! Ocean physics
[12377]	472	CALL zdf_phy_init( Nnn ) ! Vertical physics
[12482]	473
[2082]	474	! ! Lateral physics
[9019]	475	CALL ldf_tra_init ! Lateral ocean tracer physics
	476	CALL ldf_eiv_init ! eddy induced velocity param.
	477	CALL ldf_dyn_init ! Lateral ocean momentum physics
[2082]	478
[9019]	479	! ! Active tracers
	480	IF( ln_traqsr ) CALL tra_qsr_init ! penetrative solar radiation qsr
	481	CALL tra_bbc_init ! bottom heat flux
[10350]	482	CALL tra_bbl_init ! advective (and/or diffusive) bottom boundary layer scheme
[9019]	483	CALL tra_dmp_init ! internal tracer damping
	484	CALL tra_adv_init ! horizontal & vertical advection
	485	CALL tra_ldf_init ! lateral mixing
[2027]	486
[9019]	487	! ! Dynamics
[12377]	488	IF( lk_c1d ) CALL dyn_dmp_init ! internal momentum damping
	489	CALL dyn_adv_init ! advection (vector or flux form)
	490	CALL dyn_vor_init ! vorticity term including Coriolis
	491	CALL dyn_ldf_init ! lateral mixing
	492	CALL dyn_hpg_init( Nnn ) ! horizontal gradient of Hydrostatic pressure
	493	CALL dyn_spg_init ! surface pressure gradient
[3764]	494
[5836]	495	#if defined key_top
	496	! ! Passive tracers
[12377]	497	CALL trc_init( Nbb, Nnn, Naa )
[5836]	498	#endif
[9019]	499	IF( l_ldfslp ) CALL ldf_slp_init ! slope of lateral mixing
[5836]	500
	501	! ! Icebergs
[12724]	502	CALL icb_init( rn_Dt, nit000) ! initialise icebergs instance
[5836]	503
[12377]	504	! ice shelf
	505	CALL isf_init( Nbb, Nnn, Naa )
	506
[5836]	507	! ! Misc. options
[9019]	508	CALL sto_par_init ! Stochastic parametrization
	509	IF( ln_sto_eos ) CALL sto_pts_init ! RRandom T/S fluctuations
[12482]	510
[5836]	511	! ! Diagnostics
[12377]	512	CALL flo_init( Nnn ) ! drifting Floats
[9019]	513	IF( ln_diacfl ) CALL dia_cfl_init ! Initialise CFL diagnostics
[12377]	514	! CALL dia_ptr_init ! Poleward TRansports initialization
[11536]	515	CALL dia_dct_init ! Sections tranports
[12377]	516	CALL dia_hsb_init( Nnn ) ! heat content, salt content and volume budgets
	517	CALL trd_init( Nnn ) ! Mixed-layer/Vorticity/Integral constraints trends
	518	CALL dia_obs_init( Nnn ) ! Initialize observational data
	519	CALL dia_25h_init( Nbb ) ! 25h mean outputs
	520	CALL dia_detide_init ! Weights computation for daily detiding of model diagnostics
	521	IF( ln_diaobs ) CALL dia_obs( nit000-1, Nnn ) ! Observation operator for restart
	522	CALL dia_mlr_init ! Initialisation of IOM context management for multiple-linear-regression analysis
[6140]	523
[9019]	524	! ! Assimilation increments
[12377]	525	IF( lk_asminc ) CALL asm_inc_init( Nbb, Nnn, Nrhs ) ! Initialize assimilation increments
[1593]	526	!
[9213]	527	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	528	!
	529	IF( ln_timing ) CALL timing_stop( 'nemo_init')
	530	!
[2496]	531	END SUBROUTINE nemo_init
[467]	532
	533
[2496]	534	SUBROUTINE nemo_ctl
[467]	535	!!----------------------------------------------------------------------
[2496]	536	!! * ROUTINE nemo_ctl *
[467]	537	!!
[3764]	538	!! ** Purpose : control print setting
[467]	539	!!
[11536]	540	!! ** Method : - print namctl and namcfg information and check some consistencies
[467]	541	!!----------------------------------------------------------------------
[2442]	542	!
[2496]	543	IF(lwp) THEN ! control print
[531]	544	WRITE(numout,*)
[7646]	545	WRITE(numout,*) 'nemo_ctl: Control prints'
[9213]	546	WRITE(numout,*) '~~~~~~~~'
[1593]	547	WRITE(numout,*) ' Namelist namctl'
[12377]	548	WRITE(numout,*) ' sn_cfctl%l_glochk = ', sn_cfctl%l_glochk
	549	WRITE(numout,*) ' sn_cfctl%l_allon = ', sn_cfctl%l_allon
[10570]	550	WRITE(numout,*) ' finer control over o/p sn_cfctl%l_config = ', sn_cfctl%l_config
	551	WRITE(numout,*) ' sn_cfctl%l_runstat = ', sn_cfctl%l_runstat
	552	WRITE(numout,*) ' sn_cfctl%l_trcstat = ', sn_cfctl%l_trcstat
	553	WRITE(numout,*) ' sn_cfctl%l_oceout = ', sn_cfctl%l_oceout
	554	WRITE(numout,*) ' sn_cfctl%l_layout = ', sn_cfctl%l_layout
[12377]	555	WRITE(numout,*) ' sn_cfctl%l_prtctl = ', sn_cfctl%l_prtctl
	556	WRITE(numout,*) ' sn_cfctl%l_prttrc = ', sn_cfctl%l_prttrc
	557	WRITE(numout,*) ' sn_cfctl%l_oasout = ', sn_cfctl%l_oasout
[12482]	558	WRITE(numout,*) ' sn_cfctl%procmin = ', sn_cfctl%procmin
	559	WRITE(numout,*) ' sn_cfctl%procmax = ', sn_cfctl%procmax
	560	WRITE(numout,*) ' sn_cfctl%procincr = ', sn_cfctl%procincr
	561	WRITE(numout,*) ' sn_cfctl%ptimincr = ', sn_cfctl%ptimincr
[1601]	562	WRITE(numout,*) ' level of print nn_print = ', nn_print
	563	WRITE(numout,*) ' Start i indice for SUM control nn_ictls = ', nn_ictls
	564	WRITE(numout,*) ' End i indice for SUM control nn_ictle = ', nn_ictle
	565	WRITE(numout,*) ' Start j indice for SUM control nn_jctls = ', nn_jctls
	566	WRITE(numout,*) ' End j indice for SUM control nn_jctle = ', nn_jctle
	567	WRITE(numout,*) ' number of proc. following i nn_isplt = ', nn_isplt
	568	WRITE(numout,*) ' number of proc. following j nn_jsplt = ', nn_jsplt
[9019]	569	WRITE(numout,*) ' timing by routine ln_timing = ', ln_timing
	570	WRITE(numout,*) ' CFL diagnostics ln_diacfl = ', ln_diacfl
[531]	571	ENDIF
[2442]	572	!
[1601]	573	nprint = nn_print ! convert DOCTOR namelist names into OLD names
	574	nictls = nn_ictls
	575	nictle = nn_ictle
	576	njctls = nn_jctls
	577	njctle = nn_jctle
	578	isplt = nn_isplt
[9213]	579	jsplt = nn_jsplt
[4147]	580
	581	IF(lwp) THEN ! control print
	582	WRITE(numout,*)
	583	WRITE(numout,*) ' Namelist namcfg'
[7646]	584	WRITE(numout,*) ' read domain configuration file ln_read_cfg = ', ln_read_cfg
	585	WRITE(numout,*) ' filename to be read cn_domcfg = ', TRIM(cn_domcfg)
[9213]	586	WRITE(numout,*) ' keep closed seas in the domain (if exist) ln_closea = ', ln_closea
	587	WRITE(numout,*) ' create a configuration definition file ln_write_cfg = ', ln_write_cfg
[7646]	588	WRITE(numout,*) ' filename to be written cn_domcfg_out = ', TRIM(cn_domcfg_out)
	589	WRITE(numout,*) ' use file attribute if exists as i/p j-start ln_use_jattr = ', ln_use_jattr
[4147]	590	ENDIF
[9213]	591	IF( .NOT.ln_read_cfg ) ln_closea = .false. ! dealing possible only with a domcfg file
	592	!
[2442]	593	! ! Parameter control
[1593]	594	!
[12377]	595	IF( sn_cfctl%l_prtctl .OR. sn_cfctl%l_prttrc ) THEN ! sub-domain area indices for the control prints
[3294]	596	IF( lk_mpp .AND. jpnij > 1 ) THEN
[2496]	597	isplt = jpni ; jsplt = jpnj ; ijsplt = jpni*jpnj ! the domain is forced to the real split domain
[531]	598	ELSE
	599	IF( isplt == 1 .AND. jsplt == 1 ) THEN
[1593]	600	CALL ctl_warn( ' - isplt & jsplt are equal to 1', &
	601	& ' - the print control will be done over the whole domain' )
[531]	602	ENDIF
[1593]	603	ijsplt = isplt * jsplt ! total number of processors ijsplt
[531]	604	ENDIF
	605	IF(lwp) WRITE(numout,*)' - The total number of processors over which the'
	606	IF(lwp) WRITE(numout,*)' print control will be done is ijsplt : ', ijsplt
[1593]	607	!
	608	! ! indices used for the SUM control
	609	IF( nictls+nictle+njctls+njctle == 0 ) THEN ! print control done over the default area
[3764]	610	lsp_area = .FALSE.
[1593]	611	ELSE ! print control done over a specific area
[531]	612	lsp_area = .TRUE.
	613	IF( nictls < 1 .OR. nictls > jpiglo ) THEN
	614	CALL ctl_warn( ' - nictls must be 1<=nictls>=jpiglo, it is forced to 1' )
	615	nictls = 1
	616	ENDIF
	617	IF( nictle < 1 .OR. nictle > jpiglo ) THEN
	618	CALL ctl_warn( ' - nictle must be 1<=nictle>=jpiglo, it is forced to jpiglo' )
	619	nictle = jpiglo
	620	ENDIF
	621	IF( njctls < 1 .OR. njctls > jpjglo ) THEN
	622	CALL ctl_warn( ' - njctls must be 1<=njctls>=jpjglo, it is forced to 1' )
	623	njctls = 1
	624	ENDIF
	625	IF( njctle < 1 .OR. njctle > jpjglo ) THEN
	626	CALL ctl_warn( ' - njctle must be 1<=njctle>=jpjglo, it is forced to jpjglo' )
	627	njctle = jpjglo
	628	ENDIF
[1593]	629	ENDIF
	630	ENDIF
[2442]	631	!
[9213]	632	IF( 1._wp /= SIGN(1._wp,-0._wp) ) CALL ctl_stop( 'nemo_ctl: The intrinsec SIGN function follows f2003 standard.', &
[10425]	633	& 'Compile with key_nosignedzero enabled:', &
	634	& '--> add -Dkey_nosignedzero to the definition of %CPP in your arch file' )
[3764]	635	!
[9023]	636	#if defined key_agrif
[9124]	637	IF( ln_timing ) CALL ctl_stop( 'AGRIF not implemented with ln_timing = true')
[9023]	638	#endif
	639	!
[2496]	640	END SUBROUTINE nemo_ctl
[467]	641
	642
[2496]	643	SUBROUTINE nemo_closefile
[467]	644	!!----------------------------------------------------------------------
[2496]	645	!! * ROUTINE nemo_closefile *
[467]	646	!!
	647	!! ** Purpose : Close the files
	648	!!----------------------------------------------------------------------
[1593]	649	!
	650	IF( lk_mpp ) CALL mppsync
	651	!
[1685]	652	CALL iom_close ! close all input/output files managed by iom_*
[1593]	653	!
[4147]	654	IF( numstp /= -1 ) CLOSE( numstp ) ! time-step file
[9019]	655	IF( numrun /= -1 ) CLOSE( numrun ) ! run statistics file
[4624]	656	IF( lwm.AND.numond /= -1 ) CLOSE( numond ) ! oce output namelist
	657	IF( lwm.AND.numoni /= -1 ) CLOSE( numoni ) ! ice output namelist
[4147]	658	IF( numevo_ice /= -1 ) CLOSE( numevo_ice ) ! ice variables (temp. evolution)
	659	IF( numout /= 6 ) CLOSE( numout ) ! standard model output file
	660	IF( numdct_vol /= -1 ) CLOSE( numdct_vol ) ! volume transports
	661	IF( numdct_heat /= -1 ) CLOSE( numdct_heat ) ! heat transports
	662	IF( numdct_salt /= -1 ) CLOSE( numdct_salt ) ! salt transports
[1593]	663	!
[2442]	664	numout = 6 ! redefine numout in case it is used after this point...
	665	!
[2496]	666	END SUBROUTINE nemo_closefile
[467]	667
[2715]	668
	669	SUBROUTINE nemo_alloc
	670	!!----------------------------------------------------------------------
	671	!! * ROUTINE nemo_alloc *
	672	!!
	673	!! ** Purpose : Allocate all the dynamic arrays of the OPA modules
	674	!!
	675	!! ** Method :
	676	!!----------------------------------------------------------------------
[9213]	677	USE diawri , ONLY : dia_wri_alloc
	678	USE dom_oce , ONLY : dom_oce_alloc
	679	USE trc_oce , ONLY : trc_oce_alloc
	680	USE bdy_oce , ONLY : bdy_oce_alloc
[2715]	681	!
	682	INTEGER :: ierr
	683	!!----------------------------------------------------------------------
	684	!
[12482]	685	ierr = oce_alloc () ! ocean
[9213]	686	ierr = ierr + dia_wri_alloc()
	687	ierr = ierr + dom_oce_alloc() ! ocean domain
	688	ierr = ierr + zdf_oce_alloc() ! ocean vertical physics
	689	ierr = ierr + trc_oce_alloc() ! shared TRC / TRA arrays
	690	ierr = ierr + bdy_oce_alloc() ! bdy masks (incl. initialization)
[2715]	691	!
[10425]	692	CALL mpp_sum( 'nemogcm', ierr )
[9213]	693	IF( ierr /= 0 ) CALL ctl_stop( 'STOP', 'nemo_alloc: unable to allocate standard ocean arrays' )
[2715]	694	!
	695	END SUBROUTINE nemo_alloc
	696
[12482]	697
[10570]	698	SUBROUTINE nemo_set_cfctl(sn_cfctl, setto, for_all )
	699	!!----------------------------------------------------------------------
	700	!! * ROUTINE nemo_set_cfctl *
	701	!!
	702	!! ** Purpose : Set elements of the output control structure to setto.
	703	!! for_all should be .false. unless all areas are to be
	704	!! treated identically.
	705	!!
	706	!! ** Method : Note this routine can be used to switch on/off some
	707	!! types of output for selected areas but any output types
	708	!! that involve global communications (e.g. mpp_max, glob_sum)
	709	!! should be protected from selective switching by the
	710	!! for_all argument
	711	!!----------------------------------------------------------------------
	712	LOGICAL :: setto, for_all
[10588]	713	TYPE(sn_ctl) :: sn_cfctl
[10570]	714	!!----------------------------------------------------------------------
	715	IF( for_all ) THEN
	716	sn_cfctl%l_runstat = setto
	717	sn_cfctl%l_trcstat = setto
	718	ENDIF
	719	sn_cfctl%l_oceout = setto
	720	sn_cfctl%l_layout = setto
[12377]	721	sn_cfctl%l_prtctl = setto
	722	sn_cfctl%l_prttrc = setto
	723	sn_cfctl%l_oasout = setto
[10570]	724	END SUBROUTINE nemo_set_cfctl
	725
[3]	726	!!======================================================================
[2496]	727	END MODULE nemogcm

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