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

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source: NEMO/trunk/src/OCE/nemogcm.F90 @ 14994

Last change on this file since 14994 was 14834, checked in by hadcv, 3 years ago
#2600: Merge in dev_r14273_HPC-02_Daley_Tiling
Property svn:keywords set to `Id`
File size: 32.2 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)
	53	USE icbini ! handle bergs, initialisation
[14053]	54	USE icbstp , ONLY : icb_end ! handle bergs, close iceberg files
[6140]	55	USE cpl_oasis3 ! OASIS3 coupling
[14053]	56	USE dyndmp ! Momentum damping (C1D only)
	57	USE step_diu ! diurnal bulk SST timestepping (called from here if run offline)
	58	USE crsini ! initialise grid coarsening utility
	59	USE dia25h , ONLY : dia_25h_init ! 25h mean output (initialisation)
[6140]	60	USE c1d ! 1D configuration
	61	USE step_c1d ! Time stepping loop for the 1D configuration
[1594]	62	#if defined key_top
[6140]	63	USE trcini ! passive tracer initialisation
[1594]	64	#endif
[7646]	65	#if defined key_nemocice_decomp
	66	USE ice_domain_size, only: nx_global, ny_global
	67	#endif
[14143]	68	#if defined key_qco \|\| defined key_linssh
[14053]	69	USE stpmlf ! NEMO time-stepping (stp_MLF routine)
	70	#else
	71	USE step ! NEMO time-stepping (stp routine)
	72	#endif
[7646]	73	!
[6140]	74	USE lib_mpp ! distributed memory computing
[7646]	75	USE mppini ! shared/distributed memory setting (mpp_init routine)
[14072]	76	USE lbcnfd , ONLY : isendto, nsndto ! Setup of north fold exchanges
[7646]	77	USE lib_fortran ! Fortran utilities (allows no signed zero when 'key_nosignedzero' defined)
[14143]	78	USE halo_mng ! halo manager
[268]	79
[2715]	80	IMPLICIT NONE
[3]	81	PRIVATE
	82
[2496]	83	PUBLIC nemo_gcm ! called by model.F90
	84	PUBLIC nemo_init ! needed by AGRIF
[3764]	85	PUBLIC nemo_alloc ! needed by TAM
[467]	86
[2498]	87	CHARACTER(lc) :: cform_aaa="( /, 'AAAAAAAA', / ) " ! flag for output listing
[1593]	88
[14229]	89	#if ! defined key_mpi_off
[11536]	90	! need MPI_Wtime
[10425]	91	INCLUDE 'mpif.h'
	92	#endif
	93
[3]	94	!!----------------------------------------------------------------------
[9570]	95	!! NEMO/OCE 4.0 , NEMO Consortium (2018)
[2392]	96	!! $Id$
[10068]	97	!! Software governed by the CeCILL license (see ./LICENSE)
[3]	98	!!----------------------------------------------------------------------
	99	CONTAINS
	100
[2496]	101	SUBROUTINE nemo_gcm
[3]	102	!!----------------------------------------------------------------------
[2496]	103	!! * ROUTINE nemo_gcm *
[3]	104	!!
[3764]	105	!! ** Purpose : NEMO solves the primitive equations on an orthogonal
[1593]	106	!! curvilinear mesh on the sphere.
[3]	107	!!
	108	!! ** Method : - model general initialization
	109	!! - launch the time-stepping (stp routine)
[1593]	110	!! - finalize the run by closing files and communications
[3]	111	!!
[2715]	112	!! References : Madec, Delecluse, Imbard, and Levy, 1997: internal report, IPSL.
[1593]	113	!! Madec, 2008, internal report, IPSL.
[3]	114	!!----------------------------------------------------------------------
[7646]	115	INTEGER :: istp ! time step index
[11536]	116	REAL(wp):: zstptiming ! elapsed time for 1 time step
[389]	117	!!----------------------------------------------------------------------
[2382]	118	!
[392]	119	#if defined key_agrif
[1593]	120	CALL Agrif_Init_Grids() ! AGRIF: set the meshes
[389]	121	#endif
[1593]	122	! !-----------------------!
[2496]	123	CALL nemo_init !== Initialisations ==!
[1593]	124	! !-----------------------!
[2715]	125	#if defined key_agrif
[12377]	126	Kbb_a = Nbb; Kmm_a = Nnn; Krhs_a = Nrhs ! agrif_oce module copies of time level indices
[13216]	127	CALL Agrif_Declare_Var ! " " " " " DYN/TRA
[2715]	128	# if defined key_top
[3680]	129	CALL Agrif_Declare_Var_top ! " " " " " TOP
[2715]	130	# endif
	131	#endif
[682]	132	! check that all process are still there... If some process have an error,
	133	! they will never enter in step and other processes will wait until the end of the cpu time!
[10425]	134	CALL mpp_max( 'nemogcm', nstop )
[682]	135
[1593]	136	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	137
	138	! !-----------------------!
	139	! !== time stepping ==!
	140	! !-----------------------!
[12489]	141	!
	142	! !== set the model time-step ==!
	143	!
[900]	144	istp = nit000
[9210]	145	!
[2236]	146	#if defined key_c1d
[9210]	147	DO WHILE ( istp <= nitend .AND. nstop == 0 ) !== C1D time-stepping ==!
	148	CALL stp_c1d( istp )
	149	istp = istp + 1
	150	END DO
[2236]	151	#else
[9210]	152	!
	153	# if defined key_agrif
	154	! !== AGRIF time-stepping ==!
	155	CALL Agrif_Regrid()
[9213]	156	!
[9780]	157	! Recursive update from highest nested level to lowest:
[12377]	158	Kbb_a = Nbb; Kmm_a = Nnn; Krhs_a = Nrhs ! agrif_oce module copies of time level indices
[9780]	159	CALL Agrif_step_child_adj(Agrif_Update_All)
[14086]	160	CALL Agrif_step_child_adj(Agrif_Check_parent_bat)
[9780]	161	!
[9210]	162	DO WHILE( istp <= nitend .AND. nstop == 0 )
[14143]	163	!
	164	# if defined key_qco \|\| defined key_linssh
[13237]	165	CALL stp_MLF
[14053]	166	# else
[9210]	167	CALL stp
[14053]	168	# endif
[9210]	169	istp = istp + 1
	170	END DO
	171	!
	172	# else
	173	!
	174	IF( .NOT.ln_diurnal_only ) THEN !== Standard time-stepping ==!
	175	!
	176	DO WHILE( istp <= nitend .AND. nstop == 0 )
[14053]	177	!
[10425]	178	ncom_stp = istp
[11536]	179	IF( ln_timing ) THEN
	180	zstptiming = MPI_Wtime()
	181	IF ( istp == ( nit000 + 1 ) ) elapsed_time = zstptiming
	182	IF ( istp == nitend ) elapsed_time = zstptiming - elapsed_time
	183	ENDIF
[14053]	184	!
[14143]	185	# if defined key_qco \|\| defined key_linssh
	186	CALL stp_MLF( istp )
[14053]	187	# else
[14143]	188	CALL stp ( istp )
[14053]	189	# endif
[389]	190	istp = istp + 1
[14053]	191	!
[11536]	192	IF( lwp .AND. ln_timing ) WRITE(numtime,*) 'timing step ', istp-1, ' : ', MPI_Wtime() - zstptiming
[14053]	193	!
[389]	194	END DO
[9210]	195	!
	196	ELSE !== diurnal SST time-steeping only ==!
	197	!
	198	DO WHILE( istp <= nitend .AND. nstop == 0 )
[14072]	199	CALL stp_diurnal( istp ) ! time step only the diurnal SST
[9210]	200	istp = istp + 1
	201	END DO
	202	!
	203	ENDIF
	204	!
	205	# endif
	206	!
[2236]	207	#endif
[9210]	208	!
[6140]	209	IF( ln_diaobs ) CALL dia_obs_wri
[3609]	210	!
	211	IF( ln_icebergs ) CALL icb_end( nitend )
[3764]	212
[1593]	213	! !------------------------!
	214	! !== finalize the run ==!
	215	! !------------------------!
[7646]	216	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
[1593]	217	!
[7646]	218	IF( nstop /= 0 .AND. lwp ) THEN ! error print
[11536]	219	WRITE(ctmp1,*) ' ==>>> nemo_gcm: a total of ', nstop, ' errors have been found'
[12933]	220	IF( ngrdstop > 0 ) THEN
	221	WRITE(ctmp9,'(i2)') ngrdstop
[13011]	222	WRITE(ctmp2,*) ' E R R O R detected in Agrif grid '//TRIM(ctmp9)
	223	WRITE(ctmp3,) ' Look for "E R R O R" messages in all existing '//TRIM(ctmp9)//'_ocean_output files'
	224	CALL ctl_stop( ' ', ctmp1, ' ', ctmp2, ' ', ctmp3 )
[12933]	225	ELSE
[13011]	226	WRITE(ctmp2,) ' Look for "E R R O R" messages in all existing ocean_output files'
	227	CALL ctl_stop( ' ', ctmp1, ' ', ctmp2 )
[12933]	228	ENDIF
[389]	229	ENDIF
[1593]	230	!
[9124]	231	IF( ln_timing ) CALL timing_finalize
[3294]	232	!
[2496]	233	CALL nemo_closefile
[4990]	234	!
[14239]	235	#if defined key_xios
[9210]	236	CALL xios_finalize ! end mpp communications with xios
	237	IF( lk_oasis ) CALL cpl_finalize ! end coupling and mpp communications with OASIS
[532]	238	#else
[9210]	239	IF ( lk_oasis ) THEN ; CALL cpl_finalize ! end coupling and mpp communications with OASIS
[13011]	240	ELSEIF( lk_mpp ) THEN ; CALL mppstop ! end mpp communications
[4990]	241	ENDIF
[532]	242	#endif
[900]	243	!
[10436]	244	IF(lwm) THEN
	245	IF( nstop == 0 ) THEN ; STOP 0
[11536]	246	ELSE ; STOP 123
[10436]	247	ENDIF
[10425]	248	ENDIF
	249	!
[2496]	250	END SUBROUTINE nemo_gcm
[389]	251
	252
[2496]	253	SUBROUTINE nemo_init
[389]	254	!!----------------------------------------------------------------------
[2496]	255	!! * ROUTINE nemo_init *
[389]	256	!!
[2496]	257	!! ** Purpose : initialization of the NEMO GCM
[389]	258	!!----------------------------------------------------------------------
[11536]	259	INTEGER :: ios, ilocal_comm ! local integers
[9213]	260	!!
[14053]	261	NAMELIST/namctl/ sn_cfctl, ln_timing, ln_diacfl, nn_isplt, nn_jsplt , nn_ictls, &
	262	& nn_ictle, nn_jctls , nn_jctle
[9213]	263	NAMELIST/namcfg/ ln_read_cfg, cn_domcfg, ln_closea, ln_write_cfg, cn_domcfg_out, ln_use_jattr
[3]	264	!!----------------------------------------------------------------------
[1593]	265	!
[5407]	266	cxios_context = 'nemo'
[2496]	267	!
[11536]	268	! !-------------------------------------------------!
	269	! ! set communicator & select the local rank !
	270	! ! must be done as soon as possible to get narea !
	271	! !-------------------------------------------------!
[1593]	272	!
[14239]	273	#if defined key_xios
[2200]	274	IF( Agrif_Root() ) THEN
[5407]	275	IF( lk_oasis ) THEN
[7646]	276	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
[11536]	277	CALL xios_initialize( "not used" , local_comm =ilocal_comm ) ! send nemo communicator to xios
[4990]	278	ELSE
[11536]	279	CALL xios_initialize( "for_xios_mpi_id", return_comm=ilocal_comm ) ! nemo local communicator given by xios
[4990]	280	ENDIF
[2200]	281	ENDIF
[11536]	282	CALL mpp_start( ilocal_comm )
[532]	283	#else
[5407]	284	IF( lk_oasis ) THEN
[4990]	285	IF( Agrif_Root() ) THEN
[7646]	286	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
[4990]	287	ENDIF
[11536]	288	CALL mpp_start( ilocal_comm )
[4990]	289	ELSE
[11536]	290	CALL mpp_start( )
[2236]	291	ENDIF
[532]	292	#endif
[11536]	293	!
	294	narea = mpprank + 1 ! mpprank: the rank of proc (0 --> mppsize -1 )
	295	lwm = (narea == 1) ! control of output namelists
	296	!
	297	! !---------------------------------------------------------------!
	298	! ! Open output files, reference and configuration namelist files !
	299	! !---------------------------------------------------------------!
	300	!
	301	! open ocean.output as soon as possible to get all output prints (including errors messages)
	302	IF( lwm ) CALL ctl_opn( numout, 'ocean.output', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, -1, .FALSE. )
	303	! open reference and configuration namelist files
[12377]	304	CALL load_nml( numnam_ref, 'namelist_ref', -1, lwm )
	305	CALL load_nml( numnam_cfg, 'namelist_cfg', -1, lwm )
[11536]	306	IF( lwm ) CALL ctl_opn( numond, 'output.namelist.dyn', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, -1, .FALSE. )
	307	! open /dev/null file to be able to supress output write easily
[12641]	308	IF( Agrif_Root() ) THEN
[11536]	309	CALL ctl_opn( numnul, '/dev/null', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, -1, .FALSE. )
[12641]	310	#ifdef key_agrif
	311	ELSE
[14072]	312	numnul = Agrif_Parent(numnul)
[12641]	313	#endif
	314	ENDIF
[11536]	315	! !--------------------!
[12377]	316	! ! Open listing units ! -> need sn_cfctl from namctl to define lwp
[11536]	317	! !--------------------!
	318	!
	319	READ ( numnam_ref, namctl, IOSTAT = ios, ERR = 901 )
	320	901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in reference namelist' )
	321	READ ( numnam_cfg, namctl, IOSTAT = ios, ERR = 902 )
	322	902 IF( ios > 0 ) CALL ctl_nam ( ios , 'namctl in configuration namelist' )
	323	!
[12377]	324	! finalize the definition of namctl variables
[12933]	325	IF( narea < sn_cfctl%procmin .OR. narea > sn_cfctl%procmax .OR. MOD( narea - sn_cfctl%procmin, sn_cfctl%procincr ) /= 0 ) &
	326	& CALL nemo_set_cfctl( sn_cfctl, .FALSE. )
[11536]	327	!
[12377]	328	lwp = (narea == 1) .OR. sn_cfctl%l_oceout ! control of all listing output print
	329	!
[11536]	330	IF(lwp) THEN ! open listing units
[1593]	331	!
[14143]	332	IF( .NOT. lwm ) & ! alreay opened for narea == 1
[11536]	333	& CALL ctl_opn( numout, 'ocean.output', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, -1, .FALSE., narea )
[1593]	334	!
[1579]	335	WRITE(numout,*)
[11536]	336	WRITE(numout,*) ' CNRS - NERC - Met OFFICE - MERCATOR-ocean - CMCC'
[1593]	337	WRITE(numout,*) ' NEMO team'
[1579]	338	WRITE(numout,*) ' Ocean General Circulation Model'
[14053]	339	WRITE(numout,*) ' NEMO version 4.0 (2020) '
[1579]	340	WRITE(numout,*)
[10510]	341	WRITE(numout,*) " ._ ._ ._ ._ ._ "
	342	WRITE(numout,*) " _.-._)`\_.-._)`\_.-._)`\_.-._)`\_.-._)`\_ "
[1579]	343	WRITE(numout,*)
[10510]	344	WRITE(numout,*) " o _, _, "
	345	WRITE(numout,*) " o .' ( .-' / "
	346	WRITE(numout,*) " o _/..._'. .' / "
	347	WRITE(numout,*) " ( o .-'` ` '-./ _.' "
	348	WRITE(numout,*) " ) ( o) ;= <_ ( "
	349	WRITE(numout,*) " ( '-.,\\__ __.-;`\ '. ) "
	350	WRITE(numout,*) " ) ) \) \|`\ \) '. \ ( ( "
	351	WRITE(numout,*) " ( ( \_/ '-._\ ) ) "
[10583]	352	WRITE(numout,*) " ) ) jgs ` ( ( "
[10510]	353	WRITE(numout,*) " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ "
	354	WRITE(numout,*)
[14053]	355	!
	356	WRITE(numout,cform_aaa) ! Flag AAAAAAA
	357	!
	358	! ! Control print of the working precision
	359	WRITE(numout,*)
	360	IF( wp == dp ) THEN ; WRITE(numout,*) "par_kind : wp = Working precision = dp = double-precision"
	361	ELSE ; WRITE(numout,*) "par_kind : wp = Working precision = sp = single-precision"
[13226]	362	ENDIF
[14053]	363	WRITE(numout,) "~~~~~~~~ ***************"
	364	WRITE(numout,*)
[1593]	365	!
[473]	366	ENDIF
[10425]	367	!
[11536]	368	IF(lwm) WRITE( numond, namctl )
	369	!
	370	! !------------------------------------!
	371	! ! Set global domain size parameters !
	372	! !------------------------------------!
	373	!
	374	READ ( numnam_ref, namcfg, IOSTAT = ios, ERR = 903 )
	375	903 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in reference namelist' )
	376	READ ( numnam_cfg, namcfg, IOSTAT = ios, ERR = 904 )
[14072]	377	904 IF( ios > 0 ) CALL ctl_nam ( ios , 'namcfg in configuration namelist' )
[11536]	378	!
	379	IF( ln_read_cfg ) THEN ! Read sizes in domain configuration file
[14433]	380	CALL domain_cfg ( cn_cfg, nn_cfg, Ni0glo, Nj0glo, jpkglo, l_Iperio, l_Jperio, l_NFold, c_NFtype )
[11536]	381	ELSE ! user-defined namelist
[14433]	382	CALL usr_def_nam( cn_cfg, nn_cfg, Ni0glo, Nj0glo, jpkglo, l_Iperio, l_Jperio, l_NFold, c_NFtype )
[11536]	383	ENDIF
	384	!
	385	IF(lwm) WRITE( numond, namcfg )
	386	!
	387	! !-----------------------------------------!
	388	! ! mpp parameters and domain decomposition !
	389	! !-----------------------------------------!
	390	CALL mpp_init
[2715]	391
[14834]	392	#if defined key_loop_fusion
	393	IF( nn_hls == 1 ) THEN
	394	CALL ctl_stop( 'STOP', 'nemogcm : Loop fusion can be used only with extra-halo' )
	395	ENDIF
	396	#endif
	397
[13286]	398	CALL halo_mng_init()
[7646]	399	! Now we know the dimensions of the grid and numout has been set: we can allocate arrays
[2715]	400	CALL nemo_alloc()
	401
[12377]	402	! Initialise time level indices
[14053]	403	Nbb = 1 ; Nnn = 2 ; Naa = 3 ; Nrhs = Naa
[13216]	404	#if defined key_agrif
[14053]	405	Kbb_a = Nbb ; Kmm_a = Nnn ; Krhs_a = Nrhs ! agrif_oce module copies of time level indices
[14072]	406	#endif
[2496]	407	! !-------------------------------!
	408	! ! NEMO general initialization !
	409	! !-------------------------------!
[473]	410
[14053]	411	CALL nemo_ctl ! Control prints of namctl and namcfg
[2382]	412	!
[9213]	413	! ! General initialization
	414	IF( ln_timing ) CALL timing_init ! timing
	415	IF( ln_timing ) CALL timing_start( 'nemo_init')
[3294]	416	!
[9367]	417	CALL phy_cst ! Physical constants
	418	CALL eos_init ! Equation of state
	419	IF( lk_c1d ) CALL c1d_init ! 1D column configuration
	420	CALL wad_init ! Wetting and drying options
[13216]	421
	422	#if defined key_agrif
	423	CALL Agrif_Declare_Var_ini ! " " " " " DOM
	424	#endif
[14053]	425	CALL dom_init( Nbb, Nnn, Naa ) ! Domain
[14072]	426	IF( ln_crs ) CALL crs_init( Nnn ) ! coarsened grid: domain initialization
[12377]	427	IF( sn_cfctl%l_prtctl ) &
	428	& CALL prt_ctl_init ! Print control
[14072]	429
[12377]	430	CALL diurnal_sst_bulk_init ! diurnal sst
[14072]	431	IF( ln_diurnal ) CALL diurnal_sst_coolskin_init ! cool skin
	432	!
[12377]	433	IF( ln_diurnal_only ) THEN ! diurnal only: a subset of the initialisation routines
	434	CALL istate_init( Nbb, Nnn, Naa ) ! ocean initial state (Dynamics and tracers)
	435	CALL sbc_init( Nbb, Nnn, Naa ) ! Forcings : surface module
	436	CALL tra_qsr_init ! penetrative solar radiation qsr
	437	IF( ln_diaobs ) THEN ! Observation & model comparison
	438	CALL dia_obs_init( Nnn ) ! Initialize observational data
	439	CALL dia_obs( nit000 - 1, Nnn ) ! Observation operator for restart
[14072]	440	ENDIF
[12377]	441	IF( lk_asminc ) CALL asm_inc_init( Nbb, Nnn, Nrhs ) ! Assimilation increments
[9213]	442	!
	443	RETURN ! end of initialization
[6140]	444	ENDIF
[12377]	445	!
[13216]	446
[12377]	447	CALL istate_init( Nbb, Nnn, Naa ) ! ocean initial state (Dynamics and tracers)
[3651]	448
[14072]	449	! ! external forcing
[12377]	450	CALL tide_init ! tidal harmonics
	451	CALL sbc_init( Nbb, Nnn, Naa ) ! surface boundary conditions (including sea-ice)
	452	CALL bdy_init ! Open boundaries initialisation
[9019]	453
[5836]	454	! ! Ocean physics
[12377]	455	CALL zdf_phy_init( Nnn ) ! Vertical physics
[14072]	456
[2082]	457	! ! Lateral physics
[9019]	458	CALL ldf_tra_init ! Lateral ocean tracer physics
[13558]	459	CALL ldf_eiv_init ! eddy induced velocity param. must be done after ldf_tra_init
[9019]	460	CALL ldf_dyn_init ! Lateral ocean momentum physics
[2082]	461
[9019]	462	! ! Active tracers
	463	IF( ln_traqsr ) CALL tra_qsr_init ! penetrative solar radiation qsr
	464	CALL tra_bbc_init ! bottom heat flux
[10350]	465	CALL tra_bbl_init ! advective (and/or diffusive) bottom boundary layer scheme
[9019]	466	CALL tra_dmp_init ! internal tracer damping
	467	CALL tra_adv_init ! horizontal & vertical advection
	468	CALL tra_ldf_init ! lateral mixing
[2027]	469
[9019]	470	! ! Dynamics
[12377]	471	IF( lk_c1d ) CALL dyn_dmp_init ! internal momentum damping
	472	CALL dyn_adv_init ! advection (vector or flux form)
	473	CALL dyn_vor_init ! vorticity term including Coriolis
	474	CALL dyn_ldf_init ! lateral mixing
	475	CALL dyn_hpg_init( Nnn ) ! horizontal gradient of Hydrostatic pressure
	476	CALL dyn_spg_init ! surface pressure gradient
[3764]	477
[14032]	478	! ! Icebergs
	479	CALL icb_init( rn_Dt, nit000) ! initialise icebergs instance
	480
	481	! ice shelf
	482	CALL isf_init( Nbb, Nnn, Naa )
[5836]	483	#if defined key_top
	484	! ! Passive tracers
[12377]	485	CALL trc_init( Nbb, Nnn, Naa )
[5836]	486	#endif
[9019]	487	IF( l_ldfslp ) CALL ldf_slp_init ! slope of lateral mixing
[5836]	488
	489	! ! Misc. options
[9019]	490	CALL sto_par_init ! Stochastic parametrization
	491	IF( ln_sto_eos ) CALL sto_pts_init ! RRandom T/S fluctuations
[14072]	492
[5836]	493	! ! Diagnostics
[12377]	494	CALL flo_init( Nnn ) ! drifting Floats
[9019]	495	IF( ln_diacfl ) CALL dia_cfl_init ! Initialise CFL diagnostics
[11536]	496	CALL dia_dct_init ! Sections tranports
[12377]	497	CALL dia_hsb_init( Nnn ) ! heat content, salt content and volume budgets
	498	CALL trd_init( Nnn ) ! Mixed-layer/Vorticity/Integral constraints trends
	499	CALL dia_obs_init( Nnn ) ! Initialize observational data
	500	CALL dia_25h_init( Nbb ) ! 25h mean outputs
	501	CALL dia_detide_init ! Weights computation for daily detiding of model diagnostics
	502	IF( ln_diaobs ) CALL dia_obs( nit000-1, Nnn ) ! Observation operator for restart
	503	CALL dia_mlr_init ! Initialisation of IOM context management for multiple-linear-regression analysis
[6140]	504
[9019]	505	! ! Assimilation increments
[12377]	506	IF( lk_asminc ) CALL asm_inc_init( Nbb, Nnn, Nrhs ) ! Initialize assimilation increments
[1593]	507	!
[9213]	508	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	509	!
	510	IF( ln_timing ) CALL timing_stop( 'nemo_init')
	511	!
[2496]	512	END SUBROUTINE nemo_init
[467]	513
	514
[2496]	515	SUBROUTINE nemo_ctl
[467]	516	!!----------------------------------------------------------------------
[2496]	517	!! * ROUTINE nemo_ctl *
[467]	518	!!
[3764]	519	!! ** Purpose : control print setting
[467]	520	!!
[11536]	521	!! ** Method : - print namctl and namcfg information and check some consistencies
[467]	522	!!----------------------------------------------------------------------
[2442]	523	!
[2496]	524	IF(lwp) THEN ! control print
[531]	525	WRITE(numout,*)
[7646]	526	WRITE(numout,*) 'nemo_ctl: Control prints'
[9213]	527	WRITE(numout,*) '~~~~~~~~'
[1593]	528	WRITE(numout,*) ' Namelist namctl'
[10570]	529	WRITE(numout,*) ' sn_cfctl%l_runstat = ', sn_cfctl%l_runstat
	530	WRITE(numout,*) ' sn_cfctl%l_trcstat = ', sn_cfctl%l_trcstat
	531	WRITE(numout,*) ' sn_cfctl%l_oceout = ', sn_cfctl%l_oceout
	532	WRITE(numout,*) ' sn_cfctl%l_layout = ', sn_cfctl%l_layout
[12377]	533	WRITE(numout,*) ' sn_cfctl%l_prtctl = ', sn_cfctl%l_prtctl
	534	WRITE(numout,*) ' sn_cfctl%l_prttrc = ', sn_cfctl%l_prttrc
	535	WRITE(numout,*) ' sn_cfctl%l_oasout = ', sn_cfctl%l_oasout
[14072]	536	WRITE(numout,*) ' sn_cfctl%procmin = ', sn_cfctl%procmin
	537	WRITE(numout,*) ' sn_cfctl%procmax = ', sn_cfctl%procmax
	538	WRITE(numout,*) ' sn_cfctl%procincr = ', sn_cfctl%procincr
	539	WRITE(numout,*) ' sn_cfctl%ptimincr = ', sn_cfctl%ptimincr
[9019]	540	WRITE(numout,*) ' timing by routine ln_timing = ', ln_timing
	541	WRITE(numout,*) ' CFL diagnostics ln_diacfl = ', ln_diacfl
[531]	542	ENDIF
[2442]	543	!
[13286]	544	IF( .NOT.ln_read_cfg ) ln_closea = .false. ! dealing possible only with a domcfg file
[4147]	545	IF(lwp) THEN ! control print
	546	WRITE(numout,*)
	547	WRITE(numout,*) ' Namelist namcfg'
[7646]	548	WRITE(numout,*) ' read domain configuration file ln_read_cfg = ', ln_read_cfg
	549	WRITE(numout,*) ' filename to be read cn_domcfg = ', TRIM(cn_domcfg)
[9213]	550	WRITE(numout,*) ' keep closed seas in the domain (if exist) ln_closea = ', ln_closea
	551	WRITE(numout,*) ' create a configuration definition file ln_write_cfg = ', ln_write_cfg
[7646]	552	WRITE(numout,*) ' filename to be written cn_domcfg_out = ', TRIM(cn_domcfg_out)
	553	WRITE(numout,*) ' use file attribute if exists as i/p j-start ln_use_jattr = ', ln_use_jattr
[4147]	554	ENDIF
[9213]	555	!
	556	IF( 1._wp /= SIGN(1._wp,-0._wp) ) CALL ctl_stop( 'nemo_ctl: The intrinsec SIGN function follows f2003 standard.', &
[10425]	557	& 'Compile with key_nosignedzero enabled:', &
	558	& '--> add -Dkey_nosignedzero to the definition of %CPP in your arch file' )
[3764]	559	!
[9023]	560	#if defined key_agrif
[9124]	561	IF( ln_timing ) CALL ctl_stop( 'AGRIF not implemented with ln_timing = true')
[9023]	562	#endif
	563	!
[2496]	564	END SUBROUTINE nemo_ctl
[467]	565
	566
[2496]	567	SUBROUTINE nemo_closefile
[467]	568	!!----------------------------------------------------------------------
[2496]	569	!! * ROUTINE nemo_closefile *
[467]	570	!!
	571	!! ** Purpose : Close the files
	572	!!----------------------------------------------------------------------
[1593]	573	!
	574	IF( lk_mpp ) CALL mppsync
	575	!
[1685]	576	CALL iom_close ! close all input/output files managed by iom_*
[1593]	577	!
[4147]	578	IF( numstp /= -1 ) CLOSE( numstp ) ! time-step file
[9019]	579	IF( numrun /= -1 ) CLOSE( numrun ) ! run statistics file
[4624]	580	IF( lwm.AND.numond /= -1 ) CLOSE( numond ) ! oce output namelist
	581	IF( lwm.AND.numoni /= -1 ) CLOSE( numoni ) ! ice output namelist
[4147]	582	IF( numevo_ice /= -1 ) CLOSE( numevo_ice ) ! ice variables (temp. evolution)
	583	IF( numout /= 6 ) CLOSE( numout ) ! standard model output file
	584	IF( numdct_vol /= -1 ) CLOSE( numdct_vol ) ! volume transports
	585	IF( numdct_heat /= -1 ) CLOSE( numdct_heat ) ! heat transports
	586	IF( numdct_salt /= -1 ) CLOSE( numdct_salt ) ! salt transports
[1593]	587	!
[2442]	588	numout = 6 ! redefine numout in case it is used after this point...
	589	!
[2496]	590	END SUBROUTINE nemo_closefile
[467]	591
[2715]	592
	593	SUBROUTINE nemo_alloc
	594	!!----------------------------------------------------------------------
	595	!! * ROUTINE nemo_alloc *
	596	!!
[14227]	597	!! ** Purpose : Allocate all the dynamic arrays of the OCE modules
[2715]	598	!!
	599	!! ** Method :
	600	!!----------------------------------------------------------------------
[9213]	601	USE diawri , ONLY : dia_wri_alloc
	602	USE dom_oce , ONLY : dom_oce_alloc
	603	USE trc_oce , ONLY : trc_oce_alloc
	604	USE bdy_oce , ONLY : bdy_oce_alloc
[2715]	605	!
	606	INTEGER :: ierr
	607	!!----------------------------------------------------------------------
	608	!
[14072]	609	ierr = oce_alloc () ! ocean
[9213]	610	ierr = ierr + dia_wri_alloc()
	611	ierr = ierr + dom_oce_alloc() ! ocean domain
	612	ierr = ierr + zdf_oce_alloc() ! ocean vertical physics
	613	ierr = ierr + trc_oce_alloc() ! shared TRC / TRA arrays
	614	ierr = ierr + bdy_oce_alloc() ! bdy masks (incl. initialization)
[2715]	615	!
[10425]	616	CALL mpp_sum( 'nemogcm', ierr )
[9213]	617	IF( ierr /= 0 ) CALL ctl_stop( 'STOP', 'nemo_alloc: unable to allocate standard ocean arrays' )
[2715]	618	!
	619	END SUBROUTINE nemo_alloc
	620
[14072]	621
[12933]	622	SUBROUTINE nemo_set_cfctl(sn_cfctl, setto )
[10570]	623	!!----------------------------------------------------------------------
	624	!! * ROUTINE nemo_set_cfctl *
	625	!!
	626	!! ** Purpose : Set elements of the output control structure to setto.
	627	!!
	628	!! ** Method : Note this routine can be used to switch on/off some
[12933]	629	!! types of output for selected areas.
[10570]	630	!!----------------------------------------------------------------------
[12933]	631	TYPE(sn_ctl), INTENT(inout) :: sn_cfctl
	632	LOGICAL , INTENT(in ) :: setto
[10570]	633	!!----------------------------------------------------------------------
[12933]	634	sn_cfctl%l_runstat = setto
	635	sn_cfctl%l_trcstat = setto
[10570]	636	sn_cfctl%l_oceout = setto
	637	sn_cfctl%l_layout = setto
[12377]	638	sn_cfctl%l_prtctl = setto
	639	sn_cfctl%l_prttrc = setto
	640	sn_cfctl%l_oasout = setto
[10570]	641	END SUBROUTINE nemo_set_cfctl
	642
[3]	643	!!======================================================================
[2496]	644	END MODULE nemogcm

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