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nemogcm.F90 @ 13576

Last change on this file since 13576 was 13576, checked in by dford, 4 years ago
Update NEMO-FABM coupler for FABM v1, and introduce two-way NEMO-ERSEM coupling options. See https://code.metoffice.gov.uk/trac/utils/ticket/366.
File size: 40.6 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)
[3764]	15	!! 8.2 ! 1999-11 (M. Imbard, H. Goosse) LIM sea-ice model
	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
	30	!! 3.4 ! 2011-11 (C. Harris) decomposition changes for running with CICE
[4152]	31	!! ! 2012-05 (C. Calone, J. Simeon, G. Madec, C. Ethe) Add grid coarsening
[1593]	32	!!----------------------------------------------------------------------
[3]	33
	34	!!----------------------------------------------------------------------
[2496]	35	!! nemo_gcm : solve ocean dynamics, tracer, biogeochemistry and/or sea-ice
	36	!! nemo_init : initialization of the NEMO system
[3764]	37	!! nemo_ctl : initialisation of the contol print
[2496]	38	!! nemo_closefile : close remaining open files
[2715]	39	!! nemo_alloc : dynamical allocation
	40	!! nemo_partition : calculate MPP domain decomposition
	41	!! factorise : calculate the factors of the no. of MPI processes
[3]	42	!!----------------------------------------------------------------------
[2382]	43	USE step_oce ! module used in the ocean time stepping module
[2392]	44	USE cla ! cross land advection (tra_cla routine)
[3]	45	USE domcfg ! domain configuration (dom_cfg routine)
	46	USE mppini ! shared/distributed memory setting (mpp_init routine)
	47	USE domain ! domain initialization (dom_init routine)
[3625]	48	#if defined key_nemocice_decomp
	49	USE ice_domain_size, only: nx_global, ny_global
	50	#endif
[3651]	51	USE tideini ! tidal components initialization (tide_ini routine)
[4990]	52	USE bdyini ! open boundary cond. setting (bdy_init routine)
	53	USE bdydta ! open boundary cond. setting (bdy_dta_init routine)
	54	USE bdytides ! open boundary cond. setting (bdytide_init routine)
[3]	55	USE istate ! initial state setting (istate_init routine)
	56	USE ldfdyn ! lateral viscosity setting (ldfdyn_init routine)
	57	USE ldftra ! lateral diffusivity setting (ldftra_init routine)
[2392]	58	USE zdfini ! vertical physics setting (zdf_init routine)
[3]	59	USE phycst ! physical constant (par_cst routine)
[4990]	60	USE trdini ! dyn/tra trends initialization (trd_init routine)
[3768]	61	USE asminc ! assimilation increments
	62	USE asmbkg ! writing out state trajectory
[10728]	63	USE asmbgc ! biogeochemical assimilation increments
[2236]	64	USE diaptr ! poleward transports (dia_ptr_init routine)
[3294]	65	USE diadct ! sections transports (dia_dct_init routine)
[2236]	66	USE diaobs ! Observation diagnostics (dia_obs_init routine)
[3764]	67	USE lib_fortran ! Fortran utilities (allows no signed zero when 'key_nosignedzero' defined)
[2496]	68	USE step ! NEMO time-stepping (stp routine)
[3609]	69	USE icbini ! handle bergs, initialisation
	70	USE icbstp ! handle bergs, calving, themodynamics and transport
[11277]	71	USE sbccpl
[1359]	72	USE cpl_oasis3 ! OASIS3 coupling
[900]	73	USE c1d ! 1D configuration
	74	USE step_c1d ! Time stepping loop for the 1D configuration
[4245]	75	USE dyndmp ! Momentum damping
[1594]	76	#if defined key_top
[1593]	77	USE trcini ! passive tracer initialisation
[1594]	78	#endif
[1593]	79	USE lib_mpp ! distributed memory computing
[1412]	80	#if defined key_iomput
[3701]	81	USE xios
[1359]	82	#endif
[3651]	83	USE sbctide, ONLY: lk_tide
[4152]	84	USE crsini ! initialise grid coarsening utility
[4671]	85	USE lbcnfd, ONLY: isendto, nsndto, nfsloop, nfeloop ! Setup of north fold exchanges
[5407]	86	USE sbc_oce, ONLY: lk_oasis
[5329]	87	USE stopar
	88	USE stopts
[8059]	89	USE diatmb ! Top,middle,bottom output
	90	USE dia25h ! 25h mean output
[8561]	91	USE diaopfoam ! FOAM operational output
	92	USE diurnal_bulk ! diurnal bulk SST
[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
[3]	103	!!----------------------------------------------------------------------
[2715]	104	!! NEMO/OPA 4.0 , NEMO Consortium (2011)
[2392]	105	!! $Id$
[2329]	106	!! Software governed by the CeCILL licence (NEMOGCM/NEMO_CeCILL.txt)
[3]	107	!!----------------------------------------------------------------------
	108	CONTAINS
	109
[2496]	110	SUBROUTINE nemo_gcm
[3]	111	!!----------------------------------------------------------------------
[2496]	112	!! * ROUTINE nemo_gcm *
[3]	113	!!
[3764]	114	!! ** Purpose : NEMO solves the primitive equations on an orthogonal
[1593]	115	!! curvilinear mesh on the sphere.
[3]	116	!!
	117	!! ** Method : - model general initialization
	118	!! - launch the time-stepping (stp routine)
[1593]	119	!! - finalize the run by closing files and communications
[3]	120	!!
[2715]	121	!! References : Madec, Delecluse, Imbard, and Levy, 1997: internal report, IPSL.
[1593]	122	!! Madec, 2008, internal report, IPSL.
[3]	123	!!----------------------------------------------------------------------
	124	INTEGER :: istp ! time step index
[389]	125	!!----------------------------------------------------------------------
[2382]	126	!
[392]	127	#if defined key_agrif
[1593]	128	CALL Agrif_Init_Grids() ! AGRIF: set the meshes
[389]	129	#endif
	130
[1593]	131	! !-----------------------!
[2496]	132	CALL nemo_init !== Initialisations ==!
[1593]	133	! !-----------------------!
[2715]	134	#if defined key_agrif
[3680]	135	CALL Agrif_Declare_Var_dom ! AGRIF: set the meshes for DOM
	136	CALL Agrif_Declare_Var ! " " " " " DYN/TRA
[2715]	137	# if defined key_top
[3680]	138	CALL Agrif_Declare_Var_top ! " " " " " TOP
[2715]	139	# endif
[3680]	140	# if defined key_lim2
	141	CALL Agrif_Declare_Var_lim2 ! " " " " " LIM
	142	# endif
[2715]	143	#endif
[682]	144	! check that all process are still there... If some process have an error,
	145	! they will never enter in step and other processes will wait until the end of the cpu time!
[900]	146	IF( lk_mpp ) CALL mpp_max( nstop )
[682]	147
[1593]	148	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	149
	150	! !-----------------------!
	151	! !== time stepping ==!
	152	! !-----------------------!
[900]	153	istp = nit000
[2236]	154	#if defined key_c1d
[389]	155	DO WHILE ( istp <= nitend .AND. nstop == 0 )
[900]	156	CALL stp_c1d( istp )
[389]	157	istp = istp + 1
	158	END DO
[2236]	159	#else
[13576]	160	! Initial call to assimilation routines moved to stp
[3764]	161
[6204]	162	#if defined key_agrif
	163	CALL Agrif_Regrid()
	164	#endif
	165
[389]	166	DO WHILE ( istp <= nitend .AND. nstop == 0 )
[392]	167	#if defined key_agrif
[6204]	168	CALL stp ! AGRIF: time stepping
[389]	169	#else
[11277]	170	IF (lk_oasis) CALL sbc_cpl_snd( istp ) ! Coupling to atmos
	171	CALL stp( istp )
	172	! We don't couple on the final timestep because
	173	! our restart file has already been written
	174	! and contains all the necessary data for a
	175	! restart. sbc_cpl_snd could be called here
	176	! but it would require
	177	! a) A test to ensure it was not performed
	178	! on the very last time-step
	179	! b) the presence of another call to
	180	! sbc_cpl_snd call prior to the main DO loop
	181	! This solution produces identical results
	182	! with fewer lines of code.
[389]	183	#endif
	184	istp = istp + 1
[900]	185	IF( lk_mpp ) CALL mpp_max( nstop )
[389]	186	END DO
[2236]	187	#endif
	188
[3609]	189	IF( lk_diaobs ) CALL dia_obs_wri
	190	!
[10728]	191	IF( ( lk_asminc ).AND.( ln_balwri ) ) CALL asm_bgc_bal_wri( nitend ) ! Output balancing increments
	192	!
[3609]	193	IF( ln_icebergs ) CALL icb_end( nitend )
[3764]	194
[1593]	195	! !------------------------!
	196	! !== finalize the run ==!
	197	! !------------------------!
	198	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	199	!
	200	IF( nstop /= 0 .AND. lwp ) THEN ! error print
[682]	201	WRITE(numout,cform_err)
[3764]	202	WRITE(numout,*) nstop, ' error have been found'
[389]	203	ENDIF
[1593]	204	!
[3294]	205	#if defined key_agrif
[6204]	206	IF( .NOT. Agrif_Root() ) THEN
[5531]	207	CALL Agrif_ParentGrid_To_ChildGrid()
	208	IF( lk_diaobs ) CALL dia_obs_wri
	209	IF( nn_timing == 1 ) CALL timing_finalize
	210	CALL Agrif_ChildGrid_To_ParentGrid()
	211	ENDIF
[3294]	212	#endif
	213	IF( nn_timing == 1 ) CALL timing_finalize
	214	!
[2496]	215	CALL nemo_closefile
[4990]	216	!
[3769]	217	#if defined key_iomput
	218	CALL xios_finalize ! end mpp communications with xios
[5407]	219	IF( lk_oasis ) CALL cpl_finalize ! end coupling and mpp communications with OASIS
[532]	220	#else
[5407]	221	IF( lk_oasis ) THEN
[4990]	222	CALL cpl_finalize ! end coupling and mpp communications with OASIS
	223	ELSE
	224	IF( lk_mpp ) CALL mppstop ! end mpp communications
	225	ENDIF
[532]	226	#endif
[900]	227	!
[2496]	228	END SUBROUTINE nemo_gcm
[389]	229
	230
[2496]	231	SUBROUTINE nemo_init
[389]	232	!!----------------------------------------------------------------------
[2496]	233	!! * ROUTINE nemo_init *
[389]	234	!!
[2496]	235	!! ** Purpose : initialization of the NEMO GCM
[389]	236	!!----------------------------------------------------------------------
[2715]	237	INTEGER :: ji ! dummy loop indices
	238	INTEGER :: ilocal_comm ! local integer
[4147]	239	INTEGER :: ios
[2715]	240	CHARACTER(len=80), DIMENSION(16) :: cltxt
[4990]	241	!
	242	NAMELIST/namctl/ ln_ctl , nn_print, nn_ictls, nn_ictle, &
[3294]	243	& nn_isplt, nn_jsplt, nn_jctls, nn_jctle, &
	244	& nn_bench, nn_timing
[4147]	245	NAMELIST/namcfg/ cp_cfg, cp_cfz, jp_cfg, jpidta, jpjdta, jpkdta, jpiglo, jpjglo, &
[5118]	246	& jpizoom, jpjzoom, jperio, ln_use_jattr
[3]	247	!!----------------------------------------------------------------------
[1593]	248	!
[2496]	249	cltxt = ''
[5407]	250	cxios_context = 'nemo'
[2496]	251	!
[4147]	252	! ! Open reference namelist and configuration namelist files
	253	CALL ctl_opn( numnam_ref, 'namelist_ref', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
	254	CALL ctl_opn( numnam_cfg, 'namelist_cfg', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
[1593]	255	!
[4147]	256	REWIND( numnam_ref ) ! Namelist namctl in reference namelist : Control prints & Benchmark
	257	READ ( numnam_ref, namctl, IOSTAT = ios, ERR = 901 )
[4289]	258	901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in reference namelist', .TRUE. )
[4147]	259
	260	REWIND( numnam_cfg ) ! Namelist namctl in confguration namelist : Control prints & Benchmark
	261	READ ( numnam_cfg, namctl, IOSTAT = ios, ERR = 902 )
[4289]	262	902 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in configuration namelist', .TRUE. )
[4147]	263
[1593]	264	!
[4147]	265	REWIND( numnam_ref ) ! Namelist namcfg in reference namelist : Control prints & Benchmark
	266	READ ( numnam_ref, namcfg, IOSTAT = ios, ERR = 903 )
[4289]	267	903 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in reference namelist', .TRUE. )
[4147]	268
	269	REWIND( numnam_cfg ) ! Namelist namcfg in confguration namelist : Control prints & Benchmark
	270	READ ( numnam_cfg, namcfg, IOSTAT = ios, ERR = 904 )
[4289]	271	904 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in configuration namelist', .TRUE. )
[4309]	272
[4147]	273	! Force values for AGRIF zoom (cf. agrif_user.F90)
	274	#if defined key_agrif
	275	IF( .NOT. Agrif_Root() ) THEN
	276	jpiglo = nbcellsx + 2 + 2*nbghostcells
	277	jpjglo = nbcellsy + 2 + 2*nbghostcells
	278	jpi = ( jpiglo-2jpreci + (jpni-1+0) ) / jpni + 2jpreci
	279	jpj = ( jpjglo-2jprecj + (jpnj-1+0) ) / jpnj + 2jprecj
	280	jpidta = jpiglo
	281	jpjdta = jpjglo
	282	jpizoom = 1
	283	jpjzoom = 1
	284	nperio = 0
	285	jperio = 0
[5118]	286	ln_use_jattr = .false.
[4147]	287	ENDIF
	288	#endif
	289	!
[1593]	290	! !--------------------------------------------!
	291	! ! set communicator & select the local node !
[4624]	292	! ! NB: mynode also opens output.namelist.dyn !
	293	! ! on unit number numond on first proc !
[1593]	294	! !--------------------------------------------!
[1412]	295	#if defined key_iomput
[2200]	296	IF( Agrif_Root() ) THEN
[5407]	297	IF( lk_oasis ) THEN
	298	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
	299	CALL xios_initialize( "not used",local_comm=ilocal_comm ) ! send nemo communicator to xios
[4990]	300	ELSE
[5407]	301	CALL xios_initialize( "for_xios_mpi_id",return_comm=ilocal_comm ) ! nemo local communicator given by xios
[4990]	302	ENDIF
[2200]	303	ENDIF
[5407]	304	! Nodes selection (control print return in cltxt)
	305	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop, ilocal_comm )
[532]	306	#else
[5407]	307	IF( lk_oasis ) THEN
[4990]	308	IF( Agrif_Root() ) THEN
[5407]	309	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
[4990]	310	ENDIF
[5407]	311	! Nodes selection (control print return in cltxt)
	312	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop, ilocal_comm )
[4990]	313	ELSE
	314	ilocal_comm = 0
[5407]	315	! Nodes selection (control print return in cltxt)
	316	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop )
[2236]	317	ENDIF
[532]	318	#endif
[2715]	319	narea = narea + 1 ! mynode return the rank of proc (0 --> jpnij -1 )
[3]	320
[4624]	321	lwm = (narea == 1) ! control of output namelists
[2715]	322	lwp = (narea == 1) .OR. ln_ctl ! control of all listing output print
[1579]	323
[4624]	324	IF(lwm) THEN
	325	! write merged namelists from earlier to output namelist now that the
	326	! file has been opened in call to mynode. nammpp has already been
	327	! written in mynode (if lk_mpp_mpi)
	328	WRITE( numond, namctl )
	329	WRITE( numond, namcfg )
	330	ENDIF
	331
[3764]	332	! If dimensions of processor grid weren't specified in the namelist file
[2715]	333	! then we calculate them here now that we have our communicator size
	334	IF( (jpni < 1) .OR. (jpnj < 1) )THEN
	335	#if defined key_mpp_mpi
	336	IF( Agrif_Root() ) CALL nemo_partition(mppsize)
	337	#else
	338	jpni = 1
	339	jpnj = 1
	340	jpnij = jpni*jpnj
	341	#endif
	342	END IF
	343
	344	! Calculate domain dimensions given calculated jpni and jpnj
	345	! This used to be done in par_oce.F90 when they were parameters rather
	346	! than variables
	347	IF( Agrif_Root() ) THEN
[3294]	348	#if defined key_nemocice_decomp
[3625]	349	jpi = ( nx_global+2-2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
	350	jpj = ( ny_global+2-2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
[3294]	351	#else
[3625]	352	jpi = ( jpiglo-2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
[2715]	353	jpj = ( jpjglo-2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
[3294]	354	#endif
[6204]	355	ENDIF
[2715]	356	jpk = jpkdta ! third dim
[6204]	357	#if defined key_agrif
	358	! simple trick to use same vertical grid as parent
	359	! but different number of levels:
	360	! Save maximum number of levels in jpkdta, then define all vertical grids
	361	! with this number.
	362	! Suppress once vertical online interpolation is ok
	363	IF(.NOT.Agrif_Root()) jpkdta = Agrif_Parent(jpkdta)
	364	#endif
[2715]	365	jpim1 = jpi-1 ! inner domain indices
	366	jpjm1 = jpj-1 ! " "
	367	jpkm1 = jpk-1 ! " "
	368	jpij = jpi*jpj ! jpi x j
	369
[1593]	370	IF(lwp) THEN ! open listing units
	371	!
[1581]	372	CALL ctl_opn( numout, 'ocean.output', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE., narea )
[1593]	373	!
[1579]	374	WRITE(numout,*)
[3294]	375	WRITE(numout,*) ' CNRS - NERC - Met OFFICE - MERCATOR-ocean - INGV - CMCC'
[1593]	376	WRITE(numout,*) ' NEMO team'
[1579]	377	WRITE(numout,*) ' Ocean General Circulation Model'
[5120]	378	WRITE(numout,*) ' version 3.6 (2015) '
[1579]	379	WRITE(numout,*)
	380	WRITE(numout,*)
[3764]	381	DO ji = 1, SIZE(cltxt)
[1593]	382	IF( TRIM(cltxt(ji)) /= '' ) WRITE(numout,*) cltxt(ji) ! control print of mynode
[1579]	383	END DO
[1593]	384	WRITE(numout,cform_aaa) ! Flag AAAAAAA
	385	!
[473]	386	ENDIF
[2715]	387
[3764]	388	! Now we know the dimensions of the grid and numout has been set we can
[2715]	389	! allocate arrays
	390	CALL nemo_alloc()
	391
[2496]	392	! !-------------------------------!
	393	! ! NEMO general initialization !
	394	! !-------------------------------!
[473]	395
[2496]	396	CALL nemo_ctl ! Control prints & Benchmark
[531]	397
[2082]	398	! ! Domain decomposition
[1593]	399	IF( jpni*jpnj == jpnij ) THEN ; CALL mpp_init ! standard cutting out
	400	ELSE ; CALL mpp_init2 ! eliminate land processors
[3]	401	ENDIF
[2382]	402	!
[3294]	403	IF( nn_timing == 1 ) CALL timing_init
	404	!
[2082]	405	! ! General initialization
[2027]	406	CALL phy_cst ! Physical constants
	407	CALL eos_init ! Equation of state
[4245]	408	IF( lk_c1d ) CALL c1d_init ! 1D column configuration
[2027]	409	CALL dom_cfg ! Domain configuration
	410	CALL dom_init ! Domain
[413]	411
[3294]	412	IF( ln_nnogather ) CALL nemo_northcomms ! Initialise the northfold neighbour lists (must be done after the masks are defined)
	413
[2027]	414	IF( ln_ctl ) CALL prt_ctl_init ! Print control
	415
[3651]	416	CALL istate_init ! ocean initial state (Dynamics and tracers)
	417
[8561]	418	CALL diurnal_sst_bulk_init ! diurnal sst
	419	IF ( ln_diurnal ) CALL diurnal_sst_coolskin_init ! cool skin
	420
[4292]	421	IF( lk_tide ) CALL tide_init( nit000 ) ! Initialisation of the tidal harmonics
[3651]	422
[5123]	423	CALL sbc_init ! Forcings : surface module (clem: moved here for bdy purpose)
	424
[4990]	425	IF( lk_bdy ) CALL bdy_init ! Open boundaries initialisation
	426	IF( lk_bdy ) CALL bdy_dta_init ! Open boundaries initialisation of external data arrays
[4292]	427	IF( lk_bdy .AND. lk_tide ) &
[4990]	428	& CALL bdytide_init ! Open boundaries initialisation of tidal harmonic forcing
[2027]	429
[3294]	430	CALL dyn_nept_init ! simplified form of Neptune effect
[4152]	431	!
	432	IF( ln_crs ) CALL crs_init ! Domain initialization of coarsened grid
	433	!
	434	! Ocean physics
[2082]	435	! ! Vertical physics
	436	CALL zdf_init ! namelist read
	437	CALL zdf_bfr_init ! bottom friction
	438	IF( lk_zdfric ) CALL zdf_ric_init ! Richardson number dependent Kz
[2329]	439	IF( lk_zdftke ) CALL zdf_tke_init ! TKE closure scheme
	440	IF( lk_zdfgls ) CALL zdf_gls_init ! GLS closure scheme
	441	IF( lk_zdfkpp ) CALL zdf_kpp_init ! KPP closure scheme
[2082]	442	IF( lk_zdftmx ) CALL zdf_tmx_init ! tidal vertical mixing
[3764]	443	IF( lk_zdfddm .AND. .NOT. lk_zdfkpp ) &
[2082]	444	& CALL zdf_ddm_init ! double diffusive mixing
	445	! ! Lateral physics
	446	CALL ldf_tra_init ! Lateral ocean tracer physics
	447	CALL ldf_dyn_init ! Lateral ocean momentum physics
[2392]	448	IF( lk_ldfslp ) CALL ldf_slp_init ! slope of lateral mixing
[2082]	449
[2027]	450	! ! Active tracers
	451	CALL tra_qsr_init ! penetrative solar radiation qsr
[2325]	452	CALL tra_bbc_init ! bottom heat flux
[2027]	453	IF( lk_trabbl ) CALL tra_bbl_init ! advective (and/or diffusive) bottom boundary layer scheme
[4245]	454	CALL tra_dmp_init ! internal damping trends- tracers
[2027]	455	CALL tra_adv_init ! horizontal & vertical advection
	456	CALL tra_ldf_init ! lateral mixing
	457	CALL tra_zdf_init ! vertical mixing and after tracer fields
	458
	459	! ! Dynamics
[4245]	460	IF( lk_c1d ) CALL dyn_dmp_init ! internal damping trends- momentum
[2027]	461	CALL dyn_adv_init ! advection (vector or flux form)
[2104]	462	CALL dyn_vor_init ! vorticity term including Coriolis
[2027]	463	CALL dyn_ldf_init ! lateral mixing
[2104]	464	CALL dyn_hpg_init ! horizontal gradient of Hydrostatic pressure
[2027]	465	CALL dyn_zdf_init ! vertical diffusion
	466	CALL dyn_spg_init ! surface pressure gradient
[3764]	467
[2392]	468	! ! Misc. options
[4147]	469	IF( nn_cla == 1 .AND. cp_cfg == 'orca' .AND. jp_cfg == 2 ) CALL cla_init ! Cross Land Advection
[3609]	470	CALL icb_init( rdt, nit000) ! initialise icebergs instance
[5329]	471	CALL sto_par_init ! Stochastic parametrization
	472	IF( ln_sto_eos ) CALL sto_pts_init ! RRandom T/S fluctuations
[4147]	473
[1594]	474	#if defined key_top
[2027]	475	! ! Passive tracers
[2082]	476	CALL trc_init
[1594]	477	#endif
[4990]	478	! ! Diagnostics
[3294]	479	IF( lk_floats ) CALL flo_init ! drifting Floats
[2392]	480	IF( lk_diaar5 ) CALL dia_ar5_init ! ar5 diag
[2027]	481	CALL dia_ptr_init ! Poleward TRansports initialization
[3294]	482	IF( lk_diadct ) CALL dia_dct_init ! Sections tranports
[2148]	483	CALL dia_hsb_init ! heat content, salt content and volume budgets
[4990]	484	CALL trd_init ! Mixed-layer/Vorticity/Integral constraints trends
[2392]	485	IF( lk_diaobs ) THEN ! Observation & model comparison
[2382]	486	CALL dia_obs_init ! Initialize observational data
[13576]	487	! Initial call to dia_obs moved to stp
[3764]	488	ENDIF
[4990]	489
[13576]	490	! Initialisation of assimilation moved to stp
[9181]	491
[2382]	492	IF(lwp) WRITE(numout,*) 'Euler time step switch is ', neuler
[13576]	493
	494	! Initialisation of tmb/25h/diaopfoam outputs moved to stp
	495
[1593]	496	!
[2496]	497	END SUBROUTINE nemo_init
[467]	498
	499
[2496]	500	SUBROUTINE nemo_ctl
[467]	501	!!----------------------------------------------------------------------
[2496]	502	!! * ROUTINE nemo_ctl *
[467]	503	!!
[3764]	504	!! ** Purpose : control print setting
[467]	505	!!
[2442]	506	!! ** Method : - print namctl information and check some consistencies
[467]	507	!!----------------------------------------------------------------------
[2442]	508	!
[2496]	509	IF(lwp) THEN ! control print
[531]	510	WRITE(numout,*)
[2496]	511	WRITE(numout,*) 'nemo_ctl: Control prints & Benchmark'
[531]	512	WRITE(numout,*) '~~~~~~~ '
[1593]	513	WRITE(numout,*) ' Namelist namctl'
[1601]	514	WRITE(numout,*) ' run control (for debugging) ln_ctl = ', ln_ctl
	515	WRITE(numout,*) ' level of print nn_print = ', nn_print
	516	WRITE(numout,*) ' Start i indice for SUM control nn_ictls = ', nn_ictls
	517	WRITE(numout,*) ' End i indice for SUM control nn_ictle = ', nn_ictle
	518	WRITE(numout,*) ' Start j indice for SUM control nn_jctls = ', nn_jctls
	519	WRITE(numout,*) ' End j indice for SUM control nn_jctle = ', nn_jctle
	520	WRITE(numout,*) ' number of proc. following i nn_isplt = ', nn_isplt
	521	WRITE(numout,*) ' number of proc. following j nn_jsplt = ', nn_jsplt
	522	WRITE(numout,*) ' benchmark parameter (0/1) nn_bench = ', nn_bench
[3610]	523	WRITE(numout,*) ' timing activated (0/1) nn_timing = ', nn_timing
[531]	524	ENDIF
[2442]	525	!
[1601]	526	nprint = nn_print ! convert DOCTOR namelist names into OLD names
	527	nictls = nn_ictls
	528	nictle = nn_ictle
	529	njctls = nn_jctls
	530	njctle = nn_jctle
	531	isplt = nn_isplt
	532	jsplt = nn_jsplt
	533	nbench = nn_bench
[4147]	534
	535	IF(lwp) THEN ! control print
	536	WRITE(numout,*)
	537	WRITE(numout,*) 'namcfg : configuration initialization through namelist read'
	538	WRITE(numout,*) '~~~~~~~ '
	539	WRITE(numout,*) ' Namelist namcfg'
	540	WRITE(numout,*) ' configuration name cp_cfg = ', TRIM(cp_cfg)
	541	WRITE(numout,*) ' configuration zoom name cp_cfz = ', TRIM(cp_cfz)
	542	WRITE(numout,*) ' configuration resolution jp_cfg = ', jp_cfg
	543	WRITE(numout,*) ' 1st lateral dimension ( >= jpi ) jpidta = ', jpidta
	544	WRITE(numout,*) ' 2nd " " ( >= jpj ) jpjdta = ', jpjdta
	545	WRITE(numout,*) ' 3nd " " jpkdta = ', jpkdta
	546	WRITE(numout,*) ' 1st dimension of global domain in i jpiglo = ', jpiglo
	547	WRITE(numout,*) ' 2nd - - in j jpjglo = ', jpjglo
	548	WRITE(numout,*) ' left bottom i index of the zoom (in data domain) jpizoom = ', jpizoom
	549	WRITE(numout,*) ' left bottom j index of the zoom (in data domain) jpizoom = ', jpjzoom
	550	WRITE(numout,*) ' lateral cond. type (between 0 and 6) jperio = ', jperio
[5118]	551	WRITE(numout,*) ' use file attribute if exists as i/p j-start ln_use_jattr = ', ln_use_jattr
[4147]	552	ENDIF
[2442]	553	! ! Parameter control
[1593]	554	!
	555	IF( ln_ctl ) THEN ! sub-domain area indices for the control prints
[3294]	556	IF( lk_mpp .AND. jpnij > 1 ) THEN
[2496]	557	isplt = jpni ; jsplt = jpnj ; ijsplt = jpni*jpnj ! the domain is forced to the real split domain
[531]	558	ELSE
	559	IF( isplt == 1 .AND. jsplt == 1 ) THEN
[1593]	560	CALL ctl_warn( ' - isplt & jsplt are equal to 1', &
	561	& ' - the print control will be done over the whole domain' )
[531]	562	ENDIF
[1593]	563	ijsplt = isplt * jsplt ! total number of processors ijsplt
[531]	564	ENDIF
	565	IF(lwp) WRITE(numout,*)' - The total number of processors over which the'
	566	IF(lwp) WRITE(numout,*)' print control will be done is ijsplt : ', ijsplt
[1593]	567	!
	568	! ! indices used for the SUM control
	569	IF( nictls+nictle+njctls+njctle == 0 ) THEN ! print control done over the default area
[3764]	570	lsp_area = .FALSE.
[1593]	571	ELSE ! print control done over a specific area
[531]	572	lsp_area = .TRUE.
	573	IF( nictls < 1 .OR. nictls > jpiglo ) THEN
	574	CALL ctl_warn( ' - nictls must be 1<=nictls>=jpiglo, it is forced to 1' )
	575	nictls = 1
	576	ENDIF
	577	IF( nictle < 1 .OR. nictle > jpiglo ) THEN
	578	CALL ctl_warn( ' - nictle must be 1<=nictle>=jpiglo, it is forced to jpiglo' )
	579	nictle = jpiglo
	580	ENDIF
	581	IF( njctls < 1 .OR. njctls > jpjglo ) THEN
	582	CALL ctl_warn( ' - njctls must be 1<=njctls>=jpjglo, it is forced to 1' )
	583	njctls = 1
	584	ENDIF
	585	IF( njctle < 1 .OR. njctle > jpjglo ) THEN
	586	CALL ctl_warn( ' - njctle must be 1<=njctle>=jpjglo, it is forced to jpjglo' )
	587	njctle = jpjglo
	588	ENDIF
[1593]	589	ENDIF
	590	ENDIF
[2442]	591	!
[3764]	592	IF( nbench == 1 ) THEN ! Benchmark
[531]	593	SELECT CASE ( cp_cfg )
[1593]	594	CASE ( 'gyre' ) ; CALL ctl_warn( ' The Benchmark is activated ' )
	595	CASE DEFAULT ; CALL ctl_stop( ' The Benchmark is based on the GYRE configuration:', &
[4147]	596	& ' cp_cfg = "gyre" in namelist &namcfg or set nbench = 0' )
[531]	597	END SELECT
	598	ENDIF
[1593]	599	!
[3764]	600	IF( 1_wp /= SIGN(1._wp,-0._wp) ) CALL ctl_stop( 'nemo_ctl: The intrinsec SIGN function follows ', &
	601	& 'f2003 standard. ' , &
	602	& 'Compile with key_nosignedzero enabled' )
	603	!
[2496]	604	END SUBROUTINE nemo_ctl
[467]	605
	606
[2496]	607	SUBROUTINE nemo_closefile
[467]	608	!!----------------------------------------------------------------------
[2496]	609	!! * ROUTINE nemo_closefile *
[467]	610	!!
	611	!! ** Purpose : Close the files
	612	!!----------------------------------------------------------------------
[1593]	613	!
	614	IF( lk_mpp ) CALL mppsync
	615	!
[1685]	616	CALL iom_close ! close all input/output files managed by iom_*
[1593]	617	!
[4147]	618	IF( numstp /= -1 ) CLOSE( numstp ) ! time-step file
	619	IF( numsol /= -1 ) CLOSE( numsol ) ! solver file
	620	IF( numnam_ref /= -1 ) CLOSE( numnam_ref ) ! oce reference namelist
	621	IF( numnam_cfg /= -1 ) CLOSE( numnam_cfg ) ! oce configuration namelist
[4624]	622	IF( lwm.AND.numond /= -1 ) CLOSE( numond ) ! oce output namelist
[4147]	623	IF( numnam_ice_ref /= -1 ) CLOSE( numnam_ice_ref ) ! ice reference namelist
	624	IF( numnam_ice_cfg /= -1 ) CLOSE( numnam_ice_cfg ) ! ice configuration namelist
[4624]	625	IF( lwm.AND.numoni /= -1 ) CLOSE( numoni ) ! ice output namelist
[4147]	626	IF( numevo_ice /= -1 ) CLOSE( numevo_ice ) ! ice variables (temp. evolution)
	627	IF( numout /= 6 ) CLOSE( numout ) ! standard model output file
	628	IF( numdct_vol /= -1 ) CLOSE( numdct_vol ) ! volume transports
	629	IF( numdct_heat /= -1 ) CLOSE( numdct_heat ) ! heat transports
	630	IF( numdct_salt /= -1 ) CLOSE( numdct_salt ) ! salt transports
[3294]	631
[1593]	632	!
[2442]	633	numout = 6 ! redefine numout in case it is used after this point...
	634	!
[2496]	635	END SUBROUTINE nemo_closefile
[467]	636
[2715]	637
	638	SUBROUTINE nemo_alloc
	639	!!----------------------------------------------------------------------
	640	!! * ROUTINE nemo_alloc *
	641	!!
	642	!! ** Purpose : Allocate all the dynamic arrays of the OPA modules
	643	!!
	644	!! ** Method :
	645	!!----------------------------------------------------------------------
	646	USE diawri , ONLY: dia_wri_alloc
	647	USE dom_oce , ONLY: dom_oce_alloc
	648	USE ldfdyn_oce, ONLY: ldfdyn_oce_alloc
	649	USE ldftra_oce, ONLY: ldftra_oce_alloc
	650	USE trc_oce , ONLY: trc_oce_alloc
[8059]	651	USE diainsitutem, ONLY: insitu_tem_alloc
[3680]	652	#if defined key_diadct
	653	USE diadct , ONLY: diadct_alloc
	654	#endif
[4354]	655	#if defined key_bdy
	656	USE bdy_oce , ONLY: bdy_oce_alloc
	657	#endif
[2715]	658	!
	659	INTEGER :: ierr
	660	!!----------------------------------------------------------------------
	661	!
[3764]	662	ierr = oce_alloc () ! ocean
[2715]	663	ierr = ierr + dia_wri_alloc ()
	664	ierr = ierr + dom_oce_alloc () ! ocean domain
	665	ierr = ierr + ldfdyn_oce_alloc() ! ocean lateral physics : dynamics
	666	ierr = ierr + ldftra_oce_alloc() ! ocean lateral physics : tracers
	667	ierr = ierr + zdf_oce_alloc () ! ocean vertical physics
[8059]	668	ierr = ierr + insitu_tem_alloc()
[2715]	669	!
	670	ierr = ierr + trc_oce_alloc () ! shared TRC / TRA arrays
	671	!
[3680]	672	#if defined key_diadct
	673	ierr = ierr + diadct_alloc () !
	674	#endif
[4354]	675	#if defined key_bdy
	676	ierr = ierr + bdy_oce_alloc () ! bdy masks (incl. initialization)
	677	#endif
[3680]	678	!
[2715]	679	IF( lk_mpp ) CALL mpp_sum( ierr )
	680	IF( ierr /= 0 ) CALL ctl_stop( 'STOP', 'nemo_alloc : unable to allocate standard ocean arrays' )
	681	!
	682	END SUBROUTINE nemo_alloc
	683
	684
	685	SUBROUTINE nemo_partition( num_pes )
	686	!!----------------------------------------------------------------------
	687	!! * ROUTINE nemo_partition *
	688	!!
[3764]	689	!! ** Purpose :
[2715]	690	!!
	691	!! ** Method :
	692	!!----------------------------------------------------------------------
[4990]	693	INTEGER, INTENT(in) :: num_pes ! The number of MPI processes we have
[2715]	694	!
	695	INTEGER, PARAMETER :: nfactmax = 20
	696	INTEGER :: nfact ! The no. of factors returned
	697	INTEGER :: ierr ! Error flag
	698	INTEGER :: ji
	699	INTEGER :: idiff, mindiff, imin ! For choosing pair of factors that are closest in value
	700	INTEGER, DIMENSION(nfactmax) :: ifact ! Array of factors
	701	!!----------------------------------------------------------------------
[4990]	702	!
[2715]	703	ierr = 0
[4990]	704	!
[2715]	705	CALL factorise( ifact, nfactmax, nfact, num_pes, ierr )
[4990]	706	!
[2715]	707	IF( nfact <= 1 ) THEN
	708	WRITE (numout, *) 'WARNING: factorisation of number of PEs failed'
	709	WRITE (numout, *) ' : using grid of ',num_pes,' x 1'
	710	jpnj = 1
	711	jpni = num_pes
	712	ELSE
	713	! Search through factors for the pair that are closest in value
	714	mindiff = 1000000
	715	imin = 1
	716	DO ji = 1, nfact-1, 2
	717	idiff = ABS( ifact(ji) - ifact(ji+1) )
	718	IF( idiff < mindiff ) THEN
	719	mindiff = idiff
	720	imin = ji
	721	ENDIF
	722	END DO
	723	jpnj = ifact(imin)
	724	jpni = ifact(imin + 1)
	725	ENDIF
	726	!
	727	jpnij = jpni*jpnj
	728	!
	729	END SUBROUTINE nemo_partition
	730
	731
	732	SUBROUTINE factorise( kfax, kmaxfax, knfax, kn, kerr )
	733	!!----------------------------------------------------------------------
	734	!! * ROUTINE factorise *
	735	!!
	736	!! ** Purpose : return the prime factors of n.
[3764]	737	!! knfax factors are returned in array kfax which is of
[2715]	738	!! maximum dimension kmaxfax.
	739	!! ** Method :
	740	!!----------------------------------------------------------------------
	741	INTEGER , INTENT(in ) :: kn, kmaxfax
	742	INTEGER , INTENT( out) :: kerr, knfax
	743	INTEGER, DIMENSION(kmaxfax), INTENT( out) :: kfax
	744	!
	745	INTEGER :: ifac, jl, inu
	746	INTEGER, PARAMETER :: ntest = 14
[6204]	747	INTEGER, DIMENSION(ntest) :: ilfax
[4990]	748	!
[6204]	749	! ilfax contains the set of allowed factors.
	750	ilfax(:) = (/(2**jl,jl=ntest,1,-1)/)
[2715]	751	!!----------------------------------------------------------------------
[6204]	752	! ilfax contains the set of allowed factors.
	753	ilfax(:) = (/(2**jl,jl=ntest,1,-1)/)
[2715]	754
	755	! Clear the error flag and initialise output vars
	756	kerr = 0
	757	kfax = 1
	758	knfax = 0
	759
	760	! Find the factors of n.
	761	IF( kn == 1 ) GOTO 20
	762
	763	! nu holds the unfactorised part of the number.
	764	! knfax holds the number of factors found.
	765	! l points to the allowed factor list.
	766	! ifac holds the current factor.
	767
	768	inu = kn
	769	knfax = 0
	770
	771	DO jl = ntest, 1, -1
	772	!
	773	ifac = ilfax(jl)
	774	IF( ifac > inu ) CYCLE
	775
	776	! Test whether the factor will divide.
	777
	778	IF( MOD(inu,ifac) == 0 ) THEN
	779	!
	780	knfax = knfax + 1 ! Add the factor to the list
	781	IF( knfax > kmaxfax ) THEN
	782	kerr = 6
	783	write (,) 'FACTOR: insufficient space in factor array ', knfax
	784	return
	785	ENDIF
	786	kfax(knfax) = ifac
	787	! Store the other factor that goes with this one
	788	knfax = knfax + 1
	789	kfax(knfax) = inu / ifac
	790	!WRITE (,) 'ARPDBG, factors ',knfax-1,' & ',knfax,' are ', kfax(knfax-1),' and ',kfax(knfax)
	791	ENDIF
	792	!
	793	END DO
	794
	795	20 CONTINUE ! Label 20 is the exit point from the factor search loop.
	796	!
	797	END SUBROUTINE factorise
	798
[3294]	799	#if defined key_mpp_mpi
[4990]	800
[3294]	801	SUBROUTINE nemo_northcomms
	802	!!======================================================================
	803	!! * ROUTINE nemo_northcomms *
[4230]	804	!! nemo_northcomms : Setup for north fold exchanges with explicit
	805	!! point-to-point messaging
[3294]	806	!!=====================================================================
	807	!!----------------------------------------------------------------------
[3764]	808	!!
[3294]	809	!! ** Purpose : Initialization of the northern neighbours lists.
	810	!!----------------------------------------------------------------------
[3764]	811	!! 1.0 ! 2011-10 (A. C. Coward, NOCS & J. Donners, PRACE)
[4230]	812	!! 2.0 ! 2013-06 Setup avoiding MPI communication (I. Epicoco, S. Mocavero, CMCC)
[3294]	813	!!----------------------------------------------------------------------
	814
[4230]	815	INTEGER :: sxM, dxM, sxT, dxT, jn
	816	INTEGER :: njmppmax
[3294]	817
[4230]	818	njmppmax = MAXVAL( njmppt )
	819
	820	!initializes the north-fold communication variables
	821	isendto(:) = 0
[3294]	822	nsndto = 0
	823
[4230]	824	!if I am a process in the north
	825	IF ( njmpp == njmppmax ) THEN
	826	!sxM is the first point (in the global domain) needed to compute the
	827	!north-fold for the current process
	828	sxM = jpiglo - nimppt(narea) - nlcit(narea) + 1
	829	!dxM is the last point (in the global domain) needed to compute the
	830	!north-fold for the current process
	831	dxM = jpiglo - nimppt(narea) + 2
[3294]	832
[4230]	833	!loop over the other north-fold processes to find the processes
	834	!managing the points belonging to the sxT-dxT range
[4671]	835
	836	DO jn = 1, jpni
[4230]	837	!sxT is the first point (in the global domain) of the jn
	838	!process
[4671]	839	sxT = nfiimpp(jn, jpnj)
[4230]	840	!dxT is the last point (in the global domain) of the jn
	841	!process
[4671]	842	dxT = nfiimpp(jn, jpnj) + nfilcit(jn, jpnj) - 1
[4230]	843	IF ((sxM .gt. sxT) .AND. (sxM .lt. dxT)) THEN
	844	nsndto = nsndto + 1
[4671]	845	isendto(nsndto) = jn
[4645]	846	ELSEIF ((sxM .le. sxT) .AND. (dxM .ge. dxT)) THEN
[4230]	847	nsndto = nsndto + 1
[4671]	848	isendto(nsndto) = jn
[4230]	849	ELSEIF ((dxM .lt. dxT) .AND. (sxT .lt. dxM)) THEN
	850	nsndto = nsndto + 1
[4671]	851	isendto(nsndto) = jn
[4230]	852	END IF
	853	END DO
[4671]	854	nfsloop = 1
	855	nfeloop = nlci
	856	DO jn = 2,jpni-1
	857	IF(nfipproc(jn,jpnj) .eq. (narea - 1)) THEN
	858	IF (nfipproc(jn - 1 ,jpnj) .eq. -1) THEN
	859	nfsloop = nldi
	860	ENDIF
	861	IF (nfipproc(jn + 1,jpnj) .eq. -1) THEN
	862	nfeloop = nlei
	863	ENDIF
	864	ENDIF
	865	END DO
	866
[3294]	867	ENDIF
[4230]	868	l_north_nogather = .TRUE.
[3294]	869	END SUBROUTINE nemo_northcomms
	870	#else
	871	SUBROUTINE nemo_northcomms ! Dummy routine
	872	WRITE(,) 'nemo_northcomms: You should not have seen this print! error?'
	873	END SUBROUTINE nemo_northcomms
	874	#endif
[4990]	875
[3]	876	!!======================================================================
[2496]	877	END MODULE nemogcm
[4354]	878
	879

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