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nemogcm.F90 in branches/UKMO/AMM15_v3_6_STABLE_package/NEMOGCM/NEMO/OPA_SRC – NEMO

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source: branches/UKMO/AMM15_v3_6_STABLE_package/NEMOGCM/NEMO/OPA_SRC/nemogcm.F90 @ 8561

Last change on this file since 8561 was 8561, checked in by jgraham, 7 years ago
Updates for operational diagnostics: 25h mean diagnostics - bottom temperature (and insitu temp) Operational foam diagnostics - diaopfoam and DIU routines added.
File size: 40.4 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)
[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
[2236]	63	USE diaptr ! poleward transports (dia_ptr_init routine)
[3294]	64	USE diadct ! sections transports (dia_dct_init routine)
[2236]	65	USE diaobs ! Observation diagnostics (dia_obs_init routine)
[3764]	66	USE lib_fortran ! Fortran utilities (allows no signed zero when 'key_nosignedzero' defined)
[2496]	67	USE step ! NEMO time-stepping (stp routine)
[3609]	68	USE icbini ! handle bergs, initialisation
	69	USE icbstp ! handle bergs, calving, themodynamics and transport
[1359]	70	USE cpl_oasis3 ! OASIS3 coupling
[900]	71	USE c1d ! 1D configuration
	72	USE step_c1d ! Time stepping loop for the 1D configuration
[4245]	73	USE dyndmp ! Momentum damping
[1594]	74	#if defined key_top
[1593]	75	USE trcini ! passive tracer initialisation
[1594]	76	#endif
[1593]	77	USE lib_mpp ! distributed memory computing
[1412]	78	#if defined key_iomput
[3701]	79	USE xios
[1359]	80	#endif
[3651]	81	USE sbctide, ONLY: lk_tide
[4152]	82	USE crsini ! initialise grid coarsening utility
[4671]	83	USE lbcnfd, ONLY: isendto, nsndto, nfsloop, nfeloop ! Setup of north fold exchanges
[5407]	84	USE sbc_oce, ONLY: lk_oasis
[5329]	85	USE stopar
	86	USE stopts
[8059]	87	USE diatmb ! Top,middle,bottom output
	88	USE dia25h ! 25h mean output
[8561]	89	USE diaopfoam ! FOAM operational output
	90	USE diurnal_bulk ! diurnal bulk SST
[268]	91
[2715]	92	IMPLICIT NONE
[3]	93	PRIVATE
	94
[2496]	95	PUBLIC nemo_gcm ! called by model.F90
	96	PUBLIC nemo_init ! needed by AGRIF
[3764]	97	PUBLIC nemo_alloc ! needed by TAM
[467]	98
[2498]	99	CHARACTER(lc) :: cform_aaa="( /, 'AAAAAAAA', / ) " ! flag for output listing
[1593]	100
[3]	101	!!----------------------------------------------------------------------
[2715]	102	!! NEMO/OPA 4.0 , NEMO Consortium (2011)
[2392]	103	!! $Id$
[2329]	104	!! Software governed by the CeCILL licence (NEMOGCM/NEMO_CeCILL.txt)
[3]	105	!!----------------------------------------------------------------------
	106	CONTAINS
	107
[2496]	108	SUBROUTINE nemo_gcm
[3]	109	!!----------------------------------------------------------------------
[2496]	110	!! * ROUTINE nemo_gcm *
[3]	111	!!
[3764]	112	!! ** Purpose : NEMO solves the primitive equations on an orthogonal
[1593]	113	!! curvilinear mesh on the sphere.
[3]	114	!!
	115	!! ** Method : - model general initialization
	116	!! - launch the time-stepping (stp routine)
[1593]	117	!! - finalize the run by closing files and communications
[3]	118	!!
[2715]	119	!! References : Madec, Delecluse, Imbard, and Levy, 1997: internal report, IPSL.
[1593]	120	!! Madec, 2008, internal report, IPSL.
[3]	121	!!----------------------------------------------------------------------
	122	INTEGER :: istp ! time step index
[389]	123	!!----------------------------------------------------------------------
[2382]	124	!
[392]	125	#if defined key_agrif
[1593]	126	CALL Agrif_Init_Grids() ! AGRIF: set the meshes
[389]	127	#endif
	128
[1593]	129	! !-----------------------!
[2496]	130	CALL nemo_init !== Initialisations ==!
[1593]	131	! !-----------------------!
[2715]	132	#if defined key_agrif
[3680]	133	CALL Agrif_Declare_Var_dom ! AGRIF: set the meshes for DOM
	134	CALL Agrif_Declare_Var ! " " " " " DYN/TRA
[2715]	135	# if defined key_top
[3680]	136	CALL Agrif_Declare_Var_top ! " " " " " TOP
[2715]	137	# endif
[3680]	138	# if defined key_lim2
	139	CALL Agrif_Declare_Var_lim2 ! " " " " " LIM
	140	# endif
[2715]	141	#endif
[682]	142	! check that all process are still there... If some process have an error,
	143	! they will never enter in step and other processes will wait until the end of the cpu time!
[900]	144	IF( lk_mpp ) CALL mpp_max( nstop )
[682]	145
[1593]	146	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	147
	148	! !-----------------------!
	149	! !== time stepping ==!
	150	! !-----------------------!
[900]	151	istp = nit000
[2236]	152	#if defined key_c1d
[389]	153	DO WHILE ( istp <= nitend .AND. nstop == 0 )
[900]	154	CALL stp_c1d( istp )
[389]	155	istp = istp + 1
	156	END DO
[2236]	157	#else
	158	IF( lk_asminc ) THEN
	159	IF( ln_bkgwri ) CALL asm_bkg_wri( nit000 - 1 ) ! Output background fields
	160	IF( ln_asmdin ) THEN ! Direct initialization
	161	IF( ln_trainc ) CALL tra_asm_inc( nit000 - 1 ) ! Tracers
[3764]	162	IF( ln_dyninc ) CALL dyn_asm_inc( nit000 - 1 ) ! Dynamics
[2236]	163	IF( ln_sshinc ) CALL ssh_asm_inc( nit000 - 1 ) ! SSH
	164	ENDIF
	165	ENDIF
[3764]	166
[6204]	167	#if defined key_agrif
	168	CALL Agrif_Regrid()
	169	#endif
	170
[389]	171	DO WHILE ( istp <= nitend .AND. nstop == 0 )
[392]	172	#if defined key_agrif
[6204]	173	CALL stp ! AGRIF: time stepping
[389]	174	#else
[1593]	175	CALL stp( istp ) ! standard time stepping
[389]	176	#endif
	177	istp = istp + 1
[900]	178	IF( lk_mpp ) CALL mpp_max( nstop )
[389]	179	END DO
[2236]	180	#endif
	181
[3609]	182	IF( lk_diaobs ) CALL dia_obs_wri
	183	!
	184	IF( ln_icebergs ) CALL icb_end( nitend )
[3764]	185
[1593]	186	! !------------------------!
	187	! !== finalize the run ==!
	188	! !------------------------!
	189	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	190	!
	191	IF( nstop /= 0 .AND. lwp ) THEN ! error print
[682]	192	WRITE(numout,cform_err)
[3764]	193	WRITE(numout,*) nstop, ' error have been found'
[389]	194	ENDIF
[1593]	195	!
[3294]	196	#if defined key_agrif
[6204]	197	IF( .NOT. Agrif_Root() ) THEN
[5531]	198	CALL Agrif_ParentGrid_To_ChildGrid()
	199	IF( lk_diaobs ) CALL dia_obs_wri
	200	IF( nn_timing == 1 ) CALL timing_finalize
	201	CALL Agrif_ChildGrid_To_ParentGrid()
	202	ENDIF
[3294]	203	#endif
	204	IF( nn_timing == 1 ) CALL timing_finalize
	205	!
[2496]	206	CALL nemo_closefile
[4990]	207	!
[3769]	208	#if defined key_iomput
	209	CALL xios_finalize ! end mpp communications with xios
[5407]	210	IF( lk_oasis ) CALL cpl_finalize ! end coupling and mpp communications with OASIS
[532]	211	#else
[5407]	212	IF( lk_oasis ) THEN
[4990]	213	CALL cpl_finalize ! end coupling and mpp communications with OASIS
	214	ELSE
	215	IF( lk_mpp ) CALL mppstop ! end mpp communications
	216	ENDIF
[532]	217	#endif
[900]	218	!
[2496]	219	END SUBROUTINE nemo_gcm
[389]	220
	221
[2496]	222	SUBROUTINE nemo_init
[389]	223	!!----------------------------------------------------------------------
[2496]	224	!! * ROUTINE nemo_init *
[389]	225	!!
[2496]	226	!! ** Purpose : initialization of the NEMO GCM
[389]	227	!!----------------------------------------------------------------------
[2715]	228	INTEGER :: ji ! dummy loop indices
	229	INTEGER :: ilocal_comm ! local integer
[4147]	230	INTEGER :: ios
[2715]	231	CHARACTER(len=80), DIMENSION(16) :: cltxt
[4990]	232	!
	233	NAMELIST/namctl/ ln_ctl , nn_print, nn_ictls, nn_ictle, &
[3294]	234	& nn_isplt, nn_jsplt, nn_jctls, nn_jctle, &
	235	& nn_bench, nn_timing
[4147]	236	NAMELIST/namcfg/ cp_cfg, cp_cfz, jp_cfg, jpidta, jpjdta, jpkdta, jpiglo, jpjglo, &
[5118]	237	& jpizoom, jpjzoom, jperio, ln_use_jattr
[3]	238	!!----------------------------------------------------------------------
[1593]	239	!
[2496]	240	cltxt = ''
[5407]	241	cxios_context = 'nemo'
[2496]	242	!
[4147]	243	! ! Open reference namelist and configuration namelist files
	244	CALL ctl_opn( numnam_ref, 'namelist_ref', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
	245	CALL ctl_opn( numnam_cfg, 'namelist_cfg', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
[1593]	246	!
[4147]	247	REWIND( numnam_ref ) ! Namelist namctl in reference namelist : Control prints & Benchmark
	248	READ ( numnam_ref, namctl, IOSTAT = ios, ERR = 901 )
[4289]	249	901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in reference namelist', .TRUE. )
[4147]	250
	251	REWIND( numnam_cfg ) ! Namelist namctl in confguration namelist : Control prints & Benchmark
	252	READ ( numnam_cfg, namctl, IOSTAT = ios, ERR = 902 )
[4289]	253	902 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in configuration namelist', .TRUE. )
[4147]	254
[1593]	255	!
[4147]	256	REWIND( numnam_ref ) ! Namelist namcfg in reference namelist : Control prints & Benchmark
	257	READ ( numnam_ref, namcfg, IOSTAT = ios, ERR = 903 )
[4289]	258	903 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in reference namelist', .TRUE. )
[4147]	259
	260	REWIND( numnam_cfg ) ! Namelist namcfg in confguration namelist : Control prints & Benchmark
	261	READ ( numnam_cfg, namcfg, IOSTAT = ios, ERR = 904 )
[4289]	262	904 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in configuration namelist', .TRUE. )
[4309]	263
[4147]	264	! Force values for AGRIF zoom (cf. agrif_user.F90)
	265	#if defined key_agrif
	266	IF( .NOT. Agrif_Root() ) THEN
	267	jpiglo = nbcellsx + 2 + 2*nbghostcells
	268	jpjglo = nbcellsy + 2 + 2*nbghostcells
	269	jpi = ( jpiglo-2jpreci + (jpni-1+0) ) / jpni + 2jpreci
	270	jpj = ( jpjglo-2jprecj + (jpnj-1+0) ) / jpnj + 2jprecj
	271	jpidta = jpiglo
	272	jpjdta = jpjglo
	273	jpizoom = 1
	274	jpjzoom = 1
	275	nperio = 0
	276	jperio = 0
[5118]	277	ln_use_jattr = .false.
[4147]	278	ENDIF
	279	#endif
	280	!
[1593]	281	! !--------------------------------------------!
	282	! ! set communicator & select the local node !
[4624]	283	! ! NB: mynode also opens output.namelist.dyn !
	284	! ! on unit number numond on first proc !
[1593]	285	! !--------------------------------------------!
[1412]	286	#if defined key_iomput
[2200]	287	IF( Agrif_Root() ) THEN
[5407]	288	IF( lk_oasis ) THEN
	289	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
	290	CALL xios_initialize( "not used",local_comm=ilocal_comm ) ! send nemo communicator to xios
[4990]	291	ELSE
[5407]	292	CALL xios_initialize( "for_xios_mpi_id",return_comm=ilocal_comm ) ! nemo local communicator given by xios
[4990]	293	ENDIF
[2200]	294	ENDIF
[5407]	295	! Nodes selection (control print return in cltxt)
	296	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop, ilocal_comm )
[532]	297	#else
[5407]	298	IF( lk_oasis ) THEN
[4990]	299	IF( Agrif_Root() ) THEN
[5407]	300	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
[4990]	301	ENDIF
[5407]	302	! Nodes selection (control print return in cltxt)
	303	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop, ilocal_comm )
[4990]	304	ELSE
	305	ilocal_comm = 0
[5407]	306	! Nodes selection (control print return in cltxt)
	307	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop )
[2236]	308	ENDIF
[532]	309	#endif
[2715]	310	narea = narea + 1 ! mynode return the rank of proc (0 --> jpnij -1 )
[3]	311
[4624]	312	lwm = (narea == 1) ! control of output namelists
[2715]	313	lwp = (narea == 1) .OR. ln_ctl ! control of all listing output print
[1579]	314
[4624]	315	IF(lwm) THEN
	316	! write merged namelists from earlier to output namelist now that the
	317	! file has been opened in call to mynode. nammpp has already been
	318	! written in mynode (if lk_mpp_mpi)
	319	WRITE( numond, namctl )
	320	WRITE( numond, namcfg )
	321	ENDIF
	322
[3764]	323	! If dimensions of processor grid weren't specified in the namelist file
[2715]	324	! then we calculate them here now that we have our communicator size
	325	IF( (jpni < 1) .OR. (jpnj < 1) )THEN
	326	#if defined key_mpp_mpi
	327	IF( Agrif_Root() ) CALL nemo_partition(mppsize)
	328	#else
	329	jpni = 1
	330	jpnj = 1
	331	jpnij = jpni*jpnj
	332	#endif
	333	END IF
	334
	335	! Calculate domain dimensions given calculated jpni and jpnj
	336	! This used to be done in par_oce.F90 when they were parameters rather
	337	! than variables
	338	IF( Agrif_Root() ) THEN
[3294]	339	#if defined key_nemocice_decomp
[3625]	340	jpi = ( nx_global+2-2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
	341	jpj = ( ny_global+2-2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
[3294]	342	#else
[3625]	343	jpi = ( jpiglo-2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
[2715]	344	jpj = ( jpjglo-2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
[3294]	345	#endif
[6204]	346	ENDIF
[2715]	347	jpk = jpkdta ! third dim
[6204]	348	#if defined key_agrif
	349	! simple trick to use same vertical grid as parent
	350	! but different number of levels:
	351	! Save maximum number of levels in jpkdta, then define all vertical grids
	352	! with this number.
	353	! Suppress once vertical online interpolation is ok
	354	IF(.NOT.Agrif_Root()) jpkdta = Agrif_Parent(jpkdta)
	355	#endif
[2715]	356	jpim1 = jpi-1 ! inner domain indices
	357	jpjm1 = jpj-1 ! " "
	358	jpkm1 = jpk-1 ! " "
	359	jpij = jpi*jpj ! jpi x j
	360
[1593]	361	IF(lwp) THEN ! open listing units
	362	!
[1581]	363	CALL ctl_opn( numout, 'ocean.output', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE., narea )
[1593]	364	!
[1579]	365	WRITE(numout,*)
[3294]	366	WRITE(numout,*) ' CNRS - NERC - Met OFFICE - MERCATOR-ocean - INGV - CMCC'
[1593]	367	WRITE(numout,*) ' NEMO team'
[1579]	368	WRITE(numout,*) ' Ocean General Circulation Model'
[5120]	369	WRITE(numout,*) ' version 3.6 (2015) '
[1579]	370	WRITE(numout,*)
	371	WRITE(numout,*)
[3764]	372	DO ji = 1, SIZE(cltxt)
[1593]	373	IF( TRIM(cltxt(ji)) /= '' ) WRITE(numout,*) cltxt(ji) ! control print of mynode
[1579]	374	END DO
[1593]	375	WRITE(numout,cform_aaa) ! Flag AAAAAAA
	376	!
[473]	377	ENDIF
[2715]	378
[3764]	379	! Now we know the dimensions of the grid and numout has been set we can
[2715]	380	! allocate arrays
	381	CALL nemo_alloc()
	382
[2496]	383	! !-------------------------------!
	384	! ! NEMO general initialization !
	385	! !-------------------------------!
[473]	386
[2496]	387	CALL nemo_ctl ! Control prints & Benchmark
[531]	388
[2082]	389	! ! Domain decomposition
[1593]	390	IF( jpni*jpnj == jpnij ) THEN ; CALL mpp_init ! standard cutting out
	391	ELSE ; CALL mpp_init2 ! eliminate land processors
[3]	392	ENDIF
[2382]	393	!
[3294]	394	IF( nn_timing == 1 ) CALL timing_init
	395	!
[2082]	396	! ! General initialization
[2027]	397	CALL phy_cst ! Physical constants
	398	CALL eos_init ! Equation of state
[4245]	399	IF( lk_c1d ) CALL c1d_init ! 1D column configuration
[2027]	400	CALL dom_cfg ! Domain configuration
	401	CALL dom_init ! Domain
[413]	402
[3294]	403	IF( ln_nnogather ) CALL nemo_northcomms ! Initialise the northfold neighbour lists (must be done after the masks are defined)
	404
[2027]	405	IF( ln_ctl ) CALL prt_ctl_init ! Print control
	406
[3651]	407	CALL istate_init ! ocean initial state (Dynamics and tracers)
	408
[8561]	409	CALL diurnal_sst_bulk_init ! diurnal sst
	410	IF ( ln_diurnal ) CALL diurnal_sst_coolskin_init ! cool skin
	411
[4292]	412	IF( lk_tide ) CALL tide_init( nit000 ) ! Initialisation of the tidal harmonics
[3651]	413
[5123]	414	CALL sbc_init ! Forcings : surface module (clem: moved here for bdy purpose)
	415
[4990]	416	IF( lk_bdy ) CALL bdy_init ! Open boundaries initialisation
	417	IF( lk_bdy ) CALL bdy_dta_init ! Open boundaries initialisation of external data arrays
[4292]	418	IF( lk_bdy .AND. lk_tide ) &
[4990]	419	& CALL bdytide_init ! Open boundaries initialisation of tidal harmonic forcing
[2027]	420
[3294]	421	CALL dyn_nept_init ! simplified form of Neptune effect
[4152]	422	!
	423	IF( ln_crs ) CALL crs_init ! Domain initialization of coarsened grid
	424	!
	425	! Ocean physics
[2082]	426	! ! Vertical physics
	427	CALL zdf_init ! namelist read
	428	CALL zdf_bfr_init ! bottom friction
	429	IF( lk_zdfric ) CALL zdf_ric_init ! Richardson number dependent Kz
[2329]	430	IF( lk_zdftke ) CALL zdf_tke_init ! TKE closure scheme
	431	IF( lk_zdfgls ) CALL zdf_gls_init ! GLS closure scheme
	432	IF( lk_zdfkpp ) CALL zdf_kpp_init ! KPP closure scheme
[2082]	433	IF( lk_zdftmx ) CALL zdf_tmx_init ! tidal vertical mixing
[3764]	434	IF( lk_zdfddm .AND. .NOT. lk_zdfkpp ) &
[2082]	435	& CALL zdf_ddm_init ! double diffusive mixing
	436	! ! Lateral physics
	437	CALL ldf_tra_init ! Lateral ocean tracer physics
	438	CALL ldf_dyn_init ! Lateral ocean momentum physics
[2392]	439	IF( lk_ldfslp ) CALL ldf_slp_init ! slope of lateral mixing
[2082]	440
[2027]	441	! ! Active tracers
	442	CALL tra_qsr_init ! penetrative solar radiation qsr
[2325]	443	CALL tra_bbc_init ! bottom heat flux
[2027]	444	IF( lk_trabbl ) CALL tra_bbl_init ! advective (and/or diffusive) bottom boundary layer scheme
[4245]	445	CALL tra_dmp_init ! internal damping trends- tracers
[2027]	446	CALL tra_adv_init ! horizontal & vertical advection
	447	CALL tra_ldf_init ! lateral mixing
	448	CALL tra_zdf_init ! vertical mixing and after tracer fields
	449
	450	! ! Dynamics
[4245]	451	IF( lk_c1d ) CALL dyn_dmp_init ! internal damping trends- momentum
[2027]	452	CALL dyn_adv_init ! advection (vector or flux form)
[2104]	453	CALL dyn_vor_init ! vorticity term including Coriolis
[2027]	454	CALL dyn_ldf_init ! lateral mixing
[2104]	455	CALL dyn_hpg_init ! horizontal gradient of Hydrostatic pressure
[2027]	456	CALL dyn_zdf_init ! vertical diffusion
	457	CALL dyn_spg_init ! surface pressure gradient
[3764]	458
[2392]	459	! ! Misc. options
[4147]	460	IF( nn_cla == 1 .AND. cp_cfg == 'orca' .AND. jp_cfg == 2 ) CALL cla_init ! Cross Land Advection
[3609]	461	CALL icb_init( rdt, nit000) ! initialise icebergs instance
[5329]	462	CALL sto_par_init ! Stochastic parametrization
	463	IF( ln_sto_eos ) CALL sto_pts_init ! RRandom T/S fluctuations
[4147]	464
[1594]	465	#if defined key_top
[2027]	466	! ! Passive tracers
[2082]	467	CALL trc_init
[1594]	468	#endif
[4990]	469	! ! Diagnostics
[3294]	470	IF( lk_floats ) CALL flo_init ! drifting Floats
[2392]	471	IF( lk_diaar5 ) CALL dia_ar5_init ! ar5 diag
[2027]	472	CALL dia_ptr_init ! Poleward TRansports initialization
[3294]	473	IF( lk_diadct ) CALL dia_dct_init ! Sections tranports
[2148]	474	CALL dia_hsb_init ! heat content, salt content and volume budgets
[4990]	475	CALL trd_init ! Mixed-layer/Vorticity/Integral constraints trends
[2392]	476	IF( lk_diaobs ) THEN ! Observation & model comparison
[2382]	477	CALL dia_obs_init ! Initialize observational data
	478	CALL dia_obs( nit000 - 1 ) ! Observation operator for restart
[3764]	479	ENDIF
[4990]	480
[2382]	481	! ! Assimilation increments
[2392]	482	IF( lk_asminc ) CALL asm_inc_init ! Initialize assimilation increments
[2382]	483	IF(lwp) WRITE(numout,*) 'Euler time step switch is ', neuler
[8059]	484	CALL dia_tmb_init ! TMB outputs
	485	CALL dia_25h_init ! 25h mean outputs
[8561]	486	CALL dia_diaopfoam_init ! FOAM operational output
[1593]	487	!
[2496]	488	END SUBROUTINE nemo_init
[467]	489
	490
[2496]	491	SUBROUTINE nemo_ctl
[467]	492	!!----------------------------------------------------------------------
[2496]	493	!! * ROUTINE nemo_ctl *
[467]	494	!!
[3764]	495	!! ** Purpose : control print setting
[467]	496	!!
[2442]	497	!! ** Method : - print namctl information and check some consistencies
[467]	498	!!----------------------------------------------------------------------
[2442]	499	!
[2496]	500	IF(lwp) THEN ! control print
[531]	501	WRITE(numout,*)
[2496]	502	WRITE(numout,*) 'nemo_ctl: Control prints & Benchmark'
[531]	503	WRITE(numout,*) '~~~~~~~ '
[1593]	504	WRITE(numout,*) ' Namelist namctl'
[1601]	505	WRITE(numout,*) ' run control (for debugging) ln_ctl = ', ln_ctl
	506	WRITE(numout,*) ' level of print nn_print = ', nn_print
	507	WRITE(numout,*) ' Start i indice for SUM control nn_ictls = ', nn_ictls
	508	WRITE(numout,*) ' End i indice for SUM control nn_ictle = ', nn_ictle
	509	WRITE(numout,*) ' Start j indice for SUM control nn_jctls = ', nn_jctls
	510	WRITE(numout,*) ' End j indice for SUM control nn_jctle = ', nn_jctle
	511	WRITE(numout,*) ' number of proc. following i nn_isplt = ', nn_isplt
	512	WRITE(numout,*) ' number of proc. following j nn_jsplt = ', nn_jsplt
	513	WRITE(numout,*) ' benchmark parameter (0/1) nn_bench = ', nn_bench
[3610]	514	WRITE(numout,*) ' timing activated (0/1) nn_timing = ', nn_timing
[531]	515	ENDIF
[2442]	516	!
[1601]	517	nprint = nn_print ! convert DOCTOR namelist names into OLD names
	518	nictls = nn_ictls
	519	nictle = nn_ictle
	520	njctls = nn_jctls
	521	njctle = nn_jctle
	522	isplt = nn_isplt
	523	jsplt = nn_jsplt
	524	nbench = nn_bench
[4147]	525
	526	IF(lwp) THEN ! control print
	527	WRITE(numout,*)
	528	WRITE(numout,*) 'namcfg : configuration initialization through namelist read'
	529	WRITE(numout,*) '~~~~~~~ '
	530	WRITE(numout,*) ' Namelist namcfg'
	531	WRITE(numout,*) ' configuration name cp_cfg = ', TRIM(cp_cfg)
	532	WRITE(numout,*) ' configuration zoom name cp_cfz = ', TRIM(cp_cfz)
	533	WRITE(numout,*) ' configuration resolution jp_cfg = ', jp_cfg
	534	WRITE(numout,*) ' 1st lateral dimension ( >= jpi ) jpidta = ', jpidta
	535	WRITE(numout,*) ' 2nd " " ( >= jpj ) jpjdta = ', jpjdta
	536	WRITE(numout,*) ' 3nd " " jpkdta = ', jpkdta
	537	WRITE(numout,*) ' 1st dimension of global domain in i jpiglo = ', jpiglo
	538	WRITE(numout,*) ' 2nd - - in j jpjglo = ', jpjglo
	539	WRITE(numout,*) ' left bottom i index of the zoom (in data domain) jpizoom = ', jpizoom
	540	WRITE(numout,*) ' left bottom j index of the zoom (in data domain) jpizoom = ', jpjzoom
	541	WRITE(numout,*) ' lateral cond. type (between 0 and 6) jperio = ', jperio
[5118]	542	WRITE(numout,*) ' use file attribute if exists as i/p j-start ln_use_jattr = ', ln_use_jattr
[4147]	543	ENDIF
[2442]	544	! ! Parameter control
[1593]	545	!
	546	IF( ln_ctl ) THEN ! sub-domain area indices for the control prints
[3294]	547	IF( lk_mpp .AND. jpnij > 1 ) THEN
[2496]	548	isplt = jpni ; jsplt = jpnj ; ijsplt = jpni*jpnj ! the domain is forced to the real split domain
[531]	549	ELSE
	550	IF( isplt == 1 .AND. jsplt == 1 ) THEN
[1593]	551	CALL ctl_warn( ' - isplt & jsplt are equal to 1', &
	552	& ' - the print control will be done over the whole domain' )
[531]	553	ENDIF
[1593]	554	ijsplt = isplt * jsplt ! total number of processors ijsplt
[531]	555	ENDIF
	556	IF(lwp) WRITE(numout,*)' - The total number of processors over which the'
	557	IF(lwp) WRITE(numout,*)' print control will be done is ijsplt : ', ijsplt
[1593]	558	!
	559	! ! indices used for the SUM control
	560	IF( nictls+nictle+njctls+njctle == 0 ) THEN ! print control done over the default area
[3764]	561	lsp_area = .FALSE.
[1593]	562	ELSE ! print control done over a specific area
[531]	563	lsp_area = .TRUE.
	564	IF( nictls < 1 .OR. nictls > jpiglo ) THEN
	565	CALL ctl_warn( ' - nictls must be 1<=nictls>=jpiglo, it is forced to 1' )
	566	nictls = 1
	567	ENDIF
	568	IF( nictle < 1 .OR. nictle > jpiglo ) THEN
	569	CALL ctl_warn( ' - nictle must be 1<=nictle>=jpiglo, it is forced to jpiglo' )
	570	nictle = jpiglo
	571	ENDIF
	572	IF( njctls < 1 .OR. njctls > jpjglo ) THEN
	573	CALL ctl_warn( ' - njctls must be 1<=njctls>=jpjglo, it is forced to 1' )
	574	njctls = 1
	575	ENDIF
	576	IF( njctle < 1 .OR. njctle > jpjglo ) THEN
	577	CALL ctl_warn( ' - njctle must be 1<=njctle>=jpjglo, it is forced to jpjglo' )
	578	njctle = jpjglo
	579	ENDIF
[1593]	580	ENDIF
	581	ENDIF
[2442]	582	!
[3764]	583	IF( nbench == 1 ) THEN ! Benchmark
[531]	584	SELECT CASE ( cp_cfg )
[1593]	585	CASE ( 'gyre' ) ; CALL ctl_warn( ' The Benchmark is activated ' )
	586	CASE DEFAULT ; CALL ctl_stop( ' The Benchmark is based on the GYRE configuration:', &
[4147]	587	& ' cp_cfg = "gyre" in namelist &namcfg or set nbench = 0' )
[531]	588	END SELECT
	589	ENDIF
[1593]	590	!
[3764]	591	IF( 1_wp /= SIGN(1._wp,-0._wp) ) CALL ctl_stop( 'nemo_ctl: The intrinsec SIGN function follows ', &
	592	& 'f2003 standard. ' , &
	593	& 'Compile with key_nosignedzero enabled' )
	594	!
[2496]	595	END SUBROUTINE nemo_ctl
[467]	596
	597
[2496]	598	SUBROUTINE nemo_closefile
[467]	599	!!----------------------------------------------------------------------
[2496]	600	!! * ROUTINE nemo_closefile *
[467]	601	!!
	602	!! ** Purpose : Close the files
	603	!!----------------------------------------------------------------------
[1593]	604	!
	605	IF( lk_mpp ) CALL mppsync
	606	!
[1685]	607	CALL iom_close ! close all input/output files managed by iom_*
[1593]	608	!
[4147]	609	IF( numstp /= -1 ) CLOSE( numstp ) ! time-step file
	610	IF( numsol /= -1 ) CLOSE( numsol ) ! solver file
	611	IF( numnam_ref /= -1 ) CLOSE( numnam_ref ) ! oce reference namelist
	612	IF( numnam_cfg /= -1 ) CLOSE( numnam_cfg ) ! oce configuration namelist
[4624]	613	IF( lwm.AND.numond /= -1 ) CLOSE( numond ) ! oce output namelist
[4147]	614	IF( numnam_ice_ref /= -1 ) CLOSE( numnam_ice_ref ) ! ice reference namelist
	615	IF( numnam_ice_cfg /= -1 ) CLOSE( numnam_ice_cfg ) ! ice configuration namelist
[4624]	616	IF( lwm.AND.numoni /= -1 ) CLOSE( numoni ) ! ice output namelist
[4147]	617	IF( numevo_ice /= -1 ) CLOSE( numevo_ice ) ! ice variables (temp. evolution)
	618	IF( numout /= 6 ) CLOSE( numout ) ! standard model output file
	619	IF( numdct_vol /= -1 ) CLOSE( numdct_vol ) ! volume transports
	620	IF( numdct_heat /= -1 ) CLOSE( numdct_heat ) ! heat transports
	621	IF( numdct_salt /= -1 ) CLOSE( numdct_salt ) ! salt transports
[3294]	622
[1593]	623	!
[2442]	624	numout = 6 ! redefine numout in case it is used after this point...
	625	!
[2496]	626	END SUBROUTINE nemo_closefile
[467]	627
[2715]	628
	629	SUBROUTINE nemo_alloc
	630	!!----------------------------------------------------------------------
	631	!! * ROUTINE nemo_alloc *
	632	!!
	633	!! ** Purpose : Allocate all the dynamic arrays of the OPA modules
	634	!!
	635	!! ** Method :
	636	!!----------------------------------------------------------------------
	637	USE diawri , ONLY: dia_wri_alloc
	638	USE dom_oce , ONLY: dom_oce_alloc
	639	USE ldfdyn_oce, ONLY: ldfdyn_oce_alloc
	640	USE ldftra_oce, ONLY: ldftra_oce_alloc
	641	USE trc_oce , ONLY: trc_oce_alloc
[8059]	642	USE diainsitutem, ONLY: insitu_tem_alloc
[3680]	643	#if defined key_diadct
	644	USE diadct , ONLY: diadct_alloc
	645	#endif
[4354]	646	#if defined key_bdy
	647	USE bdy_oce , ONLY: bdy_oce_alloc
	648	#endif
[2715]	649	!
	650	INTEGER :: ierr
	651	!!----------------------------------------------------------------------
	652	!
[3764]	653	ierr = oce_alloc () ! ocean
[2715]	654	ierr = ierr + dia_wri_alloc ()
	655	ierr = ierr + dom_oce_alloc () ! ocean domain
	656	ierr = ierr + ldfdyn_oce_alloc() ! ocean lateral physics : dynamics
	657	ierr = ierr + ldftra_oce_alloc() ! ocean lateral physics : tracers
	658	ierr = ierr + zdf_oce_alloc () ! ocean vertical physics
[8059]	659	ierr = ierr + insitu_tem_alloc()
[2715]	660	!
	661	ierr = ierr + trc_oce_alloc () ! shared TRC / TRA arrays
	662	!
[3680]	663	#if defined key_diadct
	664	ierr = ierr + diadct_alloc () !
	665	#endif
[4354]	666	#if defined key_bdy
	667	ierr = ierr + bdy_oce_alloc () ! bdy masks (incl. initialization)
	668	#endif
[3680]	669	!
[2715]	670	IF( lk_mpp ) CALL mpp_sum( ierr )
	671	IF( ierr /= 0 ) CALL ctl_stop( 'STOP', 'nemo_alloc : unable to allocate standard ocean arrays' )
	672	!
	673	END SUBROUTINE nemo_alloc
	674
	675
	676	SUBROUTINE nemo_partition( num_pes )
	677	!!----------------------------------------------------------------------
	678	!! * ROUTINE nemo_partition *
	679	!!
[3764]	680	!! ** Purpose :
[2715]	681	!!
	682	!! ** Method :
	683	!!----------------------------------------------------------------------
[4990]	684	INTEGER, INTENT(in) :: num_pes ! The number of MPI processes we have
[2715]	685	!
	686	INTEGER, PARAMETER :: nfactmax = 20
	687	INTEGER :: nfact ! The no. of factors returned
	688	INTEGER :: ierr ! Error flag
	689	INTEGER :: ji
	690	INTEGER :: idiff, mindiff, imin ! For choosing pair of factors that are closest in value
	691	INTEGER, DIMENSION(nfactmax) :: ifact ! Array of factors
	692	!!----------------------------------------------------------------------
[4990]	693	!
[2715]	694	ierr = 0
[4990]	695	!
[2715]	696	CALL factorise( ifact, nfactmax, nfact, num_pes, ierr )
[4990]	697	!
[2715]	698	IF( nfact <= 1 ) THEN
	699	WRITE (numout, *) 'WARNING: factorisation of number of PEs failed'
	700	WRITE (numout, *) ' : using grid of ',num_pes,' x 1'
	701	jpnj = 1
	702	jpni = num_pes
	703	ELSE
	704	! Search through factors for the pair that are closest in value
	705	mindiff = 1000000
	706	imin = 1
	707	DO ji = 1, nfact-1, 2
	708	idiff = ABS( ifact(ji) - ifact(ji+1) )
	709	IF( idiff < mindiff ) THEN
	710	mindiff = idiff
	711	imin = ji
	712	ENDIF
	713	END DO
	714	jpnj = ifact(imin)
	715	jpni = ifact(imin + 1)
	716	ENDIF
	717	!
	718	jpnij = jpni*jpnj
	719	!
	720	END SUBROUTINE nemo_partition
	721
	722
	723	SUBROUTINE factorise( kfax, kmaxfax, knfax, kn, kerr )
	724	!!----------------------------------------------------------------------
	725	!! * ROUTINE factorise *
	726	!!
	727	!! ** Purpose : return the prime factors of n.
[3764]	728	!! knfax factors are returned in array kfax which is of
[2715]	729	!! maximum dimension kmaxfax.
	730	!! ** Method :
	731	!!----------------------------------------------------------------------
	732	INTEGER , INTENT(in ) :: kn, kmaxfax
	733	INTEGER , INTENT( out) :: kerr, knfax
	734	INTEGER, DIMENSION(kmaxfax), INTENT( out) :: kfax
	735	!
	736	INTEGER :: ifac, jl, inu
	737	INTEGER, PARAMETER :: ntest = 14
[6204]	738	INTEGER, DIMENSION(ntest) :: ilfax
[4990]	739	!
[6204]	740	! ilfax contains the set of allowed factors.
	741	ilfax(:) = (/(2**jl,jl=ntest,1,-1)/)
[2715]	742	!!----------------------------------------------------------------------
[6204]	743	! ilfax contains the set of allowed factors.
	744	ilfax(:) = (/(2**jl,jl=ntest,1,-1)/)
[2715]	745
	746	! Clear the error flag and initialise output vars
	747	kerr = 0
	748	kfax = 1
	749	knfax = 0
	750
	751	! Find the factors of n.
	752	IF( kn == 1 ) GOTO 20
	753
	754	! nu holds the unfactorised part of the number.
	755	! knfax holds the number of factors found.
	756	! l points to the allowed factor list.
	757	! ifac holds the current factor.
	758
	759	inu = kn
	760	knfax = 0
	761
	762	DO jl = ntest, 1, -1
	763	!
	764	ifac = ilfax(jl)
	765	IF( ifac > inu ) CYCLE
	766
	767	! Test whether the factor will divide.
	768
	769	IF( MOD(inu,ifac) == 0 ) THEN
	770	!
	771	knfax = knfax + 1 ! Add the factor to the list
	772	IF( knfax > kmaxfax ) THEN
	773	kerr = 6
	774	write (,) 'FACTOR: insufficient space in factor array ', knfax
	775	return
	776	ENDIF
	777	kfax(knfax) = ifac
	778	! Store the other factor that goes with this one
	779	knfax = knfax + 1
	780	kfax(knfax) = inu / ifac
	781	!WRITE (,) 'ARPDBG, factors ',knfax-1,' & ',knfax,' are ', kfax(knfax-1),' and ',kfax(knfax)
	782	ENDIF
	783	!
	784	END DO
	785
	786	20 CONTINUE ! Label 20 is the exit point from the factor search loop.
	787	!
	788	END SUBROUTINE factorise
	789
[3294]	790	#if defined key_mpp_mpi
[4990]	791
[3294]	792	SUBROUTINE nemo_northcomms
	793	!!======================================================================
	794	!! * ROUTINE nemo_northcomms *
[4230]	795	!! nemo_northcomms : Setup for north fold exchanges with explicit
	796	!! point-to-point messaging
[3294]	797	!!=====================================================================
	798	!!----------------------------------------------------------------------
[3764]	799	!!
[3294]	800	!! ** Purpose : Initialization of the northern neighbours lists.
	801	!!----------------------------------------------------------------------
[3764]	802	!! 1.0 ! 2011-10 (A. C. Coward, NOCS & J. Donners, PRACE)
[4230]	803	!! 2.0 ! 2013-06 Setup avoiding MPI communication (I. Epicoco, S. Mocavero, CMCC)
[3294]	804	!!----------------------------------------------------------------------
	805
[4230]	806	INTEGER :: sxM, dxM, sxT, dxT, jn
	807	INTEGER :: njmppmax
[3294]	808
[4230]	809	njmppmax = MAXVAL( njmppt )
	810
	811	!initializes the north-fold communication variables
	812	isendto(:) = 0
[3294]	813	nsndto = 0
	814
[4230]	815	!if I am a process in the north
	816	IF ( njmpp == njmppmax ) THEN
	817	!sxM is the first point (in the global domain) needed to compute the
	818	!north-fold for the current process
	819	sxM = jpiglo - nimppt(narea) - nlcit(narea) + 1
	820	!dxM is the last point (in the global domain) needed to compute the
	821	!north-fold for the current process
	822	dxM = jpiglo - nimppt(narea) + 2
[3294]	823
[4230]	824	!loop over the other north-fold processes to find the processes
	825	!managing the points belonging to the sxT-dxT range
[4671]	826
	827	DO jn = 1, jpni
[4230]	828	!sxT is the first point (in the global domain) of the jn
	829	!process
[4671]	830	sxT = nfiimpp(jn, jpnj)
[4230]	831	!dxT is the last point (in the global domain) of the jn
	832	!process
[4671]	833	dxT = nfiimpp(jn, jpnj) + nfilcit(jn, jpnj) - 1
[4230]	834	IF ((sxM .gt. sxT) .AND. (sxM .lt. dxT)) THEN
	835	nsndto = nsndto + 1
[4671]	836	isendto(nsndto) = jn
[4645]	837	ELSEIF ((sxM .le. sxT) .AND. (dxM .ge. dxT)) THEN
[4230]	838	nsndto = nsndto + 1
[4671]	839	isendto(nsndto) = jn
[4230]	840	ELSEIF ((dxM .lt. dxT) .AND. (sxT .lt. dxM)) THEN
	841	nsndto = nsndto + 1
[4671]	842	isendto(nsndto) = jn
[4230]	843	END IF
	844	END DO
[4671]	845	nfsloop = 1
	846	nfeloop = nlci
	847	DO jn = 2,jpni-1
	848	IF(nfipproc(jn,jpnj) .eq. (narea - 1)) THEN
	849	IF (nfipproc(jn - 1 ,jpnj) .eq. -1) THEN
	850	nfsloop = nldi
	851	ENDIF
	852	IF (nfipproc(jn + 1,jpnj) .eq. -1) THEN
	853	nfeloop = nlei
	854	ENDIF
	855	ENDIF
	856	END DO
	857
[3294]	858	ENDIF
[4230]	859	l_north_nogather = .TRUE.
[3294]	860	END SUBROUTINE nemo_northcomms
	861	#else
	862	SUBROUTINE nemo_northcomms ! Dummy routine
	863	WRITE(,) 'nemo_northcomms: You should not have seen this print! error?'
	864	END SUBROUTINE nemo_northcomms
	865	#endif
[4990]	866
[3]	867	!!======================================================================
[2496]	868	END MODULE nemogcm
[4354]	869
	870

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