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nemogcm.F90 in branches/NERC/dev_r5518_NOC_MEDUSA_Stable/NEMOGCM/NEMO/OPA_SRC – NEMO

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source: branches/NERC/dev_r5518_NOC_MEDUSA_Stable/NEMOGCM/NEMO/OPA_SRC/nemogcm.F90 @ 7516

Last change on this file since 7516 was 7516, checked in by jpalmier, 7 years ago
JPALM - remove nemogcm debug printing statements to avoid conflicts - change update field_def_dyn.xml to latest version
File size: 39.3 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
[268]	87
[2715]	88	IMPLICIT NONE
[3]	89	PRIVATE
	90
[2496]	91	PUBLIC nemo_gcm ! called by model.F90
	92	PUBLIC nemo_init ! needed by AGRIF
[3764]	93	PUBLIC nemo_alloc ! needed by TAM
[467]	94
[2498]	95	CHARACTER(lc) :: cform_aaa="( /, 'AAAAAAAA', / ) " ! flag for output listing
[1593]	96
[3]	97	!!----------------------------------------------------------------------
[2715]	98	!! NEMO/OPA 4.0 , NEMO Consortium (2011)
[2392]	99	!! $Id$
[2329]	100	!! Software governed by the CeCILL licence (NEMOGCM/NEMO_CeCILL.txt)
[3]	101	!!----------------------------------------------------------------------
	102	CONTAINS
	103
[2496]	104	SUBROUTINE nemo_gcm
[3]	105	!!----------------------------------------------------------------------
[2496]	106	!! * ROUTINE nemo_gcm *
[3]	107	!!
[3764]	108	!! ** Purpose : NEMO solves the primitive equations on an orthogonal
[1593]	109	!! curvilinear mesh on the sphere.
[3]	110	!!
	111	!! ** Method : - model general initialization
	112	!! - launch the time-stepping (stp routine)
[1593]	113	!! - finalize the run by closing files and communications
[3]	114	!!
[2715]	115	!! References : Madec, Delecluse, Imbard, and Levy, 1997: internal report, IPSL.
[1593]	116	!! Madec, 2008, internal report, IPSL.
[3]	117	!!----------------------------------------------------------------------
	118	INTEGER :: istp ! time step index
[389]	119	!!----------------------------------------------------------------------
[2382]	120	!
[392]	121	#if defined key_agrif
[1593]	122	CALL Agrif_Init_Grids() ! AGRIF: set the meshes
[389]	123	#endif
	124
[1593]	125	! !-----------------------!
[2496]	126	CALL nemo_init !== Initialisations ==!
[1593]	127	! !-----------------------!
[2715]	128	#if defined key_agrif
[3680]	129	CALL Agrif_Declare_Var_dom ! AGRIF: set the meshes for DOM
	130	CALL Agrif_Declare_Var ! " " " " " DYN/TRA
[2715]	131	# if defined key_top
[3680]	132	CALL Agrif_Declare_Var_top ! " " " " " TOP
[2715]	133	# endif
[3680]	134	# if defined key_lim2
	135	CALL Agrif_Declare_Var_lim2 ! " " " " " LIM
	136	# endif
[2715]	137	#endif
[682]	138	! check that all process are still there... If some process have an error,
	139	! they will never enter in step and other processes will wait until the end of the cpu time!
[900]	140	IF( lk_mpp ) CALL mpp_max( nstop )
[682]	141
[1593]	142	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	143
	144	! !-----------------------!
	145	! !== time stepping ==!
	146	! !-----------------------!
[900]	147	istp = nit000
[2236]	148	#if defined key_c1d
[389]	149	DO WHILE ( istp <= nitend .AND. nstop == 0 )
[900]	150	CALL stp_c1d( istp )
[389]	151	istp = istp + 1
	152	END DO
[2236]	153	#else
	154	IF( lk_asminc ) THEN
	155	IF( ln_bkgwri ) CALL asm_bkg_wri( nit000 - 1 ) ! Output background fields
	156	IF( ln_asmdin ) THEN ! Direct initialization
	157	IF( ln_trainc ) CALL tra_asm_inc( nit000 - 1 ) ! Tracers
[3764]	158	IF( ln_dyninc ) CALL dyn_asm_inc( nit000 - 1 ) ! Dynamics
[2236]	159	IF( ln_sshinc ) CALL ssh_asm_inc( nit000 - 1 ) ! SSH
	160	ENDIF
	161	ENDIF
[3764]	162
[389]	163	DO WHILE ( istp <= nitend .AND. nstop == 0 )
[392]	164	#if defined key_agrif
[1593]	165	CALL Agrif_Step( stp ) ! AGRIF: time stepping
[389]	166	#else
[1593]	167	CALL stp( istp ) ! standard time stepping
[389]	168	#endif
	169	istp = istp + 1
[900]	170	IF( lk_mpp ) CALL mpp_max( nstop )
[389]	171	END DO
[2236]	172	#endif
	173
[3609]	174	IF( lk_diaobs ) CALL dia_obs_wri
	175	!
	176	IF( ln_icebergs ) CALL icb_end( nitend )
[3764]	177
[1593]	178	! !------------------------!
	179	! !== finalize the run ==!
	180	! !------------------------!
	181	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	182	!
	183	IF( nstop /= 0 .AND. lwp ) THEN ! error print
[682]	184	WRITE(numout,cform_err)
[3764]	185	WRITE(numout,*) nstop, ' error have been found'
[389]	186	ENDIF
[1593]	187	!
[3294]	188	#if defined key_agrif
	189	CALL Agrif_ParentGrid_To_ChildGrid()
	190	IF( lk_diaobs ) CALL dia_obs_wri
	191	IF( nn_timing == 1 ) CALL timing_finalize
	192	CALL Agrif_ChildGrid_To_ParentGrid()
	193	#endif
	194	IF( nn_timing == 1 ) CALL timing_finalize
	195	!
[2496]	196	CALL nemo_closefile
[4990]	197	!
[3769]	198	#if defined key_iomput
	199	CALL xios_finalize ! end mpp communications with xios
[5407]	200	IF( lk_oasis ) CALL cpl_finalize ! end coupling and mpp communications with OASIS
[532]	201	#else
[5407]	202	IF( lk_oasis ) THEN
[4990]	203	CALL cpl_finalize ! end coupling and mpp communications with OASIS
	204	ELSE
	205	IF( lk_mpp ) CALL mppstop ! end mpp communications
	206	ENDIF
[532]	207	#endif
[900]	208	!
[2496]	209	END SUBROUTINE nemo_gcm
[389]	210
	211
[2496]	212	SUBROUTINE nemo_init
[389]	213	!!----------------------------------------------------------------------
[2496]	214	!! * ROUTINE nemo_init *
[389]	215	!!
[2496]	216	!! ** Purpose : initialization of the NEMO GCM
[389]	217	!!----------------------------------------------------------------------
[2715]	218	INTEGER :: ji ! dummy loop indices
	219	INTEGER :: ilocal_comm ! local integer
[4147]	220	INTEGER :: ios
[2715]	221	CHARACTER(len=80), DIMENSION(16) :: cltxt
[4990]	222	!
	223	NAMELIST/namctl/ ln_ctl , nn_print, nn_ictls, nn_ictle, &
[3294]	224	& nn_isplt, nn_jsplt, nn_jctls, nn_jctle, &
	225	& nn_bench, nn_timing
[4147]	226	NAMELIST/namcfg/ cp_cfg, cp_cfz, jp_cfg, jpidta, jpjdta, jpkdta, jpiglo, jpjglo, &
[5118]	227	& jpizoom, jpjzoom, jperio, ln_use_jattr
[3]	228	!!----------------------------------------------------------------------
[1593]	229	!
[2496]	230	cltxt = ''
[5407]	231	cxios_context = 'nemo'
[2496]	232	!
[4147]	233	! ! Open reference namelist and configuration namelist files
	234	CALL ctl_opn( numnam_ref, 'namelist_ref', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
	235	CALL ctl_opn( numnam_cfg, 'namelist_cfg', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
[1593]	236	!
[4147]	237	REWIND( numnam_ref ) ! Namelist namctl in reference namelist : Control prints & Benchmark
	238	READ ( numnam_ref, namctl, IOSTAT = ios, ERR = 901 )
[4289]	239	901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in reference namelist', .TRUE. )
[4147]	240
	241	REWIND( numnam_cfg ) ! Namelist namctl in confguration namelist : Control prints & Benchmark
	242	READ ( numnam_cfg, namctl, IOSTAT = ios, ERR = 902 )
[4289]	243	902 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in configuration namelist', .TRUE. )
[4147]	244
[1593]	245	!
[4147]	246	REWIND( numnam_ref ) ! Namelist namcfg in reference namelist : Control prints & Benchmark
	247	READ ( numnam_ref, namcfg, IOSTAT = ios, ERR = 903 )
[4289]	248	903 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in reference namelist', .TRUE. )
[4147]	249
	250	REWIND( numnam_cfg ) ! Namelist namcfg in confguration namelist : Control prints & Benchmark
	251	READ ( numnam_cfg, namcfg, IOSTAT = ios, ERR = 904 )
[4289]	252	904 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in configuration namelist', .TRUE. )
[4309]	253
[4147]	254	! Force values for AGRIF zoom (cf. agrif_user.F90)
	255	#if defined key_agrif
	256	IF( .NOT. Agrif_Root() ) THEN
	257	jpiglo = nbcellsx + 2 + 2*nbghostcells
	258	jpjglo = nbcellsy + 2 + 2*nbghostcells
	259	jpi = ( jpiglo-2jpreci + (jpni-1+0) ) / jpni + 2jpreci
	260	jpj = ( jpjglo-2jprecj + (jpnj-1+0) ) / jpnj + 2jprecj
	261	jpidta = jpiglo
	262	jpjdta = jpjglo
	263	jpizoom = 1
	264	jpjzoom = 1
	265	nperio = 0
	266	jperio = 0
[5118]	267	ln_use_jattr = .false.
[4147]	268	ENDIF
	269	#endif
	270	!
[1593]	271	! !--------------------------------------------!
	272	! ! set communicator & select the local node !
[4624]	273	! ! NB: mynode also opens output.namelist.dyn !
	274	! ! on unit number numond on first proc !
[1593]	275	! !--------------------------------------------!
[1412]	276	#if defined key_iomput
[2200]	277	IF( Agrif_Root() ) THEN
[5407]	278	IF( lk_oasis ) THEN
	279	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
	280	CALL xios_initialize( "not used",local_comm=ilocal_comm ) ! send nemo communicator to xios
[4990]	281	ELSE
[5407]	282	CALL xios_initialize( "for_xios_mpi_id",return_comm=ilocal_comm ) ! nemo local communicator given by xios
[4990]	283	ENDIF
[2200]	284	ENDIF
[5407]	285	! Nodes selection (control print return in cltxt)
	286	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop, ilocal_comm )
[532]	287	#else
[5407]	288	IF( lk_oasis ) THEN
[4990]	289	IF( Agrif_Root() ) THEN
[5407]	290	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
[4990]	291	ENDIF
[5407]	292	! Nodes selection (control print return in cltxt)
	293	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop, ilocal_comm )
[4990]	294	ELSE
	295	ilocal_comm = 0
[5407]	296	! Nodes selection (control print return in cltxt)
	297	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop )
[2236]	298	ENDIF
[532]	299	#endif
[2715]	300	narea = narea + 1 ! mynode return the rank of proc (0 --> jpnij -1 )
[3]	301
[4624]	302	lwm = (narea == 1) ! control of output namelists
[2715]	303	lwp = (narea == 1) .OR. ln_ctl ! control of all listing output print
[1579]	304
[4624]	305	IF(lwm) THEN
	306	! write merged namelists from earlier to output namelist now that the
	307	! file has been opened in call to mynode. nammpp has already been
	308	! written in mynode (if lk_mpp_mpi)
	309	WRITE( numond, namctl )
	310	WRITE( numond, namcfg )
	311	ENDIF
	312
[3764]	313	! If dimensions of processor grid weren't specified in the namelist file
[2715]	314	! then we calculate them here now that we have our communicator size
	315	IF( (jpni < 1) .OR. (jpnj < 1) )THEN
	316	#if defined key_mpp_mpi
	317	IF( Agrif_Root() ) CALL nemo_partition(mppsize)
	318	#else
	319	jpni = 1
	320	jpnj = 1
	321	jpnij = jpni*jpnj
	322	#endif
	323	END IF
	324
	325	! Calculate domain dimensions given calculated jpni and jpnj
	326	! This used to be done in par_oce.F90 when they were parameters rather
	327	! than variables
	328	IF( Agrif_Root() ) THEN
[3294]	329	#if defined key_nemocice_decomp
[3625]	330	jpi = ( nx_global+2-2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
	331	jpj = ( ny_global+2-2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
[3294]	332	#else
[3625]	333	jpi = ( jpiglo-2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
[2715]	334	jpj = ( jpjglo-2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
[3294]	335	#endif
[4147]	336	ENDIF
[2715]	337	jpk = jpkdta ! third dim
	338	jpim1 = jpi-1 ! inner domain indices
	339	jpjm1 = jpj-1 ! " "
	340	jpkm1 = jpk-1 ! " "
	341	jpij = jpi*jpj ! jpi x j
	342
[1593]	343	IF(lwp) THEN ! open listing units
	344	!
[1581]	345	CALL ctl_opn( numout, 'ocean.output', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE., narea )
[1593]	346	!
[1579]	347	WRITE(numout,*)
[3294]	348	WRITE(numout,*) ' CNRS - NERC - Met OFFICE - MERCATOR-ocean - INGV - CMCC'
[1593]	349	WRITE(numout,*) ' NEMO team'
[1579]	350	WRITE(numout,*) ' Ocean General Circulation Model'
[5120]	351	WRITE(numout,*) ' version 3.6 (2015) '
[1579]	352	WRITE(numout,*)
	353	WRITE(numout,*)
[3764]	354	DO ji = 1, SIZE(cltxt)
[1593]	355	IF( TRIM(cltxt(ji)) /= '' ) WRITE(numout,*) cltxt(ji) ! control print of mynode
[1579]	356	END DO
[1593]	357	WRITE(numout,cform_aaa) ! Flag AAAAAAA
	358	!
[473]	359	ENDIF
[2715]	360
[3764]	361	! Now we know the dimensions of the grid and numout has been set we can
[2715]	362	! allocate arrays
	363	CALL nemo_alloc()
	364
[2496]	365	! !-------------------------------!
	366	! ! NEMO general initialization !
	367	! !-------------------------------!
[473]	368
[2496]	369	CALL nemo_ctl ! Control prints & Benchmark
[531]	370
[2082]	371	! ! Domain decomposition
[1593]	372	IF( jpni*jpnj == jpnij ) THEN ; CALL mpp_init ! standard cutting out
	373	ELSE ; CALL mpp_init2 ! eliminate land processors
[3]	374	ENDIF
[2382]	375	!
[3294]	376	IF( nn_timing == 1 ) CALL timing_init
	377	!
[2082]	378	! ! General initialization
[2027]	379	CALL phy_cst ! Physical constants
	380	CALL eos_init ! Equation of state
[4245]	381	IF( lk_c1d ) CALL c1d_init ! 1D column configuration
[2027]	382	CALL dom_cfg ! Domain configuration
	383	CALL dom_init ! Domain
[413]	384
[3294]	385	IF( ln_nnogather ) CALL nemo_northcomms ! Initialise the northfold neighbour lists (must be done after the masks are defined)
	386
[2027]	387	IF( ln_ctl ) CALL prt_ctl_init ! Print control
	388
[3651]	389	CALL istate_init ! ocean initial state (Dynamics and tracers)
	390
[4292]	391	IF( lk_tide ) CALL tide_init( nit000 ) ! Initialisation of the tidal harmonics
[3651]	392
[5123]	393	CALL sbc_init ! Forcings : surface module (clem: moved here for bdy purpose)
	394
[4990]	395	IF( lk_bdy ) CALL bdy_init ! Open boundaries initialisation
	396	IF( lk_bdy ) CALL bdy_dta_init ! Open boundaries initialisation of external data arrays
[4292]	397	IF( lk_bdy .AND. lk_tide ) &
[4990]	398	& CALL bdytide_init ! Open boundaries initialisation of tidal harmonic forcing
[2027]	399
[3294]	400	CALL dyn_nept_init ! simplified form of Neptune effect
[4152]	401	!
	402	IF( ln_crs ) CALL crs_init ! Domain initialization of coarsened grid
	403	!
	404	! Ocean physics
[2082]	405	! ! Vertical physics
	406	CALL zdf_init ! namelist read
	407	CALL zdf_bfr_init ! bottom friction
	408	IF( lk_zdfric ) CALL zdf_ric_init ! Richardson number dependent Kz
[2329]	409	IF( lk_zdftke ) CALL zdf_tke_init ! TKE closure scheme
	410	IF( lk_zdfgls ) CALL zdf_gls_init ! GLS closure scheme
	411	IF( lk_zdfkpp ) CALL zdf_kpp_init ! KPP closure scheme
[2082]	412	IF( lk_zdftmx ) CALL zdf_tmx_init ! tidal vertical mixing
[3764]	413	IF( lk_zdfddm .AND. .NOT. lk_zdfkpp ) &
[2082]	414	& CALL zdf_ddm_init ! double diffusive mixing
	415	! ! Lateral physics
	416	CALL ldf_tra_init ! Lateral ocean tracer physics
	417	CALL ldf_dyn_init ! Lateral ocean momentum physics
[2392]	418	IF( lk_ldfslp ) CALL ldf_slp_init ! slope of lateral mixing
[2082]	419
[2027]	420	! ! Active tracers
	421	CALL tra_qsr_init ! penetrative solar radiation qsr
[2325]	422	CALL tra_bbc_init ! bottom heat flux
[2027]	423	IF( lk_trabbl ) CALL tra_bbl_init ! advective (and/or diffusive) bottom boundary layer scheme
[4245]	424	CALL tra_dmp_init ! internal damping trends- tracers
[2027]	425	CALL tra_adv_init ! horizontal & vertical advection
	426	CALL tra_ldf_init ! lateral mixing
	427	CALL tra_zdf_init ! vertical mixing and after tracer fields
	428
	429	! ! Dynamics
[4245]	430	IF( lk_c1d ) CALL dyn_dmp_init ! internal damping trends- momentum
[2027]	431	CALL dyn_adv_init ! advection (vector or flux form)
[2104]	432	CALL dyn_vor_init ! vorticity term including Coriolis
[2027]	433	CALL dyn_ldf_init ! lateral mixing
[2104]	434	CALL dyn_hpg_init ! horizontal gradient of Hydrostatic pressure
[2027]	435	CALL dyn_zdf_init ! vertical diffusion
	436	CALL dyn_spg_init ! surface pressure gradient
[3764]	437
[2392]	438	! ! Misc. options
[4147]	439	IF( nn_cla == 1 .AND. cp_cfg == 'orca' .AND. jp_cfg == 2 ) CALL cla_init ! Cross Land Advection
[3609]	440	CALL icb_init( rdt, nit000) ! initialise icebergs instance
[5329]	441	CALL sto_par_init ! Stochastic parametrization
	442	IF( ln_sto_eos ) CALL sto_pts_init ! RRandom T/S fluctuations
[4147]	443
[1594]	444	#if defined key_top
[2027]	445	! ! Passive tracers
[2082]	446	CALL trc_init
[1594]	447	#endif
[4990]	448	! ! Diagnostics
[3294]	449	IF( lk_floats ) CALL flo_init ! drifting Floats
[2392]	450	IF( lk_diaar5 ) CALL dia_ar5_init ! ar5 diag
[2027]	451	CALL dia_ptr_init ! Poleward TRansports initialization
[3294]	452	IF( lk_diadct ) CALL dia_dct_init ! Sections tranports
[2148]	453	CALL dia_hsb_init ! heat content, salt content and volume budgets
[4990]	454	CALL trd_init ! Mixed-layer/Vorticity/Integral constraints trends
[2392]	455	IF( lk_diaobs ) THEN ! Observation & model comparison
[2382]	456	CALL dia_obs_init ! Initialize observational data
	457	CALL dia_obs( nit000 - 1 ) ! Observation operator for restart
[3764]	458	ENDIF
[7516]	459
[2382]	460	! ! Assimilation increments
[2392]	461	IF( lk_asminc ) CALL asm_inc_init ! Initialize assimilation increments
[2382]	462	IF(lwp) WRITE(numout,*) 'Euler time step switch is ', neuler
[1593]	463	!
[2496]	464	END SUBROUTINE nemo_init
[467]	465
	466
[2496]	467	SUBROUTINE nemo_ctl
[467]	468	!!----------------------------------------------------------------------
[2496]	469	!! * ROUTINE nemo_ctl *
[467]	470	!!
[3764]	471	!! ** Purpose : control print setting
[467]	472	!!
[2442]	473	!! ** Method : - print namctl information and check some consistencies
[467]	474	!!----------------------------------------------------------------------
[2442]	475	!
[2496]	476	IF(lwp) THEN ! control print
[531]	477	WRITE(numout,*)
[2496]	478	WRITE(numout,*) 'nemo_ctl: Control prints & Benchmark'
[531]	479	WRITE(numout,*) '~~~~~~~ '
[1593]	480	WRITE(numout,*) ' Namelist namctl'
[1601]	481	WRITE(numout,*) ' run control (for debugging) ln_ctl = ', ln_ctl
	482	WRITE(numout,*) ' level of print nn_print = ', nn_print
	483	WRITE(numout,*) ' Start i indice for SUM control nn_ictls = ', nn_ictls
	484	WRITE(numout,*) ' End i indice for SUM control nn_ictle = ', nn_ictle
	485	WRITE(numout,*) ' Start j indice for SUM control nn_jctls = ', nn_jctls
	486	WRITE(numout,*) ' End j indice for SUM control nn_jctle = ', nn_jctle
	487	WRITE(numout,*) ' number of proc. following i nn_isplt = ', nn_isplt
	488	WRITE(numout,*) ' number of proc. following j nn_jsplt = ', nn_jsplt
	489	WRITE(numout,*) ' benchmark parameter (0/1) nn_bench = ', nn_bench
[3610]	490	WRITE(numout,*) ' timing activated (0/1) nn_timing = ', nn_timing
[531]	491	ENDIF
[2442]	492	!
[1601]	493	nprint = nn_print ! convert DOCTOR namelist names into OLD names
	494	nictls = nn_ictls
	495	nictle = nn_ictle
	496	njctls = nn_jctls
	497	njctle = nn_jctle
	498	isplt = nn_isplt
	499	jsplt = nn_jsplt
	500	nbench = nn_bench
[4147]	501
	502	IF(lwp) THEN ! control print
	503	WRITE(numout,*)
	504	WRITE(numout,*) 'namcfg : configuration initialization through namelist read'
	505	WRITE(numout,*) '~~~~~~~ '
	506	WRITE(numout,*) ' Namelist namcfg'
	507	WRITE(numout,*) ' configuration name cp_cfg = ', TRIM(cp_cfg)
	508	WRITE(numout,*) ' configuration zoom name cp_cfz = ', TRIM(cp_cfz)
	509	WRITE(numout,*) ' configuration resolution jp_cfg = ', jp_cfg
	510	WRITE(numout,*) ' 1st lateral dimension ( >= jpi ) jpidta = ', jpidta
	511	WRITE(numout,*) ' 2nd " " ( >= jpj ) jpjdta = ', jpjdta
	512	WRITE(numout,*) ' 3nd " " jpkdta = ', jpkdta
	513	WRITE(numout,*) ' 1st dimension of global domain in i jpiglo = ', jpiglo
	514	WRITE(numout,*) ' 2nd - - in j jpjglo = ', jpjglo
	515	WRITE(numout,*) ' left bottom i index of the zoom (in data domain) jpizoom = ', jpizoom
	516	WRITE(numout,*) ' left bottom j index of the zoom (in data domain) jpizoom = ', jpjzoom
	517	WRITE(numout,*) ' lateral cond. type (between 0 and 6) jperio = ', jperio
[5118]	518	WRITE(numout,*) ' use file attribute if exists as i/p j-start ln_use_jattr = ', ln_use_jattr
[4147]	519	ENDIF
[2442]	520	! ! Parameter control
[1593]	521	!
	522	IF( ln_ctl ) THEN ! sub-domain area indices for the control prints
[3294]	523	IF( lk_mpp .AND. jpnij > 1 ) THEN
[2496]	524	isplt = jpni ; jsplt = jpnj ; ijsplt = jpni*jpnj ! the domain is forced to the real split domain
[531]	525	ELSE
	526	IF( isplt == 1 .AND. jsplt == 1 ) THEN
[1593]	527	CALL ctl_warn( ' - isplt & jsplt are equal to 1', &
	528	& ' - the print control will be done over the whole domain' )
[531]	529	ENDIF
[1593]	530	ijsplt = isplt * jsplt ! total number of processors ijsplt
[531]	531	ENDIF
	532	IF(lwp) WRITE(numout,*)' - The total number of processors over which the'
	533	IF(lwp) WRITE(numout,*)' print control will be done is ijsplt : ', ijsplt
[1593]	534	!
	535	! ! indices used for the SUM control
	536	IF( nictls+nictle+njctls+njctle == 0 ) THEN ! print control done over the default area
[3764]	537	lsp_area = .FALSE.
[1593]	538	ELSE ! print control done over a specific area
[531]	539	lsp_area = .TRUE.
	540	IF( nictls < 1 .OR. nictls > jpiglo ) THEN
	541	CALL ctl_warn( ' - nictls must be 1<=nictls>=jpiglo, it is forced to 1' )
	542	nictls = 1
	543	ENDIF
	544	IF( nictle < 1 .OR. nictle > jpiglo ) THEN
	545	CALL ctl_warn( ' - nictle must be 1<=nictle>=jpiglo, it is forced to jpiglo' )
	546	nictle = jpiglo
	547	ENDIF
	548	IF( njctls < 1 .OR. njctls > jpjglo ) THEN
	549	CALL ctl_warn( ' - njctls must be 1<=njctls>=jpjglo, it is forced to 1' )
	550	njctls = 1
	551	ENDIF
	552	IF( njctle < 1 .OR. njctle > jpjglo ) THEN
	553	CALL ctl_warn( ' - njctle must be 1<=njctle>=jpjglo, it is forced to jpjglo' )
	554	njctle = jpjglo
	555	ENDIF
[1593]	556	ENDIF
	557	ENDIF
[2442]	558	!
[3764]	559	IF( nbench == 1 ) THEN ! Benchmark
[531]	560	SELECT CASE ( cp_cfg )
[1593]	561	CASE ( 'gyre' ) ; CALL ctl_warn( ' The Benchmark is activated ' )
	562	CASE DEFAULT ; CALL ctl_stop( ' The Benchmark is based on the GYRE configuration:', &
[4147]	563	& ' cp_cfg = "gyre" in namelist &namcfg or set nbench = 0' )
[531]	564	END SELECT
	565	ENDIF
[1593]	566	!
[3764]	567	IF( 1_wp /= SIGN(1._wp,-0._wp) ) CALL ctl_stop( 'nemo_ctl: The intrinsec SIGN function follows ', &
	568	& 'f2003 standard. ' , &
	569	& 'Compile with key_nosignedzero enabled' )
	570	!
[2496]	571	END SUBROUTINE nemo_ctl
[467]	572
	573
[2496]	574	SUBROUTINE nemo_closefile
[467]	575	!!----------------------------------------------------------------------
[2496]	576	!! * ROUTINE nemo_closefile *
[467]	577	!!
	578	!! ** Purpose : Close the files
	579	!!----------------------------------------------------------------------
[1593]	580	!
	581	IF( lk_mpp ) CALL mppsync
	582	!
[1685]	583	CALL iom_close ! close all input/output files managed by iom_*
[1593]	584	!
[4147]	585	IF( numstp /= -1 ) CLOSE( numstp ) ! time-step file
	586	IF( numsol /= -1 ) CLOSE( numsol ) ! solver file
	587	IF( numnam_ref /= -1 ) CLOSE( numnam_ref ) ! oce reference namelist
	588	IF( numnam_cfg /= -1 ) CLOSE( numnam_cfg ) ! oce configuration namelist
[4624]	589	IF( lwm.AND.numond /= -1 ) CLOSE( numond ) ! oce output namelist
[4147]	590	IF( numnam_ice_ref /= -1 ) CLOSE( numnam_ice_ref ) ! ice reference namelist
	591	IF( numnam_ice_cfg /= -1 ) CLOSE( numnam_ice_cfg ) ! ice configuration namelist
[4624]	592	IF( lwm.AND.numoni /= -1 ) CLOSE( numoni ) ! ice output namelist
[4147]	593	IF( numevo_ice /= -1 ) CLOSE( numevo_ice ) ! ice variables (temp. evolution)
	594	IF( numout /= 6 ) CLOSE( numout ) ! standard model output file
	595	IF( numdct_vol /= -1 ) CLOSE( numdct_vol ) ! volume transports
	596	IF( numdct_heat /= -1 ) CLOSE( numdct_heat ) ! heat transports
	597	IF( numdct_salt /= -1 ) CLOSE( numdct_salt ) ! salt transports
[3294]	598
[1593]	599	!
[2442]	600	numout = 6 ! redefine numout in case it is used after this point...
	601	!
[2496]	602	END SUBROUTINE nemo_closefile
[467]	603
[2715]	604
	605	SUBROUTINE nemo_alloc
	606	!!----------------------------------------------------------------------
	607	!! * ROUTINE nemo_alloc *
	608	!!
	609	!! ** Purpose : Allocate all the dynamic arrays of the OPA modules
	610	!!
	611	!! ** Method :
	612	!!----------------------------------------------------------------------
	613	USE diawri , ONLY: dia_wri_alloc
	614	USE dom_oce , ONLY: dom_oce_alloc
	615	USE ldfdyn_oce, ONLY: ldfdyn_oce_alloc
	616	USE ldftra_oce, ONLY: ldftra_oce_alloc
	617	USE trc_oce , ONLY: trc_oce_alloc
[3680]	618	#if defined key_diadct
	619	USE diadct , ONLY: diadct_alloc
	620	#endif
[4354]	621	#if defined key_bdy
	622	USE bdy_oce , ONLY: bdy_oce_alloc
	623	#endif
[2715]	624	!
	625	INTEGER :: ierr
	626	!!----------------------------------------------------------------------
	627	!
[3764]	628	ierr = oce_alloc () ! ocean
[2715]	629	ierr = ierr + dia_wri_alloc ()
	630	ierr = ierr + dom_oce_alloc () ! ocean domain
	631	ierr = ierr + ldfdyn_oce_alloc() ! ocean lateral physics : dynamics
	632	ierr = ierr + ldftra_oce_alloc() ! ocean lateral physics : tracers
	633	ierr = ierr + zdf_oce_alloc () ! ocean vertical physics
	634	!
	635	ierr = ierr + trc_oce_alloc () ! shared TRC / TRA arrays
	636	!
[3680]	637	#if defined key_diadct
	638	ierr = ierr + diadct_alloc () !
	639	#endif
[4354]	640	#if defined key_bdy
	641	ierr = ierr + bdy_oce_alloc () ! bdy masks (incl. initialization)
	642	#endif
[3680]	643	!
[2715]	644	IF( lk_mpp ) CALL mpp_sum( ierr )
	645	IF( ierr /= 0 ) CALL ctl_stop( 'STOP', 'nemo_alloc : unable to allocate standard ocean arrays' )
	646	!
	647	END SUBROUTINE nemo_alloc
	648
	649
	650	SUBROUTINE nemo_partition( num_pes )
	651	!!----------------------------------------------------------------------
	652	!! * ROUTINE nemo_partition *
	653	!!
[3764]	654	!! ** Purpose :
[2715]	655	!!
	656	!! ** Method :
	657	!!----------------------------------------------------------------------
[4990]	658	INTEGER, INTENT(in) :: num_pes ! The number of MPI processes we have
[2715]	659	!
	660	INTEGER, PARAMETER :: nfactmax = 20
	661	INTEGER :: nfact ! The no. of factors returned
	662	INTEGER :: ierr ! Error flag
	663	INTEGER :: ji
	664	INTEGER :: idiff, mindiff, imin ! For choosing pair of factors that are closest in value
	665	INTEGER, DIMENSION(nfactmax) :: ifact ! Array of factors
	666	!!----------------------------------------------------------------------
[4990]	667	!
[2715]	668	ierr = 0
[4990]	669	!
[2715]	670	CALL factorise( ifact, nfactmax, nfact, num_pes, ierr )
[4990]	671	!
[2715]	672	IF( nfact <= 1 ) THEN
	673	WRITE (numout, *) 'WARNING: factorisation of number of PEs failed'
	674	WRITE (numout, *) ' : using grid of ',num_pes,' x 1'
	675	jpnj = 1
	676	jpni = num_pes
	677	ELSE
	678	! Search through factors for the pair that are closest in value
	679	mindiff = 1000000
	680	imin = 1
	681	DO ji = 1, nfact-1, 2
	682	idiff = ABS( ifact(ji) - ifact(ji+1) )
	683	IF( idiff < mindiff ) THEN
	684	mindiff = idiff
	685	imin = ji
	686	ENDIF
	687	END DO
	688	jpnj = ifact(imin)
	689	jpni = ifact(imin + 1)
	690	ENDIF
	691	!
	692	jpnij = jpni*jpnj
	693	!
	694	END SUBROUTINE nemo_partition
	695
	696
	697	SUBROUTINE factorise( kfax, kmaxfax, knfax, kn, kerr )
	698	!!----------------------------------------------------------------------
	699	!! * ROUTINE factorise *
	700	!!
	701	!! ** Purpose : return the prime factors of n.
[3764]	702	!! knfax factors are returned in array kfax which is of
[2715]	703	!! maximum dimension kmaxfax.
	704	!! ** Method :
	705	!!----------------------------------------------------------------------
	706	INTEGER , INTENT(in ) :: kn, kmaxfax
	707	INTEGER , INTENT( out) :: kerr, knfax
	708	INTEGER, DIMENSION(kmaxfax), INTENT( out) :: kfax
	709	!
	710	INTEGER :: ifac, jl, inu
	711	INTEGER, PARAMETER :: ntest = 14
	712	INTEGER :: ilfax(ntest)
[4990]	713	!
[2715]	714	! lfax contains the set of allowed factors.
	715	data (ilfax(jl),jl=1,ntest) / 16384, 8192, 4096, 2048, 1024, 512, 256, &
	716	& 128, 64, 32, 16, 8, 4, 2 /
	717	!!----------------------------------------------------------------------
	718
	719	! Clear the error flag and initialise output vars
	720	kerr = 0
	721	kfax = 1
	722	knfax = 0
	723
	724	! Find the factors of n.
	725	IF( kn == 1 ) GOTO 20
	726
	727	! nu holds the unfactorised part of the number.
	728	! knfax holds the number of factors found.
	729	! l points to the allowed factor list.
	730	! ifac holds the current factor.
	731
	732	inu = kn
	733	knfax = 0
	734
	735	DO jl = ntest, 1, -1
	736	!
	737	ifac = ilfax(jl)
	738	IF( ifac > inu ) CYCLE
	739
	740	! Test whether the factor will divide.
	741
	742	IF( MOD(inu,ifac) == 0 ) THEN
	743	!
	744	knfax = knfax + 1 ! Add the factor to the list
	745	IF( knfax > kmaxfax ) THEN
	746	kerr = 6
	747	write (,) 'FACTOR: insufficient space in factor array ', knfax
	748	return
	749	ENDIF
	750	kfax(knfax) = ifac
	751	! Store the other factor that goes with this one
	752	knfax = knfax + 1
	753	kfax(knfax) = inu / ifac
	754	!WRITE (,) 'ARPDBG, factors ',knfax-1,' & ',knfax,' are ', kfax(knfax-1),' and ',kfax(knfax)
	755	ENDIF
	756	!
	757	END DO
	758
	759	20 CONTINUE ! Label 20 is the exit point from the factor search loop.
	760	!
	761	END SUBROUTINE factorise
	762
[3294]	763	#if defined key_mpp_mpi
[4990]	764
[3294]	765	SUBROUTINE nemo_northcomms
	766	!!======================================================================
	767	!! * ROUTINE nemo_northcomms *
[4230]	768	!! nemo_northcomms : Setup for north fold exchanges with explicit
	769	!! point-to-point messaging
[3294]	770	!!=====================================================================
	771	!!----------------------------------------------------------------------
[3764]	772	!!
[3294]	773	!! ** Purpose : Initialization of the northern neighbours lists.
	774	!!----------------------------------------------------------------------
[3764]	775	!! 1.0 ! 2011-10 (A. C. Coward, NOCS & J. Donners, PRACE)
[4230]	776	!! 2.0 ! 2013-06 Setup avoiding MPI communication (I. Epicoco, S. Mocavero, CMCC)
[3294]	777	!!----------------------------------------------------------------------
	778
[4230]	779	INTEGER :: sxM, dxM, sxT, dxT, jn
	780	INTEGER :: njmppmax
[3294]	781
[4230]	782	njmppmax = MAXVAL( njmppt )
	783
	784	!initializes the north-fold communication variables
	785	isendto(:) = 0
[3294]	786	nsndto = 0
	787
[4230]	788	!if I am a process in the north
	789	IF ( njmpp == njmppmax ) THEN
	790	!sxM is the first point (in the global domain) needed to compute the
	791	!north-fold for the current process
	792	sxM = jpiglo - nimppt(narea) - nlcit(narea) + 1
	793	!dxM is the last point (in the global domain) needed to compute the
	794	!north-fold for the current process
	795	dxM = jpiglo - nimppt(narea) + 2
[3294]	796
[4230]	797	!loop over the other north-fold processes to find the processes
	798	!managing the points belonging to the sxT-dxT range
[4671]	799
	800	DO jn = 1, jpni
[4230]	801	!sxT is the first point (in the global domain) of the jn
	802	!process
[4671]	803	sxT = nfiimpp(jn, jpnj)
[4230]	804	!dxT is the last point (in the global domain) of the jn
	805	!process
[4671]	806	dxT = nfiimpp(jn, jpnj) + nfilcit(jn, jpnj) - 1
[4230]	807	IF ((sxM .gt. sxT) .AND. (sxM .lt. dxT)) THEN
	808	nsndto = nsndto + 1
[4671]	809	isendto(nsndto) = jn
[4645]	810	ELSEIF ((sxM .le. sxT) .AND. (dxM .ge. dxT)) THEN
[4230]	811	nsndto = nsndto + 1
[4671]	812	isendto(nsndto) = jn
[4230]	813	ELSEIF ((dxM .lt. dxT) .AND. (sxT .lt. dxM)) THEN
	814	nsndto = nsndto + 1
[4671]	815	isendto(nsndto) = jn
[4230]	816	END IF
	817	END DO
[4671]	818	nfsloop = 1
	819	nfeloop = nlci
	820	DO jn = 2,jpni-1
	821	IF(nfipproc(jn,jpnj) .eq. (narea - 1)) THEN
	822	IF (nfipproc(jn - 1 ,jpnj) .eq. -1) THEN
	823	nfsloop = nldi
	824	ENDIF
	825	IF (nfipproc(jn + 1,jpnj) .eq. -1) THEN
	826	nfeloop = nlei
	827	ENDIF
	828	ENDIF
	829	END DO
	830
[3294]	831	ENDIF
[4230]	832	l_north_nogather = .TRUE.
[3294]	833	END SUBROUTINE nemo_northcomms
	834	#else
	835	SUBROUTINE nemo_northcomms ! Dummy routine
	836	WRITE(,) 'nemo_northcomms: You should not have seen this print! error?'
	837	END SUBROUTINE nemo_northcomms
	838	#endif
[4990]	839
[3]	840	!!======================================================================
[2496]	841	END MODULE nemogcm
[4354]	842
	843

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