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nemogcm.F90 @ 5066

Last change on this file since 5066 was 5066, checked in by rfurner, 9 years ago
added current state of wetting and drying code to test...note it does not work
Property svn:keywords set to `Id`
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
[5066]	32	!! 3.6.?! 2014-09 (H. Liu) Add Wetting and Drying
[1593]	33	!!----------------------------------------------------------------------
[3]	34
	35	!!----------------------------------------------------------------------
[2496]	36	!! nemo_gcm : solve ocean dynamics, tracer, biogeochemistry and/or sea-ice
	37	!! nemo_init : initialization of the NEMO system
[3764]	38	!! nemo_ctl : initialisation of the contol print
[2496]	39	!! nemo_closefile : close remaining open files
[2715]	40	!! nemo_alloc : dynamical allocation
	41	!! nemo_partition : calculate MPP domain decomposition
	42	!! factorise : calculate the factors of the no. of MPI processes
[3]	43	!!----------------------------------------------------------------------
[2382]	44	USE step_oce ! module used in the ocean time stepping module
[888]	45	USE sbc_oce ! surface boundary condition: ocean
[2392]	46	USE cla ! cross land advection (tra_cla routine)
[3]	47	USE domcfg ! domain configuration (dom_cfg routine)
	48	USE mppini ! shared/distributed memory setting (mpp_init routine)
	49	USE domain ! domain initialization (dom_init routine)
[3625]	50	#if defined key_nemocice_decomp
	51	USE ice_domain_size, only: nx_global, ny_global
	52	#endif
[3651]	53	USE tideini ! tidal components initialization (tide_ini routine)
[3294]	54	USE bdyini ! open boundary cond. initialization (bdy_init routine)
	55	USE bdydta ! open boundary cond. initialization (bdy_dta_init routine)
[3651]	56	USE bdytides ! open boundary cond. initialization (bdytide_init routine)
[3]	57	USE istate ! initial state setting (istate_init routine)
	58	USE ldfdyn ! lateral viscosity setting (ldfdyn_init routine)
	59	USE ldftra ! lateral diffusivity setting (ldftra_init routine)
[2392]	60	USE zdfini ! vertical physics setting (zdf_init routine)
[3]	61	USE phycst ! physical constant (par_cst routine)
[2236]	62	USE trdmod ! momentum/tracers trends (trd_mod_init routine)
[3768]	63	USE asminc ! assimilation increments
	64	USE asmbkg ! writing out state trajectory
[2236]	65	USE diaptr ! poleward transports (dia_ptr_init routine)
[3294]	66	USE diadct ! sections transports (dia_dct_init routine)
[2236]	67	USE diaobs ! Observation diagnostics (dia_obs_init routine)
[3764]	68	USE lib_fortran ! Fortran utilities (allows no signed zero when 'key_nosignedzero' defined)
[2496]	69	USE step ! NEMO time-stepping (stp routine)
[3609]	70	USE icbini ! handle bergs, initialisation
	71	USE icbstp ! handle bergs, calving, themodynamics and transport
[532]	72	#if defined key_oasis3
[1359]	73	USE cpl_oasis3 ! OASIS3 coupling
[599]	74	#elif defined key_oasis4
[1359]	75	USE cpl_oasis4 ! OASIS4 coupling (not working)
[532]	76	#endif
[900]	77	USE c1d ! 1D configuration
	78	USE step_c1d ! Time stepping loop for the 1D configuration
[4245]	79	USE dyndmp ! Momentum damping
[1594]	80	#if defined key_top
[1593]	81	USE trcini ! passive tracer initialisation
[1594]	82	#endif
[1593]	83	USE lib_mpp ! distributed memory computing
[1412]	84	#if defined key_iomput
[3701]	85	USE xios
[1359]	86	#endif
[3651]	87	USE sbctide, ONLY: lk_tide
[4152]	88	USE crsini ! initialise grid coarsening utility
[4230]	89	USE lbcnfd, ONLY: isendto, nsndto ! Setup of north fold exchanges
[268]	90
[2715]	91	IMPLICIT NONE
[3]	92	PRIVATE
	93
[2496]	94	PUBLIC nemo_gcm ! called by model.F90
	95	PUBLIC nemo_init ! needed by AGRIF
[3764]	96	PUBLIC nemo_alloc ! needed by TAM
[467]	97
[2498]	98	CHARACTER(lc) :: cform_aaa="( /, 'AAAAAAAA', / ) " ! flag for output listing
[1593]	99
[3]	100	!!----------------------------------------------------------------------
[2715]	101	!! NEMO/OPA 4.0 , NEMO Consortium (2011)
[2392]	102	!! $Id$
[2329]	103	!! Software governed by the CeCILL licence (NEMOGCM/NEMO_CeCILL.txt)
[3]	104	!!----------------------------------------------------------------------
	105	CONTAINS
	106
[2496]	107	SUBROUTINE nemo_gcm
[3]	108	!!----------------------------------------------------------------------
[2496]	109	!! * ROUTINE nemo_gcm *
[3]	110	!!
[3764]	111	!! ** Purpose : NEMO solves the primitive equations on an orthogonal
[1593]	112	!! curvilinear mesh on the sphere.
[3]	113	!!
	114	!! ** Method : - model general initialization
	115	!! - launch the time-stepping (stp routine)
[1593]	116	!! - finalize the run by closing files and communications
[3]	117	!!
[2715]	118	!! References : Madec, Delecluse, Imbard, and Levy, 1997: internal report, IPSL.
[1593]	119	!! Madec, 2008, internal report, IPSL.
[3]	120	!!----------------------------------------------------------------------
	121	INTEGER :: istp ! time step index
[389]	122	!!----------------------------------------------------------------------
[2382]	123	!
[4147]	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
[4147]	142
[682]	143	! check that all process are still there... If some process have an error,
	144	! they will never enter in step and other processes will wait until the end of the cpu time!
[900]	145	IF( lk_mpp ) CALL mpp_max( nstop )
[682]	146
[1593]	147	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	148
	149	! !-----------------------!
	150	! !== time stepping ==!
	151	! !-----------------------!
[900]	152	istp = nit000
[2236]	153	#if defined key_c1d
[389]	154	DO WHILE ( istp <= nitend .AND. nstop == 0 )
[900]	155	CALL stp_c1d( istp )
[389]	156	istp = istp + 1
	157	END DO
[2236]	158	#else
	159	IF( lk_asminc ) THEN
	160	IF( ln_bkgwri ) CALL asm_bkg_wri( nit000 - 1 ) ! Output background fields
	161	IF( ln_asmdin ) THEN ! Direct initialization
	162	IF( ln_trainc ) CALL tra_asm_inc( nit000 - 1 ) ! Tracers
[3764]	163	IF( ln_dyninc ) CALL dyn_asm_inc( nit000 - 1 ) ! Dynamics
[2236]	164	IF( ln_sshinc ) CALL ssh_asm_inc( nit000 - 1 ) ! SSH
	165	ENDIF
	166	ENDIF
[3764]	167
[389]	168	DO WHILE ( istp <= nitend .AND. nstop == 0 )
[4147]	169
[392]	170	#if defined key_agrif
[1593]	171	CALL Agrif_Step( stp ) ! AGRIF: time stepping
[389]	172	#else
[1593]	173	CALL stp( istp ) ! standard time stepping
[389]	174	#endif
[4147]	175
[389]	176	istp = istp + 1
[900]	177	IF( lk_mpp ) CALL mpp_max( nstop )
[389]	178	END DO
[2236]	179	#endif
	180
[3609]	181	IF( lk_diaobs ) CALL dia_obs_wri
	182	!
	183	IF( ln_icebergs ) CALL icb_end( nitend )
[3764]	184
[1593]	185	! !------------------------!
	186	! !== finalize the run ==!
	187	! !------------------------!
	188	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	189	!
	190	IF( nstop /= 0 .AND. lwp ) THEN ! error print
[682]	191	WRITE(numout,cform_err)
[3764]	192	WRITE(numout,*) nstop, ' error have been found'
[389]	193	ENDIF
[1593]	194	!
[3294]	195	#if defined key_agrif
	196	CALL Agrif_ParentGrid_To_ChildGrid()
	197	IF( lk_diaobs ) CALL dia_obs_wri
	198	IF( nn_timing == 1 ) CALL timing_finalize
	199	CALL Agrif_ChildGrid_To_ParentGrid()
	200	#endif
	201	IF( nn_timing == 1 ) CALL timing_finalize
	202	!
[2496]	203	CALL nemo_closefile
[3769]	204	#if defined key_iomput
	205	CALL xios_finalize ! end mpp communications with xios
	206	# if defined key_oasis3 \|\| defined key_oasis4
[1976]	207	CALL cpl_prism_finalize ! end coupling and mpp communications with OASIS
[3769]	208	# endif
[532]	209	#else
[3769]	210	# if defined key_oasis3 \|\| defined key_oasis4
	211	CALL cpl_prism_finalize ! end coupling and mpp communications with OASIS
[3701]	212	# else
[1593]	213	IF( lk_mpp ) CALL mppstop ! end mpp communications
[3701]	214	# endif
[532]	215	#endif
[900]	216	!
[2496]	217	END SUBROUTINE nemo_gcm
[389]	218
	219
[2496]	220	SUBROUTINE nemo_init
[389]	221	!!----------------------------------------------------------------------
[2496]	222	!! * ROUTINE nemo_init *
[389]	223	!!
[2496]	224	!! ** Purpose : initialization of the NEMO GCM
[389]	225	!!----------------------------------------------------------------------
[2715]	226	INTEGER :: ji ! dummy loop indices
	227	INTEGER :: ilocal_comm ! local integer
[4147]	228	INTEGER :: ios
[2715]	229	CHARACTER(len=80), DIMENSION(16) :: cltxt
[1593]	230	!!
[4147]	231	NAMELIST/namctl/ ln_ctl, nn_print, nn_ictls, nn_ictle, &
[3294]	232	& nn_isplt, nn_jsplt, nn_jctls, nn_jctle, &
	233	& nn_bench, nn_timing
[4147]	234	NAMELIST/namcfg/ cp_cfg, cp_cfz, jp_cfg, jpidta, jpjdta, jpkdta, jpiglo, jpjglo, &
	235	& jpizoom, jpjzoom, jperio
[5066]	236	NAMELIST/namwad/ ln_wd, rn_wdmin1, rn_wdmin2, rn_wdld, nn_wdit
[3]	237	!!----------------------------------------------------------------------
[1593]	238	!
[2496]	239	cltxt = ''
	240	!
[4147]	241	! ! Open reference namelist and configuration namelist files
	242	CALL ctl_opn( numnam_ref, 'namelist_ref', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
	243	CALL ctl_opn( numnam_cfg, 'namelist_cfg', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
[1593]	244	!
[4147]	245	REWIND( numnam_ref ) ! Namelist namctl in reference namelist : Control prints & Benchmark
	246	READ ( numnam_ref, namctl, IOSTAT = ios, ERR = 901 )
[4289]	247	901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in reference namelist', .TRUE. )
[4147]	248
	249	REWIND( numnam_cfg ) ! Namelist namctl in confguration namelist : Control prints & Benchmark
	250	READ ( numnam_cfg, namctl, IOSTAT = ios, ERR = 902 )
[4289]	251	902 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in configuration namelist', .TRUE. )
[4147]	252
[1593]	253	!
[4147]	254	REWIND( numnam_ref ) ! Namelist namcfg in reference namelist : Control prints & Benchmark
	255	READ ( numnam_ref, namcfg, IOSTAT = ios, ERR = 903 )
[4289]	256	903 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in reference namelist', .TRUE. )
[4147]	257
	258	REWIND( numnam_cfg ) ! Namelist namcfg in confguration namelist : Control prints & Benchmark
	259	READ ( numnam_cfg, namcfg, IOSTAT = ios, ERR = 904 )
[4289]	260	904 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in configuration namelist', .TRUE. )
[4309]	261
[5066]	262	REWIND( numnam_ref ) ! Namelist namwad in reference namelist : Parameters for Wetting/Drying
	263	READ ( numnam_ref, namwad, IOSTAT = ios, ERR = 905)
	264	905 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namwad in reference namelist', lwp )
	265
	266	REWIND( numnam_cfg ) ! Namelist namwad in configuration namelist : Parameters for Wetting/Drying
	267	READ ( numnam_cfg, namwad, IOSTAT = ios, ERR = 906)
	268	906 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namwad in configuration namelist', lwp )
	269
[4147]	270	! Force values for AGRIF zoom (cf. agrif_user.F90)
	271	#if defined key_agrif
	272	IF( .NOT. Agrif_Root() ) THEN
	273	jpiglo = nbcellsx + 2 + 2*nbghostcells
	274	jpjglo = nbcellsy + 2 + 2*nbghostcells
	275	jpi = ( jpiglo-2jpreci + (jpni-1+0) ) / jpni + 2jpreci
	276	jpj = ( jpjglo-2jprecj + (jpnj-1+0) ) / jpnj + 2jprecj
	277	jpidta = jpiglo
	278	jpjdta = jpjglo
	279	jpizoom = 1
	280	jpjzoom = 1
	281	nperio = 0
	282	jperio = 0
	283	ENDIF
	284	#endif
	285	!
[1593]	286	! !--------------------------------------------!
	287	! ! set communicator & select the local node !
[4624]	288	! ! NB: mynode also opens output.namelist.dyn !
	289	! ! on unit number numond on first proc !
[1593]	290	! !--------------------------------------------!
[1412]	291	#if defined key_iomput
[2200]	292	IF( Agrif_Root() ) THEN
[1412]	293	# if defined key_oasis3 \|\| defined key_oasis4
[3701]	294	CALL cpl_prism_init( ilocal_comm ) ! nemo local communicator given by oasis
	295	CALL xios_initialize( "oceanx",local_comm=ilocal_comm )
	296	# else
	297	CALL xios_initialize( "nemo",return_comm=ilocal_comm )
[1412]	298	# endif
[2200]	299	ENDIF
[4147]	300	narea = mynode( cltxt, numnam_ref, numnam_cfg, numond , nstop, ilocal_comm ) ! Nodes selection
[532]	301	#else
[1412]	302	# if defined key_oasis3 \|\| defined key_oasis4
[2236]	303	IF( Agrif_Root() ) THEN
[2715]	304	CALL cpl_prism_init( ilocal_comm ) ! nemo local communicator given by oasis
[2236]	305	ENDIF
[4147]	306	narea = mynode( cltxt, numnam_ref, numnam_cfg, numond , nstop, ilocal_comm ) ! Nodes selection (control print return in cltxt)
[1412]	307	# else
[2082]	308	ilocal_comm = 0
[4147]	309	narea = mynode( cltxt, numnam_ref, numnam_cfg, numond , nstop ) ! Nodes selection (control print return in cltxt)
[1412]	310	# endif
[532]	311	#endif
[2715]	312	narea = narea + 1 ! mynode return the rank of proc (0 --> jpnij -1 )
[3]	313
[4624]	314	lwm = (narea == 1) ! control of output namelists
[2715]	315	lwp = (narea == 1) .OR. ln_ctl ! control of all listing output print
[1579]	316
[4624]	317	IF(lwm) THEN
	318	! write merged namelists from earlier to output namelist now that the
	319	! file has been opened in call to mynode. nammpp has already been
	320	! written in mynode (if lk_mpp_mpi)
	321	WRITE( numond, namctl )
	322	WRITE( numond, namcfg )
[5066]	323	WRITE( numond, namwad )
[4624]	324	ENDIF
	325
[3764]	326	! If dimensions of processor grid weren't specified in the namelist file
[2715]	327	! then we calculate them here now that we have our communicator size
	328	IF( (jpni < 1) .OR. (jpnj < 1) )THEN
	329	#if defined key_mpp_mpi
	330	IF( Agrif_Root() ) CALL nemo_partition(mppsize)
	331	#else
	332	jpni = 1
	333	jpnj = 1
	334	jpnij = jpni*jpnj
	335	#endif
	336	END IF
	337
	338	! Calculate domain dimensions given calculated jpni and jpnj
	339	! This used to be done in par_oce.F90 when they were parameters rather
	340	! than variables
	341	IF( Agrif_Root() ) THEN
[3294]	342	#if defined key_nemocice_decomp
[3625]	343	jpi = ( nx_global+2-2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
	344	jpj = ( ny_global+2-2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
[3294]	345	#else
[3625]	346	jpi = ( jpiglo-2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
[2715]	347	jpj = ( jpjglo-2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
[3294]	348	#endif
[4147]	349	ENDIF
[2715]	350	jpk = jpkdta ! third dim
	351	jpim1 = jpi-1 ! inner domain indices
	352	jpjm1 = jpj-1 ! " "
	353	jpkm1 = jpk-1 ! " "
	354	jpij = jpi*jpj ! jpi x j
	355
[1593]	356	IF(lwp) THEN ! open listing units
	357	!
[1581]	358	CALL ctl_opn( numout, 'ocean.output', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE., narea )
[1593]	359	!
[1579]	360	WRITE(numout,*)
[3294]	361	WRITE(numout,*) ' CNRS - NERC - Met OFFICE - MERCATOR-ocean - INGV - CMCC'
[1593]	362	WRITE(numout,*) ' NEMO team'
[1579]	363	WRITE(numout,*) ' Ocean General Circulation Model'
[3294]	364	WRITE(numout,*) ' version 3.4 (2011) '
[1579]	365	WRITE(numout,*)
	366	WRITE(numout,*)
[3764]	367	DO ji = 1, SIZE(cltxt)
[1593]	368	IF( TRIM(cltxt(ji)) /= '' ) WRITE(numout,*) cltxt(ji) ! control print of mynode
[1579]	369	END DO
[1593]	370	WRITE(numout,cform_aaa) ! Flag AAAAAAA
	371	!
[473]	372	ENDIF
[2715]	373
[3764]	374	! Now we know the dimensions of the grid and numout has been set we can
[2715]	375	! allocate arrays
	376	CALL nemo_alloc()
	377
[2496]	378	! !-------------------------------!
	379	! ! NEMO general initialization !
	380	! !-------------------------------!
[473]	381
[2496]	382	CALL nemo_ctl ! Control prints & Benchmark
[531]	383
[2082]	384	! ! Domain decomposition
[1593]	385	IF( jpni*jpnj == jpnij ) THEN ; CALL mpp_init ! standard cutting out
	386	ELSE ; CALL mpp_init2 ! eliminate land processors
[3]	387	ENDIF
[2382]	388	!
[3294]	389	IF( nn_timing == 1 ) CALL timing_init
	390	!
[2082]	391	! ! General initialization
[2027]	392	CALL phy_cst ! Physical constants
	393	CALL eos_init ! Equation of state
[4245]	394	IF( lk_c1d ) CALL c1d_init ! 1D column configuration
[2027]	395	CALL dom_cfg ! Domain configuration
	396	CALL dom_init ! Domain
[413]	397
[3294]	398	IF( ln_nnogather ) CALL nemo_northcomms ! Initialise the northfold neighbour lists (must be done after the masks are defined)
	399
[2027]	400	IF( ln_ctl ) CALL prt_ctl_init ! Print control
	401
[3651]	402	CALL istate_init ! ocean initial state (Dynamics and tracers)
	403
[4292]	404	IF( lk_tide ) CALL tide_init( nit000 ) ! Initialisation of the tidal harmonics
[3651]	405
[4292]	406	IF( lk_bdy ) CALL bdy_init ! Open boundaries initialisation
	407	IF( lk_bdy ) CALL bdy_dta_init ! Open boundaries initialisation of external data arrays
	408	IF( lk_bdy .AND. lk_tide ) &
	409	& CALL bdytide_init ! Open boundaries initialisation of tidal harmonic forcing
[2027]	410
[3294]	411	CALL dyn_nept_init ! simplified form of Neptune effect
	412
[4152]	413	!
	414	IF( ln_crs ) CALL crs_init ! Domain initialization of coarsened grid
	415	!
	416	! Ocean physics
[3764]	417	CALL sbc_init ! Forcings : surface module
[2082]	418	! ! Vertical physics
[4147]	419
[2082]	420	CALL zdf_init ! namelist read
[4147]	421
[2082]	422	CALL zdf_bfr_init ! bottom friction
[4147]	423
[2082]	424	IF( lk_zdfric ) CALL zdf_ric_init ! Richardson number dependent Kz
[2329]	425	IF( lk_zdftke ) CALL zdf_tke_init ! TKE closure scheme
	426	IF( lk_zdfgls ) CALL zdf_gls_init ! GLS closure scheme
	427	IF( lk_zdfkpp ) CALL zdf_kpp_init ! KPP closure scheme
[2082]	428	IF( lk_zdftmx ) CALL zdf_tmx_init ! tidal vertical mixing
[3764]	429	IF( lk_zdfddm .AND. .NOT. lk_zdfkpp ) &
[2082]	430	& CALL zdf_ddm_init ! double diffusive mixing
	431	! ! Lateral physics
[4708]	432	#if ! defined key_surge
[2082]	433	CALL ldf_tra_init ! Lateral ocean tracer physics
[4708]	434	#endif
[2082]	435	CALL ldf_dyn_init ! Lateral ocean momentum physics
[2392]	436	IF( lk_ldfslp ) CALL ldf_slp_init ! slope of lateral mixing
[2082]	437
[4708]	438	#if ! defined key_surge
[2027]	439	! ! Active tracers
	440	CALL tra_qsr_init ! penetrative solar radiation qsr
[2325]	441	CALL tra_bbc_init ! bottom heat flux
[2027]	442	IF( lk_trabbl ) CALL tra_bbl_init ! advective (and/or diffusive) bottom boundary layer scheme
[4245]	443	CALL tra_dmp_init ! internal damping trends- tracers
[2027]	444	CALL tra_adv_init ! horizontal & vertical advection
	445	CALL tra_ldf_init ! lateral mixing
	446	CALL tra_zdf_init ! vertical mixing and after tracer fields
[4708]	447	#endif
[2027]	448
	449	! ! Dynamics
[4245]	450	IF( lk_c1d ) CALL dyn_dmp_init ! internal damping trends- momentum
[2027]	451	CALL dyn_adv_init ! advection (vector or flux form)
[2104]	452	CALL dyn_vor_init ! vorticity term including Coriolis
[2027]	453	CALL dyn_ldf_init ! lateral mixing
[2104]	454	CALL dyn_hpg_init ! horizontal gradient of Hydrostatic pressure
[4794]	455	#if ! defined key_surge
[2027]	456	CALL dyn_zdf_init ! vertical diffusion
[4794]	457	#endif
[2027]	458	CALL dyn_spg_init ! surface pressure gradient
[3764]	459
[2392]	460	! ! Misc. options
[4147]	461	IF( nn_cla == 1 .AND. cp_cfg == 'orca' .AND. jp_cfg == 2 ) CALL cla_init ! Cross Land Advection
[3609]	462	CALL icb_init( rdt, nit000) ! initialise icebergs instance
[4147]	463
[1594]	464	#if defined key_top
[2027]	465	! ! Passive tracers
[2082]	466	CALL trc_init
[1594]	467	#endif
[4147]	468	!
	469
	470	! Diagnostics
[3294]	471	IF( lk_floats ) CALL flo_init ! drifting Floats
[2392]	472	IF( lk_diaar5 ) CALL dia_ar5_init ! ar5 diag
[2027]	473	CALL dia_ptr_init ! Poleward TRansports initialization
[3294]	474	IF( lk_diadct ) CALL dia_dct_init ! Sections tranports
[2148]	475	CALL dia_hsb_init ! heat content, salt content and volume budgets
[2027]	476	CALL trd_mod_init ! Mixed-layer/Vorticity/Integral constraints trends
[2392]	477	IF( lk_diaobs ) THEN ! Observation & model comparison
[2382]	478	CALL dia_obs_init ! Initialize observational data
	479	CALL dia_obs( nit000 - 1 ) ! Observation operator for restart
[3764]	480	ENDIF
[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
[1593]	484	!
[2496]	485	END SUBROUTINE nemo_init
[467]	486
	487
[2496]	488	SUBROUTINE nemo_ctl
[467]	489	!!----------------------------------------------------------------------
[2496]	490	!! * ROUTINE nemo_ctl *
[467]	491	!!
[3764]	492	!! ** Purpose : control print setting
[467]	493	!!
[2442]	494	!! ** Method : - print namctl information and check some consistencies
[467]	495	!!----------------------------------------------------------------------
[2442]	496	!
[2496]	497	IF(lwp) THEN ! control print
[531]	498	WRITE(numout,*)
[2496]	499	WRITE(numout,*) 'nemo_ctl: Control prints & Benchmark'
[531]	500	WRITE(numout,*) '~~~~~~~ '
[1593]	501	WRITE(numout,*) ' Namelist namctl'
[1601]	502	WRITE(numout,*) ' run control (for debugging) ln_ctl = ', ln_ctl
	503	WRITE(numout,*) ' level of print nn_print = ', nn_print
	504	WRITE(numout,*) ' Start i indice for SUM control nn_ictls = ', nn_ictls
	505	WRITE(numout,*) ' End i indice for SUM control nn_ictle = ', nn_ictle
	506	WRITE(numout,*) ' Start j indice for SUM control nn_jctls = ', nn_jctls
	507	WRITE(numout,*) ' End j indice for SUM control nn_jctle = ', nn_jctle
	508	WRITE(numout,*) ' number of proc. following i nn_isplt = ', nn_isplt
	509	WRITE(numout,*) ' number of proc. following j nn_jsplt = ', nn_jsplt
	510	WRITE(numout,*) ' benchmark parameter (0/1) nn_bench = ', nn_bench
[3610]	511	WRITE(numout,*) ' timing activated (0/1) nn_timing = ', nn_timing
[531]	512	ENDIF
[2442]	513	!
[1601]	514	nprint = nn_print ! convert DOCTOR namelist names into OLD names
	515	nictls = nn_ictls
	516	nictle = nn_ictle
	517	njctls = nn_jctls
	518	njctle = nn_jctle
	519	isplt = nn_isplt
	520	jsplt = nn_jsplt
	521	nbench = nn_bench
[4147]	522
	523	IF(lwp) THEN ! control print
	524	WRITE(numout,*)
	525	WRITE(numout,*) 'namcfg : configuration initialization through namelist read'
	526	WRITE(numout,*) '~~~~~~~ '
	527	WRITE(numout,*) ' Namelist namcfg'
	528	WRITE(numout,*) ' configuration name cp_cfg = ', TRIM(cp_cfg)
	529	WRITE(numout,*) ' configuration zoom name cp_cfz = ', TRIM(cp_cfz)
	530	WRITE(numout,*) ' configuration resolution jp_cfg = ', jp_cfg
	531	WRITE(numout,*) ' 1st lateral dimension ( >= jpi ) jpidta = ', jpidta
	532	WRITE(numout,*) ' 2nd " " ( >= jpj ) jpjdta = ', jpjdta
	533	WRITE(numout,*) ' 3nd " " jpkdta = ', jpkdta
	534	WRITE(numout,*) ' 1st dimension of global domain in i jpiglo = ', jpiglo
	535	WRITE(numout,*) ' 2nd - - in j jpjglo = ', jpjglo
	536	WRITE(numout,*) ' left bottom i index of the zoom (in data domain) jpizoom = ', jpizoom
	537	WRITE(numout,*) ' left bottom j index of the zoom (in data domain) jpizoom = ', jpjzoom
	538	WRITE(numout,*) ' lateral cond. type (between 0 and 6) jperio = ', jperio
	539	ENDIF
[5066]	540
	541	IF(lwp) THEN ! control print
	542	WRITE(numout,*)
	543	WRITE(numout,*) 'namwad : wetting and drying initialisation through namelist read'
	544	WRITE(numout,*) '~~~~~~~ '
	545	WRITE(numout,*) ' Namelist namwad'
	546	WRITE(numout,*) ' key to turn on/off wetting/drying ln_wd = ', ln_wd
	547	WRITE(numout,*) ' minimum water depth on dried cells rn_wdmin1 = ', rn_wdmin1
	548	WRITE(numout,*) ' tolerrance of min water depth on dried cells rn_wdmin2 = ', rn_wdmin2
	549	WRITE(numout,*) ' land elevation below which wad considered rn_wdld = ', rn_wdld
	550	WRITE(numout,*) ' maximum number of iteration for W/D limiter nn_wdit = ', nn_wdit
	551	ENDIF
	552
[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	!
[2496]	600	IF( lk_c1d .AND. .NOT.lk_iomput ) CALL ctl_stop( 'nemo_ctl: The 1D configuration must be used ', &
	601	& 'with the IOM Input/Output manager. ' , &
[2442]	602	& 'Compile with key_iomput enabled' )
[2409]	603	!
[3764]	604	IF( 1_wp /= SIGN(1._wp,-0._wp) ) CALL ctl_stop( 'nemo_ctl: The intrinsec SIGN function follows ', &
	605	& 'f2003 standard. ' , &
	606	& 'Compile with key_nosignedzero enabled' )
	607	!
[2496]	608	END SUBROUTINE nemo_ctl
[467]	609
	610
[2496]	611	SUBROUTINE nemo_closefile
[467]	612	!!----------------------------------------------------------------------
[2496]	613	!! * ROUTINE nemo_closefile *
[467]	614	!!
	615	!! ** Purpose : Close the files
	616	!!----------------------------------------------------------------------
[1593]	617	!
	618	IF( lk_mpp ) CALL mppsync
	619	!
[1685]	620	CALL iom_close ! close all input/output files managed by iom_*
[1593]	621	!
[4147]	622	IF( numstp /= -1 ) CLOSE( numstp ) ! time-step file
	623	IF( numsol /= -1 ) CLOSE( numsol ) ! solver file
	624	IF( numnam_ref /= -1 ) CLOSE( numnam_ref ) ! oce reference namelist
	625	IF( numnam_cfg /= -1 ) CLOSE( numnam_cfg ) ! oce configuration namelist
[4624]	626	IF( lwm.AND.numond /= -1 ) CLOSE( numond ) ! oce output namelist
[4147]	627	IF( numnam_ice_ref /= -1 ) CLOSE( numnam_ice_ref ) ! ice reference namelist
	628	IF( numnam_ice_cfg /= -1 ) CLOSE( numnam_ice_cfg ) ! ice configuration namelist
[4624]	629	IF( lwm.AND.numoni /= -1 ) CLOSE( numoni ) ! ice output namelist
[4147]	630	IF( numevo_ice /= -1 ) CLOSE( numevo_ice ) ! ice variables (temp. evolution)
	631	IF( numout /= 6 ) CLOSE( numout ) ! standard model output file
	632	IF( numdct_vol /= -1 ) CLOSE( numdct_vol ) ! volume transports
	633	IF( numdct_heat /= -1 ) CLOSE( numdct_heat ) ! heat transports
	634	IF( numdct_salt /= -1 ) CLOSE( numdct_salt ) ! salt transports
[3294]	635
[1593]	636	!
[2442]	637	numout = 6 ! redefine numout in case it is used after this point...
	638	!
[2496]	639	END SUBROUTINE nemo_closefile
[467]	640
[2715]	641
	642	SUBROUTINE nemo_alloc
	643	!!----------------------------------------------------------------------
	644	!! * ROUTINE nemo_alloc *
	645	!!
	646	!! ** Purpose : Allocate all the dynamic arrays of the OPA modules
	647	!!
	648	!! ** Method :
	649	!!----------------------------------------------------------------------
	650	USE diawri , ONLY: dia_wri_alloc
	651	USE dom_oce , ONLY: dom_oce_alloc
	652	USE ldfdyn_oce, ONLY: ldfdyn_oce_alloc
	653	USE ldftra_oce, ONLY: ldftra_oce_alloc
	654	USE trc_oce , ONLY: trc_oce_alloc
[3680]	655	#if defined key_diadct
	656	USE diadct , ONLY: diadct_alloc
	657	#endif
[4354]	658	#if defined key_bdy
	659	USE bdy_oce , ONLY: bdy_oce_alloc
	660	#endif
[2715]	661	!
	662	INTEGER :: ierr
	663	!!----------------------------------------------------------------------
	664	!
[3764]	665	ierr = oce_alloc () ! ocean
[2715]	666	ierr = ierr + dia_wri_alloc ()
	667	ierr = ierr + dom_oce_alloc () ! ocean domain
	668	ierr = ierr + ldfdyn_oce_alloc() ! ocean lateral physics : dynamics
	669	ierr = ierr + ldftra_oce_alloc() ! ocean lateral physics : tracers
	670	ierr = ierr + zdf_oce_alloc () ! ocean vertical physics
	671	!
	672	ierr = ierr + trc_oce_alloc () ! shared TRC / TRA arrays
	673	!
[3680]	674	#if defined key_diadct
	675	ierr = ierr + diadct_alloc () !
	676	#endif
[4354]	677	#if defined key_bdy
	678	ierr = ierr + bdy_oce_alloc () ! bdy masks (incl. initialization)
	679	#endif
[3680]	680	!
[2715]	681	IF( lk_mpp ) CALL mpp_sum( ierr )
	682	IF( ierr /= 0 ) CALL ctl_stop( 'STOP', 'nemo_alloc : unable to allocate standard ocean arrays' )
	683	!
	684	END SUBROUTINE nemo_alloc
	685
	686
	687	SUBROUTINE nemo_partition( num_pes )
	688	!!----------------------------------------------------------------------
	689	!! * ROUTINE nemo_partition *
	690	!!
[3764]	691	!! ** Purpose :
[2715]	692	!!
	693	!! ** Method :
	694	!!----------------------------------------------------------------------
	695	INTEGER, INTENT(in) :: num_pes ! The number of MPI processes we have
	696	!
	697	INTEGER, PARAMETER :: nfactmax = 20
	698	INTEGER :: nfact ! The no. of factors returned
	699	INTEGER :: ierr ! Error flag
	700	INTEGER :: ji
	701	INTEGER :: idiff, mindiff, imin ! For choosing pair of factors that are closest in value
	702	INTEGER, DIMENSION(nfactmax) :: ifact ! Array of factors
	703	!!----------------------------------------------------------------------
	704
	705	ierr = 0
	706
	707	CALL factorise( ifact, nfactmax, nfact, num_pes, ierr )
	708
	709	IF( nfact <= 1 ) THEN
	710	WRITE (numout, *) 'WARNING: factorisation of number of PEs failed'
	711	WRITE (numout, *) ' : using grid of ',num_pes,' x 1'
	712	jpnj = 1
	713	jpni = num_pes
	714	ELSE
	715	! Search through factors for the pair that are closest in value
	716	mindiff = 1000000
	717	imin = 1
	718	DO ji = 1, nfact-1, 2
	719	idiff = ABS( ifact(ji) - ifact(ji+1) )
	720	IF( idiff < mindiff ) THEN
	721	mindiff = idiff
	722	imin = ji
	723	ENDIF
	724	END DO
	725	jpnj = ifact(imin)
	726	jpni = ifact(imin + 1)
	727	ENDIF
	728	!
	729	jpnij = jpni*jpnj
	730	!
	731	END SUBROUTINE nemo_partition
	732
	733
	734	SUBROUTINE factorise( kfax, kmaxfax, knfax, kn, kerr )
	735	!!----------------------------------------------------------------------
	736	!! * ROUTINE factorise *
	737	!!
	738	!! ** Purpose : return the prime factors of n.
[3764]	739	!! knfax factors are returned in array kfax which is of
[2715]	740	!! maximum dimension kmaxfax.
	741	!! ** Method :
	742	!!----------------------------------------------------------------------
	743	INTEGER , INTENT(in ) :: kn, kmaxfax
	744	INTEGER , INTENT( out) :: kerr, knfax
	745	INTEGER, DIMENSION(kmaxfax), INTENT( out) :: kfax
	746	!
	747	INTEGER :: ifac, jl, inu
	748	INTEGER, PARAMETER :: ntest = 14
	749	INTEGER :: ilfax(ntest)
	750
	751	! lfax contains the set of allowed factors.
	752	data (ilfax(jl),jl=1,ntest) / 16384, 8192, 4096, 2048, 1024, 512, 256, &
	753	& 128, 64, 32, 16, 8, 4, 2 /
	754	!!----------------------------------------------------------------------
	755
	756	! Clear the error flag and initialise output vars
	757	kerr = 0
	758	kfax = 1
	759	knfax = 0
	760
	761	! Find the factors of n.
	762	IF( kn == 1 ) GOTO 20
	763
	764	! nu holds the unfactorised part of the number.
	765	! knfax holds the number of factors found.
	766	! l points to the allowed factor list.
	767	! ifac holds the current factor.
	768
	769	inu = kn
	770	knfax = 0
	771
	772	DO jl = ntest, 1, -1
	773	!
	774	ifac = ilfax(jl)
	775	IF( ifac > inu ) CYCLE
	776
	777	! Test whether the factor will divide.
	778
	779	IF( MOD(inu,ifac) == 0 ) THEN
	780	!
	781	knfax = knfax + 1 ! Add the factor to the list
	782	IF( knfax > kmaxfax ) THEN
	783	kerr = 6
	784	write (,) 'FACTOR: insufficient space in factor array ', knfax
	785	return
	786	ENDIF
	787	kfax(knfax) = ifac
	788	! Store the other factor that goes with this one
	789	knfax = knfax + 1
	790	kfax(knfax) = inu / ifac
	791	!WRITE (,) 'ARPDBG, factors ',knfax-1,' & ',knfax,' are ', kfax(knfax-1),' and ',kfax(knfax)
	792	ENDIF
	793	!
	794	END DO
	795
	796	20 CONTINUE ! Label 20 is the exit point from the factor search loop.
	797	!
	798	END SUBROUTINE factorise
	799
[3294]	800	#if defined key_mpp_mpi
	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
	835	DO jn = jpnij - jpni +1, jpnij
	836	IF ( njmppt(jn) == njmppmax ) THEN
	837	!sxT is the first point (in the global domain) of the jn
	838	!process
	839	sxT = nimppt(jn)
	840	!dxT is the last point (in the global domain) of the jn
	841	!process
	842	dxT = nimppt(jn) + nlcit(jn) - 1
	843	IF ((sxM .gt. sxT) .AND. (sxM .lt. dxT)) THEN
	844	nsndto = nsndto + 1
	845	isendto(nsndto) = jn
[4645]	846	ELSEIF ((sxM .le. sxT) .AND. (dxM .ge. dxT)) THEN
[4230]	847	nsndto = nsndto + 1
	848	isendto(nsndto) = jn
	849	ELSEIF ((dxM .lt. dxT) .AND. (sxT .lt. dxM)) THEN
	850	nsndto = nsndto + 1
	851	isendto(nsndto) = jn
	852	END IF
	853	END IF
	854	END DO
[3294]	855	ENDIF
[4230]	856	l_north_nogather = .TRUE.
[3294]	857	END SUBROUTINE nemo_northcomms
	858	#else
	859	SUBROUTINE nemo_northcomms ! Dummy routine
	860	WRITE(,) 'nemo_northcomms: You should not have seen this print! error?'
	861	END SUBROUTINE nemo_northcomms
	862	#endif
[3]	863	!!======================================================================
[2496]	864	END MODULE nemogcm
[4354]	865
	866

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