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nemogcm.F90

Last change on this file was 12784, checked in by rrenshaw, 4 years ago
fix for profiles
File size: 41.8 KB

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1	MODULE nemogcm
2	!!======================================================================
3	!! * MODULE nemogcm *
4	!! Ocean system : NEMO GCM (ocean dynamics, on-line tracers, biochemistry and sea-ice)
5	!!======================================================================
6	!! History : OPA ! 1990-10 (C. Levy, G. Madec) Original code
7	!! 7.0 ! 1991-11 (M. Imbard, C. Levy, G. Madec)
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
10	!! - ! 1992-06 (L.Terray) coupling implementation
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,
13	!! P. Delecluse, L.Terray, M.A. Filiberti, J. Vialar, A.M. Treguier, M. Levy) release 8.0
14	!! 8.1 ! 1997-06 (M. Imbard, G. Madec)
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
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
27	!! 3.3 ! 2010-05 (K. Mogensen, A. Weaver, M. Martin, D. Lea) Assimilation interface
28	!! - ! 2010-10 (C. Ethe, G. Madec) reorganisation of initialisation phase
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
31	!! ! 2012-05 (C. Calone, J. Simeon, G. Madec, C. Ethe) Add grid coarsening
32	!!----------------------------------------------------------------------
33
34	!!----------------------------------------------------------------------
35	!! nemo_gcm : solve ocean dynamics, tracer, biogeochemistry and/or sea-ice
36	!! nemo_init : initialization of the NEMO system
37	!! nemo_ctl : initialisation of the contol print
38	!! nemo_closefile : close remaining open files
39	!! nemo_alloc : dynamical allocation
40	!! nemo_partition : calculate MPP domain decomposition
41	!! factorise : calculate the factors of the no. of MPI processes
42	!!----------------------------------------------------------------------
43	USE step_oce ! module used in the ocean time stepping module
44	USE cla ! cross land advection (tra_cla routine)
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)
48	#if defined key_nemocice_decomp
49	USE ice_domain_size, only: nx_global, ny_global
50	#endif
51	USE tideini ! tidal components initialization (tide_ini routine)
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)
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)
58	USE zdfini ! vertical physics setting (zdf_init routine)
59	USE phycst ! physical constant (par_cst routine)
60	USE trdini ! dyn/tra trends initialization (trd_init routine)
61	USE asminc ! assimilation increments
62	USE asmbkg ! writing out state trajectory
63	USE asmbgc ! biogeochemical assimilation increments
64	USE diaptr ! poleward transports (dia_ptr_init routine)
65	USE diadct ! sections transports (dia_dct_init routine)
66	USE diaobs ! Observation diagnostics (dia_obs_init routine)
67	USE lib_fortran ! Fortran utilities (allows no signed zero when 'key_nosignedzero' defined)
68	USE step ! NEMO time-stepping (stp routine)
69	USE icbini ! handle bergs, initialisation
70	USE icbstp ! handle bergs, calving, themodynamics and transport
71	USE sbccpl
72	USE cpl_oasis3 ! OASIS3 coupling
73	USE c1d ! 1D configuration
74	USE step_c1d ! Time stepping loop for the 1D configuration
75	USE dyndmp ! Momentum damping
76	#if defined key_top
77	USE trcini ! passive tracer initialisation
78	#endif
79	USE lib_mpp ! distributed memory computing
80	#if defined key_iomput
81	USE xios
82	#endif
83	USE sbctide, ONLY: lk_tide
84	USE crsini ! initialise grid coarsening utility
85	USE lbcnfd, ONLY: isendto, nsndto, nfsloop, nfeloop ! Setup of north fold exchanges
86	USE sbc_oce, ONLY: lk_oasis
87	USE stopar
88	USE stopts
89	USE diatmb ! Top,middle,bottom output
90	USE diaregmean ! regional means output
91	USE diapea ! potential energy anomaly output
92	USE dia25h ! 25h mean output
93	USE diaopfoam ! FOAM operational output
94	USE diurnal_bulk ! diurnal bulk SST
95
96	IMPLICIT NONE
97	PRIVATE
98
99	PUBLIC nemo_gcm ! called by model.F90
100	PUBLIC nemo_init ! needed by AGRIF
101	PUBLIC nemo_alloc ! needed by TAM
102
103	CHARACTER(lc) :: cform_aaa="( /, 'AAAAAAAA', / ) " ! flag for output listing
104
105	!!----------------------------------------------------------------------
106	!! NEMO/OPA 4.0 , NEMO Consortium (2011)
107	!! $Id$
108	!! Software governed by the CeCILL licence (NEMOGCM/NEMO_CeCILL.txt)
109	!!----------------------------------------------------------------------
110	CONTAINS
111
112	SUBROUTINE nemo_gcm
113	!!----------------------------------------------------------------------
114	!! * ROUTINE nemo_gcm *
115	!!
116	!! ** Purpose : NEMO solves the primitive equations on an orthogonal
117	!! curvilinear mesh on the sphere.
118	!!
119	!! ** Method : - model general initialization
120	!! - launch the time-stepping (stp routine)
121	!! - finalize the run by closing files and communications
122	!!
123	!! References : Madec, Delecluse, Imbard, and Levy, 1997: internal report, IPSL.
124	!! Madec, 2008, internal report, IPSL.
125	!!----------------------------------------------------------------------
126	INTEGER :: istp ! time step index
127	!!----------------------------------------------------------------------
128	!
129	#if defined key_agrif
130	CALL Agrif_Init_Grids() ! AGRIF: set the meshes
131	#endif
132
133	! !-----------------------!
134	CALL nemo_init !== Initialisations ==!
135	! !-----------------------!
136	#if defined key_agrif
137	CALL Agrif_Declare_Var_dom ! AGRIF: set the meshes for DOM
138	CALL Agrif_Declare_Var ! " " " " " DYN/TRA
139	# if defined key_top
140	CALL Agrif_Declare_Var_top ! " " " " " TOP
141	# endif
142	# if defined key_lim2
143	CALL Agrif_Declare_Var_lim2 ! " " " " " LIM
144	# endif
145	#endif
146	! check that all process are still there... If some process have an error,
147	! they will never enter in step and other processes will wait until the end of the cpu time!
148	IF( lk_mpp ) CALL mpp_max( nstop )
149
150	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
151
152	! !-----------------------!
153	! !== time stepping ==!
154	! !-----------------------!
155	istp = nit000
156	#if defined key_c1d
157	DO WHILE ( istp <= nitend .AND. nstop == 0 )
158	CALL stp_c1d( istp )
159	istp = istp + 1
160	END DO
161	#else
162	IF( lk_asminc ) THEN
163	IF( ln_bkgwri ) CALL asm_bkg_wri( nit000 - 1 ) ! Output background fields
164	IF( ln_asmdin ) THEN ! Direct initialization
165	IF( ln_trainc ) CALL tra_asm_inc( nit000 - 1 ) ! Tracers
166	IF( ln_dyninc ) CALL dyn_asm_inc( nit000 - 1 ) ! Dynamics
167	IF( ln_sshinc ) CALL ssh_asm_inc( nit000 - 1 ) ! SSH
168	IF( lk_bgcinc ) CALL bgc_asm_inc( nit000 - 1 ) ! BGC
169	ENDIF
170	ENDIF
171
172	#if defined key_agrif
173	CALL Agrif_Regrid()
174	#endif
175
176	DO WHILE ( istp <= nitend .AND. nstop == 0 )
177	#if defined key_agrif
178	CALL stp ! AGRIF: time stepping
179	#else
180	IF (lk_oasis) CALL sbc_cpl_snd( istp ) ! Coupling to atmos
181	CALL stp( istp )
182	! We don't couple on the final timestep because
183	! our restart file has already been written
184	! and contains all the necessary data for a
185	! restart. sbc_cpl_snd could be called here
186	! but it would require
187	! a) A test to ensure it was not performed
188	! on the very last time-step
189	! b) the presence of another call to
190	! sbc_cpl_snd call prior to the main DO loop
191	! This solution produces identical results
192	! with fewer lines of code.
193	#endif
194	istp = istp + 1
195	IF( lk_mpp ) CALL mpp_max( nstop )
196	END DO
197	#endif
198
199	IF( lk_diaobs ) CALL dia_obs_wri
200	!
201	IF( ( lk_asminc ).AND.( ln_balwri ) ) CALL asm_bgc_bal_wri( nitend ) ! Output balancing increments
202	!
203	IF( ln_icebergs ) CALL icb_end( nitend )
204
205	! !------------------------!
206	! !== finalize the run ==!
207	! !------------------------!
208	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
209	!
210	IF( nstop /= 0 .AND. lwp ) THEN ! error print
211	WRITE(numout,cform_err)
212	WRITE(numout,*) nstop, ' error have been found'
213	ENDIF
214	!
215	#if defined key_agrif
216	IF( .NOT. Agrif_Root() ) THEN
217	CALL Agrif_ParentGrid_To_ChildGrid()
218	IF( lk_diaobs ) CALL dia_obs_wri
219	IF( nn_timing == 1 ) CALL timing_finalize
220	CALL Agrif_ChildGrid_To_ParentGrid()
221	ENDIF
222	#endif
223	IF( nn_timing == 1 ) CALL timing_finalize
224	!
225	CALL nemo_closefile
226	!
227	#if defined key_iomput
228	CALL xios_finalize ! end mpp communications with xios
229	IF( lk_oasis ) CALL cpl_finalize ! end coupling and mpp communications with OASIS
230	#else
231	IF( lk_oasis ) THEN
232	CALL cpl_finalize ! end coupling and mpp communications with OASIS
233	ELSE
234	IF( lk_mpp ) CALL mppstop ! end mpp communications
235	ENDIF
236	#endif
237	!
238	END SUBROUTINE nemo_gcm
239
240
241	SUBROUTINE nemo_init
242	!!----------------------------------------------------------------------
243	!! * ROUTINE nemo_init *
244	!!
245	!! ** Purpose : initialization of the NEMO GCM
246	!!----------------------------------------------------------------------
247	INTEGER :: ji ! dummy loop indices
248	INTEGER :: ilocal_comm ! local integer
249	INTEGER :: ios
250	CHARACTER(len=80), DIMENSION(16) :: cltxt
251	!
252	NAMELIST/namctl/ ln_ctl , nn_print, nn_ictls, nn_ictle, &
253	& nn_isplt, nn_jsplt, nn_jctls, nn_jctle, &
254	& nn_bench, nn_timing
255	NAMELIST/namcfg/ cp_cfg, cp_cfz, jp_cfg, jpidta, jpjdta, jpkdta, jpiglo, jpjglo, &
256	& jpizoom, jpjzoom, jperio, ln_use_jattr
257	!!----------------------------------------------------------------------
258	!
259	cltxt = ''
260	cxios_context = 'nemo'
261	!
262	! ! Open reference namelist and configuration namelist files
263	CALL ctl_opn( numnam_ref, 'namelist_ref', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
264	CALL ctl_opn( numnam_cfg, 'namelist_cfg', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
265	!
266	REWIND( numnam_ref ) ! Namelist namctl in reference namelist : Control prints & Benchmark
267	READ ( numnam_ref, namctl, IOSTAT = ios, ERR = 901 )
268	901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in reference namelist', .TRUE. )
269
270	REWIND( numnam_cfg ) ! Namelist namctl in confguration namelist : Control prints & Benchmark
271	READ ( numnam_cfg, namctl, IOSTAT = ios, ERR = 902 )
272	902 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in configuration namelist', .TRUE. )
273
274	!
275	REWIND( numnam_ref ) ! Namelist namcfg in reference namelist : Control prints & Benchmark
276	READ ( numnam_ref, namcfg, IOSTAT = ios, ERR = 903 )
277	903 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in reference namelist', .TRUE. )
278
279	REWIND( numnam_cfg ) ! Namelist namcfg in confguration namelist : Control prints & Benchmark
280	READ ( numnam_cfg, namcfg, IOSTAT = ios, ERR = 904 )
281	904 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in configuration namelist', .TRUE. )
282
283	! Force values for AGRIF zoom (cf. agrif_user.F90)
284	#if defined key_agrif
285	IF( .NOT. Agrif_Root() ) THEN
286	jpiglo = nbcellsx + 2 + 2*nbghostcells
287	jpjglo = nbcellsy + 2 + 2*nbghostcells
288	jpi = ( jpiglo-2jpreci + (jpni-1+0) ) / jpni + 2jpreci
289	jpj = ( jpjglo-2jprecj + (jpnj-1+0) ) / jpnj + 2jprecj
290	jpidta = jpiglo
291	jpjdta = jpjglo
292	jpizoom = 1
293	jpjzoom = 1
294	nperio = 0
295	jperio = 0
296	ln_use_jattr = .false.
297	ENDIF
298	#endif
299	!
300	! !--------------------------------------------!
301	! ! set communicator & select the local node !
302	! ! NB: mynode also opens output.namelist.dyn !
303	! ! on unit number numond on first proc !
304	! !--------------------------------------------!
305	#if defined key_iomput
306	IF( Agrif_Root() ) THEN
307	IF( lk_oasis ) THEN
308	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
309	CALL xios_initialize( "not used",local_comm=ilocal_comm ) ! send nemo communicator to xios
310	ELSE
311	CALL xios_initialize( "for_xios_mpi_id",return_comm=ilocal_comm ) ! nemo local communicator given by xios
312	ENDIF
313	ENDIF
314	! Nodes selection (control print return in cltxt)
315	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop, ilocal_comm )
316	#else
317	IF( lk_oasis ) THEN
318	IF( Agrif_Root() ) THEN
319	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
320	ENDIF
321	! Nodes selection (control print return in cltxt)
322	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop, ilocal_comm )
323	ELSE
324	ilocal_comm = 0
325	! Nodes selection (control print return in cltxt)
326	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop )
327	ENDIF
328	#endif
329	narea = narea + 1 ! mynode return the rank of proc (0 --> jpnij -1 )
330
331	lwm = (narea == 1) ! control of output namelists
332	lwp = (narea == 1) .OR. ln_ctl ! control of all listing output print
333
334	IF(lwm) THEN
335	! write merged namelists from earlier to output namelist now that the
336	! file has been opened in call to mynode. nammpp has already been
337	! written in mynode (if lk_mpp_mpi)
338	WRITE( numond, namctl )
339	WRITE( numond, namcfg )
340	ENDIF
341
342	! If dimensions of processor grid weren't specified in the namelist file
343	! then we calculate them here now that we have our communicator size
344	IF( (jpni < 1) .OR. (jpnj < 1) )THEN
345	#if defined key_mpp_mpi
346	IF( Agrif_Root() ) CALL nemo_partition(mppsize)
347	#else
348	jpni = 1
349	jpnj = 1
350	jpnij = jpni*jpnj
351	#endif
352	END IF
353
354	! Calculate domain dimensions given calculated jpni and jpnj
355	! This used to be done in par_oce.F90 when they were parameters rather
356	! than variables
357	IF( Agrif_Root() ) THEN
358	#if defined key_nemocice_decomp
359	jpi = ( nx_global+2-2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
360	jpj = ( ny_global+2-2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
361	#else
362	jpi = ( jpiglo-2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
363	jpj = ( jpjglo-2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
364	#endif
365	ENDIF
366	jpk = jpkdta ! third dim
367	#if defined key_agrif
368	! simple trick to use same vertical grid as parent
369	! but different number of levels:
370	! Save maximum number of levels in jpkdta, then define all vertical grids
371	! with this number.
372	! Suppress once vertical online interpolation is ok
373	IF(.NOT.Agrif_Root()) jpkdta = Agrif_Parent(jpkdta)
374	#endif
375	jpim1 = jpi-1 ! inner domain indices
376	jpjm1 = jpj-1 ! " "
377	jpkm1 = jpk-1 ! " "
378	jpij = jpi*jpj ! jpi x j
379
380	IF(lwp) THEN ! open listing units
381	!
382	CALL ctl_opn( numout, 'ocean.output', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE., narea )
383	!
384	WRITE(numout,*)
385	WRITE(numout,*) ' CNRS - NERC - Met OFFICE - MERCATOR-ocean - INGV - CMCC'
386	WRITE(numout,*) ' NEMO team'
387	WRITE(numout,*) ' Ocean General Circulation Model'
388	WRITE(numout,*) ' version 3.6 (2015) '
389	WRITE(numout,*)
390	WRITE(numout,*)
391	DO ji = 1, SIZE(cltxt)
392	IF( TRIM(cltxt(ji)) /= '' ) WRITE(numout,*) cltxt(ji) ! control print of mynode
393	END DO
394	WRITE(numout,cform_aaa) ! Flag AAAAAAA
395	!
396	ENDIF
397
398	! Now we know the dimensions of the grid and numout has been set we can
399	! allocate arrays
400	CALL nemo_alloc()
401
402	! !-------------------------------!
403	! ! NEMO general initialization !
404	! !-------------------------------!
405
406	CALL nemo_ctl ! Control prints & Benchmark
407
408	! ! Domain decomposition
409	IF( jpni*jpnj == jpnij ) THEN ; CALL mpp_init ! standard cutting out
410	ELSE ; CALL mpp_init2 ! eliminate land processors
411	ENDIF
412	!
413	IF( nn_timing == 1 ) CALL timing_init
414	!
415	! ! General initialization
416	CALL phy_cst ! Physical constants
417	CALL eos_init ! Equation of state
418	IF( lk_c1d ) CALL c1d_init ! 1D column configuration
419	CALL dom_cfg ! Domain configuration
420	CALL dom_init ! Domain
421
422	IF( ln_nnogather ) CALL nemo_northcomms ! Initialise the northfold neighbour lists (must be done after the masks are defined)
423
424	IF( ln_ctl ) CALL prt_ctl_init ! Print control
425
426	CALL istate_init ! ocean initial state (Dynamics and tracers)
427
428	CALL diurnal_sst_bulk_init ! diurnal sst
429	IF ( ln_diurnal ) CALL diurnal_sst_coolskin_init ! cool skin
430
431	IF( lk_tide ) CALL tide_init( nit000 ) ! Initialisation of the tidal harmonics
432
433	CALL sbc_init ! Forcings : surface module (clem: moved here for bdy purpose)
434
435	IF( lk_bdy ) CALL bdy_init ! Open boundaries initialisation
436	IF( lk_bdy ) CALL bdy_dta_init ! Open boundaries initialisation of external data arrays
437	IF( lk_bdy .AND. lk_tide ) &
438	& CALL bdytide_init ! Open boundaries initialisation of tidal harmonic forcing
439
440	CALL dyn_nept_init ! simplified form of Neptune effect
441	!
442	IF( ln_crs ) CALL crs_init ! Domain initialization of coarsened grid
443	!
444	! Ocean physics
445	! ! Vertical physics
446	CALL zdf_init ! namelist read
447	CALL zdf_bfr_init ! bottom friction
448	IF( lk_zdfric ) CALL zdf_ric_init ! Richardson number dependent Kz
449	IF( lk_zdftke ) CALL zdf_tke_init ! TKE closure scheme
450	IF( lk_zdfgls ) CALL zdf_gls_init ! GLS closure scheme
451	IF( lk_zdfkpp ) CALL zdf_kpp_init ! KPP closure scheme
452	IF( lk_zdftmx ) CALL zdf_tmx_init ! tidal vertical mixing
453	IF( lk_zdfddm .AND. .NOT. lk_zdfkpp ) &
454	& CALL zdf_ddm_init ! double diffusive mixing
455	! ! Lateral physics
456	CALL ldf_tra_init ! Lateral ocean tracer physics
457	CALL ldf_dyn_init ! Lateral ocean momentum physics
458	IF( lk_ldfslp ) CALL ldf_slp_init ! slope of lateral mixing
459
460	! ! Active tracers
461	CALL tra_qsr_init ! penetrative solar radiation qsr
462	CALL tra_bbc_init ! bottom heat flux
463	IF( lk_trabbl ) CALL tra_bbl_init ! advective (and/or diffusive) bottom boundary layer scheme
464	CALL tra_dmp_init ! internal damping trends- tracers
465	CALL tra_adv_init ! horizontal & vertical advection
466	CALL tra_ldf_init ! lateral mixing
467	CALL tra_zdf_init ! vertical mixing and after tracer fields
468
469	! ! Dynamics
470	IF( lk_c1d ) CALL dyn_dmp_init ! internal damping trends- momentum
471	CALL dyn_adv_init ! advection (vector or flux form)
472	CALL dyn_vor_init ! vorticity term including Coriolis
473	CALL dyn_ldf_init ! lateral mixing
474	CALL dyn_hpg_init ! horizontal gradient of Hydrostatic pressure
475	CALL dyn_zdf_init ! vertical diffusion
476	CALL dyn_spg_init ! surface pressure gradient
477
478	! ! Misc. options
479	IF( nn_cla == 1 .AND. cp_cfg == 'orca' .AND. jp_cfg == 2 ) CALL cla_init ! Cross Land Advection
480	CALL icb_init( rdt, nit000) ! initialise icebergs instance
481	CALL sto_par_init ! Stochastic parametrization
482	IF( ln_sto_eos ) CALL sto_pts_init ! RRandom T/S fluctuations
483
484	#if defined key_top
485	! ! Passive tracers
486	CALL trc_init
487	#endif
488	! ! Diagnostics
489	IF( lk_floats ) CALL flo_init ! drifting Floats
490	IF( lk_diaar5 ) CALL dia_ar5_init ! ar5 diag
491	CALL dia_ptr_init ! Poleward TRansports initialization
492	IF( lk_diadct ) CALL dia_dct_init ! Sections tranports
493	CALL dia_hsb_init ! heat content, salt content and volume budgets
494	CALL trd_init ! Mixed-layer/Vorticity/Integral constraints trends
495	IF( lk_diaobs ) THEN ! Observation & model comparison
496	CALL dia_obs_init ! Initialize observational data
497	CALL dia_obs( nit000 - 1 ) ! Observation operator for restart
498	ENDIF
499
500	! ! Assimilation increments
501	IF( lk_asminc ) THEN
502	#if defined key_shelf
503	CALL zdf_mxl_tref() ! Initialization of hmld_tref
504	#endif
505	CALL asm_inc_init ! Initialize assimilation increments
506	ENDIF
507
508	IF(lwp) WRITE(numout,*) 'Euler time step switch is ', neuler
509	CALL dia_tmb_init ! TMB outputs
510	CALL dia_regmean_init ! TMB outputs
511	CALL dia_pea_init ! TMB outputs
512	CALL dia_25h_init ! 25h mean outputs
513	CALL dia_diaopfoam_init ! FOAM operational output
514	!
515	END SUBROUTINE nemo_init
516
517
518	SUBROUTINE nemo_ctl
519	!!----------------------------------------------------------------------
520	!! * ROUTINE nemo_ctl *
521	!!
522	!! ** Purpose : control print setting
523	!!
524	!! ** Method : - print namctl information and check some consistencies
525	!!----------------------------------------------------------------------
526	!
527	IF(lwp) THEN ! control print
528	WRITE(numout,*)
529	WRITE(numout,*) 'nemo_ctl: Control prints & Benchmark'
530	WRITE(numout,*) '~~~~~~~ '
531	WRITE(numout,*) ' Namelist namctl'
532	WRITE(numout,*) ' run control (for debugging) ln_ctl = ', ln_ctl
533	WRITE(numout,*) ' level of print nn_print = ', nn_print
534	WRITE(numout,*) ' Start i indice for SUM control nn_ictls = ', nn_ictls
535	WRITE(numout,*) ' End i indice for SUM control nn_ictle = ', nn_ictle
536	WRITE(numout,*) ' Start j indice for SUM control nn_jctls = ', nn_jctls
537	WRITE(numout,*) ' End j indice for SUM control nn_jctle = ', nn_jctle
538	WRITE(numout,*) ' number of proc. following i nn_isplt = ', nn_isplt
539	WRITE(numout,*) ' number of proc. following j nn_jsplt = ', nn_jsplt
540	WRITE(numout,*) ' benchmark parameter (0/1) nn_bench = ', nn_bench
541	WRITE(numout,*) ' timing activated (0/1) nn_timing = ', nn_timing
542	ENDIF
543	!
544	nprint = nn_print ! convert DOCTOR namelist names into OLD names
545	nictls = nn_ictls
546	nictle = nn_ictle
547	njctls = nn_jctls
548	njctle = nn_jctle
549	isplt = nn_isplt
550	jsplt = nn_jsplt
551	nbench = nn_bench
552
553	IF(lwp) THEN ! control print
554	WRITE(numout,*)
555	WRITE(numout,*) 'namcfg : configuration initialization through namelist read'
556	WRITE(numout,*) '~~~~~~~ '
557	WRITE(numout,*) ' Namelist namcfg'
558	WRITE(numout,*) ' configuration name cp_cfg = ', TRIM(cp_cfg)
559	WRITE(numout,*) ' configuration zoom name cp_cfz = ', TRIM(cp_cfz)
560	WRITE(numout,*) ' configuration resolution jp_cfg = ', jp_cfg
561	WRITE(numout,*) ' 1st lateral dimension ( >= jpi ) jpidta = ', jpidta
562	WRITE(numout,*) ' 2nd " " ( >= jpj ) jpjdta = ', jpjdta
563	WRITE(numout,*) ' 3nd " " jpkdta = ', jpkdta
564	WRITE(numout,*) ' 1st dimension of global domain in i jpiglo = ', jpiglo
565	WRITE(numout,*) ' 2nd - - in j jpjglo = ', jpjglo
566	WRITE(numout,*) ' left bottom i index of the zoom (in data domain) jpizoom = ', jpizoom
567	WRITE(numout,*) ' left bottom j index of the zoom (in data domain) jpizoom = ', jpjzoom
568	WRITE(numout,*) ' lateral cond. type (between 0 and 6) jperio = ', jperio
569	WRITE(numout,*) ' use file attribute if exists as i/p j-start ln_use_jattr = ', ln_use_jattr
570	ENDIF
571	! ! Parameter control
572	!
573	IF( ln_ctl ) THEN ! sub-domain area indices for the control prints
574	IF( lk_mpp .AND. jpnij > 1 ) THEN
575	isplt = jpni ; jsplt = jpnj ; ijsplt = jpni*jpnj ! the domain is forced to the real split domain
576	ELSE
577	IF( isplt == 1 .AND. jsplt == 1 ) THEN
578	CALL ctl_warn( ' - isplt & jsplt are equal to 1', &
579	& ' - the print control will be done over the whole domain' )
580	ENDIF
581	ijsplt = isplt * jsplt ! total number of processors ijsplt
582	ENDIF
583	IF(lwp) WRITE(numout,*)' - The total number of processors over which the'
584	IF(lwp) WRITE(numout,*)' print control will be done is ijsplt : ', ijsplt
585	!
586	! ! indices used for the SUM control
587	IF( nictls+nictle+njctls+njctle == 0 ) THEN ! print control done over the default area
588	lsp_area = .FALSE.
589	ELSE ! print control done over a specific area
590	lsp_area = .TRUE.
591	IF( nictls < 1 .OR. nictls > jpiglo ) THEN
592	CALL ctl_warn( ' - nictls must be 1<=nictls>=jpiglo, it is forced to 1' )
593	nictls = 1
594	ENDIF
595	IF( nictle < 1 .OR. nictle > jpiglo ) THEN
596	CALL ctl_warn( ' - nictle must be 1<=nictle>=jpiglo, it is forced to jpiglo' )
597	nictle = jpiglo
598	ENDIF
599	IF( njctls < 1 .OR. njctls > jpjglo ) THEN
600	CALL ctl_warn( ' - njctls must be 1<=njctls>=jpjglo, it is forced to 1' )
601	njctls = 1
602	ENDIF
603	IF( njctle < 1 .OR. njctle > jpjglo ) THEN
604	CALL ctl_warn( ' - njctle must be 1<=njctle>=jpjglo, it is forced to jpjglo' )
605	njctle = jpjglo
606	ENDIF
607	ENDIF
608	ENDIF
609	!
610	IF( nbench == 1 ) THEN ! Benchmark
611	SELECT CASE ( cp_cfg )
612	CASE ( 'gyre' ) ; CALL ctl_warn( ' The Benchmark is activated ' )
613	CASE DEFAULT ; CALL ctl_stop( ' The Benchmark is based on the GYRE configuration:', &
614	& ' cp_cfg = "gyre" in namelist &namcfg or set nbench = 0' )
615	END SELECT
616	ENDIF
617	!
618	IF( 1_wp /= SIGN(1._wp,-0._wp) ) CALL ctl_stop( 'nemo_ctl: The intrinsec SIGN function follows ', &
619	& 'f2003 standard. ' , &
620	& 'Compile with key_nosignedzero enabled' )
621	!
622	END SUBROUTINE nemo_ctl
623
624
625	SUBROUTINE nemo_closefile
626	!!----------------------------------------------------------------------
627	!! * ROUTINE nemo_closefile *
628	!!
629	!! ** Purpose : Close the files
630	!!----------------------------------------------------------------------
631	!
632	IF( lk_mpp ) CALL mppsync
633	!
634	CALL iom_close ! close all input/output files managed by iom_*
635	!
636	IF( numstp /= -1 ) CLOSE( numstp ) ! time-step file
637	IF( numsol /= -1 ) CLOSE( numsol ) ! solver file
638	IF( numnam_ref /= -1 ) CLOSE( numnam_ref ) ! oce reference namelist
639	IF( numnam_cfg /= -1 ) CLOSE( numnam_cfg ) ! oce configuration namelist
640	IF( lwm.AND.numond /= -1 ) CLOSE( numond ) ! oce output namelist
641	IF( numnam_ice_ref /= -1 ) CLOSE( numnam_ice_ref ) ! ice reference namelist
642	IF( numnam_ice_cfg /= -1 ) CLOSE( numnam_ice_cfg ) ! ice configuration namelist
643	IF( lwm.AND.numoni /= -1 ) CLOSE( numoni ) ! ice output namelist
644	IF( numevo_ice /= -1 ) CLOSE( numevo_ice ) ! ice variables (temp. evolution)
645	IF( numout /= 6 ) CLOSE( numout ) ! standard model output file
646	IF( numdct_vol /= -1 ) CLOSE( numdct_vol ) ! volume transports
647	IF( numdct_heat /= -1 ) CLOSE( numdct_heat ) ! heat transports
648	IF( numdct_salt /= -1 ) CLOSE( numdct_salt ) ! salt transports
649	IF( numdct_NOOS /= -1 ) CLOSE( numdct_NOOS ) ! NOOS transports
650	IF( numdct_NOOS_h /= -1 ) CLOSE( numdct_NOOS_h ) ! NOOS transports
651	IF( numdct_in /= -1 ) CLOSE( numdct_in ) ! NOOS transports
652
653	!
654	numout = 6 ! redefine numout in case it is used after this point...
655	!
656	END SUBROUTINE nemo_closefile
657
658
659	SUBROUTINE nemo_alloc
660	!!----------------------------------------------------------------------
661	!! * ROUTINE nemo_alloc *
662	!!
663	!! ** Purpose : Allocate all the dynamic arrays of the OPA modules
664	!!
665	!! ** Method :
666	!!----------------------------------------------------------------------
667	USE diawri , ONLY: dia_wri_alloc
668	USE dom_oce , ONLY: dom_oce_alloc
669	USE ldfdyn_oce, ONLY: ldfdyn_oce_alloc
670	USE ldftra_oce, ONLY: ldftra_oce_alloc
671	USE trc_oce , ONLY: trc_oce_alloc
672	USE diainsitutem, ONLY: insitu_tem_alloc
673	#if defined key_diadct
674	USE diadct , ONLY: diadct_alloc
675	#endif
676	#if defined key_bdy
677	USE bdy_oce , ONLY: bdy_oce_alloc
678	#endif
679	!
680	INTEGER :: ierr
681	!!----------------------------------------------------------------------
682	!
683	ierr = oce_alloc () ! ocean
684	ierr = ierr + dia_wri_alloc ()
685	ierr = ierr + dom_oce_alloc () ! ocean domain
686	ierr = ierr + ldfdyn_oce_alloc() ! ocean lateral physics : dynamics
687	ierr = ierr + ldftra_oce_alloc() ! ocean lateral physics : tracers
688	ierr = ierr + zdf_oce_alloc () ! ocean vertical physics
689	ierr = ierr + insitu_tem_alloc()
690	!
691	ierr = ierr + trc_oce_alloc () ! shared TRC / TRA arrays
692	!
693	#if defined key_diadct
694	ierr = ierr + diadct_alloc () !
695	#endif
696	#if defined key_bdy
697	ierr = ierr + bdy_oce_alloc () ! bdy masks (incl. initialization)
698	#endif
699	!
700	IF( lk_mpp ) CALL mpp_sum( ierr )
701	IF( ierr /= 0 ) CALL ctl_stop( 'STOP', 'nemo_alloc : unable to allocate standard ocean arrays' )
702	!
703	END SUBROUTINE nemo_alloc
704
705
706	SUBROUTINE nemo_partition( num_pes )
707	!!----------------------------------------------------------------------
708	!! * ROUTINE nemo_partition *
709	!!
710	!! ** Purpose :
711	!!
712	!! ** Method :
713	!!----------------------------------------------------------------------
714	INTEGER, INTENT(in) :: num_pes ! The number of MPI processes we have
715	!
716	INTEGER, PARAMETER :: nfactmax = 20
717	INTEGER :: nfact ! The no. of factors returned
718	INTEGER :: ierr ! Error flag
719	INTEGER :: ji
720	INTEGER :: idiff, mindiff, imin ! For choosing pair of factors that are closest in value
721	INTEGER, DIMENSION(nfactmax) :: ifact ! Array of factors
722	!!----------------------------------------------------------------------
723	!
724	ierr = 0
725	!
726	CALL factorise( ifact, nfactmax, nfact, num_pes, ierr )
727	!
728	IF( nfact <= 1 ) THEN
729	WRITE (numout, *) 'WARNING: factorisation of number of PEs failed'
730	WRITE (numout, *) ' : using grid of ',num_pes,' x 1'
731	jpnj = 1
732	jpni = num_pes
733	ELSE
734	! Search through factors for the pair that are closest in value
735	mindiff = 1000000
736	imin = 1
737	DO ji = 1, nfact-1, 2
738	idiff = ABS( ifact(ji) - ifact(ji+1) )
739	IF( idiff < mindiff ) THEN
740	mindiff = idiff
741	imin = ji
742	ENDIF
743	END DO
744	jpnj = ifact(imin)
745	jpni = ifact(imin + 1)
746	ENDIF
747	!
748	jpnij = jpni*jpnj
749	!
750	END SUBROUTINE nemo_partition
751
752
753	SUBROUTINE factorise( kfax, kmaxfax, knfax, kn, kerr )
754	!!----------------------------------------------------------------------
755	!! * ROUTINE factorise *
756	!!
757	!! ** Purpose : return the prime factors of n.
758	!! knfax factors are returned in array kfax which is of
759	!! maximum dimension kmaxfax.
760	!! ** Method :
761	!!----------------------------------------------------------------------
762	INTEGER , INTENT(in ) :: kn, kmaxfax
763	INTEGER , INTENT( out) :: kerr, knfax
764	INTEGER, DIMENSION(kmaxfax), INTENT( out) :: kfax
765	!
766	INTEGER :: ifac, jl, inu
767	INTEGER, PARAMETER :: ntest = 14
768	INTEGER, DIMENSION(ntest) :: ilfax
769	!
770	! ilfax contains the set of allowed factors.
771	ilfax(:) = (/(2**jl,jl=ntest,1,-1)/)
772	!!----------------------------------------------------------------------
773	! ilfax contains the set of allowed factors.
774	ilfax(:) = (/(2**jl,jl=ntest,1,-1)/)
775
776	! Clear the error flag and initialise output vars
777	kerr = 0
778	kfax = 1
779	knfax = 0
780
781	! Find the factors of n.
782	IF( kn == 1 ) GOTO 20
783
784	! nu holds the unfactorised part of the number.
785	! knfax holds the number of factors found.
786	! l points to the allowed factor list.
787	! ifac holds the current factor.
788
789	inu = kn
790	knfax = 0
791
792	DO jl = ntest, 1, -1
793	!
794	ifac = ilfax(jl)
795	IF( ifac > inu ) CYCLE
796
797	! Test whether the factor will divide.
798
799	IF( MOD(inu,ifac) == 0 ) THEN
800	!
801	knfax = knfax + 1 ! Add the factor to the list
802	IF( knfax > kmaxfax ) THEN
803	kerr = 6
804	write (,) 'FACTOR: insufficient space in factor array ', knfax
805	return
806	ENDIF
807	kfax(knfax) = ifac
808	! Store the other factor that goes with this one
809	knfax = knfax + 1
810	kfax(knfax) = inu / ifac
811	!WRITE (,) 'ARPDBG, factors ',knfax-1,' & ',knfax,' are ', kfax(knfax-1),' and ',kfax(knfax)
812	ENDIF
813	!
814	END DO
815
816	20 CONTINUE ! Label 20 is the exit point from the factor search loop.
817	!
818	END SUBROUTINE factorise
819
820	#if defined key_mpp_mpi
821
822	SUBROUTINE nemo_northcomms
823	!!======================================================================
824	!! * ROUTINE nemo_northcomms *
825	!! nemo_northcomms : Setup for north fold exchanges with explicit
826	!! point-to-point messaging
827	!!=====================================================================
828	!!----------------------------------------------------------------------
829	!!
830	!! ** Purpose : Initialization of the northern neighbours lists.
831	!!----------------------------------------------------------------------
832	!! 1.0 ! 2011-10 (A. C. Coward, NOCS & J. Donners, PRACE)
833	!! 2.0 ! 2013-06 Setup avoiding MPI communication (I. Epicoco, S. Mocavero, CMCC)
834	!!----------------------------------------------------------------------
835
836	INTEGER :: sxM, dxM, sxT, dxT, jn
837	INTEGER :: njmppmax
838
839	njmppmax = MAXVAL( njmppt )
840
841	!initializes the north-fold communication variables
842	isendto(:) = 0
843	nsndto = 0
844
845	!if I am a process in the north
846	IF ( njmpp == njmppmax ) THEN
847	!sxM is the first point (in the global domain) needed to compute the
848	!north-fold for the current process
849	sxM = jpiglo - nimppt(narea) - nlcit(narea) + 1
850	!dxM is the last point (in the global domain) needed to compute the
851	!north-fold for the current process
852	dxM = jpiglo - nimppt(narea) + 2
853
854	!loop over the other north-fold processes to find the processes
855	!managing the points belonging to the sxT-dxT range
856
857	DO jn = 1, jpni
858	!sxT is the first point (in the global domain) of the jn
859	!process
860	sxT = nfiimpp(jn, jpnj)
861	!dxT is the last point (in the global domain) of the jn
862	!process
863	dxT = nfiimpp(jn, jpnj) + nfilcit(jn, jpnj) - 1
864	IF ((sxM .gt. sxT) .AND. (sxM .lt. dxT)) THEN
865	nsndto = nsndto + 1
866	isendto(nsndto) = jn
867	ELSEIF ((sxM .le. sxT) .AND. (dxM .ge. dxT)) THEN
868	nsndto = nsndto + 1
869	isendto(nsndto) = jn
870	ELSEIF ((dxM .lt. dxT) .AND. (sxT .lt. dxM)) THEN
871	nsndto = nsndto + 1
872	isendto(nsndto) = jn
873	END IF
874	END DO
875	nfsloop = 1
876	nfeloop = nlci
877	DO jn = 2,jpni-1
878	IF(nfipproc(jn,jpnj) .eq. (narea - 1)) THEN
879	IF (nfipproc(jn - 1 ,jpnj) .eq. -1) THEN
880	nfsloop = nldi
881	ENDIF
882	IF (nfipproc(jn + 1,jpnj) .eq. -1) THEN
883	nfeloop = nlei
884	ENDIF
885	ENDIF
886	END DO
887
888	ENDIF
889	l_north_nogather = .TRUE.
890	END SUBROUTINE nemo_northcomms
891	#else
892	SUBROUTINE nemo_northcomms ! Dummy routine
893	WRITE(,) 'nemo_northcomms: You should not have seen this print! error?'
894	END SUBROUTINE nemo_northcomms
895	#endif
896
897	!!======================================================================
898	END MODULE nemogcm
899
900

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