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nemogcm.F90 @ 9015

Last change on this file since 9015 was 9015, checked in by acc, 7 years ago
Branch dev_CNRS_2017. Tidy up timing calls. Correct a few inconsistent labels and fix incorrect call in trc_sub_stp. Remove timing from icethd_pnd which is not always called by all processors
Property svn:keywords set to `Id`
File size: 40.6 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 ! 2011-10 (A. C. Coward, NOCS & J. Donners, PRACE) add nemo_northcomms
31	!! - ! 2011-11 (C. Harris) decomposition changes for running with CICE
32	!! 3.6 ! 2012-05 (C. Calone, J. Simeon, G. Madec, C. Ethe) Add grid coarsening
33	!! - ! 2013-06 (I. Epicoco, S. Mocavero, CMCC) nemo_northcomms: setup avoiding MPI communication
34	!! - ! 2014-12 (G. Madec) remove KPP scheme and cross-land advection (cla)
35	!! 4.0 ! 2016-10 (G. Madec, S. Flavoni) domain configuration / user defined interface
36	!!----------------------------------------------------------------------
37
38	!!----------------------------------------------------------------------
39	!! nemo_gcm : solve ocean dynamics, tracer, biogeochemistry and/or sea-ice
40	!! nemo_init : initialization of the NEMO system
41	!! nemo_ctl : initialisation of the contol print
42	!! nemo_closefile: close remaining open files
43	!! nemo_alloc : dynamical allocation
44	!! nemo_partition: calculate MPP domain decomposition
45	!! factorise : calculate the factors of the no. of MPI processes
46	!!----------------------------------------------------------------------
47	USE step_oce ! module used in the ocean time stepping module (step.F90)
48	USE phycst ! physical constant (par_cst routine)
49	USE domain ! domain initialization (dom_init & dom_cfg routines)
50	USE usrdef_nam ! user defined configuration
51	USE tideini ! tidal components initialization (tide_ini routine)
52	USE bdy_oce, ONLY : ln_bdy
53	USE bdyini ! open boundary cond. setting (bdy_init routine)
54	USE istate ! initial state setting (istate_init routine)
55	USE ldfdyn ! lateral viscosity setting (ldfdyn_init routine)
56	USE ldftra ! lateral diffusivity setting (ldftra_init routine)
57	USE trdini ! dyn/tra trends initialization (trd_init routine)
58	USE asminc ! assimilation increments
59	USE asmbkg ! writing out state trajectory
60	USE diaptr ! poleward transports (dia_ptr_init routine)
61	USE diadct ! sections transports (dia_dct_init routine)
62	USE diaobs ! Observation diagnostics (dia_obs_init routine)
63	USE diacfl ! CFL diagnostics (dia_cfl_init routine)
64	USE step ! NEMO time-stepping (stp routine)
65	USE icbini ! handle bergs, initialisation
66	USE icbstp ! handle bergs, calving, themodynamics and transport
67	USE cpl_oasis3 ! OASIS3 coupling
68	USE c1d ! 1D configuration
69	USE step_c1d ! Time stepping loop for the 1D configuration
70	USE dyndmp ! Momentum damping
71	USE stopar ! Stochastic param.: ???
72	USE stopts ! Stochastic param.: ???
73	USE diurnal_bulk ! diurnal bulk SST
74	USE step_diu ! diurnal bulk SST timestepping (called from here if run offline)
75	USE crsini ! initialise grid coarsening utility
76	USE diatmb ! Top,middle,bottom output
77	USE dia25h ! 25h mean output
78	USE sbc_oce , ONLY : lk_oasis
79	USE wet_dry ! Wetting and drying setting (wad_init routine)
80	#if defined key_top
81	USE trcini ! passive tracer initialisation
82	#endif
83	#if defined key_nemocice_decomp
84	USE ice_domain_size, only: nx_global, ny_global
85	#endif
86	!
87	USE lib_mpp ! distributed memory computing
88	USE mppini ! shared/distributed memory setting (mpp_init routine)
89	USE lbcnfd , ONLY : isendto, nsndto, nfsloop, nfeloop ! Setup of north fold exchanges
90	USE lib_fortran ! Fortran utilities (allows no signed zero when 'key_nosignedzero' defined)
91	#if defined key_iomput
92	USE xios ! xIOserver
93	#endif
94
95	IMPLICIT NONE
96	PRIVATE
97
98	PUBLIC nemo_gcm ! called by model.F90
99	PUBLIC nemo_init ! needed by AGRIF
100	PUBLIC nemo_alloc ! needed by TAM
101
102	CHARACTER(lc) :: cform_aaa="( /, 'AAAAAAAA', / ) " ! flag for output listing
103
104	!!----------------------------------------------------------------------
105	!! NEMO/OPA 3.7 , NEMO Consortium (2016)
106	!! $Id$
107	!! Software governed by the CeCILL licence (NEMOGCM/NEMO_CeCILL.txt)
108	!!----------------------------------------------------------------------
109	CONTAINS
110
111	SUBROUTINE nemo_gcm
112	!!----------------------------------------------------------------------
113	!! * ROUTINE nemo_gcm *
114	!!
115	!! ** Purpose : NEMO solves the primitive equations on an orthogonal
116	!! curvilinear mesh on the sphere.
117	!!
118	!! ** Method : - model general initialization
119	!! - launch the time-stepping (stp routine)
120	!! - finalize the run by closing files and communications
121	!!
122	!! References : Madec, Delecluse, Imbard, and Levy, 1997: internal report, IPSL.
123	!! Madec, 2008, internal report, IPSL.
124	!!----------------------------------------------------------------------
125	INTEGER :: istp ! time step index
126	!!----------------------------------------------------------------------
127	!
128	#if defined key_agrif
129	CALL Agrif_Init_Grids() ! AGRIF: set the meshes
130	#endif
131	!
132	! !-----------------------!
133	CALL nemo_init !== Initialisations ==!
134	! !-----------------------!
135	#if defined key_agrif
136	CALL Agrif_Declare_Var_dom ! AGRIF: set the meshes for DOM
137	CALL Agrif_Declare_Var ! " " " " " DYN/TRA
138	# if defined key_top
139	CALL Agrif_Declare_Var_top ! " " " " " TOP
140	# endif
141	# if defined key_lim3
142	CALL Agrif_Declare_Var_lim3 ! " " " " " LIM3
143	# endif
144	#endif
145	! check that all process are still there... If some process have an error,
146	! they will never enter in step and other processes will wait until the end of the cpu time!
147	IF( lk_mpp ) CALL mpp_max( nstop )
148
149	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
150
151	! !-----------------------!
152	! !== time stepping ==!
153	! !-----------------------!
154	istp = nit000
155	#if defined key_c1d
156	DO WHILE ( istp <= nitend .AND. nstop == 0 )
157	CALL stp_c1d( istp )
158	istp = istp + 1
159	END DO
160	#else
161	IF( lk_asminc ) THEN
162	IF( ln_bkgwri ) CALL asm_bkg_wri( nit000 - 1 ) ! Output background fields
163	IF( ln_asmdin ) THEN ! Direct initialization
164	IF( ln_trainc ) CALL tra_asm_inc( nit000 - 1 ) ! Tracers
165	IF( ln_dyninc ) CALL dyn_asm_inc( nit000 - 1 ) ! Dynamics
166	IF( ln_sshinc ) CALL ssh_asm_inc( nit000 - 1 ) ! SSH
167	ENDIF
168	ENDIF
169
170	#if defined key_agrif
171	CALL Agrif_Regrid()
172	#endif
173
174	DO WHILE ( istp <= nitend .AND. nstop == 0 )
175	#if defined key_agrif
176	CALL stp ! AGRIF: time stepping
177	#else
178	IF ( .NOT. ln_diurnal_only ) THEN
179	CALL stp( istp ) ! standard time stepping
180	ELSE
181	CALL stp_diurnal( istp ) ! time step only the diurnal SST
182	ENDIF
183	#endif
184	istp = istp + 1
185	IF( lk_mpp ) CALL mpp_max( nstop )
186	END DO
187	#endif
188
189	IF( ln_diaobs ) CALL dia_obs_wri
190	!
191	IF( ln_icebergs ) CALL icb_end( nitend )
192
193	! !------------------------!
194	! !== finalize the run ==!
195	! !------------------------!
196	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
197	!
198	IF( nstop /= 0 .AND. lwp ) THEN ! error print
199	WRITE(numout,cform_err)
200	WRITE(numout,*) nstop, ' error have been found'
201	ENDIF
202	!
203	#if defined key_agrif
204	IF( .NOT. Agrif_Root() ) THEN
205	CALL Agrif_ParentGrid_To_ChildGrid()
206	IF( ln_diaobs ) CALL dia_obs_wri
207	IF( nn_timing == 1 ) CALL timing_finalize
208	CALL Agrif_ChildGrid_To_ParentGrid()
209	ENDIF
210	#endif
211	IF( ln_timing ) CALL timing_finalize
212	!
213	CALL nemo_closefile
214	!
215	#if defined key_iomput
216	CALL xios_finalize ! end mpp communications with xios
217	IF( lk_oasis ) CALL cpl_finalize ! end coupling and mpp communications with OASIS
218	#else
219	IF( lk_oasis ) THEN
220	CALL cpl_finalize ! end coupling and mpp communications with OASIS
221	ELSE
222	IF( lk_mpp ) CALL mppstop ! end mpp communications
223	ENDIF
224	#endif
225	!
226	END SUBROUTINE nemo_gcm
227
228
229	SUBROUTINE nemo_init
230	!!----------------------------------------------------------------------
231	!! * ROUTINE nemo_init *
232	!!
233	!! ** Purpose : initialization of the NEMO GCM
234	!!----------------------------------------------------------------------
235	INTEGER :: ji ! dummy loop indices
236	INTEGER :: ios, ilocal_comm ! local integer
237	INTEGER :: iiarea, ijarea ! local integers
238	INTEGER :: iirest, ijrest ! local integers
239	CHARACTER(len=120), DIMENSION(30) :: cltxt, cltxt2, clnam
240	!
241	NAMELIST/namctl/ ln_ctl , nn_print, nn_ictls, nn_ictle, &
242	& nn_isplt , nn_jsplt, nn_jctls, nn_jctle, &
243	& ln_timing, ln_diacfl
244	NAMELIST/namcfg/ ln_read_cfg, cn_domcfg, ln_write_cfg, cn_domcfg_out, ln_use_jattr
245	!!----------------------------------------------------------------------
246	!
247	cltxt = ''
248	cltxt2 = ''
249	clnam = ''
250	cxios_context = 'nemo'
251	!
252	! ! Open reference namelist and configuration namelist files
253	CALL ctl_opn( numnam_ref, 'namelist_ref', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
254	CALL ctl_opn( numnam_cfg, 'namelist_cfg', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
255	!
256	REWIND( numnam_ref ) ! Namelist namctl in reference namelist : Control prints
257	READ ( numnam_ref, namctl, IOSTAT = ios, ERR = 901 )
258	901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in reference namelist', .TRUE. )
259	!
260	REWIND( numnam_cfg ) ! Namelist namctl in confguration namelist
261	READ ( numnam_cfg, namctl, IOSTAT = ios, ERR = 902 )
262	902 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in configuration namelist', .TRUE. )
263	!
264	REWIND( numnam_ref ) ! Namelist namcfg in reference namelist : Control prints
265	READ ( numnam_ref, namcfg, IOSTAT = ios, ERR = 903 )
266	903 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in reference namelist', .TRUE. )
267
268	REWIND( numnam_cfg ) ! Namelist namcfg in confguration namelist : Control prints & Benchmark
269	READ ( numnam_cfg, namcfg, IOSTAT = ios, ERR = 904 )
270	904 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in configuration namelist', .TRUE. )
271
272	! !--------------------------!
273	! ! Set global domain size ! (control print return in cltxt2)
274	! !--------------------------!
275	IF( ln_read_cfg ) THEN ! Read sizes in domain configuration file
276	CALL domain_cfg ( cltxt2, cn_cfg, nn_cfg, jpiglo, jpjglo, jpkglo, jperio )
277	!
278	ELSE ! user-defined namelist
279	CALL usr_def_nam( cltxt2, clnam, cn_cfg, nn_cfg, jpiglo, jpjglo, jpkglo, jperio )
280	ENDIF
281	!
282	!
283	! !--------------------------------------------!
284	! ! set communicator & select the local node !
285	! ! NB: mynode also opens output.namelist.dyn !
286	! ! on unit number numond on first proc !
287	! !--------------------------------------------!
288	#if defined key_iomput
289	IF( Agrif_Root() ) THEN
290	IF( lk_oasis ) THEN
291	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
292	CALL xios_initialize( "not used" ,local_comm= ilocal_comm ) ! send nemo communicator to xios
293	ELSE
294	CALL xios_initialize( "for_xios_mpi_id",return_comm=ilocal_comm ) ! nemo local communicator given by xios
295	ENDIF
296	ENDIF
297	! Nodes selection (control print return in cltxt)
298	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop, ilocal_comm )
299	#else
300	IF( lk_oasis ) THEN
301	IF( Agrif_Root() ) THEN
302	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
303	ENDIF
304	! Nodes selection (control print return in cltxt)
305	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop, ilocal_comm )
306	ELSE
307	ilocal_comm = 0 ! Nodes selection (control print return in cltxt)
308	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop )
309	ENDIF
310	#endif
311
312	narea = narea + 1 ! mynode return the rank of proc (0 --> jpnij -1 )
313
314	lwm = (narea == 1) ! control of output namelists
315	lwp = (narea == 1) .OR. ln_ctl ! control of all listing output print
316
317	IF(lwm) THEN ! write merged namelists from earlier to output namelist
318	! ! now that the file has been opened in call to mynode.
319	! ! NB: nammpp has already been written in mynode (if lk_mpp_mpi)
320	WRITE( numond, namctl )
321	WRITE( numond, namcfg )
322	IF( .NOT.ln_read_cfg ) THEN
323	DO ji = 1, SIZE(clnam)
324	IF( TRIM(clnam(ji)) /= '' ) WRITE(numond, * ) clnam(ji) ! namusr_def print
325	END DO
326	ENDIF
327	ENDIF
328
329	! If dimensions of processor grid weren't specified in the namelist file
330	! then we calculate them here now that we have our communicator size
331	IF( jpni < 1 .OR. jpnj < 1 ) THEN
332	#if defined key_mpp_mpi
333	IF( Agrif_Root() ) CALL nemo_partition( mppsize )
334	#else
335	jpni = 1
336	jpnj = 1
337	jpnij = jpni*jpnj
338	#endif
339	ENDIF
340	!
341	#if defined key_agrif
342	IF( .NOT. Agrif_Root() ) THEN ! AGRIF children: specific setting (cf. agrif_user.F90)
343	jpiglo = nbcellsx + 2 + 2*nbghostcells
344	jpjglo = nbcellsy + 2 + 2*nbghostcells
345	jpi = ( jpiglo-2nn_hls + (jpni-1+0) ) / jpni + 2nn_hls
346	jpj = ( jpjglo-2nn_hls + (jpnj-1+0) ) / jpnj + 2nn_hls
347	jpimax = jpi
348	jpjmax = jpj
349	nperio = 0
350	jperio = 0
351	ln_use_jattr = .false.
352	ENDIF
353	#endif
354
355	IF( Agrif_Root() ) THEN ! AGRIF mother: specific setting from jpni and jpnj
356	iiarea = 1 + MOD( narea - 1 , jpni )
357	ijarea = 1 + ( narea - 1 ) / jpni
358	iirest = 1 + MOD( jpiglo - 2*nn_hls - 1 , jpni )
359	ijrest = 1 + MOD( jpjglo - 2*nn_hls - 1 , jpnj )
360	#if defined key_nemocice_decomp
361	jpi = ( nx_global+2-2nn_hls + (jpni-1) ) / jpni + 2nn_hls ! first dim.
362	jpj = ( ny_global+2-2nn_hls + (jpnj-1) ) / jpnj + 2nn_hls ! second dim.
363	jpimax = jpi
364	jpjmax = jpj
365	IF( iiarea == jpni ) jpi = jpiglo - (jpni - 1) * (jpi - 2*nn_hls)
366	IF( ijarea == jpnj ) jpj = jpjglo - (jpnj - 1) * (jpj - 2*nn_hls)
367	#else
368	jpi = ( jpiglo -2nn_hls + (jpni-1) ) / jpni + 2nn_hls ! first dim.
369	jpj = ( jpjglo -2nn_hls + (jpnj-1) ) / jpnj + 2nn_hls ! second dim.
370	jpimax = jpi
371	jpjmax = jpj
372	IF( iiarea > iirest ) jpi = jpi - 1
373	IF( ijarea > ijrest ) jpj = jpj - 1
374	#endif
375	ENDIF
376
377	jpk = jpkglo ! third dim
378
379	#if defined key_agrif
380	! simple trick to use same vertical grid as parent but different number of levels:
381	! Save maximum number of levels in jpkglo, then define all vertical grids with this number.
382	! Suppress once vertical online interpolation is ok
383	IF(.NOT.Agrif_Root()) jpkglo = Agrif_Parent( jpkglo )
384	#endif
385	jpim1 = jpi-1 ! inner domain indices
386	jpjm1 = jpj-1 ! " "
387	jpkm1 = MAX( 1, jpk-1 ) ! " "
388	jpij = jpi*jpj ! jpi x j
389
390	IF(lwp) THEN ! open listing units
391	!
392	CALL ctl_opn( numout, 'ocean.output', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE., narea )
393	!
394	WRITE(numout,*)
395	WRITE(numout,*) ' CNRS - NERC - Met OFFICE - MERCATOR-ocean - INGV - CMCC'
396	WRITE(numout,*) ' NEMO team'
397	WRITE(numout,*) ' Ocean General Circulation Model'
398	WRITE(numout,*) ' NEMO version 3.7 (2016) '
399	WRITE(numout,*)
400	WRITE(numout,*)
401	DO ji = 1, SIZE(cltxt)
402	IF( TRIM(cltxt (ji)) /= '' ) WRITE(numout,*) cltxt(ji) ! control print of mynode
403	END DO
404	WRITE(numout,*)
405	WRITE(numout,*)
406	DO ji = 1, SIZE(cltxt2)
407	IF( TRIM(cltxt2(ji)) /= '' ) WRITE(numout,*) cltxt2(ji) ! control print of domain size
408	END DO
409	!
410	WRITE(numout,cform_aaa) ! Flag AAAAAAA
411	!
412	ENDIF
413
414	! Now we know the dimensions of the grid and numout has been set: we can allocate arrays
415	CALL nemo_alloc()
416
417	! !-------------------------------!
418	! ! NEMO general initialization !
419	! !-------------------------------!
420
421	CALL nemo_ctl ! Control prints
422
423	! ! Domain decomposition
424	CALL mpp_init
425	IF( ln_nnogather ) CALL nemo_northcomms! northfold neighbour lists
426	!
427	IF( ln_timing ) CALL timing_init
428	!
429	! ! General initialization
430	CALL phy_cst ! Physical constants
431	CALL eos_init ! Equation of state
432	IF( lk_c1d ) CALL c1d_init ! 1D column configuration
433	CALL wad_init ! Wetting and drying options
434	CALL dom_init ! Domain
435	IF( ln_crs ) CALL crs_init ! coarsened grid: domain initialization
436	IF( ln_ctl ) CALL prt_ctl_init ! Print control
437
438	CALL diurnal_sst_bulk_init ! diurnal sst
439	IF ( ln_diurnal ) CALL diurnal_sst_coolskin_init ! cool skin
440
441	! IF ln_diurnal_only, then we only want a subset of the initialisation routines
442	IF( ln_diurnal_only ) THEN
443	CALL istate_init ! ocean initial state (Dynamics and tracers)
444	CALL sbc_init ! Forcings : surface module
445	CALL tra_qsr_init ! penetrative solar radiation qsr
446	IF( ln_diaobs ) THEN ! Observation & model comparison
447	CALL dia_obs_init ! Initialize observational data
448	CALL dia_obs( nit000 - 1 ) ! Observation operator for restart
449	ENDIF
450	! ! Assimilation increments
451	IF( lk_asminc ) CALL asm_inc_init ! Initialize assimilation increments
452
453	IF(lwp) WRITE(numout,*) 'Euler time step switch is ', neuler
454	RETURN
455	ENDIF
456
457	CALL istate_init ! ocean initial state (Dynamics and tracers)
458
459	! ! external forcing
460	CALL tide_init ! tidal harmonics
461	CALL sbc_init ! surface boundary conditions (including sea-ice)
462	CALL bdy_init ! Open boundaries initialisation
463
464	! ! Ocean physics
465	CALL zdf_phy_init ! Vertical physics
466
467	! ! Lateral physics
468	CALL ldf_tra_init ! Lateral ocean tracer physics
469	CALL ldf_eiv_init ! eddy induced velocity param.
470	CALL ldf_dyn_init ! Lateral ocean momentum physics
471
472	! ! Active tracers
473	IF( ln_traqsr ) CALL tra_qsr_init ! penetrative solar radiation qsr
474	CALL tra_bbc_init ! bottom heat flux
475	IF( ln_trabbl ) CALL tra_bbl_init ! advective (and/or diffusive) bottom boundary layer scheme
476	CALL tra_dmp_init ! internal tracer damping
477	CALL tra_adv_init ! horizontal & vertical advection
478	CALL tra_ldf_init ! lateral mixing
479
480	! ! Dynamics
481	IF( lk_c1d ) CALL dyn_dmp_init ! internal momentum damping
482	CALL dyn_adv_init ! advection (vector or flux form)
483	CALL dyn_vor_init ! vorticity term including Coriolis
484	CALL dyn_ldf_init ! lateral mixing
485	CALL dyn_hpg_init ! horizontal gradient of Hydrostatic pressure
486	CALL dyn_spg_init ! surface pressure gradient
487
488	#if defined key_top
489	! ! Passive tracers
490	CALL trc_init
491	#endif
492	IF( l_ldfslp ) CALL ldf_slp_init ! slope of lateral mixing
493
494	! ! Icebergs
495	CALL icb_init( rdt, nit000) ! initialise icebergs instance
496
497	! ! Misc. options
498	CALL sto_par_init ! Stochastic parametrization
499	IF( ln_sto_eos ) CALL sto_pts_init ! RRandom T/S fluctuations
500
501	! ! Diagnostics
502	IF( lk_floats ) CALL flo_init ! drifting Floats
503	IF( ln_diacfl ) CALL dia_cfl_init ! Initialise CFL diagnostics
504	CALL dia_ptr_init ! Poleward TRansports initialization
505	IF( lk_diadct ) CALL dia_dct_init ! Sections tranports
506	CALL dia_hsb_init ! heat content, salt content and volume budgets
507	CALL trd_init ! Mixed-layer/Vorticity/Integral constraints trends
508	CALL dia_obs_init ! Initialize observational data
509	IF( ln_diaobs ) CALL dia_obs( nit000 - 1 ) ! Observation operator for restart
510
511	! ! Assimilation increments
512	IF( lk_asminc ) CALL asm_inc_init ! Initialize assimilation increments
513	IF(lwp) WRITE(numout,*) 'Euler time step switch is ', neuler
514	CALL dia_tmb_init ! TMB outputs
515	CALL dia_25h_init ! 25h mean outputs
516	!
517	END SUBROUTINE nemo_init
518
519
520	SUBROUTINE nemo_ctl
521	!!----------------------------------------------------------------------
522	!! * ROUTINE nemo_ctl *
523	!!
524	!! ** Purpose : control print setting
525	!!
526	!! ** Method : - print namctl information and check some consistencies
527	!!----------------------------------------------------------------------
528	!
529	IF(lwp) THEN ! control print
530	WRITE(numout,*)
531	WRITE(numout,*) 'nemo_ctl: Control prints'
532	WRITE(numout,*) '~~~~~~~ '
533	WRITE(numout,*) ' Namelist namctl'
534	WRITE(numout,*) ' run control (for debugging) ln_ctl = ', ln_ctl
535	WRITE(numout,*) ' level of print nn_print = ', nn_print
536	WRITE(numout,*) ' Start i indice for SUM control nn_ictls = ', nn_ictls
537	WRITE(numout,*) ' End i indice for SUM control nn_ictle = ', nn_ictle
538	WRITE(numout,*) ' Start j indice for SUM control nn_jctls = ', nn_jctls
539	WRITE(numout,*) ' End j indice for SUM control nn_jctle = ', nn_jctle
540	WRITE(numout,*) ' number of proc. following i nn_isplt = ', nn_isplt
541	WRITE(numout,*) ' number of proc. following j nn_jsplt = ', nn_jsplt
542	WRITE(numout,*) ' timing by routine ln_timing = ', ln_timing
543	WRITE(numout,*) ' CFL diagnostics ln_diacfl = ', ln_diacfl
544	ENDIF
545	!
546	nprint = nn_print ! convert DOCTOR namelist names into OLD names
547	nictls = nn_ictls
548	nictle = nn_ictle
549	njctls = nn_jctls
550	njctle = nn_jctle
551	isplt = nn_isplt
552	jsplt = nn_jsplt
553	!!gm to be remove at the end of the 2017 merge party
554	if( ln_timing ) then ; nn_timing = 1
555	else ; nn_timing = 0
556	endif
557	!!gm end
558
559
560	IF(lwp) THEN ! control print
561	WRITE(numout,*)
562	WRITE(numout,*) 'namcfg : configuration initialization through namelist read'
563	WRITE(numout,*) '~~~~~~ '
564	WRITE(numout,*) ' Namelist namcfg'
565	WRITE(numout,*) ' read domain configuration file ln_read_cfg = ', ln_read_cfg
566	WRITE(numout,*) ' filename to be read cn_domcfg = ', TRIM(cn_domcfg)
567	WRITE(numout,*) ' write configuration definition file ln_write_cfg = ', ln_write_cfg
568	WRITE(numout,*) ' filename to be written cn_domcfg_out = ', TRIM(cn_domcfg_out)
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( 1_wp /= SIGN(1._wp,-0._wp) ) CALL ctl_stop( 'nemo_ctl: The intrinsec SIGN function follows ', &
611	& 'f2003 standard. ' , &
612	& 'Compile with key_nosignedzero enabled' )
613	!
614	END SUBROUTINE nemo_ctl
615
616
617	SUBROUTINE nemo_closefile
618	!!----------------------------------------------------------------------
619	!! * ROUTINE nemo_closefile *
620	!!
621	!! ** Purpose : Close the files
622	!!----------------------------------------------------------------------
623	!
624	IF( lk_mpp ) CALL mppsync
625	!
626	CALL iom_close ! close all input/output files managed by iom_*
627	!
628	IF( numstp /= -1 ) CLOSE( numstp ) ! time-step file
629	IF( numrun /= -1 ) CLOSE( numrun ) ! run statistics file
630	IF( numnam_ref /= -1 ) CLOSE( numnam_ref ) ! oce reference namelist
631	IF( numnam_cfg /= -1 ) CLOSE( numnam_cfg ) ! oce configuration namelist
632	IF( lwm.AND.numond /= -1 ) CLOSE( numond ) ! oce output namelist
633	IF( numnam_ice_ref /= -1 ) CLOSE( numnam_ice_ref ) ! ice reference namelist
634	IF( numnam_ice_cfg /= -1 ) CLOSE( numnam_ice_cfg ) ! ice configuration namelist
635	IF( lwm.AND.numoni /= -1 ) CLOSE( numoni ) ! ice output namelist
636	IF( numevo_ice /= -1 ) CLOSE( numevo_ice ) ! ice variables (temp. evolution)
637	IF( numout /= 6 ) CLOSE( numout ) ! standard model output file
638	IF( numdct_vol /= -1 ) CLOSE( numdct_vol ) ! volume transports
639	IF( numdct_heat /= -1 ) CLOSE( numdct_heat ) ! heat transports
640	IF( numdct_salt /= -1 ) CLOSE( numdct_salt ) ! salt transports
641	!
642	numout = 6 ! redefine numout in case it is used after this point...
643	!
644	END SUBROUTINE nemo_closefile
645
646
647	SUBROUTINE nemo_alloc
648	!!----------------------------------------------------------------------
649	!! * ROUTINE nemo_alloc *
650	!!
651	!! ** Purpose : Allocate all the dynamic arrays of the OPA modules
652	!!
653	!! ** Method :
654	!!----------------------------------------------------------------------
655	USE diawri , ONLY: dia_wri_alloc
656	USE dom_oce , ONLY: dom_oce_alloc
657	USE trc_oce , ONLY: trc_oce_alloc
658	#if defined key_diadct
659	USE diadct , ONLY: diadct_alloc
660	#endif
661	USE bdy_oce , ONLY: bdy_oce_alloc
662	!
663	INTEGER :: ierr
664	!!----------------------------------------------------------------------
665	!
666	ierr = oce_alloc () ! ocean
667	ierr = ierr + dia_wri_alloc ()
668	ierr = ierr + dom_oce_alloc () ! ocean domain
669	ierr = ierr + zdf_oce_alloc () ! ocean vertical physics
670	!
671	ierr = ierr + trc_oce_alloc () ! shared TRC / TRA arrays
672	!
673	#if defined key_diadct
674	ierr = ierr + diadct_alloc () !
675	#endif
676	ierr = ierr + bdy_oce_alloc () ! bdy masks (incl. initialization)
677	!
678	IF( lk_mpp ) CALL mpp_sum( ierr )
679	IF( ierr /= 0 ) CALL ctl_stop( 'STOP', 'nemo_alloc : unable to allocate standard ocean arrays' )
680	!
681	END SUBROUTINE nemo_alloc
682
683
684	SUBROUTINE nemo_partition( num_pes )
685	!!----------------------------------------------------------------------
686	!! * ROUTINE nemo_partition *
687	!!
688	!! ** Purpose :
689	!!
690	!! ** Method :
691	!!----------------------------------------------------------------------
692	INTEGER, INTENT(in) :: num_pes ! The number of MPI processes we have
693	!
694	INTEGER, PARAMETER :: nfactmax = 20
695	INTEGER :: nfact ! The no. of factors returned
696	INTEGER :: ierr ! Error flag
697	INTEGER :: ji
698	INTEGER :: idiff, mindiff, imin ! For choosing pair of factors that are closest in value
699	INTEGER, DIMENSION(nfactmax) :: ifact ! Array of factors
700	!!----------------------------------------------------------------------
701	!
702	ierr = 0
703	!
704	CALL factorise( ifact, nfactmax, nfact, num_pes, ierr )
705	!
706	IF( nfact <= 1 ) THEN
707	WRITE (numout, *) 'WARNING: factorisation of number of PEs failed'
708	WRITE (numout, *) ' : using grid of ',num_pes,' x 1'
709	jpnj = 1
710	jpni = num_pes
711	ELSE
712	! Search through factors for the pair that are closest in value
713	mindiff = 1000000
714	imin = 1
715	DO ji = 1, nfact-1, 2
716	idiff = ABS( ifact(ji) - ifact(ji+1) )
717	IF( idiff < mindiff ) THEN
718	mindiff = idiff
719	imin = ji
720	ENDIF
721	END DO
722	jpnj = ifact(imin)
723	jpni = ifact(imin + 1)
724	ENDIF
725	!
726	jpnij = jpni*jpnj
727	!
728	END SUBROUTINE nemo_partition
729
730
731	SUBROUTINE factorise( kfax, kmaxfax, knfax, kn, kerr )
732	!!----------------------------------------------------------------------
733	!! * ROUTINE factorise *
734	!!
735	!! ** Purpose : return the prime factors of n.
736	!! knfax factors are returned in array kfax which is of
737	!! maximum dimension kmaxfax.
738	!! ** Method :
739	!!----------------------------------------------------------------------
740	INTEGER , INTENT(in ) :: kn, kmaxfax
741	INTEGER , INTENT( out) :: kerr, knfax
742	INTEGER, DIMENSION(kmaxfax), INTENT( out) :: kfax
743	!
744	INTEGER :: ifac, jl, inu
745	INTEGER, PARAMETER :: ntest = 14
746	INTEGER, DIMENSION(ntest) :: ilfax
747	!!----------------------------------------------------------------------
748	!
749	! lfax contains the set of allowed factors.
750	ilfax(:) = (/(2**jl,jl=ntest,1,-1)/)
751	!
752	! Clear the error flag and initialise output vars
753	kerr = 0
754	kfax = 1
755	knfax = 0
756	!
757	! Find the factors of n.
758	IF( kn .NE. 1 ) THEN
759
760	! nu holds the unfactorised part of the number.
761	! knfax holds the number of factors found.
762	! l points to the allowed factor list.
763	! ifac holds the current factor.
764	!
765	inu = kn
766	knfax = 0
767	!
768	DO jl = ntest, 1, -1
769	!
770	ifac = ilfax(jl)
771	IF( ifac > inu ) CYCLE
772
773	! Test whether the factor will divide.
774
775	IF( MOD(inu,ifac) == 0 ) THEN
776	!
777	knfax = knfax + 1 ! Add the factor to the list
778	IF( knfax > kmaxfax ) THEN
779	kerr = 6
780	write (,) 'FACTOR: insufficient space in factor array ', knfax
781	return
782	ENDIF
783	kfax(knfax) = ifac
784	! Store the other factor that goes with this one
785	knfax = knfax + 1
786	kfax(knfax) = inu / ifac
787	!WRITE (,) 'ARPDBG, factors ',knfax-1,' & ',knfax,' are ', kfax(knfax-1),' and ',kfax(knfax)
788	ENDIF
789	!
790	END DO
791	!
792	ENDIF
793	!
794	END SUBROUTINE factorise
795
796	#if defined key_mpp_mpi
797
798	SUBROUTINE nemo_northcomms
799	!!----------------------------------------------------------------------
800	!! * ROUTINE nemo_northcomms *
801	!! ** Purpose : Setup for north fold exchanges with explicit
802	!! point-to-point messaging
803	!!
804	!! ** Method : Initialization of the northern neighbours lists.
805	!!----------------------------------------------------------------------
806	!! 1.0 ! 2011-10 (A. C. Coward, NOCS & J. Donners, PRACE)
807	!! 2.0 ! 2013-06 Setup avoiding MPI communication (I. Epicoco, S. Mocavero, CMCC)
808	!!----------------------------------------------------------------------
809	INTEGER :: sxM, dxM, sxT, dxT, jn
810	INTEGER :: njmppmax
811	!!----------------------------------------------------------------------
812	!
813	njmppmax = MAXVAL( njmppt )
814	!
815	!initializes the north-fold communication variables
816	isendto(:) = 0
817	nsndto = 0
818	!
819	!if I am a process in the north
820	IF ( njmpp == njmppmax ) THEN
821	!sxM is the first point (in the global domain) needed to compute the
822	!north-fold for the current process
823	sxM = jpiglo - nimppt(narea) - nlcit(narea) + 1
824	!dxM is the last point (in the global domain) needed to compute the
825	!north-fold for the current process
826	dxM = jpiglo - nimppt(narea) + 2
827
828	!loop over the other north-fold processes to find the processes
829	!managing the points belonging to the sxT-dxT range
830
831	DO jn = 1, jpni
832	!sxT is the first point (in the global domain) of the jn
833	!process
834	sxT = nfiimpp(jn, jpnj)
835	!dxT is the last point (in the global domain) of the jn
836	!process
837	dxT = nfiimpp(jn, jpnj) + nfilcit(jn, jpnj) - 1
838	IF ((sxM .gt. sxT) .AND. (sxM .lt. dxT)) THEN
839	nsndto = nsndto + 1
840	isendto(nsndto) = jn
841	ELSEIF ((sxM .le. sxT) .AND. (dxM .ge. dxT)) THEN
842	nsndto = nsndto + 1
843	isendto(nsndto) = jn
844	ELSEIF ((dxM .lt. dxT) .AND. (sxT .lt. dxM)) THEN
845	nsndto = nsndto + 1
846	isendto(nsndto) = jn
847	ENDIF
848	END DO
849	nfsloop = 1
850	nfeloop = nlci
851	DO jn = 2,jpni-1
852	IF(nfipproc(jn,jpnj) .eq. (narea - 1)) THEN
853	IF (nfipproc(jn - 1 ,jpnj) .eq. -1) THEN
854	nfsloop = nldi
855	ENDIF
856	IF (nfipproc(jn + 1,jpnj) .eq. -1) THEN
857	nfeloop = nlei
858	ENDIF
859	ENDIF
860	END DO
861
862	ENDIF
863	l_north_nogather = .TRUE.
864	END SUBROUTINE nemo_northcomms
865
866	#else
867	SUBROUTINE nemo_northcomms ! Dummy routine
868	WRITE(,) 'nemo_northcomms: You should not have seen this print! error?'
869	END SUBROUTINE nemo_northcomms
870	#endif
871
872	!!======================================================================
873	END MODULE nemogcm
874

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