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nemogcm.F90 @ 8738

Last change on this file since 8738 was 8738, checked in by dancopsey, 6 years ago
Merged in main ICEMODEL branch (branches/2017/dev_r8183_ICEMODEL) up to revision 8588
File size: 40.7 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 zdfini ! vertical physics setting (zdf_init routine)
58	USE trdini ! dyn/tra trends initialization (trd_init routine)
59	USE asminc ! assimilation increments
60	USE asmbkg ! writing out state trajectory
61	USE diaptr ! poleward transports (dia_ptr_init routine)
62	USE diadct ! sections transports (dia_dct_init routine)
63	USE diaobs ! Observation diagnostics (dia_obs_init routine)
64	USE diacfl ! CFL diagnostics (dia_cfl_init routine)
65	USE step ! NEMO time-stepping (stp routine)
66	USE icbini ! handle bergs, initialisation
67	USE icbstp ! handle bergs, calving, themodynamics and transport
68	USE cpl_oasis3 ! OASIS3 coupling
69	USE c1d ! 1D configuration
70	USE step_c1d ! Time stepping loop for the 1D configuration
71	USE dyndmp ! Momentum damping
72	USE stopar ! Stochastic param.: ???
73	USE stopts ! Stochastic param.: ???
74	USE diurnal_bulk ! diurnal bulk SST
75	USE step_diu ! diurnal bulk SST timestepping (called from here if run offline)
76	USE crsini ! initialise grid coarsening utility
77	USE diatmb ! Top,middle,bottom output
78	USE dia25h ! 25h mean output
79	USE sbc_oce , ONLY : lk_oasis
80	USE wet_dry ! Wetting and drying setting (wad_init routine)
81	#if defined key_top
82	USE trcini ! passive tracer initialisation
83	#endif
84	#if defined key_nemocice_decomp
85	USE ice_domain_size, only: nx_global, ny_global
86	#endif
87	!
88	USE lib_mpp ! distributed memory computing
89	USE mppini ! shared/distributed memory setting (mpp_init routine)
90	USE lbcnfd , ONLY : isendto, nsndto, nfsloop, nfeloop ! Setup of north fold exchanges
91	USE lib_fortran ! Fortran utilities (allows no signed zero when 'key_nosignedzero' defined)
92	#if defined key_iomput
93	USE xios ! xIOserver
94	#endif
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 3.7 , NEMO Consortium (2016)
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_lim3
143	CALL Agrif_Declare_Var_lim3 ! " " " " " LIM3
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	ENDIF
169	ENDIF
170
171	#if defined key_agrif
172	CALL Agrif_Regrid()
173	#endif
174
175	DO WHILE ( istp <= nitend .AND. nstop == 0 )
176	#if defined key_agrif
177	CALL stp ! AGRIF: time stepping
178	#else
179	IF ( .NOT. ln_diurnal_only ) THEN
180	CALL stp( istp ) ! standard time stepping
181	ELSE
182	CALL stp_diurnal( istp ) ! time step only the diurnal SST
183	ENDIF
184	#endif
185	istp = istp + 1
186	IF( lk_mpp ) CALL mpp_max( nstop )
187	END DO
188	#endif
189
190	IF( ln_diaobs ) CALL dia_obs_wri
191	!
192	IF( ln_icebergs ) CALL icb_end( nitend )
193
194	! !------------------------!
195	! !== finalize the run ==!
196	! !------------------------!
197	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
198	!
199	IF( nstop /= 0 .AND. lwp ) THEN ! error print
200	WRITE(numout,cform_err)
201	WRITE(numout,*) nstop, ' error have been found'
202	ENDIF
203	!
204	#if defined key_agrif
205	IF( .NOT. Agrif_Root() ) THEN
206	CALL Agrif_ParentGrid_To_ChildGrid()
207	IF( ln_diaobs ) CALL dia_obs_wri
208	IF( nn_timing == 1 ) CALL timing_finalize
209	CALL Agrif_ChildGrid_To_ParentGrid()
210	ENDIF
211	#endif
212	IF( nn_timing == 1 ) CALL timing_finalize
213	!
214	CALL nemo_closefile
215	!
216	#if defined key_iomput
217	CALL xios_finalize ! end mpp communications with xios
218	IF( lk_oasis ) CALL cpl_finalize ! end coupling and mpp communications with OASIS
219	#else
220	IF( lk_oasis ) THEN
221	CALL cpl_finalize ! end coupling and mpp communications with OASIS
222	ELSE
223	IF( lk_mpp ) CALL mppstop ! end mpp communications
224	ENDIF
225	#endif
226	!
227	END SUBROUTINE nemo_gcm
228
229
230	SUBROUTINE nemo_init
231	!!----------------------------------------------------------------------
232	!! * ROUTINE nemo_init *
233	!!
234	!! ** Purpose : initialization of the NEMO GCM
235	!!----------------------------------------------------------------------
236	INTEGER :: ji ! dummy loop indices
237	INTEGER :: ios, ilocal_comm ! local integer
238	CHARACTER(len=120), DIMENSION(30) :: cltxt, cltxt2, clnam
239	!
240	NAMELIST/namctl/ ln_ctl , nn_print, nn_ictls, nn_ictle, &
241	& nn_isplt , nn_jsplt, nn_jctls, nn_jctle, &
242	& nn_timing, nn_diacfl
243	NAMELIST/namcfg/ ln_read_cfg, cn_domcfg, ln_write_cfg, cn_domcfg_out, ln_use_jattr
244	!!----------------------------------------------------------------------
245	!
246	cltxt = ''
247	cltxt2 = ''
248	clnam = ''
249	cxios_context = 'nemo'
250	!
251	! ! Open reference namelist and configuration namelist files
252	CALL ctl_opn( numnam_ref, 'namelist_ref', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
253	CALL ctl_opn( numnam_cfg, 'namelist_cfg', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
254	!
255	REWIND( numnam_ref ) ! Namelist namctl in reference namelist : Control prints
256	READ ( numnam_ref, namctl, IOSTAT = ios, ERR = 901 )
257	901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in reference namelist', .TRUE. )
258	!
259	REWIND( numnam_cfg ) ! Namelist namctl in confguration namelist
260	READ ( numnam_cfg, namctl, IOSTAT = ios, ERR = 902 )
261	902 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in configuration namelist', .TRUE. )
262	!
263	REWIND( numnam_ref ) ! Namelist namcfg in reference namelist : Control prints
264	READ ( numnam_ref, namcfg, IOSTAT = ios, ERR = 903 )
265	903 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in reference namelist', .TRUE. )
266
267	REWIND( numnam_cfg ) ! Namelist namcfg in confguration namelist : Control prints & Benchmark
268	READ ( numnam_cfg, namcfg, IOSTAT = ios, ERR = 904 )
269	904 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in configuration namelist', .TRUE. )
270
271	! !--------------------------!
272	! ! Set global domain size ! (control print return in cltxt2)
273	! !--------------------------!
274	IF( ln_read_cfg ) THEN ! Read sizes in domain configuration file
275	CALL domain_cfg ( cltxt2, cn_cfg, nn_cfg, jpiglo, jpjglo, jpkglo, jperio )
276	!
277	ELSE ! user-defined namelist
278	CALL usr_def_nam( cltxt2, clnam, cn_cfg, nn_cfg, jpiglo, jpjglo, jpkglo, jperio )
279	ENDIF
280	!
281	jpk = jpkglo
282	!
283	#if defined key_agrif
284	IF( .NOT. Agrif_Root() ) THEN ! AGRIF children: specific setting (cf. agrif_user.F90)
285	jpiglo = nbcellsx + 2 + 2*nbghostcells
286	jpjglo = nbcellsy + 2 + 2*nbghostcells
287	jpi = ( jpiglo-2jpreci + (jpni-1+0) ) / jpni + 2jpreci
288	jpj = ( jpjglo-2jprecj + (jpnj-1+0) ) / jpnj + 2jprecj
289	nperio = 0
290	jperio = 0
291	ln_use_jattr = .false.
292	ENDIF
293	#endif
294	!
295	! !--------------------------------------------!
296	! ! set communicator & select the local node !
297	! ! NB: mynode also opens output.namelist.dyn !
298	! ! on unit number numond on first proc !
299	! !--------------------------------------------!
300	#if defined key_iomput
301	IF( Agrif_Root() ) THEN
302	IF( lk_oasis ) THEN
303	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
304	CALL xios_initialize( "not used" ,local_comm= ilocal_comm ) ! send nemo communicator to xios
305	ELSE
306	CALL xios_initialize( "for_xios_mpi_id",return_comm=ilocal_comm ) ! nemo local communicator given by xios
307	ENDIF
308	ENDIF
309	! Nodes selection (control print return in cltxt)
310	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop, ilocal_comm )
311	#else
312	IF( lk_oasis ) THEN
313	IF( Agrif_Root() ) THEN
314	CALL cpl_init( "oceanx", ilocal_comm ) ! nemo local communicator given by oasis
315	ENDIF
316	! Nodes selection (control print return in cltxt)
317	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop, ilocal_comm )
318	ELSE
319	ilocal_comm = 0 ! Nodes selection (control print return in cltxt)
320	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop )
321	ENDIF
322	#endif
323
324	narea = narea + 1 ! mynode return the rank of proc (0 --> jpnij -1 )
325
326	lwm = (narea == 1) ! control of output namelists
327	lwp = (narea == 1) .OR. ln_ctl ! control of all listing output print
328
329	IF(lwm) THEN ! write merged namelists from earlier to output namelist
330	! ! now that the file has been opened in call to mynode.
331	! ! NB: nammpp has already been written in mynode (if lk_mpp_mpi)
332	WRITE( numond, namctl )
333	WRITE( numond, namcfg )
334	IF( .NOT.ln_read_cfg ) THEN
335	DO ji = 1, SIZE(clnam)
336	IF( TRIM(clnam(ji)) /= '' ) WRITE(numond, * ) clnam(ji) ! namusr_def print
337	END DO
338	ENDIF
339	ENDIF
340
341	! If dimensions of processor grid weren't specified in the namelist file
342	! then we calculate them here now that we have our communicator size
343	IF( jpni < 1 .OR. jpnj < 1 ) THEN
344	#if defined key_mpp_mpi
345	IF( Agrif_Root() ) CALL nemo_partition( mppsize )
346	#else
347	jpni = 1
348	jpnj = 1
349	jpnij = jpni*jpnj
350	#endif
351	ENDIF
352
353	IF( Agrif_Root() ) THEN ! AGRIF mother: specific setting from jpni and jpnj
354	#if defined key_nemocice_decomp
355	jpi = ( nx_global+2-2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
356	jpj = ( ny_global+2-2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
357	#else
358	jpi = ( jpiglo -2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
359	jpj = ( jpjglo -2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
360	#endif
361	ENDIF
362
363	!!gm ??? why here it has already been done in line 301 !
364	jpk = jpkglo ! third dim
365	!!gm end
366
367	#if defined key_agrif
368	! simple trick to use same vertical grid as parent but different number of levels:
369	! Save maximum number of levels in jpkglo, then define all vertical grids with this number.
370	! Suppress once vertical online interpolation is ok
371	IF(.NOT.Agrif_Root()) jpkglo = Agrif_Parent( jpkglo )
372	#endif
373	jpim1 = jpi-1 ! inner domain indices
374	jpjm1 = jpj-1 ! " "
375	jpkm1 = MAX( 1, jpk-1 ) ! " "
376	jpij = jpi*jpj ! jpi x j
377
378	IF(lwp) THEN ! open listing units
379	!
380	CALL ctl_opn( numout, 'ocean.output', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE., narea )
381	!
382	WRITE(numout,*)
383	WRITE(numout,*) ' CNRS - NERC - Met OFFICE - MERCATOR-ocean - INGV - CMCC'
384	WRITE(numout,*) ' NEMO team'
385	WRITE(numout,*) ' Ocean General Circulation Model'
386	WRITE(numout,*) ' NEMO version 3.7 (2016) '
387	WRITE(numout,*)
388	WRITE(numout,*)
389	DO ji = 1, SIZE(cltxt)
390	IF( TRIM(cltxt (ji)) /= '' ) WRITE(numout,*) cltxt(ji) ! control print of mynode
391	END DO
392	WRITE(numout,*)
393	WRITE(numout,*)
394	DO ji = 1, SIZE(cltxt2)
395	IF( TRIM(cltxt2(ji)) /= '' ) WRITE(numout,*) cltxt2(ji) ! control print of domain size
396	END DO
397	!
398	WRITE(numout,cform_aaa) ! Flag AAAAAAA
399	!
400	ENDIF
401
402	! Now we know the dimensions of the grid and numout has been set: we can allocate arrays
403	CALL nemo_alloc()
404
405	! !-------------------------------!
406	! ! NEMO general initialization !
407	! !-------------------------------!
408
409	CALL nemo_ctl ! Control prints
410
411	! ! Domain decomposition
412	IF( jpni*jpnj == jpnij ) THEN ; CALL mpp_init ! standard cutting out
413	ELSE ; CALL mpp_init2 ! eliminate land processors
414	ENDIF
415	!
416	IF( nn_timing == 1 ) CALL timing_init
417	!
418	! ! General initialization
419	CALL phy_cst ! Physical constants
420	CALL eos_init ! Equation of state
421	IF( lk_c1d ) CALL c1d_init ! 1D column configuration
422	CALL wad_init ! Wetting and drying options
423	CALL dom_init ! Domain
424	IF( ln_crs ) CALL crs_init ! coarsened grid: domain initialization
425	IF( ln_nnogather ) CALL nemo_northcomms! northfold neighbour lists (must be done after the masks are defined)
426	IF( ln_ctl ) CALL prt_ctl_init ! Print control
427
428	CALL diurnal_sst_bulk_init ! diurnal sst
429	IF ( ln_diurnal ) CALL diurnal_sst_coolskin_init ! cool skin
430
431	! IF ln_diurnal_only, then we only want a subset of the initialisation routines
432	IF ( ln_diurnal_only ) THEN
433	CALL istate_init ! ocean initial state (Dynamics and tracers)
434	CALL sbc_init ! Forcings : surface module
435	CALL tra_qsr_init ! penetrative solar radiation qsr
436	IF( ln_diaobs ) THEN ! Observation & model comparison
437	CALL dia_obs_init ! Initialize observational data
438	CALL dia_obs( nit000 - 1 ) ! Observation operator for restart
439	ENDIF
440	! ! Assimilation increments
441	IF( lk_asminc ) CALL asm_inc_init ! Initialize assimilation increments
442
443	IF(lwp) WRITE(numout,*) 'Euler time step switch is ', neuler
444	RETURN
445	ENDIF
446
447	CALL istate_init ! ocean initial state (Dynamics and tracers)
448
449	! ! external forcing
450	!!gm to be added : creation and call of sbc_apr_init
451	CALL tide_init ! tidal harmonics
452	CALL sbc_init ! surface boundary conditions (including sea-ice)
453	CALL bdy_init ! Open boundaries initialisation
454	! ! Ocean physics
455	! ! Vertical physics
456	CALL zdf_init ! namelist read
457	CALL zdf_bfr_init ! bottom friction
458	IF( lk_zdfric ) CALL zdf_ric_init ! Richardson number dependent Kz
459	IF( lk_zdftke ) CALL zdf_tke_init ! TKE closure scheme
460	IF( lk_zdfgls ) CALL zdf_gls_init ! GLS closure scheme
461	IF( lk_zdftmx ) CALL zdf_tmx_init ! tidal vertical mixing
462	IF( lk_zdfddm ) CALL zdf_ddm_init ! double diffusive mixing
463
464	! ! Lateral physics
465	CALL ldf_tra_init ! Lateral ocean tracer physics
466	CALL ldf_eiv_init ! eddy induced velocity param.
467	CALL ldf_dyn_init ! Lateral ocean momentum physics
468
469	! ! Active tracers
470	CALL tra_qsr_init ! penetrative solar radiation qsr
471	CALL tra_bbc_init ! bottom heat flux
472	IF( lk_trabbl ) CALL tra_bbl_init ! advective (and/or diffusive) bottom boundary layer scheme
473	CALL tra_dmp_init ! internal tracer damping
474	CALL tra_adv_init ! horizontal & vertical advection
475	CALL tra_ldf_init ! lateral mixing
476	CALL tra_zdf_init ! vertical mixing and after tracer fields
477
478	! ! Dynamics
479	IF( lk_c1d ) CALL dyn_dmp_init ! internal momentum damping
480	CALL dyn_adv_init ! advection (vector or flux form)
481	CALL dyn_vor_init ! vorticity term including Coriolis
482	CALL dyn_ldf_init ! lateral mixing
483	CALL dyn_hpg_init ! horizontal gradient of Hydrostatic pressure
484	CALL dyn_zdf_init ! vertical diffusion
485	CALL dyn_spg_init ! surface pressure gradient
486
487	#if defined key_top
488	! ! Passive tracers
489	CALL trc_init
490	#endif
491	IF( l_ldfslp ) CALL ldf_slp_init ! slope of lateral mixing
492
493	! ! Icebergs
494	CALL icb_init( rdt, nit000) ! initialise icebergs instance
495
496	! ! Misc. options
497	CALL sto_par_init ! Stochastic parametrization
498	IF( ln_sto_eos ) CALL sto_pts_init ! RRandom T/S fluctuations
499
500	! ! Diagnostics
501	IF( lk_floats ) CALL flo_init ! drifting Floats
502	CALL dia_cfl_init ! Initialise CFL diagnostics
503	CALL dia_ptr_init ! Poleward TRansports initialization
504	IF( lk_diadct ) CALL dia_dct_init ! Sections tranports
505	CALL dia_hsb_init ! heat content, salt content and volume budgets
506	CALL trd_init ! Mixed-layer/Vorticity/Integral constraints trends
507	CALL dia_obs_init ! Initialize observational data
508	IF( ln_diaobs ) CALL dia_obs( nit000 - 1 ) ! Observation operator for restart
509
510	! ! Assimilation increments
511	IF( lk_asminc ) CALL asm_inc_init ! Initialize assimilation increments
512	IF(lwp) WRITE(numout,*) 'Euler time step switch is ', neuler
513	CALL dia_tmb_init ! TMB outputs
514	CALL dia_25h_init ! 25h mean outputs
515	!
516	END SUBROUTINE nemo_init
517
518
519	SUBROUTINE nemo_ctl
520	!!----------------------------------------------------------------------
521	!! * ROUTINE nemo_ctl *
522	!!
523	!! ** Purpose : control print setting
524	!!
525	!! ** Method : - print namctl information and check some consistencies
526	!!----------------------------------------------------------------------
527	!
528	IF(lwp) THEN ! control print
529	WRITE(numout,*)
530	WRITE(numout,*) 'nemo_ctl: Control prints'
531	WRITE(numout,*) '~~~~~~~ '
532	WRITE(numout,*) ' Namelist namctl'
533	WRITE(numout,*) ' run control (for debugging) ln_ctl = ', ln_ctl
534	WRITE(numout,*) ' level of print nn_print = ', nn_print
535	WRITE(numout,*) ' Start i indice for SUM control nn_ictls = ', nn_ictls
536	WRITE(numout,*) ' End i indice for SUM control nn_ictle = ', nn_ictle
537	WRITE(numout,*) ' Start j indice for SUM control nn_jctls = ', nn_jctls
538	WRITE(numout,*) ' End j indice for SUM control nn_jctle = ', nn_jctle
539	WRITE(numout,*) ' number of proc. following i nn_isplt = ', nn_isplt
540	WRITE(numout,*) ' number of proc. following j nn_jsplt = ', nn_jsplt
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
552	IF(lwp) THEN ! control print
553	WRITE(numout,*)
554	WRITE(numout,*) 'namcfg : configuration initialization through namelist read'
555	WRITE(numout,*) '~~~~~~ '
556	WRITE(numout,*) ' Namelist namcfg'
557	WRITE(numout,*) ' read domain configuration file ln_read_cfg = ', ln_read_cfg
558	WRITE(numout,*) ' filename to be read cn_domcfg = ', TRIM(cn_domcfg)
559	WRITE(numout,*) ' write configuration definition file ln_write_cfg = ', ln_write_cfg
560	WRITE(numout,*) ' filename to be written cn_domcfg_out = ', TRIM(cn_domcfg_out)
561	WRITE(numout,*) ' use file attribute if exists as i/p j-start ln_use_jattr = ', ln_use_jattr
562	ENDIF
563	! ! Parameter control
564	!
565	IF( ln_ctl ) THEN ! sub-domain area indices for the control prints
566	IF( lk_mpp .AND. jpnij > 1 ) THEN
567	isplt = jpni ; jsplt = jpnj ; ijsplt = jpni*jpnj ! the domain is forced to the real split domain
568	ELSE
569	IF( isplt == 1 .AND. jsplt == 1 ) THEN
570	CALL ctl_warn( ' - isplt & jsplt are equal to 1', &
571	& ' - the print control will be done over the whole domain' )
572	ENDIF
573	ijsplt = isplt * jsplt ! total number of processors ijsplt
574	ENDIF
575	IF(lwp) WRITE(numout,*)' - The total number of processors over which the'
576	IF(lwp) WRITE(numout,*)' print control will be done is ijsplt : ', ijsplt
577	!
578	! ! indices used for the SUM control
579	IF( nictls+nictle+njctls+njctle == 0 ) THEN ! print control done over the default area
580	lsp_area = .FALSE.
581	ELSE ! print control done over a specific area
582	lsp_area = .TRUE.
583	IF( nictls < 1 .OR. nictls > jpiglo ) THEN
584	CALL ctl_warn( ' - nictls must be 1<=nictls>=jpiglo, it is forced to 1' )
585	nictls = 1
586	ENDIF
587	IF( nictle < 1 .OR. nictle > jpiglo ) THEN
588	CALL ctl_warn( ' - nictle must be 1<=nictle>=jpiglo, it is forced to jpiglo' )
589	nictle = jpiglo
590	ENDIF
591	IF( njctls < 1 .OR. njctls > jpjglo ) THEN
592	CALL ctl_warn( ' - njctls must be 1<=njctls>=jpjglo, it is forced to 1' )
593	njctls = 1
594	ENDIF
595	IF( njctle < 1 .OR. njctle > jpjglo ) THEN
596	CALL ctl_warn( ' - njctle must be 1<=njctle>=jpjglo, it is forced to jpjglo' )
597	njctle = jpjglo
598	ENDIF
599	ENDIF
600	ENDIF
601	!
602	IF( 1_wp /= SIGN(1._wp,-0._wp) ) CALL ctl_stop( 'nemo_ctl: The intrinsec SIGN function follows ', &
603	& 'f2003 standard. ' , &
604	& 'Compile with key_nosignedzero enabled' )
605	!
606	END SUBROUTINE nemo_ctl
607
608
609	SUBROUTINE nemo_closefile
610	!!----------------------------------------------------------------------
611	!! * ROUTINE nemo_closefile *
612	!!
613	!! ** Purpose : Close the files
614	!!----------------------------------------------------------------------
615	!
616	IF( lk_mpp ) CALL mppsync
617	!
618	CALL iom_close ! close all input/output files managed by iom_*
619	!
620	IF( numstp /= -1 ) CLOSE( numstp ) ! time-step file
621	IF( numrun /= -1 ) CLOSE( numrun ) ! run statistics file
622	IF( numnam_ref /= -1 ) CLOSE( numnam_ref ) ! oce reference namelist
623	IF( numnam_cfg /= -1 ) CLOSE( numnam_cfg ) ! oce configuration namelist
624	IF( lwm.AND.numond /= -1 ) CLOSE( numond ) ! oce output namelist
625	IF( numnam_ice_ref /= -1 ) CLOSE( numnam_ice_ref ) ! ice reference namelist
626	IF( numnam_ice_cfg /= -1 ) CLOSE( numnam_ice_cfg ) ! ice configuration namelist
627	IF( lwm.AND.numoni /= -1 ) CLOSE( numoni ) ! ice output namelist
628	IF( numevo_ice /= -1 ) CLOSE( numevo_ice ) ! ice variables (temp. evolution)
629	IF( numout /= 6 ) CLOSE( numout ) ! standard model output file
630	IF( numdct_vol /= -1 ) CLOSE( numdct_vol ) ! volume transports
631	IF( numdct_heat /= -1 ) CLOSE( numdct_heat ) ! heat transports
632	IF( numdct_salt /= -1 ) CLOSE( numdct_salt ) ! salt transports
633	!
634	numout = 6 ! redefine numout in case it is used after this point...
635	!
636	END SUBROUTINE nemo_closefile
637
638
639	SUBROUTINE nemo_alloc
640	!!----------------------------------------------------------------------
641	!! * ROUTINE nemo_alloc *
642	!!
643	!! ** Purpose : Allocate all the dynamic arrays of the OPA modules
644	!!
645	!! ** Method :
646	!!----------------------------------------------------------------------
647	USE diawri , ONLY: dia_wri_alloc
648	USE dom_oce , ONLY: dom_oce_alloc
649	USE trc_oce , ONLY: trc_oce_alloc
650	#if defined key_diadct
651	USE diadct , ONLY: diadct_alloc
652	#endif
653	USE bdy_oce , ONLY: bdy_oce_alloc
654	!
655	INTEGER :: ierr
656	!!----------------------------------------------------------------------
657	!
658	ierr = oce_alloc () ! ocean
659	ierr = ierr + dia_wri_alloc ()
660	ierr = ierr + dom_oce_alloc () ! ocean domain
661	ierr = ierr + zdf_oce_alloc () ! ocean vertical physics
662	!
663	ierr = ierr + trc_oce_alloc () ! shared TRC / TRA arrays
664	!
665	#if defined key_diadct
666	ierr = ierr + diadct_alloc () !
667	#endif
668	ierr = ierr + bdy_oce_alloc () ! bdy masks (incl. initialization)
669	!
670	IF( lk_mpp ) CALL mpp_sum( ierr )
671	IF( ierr /= 0 ) CALL ctl_stop( 'STOP', 'nemo_alloc : unable to allocate standard ocean arrays' )
672	!
673	END SUBROUTINE nemo_alloc
674
675
676	SUBROUTINE nemo_partition( num_pes )
677	!!----------------------------------------------------------------------
678	!! * ROUTINE nemo_partition *
679	!!
680	!! ** Purpose :
681	!!
682	!! ** Method :
683	!!----------------------------------------------------------------------
684	INTEGER, INTENT(in) :: num_pes ! The number of MPI processes we have
685	!
686	INTEGER, PARAMETER :: nfactmax = 20
687	INTEGER :: nfact ! The no. of factors returned
688	INTEGER :: ierr ! Error flag
689	INTEGER :: ji
690	INTEGER :: idiff, mindiff, imin ! For choosing pair of factors that are closest in value
691	INTEGER, DIMENSION(nfactmax) :: ifact ! Array of factors
692	!!----------------------------------------------------------------------
693	!
694	ierr = 0
695	!
696	CALL factorise( ifact, nfactmax, nfact, num_pes, ierr )
697	!
698	IF( nfact <= 1 ) THEN
699	WRITE (numout, *) 'WARNING: factorisation of number of PEs failed'
700	WRITE (numout, *) ' : using grid of ',num_pes,' x 1'
701	jpnj = 1
702	jpni = num_pes
703	ELSE
704	! Search through factors for the pair that are closest in value
705	mindiff = 1000000
706	imin = 1
707	DO ji = 1, nfact-1, 2
708	idiff = ABS( ifact(ji) - ifact(ji+1) )
709	IF( idiff < mindiff ) THEN
710	mindiff = idiff
711	imin = ji
712	ENDIF
713	END DO
714	jpnj = ifact(imin)
715	jpni = ifact(imin + 1)
716	ENDIF
717	!
718	jpnij = jpni*jpnj
719	!
720	END SUBROUTINE nemo_partition
721
722
723	SUBROUTINE factorise( kfax, kmaxfax, knfax, kn, kerr )
724	!!----------------------------------------------------------------------
725	!! * ROUTINE factorise *
726	!!
727	!! ** Purpose : return the prime factors of n.
728	!! knfax factors are returned in array kfax which is of
729	!! maximum dimension kmaxfax.
730	!! ** Method :
731	!!----------------------------------------------------------------------
732	INTEGER , INTENT(in ) :: kn, kmaxfax
733	INTEGER , INTENT( out) :: kerr, knfax
734	INTEGER, DIMENSION(kmaxfax), INTENT( out) :: kfax
735	!
736	INTEGER :: ifac, jl, inu
737	INTEGER, PARAMETER :: ntest = 14
738	INTEGER, DIMENSION(ntest) :: ilfax
739	!!----------------------------------------------------------------------
740	!
741	! lfax contains the set of allowed factors.
742	ilfax(:) = (/(2**jl,jl=ntest,1,-1)/)
743	!
744	! Clear the error flag and initialise output vars
745	kerr = 0
746	kfax = 1
747	knfax = 0
748	!
749	! Find the factors of n.
750	IF( kn == 1 ) GOTO 20
751
752	! nu holds the unfactorised part of the number.
753	! knfax holds the number of factors found.
754	! l points to the allowed factor list.
755	! ifac holds the current factor.
756	!
757	inu = kn
758	knfax = 0
759	!
760	DO jl = ntest, 1, -1
761	!
762	ifac = ilfax(jl)
763	IF( ifac > inu ) CYCLE
764
765	! Test whether the factor will divide.
766
767	IF( MOD(inu,ifac) == 0 ) THEN
768	!
769	knfax = knfax + 1 ! Add the factor to the list
770	IF( knfax > kmaxfax ) THEN
771	kerr = 6
772	write (,) 'FACTOR: insufficient space in factor array ', knfax
773	return
774	ENDIF
775	kfax(knfax) = ifac
776	! Store the other factor that goes with this one
777	knfax = knfax + 1
778	kfax(knfax) = inu / ifac
779	!WRITE (,) 'ARPDBG, factors ',knfax-1,' & ',knfax,' are ', kfax(knfax-1),' and ',kfax(knfax)
780	ENDIF
781	!
782	END DO
783	!
784	20 CONTINUE ! Label 20 is the exit point from the factor search loop.
785	!
786	END SUBROUTINE factorise
787
788	#if defined key_mpp_mpi
789
790	SUBROUTINE nemo_northcomms
791	!!----------------------------------------------------------------------
792	!! * ROUTINE nemo_northcomms *
793	!! ** Purpose : Setup for north fold exchanges with explicit
794	!! point-to-point messaging
795	!!
796	!! ** Method : Initialization of the northern neighbours lists.
797	!!----------------------------------------------------------------------
798	!! 1.0 ! 2011-10 (A. C. Coward, NOCS & J. Donners, PRACE)
799	!! 2.0 ! 2013-06 Setup avoiding MPI communication (I. Epicoco, S. Mocavero, CMCC)
800	!!----------------------------------------------------------------------
801	INTEGER :: sxM, dxM, sxT, dxT, jn
802	INTEGER :: njmppmax
803	!!----------------------------------------------------------------------
804	!
805	njmppmax = MAXVAL( njmppt )
806	!
807	!initializes the north-fold communication variables
808	isendto(:) = 0
809	nsndto = 0
810	!
811	!if I am a process in the north
812	IF ( njmpp == njmppmax ) THEN
813	!sxM is the first point (in the global domain) needed to compute the
814	!north-fold for the current process
815	sxM = jpiglo - nimppt(narea) - nlcit(narea) + 1
816	!dxM is the last point (in the global domain) needed to compute the
817	!north-fold for the current process
818	dxM = jpiglo - nimppt(narea) + 2
819
820	!loop over the other north-fold processes to find the processes
821	!managing the points belonging to the sxT-dxT range
822
823	DO jn = 1, jpni
824	!sxT is the first point (in the global domain) of the jn
825	!process
826	sxT = nfiimpp(jn, jpnj)
827	!dxT is the last point (in the global domain) of the jn
828	!process
829	dxT = nfiimpp(jn, jpnj) + nfilcit(jn, jpnj) - 1
830	IF ((sxM .gt. sxT) .AND. (sxM .lt. dxT)) THEN
831	nsndto = nsndto + 1
832	isendto(nsndto) = jn
833	ELSEIF ((sxM .le. sxT) .AND. (dxM .ge. dxT)) THEN
834	nsndto = nsndto + 1
835	isendto(nsndto) = jn
836	ELSEIF ((dxM .lt. dxT) .AND. (sxT .lt. dxM)) THEN
837	nsndto = nsndto + 1
838	isendto(nsndto) = jn
839	ENDIF
840	END DO
841	nfsloop = 1
842	nfeloop = nlci
843	DO jn = 2,jpni-1
844	IF(nfipproc(jn,jpnj) .eq. (narea - 1)) THEN
845	IF (nfipproc(jn - 1 ,jpnj) .eq. -1) THEN
846	nfsloop = nldi
847	ENDIF
848	IF (nfipproc(jn + 1,jpnj) .eq. -1) THEN
849	nfeloop = nlei
850	ENDIF
851	ENDIF
852	END DO
853
854	ENDIF
855	l_north_nogather = .TRUE.
856	END SUBROUTINE nemo_northcomms
857
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
863
864	!!======================================================================
865	END MODULE nemogcm
866

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