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nemogcm.F90 @ 8734

Last change on this file since 8734 was 8731, checked in by dancopsey, 7 years ago
Merged in NEMO3.6 version of this branch (dev_r5518_GC3_couple_pkg)
File size: 41.6 KB

Line
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	USE sbccpl
93	#if defined key_iomput
94	USE xios ! xIOserver
95	#endif
96
97	IMPLICIT NONE
98	PRIVATE
99
100	PUBLIC nemo_gcm ! called by model.F90
101	PUBLIC nemo_init ! needed by AGRIF
102	PUBLIC nemo_alloc ! needed by TAM
103
104	CHARACTER(lc) :: cform_aaa="( /, 'AAAAAAAA', / ) " ! flag for output listing
105
106	!!----------------------------------------------------------------------
107	!! NEMO/OPA 3.7 , NEMO Consortium (2016)
108	!! $Id$
109	!! Software governed by the CeCILL licence (NEMOGCM/NEMO_CeCILL.txt)
110	!!----------------------------------------------------------------------
111	CONTAINS
112
113	SUBROUTINE nemo_gcm
114	!!----------------------------------------------------------------------
115	!! * ROUTINE nemo_gcm *
116	!!
117	!! ** Purpose : NEMO solves the primitive equations on an orthogonal
118	!! curvilinear mesh on the sphere.
119	!!
120	!! ** Method : - model general initialization
121	!! - launch the time-stepping (stp routine)
122	!! - finalize the run by closing files and communications
123	!!
124	!! References : Madec, Delecluse, Imbard, and Levy, 1997: internal report, IPSL.
125	!! Madec, 2008, internal report, IPSL.
126	!!----------------------------------------------------------------------
127	INTEGER :: istp ! time step index
128	!!----------------------------------------------------------------------
129	!
130	#if defined key_agrif
131	CALL Agrif_Init_Grids() ! AGRIF: set the meshes
132	#endif
133	!
134	! !-----------------------!
135	CALL nemo_init !== Initialisations ==!
136	! !-----------------------!
137	#if defined key_agrif
138	CALL Agrif_Declare_Var_dom ! AGRIF: set the meshes for DOM
139	CALL Agrif_Declare_Var ! " " " " " DYN/TRA
140	# if defined key_top
141	CALL Agrif_Declare_Var_top ! " " " " " TOP
142	# endif
143	# if defined key_lim2
144	CALL Agrif_Declare_Var_lim2 ! " " " " " LIM2
145	# endif
146	# if defined key_lim3
147	CALL Agrif_Declare_Var_lim3 ! " " " " " LIM3
148	# endif
149	#endif
150	! check that all process are still there... If some process have an error,
151	! they will never enter in step and other processes will wait until the end of the cpu time!
152	IF( lk_mpp ) CALL mpp_max( nstop )
153
154	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
155
156	! !-----------------------!
157	! !== time stepping ==!
158	! !-----------------------!
159	istp = nit000
160	#if defined key_c1d
161	DO WHILE ( istp <= nitend .AND. nstop == 0 )
162	CALL stp_c1d( istp )
163	istp = istp + 1
164	END DO
165	#else
166	IF( lk_asminc ) THEN
167	IF( ln_bkgwri ) CALL asm_bkg_wri( nit000 - 1 ) ! Output background fields
168	IF( ln_asmdin ) THEN ! Direct initialization
169	IF( ln_trainc ) CALL tra_asm_inc( nit000 - 1 ) ! Tracers
170	IF( ln_dyninc ) CALL dyn_asm_inc( nit000 - 1 ) ! Dynamics
171	IF( ln_sshinc ) CALL ssh_asm_inc( nit000 - 1 ) ! SSH
172	ENDIF
173	ENDIF
174
175	#if defined key_agrif
176	CALL Agrif_Regrid()
177	#endif
178
179	DO WHILE ( istp <= nitend .AND. nstop == 0 )
180	#if defined key_agrif
181	CALL stp ! AGRIF: time stepping
182	#else
183	IF ( .NOT. ln_diurnal_only ) THEN
184	IF (lk_oasis) CALL sbc_cpl_snd( istp ) ! Coupling to atmos
185	CALL stp( istp ) ! standard time stepping
186	! We don't couple on the final timestep because
187	! our restart file has already been written
188	! and contains all the necessary data for a
189	! restart. sbc_cpl_snd could be called here
190	! but it would require
191	! a) A test to ensure it was not performed
192	! on the very last time-step
193	! b) the presence of another call to
194	! sbc_cpl_snd call prior to the main DO loop
195	! This solution produces identical results
196	! with fewer lines of code.
197	ELSE
198	CALL stp_diurnal( istp ) ! time step only the diurnal SST
199	ENDIF
200	#endif
201	istp = istp + 1
202	IF( lk_mpp ) CALL mpp_max( nstop )
203	END DO
204	#endif
205
206	IF( ln_diaobs ) CALL dia_obs_wri
207	!
208	IF( ln_icebergs ) CALL icb_end( nitend )
209
210	! !------------------------!
211	! !== finalize the run ==!
212	! !------------------------!
213	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
214	!
215	IF( nstop /= 0 .AND. lwp ) THEN ! error print
216	WRITE(numout,cform_err)
217	WRITE(numout,*) nstop, ' error have been found'
218	ENDIF
219	!
220	#if defined key_agrif
221	IF( .NOT. Agrif_Root() ) THEN
222	CALL Agrif_ParentGrid_To_ChildGrid()
223	IF( ln_diaobs ) CALL dia_obs_wri
224	IF( nn_timing == 1 ) CALL timing_finalize
225	CALL Agrif_ChildGrid_To_ParentGrid()
226	ENDIF
227	#endif
228	IF( nn_timing == 1 ) CALL timing_finalize
229	!
230	CALL nemo_closefile
231	!
232	#if defined key_iomput
233	CALL xios_finalize ! end mpp communications with xios
234	IF( lk_oasis ) CALL cpl_finalize ! end coupling and mpp communications with OASIS
235	#else
236	IF( lk_oasis ) THEN
237	CALL cpl_finalize ! end coupling and mpp communications with OASIS
238	ELSE
239	IF( lk_mpp ) CALL mppstop ! end mpp communications
240	ENDIF
241	#endif
242	!
243	END SUBROUTINE nemo_gcm
244
245
246	SUBROUTINE nemo_init
247	!!----------------------------------------------------------------------
248	!! * ROUTINE nemo_init *
249	!!
250	!! ** Purpose : initialization of the NEMO GCM
251	!!----------------------------------------------------------------------
252	INTEGER :: ji ! dummy loop indices
253	INTEGER :: ios, ilocal_comm ! local integer
254	CHARACTER(len=120), DIMENSION(30) :: cltxt, cltxt2, clnam
255	!
256	NAMELIST/namctl/ ln_ctl , nn_print, nn_ictls, nn_ictle, &
257	& nn_isplt , nn_jsplt, nn_jctls, nn_jctle, &
258	& nn_timing, nn_diacfl
259	NAMELIST/namcfg/ ln_read_cfg, cn_domcfg, ln_write_cfg, cn_domcfg_out, ln_use_jattr
260	!!----------------------------------------------------------------------
261	!
262	cltxt = ''
263	cltxt2 = ''
264	clnam = ''
265	cxios_context = 'nemo'
266	!
267	! ! Open reference namelist and configuration namelist files
268	CALL ctl_opn( numnam_ref, 'namelist_ref', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
269	CALL ctl_opn( numnam_cfg, 'namelist_cfg', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
270	!
271	REWIND( numnam_ref ) ! Namelist namctl in reference namelist : Control prints
272	READ ( numnam_ref, namctl, IOSTAT = ios, ERR = 901 )
273	901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in reference namelist', .TRUE. )
274	!
275	REWIND( numnam_cfg ) ! Namelist namctl in confguration namelist
276	READ ( numnam_cfg, namctl, IOSTAT = ios, ERR = 902 )
277	902 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namctl in configuration namelist', .TRUE. )
278	!
279	REWIND( numnam_ref ) ! Namelist namcfg in reference namelist : Control prints
280	READ ( numnam_ref, namcfg, IOSTAT = ios, ERR = 903 )
281	903 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in reference namelist', .TRUE. )
282
283	REWIND( numnam_cfg ) ! Namelist namcfg in confguration namelist : Control prints & Benchmark
284	READ ( numnam_cfg, namcfg, IOSTAT = ios, ERR = 904 )
285	904 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namcfg in configuration namelist', .TRUE. )
286
287	! !--------------------------!
288	! ! Set global domain size ! (control print return in cltxt2)
289	! !--------------------------!
290	IF( ln_read_cfg ) THEN ! Read sizes in domain configuration file
291	CALL domain_cfg ( cltxt2, cn_cfg, nn_cfg, jpiglo, jpjglo, jpkglo, jperio )
292	!
293	ELSE ! user-defined namelist
294	CALL usr_def_nam( cltxt2, clnam, cn_cfg, nn_cfg, jpiglo, jpjglo, jpkglo, jperio )
295	ENDIF
296	!
297	jpk = jpkglo
298	!
299	#if defined key_agrif
300	IF( .NOT. Agrif_Root() ) THEN ! AGRIF children: specific setting (cf. agrif_user.F90)
301	jpiglo = nbcellsx + 2 + 2*nbghostcells
302	jpjglo = nbcellsy + 2 + 2*nbghostcells
303	jpi = ( jpiglo-2jpreci + (jpni-1+0) ) / jpni + 2jpreci
304	jpj = ( jpjglo-2jprecj + (jpnj-1+0) ) / jpnj + 2jprecj
305	nperio = 0
306	jperio = 0
307	ln_use_jattr = .false.
308	ENDIF
309	#endif
310	!
311	! !--------------------------------------------!
312	! ! set communicator & select the local node !
313	! ! NB: mynode also opens output.namelist.dyn !
314	! ! on unit number numond on first proc !
315	! !--------------------------------------------!
316	#if defined key_iomput
317	IF( Agrif_Root() ) THEN
318	IF( lk_oasis ) THEN
319	CALL cpl_init( "toyoce", ilocal_comm ) ! nemo local communicator given by oasis
320	CALL xios_initialize( "not used" ,local_comm= ilocal_comm ) ! send nemo communicator to xios
321	ELSE
322	CALL xios_initialize( "for_xios_mpi_id",return_comm=ilocal_comm ) ! nemo local communicator given by xios
323	ENDIF
324	ENDIF
325	! Nodes selection (control print return in cltxt)
326	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop, ilocal_comm )
327	#else
328	IF( lk_oasis ) THEN
329	IF( Agrif_Root() ) THEN
330	CALL cpl_init( "toyoce", ilocal_comm ) ! nemo local communicator given by oasis
331	ENDIF
332	! Nodes selection (control print return in cltxt)
333	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop, ilocal_comm )
334	ELSE
335	ilocal_comm = 0 ! Nodes selection (control print return in cltxt)
336	narea = mynode( cltxt, 'output.namelist.dyn', numnam_ref, numnam_cfg, numond , nstop )
337	ENDIF
338	#endif
339
340	narea = narea + 1 ! mynode return the rank of proc (0 --> jpnij -1 )
341
342	lwm = (narea == 1) ! control of output namelists
343	lwp = (narea == 1) .OR. ln_ctl ! control of all listing output print
344
345	IF(lwm) THEN ! write merged namelists from earlier to output namelist
346	! ! now that the file has been opened in call to mynode.
347	! ! NB: nammpp has already been written in mynode (if lk_mpp_mpi)
348	WRITE( numond, namctl )
349	WRITE( numond, namcfg )
350	IF( .NOT.ln_read_cfg ) THEN
351	DO ji = 1, SIZE(clnam)
352	IF( TRIM(clnam(ji)) /= '' ) WRITE(numond, * ) clnam(ji) ! namusr_def print
353	END DO
354	ENDIF
355	ENDIF
356
357	! If dimensions of processor grid weren't specified in the namelist file
358	! then we calculate them here now that we have our communicator size
359	IF( jpni < 1 .OR. jpnj < 1 ) THEN
360	#if defined key_mpp_mpi
361	IF( Agrif_Root() ) CALL nemo_partition( mppsize )
362	#else
363	jpni = 1
364	jpnj = 1
365	jpnij = jpni*jpnj
366	#endif
367	ENDIF
368
369	IF( Agrif_Root() ) THEN ! AGRIF mother: specific setting from jpni and jpnj
370	#if defined key_nemocice_decomp
371	jpi = ( nx_global+2-2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
372	jpj = ( ny_global+2-2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
373	#else
374	jpi = ( jpiglo -2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
375	jpj = ( jpjglo -2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
376	#endif
377	ENDIF
378
379	!!gm ??? why here it has already been done in line 301 !
380	jpk = jpkglo ! third dim
381	!!gm end
382
383	#if defined key_agrif
384	! simple trick to use same vertical grid as parent but different number of levels:
385	! Save maximum number of levels in jpkglo, then define all vertical grids with this number.
386	! Suppress once vertical online interpolation is ok
387	IF(.NOT.Agrif_Root()) jpkglo = Agrif_Parent( jpkglo )
388	#endif
389	jpim1 = jpi-1 ! inner domain indices
390	jpjm1 = jpj-1 ! " "
391	jpkm1 = MAX( 1, jpk-1 ) ! " "
392	jpij = jpi*jpj ! jpi x j
393
394	IF(lwp) THEN ! open listing units
395	!
396	CALL ctl_opn( numout, 'ocean.output', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE., narea )
397	!
398	WRITE(numout,*)
399	WRITE(numout,*) ' CNRS - NERC - Met OFFICE - MERCATOR-ocean - INGV - CMCC'
400	WRITE(numout,*) ' NEMO team'
401	WRITE(numout,*) ' Ocean General Circulation Model'
402	WRITE(numout,*) ' NEMO version 3.7 (2016) '
403	WRITE(numout,*)
404	WRITE(numout,*)
405	DO ji = 1, SIZE(cltxt)
406	IF( TRIM(cltxt (ji)) /= '' ) WRITE(numout,*) cltxt(ji) ! control print of mynode
407	END DO
408	WRITE(numout,*)
409	WRITE(numout,*)
410	DO ji = 1, SIZE(cltxt2)
411	IF( TRIM(cltxt2(ji)) /= '' ) WRITE(numout,*) cltxt2(ji) ! control print of domain size
412	END DO
413	!
414	WRITE(numout,cform_aaa) ! Flag AAAAAAA
415	!
416	ENDIF
417
418	! Now we know the dimensions of the grid and numout has been set: we can allocate arrays
419	CALL nemo_alloc()
420
421	! !-------------------------------!
422	! ! NEMO general initialization !
423	! !-------------------------------!
424
425	CALL nemo_ctl ! Control prints
426
427	! ! Domain decomposition
428	IF( jpni*jpnj == jpnij ) THEN ; CALL mpp_init ! standard cutting out
429	ELSE ; CALL mpp_init2 ! eliminate land processors
430	ENDIF
431	!
432	IF( nn_timing == 1 ) CALL timing_init
433	!
434	! ! General initialization
435	CALL phy_cst ! Physical constants
436	CALL eos_init ! Equation of state
437	IF( lk_c1d ) CALL c1d_init ! 1D column configuration
438	CALL wad_init ! Wetting and drying options
439	CALL dom_init ! Domain
440	IF( ln_crs ) CALL crs_init ! coarsened grid: domain initialization
441	IF( ln_nnogather ) CALL nemo_northcomms! northfold neighbour lists (must be done after the masks are defined)
442	IF( ln_ctl ) CALL prt_ctl_init ! Print control
443
444	CALL diurnal_sst_bulk_init ! diurnal sst
445	IF ( ln_diurnal ) CALL diurnal_sst_coolskin_init ! cool skin
446
447	! IF ln_diurnal_only, then we only want a subset of the initialisation routines
448	IF ( ln_diurnal_only ) THEN
449	CALL istate_init ! ocean initial state (Dynamics and tracers)
450	CALL sbc_init ! Forcings : surface module
451	CALL tra_qsr_init ! penetrative solar radiation qsr
452	IF( ln_diaobs ) THEN ! Observation & model comparison
453	CALL dia_obs_init ! Initialize observational data
454	CALL dia_obs( nit000 - 1 ) ! Observation operator for restart
455	ENDIF
456	! ! Assimilation increments
457	IF( lk_asminc ) CALL asm_inc_init ! Initialize assimilation increments
458
459	IF(lwp) WRITE(numout,*) 'Euler time step switch is ', neuler
460	RETURN
461	ENDIF
462
463	CALL istate_init ! ocean initial state (Dynamics and tracers)
464
465	! ! external forcing
466	!!gm to be added : creation and call of sbc_apr_init
467	CALL tide_init ! tidal harmonics
468	CALL sbc_init ! surface boundary conditions (including sea-ice)
469	CALL bdy_init ! Open boundaries initialisation
470	! ! Ocean physics
471	! ! Vertical physics
472	CALL zdf_init ! namelist read
473	CALL zdf_bfr_init ! bottom friction
474	IF( lk_zdfric ) CALL zdf_ric_init ! Richardson number dependent Kz
475	IF( lk_zdftke ) CALL zdf_tke_init ! TKE closure scheme
476	IF( lk_zdfgls ) CALL zdf_gls_init ! GLS closure scheme
477	IF( lk_zdftmx ) CALL zdf_tmx_init ! tidal vertical mixing
478	IF( lk_zdfddm ) CALL zdf_ddm_init ! double diffusive mixing
479
480	! ! Lateral physics
481	CALL ldf_tra_init ! Lateral ocean tracer physics
482	CALL ldf_eiv_init ! eddy induced velocity param.
483	CALL ldf_dyn_init ! Lateral ocean momentum physics
484
485	! ! Active tracers
486	CALL tra_qsr_init ! penetrative solar radiation qsr
487	CALL tra_bbc_init ! bottom heat flux
488	IF( lk_trabbl ) CALL tra_bbl_init ! advective (and/or diffusive) bottom boundary layer scheme
489	CALL tra_dmp_init ! internal tracer damping
490	CALL tra_adv_init ! horizontal & vertical advection
491	CALL tra_ldf_init ! lateral mixing
492	CALL tra_zdf_init ! vertical mixing and after tracer fields
493
494	! ! Dynamics
495	IF( lk_c1d ) CALL dyn_dmp_init ! internal momentum damping
496	CALL dyn_adv_init ! advection (vector or flux form)
497	CALL dyn_vor_init ! vorticity term including Coriolis
498	CALL dyn_ldf_init ! lateral mixing
499	CALL dyn_hpg_init ! horizontal gradient of Hydrostatic pressure
500	CALL dyn_zdf_init ! vertical diffusion
501	CALL dyn_spg_init ! surface pressure gradient
502
503	#if defined key_top
504	! ! Passive tracers
505	CALL trc_init
506	#endif
507	IF( l_ldfslp ) CALL ldf_slp_init ! slope of lateral mixing
508
509	! ! Icebergs
510	CALL icb_init( rdt, nit000) ! initialise icebergs instance
511
512	! ! Misc. options
513	CALL sto_par_init ! Stochastic parametrization
514	IF( ln_sto_eos ) CALL sto_pts_init ! RRandom T/S fluctuations
515
516	! ! Diagnostics
517	IF( lk_floats ) CALL flo_init ! drifting Floats
518	CALL dia_cfl_init ! Initialise CFL diagnostics
519	CALL dia_ptr_init ! Poleward TRansports initialization
520	IF( lk_diadct ) CALL dia_dct_init ! Sections tranports
521	CALL dia_hsb_init ! heat content, salt content and volume budgets
522	CALL trd_init ! Mixed-layer/Vorticity/Integral constraints trends
523	CALL dia_obs_init ! Initialize observational data
524	IF( ln_diaobs ) CALL dia_obs( nit000 - 1 ) ! Observation operator for restart
525
526	! ! Assimilation increments
527	IF( lk_asminc ) CALL asm_inc_init ! Initialize assimilation increments
528	IF(lwp) WRITE(numout,*) 'Euler time step switch is ', neuler
529	CALL dia_tmb_init ! TMB outputs
530	CALL dia_25h_init ! 25h mean outputs
531
532	IF (nstop > 0) THEN
533	CALL CTL_STOP('STOP','Critical errors in NEMO initialisation')
534	END IF
535
536	!
537	END SUBROUTINE nemo_init
538
539
540	SUBROUTINE nemo_ctl
541	!!----------------------------------------------------------------------
542	!! * ROUTINE nemo_ctl *
543	!!
544	!! ** Purpose : control print setting
545	!!
546	!! ** Method : - print namctl information and check some consistencies
547	!!----------------------------------------------------------------------
548	!
549	IF(lwp) THEN ! control print
550	WRITE(numout,*)
551	WRITE(numout,*) 'nemo_ctl: Control prints'
552	WRITE(numout,*) '~~~~~~~ '
553	WRITE(numout,*) ' Namelist namctl'
554	WRITE(numout,*) ' run control (for debugging) ln_ctl = ', ln_ctl
555	WRITE(numout,*) ' level of print nn_print = ', nn_print
556	WRITE(numout,*) ' Start i indice for SUM control nn_ictls = ', nn_ictls
557	WRITE(numout,*) ' End i indice for SUM control nn_ictle = ', nn_ictle
558	WRITE(numout,*) ' Start j indice for SUM control nn_jctls = ', nn_jctls
559	WRITE(numout,*) ' End j indice for SUM control nn_jctle = ', nn_jctle
560	WRITE(numout,*) ' number of proc. following i nn_isplt = ', nn_isplt
561	WRITE(numout,*) ' number of proc. following j nn_jsplt = ', nn_jsplt
562	WRITE(numout,*) ' timing activated (0/1) nn_timing = ', nn_timing
563	ENDIF
564	!
565	nprint = nn_print ! convert DOCTOR namelist names into OLD names
566	nictls = nn_ictls
567	nictle = nn_ictle
568	njctls = nn_jctls
569	njctle = nn_jctle
570	isplt = nn_isplt
571	jsplt = nn_jsplt
572
573	IF(lwp) THEN ! control print
574	WRITE(numout,*)
575	WRITE(numout,*) 'namcfg : configuration initialization through namelist read'
576	WRITE(numout,*) '~~~~~~ '
577	WRITE(numout,*) ' Namelist namcfg'
578	WRITE(numout,*) ' read domain configuration file ln_read_cfg = ', ln_read_cfg
579	WRITE(numout,*) ' filename to be read cn_domcfg = ', TRIM(cn_domcfg)
580	WRITE(numout,*) ' write configuration definition file ln_write_cfg = ', ln_write_cfg
581	WRITE(numout,*) ' filename to be written cn_domcfg_out = ', TRIM(cn_domcfg_out)
582	WRITE(numout,*) ' use file attribute if exists as i/p j-start ln_use_jattr = ', ln_use_jattr
583	ENDIF
584	! ! Parameter control
585	!
586	IF( ln_ctl ) THEN ! sub-domain area indices for the control prints
587	IF( lk_mpp .AND. jpnij > 1 ) THEN
588	isplt = jpni ; jsplt = jpnj ; ijsplt = jpni*jpnj ! the domain is forced to the real split domain
589	ELSE
590	IF( isplt == 1 .AND. jsplt == 1 ) THEN
591	CALL ctl_warn( ' - isplt & jsplt are equal to 1', &
592	& ' - the print control will be done over the whole domain' )
593	ENDIF
594	ijsplt = isplt * jsplt ! total number of processors ijsplt
595	ENDIF
596	IF(lwp) WRITE(numout,*)' - The total number of processors over which the'
597	IF(lwp) WRITE(numout,*)' print control will be done is ijsplt : ', ijsplt
598	!
599	! ! indices used for the SUM control
600	IF( nictls+nictle+njctls+njctle == 0 ) THEN ! print control done over the default area
601	lsp_area = .FALSE.
602	ELSE ! print control done over a specific area
603	lsp_area = .TRUE.
604	IF( nictls < 1 .OR. nictls > jpiglo ) THEN
605	CALL ctl_warn( ' - nictls must be 1<=nictls>=jpiglo, it is forced to 1' )
606	nictls = 1
607	ENDIF
608	IF( nictle < 1 .OR. nictle > jpiglo ) THEN
609	CALL ctl_warn( ' - nictle must be 1<=nictle>=jpiglo, it is forced to jpiglo' )
610	nictle = jpiglo
611	ENDIF
612	IF( njctls < 1 .OR. njctls > jpjglo ) THEN
613	CALL ctl_warn( ' - njctls must be 1<=njctls>=jpjglo, it is forced to 1' )
614	njctls = 1
615	ENDIF
616	IF( njctle < 1 .OR. njctle > jpjglo ) THEN
617	CALL ctl_warn( ' - njctle must be 1<=njctle>=jpjglo, it is forced to jpjglo' )
618	njctle = jpjglo
619	ENDIF
620	ENDIF
621	ENDIF
622	!
623	IF( 1_wp /= SIGN(1._wp,-0._wp) ) CALL ctl_stop( 'nemo_ctl: The intrinsec SIGN function follows ', &
624	& 'f2003 standard. ' , &
625	& 'Compile with key_nosignedzero enabled' )
626	!
627	END SUBROUTINE nemo_ctl
628
629
630	SUBROUTINE nemo_closefile
631	!!----------------------------------------------------------------------
632	!! * ROUTINE nemo_closefile *
633	!!
634	!! ** Purpose : Close the files
635	!!----------------------------------------------------------------------
636	!
637	IF( lk_mpp ) CALL mppsync
638	!
639	CALL iom_close ! close all input/output files managed by iom_*
640	!
641	IF( numstp /= -1 ) CLOSE( numstp ) ! time-step file
642	IF( numsol /= -1 ) CLOSE( numsol ) ! solver file
643	IF( numnam_ref /= -1 ) CLOSE( numnam_ref ) ! oce reference namelist
644	IF( numnam_cfg /= -1 ) CLOSE( numnam_cfg ) ! oce configuration namelist
645	IF( lwm.AND.numond /= -1 ) CLOSE( numond ) ! oce output namelist
646	IF( numnam_ice_ref /= -1 ) CLOSE( numnam_ice_ref ) ! ice reference namelist
647	IF( numnam_ice_cfg /= -1 ) CLOSE( numnam_ice_cfg ) ! ice configuration namelist
648	IF( lwm.AND.numoni /= -1 ) CLOSE( numoni ) ! ice output namelist
649	IF( numevo_ice /= -1 ) CLOSE( numevo_ice ) ! ice variables (temp. evolution)
650	IF( numout /= 6 ) CLOSE( numout ) ! standard model output file
651	IF( numdct_vol /= -1 ) CLOSE( numdct_vol ) ! volume transports
652	IF( numdct_heat /= -1 ) CLOSE( numdct_heat ) ! heat transports
653	IF( numdct_salt /= -1 ) CLOSE( numdct_salt ) ! salt transports
654	!
655	numout = 6 ! redefine numout in case it is used after this point...
656	!
657	END SUBROUTINE nemo_closefile
658
659
660	SUBROUTINE nemo_alloc
661	!!----------------------------------------------------------------------
662	!! * ROUTINE nemo_alloc *
663	!!
664	!! ** Purpose : Allocate all the dynamic arrays of the OPA modules
665	!!
666	!! ** Method :
667	!!----------------------------------------------------------------------
668	USE diawri , ONLY: dia_wri_alloc
669	USE dom_oce , ONLY: dom_oce_alloc
670	USE trc_oce , ONLY: trc_oce_alloc
671	#if defined key_diadct
672	USE diadct , ONLY: diadct_alloc
673	#endif
674	USE bdy_oce , ONLY: bdy_oce_alloc
675	!
676	INTEGER :: ierr
677	!!----------------------------------------------------------------------
678	!
679	ierr = oce_alloc () ! ocean
680	ierr = ierr + dia_wri_alloc ()
681	ierr = ierr + dom_oce_alloc () ! ocean domain
682	ierr = ierr + zdf_oce_alloc () ! ocean vertical physics
683	!
684	ierr = ierr + trc_oce_alloc () ! shared TRC / TRA arrays
685	!
686	#if defined key_diadct
687	ierr = ierr + diadct_alloc () !
688	#endif
689	ierr = ierr + bdy_oce_alloc () ! bdy masks (incl. initialization)
690	!
691	IF( lk_mpp ) CALL mpp_sum( ierr )
692	IF( ierr /= 0 ) CALL ctl_stop( 'STOP', 'nemo_alloc : unable to allocate standard ocean arrays' )
693	!
694	END SUBROUTINE nemo_alloc
695
696
697	SUBROUTINE nemo_partition( num_pes )
698	!!----------------------------------------------------------------------
699	!! * ROUTINE nemo_partition *
700	!!
701	!! ** Purpose :
702	!!
703	!! ** Method :
704	!!----------------------------------------------------------------------
705	INTEGER, INTENT(in) :: num_pes ! The number of MPI processes we have
706	!
707	INTEGER, PARAMETER :: nfactmax = 20
708	INTEGER :: nfact ! The no. of factors returned
709	INTEGER :: ierr ! Error flag
710	INTEGER :: ji
711	INTEGER :: idiff, mindiff, imin ! For choosing pair of factors that are closest in value
712	INTEGER, DIMENSION(nfactmax) :: ifact ! Array of factors
713	!!----------------------------------------------------------------------
714	!
715	ierr = 0
716	!
717	CALL factorise( ifact, nfactmax, nfact, num_pes, ierr )
718	!
719	IF( nfact <= 1 ) THEN
720	WRITE (numout, *) 'WARNING: factorisation of number of PEs failed'
721	WRITE (numout, *) ' : using grid of ',num_pes,' x 1'
722	jpnj = 1
723	jpni = num_pes
724	ELSE
725	! Search through factors for the pair that are closest in value
726	mindiff = 1000000
727	imin = 1
728	DO ji = 1, nfact-1, 2
729	idiff = ABS( ifact(ji) - ifact(ji+1) )
730	IF( idiff < mindiff ) THEN
731	mindiff = idiff
732	imin = ji
733	ENDIF
734	END DO
735	jpnj = ifact(imin)
736	jpni = ifact(imin + 1)
737	ENDIF
738	!
739	jpnij = jpni*jpnj
740	!
741	END SUBROUTINE nemo_partition
742
743
744	SUBROUTINE factorise( kfax, kmaxfax, knfax, kn, kerr )
745	!!----------------------------------------------------------------------
746	!! * ROUTINE factorise *
747	!!
748	!! ** Purpose : return the prime factors of n.
749	!! knfax factors are returned in array kfax which is of
750	!! maximum dimension kmaxfax.
751	!! ** Method :
752	!!----------------------------------------------------------------------
753	INTEGER , INTENT(in ) :: kn, kmaxfax
754	INTEGER , INTENT( out) :: kerr, knfax
755	INTEGER, DIMENSION(kmaxfax), INTENT( out) :: kfax
756	!
757	INTEGER :: ifac, jl, inu
758	INTEGER, PARAMETER :: ntest = 14
759	INTEGER, DIMENSION(ntest) :: ilfax
760	!!----------------------------------------------------------------------
761	!
762	! lfax contains the set of allowed factors.
763	ilfax(:) = (/(2**jl,jl=ntest,1,-1)/)
764	!
765	! Clear the error flag and initialise output vars
766	kerr = 0
767	kfax = 1
768	knfax = 0
769	!
770	! Find the factors of n.
771	IF( kn == 1 ) GOTO 20
772
773	! nu holds the unfactorised part of the number.
774	! knfax holds the number of factors found.
775	! l points to the allowed factor list.
776	! ifac holds the current factor.
777	!
778	inu = kn
779	knfax = 0
780	!
781	DO jl = ntest, 1, -1
782	!
783	ifac = ilfax(jl)
784	IF( ifac > inu ) CYCLE
785
786	! Test whether the factor will divide.
787
788	IF( MOD(inu,ifac) == 0 ) THEN
789	!
790	knfax = knfax + 1 ! Add the factor to the list
791	IF( knfax > kmaxfax ) THEN
792	kerr = 6
793	write (,) 'FACTOR: insufficient space in factor array ', knfax
794	return
795	ENDIF
796	kfax(knfax) = ifac
797	! Store the other factor that goes with this one
798	knfax = knfax + 1
799	kfax(knfax) = inu / ifac
800	!WRITE (,) 'ARPDBG, factors ',knfax-1,' & ',knfax,' are ', kfax(knfax-1),' and ',kfax(knfax)
801	ENDIF
802	!
803	END DO
804	!
805	20 CONTINUE ! Label 20 is the exit point from the factor search loop.
806	!
807	END SUBROUTINE factorise
808
809	#if defined key_mpp_mpi
810
811	SUBROUTINE nemo_northcomms
812	!!----------------------------------------------------------------------
813	!! * ROUTINE nemo_northcomms *
814	!! ** Purpose : Setup for north fold exchanges with explicit
815	!! point-to-point messaging
816	!!
817	!! ** Method : Initialization of the northern neighbours lists.
818	!!----------------------------------------------------------------------
819	!! 1.0 ! 2011-10 (A. C. Coward, NOCS & J. Donners, PRACE)
820	!! 2.0 ! 2013-06 Setup avoiding MPI communication (I. Epicoco, S. Mocavero, CMCC)
821	!!----------------------------------------------------------------------
822	INTEGER :: sxM, dxM, sxT, dxT, jn
823	INTEGER :: njmppmax
824	!!----------------------------------------------------------------------
825	!
826	njmppmax = MAXVAL( njmppt )
827	!
828	!initializes the north-fold communication variables
829	isendto(:) = 0
830	nsndto = 0
831	!
832	!if I am a process in the north
833	IF ( njmpp == njmppmax ) THEN
834	!sxM is the first point (in the global domain) needed to compute the
835	!north-fold for the current process
836	sxM = jpiglo - nimppt(narea) - nlcit(narea) + 1
837	!dxM is the last point (in the global domain) needed to compute the
838	!north-fold for the current process
839	dxM = jpiglo - nimppt(narea) + 2
840
841	!loop over the other north-fold processes to find the processes
842	!managing the points belonging to the sxT-dxT range
843
844	DO jn = 1, jpni
845	!sxT is the first point (in the global domain) of the jn
846	!process
847	sxT = nfiimpp(jn, jpnj)
848	!dxT is the last point (in the global domain) of the jn
849	!process
850	dxT = nfiimpp(jn, jpnj) + nfilcit(jn, jpnj) - 1
851	IF ((sxM .gt. sxT) .AND. (sxM .lt. dxT)) THEN
852	nsndto = nsndto + 1
853	isendto(nsndto) = jn
854	ELSEIF ((sxM .le. sxT) .AND. (dxM .ge. dxT)) THEN
855	nsndto = nsndto + 1
856	isendto(nsndto) = jn
857	ELSEIF ((dxM .lt. dxT) .AND. (sxT .lt. dxM)) THEN
858	nsndto = nsndto + 1
859	isendto(nsndto) = jn
860	ENDIF
861	END DO
862	nfsloop = 1
863	nfeloop = nlci
864	DO jn = 2,jpni-1
865	IF(nfipproc(jn,jpnj) .eq. (narea - 1)) THEN
866	IF (nfipproc(jn - 1 ,jpnj) .eq. -1) THEN
867	nfsloop = nldi
868	ENDIF
869	IF (nfipproc(jn + 1,jpnj) .eq. -1) THEN
870	nfeloop = nlei
871	ENDIF
872	ENDIF
873	END DO
874
875	ENDIF
876	l_north_nogather = .TRUE.
877	END SUBROUTINE nemo_northcomms
878
879	#else
880	SUBROUTINE nemo_northcomms ! Dummy routine
881	WRITE(,) 'nemo_northcomms: You should not have seen this print! error?'
882	END SUBROUTINE nemo_northcomms
883	#endif
884
885	!!======================================================================
886	END MODULE nemogcm
887

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