Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
MODULE iom_nf90
!!======================================================================
!! *** MODULE iom_nf90 ***
!! Input/Output manager : Library to read input files with NF90 (only fliocom module)
!!======================================================================
!! History : 9.0 ! 05 12 (J. Belier) Original code
!! 9.0 ! 06 02 (S. Masson) Adaptation to NEMO
!! " ! 07 07 (D. Storkey) Changes to iom_nf90_gettime
!! 3.6 ! 2015-15 (J. Harle) Added procedure to read REAL attributes
!! 4.0 ! 2017-11 (M. Andrejczuk) Extend IOM interface to write any 3D fields
!!----------------------------------------------------------------------
!!----------------------------------------------------------------------
!! iom_open : open a file read only
!! iom_close : close a file or all files opened by iom
!! iom_get : read a field (interfaced to several routines)
!! iom_varid : get the id of a variable in a file
!! iom_rstput : write a field in a restart file (interfaced to several routines)
!!----------------------------------------------------------------------
USE dom_oce ! ocean space and time domain
!USE sbc_oce, ONLY: ght_abl ! abl vertical level number and height
USE lbclnk ! lateal boundary condition / mpp exchanges
USE iom_def ! iom variables definitions
USE netcdf ! NetCDF library
USE in_out_manager ! I/O manager
USE lib_mpp ! MPP library
IMPLICIT NONE
PRIVATE
PUBLIC iom_nf90_open , iom_nf90_close, iom_nf90_varid, iom_nf90_get, iom_nf90_rstput
PUBLIC iom_nf90_chkatt, iom_nf90_getatt, iom_nf90_putatt
INTERFACE iom_nf90_get
MODULE PROCEDURE iom_nf90_g0d_sp
MODULE PROCEDURE iom_nf90_g0d_dp, iom_nf90_g123d_dp
END INTERFACE
INTERFACE iom_nf90_rstput
MODULE PROCEDURE iom_nf90_rp0123d_dp
END INTERFACE
!!----------------------------------------------------------------------
!! NEMO/OCE 4.0 , NEMO Consortium (2018)
!! $Id: iom_nf90.F90 13286 2020-07-09 15:48:29Z smasson $
!! Software governed by the CeCILL license (see ./LICENSE)
!!----------------------------------------------------------------------
CONTAINS
SUBROUTINE iom_nf90_open( cdname, kiomid, ldwrt, ldok, kdlev, cdcomp )
!!---------------------------------------------------------------------
!! *** SUBROUTINE iom_open ***
!!
!! ** Purpose : open an input file with NF90
!!---------------------------------------------------------------------
CHARACTER(len=*) , INTENT(inout) :: cdname ! File name
INTEGER , INTENT( out) :: kiomid ! nf90 identifier of the opened file
LOGICAL , INTENT(in ) :: ldwrt ! read or write the file?
LOGICAL , INTENT(in ) :: ldok ! check the existence
INTEGER , INTENT(in ), OPTIONAL :: kdlev ! size of the ice/abl third dimension
CHARACTER(len=3) , INTENT(in ), OPTIONAL :: cdcomp ! name of component calling iom_nf90_open
CHARACTER(LEN=256) :: clinfo ! info character
CHARACTER(LEN=256) :: cltmp ! temporary character
CHARACTER(LEN=12 ) :: clfmt ! writing format
CHARACTER(LEN=3 ) :: clcomp ! name of component calling iom_nf90_open
INTEGER :: idg ! number of digits
INTEGER :: iln ! lengths of character
INTEGER :: istop ! temporary storage of nstop
INTEGER :: if90id ! nf90 identifier of the opened file
INTEGER :: idmy ! dummy variable
INTEGER :: jl ! loop variable
INTEGER :: ichunk ! temporary storage of nn_chunksz
INTEGER :: imode ! creation mode flag: NF90_CLOBBER or NF90_NOCLOBBER or NF90_HDF5
INTEGER :: ihdf5 ! local variable for retrieval of value for NF90_HDF5
LOGICAL :: llclobber ! local definition of ln_clobber
!---------------------------------------------------------------------
!
clinfo = ' iom_nf90_open ~~~ '
istop = nstop ! store the actual value of nstop
!
! !number of vertical levels
IF( PRESENT(cdcomp) ) THEN
IF( .NOT. PRESENT(kdlev) ) CALL ctl_stop( 'iom_nf90_open: cdcomp and kdlev must both be present' )
clcomp = cdcomp ! use input value
ELSE
clcomp = 'OCE' ! by default
ENDIF
!
IF( nn_chunksz > 0 ) THEN ; ichunk = nn_chunksz
ELSE ; ichunk = NF90_SIZEHINT_DEFAULT
ENDIF
!
llclobber = ldwrt .AND. ln_clobber
IF( ldok .AND. .NOT. llclobber ) THEN !== Open existing file ==!
! !=========================!
IF( ldwrt ) THEN ! ... in write mode
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' open existing file: '//TRIM(cdname)//' in WRITE mode'
IF( snc4set%luse ) THEN
CALL iom_nf90_check(NF90_OPEN( TRIM(cdname), NF90_WRITE , if90id ), clinfo)
ELSE
CALL iom_nf90_check(NF90_OPEN( TRIM(cdname), NF90_WRITE , if90id, chunksize = ichunk ), clinfo)
ENDIF
CALL iom_nf90_check(NF90_SET_FILL( if90id, NF90_NOFILL, idmy ), clinfo)
ELSE ! ... in read mode
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' open existing file: '//TRIM(cdname)//' in READ mode'
CALL iom_nf90_check(NF90_OPEN( TRIM(cdname), NF90_NOWRITE, if90id, chunksize = ichunk ), clinfo)
ENDIF
ELSE !== the file doesn't exist ==! (or we overwrite it)
! !============================!
iln = INDEX( cdname, '.nc' )
IF( ldwrt ) THEN !* the file should be open in write mode so we create it...
IF( jpnij > 1 ) THEN
idg = MAX( INT(LOG10(REAL(MAX(1,jpnij-1),wp))) + 1, 4 ) ! how many digits to we need to write? min=4, max=9
WRITE(clfmt, "('(a,a,i', i1, '.', i1, ',a)')") idg, idg ! '(a,a,ix.x,a)'
WRITE(cltmp,clfmt) cdname(1:iln-1), '_', narea-1, '.nc'
cdname = TRIM(cltmp)
ENDIF
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' create new file: '//TRIM(cdname)//' in WRITE mode'
IF( llclobber ) THEN ; imode = IOR( NF90_64BIT_OFFSET, NF90_CLOBBER )
ELSE ; imode = IOR( NF90_64BIT_OFFSET, NF90_NOCLOBBER )
ENDIF
IF( snc4set%luse ) THEN
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' creating file: '//TRIM(cdname)//' in hdf5 (netcdf4) mode'
CALL GET_NF90_SYMBOL("NF90_HDF5", ihdf5)
IF( llclobber ) THEN ; imode = IOR(ihdf5, NF90_CLOBBER)
ELSE ; imode = IOR(ihdf5, NF90_NOCLOBBER)
ENDIF
CALL iom_nf90_check(NF90_CREATE( TRIM(cdname), imode, if90id ), clinfo)
ELSE
CALL iom_nf90_check(NF90_CREATE( TRIM(cdname), imode, if90id, chunksize = ichunk ), clinfo)
ENDIF
CALL iom_nf90_check(NF90_SET_FILL( if90id, NF90_NOFILL, idmy ), clinfo)
! define dimensions
CALL iom_nf90_check(NF90_DEF_DIM( if90id, 'x', Ni_0, idmy ), clinfo)
CALL iom_nf90_check(NF90_DEF_DIM( if90id, 'y', Nj_0, idmy ), clinfo)
SELECT CASE (clcomp)
CASE ('OCE') ; CALL iom_nf90_check(NF90_DEF_DIM( if90id, 'nav_lev', jpk, idmy ), clinfo)
CASE ('ICE') ; CALL iom_nf90_check(NF90_DEF_DIM( if90id, 'numcat', kdlev, idmy ), clinfo)
CASE ('ABL') ; CALL iom_nf90_check(NF90_DEF_DIM( if90id, 'nav_lev', kdlev, idmy ), clinfo)
CASE ('SED') ; CALL iom_nf90_check(NF90_DEF_DIM( if90id, 'numsed', kdlev, idmy ), clinfo)
CASE DEFAULT ; CALL ctl_stop( 'iom_nf90_open unknown component type' )
END SELECT
CALL iom_nf90_check(NF90_DEF_DIM( if90id, 'time_counter', NF90_UNLIMITED, idmy ), clinfo)
! global attributes
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_number_total' , jpnij ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_number' , narea-1 ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_dimensions_ids' , (/ 1 , 2 /) ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_size_global' , (/ Ni0glo , Nj0glo /) ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_size_local' , (/ Ni_0 , Nj_0 /) ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_position_first' , (/ mig0(Nis0), mjg0(Njs0) /) ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_position_last' , (/ mig0(Nie0), mjg0(Nje0) /) ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_halo_size_start', (/ 0 , 0 /) ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_halo_size_end' , (/ 0 , 0 /) ), clinfo)
CALL iom_nf90_check(NF90_PUT_ATT( if90id, NF90_GLOBAL, 'DOMAIN_type' , 'BOX' ), clinfo)
ELSE !* the file should be open for read mode so it must exist...
CALL ctl_stop( TRIM(clinfo), ' should be impossible case...' )
ENDIF
ENDIF
!
! start to fill file informations
! =============
IF( istop == nstop ) THEN ! no error within this routine
!does not work with some compilers kiomid = MINLOC(iom_file(:)%nfid, dim = 1)
kiomid = 0
DO jl = jpmax_files, 1, -1
IF( iom_file(jl)%nfid == 0 ) kiomid = jl
ENDDO
iom_file(kiomid)%name = TRIM(cdname)
iom_file(kiomid)%comp = clcomp
iom_file(kiomid)%nfid = if90id
iom_file(kiomid)%nvars = 0
iom_file(kiomid)%irec = -1 ! useless for NetCDF files, used to know if the file is in define mode
CALL iom_nf90_check(NF90_Inquire(if90id, unlimitedDimId = iom_file(kiomid)%iduld), clinfo)
IF( iom_file(kiomid)%iduld .GE. 0 ) THEN
CALL iom_nf90_check(NF90_Inquire_Dimension(if90id, iom_file(kiomid)%iduld, &
& name = iom_file(kiomid)%uldname, &
& len = iom_file(kiomid)%lenuld ), clinfo )
ENDIF
IF(lwp) WRITE(numout,*) ' ---> '//TRIM(cdname)//' OK'
ELSE
kiomid = 0 ! return error flag
ENDIF
!
END SUBROUTINE iom_nf90_open
SUBROUTINE iom_nf90_close( kiomid )
!!--------------------------------------------------------------------
!! *** SUBROUTINE iom_nf90_close ***
!!
!! ** Purpose : close an input file with NF90
!!--------------------------------------------------------------------
INTEGER, INTENT(in) :: kiomid ! iom identifier of the file to be closed
CHARACTER(LEN=100) :: clinfo ! info character
!---------------------------------------------------------------------
clinfo = ' iom_nf90_close , file: '//TRIM(iom_file(kiomid)%name)
CALL iom_nf90_check(NF90_CLOSE(iom_file(kiomid)%nfid), clinfo)
END SUBROUTINE iom_nf90_close
FUNCTION iom_nf90_varid ( kiomid, cdvar, kiv, kdimsz, kndims, lduld )
!!-----------------------------------------------------------------------
!! *** FUNCTION iom_varid ***
!!
!! ** Purpose : get the id of a variable in a file with NF90
!!-----------------------------------------------------------------------
INTEGER , INTENT(in ) :: kiomid ! file Identifier
CHARACTER(len=*) , INTENT(in ) :: cdvar ! name of the variable
INTEGER , INTENT(in ) :: kiv !
INTEGER, DIMENSION(:), INTENT( out), OPTIONAL :: kdimsz ! size of each dimension
INTEGER , INTENT( out), OPTIONAL :: kndims ! number of dimensions
LOGICAL , INTENT( out), OPTIONAL :: lduld ! true if the last dimension is unlimited (time)
!
INTEGER :: iom_nf90_varid ! iom variable Id
INTEGER :: if90id ! nf90 file identifier
INTEGER :: ji ! dummy loop index
INTEGER :: ivarid ! NetCDF variable Id
INTEGER :: i_nvd ! number of dimension of the variable
INTEGER, DIMENSION(jpmax_dims) :: idimid ! dimension ids of the variable
LOGICAL :: llok ! ok test
CHARACTER(LEN=100) :: clinfo ! info character
!!-----------------------------------------------------------------------
clinfo = ' iom_nf90_varid, file: '//TRIM(iom_file(kiomid)%name)//', var: '//TRIM(cdvar)
iom_nf90_varid = 0 ! default definition
IF( PRESENT(kdimsz) ) kdimsz(:) = 0 ! default definition
if90id = iom_file(kiomid)%nfid ! get back NetCDF file id
!
llok = NF90_INQ_VARID( if90id, TRIM(cdvar), ivarid ) == nf90_noerr ! does the variable exist in the file
IF( llok ) THEN
iom_nf90_varid = kiv
iom_file(kiomid)%nvars = kiv
iom_file(kiomid)%nvid(kiv) = ivarid
iom_file(kiomid)%cn_var(kiv) = TRIM(cdvar)
CALL iom_nf90_check(NF90_Inquire_Variable(if90id, ivarid, ndims = i_nvd), clinfo) ! number of dimensions
iom_file(kiomid)%ndims(kiv) = i_nvd
CALL iom_nf90_check(NF90_Inquire_Variable(if90id, ivarid, dimids = idimid(1:i_nvd)), clinfo) ! dimensions ids
iom_file(kiomid)%luld(kiv) = .FALSE. ! default value
iom_file(kiomid)%dimsz(:,kiv) = 0 ! reset dimsz in case previously used
DO ji = 1, i_nvd ! dimensions size
CALL iom_nf90_check(NF90_Inquire_Dimension(if90id, idimid(ji), len = iom_file(kiomid)%dimsz(ji,kiv)), clinfo)
IF( idimid(ji) == iom_file(kiomid)%iduld ) iom_file(kiomid)%luld(kiv) = .TRUE. ! unlimited dimension?
END DO
!---------- Deal with scale_factor and add_offset
llok = NF90_Inquire_attribute(if90id, ivarid, 'scale_factor') == nf90_noerr
IF( llok) THEN
CALL iom_nf90_check(NF90_GET_ATT(if90id, ivarid, 'scale_factor', iom_file(kiomid)%scf(kiv)), clinfo)
ELSE
iom_file(kiomid)%scf(kiv) = 1.
END IF
llok = NF90_Inquire_attribute(if90id, ivarid, 'add_offset') == nf90_noerr
IF( llok ) THEN
CALL iom_nf90_check(NF90_GET_ATT(if90id, ivarid, 'add_offset', iom_file(kiomid)%ofs(kiv)), clinfo)
ELSE
iom_file(kiomid)%ofs(kiv) = 0.
END IF
! return the simension size
IF( PRESENT(kdimsz) ) THEN
IF( i_nvd <= SIZE(kdimsz) ) THEN
kdimsz(1:i_nvd) = iom_file(kiomid)%dimsz(1:i_nvd,kiv)
ELSE
WRITE(ctmp1,*) i_nvd, SIZE(kdimsz)
CALL ctl_stop( TRIM(clinfo), 'error in kdimsz size'//TRIM(ctmp1) )
ENDIF
ENDIF
IF( PRESENT(kndims) ) kndims = iom_file(kiomid)%ndims(kiv)
IF( PRESENT( lduld) ) lduld = iom_file(kiomid)%luld(kiv)
ELSE
iom_nf90_varid = -1 ! variable not found, return error code: -1
ENDIF
!
END FUNCTION iom_nf90_varid
!!----------------------------------------------------------------------
!! INTERFACE iom_nf90_get
!!----------------------------------------------------------------------
SUBROUTINE iom_nf90_g0d_sp( kiomid, kvid, pvar, kstart )
!!-----------------------------------------------------------------------
!! *** ROUTINE iom_nf90_g0d ***
!!
!! ** Purpose : read a scalar with NF90
!!-----------------------------------------------------------------------
INTEGER , INTENT(in ) :: kiomid ! Identifier of the file
INTEGER , INTENT(in ) :: kvid ! variable id
REAL(sp), INTENT( out) :: pvar ! read field
INTEGER , DIMENSION(1), INTENT(in ), OPTIONAL :: kstart ! start position of the reading in each axis
!
CHARACTER(LEN=100) :: clinfo ! info character
!---------------------------------------------------------------------
clinfo = 'iom_nf90_g0d , file: '//TRIM(iom_file(kiomid)%name)//', var: '//TRIM(iom_file(kiomid)%cn_var(kvid))
CALL iom_nf90_check(NF90_GET_VAR(iom_file(kiomid)%nfid, iom_file(kiomid)%nvid(kvid), pvar, start = kstart), clinfo )
END SUBROUTINE iom_nf90_g0d_sp
SUBROUTINE iom_nf90_g0d_dp( kiomid, kvid, pvar, kstart )
!!-----------------------------------------------------------------------
!! *** ROUTINE iom_nf90_g0d ***
!!
!! ** Purpose : read a scalar with NF90
!!-----------------------------------------------------------------------
INTEGER , INTENT(in ) :: kiomid ! Identifier of the file
INTEGER , INTENT(in ) :: kvid ! variable id
REAL(dp), INTENT( out) :: pvar ! read field
INTEGER , DIMENSION(1), INTENT(in ), OPTIONAL :: kstart ! start position of the reading in each axis
!
CHARACTER(LEN=100) :: clinfo ! info character
!---------------------------------------------------------------------
clinfo = 'iom_nf90_g0d , file: '//TRIM(iom_file(kiomid)%name)//', var: '//TRIM(iom_file(kiomid)%cn_var(kvid))
CALL iom_nf90_check(NF90_GET_VAR(iom_file(kiomid)%nfid, iom_file(kiomid)%nvid(kvid), pvar, start = kstart), clinfo )
END SUBROUTINE iom_nf90_g0d_dp
SUBROUTINE iom_nf90_g123d_dp( kiomid, kvid, knbdim, kstart, kcount, kx1, kx2, ky1, ky2, &
& pv_r1d, pv_r2d, pv_r3d )
!!-----------------------------------------------------------------------
!! *** ROUTINE iom_nf90_g123d ***
!!
!! ** Purpose : read a 1D/2D/3D variable with NF90
!!
!! ** Method : read ONE record at each CALL
!!-----------------------------------------------------------------------
INTEGER , INTENT(in ) :: kiomid ! iom identifier of the file
INTEGER , INTENT(in ) :: kvid ! Name of the variable
INTEGER , INTENT(in ) :: knbdim ! number of dimensions of the variable
INTEGER , DIMENSION(:) , INTENT(in ) :: kstart ! start position of the reading in each axis
INTEGER , DIMENSION(:) , INTENT(in ) :: kcount ! number of points to be read in each axis
INTEGER , INTENT(in ) :: kx1, kx2, ky1, ky2 ! subdomain indexes
REAL(dp), DIMENSION(:) , INTENT( out), OPTIONAL :: pv_r1d ! read field (1D case)
REAL(dp), DIMENSION(:,:) , INTENT( out), OPTIONAL :: pv_r2d ! read field (2D case)
REAL(dp), DIMENSION(:,:,:) , INTENT( out), OPTIONAL :: pv_r3d ! read field (3D case)
!
CHARACTER(LEN=100) :: clinfo ! info character
INTEGER :: if90id ! nf90 identifier of the opened file
INTEGER :: ivid ! nf90 variable id
!---------------------------------------------------------------------
clinfo = 'iom_nf90_g123d , file: '//TRIM(iom_file(kiomid)%name)//', var: '//TRIM(iom_file(kiomid)%cn_var(kvid))
if90id = iom_file(kiomid)%nfid ! get back NetCDF file id
ivid = iom_file(kiomid)%nvid(kvid) ! get back NetCDF var id
!
IF( PRESENT(pv_r1d) ) THEN
CALL iom_nf90_check( NF90_GET_VAR(if90id, ivid, pv_r1d(: ), start = kstart(1:knbdim), &
& count = kcount(1:knbdim)), clinfo )
ELSEIF( PRESENT(pv_r2d) ) THEN
CALL iom_nf90_check( NF90_GET_VAR(if90id, ivid, pv_r2d(kx1:kx2,ky1:ky2 ), start = kstart(1:knbdim), &
& count = kcount(1:knbdim)), clinfo )
ELSEIF( PRESENT(pv_r3d) ) THEN
CALL iom_nf90_check( NF90_GET_VAR(if90id, ivid, pv_r3d(kx1:kx2,ky1:ky2,:), start = kstart(1:knbdim), &
& count = kcount(1:knbdim)), clinfo )
ENDIF
!
END SUBROUTINE iom_nf90_g123d_dp
SUBROUTINE iom_nf90_chkatt( kiomid, cdatt, llok, ksize, cdvar )
!!-----------------------------------------------------------------------
!! *** ROUTINE iom_nf90_chkatt ***
!!
!! ** Purpose : check existence of attribute with NF90
!! (either a global attribute (default) or a variable
!! attribute if optional variable name is supplied (cdvar))
!!-----------------------------------------------------------------------
INTEGER , INTENT(in ) :: kiomid ! Identifier of the file
CHARACTER(len=*), INTENT(in ) :: cdatt ! attribute name
LOGICAL , INTENT( out) :: llok ! error code
INTEGER , INTENT( out), OPTIONAL &
& :: ksize ! attribute size
CHARACTER(len=*), INTENT(in ), OPTIONAL &
& :: cdvar ! name of the variable
!
INTEGER :: if90id ! temporary integer
INTEGER :: isize ! temporary integer
INTEGER :: ivarid ! NetCDF variable Id
!---------------------------------------------------------------------
!
if90id = iom_file(kiomid)%nfid
IF( PRESENT(cdvar) ) THEN
! check the variable exists in the file
llok = NF90_INQ_VARID( if90id, TRIM(cdvar), ivarid ) == nf90_noerr
IF( llok ) &
! check the variable has the attribute required
llok = NF90_Inquire_attribute(if90id, ivarid, cdatt, len=isize ) == nf90_noerr
ELSE
llok = NF90_Inquire_attribute(if90id, NF90_GLOBAL, cdatt, len=isize ) == nf90_noerr
ENDIF
!
IF( PRESENT(ksize) ) ksize = isize
!
IF( .not. llok) &
CALL ctl_warn('iom_nf90_chkatt: no attribute '//cdatt//' found')
!
END SUBROUTINE iom_nf90_chkatt
!!----------------------------------------------------------------------
!! INTERFACE iom_nf90_getatt
!!----------------------------------------------------------------------
SUBROUTINE iom_nf90_getatt( kiomid, cdatt, katt0d, katt1d, patt0d, patt1d, cdatt0d, cdvar)
!!-----------------------------------------------------------------------
!! *** ROUTINE iom_nf90_getatt ***
!!
!! ** Purpose : read an attribute with NF90
!! (either a global attribute (default) or a variable
!! attribute if optional variable name is supplied (cdvar))
!!-----------------------------------------------------------------------
INTEGER , INTENT(in ) :: kiomid ! Identifier of the file
CHARACTER(len=*) , INTENT(in ) :: cdatt ! attribute name
INTEGER , INTENT( out), OPTIONAL :: katt0d ! read scalar integer
INTEGER, DIMENSION(:) , INTENT( out), OPTIONAL :: katt1d ! read 1d array integer
REAL(wp) , INTENT( out), OPTIONAL :: patt0d ! read scalar real
REAL(wp), DIMENSION(:), INTENT( out), OPTIONAL :: patt1d ! read 1d array real
CHARACTER(len=*) , INTENT( out), OPTIONAL :: cdatt0d ! read character
CHARACTER(len=*) , INTENT(in ), OPTIONAL :: cdvar ! name of the variable
!
INTEGER :: if90id ! temporary integer
INTEGER :: ivarid ! NetCDF variable Id
LOGICAL :: llok ! temporary logical
CHARACTER(LEN=100) :: clinfo ! info character
!---------------------------------------------------------------------
!
if90id = iom_file(kiomid)%nfid
IF( PRESENT(cdvar) ) THEN
! check the variable exists in the file
llok = NF90_INQ_VARID( if90id, TRIM(cdvar), ivarid ) == nf90_noerr
IF( llok ) THEN
! check the variable has the attribute required
llok = NF90_Inquire_attribute(if90id, ivarid, cdatt) == nf90_noerr
ELSE
CALL ctl_warn('iom_nf90_getatt: no variable '//TRIM(cdvar)//' found')
ENDIF
ELSE
llok = NF90_Inquire_attribute(if90id, NF90_GLOBAL, cdatt) == nf90_noerr
ivarid = NF90_GLOBAL
ENDIF
!
IF( llok) THEN
clinfo = 'iom_nf90_getatt, file: '//TRIM(iom_file(kiomid)%name)//', att: '//TRIM(cdatt)
IF(PRESENT( katt0d)) CALL iom_nf90_check(NF90_GET_ATT(if90id, ivarid, cdatt, values = katt0d), clinfo)
IF(PRESENT( katt1d)) CALL iom_nf90_check(NF90_GET_ATT(if90id, ivarid, cdatt, values = katt1d), clinfo)
IF(PRESENT( patt0d)) CALL iom_nf90_check(NF90_GET_ATT(if90id, ivarid, cdatt, values = patt0d), clinfo)
IF(PRESENT( patt1d)) CALL iom_nf90_check(NF90_GET_ATT(if90id, ivarid, cdatt, values = patt1d), clinfo)
IF(PRESENT(cdatt0d)) CALL iom_nf90_check(NF90_GET_ATT(if90id, ivarid, cdatt, values = cdatt0d), clinfo)
ELSE
CALL ctl_warn('iom_nf90_getatt: no attribute '//TRIM(cdatt)//' found')
IF(PRESENT( katt0d)) katt0d = -999
IF(PRESENT( katt1d)) katt1d(:) = -999
IF(PRESENT( patt0d)) patt0d = -999._wp
IF(PRESENT( patt1d)) patt1d(:) = -999._wp
IF(PRESENT(cdatt0d)) cdatt0d = '!'
ENDIF
!
END SUBROUTINE iom_nf90_getatt
SUBROUTINE iom_nf90_putatt( kiomid, cdatt, katt0d, katt1d, patt0d, patt1d, cdatt0d, cdvar)
!!-----------------------------------------------------------------------
!! *** ROUTINE iom_nf90_putatt ***
!!
!! ** Purpose : write an attribute with NF90
!! (either a global attribute (default) or a variable
!! attribute if optional variable name is supplied (cdvar))
!!-----------------------------------------------------------------------
INTEGER , INTENT(in ) :: kiomid ! Identifier of the file
CHARACTER(len=*) , INTENT(in ) :: cdatt ! attribute name
INTEGER , INTENT(in ), OPTIONAL :: katt0d ! read scalar integer
INTEGER, DIMENSION(:) , INTENT(in ), OPTIONAL :: katt1d ! read 1d array integer
REAL(wp) , INTENT(in ), OPTIONAL :: patt0d ! read scalar real
REAL(wp), DIMENSION(:), INTENT(in ), OPTIONAL :: patt1d ! read 1d array real
CHARACTER(len=*) , INTENT(in ), OPTIONAL :: cdatt0d ! read character
CHARACTER(len=*) , INTENT(in ), OPTIONAL :: cdvar ! name of the variable
!
INTEGER :: if90id ! temporary integer
INTEGER :: ivarid ! NetCDF variable Id
INTEGER :: isize ! Attribute size
INTEGER :: itype ! Attribute type
LOGICAL :: llok ! temporary logical
LOGICAL :: llatt ! temporary logical
LOGICAL :: lldata ! temporary logical
CHARACTER(LEN=100) :: clinfo ! info character
!---------------------------------------------------------------------
!
if90id = iom_file(kiomid)%nfid
IF( PRESENT(cdvar) ) THEN
llok = NF90_INQ_VARID( if90id, TRIM(cdvar), ivarid ) == nf90_noerr ! is the variable in the file?
IF( .NOT. llok ) THEN
CALL ctl_warn('iom_nf90_putatt: no variable '//TRIM(cdvar)//' found' &
& , ' no attribute '//cdatt//' written' )
RETURN
ENDIF
ELSE
ivarid = NF90_GLOBAL
ENDIF
llatt = NF90_Inquire_attribute(if90id, ivarid, cdatt, len = isize, xtype = itype ) == nf90_noerr
!
! trick: irec used to know if the file is in define mode or not
lldata = iom_file(kiomid)%irec /= -1 ! default: go back in define mode if in data mode
IF( lldata .AND. llatt ) THEN ! attribute already there. Do we really need to go back in define mode?
! do we have the appropriate type?
IF(PRESENT( katt0d) .OR. PRESENT( katt1d)) llok = itype == NF90_INT
IF(PRESENT( patt0d) .OR. PRESENT( patt1d)) llok = itype == NF90_DOUBLE
IF(PRESENT(cdatt0d) ) llok = itype == NF90_CHAR
! and do we have the appropriate size?
IF(PRESENT( katt0d)) llok = llok .AND. isize == 1
IF(PRESENT( katt1d)) llok = llok .AND. isize == SIZE(katt1d)
IF(PRESENT( patt0d)) llok = llok .AND. isize == 1
IF(PRESENT( patt1d)) llok = llok .AND. isize == SIZE(patt1d)
IF(PRESENT(cdatt0d)) llok = llok .AND. isize == LEN_TRIM(cdatt0d)
!
lldata = .NOT. llok
ENDIF
!
clinfo = 'iom_nf90_putatt, file: '//TRIM(iom_file(kiomid)%name)//', att: '//TRIM(cdatt)
IF(lldata) CALL iom_nf90_check(NF90_REDEF( if90id ), clinfo) ! leave data mode to define mode
!
IF(PRESENT( katt0d)) CALL iom_nf90_check(NF90_PUT_ATT(if90id, ivarid, cdatt, values = katt0d) , clinfo)
IF(PRESENT( katt1d)) CALL iom_nf90_check(NF90_PUT_ATT(if90id, ivarid, cdatt, values = katt1d) , clinfo)
IF(PRESENT( patt0d)) CALL iom_nf90_check(NF90_PUT_ATT(if90id, ivarid, cdatt, values = patt0d) , clinfo)
IF(PRESENT( patt1d)) CALL iom_nf90_check(NF90_PUT_ATT(if90id, ivarid, cdatt, values = patt1d) , clinfo)
IF(PRESENT(cdatt0d)) CALL iom_nf90_check(NF90_PUT_ATT(if90id, ivarid, cdatt, values = trim(cdatt0d)), clinfo)
!
IF(lldata) CALL iom_nf90_check(NF90_ENDDEF( if90id ), clinfo) ! leave define mode to data mode
!
END SUBROUTINE iom_nf90_putatt
SUBROUTINE iom_nf90_rp0123d_dp( kt, kwrite, kiomid, cdvar , kvid , ktype, &
& pv_r0d, pv_r1d, pv_r2d, pv_r3d )
!!--------------------------------------------------------------------
!! *** SUBROUTINE iom_nf90_rstput ***
!!
!! ** Purpose : read the time axis cdvar in the file
!!--------------------------------------------------------------------
INTEGER , INTENT(in) :: kt ! ocean time-step
INTEGER , INTENT(in) :: kwrite ! writing time-step
INTEGER , INTENT(in) :: kiomid ! Identifier of the file
CHARACTER(len=*) , INTENT(in) :: cdvar ! variable name
INTEGER , INTENT(in) :: kvid ! variable id
INTEGER , INTENT(in), OPTIONAL :: ktype ! variable type (default R8)
REAL(dp) , INTENT(in), OPTIONAL :: pv_r0d ! written Od field
REAL(dp), DIMENSION( :), INTENT(in), OPTIONAL :: pv_r1d ! written 1d field
REAL(dp), DIMENSION(:, : ), INTENT(in), OPTIONAL :: pv_r2d ! written 2d field
REAL(dp), DIMENSION(:, :, :), INTENT(in), OPTIONAL :: pv_r3d ! written 3d field
!
INTEGER :: idims ! number of dimension
INTEGER :: idvar ! variable id
INTEGER :: jd ! dimension loop counter
INTEGER :: ix1, ix2, iy1, iy2 ! subdomain indexes
INTEGER, DIMENSION(4) :: idimsz ! dimensions size
INTEGER, DIMENSION(4) :: idimid ! dimensions id
CHARACTER(LEN=256) :: clinfo ! info character
INTEGER :: if90id ! nf90 file identifier
INTEGER :: itype ! variable type
INTEGER, DIMENSION(4) :: ichunksz ! NetCDF4 chunk sizes. Will be computed using
! ! nn_nchunks_[i,j,k,t] namelist parameters
INTEGER :: ichunkalg, ishuffle, ideflate, ideflate_level
! ! NetCDF4 internally fixed parameters
LOGICAL :: lchunk ! logical switch to activate chunking and compression
! ! when appropriate (currently chunking is applied to 4d fields only)
INTEGER :: idlv ! local variable
CHARACTER(LEN=256) :: ccname ! local variable
!---------------------------------------------------------------------
!
clinfo = ' iom_nf90_rp0123d, file: '//TRIM(iom_file(kiomid)%name)//', var: '//TRIM(cdvar)
if90id = iom_file(kiomid)%nfid
!
! define dimension variables if it is not already done
! ==========================
IF( iom_file(kiomid)%nvars == 0 ) THEN
! are we in define mode?
IF( iom_file(kiomid)%irec /= -1 ) THEN ! trick: irec used to know if the file is in define mode or not
CALL iom_nf90_check(NF90_REDEF( if90id ), clinfo) ; iom_file(kiomid)%irec = -1
ENDIF
! define the dimension variables if it is not already done
DO jd = 1, 2
CALL iom_nf90_check(NF90_INQUIRE_DIMENSION(if90id,jd,iom_file(kiomid)%cn_var(jd),iom_file(kiomid)%dimsz(jd,jd)),clinfo)
ccname = TRIM(iom_file(kiomid)%cn_var(jd))
IF ( ccname == 'x') ccname = 'nav_lon'
IF ( ccname == 'y') ccname = 'nav_lat'
CALL iom_nf90_check(NF90_DEF_VAR( if90id, ccname, NF90_FLOAT , (/ 1, 2 /), &
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
& iom_file(kiomid)%nvid(jd) ), clinfo)
END DO
iom_file(kiomid)%dimsz(2,1) = iom_file(kiomid)%dimsz(2,2) ! second dim of first variable
iom_file(kiomid)%dimsz(1,2) = iom_file(kiomid)%dimsz(1,1) ! first dim of second variable
DO jd = 3, 4
CALL iom_nf90_check(NF90_INQUIRE_DIMENSION(if90id,jd,iom_file(kiomid)%cn_var(jd),iom_file(kiomid)%dimsz(1,jd)), clinfo)
CALL iom_nf90_check(NF90_DEF_VAR( if90id, TRIM(iom_file(kiomid)%cn_var(jd)), NF90_FLOAT , (/ jd /), &
& iom_file(kiomid)%nvid(jd) ), clinfo)
END DO
! update informations structure related the dimension variable we just added...
iom_file(kiomid)%nvars = 4
iom_file(kiomid)%luld(1:4) = (/ .FALSE., .FALSE., .FALSE., .TRUE. /)
iom_file(kiomid)%ndims(1:4) = (/ 2, 2, 1, 1 /)
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' define dimension variables done'
ENDIF
! define the data if it is not already done
! ===============
IF( kvid <= 0 ) THEN
!
! NetCDF4 chunking and compression fixed settings
ichunkalg = 0
ishuffle = 1
ideflate = 1
ideflate_level = 1
!
idvar = iom_file(kiomid)%nvars + 1
! are we in define mode?
IF( iom_file(kiomid)%irec /= -1 ) THEN ! trick: irec used to know if the file is in define mode or not
CALL iom_nf90_check(NF90_REDEF( if90id ), clinfo) ; iom_file(kiomid)%irec = -1
ENDIF
! variable definition
IF( PRESENT(pv_r0d) ) THEN ; idims = 0
ELSEIF( PRESENT(pv_r1d) ) THEN
idims = 2 ; idimid(1:idims) = (/3,4/)
ELSEIF( PRESENT(pv_r2d) ) THEN ; idims = 3 ; idimid(1:idims) = (/1,2,4/)
ELSEIF( PRESENT(pv_r3d) ) THEN
idims = 4 ; idimid(1:idims) = (/1,2,3,4/)
ENDIF
IF( PRESENT(ktype) ) THEN ! variable external type
SELECT CASE (ktype)
CASE (jp_r8) ; itype = NF90_DOUBLE
CASE (jp_r4) ; itype = NF90_FLOAT
CASE (jp_i4) ; itype = NF90_INT
CASE (jp_i2) ; itype = NF90_SHORT
CASE (jp_i1) ; itype = NF90_BYTE
CASE DEFAULT ; CALL ctl_stop( TRIM(clinfo)//' unknown variable type' )
END SELECT
ELSE
itype = NF90_DOUBLE
ENDIF
IF( PRESENT(pv_r0d) ) THEN
CALL iom_nf90_check(NF90_DEF_VAR( if90id, TRIM(cdvar), itype, &
& iom_file(kiomid)%nvid(idvar) ), clinfo )
ELSE
CALL iom_nf90_check(NF90_DEF_VAR( if90id, TRIM(cdvar), itype, idimid(1:idims), &
& iom_file(kiomid)%nvid(idvar) ), clinfo )
ENDIF
lchunk = .false.
IF( snc4set%luse .AND. idims == 4 ) lchunk = .true.
! update informations structure related the new variable we want to add...
iom_file(kiomid)%nvars = idvar
iom_file(kiomid)%cn_var(idvar) = TRIM(cdvar)
iom_file(kiomid)%scf(idvar) = 1.
iom_file(kiomid)%ofs(idvar) = 0.
iom_file(kiomid)%ndims(idvar) = idims
IF( .NOT. PRESENT(pv_r0d) ) THEN ; iom_file(kiomid)%luld(idvar) = .TRUE.
ELSE ; iom_file(kiomid)%luld(idvar) = .FALSE.
ENDIF
DO jd = 1, idims
CALL iom_nf90_check(NF90_INQUIRE_DIMENSION( if90id, idimid(jd), len = iom_file(kiomid)%dimsz(jd,idvar) ), clinfo)
IF ( lchunk ) ichunksz(jd) = iom_file(kiomid)%dimsz(jd,idvar)
END DO
IF ( lchunk ) THEN
! Calculate chunk sizes by partitioning each dimension as requested in namnc4 namelist
! Disallow very small chunk sizes and prevent chunk sizes larger than each individual dimension
ichunksz(1) = MIN( ichunksz(1),MAX( (ichunksz(1)-1)/snc4set%ni + 1 ,16 ) ) ! Suggested default nc4set%ni=4
ichunksz(2) = MIN( ichunksz(2),MAX( (ichunksz(2)-1)/snc4set%nj + 1 ,16 ) ) ! Suggested default nc4set%nj=2
ichunksz(3) = MIN( ichunksz(3),MAX( (ichunksz(3)-1)/snc4set%nk + 1 , 1 ) ) ! Suggested default nc4set%nk=6
ichunksz(4) = 1 ! Do not allow chunks to span the
! ! unlimited dimension
CALL iom_nf90_check(SET_NF90_DEF_VAR_CHUNKING(if90id, idvar, ichunkalg, ichunksz), clinfo)
CALL iom_nf90_check(SET_NF90_DEF_VAR_DEFLATE(if90id, idvar, ishuffle, ideflate, ideflate_level), clinfo)
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' chunked ok. Chunks sizes: ', ichunksz
ENDIF
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' defined ok'
ELSE
idvar = kvid
ENDIF
!
! time step kwrite : write the variable
IF( kt == kwrite ) THEN
! are we in write mode?
IF( iom_file(kiomid)%irec == -1 ) THEN ! trick: irec used to know if the file is in define mode or not
CALL iom_nf90_check(NF90_ENDDEF( if90id ), clinfo) ; iom_file(kiomid)%irec = 0
ENDIF
! on what kind of domain must the data be written?
IF( PRESENT(pv_r2d) .OR. PRESENT(pv_r3d) ) THEN
idimsz(1:2) = iom_file(kiomid)%dimsz(1:2,idvar)
IF( idimsz(1) == Ni_0 .AND. idimsz(2) == Nj_0 ) THEN
ix1 = Nis0 ; ix2 = Nie0 ; iy1 = Njs0 ; iy2 = Nje0
ELSEIF( idimsz(1) == jpi .AND. idimsz(2) == jpj ) THEN
ix1 = 1 ; ix2 = jpi ; iy1 = 1 ; iy2 = jpj
ELSEIF( idimsz(1) == jpi .AND. idimsz(2) == jpj ) THEN
ix1 = 1 ; ix2 = jpi ; iy1 = 1 ; iy2 = jpj
ELSE
CALL ctl_stop( 'iom_nf90_rp0123d: should have been an impossible case...' )
ENDIF
! write dimension variables if it is not already done
! =============
! trick: is defined to 0 => dimension variable are defined but not yet written
IF( iom_file(kiomid)%dimsz(1, 4) == 0 ) THEN ! time_counter = 0
CALL iom_nf90_check( NF90_PUT_VAR( if90id, 1, glamt(ix1:ix2, iy1:iy2) ), clinfo )
CALL iom_nf90_check( NF90_PUT_VAR( if90id, 2, gphit(ix1:ix2, iy1:iy2) ), clinfo )
SELECT CASE (iom_file(kiomid)%comp)
CASE ('OCE')
CALL iom_nf90_check( NF90_PUT_VAR( if90id, 3, gdept_1d ), clinfo )
! CASE ('ABL')
! CALL iom_nf90_check( NF90_PUT_VAR( if90id, 3, ght_abl ), clinfo )
CASE DEFAULT
CALL iom_nf90_check( NF90_PUT_VAR( if90id, 3, (/ (idlv, idlv = 1,iom_file(kiomid)%dimsz(1,3)) /) ), clinfo )
END SELECT
! "wrong" value: to be improved but not really useful...
CALL iom_nf90_check( NF90_PUT_VAR( if90id, 4, kt ), clinfo )
! update the size of the variable corresponding to the unlimited dimension
iom_file(kiomid)%dimsz(1, 4) = 1 ! so we don't enter this IF case any more...
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' write dimension variables done'
ENDIF
ENDIF
! write the data
! =============
IF( PRESENT(pv_r0d) ) THEN
CALL iom_nf90_check( NF90_PUT_VAR( if90id, idvar, pv_r0d ), clinfo )
ELSEIF( PRESENT(pv_r1d) ) THEN
CALL iom_nf90_check( NF90_PUT_VAR( if90id, idvar, pv_r1d(:) ), clinfo )
ELSEIF( PRESENT(pv_r2d) ) THEN
CALL iom_nf90_check( NF90_PUT_VAR( if90id, idvar, pv_r2d(ix1:ix2,iy1:iy2) ), clinfo )
ELSEIF( PRESENT(pv_r3d) ) THEN
CALL iom_nf90_check( NF90_PUT_VAR( if90id, idvar, pv_r3d(ix1:ix2,iy1:iy2,:) ), clinfo )
ENDIF
! add 1 to the size of the temporal dimension (not really useful...)
IF( iom_file(kiomid)%luld(idvar) ) iom_file(kiomid)%dimsz(iom_file(kiomid)%ndims(idvar), idvar) &
& = iom_file(kiomid)%dimsz(iom_file(kiomid)%ndims(idvar), idvar) + 1
IF(lwp) WRITE(numout,*) TRIM(clinfo)//' written ok'
ENDIF
!
END SUBROUTINE iom_nf90_rp0123d_dp
SUBROUTINE iom_nf90_check( kstatus, cdinfo )
!!--------------------------------------------------------------------
!! *** SUBROUTINE iom_nf90_check ***
!!
!! ** Purpose : check nf90 errors
!!--------------------------------------------------------------------
INTEGER, INTENT(in) :: kstatus
CHARACTER(LEN=*), INTENT(in) :: cdinfo
!---------------------------------------------------------------------
IF(kstatus /= nf90_noerr) CALL ctl_stop( 'iom_nf90_check : '//TRIM(nf90_strerror(kstatus)), TRIM(cdinfo) )
END SUBROUTINE iom_nf90_check
!!======================================================================
END MODULE iom_nf90