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diaobs.F90 in branches/UKMO/dev_r5518_obs_oper_update_bgc3d/NEMOGCM/NEMO/OPA_SRC/OBS – NEMO

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source: branches/UKMO/dev_r5518_obs_oper_update_bgc3d/NEMOGCM/NEMO/OPA_SRC/OBS/diaobs.F90 @ 9202

Last change on this file since 9202 was 9202, checked in by dford, 6 years ago
Modify obs_rea_prof to loop over an arbitrary number of variables.
File size: 83.8 KB

Line
1	MODULE diaobs
2	!!======================================================================
3	!! * MODULE diaobs *
4	!! Observation diagnostics: Computation of the misfit between data and
5	!! their model equivalent
6	!!======================================================================
7
8	!!----------------------------------------------------------------------
9	!! dia_obs_init : Reading and prepare observations
10	!! dia_obs : Compute model equivalent to observations
11	!! dia_obs_wri : Write observational diagnostics
12	!! ini_date : Compute the initial date YYYYMMDD.HHMMSS
13	!! fin_date : Compute the final date YYYYMMDD.HHMMSS
14	!!----------------------------------------------------------------------
15	!! * Modules used
16	USE wrk_nemo ! Memory Allocation
17	USE par_kind ! Precision variables
18	USE in_out_manager ! I/O manager
19	USE par_oce
20	USE dom_oce ! Ocean space and time domain variables
21	USE obs_read_prof ! Reading and allocation of profile obs
22	USE obs_read_surf ! Reading and allocation of surface obs
23	USE obs_readmdt ! Reading and allocation of MDT for SLA.
24	USE obs_prep ! Preparation of obs. (grid search etc).
25	USE obs_oper ! Observation operators
26	USE obs_write ! Writing of observation related diagnostics
27	USE obs_grid ! Grid searching
28	USE obs_read_altbias ! Bias treatment for altimeter
29	USE obs_sstbias ! Bias correction routine for SST
30	USE obs_profiles_def ! Profile data definitions
31	USE obs_surf_def ! Surface data definitions
32	USE obs_types ! Definitions for observation types
33	USE mpp_map ! MPP mapping
34	USE lib_mpp ! For ctl_warn/stop
35
36	IMPLICIT NONE
37
38	!! * Routine accessibility
39	PRIVATE
40	PUBLIC dia_obs_init, & ! Initialize and read observations
41	& dia_obs, & ! Compute model equivalent to observations
42	& dia_obs_wri, & ! Write model equivalent to observations
43	& dia_obs_dealloc ! Deallocate dia_obs data
44
45	!! * Module variables
46	LOGICAL, PUBLIC :: &
47	& lk_diaobs = .TRUE. !: Include this for backwards compatibility at NEMO 3.6.
48	LOGICAL :: ln_diaobs !: Logical switch for the obs operator
49	LOGICAL :: ln_sstnight !: Logical switch for night mean SST obs
50	LOGICAL :: ln_default_fp_indegs !: T=> Default obs footprint size specified in degrees, F=> in metres
51	LOGICAL :: ln_sla_fp_indegs !: T=> SLA obs footprint size specified in degrees, F=> in metres
52	LOGICAL :: ln_sst_fp_indegs !: T=> SST obs footprint size specified in degrees, F=> in metres
53	LOGICAL :: ln_sss_fp_indegs !: T=> SSS obs footprint size specified in degrees, F=> in metres
54	LOGICAL :: ln_sic_fp_indegs !: T=> sea-ice obs footprint size specified in degrees, F=> in metres
55
56	REAL(wp) :: rn_default_avglamscl !: Default E/W diameter of observation footprint
57	REAL(wp) :: rn_default_avgphiscl !: Default N/S diameter of observation footprint
58	REAL(wp) :: rn_sla_avglamscl !: E/W diameter of SLA observation footprint
59	REAL(wp) :: rn_sla_avgphiscl !: N/S diameter of SLA observation footprint
60	REAL(wp) :: rn_sst_avglamscl !: E/W diameter of SST observation footprint
61	REAL(wp) :: rn_sst_avgphiscl !: N/S diameter of SST observation footprint
62	REAL(wp) :: rn_sss_avglamscl !: E/W diameter of SSS observation footprint
63	REAL(wp) :: rn_sss_avgphiscl !: N/S diameter of SSS observation footprint
64	REAL(wp) :: rn_sic_avglamscl !: E/W diameter of sea-ice observation footprint
65	REAL(wp) :: rn_sic_avgphiscl !: N/S diameter of sea-ice observation footprint
66
67	INTEGER :: nn_1dint !: Vertical interpolation method
68	INTEGER :: nn_2dint_default !: Default horizontal interpolation method
69	INTEGER :: nn_2dint_sla !: SLA horizontal interpolation method (-1 = default)
70	INTEGER :: nn_2dint_sst !: SST horizontal interpolation method (-1 = default)
71	INTEGER :: nn_2dint_sss !: SSS horizontal interpolation method (-1 = default)
72	INTEGER :: nn_2dint_sic !: Seaice horizontal interpolation method (-1 = default)
73
74	INTEGER, DIMENSION(imaxavtypes) :: &
75	& nn_profdavtypes !: Profile data types representing a daily average
76	INTEGER :: nproftypes !: Number of profile obs types
77	INTEGER :: nsurftypes !: Number of surface obs types
78	INTEGER, DIMENSION(:), ALLOCATABLE :: &
79	& nvarsprof, & !: Number of profile variables
80	& nvarssurf !: Number of surface variables
81	INTEGER, DIMENSION(:), ALLOCATABLE :: &
82	& nextrprof, & !: Number of profile extra variables
83	& nextrsurf !: Number of surface extra variables
84	INTEGER, DIMENSION(:), ALLOCATABLE :: &
85	& n2dintsurf !: Interpolation option for surface variables
86	REAL(wp), DIMENSION(:), ALLOCATABLE :: &
87	& ravglamscl, & !: E/W diameter of averaging footprint for surface variables
88	& ravgphiscl !: N/S diameter of averaging footprint for surface variables
89	LOGICAL, DIMENSION(:), ALLOCATABLE :: &
90	& lfpindegs, & !: T=> surface obs footprint size specified in degrees, F=> in metres
91	& llnightav !: Logical for calculating night-time averages
92
93	TYPE(obs_surf), PUBLIC, POINTER, DIMENSION(:) :: &
94	& surfdata, & !: Initial surface data
95	& surfdataqc !: Surface data after quality control
96	TYPE(obs_prof), PUBLIC, POINTER, DIMENSION(:) :: &
97	& profdata, & !: Initial profile data
98	& profdataqc !: Profile data after quality control
99
100	CHARACTER(len=8), PUBLIC, DIMENSION(:), ALLOCATABLE :: &
101	& cobstypesprof, & !: Profile obs types
102	& cobstypessurf !: Surface obs types
103
104	!!----------------------------------------------------------------------
105	!! NEMO/OPA 3.3 , NEMO Consortium (2010)
106	!! $Id$
107	!! Software governed by the CeCILL licence (NEMOGCM/NEMO_CeCILL.txt)
108	!!----------------------------------------------------------------------
109
110	!! * Substitutions
111	# include "domzgr_substitute.h90"
112	CONTAINS
113
114	SUBROUTINE dia_obs_init
115	!!----------------------------------------------------------------------
116	!! * ROUTINE dia_obs_init *
117	!!
118	!! ** Purpose : Initialize and read observations
119	!!
120	!! ** Method : Read the namelist and call reading routines
121	!!
122	!! ** Action : Read the namelist and call reading routines
123	!!
124	!! History :
125	!! ! 06-03 (K. Mogensen) Original code
126	!! ! 06-05 (A. Weaver) Reformatted
127	!! ! 06-10 (A. Weaver) Cleaning and add controls
128	!! ! 07-03 (K. Mogensen) General handling of profiles
129	!! ! 14-08 (J.While) Incorporated SST bias correction
130	!! ! 15-02 (M. Martin) Simplification of namelist and code
131	!!----------------------------------------------------------------------
132
133	IMPLICIT NONE
134
135	!! * Local declarations
136	INTEGER, PARAMETER :: &
137	& jpmaxnfiles = 1000 ! Maximum number of files for each obs type
138	INTEGER, DIMENSION(:), ALLOCATABLE :: &
139	& ifilesprof, & ! Number of profile files
140	& ifilessurf ! Number of surface files
141	INTEGER :: ios ! Local integer output status for namelist read
142	INTEGER :: jtype ! Counter for obs types
143	INTEGER :: jvar ! Counter for variables
144	INTEGER :: jfile ! Counter for files
145	INTEGER :: jnumsstbias ! Number of SST bias files to read and apply
146	INTEGER :: n2dint_type ! Local version of nn_2dint*
147
148	CHARACTER(len=128), DIMENSION(jpmaxnfiles) :: &
149	& cn_profbfiles, & ! T/S profile input filenames
150	& cn_sstfbfiles, & ! Sea surface temperature input filenames
151	& cn_slafbfiles, & ! Sea level anomaly input filenames
152	& cn_sicfbfiles, & ! Seaice concentration input filenames
153	& cn_velfbfiles, & ! Velocity profile input filenames
154	& cn_sssfbfiles, & ! Sea surface salinity input filenames
155	& cn_slchltotfbfiles, & ! Surface total log10(chlorophyll) input filenames
156	& cn_slchldiafbfiles, & ! Surface diatom log10(chlorophyll) input filenames
157	& cn_slchlnonfbfiles, & ! Surface non-diatom log10(chlorophyll) input filenames
158	& cn_slchldinfbfiles, & ! Surface dinoflagellate log10(chlorophyll) input filenames
159	& cn_slchlmicfbfiles, & ! Surface microphytoplankton log10(chlorophyll) input filenames
160	& cn_slchlnanfbfiles, & ! Surface nanophytoplankton log10(chlorophyll) input filenames
161	& cn_slchlpicfbfiles, & ! Surface picophytoplankton log10(chlorophyll) input filenames
162	& cn_schltotfbfiles, & ! Surface total chlorophyll input filenames
163	& cn_sspmfbfiles, & ! Surface suspended particulate matter input filenames
164	& cn_sfco2fbfiles, & ! Surface fugacity of carbon dioxide input filenames
165	& cn_spco2fbfiles, & ! Surface partial pressure of carbon dioxide input filenames
166	& cn_plchltotfbfiles, & ! Profile total log10(chlorophyll) input filenames
167	& cn_pchltotfbfiles, & ! Profile total chlorophyll input filenames
168	& cn_pno3fbfiles, & ! Profile nitrate input filenames
169	& cn_psi4fbfiles, & ! Profile silicate input filenames
170	& cn_ppo4fbfiles, & ! Profile phosphate input filenames
171	& cn_pdicfbfiles, & ! Profile dissolved inorganic carbon input filenames
172	& cn_palkfbfiles, & ! Profile alkalinity input filenames
173	& cn_pphfbfiles, & ! Profile pH input filenames
174	& cn_po2fbfiles, & ! Profile dissolved oxygen input filenames
175	& cn_sstbiasfiles ! SST bias input filenames
176
177	CHARACTER(LEN=128) :: &
178	& cn_altbiasfile ! Altimeter bias input filename
179
180
181	LOGICAL :: ln_t3d ! Logical switch for temperature profiles
182	LOGICAL :: ln_s3d ! Logical switch for salinity profiles
183	LOGICAL :: ln_sla ! Logical switch for sea level anomalies
184	LOGICAL :: ln_sst ! Logical switch for sea surface temperature
185	LOGICAL :: ln_sic ! Logical switch for sea ice concentration
186	LOGICAL :: ln_sss ! Logical switch for sea surface salinity obs
187	LOGICAL :: ln_vel3d ! Logical switch for velocity (u,v) obs
188	LOGICAL :: ln_slchltot ! Logical switch for surface total log10(chlorophyll) obs
189	LOGICAL :: ln_slchldia ! Logical switch for surface diatom log10(chlorophyll) obs
190	LOGICAL :: ln_slchlnon ! Logical switch for surface non-diatom log10(chlorophyll) obs
191	LOGICAL :: ln_slchldin ! Logical switch for surface dinoflagellate log10(chlorophyll) obs
192	LOGICAL :: ln_slchlmic ! Logical switch for surface microphytoplankton log10(chlorophyll) obs
193	LOGICAL :: ln_slchlnan ! Logical switch for surface nanophytoplankton log10(chlorophyll) obs
194	LOGICAL :: ln_slchlpic ! Logical switch for surface picophytoplankton log10(chlorophyll) obs
195	LOGICAL :: ln_schltot ! Logical switch for surface total chlorophyll obs
196	LOGICAL :: ln_sspm ! Logical switch for surface suspended particulate matter obs
197	LOGICAL :: ln_sfco2 ! Logical switch for surface fugacity of carbon dioxide obs
198	LOGICAL :: ln_spco2 ! Logical switch for surface partial pressure of carbon dioxide obs
199	LOGICAL :: ln_plchltot ! Logical switch for profile total log10(chlorophyll) obs
200	LOGICAL :: ln_pchltot ! Logical switch for profile total chlorophyll obs
201	LOGICAL :: ln_pno3 ! Logical switch for profile nitrate obs
202	LOGICAL :: ln_psi4 ! Logical switch for profile silicate obs
203	LOGICAL :: ln_ppo4 ! Logical switch for profile phosphate obs
204	LOGICAL :: ln_pdic ! Logical switch for profile dissolved inorganic carbon obs
205	LOGICAL :: ln_palk ! Logical switch for profile alkalinity obs
206	LOGICAL :: ln_pph ! Logical switch for profile pH obs
207	LOGICAL :: ln_po2 ! Logical switch for profile dissolved oxygen obs
208	LOGICAL :: ln_nea ! Logical switch to remove obs near land
209	LOGICAL :: ln_altbias ! Logical switch for altimeter bias
210	LOGICAL :: ln_sstbias ! Logical switch for bias correction of SST
211	LOGICAL :: ln_ignmis ! Logical switch for ignoring missing files
212	LOGICAL :: ln_s_at_t ! Logical switch to compute model S at T obs
213	LOGICAL :: ln_bound_reject ! Logical switch for rejecting obs near the boundary
214
215	REAL(dp) :: rn_dobsini ! Obs window start date YYYYMMDD.HHMMSS
216	REAL(dp) :: rn_dobsend ! Obs window end date YYYYMMDD.HHMMSS
217
218	REAL(wp) :: rtype_avglamscl ! Local version of rn_*_avglamscl
219	REAL(wp) :: rtype_avgphiscl ! Local version of rn_*_avgphiscl
220
221	CHARACTER(len=128), DIMENSION(:,:), ALLOCATABLE :: &
222	& clproffiles, & ! Profile filenames
223	& clsurffiles ! Surface filenames
224
225	LOGICAL, DIMENSION(:), ALLOCATABLE :: llvar ! Logical for profile variable read
226	LOGICAL :: ltype_fp_indegs ! Local version of ln_*_fp_indegs
227	LOGICAL :: ltype_night ! Local version of ln_sstnight (false for other variables)
228
229	REAL(wp), POINTER, DIMENSION(:,:) :: &
230	& zglam1, & ! Model longitudes for profile variable 1
231	& zglam2 ! Model longitudes for profile variable 2
232	REAL(wp), POINTER, DIMENSION(:,:) :: &
233	& zgphi1, & ! Model latitudes for profile variable 1
234	& zgphi2 ! Model latitudes for profile variable 2
235	REAL(wp), POINTER, DIMENSION(:,:,:) :: &
236	& zmask1, & ! Model land/sea mask associated with variable 1
237	& zmask2 ! Model land/sea mask associated with variable 2
238
239
240	NAMELIST/namobs/ln_diaobs, ln_t3d, ln_s3d, ln_sla, &
241	& ln_sst, ln_sic, ln_sss, ln_vel3d, &
242	& ln_slchltot, ln_slchldia, ln_slchlnon, &
243	& ln_slchldin, ln_slchlmic, ln_slchlnan, &
244	& ln_slchlpic, ln_schltot, &
245	& ln_sspm, ln_sfco2, ln_spco2, &
246	& ln_plchltot, ln_pchltot, ln_pno3, &
247	& ln_psi4, ln_ppo4, ln_pdic, &
248	& ln_palk, ln_pph, ln_po2, &
249	& ln_altbias, ln_sstbias, ln_nea, &
250	& ln_grid_global, ln_grid_search_lookup, &
251	& ln_ignmis, ln_s_at_t, ln_bound_reject, &
252	& ln_sstnight, ln_default_fp_indegs, &
253	& ln_sla_fp_indegs, ln_sst_fp_indegs, &
254	& ln_sss_fp_indegs, ln_sic_fp_indegs, &
255	& cn_profbfiles, cn_slafbfiles, &
256	& cn_sstfbfiles, cn_sicfbfiles, &
257	& cn_velfbfiles, cn_sssfbfiles, &
258	& cn_slchltotfbfiles, cn_slchldiafbfiles, &
259	& cn_slchlnonfbfiles, cn_slchldinfbfiles, &
260	& cn_slchlmicfbfiles, cn_slchlnanfbfiles, &
261	& cn_slchlpicfbfiles, &
262	& cn_schltotfbfiles, cn_sspmfbfiles, &
263	& cn_sfco2fbfiles, cn_spco2fbfiles, &
264	& cn_plchltotfbfiles, cn_pchltotfbfiles, &
265	& cn_pno3fbfiles, cn_psi4fbfiles, cn_ppo4fbfiles, &
266	& cn_pdicfbfiles, cn_palkfbfiles, cn_pphfbfiles, &
267	& cn_po2fbfiles, &
268	& cn_sstbiasfiles, cn_altbiasfile, &
269	& cn_gridsearchfile, rn_gridsearchres, &
270	& rn_dobsini, rn_dobsend, &
271	& rn_default_avglamscl, rn_default_avgphiscl, &
272	& rn_sla_avglamscl, rn_sla_avgphiscl, &
273	& rn_sst_avglamscl, rn_sst_avgphiscl, &
274	& rn_sss_avglamscl, rn_sss_avgphiscl, &
275	& rn_sic_avglamscl, rn_sic_avgphiscl, &
276	& nn_1dint, nn_2dint_default, &
277	& nn_2dint_sla, nn_2dint_sst, &
278	& nn_2dint_sss, nn_2dint_sic, &
279	& nn_msshc, rn_mdtcorr, rn_mdtcutoff, &
280	& nn_profdavtypes
281
282	CALL wrk_alloc( jpi, jpj, zglam1 )
283	CALL wrk_alloc( jpi, jpj, zglam2 )
284	CALL wrk_alloc( jpi, jpj, zgphi1 )
285	CALL wrk_alloc( jpi, jpj, zgphi2 )
286	CALL wrk_alloc( jpi, jpj, jpk, zmask1 )
287	CALL wrk_alloc( jpi, jpj, jpk, zmask2 )
288
289	!-----------------------------------------------------------------------
290	! Read namelist parameters
291	!-----------------------------------------------------------------------
292
293	! Some namelist arrays need initialising
294	cn_profbfiles(:) = ''
295	cn_slafbfiles(:) = ''
296	cn_sstfbfiles(:) = ''
297	cn_sicfbfiles(:) = ''
298	cn_velfbfiles(:) = ''
299	cn_sssfbfiles(:) = ''
300	cn_slchltotfbfiles(:) = ''
301	cn_slchldiafbfiles(:) = ''
302	cn_slchlnonfbfiles(:) = ''
303	cn_slchldinfbfiles(:) = ''
304	cn_slchlmicfbfiles(:) = ''
305	cn_slchlnanfbfiles(:) = ''
306	cn_slchlpicfbfiles(:) = ''
307	cn_schltotfbfiles(:) = ''
308	cn_sspmfbfiles(:) = ''
309	cn_sfco2fbfiles(:) = ''
310	cn_spco2fbfiles(:) = ''
311	cn_plchltotfbfiles(:) = ''
312	cn_pchltotfbfiles(:) = ''
313	cn_pno3fbfiles(:) = ''
314	cn_psi4fbfiles(:) = ''
315	cn_ppo4fbfiles(:) = ''
316	cn_pdicfbfiles(:) = ''
317	cn_palkfbfiles(:) = ''
318	cn_pphfbfiles(:) = ''
319	cn_po2fbfiles(:) = ''
320	cn_sstbiasfiles(:) = ''
321	nn_profdavtypes(:) = -1
322
323	CALL ini_date( rn_dobsini )
324	CALL fin_date( rn_dobsend )
325
326	! Read namelist namobs : control observation diagnostics
327	REWIND( numnam_ref ) ! Namelist namobs in reference namelist
328	READ ( numnam_ref, namobs, IOSTAT = ios, ERR = 901)
329	901 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namobs in reference namelist', lwp )
330
331	REWIND( numnam_cfg ) ! Namelist namobs in configuration namelist
332	READ ( numnam_cfg, namobs, IOSTAT = ios, ERR = 902 )
333	902 IF( ios /= 0 ) CALL ctl_nam ( ios , 'namobs in configuration namelist', lwp )
334	IF(lwm) WRITE ( numond, namobs )
335
336	lk_diaobs = .FALSE.
337	#if defined key_diaobs
338	IF ( ln_diaobs ) lk_diaobs = .TRUE.
339	#endif
340
341	IF ( .NOT. lk_diaobs ) THEN
342	IF(lwp) WRITE(numout,cform_war)
343	IF(lwp) WRITE(numout,*)' ln_diaobs is set to false or key_diaobs is not set, so not calling dia_obs'
344	RETURN
345	ENDIF
346
347	IF(lwp) THEN
348	WRITE(numout,*)
349	WRITE(numout,*) 'dia_obs_init : Observation diagnostic initialization'
350	WRITE(numout,*) '~~~~~~~~~~~~'
351	WRITE(numout,*) ' Namelist namobs : set observation diagnostic parameters'
352	WRITE(numout,*) ' Logical switch for T profile observations ln_t3d = ', ln_t3d
353	WRITE(numout,*) ' Logical switch for S profile observations ln_s3d = ', ln_s3d
354	WRITE(numout,*) ' Logical switch for SLA observations ln_sla = ', ln_sla
355	WRITE(numout,*) ' Logical switch for SST observations ln_sst = ', ln_sst
356	WRITE(numout,*) ' Logical switch for Sea Ice observations ln_sic = ', ln_sic
357	WRITE(numout,*) ' Logical switch for velocity observations ln_vel3d = ', ln_vel3d
358	WRITE(numout,*) ' Logical switch for SSS observations ln_sss = ', ln_sss
359	WRITE(numout,*) ' Logical switch for surface total logchl obs ln_slchltot = ', ln_slchltot
360	WRITE(numout,*) ' Logical switch for surface diatom logchl obs ln_slchldia = ', ln_slchldia
361	WRITE(numout,*) ' Logical switch for surface non-diatom logchl obs ln_slchlnon = ', ln_slchlnon
362	WRITE(numout,*) ' Logical switch for surface dino logchl obs ln_slchldin = ', ln_slchldin
363	WRITE(numout,*) ' Logical switch for surface micro logchl obs ln_slchlmic = ', ln_slchlmic
364	WRITE(numout,*) ' Logical switch for surface nano logchl obs ln_slchlnan = ', ln_slchlnan
365	WRITE(numout,*) ' Logical switch for surface pico logchl obs ln_slchlpic = ', ln_slchlpic
366	WRITE(numout,*) ' Logical switch for surface total chl obs ln_schltot = ', ln_schltot
367	WRITE(numout,*) ' Logical switch for surface SPM observations ln_sspm = ', ln_sspm
368	WRITE(numout,*) ' Logical switch for surface fCO2 observations ln_sfco2 = ', ln_sfco2
369	WRITE(numout,*) ' Logical switch for surface pCO2 observations ln_spco2 = ', ln_spco2
370	WRITE(numout,*) ' Logical switch for profile total logchl obs ln_plchltot = ', ln_plchltot
371	WRITE(numout,*) ' Logical switch for profile total chl obs ln_pchltot = ', ln_pchltot
372	WRITE(numout,*) ' Logical switch for profile nitrate obs ln_pno3 = ', ln_pno3
373	WRITE(numout,*) ' Logical switch for profile silicate obs ln_psi4 = ', ln_psi4
374	WRITE(numout,*) ' Logical switch for profile phosphate obs ln_ppo4 = ', ln_ppo4
375	WRITE(numout,*) ' Logical switch for profile DIC obs ln_pdic = ', ln_pdic
376	WRITE(numout,*) ' Logical switch for profile alkalinity obs ln_palk = ', ln_palk
377	WRITE(numout,*) ' Logical switch for profile pH obs ln_pph = ', ln_pph
378	WRITE(numout,*) ' Logical switch for profile oxygen obs ln_po2 = ', ln_po2
379	WRITE(numout,*) ' Global distribution of observations ln_grid_global = ', ln_grid_global
380	WRITE(numout,*) ' Logical switch for obs grid search lookup ln_grid_search_lookup = ', ln_grid_search_lookup
381	IF (ln_grid_search_lookup) &
382	WRITE(numout,*) ' Grid search lookup file header cn_gridsearchfile = ', cn_gridsearchfile
383	WRITE(numout,*) ' Initial date in window YYYYMMDD.HHMMSS rn_dobsini = ', rn_dobsini
384	WRITE(numout,*) ' Final date in window YYYYMMDD.HHMMSS rn_dobsend = ', rn_dobsend
385	WRITE(numout,*) ' Type of vertical interpolation method nn_1dint = ', nn_1dint
386	WRITE(numout,*) ' Default horizontal interpolation method nn_2dint_default = ', nn_2dint_default
387	WRITE(numout,*) ' Type of horizontal interpolation method for SLA nn_2dint_sla = ', nn_2dint_sla
388	WRITE(numout,*) ' Type of horizontal interpolation method for SST nn_2dint_sst = ', nn_2dint_sst
389	WRITE(numout,*) ' Type of horizontal interpolation method for SSS nn_2dint_sss = ', nn_2dint_sss
390	WRITE(numout,*) ' Type of horizontal interpolation method for SIC nn_2dint_sic = ', nn_2dint_sic
391	WRITE(numout,*) ' Default E/W diameter of obs footprint rn_default_avglamscl = ', rn_default_avglamscl
392	WRITE(numout,*) ' Default N/S diameter of obs footprint rn_default_avgphiscl = ', rn_default_avgphiscl
393	WRITE(numout,*) ' Default obs footprint in deg [T] or m [F] ln_default_fp_indegs = ', ln_default_fp_indegs
394	WRITE(numout,*) ' SLA E/W diameter of obs footprint rn_sla_avglamscl = ', rn_sla_avglamscl
395	WRITE(numout,*) ' SLA N/S diameter of obs footprint rn_sla_avgphiscl = ', rn_sla_avgphiscl
396	WRITE(numout,*) ' SLA obs footprint in deg [T] or m [F] ln_sla_fp_indegs = ', ln_sla_fp_indegs
397	WRITE(numout,*) ' SST E/W diameter of obs footprint rn_sst_avglamscl = ', rn_sst_avglamscl
398	WRITE(numout,*) ' SST N/S diameter of obs footprint rn_sst_avgphiscl = ', rn_sst_avgphiscl
399	WRITE(numout,*) ' SST obs footprint in deg [T] or m [F] ln_sst_fp_indegs = ', ln_sst_fp_indegs
400	WRITE(numout,*) ' SIC E/W diameter of obs footprint rn_sic_avglamscl = ', rn_sic_avglamscl
401	WRITE(numout,*) ' SIC N/S diameter of obs footprint rn_sic_avgphiscl = ', rn_sic_avgphiscl
402	WRITE(numout,*) ' SIC obs footprint in deg [T] or m [F] ln_sic_fp_indegs = ', ln_sic_fp_indegs
403	WRITE(numout,*) ' Rejection of observations near land switch ln_nea = ', ln_nea
404	WRITE(numout,*) ' Rejection of obs near open bdys ln_bound_reject = ', ln_bound_reject
405	WRITE(numout,*) ' MSSH correction scheme nn_msshc = ', nn_msshc
406	WRITE(numout,*) ' MDT correction rn_mdtcorr = ', rn_mdtcorr
407	WRITE(numout,*) ' MDT cutoff for computed correction rn_mdtcutoff = ', rn_mdtcutoff
408	WRITE(numout,*) ' Logical switch for alt bias ln_altbias = ', ln_altbias
409	WRITE(numout,*) ' Logical switch for sst bias ln_sstbias = ', ln_sstbias
410	WRITE(numout,*) ' Logical switch for ignoring missing files ln_ignmis = ', ln_ignmis
411	WRITE(numout,*) ' Daily average types nn_profdavtypes = ', nn_profdavtypes
412	WRITE(numout,*) ' Logical switch for night-time SST obs ln_sstnight = ', ln_sstnight
413	ENDIF
414	!-----------------------------------------------------------------------
415	! Set up list of observation types to be used
416	! and the files associated with each type
417	!-----------------------------------------------------------------------
418
419	nproftypes = COUNT( (/ln_t3d .OR. ln_s3d, ln_vel3d, ln_plchltot, &
420	& ln_pchltot, ln_pno3, ln_psi4, ln_ppo4, &
421	& ln_pdic, ln_palk, ln_pph, ln_po2 /) )
422	nsurftypes = COUNT( (/ln_sla, ln_sst, ln_sic, ln_sss, &
423	& ln_slchltot, ln_slchldia, ln_slchlnon, ln_slchldin, &
424	& ln_slchlmic, ln_slchlnan, ln_slchlpic, ln_schltot, &
425	& ln_sspm, ln_sfco2, ln_spco2 /) )
426
427	IF ( nproftypes == 0 .AND. nsurftypes == 0 ) THEN
428	IF(lwp) WRITE(numout,cform_war)
429	IF(lwp) WRITE(numout,*) ' ln_diaobs is set to true, but all obs operator logical flags', &
430	& ' are set to .FALSE. so turning off calls to dia_obs'
431	nwarn = nwarn + 1
432	lk_diaobs = .FALSE.
433	RETURN
434	ENDIF
435
436	IF(lwp) WRITE(numout,*) ' Number of profile obs types: ',nproftypes
437	IF ( nproftypes > 0 ) THEN
438
439	ALLOCATE( cobstypesprof(nproftypes) )
440	ALLOCATE( ifilesprof(nproftypes) )
441	ALLOCATE( clproffiles(nproftypes,jpmaxnfiles) )
442
443	jtype = 0
444	IF (ln_t3d .OR. ln_s3d) THEN
445	jtype = jtype + 1
446	cobstypesprof(jtype) = 'prof'
447	clproffiles(jtype,:) = cn_profbfiles
448	ENDIF
449	IF (ln_vel3d) THEN
450	jtype = jtype + 1
451	cobstypesprof(jtype) = 'vel'
452	clproffiles(jtype,:) = cn_velfbfiles
453	ENDIF
454	IF (ln_plchltot) THEN
455	jtype = jtype + 1
456	cobstypesprof(jtype) = 'plchltot'
457	clproffiles(jtype,:) = cn_plchltotfbfiles
458	ENDIF
459	IF (ln_pchltot) THEN
460	jtype = jtype + 1
461	cobstypesprof(jtype) = 'pchltot'
462	clproffiles(jtype,:) = cn_pchltotfbfiles
463	ENDIF
464	IF (ln_pno3) THEN
465	jtype = jtype + 1
466	cobstypesprof(jtype) = 'pno3'
467	clproffiles(jtype,:) = cn_pno3fbfiles
468	ENDIF
469	IF (ln_psi4) THEN
470	jtype = jtype + 1
471	cobstypesprof(jtype) = 'psi4'
472	clproffiles(jtype,:) = cn_psi4fbfiles
473	ENDIF
474	IF (ln_ppo4) THEN
475	jtype = jtype + 1
476	cobstypesprof(jtype) = 'ppo4'
477	clproffiles(jtype,:) = cn_ppo4fbfiles
478	ENDIF
479	IF (ln_pdic) THEN
480	jtype = jtype + 1
481	cobstypesprof(jtype) = 'pdic'
482	clproffiles(jtype,:) = cn_pdicfbfiles
483	ENDIF
484	IF (ln_palk) THEN
485	jtype = jtype + 1
486	cobstypesprof(jtype) = 'palk'
487	clproffiles(jtype,:) = cn_palkfbfiles
488	ENDIF
489	IF (ln_pph) THEN
490	jtype = jtype + 1
491	cobstypesprof(jtype) = 'pph'
492	clproffiles(jtype,:) = cn_pphfbfiles
493	ENDIF
494	IF (ln_po2) THEN
495	jtype = jtype + 1
496	cobstypesprof(jtype) = 'po2'
497	clproffiles(jtype,:) = cn_po2fbfiles
498	ENDIF
499
500	CALL obs_settypefiles( nproftypes, jpmaxnfiles, ifilesprof, cobstypesprof, clproffiles )
501
502	ENDIF
503
504	IF(lwp) WRITE(numout,*)' Number of surface obs types: ',nsurftypes
505	IF ( nsurftypes > 0 ) THEN
506
507	ALLOCATE( cobstypessurf(nsurftypes) )
508	ALLOCATE( ifilessurf(nsurftypes) )
509	ALLOCATE( clsurffiles(nsurftypes, jpmaxnfiles) )
510	ALLOCATE(n2dintsurf(nsurftypes))
511	ALLOCATE(ravglamscl(nsurftypes))
512	ALLOCATE(ravgphiscl(nsurftypes))
513	ALLOCATE(lfpindegs(nsurftypes))
514	ALLOCATE(llnightav(nsurftypes))
515
516	jtype = 0
517	IF (ln_sla) THEN
518	jtype = jtype + 1
519	cobstypessurf(jtype) = 'sla'
520	clsurffiles(jtype,:) = cn_slafbfiles
521	ENDIF
522	IF (ln_sst) THEN
523	jtype = jtype + 1
524	cobstypessurf(jtype) = 'sst'
525	clsurffiles(jtype,:) = cn_sstfbfiles
526	ENDIF
527	IF (ln_sic) THEN
528	jtype = jtype + 1
529	cobstypessurf(jtype) = 'sic'
530	clsurffiles(jtype,:) = cn_sicfbfiles
531	ENDIF
532	IF (ln_sss) THEN
533	jtype = jtype + 1
534	cobstypessurf(jtype) = 'sss'
535	clsurffiles(jtype,:) = cn_sssfbfiles
536	ENDIF
537	IF (ln_slchltot) THEN
538	jtype = jtype + 1
539	cobstypessurf(jtype) = 'slchltot'
540	clsurffiles(jtype,:) = cn_slchltotfbfiles
541	ENDIF
542	IF (ln_slchldia) THEN
543	jtype = jtype + 1
544	cobstypessurf(jtype) = 'slchldia'
545	clsurffiles(jtype,:) = cn_slchldiafbfiles
546	ENDIF
547	IF (ln_slchlnon) THEN
548	jtype = jtype + 1
549	cobstypessurf(jtype) = 'slchlnon'
550	clsurffiles(jtype,:) = cn_slchlnonfbfiles
551	ENDIF
552	IF (ln_slchldin) THEN
553	jtype = jtype + 1
554	cobstypessurf(jtype) = 'slchldin'
555	clsurffiles(jtype,:) = cn_slchldinfbfiles
556	ENDIF
557	IF (ln_slchlmic) THEN
558	jtype = jtype + 1
559	cobstypessurf(jtype) = 'slchlmic'
560	clsurffiles(jtype,:) = cn_slchlmicfbfiles
561	ENDIF
562	IF (ln_slchlnan) THEN
563	jtype = jtype + 1
564	cobstypessurf(jtype) = 'slchlnan'
565	clsurffiles(jtype,:) = cn_slchlnanfbfiles
566	ENDIF
567	IF (ln_slchlpic) THEN
568	jtype = jtype + 1
569	cobstypessurf(jtype) = 'slchlpic'
570	clsurffiles(jtype,:) = cn_slchlpicfbfiles
571	ENDIF
572	IF (ln_schltot) THEN
573	jtype = jtype + 1
574	cobstypessurf(jtype) = 'schltot'
575	clsurffiles(jtype,:) = cn_schltotfbfiles
576	ENDIF
577	IF (ln_sspm) THEN
578	jtype = jtype + 1
579	cobstypessurf(jtype) = 'sspm'
580	clsurffiles(jtype,:) = cn_sspmfbfiles
581	ENDIF
582	IF (ln_sfco2) THEN
583	jtype = jtype + 1
584	cobstypessurf(jtype) = 'sfco2'
585	clsurffiles(jtype,:) = cn_sfco2fbfiles
586	ENDIF
587	IF (ln_spco2) THEN
588	jtype = jtype + 1
589	cobstypessurf(jtype) = 'spco2'
590	clsurffiles(jtype,:) = cn_spco2fbfiles
591	ENDIF
592
593	CALL obs_settypefiles( nsurftypes, jpmaxnfiles, ifilessurf, cobstypessurf, clsurffiles )
594
595	DO jtype = 1, nsurftypes
596
597	IF ( TRIM(cobstypessurf(jtype)) == 'sla' ) THEN
598	IF ( nn_2dint_sla == -1 ) THEN
599	n2dint_type = nn_2dint_default
600	ELSE
601	n2dint_type = nn_2dint_sla
602	ENDIF
603	rtype_avglamscl = rn_sla_avglamscl
604	rtype_avgphiscl = rn_sla_avgphiscl
605	ltype_fp_indegs = ln_sla_fp_indegs
606	ltype_night = .FALSE.
607	ELSE IF ( TRIM(cobstypessurf(jtype)) == 'sst' ) THEN
608	IF ( nn_2dint_sst == -1 ) THEN
609	n2dint_type = nn_2dint_default
610	ELSE
611	n2dint_type = nn_2dint_sst
612	ENDIF
613	rtype_avglamscl = rn_sst_avglamscl
614	rtype_avgphiscl = rn_sst_avgphiscl
615	ltype_fp_indegs = ln_sst_fp_indegs
616	ltype_night = ln_sstnight
617	ELSE IF ( TRIM(cobstypessurf(jtype)) == 'sic' ) THEN
618	IF ( nn_2dint_sic == -1 ) THEN
619	n2dint_type = nn_2dint_default
620	ELSE
621	n2dint_type = nn_2dint_sic
622	ENDIF
623	rtype_avglamscl = rn_sic_avglamscl
624	rtype_avgphiscl = rn_sic_avgphiscl
625	ltype_fp_indegs = ln_sic_fp_indegs
626	ltype_night = .FALSE.
627	ELSE IF ( TRIM(cobstypessurf(jtype)) == 'sss' ) THEN
628	IF ( nn_2dint_sss == -1 ) THEN
629	n2dint_type = nn_2dint_default
630	ELSE
631	n2dint_type = nn_2dint_sss
632	ENDIF
633	rtype_avglamscl = rn_sss_avglamscl
634	rtype_avgphiscl = rn_sss_avgphiscl
635	ltype_fp_indegs = ln_sss_fp_indegs
636	ltype_night = .FALSE.
637	ELSE
638	n2dint_type = nn_2dint_default
639	rtype_avglamscl = rn_default_avglamscl
640	rtype_avgphiscl = rn_default_avgphiscl
641	ltype_fp_indegs = ln_default_fp_indegs
642	ltype_night = .FALSE.
643	ENDIF
644
645	CALL obs_setinterpopts( nsurftypes, jtype, TRIM(cobstypessurf(jtype)), &
646	& nn_2dint_default, n2dint_type, &
647	& rtype_avglamscl, rtype_avgphiscl, &
648	& ltype_fp_indegs, ltype_night, &
649	& n2dintsurf, ravglamscl, ravgphiscl, &
650	& lfpindegs, llnightav )
651
652	END DO
653
654	ENDIF
655
656	IF(lwp) WRITE(numout,*) '~~~~~~~~~~~~'
657
658
659	!-----------------------------------------------------------------------
660	! Obs operator parameter checking and initialisations
661	!-----------------------------------------------------------------------
662
663	IF ( ln_vel3d .AND. ( .NOT. ln_grid_global ) ) THEN
664	CALL ctl_stop( 'Velocity data only works with ln_grid_global=.true.' )
665	RETURN
666	ENDIF
667
668	IF ( ( nn_1dint < 0 ) .OR. ( nn_1dint > 1 ) ) THEN
669	CALL ctl_stop(' Choice of vertical (1D) interpolation method', &
670	& ' is not available')
671	ENDIF
672
673	IF ( ( nn_2dint_default < 0 ) .OR. ( nn_2dint_default > 6 ) ) THEN
674	CALL ctl_stop(' Choice of default horizontal (2D) interpolation method', &
675	& ' is not available')
676	ENDIF
677
678	CALL obs_typ_init
679
680	CALL mppmap_init
681
682	CALL obs_grid_setup( )
683
684	!-----------------------------------------------------------------------
685	! Depending on switches read the various observation types
686	!-----------------------------------------------------------------------
687
688	IF ( nproftypes > 0 ) THEN
689
690	ALLOCATE(profdata(nproftypes))
691	ALLOCATE(profdataqc(nproftypes))
692	ALLOCATE(nvarsprof(nproftypes))
693	ALLOCATE(nextrprof(nproftypes))
694
695	DO jtype = 1, nproftypes
696
697	IF ( TRIM(cobstypesprof(jtype)) == 'prof' ) THEN
698	nvarsprof(jtype) = 2
699	nextrprof(jtype) = 1
700	ALLOCATE(llvar(nvarsprof(jtype)))
701	llvar(1) = ln_t3d
702	llvar(2) = ln_s3d
703	zglam1 = glamt
704	zgphi1 = gphit
705	zmask1 = tmask
706	zglam2 = glamt
707	zgphi2 = gphit
708	zmask2 = tmask
709	ELSE IF ( TRIM(cobstypesprof(jtype)) == 'vel' ) THEN
710	nvarsprof(jtype) = 2
711	nextrprof(jtype) = 2
712	ALLOCATE(llvar(nvarsprof(jtype)))
713	llvar(1) = ln_vel3d
714	llvar(2) = ln_vel3d
715	zglam1 = glamu
716	zgphi1 = gphiu
717	zmask1 = umask
718	zglam2 = glamv
719	zgphi2 = gphiv
720	zmask2 = vmask
721	ELSE
722	nvarsprof(jtype) = 1
723	nextrprof(jtype) = 0
724	ALLOCATE(llvar(nvarsprof(jtype)))
725	llvar(1) = .TRUE.
726	zglam1 = glamt
727	zgphi1 = gphit
728	zmask1 = tmask
729	zglam2 = glamt
730	zgphi2 = gphit
731	zmask2 = tmask
732	ENDIF
733
734	!Read in profile or profile obs types
735	CALL obs_rea_prof( profdata(jtype), ifilesprof(jtype), &
736	& clproffiles(jtype,1:ifilesprof(jtype)), &
737	& nvarsprof(jtype), nextrprof(jtype), nitend-nit000+2, &
738	& rn_dobsini, rn_dobsend, llvar, &
739	& ln_ignmis, ln_s_at_t, .FALSE., &
740	& kdailyavtypes = nn_profdavtypes )
741
742	DO jvar = 1, nvarsprof(jtype)
743	CALL obs_prof_staend( profdata(jtype), jvar )
744	END DO
745
746	CALL obs_pre_prof( profdata(jtype), profdataqc(jtype), &
747	& llvar(1), llvar(2), &
748	& jpi, jpj, jpk, &
749	& zmask1, zglam1, zgphi1, zmask2, zglam2, zgphi2, &
750	& ln_nea, ln_bound_reject, &
751	& kdailyavtypes = nn_profdavtypes )
752
753	! Is allocating and deallocating repeatedly in a loop good practice?
754	DEALLOCATE(llvar)
755
756	END DO
757
758	DEALLOCATE( ifilesprof, clproffiles )
759
760	ENDIF
761
762	IF ( nsurftypes > 0 ) THEN
763
764	ALLOCATE(surfdata(nsurftypes))
765	ALLOCATE(surfdataqc(nsurftypes))
766	ALLOCATE(nvarssurf(nsurftypes))
767	ALLOCATE(nextrsurf(nsurftypes))
768
769	DO jtype = 1, nsurftypes
770
771	nvarssurf(jtype) = 1
772	nextrsurf(jtype) = 0
773	IF ( TRIM(cobstypessurf(jtype)) == 'sla' ) nextrsurf(jtype) = 2
774
775	!Read in surface obs types
776	CALL obs_rea_surf( surfdata(jtype), ifilessurf(jtype), &
777	& clsurffiles(jtype,1:ifilessurf(jtype)), &
778	& nvarssurf(jtype), nextrsurf(jtype), nitend-nit000+2, &
779	& rn_dobsini, rn_dobsend, ln_ignmis, .FALSE., llnightav(jtype) )
780
781	CALL obs_pre_surf( surfdata(jtype), surfdataqc(jtype), ln_nea, ln_bound_reject )
782
783	IF ( TRIM(cobstypessurf(jtype)) == 'sla' ) THEN
784	CALL obs_rea_mdt( surfdataqc(jtype), n2dintsurf(jtype) )
785	IF ( ln_altbias ) &
786	& CALL obs_rea_altbias ( surfdataqc(jtype), n2dintsurf(jtype), cn_altbiasfile )
787	ENDIF
788
789	IF ( TRIM(cobstypessurf(jtype)) == 'sst' .AND. ln_sstbias ) THEN
790	jnumsstbias = 0
791	DO jfile = 1, jpmaxnfiles
792	IF ( TRIM(cn_sstbiasfiles(jfile)) /= '' ) &
793	& jnumsstbias = jnumsstbias + 1
794	END DO
795	IF ( jnumsstbias == 0 ) THEN
796	CALL ctl_stop("ln_sstbias set but no bias files to read in")
797	ENDIF
798
799	CALL obs_app_sstbias( surfdataqc(jtype), n2dintsurf(jtype), &
800	& jnumsstbias, cn_sstbiasfiles(1:jnumsstbias) )
801
802	ENDIF
803
804	END DO
805
806	DEALLOCATE( ifilessurf, clsurffiles )
807
808	ENDIF
809
810	CALL wrk_dealloc( jpi, jpj, zglam1 )
811	CALL wrk_dealloc( jpi, jpj, zglam2 )
812	CALL wrk_dealloc( jpi, jpj, zgphi1 )
813	CALL wrk_dealloc( jpi, jpj, zgphi2 )
814	CALL wrk_dealloc( jpi, jpj, jpk, zmask1 )
815	CALL wrk_dealloc( jpi, jpj, jpk, zmask2 )
816
817	END SUBROUTINE dia_obs_init
818
819	SUBROUTINE dia_obs( kstp )
820	!!----------------------------------------------------------------------
821	!! * ROUTINE dia_obs *
822	!!
823	!! ** Purpose : Call the observation operators on each time step
824	!!
825	!! ** Method : Call the observation operators on each time step to
826	!! compute the model equivalent of the following data:
827	!! - Profile data, currently T/S or U/V
828	!! - Surface data, currently SST, SLA or sea-ice concentration.
829	!!
830	!! ** Action :
831	!!
832	!! History :
833	!! ! 06-03 (K. Mogensen) Original code
834	!! ! 06-05 (K. Mogensen) Reformatted
835	!! ! 06-10 (A. Weaver) Cleaning
836	!! ! 07-03 (K. Mogensen) General handling of profiles
837	!! ! 07-04 (G. Smith) Generalized surface operators
838	!! ! 08-10 (M. Valdivieso) obs operator for velocity profiles
839	!! ! 15-08 (M. Martin) Combined surface/profile routines.
840	!!----------------------------------------------------------------------
841	!! * Modules used
842	USE phycst, ONLY : & ! Physical constants
843	& rday
844	USE oce, ONLY : & ! Ocean dynamics and tracers variables
845	& tsn, &
846	& un, &
847	& vn, &
848	& sshn
849	#if defined key_lim3
850	USE ice, ONLY : & ! LIM3 Ice model variables
851	& frld
852	#endif
853	#if defined key_lim2
854	USE ice_2, ONLY : & ! LIM2 Ice model variables
855	& frld
856	#endif
857	#if defined key_cice
858	USE sbc_oce, ONLY : fr_i ! ice fraction
859	#endif
860	#if defined key_hadocc
861	USE trc, ONLY : & ! HadOCC variables
862	& trn, &
863	& HADOCC_CHL, &
864	& HADOCC_FCO2, &
865	& HADOCC_PCO2, &
866	& HADOCC_FILL_FLT
867	USE par_hadocc
868	#elif defined key_medusa && defined key_foam_medusa
869	USE trc, ONLY : & ! MEDUSA variables
870	& trn
871	USE par_medusa
872	#if defined key_roam
873	USE sms_medusa, ONLY: &
874	& f2_pco2w, &
875	& f2_fco2w, &
876	& f3_pH
877	#endif
878	#elif defined key_fabm
879	USE fabm
880	USE par_fabm
881	#endif
882	#if defined key_spm
883	USE par_spm, ONLY: & ! ERSEM/SPM sediments
884	& jp_spm
885	USE trc, ONLY : &
886	& trn
887	#endif
888
889	IMPLICIT NONE
890
891	!! * Arguments
892	INTEGER, INTENT(IN) :: kstp ! Current timestep
893	!! * Local declarations
894	INTEGER :: idaystp ! Number of timesteps per day
895	INTEGER :: jtype ! Data loop variable
896	INTEGER :: jvar ! Variable number
897	INTEGER :: ji, jj ! Loop counters
898	REAL(wp) :: tiny ! small number
899	REAL(wp), POINTER, DIMENSION(:,:,:) :: &
900	& zprofvar1, & ! Model values for 1st variable in a prof ob
901	& zprofvar2 ! Model values for 2nd variable in a prof ob
902	REAL(wp), POINTER, DIMENSION(:,:,:) :: &
903	& zprofmask1, & ! Mask associated with zprofvar1
904	& zprofmask2 ! Mask associated with zprofvar2
905	REAL(wp), POINTER, DIMENSION(:,:) :: &
906	& zsurfvar, & ! Model values equivalent to surface ob.
907	& zsurfmask ! Mask associated with surface variable
908	REAL(wp), POINTER, DIMENSION(:,:) :: &
909	& zglam1, & ! Model longitudes for prof variable 1
910	& zglam2, & ! Model longitudes for prof variable 2
911	& zgphi1, & ! Model latitudes for prof variable 1
912	& zgphi2 ! Model latitudes for prof variable 2
913	LOGICAL :: llog10 ! Perform log10 transform of variable
914
915
916	!Allocate local work arrays
917	CALL wrk_alloc( jpi, jpj, jpk, zprofvar1 )
918	CALL wrk_alloc( jpi, jpj, jpk, zprofvar2 )
919	CALL wrk_alloc( jpi, jpj, jpk, zprofmask1 )
920	CALL wrk_alloc( jpi, jpj, jpk, zprofmask2 )
921	CALL wrk_alloc( jpi, jpj, zsurfvar )
922	CALL wrk_alloc( jpi, jpj, zsurfmask )
923	CALL wrk_alloc( jpi, jpj, zglam1 )
924	CALL wrk_alloc( jpi, jpj, zglam2 )
925	CALL wrk_alloc( jpi, jpj, zgphi1 )
926	CALL wrk_alloc( jpi, jpj, zgphi2 )
927
928	IF(lwp) THEN
929	WRITE(numout,*)
930	WRITE(numout,*) 'dia_obs : Call the observation operators', kstp
931	WRITE(numout,*) '~~~~~~~'
932	CALL FLUSH(numout)
933	ENDIF
934
935	idaystp = NINT( rday / rdt )
936
937	!-----------------------------------------------------------------------
938	! Call the profile and surface observation operators
939	!-----------------------------------------------------------------------
940
941	IF ( nproftypes > 0 ) THEN
942
943	DO jtype = 1, nproftypes
944
945	SELECT CASE ( TRIM(cobstypesprof(jtype)) )
946	CASE('prof')
947	zprofvar1(:,:,:) = tsn(:,:,:,jp_tem)
948	zprofvar2(:,:,:) = tsn(:,:,:,jp_sal)
949	zprofmask1(:,:,:) = tmask(:,:,:)
950	zprofmask2(:,:,:) = tmask(:,:,:)
951	zglam1(:,:) = glamt(:,:)
952	zglam2(:,:) = glamt(:,:)
953	zgphi1(:,:) = gphit(:,:)
954	zgphi2(:,:) = gphit(:,:)
955	CASE('vel')
956	zprofvar1(:,:,:) = un(:,:,:)
957	zprofvar2(:,:,:) = vn(:,:,:)
958	zprofmask1(:,:,:) = umask(:,:,:)
959	zprofmask2(:,:,:) = vmask(:,:,:)
960	zglam1(:,:) = glamu(:,:)
961	zglam2(:,:) = glamv(:,:)
962	zgphi1(:,:) = gphiu(:,:)
963	zgphi2(:,:) = gphiv(:,:)
964
965	CASE('plchltot')
966	#if defined key_hadocc
967	! Chlorophyll from HadOCC
968	zprofvar1(:,:,:) = HADOCC_CHL(:,:,:)
969	#elif defined key_medusa && defined key_foam_medusa
970	! Add non-diatom and diatom chlorophyll from MEDUSA
971	zprofvar1(:,:,:) = trn(:,:,:,jpchn) + trn(:,:,:,jpchd)
972	#elif defined key_fabm
973	! Add all chlorophyll groups from ERSEM
974	zprofvar1(:,:,:) = trn(:,:,:,jp_fabm_chl1) + trn(:,:,:,jp_fabm_chl2) + &
975	& trn(:,:,:,jp_fabm_chl3) + trn(:,:,:,jp_fabm_chl4)
976	#else
977	CALL ctl_stop( ' Trying to run plchltot observation operator', &
978	& ' but no biogeochemical model appears to have been defined' )
979	#endif
980	zprofmask1(:,:,:) = tmask(:,:,:)
981	! Take the log10 where we can, otherwise exclude
982	tiny = 1.0e-20
983	WHERE(zprofvar1(:,:,:) > tiny .AND. zprofvar1(:,:,:) /= obfillflt )
984	zprofvar1(:,:,:) = LOG10(zprofvar1(:,:,:))
985	ELSEWHERE
986	zprofvar1(:,:,:) = obfillflt
987	zprofmask1(:,:,:) = 0
988	END WHERE
989	zglam1(:,:) = glamt(:,:)
990	zgphi1(:,:) = gphit(:,:)
991
992	CASE('pchltot')
993	#if defined key_hadocc
994	! Chlorophyll from HadOCC
995	zprofvar1(:,:,:) = HADOCC_CHL(:,:,:)
996	#elif defined key_medusa && defined key_foam_medusa
997	! Add non-diatom and diatom chlorophyll from MEDUSA
998	zprofvar1(:,:,:) = trn(:,:,:,jpchn) + trn(:,:,:,jpchd)
999	#elif defined key_fabm
1000	! Add all chlorophyll groups from ERSEM
1001	zprofvar1(:,:,:) = trn(:,:,:,jp_fabm_chl1) + trn(:,:,:,jp_fabm_chl2) + &
1002	& trn(:,:,:,jp_fabm_chl3) + trn(:,:,:,jp_fabm_chl4)
1003	#else
1004	CALL ctl_stop( ' Trying to run pchltot observation operator', &
1005	& ' but no biogeochemical model appears to have been defined' )
1006	#endif
1007	zprofmask1(:,:,:) = tmask(:,:,:)
1008	zglam1(:,:) = glamt(:,:)
1009	zgphi1(:,:) = gphit(:,:)
1010
1011	CASE('pno3')
1012	#if defined key_hadocc
1013	! Dissolved inorganic nitrogen from HadOCC
1014	zprofvar1(:,:,:) = trn(:,:,:,jp_had_nut)
1015	#elif defined key_medusa && defined key_foam_medusa
1016	! Dissolved inorganic nitrogen from MEDUSA
1017	zprofvar1(:,:,:) = trn(:,:,:,jpdin)
1018	#elif defined key_fabm
1019	! Nitrate from ERSEM
1020	zprofvar1(:,:,:) = trn(:,:,:,jp_fabm_n3n)
1021	#else
1022	CALL ctl_stop( ' Trying to run pno3 observation operator', &
1023	& ' but no biogeochemical model appears to have been defined' )
1024	#endif
1025	zprofmask1(:,:,:) = tmask(:,:,:)
1026	zglam1(:,:) = glamt(:,:)
1027	zgphi1(:,:) = gphit(:,:)
1028
1029	CASE('psi4')
1030	#if defined key_hadocc
1031	CALL ctl_stop( ' Trying to run psi4 observation operator', &
1032	& ' but HadOCC does not simulate silicate' )
1033	#elif defined key_medusa && defined key_foam_medusa
1034	! Silicate from MEDUSA
1035	zprofvar1(:,:,:) = trn(:,:,:,jpsil)
1036	#elif defined key_fabm
1037	! Silicate from ERSEM
1038	zprofvar1(:,:,:) = trn(:,:,:,jp_fabm_n5s)
1039	#else
1040	CALL ctl_stop( ' Trying to run psi4 observation operator', &
1041	& ' but no biogeochemical model appears to have been defined' )
1042	#endif
1043	zprofmask1(:,:,:) = tmask(:,:,:)
1044	zglam1(:,:) = glamt(:,:)
1045	zgphi1(:,:) = gphit(:,:)
1046
1047	CASE('ppo4')
1048	#if defined key_hadocc
1049	CALL ctl_stop( ' Trying to run ppo4 observation operator', &
1050	& ' but HadOCC does not simulate phosphate' )
1051	#elif defined key_medusa && defined key_foam_medusa
1052	CALL ctl_stop( ' Trying to run ppo4 observation operator', &
1053	& ' but MEDUSA does not simulate phosphate' )
1054	#elif defined key_fabm
1055	! Phosphate from ERSEM
1056	zprofvar1(:,:,:) = trn(:,:,:,jp_fabm_n1p)
1057	#else
1058	CALL ctl_stop( ' Trying to run ppo4 observation operator', &
1059	& ' but no biogeochemical model appears to have been defined' )
1060	#endif
1061	zprofmask1(:,:,:) = tmask(:,:,:)
1062	zglam1(:,:) = glamt(:,:)
1063	zgphi1(:,:) = gphit(:,:)
1064
1065	CASE('pdic')
1066	#if defined key_hadocc
1067	! Dissolved inorganic carbon from HadOCC
1068	zprofvar1(:,:,:) = trn(:,:,:,jp_had_dic)
1069	#elif defined key_medusa && defined key_foam_medusa
1070	! Dissolved inorganic carbon from MEDUSA
1071	zprofvar1(:,:,:) = trn(:,:,:,jpdic)
1072	#elif defined key_fabm
1073	! Dissolved inorganic carbon from ERSEM
1074	zprofvar1(:,:,:) = trn(:,:,:,jp_fabm_o3c)
1075	#else
1076	CALL ctl_stop( ' Trying to run pdic observation operator', &
1077	& ' but no biogeochemical model appears to have been defined' )
1078	#endif
1079	zprofmask1(:,:,:) = tmask(:,:,:)
1080	zglam1(:,:) = glamt(:,:)
1081	zgphi1(:,:) = gphit(:,:)
1082
1083	CASE('palk')
1084	#if defined key_hadocc
1085	! Alkalinity from HadOCC
1086	zprofvar1(:,:,:) = trn(:,:,:,jp_had_alk)
1087	#elif defined key_medusa && defined key_foam_medusa
1088	! Alkalinity from MEDUSA
1089	zprofvar1(:,:,:) = trn(:,:,:,jpalk)
1090	#elif defined key_fabm
1091	! Alkalinity from ERSEM
1092	zprofvar1(:,:,:) = trn(:,:,:,jp_fabm_o3a)
1093	#else
1094	CALL ctl_stop( ' Trying to run palk observation operator', &
1095	& ' but no biogeochemical model appears to have been defined' )
1096	#endif
1097	zprofmask1(:,:,:) = tmask(:,:,:)
1098	zglam1(:,:) = glamt(:,:)
1099	zgphi1(:,:) = gphit(:,:)
1100
1101	CASE('pph')
1102	#if defined key_hadocc
1103	CALL ctl_stop( ' Trying to run pph observation operator', &
1104	& ' but HadOCC has no pH diagnostic defined' )
1105	#elif defined key_medusa && defined key_foam_medusa
1106	! pH from MEDUSA
1107	zprofvar1(:,:,:) = f3_pH(:,:,:)
1108	#elif defined key_fabm
1109	! pH from ERSEM
1110	zprofvar1(:,:,:) = trn(:,:,:,jp_fabm_o3ph)
1111	#else
1112	CALL ctl_stop( ' Trying to run pph observation operator', &
1113	& ' but no biogeochemical model appears to have been defined' )
1114	#endif
1115	zprofmask1(:,:,:) = tmask(:,:,:)
1116	zglam1(:,:) = glamt(:,:)
1117	zgphi1(:,:) = gphit(:,:)
1118
1119	CASE('po2')
1120	#if defined key_hadocc
1121	CALL ctl_stop( ' Trying to run po2 observation operator', &
1122	& ' but HadOCC does not simulate oxygen' )
1123	#elif defined key_medusa && defined key_foam_medusa
1124	! Oxygen from MEDUSA
1125	zprofvar1(:,:,:) = trn(:,:,:,jpoxy)
1126	#elif defined key_fabm
1127	! Oxygen from ERSEM
1128	zprofvar1(:,:,:) = trn(:,:,:,jp_fabm_o2o)
1129	#else
1130	CALL ctl_stop( ' Trying to run po2 observation operator', &
1131	& ' but no biogeochemical model appears to have been defined' )
1132	#endif
1133	zprofmask1(:,:,:) = tmask(:,:,:)
1134	zglam1(:,:) = glamt(:,:)
1135	zgphi1(:,:) = gphit(:,:)
1136
1137	CASE DEFAULT
1138	CALL ctl_stop( 'Unknown profile observation type '//TRIM(cobstypesprof(jtype))//' in dia_obs' )
1139	END SELECT
1140
1141	IF ( ( TRIM(cobstypesprof(jtype)) /= 'prof' ) .AND. ( TRIM(cobstypesprof(jtype)) /= 'vel' ) ) THEN
1142	zprofvar2(:,:,:) = zprofvar1(:,:,:)
1143	zprofmask2(:,:,:) = zprofmask1(:,:,:)
1144	zglam2(:,:) = zglam1(:,:)
1145	zgphi2(:,:) = zgphi1(:,:)
1146	ENDIF
1147
1148	CALL obs_prof_opt( profdataqc(jtype), kstp, jpi, jpj, jpk, &
1149	& nit000, idaystp, &
1150	& zprofvar1, zprofvar2, &
1151	& fsdept(:,:,:), fsdepw(:,:,:), &
1152	& zprofmask1, zprofmask2, &
1153	& zglam1, zglam2, zgphi1, zgphi2, &
1154	& nn_1dint, nn_2dint_default, &
1155	& kdailyavtypes = nn_profdavtypes )
1156
1157	END DO
1158
1159	ENDIF
1160
1161	IF ( nsurftypes > 0 ) THEN
1162
1163	DO jtype = 1, nsurftypes
1164
1165	!Defaults which might be changed
1166	zsurfmask(:,:) = tmask(:,:,1)
1167	llog10 = .FALSE.
1168
1169	SELECT CASE ( TRIM(cobstypessurf(jtype)) )
1170	CASE('sst')
1171	zsurfvar(:,:) = tsn(:,:,1,jp_tem)
1172	CASE('sla')
1173	zsurfvar(:,:) = sshn(:,:)
1174	CASE('sss')
1175	zsurfvar(:,:) = tsn(:,:,1,jp_sal)
1176	CASE('sic')
1177	IF ( kstp == 0 ) THEN
1178	IF ( lwp .AND. surfdataqc(jtype)%nsstpmpp(1) > 0 ) THEN
1179	CALL ctl_warn( 'Sea-ice not initialised on zeroth '// &
1180	& 'time-step but some obs are valid then.' )
1181	WRITE(numout,*)surfdataqc(jtype)%nsstpmpp(1), &
1182	& ' sea-ice obs will be missed'
1183	ENDIF
1184	surfdataqc(jtype)%nsurfup = surfdataqc(jtype)%nsurfup + &
1185	& surfdataqc(jtype)%nsstp(1)
1186	CYCLE
1187	ELSE
1188	#if defined key_cice
1189	zsurfvar(:,:) = fr_i(:,:)
1190	#elif defined key_lim2 \|\| defined key_lim3
1191	zsurfvar(:,:) = 1._wp - frld(:,:)
1192	#else
1193	CALL ctl_stop( ' Trying to run sea-ice observation operator', &
1194	& ' but no sea-ice model appears to have been defined' )
1195	#endif
1196	ENDIF
1197
1198	CASE('slchltot')
1199	#if defined key_hadocc
1200	! Surface chlorophyll from HadOCC
1201	zsurfvar(:,:) = HADOCC_CHL(:,:,1)
1202	#elif defined key_medusa && defined key_foam_medusa
1203	! Add non-diatom and diatom surface chlorophyll from MEDUSA
1204	zsurfvar(:,:) = trn(:,:,1,jpchn) + trn(:,:,1,jpchd)
1205	#elif defined key_fabm
1206	! Add all surface chlorophyll groups from ERSEM
1207	zsurfvar(:,:) = trn(:,:,1,jp_fabm_chl1) + trn(:,:,1,jp_fabm_chl2) + &
1208	& trn(:,:,1,jp_fabm_chl3) + trn(:,:,1,jp_fabm_chl4)
1209	#else
1210	CALL ctl_stop( ' Trying to run slchltot observation operator', &
1211	& ' but no biogeochemical model appears to have been defined' )
1212	#endif
1213	llog10 = .TRUE.
1214
1215	CASE('slchldia')
1216	#if defined key_hadocc
1217	CALL ctl_stop( ' Trying to run slchldia observation operator', &
1218	& ' but HadOCC does not explicitly simulate diatoms' )
1219	#elif defined key_medusa && defined key_foam_medusa
1220	! Diatom surface chlorophyll from MEDUSA
1221	zsurfvar(:,:) = trn(:,:,1,jpchd)
1222	#elif defined key_fabm
1223	! Diatom surface chlorophyll from ERSEM
1224	zsurfvar(:,:) = trn(:,:,1,jp_fabm_chl1)
1225	#else
1226	CALL ctl_stop( ' Trying to run slchldia observation operator', &
1227	& ' but no biogeochemical model appears to have been defined' )
1228	#endif
1229	llog10 = .TRUE.
1230
1231	CASE('slchlnon')
1232	#if defined key_hadocc
1233	CALL ctl_stop( ' Trying to run slchlnon observation operator', &
1234	& ' but HadOCC does not explicitly simulate non-diatoms' )
1235	#elif defined key_medusa && defined key_foam_medusa
1236	! Non-diatom surface chlorophyll from MEDUSA
1237	zsurfvar(:,:) = trn(:,:,1,jpchn)
1238	#elif defined key_fabm
1239	! Add all non-diatom surface chlorophyll groups from ERSEM
1240	zsurfvar(:,:) = trn(:,:,1,jp_fabm_chl2) + &
1241	& trn(:,:,1,jp_fabm_chl3) + trn(:,:,1,jp_fabm_chl4)
1242	#else
1243	CALL ctl_stop( ' Trying to run slchlnon observation operator', &
1244	& ' but no biogeochemical model appears to have been defined' )
1245	#endif
1246	llog10 = .TRUE.
1247
1248	CASE('slchldin')
1249	#if defined key_hadocc
1250	CALL ctl_stop( ' Trying to run slchldin observation operator', &
1251	& ' but HadOCC does not explicitly simulate dinoflagellates' )
1252	#elif defined key_medusa && defined key_foam_medusa
1253	CALL ctl_stop( ' Trying to run slchldin observation operator', &
1254	& ' but MEDUSA does not explicitly simulate dinoflagellates' )
1255	#elif defined key_fabm
1256	! Dinoflagellate surface chlorophyll from ERSEM
1257	zsurfvar(:,:) = trn(:,:,1,jp_fabm_chl4)
1258	#else
1259	CALL ctl_stop( ' Trying to run slchldin observation operator', &
1260	& ' but no biogeochemical model appears to have been defined' )
1261	#endif
1262	llog10 = .TRUE.
1263
1264	CASE('slchlmic')
1265	#if defined key_hadocc
1266	CALL ctl_stop( ' Trying to run slchlmic observation operator', &
1267	& ' but HadOCC does not explicitly simulate microphytoplankton' )
1268	#elif defined key_medusa && defined key_foam_medusa
1269	CALL ctl_stop( ' Trying to run slchlmic observation operator', &
1270	& ' but MEDUSA does not explicitly simulate microphytoplankton' )
1271	#elif defined key_fabm
1272	! Add diatom and dinoflagellate surface chlorophyll from ERSEM
1273	zsurfvar(:,:) = trn(:,:,1,jp_fabm_chl1) + trn(:,:,1,jp_fabm_chl4)
1274	#else
1275	CALL ctl_stop( ' Trying to run slchlmic observation operator', &
1276	& ' but no biogeochemical model appears to have been defined' )
1277	#endif
1278	llog10 = .TRUE.
1279
1280	CASE('slchlnan')
1281	#if defined key_hadocc
1282	CALL ctl_stop( ' Trying to run slchlnan observation operator', &
1283	& ' but HadOCC does not explicitly simulate nanophytoplankton' )
1284	#elif defined key_medusa && defined key_foam_medusa
1285	CALL ctl_stop( ' Trying to run slchlnan observation operator', &
1286	& ' but MEDUSA does not explicitly simulate nanophytoplankton' )
1287	#elif defined key_fabm
1288	! Nanophytoplankton surface chlorophyll from ERSEM
1289	zsurfvar(:,:) = trn(:,:,1,jp_fabm_chl2)
1290	#else
1291	CALL ctl_stop( ' Trying to run slchlnan observation operator', &
1292	& ' but no biogeochemical model appears to have been defined' )
1293	#endif
1294	llog10 = .TRUE.
1295
1296	CASE('slchlpic')
1297	#if defined key_hadocc
1298	CALL ctl_stop( ' Trying to run slchlpic observation operator', &
1299	& ' but HadOCC does not explicitly simulate picophytoplankton' )
1300	#elif defined key_medusa && defined key_foam_medusa
1301	CALL ctl_stop( ' Trying to run slchlpic observation operator', &
1302	& ' but MEDUSA does not explicitly simulate picophytoplankton' )
1303	#elif defined key_fabm
1304	! Picophytoplankton surface chlorophyll from ERSEM
1305	zsurfvar(:,:) = trn(:,:,1,jp_fabm_chl3)
1306	#else
1307	CALL ctl_stop( ' Trying to run slchlpic observation operator', &
1308	& ' but no biogeochemical model appears to have been defined' )
1309	#endif
1310	llog10 = .TRUE.
1311
1312	CASE('schltot')
1313	#if defined key_hadocc
1314	! Surface chlorophyll from HadOCC
1315	zsurfvar(:,:) = HADOCC_CHL(:,:,1)
1316	#elif defined key_medusa && defined key_foam_medusa
1317	! Add non-diatom and diatom surface chlorophyll from MEDUSA
1318	zsurfvar(:,:) = trn(:,:,1,jpchn) + trn(:,:,1,jpchd)
1319	#elif defined key_fabm
1320	! Add all surface chlorophyll groups from ERSEM
1321	zsurfvar(:,:) = trn(:,:,1,jp_fabm_chl1) + trn(:,:,1,jp_fabm_chl2) + &
1322	& trn(:,:,1,jp_fabm_chl3) + trn(:,:,1,jp_fabm_chl4)
1323	#else
1324	CALL ctl_stop( ' Trying to run schltot observation operator', &
1325	& ' but no biogeochemical model appears to have been defined' )
1326	#endif
1327
1328	CASE('sspm')
1329	#if defined key_spm
1330	zsurfvar(:,:) = 0.0
1331	DO jn = 1, jp_spm
1332	zsurfvar(:,:) = zsurfvar(:,:) + trn(:,:,1,jn) ! sum SPM sizes
1333	END DO
1334	#else
1335	CALL ctl_stop( ' Trying to run sspm observation operator', &
1336	& ' but no spm model appears to have been defined' )
1337	#endif
1338
1339	CASE('sfco2')
1340	#if defined key_hadocc
1341	zsurfvar(:,:) = HADOCC_FCO2(:,:) ! fCO2 from HadOCC
1342	IF ( ( MINVAL( HADOCC_FCO2 ) == HADOCC_FILL_FLT ) .AND. &
1343	& ( MAXVAL( HADOCC_FCO2 ) == HADOCC_FILL_FLT ) ) THEN
1344	zsurfvar(:,:) = obfillflt
1345	zsurfmask(:,:) = 0
1346	CALL ctl_warn( ' HadOCC fCO2 values masked out for observation operator', &
1347	& ' as HADOCC_FCO2(:,:) == HADOCC_FILL_FLT' )
1348	ENDIF
1349	#elif defined key_medusa && defined key_foam_medusa && defined key_roam
1350	zsurfvar(:,:) = f2_fco2w(:,:)
1351	#elif defined key_fabm
1352	! First, get pCO2 from FABM
1353	pco2_3d(:,:,:) = fabm_get_bulk_diagnostic_data(model, jp_fabm_o3pc)
1354	zsurfvar(:,:) = pco2_3d(:,:,1)
1355	! Now, convert pCO2 to fCO2, based on SST in K. This follows the standard methodology of:
1356	! Pierrot et al. (2009), Recommendations for autonomous underway pCO2 measuring systems
1357	! and data reduction routines, Deep-Sea Research II, 56: 512-522.
1358	! and
1359	! Weiss (1974), Carbon dioxide in water and seawater: the solubility of a non-ideal gas,
1360	! Marine Chemistry, 2: 203-215.
1361	! In the implementation below, atmospheric pressure has been assumed to be 1 atm and so
1362	! not explicitly included - atmospheric pressure is not necessarily available so this is
1363	! the best assumption.
1364	! Further, the (1-xCO2)^2 term has been neglected. This is common practice
1365	! (see e.g. Zeebe and Wolf-Gladrow (2001), CO2 in Seawater: Equilibrium, Kinetics, Isotopes)
1366	! because xCO2 in atm is ~0, and so this term will only affect the result to the 3rd decimal
1367	! place for typical values, and xCO2 would need to be approximated from pCO2 anyway.
1368	zsurfvar(:,:) = zsurfvar(:,:) * EXP((-1636.75 + &
1369	& 12.0408 * (tsn(:,:,1,jp_tem)+rt0) - &
1370	& 0.0327957 * (tsn(:,:,1,jp_tem)+rt0)*(tsn(:,:,1,jp_tem)+rt0) + &
1371	& 0.0000316528 * (tsn(:,:,1,jp_tem)+rt0)(tsn(:,:,1,jp_tem)+rt0)(tsn(:,:,1,jp_tem)+rt0) + &
1372	& 2.0 * (57.7 - 0.118 * (tsn(:,:,1,jp_tem)+rt0))) / &
1373	& (82.0578 * (tsn(:,:,1,jp_tem)+rt0)))
1374	#else
1375	CALL ctl_stop( ' Trying to run sfco2 observation operator', &
1376	& ' but no biogeochemical model appears to have been defined' )
1377	#endif
1378
1379	CASE('spco2')
1380	#if defined key_hadocc
1381	zsurfvar(:,:) = HADOCC_PCO2(:,:) ! pCO2 from HadOCC
1382	IF ( ( MINVAL( HADOCC_PCO2 ) == HADOCC_FILL_FLT ) .AND. &
1383	& ( MAXVAL( HADOCC_PCO2 ) == HADOCC_FILL_FLT ) ) THEN
1384	zsurfvar(:,:) = obfillflt
1385	zsurfmask(:,:) = 0
1386	CALL ctl_warn( ' HadOCC pCO2 values masked out for observation operator', &
1387	& ' as HADOCC_PCO2(:,:) == HADOCC_FILL_FLT' )
1388	ENDIF
1389	#elif defined key_medusa && defined key_foam_medusa && defined key_roam
1390	zsurfvar(:,:) = f2_pco2w(:,:)
1391	#elif defined key_fabm
1392	pco2_3d(:,:,:) = fabm_get_bulk_diagnostic_data(model, jp_fabm_o3pc)
1393	zsurfvar(:,:) = pco2_3d(:,:,1)
1394	#else
1395	CALL ctl_stop( ' Trying to run spco2 observation operator', &
1396	& ' but no biogeochemical model appears to have been defined' )
1397	#endif
1398
1399	CASE DEFAULT
1400
1401	CALL ctl_stop( 'Unknown surface observation type '//TRIM(cobstypessurf(jtype))//' in dia_obs' )
1402
1403	END SELECT
1404
1405	IF ( llog10 ) THEN
1406	! Take the log10 where we can, otherwise exclude
1407	tiny = 1.0e-20
1408	WHERE(zsurfvar(:,:) > tiny .AND. zsurfvar(:,:) /= obfillflt )
1409	zsurfvar(:,:) = LOG10(zsurfvar(:,:))
1410	ELSEWHERE
1411	zsurfvar(:,:) = obfillflt
1412	zsurfmask(:,:) = 0
1413	END WHERE
1414	ENDIF
1415
1416	CALL obs_surf_opt( surfdataqc(jtype), kstp, jpi, jpj, &
1417	& nit000, idaystp, zsurfvar, zsurfmask, &
1418	& n2dintsurf(jtype), llnightav(jtype), &
1419	& ravglamscl(jtype), ravgphiscl(jtype), &
1420	& lfpindegs(jtype) )
1421
1422	END DO
1423
1424	ENDIF
1425
1426	CALL wrk_dealloc( jpi, jpj, jpk, zprofvar1 )
1427	CALL wrk_dealloc( jpi, jpj, jpk, zprofvar2 )
1428	CALL wrk_dealloc( jpi, jpj, jpk, zprofmask1 )
1429	CALL wrk_dealloc( jpi, jpj, jpk, zprofmask2 )
1430	CALL wrk_dealloc( jpi, jpj, zsurfvar )
1431	CALL wrk_dealloc( jpi, jpj, zsurfmask )
1432	CALL wrk_dealloc( jpi, jpj, zglam1 )
1433	CALL wrk_dealloc( jpi, jpj, zglam2 )
1434	CALL wrk_dealloc( jpi, jpj, zgphi1 )
1435	CALL wrk_dealloc( jpi, jpj, zgphi2 )
1436
1437	END SUBROUTINE dia_obs
1438
1439	SUBROUTINE dia_obs_wri
1440	!!----------------------------------------------------------------------
1441	!! * ROUTINE dia_obs_wri *
1442	!!
1443	!! ** Purpose : Call observation diagnostic output routines
1444	!!
1445	!! ** Method : Call observation diagnostic output routines
1446	!!
1447	!! ** Action :
1448	!!
1449	!! History :
1450	!! ! 06-03 (K. Mogensen) Original code
1451	!! ! 06-05 (K. Mogensen) Reformatted
1452	!! ! 06-10 (A. Weaver) Cleaning
1453	!! ! 07-03 (K. Mogensen) General handling of profiles
1454	!! ! 08-09 (M. Valdivieso) Velocity component (U,V) profiles
1455	!! ! 15-08 (M. Martin) Combined writing for prof and surf types
1456	!!----------------------------------------------------------------------
1457	!! * Modules used
1458	USE obs_rot_vel ! Rotation of velocities
1459
1460	IMPLICIT NONE
1461
1462	!! * Local declarations
1463	INTEGER :: jtype ! Data set loop variable
1464	INTEGER :: jo, jvar, jk
1465	REAL(wp), DIMENSION(:), ALLOCATABLE :: &
1466	& zu, &
1467	& zv
1468
1469	!-----------------------------------------------------------------------
1470	! Depending on switches call various observation output routines
1471	!-----------------------------------------------------------------------
1472
1473	IF ( nproftypes > 0 ) THEN
1474
1475	DO jtype = 1, nproftypes
1476
1477	IF ( TRIM(cobstypesprof(jtype)) == 'vel' ) THEN
1478
1479	! For velocity data, rotate the model velocities to N/S, E/W
1480	! using the compressed data structure.
1481	ALLOCATE( &
1482	& zu(profdataqc(jtype)%nvprot(1)), &
1483	& zv(profdataqc(jtype)%nvprot(2)) &
1484	& )
1485
1486	CALL obs_rotvel( profdataqc(jtype), nn_2dint_default, zu, zv )
1487
1488	DO jo = 1, profdataqc(jtype)%nprof
1489	DO jvar = 1, 2
1490	DO jk = profdataqc(jtype)%npvsta(jo,jvar), profdataqc(jtype)%npvend(jo,jvar)
1491
1492	IF ( jvar == 1 ) THEN
1493	profdataqc(jtype)%var(jvar)%vmod(jk) = zu(jk)
1494	ELSE
1495	profdataqc(jtype)%var(jvar)%vmod(jk) = zv(jk)
1496	ENDIF
1497
1498	END DO
1499	END DO
1500	END DO
1501
1502	DEALLOCATE( zu )
1503	DEALLOCATE( zv )
1504
1505	END IF
1506
1507	CALL obs_prof_decompress( profdataqc(jtype), &
1508	& profdata(jtype), .TRUE., numout )
1509
1510	CALL obs_wri_prof( profdata(jtype) )
1511
1512	END DO
1513
1514	ENDIF
1515
1516	IF ( nsurftypes > 0 ) THEN
1517
1518	DO jtype = 1, nsurftypes
1519
1520	CALL obs_surf_decompress( surfdataqc(jtype), &
1521	& surfdata(jtype), .TRUE., numout )
1522
1523	CALL obs_wri_surf( surfdata(jtype) )
1524
1525	END DO
1526
1527	ENDIF
1528
1529	END SUBROUTINE dia_obs_wri
1530
1531	SUBROUTINE dia_obs_dealloc
1532	IMPLICIT NONE
1533	!!----------------------------------------------------------------------
1534	!! * ROUTINE dia_obs_dealloc *
1535	!!
1536	!! ** Purpose : To deallocate data to enable the obs_oper online loop.
1537	!! Specifically: dia_obs_init --> dia_obs --> dia_obs_wri
1538	!!
1539	!! ** Method : Clean up various arrays left behind by the obs_oper.
1540	!!
1541	!! ** Action :
1542	!!
1543	!!----------------------------------------------------------------------
1544	! obs_grid deallocation
1545	CALL obs_grid_deallocate
1546
1547	! diaobs deallocation
1548	IF ( nproftypes > 0 ) &
1549	& DEALLOCATE( cobstypesprof, profdata, profdataqc, nvarsprof, nextrprof )
1550
1551	IF ( nsurftypes > 0 ) &
1552	& DEALLOCATE( cobstypessurf, surfdata, surfdataqc, nvarssurf, nextrsurf, &
1553	& n2dintsurf, ravglamscl, ravgphiscl, lfpindegs, llnightav )
1554
1555	END SUBROUTINE dia_obs_dealloc
1556
1557	SUBROUTINE ini_date( ddobsini )
1558	!!----------------------------------------------------------------------
1559	!! * ROUTINE ini_date *
1560	!!
1561	!! ** Purpose : Get initial date in double precision YYYYMMDD.HHMMSS format
1562	!!
1563	!! ** Method : Get initial date in double precision YYYYMMDD.HHMMSS format
1564	!!
1565	!! ** Action : Get initial date in double precision YYYYMMDD.HHMMSS format
1566	!!
1567	!! History :
1568	!! ! 06-03 (K. Mogensen) Original code
1569	!! ! 06-05 (K. Mogensen) Reformatted
1570	!! ! 06-10 (A. Weaver) Cleaning
1571	!! ! 06-10 (G. Smith) Calculates initial date the same as method for final date
1572	!! ! 10-05 (D. Lea) Update to month length calculation for NEMO vn3.2
1573	!!----------------------------------------------------------------------
1574	USE phycst, ONLY : & ! Physical constants
1575	& rday
1576	USE dom_oce, ONLY : & ! Ocean space and time domain variables
1577	& rdt
1578
1579	IMPLICIT NONE
1580
1581	!! * Arguments
1582	REAL(dp), INTENT(OUT) :: ddobsini ! Initial date in YYYYMMDD.HHMMSS
1583
1584	!! * Local declarations
1585	INTEGER :: iyea ! date - (year, month, day, hour, minute)
1586	INTEGER :: imon
1587	INTEGER :: iday
1588	INTEGER :: ihou
1589	INTEGER :: imin
1590	INTEGER :: imday ! Number of days in month.
1591	INTEGER, DIMENSION(12) :: &
1592	& imonth_len ! Length in days of the months of the current year
1593	REAL(wp) :: zdayfrc ! Fraction of day
1594
1595	!----------------------------------------------------------------------
1596	! Initial date initialization (year, month, day, hour, minute)
1597	! (This assumes that the initial date is for 00z))
1598	!----------------------------------------------------------------------
1599	iyea = ndate0 / 10000
1600	imon = ( ndate0 - iyea * 10000 ) / 100
1601	iday = ndate0 - iyea * 10000 - imon * 100
1602	ihou = 0
1603	imin = 0
1604
1605	!----------------------------------------------------------------------
1606	! Compute number of days + number of hours + min since initial time
1607	!----------------------------------------------------------------------
1608	iday = iday + ( nit000 -1 ) * rdt / rday
1609	zdayfrc = ( nit000 -1 ) * rdt / rday
1610	zdayfrc = zdayfrc - aint(zdayfrc)
1611	ihou = int( zdayfrc * 24 )
1612	imin = int( (zdayfrc * 24 - ihou) * 60 )
1613
1614	!-----------------------------------------------------------------------
1615	! Convert number of days (iday) into a real date
1616	!----------------------------------------------------------------------
1617
1618	CALL calc_month_len( iyea, imonth_len )
1619
1620	DO WHILE ( iday > imonth_len(imon) )
1621	iday = iday - imonth_len(imon)
1622	imon = imon + 1
1623	IF ( imon > 12 ) THEN
1624	imon = 1
1625	iyea = iyea + 1
1626	CALL calc_month_len( iyea, imonth_len ) ! update month lengths
1627	ENDIF
1628	END DO
1629
1630	!----------------------------------------------------------------------
1631	! Convert it into YYYYMMDD.HHMMSS format.
1632	!----------------------------------------------------------------------
1633	ddobsini = iyea * 10000_dp + imon * 100_dp + &
1634	& iday + ihou * 0.01_dp + imin * 0.0001_dp
1635
1636
1637	END SUBROUTINE ini_date
1638
1639	SUBROUTINE fin_date( ddobsfin )
1640	!!----------------------------------------------------------------------
1641	!! * ROUTINE fin_date *
1642	!!
1643	!! ** Purpose : Get final date in double precision YYYYMMDD.HHMMSS format
1644	!!
1645	!! ** Method : Get final date in double precision YYYYMMDD.HHMMSS format
1646	!!
1647	!! ** Action : Get final date in double precision YYYYMMDD.HHMMSS format
1648	!!
1649	!! History :
1650	!! ! 06-03 (K. Mogensen) Original code
1651	!! ! 06-05 (K. Mogensen) Reformatted
1652	!! ! 06-10 (A. Weaver) Cleaning
1653	!! ! 10-05 (D. Lea) Update to month length calculation for NEMO vn3.2
1654	!!----------------------------------------------------------------------
1655	USE phycst, ONLY : & ! Physical constants
1656	& rday
1657	USE dom_oce, ONLY : & ! Ocean space and time domain variables
1658	& rdt
1659
1660	IMPLICIT NONE
1661
1662	!! * Arguments
1663	REAL(dp), INTENT(OUT) :: ddobsfin ! Final date in YYYYMMDD.HHMMSS
1664
1665	!! * Local declarations
1666	INTEGER :: iyea ! date - (year, month, day, hour, minute)
1667	INTEGER :: imon
1668	INTEGER :: iday
1669	INTEGER :: ihou
1670	INTEGER :: imin
1671	INTEGER :: imday ! Number of days in month.
1672	INTEGER, DIMENSION(12) :: &
1673	& imonth_len ! Length in days of the months of the current year
1674	REAL(wp) :: zdayfrc ! Fraction of day
1675
1676	!-----------------------------------------------------------------------
1677	! Initial date initialization (year, month, day, hour, minute)
1678	! (This assumes that the initial date is for 00z)
1679	!-----------------------------------------------------------------------
1680	iyea = ndate0 / 10000
1681	imon = ( ndate0 - iyea * 10000 ) / 100
1682	iday = ndate0 - iyea * 10000 - imon * 100
1683	ihou = 0
1684	imin = 0
1685
1686	!-----------------------------------------------------------------------
1687	! Compute number of days + number of hours + min since initial time
1688	!-----------------------------------------------------------------------
1689	iday = iday + nitend * rdt / rday
1690	zdayfrc = nitend * rdt / rday
1691	zdayfrc = zdayfrc - AINT( zdayfrc )
1692	ihou = INT( zdayfrc * 24 )
1693	imin = INT( ( zdayfrc * 24 - ihou ) * 60 )
1694
1695	!-----------------------------------------------------------------------
1696	! Convert number of days (iday) into a real date
1697	!----------------------------------------------------------------------
1698
1699	CALL calc_month_len( iyea, imonth_len )
1700
1701	DO WHILE ( iday > imonth_len(imon) )
1702	iday = iday - imonth_len(imon)
1703	imon = imon + 1
1704	IF ( imon > 12 ) THEN
1705	imon = 1
1706	iyea = iyea + 1
1707	CALL calc_month_len( iyea, imonth_len ) ! update month lengths
1708	ENDIF
1709	END DO
1710
1711	!-----------------------------------------------------------------------
1712	! Convert it into YYYYMMDD.HHMMSS format
1713	!-----------------------------------------------------------------------
1714	ddobsfin = iyea * 10000_dp + imon * 100_dp + iday &
1715	& + ihou * 0.01_dp + imin * 0.0001_dp
1716
1717	END SUBROUTINE fin_date
1718
1719	SUBROUTINE obs_settypefiles( ntypes, jpmaxnfiles, ifiles, cobstypes, cfiles )
1720
1721	INTEGER, INTENT(IN) :: ntypes ! Total number of obs types
1722	INTEGER, INTENT(IN) :: jpmaxnfiles ! Maximum number of files allowed for each type
1723	INTEGER, DIMENSION(ntypes), INTENT(OUT) :: &
1724	& ifiles ! Out number of files for each type
1725	CHARACTER(len=8), DIMENSION(ntypes), INTENT(IN) :: &
1726	& cobstypes ! List of obs types
1727	CHARACTER(len=128), DIMENSION(ntypes, jpmaxnfiles), INTENT(IN) :: &
1728	& cfiles ! List of files for all types
1729
1730	!Local variables
1731	INTEGER :: jfile
1732	INTEGER :: jtype
1733
1734	DO jtype = 1, ntypes
1735
1736	ifiles(jtype) = 0
1737	DO jfile = 1, jpmaxnfiles
1738	IF ( trim(cfiles(jtype,jfile)) /= '' ) &
1739	ifiles(jtype) = ifiles(jtype) + 1
1740	END DO
1741
1742	IF ( ifiles(jtype) == 0 ) THEN
1743	CALL ctl_stop( 'Logical for observation type '//TRIM(cobstypes(jtype))// &
1744	& ' set to true but no files available to read' )
1745	ENDIF
1746
1747	IF(lwp) THEN
1748	WRITE(numout,*) ' '//cobstypes(jtype)//' input observation file names:'
1749	DO jfile = 1, ifiles(jtype)
1750	WRITE(numout,*) ' '//TRIM(cfiles(jtype,jfile))
1751	END DO
1752	ENDIF
1753
1754	END DO
1755
1756	END SUBROUTINE obs_settypefiles
1757
1758	SUBROUTINE obs_setinterpopts( ntypes, jtype, ctypein, &
1759	& n2dint_default, n2dint_type, &
1760	& ravglamscl_type, ravgphiscl_type, &
1761	& lfp_indegs_type, lavnight_type, &
1762	& n2dint, ravglamscl, ravgphiscl, &
1763	& lfpindegs, lavnight )
1764
1765	INTEGER, INTENT(IN) :: ntypes ! Total number of obs types
1766	INTEGER, INTENT(IN) :: jtype ! Index of the current type of obs
1767	INTEGER, INTENT(IN) :: n2dint_default ! Default option for interpolation type
1768	INTEGER, INTENT(IN) :: n2dint_type ! Option for interpolation type
1769	REAL(wp), INTENT(IN) :: &
1770	& ravglamscl_type, & !E/W diameter of obs footprint for this type
1771	& ravgphiscl_type !N/S diameter of obs footprint for this type
1772	LOGICAL, INTENT(IN) :: lfp_indegs_type !T=> footprint in degrees, F=> in metres
1773	LOGICAL, INTENT(IN) :: lavnight_type !T=> obs represent night time average
1774	CHARACTER(len=8), INTENT(IN) :: ctypein
1775
1776	INTEGER, DIMENSION(ntypes), INTENT(INOUT) :: &
1777	& n2dint
1778	REAL(wp), DIMENSION(ntypes), INTENT(INOUT) :: &
1779	& ravglamscl, ravgphiscl
1780	LOGICAL, DIMENSION(ntypes), INTENT(INOUT) :: &
1781	& lfpindegs, lavnight
1782
1783	lavnight(jtype) = lavnight_type
1784
1785	IF ( (n2dint_type >= 0) .AND. (n2dint_type <= 6) ) THEN
1786	n2dint(jtype) = n2dint_type
1787	ELSE IF ( n2dint_type == -1 ) THEN
1788	n2dint(jtype) = n2dint_default
1789	ELSE
1790	CALL ctl_stop(' Choice of '//TRIM(ctypein)//' horizontal (2D) interpolation method', &
1791	& ' is not available')
1792	ENDIF
1793
1794	! For averaging observation footprints set options for size of footprint
1795	IF ( (n2dint(jtype) > 4) .AND. (n2dint(jtype) <= 6) ) THEN
1796	IF ( ravglamscl_type > 0._wp ) THEN
1797	ravglamscl(jtype) = ravglamscl_type
1798	ELSE
1799	CALL ctl_stop( 'Incorrect value set for averaging footprint '// &
1800	'scale (ravglamscl) for observation type '//TRIM(ctypein) )
1801	ENDIF
1802
1803	IF ( ravgphiscl_type > 0._wp ) THEN
1804	ravgphiscl(jtype) = ravgphiscl_type
1805	ELSE
1806	CALL ctl_stop( 'Incorrect value set for averaging footprint '// &
1807	'scale (ravgphiscl) for observation type '//TRIM(ctypein) )
1808	ENDIF
1809
1810	lfpindegs(jtype) = lfp_indegs_type
1811
1812	ENDIF
1813
1814	! Write out info
1815	IF(lwp) THEN
1816	IF ( n2dint(jtype) <= 4 ) THEN
1817	WRITE(numout,*) ' '//TRIM(ctypein)// &
1818	& ' model counterparts will be interpolated horizontally'
1819	ELSE IF ( n2dint(jtype) <= 6 ) THEN
1820	WRITE(numout,*) ' '//TRIM(ctypein)// &
1821	& ' model counterparts will be averaged horizontally'
1822	WRITE(numout,*) ' '//' with E/W scale: ',ravglamscl(jtype)
1823	WRITE(numout,*) ' '//' with N/S scale: ',ravgphiscl(jtype)
1824	IF ( lfpindegs(jtype) ) THEN
1825	WRITE(numout,*) ' '//' (in degrees)'
1826	ELSE
1827	WRITE(numout,*) ' '//' (in metres)'
1828	ENDIF
1829	ENDIF
1830	ENDIF
1831
1832	END SUBROUTINE obs_setinterpopts
1833
1834	END MODULE diaobs

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