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source: palm/trunk/UTIL/inifor/src/io.f90 @ 2947

Last change on this file since 2947 was 2718, checked in by maronga, 7 years ago
deleting of deprecated files; headers updated where needed
Property svn:keywords set to `Id`
File size: 31.4 KB

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1	!> @file src/io.f90
2	!------------------------------------------------------------------------------!
3	! This file is part of the PALM model system.
4	!
5	! PALM is free software: you can redistribute it and/or modify it under the
6	! terms of the GNU General Public License as published by the Free Software
7	! Foundation, either version 3 of the License, or (at your option) any later
8	! version.
9	!
10	! PALM is distributed in the hope that it will be useful, but WITHOUT ANY
11	! WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
12	! A PARTICULAR PURPOSE. See the GNU General Public License for more details.
13	!
14	! You should have received a copy of the GNU General Public License along with
15	! PALM. If not, see <http://www.gnu.org/licenses/>.
16	!
17	! Copyright 2017-2018 Leibniz Universitaet Hannover
18	! Copyright 2017-2018 Deutscher Wetterdienst Offenbach
19	!------------------------------------------------------------------------------!
20	!
21	! Current revisions:
22	! -----------------
23	!
24	!
25	! Former revisions:
26	! -----------------
27	! $Id: io.f90 2718 2018-01-02 08:49:38Z suehring $
28	! Initial revision
29	!
30	!
31	!
32	! Authors:
33	! --------
34	! @author Eckhard Kadasch
35	!
36	! Description:
37	! ------------
38	!> The io module contains the functions needed to read and write netCDF data in
39	!> INIFOR.
40	!------------------------------------------------------------------------------!
41	MODULE io
42
43	USE control
44	USE defs, &
45	ONLY: DATE, SNAME, PATH, PI, dp, TO_RADIANS, TO_DEGREES, VERSION
46	USE netcdf
47	USE types
48	USE util, &
49	ONLY: reverse, str
50
51	IMPLICIT NONE
52
53	CONTAINS
54
55	SUBROUTINE netcdf_define_variable(var, ncid)
56
57	TYPE(nc_var), INTENT(INOUT) :: var
58	INTEGER, INTENT(IN) :: ncid
59
60	CALL check(nf90_def_var(ncid, var % name, NF90_FLOAT, var % dimids(1:var % ndim), var % varid))
61	CALL check(nf90_put_att(ncid, var % varid, "standard_name", var % standard_name))
62	CALL check(nf90_put_att(ncid, var % varid, "long_name", var % long_name))
63	CALL check(nf90_put_att(ncid, var % varid, "units", var % units))
64	CALL check(nf90_put_att(ncid, var % varid, "lod", var % lod))
65	CALL check(nf90_put_att(ncid, var % varid, "source", var % source))
66	CALL check(nf90_put_att(ncid, var % varid, "_FillValue", NF90_FILL_REAL))
67
68	END SUBROUTINE netcdf_define_variable
69
70
71	SUBROUTINE netcdf_get_dimensions(var, ncid)
72
73	TYPE(nc_var), INTENT(INOUT) :: var
74	INTEGER, INTENT(IN) :: ncid
75	INTEGER :: i
76	CHARACTER(SNAME) :: null
77
78	! Remember dimension lenghts for NetCDF writing routine
79	DO i = 1, var % ndim
80	CALL check(nf90_inquire_dimension(ncid, var % dimids(i), &
81	name = null, &
82	len = var % dimlen(i) ) )
83	END DO
84
85	END SUBROUTINE netcdf_get_dimensions
86
87
88	!------------------------------------------------------------------------------!
89	! Description:
90	! ------------
91	!> This routine initializes Inifor. This includes parsing command-line
92	!> arguments, setting the names of the input and output file names as well as
93	!> the name of the input namelist and, subsequently, reading in and setting grid
94	!> parameters for the PALM-4U computational grid.
95	!------------------------------------------------------------------------------!
96	SUBROUTINE parse_command_line_arguments( start_date, hhl_file, &
97	soiltyp_file, static_driver_file, input_path, output_file, &
98	namelist_file, ug, vg, p0, z0, mode )
99
100	CHARACTER(LEN=PATH), INTENT(INOUT) :: hhl_file, soiltyp_file, &
101	static_driver_file, input_path, output_file, namelist_file
102	CHARACTER(LEN=SNAME), INTENT(INOUT) :: mode
103	REAL(dp), INTENT(INOUT) :: ug, vg, p0, z0
104	CHARACTER(LEN=DATE), INTENT(INOUT) :: start_date
105
106	CHARACTER(LEN=PATH) :: option, arg
107	INTEGER :: arg_count, i
108
109	arg_count = COMMAND_ARGUMENT_COUNT()
110	IF (arg_count .GT. 0) THEN
111
112	! Every option should have an argument.
113	IF ( MOD(arg_count, 2) .NE. 0 ) THEN
114	message = "Syntax error in command line."
115	CALL abort('parse_command_line_arguments', message)
116	END IF
117
118	message = "The -clon and -clat command line options are depricated. " // &
119	"Please remove them form your inifor command and specify the " // &
120	"location of the PALM-4U origin either" // NEW_LINE(' ') // &
121	" - by setting the namelist parameters 'origin_lon' and 'origin_lat, or'" // NEW_LINE(' ') // &
122	" - by providing a static driver netCDF file via the -static command-line option."
123
124	! Loop through option/argument pairs.
125	DO i = 1, arg_count, 2
126
127	CALL GET_COMMAND_ARGUMENT( i, option )
128	CALL GET_COMMAND_ARGUMENT( i+1, arg )
129
130	SELECT CASE( TRIM(option) )
131
132	CASE( '-date' )
133	start_date = TRIM(arg)
134
135	! Elevation of the PALM-4U domain above sea level
136	CASE( '-z0' )
137	READ(arg, *) z0
138
139	! surface pressure, at z0
140	CASE( '-p0' )
141	READ(arg, *) p0
142
143	! surface pressure, at z0
144	CASE( '-ug' )
145	READ(arg, *) ug
146
147	! surface pressure, at z0
148	CASE( '-vg' )
149	READ(arg, *) vg
150
151	! Domain centre geographical longitude
152	CASE( '-clon' )
153	CALL abort('parse_command_line_arguments', message)
154	!READ(arg, *) lambda_cg
155	!lambda_cg = lambda_cg * TO_RADIANS
156
157	! Domain centre geographical latitude
158	CASE( '-clat' )
159	CALL abort('parse_command_line_arguments', message)
160	!READ(arg, *) phi_cg
161	!phi_cg = phi_cg * TO_RADIANS
162
163	CASE( '-path' )
164	input_path = TRIM(arg)
165
166	CASE( '-hhl' )
167	hhl_file = TRIM(arg)
168
169	CASE( '-static' )
170	static_driver_file = TRIM(arg)
171
172	CASE( '-soil' )
173	soiltyp_file = TRIM(arg)
174
175	CASE( '-o' )
176	output_file = TRIM(arg)
177
178	CASE( '-n' )
179	namelist_file = TRIM(arg)
180
181	! Initialization mode: 'profile' / 'volume'
182	CASE( '-mode' )
183	mode = TRIM(arg)
184
185	SELECT CASE( TRIM(mode) )
186
187	CASE( 'profile' )
188
189	CASE DEFAULT
190	message = "Mode '" // TRIM(mode) // "' is not supported. " //&
191	"Currently, '-mode profile' is the only supported option. " //&
192	"Select this one or omit the -mode option entirely."
193	CALL abort( 'parse_command_line_arguments', message )
194	END SELECT
195
196	CASE DEFAULT
197	message = "unknown option '" // TRIM(option(2:)) // "'."
198	CALL abort('parse_command_line_arguments', message)
199
200	END SELECT
201
202	END DO
203
204	ELSE
205
206	message = "No arguments present, using default input and output files"
207	CALL report('parse_command_line_arguments', message)
208
209	END IF
210
211	END SUBROUTINE parse_command_line_arguments
212
213
214	!------------------------------------------------------------------------------!
215	! Description:
216	! ------------
217	!> This routine initializes the Inifor output file, i.e. the PALM-4U
218	!> initializing and forcing data as a NetCDF file.
219	!>
220	!> Besides writing metadata, such as global attributes, coordinates, variables,
221	!> in the NetCDF file, various NetCDF IDs are saved for later, when Inifor
222	!> writes the actual data.
223	!------------------------------------------------------------------------------!
224	SUBROUTINE setup_netcdf_dimensions(output_file, palm_grid)
225
226	TYPE(nc_file), INTENT(INOUT) :: output_file
227	TYPE(grid_definition), INTENT(IN) :: palm_grid
228
229	CHARACTER (LEN=SNAME) :: date
230	INTEGER :: ncid, nx, ny, nz, nt, dimids(3), dimvarids(3)
231	REAL(dp) :: z0
232
233	! Create the NetCDF file. NF90_CLOBBER selects overwrite mode.
234	CALL check(nf90_create(TRIM(output_file % name), OR(NF90_CLOBBER, NF90_HDF5), ncid))
235
236	!
237	!------------------------------------------------------------------------------
238	!- Section 1: Write global NetCDF attributes
239	!------------------------------------------------------------------------------
240	CALL date_and_time(date)
241	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'title', 'PALM input file for scenario ...'))
242	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'institution', 'Deutscher Wetterdienst, Offenbach'))
243	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'author', 'Eckhard Kadasch, eckhard.kadasch@dwd.de'))
244	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'history', 'Created on '//date))
245	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'references', '--'))
246	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'comment', '--'))
247	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'origin_lat', '--'))
248	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'origin_lon', '--'))
249	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'inifor_version', TRIM(VERSION)))
250	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'palm_version', '--'))
251
252	!
253	!------------------------------------------------------------------------------
254	!- Section 2: Define NetCDF dimensions and coordinates
255	!------------------------------------------------------------------------------
256	nt = SIZE(output_file % time)
257	nx = palm_grid % nx
258	ny = palm_grid % ny
259	nz = palm_grid % nz
260	z0 = palm_grid % z0
261
262	!
263	!------------------------------------------------------------------------------
264	!- Section 2a: Define dimensions for cell centers (scalars in soil and atmosph.)
265	!------------------------------------------------------------------------------
266	dimids = (/0, 0, 0/) ! reset dimids
267	CALL check( nf90_def_dim(ncid, "x", nx+1, dimids(1)) )
268	CALL check( nf90_def_dim(ncid, "y", ny+1, dimids(2)) )
269	CALL check( nf90_def_dim(ncid, "z", nz+1, dimids(3)) )
270	output_file % dimids_scl = dimids ! save dimids for later
271
272	dimvarids = (/0, 0, 0/) ! reset dimvarids
273	CALL check(nf90_def_var(ncid, "x", NF90_FLOAT, dimids(1), dimvarids(1)))
274	CALL check(nf90_put_att(ncid, dimvarids(1), "standard_name", "x coordinate of cell centers"))
275	CALL check(nf90_put_att(ncid, dimvarids(1), "units", "m"))
276
277	CALL check(nf90_def_var(ncid, "y", NF90_FLOAT, dimids(2), dimvarids(2)))
278	CALL check(nf90_put_att(ncid, dimvarids(2), "standard_name", "y coordinate of cell centers"))
279	CALL check(nf90_put_att(ncid, dimvarids(2), "units", "m"))
280
281	CALL check(nf90_def_var(ncid, "z", NF90_FLOAT, dimids(3), dimvarids(3)))
282	CALL check(nf90_put_att(ncid, dimvarids(3), "standard_name", "z coordinate of cell centers"))
283	CALL check(nf90_put_att(ncid, dimvarids(3), "units", "m"))
284	output_file % dimvarids_scl = dimvarids ! save dimvarids for later
285
286	! overwrite third dimid with the one of depth
287	CALL check(nf90_def_dim(ncid, "depth", SIZE(palm_grid % depths), dimids(3)) )
288	output_file % dimids_soil = dimids ! save dimids for later
289
290	! overwrite third dimvarid with the one of depth
291	CALL check(nf90_def_var(ncid, "depth", NF90_FLOAT, output_file % dimids_soil(3), dimvarids(3)))
292	CALL check(nf90_put_att(ncid, dimvarids(3), "standard_name", "depth_below_land"))
293	CALL check(nf90_put_att(ncid, dimvarids(3), "positive", "down"))
294	CALL check(nf90_put_att(ncid, dimvarids(3), "units", "m"))
295	output_file % dimvarids_soil = dimvarids ! save dimvarids for later
296	!
297	!------------------------------------------------------------------------------
298	!- Section 2b: Define dimensions for cell faces/velocities
299	!------------------------------------------------------------------------------
300	dimids = (/0, 0, 0/) ! reset dimids
301	CALL check(nf90_def_dim(ncid, "xu", nx, dimids(1)) )
302	CALL check(nf90_def_dim(ncid, "yv", ny, dimids(2)) )
303	CALL check(nf90_def_dim(ncid, "zw", nz, dimids(3)) )
304	output_file % dimids_vel = dimids ! save dimids for later
305
306	dimvarids = (/0, 0, 0/) ! reset dimvarids
307	CALL check(nf90_def_var(ncid, "xu", NF90_FLOAT, dimids(1), dimvarids(1)))
308	CALL check(nf90_put_att(ncid, dimvarids(1), "standard_name", "x coordinate of cell faces"))
309	CALL check(nf90_put_att(ncid, dimvarids(1), "units", "m"))
310
311	CALL check(nf90_def_var(ncid, "yv", NF90_FLOAT, dimids(2), dimvarids(2)))
312	CALL check(nf90_put_att(ncid, dimvarids(2), "standard_name", "y coordinate of cell faces"))
313	CALL check(nf90_put_att(ncid, dimvarids(2), "units", "m"))
314
315	CALL check(nf90_def_var(ncid, "zw", NF90_FLOAT, dimids(3), dimvarids(3)))
316	CALL check(nf90_put_att(ncid, dimvarids(3), "standard_name", "z coordinate of cell faces"))
317	CALL check(nf90_put_att(ncid, dimvarids(3), "units", "m"))
318	output_file % dimvarids_vel = dimvarids ! save dimvarids for later
319
320	!
321	!------------------------------------------------------------------------------
322	!- Section 2c: Define time dimension
323	!------------------------------------------------------------------------------
324	CALL check(nf90_def_dim(ncid, "time", nt, output_file % dimid_time) )
325	CALL check(nf90_def_var(ncid, "time", NF90_FLOAT, &
326	output_file % dimid_time, &
327	output_file % dimvarid_time))
328	CALL check(nf90_put_att(ncid, output_file % dimvarid_time, "standard_name", "time"))
329	CALL check(nf90_put_att(ncid, output_file % dimvarid_time, "long_name", "time"))
330	CALL check(nf90_put_att(ncid, output_file % dimvarid_time, "units", "seconds since..."))
331
332	CALL check(nf90_enddef(ncid))
333
334	!
335	!------------------------------------------------------------------------------
336	!- Section 3: Write grid coordinates
337	!------------------------------------------------------------------------------
338	CALL check(nf90_put_var(ncid, output_file % dimvarids_scl(1), palm_grid%x))
339	CALL check(nf90_put_var(ncid, output_file % dimvarids_scl(2), palm_grid%y))
340	CALL check(nf90_put_var(ncid, output_file % dimvarids_scl(3), palm_grid%z))
341
342	CALL check(nf90_put_var(ncid, output_file % dimvarids_vel(1), palm_grid%xu))
343	CALL check(nf90_put_var(ncid, output_file % dimvarids_vel(2), palm_grid%yv))
344	CALL check(nf90_put_var(ncid, output_file % dimvarids_vel(3), palm_grid%zw))
345
346	! TODO Read in soil depths from input file before this.
347	CALL check(nf90_put_var(ncid, output_file % dimvarids_soil(3), palm_grid%depths))
348
349	! Write time vector
350	CALL check(nf90_put_var(ncid, output_file % dimvarid_time, output_file % time))
351
352	! Close the file
353	CALL check(nf90_close(ncid))
354
355	END SUBROUTINE setup_netcdf_dimensions
356
357
358	SUBROUTINE setup_netcdf_variables(filename, output_variable_table)
359
360	CHARACTER (LEN=*), INTENT(IN) :: filename
361	TYPE(nc_var), INTENT(INOUT), TARGET :: output_variable_table(:)
362	TYPE(nc_var), POINTER :: var
363	INTEGER :: i, ncid
364
365	message = "Initializing PALM-4U forcing file '" // TRIM(filename) // "'."
366	CALL report('setup_netcdf_variables', message)
367
368	CALL check(nf90_open(TRIM(filename), NF90_WRITE, ncid))
369	CALL check(nf90_redef(ncid))
370
371	DO i = 1, SIZE(output_variable_table)
372
373	var => output_variable_table(i)
374
375	IF ( var % to_be_processed ) THEN
376	message = "Defining variable #" // TRIM(str(i)) // " '" // TRIM(var%name) // "'."
377	CALL report('setup_netcdf_variables', message)
378
379	CALL netcdf_define_variable(var, ncid)
380	CALL netcdf_get_dimensions(var, ncid)
381	END IF
382
383	END DO
384
385	CALL check(nf90_enddef(ncid))
386	CALL check(nf90_close(ncid))
387
388	message = "Forcing file '" // TRIM(filename) // "' initialized successfully."
389	CALL report('setup_netcdf_variables', message)
390
391	END SUBROUTINE setup_netcdf_variables
392
393
394	!------------------------------------------------------------------------------!
395	! Description:
396	! ------------
397	!> This routine reads and returns all input variables of the given IO group
398	!> It accomodates the data by allocating a container variable that represents a
399	!> list of arrays of the same length as the groups variable list. (This list
400	!> will typically contain one or two items.) After the container, its members
401	!> are allocated one by one with the appropriate, possibly different,
402	!> dimensions.
403	!>
404	!> The 'group' is an INTENT(INOUT) variable so that 'get_netcdf_variable()' can
405	!> record netCDF IDs in the 'in_var_list()' member variable.
406	!------------------------------------------------------------------------------!
407	SUBROUTINE read_input_variables(group, iter, buffer)
408	TYPE(io_group), INTENT(INOUT), TARGET :: group
409	INTEGER, INTENT(IN) :: iter
410	TYPE(container), ALLOCATABLE, INTENT(INOUT) :: buffer(:)
411	INTEGER :: hour, buf_id
412	TYPE(nc_var), POINTER :: input_var
413	CHARACTER(LEN=PATH), POINTER :: input_file
414	INTEGER :: ivar, nbuffers
415
416	message = "Reading data for I/O group '" // TRIM(group % in_var_list(1) % name) // "'."
417	CALL report('read_input_variables', message)
418
419	input_file => group % in_files(iter)
420
421	!
422	!------------------------------------------------------------------------------
423	!- Section 1: Load input buffers for accumulated variables
424	!------------------------------------------------------------------------------
425	IF (group % kind == 'running average' .OR. &
426	group % kind == 'accumulated') THEN ! radiation budgets, precipitation
427
428	IF (SIZE(group % in_var_list) .GT. 1 ) THEN
429	message = "I/O groups may not contain more than one " // &
430	"accumulated variable. Group '" // TRIM(group % kind) //&
431	"' contains " // &
432	TRIM( str(SIZE(group % in_var_list)) ) // "."
433	CALL abort('read_input_variables \| accumulation', message)
434	END IF
435
436	! use two buffer arrays
437	nbuffers = 2
438	IF ( .NOT. ALLOCATED( buffer ) ) ALLOCATE( buffer(nbuffers) )
439
440	! chose correct buffer array
441	hour = iter - 1! hour of the day
442	buf_id = select_buffer(hour)
443
444	CALL run_control('time', 'read')
445	IF ( ALLOCATED(buffer(buf_id) % array) ) DEALLOCATE(buffer(buf_id) % array)
446	CALL run_control('time', 'alloc')
447
448	input_var => group % in_var_list(1)
449	buffer(buf_id) % array = get_netcdf_variable( input_file, input_var )
450	CALL report('read_input_variables', "Read accumulated " // TRIM(group % in_var_list(1) % name))
451
452	IF ( input_var % is_upside_down ) CALL reverse(buffer(buf_id) % array)
453	CALL run_control('time', 'comp')
454
455	!------------------------------------------------------------------------------
456	!- Section 2: Load input buffers for normal I/O groups
457	!------------------------------------------------------------------------------
458	ELSE
459
460	nbuffers = SIZE( group % in_var_list )
461	ALLOCATE( buffer(nbuffers) )
462	CALL run_control('time', 'alloc')
463
464	DO ivar = 1, nbuffers
465
466	input_var => group % in_var_list(ivar)
467
468	! Check wheather P or PP is present in input file
469	IF (input_var % name == 'P') THEN
470	input_var % name = TRIM( get_pressure_var(input_file) )
471	CALL run_control('time', 'read')
472	END IF
473
474	buffer(ivar) % array = get_netcdf_variable( input_file, input_var )
475
476	IF ( input_var % is_upside_down ) CALL reverse(buffer(ivar) % array)
477	CALL run_control('time', 'comp')
478
479	END DO
480	END IF
481
482	END SUBROUTINE read_input_variables
483
484
485	INTEGER FUNCTION select_buffer(hour)
486	INTEGER, INTENT(IN) :: hour
487	INTEGER :: step
488
489	select_buffer = 0
490	step = MODULO(hour, 3) + 1
491
492	SELECT CASE(step)
493	CASE(1, 3)
494	select_buffer = 1
495	CASE(2)
496	select_buffer = 2
497	CASE DEFAULT
498	message = "Invalid step '" // TRIM(str(step))
499	CALL abort('select_buffer', message)
500	END SELECT
501	END FUNCTION select_buffer
502
503
504	!------------------------------------------------------------------------------!
505	! Description:
506	! ------------
507	!> Checks if the input_file contains the absolute pressure, 'P', or the pressure
508	!> perturbation, 'PP', and returns the appropriate string.
509	!------------------------------------------------------------------------------!
510	CHARACTER(LEN=2) FUNCTION get_pressure_var(input_file) RESULT(var)
511	CHARACTER(LEN=*) :: input_file
512	INTEGER :: ncid, varid
513
514	CALL check(nf90_open( TRIM(input_file), NF90_NOWRITE, ncid ))
515	IF ( nf90_inq_varid( ncid, 'P', varid ) .EQ. NF90_NOERR ) THEN
516
517	var = 'P'
518
519	ELSE IF ( nf90_inq_varid( ncid, 'PP', varid ) .EQ. NF90_NOERR ) THEN
520
521	var = 'PP'
522	CALL report('get_pressure_var', 'Using PP instead of P')
523
524	ELSE
525
526	message = "Failed to read '" // TRIM(var) // &
527	"' from file '" // TRIM(input_file) // "'."
528	CALL abort('get_pressure_var', message)
529
530	END IF
531
532	CALL check(nf90_close(ncid))
533
534	END FUNCTION get_pressure_var
535
536
537	FUNCTION get_netcdf_attribute(filename, attribute) RESULT(attribute_value)
538
539	CHARACTER(LEN=*), INTENT(IN) :: filename, attribute
540	REAL(dp) :: attribute_value
541
542	INTEGER :: ncid
543
544	IF ( nf90_open( TRIM(filename), NF90_NOWRITE, ncid ) == NF90_NOERR ) THEN
545
546	CALL check(nf90_get_att(ncid, NF90_GLOBAL, TRIM(attribute), attribute_value))
547
548	ELSE
549
550	message = "Failed to read '" // TRIM(attribute) // &
551	"' from file '" // TRIM(filename) // "'."
552	CALL abort('get_netcdf_attribute', message)
553
554	END IF
555
556	END FUNCTION get_netcdf_attribute
557
558
559
560	FUNCTION get_netcdf_variable(in_file, in_var) RESULT(buffer)
561
562	CHARACTER(LEN=PATH), INTENT(IN) :: in_file
563	TYPE(nc_var), INTENT(INOUT) :: in_var
564	REAL(dp), ALLOCATABLE :: buffer(:,:,:)
565	INTEGER :: i, ncid, start(3)
566
567
568	! Read in_var NetCDF attributes
569	IF ( nf90_open( TRIM(in_file), NF90_NOWRITE, ncid ) .EQ. NF90_NOERR .AND. &
570	nf90_inq_varid( ncid, in_var % name, in_var % varid ) .EQ. NF90_NOERR ) THEN
571
572	CALL check(nf90_get_att(ncid, in_var % varid, "long_name", in_var % long_name))
573	CALL check(nf90_get_att(ncid, in_var % varid, "units", in_var % units))
574
575	! Read in_var NetCDF dimensions
576	CALL check(nf90_inquire_variable( ncid, in_var % varid, &
577	ndims = in_var % ndim, &
578	dimids = in_var % dimids ))
579
580	DO i = 1, in_var % ndim
581	CALL check(nf90_inquire_dimension( ncid, in_var % dimids(i), &
582	name = in_var % dimname(i), &
583	len = in_var % dimlen(i) ))
584	END DO
585
586	start = (/ 1, 1, 1 /)
587	IF ( TRIM(in_var % name) .EQ. 'T_SO' ) THEN
588	! Skip depth = 0.0 for T_SO and reduce number of depths from 9 to 8
589	in_var % dimlen(3) = in_var % dimlen(3) - 1
590
591	! Start reading from second level, e.g. depth = 0.005 instead of 0.0
592	start(3) = 2
593	END IF
594
595	SELECT CASE(in_var % ndim)
596
597	CASE (2)
598
599	ALLOCATE( buffer( in_var % dimlen(1), &
600	in_var % dimlen(2), &
601	1 ) )
602
603	CASE (3)
604
605	ALLOCATE( buffer( in_var % dimlen(1), &
606	in_var % dimlen(2), &
607	in_var % dimlen(3) ) )
608	CASE (4)
609
610	ALLOCATE( buffer( in_var % dimlen(1), &
611	in_var % dimlen(2), &
612	in_var % dimlen(3) ) )
613	CASE DEFAULT
614
615	message = "Failed reading NetCDF variable " // &
616	TRIM(in_var % name) // " with " // TRIM(str(in_var%ndim)) // &
617	" dimensions because only two- and and three-dimensional" // &
618	" variables are supported."
619	CALL abort('get_netcdf_variable', message)
620
621	END SELECT
622	CALL run_control('time', 'alloc')
623
624	! TODO: Check for matching dimensions of buffer and var
625	CALL check(nf90_get_var( ncid, in_var % varid, buffer, &
626	start = start, &
627	count = in_var % dimlen(1:3) ) )
628
629	CALL run_control('time', 'read')
630	ELSE
631
632	message = "Failed to read '" // TRIM(in_var % name) // &
633	"' from file '" // TRIM(in_file) // "'."
634	CALL report('get_netcdf_variable', message)
635
636	END IF
637
638	CALL check(nf90_close(ncid))
639
640	CALL run_control('time', 'read')
641
642	END FUNCTION get_netcdf_variable
643
644
645	SUBROUTINE update_output(var, array, iter, output_file)
646	TYPE(nc_var), INTENT(IN) :: var
647	REAL(dp), INTENT(IN) :: array(:,:,:)
648	INTEGER, INTENT(IN) :: iter
649	TYPE(nc_file), INTENT(IN) :: output_file
650
651	INTEGER :: ncid, ndim, start(4), count(4)
652	LOGICAL :: var_is_time_dependent
653
654	var_is_time_dependent = ( &
655	var % dimids( var % ndim ) == output_file % dimid_time &
656	)
657
658	! Skip time dimension for output
659	IF ( var_is_time_dependent ) THEN
660	ndim = var % ndim - 1
661	ELSE
662	ndim = var % ndim
663	END IF
664
665	start(:) = (/1,1,1,1/)
666	start(ndim+1) = iter
667	count(1:ndim) = var%dimlen(1:ndim)
668
669	CALL check(nf90_open(output_file % name, NF90_WRITE, ncid))
670
671	! Reduce dimension of output array according to variable kind
672	SELECT CASE (TRIM(var % kind))
673
674	CASE ( 'init scalar profile', 'init u profile', 'init v profile', &
675	'init w profile' )
676
677	CALL check(nf90_put_var( ncid, var%varid, array(1,1,:) ) )
678
679	CASE ( 'init soil', 'init scalar', 'init u', 'init v', 'init w' )
680
681	CALL check(nf90_put_var( ncid, var%varid, array(:,:,:) ) )
682
683	CASE( 'left scalar', 'right scalar', 'left w', 'right w' )
684
685	CALL check(nf90_put_var( ncid, var%varid, array(1,:,:), &
686	start=start(1:ndim+1), &
687	count=count(1:ndim) ) )
688
689
690	IF (.NOT. SIZE(array, 2) .EQ. var % dimlen(1)) THEN
691	PRINT *, "inifor: update_output: Dimension ", 1, " of variable ", &
692	TRIM(var % name), " (", var % dimlen(1), &
693	") does not match the dimension of the output array (", &
694	SIZE(array, 2), ")."
695	STOP
696	END IF
697
698
699	CASE( 'north scalar', 'south scalar', 'north w', 'south w' )
700
701	CALL check(nf90_put_var( ncid, var%varid, array(:,1,:), &
702	start=start(1:ndim+1), &
703	count=count(1:ndim) ) )
704
705
706	CASE( 'surface forcing', 'top scalar', 'top w' )
707
708	CALL check(nf90_put_var( ncid, var%varid, array(:,:,1), &
709	start=start(1:ndim+1), &
710	count=count(1:ndim) ) )
711
712	CASE ( 'left u', 'right u', 'left v', 'right v' )
713
714	CALL check(nf90_put_var( ncid, var%varid, array(1,:,:), &
715	start=start(1:ndim+1), &
716	count=count(1:ndim) ) )
717
718	CASE ( 'north u', 'south u', 'north v', 'south v' )
719
720	CALL check(nf90_put_var( ncid, var%varid, array(:,1,:), &
721	start=start(1:ndim+1), &
722	count=count(1:ndim) ) )
723
724	CASE ( 'top u', 'top v' )
725
726	CALL check(nf90_put_var( ncid, var%varid, array(:,:,1), &
727	start=start(1:ndim+1), &
728	count=count(1:ndim) ) )
729
730	CASE ( 'time series' )
731
732	CALL check(nf90_put_var( ncid, var%varid, array(1,1,1), &
733	start=start(1:ndim+1) ) )
734
735	CASE ( 'profile' )
736
737	CALL check(nf90_put_var( ncid, var%varid, array(1,1,:), &
738	start=start(1:ndim+1), &
739	count=count(1:ndim) ) )
740
741	CASE DEFAULT
742
743	message = "Variable kind '" // TRIM(var % kind) // &
744	"' not recognized."
745	CALL abort('update_output', message)
746
747	END SELECT
748
749	CALL check(nf90_close(ncid))
750
751	END SUBROUTINE update_output
752
753
754	SUBROUTINE write_netcdf_variable_2d(var, iter, output_file, buffer)
755	TYPE(nc_var), INTENT(IN) :: var
756	INTEGER, INTENT(IN) :: iter
757	TYPE(nc_file), INTENT(IN) :: output_file
758	REAL(dp), INTENT(IN) :: buffer(:,:,:)
759
760	INTEGER :: ncid, ndim_out, start(4), count(4)
761	LOGICAL :: last_dimension_is_time
762
763	ndim_out = var % ndim
764
765	last_dimension_is_time = var % dimids( var % ndim ) == output_file % dimid_time
766	IF ( last_dimension_is_time ) THEN
767	ndim_out = ndim_out - 1
768	END IF
769
770	start(:) = (/1,1,1,iter/)
771	count(1:ndim_out) = var%dimlen(1:ndim_out)
772
773	CALL check(nf90_open(output_file % name, NF90_WRITE, ncid))
774
775	IF (TRIM(var % kind) .EQ. 'left/right scalar') THEN
776
777	CALL check(nf90_put_var( ncid, var%varid, buffer(1,:,:) ) )
778
779	ELSE IF (TRIM(var % kind) .EQ. 'north/south scalar') THEN
780
781	CALL check(nf90_put_var( ncid, var%varid, buffer(:,1,:) ) )
782
783	ELSE IF (TRIM(var % kind) .EQ. 'top scalar') THEN
784
785	CALL check(nf90_put_var( ncid, var%varid, buffer(:,:,1) ) )
786	ELSE
787
788	CALL check(nf90_put_var( ncid, var%varid, buffer ) )
789
790	END IF
791	CALL check(nf90_close(ncid))
792
793	END SUBROUTINE write_netcdf_variable_2d
794
795
796	SUBROUTINE check(status)
797
798	INTEGER, INTENT(IN) :: status
799
800	IF (status /= nf90_noerr) THEN
801	message = "NetCDF API call failed with error: " // &
802	TRIM( nf90_strerror(status) )
803	CALL abort('io.check', message)
804	END IF
805
806	END SUBROUTINE check
807
808	END MODULE io

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