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source: palm/trunk/UTIL/inifor/src/io.f90 @ 3262

Last change on this file since 3262 was 3262, checked in by eckhard, 6 years ago
Removed unnecessary file check
Property svn:keywords set to `Id`
File size: 34.1 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 3262 2018-09-19 15:47:15Z eckhard $
28	! Removed unnecessary check for output file
29	!
30	! 3183 2018-07-27 14:25:55Z suehring
31	! Introduced new PALM grid stretching
32	! Updated variable names and metadata for PIDS v1.9 compatibility
33	! Improved handling of the start date string
34	! Better compatibility with older Intel compilers:
35	! - avoiding implicit array allocation with new get_netcdf_variable()
36	! subroutine instead of function
37	! Improved command line interface:
38	! - Added configuration validation
39	! - New options to configure input file prefixes
40	! - GNU-style short and long option names
41	! - Added version and copyright output
42	!
43	!
44	! 3182 2018-07-27 13:36:03Z suehring
45	! Initial revision
46	!
47	!
48	!
49	! Authors:
50	! --------
51	! @author Eckhard Kadasch
52	!
53	! Description:
54	! ------------
55	!> The io module contains the functions needed to read and write netCDF data in
56	!> INIFOR.
57	!------------------------------------------------------------------------------!
58	MODULE io
59
60	USE control
61	USE defs, &
62	ONLY: DATE, SNAME, PATH, PI, dp, hp, TO_RADIANS, TO_DEGREES, VERSION
63	USE netcdf
64	USE types
65	USE util, &
66	ONLY: reverse, str, real_to_str
67
68	IMPLICIT NONE
69
70	INTERFACE get_netcdf_variable
71	MODULE PROCEDURE get_netcdf_variable_int
72	MODULE PROCEDURE get_netcdf_variable_real
73	END INTERFACE get_netcdf_variable
74
75	PRIVATE :: get_netcdf_variable_int, get_netcdf_variable_real
76
77	CONTAINS
78
79	SUBROUTINE get_netcdf_variable_int(in_file, in_var, buffer)
80
81	CHARACTER(LEN=PATH), INTENT(IN) :: in_file
82	TYPE(nc_var), INTENT(INOUT) :: in_var
83	INTEGER(hp), ALLOCATABLE, INTENT(INOUT) :: buffer(:,:,:)
84
85	INCLUDE 'get_netcdf_variable.inc'
86
87	END SUBROUTINE get_netcdf_variable_int
88
89
90	SUBROUTINE get_netcdf_variable_real(in_file, in_var, buffer)
91
92	CHARACTER(LEN=PATH), INTENT(IN) :: in_file
93	TYPE(nc_var), INTENT(INOUT) :: in_var
94	REAL(dp), ALLOCATABLE, INTENT(INOUT) :: buffer(:,:,:)
95
96	INCLUDE 'get_netcdf_variable.inc'
97
98	END SUBROUTINE get_netcdf_variable_real
99
100
101	SUBROUTINE netcdf_define_variable(var, ncid)
102
103	TYPE(nc_var), INTENT(INOUT) :: var
104	INTEGER, INTENT(IN) :: ncid
105
106	CALL check(nf90_def_var(ncid, var % name, NF90_FLOAT, var % dimids(1:var % ndim), var % varid))
107	CALL check(nf90_put_att(ncid, var % varid, "long_name", var % long_name))
108	CALL check(nf90_put_att(ncid, var % varid, "units", var % units))
109	IF ( var % lod .GE. 0 ) THEN
110	CALL check(nf90_put_att(ncid, var % varid, "lod", var % lod))
111	END IF
112	CALL check(nf90_put_att(ncid, var % varid, "source", var % source))
113	CALL check(nf90_put_att(ncid, var % varid, "_FillValue", NF90_FILL_REAL))
114
115	END SUBROUTINE netcdf_define_variable
116
117
118	SUBROUTINE netcdf_get_dimensions(var, ncid)
119
120	TYPE(nc_var), INTENT(INOUT) :: var
121	INTEGER, INTENT(IN) :: ncid
122	INTEGER :: i
123	CHARACTER(SNAME) :: null
124
125	! Remember dimension lenghts for NetCDF writing routine
126	DO i = 1, var % ndim
127	CALL check(nf90_inquire_dimension(ncid, var % dimids(i), &
128	name = null, &
129	len = var % dimlen(i) ) )
130	END DO
131
132	END SUBROUTINE netcdf_get_dimensions
133
134
135	!------------------------------------------------------------------------------!
136	! Description:
137	! ------------
138	!> This routine initializes Inifor. This includes parsing command-line
139	!> arguments, setting the names of the input and output file names as well as
140	!> the name of the input namelist and, subsequently, reading in and setting grid
141	!> parameters for the PALM-4U computational grid.
142	!------------------------------------------------------------------------------!
143	SUBROUTINE parse_command_line_arguments( cfg )
144
145	TYPE(inifor_config), INTENT(INOUT) :: cfg
146
147	CHARACTER(LEN=PATH) :: option, arg
148	INTEGER :: arg_count, i
149
150	arg_count = COMMAND_ARGUMENT_COUNT()
151	IF (arg_count .GT. 0) THEN
152
153	! Every option should have an argument.
154	!IF ( MOD(arg_count, 2) .NE. 0 ) THEN
155	! message = "Syntax error in command line."
156	! CALL abort('parse_command_line_arguments', message)
157	!END IF
158
159	message = "The -clon and -clat command line options are depricated. " // &
160	"Please remove them form your inifor command and specify the " // &
161	"location of the PALM-4U origin either" // NEW_LINE(' ') // &
162	" - by setting the namelist parameters 'longitude' and 'latitude', or" // NEW_LINE(' ') // &
163	" - by providing a static driver netCDF file via the -static command-line option."
164
165	i = 1
166	DO WHILE (i .LE. arg_count)
167
168	CALL GET_COMMAND_ARGUMENT( i, option )
169
170	SELECT CASE( TRIM(option) )
171
172	CASE( '-date', '-d', '--date' )
173	CALL get_option_argument( i, arg )
174	cfg % start_date = TRIM(arg)
175
176	! Elevation of the PALM-4U domain above sea level
177	CASE( '-z0', '-z', '--elevation' )
178	CALL get_option_argument( i, arg )
179	READ(arg, *) cfg % z0
180
181	! surface pressure, at z0
182	CASE( '-p0', '-r', '--surface-pressure' )
183	CALL get_option_argument( i, arg )
184	READ(arg, *) cfg % p0
185
186	! geostrophic wind in x direction
187	CASE( '-ug', '-u', '--geostrophic-u' )
188	CALL get_option_argument( i, arg )
189	READ(arg, *) cfg % ug
190
191	! geostrophic wind in y direction
192	CASE( '-vg', '-v', '--geostrophic-v' )
193	CALL get_option_argument( i, arg )
194	READ(arg, *) cfg % vg
195
196	! domain centre geographical longitude and latitude
197	CASE( '-clon', '-clat' )
198	CALL abort('parse_command_line_arguments', message)
199	!READ(arg, *) lambda_cg
200	!lambda_cg = lambda_cg * TO_RADIANS
201	!READ(arg, *) phi_cg
202	!phi_cg = phi_cg * TO_RADIANS
203
204	CASE( '-path', '-p', '--path' )
205	CALL get_option_argument( i, arg )
206	cfg % input_path = TRIM(arg)
207
208	CASE( '-hhl', '-l', '--hhl-file' )
209	CALL get_option_argument( i, arg )
210	cfg % hhl_file = TRIM(arg)
211
212	CASE( '-static', '-t', '--static-driver' )
213	CALL get_option_argument( i, arg )
214	cfg % static_driver_file = TRIM(arg)
215
216	CASE( '-soil', '-s', '--soil-file')
217	CALL get_option_argument( i, arg )
218	cfg % soiltyp_file = TRIM(arg)
219
220	CASE( '--flow-prefix')
221	CALL get_option_argument( i, arg )
222	cfg % flow_prefix = TRIM(arg)
223
224	CASE( '--radiation-prefix')
225	CALL get_option_argument( i, arg )
226	cfg % radiation_prefix = TRIM(arg)
227
228	CASE( '--soil-prefix')
229	CALL get_option_argument( i, arg )
230	cfg % soil_prefix = TRIM(arg)
231
232	CASE( '--soilmoisture-prefix')
233	CALL get_option_argument( i, arg )
234	cfg % soilmoisture_prefix = TRIM(arg)
235
236	CASE( '-o', '--output' )
237	CALL get_option_argument( i, arg )
238	cfg % output_file = TRIM(arg)
239
240	CASE( '-n', '--namelist' )
241	CALL get_option_argument( i, arg )
242	cfg % namelist_file = TRIM(arg)
243
244	! initial condition mode: 'profile' / 'volume'
245	CASE( '-mode', '-i', '--init-mode' )
246	CALL get_option_argument( i, arg )
247	cfg % ic_mode = TRIM(arg)
248
249	! boundary conditions / forcing mode: 'ideal' / 'real'
250	CASE( '-f', '--forcing-mode' )
251	CALL get_option_argument( i, arg )
252	cfg % bc_mode = TRIM(arg)
253
254	CASE( '--version' )
255	CALL print_version()
256	STOP
257
258	CASE( '--help' )
259	CALL print_version()
260	PRINT *, ""
261	PRINT *, "For a list of command-line options have a look at the README file."
262	STOP
263
264	CASE DEFAULT
265	message = "unknown option '" // TRIM(option) // "'."
266	CALL abort('parse_command_line_arguments', message)
267
268	END SELECT
269
270	i = i + 1
271
272	END DO
273
274	ELSE
275
276	message = "No arguments present, using default input and output files"
277	CALL report('parse_command_line_arguments', message)
278
279	END IF
280
281	END SUBROUTINE parse_command_line_arguments
282
283
284	SUBROUTINE get_option_argument(i, arg)
285	CHARACTER(LEN=PATH), INTENT(INOUT) :: arg
286	INTEGER, INTENT(INOUT) :: i
287
288	i = i + 1
289	CALL GET_COMMAND_ARGUMENT(i, arg)
290
291	END SUBROUTINE
292
293
294	SUBROUTINE validate_config(cfg)
295	TYPE(inifor_config), INTENT(IN) :: cfg
296	LOGICAL :: all_files_present
297
298	all_files_present = .TRUE.
299	all_files_present = all_files_present .AND. file_present(cfg % hhl_file)
300	all_files_present = all_files_present .AND. file_present(cfg % namelist_file)
301	all_files_present = all_files_present .AND. file_present(cfg % soiltyp_file)
302
303	! Only check optional static driver file name, if it has been given.
304	IF (TRIM(cfg % static_driver_file) .NE. '') THEN
305	all_files_present = all_files_present .AND. file_present(cfg % static_driver_file)
306	END IF
307
308	IF (.NOT. all_files_present) THEN
309	message = "INIFOR configuration invalid; some input files are missing."
310	CALL abort( 'validate_config', message )
311	END IF
312
313
314	SELECT CASE( TRIM(cfg % ic_mode) )
315	CASE( 'profile', 'volume')
316	CASE DEFAULT
317	message = "Initialization mode '" // TRIM(cfg % ic_mode) //&
318	"' is not supported. " //&
319	"Please select either 'profile' or 'volume', " //&
320	"or omit the -i/--init-mode/-mode option entirely, which corresponds "//&
321	"to the latter."
322	CALL abort( 'validate_config', message )
323	END SELECT
324
325
326	SELECT CASE( TRIM(cfg % bc_mode) )
327	CASE( 'real', 'ideal')
328	CASE DEFAULT
329	message = "Forcing mode '" // TRIM(cfg % bc_mode) //&
330	"' is not supported. " //&
331	"Please select either 'real' or 'ideal', " //&
332	"or omit the -f/--forcing-mode option entirely, which corresponds "//&
333	"to the latter."
334	CALL abort( 'validate_config', message )
335	END SELECT
336
337
338	END SUBROUTINE validate_config
339
340
341	LOGICAL FUNCTION file_present(filename)
342	CHARACTER(LEN=PATH), INTENT(IN) :: filename
343
344	INQUIRE(FILE=filename, EXIST=file_present)
345
346	IF (.NOT. file_present) THEN
347	message = "The given file '" // "' does not exist."
348	CALL report('file_present', message)
349	END IF
350
351	END FUNCTION file_present
352
353
354	!------------------------------------------------------------------------------!
355	! Description:
356	! ------------
357	!> This routine initializes the Inifor output file, i.e. the PALM-4U
358	!> initializing and forcing data as a NetCDF file.
359	!>
360	!> Besides writing metadata, such as global attributes, coordinates, variables,
361	!> in the NetCDF file, various NetCDF IDs are saved for later, when Inifor
362	!> writes the actual data.
363	!------------------------------------------------------------------------------!
364	SUBROUTINE setup_netcdf_dimensions(output_file, palm_grid, &
365	start_date_string, origin_lon, origin_lat)
366
367	TYPE(nc_file), INTENT(INOUT) :: output_file
368	TYPE(grid_definition), INTENT(IN) :: palm_grid
369	CHARACTER (LEN=DATE), INTENT(IN) :: start_date_string
370	REAL(dp), INTENT(IN) :: origin_lon, origin_lat
371
372	CHARACTER (LEN=8) :: date_string
373	CHARACTER (LEN=10) :: time_string
374	CHARACTER (LEN=5) :: zone_string
375	CHARACTER (LEN=SNAME) :: history_string
376	INTEGER :: ncid, nx, ny, nz, nt, dimids(3), dimvarids(3)
377	REAL(dp) :: z0
378
379	message = "Initializing PALM-4U dynamic driver file '" // &
380	TRIM(output_file % name) // "' and setting up dimensions."
381	CALL report('setup_netcdf_dimensions', message)
382
383	! Create the NetCDF file. NF90_CLOBBER selects overwrite mode.
384	#if defined( __netcdf4 )
385	CALL check(nf90_create(TRIM(output_file % name), OR(NF90_CLOBBER, NF90_HDF5), ncid))
386	#else
387	CALL check(nf90_create(TRIM(output_file % name), NF90_CLOBBER, ncid))
388	#endif
389
390	!
391	!------------------------------------------------------------------------------
392	!- Section 1: Write global NetCDF attributes
393	!------------------------------------------------------------------------------
394	CALL date_and_time(DATE=date_string, TIME=time_string, ZONE=zone_string)
395	history_string = &
396	'Created on '// date_string // &
397	' at ' // time_string(1:2) // ':' // time_string(3:4) // &
398	' (UTC' // zone_string // ')'
399
400	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'title', 'PALM input file for scenario ...'))
401	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'institution', 'Deutscher Wetterdienst, Offenbach'))
402	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'author', 'Eckhard Kadasch, eckhard.kadasch@dwd.de'))
403	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'history', TRIM(history_string)))
404	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'references', '--'))
405	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'comment', '--'))
406	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'origin_lat', TRIM(real_to_str(origin_lat*TO_DEGREES, '(F18.13)'))))
407	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'origin_lon', TRIM(real_to_str(origin_lon*TO_DEGREES, '(F18.13)'))))
408	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'inifor_version', TRIM(VERSION)))
409	CALL check(nf90_put_att(ncid, NF90_GLOBAL, 'palm_version', '--'))
410
411	!
412	!------------------------------------------------------------------------------
413	!- Section 2: Define NetCDF dimensions and coordinates
414	!------------------------------------------------------------------------------
415	nt = SIZE(output_file % time)
416	nx = palm_grid % nx
417	ny = palm_grid % ny
418	nz = palm_grid % nz
419	z0 = palm_grid % z0
420
421	!
422	!------------------------------------------------------------------------------
423	!- Section 2a: Define dimensions for cell centers (scalars in soil and atmosph.)
424	!------------------------------------------------------------------------------
425	dimids = (/0, 0, 0/) ! reset dimids
426	CALL check( nf90_def_dim(ncid, "x", nx+1, dimids(1)) )
427	CALL check( nf90_def_dim(ncid, "y", ny+1, dimids(2)) )
428	CALL check( nf90_def_dim(ncid, "z", nz, dimids(3)) )
429	output_file % dimids_scl = dimids ! save dimids for later
430
431	dimvarids = (/0, 0, 0/) ! reset dimvarids
432	CALL check(nf90_def_var(ncid, "x", NF90_FLOAT, dimids(1), dimvarids(1)))
433	CALL check(nf90_put_att(ncid, dimvarids(1), "standard_name", "x coordinate of cell centers"))
434	CALL check(nf90_put_att(ncid, dimvarids(1), "units", "m"))
435
436	CALL check(nf90_def_var(ncid, "y", NF90_FLOAT, dimids(2), dimvarids(2)))
437	CALL check(nf90_put_att(ncid, dimvarids(2), "standard_name", "y coordinate of cell centers"))
438	CALL check(nf90_put_att(ncid, dimvarids(2), "units", "m"))
439
440	CALL check(nf90_def_var(ncid, "z", NF90_FLOAT, dimids(3), dimvarids(3)))
441	CALL check(nf90_put_att(ncid, dimvarids(3), "standard_name", "z coordinate of cell centers"))
442	CALL check(nf90_put_att(ncid, dimvarids(3), "units", "m"))
443	output_file % dimvarids_scl = dimvarids ! save dimvarids for later
444
445	! overwrite third dimid with the one of depth
446	CALL check(nf90_def_dim(ncid, "zsoil", SIZE(palm_grid % depths), dimids(3)) )
447	output_file % dimids_soil = dimids ! save dimids for later
448
449	! overwrite third dimvarid with the one of depth
450	CALL check(nf90_def_var(ncid, "zsoil", NF90_FLOAT, output_file % dimids_soil(3), dimvarids(3)))
451	CALL check(nf90_put_att(ncid, dimvarids(3), "standard_name", "depth_below_land"))
452	CALL check(nf90_put_att(ncid, dimvarids(3), "positive", "down"))
453	CALL check(nf90_put_att(ncid, dimvarids(3), "units", "m"))
454	output_file % dimvarids_soil = dimvarids ! save dimvarids for later
455	!
456	!------------------------------------------------------------------------------
457	!- Section 2b: Define dimensions for cell faces/velocities
458	!------------------------------------------------------------------------------
459	dimids = (/0, 0, 0/) ! reset dimids
460	CALL check(nf90_def_dim(ncid, "xu", nx, dimids(1)) )
461	CALL check(nf90_def_dim(ncid, "yv", ny, dimids(2)) )
462	CALL check(nf90_def_dim(ncid, "zw", nz-1, dimids(3)) )
463	output_file % dimids_vel = dimids ! save dimids for later
464
465	dimvarids = (/0, 0, 0/) ! reset dimvarids
466	CALL check(nf90_def_var(ncid, "xu", NF90_FLOAT, dimids(1), dimvarids(1)))
467	CALL check(nf90_put_att(ncid, dimvarids(1), "standard_name", "x coordinate of cell faces"))
468	CALL check(nf90_put_att(ncid, dimvarids(1), "units", "m"))
469
470	CALL check(nf90_def_var(ncid, "yv", NF90_FLOAT, dimids(2), dimvarids(2)))
471	CALL check(nf90_put_att(ncid, dimvarids(2), "standard_name", "y coordinate of cell faces"))
472	CALL check(nf90_put_att(ncid, dimvarids(2), "units", "m"))
473
474	CALL check(nf90_def_var(ncid, "zw", NF90_FLOAT, dimids(3), dimvarids(3)))
475	CALL check(nf90_put_att(ncid, dimvarids(3), "standard_name", "z coordinate of cell faces"))
476	CALL check(nf90_put_att(ncid, dimvarids(3), "units", "m"))
477	output_file % dimvarids_vel = dimvarids ! save dimvarids for later
478
479	!
480	!------------------------------------------------------------------------------
481	!- Section 2c: Define time dimension
482	!------------------------------------------------------------------------------
483	CALL check(nf90_def_dim(ncid, "time", nt, output_file % dimid_time) )
484	CALL check(nf90_def_var(ncid, "time", NF90_FLOAT, &
485	output_file % dimid_time, &
486	output_file % dimvarid_time))
487	CALL check(nf90_put_att(ncid, output_file % dimvarid_time, "standard_name", "time"))
488	CALL check(nf90_put_att(ncid, output_file % dimvarid_time, "long_name", "time"))
489	CALL check(nf90_put_att(ncid, output_file % dimvarid_time, "units", &
490	"seconds since " // start_date_string // " UTC"))
491
492	CALL check(nf90_enddef(ncid))
493
494	!
495	!------------------------------------------------------------------------------
496	!- Section 3: Write grid coordinates
497	!------------------------------------------------------------------------------
498	CALL check(nf90_put_var(ncid, output_file % dimvarids_scl(1), palm_grid%x))
499	CALL check(nf90_put_var(ncid, output_file % dimvarids_scl(2), palm_grid%y))
500	CALL check(nf90_put_var(ncid, output_file % dimvarids_scl(3), palm_grid%z))
501
502	CALL check(nf90_put_var(ncid, output_file % dimvarids_vel(1), palm_grid%xu))
503	CALL check(nf90_put_var(ncid, output_file % dimvarids_vel(2), palm_grid%yv))
504	CALL check(nf90_put_var(ncid, output_file % dimvarids_vel(3), palm_grid%zw))
505
506	! TODO Read in soil depths from input file before this.
507	CALL check(nf90_put_var(ncid, output_file % dimvarids_soil(3), palm_grid%depths))
508
509	! Write time vector
510	CALL check(nf90_put_var(ncid, output_file % dimvarid_time, output_file % time))
511
512	! Close the file
513	CALL check(nf90_close(ncid))
514
515	END SUBROUTINE setup_netcdf_dimensions
516
517
518	SUBROUTINE setup_netcdf_variables(filename, output_variable_table)
519
520	CHARACTER (LEN=*), INTENT(IN) :: filename
521	TYPE(nc_var), INTENT(INOUT), TARGET :: output_variable_table(:)
522	TYPE(nc_var), POINTER :: var
523	INTEGER :: i, ncid
524
525	message = "Defining variables in dynamic driver '" // TRIM(filename) // "'."
526	CALL report('setup_netcdf_variables', message)
527
528	CALL check(nf90_open(TRIM(filename), NF90_WRITE, ncid))
529	CALL check(nf90_redef(ncid))
530
531	DO i = 1, SIZE(output_variable_table)
532
533	var => output_variable_table(i)
534
535	IF ( var % to_be_processed ) THEN
536	message = " variable #" // TRIM(str(i)) // " '" // TRIM(var%name) // "'."
537	CALL report('setup_netcdf_variables', message)
538
539	CALL netcdf_define_variable(var, ncid)
540	CALL netcdf_get_dimensions(var, ncid)
541	END IF
542
543	END DO
544
545	CALL check(nf90_enddef(ncid))
546	CALL check(nf90_close(ncid))
547
548	message = "Dynamic driver '" // TRIM(filename) // "' initialized successfully."
549	CALL report('setup_netcdf_variables', message)
550
551	END SUBROUTINE setup_netcdf_variables
552
553
554	!------------------------------------------------------------------------------!
555	! Description:
556	! ------------
557	!> This routine reads and returns all input variables of the given IO group
558	!> It accomodates the data by allocating a container variable that represents a
559	!> list of arrays of the same length as the groups variable list. (This list
560	!> will typically contain one or two items.) After the container, its members
561	!> are allocated one by one with the appropriate, possibly different,
562	!> dimensions.
563	!>
564	!> The 'group' is an INTENT(INOUT) variable so that 'get_netcdf_variable()' can
565	!> record netCDF IDs in the 'in_var_list()' member variable.
566	!------------------------------------------------------------------------------!
567	SUBROUTINE read_input_variables(group, iter, buffer)
568	TYPE(io_group), INTENT(INOUT), TARGET :: group
569	INTEGER, INTENT(IN) :: iter
570	TYPE(container), ALLOCATABLE, INTENT(INOUT) :: buffer(:)
571	INTEGER :: hour, buf_id
572	TYPE(nc_var), POINTER :: input_var
573	CHARACTER(LEN=PATH), POINTER :: input_file
574	INTEGER :: ivar, nbuffers
575
576	message = "Reading data for I/O group '" // TRIM(group % in_var_list(1) % name) // "'."
577	CALL report('read_input_variables', message)
578
579	input_file => group % in_files(iter)
580
581	!
582	!------------------------------------------------------------------------------
583	!- Section 1: Load input buffers for accumulated variables
584	!------------------------------------------------------------------------------
585	IF (group % kind == 'running average' .OR. &
586	group % kind == 'accumulated') THEN ! radiation budgets, precipitation
587
588	IF (SIZE(group % in_var_list) .GT. 1 ) THEN
589	message = "I/O groups may not contain more than one " // &
590	"accumulated variable. Group '" // TRIM(group % kind) //&
591	"' contains " // &
592	TRIM( str(SIZE(group % in_var_list)) ) // "."
593	CALL abort('read_input_variables \| accumulation', message)
594	END IF
595
596	! use two buffer arrays
597	nbuffers = 2
598	IF ( .NOT. ALLOCATED( buffer ) ) ALLOCATE( buffer(nbuffers) )
599
600	! chose correct buffer array
601	hour = iter - 1! hour of the day
602	buf_id = select_buffer(hour)
603
604	CALL run_control('time', 'read')
605	IF ( ALLOCATED(buffer(buf_id) % array) ) DEALLOCATE(buffer(buf_id) % array)
606	CALL run_control('time', 'alloc')
607
608	input_var => group % in_var_list(1)
609	CALL get_netcdf_variable(input_file, input_var, buffer(buf_id) % array)
610	CALL report('read_input_variables', "Read accumulated " // TRIM(group % in_var_list(1) % name))
611
612	IF ( input_var % is_upside_down ) CALL reverse(buffer(buf_id) % array)
613	CALL run_control('time', 'comp')
614
615	!------------------------------------------------------------------------------
616	!- Section 2: Load input buffers for normal I/O groups
617	!------------------------------------------------------------------------------
618	ELSE
619
620	nbuffers = SIZE( group % in_var_list )
621	ALLOCATE( buffer(nbuffers) )
622	CALL run_control('time', 'alloc')
623
624	DO ivar = 1, nbuffers
625
626	input_var => group % in_var_list(ivar)
627
628	! Check wheather P or PP is present in input file
629	IF (input_var % name == 'P') THEN
630	input_var % name = TRIM( get_pressure_var(input_file) )
631	CALL run_control('time', 'read')
632	END IF
633
634	CALL get_netcdf_variable(input_file, input_var, buffer(ivar) % array)
635
636	IF ( input_var % is_upside_down ) CALL reverse(buffer(ivar) % array)
637	CALL run_control('time', 'comp')
638
639	END DO
640	END IF
641
642	END SUBROUTINE read_input_variables
643
644
645	INTEGER FUNCTION select_buffer(hour)
646	INTEGER, INTENT(IN) :: hour
647	INTEGER :: step
648
649	select_buffer = 0
650	step = MODULO(hour, 3) + 1
651
652	SELECT CASE(step)
653	CASE(1, 3)
654	select_buffer = 1
655	CASE(2)
656	select_buffer = 2
657	CASE DEFAULT
658	message = "Invalid step '" // TRIM(str(step))
659	CALL abort('select_buffer', message)
660	END SELECT
661	END FUNCTION select_buffer
662
663
664	!------------------------------------------------------------------------------!
665	! Description:
666	! ------------
667	!> Checks if the input_file contains the absolute pressure, 'P', or the pressure
668	!> perturbation, 'PP', and returns the appropriate string.
669	!------------------------------------------------------------------------------!
670	CHARACTER(LEN=2) FUNCTION get_pressure_var(input_file) RESULT(var)
671	CHARACTER(LEN=*) :: input_file
672	INTEGER :: ncid, varid
673
674	CALL check(nf90_open( TRIM(input_file), NF90_NOWRITE, ncid ))
675	IF ( nf90_inq_varid( ncid, 'P', varid ) .EQ. NF90_NOERR ) THEN
676
677	var = 'P'
678
679	ELSE IF ( nf90_inq_varid( ncid, 'PP', varid ) .EQ. NF90_NOERR ) THEN
680
681	var = 'PP'
682	CALL report('get_pressure_var', 'Using PP instead of P')
683
684	ELSE
685
686	message = "Failed to read '" // TRIM(var) // &
687	"' from file '" // TRIM(input_file) // "'."
688	CALL abort('get_pressure_var', message)
689
690	END IF
691
692	CALL check(nf90_close(ncid))
693
694	END FUNCTION get_pressure_var
695
696
697	FUNCTION get_netcdf_attribute(filename, attribute) RESULT(attribute_value)
698
699	CHARACTER(LEN=*), INTENT(IN) :: filename, attribute
700	REAL(dp) :: attribute_value
701
702	INTEGER :: ncid
703
704	IF ( nf90_open( TRIM(filename), NF90_NOWRITE, ncid ) == NF90_NOERR ) THEN
705
706	CALL check(nf90_get_att(ncid, NF90_GLOBAL, TRIM(attribute), attribute_value))
707	CALL check(nf90_close(ncid))
708
709	ELSE
710
711	message = "Failed to read '" // TRIM(attribute) // &
712	"' from file '" // TRIM(filename) // "'."
713	CALL abort('get_netcdf_attribute', message)
714
715	END IF
716
717	END FUNCTION get_netcdf_attribute
718
719
720	SUBROUTINE update_output(var, array, iter, output_file)
721	TYPE(nc_var), INTENT(IN) :: var
722	REAL(dp), INTENT(IN) :: array(:,:,:)
723	INTEGER, INTENT(IN) :: iter
724	TYPE(nc_file), INTENT(IN) :: output_file
725
726	INTEGER :: ncid, ndim, start(4), count(4)
727	LOGICAL :: var_is_time_dependent
728
729	var_is_time_dependent = ( &
730	var % dimids( var % ndim ) == output_file % dimid_time &
731	)
732
733	! Skip time dimension for output
734	ndim = var % ndim
735	IF ( var_is_time_dependent ) ndim = var % ndim - 1
736
737	start(:) = (/1,1,1,1/)
738	start(ndim+1) = iter
739	count(1:ndim) = var%dimlen(1:ndim)
740
741	CALL check(nf90_open(output_file % name, NF90_WRITE, ncid))
742
743	! Reduce dimension of output array according to variable kind
744	SELECT CASE (TRIM(var % kind))
745
746	CASE ( 'init scalar profile', 'init u profile', 'init v profile', &
747	'init w profile' )
748
749	CALL check(nf90_put_var( ncid, var%varid, array(1,1,:) ) )
750
751	CASE ( 'init soil', 'init scalar', 'init u', 'init v', 'init w' )
752
753	CALL check(nf90_put_var( ncid, var%varid, array(:,:,:) ) )
754
755	CASE( 'left scalar', 'right scalar', 'left w', 'right w' )
756
757	CALL check(nf90_put_var( ncid, var%varid, array(1,:,:), &
758	start=start(1:ndim+1), &
759	count=count(1:ndim) ) )
760
761
762	IF (.NOT. SIZE(array, 2) .EQ. var % dimlen(1)) THEN
763	PRINT *, "inifor: update_output: Dimension ", 1, " of variable ", &
764	TRIM(var % name), " (", var % dimlen(1), &
765	") does not match the dimension of the output array (", &
766	SIZE(array, 2), ")."
767	STOP
768	END IF
769
770
771	CASE( 'north scalar', 'south scalar', 'north w', 'south w' )
772
773	CALL check(nf90_put_var( ncid, var%varid, array(:,1,:), &
774	start=start(1:ndim+1), &
775	count=count(1:ndim) ) )
776
777
778	CASE( 'surface forcing', 'top scalar', 'top w' )
779
780	CALL check(nf90_put_var( ncid, var%varid, array(:,:,1), &
781	start=start(1:ndim+1), &
782	count=count(1:ndim) ) )
783
784	CASE ( 'left u', 'right u', 'left v', 'right v' )
785
786	CALL check(nf90_put_var( ncid, var%varid, array(1,:,:), &
787	start=start(1:ndim+1), &
788	count=count(1:ndim) ) )
789
790	CASE ( 'north u', 'south u', 'north v', 'south v' )
791
792	CALL check(nf90_put_var( ncid, var%varid, array(:,1,:), &
793	start=start(1:ndim+1), &
794	count=count(1:ndim) ) )
795
796	CASE ( 'top u', 'top v' )
797
798	CALL check(nf90_put_var( ncid, var%varid, array(:,:,1), &
799	start=start(1:ndim+1), &
800	count=count(1:ndim) ) )
801
802	CASE ( 'time series' )
803
804	CALL check(nf90_put_var( ncid, var%varid, array(1,1,1), &
805	start=start(1:ndim+1) ) )
806
807	CASE ( 'constant scalar profile' )
808
809	CALL check(nf90_put_var( ncid, var%varid, array(1,1,:), &
810	start=start(1:ndim+1), &
811	count=count(1:ndim) ) )
812
813	CASE ( 'large-scale scalar forcing', 'large-scale w forcing' )
814
815	message = "Doing nothing in terms of writing large-scale forings."
816	CALL report('update_output', message)
817
818	CASE DEFAULT
819
820	message = "Variable kind '" // TRIM(var % kind) // &
821	"' not recognized."
822	CALL abort('update_output', message)
823
824	END SELECT
825
826	CALL check(nf90_close(ncid))
827
828	END SUBROUTINE update_output
829
830
831	SUBROUTINE write_netcdf_variable_2d(var, iter, output_file, buffer)
832	TYPE(nc_var), INTENT(IN) :: var
833	INTEGER, INTENT(IN) :: iter
834	TYPE(nc_file), INTENT(IN) :: output_file
835	REAL(dp), INTENT(IN) :: buffer(:,:,:)
836
837	INTEGER :: ncid, ndim_out, start(4), count(4)
838	LOGICAL :: last_dimension_is_time
839
840	ndim_out = var % ndim
841
842	last_dimension_is_time = var % dimids( var % ndim ) == output_file % dimid_time
843	IF ( last_dimension_is_time ) THEN
844	ndim_out = ndim_out - 1
845	END IF
846
847	start(:) = (/1,1,1,iter/)
848	count(1:ndim_out) = var%dimlen(1:ndim_out)
849
850	CALL check(nf90_open(output_file % name, NF90_WRITE, ncid))
851
852	IF (TRIM(var % kind) .EQ. 'left/right scalar') THEN
853
854	CALL check(nf90_put_var( ncid, var%varid, buffer(1,:,:) ) )
855
856	ELSE IF (TRIM(var % kind) .EQ. 'north/south scalar') THEN
857
858	CALL check(nf90_put_var( ncid, var%varid, buffer(:,1,:) ) )
859
860	ELSE IF (TRIM(var % kind) .EQ. 'top scalar') THEN
861
862	CALL check(nf90_put_var( ncid, var%varid, buffer(:,:,1) ) )
863	ELSE
864
865	CALL check(nf90_put_var( ncid, var%varid, buffer ) )
866
867	END IF
868	CALL check(nf90_close(ncid))
869
870	END SUBROUTINE write_netcdf_variable_2d
871
872
873	SUBROUTINE check(status)
874
875	INTEGER, INTENT(IN) :: status
876
877	IF (status /= nf90_noerr) THEN
878	message = "NetCDF API call failed with error: " // &
879	TRIM( nf90_strerror(status) )
880	CALL abort('io.check', message)
881	END IF
882
883	END SUBROUTINE check
884
885	END MODULE io

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