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source: palm/trunk/UTIL/inifor/src/io.f90 @ 2954

Last change on this file since 2954 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

Rev	Line
[2696]	1	!> @file src/io.f90
	2	!------------------------------------------------------------------------------!
[2718]	3	! This file is part of the PALM model system.
[2696]	4	!
[2718]	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
[2696]	8	! version.
	9	!
[2718]	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.
[2696]	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	!
[2718]	17	! Copyright 2017-2018 Leibniz Universitaet Hannover
	18	! Copyright 2017-2018 Deutscher Wetterdienst Offenbach
[2696]	19	!------------------------------------------------------------------------------!
	20	!
	21	! Current revisions:
	22	! -----------------
	23	!
	24	!
	25	! Former revisions:
	26	! -----------------
	27	! $Id: io.f90 2718 2018-01-02 08:49:38Z schwenkel $
	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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