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hdf5_wrapper.F
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1!--------------------------------------------------------------------------------------------------!
2! CP2K: A general program to perform molecular dynamics simulations !
3! Copyright 2000-2025 CP2K developers group <https://cp2k.org> !
4! !
5! SPDX-License-Identifier: GPL-2.0-or-later !
6!--------------------------------------------------------------------------------------------------!
7
8! **************************************************************************************************
9!> \brief A wrapper around the HDF5 Fortran API
10!> \par History
11!> 04.2023 created [SB]
12!> \author Stefano Battaglia
13! **************************************************************************************************
14MODULE hdf5_wrapper
15
16#ifdef __HDF5
17 USE hdf5, ONLY: &
18 h5aclose_f, h5acreate_f, h5aopen_f, h5aread_f, h5awrite_f, h5close_f, h5dclose_f, &
19 h5dcreate_f, h5dget_space_f, h5dopen_f, h5dread_f, h5dwrite_f, h5f_acc_rdonly_f, &
20 h5f_acc_trunc_f, h5fclose_f, h5fcreate_f, h5fopen_f, h5gclose_f, h5gcreate_f, h5gopen_f, &
21 h5open_f, h5s_scalar_f, h5sclose_f, h5screate_f, h5screate_simple_f, &
22 h5sget_simple_extent_npoints_f, h5t_c_s1, h5t_cset_utf8_f, h5t_enum_f, h5t_native_double, &
23 h5t_native_integer, h5t_str_nullpad_f, h5t_string, h5tclose_f, h5tcopy_f, h5tcreate_f, &
24 h5tenum_insert_f, h5tset_cset_f, h5tset_size_f, h5tset_strpad_f, hid_t, hsize_t, size_t
25#endif
26 USE iso_c_binding, ONLY: c_loc, &
27 c_ptr
28 USE kinds, ONLY: dp
29#include "./base/base_uses.f90"
30
31 IMPLICIT NONE
32
33 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'hdf5_wrapper'
34#ifdef __HDF5
35 INTEGER, PARAMETER, PUBLIC :: hdf5_id = hid_t
36#endif
37
38CONTAINS
39
40#ifdef __HDF5
41! **************************************************************************************************
42!> \brief Initialize the HDF5 fortran API
43! **************************************************************************************************
44 SUBROUTINE h5open()
45 INTEGER :: error
46
47 CALL h5open_f(error)
48 IF (error < 0) cpabort('ERROR: failed to initialize HDF5 interface')
49
50 END SUBROUTINE h5open
51
52! **************************************************************************************************
53!> \brief Close the HDF5 fortran API
54! **************************************************************************************************
55 SUBROUTINE h5close()
56 INTEGER :: error
57
58 CALL h5close_f(error)
59 IF (error < 0) cpabort('ERROR: failed to close HDF5 interface')
60
61 END SUBROUTINE h5close
62
63! **************************************************************************************************
64!> \brief Create a HDF5 file
65!> \param filename the name of the hdf5 file
66!> \param file_id the file id of the hdf5 file
67! **************************************************************************************************
68 SUBROUTINE h5fcreate(filename, file_id)
69 CHARACTER(LEN=*), INTENT(IN) :: filename
70 INTEGER(KIND=hid_t), INTENT(OUT) :: file_id
71
72 INTEGER :: error
73
74 CALL h5fcreate_f(filename, h5f_acc_trunc_f, file_id, error)
75 IF (error < 0) cpabort('ERROR: failed to create HDF5 file')
76
77 END SUBROUTINE h5fcreate
78
79! **************************************************************************************************
80!> \brief Open a HDF5 file
81!> \param filename the name of the hdf5 file
82!> \param file_id the file id of the hdf5 file
83! **************************************************************************************************
84 SUBROUTINE h5fopen(filename, file_id)
85 CHARACTER(LEN=*), INTENT(IN) :: filename
86 INTEGER(KIND=hid_t), INTENT(OUT) :: file_id
87
88 INTEGER :: error
89
90 CALL h5fopen_f(trim(filename), h5f_acc_rdonly_f, file_id, error)
91 IF (error < 0) cpabort('ERROR: failed to open HDF5 file')
92
93 END SUBROUTINE h5fopen
94
95! **************************************************************************************************
96!> \brief Close a HDF5 file
97!> \param file_id the file id of the hdf5 file
98! **************************************************************************************************
99 SUBROUTINE h5fclose(file_id)
100 INTEGER(KIND=hid_t), INTENT(IN) :: file_id
101
102 INTEGER :: error
103
104 CALL h5fclose_f(file_id, error)
105 IF (error < 0) cpabort('ERROR: failed to close HDF5 file')
106
107 END SUBROUTINE h5fclose
108
109! **************************************************************************************************
110!> \brief Create a HDF5 group
111!> \param loc_id file or group identifier
112!> \param name name of the group
113!> \param grp_id group identifier
114! **************************************************************************************************
115 SUBROUTINE h5gcreate(loc_id, name, grp_id)
116 INTEGER(KIND=hid_t), INTENT(IN) :: loc_id
117 CHARACTER(LEN=*), INTENT(IN) :: name
118 INTEGER(KIND=hid_t), INTENT(OUT) :: grp_id
119
120 INTEGER :: error
121
122 CALL h5gcreate_f(loc_id, name, grp_id, error)
123 IF (error < 0) cpabort('ERROR: failed to create HDF5 group')
124
125 END SUBROUTINE h5gcreate
126
127! **************************************************************************************************
128!> \brief Open a HDF5 group
129!> \param loc_id file or group identifier
130!> \param name name of the group
131!> \param grp_id group identifier
132! **************************************************************************************************
133 SUBROUTINE h5gopen(loc_id, name, grp_id)
134 INTEGER(KIND=hid_t), INTENT(IN) :: loc_id
135 CHARACTER(LEN=*), INTENT(IN) :: name
136 INTEGER(KIND=hid_t), INTENT(OUT) :: grp_id
137
138 INTEGER :: error
139
140 CALL h5gopen_f(loc_id, name, grp_id, error)
141 IF (error < 0) cpabort('ERROR: failed to open HDF5 group')
142
143 END SUBROUTINE h5gopen
144
145! **************************************************************************************************
146!> \brief Close a HDF5 group
147!> \param grp_id group identifier
148! **************************************************************************************************
149 SUBROUTINE h5gclose(grp_id)
150 INTEGER(KIND=hid_t), INTENT(IN) :: grp_id
151
152 INTEGER :: error
153
154 CALL h5gclose_f(grp_id, error)
155 IF (error < 0) cpabort('ERROR: failed to close HDF5 group')
156
157 END SUBROUTINE h5gclose
158
159! **************************************************************************************************
160!> \brief Write a variable-length string attribute
161!> \param loc_id either file id or group id
162!> \param attr_name the name of the attribute
163!> \param attr_data the attribute data, i.e. the string to write
164! **************************************************************************************************
165 SUBROUTINE h5awrite_varlen_string(loc_id, attr_name, attr_data)
166 INTEGER(KIND=hid_t), INTENT(IN) :: loc_id
167 CHARACTER(LEN=*), INTENT(IN) :: attr_name
168 CHARACTER(LEN=*), INTENT(IN), TARGET :: attr_data
169
170 INTEGER :: error, output_unit
171 INTEGER(KIND=hid_t) :: attr_id, space_id, type_id
172 TYPE(c_ptr) :: buffer
173 TYPE(c_ptr), TARGET :: in_between_ptr
174
175 ! create a scalar dataspace
176 CALL h5screate_f(h5s_scalar_f, space_id, error)
177 IF (error < 0) THEN
178 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
179 ' ERROR: failed to create HDF5 dataspace'
180 RETURN
181 END IF
182
183 ! create a variable-length string type
184 CALL h5tcopy_f(h5t_string, type_id, error)
185 CALL h5tset_cset_f(type_id, h5t_cset_utf8_f, error)
186 CALL h5tset_strpad_f(type_id, h5t_str_nullpad_f, error)
187
188 ! create the attribute
189 CALL h5acreate_f(loc_id, attr_name, type_id, space_id, attr_id, error)
190 IF (error < 0) THEN
191 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
192 ' ERROR: failed to create HDF5 attribute'
193 RETURN
194 END IF
195
196 ! weird in-between pointer needed for variable-length
197 ! string to a scalar dataspace
198 in_between_ptr = c_loc(attr_data)
199 ! the actual pointer to be passed
200 buffer = c_loc(in_between_ptr)
201
202 ! write the string attribute to file
203 CALL h5awrite_f(attr_id, type_id, buffer, error)
204 IF (error < 0) THEN
205 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
206 ' ERROR: failed to write HDF5 attribute'
207 RETURN
208 END IF
209
210 ! close attribute
211 CALL h5aclose_f(attr_id, error)
212 IF (error < 0) THEN
213 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
214 ' ERROR: failed to close HDF5 attribute'
215 RETURN
216 END IF
217
218 ! close dataspace
219 CALL h5sclose_f(space_id, error)
220 IF (error < 0) THEN
221 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
222 ' ERROR: failed to close HDF5 dataspace'
223 RETURN
224 END IF
225
226 ! close datatype
227 CALL h5tclose_f(type_id, error)
228 IF (error < 0) THEN
229 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
230 ' ERROR: failed to close HDF5 datatype'
231 RETURN
232 END IF
233
234 END SUBROUTINE h5awrite_varlen_string
235
236! **************************************************************************************************
237!> \brief Write a fixed-length string attribute
238!> \param loc_id either file id or group id
239!> \param attr_name the name of the attribute
240!> \param attr_data the attribute data, i.e. the string to write
241! **************************************************************************************************
242 SUBROUTINE h5awrite_fixlen_string(loc_id, attr_name, attr_data)
243 INTEGER(KIND=hid_t), INTENT(IN) :: loc_id
244 CHARACTER(LEN=*), INTENT(IN) :: attr_name
245 CHARACTER(LEN=*), INTENT(IN), TARGET :: attr_data
246
247 INTEGER :: error, output_unit
248 INTEGER(KIND=hid_t) :: attr_id, space_id, type_id
249 TYPE(c_ptr) :: buffer
250
251 ! create a scalar dataspace
252 CALL h5screate_f(h5s_scalar_f, space_id, error)
253 IF (error < 0) THEN
254 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
255 ' ERROR: failed to create HDF5 dataspace'
256 RETURN
257 END IF
258
259 ! create a fixed-length string datatype
260 CALL h5tcopy_f(h5t_c_s1, type_id, error)
261 CALL h5tset_cset_f(type_id, h5t_cset_utf8_f, error)
262 CALL h5tset_size_f(type_id, len(attr_data, size_t), error)
263
264 ! create the attribute
265 CALL h5acreate_f(loc_id, attr_name, type_id, space_id, attr_id, error)
266 IF (error < 0) THEN
267 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
268 ' ERROR: failed to create HDF5 attribute'
269 RETURN
270 END IF
271
272 ! the actual pointer to be passed
273 buffer = c_loc(attr_data)
274
275 ! write the string attribute to file
276 CALL h5awrite_f(attr_id, type_id, buffer, error)
277 IF (error < 0) THEN
278 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
279 ' ERROR: failed to write HDF5 attribute'
280 RETURN
281 END IF
282
283 ! close attribute
284 CALL h5aclose_f(attr_id, error)
285 IF (error < 0) THEN
286 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
287 ' ERROR: failed to close HDF5 attribute'
288 RETURN
289 END IF
290
291 ! close dataspace
292 CALL h5sclose_f(space_id, error)
293 IF (error < 0) THEN
294 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
295 ' ERROR: failed to close HDF5 dataspace'
296 RETURN
297 END IF
298
299 ! close datatype
300 CALL h5tclose_f(type_id, error)
301 IF (error < 0) THEN
302 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
303 ' ERROR: failed to close HDF5 datatype'
304 RETURN
305 END IF
306
307 END SUBROUTINE h5awrite_fixlen_string
308
309! **************************************************************************************************
310!> \brief Write a boolean attribute
311!> \param loc_id either file id or group id
312!> \param attr_name the name of the attribute
313!> \param attr_data the attribute data, i.e. the logical to write (.true. or .false.)
314! **************************************************************************************************
315 SUBROUTINE h5awrite_boolean(loc_id, attr_name, attr_data)
316 INTEGER(KIND=hid_t), INTENT(IN) :: loc_id
317 CHARACTER(LEN=*), INTENT(IN) :: attr_name
318 LOGICAL, INTENT(IN) :: attr_data
319
320 INTEGER :: error, output_unit
321 INTEGER(KIND=hid_t) :: attr_id, space_id, type_id
322 INTEGER, TARGET :: attr_data_to_int
323 TYPE(c_ptr) :: buffer
324
325 ! 8-bit integers in enum bool_type
326
327 ! create a scalar dataspace
328 CALL h5screate_f(h5s_scalar_f, space_id, error)
329 IF (error < 0) THEN
330 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
331 ' ERROR: failed to create HDF5 dataspace'
332 RETURN
333 END IF
334
335 ! create the datatype
336 CALL h5tcreate_f(h5t_enum_f, int(1, size_t), type_id, error)
337 CALL h5tenum_insert_f(type_id, "FALSE", 0, error)
338 CALL h5tenum_insert_f(type_id, "TRUE", 1, error)
339
340 IF (attr_data) THEN
341 attr_data_to_int = 1
342 ELSE
343 attr_data_to_int = 0
344 END IF
345 ! the C pointer to the actual data
346 buffer = c_loc(attr_data_to_int)
347
348 ! create the attribute
349 CALL h5acreate_f(loc_id, attr_name, type_id, space_id, attr_id, error)
350 IF (error < 0) THEN
351 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
352 ' ERROR: failed to create HDF5 attribute'
353 RETURN
354 END IF
355
356 ! write the string attribute to file
357 CALL h5awrite_f(attr_id, type_id, buffer, error)
358 IF (error < 0) THEN
359 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
360 ' ERROR: failed to write HDF5 attribute'
361 RETURN
362 END IF
363
364 ! close attribute
365 CALL h5aclose_f(attr_id, error)
366 IF (error < 0) THEN
367 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
368 ' ERROR: failed to close HDF5 attribute'
369 RETURN
370 END IF
371
372 ! close dataspace
373 CALL h5sclose_f(space_id, error)
374 IF (error < 0) THEN
375 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
376 ' ERROR: failed to close HDF5 dataspace'
377 RETURN
378 END IF
379
380 ! close datatype
381 CALL h5tclose_f(type_id, error)
382 IF (error < 0) THEN
383 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
384 ' ERROR: failed to close HDF5 datatype'
385 RETURN
386 END IF
387
388 END SUBROUTINE h5awrite_boolean
389
390! **************************************************************************************************
391!> \brief Write a (scalar) integer attribute
392!> \param loc_id either file id or group id
393!> \param attr_name the name of the attribute
394!> \param attr_data the attribute data, i.e. the integer to write
395! **************************************************************************************************
396 SUBROUTINE h5awrite_integer_scalar(loc_id, attr_name, attr_data)
397 INTEGER(KIND=hid_t), INTENT(IN) :: loc_id
398 CHARACTER(LEN=*), INTENT(IN) :: attr_name
399 INTEGER, INTENT(IN), TARGET :: attr_data
400
401 INTEGER :: error, output_unit
402 INTEGER(KIND=hid_t) :: attr_id, space_id, type_id
403 TYPE(c_ptr) :: buffer
404
405 ! create a scalar dataspace
406 CALL h5screate_f(h5s_scalar_f, space_id, error)
407 IF (error < 0) THEN
408 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
409 ' ERROR: failed to create HDF5 dataspace'
410 RETURN
411 END IF
412
413 ! the C pointer to the actual data
414 buffer = c_loc(attr_data)
415
416 ! set the type of data
417 type_id = h5t_native_integer
418
419 ! create the attribute
420 CALL h5acreate_f(loc_id, attr_name, type_id, space_id, attr_id, error)
421 IF (error < 0) THEN
422 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
423 ' ERROR: failed to create HDF5 attribute'
424 RETURN
425 END IF
426
427 ! write the string attribute to file
428 CALL h5awrite_f(attr_id, type_id, buffer, error)
429 IF (error < 0) THEN
430 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
431 ' ERROR: failed to write HDF5 attribute'
432 RETURN
433 END IF
434
435 ! close attribute
436 CALL h5aclose_f(attr_id, error)
437 IF (error < 0) THEN
438 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
439 ' ERROR: failed to close HDF5 attribute'
440 RETURN
441 END IF
442
443 ! close dataspace
444 CALL h5sclose_f(space_id, error)
445 IF (error < 0) THEN
446 WRITE (unit=output_unit, fmt="(/,T5,A,/)") &
447 ' ERROR: failed to close HDF5 dataspace'
448 RETURN
449 END IF
450
451 END SUBROUTINE h5awrite_integer_scalar
452
453! **************************************************************************************************
454!> \brief Write a (scalar) double precision attribute
455!> \param loc_id either file id or group id
456!> \param attr_name the name of the attribute
457!> \param attr_data the attribute data, i.e. the double to write
458! **************************************************************************************************
459 SUBROUTINE h5awrite_double_scalar(loc_id, attr_name, attr_data)
460 INTEGER(KIND=hid_t), INTENT(IN) :: loc_id
461 CHARACTER(LEN=*), INTENT(IN) :: attr_name
462 REAL(KIND=dp), INTENT(IN), TARGET :: attr_data
463
464 INTEGER :: error
465 INTEGER(KIND=hid_t) :: attr_id, space_id, type_id
466 TYPE(c_ptr) :: buffer
467
468 ! create a scalar dataspace
469 CALL h5screate_f(h5s_scalar_f, space_id, error)
470 IF (error < 0) cpabort('ERROR: failed to create HDF5 dataspace')
471
472 ! the C pointer to the actual data
473 buffer = c_loc(attr_data)
474
475 ! set the type of data
476 type_id = h5t_native_double
477
478 ! create the attribute
479 CALL h5acreate_f(loc_id, attr_name, type_id, space_id, attr_id, error)
480 IF (error < 0) cpabort('ERROR: failed to create HDF5 attribute')
481
482 ! write the string attribute to file
483 CALL h5awrite_f(attr_id, type_id, buffer, error)
484 IF (error < 0) cpabort('ERROR: failed to write HDF5 attribute')
485
486 ! close attribute
487 CALL h5aclose_f(attr_id, error)
488 IF (error < 0) cpabort('ERROR: failed to close HDF5 attribute')
489
490 ! close dataspace
491 CALL h5sclose_f(space_id, error)
492 IF (error < 0) cpabort('ERROR: failed to close HDF5 dataspace')
493
494 END SUBROUTINE h5awrite_double_scalar
495
496! **************************************************************************************************
497!> \brief Write an array of fixed-length string attribute
498!> \param loc_id either file id or group id
499!> \param attr_name the name of the attribute
500!> \param attr_data the attribute data, i.e. the array of strings
501! **************************************************************************************************
502 SUBROUTINE h5awrite_string_simple(loc_id, attr_name, attr_data)
503 INTEGER(KIND=hid_t), INTENT(IN) :: loc_id
504 CHARACTER(LEN=*), INTENT(IN) :: attr_name
505 CHARACTER(LEN=*), DIMENSION(:), INTENT(IN), TARGET :: attr_data
506
507 INTEGER :: error
508 INTEGER(KIND=hid_t) :: attr_id, space_id, type_id
509 INTEGER(KIND=hsize_t), DIMENSION(2) :: dims
510 TYPE(c_ptr) :: buffer
511
512 dims(1) = len(attr_data(1), kind=hsize_t) ! length of a string entry
513 dims(2) = SIZE(attr_data, kind=hsize_t) ! length of array of strings
514
515 ! create a fixed-length string datatype
516 CALL h5tcopy_f(h5t_c_s1, type_id, error)
517 CALL h5tset_cset_f(type_id, h5t_cset_utf8_f, error)
518 CALL h5tset_size_f(type_id, int(dims(1), size_t), error)
519
520 ! create a simple dataspace
521 CALL h5screate_simple_f(1, dims(2:2), space_id, error)
522 IF (error < 0) cpabort('ERROR: failed to create HDF5 dataspace')
523
524 ! create the atrtibute
525 CALL h5acreate_f(loc_id, attr_name, type_id, space_id, attr_id, error)
526 IF (error < 0) cpabort('ERROR: failed to create HDF5 attribute')
527
528 ! the actual pointer to be passed
529 buffer = c_loc(attr_data(1))
530
531 ! write the string array attribute to file
532 CALL h5awrite_f(attr_id, type_id, buffer, error)
533 IF (error < 0) cpabort('ERROR: failed to write HDF5 attribute')
534
535 ! close attribute
536 CALL h5aclose_f(attr_id, error)
537 IF (error < 0) cpabort('ERROR: failed to close HDF5 attribute')
538
539 ! close dataspace
540 CALL h5sclose_f(space_id, error)
541 IF (error < 0) cpabort('ERROR: failed to close HDF5 dataspace')
542
543 ! close datatype
544 CALL h5tclose_f(type_id, error)
545 IF (error < 0) cpabort('ERROR: failed to close HDF5 datatype')
546
547 END SUBROUTINE h5awrite_string_simple
548
549! **************************************************************************************************
550!> \brief Write an array of doubles attribute
551!> \param loc_id either file id or group id
552!> \param attr_name the name of the attribute
553!> \param attr_data the attribute data, i.e. the array of doubles
554! **************************************************************************************************
555 SUBROUTINE h5awrite_double_simple(loc_id, attr_name, attr_data)
556 INTEGER(KIND=hid_t), INTENT(IN) :: loc_id
557 CHARACTER(LEN=*), INTENT(IN) :: attr_name
558 REAL(KIND=dp), DIMENSION(:), INTENT(IN), TARGET :: attr_data
559
560 INTEGER :: error
561 INTEGER(KIND=hid_t) :: attr_id, space_id, type_id
562 INTEGER(KIND=hsize_t), DIMENSION(1) :: dims
563 TYPE(c_ptr) :: buffer
564
565 dims(1) = SIZE(attr_data, kind=hsize_t) ! length of array of strings
566
567 ! set the type of data
568 type_id = h5t_native_double
569
570 ! create a simple dataspace
571 CALL h5screate_simple_f(1, dims, space_id, error)
572 IF (error < 0) cpabort('ERROR: failed to create HDF5 dataspace')
573
574 ! create the atrtibute
575 CALL h5acreate_f(loc_id, attr_name, type_id, space_id, attr_id, error)
576 IF (error < 0) cpabort('ERROR: failed to create HDF5 attribute')
577
578 ! the actual pointer to be passed
579 buffer = c_loc(attr_data(1))
580
581 ! write the string array attribute to file
582 CALL h5awrite_f(attr_id, type_id, buffer, error)
583 IF (error < 0) cpabort('ERROR: failed to write HDF5 attribute')
584
585 ! close attribute
586 CALL h5aclose_f(attr_id, error)
587 IF (error < 0) cpabort('ERROR: failed to close HDF5 attribute')
588
589 ! close dataspace
590 CALL h5sclose_f(space_id, error)
591 IF (error < 0) cpabort('ERROR: failed to close HDF5 dataspace')
592
593 END SUBROUTINE h5awrite_double_simple
594
595! **************************************************************************************************
596!> \brief Write an array of integers attribute
597!> \param loc_id either file id or group id
598!> \param attr_name the name of the attribute
599!> \param attr_data the attribute data, i.e. the array of integers
600! **************************************************************************************************
601 SUBROUTINE h5awrite_integer_simple(loc_id, attr_name, attr_data)
602 INTEGER(KIND=hid_t), INTENT(IN) :: loc_id
603 CHARACTER(LEN=*), INTENT(IN) :: attr_name
604 INTEGER, DIMENSION(:), INTENT(IN), TARGET :: attr_data
605
606 INTEGER :: error
607 INTEGER(KIND=hid_t) :: attr_id, space_id, type_id
608 INTEGER(KIND=hsize_t), DIMENSION(1) :: dims
609 TYPE(c_ptr) :: buffer
610
611 dims(1) = SIZE(attr_data, kind=hsize_t) ! length of array of strings
612
613 ! set the type of data
614 type_id = h5t_native_integer
615
616 ! create a simple dataspace
617 CALL h5screate_simple_f(1, dims, space_id, error)
618 IF (error < 0) cpabort('ERROR: failed to create HDF5 dataspace')
619
620 ! create the atrtibute
621 CALL h5acreate_f(loc_id, attr_name, type_id, space_id, attr_id, error)
622 IF (error < 0) cpabort('ERROR: failed to create HDF5 attribute')
623
624 ! the actual pointer to be passed
625 buffer = c_loc(attr_data(1))
626
627 ! write the string array attribute to file
628 CALL h5awrite_f(attr_id, type_id, buffer, error)
629 IF (error < 0) cpabort('ERROR: failed to write HDF5 attribute')
630
631 ! close attribute
632 CALL h5aclose_f(attr_id, error)
633 IF (error < 0) cpabort('ERROR: failed to close HDF5 attribute')
634
635 ! close dataspace
636 CALL h5sclose_f(space_id, error)
637 IF (error < 0) cpabort('ERROR: failed to close HDF5 dataspace')
638
639 END SUBROUTINE h5awrite_integer_simple
640
641! **************************************************************************************************
642!> \brief Write a dataset containing an array of doubles
643!> \param loc_id either file id or group id
644!> \param dset_name the name of the dataset
645!> \param dset_data the dataset data, i.e. the array of doubles
646! **************************************************************************************************
647 SUBROUTINE h5dwrite_double_simple(loc_id, dset_name, dset_data)
648 INTEGER(KIND=hid_t), INTENT(IN) :: loc_id
649 CHARACTER(LEN=*), INTENT(IN) :: dset_name
650 REAL(KIND=dp), DIMENSION(:), INTENT(IN), TARGET :: dset_data
651
652 INTEGER :: error
653 INTEGER(KIND=hid_t) :: dset_id, space_id, type_id
654 INTEGER(KIND=hsize_t), DIMENSION(1) :: dims
655 TYPE(c_ptr) :: buffer
656
657 dims(1) = SIZE(dset_data, kind=hsize_t) ! length of array
658
659 ! set the type of data
660 type_id = h5t_native_double
661
662 ! create a simple dataspace
663 CALL h5screate_simple_f(1, dims, space_id, error)
664 IF (error < 0) cpabort('ERROR: failed to create HDF5 dataspace')
665
666 ! create the dataset
667 CALL h5dcreate_f(loc_id, dset_name, type_id, space_id, dset_id, error)
668 IF (error < 0) cpabort('ERROR: failed to create HDF5 dataset')
669
670 ! the actual pointer to be passed
671 buffer = c_loc(dset_data(1))
672
673 ! write the string array attribute to file
674 CALL h5dwrite_f(dset_id, type_id, buffer, error)
675 IF (error < 0) cpabort('ERROR: failed to write HDF5 dataset')
676
677 ! close dataset
678 CALL h5dclose_f(dset_id, error)
679 IF (error < 0) cpabort('ERROR: failed to close HDF5 dataset')
680
681 ! close dataspace
682 CALL h5sclose_f(space_id, error)
683 IF (error < 0) cpabort('ERROR: failed to close HDF5 dataspace')
684
685 END SUBROUTINE h5dwrite_double_simple
686
687! **************************************************************************************************
688!> \brief Read a dataset containing an array of doubles
689!> \param loc_id either file id or group id
690!> \param dset_name the name of the dataset
691!> \param dset_data where the read dataset data will be written
692! **************************************************************************************************
693 SUBROUTINE h5dread_double_simple(loc_id, dset_name, dset_data)
694 INTEGER(KIND=hid_t), INTENT(IN) :: loc_id
695 CHARACTER(LEN=*), INTENT(IN) :: dset_name
696 REAL(KIND=dp), DIMENSION(:), INTENT(OUT) :: dset_data
697
698 INTEGER :: error
699 INTEGER(KIND=hid_t) :: dset_id, npoints, space_id, type_id
700 INTEGER(KIND=hsize_t), DIMENSION(1) :: dims
701
702 dims(1) = SIZE(dset_data, kind=hsize_t) ! length of array
703
704 ! set the type of data
705 type_id = h5t_native_double
706
707 ! open the dataset
708 CALL h5dopen_f(loc_id, dset_name, dset_id, error)
709 IF (error < 0) cpabort('ERROR: failed to open HDF5 dataset')
710
711 ! get information on the dataspace
712 CALL h5dget_space_f(dset_id, space_id, error)
713 IF (error < 0) cpabort('ERROR: failed to fetch HDF5 dataspace info')
714
715 ! get dataspace dims
716 CALL h5sget_simple_extent_npoints_f(space_id, npoints, error)
717 IF (error < 0) cpabort('ERROR: failed to fetch HDF5 dataspace dimension')
718
719 ! read the data
720 CALL h5dread_f(dset_id, type_id, dset_data, dims, error)
721 IF (error < 0) cpabort('ERROR: failed to read HDF5 dataset')
722
723 ! close dataset
724 CALL h5dclose_f(dset_id, error)
725 IF (error < 0) cpabort('ERROR: failed to close HDF5 dataset')
726
727 ! close dataspace
728 CALL h5sclose_f(space_id, error)
729 IF (error < 0) cpabort('ERROR: failed to close HDF5 dataspace')
730
731 END SUBROUTINE h5dread_double_simple
732
733! **************************************************************************************************
734!> \brief Read an attribute containing a scalar double
735!> \param loc_id either file id or group id
736!> \param attr_name ...
737!> \param attr_data ...
738! **************************************************************************************************
739 SUBROUTINE h5aread_double_scalar(loc_id, attr_name, attr_data)
740 INTEGER(KIND=hid_t), INTENT(IN) :: loc_id
741 CHARACTER(LEN=*), INTENT(IN) :: attr_name
742 REAL(KIND=dp), INTENT(OUT), TARGET :: attr_data
743
744 INTEGER :: error
745 INTEGER(KIND=hid_t) :: attr_id, type_id
746 TYPE(c_ptr) :: buffer
747
748 ! set the type of data
749 type_id = h5t_native_double
750
751 ! open the attribute
752 CALL h5aopen_f(loc_id, attr_name, attr_id, error)
753 IF (error < 0) cpabort('ERROR: failed to open HDF5 attribute')
754
755 buffer = c_loc(attr_data)
756 ! read the data
757 CALL h5aread_f(attr_id, type_id, buffer, error)
758 IF (error < 0) cpabort('ERROR: failed to read HDF5 attribute')
759
760 ! close the attribute
761 CALL h5aclose_f(attr_id, error)
762 IF (error < 0) cpabort('ERROR: failed to close HDF5 attribute')
763
764 END SUBROUTINE h5aread_double_scalar
765
766#endif
767
768END MODULE hdf5_wrapper
hdf5_wrapper
A wrapper around the HDF5 Fortran API.
Definition hdf5_wrapper.F:14
kinds
Defines the basic variable types.
Definition kinds.F:23
kinds::dp
integer, parameter, public dp
Definition kinds.F:34