fileio_binary.f90
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1!#############################################################################
2!# #
3!# fosite - 3D hydrodynamical simulation program #
4!# module: fileio_binary.f90 #
5!# #
6!# Copyright (C) 2015-2024 #
7!# Manuel Jung <mjung@astrophysik.uni-kiel.de> #
8!# Jannes Klee <jklee@astrophysik.uni-kiel.de> #
9!# Tobias Illenseer <tillense@astrophysik.uni-kiel.de> #
10!# #
11!# This program is free software; you can redistribute it and/or modify #
12!# it under the terms of the GNU General Public License as published by #
13!# the Free Software Foundation; either version 2 of the License, or (at #
14!# your option) any later version. #
15!# #
16!# This program is distributed in the hope that it will be useful, but #
17!# WITHOUT ANY WARRANTY; without even the implied warranty of #
18!# MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, GOOD TITLE or #
19!# NON INFRINGEMENT. See the GNU General Public License for more #
20!# details. #
21!# #
22!# You should have received a copy of the GNU General Public License #
23!# along with this program; if not, write to the Free Software #
24!# Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. #
25!# #
26!#############################################################################
27!----------------------------------------------------------------------------!
59!----------------------------------------------------------------------------!
60#define HAVE_VTK
61MODULE fileio_binary_mod
62 USE fileio_base_mod
63 USE geometry_base_mod
64 USE mesh_base_mod
65 USE physics_base_mod
66 USE timedisc_base_mod
67 USE fluxes_base_mod
68 USE sources_generic_mod
69 USE common_dict
70#ifdef PARALLEL
71#ifdef HAVE_MPI_MOD
72 USE mpi
73#endif
74#endif
75 IMPLICIT NONE
76#ifdef PARALLEL
77#ifdef HAVE_MPIF_H
78 include 'mpif.h'
79#endif
80#endif
81 !--------------------------------------------------------------------------!
82 PRIVATE
83 CHARACTER, PARAMETER :: lf = achar(10)
84 !--------------------------------------------------------------------------!
86 TYPE, EXTENDS(fileio_base) :: fileio_binary
88 CHARACTER(LEN=12) :: realfmt
89 CHARACTER(LEN=14) :: endianness
90 INTEGER :: realsize
91 INTEGER :: intsize
92#ifdef PARALLEL
93 LOGICAL :: first
94 INTEGER :: cbufsize, & !< size of corner output
95 clsizes(3)
96 INTEGER(KIND=MPI_OFFSET_KIND) :: offset
97#else
98 INTEGER :: offset
99#endif
100 CONTAINS
102 PROCEDURE :: initfileio_deferred => initfileio_binary
103 PROCEDURE :: writeheader
104 !PROCEDURE :: ReadHeader
105 !PROCEDURE :: WriteTimestamp
106 !PROCEDURE :: ReadTimestamp
107 PROCEDURE :: writedataset_deferred => writedataset_binary
108 !PROCEDURE :: ReadDataset
109 final :: finalize
110 !PRIVATE
111 PROCEDURE :: hasmeshdims
112 PROCEDURE :: hascornerdims
113 PROCEDURE :: setoutputdims
114 PROCEDURE :: writenode
115 PROCEDURE :: writekey
116 PROCEDURE :: writedataattributes
117 END TYPE
118 !--------------------------------------------------------------------------!
119 PUBLIC :: &
120 ! types
121 fileio_binary
122 !--------------------------------------------------------------------------!
123
124CONTAINS
129 SUBROUTINE initfileio_binary(this,Mesh,Physics,Timedisc,Sources,config,IO)
130 IMPLICIT NONE
131 !------------------------------------------------------------------------!
132 CLASS(fileio_binary), INTENT(INOUT) :: this
133 CLASS(mesh_base), INTENT(IN) :: Mesh
134 CLASS(physics_base), INTENT(IN) :: Physics
135 CLASS(timedisc_base), INTENT(IN) :: Timedisc
136 CLASS(sources_list), ALLOCATABLE, INTENT(IN) :: Sources
137 TYPE(dict_typ), INTENT(IN), POINTER :: config,IO
138 !------------------------------------------------------------------------!
139#ifdef PARALLEL
140 INTEGER, DIMENSION(3) :: gsizes,lsizes,indices
141#endif
142 CHARACTER(LEN=1),DIMENSION(:),POINTER :: mold
143 REAL :: r
144 INTEGER :: i,err
145 !------------------------------------------------------------------------!
146 IF (.NOT.this%Initialized()) &
147 CALL this%InitFileio(mesh,physics,timedisc,sources,config,io,"binary","bin",textfile=.false.)
148
149 ! We mark the endianess similar to the TIFF format
150 ! See: http://en.wikipedia.org/wiki/Endianness#Endianness_in_files_and_byte_swap
151 ! II == Intel Format == Little Endian
152 ! MM == Motorola Format == Big Endian
153 CALL this%GetEndianness(this%endianness, 'II','MM')
154 this%realsize = SIZE(transfer(r, mold))
155 this%intsize = SIZE(transfer(i, mold))
156
157 SELECT CASE(this%realsize)
158 CASE(4,8)
159 WRITE(this%realfmt,'(A,I1,A)') '"',this%realsize,'"'
160 CASE DEFAULT
161 CALL this%Error("fileio_binary::InitFileIO_binary","Only single and double precision are allowed")
162 END SELECT
163
164 ! set local array dimensions (frequently used)
165 this%INUM = mesh%IMAX-mesh%IMIN+1
166 this%JNUM = mesh%JMAX-mesh%JMIN+1
167 this%KNUM = mesh%KMAX-mesh%KMIN+1
168
169#ifdef PARALLEL
170 ! create the data type for the distributed array of
171 ! coordinates and simulation data
172 gsizes(1:3) = (/ mesh%INUM, mesh%JNUM, mesh%KNUM /)
173 lsizes(1:3) = (/ this%INUM, this%JNUM, this%KNUM /)
174 indices(1:3) = (/ mesh%IMIN-1, mesh%JMIN-1, mesh%KMIN-1 /)
175 this%bufsize = product(lsizes)
176 this%err = 0
177 SELECT TYPE(df=>this%datafile)
178 CLASS IS(filehandle_mpi)
179 CALL mpi_type_create_subarray(3, gsizes, lsizes, indices, mpi_order_fortran,&
180 default_mpi_real,df%filetype,this%err)
181 IF (this%err.EQ.0) CALL mpi_type_commit(df%filetype,this%err)
182 END SELECT
183
184 ! create the data type for the distributed array of
185 ! mesh corner positions
186 this%clsizes(:) = lsizes(:)
187 WHERE ((/mesh%INUM,mesh%JNUM,mesh%KNUM/).GT.1)
188 ! add +1 to the global size if dimension has real extend,i.e. not one cell
189 gsizes(:) = gsizes(:)+1
190 WHERE ((/mesh%INUM,mesh%JNUM,mesh%KNUM/).EQ.(/mesh%IMAX,mesh%JMAX,mesh%KMAX/))
191 ! add +1 to the local size if process contains the outermost domain
192 this%clsizes(:) = lsizes(:)+1
193 END WHERE
194 END WHERE
195 this%cbufsize = product(this%clsizes)
196 SELECT TYPE(df=>this%datafile)
197 CLASS IS(filehandle_mpi)
198 IF (this%err.EQ.0) CALL mpi_type_create_subarray(3, gsizes, this%clsizes, indices, mpi_order_fortran,&
199 default_mpi_real,df%cfiletype,this%err)
200 IF (this%err.EQ.0) CALL mpi_type_commit(df%cfiletype,this%err)
201 END SELECT
202
203 IF (this%err.NE.0) &
204 CALL this%Error("fileio_binary::InitFileIO_binary","creating MPI data types failed")
205 this%first = .true.
206#endif
207 END SUBROUTINE initfileio_binary
208
215 SUBROUTINE writeheader(this,Mesh,Physics,Header,IO)
216 IMPLICIT NONE
217 !------------------------------------------------------------------------!
218 CLASS(fileio_binary), INTENT(INOUT) :: this
219 CLASS(mesh_base), INTENT(IN) :: Mesh
220 CLASS(physics_base), INTENT(IN) :: Physics
221 TYPE(dict_typ), POINTER :: Header,IO
222 !------------------------------------------------------------------------!
223 CHARACTER(LEN=6) :: magic = "FOSITE"
224 CHARACTER(LEN=1) :: version = achar(0)
225 CHARACTER(LEN=4) :: sizes
226 CHARACTER(LEN=13) :: sheader
227 !------------------------------------------------------------------------!
228 WRITE(sizes, '(I2,I2)') this%realsize, this%intsize
229 sheader = magic // this%endianness(1:2) // version // sizes
230 this%offset = 0
231 SELECT TYPE(df=>this%datafile)
232#ifndef PARALLEL
233 CLASS IS(filehandle_fortran)
234 WRITE (unit=df%GetUnitNumber(),iostat=this%err) sheader
235#else
236 CLASS IS(filehandle_mpi)
237 CALL mpi_file_set_view(df%GetUnitNumber(),this%offset,mpi_byte,&
238 mpi_byte, 'native', mpi_info_null, this%err)
239 IF (this%GetRank().EQ.0) &
240 CALL mpi_file_write(df%GetUnitNumber(),sheader,len(sheader),mpi_byte, &
241 df%status,this%err)
242#endif
243 CLASS DEFAULT
244 CALL this%Error("fileio_binary::WriteHeader","unknown file handle")
245 END SELECT
246 this%offset = this%offset + len(sheader)
247 END SUBROUTINE writeheader
248
249! !> \public Reads the header of a file (not yet implemented)
250! !!
251! SUBROUTINE ReadHeader_binary(this,success)
252! IMPLICIT NONE
253! !------------------------------------------------------------------------!
254! TYPE(FileIO_TYP) :: this !< \param [in,out] this fileio type
255! LOGICAL :: success !< \param [out] success
256! !------------------------------------------------------------------------!
257! INTENT(OUT) :: success
258! INTENT(INOUT) :: this
259! !------------------------------------------------------------------------!
260! success = .FALSE.
261! END SUBROUTINE ReadHeader_binary
262!
263! !> \public Writes the timestep (not yet implemented)
264! !!
265! SUBROUTINE WriteTimestamp_binary(this,time)
266! IMPLICIT NONE
267! !------------------------------------------------------------------------!
268! TYPE(FileIO_TYP) :: this !< \param [in,out] this fileio type
269! REAL :: time !< \param [in] time
270! !------------------------------------------------------------------------!
271! INTENT(IN) :: time
272! INTENT(INOUT) :: this
273! !------------------------------------------------------------------------!
274! END SUBROUTINE WriteTimestamp_binary
275!
276! !> \public Writes the timestep (not yet implemented)
277! !!
278! SUBROUTINE ReadTimestamp_binary(this,time)
279! IMPLICIT NONE
280! !------------------------------------------------------------------------!
281! TYPE(FileIO_TYP) :: this !< \param [in,out] this fileio type
282! REAL :: time !< \param [out] time
283! !------------------------------------------------------------------------!
284! INTENT(OUT) :: time
285! INTENT(INOUT) :: this
286! !------------------------------------------------------------------------!
287! END SUBROUTINE ReadTimestamp_binary
288
289
298 SUBROUTINE writekey(this,key,type,bytes,dims)
299 IMPLICIT NONE
300 !------------------------------------------------------------------------!
301 CLASS(fileio_binary), INTENT(INOUT) :: this
302 CHARACTER(LEN=*) :: key
303 INTEGER :: type,bytes
304 INTEGER, DIMENSION(5), OPTIONAL :: dims
305 INTEGER :: bufsize
306 CHARACTER(LEN=1), DIMENSION(:), ALLOCATABLE :: buf
307 !------------------------------------------------------------------------!
308 INTEGER :: keylen,l,b,o
309 !------------------------------------------------------------------------!
310 INTENT(IN) :: key,type,bytes
311 !------------------------------------------------------------------------!
312 keylen = len_trim(key)
313 IF(PRESENT(dims)) THEN
314 l = 3
315 IF(dims(4).GT.1) l = 4
316 IF(dims(5).GT.1) l = 5
317 ELSE
318 l = 0
319 END IF
320 b = bytes + l * this%intsize
321 bufsize = (3+l) * this%intsize + keylen
322 ALLOCATE(buf(bufsize))
323 o = 1
324 CALL append(buf,o,transfer(keylen,buf))
325 CALL append(buf,o,transfer(trim(key),buf))
326 CALL append(buf,o,transfer(type,buf))
327 CALL append(buf,o,transfer(b,buf))
328 IF(l.GT.0) THEN
329 CALL append(buf,o,transfer(dims(1:l),buf))
330 END IF
331
332 SELECT TYPE(df=>this%datafile)
333#ifndef PARALLEL
334 CLASS IS(filehandle_fortran)
335 WRITE (unit=df%GetUnitNumber(),iostat=this%err) buf
336#else
337 CLASS IS(filehandle_mpi)
338 CALL mpi_file_set_view(df%GetUnitNumber(),this%offset,mpi_byte,&
339 mpi_byte, 'native', mpi_info_null, this%err)
340 IF (this%GetRank().EQ.0) &
341 CALL mpi_file_write(df%GetUnitNumber(),buf,bufsize,mpi_byte, &
342 df%status,this%err)
343#endif
344 CLASS DEFAULT
345 CALL this%Error("fileio_binary::WriteKey","unknown file handle")
346 END SELECT
347
348 DEALLOCATE(buf)
349 this%offset = this%offset + bufsize
350
351 CONTAINS
352 SUBROUTINE append(buffer,i,d)
353 IMPLICIT NONE
354 !--------------------------------------------------------------------!
355 CHARACTER(LEN=1), DIMENSION(:) :: buffer,d
356 INTEGER :: i,s
357 !--------------------------------------------------------------------!
358 s = SIZE(d)
359 buffer(i:i+s-1) = d
360 o = o + s
361 END SUBROUTINE
362 END SUBROUTINE writekey
363
364
367 RECURSIVE SUBROUTINE writedataattributes(this,Mesh,config,path)
368 IMPLICIT NONE
369 !------------------------------------------------------------------------!
370 CLASS(fileio_binary), INTENT(INOUT) :: this
371 CLASS(mesh_base), INTENT(IN) :: mesh
372 TYPE(dict_typ), POINTER :: config
373 CHARACTER(LEN=*), OPTIONAL :: path
374 !------------------------------------------------------------------------!
375 CHARACTER(LEN=MAX_CHAR_LEN) :: str, key
376 TYPE(dict_typ), POINTER :: node
377 !------------------------------------------------------------------------!
378 INTENT(IN) :: path
379 !------------------------------------------------------------------------!
380 IF(PRESENT(path)) THEN
381 str = path
382 ELSE
383 str = ""
384 ENDIF
385 node => config
386 DO WHILE(ASSOCIATED(node))
387 key = trim(str)//"/"//trim(getkey(node))
388
389 CALL this%WriteNode(mesh,key,node)
390
391 IF(haschild(node)) THEN
392 CALL this%WriteDataAttributes(mesh, getchild(node), key)
393 END IF
394 node=>getnext(node)
395 END DO
396 END SUBROUTINE writedataattributes
397
398 SUBROUTINE writenode(this,Mesh,key,node)
399 IMPLICIT NONE
400 !------------------------------------------------------------------------!
401 CLASS(fileio_binary), INTENT(INOUT) :: this
402 CLASS(mesh_base), INTENT(IN) :: Mesh
403 CHARACTER(LEN=MAX_CHAR_LEN) :: key
404 TYPE(dict_typ), POINTER :: node
405 !------------------------------------------------------------------------!
406 TYPE(real_t) :: ptr0
407 TYPE(int_t) :: ptrint
408 REAL, DIMENSION(:,:), POINTER, CONTIGUOUS :: ptr2
409 REAL, DIMENSION(:,:,:), POINTER :: ptr3
410 REAL, DIMENSION(:,:,:,:), POINTER :: ptr4
411 REAL, DIMENSION(:,:,:,:,:), POINTER :: ptr5
412 INTEGER, DIMENSION(5) :: dims
413 INTEGER :: bytes,k,l
414 CHARACTER(LEN=1), DIMENSION(:), POINTER :: val
415#ifdef PARALLEL
416 INTEGER(KIND=MPI_OFFSET_KIND) :: omax,omin
417#endif
418 !------------------------------------------------------------------------!
419 INTENT(IN) :: key
420 !------------------------------------------------------------------------!
421 dims(:) = 1
422 NULLIFY(ptr2,ptr3,ptr4,ptr5)
423
424 SELECT CASE(getdatatype(node))
425 CASE(dict_real_twod)
426 CALL getattr(node,key,ptr2)
427 dims(1:2) = shape(ptr2)
428 CASE(dict_real_threed)
429 CALL getattr(node,key,ptr3)
430 dims(1:3) = shape(ptr3)
431 CASE(dict_real_fourd)
432 CALL getattr(node,key,ptr4)
433 dims(1:4) = shape(ptr4)
434 CASE(dict_real_fived)
435 CALL getattr(node,key,ptr5)
436 dims(1:5) = shape(ptr5)
437 END SELECT
438
439 IF(product(dims).GT.1) THEN
440 CALL this%SetOutputDims(mesh,dims)
441 bytes = product(dims(1:3)) * this%realsize
442 CALL this%WriteKey(key,getdatatype(node),&
443 product(dims)*this%realsize,dims)
444 DO l=1,dims(5)
445 DO k=1,dims(4)
446 IF(ASSOCIATED(ptr4)) THEN
447 ptr3 => ptr4(:,:,:,k)
448 ELSE IF(ASSOCIATED(ptr5)) THEN
449 ptr3 => ptr5(:,:,:,k,l)
450 ELSE IF(ASSOCIATED(ptr2)) THEN
451 ptr3(1:dims(1),1:dims(2),1:1) => ptr2
452 END IF
453 SELECT TYPE(df=>this%datafile)
454#ifndef PARALLEL
455 CLASS IS(filehandle_fortran)
456 WRITE (unit=df%GetUnitNumber(),iostat=this%err) ptr3
457#else
458 CLASS IS(filehandle_mpi)
459 IF(this%HasMeshDims(mesh,shape(ptr3))) THEN
460 CALL mpi_file_set_view(df%GetUnitNumber(),this%offset,default_mpi_real,&
461 df%filetype, 'native', mpi_info_null, this%err)
462 CALL mpi_file_write_all(df%GetUnitNumber(),ptr3,this%bufsize,&
463 default_mpi_real,df%status,this%err)
464
465 ELSE IF(this%HasCornerDims(mesh,shape(ptr3))) THEN
466 CALL mpi_file_set_view(df%GetUnitNumber(),this%offset,default_mpi_real,&
467 df%cfiletype, 'native', mpi_info_null, this%err)
468 CALL mpi_file_write_all(df%GetUnitNumber(),ptr3(1:this%clsizes(1),1:this%clsizes(2),1:this%clsizes(3)),&
469 this%cbufsize,default_mpi_real,df%status,this%err)
470 ELSE
471 CALL mpi_file_set_view(df%GetUnitNumber(),this%offset,mpi_byte,&
472 mpi_byte, 'native', mpi_info_null, this%err)
473 IF(this%GetRank().EQ.0) THEN
474 CALL mpi_file_write(df%GetUnitNumber(),ptr3,bytes,mpi_byte, &
475 df%status,this%err)
476 END IF
477 END IF
478#endif
479 CLASS DEFAULT
480 CALL this%Error("fileio_binary::WriteNode","unknown file handle")
481 END SELECT
482 this%offset = this%offset + bytes
483 END DO
484 END DO
485 ELSE
486 SELECT CASE(getdatatype(node))
487 CASE(dict_real_p)
488 CALL getattr(node,key,ptr0)
489 bytes = this%realsize
490 CALL this%WriteKey(key,dict_real,bytes)
491 SELECT TYPE(df=>this%datafile)
492#ifndef PARALLEL
493 CLASS IS(filehandle_fortran)
494 WRITE (unit=df%GetUnitNumber(),iostat=this%err) ptr0%p
495#else
496 CLASS IS(filehandle_mpi)
497 CALL mpi_file_set_view(df%GetUnitNumber(),this%offset,mpi_byte,&
498 mpi_byte, 'native', mpi_info_null, this%err)
499 IF(this%GetRank().EQ.0) &
500 CALL mpi_file_write(df%GetUnitNumber(),ptr0%p,bytes,mpi_byte, &
501 df%status,this%err)
502#endif
503 CLASS DEFAULT
504 CALL this%Error("fileio_binary::WriteNode","unknown file handle")
505 END SELECT
506 CASE(dict_int_p)
507 CALL getattr(node,key,ptrint)
508 bytes = this%intsize
509 CALL this%WriteKey(key,dict_int,bytes)
510 SELECT TYPE(df=>this%datafile)
511#ifndef PARALLEL
512 CLASS IS(filehandle_fortran)
513 WRITE (unit=df%GetUnitNumber(),iostat=this%err) ptrint%p
514#else
515 CLASS IS(filehandle_mpi)
516 CALL mpi_file_set_view(df%GetUnitNumber(),this%offset,mpi_byte,&
517 mpi_byte, 'native', mpi_info_null, this%err)
518 IF(this%GetRank().EQ.0) &
519 CALL mpi_file_write(df%GetUnitNumber(),ptrint%p,bytes,mpi_byte, &
520 df%status,this%err)
521#endif
522 CLASS DEFAULT
523 CALL this%Error("fileio_binary::WriteNode","unknown file handle")
524 END SELECT
525 CASE DEFAULT
526 val => getdata(node)
527 IF(ASSOCIATED(val)) THEN
528 bytes = SIZE(val)
529 ELSE
530 bytes = 0
531 END IF
532 CALL this%WriteKey(key,getdatatype(node),bytes)
533 IF(bytes.GT.0) THEN
534 SELECT TYPE(df=>this%datafile)
535#ifndef PARALLEL
536 CLASS IS(filehandle_fortran)
537 WRITE (unit=df%GetUnitNumber(),iostat=this%err) val
538#else
539 CLASS IS(filehandle_mpi)
540 CALL mpi_file_set_view(df%GetUnitNumber(),this%offset,mpi_byte,&
541 mpi_byte, 'native', mpi_info_null, this%err)
542 IF(this%GetRank().EQ.0) THEN
543 CALL mpi_file_write(df%GetUnitNumber(),val,bytes,mpi_byte, &
544 df%status,this%err)
545 END IF
546#endif
547 CLASS DEFAULT
548 CALL this%Error("fileio_binary::WriteNode","unknown file handle")
549 END SELECT
550 END IF
551 END SELECT
552 this%offset = this%offset + bytes
553 END IF
554#ifdef PARALLEL
555 IF(this%first) THEN
556 ! If MPI is used and this is the first output of the run,
557 ! it is checked, if the offsets of the different nodes are still
558 ! in sync. They can get easily out of sync if an output array is not
559 ! a mesh or corner array, but still has a different size on some nodes.
560 ! This easily happens, e.g. if one forgets to specify the subarray limits.
561 ! output_array(Mesh%IMIN:Mesh%IMAX,Mesh%JMIN:Mesh%JMAX)
562 ! The array would without them be interpreted as generic 2D array in
563 ! this case and therefore the calculated size could be different on
564 ! different nodes.
565 CALL mpi_allreduce(this%offset,omax,1,mpi_offset,mpi_max,&
566 mesh%comm_cart,this%err)
567 CALL mpi_allreduce(this%offset,omin,1,mpi_offset,mpi_min,&
568 mesh%comm_cart,this%err)
569 IF((this%offset.NE.omax).OR.(this%offset.NE.omin)) &
570 CALL this%Error("WriteNode_binary",&
571 "The offsets on different nodes are not in sync anymore." // lf &
572 //"The last key was '" // trim(key) // "'.")
573 END IF
574#endif
575 END SUBROUTINE writenode
576
577 FUNCTION hasmeshdims(this,Mesh,dims) RESULT(res)
578 IMPLICIT NONE
579 !------------------------------------------------------------------------!
580 CLASS(fileio_binary), INTENT(INOUT) :: this
581 CLASS(mesh_base), INTENT(IN) :: mesh
582 INTEGER, DIMENSION(:), INTENT(IN) :: dims
583 LOGICAL :: res
584 !------------------------------------------------------------------------!
585 IF(SIZE(dims).GE.3) THEN
586 res = all(dims(1:3).EQ.(/mesh%IMAX-mesh%IMIN+1, &
587 mesh%JMAX-mesh%JMIN+1, &
588 mesh%KMAX-mesh%KMIN+1/))
589 ELSE
590 res = .false.
591 END IF
592 END FUNCTION hasmeshdims
593
594
595 FUNCTION hascornerdims(this,Mesh,dims) RESULT(res)
596 IMPLICIT NONE
597 !------------------------------------------------------------------------!
598 CLASS(fileio_binary), INTENT(INOUT) :: this
599 CLASS(mesh_base), INTENT(IN) :: mesh
600 INTEGER, DIMENSION(:) :: dims
601 LOGICAL :: res
602 !------------------------------------------------------------------------!
603 INTENT(IN) :: dims
604 !------------------------------------------------------------------------!
605 IF(SIZE(dims).GE.3) THEN
606 ! remark: xP1 = 1 if xNUM > 1 and 0 if xNUM = 1 for x=I,J,K
607 res = all(dims(1:3).EQ.(/mesh%IMAX-mesh%IMIN+mesh%IP1+1, &
608 mesh%JMAX-mesh%JMIN+mesh%JP1+1, &
609 mesh%KMAX-mesh%KMIN+mesh%KP1+1/))
610 ELSE
611 res = .false.
612 END IF
613 END FUNCTION hascornerdims
614
615
616 SUBROUTINE setoutputdims(this,Mesh,dims)
617 IMPLICIT NONE
618 !------------------------------------------------------------------------!
619 CLASS(fileio_binary), INTENT(INOUT) :: this
620 CLASS(mesh_base), INTENT(IN) :: Mesh
621 INTEGER, DIMENSION(:), INTENT(INOUT):: dims
622 !------------------------------------------------------------------------!
623 IF(this%HasMeshDims(mesh,dims)) THEN
624 dims(1:3) = (/mesh%INUM,mesh%JNUM,mesh%KNUM/)
625 ELSE IF(this%HasCornerDims(mesh,dims)) THEN
626 dims(1:3) = (/mesh%INUM,mesh%JNUM,mesh%KNUM/)
627 WHERE ((/mesh%INUM,mesh%JNUM,mesh%KNUM/).GT.1)
628 ! add +1 to the global size to write one additional data point
629 ! in each dimension which has extend larger than 1
630 dims(1:3) = dims(1:3) + 1
631 END WHERE
632 END IF
633 END SUBROUTINE setoutputdims
634
635
638 SUBROUTINE writedataset_binary(this,Mesh,Physics,Fluxes,Timedisc,Header,IO)
639 IMPLICIT NONE
640 !------------------------------------------------------------------------!
641 CLASS(fileio_binary), INTENT(INOUT) :: this
642 CLASS(mesh_base), INTENT(IN) :: Mesh
643 CLASS(physics_base), INTENT(INOUT) :: Physics
644 CLASS(fluxes_base), INTENT(IN) :: Fluxes
645 CLASS(timedisc_base), INTENT(IN) :: Timedisc
646 TYPE(dict_typ), POINTER :: Header,IO
647 !------------------------------------------------------------------------!
648 CALL this%WriteDataAttributes(mesh,io)
649
650#ifdef PARALLEL
651 this%first = .false.
652#endif
653 END SUBROUTINE writedataset_binary
654
655! !> \public Reads the data arrays from file (not yet implemented)
656! !!
657! SUBROUTINE ReadDataset_binary(this,Mesh,Physics,Timedisc)
658! IMPLICIT NONE
659! !------------------------------------------------------------------------!
660! TYPE(FileIO_TYP) :: this !< \param [in,out] this fileio type
661! TYPE(Mesh_TYP) :: Mesh !< \param [in] mesh mesh type
662! TYPE(Physics_TYP) :: Physics !< \param [in] physics physics type
663! TYPE(Timedisc_TYP):: Timedisc !< \param [in,out] timedisc timedisc type
664! !------------------------------------------------------------------------!
665! INTENT(IN) :: Mesh,Physics
666! INTENT(INOUT) :: this,Timedisc
667! !------------------------------------------------------------------------!
668! END SUBROUTINE ReadDataset_binary
669
672 SUBROUTINE finalize(this)
673 IMPLICIT NONE
674 !------------------------------------------------------------------------!
675 TYPE(fileio_binary), INTENT(INOUT) :: this
676 !------------------------------------------------------------------------!
677#ifdef PARALLEL
678 SELECT TYPE(df=>this%datafile)
679 CLASS IS(filehandle_mpi)
680 CALL mpi_type_free(df%cfiletype,this%err)
681 CALL mpi_type_free(df%filetype,this%err)
682 END SELECT
683#endif
684 CALL this%Finalize_base()
685 END SUBROUTINE finalize
686
687END MODULE fileio_binary_mod
common_dict
Dictionary for generic data types.
Definition: common_dict.f90:61
common_dict::dict_real
integer, parameter, public dict_real
Definition: common_dict.f90:95
common_dict::getdata
pointer, public getdata(root)
Return the datatype of node 'root'.
Definition: common_dict.f90:460
common_dict::haschild
logical function, public haschild(root)
Check if the node 'root' has one or more children.
Definition: common_dict.f90:470
common_dict::dict_real_fourd
integer, parameter, public dict_real_fourd
Definition: common_dict.f90:101
common_dict::dict_real_threed
integer, parameter, public dict_real_threed
Definition: common_dict.f90:100
common_dict::dict_int_p
integer, parameter, public dict_int_p
Definition: common_dict.f90:104
common_dict::getdatatype
integer function, public getdatatype(root)
Return the datatype of node 'root'.
Definition: common_dict.f90:450
common_dict::getkey
function, public getkey(root)
Get the key of pointer 'root'.
Definition: common_dict.f90:424
common_dict::dict_real_fived
integer, parameter, public dict_real_fived
Definition: common_dict.f90:105
common_dict::dict_real_twod
integer, parameter, public dict_real_twod
Definition: common_dict.f90:99
common_dict::dict_real_p
integer, parameter, public dict_real_p
Definition: common_dict.f90:103
common_dict::getnext
type(dict_typ) function, pointer, public getnext(root)
Get the pointer to the next child.
Definition: common_dict.f90:392
common_dict::this
type(logging_base), save this
Definition: common_dict.f90:149
common_dict::dict_int
integer, parameter, public dict_int
Definition: common_dict.f90:94
common_dict::getchild
type(dict_typ) function, pointer, public getchild(root)
Get the pointer to a direct child of the pointer 'root'.
Definition: common_dict.f90:415
fileio_base_mod
Generic file I/O module.
Definition: fileio_base.f90:54
fileio_base_mod::append
integer, parameter append
read/write access at end
Definition: fileio_base.f90:277
fileio_binary_mod
module for binary file I/O
Definition: fileio_binary.f90:61
fileio_binary_mod::writedataattributes
recursive subroutine writedataattributes(this, Mesh, config, path)
Writes data attributes to a file.
Definition: fileio_binary.f90:368
fileio_binary_mod::initfileio_binary
subroutine initfileio_binary(this, Mesh, Physics, Timedisc, Sources, config, IO)
Constructor for the binary file I/O.
Definition: fileio_binary.f90:130
fileio_binary_mod::writekey
subroutine writekey(this, key, type, bytes, dims)
Writes key structure This subroutine writes the the key, data type and data sizes....
Definition: fileio_binary.f90:299
fileio_binary_mod::writeheader
subroutine writeheader(this, Mesh, Physics, Header, IO)
Write the file header The header is written in ASCII and is 13 Byte long. First a "magic" identifier ...
Definition: fileio_binary.f90:216
fileio_binary_mod::setoutputdims
subroutine setoutputdims(this, Mesh, dims)
Definition: fileio_binary.f90:617
fileio_binary_mod::lf
character, parameter lf
line feed
Definition: fileio_binary.f90:83
fileio_binary_mod::finalize
subroutine finalize(this)
Closes the file I/O.
Definition: fileio_binary.f90:673
fileio_binary_mod::writenode
subroutine writenode(this, Mesh, key, node)
Definition: fileio_binary.f90:399
fileio_binary_mod::hasmeshdims
logical function hasmeshdims(this, Mesh, dims)
Definition: fileio_binary.f90:578
fileio_binary_mod::hascornerdims
logical function hascornerdims(this, Mesh, dims)
Definition: fileio_binary.f90:596
fileio_binary_mod::writedataset_binary
subroutine writedataset_binary(this, Mesh, Physics, Fluxes, Timedisc, Header, IO)
Writes all desired data arrays to a file.
Definition: fileio_binary.f90:639
fluxes_base_mod
base module for numerical flux functions
Definition: fluxes_base.f90:39
geometry_base_mod
base class for geometrical properties
Definition: geometry_base.f90:36
mesh_base_mod
basic mesh module
Definition: mesh_base.f90:72
physics_base_mod
Basic physics module.
Definition: physics_base.f90:55
sources_generic_mod
module to manage list of source terms
Definition: sources_generic.f90:37
timedisc_base_mod
Definition: timedisc_base.f90:57
common_dict::dict_typ
Definition: common_dict.f90:123
common_dict::int_t
Definition: common_dict.f90:134
common_dict::real_t
Definition: common_dict.f90:131
fileio_base_mod::filehandle_fortran
class for Fortran file handle
Definition: fileio_base.f90:99
fileio_base_mod::filehandle_mpi
class for MPI file handle
Definition: fileio_base.f90:123
fileio_base_mod::fileio_base
FileIO base class.
Definition: fileio_base.f90:139
fileio_binary_mod::fileio_binary
FileIO binary class.
Definition: fileio_binary.f90:86
fluxes_base_mod::fluxes_base
Definition: fluxes_base.f90:61
mesh_base_mod::mesh_base
mesh data structure
Definition: mesh_base.f90:122
physics_base_mod::physics_base
Definition: physics_base.f90:69
sources_generic_mod::sources_list
container class to manage the list of source terms
Definition: sources_generic.f90:58
timedisc_base_mod::timedisc_base
Definition: timedisc_base.f90:84
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