Neko 1.99.2
A portable framework for high-order spectral element flow simulations
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nmsh_file.f90
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34module nmsh_file
35 use generic_file, only : generic_file_t
36 use comm, only : neko_comm, pe_rank, pe_size
37 use num_types, only : rp, dp, i4, i8
38 use mesh, only : mesh_t, neko_msh_max_zlbls
39 use utils, only : neko_error
40 use point, only : point_t
41 use tuple, only : tuple4_i4_t
42 use nmsh, only : nmsh_hex_t, nmsh_quad_t, nmsh_zone_t, nmsh_curve_el_t
43 use element, only : element_t
44 use datadist, only : linear_dist_t
45 use neko_mpi_types, only : mpi_nmsh_hex, mpi_nmsh_quad, mpi_nmsh_zone, &
46 mpi_nmsh_curve, mpi_integer_size
47 use mpi_f08, only : mpi_wtime, mpi_status, mpi_file, mpi_offset_kind, &
48 mpi_mode_wronly, mpi_mode_create, mpi_mode_rdonly, mpi_info_null, &
49 mpi_file_open, mpi_file_close, mpi_file_read_all, mpi_file_write_all, &
50 mpi_file_write_at_all, mpi_file_read_at_all, mpi_integer, mpi_sum, &
51 mpi_exscan, mpi_barrier, mpi_type_size, mpi_allreduce, mpi_file_sync
52 use logger, only : neko_log, log_size
53 implicit none
54
55 private
58 integer, parameter :: max_write_nel = 8000000
60 type, public, extends(generic_file_t) :: nmsh_file_t
61 contains
62 procedure :: read => nmsh_file_read
63 procedure :: write => nmsh_file_write
64 end type nmsh_file_t
65
66contains
67
69 subroutine nmsh_file_read(this, data)
70 class(nmsh_file_t) :: this
71 class(*), target, intent(inout) :: data
72 type(nmsh_hex_t), allocatable :: nmsh_hex(:)
73 type(nmsh_quad_t), allocatable :: nmsh_quad(:)
74 type(nmsh_zone_t), allocatable :: nmsh_zone(:)
75 type(nmsh_curve_el_t), allocatable :: nmsh_curve(:)
76 type(mesh_t), pointer :: msh
77 type(mpi_status) :: status
78 type(mpi_file) :: fh
79 integer (kind=MPI_OFFSET_KIND) :: mpi_offset, mpi_el_offset
80 integer :: i, j, ierr, element_offset
81 integer :: nmsh_quad_size, nmsh_hex_size, nmsh_zone_size
82 integer :: nelv, gdim, nzones, ncurves
83 integer :: el_idx, el_idx_glb
84 type(point_t), target :: p(8)
85 type(linear_dist_t) :: dist
86 character(len=LOG_SIZE) :: log_buf
87 real(kind=rp) :: t_start, t_end
88
89 call this%check_exists()
90
91 select type (data)
92 type is (mesh_t)
93 msh => data
94 class default
95 call neko_error('Invalid output data')
96 end select
97
98
99 call neko_log%section("Mesh")
100 call neko_log%message('Reading a binary Neko file ' // this%get_fname())
101
102 call mpi_type_size(mpi_nmsh_hex, nmsh_hex_size, ierr)
103 call mpi_type_size(mpi_nmsh_quad, nmsh_quad_size, ierr)
104 call mpi_type_size(mpi_nmsh_zone, nmsh_zone_size, ierr)
105
106 call mpi_file_open(neko_comm, trim(this%get_fname()), &
107 mpi_mode_rdonly, mpi_info_null, fh, ierr)
108
109 if (ierr > 0) then
110 call neko_error('Could not open the mesh file ' // this%get_fname() // &
111 'for reading!')
112 end if
113 call mpi_file_read_all(fh, nelv, 1, mpi_integer, status, ierr)
114 call mpi_file_read_all(fh, gdim, 1, mpi_integer, status, ierr)
115
116 write(log_buf,1) gdim, nelv
1171 format('gdim = ', i1, ', nelements = ', i9)
118 call neko_log%message(log_buf)
119
120 if (gdim .eq. 2) then
121 call mpi_file_close(fh, ierr)
122 call nmsh_file_read_2d(this, msh)
123 else
124
125 dist = linear_dist_t(nelv, pe_rank, pe_size, neko_comm)
126 nelv = dist%num_local()
127 element_offset = dist%start_idx()
128
129 call msh%init(gdim, nelv)
130
131 call neko_log%message('Reading elements')
132
133 if (msh%gdim .eq. 2) then
134 allocate(nmsh_quad(msh%nelv))
135 mpi_offset = int(2 * mpi_integer_size, i8) + &
136 int(element_offset, i8) * int(nmsh_quad_size, i8)
137 call mpi_file_read_at_all(fh, mpi_offset, &
138 nmsh_quad, msh%nelv, mpi_nmsh_quad, status, ierr)
139 do i = 1, nelv
140 do j = 1, 4
141 call p(j)%init(nmsh_quad(i)%v(j)%v_xyz, nmsh_quad(i)%v(j)%v_idx)
142 end do
143 ! swap vertices to keep symmetric vertex numbering in neko
144 call msh%add_element(i, nmsh_quad(i)%el_idx, &
145 p(1), p(2), p(4), p(3))
146 end do
147 deallocate(nmsh_quad)
148 mpi_el_offset = int(2 * mpi_integer_size, i8) + &
149 int(dist%num_global(), i8) * int(nmsh_quad_size, i8)
150 else if (msh%gdim .eq. 3) then
151 allocate(nmsh_hex(msh%nelv))
152 mpi_offset = int(2 * mpi_integer_size, i8) + &
153 int(element_offset, i8) * int(nmsh_hex_size, i8)
154 call mpi_file_read_at_all(fh, mpi_offset, &
155 nmsh_hex, msh%nelv, mpi_nmsh_hex, status, ierr)
156 do i = 1, nelv
157 do j = 1, 8
158 call p(j)%init(nmsh_hex(i)%v(j)%v_xyz, nmsh_hex(i)%v(j)%v_idx)
159 end do
160 ! swap vertices to keep symmetric vertex numbering in neko
161 call msh%add_element(i, nmsh_hex(i)%el_idx, &
162 p(1), p(2), p(4), p(3), p(5), p(6), p(8), p(7))
163 end do
164 deallocate(nmsh_hex)
165 mpi_el_offset = int(2 * mpi_integer_size, i8) + &
166 int(dist%num_global(), i8) * int(nmsh_hex_size, i8)
167 else
168 if (pe_rank .eq. 0) call neko_error('Invalid dimension of mesh')
169 end if
170 call neko_log%message('Reading BC/zone data')
171
172 mpi_offset = mpi_el_offset
173 call mpi_file_read_at_all(fh, mpi_offset, &
174 nzones, 1, mpi_integer, status, ierr)
175 if (nzones .gt. 0) then
176 allocate(nmsh_zone(nzones))
177
183 mpi_offset = mpi_el_offset + int(mpi_integer_size, i8)
184 call mpi_file_read_at_all(fh, mpi_offset, &
185 nmsh_zone, nzones, mpi_nmsh_zone, status, ierr)
186
187 do i = 1, nzones
188 el_idx_glb = nmsh_zone(i)%e
189 if (msh%htel%get(el_idx_glb, el_idx) .eq. 0) then
190 select case (nmsh_zone(i)%type)
191 case (5)
192 call msh%mark_periodic_facet(nmsh_zone(i)%f, el_idx, &
193 nmsh_zone(i)%p_f, nmsh_zone(i)%p_e, &
194 nmsh_zone(i)%glb_pt_ids)
195 case (7)
196 call msh%mark_labeled_facet(nmsh_zone(i)%f, el_idx, &
197 nmsh_zone(i)%p_f)
198 end select
199 end if
200 end do
201 !Apply facets, important that marking is finished
202 do i = 1, nzones
203 el_idx_glb = nmsh_zone(i)%e
204 if (msh%htel%get(el_idx_glb, el_idx) .eq. 0) then
205 select case (nmsh_zone(i)%type)
206 case (5)
207 call msh%apply_periodic_facet(nmsh_zone(i)%f, el_idx, &
208 nmsh_zone(i)%p_f, nmsh_zone(i)%p_e, &
209 nmsh_zone(i)%glb_pt_ids)
210 end select
211 end if
212 end do
213
214 deallocate(nmsh_zone)
215 end if
216 call neko_log%message('Reading deformation data')
217
218 mpi_offset = mpi_el_offset + int(mpi_integer_size, i8) + &
219 int(nzones, i8)*int(nmsh_zone_size, i8)
220 call mpi_file_read_at_all(fh, mpi_offset, &
221 ncurves, 1, mpi_integer, status, ierr)
222
223 if (ncurves .gt. 0) then
224
225 allocate(nmsh_curve(ncurves))
226 mpi_offset = mpi_el_offset + int(2 * mpi_integer_size, i8) + &
227 int(nzones, i8)*int(nmsh_zone_size, i8)
228 call mpi_file_read_at_all(fh, mpi_offset, &
229 nmsh_curve, ncurves, mpi_nmsh_curve, status, ierr)
230
231 do i = 1, ncurves
232 el_idx_glb = nmsh_curve(i)%e
233 if (msh%htel%get(el_idx_glb, el_idx) .eq. 0) then
234 call msh%mark_curve_element(el_idx, &
235 nmsh_curve(i)%curve_data, nmsh_curve(i)%type)
236 end if
237
238 end do
239
240 deallocate(nmsh_curve)
241 end if
242
243 call mpi_file_close(fh, ierr)
244 call neko_log%message('Mesh read, setting up connectivity')
245
246 t_start = mpi_wtime()
247 call msh%finalize()
248 call mpi_barrier(neko_comm, ierr)
249 t_end = mpi_wtime()
250 write(log_buf, '(A)') 'Done setting up mesh and connectivity'
251 call neko_log%message(log_buf)
252 write(log_buf, '(A,F9.6)') &
253 'Mesh and connectivity setup (excluding read) time (s): ', &
254 t_end - t_start
255 call neko_log%message(log_buf)
256
257 call neko_log%end_section()
258 end if
259
260 end subroutine nmsh_file_read
261
263 subroutine nmsh_file_read_2d(this, msh)
264 class(nmsh_file_t) :: this
265 type(mesh_t), pointer, intent(inout) :: msh
266 type(nmsh_hex_t), allocatable :: nmsh_hex(:)
267 type(nmsh_quad_t), allocatable :: nmsh_quad(:)
268 type(nmsh_zone_t), allocatable :: nmsh_zone(:)
269 type(nmsh_curve_el_t), allocatable :: nmsh_curve(:)
270 type(mpi_status) :: status
271 type(mpi_file) :: fh
272 integer (kind=MPI_OFFSET_KIND) :: mpi_offset, mpi_el_offset
273 integer :: i, j, ierr, element_offset, id
274 integer :: nmsh_quad_size, nmsh_hex_size, nmsh_zone_size
275 integer :: nelv, gdim, nzones, ncurves, ids(4)
276 integer :: el_idx_glb, el_idx
277 type(point_t) :: p(8)
278 type(linear_dist_t) :: dist
279 character(len=LOG_SIZE) :: log_buf
280 real(kind=rp) :: depth = 1d0
281 real(kind=dp) :: coord(3)
282 type(tuple4_i4_t) :: glb_pt_ids
283
284
285 call mpi_type_size(mpi_nmsh_hex, nmsh_hex_size, ierr)
286 call mpi_type_size(mpi_nmsh_quad, nmsh_quad_size, ierr)
287 call mpi_type_size(mpi_nmsh_zone, nmsh_zone_size, ierr)
288
289 call mpi_file_open(neko_comm, trim(this%get_fname()), &
290 mpi_mode_rdonly, mpi_info_null, fh, ierr)
291 call mpi_file_read_all(fh, nelv, 1, mpi_integer, status, ierr)
292 call mpi_file_read_all(fh, gdim, 1, mpi_integer, status, ierr)
293
294 write(log_buf,2) gdim
2952 format('gdim = ', i1, ', no full 2d support, creating thin slab')
296 call neko_log%message(log_buf)
297 gdim = 3
298
299 dist = linear_dist_t(nelv, pe_rank, pe_size, neko_comm)
300 nelv = dist%num_local()
301 element_offset = dist%start_idx()
302
303 call msh%init(gdim, nelv)
304
305 allocate(nmsh_quad(msh%nelv))
306 mpi_offset = int(2 * mpi_integer_size, i8) + &
307 int(element_offset, i8) * int(nmsh_quad_size, i8)
308 call mpi_file_read_at_all(fh, mpi_offset, &
309 nmsh_quad, msh%nelv, mpi_nmsh_quad, status, ierr)
310 do i = 1, nelv
311 do j = 1, 4
312 coord = nmsh_quad(i)%v(j)%v_xyz
313 coord(3) = 0_rp
314 call p(j)%init(coord, nmsh_quad(i)%v(j)%v_idx)
315 end do
316 do j = 1, 4
317 coord = nmsh_quad(i)%v(j)%v_xyz
318 coord(3) = depth
319 id = nmsh_quad(i)%v(j)%v_idx+msh%glb_nelv*8
320 call p(j+4)%init(coord, id)
321 end do
322 ! swap vertices to keep symmetric vertex numbering in neko
323 call msh%add_element(i, nmsh_quad(i)%el_idx, &
324 p(1), p(2), p(4), p(3), p(5), p(6), p(8), p(7))
325 end do
326 deallocate(nmsh_quad)
327 mpi_el_offset = int(2 * mpi_integer_size, i8) + &
328 int(dist%num_global(), i8) * int(nmsh_quad_size, i8)
329
330 mpi_offset = mpi_el_offset
331 call mpi_file_read_at_all(fh, mpi_offset, &
332 nzones, 1, mpi_integer, status, ierr)
333 if (nzones .gt. 0) then
334 allocate(nmsh_zone(nzones))
335
341 mpi_offset = mpi_el_offset + int(mpi_integer_size, i8)
342 call mpi_file_read_at_all(fh, mpi_offset, &
343 nmsh_zone, nzones, mpi_nmsh_zone, status, ierr)
344
345 do i = 1, nzones
346 el_idx_glb = nmsh_zone(i)%e
347 if (msh%htel%get(el_idx_glb, el_idx) .eq. 0) then
348 select case (nmsh_zone(i)%type)
349 case (5)
350 nmsh_zone(i)%glb_pt_ids(3) = nmsh_zone(i)%glb_pt_ids(1) + &
351 msh%glb_nelv * 8
352 nmsh_zone(i)%glb_pt_ids(4) = nmsh_zone(i)%glb_pt_ids(2) + &
353 msh%glb_nelv * 8
354 if (nmsh_zone(i)%f .eq. 1 .or. nmsh_zone(i)%f .eq. 2) then
355 ids(1) = nmsh_zone(i)%glb_pt_ids(1)
356 ids(2) = nmsh_zone(i)%glb_pt_ids(3)
357 ids(3) = nmsh_zone(i)%glb_pt_ids(4)
358 ids(4) = nmsh_zone(i)%glb_pt_ids(2)
359 else
360 ids(1) = nmsh_zone(i)%glb_pt_ids(1)
361 ids(2) = nmsh_zone(i)%glb_pt_ids(2)
362 ids(3) = nmsh_zone(i)%glb_pt_ids(4)
363 ids(4) = nmsh_zone(i)%glb_pt_ids(3)
364 end if
365 nmsh_zone(i)%glb_pt_ids = ids
366 call msh%mark_periodic_facet(nmsh_zone(i)%f, el_idx, &
367 nmsh_zone(i)%p_f, nmsh_zone(i)%p_e, ids)
368 case (7)
369 call msh%mark_labeled_facet(nmsh_zone(i)%f, el_idx, &
370 nmsh_zone(i)%p_f)
371 end select
372 end if
373 end do
374 !Apply facets, important that marking is finished
375 do i = 1, nzones
376 el_idx_glb = nmsh_zone(i)%e
377 if (msh%htel%get(el_idx_glb, el_idx) .eq. 0) then
378 select case (nmsh_zone(i)%type)
379 case (5)
380 call msh%apply_periodic_facet(nmsh_zone(i)%f, el_idx, &
381 nmsh_zone(i)%p_f, nmsh_zone(i)%p_e, &
382 nmsh_zone(i)%glb_pt_ids)
383 end select
384 end if
385 end do
386 !Do the same for extruded 3d points
387 do el_idx = 1, nelv
388 call msh%elements(el_idx)%e%facet_order(glb_pt_ids,5)
389 call msh%mark_periodic_facet(6, el_idx, &
390 5, el_idx, glb_pt_ids%x)
391 call msh%elements(el_idx)%e%facet_order(glb_pt_ids,5)
392 call msh%mark_periodic_facet(5, el_idx, &
393 6, el_idx, glb_pt_ids%x)
394 end do
395 do el_idx = 1, nelv
396 call msh%elements(el_idx)%e%facet_order(glb_pt_ids,5)
397 call msh%apply_periodic_facet(6, el_idx, &
398 5, el_idx, glb_pt_ids%x)
399 call msh%elements(el_idx)%e%facet_order(glb_pt_ids,5)
400 call msh%apply_periodic_facet(5, el_idx, &
401 6, el_idx, glb_pt_ids%x)
402 end do
403
404 deallocate(nmsh_zone)
405 end if
406
407 mpi_offset = mpi_el_offset + &
408 int(mpi_integer_size, i8) + int(nzones, i8)*int(nmsh_zone_size, i8)
409 call mpi_file_read_at_all(fh, mpi_offset, &
410 ncurves, 1, mpi_integer, status, ierr)
411
412 if (ncurves .gt. 0) then
413
414 allocate(nmsh_curve(ncurves))
415 mpi_offset = mpi_el_offset + &
416 int(2*mpi_integer_size, i8) + &
417 int(nzones, i8)*int(nmsh_zone_size, i8)
418 call mpi_file_read_at_all(fh, mpi_offset, &
419 nmsh_curve, ncurves, mpi_nmsh_curve, status, ierr)
420
421 do i = 1, ncurves
422 el_idx_glb = nmsh_curve(i)%e
423 if (msh%htel%get(el_idx_glb, el_idx) .eq. 0) then
424 call msh%mark_curve_element(el_idx, &
425 nmsh_curve(i)%curve_data, nmsh_curve(i)%type)
426 end if
427 end do
428
429 deallocate(nmsh_curve)
430 end if
431
432 call mpi_file_close(fh, ierr)
433
434 call msh%finalize()
435
436 call neko_log%end_section()
437
438 end subroutine nmsh_file_read_2d
439
440
442 subroutine nmsh_file_write(this, data, t)
443 class(nmsh_file_t), intent(inout) :: this
444 class(*), target, intent(in) :: data
445 real(kind=rp), intent(in), optional :: t
446 type(nmsh_quad_t), allocatable :: nmsh_quad(:)
447 type(nmsh_hex_t), allocatable :: nmsh_hex(:)
448 type(nmsh_zone_t), allocatable :: nmsh_zone(:)
449 type(nmsh_curve_el_t), allocatable :: nmsh_curve(:)
450 type(mesh_t), pointer :: msh
451 type(mpi_status) :: status
452 type(mpi_file) :: fh
453 integer (kind=MPI_OFFSET_KIND) :: mpi_offset, mpi_el_offset
454 integer :: i, j, ierr, k
455 integer :: nmsh_quad_size, nmsh_hex_size, nmsh_zone_size, nmsh_curve_size
456 integer :: nzones, nzones_glb, nzones_offset
457 integer :: ncurves, ncurves_glb, ncurves_offset
458 integer :: el_idx, el_idx_glb
459 class(element_t), pointer :: ep
460 integer(i4), dimension(8), parameter :: vcyc_to_sym = &
461 [1, 2, 4, 3, 5, 6, 8, 7] ! cyclic to symmetric vertex mapping
462
463 select type (data)
464 type is (mesh_t)
465 msh => data
466 class default
467 call neko_error('Invalid output data')
468 end select
469
470 call mpi_type_size(mpi_nmsh_quad, nmsh_quad_size, ierr)
471 call mpi_type_size(mpi_nmsh_hex, nmsh_hex_size, ierr)
472 call mpi_type_size(mpi_nmsh_zone, nmsh_zone_size, ierr)
473 call mpi_type_size(mpi_nmsh_curve, nmsh_curve_size, ierr)
474
475 call neko_log%message('Writing data as a binary Neko file ' // &
476 this%get_fname())
477
478 call mpi_file_open(neko_comm, trim(this%get_fname()), &
479 mpi_mode_wronly + mpi_mode_create, mpi_info_null, fh, ierr)
480
481 call mpi_file_write_all(fh, msh%glb_nelv, 1, mpi_integer, status, ierr)
482 call mpi_file_write_all(fh, msh%gdim, 1, mpi_integer, status, ierr)
483
484 call msh%reset_periodic_ids()
485
486 if (msh%gdim .eq. 2) then
487 allocate(nmsh_quad(msh%nelv))
488 do i = 1, msh%nelv
489 ep => msh%elements(i)%e
490 nmsh_quad(i)%el_idx = ep%id()
491 do j = 1, 4
492 nmsh_quad(i)%v(j)%v_idx = ep%pts(vcyc_to_sym(j))%p%id()
493 nmsh_quad(i)%v(j)%v_xyz = ep%pts(vcyc_to_sym(j))%p%x
494 end do
495 end do
496 mpi_offset = int(2 * mpi_integer_size, i8) + &
497 int(msh%offset_el, i8) * int(nmsh_quad_size, i8)
498 call mpi_file_write_at_all(fh, mpi_offset, &
499 nmsh_quad, msh%nelv, mpi_nmsh_quad, status, ierr)
500 deallocate(nmsh_quad)
501 mpi_el_offset = int(2 * mpi_integer_size, i8) + &
502 int(msh%glb_nelv, i8) * int(nmsh_quad_size, i8)
503 else if (msh%gdim .eq. 3) then
504 allocate(nmsh_hex(msh%nelv))
505 do i = 1, msh%nelv
506 ep => msh%elements(i)%e
507 nmsh_hex(i)%el_idx = ep%id()
508 do j = 1, 8
509 nmsh_hex(i)%v(j)%v_idx = ep%pts(vcyc_to_sym(j))%p%id()
510 nmsh_hex(i)%v(j)%v_xyz = ep%pts(vcyc_to_sym(j))%p%x
511 end do
512 end do
513 mpi_offset = int(2 * mpi_integer_size, i8) + &
514 int(msh%offset_el, i8) * int(nmsh_hex_size, i8)
515 call mpi_file_write_at_all(fh, mpi_offset, &
516 nmsh_hex, min(msh%nelv, max_write_nel), mpi_nmsh_hex, status, ierr)
517 do i = 1, msh%nelv/max_write_nel
518 mpi_offset = int(2 * mpi_integer_size, i8) + &
519 int(msh%offset_el+i*max_write_nel, i8) * int(nmsh_hex_size, i8)
520 call mpi_file_write_at_all(fh, mpi_offset, &
521 nmsh_hex(i*max_write_nel+1), &
522 min(msh%nelv-i*max_write_nel, max_write_nel), &
523 mpi_nmsh_hex, status, ierr)
524 end do
525 deallocate(nmsh_hex)
526 mpi_el_offset = int(2 * mpi_integer_size, i8) + &
527 int(msh%glb_nelv, i8) * int(nmsh_hex_size, i8)
528 else
529 call neko_error('Invalid dimension of mesh')
530 end if
531
532 nzones = msh%periodic%size
533 do i = 1, neko_msh_max_zlbls
534 nzones = nzones + msh%labeled_zones(i)%size
535 end do
536
537 call mpi_allreduce(nzones, nzones_glb, 1, &
538 mpi_integer, mpi_sum, neko_comm, ierr)
539
540 nzones_offset = 0
541 call mpi_exscan(nzones, nzones_offset, 1, &
542 mpi_integer, mpi_sum, neko_comm, ierr)
543
544 mpi_offset = mpi_el_offset
545 call mpi_file_write_at_all(fh, mpi_offset, &
546 nzones_glb, 1, mpi_integer, status, ierr)
547
548 if (nzones_glb .gt. 0) then
549 allocate(nmsh_zone(nzones))
550
551 if (nzones .gt. 0) then
552 nmsh_zone(:)%type = 0
553
554 j = 1
555 do i = 1, msh%periodic%size
556 nmsh_zone(j)%e = msh%elements(msh%periodic%facet_el(i)%x(2))%e%id()
557 nmsh_zone(j)%f = msh%periodic%facet_el(i)%x(1)
558 nmsh_zone(j)%p_e = msh%periodic%p_facet_el(i)%x(2)
559 nmsh_zone(j)%p_f = msh%periodic%p_facet_el(i)%x(1)
560 nmsh_zone(j)%glb_pt_ids = msh%periodic%p_ids(i)%x
561 nmsh_zone(j)%type = 5
562 j = j + 1
563 end do
564
565 do k = 1, neko_msh_max_zlbls
566 do i = 1, msh%labeled_zones(k)%size
567 nmsh_zone(j)%e = &
568 msh%elements(msh%labeled_zones(k)%facet_el(i)%x(2))%e%id()
569 nmsh_zone(j)%f = msh%labeled_zones(k)%facet_el(i)%x(1)
570 nmsh_zone(j)%p_f = k
571 nmsh_zone(j)%type = 7
572 j = j + 1
573 end do
574 end do
575 end if
576
577 mpi_offset = mpi_el_offset + int(mpi_integer_size, i8) + &
578 int(nzones_offset, i8) * int(nmsh_zone_size, i8)
579 call mpi_file_write_at_all(fh, mpi_offset, &
580 nmsh_zone, nzones, mpi_nmsh_zone, status, ierr)
581
582 deallocate(nmsh_zone)
583 end if
584
585 ncurves = msh%curve%size
586
587
588 call mpi_allreduce(ncurves, ncurves_glb, 1, &
589 mpi_integer, mpi_sum, neko_comm, ierr)
590
591 ncurves_offset = 0
592 call mpi_exscan(ncurves, ncurves_offset, 1, &
593 mpi_integer, mpi_sum, neko_comm, ierr)
594
595 mpi_offset = mpi_el_offset + int(mpi_integer_size, i8) + &
596 int(nzones_glb, i8)*int(nmsh_zone_size, i8)
597
598 call mpi_file_write_at_all(fh, mpi_offset, &
599 ncurves_glb, 1, mpi_integer, status, ierr)
600
601 if (ncurves_glb .gt. 0) then
602
603 allocate(nmsh_curve(ncurves))
604
605 do i = 1, ncurves
606 nmsh_curve(i)%type = 0
607 end do
608
609 do i = 1, ncurves
610 nmsh_curve(i)%e = msh%elements(msh%curve%curve_el(i)%el_idx)%e%id()
611 nmsh_curve(i)%curve_data = msh%curve%curve_el(i)%curve_data
612 nmsh_curve(i)%type = msh%curve%curve_el(i)%curve_type
613 end do
614
615 mpi_offset = mpi_el_offset + int(2*mpi_integer_size, i8) + &
616 int(nzones_glb, i8) * int(nmsh_zone_size, i8) + &
617 int(ncurves_offset, i8) * int(nmsh_curve_size, i8)
618
619 call mpi_file_write_at_all(fh, mpi_offset, &
620 nmsh_curve, ncurves, mpi_nmsh_curve, status, ierr)
621 deallocate(nmsh_curve)
622 end if
623
624 call mpi_file_sync(fh, ierr)
625 call mpi_file_close(fh, ierr)
626 call neko_log%message('Done')
627
628 !
629 ! Re-apply periodic facets
630 ! (necessary if the mesh is going to be used after I/O)
631 !
632 do i = 1, msh%periodic%size
633 el_idx_glb = msh%elements(msh%periodic%facet_el(i)%x(2))%e%id()
634 if (msh%htel%get(el_idx_glb, el_idx) .eq. 0) then
635 call msh%apply_periodic_facet(msh%periodic%facet_el(i)%x(1), el_idx, &
636 msh%periodic%p_facet_el(i)%x(1), &
637 msh%periodic%p_facet_el(i)%x(2), msh%periodic%p_ids(i)%x)
638 end if
639 end do
640
641 end subroutine nmsh_file_write
642
643end module nmsh_file
utils::neko_error
Definition utils.f90:42
comm
Definition comm.F90:1
comm::pe_size
integer, public pe_size
MPI size of communicator.
Definition comm.F90:59
comm::pe_rank
integer, public pe_rank
MPI rank.
Definition comm.F90:56
comm::neko_comm
type(mpi_comm), public neko_comm
MPI communicator.
Definition comm.F90:43
datadist
Defines practical data distributions.
Definition datadist.f90:34
generic_file
Definition generic_file.f90:33
logger
Logging routines.
Definition log.f90:34
logger::neko_log
type(log_t), public neko_log
Global log stream.
Definition log.f90:77
logger::log_size
integer, parameter, public log_size
Definition log.f90:46
mesh
Defines a mesh.
Definition mesh.f90:34
mesh::neko_msh_max_zlbls
integer, parameter, public neko_msh_max_zlbls
Max num. zone labels.
Definition mesh.f90:63
neko_mpi_types
MPI derived types.
Definition mpi_types.f90:34
neko_mpi_types::mpi_nmsh_hex
type(mpi_datatype), public mpi_nmsh_hex
MPI derived type for 3D Neko nmsh data.
Definition mpi_types.f90:47
neko_mpi_types::mpi_nmsh_quad
type(mpi_datatype), public mpi_nmsh_quad
MPI derived type for 2D Neko nmsh data.
Definition mpi_types.f90:48
neko_mpi_types::mpi_nmsh_curve
type(mpi_datatype), public mpi_nmsh_curve
MPI derived type for Neko nmsh curved elements.
Definition mpi_types.f90:50
neko_mpi_types::mpi_integer_size
integer, public mpi_integer_size
Size of MPI type integer.
Definition mpi_types.f90:68
neko_mpi_types::mpi_nmsh_zone
type(mpi_datatype), public mpi_nmsh_zone
MPI derived type for Neko nmsh zone data.
Definition mpi_types.f90:49
nmsh_file
Neko binary mesh data.
Definition nmsh_file.f90:34
nmsh_file::nmsh_file_write
subroutine nmsh_file_write(this, data, t)
Write a mesh from to a binary Neko nmsh file.
Definition nmsh_file.f90:443
nmsh_file::nmsh_file_read
subroutine nmsh_file_read(this, data)
Load a mesh from a binary Neko nmsh file.
Definition nmsh_file.f90:70
nmsh_file::max_write_nel
integer, parameter max_write_nel
Specifices the maximum number of elements any rank is allowed to write (for nmsh)....
Definition nmsh_file.f90:58
nmsh_file::nmsh_file_read_2d
subroutine nmsh_file_read_2d(this, msh)
Load a mesh from a binary Neko nmsh file.
Definition nmsh_file.f90:264
nmsh
Neko binary mesh format.
Definition nmsh.f90:2
num_types
Definition num_types.f90:1
num_types::i8
integer, parameter, public i8
Definition num_types.f90:7
num_types::i4
integer, parameter, public i4
Definition num_types.f90:6
num_types::dp
integer, parameter, public dp
Definition num_types.f90:9
num_types::rp
integer, parameter, public rp
Global precision used in computations.
Definition num_types.f90:12
point
Implements a point.
Definition point.f90:35
tuple
Implements a n-tuple.
Definition tuple.f90:34
utils
Utilities.
Definition utils.f90:35
datadist::linear_dist_t
Load-balanced linear distribution .
Definition datadist.f90:50
element::element_t
Base type for an element.
Definition element.f90:44
generic_file::generic_file_t
A generic file handler.
Definition generic_file.f90:42
mesh::mesh_t
Definition mesh.f90:71
nmsh::nmsh_curve_el_t
Neko curve data.
Definition nmsh.f90:39
nmsh::nmsh_hex_t
Neko hex element data.
Definition nmsh.f90:24
nmsh::nmsh_quad_t
Neko quad element data.
Definition nmsh.f90:19
nmsh::nmsh_zone_t
Neko zone data.
Definition nmsh.f90:29
nmsh_file::nmsh_file_t
Interface for Neko nmsh files.
Definition nmsh_file.f90:60
point::point_t
A point in with coordinates .
Definition point.f90:43
tuple::tuple4_i4_t
Integer based 4-tuple.
Definition tuple.f90:69