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input_cp2k_binary_restarts.F
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1!--------------------------------------------------------------------------------------------------!
2! CP2K: A general program to perform molecular dynamics simulations !
3! Copyright 2000-2024 CP2K developers group <https://cp2k.org> !
4! !
5! SPDX-License-Identifier: GPL-2.0-or-later !
6!--------------------------------------------------------------------------------------------------!
7
8! **************************************************************************************************
9!> \brief Routines to read the binary restart file of CP2K
10!> \author Matthias Krack (MK)
11!> \par History
12!> - Creation (17.02.2011,MK)
13!> \version 1.0
14! **************************************************************************************************
15MODULE input_cp2k_binary_restarts
16
17 USE cp_files, ONLY: close_file,&
18 open_file
19 USE cp_log_handling, ONLY: cp_get_default_logger,&
20 cp_logger_get_default_io_unit,&
21 cp_logger_type,&
22 cp_to_string
23 USE cp_output_handling, ONLY: cp_print_key_unit_nr,&
24 debug_print_level
25 USE extended_system_types, ONLY: lnhc_parameters_type
26 USE input_section_types, ONLY: section_vals_type,&
27 section_vals_val_get
28 USE kinds, ONLY: default_path_length,&
29 default_string_length,&
30 dp
31 USE message_passing, ONLY: mp_para_env_type
32 USE particle_types, ONLY: particle_type
33 USE physcon, ONLY: angstrom
34 USE print_messages, ONLY: print_message
35 USE string_table, ONLY: id2str,&
36 s2s,&
37 str2id
38 USE topology_types, ONLY: atom_info_type,&
39 topology_parameters_type
40#include "./base/base_uses.f90"
41
42 IMPLICIT NONE
43
44 PRIVATE
45
46 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'input_cp2k_binary_restarts'
47
48 PUBLIC :: read_binary_coordinates, &
49 read_binary_cs_coordinates, &
50 read_binary_thermostats_nose, &
51 read_binary_velocities
52
53CONTAINS
54
55! **************************************************************************************************
56!> \brief Read the input section &COORD from an external file written in
57!> binary format.
58!> \param topology ...
59!> \param root_section ...
60!> \param para_env ...
61!> \param subsys_section ...
62!> \param binary_file_read ...
63!> \par History
64!> - Creation (10.02.2011,MK)
65!> \author Matthias Krack (MK)
66!> \version 1.0
67! **************************************************************************************************
68 SUBROUTINE read_binary_coordinates(topology, root_section, para_env, &
69 subsys_section, binary_file_read)
70
71 TYPE(topology_parameters_type) :: topology
72 TYPE(section_vals_type), POINTER :: root_section
73 TYPE(mp_para_env_type), POINTER :: para_env
74 TYPE(section_vals_type), POINTER :: subsys_section
75 LOGICAL, INTENT(OUT) :: binary_file_read
76
77 CHARACTER(LEN=*), PARAMETER :: routinen = 'read_binary_coordinates'
78
79 CHARACTER(LEN=default_path_length) :: binary_restart_file_name
80 CHARACTER(LEN=default_string_length) :: string
81 INTEGER :: handle, iatom, ikind, input_unit, istat, &
82 iw, natom, natomkind, ncore, &
83 nmolecule, nmoleculekind, nshell
84 INTEGER, ALLOCATABLE, DIMENSION(:) :: ibuf, id_name
85 TYPE(atom_info_type), POINTER :: atom_info
86 TYPE(cp_logger_type), POINTER :: logger
87
88 CALL timeset(routinen, handle)
89
90 NULLIFY (logger)
91 cpassert(ASSOCIATED(root_section))
92 cpassert(ASSOCIATED(para_env))
93 cpassert(ASSOCIATED(subsys_section))
94 logger => cp_get_default_logger()
95
96 binary_file_read = .false.
97
98 CALL section_vals_val_get(root_section, "EXT_RESTART%BINARY_RESTART_FILE_NAME", &
99 c_val=binary_restart_file_name)
100
101 IF (trim(adjustl(binary_restart_file_name)) == "") THEN
102 CALL timestop(handle)
103 RETURN
104 END IF
105
106 iw = cp_print_key_unit_nr(logger, subsys_section, "PRINT%TOPOLOGY_INFO/XYZ_INFO", &
107 extension=".subsysLog")
108
109 natomkind = 0
110 natom = 0
111 ncore = 0
112 nshell = 0
113 nmoleculekind = 0
114 nmolecule = 0
115
116 ! Open binary restart file and read number atomic kinds, atoms, etc.
117 IF (para_env%is_source()) THEN
118 CALL open_file(file_name=binary_restart_file_name, &
119 file_status="OLD", &
120 file_form="UNFORMATTED", &
121 file_action="READWRITE", &
122 file_position="REWIND", &
123 unit_number=input_unit, &
124 debug=iw)
125 READ (unit=input_unit, iostat=istat) &
126 natomkind, natom, ncore, nshell, nmoleculekind, nmolecule
127 IF (istat /= 0) THEN
128 CALL stop_read("natomkind,natom,ncore,nshell,nmoleculekind,nmolecule "// &
129 "(IOSTAT = "//trim(adjustl(cp_to_string(istat)))//")", &
130 input_unit)
131 END IF
132 IF (iw > 0) THEN
133 WRITE (unit=iw, fmt="(T2,A,T71,I10)") &
134 "Number of atomic kinds:", natomkind, &
135 "Number of atoms:", natom, &
136 "Number of cores (only core-shell model):", ncore, &
137 "Number of shells (only core-shell model):", nshell, &
138 "Number of molecule kinds:", nmoleculekind, &
139 "Number of molecules", nmolecule
140 END IF
141 END IF
142
143 CALL para_env%bcast(natomkind)
144 CALL para_env%bcast(natom)
145 CALL para_env%bcast(ncore)
146 CALL para_env%bcast(nshell)
147 CALL para_env%bcast(nmoleculekind)
148 CALL para_env%bcast(nmolecule)
149
150 ALLOCATE (id_name(natomkind))
151 ! Read atomic kind names
152 DO ikind = 1, natomkind
153 IF (para_env%is_source()) THEN
154 READ (unit=input_unit, iostat=istat) string
155 IF (istat /= 0) CALL stop_read("string (IOSTAT = "// &
156 trim(adjustl(cp_to_string(istat)))//")", &
157 input_unit)
158 END IF
159 CALL para_env%bcast(string)
160 id_name(ikind) = str2id(string)
161 END DO
162
163 ! Allocate and initialise atom_info array
164 atom_info => topology%atom_info
165 ALLOCATE (atom_info%id_molname(natom))
166 atom_info%id_molname(:) = 0
167 ALLOCATE (atom_info%id_resname(natom))
168 atom_info%id_resname(:) = 0
169 ALLOCATE (atom_info%resid(natom))
170 atom_info%resid = 1
171 ALLOCATE (atom_info%id_atmname(natom))
172 atom_info%id_atmname = 0
173 ALLOCATE (atom_info%r(3, natom))
174 atom_info%r(:, :) = 0.0_dp
175 ALLOCATE (atom_info%atm_mass(natom))
176 atom_info%atm_mass(:) = huge(0.0_dp)
177 ALLOCATE (atom_info%atm_charge(natom))
178 atom_info%atm_charge(:) = -huge(0.0_dp)
179 ALLOCATE (atom_info%occup(natom))
180 atom_info%occup(:) = 0.0_dp
181 ALLOCATE (atom_info%beta(natom))
182 atom_info%beta(:) = 0.0_dp
183 ALLOCATE (atom_info%id_element(natom))
184 atom_info%id_element(:) = 0
185 ALLOCATE (ibuf(natom))
186
187 ! Read atomic kind number of each atom
188 IF (para_env%is_source()) THEN
189 READ (unit=input_unit, iostat=istat) ibuf(1:natom)
190 IF (istat /= 0) CALL stop_read("ibuf (IOSTAT = "// &
191 trim(adjustl(cp_to_string(istat)))//")", &
192 input_unit)
193 END IF
194 CALL para_env%bcast(ibuf)
195 DO iatom = 1, natom
196 ikind = ibuf(iatom)
197 atom_info%id_atmname(iatom) = id_name(ikind)
198 atom_info%id_element(iatom) = id_name(ikind)
199 END DO
200 DEALLOCATE (id_name)
201
202 ! Read atomic coordinates
203 IF (para_env%is_source()) THEN
204 READ (unit=input_unit, iostat=istat) atom_info%r(1:3, 1:natom)
205 IF (istat /= 0) CALL stop_read("atom_info%r(1:3,1:natom) (IOSTAT = "// &
206 trim(adjustl(cp_to_string(istat)))//")", &
207 input_unit)
208 END IF
209 CALL para_env%bcast(atom_info%r)
210
211 ! Read molecule information if available
212 IF (nmolecule > 0) THEN
213 ALLOCATE (id_name(nmoleculekind))
214 ! Read molecule kind names
215 DO ikind = 1, nmoleculekind
216 IF (para_env%is_source()) THEN
217 READ (unit=input_unit, iostat=istat) string
218 IF (istat /= 0) CALL stop_read("string (IOSTAT = "// &
219 trim(adjustl(cp_to_string(istat)))//")", &
220 input_unit)
221 END IF
222 CALL para_env%bcast(string)
223 id_name(ikind) = str2id(string)
224 END DO
225 ! Read molecule kind numbers
226 IF (para_env%is_source()) THEN
227 READ (unit=input_unit, iostat=istat) ibuf(1:natom)
228 IF (istat /= 0) CALL stop_read("ibuf(1:natom) (IOSTAT = "// &
229 trim(adjustl(cp_to_string(istat)))//")", &
230 input_unit)
231 END IF
232 CALL para_env%bcast(ibuf)
233 DO iatom = 1, natom
234 ikind = ibuf(iatom)
235 atom_info%id_molname(iatom) = id_name(ikind)
236 END DO
237 DEALLOCATE (id_name)
238 ! Read molecule index which is used also as residue id
239 IF (para_env%is_source()) THEN
240 READ (unit=input_unit, iostat=istat) atom_info%resid(1:natom)
241 IF (istat /= 0) CALL stop_read("atom_info%resid(1:natom) (IOSTAT = "// &
242 trim(adjustl(cp_to_string(istat)))//")", &
243 input_unit)
244 END IF
245 CALL para_env%bcast(atom_info%resid)
246 DO iatom = 1, natom
247 atom_info%id_resname(iatom) = str2id(s2s(cp_to_string(atom_info%resid(iatom))))
248 END DO
249 END IF
250 DEALLOCATE (ibuf)
251
252 !MK to be checked ...
253 topology%aa_element = .true.
254 topology%molname_generated = .false.
255 topology%natoms = natom
256
257 IF (iw > 0) THEN
258 WRITE (unit=iw, fmt="(T2,A)") &
259 "BEGIN of COORD section data [Angstrom] read in binary format from file "// &
260 trim(binary_restart_file_name)
261 DO iatom = 1, natom
262 WRITE (unit=iw, fmt="(T2,A2,3(1X,ES25.16),2(1X,A))") &
263 trim(adjustl(id2str(atom_info%id_atmname(iatom)))), &
264 atom_info%r(1:3, iatom)*angstrom, &
265 trim(adjustl(id2str(atom_info%id_molname(iatom)))), &
266 trim(adjustl(id2str(atom_info%id_resname(iatom))))
267 END DO
268 WRITE (unit=iw, fmt="(T2,A)") &
269 "END of COORD section data [Angstrom] read from binary restart file "// &
270 trim(binary_restart_file_name)
271 END IF
272
273 IF (para_env%is_source()) CALL close_file(unit_number=input_unit, &
274 keep_preconnection=.true.)
275
276 binary_file_read = .true.
277
278 CALL timestop(handle)
279
280 END SUBROUTINE read_binary_coordinates
281
282! **************************************************************************************************
283!> \brief Read the input section &CORE_COORD or &SHELL_COORD from an external
284!> file written in binary format.
285!> \param prefix ...
286!> \param particle_set ...
287!> \param root_section ...
288!> \param subsys_section ...
289!> \param binary_file_read ...
290!> \par History
291!> - Creation (17.02.2011,MK)
292!> \author Matthias Krack (MK)
293!> \version 1.0
294! **************************************************************************************************
295 SUBROUTINE read_binary_cs_coordinates(prefix, particle_set, root_section, &
296 subsys_section, binary_file_read)
297
298 CHARACTER(LEN=*), INTENT(IN) :: prefix
299 TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
300 TYPE(section_vals_type), POINTER :: root_section, subsys_section
301 LOGICAL, INTENT(OUT) :: binary_file_read
302
303 CHARACTER(LEN=*), PARAMETER :: routinen = 'read_binary_cs_coordinates'
304
305 CHARACTER(LEN=default_path_length) :: binary_restart_file_name, message
306 CHARACTER(LEN=default_string_length) :: section_label, section_name
307 INTEGER :: handle, input_unit, iparticle, istat, &
308 iw, nbuf, nparticle
309 INTEGER, ALLOCATABLE, DIMENSION(:) :: ibuf
310 LOGICAL :: exit_routine
311 REAL(kind=dp), ALLOCATABLE, DIMENSION(:, :) :: rbuf
312 TYPE(cp_logger_type), POINTER :: logger
313 TYPE(mp_para_env_type), POINTER :: para_env
314
315 CALL timeset(routinen, handle)
316
317 NULLIFY (logger)
318 cpassert(ASSOCIATED(root_section))
319 cpassert(ASSOCIATED(subsys_section))
320 logger => cp_get_default_logger()
321 para_env => logger%para_env
322
323 binary_file_read = .false.
324
325 IF (ASSOCIATED(particle_set)) THEN
326 exit_routine = .false.
327 nparticle = SIZE(particle_set)
328 ELSE
329 exit_routine = .true.
330 nparticle = 0
331 END IF
332
333 CALL section_vals_val_get(root_section, "EXT_RESTART%BINARY_RESTART_FILE_NAME", &
334 c_val=binary_restart_file_name)
335
336 IF (trim(adjustl(binary_restart_file_name)) == "") THEN
337 CALL timestop(handle)
338 RETURN
339 END IF
340
341 iw = cp_print_key_unit_nr(logger, subsys_section, "PRINT%TOPOLOGY_INFO/XYZ_INFO", &
342 extension=".subsysLog")
343
344 section_name = prefix//" COORDINATES"
345
346 ! Open binary restart file at last position
347 IF (para_env%is_source()) THEN
348 CALL open_file(file_name=trim(binary_restart_file_name), &
349 file_status="OLD", &
350 file_form="UNFORMATTED", &
351 file_action="READWRITE", &
352 file_position="ASIS", &
353 unit_number=input_unit, &
354 debug=iw)
355 READ (unit=input_unit, iostat=istat) section_label, nbuf
356 IF (istat /= 0) CALL stop_read("section_label, nbuf -> "//trim(section_label)//", "// &
357 trim(adjustl(cp_to_string(nbuf)))// &
358 " (IOSTAT = "//trim(adjustl(cp_to_string(istat)))//"). "// &
359 "Section "//trim(adjustl(section_name))//" was expected.", &
360 input_unit)
361 IF (trim(section_label) == trim(section_name)) THEN
362 IF (nbuf /= nparticle) THEN
363 IF (iw > 0) THEN
364 message = "INFO: The requested number of "//trim(section_name)//" ("// &
365 trim(adjustl(cp_to_string(nparticle)))//") does not match the "// &
366 "number ("//trim(adjustl(cp_to_string(nbuf)))//") available from the "// &
367 "binary restart file <"//trim(binary_restart_file_name)// &
368 ">. The restart file information is ignored."
369 CALL print_message(message, iw, 1, 1, 1)
370 END IF
371 ! Ignore this section
372 IF (nbuf > 0) THEN
373 ! Perform dummy read
374 ALLOCATE (rbuf(3, nbuf))
375 READ (unit=input_unit, iostat=istat) rbuf(1:3, 1:nbuf)
376 IF (istat /= 0) CALL stop_read("rbuf(1:3,1:nbuf) -> "//prefix// &
377 " coordinates (IOSTAT = "// &
378 trim(adjustl(cp_to_string(istat)))//")", &
379 input_unit)
380 DEALLOCATE (rbuf)
381 ALLOCATE (ibuf(nbuf))
382 READ (unit=input_unit, iostat=istat) ibuf(1:nbuf)
383 IF (istat /= 0) CALL stop_read("ibuf(1:nparticle) -> atomic indices of the "// &
384 trim(section_name)//" (IOSTAT = "// &
385 trim(adjustl(cp_to_string(istat)))//")", &
386 input_unit)
387 DEALLOCATE (ibuf)
388 END IF
389 exit_routine = .true.
390 ELSE
391 IF (iw > 0) THEN
392 WRITE (unit=iw, fmt="(T2,A,T71,I10)") &
393 "Number of "//prefix//" particles:", nparticle
394 END IF
395 IF (nparticle == 0) exit_routine = .true.
396 END IF
397 ELSE
398 CALL cp_abort(__location__, &
399 "Section label <"//trim(section_label)//"> read from the "// &
400 "binary restart file <"//trim(binary_restart_file_name)// &
401 "> does not match the requested section name <"// &
402 trim(section_name)//">.")
403 END IF
404 END IF
405
406 CALL para_env%bcast(exit_routine)
407 IF (exit_routine) THEN
408 IF (para_env%is_source()) CALL close_file(unit_number=input_unit, &
409 keep_preconnection=.true.)
410 CALL timestop(handle)
411 RETURN
412 END IF
413
414 cpassert(nparticle > 0)
415
416 ALLOCATE (rbuf(3, nparticle))
417
418 IF (para_env%is_source()) THEN
419 READ (unit=input_unit, iostat=istat) rbuf(1:3, 1:nparticle)
420 IF (istat /= 0) CALL stop_read("rbuf(1:3,1:nparticle) -> "//prefix// &
421 " coordinates (IOSTAT = "// &
422 trim(adjustl(cp_to_string(istat)))//")", &
423 input_unit)
424 END IF
425 CALL para_env%bcast(rbuf)
426
427 DO iparticle = 1, nparticle
428 particle_set(iparticle)%r(1:3) = rbuf(1:3, iparticle)
429 END DO
430
431 DEALLOCATE (rbuf)
432
433 ALLOCATE (ibuf(nparticle))
434
435 IF (para_env%is_source()) THEN
436 READ (unit=input_unit, iostat=istat) ibuf(1:nparticle)
437 IF (istat /= 0) CALL stop_read("ibuf(1:nparticle) -> atomic indices of the "// &
438 trim(section_name)//" (IOSTAT = "// &
439 trim(adjustl(cp_to_string(istat)))//")", &
440 input_unit)
441 END IF
442
443 CALL para_env%bcast(ibuf)
444
445 DO iparticle = 1, nparticle
446 particle_set(iparticle)%atom_index = ibuf(iparticle)
447 END DO
448
449 DEALLOCATE (ibuf)
450
451 IF (iw > 0) THEN
452 WRITE (unit=iw, fmt="(T2,A)") &
453 "BEGIN of "//trim(adjustl(section_name))// &
454 " section data [Angstrom] read in binary format from file "// &
455 trim(binary_restart_file_name)
456 DO iparticle = 1, nparticle
457 WRITE (unit=iw, fmt="(T2,A2,3(1X,ES25.16),1X,I0)") &
458 trim(adjustl(particle_set(iparticle)%atomic_kind%name)), &
459 particle_set(iparticle)%r(1:3)*angstrom, &
460 particle_set(iparticle)%atom_index
461 END DO
462 WRITE (unit=iw, fmt="(T2,A)") &
463 "END of "//trim(adjustl(section_name))// &
464 " section data [Angstrom] read from binary restart file "// &
465 trim(binary_restart_file_name)
466 END IF
467
468 IF (para_env%is_source()) CALL close_file(unit_number=input_unit, &
469 keep_preconnection=.true.)
470
471 binary_file_read = .true.
472
473 CALL timestop(handle)
474
475 END SUBROUTINE read_binary_cs_coordinates
476
477! **************************************************************************************************
478!> \brief Read the input section &VELOCITY, &CORE_VELOCITY, or
479!> &SHELL_VELOCITY from an external file written in binary format.
480!> \param prefix ...
481!> \param particle_set ...
482!> \param root_section ...
483!> \param para_env ...
484!> \param subsys_section ...
485!> \param binary_file_read ...
486!> \par History
487!> - Creation (17.02.2011,MK)
488!> \author Matthias Krack (MK)
489!> \version 1.0
490! **************************************************************************************************
491 SUBROUTINE read_binary_velocities(prefix, particle_set, root_section, para_env, &
492 subsys_section, binary_file_read)
493
494 CHARACTER(LEN=*), INTENT(IN) :: prefix
495 TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
496 TYPE(section_vals_type), POINTER :: root_section
497 TYPE(mp_para_env_type), POINTER :: para_env
498 TYPE(section_vals_type), POINTER :: subsys_section
499 LOGICAL, INTENT(OUT) :: binary_file_read
500
501 CHARACTER(LEN=*), PARAMETER :: routinen = 'read_binary_velocities'
502
503 CHARACTER(LEN=default_path_length) :: binary_restart_file_name, message
504 CHARACTER(LEN=default_string_length) :: section_label, section_name
505 INTEGER :: handle, i, input_unit, iparticle, istat, &
506 iw, nbuf, nparticle
507 LOGICAL :: have_velocities
508 REAL(kind=dp), ALLOCATABLE, DIMENSION(:, :) :: rbuf
509 TYPE(cp_logger_type), POINTER :: logger
510
511 CALL timeset(routinen, handle)
512
513 NULLIFY (logger)
514 cpassert(ASSOCIATED(root_section))
515 cpassert(ASSOCIATED(para_env))
516 cpassert(ASSOCIATED(subsys_section))
517 logger => cp_get_default_logger()
518
519 binary_file_read = .false.
520
521 CALL section_vals_val_get(root_section, "EXT_RESTART%BINARY_RESTART_FILE_NAME", &
522 c_val=binary_restart_file_name)
523
524 IF (trim(adjustl(binary_restart_file_name)) == "") THEN
525 CALL timestop(handle)
526 RETURN
527 END IF
528
529 iw = cp_print_key_unit_nr(logger, subsys_section, "PRINT%TOPOLOGY_INFO/XYZ_INFO", &
530 extension=".subsysLog")
531
532 IF (len_trim(prefix) == 0) THEN
533 section_name = "VELOCITIES"
534 ELSE
535 section_name = prefix//" VELOCITIES"
536 END IF
537
538 have_velocities = .false.
539
540 IF (ASSOCIATED(particle_set)) THEN
541 nparticle = SIZE(particle_set)
542 ELSE
543 nparticle = 0
544 END IF
545
546 ! Open binary restart file at last position and check if there are
547 ! velocities available
548 IF (para_env%is_source()) THEN
549 CALL open_file(file_name=binary_restart_file_name, &
550 file_status="OLD", &
551 file_form="UNFORMATTED", &
552 file_action="READWRITE", &
553 file_position="ASIS", &
554 unit_number=input_unit, &
555 debug=iw)
556 DO
557 READ (unit=input_unit, iostat=istat) section_label, nbuf
558 IF (istat /= 0) CALL stop_read("section_label, nbuf -> "//trim(section_label)//", "// &
559 trim(adjustl(cp_to_string(nbuf)))// &
560 " (IOSTAT = "//trim(adjustl(cp_to_string(istat)))//"). "// &
561 "Section "//trim(adjustl(section_name))//" was expected.", &
562 input_unit)
563 IF (index(section_label, "THERMOSTAT") > 0) THEN
564 IF (nbuf > 0) THEN
565 ! Ignore thermostat information
566 ALLOCATE (rbuf(nbuf, 1))
567 ! Perform dummy read
568 DO i = 1, 4
569 READ (unit=input_unit, iostat=istat) rbuf(1:nbuf, 1)
570 IF (istat /= 0) CALL stop_read("rbuf(1:nbuf,1) -> "// &
571 trim(adjustl(section_label))// &
572 " (IOSTAT = "//trim(adjustl(cp_to_string(istat)))//")", &
573 input_unit)
574 END DO
575 DEALLOCATE (rbuf)
576 IF (iw > 0) THEN
577 message = "INFO: Ignoring section <"//trim(adjustl(section_label))// &
578 "> from binary restart file <"//trim(binary_restart_file_name)//">."
579 CALL print_message(message, iw, 1, 1, 1)
580 END IF
581 END IF
582 cycle
583 ELSE IF (index(section_label, "VELOCIT") == 0) THEN
584 CALL cp_abort(__location__, &
585 "Section label <"//trim(section_label)//"> read from the "// &
586 "binary restart file <"//trim(binary_restart_file_name)// &
587 "> does not match the requested section name <"// &
588 trim(section_name)//">.")
589 ELSE
590 IF (nbuf > 0) have_velocities = .true.
591 EXIT
592 END IF
593 END DO
594 END IF
595
596 CALL para_env%bcast(nbuf)
597 CALL para_env%bcast(have_velocities)
598
599 IF (have_velocities) THEN
600
601 ALLOCATE (rbuf(3, nbuf))
602
603 IF (para_env%is_source()) THEN
604 READ (unit=input_unit, iostat=istat) rbuf(1:3, 1:nbuf)
605 IF (istat /= 0) CALL stop_read("rbuf(1:3,1:nbuf) -> "// &
606 trim(adjustl(section_name))// &
607 " (IOSTAT = "//trim(adjustl(cp_to_string(istat)))//")", &
608 input_unit)
609 END IF
610
611 IF (nbuf == nparticle) THEN
612 CALL para_env%bcast(rbuf)
613 DO iparticle = 1, nparticle
614 particle_set(iparticle)%v(1:3) = rbuf(1:3, iparticle)
615 END DO
616 ELSE
617 IF (iw > 0) THEN
618 message = "INFO: The requested number of "//trim(adjustl(section_name))// &
619 " ("//trim(adjustl(cp_to_string(nparticle)))//") does not match the "// &
620 "number ("//trim(adjustl(cp_to_string(nbuf)))//") available from the "// &
621 "binary restart file <"//trim(binary_restart_file_name)// &
622 ">. The restart file information is ignored."
623 CALL print_message(message, iw, 1, 1, 1)
624 END IF
625 END IF
626
627 DEALLOCATE (rbuf)
628
629 END IF
630
631 IF (nbuf == nparticle) THEN
632 IF (iw > 0) THEN
633 WRITE (unit=iw, fmt="(T2,A)") &
634 "BEGIN of "//trim(adjustl(section_name))// &
635 " section data [a.u.] read in binary format from file "// &
636 trim(binary_restart_file_name)
637 IF (have_velocities) THEN
638 DO iparticle = 1, nparticle
639 WRITE (unit=iw, fmt="(T2,A2,3(1X,ES25.16))") &
640 trim(adjustl(particle_set(iparticle)%atomic_kind%name)), &
641 particle_set(iparticle)%v(1:3)
642 END DO
643 ELSE
644 WRITE (unit=iw, fmt="(A)") &
645 "# No "//trim(adjustl(section_name))//" available"
646 END IF
647 WRITE (unit=iw, fmt="(T2,A)") &
648 "END of "//trim(adjustl(section_name))// &
649 " section data [a.u.] read from binary restart file "// &
650 trim(binary_restart_file_name)
651 END IF
652 binary_file_read = .true.
653 END IF
654
655 IF (para_env%is_source()) CALL close_file(unit_number=input_unit, &
656 keep_preconnection=.true.)
657
658 CALL timestop(handle)
659
660 END SUBROUTINE read_binary_velocities
661
662! **************************************************************************************************
663!> \brief Read the input section &THERMOSTAT for Nose thermostats from an
664!> external file written in binary format.
665!> \param prefix ...
666!> \param nhc ...
667!> \param binary_restart_file_name ...
668!> \param restart ...
669!> \param para_env ...
670!> \par History
671!> - Creation (28.02.2011,MK)
672!> \author Matthias Krack (MK)
673!> \version 1.0
674! **************************************************************************************************
675 SUBROUTINE read_binary_thermostats_nose(prefix, nhc, binary_restart_file_name, &
676 restart, para_env)
677
678 CHARACTER(LEN=*), INTENT(IN) :: prefix
679 TYPE(lnhc_parameters_type), POINTER :: nhc
680 CHARACTER(LEN=*), INTENT(IN) :: binary_restart_file_name
681 LOGICAL, INTENT(OUT) :: restart
682 TYPE(mp_para_env_type), POINTER :: para_env
683
684 CHARACTER(LEN=*), PARAMETER :: routinen = 'read_binary_thermostats_nose'
685
686 CHARACTER(LEN=default_string_length) :: section_label, section_name
687 INTEGER :: handle, i, idx, input_unit, istat, j, &
688 nhc_size, output_unit
689 LOGICAL :: debug
690 REAL(kind=dp), ALLOCATABLE, DIMENSION(:) :: rbuf
691 TYPE(cp_logger_type), POINTER :: logger
692
693 CALL timeset(routinen, handle)
694
695 cpassert(ASSOCIATED(nhc))
696 cpassert(ASSOCIATED(para_env))
697
698 ! Set to .TRUE. for debug mode, i.e. all data read are written to stdout
699 NULLIFY (logger)
700 logger => cp_get_default_logger()
701 output_unit = cp_logger_get_default_io_unit(logger)
702
703 IF (logger%iter_info%print_level >= debug_print_level) THEN
704 debug = .true.
705 ELSE
706 debug = .false.
707 END IF
708
709 restart = .false.
710
711 section_name = prefix//" THERMOSTATS"
712
713 ! Open binary restart file at last position
714 IF (para_env%is_source()) THEN
715 CALL open_file(file_name=binary_restart_file_name, &
716 file_status="OLD", &
717 file_form="UNFORMATTED", &
718 file_action="READWRITE", &
719 file_position="ASIS", &
720 unit_number=input_unit)
721 READ (unit=input_unit, iostat=istat) section_label, nhc_size
722 IF (istat /= 0) CALL stop_read("nhc_size (IOSTAT = "// &
723 trim(adjustl(cp_to_string(istat)))//")", &
724 input_unit)
725 IF (index(section_label, "THERMOSTAT") == 0) THEN
726 CALL cp_abort(__location__, &
727 "Section label <"//trim(section_label)//"> read from the "// &
728 "binary restart file <"//trim(binary_restart_file_name)// &
729 "> does not match the requested section name <"// &
730 trim(section_name)//">.")
731 END IF
732 IF (debug .AND. output_unit > 0) THEN
733 WRITE (unit=output_unit, fmt="(T2,A,/,T2,A,I0)") &
734 "BEGIN of "//trim(adjustl(section_label))// &
735 " section data read in binary format from file "// &
736 trim(binary_restart_file_name), &
737 "# nhc_size = ", nhc_size
738 END IF
739 END IF
740
741 CALL para_env%bcast(nhc_size)
742
743 IF (nhc_size > 0) THEN
744
745 ALLOCATE (rbuf(nhc_size))
746 rbuf(:) = 0.0_dp
747
748 ! Read NHC section &COORD
749 IF (para_env%is_source()) THEN
750 READ (unit=input_unit, iostat=istat) rbuf(1:nhc_size)
751 IF (istat /= 0) CALL stop_read("eta -> rbuf (IOSTAT = "// &
752 trim(adjustl(cp_to_string(istat)))//")", &
753 input_unit)
754 IF (debug .AND. output_unit > 0) THEN
755 WRITE (unit=output_unit, fmt="(T2,A,/,(4(1X,ES25.16)))") &
756 "&COORD", rbuf(1:nhc_size)
757 END IF
758 END IF
759 CALL para_env%bcast(rbuf)
760 DO i = 1, SIZE(nhc%nvt, 2)
761 idx = (nhc%map_info%index(i) - 1)*nhc%nhc_len
762 DO j = 1, SIZE(nhc%nvt, 1)
763 idx = idx + 1
764 nhc%nvt(j, i)%eta = rbuf(idx)
765 END DO
766 END DO
767
768 ! Read NHC section &VELOCITY
769 IF (para_env%is_source()) THEN
770 READ (unit=input_unit, iostat=istat) rbuf(1:nhc_size)
771 IF (istat /= 0) CALL stop_read("veta -> rbuf (IOSTAT = "// &
772 trim(adjustl(cp_to_string(istat)))//")", &
773 input_unit)
774 IF (debug .AND. output_unit > 0) THEN
775 WRITE (unit=output_unit, fmt="(T2,A,/,(4(1X,ES25.16)))") &
776 "&VELOCITY", rbuf(1:nhc_size)
777 END IF
778 END IF
779 CALL para_env%bcast(rbuf)
780 DO i = 1, SIZE(nhc%nvt, 2)
781 idx = (nhc%map_info%index(i) - 1)*nhc%nhc_len
782 DO j = 1, SIZE(nhc%nvt, 1)
783 idx = idx + 1
784 nhc%nvt(j, i)%v = rbuf(idx)
785 END DO
786 END DO
787
788 ! Read NHC section &MASS
789 IF (para_env%is_source()) THEN
790 READ (unit=input_unit, iostat=istat) rbuf(1:nhc_size)
791 IF (istat /= 0) CALL stop_read("mnhc -> rbuf (IOSTAT = "// &
792 trim(adjustl(cp_to_string(istat)))//")", &
793 input_unit)
794 IF (debug .AND. output_unit > 0) THEN
795 WRITE (unit=output_unit, fmt="(T2,A,/,(4(1X,ES25.16)))") &
796 "&MASS:", rbuf(1:nhc_size)
797 END IF
798 END IF
799 CALL para_env%bcast(rbuf)
800 DO i = 1, SIZE(nhc%nvt, 2)
801 idx = (nhc%map_info%index(i) - 1)*nhc%nhc_len
802 DO j = 1, SIZE(nhc%nvt, 1)
803 idx = idx + 1
804 nhc%nvt(j, i)%mass = rbuf(idx)
805 END DO
806 END DO
807
808 ! Read NHC section &FORCE
809 IF (para_env%is_source()) THEN
810 READ (unit=input_unit, iostat=istat) rbuf(1:nhc_size)
811 IF (istat /= 0) CALL stop_read("fnhc -> rbuf (IOSTAT = "// &
812 trim(adjustl(cp_to_string(istat)))//")", &
813 input_unit)
814 IF (debug .AND. output_unit > 0) THEN
815 WRITE (unit=output_unit, fmt="(T2,A,/,(4(1X,ES25.16)))") &
816 "&FORCE", rbuf(1:nhc_size)
817 END IF
818 END IF
819 CALL para_env%bcast(rbuf)
820 DO i = 1, SIZE(nhc%nvt, 2)
821 idx = (nhc%map_info%index(i) - 1)*nhc%nhc_len
822 DO j = 1, SIZE(nhc%nvt, 1)
823 idx = idx + 1
824 nhc%nvt(j, i)%f = rbuf(idx)
825 END DO
826 END DO
827
828 DEALLOCATE (rbuf)
829
830 restart = .true.
831
832 END IF
833
834 IF (para_env%is_source()) THEN
835 IF (debug .AND. output_unit > 0) THEN
836 WRITE (unit=output_unit, fmt="(T2,A)") &
837 "END of"//trim(adjustl(section_label))// &
838 " section data read in binary format from file "// &
839 trim(binary_restart_file_name)
840 END IF
841 CALL close_file(unit_number=input_unit, &
842 keep_preconnection=.true.)
843 END IF
844
845 CALL timestop(handle)
846
847 END SUBROUTINE read_binary_thermostats_nose
848
849! **************************************************************************************************
850!> \brief Print an error message and stop the program execution in case of a
851!> read error.
852!> \param object ...
853!> \param unit_number ...
854!> \par History
855!> - Creation (15.02.2011,MK)
856!> \author Matthias Krack (MK)
857!> \note
858!> object : Name of the data object for which I/O operation failed
859!> unit_number: Logical unit number of the file read from
860! **************************************************************************************************
861 SUBROUTINE stop_read(object, unit_number)
862 CHARACTER(LEN=*), INTENT(IN) :: object
863 INTEGER, INTENT(IN) :: unit_number
864
865 CHARACTER(LEN=2*default_path_length) :: message
866 CHARACTER(LEN=default_path_length) :: file_name
867 LOGICAL :: file_exists
868
869 IF (unit_number >= 0) THEN
870 INQUIRE (unit=unit_number, exist=file_exists)
871 ELSE
872 file_exists = .false.
873 END IF
874 IF (file_exists) THEN
875 INQUIRE (unit=unit_number, name=file_name)
876 WRITE (unit=message, fmt="(A)") &
877 "An error occurred reading data object <"//trim(adjustl(object))// &
878 "> from file <"//trim(adjustl(file_name))//">"
879 ELSE
880 WRITE (unit=message, fmt="(A,I0,A)") &
881 "Could not read data object <"//trim(adjustl(object))// &
882 "> from logical unit ", unit_number, ". The I/O unit does not exist."
883 END IF
884
885 cpabort(message)
886
887 END SUBROUTINE stop_read
888
889END MODULE input_cp2k_binary_restarts
idx
static GRID_HOST_DEVICE int idx(const orbital a)
Return coset index of given orbital angular momentum.
Definition grid_common.h:153
cp_log_handling::cp_to_string
Definition cp_log_handling.F:90
cp_files
Utility routines to open and close files. Tracking of preconnections.
Definition cp_files.F:16
cp_files::open_file
subroutine, public open_file(file_name, file_status, file_form, file_action, file_position, file_pad, unit_number, debug, skip_get_unit_number, file_access)
Opens the requested file using a free unit number.
Definition cp_files.F:308
cp_files::close_file
subroutine, public close_file(unit_number, file_status, keep_preconnection)
Close an open file given by its logical unit number. Optionally, keep the file and unit preconnected.
Definition cp_files.F:119
cp_files::file_exists
logical function, public file_exists(file_name)
Checks if file exists, considering also the file discovery mechanism.
Definition cp_files.F:494
cp_log_handling
various routines to log and control the output. The idea is that decisions about where to log should ...
Definition cp_log_handling.F:41
cp_log_handling::cp_logger_get_default_io_unit
integer function, public cp_logger_get_default_io_unit(logger)
returns the unit nr for the ionode (-1 on all other processors) skips as well checks if the procs cal...
Definition cp_log_handling.F:515
cp_log_handling::cp_get_default_logger
type(cp_logger_type) function, pointer, public cp_get_default_logger()
returns the default logger
Definition cp_log_handling.F:234
cp_output_handling
routines to handle the output, The idea is to remove the decision of wheter to output and what to out...
Definition cp_output_handling.F:25
cp_output_handling::debug_print_level
integer, parameter, public debug_print_level
Definition cp_output_handling.F:73
cp_output_handling::cp_print_key_unit_nr
integer function, public cp_print_key_unit_nr(logger, basis_section, print_key_path, extension, middle_name, local, log_filename, ignore_should_output, file_form, file_position, file_action, file_status, do_backup, on_file, is_new_file, mpi_io, fout)
...
Definition cp_output_handling.F:803
extended_system_types
Lumps all possible extended system variables into one type for easy access and passing.
Definition extended_system_types.F:17
input_cp2k_binary_restarts
Routines to read the binary restart file of CP2K.
Definition input_cp2k_binary_restarts.F:15
input_cp2k_binary_restarts::read_binary_thermostats_nose
subroutine, public read_binary_thermostats_nose(prefix, nhc, binary_restart_file_name, restart, para_env)
Read the input section &THERMOSTAT for Nose thermostats from an external file written in binary forma...
Definition input_cp2k_binary_restarts.F:677
input_cp2k_binary_restarts::read_binary_coordinates
subroutine, public read_binary_coordinates(topology, root_section, para_env, subsys_section, binary_file_read)
Read the input section &COORD from an external file written in binary format.
Definition input_cp2k_binary_restarts.F:70
input_cp2k_binary_restarts::read_binary_velocities
subroutine, public read_binary_velocities(prefix, particle_set, root_section, para_env, subsys_section, binary_file_read)
Read the input section &VELOCITY, &CORE_VELOCITY, or &SHELL_VELOCITY from an external file written in...
Definition input_cp2k_binary_restarts.F:493
input_cp2k_binary_restarts::read_binary_cs_coordinates
subroutine, public read_binary_cs_coordinates(prefix, particle_set, root_section, subsys_section, binary_file_read)
Read the input section &CORE_COORD or &SHELL_COORD from an external file written in binary format.
Definition input_cp2k_binary_restarts.F:297
input_section_types
objects that represent the structure of input sections and the data contained in an input section
Definition input_section_types.F:15
input_section_types::section_vals_val_get
subroutine, public section_vals_val_get(section_vals, keyword_name, i_rep_section, i_rep_val, n_rep_val, val, l_val, i_val, r_val, c_val, l_vals, i_vals, r_vals, c_vals, explicit)
returns the requested value
Definition input_section_types.F:1040
kinds
Defines the basic variable types.
Definition kinds.F:23
kinds::dp
integer, parameter, public dp
Definition kinds.F:34
kinds::default_string_length
integer, parameter, public default_string_length
Definition kinds.F:57
kinds::default_path_length
integer, parameter, public default_path_length
Definition kinds.F:58
message_passing
Interface to the message passing library MPI.
Definition message_passing.F:23
particle_types
Define the data structure for the particle information.
Definition particle_types.F:19
physcon
Definition of physical constants:
Definition physcon.F:68
physcon::angstrom
real(kind=dp), parameter, public angstrom
Definition physcon.F:144
print_messages
Perform an abnormal program termination.
Definition print_messages.F:21
print_messages::print_message
subroutine, public print_message(message, output_unit, declev, before, after)
Perform a basic blocking of the text in message and print it optionally decorated with a frame of sta...
Definition print_messages.F:56
string_table
generates a unique id number for a string (str2id) that can be used two compare two strings....
Definition string_table.F:22
string_table::s2s
character(len=default_string_length) function, public s2s(str)
converts a string in a string of default_string_length
Definition string_table.F:141
string_table::str2id
integer function, public str2id(str)
returns a unique id for a given string, and stores the string for later retrieval using the id.
Definition string_table.F:72
string_table::id2str
character(len=default_string_length) function, public id2str(id)
returns the string associated with a given id
Definition string_table.F:115
topology_types
Definition topology_types.F:18
topology
Control for reading in different topologies and coordinates.
Definition topology.F:13
cp_log_handling::cp_logger_type
type of a logger, at the moment it contains just a print level starting at which level it should be l...
Definition cp_log_handling.F:140
extended_system_types::lnhc_parameters_type
Definition extended_system_types.F:75
input_section_types::section_vals_type
stores the values of a section
Definition input_section_types.F:126
message_passing::mp_para_env_type
stores all the informations relevant to an mpi environment
Definition message_passing.F:763
particle_types::particle_type
Definition particle_types.F:35
topology_types::atom_info_type
Definition topology_types.F:35
topology_types::topology_parameters_type
Definition topology_types.F:142