(git:374b731)
Loading...
Searching...
No Matches
pint_io.F
Go to the documentation of this file.
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 I/O subroutines for pint_env
10!> \author Lukasz Walewski
11!> \date 2009-06-04
12! **************************************************************************************************
13MODULE pint_io
14
15 USE cell_types, ONLY: cell_type
16 USE cp_log_handling, ONLY: cp_get_default_logger,&
17 cp_logger_get_default_unit_nr,&
18 cp_logger_type
19 USE cp_output_handling, ONLY: cp_p_file,&
20 cp_print_key_finished_output,&
21 cp_print_key_should_output,&
22 cp_print_key_unit_nr
23 USE cp_subsys_types, ONLY: cp_subsys_get,&
24 cp_subsys_type
25 USE cp_units, ONLY: cp_unit_from_cp2k
26 USE f77_interface, ONLY: f_env_add_defaults,&
27 f_env_rm_defaults,&
28 f_env_type
29 USE force_env_types, ONLY: force_env_get
30 USE input_constants, ONLY: dump_atomic,&
31 dump_dcd,&
32 dump_dcd_aligned_cell,&
33 dump_xmol
34 USE input_section_types, ONLY: section_vals_get_subs_vals,&
35 section_vals_type,&
36 section_vals_val_get
37 USE kinds, ONLY: default_string_length,&
38 dp
39 USE machine, ONLY: m_flush
40 USE particle_list_types, ONLY: particle_list_type
41 USE particle_methods, ONLY: write_particle_coordinates
42 USE pint_public, ONLY: pint_com_pos
43 USE pint_transformations, ONLY: pint_u2x
44 USE pint_types, ONLY: e_conserved_id,&
45 e_kin_thermo_id,&
46 e_kin_virial_id,&
47 e_potential_id,&
48 pint_env_type
49#include "../base/base_uses.f90"
50
51 IMPLICIT NONE
52
53 PRIVATE
54
55 LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .true.
56 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'pint_io'
57
58 PUBLIC :: pint_write_line
59 PUBLIC :: pint_write_centroids
60 PUBLIC :: pint_write_trajectory
61 PUBLIC :: pint_write_com
62 PUBLIC :: pint_write_ener
63 PUBLIC :: pint_write_action
64 PUBLIC :: pint_write_step_info
65 PUBLIC :: pint_write_rgyr
66
67CONTAINS
68
69! ***************************************************************************
70!> \brief Writes out a line of text to the default output unit.
71!> \param line ...
72!> \date 2009-07-10
73!> \author Lukasz Walewski
74! **************************************************************************************************
75 SUBROUTINE pint_write_line(line)
76
77 CHARACTER(len=*), INTENT(IN) :: line
78
79 CHARACTER(len=default_string_length) :: my_label
80 INTEGER :: unit_nr
81 TYPE(cp_logger_type), POINTER :: logger
82
83 NULLIFY (logger)
84 logger => cp_get_default_logger()
85 my_label = "PINT|"
86
87 IF (logger%para_env%is_source()) THEN
88 unit_nr = cp_logger_get_default_unit_nr(logger)
89 WRITE (unit_nr, '(T2,A)') trim(my_label)//" "//trim(line)
90 END IF
91
92 END SUBROUTINE pint_write_line
93
94! ***************************************************************************
95!> \brief Write out the trajectory of the centroid (positions and velocities)
96!> \param pint_env ...
97!> \par History
98!> various bug fixes - hforbert
99!> 2010-11-25 rewritten, added support for velocity printing,
100!> calc of the stddev of the beads turned off [lwalewski]
101!> \author fawzi
102! **************************************************************************************************
103 SUBROUTINE pint_write_centroids(pint_env)
104 TYPE(pint_env_type), INTENT(IN) :: pint_env
105
106 CHARACTER(len=*), PARAMETER :: routinen = 'pint_write_centroids'
107 INTEGER, PARAMETER :: n_ids = 2, pos_id = 1, vel_id = 2
108
109 CHARACTER(len=default_string_length) :: ext, form, my_middle_name, unit_str
110 CHARACTER(len=default_string_length), DIMENSION(2) :: content_id, middle_name, sect_path, title
111 INTEGER :: handle, handle1, iat, ib, id, idim, &
112 idir, ierr, outformat, should_output, &
113 unit_nr
114 LOGICAL :: new_file, print_kind
115 REAL(kind=dp) :: nb, ss, unit_conv, vv
116 TYPE(cell_type), POINTER :: cell
117 TYPE(cp_logger_type), POINTER :: logger
118 TYPE(cp_subsys_type), POINTER :: subsys
119 TYPE(f_env_type), POINTER :: f_env
120 TYPE(particle_list_type), POINTER :: particles
121 TYPE(section_vals_type), POINTER :: print_key
122
123 CALL timeset(routinen, handle1)
124
125 sect_path(pos_id) = "MOTION%PINT%PRINT%CENTROID_POS"
126 sect_path(vel_id) = "MOTION%PINT%PRINT%CENTROID_VEL"
127 middle_name(pos_id) = "centroid-pos"
128 middle_name(vel_id) = "centroid-vel"
129 content_id(pos_id) = "POS"
130 content_id(vel_id) = "VEL"
131 WRITE (unit=title(pos_id), fmt="(A,I8,A,F20.10)") &
132 " i =", pint_env%iter, &
133 ", E =", sum(pint_env%e_pot_bead)*pint_env%propagator%physpotscale
134 WRITE (unit=title(vel_id), fmt="(A,I8,A,F20.10,A,F20.10)") &
135 " i =", pint_env%iter, &
136 ", E_trm =", pint_env%energy(e_kin_thermo_id), &
137 ", E_vir =", pint_env%energy(e_kin_virial_id)
138
139 NULLIFY (logger)
140 logger => cp_get_default_logger()
141
142 CALL pint_u2x(pint_env, ux=pint_env%uv, x=pint_env%v)
143
144 ! iterate over the properties that we know how to print
145 ! (currently positions and velocities)
146 DO id = 1, n_ids
147
148 print_key => section_vals_get_subs_vals(pint_env%input, &
149 trim(sect_path(id)))
150
151 should_output = cp_print_key_should_output( &
152 iteration_info=logger%iter_info, &
153 basis_section=print_key)
154 IF (.NOT. btest(should_output, cp_p_file)) CONTINUE
155
156 print_kind = .false.
157
158 ! get units of measure for output (if available)
159 CALL section_vals_val_get(print_key, "UNIT", &
160 c_val=unit_str)
161 unit_conv = cp_unit_from_cp2k(1.0_dp, trim(unit_str))
162
163 ! get the format for output
164 CALL section_vals_val_get(print_key, "FORMAT", i_val=outformat)
165
166 SELECT CASE (outformat)
167 CASE (dump_dcd, dump_dcd_aligned_cell)
168 form = "UNFORMATTED"
169 ext = ".dcd"
170 CASE (dump_atomic)
171 form = "FORMATTED"
172 ext = ""
173 CASE (dump_xmol)
174 CALL section_vals_val_get(print_key, "PRINT_ATOM_KIND", &
175 l_val=print_kind)
176 form = "FORMATTED"
177 ext = ".xyz"
178 CASE default
179 cpabort("")
180 END SELECT
181
182 NULLIFY (f_env, cell, subsys)
183 CALL f_env_add_defaults(f_env_id=pint_env%replicas%f_env_id, &
184 f_env=f_env, handle=handle)
185 CALL force_env_get(force_env=f_env%force_env, &
186 cell=cell, subsys=subsys)
187 CALL cp_subsys_get(subsys, particles=particles)
188
189 ! calculate and copy the requested property
190 ! to the particles structure
191 nb = real(pint_env%p, dp)
192 idim = 0
193 DO iat = 1, pint_env%ndim/3
194 DO idir = 1, 3
195 idim = idim + 1
196 ss = 0.0_dp
197 vv = 0.0_dp
198! ss2=0.0_dp
199 DO ib = 1, pint_env%p
200 ss = ss + pint_env%x(ib, idim)
201 vv = vv + pint_env%v(ib, idim)
202! ss2=ss2+pint_env%x(ib,idim)**2
203 END DO
204 particles%els(iat)%r(idir) = ss/nb
205 particles%els(iat)%v(idir) = vv/nb
206! particles%els(iat)%v(idir)=SQRT(ss2/nb-(ss/nb)**2)
207 END DO
208 END DO
209
210 ! set up the output unit number and file name
211 ! for the current property
212 my_middle_name = trim(middle_name(id))
213 unit_nr = cp_print_key_unit_nr(logger=logger, &
214 basis_section=print_key, print_key_path="", &
215 extension=trim(ext), middle_name=trim(my_middle_name), &
216 local=.false., file_form=form, is_new_file=new_file)
217
218 ! don't write the 0-th frame if the file already exists
219 IF (.NOT. new_file .AND. (pint_env%iter .LE. pint_env%first_step)) THEN
220 CALL cp_print_key_finished_output(unit_nr, logger, &
221 print_key)
222 CONTINUE
223 END IF
224
225 ! actually perform the i/o - on the ionode only
226 IF (unit_nr > 0) THEN
227
228 CALL write_particle_coordinates( &
229 particles%els, &
230 iunit=unit_nr, &
231 output_format=outformat, &
232 content=content_id(id), &
233 title=title(id), &
234 cell=cell, &
235 unit_conv=unit_conv, &
236 print_kind=print_kind)
237
238 CALL cp_print_key_finished_output(unit_nr, logger, &
239 print_key, "", local=.false.)
240
241 END IF
242
243 CALL f_env_rm_defaults(f_env, ierr, handle)
244 cpassert(ierr == 0)
245
246 END DO
247
248 CALL timestop(handle1)
249 END SUBROUTINE pint_write_centroids
250
251! ***************************************************************************
252!> \brief Write out the trajectory of the beads (positions and velocities)
253!> \param pint_env ...
254!> \par History
255!> 2010-11-25 added support for velocity printing [lwalewski]
256!> \author hforbert
257! **************************************************************************************************
258 SUBROUTINE pint_write_trajectory(pint_env)
259 TYPE(pint_env_type), INTENT(IN) :: pint_env
260
261 CHARACTER(len=*), PARAMETER :: routinen = 'pint_write_trajectory'
262 INTEGER, PARAMETER :: force_id = 3, n_ids = 3, pos_id = 1, &
263 vel_id = 2
264
265 CHARACTER(len=default_string_length) :: ext, form, ib_str, my_middle_name, &
266 title, unit_str
267 CHARACTER(len=default_string_length), DIMENSION(3) :: content_id, middle_name, sect_path
268 INTEGER :: handle, handle1, iat, ib, id, idim, &
269 idir, ierr, imag_stride, outformat, &
270 should_output, unit_nr
271 LOGICAL :: new_file
272 REAL(kind=dp) :: unit_conv
273 TYPE(cell_type), POINTER :: cell
274 TYPE(cp_logger_type), POINTER :: logger
275 TYPE(cp_subsys_type), POINTER :: subsys
276 TYPE(f_env_type), POINTER :: f_env
277 TYPE(particle_list_type), POINTER :: particles
278 TYPE(section_vals_type), POINTER :: print_key
279
280 CALL timeset(routinen, handle1)
281
282 sect_path(pos_id) = "MOTION%PRINT%TRAJECTORY"
283 sect_path(vel_id) = "MOTION%PRINT%VELOCITIES"
284 sect_path(force_id) = "MOTION%PRINT%FORCES"
285 middle_name(pos_id) = "pos-"
286 middle_name(vel_id) = "vel-"
287 middle_name(force_id) = "force-"
288 content_id(pos_id) = "POS"
289 content_id(vel_id) = "VEL"
290 content_id(force_id) = "FORCE"
291
292 NULLIFY (logger)
293 logger => cp_get_default_logger()
294
295 CALL pint_u2x(pint_env, ux=pint_env%uv, x=pint_env%v)
296
297 ! iterate over the properties that we know how to print
298 ! (currently positions and velocities)
299 DO id = 1, n_ids
300
301 print_key => section_vals_get_subs_vals(pint_env%input, &
302 trim(sect_path(id)))
303
304 should_output = cp_print_key_should_output( &
305 iteration_info=logger%iter_info, &
306 basis_section=print_key)
307 IF (.NOT. btest(should_output, cp_p_file)) CONTINUE
308
309 ! get units of measure for output (if available)
310 CALL section_vals_val_get(print_key, "UNIT", &
311 c_val=unit_str)
312 unit_conv = cp_unit_from_cp2k(1.0_dp, trim(unit_str))
313
314 ! get the format for output
315 CALL section_vals_val_get(print_key, "FORMAT", i_val=outformat)
316
317 SELECT CASE (outformat)
318 CASE (dump_dcd, dump_dcd_aligned_cell)
319 form = "UNFORMATTED"
320 ext = ".dcd"
321 CASE (dump_atomic)
322 form = "FORMATTED"
323 ext = ""
324 CASE (dump_xmol)
325 form = "FORMATTED"
326 ext = ".xyz"
327 CASE default
328 cpabort("")
329 END SELECT
330
331 NULLIFY (f_env, cell, subsys)
332 CALL f_env_add_defaults(f_env_id=pint_env%replicas%f_env_id, &
333 f_env=f_env, handle=handle)
334 CALL force_env_get(force_env=f_env%force_env, &
335 cell=cell, subsys=subsys)
336 CALL cp_subsys_get(subsys, particles=particles)
337
338 !Get print stride for bead trajectories
339 CALL section_vals_val_get(pint_env%input, &
340 "MOTION%PINT%PRINT%IMAGINARY_TIME_STRIDE", &
341 i_val=imag_stride)
342
343 ! iterate over beads
344 DO ib = 1, pint_env%p, imag_stride
345
346 ! copy the requested property of the current bead
347 ! to the particles structure
348 idim = 0
349 DO iat = 1, pint_env%ndim/3
350 DO idir = 1, 3
351 idim = idim + 1
352 particles%els(iat)%r(idir) = pint_env%x(ib, idim)
353 particles%els(iat)%v(idir) = pint_env%v(ib, idim)
354 particles%els(iat)%f(idir) = pint_env%f(ib, idim)
355 END DO
356 END DO
357
358 ! set up the output unit number and file name
359 ! for the current property and bead
360 ib_str = ""
361 WRITE (ib_str, *) ib
362 my_middle_name = trim(middle_name(id))//trim(adjustl(ib_str))
363 unit_nr = cp_print_key_unit_nr(logger=logger, &
364 basis_section=print_key, print_key_path="", &
365 extension=trim(ext), middle_name=trim(my_middle_name), &
366 local=.false., file_form=form, is_new_file=new_file)
367
368 ! don't write the 0-th frame if the file already exists
369 IF (.NOT. new_file .AND. (pint_env%iter .LE. pint_env%first_step)) THEN
370 CALL cp_print_key_finished_output(unit_nr, logger, &
371 print_key)
372 CONTINUE
373 END IF
374
375 ! actually perform the i/o - on the ionode only
376 IF (unit_nr > 0) THEN
377
378 IF (outformat == dump_xmol) THEN
379 WRITE (unit=title, fmt="(A,I8,A,F20.10)") &
380 " i =", pint_env%iter, &
381 ", E =", pint_env%e_pot_bead(ib)
382 END IF
383
384 CALL write_particle_coordinates( &
385 particles%els, &
386 iunit=unit_nr, &
387 output_format=outformat, &
388 content=content_id(id), &
389 title=title, &
390 cell=cell, &
391 unit_conv=unit_conv)
392
393 CALL cp_print_key_finished_output(unit_nr, logger, &
394 print_key, "", local=.false.)
395
396 END IF
397
398 END DO
399
400 CALL f_env_rm_defaults(f_env, ierr, handle)
401 cpassert(ierr == 0)
402
403 END DO
404
405 CALL timestop(handle1)
406 END SUBROUTINE pint_write_trajectory
407
408! ***************************************************************************
409!> \brief Write center of mass (COM) position according to PINT%PRINT%COM
410!> \param pint_env ...
411!> \date 2010-02-17
412!> \author Lukasz Walewski
413! **************************************************************************************************
414 SUBROUTINE pint_write_com(pint_env)
415
416 TYPE(pint_env_type), INTENT(IN) :: pint_env
417
418 CHARACTER(len=default_string_length) :: stmp1, stmp2
419 INTEGER :: ic, unit_nr
420 LOGICAL :: new_file, should_output
421 REAL(kind=dp), DIMENSION(3) :: com_r
422 TYPE(cp_logger_type), POINTER :: logger
423 TYPE(section_vals_type), POINTER :: print_key
424
425 NULLIFY (logger)
426 logger => cp_get_default_logger()
427
428 ! decide whether to write anything or not
429 NULLIFY (print_key)
430 print_key => section_vals_get_subs_vals(pint_env%input, &
431 "MOTION%PINT%PRINT%COM")
432 should_output = btest(cp_print_key_should_output( &
433 iteration_info=logger%iter_info, &
434 basis_section=print_key), cp_p_file)
435 IF (.NOT. should_output) THEN
436 RETURN
437 END IF
438
439 com_r = pint_com_pos(pint_env)
440 DO ic = 1, 3
441 com_r(ic) = cp_unit_from_cp2k(com_r(ic), "angstrom")
442 END DO
443
444 unit_nr = cp_print_key_unit_nr(logger, print_key, is_new_file=new_file, &
445 middle_name="com-pos", extension=".xyz")
446
447 ! don't write the 0-th frame if the file already exists
448 IF (.NOT. new_file .AND. (pint_env%iter .LE. pint_env%first_step)) THEN
449 CALL cp_print_key_finished_output(unit_nr, logger, &
450 print_key)
451 RETURN
452 END IF
453
454 ! actually perform the i/o - on the ionode only
455 IF (unit_nr > 0) THEN
456
457 WRITE (unit_nr, '(I2)') 1
458 WRITE (stmp1, *) pint_env%iter
459 WRITE (stmp2, '(F20.10)') pint_env%energy(e_conserved_id)
460 WRITE (unit_nr, '(4A)') " Iteration = ", trim(adjustl(stmp1)), &
461 ", E_conserved = ", trim(adjustl(stmp2))
462 WRITE (unit_nr, '(A2,3(1X,F20.10))') "X ", (com_r(ic), ic=1, 3)
463
464 CALL m_flush(unit_nr)
465
466 END IF
467
468 CALL cp_print_key_finished_output(unit_nr, logger, print_key)
469
470 END SUBROUTINE pint_write_com
471
472! ***************************************************************************
473!> \brief Writes out the energies according to PINT%PRINT%ENERGY
474!> \param pint_env path integral environment
475!> \par History
476!> various bug fixes [hforbert]
477!> 2009-11-16 energy components calc moved out of here [lwalewski]
478!> \author fawzi
479! **************************************************************************************************
480 SUBROUTINE pint_write_ener(pint_env)
481 TYPE(pint_env_type), INTENT(IN) :: pint_env
482
483 INTEGER :: ndof, unit_nr
484 LOGICAL :: file_is_new
485 REAL(kind=dp) :: t, temp
486 TYPE(cp_logger_type), POINTER :: logger
487 TYPE(section_vals_type), POINTER :: print_key
488
489 NULLIFY (print_key, logger)
490 print_key => section_vals_get_subs_vals(pint_env%input, &
491 "MOTION%PINT%PRINT%ENERGY")
492 logger => cp_get_default_logger()
493 IF (btest(cp_print_key_should_output(iteration_info=logger%iter_info, &
494 basis_section=print_key), cp_p_file)) THEN
495
496 unit_nr = cp_print_key_unit_nr(logger, print_key, middle_name="energy", &
497 extension=".dat", is_new_file=file_is_new)
498
499 ! don't write the 0-th frame if the file already exists
500 IF (.NOT. file_is_new .AND. (pint_env%iter .LE. pint_env%first_step)) THEN
501 CALL cp_print_key_finished_output(unit_nr, logger, &
502 print_key)
503 RETURN
504 END IF
505
506 ! cp_print_key_unit_nr returns -1 on nodes other than logger%para_env%is_source()
507 IF (unit_nr > 0) THEN
508
509 ! please keep the format explanation up to date
510 ! keep the constant of motion the true constant of motion !
511 IF (file_is_new) THEN
512 WRITE (unit_nr, "(A8,1X,A12,1X,5(A20,1X),A12)") &
513 "# StepNr", &
514 " Time [fs]", &
515 " Kinetic [a.u.]", &
516 " VirialKin [a.u.]", &
517 " Temperature [K]", &
518 " Potential [a.u.]", &
519 " ConsQty [a.u.]", &
520 " CPU [s]"
521 END IF
522
523 t = cp_unit_from_cp2k(pint_env%t, "fs")
524
525 ndof = pint_env%p
526 IF (pint_env%first_propagated_mode .EQ. 2) THEN
527 ndof = ndof - 1
528 END IF
529 temp = cp_unit_from_cp2k(2.0_dp*pint_env%e_kin_beads/ &
530 REAL(ndof, dp)/REAL(pint_env%ndim, dp), &
531 "K")*pint_env%propagator%temp_sim2phys
532
533 WRITE (unit_nr, "(I8,1X,F12.3,1X,5(F20.9,1X),F12.1)") &
534 pint_env%iter, &
535 t, &
536 pint_env%energy(e_kin_thermo_id), &
537 pint_env%energy(e_kin_virial_id), &
538 temp, &
539 pint_env%energy(e_potential_id), &
540 pint_env%energy(e_conserved_id), &
541 pint_env%time_per_step
542 CALL m_flush(unit_nr)
543
544 END IF
545
546 CALL cp_print_key_finished_output(unit_nr, logger, print_key)
547 END IF
548
549 END SUBROUTINE pint_write_ener
550
551! ***************************************************************************
552!> \brief Writes out the actions according to PINT%PRINT%ACTION
553!> \param pint_env path integral environment
554!> \author Felix Uhl
555! **************************************************************************************************
556 SUBROUTINE pint_write_action(pint_env)
557 TYPE(pint_env_type), INTENT(IN) :: pint_env
558
559 INTEGER :: unit_nr
560 LOGICAL :: file_is_new
561 REAL(kind=dp) :: t
562 TYPE(cp_logger_type), POINTER :: logger
563 TYPE(section_vals_type), POINTER :: print_key
564
565 NULLIFY (print_key, logger)
566 print_key => section_vals_get_subs_vals(pint_env%input, &
567 "MOTION%PINT%PRINT%ACTION")
568 logger => cp_get_default_logger()
569 IF (btest(cp_print_key_should_output(iteration_info=logger%iter_info, &
570 basis_section=print_key), cp_p_file)) THEN
571
572 unit_nr = cp_print_key_unit_nr(logger, print_key, middle_name="action", &
573 extension=".dat", is_new_file=file_is_new)
574
575 ! don't write the 0-th frame if the file already exists
576 IF (.NOT. file_is_new .AND. (pint_env%iter .LE. pint_env%first_step)) THEN
577 CALL cp_print_key_finished_output(unit_nr, logger, &
578 print_key)
579 RETURN
580 END IF
581
582 ! cp_print_key_unit_nr returns -1 on nodes other than logger%para_env%is_source()
583 IF (unit_nr > 0) THEN
584
585 ! please keep the format explanation up to date
586 ! keep the constant of motion the true constant of motion !
587 IF (file_is_new) THEN
588 WRITE (unit_nr, "(A8,1X,A12,1X,2(A25,1X))") &
589 "# StepNr", &
590 " Time [fs]", &
591 " Link Action [a.u.]", &
592 " Potential Action [a.u.]"
593 END IF
594
595 t = cp_unit_from_cp2k(pint_env%t, "fs")
596
597 WRITE (unit_nr, "(I8,1X,F12.3,1X,5(F20.9,1X),F12.1)") &
598 pint_env%iter, &
599 t, &
600 pint_env%link_action, &
601 pint_env%pot_action
602 CALL m_flush(unit_nr)
603
604 END IF
605
606 CALL cp_print_key_finished_output(unit_nr, logger, print_key)
607 END IF
608
609 END SUBROUTINE pint_write_action
610
611! ***************************************************************************
612!> \brief Write step info to the output file.
613!> \param pint_env ...
614!> \date 2009-11-16
615!> \par History
616!> 2010-01-27 getting default unit nr now only on ionode [lwalewski]
617!> \author Lukasz Walewski
618! **************************************************************************************************
619 SUBROUTINE pint_write_step_info(pint_env)
620 TYPE(pint_env_type), INTENT(IN) :: pint_env
621
622 CHARACTER(len=default_string_length) :: msgstr, stmp, time_unit
623 INTEGER :: unit_nr
624 REAL(kind=dp) :: time_used
625 TYPE(cp_logger_type), POINTER :: logger
626
627 unit_nr = 0
628 NULLIFY (logger)
629 logger => cp_get_default_logger()
630
631 time_used = pint_env%time_per_step
632 time_unit = "sec"
633 IF (time_used .GE. 60.0_dp) THEN
634 time_used = time_used/60.0_dp
635 time_unit = "min"
636 END IF
637 IF (time_used .GE. 60.0_dp) THEN
638 time_used = time_used/60.0_dp
639 time_unit = "hours"
640 END IF
641 msgstr = "PINT step"
642 stmp = ""
643 WRITE (stmp, *) pint_env%iter
644 msgstr = trim(adjustl(msgstr))//" "//trim(adjustl(stmp))//" of"
645 stmp = ""
646 WRITE (stmp, *) pint_env%last_step
647 msgstr = trim(adjustl(msgstr))//" "//trim(adjustl(stmp))//" in"
648 stmp = ""
649 WRITE (stmp, '(F20.1)') time_used
650 msgstr = trim(adjustl(msgstr))//" "//trim(adjustl(stmp))
651 msgstr = trim(adjustl(msgstr))//" "//trim(adjustl(time_unit))//"."
652
653 IF (logger%para_env%is_source()) THEN
654 unit_nr = cp_logger_get_default_unit_nr(logger)
655 WRITE (unit_nr, '(T2,A)') "PINT| "//trim(adjustl(msgstr))
656 END IF
657
658 ! print out the total energy - for regtest evaluation
659 stmp = ""
660 WRITE (stmp, *) pint_env%energy(e_conserved_id)
661 msgstr = "Total energy = "//trim(adjustl(stmp))
662 IF (logger%para_env%is_source()) THEN
663 WRITE (unit_nr, '(T2,A)') "PINT| "//trim(adjustl(msgstr))
664 END IF
665
666 END SUBROUTINE pint_write_step_info
667
668! ***************************************************************************
669!> \brief Write radii of gyration according to PINT%PRINT%CENTROID_GYR
670!> \param pint_env ...
671!> \date 2011-01-07
672!> \author Lukasz Walewski
673! **************************************************************************************************
674 SUBROUTINE pint_write_rgyr(pint_env)
675
676 TYPE(pint_env_type), INTENT(IN) :: pint_env
677
678 CHARACTER(len=default_string_length) :: unit_str
679 INTEGER :: ia, ib, ic, idim, unit_nr
680 LOGICAL :: new_file, should_output
681 REAL(kind=dp) :: nb, ss, unit_conv
682 TYPE(cp_logger_type), POINTER :: logger
683 TYPE(section_vals_type), POINTER :: print_key
684
685 NULLIFY (logger)
686 logger => cp_get_default_logger()
687
688 ! decide whether to write anything or not
689 NULLIFY (print_key)
690 print_key => section_vals_get_subs_vals(pint_env%input, &
691 "MOTION%PINT%PRINT%CENTROID_GYR")
692 should_output = btest(cp_print_key_should_output( &
693 iteration_info=logger%iter_info, &
694 basis_section=print_key), cp_p_file)
695 IF (.NOT. should_output) THEN
696 RETURN
697 END IF
698
699 ! get the units conversion factor
700 CALL section_vals_val_get(print_key, "UNIT", c_val=unit_str)
701 unit_conv = cp_unit_from_cp2k(1.0_dp, trim(unit_str))
702
703 ! calculate the centroid positions
704 nb = real(pint_env%p, dp)
705 idim = 0
706 DO ia = 1, pint_env%ndim/3
707 DO ic = 1, 3
708 idim = idim + 1
709 ss = 0.0_dp
710 DO ib = 1, pint_env%p
711 ss = ss + pint_env%x(ib, idim)
712 END DO
713 pint_env%rtmp_ndim(idim) = ss/nb
714 END DO
715 END DO
716
717 ! calculate the radii of gyration
718 idim = 0
719 DO ia = 1, pint_env%ndim/3
720 ss = 0.0_dp
721 DO ic = 1, 3
722 idim = idim + 1
723 DO ib = 1, pint_env%p
724 ss = ss + (pint_env%x(ib, idim) - pint_env%rtmp_ndim(idim))**2
725 END DO
726 END DO
727 pint_env%rtmp_natom(ia) = sqrt(ss/nb)*unit_conv
728 END DO
729
730 unit_nr = cp_print_key_unit_nr(logger, print_key, is_new_file=new_file, &
731 middle_name="centroid-gyr", extension=".dat")
732
733 ! don't write the 0-th frame if the file already exists
734 IF (.NOT. new_file .AND. (pint_env%iter .LE. pint_env%first_step)) THEN
735 CALL cp_print_key_finished_output(unit_nr, logger, &
736 print_key)
737 RETURN
738 END IF
739
740 ! actually perform the i/o - on the ionode only
741 IF (unit_nr > 0) THEN
742
743 DO ia = 1, pint_env%ndim/3
744 WRITE (unit_nr, '(F20.10,1X)', advance='NO') pint_env%rtmp_natom(ia)
745 END DO
746 WRITE (unit_nr, '(A)') ""
747
748 CALL m_flush(unit_nr)
749
750 END IF
751
752 CALL cp_print_key_finished_output(unit_nr, logger, print_key)
753
754 END SUBROUTINE pint_write_rgyr
755
756END MODULE pint_io
cell_types
Handles all functions related to the CELL.
Definition cell_types.F:15
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_unit_nr
recursive integer function, public cp_logger_get_default_unit_nr(logger, local, skip_not_ionode)
asks the default unit number of the given logger. try to use cp_logger_get_unit_nr
Definition cp_log_handling.F:567
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::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
cp_output_handling::cp_print_key_finished_output
subroutine, public cp_print_key_finished_output(unit_nr, logger, basis_section, print_key_path, local, ignore_should_output, on_file, mpi_io)
should be called after you finish working with a unit obtained with cp_print_key_unit_nr,...
Definition cp_output_handling.F:1013
cp_output_handling::cp_p_file
integer, parameter, public cp_p_file
Definition cp_output_handling.F:103
cp_output_handling::cp_print_key_should_output
integer function, public cp_print_key_should_output(iteration_info, basis_section, print_key_path, used_print_key, first_time)
returns what should be done with the given property if btest(res,cp_p_store) then the property should...
Definition cp_output_handling.F:345
cp_subsys_types
types that represent a subsys, i.e. a part of the system
Definition cp_subsys_types.F:16
cp_subsys_types::cp_subsys_get
subroutine, public cp_subsys_get(subsys, ref_count, atomic_kinds, atomic_kind_set, particles, particle_set, local_particles, molecules, molecule_set, molecule_kinds, molecule_kind_set, local_molecules, para_env, colvar_p, shell_particles, core_particles, gci, multipoles, natom, nparticle, ncore, nshell, nkind, atprop, virial, results, cell)
returns information about various attributes of the given subsys
Definition cp_subsys_types.F:345
cp_units
unit conversion facility
Definition cp_units.F:30
cp_units::cp_unit_from_cp2k
real(kind=dp) function, public cp_unit_from_cp2k(value, unit_str, defaults, power)
converts from the internal cp2k units to the given unit
Definition cp_units.F:1179
f77_interface
interface to use cp2k as library
Definition f77_interface.F:20
f77_interface::f_env_add_defaults
subroutine, public f_env_add_defaults(f_env_id, f_env, handle)
adds the default environments of the f_env to the stack of the defaults, and returns a new error and ...
Definition f77_interface.F:450
f77_interface::f_env_rm_defaults
subroutine, public f_env_rm_defaults(f_env, ierr, handle)
removes the default environments of the f_env to the stack of the defaults, and sets ierr accordingly...
Definition f77_interface.F:494
force_env_types
Interface for the force calculations.
Definition force_env_types.F:18
force_env_types::force_env_get
recursive subroutine, public force_env_get(force_env, in_use, fist_env, qs_env, meta_env, fp_env, subsys, para_env, potential_energy, additional_potential, kinetic_energy, harmonic_shell, kinetic_shell, cell, sub_force_env, qmmm_env, qmmmx_env, eip_env, pwdft_env, globenv, input, force_env_section, method_name_id, root_section, mixed_env, nnp_env, embed_env)
returns various attributes about the force environment
Definition force_env_types.F:329
input_constants
collects all constants needed in input so that they can be used without circular dependencies
Definition input_constants.F:17
input_constants::dump_xmol
integer, parameter, public dump_xmol
Definition input_constants.F:375
input_constants::dump_atomic
integer, parameter, public dump_atomic
Definition input_constants.F:375
input_constants::dump_dcd_aligned_cell
integer, parameter, public dump_dcd_aligned_cell
Definition input_constants.F:375
input_constants::dump_dcd
integer, parameter, public dump_dcd
Definition input_constants.F:375
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_get_subs_vals
recursive type(section_vals_type) function, pointer, public section_vals_get_subs_vals(section_vals, subsection_name, i_rep_section, can_return_null)
returns the values of the requested subsection
Definition input_section_types.F:724
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
machine
Machine interface based on Fortran 2003 and POSIX.
Definition machine.F:17
machine::m_flush
subroutine, public m_flush(lunit)
flushes units if the &GLOBAL flag is set accordingly
Definition machine.F:106
particle_list_types
represent a simple array based list of the given type
Definition particle_list_types.F:15
particle_methods
Define methods related to particle_type.
Definition particle_methods.F:14
particle_methods::write_particle_coordinates
subroutine, public write_particle_coordinates(particle_set, iunit, output_format, content, title, cell, array, unit_conv, charge_occup, charge_beta, charge_extended, print_kind)
Should be able to write a few formats e.g. xmol, and some binary format (dcd) some format can be used...
Definition particle_methods.F:183
pint_io
I/O subroutines for pint_env.
Definition pint_io.F:13
pint_io::pint_write_action
subroutine, public pint_write_action(pint_env)
Writes out the actions according to PINTPRINTACTION.
Definition pint_io.F:557
pint_io::pint_write_centroids
subroutine, public pint_write_centroids(pint_env)
Write out the trajectory of the centroid (positions and velocities)
Definition pint_io.F:104
pint_io::pint_write_rgyr
subroutine, public pint_write_rgyr(pint_env)
Write radii of gyration according to PINTPRINTCENTROID_GYR.
Definition pint_io.F:675
pint_io::pint_write_step_info
subroutine, public pint_write_step_info(pint_env)
Write step info to the output file.
Definition pint_io.F:620
pint_io::pint_write_ener
subroutine, public pint_write_ener(pint_env)
Writes out the energies according to PINTPRINTENERGY.
Definition pint_io.F:481
pint_io::pint_write_line
subroutine, public pint_write_line(line)
Writes out a line of text to the default output unit.
Definition pint_io.F:76
pint_io::pint_write_trajectory
subroutine, public pint_write_trajectory(pint_env)
Write out the trajectory of the beads (positions and velocities)
Definition pint_io.F:259
pint_io::pint_write_com
subroutine, public pint_write_com(pint_env)
Write center of mass (COM) position according to PINTPRINTCOM.
Definition pint_io.F:415
pint_public
Public path integral routines that can be called from other modules.
Definition pint_public.F:15
pint_public::pint_com_pos
pure real(kind=dp) function, dimension(3), public pint_com_pos(pint_env)
Return the center of mass of the PI system.
Definition pint_public.F:45
pint_transformations
Definition pint_transformations.F:8
pint_transformations::pint_u2x
subroutine, public pint_u2x(pint_env, ux, x)
transform from the u variable to the x (inverse of x2u)
Definition pint_transformations.F:75
pint_types
Definition pint_types.F:8
pint_types::e_kin_thermo_id
integer, parameter, public e_kin_thermo_id
Definition pint_types.F:25
pint_types::e_conserved_id
integer, parameter, public e_conserved_id
Definition pint_types.F:25
pint_types::e_potential_id
integer, parameter, public e_potential_id
Definition pint_types.F:25
pint_types::e_kin_virial_id
integer, parameter, public e_kin_virial_id
Definition pint_types.F:25
cell_types::cell_type
Type defining parameters related to the simulation cell.
Definition cell_types.F:55
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
cp_subsys_types::cp_subsys_type
represents a system: atoms, molecules, their pos,vel,...
Definition cp_subsys_types.F:89
f77_interface::f_env_type
Definition f77_interface.F:158
input_section_types::section_vals_type
stores the values of a section
Definition input_section_types.F:126
particle_list_types::particle_list_type
represent a list of objects
Definition particle_list_types.F:46
pint_types::pint_env_type
environment for a path integral run
Definition pint_types.F:112