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neb_io.F
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1!--------------------------------------------------------------------------------------------------!
2! CP2K: A general program to perform molecular dynamics simulations !
3! Copyright 2000-2025 CP2K developers group <https://cp2k.org> !
4! !
5! SPDX-License-Identifier: GPL-2.0-or-later !
6!--------------------------------------------------------------------------------------------------!
7
8! **************************************************************************************************
9!> \brief I/O Module for Nudged Elastic Band Calculation
10!> \note
11!> Numerical accuracy for parallel runs:
12!> Each replica starts the SCF run from the one optimized
13!> in a previous run. It may happen then energies and derivatives
14!> of a serial run and a parallel run could be slightly different
15!> 'cause of a different starting density matrix.
16!> Exact results are obtained using:
17!> EXTRAPOLATION USE_GUESS in QS section (Teo 09.2006)
18!> \author Teodoro Laino 10.2006
19! **************************************************************************************************
20MODULE neb_io
21 USE cell_types, ONLY: cell_type
22 USE cp2k_info, ONLY: get_runtime_info
23 USE cp_files, ONLY: close_file,&
24 open_file
25 USE cp_log_handling, ONLY: cp_add_default_logger,&
26 cp_get_default_logger,&
27 cp_logger_type,&
28 cp_rm_default_logger,&
29 cp_to_string
30 USE cp_output_handling, ONLY: cp_print_key_finished_output,&
31 cp_print_key_unit_nr
32 USE cp_units, ONLY: cp_unit_from_cp2k
33 USE f77_interface, ONLY: f_env_add_defaults,&
34 f_env_rm_defaults,&
35 f_env_type
36 USE force_env_types, ONLY: force_env_get,&
37 use_mixed_force
38 USE header, ONLY: cp2k_footer
39 USE input_constants, ONLY: band_md_opt,&
40 do_sm,&
41 dump_xmol,&
42 pot_neb_fe,&
43 pot_neb_full,&
44 pot_neb_me
45 USE input_cp2k_neb, ONLY: create_band_section
46 USE input_cp2k_restarts, ONLY: write_restart
47 USE input_enumeration_types, ONLY: enum_i2c,&
48 enumeration_type
49 USE input_keyword_types, ONLY: keyword_get,&
50 keyword_type
51 USE input_section_types, ONLY: section_get_keyword,&
52 section_release,&
53 section_type,&
54 section_vals_get,&
55 section_vals_get_subs_vals,&
56 section_vals_type,&
57 section_vals_val_get,&
58 section_vals_val_set
59 USE kinds, ONLY: default_path_length,&
60 default_string_length,&
61 dp
62 USE machine, ONLY: m_flush
63 USE neb_md_utils, ONLY: get_temperatures
64 USE neb_types, ONLY: neb_type,&
65 neb_var_type
66 USE particle_methods, ONLY: write_particle_coordinates
67 USE particle_types, ONLY: get_particle_pos_or_vel,&
68 particle_type
69 USE physcon, ONLY: angstrom
70 USE replica_types, ONLY: replica_env_type
71#include "../base/base_uses.f90"
72
73 IMPLICIT NONE
74 PRIVATE
75 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'neb_io'
76
77 PUBLIC :: read_neb_section, &
78 dump_neb_info, &
79 dump_replica_coordinates, &
80 handle_band_file_names, &
81 neb_rep_env_map_info
82
83CONTAINS
84
85! **************************************************************************************************
86!> \brief Read data from the NEB input section
87!> \param neb_env ...
88!> \param neb_section ...
89!> \author Teodoro Laino 09.2006
90! **************************************************************************************************
91 SUBROUTINE read_neb_section(neb_env, neb_section)
92 TYPE(neb_type), POINTER :: neb_env
93 TYPE(section_vals_type), POINTER :: neb_section
94
95 LOGICAL :: explicit
96 TYPE(section_vals_type), POINTER :: wrk_section
97
98 cpassert(ASSOCIATED(neb_env))
99 neb_env%istep = 0
100 CALL section_vals_val_get(neb_section, "BAND_TYPE", i_val=neb_env%id_type)
101 CALL section_vals_val_get(neb_section, "NUMBER_OF_REPLICA", i_val=neb_env%number_of_replica)
102 CALL section_vals_val_get(neb_section, "K_SPRING", r_val=neb_env%K)
103 CALL section_vals_val_get(neb_section, "ROTATE_FRAMES", l_val=neb_env%rotate_frames)
104 CALL section_vals_val_get(neb_section, "ALIGN_FRAMES", l_val=neb_env%align_frames)
105 CALL section_vals_val_get(neb_section, "OPTIMIZE_BAND%OPTIMIZE_END_POINTS", l_val=neb_env%optimize_end_points)
106 ! Climb Image NEB
107 CALL section_vals_val_get(neb_section, "CI_NEB%NSTEPS_IT", i_val=neb_env%nsteps_it)
108 ! Band Optimization Type
109 CALL section_vals_val_get(neb_section, "OPTIMIZE_BAND%OPT_TYPE", i_val=neb_env%opt_type)
110 ! Use colvars
111 CALL section_vals_val_get(neb_section, "USE_COLVARS", l_val=neb_env%use_colvar)
112 CALL section_vals_val_get(neb_section, "POT_TYPE", i_val=neb_env%pot_type)
113 ! Before continuing let's do some consistency check between keywords
114 IF (neb_env%pot_type /= pot_neb_full) THEN
115 ! Requires the use of colvars
116 IF (.NOT. neb_env%use_colvar) &
117 CALL cp_abort(__location__, &
118 "A potential energy function based on free energy or minimum energy"// &
119 " was requested without enabling the usage of COLVARS. Both methods"// &
120 " are based on COLVARS definition.")
121 ! Moreover let's check if the proper sections have been defined..
122 SELECT CASE (neb_env%pot_type)
123 CASE (pot_neb_fe)
124 wrk_section => section_vals_get_subs_vals(neb_env%root_section, "MOTION%MD")
125 CALL section_vals_get(wrk_section, explicit=explicit)
126 IF (.NOT. explicit) &
127 CALL cp_abort(__location__, &
128 "A free energy BAND (colvars projected) calculation is requested"// &
129 " but NONE MD section was defined in the input.")
130 CASE (pot_neb_me)
131 wrk_section => section_vals_get_subs_vals(neb_env%root_section, "MOTION%GEO_OPT")
132 CALL section_vals_get(wrk_section, explicit=explicit)
133 IF (.NOT. explicit) &
134 CALL cp_abort(__location__, &
135 "A minimum energy BAND (colvars projected) calculation is requested"// &
136 " but NONE GEO_OPT section was defined in the input.")
137 END SELECT
138 ELSE
139 IF (neb_env%use_colvar) &
140 CALL cp_abort(__location__, &
141 "A band calculation was requested with a full potential energy. USE_COLVAR cannot"// &
142 " be set for this kind of calculation!")
143 END IF
144 ! String Method
145 CALL section_vals_val_get(neb_section, "STRING_METHOD%SMOOTHING", r_val=neb_env%smoothing)
146 CALL section_vals_val_get(neb_section, "STRING_METHOD%SPLINE_ORDER", i_val=neb_env%spline_order)
147 neb_env%reparametrize_frames = .false.
148 IF (neb_env%id_type == do_sm) THEN
149 neb_env%reparametrize_frames = .true.
150 END IF
151 END SUBROUTINE read_neb_section
152
153! **************************************************************************************************
154!> \brief dump print info of a NEB run
155!> \param neb_env ...
156!> \param coords ...
157!> \param vels ...
158!> \param forces ...
159!> \param particle_set ...
160!> \param logger ...
161!> \param istep ...
162!> \param energies ...
163!> \param distances ...
164!> \param output_unit ...
165!> \author Teodoro Laino 09.2006
166! **************************************************************************************************
167 SUBROUTINE dump_neb_info(neb_env, coords, vels, forces, particle_set, logger, &
168 istep, energies, distances, output_unit)
169 TYPE(neb_type), POINTER :: neb_env
170 TYPE(neb_var_type), POINTER :: coords
171 TYPE(neb_var_type), OPTIONAL, POINTER :: vels, forces
172 TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
173 TYPE(cp_logger_type), POINTER :: logger
174 INTEGER, INTENT(IN) :: istep
175 REAL(kind=dp), DIMENSION(:), INTENT(IN) :: energies, distances
176 INTEGER, INTENT(IN) :: output_unit
177
178 CHARACTER(len=*), PARAMETER :: routinen = 'dump_neb_info'
179
180 CHARACTER(LEN=20) :: mytype
181 CHARACTER(LEN=default_string_length) :: line, title, unit_str
182 INTEGER :: crd, ener, frc, handle, i, irep, ndig, &
183 ndigl, ttst, vel
184 LOGICAL :: explicit, lval, print_kind
185 REAL(kind=dp) :: f_ann, tmp_r1, unit_conv
186 REAL(kind=dp), ALLOCATABLE, DIMENSION(:) :: ekin, temperatures
187 TYPE(cell_type), POINTER :: cell
188 TYPE(enumeration_type), POINTER :: enum
189 TYPE(keyword_type), POINTER :: keyword
190 TYPE(section_type), POINTER :: section
191 TYPE(section_vals_type), POINTER :: tc_section, vc_section
192
193 CALL timeset(routinen, handle)
194 ndig = ceiling(log10(real(neb_env%number_of_replica + 1, kind=dp)))
195 CALL force_env_get(neb_env%force_env, cell=cell)
196 DO irep = 1, neb_env%number_of_replica
197 ndigl = ceiling(log10(real(irep + 1, kind=dp)))
198 WRITE (line, '(A,'//cp_to_string(ndig)//'("0"),T'//cp_to_string(11 + ndig + 1 - ndigl)//',I0)') "Replica_nr_", irep
199 crd = cp_print_key_unit_nr(logger, neb_env%motion_print_section, "TRAJECTORY", &
200 extension=".xyz", file_form="FORMATTED", middle_name="pos-"//trim(line))
201 IF (PRESENT(vels)) THEN
202 vel = cp_print_key_unit_nr(logger, neb_env%motion_print_section, "VELOCITIES", &
203 extension=".xyz", file_form="FORMATTED", middle_name="vel-"//trim(line))
204 END IF
205 IF (PRESENT(forces)) THEN
206 frc = cp_print_key_unit_nr(logger, neb_env%motion_print_section, "FORCES", &
207 extension=".xyz", file_form="FORMATTED", middle_name="force-"//trim(line))
208 END IF
209 ! Dump Trajectory
210 IF (crd > 0) THEN
211 ! Gather units of measure for output
212 CALL section_vals_val_get(neb_env%motion_print_section, "TRAJECTORY%UNIT", &
213 c_val=unit_str)
214 CALL section_vals_val_get(neb_env%motion_print_section, "TRAJECTORY%PRINT_ATOM_KIND", &
215 l_val=print_kind)
216 unit_conv = cp_unit_from_cp2k(1.0_dp, trim(unit_str))
217 ! This information can be digested by Molden
218 WRITE (unit=title, fmt="(A,I8,A,F20.10)") " i =", istep, ", E =", energies(irep)
219 CALL write_particle_coordinates(particle_set, crd, dump_xmol, "POS", title, &
220 cell=cell, array=coords%xyz(:, irep), unit_conv=unit_conv, &
221 print_kind=print_kind)
222 CALL m_flush(crd)
223 END IF
224 ! Dump Velocities
225 IF (vel > 0 .AND. PRESENT(vels)) THEN
226 ! Gather units of measure for output
227 CALL section_vals_val_get(neb_env%motion_print_section, "VELOCITIES%UNIT", &
228 c_val=unit_str)
229 CALL section_vals_val_get(neb_env%motion_print_section, "VELOCITIES%PRINT_ATOM_KIND", &
230 l_val=print_kind)
231 unit_conv = cp_unit_from_cp2k(1.0_dp, trim(unit_str))
232 WRITE (unit=title, fmt="(A,I8,A,F20.10)") " i =", istep, ", E =", energies(irep)
233 CALL write_particle_coordinates(particle_set, vel, dump_xmol, "VEL", title, &
234 cell=cell, array=vels%xyz(:, irep), unit_conv=unit_conv, &
235 print_kind=print_kind)
236 CALL m_flush(vel)
237 END IF
238 ! Dump Forces
239 IF (frc > 0 .AND. PRESENT(forces)) THEN
240 ! Gather units of measure for output
241 CALL section_vals_val_get(neb_env%motion_print_section, "FORCES%UNIT", &
242 c_val=unit_str)
243 CALL section_vals_val_get(neb_env%motion_print_section, "FORCES%PRINT_ATOM_KIND", &
244 l_val=print_kind)
245 unit_conv = cp_unit_from_cp2k(1.0_dp, trim(unit_str))
246 WRITE (unit=title, fmt="(A,I8,A,F20.10)") " i =", istep, ", E =", energies(irep)
247 CALL write_particle_coordinates(particle_set, frc, dump_xmol, "FRC", title, &
248 cell=cell, array=forces%xyz(:, irep), unit_conv=unit_conv, &
249 print_kind=print_kind)
250 CALL m_flush(frc)
251 END IF
252 CALL cp_print_key_finished_output(crd, logger, neb_env%motion_print_section, &
253 "TRAJECTORY")
254 IF (PRESENT(vels)) THEN
255 CALL cp_print_key_finished_output(vel, logger, neb_env%motion_print_section, &
256 "VELOCITIES")
257 END IF
258 IF (PRESENT(forces)) THEN
259 CALL cp_print_key_finished_output(frc, logger, neb_env%motion_print_section, &
260 "FORCES")
261 END IF
262 END DO
263 ! NEB summary info on screen
264 IF (output_unit > 0) THEN
265 tc_section => section_vals_get_subs_vals(neb_env%neb_section, "OPTIMIZE_BAND%MD%TEMP_CONTROL")
266 vc_section => section_vals_get_subs_vals(neb_env%neb_section, "OPTIMIZE_BAND%MD%VEL_CONTROL")
267 ALLOCATE (temperatures(neb_env%number_of_replica))
268 ALLOCATE (ekin(neb_env%number_of_replica))
269 CALL get_temperatures(vels, particle_set, temperatures, ekin=ekin)
270 WRITE (output_unit, '(/)', advance="NO")
271 WRITE (output_unit, fmt='(A,A)') ' **************************************', &
272 '*****************************************'
273 NULLIFY (section, keyword, enum)
274 CALL create_band_section(section)
275 keyword => section_get_keyword(section, "BAND_TYPE")
276 CALL keyword_get(keyword, enum=enum)
277 mytype = trim(enum_i2c(enum, neb_env%id_type))
278 WRITE (output_unit, fmt='(A,T61,A)') &
279 ' BAND TYPE =', adjustr(mytype)
280 CALL section_release(section)
281 WRITE (output_unit, fmt='(A,T61,A)') &
282 ' BAND TYPE OPTIMIZATION =', adjustr(neb_env%opt_type_label(1:20))
283 WRITE (output_unit, '( A,T71,I10 )') &
284 ' STEP NUMBER =', istep
285 IF (neb_env%rotate_frames) WRITE (output_unit, '( A,T71,L10 )') &
286 ' RMSD DISTANCE DEFINITION =', neb_env%rotate_frames
287 ! velocity control parameters output
288 CALL section_vals_get(vc_section, explicit=explicit)
289 IF (explicit) THEN
290 CALL section_vals_val_get(vc_section, "PROJ_VELOCITY_VERLET", l_val=lval)
291 IF (lval) WRITE (output_unit, '( A,T71,L10 )') &
292 ' PROJECTED VELOCITY VERLET =', lval
293 CALL section_vals_val_get(vc_section, "SD_LIKE", l_val=lval)
294 IF (lval) WRITE (output_unit, '( A,T71,L10)') &
295 ' STEEPEST DESCENT LIKE =', lval
296 CALL section_vals_val_get(vc_section, "ANNEALING", r_val=f_ann)
297 IF (f_ann /= 1.0_dp) THEN
298 WRITE (output_unit, '( A,T71,F10.5)') &
299 ' ANNEALING FACTOR = ', f_ann
300 END IF
301 END IF
302 ! temperature control parameters output
303 CALL section_vals_get(tc_section, explicit=explicit)
304 IF (explicit) THEN
305 CALL section_vals_val_get(tc_section, "TEMP_TOL_STEPS", i_val=ttst)
306 IF (istep <= ttst) THEN
307 CALL section_vals_val_get(tc_section, "TEMPERATURE", r_val=f_ann)
308 tmp_r1 = cp_unit_from_cp2k(f_ann, "K")
309 WRITE (output_unit, '( A,T71,F10.5)') &
310 ' TEMPERATURE TARGET =', tmp_r1
311 END IF
312 END IF
313 WRITE (output_unit, '( A,T71,I10 )') &
314 ' NUMBER OF NEB REPLICA =', neb_env%number_of_replica
315 WRITE (output_unit, '( A,T17,4F16.6)') &
316 ' DISTANCES REP =', distances(1:min(4, SIZE(distances)))
317 IF (SIZE(distances) > 4) THEN
318 WRITE (output_unit, '( T17,4F16.6)') distances(5:SIZE(distances))
319 END IF
320 WRITE (output_unit, '( A,T17,4F16.6)') &
321 ' ENERGIES [au] =', energies(1:min(4, SIZE(energies)))
322 IF (SIZE(energies) > 4) THEN
323 WRITE (output_unit, '( T17,4F16.6)') energies(5:SIZE(energies))
324 END IF
325 IF (neb_env%opt_type == band_md_opt) THEN
326 WRITE (output_unit, '( A,T33,4(1X,F11.5))') &
327 ' REPLICA TEMPERATURES (K) =', temperatures(1:min(4, SIZE(temperatures)))
328 DO i = 5, SIZE(temperatures), 4
329 WRITE (output_unit, '( T33,4(1X,F11.5))') &
330 temperatures(i:min(i + 3, SIZE(temperatures)))
331 END DO
332 END IF
333 WRITE (output_unit, '( A,T56,F25.14)') &
334 ' BAND TOTAL ENERGY [au] =', sum(energies(:) + ekin(:)) + &
335 neb_env%spring_energy
336 WRITE (output_unit, fmt='(A,A)') ' **************************************', &
337 '*****************************************'
338 DEALLOCATE (ekin)
339 DEALLOCATE (temperatures)
340 END IF
341 ! Ener file
342 ener = cp_print_key_unit_nr(logger, neb_env%neb_section, "ENERGY", &
343 extension=".ener", file_form="FORMATTED")
344 IF (ener > 0) THEN
345 WRITE (line, '(I0)') 2*neb_env%number_of_replica - 1
346 WRITE (ener, '(I10,'//trim(line)//'(1X,F20.9))') istep, &
347 energies, distances
348 END IF
349 CALL cp_print_key_finished_output(ener, logger, neb_env%neb_section, &
350 "ENERGY")
351
352 ! Dump Restarts
353 CALL cp_add_default_logger(logger)
354 CALL write_restart(force_env=neb_env%force_env, &
355 root_section=neb_env%root_section, &
356 coords=coords, &
357 vels=vels)
358 CALL cp_rm_default_logger()
359
360 CALL timestop(handle)
361
362 END SUBROUTINE dump_neb_info
363
364! **************************************************************************************************
365!> \brief dump coordinates of a replica NEB
366!> \param particle_set ...
367!> \param coords ...
368!> \param i_rep ...
369!> \param ienum ...
370!> \param iw ...
371!> \param use_colvar ...
372!> \author Teodoro Laino 09.2006
373! **************************************************************************************************
374 SUBROUTINE dump_replica_coordinates(particle_set, coords, i_rep, ienum, iw, use_colvar)
375
376 TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
377 TYPE(neb_var_type), POINTER :: coords
378 INTEGER, INTENT(IN) :: i_rep, ienum, iw
379 LOGICAL, INTENT(IN) :: use_colvar
380
381 INTEGER :: iatom, j
382 REAL(kind=dp), DIMENSION(3) :: r
383
384 IF (iw > 0) THEN
385 WRITE (iw, '(/,T2,"NEB|",75("*"))')
386 WRITE (iw, '(T2,"NEB|",1X,A,I0,A)') &
387 "Geometry for Replica Nr. ", ienum, " in Angstrom"
388 DO iatom = 1, SIZE(particle_set)
389 r(1:3) = get_particle_pos_or_vel(iatom, particle_set, coords%xyz(:, i_rep))
390 WRITE (iw, '(T2,"NEB|",1X,A10,5X,3F15.9)') &
391 trim(particle_set(iatom)%atomic_kind%name), r(1:3)*angstrom
392 END DO
393 IF (use_colvar) THEN
394 WRITE (iw, '(/,T2,"NEB|",1X,A10)') "COLLECTIVE VARIABLES:"
395 WRITE (iw, '(T2,"NEB|",16X,3F15.9)') &
396 (coords%int(j, i_rep), j=1, SIZE(coords%int(:, :), 1))
397 END IF
398 WRITE (iw, '(T2,"NEB|",75("*"))')
399 CALL m_flush(iw)
400 END IF
401
402 END SUBROUTINE dump_replica_coordinates
403
404! **************************************************************************************************
405!> \brief Handles the correct file names during a band calculation
406!> \param rep_env ...
407!> \param irep ...
408!> \param n_rep ...
409!> \param istep ...
410!> \author Teodoro Laino 06.2009
411! **************************************************************************************************
412 SUBROUTINE handle_band_file_names(rep_env, irep, n_rep, istep)
413 TYPE(replica_env_type), POINTER :: rep_env
414 INTEGER, INTENT(IN) :: irep, n_rep, istep
415
416 CHARACTER(len=*), PARAMETER :: routinen = 'handle_band_file_names'
417
418 CHARACTER(LEN=default_path_length) :: output_file_path, replica_proj_name
419 INTEGER :: handle, handle2, i, ierr, j, lp, unit_nr
420 TYPE(cp_logger_type), POINTER :: logger, sub_logger
421 TYPE(f_env_type), POINTER :: f_env
422 TYPE(section_vals_type), POINTER :: root_section
423
424 CALL timeset(routinen, handle)
425 CALL f_env_add_defaults(f_env_id=rep_env%f_env_id, f_env=f_env, &
426 handle=handle2)
427 logger => cp_get_default_logger()
428 CALL force_env_get(f_env%force_env, root_section=root_section)
429 j = irep + (rep_env%local_rep_indices(1) - 1)
430 ! Get replica_project_name
431 replica_proj_name = get_replica_project_name(rep_env, n_rep, j)
432 lp = len_trim(replica_proj_name)
433 CALL section_vals_val_set(root_section, "GLOBAL%PROJECT_NAME", &
434 c_val=trim(replica_proj_name))
435 logger%iter_info%project_name = replica_proj_name
436
437 ! We change the file on which is pointing the global logger and error
438 output_file_path = replica_proj_name(1:lp)//".out"
439 CALL section_vals_val_set(root_section, "GLOBAL%OUTPUT_FILE_NAME", &
440 c_val=trim(output_file_path))
441 IF (logger%default_global_unit_nr > 0) THEN
442 CALL close_file(logger%default_global_unit_nr)
443 CALL open_file(file_name=output_file_path, file_status="UNKNOWN", &
444 file_action="WRITE", file_position="APPEND", &
445 unit_number=logger%default_global_unit_nr, &
446 skip_get_unit_number=.true.)
447 WRITE (unit=logger%default_global_unit_nr, fmt="(/,(T2,A79))") &
448 "*******************************************************************************", &
449 "** BAND EVALUATION OF ENERGIES AND FORCES **", &
450 "*******************************************************************************"
451 WRITE (unit=logger%default_global_unit_nr, fmt="(T2,A,T79,A)") "**", "**"
452 WRITE (unit=logger%default_global_unit_nr, fmt="(T2,A,T79,A)") "**", "**"
453 WRITE (unit=logger%default_global_unit_nr, fmt="(T2,A,I5,T41,A,I5,T79,A)") &
454 "** Replica Env Nr. :", rep_env%local_rep_indices(1) - 1, "Replica Band Nr. :", j, "**"
455 WRITE (unit=logger%default_global_unit_nr, fmt="(T2,A,I5,T79,A)") &
456 "** Band Step Nr. :", istep, "**"
457 WRITE (unit=logger%default_global_unit_nr, fmt="(T2,A79)") &
458 "*******************************************************************************"
459 END IF
460
461 ! Handle specific case for mixed_env
462 SELECT CASE (f_env%force_env%in_use)
463 CASE (use_mixed_force)
464 DO i = 1, f_env%force_env%mixed_env%ngroups
465 IF (modulo(i - 1, f_env%force_env%mixed_env%ngroups) == &
466 f_env%force_env%mixed_env%group_distribution(f_env%force_env%mixed_env%para_env%mepos)) THEN
467 sub_logger => f_env%force_env%mixed_env%sub_logger(i)%p
468 sub_logger%iter_info%project_name = replica_proj_name(1:lp)//"-r-"//trim(adjustl(cp_to_string(i)))
469
470 unit_nr = sub_logger%default_global_unit_nr
471 IF (unit_nr > 0) THEN
472 CALL close_file(unit_nr)
473
474 output_file_path = replica_proj_name(1:lp)//"-r-"//trim(adjustl(cp_to_string(i)))//".out"
475 CALL open_file(file_name=output_file_path, file_status="UNKNOWN", &
476 file_action="WRITE", file_position="APPEND", &
477 unit_number=unit_nr, skip_get_unit_number=.true.)
478 END IF
479 END IF
480 END DO
481 END SELECT
482
483 CALL f_env_rm_defaults(f_env=f_env, ierr=ierr, handle=handle2)
484 cpassert(ierr == 0)
485 CALL timestop(handle)
486
487 END SUBROUTINE handle_band_file_names
488
489! **************************************************************************************************
490!> \brief Constructs project names for BAND replicas
491!> \param rep_env ...
492!> \param n_rep ...
493!> \param j ...
494!> \return ...
495!> \author Teodoro Laino 06.2009
496! **************************************************************************************************
497 FUNCTION get_replica_project_name(rep_env, n_rep, j) RESULT(replica_proj_name)
498 TYPE(replica_env_type), POINTER :: rep_env
499 INTEGER, INTENT(IN) :: n_rep, j
500 CHARACTER(LEN=default_path_length) :: replica_proj_name
501
502 CHARACTER(LEN=default_string_length) :: padding
503 INTEGER :: i, lp, ndigits
504
505! Setup new replica project name and output file
506
507 replica_proj_name = rep_env%original_project_name
508 ! Find padding
509 ndigits = ceiling(log10(real(n_rep + 1, kind=dp))) - &
510 ceiling(log10(real(j + 1, kind=dp)))
511 padding = ""
512 DO i = 1, ndigits
513 padding(i:i) = "0"
514 END DO
515 lp = len_trim(replica_proj_name)
516 replica_proj_name(lp + 1:len(replica_proj_name)) = "-BAND"// &
517 trim(padding)//adjustl(cp_to_string(j))
518 END FUNCTION get_replica_project_name
519
520! **************************************************************************************************
521!> \brief Print some mapping infos in the replica_env setup output files
522!> i.e. prints in which files one can find information for each band
523!> replica
524!> \param rep_env ...
525!> \param neb_env ...
526!> \author Teodoro Laino 06.2009
527! **************************************************************************************************
528 SUBROUTINE neb_rep_env_map_info(rep_env, neb_env)
529 TYPE(replica_env_type), POINTER :: rep_env
530 TYPE(neb_type), POINTER :: neb_env
531
532 CHARACTER(LEN=default_path_length) :: replica_proj_name
533 INTEGER :: handle2, ierr, irep, n_rep, n_rep_neb, &
534 output_unit
535 TYPE(cp_logger_type), POINTER :: logger
536 TYPE(f_env_type), POINTER :: f_env
537
538 n_rep_neb = neb_env%number_of_replica
539 n_rep = rep_env%nrep
540 CALL f_env_add_defaults(f_env_id=rep_env%f_env_id, f_env=f_env, &
541 handle=handle2)
542 logger => cp_get_default_logger()
543 output_unit = logger%default_global_unit_nr
544 IF (output_unit > 0) THEN
545 WRITE (unit=output_unit, fmt='(/,(T2,A79))') &
546 "*******************************************************************************", &
547 "** MAPPING OF BAND REPLICA TO REPLICA ENV **", &
548 "*******************************************************************************"
549 WRITE (unit=output_unit, fmt='(T2,A,I6,T32,A,T79,A)') &
550 "** Replica Env Nr.: ", rep_env%local_rep_indices(1) - 1, &
551 "working on the following BAND replicas", "**"
552 WRITE (unit=output_unit, fmt='(T2,A79)') &
553 "** **"
554 END IF
555 DO irep = 1, n_rep_neb, n_rep
556 replica_proj_name = get_replica_project_name(rep_env, n_rep_neb, irep + rep_env%local_rep_indices(1) - 1)
557 IF (output_unit > 0) THEN
558 WRITE (unit=output_unit, fmt='(T2,A,I6,T32,A,T79,A)') &
559 "** Band Replica Nr.: ", irep + rep_env%local_rep_indices(1) - 1, &
560 "Output available on file: "//trim(replica_proj_name)//".out", "**"
561 END IF
562 END DO
563 IF (output_unit > 0) THEN
564 WRITE (unit=output_unit, fmt='(T2,A79)') &
565 "** **", &
566 "*******************************************************************************"
567 WRITE (unit=output_unit, fmt='(/)')
568 END IF
569 ! update runtime info before printing the footer
570 CALL get_runtime_info()
571 ! print footer
572 CALL cp2k_footer(output_unit)
573 CALL f_env_rm_defaults(f_env=f_env, ierr=ierr, handle=handle2)
574 cpassert(ierr == 0)
575 END SUBROUTINE neb_rep_env_map_info
576
577END MODULE neb_io
modulo
static GRID_HOST_DEVICE int modulo(int a, int m)
Equivalent of Fortran's MODULO, which always return a positive number. https://gcc....
Definition grid_common.h:120
cp_log_handling::cp_to_string
Definition cp_log_handling.F:90
cell_types
Handles all functions related to the CELL.
Definition cell_types.F:15
cp2k_info
some minimal info about CP2K, including its version and license
Definition cp2k_info.F:16
cp2k_info::get_runtime_info
subroutine, public get_runtime_info()
...
Definition cp2k_info.F:328
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_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_rm_default_logger
subroutine, public cp_rm_default_logger()
the cousin of cp_add_default_logger, decrements the stack, so that the default logger is what it has ...
Definition cp_log_handling.F:213
cp_log_handling::cp_add_default_logger
subroutine, public cp_add_default_logger(logger)
adds a default logger. MUST be called before logging occours
Definition cp_log_handling.F:188
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:853
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:1063
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:452
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:496
force_env_types
Interface for the force calculations.
Definition force_env_types.F:18
force_env_types::use_mixed_force
integer, parameter, public use_mixed_force
Definition force_env_types.F:83
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, ipi_env)
returns various attributes about the force environment
Definition force_env_types.F:342
header::cp2k_footer
subroutine, public cp2k_footer(iw, wdir)
...
Definition header.F:69
input_constants
collects all constants needed in input so that they can be used without circular dependencies
Definition input_constants.F:17
input_constants::pot_neb_me
integer, parameter, public pot_neb_me
Definition input_constants.F:191
input_constants::band_md_opt
integer, parameter, public band_md_opt
Definition input_constants.F:64
input_constants::pot_neb_fe
integer, parameter, public pot_neb_fe
Definition input_constants.F:191
input_constants::dump_xmol
integer, parameter, public dump_xmol
Definition input_constants.F:376
input_constants::do_sm
integer, parameter, public do_sm
Definition input_constants.F:184
input_constants::pot_neb_full
integer, parameter, public pot_neb_full
Definition input_constants.F:191
input_cp2k_neb
Definition input_cp2k_neb.F:14
input_cp2k_neb::create_band_section
subroutine, public create_band_section(section)
creates the section for a BAND run
Definition input_cp2k_neb.F:60
input_cp2k_restarts
Set of routines to dump the restart file of CP2K.
Definition input_cp2k_restarts.F:13
input_cp2k_restarts::write_restart
subroutine, public write_restart(md_env, force_env, root_section, coords, vels, pint_env, helium_env)
checks if a restart needs to be written and does so, updating all necessary fields in the input file....
Definition input_cp2k_restarts.F:112
input_enumeration_types
represents an enumeration, i.e. a mapping between integers and strings
Definition input_enumeration_types.F:14
input_enumeration_types::enum_i2c
character(len=default_string_length) function, public enum_i2c(enum, i)
maps an integer to a string
Definition input_enumeration_types.F:152
input_keyword_types
represents keywords in an input
Definition input_keyword_types.F:14
input_keyword_types::keyword_get
subroutine, public keyword_get(keyword, names, usage, description, type_of_var, n_var, default_value, lone_keyword_value, repeats, enum, citations)
...
Definition input_keyword_types.F:480
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_set
subroutine, public section_vals_val_set(section_vals, keyword_name, i_rep_section, i_rep_val, val, l_val, i_val, r_val, c_val, l_vals_ptr, i_vals_ptr, r_vals_ptr, c_vals_ptr)
sets the requested value
Definition input_section_types.F:1223
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:731
input_section_types::section_release
recursive subroutine, public section_release(section)
releases the given keyword list (see doc/ReferenceCounting.html)
Definition input_section_types.F:238
input_section_types::section_get_keyword
recursive type(keyword_type) function, pointer, public section_get_keyword(section, keyword_name)
returns the requested keyword
Definition input_section_types.F:478
input_section_types::section_vals_get
subroutine, public section_vals_get(section_vals, ref_count, n_repetition, n_subs_vals_rep, section, explicit)
returns various attributes about the section_vals
Definition input_section_types.F:704
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:1047
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
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:130
neb_io
I/O Module for Nudged Elastic Band Calculation.
Definition neb_io.F:20
neb_io::read_neb_section
subroutine, public read_neb_section(neb_env, neb_section)
Read data from the NEB input section.
Definition neb_io.F:92
neb_io::dump_replica_coordinates
subroutine, public dump_replica_coordinates(particle_set, coords, i_rep, ienum, iw, use_colvar)
dump coordinates of a replica NEB
Definition neb_io.F:375
neb_io::neb_rep_env_map_info
subroutine, public neb_rep_env_map_info(rep_env, neb_env)
Print some mapping infos in the replica_env setup output files i.e. prints in which files one can fin...
Definition neb_io.F:529
neb_io::dump_neb_info
subroutine, public dump_neb_info(neb_env, coords, vels, forces, particle_set, logger, istep, energies, distances, output_unit)
dump print info of a NEB run
Definition neb_io.F:169
neb_io::handle_band_file_names
subroutine, public handle_band_file_names(rep_env, irep, n_rep, istep)
Handles the correct file names during a band calculation.
Definition neb_io.F:413
neb_md_utils
Module with utility to perform MD Nudged Elastic Band Calculation.
Definition neb_md_utils.F:20
neb_md_utils::get_temperatures
subroutine, public get_temperatures(vels, particle_set, temperatures, ekin, factor)
Computes temperatures.
Definition neb_md_utils.F:272
neb_types
Typo for Nudged Elastic Band Calculation.
Definition neb_types.F:20
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
particle_types
Define the data structure for the particle information.
Definition particle_types.F:19
particle_types::get_particle_pos_or_vel
pure real(kind=dp) function, dimension(3), public get_particle_pos_or_vel(iatom, particle_set, vector)
Return the atomic position or velocity of atom iatom in x from a packed vector even if core-shell par...
Definition particle_types.F:181
physcon
Definition of physical constants:
Definition physcon.F:68
physcon::angstrom
real(kind=dp), parameter, public angstrom
Definition physcon.F:144
replica_types
types used to handle many replica of the same system that differ only in atom positions,...
Definition replica_types.F:21
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
f77_interface::f_env_type
Definition f77_interface.F:163
input_enumeration_types::enumeration_type
Definition input_enumeration_types.F:43
input_keyword_types::keyword_type
represent a keyword in the input
Definition input_keyword_types.F:88
input_section_types::section_type
represent a section of the input file
Definition input_section_types.F:102
input_section_types::section_vals_type
stores the values of a section
Definition input_section_types.F:127
neb_types::neb_type
Definition neb_types.F:43
neb_types::neb_var_type
Definition neb_types.F:68
particle_types::particle_type
Definition particle_types.F:35
replica_types::replica_env_type
keeps replicated information about the replicas
Definition replica_types.F:96