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nnp_environment.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 Methods dealing with Neural Network potentials
10!> \author Christoph Schran (christoph.schran@rub.de)
11!> \date 2020-10-10
12! **************************************************************************************************
13MODULE nnp_environment
14
15 USE atomic_kind_types, ONLY: atomic_kind_type
16 USE bibliography, ONLY: behler2007,&
17 behler2011,&
18 schran2020a,&
19 schran2020b,&
20 cite_reference
21 USE cell_methods, ONLY: read_cell,&
22 write_cell
23 USE cell_types, ONLY: cell_release,&
24 cell_type,&
25 get_cell
26 USE cp_log_handling, ONLY: cp_get_default_logger,&
27 cp_logger_get_default_unit_nr,&
28 cp_logger_type
29 USE cp_parser_methods, ONLY: parser_read_line,&
30 parser_search_string
31 USE cp_parser_types, ONLY: cp_parser_type,&
32 parser_create,&
33 parser_release,&
34 parser_reset
35 USE cp_subsys_methods, ONLY: cp_subsys_create
36 USE cp_subsys_types, ONLY: cp_subsys_set,&
37 cp_subsys_type
38 USE distribution_1d_types, ONLY: distribution_1d_release,&
39 distribution_1d_type
40 USE distribution_methods, ONLY: distribute_molecules_1d
41 USE input_section_types, ONLY: section_vals_get,&
42 section_vals_get_subs_vals,&
43 section_vals_type,&
44 section_vals_val_get
45 USE kinds, ONLY: default_path_length,&
46 dp
47 USE message_passing, ONLY: mp_para_env_type
48 USE molecule_kind_types, ONLY: molecule_kind_type,&
49 write_molecule_kind_set
50 USE molecule_types, ONLY: molecule_type
51 USE nnp_acsf, ONLY: nnp_init_acsf_groups,&
52 nnp_sort_acsf,&
53 nnp_sort_ele,&
54 nnp_write_acsf
55 USE nnp_environment_types, ONLY: &
56 nnp_actfnct_cos, nnp_actfnct_exp, nnp_actfnct_gaus, nnp_actfnct_invsig, nnp_actfnct_lin, &
57 nnp_actfnct_quad, nnp_actfnct_sig, nnp_actfnct_softplus, nnp_actfnct_tanh, nnp_env_set, &
58 nnp_type
59 USE nnp_model, ONLY: nnp_write_arc
60 USE particle_methods, ONLY: write_fist_particle_coordinates,&
61 write_particle_distances,&
62 write_structure_data
63 USE particle_types, ONLY: particle_type
64 USE periodic_table, ONLY: get_ptable_info
65#include "./base/base_uses.f90"
66
67 IMPLICIT NONE
68
69 PRIVATE
70
71 LOGICAL, PARAMETER, PRIVATE :: debug_this_module = .true.
72 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'nnp_environment'
73
74 PUBLIC :: nnp_init
75 PUBLIC :: nnp_init_model
76
77CONTAINS
78
79! **************************************************************************************************
80!> \brief Read and initialize all the information for neural network potentials
81!> \param nnp_env ...
82!> \param root_section ...
83!> \param para_env ...
84!> \param force_env_section ...
85!> \param subsys_section ...
86!> \param use_motion_section ...
87!> \date 2020-10-10
88!> \author Christoph Schran (christoph.schran@rub.de)
89! **************************************************************************************************
90 SUBROUTINE nnp_init(nnp_env, root_section, para_env, force_env_section, subsys_section, &
91 use_motion_section)
92 TYPE(nnp_type), INTENT(INOUT), POINTER :: nnp_env
93 TYPE(section_vals_type), INTENT(IN), POINTER :: root_section
94 TYPE(mp_para_env_type), INTENT(IN), POINTER :: para_env
95 TYPE(section_vals_type), INTENT(INOUT), POINTER :: force_env_section, subsys_section
96 LOGICAL, INTENT(IN) :: use_motion_section
97
98 CHARACTER(len=*), PARAMETER :: routinen = 'nnp_init'
99
100 INTEGER :: handle
101 LOGICAL :: explicit, use_ref_cell
102 REAL(kind=dp), DIMENSION(3) :: abc
103 TYPE(cell_type), POINTER :: cell, cell_ref
104 TYPE(cp_subsys_type), POINTER :: subsys
105 TYPE(section_vals_type), POINTER :: cell_section, nnp_section
106
107 CALL timeset(routinen, handle)
108 CALL cite_reference(behler2007)
109 CALL cite_reference(behler2011)
110 CALL cite_reference(schran2020a)
111 CALL cite_reference(schran2020b)
112
113 cpassert(ASSOCIATED(nnp_env))
114
115 NULLIFY (cell_section, nnp_section, cell, cell_ref, subsys)
116
117 IF (.NOT. ASSOCIATED(subsys_section)) THEN
118 subsys_section => section_vals_get_subs_vals(force_env_section, "SUBSYS")
119 END IF
120 cell_section => section_vals_get_subs_vals(subsys_section, "CELL")
121 nnp_section => section_vals_get_subs_vals(force_env_section, "NNP")
122 CALL section_vals_get(nnp_section, explicit=explicit)
123 IF (.NOT. explicit) THEN
124 cpwarn("NNP section not explicitly stated. Using default file names.")
125 END IF
126
127 CALL nnp_env_set(nnp_env=nnp_env, nnp_input=nnp_section, &
128 force_env_input=force_env_section)
129
130 CALL read_cell(cell=cell, cell_ref=cell_ref, use_ref_cell=use_ref_cell, cell_section=cell_section, &
131 para_env=para_env)
132 CALL get_cell(cell=cell, abc=abc)
133 CALL write_cell(cell=cell, subsys_section=subsys_section)
134
135 CALL cp_subsys_create(subsys, para_env, root_section, &
136 force_env_section=force_env_section, subsys_section=subsys_section, &
137 use_motion_section=use_motion_section)
138
139 CALL nnp_init_subsys(nnp_env=nnp_env, subsys=subsys, cell=cell, &
140 cell_ref=cell_ref, use_ref_cell=use_ref_cell, &
141 subsys_section=subsys_section)
142
143 CALL cell_release(cell)
144 CALL cell_release(cell_ref)
145
146 CALL timestop(handle)
147
148 END SUBROUTINE nnp_init
149
150! **************************************************************************************************
151!> \brief Read and initialize all the information for neural network potentials
152!> \param nnp_env ...
153!> \param subsys ...
154!> \param cell ...
155!> \param cell_ref ...
156!> \param use_ref_cell ...
157!> \param subsys_section ...
158!> \date 2020-10-10
159!> \author Christoph Schran (christoph.schran@rub.de)
160! **************************************************************************************************
161 SUBROUTINE nnp_init_subsys(nnp_env, subsys, cell, cell_ref, use_ref_cell, subsys_section)
162 TYPE(nnp_type), INTENT(INOUT), POINTER :: nnp_env
163 TYPE(cp_subsys_type), INTENT(IN), POINTER :: subsys
164 TYPE(cell_type), INTENT(INOUT), POINTER :: cell, cell_ref
165 LOGICAL, INTENT(IN) :: use_ref_cell
166 TYPE(section_vals_type), INTENT(IN), POINTER :: subsys_section
167
168 CHARACTER(len=*), PARAMETER :: routinen = 'nnp_init_subsys'
169
170 INTEGER :: handle, natom
171 TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
172 TYPE(distribution_1d_type), POINTER :: local_molecules, local_particles
173 TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
174 TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
175 TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
176
177 CALL timeset(routinen, handle)
178
179 NULLIFY (atomic_kind_set, molecule_kind_set, particle_set, molecule_set, &
180 local_molecules, local_particles)
181
182 particle_set => subsys%particles%els
183 atomic_kind_set => subsys%atomic_kinds%els
184 molecule_kind_set => subsys%molecule_kinds%els
185 molecule_set => subsys%molecules%els
186
187 !Print the molecule kind set
188 CALL write_molecule_kind_set(molecule_kind_set, subsys_section)
189
190 !Print the atomic coordinates
191 CALL write_fist_particle_coordinates(particle_set, subsys_section)
192 CALL write_particle_distances(particle_set, cell=cell, &
193 subsys_section=subsys_section)
194 CALL write_structure_data(particle_set, cell=cell, &
195 input_section=subsys_section)
196
197 !Distribute molecules and atoms using the new data structures
198 CALL distribute_molecules_1d(atomic_kind_set=atomic_kind_set, &
199 particle_set=particle_set, &
200 local_particles=local_particles, &
201 molecule_kind_set=molecule_kind_set, &
202 molecule_set=molecule_set, &
203 local_molecules=local_molecules, &
204 force_env_section=nnp_env%force_env_input)
205
206 natom = SIZE(particle_set)
207
208 ALLOCATE (nnp_env%nnp_forces(3, natom))
209
210 nnp_env%nnp_forces(:, :) = 0.0_dp
211
212 nnp_env%nnp_potential_energy = 0.0_dp
213
214 ! Set up arrays for calculation:
215 nnp_env%num_atoms = natom
216 ALLOCATE (nnp_env%ele_ind(natom))
217 ALLOCATE (nnp_env%nuc_atoms(natom))
218 ALLOCATE (nnp_env%coord(3, natom))
219 ALLOCATE (nnp_env%atoms(natom))
220 ALLOCATE (nnp_env%sort(natom))
221 ALLOCATE (nnp_env%sort_inv(natom))
222
223 CALL cp_subsys_set(subsys, cell=cell)
224
225 CALL nnp_env_set(nnp_env=nnp_env, subsys=subsys, &
226 cell_ref=cell_ref, use_ref_cell=use_ref_cell, &
227 local_molecules=local_molecules, &
228 local_particles=local_particles)
229
230 CALL distribution_1d_release(local_particles)
231 CALL distribution_1d_release(local_molecules)
232
233 CALL nnp_init_model(nnp_env=nnp_env, printtag="NNP")
234
235 CALL timestop(handle)
236
237 END SUBROUTINE nnp_init_subsys
238
239! **************************************************************************************************
240!> \brief Initialize the Neural Network Potential
241!> \param nnp_env ...
242!> \param printtag ...
243!> \date 2020-10-10
244!> \author Christoph Schran (christoph.schran@rub.de)
245! **************************************************************************************************
246 SUBROUTINE nnp_init_model(nnp_env, printtag)
247 TYPE(nnp_type), INTENT(INOUT), POINTER :: nnp_env
248 CHARACTER(LEN=*), INTENT(IN) :: printtag
249
250 CHARACTER(len=*), PARAMETER :: routinen = 'nnp_init_model'
251 INTEGER, PARAMETER :: def_str_len = 256, &
252 default_path_length = 256
253
254 CHARACTER(len=1), ALLOCATABLE, DIMENSION(:) :: cactfnct
255 CHARACTER(len=2) :: ele
256 CHARACTER(len=def_str_len) :: dummy, line
257 CHARACTER(len=default_path_length) :: base_name, file_name
258 INTEGER :: handle, i, i_com, io, iweight, j, k, l, &
259 n_weight, nele, nuc_ele, symfnct_type, &
260 unit_nr
261 LOGICAL :: at_end, atom_e_found, explicit, first, &
262 found
263 REAL(kind=dp) :: energy
264 REAL(kind=dp), ALLOCATABLE, DIMENSION(:) :: weights
265 REAL(kind=dp), DIMENSION(7) :: test_array
266 REAL(kind=dp), DIMENSION(:), POINTER :: work
267 TYPE(cp_logger_type), POINTER :: logger
268 TYPE(cp_parser_type) :: parser
269 TYPE(section_vals_type), POINTER :: bias_section, model_section
270
271 CALL timeset(routinen, handle)
272
273 NULLIFY (logger)
274
275 logger => cp_get_default_logger()
276
277 IF (logger%para_env%is_source()) THEN
278 unit_nr = cp_logger_get_default_unit_nr(logger)
279 WRITE (unit_nr, *) ""
280 WRITE (unit_nr, *) trim(printtag)//"| Neural Network Potential Force Environment"
281 END IF
282
283 model_section => section_vals_get_subs_vals(nnp_env%nnp_input, "MODEL")
284 CALL section_vals_get(model_section, n_repetition=nnp_env%n_committee)
285 ALLOCATE (nnp_env%atomic_energy(nnp_env%num_atoms, nnp_env%n_committee))
286 ALLOCATE (nnp_env%committee_energy(nnp_env%n_committee))
287 ALLOCATE (nnp_env%myforce(3, nnp_env%num_atoms, nnp_env%n_committee))
288 ALLOCATE (nnp_env%committee_forces(3, nnp_env%num_atoms, nnp_env%n_committee))
289 ALLOCATE (nnp_env%committee_stress(3, 3, nnp_env%n_committee))
290
291 CALL section_vals_val_get(nnp_env%nnp_input, "NNP_INPUT_FILE_NAME", c_val=file_name)
292 CALL parser_create(parser, file_name, para_env=logger%para_env)
293
294 ! read number of elements and cut_type and check for scale and center
295 nnp_env%scale_acsf = .false.
296 nnp_env%scale_sigma_acsf = .false.
297 ! Defaults for scale min and max:
298 nnp_env%scmin = 0.0_dp
299 nnp_env%scmax = 1.0_dp
300 nnp_env%center_acsf = .false.
301 nnp_env%normnodes = .false.
302 nnp_env%n_hlayer = 0
303
304 IF (logger%para_env%is_source()) THEN
305 unit_nr = cp_logger_get_default_unit_nr(logger)
306 WRITE (unit_nr, *) trim(printtag)//"| Reading NNP input from file: ", trim(file_name)
307 END IF
308
309 CALL parser_search_string(parser, "number_of_elements", .true., found, line, &
310 search_from_begin_of_file=.true.)
311 IF (found) THEN
312 READ (line, *) dummy, nnp_env%n_ele
313 ELSE
314 CALL cp_abort(__location__, trim(printtag)// &
315 "| number of elements missing in NNP_INPUT_FILE")
316 END IF
317
318 CALL parser_search_string(parser, "scale_symmetry_functions_sigma", .true., found, &
319 search_from_begin_of_file=.true.)
320 nnp_env%scale_sigma_acsf = found
321
322 CALL parser_search_string(parser, "scale_symmetry_functions", .true., found, &
323 search_from_begin_of_file=.true.)
324 nnp_env%scale_acsf = found
325
326 ! Test if there are two keywords of this:
327 CALL parser_search_string(parser, "scale_symmetry_functions", .true., found)
328 IF (found .AND. nnp_env%scale_sigma_acsf) THEN
329 cpwarn('Two scaling keywords in the input, we will ignore sigma scaling in this case')
330 nnp_env%scale_sigma_acsf = .false.
331 ELSE IF (.NOT. found .AND. nnp_env%scale_sigma_acsf) THEN
332 nnp_env%scale_acsf = .false.
333 END IF
334
335 CALL parser_search_string(parser, "scale_min_short_atomic", .true., found, line, &
336 search_from_begin_of_file=.true.)
337 IF (found) READ (line, *) dummy, nnp_env%scmin
338
339 CALL parser_search_string(parser, "scale_max_short_atomic", .true., found, line, &
340 search_from_begin_of_file=.true.)
341 IF (found) READ (line, *) dummy, nnp_env%scmax
342
343 CALL parser_search_string(parser, "center_symmetry_functions", .true., found, &
344 search_from_begin_of_file=.true.)
345 nnp_env%center_acsf = found
346 ! n2p2 overwrites sigma scaling, if centering is requested:
347 IF (nnp_env%scale_sigma_acsf .AND. nnp_env%center_acsf) THEN
348 nnp_env%scale_sigma_acsf = .false.
349 END IF
350 ! Print warning if centering and scaling is requested:
351 IF (nnp_env%center_acsf .AND. nnp_env%scale_acsf) THEN
352 IF ((abs(nnp_env%scmin) > epsilon(0.0_dp)*1.0e+4_dp) .OR. (abs(nnp_env%scmax - 1.0_dp) > epsilon(0.0_dp)*1.0e+4_dp)) THEN
353 CALL cp_warn(__location__, &
354 "Centering and scaling of symmetry functions requested while scale_min_short_atomic != 0 and/or "// &
355 "scale_max_short_atomic != 1. Make sure that scaling and centering of symmetry functions in CP2K "// &
356 "is consistent with your training code. "// &
357 "In CP2K: G* = (G - ave(G)) / (max(G) - min(G)) * (Smax - Smin) + Smin")
358 END IF
359 END IF
360
361 CALL parser_search_string(parser, "normalize_nodes", .true., found, &
362 search_from_begin_of_file=.true.)
363 nnp_env%normnodes = found
364
365 CALL parser_search_string(parser, "cutoff_type", .true., found, line, &
366 search_from_begin_of_file=.true.)
367 IF (found) THEN
368 READ (line, *) dummy, nnp_env%cut_type
369 ELSE
370 CALL cp_abort(__location__, trim(printtag)// &
371 "| no cutoff type specified in NNP_INPUT_FILE")
372 END IF
373
374 CALL parser_search_string(parser, "global_hidden_layers_short", .true., found, line, &
375 search_from_begin_of_file=.true.)
376 IF (found) THEN
377 READ (line, *) dummy, nnp_env%n_hlayer
378 ELSE
379 CALL cp_abort(__location__, trim(printtag)// &
380 "| number of hidden layers missing in NNP_INPUT_FILE")
381 END IF
382 nnp_env%n_layer = nnp_env%n_hlayer + 2
383
384 nele = nnp_env%n_ele
385 ALLOCATE (nnp_env%rad(nele))
386 ALLOCATE (nnp_env%ang(nele))
387 ALLOCATE (nnp_env%n_rad(nele))
388 ALLOCATE (nnp_env%n_ang(nele))
389 ALLOCATE (nnp_env%actfnct(nnp_env%n_hlayer + 1))
390 ALLOCATE (cactfnct(nnp_env%n_hlayer + 1))
391 ALLOCATE (nnp_env%ele(nele))
392 ALLOCATE (nnp_env%nuc_ele(nele))
393 ALLOCATE (nnp_env%arc(nele))
394 DO i = 1, nele
395 ALLOCATE (nnp_env%arc(i)%layer(nnp_env%n_layer))
396 ALLOCATE (nnp_env%arc(i)%n_nodes(nnp_env%n_layer))
397 END DO
398 ALLOCATE (nnp_env%n_hnodes(nnp_env%n_hlayer))
399 ALLOCATE (nnp_env%atom_energies(nele))
400 nnp_env%atom_energies = 0.0_dp
401
402 ! read elements, broadcast and sort
403 CALL parser_reset(parser)
404 DO
405 CALL parser_search_string(parser, "elements", .true., found, line)
406 IF (found) THEN
407 READ (line, *) dummy
408 IF (trim(adjustl(dummy)) == "elements") THEN
409 READ (line, *) dummy, nnp_env%ele(:)
410 CALL nnp_sort_ele(nnp_env%ele, nnp_env%nuc_ele)
411 EXIT
412 END IF
413 ELSE
414 CALL cp_abort(__location__, trim(printtag)// &
415 "| elements not specified in NNP_INPUT_FILE")
416 END IF
417 END DO
418
419 CALL parser_search_string(parser, "remove_atom_energies", .true., atom_e_found, &
420 search_from_begin_of_file=.true.)
421
422 IF (atom_e_found) THEN
423 CALL parser_reset(parser)
424 i = 0
425 DO
426 CALL parser_search_string(parser, "atom_energy", .true., found, line)
427 IF (found) THEN
428 READ (line, *) dummy, ele, energy
429 DO j = 1, nele
430 IF (nnp_env%ele(j) == trim(ele)) THEN
431 i = i + 1
432 nnp_env%atom_energies(j) = energy
433 END IF
434 END DO
435 IF (i == nele) EXIT
436 ELSE
437 CALL cp_abort(__location__, trim(printtag)// &
438 "| atom energies are not specified")
439 END IF
440 END DO
441 END IF
442
443 CALL parser_search_string(parser, "global_nodes_short", .true., found, line, &
444 search_from_begin_of_file=.true.)
445 IF (found) THEN
446 READ (line, *) dummy, nnp_env%n_hnodes(:)
447 ELSE
448 CALL cp_abort(__location__, trim(printtag)// &
449 "NNP| global_nodes_short not specified in NNP_INPUT_FILE")
450 END IF
451
452 CALL parser_search_string(parser, "global_activation_short", .true., found, line, &
453 search_from_begin_of_file=.true.)
454 IF (found) THEN
455 READ (line, *) dummy, cactfnct(:)
456 ELSE
457 CALL cp_abort(__location__, trim(printtag)// &
458 "| global_activation_short not specified in NNP_INPUT_FILE")
459 END IF
460
461 DO i = 1, nnp_env%n_hlayer + 1
462 SELECT CASE (cactfnct(i))
463 CASE ("t")
464 nnp_env%actfnct(i) = nnp_actfnct_tanh
465 CASE ("g")
466 nnp_env%actfnct(i) = nnp_actfnct_gaus
467 CASE ("l")
468 nnp_env%actfnct(i) = nnp_actfnct_lin
469 CASE ("c")
470 nnp_env%actfnct(i) = nnp_actfnct_cos
471 CASE ("s")
472 nnp_env%actfnct(i) = nnp_actfnct_sig
473 CASE ("S")
474 nnp_env%actfnct(i) = nnp_actfnct_invsig
475 CASE ("e")
476 nnp_env%actfnct(i) = nnp_actfnct_exp
477 CASE ("p")
478 nnp_env%actfnct(i) = nnp_actfnct_softplus
479 CASE ("h")
480 nnp_env%actfnct(i) = nnp_actfnct_quad
481 CASE DEFAULT
482 CALL cp_abort(__location__, trim(printtag)// &
483 "| Activation function unkown")
484 END SELECT
485 END DO
486
487 ! determine n_rad and n_ang
488 DO i = 1, nele
489 nnp_env%n_rad(i) = 0
490 nnp_env%n_ang(i) = 0
491 END DO
492
493 ! count symfunctions
494 CALL parser_reset(parser)
495 first = .true.
496 DO
497 CALL parser_search_string(parser, "symfunction_short", .true., found, line)
498 IF (found) THEN
499 READ (line, *) dummy, ele, symfnct_type
500 DO i = 1, nele
501 IF (trim(ele) .EQ. nnp_env%ele(i)) THEN
502 IF (symfnct_type .EQ. 2) THEN
503 nnp_env%n_rad(i) = nnp_env%n_rad(i) + 1
504 ELSE IF (symfnct_type .EQ. 3) THEN
505 nnp_env%n_ang(i) = nnp_env%n_ang(i) + 1
506 ELSE
507 CALL cp_abort(__location__, trim(printtag)// &
508 "| Symmetry function type not supported")
509 END IF
510 END IF
511 END DO
512 first = .false.
513 ELSE
514 IF (first) CALL cp_abort(__location__, trim(printtag)// &
515 "| no symfunction_short specified in NNP_INPUT_FILE")
516 ! no additional symfnct found
517 EXIT
518 END IF
519 END DO
520
521 DO i = 1, nele
522 ALLOCATE (nnp_env%rad(i)%y(nnp_env%n_rad(i)))
523 ALLOCATE (nnp_env%rad(i)%funccut(nnp_env%n_rad(i)))
524 ALLOCATE (nnp_env%rad(i)%eta(nnp_env%n_rad(i)))
525 ALLOCATE (nnp_env%rad(i)%rs(nnp_env%n_rad(i)))
526 ALLOCATE (nnp_env%rad(i)%loc_min(nnp_env%n_rad(i)))
527 ALLOCATE (nnp_env%rad(i)%loc_max(nnp_env%n_rad(i)))
528 ALLOCATE (nnp_env%rad(i)%loc_av(nnp_env%n_rad(i)))
529 ALLOCATE (nnp_env%rad(i)%sigma(nnp_env%n_rad(i)))
530 ALLOCATE (nnp_env%rad(i)%ele(nnp_env%n_rad(i)))
531 ALLOCATE (nnp_env%rad(i)%nuc_ele(nnp_env%n_rad(i)))
532 nnp_env%rad(i)%funccut = 0.0_dp
533 nnp_env%rad(i)%eta = 0.0_dp
534 nnp_env%rad(i)%rs = 0.0_dp
535 nnp_env%rad(i)%ele = 'X'
536 nnp_env%rad(i)%nuc_ele = 0
537
538 ALLOCATE (nnp_env%ang(i)%y(nnp_env%n_ang(i)))
539 ALLOCATE (nnp_env%ang(i)%funccut(nnp_env%n_ang(i)))
540 ALLOCATE (nnp_env%ang(i)%eta(nnp_env%n_ang(i)))
541 ALLOCATE (nnp_env%ang(i)%zeta(nnp_env%n_ang(i)))
542 ALLOCATE (nnp_env%ang(i)%prefzeta(nnp_env%n_ang(i)))
543 ALLOCATE (nnp_env%ang(i)%lam(nnp_env%n_ang(i)))
544 ALLOCATE (nnp_env%ang(i)%loc_min(nnp_env%n_ang(i)))
545 ALLOCATE (nnp_env%ang(i)%loc_max(nnp_env%n_ang(i)))
546 ALLOCATE (nnp_env%ang(i)%loc_av(nnp_env%n_ang(i)))
547 ALLOCATE (nnp_env%ang(i)%sigma(nnp_env%n_ang(i)))
548 ALLOCATE (nnp_env%ang(i)%ele1(nnp_env%n_ang(i)))
549 ALLOCATE (nnp_env%ang(i)%ele2(nnp_env%n_ang(i)))
550 ALLOCATE (nnp_env%ang(i)%nuc_ele1(nnp_env%n_ang(i)))
551 ALLOCATE (nnp_env%ang(i)%nuc_ele2(nnp_env%n_ang(i)))
552 nnp_env%ang(i)%funccut = 0.0_dp
553 nnp_env%ang(i)%eta = 0.0_dp
554 nnp_env%ang(i)%zeta = 0.0_dp
555 nnp_env%ang(i)%prefzeta = 1.0_dp
556 nnp_env%ang(i)%lam = 0.0_dp
557 nnp_env%ang(i)%ele1 = 'X'
558 nnp_env%ang(i)%ele2 = 'X'
559 nnp_env%ang(i)%nuc_ele1 = 0
560 nnp_env%ang(i)%nuc_ele2 = 0
561
562 ! set number of nodes
563 nnp_env%arc(i)%n_nodes(1) = nnp_env%n_rad(i) + nnp_env%n_ang(i)
564 nnp_env%arc(i)%n_nodes(2:nnp_env%n_layer - 1) = nnp_env%n_hnodes
565 nnp_env%arc(i)%n_nodes(nnp_env%n_layer) = 1
566 DO j = 1, nnp_env%n_layer
567 ALLOCATE (nnp_env%arc(i)%layer(j)%node(nnp_env%arc(i)%n_nodes(j)))
568 ALLOCATE (nnp_env%arc(i)%layer(j)%node_grad(nnp_env%arc(i)%n_nodes(j)))
569 ALLOCATE (nnp_env%arc(i)%layer(j)%tmp_der(nnp_env%arc(i)%n_nodes(1), nnp_env%arc(i)%n_nodes(j)))
570 END DO
571 END DO
572
573 ! read, bcast and sort symfnct parameters
574 DO i = 1, nele
575 nnp_env%n_rad(i) = 0
576 nnp_env%n_ang(i) = 0
577 END DO
578 CALL parser_reset(parser)
579 first = .true.
580 nnp_env%max_cut = 0.0_dp
581 DO
582 CALL parser_search_string(parser, "symfunction_short", .true., found, line)
583 IF (found) THEN
584 READ (line, *) dummy, ele, symfnct_type
585 DO i = 1, nele
586 IF (trim(ele) .EQ. nnp_env%ele(i)) THEN
587 IF (symfnct_type .EQ. 2) THEN
588 nnp_env%n_rad(i) = nnp_env%n_rad(i) + 1
589 READ (line, *) dummy, ele, symfnct_type, &
590 nnp_env%rad(i)%ele(nnp_env%n_rad(i)), &
591 nnp_env%rad(i)%eta(nnp_env%n_rad(i)), &
592 nnp_env%rad(i)%rs(nnp_env%n_rad(i)), &
593 nnp_env%rad(i)%funccut(nnp_env%n_rad(i))
594 IF (nnp_env%max_cut < nnp_env%rad(i)%funccut(nnp_env%n_rad(i))) THEN
595 nnp_env%max_cut = nnp_env%rad(i)%funccut(nnp_env%n_rad(i))
596 END IF
597 ELSE IF (symfnct_type .EQ. 3) THEN
598 nnp_env%n_ang(i) = nnp_env%n_ang(i) + 1
599 READ (line, *) dummy, ele, symfnct_type, &
600 nnp_env%ang(i)%ele1(nnp_env%n_ang(i)), &
601 nnp_env%ang(i)%ele2(nnp_env%n_ang(i)), &
602 nnp_env%ang(i)%eta(nnp_env%n_ang(i)), &
603 nnp_env%ang(i)%lam(nnp_env%n_ang(i)), &
604 nnp_env%ang(i)%zeta(nnp_env%n_ang(i)), &
605 nnp_env%ang(i)%funccut(nnp_env%n_ang(i))
606 nnp_env%ang(i)%prefzeta(nnp_env%n_ang(i)) = &
607 2.0_dp**(1.0_dp - nnp_env%ang(i)%zeta(nnp_env%n_ang(i)))
608 IF (nnp_env%max_cut < nnp_env%ang(i)%funccut(nnp_env%n_ang(i))) THEN
609 nnp_env%max_cut = nnp_env%ang(i)%funccut(nnp_env%n_ang(i))
610 END IF
611 ELSE
612 CALL cp_abort(__location__, trim(printtag)// &
613 "| Symmetry function type not supported")
614 END IF
615 END IF
616 END DO
617 first = .false.
618 ELSE
619 IF (first) CALL cp_abort(__location__, trim(printtag)// &
620 "| no symfunction_short specified in NNP_INPUT_FILE")
621 ! no additional symfnct found
622 EXIT
623 END IF
624 END DO
625
626 DO i = 1, nele
627 DO j = 1, nnp_env%n_rad(i)
628 CALL get_ptable_info(nnp_env%rad(i)%ele(j), number=nnp_env%rad(i)%nuc_ele(j))
629 END DO
630 DO j = 1, nnp_env%n_ang(i)
631 CALL get_ptable_info(nnp_env%ang(i)%ele1(j), number=nnp_env%ang(i)%nuc_ele1(j))
632 CALL get_ptable_info(nnp_env%ang(i)%ele2(j), number=nnp_env%ang(i)%nuc_ele2(j))
633 ! sort ele1 and ele2
634 IF (nnp_env%ang(i)%nuc_ele1(j) .GT. nnp_env%ang(i)%nuc_ele2(j)) THEN
635 ele = nnp_env%ang(i)%ele1(j)
636 nnp_env%ang(i)%ele1(j) = nnp_env%ang(i)%ele2(j)
637 nnp_env%ang(i)%ele2(j) = ele
638 nuc_ele = nnp_env%ang(i)%nuc_ele1(j)
639 nnp_env%ang(i)%nuc_ele1(j) = nnp_env%ang(i)%nuc_ele2(j)
640 nnp_env%ang(i)%nuc_ele2(j) = nuc_ele
641 END IF
642 END DO
643 END DO
644 ! Done with input.nn file
645 CALL parser_release(parser)
646
647 ! sort symmetry functions and output information
648 CALL nnp_sort_acsf(nnp_env)
649 CALL nnp_write_acsf(nnp_env, logger%para_env, printtag)
650 CALL nnp_write_arc(nnp_env, logger%para_env, printtag)
651
652 ! read scaling information from file
653 IF (nnp_env%scale_acsf .OR. nnp_env%center_acsf .OR. nnp_env%scale_sigma_acsf) THEN
654 IF (logger%para_env%is_source()) THEN
655 WRITE (unit_nr, *) trim(printtag)//"| Reading scaling information from file: ", trim(file_name)
656 END IF
657 CALL section_vals_val_get(nnp_env%nnp_input, "SCALE_FILE_NAME", &
658 c_val=file_name)
659 CALL parser_create(parser, file_name, para_env=logger%para_env)
660
661 ! Get number of elements in scaling file
662 CALL parser_read_line(parser, 1)
663 k = 0
664 DO WHILE (k < 7)
665 READ (parser%input_line, *, iostat=io) test_array(1:k)
666 IF (io == -1) EXIT
667 k = k + 1
668 END DO
669 k = k - 1
670
671 IF (k == 5 .AND. nnp_env%scale_sigma_acsf) THEN
672 cpabort("Sigma scaling requested, but scaling.data does not contain sigma.")
673 END IF
674
675 CALL parser_reset(parser)
676 DO i = 1, nnp_env%n_ele
677 DO j = 1, nnp_env%n_rad(i)
678 CALL parser_read_line(parser, 1)
679 IF (nnp_env%scale_sigma_acsf) THEN
680 READ (parser%input_line, *) dummy, dummy, &
681 nnp_env%rad(i)%loc_min(j), &
682 nnp_env%rad(i)%loc_max(j), &
683 nnp_env%rad(i)%loc_av(j), &
684 nnp_env%rad(i)%sigma(j)
685 ELSE
686 READ (parser%input_line, *) dummy, dummy, &
687 nnp_env%rad(i)%loc_min(j), &
688 nnp_env%rad(i)%loc_max(j), &
689 nnp_env%rad(i)%loc_av(j)
690 END IF
691 END DO
692 DO j = 1, nnp_env%n_ang(i)
693 CALL parser_read_line(parser, 1)
694 IF (nnp_env%scale_sigma_acsf) THEN
695 READ (parser%input_line, *) dummy, dummy, &
696 nnp_env%ang(i)%loc_min(j), &
697 nnp_env%ang(i)%loc_max(j), &
698 nnp_env%ang(i)%loc_av(j), &
699 nnp_env%ang(i)%sigma(j)
700 ELSE
701 READ (parser%input_line, *) dummy, dummy, &
702 nnp_env%ang(i)%loc_min(j), &
703 nnp_env%ang(i)%loc_max(j), &
704 nnp_env%ang(i)%loc_av(j)
705 END IF
706 END DO
707 END DO
708 CALL parser_release(parser)
709 END IF
710
711 CALL nnp_init_acsf_groups(nnp_env)
712
713 ! read weights from file
714 DO i = 1, nnp_env%n_ele
715 DO j = 2, nnp_env%n_layer
716 ALLOCATE (nnp_env%arc(i)%layer(j)%weights(nnp_env%arc(i)%n_nodes(j - 1), &
717 nnp_env%arc(i)%n_nodes(j), nnp_env%n_committee))
718 ALLOCATE (nnp_env%arc(i)%layer(j)%bweights(nnp_env%arc(i)%n_nodes(j), nnp_env%n_committee))
719 END DO
720 END DO
721 DO i_com = 1, nnp_env%n_committee
722 CALL section_vals_val_get(model_section, "WEIGHTS", c_val=base_name, i_rep_section=i_com)
723 IF (logger%para_env%is_source()) THEN
724 WRITE (unit_nr, *) trim(printtag)//"| Initializing weights for model: ", i_com
725 END IF
726 DO i = 1, nnp_env%n_ele
727 WRITE (file_name, '(A,I0.3,A)') trim(base_name)//".", nnp_env%nuc_ele(i), ".data"
728 IF (logger%para_env%is_source()) THEN
729 WRITE (unit_nr, *) trim(printtag)//"| Reading weights from file: ", trim(file_name)
730 END IF
731 CALL parser_create(parser, file_name, para_env=logger%para_env)
732 n_weight = 0
733 DO WHILE (.true.)
734 CALL parser_read_line(parser, 1, at_end)
735 IF (at_end) EXIT
736 n_weight = n_weight + 1
737 END DO
738
739 ALLOCATE (weights(n_weight))
740
741 CALL parser_reset(parser)
742 DO j = 1, n_weight
743 CALL parser_read_line(parser, 1)
744 READ (parser%input_line, *) weights(j)
745 END DO
746 CALL parser_release(parser)
747
748 ! sort weights into corresponding arrays
749 iweight = 0
750 DO j = 2, nnp_env%n_layer
751 DO k = 1, nnp_env%arc(i)%n_nodes(j - 1)
752 DO l = 1, nnp_env%arc(i)%n_nodes(j)
753 iweight = iweight + 1
754 nnp_env%arc(i)%layer(j)%weights(k, l, i_com) = weights(iweight)
755 END DO
756 END DO
757
758 DO k = 1, nnp_env%arc(i)%n_nodes(j)
759 iweight = iweight + 1
760 nnp_env%arc(i)%layer(j)%bweights(k, i_com) = weights(iweight)
761 END DO
762 END DO
763
764 DEALLOCATE (weights)
765 END DO
766 END DO
767
768 !Initialize extrapolation counter
769 nnp_env%expol = 0
770
771 ! Bias the standard deviation of committee disagreement
772 NULLIFY (bias_section)
773 explicit = .false.
774 !HELIUM NNP does atm not allow for bias (not even defined)
775 bias_section => section_vals_get_subs_vals(nnp_env%nnp_input, "BIAS", can_return_null=.true.)
776 IF (ASSOCIATED(bias_section)) CALL section_vals_get(bias_section, explicit=explicit)
777 nnp_env%bias = .false.
778 IF (explicit) THEN
779 IF (nnp_env%n_committee > 1) THEN
780 IF (logger%para_env%is_source()) THEN
781 WRITE (unit_nr, *) "NNP| Biasing of committee disagreement enabled"
782 END IF
783 nnp_env%bias = .true.
784 ALLOCATE (nnp_env%bias_forces(3, nnp_env%num_atoms))
785 ALLOCATE (nnp_env%bias_e_avrg(nnp_env%n_committee))
786 CALL section_vals_val_get(bias_section, "SIGMA_0", r_val=nnp_env%bias_sigma0)
787 CALL section_vals_val_get(bias_section, "K_B", r_val=nnp_env%bias_kb)
788 nnp_env%bias_e_avrg(:) = 0.0_dp
789 CALL section_vals_val_get(bias_section, "ALIGN_NNP_ENERGIES", explicit=explicit)
790 nnp_env%bias_align = explicit
791 IF (explicit) THEN
792 NULLIFY (work)
793 CALL section_vals_val_get(bias_section, "ALIGN_NNP_ENERGIES", r_vals=work)
794 IF (SIZE(work) .NE. nnp_env%n_committee) THEN
795 cpabort("ALIGN_NNP_ENERGIES size mismatch wrt committee size.")
796 END IF
797 nnp_env%bias_e_avrg(:) = work
798 IF (logger%para_env%is_source()) THEN
799 WRITE (unit_nr, *) trim(printtag)//"| Biasing is aligned by shifting the energy prediction of the C-NNP members"
800 END IF
801 END IF
802 ELSE
803 cpwarn("NNP committee size is 1, BIAS section is ignored.")
804 END IF
805 END IF
806
807 IF (logger%para_env%is_source()) THEN
808 WRITE (unit_nr, *) trim(printtag)//"| NNP force environment initialized"
809 END IF
810
811 CALL timestop(handle)
812
813 END SUBROUTINE nnp_init_model
814
815END MODULE nnp_environment
atomic_kind_types
Define the atomic kind types and their sub types.
Definition atomic_kind_types.F:23
bibliography
collects all references to literature in CP2K as new algorithms / method are included from literature...
Definition bibliography.F:21
bibliography::schran2020b
integer, save, public schran2020b
Definition bibliography.F:36
bibliography::schran2020a
integer, save, public schran2020a
Definition bibliography.F:36
bibliography::behler2011
integer, save, public behler2011
Definition bibliography.F:36
bibliography::behler2007
integer, save, public behler2007
Definition bibliography.F:36
cell_methods
Handles all functions related to the CELL.
Definition cell_methods.F:15
cell_methods::read_cell
recursive subroutine, public read_cell(cell, cell_ref, use_ref_cell, cell_section, check_for_ref, para_env)
...
Definition cell_methods.F:272
cell_methods::write_cell
subroutine, public write_cell(cell, subsys_section, tag)
Write the cell parameters to the output unit.
Definition cell_methods.F:731
cell_types
Handles all functions related to the CELL.
Definition cell_types.F:15
cell_types::cell_release
subroutine, public cell_release(cell)
releases the given cell (see doc/ReferenceCounting.html)
Definition cell_types.F:559
cell_types::get_cell
subroutine, public get_cell(cell, alpha, beta, gamma, deth, orthorhombic, abc, periodic, h, h_inv, symmetry_id, tag)
Get informations about a simulation cell.
Definition cell_types.F:195
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_parser_methods
Utility routines to read data from files. Kept as close as possible to the old parser because.
Definition cp_parser_methods.F:20
cp_parser_methods::parser_read_line
subroutine, public parser_read_line(parser, nline, at_end)
Read the next line from a logical unit "unit" (I/O node only). Skip (nline-1) lines and skip also all...
Definition cp_parser_methods.F:147
cp_parser_methods::parser_search_string
subroutine, public parser_search_string(parser, string, ignore_case, found, line, begin_line, search_from_begin_of_file)
Search a string pattern in a file defined by its logical unit number "unit". A case sensitive search ...
Definition cp_parser_methods.F:786
cp_parser_types
Utility routines to read data from files. Kept as close as possible to the old parser because.
Definition cp_parser_types.F:21
cp_parser_types::parser_reset
subroutine, public parser_reset(parser)
Resets the parser: rewinding the unit and re-initializing all parser structures.
Definition cp_parser_types.F:228
cp_parser_types::parser_release
subroutine, public parser_release(parser)
releases the parser
Definition cp_parser_types.F:109
cp_parser_types::parser_create
subroutine, public parser_create(parser, file_name, unit_nr, para_env, end_section_label, separator_chars, comment_char, continuation_char, quote_char, section_char, parse_white_lines, initial_variables, apply_preprocessing)
Start a parser run. Initial variables allow to @SET stuff before opening the file.
Definition cp_parser_types.F:147
cp_subsys_methods
Initialize a small environment for a particular calculation.
Definition cp_subsys_methods.F:15
cp_subsys_methods::cp_subsys_create
subroutine, public cp_subsys_create(subsys, para_env, root_section, force_env_section, subsys_section, use_motion_section, qmmm, qmmm_env, exclusions, elkind)
Creates allocates and fills subsys from given input.
Definition cp_subsys_methods.F:96
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_set
subroutine, public cp_subsys_set(subsys, atomic_kinds, particles, local_particles, molecules, molecule_kinds, local_molecules, para_env, colvar_p, shell_particles, core_particles, gci, multipoles, results, cell)
sets various propreties of the subsys
Definition cp_subsys_types.F:205
distribution_1d_types
stores a lists of integer that are local to a processor. The idea is that these integers represent ob...
Definition distribution_1d_types.F:24
distribution_1d_types::distribution_1d_release
subroutine, public distribution_1d_release(distribution_1d)
releases the given distribution_1d
Definition distribution_1d_types.F:149
distribution_methods
Distribution methods for atoms, particles, or molecules.
Definition distribution_methods.F:15
distribution_methods::distribute_molecules_1d
subroutine, public distribute_molecules_1d(atomic_kind_set, particle_set, local_particles, molecule_kind_set, molecule_set, local_molecules, force_env_section, prev_molecule_kind_set, prev_local_molecules)
Distribute molecules and particles.
Definition distribution_methods.F:108
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:731
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_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
molecule_kind_types
Define the molecule kind structure types and the corresponding functionality.
Definition molecule_kind_types.F:16
molecule_kind_types::write_molecule_kind_set
subroutine, public write_molecule_kind_set(molecule_kind_set, subsys_section)
Write a moleculeatomic kind set data set to the output unit.
Definition molecule_kind_types.F:966
molecule_types
Define the data structure for the molecule information.
Definition molecule_types.F:16
nnp_acsf
Functionality for atom centered symmetry functions for neural network potentials.
Definition nnp_acsf.F:14
nnp_acsf::nnp_write_acsf
subroutine, public nnp_write_acsf(nnp, para_env, printtag)
Write symmetry function information.
Definition nnp_acsf.F:1197
nnp_acsf::nnp_init_acsf_groups
subroutine, public nnp_init_acsf_groups(nnp)
Initialize symmetry function groups.
Definition nnp_acsf.F:1055
nnp_acsf::nnp_sort_acsf
subroutine, public nnp_sort_acsf(nnp)
Sort symmetry functions according to different criteria.
Definition nnp_acsf.F:796
nnp_acsf::nnp_sort_ele
subroutine, public nnp_sort_ele(ele, nuc_ele)
Sort element array according to atomic number.
Definition nnp_acsf.F:756
nnp_environment_types
Data types for neural network potentials.
Definition nnp_environment_types.F:13
nnp_environment_types::nnp_actfnct_lin
integer, parameter, public nnp_actfnct_lin
Definition nnp_environment_types.F:67
nnp_environment_types::nnp_env_set
subroutine, public nnp_env_set(nnp_env, nnp_forces, subsys, atomic_kind_set, particle_set, local_particles, molecule_kind_set, molecule_set, local_molecules, nnp_input, force_env_input, cell, cell_ref, use_ref_cell, nnp_potential_energy)
Sets various attributes of the nnp environment.
Definition nnp_environment_types.F:506
nnp_environment_types::nnp_actfnct_cos
integer, parameter, public nnp_actfnct_cos
Definition nnp_environment_types.F:67
nnp_environment_types::nnp_actfnct_invsig
integer, parameter, public nnp_actfnct_invsig
Definition nnp_environment_types.F:67
nnp_environment_types::nnp_actfnct_sig
integer, parameter, public nnp_actfnct_sig
Definition nnp_environment_types.F:67
nnp_environment_types::nnp_actfnct_exp
integer, parameter, public nnp_actfnct_exp
Definition nnp_environment_types.F:67
nnp_environment_types::nnp_actfnct_softplus
integer, parameter, public nnp_actfnct_softplus
Definition nnp_environment_types.F:67
nnp_environment_types::nnp_actfnct_quad
integer, parameter, public nnp_actfnct_quad
Definition nnp_environment_types.F:67
nnp_environment_types::nnp_actfnct_gaus
integer, parameter, public nnp_actfnct_gaus
Definition nnp_environment_types.F:67
nnp_environment_types::nnp_actfnct_tanh
integer, parameter, public nnp_actfnct_tanh
Definition nnp_environment_types.F:67
nnp_environment
Methods dealing with Neural Network potentials.
Definition nnp_environment.F:13
nnp_environment::nnp_init_model
subroutine, public nnp_init_model(nnp_env, printtag)
Initialize the Neural Network Potential.
Definition nnp_environment.F:247
nnp_environment::nnp_init
subroutine, public nnp_init(nnp_env, root_section, para_env, force_env_section, subsys_section, use_motion_section)
Read and initialize all the information for neural network potentials.
Definition nnp_environment.F:92
nnp_model
Methods dealing with core routines for artificial neural networks.
Definition nnp_model.F:13
nnp_model::nnp_write_arc
subroutine, public nnp_write_arc(nnp, para_env, printtag)
Write neural network architecture information.
Definition nnp_model.F:47
particle_methods
Define methods related to particle_type.
Definition particle_methods.F:14
particle_methods::write_fist_particle_coordinates
subroutine, public write_fist_particle_coordinates(particle_set, subsys_section, charges)
Write the atomic coordinates to the output unit.
Definition particle_methods.F:484
particle_methods::write_structure_data
subroutine, public write_structure_data(particle_set, cell, input_section)
Write structure data requested by a separate structure data input section to the output unit....
Definition particle_methods.F:786
particle_methods::write_particle_distances
subroutine, public write_particle_distances(particle_set, cell, subsys_section)
Write the matrix of the particle distances to the output unit.
Definition particle_methods.F:606
particle_types
Define the data structure for the particle information.
Definition particle_types.F:19
periodic_table
Periodic Table related data definitions.
Definition periodic_table.F:28
periodic_table::get_ptable_info
subroutine, public get_ptable_info(symbol, number, amass, ielement, covalent_radius, metallic_radius, vdw_radius, found)
Pass information about the kind given the element symbol.
Definition periodic_table.F:85
atomic_kind_types::atomic_kind_type
Provides all information about an atomic kind.
Definition atomic_kind_types.F:45
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_parser_types::cp_parser_type
represent a parser
Definition cp_parser_types.F:77
cp_subsys_types::cp_subsys_type
represents a system: atoms, molecules, their pos,vel,...
Definition cp_subsys_types.F:89
distribution_1d_types::distribution_1d_type
structure to store local (to a processor) ordered lists of integers.
Definition distribution_1d_types.F:62
input_section_types::section_vals_type
stores the values of a section
Definition input_section_types.F:127
message_passing::mp_para_env_type
stores all the informations relevant to an mpi environment
Definition message_passing.F:763
molecule_kind_types::molecule_kind_type
Definition molecule_kind_types.F:161
molecule_types::molecule_type
Definition molecule_types.F:110
nnp_environment_types::nnp_type
Main data type collecting all relevant data for neural network potentials.
Definition nnp_environment_types.F:83
particle_types::particle_type
Definition particle_types.F:35