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colvar_utils.F
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1!--------------------------------------------------------------------------------------------------!
2! CP2K: A general program to perform molecular dynamics simulations !
3! Copyright 2000-2024 CP2K developers group <https://cp2k.org> !
4! !
5! SPDX-License-Identifier: GPL-2.0-or-later !
6!--------------------------------------------------------------------------------------------------!
7
8! **************************************************************************************************
9!> \brief evaluations of colvar for internal coordinates schemes
10!> \par History
11!> 05-2007 created [tlaino]
12!> \author Teodoro Laino - Zurich University (2007) [tlaino]
13! **************************************************************************************************
14MODULE colvar_utils
15 USE cell_types, ONLY: cell_type
16 USE colvar_methods, ONLY: colvar_eval_mol_f
17 USE colvar_types, ONLY: &
18 colvar_counters, colvar_setup, colvar_type, coord_colvar_id, distance_from_path_colvar_id, &
19 gyration_colvar_id, mindist_colvar_id, population_colvar_id, reaction_path_colvar_id, &
20 rmsd_colvar_id
21 USE cp_subsys_types, ONLY: cp_subsys_get,&
22 cp_subsys_type
23 USE distribution_1d_types, ONLY: distribution_1d_type
24 USE force_env_types, ONLY: force_env_get,&
25 force_env_type
26 USE input_constants, ONLY: rmsd_all,&
27 rmsd_list
28 USE kinds, ONLY: dp
29 USE mathlib, ONLY: invert_matrix
30 USE memory_utilities, ONLY: reallocate
31 USE molecule_kind_list_types, ONLY: molecule_kind_list_type
32 USE molecule_kind_types, ONLY: colvar_constraint_type,&
33 fixd_constraint_type,&
34 get_molecule_kind,&
35 molecule_kind_type
36 USE molecule_list_types, ONLY: molecule_list_type
37 USE molecule_types, ONLY: get_molecule,&
38 global_constraint_type,&
39 local_colvar_constraint_type,&
40 molecule_type
41 USE particle_list_types, ONLY: particle_list_type
42 USE particle_types, ONLY: particle_type
43 USE rmsd, ONLY: rmsd3
44 USE string_utilities, ONLY: uppercase
45 USE util, ONLY: sort
46#include "./base/base_uses.f90"
47
48 IMPLICIT NONE
49
50 PRIVATE
51 PUBLIC :: number_of_colvar, &
52 eval_colvar, &
53 set_colvars_target, &
54 get_clv_force, &
55 post_process_colvar
56
57 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'colvar_utils'
58
59CONTAINS
60
61! **************************************************************************************************
62!> \brief Gives back the number of colvar defined for a force_eval
63!> \param force_env ...
64!> \param only_intra_colvar ...
65!> \param unique ...
66!> \return ...
67!> \author Teodoro Laino 05.2007 [tlaino] - Zurich University
68! **************************************************************************************************
69 FUNCTION number_of_colvar(force_env, only_intra_colvar, unique) RESULT(ntot)
70 TYPE(force_env_type), POINTER :: force_env
71 LOGICAL, INTENT(IN), OPTIONAL :: only_intra_colvar, unique
72 INTEGER :: ntot
73
74 CHARACTER(LEN=*), PARAMETER :: routinen = 'number_of_colvar'
75
76 INTEGER :: handle, ikind, imol
77 LOGICAL :: my_unique, skip_inter_colvar
78 TYPE(colvar_counters) :: ncolv
79 TYPE(cp_subsys_type), POINTER :: subsys
80 TYPE(global_constraint_type), POINTER :: gci
81 TYPE(molecule_kind_list_type), POINTER :: molecule_kinds
82 TYPE(molecule_kind_type), POINTER :: molecule_kind, molecule_kind_set(:)
83 TYPE(molecule_list_type), POINTER :: molecules
84 TYPE(molecule_type), POINTER :: molecule, molecule_set(:)
85
86 NULLIFY (subsys, molecules, molecule_kind, molecule, molecule_set, gci)
87 CALL timeset(routinen, handle)
88 skip_inter_colvar = .false.
89 my_unique = .false.
90 IF (PRESENT(only_intra_colvar)) skip_inter_colvar = only_intra_colvar
91 IF (PRESENT(unique)) my_unique = unique
92 ntot = 0
93 CALL force_env_get(force_env=force_env, subsys=subsys)
94 CALL cp_subsys_get(subsys=subsys, molecules=molecules, gci=gci, &
95 molecule_kinds=molecule_kinds)
96
97 molecule_set => molecules%els
98 ! Intramolecular Colvar
99 IF (my_unique) THEN
100 molecule_kind_set => molecule_kinds%els
101 DO ikind = 1, molecule_kinds%n_els
102 molecule_kind => molecule_kind_set(ikind)
103 CALL get_molecule_kind(molecule_kind, ncolv=ncolv)
104 ntot = ntot + ncolv%ntot
105 END DO
106 ELSE
107 mol: DO imol = 1, SIZE(molecule_set)
108 molecule => molecule_set(imol)
109 molecule_kind => molecule%molecule_kind
110
111 CALL get_molecule_kind(molecule_kind, &
112 ncolv=ncolv)
113 ntot = ntot + ncolv%ntot
114 END DO mol
115 END IF
116 ! Intermolecular Colvar
117 IF (.NOT. skip_inter_colvar) THEN
118 IF (ASSOCIATED(gci)) THEN
119 ntot = ntot + gci%ncolv%ntot
120 END IF
121 END IF
122 CALL timestop(handle)
123
124 END FUNCTION number_of_colvar
125
126! **************************************************************************************************
127!> \brief Set the value of target for constraints/restraints
128!> \param targets ...
129!> \param force_env ...
130!> \author Teodoro Laino 05.2007 [tlaino] - Zurich University
131! **************************************************************************************************
132 SUBROUTINE set_colvars_target(targets, force_env)
133 REAL(kind=dp), DIMENSION(:), INTENT(IN) :: targets
134 TYPE(force_env_type), POINTER :: force_env
135
136 CHARACTER(LEN=*), PARAMETER :: routinen = 'set_colvars_target'
137
138 INTEGER :: handle, i, ikind, ind, nkind
139 TYPE(cell_type), POINTER :: cell
140 TYPE(colvar_constraint_type), DIMENSION(:), &
141 POINTER :: colv_list
142 TYPE(colvar_counters) :: ncolv
143 TYPE(cp_subsys_type), POINTER :: subsys
144 TYPE(global_constraint_type), POINTER :: gci
145 TYPE(molecule_kind_list_type), POINTER :: molecule_kinds
146 TYPE(molecule_kind_type), POINTER :: molecule_kind
147
148 NULLIFY (cell, subsys, molecule_kinds, molecule_kind, gci, colv_list)
149 CALL timeset(routinen, handle)
150 CALL force_env_get(force_env=force_env, subsys=subsys, cell=cell)
151 CALL cp_subsys_get(subsys=subsys, gci=gci, molecule_kinds=molecule_kinds)
152
153 nkind = molecule_kinds%n_els
154 ! Set Target for Intramolecular Colvars
155 mol: DO ikind = 1, nkind
156 molecule_kind => molecule_kinds%els(ikind)
157 CALL get_molecule_kind(molecule_kind, &
158 colv_list=colv_list, &
159 ncolv=ncolv)
160 IF (ncolv%ntot /= 0) THEN
161 DO i = 1, SIZE(colv_list)
162 ind = colv_list(i)%inp_seq_num
163 colv_list(i)%expected_value = targets(ind)
164 END DO
165 END IF
166 END DO mol
167 ! Set Target for Intermolecular Colvars
168 IF (ASSOCIATED(gci)) THEN
169 IF (gci%ncolv%ntot /= 0) THEN
170 colv_list => gci%colv_list
171 DO i = 1, SIZE(colv_list)
172 ind = colv_list(i)%inp_seq_num
173 colv_list(i)%expected_value = targets(ind)
174 END DO
175 END IF
176 END IF
177 CALL timestop(handle)
178
179 END SUBROUTINE set_colvars_target
180
181! **************************************************************************************************
182!> \brief Computes the values of colvars and the Wilson matrix B and its invers A
183!> \param force_env ...
184!> \param coords ...
185!> \param cvalues ...
186!> \param Bmatrix ...
187!> \param MassI ...
188!> \param Amatrix ...
189!> \author Teodoro Laino 05.2007 [tlaino] - Zurich University
190! **************************************************************************************************
191 SUBROUTINE eval_colvar(force_env, coords, cvalues, Bmatrix, MassI, Amatrix)
192
193 TYPE(force_env_type), POINTER :: force_env
194 REAL(kind=dp), DIMENSION(:), INTENT(IN), OPTIONAL :: coords
195 REAL(kind=dp), DIMENSION(:), INTENT(OUT) :: cvalues
196 REAL(kind=dp), DIMENSION(:, :), OPTIONAL, POINTER :: bmatrix
197 REAL(kind=dp), DIMENSION(:), OPTIONAL, POINTER :: massi
198 REAL(kind=dp), DIMENSION(:, :), OPTIONAL, POINTER :: amatrix
199
200 CHARACTER(LEN=*), PARAMETER :: routinen = 'eval_colvar'
201
202 INTEGER :: handle, i, ikind, imol, n_tot, natom, &
203 nkind, nmol_per_kind, offset
204 INTEGER, DIMENSION(:), POINTER :: map, wrk
205 LOGICAL :: check
206 REAL(kind=dp) :: inv_error
207 REAL(kind=dp), ALLOCATABLE, DIMENSION(:, :) :: bwrk, gmatrix, gmatrix_i
208 REAL(kind=dp), DIMENSION(:), POINTER :: rwrk
209 TYPE(cell_type), POINTER :: cell
210 TYPE(colvar_counters) :: ncolv
211 TYPE(cp_subsys_type), POINTER :: subsys
212 TYPE(distribution_1d_type), POINTER :: local_molecules
213 TYPE(global_constraint_type), POINTER :: gci
214 TYPE(molecule_kind_list_type), POINTER :: molecule_kinds
215 TYPE(molecule_kind_type), POINTER :: molecule_kind
216 TYPE(molecule_list_type), POINTER :: molecules
217 TYPE(molecule_type), POINTER :: molecule, molecule_set(:)
218 TYPE(particle_list_type), POINTER :: particles
219 TYPE(particle_type), POINTER :: particle_set(:)
220
221 NULLIFY (cell, subsys, local_molecules, molecule_kinds, &
222 molecules, molecule_kind, molecule, &
223 molecule_set, particles, particle_set, gci)
224 IF (PRESENT(bmatrix)) THEN
225 check = ASSOCIATED(bmatrix)
226 cpassert(check)
227 bmatrix = 0.0_dp
228 END IF
229 CALL timeset(routinen, handle)
230 ALLOCATE (map(SIZE(cvalues)))
231 map = huge(0) ! init all, since used in a sort, but not all set in parallel.
232 CALL force_env_get(force_env=force_env, subsys=subsys, cell=cell)
233 n_tot = 0
234 cvalues = 0.0_dp
235 CALL cp_subsys_get(subsys=subsys, &
236 particles=particles, &
237 molecules=molecules, &
238 local_molecules=local_molecules, &
239 gci=gci, &
240 molecule_kinds=molecule_kinds)
241
242 nkind = molecule_kinds%n_els
243 particle_set => particles%els
244 molecule_set => molecules%els
245 ! Intramolecular Colvars
246 IF (number_of_colvar(force_env, only_intra_colvar=.true.) /= 0) THEN
247 mol: DO ikind = 1, nkind
248 nmol_per_kind = local_molecules%n_el(ikind)
249 DO imol = 1, nmol_per_kind
250 i = local_molecules%list(ikind)%array(imol)
251 molecule => molecule_set(i)
252 molecule_kind => molecule%molecule_kind
253
254 CALL get_molecule_kind(molecule_kind, &
255 ncolv=ncolv)
256 offset = get_colvar_offset(i, molecule_set)
257 ! Collective variables
258 IF (ncolv%ntot /= 0) THEN
259 CALL eval_colv_int(molecule, particle_set, coords, cell, cvalues, &
260 bmatrix, offset, n_tot, map)
261 END IF
262 END DO
263 END DO mol
264 CALL force_env%para_env%sum(n_tot)
265 CALL force_env%para_env%sum(cvalues)
266 IF (PRESENT(bmatrix)) CALL force_env%para_env%sum(bmatrix)
267 END IF
268 offset = n_tot
269 ! Intermolecular Colvars
270 IF (ASSOCIATED(gci)) THEN
271 IF (gci%ncolv%ntot /= 0) THEN
272 CALL eval_colv_ext(gci, particle_set, coords, cell, cvalues, &
273 bmatrix, offset, n_tot, map)
274 END IF
275 END IF
276 cpassert(n_tot == SIZE(cvalues))
277 ! Sort values of Collective Variables according the order of the input
278 ! sections
279 ALLOCATE (wrk(SIZE(cvalues)))
280 ALLOCATE (rwrk(SIZE(cvalues)))
281 CALL sort(map, SIZE(map), wrk)
282 rwrk = cvalues
283 DO i = 1, SIZE(wrk)
284 cvalues(i) = rwrk(wrk(i))
285 END DO
286 ! check and sort on Bmatrix
287 IF (PRESENT(bmatrix)) THEN
288 check = n_tot == SIZE(bmatrix, 2)
289 cpassert(check)
290 ALLOCATE (bwrk(SIZE(bmatrix, 1), SIZE(bmatrix, 2)))
291 bwrk(:, :) = bmatrix
292 DO i = 1, SIZE(wrk)
293 bmatrix(:, i) = bwrk(:, wrk(i))
294 END DO
295 DEALLOCATE (bwrk)
296 END IF
297 DEALLOCATE (rwrk)
298 DEALLOCATE (wrk)
299 DEALLOCATE (map)
300 ! Construction of the Amatrix
301 IF (PRESENT(bmatrix) .AND. PRESENT(amatrix)) THEN
302 cpassert(ASSOCIATED(amatrix))
303 check = SIZE(bmatrix, 1) == SIZE(amatrix, 2)
304 cpassert(check)
305 check = SIZE(bmatrix, 2) == SIZE(amatrix, 1)
306 cpassert(check)
307 ALLOCATE (gmatrix(n_tot, n_tot))
308 ALLOCATE (gmatrix_i(n_tot, n_tot))
309 gmatrix(:, :) = matmul(transpose(bmatrix), bmatrix)
310 CALL invert_matrix(gmatrix, gmatrix_i, inv_error)
311 IF (abs(inv_error) > 1.0e-8_dp) &
312 cpwarn("Error in inverting the Gmatrix larger than 1.0E-8!")
313 amatrix = matmul(gmatrix_i, transpose(bmatrix))
314 DEALLOCATE (gmatrix_i)
315 DEALLOCATE (gmatrix)
316 END IF
317 IF (PRESENT(massi)) THEN
318 natom = SIZE(particle_set)
319 cpassert(ASSOCIATED(massi))
320 cpassert(SIZE(massi) == natom*3)
321 DO i = 1, natom
322 massi((i - 1)*3 + 1) = 1.0_dp/particle_set(i)%atomic_kind%mass
323 massi((i - 1)*3 + 2) = 1.0_dp/particle_set(i)%atomic_kind%mass
324 massi((i - 1)*3 + 3) = 1.0_dp/particle_set(i)%atomic_kind%mass
325 END DO
326 END IF
327 CALL timestop(handle)
328
329 END SUBROUTINE eval_colvar
330
331! **************************************************************************************************
332!> \brief Computes the offset of the colvar for the specific molecule
333!> \param i ...
334!> \param molecule_set ...
335!> \return ...
336!> \author Teodoro Laino 05.2007 [tlaino] - Zurich University
337! **************************************************************************************************
338 FUNCTION get_colvar_offset(i, molecule_set) RESULT(offset)
339 INTEGER, INTENT(IN) :: i
340 TYPE(molecule_type), POINTER :: molecule_set(:)
341 INTEGER :: offset
342
343 INTEGER :: j
344 TYPE(colvar_counters) :: ncolv
345 TYPE(molecule_kind_type), POINTER :: molecule_kind
346 TYPE(molecule_type), POINTER :: molecule
347
348 offset = 0
349 DO j = 1, i - 1
350 molecule => molecule_set(j)
351 molecule_kind => molecule%molecule_kind
352 CALL get_molecule_kind(molecule_kind, &
353 ncolv=ncolv)
354 offset = offset + ncolv%ntot
355 END DO
356
357 END FUNCTION get_colvar_offset
358
359! **************************************************************************************************
360!> \brief Computes Intramolecular colvar
361!> \param molecule ...
362!> \param particle_set ...
363!> \param coords ...
364!> \param cell ...
365!> \param cvalues ...
366!> \param Bmatrix ...
367!> \param offset ...
368!> \param n_tot ...
369!> \param map ...
370!> \author Teodoro Laino 05.2007 [tlaino] - Zurich University
371! **************************************************************************************************
372 SUBROUTINE eval_colv_int(molecule, particle_set, coords, cell, cvalues, &
373 Bmatrix, offset, n_tot, map)
374
375 TYPE(molecule_type), POINTER :: molecule
376 TYPE(particle_type), POINTER :: particle_set(:)
377 REAL(kind=dp), DIMENSION(:), INTENT(IN), OPTIONAL :: coords
378 TYPE(cell_type), POINTER :: cell
379 REAL(kind=dp), DIMENSION(:), INTENT(INOUT) :: cvalues
380 REAL(kind=dp), DIMENSION(:, :), OPTIONAL, POINTER :: bmatrix
381 INTEGER, INTENT(IN) :: offset
382 INTEGER, INTENT(INOUT) :: n_tot
383 INTEGER, DIMENSION(:), POINTER :: map
384
385 TYPE(colvar_constraint_type), POINTER :: colv_list(:)
386 TYPE(fixd_constraint_type), DIMENSION(:), POINTER :: fixd_list
387 TYPE(local_colvar_constraint_type), POINTER :: lcolv(:)
388 TYPE(molecule_kind_type), POINTER :: molecule_kind
389
390 NULLIFY (fixd_list)
391
392 molecule_kind => molecule%molecule_kind
393 CALL get_molecule_kind(molecule_kind, colv_list=colv_list, fixd_list=fixd_list)
394 CALL get_molecule(molecule, lcolv=lcolv)
395 CALL eval_colv_low(colv_list, fixd_list, lcolv, particle_set, &
396 coords, cell, cvalues, bmatrix, offset, n_tot, map)
397
398 END SUBROUTINE eval_colv_int
399
400! **************************************************************************************************
401!> \brief Computes Intermolecular colvar
402!> \param gci ...
403!> \param particle_set ...
404!> \param coords ...
405!> \param cell ...
406!> \param cvalues ...
407!> \param Bmatrix ...
408!> \param offset ...
409!> \param n_tot ...
410!> \param map ...
411!> \author Teodoro Laino 05.2007 [tlaino] - Zurich University
412! **************************************************************************************************
413 SUBROUTINE eval_colv_ext(gci, particle_set, coords, cell, cvalues, &
414 Bmatrix, offset, n_tot, map)
415 TYPE(global_constraint_type), POINTER :: gci
416 TYPE(particle_type), POINTER :: particle_set(:)
417 REAL(kind=dp), DIMENSION(:), INTENT(IN), OPTIONAL :: coords
418 TYPE(cell_type), POINTER :: cell
419 REAL(kind=dp), DIMENSION(:), INTENT(INOUT) :: cvalues
420 REAL(kind=dp), DIMENSION(:, :), OPTIONAL, POINTER :: bmatrix
421 INTEGER, INTENT(IN) :: offset
422 INTEGER, INTENT(INOUT) :: n_tot
423 INTEGER, DIMENSION(:), POINTER :: map
424
425 TYPE(colvar_constraint_type), POINTER :: colv_list(:)
426 TYPE(fixd_constraint_type), DIMENSION(:), POINTER :: fixd_list
427 TYPE(local_colvar_constraint_type), POINTER :: lcolv(:)
428
429 colv_list => gci%colv_list
430 fixd_list => gci%fixd_list
431 lcolv => gci%lcolv
432 CALL eval_colv_low(colv_list, fixd_list, lcolv, particle_set, &
433 coords, cell, cvalues, bmatrix, offset, n_tot, map)
434
435 END SUBROUTINE eval_colv_ext
436
437! **************************************************************************************************
438!> \brief Real evaluation of colvar and of the Wilson-Eliashevich Matrix
439!> B_ik : i: internal coordinates
440!> k: cartesian coordinates
441!> \param colv_list ...
442!> \param fixd_list ...
443!> \param lcolv ...
444!> \param particle_set ...
445!> \param coords ...
446!> \param cell ...
447!> \param cvalues ...
448!> \param Bmatrix ...
449!> \param offset ...
450!> \param n_tot ...
451!> \param map ...
452!> \author Teodoro Laino 05.2007 [tlaino] - Zurich University
453! **************************************************************************************************
454 SUBROUTINE eval_colv_low(colv_list, fixd_list, lcolv, particle_set, coords, &
455 cell, cvalues, Bmatrix, offset, n_tot, map)
456
457 TYPE(colvar_constraint_type), POINTER :: colv_list(:)
458 TYPE(fixd_constraint_type), DIMENSION(:), POINTER :: fixd_list
459 TYPE(local_colvar_constraint_type), POINTER :: lcolv(:)
460 TYPE(particle_type), POINTER :: particle_set(:)
461 REAL(kind=dp), DIMENSION(:), INTENT(IN), OPTIONAL :: coords
462 TYPE(cell_type), POINTER :: cell
463 REAL(kind=dp), DIMENSION(:), INTENT(INOUT) :: cvalues
464 REAL(kind=dp), DIMENSION(:, :), OPTIONAL, POINTER :: bmatrix
465 INTEGER, INTENT(IN) :: offset
466 INTEGER, INTENT(INOUT) :: n_tot
467 INTEGER, DIMENSION(:), POINTER :: map
468
469 INTEGER :: iatm, iconst, ind, ival
470
471 ival = offset
472 DO iconst = 1, SIZE(colv_list)
473 n_tot = n_tot + 1
474 ival = ival + 1
475 ! Update colvar
476 IF (PRESENT(coords)) THEN
477 CALL colvar_eval_mol_f(lcolv(iconst)%colvar, cell, particles=particle_set, &
478 pos=reshape(coords, (/3, SIZE(particle_set)/)), fixd_list=fixd_list)
479 ELSE
480 CALL colvar_eval_mol_f(lcolv(iconst)%colvar, cell, particles=particle_set, &
481 fixd_list=fixd_list)
482 END IF
483 cvalues(ival) = lcolv(iconst)%colvar%ss
484 map(ival) = colv_list(iconst)%inp_seq_num
485 ! Build the Wilson-Eliashevich Matrix
486 IF (PRESENT(bmatrix)) THEN
487 DO iatm = 1, SIZE(lcolv(iconst)%colvar%i_atom)
488 ind = (lcolv(iconst)%colvar%i_atom(iatm) - 1)*3
489 bmatrix(ind + 1, ival) = lcolv(iconst)%colvar%dsdr(1, iatm)
490 bmatrix(ind + 2, ival) = lcolv(iconst)%colvar%dsdr(2, iatm)
491 bmatrix(ind + 3, ival) = lcolv(iconst)%colvar%dsdr(3, iatm)
492 END DO
493 END IF
494 END DO
495
496 END SUBROUTINE eval_colv_low
497
498! **************************************************************************************************
499!> \brief Computes the forces in the frame of collective variables, and additional
500!> also the local metric tensor
501!> \param force_env ...
502!> \param forces ...
503!> \param coords ...
504!> \param nsize_xyz ...
505!> \param nsize_int ...
506!> \param cvalues ...
507!> \param Mmatrix ...
508!> \author Teodoro Laino 05.2007
509! **************************************************************************************************
510 SUBROUTINE get_clv_force(force_env, forces, coords, nsize_xyz, nsize_int, cvalues, &
511 Mmatrix)
512 TYPE(force_env_type), POINTER :: force_env
513 REAL(kind=dp), DIMENSION(:), INTENT(INOUT), &
514 OPTIONAL :: forces, coords
515 INTEGER, INTENT(IN) :: nsize_xyz, nsize_int
516 REAL(kind=dp), DIMENSION(:), INTENT(OUT) :: cvalues, mmatrix
517
518 INTEGER :: i, j, k
519 REAL(kind=dp) :: tmp
520 REAL(kind=dp), DIMENSION(:), POINTER :: massi, wrk
521 REAL(kind=dp), DIMENSION(:, :), POINTER :: amatrix, bmatrix
522
523 ALLOCATE (bmatrix(nsize_xyz, nsize_int))
524 ALLOCATE (massi(nsize_xyz))
525 ! Transform gradients if requested
526 IF (PRESENT(forces)) THEN
527 ALLOCATE (wrk(nsize_int))
528 ALLOCATE (amatrix(nsize_int, nsize_xyz))
529 ! Compute the transformation matrices and the inverse mass diagonal Matrix
530 CALL eval_colvar(force_env, coords, cvalues, bmatrix, massi, amatrix)
531 wrk = matmul(amatrix, forces)
532 forces = 0.0_dp
533 forces(1:nsize_int) = wrk
534 DEALLOCATE (amatrix)
535 DEALLOCATE (wrk)
536 ELSE
537 ! Compute the transformation matrices and the inverse mass diagonal Matrix
538 CALL eval_colvar(force_env, coords, cvalues, bmatrix, massi)
539 END IF
540 ! Compute the Metric Tensor
541 DO i = 1, nsize_int
542 DO j = 1, i
543 tmp = 0.0_dp
544 DO k = 1, nsize_xyz
545 tmp = tmp + bmatrix(k, j)*massi(k)*bmatrix(k, i)
546 END DO
547 mmatrix((i - 1)*nsize_int + j) = tmp
548 mmatrix((j - 1)*nsize_int + i) = tmp
549 END DO
550 END DO
551 DEALLOCATE (massi)
552 DEALLOCATE (bmatrix)
553 END SUBROUTINE get_clv_force
554
555! **************************************************************************************************
556!> \brief Complete the description of the COORDINATION colvar when
557!> defined using KINDS
558!> \param colvar ...
559!> \param particles ...
560!> \par History
561!> 1.2009 Fabio Sterpone : Added a part for population
562!> 10.2014 Moved out of colvar_types.F [Ole Schuett]
563!> \author Teodoro Laino - 07.2007
564! **************************************************************************************************
565 SUBROUTINE post_process_colvar(colvar, particles)
566 TYPE(colvar_type), POINTER :: colvar
567 TYPE(particle_type), DIMENSION(:), OPTIONAL, &
568 POINTER :: particles
569
570 CHARACTER(len=3) :: name_kind
571 INTEGER :: i, ii, j, natoms, nkinds, nr_frame, stat
572
573 natoms = SIZE(particles)
574 IF (colvar%type_id == coord_colvar_id) THEN
575 IF (colvar%coord_param%use_kinds_from .OR. colvar%coord_param%use_kinds_to) THEN
576 ! Atoms from
577 IF (colvar%coord_param%use_kinds_from) THEN
578 colvar%coord_param%use_kinds_from = .false.
579 nkinds = SIZE(colvar%coord_param%c_kinds_from)
580 DO i = 1, natoms
581 DO j = 1, nkinds
582 name_kind = trim(particles(i)%atomic_kind%name)
583 CALL uppercase(name_kind)
584 IF (trim(colvar%coord_param%c_kinds_from(j)) == name_kind) THEN
585 CALL reallocate(colvar%coord_param%i_at_from, 1, colvar%coord_param%n_atoms_from + 1)
586 colvar%coord_param%n_atoms_from = colvar%coord_param%n_atoms_from + 1
587 colvar%coord_param%i_at_from(colvar%coord_param%n_atoms_from) = i
588 END IF
589 END DO
590 END DO
591 stat = colvar%coord_param%n_atoms_from
592 cpassert(stat /= 0)
593 END IF
594 ! Atoms to
595 IF (colvar%coord_param%use_kinds_to) THEN
596 colvar%coord_param%use_kinds_to = .false.
597 nkinds = SIZE(colvar%coord_param%c_kinds_to)
598 DO i = 1, natoms
599 DO j = 1, nkinds
600 name_kind = trim(particles(i)%atomic_kind%name)
601 CALL uppercase(name_kind)
602 IF (trim(colvar%coord_param%c_kinds_to(j)) == name_kind) THEN
603 CALL reallocate(colvar%coord_param%i_at_to, 1, colvar%coord_param%n_atoms_to + 1)
604 colvar%coord_param%n_atoms_to = colvar%coord_param%n_atoms_to + 1
605 colvar%coord_param%i_at_to(colvar%coord_param%n_atoms_to) = i
606 END IF
607 END DO
608 END DO
609 stat = colvar%coord_param%n_atoms_to
610 cpassert(stat /= 0)
611 END IF
612 ! Atoms to b
613 IF (colvar%coord_param%use_kinds_to_b) THEN
614 colvar%coord_param%use_kinds_to_b = .false.
615 nkinds = SIZE(colvar%coord_param%c_kinds_to_b)
616 DO i = 1, natoms
617 DO j = 1, nkinds
618 name_kind = trim(particles(i)%atomic_kind%name)
619 CALL uppercase(name_kind)
620 IF (trim(colvar%coord_param%c_kinds_to_b(j)) == name_kind) THEN
621 CALL reallocate(colvar%coord_param%i_at_to_b, 1, colvar%coord_param%n_atoms_to_b + 1)
622 colvar%coord_param%n_atoms_to_b = colvar%coord_param%n_atoms_to_b + 1
623 colvar%coord_param%i_at_to_b(colvar%coord_param%n_atoms_to_b) = i
624 END IF
625 END DO
626 END DO
627 stat = colvar%coord_param%n_atoms_to_b
628 cpassert(stat /= 0)
629 END IF
630
631 ! Setup the colvar
632 CALL colvar_setup(colvar)
633 END IF
634 END IF
635
636 IF (colvar%type_id == mindist_colvar_id) THEN
637 IF (colvar%mindist_param%use_kinds_from .OR. colvar%mindist_param%use_kinds_to) THEN
638 ! Atoms from
639 IF (colvar%mindist_param%use_kinds_from) THEN
640 colvar%mindist_param%use_kinds_from = .false.
641 nkinds = SIZE(colvar%mindist_param%k_coord_from)
642 DO i = 1, natoms
643 DO j = 1, nkinds
644 name_kind = trim(particles(i)%atomic_kind%name)
645 CALL uppercase(name_kind)
646 IF (trim(colvar%mindist_param%k_coord_from(j)) == name_kind) THEN
647 CALL reallocate(colvar%mindist_param%i_coord_from, 1, colvar%mindist_param%n_coord_from + 1)
648 colvar%mindist_param%n_coord_from = colvar%mindist_param%n_coord_from + 1
649 colvar%mindist_param%i_coord_from(colvar%mindist_param%n_coord_from) = i
650 END IF
651 END DO
652 END DO
653 stat = colvar%mindist_param%n_coord_from
654 cpassert(stat /= 0)
655 END IF
656 ! Atoms to
657 IF (colvar%mindist_param%use_kinds_to) THEN
658 colvar%mindist_param%use_kinds_to = .false.
659 nkinds = SIZE(colvar%mindist_param%k_coord_to)
660 DO i = 1, natoms
661 DO j = 1, nkinds
662 name_kind = trim(particles(i)%atomic_kind%name)
663 CALL uppercase(name_kind)
664 IF (trim(colvar%mindist_param%k_coord_to(j)) == name_kind) THEN
665 CALL reallocate(colvar%mindist_param%i_coord_to, 1, colvar%mindist_param%n_coord_to + 1)
666 colvar%mindist_param%n_coord_to = colvar%mindist_param%n_coord_to + 1
667 colvar%mindist_param%i_coord_to(colvar%mindist_param%n_coord_to) = i
668 END IF
669 END DO
670 END DO
671 stat = colvar%mindist_param%n_coord_to
672 cpassert(stat /= 0)
673 END IF
674 ! Setup the colvar
675 CALL colvar_setup(colvar)
676 END IF
677 END IF
678
679 IF (colvar%type_id == population_colvar_id) THEN
680
681 IF (colvar%population_param%use_kinds_from .OR. colvar%population_param%use_kinds_to) THEN
682 ! Atoms from
683 IF (colvar%population_param%use_kinds_from) THEN
684 colvar%population_param%use_kinds_from = .false.
685 nkinds = SIZE(colvar%population_param%c_kinds_from)
686 DO i = 1, natoms
687 DO j = 1, nkinds
688 name_kind = trim(particles(i)%atomic_kind%name)
689 CALL uppercase(name_kind)
690 IF (trim(colvar%population_param%c_kinds_from(j)) == name_kind) THEN
691 CALL reallocate(colvar%population_param%i_at_from, 1, colvar%population_param%n_atoms_from + 1)
692 colvar%population_param%n_atoms_from = colvar%population_param%n_atoms_from + 1
693 colvar%population_param%i_at_from(colvar%population_param%n_atoms_from) = i
694 END IF
695 END DO
696 END DO
697 stat = colvar%population_param%n_atoms_from
698 cpassert(stat /= 0)
699 END IF
700 ! Atoms to
701 IF (colvar%population_param%use_kinds_to) THEN
702 colvar%population_param%use_kinds_to = .false.
703 nkinds = SIZE(colvar%population_param%c_kinds_to)
704 DO i = 1, natoms
705 DO j = 1, nkinds
706 name_kind = trim(particles(i)%atomic_kind%name)
707 CALL uppercase(name_kind)
708 IF (trim(colvar%population_param%c_kinds_to(j)) == name_kind) THEN
709 CALL reallocate(colvar%population_param%i_at_to, 1, colvar%population_param%n_atoms_to + 1)
710 colvar%population_param%n_atoms_to = colvar%population_param%n_atoms_to + 1
711 colvar%population_param%i_at_to(colvar%population_param%n_atoms_to) = i
712 END IF
713 END DO
714 END DO
715 stat = colvar%population_param%n_atoms_to
716 cpassert(stat /= 0)
717 END IF
718 ! Setup the colvar
719 CALL colvar_setup(colvar)
720 END IF
721
722 END IF
723
724 IF (colvar%type_id == gyration_colvar_id) THEN
725
726 IF (colvar%gyration_param%use_kinds) THEN
727 ! Atoms from
728 IF (colvar%gyration_param%use_kinds) THEN
729 colvar%gyration_param%use_kinds = .false.
730 nkinds = SIZE(colvar%gyration_param%c_kinds)
731 DO i = 1, natoms
732 DO j = 1, nkinds
733 name_kind = trim(particles(i)%atomic_kind%name)
734 CALL uppercase(name_kind)
735 IF (trim(colvar%gyration_param%c_kinds(j)) == name_kind) THEN
736 CALL reallocate(colvar%gyration_param%i_at, 1, colvar%gyration_param%n_atoms + 1)
737 colvar%gyration_param%n_atoms = colvar%gyration_param%n_atoms + 1
738 colvar%gyration_param%i_at(colvar%gyration_param%n_atoms) = i
739 END IF
740 END DO
741 END DO
742 stat = colvar%gyration_param%n_atoms
743 cpassert(stat /= 0)
744 END IF
745 ! Setup the colvar
746 CALL colvar_setup(colvar)
747 END IF
748 END IF
749
750 IF (colvar%type_id == rmsd_colvar_id) THEN
751 IF (colvar%rmsd_param%subset == rmsd_all .OR. colvar%rmsd_param%subset == rmsd_list) THEN
752 ! weights are masses
753 DO i = 1, SIZE(colvar%rmsd_param%i_rmsd)
754 ii = colvar%rmsd_param%i_rmsd(i)
755 colvar%rmsd_param%weights(ii) = particles(ii)%atomic_kind%mass
756 END DO
757 END IF
758
759 IF (colvar%rmsd_param%align_frames) THEN
760 nr_frame = SIZE(colvar%rmsd_param%r_ref, 2)
761 DO i = 2, nr_frame
762 CALL rmsd3(particles, colvar%rmsd_param%r_ref(:, i), colvar%rmsd_param%r_ref(:, 1), -1, &
763 rotate=.true.)
764 END DO
765 END IF
766
767 END IF
768
769 IF (colvar%type_id == distance_from_path_colvar_id .OR. colvar%type_id == reaction_path_colvar_id) THEN
770 IF (colvar%reaction_path_param%dist_rmsd .OR. colvar%reaction_path_param%rmsd) THEN
771 IF (colvar%reaction_path_param%align_frames) THEN
772 nr_frame = colvar%reaction_path_param%nr_frames
773 DO i = 2, nr_frame
774 CALL rmsd3(particles, colvar%reaction_path_param%r_ref(:, i), colvar%reaction_path_param%r_ref(:, 1), -1, &
775 rotate=.true.)
776 END DO
777 END IF
778 END IF
779 END IF
780
781 END SUBROUTINE post_process_colvar
782
783END MODULE colvar_utils
mathlib::invert_matrix
Definition mathlib.F:69
memory_utilities::reallocate
Definition memory_utilities.F:27
cell_types
Handles all functions related to the CELL.
Definition cell_types.F:15
colvar_methods
defines collective variables s({R}) and the derivative of this variable wrt R these can then be used ...
Definition colvar_methods.F:16
colvar_methods::colvar_eval_mol_f
subroutine, public colvar_eval_mol_f(colvar, cell, particles, pos, fixd_list)
evaluates the derivatives (dsdr) given and due to the given colvar variables in a molecular environme...
Definition colvar_methods.F:1631
colvar_types
Initialize the collective variables types.
Definition colvar_types.F:15
colvar_types::population_colvar_id
integer, parameter, public population_colvar_id
Definition colvar_types.F:56
colvar_types::distance_from_path_colvar_id
integer, parameter, public distance_from_path_colvar_id
Definition colvar_types.F:56
colvar_types::rmsd_colvar_id
integer, parameter, public rmsd_colvar_id
Definition colvar_types.F:56
colvar_types::mindist_colvar_id
integer, parameter, public mindist_colvar_id
Definition colvar_types.F:56
colvar_types::gyration_colvar_id
integer, parameter, public gyration_colvar_id
Definition colvar_types.F:56
colvar_types::coord_colvar_id
integer, parameter, public coord_colvar_id
Definition colvar_types.F:56
colvar_types::colvar_setup
subroutine, public colvar_setup(colvar)
Finalize the setup of the collective variable.
Definition colvar_types.F:502
colvar_types::reaction_path_colvar_id
integer, parameter, public reaction_path_colvar_id
Definition colvar_types.F:56
colvar_utils
evaluations of colvar for internal coordinates schemes
Definition colvar_utils.F:14
colvar_utils::eval_colvar
subroutine, public eval_colvar(force_env, coords, cvalues, bmatrix, massi, amatrix)
Computes the values of colvars and the Wilson matrix B and its invers A.
Definition colvar_utils.F:192
colvar_utils::post_process_colvar
subroutine, public post_process_colvar(colvar, particles)
Complete the description of the COORDINATION colvar when defined using KINDS.
Definition colvar_utils.F:566
colvar_utils::number_of_colvar
integer function, public number_of_colvar(force_env, only_intra_colvar, unique)
Gives back the number of colvar defined for a force_eval.
Definition colvar_utils.F:70
colvar_utils::get_clv_force
subroutine, public get_clv_force(force_env, forces, coords, nsize_xyz, nsize_int, cvalues, mmatrix)
Computes the forces in the frame of collective variables, and additional also the local metric tensor...
Definition colvar_utils.F:512
colvar_utils::set_colvars_target
subroutine, public set_colvars_target(targets, force_env)
Set the value of target for constraints/restraints.
Definition colvar_utils.F:133
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
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
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::rmsd_list
integer, parameter, public rmsd_list
Definition input_constants.F:87
input_constants::rmsd_all
integer, parameter, public rmsd_all
Definition input_constants.F:87
kinds
Defines the basic variable types.
Definition kinds.F:23
kinds::dp
integer, parameter, public dp
Definition kinds.F:34
mathlib
Collection of simple mathematical functions and subroutines.
Definition mathlib.F:15
memory_utilities
Utility routines for the memory handling.
Definition memory_utilities.F:14
molecule_kind_list_types
represent a simple array based list of the given type
Definition molecule_kind_list_types.F:15
molecule_kind_types
Define the molecule kind structure types and the corresponding functionality.
Definition molecule_kind_types.F:16
molecule_kind_types::get_molecule_kind
subroutine, public get_molecule_kind(molecule_kind, atom_list, bond_list, bend_list, ub_list, impr_list, opbend_list, colv_list, fixd_list, g3x3_list, g4x6_list, vsite_list, torsion_list, shell_list, name, mass, charge, kind_number, natom, nbend, nbond, nub, nimpr, nopbend, nconstraint, nconstraint_fixd, nfixd, ncolv, ng3x3, ng4x6, nvsite, nfixd_restraint, ng3x3_restraint, ng4x6_restraint, nvsite_restraint, nrestraints, nmolecule, nsgf, nshell, ntorsion, molecule_list, nelectron, nelectron_alpha, nelectron_beta, bond_kind_set, bend_kind_set, ub_kind_set, impr_kind_set, opbend_kind_set, torsion_kind_set, molname_generated)
Get informations about a molecule kind.
Definition molecule_kind_types.F:510
molecule_list_types
represent a simple array based list of the given type
Definition molecule_list_types.F:15
molecule_types
Define the data structure for the molecule information.
Definition molecule_types.F:16
molecule_types::get_molecule
subroutine, public get_molecule(molecule, molecule_kind, lmi, lci, lg3x3, lg4x6, lcolv, first_atom, last_atom, first_shell, last_shell)
Get components from a molecule data set.
Definition molecule_types.F:277
particle_list_types
represent a simple array based list of the given type
Definition particle_list_types.F:15
particle_types
Define the data structure for the particle information.
Definition particle_types.F:19
rmsd
Defines functions to perform rmsd in 3D.
Definition rmsd.F:12
rmsd::rmsd3
subroutine, public rmsd3(particle_set, r, r0, output_unit, weights, my_val, rotate, transl, rot, drmsd3)
Computes the RMSD in 3D. Provides also derivatives.
Definition rmsd.F:53
string_utilities
Utilities for string manipulations.
Definition string_utilities.F:16
string_utilities::uppercase
elemental subroutine, public uppercase(string)
Convert all lower case characters in a string to upper case.
Definition string_utilities.F:3361
util
All kind of helpful little routines.
Definition util.F:14
cell_types::cell_type
Type defining parameters related to the simulation cell.
Definition cell_types.F:55
colvar_types::colvar_counters
Definition colvar_types.F:388
colvar_types::colvar_type
parameters for a collective variable
Definition colvar_types.F:346
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
force_env_types::force_env_type
wrapper to abstract the force evaluation of the various methods
Definition force_env_types.F:139
molecule_kind_list_types::molecule_kind_list_type
represent a list of objects
Definition molecule_kind_list_types.F:45
molecule_kind_types::colvar_constraint_type
Definition molecule_kind_types.F:117
molecule_kind_types::fixd_constraint_type
Definition molecule_kind_types.F:149
molecule_kind_types::molecule_kind_type
Definition molecule_kind_types.F:161
molecule_list_types::molecule_list_type
represent a list of objects
Definition molecule_list_types.F:46
molecule_types::global_constraint_type
Definition molecule_types.F:93
molecule_types::local_colvar_constraint_type
Definition molecule_types.F:41
molecule_types::molecule_type
Definition molecule_types.F:110
particle_list_types::particle_list_type
represent a list of objects
Definition particle_list_types.F:46
particle_types::particle_type
Definition particle_types.F:35