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colvar_types.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 Initialize the collective variables types
10!> \par History
11!> 5.2004 created [fawzi and alessandro]
12!> 1.2009 Fabio Sterpone : added the population COLVAR
13!> \author Teodoro Laino
14! **************************************************************************************************
15MODULE colvar_types
16
17 USE input_section_types, ONLY: section_vals_type
18 USE kinds, ONLY: default_path_length,&
19 default_string_length,&
20 dp
21 USE particle_types, ONLY: particle_type
22#include "../base/base_uses.f90"
23
24 IMPLICIT NONE
25
26 PRIVATE
27
28 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'colvar_types'
29
30 INTEGER, PARAMETER, PUBLIC :: plane_def_atoms = 0, &
31 plane_def_vec = 1
32
33 INTEGER, PARAMETER, PUBLIC :: do_clv_geo_center = 0, &
34 do_clv_fix_point = 1, &
35 do_clv_xyz = 0, &
36 do_clv_x = 1, &
37 do_clv_y = 2, &
38 do_clv_z = 3, &
39 do_clv_xy = 4, &
40 do_clv_xz = 5, &
41 do_clv_yz = 6
42 PUBLIC :: colvar_type, &
43 colvar_p_type, &
44 colvar_p_reallocate, &
45 colvar_p_release, &
46 colvar_create, &
47 colvar_clone, &
48 colvar_setup, &
49 colvar_release, &
50 colvar_counters, &
51 eval_point_der, &
52 eval_point_pos, &
53 eval_point_mass, &
54 diff_colvar
55
56 INTEGER, PARAMETER, PUBLIC :: no_colvar_id = -2, &
57 dist_colvar_id = 1, &
58 coord_colvar_id = 2, &
59 torsion_colvar_id = 3, &
60 angle_colvar_id = 4, &
61 plane_distance_colvar_id = 5, &
62 rotation_colvar_id = 6, &
63 dfunct_colvar_id = 7, &
64 qparm_colvar_id = 8, &
65 hydronium_shell_colvar_id = 9, &
66 reaction_path_colvar_id = 10, &
67 combine_colvar_id = 11, &
68 population_colvar_id = 12, &
69 plane_plane_angle_colvar_id = 13, &
70 gyration_colvar_id = 14, &
71 rmsd_colvar_id = 15, &
72 distance_from_path_colvar_id = 16, &
73 xyz_diag_colvar_id = 17, &
74 xyz_outerdiag_colvar_id = 18, &
75 u_colvar_id = 19, &
76 wc_colvar_id = 20, &
77 hbp_colvar_id = 21, &
78 ring_puckering_colvar_id = 22, &
79 mindist_colvar_id = 23, &
80 acid_hyd_dist_colvar_id = 24, &
81 acid_hyd_shell_colvar_id = 25, &
82 hydronium_dist_colvar_id = 26
83
84! **************************************************************************************************
85!> \brief parameters for the distance collective variable
86!> \param i_at ,j_at: indexes of the two atoms between which you calculate
87!> the distance
88!> \author alessandro laio and fawzi mohamed
89! **************************************************************************************************
90 TYPE dist_colvar_type
91 INTEGER :: i_at = 0, j_at = 0, axis_id = 0
92 LOGICAL :: sign_d = .false.
93 END TYPE dist_colvar_type
94
95! **************************************************************************************************
96 TYPE coord_colvar_type
97 LOGICAL :: do_chain = .false., use_kinds_from = .false., use_kinds_to = .false., &
98 use_kinds_to_b = .false.
99 INTEGER :: n_atoms_to = 0, &
100 n_atoms_from = 0, &
101 nncrd = 0, &
102 ndcrd = 0, &
103 n_atoms_to_b = 0, &
104 nncrd_b = 0, &
105 ndcrd_b = 0
106 INTEGER, POINTER, DIMENSION(:) :: i_at_from => null(), &
107 i_at_to => null(), &
108 i_at_to_b => null()
109 CHARACTER(LEN=default_string_length), DIMENSION(:), POINTER :: c_kinds_from => null(), &
110 c_kinds_to => null(), &
111 c_kinds_to_b => null()
112 REAL(kind=dp) :: r_0 = 0.0_dp, r_0_b = 0.0_dp
113 END TYPE coord_colvar_type
114
115! **************************************************************************************************
116 TYPE population_colvar_type
117 LOGICAL :: use_kinds_from = .false., use_kinds_to = .false.
118 INTEGER :: n_atoms_to = 0, &
119 n_atoms_from = 0, &
120 nncrd = 0, &
121 ndcrd = 0, &
122 n0 = 0
123 INTEGER, POINTER, DIMENSION(:) :: i_at_from => null(), &
124 i_at_to => null()
125 CHARACTER(LEN=default_string_length), DIMENSION(:), POINTER :: c_kinds_from => null(), &
126 c_kinds_to => null()
127 REAL(kind=dp) :: r_0 = 0.0_dp, sigma = 0.0_dp
128 END TYPE population_colvar_type
129
130! **************************************************************************************************
131 TYPE gyration_colvar_type
132 LOGICAL :: use_kinds = .false.
133 INTEGER :: n_atoms = 0
134 INTEGER, POINTER, DIMENSION(:) :: i_at => null()
135 CHARACTER(LEN=default_string_length), DIMENSION(:), POINTER :: c_kinds => null()
136 END TYPE gyration_colvar_type
137
138! **************************************************************************************************
139 TYPE torsion_colvar_type
140 REAL(kind=dp) :: o0 = 0.0_dp
141 INTEGER, DIMENSION(4) :: i_at_tors = 0
142 END TYPE torsion_colvar_type
143
144! **************************************************************************************************
145 TYPE plane_distance_colvar_type
146 LOGICAL :: use_pbc = .false.
147 INTEGER, DIMENSION(3) :: plane = -1
148 INTEGER :: point = -1
149 END TYPE plane_distance_colvar_type
150
151! **************************************************************************************************
152 TYPE plane_def_type
153 INTEGER :: type_of_def = -1
154 INTEGER, DIMENSION(3) :: points = 0
155 REAL(kind=dp), DIMENSION(3) :: normal_vec = 0.0_dp
156 END TYPE plane_def_type
157
158 TYPE plane_plane_angle_colvar_type
159 TYPE(plane_def_type) :: plane1 = plane_def_type(), plane2 = plane_def_type()
160 END TYPE plane_plane_angle_colvar_type
161
162! **************************************************************************************************
163 TYPE angle_colvar_type
164 INTEGER, DIMENSION(3) :: i_at_angle = 0
165 END TYPE angle_colvar_type
166
167! **************************************************************************************************
168 TYPE rotation_colvar_type
169 INTEGER :: i_at1_bond1 = 0, &
170 i_at2_bond1 = 0, &
171 i_at1_bond2 = 0, &
172 i_at2_bond2 = 0
173 END TYPE rotation_colvar_type
174
175! **************************************************************************************************
176 TYPE dfunct_colvar_type
177 INTEGER, DIMENSION(4) :: i_at_dfunct = 0
178 LOGICAL :: use_pbc = .false.
179 REAL(kind=dp) :: coeff = 0.0_dp
180 END TYPE dfunct_colvar_type
181
182! **************************************************************************************************
183 TYPE qparm_colvar_type
184 INTEGER :: l = 0
185 INTEGER :: n_atoms_to = 0, &
186 n_atoms_from = 0
187 INTEGER, POINTER, DIMENSION(:) :: i_at_from => null(), &
188 i_at_to => null()
189 REAL(kind=dp) :: rcut = 0.0_dp, rstart = 0.0_dp
190 LOGICAL :: include_images = .false.
191 END TYPE qparm_colvar_type
192
193! **************************************************************************************************
194 TYPE hydronium_shell_colvar_type
195 INTEGER :: n_oxygens = -1, &
196 n_hydrogens = -1, &
197 poh = -1, qoh = -1, poo = -1, qoo = -1, &
198 pm = -1, qm = -1
199 INTEGER, POINTER, DIMENSION(:) :: i_oxygens => null(), &
200 i_hydrogens => null()
201 REAL(kind=dp) :: roo = 0.0_dp, roh = 0.0_dp, lambda = 0.0_dp, nh = 0.0_dp
202 END TYPE hydronium_shell_colvar_type
203
204! **************************************************************************************************
205 TYPE hydronium_dist_colvar_type
206 INTEGER :: n_oxygens = -1, &
207 n_hydrogens = -1, &
208 poh = -1, qoh = -1, &
209 pf = -1, qf = -1, pm = -1, qm = -1
210 INTEGER, POINTER, DIMENSION(:) :: i_oxygens => null(), &
211 i_hydrogens => null()
212 REAL(kind=dp) :: roh = 0.0_dp, lambda = 0.0_dp, nh = 0.0_dp, nn = 0.0_dp
213 END TYPE hydronium_dist_colvar_type
214
215! **************************************************************************************************
216 TYPE acid_hyd_dist_colvar_type
217 INTEGER :: n_oxygens_water = -1, &
218 n_oxygens_acid = -1, &
219 n_hydrogens = -1, &
220 pwoh = -1, qwoh = -1, paoh = -1, qaoh = -1, pcut = -1, qcut = -1
221 INTEGER, POINTER, DIMENSION(:) :: i_oxygens_water => null(), i_oxygens_acid => null(), &
222 i_hydrogens => null()
223 REAL(kind=dp) :: rwoh = 0.0_dp, raoh = 0.0_dp, lambda = 0.0_dp, nc = 0.0_dp
224 END TYPE acid_hyd_dist_colvar_type
225
226! **************************************************************************************************
227 TYPE acid_hyd_shell_colvar_type
228 INTEGER :: n_oxygens_water = -1, &
229 n_oxygens_acid = -1, &
230 n_hydrogens = -1, &
231 pwoh = -1, qwoh = -1, paoh = -1, qaoh = -1, &
232 poo = -1, qoo = -1, pcut = -1, qcut = -1, pm = -1, qm = -1
233 INTEGER, POINTER, DIMENSION(:) :: i_oxygens_water => null(), i_oxygens_acid => null(), &
234 i_hydrogens => null()
235 REAL(kind=dp) :: rwoh = 0.0_dp, raoh = 0.0_dp, roo = 0.0_dp, lambda = 0.0_dp, nc = 0.0_dp, nh = 0.0_dp
236 END TYPE acid_hyd_shell_colvar_type
237
238! **************************************************************************************************
239 TYPE reaction_path_colvar_type
240 INTEGER :: type_id = -1
241 INTEGER :: n_components = -1, nr_frames = -1, subset = -1
242 INTEGER, DIMENSION(2) :: function_bounds = -1
243 INTEGER, POINTER, DIMENSION(:) :: i_rmsd => null()
244 LOGICAL :: align_frames = .false., dist_rmsd = .false., rmsd = .false.
245 REAL(kind=dp), DIMENSION(:, :), POINTER :: f_vals => null()
246 REAL(kind=dp), DIMENSION(:, :), POINTER :: r_ref => null()
247 REAL(kind=dp) :: lambda = 0.0_dp
248 REAL(kind=dp) :: step_size = 0.0_dp
249 TYPE(colvar_p_type), POINTER, DIMENSION(:) :: colvar_p => null()
250 END TYPE reaction_path_colvar_type
251
252! **************************************************************************************************
253 TYPE combine_colvar_type
254 INTEGER :: type_id = -1
255 TYPE(colvar_p_type), POINTER, DIMENSION(:) :: colvar_p => null()
256 REAL(kind=dp) :: lerr = 0.0_dp, dx = 0.0_dp
257 CHARACTER(LEN=default_path_length) :: function = ""
258 CHARACTER(LEN=default_string_length), &
259 DIMENSION(:), POINTER :: c_parameters => null(), variables => null()
260 REAL(kind=dp), DIMENSION(:), POINTER :: v_parameters => null()
261 END TYPE combine_colvar_type
262! **************************************************************************************************
263 TYPE rmsd_colvar_type
264 INTEGER :: n_atoms = 0, nr_frames = 0, subset = 0
265 INTEGER, POINTER, DIMENSION(:) :: i_rmsd => null()
266 LOGICAL :: align_frames = .false.
267 REAL(kind=dp), DIMENSION(:), POINTER :: weights => null()
268 REAL(kind=dp), DIMENSION(:, :), POINTER :: r_ref => null()
269 END TYPE rmsd_colvar_type
270
271! **************************************************************************************************
272 TYPE point_type
273 INTEGER :: type_id = -1
274 INTEGER, DIMENSION(:), POINTER :: atoms => null()
275 REAL(kind=dp), DIMENSION(:), POINTER :: weights => null()
276 REAL(kind=dp), DIMENSION(3) :: r = 0.0_dp
277 END TYPE point_type
278
279! **************************************************************************************************
280 TYPE xyz_diag_colvar_type
281 LOGICAL :: use_pbc = .false.
282 LOGICAL :: use_absolute_position = .false.
283 INTEGER :: i_atom = 0
284 INTEGER :: component = 0
285 REAL(kind=dp), DIMENSION(3) :: r0 = 0.0_dp
286 END TYPE xyz_diag_colvar_type
287
288! **************************************************************************************************
289 TYPE xyz_outerdiag_colvar_type
290 LOGICAL :: use_pbc = .false.
291 INTEGER, DIMENSION(2) :: i_atoms = 0
292 INTEGER, DIMENSION(2) :: components = 0
293 REAL(kind=dp), DIMENSION(3, 2) :: r0 = 0.0_dp
294 END TYPE xyz_outerdiag_colvar_type
295
296! **************************************************************************************************
297 TYPE u_colvar_type
298 TYPE(section_vals_type), POINTER :: mixed_energy_section => null()
299 INTEGER :: natom = -1
300 END TYPE u_colvar_type
301
302! **************************************************************************************************
303 TYPE wc_colvar_type
304 INTEGER :: ids(3) = -1 ! first is the Od, second the H, third the Oa
305 REAL(kind=dp) :: ewc = 0.0_dp
306 REAL(kind=dp) :: rcut = 0.0_dp
307 END TYPE wc_colvar_type
308
309! **************************************************************************************************
310 TYPE hbp_colvar_type
311 INTEGER :: npoints = -1 ! number of the points in the path
312 INTEGER, POINTER :: ids(:, :) => null() ! first is the Od, second the H,
313 ! third the Oa and contains a row for each intermediate point in the path
314 REAL(kind=dp), POINTER :: ewc(:) => null() ! one for each point in the path
315 REAL(kind=dp) :: rcut = 0.0_dp
316 REAL(kind=dp) :: shift = 0.0_dp ! shift applied for each term in the collective variable
317 END TYPE hbp_colvar_type
318
319! **************************************************************************************************
320 TYPE ring_puckering_colvar_type
321 INTEGER :: nring = -1
322 INTEGER, POINTER, DIMENSION(:) :: atoms => null()
323 INTEGER :: iq = -1
324 END TYPE ring_puckering_colvar_type
325
326! **************************************************************************************************
327 TYPE mindist_colvar_type
328 LOGICAL :: use_kinds_from = .false., use_kinds_to = .false.
329 INTEGER :: n_coord_to = 0, &
330 n_coord_from = 0, &
331 n_dist_from = 0, &
332 p_exp = 0, &
333 q_exp = 0
334 INTEGER, POINTER, DIMENSION(:) :: i_coord_from => null(), &
335 i_coord_to => null(), &
336 i_dist_from => null()
337 CHARACTER(LEN=default_string_length), DIMENSION(:), POINTER :: k_coord_from => null(), &
338 k_coord_to => null()
339 REAL(kind=dp) :: lambda = 0.0_dp, r_cut = 0.0_dp
340 END TYPE mindist_colvar_type
341
342! **************************************************************************************************
343!> \brief parameters for a collective variable
344!> \author alessandro laio and fawzi mohamed
345! **************************************************************************************************
346 TYPE colvar_type
347 INTEGER :: type_id = -1
348 LOGICAL :: use_points = .false.
349 REAL(kind=dp) :: ss = 0.0_dp ! Value of the colvar
350 REAL(kind=dp), DIMENSION(:, :), POINTER :: dsdr => null() ! Derivative of colvar (3,:)
351 INTEGER, DIMENSION(:), POINTER :: i_atom => null() ! Mapping of dsdr
352 INTEGER :: n_atom_s = -1
353 ! Available COLVAR types
354 TYPE(dist_colvar_type), POINTER :: dist_param => null()
355 TYPE(coord_colvar_type), POINTER :: coord_param => null()
356 TYPE(population_colvar_type), POINTER :: population_param => null()
357 TYPE(gyration_colvar_type), POINTER :: gyration_param => null()
358 TYPE(torsion_colvar_type), POINTER :: torsion_param => null()
359 TYPE(angle_colvar_type), POINTER :: angle_param => null()
360 TYPE(plane_distance_colvar_type), POINTER :: plane_distance_param => null()
361 TYPE(plane_plane_angle_colvar_type), POINTER :: plane_plane_angle_param => null()
362 TYPE(rotation_colvar_type), POINTER :: rotation_param => null()
363 TYPE(dfunct_colvar_type), POINTER :: dfunct_param => null()
364 TYPE(qparm_colvar_type), POINTER :: qparm_param => null()
365 TYPE(hydronium_shell_colvar_type), POINTER :: hydronium_shell_param => null()
366 TYPE(hydronium_dist_colvar_type), POINTER :: hydronium_dist_param => null()
367 TYPE(acid_hyd_dist_colvar_type), POINTER :: acid_hyd_dist_param => null()
368 TYPE(acid_hyd_shell_colvar_type), POINTER :: acid_hyd_shell_param => null()
369 TYPE(reaction_path_colvar_type), POINTER :: reaction_path_param => null()
370 TYPE(combine_colvar_type), POINTER :: combine_cvs_param => null()
371 TYPE(rmsd_colvar_type), POINTER :: rmsd_param => null()
372 TYPE(xyz_diag_colvar_type), POINTER :: xyz_diag_param => null()
373 TYPE(xyz_outerdiag_colvar_type), POINTER :: xyz_outerdiag_param => null()
374 TYPE(u_colvar_type), POINTER :: u_param => null()
375 TYPE(point_type), DIMENSION(:), POINTER :: points => null()
376 TYPE(wc_colvar_type), POINTER :: wc => null()
377 TYPE(hbp_colvar_type), POINTER :: hbp => null()
378 TYPE(ring_puckering_colvar_type), POINTER :: ring_puckering_param => null()
379 TYPE(mindist_colvar_type), POINTER :: mindist_param => null()
380 END TYPE colvar_type
381
382! **************************************************************************************************
383 TYPE colvar_p_type
384 TYPE(colvar_type), POINTER :: colvar => null()
385 END TYPE colvar_p_type
386
387! **************************************************************************************************
388 TYPE colvar_counters
389 INTEGER :: ndist = 0
390 INTEGER :: nangle = 0
391 INTEGER :: ntorsion = 0
392 INTEGER :: ncoord = 0
393 INTEGER :: nplane_dist = 0
394 INTEGER :: nplane_angle = 0
395 INTEGER :: nrot = 0
396 INTEGER :: ndfunct = 0
397 INTEGER :: nqparm = 0
398 INTEGER :: nhydronium_shell = 0
399 INTEGER :: nhydronium_dist = 0
400 INTEGER :: nacid_hyd_dist = 0
401 INTEGER :: nacid_hyd_shell = 0
402 INTEGER :: nreactionpath = 0
403 INTEGER :: ncombinecvs = 0
404 INTEGER :: nrestraint = 0
405 INTEGER :: npopulation = 0
406 INTEGER :: ngyration = 0
407 INTEGER :: nxyz_diag = 0
408 INTEGER :: nxyz_outerdiag = 0
409 INTEGER :: ntot = 0
410 END TYPE colvar_counters
411
412CONTAINS
413
414! **************************************************************************************************
415!> \brief initializes a colvar_param type
416!> \param colvar the colvat to initialize
417!> \param colvar_id ...
418!> \author alessandro laio and fawzi mohamed
419! **************************************************************************************************
420 SUBROUTINE colvar_create(colvar, colvar_id)
421 TYPE(colvar_type), POINTER :: colvar
422 INTEGER, INTENT(in) :: colvar_id
423
424 cpassert(.NOT. ASSOCIATED(colvar))
425 ALLOCATE (colvar)
426 colvar%type_id = colvar_id
427 colvar%use_points = .false.
428 SELECT CASE (colvar_id)
429 CASE (dist_colvar_id)
430 ALLOCATE (colvar%dist_param)
431 colvar%dist_param%axis_id = do_clv_xyz
432 colvar%dist_param%sign_d = .false.
433 CASE (coord_colvar_id)
434 ALLOCATE (colvar%coord_param)
435 CASE (population_colvar_id)
436 ALLOCATE (colvar%population_param)
437 CASE (gyration_colvar_id)
438 ALLOCATE (colvar%gyration_param)
439 CASE (angle_colvar_id)
440 ALLOCATE (colvar%angle_param)
441 CASE (torsion_colvar_id)
442 ALLOCATE (colvar%torsion_param)
443 CASE (plane_distance_colvar_id)
444 ALLOCATE (colvar%plane_distance_param)
445 CASE (plane_plane_angle_colvar_id)
446 ALLOCATE (colvar%plane_plane_angle_param)
447 CASE (rotation_colvar_id)
448 ALLOCATE (colvar%rotation_param)
449 CASE (dfunct_colvar_id)
450 ALLOCATE (colvar%dfunct_param)
451 CASE (qparm_colvar_id)
452 ALLOCATE (colvar%qparm_param)
453 CASE (xyz_diag_colvar_id)
454 ALLOCATE (colvar%xyz_diag_param)
455 ! Initialize r0 with dummy..
456 colvar%xyz_diag_param%r0 = huge(0.0_dp)
457 CASE (xyz_outerdiag_colvar_id)
458 ALLOCATE (colvar%xyz_outerdiag_param)
459 ! Initialize r0 with dummy..
460 colvar%xyz_outerdiag_param%r0 = huge(0.0_dp)
461 CASE (u_colvar_id)
462 ALLOCATE (colvar%u_param)
463 NULLIFY (colvar%u_param%mixed_energy_section)
464 CASE (hydronium_shell_colvar_id)
465 ALLOCATE (colvar%hydronium_shell_param)
466 CASE (hydronium_dist_colvar_id)
467 ALLOCATE (colvar%hydronium_dist_param)
468 CASE (acid_hyd_dist_colvar_id)
469 ALLOCATE (colvar%acid_hyd_dist_param)
470 CASE (acid_hyd_shell_colvar_id)
471 ALLOCATE (colvar%acid_hyd_shell_param)
472 CASE (reaction_path_colvar_id)
473 ALLOCATE (colvar%reaction_path_param)
474 CASE (distance_from_path_colvar_id)
475 ALLOCATE (colvar%reaction_path_param)
476 CASE (combine_colvar_id)
477 ALLOCATE (colvar%combine_cvs_param)
478 CASE (rmsd_colvar_id)
479 ALLOCATE (colvar%rmsd_param)
480 CASE (wc_colvar_id)
481 ALLOCATE (colvar%Wc)
482 CASE (hbp_colvar_id)
483 ALLOCATE (colvar%HBP)
484 CASE (ring_puckering_colvar_id)
485 ALLOCATE (colvar%ring_puckering_param)
486 CASE (mindist_colvar_id)
487 ALLOCATE (colvar%mindist_param)
488 CASE (no_colvar_id)
489 ! Do nothing
490 CASE DEFAULT
491 cpabort("")
492 END SELECT
493
494 END SUBROUTINE colvar_create
495
496! **************************************************************************************************
497!> \brief Finalize the setup of the collective variable
498!> \param colvar the colvar to initialize
499!> \author Teodoro Laino, [teo] 09.03.2006
500! **************************************************************************************************
501 SUBROUTINE colvar_setup(colvar)
502 TYPE(colvar_type), INTENT(INOUT) :: colvar
503
504 INTEGER :: i, idum, iend, ii, istart, j, np, stat
505 INTEGER, DIMENSION(:), POINTER :: list
506
507 SELECT CASE (colvar%type_id)
508 CASE (dist_colvar_id)
509 np = 2
510 i = colvar%dist_param%i_at
511 j = colvar%dist_param%j_at
512 ! Number of real atoms involved in the colvar
513 colvar%n_atom_s = colv_size(colvar, i) + &
514 colv_size(colvar, j)
515 ! Create a List of points...
516 ALLOCATE (list(np))
517 list(1) = colvar%dist_param%i_at
518 list(2) = colvar%dist_param%j_at
519 CASE (coord_colvar_id)
520 np = colvar%coord_param%n_atoms_from + colvar%coord_param%n_atoms_to &
521 + colvar%coord_param%n_atoms_to_b
522 ! Number of real atoms involved in the colvar
523 colvar%n_atom_s = 0
524 DO ii = 1, colvar%coord_param%n_atoms_from
525 i = colvar%coord_param%i_at_from(ii)
526 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
527 END DO
528 DO ii = 1, colvar%coord_param%n_atoms_to
529 i = colvar%coord_param%i_at_to(ii)
530 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
531 END DO
532 IF (colvar%coord_param%n_atoms_to_b /= 0) THEN
533 DO ii = 1, colvar%coord_param%n_atoms_to_b
534 i = colvar%coord_param%i_at_to_b(ii)
535 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
536 END DO
537 END IF
538 ! Create a List of points...
539 ALLOCATE (list(np))
540 idum = 0
541 DO ii = 1, colvar%coord_param%n_atoms_from
542 idum = idum + 1
543 i = colvar%coord_param%i_at_from(ii)
544 list(idum) = i
545 END DO
546 DO ii = 1, colvar%coord_param%n_atoms_to
547 idum = idum + 1
548 i = colvar%coord_param%i_at_to(ii)
549 list(idum) = i
550 END DO
551 IF (colvar%coord_param%n_atoms_to_b /= 0) THEN
552 DO ii = 1, colvar%coord_param%n_atoms_to_b
553 idum = idum + 1
554 i = colvar%coord_param%i_at_to_b(ii)
555 list(idum) = i
556 END DO
557 END IF
558 cpassert(idum == np)
559 CASE (population_colvar_id)
560 np = colvar%population_param%n_atoms_from + colvar%population_param%n_atoms_to
561 ! Number of real atoms involved in the colvar
562 colvar%n_atom_s = 0
563 DO ii = 1, colvar%population_param%n_atoms_from
564 i = colvar%population_param%i_at_from(ii)
565 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
566 END DO
567 DO ii = 1, colvar%population_param%n_atoms_to
568 i = colvar%population_param%i_at_to(ii)
569 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
570 END DO
571 ! Create a List of points...
572 ALLOCATE (list(np))
573 idum = 0
574 DO ii = 1, colvar%population_param%n_atoms_from
575 idum = idum + 1
576 i = colvar%population_param%i_at_from(ii)
577 list(idum) = i
578 END DO
579 DO ii = 1, colvar%population_param%n_atoms_to
580 idum = idum + 1
581 i = colvar%population_param%i_at_to(ii)
582 list(idum) = i
583 END DO
584 cpassert(idum == np)
585 CASE (gyration_colvar_id)
586 np = colvar%gyration_param%n_atoms
587 ! Number of real atoms involved in the colvar
588 colvar%n_atom_s = 0
589 DO ii = 1, colvar%gyration_param%n_atoms
590 i = colvar%gyration_param%i_at(ii)
591 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
592 END DO
593 ! Create a List of points...
594 ALLOCATE (list(np))
595 idum = 0
596 DO ii = 1, colvar%gyration_param%n_atoms
597 idum = idum + 1
598 i = colvar%gyration_param%i_at(ii)
599 list(idum) = i
600 END DO
601 cpassert(idum == np)
602 CASE (angle_colvar_id)
603 np = 3
604 ! Number of real atoms involved in the colvar
605 colvar%n_atom_s = 0
606 DO ii = 1, 3
607 i = colvar%angle_param%i_at_angle(ii)
608 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
609 END DO
610 ! Create a List of points...
611 ALLOCATE (list(np))
612 idum = 0
613 DO ii = 1, 3
614 idum = idum + 1
615 i = colvar%angle_param%i_at_angle(ii)
616 list(idum) = i
617 END DO
618 cpassert(idum == np)
619 CASE (torsion_colvar_id)
620 np = 4
621 ! Number of real atoms involved in the colvar
622 colvar%n_atom_s = 0
623 DO ii = 1, 4
624 i = colvar%torsion_param%i_at_tors(ii)
625 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
626 END DO
627 ! Create a List of points...
628 ALLOCATE (list(np))
629 idum = 0
630 DO ii = 1, 4
631 idum = idum + 1
632 i = colvar%torsion_param%i_at_tors(ii)
633 list(idum) = i
634 END DO
635 cpassert(idum == np)
636 CASE (plane_distance_colvar_id)
637 np = 4
638 ! Number of real atoms involved in the colvar
639 colvar%n_atom_s = 0
640 DO ii = 1, 3
641 i = colvar%plane_distance_param%plane(ii)
642 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
643 END DO
644 i = colvar%plane_distance_param%point
645 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
646 ! Create a List of points...
647 ALLOCATE (list(np))
648 idum = 0
649 DO ii = 1, 3
650 idum = idum + 1
651 i = colvar%plane_distance_param%plane(ii)
652 list(idum) = i
653 END DO
654 i = colvar%plane_distance_param%point
655 list(4) = i
656 idum = idum + 1
657 cpassert(idum == np)
658 CASE (plane_plane_angle_colvar_id)
659 np = 0
660 IF (colvar%plane_plane_angle_param%plane1%type_of_def == plane_def_atoms) np = np + 3
661 IF (colvar%plane_plane_angle_param%plane2%type_of_def == plane_def_atoms) np = np + 3
662 ! if np is equal to zero this means that this is not a COLLECTIVE variable..
663 IF (np == 0) &
664 CALL cp_abort(__location__, &
665 "PLANE_PLANE_ANGLE Colvar defined using two normal vectors! This is "// &
666 "not a COLLECTIVE VARIABLE! One of the two planes must be defined "// &
667 "using atomic positions.")
668
669 ! Number of real atoms involved in the colvar
670 colvar%n_atom_s = 0
671 IF (colvar%plane_plane_angle_param%plane1%type_of_def == plane_def_atoms) THEN
672 DO ii = 1, 3
673 i = colvar%plane_plane_angle_param%plane1%points(ii)
674 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
675 END DO
676 END IF
677 IF (colvar%plane_plane_angle_param%plane2%type_of_def == plane_def_atoms) THEN
678 DO ii = 1, 3
679 i = colvar%plane_plane_angle_param%plane2%points(ii)
680 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
681 END DO
682 END IF
683
684 ! Create a List of points...
685 ALLOCATE (list(np))
686 idum = 0
687 IF (colvar%plane_plane_angle_param%plane1%type_of_def == plane_def_atoms) THEN
688 DO ii = 1, 3
689 idum = idum + 1
690 i = colvar%plane_plane_angle_param%plane1%points(ii)
691 list(idum) = i
692 END DO
693 END IF
694 IF (colvar%plane_plane_angle_param%plane2%type_of_def == plane_def_atoms) THEN
695 DO ii = 1, 3
696 idum = idum + 1
697 i = colvar%plane_plane_angle_param%plane2%points(ii)
698 list(idum) = i
699 END DO
700 END IF
701 cpassert(idum == np)
702 CASE (dfunct_colvar_id)
703 np = 4
704 ! Number of real atoms involved in the colvar
705 colvar%n_atom_s = 0
706 DO ii = 1, 4
707 i = colvar%dfunct_param%i_at_dfunct(ii)
708 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
709 END DO
710 ! Create a List of points...
711 ALLOCATE (list(np))
712 idum = 0
713 DO ii = 1, 4
714 idum = idum + 1
715 i = colvar%dfunct_param%i_at_dfunct(ii)
716 list(idum) = i
717 END DO
718 cpassert(idum == np)
719 CASE (rotation_colvar_id)
720 np = 4
721 ! Number of real atoms involved in the colvar
722 colvar%n_atom_s = 0
723 i = colvar%rotation_param%i_at1_bond1
724 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
725 i = colvar%rotation_param%i_at2_bond1
726 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
727 i = colvar%rotation_param%i_at1_bond2
728 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
729 i = colvar%rotation_param%i_at2_bond2
730 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
731 ! Create a List of points...
732 ALLOCATE (list(np))
733 i = colvar%rotation_param%i_at1_bond1
734 list(1) = i
735 i = colvar%rotation_param%i_at2_bond1
736 list(2) = i
737 i = colvar%rotation_param%i_at1_bond2
738 list(3) = i
739 i = colvar%rotation_param%i_at2_bond2
740 list(4) = i
741 CASE (qparm_colvar_id)
742 np = colvar%qparm_param%n_atoms_from + colvar%qparm_param%n_atoms_to
743 ! Number of real atoms involved in the colvar
744 colvar%n_atom_s = 0
745 DO ii = 1, colvar%qparm_param%n_atoms_from
746 i = colvar%qparm_param%i_at_from(ii)
747 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
748 END DO
749 DO ii = 1, colvar%qparm_param%n_atoms_to
750 i = colvar%qparm_param%i_at_to(ii)
751 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
752 END DO
753 ! Create a List of points...
754 ALLOCATE (list(np))
755 idum = 0
756 DO ii = 1, colvar%qparm_param%n_atoms_from
757 idum = idum + 1
758 i = colvar%qparm_param%i_at_from(ii)
759 list(idum) = i
760 END DO
761 DO ii = 1, colvar%qparm_param%n_atoms_to
762 idum = idum + 1
763 i = colvar%qparm_param%i_at_to(ii)
764 list(idum) = i
765 END DO
766 cpassert(idum == np)
767 CASE (hydronium_shell_colvar_id)
768 np = colvar%hydronium_shell_param%n_oxygens + colvar%hydronium_shell_param%n_hydrogens
769 ALLOCATE (list(np))
770 CALL setup_hydronium_colvars(colvar, hydronium_shell_colvar_id, list)
771 CASE (hydronium_dist_colvar_id)
772 np = colvar%hydronium_dist_param%n_oxygens + colvar%hydronium_dist_param%n_hydrogens
773 ALLOCATE (list(np))
774 CALL setup_hydronium_colvars(colvar, hydronium_dist_colvar_id, list)
775 CASE (acid_hyd_dist_colvar_id)
776 np = colvar%acid_hyd_dist_param%n_oxygens_water &
777 + colvar%acid_hyd_dist_param%n_oxygens_acid &
778 + colvar%acid_hyd_dist_param%n_hydrogens
779 ALLOCATE (list(np))
780 CALL setup_acid_hydronium_colvars(colvar, acid_hyd_dist_colvar_id, list)
781 CASE (acid_hyd_shell_colvar_id)
782 np = colvar%acid_hyd_shell_param%n_oxygens_water &
783 + colvar%acid_hyd_shell_param%n_oxygens_acid &
784 + colvar%acid_hyd_shell_param%n_hydrogens
785 ALLOCATE (list(np))
786 CALL setup_acid_hydronium_colvars(colvar, acid_hyd_shell_colvar_id, list)
787 CASE (rmsd_colvar_id)
788 np = colvar%rmsd_param%n_atoms
789 ! Number of real atoms involved in the colvar
790 colvar%n_atom_s = 0
791 DO ii = 1, colvar%rmsd_param%n_atoms
792 i = colvar%rmsd_param%i_rmsd(ii)
793 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
794 END DO
795 ! Create a List of points...
796 ALLOCATE (list(np))
797 idum = 0
798 DO ii = 1, colvar%rmsd_param%n_atoms
799 idum = idum + 1
800 i = colvar%rmsd_param%i_rmsd(ii)
801 list(idum) = i
802 END DO
803 CASE (reaction_path_colvar_id, distance_from_path_colvar_id)
804 colvar%n_atom_s = 0
805 IF (colvar%reaction_path_param%dist_rmsd .OR. colvar%reaction_path_param%rmsd) THEN
806 colvar%n_atom_s = colvar%reaction_path_param%n_components
807 ELSE
808 DO ii = 1, SIZE(colvar%reaction_path_param%colvar_p)
809 colvar%n_atom_s = colvar%n_atom_s + colvar%reaction_path_param%colvar_p(ii)%colvar%n_atom_s
810 END DO
811 END IF
812 ALLOCATE (list(colvar%n_atom_s))
813 idum = 0
814 IF (colvar%reaction_path_param%dist_rmsd .OR. colvar%reaction_path_param%rmsd) THEN
815 DO ii = 1, SIZE(colvar%reaction_path_param%i_rmsd)
816 idum = idum + 1
817 i = colvar%reaction_path_param%i_rmsd(ii)
818 list(idum) = i
819 END DO
820 ELSE
821 DO ii = 1, SIZE(colvar%reaction_path_param%colvar_p)
822 DO j = 1, colvar%reaction_path_param%colvar_p(ii)%colvar%n_atom_s
823 idum = idum + 1
824 list(idum) = colvar%reaction_path_param%colvar_p(ii)%colvar%i_atom(j)
825 END DO
826 END DO
827 END IF
828 CASE (xyz_diag_colvar_id)
829 np = 1
830 ! Number of real atoms involved in the colvar
831 colvar%n_atom_s = 0
832 i = colvar%xyz_diag_param%i_atom
833 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
834 ! Create a List of points...
835 ALLOCATE (list(np))
836 i = colvar%xyz_diag_param%i_atom
837 list(1) = i
838 CASE (xyz_outerdiag_colvar_id)
839 np = 2
840 ! Number of real atoms involved in the colvar
841 colvar%n_atom_s = 0
842 i = colvar%xyz_outerdiag_param%i_atoms(1)
843 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
844 i = colvar%xyz_outerdiag_param%i_atoms(2)
845 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
846 ! Create a List of points...
847 ALLOCATE (list(np))
848 i = colvar%xyz_outerdiag_param%i_atoms(1)
849 list(1) = i
850 i = colvar%xyz_outerdiag_param%i_atoms(2)
851 list(2) = i
852 CASE (u_colvar_id)
853 np = 1; ALLOCATE (list(np), stat=stat)
854 cpassert(stat == 0)
855 colvar%n_atom_s = np; list(1) = 1
856 CASE (wc_colvar_id)
857 np = 3
858 ! Number of real atoms involved in the colvar
859 colvar%n_atom_s = 0
860 DO ii = 1, 3
861 i = colvar%Wc%ids(ii)
862 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
863 END DO
864 ! Create a List of points...
865 ALLOCATE (list(np))
866 idum = 0
867 DO ii = 1, 3
868 idum = idum + 1
869 i = colvar%Wc%ids(ii)
870 list(idum) = i
871 END DO
872 cpassert(idum == np)
873 CASE (hbp_colvar_id)
874 np = 3*colvar%HBP%nPoints
875 ! Number of real atoms involved in the colvar
876 colvar%n_atom_s = 0
877 DO j = 1, colvar%HBP%nPoints
878 DO ii = 1, 3
879 i = colvar%HBP%ids(j, ii)
880 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
881 END DO
882 END DO
883 ! Create a List of points...
884 ALLOCATE (list(np))
885 idum = 0
886 DO j = 1, colvar%HBP%nPoints
887 DO ii = 1, 3
888 idum = idum + 1
889 i = colvar%HBP%ids(j, ii)
890 list(idum) = i
891 END DO
892 END DO
893 cpassert(idum == np)
894 CASE (ring_puckering_colvar_id)
895 np = colvar%ring_puckering_param%nring
896 ! Number of real atoms involved in the colvar
897 colvar%n_atom_s = 0
898 DO ii = 1, colvar%ring_puckering_param%nring
899 i = colvar%ring_puckering_param%atoms(ii)
900 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
901 END DO
902 ! Create a List of points...
903 ALLOCATE (list(np))
904 idum = 0
905 DO ii = 1, colvar%ring_puckering_param%nring
906 idum = idum + 1
907 i = colvar%ring_puckering_param%atoms(ii)
908 list(idum) = i
909 END DO
910 cpassert(idum == np)
911 CASE (mindist_colvar_id)
912 np = colvar%mindist_param%n_dist_from + &
913 colvar%mindist_param%n_coord_from + colvar%mindist_param%n_coord_to
914 ! Number of real atoms involved in the colvar
915 colvar%n_atom_s = 0
916 DO ii = 1, colvar%mindist_param%n_dist_from
917 i = colvar%mindist_param%i_dist_from(ii)
918 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
919 END DO
920 DO ii = 1, colvar%mindist_param%n_coord_from
921 i = colvar%mindist_param%i_coord_from(ii)
922 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
923 END DO
924 DO ii = 1, colvar%mindist_param%n_coord_to
925 i = colvar%mindist_param%i_coord_to(ii)
926 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
927 END DO
928 ! Create a List of points...
929 ALLOCATE (list(np))
930 idum = 0
931 DO ii = 1, colvar%mindist_param%n_dist_from
932 idum = idum + 1
933 i = colvar%mindist_param%i_dist_from(ii)
934 list(idum) = i
935 END DO
936 DO ii = 1, colvar%mindist_param%n_coord_from
937 idum = idum + 1
938 i = colvar%mindist_param%i_coord_from(ii)
939 list(idum) = i
940 END DO
941 DO ii = 1, colvar%mindist_param%n_coord_to
942 idum = idum + 1
943 i = colvar%mindist_param%i_coord_to(ii)
944 list(idum) = i
945 END DO
946 cpassert(idum == np)
947 CASE (combine_colvar_id)
948 colvar%n_atom_s = 0
949 DO ii = 1, SIZE(colvar%combine_cvs_param%colvar_p)
950 colvar%n_atom_s = colvar%n_atom_s + colvar%combine_cvs_param%colvar_p(ii)%colvar%n_atom_s
951 END DO
952 ALLOCATE (list(colvar%n_atom_s))
953 idum = 0
954 DO ii = 1, SIZE(colvar%combine_cvs_param%colvar_p)
955 DO j = 1, colvar%combine_cvs_param%colvar_p(ii)%colvar%n_atom_s
956 idum = idum + 1
957 list(idum) = colvar%combine_cvs_param%colvar_p(ii)%colvar%i_atom(j)
958 END DO
959 END DO
960 END SELECT
961
962 IF (ASSOCIATED(colvar%dsdr)) THEN
963 DEALLOCATE (colvar%dsdr)
964 END IF
965 IF (ASSOCIATED(colvar%i_atom)) THEN
966 DEALLOCATE (colvar%i_atom)
967 END IF
968 ALLOCATE (colvar%dsdr(3, colvar%n_atom_s))
969 ALLOCATE (colvar%i_atom(colvar%n_atom_s))
970 ! And now map real atoms
971 istart = 0
972 iend = 0
973 DO i = 1, SIZE(list)
974 IF (.NOT. colvar%use_points) THEN
975 ! No point centers
976 colvar%i_atom(i) = list(i)
977 iend = iend + 1
978 ELSE
979 IF (ASSOCIATED(colvar%points(list(i))%atoms)) THEN
980 iend = istart + SIZE(colvar%points(list(i))%atoms)
981 colvar%i_atom(istart + 1:iend) = colvar%points(list(i))%atoms
982 istart = iend
983 END IF
984 END IF
985 END DO
986 cpassert(iend == colvar%n_atom_s)
987 DEALLOCATE (list)
988
989 END SUBROUTINE colvar_setup
990
991! **************************************************************************************************
992!> \brief Finalize the setup of the collective variable for the autoionization of water
993!> \param colvar the colvar to initialize
994!> \param colvar_id ...
995!> \param list ...
996!> \author Dorothea Golze
997! **************************************************************************************************
998 SUBROUTINE setup_hydronium_colvars(colvar, colvar_id, list)
999 TYPE(colvar_type), INTENT(INOUT) :: colvar
1000 INTEGER, INTENT(IN) :: colvar_id
1001 INTEGER, DIMENSION(:), INTENT(INOUT) :: list
1002
1003 INTEGER :: i, idum, ii, n_hydrogens, n_oxygens, np
1004 INTEGER, DIMENSION(:), POINTER :: i_hydrogens, i_oxygens
1005
1006 NULLIFY (i_oxygens, i_hydrogens)
1007
1008 SELECT CASE (colvar_id)
1009 CASE (hydronium_shell_colvar_id)
1010 n_oxygens = colvar%hydronium_shell_param%n_oxygens
1011 n_hydrogens = colvar%hydronium_shell_param%n_hydrogens
1012 i_oxygens => colvar%hydronium_shell_param%i_oxygens
1013 i_hydrogens => colvar%hydronium_shell_param%i_hydrogens
1014 CASE (hydronium_dist_colvar_id)
1015 n_oxygens = colvar%hydronium_dist_param%n_oxygens
1016 n_hydrogens = colvar%hydronium_dist_param%n_hydrogens
1017 i_oxygens => colvar%hydronium_dist_param%i_oxygens
1018 i_hydrogens => colvar%hydronium_dist_param%i_hydrogens
1019 END SELECT
1020
1021 np = n_oxygens + n_hydrogens
1022 ! Number of real atoms involved in the colvar
1023 colvar%n_atom_s = 0
1024 DO ii = 1, n_oxygens
1025 i = i_oxygens(ii)
1026 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
1027 END DO
1028 DO ii = 1, n_hydrogens
1029 i = i_hydrogens(ii)
1030 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
1031 END DO
1032 idum = 0
1033 DO ii = 1, n_oxygens
1034 idum = idum + 1
1035 i = i_oxygens(ii)
1036 list(idum) = i
1037 IF (any(i_hydrogens == i)) &
1038 cpabort("COLVAR: atoms doubled in OXYGENS and HYDROGENS list")
1039 END DO
1040 DO ii = 1, n_hydrogens
1041 idum = idum + 1
1042 i = i_hydrogens(ii)
1043 list(idum) = i
1044 END DO
1045 cpassert(idum == np)
1046 DO i = 1, np
1047 DO ii = i + 1, np
1048 IF (list(i) == list(ii)) THEN
1049 IF (i <= n_oxygens) &
1050 cpabort("atoms doubled in OXYGENS list")
1051 IF (i > n_oxygens) &
1052 cpabort("atoms doubled in HYDROGENS list")
1053 END IF
1054 END DO
1055 END DO
1056
1057 END SUBROUTINE setup_hydronium_colvars
1058
1059! **************************************************************************************************
1060!> \brief Finalize the setup of the collective variable for the dissociation
1061!> of a carboxylic acid in water
1062!> \param colvar the colvar to initialize
1063!> \param colvar_id ...
1064!> \param list ...
1065!> \author Dorothea Golze
1066! **************************************************************************************************
1067 SUBROUTINE setup_acid_hydronium_colvars(colvar, colvar_id, list)
1068 TYPE(colvar_type), INTENT(INOUT) :: colvar
1069 INTEGER, INTENT(IN) :: colvar_id
1070 INTEGER, DIMENSION(:), INTENT(INOUT) :: list
1071
1072 INTEGER :: i, idum, ii, n_hydrogens, &
1073 n_oxygens_acid, n_oxygens_water, np
1074 INTEGER, DIMENSION(:), POINTER :: i_hydrogens, i_oxygens_acid, &
1075 i_oxygens_water
1076
1077 NULLIFY (i_oxygens_water, i_oxygens_acid, i_hydrogens)
1078
1079 SELECT CASE (colvar_id)
1080 CASE (acid_hyd_dist_colvar_id)
1081 n_oxygens_water = colvar%acid_hyd_dist_param%n_oxygens_water
1082 n_oxygens_acid = colvar%acid_hyd_dist_param%n_oxygens_acid
1083 n_hydrogens = colvar%acid_hyd_dist_param%n_hydrogens
1084 i_oxygens_water => colvar%acid_hyd_dist_param%i_oxygens_water
1085 i_oxygens_acid => colvar%acid_hyd_dist_param%i_oxygens_acid
1086 i_hydrogens => colvar%acid_hyd_dist_param%i_hydrogens
1087 CASE (acid_hyd_shell_colvar_id)
1088 n_oxygens_water = colvar%acid_hyd_shell_param%n_oxygens_water
1089 n_oxygens_acid = colvar%acid_hyd_shell_param%n_oxygens_acid
1090 n_hydrogens = colvar%acid_hyd_shell_param%n_hydrogens
1091 i_oxygens_water => colvar%acid_hyd_shell_param%i_oxygens_water
1092 i_oxygens_acid => colvar%acid_hyd_shell_param%i_oxygens_acid
1093 i_hydrogens => colvar%acid_hyd_shell_param%i_hydrogens
1094 END SELECT
1095
1096 np = n_oxygens_water + n_oxygens_acid + n_hydrogens
1097 ! Number of real atoms involved in the colvar
1098 colvar%n_atom_s = 0
1099 DO ii = 1, n_oxygens_water
1100 i = i_oxygens_water(ii)
1101 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
1102 END DO
1103 DO ii = 1, n_oxygens_acid
1104 i = i_oxygens_acid(ii)
1105 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
1106 END DO
1107 DO ii = 1, n_hydrogens
1108 i = i_hydrogens(ii)
1109 colvar%n_atom_s = colvar%n_atom_s + colv_size(colvar, i)
1110 END DO
1111 idum = 0
1112 DO ii = 1, n_oxygens_water
1113 idum = idum + 1
1114 i = i_oxygens_water(ii)
1115 list(idum) = i
1116 IF (any(i_hydrogens == i)) &
1117 cpabort("COLVAR: atoms doubled in OXYGENS_WATER and HYDROGENS list")
1118 IF (any(i_oxygens_acid == i)) &
1119 cpabort("COLVAR: atoms doubled in OXYGENS_WATER and OXYGENS_ACID list")
1120 END DO
1121 DO ii = 1, n_oxygens_acid
1122 idum = idum + 1
1123 i = i_oxygens_acid(ii)
1124 list(idum) = i
1125 IF (any(i_hydrogens == i)) &
1126 cpabort("COLVAR: atoms doubled in OXYGENS_ACID and HYDROGENS list")
1127 END DO
1128 DO ii = 1, n_hydrogens
1129 idum = idum + 1
1130 i = i_hydrogens(ii)
1131 list(idum) = i
1132 END DO
1133 cpassert(idum == np)
1134 DO i = 1, np
1135 DO ii = i + 1, np
1136 IF (list(i) == list(ii)) THEN
1137 IF (i <= n_oxygens_water) &
1138 cpabort("atoms doubled in OXYGENS_WATER list")
1139 IF (i > n_oxygens_water .AND. i <= n_oxygens_water + n_oxygens_acid) &
1140 cpabort("atoms doubled in OXYGENS_ACID list")
1141 IF (i > n_oxygens_water + n_oxygens_acid) &
1142 cpabort("atoms doubled in HYDROGENS list")
1143 END IF
1144 END DO
1145 END DO
1146
1147 END SUBROUTINE setup_acid_hydronium_colvars
1148
1149! **************************************************************************************************
1150!> \brief Gives back the size of an array of integer. If not associated gives back 1
1151!> \param colvar ...
1152!> \param i ...
1153!> \return ...
1154!> \author Teodoro Laino - 03.2007
1155! **************************************************************************************************
1156 FUNCTION colv_size(colvar, i) RESULT(my_size)
1157 TYPE(colvar_type), INTENT(IN) :: colvar
1158 INTEGER :: i, my_size
1159
1160 my_size = 1
1161 IF (ASSOCIATED(colvar%points)) THEN
1162 IF (ASSOCIATED(colvar%points(i)%atoms)) THEN
1163 my_size = SIZE(colvar%points(i)%atoms)
1164 ELSE
1165 my_size = 0
1166 END IF
1167 END IF
1168 END FUNCTION colv_size
1169
1170! **************************************************************************************************
1171!> \brief releases the memory that might have been allocated by the colvar
1172!> \param colvar the colvar to deallocate
1173!> \author alessandro laio and fawzi mohamed
1174! **************************************************************************************************
1175 RECURSIVE SUBROUTINE colvar_release(colvar)
1176 TYPE(colvar_type), POINTER :: colvar
1177
1178 INTEGER :: i
1179
1180 cpassert(ASSOCIATED(colvar))
1181 IF (ASSOCIATED(colvar%dsdr)) THEN
1182 DEALLOCATE (colvar%dsdr)
1183 END IF
1184 IF (ASSOCIATED(colvar%i_atom)) THEN
1185 DEALLOCATE (colvar%i_atom)
1186 END IF
1187 IF (ASSOCIATED(colvar%points)) THEN
1188 DO i = 1, SIZE(colvar%points)
1189 IF (ASSOCIATED(colvar%points(i)%atoms)) THEN
1190 DEALLOCATE (colvar%points(i)%atoms)
1191 END IF
1192 IF (ASSOCIATED(colvar%points(i)%weights)) THEN
1193 DEALLOCATE (colvar%points(i)%weights)
1194 END IF
1195 END DO
1196 DEALLOCATE (colvar%points)
1197 END IF
1198 SELECT CASE (colvar%type_id)
1199 CASE (dist_colvar_id)
1200 DEALLOCATE (colvar%dist_param)
1201 CASE (coord_colvar_id)
1202 IF (ASSOCIATED(colvar%coord_param%i_at_from)) THEN
1203 DEALLOCATE (colvar%coord_param%i_at_from)
1204 END IF
1205 IF (ASSOCIATED(colvar%coord_param%i_at_to)) THEN
1206 DEALLOCATE (colvar%coord_param%i_at_to)
1207 END IF
1208 IF (ASSOCIATED(colvar%coord_param%c_kinds_from)) THEN
1209 DEALLOCATE (colvar%coord_param%c_kinds_from)
1210 END IF
1211 IF (ASSOCIATED(colvar%coord_param%c_kinds_to)) THEN
1212 DEALLOCATE (colvar%coord_param%c_kinds_to)
1213 END IF
1214 IF (ASSOCIATED(colvar%coord_param%i_at_to_b)) THEN
1215 DEALLOCATE (colvar%coord_param%i_at_to_b)
1216 END IF
1217 IF (ASSOCIATED(colvar%coord_param%c_kinds_to_b)) THEN
1218 DEALLOCATE (colvar%coord_param%c_kinds_to_b)
1219 END IF
1220 DEALLOCATE (colvar%coord_param)
1221 CASE (population_colvar_id)
1222 IF (ASSOCIATED(colvar%population_param%i_at_from)) THEN
1223 DEALLOCATE (colvar%population_param%i_at_from)
1224 END IF
1225 IF (ASSOCIATED(colvar%population_param%i_at_to)) THEN
1226 DEALLOCATE (colvar%population_param%i_at_to)
1227 END IF
1228 IF (ASSOCIATED(colvar%population_param%c_kinds_from)) THEN
1229 DEALLOCATE (colvar%population_param%c_kinds_from)
1230 END IF
1231 IF (ASSOCIATED(colvar%population_param%c_kinds_to)) THEN
1232 DEALLOCATE (colvar%population_param%c_kinds_to)
1233 END IF
1234 DEALLOCATE (colvar%population_param)
1235 CASE (gyration_colvar_id)
1236 IF (ASSOCIATED(colvar%gyration_param%i_at)) THEN
1237 DEALLOCATE (colvar%gyration_param%i_at)
1238 END IF
1239 IF (ASSOCIATED(colvar%gyration_param%c_kinds)) THEN
1240 DEALLOCATE (colvar%gyration_param%c_kinds)
1241 END IF
1242 DEALLOCATE (colvar%gyration_param)
1243 CASE (angle_colvar_id)
1244 DEALLOCATE (colvar%angle_param)
1245 CASE (torsion_colvar_id)
1246 DEALLOCATE (colvar%torsion_param)
1247 CASE (plane_distance_colvar_id)
1248 DEALLOCATE (colvar%plane_distance_param)
1249 CASE (plane_plane_angle_colvar_id)
1250 DEALLOCATE (colvar%plane_plane_angle_param)
1251 CASE (dfunct_colvar_id)
1252 DEALLOCATE (colvar%dfunct_param)
1253 CASE (rotation_colvar_id)
1254 DEALLOCATE (colvar%rotation_param)
1255 CASE (qparm_colvar_id)
1256 DEALLOCATE (colvar%qparm_param%i_at_from)
1257 DEALLOCATE (colvar%qparm_param%i_at_to)
1258 DEALLOCATE (colvar%qparm_param)
1259 CASE (xyz_diag_colvar_id)
1260 DEALLOCATE (colvar%xyz_diag_param)
1261 CASE (xyz_outerdiag_colvar_id)
1262 DEALLOCATE (colvar%xyz_outerdiag_param)
1263 CASE (u_colvar_id)
1264 NULLIFY (colvar%u_param%mixed_energy_section)
1265 DEALLOCATE (colvar%u_param)
1266 CASE (hydronium_shell_colvar_id)
1267 DEALLOCATE (colvar%hydronium_shell_param%i_oxygens)
1268 DEALLOCATE (colvar%hydronium_shell_param%i_hydrogens)
1269 DEALLOCATE (colvar%hydronium_shell_param)
1270 CASE (hydronium_dist_colvar_id)
1271 DEALLOCATE (colvar%hydronium_dist_param%i_oxygens)
1272 DEALLOCATE (colvar%hydronium_dist_param%i_hydrogens)
1273 DEALLOCATE (colvar%hydronium_dist_param)
1274 CASE (acid_hyd_dist_colvar_id)
1275 DEALLOCATE (colvar%acid_hyd_dist_param%i_oxygens_water)
1276 DEALLOCATE (colvar%acid_hyd_dist_param%i_oxygens_acid)
1277 DEALLOCATE (colvar%acid_hyd_dist_param%i_hydrogens)
1278 DEALLOCATE (colvar%acid_hyd_dist_param)
1279 CASE (acid_hyd_shell_colvar_id)
1280 DEALLOCATE (colvar%acid_hyd_shell_param%i_oxygens_water)
1281 DEALLOCATE (colvar%acid_hyd_shell_param%i_oxygens_acid)
1282 DEALLOCATE (colvar%acid_hyd_shell_param%i_hydrogens)
1283 DEALLOCATE (colvar%acid_hyd_shell_param)
1284 CASE (reaction_path_colvar_id, distance_from_path_colvar_id)
1285 IF (colvar%reaction_path_param%dist_rmsd .OR. colvar%reaction_path_param%rmsd) THEN
1286 DEALLOCATE (colvar%reaction_path_param%r_ref)
1287 DEALLOCATE (colvar%reaction_path_param%i_rmsd)
1288 ELSE
1289 DO i = 1, SIZE(colvar%reaction_path_param%colvar_p)
1290 CALL colvar_release(colvar%reaction_path_param%colvar_p(i)%colvar)
1291 END DO
1292 DEALLOCATE (colvar%reaction_path_param%colvar_p)
1293 DEALLOCATE (colvar%reaction_path_param%f_vals)
1294 END IF
1295 DEALLOCATE (colvar%reaction_path_param)
1296 CASE (combine_colvar_id)
1297 DO i = 1, SIZE(colvar%combine_cvs_param%colvar_p)
1298 CALL colvar_release(colvar%combine_cvs_param%colvar_p(i)%colvar)
1299 END DO
1300 DEALLOCATE (colvar%combine_cvs_param%colvar_p)
1301 DEALLOCATE (colvar%combine_cvs_param%c_parameters)
1302 DEALLOCATE (colvar%combine_cvs_param%v_parameters)
1303 DEALLOCATE (colvar%combine_cvs_param%variables)
1304 DEALLOCATE (colvar%combine_cvs_param)
1305 CASE (rmsd_colvar_id)
1306 DEALLOCATE (colvar%rmsd_param%weights)
1307 DEALLOCATE (colvar%rmsd_param%r_ref)
1308 DEALLOCATE (colvar%rmsd_param%i_rmsd)
1309 DEALLOCATE (colvar%rmsd_param)
1310 CASE (wc_colvar_id)
1311 DEALLOCATE (colvar%Wc)
1312 CASE (hbp_colvar_id)
1313 DEALLOCATE (colvar%HBP%ewc)
1314 DEALLOCATE (colvar%HBP%ids)
1315 DEALLOCATE (colvar%HBP)
1316 CASE (ring_puckering_colvar_id)
1317 DEALLOCATE (colvar%ring_puckering_param%atoms)
1318 DEALLOCATE (colvar%ring_puckering_param)
1319 CASE (mindist_colvar_id)
1320 IF (ASSOCIATED(colvar%mindist_param%i_dist_from)) THEN
1321 DEALLOCATE (colvar%mindist_param%i_dist_from)
1322 END IF
1323 IF (ASSOCIATED(colvar%mindist_param%i_coord_from)) THEN
1324 DEALLOCATE (colvar%mindist_param%i_coord_from)
1325 END IF
1326 IF (ASSOCIATED(colvar%mindist_param%i_coord_to)) THEN
1327 DEALLOCATE (colvar%mindist_param%i_coord_to)
1328 END IF
1329 IF (ASSOCIATED(colvar%mindist_param%k_coord_from)) THEN
1330 DEALLOCATE (colvar%mindist_param%k_coord_from)
1331 END IF
1332 IF (ASSOCIATED(colvar%mindist_param%k_coord_to)) THEN
1333 DEALLOCATE (colvar%mindist_param%k_coord_to)
1334 END IF
1335 DEALLOCATE (colvar%mindist_param)
1336 CASE (no_colvar_id)
1337 ! Do nothing
1338 CASE default
1339 cpabort("")
1340 END SELECT
1341 DEALLOCATE (colvar)
1342
1343 END SUBROUTINE colvar_release
1344
1345! **************************************************************************************************
1346!> \brief Clone a colvar type
1347!> \param colvar_out ...
1348!> \param colvar_in the colvar to deallocate
1349!> \param i_atom_offset ...
1350!> \author Teodoro Laino [tlaino] 04.2006
1351! **************************************************************************************************
1352 RECURSIVE SUBROUTINE colvar_clone(colvar_out, colvar_in, i_atom_offset)
1353 TYPE(colvar_type), INTENT(INOUT), POINTER :: colvar_out
1354 TYPE(colvar_type), INTENT(IN) :: colvar_in
1355 INTEGER, INTENT(IN), OPTIONAL :: i_atom_offset
1356
1357 INTEGER :: i, my_offset, ndim, ndim2, stat
1358
1359 my_offset = 0
1360 IF (PRESENT(i_atom_offset)) my_offset = i_atom_offset
1361 CALL colvar_create(colvar_out, colvar_in%type_id)
1362 CALL colvar_clone_points(colvar_out, colvar_in, my_offset)
1363 IF (colvar_in%use_points) my_offset = 0
1364 SELECT CASE (colvar_out%type_id)
1365 CASE (dist_colvar_id)
1366 colvar_out%dist_param%i_at = colvar_in%dist_param%i_at + my_offset
1367 colvar_out%dist_param%j_at = colvar_in%dist_param%j_at + my_offset
1368 colvar_out%dist_param%axis_id = colvar_in%dist_param%axis_id
1369 colvar_out%dist_param%sign_d = colvar_in%dist_param%sign_d
1370 CASE (coord_colvar_id)
1371 colvar_out%coord_param%n_atoms_to = colvar_in%coord_param%n_atoms_to
1372 colvar_out%coord_param%n_atoms_to_b = colvar_in%coord_param%n_atoms_to_b
1373 colvar_out%coord_param%n_atoms_from = colvar_in%coord_param%n_atoms_from
1374 colvar_out%coord_param%nncrd = colvar_in%coord_param%nncrd
1375 colvar_out%coord_param%ndcrd = colvar_in%coord_param%ndcrd
1376 colvar_out%coord_param%r_0 = colvar_in%coord_param%r_0
1377 colvar_out%coord_param%nncrd_b = colvar_in%coord_param%nncrd_b
1378 colvar_out%coord_param%ndcrd_b = colvar_in%coord_param%ndcrd_b
1379 colvar_out%coord_param%r_0_b = colvar_in%coord_param%r_0_b
1380 colvar_out%coord_param%use_kinds_from = colvar_in%coord_param%use_kinds_from
1381 colvar_out%coord_param%use_kinds_to = colvar_in%coord_param%use_kinds_to
1382 colvar_out%coord_param%use_kinds_to_b = colvar_in%coord_param%use_kinds_to_b
1383 IF (colvar_in%coord_param%use_kinds_from) THEN
1384 ! KINDS
1385 ndim = SIZE(colvar_in%coord_param%c_kinds_from)
1386 ALLOCATE (colvar_out%coord_param%c_kinds_from(ndim))
1387 colvar_out%coord_param%c_kinds_from = colvar_in%coord_param%c_kinds_from
1388 ELSE
1389 ! INDEX
1390 ndim = SIZE(colvar_in%coord_param%i_at_from)
1391 ALLOCATE (colvar_out%coord_param%i_at_from(ndim))
1392 colvar_out%coord_param%i_at_from = colvar_in%coord_param%i_at_from + my_offset
1393 END IF
1394 IF (colvar_in%coord_param%use_kinds_to) THEN
1395 ! KINDS
1396 ndim = SIZE(colvar_in%coord_param%c_kinds_to)
1397 ALLOCATE (colvar_out%coord_param%c_kinds_to(ndim))
1398 colvar_out%coord_param%c_kinds_to = colvar_in%coord_param%c_kinds_to
1399 ELSE
1400 ! INDEX
1401 ndim = SIZE(colvar_in%coord_param%i_at_to)
1402 ALLOCATE (colvar_out%coord_param%i_at_to(ndim))
1403 colvar_out%coord_param%i_at_to = colvar_in%coord_param%i_at_to + my_offset
1404 END IF
1405 IF (colvar_in%coord_param%use_kinds_to_b) THEN
1406 ! KINDS
1407 ndim = SIZE(colvar_in%coord_param%c_kinds_to_b)
1408 ALLOCATE (colvar_out%coord_param%c_kinds_to_b(ndim))
1409 colvar_out%coord_param%c_kinds_to_b = colvar_in%coord_param%c_kinds_to_b
1410 ELSEIF (ASSOCIATED(colvar_in%coord_param%i_at_to_b)) THEN
1411 ! INDEX
1412 ndim = SIZE(colvar_in%coord_param%i_at_to_b)
1413 ALLOCATE (colvar_out%coord_param%i_at_to_b(ndim))
1414 colvar_out%coord_param%i_at_to_b = colvar_in%coord_param%i_at_to_b + my_offset
1415 END IF
1416
1417 CASE (population_colvar_id)
1418 colvar_out%population_param%n_atoms_to = colvar_in%population_param%n_atoms_to
1419 colvar_out%population_param%n_atoms_from = colvar_in%population_param%n_atoms_from
1420 colvar_out%population_param%nncrd = colvar_in%population_param%nncrd
1421 colvar_out%population_param%ndcrd = colvar_in%population_param%ndcrd
1422 colvar_out%population_param%r_0 = colvar_in%population_param%r_0
1423 colvar_out%population_param%use_kinds_from = colvar_in%population_param%use_kinds_from
1424 colvar_out%population_param%use_kinds_to = colvar_in%population_param%use_kinds_to
1425 IF (colvar_in%population_param%use_kinds_from) THEN
1426 ! KINDS
1427 ndim = SIZE(colvar_in%population_param%c_kinds_from)
1428 ALLOCATE (colvar_out%population_param%c_kinds_from(ndim))
1429 colvar_out%population_param%c_kinds_from = colvar_in%population_param%c_kinds_from
1430 ELSE
1431 ! INDEX
1432 ndim = SIZE(colvar_in%population_param%i_at_from)
1433 ALLOCATE (colvar_out%population_param%i_at_from(ndim))
1434 colvar_out%population_param%i_at_from = colvar_in%population_param%i_at_from + my_offset
1435 END IF
1436 IF (colvar_in%population_param%use_kinds_to) THEN
1437 ! KINDS
1438 ndim = SIZE(colvar_in%population_param%c_kinds_to)
1439 ALLOCATE (colvar_out%population_param%c_kinds_to(ndim))
1440 colvar_out%population_param%c_kinds_to = colvar_in%population_param%c_kinds_to
1441 ELSE
1442 ! INDEX
1443 ndim = SIZE(colvar_in%population_param%i_at_to)
1444 ALLOCATE (colvar_out%population_param%i_at_to(ndim))
1445 colvar_out%population_param%i_at_to = colvar_in%population_param%i_at_to + my_offset
1446 END IF
1447
1448 CASE (gyration_colvar_id)
1449 colvar_out%gyration_param%n_atoms = colvar_in%gyration_param%n_atoms
1450 colvar_out%gyration_param%use_kinds = colvar_in%gyration_param%use_kinds
1451 IF (colvar_in%gyration_param%use_kinds) THEN
1452 ! KINDS
1453 ndim = SIZE(colvar_in%gyration_param%c_kinds)
1454 ALLOCATE (colvar_out%gyration_param%c_kinds(ndim))
1455 colvar_out%gyration_param%c_kinds = colvar_in%gyration_param%c_kinds
1456 ELSE
1457 ! INDEX
1458 ndim = SIZE(colvar_in%gyration_param%i_at)
1459 ALLOCATE (colvar_out%gyration_param%i_at(ndim))
1460 colvar_out%gyration_param%i_at = colvar_in%gyration_param%i_at + my_offset
1461 END IF
1462 CASE (angle_colvar_id)
1463 colvar_out%angle_param%i_at_angle = colvar_in%angle_param%i_at_angle + my_offset
1464 CASE (torsion_colvar_id)
1465 colvar_out%torsion_param%i_at_tors = colvar_in%torsion_param%i_at_tors + my_offset
1466 colvar_out%torsion_param%o0 = colvar_in%torsion_param%o0
1467 CASE (plane_distance_colvar_id)
1468 colvar_out%plane_distance_param%use_pbc = colvar_in%plane_distance_param%use_pbc
1469 colvar_out%plane_distance_param%plane = colvar_in%plane_distance_param%plane + my_offset
1470 colvar_out%plane_distance_param%point = colvar_in%plane_distance_param%point + my_offset
1471 CASE (plane_plane_angle_colvar_id)
1472 colvar_out%plane_plane_angle_param%plane1%type_of_def = colvar_in%plane_plane_angle_param%plane1%type_of_def
1473 IF (colvar_out%plane_plane_angle_param%plane1%type_of_def == plane_def_vec) THEN
1474 colvar_out%plane_plane_angle_param%plane1%normal_vec = colvar_in%plane_plane_angle_param%plane1%normal_vec
1475 ELSE
1476 colvar_out%plane_plane_angle_param%plane1%points = colvar_in%plane_plane_angle_param%plane1%points + my_offset
1477 END IF
1478
1479 colvar_out%plane_plane_angle_param%plane2%type_of_def = colvar_in%plane_plane_angle_param%plane2%type_of_def
1480 IF (colvar_out%plane_plane_angle_param%plane2%type_of_def == plane_def_vec) THEN
1481 colvar_out%plane_plane_angle_param%plane2%normal_vec = colvar_in%plane_plane_angle_param%plane2%normal_vec
1482 ELSE
1483 colvar_out%plane_plane_angle_param%plane2%points = colvar_in%plane_plane_angle_param%plane2%points + my_offset
1484 END IF
1485 CASE (rotation_colvar_id)
1486 colvar_out%rotation_param%i_at1_bond1 = colvar_in%rotation_param%i_at1_bond1 + my_offset
1487 colvar_out%rotation_param%i_at2_bond1 = colvar_in%rotation_param%i_at2_bond1 + my_offset
1488 colvar_out%rotation_param%i_at1_bond2 = colvar_in%rotation_param%i_at1_bond2 + my_offset
1489 colvar_out%rotation_param%i_at2_bond2 = colvar_in%rotation_param%i_at2_bond2 + my_offset
1490 CASE (dfunct_colvar_id)
1491 colvar_out%dfunct_param%i_at_dfunct = colvar_in%dfunct_param%i_at_dfunct + my_offset
1492 colvar_out%dfunct_param%coeff = colvar_in%dfunct_param%coeff
1493 colvar_out%dfunct_param%use_pbc = colvar_in%dfunct_param%use_pbc
1494 CASE (qparm_colvar_id)
1495 colvar_out%qparm_param%n_atoms_to = colvar_in%qparm_param%n_atoms_to
1496 colvar_out%qparm_param%n_atoms_from = colvar_in%qparm_param%n_atoms_from
1497 colvar_out%qparm_param%rcut = colvar_in%qparm_param%rcut
1498 colvar_out%qparm_param%l = colvar_in%qparm_param%l
1499 colvar_out%qparm_param%rstart = colvar_in%qparm_param%rstart
1500 colvar_out%qparm_param%include_images = colvar_in%qparm_param%include_images
1501 ndim = SIZE(colvar_in%qparm_param%i_at_from)
1502 ALLOCATE (colvar_out%qparm_param%i_at_from(ndim))
1503 ndim = SIZE(colvar_in%qparm_param%i_at_to)
1504 ALLOCATE (colvar_out%qparm_param%i_at_to(ndim))
1505 colvar_out%qparm_param%i_at_from = colvar_in%qparm_param%i_at_from + my_offset
1506 colvar_out%qparm_param%i_at_to = colvar_in%qparm_param%i_at_from + my_offset
1507 CASE (xyz_diag_colvar_id)
1508 colvar_out%xyz_diag_param%i_atom = colvar_in%xyz_diag_param%i_atom + my_offset
1509 colvar_out%xyz_diag_param%component = colvar_in%xyz_diag_param%component
1510 colvar_out%xyz_diag_param%r0 = colvar_in%xyz_diag_param%r0
1511 colvar_out%xyz_diag_param%use_pbc = colvar_in%xyz_diag_param%use_pbc
1512 colvar_out%xyz_diag_param%use_absolute_position = colvar_in%xyz_diag_param%use_absolute_position
1513 CASE (xyz_outerdiag_colvar_id)
1514 colvar_out%xyz_outerdiag_param%i_atoms = colvar_in%xyz_outerdiag_param%i_atoms + my_offset
1515 colvar_out%xyz_outerdiag_param%components = colvar_in%xyz_outerdiag_param%components
1516 colvar_out%xyz_outerdiag_param%r0 = colvar_in%xyz_outerdiag_param%r0
1517 colvar_out%xyz_outerdiag_param%use_pbc = colvar_in%xyz_outerdiag_param%use_pbc
1518 CASE (u_colvar_id)
1519 colvar_out%u_param%natom = colvar_in%u_param%natom
1520 CASE (hydronium_shell_colvar_id)
1521 colvar_out%hydronium_shell_param%n_hydrogens = colvar_in%hydronium_shell_param%n_hydrogens
1522 colvar_out%hydronium_shell_param%n_oxygens = colvar_in%hydronium_shell_param%n_oxygens
1523 colvar_out%hydronium_shell_param%nh = colvar_in%hydronium_shell_param%nh
1524 colvar_out%hydronium_shell_param%poh = colvar_in%hydronium_shell_param%poh
1525 colvar_out%hydronium_shell_param%poo = colvar_in%hydronium_shell_param%poo
1526 colvar_out%hydronium_shell_param%qoh = colvar_in%hydronium_shell_param%qoh
1527 colvar_out%hydronium_shell_param%qoo = colvar_in%hydronium_shell_param%qoo
1528 colvar_out%hydronium_shell_param%pm = colvar_in%hydronium_shell_param%pm
1529 colvar_out%hydronium_shell_param%qm = colvar_in%hydronium_shell_param%qm
1530 colvar_out%hydronium_shell_param%roo = colvar_in%hydronium_shell_param%roo
1531 colvar_out%hydronium_shell_param%roh = colvar_in%hydronium_shell_param%roh
1532 colvar_out%hydronium_shell_param%lambda = colvar_in%hydronium_shell_param%lambda
1533 ndim = SIZE(colvar_in%hydronium_shell_param%i_oxygens)
1534 ALLOCATE (colvar_out%hydronium_shell_param%i_oxygens(ndim))
1535 ndim = SIZE(colvar_in%hydronium_shell_param%i_hydrogens)
1536 ALLOCATE (colvar_out%hydronium_shell_param%i_hydrogens(ndim))
1537 colvar_out%hydronium_shell_param%i_oxygens = colvar_in%hydronium_shell_param%i_oxygens + my_offset
1538 colvar_out%hydronium_shell_param%i_hydrogens = colvar_in%hydronium_shell_param%i_hydrogens + my_offset
1539 CASE (hydronium_dist_colvar_id)
1540 colvar_out%hydronium_dist_param%n_hydrogens = colvar_in%hydronium_dist_param%n_hydrogens
1541 colvar_out%hydronium_dist_param%n_oxygens = colvar_in%hydronium_dist_param%n_oxygens
1542 colvar_out%hydronium_dist_param%nh = colvar_in%hydronium_dist_param%nh
1543 colvar_out%hydronium_dist_param%nn = colvar_in%hydronium_dist_param%nn
1544 colvar_out%hydronium_dist_param%poh = colvar_in%hydronium_dist_param%poh
1545 colvar_out%hydronium_dist_param%qoh = colvar_in%hydronium_dist_param%qoh
1546 colvar_out%hydronium_dist_param%pf = colvar_in%hydronium_dist_param%pf
1547 colvar_out%hydronium_dist_param%qf = colvar_in%hydronium_dist_param%qf
1548 colvar_out%hydronium_dist_param%pm = colvar_in%hydronium_dist_param%pm
1549 colvar_out%hydronium_dist_param%qm = colvar_in%hydronium_dist_param%qm
1550 colvar_out%hydronium_dist_param%roh = colvar_in%hydronium_dist_param%roh
1551 colvar_out%hydronium_dist_param%lambda = colvar_in%hydronium_dist_param%lambda
1552 ndim = SIZE(colvar_in%hydronium_dist_param%i_oxygens)
1553 ALLOCATE (colvar_out%hydronium_dist_param%i_oxygens(ndim))
1554 ndim = SIZE(colvar_in%hydronium_dist_param%i_hydrogens)
1555 ALLOCATE (colvar_out%hydronium_dist_param%i_hydrogens(ndim))
1556 colvar_out%hydronium_dist_param%i_oxygens = colvar_in%hydronium_dist_param%i_oxygens + my_offset
1557 colvar_out%hydronium_dist_param%i_hydrogens = colvar_in%hydronium_dist_param%i_hydrogens + my_offset
1558 CASE (acid_hyd_dist_colvar_id)
1559 colvar_out%acid_hyd_dist_param%n_hydrogens = colvar_in%acid_hyd_dist_param%n_hydrogens
1560 colvar_out%acid_hyd_dist_param%n_oxygens_water = colvar_in%acid_hyd_dist_param%n_oxygens_water
1561 colvar_out%acid_hyd_dist_param%n_oxygens_acid = colvar_in%acid_hyd_dist_param%n_oxygens_acid
1562 colvar_out%acid_hyd_dist_param%nc = colvar_in%acid_hyd_dist_param%nc
1563 colvar_out%acid_hyd_dist_param%pwoh = colvar_in%acid_hyd_dist_param%pwoh
1564 colvar_out%acid_hyd_dist_param%qwoh = colvar_in%acid_hyd_dist_param%qwoh
1565 colvar_out%acid_hyd_dist_param%paoh = colvar_in%acid_hyd_dist_param%paoh
1566 colvar_out%acid_hyd_dist_param%qaoh = colvar_in%acid_hyd_dist_param%qaoh
1567 colvar_out%acid_hyd_dist_param%pcut = colvar_in%acid_hyd_dist_param%pcut
1568 colvar_out%acid_hyd_dist_param%qcut = colvar_in%acid_hyd_dist_param%qcut
1569 colvar_out%acid_hyd_dist_param%rwoh = colvar_in%acid_hyd_dist_param%rwoh
1570 colvar_out%acid_hyd_dist_param%raoh = colvar_in%acid_hyd_dist_param%raoh
1571 colvar_out%acid_hyd_dist_param%lambda = colvar_in%acid_hyd_dist_param%lambda
1572 ndim = SIZE(colvar_in%acid_hyd_dist_param%i_oxygens_water)
1573 ALLOCATE (colvar_out%acid_hyd_dist_param%i_oxygens_water(ndim))
1574 ndim = SIZE(colvar_in%acid_hyd_dist_param%i_oxygens_acid)
1575 ALLOCATE (colvar_out%acid_hyd_dist_param%i_oxygens_acid(ndim))
1576 ndim = SIZE(colvar_in%acid_hyd_dist_param%i_hydrogens)
1577 ALLOCATE (colvar_out%acid_hyd_dist_param%i_hydrogens(ndim))
1578 colvar_out%acid_hyd_dist_param%i_oxygens_water = colvar_in%acid_hyd_dist_param%i_oxygens_water + my_offset
1579 colvar_out%acid_hyd_dist_param%i_oxygens_acid = colvar_in%acid_hyd_dist_param%i_oxygens_acid + my_offset
1580 colvar_out%acid_hyd_dist_param%i_hydrogens = colvar_in%acid_hyd_dist_param%i_hydrogens + my_offset
1581 CASE (acid_hyd_shell_colvar_id)
1582 colvar_out%acid_hyd_shell_param%n_hydrogens = colvar_in%acid_hyd_shell_param%n_hydrogens
1583 colvar_out%acid_hyd_shell_param%n_oxygens_water = colvar_in%acid_hyd_shell_param%n_oxygens_water
1584 colvar_out%acid_hyd_shell_param%n_oxygens_acid = colvar_in%acid_hyd_shell_param%n_oxygens_acid
1585 colvar_out%acid_hyd_shell_param%nc = colvar_in%acid_hyd_shell_param%nc
1586 colvar_out%acid_hyd_shell_param%nh = colvar_in%acid_hyd_shell_param%nh
1587 colvar_out%acid_hyd_shell_param%pwoh = colvar_in%acid_hyd_shell_param%pwoh
1588 colvar_out%acid_hyd_shell_param%qwoh = colvar_in%acid_hyd_shell_param%qwoh
1589 colvar_out%acid_hyd_shell_param%paoh = colvar_in%acid_hyd_shell_param%paoh
1590 colvar_out%acid_hyd_shell_param%qaoh = colvar_in%acid_hyd_shell_param%qaoh
1591 colvar_out%acid_hyd_shell_param%poo = colvar_in%acid_hyd_shell_param%poo
1592 colvar_out%acid_hyd_shell_param%qoo = colvar_in%acid_hyd_shell_param%qoo
1593 colvar_out%acid_hyd_shell_param%pm = colvar_in%acid_hyd_shell_param%pm
1594 colvar_out%acid_hyd_shell_param%qm = colvar_in%acid_hyd_shell_param%qm
1595 colvar_out%acid_hyd_shell_param%pcut = colvar_in%acid_hyd_shell_param%pcut
1596 colvar_out%acid_hyd_shell_param%qcut = colvar_in%acid_hyd_shell_param%qcut
1597 colvar_out%acid_hyd_shell_param%rwoh = colvar_in%acid_hyd_shell_param%rwoh
1598 colvar_out%acid_hyd_shell_param%raoh = colvar_in%acid_hyd_shell_param%raoh
1599 colvar_out%acid_hyd_shell_param%roo = colvar_in%acid_hyd_shell_param%roo
1600 colvar_out%acid_hyd_shell_param%lambda = colvar_in%acid_hyd_shell_param%lambda
1601 ndim = SIZE(colvar_in%acid_hyd_shell_param%i_oxygens_water)
1602 ALLOCATE (colvar_out%acid_hyd_shell_param%i_oxygens_water(ndim))
1603 ndim = SIZE(colvar_in%acid_hyd_shell_param%i_oxygens_acid)
1604 ALLOCATE (colvar_out%acid_hyd_shell_param%i_oxygens_acid(ndim))
1605 ndim = SIZE(colvar_in%acid_hyd_shell_param%i_hydrogens)
1606 ALLOCATE (colvar_out%acid_hyd_shell_param%i_hydrogens(ndim))
1607 colvar_out%acid_hyd_shell_param%i_oxygens_water = colvar_in%acid_hyd_shell_param%i_oxygens_water + my_offset
1608 colvar_out%acid_hyd_shell_param%i_oxygens_acid = colvar_in%acid_hyd_shell_param%i_oxygens_acid + my_offset
1609 colvar_out%acid_hyd_shell_param%i_hydrogens = colvar_in%acid_hyd_shell_param%i_hydrogens + my_offset
1610 CASE (reaction_path_colvar_id, distance_from_path_colvar_id)
1611 colvar_out%reaction_path_param%dist_rmsd = colvar_in%reaction_path_param%dist_rmsd
1612 colvar_out%reaction_path_param%rmsd = colvar_in%reaction_path_param%rmsd
1613 colvar_out%reaction_path_param%nr_frames = colvar_in%reaction_path_param%nr_frames
1614 IF (colvar_in%reaction_path_param%dist_rmsd .OR. colvar_in%reaction_path_param%rmsd) THEN
1615 colvar_out%reaction_path_param%align_frames = colvar_in%reaction_path_param%align_frames
1616 colvar_out%reaction_path_param%subset = colvar_in%reaction_path_param%subset
1617 ndim = SIZE(colvar_in%reaction_path_param%i_rmsd)
1618 ALLOCATE (colvar_out%reaction_path_param%i_rmsd(ndim), stat=stat)
1619 colvar_out%reaction_path_param%i_rmsd = colvar_in%reaction_path_param%i_rmsd
1620 ndim = SIZE(colvar_in%reaction_path_param%r_ref, 1)
1621 ndim2 = SIZE(colvar_in%reaction_path_param%r_ref, 2)
1622 ALLOCATE (colvar_out%reaction_path_param%r_ref(ndim, ndim2), stat=stat)
1623 colvar_out%reaction_path_param%r_ref = colvar_in%reaction_path_param%r_ref
1624 ELSE
1625 ndim = SIZE(colvar_in%reaction_path_param%colvar_p)
1626 ALLOCATE (colvar_out%reaction_path_param%colvar_p(ndim))
1627 DO i = 1, ndim
1628 CALL colvar_clone(colvar_out%reaction_path_param%colvar_p(i)%colvar, &
1629 colvar_in%reaction_path_param%colvar_p(i)%colvar, &
1630 my_offset)
1631 END DO
1632 colvar_out%reaction_path_param%function_bounds = colvar_in%reaction_path_param%function_bounds
1633 ndim = SIZE(colvar_in%reaction_path_param%f_vals, 1)
1634 ndim2 = SIZE(colvar_in%reaction_path_param%f_vals, 2)
1635 ALLOCATE (colvar_out%reaction_path_param%f_vals(ndim, ndim2))
1636 colvar_out%reaction_path_param%f_vals = colvar_in%reaction_path_param%f_vals
1637 END IF
1638 colvar_out%reaction_path_param%step_size = colvar_in%reaction_path_param%step_size
1639 colvar_out%reaction_path_param%n_components = colvar_in%reaction_path_param%n_components
1640 colvar_out%reaction_path_param%lambda = colvar_in%reaction_path_param%lambda
1641 CASE (combine_colvar_id)
1642 ndim = SIZE(colvar_in%combine_cvs_param%colvar_p)
1643 ALLOCATE (colvar_out%combine_cvs_param%colvar_p(ndim))
1644 DO i = 1, ndim
1645 CALL colvar_clone(colvar_out%combine_cvs_param%colvar_p(i)%colvar, &
1646 colvar_in%combine_cvs_param%colvar_p(i)%colvar, &
1647 my_offset)
1648 END DO
1649 colvar_out%combine_cvs_param%lerr = colvar_in%combine_cvs_param%lerr
1650 colvar_out%combine_cvs_param%dx = colvar_in%combine_cvs_param%dx
1651 colvar_out%combine_cvs_param%function = colvar_in%combine_cvs_param%function
1652 !
1653 ndim = SIZE(colvar_in%combine_cvs_param%c_parameters)
1654 ALLOCATE (colvar_out%combine_cvs_param%c_parameters(ndim))
1655 colvar_out%combine_cvs_param%c_parameters = colvar_in%combine_cvs_param%c_parameters
1656 !
1657 ndim = SIZE(colvar_in%combine_cvs_param%v_parameters)
1658 ALLOCATE (colvar_out%combine_cvs_param%v_parameters(ndim))
1659 colvar_out%combine_cvs_param%v_parameters = colvar_in%combine_cvs_param%v_parameters
1660 !
1661 ndim = SIZE(colvar_in%combine_cvs_param%variables)
1662 ALLOCATE (colvar_out%combine_cvs_param%variables(ndim))
1663 colvar_out%combine_cvs_param%variables = colvar_in%combine_cvs_param%variables
1664 CASE (rmsd_colvar_id)
1665 colvar_out%rmsd_param%n_atoms = colvar_in%rmsd_param%n_atoms
1666 colvar_out%rmsd_param%align_frames = colvar_in%rmsd_param%align_frames
1667 colvar_out%rmsd_param%nr_frames = colvar_in%rmsd_param%nr_frames
1668 colvar_out%rmsd_param%subset = colvar_in%rmsd_param%subset
1669 ! INDEX
1670 ndim = SIZE(colvar_in%rmsd_param%i_rmsd)
1671 ALLOCATE (colvar_out%rmsd_param%i_rmsd(ndim))
1672 colvar_out%rmsd_param%i_rmsd = colvar_in%rmsd_param%i_rmsd + my_offset
1673 ! A and Bconfigurations and weights
1674 ndim = SIZE(colvar_in%rmsd_param%weights)
1675 ALLOCATE (colvar_out%rmsd_param%weights(ndim))
1676 colvar_out%rmsd_param%weights = colvar_in%rmsd_param%weights
1677 ndim = SIZE(colvar_in%rmsd_param%r_ref, 1)
1678 ndim2 = SIZE(colvar_in%rmsd_param%r_ref, 2)
1679 ALLOCATE (colvar_out%rmsd_param%r_ref(ndim, ndim2))
1680 colvar_out%rmsd_param%r_ref = colvar_in%rmsd_param%r_ref
1681 CASE (wc_colvar_id)
1682 colvar_out%Wc%ids = colvar_in%Wc%ids + my_offset
1683 colvar_out%Wc%rcut = colvar_in%Wc%rcut
1684 CASE (hbp_colvar_id)
1685 ndim = colvar_out%HBP%nPoints
1686 ALLOCATE (colvar_out%HBP%ids(ndim, 3))
1687 ALLOCATE (colvar_out%HBP%ewc(ndim))
1688 colvar_out%HBP%ids = colvar_in%HBP%ids + my_offset
1689 colvar_out%HBP%ewc = colvar_in%HBP%ewc + my_offset
1690 colvar_out%HBP%nPoints = colvar_in%HBP%nPoints
1691 colvar_out%HBP%rcut = colvar_in%HBP%rcut
1692 colvar_out%HBP%shift = colvar_in%HBP%shift
1693 CASE (ring_puckering_colvar_id)
1694 ndim = colvar_in%ring_puckering_param%nring
1695 colvar_out%ring_puckering_param%nring = colvar_in%ring_puckering_param%nring
1696 colvar_out%ring_puckering_param%iq = colvar_in%ring_puckering_param%iq
1697 ALLOCATE (colvar_out%ring_puckering_param%atoms(ndim))
1698 colvar_out%ring_puckering_param%atoms = colvar_in%ring_puckering_param%atoms + my_offset
1699 CASE (mindist_colvar_id)
1700 colvar_out%mindist_param%n_dist_from = colvar_in%mindist_param%n_dist_from
1701 colvar_out%mindist_param%n_coord_to = colvar_in%mindist_param%n_coord_to
1702 colvar_out%mindist_param%n_coord_from = colvar_in%mindist_param%n_coord_from
1703 colvar_out%mindist_param%p_exp = colvar_in%mindist_param%p_exp
1704 colvar_out%mindist_param%q_exp = colvar_in%mindist_param%q_exp
1705 colvar_out%mindist_param%r_cut = colvar_in%mindist_param%r_cut
1706 colvar_out%mindist_param%lambda = colvar_in%mindist_param%lambda
1707 colvar_out%mindist_param%use_kinds_from = colvar_in%mindist_param%use_kinds_from
1708 colvar_out%mindist_param%use_kinds_to = colvar_in%mindist_param%use_kinds_to
1709 ! INDEX
1710 ndim = SIZE(colvar_in%mindist_param%i_dist_from)
1711 ALLOCATE (colvar_out%mindist_param%i_dist_from(ndim))
1712 colvar_out%mindist_param%i_dist_from = colvar_in%mindist_param%i_dist_from + my_offset
1713 IF (colvar_in%mindist_param%use_kinds_from) THEN
1714 ! KINDS
1715 ndim = SIZE(colvar_in%mindist_param%k_coord_from)
1716 ALLOCATE (colvar_out%mindist_param%k_coord_from(ndim))
1717 colvar_out%mindist_param%k_coord_from = colvar_in%mindist_param%k_coord_from
1718 ELSE
1719 ! INDEX
1720 ndim = SIZE(colvar_in%mindist_param%i_coord_from)
1721 ALLOCATE (colvar_out%mindist_param%i_coord_from(ndim))
1722 colvar_out%mindist_param%i_coord_from = colvar_in%mindist_param%i_coord_from + my_offset
1723 END IF
1724 IF (colvar_in%mindist_param%use_kinds_to) THEN
1725 ! KINDS
1726 ndim = SIZE(colvar_in%mindist_param%k_coord_to)
1727 ALLOCATE (colvar_out%mindist_param%k_coord_to(ndim))
1728 colvar_out%mindist_param%k_coord_to = colvar_in%mindist_param%k_coord_to
1729 ELSE
1730 ! INDEX
1731 ndim = SIZE(colvar_in%mindist_param%i_coord_to)
1732 ALLOCATE (colvar_out%mindist_param%i_coord_to(ndim))
1733 colvar_out%mindist_param%i_coord_to = colvar_in%mindist_param%i_coord_to + my_offset
1734 END IF
1735
1736 END SELECT
1737 CALL colvar_setup(colvar_out)
1738 END SUBROUTINE colvar_clone
1739
1740! **************************************************************************************************
1741!> \brief Clone points type of a colvar type
1742!> \param colvar_out ...
1743!> \param colvar_in the colvar to deallocate
1744!> \param offset ...
1745!> \author Teodoro Laino [tlaino] 03.2007
1746! **************************************************************************************************
1747 SUBROUTINE colvar_clone_points(colvar_out, colvar_in, offset)
1748 TYPE(colvar_type), INTENT(INOUT) :: colvar_out
1749 TYPE(colvar_type), INTENT(IN) :: colvar_in
1750 INTEGER, INTENT(IN) :: offset
1751
1752 INTEGER :: i, natoms, npoints
1753
1754 colvar_out%use_points = colvar_in%use_points
1755 IF (colvar_in%use_points) THEN
1756 cpassert(ASSOCIATED(colvar_in%points))
1757 npoints = SIZE(colvar_in%points)
1758 ALLOCATE (colvar_out%points(npoints))
1759 DO i = 1, npoints
1760 IF (ASSOCIATED(colvar_in%points(i)%atoms)) THEN
1761 natoms = SIZE(colvar_in%points(i)%atoms)
1762 ALLOCATE (colvar_out%points(i)%atoms(natoms))
1763 colvar_out%points(i)%atoms = colvar_in%points(i)%atoms + offset
1764 ELSE
1765 NULLIFY (colvar_out%points(i)%atoms)
1766 END IF
1767 IF (ASSOCIATED(colvar_in%points(i)%weights)) THEN
1768 natoms = SIZE(colvar_in%points(i)%weights)
1769 ALLOCATE (colvar_out%points(i)%weights(natoms))
1770 colvar_out%points(i)%weights = colvar_in%points(i)%weights
1771 ELSE
1772 NULLIFY (colvar_out%points(i)%weights)
1773 END IF
1774 colvar_out%points(i)%type_id = colvar_in%points(i)%type_id
1775 colvar_out%points(i)%r = colvar_in%points(i)%r
1776 END DO
1777 ELSE
1778 NULLIFY (colvar_out%points)
1779 END IF
1780
1781 END SUBROUTINE colvar_clone_points
1782
1783! **************************************************************************************************
1784!> \brief Change the dimension of a colvar_p_type
1785!> \param colvar_set ...
1786!> \param lb1_new ...
1787!> \param ub1_new ...
1788!> \author Teodoro Laino [tlaino] 04.2006
1789! **************************************************************************************************
1790 SUBROUTINE colvar_p_reallocate(colvar_set, lb1_new, ub1_new)
1791 TYPE(colvar_p_type), DIMENSION(:), POINTER :: colvar_set
1792 INTEGER, INTENT(IN) :: lb1_new, ub1_new
1793
1794 INTEGER :: j, lb1, lb1_old, ub1, ub1_old
1795 TYPE(colvar_p_type), DIMENSION(:), POINTER :: work
1796
1797 NULLIFY (work)
1798 IF (ASSOCIATED(colvar_set)) THEN
1799 lb1_old = lbound(colvar_set, 1)
1800 ub1_old = ubound(colvar_set, 1)
1801 lb1 = max(lb1_new, lb1_old)
1802 ub1 = min(ub1_new, ub1_old)
1803 ALLOCATE (work(lb1:ub1))
1804 DO j = lb1, ub1
1805 CALL colvar_clone(work(j)%colvar, colvar_set(j)%colvar)
1806 END DO
1807 DO j = lb1, ub1
1808 CALL colvar_release(colvar_set(j)%colvar)
1809 END DO
1810 DEALLOCATE (colvar_set)
1811 END IF
1812
1813 ALLOCATE (colvar_set(lb1_new:ub1_new))
1814
1815 IF (ASSOCIATED(work)) THEN
1816 lb1 = max(lb1_new, lb1_old)
1817 ub1 = min(ub1_new, ub1_old)
1818 DO j = lb1, ub1
1819 CALL colvar_clone(colvar_set(j)%colvar, work(j)%colvar)
1820 END DO
1821 DO j = lb1, ub1
1822 CALL colvar_release(work(j)%colvar)
1823 END DO
1824 DEALLOCATE (work)
1825 END IF
1826 END SUBROUTINE colvar_p_reallocate
1827
1828! **************************************************************************************************
1829!> \brief Deallocate a set of colvar_p_type
1830!> \param colvar_p ...
1831!> \par History
1832!> 07.2003 created [fawzi]
1833!> 01.2014 moved from cp_subsys_release() into separate routine.
1834!> \author Ole Schuett
1835! **************************************************************************************************
1836 SUBROUTINE colvar_p_release(colvar_p)
1837 TYPE(colvar_p_type), DIMENSION(:), POINTER :: colvar_p
1838
1839 INTEGER :: i
1840
1841! Colvar info
1842
1843 IF (ASSOCIATED(colvar_p)) THEN
1844 DO i = 1, SIZE(colvar_p)
1845 IF (ASSOCIATED(colvar_p(i)%colvar)) &
1846 CALL colvar_release(colvar_p(i)%colvar)
1847 END DO
1848 DEALLOCATE (colvar_p)
1849 END IF
1850 END SUBROUTINE colvar_p_release
1851
1852! **************************************************************************************************
1853!> \brief Evaluate the position of the geometrical point
1854!> \param point ...
1855!> \param particles ...
1856!> \param r ...
1857!> \author Teodoro Laino - 03.2007
1858! **************************************************************************************************
1859 SUBROUTINE eval_point_pos(point, particles, r)
1860 TYPE(point_type), INTENT(IN) :: point
1861 TYPE(particle_type), DIMENSION(:), INTENT(IN) :: particles
1862 REAL(kind=dp), DIMENSION(3), INTENT(OUT) :: r
1863
1864 INTEGER :: i
1865
1866 SELECT CASE (point%type_id)
1867 CASE (do_clv_geo_center)
1868 r = 0.0_dp
1869 DO i = 1, SIZE(point%atoms)
1870 r = r + particles(point%atoms(i))%r*point%weights(i)
1871 END DO
1872 CASE (do_clv_fix_point)
1873 r = point%r
1874 END SELECT
1875
1876 END SUBROUTINE eval_point_pos
1877
1878! **************************************************************************************************
1879!> \brief ...
1880!> \param point ...
1881!> \param particles ...
1882!> \param m ...
1883! **************************************************************************************************
1884 SUBROUTINE eval_point_mass(point, particles, m)
1885 TYPE(point_type), INTENT(IN) :: point
1886 TYPE(particle_type), DIMENSION(:), INTENT(IN) :: particles
1887 REAL(kind=dp), INTENT(OUT) :: m
1888
1889 INTEGER :: i
1890
1891 SELECT CASE (point%type_id)
1892 CASE (do_clv_geo_center)
1893 m = 0.0_dp
1894 DO i = 1, SIZE(point%atoms)
1895 m = m + particles(point%atoms(i))%atomic_kind%mass*point%weights(i)
1896 END DO
1897 CASE (do_clv_fix_point)
1898 m = 0.0_dp
1899 END SELECT
1900
1901 END SUBROUTINE eval_point_mass
1902
1903! **************************************************************************************************
1904!> \brief Evaluate the position of the geometrical point
1905!> \param points ...
1906!> \param i ...
1907!> \param dsdr ...
1908!> \param f ...
1909!> \author Teodoro Laino - 03.2007
1910! **************************************************************************************************
1911 SUBROUTINE eval_point_der(points, i, dsdr, f)
1912 TYPE(point_type), DIMENSION(:), INTENT(IN) :: points
1913 INTEGER, INTENT(IN) :: i
1914 REAL(kind=dp), DIMENSION(:, :), INTENT(INOUT) :: dsdr
1915 REAL(kind=dp), DIMENSION(3), INTENT(IN) :: f
1916
1917 INTEGER :: ind, j
1918 REAL(kind=dp) :: fac
1919
1920 SELECT CASE (points(i)%type_id)
1921 CASE (do_clv_geo_center)
1922 ind = 0
1923 DO j = 1, i - 1
1924 IF (ASSOCIATED(points(j)%atoms)) THEN
1925 ind = ind + SIZE(points(j)%atoms)
1926 END IF
1927 END DO
1928 DO j = 1, SIZE(points(i)%atoms)
1929 fac = points(i)%weights(j)
1930 dsdr(:, ind + j) = dsdr(:, ind + j) + f*fac
1931 END DO
1932 CASE (do_clv_fix_point)
1933 ! Do nothing if it's a fixed point in space
1934 END SELECT
1935
1936 END SUBROUTINE eval_point_der
1937
1938! **************************************************************************************************
1939!> \brief subtract b from the ss value of a colvar: general function for handling
1940!> periodic/non-periodic colvar
1941!> \param colvar ...
1942!> \param b ...
1943!> \return ...
1944!> \author Teodoro Laino [tlaino] - University of Zurich 10.2008
1945! **************************************************************************************************
1946 FUNCTION diff_colvar(colvar, b) RESULT(diff)
1947 TYPE(colvar_type), INTENT(IN) :: colvar
1948 REAL(kind=dp), INTENT(IN) :: b
1949 REAL(kind=dp) :: diff
1950
1951 diff = colvar%ss - b
1952 IF (colvar%type_id == torsion_colvar_id) THEN
1953 ! The difference of a periodic COLVAR is always within [-pi,pi]
1954 diff = sign(1.0_dp, asin(sin(diff)))*acos(cos(diff))
1955 END IF
1956 END FUNCTION diff_colvar
1957
1958END MODULE colvar_types
fac
static GRID_HOST_DEVICE double fac(const int i)
Factorial function, e.g. fac(5) = 5! = 120.
Definition grid_common.h:48
colvar_types
Initialize the collective variables types.
Definition colvar_types.F:15
colvar_types::ring_puckering_colvar_id
integer, parameter, public ring_puckering_colvar_id
Definition colvar_types.F:56
colvar_types::population_colvar_id
integer, parameter, public population_colvar_id
Definition colvar_types.F:56
colvar_types::do_clv_geo_center
integer, parameter, public do_clv_geo_center
Definition colvar_types.F:33
colvar_types::colvar_release
recursive subroutine, public colvar_release(colvar)
releases the memory that might have been allocated by the colvar
Definition colvar_types.F:1176
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::wc_colvar_id
integer, parameter, public wc_colvar_id
Definition colvar_types.F:56
colvar_types::acid_hyd_dist_colvar_id
integer, parameter, public acid_hyd_dist_colvar_id
Definition colvar_types.F:56
colvar_types::xyz_outerdiag_colvar_id
integer, parameter, public xyz_outerdiag_colvar_id
Definition colvar_types.F:56
colvar_types::do_clv_xyz
integer, parameter, public do_clv_xyz
Definition colvar_types.F:33
colvar_types::do_clv_xz
integer, parameter, public do_clv_xz
Definition colvar_types.F:33
colvar_types::diff_colvar
real(kind=dp) function, public diff_colvar(colvar, b)
subtract b from the ss value of a colvar: general function for handling periodic/non-periodic colvar
Definition colvar_types.F:1947
colvar_types::plane_plane_angle_colvar_id
integer, parameter, public plane_plane_angle_colvar_id
Definition colvar_types.F:56
colvar_types::colvar_create
subroutine, public colvar_create(colvar, colvar_id)
initializes a colvar_param type
Definition colvar_types.F:421
colvar_types::plane_distance_colvar_id
integer, parameter, public plane_distance_colvar_id
Definition colvar_types.F:56
colvar_types::combine_colvar_id
integer, parameter, public combine_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::hbp_colvar_id
integer, parameter, public hbp_colvar_id
Definition colvar_types.F:56
colvar_types::rotation_colvar_id
integer, parameter, public rotation_colvar_id
Definition colvar_types.F:56
colvar_types::colvar_clone
recursive subroutine, public colvar_clone(colvar_out, colvar_in, i_atom_offset)
Clone a colvar type.
Definition colvar_types.F:1353
colvar_types::hydronium_dist_colvar_id
integer, parameter, public hydronium_dist_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::do_clv_fix_point
integer, parameter, public do_clv_fix_point
Definition colvar_types.F:33
colvar_types::do_clv_z
integer, parameter, public do_clv_z
Definition colvar_types.F:33
colvar_types::eval_point_pos
subroutine, public eval_point_pos(point, particles, r)
Evaluate the position of the geometrical point.
Definition colvar_types.F:1860
colvar_types::plane_def_atoms
integer, parameter, public plane_def_atoms
Definition colvar_types.F:30
colvar_types::do_clv_yz
integer, parameter, public do_clv_yz
Definition colvar_types.F:33
colvar_types::dfunct_colvar_id
integer, parameter, public dfunct_colvar_id
Definition colvar_types.F:56
colvar_types::colvar_p_reallocate
subroutine, public colvar_p_reallocate(colvar_set, lb1_new, ub1_new)
Change the dimension of a colvar_p_type.
Definition colvar_types.F:1791
colvar_types::colvar_p_release
subroutine, public colvar_p_release(colvar_p)
Deallocate a set of colvar_p_type.
Definition colvar_types.F:1837
colvar_types::no_colvar_id
integer, parameter, public no_colvar_id
Definition colvar_types.F:56
colvar_types::angle_colvar_id
integer, parameter, public angle_colvar_id
Definition colvar_types.F:56
colvar_types::qparm_colvar_id
integer, parameter, public qparm_colvar_id
Definition colvar_types.F:56
colvar_types::eval_point_der
subroutine, public eval_point_der(points, i, dsdr, f)
Evaluate the position of the geometrical point.
Definition colvar_types.F:1912
colvar_types::eval_point_mass
subroutine, public eval_point_mass(point, particles, m)
...
Definition colvar_types.F:1885
colvar_types::dist_colvar_id
integer, parameter, public dist_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::do_clv_xy
integer, parameter, public do_clv_xy
Definition colvar_types.F:33
colvar_types::u_colvar_id
integer, parameter, public u_colvar_id
Definition colvar_types.F:56
colvar_types::hydronium_shell_colvar_id
integer, parameter, public hydronium_shell_colvar_id
Definition colvar_types.F:56
colvar_types::torsion_colvar_id
integer, parameter, public torsion_colvar_id
Definition colvar_types.F:56
colvar_types::do_clv_y
integer, parameter, public do_clv_y
Definition colvar_types.F:33
colvar_types::plane_def_vec
integer, parameter, public plane_def_vec
Definition colvar_types.F:30
colvar_types::xyz_diag_colvar_id
integer, parameter, public xyz_diag_colvar_id
Definition colvar_types.F:56
colvar_types::reaction_path_colvar_id
integer, parameter, public reaction_path_colvar_id
Definition colvar_types.F:56
colvar_types::do_clv_x
integer, parameter, public do_clv_x
Definition colvar_types.F:33
colvar_types::acid_hyd_shell_colvar_id
integer, parameter, public acid_hyd_shell_colvar_id
Definition colvar_types.F:56
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
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
list
An array-based list which grows on demand. When the internal array is full, a new array of twice the ...
Definition list.F:24
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
colvar_types::colvar_counters
Definition colvar_types.F:388
colvar_types::colvar_p_type
Definition colvar_types.F:383
colvar_types::colvar_type
parameters for a collective variable
Definition colvar_types.F:346
input_section_types::section_vals_type
stores the values of a section
Definition input_section_types.F:126
particle_types::particle_type
Definition particle_types.F:35