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topology_constraint_util.F
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1!--------------------------------------------------------------------------------------------------!
2! CP2K: A general program to perform molecular dynamics simulations !
3! Copyright 2000-2026 CP2K developers group <https://cp2k.org> !
4! !
5! SPDX-License-Identifier: GPL-2.0-or-later !
6!--------------------------------------------------------------------------------------------------!
7
8! **************************************************************************************************
9!> \brief Collection of subroutine needed for topology related things
10!> \par History
11!> jgh (23-05-2004) Last atom of molecule information added
12! **************************************************************************************************
13MODULE topology_constraint_util
14 USE atomic_kind_types, ONLY: atomic_kind_type,&
15 get_atomic_kind,&
16 is_hydrogen
17 USE cell_types, ONLY: cell_transform_input_cartesian,&
18 use_perd_x,&
19 use_perd_xy,&
20 use_perd_xyz,&
21 use_perd_xz,&
22 use_perd_y,&
23 use_perd_yz,&
24 use_perd_z
25 USE colvar_methods, ONLY: colvar_eval_mol_f
26 USE colvar_types, ONLY: &
27 colvar_clone, colvar_counters, colvar_create, colvar_p_reallocate, colvar_release, &
28 colvar_setup, colvar_type, dist_colvar_id, torsion_colvar_id, xyz_diag_colvar_id, &
29 xyz_outerdiag_colvar_id
30 USE colvar_utils, ONLY: post_process_colvar
31 USE cp_log_handling, ONLY: cp_get_default_logger,&
32 cp_logger_type,&
33 cp_to_string
34 USE cp_output_handling, ONLY: cp_print_key_finished_output,&
35 cp_print_key_unit_nr
36 USE input_constants, ONLY: do_constr_atomic,&
37 do_constr_molec
38 USE input_section_types, ONLY: section_vals_get,&
39 section_vals_get_subs_vals,&
40 section_vals_type,&
41 section_vals_val_get,&
42 section_vals_val_set
43 USE kinds, ONLY: default_string_length,&
44 dp
45 USE memory_utilities, ONLY: reallocate
46 USE molecule_kind_types, ONLY: &
47 atom_type, bond_type, colvar_constraint_type, fixd_constraint_type, g3x3_constraint_type, &
48 g4x6_constraint_type, get_molecule_kind, molecule_kind_type, set_molecule_kind, &
49 setup_colvar_counters, vsite_constraint_type
50 USE molecule_types, ONLY: get_molecule,&
51 global_constraint_type,&
52 local_colvar_constraint_type,&
53 local_constraint_type,&
54 local_g3x3_constraint_type,&
55 local_g4x6_constraint_type,&
56 molecule_type,&
57 set_molecule
58 USE particle_types, ONLY: particle_type
59 USE qmmm_ff_fist, ONLY: qmmm_ff_precond_only_qm
60 USE qmmm_types_low, ONLY: qmmm_env_mm_type
61 USE topology_types, ONLY: constr_list_type,&
62 constraint_info_type,&
63 topology_parameters_type
64#include "./base/base_uses.f90"
65
66 IMPLICIT NONE
67
68 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'topology_constraint_util'
69
70 PRIVATE
71 PUBLIC :: topology_constraint_pack
72
73CONTAINS
74
75! **************************************************************************************************
76!> \brief Pack in all the information needed for the constraints
77!> \param molecule_kind_set ...
78!> \param molecule_set ...
79!> \param topology ...
80!> \param qmmm_env ...
81!> \param particle_set ...
82!> \param input_file ...
83!> \param subsys_section ...
84!> \param gci ...
85! **************************************************************************************************
86 SUBROUTINE topology_constraint_pack(molecule_kind_set, molecule_set, &
87 topology, qmmm_env, particle_set, input_file, subsys_section, gci)
88 TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
89 TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
90 TYPE(topology_parameters_type), INTENT(INOUT) :: topology
91 TYPE(qmmm_env_mm_type), OPTIONAL, POINTER :: qmmm_env
92 TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
93 TYPE(section_vals_type), POINTER :: input_file, subsys_section
94 TYPE(global_constraint_type), POINTER :: gci
95
96 CHARACTER(len=*), PARAMETER :: routinen = 'topology_constraint_pack'
97
98 CHARACTER(LEN=2) :: element_symbol
99 CHARACTER(LEN=default_string_length) :: molname, name
100 CHARACTER(LEN=default_string_length), &
101 DIMENSION(:), POINTER :: atom_typeh, cnds
102 INTEGER :: cind, first, first_atom, gind, handle, handle2, i, ii, itype, iw, j, k, k1loc, &
103 k2loc, kk, last, last_atom, m, n_start_colv, natom, nbond, ncolv_glob, ncolv_mol, &
104 nfixd_list_gci, nfixd_restart, nfixd_restraint, nfixed_atoms, ng3x3, ng3x3_restraint, &
105 ng4x6, ng4x6_restraint, nhdist, nmolecule, nrep, nvsite, nvsite_restraint, offset
106 INTEGER, DIMENSION(:), POINTER :: constr_x_glob, inds, molecule_list
107 LOGICAL :: exclude_mm, exclude_qm, fix_atom_mm, fix_atom_molname, fix_atom_qm, &
108 fix_atom_qmmm, fix_fixed_atom, found_molname, is_qm, ishbond, ldummy, &
109 restart_restraint_clv, restart_restraint_pos, use_clv_info
110 LOGICAL, ALLOCATABLE, DIMENSION(:) :: missed_molname
111 REAL(kind=dp) :: rmod, rvec(3)
112 REAL(kind=dp), DIMENSION(:), POINTER :: hdist, r
113 TYPE(atom_type), DIMENSION(:), POINTER :: atom_list
114 TYPE(atomic_kind_type), POINTER :: atomic_kind
115 TYPE(bond_type), DIMENSION(:), POINTER :: bond_list
116 TYPE(colvar_constraint_type), DIMENSION(:), &
117 POINTER :: colv_list
118 TYPE(colvar_counters) :: ncolv
119 TYPE(constr_list_type), DIMENSION(:), POINTER :: constr_x_mol
120 TYPE(constraint_info_type), POINTER :: cons_info
121 TYPE(cp_logger_type), POINTER :: logger
122 TYPE(fixd_constraint_type), DIMENSION(:), POINTER :: fixd_list, fixd_list_gci
123 TYPE(g3x3_constraint_type), DIMENSION(:), POINTER :: g3x3_list
124 TYPE(g4x6_constraint_type), DIMENSION(:), POINTER :: g4x6_list
125 TYPE(local_colvar_constraint_type), DIMENSION(:), &
126 POINTER :: lcolv
127 TYPE(local_constraint_type), POINTER :: lci
128 TYPE(local_g3x3_constraint_type), DIMENSION(:), &
129 POINTER :: lg3x3
130 TYPE(local_g4x6_constraint_type), DIMENSION(:), &
131 POINTER :: lg4x6
132 TYPE(molecule_kind_type), POINTER :: molecule_kind
133 TYPE(molecule_type), POINTER :: molecule
134 TYPE(section_vals_type), POINTER :: colvar_func_info, colvar_rest, &
135 fixd_restr_rest, hbonds_section
136 TYPE(vsite_constraint_type), DIMENSION(:), POINTER :: vsite_list
137
138 NULLIFY (logger, constr_x_mol, constr_x_glob)
139 logger => cp_get_default_logger()
140 iw = cp_print_key_unit_nr(logger, subsys_section, "PRINT%TOPOLOGY_INFO/UTIL_INFO", &
141 extension=".subsysLog")
142 CALL timeset(routinen, handle)
143 CALL timeset(routinen//"_1", handle2)
144
145 cons_info => topology%cons_info
146 hbonds_section => section_vals_get_subs_vals(input_file, &
147 "MOTION%CONSTRAINT%HBONDS")
148 fixd_restr_rest => section_vals_get_subs_vals(input_file, &
149 "MOTION%CONSTRAINT%FIX_ATOM_RESTART")
150 CALL section_vals_get(fixd_restr_rest, explicit=restart_restraint_pos)
151 colvar_rest => section_vals_get_subs_vals(input_file, &
152 "MOTION%CONSTRAINT%COLVAR_RESTART")
153 CALL section_vals_get(colvar_rest, explicit=restart_restraint_clv)
154 colvar_func_info => section_vals_get_subs_vals(subsys_section, &
155 "COLVAR%COLVAR_FUNC_INFO")
156 CALL section_vals_get(colvar_func_info, explicit=use_clv_info)
157 !-----------------------------------------------------------------------------
158 !-----------------------------------------------------------------------------
159 ! 1. NULLIFY the molecule_set(imol)%lci via set_molecule_set
160 !-----------------------------------------------------------------------------
161 DO i = 1, topology%nmol
162 molecule => molecule_set(i)
163 NULLIFY (lci)
164 ! only allocate the lci if constraints are active. Can this stuff be distributed ?
165 IF (topology%const_atom .OR. topology%const_hydr .OR. &
166 topology%const_33 .OR. topology%const_46 .OR. &
167 topology%const_colv .OR. topology%const_vsite) THEN
168 ALLOCATE (lci)
169 NULLIFY (lci%lcolv)
170 NULLIFY (lci%lg3x3)
171 NULLIFY (lci%lg4x6)
172 END IF
173 CALL set_molecule(molecule, lci=lci)
174 END DO
175 ALLOCATE (gci)
176 NULLIFY (gci%lcolv, &
177 gci%lg3x3, &
178 gci%lg4x6, &
179 gci%fixd_list, &
180 gci%colv_list, &
181 gci%g3x3_list, &
182 gci%g4x6_list, &
183 gci%vsite_list)
184 gci%ntot = 0
185 gci%ng3x3 = 0
186 gci%ng4x6 = 0
187 gci%nvsite = 0
188 gci%ng3x3_restraint = 0
189 gci%ng4x6_restraint = 0
190 gci%nvsite_restraint = 0
191 CALL setup_colvar_counters(gci%colv_list, gci%ncolv)
192 gci%nrestraint = gci%ng3x3_restraint + &
193 gci%ng4x6_restraint + &
194 gci%nvsite_restraint + &
195 gci%ncolv%nrestraint
196 CALL timestop(handle2)
197 CALL timeset(routinen//"_2", handle2)
198 !-----------------------------------------------------------------------------
199 !-----------------------------------------------------------------------------
200 ! 2. Add more stuff to COLVAR constraint if constraint hydrogen is on
201 !-----------------------------------------------------------------------------
202 IF (topology%const_hydr) THEN
203 topology%const_colv = .true.
204 NULLIFY (atom_typeh, hdist)
205 ALLOCATE (constr_x_mol(SIZE(molecule_kind_set)))
206 DO i = 1, SIZE(molecule_kind_set)
207 ALLOCATE (constr_x_mol(i)%constr(1))
208 constr_x_mol(i)%constr(1) = 1
209 END DO
210 CALL section_vals_val_get(hbonds_section, "MOLECULE", n_rep_val=nrep)
211 IF (nrep /= 0) THEN
212 NULLIFY (inds)
213 DO i = 1, SIZE(molecule_kind_set)
214 constr_x_mol(i)%constr(1) = 0
215 END DO
216 CALL section_vals_val_get(hbonds_section, "MOLECULE", i_vals=inds)
217 DO i = 1, SIZE(inds)
218 constr_x_mol(inds(i))%constr(1) = 1
219 END DO
220 ELSE
221 CALL section_vals_val_get(hbonds_section, "MOLNAME", n_rep_val=nrep)
222 IF (nrep /= 0) THEN
223 NULLIFY (cnds)
224 DO i = 1, SIZE(molecule_kind_set)
225 constr_x_mol(i)%constr(1) = 0
226 END DO
227 CALL section_vals_val_get(hbonds_section, "MOLNAME", c_vals=cnds)
228 DO i = 1, SIZE(cnds)
229 found_molname = .false.
230 DO k = 1, SIZE(molecule_kind_set)
231 molecule_kind => molecule_kind_set(k)
232 name = molecule_kind%name
233 ldummy = qmmm_ff_precond_only_qm(id1=name)
234 IF (cnds(i) == name) THEN
235 constr_x_mol(k)%constr(1) = 1
236 found_molname = .true.
237 END IF
238 END DO
239 CALL print_warning_molname(found_molname, cnds(i))
240 END DO
241 END IF
242 END IF
243 CALL section_vals_val_get(hbonds_section, "ATOM_TYPE", n_rep_val=nrep)
244 IF (nrep /= 0) &
245 CALL section_vals_val_get(hbonds_section, "ATOM_TYPE", c_vals=atom_typeh)
246 CALL section_vals_val_get(hbonds_section, "TARGETS", n_rep_val=nrep)
247 IF (nrep /= 0) &
248 CALL section_vals_val_get(hbonds_section, "TARGETS", r_vals=hdist)
249 IF (ASSOCIATED(hdist)) THEN
250 cpassert(SIZE(hdist) == SIZE(atom_typeh))
251 END IF
252 CALL section_vals_val_get(hbonds_section, "exclude_qm", l_val=exclude_qm)
253 CALL section_vals_val_get(hbonds_section, "exclude_mm", l_val=exclude_mm)
254 nhdist = 0
255 DO i = 1, SIZE(molecule_kind_set)
256 molecule_kind => molecule_kind_set(i)
257 IF (constr_x_mol(i)%constr(1) == 0) cycle
258 CALL get_molecule_kind(molecule_kind=molecule_kind, &
259 bond_list=bond_list, nbond=nbond, atom_list=atom_list, &
260 molecule_list=molecule_list)
261 ! Let's tag all requested atoms involving Hydrogen
262 ! on the first molecule of this kind
263 molecule => molecule_set(molecule_list(1))
264 CALL get_molecule(molecule, first_atom=first_atom, last_atom=last_atom)
265 natom = last_atom - first_atom + 1
266 DO k = 1, nbond
267 ishbond = .false.
268 j = bond_list(k)%a
269 IF (j < 1 .OR. j > natom) cycle
270 atomic_kind => atom_list(j)%atomic_kind
271 CALL get_atomic_kind(atomic_kind=atomic_kind, name=name)
272 is_qm = qmmm_ff_precond_only_qm(id1=name)
273 IF ((name(1:1) == "H") .OR. is_hydrogen(atomic_kind)) ishbond = .true.
274 IF (is_qm .AND. exclude_qm) ishbond = .false.
275 IF (.NOT. (is_qm) .AND. exclude_mm) ishbond = .false.
276 IF (.NOT. ishbond) THEN
277 j = bond_list(k)%b
278 IF (j < 1 .OR. j > natom) cycle
279 atomic_kind => atom_list(j)%atomic_kind
280 CALL get_atomic_kind(atomic_kind=atomic_kind, name=name)
281 is_qm = qmmm_ff_precond_only_qm(id1=name)
282 IF ((name(1:1) == "H") .OR. is_hydrogen(atomic_kind)) ishbond = .true.
283 IF (is_qm .AND. exclude_qm) ishbond = .false.
284 IF (.NOT. (is_qm) .AND. exclude_mm) ishbond = .false.
285 END IF
286 IF (ishbond) THEN
287 nhdist = nhdist + 1
288 END IF
289 END DO
290 END DO
291 n_start_colv = cons_info%nconst_colv
292 cons_info%nconst_colv = nhdist + n_start_colv
293 CALL reallocate(cons_info%const_colv_mol, 1, cons_info%nconst_colv)
294 CALL reallocate(cons_info%const_colv_molname, 1, cons_info%nconst_colv)
295 CALL reallocate(cons_info%const_colv_target, 1, cons_info%nconst_colv)
296 CALL reallocate(cons_info%const_colv_target_growth, 1, cons_info%nconst_colv)
297 CALL colvar_p_reallocate(cons_info%colvar_set, 1, cons_info%nconst_colv)
298 ! Fill in Restraints info
299 CALL reallocate(cons_info%colv_intermolecular, 1, cons_info%nconst_colv)
300 CALL reallocate(cons_info%colv_restraint, 1, cons_info%nconst_colv)
301 CALL reallocate(cons_info%colv_k0, 1, cons_info%nconst_colv)
302 CALL reallocate(cons_info%colv_exclude_qm, 1, cons_info%nconst_colv)
303 CALL reallocate(cons_info%colv_exclude_mm, 1, cons_info%nconst_colv)
304 ! Bonds involving hydrogens are by their nature only intramolecular
305 cons_info%colv_intermolecular(n_start_colv + 1:cons_info%nconst_colv) = .false.
306 cons_info%colv_exclude_qm(n_start_colv + 1:cons_info%nconst_colv) = .false.
307 cons_info%colv_exclude_mm(n_start_colv + 1:cons_info%nconst_colv) = .false.
308 cons_info%colv_restraint(n_start_colv + 1:cons_info%nconst_colv) = cons_info%hbonds_restraint
309 cons_info%colv_k0(n_start_colv + 1:cons_info%nconst_colv) = cons_info%hbonds_k0
310 !
311 nhdist = 0
312 DO i = 1, SIZE(molecule_kind_set)
313 IF (constr_x_mol(i)%constr(1) == 0) cycle
314 molecule_kind => molecule_kind_set(i)
315 CALL get_molecule_kind(molecule_kind=molecule_kind, &
316 bond_list=bond_list, nbond=nbond, atom_list=atom_list, &
317 molecule_list=molecule_list)
318 molecule => molecule_set(molecule_list(1))
319 CALL get_molecule(molecule, first_atom=first_atom, last_atom=last_atom)
320 natom = last_atom - first_atom + 1
321 offset = first_atom - 1
322 DO k = 1, nbond
323 ishbond = .false.
324 j = bond_list(k)%a
325 IF (j < 1 .OR. j > natom) cycle
326 atomic_kind => atom_list(j)%atomic_kind
327 CALL get_atomic_kind(atomic_kind=atomic_kind, name=name)
328 is_qm = qmmm_ff_precond_only_qm(id1=name)
329 IF ((name(1:1) == "H") .OR. is_hydrogen(atomic_kind)) ishbond = .true.
330 IF (is_qm .AND. exclude_qm) ishbond = .false.
331 IF (.NOT. (is_qm) .AND. exclude_mm) ishbond = .false.
332 IF (.NOT. ishbond) THEN
333 j = bond_list(k)%b
334 IF (j < 1 .OR. j > natom) cycle
335 atomic_kind => atom_list(j)%atomic_kind
336 CALL get_atomic_kind(atomic_kind=atomic_kind, name=name)
337 is_qm = qmmm_ff_precond_only_qm(id1=name)
338 IF ((name(1:1) == "H") .OR. is_hydrogen(atomic_kind)) ishbond = .true.
339 IF (is_qm .AND. exclude_qm) ishbond = .false.
340 IF (.NOT. (is_qm) .AND. exclude_mm) ishbond = .false.
341 END IF
342 IF (ishbond) THEN
343 nhdist = nhdist + 1
344 rvec = particle_set(offset + bond_list(k)%a)%r - particle_set(offset + bond_list(k)%b)%r
345 rmod = sqrt(dot_product(rvec, rvec))
346 IF (ASSOCIATED(hdist)) THEN
347 IF (SIZE(hdist) > 0) THEN
348 IF (bond_list(k)%a == j) atomic_kind => atom_list(bond_list(k)%b)%atomic_kind
349 IF (bond_list(k)%b == j) atomic_kind => atom_list(bond_list(k)%a)%atomic_kind
350 CALL get_atomic_kind(atomic_kind=atomic_kind, &
351 name=name, element_symbol=element_symbol)
352 ldummy = qmmm_ff_precond_only_qm(id1=name)
353 DO m = 1, SIZE(hdist)
354 IF (trim(name) == trim(atom_typeh(m))) EXIT
355 IF (trim(element_symbol) == trim(atom_typeh(m))) EXIT
356 END DO
357 IF (m <= SIZE(hdist)) THEN
358 rmod = hdist(m)
359 END IF
360 END IF
361 END IF
362 cons_info%const_colv_mol(nhdist + n_start_colv) = i
363 cons_info%const_colv_molname(nhdist + n_start_colv) = "UNDEF"
364 cons_info%const_colv_target(nhdist + n_start_colv) = rmod
365 cons_info%const_colv_target_growth(nhdist + n_start_colv) = 0.0_dp
366 CALL colvar_create(cons_info%colvar_set(nhdist + n_start_colv)%colvar, &
367 dist_colvar_id)
368 cons_info%colvar_set(nhdist + n_start_colv)%colvar%dist_param%i_at = bond_list(k)%a
369 cons_info%colvar_set(nhdist + n_start_colv)%colvar%dist_param%j_at = bond_list(k)%b
370 CALL colvar_setup(cons_info%colvar_set(nhdist + n_start_colv)%colvar)
371 END IF
372 END DO
373 END DO
374 DO j = 1, SIZE(constr_x_mol)
375 DEALLOCATE (constr_x_mol(j)%constr)
376 END DO
377 DEALLOCATE (constr_x_mol)
378 END IF
379
380 CALL timestop(handle2)
381 CALL timeset(routinen//"_3", handle2)
382 !-----------------------------------------------------------------------------
383 !-----------------------------------------------------------------------------
384 ! 3. Set the COLVAR constraint molecule_kind_set(ikind)%colv_list
385 !-----------------------------------------------------------------------------
386 IF (topology%const_colv) THEN
387 ! Post Process of COLVARS..
388 DO ii = 1, SIZE(cons_info%colvar_set)
389 CALL post_process_colvar(cons_info%colvar_set(ii)%colvar, particle_set)
390 END DO
391 ! Real constraint/restraint part..
392 CALL give_constraint_array(cons_info%const_colv_mol, &
393 cons_info%const_colv_molname, &
394 cons_info%colv_intermolecular, &
395 constr_x_mol, &
396 constr_x_glob, &
397 molecule_kind_set, &
398 cons_info%colv_exclude_qm, &
399 cons_info%colv_exclude_mm)
400 ! Intramolecular constraints
401 gind = 0
402 cind = 0
403 DO ii = 1, SIZE(molecule_kind_set)
404 molecule_kind => molecule_kind_set(ii)
405 CALL get_molecule_kind(molecule_kind=molecule_kind, &
406 nmolecule=nmolecule, molecule_list=molecule_list)
407 ncolv_mol = SIZE(constr_x_mol(ii)%constr)
408 ALLOCATE (colv_list(ncolv_mol))
409 ! Starting index of the first molecule of this kind.
410 ! We need the index if no target is provided in the input file
411 ! for the collective variable.. The target will be computed on the
412 ! first molecule of the kind...
413 molecule => molecule_set(molecule_list(1))
414 CALL get_molecule(molecule, first_atom=first_atom)
415 CALL setup_colv_list(colv_list, constr_x_mol(ii)%constr, gind, &
416 cons_info, topology, particle_set, restart_restraint_clv, &
417 colvar_rest, first_atom)
418 CALL setup_colvar_counters(colv_list, ncolv)
419 CALL set_molecule_kind(molecule_kind, colv_list=colv_list, ncolv=ncolv)
420 DO j = 1, nmolecule
421 molecule => molecule_set(molecule_list(j))
422 CALL get_molecule(molecule, first_atom=first_atom, last_atom=last_atom)
423 ALLOCATE (lcolv(ncolv_mol))
424 CALL setup_lcolv(lcolv, constr_x_mol(ii)%constr, first_atom, last_atom, &
425 cons_info, particle_set, colvar_func_info, use_clv_info, cind)
426 CALL set_molecule(molecule=molecule, lcolv=lcolv)
427 END DO
428 END DO
429 DO j = 1, SIZE(constr_x_mol)
430 DEALLOCATE (constr_x_mol(j)%constr)
431 END DO
432 DEALLOCATE (constr_x_mol)
433 ! Intermolecular constraints
434 ncolv_glob = 0
435 IF (ASSOCIATED(constr_x_glob)) THEN
436 ncolv_glob = SIZE(constr_x_glob)
437 ALLOCATE (colv_list(ncolv_glob))
438 CALL setup_colv_list(colv_list, constr_x_glob, gind, cons_info, &
439 topology, particle_set, restart_restraint_clv, colvar_rest, &
440 first_atom=1)
441 CALL setup_colvar_counters(colv_list, ncolv)
442 ALLOCATE (lcolv(ncolv_glob))
443 CALL setup_lcolv(lcolv, constr_x_glob, 1, SIZE(particle_set), cons_info, &
444 particle_set, colvar_func_info, use_clv_info, cind)
445 gci%colv_list => colv_list
446 gci%lcolv => lcolv
447 gci%ncolv = ncolv
448 ! Total number of Intermolecular constraints
449 gci%ntot = gci%ncolv%ntot + gci%ntot
450 DEALLOCATE (constr_x_glob)
451 END IF
452 END IF
453
454 CALL timestop(handle2)
455 CALL timeset(routinen//"_4", handle2)
456 !-----------------------------------------------------------------------------
457 !-----------------------------------------------------------------------------
458 ! 4. Set the group 3x3 constraint g3x3_list
459 !-----------------------------------------------------------------------------
460 IF (topology%const_33) THEN
461 CALL give_constraint_array(cons_info%const_g33_mol, &
462 cons_info%const_g33_molname, &
463 cons_info%g33_intermolecular, &
464 constr_x_mol, &
465 constr_x_glob, &
466 molecule_kind_set, &
467 cons_info%g33_exclude_qm, &
468 cons_info%g33_exclude_mm)
469 ! Intramolecular constraints
470 DO ii = 1, SIZE(molecule_kind_set)
471 molecule_kind => molecule_kind_set(ii)
472 CALL get_molecule_kind(molecule_kind=molecule_kind, &
473 nmolecule=nmolecule, &
474 molecule_list=molecule_list)
475 ng3x3 = SIZE(constr_x_mol(ii)%constr)
476 ALLOCATE (g3x3_list(ng3x3))
477 CALL setup_g3x3_list(g3x3_list, constr_x_mol(ii)%constr, cons_info, ng3x3_restraint)
478 CALL set_molecule_kind(molecule_kind, ng3x3=ng3x3, ng3x3_restraint=ng3x3_restraint, g3x3_list=g3x3_list)
479 DO j = 1, nmolecule
480 molecule => molecule_set(molecule_list(j))
481 CALL get_molecule(molecule, first_atom=first_atom, last_atom=last_atom)
482 ALLOCATE (lg3x3(ng3x3))
483 CALL setup_lg3x3(lg3x3, g3x3_list, first_atom, last_atom)
484 CALL set_molecule(molecule=molecule, lg3x3=lg3x3)
485 END DO
486 END DO
487 DO j = 1, SIZE(constr_x_mol)
488 DEALLOCATE (constr_x_mol(j)%constr)
489 END DO
490 DEALLOCATE (constr_x_mol)
491 ! Intermolecular constraints
492 IF (ASSOCIATED(constr_x_glob)) THEN
493 ng3x3 = SIZE(constr_x_glob)
494 ALLOCATE (g3x3_list(ng3x3))
495 CALL setup_g3x3_list(g3x3_list, constr_x_glob, cons_info, ng3x3_restraint)
496 ALLOCATE (lg3x3(ng3x3))
497 CALL setup_lg3x3(lg3x3, g3x3_list, first_atom, last_atom)
498 gci%g3x3_list => g3x3_list
499 gci%lg3x3 => lg3x3
500 gci%ng3x3 = ng3x3
501 gci%ng3x3_restraint = ng3x3_restraint
502 ! Total number of Intermolecular constraints
503 gci%ntot = 3*gci%ng3x3 + gci%ntot
504 DEALLOCATE (constr_x_glob)
505 END IF
506 END IF
507
508 CALL timestop(handle2)
509 CALL timeset(routinen//"_5", handle2)
510 !-----------------------------------------------------------------------------
511 !-----------------------------------------------------------------------------
512 ! 5. Set the group 4x6 constraint g4x6_list
513 !-----------------------------------------------------------------------------
514 IF (topology%const_46) THEN
515 CALL give_constraint_array(cons_info%const_g46_mol, &
516 cons_info%const_g46_molname, &
517 cons_info%g46_intermolecular, &
518 constr_x_mol, &
519 constr_x_glob, &
520 molecule_kind_set, &
521 cons_info%g46_exclude_qm, &
522 cons_info%g46_exclude_mm)
523 ! Intramolecular constraints
524 DO ii = 1, SIZE(molecule_kind_set)
525 molecule_kind => molecule_kind_set(ii)
526 CALL get_molecule_kind(molecule_kind=molecule_kind, &
527 nmolecule=nmolecule, molecule_list=molecule_list)
528 ng4x6 = SIZE(constr_x_mol(ii)%constr)
529 ALLOCATE (g4x6_list(ng4x6))
530 CALL setup_g4x6_list(g4x6_list, constr_x_mol(ii)%constr, cons_info, ng4x6_restraint)
531 CALL set_molecule_kind(molecule_kind, ng4x6=ng4x6, ng4x6_restraint=ng4x6_restraint, g4x6_list=g4x6_list)
532 DO j = 1, nmolecule
533 molecule => molecule_set(molecule_list(j))
534 CALL get_molecule(molecule, first_atom=first_atom, last_atom=last_atom)
535 ALLOCATE (lg4x6(ng4x6))
536 CALL setup_lg4x6(lg4x6, g4x6_list, first_atom, last_atom)
537 CALL set_molecule(molecule=molecule, lg4x6=lg4x6)
538 END DO
539 END DO
540 DO j = 1, SIZE(constr_x_mol)
541 DEALLOCATE (constr_x_mol(j)%constr)
542 END DO
543 DEALLOCATE (constr_x_mol)
544 ! Intermolecular constraints
545 IF (ASSOCIATED(constr_x_glob)) THEN
546 ng4x6 = SIZE(constr_x_glob)
547 ALLOCATE (g4x6_list(ng4x6))
548 CALL setup_g4x6_list(g4x6_list, constr_x_glob, cons_info, ng4x6_restraint)
549 ALLOCATE (lg4x6(ng4x6))
550 CALL setup_lg4x6(lg4x6, g4x6_list, first_atom, last_atom)
551 gci%g4x6_list => g4x6_list
552 gci%lg4x6 => lg4x6
553 gci%ng4x6 = ng4x6
554 gci%ng4x6_restraint = ng4x6_restraint
555 ! Total number of Intermolecular constraints
556 gci%ntot = 6*gci%ng4x6 + gci%ntot
557 DEALLOCATE (constr_x_glob)
558 END IF
559 END IF
560
561 CALL timestop(handle2)
562 CALL timeset(routinen//"_6", handle2)
563 !-----------------------------------------------------------------------------
564 !-----------------------------------------------------------------------------
565 ! 6. Set the group vsite constraint vsite_list
566 !-----------------------------------------------------------------------------
567 IF (topology%const_vsite) THEN
568 CALL give_constraint_array(cons_info%const_vsite_mol, &
569 cons_info%const_vsite_molname, &
570 cons_info%vsite_intermolecular, &
571 constr_x_mol, &
572 constr_x_glob, &
573 molecule_kind_set, &
574 cons_info%vsite_exclude_qm, &
575 cons_info%vsite_exclude_mm)
576 ! Intramolecular constraints
577 DO ii = 1, SIZE(molecule_kind_set)
578 molecule_kind => molecule_kind_set(ii)
579 CALL get_molecule_kind(molecule_kind=molecule_kind, &
580 nmolecule=nmolecule, molecule_list=molecule_list)
581 nvsite = SIZE(constr_x_mol(ii)%constr)
582 ALLOCATE (vsite_list(nvsite))
583 CALL setup_vsite_list(vsite_list, constr_x_mol(ii)%constr, cons_info, nvsite_restraint)
584 CALL set_molecule_kind(molecule_kind, nvsite=nvsite, nvsite_restraint=nvsite_restraint, &
585 vsite_list=vsite_list)
586 END DO
587 DO j = 1, SIZE(constr_x_mol)
588 DEALLOCATE (constr_x_mol(j)%constr)
589 END DO
590 DEALLOCATE (constr_x_mol)
591 ! Intermolecular constraints
592 IF (ASSOCIATED(constr_x_glob)) THEN
593 nvsite = SIZE(constr_x_glob)
594 ALLOCATE (vsite_list(nvsite))
595 CALL setup_vsite_list(vsite_list, constr_x_glob, cons_info, nvsite_restraint)
596 gci%vsite_list => vsite_list
597 gci%nvsite = nvsite
598 gci%nvsite_restraint = nvsite_restraint
599 ! Total number of Intermolecular constraints
600 gci%ntot = gci%nvsite + gci%ntot
601 DEALLOCATE (constr_x_glob)
602 END IF
603 END IF
604 CALL timestop(handle2)
605 CALL timeset(routinen//"_7", handle2)
606 !-----------------------------------------------------------------------------
607 !-----------------------------------------------------------------------------
608 ! 7. Set the group fixed_atom constraint fixd_list
609 !-----------------------------------------------------------------------------
610 IF (topology%const_atom) THEN
611 ALLOCATE (fixd_list_gci(SIZE(particle_set)))
612 nfixd_list_gci = 0
613 ALLOCATE (missed_molname(SIZE(cons_info%fixed_molnames, 1)))
614 missed_molname = .true.
615 nfixd_restart = 0
616 DO i = 1, SIZE(molecule_kind_set)
617 molecule_kind => molecule_kind_set(i)
618 CALL get_molecule_kind(molecule_kind=molecule_kind, &
619 nmolecule=nmolecule, molecule_list=molecule_list, name=molname)
620 is_qm = qmmm_ff_precond_only_qm(id1=molname)
621 WHERE (molname == cons_info%fixed_molnames)
622 missed_molname = .false.
623 END WHERE
624 ! Try to figure out how many atoms of the list belong to this molecule_kind
625 nfixed_atoms = 0
626 DO j = 1, nmolecule
627 molecule => molecule_set(molecule_list(j))
628 CALL get_molecule(molecule, first_atom=first, last_atom=last)
629 fix_atom_molname = .false.
630 IF (ASSOCIATED(cons_info%fixed_molnames)) THEN
631 DO k = 1, SIZE(cons_info%fixed_molnames)
632 IF (cons_info%fixed_molnames(k) == molname) THEN
633 fix_atom_molname = .true.
634 IF (is_qm .AND. cons_info%fixed_exclude_qm(k)) fix_atom_molname = .false.
635 IF ((.NOT. is_qm) .AND. cons_info%fixed_exclude_mm(k)) fix_atom_molname = .false.
636 END IF
637 END DO
638 END IF
639 DO k = first, last
640 fix_atom_qmmm = .false.
641 IF (PRESENT(qmmm_env)) THEN
642 SELECT CASE (cons_info%freeze_qm)
643 CASE (do_constr_atomic)
644 IF (any(qmmm_env%qm_atom_index == k)) fix_atom_qmmm = .true.
645 CASE (do_constr_molec)
646 IF (any(qmmm_env%qm_molecule_index == molecule_list(j))) fix_atom_qmmm = .true.
647 END SELECT
648 SELECT CASE (cons_info%freeze_mm)
649 CASE (do_constr_atomic)
650 IF (all(qmmm_env%qm_atom_index /= k)) fix_atom_qmmm = .true.
651 CASE (do_constr_molec)
652 IF (all(qmmm_env%qm_molecule_index /= molecule_list(j))) fix_atom_qmmm = .true.
653 END SELECT
654 END IF
655 IF (any(cons_info%fixed_atoms == k) .OR. fix_atom_qmmm .OR. fix_atom_molname) THEN
656 nfixed_atoms = nfixed_atoms + 1
657 END IF
658 END DO
659 END DO
660 ALLOCATE (fixd_list(nfixed_atoms))
661 kk = 0
662 nfixd_restraint = 0
663 IF (nfixed_atoms /= 0) THEN
664 DO j = 1, nmolecule
665 molecule => molecule_set(molecule_list(j))
666 CALL get_molecule(molecule, first_atom=first, last_atom=last)
667 fix_atom_molname = .false.
668 IF (ASSOCIATED(cons_info%fixed_molnames)) THEN
669 DO k1loc = 1, SIZE(cons_info%fixed_molnames)
670 IF (cons_info%fixed_molnames(k1loc) == molname) THEN
671 fix_atom_molname = .true.
672 itype = cons_info%fixed_mol_type(k1loc)
673 EXIT
674 END IF
675 END DO
676 END IF
677 DO k = first, last
678 ! FIXED LIST ATOMS
679 fix_fixed_atom = .false.
680 DO k2loc = 1, SIZE(cons_info%fixed_atoms)
681 IF (cons_info%fixed_atoms(k2loc) == k) THEN
682 fix_fixed_atom = .true.
683 itype = cons_info%fixed_type(k2loc)
684 EXIT
685 END IF
686 END DO
687 ! QMMM FIXED ATOMS (QM OR MM)
688 fix_atom_qmmm = .false.
689 fix_atom_mm = .false.
690 fix_atom_qm = .false.
691 IF (PRESENT(qmmm_env)) THEN
692 SELECT CASE (cons_info%freeze_qm)
693 CASE (do_constr_atomic)
694 IF (any(qmmm_env%qm_atom_index == k)) THEN
695 fix_atom_qmmm = .true.
696 fix_atom_qm = .true.
697 itype = cons_info%freeze_qm_type
698 END IF
699 CASE (do_constr_molec)
700 IF (any(qmmm_env%qm_molecule_index == molecule_list(j))) THEN
701 fix_atom_qmmm = .true.
702 fix_atom_qm = .true.
703 itype = cons_info%freeze_qm_type
704 END IF
705 END SELECT
706 SELECT CASE (cons_info%freeze_mm)
707 CASE (do_constr_atomic)
708 IF (all(qmmm_env%qm_atom_index /= k)) THEN
709 fix_atom_qmmm = .true.
710 fix_atom_mm = .true.
711 itype = cons_info%freeze_mm_type
712 END IF
713 CASE (do_constr_molec)
714 IF (all(qmmm_env%qm_molecule_index /= molecule_list(j))) THEN
715 fix_atom_qmmm = .true.
716 fix_atom_mm = .true.
717 itype = cons_info%freeze_mm_type
718 END IF
719 END SELECT
720 ! We should never reach this point but let's check it anyway
721 IF (fix_atom_qm .AND. fix_atom_mm) THEN
722 CALL cp_abort(__location__, &
723 "Atom number: "//cp_to_string(k)// &
724 " has been defined both QM and MM. General Error!")
725 END IF
726 END IF
727 ! Check that the fixed atom constraint/restraint is unique
728 IF ((fix_fixed_atom .AND. fix_atom_qmmm) .OR. (fix_fixed_atom .AND. fix_atom_molname) &
729 .OR. (fix_atom_qmmm .AND. fix_atom_molname)) THEN
730 CALL cp_abort(__location__, &
731 "Atom number: "//cp_to_string(k)// &
732 " has been constrained/restrained to be fixed in more than one"// &
733 " input section. Check and correct your input file!")
734 END IF
735 ! Let's store the atom index
736 IF (fix_fixed_atom .OR. fix_atom_qmmm .OR. fix_atom_molname) THEN
737 IF (ASSOCIATED(topology%cell_muc)) THEN
738 IF (topology%cell_muc%input_cell_canonicalized .AND. itype /= use_perd_xyz) THEN
739 CALL cp_abort(__location__, &
740 "Partial FIXED_ATOMS components cannot be transformed "// &
741 "after CELL%CANONICALIZE. Use COMPONENTS_TO_FIX XYZ or "// &
742 "disable CELL%CANONICALIZE for this input.")
743 END IF
744 END IF
745 kk = kk + 1
746 fixd_list(kk)%fixd = k
747 fixd_list(kk)%coord = particle_set(k)%r
748 fixd_list(kk)%itype = itype
749 ! Possibly Restraint
750 IF (fix_fixed_atom) THEN
751 fixd_list(kk)%restraint%active = cons_info%fixed_restraint(k2loc)
752 fixd_list(kk)%restraint%k0 = cons_info%fixed_k0(k2loc)
753 ELSEIF (fix_atom_qm) THEN
754 fixd_list(kk)%restraint%active = cons_info%fixed_qm_restraint
755 fixd_list(kk)%restraint%k0 = cons_info%fixed_qm_k0
756 ELSEIF (fix_atom_mm) THEN
757 fixd_list(kk)%restraint%active = cons_info%fixed_mm_restraint
758 fixd_list(kk)%restraint%k0 = cons_info%fixed_mm_k0
759 ELSEIF (fix_atom_molname) THEN
760 fixd_list(kk)%restraint%active = cons_info%fixed_mol_restraint(k1loc)
761 fixd_list(kk)%restraint%k0 = cons_info%fixed_mol_k0(k1loc)
762 ELSE
763 ! Should never reach this point
764 cpabort("")
765 END IF
766 IF (fixd_list(kk)%restraint%active) THEN
767 nfixd_restraint = nfixd_restraint + 1
768 nfixd_restart = nfixd_restart + 1
769 ! Check that we use the components that we really want..
770 SELECT CASE (itype)
771 CASE (use_perd_x)
772 fixd_list(kk)%coord(2) = huge(0.0_dp)
773 fixd_list(kk)%coord(3) = huge(0.0_dp)
774 CASE (use_perd_y)
775 fixd_list(kk)%coord(1) = huge(0.0_dp)
776 fixd_list(kk)%coord(3) = huge(0.0_dp)
777 CASE (use_perd_z)
778 fixd_list(kk)%coord(1) = huge(0.0_dp)
779 fixd_list(kk)%coord(2) = huge(0.0_dp)
780 CASE (use_perd_xy)
781 fixd_list(kk)%coord(3) = huge(0.0_dp)
782 CASE (use_perd_xz)
783 fixd_list(kk)%coord(2) = huge(0.0_dp)
784 CASE (use_perd_yz)
785 fixd_list(kk)%coord(1) = huge(0.0_dp)
786 END SELECT
787 IF (restart_restraint_pos) THEN
788 ! Read coord0 value for restraint
789 CALL section_vals_val_get(fixd_restr_rest, "_DEFAULT_KEYWORD_", &
790 i_rep_val=nfixd_restart, r_vals=r)
791 SELECT CASE (itype)
792 CASE (use_perd_x)
793 cpassert(SIZE(r) == 1)
794 fixd_list(kk)%coord(1) = r(1)
795 CASE (use_perd_y)
796 cpassert(SIZE(r) == 1)
797 fixd_list(kk)%coord(2) = r(1)
798 CASE (use_perd_z)
799 cpassert(SIZE(r) == 1)
800 fixd_list(kk)%coord(3) = r(1)
801 CASE (use_perd_xy)
802 cpassert(SIZE(r) == 2)
803 fixd_list(kk)%coord(1) = r(1)
804 fixd_list(kk)%coord(2) = r(2)
805 CASE (use_perd_xz)
806 cpassert(SIZE(r) == 2)
807 fixd_list(kk)%coord(1) = r(1)
808 fixd_list(kk)%coord(3) = r(2)
809 CASE (use_perd_yz)
810 cpassert(SIZE(r) == 2)
811 fixd_list(kk)%coord(2) = r(1)
812 fixd_list(kk)%coord(3) = r(2)
813 CASE (use_perd_xyz)
814 cpassert(SIZE(r) == 3)
815 fixd_list(kk)%coord(1:3) = r(1:3)
816 IF (ASSOCIATED(topology%cell_muc)) &
817 CALL cell_transform_input_cartesian(topology%cell_muc, fixd_list(kk)%coord)
818 END SELECT
819 ELSE
820 ! Write coord0 value for restraint
821 SELECT CASE (itype)
822 CASE (use_perd_x)
823 ALLOCATE (r(1))
824 r(1) = fixd_list(kk)%coord(1)
825 CASE (use_perd_y)
826 ALLOCATE (r(1))
827 r(1) = fixd_list(kk)%coord(2)
828 CASE (use_perd_z)
829 ALLOCATE (r(1))
830 r(1) = fixd_list(kk)%coord(3)
831 CASE (use_perd_xy)
832 ALLOCATE (r(2))
833 r(1) = fixd_list(kk)%coord(1)
834 r(2) = fixd_list(kk)%coord(2)
835 CASE (use_perd_xz)
836 ALLOCATE (r(2))
837 r(1) = fixd_list(kk)%coord(1)
838 r(2) = fixd_list(kk)%coord(3)
839 CASE (use_perd_yz)
840 ALLOCATE (r(2))
841 r(1) = fixd_list(kk)%coord(1)
842 r(2) = fixd_list(kk)%coord(3)
843 CASE (use_perd_xyz)
844 ALLOCATE (r(3))
845 r(1:3) = fixd_list(kk)%coord(1:3)
846 END SELECT
847 CALL section_vals_val_set(fixd_restr_rest, "_DEFAULT_KEYWORD_", &
848 i_rep_val=nfixd_restart, r_vals_ptr=r)
849 END IF
850 END IF
851 END IF
852 END DO
853 END DO
854 END IF
855 IF (iw > 0) THEN
856 WRITE (iw, *) "MOLECULE KIND:", i, " NR. FIXED ATOMS:", SIZE(fixd_list(:)%fixd), " LIST::", fixd_list(:)%fixd
857 END IF
858 CALL set_molecule_kind(molecule_kind, nfixd=nfixed_atoms, nfixd_restraint=nfixd_restraint, &
859 fixd_list=fixd_list)
860 fixd_list_gci(nfixd_list_gci + 1:nfixd_list_gci + nfixed_atoms) = fixd_list
861 nfixd_list_gci = nfixd_list_gci + nfixed_atoms
862 END DO
863 IF (iw > 0) THEN
864 WRITE (iw, *) "TOTAL NUMBER OF FIXED ATOMS:", nfixd_list_gci
865 END IF
866 cpassert(count(missed_molname) == 0)
867 DEALLOCATE (missed_molname)
868 ! Intermolecular constraints
869 IF (gci%ntot /= 0) THEN
870 ALLOCATE (fixd_list(nfixd_list_gci))
871 fixd_list(1:nfixd_list_gci) = fixd_list_gci(1:nfixd_list_gci)
872 gci%fixd_list => fixd_list
873 END IF
874 DEALLOCATE (fixd_list_gci)
875 END IF
876 ! Final setup of the number of possible restraints
877 gci%nrestraint = gci%ng3x3_restraint + &
878 gci%ng4x6_restraint + &
879 gci%nvsite_restraint + &
880 gci%ncolv%nrestraint
881 CALL cp_print_key_finished_output(iw, logger, subsys_section, &
882 "PRINT%TOPOLOGY_INFO/UTIL_INFO")
883 CALL timestop(handle2)
884 CALL timestop(handle)
885 END SUBROUTINE topology_constraint_pack
886
887! **************************************************************************************************
888!> \brief Setup the colv_list for the packing of constraints
889!> \param colv_list ...
890!> \param ilist ...
891!> \param gind ...
892!> \param cons_info ...
893!> \param topology ...
894!> \param particle_set ...
895!> \param restart_restraint_clv ...
896!> \param colvar_rest ...
897!> \param first_atom ...
898!> \par History
899!> Updated 2007 for intermolecular constraints
900!> \author Teodoro Laino [2007]
901! **************************************************************************************************
902 SUBROUTINE setup_colv_list(colv_list, ilist, gind, cons_info, topology, &
903 particle_set, restart_restraint_clv, colvar_rest, first_atom)
904
905 TYPE(colvar_constraint_type), DIMENSION(:), &
906 POINTER :: colv_list
907 INTEGER, DIMENSION(:), POINTER :: ilist
908 INTEGER, INTENT(INOUT) :: gind
909 TYPE(constraint_info_type), POINTER :: cons_info
910 TYPE(topology_parameters_type), INTENT(INOUT) :: topology
911 TYPE(particle_type), DIMENSION(:), OPTIONAL, &
912 POINTER :: particle_set
913 LOGICAL, INTENT(IN) :: restart_restraint_clv
914 TYPE(section_vals_type), POINTER :: colvar_rest
915 INTEGER, INTENT(IN) :: first_atom
916
917 INTEGER :: j, kdim, kk, ncolv_mol
918 REAL(kind=dp) :: rmod
919 TYPE(colvar_type), POINTER :: local_colvar
920
921 ncolv_mol = 0
922 DO kk = 1, SIZE(ilist)
923 j = ilist(kk)
924 ncolv_mol = ncolv_mol + 1
925 kdim = SIZE(cons_info%colvar_set(j)%colvar%i_atom)
926 ALLOCATE (colv_list(ncolv_mol)%i_atoms(kdim))
927 colv_list(ncolv_mol)%inp_seq_num = j
928 colv_list(ncolv_mol)%type_id = cons_info%colvar_set(j)%colvar%type_id
929 colv_list(ncolv_mol)%i_atoms = cons_info%colvar_set(j)%colvar%i_atom
930 colv_list(ncolv_mol)%use_points = cons_info%colvar_set(j)%colvar%use_points
931 ! Restraint
932 colv_list(ncolv_mol)%restraint%active = cons_info%colv_restraint(j)
933 colv_list(ncolv_mol)%restraint%k0 = cons_info%colv_k0(j)
934 IF (cons_info%const_colv_target(j) == -huge(0.0_dp)) THEN
935 ! Let's compute the value..
936 NULLIFY (local_colvar)
937 CALL colvar_clone(local_colvar, cons_info%colvar_set(j)%colvar, &
938 i_atom_offset=first_atom - 1)
939 CALL colvar_eval_mol_f(local_colvar, topology%cell, particle_set)
940 colv_list(ncolv_mol)%expected_value = local_colvar%ss
941 CALL colvar_release(local_colvar)
942 ELSE
943 colv_list(ncolv_mol)%expected_value = cons_info%const_colv_target(j)
944 END IF
945 colv_list(ncolv_mol)%expected_value_growth_speed = cons_info%const_colv_target_growth(j)
946 ! In case of Restraint let's check for possible restart values
947 IF (colv_list(ncolv_mol)%restraint%active .AND. &
948 (colv_list(ncolv_mol)%expected_value_growth_speed == 0.0_dp)) THEN
949 gind = gind + 1
950 IF (restart_restraint_clv) THEN
951 CALL section_vals_val_get(colvar_rest, "_DEFAULT_KEYWORD_", &
952 i_rep_val=gind, r_val=rmod)
953 colv_list(ncolv_mol)%expected_value = rmod
954 ELSE
955 rmod = colv_list(ncolv_mol)%expected_value
956 CALL section_vals_val_set(colvar_rest, "_DEFAULT_KEYWORD_", &
957 i_rep_val=gind, r_val=rmod)
958 END IF
959 END IF
960 ! Only if torsion let's take into account the singularity in the definition
961 ! of the dihedral
962 IF (cons_info%colvar_set(j)%colvar%type_id == torsion_colvar_id) THEN
963 cons_info%colvar_set(j)%colvar%torsion_param%o0 = colv_list(ncolv_mol)%expected_value
964 END IF
965 END DO
966 END SUBROUTINE setup_colv_list
967
968! **************************************************************************************************
969!> \brief Setup the g3x3_list for the packing of constraints
970!> \param g3x3_list ...
971!> \param ilist ...
972!> \param cons_info ...
973!> \param ng3x3_restraint ...
974!> \par History
975!> Updated 2007 for intermolecular constraints
976!> \author Teodoro Laino [2007]
977! **************************************************************************************************
978 SUBROUTINE setup_g3x3_list(g3x3_list, ilist, cons_info, ng3x3_restraint)
979 TYPE(g3x3_constraint_type), DIMENSION(:), POINTER :: g3x3_list
980 INTEGER, DIMENSION(:), POINTER :: ilist
981 TYPE(constraint_info_type), POINTER :: cons_info
982 INTEGER, INTENT(OUT) :: ng3x3_restraint
983
984 INTEGER :: j, ng3x3
985
986 ng3x3_restraint = 0
987 DO ng3x3 = 1, SIZE(ilist)
988 j = ilist(ng3x3)
989 g3x3_list(ng3x3)%a = cons_info%const_g33_a(j)
990 g3x3_list(ng3x3)%b = cons_info%const_g33_b(j)
991 g3x3_list(ng3x3)%c = cons_info%const_g33_c(j)
992 g3x3_list(ng3x3)%dab = cons_info%const_g33_dab(j)
993 g3x3_list(ng3x3)%dac = cons_info%const_g33_dac(j)
994 g3x3_list(ng3x3)%dbc = cons_info%const_g33_dbc(j)
995 ! Restraint
996 g3x3_list(ng3x3)%restraint%active = cons_info%g33_restraint(j)
997 g3x3_list(ng3x3)%restraint%k0 = cons_info%g33_k0(j)
998 IF (g3x3_list(ng3x3)%restraint%active) ng3x3_restraint = ng3x3_restraint + 1
999 END DO
1000
1001 END SUBROUTINE setup_g3x3_list
1002
1003! **************************************************************************************************
1004!> \brief Setup the g4x6_list for the packing of constraints
1005!> \param g4x6_list ...
1006!> \param ilist ...
1007!> \param cons_info ...
1008!> \param ng4x6_restraint ...
1009!> \par History
1010!> Updated 2007 for intermolecular constraints
1011!> \author Teodoro Laino [2007]
1012! **************************************************************************************************
1013 SUBROUTINE setup_g4x6_list(g4x6_list, ilist, cons_info, ng4x6_restraint)
1014 TYPE(g4x6_constraint_type), DIMENSION(:), POINTER :: g4x6_list
1015 INTEGER, DIMENSION(:), POINTER :: ilist
1016 TYPE(constraint_info_type), POINTER :: cons_info
1017 INTEGER, INTENT(OUT) :: ng4x6_restraint
1018
1019 INTEGER :: j, ng4x6
1020
1021 ng4x6 = 0
1022 ng4x6_restraint = 0
1023 DO ng4x6 = 1, SIZE(ilist)
1024 j = ilist(ng4x6)
1025 g4x6_list(ng4x6)%a = cons_info%const_g46_a(j)
1026 g4x6_list(ng4x6)%b = cons_info%const_g46_b(j)
1027 g4x6_list(ng4x6)%c = cons_info%const_g46_c(j)
1028 g4x6_list(ng4x6)%d = cons_info%const_g46_d(j)
1029 g4x6_list(ng4x6)%dab = cons_info%const_g46_dab(j)
1030 g4x6_list(ng4x6)%dac = cons_info%const_g46_dac(j)
1031 g4x6_list(ng4x6)%dbc = cons_info%const_g46_dbc(j)
1032 g4x6_list(ng4x6)%dad = cons_info%const_g46_dad(j)
1033 g4x6_list(ng4x6)%dbd = cons_info%const_g46_dbd(j)
1034 g4x6_list(ng4x6)%dcd = cons_info%const_g46_dcd(j)
1035 ! Restraint
1036 g4x6_list(ng4x6)%restraint%active = cons_info%g46_restraint(j)
1037 g4x6_list(ng4x6)%restraint%k0 = cons_info%g46_k0(j)
1038 IF (g4x6_list(ng4x6)%restraint%active) ng4x6_restraint = ng4x6_restraint + 1
1039 END DO
1040
1041 END SUBROUTINE setup_g4x6_list
1042
1043! **************************************************************************************************
1044!> \brief Setup the vsite_list for the packing of constraints
1045!> \param vsite_list ...
1046!> \param ilist ...
1047!> \param cons_info ...
1048!> \param nvsite_restraint ...
1049!> \par History
1050!> \author Marcel Baer [2008]
1051! **************************************************************************************************
1052 SUBROUTINE setup_vsite_list(vsite_list, ilist, cons_info, nvsite_restraint)
1053 TYPE(vsite_constraint_type), DIMENSION(:), POINTER :: vsite_list
1054 INTEGER, DIMENSION(:), POINTER :: ilist
1055 TYPE(constraint_info_type), POINTER :: cons_info
1056 INTEGER, INTENT(OUT) :: nvsite_restraint
1057
1058 INTEGER :: j, nvsite
1059
1060 nvsite = 0
1061 nvsite_restraint = 0
1062 DO nvsite = 1, SIZE(ilist)
1063 j = ilist(nvsite)
1064 vsite_list(nvsite)%a = cons_info%const_vsite_a(j)
1065 vsite_list(nvsite)%b = cons_info%const_vsite_b(j)
1066 vsite_list(nvsite)%c = cons_info%const_vsite_c(j)
1067 vsite_list(nvsite)%d = cons_info%const_vsite_d(j)
1068 vsite_list(nvsite)%wbc = cons_info%const_vsite_wbc(j)
1069 vsite_list(nvsite)%wdc = cons_info%const_vsite_wdc(j)
1070 ! Restraint
1071 vsite_list(nvsite)%restraint%active = cons_info%vsite_restraint(j)
1072 vsite_list(nvsite)%restraint%k0 = cons_info%vsite_k0(j)
1073 IF (vsite_list(nvsite)%restraint%active) nvsite_restraint = nvsite_restraint + 1
1074 END DO
1075
1076 END SUBROUTINE setup_vsite_list
1077! **************************************************************************************************
1078!> \brief Setup the lcolv for the packing of constraints
1079!> \param lcolv ...
1080!> \param ilist ...
1081!> \param first_atom ...
1082!> \param last_atom ...
1083!> \param cons_info ...
1084!> \param particle_set ...
1085!> \param colvar_func_info ...
1086!> \param use_clv_info ...
1087!> \param cind ...
1088!> \par History
1089!> Updated 2007 for intermolecular constraints
1090!> \author Teodoro Laino [2007]
1091! **************************************************************************************************
1092 SUBROUTINE setup_lcolv(lcolv, ilist, first_atom, last_atom, cons_info, &
1093 particle_set, colvar_func_info, use_clv_info, &
1094 cind)
1095 TYPE(local_colvar_constraint_type), DIMENSION(:), &
1096 POINTER :: lcolv
1097 INTEGER, DIMENSION(:), POINTER :: ilist
1098 INTEGER, INTENT(IN) :: first_atom, last_atom
1099 TYPE(constraint_info_type), POINTER :: cons_info
1100 TYPE(particle_type), DIMENSION(:), OPTIONAL, &
1101 POINTER :: particle_set
1102 TYPE(section_vals_type), POINTER :: colvar_func_info
1103 LOGICAL, INTENT(IN) :: use_clv_info
1104 INTEGER, INTENT(INOUT) :: cind
1105
1106 INTEGER :: ind, k, kk
1107 REAL(kind=dp), DIMENSION(:), POINTER :: r_vals
1108
1109 DO kk = 1, SIZE(ilist)
1110 k = ilist(kk)
1111 lcolv(kk)%init = .false.
1112 lcolv(kk)%lambda = 0.0_dp
1113 lcolv(kk)%sigma = 0.0_dp
1114
1115 ! Set Up colvar variable
1116 NULLIFY (lcolv(kk)%colvar, lcolv(kk)%colvar_old)
1117 ! Colvar
1118 CALL colvar_clone(lcolv(kk)%colvar, cons_info%colvar_set(k)%colvar, &
1119 i_atom_offset=first_atom - 1)
1120
1121 ! Some COLVARS may need additional information for evaluating the
1122 ! functional form: this is the case for COLVARS which depend on the
1123 ! initial position of the atoms: This information is stored in a proper
1124 ! container in the COLVAR_RESTART section..
1125 IF ((lcolv(kk)%colvar%type_id == xyz_diag_colvar_id) .OR. &
1126 (lcolv(kk)%colvar%type_id == xyz_outerdiag_colvar_id)) THEN
1127 cind = cind + 1
1128 IF (use_clv_info) THEN
1129 CALL section_vals_val_get(colvar_func_info, "_DEFAULT_KEYWORD_", &
1130 i_rep_val=cind, r_vals=r_vals)
1131 SELECT CASE (lcolv(kk)%colvar%type_id)
1132 CASE (xyz_diag_colvar_id)
1133 cpassert(SIZE(r_vals) == 3)
1134 lcolv(kk)%colvar%xyz_diag_param%r0 = r_vals
1135 CASE (xyz_outerdiag_colvar_id)
1136 cpassert(SIZE(r_vals) == 6)
1137 lcolv(kk)%colvar%xyz_outerdiag_param%r0(:, 1) = r_vals(1:3)
1138 lcolv(kk)%colvar%xyz_outerdiag_param%r0(:, 2) = r_vals(4:6)
1139 END SELECT
1140 ELSE
1141 SELECT CASE (lcolv(kk)%colvar%type_id)
1142 CASE (xyz_diag_colvar_id)
1143 ALLOCATE (r_vals(3))
1144 ind = first_atom - 1 + lcolv(kk)%colvar%xyz_diag_param%i_atom
1145 r_vals = particle_set(ind)%r
1146 lcolv(kk)%colvar%xyz_diag_param%r0 = r_vals
1147 CASE (xyz_outerdiag_colvar_id)
1148 ALLOCATE (r_vals(6))
1149 ind = first_atom - 1 + lcolv(kk)%colvar%xyz_outerdiag_param%i_atoms(1)
1150 r_vals(1:3) = particle_set(ind)%r
1151 ind = first_atom - 1 + lcolv(kk)%colvar%xyz_outerdiag_param%i_atoms(2)
1152 r_vals(4:6) = particle_set(ind)%r
1153 lcolv(kk)%colvar%xyz_outerdiag_param%r0(:, 1) = r_vals(1:3)
1154 lcolv(kk)%colvar%xyz_outerdiag_param%r0(:, 2) = r_vals(4:6)
1155 END SELECT
1156 CALL section_vals_val_set(colvar_func_info, "_DEFAULT_KEYWORD_", &
1157 i_rep_val=cind, r_vals_ptr=r_vals)
1158 END IF
1159 END IF
1160
1161 ! Setup Colvar_old
1162 CALL colvar_clone(lcolv(kk)%colvar_old, lcolv(kk)%colvar)
1163
1164 ! Check for consistency in the constraint definition
1165 IF (any(lcolv(kk)%colvar%i_atom > last_atom) .OR. &
1166 any(lcolv(kk)%colvar%i_atom < first_atom)) THEN
1167 WRITE (*, '(T5,"|",T8,A)') "Error in constraints setup!"
1168 WRITE (*, '(T5,"|",T8,A)') "A constraint has been defined for a molecule type", &
1169 " but the atoms specified in the constraint and the atoms defined for", &
1170 " the molecule DO NOT match!", &
1171 "This could be very probable due to a wrong connectivity, or an error", &
1172 " in the constraint specification in the input file.", &
1173 " Please check it carefully!"
1174 cpabort("")
1175 END IF
1176 END DO
1177 END SUBROUTINE setup_lcolv
1178
1179! **************************************************************************************************
1180!> \brief Setup the lg3x3 for the packing of constraints
1181!> \param lg3x3 ...
1182!> \param g3x3_list ...
1183!> \param first_atom ...
1184!> \param last_atom ...
1185!> \par History
1186!> Updated 2007 for intermolecular constraints
1187!> \author Teodoro Laino [2007]
1188! **************************************************************************************************
1189 SUBROUTINE setup_lg3x3(lg3x3, g3x3_list, first_atom, last_atom)
1190 TYPE(local_g3x3_constraint_type), DIMENSION(:), &
1191 POINTER :: lg3x3
1192 TYPE(g3x3_constraint_type), DIMENSION(:), POINTER :: g3x3_list
1193 INTEGER, INTENT(IN) :: first_atom, last_atom
1194
1195 INTEGER :: kk
1196
1197 DO kk = 1, SIZE(lg3x3)
1198 lg3x3(kk)%init = .false.
1199 lg3x3(kk)%scale = 0.0_dp
1200 lg3x3(kk)%scale_old = 0.0_dp
1201 lg3x3(kk)%fa = 0.0_dp
1202 lg3x3(kk)%fb = 0.0_dp
1203 lg3x3(kk)%fc = 0.0_dp
1204 lg3x3(kk)%ra_old = 0.0_dp
1205 lg3x3(kk)%rb_old = 0.0_dp
1206 lg3x3(kk)%rc_old = 0.0_dp
1207 lg3x3(kk)%va = 0.0_dp
1208 lg3x3(kk)%vb = 0.0_dp
1209 lg3x3(kk)%vc = 0.0_dp
1210 lg3x3(kk)%lambda = 0.0_dp
1211 IF ((g3x3_list(kk)%a + first_atom - 1 < first_atom) .OR. &
1212 (g3x3_list(kk)%b + first_atom - 1 < first_atom) .OR. &
1213 (g3x3_list(kk)%c + first_atom - 1 < first_atom) .OR. &
1214 (g3x3_list(kk)%a + first_atom - 1 > last_atom) .OR. &
1215 (g3x3_list(kk)%b + first_atom - 1 > last_atom) .OR. &
1216 (g3x3_list(kk)%c + first_atom - 1 > last_atom)) THEN
1217 WRITE (*, '(T5,"|",T8,A)') "Error in constraints setup!"
1218 WRITE (*, '(T5,"|",T8,A)') "A constraint has been defined for a molecule type", &
1219 " but the atoms specified in the constraint and the atoms defined for", &
1220 " the molecule DO NOT match!", &
1221 "This could be very probable due to a wrong connectivity, or an error", &
1222 " in the constraint specification in the input file.", &
1223 " Please check it carefully!"
1224 cpabort("")
1225 END IF
1226 END DO
1227
1228 END SUBROUTINE setup_lg3x3
1229
1230! **************************************************************************************************
1231!> \brief Setup the lg4x6 for the packing of constraints
1232!> \param lg4x6 ...
1233!> \param g4x6_list ...
1234!> \param first_atom ...
1235!> \param last_atom ...
1236!> \par History
1237!> Updated 2007 for intermolecular constraints
1238!> \author Teodoro Laino [2007]
1239! **************************************************************************************************
1240 SUBROUTINE setup_lg4x6(lg4x6, g4x6_list, first_atom, last_atom)
1241 TYPE(local_g4x6_constraint_type), DIMENSION(:), &
1242 POINTER :: lg4x6
1243 TYPE(g4x6_constraint_type), DIMENSION(:), POINTER :: g4x6_list
1244 INTEGER, INTENT(IN) :: first_atom, last_atom
1245
1246 INTEGER :: kk
1247
1248 DO kk = 1, SIZE(lg4x6)
1249 lg4x6(kk)%init = .false.
1250 lg4x6(kk)%scale = 0.0_dp
1251 lg4x6(kk)%scale_old = 0.0_dp
1252 lg4x6(kk)%fa = 0.0_dp
1253 lg4x6(kk)%fb = 0.0_dp
1254 lg4x6(kk)%fc = 0.0_dp
1255 lg4x6(kk)%fd = 0.0_dp
1256 lg4x6(kk)%fe = 0.0_dp
1257 lg4x6(kk)%ff = 0.0_dp
1258 lg4x6(kk)%ra_old = 0.0_dp
1259 lg4x6(kk)%rb_old = 0.0_dp
1260 lg4x6(kk)%rc_old = 0.0_dp
1261 lg4x6(kk)%rd_old = 0.0_dp
1262 lg4x6(kk)%re_old = 0.0_dp
1263 lg4x6(kk)%rf_old = 0.0_dp
1264 lg4x6(kk)%va = 0.0_dp
1265 lg4x6(kk)%vb = 0.0_dp
1266 lg4x6(kk)%vc = 0.0_dp
1267 lg4x6(kk)%vd = 0.0_dp
1268 lg4x6(kk)%ve = 0.0_dp
1269 lg4x6(kk)%vf = 0.0_dp
1270 lg4x6(kk)%lambda = 0.0_dp
1271 IF ((g4x6_list(kk)%a + first_atom - 1 < first_atom) .OR. &
1272 (g4x6_list(kk)%b + first_atom - 1 < first_atom) .OR. &
1273 (g4x6_list(kk)%c + first_atom - 1 < first_atom) .OR. &
1274 (g4x6_list(kk)%d + first_atom - 1 < first_atom) .OR. &
1275 (g4x6_list(kk)%a + first_atom - 1 > last_atom) .OR. &
1276 (g4x6_list(kk)%b + first_atom - 1 > last_atom) .OR. &
1277 (g4x6_list(kk)%c + first_atom - 1 > last_atom) .OR. &
1278 (g4x6_list(kk)%d + first_atom - 1 > last_atom)) THEN
1279 WRITE (*, '(T5,"|",T8,A)') "Error in constraints setup!"
1280 WRITE (*, '(T5,"|",T8,A)') "A constrained has been defined for a molecule type", &
1281 " but the atoms specified in the constraint and the atoms defined for", &
1282 " the molecule DO NOT match!", &
1283 "This could be very probable due to a wrong connectivity, or an error", &
1284 " in the constraint specification in the input file.", &
1285 " Please check it carefully!"
1286 cpabort("")
1287 END IF
1288 END DO
1289
1290 END SUBROUTINE setup_lg4x6
1291
1292! **************************************************************************************************
1293!> \brief Gives back a list of molecule to which apply the constraint
1294!> \param const_mol ...
1295!> \param const_molname ...
1296!> \param const_intermolecular ...
1297!> \param constr_x_mol ...
1298!> \param constr_x_glob ...
1299!> \param molecule_kind_set ...
1300!> \param exclude_qm ...
1301!> \param exclude_mm ...
1302!> \par History
1303!> Updated 2007 for intermolecular constraints
1304!> \author Teodoro Laino [2006]
1305! **************************************************************************************************
1306 SUBROUTINE give_constraint_array(const_mol, const_molname, const_intermolecular, &
1307 constr_x_mol, constr_x_glob, molecule_kind_set, exclude_qm, exclude_mm)
1308
1309 INTEGER, DIMENSION(:), POINTER :: const_mol
1310 CHARACTER(LEN=default_string_length), &
1311 DIMENSION(:), POINTER :: const_molname
1312 LOGICAL, DIMENSION(:), POINTER :: const_intermolecular
1313 TYPE(constr_list_type), DIMENSION(:), POINTER :: constr_x_mol
1314 INTEGER, DIMENSION(:), POINTER :: constr_x_glob
1315 TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
1316 LOGICAL, DIMENSION(:), POINTER :: exclude_qm, exclude_mm
1317
1318 CHARACTER(len=*), PARAMETER :: routinen = 'give_constraint_array'
1319
1320 CHARACTER(LEN=default_string_length) :: myname, name
1321 INTEGER :: handle, i, iglob, isize, k
1322 LOGICAL :: found_molname, is_qm
1323 TYPE(molecule_kind_type), POINTER :: molecule_kind
1324
1325 CALL timeset(routinen, handle)
1326 NULLIFY (molecule_kind)
1327 ALLOCATE (constr_x_mol(SIZE(molecule_kind_set)))
1328 DO i = 1, SIZE(constr_x_mol)
1329 NULLIFY (constr_x_mol(i)%constr)
1330 ALLOCATE (constr_x_mol(i)%constr(0))
1331 END DO
1332 cpassert(SIZE(const_mol) == SIZE(const_molname))
1333 iglob = 0
1334 DO i = 1, SIZE(const_mol)
1335 IF (const_intermolecular(i)) THEN
1336 ! Intermolecular constraint
1337 iglob = iglob + 1
1338 CALL reallocate(constr_x_glob, 1, iglob)
1339 constr_x_glob(iglob) = i
1340 ELSE
1341 ! Intramolecular constraint
1342 IF (const_mol(i) /= 0) THEN
1343 k = const_mol(i)
1344 IF (k > SIZE(molecule_kind_set)) &
1345 CALL cp_abort(__location__, &
1346 "A constraint has been specified providing the molecule index. But the"// &
1347 " molecule index ("//cp_to_string(k)//") is out of range of the possible"// &
1348 " molecule kinds ("//cp_to_string(SIZE(molecule_kind_set))//").")
1349 isize = SIZE(constr_x_mol(k)%constr)
1350 CALL reallocate(constr_x_mol(k)%constr, 1, isize + 1)
1351 constr_x_mol(k)%constr(isize + 1) = i
1352 ELSE
1353 myname = const_molname(i)
1354 found_molname = .false.
1355 DO k = 1, SIZE(molecule_kind_set)
1356 molecule_kind => molecule_kind_set(k)
1357 name = molecule_kind%name
1358 is_qm = qmmm_ff_precond_only_qm(id1=name)
1359 IF (is_qm .AND. exclude_qm(i)) cycle
1360 IF (.NOT. is_qm .AND. exclude_mm(i)) cycle
1361 IF (name == myname) THEN
1362 isize = SIZE(constr_x_mol(k)%constr)
1363 CALL reallocate(constr_x_mol(k)%constr, 1, isize + 1)
1364 constr_x_mol(k)%constr(isize + 1) = i
1365 found_molname = .true.
1366 END IF
1367 END DO
1368 CALL print_warning_molname(found_molname, myname)
1369 END IF
1370 END IF
1371 END DO
1372 CALL timestop(handle)
1373 END SUBROUTINE give_constraint_array
1374
1375! **************************************************************************************************
1376!> \brief Prints a warning message if undefined molnames are used to define constraints
1377!> \param found ...
1378!> \param name ...
1379!> \author Teodoro Laino [2007] - Zurich University
1380! **************************************************************************************************
1381 SUBROUTINE print_warning_molname(found, name)
1382 LOGICAL, INTENT(IN) :: found
1383 CHARACTER(LEN=*), INTENT(IN) :: name
1384
1385 IF (.NOT. found) &
1386 CALL cp_warn(__location__, &
1387 " MOLNAME ("//trim(name)//") was defined for constraints, but this molecule name "// &
1388 "is not defined. Please check carefully your PDB, PSF (has priority over PDB) or "// &
1389 "input driven CP2K coordinates. In case you may not find the reason for this warning "// &
1390 "it may be a good idea to print all molecule information (including kind name) activating "// &
1391 "the print_key MOLECULES specific of the SUBSYS%PRINT section. ")
1392
1393 END SUBROUTINE print_warning_molname
1394
1395END MODULE topology_constraint_util
cp_log_handling::cp_to_string
Definition cp_log_handling.F:90
memory_utilities::reallocate
Definition memory_utilities.F:27
atomic_kind_types
Define the atomic kind types and their sub types.
Definition atomic_kind_types.F:23
atomic_kind_types::get_atomic_kind
subroutine, public get_atomic_kind(atomic_kind, fist_potential, element_symbol, name, mass, kind_number, natom, atom_list, rcov, rvdw, z, qeff, apol, cpol, mm_radius, shell, shell_active, damping)
Get attributes of an atomic kind.
Definition atomic_kind_types.F:138
atomic_kind_types::is_hydrogen
elemental logical function, public is_hydrogen(atomic_kind)
Determines if the atomic_kind is HYDROGEN.
Definition atomic_kind_types.F:380
cell_types
Handles all functions related to the CELL.
Definition cell_types.F:15
cell_types::use_perd_xyz
integer, parameter, public use_perd_xyz
Definition cell_types.F:42
cell_types::use_perd_y
integer, parameter, public use_perd_y
Definition cell_types.F:42
cell_types::use_perd_xz
integer, parameter, public use_perd_xz
Definition cell_types.F:42
cell_types::use_perd_x
integer, parameter, public use_perd_x
Definition cell_types.F:42
cell_types::use_perd_z
integer, parameter, public use_perd_z
Definition cell_types.F:42
cell_types::use_perd_yz
integer, parameter, public use_perd_yz
Definition cell_types.F:42
cell_types::use_perd_xy
integer, parameter, public use_perd_xy
Definition cell_types.F:42
cell_types::cell_transform_input_cartesian
subroutine, public cell_transform_input_cartesian(cell, vector)
Transform a Cartesian real-space vector from the user input cell frame into CP2K's canonical internal...
Definition cell_types.F:261
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:1646
colvar_types
Initialize the collective variables types.
Definition colvar_types.F:15
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::xyz_outerdiag_colvar_id
integer, parameter, public xyz_outerdiag_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::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::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::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::torsion_colvar_id
integer, parameter, public torsion_colvar_id
Definition colvar_types.F:56
colvar_types::xyz_diag_colvar_id
integer, parameter, public xyz_diag_colvar_id
Definition colvar_types.F:56
colvar_utils
evaluations of colvar for internal coordinates schemes
Definition colvar_utils.F:14
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:567
cp_log_handling
various routines to log and control the output. The idea is that decisions about where to log should ...
Definition cp_log_handling.F:41
cp_log_handling::cp_get_default_logger
type(cp_logger_type) function, pointer, public cp_get_default_logger()
returns the default logger
Definition cp_log_handling.F:234
cp_output_handling
routines to handle the output, The idea is to remove the decision of wheter to output and what to out...
Definition cp_output_handling.F:25
cp_output_handling::cp_print_key_unit_nr
integer function, public cp_print_key_unit_nr(logger, basis_section, print_key_path, extension, middle_name, local, log_filename, ignore_should_output, file_form, file_position, file_action, file_status, do_backup, on_file, is_new_file, mpi_io, fout)
...
Definition cp_output_handling.F:853
cp_output_handling::cp_print_key_finished_output
subroutine, public cp_print_key_finished_output(unit_nr, logger, basis_section, print_key_path, local, ignore_should_output, on_file, mpi_io)
should be called after you finish working with a unit obtained with cp_print_key_unit_nr,...
Definition cp_output_handling.F:1067
input_constants
collects all constants needed in input so that they can be used without circular dependencies
Definition input_constants.F:17
input_constants::do_constr_atomic
integer, parameter, public do_constr_atomic
Definition input_constants.F:80
input_constants::do_constr_molec
integer, parameter, public do_constr_molec
Definition input_constants.F:80
input_section_types
objects that represent the structure of input sections and the data contained in an input section
Definition input_section_types.F:15
input_section_types::section_vals_val_set
subroutine, public section_vals_val_set(section_vals, keyword_name, i_rep_section, i_rep_val, val, l_val, i_val, r_val, c_val, l_vals_ptr, i_vals_ptr, r_vals_ptr, c_vals_ptr)
sets the requested value
Definition input_section_types.F:1223
input_section_types::section_vals_get_subs_vals
recursive type(section_vals_type) function, pointer, public section_vals_get_subs_vals(section_vals, subsection_name, i_rep_section, can_return_null)
returns the values of the requested subsection
Definition input_section_types.F:731
input_section_types::section_vals_get
subroutine, public section_vals_get(section_vals, ref_count, n_repetition, n_subs_vals_rep, section, explicit)
returns various attributes about the section_vals
Definition input_section_types.F:704
input_section_types::section_vals_val_get
subroutine, public section_vals_val_get(section_vals, keyword_name, i_rep_section, i_rep_val, n_rep_val, val, l_val, i_val, r_val, c_val, l_vals, i_vals, r_vals, c_vals, explicit)
returns the requested value
Definition input_section_types.F:1047
kinds
Defines the basic variable types.
Definition kinds.F:23
kinds::dp
integer, parameter, public dp
Definition kinds.F:34
kinds::default_string_length
integer, parameter, public default_string_length
Definition kinds.F:57
memory_utilities
Utility routines for the memory handling.
Definition memory_utilities.F:14
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:512
molecule_kind_types::setup_colvar_counters
subroutine, public setup_colvar_counters(colv_list, ncolv)
...
Definition molecule_kind_types.F:241
molecule_kind_types::set_molecule_kind
subroutine, public set_molecule_kind(molecule_kind, name, mass, charge, kind_number, molecule_list, atom_list, nbond, bond_list, nbend, bend_list, nub, ub_list, nimpr, impr_list, nopbend, opbend_list, ntorsion, torsion_list, fixd_list, ncolv, colv_list, ng3x3, g3x3_list, ng4x6, nfixd, g4x6_list, nvsite, vsite_list, ng3x3_restraint, ng4x6_restraint, nfixd_restraint, nshell, shell_list, nvsite_restraint, bond_kind_set, bend_kind_set, ub_kind_set, torsion_kind_set, impr_kind_set, opbend_kind_set, nelectron, nsgf, molname_generated)
Set the components of a molecule kind.
Definition molecule_kind_types.F:781
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:327
molecule_types::set_molecule
subroutine, public set_molecule(molecule, molecule_kind, lmi, lci, lcolv, lg3x3, lg4x6)
Set a molecule data set.
Definition molecule_types.F:387
particle_types
Define the data structure for the particle information.
Definition particle_types.F:19
qmmm_ff_fist
Definition qmmm_ff_fist.F:11
qmmm_ff_fist::qmmm_ff_precond_only_qm
logical function, public qmmm_ff_precond_only_qm(id1, id2, id3, id4, is_link)
This function handles the atom names and modifies the "_QM_" prefix, in order to find the parameters ...
Definition qmmm_ff_fist.F:39
qmmm_types_low
Definition qmmm_types_low.F:13
topology_constraint_util
Collection of subroutine needed for topology related things.
Definition topology_constraint_util.F:13
topology_constraint_util::topology_constraint_pack
subroutine, public topology_constraint_pack(molecule_kind_set, molecule_set, topology, qmmm_env, particle_set, input_file, subsys_section, gci)
Pack in all the information needed for the constraints.
Definition topology_constraint_util.F:88
topology_types
Definition topology_types.F:18
topology
Control for reading in different topologies and coordinates.
Definition topology.F:13
atomic_kind_types::atomic_kind_type
Provides all information about an atomic kind.
Definition atomic_kind_types.F:45
colvar_types::colvar_counters
Definition colvar_types.F:388
colvar_types::colvar_type
parameters for a collective variable
Definition colvar_types.F:346
cp_log_handling::cp_logger_type
type of a logger, at the moment it contains just a print level starting at which level it should be l...
Definition cp_log_handling.F:140
input_section_types::section_vals_type
stores the values of a section
Definition input_section_types.F:127
molecule_kind_types::atom_type
Definition molecule_kind_types.F:58
molecule_kind_types::bond_type
Definition molecule_kind_types.F:69
molecule_kind_types::colvar_constraint_type
Definition molecule_kind_types.F:111
molecule_kind_types::fixd_constraint_type
Definition molecule_kind_types.F:140
molecule_kind_types::g3x3_constraint_type
Definition molecule_kind_types.F:121
molecule_kind_types::g4x6_constraint_type
Definition molecule_kind_types.F:127
molecule_kind_types::molecule_kind_type
Definition molecule_kind_types.F:151
molecule_kind_types::vsite_constraint_type
Definition molecule_kind_types.F:134
molecule_types::global_constraint_type
Definition molecule_types.F:134
molecule_types::local_colvar_constraint_type
Definition molecule_types.F:40
molecule_types::local_constraint_type
Definition molecule_types.F:125
molecule_types::local_g3x3_constraint_type
Definition molecule_types.F:48
molecule_types::local_g4x6_constraint_type
Definition molecule_types.F:76
molecule_types::molecule_type
Definition molecule_types.F:159
particle_types::particle_type
Definition particle_types.F:35
qmmm_types_low::qmmm_env_mm_type
...
Definition qmmm_types_low.F:238
topology_types::constr_list_type
Definition topology_types.F:181
topology_types::constraint_info_type
Definition topology_types.F:65
topology_types::topology_parameters_type
Definition topology_types.F:143