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molecule_types.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 Define the data structure for the molecule information.
10!> \par History
11!> JGH (22.05.2004) add last_atom information
12!> Teodoro Laino [tlaino] 12.2008 - Preparing for VIRTUAL SITE constraints
13!> (patch by Marcel Baer)
14!> \author Matthias Krack (29.08.2003)
15! **************************************************************************************************
16MODULE molecule_types
17
18 USE colvar_types, ONLY: colvar_counters,&
19 colvar_release,&
20 colvar_type
21 USE kinds, ONLY: dp
22 USE molecule_kind_types, ONLY: colvar_constraint_type,&
23 fixd_constraint_type,&
24 g3x3_constraint_type,&
25 g4x6_constraint_type,&
26 get_molecule_kind,&
27 molecule_kind_type,&
28 vsite_constraint_type
29#include "../base/base_uses.f90"
30
31 IMPLICIT NONE
32
33 PRIVATE
34
35 ! Global parameters (in this module)
36
37 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'molecule_types'
38
39 ! Molecular constraint types
40 TYPE local_colvar_constraint_type
41 TYPE(colvar_type), POINTER :: colvar => null(), &
42 colvar_old => null()
43 REAL(kind=dp) :: lambda = 0.0_dp, &
44 sigma = 0.0_dp
45 LOGICAL :: init = .false.
46 END TYPE local_colvar_constraint_type
47
48 TYPE local_g3x3_constraint_type
49 LOGICAL :: init = .false.
50 REAL(kind=dp) :: scale = 0.0_dp, &
51 imass1 = 0.0_dp, &
52 imass2 = 0.0_dp, &
53 imass3 = 0.0_dp, &
54 scale_old = 0.0_dp
55 REAL(kind=dp), DIMENSION(3) :: fa = 0.0_dp, &
56 fb = 0.0_dp, &
57 fc = 0.0_dp, &
58 f_roll1 = 0.0_dp, &
59 f_roll2 = 0.0_dp, &
60 f_roll3 = 0.0_dp, &
61 ra_old = 0.0_dp, &
62 rb_old = 0.0_dp, &
63 rc_old = 0.0_dp, &
64 r0_12 = 0.0_dp, &
65 r0_13 = 0.0_dp, &
66 r0_23 = 0.0_dp, &
67 va = 0.0_dp, &
68 vb = 0.0_dp, &
69 vc = 0.0_dp, &
70 del_lambda = 0.0_dp, &
71 lambda = 0.0_dp, &
72 lambda_old = 0.0_dp
73 REAL(kind=dp), DIMENSION(3, 3) :: amat = 0.0_dp
74 END TYPE local_g3x3_constraint_type
75
76 TYPE local_g4x6_constraint_type
77 LOGICAL :: init = .false.
78 REAL(kind=dp) :: scale = 0.0_dp, &
79 scale_old = 0.0_dp, &
80 imass1 = 0.0_dp, &
81 imass2 = 0.0_dp, &
82 imass3 = 0.0_dp, &
83 imass4 = 0.0_dp
84 REAL(kind=dp), DIMENSION(3) :: fa = 0.0_dp, &
85 fb = 0.0_dp, &
86 fc = 0.0_dp, &
87 fd = 0.0_dp, &
88 fe = 0.0_dp, &
89 ff = 0.0_dp, &
90 f_roll1 = 0.0_dp, &
91 f_roll2 = 0.0_dp, &
92 f_roll3 = 0.0_dp, &
93 f_roll4 = 0.0_dp, &
94 f_roll5 = 0.0_dp, &
95 f_roll6 = 0.0_dp, &
96 ra_old = 0.0_dp, &
97 rb_old = 0.0_dp, &
98 rc_old = 0.0_dp, &
99 rd_old = 0.0_dp, &
100 re_old = 0.0_dp, &
101 rf_old = 0.0_dp, &
102 va = 0.0_dp, &
103 vb = 0.0_dp, &
104 vc = 0.0_dp, &
105 vd = 0.0_dp, &
106 ve = 0.0_dp, &
107 vf = 0.0_dp, &
108 r0_12 = 0.0_dp, &
109 r0_13 = 0.0_dp, &
110 r0_14 = 0.0_dp, &
111 r0_23 = 0.0_dp, &
112 r0_24 = 0.0_dp, &
113 r0_34 = 0.0_dp
114 REAL(kind=dp), DIMENSION(6) :: del_lambda = 0.0_dp, &
115 lambda = 0.0_dp, &
116 lambda_old = 0.0_dp
117 REAL(kind=dp), DIMENSION(6, 6) :: amat = 0.0_dp
118 END TYPE local_g4x6_constraint_type
119
120 TYPE local_states_type
121 INTEGER :: nstates = 0 ! Kohn-Sham states for molecule
122 INTEGER, DIMENSION(:), POINTER :: states => null() ! indices of Kohn-Sham states for molecule
123 END TYPE local_states_type
124
125 TYPE local_constraint_type
126 TYPE(local_colvar_constraint_type), &
127 DIMENSION(:), POINTER :: lcolv => null()
128 TYPE(local_g3x3_constraint_type), DIMENSION(:), &
129 POINTER :: lg3x3 => null()
130 TYPE(local_g4x6_constraint_type), DIMENSION(:), &
131 POINTER :: lg4x6 => null()
132 END TYPE local_constraint_type
133
134 TYPE global_constraint_type
135 TYPE(colvar_counters) :: ncolv = colvar_counters()
136 INTEGER :: ntot = 0, &
137 nrestraint = 0, &
138 ng3x3 = 0, &
139 ng3x3_restraint = 0, &
140 ng4x6 = 0, &
141 ng4x6_restraint = 0, &
142 nvsite = 0, &
143 nvsite_restraint = 0
144 TYPE(fixd_constraint_type), DIMENSION(:), POINTER :: fixd_list => null()
145 TYPE(colvar_constraint_type), DIMENSION(:), &
146 POINTER :: colv_list => null()
147 TYPE(g3x3_constraint_type), DIMENSION(:), POINTER :: g3x3_list => null()
148 TYPE(g4x6_constraint_type), DIMENSION(:), POINTER :: g4x6_list => null()
149 TYPE(vsite_constraint_type), DIMENSION(:), POINTER :: vsite_list => null()
150 TYPE(local_colvar_constraint_type), &
151 DIMENSION(:), POINTER :: lcolv => null()
152 TYPE(local_g3x3_constraint_type), DIMENSION(:), &
153 POINTER :: lg3x3 => null()
154 TYPE(local_g4x6_constraint_type), DIMENSION(:), &
155 POINTER :: lg4x6 => null()
156 END TYPE global_constraint_type
157
158 ! Molecule type
159 TYPE molecule_type
160 TYPE(molecule_kind_type), POINTER :: molecule_kind => null() ! pointer to molecule kind information
161 TYPE(local_states_type), DIMENSION(:), POINTER :: lmi => null() ! local (spin)-states information
162 TYPE(local_constraint_type), POINTER :: lci => null() ! local molecule constraint info
163 INTEGER :: first_atom = 0 ! global index of first atom in molecule
164 INTEGER :: last_atom = 0 ! global index of last atom in molecule
165 INTEGER :: first_shell = 0 ! global index of first shell atom in molecule
166 INTEGER :: last_shell = 0 ! global index of last shell atom in molecule
167 END TYPE molecule_type
168
169 ! Public data types
170
171 PUBLIC :: local_colvar_constraint_type, &
172 local_g3x3_constraint_type, &
173 local_g4x6_constraint_type, &
174 local_constraint_type, &
175 local_states_type, &
176 global_constraint_type, &
177 molecule_type
178
179 ! Public subroutines
180
181 PUBLIC :: deallocate_global_constraint, &
182 allocate_molecule_set, &
183 deallocate_molecule_set, &
184 get_molecule, &
185 set_molecule, &
186 set_molecule_set, &
187 molecule_of_atom, &
188 get_molecule_set_info, &
189 get_domain_set_info
190
191CONTAINS
192
193! **************************************************************************************************
194!> \brief Deallocate a global constraint.
195!> \param gci ...
196!> \par History
197!> 07.2003 created [fawzi]
198!> 01.2014 moved from cp_subsys_release() into separate routine.
199!> \author Ole Schuett
200! **************************************************************************************************
201 SUBROUTINE deallocate_global_constraint(gci)
202 TYPE(global_constraint_type), POINTER :: gci
203
204 INTEGER :: i
205
206 IF (ASSOCIATED(gci)) THEN
207 ! List of constraints
208 IF (ASSOCIATED(gci%colv_list)) THEN
209 DO i = 1, SIZE(gci%colv_list)
210 DEALLOCATE (gci%colv_list(i)%i_atoms)
211 END DO
212 DEALLOCATE (gci%colv_list)
213 END IF
214
215 IF (ASSOCIATED(gci%g3x3_list)) THEN
216 DEALLOCATE (gci%g3x3_list)
217 END IF
218
219 IF (ASSOCIATED(gci%g4x6_list)) THEN
220 DEALLOCATE (gci%g4x6_list)
221 END IF
222
223 ! Local information
224 IF (ASSOCIATED(gci%lcolv)) THEN
225 DO i = 1, SIZE(gci%lcolv)
226 CALL colvar_release(gci%lcolv(i)%colvar)
227 CALL colvar_release(gci%lcolv(i)%colvar_old)
228 END DO
229 DEALLOCATE (gci%lcolv)
230 END IF
231
232 IF (ASSOCIATED(gci%lg3x3)) THEN
233 DEALLOCATE (gci%lg3x3)
234 END IF
235
236 IF (ASSOCIATED(gci%lg4x6)) THEN
237 DEALLOCATE (gci%lg4x6)
238 END IF
239
240 IF (ASSOCIATED(gci%fixd_list)) THEN
241 DEALLOCATE (gci%fixd_list)
242 END IF
243
244 DEALLOCATE (gci)
245 END IF
246 END SUBROUTINE deallocate_global_constraint
247
248! **************************************************************************************************
249!> \brief Allocate a molecule set.
250!> \param molecule_set ...
251!> \param nmolecule ...
252!> \date 29.08.2003
253!> \author Matthias Krack
254!> \version 1.0
255! **************************************************************************************************
256 SUBROUTINE allocate_molecule_set(molecule_set, nmolecule)
257 TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
258 INTEGER, INTENT(IN) :: nmolecule
259
260 IF (ASSOCIATED(molecule_set)) CALL deallocate_molecule_set(molecule_set)
261
262 ALLOCATE (molecule_set(nmolecule))
263
264 END SUBROUTINE allocate_molecule_set
265
266! **************************************************************************************************
267!> \brief Deallocate a molecule set.
268!> \param molecule_set ...
269!> \date 29.08.2003
270!> \author Matthias Krack
271!> \version 1.0
272! **************************************************************************************************
273 SUBROUTINE deallocate_molecule_set(molecule_set)
274 TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
275
276 INTEGER :: imolecule, j
277
278 IF (ASSOCIATED(molecule_set)) THEN
279
280 DO imolecule = 1, SIZE(molecule_set)
281 IF (ASSOCIATED(molecule_set(imolecule)%lmi)) THEN
282 DO j = 1, SIZE(molecule_set(imolecule)%lmi)
283 IF (ASSOCIATED(molecule_set(imolecule)%lmi(j)%states)) THEN
284 DEALLOCATE (molecule_set(imolecule)%lmi(j)%states)
285 END IF
286 END DO
287 DEALLOCATE (molecule_set(imolecule)%lmi)
288 END IF
289 IF (ASSOCIATED(molecule_set(imolecule)%lci)) THEN
290 IF (ASSOCIATED(molecule_set(imolecule)%lci%lcolv)) THEN
291 DO j = 1, SIZE(molecule_set(imolecule)%lci%lcolv)
292 CALL colvar_release(molecule_set(imolecule)%lci%lcolv(j)%colvar)
293 CALL colvar_release(molecule_set(imolecule)%lci%lcolv(j)%colvar_old)
294 END DO
295 DEALLOCATE (molecule_set(imolecule)%lci%lcolv)
296 END IF
297 IF (ASSOCIATED(molecule_set(imolecule)%lci%lg3x3)) THEN
298 DEALLOCATE (molecule_set(imolecule)%lci%lg3x3)
299 END IF
300 IF (ASSOCIATED(molecule_set(imolecule)%lci%lg4x6)) THEN
301 DEALLOCATE (molecule_set(imolecule)%lci%lg4x6)
302 END IF
303 DEALLOCATE (molecule_set(imolecule)%lci)
304 END IF
305 END DO
306 DEALLOCATE (molecule_set)
307
308 END IF
309 NULLIFY (molecule_set)
310
311 END SUBROUTINE deallocate_molecule_set
312
313! **************************************************************************************************
314!> \brief Get components from a molecule data set.
315!> \param molecule ...
316!> \param molecule_kind ...
317!> \param lmi ...
318!> \param lci ...
319!> \param lg3x3 ...
320!> \param lg4x6 ...
321!> \param lcolv ...
322!> \param first_atom ...
323!> \param last_atom ...
324!> \param first_shell ...
325!> \param last_shell ...
326!> \date 29.08.2003
327!> \author Matthias Krack
328!> \version 1.0
329! **************************************************************************************************
330 SUBROUTINE get_molecule(molecule, molecule_kind, lmi, lci, lg3x3, lg4x6, lcolv, &
331 first_atom, last_atom, first_shell, last_shell)
332
333 TYPE(molecule_type), INTENT(IN) :: molecule
334 TYPE(molecule_kind_type), OPTIONAL, POINTER :: molecule_kind
335 TYPE(local_states_type), DIMENSION(:), OPTIONAL, &
336 POINTER :: lmi
337 TYPE(local_constraint_type), OPTIONAL, POINTER :: lci
338 TYPE(local_g3x3_constraint_type), OPTIONAL, &
339 POINTER :: lg3x3(:)
340 TYPE(local_g4x6_constraint_type), OPTIONAL, &
341 POINTER :: lg4x6(:)
342 TYPE(local_colvar_constraint_type), DIMENSION(:), &
343 OPTIONAL, POINTER :: lcolv
344 INTEGER, OPTIONAL :: first_atom, last_atom, first_shell, &
345 last_shell
346
347 IF (PRESENT(first_atom)) first_atom = molecule%first_atom
348 IF (PRESENT(last_atom)) last_atom = molecule%last_atom
349 IF (PRESENT(first_shell)) first_shell = molecule%first_shell
350 IF (PRESENT(last_shell)) last_shell = molecule%last_shell
351 IF (PRESENT(molecule_kind)) molecule_kind => molecule%molecule_kind
352 IF (PRESENT(lmi)) lmi => molecule%lmi
353 IF (PRESENT(lci)) lci => molecule%lci
354 IF (PRESENT(lcolv)) THEN
355 IF (ASSOCIATED(molecule%lci)) THEN
356 lcolv => molecule%lci%lcolv
357 ELSE
358 cpabort("The pointer lci is not associated")
359 END IF
360 END IF
361 IF (PRESENT(lg3x3)) THEN
362 IF (ASSOCIATED(molecule%lci)) THEN
363 lg3x3 => molecule%lci%lg3x3
364 ELSE
365 cpabort("The pointer lci is not associated")
366 END IF
367 END IF
368 IF (PRESENT(lg4x6)) THEN
369 IF (ASSOCIATED(molecule%lci)) THEN
370 lg4x6 => molecule%lci%lg4x6
371 ELSE
372 cpabort("The pointer lci is not associated")
373 END IF
374 END IF
375
376 END SUBROUTINE get_molecule
377
378! **************************************************************************************************
379!> \brief Set a molecule data set.
380!> \param molecule ...
381!> \param molecule_kind ...
382!> \param lmi ...
383!> \param lci ...
384!> \param lcolv ...
385!> \param lg3x3 ...
386!> \param lg4x6 ...
387!> \date 29.08.2003
388!> \author Matthias Krack
389!> \version 1.0
390! **************************************************************************************************
391 SUBROUTINE set_molecule(molecule, molecule_kind, lmi, lci, lcolv, lg3x3, lg4x6)
392 TYPE(molecule_type), INTENT(INOUT) :: molecule
393 TYPE(molecule_kind_type), OPTIONAL, POINTER :: molecule_kind
394 TYPE(local_states_type), DIMENSION(:), OPTIONAL, &
395 POINTER :: lmi
396 TYPE(local_constraint_type), OPTIONAL, POINTER :: lci
397 TYPE(local_colvar_constraint_type), DIMENSION(:), &
398 OPTIONAL, POINTER :: lcolv
399 TYPE(local_g3x3_constraint_type), OPTIONAL, &
400 POINTER :: lg3x3(:)
401 TYPE(local_g4x6_constraint_type), OPTIONAL, &
402 POINTER :: lg4x6(:)
403
404 IF (PRESENT(molecule_kind)) molecule%molecule_kind => molecule_kind
405 IF (PRESENT(lmi)) molecule%lmi => lmi
406 IF (PRESENT(lci)) molecule%lci => lci
407 IF (PRESENT(lcolv)) THEN
408 IF (ASSOCIATED(molecule%lci)) THEN
409 molecule%lci%lcolv => lcolv
410 ELSE
411 cpabort("The pointer lci is not associated")
412 END IF
413 END IF
414 IF (PRESENT(lg3x3)) THEN
415 IF (ASSOCIATED(molecule%lci)) THEN
416 molecule%lci%lg3x3 => lg3x3
417 ELSE
418 cpabort("The pointer lci is not associated")
419 END IF
420 END IF
421 IF (PRESENT(lg4x6)) THEN
422 IF (ASSOCIATED(molecule%lci)) THEN
423 molecule%lci%lg4x6 => lg4x6
424 ELSE
425 cpabort("The pointer lci is not associated")
426 END IF
427 END IF
428
429 END SUBROUTINE set_molecule
430
431! **************************************************************************************************
432!> \brief Set a molecule data set.
433!> \param molecule_set ...
434!> \param first_atom ...
435!> \param last_atom ...
436!> \date 29.08.2003
437!> \author Matthias Krack
438!> \version 1.0
439! **************************************************************************************************
440 SUBROUTINE set_molecule_set(molecule_set, first_atom, last_atom)
441 TYPE(molecule_type), DIMENSION(:), INTENT(INOUT) :: molecule_set
442 INTEGER, DIMENSION(:), INTENT(IN), OPTIONAL :: first_atom, last_atom
443
444 INTEGER :: imolecule
445
446 IF (PRESENT(first_atom)) THEN
447 IF (SIZE(first_atom) /= SIZE(molecule_set)) THEN
448 CALL cp_abort(__location__, &
449 "The sizes of first_atom and molecule_set "// &
450 "are different")
451 END IF
452
453 DO imolecule = 1, SIZE(molecule_set)
454 molecule_set(imolecule)%first_atom = first_atom(imolecule)
455 END DO
456 END IF
457
458 IF (PRESENT(last_atom)) THEN
459 IF (SIZE(last_atom) /= SIZE(molecule_set)) THEN
460 CALL cp_abort(__location__, &
461 "The sizes of last_atom and molecule_set "// &
462 "are different")
463 END IF
464
465 DO imolecule = 1, SIZE(molecule_set)
466 molecule_set(imolecule)%last_atom = last_atom(imolecule)
467 END DO
468 END IF
469
470 END SUBROUTINE set_molecule_set
471
472! **************************************************************************************************
473!> \brief finds for each atom the molecule it belongs to
474!> \param molecule_set ...
475!> \param atom_to_mol ...
476! **************************************************************************************************
477 SUBROUTINE molecule_of_atom(molecule_set, atom_to_mol)
478 TYPE(molecule_type), DIMENSION(:), INTENT(IN) :: molecule_set
479 INTEGER, DIMENSION(:), INTENT(OUT) :: atom_to_mol
480
481 INTEGER :: first_atom, iatom, imol, last_atom
482
483 DO imol = 1, SIZE(molecule_set)
484 CALL get_molecule(molecule=molecule_set(imol), first_atom=first_atom, last_atom=last_atom)
485 DO iatom = first_atom, last_atom
486 atom_to_mol(iatom) = imol
487 END DO ! iatom
488 END DO ! imol
489
490 END SUBROUTINE molecule_of_atom
491
492! **************************************************************************************************
493!> \brief returns information about molecules in the set.
494!> \param molecule_set ...
495!> \param atom_to_mol ...
496!> \param mol_to_first_atom ...
497!> \param mol_to_last_atom ...
498!> \param mol_to_nelectrons ...
499!> \param mol_to_nbasis ...
500!> \param mol_to_charge ...
501!> \param mol_to_multiplicity ...
502!> \par History
503!> 2011.06 created [Rustam Z Khaliullin]
504!> \author Rustam Z Khaliullin
505! **************************************************************************************************
506 SUBROUTINE get_molecule_set_info(molecule_set, atom_to_mol, mol_to_first_atom, &
507 mol_to_last_atom, mol_to_nelectrons, mol_to_nbasis, mol_to_charge, &
508 mol_to_multiplicity)
509
510 TYPE(molecule_type), DIMENSION(:), INTENT(IN) :: molecule_set
511 INTEGER, DIMENSION(:), INTENT(OUT), OPTIONAL :: atom_to_mol, mol_to_first_atom, &
512 mol_to_last_atom, mol_to_nelectrons, mol_to_nbasis, mol_to_charge, mol_to_multiplicity
513
514 INTEGER :: first_atom, iatom, imol, last_atom, &
515 nbasis, nelec
516 REAL(kind=dp) :: charge
517 TYPE(molecule_kind_type), POINTER :: imol_kind
518
519 DO imol = 1, SIZE(molecule_set)
520
521 CALL get_molecule(molecule=molecule_set(imol), molecule_kind=imol_kind, &
522 first_atom=first_atom, last_atom=last_atom)
523
524 IF (PRESENT(mol_to_nelectrons)) THEN
525 CALL get_molecule_kind(imol_kind, nelectron=nelec)
526 mol_to_nelectrons(imol) = nelec
527 END IF
528
529 IF (PRESENT(mol_to_multiplicity)) THEN
530 ! RZK-warning: At the moment we can only get the total number
531 ! of electrons (alpha+beta) and we do not have a way to get the multiplicity of mols.
532 ! Therefore, the best we can do is to assume the singlet state for even number of electrons
533 ! and doublet state for odd number of electrons (assume ne_alpha > ne_beta).
534 ! The best way to implement a correct multiplicity subroutine in the future is to get
535 ! the number of alpha and beta e- for each atom from init_atom_electronic_state. This way (as opposed to
536 ! reading the multiplicities from file) the number of occupied and virtual orbitals
537 ! will be consistent with atomic guess. A guess with broken symmetry will be easy to
538 ! implement as well.
539 CALL get_molecule_kind(imol_kind, nelectron=nelec)
540 IF (mod(nelec, 2) == 0) THEN
541 mol_to_multiplicity(imol) = 1
542 ELSE
543 mol_to_multiplicity(imol) = 2
544 END IF
545 END IF
546
547 IF (PRESENT(mol_to_charge)) THEN
548 CALL get_molecule_kind(imol_kind, charge=charge)
549 mol_to_charge(imol) = nint(charge)
550 END IF
551
552 IF (PRESENT(mol_to_nbasis)) THEN
553 CALL get_molecule_kind(imol_kind, nsgf=nbasis)
554 mol_to_nbasis(imol) = nbasis
555 END IF
556
557 IF (PRESENT(mol_to_first_atom)) THEN
558 mol_to_first_atom(imol) = first_atom
559 END IF
560
561 IF (PRESENT(mol_to_last_atom)) THEN
562 mol_to_last_atom(imol) = last_atom
563 END IF
564
565 IF (PRESENT(atom_to_mol)) THEN
566 DO iatom = first_atom, last_atom
567 atom_to_mol(iatom) = imol
568 END DO ! iatom
569 END IF
570
571 END DO ! imol
572
573 END SUBROUTINE get_molecule_set_info
574
575! **************************************************************************************************
576!> \brief ...
577!> \param molecule_set ...
578!> \param atom_to_mol ...
579!> \param mol_to_first_atom ...
580!> \param mol_to_last_atom ...
581!> \param mol_to_nelectrons ...
582!> \param mol_to_nbasis ...
583!> \param mol_to_charge ...
584!> \param mol_to_multiplicity ...
585! **************************************************************************************************
586 SUBROUTINE get_domain_set_info(molecule_set, atom_to_mol, mol_to_first_atom, &
587 mol_to_last_atom, mol_to_nelectrons, mol_to_nbasis, mol_to_charge, &
588 mol_to_multiplicity)
589
590 TYPE(molecule_type), DIMENSION(:), INTENT(IN) :: molecule_set
591 INTEGER, DIMENSION(:), INTENT(OUT), OPTIONAL :: atom_to_mol, mol_to_first_atom, &
592 mol_to_last_atom, mol_to_nelectrons, mol_to_nbasis, mol_to_charge, mol_to_multiplicity
593
594 INTEGER :: first_atom, iatom, imol, last_atom, &
595 nbasis, nelec
596 REAL(kind=dp) :: charge
597 TYPE(molecule_kind_type), POINTER :: imol_kind
598
599 DO imol = 1, SIZE(molecule_set)
600
601 CALL get_molecule(molecule=molecule_set(imol), molecule_kind=imol_kind, &
602 first_atom=first_atom, last_atom=last_atom)
603
604 IF (PRESENT(mol_to_nelectrons)) THEN
605 CALL get_molecule_kind(imol_kind, nelectron=nelec)
606 mol_to_nelectrons(imol) = nelec
607 END IF
608
609 IF (PRESENT(mol_to_multiplicity)) THEN
610 ! RZK-warning: At the moment we can only get the total number
611 ! of electrons (alpha+beta) and we do not have a way to get the multiplicity of mols.
612 ! Therefore, the best we can do is to assume the singlet state for even number of electrons
613 ! and doublet state for odd number of electrons (assume ne_alpha > ne_beta).
614 ! The best way to implement a correct multiplicity subroutine in the future is to get
615 ! the number of alpha and beta e- for each atom from init_atom_electronic_state. This way (as opposed to
616 ! reading the multiplicities from file) the number of occupied and virtual orbitals
617 ! will be consistent with atomic guess. A guess with broken symmetry will be easy to
618 ! implement as well.
619 CALL get_molecule_kind(imol_kind, nelectron=nelec)
620 IF (mod(nelec, 2) == 0) THEN
621 mol_to_multiplicity(imol) = 1
622 ELSE
623 mol_to_multiplicity(imol) = 2
624 END IF
625 END IF
626
627 IF (PRESENT(mol_to_charge)) THEN
628 CALL get_molecule_kind(imol_kind, charge=charge)
629 mol_to_charge(imol) = nint(charge)
630 END IF
631
632 IF (PRESENT(mol_to_nbasis)) THEN
633 CALL get_molecule_kind(imol_kind, nsgf=nbasis)
634 mol_to_nbasis(imol) = nbasis
635 END IF
636
637 IF (PRESENT(mol_to_first_atom)) THEN
638 mol_to_first_atom(imol) = first_atom
639 END IF
640
641 IF (PRESENT(mol_to_last_atom)) THEN
642 mol_to_last_atom(imol) = last_atom
643 END IF
644
645 IF (PRESENT(atom_to_mol)) THEN
646 DO iatom = first_atom, last_atom
647 atom_to_mol(iatom) = imol
648 END DO ! iatom
649 END IF
650
651 END DO ! imol
652
653 END SUBROUTINE get_domain_set_info
654
655END MODULE molecule_types
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:1186
kinds
Defines the basic variable types.
Definition kinds.F:23
kinds::dp
integer, parameter, public dp
Definition kinds.F:34
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:513
molecule_types
Define the data structure for the molecule information.
Definition molecule_types.F:16
molecule_types::deallocate_molecule_set
subroutine, public deallocate_molecule_set(molecule_set)
Deallocate a molecule set.
Definition molecule_types.F:274
molecule_types::get_domain_set_info
subroutine, public get_domain_set_info(molecule_set, atom_to_mol, mol_to_first_atom, mol_to_last_atom, mol_to_nelectrons, mol_to_nbasis, mol_to_charge, mol_to_multiplicity)
...
Definition molecule_types.F:589
molecule_types::deallocate_global_constraint
subroutine, public deallocate_global_constraint(gci)
Deallocate a global constraint.
Definition molecule_types.F:202
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:332
molecule_types::allocate_molecule_set
subroutine, public allocate_molecule_set(molecule_set, nmolecule)
Allocate a molecule set.
Definition molecule_types.F:257
molecule_types::molecule_of_atom
subroutine, public molecule_of_atom(molecule_set, atom_to_mol)
finds for each atom the molecule it belongs to
Definition molecule_types.F:478
molecule_types::set_molecule_set
subroutine, public set_molecule_set(molecule_set, first_atom, last_atom)
Set a molecule data set.
Definition molecule_types.F:441
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:392
molecule_types::get_molecule_set_info
subroutine, public get_molecule_set_info(molecule_set, atom_to_mol, mol_to_first_atom, mol_to_last_atom, mol_to_nelectrons, mol_to_nbasis, mol_to_charge, mol_to_multiplicity)
returns information about molecules in the set.
Definition molecule_types.F:509
colvar_types::colvar_counters
Definition colvar_types.F:388
colvar_types::colvar_type
parameters for a collective variable
Definition colvar_types.F:346
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::local_states_type
Definition molecule_types.F:120
molecule_types::molecule_type
Definition molecule_types.F:159