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topology_types.F
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1!--------------------------------------------------------------------------------------------------!
2! CP2K: A general program to perform molecular dynamics simulations !
3! Copyright 2000-2024 CP2K developers group <https://cp2k.org> !
4! !
5! SPDX-License-Identifier: GPL-2.0-or-later !
6!--------------------------------------------------------------------------------------------------!
7
8! **************************************************************************************************
9!> \par History
10!> JGH (30.11.2001) : new entries in setup_parameters_type
11!> change name from input_file_name to coord_...
12!> added topology file
13!> added atom_names
14!> Teodoro Laino [tlaino] 12.2008 - Preparing for VIRTUAL SITE constraints
15!> (patch by Marcel Baer)
16!> \author CJM & JGH
17! **************************************************************************************************
18MODULE topology_types
19 USE cell_types, ONLY: cell_release,&
20 cell_type
21 USE colvar_types, ONLY: colvar_p_type,&
22 colvar_release
23 USE input_constants, ONLY: do_bondparm_covalent,&
24 do_conn_generate,&
25 do_constr_none,&
26 do_skip_13
27 USE kinds, ONLY: default_path_length,&
28 default_string_length,&
29 dp
30#include "./base/base_uses.f90"
31
32 IMPLICIT NONE
33
34! **************************************************************************************************
35 TYPE atom_info_type
36 INTEGER, DIMENSION(:), POINTER :: id_molname
37 INTEGER, DIMENSION(:), POINTER :: id_resname
38 INTEGER, DIMENSION(:), POINTER :: id_atmname
39 INTEGER, DIMENSION(:), POINTER :: id_atom_names
40 INTEGER, DIMENSION(:), POINTER :: id_element
41 INTEGER, POINTER :: resid(:)
42 REAL(kind=dp), DIMENSION(:, :), POINTER :: r
43 INTEGER, POINTER :: map_mol_typ(:)
44 INTEGER, POINTER :: map_mol_num(:)
45 INTEGER, POINTER :: map_mol_res(:)
46 REAL(kind=dp), POINTER :: atm_charge(:)
47 REAL(kind=dp), POINTER :: atm_mass(:)
48 REAL(kind=dp), POINTER :: occup(:)
49 REAL(kind=dp), POINTER :: beta(:)
50 END TYPE atom_info_type
51
52! **************************************************************************************************
53 TYPE connectivity_info_type
54 INTEGER, POINTER :: bond_a(:), bond_b(:), bond_type(:)
55 INTEGER, POINTER :: ub_a(:), ub_b(:), ub_c(:)
56 INTEGER, POINTER :: theta_a(:), theta_b(:), theta_c(:), theta_type(:)
57 INTEGER, POINTER :: phi_a(:), phi_b(:), phi_c(:), phi_d(:), phi_type(:)
58 INTEGER, POINTER :: impr_a(:), impr_b(:), impr_c(:), impr_d(:), impr_type(:)
59 INTEGER, POINTER :: onfo_a(:), onfo_b(:)
60 INTEGER, POINTER :: c_bond_a(:), c_bond_b(:), c_bond_type(:)
61 END TYPE connectivity_info_type
62
63! **************************************************************************************************
64 TYPE constraint_info_type
65 ! Bonds involving Hydrogens
66 LOGICAL :: hbonds_restraint ! Restraints control
67 REAL(kind=dp) :: hbonds_k0 ! Restraints control
68 ! Fixed Atoms
69 INTEGER :: nfixed_atoms
70 INTEGER, POINTER :: fixed_atoms(:), fixed_type(:), fixed_mol_type(:)
71 LOGICAL, POINTER :: fixed_restraint(:) ! Restraints control
72 REAL(kind=dp), POINTER :: fixed_k0(:) ! Restraints control
73 ! Freeze QM or MM
74 INTEGER :: freeze_qm, freeze_mm, freeze_qm_type, freeze_mm_type
75 LOGICAL :: fixed_mm_restraint, fixed_qm_restraint ! Restraints control
76 REAL(kind=dp) :: fixed_mm_k0, fixed_qm_k0 ! Restraints control
77 ! Freeze with molnames
78 LOGICAL, POINTER :: fixed_mol_restraint(:) ! Restraints control
79 REAL(kind=dp), POINTER :: fixed_mol_k0(:) ! Restraints control
80 CHARACTER(LEN=default_string_length), POINTER :: fixed_molnames(:)
81 LOGICAL, POINTER, DIMENSION(:) :: fixed_exclude_qm, fixed_exclude_mm
82 ! Collective constraints
83 INTEGER :: nconst_colv
84 INTEGER, POINTER :: const_colv_mol(:)
85 CHARACTER(LEN=default_string_length), POINTER :: const_colv_molname(:)
86 REAL(kind=dp), POINTER :: const_colv_target(:)
87 REAL(kind=dp), POINTER :: const_colv_target_growth(:)
88 TYPE(colvar_p_type), POINTER, DIMENSION(:) :: colvar_set
89 LOGICAL, POINTER :: colv_intermolecular(:)
90 LOGICAL, POINTER :: colv_restraint(:) ! Restraints control
91 REAL(kind=dp), POINTER :: colv_k0(:) ! Restraints control
92 LOGICAL, POINTER, DIMENSION(:) :: colv_exclude_qm, colv_exclude_mm
93 ! G3x3
94 INTEGER :: nconst_g33
95 INTEGER, POINTER :: const_g33_mol(:)
96 CHARACTER(LEN=default_string_length), POINTER :: const_g33_molname(:)
97 INTEGER, POINTER :: const_g33_a(:)
98 INTEGER, POINTER :: const_g33_b(:)
99 INTEGER, POINTER :: const_g33_c(:)
100 REAL(kind=dp), POINTER :: const_g33_dab(:)
101 REAL(kind=dp), POINTER :: const_g33_dac(:)
102 REAL(kind=dp), POINTER :: const_g33_dbc(:)
103 LOGICAL, POINTER :: g33_intermolecular(:)
104 LOGICAL, POINTER :: g33_restraint(:) ! Restraints control
105 REAL(kind=dp), POINTER :: g33_k0(:) ! Restraints control
106 LOGICAL, POINTER, DIMENSION(:) :: g33_exclude_qm, g33_exclude_mm
107 ! G4x6
108 INTEGER :: nconst_g46
109 INTEGER, POINTER :: const_g46_mol(:)
110 CHARACTER(LEN=default_string_length), POINTER :: const_g46_molname(:)
111 INTEGER, POINTER :: const_g46_a(:)
112 INTEGER, POINTER :: const_g46_b(:)
113 INTEGER, POINTER :: const_g46_c(:)
114 INTEGER, POINTER :: const_g46_d(:)
115 REAL(kind=dp), POINTER :: const_g46_dab(:)
116 REAL(kind=dp), POINTER :: const_g46_dac(:)
117 REAL(kind=dp), POINTER :: const_g46_dbc(:)
118 REAL(kind=dp), POINTER :: const_g46_dad(:)
119 REAL(kind=dp), POINTER :: const_g46_dbd(:)
120 REAL(kind=dp), POINTER :: const_g46_dcd(:)
121 LOGICAL, POINTER :: g46_intermolecular(:)
122 LOGICAL, POINTER :: g46_restraint(:) ! Restraints control
123 REAL(kind=dp), POINTER :: g46_k0(:) ! Restraints control
124 LOGICAL, POINTER, DIMENSION(:) :: g46_exclude_qm, g46_exclude_mm
125 ! virtual_site
126 INTEGER :: nconst_vsite
127 INTEGER, POINTER :: const_vsite_mol(:)
128 CHARACTER(LEN=default_string_length), POINTER :: const_vsite_molname(:)
129 INTEGER, POINTER :: const_vsite_a(:)
130 INTEGER, POINTER :: const_vsite_b(:)
131 INTEGER, POINTER :: const_vsite_c(:)
132 INTEGER, POINTER :: const_vsite_d(:)
133 REAL(kind=dp), POINTER :: const_vsite_wbc(:)
134 REAL(kind=dp), POINTER :: const_vsite_wdc(:)
135 LOGICAL, POINTER :: vsite_intermolecular(:)
136 LOGICAL, POINTER :: vsite_restraint(:) ! Restraints control
137 REAL(kind=dp), POINTER :: vsite_k0(:) ! Restraints control
138 LOGICAL, POINTER, DIMENSION(:) :: vsite_exclude_qm, vsite_exclude_mm
139 END TYPE constraint_info_type
140
141! **************************************************************************************************
142 TYPE topology_parameters_type
143 TYPE(atom_info_type), POINTER :: atom_info
144 TYPE(connectivity_info_type), POINTER :: conn_info
145 TYPE(constraint_info_type), POINTER :: cons_info
146 TYPE(cell_type), POINTER :: cell, cell_ref, cell_muc
147 INTEGER :: conn_type
148 INTEGER :: coord_type
149 INTEGER :: exclude_vdw
150 INTEGER :: exclude_ei
151 INTEGER :: bondparm_type
152 !TRY TO REMOVE THIS FIVE VARIABLE IN THE FUTURE
153 INTEGER :: natoms, natom_type
154 INTEGER :: nmol, nmol_type, nmol_conn
155 !TRY TO REMOVE THIS FIVE VARIABLE IN THE FUTURE
156 LOGICAL :: aa_element
157 LOGICAL :: molname_generated
158 REAL(kind=dp) :: bondparm_factor
159 LOGICAL :: create_molecules
160 LOGICAL :: reorder_atom
161 LOGICAL :: molecules_check
162 LOGICAL :: coordinate
163 LOGICAL :: use_g96_velocity
164 CHARACTER(LEN=default_path_length) :: coord_file_name
165 CHARACTER(LEN=default_path_length) :: conn_file_name
166 LOGICAL :: const_atom
167 LOGICAL :: const_hydr
168 LOGICAL :: const_colv
169 LOGICAL :: const_33
170 LOGICAL :: const_46
171 LOGICAL :: const_vsite
172 LOGICAL :: charge_occup
173 LOGICAL :: charge_beta
174 LOGICAL :: charge_extended
175 LOGICAL :: para_res
176 END TYPE topology_parameters_type
177
178! **************************************************************************************************
179 TYPE constr_list_type
180 INTEGER, DIMENSION(:), POINTER :: constr
181 END TYPE constr_list_type
182
183 PUBLIC :: atom_info_type, &
184 connectivity_info_type, &
185 constraint_info_type, &
186 topology_parameters_type, &
187 constr_list_type
188
189 PUBLIC :: init_topology, &
190 deallocate_topology, &
191 pre_read_topology
192
193 CHARACTER(len=*), PARAMETER, PRIVATE :: modulen = 'topology_types'
194 PRIVATE
195
196CONTAINS
197
198! **************************************************************************************************
199!> \brief 1. Just NULLIFY and zero all the stuff
200!> \param topology ...
201!> \par History
202!> none
203! **************************************************************************************************
204 SUBROUTINE init_topology(topology)
205 TYPE(topology_parameters_type), INTENT(INOUT) :: topology
206
207!-----------------------------------------------------------------------------
208! 1. Nullify and allocate things in topology
209!-----------------------------------------------------------------------------
210
211 ALLOCATE (topology%atom_info)
212 ALLOCATE (topology%conn_info)
213 ALLOCATE (topology%cons_info)
214 !-----------------------------------------------------------------------------
215 ! 2. Initialize and Nullify things in topology
216 !-----------------------------------------------------------------------------
217 NULLIFY (topology%cell, topology%cell_ref, topology%cell_muc)
218 topology%natoms = 0
219 topology%natom_type = 0
220 topology%nmol = 0
221 topology%nmol_type = 0
222 topology%nmol_conn = 0
223 topology%bondparm_type = do_bondparm_covalent
224 topology%reorder_atom = .false.
225 topology%create_molecules = .false.
226 topology%molecules_check = .false.
227 topology%coordinate = .false.
228 topology%use_g96_velocity = .false.
229 topology%coord_type = -1
230 topology%coord_file_name = ''
231 topology%conn_type = do_conn_generate
232 topology%conn_file_name = 'OFF'
233 topology%const_atom = .false.
234 topology%const_hydr = .false.
235 topology%const_colv = .false.
236 topology%const_33 = .false.
237 topology%const_46 = .false.
238 topology%const_vsite = .false.
239 topology%charge_occup = .false.
240 topology%charge_beta = .false.
241 topology%charge_extended = .false.
242 topology%para_res = .false.
243 topology%molname_generated = .false.
244 topology%aa_element = .false.
245 topology%exclude_vdw = do_skip_13
246 topology%exclude_ei = do_skip_13
247 !-----------------------------------------------------------------------------
248 ! 3. Initialize and Nullify things in topology%atom_info
249 !-----------------------------------------------------------------------------
250 NULLIFY (topology%atom_info%id_molname)
251 NULLIFY (topology%atom_info%id_resname)
252 NULLIFY (topology%atom_info%resid)
253 NULLIFY (topology%atom_info%id_atmname)
254 NULLIFY (topology%atom_info%id_atom_names)
255 NULLIFY (topology%atom_info%r)
256 NULLIFY (topology%atom_info%map_mol_typ)
257 NULLIFY (topology%atom_info%map_mol_num)
258 NULLIFY (topology%atom_info%map_mol_res)
259 NULLIFY (topology%atom_info%atm_charge)
260 NULLIFY (topology%atom_info%atm_mass)
261 NULLIFY (topology%atom_info%occup)
262 NULLIFY (topology%atom_info%beta)
263 NULLIFY (topology%atom_info%id_element)
264 !-----------------------------------------------------------------------------
265 ! 4. Initialize and Nullify things in topology%conn_info
266 !-----------------------------------------------------------------------------
267 NULLIFY (topology%conn_info%bond_a)
268 NULLIFY (topology%conn_info%bond_b)
269 NULLIFY (topology%conn_info%bond_type)
270 NULLIFY (topology%conn_info%ub_a)
271 NULLIFY (topology%conn_info%ub_b)
272 NULLIFY (topology%conn_info%ub_c)
273 NULLIFY (topology%conn_info%theta_a)
274 NULLIFY (topology%conn_info%theta_b)
275 NULLIFY (topology%conn_info%theta_c)
276 NULLIFY (topology%conn_info%theta_type)
277 NULLIFY (topology%conn_info%phi_a)
278 NULLIFY (topology%conn_info%phi_b)
279 NULLIFY (topology%conn_info%phi_c)
280 NULLIFY (topology%conn_info%phi_d)
281 NULLIFY (topology%conn_info%phi_type)
282 NULLIFY (topology%conn_info%impr_a)
283 NULLIFY (topology%conn_info%impr_b)
284 NULLIFY (topology%conn_info%impr_c)
285 NULLIFY (topology%conn_info%impr_d)
286 NULLIFY (topology%conn_info%impr_type)
287 NULLIFY (topology%conn_info%onfo_a)
288 NULLIFY (topology%conn_info%onfo_b)
289 NULLIFY (topology%conn_info%c_bond_a)
290 NULLIFY (topology%conn_info%c_bond_b)
291 NULLIFY (topology%conn_info%c_bond_type)
292 !-----------------------------------------------------------------------------
293 ! 5. Initialize and Nullify things in topology%cons_info
294 !-----------------------------------------------------------------------------
295 CALL init_constraint(topology%cons_info)
296 END SUBROUTINE init_topology
297
298! **************************************************************************************************
299!> \brief 1. Just NULLIFY and zero all the stuff
300!> \param constraint_info ...
301!> \par History
302!> none
303! **************************************************************************************************
304 SUBROUTINE init_constraint(constraint_info)
305 TYPE(constraint_info_type), POINTER :: constraint_info
306
307! Bonds involving Hydrogens
308
309 constraint_info%hbonds_restraint = .false.
310 ! Fixed Atoms
311 constraint_info%nfixed_atoms = 0
312 constraint_info%freeze_mm = do_constr_none
313 constraint_info%freeze_qm = do_constr_none
314 NULLIFY (constraint_info%fixed_atoms)
315 NULLIFY (constraint_info%fixed_type)
316 NULLIFY (constraint_info%fixed_mol_type)
317 NULLIFY (constraint_info%fixed_molnames)
318 NULLIFY (constraint_info%fixed_restraint)
319 NULLIFY (constraint_info%fixed_k0)
320 NULLIFY (constraint_info%fixed_mol_restraint)
321 NULLIFY (constraint_info%fixed_mol_k0)
322 NULLIFY (constraint_info%fixed_exclude_qm, constraint_info%fixed_exclude_mm)
323 ! Collective Constraints
324 constraint_info%nconst_colv = 0
325 NULLIFY (constraint_info%colvar_set)
326 NULLIFY (constraint_info%const_colv_mol)
327 NULLIFY (constraint_info%const_colv_molname)
328 NULLIFY (constraint_info%const_colv_target)
329 NULLIFY (constraint_info%const_colv_target_growth)
330 NULLIFY (constraint_info%colv_intermolecular)
331 NULLIFY (constraint_info%colv_restraint)
332 NULLIFY (constraint_info%colv_k0)
333 NULLIFY (constraint_info%colv_exclude_qm, constraint_info%colv_exclude_mm)
334 ! G3x3
335 constraint_info%nconst_g33 = 0
336 NULLIFY (constraint_info%const_g33_mol)
337 NULLIFY (constraint_info%const_g33_molname)
338 NULLIFY (constraint_info%const_g33_a)
339 NULLIFY (constraint_info%const_g33_b)
340 NULLIFY (constraint_info%const_g33_c)
341 NULLIFY (constraint_info%const_g33_dab)
342 NULLIFY (constraint_info%const_g33_dac)
343 NULLIFY (constraint_info%const_g33_dbc)
344 NULLIFY (constraint_info%g33_intermolecular)
345 NULLIFY (constraint_info%g33_restraint)
346 NULLIFY (constraint_info%g33_k0)
347 NULLIFY (constraint_info%g33_exclude_qm, constraint_info%g33_exclude_mm)
348 ! G4x6
349 constraint_info%nconst_g46 = 0
350 NULLIFY (constraint_info%const_g46_mol)
351 NULLIFY (constraint_info%const_g46_molname)
352 NULLIFY (constraint_info%const_g46_a)
353 NULLIFY (constraint_info%const_g46_b)
354 NULLIFY (constraint_info%const_g46_c)
355 NULLIFY (constraint_info%const_g46_d)
356 NULLIFY (constraint_info%const_g46_dab)
357 NULLIFY (constraint_info%const_g46_dac)
358 NULLIFY (constraint_info%const_g46_dbc)
359 NULLIFY (constraint_info%const_g46_dad)
360 NULLIFY (constraint_info%const_g46_dbd)
361 NULLIFY (constraint_info%const_g46_dcd)
362 NULLIFY (constraint_info%g46_intermolecular)
363 NULLIFY (constraint_info%g46_restraint)
364 NULLIFY (constraint_info%g46_k0)
365 NULLIFY (constraint_info%g46_exclude_qm, constraint_info%g46_exclude_mm)
366 ! virtual_site
367 constraint_info%nconst_vsite = 0
368 NULLIFY (constraint_info%const_vsite_mol)
369 NULLIFY (constraint_info%const_vsite_molname)
370 NULLIFY (constraint_info%const_vsite_a)
371 NULLIFY (constraint_info%const_vsite_b)
372 NULLIFY (constraint_info%const_vsite_c)
373 NULLIFY (constraint_info%const_vsite_d)
374 NULLIFY (constraint_info%const_vsite_wbc)
375 NULLIFY (constraint_info%const_vsite_wdc)
376 NULLIFY (constraint_info%vsite_intermolecular)
377 NULLIFY (constraint_info%vsite_restraint)
378 NULLIFY (constraint_info%vsite_k0)
379 NULLIFY (constraint_info%vsite_exclude_qm, constraint_info%vsite_exclude_mm)
380
381 END SUBROUTINE init_constraint
382
383! **************************************************************************************************
384!> \brief 1. Just DEALLOCATE all the stuff
385!> \param topology ...
386!> \par History
387!> none
388! **************************************************************************************************
389 SUBROUTINE deallocate_topology(topology)
390 TYPE(topology_parameters_type), INTENT(INOUT) :: topology
391
392!-----------------------------------------------------------------------------
393! 1. DEALLOCATE things in topology%atom_info
394!-----------------------------------------------------------------------------
395
396 IF (ASSOCIATED(topology%atom_info%id_molname)) THEN
397 DEALLOCATE (topology%atom_info%id_molname)
398 END IF
399 IF (ASSOCIATED(topology%atom_info%id_resname)) THEN
400 DEALLOCATE (topology%atom_info%id_resname)
401 END IF
402 IF (ASSOCIATED(topology%atom_info%resid)) THEN
403 DEALLOCATE (topology%atom_info%resid)
404 END IF
405 IF (ASSOCIATED(topology%atom_info%id_atmname)) THEN
406 DEALLOCATE (topology%atom_info%id_atmname)
407 END IF
408 IF (ASSOCIATED(topology%atom_info%id_atom_names)) THEN
409 DEALLOCATE (topology%atom_info%id_atom_names)
410 END IF
411 IF (ASSOCIATED(topology%atom_info%r)) THEN
412 DEALLOCATE (topology%atom_info%r)
413 END IF
414 IF (ASSOCIATED(topology%atom_info%map_mol_typ)) THEN
415 DEALLOCATE (topology%atom_info%map_mol_typ)
416 END IF
417 IF (ASSOCIATED(topology%atom_info%map_mol_num)) THEN
418 DEALLOCATE (topology%atom_info%map_mol_num)
419 END IF
420 IF (ASSOCIATED(topology%atom_info%map_mol_res)) THEN
421 DEALLOCATE (topology%atom_info%map_mol_res)
422 END IF
423 IF (ASSOCIATED(topology%atom_info%atm_charge)) THEN
424 DEALLOCATE (topology%atom_info%atm_charge)
425 END IF
426 IF (ASSOCIATED(topology%atom_info%atm_mass)) THEN
427 DEALLOCATE (topology%atom_info%atm_mass)
428 END IF
429 IF (ASSOCIATED(topology%atom_info%occup)) THEN
430 DEALLOCATE (topology%atom_info%occup)
431 END IF
432 IF (ASSOCIATED(topology%atom_info%beta)) THEN
433 DEALLOCATE (topology%atom_info%beta)
434 END IF
435 IF (ASSOCIATED(topology%atom_info%id_element)) THEN
436 DEALLOCATE (topology%atom_info%id_element)
437 END IF
438 !-----------------------------------------------------------------------------
439 ! 2. DEALLOCATE things in topology%conn_info
440 !-----------------------------------------------------------------------------
441 IF (ASSOCIATED(topology%conn_info%bond_a)) THEN
442 DEALLOCATE (topology%conn_info%bond_a)
443 END IF
444 IF (ASSOCIATED(topology%conn_info%bond_b)) THEN
445 DEALLOCATE (topology%conn_info%bond_b)
446 END IF
447 IF (ASSOCIATED(topology%conn_info%bond_type)) THEN
448 DEALLOCATE (topology%conn_info%bond_type)
449 END IF
450 IF (ASSOCIATED(topology%conn_info%ub_a)) THEN
451 DEALLOCATE (topology%conn_info%ub_a)
452 END IF
453 IF (ASSOCIATED(topology%conn_info%ub_b)) THEN
454 DEALLOCATE (topology%conn_info%ub_b)
455 END IF
456 IF (ASSOCIATED(topology%conn_info%ub_c)) THEN
457 DEALLOCATE (topology%conn_info%ub_c)
458 END IF
459 IF (ASSOCIATED(topology%conn_info%theta_a)) THEN
460 DEALLOCATE (topology%conn_info%theta_a)
461 END IF
462 IF (ASSOCIATED(topology%conn_info%theta_b)) THEN
463 DEALLOCATE (topology%conn_info%theta_b)
464 END IF
465 IF (ASSOCIATED(topology%conn_info%theta_c)) THEN
466 DEALLOCATE (topology%conn_info%theta_c)
467 END IF
468 IF (ASSOCIATED(topology%conn_info%theta_type)) THEN
469 DEALLOCATE (topology%conn_info%theta_type)
470 END IF
471 IF (ASSOCIATED(topology%conn_info%phi_a)) THEN
472 DEALLOCATE (topology%conn_info%phi_a)
473 END IF
474 IF (ASSOCIATED(topology%conn_info%phi_b)) THEN
475 DEALLOCATE (topology%conn_info%phi_b)
476 END IF
477 IF (ASSOCIATED(topology%conn_info%phi_c)) THEN
478 DEALLOCATE (topology%conn_info%phi_c)
479 END IF
480 IF (ASSOCIATED(topology%conn_info%phi_d)) THEN
481 DEALLOCATE (topology%conn_info%phi_d)
482 END IF
483 IF (ASSOCIATED(topology%conn_info%phi_type)) THEN
484 DEALLOCATE (topology%conn_info%phi_type)
485 END IF
486 IF (ASSOCIATED(topology%conn_info%impr_a)) THEN
487 DEALLOCATE (topology%conn_info%impr_a)
488 END IF
489 IF (ASSOCIATED(topology%conn_info%impr_b)) THEN
490 DEALLOCATE (topology%conn_info%impr_b)
491 END IF
492 IF (ASSOCIATED(topology%conn_info%impr_c)) THEN
493 DEALLOCATE (topology%conn_info%impr_c)
494 END IF
495 IF (ASSOCIATED(topology%conn_info%impr_d)) THEN
496 DEALLOCATE (topology%conn_info%impr_d)
497 END IF
498 IF (ASSOCIATED(topology%conn_info%impr_type)) THEN
499 DEALLOCATE (topology%conn_info%impr_type)
500 END IF
501 IF (ASSOCIATED(topology%conn_info%onfo_a)) THEN
502 DEALLOCATE (topology%conn_info%onfo_a)
503 END IF
504 IF (ASSOCIATED(topology%conn_info%onfo_b)) THEN
505 DEALLOCATE (topology%conn_info%onfo_b)
506 END IF
507 IF (ASSOCIATED(topology%conn_info%c_bond_a)) THEN
508 DEALLOCATE (topology%conn_info%c_bond_a)
509 END IF
510 IF (ASSOCIATED(topology%conn_info%c_bond_b)) THEN
511 DEALLOCATE (topology%conn_info%c_bond_b)
512 END IF
513 IF (ASSOCIATED(topology%conn_info%c_bond_type)) THEN
514 DEALLOCATE (topology%conn_info%c_bond_type)
515 END IF
516 !-----------------------------------------------------------------------------
517 ! 3. DEALLOCATE things in topology%cons_info
518 !-----------------------------------------------------------------------------
519 IF (ASSOCIATED(topology%cons_info)) &
520 CALL deallocate_constraint(topology%cons_info)
521 !-----------------------------------------------------------------------------
522 ! 4. DEALLOCATE things in topology
523 !-----------------------------------------------------------------------------
524 CALL cell_release(topology%cell)
525 CALL cell_release(topology%cell_ref)
526 CALL cell_release(topology%cell_muc)
527 IF (ASSOCIATED(topology%atom_info)) THEN
528 DEALLOCATE (topology%atom_info)
529 END IF
530 IF (ASSOCIATED(topology%conn_info)) THEN
531 DEALLOCATE (topology%conn_info)
532 END IF
533 IF (ASSOCIATED(topology%cons_info)) THEN
534 DEALLOCATE (topology%cons_info)
535 END IF
536
537 END SUBROUTINE deallocate_topology
538
539! **************************************************************************************************
540!> \brief 1. Just DEALLOCATE all the stuff
541!> \param constraint_info ...
542!> \par History
543!> none
544! **************************************************************************************************
545 SUBROUTINE deallocate_constraint(constraint_info)
546 TYPE(constraint_info_type), POINTER :: constraint_info
547
548 INTEGER :: i
549
550! Fixed Atoms
551
552 IF (ASSOCIATED(constraint_info%fixed_atoms)) THEN
553 DEALLOCATE (constraint_info%fixed_atoms)
554 END IF
555 IF (ASSOCIATED(constraint_info%fixed_type)) THEN
556 DEALLOCATE (constraint_info%fixed_type)
557 END IF
558 IF (ASSOCIATED(constraint_info%fixed_molnames)) THEN
559 DEALLOCATE (constraint_info%fixed_molnames)
560 END IF
561 IF (ASSOCIATED(constraint_info%fixed_mol_type)) THEN
562 DEALLOCATE (constraint_info%fixed_mol_type)
563 END IF
564 IF (ASSOCIATED(constraint_info%fixed_restraint)) THEN
565 DEALLOCATE (constraint_info%fixed_restraint)
566 END IF
567 IF (ASSOCIATED(constraint_info%fixed_k0)) THEN
568 DEALLOCATE (constraint_info%fixed_k0)
569 END IF
570 IF (ASSOCIATED(constraint_info%fixed_mol_restraint)) THEN
571 DEALLOCATE (constraint_info%fixed_mol_restraint)
572 END IF
573 IF (ASSOCIATED(constraint_info%fixed_mol_k0)) THEN
574 DEALLOCATE (constraint_info%fixed_mol_k0)
575 END IF
576 IF (ASSOCIATED(constraint_info%fixed_exclude_qm)) THEN
577 DEALLOCATE (constraint_info%fixed_exclude_qm)
578 END IF
579 IF (ASSOCIATED(constraint_info%fixed_exclude_mm)) THEN
580 DEALLOCATE (constraint_info%fixed_exclude_mm)
581 END IF
582 ! Collective Constraint
583 IF (ASSOCIATED(constraint_info%colvar_set)) THEN
584 DO i = 1, SIZE(constraint_info%colvar_set)
585 IF (ASSOCIATED(constraint_info%colvar_set(i)%colvar)) THEN
586 CALL colvar_release(constraint_info%colvar_set(i)%colvar)
587 NULLIFY (constraint_info%colvar_set(i)%colvar)
588 END IF
589 END DO
590 DEALLOCATE (constraint_info%colvar_set)
591 END IF
592 IF (ASSOCIATED(constraint_info%const_colv_mol)) THEN
593 DEALLOCATE (constraint_info%const_colv_mol)
594 END IF
595 IF (ASSOCIATED(constraint_info%const_colv_molname)) THEN
596 DEALLOCATE (constraint_info%const_colv_molname)
597 END IF
598 IF (ASSOCIATED(constraint_info%const_colv_target)) THEN
599 DEALLOCATE (constraint_info%const_colv_target)
600 END IF
601 IF (ASSOCIATED(constraint_info%const_colv_target_growth)) THEN
602 DEALLOCATE (constraint_info%const_colv_target_growth)
603 END IF
604 IF (ASSOCIATED(constraint_info%colv_intermolecular)) THEN
605 DEALLOCATE (constraint_info%colv_intermolecular)
606 END IF
607 IF (ASSOCIATED(constraint_info%colv_restraint)) THEN
608 DEALLOCATE (constraint_info%colv_restraint)
609 END IF
610 IF (ASSOCIATED(constraint_info%colv_k0)) THEN
611 DEALLOCATE (constraint_info%colv_k0)
612 END IF
613 IF (ASSOCIATED(constraint_info%colv_exclude_qm)) THEN
614 DEALLOCATE (constraint_info%colv_exclude_qm)
615 END IF
616 IF (ASSOCIATED(constraint_info%colv_exclude_mm)) THEN
617 DEALLOCATE (constraint_info%colv_exclude_mm)
618 END IF
619 ! G3x3
620 IF (ASSOCIATED(constraint_info%const_g33_mol)) THEN
621 DEALLOCATE (constraint_info%const_g33_mol)
622 END IF
623 IF (ASSOCIATED(constraint_info%const_g33_molname)) THEN
624 DEALLOCATE (constraint_info%const_g33_molname)
625 END IF
626 IF (ASSOCIATED(constraint_info%const_g33_a)) THEN
627 DEALLOCATE (constraint_info%const_g33_a)
628 END IF
629 IF (ASSOCIATED(constraint_info%const_g33_b)) THEN
630 DEALLOCATE (constraint_info%const_g33_b)
631 END IF
632 IF (ASSOCIATED(constraint_info%const_g33_c)) THEN
633 DEALLOCATE (constraint_info%const_g33_c)
634 END IF
635 IF (ASSOCIATED(constraint_info%const_g33_dab)) THEN
636 DEALLOCATE (constraint_info%const_g33_dab)
637 END IF
638 IF (ASSOCIATED(constraint_info%const_g33_dac)) THEN
639 DEALLOCATE (constraint_info%const_g33_dac)
640 END IF
641 IF (ASSOCIATED(constraint_info%const_g33_dbc)) THEN
642 DEALLOCATE (constraint_info%const_g33_dbc)
643 END IF
644 IF (ASSOCIATED(constraint_info%g33_intermolecular)) THEN
645 DEALLOCATE (constraint_info%g33_intermolecular)
646 END IF
647 IF (ASSOCIATED(constraint_info%g33_restraint)) THEN
648 DEALLOCATE (constraint_info%g33_restraint)
649 END IF
650 IF (ASSOCIATED(constraint_info%g33_k0)) THEN
651 DEALLOCATE (constraint_info%g33_k0)
652 END IF
653 IF (ASSOCIATED(constraint_info%g33_exclude_qm)) THEN
654 DEALLOCATE (constraint_info%g33_exclude_qm)
655 END IF
656 IF (ASSOCIATED(constraint_info%g33_exclude_mm)) THEN
657 DEALLOCATE (constraint_info%g33_exclude_mm)
658 END IF
659 ! G4x6
660 IF (ASSOCIATED(constraint_info%const_g46_mol)) THEN
661 DEALLOCATE (constraint_info%const_g46_mol)
662 END IF
663 IF (ASSOCIATED(constraint_info%const_g46_molname)) THEN
664 DEALLOCATE (constraint_info%const_g46_molname)
665 END IF
666 IF (ASSOCIATED(constraint_info%const_g46_a)) THEN
667 DEALLOCATE (constraint_info%const_g46_a)
668 END IF
669 IF (ASSOCIATED(constraint_info%const_g46_b)) THEN
670 DEALLOCATE (constraint_info%const_g46_b)
671 END IF
672 IF (ASSOCIATED(constraint_info%const_g46_c)) THEN
673 DEALLOCATE (constraint_info%const_g46_c)
674 END IF
675 IF (ASSOCIATED(constraint_info%const_g46_d)) THEN
676 DEALLOCATE (constraint_info%const_g46_d)
677 END IF
678 IF (ASSOCIATED(constraint_info%const_g46_dab)) THEN
679 DEALLOCATE (constraint_info%const_g46_dab)
680 END IF
681 IF (ASSOCIATED(constraint_info%const_g46_dac)) THEN
682 DEALLOCATE (constraint_info%const_g46_dac)
683 END IF
684 IF (ASSOCIATED(constraint_info%const_g46_dbc)) THEN
685 DEALLOCATE (constraint_info%const_g46_dbc)
686 END IF
687 IF (ASSOCIATED(constraint_info%const_g46_dad)) THEN
688 DEALLOCATE (constraint_info%const_g46_dad)
689 END IF
690 IF (ASSOCIATED(constraint_info%const_g46_dbd)) THEN
691 DEALLOCATE (constraint_info%const_g46_dbd)
692 END IF
693 IF (ASSOCIATED(constraint_info%const_g46_dcd)) THEN
694 DEALLOCATE (constraint_info%const_g46_dcd)
695 END IF
696 IF (ASSOCIATED(constraint_info%g46_intermolecular)) THEN
697 DEALLOCATE (constraint_info%g46_intermolecular)
698 END IF
699 IF (ASSOCIATED(constraint_info%g46_restraint)) THEN
700 DEALLOCATE (constraint_info%g46_restraint)
701 END IF
702 IF (ASSOCIATED(constraint_info%g46_k0)) THEN
703 DEALLOCATE (constraint_info%g46_k0)
704 END IF
705 IF (ASSOCIATED(constraint_info%g46_exclude_qm)) THEN
706 DEALLOCATE (constraint_info%g46_exclude_qm)
707 END IF
708 IF (ASSOCIATED(constraint_info%g46_exclude_mm)) THEN
709 DEALLOCATE (constraint_info%g46_exclude_mm)
710 END IF
711 ! virtual_site
712 IF (ASSOCIATED(constraint_info%const_vsite_mol)) THEN
713 DEALLOCATE (constraint_info%const_vsite_mol)
714 END IF
715 IF (ASSOCIATED(constraint_info%const_vsite_molname)) THEN
716 DEALLOCATE (constraint_info%const_vsite_molname)
717 END IF
718 IF (ASSOCIATED(constraint_info%const_vsite_a)) THEN
719 DEALLOCATE (constraint_info%const_vsite_a)
720 END IF
721 IF (ASSOCIATED(constraint_info%const_vsite_b)) THEN
722 DEALLOCATE (constraint_info%const_vsite_b)
723 END IF
724 IF (ASSOCIATED(constraint_info%const_vsite_c)) THEN
725 DEALLOCATE (constraint_info%const_vsite_c)
726 END IF
727 IF (ASSOCIATED(constraint_info%const_vsite_d)) THEN
728 DEALLOCATE (constraint_info%const_vsite_d)
729 END IF
730 IF (ASSOCIATED(constraint_info%const_vsite_wbc)) THEN
731 DEALLOCATE (constraint_info%const_vsite_wbc)
732 END IF
733 IF (ASSOCIATED(constraint_info%const_vsite_wdc)) THEN
734 DEALLOCATE (constraint_info%const_vsite_wdc)
735 END IF
736 IF (ASSOCIATED(constraint_info%vsite_intermolecular)) THEN
737 DEALLOCATE (constraint_info%vsite_intermolecular)
738 END IF
739 IF (ASSOCIATED(constraint_info%vsite_restraint)) THEN
740 DEALLOCATE (constraint_info%vsite_restraint)
741 END IF
742 IF (ASSOCIATED(constraint_info%vsite_k0)) THEN
743 DEALLOCATE (constraint_info%vsite_k0)
744 END IF
745 IF (ASSOCIATED(constraint_info%vsite_exclude_qm)) THEN
746 DEALLOCATE (constraint_info%vsite_exclude_qm)
747 END IF
748 IF (ASSOCIATED(constraint_info%vsite_exclude_mm)) THEN
749 DEALLOCATE (constraint_info%vsite_exclude_mm)
750 END IF
751 END SUBROUTINE deallocate_constraint
752
753! **************************************************************************************************
754!> \brief Deallocate possibly allocated arrays before reading topology
755!> \param topology ...
756!> \par History
757!> none
758! **************************************************************************************************
759 SUBROUTINE pre_read_topology(topology)
760 TYPE(topology_parameters_type), INTENT(INOUT) :: topology
761
762 TYPE(atom_info_type), POINTER :: atom_info
763
764 atom_info => topology%atom_info
765
766 IF (ASSOCIATED(atom_info%id_molname)) THEN
767 DEALLOCATE (atom_info%id_molname)
768 END IF
769
770 IF (ASSOCIATED(atom_info%resid)) THEN
771 DEALLOCATE (atom_info%resid)
772 END IF
773
774 IF (ASSOCIATED(atom_info%id_resname)) THEN
775 DEALLOCATE (atom_info%id_resname)
776 END IF
777
778 IF (ASSOCIATED(atom_info%id_atmname)) THEN
779 DEALLOCATE (atom_info%id_atmname)
780 END IF
781
782 IF (ASSOCIATED(atom_info%atm_charge)) THEN
783 DEALLOCATE (atom_info%atm_charge)
784 END IF
785
786 IF (ASSOCIATED(atom_info%atm_mass)) THEN
787 DEALLOCATE (atom_info%atm_mass)
788 END IF
789
790 END SUBROUTINE pre_read_topology
791
792END MODULE topology_types
cell_types
Handles all functions related to the CELL.
Definition cell_types.F:15
cell_types::cell_release
subroutine, public cell_release(cell)
releases the given cell (see doc/ReferenceCounting.html)
Definition cell_types.F:559
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
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_skip_13
integer, parameter, public do_skip_13
Definition input_constants.F:412
input_constants::do_bondparm_covalent
integer, parameter, public do_bondparm_covalent
Definition input_constants.F:412
input_constants::do_conn_generate
integer, parameter, public do_conn_generate
Definition input_constants.F:412
input_constants::do_constr_none
integer, parameter, public do_constr_none
Definition input_constants.F:79
kinds
Defines the basic variable types.
Definition kinds.F:23
kinds::dp
integer, parameter, public dp
Definition kinds.F:34
kinds::default_string_length
integer, parameter, public default_string_length
Definition kinds.F:57
kinds::default_path_length
integer, parameter, public default_path_length
Definition kinds.F:58
topology_types
Definition topology_types.F:18
topology_types::deallocate_topology
subroutine, public deallocate_topology(topology)
Just DEALLOCATE all the stuff
Definition topology_types.F:390
topology_types::pre_read_topology
subroutine, public pre_read_topology(topology)
Deallocate possibly allocated arrays before reading topology.
Definition topology_types.F:760
topology_types::init_topology
subroutine, public init_topology(topology)
Just NULLIFY and zero all the stuff
Definition topology_types.F:205
topology
Control for reading in different topologies and coordinates.
Definition topology.F:13
cell_types::cell_type
Type defining parameters related to the simulation cell.
Definition cell_types.F:55
colvar_types::colvar_p_type
Definition colvar_types.F:383
topology_types::atom_info_type
Definition topology_types.F:35
topology_types::connectivity_info_type
Definition topology_types.F:53
topology_types::constr_list_type
Definition topology_types.F:179
topology_types::constraint_info_type
Definition topology_types.F:64
topology_types::topology_parameters_type
Definition topology_types.F:142