(git:ccc2433)
molecule_types.F
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1 !--------------------------------------------------------------------------------------------------!
2 ! CP2K: A general program to perform molecular dynamics simulations !
3 ! Copyright 2000-2024 CP2K developers group <https://cp2k.org> !
4 ! !
5 ! SPDX-License-Identifier: GPL-2.0-or-later !
6 !--------------------------------------------------------------------------------------------------!
7 
8 ! **************************************************************************************************
9 !> \brief 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 MK (29.08.2003)
15 ! **************************************************************************************************
16 MODULE 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 ! *** Data types ***
40 ! **************************************************************************************************
41  TYPE local_colvar_constraint_type
42  LOGICAL :: init = .false.
43  TYPE(colvar_type), POINTER :: colvar => null()
44  TYPE(colvar_type), POINTER :: colvar_old => null()
45  REAL(KIND=dp) :: lambda = 0.0_dp, sigma = 0.0_dp
46  END TYPE local_colvar_constraint_type
47 
48 ! **************************************************************************************************
49  TYPE local_g3x3_constraint_type
50  LOGICAL :: init = .false.
51  REAL(KIND=dp) :: scale = 0.0_dp, scale_old = 0.0_dp, &
52  imass1 = 0.0_dp, imass2 = 0.0_dp, imass3 = 0.0_dp
53  REAL(KIND=dp), DIMENSION(3) :: fa = 0.0_dp, fb = 0.0_dp, fc = 0.0_dp, &
54  f_roll1 = 0.0_dp, f_roll2 = 0.0_dp, f_roll3 = 0.0_dp, &
55  ra_old = 0.0_dp, rb_old = 0.0_dp, rc_old = 0.0_dp, &
56  va = 0.0_dp, vb = 0.0_dp, vc = 0.0_dp, &
57  lambda = 0.0_dp, del_lambda = 0.0_dp, lambda_old = 0.0_dp, &
58  r0_12 = 0.0_dp, r0_13 = 0.0_dp, r0_23 = 0.0_dp
59  REAL(KIND=dp), DIMENSION(3, 3) :: amat = 0.0_dp
60  END TYPE local_g3x3_constraint_type
61 
62 ! **************************************************************************************************
63  TYPE local_g4x6_constraint_type
64  LOGICAL :: init = .false.
65  REAL(KIND=dp) :: scale = 0.0_dp, scale_old = 0.0_dp, imass1 = 0.0_dp, &
66  imass2 = 0.0_dp, imass3 = 0.0_dp, imass4 = 0.0_dp
67  REAL(KIND=dp), DIMENSION(3) :: fa = 0.0_dp, fb = 0.0_dp, fc = 0.0_dp, fd = 0.0_dp, fe = 0.0_dp, ff = 0.0_dp, &
68  f_roll1 = 0.0_dp, f_roll2 = 0.0_dp, f_roll3 = 0.0_dp, &
69  f_roll4 = 0.0_dp, f_roll5 = 0.0_dp, f_roll6 = 0.0_dp, &
70  ra_old = 0.0_dp, rb_old = 0.0_dp, rc_old = 0.0_dp, &
71  rd_old = 0.0_dp, re_old = 0.0_dp, rf_old = 0.0_dp, &
72  va = 0.0_dp, vb = 0.0_dp, vc = 0.0_dp, vd = 0.0_dp, ve = 0.0_dp, vf = 0.0_dp, &
73  r0_12 = 0.0_dp, r0_13 = 0.0_dp, r0_14 = 0.0_dp, &
74  r0_23 = 0.0_dp, r0_24 = 0.0_dp, r0_34 = 0.0_dp
75  REAL(KIND=dp), DIMENSION(6) :: lambda = 0.0_dp, del_lambda = 0.0_dp, lambda_old = 0.0_dp
76  REAL(KIND=dp), DIMENSION(6, 6) :: amat = 0.0_dp
77  END TYPE local_g4x6_constraint_type
78 
79 ! **************************************************************************************************
80  TYPE local_states_type
81  INTEGER, DIMENSION(:), POINTER :: states => null() ! indices of Kohn-Sham states for molecule
82  INTEGER :: nstates = 0 ! Kohn-Sham states for molecule
83  END TYPE local_states_type
84 
85 ! **************************************************************************************************
86  TYPE local_constraint_type
87  TYPE(local_colvar_constraint_type), DIMENSION(:), POINTER :: lcolv => null()
88  TYPE(local_g3x3_constraint_type), DIMENSION(:), POINTER :: lg3x3 => null()
89  TYPE(local_g4x6_constraint_type), DIMENSION(:), POINTER :: lg4x6 => null()
90  END TYPE local_constraint_type
91 
92 ! **************************************************************************************************
93  TYPE global_constraint_type
94  TYPE(colvar_counters) :: ncolv = colvar_counters()
95  INTEGER :: ntot = 0, nrestraint = 0
96  INTEGER :: ng3x3 = 0, ng3x3_restraint = 0
97  INTEGER :: ng4x6 = 0, ng4x6_restraint = 0
98  INTEGER :: nvsite = 0, nvsite_restraint = 0
99  TYPE(fixd_constraint_type), DIMENSION(:), POINTER :: fixd_list => null()
100  TYPE(colvar_constraint_type), DIMENSION(:), POINTER :: colv_list => null()
101  TYPE(g3x3_constraint_type), DIMENSION(:), POINTER :: g3x3_list => null()
102  TYPE(g4x6_constraint_type), DIMENSION(:), POINTER :: g4x6_list => null()
103  TYPE(vsite_constraint_type), DIMENSION(:), POINTER :: vsite_list => null()
104  TYPE(local_colvar_constraint_type), DIMENSION(:), POINTER :: lcolv => null()
105  TYPE(local_g3x3_constraint_type), DIMENSION(:), POINTER :: lg3x3 => null()
106  TYPE(local_g4x6_constraint_type), DIMENSION(:), POINTER :: lg4x6 => null()
107  END TYPE global_constraint_type
108 
109 ! **************************************************************************************************
110  TYPE molecule_type
111  TYPE(molecule_kind_type), POINTER :: molecule_kind => null() ! pointer to molecule kind information
112  TYPE(local_states_type), DIMENSION(:), POINTER :: lmi => null() ! local (spin)-states information
113  TYPE(local_constraint_type), POINTER :: lci => null() ! local molecule constraint info
114  INTEGER :: first_atom = 0 ! global index of first atom in molecule
115  INTEGER :: last_atom = 0 ! global index of last atom in molecule
116  INTEGER :: first_shell = 0 ! global index of first shell atom in molecule
117  INTEGER :: last_shell = 0 ! global index of last shell atom in molecule
118  END TYPE molecule_type
119 
120 ! *** Public data types ***
121 
122  PUBLIC :: local_colvar_constraint_type, &
123  local_g3x3_constraint_type, &
124  local_g4x6_constraint_type, &
125  local_constraint_type, &
126  local_states_type, &
127  global_constraint_type, &
128  molecule_type
129 
130 ! *** Public subroutines ***
131 
132  PUBLIC :: deallocate_global_constraint, &
133  allocate_molecule_set, &
134  deallocate_molecule_set, &
135  get_molecule, &
136  set_molecule, &
137  set_molecule_set, &
138  molecule_of_atom, &
139  get_molecule_set_info
140 
141 CONTAINS
142 
143 ! **************************************************************************************************
144 !> \brief Deallocate a global constraint.
145 !> \param gci ...
146 !> \par History
147 !> 07.2003 created [fawzi]
148 !> 01.2014 moved from cp_subsys_release() into separate routine.
149 !> \author Ole Schuett
150 ! **************************************************************************************************
151  SUBROUTINE deallocate_global_constraint(gci)
152  TYPE(global_constraint_type), POINTER :: gci
153 
154  INTEGER :: i
155 
156  IF (ASSOCIATED(gci)) THEN
157  ! List of constraints
158  IF (ASSOCIATED(gci%colv_list)) THEN
159  DO i = 1, SIZE(gci%colv_list)
160  DEALLOCATE (gci%colv_list(i)%i_atoms)
161  END DO
162  DEALLOCATE (gci%colv_list)
163  END IF
164 
165  IF (ASSOCIATED(gci%g3x3_list)) &
166  DEALLOCATE (gci%g3x3_list)
167 
168  IF (ASSOCIATED(gci%g4x6_list)) &
169  DEALLOCATE (gci%g4x6_list)
170 
171  ! Local information
172  IF (ASSOCIATED(gci%lcolv)) THEN
173  DO i = 1, SIZE(gci%lcolv)
174  CALL colvar_release(gci%lcolv(i)%colvar)
175  CALL colvar_release(gci%lcolv(i)%colvar_old)
176  END DO
177  DEALLOCATE (gci%lcolv)
178  END IF
179 
180  IF (ASSOCIATED(gci%lg3x3)) &
181  DEALLOCATE (gci%lg3x3)
182 
183  IF (ASSOCIATED(gci%lg4x6)) &
184  DEALLOCATE (gci%lg4x6)
185 
186  IF (ASSOCIATED(gci%fixd_list)) &
187  DEALLOCATE (gci%fixd_list)
188 
189  DEALLOCATE (gci)
190  END IF
191  END SUBROUTINE deallocate_global_constraint
192 
193 ! **************************************************************************************************
194 !> \brief Allocate a molecule set.
195 !> \param molecule_set ...
196 !> \param nmolecule ...
197 !> \date 29.08.2003
198 !> \author MK
199 !> \version 1.0
200 ! **************************************************************************************************
201  SUBROUTINE allocate_molecule_set(molecule_set, nmolecule)
202  TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
203  INTEGER, INTENT(IN) :: nmolecule
204 
205  IF (ASSOCIATED(molecule_set)) CALL deallocate_molecule_set(molecule_set)
206 
207  ALLOCATE (molecule_set(nmolecule))
208 
209  END SUBROUTINE allocate_molecule_set
210 
211 ! **************************************************************************************************
212 !> \brief Deallocate a molecule set.
213 !> \param molecule_set ...
214 !> \date 29.08.2003
215 !> \author MK
216 !> \version 1.0
217 ! **************************************************************************************************
218  SUBROUTINE deallocate_molecule_set(molecule_set)
219  TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
220 
221  INTEGER :: imolecule, j
222 
223  IF (ASSOCIATED(molecule_set)) THEN
224 
225  DO imolecule = 1, SIZE(molecule_set)
226  IF (ASSOCIATED(molecule_set(imolecule)%lmi)) THEN
227  DO j = 1, SIZE(molecule_set(imolecule)%lmi)
228  IF (ASSOCIATED(molecule_set(imolecule)%lmi(j)%states)) THEN
229  DEALLOCATE (molecule_set(imolecule)%lmi(j)%states)
230  END IF
231  END DO
232  DEALLOCATE (molecule_set(imolecule)%lmi)
233  END IF
234  IF (ASSOCIATED(molecule_set(imolecule)%lci)) THEN
235  IF (ASSOCIATED(molecule_set(imolecule)%lci%lcolv)) THEN
236  DO j = 1, SIZE(molecule_set(imolecule)%lci%lcolv)
237  CALL colvar_release(molecule_set(imolecule)%lci%lcolv(j)%colvar)
238  CALL colvar_release(molecule_set(imolecule)%lci%lcolv(j)%colvar_old)
239  END DO
240  DEALLOCATE (molecule_set(imolecule)%lci%lcolv)
241  END IF
242  IF (ASSOCIATED(molecule_set(imolecule)%lci%lg3x3)) THEN
243  DEALLOCATE (molecule_set(imolecule)%lci%lg3x3)
244  END IF
245  IF (ASSOCIATED(molecule_set(imolecule)%lci%lg4x6)) THEN
246  DEALLOCATE (molecule_set(imolecule)%lci%lg4x6)
247  END IF
248  DEALLOCATE (molecule_set(imolecule)%lci)
249  END IF
250  END DO
251  DEALLOCATE (molecule_set)
252 
253  END IF
254  NULLIFY (molecule_set)
255 
256  END SUBROUTINE deallocate_molecule_set
257 
258 ! **************************************************************************************************
259 !> \brief Get components from a molecule data set.
260 !> \param molecule ...
261 !> \param molecule_kind ...
262 !> \param lmi ...
263 !> \param lci ...
264 !> \param lg3x3 ...
265 !> \param lg4x6 ...
266 !> \param lcolv ...
267 !> \param first_atom ...
268 !> \param last_atom ...
269 !> \param first_shell ...
270 !> \param last_shell ...
271 !> \date 29.08.2003
272 !> \author MK
273 !> \version 1.0
274 ! **************************************************************************************************
275  SUBROUTINE get_molecule(molecule, molecule_kind, lmi, lci, lg3x3, lg4x6, lcolv, &
276  first_atom, last_atom, first_shell, last_shell)
277 
278  TYPE(molecule_type), INTENT(IN) :: molecule
279  TYPE(molecule_kind_type), OPTIONAL, POINTER :: molecule_kind
280  TYPE(local_states_type), DIMENSION(:), OPTIONAL, &
281  POINTER :: lmi
282  TYPE(local_constraint_type), OPTIONAL, POINTER :: lci
283  TYPE(local_g3x3_constraint_type), OPTIONAL, &
284  POINTER :: lg3x3(:)
285  TYPE(local_g4x6_constraint_type), OPTIONAL, &
286  POINTER :: lg4x6(:)
287  TYPE(local_colvar_constraint_type), DIMENSION(:), &
288  OPTIONAL, POINTER :: lcolv
289  INTEGER, OPTIONAL :: first_atom, last_atom, first_shell, &
290  last_shell
291 
292  IF (PRESENT(first_atom)) first_atom = molecule%first_atom
293  IF (PRESENT(last_atom)) last_atom = molecule%last_atom
294  IF (PRESENT(first_shell)) first_shell = molecule%first_shell
295  IF (PRESENT(last_shell)) last_shell = molecule%last_shell
296  IF (PRESENT(molecule_kind)) molecule_kind => molecule%molecule_kind
297  IF (PRESENT(lmi)) lmi => molecule%lmi
298  IF (PRESENT(lci)) lci => molecule%lci
299  IF (PRESENT(lcolv)) THEN
300  IF (ASSOCIATED(molecule%lci)) THEN
301  lcolv => molecule%lci%lcolv
302  ELSE
303  cpabort("The pointer lci is not associated")
304  END IF
305  END IF
306  IF (PRESENT(lg3x3)) THEN
307  IF (ASSOCIATED(molecule%lci)) THEN
308  lg3x3 => molecule%lci%lg3x3
309  ELSE
310  cpabort("The pointer lci is not associated")
311  END IF
312  END IF
313  IF (PRESENT(lg4x6)) THEN
314  IF (ASSOCIATED(molecule%lci)) THEN
315  lg4x6 => molecule%lci%lg4x6
316  ELSE
317  cpabort("The pointer lci is not associated")
318  END IF
319  END IF
320 
321  END SUBROUTINE get_molecule
322 
323 ! **************************************************************************************************
324 !> \brief Set a molecule data set.
325 !> \param molecule ...
326 !> \param molecule_kind ...
327 !> \param lmi ...
328 !> \param lci ...
329 !> \param lcolv ...
330 !> \param lg3x3 ...
331 !> \param lg4x6 ...
332 !> \date 29.08.2003
333 !> \author MK
334 !> \version 1.0
335 ! **************************************************************************************************
336  SUBROUTINE set_molecule(molecule, molecule_kind, lmi, lci, lcolv, lg3x3, lg4x6)
337  TYPE(molecule_type), INTENT(INOUT) :: molecule
338  TYPE(molecule_kind_type), OPTIONAL, POINTER :: molecule_kind
339  TYPE(local_states_type), DIMENSION(:), OPTIONAL, &
340  POINTER :: lmi
341  TYPE(local_constraint_type), OPTIONAL, POINTER :: lci
342  TYPE(local_colvar_constraint_type), DIMENSION(:), &
343  OPTIONAL, POINTER :: lcolv
344  TYPE(local_g3x3_constraint_type), OPTIONAL, &
345  POINTER :: lg3x3(:)
346  TYPE(local_g4x6_constraint_type), OPTIONAL, &
347  POINTER :: lg4x6(:)
348 
349  IF (PRESENT(molecule_kind)) molecule%molecule_kind => molecule_kind
350  IF (PRESENT(lmi)) molecule%lmi => lmi
351  IF (PRESENT(lci)) molecule%lci => lci
352  IF (PRESENT(lcolv)) THEN
353  IF (ASSOCIATED(molecule%lci)) THEN
354  molecule%lci%lcolv => lcolv
355  ELSE
356  cpabort("The pointer lci is not associated")
357  END IF
358  END IF
359  IF (PRESENT(lg3x3)) THEN
360  IF (ASSOCIATED(molecule%lci)) THEN
361  molecule%lci%lg3x3 => lg3x3
362  ELSE
363  cpabort("The pointer lci is not associated")
364  END IF
365  END IF
366  IF (PRESENT(lg4x6)) THEN
367  IF (ASSOCIATED(molecule%lci)) THEN
368  molecule%lci%lg4x6 => lg4x6
369  ELSE
370  cpabort("The pointer lci is not associated")
371  END IF
372  END IF
373 
374  END SUBROUTINE set_molecule
375 
376 ! **************************************************************************************************
377 !> \brief Set a molecule data set.
378 !> \param molecule_set ...
379 !> \param first_atom ...
380 !> \param last_atom ...
381 !> \date 29.08.2003
382 !> \author MK
383 !> \version 1.0
384 ! **************************************************************************************************
385  SUBROUTINE set_molecule_set(molecule_set, first_atom, last_atom)
386  TYPE(molecule_type), DIMENSION(:), INTENT(INOUT) :: molecule_set
387  INTEGER, DIMENSION(:), INTENT(IN), OPTIONAL :: first_atom, last_atom
388 
389  INTEGER :: imolecule
390 
391  IF (PRESENT(first_atom)) THEN
392  IF (SIZE(first_atom) /= SIZE(molecule_set)) THEN
393  CALL cp_abort(__location__, &
394  "The sizes of first_atom and molecule_set "// &
395  "are different")
396  END IF
397 
398  DO imolecule = 1, SIZE(molecule_set)
399  molecule_set(imolecule)%first_atom = first_atom(imolecule)
400  END DO
401  END IF
402 
403  IF (PRESENT(last_atom)) THEN
404  IF (SIZE(last_atom) /= SIZE(molecule_set)) THEN
405  CALL cp_abort(__location__, &
406  "The sizes of last_atom and molecule_set "// &
407  "are different")
408  END IF
409 
410  DO imolecule = 1, SIZE(molecule_set)
411  molecule_set(imolecule)%last_atom = last_atom(imolecule)
412  END DO
413  END IF
414 
415  END SUBROUTINE set_molecule_set
416 
417 ! **************************************************************************************************
418 !> \brief finds for each atom the molecule it belongs to
419 !> \param molecule_set ...
420 !> \param atom_to_mol ...
421 ! **************************************************************************************************
422  SUBROUTINE molecule_of_atom(molecule_set, atom_to_mol)
423  TYPE(molecule_type), DIMENSION(:), INTENT(IN) :: molecule_set
424  INTEGER, DIMENSION(:), INTENT(OUT) :: atom_to_mol
425 
426  INTEGER :: first_atom, iatom, imol, last_atom
427 
428  DO imol = 1, SIZE(molecule_set)
429  CALL get_molecule(molecule=molecule_set(imol), first_atom=first_atom, last_atom=last_atom)
430  DO iatom = first_atom, last_atom
431  atom_to_mol(iatom) = imol
432  END DO ! iatom
433  END DO ! imol
434 
435  END SUBROUTINE molecule_of_atom
436 
437 ! **************************************************************************************************
438 !> \brief returns information about molecules in the set.
439 !> \param molecule_set ...
440 !> \param atom_to_mol ...
441 !> \param mol_to_first_atom ...
442 !> \param mol_to_last_atom ...
443 !> \param mol_to_nelectrons ...
444 !> \param mol_to_nbasis ...
445 !> \param mol_to_charge ...
446 !> \param mol_to_multiplicity ...
447 !> \par History
448 !> 2011.06 created [Rustam Z Khaliullin]
449 !> \author Rustam Z Khaliullin
450 ! **************************************************************************************************
451  SUBROUTINE get_molecule_set_info(molecule_set, atom_to_mol, mol_to_first_atom, &
452  mol_to_last_atom, mol_to_nelectrons, mol_to_nbasis, mol_to_charge, &
453  mol_to_multiplicity)
454 
455  TYPE(molecule_type), DIMENSION(:), INTENT(IN) :: molecule_set
456  INTEGER, DIMENSION(:), INTENT(OUT), OPTIONAL :: atom_to_mol, mol_to_first_atom, &
457  mol_to_last_atom, mol_to_nelectrons, mol_to_nbasis, mol_to_charge, mol_to_multiplicity
458 
459  INTEGER :: first_atom, iatom, imol, last_atom, &
460  nbasis, nelec
461  REAL(kind=dp) :: charge
462  TYPE(molecule_kind_type), POINTER :: imol_kind
463 
464  DO imol = 1, SIZE(molecule_set)
465 
466  CALL get_molecule(molecule=molecule_set(imol), molecule_kind=imol_kind, &
467  first_atom=first_atom, last_atom=last_atom)
468 
469  IF (PRESENT(mol_to_nelectrons)) THEN
470  CALL get_molecule_kind(imol_kind, nelectron=nelec)
471  mol_to_nelectrons(imol) = nelec
472  END IF
473 
474  IF (PRESENT(mol_to_multiplicity)) THEN
475  ! RZK-warning: At the moment we can only get the total number
476  ! of electrons (alpha+beta) and we do not have a way to get the multiplicity of mols.
477  ! Therefore, the best we can do is to assume the singlet state for even number of electrons
478  ! and doublet state for odd number of electrons (assume ne_alpha > ne_beta).
479  ! The best way to implement a correct multiplicity subroutine in the future is to get
480  ! the number of alpha and beta e- for each atom from init_atom_electronic_state. This way (as opposed to
481  ! reading the multiplicities from file) the number of occupied and virtual orbitals
482  ! will be consistent with atomic guess. A guess with broken symmetry will be easy to
483  ! implement as well.
484  CALL get_molecule_kind(imol_kind, nelectron=nelec)
485  IF (mod(nelec, 2) .EQ. 0) THEN
486  mol_to_multiplicity(imol) = 1
487  ELSE
488  mol_to_multiplicity(imol) = 2
489  END IF
490  END IF
491 
492  IF (PRESENT(mol_to_charge)) THEN
493  CALL get_molecule_kind(imol_kind, charge=charge)
494  mol_to_charge(imol) = nint(charge)
495  END IF
496 
497  IF (PRESENT(mol_to_nbasis)) THEN
498  CALL get_molecule_kind(imol_kind, nsgf=nbasis)
499  mol_to_nbasis(imol) = nbasis
500  END IF
501 
502  IF (PRESENT(mol_to_first_atom)) THEN
503  mol_to_first_atom(imol) = first_atom
504  END IF
505 
506  IF (PRESENT(mol_to_last_atom)) THEN
507  mol_to_last_atom(imol) = last_atom
508  END IF
509 
510  IF (PRESENT(atom_to_mol)) THEN
511  DO iatom = first_atom, last_atom
512  atom_to_mol(iatom) = imol
513  END DO ! iatom
514  END IF
515 
516  END DO ! imol
517 
518  END SUBROUTINE get_molecule_set_info
519 
520 END 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:1176
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:510
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:219
molecule_types::deallocate_global_constraint
subroutine, public deallocate_global_constraint(gci)
Deallocate a global constraint.
Definition: molecule_types.F:152
molecule_types::get_molecule
subroutine, public get_molecule(molecule, molecule_kind, lmi, lci, lg3x3, lg4x6, lcolv, first_atom, last_atom, first_shell, last_shell)
Get components from a molecule data set.
Definition: molecule_types.F:277
molecule_types::allocate_molecule_set
subroutine, public allocate_molecule_set(molecule_set, nmolecule)
Allocate a molecule set.
Definition: molecule_types.F:202
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:423
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:386
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:337
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:454