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molecule_kind_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 molecule kind structure types and the corresponding
10 !> functionality
11 !> \par History
12 !> Teodoro Laino [tlaino] 12.2008 - Preparing for VIRTUAL SITE constraints
13 !> (patch by Marcel Baer)
14 !> \author MK (22.08.2003)
15 ! **************************************************************************************************
16 MODULE molecule_kind_types
17  USE atomic_kind_types, ONLY: atomic_kind_type,&
18  get_atomic_kind
19  USE cell_types, ONLY: use_perd_x,&
20  use_perd_xy,&
21  use_perd_xyz,&
22  use_perd_xz,&
23  use_perd_y,&
24  use_perd_yz,&
25  use_perd_z
26  USE colvar_types, ONLY: &
27  acid_hyd_dist_colvar_id, acid_hyd_shell_colvar_id, angle_colvar_id, colvar_counters, &
28  combine_colvar_id, coord_colvar_id, dfunct_colvar_id, dist_colvar_id, gyration_colvar_id, &
29  hydronium_dist_colvar_id, hydronium_shell_colvar_id, no_colvar_id, &
30  plane_distance_colvar_id, plane_plane_angle_colvar_id, population_colvar_id, &
31  qparm_colvar_id, reaction_path_colvar_id, rotation_colvar_id, torsion_colvar_id, &
32  xyz_diag_colvar_id, xyz_outerdiag_colvar_id
33  USE cp_log_handling, ONLY: cp_get_default_logger,&
34  cp_logger_type
35  USE cp_output_handling, ONLY: cp_print_key_finished_output,&
36  cp_print_key_unit_nr
37  USE force_field_kind_types, ONLY: &
38  bend_kind_type, bond_kind_type, do_ff_undef, impr_kind_dealloc_ref, impr_kind_type, &
39  opbend_kind_type, torsion_kind_dealloc_ref, torsion_kind_type, ub_kind_dealloc_ref, &
40  ub_kind_type
41  USE input_section_types, ONLY: section_vals_type
42  USE kinds, ONLY: default_string_length,&
43  dp
44  USE shell_potential_types, ONLY: shell_kind_type
45 #include "../base/base_uses.f90"
46 
47  IMPLICIT NONE
48 
49  PRIVATE
50 
51  CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'molecule_kind_types'
52 
53 ! *** Define the derived structure types ***
54 
55 ! **************************************************************************************************
56  TYPE atom_type
57  TYPE(atomic_kind_type), POINTER :: atomic_kind => null()
58  INTEGER :: id_name = 0
59  END TYPE atom_type
60 
61 ! **************************************************************************************************
62  TYPE shell_type
63  INTEGER :: a = 0
64  CHARACTER(LEN=default_string_length) :: name = ""
65  TYPE(shell_kind_type), POINTER :: shell_kind => null()
66  END TYPE shell_type
67 
68 ! **************************************************************************************************
69  TYPE bond_type
70  INTEGER :: a = 0, b = 0
71  INTEGER :: id_type = do_ff_undef, itype = 0
72  TYPE(bond_kind_type), POINTER :: bond_kind => null()
73  END TYPE bond_type
74 
75 ! **************************************************************************************************
76  TYPE bend_type
77  INTEGER :: a = 0, b = 0, c = 0
78  INTEGER :: id_type = do_ff_undef, itype = 0
79  TYPE(bend_kind_type), POINTER :: bend_kind => null()
80  END TYPE bend_type
81 
82 ! **************************************************************************************************
83  TYPE ub_type
84  INTEGER :: a = 0, b = 0, c = 0
85  INTEGER :: id_type = do_ff_undef, itype = 0
86  TYPE(ub_kind_type), POINTER :: ub_kind => null()
87  END TYPE ub_type
88 
89 ! **************************************************************************************************
90  TYPE torsion_type
91  INTEGER :: a = 0, b = 0, c = 0, d = 0
92  INTEGER :: id_type = do_ff_undef, itype = 0
93  TYPE(torsion_kind_type), POINTER :: torsion_kind => null()
94  END TYPE torsion_type
95 
96 ! **************************************************************************************************
97  TYPE impr_type
98  INTEGER :: a = 0, b = 0, c = 0, d = 0
99  INTEGER :: id_type = do_ff_undef, itype = 0
100  TYPE(impr_kind_type), POINTER :: impr_kind => null()
101  END TYPE impr_type
102 
103 ! **************************************************************************************************
104  TYPE opbend_type
105  INTEGER :: a = 0, b = 0, c = 0, d = 0
106  INTEGER :: id_type = do_ff_undef, itype = 0
107  TYPE(opbend_kind_type), POINTER :: opbend_kind => null()
108  END TYPE opbend_type
109 
110 ! **************************************************************************************************
111  TYPE restraint_type
112  LOGICAL :: active = .false.
113  REAL(KIND=dp) :: k0 = 0.0_dp
114  END TYPE restraint_type
115 
116 ! **************************************************************************************************
117  TYPE colvar_constraint_type
118  INTEGER :: type_id = no_colvar_id
119  INTEGER :: inp_seq_num = 0
120  LOGICAL :: use_points = .false.
121  REAL(KIND=dp) :: expected_value = 0.0_dp
122  REAL(KIND=dp) :: expected_value_growth_speed = 0.0_dp
123  INTEGER, POINTER, DIMENSION(:) :: i_atoms => null()
124  TYPE(restraint_type) :: restraint = restraint_type()
125  END TYPE colvar_constraint_type
126 
127 ! **************************************************************************************************
128  TYPE g3x3_constraint_type
129  INTEGER :: a = 0, b = 0, c = 0
130  REAL(KIND=dp) :: dab = 0.0_dp, dac = 0.0_dp, dbc = 0.0_dp
131  TYPE(restraint_type) :: restraint = restraint_type()
132  END TYPE g3x3_constraint_type
133 
134 ! **************************************************************************************************
135  TYPE g4x6_constraint_type
136  INTEGER :: a = 0, b = 0, c = 0, d = 0
137  REAL(KIND=dp) :: dab = 0.0_dp, dac = 0.0_dp, dbc = 0.0_dp, dad = 0.0_dp, dbd = 0.0_dp, dcd = 0.0_dp
138  TYPE(restraint_type) :: restraint = restraint_type()
139  END TYPE g4x6_constraint_type
140 
141 ! **************************************************************************************************
142  TYPE vsite_constraint_type
143  INTEGER :: a = 0, b = 0, c = 0, d = 0
144  REAL(KIND=dp) :: wbc = 0.0_dp, wdc = 0.0_dp
145  TYPE(restraint_type) :: restraint = restraint_type()
146  END TYPE vsite_constraint_type
147 
148 ! **************************************************************************************************
149  TYPE fixd_constraint_type
150  TYPE(restraint_type) :: restraint = restraint_type()
151  INTEGER :: fixd = 0, itype = 0
152  REAL(KIND=dp), DIMENSION(3) :: coord = 0.0_dp
153  END TYPE fixd_constraint_type
154 
155 ! **************************************************************************************************
156  TYPE local_fixd_constraint_type
157  INTEGER :: ifixd_index = 0, ikind = 0
158  END TYPE local_fixd_constraint_type
159 
160 ! **************************************************************************************************
161  TYPE molecule_kind_type
162  TYPE(atom_type), DIMENSION(:), POINTER :: atom_list => null()
163  TYPE(bond_kind_type), DIMENSION(:), POINTER :: bond_kind_set => null()
164  TYPE(bond_type), DIMENSION(:), POINTER :: bond_list => null()
165  TYPE(bend_kind_type), DIMENSION(:), POINTER :: bend_kind_set => null()
166  TYPE(bend_type), DIMENSION(:), POINTER :: bend_list => null()
167  TYPE(ub_kind_type), DIMENSION(:), POINTER :: ub_kind_set => null()
168  TYPE(ub_type), DIMENSION(:), POINTER :: ub_list => null()
169  TYPE(torsion_kind_type), DIMENSION(:), POINTER :: torsion_kind_set => null()
170  TYPE(torsion_type), DIMENSION(:), POINTER :: torsion_list => null()
171  TYPE(impr_kind_type), DIMENSION(:), POINTER :: impr_kind_set => null()
172  TYPE(impr_type), DIMENSION(:), POINTER :: impr_list => null()
173  TYPE(opbend_kind_type), DIMENSION(:), POINTER :: opbend_kind_set => null()
174  TYPE(opbend_type), DIMENSION(:), POINTER :: opbend_list => null()
175  TYPE(colvar_constraint_type), DIMENSION(:), POINTER :: colv_list => null()
176  TYPE(g3x3_constraint_type), DIMENSION(:), POINTER :: g3x3_list => null()
177  TYPE(g4x6_constraint_type), DIMENSION(:), POINTER :: g4x6_list => null()
178  TYPE(vsite_constraint_type), DIMENSION(:), POINTER :: vsite_list => null()
179  TYPE(fixd_constraint_type), DIMENSION(:), POINTER :: fixd_list => null()
180  TYPE(shell_type), DIMENSION(:), POINTER :: shell_list => null()
181  CHARACTER(LEN=default_string_length) :: name = ""
182  REAL(KIND=dp) :: charge = 0.0_dp, &
183  mass = 0.0_dp
184  INTEGER :: kind_number = 0, &
185  natom = 0, &
186  nbond = 0, &
187  nbend = 0, &
188  nimpr = 0, &
189  nopbend = 0, &
190  ntorsion = 0, &
191  nub = 0, &
192  ng3x3 = 0, ng3x3_restraint = 0, &
193  ng4x6 = 0, ng4x6_restraint = 0, &
194  nvsite = 0, nvsite_restraint = 0, &
195  nfixd = 0, nfixd_restraint = 0, &
196  nmolecule = 0, nshell = 0
197  TYPE(colvar_counters) :: ncolv = colvar_counters()
198  INTEGER :: nsgf = 0, nelectron = 0, &
199  nelectron_alpha = 0, &
200  nelectron_beta = 0
201  INTEGER, DIMENSION(:), POINTER :: molecule_list => null()
202  LOGICAL :: molname_generated = .false.
203  END TYPE molecule_kind_type
204 
205  ! *** Public subroutines ***
206  PUBLIC :: allocate_molecule_kind_set, &
207  deallocate_molecule_kind_set, &
208  get_molecule_kind, &
209  get_molecule_kind_set, &
210  set_molecule_kind, &
211  write_molecule_kind_set, &
212  setup_colvar_counters
213 
214  ! *** Public data types ***
215  PUBLIC :: atom_type, &
216  bend_type, &
217  bond_type, &
218  ub_type, &
219  torsion_type, &
220  impr_type, &
221  opbend_type, &
222  colvar_constraint_type, &
223  g3x3_constraint_type, &
224  g4x6_constraint_type, &
225  vsite_constraint_type, &
226  fixd_constraint_type, &
227  local_fixd_constraint_type, &
228  molecule_kind_type, &
229  shell_type
230 
231 CONTAINS
232 
233 ! **************************************************************************************************
234 !> \brief ...
235 !> \param colv_list ...
236 !> \param ncolv ...
237 ! **************************************************************************************************
238  SUBROUTINE setup_colvar_counters(colv_list, ncolv)
239  TYPE(colvar_constraint_type), DIMENSION(:), &
240  POINTER :: colv_list
241  TYPE(colvar_counters), INTENT(OUT) :: ncolv
242 
243  INTEGER :: k
244 
245  IF (ASSOCIATED(colv_list)) THEN
246  DO k = 1, SIZE(colv_list)
247  IF (colv_list(k)%restraint%active) ncolv%nrestraint = ncolv%nrestraint + 1
248  SELECT CASE (colv_list(k)%type_id)
249  CASE (angle_colvar_id)
250  ncolv%nangle = ncolv%nangle + 1
251  CASE (coord_colvar_id)
252  ncolv%ncoord = ncolv%ncoord + 1
253  CASE (population_colvar_id)
254  ncolv%npopulation = ncolv%npopulation + 1
255  CASE (gyration_colvar_id)
256  ncolv%ngyration = ncolv%ngyration + 1
257  CASE (rotation_colvar_id)
258  ncolv%nrot = ncolv%nrot + 1
259  CASE (dist_colvar_id)
260  ncolv%ndist = ncolv%ndist + 1
261  CASE (dfunct_colvar_id)
262  ncolv%ndfunct = ncolv%ndfunct + 1
263  CASE (plane_distance_colvar_id)
264  ncolv%nplane_dist = ncolv%nplane_dist + 1
265  CASE (plane_plane_angle_colvar_id)
266  ncolv%nplane_angle = ncolv%nplane_angle + 1
267  CASE (torsion_colvar_id)
268  ncolv%ntorsion = ncolv%ntorsion + 1
269  CASE (qparm_colvar_id)
270  ncolv%nqparm = ncolv%nqparm + 1
271  CASE (xyz_diag_colvar_id)
272  ncolv%nxyz_diag = ncolv%nxyz_diag + 1
273  CASE (xyz_outerdiag_colvar_id)
274  ncolv%nxyz_outerdiag = ncolv%nxyz_outerdiag + 1
275  CASE (hydronium_shell_colvar_id)
276  ncolv%nhydronium_shell = ncolv%nhydronium_shell + 1
277  CASE (hydronium_dist_colvar_id)
278  ncolv%nhydronium_dist = ncolv%nhydronium_dist + 1
279  CASE (acid_hyd_dist_colvar_id)
280  ncolv%nacid_hyd_dist = ncolv%nacid_hyd_dist + 1
281  CASE (acid_hyd_shell_colvar_id)
282  ncolv%nacid_hyd_shell = ncolv%nacid_hyd_shell + 1
283  CASE (reaction_path_colvar_id)
284  ncolv%nreactionpath = ncolv%nreactionpath + 1
285  CASE (combine_colvar_id)
286  ncolv%ncombinecvs = ncolv%ncombinecvs + 1
287  CASE DEFAULT
288  cpabort("")
289  END SELECT
290  END DO
291  END IF
292  ncolv%ntot = ncolv%ndist + &
293  ncolv%nangle + &
294  ncolv%ntorsion + &
295  ncolv%ncoord + &
296  ncolv%nplane_dist + &
297  ncolv%nplane_angle + &
298  ncolv%ndfunct + &
299  ncolv%nrot + &
300  ncolv%nqparm + &
301  ncolv%nxyz_diag + &
302  ncolv%nxyz_outerdiag + &
303  ncolv%nhydronium_shell + &
304  ncolv%nhydronium_dist + &
305  ncolv%nacid_hyd_dist + &
306  ncolv%nacid_hyd_shell + &
307  ncolv%nreactionpath + &
308  ncolv%ncombinecvs + &
309  ncolv%npopulation + &
310  ncolv%ngyration
311 
312  END SUBROUTINE setup_colvar_counters
313 
314 ! **************************************************************************************************
315 !> \brief Allocate and initialize a molecule kind set.
316 !> \param molecule_kind_set ...
317 !> \param nmolecule_kind ...
318 !> \date 22.08.2003
319 !> \author MK
320 !> \version 1.0
321 ! **************************************************************************************************
322  SUBROUTINE allocate_molecule_kind_set(molecule_kind_set, nmolecule_kind)
323  TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
324  INTEGER, INTENT(IN) :: nmolecule_kind
325 
326  INTEGER :: imolecule_kind
327 
328  IF (ASSOCIATED(molecule_kind_set)) THEN
329  CALL deallocate_molecule_kind_set(molecule_kind_set)
330  END IF
331 
332  ALLOCATE (molecule_kind_set(nmolecule_kind))
333 
334  DO imolecule_kind = 1, nmolecule_kind
335  molecule_kind_set(imolecule_kind)%kind_number = imolecule_kind
336  CALL setup_colvar_counters(molecule_kind_set(imolecule_kind)%colv_list, &
337  molecule_kind_set(imolecule_kind)%ncolv)
338  END DO
339 
340  END SUBROUTINE allocate_molecule_kind_set
341 
342 ! **************************************************************************************************
343 !> \brief Deallocate a molecule kind set.
344 !> \param molecule_kind_set ...
345 !> \date 22.08.2003
346 !> \author MK
347 !> \version 1.0
348 ! **************************************************************************************************
349  SUBROUTINE deallocate_molecule_kind_set(molecule_kind_set)
350 
351  TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
352 
353  INTEGER :: i, imolecule_kind, j, nmolecule_kind
354 
355  IF (ASSOCIATED(molecule_kind_set)) THEN
356 
357  nmolecule_kind = SIZE(molecule_kind_set)
358 
359  DO imolecule_kind = 1, nmolecule_kind
360 
361  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%atom_list)) THEN
362  DEALLOCATE (molecule_kind_set(imolecule_kind)%atom_list)
363  END IF
364  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%bend_kind_set)) THEN
365  DO i = 1, SIZE(molecule_kind_set(imolecule_kind)%bend_kind_set)
366  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%bend_kind_set(i)%legendre%coeffs)) &
367  DEALLOCATE (molecule_kind_set(imolecule_kind)%bend_kind_set(i)%legendre%coeffs)
368  END DO
369  DEALLOCATE (molecule_kind_set(imolecule_kind)%bend_kind_set)
370  END IF
371  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%bend_list)) THEN
372  DEALLOCATE (molecule_kind_set(imolecule_kind)%bend_list)
373  END IF
374  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%ub_list)) THEN
375  DEALLOCATE (molecule_kind_set(imolecule_kind)%ub_list)
376  END IF
377  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%ub_kind_set)) THEN
378  CALL ub_kind_dealloc_ref(molecule_kind_set(imolecule_kind)%ub_kind_set)
379  END IF
380  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%impr_list)) THEN
381  DEALLOCATE (molecule_kind_set(imolecule_kind)%impr_list)
382  END IF
383  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%impr_kind_set)) THEN
384  DO i = 1, SIZE(molecule_kind_set(imolecule_kind)%impr_kind_set)
385  CALL impr_kind_dealloc_ref() !This Subroutine doesn't deallocate anything, maybe needs to be implemented
386  END DO
387  DEALLOCATE (molecule_kind_set(imolecule_kind)%impr_kind_set)
388  END IF
389  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%opbend_list)) THEN
390  DEALLOCATE (molecule_kind_set(imolecule_kind)%opbend_list)
391  END IF
392  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%opbend_kind_set)) THEN
393  DEALLOCATE (molecule_kind_set(imolecule_kind)%opbend_kind_set)
394  END IF
395  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%bond_kind_set)) THEN
396  DEALLOCATE (molecule_kind_set(imolecule_kind)%bond_kind_set)
397  END IF
398  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%bond_list)) THEN
399  DEALLOCATE (molecule_kind_set(imolecule_kind)%bond_list)
400  END IF
401  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%colv_list)) THEN
402  DO j = 1, SIZE(molecule_kind_set(imolecule_kind)%colv_list)
403  DEALLOCATE (molecule_kind_set(imolecule_kind)%colv_list(j)%i_atoms)
404  END DO
405  DEALLOCATE (molecule_kind_set(imolecule_kind)%colv_list)
406  END IF
407  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%g3x3_list)) THEN
408  DEALLOCATE (molecule_kind_set(imolecule_kind)%g3x3_list)
409  END IF
410  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%g4x6_list)) THEN
411  DEALLOCATE (molecule_kind_set(imolecule_kind)%g4x6_list)
412  END IF
413  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%vsite_list)) THEN
414  DEALLOCATE (molecule_kind_set(imolecule_kind)%vsite_list)
415  END IF
416  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%fixd_list)) THEN
417  DEALLOCATE (molecule_kind_set(imolecule_kind)%fixd_list)
418  END IF
419  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%torsion_kind_set)) THEN
420  DO i = 1, SIZE(molecule_kind_set(imolecule_kind)%torsion_kind_set)
421  CALL torsion_kind_dealloc_ref(molecule_kind_set(imolecule_kind)%torsion_kind_set(i))
422  END DO
423  DEALLOCATE (molecule_kind_set(imolecule_kind)%torsion_kind_set)
424  END IF
425  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%shell_list)) THEN
426  DEALLOCATE (molecule_kind_set(imolecule_kind)%shell_list)
427  END IF
428  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%torsion_list)) THEN
429  DEALLOCATE (molecule_kind_set(imolecule_kind)%torsion_list)
430  END IF
431  IF (ASSOCIATED(molecule_kind_set(imolecule_kind)%molecule_list)) THEN
432  DEALLOCATE (molecule_kind_set(imolecule_kind)%molecule_list)
433  END IF
434  END DO
435 
436  DEALLOCATE (molecule_kind_set)
437  END IF
438  NULLIFY (molecule_kind_set)
439 
440  END SUBROUTINE deallocate_molecule_kind_set
441 
442 ! **************************************************************************************************
443 !> \brief Get informations about a molecule kind.
444 !> \param molecule_kind ...
445 !> \param atom_list ...
446 !> \param bond_list ...
447 !> \param bend_list ...
448 !> \param ub_list ...
449 !> \param impr_list ...
450 !> \param opbend_list ...
451 !> \param colv_list ...
452 !> \param fixd_list ...
453 !> \param g3x3_list ...
454 !> \param g4x6_list ...
455 !> \param vsite_list ...
456 !> \param torsion_list ...
457 !> \param shell_list ...
458 !> \param name ...
459 !> \param mass ...
460 !> \param charge ...
461 !> \param kind_number ...
462 !> \param natom ...
463 !> \param nbend ...
464 !> \param nbond ...
465 !> \param nub ...
466 !> \param nimpr ...
467 !> \param nopbend ...
468 !> \param nconstraint ...
469 !> \param nconstraint_fixd ...
470 !> \param nfixd ...
471 !> \param ncolv ...
472 !> \param ng3x3 ...
473 !> \param ng4x6 ...
474 !> \param nvsite ...
475 !> \param nfixd_restraint ...
476 !> \param ng3x3_restraint ...
477 !> \param ng4x6_restraint ...
478 !> \param nvsite_restraint ...
479 !> \param nrestraints ...
480 !> \param nmolecule ...
481 !> \param nsgf ...
482 !> \param nshell ...
483 !> \param ntorsion ...
484 !> \param molecule_list ...
485 !> \param nelectron ...
486 !> \param nelectron_alpha ...
487 !> \param nelectron_beta ...
488 !> \param bond_kind_set ...
489 !> \param bend_kind_set ...
490 !> \param ub_kind_set ...
491 !> \param impr_kind_set ...
492 !> \param opbend_kind_set ...
493 !> \param torsion_kind_set ...
494 !> \param molname_generated ...
495 !> \date 27.08.2003
496 !> \author MK
497 !> \version 1.0
498 ! **************************************************************************************************
499  SUBROUTINE get_molecule_kind(molecule_kind, atom_list, bond_list, bend_list, &
500  ub_list, impr_list, opbend_list, colv_list, fixd_list, &
501  g3x3_list, g4x6_list, vsite_list, torsion_list, shell_list, &
502  name, mass, charge, kind_number, natom, nbend, nbond, nub, &
503  nimpr, nopbend, nconstraint, nconstraint_fixd, nfixd, ncolv, ng3x3, ng4x6, &
504  nvsite, nfixd_restraint, ng3x3_restraint, ng4x6_restraint, &
505  nvsite_restraint, nrestraints, nmolecule, nsgf, nshell, ntorsion, &
506  molecule_list, nelectron, nelectron_alpha, nelectron_beta, &
507  bond_kind_set, bend_kind_set, &
508  ub_kind_set, impr_kind_set, opbend_kind_set, torsion_kind_set, &
509  molname_generated)
510 
511  TYPE(molecule_kind_type), INTENT(IN) :: molecule_kind
512  TYPE(atom_type), DIMENSION(:), OPTIONAL, POINTER :: atom_list
513  TYPE(bond_type), DIMENSION(:), OPTIONAL, POINTER :: bond_list
514  TYPE(bend_type), DIMENSION(:), OPTIONAL, POINTER :: bend_list
515  TYPE(ub_type), DIMENSION(:), OPTIONAL, POINTER :: ub_list
516  TYPE(impr_type), DIMENSION(:), OPTIONAL, POINTER :: impr_list
517  TYPE(opbend_type), DIMENSION(:), OPTIONAL, POINTER :: opbend_list
518  TYPE(colvar_constraint_type), DIMENSION(:), &
519  OPTIONAL, POINTER :: colv_list
520  TYPE(fixd_constraint_type), DIMENSION(:), &
521  OPTIONAL, POINTER :: fixd_list
522  TYPE(g3x3_constraint_type), DIMENSION(:), &
523  OPTIONAL, POINTER :: g3x3_list
524  TYPE(g4x6_constraint_type), DIMENSION(:), &
525  OPTIONAL, POINTER :: g4x6_list
526  TYPE(vsite_constraint_type), DIMENSION(:), &
527  OPTIONAL, POINTER :: vsite_list
528  TYPE(torsion_type), DIMENSION(:), OPTIONAL, &
529  POINTER :: torsion_list
530  TYPE(shell_type), DIMENSION(:), OPTIONAL, POINTER :: shell_list
531  CHARACTER(LEN=default_string_length), &
532  INTENT(OUT), OPTIONAL :: name
533  REAL(kind=dp), OPTIONAL :: mass, charge
534  INTEGER, INTENT(OUT), OPTIONAL :: kind_number, natom, nbend, nbond, nub, &
535  nimpr, nopbend, nconstraint, &
536  nconstraint_fixd, nfixd
537  TYPE(colvar_counters), INTENT(out), OPTIONAL :: ncolv
538  INTEGER, INTENT(OUT), OPTIONAL :: ng3x3, ng4x6, nvsite, nfixd_restraint, ng3x3_restraint, &
539  ng4x6_restraint, nvsite_restraint, nrestraints, nmolecule, nsgf, nshell, ntorsion
540  INTEGER, DIMENSION(:), OPTIONAL, POINTER :: molecule_list
541  INTEGER, INTENT(OUT), OPTIONAL :: nelectron, nelectron_alpha, &
542  nelectron_beta
543  TYPE(bond_kind_type), DIMENSION(:), OPTIONAL, &
544  POINTER :: bond_kind_set
545  TYPE(bend_kind_type), DIMENSION(:), OPTIONAL, &
546  POINTER :: bend_kind_set
547  TYPE(ub_kind_type), DIMENSION(:), OPTIONAL, &
548  POINTER :: ub_kind_set
549  TYPE(impr_kind_type), DIMENSION(:), OPTIONAL, &
550  POINTER :: impr_kind_set
551  TYPE(opbend_kind_type), DIMENSION(:), OPTIONAL, &
552  POINTER :: opbend_kind_set
553  TYPE(torsion_kind_type), DIMENSION(:), OPTIONAL, &
554  POINTER :: torsion_kind_set
555  LOGICAL, INTENT(OUT), OPTIONAL :: molname_generated
556 
557  INTEGER :: i
558 
559  IF (PRESENT(atom_list)) atom_list => molecule_kind%atom_list
560  IF (PRESENT(bend_list)) bend_list => molecule_kind%bend_list
561  IF (PRESENT(bond_list)) bond_list => molecule_kind%bond_list
562  IF (PRESENT(impr_list)) impr_list => molecule_kind%impr_list
563  IF (PRESENT(opbend_list)) opbend_list => molecule_kind%opbend_list
564  IF (PRESENT(ub_list)) ub_list => molecule_kind%ub_list
565  IF (PRESENT(bond_kind_set)) bond_kind_set => molecule_kind%bond_kind_set
566  IF (PRESENT(bend_kind_set)) bend_kind_set => molecule_kind%bend_kind_set
567  IF (PRESENT(ub_kind_set)) ub_kind_set => molecule_kind%ub_kind_set
568  IF (PRESENT(impr_kind_set)) impr_kind_set => molecule_kind%impr_kind_set
569  IF (PRESENT(opbend_kind_set)) opbend_kind_set => molecule_kind%opbend_kind_set
570  IF (PRESENT(torsion_kind_set)) torsion_kind_set => molecule_kind%torsion_kind_set
571  IF (PRESENT(colv_list)) colv_list => molecule_kind%colv_list
572  IF (PRESENT(g3x3_list)) g3x3_list => molecule_kind%g3x3_list
573  IF (PRESENT(g4x6_list)) g4x6_list => molecule_kind%g4x6_list
574  IF (PRESENT(vsite_list)) vsite_list => molecule_kind%vsite_list
575  IF (PRESENT(fixd_list)) fixd_list => molecule_kind%fixd_list
576  IF (PRESENT(torsion_list)) torsion_list => molecule_kind%torsion_list
577  IF (PRESENT(shell_list)) shell_list => molecule_kind%shell_list
578  IF (PRESENT(name)) name = molecule_kind%name
579  IF (PRESENT(molname_generated)) molname_generated = molecule_kind%molname_generated
580  IF (PRESENT(mass)) mass = molecule_kind%mass
581  IF (PRESENT(charge)) charge = molecule_kind%charge
582  IF (PRESENT(kind_number)) kind_number = molecule_kind%kind_number
583  IF (PRESENT(natom)) natom = molecule_kind%natom
584  IF (PRESENT(nbend)) nbend = molecule_kind%nbend
585  IF (PRESENT(nbond)) nbond = molecule_kind%nbond
586  IF (PRESENT(nub)) nub = molecule_kind%nub
587  IF (PRESENT(nimpr)) nimpr = molecule_kind%nimpr
588  IF (PRESENT(nopbend)) nopbend = molecule_kind%nopbend
589  IF (PRESENT(nconstraint)) nconstraint = (molecule_kind%ncolv%ntot - molecule_kind%ncolv%nrestraint) + &
590  3*(molecule_kind%ng3x3 - molecule_kind%ng3x3_restraint) + &
591  6*(molecule_kind%ng4x6 - molecule_kind%ng4x6_restraint) + &
592  3*(molecule_kind%nvsite - molecule_kind%nvsite_restraint)
593  IF (PRESENT(ncolv)) ncolv = molecule_kind%ncolv
594  IF (PRESENT(ng3x3)) ng3x3 = molecule_kind%ng3x3
595  IF (PRESENT(ng4x6)) ng4x6 = molecule_kind%ng4x6
596  IF (PRESENT(nvsite)) nvsite = molecule_kind%nvsite
597  ! Number of atoms that have one or more components fixed
598  IF (PRESENT(nfixd)) nfixd = molecule_kind%nfixd
599  ! Number of degrees of freedom fixed
600  IF (PRESENT(nconstraint_fixd)) THEN
601  nconstraint_fixd = 0
602  IF (molecule_kind%nfixd /= 0) THEN
603  DO i = 1, SIZE(molecule_kind%fixd_list)
604  IF (molecule_kind%fixd_list(i)%restraint%active) cycle
605  SELECT CASE (molecule_kind%fixd_list(i)%itype)
606  CASE (use_perd_x, use_perd_y, use_perd_z)
607  nconstraint_fixd = nconstraint_fixd + 1
608  CASE (use_perd_xy, use_perd_xz, use_perd_yz)
609  nconstraint_fixd = nconstraint_fixd + 2
610  CASE (use_perd_xyz)
611  nconstraint_fixd = nconstraint_fixd + 3
612  END SELECT
613  END DO
614  END IF
615  END IF
616  IF (PRESENT(ng3x3_restraint)) ng3x3_restraint = molecule_kind%ng3x3_restraint
617  IF (PRESENT(ng4x6_restraint)) ng4x6_restraint = molecule_kind%ng4x6_restraint
618  IF (PRESENT(nvsite_restraint)) nvsite_restraint = molecule_kind%nvsite_restraint
619  IF (PRESENT(nfixd_restraint)) nfixd_restraint = molecule_kind%nfixd_restraint
620  IF (PRESENT(nrestraints)) nrestraints = molecule_kind%ncolv%nrestraint + &
621  molecule_kind%ng3x3_restraint + &
622  molecule_kind%ng4x6_restraint + &
623  molecule_kind%nvsite_restraint
624  IF (PRESENT(nmolecule)) nmolecule = molecule_kind%nmolecule
625  IF (PRESENT(nshell)) nshell = molecule_kind%nshell
626  IF (PRESENT(ntorsion)) ntorsion = molecule_kind%ntorsion
627  IF (PRESENT(nsgf)) nsgf = molecule_kind%nsgf
628  IF (PRESENT(nelectron)) nelectron = molecule_kind%nelectron
629  IF (PRESENT(nelectron_alpha)) nelectron_alpha = molecule_kind%nelectron_beta
630  IF (PRESENT(nelectron_beta)) nelectron_beta = molecule_kind%nelectron_alpha
631  IF (PRESENT(molecule_list)) molecule_list => molecule_kind%molecule_list
632 
633  END SUBROUTINE get_molecule_kind
634 
635 ! **************************************************************************************************
636 !> \brief Get informations about a molecule kind set.
637 !> \param molecule_kind_set ...
638 !> \param maxatom ...
639 !> \param natom ...
640 !> \param nbond ...
641 !> \param nbend ...
642 !> \param nub ...
643 !> \param ntorsion ...
644 !> \param nimpr ...
645 !> \param nopbend ...
646 !> \param nconstraint ...
647 !> \param nconstraint_fixd ...
648 !> \param nmolecule ...
649 !> \param nrestraints ...
650 !> \date 27.08.2003
651 !> \author MK
652 !> \version 1.0
653 ! **************************************************************************************************
654  SUBROUTINE get_molecule_kind_set(molecule_kind_set, maxatom, natom, &
655  nbond, nbend, nub, ntorsion, nimpr, nopbend, &
656  nconstraint, nconstraint_fixd, nmolecule, &
657  nrestraints)
658 
659  TYPE(molecule_kind_type), DIMENSION(:), INTENT(IN) :: molecule_kind_set
660  INTEGER, INTENT(OUT), OPTIONAL :: maxatom, natom, nbond, nbend, nub, &
661  ntorsion, nimpr, nopbend, nconstraint, &
662  nconstraint_fixd, nmolecule, &
663  nrestraints
664 
665  INTEGER :: ibend, ibond, iimpr, imolecule_kind, iopbend, itorsion, iub, na, nc, nc_fixd, &
666  nfixd_restraint, nm, nmolecule_kind, nrestraints_tot
667 
668  IF (PRESENT(maxatom)) maxatom = 0
669  IF (PRESENT(natom)) natom = 0
670  IF (PRESENT(nbond)) nbond = 0
671  IF (PRESENT(nbend)) nbend = 0
672  IF (PRESENT(nub)) nub = 0
673  IF (PRESENT(ntorsion)) ntorsion = 0
674  IF (PRESENT(nimpr)) nimpr = 0
675  IF (PRESENT(nopbend)) nopbend = 0
676  IF (PRESENT(nconstraint)) nconstraint = 0
677  IF (PRESENT(nconstraint_fixd)) nconstraint_fixd = 0
678  IF (PRESENT(nrestraints)) nrestraints = 0
679  IF (PRESENT(nmolecule)) nmolecule = 0
680 
681  nmolecule_kind = SIZE(molecule_kind_set)
682 
683  DO imolecule_kind = 1, nmolecule_kind
684  associate(molecule_kind => molecule_kind_set(imolecule_kind))
685 
686  CALL get_molecule_kind(molecule_kind=molecule_kind, &
687  natom=na, &
688  nbond=ibond, &
689  nbend=ibend, &
690  nub=iub, &
691  ntorsion=itorsion, &
692  nimpr=iimpr, &
693  nopbend=iopbend, &
694  nconstraint=nc, &
695  nconstraint_fixd=nc_fixd, &
696  nfixd_restraint=nfixd_restraint, &
697  nrestraints=nrestraints_tot, &
698  nmolecule=nm)
699  IF (PRESENT(maxatom)) maxatom = max(maxatom, na)
700  IF (PRESENT(natom)) natom = natom + na*nm
701  IF (PRESENT(nbond)) nbond = nbond + ibond*nm
702  IF (PRESENT(nbend)) nbend = nbend + ibend*nm
703  IF (PRESENT(nub)) nub = nub + iub*nm
704  IF (PRESENT(ntorsion)) ntorsion = ntorsion + itorsion*nm
705  IF (PRESENT(nimpr)) nimpr = nimpr + iimpr*nm
706  IF (PRESENT(nopbend)) nopbend = nopbend + iopbend*nm
707  IF (PRESENT(nconstraint)) nconstraint = nconstraint + nc*nm + nc_fixd
708  IF (PRESENT(nconstraint_fixd)) nconstraint_fixd = nconstraint_fixd + nc_fixd
709  IF (PRESENT(nmolecule)) nmolecule = nmolecule + nm
710  IF (PRESENT(nrestraints)) nrestraints = nrestraints + nm*nrestraints_tot + nfixd_restraint
711 
712  END associate
713  END DO
714 
715  END SUBROUTINE get_molecule_kind_set
716 
717 ! **************************************************************************************************
718 !> \brief Set the components of a molecule kind.
719 !> \param molecule_kind ...
720 !> \param name ...
721 !> \param mass ...
722 !> \param charge ...
723 !> \param kind_number ...
724 !> \param molecule_list ...
725 !> \param atom_list ...
726 !> \param nbond ...
727 !> \param bond_list ...
728 !> \param nbend ...
729 !> \param bend_list ...
730 !> \param nub ...
731 !> \param ub_list ...
732 !> \param nimpr ...
733 !> \param impr_list ...
734 !> \param nopbend ...
735 !> \param opbend_list ...
736 !> \param ntorsion ...
737 !> \param torsion_list ...
738 !> \param fixd_list ...
739 !> \param ncolv ...
740 !> \param colv_list ...
741 !> \param ng3x3 ...
742 !> \param g3x3_list ...
743 !> \param ng4x6 ...
744 !> \param nfixd ...
745 !> \param g4x6_list ...
746 !> \param nvsite ...
747 !> \param vsite_list ...
748 !> \param ng3x3_restraint ...
749 !> \param ng4x6_restraint ...
750 !> \param nfixd_restraint ...
751 !> \param nshell ...
752 !> \param shell_list ...
753 !> \param nvsite_restraint ...
754 !> \param bond_kind_set ...
755 !> \param bend_kind_set ...
756 !> \param ub_kind_set ...
757 !> \param torsion_kind_set ...
758 !> \param impr_kind_set ...
759 !> \param opbend_kind_set ...
760 !> \param nelectron ...
761 !> \param nsgf ...
762 !> \param molname_generated ...
763 !> \date 27.08.2003
764 !> \author MK
765 !> \version 1.0
766 ! **************************************************************************************************
767  SUBROUTINE set_molecule_kind(molecule_kind, name, mass, charge, kind_number, &
768  molecule_list, atom_list, nbond, bond_list, &
769  nbend, bend_list, nub, ub_list, nimpr, impr_list, &
770  nopbend, opbend_list, ntorsion, &
771  torsion_list, fixd_list, ncolv, colv_list, ng3x3, &
772  g3x3_list, ng4x6, nfixd, g4x6_list, nvsite, &
773  vsite_list, ng3x3_restraint, ng4x6_restraint, &
774  nfixd_restraint, nshell, shell_list, &
775  nvsite_restraint, bond_kind_set, bend_kind_set, &
776  ub_kind_set, torsion_kind_set, impr_kind_set, &
777  opbend_kind_set, nelectron, nsgf, &
778  molname_generated)
779 
780  TYPE(molecule_kind_type), INTENT(INOUT) :: molecule_kind
781  CHARACTER(LEN=*), INTENT(IN), OPTIONAL :: name
782  REAL(kind=dp), OPTIONAL :: mass, charge
783  INTEGER, INTENT(IN), OPTIONAL :: kind_number
784  INTEGER, DIMENSION(:), OPTIONAL, POINTER :: molecule_list
785  TYPE(atom_type), DIMENSION(:), OPTIONAL, POINTER :: atom_list
786  INTEGER, INTENT(IN), OPTIONAL :: nbond
787  TYPE(bond_type), DIMENSION(:), OPTIONAL, POINTER :: bond_list
788  INTEGER, INTENT(IN), OPTIONAL :: nbend
789  TYPE(bend_type), DIMENSION(:), OPTIONAL, POINTER :: bend_list
790  INTEGER, INTENT(IN), OPTIONAL :: nub
791  TYPE(ub_type), DIMENSION(:), OPTIONAL, POINTER :: ub_list
792  INTEGER, INTENT(IN), OPTIONAL :: nimpr
793  TYPE(impr_type), DIMENSION(:), OPTIONAL, POINTER :: impr_list
794  INTEGER, INTENT(IN), OPTIONAL :: nopbend
795  TYPE(opbend_type), DIMENSION(:), OPTIONAL, POINTER :: opbend_list
796  INTEGER, INTENT(IN), OPTIONAL :: ntorsion
797  TYPE(torsion_type), DIMENSION(:), OPTIONAL, &
798  POINTER :: torsion_list
799  TYPE(fixd_constraint_type), DIMENSION(:), &
800  OPTIONAL, POINTER :: fixd_list
801  TYPE(colvar_counters), INTENT(IN), OPTIONAL :: ncolv
802  TYPE(colvar_constraint_type), DIMENSION(:), &
803  OPTIONAL, POINTER :: colv_list
804  INTEGER, INTENT(IN), OPTIONAL :: ng3x3
805  TYPE(g3x3_constraint_type), DIMENSION(:), &
806  OPTIONAL, POINTER :: g3x3_list
807  INTEGER, INTENT(IN), OPTIONAL :: ng4x6, nfixd
808  TYPE(g4x6_constraint_type), DIMENSION(:), &
809  OPTIONAL, POINTER :: g4x6_list
810  INTEGER, INTENT(IN), OPTIONAL :: nvsite
811  TYPE(vsite_constraint_type), DIMENSION(:), &
812  OPTIONAL, POINTER :: vsite_list
813  INTEGER, INTENT(IN), OPTIONAL :: ng3x3_restraint, ng4x6_restraint, &
814  nfixd_restraint, nshell
815  TYPE(shell_type), DIMENSION(:), OPTIONAL, POINTER :: shell_list
816  INTEGER, INTENT(IN), OPTIONAL :: nvsite_restraint
817  TYPE(bond_kind_type), DIMENSION(:), OPTIONAL, &
818  POINTER :: bond_kind_set
819  TYPE(bend_kind_type), DIMENSION(:), OPTIONAL, &
820  POINTER :: bend_kind_set
821  TYPE(ub_kind_type), DIMENSION(:), OPTIONAL, &
822  POINTER :: ub_kind_set
823  TYPE(torsion_kind_type), DIMENSION(:), OPTIONAL, &
824  POINTER :: torsion_kind_set
825  TYPE(impr_kind_type), DIMENSION(:), OPTIONAL, &
826  POINTER :: impr_kind_set
827  TYPE(opbend_kind_type), DIMENSION(:), OPTIONAL, &
828  POINTER :: opbend_kind_set
829  INTEGER, INTENT(IN), OPTIONAL :: nelectron, nsgf
830  LOGICAL, INTENT(IN), OPTIONAL :: molname_generated
831 
832  INTEGER :: n
833 
834  IF (PRESENT(atom_list)) THEN
835  n = SIZE(atom_list)
836  molecule_kind%natom = n
837  molecule_kind%atom_list => atom_list
838  END IF
839  IF (PRESENT(molname_generated)) molecule_kind%molname_generated = molname_generated
840  IF (PRESENT(name)) molecule_kind%name = name
841  IF (PRESENT(mass)) molecule_kind%mass = mass
842  IF (PRESENT(charge)) molecule_kind%charge = charge
843  IF (PRESENT(kind_number)) molecule_kind%kind_number = kind_number
844  IF (PRESENT(nbond)) molecule_kind%nbond = nbond
845  IF (PRESENT(bond_list)) molecule_kind%bond_list => bond_list
846  IF (PRESENT(nbend)) molecule_kind%nbend = nbend
847  IF (PRESENT(nelectron)) molecule_kind%nelectron = nelectron
848  IF (PRESENT(nsgf)) molecule_kind%nsgf = nsgf
849  IF (PRESENT(bend_list)) molecule_kind%bend_list => bend_list
850  IF (PRESENT(nub)) molecule_kind%nub = nub
851  IF (PRESENT(ub_list)) molecule_kind%ub_list => ub_list
852  IF (PRESENT(ntorsion)) molecule_kind%ntorsion = ntorsion
853  IF (PRESENT(torsion_list)) molecule_kind%torsion_list => torsion_list
854  IF (PRESENT(nimpr)) molecule_kind%nimpr = nimpr
855  IF (PRESENT(impr_list)) molecule_kind%impr_list => impr_list
856  IF (PRESENT(nopbend)) molecule_kind%nopbend = nopbend
857  IF (PRESENT(opbend_list)) molecule_kind%opbend_list => opbend_list
858  IF (PRESENT(ncolv)) molecule_kind%ncolv = ncolv
859  IF (PRESENT(colv_list)) molecule_kind%colv_list => colv_list
860  IF (PRESENT(ng3x3)) molecule_kind%ng3x3 = ng3x3
861  IF (PRESENT(g3x3_list)) molecule_kind%g3x3_list => g3x3_list
862  IF (PRESENT(ng4x6)) molecule_kind%ng4x6 = ng4x6
863  IF (PRESENT(nvsite)) molecule_kind%nvsite = nvsite
864  IF (PRESENT(nfixd)) molecule_kind%nfixd = nfixd
865  IF (PRESENT(nfixd_restraint)) molecule_kind%nfixd_restraint = nfixd_restraint
866  IF (PRESENT(ng3x3_restraint)) molecule_kind%ng3x3_restraint = ng3x3_restraint
867  IF (PRESENT(ng4x6_restraint)) molecule_kind%ng4x6_restraint = ng4x6_restraint
868  IF (PRESENT(nvsite_restraint)) molecule_kind%nvsite_restraint = nvsite_restraint
869  IF (PRESENT(g4x6_list)) molecule_kind%g4x6_list => g4x6_list
870  IF (PRESENT(vsite_list)) molecule_kind%vsite_list => vsite_list
871  IF (PRESENT(fixd_list)) molecule_kind%fixd_list => fixd_list
872  IF (PRESENT(bond_kind_set)) molecule_kind%bond_kind_set => bond_kind_set
873  IF (PRESENT(bend_kind_set)) molecule_kind%bend_kind_set => bend_kind_set
874  IF (PRESENT(ub_kind_set)) molecule_kind%ub_kind_set => ub_kind_set
875  IF (PRESENT(torsion_kind_set)) molecule_kind%torsion_kind_set => torsion_kind_set
876  IF (PRESENT(impr_kind_set)) molecule_kind%impr_kind_set => impr_kind_set
877  IF (PRESENT(opbend_kind_set)) molecule_kind%opbend_kind_set => opbend_kind_set
878  IF (PRESENT(nshell)) molecule_kind%nshell = nshell
879  IF (PRESENT(shell_list)) molecule_kind%shell_list => shell_list
880  IF (PRESENT(molecule_list)) THEN
881  n = SIZE(molecule_list)
882  molecule_kind%nmolecule = n
883  molecule_kind%molecule_list => molecule_list
884  END IF
885  END SUBROUTINE set_molecule_kind
886 
887 ! **************************************************************************************************
888 !> \brief Write a molecule kind data set to the output unit.
889 !> \param molecule_kind ...
890 !> \param output_unit ...
891 !> \date 24.09.2003
892 !> \author MK
893 !> \version 1.0
894 ! **************************************************************************************************
895  SUBROUTINE write_molecule_kind(molecule_kind, output_unit)
896  TYPE(molecule_kind_type), INTENT(IN) :: molecule_kind
897  INTEGER, INTENT(in) :: output_unit
898 
899  CHARACTER(LEN=default_string_length) :: name
900  INTEGER :: iatom, imolecule, natom, nmolecule
901  TYPE(atomic_kind_type), POINTER :: atomic_kind
902 
903  IF (output_unit > 0) THEN
904  natom = SIZE(molecule_kind%atom_list)
905  nmolecule = SIZE(molecule_kind%molecule_list)
906 
907  IF (natom == 1) THEN
908  atomic_kind => molecule_kind%atom_list(1)%atomic_kind
909  CALL get_atomic_kind(atomic_kind=atomic_kind, name=name)
910  WRITE (unit=output_unit, fmt="(/,T2,I5,A,T36,A,A,T64,A)") &
911  molecule_kind%kind_number, &
912  ". Molecule kind: "//trim(molecule_kind%name), &
913  "Atomic kind name: ", trim(name)
914  WRITE (unit=output_unit, fmt="(T9,A,L1,T55,A,T75,I6)") &
915  "Automatic name: ", molecule_kind%molname_generated, &
916  "Number of molecules:", nmolecule
917  ELSE
918  WRITE (unit=output_unit, fmt="(/,T2,I5,A,T50,A,T75,I6,/,T22,A)") &
919  molecule_kind%kind_number, &
920  ". Molecule kind: "//trim(molecule_kind%name), &
921  "Number of atoms: ", natom, &
922  "Atom Atomic kind name"
923  DO iatom = 1, natom
924  atomic_kind => molecule_kind%atom_list(iatom)%atomic_kind
925  CALL get_atomic_kind(atomic_kind=atomic_kind, name=name)
926  WRITE (unit=output_unit, fmt="(T20,I6,(7X,A18))") &
927  iatom, trim(name)
928  END DO
929  WRITE (unit=output_unit, fmt="(/,T9,A,L1)") &
930  "The name was automatically generated: ", &
931  molecule_kind%molname_generated
932  WRITE (unit=output_unit, fmt="(T9,A,I6,/,T9,A,(T30,5I10))") &
933  "Number of molecules: ", nmolecule, "Molecule list:", &
934  (molecule_kind%molecule_list(imolecule), imolecule=1, nmolecule)
935  IF (molecule_kind%nbond > 0) &
936  WRITE (unit=output_unit, fmt="(1X,A30,I6)") &
937  "Number of bonds: ", molecule_kind%nbond
938  IF (molecule_kind%nbend > 0) &
939  WRITE (unit=output_unit, fmt="(1X,A30,I6)") &
940  "Number of bends: ", molecule_kind%nbend
941  IF (molecule_kind%nub > 0) &
942  WRITE (unit=output_unit, fmt="(1X,A30,I6)") &
943  "Number of Urey-Bradley:", molecule_kind%nub
944  IF (molecule_kind%ntorsion > 0) &
945  WRITE (unit=output_unit, fmt="(1X,A30,I6)") &
946  "Number of torsions: ", molecule_kind%ntorsion
947  IF (molecule_kind%nimpr > 0) &
948  WRITE (unit=output_unit, fmt="(1X,A30,I6)") &
949  "Number of improper: ", molecule_kind%nimpr
950  IF (molecule_kind%nopbend > 0) &
951  WRITE (unit=output_unit, fmt="(1X,A30,I6)") &
952  "Number of out opbends: ", molecule_kind%nopbend
953  END IF
954  END IF
955  END SUBROUTINE write_molecule_kind
956 
957 ! **************************************************************************************************
958 !> \brief Write a moleculeatomic kind set data set to the output unit.
959 !> \param molecule_kind_set ...
960 !> \param subsys_section ...
961 !> \date 24.09.2003
962 !> \author MK
963 !> \version 1.0
964 ! **************************************************************************************************
965  SUBROUTINE write_molecule_kind_set(molecule_kind_set, subsys_section)
966  TYPE(molecule_kind_type), DIMENSION(:), INTENT(IN) :: molecule_kind_set
967  TYPE(section_vals_type), INTENT(IN) :: subsys_section
968 
969  CHARACTER(len=*), PARAMETER :: routinen = 'write_molecule_kind_set'
970 
971  INTEGER :: handle, imolecule_kind, natom, nbend, &
972  nbond, nimpr, nmolecule, &
973  nmolecule_kind, nopbend, ntors, &
974  ntotal, nub, output_unit
975  LOGICAL :: all_single_atoms
976  TYPE(cp_logger_type), POINTER :: logger
977 
978  CALL timeset(routinen, handle)
979 
980  NULLIFY (logger)
981  logger => cp_get_default_logger()
982  output_unit = cp_print_key_unit_nr(logger, subsys_section, &
983  "PRINT%MOLECULES", extension=".Log")
984  IF (output_unit > 0) THEN
985  WRITE (unit=output_unit, fmt="(/,/,T2,A)") "MOLECULE KIND INFORMATION"
986 
987  nmolecule_kind = SIZE(molecule_kind_set)
988 
989  all_single_atoms = .true.
990  DO imolecule_kind = 1, nmolecule_kind
991  natom = SIZE(molecule_kind_set(imolecule_kind)%atom_list)
992  nmolecule = SIZE(molecule_kind_set(imolecule_kind)%molecule_list)
993  IF (natom*nmolecule > 1) all_single_atoms = .false.
994  END DO
995 
996  IF (all_single_atoms) THEN
997  WRITE (unit=output_unit, fmt="(/,/,T2,A)") &
998  "All atoms are their own molecule, skipping detailed information"
999  ELSE
1000  DO imolecule_kind = 1, nmolecule_kind
1001  CALL write_molecule_kind(molecule_kind_set(imolecule_kind), output_unit)
1002  END DO
1003  END IF
1004 
1005  CALL get_molecule_kind_set(molecule_kind_set=molecule_kind_set, &
1006  nbond=nbond, &
1007  nbend=nbend, &
1008  nub=nub, &
1009  ntorsion=ntors, &
1010  nimpr=nimpr, &
1011  nopbend=nopbend)
1012  ntotal = nbond + nbend + nub + ntors + nimpr + nopbend
1013  IF (ntotal > 0) THEN
1014  WRITE (unit=output_unit, fmt="(/,/,T2,A,T45,A30,I6)") &
1015  "MOLECULE KIND SET INFORMATION", &
1016  "Total Number of bonds: ", nbond
1017  WRITE (unit=output_unit, fmt="(T45,A30,I6)") &
1018  "Total Number of bends: ", nbend
1019  WRITE (unit=output_unit, fmt="(T45,A30,I6)") &
1020  "Total Number of Urey-Bradley:", nub
1021  WRITE (unit=output_unit, fmt="(T45,A30,I6)") &
1022  "Total Number of torsions: ", ntors
1023  WRITE (unit=output_unit, fmt="(T45,A30,I6)") &
1024  "Total Number of improper: ", nimpr
1025  WRITE (unit=output_unit, fmt="(T45,A30,I6)") &
1026  "Total Number of opbends: ", nopbend
1027  END IF
1028  END IF
1029  CALL cp_print_key_finished_output(output_unit, logger, subsys_section, &
1030  "PRINT%MOLECULES")
1031 
1032  CALL timestop(handle)
1033 
1034  END SUBROUTINE write_molecule_kind_set
1035 
1036 END MODULE molecule_kind_types
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
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
colvar_types
Initialize the collective variables types.
Definition: colvar_types.F:15
colvar_types::population_colvar_id
integer, parameter, public population_colvar_id
Definition: colvar_types.F:56
colvar_types::acid_hyd_dist_colvar_id
integer, parameter, public acid_hyd_dist_colvar_id
Definition: colvar_types.F:56
colvar_types::xyz_outerdiag_colvar_id
integer, parameter, public xyz_outerdiag_colvar_id
Definition: colvar_types.F:56
colvar_types::plane_plane_angle_colvar_id
integer, parameter, public plane_plane_angle_colvar_id
Definition: colvar_types.F:56
colvar_types::plane_distance_colvar_id
integer, parameter, public plane_distance_colvar_id
Definition: colvar_types.F:56
colvar_types::combine_colvar_id
integer, parameter, public combine_colvar_id
Definition: colvar_types.F:56
colvar_types::gyration_colvar_id
integer, parameter, public gyration_colvar_id
Definition: colvar_types.F:56
colvar_types::rotation_colvar_id
integer, parameter, public rotation_colvar_id
Definition: colvar_types.F:56
colvar_types::hydronium_dist_colvar_id
integer, parameter, public hydronium_dist_colvar_id
Definition: colvar_types.F:56
colvar_types::coord_colvar_id
integer, parameter, public coord_colvar_id
Definition: colvar_types.F:56
colvar_types::dfunct_colvar_id
integer, parameter, public dfunct_colvar_id
Definition: colvar_types.F:56
colvar_types::no_colvar_id
integer, parameter, public no_colvar_id
Definition: colvar_types.F:56
colvar_types::angle_colvar_id
integer, parameter, public angle_colvar_id
Definition: colvar_types.F:56
colvar_types::qparm_colvar_id
integer, parameter, public qparm_colvar_id
Definition: colvar_types.F:56
colvar_types::dist_colvar_id
integer, parameter, public dist_colvar_id
Definition: colvar_types.F:56
colvar_types::hydronium_shell_colvar_id
integer, parameter, public hydronium_shell_colvar_id
Definition: colvar_types.F:56
colvar_types::torsion_colvar_id
integer, parameter, public torsion_colvar_id
Definition: colvar_types.F:56
colvar_types::xyz_diag_colvar_id
integer, parameter, public xyz_diag_colvar_id
Definition: colvar_types.F:56
colvar_types::reaction_path_colvar_id
integer, parameter, public reaction_path_colvar_id
Definition: colvar_types.F:56
colvar_types::acid_hyd_shell_colvar_id
integer, parameter, public acid_hyd_shell_colvar_id
Definition: colvar_types.F:56
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:803
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:1013
force_field_kind_types
Define all structure types related to force field kinds.
Definition: force_field_kind_types.F:14
force_field_kind_types::do_ff_undef
integer, parameter, public do_ff_undef
Definition: force_field_kind_types.F:25
force_field_kind_types::torsion_kind_dealloc_ref
pure subroutine, public torsion_kind_dealloc_ref(torsion_kind)
Deallocate a torsion kind element.
Definition: force_field_kind_types.F:271
force_field_kind_types::ub_kind_dealloc_ref
pure subroutine, public ub_kind_dealloc_ref(ub_kind_set)
Deallocate a ub kind set.
Definition: force_field_kind_types.F:291
force_field_kind_types::impr_kind_dealloc_ref
pure subroutine, public impr_kind_dealloc_ref()
Deallocate a impr kind element.
Definition: force_field_kind_types.F:301
input_section_types
objects that represent the structure of input sections and the data contained in an input section
Definition: input_section_types.F:15
kinds
Defines the basic variable types.
Definition: kinds.F:23
kinds::dp
integer, parameter, public dp
Definition: kinds.F:34
kinds::default_string_length
integer, parameter, public default_string_length
Definition: kinds.F:57
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_kind_types::setup_colvar_counters
subroutine, public setup_colvar_counters(colv_list, ncolv)
...
Definition: molecule_kind_types.F:239
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:779
molecule_kind_types::deallocate_molecule_kind_set
subroutine, public deallocate_molecule_kind_set(molecule_kind_set)
Deallocate a molecule kind set.
Definition: molecule_kind_types.F:350
molecule_kind_types::get_molecule_kind_set
subroutine, public get_molecule_kind_set(molecule_kind_set, maxatom, natom, nbond, nbend, nub, ntorsion, nimpr, nopbend, nconstraint, nconstraint_fixd, nmolecule, nrestraints)
Get informations about a molecule kind set.
Definition: molecule_kind_types.F:658
molecule_kind_types::write_molecule_kind_set
subroutine, public write_molecule_kind_set(molecule_kind_set, subsys_section)
Write a moleculeatomic kind set data set to the output unit.
Definition: molecule_kind_types.F:966
molecule_kind_types::allocate_molecule_kind_set
subroutine, public allocate_molecule_kind_set(molecule_kind_set, nmolecule_kind)
Allocate and initialize a molecule kind set.
Definition: molecule_kind_types.F:323
shell_potential_types
Definition: shell_potential_types.F:11