(git:b195825)
topology_input.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 Reads the input sections "topology"
10 !> \par History
11 !> JGH (26-01-2002) Added read_topology_section
12 !> \author JGH
13 ! **************************************************************************************************
14 MODULE topology_input
15  USE colvar_types, ONLY: colvar_clone,&
16  colvar_p_type
17  USE cp_log_handling, ONLY: cp_logger_get_default_io_unit,&
18  cp_to_string
19  USE input_constants, ONLY: do_conn_generate,&
20  do_conn_mol_set,&
21  do_conn_off,&
22  do_conn_user,&
23  do_constr_none,&
24  do_coord_off
25  USE input_section_types, ONLY: section_vals_get,&
26  section_vals_get_subs_vals,&
27  section_vals_type,&
28  section_vals_val_get,&
29  section_vals_val_unset
30  USE kinds, ONLY: default_string_length,&
31  dp
32  USE memory_utilities, ONLY: reallocate
33  USE topology_types, ONLY: constraint_info_type,&
34  topology_parameters_type
35 #include "./base/base_uses.f90"
36 
37  IMPLICIT NONE
38 
39  CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'topology_input'
40 
41  PRIVATE
42  PUBLIC :: read_topology_section, read_constraints_section
43 
44 CONTAINS
45 
46 ! **************************************************************************************************
47 !> \brief reads the input section topology
48 !> \param topology ...
49 !> \param topology_section ...
50 !> \par History
51 !> none
52 !> \author JGH (26-01-2002)
53 ! **************************************************************************************************
54  SUBROUTINE read_topology_section(topology, topology_section)
55  TYPE(topology_parameters_type) :: topology
56  TYPE(section_vals_type), POINTER :: topology_section
57 
58  CHARACTER(len=*), PARAMETER :: routinen = 'read_topology_section'
59 
60  INTEGER :: handle, ival
61 
62  CALL timeset(routinen, handle)
63  CALL section_vals_val_get(topology_section, "CHARGE_OCCUP", l_val=topology%charge_occup)
64  CALL section_vals_val_get(topology_section, "CHARGE_BETA", l_val=topology%charge_beta)
65  CALL section_vals_val_get(topology_section, "CHARGE_EXTENDED", l_val=topology%charge_extended)
66  ival = count((/topology%charge_occup, topology%charge_beta, topology%charge_extended/))
67  IF (ival > 1) &
68  cpabort("Only one between <CHARGE_OCCUP,CHARGE_BETA,CHARGE_EXTENDED> can be defined! ")
69  CALL section_vals_val_get(topology_section, "PARA_RES", l_val=topology%para_res)
70  CALL section_vals_val_get(topology_section, "GENERATE%REORDER", l_val=topology%reorder_atom)
71  CALL section_vals_val_get(topology_section, "GENERATE%CREATE_MOLECULES", l_val=topology%create_molecules)
72  CALL section_vals_val_get(topology_section, "MOL_CHECK", l_val=topology%molecules_check)
73  CALL section_vals_val_get(topology_section, "USE_G96_VELOCITY", l_val=topology%use_g96_velocity)
74  CALL section_vals_val_get(topology_section, "COORD_FILE_FORMAT", i_val=topology%coord_type)
75  SELECT CASE (topology%coord_type)
76  CASE (do_coord_off)
77  ! Do Nothing
78  CASE DEFAULT
79  topology%coordinate = .true.
80  CALL section_vals_val_get(topology_section, "COORD_FILE_NAME", c_val=topology%coord_file_name)
81  END SELECT
82  CALL section_vals_val_get(topology_section, "CONN_FILE_FORMAT", i_val=topology%conn_type)
83  SELECT CASE (topology%conn_type)
84  CASE (do_conn_off, do_conn_generate, do_conn_mol_set, do_conn_user)
85  ! Do Nothing
86  CASE DEFAULT
87  CALL section_vals_val_get(topology_section, "CONN_FILE_NAME", c_val=topology%conn_file_name)
88  END SELECT
89  CALL section_vals_val_get(topology_section, "EXCLUDE_VDW", i_val=topology%exclude_vdw)
90  CALL section_vals_val_get(topology_section, "EXCLUDE_EI", i_val=topology%exclude_ei)
91  CALL section_vals_val_get(topology_section, "GENERATE%BONDPARM", i_val=topology%bondparm_type)
92  CALL section_vals_val_get(topology_section, "GENERATE%BONDPARM_FACTOR", r_val=topology%bondparm_factor)
93  CALL timestop(handle)
94  END SUBROUTINE read_topology_section
95 
96 ! **************************************************************************************************
97 !> \brief Read all the distance parameters. Put them in the
98 !> constraint_distance array.
99 !> \param topology ...
100 !> \param colvar_p ...
101 !> \param constraint_section ...
102 !> \par History
103 !> JGH (26-01-2002) Distance parameters are now stored in tables. The position
104 !> within the table is used as handle for the topology
105 !> teo Read the CONSTRAINT section within the new input style
106 !> \author teo
107 ! **************************************************************************************************
108  SUBROUTINE read_constraints_section(topology, colvar_p, constraint_section)
109 
110  TYPE(topology_parameters_type), INTENT(INOUT) :: topology
111  TYPE(colvar_p_type), DIMENSION(:), POINTER :: colvar_p
112  TYPE(section_vals_type), POINTER :: constraint_section
113 
114  CHARACTER(LEN=default_string_length), &
115  DIMENSION(:), POINTER :: tmpstringlist
116  INTEGER :: icolvar, ig, isize, isize_old, itype, &
117  jg, msize, msize_old, n_rep, ncons, &
118  nrep
119  INTEGER, DIMENSION(:), POINTER :: ilist, tmplist
120  LOGICAL :: explicit
121  REAL(kind=dp), DIMENSION(:), POINTER :: rlist
122  TYPE(constraint_info_type), POINTER :: cons_info
123  TYPE(section_vals_type), POINTER :: collective_section, fix_atom_section, &
124  g3x3_section, g4x6_section, &
125  hbonds_section, vsite_section
126 
127  cons_info => topology%cons_info
128  IF (ASSOCIATED(constraint_section)) THEN
129  hbonds_section => section_vals_get_subs_vals(constraint_section, "HBONDS")
130  g3x3_section => section_vals_get_subs_vals(constraint_section, "G3X3")
131  g4x6_section => section_vals_get_subs_vals(constraint_section, "G4X6")
132  vsite_section => section_vals_get_subs_vals(constraint_section, "VIRTUAL_SITE")
133  fix_atom_section => section_vals_get_subs_vals(constraint_section, "FIXED_ATOMS")
134  collective_section => section_vals_get_subs_vals(constraint_section, "COLLECTIVE")
135  ! HBONDS
136  CALL section_vals_get(hbonds_section, explicit=topology%const_hydr)
137  CALL check_restraint(hbonds_section, &
138  is_restraint=cons_info%hbonds_restraint, &
139  k0=cons_info%hbonds_k0, &
140  label="HBONDS")
141  ! G3X3
142  CALL section_vals_get(g3x3_section, explicit=explicit, n_repetition=ncons)
143  IF (explicit) THEN
144  topology%const_33 = .true.
145  cons_info%nconst_g33 = ncons
146  !
147  ALLOCATE (cons_info%const_g33_mol(ncons))
148  ALLOCATE (cons_info%const_g33_molname(ncons))
149  ALLOCATE (cons_info%const_g33_a(ncons))
150  ALLOCATE (cons_info%const_g33_b(ncons))
151  ALLOCATE (cons_info%const_g33_c(ncons))
152  ALLOCATE (cons_info%const_g33_dab(ncons))
153  ALLOCATE (cons_info%const_g33_dac(ncons))
154  ALLOCATE (cons_info%const_g33_dbc(ncons))
155  ALLOCATE (cons_info%g33_intermolecular(ncons))
156  ALLOCATE (cons_info%g33_restraint(ncons))
157  ALLOCATE (cons_info%g33_k0(ncons))
158  ALLOCATE (cons_info%g33_exclude_qm(ncons))
159  ALLOCATE (cons_info%g33_exclude_mm(ncons))
160  DO ig = 1, ncons
161  CALL check_restraint(g3x3_section, &
162  is_restraint=cons_info%g33_restraint(ig), &
163  k0=cons_info%g33_k0(ig), &
164  i_rep_section=ig, &
165  label="G3X3")
166  cons_info%const_g33_mol(ig) = 0
167  cons_info%const_g33_molname(ig) = "UNDEF"
168  ! Exclude QM or MM
169  CALL section_vals_val_get(g3x3_section, "EXCLUDE_QM", i_rep_section=ig, &
170  l_val=cons_info%g33_exclude_qm(ig))
171  CALL section_vals_val_get(g3x3_section, "EXCLUDE_MM", i_rep_section=ig, &
172  l_val=cons_info%g33_exclude_mm(ig))
173  ! Intramolecular restraint
174  CALL section_vals_val_get(g3x3_section, "INTERMOLECULAR", i_rep_section=ig, &
175  l_val=cons_info%g33_intermolecular(ig))
176  ! If it is intramolecular let's unset (in case user did it)
177  ! the molecule and molname field
178  IF (cons_info%g33_intermolecular(ig)) THEN
179  CALL section_vals_val_unset(g3x3_section, "MOLECULE", i_rep_section=ig)
180  CALL section_vals_val_unset(g3x3_section, "MOLNAME", i_rep_section=ig)
181  END IF
182  ! Let's tag to which molecule we want to apply constraints
183  CALL section_vals_val_get(g3x3_section, "MOLECULE", i_rep_section=ig, &
184  n_rep_val=nrep)
185  IF (nrep /= 0) THEN
186  CALL section_vals_val_get(g3x3_section, "MOLECULE", i_rep_section=ig, &
187  i_val=cons_info%const_g33_mol(ig))
188  END IF
189  CALL section_vals_val_get(g3x3_section, "MOLNAME", i_rep_section=ig, &
190  n_rep_val=nrep)
191  IF (nrep /= 0) THEN
192  CALL section_vals_val_get(g3x3_section, "MOLNAME", i_rep_section=ig, &
193  c_val=cons_info%const_g33_molname(ig))
194  END IF
195  IF ((cons_info%const_g33_mol(ig) /= 0) .AND. (cons_info%const_g33_molname(ig) /= "UNDEF")) THEN
196  cpabort("")
197  END IF
198  IF ((cons_info%const_g33_mol(ig) == 0) .AND. (cons_info%const_g33_molname(ig) == "UNDEF") .AND. &
199  (.NOT. cons_info%g33_intermolecular(ig))) THEN
200  cpabort("")
201  END IF
202  CALL section_vals_val_get(g3x3_section, "ATOMS", i_rep_section=ig, &
203  i_vals=ilist)
204  CALL section_vals_val_get(g3x3_section, "DISTANCES", i_rep_section=ig, &
205  r_vals=rlist)
206  cons_info%const_g33_a(ig) = ilist(1)
207  cons_info%const_g33_b(ig) = ilist(2)
208  cons_info%const_g33_c(ig) = ilist(3)
209 
210  cons_info%const_g33_dab(ig) = rlist(1)
211  cons_info%const_g33_dac(ig) = rlist(2)
212  cons_info%const_g33_dbc(ig) = rlist(3)
213  END DO
214  END IF
215  ! G4X6
216  CALL section_vals_get(g4x6_section, explicit=explicit, n_repetition=ncons)
217  IF (explicit) THEN
218  topology%const_46 = .true.
219  cons_info%nconst_g46 = ncons
220  !
221  ALLOCATE (cons_info%const_g46_mol(ncons))
222  ALLOCATE (cons_info%const_g46_molname(ncons))
223  ALLOCATE (cons_info%const_g46_a(ncons))
224  ALLOCATE (cons_info%const_g46_b(ncons))
225  ALLOCATE (cons_info%const_g46_c(ncons))
226  ALLOCATE (cons_info%const_g46_d(ncons))
227  ALLOCATE (cons_info%const_g46_dab(ncons))
228  ALLOCATE (cons_info%const_g46_dac(ncons))
229  ALLOCATE (cons_info%const_g46_dbc(ncons))
230  ALLOCATE (cons_info%const_g46_dad(ncons))
231  ALLOCATE (cons_info%const_g46_dbd(ncons))
232  ALLOCATE (cons_info%const_g46_dcd(ncons))
233  ALLOCATE (cons_info%g46_intermolecular(ncons))
234  ALLOCATE (cons_info%g46_restraint(ncons))
235  ALLOCATE (cons_info%g46_k0(ncons))
236  ALLOCATE (cons_info%g46_exclude_qm(ncons))
237  ALLOCATE (cons_info%g46_exclude_mm(ncons))
238  DO ig = 1, ncons
239  CALL check_restraint(g4x6_section, &
240  is_restraint=cons_info%g46_restraint(ig), &
241  k0=cons_info%g46_k0(ig), &
242  i_rep_section=ig, &
243  label="G4X6")
244  cons_info%const_g46_mol(ig) = 0
245  cons_info%const_g46_molname(ig) = "UNDEF"
246  ! Exclude QM or MM
247  CALL section_vals_val_get(g4x6_section, "EXCLUDE_QM", i_rep_section=ig, &
248  l_val=cons_info%g46_exclude_qm(ig))
249  CALL section_vals_val_get(g4x6_section, "EXCLUDE_MM", i_rep_section=ig, &
250  l_val=cons_info%g46_exclude_mm(ig))
251  ! Intramolecular restraint
252  CALL section_vals_val_get(g4x6_section, "INTERMOLECULAR", i_rep_section=ig, &
253  l_val=cons_info%g46_intermolecular(ig))
254  ! If it is intramolecular let's unset (in case user did it)
255  ! the molecule and molname field
256  IF (cons_info%g46_intermolecular(ig)) THEN
257  CALL section_vals_val_unset(g4x6_section, "MOLECULE", i_rep_section=ig)
258  CALL section_vals_val_unset(g4x6_section, "MOLNAME", i_rep_section=ig)
259  END IF
260  ! Let's tag to which molecule we want to apply constraints
261  CALL section_vals_val_get(g4x6_section, "MOLECULE", i_rep_section=ig, &
262  n_rep_val=nrep)
263  IF (nrep /= 0) THEN
264  CALL section_vals_val_get(g4x6_section, "MOLECULE", i_rep_section=ig, &
265  i_val=cons_info%const_g46_mol(ig))
266  END IF
267  CALL section_vals_val_get(g4x6_section, "MOLNAME", i_rep_section=ig, &
268  n_rep_val=nrep)
269  IF (nrep /= 0) THEN
270  CALL section_vals_val_get(g4x6_section, "MOLNAME", i_rep_section=ig, &
271  c_val=cons_info%const_g46_molname(ig))
272  END IF
273  IF ((cons_info%const_g46_mol(ig) /= 0) .AND. (cons_info%const_g46_molname(ig) /= "UNDEF")) THEN
274  cpabort("")
275  END IF
276  IF ((cons_info%const_g46_mol(ig) == 0) .AND. (cons_info%const_g46_molname(ig) == "UNDEF") .AND. &
277  (.NOT. cons_info%g46_intermolecular(ig))) THEN
278  cpabort("")
279  END IF
280  CALL section_vals_val_get(g4x6_section, "ATOMS", i_rep_section=ig, &
281  i_vals=ilist)
282  CALL section_vals_val_get(g4x6_section, "DISTANCES", i_rep_section=ig, &
283  r_vals=rlist)
284  cons_info%const_g46_a(ig) = ilist(1)
285  cons_info%const_g46_b(ig) = ilist(2)
286  cons_info%const_g46_c(ig) = ilist(3)
287  cons_info%const_g46_d(ig) = ilist(4)
288  cons_info%const_g46_dab(ig) = rlist(1)
289  cons_info%const_g46_dac(ig) = rlist(2)
290  cons_info%const_g46_dad(ig) = rlist(3)
291  cons_info%const_g46_dbc(ig) = rlist(4)
292  cons_info%const_g46_dbd(ig) = rlist(5)
293  cons_info%const_g46_dcd(ig) = rlist(6)
294  END DO
295  END IF
296  ! virtual
297  CALL section_vals_get(vsite_section, explicit=explicit, n_repetition=ncons)
298  IF (explicit) THEN
299  topology%const_vsite = .true.
300  cons_info%nconst_vsite = ncons
301  !
302  ALLOCATE (cons_info%const_vsite_mol(ncons))
303  ALLOCATE (cons_info%const_vsite_molname(ncons))
304  ALLOCATE (cons_info%const_vsite_a(ncons))
305  ALLOCATE (cons_info%const_vsite_b(ncons))
306  ALLOCATE (cons_info%const_vsite_c(ncons))
307  ALLOCATE (cons_info%const_vsite_d(ncons))
308  ALLOCATE (cons_info%const_vsite_wbc(ncons))
309  ALLOCATE (cons_info%const_vsite_wdc(ncons))
310  ALLOCATE (cons_info%vsite_intermolecular(ncons))
311  ALLOCATE (cons_info%vsite_restraint(ncons))
312  ALLOCATE (cons_info%vsite_k0(ncons))
313  ALLOCATE (cons_info%vsite_exclude_qm(ncons))
314  ALLOCATE (cons_info%vsite_exclude_mm(ncons))
315  DO ig = 1, ncons
316  CALL check_restraint(vsite_section, &
317  is_restraint=cons_info%vsite_restraint(ig), &
318  k0=cons_info%vsite_k0(ig), &
319  i_rep_section=ig, &
320  label="Virtual_SITE")
321  cons_info%const_vsite_mol(ig) = 0
322  cons_info%const_vsite_molname(ig) = "UNDEF"
323  ! Exclude QM or MM
324  CALL section_vals_val_get(vsite_section, "EXCLUDE_QM", i_rep_section=ig, &
325  l_val=cons_info%vsite_exclude_qm(ig))
326  CALL section_vals_val_get(vsite_section, "EXCLUDE_MM", i_rep_section=ig, &
327  l_val=cons_info%vsite_exclude_mm(ig))
328  ! Intramolecular restraint
329  CALL section_vals_val_get(vsite_section, "INTERMOLECULAR", i_rep_section=ig, &
330  l_val=cons_info%vsite_intermolecular(ig))
331  ! If it is intramolecular let's unset (in case user did it)
332  ! the molecule and molname field
333  IF (cons_info%vsite_intermolecular(ig)) THEN
334  CALL section_vals_val_unset(vsite_section, "MOLECULE", i_rep_section=ig)
335  CALL section_vals_val_unset(vsite_section, "MOLNAME", i_rep_section=ig)
336  END IF
337  ! Let's tag to which molecule we want to apply constraints
338  CALL section_vals_val_get(vsite_section, "MOLECULE", i_rep_section=ig, &
339  n_rep_val=nrep)
340  IF (nrep /= 0) THEN
341  CALL section_vals_val_get(vsite_section, "MOLECULE", i_rep_section=ig, &
342  i_val=cons_info%const_vsite_mol(ig))
343  END IF
344  CALL section_vals_val_get(vsite_section, "MOLNAME", i_rep_section=ig, &
345  n_rep_val=nrep)
346  IF (nrep /= 0) THEN
347  CALL section_vals_val_get(vsite_section, "MOLNAME", i_rep_section=ig, &
348  c_val=cons_info%const_vsite_molname(ig))
349  END IF
350  IF ((cons_info%const_vsite_mol(ig) /= 0) .AND. (cons_info%const_vsite_molname(ig) /= "UNDEF")) THEN
351  cpabort("")
352  END IF
353  IF ((cons_info%const_vsite_mol(ig) == 0) .AND. (cons_info%const_vsite_molname(ig) == "UNDEF") .AND. &
354  (.NOT. cons_info%vsite_intermolecular(ig))) THEN
355  cpabort("")
356  END IF
357  CALL section_vals_val_get(vsite_section, "ATOMS", i_rep_section=ig, &
358  i_vals=ilist)
359  CALL section_vals_val_get(vsite_section, "PARAMETERS", i_rep_section=ig, &
360  r_vals=rlist)
361  cons_info%const_vsite_a(ig) = ilist(1)
362  cons_info%const_vsite_b(ig) = ilist(2)
363  cons_info%const_vsite_c(ig) = ilist(3)
364  cons_info%const_vsite_d(ig) = ilist(4)
365  cons_info%const_vsite_wbc(ig) = rlist(1)
366  cons_info%const_vsite_wdc(ig) = rlist(2)
367  END DO
368  END IF
369  ! FIXED ATOMS
370  CALL section_vals_get(fix_atom_section, explicit=explicit, n_repetition=ncons)
371  IF (explicit) THEN
372  NULLIFY (tmplist, tmpstringlist)
373  isize = 0
374  msize = 0
375  ALLOCATE (cons_info%fixed_atoms(isize))
376  ALLOCATE (cons_info%fixed_type(isize))
377  ALLOCATE (cons_info%fixed_restraint(isize))
378  ALLOCATE (cons_info%fixed_k0(isize))
379  ALLOCATE (cons_info%fixed_molnames(msize))
380  ALLOCATE (cons_info%fixed_mol_type(isize))
381  ALLOCATE (cons_info%fixed_mol_restraint(msize))
382  ALLOCATE (cons_info%fixed_mol_k0(msize))
383  ALLOCATE (cons_info%fixed_exclude_qm(ncons))
384  ALLOCATE (cons_info%fixed_exclude_mm(ncons))
385  DO ig = 1, ncons
386  isize_old = isize
387  msize_old = msize
388  CALL section_vals_val_get(fix_atom_section, "COMPONENTS_TO_FIX", i_rep_section=ig, &
389  i_val=itype)
390  CALL section_vals_val_get(fix_atom_section, "LIST", i_rep_section=ig, &
391  n_rep_val=n_rep)
392  DO jg = 1, n_rep
393  CALL section_vals_val_get(fix_atom_section, "LIST", i_rep_section=ig, &
394  i_rep_val=jg, i_vals=tmplist)
395  CALL reallocate(cons_info%fixed_atoms, 1, isize + SIZE(tmplist))
396  cons_info%fixed_atoms(isize + 1:isize + SIZE(tmplist)) = tmplist
397  CALL reallocate(cons_info%fixed_restraint, 1, isize + SIZE(tmplist))
398  CALL reallocate(cons_info%fixed_k0, 1, isize + SIZE(tmplist))
399  CALL reallocate(cons_info%fixed_type, 1, isize + SIZE(tmplist))
400  cons_info%fixed_type(isize + 1:isize + SIZE(tmplist)) = itype
401  isize = SIZE(cons_info%fixed_atoms)
402  END DO
403  !Check for restraints
404  IF ((isize - isize_old) > 0) THEN
405  CALL check_restraint(fix_atom_section, &
406  is_restraint=cons_info%fixed_restraint(isize_old + 1), &
407  k0=cons_info%fixed_k0(isize_old + 1), &
408  i_rep_section=ig, &
409  label="FIXED ATOM")
410  cons_info%fixed_restraint(isize_old + 1:isize) = cons_info%fixed_restraint(isize_old + 1)
411  cons_info%fixed_k0(isize_old + 1:isize) = cons_info%fixed_k0(isize_old + 1)
412  END IF
413  CALL section_vals_val_get(fix_atom_section, "MOLNAME", i_rep_section=ig, &
414  n_rep_val=n_rep)
415  IF (n_rep /= 0) THEN
416  DO jg = 1, n_rep
417  CALL section_vals_val_get(fix_atom_section, "MOLNAME", i_rep_section=ig, &
418  i_rep_val=jg, c_vals=tmpstringlist)
419  CALL reallocate(cons_info%fixed_molnames, 1, msize + SIZE(tmpstringlist, 1))
420  CALL reallocate(cons_info%fixed_mol_type, 1, msize + SIZE(tmpstringlist, 1))
421  CALL reallocate(cons_info%fixed_mol_restraint, 1, msize + SIZE(tmpstringlist, 1))
422  CALL reallocate(cons_info%fixed_mol_k0, 1, msize + SIZE(tmpstringlist, 1))
423  cons_info%fixed_molnames(msize + 1:msize + SIZE(tmpstringlist, 1)) = tmpstringlist
424  cons_info%fixed_mol_type(msize + 1:msize + SIZE(tmpstringlist, 1)) = itype
425  msize = SIZE(cons_info%fixed_molnames)
426  END DO
427  ! Exclude QM or MM work only if defined MOLNAME
428  CALL reallocate(cons_info%fixed_exclude_qm, 1, msize)
429  CALL reallocate(cons_info%fixed_exclude_mm, 1, msize)
430  CALL section_vals_val_get(fix_atom_section, "EXCLUDE_QM", i_rep_section=ig, &
431  l_val=cons_info%fixed_exclude_qm(msize_old + 1))
432  CALL section_vals_val_get(fix_atom_section, "EXCLUDE_MM", i_rep_section=ig, &
433  l_val=cons_info%fixed_exclude_mm(msize_old + 1))
434  cons_info%fixed_exclude_qm(msize_old + 1:msize) = cons_info%fixed_exclude_qm(msize_old + 1)
435  cons_info%fixed_exclude_mm(msize_old + 1:msize) = cons_info%fixed_exclude_mm(msize_old + 1)
436  END IF
437  !Check for restraints
438  IF (n_rep /= 0) THEN
439  CALL check_restraint(fix_atom_section, &
440  is_restraint=cons_info%fixed_mol_restraint(msize_old + 1), &
441  k0=cons_info%fixed_mol_k0(msize_old + 1), &
442  i_rep_section=ig, &
443  label="FIXED ATOM")
444  cons_info%fixed_mol_restraint(msize_old + 1:msize) = cons_info%fixed_mol_restraint(msize_old + 1)
445  cons_info%fixed_mol_k0(msize_old + 1:msize) = cons_info%fixed_mol_k0(msize_old + 1)
446  END IF
447  CALL section_vals_val_get(fix_atom_section, "MM_SUBSYS", i_rep_section=ig, &
448  n_rep_val=nrep, explicit=explicit)
449  IF (nrep == 1 .AND. explicit) THEN
450  cpassert(cons_info%freeze_mm == do_constr_none)
451  CALL section_vals_val_get(fix_atom_section, "MM_SUBSYS", i_val=cons_info%freeze_mm, &
452  i_rep_section=ig)
453  cons_info%freeze_mm_type = itype
454  END IF
455  CALL section_vals_val_get(fix_atom_section, "QM_SUBSYS", i_rep_section=ig, &
456  n_rep_val=nrep, explicit=explicit)
457  IF (nrep == 1 .AND. explicit) THEN
458  cpassert(cons_info%freeze_qm == do_constr_none)
459  CALL section_vals_val_get(fix_atom_section, "QM_SUBSYS", i_val=cons_info%freeze_qm, &
460  i_rep_section=ig)
461  cons_info%freeze_qm_type = itype
462  END IF
463  IF (cons_info%freeze_mm /= do_constr_none) THEN
464  CALL check_restraint(fix_atom_section, &
465  is_restraint=cons_info%fixed_mm_restraint, &
466  k0=cons_info%fixed_mm_k0, &
467  i_rep_section=ig, &
468  label="FIXED ATOM")
469  END IF
470  IF (cons_info%freeze_qm /= do_constr_none) THEN
471  CALL check_restraint(fix_atom_section, &
472  is_restraint=cons_info%fixed_qm_restraint, &
473  k0=cons_info%fixed_qm_k0, &
474  i_rep_section=ig, &
475  label="FIXED ATOM")
476  END IF
477 
478  END DO
479  IF ((isize /= 0) .OR. (msize /= 0) .OR. &
480  (cons_info%freeze_mm /= do_constr_none) .OR. &
481  (cons_info%freeze_qm /= do_constr_none)) THEN
482  topology%const_atom = .true.
483  END IF
484  END IF
485  ! Collective Constraints
486  CALL section_vals_get(collective_section, explicit=explicit, n_repetition=ncons)
487  IF (explicit) THEN
488  topology%const_colv = .true.
489  DO ig = 1, ncons
490  CALL section_vals_val_get(collective_section, "COLVAR", i_rep_section=ig, i_val=icolvar)
491  cpassert(icolvar <= SIZE(colvar_p))
492  END DO
493  cons_info%nconst_colv = ncons
494  ALLOCATE (cons_info%const_colv_mol(ncons))
495  ALLOCATE (cons_info%const_colv_molname(ncons))
496  ALLOCATE (cons_info%const_colv_target(ncons))
497  ALLOCATE (cons_info%const_colv_target_growth(ncons))
498  ALLOCATE (cons_info%colvar_set(ncons))
499  ALLOCATE (cons_info%colv_intermolecular(ncons))
500  ALLOCATE (cons_info%colv_restraint(ncons))
501  ALLOCATE (cons_info%colv_k0(ncons))
502  ALLOCATE (cons_info%colv_exclude_qm(ncons))
503  ALLOCATE (cons_info%colv_exclude_mm(ncons))
504  DO ig = 1, ncons
505  CALL check_restraint(collective_section, &
506  is_restraint=cons_info%colv_restraint(ig), &
507  k0=cons_info%colv_k0(ig), &
508  i_rep_section=ig, &
509  label="COLLECTIVE")
510  cons_info%const_colv_mol(ig) = 0
511  cons_info%const_colv_molname(ig) = "UNDEF"
512  ! Exclude QM or MM
513  CALL section_vals_val_get(collective_section, "EXCLUDE_QM", i_rep_section=ig, &
514  l_val=cons_info%colv_exclude_qm(ig))
515  CALL section_vals_val_get(collective_section, "EXCLUDE_MM", i_rep_section=ig, &
516  l_val=cons_info%colv_exclude_mm(ig))
517  ! Intramolecular restraint
518  CALL section_vals_val_get(collective_section, "INTERMOLECULAR", i_rep_section=ig, &
519  l_val=cons_info%colv_intermolecular(ig))
520  ! If it is intramolecular let's unset (in case user did it)
521  ! the molecule and molname field
522  IF (cons_info%colv_intermolecular(ig)) THEN
523  CALL section_vals_val_unset(collective_section, "MOLECULE", i_rep_section=ig)
524  CALL section_vals_val_unset(collective_section, "MOLNAME", i_rep_section=ig)
525  END IF
526  ! Let's tag to which molecule we want to apply constraints
527  CALL section_vals_val_get(collective_section, "MOLECULE", i_rep_section=ig, &
528  n_rep_val=nrep)
529  IF (nrep /= 0) THEN
530  CALL section_vals_val_get(collective_section, "MOLECULE", i_rep_section=ig, &
531  i_val=cons_info%const_colv_mol(ig))
532  END IF
533  CALL section_vals_val_get(collective_section, "MOLNAME", i_rep_section=ig, &
534  n_rep_val=nrep)
535  IF (nrep /= 0) THEN
536  CALL section_vals_val_get(collective_section, "MOLNAME", i_rep_section=ig, &
537  c_val=cons_info%const_colv_molname(ig))
538  END IF
539  IF (((cons_info%const_colv_mol(ig) /= 0) .AND. (cons_info%const_colv_molname(ig) /= "UNDEF"))) THEN
540  cpabort("Both MOLNAME and MOLECULE specified for CONSTRAINT section. ")
541  END IF
542  IF ((cons_info%const_colv_mol(ig) == 0) .AND. (cons_info%const_colv_molname(ig) == "UNDEF") .AND. &
543  (.NOT. cons_info%colv_intermolecular(ig))) THEN
544  CALL cp_abort(__location__, &
545  "Constraint section error: you have to specify at least one of the "// &
546  "following keywords: MOLECULE, MOLNAME or INTERMOLECULAR! ")
547  END IF
548  NULLIFY (cons_info%colvar_set(ig)%colvar)
549  CALL section_vals_val_get(collective_section, "COLVAR", i_rep_section=ig, &
550  i_val=icolvar)
551  CALL colvar_clone(cons_info%colvar_set(ig)%colvar, &
552  colvar_p(icolvar)%colvar)
553  CALL section_vals_val_get(collective_section, "TARGET", &
554  n_rep_val=n_rep, i_rep_section=ig)
555  IF (n_rep /= 0) THEN
556  CALL section_vals_val_get(collective_section, "TARGET", &
557  r_val=cons_info%const_colv_target(ig), i_rep_section=ig)
558  ELSE
559  cons_info%const_colv_target(ig) = -huge(0.0_dp)
560  END IF
561  CALL section_vals_val_get(collective_section, "TARGET_GROWTH", &
562  r_val=cons_info%const_colv_target_growth(ig), i_rep_section=ig)
563  END DO
564  END IF
565  END IF
566 
567  END SUBROUTINE read_constraints_section
568 
569 ! **************************************************************************************************
570 !> \brief Reads input and decides if apply restraints instead of constraints
571 !> \param cons_section ...
572 !> \param is_restraint ...
573 !> \param k0 ...
574 !> \param i_rep_section ...
575 !> \param label ...
576 !> \author teo
577 ! **************************************************************************************************
578  SUBROUTINE check_restraint(cons_section, is_restraint, k0, i_rep_section, label)
579  TYPE(section_vals_type), POINTER :: cons_section
580  LOGICAL, INTENT(OUT) :: is_restraint
581  REAL(kind=dp), INTENT(OUT) :: k0
582  INTEGER, INTENT(IN), OPTIONAL :: i_rep_section
583  CHARACTER(LEN=*), INTENT(IN) :: label
584 
585  CHARACTER(LEN=default_string_length) :: nlabel
586  INTEGER :: output_unit
587  LOGICAL :: explicit
588  TYPE(section_vals_type), POINTER :: restraint_section
589 
590  is_restraint = .false.
591  output_unit = cp_logger_get_default_io_unit()
592  CALL section_vals_get(cons_section, explicit=explicit)
593  IF (explicit) THEN
594  restraint_section => section_vals_get_subs_vals(cons_section, "RESTRAINT", &
595  i_rep_section=i_rep_section)
596  CALL section_vals_get(restraint_section, explicit=is_restraint)
597  IF (is_restraint) THEN
598  CALL section_vals_val_get(restraint_section, "K", r_val=k0)
599  IF (output_unit > 0) THEN
600  nlabel = cp_to_string(i_rep_section)
601  WRITE (output_unit, fmt='(T2,"RESTRAINT|",1X,A,F9.6)') &
602  "Active restraint on "//label//" section Nr."// &
603  trim(nlabel)//". K [a.u.]=", k0
604  END IF
605  END IF
606  END IF
607  END SUBROUTINE check_restraint
608 
609 END MODULE topology_input
610 
colvar_types
Initialize the collective variables types.
Definition: colvar_types.F:15
colvar_types::colvar_clone
recursive subroutine, public colvar_clone(colvar_out, colvar_in, i_atom_offset)
Clone a colvar type.
Definition: colvar_types.F:1353
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_logger_get_default_io_unit
integer function, public cp_logger_get_default_io_unit(logger)
returns the unit nr for the ionode (-1 on all other processors) skips as well checks if the procs cal...
Definition: cp_log_handling.F:515
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_conn_off
integer, parameter, public do_conn_off
Definition: input_constants.F:412
input_constants::do_conn_user
integer, parameter, public do_conn_user
Definition: input_constants.F:412
input_constants::do_conn_generate
integer, parameter, public do_conn_generate
Definition: input_constants.F:412
input_constants::do_conn_mol_set
integer, parameter, public do_conn_mol_set
Definition: input_constants.F:412
input_constants::do_constr_none
integer, parameter, public do_constr_none
Definition: input_constants.F:79
input_constants::do_coord_off
integer, parameter, public do_coord_off
Definition: input_constants.F:412
input_section_types
objects that represent the structure of input sections and the data contained in an input section
Definition: input_section_types.F:15
input_section_types::section_vals_val_unset
subroutine, public section_vals_val_unset(section_vals, keyword_name, i_rep_section, i_rep_val)
unsets (removes) the requested value (if it is a keyword repetitions removes the repetition,...
Definition: input_section_types.F:1347
input_section_types::section_vals_get_subs_vals
recursive type(section_vals_type) function, pointer, public section_vals_get_subs_vals(section_vals, subsection_name, i_rep_section, can_return_null)
returns the values of the requested subsection
Definition: input_section_types.F:724
input_section_types::section_vals_get
subroutine, public section_vals_get(section_vals, ref_count, n_repetition, n_subs_vals_rep, section, explicit)
returns various attributes about the section_vals
Definition: input_section_types.F:697
input_section_types::section_vals_val_get
subroutine, public section_vals_val_get(section_vals, keyword_name, i_rep_section, i_rep_val, n_rep_val, val, l_val, i_val, r_val, c_val, l_vals, i_vals, r_vals, c_vals, explicit)
returns the requested value
Definition: input_section_types.F:1040
kinds
Defines the basic variable types.
Definition: kinds.F:23
kinds::dp
integer, parameter, public dp
Definition: kinds.F:34
kinds::default_string_length
integer, parameter, public default_string_length
Definition: kinds.F:57
memory_utilities
Utility routines for the memory handling.
Definition: memory_utilities.F:14
topology_input
Reads the input sections "topology".
Definition: topology_input.F:14
topology_input::read_topology_section
subroutine, public read_topology_section(topology, topology_section)
reads the input section topology
Definition: topology_input.F:55
topology_input::read_constraints_section
subroutine, public read_constraints_section(topology, colvar_p, constraint_section)
Read all the distance parameters. Put them in the constraint_distance array.
Definition: topology_input.F:109
topology_types
Definition: topology_types.F:18
topology
Control for reading in different topologies and coordinates.
Definition: topology.F:13
topology_types::constraint_info_type
Definition: topology_types.F:64
topology_types::topology_parameters_type
Definition: topology_types.F:142