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topology_input.F
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1!--------------------------------------------------------------------------------------------------!
2! CP2K: A general program to perform molecular dynamics simulations !
3! Copyright 2000-2026 CP2K developers group <https://cp2k.org> !
4! !
5! SPDX-License-Identifier: GPL-2.0-or-later !
6!--------------------------------------------------------------------------------------------------!
7
8! **************************************************************************************************
9!> \brief Reads the input sections "topology"
10!> \par History
11!> JGH (26-01-2002) Added read_topology_section
12!> \author JGH
13! **************************************************************************************************
14MODULE 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
44CONTAINS
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) THEN
68 cpabort("Only one between <CHARGE_OCCUP,CHARGE_BETA,CHARGE_EXTENDED> can be defined! ")
69 END IF
70 CALL section_vals_val_get(topology_section, "PARA_RES", l_val=topology%para_res)
71 CALL section_vals_val_get(topology_section, "GENERATE%REORDER", l_val=topology%reorder_atom)
72 CALL section_vals_val_get(topology_section, "GENERATE%CREATE_MOLECULES", l_val=topology%create_molecules)
73 CALL section_vals_val_get(topology_section, "MOL_CHECK", l_val=topology%molecules_check)
74 CALL section_vals_val_get(topology_section, "USE_G96_VELOCITY", l_val=topology%use_g96_velocity)
75 CALL section_vals_val_get(topology_section, "COORD_FILE_FORMAT", i_val=topology%coord_type)
76 SELECT CASE (topology%coord_type)
77 CASE (do_coord_off)
78 ! Do Nothing
79 CASE DEFAULT
80 topology%coordinate = .true.
81 CALL section_vals_val_get(topology_section, "COORD_FILE_NAME", c_val=topology%coord_file_name)
82 END SELECT
83 CALL section_vals_val_get(topology_section, "CONN_FILE_FORMAT", i_val=topology%conn_type)
84 SELECT CASE (topology%conn_type)
85 CASE (do_conn_off, do_conn_generate, do_conn_mol_set, do_conn_user)
86 ! Do Nothing
87 CASE DEFAULT
88 CALL section_vals_val_get(topology_section, "CONN_FILE_NAME", c_val=topology%conn_file_name)
89 END SELECT
90 CALL section_vals_val_get(topology_section, "EXCLUDE_VDW", i_val=topology%exclude_vdw)
91 CALL section_vals_val_get(topology_section, "EXCLUDE_EI", i_val=topology%exclude_ei)
92 CALL section_vals_val_get(topology_section, "GENERATE%BONDPARM", i_val=topology%bondparm_type)
93 CALL section_vals_val_get(topology_section, "GENERATE%BONDPARM_FACTOR", r_val=topology%bondparm_factor)
94 CALL timestop(handle)
95 END SUBROUTINE read_topology_section
96
97! **************************************************************************************************
98!> \brief Read all the distance parameters. Put them in the
99!> constraint_distance array.
100!> \param topology ...
101!> \param colvar_p ...
102!> \param constraint_section ...
103!> \par History
104!> JGH (26-01-2002) Distance parameters are now stored in tables. The position
105!> within the table is used as handle for the topology
106!> teo Read the CONSTRAINT section within the new input style
107!> \author teo
108! **************************************************************************************************
109 SUBROUTINE read_constraints_section(topology, colvar_p, constraint_section)
110
111 TYPE(topology_parameters_type), INTENT(INOUT) :: topology
112 TYPE(colvar_p_type), DIMENSION(:), POINTER :: colvar_p
113 TYPE(section_vals_type), POINTER :: constraint_section
114
115 CHARACTER(LEN=default_string_length), &
116 DIMENSION(:), POINTER :: tmpstringlist
117 INTEGER :: icolvar, ig, isize, isize_old, itype, &
118 jg, msize, msize_old, n_rep, ncons, &
119 nrep
120 INTEGER, DIMENSION(:), POINTER :: ilist, tmplist
121 LOGICAL :: explicit
122 REAL(kind=dp), DIMENSION(:), POINTER :: rlist
123 TYPE(constraint_info_type), POINTER :: cons_info
124 TYPE(section_vals_type), POINTER :: collective_section, fix_atom_section, &
125 g3x3_section, g4x6_section, &
126 hbonds_section, vsite_section
127
128 cons_info => topology%cons_info
129 IF (ASSOCIATED(constraint_section)) THEN
130 hbonds_section => section_vals_get_subs_vals(constraint_section, "HBONDS")
131 g3x3_section => section_vals_get_subs_vals(constraint_section, "G3X3")
132 g4x6_section => section_vals_get_subs_vals(constraint_section, "G4X6")
133 vsite_section => section_vals_get_subs_vals(constraint_section, "VIRTUAL_SITE")
134 fix_atom_section => section_vals_get_subs_vals(constraint_section, "FIXED_ATOMS")
135 collective_section => section_vals_get_subs_vals(constraint_section, "COLLECTIVE")
136 ! HBONDS
137 CALL section_vals_get(hbonds_section, explicit=topology%const_hydr)
138 CALL check_restraint(hbonds_section, &
139 is_restraint=cons_info%hbonds_restraint, &
140 k0=cons_info%hbonds_k0, &
141 label="HBONDS")
142 ! G3X3
143 CALL section_vals_get(g3x3_section, explicit=explicit, n_repetition=ncons)
144 IF (explicit) THEN
145 topology%const_33 = .true.
146 cons_info%nconst_g33 = ncons
147 !
148 ALLOCATE (cons_info%const_g33_mol(ncons))
149 ALLOCATE (cons_info%const_g33_molname(ncons))
150 ALLOCATE (cons_info%const_g33_a(ncons))
151 ALLOCATE (cons_info%const_g33_b(ncons))
152 ALLOCATE (cons_info%const_g33_c(ncons))
153 ALLOCATE (cons_info%const_g33_dab(ncons))
154 ALLOCATE (cons_info%const_g33_dac(ncons))
155 ALLOCATE (cons_info%const_g33_dbc(ncons))
156 ALLOCATE (cons_info%g33_intermolecular(ncons))
157 ALLOCATE (cons_info%g33_restraint(ncons))
158 ALLOCATE (cons_info%g33_k0(ncons))
159 ALLOCATE (cons_info%g33_exclude_qm(ncons))
160 ALLOCATE (cons_info%g33_exclude_mm(ncons))
161 DO ig = 1, ncons
162 CALL check_restraint(g3x3_section, &
163 is_restraint=cons_info%g33_restraint(ig), &
164 k0=cons_info%g33_k0(ig), &
165 i_rep_section=ig, &
166 label="G3X3")
167 cons_info%const_g33_mol(ig) = 0
168 cons_info%const_g33_molname(ig) = "UNDEF"
169 ! Exclude QM or MM
170 CALL section_vals_val_get(g3x3_section, "EXCLUDE_QM", i_rep_section=ig, &
171 l_val=cons_info%g33_exclude_qm(ig))
172 CALL section_vals_val_get(g3x3_section, "EXCLUDE_MM", i_rep_section=ig, &
173 l_val=cons_info%g33_exclude_mm(ig))
174 ! Intramolecular restraint
175 CALL section_vals_val_get(g3x3_section, "INTERMOLECULAR", i_rep_section=ig, &
176 l_val=cons_info%g33_intermolecular(ig))
177 ! If it is intramolecular let's unset (in case user did it)
178 ! the molecule and molname field
179 IF (cons_info%g33_intermolecular(ig)) THEN
180 CALL section_vals_val_unset(g3x3_section, "MOLECULE", i_rep_section=ig)
181 CALL section_vals_val_unset(g3x3_section, "MOLNAME", i_rep_section=ig)
182 END IF
183 ! Let's tag to which molecule we want to apply constraints
184 CALL section_vals_val_get(g3x3_section, "MOLECULE", i_rep_section=ig, &
185 n_rep_val=nrep)
186 IF (nrep /= 0) THEN
187 CALL section_vals_val_get(g3x3_section, "MOLECULE", i_rep_section=ig, &
188 i_val=cons_info%const_g33_mol(ig))
189 END IF
190 CALL section_vals_val_get(g3x3_section, "MOLNAME", i_rep_section=ig, &
191 n_rep_val=nrep)
192 IF (nrep /= 0) THEN
193 CALL section_vals_val_get(g3x3_section, "MOLNAME", i_rep_section=ig, &
194 c_val=cons_info%const_g33_molname(ig))
195 END IF
196 IF ((cons_info%const_g33_mol(ig) /= 0) .AND. (cons_info%const_g33_molname(ig) /= "UNDEF")) THEN
197 CALL cp_abort(__location__, &
198 "Invalid G3X3 constraint section "//cp_to_string(ig)//": "// &
199 "check MOLECULE and MOLNAME setup!")
200 END IF
201 IF ((cons_info%const_g33_mol(ig) == 0) .AND. (cons_info%const_g33_molname(ig) == "UNDEF") .AND. &
202 (.NOT. cons_info%g33_intermolecular(ig))) THEN
203 CALL cp_abort(__location__, &
204 "Invalid G3X3 constraint section "//cp_to_string(ig)//": "// &
205 "check MOLECULE and MOLNAME setup!")
206 END IF
207 CALL section_vals_val_get(g3x3_section, "ATOMS", i_rep_section=ig, &
208 i_vals=ilist)
209 CALL section_vals_val_get(g3x3_section, "DISTANCES", i_rep_section=ig, &
210 r_vals=rlist)
211 cons_info%const_g33_a(ig) = ilist(1)
212 cons_info%const_g33_b(ig) = ilist(2)
213 cons_info%const_g33_c(ig) = ilist(3)
214
215 cons_info%const_g33_dab(ig) = rlist(1)
216 cons_info%const_g33_dac(ig) = rlist(2)
217 cons_info%const_g33_dbc(ig) = rlist(3)
218 END DO
219 END IF
220 ! G4X6
221 CALL section_vals_get(g4x6_section, explicit=explicit, n_repetition=ncons)
222 IF (explicit) THEN
223 topology%const_46 = .true.
224 cons_info%nconst_g46 = ncons
225 !
226 ALLOCATE (cons_info%const_g46_mol(ncons))
227 ALLOCATE (cons_info%const_g46_molname(ncons))
228 ALLOCATE (cons_info%const_g46_a(ncons))
229 ALLOCATE (cons_info%const_g46_b(ncons))
230 ALLOCATE (cons_info%const_g46_c(ncons))
231 ALLOCATE (cons_info%const_g46_d(ncons))
232 ALLOCATE (cons_info%const_g46_dab(ncons))
233 ALLOCATE (cons_info%const_g46_dac(ncons))
234 ALLOCATE (cons_info%const_g46_dbc(ncons))
235 ALLOCATE (cons_info%const_g46_dad(ncons))
236 ALLOCATE (cons_info%const_g46_dbd(ncons))
237 ALLOCATE (cons_info%const_g46_dcd(ncons))
238 ALLOCATE (cons_info%g46_intermolecular(ncons))
239 ALLOCATE (cons_info%g46_restraint(ncons))
240 ALLOCATE (cons_info%g46_k0(ncons))
241 ALLOCATE (cons_info%g46_exclude_qm(ncons))
242 ALLOCATE (cons_info%g46_exclude_mm(ncons))
243 DO ig = 1, ncons
244 CALL check_restraint(g4x6_section, &
245 is_restraint=cons_info%g46_restraint(ig), &
246 k0=cons_info%g46_k0(ig), &
247 i_rep_section=ig, &
248 label="G4X6")
249 cons_info%const_g46_mol(ig) = 0
250 cons_info%const_g46_molname(ig) = "UNDEF"
251 ! Exclude QM or MM
252 CALL section_vals_val_get(g4x6_section, "EXCLUDE_QM", i_rep_section=ig, &
253 l_val=cons_info%g46_exclude_qm(ig))
254 CALL section_vals_val_get(g4x6_section, "EXCLUDE_MM", i_rep_section=ig, &
255 l_val=cons_info%g46_exclude_mm(ig))
256 ! Intramolecular restraint
257 CALL section_vals_val_get(g4x6_section, "INTERMOLECULAR", i_rep_section=ig, &
258 l_val=cons_info%g46_intermolecular(ig))
259 ! If it is intramolecular let's unset (in case user did it)
260 ! the molecule and molname field
261 IF (cons_info%g46_intermolecular(ig)) THEN
262 CALL section_vals_val_unset(g4x6_section, "MOLECULE", i_rep_section=ig)
263 CALL section_vals_val_unset(g4x6_section, "MOLNAME", i_rep_section=ig)
264 END IF
265 ! Let's tag to which molecule we want to apply constraints
266 CALL section_vals_val_get(g4x6_section, "MOLECULE", i_rep_section=ig, &
267 n_rep_val=nrep)
268 IF (nrep /= 0) THEN
269 CALL section_vals_val_get(g4x6_section, "MOLECULE", i_rep_section=ig, &
270 i_val=cons_info%const_g46_mol(ig))
271 END IF
272 CALL section_vals_val_get(g4x6_section, "MOLNAME", i_rep_section=ig, &
273 n_rep_val=nrep)
274 IF (nrep /= 0) THEN
275 CALL section_vals_val_get(g4x6_section, "MOLNAME", i_rep_section=ig, &
276 c_val=cons_info%const_g46_molname(ig))
277 END IF
278 IF ((cons_info%const_g46_mol(ig) /= 0) .AND. (cons_info%const_g46_molname(ig) /= "UNDEF")) THEN
279 CALL cp_abort(__location__, &
280 "Invalid G4X6 constraint section "//cp_to_string(ig)//": "// &
281 "check MOLECULE and MOLNAME setup!")
282 END IF
283 IF ((cons_info%const_g46_mol(ig) == 0) .AND. (cons_info%const_g46_molname(ig) == "UNDEF") .AND. &
284 (.NOT. cons_info%g46_intermolecular(ig))) THEN
285 CALL cp_abort(__location__, &
286 "Invalid G4X6 constraint section "//cp_to_string(ig)//": "// &
287 "check MOLECULE and MOLNAME setup!")
288 END IF
289 CALL section_vals_val_get(g4x6_section, "ATOMS", i_rep_section=ig, &
290 i_vals=ilist)
291 CALL section_vals_val_get(g4x6_section, "DISTANCES", i_rep_section=ig, &
292 r_vals=rlist)
293 cons_info%const_g46_a(ig) = ilist(1)
294 cons_info%const_g46_b(ig) = ilist(2)
295 cons_info%const_g46_c(ig) = ilist(3)
296 cons_info%const_g46_d(ig) = ilist(4)
297 cons_info%const_g46_dab(ig) = rlist(1)
298 cons_info%const_g46_dac(ig) = rlist(2)
299 cons_info%const_g46_dad(ig) = rlist(3)
300 cons_info%const_g46_dbc(ig) = rlist(4)
301 cons_info%const_g46_dbd(ig) = rlist(5)
302 cons_info%const_g46_dcd(ig) = rlist(6)
303 END DO
304 END IF
305 ! virtual
306 CALL section_vals_get(vsite_section, explicit=explicit, n_repetition=ncons)
307 IF (explicit) THEN
308 topology%const_vsite = .true.
309 cons_info%nconst_vsite = ncons
310 !
311 ALLOCATE (cons_info%const_vsite_mol(ncons))
312 ALLOCATE (cons_info%const_vsite_molname(ncons))
313 ALLOCATE (cons_info%const_vsite_a(ncons))
314 ALLOCATE (cons_info%const_vsite_b(ncons))
315 ALLOCATE (cons_info%const_vsite_c(ncons))
316 ALLOCATE (cons_info%const_vsite_d(ncons))
317 ALLOCATE (cons_info%const_vsite_wbc(ncons))
318 ALLOCATE (cons_info%const_vsite_wdc(ncons))
319 ALLOCATE (cons_info%vsite_intermolecular(ncons))
320 ALLOCATE (cons_info%vsite_restraint(ncons))
321 ALLOCATE (cons_info%vsite_k0(ncons))
322 ALLOCATE (cons_info%vsite_exclude_qm(ncons))
323 ALLOCATE (cons_info%vsite_exclude_mm(ncons))
324 DO ig = 1, ncons
325 CALL check_restraint(vsite_section, &
326 is_restraint=cons_info%vsite_restraint(ig), &
327 k0=cons_info%vsite_k0(ig), &
328 i_rep_section=ig, &
329 label="Virtual_SITE")
330 cons_info%const_vsite_mol(ig) = 0
331 cons_info%const_vsite_molname(ig) = "UNDEF"
332 ! Exclude QM or MM
333 CALL section_vals_val_get(vsite_section, "EXCLUDE_QM", i_rep_section=ig, &
334 l_val=cons_info%vsite_exclude_qm(ig))
335 CALL section_vals_val_get(vsite_section, "EXCLUDE_MM", i_rep_section=ig, &
336 l_val=cons_info%vsite_exclude_mm(ig))
337 ! Intramolecular restraint
338 CALL section_vals_val_get(vsite_section, "INTERMOLECULAR", i_rep_section=ig, &
339 l_val=cons_info%vsite_intermolecular(ig))
340 ! If it is intramolecular let's unset (in case user did it)
341 ! the molecule and molname field
342 IF (cons_info%vsite_intermolecular(ig)) THEN
343 CALL section_vals_val_unset(vsite_section, "MOLECULE", i_rep_section=ig)
344 CALL section_vals_val_unset(vsite_section, "MOLNAME", i_rep_section=ig)
345 END IF
346 ! Let's tag to which molecule we want to apply constraints
347 CALL section_vals_val_get(vsite_section, "MOLECULE", i_rep_section=ig, &
348 n_rep_val=nrep)
349 IF (nrep /= 0) THEN
350 CALL section_vals_val_get(vsite_section, "MOLECULE", i_rep_section=ig, &
351 i_val=cons_info%const_vsite_mol(ig))
352 END IF
353 CALL section_vals_val_get(vsite_section, "MOLNAME", i_rep_section=ig, &
354 n_rep_val=nrep)
355 IF (nrep /= 0) THEN
356 CALL section_vals_val_get(vsite_section, "MOLNAME", i_rep_section=ig, &
357 c_val=cons_info%const_vsite_molname(ig))
358 END IF
359 IF ((cons_info%const_vsite_mol(ig) /= 0) .AND. (cons_info%const_vsite_molname(ig) /= "UNDEF")) THEN
360 CALL cp_abort(__location__, &
361 "Invalid VIRTUAL_SITE constraint section "//cp_to_string(ig)//": "// &
362 "check MOLECULE and MOLNAME setup!")
363 END IF
364 IF ((cons_info%const_vsite_mol(ig) == 0) .AND. (cons_info%const_vsite_molname(ig) == "UNDEF") .AND. &
365 (.NOT. cons_info%vsite_intermolecular(ig))) THEN
366 CALL cp_abort(__location__, &
367 "Invalid VIRTUAL_SITE constraint section "//cp_to_string(ig)//": "// &
368 "check MOLECULE and MOLNAME setup!")
369 END IF
370 CALL section_vals_val_get(vsite_section, "ATOMS", i_rep_section=ig, &
371 i_vals=ilist)
372 CALL section_vals_val_get(vsite_section, "PARAMETERS", i_rep_section=ig, &
373 r_vals=rlist)
374 cons_info%const_vsite_a(ig) = ilist(1)
375 cons_info%const_vsite_b(ig) = ilist(2)
376 cons_info%const_vsite_c(ig) = ilist(3)
377 cons_info%const_vsite_d(ig) = ilist(4)
378 cons_info%const_vsite_wbc(ig) = rlist(1)
379 cons_info%const_vsite_wdc(ig) = rlist(2)
380 END DO
381 END IF
382 ! FIXED ATOMS
383 CALL section_vals_get(fix_atom_section, explicit=explicit, n_repetition=ncons)
384 IF (explicit) THEN
385 NULLIFY (tmplist, tmpstringlist)
386 isize = 0
387 msize = 0
388 ALLOCATE (cons_info%fixed_atoms(isize))
389 ALLOCATE (cons_info%fixed_type(isize))
390 ALLOCATE (cons_info%fixed_restraint(isize))
391 ALLOCATE (cons_info%fixed_k0(isize))
392 ALLOCATE (cons_info%fixed_molnames(msize))
393 ALLOCATE (cons_info%fixed_mol_type(isize))
394 ALLOCATE (cons_info%fixed_mol_restraint(msize))
395 ALLOCATE (cons_info%fixed_mol_k0(msize))
396 ALLOCATE (cons_info%fixed_exclude_qm(ncons))
397 ALLOCATE (cons_info%fixed_exclude_mm(ncons))
398 DO ig = 1, ncons
399 isize_old = isize
400 msize_old = msize
401 CALL section_vals_val_get(fix_atom_section, "COMPONENTS_TO_FIX", i_rep_section=ig, &
402 i_val=itype)
403 CALL section_vals_val_get(fix_atom_section, "LIST", i_rep_section=ig, &
404 n_rep_val=n_rep)
405 DO jg = 1, n_rep
406 CALL section_vals_val_get(fix_atom_section, "LIST", i_rep_section=ig, &
407 i_rep_val=jg, i_vals=tmplist)
408 CALL reallocate(cons_info%fixed_atoms, 1, isize + SIZE(tmplist))
409 cons_info%fixed_atoms(isize + 1:isize + SIZE(tmplist)) = tmplist
410 CALL reallocate(cons_info%fixed_restraint, 1, isize + SIZE(tmplist))
411 CALL reallocate(cons_info%fixed_k0, 1, isize + SIZE(tmplist))
412 CALL reallocate(cons_info%fixed_type, 1, isize + SIZE(tmplist))
413 cons_info%fixed_type(isize + 1:isize + SIZE(tmplist)) = itype
414 isize = SIZE(cons_info%fixed_atoms)
415 END DO
416 !Check for restraints
417 IF ((isize - isize_old) > 0) THEN
418 CALL check_restraint(fix_atom_section, &
419 is_restraint=cons_info%fixed_restraint(isize_old + 1), &
420 k0=cons_info%fixed_k0(isize_old + 1), &
421 i_rep_section=ig, &
422 label="FIXED ATOM")
423 cons_info%fixed_restraint(isize_old + 1:isize) = cons_info%fixed_restraint(isize_old + 1)
424 cons_info%fixed_k0(isize_old + 1:isize) = cons_info%fixed_k0(isize_old + 1)
425 END IF
426 CALL section_vals_val_get(fix_atom_section, "MOLNAME", i_rep_section=ig, &
427 n_rep_val=n_rep)
428 IF (n_rep /= 0) THEN
429 DO jg = 1, n_rep
430 CALL section_vals_val_get(fix_atom_section, "MOLNAME", i_rep_section=ig, &
431 i_rep_val=jg, c_vals=tmpstringlist)
432 CALL reallocate(cons_info%fixed_molnames, 1, msize + SIZE(tmpstringlist, 1))
433 CALL reallocate(cons_info%fixed_mol_type, 1, msize + SIZE(tmpstringlist, 1))
434 CALL reallocate(cons_info%fixed_mol_restraint, 1, msize + SIZE(tmpstringlist, 1))
435 CALL reallocate(cons_info%fixed_mol_k0, 1, msize + SIZE(tmpstringlist, 1))
436 cons_info%fixed_molnames(msize + 1:msize + SIZE(tmpstringlist, 1)) = tmpstringlist
437 cons_info%fixed_mol_type(msize + 1:msize + SIZE(tmpstringlist, 1)) = itype
438 msize = SIZE(cons_info%fixed_molnames)
439 END DO
440 ! Exclude QM or MM work only if defined MOLNAME
441 CALL reallocate(cons_info%fixed_exclude_qm, 1, msize)
442 CALL reallocate(cons_info%fixed_exclude_mm, 1, msize)
443 CALL section_vals_val_get(fix_atom_section, "EXCLUDE_QM", i_rep_section=ig, &
444 l_val=cons_info%fixed_exclude_qm(msize_old + 1))
445 CALL section_vals_val_get(fix_atom_section, "EXCLUDE_MM", i_rep_section=ig, &
446 l_val=cons_info%fixed_exclude_mm(msize_old + 1))
447 cons_info%fixed_exclude_qm(msize_old + 1:msize) = cons_info%fixed_exclude_qm(msize_old + 1)
448 cons_info%fixed_exclude_mm(msize_old + 1:msize) = cons_info%fixed_exclude_mm(msize_old + 1)
449 END IF
450 !Check for restraints
451 IF (n_rep /= 0) THEN
452 CALL check_restraint(fix_atom_section, &
453 is_restraint=cons_info%fixed_mol_restraint(msize_old + 1), &
454 k0=cons_info%fixed_mol_k0(msize_old + 1), &
455 i_rep_section=ig, &
456 label="FIXED ATOM")
457 cons_info%fixed_mol_restraint(msize_old + 1:msize) = cons_info%fixed_mol_restraint(msize_old + 1)
458 cons_info%fixed_mol_k0(msize_old + 1:msize) = cons_info%fixed_mol_k0(msize_old + 1)
459 END IF
460 CALL section_vals_val_get(fix_atom_section, "MM_SUBSYS", i_rep_section=ig, &
461 n_rep_val=nrep, explicit=explicit)
462 IF (nrep == 1 .AND. explicit) THEN
463 cpassert(cons_info%freeze_mm == do_constr_none)
464 CALL section_vals_val_get(fix_atom_section, "MM_SUBSYS", i_val=cons_info%freeze_mm, &
465 i_rep_section=ig)
466 cons_info%freeze_mm_type = itype
467 END IF
468 CALL section_vals_val_get(fix_atom_section, "QM_SUBSYS", i_rep_section=ig, &
469 n_rep_val=nrep, explicit=explicit)
470 IF (nrep == 1 .AND. explicit) THEN
471 cpassert(cons_info%freeze_qm == do_constr_none)
472 CALL section_vals_val_get(fix_atom_section, "QM_SUBSYS", i_val=cons_info%freeze_qm, &
473 i_rep_section=ig)
474 cons_info%freeze_qm_type = itype
475 END IF
476 IF (cons_info%freeze_mm /= do_constr_none) THEN
477 CALL check_restraint(fix_atom_section, &
478 is_restraint=cons_info%fixed_mm_restraint, &
479 k0=cons_info%fixed_mm_k0, &
480 i_rep_section=ig, &
481 label="FIXED ATOM")
482 END IF
483 IF (cons_info%freeze_qm /= do_constr_none) THEN
484 CALL check_restraint(fix_atom_section, &
485 is_restraint=cons_info%fixed_qm_restraint, &
486 k0=cons_info%fixed_qm_k0, &
487 i_rep_section=ig, &
488 label="FIXED ATOM")
489 END IF
490
491 END DO
492 IF ((isize /= 0) .OR. (msize /= 0) .OR. &
493 (cons_info%freeze_mm /= do_constr_none) .OR. &
494 (cons_info%freeze_qm /= do_constr_none)) THEN
495 topology%const_atom = .true.
496 END IF
497 END IF
498 ! Collective Constraints
499 CALL section_vals_get(collective_section, explicit=explicit, n_repetition=ncons)
500 IF (explicit) THEN
501 topology%const_colv = .true.
502 DO ig = 1, ncons
503 CALL section_vals_val_get(collective_section, "COLVAR", i_rep_section=ig, i_val=icolvar)
504 IF (icolvar > SIZE(colvar_p)) THEN
505 cpabort("More collective constraints than collective variables specified.")
506 END IF
507 END DO
508 cons_info%nconst_colv = ncons
509 ALLOCATE (cons_info%const_colv_mol(ncons))
510 ALLOCATE (cons_info%const_colv_molname(ncons))
511 ALLOCATE (cons_info%const_colv_target(ncons))
512 ALLOCATE (cons_info%const_colv_target_growth(ncons))
513 ALLOCATE (cons_info%colvar_set(ncons))
514 ALLOCATE (cons_info%colv_intermolecular(ncons))
515 ALLOCATE (cons_info%colv_restraint(ncons))
516 ALLOCATE (cons_info%colv_k0(ncons))
517 ALLOCATE (cons_info%colv_exclude_qm(ncons))
518 ALLOCATE (cons_info%colv_exclude_mm(ncons))
519 DO ig = 1, ncons
520 CALL check_restraint(collective_section, &
521 is_restraint=cons_info%colv_restraint(ig), &
522 k0=cons_info%colv_k0(ig), &
523 i_rep_section=ig, &
524 label="COLLECTIVE")
525 cons_info%const_colv_mol(ig) = 0
526 cons_info%const_colv_molname(ig) = "UNDEF"
527 ! Exclude QM or MM
528 CALL section_vals_val_get(collective_section, "EXCLUDE_QM", i_rep_section=ig, &
529 l_val=cons_info%colv_exclude_qm(ig))
530 CALL section_vals_val_get(collective_section, "EXCLUDE_MM", i_rep_section=ig, &
531 l_val=cons_info%colv_exclude_mm(ig))
532 ! Intramolecular restraint
533 CALL section_vals_val_get(collective_section, "INTERMOLECULAR", i_rep_section=ig, &
534 l_val=cons_info%colv_intermolecular(ig))
535 ! If it is intramolecular let's unset (in case user did it)
536 ! the molecule and molname field
537 IF (cons_info%colv_intermolecular(ig)) THEN
538 CALL section_vals_val_unset(collective_section, "MOLECULE", i_rep_section=ig)
539 CALL section_vals_val_unset(collective_section, "MOLNAME", i_rep_section=ig)
540 END IF
541 ! Let's tag to which molecule we want to apply constraints
542 CALL section_vals_val_get(collective_section, "MOLECULE", i_rep_section=ig, &
543 n_rep_val=nrep)
544 IF (nrep /= 0) THEN
545 CALL section_vals_val_get(collective_section, "MOLECULE", i_rep_section=ig, &
546 i_val=cons_info%const_colv_mol(ig))
547 END IF
548 CALL section_vals_val_get(collective_section, "MOLNAME", i_rep_section=ig, &
549 n_rep_val=nrep)
550 IF (nrep /= 0) THEN
551 CALL section_vals_val_get(collective_section, "MOLNAME", i_rep_section=ig, &
552 c_val=cons_info%const_colv_molname(ig))
553 END IF
554 IF (((cons_info%const_colv_mol(ig) /= 0) .AND. (cons_info%const_colv_molname(ig) /= "UNDEF"))) THEN
555 cpabort("Both MOLNAME and MOLECULE specified for CONSTRAINT section. ")
556 END IF
557 IF ((cons_info%const_colv_mol(ig) == 0) .AND. (cons_info%const_colv_molname(ig) == "UNDEF") .AND. &
558 (.NOT. cons_info%colv_intermolecular(ig))) THEN
559 CALL cp_abort(__location__, &
560 "Constraint section error: you have to specify at least one of the "// &
561 "following keywords: MOLECULE, MOLNAME or INTERMOLECULAR! ")
562 END IF
563 NULLIFY (cons_info%colvar_set(ig)%colvar)
564 CALL section_vals_val_get(collective_section, "COLVAR", i_rep_section=ig, &
565 i_val=icolvar)
566 CALL colvar_clone(cons_info%colvar_set(ig)%colvar, &
567 colvar_p(icolvar)%colvar)
568 CALL section_vals_val_get(collective_section, "TARGET", &
569 n_rep_val=n_rep, i_rep_section=ig)
570 IF (n_rep /= 0) THEN
571 CALL section_vals_val_get(collective_section, "TARGET", &
572 r_val=cons_info%const_colv_target(ig), i_rep_section=ig)
573 ELSE
574 cons_info%const_colv_target(ig) = -huge(0.0_dp)
575 END IF
576 CALL section_vals_val_get(collective_section, "TARGET_GROWTH", &
577 r_val=cons_info%const_colv_target_growth(ig), i_rep_section=ig)
578 END DO
579 END IF
580 END IF
581
582 END SUBROUTINE read_constraints_section
583
584! **************************************************************************************************
585!> \brief Reads input and decides if apply restraints instead of constraints
586!> \param cons_section ...
587!> \param is_restraint ...
588!> \param k0 ...
589!> \param i_rep_section ...
590!> \param label ...
591!> \author teo
592! **************************************************************************************************
593 SUBROUTINE check_restraint(cons_section, is_restraint, k0, i_rep_section, label)
594 TYPE(section_vals_type), POINTER :: cons_section
595 LOGICAL, INTENT(OUT) :: is_restraint
596 REAL(kind=dp), INTENT(OUT) :: k0
597 INTEGER, INTENT(IN), OPTIONAL :: i_rep_section
598 CHARACTER(LEN=*), INTENT(IN) :: label
599
600 CHARACTER(LEN=default_string_length) :: nlabel
601 INTEGER :: output_unit
602 LOGICAL :: explicit
603 TYPE(section_vals_type), POINTER :: restraint_section
604
605 is_restraint = .false.
606 output_unit = cp_logger_get_default_io_unit()
607 CALL section_vals_get(cons_section, explicit=explicit)
608 IF (explicit) THEN
609 restraint_section => section_vals_get_subs_vals(cons_section, "RESTRAINT", &
610 i_rep_section=i_rep_section)
611 CALL section_vals_get(restraint_section, explicit=is_restraint)
612 IF (is_restraint) THEN
613 CALL section_vals_val_get(restraint_section, "K", r_val=k0)
614 IF (output_unit > 0) THEN
615 nlabel = cp_to_string(i_rep_section)
616 WRITE (output_unit, fmt='(T2,"RESTRAINT|",1X,A,F9.6)') &
617 "Active restraint on "//label//" section Nr."// &
618 trim(nlabel)//". K [a.u.]=", k0
619 END IF
620 END IF
621 END IF
622 END SUBROUTINE check_restraint
623
624END MODULE topology_input
625
cp_log_handling::cp_to_string
Definition cp_log_handling.F:90
memory_utilities::reallocate
Definition memory_utilities.F:27
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:1363
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:523
input_constants
collects all constants needed in input so that they can be used without circular dependencies
Definition input_constants.F:18
input_constants::do_conn_off
integer, parameter, public do_conn_off
Definition input_constants.F:427
input_constants::do_conn_user
integer, parameter, public do_conn_user
Definition input_constants.F:427
input_constants::do_conn_generate
integer, parameter, public do_conn_generate
Definition input_constants.F:427
input_constants::do_conn_mol_set
integer, parameter, public do_conn_mol_set
Definition input_constants.F:427
input_constants::do_constr_none
integer, parameter, public do_constr_none
Definition input_constants.F:84
input_constants::do_coord_off
integer, parameter, public do_coord_off
Definition input_constants.F:427
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:1369
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:735
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:708
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:1052
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:110
topology_types
Definition topology_types.F:18
topology
Control for reading in different topologies and coordinates.
Definition topology.F:13
colvar_types::colvar_p_type
Definition colvar_types.F:383
input_section_types::section_vals_type
stores the values of a section
Definition input_section_types.F:127
topology_types::constraint_info_type
Definition topology_types.F:65
topology_types::topology_parameters_type
Definition topology_types.F:144