(git:374b731)
Loading...
Searching...
No Matches
topology_input.F
Go to the documentation of this file.
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! **************************************************************************************************
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) &
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
609END MODULE topology_input
610
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: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
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:126
topology_types::constraint_info_type
Definition topology_types.F:64
topology_types::topology_parameters_type
Definition topology_types.F:142