Line data Source code
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 : ! **************************************************************************************************
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 10854 : 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 10854 : CALL timeset(routineN, handle)
63 10854 : CALL section_vals_val_get(topology_section, "CHARGE_OCCUP", l_val=topology%charge_occup)
64 10854 : CALL section_vals_val_get(topology_section, "CHARGE_BETA", l_val=topology%charge_beta)
65 10854 : CALL section_vals_val_get(topology_section, "CHARGE_EXTENDED", l_val=topology%charge_extended)
66 43416 : ival = COUNT([topology%charge_occup, topology%charge_beta, topology%charge_extended])
67 10854 : IF (ival > 1) &
68 0 : CPABORT("Only one between <CHARGE_OCCUP,CHARGE_BETA,CHARGE_EXTENDED> can be defined! ")
69 10854 : CALL section_vals_val_get(topology_section, "PARA_RES", l_val=topology%para_res)
70 10854 : CALL section_vals_val_get(topology_section, "GENERATE%REORDER", l_val=topology%reorder_atom)
71 10854 : CALL section_vals_val_get(topology_section, "GENERATE%CREATE_MOLECULES", l_val=topology%create_molecules)
72 10854 : CALL section_vals_val_get(topology_section, "MOL_CHECK", l_val=topology%molecules_check)
73 10854 : CALL section_vals_val_get(topology_section, "USE_G96_VELOCITY", l_val=topology%use_g96_velocity)
74 10854 : CALL section_vals_val_get(topology_section, "COORD_FILE_FORMAT", i_val=topology%coord_type)
75 12781 : SELECT CASE (topology%coord_type)
76 : CASE (do_coord_off)
77 : ! Do Nothing
78 : CASE DEFAULT
79 1927 : topology%coordinate = .TRUE.
80 10854 : CALL section_vals_val_get(topology_section, "COORD_FILE_NAME", c_val=topology%coord_file_name)
81 : END SELECT
82 10854 : CALL section_vals_val_get(topology_section, "CONN_FILE_FORMAT", i_val=topology%conn_type)
83 11378 : 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 10854 : CALL section_vals_val_get(topology_section, "CONN_FILE_NAME", c_val=topology%conn_file_name)
88 : END SELECT
89 10854 : CALL section_vals_val_get(topology_section, "EXCLUDE_VDW", i_val=topology%exclude_vdw)
90 10854 : CALL section_vals_val_get(topology_section, "EXCLUDE_EI", i_val=topology%exclude_ei)
91 10854 : CALL section_vals_val_get(topology_section, "GENERATE%BONDPARM", i_val=topology%bondparm_type)
92 10854 : CALL section_vals_val_get(topology_section, "GENERATE%BONDPARM_FACTOR", r_val=topology%bondparm_factor)
93 10854 : CALL timestop(handle)
94 10854 : 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 10854 : 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 10854 : DIMENSION(:), POINTER :: tmpstringlist
116 : INTEGER :: icolvar, ig, isize, isize_old, itype, &
117 : jg, msize, msize_old, n_rep, ncons, &
118 : nrep
119 10854 : INTEGER, DIMENSION(:), POINTER :: ilist, tmplist
120 : LOGICAL :: explicit
121 10854 : 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 10854 : cons_info => topology%cons_info
128 63449 : IF (ASSOCIATED(constraint_section)) THEN
129 10519 : hbonds_section => section_vals_get_subs_vals(constraint_section, "HBONDS")
130 10519 : g3x3_section => section_vals_get_subs_vals(constraint_section, "G3X3")
131 10519 : g4x6_section => section_vals_get_subs_vals(constraint_section, "G4X6")
132 10519 : vsite_section => section_vals_get_subs_vals(constraint_section, "VIRTUAL_SITE")
133 10519 : fix_atom_section => section_vals_get_subs_vals(constraint_section, "FIXED_ATOMS")
134 10519 : collective_section => section_vals_get_subs_vals(constraint_section, "COLLECTIVE")
135 : ! HBONDS
136 10519 : 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 10519 : label="HBONDS")
141 : ! G3X3
142 10519 : CALL section_vals_get(g3x3_section, explicit=explicit, n_repetition=ncons)
143 10519 : IF (explicit) THEN
144 156 : topology%const_33 = .TRUE.
145 156 : cons_info%nconst_g33 = ncons
146 : !
147 468 : ALLOCATE (cons_info%const_g33_mol(ncons))
148 468 : ALLOCATE (cons_info%const_g33_molname(ncons))
149 312 : ALLOCATE (cons_info%const_g33_a(ncons))
150 312 : ALLOCATE (cons_info%const_g33_b(ncons))
151 312 : ALLOCATE (cons_info%const_g33_c(ncons))
152 468 : ALLOCATE (cons_info%const_g33_dab(ncons))
153 312 : ALLOCATE (cons_info%const_g33_dac(ncons))
154 312 : ALLOCATE (cons_info%const_g33_dbc(ncons))
155 312 : ALLOCATE (cons_info%g33_intermolecular(ncons))
156 312 : ALLOCATE (cons_info%g33_restraint(ncons))
157 312 : ALLOCATE (cons_info%g33_k0(ncons))
158 312 : ALLOCATE (cons_info%g33_exclude_qm(ncons))
159 312 : ALLOCATE (cons_info%g33_exclude_mm(ncons))
160 316 : 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, &
165 160 : label="G3X3")
166 160 : cons_info%const_g33_mol(ig) = 0
167 160 : 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, &
170 160 : l_val=cons_info%g33_exclude_qm(ig))
171 : CALL section_vals_val_get(g3x3_section, "EXCLUDE_MM", i_rep_section=ig, &
172 160 : l_val=cons_info%g33_exclude_mm(ig))
173 : ! Intramolecular restraint
174 : CALL section_vals_val_get(g3x3_section, "INTERMOLECULAR", i_rep_section=ig, &
175 160 : 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
178 160 : IF (cons_info%g33_intermolecular(ig)) THEN
179 4 : CALL section_vals_val_unset(g3x3_section, "MOLECULE", i_rep_section=ig)
180 4 : 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, &
184 160 : n_rep_val=nrep)
185 160 : IF (nrep /= 0) THEN
186 : CALL section_vals_val_get(g3x3_section, "MOLECULE", i_rep_section=ig, &
187 120 : i_val=cons_info%const_g33_mol(ig))
188 : END IF
189 : CALL section_vals_val_get(g3x3_section, "MOLNAME", i_rep_section=ig, &
190 160 : n_rep_val=nrep)
191 160 : IF (nrep /= 0) THEN
192 : CALL section_vals_val_get(g3x3_section, "MOLNAME", i_rep_section=ig, &
193 36 : c_val=cons_info%const_g33_molname(ig))
194 : END IF
195 160 : IF ((cons_info%const_g33_mol(ig) /= 0) .AND. (cons_info%const_g33_molname(ig) /= "UNDEF")) THEN
196 : CALL cp_abort(__LOCATION__, &
197 : "Invalid G3X3 constraint section "//cp_to_string(ig)//": "// &
198 0 : "check MOLECULE and MOLNAME setup!")
199 : END IF
200 160 : IF ((cons_info%const_g33_mol(ig) == 0) .AND. (cons_info%const_g33_molname(ig) == "UNDEF") .AND. &
201 : (.NOT. cons_info%g33_intermolecular(ig))) THEN
202 : CALL cp_abort(__LOCATION__, &
203 : "Invalid G3X3 constraint section "//cp_to_string(ig)//": "// &
204 0 : "check MOLECULE and MOLNAME setup!")
205 : END IF
206 : CALL section_vals_val_get(g3x3_section, "ATOMS", i_rep_section=ig, &
207 160 : i_vals=ilist)
208 : CALL section_vals_val_get(g3x3_section, "DISTANCES", i_rep_section=ig, &
209 160 : r_vals=rlist)
210 160 : cons_info%const_g33_a(ig) = ilist(1)
211 160 : cons_info%const_g33_b(ig) = ilist(2)
212 160 : cons_info%const_g33_c(ig) = ilist(3)
213 :
214 160 : cons_info%const_g33_dab(ig) = rlist(1)
215 160 : cons_info%const_g33_dac(ig) = rlist(2)
216 636 : cons_info%const_g33_dbc(ig) = rlist(3)
217 : END DO
218 : END IF
219 : ! G4X6
220 10519 : CALL section_vals_get(g4x6_section, explicit=explicit, n_repetition=ncons)
221 10519 : IF (explicit) THEN
222 16 : topology%const_46 = .TRUE.
223 16 : cons_info%nconst_g46 = ncons
224 : !
225 48 : ALLOCATE (cons_info%const_g46_mol(ncons))
226 48 : ALLOCATE (cons_info%const_g46_molname(ncons))
227 32 : ALLOCATE (cons_info%const_g46_a(ncons))
228 32 : ALLOCATE (cons_info%const_g46_b(ncons))
229 32 : ALLOCATE (cons_info%const_g46_c(ncons))
230 32 : ALLOCATE (cons_info%const_g46_d(ncons))
231 48 : ALLOCATE (cons_info%const_g46_dab(ncons))
232 32 : ALLOCATE (cons_info%const_g46_dac(ncons))
233 32 : ALLOCATE (cons_info%const_g46_dbc(ncons))
234 32 : ALLOCATE (cons_info%const_g46_dad(ncons))
235 32 : ALLOCATE (cons_info%const_g46_dbd(ncons))
236 32 : ALLOCATE (cons_info%const_g46_dcd(ncons))
237 32 : ALLOCATE (cons_info%g46_intermolecular(ncons))
238 32 : ALLOCATE (cons_info%g46_restraint(ncons))
239 32 : ALLOCATE (cons_info%g46_k0(ncons))
240 32 : ALLOCATE (cons_info%g46_exclude_qm(ncons))
241 32 : ALLOCATE (cons_info%g46_exclude_mm(ncons))
242 32 : DO ig = 1, ncons
243 : CALL check_restraint(g4x6_section, &
244 : is_restraint=cons_info%g46_restraint(ig), &
245 : k0=cons_info%g46_k0(ig), &
246 : i_rep_section=ig, &
247 16 : label="G4X6")
248 16 : cons_info%const_g46_mol(ig) = 0
249 16 : cons_info%const_g46_molname(ig) = "UNDEF"
250 : ! Exclude QM or MM
251 : CALL section_vals_val_get(g4x6_section, "EXCLUDE_QM", i_rep_section=ig, &
252 16 : l_val=cons_info%g46_exclude_qm(ig))
253 : CALL section_vals_val_get(g4x6_section, "EXCLUDE_MM", i_rep_section=ig, &
254 16 : l_val=cons_info%g46_exclude_mm(ig))
255 : ! Intramolecular restraint
256 : CALL section_vals_val_get(g4x6_section, "INTERMOLECULAR", i_rep_section=ig, &
257 16 : l_val=cons_info%g46_intermolecular(ig))
258 : ! If it is intramolecular let's unset (in case user did it)
259 : ! the molecule and molname field
260 16 : IF (cons_info%g46_intermolecular(ig)) THEN
261 4 : CALL section_vals_val_unset(g4x6_section, "MOLECULE", i_rep_section=ig)
262 4 : CALL section_vals_val_unset(g4x6_section, "MOLNAME", i_rep_section=ig)
263 : END IF
264 : ! Let's tag to which molecule we want to apply constraints
265 : CALL section_vals_val_get(g4x6_section, "MOLECULE", i_rep_section=ig, &
266 16 : n_rep_val=nrep)
267 16 : IF (nrep /= 0) THEN
268 : CALL section_vals_val_get(g4x6_section, "MOLECULE", i_rep_section=ig, &
269 8 : i_val=cons_info%const_g46_mol(ig))
270 : END IF
271 : CALL section_vals_val_get(g4x6_section, "MOLNAME", i_rep_section=ig, &
272 16 : n_rep_val=nrep)
273 16 : IF (nrep /= 0) THEN
274 : CALL section_vals_val_get(g4x6_section, "MOLNAME", i_rep_section=ig, &
275 4 : c_val=cons_info%const_g46_molname(ig))
276 : END IF
277 16 : IF ((cons_info%const_g46_mol(ig) /= 0) .AND. (cons_info%const_g46_molname(ig) /= "UNDEF")) THEN
278 : CALL cp_abort(__LOCATION__, &
279 : "Invalid G4X6 constraint section "//cp_to_string(ig)//": "// &
280 0 : "check MOLECULE and MOLNAME setup!")
281 : END IF
282 16 : IF ((cons_info%const_g46_mol(ig) == 0) .AND. (cons_info%const_g46_molname(ig) == "UNDEF") .AND. &
283 : (.NOT. cons_info%g46_intermolecular(ig))) THEN
284 : CALL cp_abort(__LOCATION__, &
285 : "Invalid G4X6 constraint section "//cp_to_string(ig)//": "// &
286 0 : "check MOLECULE and MOLNAME setup!")
287 : END IF
288 : CALL section_vals_val_get(g4x6_section, "ATOMS", i_rep_section=ig, &
289 16 : i_vals=ilist)
290 : CALL section_vals_val_get(g4x6_section, "DISTANCES", i_rep_section=ig, &
291 16 : r_vals=rlist)
292 16 : cons_info%const_g46_a(ig) = ilist(1)
293 16 : cons_info%const_g46_b(ig) = ilist(2)
294 16 : cons_info%const_g46_c(ig) = ilist(3)
295 16 : cons_info%const_g46_d(ig) = ilist(4)
296 16 : cons_info%const_g46_dab(ig) = rlist(1)
297 16 : cons_info%const_g46_dac(ig) = rlist(2)
298 16 : cons_info%const_g46_dad(ig) = rlist(3)
299 16 : cons_info%const_g46_dbc(ig) = rlist(4)
300 16 : cons_info%const_g46_dbd(ig) = rlist(5)
301 64 : cons_info%const_g46_dcd(ig) = rlist(6)
302 : END DO
303 : END IF
304 : ! virtual
305 10519 : CALL section_vals_get(vsite_section, explicit=explicit, n_repetition=ncons)
306 10519 : IF (explicit) THEN
307 8 : topology%const_vsite = .TRUE.
308 8 : cons_info%nconst_vsite = ncons
309 : !
310 24 : ALLOCATE (cons_info%const_vsite_mol(ncons))
311 24 : ALLOCATE (cons_info%const_vsite_molname(ncons))
312 16 : ALLOCATE (cons_info%const_vsite_a(ncons))
313 16 : ALLOCATE (cons_info%const_vsite_b(ncons))
314 16 : ALLOCATE (cons_info%const_vsite_c(ncons))
315 16 : ALLOCATE (cons_info%const_vsite_d(ncons))
316 24 : ALLOCATE (cons_info%const_vsite_wbc(ncons))
317 16 : ALLOCATE (cons_info%const_vsite_wdc(ncons))
318 16 : ALLOCATE (cons_info%vsite_intermolecular(ncons))
319 16 : ALLOCATE (cons_info%vsite_restraint(ncons))
320 16 : ALLOCATE (cons_info%vsite_k0(ncons))
321 16 : ALLOCATE (cons_info%vsite_exclude_qm(ncons))
322 16 : ALLOCATE (cons_info%vsite_exclude_mm(ncons))
323 16 : DO ig = 1, ncons
324 : CALL check_restraint(vsite_section, &
325 : is_restraint=cons_info%vsite_restraint(ig), &
326 : k0=cons_info%vsite_k0(ig), &
327 : i_rep_section=ig, &
328 8 : label="Virtual_SITE")
329 8 : cons_info%const_vsite_mol(ig) = 0
330 8 : cons_info%const_vsite_molname(ig) = "UNDEF"
331 : ! Exclude QM or MM
332 : CALL section_vals_val_get(vsite_section, "EXCLUDE_QM", i_rep_section=ig, &
333 8 : l_val=cons_info%vsite_exclude_qm(ig))
334 : CALL section_vals_val_get(vsite_section, "EXCLUDE_MM", i_rep_section=ig, &
335 8 : l_val=cons_info%vsite_exclude_mm(ig))
336 : ! Intramolecular restraint
337 : CALL section_vals_val_get(vsite_section, "INTERMOLECULAR", i_rep_section=ig, &
338 8 : l_val=cons_info%vsite_intermolecular(ig))
339 : ! If it is intramolecular let's unset (in case user did it)
340 : ! the molecule and molname field
341 8 : IF (cons_info%vsite_intermolecular(ig)) THEN
342 0 : CALL section_vals_val_unset(vsite_section, "MOLECULE", i_rep_section=ig)
343 0 : CALL section_vals_val_unset(vsite_section, "MOLNAME", i_rep_section=ig)
344 : END IF
345 : ! Let's tag to which molecule we want to apply constraints
346 : CALL section_vals_val_get(vsite_section, "MOLECULE", i_rep_section=ig, &
347 8 : n_rep_val=nrep)
348 8 : IF (nrep /= 0) THEN
349 : CALL section_vals_val_get(vsite_section, "MOLECULE", i_rep_section=ig, &
350 8 : i_val=cons_info%const_vsite_mol(ig))
351 : END IF
352 : CALL section_vals_val_get(vsite_section, "MOLNAME", i_rep_section=ig, &
353 8 : n_rep_val=nrep)
354 8 : IF (nrep /= 0) THEN
355 : CALL section_vals_val_get(vsite_section, "MOLNAME", i_rep_section=ig, &
356 0 : c_val=cons_info%const_vsite_molname(ig))
357 : END IF
358 8 : IF ((cons_info%const_vsite_mol(ig) /= 0) .AND. (cons_info%const_vsite_molname(ig) /= "UNDEF")) THEN
359 : CALL cp_abort(__LOCATION__, &
360 : "Invalid VIRTUAL_SITE constraint section "//cp_to_string(ig)//": "// &
361 0 : "check MOLECULE and MOLNAME setup!")
362 : END IF
363 8 : IF ((cons_info%const_vsite_mol(ig) == 0) .AND. (cons_info%const_vsite_molname(ig) == "UNDEF") .AND. &
364 : (.NOT. cons_info%vsite_intermolecular(ig))) THEN
365 : CALL cp_abort(__LOCATION__, &
366 : "Invalid VIRTUAL_SITE constraint section "//cp_to_string(ig)//": "// &
367 0 : "check MOLECULE and MOLNAME setup!")
368 : END IF
369 : CALL section_vals_val_get(vsite_section, "ATOMS", i_rep_section=ig, &
370 8 : i_vals=ilist)
371 : CALL section_vals_val_get(vsite_section, "PARAMETERS", i_rep_section=ig, &
372 8 : r_vals=rlist)
373 8 : cons_info%const_vsite_a(ig) = ilist(1)
374 8 : cons_info%const_vsite_b(ig) = ilist(2)
375 8 : cons_info%const_vsite_c(ig) = ilist(3)
376 8 : cons_info%const_vsite_d(ig) = ilist(4)
377 8 : cons_info%const_vsite_wbc(ig) = rlist(1)
378 32 : cons_info%const_vsite_wdc(ig) = rlist(2)
379 : END DO
380 : END IF
381 : ! FIXED ATOMS
382 10519 : CALL section_vals_get(fix_atom_section, explicit=explicit, n_repetition=ncons)
383 10519 : IF (explicit) THEN
384 110 : NULLIFY (tmplist, tmpstringlist)
385 110 : isize = 0
386 110 : msize = 0
387 110 : ALLOCATE (cons_info%fixed_atoms(isize))
388 110 : ALLOCATE (cons_info%fixed_type(isize))
389 110 : ALLOCATE (cons_info%fixed_restraint(isize))
390 110 : ALLOCATE (cons_info%fixed_k0(isize))
391 110 : ALLOCATE (cons_info%fixed_molnames(msize))
392 110 : ALLOCATE (cons_info%fixed_mol_type(isize))
393 110 : ALLOCATE (cons_info%fixed_mol_restraint(msize))
394 110 : ALLOCATE (cons_info%fixed_mol_k0(msize))
395 330 : ALLOCATE (cons_info%fixed_exclude_qm(ncons))
396 220 : ALLOCATE (cons_info%fixed_exclude_mm(ncons))
397 246 : DO ig = 1, ncons
398 136 : isize_old = isize
399 136 : msize_old = msize
400 : CALL section_vals_val_get(fix_atom_section, "COMPONENTS_TO_FIX", i_rep_section=ig, &
401 136 : i_val=itype)
402 : CALL section_vals_val_get(fix_atom_section, "LIST", i_rep_section=ig, &
403 136 : n_rep_val=n_rep)
404 254 : DO jg = 1, n_rep
405 : CALL section_vals_val_get(fix_atom_section, "LIST", i_rep_section=ig, &
406 118 : i_rep_val=jg, i_vals=tmplist)
407 118 : CALL reallocate(cons_info%fixed_atoms, 1, isize + SIZE(tmplist))
408 20142 : cons_info%fixed_atoms(isize + 1:isize + SIZE(tmplist)) = tmplist
409 118 : CALL reallocate(cons_info%fixed_restraint, 1, isize + SIZE(tmplist))
410 118 : CALL reallocate(cons_info%fixed_k0, 1, isize + SIZE(tmplist))
411 118 : CALL reallocate(cons_info%fixed_type, 1, isize + SIZE(tmplist))
412 10130 : cons_info%fixed_type(isize + 1:isize + SIZE(tmplist)) = itype
413 254 : isize = SIZE(cons_info%fixed_atoms)
414 : END DO
415 : !Check for restraints
416 136 : IF ((isize - isize_old) > 0) THEN
417 : CALL check_restraint(fix_atom_section, &
418 : is_restraint=cons_info%fixed_restraint(isize_old + 1), &
419 : k0=cons_info%fixed_k0(isize_old + 1), &
420 : i_rep_section=ig, &
421 112 : label="FIXED ATOM")
422 10124 : cons_info%fixed_restraint(isize_old + 1:isize) = cons_info%fixed_restraint(isize_old + 1)
423 10124 : cons_info%fixed_k0(isize_old + 1:isize) = cons_info%fixed_k0(isize_old + 1)
424 : END IF
425 : CALL section_vals_val_get(fix_atom_section, "MOLNAME", i_rep_section=ig, &
426 136 : n_rep_val=n_rep)
427 136 : IF (n_rep /= 0) THEN
428 12 : DO jg = 1, n_rep
429 : CALL section_vals_val_get(fix_atom_section, "MOLNAME", i_rep_section=ig, &
430 6 : i_rep_val=jg, c_vals=tmpstringlist)
431 6 : CALL reallocate(cons_info%fixed_molnames, 1, msize + SIZE(tmpstringlist, 1))
432 6 : CALL reallocate(cons_info%fixed_mol_type, 1, msize + SIZE(tmpstringlist, 1))
433 6 : CALL reallocate(cons_info%fixed_mol_restraint, 1, msize + SIZE(tmpstringlist, 1))
434 6 : CALL reallocate(cons_info%fixed_mol_k0, 1, msize + SIZE(tmpstringlist, 1))
435 18 : cons_info%fixed_molnames(msize + 1:msize + SIZE(tmpstringlist, 1)) = tmpstringlist
436 12 : cons_info%fixed_mol_type(msize + 1:msize + SIZE(tmpstringlist, 1)) = itype
437 12 : msize = SIZE(cons_info%fixed_molnames)
438 : END DO
439 : ! Exclude QM or MM work only if defined MOLNAME
440 6 : CALL reallocate(cons_info%fixed_exclude_qm, 1, msize)
441 6 : CALL reallocate(cons_info%fixed_exclude_mm, 1, msize)
442 : CALL section_vals_val_get(fix_atom_section, "EXCLUDE_QM", i_rep_section=ig, &
443 6 : l_val=cons_info%fixed_exclude_qm(msize_old + 1))
444 : CALL section_vals_val_get(fix_atom_section, "EXCLUDE_MM", i_rep_section=ig, &
445 6 : l_val=cons_info%fixed_exclude_mm(msize_old + 1))
446 12 : cons_info%fixed_exclude_qm(msize_old + 1:msize) = cons_info%fixed_exclude_qm(msize_old + 1)
447 12 : cons_info%fixed_exclude_mm(msize_old + 1:msize) = cons_info%fixed_exclude_mm(msize_old + 1)
448 : END IF
449 : !Check for restraints
450 136 : IF (n_rep /= 0) THEN
451 : CALL check_restraint(fix_atom_section, &
452 : is_restraint=cons_info%fixed_mol_restraint(msize_old + 1), &
453 : k0=cons_info%fixed_mol_k0(msize_old + 1), &
454 : i_rep_section=ig, &
455 6 : label="FIXED ATOM")
456 12 : cons_info%fixed_mol_restraint(msize_old + 1:msize) = cons_info%fixed_mol_restraint(msize_old + 1)
457 12 : cons_info%fixed_mol_k0(msize_old + 1:msize) = cons_info%fixed_mol_k0(msize_old + 1)
458 : END IF
459 : CALL section_vals_val_get(fix_atom_section, "MM_SUBSYS", i_rep_section=ig, &
460 136 : n_rep_val=nrep, explicit=explicit)
461 136 : IF (nrep == 1 .AND. explicit) THEN
462 16 : CPASSERT(cons_info%freeze_mm == do_constr_none)
463 : CALL section_vals_val_get(fix_atom_section, "MM_SUBSYS", i_val=cons_info%freeze_mm, &
464 16 : i_rep_section=ig)
465 16 : cons_info%freeze_mm_type = itype
466 : END IF
467 : CALL section_vals_val_get(fix_atom_section, "QM_SUBSYS", i_rep_section=ig, &
468 136 : n_rep_val=nrep, explicit=explicit)
469 136 : IF (nrep == 1 .AND. explicit) THEN
470 2 : CPASSERT(cons_info%freeze_qm == do_constr_none)
471 : CALL section_vals_val_get(fix_atom_section, "QM_SUBSYS", i_val=cons_info%freeze_qm, &
472 2 : i_rep_section=ig)
473 2 : cons_info%freeze_qm_type = itype
474 : END IF
475 136 : IF (cons_info%freeze_mm /= do_constr_none) THEN
476 : CALL check_restraint(fix_atom_section, &
477 : is_restraint=cons_info%fixed_mm_restraint, &
478 : k0=cons_info%fixed_mm_k0, &
479 : i_rep_section=ig, &
480 28 : label="FIXED ATOM")
481 : END IF
482 790 : IF (cons_info%freeze_qm /= do_constr_none) THEN
483 : CALL check_restraint(fix_atom_section, &
484 : is_restraint=cons_info%fixed_qm_restraint, &
485 : k0=cons_info%fixed_qm_k0, &
486 : i_rep_section=ig, &
487 2 : label="FIXED ATOM")
488 : END IF
489 :
490 : END DO
491 : IF ((isize /= 0) .OR. (msize /= 0) .OR. &
492 110 : (cons_info%freeze_mm /= do_constr_none) .OR. &
493 : (cons_info%freeze_qm /= do_constr_none)) THEN
494 110 : topology%const_atom = .TRUE.
495 : END IF
496 : END IF
497 : ! Collective Constraints
498 10519 : CALL section_vals_get(collective_section, explicit=explicit, n_repetition=ncons)
499 10519 : IF (explicit) THEN
500 120 : topology%const_colv = .TRUE.
501 390 : DO ig = 1, ncons
502 270 : CALL section_vals_val_get(collective_section, "COLVAR", i_rep_section=ig, i_val=icolvar)
503 390 : IF (icolvar > SIZE(colvar_p)) THEN
504 0 : CPABORT("More collective constraints than collective variables specified.")
505 : END IF
506 : END DO
507 120 : cons_info%nconst_colv = ncons
508 360 : ALLOCATE (cons_info%const_colv_mol(ncons))
509 360 : ALLOCATE (cons_info%const_colv_molname(ncons))
510 360 : ALLOCATE (cons_info%const_colv_target(ncons))
511 240 : ALLOCATE (cons_info%const_colv_target_growth(ncons))
512 510 : ALLOCATE (cons_info%colvar_set(ncons))
513 240 : ALLOCATE (cons_info%colv_intermolecular(ncons))
514 240 : ALLOCATE (cons_info%colv_restraint(ncons))
515 240 : ALLOCATE (cons_info%colv_k0(ncons))
516 240 : ALLOCATE (cons_info%colv_exclude_qm(ncons))
517 240 : ALLOCATE (cons_info%colv_exclude_mm(ncons))
518 390 : DO ig = 1, ncons
519 : CALL check_restraint(collective_section, &
520 : is_restraint=cons_info%colv_restraint(ig), &
521 : k0=cons_info%colv_k0(ig), &
522 : i_rep_section=ig, &
523 270 : label="COLLECTIVE")
524 270 : cons_info%const_colv_mol(ig) = 0
525 270 : cons_info%const_colv_molname(ig) = "UNDEF"
526 : ! Exclude QM or MM
527 : CALL section_vals_val_get(collective_section, "EXCLUDE_QM", i_rep_section=ig, &
528 270 : l_val=cons_info%colv_exclude_qm(ig))
529 : CALL section_vals_val_get(collective_section, "EXCLUDE_MM", i_rep_section=ig, &
530 270 : l_val=cons_info%colv_exclude_mm(ig))
531 : ! Intramolecular restraint
532 : CALL section_vals_val_get(collective_section, "INTERMOLECULAR", i_rep_section=ig, &
533 270 : l_val=cons_info%colv_intermolecular(ig))
534 : ! If it is intramolecular let's unset (in case user did it)
535 : ! the molecule and molname field
536 270 : IF (cons_info%colv_intermolecular(ig)) THEN
537 66 : CALL section_vals_val_unset(collective_section, "MOLECULE", i_rep_section=ig)
538 66 : CALL section_vals_val_unset(collective_section, "MOLNAME", i_rep_section=ig)
539 : END IF
540 : ! Let's tag to which molecule we want to apply constraints
541 : CALL section_vals_val_get(collective_section, "MOLECULE", i_rep_section=ig, &
542 270 : n_rep_val=nrep)
543 270 : IF (nrep /= 0) THEN
544 : CALL section_vals_val_get(collective_section, "MOLECULE", i_rep_section=ig, &
545 160 : i_val=cons_info%const_colv_mol(ig))
546 : END IF
547 : CALL section_vals_val_get(collective_section, "MOLNAME", i_rep_section=ig, &
548 270 : n_rep_val=nrep)
549 270 : IF (nrep /= 0) THEN
550 : CALL section_vals_val_get(collective_section, "MOLNAME", i_rep_section=ig, &
551 44 : c_val=cons_info%const_colv_molname(ig))
552 : END IF
553 270 : IF (((cons_info%const_colv_mol(ig) /= 0) .AND. (cons_info%const_colv_molname(ig) /= "UNDEF"))) THEN
554 0 : CPABORT("Both MOLNAME and MOLECULE specified for CONSTRAINT section. ")
555 : END IF
556 270 : IF ((cons_info%const_colv_mol(ig) == 0) .AND. (cons_info%const_colv_molname(ig) == "UNDEF") .AND. &
557 : (.NOT. cons_info%colv_intermolecular(ig))) THEN
558 : CALL cp_abort(__LOCATION__, &
559 : "Constraint section error: you have to specify at least one of the "// &
560 0 : "following keywords: MOLECULE, MOLNAME or INTERMOLECULAR! ")
561 : END IF
562 270 : NULLIFY (cons_info%colvar_set(ig)%colvar)
563 : CALL section_vals_val_get(collective_section, "COLVAR", i_rep_section=ig, &
564 270 : i_val=icolvar)
565 : CALL colvar_clone(cons_info%colvar_set(ig)%colvar, &
566 270 : colvar_p(icolvar)%colvar)
567 : CALL section_vals_val_get(collective_section, "TARGET", &
568 270 : n_rep_val=n_rep, i_rep_section=ig)
569 270 : IF (n_rep /= 0) THEN
570 : CALL section_vals_val_get(collective_section, "TARGET", &
571 168 : r_val=cons_info%const_colv_target(ig), i_rep_section=ig)
572 : ELSE
573 102 : cons_info%const_colv_target(ig) = -HUGE(0.0_dp)
574 : END IF
575 : CALL section_vals_val_get(collective_section, "TARGET_GROWTH", &
576 1470 : r_val=cons_info%const_colv_target_growth(ig), i_rep_section=ig)
577 : END DO
578 : END IF
579 : END IF
580 :
581 10854 : END SUBROUTINE read_constraints_section
582 :
583 : ! **************************************************************************************************
584 : !> \brief Reads input and decides if apply restraints instead of constraints
585 : !> \param cons_section ...
586 : !> \param is_restraint ...
587 : !> \param k0 ...
588 : !> \param i_rep_section ...
589 : !> \param label ...
590 : !> \author teo
591 : ! **************************************************************************************************
592 22242 : SUBROUTINE check_restraint(cons_section, is_restraint, k0, i_rep_section, label)
593 : TYPE(section_vals_type), POINTER :: cons_section
594 : LOGICAL, INTENT(OUT) :: is_restraint
595 : REAL(KIND=dp), INTENT(OUT) :: k0
596 : INTEGER, INTENT(IN), OPTIONAL :: i_rep_section
597 : CHARACTER(LEN=*), INTENT(IN) :: label
598 :
599 : CHARACTER(LEN=default_string_length) :: nlabel
600 : INTEGER :: output_unit
601 : LOGICAL :: explicit
602 : TYPE(section_vals_type), POINTER :: restraint_section
603 :
604 11121 : is_restraint = .FALSE.
605 11121 : output_unit = cp_logger_get_default_io_unit()
606 11121 : CALL section_vals_get(cons_section, explicit=explicit)
607 11121 : IF (explicit) THEN
608 : restraint_section => section_vals_get_subs_vals(cons_section, "RESTRAINT", &
609 618 : i_rep_section=i_rep_section)
610 618 : CALL section_vals_get(restraint_section, explicit=is_restraint)
611 618 : IF (is_restraint) THEN
612 124 : CALL section_vals_val_get(restraint_section, "K", r_val=k0)
613 124 : IF (output_unit > 0) THEN
614 64 : nlabel = cp_to_string(i_rep_section)
615 : WRITE (output_unit, FMT='(T2,"RESTRAINT|",1X,A,F9.6)') &
616 : "Active restraint on "//label//" section Nr."// &
617 64 : TRIM(nlabel)//". K [a.u.]=", k0
618 : END IF
619 : END IF
620 : END IF
621 11121 : END SUBROUTINE check_restraint
622 :
623 : END MODULE topology_input
624 :
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