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input_cp2k_colvar.F
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1!--------------------------------------------------------------------------------------------------!
2! CP2K: A general program to perform molecular dynamics simulations !
3! Copyright 2000-2024 CP2K developers group <https://cp2k.org> !
4! !
5! SPDX-License-Identifier: GPL-2.0-or-later !
6!--------------------------------------------------------------------------------------------------!
7
8! **************************************************************************************************
9!> \par History
10!> - taken out of input_cp2k_motion
11!> \author teo & fawzi
12! **************************************************************************************************
13MODULE input_cp2k_colvar
14 USE bibliography, ONLY: branduardi2007
15 USE colvar_types, ONLY: &
16 do_clv_fix_point, do_clv_geo_center, do_clv_x, do_clv_xy, do_clv_xyz, do_clv_xz, do_clv_y, &
17 do_clv_yz, do_clv_z, plane_def_atoms, plane_def_vec
18 USE cp_output_handling, ONLY: add_last_numeric,&
19 cp_print_key_section_create,&
20 high_print_level,&
21 low_print_level
22 USE cp_units, ONLY: cp_unit_to_cp2k
23 USE input_constants, ONLY: gaussian,&
24 numerical,&
25 rmsd_all,&
26 rmsd_list,&
27 rmsd_weightlist
28 USE input_keyword_types, ONLY: keyword_create,&
29 keyword_release,&
30 keyword_type
31 USE input_section_types, ONLY: section_add_keyword,&
32 section_add_subsection,&
33 section_create,&
34 section_release,&
35 section_type
36 USE input_val_types, ONLY: char_t,&
37 integer_t,&
38 lchar_t,&
39 real_t
40 USE kinds, ONLY: dp
41 USE string_utilities, ONLY: s2a
42#include "./base/base_uses.f90"
43
44 IMPLICIT NONE
45 PRIVATE
46
47 LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .false.
48 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'input_cp2k_colvar'
49
50 PUBLIC :: create_colvar_section, &
51 create_colvar_xyz_d_section, &
52 create_colvar_xyz_od_section
53
54CONTAINS
55
56! **************************************************************************************************
57!> \brief creates the colvar section
58!> \param section the section to be created
59!> \param skip_recursive_colvar ...
60!> \author teo
61! **************************************************************************************************
62 RECURSIVE SUBROUTINE create_colvar_section(section, skip_recursive_colvar)
63 TYPE(section_type), POINTER :: section
64 LOGICAL, OPTIONAL :: skip_recursive_colvar
65
66 LOGICAL :: skip
67 TYPE(section_type), POINTER :: print_key, subsection
68
69 skip = .false.
70 IF (PRESENT(skip_recursive_colvar)) skip = skip_recursive_colvar
71 cpassert(.NOT. ASSOCIATED(section))
72 CALL section_create(section, __location__, name="COLVAR", &
73 description="This section specifies the nature of the collective variables.", &
74 n_keywords=1, n_subsections=1, repeats=.true.)
75 NULLIFY (subsection, print_key)
76
77 CALL create_colvar_var_section(subsection=subsection, &
78 section=section, skip_recursive_colvar=skip)
79
80 CALL section_create(subsection, __location__, name="PRINT", &
81 description="Controls the printing of the colvar specifications", &
82 n_keywords=0, n_subsections=1, repeats=.true.)
83 NULLIFY (print_key)
84 CALL cp_print_key_section_create(print_key, __location__, "PROGRAM_RUN_INFO", &
85 description="Controls the printing of basic information during colvar setup.", &
86 print_level=low_print_level, add_last=add_last_numeric, filename="__STD_OUT__")
87 CALL section_add_subsection(subsection, print_key)
88 CALL section_release(print_key)
89 CALL section_add_subsection(section, subsection)
90 CALL section_release(subsection)
91
92 CALL create_clv_info_section(subsection)
93 CALL section_add_subsection(section, subsection)
94 CALL section_release(subsection)
95
96 END SUBROUTINE create_colvar_section
97
98! **************************************************************************************************
99!> \brief Create the restart section for colvar restraints
100!> This section will be only used for restraint restarts.
101!> Constraints are handled automatically
102!> \param section the section to create
103!> \author Teodoro Laino 08.2006
104! **************************************************************************************************
105 SUBROUTINE create_clv_info_section(section)
106 TYPE(section_type), POINTER :: section
107
108 TYPE(keyword_type), POINTER :: keyword
109
110 cpassert(.NOT. ASSOCIATED(section))
111 NULLIFY (keyword)
112 CALL section_create(section, __location__, name="COLVAR_FUNC_INFO", &
113 description="Specify further data possibly used by colvars, depending "// &
114 "on the starting geometry, for computing the functions value.", &
115 n_subsections=0, repeats=.false.)
116
117 CALL keyword_create(keyword, __location__, name="_DEFAULT_KEYWORD_", &
118 description="Colvar function data."// &
119 " The order is an internal order. So if you decide to edit/modify/add these values by hand"// &
120 " you should know very well what you are doing.!", repeats=.true., &
121 usage="{Real} ...", type_of_var=real_t, n_var=-1)
122 CALL section_add_keyword(section, keyword)
123 CALL keyword_release(keyword)
124
125 END SUBROUTINE create_clv_info_section
126
127! **************************************************************************************************
128!> \brief creates the collective variables for the colvar section
129!> \param subsection ...
130!> \param section the section to be created
131!> \param skip_recursive_colvar ...
132!> \author teo
133! **************************************************************************************************
134 RECURSIVE SUBROUTINE create_colvar_var_section(subsection, section, skip_recursive_colvar)
135 TYPE(section_type), POINTER :: subsection, section
136 LOGICAL, INTENT(IN) :: skip_recursive_colvar
137
138 cpassert(.NOT. ASSOCIATED(subsection))
139 cpassert(ASSOCIATED(section))
140
141 CALL create_colvar_dist_section(subsection)
142 CALL section_add_subsection(section, subsection)
143 CALL section_release(subsection)
144
145 CALL create_colvar_angle_section(subsection)
146 CALL section_add_subsection(section, subsection)
147 CALL section_release(subsection)
148
149 CALL create_colvar_torsion_section(subsection)
150 CALL section_add_subsection(section, subsection)
151 CALL section_release(subsection)
152
153 CALL create_colvar_coord_section(subsection)
154 CALL section_add_subsection(section, subsection)
155 CALL section_release(subsection)
156
157 CALL create_colvar_pop_section(subsection)
158 CALL section_add_subsection(section, subsection)
159 CALL section_release(subsection)
160
161 CALL create_colvar_gyr_section(subsection)
162 CALL section_add_subsection(section, subsection)
163 CALL section_release(subsection)
164
165 CALL create_colvar_d_pl_section(subsection)
166 CALL section_add_subsection(section, subsection)
167 CALL section_release(subsection)
168
169 CALL create_colvar_a_pl_section(subsection)
170 CALL section_add_subsection(section, subsection)
171 CALL section_release(subsection)
172
173 CALL create_colvar_rot_section(subsection)
174 CALL section_add_subsection(section, subsection)
175 CALL section_release(subsection)
176
177 CALL create_colvar_dfunct_section(subsection)
178 CALL section_add_subsection(section, subsection)
179 CALL section_release(subsection)
180
181 CALL create_colvar_qparm_section(subsection)
182 CALL section_add_subsection(section, subsection)
183 CALL section_release(subsection)
184
185 CALL create_colvar_hydronium_shell_section(subsection)
186 CALL section_add_subsection(section, subsection)
187 CALL section_release(subsection)
188
189 CALL create_colvar_hydronium_dist_section(subsection)
190 CALL section_add_subsection(section, subsection)
191 CALL section_release(subsection)
192
193 CALL create_colvar_acid_hyd_dist_section(subsection)
194 CALL section_add_subsection(section, subsection)
195 CALL section_release(subsection)
196
197 CALL create_colvar_acid_hyd_shell_section(subsection)
198 CALL section_add_subsection(section, subsection)
199 CALL section_release(subsection)
200
201 CALL create_colvar_rmsd_section(subsection)
202 CALL section_add_subsection(section, subsection)
203 CALL section_release(subsection)
204
205 CALL create_colvar_xyz_d_section(subsection)
206 CALL section_add_subsection(section, subsection)
207 CALL section_release(subsection)
208
209 CALL create_colvar_xyz_od_section(subsection)
210 CALL section_add_subsection(section, subsection)
211 CALL section_release(subsection)
212
213 CALL create_colvar_u_section(subsection)
214 CALL section_add_subsection(section, subsection)
215 CALL section_release(subsection)
216
217 CALL create_colvar_wc_section(subsection)
218 CALL section_add_subsection(section, subsection)
219 CALL section_release(subsection)
220
221 CALL create_colvar_hbp_section(subsection)
222 CALL section_add_subsection(section, subsection)
223 CALL section_release(subsection)
224
225 CALL create_colvar_ring_puckering_section(subsection)
226 CALL section_add_subsection(section, subsection)
227 CALL section_release(subsection)
228
229 CALL create_colvar_cond_dist_section(subsection)
230 CALL section_add_subsection(section, subsection)
231 CALL section_release(subsection)
232
233 IF (.NOT. skip_recursive_colvar) THEN
234 CALL create_colvar_rpath_section(subsection)
235 CALL section_add_subsection(section, subsection)
236 CALL section_release(subsection)
237
238 CALL create_colvar_dpath_section(subsection)
239 CALL section_add_subsection(section, subsection)
240 CALL section_release(subsection)
241
242 CALL create_colvar_comb_section(subsection)
243 CALL section_add_subsection(section, subsection)
244 CALL section_release(subsection)
245 END IF
246
247 END SUBROUTINE create_colvar_var_section
248
249! **************************************************************************************************
250!> \brief collective variables specifying coordination
251!> \param section the section to be created
252!> \author teo
253! **************************************************************************************************
254 SUBROUTINE create_colvar_coord_section(section)
255 TYPE(section_type), POINTER :: section
256
257 TYPE(keyword_type), POINTER :: keyword
258 TYPE(section_type), POINTER :: subsection
259
260 cpassert(.NOT. ASSOCIATED(section))
261 CALL section_create(section, __location__, name="coordination", &
262 description="Section to define the coordination number as a collective variable.", &
263 n_keywords=1, n_subsections=0, repeats=.false.)
264
265 NULLIFY (subsection, keyword)
266
267 CALL keyword_create(keyword, __location__, name="ATOMS_FROM", &
268 variants=(/"POINTS_FROM"/), &
269 description="Specify indexes of atoms/points building the coordination variable. ", &
270 usage="ATOMS_FROM {integer} {integer} ..", repeats=.true., &
271 n_var=-1, type_of_var=integer_t)
272 CALL section_add_keyword(section, keyword)
273 CALL keyword_release(keyword)
274
275 CALL keyword_create(keyword, __location__, name="ATOMS_TO", &
276 variants=(/"POINTS_TO"/), &
277 description="Specify indexes of atoms/points building the coordination variable. ", &
278 usage="ATOMS_TO {integer} {integer} ..", repeats=.true., &
279 n_var=-1, type_of_var=integer_t)
280 CALL section_add_keyword(section, keyword)
281 CALL keyword_release(keyword)
282
283 CALL keyword_create(keyword, __location__, name="ATOMS_TO_B", &
284 variants=(/"POINTS_TO_B"/), &
285 description="For the CV given by the multiplication of two coorination numbers,"// &
286 " here specify indexes of the third set of atoms/points. ", &
287 usage="ATOMS_TO_B {integer} {integer} ..", repeats=.true., &
288 n_var=-1, type_of_var=integer_t)
289 CALL section_add_keyword(section, keyword)
290 CALL keyword_release(keyword)
291
292 CALL keyword_create(keyword, __location__, name="KINDS_FROM", &
293 description="Specify alternatively kinds of atoms building the coordination variable.", &
294 usage="KINDS_FROM {CHAR} {CHAR} ..", repeats=.true., &
295 n_var=-1, type_of_var=char_t)
296 CALL section_add_keyword(section, keyword)
297 CALL keyword_release(keyword)
298
299 CALL keyword_create(keyword, __location__, name="KINDS_TO", &
300 description="Specify alternatively kinds of atoms building the coordination variable.", &
301 usage="KINDS_TO {CHAR} {CHAR} ..", repeats=.true., &
302 n_var=-1, type_of_var=char_t)
303 CALL section_add_keyword(section, keyword)
304 CALL keyword_release(keyword)
305
306 CALL keyword_create(keyword, __location__, name="KINDS_TO_B", &
307 description="For the CV given by the multiplication of two coorination numbers,"// &
308 " here specify alternatively kinds of atoms building the coordination variable.", &
309 usage="KINDS_TO_B {CHAR} {CHAR} ..", repeats=.true., &
310 n_var=-1, type_of_var=char_t)
311 CALL section_add_keyword(section, keyword)
312 CALL keyword_release(keyword)
313
314 ! Must be present in each colvar and handled properly
315 CALL create_point_section(subsection)
316 CALL section_add_subsection(section, subsection)
317 CALL section_release(subsection)
318
319 CALL keyword_create(keyword, __location__, name="R0", &
320 variants=(/"R_0"/), &
321 description="Specify the R0 parameter in the coordination function.", &
322 usage="R0 {real}", default_r_val=3.0_dp, &
323 unit_str="bohr", n_var=1)
324 CALL section_add_keyword(section, keyword)
325 CALL keyword_release(keyword)
326
327 CALL keyword_create(keyword, __location__, name="NN", &
328 variants=(/"EXPON_NUMERATOR"/), &
329 description="Sets the value of the numerator of the exponential factor"// &
330 " in the coordination FUNCTION.", &
331 usage="NN {integer}", default_i_val=6, &
332 n_var=1)
333 CALL section_add_keyword(section, keyword)
334 CALL keyword_release(keyword)
335
336 CALL keyword_create(keyword, __location__, name="ND", &
337 variants=(/"EXPON_DENOMINATOR"/), &
338 description="Sets the value of the denominator of the exponential factor"// &
339 " in the coordination FUNCTION.", &
340 usage="ND {integer}", default_i_val=12, &
341 n_var=1)
342 CALL section_add_keyword(section, keyword)
343 CALL keyword_release(keyword)
344
345 CALL keyword_create(keyword, __location__, name="R0_B", &
346 variants=(/"R_0_B"/), &
347 description="For the CV given by the multiplication of two coorination numbers,"// &
348 " specify the R0 parameter in the second coordination function.", &
349 usage="R0_B {real}", default_r_val=3.0_dp, &
350 unit_str="bohr", n_var=1)
351 CALL section_add_keyword(section, keyword)
352 CALL keyword_release(keyword)
353
354 CALL keyword_create(keyword, __location__, name="NN_B", &
355 variants=(/"EXPON_NUMERATOR_B"/), &
356 description="For the CV given by the multiplication of two coorination numbers,"// &
357 " Sets the value of the numerator of the exponential factor"// &
358 " in the coordination FUNCTION.", &
359 usage="NN_B {integer}", default_i_val=6, &
360 n_var=1)
361 CALL section_add_keyword(section, keyword)
362 CALL keyword_release(keyword)
363
364 CALL keyword_create(keyword, __location__, name="ND_B", &
365 variants=(/"EXPON_DENOMINATOR_B"/), &
366 description="For the CV given by the multiplication of two coorination numbers,"// &
367 " Sets the value of the denominator of the exponential factor"// &
368 " in the coordination FUNCTION.", &
369 usage="ND_B {integer}", default_i_val=12, &
370 n_var=1)
371 CALL section_add_keyword(section, keyword)
372 CALL keyword_release(keyword)
373
374 END SUBROUTINE create_colvar_coord_section
375
376! **************************************************************************************************
377!> \brief ...
378!> \param section ...
379! **************************************************************************************************
380 SUBROUTINE create_colvar_cond_dist_section(section)
381 TYPE(section_type), POINTER :: section
382
383 TYPE(keyword_type), POINTER :: keyword
384 TYPE(section_type), POINTER :: subsection
385
386 cpassert(.NOT. ASSOCIATED(section))
387 CALL section_create(section, __location__, name="CONDITIONED_DISTANCE", &
388 description="Section to define the conditioned distance as a collective variable.", &
389 n_keywords=1, n_subsections=0, repeats=.false.)
390
391 NULLIFY (subsection, keyword)
392
393 CALL keyword_create(keyword, __location__, name="ATOMS_DISTANCE", &
394 description="Specify indexes of atoms/points from which the distance is computed. ", &
395 usage="ATOMS_DISTANCE {integer} {integer} ..", repeats=.true., &
396 n_var=-1, type_of_var=integer_t)
397 CALL section_add_keyword(section, keyword)
398 CALL keyword_release(keyword)
399
400 CALL keyword_create(keyword, __location__, name="ATOMS_FROM", &
401 variants=(/"POINTS_FROM"/), &
402 description="Specify indexes of atoms/points building the coordination variable. ", &
403 usage="ATOMS_FROM {integer} {integer} ..", repeats=.true., &
404 n_var=-1, type_of_var=integer_t)
405 CALL section_add_keyword(section, keyword)
406 CALL keyword_release(keyword)
407
408 CALL keyword_create(keyword, __location__, name="ATOMS_TO", &
409 variants=(/"POINTS_TO"/), &
410 description="Specify indexes of atoms/points building the coordination variable. ", &
411 usage="ATOMS_TO {integer} {integer} ..", repeats=.true., &
412 n_var=-1, type_of_var=integer_t)
413 CALL section_add_keyword(section, keyword)
414 CALL keyword_release(keyword)
415
416 CALL keyword_create(keyword, __location__, name="KINDS_FROM", &
417 description="Specify alternatively kinds of atoms building the coordination variable.", &
418 usage="KINDS_FROM {CHAR} {CHAR} ..", repeats=.true., &
419 n_var=-1, type_of_var=char_t)
420 CALL section_add_keyword(section, keyword)
421 CALL keyword_release(keyword)
422
423 CALL keyword_create(keyword, __location__, name="KINDS_TO", &
424 description="Specify alternatively kinds of atoms building the coordination variable.", &
425 usage="KINDS_TO {CHAR} {CHAR} ..", repeats=.true., &
426 n_var=-1, type_of_var=char_t)
427 CALL section_add_keyword(section, keyword)
428 CALL keyword_release(keyword)
429
430 ! Must be present in each colvar and handled properly
431 CALL create_point_section(subsection)
432 CALL section_add_subsection(section, subsection)
433 CALL section_release(subsection)
434
435 CALL keyword_create(keyword, __location__, name="R0", &
436 variants=(/"R_0"/), &
437 description="Specify the R0 parameter in the coordination function.", &
438 usage="R0 {real}", default_r_val=3.0_dp, &
439 unit_str="bohr", n_var=1)
440 CALL section_add_keyword(section, keyword)
441 CALL keyword_release(keyword)
442
443 CALL keyword_create(keyword, __location__, name="NN", &
444 variants=(/"EXPON_NUMERATOR"/), &
445 description="Sets the value of the numerator of the exponential factor"// &
446 " in the coordination FUNCTION.", &
447 usage="NN {integer}", default_i_val=6, &
448 n_var=1)
449 CALL section_add_keyword(section, keyword)
450 CALL keyword_release(keyword)
451
452 CALL keyword_create(keyword, __location__, name="ND", &
453 variants=(/"EXPON_DENOMINATOR"/), &
454 description="Sets the value of the denominator of the exponential factor"// &
455 " in the coordination FUNCTION.", &
456 usage="ND {integer}", default_i_val=12, &
457 n_var=1)
458 CALL section_add_keyword(section, keyword)
459 CALL keyword_release(keyword)
460
461 CALL keyword_create(keyword, __location__, name="LAMBDA", &
462 description="Specify the lambda parameter at the exponent of the conditioned distance function.", &
463 usage="R0 {real}", default_r_val=3.0_dp, &
464 unit_str="bohr", n_var=1)
465 CALL section_add_keyword(section, keyword)
466 CALL keyword_release(keyword)
467
468 END SUBROUTINE create_colvar_cond_dist_section
469
470! **************************************************************************************************
471!> \brief collective variables specifying population of a specie based on coordination
472!> \param section the section to be created
473!> \date 01.2009
474!> \author Fabio Sterpone
475! **************************************************************************************************
476 SUBROUTINE create_colvar_pop_section(section)
477 TYPE(section_type), POINTER :: section
478
479 TYPE(keyword_type), POINTER :: keyword
480 TYPE(section_type), POINTER :: subsection
481
482 cpassert(.NOT. ASSOCIATED(section))
483 CALL section_create(section, __location__, name="population", &
484 description="Section to define the population of specie as a collective variable. "// &
485 "See also <https://doi.org/10.1021/jp3019588>.", &
486 n_keywords=1, n_subsections=0, repeats=.false.)
487
488 NULLIFY (subsection, keyword)
489
490 CALL keyword_create(keyword, __location__, name="ATOMS_FROM", &
491 variants=(/"POINTS_FROM"/), &
492 description="Specify indexes of atoms/points building the coordination variable. ", &
493 usage="ATOMS_FROM {integer} {integer} ..", repeats=.true., &
494 n_var=-1, type_of_var=integer_t)
495 CALL section_add_keyword(section, keyword)
496 CALL keyword_release(keyword)
497
498 CALL keyword_create(keyword, __location__, name="ATOMS_TO", &
499 variants=(/"POINTS_TO"/), &
500 description="Specify indexes of atoms/points building the coordination variable. ", &
501 usage="ATOMS_TO {integer} {integer} ..", repeats=.true., &
502 n_var=-1, type_of_var=integer_t)
503 CALL section_add_keyword(section, keyword)
504 CALL keyword_release(keyword)
505
506 CALL keyword_create(keyword, __location__, name="KINDS_FROM", &
507 description="Specify alternatively kinds of atoms building the coordination variable.", &
508 usage="KINDS_FROM {CHAR} {CHAR} ..", repeats=.true., &
509 n_var=-1, type_of_var=char_t)
510 CALL section_add_keyword(section, keyword)
511 CALL keyword_release(keyword)
512
513 CALL keyword_create(keyword, __location__, name="KINDS_TO", &
514 description="Specify alternatively kinds of atoms building the coordination variable.", &
515 usage="KINDS_TO {CHAR} {CHAR} ..", repeats=.true., &
516 n_var=-1, type_of_var=char_t)
517 CALL section_add_keyword(section, keyword)
518 CALL keyword_release(keyword)
519
520 ! Must be present in each colvar and handled properly
521 CALL create_point_section(subsection)
522 CALL section_add_subsection(section, subsection)
523 CALL section_release(subsection)
524
525 CALL keyword_create(keyword, __location__, name="R0", &
526 variants=(/"R_0"/), &
527 description="Specify the R0 parameter in the coordination function.", &
528 usage="R0 {real}", default_r_val=3.0_dp, &
529 n_var=1)
530 CALL section_add_keyword(section, keyword)
531 CALL keyword_release(keyword)
532
533 CALL keyword_create(keyword, __location__, name="NN", &
534 variants=(/"EXPON_NUMERATOR"/), &
535 description="Sets the value of the numerator of the exponential factor"// &
536 " in the coordination FUNCTION.", &
537 usage="NN {integer}", default_i_val=6, &
538 n_var=1)
539 CALL section_add_keyword(section, keyword)
540 CALL keyword_release(keyword)
541
542 CALL keyword_create(keyword, __location__, name="ND", &
543 variants=(/"EXPON_DENOMINATOR"/), &
544 description="Sets the value of the denominator of the exponential factor"// &
545 " in the coordination FUNCTION.", &
546 usage="ND {integer}", default_i_val=12, &
547 n_var=1)
548 CALL section_add_keyword(section, keyword)
549 CALL keyword_release(keyword)
550
551 CALL keyword_create(keyword, __location__, name="n0", &
552 variants=(/"n_0"/), &
553 description="Specify the n0 parameter that sets the coordination of the species.", &
554 usage="n0 {integer}", default_i_val=4, &
555 n_var=1)
556 CALL section_add_keyword(section, keyword)
557 CALL keyword_release(keyword)
558
559 CALL keyword_create(keyword, __location__, name="SIGMA", &
560 description="Specify the gaussian width of used to build the population istogram.", &
561 usage="SIGMA {real}", default_r_val=0.5_dp, &
562 n_var=1)
563 CALL section_add_keyword(section, keyword)
564 CALL keyword_release(keyword)
565
566 END SUBROUTINE create_colvar_pop_section
567
568! **************************************************************************************************
569!> \brief ...
570!> \param section ...
571! **************************************************************************************************
572 SUBROUTINE create_colvar_gyr_section(section)
573 TYPE(section_type), POINTER :: section
574
575 TYPE(keyword_type), POINTER :: keyword
576 TYPE(section_type), POINTER :: subsection
577
578 cpassert(.NOT. ASSOCIATED(section))
579 CALL section_create(section, __location__, name="GYRATION_RADIUS", &
580 description="Section to define the gyration radius as a collective variable.", &
581 n_keywords=1, n_subsections=0, repeats=.false.)
582
583 NULLIFY (subsection, keyword)
584
585 CALL keyword_create(keyword, __location__, name="ATOMS", &
586 variants=(/"POINTS"/), &
587 description="Specify indexes of atoms/points defyining the gyration radius variable. ", &
588 usage="ATOMS {integer} {integer} ..", repeats=.true., &
589 n_var=-1, type_of_var=integer_t)
590 CALL section_add_keyword(section, keyword)
591 CALL keyword_release(keyword)
592
593 CALL keyword_create(keyword, __location__, name="KINDS", &
594 description="Specify alternatively kinds of atoms defining the gyration radius.", &
595 usage="KINDS {CHAR} {CHAR} ..", repeats=.true., &
596 n_var=-1, type_of_var=char_t)
597 CALL section_add_keyword(section, keyword)
598 CALL keyword_release(keyword)
599
600 ! Must be present in each colvar and handled properly
601 CALL create_point_section(subsection)
602 CALL section_add_subsection(section, subsection)
603 CALL section_release(subsection)
604
605 END SUBROUTINE create_colvar_gyr_section
606
607! **************************************************************************************************
608!> \brief collective variables specifying torsion
609!> \param section the section to be created
610!> \author teo
611! **************************************************************************************************
612 SUBROUTINE create_colvar_dfunct_section(section)
613 TYPE(section_type), POINTER :: section
614
615 TYPE(keyword_type), POINTER :: keyword
616 TYPE(section_type), POINTER :: subsection
617
618 cpassert(.NOT. ASSOCIATED(section))
619 CALL section_create(section, __location__, name="DISTANCE_FUNCTION", &
620 description="Section to define functions between two distances as collective variables."// &
621 " The function is defined as d1+coeff*d2", &
622 n_keywords=1, n_subsections=0, repeats=.false.)
623
624 NULLIFY (keyword, subsection)
625
626 CALL keyword_create(keyword, __location__, name="ATOMS", &
627 variants=(/"POINTS"/), &
628 description="Specifies the indexes of atoms/points for the two bonds d1=(1-2) d2=(3-4).", &
629 usage="ATOMS {integer} {integer} {integer} {integer}", &
630 n_var=4, type_of_var=integer_t)
631 CALL section_add_keyword(section, keyword)
632 CALL keyword_release(keyword)
633
634 CALL keyword_create(keyword, __location__, name="COEFFICIENT", &
635 description="Specifies the coefficient in the function for the constraint."// &
636 " -1.0 has to be used for distance difference, 1.0 for distance addition", &
637 usage="COEFFICIENT {real}", &
638 type_of_var=real_t)
639 CALL section_add_keyword(section, keyword)
640 CALL keyword_release(keyword)
641
642 CALL keyword_create(keyword, __location__, name="PBC", &
643 description="Whether periodic boundary conditions should be applied on the "// &
644 "atomic position before computing the colvar or not.", &
645 usage="PBC", &
646 default_l_val=.true., lone_keyword_l_val=.true.)
647 CALL section_add_keyword(section, keyword)
648 CALL keyword_release(keyword)
649
650 ! Must be present in each colvar and handled properly
651 CALL create_point_section(subsection)
652 CALL section_add_subsection(section, subsection)
653 CALL section_release(subsection)
654
655 END SUBROUTINE create_colvar_dfunct_section
656
657! **************************************************************************************************
658!> \brief collective variables specifying torsion
659!> \param section the section to be created
660!> \author teo
661! **************************************************************************************************
662 SUBROUTINE create_colvar_torsion_section(section)
663 TYPE(section_type), POINTER :: section
664
665 TYPE(keyword_type), POINTER :: keyword
666 TYPE(section_type), POINTER :: subsection
667
668 cpassert(.NOT. ASSOCIATED(section))
669 CALL section_create(section, __location__, name="torsion", &
670 description="Section to define the torsion as a collective variables.", &
671 n_keywords=1, n_subsections=0, repeats=.false.)
672
673 NULLIFY (keyword, subsection)
674
675 CALL keyword_create(keyword, __location__, name="ATOMS", &
676 variants=(/"POINTS"/), &
677 description="Specifies the indexes of atoms/points defining the torsion.", &
678 usage="ATOMS {integer} {integer} {integer} {integer}", &
679 n_var=4, type_of_var=integer_t)
680 CALL section_add_keyword(section, keyword)
681 CALL keyword_release(keyword)
682
683 ! Must be present in each colvar and handled properly
684 CALL create_point_section(subsection)
685 CALL section_add_subsection(section, subsection)
686 CALL section_release(subsection)
687
688 END SUBROUTINE create_colvar_torsion_section
689
690! **************************************************************************************************
691!> \brief collective variables specifying torsion
692!> \param section the section to be created
693!> \author teo
694! **************************************************************************************************
695 SUBROUTINE create_colvar_rot_section(section)
696 TYPE(section_type), POINTER :: section
697
698 TYPE(keyword_type), POINTER :: keyword
699 TYPE(section_type), POINTER :: subsection
700
701 cpassert(.NOT. ASSOCIATED(section))
702 CALL section_create(section, __location__, name="bond_rotation", &
703 description="Section to define the rotation of a bond/line with respect to"// &
704 " another bond/line", &
705 n_keywords=1, n_subsections=0, repeats=.false.)
706
707 NULLIFY (keyword, subsection)
708
709 CALL keyword_create(keyword, __location__, name="P1_BOND1", &
710 description="Specifies the index of atom/point defining the first point"// &
711 " of the first bond/line.", &
712 usage="P1_BOND1 {integer}", &
713 n_var=1, type_of_var=integer_t)
714 CALL section_add_keyword(section, keyword)
715 CALL keyword_release(keyword)
716
717 CALL keyword_create(keyword, __location__, name="P2_BOND1", &
718 description="Specifies the index of atom/point defining the second point"// &
719 " of the first bond/line.", &
720 usage="P2_BOND1 {integer}", &
721 n_var=1, type_of_var=integer_t)
722 CALL section_add_keyword(section, keyword)
723 CALL keyword_release(keyword)
724
725 CALL keyword_create(keyword, __location__, name="P1_BOND2", &
726 description="Specifies the index of atom/point defining the first point"// &
727 " of the second bond/line.", &
728 usage="P1_BOND2 {integer}", &
729 n_var=1, type_of_var=integer_t)
730 CALL section_add_keyword(section, keyword)
731 CALL keyword_release(keyword)
732
733 CALL keyword_create(keyword, __location__, name="P2_BOND2", &
734 description="Specifies the index of atom/point defining the second point"// &
735 " of the second bond/line.", &
736 usage="P2_BOND2 {integer}", &
737 n_var=1, type_of_var=integer_t)
738 CALL section_add_keyword(section, keyword)
739 CALL keyword_release(keyword)
740
741 ! Must be present in each colvar and handled properly
742 CALL create_point_section(subsection)
743 CALL section_add_subsection(section, subsection)
744 CALL section_release(subsection)
745
746 END SUBROUTINE create_colvar_rot_section
747
748! **************************************************************************************************
749!> \brief collective variables specifying angles
750!> \param section the section to be created
751!> \author teo
752! **************************************************************************************************
753 SUBROUTINE create_colvar_angle_section(section)
754 TYPE(section_type), POINTER :: section
755
756 TYPE(keyword_type), POINTER :: keyword
757 TYPE(section_type), POINTER :: subsection
758
759 cpassert(.NOT. ASSOCIATED(section))
760 CALL section_create(section, __location__, name="angle", &
761 description="Section to define the angle as a collective variables.", &
762 n_keywords=1, n_subsections=0, repeats=.false.)
763 NULLIFY (keyword, subsection)
764
765 CALL keyword_create(keyword, __location__, name="ATOMS", &
766 variants=(/"POINTS"/), &
767 description="Specifies the indexes of atoms/points defining the angle.", &
768 usage="ATOMS {integer} {integer} {integer}", &
769 n_var=3, type_of_var=integer_t)
770 CALL section_add_keyword(section, keyword)
771 CALL keyword_release(keyword)
772
773 ! Must be present in each colvar and handled properly
774 CALL create_point_section(subsection)
775 CALL section_add_subsection(section, subsection)
776 CALL section_release(subsection)
777
778 END SUBROUTINE create_colvar_angle_section
779
780! **************************************************************************************************
781!> \brief creates the colvar section regarded to the collective variables dist
782!> \param section the section to be created
783!> \author teo
784! **************************************************************************************************
785 SUBROUTINE create_colvar_dist_section(section)
786 TYPE(section_type), POINTER :: section
787
788 TYPE(keyword_type), POINTER :: keyword
789 TYPE(section_type), POINTER :: subsection
790
791 cpassert(.NOT. ASSOCIATED(section))
792 CALL section_create(section, __location__, name="distance", &
793 description="Section to define the distance as a collective variables.", &
794 n_keywords=1, n_subsections=0, repeats=.false.)
795 NULLIFY (keyword, subsection)
796
797 CALL keyword_create(keyword, __location__, name="ATOMS", &
798 variants=(/"POINTS"/), &
799 description="Specifies the indexes of atoms/points defining the distance.", &
800 usage="ATOMS {integer} {integer}", &
801 n_var=2, type_of_var=integer_t)
802 CALL section_add_keyword(section, keyword)
803 CALL keyword_release(keyword)
804 CALL keyword_create(keyword, __location__, name="AXIS", &
805 description="Define the axes along which the colvar should be evaluated", &
806 usage="AXIS (XYZ | X | Y | Z | XY| XZ | YZ)", &
807 enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
808 enum_i_vals=(/do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz/), &
809 default_i_val=do_clv_xyz)
810 CALL section_add_keyword(section, keyword)
811 CALL keyword_release(keyword)
812
813 CALL keyword_create(keyword, __location__, name="SIGN", &
814 description="Whether the distance along one Cartesian axis has to be considered with sign."// &
815 " This option is valid if only one dimension is selected.", &
816 usage="SIGN", &
817 default_l_val=.false., lone_keyword_l_val=.true.)
818 CALL section_add_keyword(section, keyword)
819 CALL keyword_release(keyword)
820
821 ! Must be present in each colvar and handled properly
822 CALL create_point_section(subsection)
823 CALL section_add_subsection(section, subsection)
824 CALL section_release(subsection)
825
826 END SUBROUTINE create_colvar_dist_section
827
828! **************************************************************************************************
829!> \brief creates the colvar section regarded to the collective variables dist
830!> \param section the section to be created
831!> \author teo
832! **************************************************************************************************
833 SUBROUTINE create_colvar_xyz_d_section(section)
834 TYPE(section_type), POINTER :: section
835
836 TYPE(keyword_type), POINTER :: keyword
837 TYPE(section_type), POINTER :: subsection
838
839 cpassert(.NOT. ASSOCIATED(section))
840 CALL section_create(section, __location__, name="XYZ_DIAG", &
841 description="Section to define the distance of an atom from its starting "// &
842 "position ((X-X(0))^2+(Y-Y(0))^2+(Z-Z(0))^2) or part of its components as a collective variable. "// &
843 "If absolute_position is specified, instead the CV is represented by the "// &
844 "instantaneous position of the atom (only available for X, Y or Z components).", &
845 n_keywords=1, n_subsections=0, repeats=.false.)
846 NULLIFY (keyword, subsection)
847
848 CALL keyword_create(keyword, __location__, name="ATOM", &
849 variants=(/"POINT"/), &
850 description="Specifies the index of the atom/point.", &
851 usage="ATOM {integer}", &
852 n_var=1, type_of_var=integer_t)
853 CALL section_add_keyword(section, keyword)
854 CALL keyword_release(keyword)
855
856 CALL keyword_create(keyword, __location__, name="COMPONENT", &
857 description="Define the component of the position vector which will be used "// &
858 "as a colvar.", &
859 usage="AXIS (XYZ | X | Y | Z | XY| XZ | YZ)", &
860 enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
861 enum_i_vals=(/do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz/), &
862 default_i_val=do_clv_xyz)
863 CALL section_add_keyword(section, keyword)
864 CALL keyword_release(keyword)
865
866 CALL keyword_create(keyword, __location__, name="PBC", &
867 description="Whether periodic boundary conditions should be applied on the "// &
868 "atomic position before computing the colvar or not.", &
869 usage="PBC", &
870 default_l_val=.true., lone_keyword_l_val=.true.)
871 CALL section_add_keyword(section, keyword)
872 CALL keyword_release(keyword)
873
874 CALL keyword_create(keyword, __location__, name="ABSOLUTE_POSITION", &
875 description="If enabled, the absolute position of the atoms will be used. ", &
876 usage="ABSOLUTE_POSITION", &
877 default_l_val=.false., lone_keyword_l_val=.true.)
878 CALL section_add_keyword(section, keyword)
879 CALL keyword_release(keyword)
880
881 ! Must be present in each colvar and handled properly
882 CALL create_point_section(subsection)
883 CALL section_add_subsection(section, subsection)
884 CALL section_release(subsection)
885
886 END SUBROUTINE create_colvar_xyz_d_section
887
888! **************************************************************************************************
889!> \brief creates the colvar section regarded to the collective variables dist
890!> \param section the section to be created
891!> \author teo
892! **************************************************************************************************
893 SUBROUTINE create_colvar_xyz_od_section(section)
894 TYPE(section_type), POINTER :: section
895
896 TYPE(keyword_type), POINTER :: keyword
897 TYPE(section_type), POINTER :: subsection
898
899 cpassert(.NOT. ASSOCIATED(section))
900 CALL section_create(section, __location__, name="XYZ_OUTERDIAG", &
901 description="Section to define the cross term (XA-XA(0))*(XB-XB(0))+(XA-XA(0))*(YB-YB(0))"// &
902 " or part of its components as a collective variable. The final term is given by the product"// &
903 " of the components of A with the components of B.", &
904 n_keywords=1, n_subsections=0, repeats=.false.)
905 NULLIFY (keyword, subsection)
906
907 CALL keyword_create(keyword, __location__, name="ATOMS", &
908 variants=(/"POINTS"/), &
909 description="Specifies the index of the atoms/points A and B.", &
910 usage="ATOMS {integer} {integer}", &
911 n_var=2, type_of_var=integer_t)
912 CALL section_add_keyword(section, keyword)
913 CALL keyword_release(keyword)
914
915 CALL keyword_create(keyword, __location__, name="COMPONENT_A", &
916 description="Define the component of the position vector which will be used "// &
917 "as a colvar for atom A.", &
918 usage="AXIS (XYZ | X | Y | Z | XY| XZ | YZ)", &
919 enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
920 enum_i_vals=(/do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz/), &
921 default_i_val=do_clv_xyz)
922 CALL section_add_keyword(section, keyword)
923 CALL keyword_release(keyword)
924
925 CALL keyword_create(keyword, __location__, name="COMPONENT_B", &
926 description="Define the component of the position vector which will be used "// &
927 "as a colvar for atom B.", &
928 usage="AXIS (XYZ | X | Y | Z | XY| XZ | YZ)", &
929 enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
930 enum_i_vals=(/do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz/), &
931 default_i_val=do_clv_xyz)
932 CALL section_add_keyword(section, keyword)
933 CALL keyword_release(keyword)
934
935 CALL keyword_create(keyword, __location__, name="PBC", &
936 description="Whether periodic boundary conditions should be applied on the "// &
937 "atomic position before computing the colvar or not.", &
938 usage="PBC", &
939 default_l_val=.true., lone_keyword_l_val=.true.)
940 CALL section_add_keyword(section, keyword)
941 CALL keyword_release(keyword)
942
943 ! Must be present in each colvar and handled properly
944 CALL create_point_section(subsection)
945 CALL section_add_subsection(section, subsection)
946 CALL section_release(subsection)
947
948 END SUBROUTINE create_colvar_xyz_od_section
949
950! **************************************************************************************************
951!> \brief energy as collective variable
952!> \param section the section to be created
953!> \author Sebastiano Caravati
954! **************************************************************************************************
955 SUBROUTINE create_colvar_u_section(section)
956 TYPE(section_type), POINTER :: section
957
958 TYPE(keyword_type), POINTER :: keyword
959 TYPE(section_type), POINTER :: subsection
960
961 cpassert(.NOT. ASSOCIATED(section))
962 CALL section_create(section, __location__, name="u", &
963 description="Section to define the energy as a generalized collective variable.", &
964 n_keywords=0, n_subsections=0, repeats=.false.)
965
966 NULLIFY (subsection, keyword)
967 CALL section_create(subsection, __location__, name="MIXED", &
968 description="This section allows to use any function of the energy subsystems"// &
969 " in a mixed_env calculation as a collective variable.", &
970 n_keywords=1, n_subsections=0, repeats=.false.)
971
972 CALL keyword_create(keyword, __location__, name="ENERGY_FUNCTION", &
973 description="Specifies the functional form of the collective variable in mathematical notation.", &
974 usage="ENERGY_FUNCTION (E1+E2-LOG(E1/E2))", type_of_var=lchar_t, &
975 n_var=1)
976 CALL section_add_keyword(subsection, keyword)
977 CALL keyword_release(keyword)
978
979 CALL keyword_create(keyword, __location__, name="VARIABLES", &
980 description="Defines the variables of the functional form. To allow an efficient"// &
981 " mapping the order of the energy variables will be considered identical to the"// &
982 " order of the force_eval in the force_eval_order list.", &
983 usage="VARIABLES x", type_of_var=char_t, &
984 n_var=-1)
985 CALL section_add_keyword(subsection, keyword)
986 CALL keyword_release(keyword)
987
988 CALL keyword_create(keyword, __location__, name="PARAMETERS", &
989 description="Defines the parameters of the functional form", &
990 usage="PARAMETERS a b D", type_of_var=char_t, &
991 n_var=-1, repeats=.true.)
992 CALL section_add_keyword(subsection, keyword)
993 CALL keyword_release(keyword)
994
995 CALL keyword_create(keyword, __location__, name="VALUES", &
996 description="Defines the values of parameter of the functional form", &
997 usage="VALUES ", type_of_var=real_t, &
998 n_var=-1, repeats=.true., unit_str="internal_cp2k")
999 CALL section_add_keyword(subsection, keyword)
1000 CALL keyword_release(keyword)
1001
1002 CALL keyword_create(keyword, __location__, name="UNITS", &
1003 description="Optionally, allows to define valid CP2K unit strings for each parameter value. "// &
1004 "It is assumed that the corresponding parameter value is specified in this unit.", &
1005 usage="UNITS angstrom eV*angstrom^-1 angstrom^1 K", type_of_var=char_t, &
1006 n_var=-1, repeats=.true.)
1007 CALL section_add_keyword(subsection, keyword)
1008 CALL keyword_release(keyword)
1009
1010 CALL keyword_create(keyword, __location__, name="DX", &
1011 description="Parameter used for computing the derivative with the Ridders' method.", &
1012 usage="DX <REAL>", default_r_val=0.1_dp, unit_str="bohr")
1013 CALL section_add_keyword(subsection, keyword)
1014 CALL keyword_release(keyword)
1015
1016 CALL keyword_create(keyword, __location__, name="ERROR_LIMIT", &
1017 description="Checks that the error in computing the derivative is not larger than "// &
1018 "the value set; in case error is larger a warning message is printed.", &
1019 usage="ERROR_LIMIT <REAL>", default_r_val=1.0e-12_dp)
1020 CALL section_add_keyword(subsection, keyword)
1021 CALL keyword_release(keyword)
1022
1023 CALL section_add_subsection(section, subsection)
1024 CALL section_release(subsection)
1025
1026 END SUBROUTINE create_colvar_u_section
1027
1028! **************************************************************************************************
1029!> \brief creates the colvar section regarded to the collective variables distance
1030!> of a point from a plane
1031!> \param section the section to be created
1032!> \author teo
1033! **************************************************************************************************
1034 SUBROUTINE create_colvar_d_pl_section(section)
1035 TYPE(section_type), POINTER :: section
1036
1037 TYPE(keyword_type), POINTER :: keyword
1038 TYPE(section_type), POINTER :: subsection
1039
1040 cpassert(.NOT. ASSOCIATED(section))
1041 CALL section_create(section, __location__, name="distance_point_plane", &
1042 description="Section to define the distance of a point from a plane "// &
1043 "as a collective variables.", &
1044 n_keywords=1, n_subsections=0, repeats=.false.)
1045 NULLIFY (keyword, subsection)
1046
1047 CALL keyword_create(keyword, __location__, name="PBC", &
1048 description="Whether periodic boundary conditions should be applied on the "// &
1049 "atomic position before computing the colvar or not.", &
1050 usage="PBC", &
1051 default_l_val=.true., lone_keyword_l_val=.true.)
1052 CALL section_add_keyword(section, keyword)
1053 CALL keyword_release(keyword)
1054
1055 CALL keyword_create(keyword, __location__, name="ATOMS_PLANE", &
1056 variants=(/"POINTS_PLANE"/), &
1057 description="Specifies the indexes of atoms/points defining the plane.", &
1058 usage="ATOMS_PLANE <INTEGER> <INTEGER> <INTEGER>", &
1059 n_var=3, type_of_var=integer_t)
1060 CALL section_add_keyword(section, keyword)
1061 CALL keyword_release(keyword)
1062
1063 CALL keyword_create(keyword, __location__, name="ATOM_POINT", &
1064 variants=(/"POINT_POINT"/), &
1065 description="Specifies the atom/point index defining the point.", &
1066 usage="ATOM_POINT <INTEGER>", &
1067 n_var=1, type_of_var=integer_t)
1068 CALL section_add_keyword(section, keyword)
1069 CALL keyword_release(keyword)
1070
1071 ! Must be present in each colvar and handled properly
1072 CALL create_point_section(subsection)
1073 CALL section_add_subsection(section, subsection)
1074 CALL section_release(subsection)
1075
1076 END SUBROUTINE create_colvar_d_pl_section
1077
1078! **************************************************************************************************
1079!> \brief creates the colvar section regarded to the collective variables
1080!> angles betweem two planes
1081!> \param section the section to be created
1082!> \author teo
1083! **************************************************************************************************
1084 SUBROUTINE create_colvar_a_pl_section(section)
1085 TYPE(section_type), POINTER :: section
1086
1087 TYPE(keyword_type), POINTER :: keyword
1088 TYPE(section_type), POINTER :: subsection
1089
1090 cpassert(.NOT. ASSOCIATED(section))
1091 CALL section_create(section, __location__, name="angle_plane_plane", &
1092 description="This section defines the angle between two planes "// &
1093 "as a collective variables.", &
1094 n_keywords=1, n_subsections=0, repeats=.false.)
1095 NULLIFY (keyword, subsection)
1096
1097 CALL section_create(subsection, __location__, name="PLANE", &
1098 description="This section defines the plane. When using this colvar, "// &
1099 "two plane section must be defined!", &
1100 n_keywords=1, n_subsections=0, repeats=.true.)
1101
1102 CALL keyword_create(keyword, __location__, name="DEF_TYPE", &
1103 description="Specify how the plane is defined: either by 3 atoms or by a fixed normal "// &
1104 "vector. At least one plane must be defined through atoms.", &
1105 usage="DEF_TYPE ATOMS", &
1106 default_i_val=plane_def_atoms, &
1107 enum_c_vals=s2a("ATOMS", "VECTOR"), &
1108 enum_desc=s2a("Plane defined by the position of 3 atoms", &
1109 "Plane defined by a fixed normal vector"), &
1110 enum_i_vals=(/plane_def_atoms, plane_def_vec/))
1111 CALL section_add_keyword(subsection, keyword)
1112 CALL keyword_release(keyword)
1113
1114 CALL keyword_create(keyword, __location__, name="ATOMS", &
1115 description="Specifies the indexes of 3 atoms/points defining the plane.", &
1116 usage="ATOMS <INTEGER> <INTEGER> <INTEGER>", &
1117 n_var=3, type_of_var=integer_t)
1118 CALL section_add_keyword(subsection, keyword)
1119 CALL keyword_release(keyword)
1120
1121 CALL keyword_create(keyword, __location__, name="NORMAL_VECTOR", &
1122 description="Alternatively to 3 atoms/points one can define one of the two, "// &
1123 "planes by defining its NORMAL vector.", &
1124 usage="NORMAL_VECTOR 0.0 1.0 0.0", &
1125 n_var=3, type_of_var=real_t)
1126 CALL section_add_keyword(subsection, keyword)
1127 CALL keyword_release(keyword)
1128 CALL section_add_subsection(section, subsection)
1129 CALL section_release(subsection)
1130
1131 ! Must be present in each colvar and handled properly
1132 CALL create_point_section(subsection)
1133 CALL section_add_subsection(section, subsection)
1134 CALL section_release(subsection)
1135 END SUBROUTINE create_colvar_a_pl_section
1136
1137! **************************************************************************************************
1138!> \brief create a geometrical point as a function of several atom coordinates
1139!> \param section the section to be created
1140!> \author teo
1141! **************************************************************************************************
1142 SUBROUTINE create_point_section(section)
1143 TYPE(section_type), POINTER :: section
1144
1145 TYPE(keyword_type), POINTER :: keyword
1146
1147 cpassert(.NOT. ASSOCIATED(section))
1148 CALL section_create(section, __location__, name="POINT", &
1149 description="Enables the possibility to use geometrical centers instead of single atoms"// &
1150 " to define colvars", &
1151 n_keywords=1, n_subsections=0, repeats=.true.)
1152
1153 NULLIFY (keyword)
1154
1155 CALL keyword_create(keyword, __location__, name="TYPE", &
1156 description="Chooses the type of geometrical point", &
1157 usage="type (GEO_CENTER|FIX_POINT)", &
1158 enum_c_vals=s2a("GEO_CENTER", "FIX_POINT"), &
1159 enum_desc=s2a("Computes the geometrical center of the listed atoms", &
1160 "Defines a fixed point in space"), &
1161 enum_i_vals=(/do_clv_geo_center, do_clv_fix_point/), &
1162 default_i_val=do_clv_geo_center)
1163 CALL section_add_keyword(section, keyword)
1164 CALL keyword_release(keyword)
1165
1166 CALL keyword_create(keyword, __location__, name="ATOMS", &
1167 description="Specifies the indexes of atoms defining the geometrical center", &
1168 usage="ATOMS {integer} {integer} {integer} {integer}", &
1169 n_var=-1, type_of_var=integer_t, repeats=.true.)
1170 CALL section_add_keyword(section, keyword)
1171 CALL keyword_release(keyword)
1172
1173 CALL keyword_create( &
1174 keyword, __location__, name="WEIGHTS", &
1175 description="Specifies the weights for a weighted geometrical center. Default is 1/natoms for every atom", &
1176 usage="WEIGHTS {real} {real} {real} {real}", &
1177 n_var=-1, type_of_var=real_t, repeats=.true.)
1178 CALL section_add_keyword(section, keyword)
1179 CALL keyword_release(keyword)
1180
1181 CALL keyword_create(keyword, __location__, name="XYZ", &
1182 description="Specifies the xyz of the fixed point (if the case)", &
1183 usage="XYZ {real} {real} {real}", &
1184 n_var=3, type_of_var=real_t, unit_str="bohr", &
1185 repeats=.false.)
1186 CALL section_add_keyword(section, keyword)
1187 CALL keyword_release(keyword)
1188
1189 END SUBROUTINE create_point_section
1190
1191! **************************************************************************************************
1192!> \brief collective variables specifying torsion
1193!> \param section the section to be created
1194!> \author teo
1195! **************************************************************************************************
1196 SUBROUTINE create_colvar_qparm_section(section)
1197 TYPE(section_type), POINTER :: section
1198
1199 TYPE(keyword_type), POINTER :: keyword
1200 TYPE(section_type), POINTER :: subsection
1201
1202 cpassert(.NOT. ASSOCIATED(section))
1203 CALL section_create(section, __location__, name="qparm", &
1204 description="Section to define the Q parameter (crystalline order parameter) as a collective variable.", &
1205 n_keywords=1, n_subsections=0, repeats=.false.)
1206
1207 NULLIFY (keyword, subsection)
1208
1209 CALL keyword_create(keyword, __location__, name="ATOMS_FROM", &
1210 variants=(/"POINTS_FROM"/), &
1211 description="Specify indexes of atoms/points building the coordination variable. ", &
1212 usage="ATOMS_FROM {integer} {integer} ..", repeats=.true., &
1213 n_var=-1, type_of_var=integer_t)
1214 CALL section_add_keyword(section, keyword)
1215 CALL keyword_release(keyword)
1216
1217 CALL keyword_create(keyword, __location__, name="ATOMS_TO", &
1218 variants=(/"POINTS_TO"/), &
1219 description="Specify indexes of atoms/points building the coordination variable. ", &
1220 usage="ATOMS_TO {integer} {integer} ..", repeats=.true., &
1221 n_var=-1, type_of_var=integer_t)
1222 CALL section_add_keyword(section, keyword)
1223 CALL keyword_release(keyword)
1224
1225 CALL keyword_create(keyword, __location__, name="RCUT", &
1226 description="Specifies the distance cutoff for neighbors. "// &
1227 "Cutoff function is exactly zero for all neighbors beyond RCUT.", &
1228 usage="RCUT {real}", &
1229 n_var=1, unit_str="angstrom", type_of_var=real_t)
1230 CALL section_add_keyword(section, keyword)
1231 CALL keyword_release(keyword)
1232
1233 CALL keyword_create(keyword, __location__, name="INCLUDE_IMAGES", &
1234 description="Whether to include periodic images of ATOMS_TO into the neighbor list.", &
1235 usage="INCLUDE_IMAGES", &
1236 default_l_val=.false., lone_keyword_l_val=.true.)
1237 CALL section_add_keyword(section, keyword)
1238 CALL keyword_release(keyword)
1239
1240 CALL keyword_create(keyword, __location__, name="RSTART", &
1241 description="Specifies the distance cutoff for neighbors. "// &
1242 "Cutoff function is exactly 1 for all neighbors closer than RSTART.", &
1243 usage="RSTART {real}", &
1244 n_var=1, unit_str="angstrom", type_of_var=real_t)
1245 CALL section_add_keyword(section, keyword)
1246 CALL keyword_release(keyword)
1247
1248 CALL keyword_create(keyword, __location__, name="L", &
1249 description="Specifies the L spherical harmonics from Ylm.", &
1250 usage="L {integer}", &
1251 n_var=1, type_of_var=integer_t)
1252 CALL section_add_keyword(section, keyword)
1253 CALL keyword_release(keyword)
1254
1255 !CALL keyword_create(keyword, __LOCATION__, name="ALPHA", &
1256 ! description="Specifies the width of the Fermi-Dirac style smearing around RCUT.", &
1257 ! usage="ALPHA {real}", unit_str="angstrom^-1", default_r_val=0.0_dp)
1258 !CALL section_add_keyword(section, keyword)
1259 !CALL keyword_release(keyword)
1260
1261 ! Must be present in each colvar and handled properly
1262 CALL create_point_section(subsection)
1263 CALL section_add_subsection(section, subsection)
1264 CALL section_release(subsection)
1265
1266 END SUBROUTINE create_colvar_qparm_section
1267
1268! **************************************************************************************************
1269!> \brief collective variables specifying hydronium solvation
1270!> \param section the section to be created
1271!> \author Marcel Baer
1272! **************************************************************************************************
1273 SUBROUTINE create_colvar_hydronium_shell_section(section)
1274 TYPE(section_type), POINTER :: section
1275
1276 TYPE(keyword_type), POINTER :: keyword
1277
1278 cpassert(.NOT. ASSOCIATED(section))
1279 CALL section_create(section, __location__, name="HYDRONIUM_SHELL", &
1280 description="Section to define the formation of a hydronium as a"// &
1281 " collective variable. Number of oxygens in the 1st shell of the"// &
1282 " hydronium. Adapted from Equation (3) in Supplementary Info of"// &
1283 " J. Am. Chem. Soc.,128, 2006, 11318, i.e. omitting the cutoff function"// &
1284 " and summing only over the oxygens of water.", &
1285 n_keywords=1, n_subsections=0, repeats=.false.)
1286
1287 NULLIFY (keyword)
1288
1289 CALL keyword_create(keyword, __location__, name="OXYGENS", &
1290 description="Specifies indexes of atoms building the coordination variable."// &
1291 " Oxygens of the water molecules.", &
1292 usage="OXYGENS {integer} {integer} ..", repeats=.true., &
1293 n_var=-1, type_of_var=integer_t)
1294 CALL section_add_keyword(section, keyword)
1295 CALL keyword_release(keyword)
1296
1297 CALL keyword_create(keyword, __location__, name="HYDROGENS", &
1298 description="Specifies indexes of atoms building the coordination variable."// &
1299 " Hydrogens of the water molecules.", &
1300 usage="HYDROGENS {integer} {integer} ..", repeats=.true., &
1301 n_var=-1, type_of_var=integer_t)
1302 CALL section_add_keyword(section, keyword)
1303 CALL keyword_release(keyword)
1304
1305 CALL keyword_create(keyword, __location__, name="ROO", &
1306 description="Specifies the rc parameter in the coordination function:"// &
1307 " number of oxygens per water oxygen.", &
1308 usage="ROO {real}", default_r_val=cp_unit_to_cp2k(value=3.0_dp, &
1309 unit_str="bohr"), unit_str="bohr", n_var=1)
1310 CALL section_add_keyword(section, keyword)
1311 CALL keyword_release(keyword)
1312
1313 CALL keyword_create(keyword, __location__, name="pOO", &
1314 variants=(/"EXPON_NUMERATORA"/), &
1315 description="Sets the value of the numerator of the exponential factor"// &
1316 " in the coordination function: number of oxygens per water oxygen.", &
1317 usage="pOO {integer}", default_i_val=6, &
1318 n_var=1)
1319 CALL section_add_keyword(section, keyword)
1320 CALL keyword_release(keyword)
1321
1322 CALL keyword_create(keyword, __location__, name="qOO", &
1323 variants=(/"EXPON_DENOMINATORA"/), &
1324 description="Sets the value of the denominator of the exponential factor"// &
1325 " in the coordination function: number of oxygens per water oxygen.", &
1326 usage="qOO {integer}", default_i_val=12, &
1327 n_var=1)
1328 CALL section_add_keyword(section, keyword)
1329 CALL keyword_release(keyword)
1330
1331 CALL keyword_create(keyword, __location__, name="ROH", &
1332 description="Specifies the rc parameter in the coordination function:"// &
1333 " number of hydrogens per water molecule.", &
1334 usage="ROH {real}", default_r_val=cp_unit_to_cp2k(value=3.0_dp, &
1335 unit_str="bohr"), unit_str="bohr", n_var=1)
1336 CALL section_add_keyword(section, keyword)
1337 CALL keyword_release(keyword)
1338
1339 CALL keyword_create(keyword, __location__, name="pOH", &
1340 variants=(/"EXPON_NUMERATORB"/), &
1341 description="Sets the value of the numerator of the exponential factor"// &
1342 " in the coordination function: number of hydrogens per water molecule.", &
1343 usage="pOH {integer}", default_i_val=6, &
1344 n_var=1)
1345 CALL section_add_keyword(section, keyword)
1346 CALL keyword_release(keyword)
1347
1348 CALL keyword_create(keyword, __location__, name="qOH", &
1349 variants=(/"EXPON_DENOMINATORB"/), &
1350 description="Sets the value of the denominator of the exponential factor"// &
1351 " in the coordination function: number of hydrogens per water molecule.", &
1352 usage="qOH {integer}", default_i_val=12, &
1353 n_var=1)
1354 CALL section_add_keyword(section, keyword)
1355 CALL keyword_release(keyword)
1356
1357 CALL keyword_create(keyword, __location__, name="NH", &
1358 description="Specifies the NH parameter in the M function.", &
1359 usage="NH {real}", default_r_val=3.0_dp, &
1360 n_var=1)
1361 CALL section_add_keyword(section, keyword)
1362 CALL keyword_release(keyword)
1363
1364 CALL keyword_create(keyword, __location__, name="pM", &
1365 variants=(/"EXPON_NUMERATOR"/), &
1366 description="Sets the value of the numerator of the exponential factor"// &
1367 " in the M function.", &
1368 usage="pM {integer}", default_i_val=8, &
1369 n_var=1)
1370 CALL section_add_keyword(section, keyword)
1371 CALL keyword_release(keyword)
1372
1373 CALL keyword_create(keyword, __location__, name="qM", &
1374 variants=(/"EXPON_DENOMINATOR"/), &
1375 description="Sets the value of the denominator of the exponential factor"// &
1376 " in the M function.", &
1377 usage="qM {integer}", default_i_val=16, &
1378 n_var=1)
1379 CALL section_add_keyword(section, keyword)
1380 CALL keyword_release(keyword)
1381
1382 CALL keyword_create(keyword, __location__, name="LAMBDA", &
1383 description="Specify the LAMBDA parameter in the hydronium function.", &
1384 usage="LAMBDA {real}", default_r_val=10.0_dp, &
1385 n_var=1)
1386 CALL section_add_keyword(section, keyword)
1387 CALL keyword_release(keyword)
1388
1389 END SUBROUTINE create_colvar_hydronium_shell_section
1390
1391! **************************************************************************************************
1392!> \brief collective variables specifying the distance between hydronium and hydroxide ion
1393!> \param section the section to be created
1394!> \author Dorothea Golze
1395! **************************************************************************************************
1396 SUBROUTINE create_colvar_hydronium_dist_section(section)
1397 TYPE(section_type), POINTER :: section
1398
1399 TYPE(keyword_type), POINTER :: keyword
1400
1401 cpassert(.NOT. ASSOCIATED(section))
1402 CALL section_create(section, __location__, name="HYDRONIUM_DISTANCE", &
1403 description="Section to define the formation of a hydronium as a"// &
1404 " collective variable. Distance between hydronium and hydroxide ion"// &
1405 " Experimental at this point, i.e. not proved to be an effective"// &
1406 " collective variable.", &
1407 n_keywords=1, n_subsections=0, repeats=.false.)
1408
1409 NULLIFY (keyword)
1410
1411 CALL keyword_create(keyword, __location__, name="OXYGENS", &
1412 description="Specifies indexes of atoms building the coordination variable."// &
1413 " Oxygens of the water molecules.", &
1414 usage="OXYGENS {integer} {integer} ..", repeats=.true., &
1415 n_var=-1, type_of_var=integer_t)
1416 CALL section_add_keyword(section, keyword)
1417 CALL keyword_release(keyword)
1418
1419 CALL keyword_create(keyword, __location__, name="HYDROGENS", &
1420 description="Specifies indexes of atoms building the coordination variable."// &
1421 " Hydrogens of the water molecules.", &
1422 usage="HYDROGENS {integer} {integer} ..", repeats=.true., &
1423 n_var=-1, type_of_var=integer_t)
1424 CALL section_add_keyword(section, keyword)
1425 CALL keyword_release(keyword)
1426
1427 CALL keyword_create(keyword, __location__, name="ROH", &
1428 description="Specifies the rc parameter in the coordination function:"// &
1429 " number of hydrogens per water molecule.", &
1430 usage="ROH {real}", default_r_val=cp_unit_to_cp2k(value=2.4_dp, &
1431 unit_str="bohr"), unit_str="bohr", n_var=1)
1432 CALL section_add_keyword(section, keyword)
1433 CALL keyword_release(keyword)
1434
1435 CALL keyword_create(keyword, __location__, name="pOH", &
1436 description="Sets the value of the numerator of the exponential factor"// &
1437 " in the coordination function: number of hydrogens per water molecule.", &
1438 usage="pOH {integer}", default_i_val=6, &
1439 n_var=1)
1440 CALL section_add_keyword(section, keyword)
1441 CALL keyword_release(keyword)
1442
1443 CALL keyword_create(keyword, __location__, name="qOH", &
1444 description="Sets the value of the denominator of the exponential factor"// &
1445 " in the coordination function: number of hydrogens per water molecule.", &
1446 usage="qOH {integer}", default_i_val=12, &
1447 n_var=1)
1448 CALL section_add_keyword(section, keyword)
1449 CALL keyword_release(keyword)
1450
1451 CALL keyword_create(keyword, __location__, name="NH", &
1452 description="Specifies the NH parameter in the M function.", &
1453 usage="NH {real}", default_r_val=2.2_dp, &
1454 n_var=1)
1455 CALL section_add_keyword(section, keyword)
1456 CALL keyword_release(keyword)
1457
1458 CALL keyword_create(keyword, __location__, name="pM", &
1459 description="Sets the value of the numerator of the exponential factor"// &
1460 " in the M function.", &
1461 usage="pM {integer}", default_i_val=8, &
1462 n_var=1)
1463 CALL section_add_keyword(section, keyword)
1464 CALL keyword_release(keyword)
1465
1466 CALL keyword_create(keyword, __location__, name="qM", &
1467 description="Sets the value of the denominator of the exponential factor"// &
1468 " in the M function.", &
1469 usage="qM {integer}", default_i_val=16, &
1470 n_var=1)
1471 CALL section_add_keyword(section, keyword)
1472 CALL keyword_release(keyword)
1473
1474 CALL keyword_create(keyword, __location__, name="NN", &
1475 description="Specifies the NN parameter in the F function.", &
1476 usage="NN {real}", default_r_val=1.5_dp, &
1477 n_var=1)
1478 CALL section_add_keyword(section, keyword)
1479 CALL keyword_release(keyword)
1480
1481 CALL keyword_create(keyword, __location__, name="pF", &
1482 description="Sets the value of the numerator of the exponential factor"// &
1483 " in the F function.", &
1484 usage="pF {integer}", default_i_val=8, &
1485 n_var=1)
1486 CALL section_add_keyword(section, keyword)
1487 CALL keyword_release(keyword)
1488
1489 CALL keyword_create(keyword, __location__, name="qF", &
1490 description="Sets the value of the denominator of the exponential factor"// &
1491 " in the F function.", &
1492 usage="qF {integer}", default_i_val=16, &
1493 n_var=1)
1494 CALL section_add_keyword(section, keyword)
1495 CALL keyword_release(keyword)
1496
1497 CALL keyword_create(keyword, __location__, name="LAMBDA", &
1498 description="Specify the LAMBDA parameter in the hydronium function.", &
1499 usage="LAMBDA {real}", default_r_val=20.0_dp, &
1500 n_var=1)
1501 CALL section_add_keyword(section, keyword)
1502 CALL keyword_release(keyword)
1503
1504 END SUBROUTINE create_colvar_hydronium_dist_section
1505
1506! **************************************************************************************************
1507!> \brief collective variables specifying the solvation of carboxylic acid;
1508!> distance between hydronium ion and acetate ion; Equation (2) in
1509!> Supplementary Information of J. Am. Chem. Soc.,128, 2006, 11318
1510!> \param section the section to be created
1511!> \author Dorothea Golze
1512! **************************************************************************************************
1513 SUBROUTINE create_colvar_acid_hyd_dist_section(section)
1514 TYPE(section_type), POINTER :: section
1515
1516 TYPE(keyword_type), POINTER :: keyword
1517
1518 cpassert(.NOT. ASSOCIATED(section))
1519 CALL section_create(section, __location__, name="ACID_HYDRONIUM_DISTANCE", &
1520 description="Section to define the dissociation of a carboxylic acid in"// &
1521 " water. Distance between hydronium ion and acetate ion. Equation (2)"// &
1522 " in Supplementary Info of J. Am. Chem. Soc.,128, 2006, 11318.", &
1523 n_keywords=1, n_subsections=0, repeats=.false.)
1524
1525 NULLIFY (keyword)
1526
1527 CALL keyword_create(keyword, __location__, name="OXYGENS_WATER", &
1528 description="Specifies indexes of atoms building the coordination variable."// &
1529 " Oxygens of the water molecules. ", &
1530 usage="OXYGENS {integer} {integer} ..", repeats=.true., &
1531 n_var=-1, type_of_var=integer_t)
1532 CALL section_add_keyword(section, keyword)
1533 CALL keyword_release(keyword)
1534
1535 CALL keyword_create(keyword, __location__, name="OXYGENS_ACID", &
1536 description="Specifies indexes of atoms building the coordination variable."// &
1537 " Oxygens of the carboxyl groups.", &
1538 usage="OXYGENS {integer} {integer} ..", repeats=.true., &
1539 n_var=-1, type_of_var=integer_t)
1540 CALL section_add_keyword(section, keyword)
1541 CALL keyword_release(keyword)
1542
1543 CALL keyword_create(keyword, __location__, name="HYDROGENS", &
1544 description="Specifies indexes of atoms building the coordination variable."// &
1545 " Hydrogens of the water molecules and of the carboxyl groups.", &
1546 usage="HYDROGENS {integer} {integer} ..", repeats=.true., &
1547 n_var=-1, type_of_var=integer_t)
1548 CALL section_add_keyword(section, keyword)
1549 CALL keyword_release(keyword)
1550
1551 CALL keyword_create(keyword, __location__, name="pWOH", &
1552 description="Sets the value of the numerator of the exponential factor"// &
1553 " in the coordination function: number of hydrogens per water molecule.", &
1554 usage="pWOH {integer}", default_i_val=8, &
1555 n_var=1)
1556 CALL section_add_keyword(section, keyword)
1557 CALL keyword_release(keyword)
1558
1559 CALL keyword_create(keyword, __location__, name="qWOH", &
1560 description="Sets the value of the denominator of the exponential factor"// &
1561 " in the coordination function: number of hydrogens per water molecule.", &
1562 usage="qWOH {integer}", default_i_val=16, &
1563 n_var=1)
1564 CALL section_add_keyword(section, keyword)
1565 CALL keyword_release(keyword)
1566
1567 CALL keyword_create(keyword, __location__, name="RWOH", &
1568 description="Specify the rc parameter in the coordination function:"// &
1569 " number of hydrogens per water molecule.", &
1570 usage="RWOH {real}", default_r_val=cp_unit_to_cp2k(value=2.4_dp, &
1571 unit_str="bohr"), unit_str="bohr", n_var=1)
1572 CALL section_add_keyword(section, keyword)
1573 CALL keyword_release(keyword)
1574
1575 CALL keyword_create(keyword, __location__, name="pAOH", &
1576 description="Sets the value of the numerator of the exponential factor"// &
1577 " in the coordination function: number of hydrogens per carboxyl group.", &
1578 usage="pAOH {integer}", default_i_val=6, &
1579 n_var=1)
1580 CALL section_add_keyword(section, keyword)
1581 CALL keyword_release(keyword)
1582
1583 CALL keyword_create(keyword, __location__, name="qAOH", &
1584 description="Sets the value of the denominator of the exponential factor"// &
1585 " in the coordination function: number of hydrogens per carboxyl group.", &
1586 usage="qAOH {integer}", default_i_val=14, &
1587 n_var=1)
1588 CALL section_add_keyword(section, keyword)
1589 CALL keyword_release(keyword)
1590
1591 CALL keyword_create(keyword, __location__, name="RAOH", &
1592 description="Specify the rc parameter in the coordination function:"// &
1593 " number of hydrogens per carboxyl group.", &
1594 usage="RAOH {real}", default_r_val=cp_unit_to_cp2k(value=2.4_dp, &
1595 unit_str="bohr"), unit_str="bohr", n_var=1)
1596 CALL section_add_keyword(section, keyword)
1597 CALL keyword_release(keyword)
1598
1599 CALL keyword_create(keyword, __location__, name="pCUT", &
1600 description="Sets the value of the numerator of the exponential factor"// &
1601 " in the cutoff function.", &
1602 usage="pCUT {integer}", default_i_val=6, &
1603 n_var=1)
1604 CALL section_add_keyword(section, keyword)
1605 CALL keyword_release(keyword)
1606
1607 CALL keyword_create(keyword, __location__, name="qCUT", &
1608 description="Sets the value of the denominator of the exponential factor"// &
1609 " in the cutoff function.", &
1610 usage="qCUT {integer}", default_i_val=12, &
1611 n_var=1)
1612 CALL section_add_keyword(section, keyword)
1613 CALL keyword_release(keyword)
1614
1615 CALL keyword_create(keyword, __location__, name="NC", &
1616 description="Specifies the NC parameter in the cutoff function.", &
1617 usage="NC {real}", default_r_val=0.56_dp, &
1618 n_var=1)
1619 CALL section_add_keyword(section, keyword)
1620 CALL keyword_release(keyword)
1621
1622 CALL keyword_create(keyword, __location__, name="LAMBDA", &
1623 variants=(/"LAMBDA"/), &
1624 description="Specifies the LAMBDA parameter carboxylic acid function.", &
1625 usage="LAMBDA {real}", default_r_val=20.0_dp, &
1626 n_var=1)
1627 CALL section_add_keyword(section, keyword)
1628 CALL keyword_release(keyword)
1629
1630 END SUBROUTINE create_colvar_acid_hyd_dist_section
1631
1632! **************************************************************************************************
1633!> \brief collective variables specifying the solvation of carboxylic acid;
1634!> number of oxygens in the 1st shell of the hydronium; Equation (3) in
1635!> Supplementary Information of J. Am. Chem. Soc.,128, 2006, 11318
1636!> \param section the section to be created
1637!> \author Dorothea Golze
1638! **************************************************************************************************
1639 SUBROUTINE create_colvar_acid_hyd_shell_section(section)
1640 TYPE(section_type), POINTER :: section
1641
1642 TYPE(keyword_type), POINTER :: keyword
1643
1644 cpassert(.NOT. ASSOCIATED(section))
1645 CALL section_create(section, __location__, name="ACID_HYDRONIUM_SHELL", &
1646 description="Section to define the dissociation of a carboxylic acid in"// &
1647 " water. Number of oxygens in the 1st shell of the hydronium. Equation (3)"// &
1648 " in Supplementary Info of J. Am. Chem. Soc.,128, 2006, 11318. Similar to"// &
1649 " the HYDRONIUM colvar, but with modification for the acid.", &
1650 n_keywords=1, n_subsections=0, repeats=.false.)
1651
1652 NULLIFY (keyword)
1653
1654 CALL keyword_create(keyword, __location__, name="OXYGENS_WATER", &
1655 description="Specifies indexes of atoms building the coordination variable."// &
1656 " Oxygens of the water molecules. ", &
1657 usage="OXYGENS {integer} {integer} ..", repeats=.true., &
1658 n_var=-1, type_of_var=integer_t)
1659 CALL section_add_keyword(section, keyword)
1660 CALL keyword_release(keyword)
1661
1662 CALL keyword_create(keyword, __location__, name="OXYGENS_ACID", &
1663 description="Specifies indexes of atoms building the coordination variable."// &
1664 " Oxygens of the carboxyl groups.", &
1665 usage="OXYGENS {integer} {integer} ..", repeats=.true., &
1666 n_var=-1, type_of_var=integer_t)
1667 CALL section_add_keyword(section, keyword)
1668 CALL keyword_release(keyword)
1669
1670 CALL keyword_create(keyword, __location__, name="HYDROGENS", &
1671 description="Specifies indexes of atoms building the coordination variable."// &
1672 " Hydrogens of the water molecules and of the carboxyl groups.", &
1673 usage="HYDROGENS {integer} {integer} ..", repeats=.true., &
1674 n_var=-1, type_of_var=integer_t)
1675 CALL section_add_keyword(section, keyword)
1676 CALL keyword_release(keyword)
1677
1678 CALL keyword_create(keyword, __location__, name="pWOH", &
1679 description="Sets the value of the numerator of the exponential factor"// &
1680 " in the coordination function: number of hydrogens per water molecule.", &
1681 usage="pWOH {integer}", default_i_val=8, &
1682 n_var=1)
1683 CALL section_add_keyword(section, keyword)
1684 CALL keyword_release(keyword)
1685
1686 CALL keyword_create(keyword, __location__, name="qWOH", &
1687 description="Sets the value of the denominator of the exponential factor"// &
1688 " in the coordination function: number of hydrogens per water molecule.", &
1689 usage="qWOH {integer}", default_i_val=16, &
1690 n_var=1)
1691 CALL section_add_keyword(section, keyword)
1692 CALL keyword_release(keyword)
1693
1694 CALL keyword_create(keyword, __location__, name="RWOH", &
1695 description="Specifies the rc parameter in the coordination function:"// &
1696 " number of hydrogens per water molecule.", &
1697 usage="RWOH {real}", default_r_val=cp_unit_to_cp2k(value=2.4_dp, &
1698 unit_str="bohr"), unit_str="bohr", n_var=1)
1699 CALL section_add_keyword(section, keyword)
1700 CALL keyword_release(keyword)
1701
1702 CALL keyword_create(keyword, __location__, name="pAOH", &
1703 description="Sets the value of the numerator of the exponential factor"// &
1704 " in the coordination function: number of hydrogens per carboxyl group.", &
1705 usage="pAOH {integer}", default_i_val=6, &
1706 n_var=1)
1707 CALL section_add_keyword(section, keyword)
1708 CALL keyword_release(keyword)
1709
1710 CALL keyword_create(keyword, __location__, name="qAOH", &
1711 description="Sets the value of the denominator of the exponential factor"// &
1712 " in the coordination function: number of hydrogens per carboxyl group.", &
1713 usage="qAOH {integer}", default_i_val=14, &
1714 n_var=1)
1715 CALL section_add_keyword(section, keyword)
1716 CALL keyword_release(keyword)
1717
1718 CALL keyword_create(keyword, __location__, name="RAOH", &
1719 description="Specifies the rc parameter in the coordination function:"// &
1720 " number of hydrogens per carboxyl group.", &
1721 usage="RAOH {real}", default_r_val=cp_unit_to_cp2k(value=2.4_dp, &
1722 unit_str="bohr"), unit_str="bohr", n_var=1)
1723 CALL section_add_keyword(section, keyword)
1724 CALL keyword_release(keyword)
1725
1726 CALL keyword_create(keyword, __location__, name="pOO", &
1727 description="Sets the value of the numerator of the exponential factor"// &
1728 " in the coordination function: number of oxygens per water oxygen.", &
1729 usage="pOO {integer}", default_i_val=6, &
1730 n_var=1)
1731 CALL section_add_keyword(section, keyword)
1732 CALL keyword_release(keyword)
1733
1734 CALL keyword_create(keyword, __location__, name="qOO", &
1735 description="Sets the value of the denominator of the exponential factor"// &
1736 " in the coordination function: number of oxygens per water oxygen.", &
1737 usage="qOO {integer}", default_i_val=12, &
1738 n_var=1)
1739 CALL section_add_keyword(section, keyword)
1740 CALL keyword_release(keyword)
1741
1742 CALL keyword_create(keyword, __location__, name="ROO", &
1743 description="Specifies the rc parameter in the coordination function:"// &
1744 " number of oxygens per water oxygen.", &
1745 usage="ROO {real}", default_r_val=cp_unit_to_cp2k(value=5.5_dp, &
1746 unit_str="bohr"), unit_str="bohr", n_var=1)
1747 CALL section_add_keyword(section, keyword)
1748 CALL keyword_release(keyword)
1749
1750 CALL keyword_create(keyword, __location__, name="pM", &
1751 description="Sets the value of the numerator of the exponential factor"// &
1752 " in the M function.", &
1753 usage="pM {integer}", default_i_val=8, &
1754 n_var=1)
1755 CALL section_add_keyword(section, keyword)
1756 CALL keyword_release(keyword)
1757
1758 CALL keyword_create(keyword, __location__, name="qM", &
1759 description="Sets the value of the denominator of the exponential factor"// &
1760 " in the M function.", &
1761 usage="qM {integer}", default_i_val=16, &
1762 n_var=1)
1763 CALL section_add_keyword(section, keyword)
1764 CALL keyword_release(keyword)
1765
1766 CALL keyword_create(keyword, __location__, name="NH", &
1767 description="Specifies the NH parameter in the M function.", &
1768 usage="NH {real}", default_r_val=2.2_dp, &
1769 n_var=1)
1770 CALL section_add_keyword(section, keyword)
1771 CALL keyword_release(keyword)
1772
1773 CALL keyword_create(keyword, __location__, name="pCUT", &
1774 description="Sets the value of the numerator of the exponential factor"// &
1775 " in the cutoff function.", &
1776 usage="pCUT {integer}", default_i_val=6, &
1777 n_var=1)
1778 CALL section_add_keyword(section, keyword)
1779 CALL keyword_release(keyword)
1780
1781 CALL keyword_create(keyword, __location__, name="qCUT", &
1782 description="Sets the value of the denominator of the exponential factor"// &
1783 " in the cutoff function.", &
1784 usage="qCUT {integer}", default_i_val=12, &
1785 n_var=1)
1786 CALL section_add_keyword(section, keyword)
1787 CALL keyword_release(keyword)
1788
1789 CALL keyword_create(keyword, __location__, name="NC", &
1790 description="Specifies the NC parameter in the cutoff function.", &
1791 usage="NC {real}", default_r_val=0.9_dp, &
1792 n_var=1)
1793 CALL section_add_keyword(section, keyword)
1794 CALL keyword_release(keyword)
1795
1796 CALL keyword_create(keyword, __location__, name="LAMBDA", &
1797 variants=(/"LAMBDA"/), &
1798 description="Specifies the LAMBDA parameter carboxylic acid function.", &
1799 usage="LAMBDA {real}", default_r_val=10.0_dp, &
1800 n_var=1)
1801 CALL section_add_keyword(section, keyword)
1802 CALL keyword_release(keyword)
1803
1804 END SUBROUTINE create_colvar_acid_hyd_shell_section
1805
1806! **************************************************************************************************
1807!> \brief ...
1808!> \param section ...
1809! **************************************************************************************************
1810 SUBROUTINE create_colvar_rmsd_section(section)
1811 TYPE(section_type), POINTER :: section
1812
1813 TYPE(keyword_type), POINTER :: keyword
1814 TYPE(section_type), POINTER :: subsection, subsubsection
1815
1816 cpassert(.NOT. ASSOCIATED(section))
1817 CALL section_create(section, __location__, name="rmsd", &
1818 description="Section to define a CV as function of RMSD computed with respect to"// &
1819 " given reference configurations. For 2 configurations the colvar is equal to:"// &
1820 " ss = (RMSDA-RMSDB)/(RMSDA+RMSDB), while if only 1 configuration is given, then the"// &
1821 " colvar is just the RMSD from that frame.", &
1822 n_keywords=1, n_subsections=0, repeats=.false.)
1823
1824 NULLIFY (keyword, subsection, subsubsection)
1825 CALL keyword_create(keyword, __location__, name="SUBSET_TYPE", &
1826 description="Define the subsytem used to compute the RMSD", &
1827 usage="SUBSET_TYPE ALL", &
1828 enum_c_vals=s2a("ALL", "LIST", "WEIGHT_LIST"), &
1829 enum_i_vals=(/rmsd_all, rmsd_list, rmsd_weightlist/), &
1830 default_i_val=rmsd_all)
1831 CALL section_add_keyword(section, keyword)
1832 CALL keyword_release(keyword)
1833
1834 CALL keyword_create(keyword, __location__, name="ALIGN_FRAMES", &
1835 description="Whether the reference frames should be aligned to minimize the RMSD", &
1836 usage="ALIGN_FRAME", &
1837 default_l_val=.false., lone_keyword_l_val=.true.)
1838 CALL section_add_keyword(section, keyword)
1839 CALL keyword_release(keyword)
1840
1841 CALL keyword_create(keyword, __location__, name="ATOMS", &
1842 description="Specify indexes of atoms building the subset. ", &
1843 usage="ATOMS {integer} {integer} ..", repeats=.true., &
1844 n_var=-1, type_of_var=integer_t)
1845 CALL section_add_keyword(section, keyword)
1846 CALL keyword_release(keyword)
1847
1848 CALL keyword_create(keyword, __location__, name="WEIGHTS", &
1849 description="Specify weights of atoms building the subset. ", &
1850 usage="weightS {real} {real} ..", repeats=.true., &
1851 n_var=-1, type_of_var=real_t)
1852 CALL section_add_keyword(section, keyword)
1853 CALL keyword_release(keyword)
1854
1855 CALL section_create(subsection, __location__, name="FRAME", &
1856 description="Specify coordinates of the frame (number of frames can be either 1 or 2)", &
1857 repeats=.true.)
1858
1859 CALL keyword_create(keyword, __location__, name="COORD_FILE_NAME", &
1860 description="Name of the xyz file with coordinates (alternative to &COORD section)", &
1861 usage="COORD_FILE_NAME <CHAR>", &
1862 default_lc_val="")
1863 CALL section_add_keyword(subsection, keyword)
1864 CALL keyword_release(keyword)
1865
1866 CALL create_coord_section_cv(subsubsection, "RMSD")
1867 CALL section_add_subsection(subsection, subsubsection)
1868 CALL section_release(subsubsection)
1869
1870 CALL section_add_subsection(section, subsection)
1871 CALL section_release(subsection)
1872
1873 END SUBROUTINE create_colvar_rmsd_section
1874
1875! **************************************************************************************************
1876!> \brief collective variables specifying the space orthogonal to the reaction path
1877!> in the space spanned by the involved collective coordinates
1878!> \param section the section to be created
1879!> \author fschiff
1880! **************************************************************************************************
1881 SUBROUTINE create_colvar_rpath_section(section)
1882 TYPE(section_type), POINTER :: section
1883
1884 cpassert(.NOT. ASSOCIATED(section))
1885 CALL section_create(section, __location__, name="REACTION_PATH", &
1886 description="Section defining a one dimensional reaction path in an Q-dimensional space of colvars. "// &
1887 "Constraining this colvar, allows to sample the space orthogonal to the reaction path, "// &
1888 "both in the Q-dimensional colvar and 3N-Q remaining coordinates. "// &
1889 "For the details of the function see cited literature.", &
1890 n_keywords=1, n_subsections=0, repeats=.false., &
1891 citations=(/branduardi2007/))
1892
1893 CALL keywords_colvar_path(section)
1894 END SUBROUTINE create_colvar_rpath_section
1895
1896! **************************************************************************************************
1897!> \brief Distance from reaction path
1898!> \param section the section to be created
1899!> \author 01.2010
1900! **************************************************************************************************
1901 SUBROUTINE create_colvar_dpath_section(section)
1902 TYPE(section_type), POINTER :: section
1903
1904 cpassert(.NOT. ASSOCIATED(section))
1905 CALL section_create(section, __location__, name="DISTANCE_FROM_PATH", &
1906 description="Section defining the distance from a one dimensional reaction "// &
1907 "path in an Q-dimensional space of colvars. "// &
1908 "Constraining this colvar, allows to sample the space equidistant to the reaction path, "// &
1909 "both in the Q-dimensional colvar and 3N-Q remaining coordinates. "// &
1910 "For the details of the function see cited literature.", &
1911 n_keywords=1, n_subsections=0, repeats=.false., &
1912 citations=(/branduardi2007/))
1913
1914 CALL keywords_colvar_path(section)
1915 END SUBROUTINE create_colvar_dpath_section
1916
1917! **************************************************************************************************
1918!> \brief Section describinf keywords for both reaction path and distance from reaction path
1919!> \param section the section to be created
1920!> \author 01.2010
1921! **************************************************************************************************
1922 SUBROUTINE keywords_colvar_path(section)
1923
1924 TYPE(section_type), POINTER :: section
1925
1926 TYPE(keyword_type), POINTER :: keyword
1927 TYPE(section_type), POINTER :: print_key, subsection, subsubsection
1928
1929 NULLIFY (keyword, subsection, subsubsection, print_key)
1930 CALL create_colvar_section(subsection, skip_recursive_colvar=.true.)
1931 CALL section_add_subsection(section, subsection)
1932 CALL section_release(subsection)
1933
1934 CALL keyword_create(keyword, __location__, name="DISTANCES_RMSD", &
1935 description=" ", &
1936 usage="DISTANCES_RMSD T", &
1937 default_l_val=.false., lone_keyword_l_val=.true.)
1938 CALL section_add_keyword(section, keyword)
1939 CALL keyword_release(keyword)
1940
1941 CALL keyword_create(keyword, __location__, name="RMSD", &
1942 description=" ", &
1943 usage="RMSD T", &
1944 default_l_val=.false., lone_keyword_l_val=.true.)
1945 CALL section_add_keyword(section, keyword)
1946 CALL keyword_release(keyword)
1947
1948 CALL keyword_create(keyword, __location__, name="SUBSET_TYPE", &
1949 description="Define the subsytem used to compute the RMSD", &
1950 usage="SUBSET_TYPE ALL", &
1951 enum_c_vals=s2a("ALL", "LIST"), &
1952 enum_i_vals=(/rmsd_all, rmsd_list/), &
1953 default_i_val=rmsd_all)
1954 CALL section_add_keyword(section, keyword)
1955 CALL keyword_release(keyword)
1956
1957 CALL keyword_create(keyword, __location__, name="ALIGN_FRAMES", &
1958 description="Whether the reference frames should be aligned to minimize the RMSD", &
1959 usage="ALIGN_FRAME", &
1960 default_l_val=.false., lone_keyword_l_val=.true.)
1961 CALL section_add_keyword(section, keyword)
1962 CALL keyword_release(keyword)
1963
1964 CALL keyword_create(keyword, __location__, name="ATOMS", &
1965 description="Specify indexes of atoms building the subset. ", &
1966 usage="ATOMS {integer} {integer} ..", repeats=.true., &
1967 n_var=-1, type_of_var=integer_t)
1968 CALL section_add_keyword(section, keyword)
1969 CALL keyword_release(keyword)
1970
1971 CALL section_create(subsection, __location__, name="FRAME", &
1972 description="Specify coordinates of the frame", &
1973 repeats=.true.)
1974
1975 CALL keyword_create(keyword, __location__, name="COORD_FILE_NAME", &
1976 description="Name of the xyz file with coordinates (alternative to &COORD section)", &
1977 usage="COORD_FILE_NAME <CHAR>", &
1978 default_lc_val="")
1979 CALL section_add_keyword(subsection, keyword)
1980 CALL keyword_release(keyword)
1981
1982 CALL create_coord_section_cv(subsubsection, "RMSD")
1983 CALL section_add_subsection(subsection, subsubsection)
1984 CALL section_release(subsubsection)
1985
1986 CALL section_add_subsection(section, subsection)
1987 CALL section_release(subsection)
1988
1989 CALL keyword_create(keyword, __location__, name="FUNCTION", &
1990 description="Specifies the ith element of the vector valued function that defines the reaction path. "// &
1991 "This keyword needs to repeat exactly Q times, and the order must match the order of the colvars. "// &
1992 "The VARIABLE (e.g. T) which parametrises the curve can be used as the target of a constraint.", &
1993 usage="FUNCTION (sin(T+2)+2*T)", type_of_var=lchar_t, &
1994 n_var=1, default_lc_val="0", repeats=.true.)
1995 CALL section_add_keyword(section, keyword)
1996 CALL keyword_release(keyword)
1997
1998 CALL keyword_create(keyword, __location__, name="VARIABLE", &
1999 description="Specifies the name of the variable that parametrises the FUNCTION "// &
2000 "defining the reaction path.", &
2001 usage="VARIABLE T", type_of_var=char_t, &
2002 n_var=1, repeats=.false.)
2003 CALL section_add_keyword(section, keyword)
2004 CALL keyword_release(keyword)
2005
2006 CALL keyword_create( &
2007 keyword, __location__, name="LAMBDA", &
2008 description="Specifies the exponent of the Gaussian used in the integral representation of the colvar. "// &
2009 "The shape of the space orthogonal to the reaction path is defined by this choice. "// &
2010 "In the limit of large values, it is given by the plane orthogonal to the path. "// &
2011 "In practice, modest values are required for stable numerical integration.", &
2012 usage="LAMBDA {real}", &
2013 type_of_var=real_t, default_r_val=5.0_dp)
2014 CALL section_add_keyword(section, keyword)
2015 CALL keyword_release(keyword)
2016
2017 CALL keyword_create(keyword, __location__, name="STEP_SIZE", &
2018 description="Step size in the numerical integration, "// &
2019 "a few thousand points are common, and the proper number also depends on LAMBDA.", &
2020 usage="STEP_SIZE {real}", &
2021 type_of_var=real_t, default_r_val=0.01_dp)
2022 CALL section_add_keyword(section, keyword)
2023 CALL keyword_release(keyword)
2024
2025 CALL keyword_create(keyword, __location__, name="RANGE", &
2026 description="The range of VARIABLE used for the parametrisation.", &
2027 usage="RANGE <REAL> <REAL>", &
2028 n_var=2, type_of_var=real_t)
2029 CALL section_add_keyword(section, keyword)
2030 CALL keyword_release(keyword)
2031
2032 CALL cp_print_key_section_create( &
2033 print_key, __location__, name="MAP", &
2034 description="Activating this print key will print once a file with the values of the FUNCTION on a grid "// &
2035 "of COLVAR values in a specified range. "// &
2036 "GRID_SPACING and RANGE for every COLVAR has to be specified again in the same order as they are in the input.", &
2037 print_level=high_print_level, filename="PATH")
2038
2039 CALL keyword_create(keyword, __location__, name="RANGE", &
2040 description="The range of of the grid of the COLVAR.", &
2041 usage="RANGE <REAL> <REAL>", &
2042 n_var=2, type_of_var=real_t, repeats=.true.)
2043 CALL section_add_keyword(print_key, keyword)
2044 CALL keyword_release(keyword)
2045
2046 CALL keyword_create(keyword, __location__, name="GRID_SPACING", &
2047 description="Distance between two gridpoints for the grid on the COLVAR", &
2048 usage="STEP_SIZE {real}", repeats=.true., &
2049 type_of_var=real_t, default_r_val=0.01_dp)
2050 CALL section_add_keyword(print_key, keyword)
2051 CALL keyword_release(keyword)
2052
2053 CALL section_add_subsection(section, print_key)
2054 CALL section_release(print_key)
2055
2056 END SUBROUTINE keywords_colvar_path
2057
2058! **************************************************************************************************
2059!> \brief Colvar allowing a combination of COLVARS
2060!> \param section the section to be created
2061!> \author Teodoro Laino [tlaino] - 12.2008
2062! **************************************************************************************************
2063 SUBROUTINE create_colvar_comb_section(section)
2064 TYPE(section_type), POINTER :: section
2065
2066 TYPE(keyword_type), POINTER :: keyword
2067 TYPE(section_type), POINTER :: subsection
2068
2069 cpassert(.NOT. ASSOCIATED(section))
2070 CALL section_create(section, __location__, name="COMBINE_COLVAR", &
2071 description="Allows the possibility to combine several COLVARs into one COLVAR "// &
2072 "with a generic function.", &
2073 n_keywords=1, n_subsections=0, repeats=.false.)
2074
2075 NULLIFY (keyword, subsection)
2076 CALL create_colvar_section(subsection, skip_recursive_colvar=.true.)
2077 CALL section_add_subsection(section, subsection)
2078 CALL section_release(subsection)
2079
2080 CALL keyword_create(keyword, __location__, name="FUNCTION", &
2081 description="Specifies the function used to combine different COLVARs into one.", &
2082 ! **************************************************************************************************
2083 !> \brief ...
2084 !> \param CV1^2 ...
2085 !> \param CV2^2 ...
2086 !> \param " ...
2087 !> \param type_of_var=lchar_t ...
2088 !> \param n_var=1 ...
2089 !> \param error=error ...
2090 ! **************************************************************************************************
2091 usage="FUNCTION SQRT(CV1^2+CV2^2)", type_of_var=lchar_t, &
2092 n_var=1)
2093 CALL section_add_keyword(section, keyword)
2094 CALL keyword_release(keyword)
2095
2096 CALL keyword_create(keyword, __location__, name="VARIABLES", &
2097 description="Specifies the name of the variable that parametrises the FUNCTION "// &
2098 "defining how COLVARS should be combined. The matching follows the same order of the "// &
2099 "COLVARS definition in the input file.", &
2100 usage="VARIABLE CV1 CV2 CV3", type_of_var=char_t, n_var=-1, repeats=.false.)
2101 CALL section_add_keyword(section, keyword)
2102 CALL keyword_release(keyword)
2103
2104 CALL keyword_create(keyword, __location__, name="PARAMETERS", &
2105 description="Defines the parameters of the functional form", &
2106 usage="PARAMETERS a b D", type_of_var=char_t, &
2107 n_var=-1, repeats=.true.)
2108 CALL section_add_keyword(section, keyword)
2109 CALL keyword_release(keyword)
2110
2111 CALL keyword_create(keyword, __location__, name="VALUES", &
2112 description="Defines the values of parameter of the functional form", &
2113 usage="VALUES ", type_of_var=real_t, &
2114 n_var=-1, repeats=.true., unit_str="internal_cp2k")
2115 CALL section_add_keyword(section, keyword)
2116 CALL keyword_release(keyword)
2117
2118 CALL keyword_create(keyword, __location__, name="DX", &
2119 description="Parameter used for computing the derivative of the combination "// &
2120 "of COLVARs with the Ridders' method.", &
2121 usage="DX <REAL>", default_r_val=0.1_dp, unit_str="bohr")
2122 CALL section_add_keyword(section, keyword)
2123 CALL keyword_release(keyword)
2124
2125 CALL keyword_create(keyword, __location__, name="ERROR_LIMIT", &
2126 description="Checks that the error in computing the derivative is not larger than "// &
2127 "the value set; in case error is larger a warning message is printed.", &
2128 usage="ERROR_LIMIT <REAL>", default_r_val=1.0e-12_dp)
2129 CALL section_add_keyword(section, keyword)
2130 CALL keyword_release(keyword)
2131
2132 END SUBROUTINE create_colvar_comb_section
2133
2134! **************************************************************************************************
2135!> \brief Creates the coord section
2136!> \param section the section to create
2137!> \param name ...
2138!> \author teo
2139! **************************************************************************************************
2140 SUBROUTINE create_coord_section_cv(section, name)
2141 TYPE(section_type), POINTER :: section
2142 CHARACTER(LEN=*), INTENT(IN) :: name
2143
2144 TYPE(keyword_type), POINTER :: keyword
2145
2146 cpassert(.NOT. ASSOCIATED(section))
2147 CALL section_create(section, __location__, name="coord", &
2148 description="The positions for "//trim(name)//" used for restart", &
2149 n_keywords=1, n_subsections=0, repeats=.false.)
2150 NULLIFY (keyword)
2151
2152 CALL keyword_create(keyword, __location__, name="_DEFAULT_KEYWORD_", &
2153 description="Specify positions of the system", repeats=.true., &
2154 usage="{Real} ...", type_of_var=real_t, n_var=-1)
2155 CALL section_add_keyword(section, keyword)
2156 CALL keyword_release(keyword)
2157
2158 END SUBROUTINE create_coord_section_cv
2159
2160! **************************************************************************************************
2161!> \brief collective variables specifying h bonds
2162!> \param section the section to be created
2163!> \author alin m elena
2164! **************************************************************************************************
2165 SUBROUTINE create_colvar_wc_section(section)
2166 TYPE(section_type), POINTER :: section
2167
2168 TYPE(keyword_type), POINTER :: keyword
2169 TYPE(section_type), POINTER :: subsection
2170
2171 cpassert(.NOT. ASSOCIATED(section))
2172 CALL section_create(section, __location__, name="wc", &
2173 description="Section to define the hbond wannier centre as a collective variables.", &
2174 n_keywords=1, n_subsections=0, repeats=.false.)
2175 NULLIFY (keyword, subsection)
2176
2177 CALL keyword_create(keyword, __location__, name="RCUT", &
2178 description="Parameter used for computing the cutoff radius for searching "// &
2179 "the wannier centres around an atom", &
2180 usage="RCUT <REAL>", default_r_val=0.529177208590000_dp, unit_str="angstrom", &
2181 type_of_var=real_t, repeats=.false.)
2182 CALL section_add_keyword(section, keyword)
2183 CALL keyword_release(keyword)
2184
2185 CALL keyword_create(keyword, __location__, name="ATOMS", &
2186 variants=(/"POINTS"/), &
2187 description="Specifies the indexes of atoms/points defining the bond (Od, H, Oa).", &
2188 usage="ATOMS {integer} {integer} {integer}", &
2189 n_var=3, type_of_var=integer_t, repeats=.true.)
2190 CALL section_add_keyword(section, keyword)
2191 CALL keyword_release(keyword)
2192
2193 ! Must be present in each colvar and handled properly
2194 CALL create_point_section(subsection)
2195 CALL section_add_subsection(section, subsection)
2196 CALL section_release(subsection)
2197
2198 END SUBROUTINE create_colvar_wc_section
2199
2200 ! **************************************************************************************************
2201!> \brief collective variables specifying h bonds= wire
2202!> \param section the section to be created
2203!> \author alin m elena
2204! **************************************************************************************************
2205 SUBROUTINE create_colvar_hbp_section(section)
2206 TYPE(section_type), POINTER :: section
2207
2208 TYPE(keyword_type), POINTER :: keyword
2209 TYPE(section_type), POINTER :: subsection
2210
2211 cpassert(.NOT. ASSOCIATED(section))
2212 CALL section_create(section, __location__, name="hbp", &
2213 description="Section to define the hbond wannier centre as a collective variables.", &
2214 n_keywords=1, n_subsections=0, repeats=.false.)
2215 NULLIFY (keyword, subsection)
2216
2217 CALL keyword_create(keyword, __location__, name="RCUT", &
2218 description="Parameter used for computing the cutoff radius for searching "// &
2219 "the wannier centres around an atom", &
2220 usage="RCUT <REAL>", default_r_val=0.529177208590000_dp, unit_str="angstrom", &
2221 type_of_var=real_t, repeats=.false.)
2222 CALL section_add_keyword(section, keyword)
2223 CALL keyword_release(keyword)
2224
2225 CALL keyword_create(keyword, __location__, name="SHIFT", &
2226 description="Parameter used for shifting each term in the sum ", &
2227 usage="SHIFT <REAL>", default_r_val=0.5_dp, &
2228 type_of_var=real_t, repeats=.false.)
2229 CALL section_add_keyword(section, keyword)
2230 CALL keyword_release(keyword)
2231
2232 CALL keyword_create(keyword, __location__, name="NPOINTS", &
2233 description="The number of points in the path", &
2234 usage="NPOINTS {integer}", default_i_val=-1, &
2235 n_var=1, type_of_var=integer_t, repeats=.false.)
2236 CALL section_add_keyword(section, keyword)
2237 CALL keyword_release(keyword)
2238
2239 CALL keyword_create(keyword, __location__, name="ATOMS", &
2240 variants=(/"POINTS"/), &
2241 description="Specifies the indexes of atoms/points defining the bond (Od, H, Oa).", &
2242 usage="ATOMS {integer} {integer} {integer}", &
2243 n_var=3, type_of_var=integer_t, repeats=.true.)
2244 CALL section_add_keyword(section, keyword)
2245 CALL keyword_release(keyword)
2246
2247 ! Must be present in each colvar and handled properly
2248 CALL create_point_section(subsection)
2249 CALL section_add_subsection(section, subsection)
2250 CALL section_release(subsection)
2251
2252 END SUBROUTINE create_colvar_hbp_section
2253
2254! **************************************************************************************************
2255!> \brief collective variables specifying ring puckering
2256!> \brief D. Cremer and J.A. Pople, JACS 97 1354 (1975)
2257!> \param section the section to be created
2258!> \author Marcel Baer
2259! **************************************************************************************************
2260 SUBROUTINE create_colvar_ring_puckering_section(section)
2261 TYPE(section_type), POINTER :: section
2262
2263 TYPE(keyword_type), POINTER :: keyword
2264 TYPE(section_type), POINTER :: subsection
2265
2266 cpassert(.NOT. ASSOCIATED(section))
2267 CALL section_create(section, __location__, name="RING_PUCKERING", &
2268 description="Section to define general ring puckering collective variables.", &
2269 n_keywords=1, n_subsections=0, repeats=.false.)
2270
2271 NULLIFY (keyword, subsection)
2272
2273 CALL keyword_create(keyword, __location__, name="ATOMS", &
2274 variants=(/"POINTS"/), &
2275 description="Specifies the indexes of atoms/points defining the ring. "// &
2276 "At least 4 Atoms are needed.", &
2277 usage="ATOMS {integer} {integer} {integer} ..", &
2278 n_var=-1, type_of_var=integer_t)
2279 CALL section_add_keyword(section, keyword)
2280 CALL keyword_release(keyword)
2281
2282 CALL keyword_create(keyword, __location__, name="COORDINATE", &
2283 description="Indicate the coordinate to be used. Follow the Cremer-Pople definition for a N ring. "// &
2284 "0 is the total puckering variable Q, "// &
2285 "2..[N/2] are puckering coordinates. "// &
2286 "-2..-[N/2-1] are puckering angles.", &
2287 usage="COORDINATE {integer}", default_i_val=0, &
2288 n_var=1)
2289 CALL section_add_keyword(section, keyword)
2290 CALL keyword_release(keyword)
2291
2292 ! Must be present in each colvar and handled properly
2293 CALL create_point_section(subsection)
2294 CALL section_add_subsection(section, subsection)
2295 CALL section_release(subsection)
2296
2297 END SUBROUTINE create_colvar_ring_puckering_section
2298
2299! **************************************************************************************************
2300
2301END MODULE input_cp2k_colvar
string_utilities::s2a
Definition string_utilities.F:48
bibliography
collects all references to literature in CP2K as new algorithms / method are included from literature...
Definition bibliography.F:28
bibliography::branduardi2007
integer, save, public branduardi2007
Definition bibliography.F:43
colvar_types
Initialize the collective variables types.
Definition colvar_types.F:15
colvar_types::do_clv_geo_center
integer, parameter, public do_clv_geo_center
Definition colvar_types.F:33
colvar_types::do_clv_xyz
integer, parameter, public do_clv_xyz
Definition colvar_types.F:33
colvar_types::do_clv_xz
integer, parameter, public do_clv_xz
Definition colvar_types.F:33
colvar_types::do_clv_fix_point
integer, parameter, public do_clv_fix_point
Definition colvar_types.F:33
colvar_types::do_clv_z
integer, parameter, public do_clv_z
Definition colvar_types.F:33
colvar_types::plane_def_atoms
integer, parameter, public plane_def_atoms
Definition colvar_types.F:30
colvar_types::do_clv_yz
integer, parameter, public do_clv_yz
Definition colvar_types.F:33
colvar_types::do_clv_xy
integer, parameter, public do_clv_xy
Definition colvar_types.F:33
colvar_types::do_clv_y
integer, parameter, public do_clv_y
Definition colvar_types.F:33
colvar_types::plane_def_vec
integer, parameter, public plane_def_vec
Definition colvar_types.F:30
colvar_types::do_clv_x
integer, parameter, public do_clv_x
Definition colvar_types.F:33
cp_output_handling
routines to handle the output, The idea is to remove the decision of wheter to output and what to out...
Definition cp_output_handling.F:25
cp_output_handling::low_print_level
integer, parameter, public low_print_level
Definition cp_output_handling.F:73
cp_output_handling::high_print_level
integer, parameter, public high_print_level
Definition cp_output_handling.F:73
cp_output_handling::add_last_numeric
integer, parameter, public add_last_numeric
Definition cp_output_handling.F:70
cp_output_handling::cp_print_key_section_create
subroutine, public cp_print_key_section_create(print_key_section, location, name, description, print_level, each_iter_names, each_iter_values, add_last, filename, common_iter_levels, citations, unit_str)
creates a print_key section
Definition cp_output_handling.F:174
cp_units
unit conversion facility
Definition cp_units.F:30
cp_units::cp_unit_to_cp2k
real(kind=dp) function, public cp_unit_to_cp2k(value, unit_str, defaults, power)
converts to the internal cp2k units to the given unit
Definition cp_units.F:1150
input_constants
collects all constants needed in input so that they can be used without circular dependencies
Definition input_constants.F:17
input_constants::rmsd_weightlist
integer, parameter, public rmsd_weightlist
Definition input_constants.F:87
input_constants::rmsd_list
integer, parameter, public rmsd_list
Definition input_constants.F:87
input_constants::rmsd_all
integer, parameter, public rmsd_all
Definition input_constants.F:87
input_constants::gaussian
integer, parameter, public gaussian
Definition input_constants.F:153
input_constants::numerical
integer, parameter, public numerical
Definition input_constants.F:153
input_cp2k_colvar
Definition input_cp2k_colvar.F:13
input_cp2k_colvar::create_colvar_xyz_d_section
subroutine, public create_colvar_xyz_d_section(section)
creates the colvar section regarded to the collective variables dist
Definition input_cp2k_colvar.F:834
input_cp2k_colvar::create_colvar_section
recursive subroutine, public create_colvar_section(section, skip_recursive_colvar)
creates the colvar section
Definition input_cp2k_colvar.F:63
input_cp2k_colvar::create_colvar_xyz_od_section
subroutine, public create_colvar_xyz_od_section(section)
creates the colvar section regarded to the collective variables dist
Definition input_cp2k_colvar.F:894
input_keyword_types
represents keywords in an input
Definition input_keyword_types.F:14
input_keyword_types::keyword_release
subroutine, public keyword_release(keyword)
releases the given keyword (see doc/ReferenceCounting.html)
Definition input_keyword_types.F:426
input_keyword_types::keyword_create
subroutine, public keyword_create(keyword, location, name, description, usage, type_of_var, n_var, repeats, variants, default_val, default_l_val, default_r_val, default_lc_val, default_c_val, default_i_val, default_l_vals, default_r_vals, default_c_vals, default_i_vals, lone_keyword_val, lone_keyword_l_val, lone_keyword_r_val, lone_keyword_c_val, lone_keyword_i_val, lone_keyword_l_vals, lone_keyword_r_vals, lone_keyword_c_vals, lone_keyword_i_vals, enum_c_vals, enum_i_vals, enum, enum_strict, enum_desc, unit_str, citations, deprecation_notice, removed)
creates a keyword object
Definition input_keyword_types.F:155
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_create
subroutine, public section_create(section, location, name, description, n_keywords, n_subsections, repeats, citations)
creates a list of keywords
Definition input_section_types.F:156
input_section_types::section_add_keyword
subroutine, public section_add_keyword(section, keyword)
adds a keyword to the given section
Definition input_section_types.F:504
input_section_types::section_add_subsection
subroutine, public section_add_subsection(section, subsection)
adds a subsection to the given section
Definition input_section_types.F:560
input_section_types::section_release
recursive subroutine, public section_release(section)
releases the given keyword list (see doc/ReferenceCounting.html)
Definition input_section_types.F:231
input_val_types
a wrapper for basic fortran types.
Definition input_val_types.F:14
input_val_types::real_t
integer, parameter, public real_t
Definition input_val_types.F:41
input_val_types::lchar_t
integer, parameter, public lchar_t
Definition input_val_types.F:41
input_val_types::char_t
integer, parameter, public char_t
Definition input_val_types.F:41
input_val_types::integer_t
integer, parameter, public integer_t
Definition input_val_types.F:41
kinds
Defines the basic variable types.
Definition kinds.F:23
kinds::dp
integer, parameter, public dp
Definition kinds.F:34
string_utilities
Utilities for string manipulations.
Definition string_utilities.F:16
input_keyword_types::keyword_type
represent a keyword in the input
Definition input_keyword_types.F:88
input_section_types::section_type
represent a section of the input file
Definition input_section_types.F:102