Line data Source code
1 : !--------------------------------------------------------------------------------------------------!
2 : ! CP2K: A general program to perform molecular dynamics simulations !
3 : ! Copyright 2000-2026 CP2K developers group <https://cp2k.org> !
4 : ! !
5 : ! SPDX-License-Identifier: GPL-2.0-or-later !
6 : !--------------------------------------------------------------------------------------------------!
7 :
8 : ! **************************************************************************************************
9 : !> \par History
10 : !> - taken out of input_cp2k_motion
11 : !> \author teo & fawzi
12 : ! **************************************************************************************************
13 : MODULE input_cp2k_colvar
14 : USE bibliography, ONLY: Branduardi2007,&
15 : Zhang2025
16 : USE colvar_types, ONLY: &
17 : do_clv_fix_point, do_clv_geo_center, do_clv_x, do_clv_xy, do_clv_xyz, do_clv_xz, do_clv_y, &
18 : do_clv_yz, do_clv_z, plane_def_atoms, plane_def_vec
19 : USE cp_output_handling, ONLY: add_last_numeric,&
20 : cp_print_key_section_create,&
21 : high_print_level,&
22 : low_print_level
23 : USE cp_units, ONLY: cp_unit_to_cp2k
24 : USE fparser, ONLY: docf
25 : USE input_constants, ONLY: gaussian,&
26 : numerical,&
27 : rmsd_all,&
28 : rmsd_list,&
29 : rmsd_weightlist
30 : USE input_keyword_types, ONLY: keyword_create,&
31 : keyword_release,&
32 : keyword_type
33 : USE input_section_types, ONLY: section_add_keyword,&
34 : section_add_subsection,&
35 : section_create,&
36 : section_release,&
37 : section_type
38 : USE input_val_types, ONLY: char_t,&
39 : integer_t,&
40 : lchar_t,&
41 : real_t
42 : USE kinds, ONLY: dp
43 : USE string_utilities, ONLY: s2a
44 : #include "./base/base_uses.f90"
45 :
46 : IMPLICIT NONE
47 : PRIVATE
48 :
49 : LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .FALSE.
50 : CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'input_cp2k_colvar'
51 :
52 : PUBLIC :: create_colvar_section, &
53 : create_colvar_xyz_d_section, &
54 : create_colvar_xyz_od_section
55 :
56 : CONTAINS
57 :
58 : ! **************************************************************************************************
59 : !> \brief creates the colvar section
60 : !> \param section the section to be created
61 : !> \param skip_recursive_colvar ...
62 : !> \author teo
63 : ! **************************************************************************************************
64 5520 : RECURSIVE SUBROUTINE create_colvar_section(section, skip_recursive_colvar)
65 : TYPE(section_type), POINTER :: section
66 : LOGICAL, OPTIONAL :: skip_recursive_colvar
67 :
68 : LOGICAL :: skip
69 : TYPE(section_type), POINTER :: print_key, subsection
70 :
71 5520 : skip = .FALSE.
72 5520 : IF (PRESENT(skip_recursive_colvar)) skip = skip_recursive_colvar
73 5520 : CPASSERT(.NOT. ASSOCIATED(section))
74 : CALL section_create(section, __LOCATION__, name="COLVAR", &
75 : description="This section specifies the nature of the collective variables.", &
76 5520 : n_keywords=1, n_subsections=1, repeats=.TRUE.)
77 5520 : NULLIFY (subsection, print_key)
78 :
79 : CALL create_colvar_var_section(subsection=subsection, &
80 5520 : section=section, skip_recursive_colvar=skip)
81 :
82 : CALL section_create(subsection, __LOCATION__, name="PRINT", &
83 : description="Controls the printing of the colvar specifications", &
84 5520 : n_keywords=0, n_subsections=1, repeats=.TRUE.)
85 5520 : NULLIFY (print_key)
86 : CALL cp_print_key_section_create(print_key, __LOCATION__, "PROGRAM_RUN_INFO", &
87 : description="Controls the printing of basic information during colvar setup.", &
88 5520 : print_level=low_print_level, add_last=add_last_numeric, filename="__STD_OUT__")
89 5520 : CALL section_add_subsection(subsection, print_key)
90 5520 : CALL section_release(print_key)
91 5520 : CALL section_add_subsection(section, subsection)
92 5520 : CALL section_release(subsection)
93 :
94 5520 : CALL create_clv_info_section(subsection)
95 5520 : CALL section_add_subsection(section, subsection)
96 5520 : CALL section_release(subsection)
97 :
98 5520 : END SUBROUTINE create_colvar_section
99 :
100 : ! **************************************************************************************************
101 : !> \brief Create the restart section for colvar restraints
102 : !> This section will be only used for restraint restarts.
103 : !> Constraints are handled automatically
104 : !> \param section the section to create
105 : !> \author Teodoro Laino 08.2006
106 : ! **************************************************************************************************
107 5520 : SUBROUTINE create_clv_info_section(section)
108 : TYPE(section_type), POINTER :: section
109 :
110 : TYPE(keyword_type), POINTER :: keyword
111 :
112 5520 : CPASSERT(.NOT. ASSOCIATED(section))
113 5520 : NULLIFY (keyword)
114 : CALL section_create(section, __LOCATION__, name="COLVAR_FUNC_INFO", &
115 : description="Specify further data possibly used by colvars, depending "// &
116 : "on the starting geometry, for computing the functions value.", &
117 5520 : n_subsections=0, repeats=.FALSE.)
118 :
119 : CALL keyword_create(keyword, __LOCATION__, name="_DEFAULT_KEYWORD_", &
120 : description="Colvar function data."// &
121 : " The order is an internal order. So if you decide to edit/modify/add these values by hand"// &
122 : " you should know very well what you are doing.!", repeats=.TRUE., &
123 5520 : usage="{Real} ...", type_of_var=real_t, n_var=-1)
124 5520 : CALL section_add_keyword(section, keyword)
125 5520 : CALL keyword_release(keyword)
126 :
127 5520 : END SUBROUTINE create_clv_info_section
128 :
129 : ! **************************************************************************************************
130 : !> \brief creates the collective variables for the colvar section
131 : !> \param subsection ...
132 : !> \param section the section to be created
133 : !> \param skip_recursive_colvar ...
134 : !> \author teo
135 : ! **************************************************************************************************
136 5520 : RECURSIVE SUBROUTINE create_colvar_var_section(subsection, section, skip_recursive_colvar)
137 : TYPE(section_type), POINTER :: subsection, section
138 : LOGICAL, INTENT(IN) :: skip_recursive_colvar
139 :
140 5520 : CPASSERT(.NOT. ASSOCIATED(subsection))
141 5520 : CPASSERT(ASSOCIATED(section))
142 :
143 5520 : CALL create_colvar_dist_section(subsection)
144 5520 : CALL section_add_subsection(section, subsection)
145 5520 : CALL section_release(subsection)
146 :
147 5520 : CALL create_colvar_angle_section(subsection)
148 5520 : CALL section_add_subsection(section, subsection)
149 5520 : CALL section_release(subsection)
150 :
151 5520 : CALL create_colvar_torsion_section(subsection)
152 5520 : CALL section_add_subsection(section, subsection)
153 5520 : CALL section_release(subsection)
154 :
155 5520 : CALL create_colvar_coord_section(subsection)
156 5520 : CALL section_add_subsection(section, subsection)
157 5520 : CALL section_release(subsection)
158 :
159 5520 : CALL create_colvar_pop_section(subsection)
160 5520 : CALL section_add_subsection(section, subsection)
161 5520 : CALL section_release(subsection)
162 :
163 5520 : CALL create_colvar_gyr_section(subsection)
164 5520 : CALL section_add_subsection(section, subsection)
165 5520 : CALL section_release(subsection)
166 :
167 5520 : CALL create_colvar_d_pl_section(subsection)
168 5520 : CALL section_add_subsection(section, subsection)
169 5520 : CALL section_release(subsection)
170 :
171 5520 : CALL create_colvar_a_pl_section(subsection)
172 5520 : CALL section_add_subsection(section, subsection)
173 5520 : CALL section_release(subsection)
174 :
175 5520 : CALL create_colvar_rot_section(subsection)
176 5520 : CALL section_add_subsection(section, subsection)
177 5520 : CALL section_release(subsection)
178 :
179 5520 : CALL create_colvar_dfunct_section(subsection)
180 5520 : CALL section_add_subsection(section, subsection)
181 5520 : CALL section_release(subsection)
182 :
183 5520 : CALL create_colvar_qparm_section(subsection)
184 5520 : CALL section_add_subsection(section, subsection)
185 5520 : CALL section_release(subsection)
186 :
187 5520 : CALL create_colvar_hydronium_shell_section(subsection)
188 5520 : CALL section_add_subsection(section, subsection)
189 5520 : CALL section_release(subsection)
190 :
191 5520 : CALL create_colvar_hydronium_dist_section(subsection)
192 5520 : CALL section_add_subsection(section, subsection)
193 5520 : CALL section_release(subsection)
194 :
195 5520 : CALL create_colvar_acid_hyd_dist_section(subsection)
196 5520 : CALL section_add_subsection(section, subsection)
197 5520 : CALL section_release(subsection)
198 :
199 5520 : CALL create_colvar_acid_hyd_shell_section(subsection)
200 5520 : CALL section_add_subsection(section, subsection)
201 5520 : CALL section_release(subsection)
202 :
203 5520 : CALL create_colvar_rmsd_section(subsection)
204 5520 : CALL section_add_subsection(section, subsection)
205 5520 : CALL section_release(subsection)
206 :
207 5520 : CALL create_colvar_xyz_d_section(subsection)
208 5520 : CALL section_add_subsection(section, subsection)
209 5520 : CALL section_release(subsection)
210 :
211 5520 : CALL create_colvar_xyz_od_section(subsection)
212 5520 : CALL section_add_subsection(section, subsection)
213 5520 : CALL section_release(subsection)
214 :
215 5520 : CALL create_colvar_u_section(subsection)
216 5520 : CALL section_add_subsection(section, subsection)
217 5520 : CALL section_release(subsection)
218 :
219 5520 : CALL create_colvar_wc_section(subsection)
220 5520 : CALL section_add_subsection(section, subsection)
221 5520 : CALL section_release(subsection)
222 :
223 5520 : CALL create_colvar_hbp_section(subsection)
224 5520 : CALL section_add_subsection(section, subsection)
225 5520 : CALL section_release(subsection)
226 :
227 5520 : CALL create_colvar_ring_puckering_section(subsection)
228 5520 : CALL section_add_subsection(section, subsection)
229 5520 : CALL section_release(subsection)
230 :
231 5520 : CALL create_colvar_cond_dist_section(subsection)
232 5520 : CALL section_add_subsection(section, subsection)
233 5520 : CALL section_release(subsection)
234 :
235 5520 : CALL create_voronoiipz_section(subsection)
236 5520 : CALL section_add_subsection(section, subsection)
237 5520 : CALL section_release(subsection)
238 :
239 5520 : IF (.NOT. skip_recursive_colvar) THEN
240 1380 : CALL create_colvar_rpath_section(subsection)
241 1380 : CALL section_add_subsection(section, subsection)
242 1380 : CALL section_release(subsection)
243 :
244 1380 : CALL create_colvar_dpath_section(subsection)
245 1380 : CALL section_add_subsection(section, subsection)
246 1380 : CALL section_release(subsection)
247 :
248 1380 : CALL create_colvar_comb_section(subsection)
249 1380 : CALL section_add_subsection(section, subsection)
250 1380 : CALL section_release(subsection)
251 : END IF
252 :
253 5520 : END SUBROUTINE create_colvar_var_section
254 :
255 : ! **************************************************************************************************
256 : !> \brief collective variables specifying coordination
257 : !> \param section the section to be created
258 : !> \author teo
259 : ! **************************************************************************************************
260 5520 : SUBROUTINE create_colvar_coord_section(section)
261 : TYPE(section_type), POINTER :: section
262 :
263 : TYPE(keyword_type), POINTER :: keyword
264 : TYPE(section_type), POINTER :: subsection
265 :
266 5520 : CPASSERT(.NOT. ASSOCIATED(section))
267 : CALL section_create(section, __LOCATION__, name="coordination", &
268 : description="Section to define the coordination number as a collective variable.", &
269 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
270 :
271 5520 : NULLIFY (subsection, keyword)
272 :
273 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_FROM", &
274 : variants=["POINTS_FROM"], &
275 : description="Specify indexes of atoms/points building the coordination variable. ", &
276 : usage="ATOMS_FROM {integer} {integer} ..", repeats=.TRUE., &
277 11040 : n_var=-1, type_of_var=integer_t)
278 5520 : CALL section_add_keyword(section, keyword)
279 5520 : CALL keyword_release(keyword)
280 :
281 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_TO", &
282 : variants=["POINTS_TO"], &
283 : description="Specify indexes of atoms/points building the coordination variable. ", &
284 : usage="ATOMS_TO {integer} {integer} ..", repeats=.TRUE., &
285 11040 : n_var=-1, type_of_var=integer_t)
286 5520 : CALL section_add_keyword(section, keyword)
287 5520 : CALL keyword_release(keyword)
288 :
289 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_TO_B", &
290 : variants=["POINTS_TO_B"], &
291 : description="For the CV given by the multiplication of two coorination numbers,"// &
292 : " here specify indexes of the third set of atoms/points. ", &
293 : usage="ATOMS_TO_B {integer} {integer} ..", repeats=.TRUE., &
294 11040 : n_var=-1, type_of_var=integer_t)
295 5520 : CALL section_add_keyword(section, keyword)
296 5520 : CALL keyword_release(keyword)
297 :
298 : CALL keyword_create(keyword, __LOCATION__, name="KINDS_FROM", &
299 : description="Specify alternatively kinds of atoms building the coordination variable.", &
300 : usage="KINDS_FROM {CHAR} {CHAR} ..", repeats=.TRUE., &
301 5520 : n_var=-1, type_of_var=char_t)
302 5520 : CALL section_add_keyword(section, keyword)
303 5520 : CALL keyword_release(keyword)
304 :
305 : CALL keyword_create(keyword, __LOCATION__, name="KINDS_TO", &
306 : description="Specify alternatively kinds of atoms building the coordination variable.", &
307 : usage="KINDS_TO {CHAR} {CHAR} ..", repeats=.TRUE., &
308 5520 : n_var=-1, type_of_var=char_t)
309 5520 : CALL section_add_keyword(section, keyword)
310 5520 : CALL keyword_release(keyword)
311 :
312 : CALL keyword_create(keyword, __LOCATION__, name="KINDS_TO_B", &
313 : description="For the CV given by the multiplication of two coorination numbers,"// &
314 : " here specify alternatively kinds of atoms building the coordination variable.", &
315 : usage="KINDS_TO_B {CHAR} {CHAR} ..", repeats=.TRUE., &
316 5520 : n_var=-1, type_of_var=char_t)
317 5520 : CALL section_add_keyword(section, keyword)
318 5520 : CALL keyword_release(keyword)
319 :
320 : ! Must be present in each colvar and handled properly
321 5520 : CALL create_point_section(subsection)
322 5520 : CALL section_add_subsection(section, subsection)
323 5520 : CALL section_release(subsection)
324 :
325 : CALL keyword_create(keyword, __LOCATION__, name="R0", &
326 : variants=["R_0"], &
327 : description="Specify the R0 parameter in the coordination function.", &
328 : usage="R0 {real}", default_r_val=3.0_dp, &
329 11040 : unit_str="bohr", n_var=1)
330 5520 : CALL section_add_keyword(section, keyword)
331 5520 : CALL keyword_release(keyword)
332 :
333 : CALL keyword_create(keyword, __LOCATION__, name="NN", &
334 : variants=["EXPON_NUMERATOR"], &
335 : description="Sets the value of the numerator of the exponential factor"// &
336 : " in the coordination FUNCTION.", &
337 : usage="NN {integer}", default_i_val=6, &
338 11040 : n_var=1)
339 5520 : CALL section_add_keyword(section, keyword)
340 5520 : CALL keyword_release(keyword)
341 :
342 : CALL keyword_create(keyword, __LOCATION__, name="ND", &
343 : variants=["EXPON_DENOMINATOR"], &
344 : description="Sets the value of the denominator of the exponential factor"// &
345 : " in the coordination FUNCTION.", &
346 : usage="ND {integer}", default_i_val=12, &
347 11040 : n_var=1)
348 5520 : CALL section_add_keyword(section, keyword)
349 5520 : CALL keyword_release(keyword)
350 :
351 : CALL keyword_create(keyword, __LOCATION__, name="R0_B", &
352 : variants=["R_0_B"], &
353 : description="For the CV given by the multiplication of two coorination numbers,"// &
354 : " specify the R0 parameter in the second coordination function.", &
355 : usage="R0_B {real}", default_r_val=3.0_dp, &
356 11040 : unit_str="bohr", n_var=1)
357 5520 : CALL section_add_keyword(section, keyword)
358 5520 : CALL keyword_release(keyword)
359 :
360 : CALL keyword_create(keyword, __LOCATION__, name="NN_B", &
361 : variants=["EXPON_NUMERATOR_B"], &
362 : description="For the CV given by the multiplication of two coorination numbers,"// &
363 : " Sets the value of the numerator of the exponential factor"// &
364 : " in the coordination FUNCTION.", &
365 : usage="NN_B {integer}", default_i_val=6, &
366 11040 : n_var=1)
367 5520 : CALL section_add_keyword(section, keyword)
368 5520 : CALL keyword_release(keyword)
369 :
370 : CALL keyword_create(keyword, __LOCATION__, name="ND_B", &
371 : variants=["EXPON_DENOMINATOR_B"], &
372 : description="For the CV given by the multiplication of two coorination numbers,"// &
373 : " Sets the value of the denominator of the exponential factor"// &
374 : " in the coordination FUNCTION.", &
375 : usage="ND_B {integer}", default_i_val=12, &
376 11040 : n_var=1)
377 5520 : CALL section_add_keyword(section, keyword)
378 5520 : CALL keyword_release(keyword)
379 :
380 5520 : END SUBROUTINE create_colvar_coord_section
381 :
382 : ! **************************************************************************************************
383 : !> \brief ...
384 : !> \param section ...
385 : ! **************************************************************************************************
386 5520 : SUBROUTINE create_colvar_cond_dist_section(section)
387 : TYPE(section_type), POINTER :: section
388 :
389 : TYPE(keyword_type), POINTER :: keyword
390 : TYPE(section_type), POINTER :: subsection
391 :
392 5520 : CPASSERT(.NOT. ASSOCIATED(section))
393 : CALL section_create(section, __LOCATION__, name="CONDITIONED_DISTANCE", &
394 : description="Section to define the conditioned distance as a collective variable.", &
395 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
396 :
397 5520 : NULLIFY (subsection, keyword)
398 :
399 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_DISTANCE", &
400 : description="Specify indexes of atoms/points from which the distance is computed. ", &
401 : usage="ATOMS_DISTANCE {integer} {integer} ..", repeats=.TRUE., &
402 5520 : n_var=-1, type_of_var=integer_t)
403 5520 : CALL section_add_keyword(section, keyword)
404 5520 : CALL keyword_release(keyword)
405 :
406 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_FROM", &
407 : variants=["POINTS_FROM"], &
408 : description="Specify indexes of atoms/points building the coordination variable. ", &
409 : usage="ATOMS_FROM {integer} {integer} ..", repeats=.TRUE., &
410 11040 : n_var=-1, type_of_var=integer_t)
411 5520 : CALL section_add_keyword(section, keyword)
412 5520 : CALL keyword_release(keyword)
413 :
414 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_TO", &
415 : variants=["POINTS_TO"], &
416 : description="Specify indexes of atoms/points building the coordination variable. ", &
417 : usage="ATOMS_TO {integer} {integer} ..", repeats=.TRUE., &
418 11040 : n_var=-1, type_of_var=integer_t)
419 5520 : CALL section_add_keyword(section, keyword)
420 5520 : CALL keyword_release(keyword)
421 :
422 : CALL keyword_create(keyword, __LOCATION__, name="KINDS_FROM", &
423 : description="Specify alternatively kinds of atoms building the coordination variable.", &
424 : usage="KINDS_FROM {CHAR} {CHAR} ..", repeats=.TRUE., &
425 5520 : n_var=-1, type_of_var=char_t)
426 5520 : CALL section_add_keyword(section, keyword)
427 5520 : CALL keyword_release(keyword)
428 :
429 : CALL keyword_create(keyword, __LOCATION__, name="KINDS_TO", &
430 : description="Specify alternatively kinds of atoms building the coordination variable.", &
431 : usage="KINDS_TO {CHAR} {CHAR} ..", repeats=.TRUE., &
432 5520 : n_var=-1, type_of_var=char_t)
433 5520 : CALL section_add_keyword(section, keyword)
434 5520 : CALL keyword_release(keyword)
435 :
436 : ! Must be present in each colvar and handled properly
437 5520 : CALL create_point_section(subsection)
438 5520 : CALL section_add_subsection(section, subsection)
439 5520 : CALL section_release(subsection)
440 :
441 : CALL keyword_create(keyword, __LOCATION__, name="R0", &
442 : variants=["R_0"], &
443 : description="Specify the R0 parameter in the coordination function.", &
444 : usage="R0 {real}", default_r_val=3.0_dp, &
445 11040 : unit_str="bohr", n_var=1)
446 5520 : CALL section_add_keyword(section, keyword)
447 5520 : CALL keyword_release(keyword)
448 :
449 : CALL keyword_create(keyword, __LOCATION__, name="NN", &
450 : variants=["EXPON_NUMERATOR"], &
451 : description="Sets the value of the numerator of the exponential factor"// &
452 : " in the coordination FUNCTION.", &
453 : usage="NN {integer}", default_i_val=6, &
454 11040 : n_var=1)
455 5520 : CALL section_add_keyword(section, keyword)
456 5520 : CALL keyword_release(keyword)
457 :
458 : CALL keyword_create(keyword, __LOCATION__, name="ND", &
459 : variants=["EXPON_DENOMINATOR"], &
460 : description="Sets the value of the denominator of the exponential factor"// &
461 : " in the coordination FUNCTION.", &
462 : usage="ND {integer}", default_i_val=12, &
463 11040 : n_var=1)
464 5520 : CALL section_add_keyword(section, keyword)
465 5520 : CALL keyword_release(keyword)
466 :
467 : CALL keyword_create(keyword, __LOCATION__, name="LAMBDA", &
468 : description="Specify the lambda parameter at the exponent of the conditioned distance function.", &
469 : usage="LAMBDA {real}", default_r_val=3.0_dp, &
470 5520 : unit_str="bohr", n_var=1)
471 5520 : CALL section_add_keyword(section, keyword)
472 5520 : CALL keyword_release(keyword)
473 :
474 5520 : END SUBROUTINE create_colvar_cond_dist_section
475 :
476 : ! **************************************************************************************************
477 : !> \brief collective variables specifying population of a specie based on coordination
478 : !> \param section the section to be created
479 : !> \date 01.2009
480 : !> \author Fabio Sterpone
481 : ! **************************************************************************************************
482 5520 : SUBROUTINE create_colvar_pop_section(section)
483 : TYPE(section_type), POINTER :: section
484 :
485 : TYPE(keyword_type), POINTER :: keyword
486 : TYPE(section_type), POINTER :: subsection
487 :
488 5520 : CPASSERT(.NOT. ASSOCIATED(section))
489 : CALL section_create(section, __LOCATION__, name="population", &
490 : description="Section to define the population of specie as a collective variable. "// &
491 : "See also <https://doi.org/10.1021/jp3019588>.", &
492 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
493 :
494 5520 : NULLIFY (subsection, keyword)
495 :
496 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_FROM", &
497 : variants=["POINTS_FROM"], &
498 : description="Specify indexes of atoms/points building the coordination variable. ", &
499 : usage="ATOMS_FROM {integer} {integer} ..", repeats=.TRUE., &
500 11040 : n_var=-1, type_of_var=integer_t)
501 5520 : CALL section_add_keyword(section, keyword)
502 5520 : CALL keyword_release(keyword)
503 :
504 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_TO", &
505 : variants=["POINTS_TO"], &
506 : description="Specify indexes of atoms/points building the coordination variable. ", &
507 : usage="ATOMS_TO {integer} {integer} ..", repeats=.TRUE., &
508 11040 : n_var=-1, type_of_var=integer_t)
509 5520 : CALL section_add_keyword(section, keyword)
510 5520 : CALL keyword_release(keyword)
511 :
512 : CALL keyword_create(keyword, __LOCATION__, name="KINDS_FROM", &
513 : description="Specify alternatively kinds of atoms building the coordination variable.", &
514 : usage="KINDS_FROM {CHAR} {CHAR} ..", repeats=.TRUE., &
515 5520 : n_var=-1, type_of_var=char_t)
516 5520 : CALL section_add_keyword(section, keyword)
517 5520 : CALL keyword_release(keyword)
518 :
519 : CALL keyword_create(keyword, __LOCATION__, name="KINDS_TO", &
520 : description="Specify alternatively kinds of atoms building the coordination variable.", &
521 : usage="KINDS_TO {CHAR} {CHAR} ..", repeats=.TRUE., &
522 5520 : n_var=-1, type_of_var=char_t)
523 5520 : CALL section_add_keyword(section, keyword)
524 5520 : CALL keyword_release(keyword)
525 :
526 : ! Must be present in each colvar and handled properly
527 5520 : CALL create_point_section(subsection)
528 5520 : CALL section_add_subsection(section, subsection)
529 5520 : CALL section_release(subsection)
530 :
531 : CALL keyword_create(keyword, __LOCATION__, name="R0", &
532 : variants=["R_0"], &
533 : description="Specify the R0 parameter in the coordination function.", &
534 : usage="R0 {real}", default_r_val=3.0_dp, &
535 11040 : n_var=1)
536 5520 : CALL section_add_keyword(section, keyword)
537 5520 : CALL keyword_release(keyword)
538 :
539 : CALL keyword_create(keyword, __LOCATION__, name="NN", &
540 : variants=["EXPON_NUMERATOR"], &
541 : description="Sets the value of the numerator of the exponential factor"// &
542 : " in the coordination FUNCTION.", &
543 : usage="NN {integer}", default_i_val=6, &
544 11040 : n_var=1)
545 5520 : CALL section_add_keyword(section, keyword)
546 5520 : CALL keyword_release(keyword)
547 :
548 : CALL keyword_create(keyword, __LOCATION__, name="ND", &
549 : variants=["EXPON_DENOMINATOR"], &
550 : description="Sets the value of the denominator of the exponential factor"// &
551 : " in the coordination FUNCTION.", &
552 : usage="ND {integer}", default_i_val=12, &
553 11040 : n_var=1)
554 5520 : CALL section_add_keyword(section, keyword)
555 5520 : CALL keyword_release(keyword)
556 :
557 : CALL keyword_create(keyword, __LOCATION__, name="n0", &
558 : variants=["n_0"], &
559 : description="Specify the n0 parameter that sets the coordination of the species.", &
560 : usage="n0 {integer}", default_i_val=4, &
561 11040 : n_var=1)
562 5520 : CALL section_add_keyword(section, keyword)
563 5520 : CALL keyword_release(keyword)
564 :
565 : CALL keyword_create(keyword, __LOCATION__, name="SIGMA", &
566 : description="Specify the gaussian width of used to build the population istogram.", &
567 : usage="SIGMA {real}", default_r_val=0.5_dp, &
568 5520 : n_var=1)
569 5520 : CALL section_add_keyword(section, keyword)
570 5520 : CALL keyword_release(keyword)
571 :
572 5520 : END SUBROUTINE create_colvar_pop_section
573 :
574 : ! **************************************************************************************************
575 : !> \brief ...
576 : !> \param section ...
577 : ! **************************************************************************************************
578 5520 : SUBROUTINE create_colvar_gyr_section(section)
579 : TYPE(section_type), POINTER :: section
580 :
581 : TYPE(keyword_type), POINTER :: keyword
582 : TYPE(section_type), POINTER :: subsection
583 :
584 5520 : CPASSERT(.NOT. ASSOCIATED(section))
585 : CALL section_create(section, __LOCATION__, name="GYRATION_RADIUS", &
586 : description="Section to define the gyration radius as a collective variable.", &
587 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
588 :
589 5520 : NULLIFY (subsection, keyword)
590 :
591 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
592 : variants=["POINTS"], &
593 : description="Specify indexes of atoms/points defyining the gyration radius variable. ", &
594 : usage="ATOMS {integer} {integer} ..", repeats=.TRUE., &
595 11040 : n_var=-1, type_of_var=integer_t)
596 5520 : CALL section_add_keyword(section, keyword)
597 5520 : CALL keyword_release(keyword)
598 :
599 : CALL keyword_create(keyword, __LOCATION__, name="KINDS", &
600 : description="Specify alternatively kinds of atoms defining the gyration radius.", &
601 : usage="KINDS {CHAR} {CHAR} ..", repeats=.TRUE., &
602 5520 : n_var=-1, type_of_var=char_t)
603 5520 : CALL section_add_keyword(section, keyword)
604 5520 : CALL keyword_release(keyword)
605 :
606 : ! Must be present in each colvar and handled properly
607 5520 : CALL create_point_section(subsection)
608 5520 : CALL section_add_subsection(section, subsection)
609 5520 : CALL section_release(subsection)
610 :
611 5520 : END SUBROUTINE create_colvar_gyr_section
612 :
613 : ! **************************************************************************************************
614 : !> \brief collective variables specifying torsion
615 : !> \param section the section to be created
616 : !> \author teo
617 : ! **************************************************************************************************
618 5520 : SUBROUTINE create_colvar_dfunct_section(section)
619 : TYPE(section_type), POINTER :: section
620 :
621 : TYPE(keyword_type), POINTER :: keyword
622 : TYPE(section_type), POINTER :: subsection
623 :
624 5520 : CPASSERT(.NOT. ASSOCIATED(section))
625 : CALL section_create(section, __LOCATION__, name="DISTANCE_FUNCTION", &
626 : description="Section to define functions between two distances as collective variables."// &
627 : " The function is defined as d1+coeff*d2", &
628 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
629 :
630 5520 : NULLIFY (keyword, subsection)
631 :
632 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
633 : variants=["POINTS"], &
634 : description="Specifies the indexes of atoms/points for the two bonds d1=(1-2) d2=(3-4).", &
635 : usage="ATOMS {integer} {integer} {integer} {integer}", &
636 11040 : n_var=4, type_of_var=integer_t)
637 5520 : CALL section_add_keyword(section, keyword)
638 5520 : CALL keyword_release(keyword)
639 :
640 : CALL keyword_create(keyword, __LOCATION__, name="COEFFICIENT", &
641 : description="Specifies the coefficient in the function for the constraint."// &
642 : " -1.0 has to be used for distance difference, 1.0 for distance addition", &
643 : usage="COEFFICIENT {real}", &
644 5520 : type_of_var=real_t)
645 5520 : CALL section_add_keyword(section, keyword)
646 5520 : CALL keyword_release(keyword)
647 :
648 : CALL keyword_create(keyword, __LOCATION__, name="PBC", &
649 : description="Whether periodic boundary conditions should be applied on the "// &
650 : "atomic position before computing the colvar or not.", &
651 : usage="PBC", &
652 5520 : default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
653 5520 : CALL section_add_keyword(section, keyword)
654 5520 : CALL keyword_release(keyword)
655 :
656 : ! Must be present in each colvar and handled properly
657 5520 : CALL create_point_section(subsection)
658 5520 : CALL section_add_subsection(section, subsection)
659 5520 : CALL section_release(subsection)
660 :
661 5520 : END SUBROUTINE create_colvar_dfunct_section
662 :
663 : ! **************************************************************************************************
664 : !> \brief collective variables specifying torsion
665 : !> \param section the section to be created
666 : !> \author teo
667 : ! **************************************************************************************************
668 5520 : SUBROUTINE create_colvar_torsion_section(section)
669 : TYPE(section_type), POINTER :: section
670 :
671 : TYPE(keyword_type), POINTER :: keyword
672 : TYPE(section_type), POINTER :: subsection
673 :
674 5520 : CPASSERT(.NOT. ASSOCIATED(section))
675 : CALL section_create(section, __LOCATION__, name="torsion", &
676 : description="Section to define the torsion as a collective variables.", &
677 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
678 :
679 5520 : NULLIFY (keyword, subsection)
680 :
681 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
682 : variants=["POINTS"], &
683 : description="Specifies the indexes of atoms/points defining the torsion.", &
684 : usage="ATOMS {integer} {integer} {integer} {integer}", &
685 11040 : n_var=4, type_of_var=integer_t)
686 5520 : CALL section_add_keyword(section, keyword)
687 5520 : CALL keyword_release(keyword)
688 :
689 : ! Must be present in each colvar and handled properly
690 5520 : CALL create_point_section(subsection)
691 5520 : CALL section_add_subsection(section, subsection)
692 5520 : CALL section_release(subsection)
693 :
694 5520 : END SUBROUTINE create_colvar_torsion_section
695 :
696 : ! **************************************************************************************************
697 : !> \brief collective variables specifying torsion
698 : !> \param section the section to be created
699 : !> \author teo
700 : ! **************************************************************************************************
701 5520 : SUBROUTINE create_colvar_rot_section(section)
702 : TYPE(section_type), POINTER :: section
703 :
704 : TYPE(keyword_type), POINTER :: keyword
705 : TYPE(section_type), POINTER :: subsection
706 :
707 5520 : CPASSERT(.NOT. ASSOCIATED(section))
708 : CALL section_create(section, __LOCATION__, name="bond_rotation", &
709 : description="Section to define the rotation of a bond/line with respect to"// &
710 : " another bond/line", &
711 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
712 :
713 5520 : NULLIFY (keyword, subsection)
714 :
715 : CALL keyword_create(keyword, __LOCATION__, name="P1_BOND1", &
716 : description="Specifies the index of atom/point defining the first point"// &
717 : " of the first bond/line.", &
718 : usage="P1_BOND1 {integer}", &
719 5520 : n_var=1, type_of_var=integer_t)
720 5520 : CALL section_add_keyword(section, keyword)
721 5520 : CALL keyword_release(keyword)
722 :
723 : CALL keyword_create(keyword, __LOCATION__, name="P2_BOND1", &
724 : description="Specifies the index of atom/point defining the second point"// &
725 : " of the first bond/line.", &
726 : usage="P2_BOND1 {integer}", &
727 5520 : n_var=1, type_of_var=integer_t)
728 5520 : CALL section_add_keyword(section, keyword)
729 5520 : CALL keyword_release(keyword)
730 :
731 : CALL keyword_create(keyword, __LOCATION__, name="P1_BOND2", &
732 : description="Specifies the index of atom/point defining the first point"// &
733 : " of the second bond/line.", &
734 : usage="P1_BOND2 {integer}", &
735 5520 : n_var=1, type_of_var=integer_t)
736 5520 : CALL section_add_keyword(section, keyword)
737 5520 : CALL keyword_release(keyword)
738 :
739 : CALL keyword_create(keyword, __LOCATION__, name="P2_BOND2", &
740 : description="Specifies the index of atom/point defining the second point"// &
741 : " of the second bond/line.", &
742 : usage="P2_BOND2 {integer}", &
743 5520 : n_var=1, type_of_var=integer_t)
744 5520 : CALL section_add_keyword(section, keyword)
745 5520 : CALL keyword_release(keyword)
746 :
747 : ! Must be present in each colvar and handled properly
748 5520 : CALL create_point_section(subsection)
749 5520 : CALL section_add_subsection(section, subsection)
750 5520 : CALL section_release(subsection)
751 :
752 5520 : END SUBROUTINE create_colvar_rot_section
753 :
754 : ! **************************************************************************************************
755 : !> \brief collective variables specifying angles
756 : !> \param section the section to be created
757 : !> \author teo
758 : ! **************************************************************************************************
759 5520 : SUBROUTINE create_colvar_angle_section(section)
760 : TYPE(section_type), POINTER :: section
761 :
762 : TYPE(keyword_type), POINTER :: keyword
763 : TYPE(section_type), POINTER :: subsection
764 :
765 5520 : CPASSERT(.NOT. ASSOCIATED(section))
766 : CALL section_create(section, __LOCATION__, name="angle", &
767 : description="Section to define the angle as a collective variables.", &
768 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
769 5520 : NULLIFY (keyword, subsection)
770 :
771 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
772 : variants=["POINTS"], &
773 : description="Specifies the indexes of atoms/points defining the angle.", &
774 : usage="ATOMS {integer} {integer} {integer}", &
775 11040 : n_var=3, type_of_var=integer_t)
776 5520 : CALL section_add_keyword(section, keyword)
777 5520 : CALL keyword_release(keyword)
778 :
779 : ! Must be present in each colvar and handled properly
780 5520 : CALL create_point_section(subsection)
781 5520 : CALL section_add_subsection(section, subsection)
782 5520 : CALL section_release(subsection)
783 :
784 5520 : END SUBROUTINE create_colvar_angle_section
785 :
786 : ! **************************************************************************************************
787 : !> \brief creates the colvar section regarded to the collective variables dist
788 : !> \param section the section to be created
789 : !> \author teo
790 : ! **************************************************************************************************
791 5520 : SUBROUTINE create_colvar_dist_section(section)
792 : TYPE(section_type), POINTER :: section
793 :
794 : TYPE(keyword_type), POINTER :: keyword
795 : TYPE(section_type), POINTER :: subsection
796 :
797 5520 : CPASSERT(.NOT. ASSOCIATED(section))
798 : CALL section_create(section, __LOCATION__, name="distance", &
799 : description="Section to define the distance as a collective variables.", &
800 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
801 5520 : NULLIFY (keyword, subsection)
802 :
803 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
804 : variants=["POINTS"], &
805 : description="Specifies the indexes of atoms/points defining the distance.", &
806 : usage="ATOMS {integer} {integer}", &
807 11040 : n_var=2, type_of_var=integer_t)
808 5520 : CALL section_add_keyword(section, keyword)
809 5520 : CALL keyword_release(keyword)
810 : CALL keyword_create(keyword, __LOCATION__, name="AXIS", &
811 : description="Define the axes along which the colvar should be evaluated", &
812 : usage="AXIS (XYZ | X | Y | Z | XY| XZ | YZ)", &
813 : enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
814 : enum_i_vals=[do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz], &
815 5520 : default_i_val=do_clv_xyz)
816 5520 : CALL section_add_keyword(section, keyword)
817 5520 : CALL keyword_release(keyword)
818 :
819 : CALL keyword_create(keyword, __LOCATION__, name="SIGN", &
820 : description="Whether the distance along one Cartesian axis has to be considered with sign."// &
821 : " This option is valid if only one dimension is selected.", &
822 : usage="SIGN", &
823 5520 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
824 5520 : CALL section_add_keyword(section, keyword)
825 5520 : CALL keyword_release(keyword)
826 :
827 : ! Must be present in each colvar and handled properly
828 5520 : CALL create_point_section(subsection)
829 5520 : CALL section_add_subsection(section, subsection)
830 5520 : CALL section_release(subsection)
831 :
832 5520 : END SUBROUTINE create_colvar_dist_section
833 :
834 : ! **************************************************************************************************
835 : !> \brief creates the colvar section regarded to the collective variables dist
836 : !> \param section the section to be created
837 : !> \author teo
838 : ! **************************************************************************************************
839 5523 : SUBROUTINE create_colvar_xyz_d_section(section)
840 : TYPE(section_type), POINTER :: section
841 :
842 : TYPE(keyword_type), POINTER :: keyword
843 : TYPE(section_type), POINTER :: subsection
844 :
845 5523 : CPASSERT(.NOT. ASSOCIATED(section))
846 : CALL section_create(section, __LOCATION__, name="XYZ_DIAG", &
847 : description="Section to define the distance of an atom from its starting "// &
848 : "position ((X-X(0))^2+(Y-Y(0))^2+(Z-Z(0))^2) or part of its components as a collective variable. "// &
849 : "If absolute_position is specified, instead the CV is represented by the "// &
850 : "instantaneous position of the atom (only available for X, Y or Z components).", &
851 5523 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
852 5523 : NULLIFY (keyword, subsection)
853 :
854 : CALL keyword_create(keyword, __LOCATION__, name="ATOM", &
855 : variants=["POINT"], &
856 : description="Specifies the index of the atom/point.", &
857 : usage="ATOM {integer}", &
858 11046 : n_var=1, type_of_var=integer_t)
859 5523 : CALL section_add_keyword(section, keyword)
860 5523 : CALL keyword_release(keyword)
861 :
862 : CALL keyword_create(keyword, __LOCATION__, name="COMPONENT", &
863 : description="Define the component of the position vector which will be used "// &
864 : "as a colvar.", &
865 : usage="COMPONENT (XYZ | X | Y | Z | XY| XZ | YZ)", &
866 : enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
867 : enum_i_vals=[do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz], &
868 5523 : default_i_val=do_clv_xyz)
869 5523 : CALL section_add_keyword(section, keyword)
870 5523 : CALL keyword_release(keyword)
871 :
872 : CALL keyword_create(keyword, __LOCATION__, name="PBC", &
873 : description="Whether periodic boundary conditions should be applied on the "// &
874 : "atomic position before computing the colvar or not.", &
875 : usage="PBC", &
876 5523 : default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
877 5523 : CALL section_add_keyword(section, keyword)
878 5523 : CALL keyword_release(keyword)
879 :
880 : CALL keyword_create(keyword, __LOCATION__, name="ABSOLUTE_POSITION", &
881 : description="If enabled, the absolute position of the atoms will be used. ", &
882 : usage="ABSOLUTE_POSITION", &
883 5523 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
884 5523 : CALL section_add_keyword(section, keyword)
885 5523 : CALL keyword_release(keyword)
886 :
887 : ! Must be present in each colvar and handled properly
888 5523 : CALL create_point_section(subsection)
889 5523 : CALL section_add_subsection(section, subsection)
890 5523 : CALL section_release(subsection)
891 :
892 5523 : END SUBROUTINE create_colvar_xyz_d_section
893 :
894 : ! **************************************************************************************************
895 : !> \brief creates the colvar section regarded to the collective variables dist
896 : !> \param section the section to be created
897 : !> \author teo
898 : ! **************************************************************************************************
899 5523 : SUBROUTINE create_colvar_xyz_od_section(section)
900 : TYPE(section_type), POINTER :: section
901 :
902 : TYPE(keyword_type), POINTER :: keyword
903 : TYPE(section_type), POINTER :: subsection
904 :
905 5523 : CPASSERT(.NOT. ASSOCIATED(section))
906 : CALL section_create(section, __LOCATION__, name="XYZ_OUTERDIAG", &
907 : description="Section to define the cross term (XA-XA(0))*(XB-XB(0))+(XA-XA(0))*(YB-YB(0))"// &
908 : " or part of its components as a collective variable. The final term is given by the product"// &
909 : " of the components of A with the components of B.", &
910 5523 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
911 5523 : NULLIFY (keyword, subsection)
912 :
913 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
914 : variants=["POINTS"], &
915 : description="Specifies the index of the atoms/points A and B.", &
916 : usage="ATOMS {integer} {integer}", &
917 11046 : n_var=2, type_of_var=integer_t)
918 5523 : CALL section_add_keyword(section, keyword)
919 5523 : CALL keyword_release(keyword)
920 :
921 : CALL keyword_create(keyword, __LOCATION__, name="COMPONENT_A", &
922 : description="Define the component of the position vector which will be used "// &
923 : "as a colvar for atom A.", &
924 : usage="COMPONENT_A (XYZ | X | Y | Z | XY| XZ | YZ)", &
925 : enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
926 : enum_i_vals=[do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz], &
927 5523 : default_i_val=do_clv_xyz)
928 5523 : CALL section_add_keyword(section, keyword)
929 5523 : CALL keyword_release(keyword)
930 :
931 : CALL keyword_create(keyword, __LOCATION__, name="COMPONENT_B", &
932 : description="Define the component of the position vector which will be used "// &
933 : "as a colvar for atom B.", &
934 : usage="COMPONENT_B (XYZ | X | Y | Z | XY| XZ | YZ)", &
935 : enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
936 : enum_i_vals=[do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz], &
937 5523 : default_i_val=do_clv_xyz)
938 5523 : CALL section_add_keyword(section, keyword)
939 5523 : CALL keyword_release(keyword)
940 :
941 : CALL keyword_create(keyword, __LOCATION__, name="PBC", &
942 : description="Whether periodic boundary conditions should be applied on the "// &
943 : "atomic position before computing the colvar or not.", &
944 : usage="PBC", &
945 5523 : default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
946 5523 : CALL section_add_keyword(section, keyword)
947 5523 : CALL keyword_release(keyword)
948 :
949 : ! Must be present in each colvar and handled properly
950 5523 : CALL create_point_section(subsection)
951 5523 : CALL section_add_subsection(section, subsection)
952 5523 : CALL section_release(subsection)
953 :
954 5523 : END SUBROUTINE create_colvar_xyz_od_section
955 :
956 : ! **************************************************************************************************
957 : !> \brief energy as collective variable
958 : !> \param section the section to be created
959 : !> \author Sebastiano Caravati
960 : ! **************************************************************************************************
961 5520 : SUBROUTINE create_colvar_u_section(section)
962 : TYPE(section_type), POINTER :: section
963 :
964 : TYPE(keyword_type), POINTER :: keyword
965 : TYPE(section_type), POINTER :: subsection
966 :
967 5520 : CPASSERT(.NOT. ASSOCIATED(section))
968 : CALL section_create(section, __LOCATION__, name="u", &
969 : description="Section to define the energy as a generalized collective variable.", &
970 5520 : n_keywords=0, n_subsections=0, repeats=.FALSE.)
971 :
972 5520 : NULLIFY (subsection, keyword)
973 : CALL section_create(subsection, __LOCATION__, name="MIXED", &
974 : description="This section allows to use any function of the energy subsystems"// &
975 : " in a mixed_env calculation as a collective variable.", &
976 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
977 :
978 : CALL keyword_create(keyword, __LOCATION__, name="ENERGY_FUNCTION", &
979 : description="Specifies the functional form of the collective variable in mathematical notation.", &
980 : usage="ENERGY_FUNCTION (E1+E2-LOG(E1/E2))", type_of_var=lchar_t, &
981 5520 : n_var=1)
982 5520 : CALL section_add_keyword(subsection, keyword)
983 5520 : CALL keyword_release(keyword)
984 :
985 : CALL keyword_create(keyword, __LOCATION__, name="VARIABLES", &
986 : description="Defines the variables of the functional form. To allow an efficient"// &
987 : " mapping the order of the energy variables will be considered identical to the"// &
988 : " order of the force_eval in the force_eval_order list.", &
989 : usage="VARIABLES x", type_of_var=char_t, &
990 5520 : n_var=-1)
991 5520 : CALL section_add_keyword(subsection, keyword)
992 5520 : CALL keyword_release(keyword)
993 :
994 : CALL keyword_create(keyword, __LOCATION__, name="PARAMETERS", &
995 : description="Defines the parameters of the functional form", &
996 : usage="PARAMETERS a b D", type_of_var=char_t, &
997 5520 : n_var=-1, repeats=.TRUE.)
998 5520 : CALL section_add_keyword(subsection, keyword)
999 5520 : CALL keyword_release(keyword)
1000 :
1001 : CALL keyword_create(keyword, __LOCATION__, name="VALUES", &
1002 : description="Defines the values of parameter of the functional form", &
1003 : usage="VALUES ", type_of_var=real_t, &
1004 5520 : n_var=-1, repeats=.TRUE., unit_str="internal_cp2k")
1005 5520 : CALL section_add_keyword(subsection, keyword)
1006 5520 : CALL keyword_release(keyword)
1007 :
1008 : CALL keyword_create(keyword, __LOCATION__, name="UNITS", &
1009 : description="Optionally, allows to define valid CP2K unit strings for each parameter value. "// &
1010 : "It is assumed that the corresponding parameter value is specified in this unit.", &
1011 : usage="UNITS angstrom eV*angstrom^-1 angstrom^1 K", type_of_var=char_t, &
1012 5520 : n_var=-1, repeats=.TRUE.)
1013 5520 : CALL section_add_keyword(subsection, keyword)
1014 5520 : CALL keyword_release(keyword)
1015 :
1016 : CALL keyword_create(keyword, __LOCATION__, name="DX", &
1017 : description="Parameter used for computing the derivative with the Ridders' method.", &
1018 5520 : usage="DX <REAL>", default_r_val=0.1_dp, unit_str="bohr")
1019 5520 : CALL section_add_keyword(subsection, keyword)
1020 5520 : CALL keyword_release(keyword)
1021 :
1022 : CALL keyword_create(keyword, __LOCATION__, name="ERROR_LIMIT", &
1023 : description="Checks that the error in computing the derivative is not larger than "// &
1024 : "the value set; in case error is larger a warning message is printed.", &
1025 5520 : usage="ERROR_LIMIT <REAL>", default_r_val=1.0E-12_dp)
1026 5520 : CALL section_add_keyword(subsection, keyword)
1027 5520 : CALL keyword_release(keyword)
1028 :
1029 5520 : CALL section_add_subsection(section, subsection)
1030 5520 : CALL section_release(subsection)
1031 :
1032 5520 : END SUBROUTINE create_colvar_u_section
1033 :
1034 : ! **************************************************************************************************
1035 : !> \brief creates the colvar section regarded to the collective variables distance
1036 : !> of a point from a plane
1037 : !> \param section the section to be created
1038 : !> \author teo
1039 : ! **************************************************************************************************
1040 5520 : SUBROUTINE create_colvar_d_pl_section(section)
1041 : TYPE(section_type), POINTER :: section
1042 :
1043 : TYPE(keyword_type), POINTER :: keyword
1044 : TYPE(section_type), POINTER :: subsection
1045 :
1046 5520 : CPASSERT(.NOT. ASSOCIATED(section))
1047 : CALL section_create(section, __LOCATION__, name="distance_point_plane", &
1048 : description="Section to define the distance of a point from a plane "// &
1049 : "as a collective variables.", &
1050 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1051 5520 : NULLIFY (keyword, subsection)
1052 :
1053 : CALL keyword_create(keyword, __LOCATION__, name="PBC", &
1054 : description="Whether periodic boundary conditions should be applied on the "// &
1055 : "atomic position before computing the colvar or not.", &
1056 : usage="PBC", &
1057 5520 : default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
1058 5520 : CALL section_add_keyword(section, keyword)
1059 5520 : CALL keyword_release(keyword)
1060 :
1061 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_PLANE", &
1062 : variants=["POINTS_PLANE"], &
1063 : description="Specifies the indexes of atoms/points defining the plane.", &
1064 : usage="ATOMS_PLANE <INTEGER> <INTEGER> <INTEGER>", &
1065 11040 : n_var=3, type_of_var=integer_t)
1066 5520 : CALL section_add_keyword(section, keyword)
1067 5520 : CALL keyword_release(keyword)
1068 :
1069 : CALL keyword_create(keyword, __LOCATION__, name="ATOM_POINT", &
1070 : variants=["POINT_POINT"], &
1071 : description="Specifies the atom/point index defining the point.", &
1072 : usage="ATOM_POINT <INTEGER>", &
1073 11040 : n_var=1, type_of_var=integer_t)
1074 5520 : CALL section_add_keyword(section, keyword)
1075 5520 : CALL keyword_release(keyword)
1076 :
1077 : ! Must be present in each colvar and handled properly
1078 5520 : CALL create_point_section(subsection)
1079 5520 : CALL section_add_subsection(section, subsection)
1080 5520 : CALL section_release(subsection)
1081 :
1082 5520 : END SUBROUTINE create_colvar_d_pl_section
1083 :
1084 : ! **************************************************************************************************
1085 : !> \brief creates the colvar section regarded to the collective variables
1086 : !> angles betweem two planes
1087 : !> \param section the section to be created
1088 : !> \author teo
1089 : ! **************************************************************************************************
1090 5520 : SUBROUTINE create_colvar_a_pl_section(section)
1091 : TYPE(section_type), POINTER :: section
1092 :
1093 : TYPE(keyword_type), POINTER :: keyword
1094 : TYPE(section_type), POINTER :: subsection
1095 :
1096 5520 : CPASSERT(.NOT. ASSOCIATED(section))
1097 : CALL section_create(section, __LOCATION__, name="angle_plane_plane", &
1098 : description="This section defines the angle between two planes "// &
1099 : "as a collective variables.", &
1100 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1101 5520 : NULLIFY (keyword, subsection)
1102 :
1103 : CALL section_create(subsection, __LOCATION__, name="PLANE", &
1104 : description="This section defines the plane. When using this colvar, "// &
1105 : "two plane section must be defined!", &
1106 5520 : n_keywords=1, n_subsections=0, repeats=.TRUE.)
1107 :
1108 : CALL keyword_create(keyword, __LOCATION__, name="DEF_TYPE", &
1109 : description="Specify how the plane is defined: either by 3 atoms or by a fixed normal "// &
1110 : "vector. At least one plane must be defined through atoms.", &
1111 : usage="DEF_TYPE ATOMS", &
1112 : default_i_val=plane_def_atoms, &
1113 : enum_c_vals=s2a("ATOMS", "VECTOR"), &
1114 : enum_desc=s2a("Plane defined by the position of 3 atoms", &
1115 : "Plane defined by a fixed normal vector"), &
1116 5520 : enum_i_vals=[plane_def_atoms, plane_def_vec])
1117 5520 : CALL section_add_keyword(subsection, keyword)
1118 5520 : CALL keyword_release(keyword)
1119 :
1120 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
1121 : description="Specifies the indexes of 3 atoms/points defining the plane.", &
1122 : usage="ATOMS <INTEGER> <INTEGER> <INTEGER>", &
1123 5520 : n_var=3, type_of_var=integer_t)
1124 5520 : CALL section_add_keyword(subsection, keyword)
1125 5520 : CALL keyword_release(keyword)
1126 :
1127 : CALL keyword_create(keyword, __LOCATION__, name="NORMAL_VECTOR", &
1128 : description="Alternatively to 3 atoms/points one can define one of the two, "// &
1129 : "planes by defining its NORMAL vector.", &
1130 : usage="NORMAL_VECTOR 0.0 1.0 0.0", &
1131 5520 : n_var=3, type_of_var=real_t)
1132 5520 : CALL section_add_keyword(subsection, keyword)
1133 5520 : CALL keyword_release(keyword)
1134 5520 : CALL section_add_subsection(section, subsection)
1135 5520 : CALL section_release(subsection)
1136 :
1137 : ! Must be present in each colvar and handled properly
1138 5520 : CALL create_point_section(subsection)
1139 5520 : CALL section_add_subsection(section, subsection)
1140 5520 : CALL section_release(subsection)
1141 5520 : END SUBROUTINE create_colvar_a_pl_section
1142 :
1143 : ! **************************************************************************************************
1144 : !> \brief create a geometrical point as a function of several atom coordinates
1145 : !> \param section the section to be created
1146 : !> \author teo
1147 : ! **************************************************************************************************
1148 93846 : SUBROUTINE create_point_section(section)
1149 : TYPE(section_type), POINTER :: section
1150 :
1151 : TYPE(keyword_type), POINTER :: keyword
1152 :
1153 93846 : CPASSERT(.NOT. ASSOCIATED(section))
1154 : CALL section_create(section, __LOCATION__, name="POINT", &
1155 : description="Enables the possibility to use geometrical centers instead of single atoms"// &
1156 : " to define colvars", &
1157 93846 : n_keywords=1, n_subsections=0, repeats=.TRUE.)
1158 :
1159 93846 : NULLIFY (keyword)
1160 :
1161 : CALL keyword_create(keyword, __LOCATION__, name="TYPE", &
1162 : description="Chooses the type of geometrical point", &
1163 : usage="type (GEO_CENTER|FIX_POINT)", &
1164 : enum_c_vals=s2a("GEO_CENTER", "FIX_POINT"), &
1165 : enum_desc=s2a("Computes the geometrical center of the listed atoms", &
1166 : "Defines a fixed point in space"), &
1167 : enum_i_vals=[do_clv_geo_center, do_clv_fix_point], &
1168 93846 : default_i_val=do_clv_geo_center)
1169 93846 : CALL section_add_keyword(section, keyword)
1170 93846 : CALL keyword_release(keyword)
1171 :
1172 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
1173 : description="Specifies the indexes of atoms defining the geometrical center", &
1174 : usage="ATOMS {integer} {integer} {integer} {integer}", &
1175 93846 : n_var=-1, type_of_var=integer_t, repeats=.TRUE.)
1176 93846 : CALL section_add_keyword(section, keyword)
1177 93846 : CALL keyword_release(keyword)
1178 :
1179 : CALL keyword_create( &
1180 : keyword, __LOCATION__, name="WEIGHTS", &
1181 : description="Specifies the weights for a weighted geometrical center. Default is 1/natoms for every atom", &
1182 : usage="WEIGHTS {real} {real} {real} {real}", &
1183 93846 : n_var=-1, type_of_var=real_t, repeats=.TRUE.)
1184 93846 : CALL section_add_keyword(section, keyword)
1185 93846 : CALL keyword_release(keyword)
1186 :
1187 : CALL keyword_create(keyword, __LOCATION__, name="XYZ", &
1188 : description="Specifies the xyz of the fixed point (if the case)", &
1189 : usage="XYZ {real} {real} {real}", &
1190 : n_var=3, type_of_var=real_t, unit_str="bohr", &
1191 93846 : repeats=.FALSE.)
1192 93846 : CALL section_add_keyword(section, keyword)
1193 93846 : CALL keyword_release(keyword)
1194 :
1195 93846 : END SUBROUTINE create_point_section
1196 :
1197 : ! **************************************************************************************************
1198 : !> \brief collective variables specifying torsion
1199 : !> \param section the section to be created
1200 : !> \author teo
1201 : ! **************************************************************************************************
1202 5520 : SUBROUTINE create_colvar_qparm_section(section)
1203 : TYPE(section_type), POINTER :: section
1204 :
1205 : TYPE(keyword_type), POINTER :: keyword
1206 : TYPE(section_type), POINTER :: subsection
1207 :
1208 5520 : CPASSERT(.NOT. ASSOCIATED(section))
1209 : CALL section_create(section, __LOCATION__, name="qparm", &
1210 : description="Section to define the Q parameter (crystalline order parameter) as a collective variable.", &
1211 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1212 :
1213 5520 : NULLIFY (keyword, subsection)
1214 :
1215 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_FROM", &
1216 : variants=["POINTS_FROM"], &
1217 : description="Specify indexes of atoms/points building the coordination variable. ", &
1218 : usage="ATOMS_FROM {integer} {integer} ..", repeats=.TRUE., &
1219 11040 : n_var=-1, type_of_var=integer_t)
1220 5520 : CALL section_add_keyword(section, keyword)
1221 5520 : CALL keyword_release(keyword)
1222 :
1223 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_TO", &
1224 : variants=["POINTS_TO"], &
1225 : description="Specify indexes of atoms/points building the coordination variable. ", &
1226 : usage="ATOMS_TO {integer} {integer} ..", repeats=.TRUE., &
1227 11040 : n_var=-1, type_of_var=integer_t)
1228 5520 : CALL section_add_keyword(section, keyword)
1229 5520 : CALL keyword_release(keyword)
1230 :
1231 : CALL keyword_create(keyword, __LOCATION__, name="RCUT", &
1232 : description="Specifies the distance cutoff for neighbors. "// &
1233 : "Cutoff function is exactly zero for all neighbors beyond RCUT.", &
1234 : usage="RCUT {real}", &
1235 5520 : n_var=1, unit_str="angstrom", type_of_var=real_t)
1236 5520 : CALL section_add_keyword(section, keyword)
1237 5520 : CALL keyword_release(keyword)
1238 :
1239 : CALL keyword_create(keyword, __LOCATION__, name="INCLUDE_IMAGES", &
1240 : description="Whether to include periodic images of ATOMS_TO into the neighbor list.", &
1241 : usage="INCLUDE_IMAGES", &
1242 5520 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
1243 5520 : CALL section_add_keyword(section, keyword)
1244 5520 : CALL keyword_release(keyword)
1245 :
1246 : CALL keyword_create(keyword, __LOCATION__, name="RSTART", &
1247 : description="Specifies the distance cutoff for neighbors. "// &
1248 : "Cutoff function is exactly 1 for all neighbors closer than RSTART.", &
1249 : usage="RSTART {real}", &
1250 5520 : n_var=1, unit_str="angstrom", type_of_var=real_t)
1251 5520 : CALL section_add_keyword(section, keyword)
1252 5520 : CALL keyword_release(keyword)
1253 :
1254 : CALL keyword_create(keyword, __LOCATION__, name="L", &
1255 : description="Specifies the L spherical harmonics from Ylm.", &
1256 : usage="L {integer}", &
1257 5520 : n_var=1, type_of_var=integer_t)
1258 5520 : CALL section_add_keyword(section, keyword)
1259 5520 : CALL keyword_release(keyword)
1260 :
1261 : !CALL keyword_create(keyword, __LOCATION__, name="ALPHA", &
1262 : ! description="Specifies the width of the Fermi-Dirac style smearing around RCUT.", &
1263 : ! usage="ALPHA {real}", unit_str="angstrom^-1", default_r_val=0.0_dp)
1264 : !CALL section_add_keyword(section, keyword)
1265 : !CALL keyword_release(keyword)
1266 :
1267 : ! Must be present in each colvar and handled properly
1268 5520 : CALL create_point_section(subsection)
1269 5520 : CALL section_add_subsection(section, subsection)
1270 5520 : CALL section_release(subsection)
1271 :
1272 5520 : END SUBROUTINE create_colvar_qparm_section
1273 :
1274 : ! **************************************************************************************************
1275 : !> \brief collective variables specifying hydronium solvation
1276 : !> \param section the section to be created
1277 : !> \author Marcel Baer
1278 : ! **************************************************************************************************
1279 5520 : SUBROUTINE create_colvar_hydronium_shell_section(section)
1280 : TYPE(section_type), POINTER :: section
1281 :
1282 : TYPE(keyword_type), POINTER :: keyword
1283 :
1284 5520 : CPASSERT(.NOT. ASSOCIATED(section))
1285 : CALL section_create(section, __LOCATION__, name="HYDRONIUM_SHELL", &
1286 : description="Section to define the formation of a hydronium as a"// &
1287 : " collective variable. Number of oxygens in the 1st shell of the"// &
1288 : " hydronium. Adapted from Equation (3) in Supplementary Info of"// &
1289 : " J. Am. Chem. Soc.,128, 2006, 11318, i.e. omitting the cutoff function"// &
1290 : " and summing only over the oxygens of water.", &
1291 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1292 :
1293 5520 : NULLIFY (keyword)
1294 :
1295 : CALL keyword_create(keyword, __LOCATION__, name="OXYGENS", &
1296 : description="Specifies indexes of atoms building the coordination variable."// &
1297 : " Oxygens of the water molecules.", &
1298 : usage="OXYGENS {integer} {integer} ..", repeats=.TRUE., &
1299 5520 : n_var=-1, type_of_var=integer_t)
1300 5520 : CALL section_add_keyword(section, keyword)
1301 5520 : CALL keyword_release(keyword)
1302 :
1303 : CALL keyword_create(keyword, __LOCATION__, name="HYDROGENS", &
1304 : description="Specifies indexes of atoms building the coordination variable."// &
1305 : " Hydrogens of the water molecules.", &
1306 : usage="HYDROGENS {integer} {integer} ..", repeats=.TRUE., &
1307 5520 : n_var=-1, type_of_var=integer_t)
1308 5520 : CALL section_add_keyword(section, keyword)
1309 5520 : CALL keyword_release(keyword)
1310 :
1311 : CALL keyword_create(keyword, __LOCATION__, name="ROO", &
1312 : description="Specifies the rc parameter in the coordination function:"// &
1313 : " number of oxygens per water oxygen.", &
1314 : usage="ROO {real}", default_r_val=cp_unit_to_cp2k(value=3.0_dp, &
1315 5520 : unit_str="bohr"), unit_str="bohr", n_var=1)
1316 5520 : CALL section_add_keyword(section, keyword)
1317 5520 : CALL keyword_release(keyword)
1318 :
1319 : CALL keyword_create(keyword, __LOCATION__, name="pOO", &
1320 : variants=["EXPON_NUMERATORA"], &
1321 : description="Sets the value of the numerator of the exponential factor"// &
1322 : " in the coordination function: number of oxygens per water oxygen.", &
1323 : usage="pOO {integer}", default_i_val=6, &
1324 11040 : n_var=1)
1325 5520 : CALL section_add_keyword(section, keyword)
1326 5520 : CALL keyword_release(keyword)
1327 :
1328 : CALL keyword_create(keyword, __LOCATION__, name="qOO", &
1329 : variants=["EXPON_DENOMINATORA"], &
1330 : description="Sets the value of the denominator of the exponential factor"// &
1331 : " in the coordination function: number of oxygens per water oxygen.", &
1332 : usage="qOO {integer}", default_i_val=12, &
1333 11040 : n_var=1)
1334 5520 : CALL section_add_keyword(section, keyword)
1335 5520 : CALL keyword_release(keyword)
1336 :
1337 : CALL keyword_create(keyword, __LOCATION__, name="ROH", &
1338 : description="Specifies the rc parameter in the coordination function:"// &
1339 : " number of hydrogens per water molecule.", &
1340 : usage="ROH {real}", default_r_val=cp_unit_to_cp2k(value=3.0_dp, &
1341 5520 : unit_str="bohr"), unit_str="bohr", n_var=1)
1342 5520 : CALL section_add_keyword(section, keyword)
1343 5520 : CALL keyword_release(keyword)
1344 :
1345 : CALL keyword_create(keyword, __LOCATION__, name="pOH", &
1346 : variants=["EXPON_NUMERATORB"], &
1347 : description="Sets the value of the numerator of the exponential factor"// &
1348 : " in the coordination function: number of hydrogens per water molecule.", &
1349 : usage="pOH {integer}", default_i_val=6, &
1350 11040 : n_var=1)
1351 5520 : CALL section_add_keyword(section, keyword)
1352 5520 : CALL keyword_release(keyword)
1353 :
1354 : CALL keyword_create(keyword, __LOCATION__, name="qOH", &
1355 : variants=["EXPON_DENOMINATORB"], &
1356 : description="Sets the value of the denominator of the exponential factor"// &
1357 : " in the coordination function: number of hydrogens per water molecule.", &
1358 : usage="qOH {integer}", default_i_val=12, &
1359 11040 : n_var=1)
1360 5520 : CALL section_add_keyword(section, keyword)
1361 5520 : CALL keyword_release(keyword)
1362 :
1363 : CALL keyword_create(keyword, __LOCATION__, name="NH", &
1364 : description="Specifies the NH parameter in the M function.", &
1365 : usage="NH {real}", default_r_val=3.0_dp, &
1366 5520 : n_var=1)
1367 5520 : CALL section_add_keyword(section, keyword)
1368 5520 : CALL keyword_release(keyword)
1369 :
1370 : CALL keyword_create(keyword, __LOCATION__, name="pM", &
1371 : variants=["EXPON_NUMERATOR"], &
1372 : description="Sets the value of the numerator of the exponential factor"// &
1373 : " in the M function.", &
1374 : usage="pM {integer}", default_i_val=8, &
1375 11040 : n_var=1)
1376 5520 : CALL section_add_keyword(section, keyword)
1377 5520 : CALL keyword_release(keyword)
1378 :
1379 : CALL keyword_create(keyword, __LOCATION__, name="qM", &
1380 : variants=["EXPON_DENOMINATOR"], &
1381 : description="Sets the value of the denominator of the exponential factor"// &
1382 : " in the M function.", &
1383 : usage="qM {integer}", default_i_val=16, &
1384 11040 : n_var=1)
1385 5520 : CALL section_add_keyword(section, keyword)
1386 5520 : CALL keyword_release(keyword)
1387 :
1388 : CALL keyword_create(keyword, __LOCATION__, name="LAMBDA", &
1389 : description="Specify the LAMBDA parameter in the hydronium function.", &
1390 : usage="LAMBDA {real}", default_r_val=10.0_dp, &
1391 5520 : n_var=1)
1392 5520 : CALL section_add_keyword(section, keyword)
1393 5520 : CALL keyword_release(keyword)
1394 :
1395 5520 : END SUBROUTINE create_colvar_hydronium_shell_section
1396 :
1397 : ! **************************************************************************************************
1398 : !> \brief collective variables specifying the distance between hydronium and hydroxide ion
1399 : !> \param section the section to be created
1400 : !> \author Dorothea Golze
1401 : ! **************************************************************************************************
1402 5520 : SUBROUTINE create_colvar_hydronium_dist_section(section)
1403 : TYPE(section_type), POINTER :: section
1404 :
1405 : TYPE(keyword_type), POINTER :: keyword
1406 :
1407 5520 : CPASSERT(.NOT. ASSOCIATED(section))
1408 : CALL section_create(section, __LOCATION__, name="HYDRONIUM_DISTANCE", &
1409 : description="Section to define the formation of a hydronium as a"// &
1410 : " collective variable. Distance between hydronium and hydroxide ion"// &
1411 : " Experimental at this point, i.e. not proved to be an effective"// &
1412 : " collective variable.", &
1413 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1414 :
1415 5520 : NULLIFY (keyword)
1416 :
1417 : CALL keyword_create(keyword, __LOCATION__, name="OXYGENS", &
1418 : description="Specifies indexes of atoms building the coordination variable."// &
1419 : " Oxygens of the water molecules.", &
1420 : usage="OXYGENS {integer} {integer} ..", repeats=.TRUE., &
1421 5520 : n_var=-1, type_of_var=integer_t)
1422 5520 : CALL section_add_keyword(section, keyword)
1423 5520 : CALL keyword_release(keyword)
1424 :
1425 : CALL keyword_create(keyword, __LOCATION__, name="HYDROGENS", &
1426 : description="Specifies indexes of atoms building the coordination variable."// &
1427 : " Hydrogens of the water molecules.", &
1428 : usage="HYDROGENS {integer} {integer} ..", repeats=.TRUE., &
1429 5520 : n_var=-1, type_of_var=integer_t)
1430 5520 : CALL section_add_keyword(section, keyword)
1431 5520 : CALL keyword_release(keyword)
1432 :
1433 : CALL keyword_create(keyword, __LOCATION__, name="ROH", &
1434 : description="Specifies the rc parameter in the coordination function:"// &
1435 : " number of hydrogens per water molecule.", &
1436 : usage="ROH {real}", default_r_val=cp_unit_to_cp2k(value=2.4_dp, &
1437 5520 : unit_str="bohr"), unit_str="bohr", n_var=1)
1438 5520 : CALL section_add_keyword(section, keyword)
1439 5520 : CALL keyword_release(keyword)
1440 :
1441 : CALL keyword_create(keyword, __LOCATION__, name="pOH", &
1442 : description="Sets the value of the numerator of the exponential factor"// &
1443 : " in the coordination function: number of hydrogens per water molecule.", &
1444 : usage="pOH {integer}", default_i_val=6, &
1445 5520 : n_var=1)
1446 5520 : CALL section_add_keyword(section, keyword)
1447 5520 : CALL keyword_release(keyword)
1448 :
1449 : CALL keyword_create(keyword, __LOCATION__, name="qOH", &
1450 : description="Sets the value of the denominator of the exponential factor"// &
1451 : " in the coordination function: number of hydrogens per water molecule.", &
1452 : usage="qOH {integer}", default_i_val=12, &
1453 5520 : n_var=1)
1454 5520 : CALL section_add_keyword(section, keyword)
1455 5520 : CALL keyword_release(keyword)
1456 :
1457 : CALL keyword_create(keyword, __LOCATION__, name="NH", &
1458 : description="Specifies the NH parameter in the M function.", &
1459 : usage="NH {real}", default_r_val=2.2_dp, &
1460 5520 : n_var=1)
1461 5520 : CALL section_add_keyword(section, keyword)
1462 5520 : CALL keyword_release(keyword)
1463 :
1464 : CALL keyword_create(keyword, __LOCATION__, name="pM", &
1465 : description="Sets the value of the numerator of the exponential factor"// &
1466 : " in the M function.", &
1467 : usage="pM {integer}", default_i_val=8, &
1468 5520 : n_var=1)
1469 5520 : CALL section_add_keyword(section, keyword)
1470 5520 : CALL keyword_release(keyword)
1471 :
1472 : CALL keyword_create(keyword, __LOCATION__, name="qM", &
1473 : description="Sets the value of the denominator of the exponential factor"// &
1474 : " in the M function.", &
1475 : usage="qM {integer}", default_i_val=16, &
1476 5520 : n_var=1)
1477 5520 : CALL section_add_keyword(section, keyword)
1478 5520 : CALL keyword_release(keyword)
1479 :
1480 : CALL keyword_create(keyword, __LOCATION__, name="NN", &
1481 : description="Specifies the NN parameter in the F function.", &
1482 : usage="NN {real}", default_r_val=1.5_dp, &
1483 5520 : n_var=1)
1484 5520 : CALL section_add_keyword(section, keyword)
1485 5520 : CALL keyword_release(keyword)
1486 :
1487 : CALL keyword_create(keyword, __LOCATION__, name="pF", &
1488 : description="Sets the value of the numerator of the exponential factor"// &
1489 : " in the F function.", &
1490 : usage="pF {integer}", default_i_val=8, &
1491 5520 : n_var=1)
1492 5520 : CALL section_add_keyword(section, keyword)
1493 5520 : CALL keyword_release(keyword)
1494 :
1495 : CALL keyword_create(keyword, __LOCATION__, name="qF", &
1496 : description="Sets the value of the denominator of the exponential factor"// &
1497 : " in the F function.", &
1498 : usage="qF {integer}", default_i_val=16, &
1499 5520 : n_var=1)
1500 5520 : CALL section_add_keyword(section, keyword)
1501 5520 : CALL keyword_release(keyword)
1502 :
1503 : CALL keyword_create(keyword, __LOCATION__, name="LAMBDA", &
1504 : description="Specify the LAMBDA parameter in the hydronium function.", &
1505 : usage="LAMBDA {real}", default_r_val=20.0_dp, &
1506 5520 : n_var=1)
1507 5520 : CALL section_add_keyword(section, keyword)
1508 5520 : CALL keyword_release(keyword)
1509 :
1510 5520 : END SUBROUTINE create_colvar_hydronium_dist_section
1511 :
1512 : ! **************************************************************************************************
1513 : !> \brief collective variables specifying the solvation of carboxylic acid;
1514 : !> distance between hydronium ion and acetate ion; Equation (2) in
1515 : !> Supplementary Information of J. Am. Chem. Soc.,128, 2006, 11318
1516 : !> \param section the section to be created
1517 : !> \author Dorothea Golze
1518 : ! **************************************************************************************************
1519 5520 : SUBROUTINE create_colvar_acid_hyd_dist_section(section)
1520 : TYPE(section_type), POINTER :: section
1521 :
1522 : TYPE(keyword_type), POINTER :: keyword
1523 :
1524 5520 : CPASSERT(.NOT. ASSOCIATED(section))
1525 : CALL section_create(section, __LOCATION__, name="ACID_HYDRONIUM_DISTANCE", &
1526 : description="Section to define the dissociation of a carboxylic acid in"// &
1527 : " water. Distance between hydronium ion and acetate ion. Equation (2)"// &
1528 : " in Supplementary Info of J. Am. Chem. Soc.,128, 2006, 11318.", &
1529 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1530 :
1531 5520 : NULLIFY (keyword)
1532 :
1533 : CALL keyword_create(keyword, __LOCATION__, name="OXYGENS_WATER", &
1534 : description="Specifies indexes of atoms building the coordination variable."// &
1535 : " Oxygens of the water molecules. ", &
1536 : usage="OXYGENS_WATER {integer} {integer} ..", repeats=.TRUE., &
1537 5520 : n_var=-1, type_of_var=integer_t)
1538 5520 : CALL section_add_keyword(section, keyword)
1539 5520 : CALL keyword_release(keyword)
1540 :
1541 : CALL keyword_create(keyword, __LOCATION__, name="OXYGENS_ACID", &
1542 : description="Specifies indexes of atoms building the coordination variable."// &
1543 : " Oxygens of the carboxyl groups.", &
1544 : usage="OXYGENS_ACID {integer} {integer} ..", repeats=.TRUE., &
1545 5520 : n_var=-1, type_of_var=integer_t)
1546 5520 : CALL section_add_keyword(section, keyword)
1547 5520 : CALL keyword_release(keyword)
1548 :
1549 : CALL keyword_create(keyword, __LOCATION__, name="HYDROGENS", &
1550 : description="Specifies indexes of atoms building the coordination variable."// &
1551 : " Hydrogens of the water molecules and of the carboxyl groups.", &
1552 : usage="HYDROGENS {integer} {integer} ..", repeats=.TRUE., &
1553 5520 : n_var=-1, type_of_var=integer_t)
1554 5520 : CALL section_add_keyword(section, keyword)
1555 5520 : CALL keyword_release(keyword)
1556 :
1557 : CALL keyword_create(keyword, __LOCATION__, name="pWOH", &
1558 : description="Sets the value of the numerator of the exponential factor"// &
1559 : " in the coordination function: number of hydrogens per water molecule.", &
1560 : usage="pWOH {integer}", default_i_val=8, &
1561 5520 : n_var=1)
1562 5520 : CALL section_add_keyword(section, keyword)
1563 5520 : CALL keyword_release(keyword)
1564 :
1565 : CALL keyword_create(keyword, __LOCATION__, name="qWOH", &
1566 : description="Sets the value of the denominator of the exponential factor"// &
1567 : " in the coordination function: number of hydrogens per water molecule.", &
1568 : usage="qWOH {integer}", default_i_val=16, &
1569 5520 : n_var=1)
1570 5520 : CALL section_add_keyword(section, keyword)
1571 5520 : CALL keyword_release(keyword)
1572 :
1573 : CALL keyword_create(keyword, __LOCATION__, name="RWOH", &
1574 : description="Specify the rc parameter in the coordination function:"// &
1575 : " number of hydrogens per water molecule.", &
1576 : usage="RWOH {real}", default_r_val=cp_unit_to_cp2k(value=2.4_dp, &
1577 5520 : unit_str="bohr"), unit_str="bohr", n_var=1)
1578 5520 : CALL section_add_keyword(section, keyword)
1579 5520 : CALL keyword_release(keyword)
1580 :
1581 : CALL keyword_create(keyword, __LOCATION__, name="pAOH", &
1582 : description="Sets the value of the numerator of the exponential factor"// &
1583 : " in the coordination function: number of hydrogens per carboxyl group.", &
1584 : usage="pAOH {integer}", default_i_val=6, &
1585 5520 : n_var=1)
1586 5520 : CALL section_add_keyword(section, keyword)
1587 5520 : CALL keyword_release(keyword)
1588 :
1589 : CALL keyword_create(keyword, __LOCATION__, name="qAOH", &
1590 : description="Sets the value of the denominator of the exponential factor"// &
1591 : " in the coordination function: number of hydrogens per carboxyl group.", &
1592 : usage="qAOH {integer}", default_i_val=14, &
1593 5520 : n_var=1)
1594 5520 : CALL section_add_keyword(section, keyword)
1595 5520 : CALL keyword_release(keyword)
1596 :
1597 : CALL keyword_create(keyword, __LOCATION__, name="RAOH", &
1598 : description="Specify the rc parameter in the coordination function:"// &
1599 : " number of hydrogens per carboxyl group.", &
1600 : usage="RAOH {real}", default_r_val=cp_unit_to_cp2k(value=2.4_dp, &
1601 5520 : unit_str="bohr"), unit_str="bohr", n_var=1)
1602 5520 : CALL section_add_keyword(section, keyword)
1603 5520 : CALL keyword_release(keyword)
1604 :
1605 : CALL keyword_create(keyword, __LOCATION__, name="pCUT", &
1606 : description="Sets the value of the numerator of the exponential factor"// &
1607 : " in the cutoff function.", &
1608 : usage="pCUT {integer}", default_i_val=6, &
1609 5520 : n_var=1)
1610 5520 : CALL section_add_keyword(section, keyword)
1611 5520 : CALL keyword_release(keyword)
1612 :
1613 : CALL keyword_create(keyword, __LOCATION__, name="qCUT", &
1614 : description="Sets the value of the denominator of the exponential factor"// &
1615 : " in the cutoff function.", &
1616 : usage="qCUT {integer}", default_i_val=12, &
1617 5520 : n_var=1)
1618 5520 : CALL section_add_keyword(section, keyword)
1619 5520 : CALL keyword_release(keyword)
1620 :
1621 : CALL keyword_create(keyword, __LOCATION__, name="NC", &
1622 : description="Specifies the NC parameter in the cutoff function.", &
1623 : usage="NC {real}", default_r_val=0.56_dp, &
1624 5520 : n_var=1)
1625 5520 : CALL section_add_keyword(section, keyword)
1626 5520 : CALL keyword_release(keyword)
1627 :
1628 : CALL keyword_create(keyword, __LOCATION__, name="LAMBDA", &
1629 : variants=["LAMBDA"], &
1630 : description="Specifies the LAMBDA parameter carboxylic acid function.", &
1631 : usage="LAMBDA {real}", default_r_val=20.0_dp, &
1632 11040 : n_var=1)
1633 5520 : CALL section_add_keyword(section, keyword)
1634 5520 : CALL keyword_release(keyword)
1635 :
1636 5520 : END SUBROUTINE create_colvar_acid_hyd_dist_section
1637 :
1638 : ! **************************************************************************************************
1639 : !> \brief collective variables specifying the solvation of carboxylic acid;
1640 : !> number of oxygens in the 1st shell of the hydronium; Equation (3) in
1641 : !> Supplementary Information of J. Am. Chem. Soc.,128, 2006, 11318
1642 : !> \param section the section to be created
1643 : !> \author Dorothea Golze
1644 : ! **************************************************************************************************
1645 5520 : SUBROUTINE create_colvar_acid_hyd_shell_section(section)
1646 : TYPE(section_type), POINTER :: section
1647 :
1648 : TYPE(keyword_type), POINTER :: keyword
1649 :
1650 5520 : CPASSERT(.NOT. ASSOCIATED(section))
1651 : CALL section_create(section, __LOCATION__, name="ACID_HYDRONIUM_SHELL", &
1652 : description="Section to define the dissociation of a carboxylic acid in"// &
1653 : " water. Number of oxygens in the 1st shell of the hydronium. Equation (3)"// &
1654 : " in Supplementary Info of J. Am. Chem. Soc.,128, 2006, 11318. Similar to"// &
1655 : " the HYDRONIUM colvar, but with modification for the acid.", &
1656 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1657 :
1658 5520 : NULLIFY (keyword)
1659 :
1660 : CALL keyword_create(keyword, __LOCATION__, name="OXYGENS_WATER", &
1661 : description="Specifies indexes of atoms building the coordination variable."// &
1662 : " Oxygens of the water molecules. ", &
1663 : usage="OXYGENS_WATER {integer} {integer} ..", repeats=.TRUE., &
1664 5520 : n_var=-1, type_of_var=integer_t)
1665 5520 : CALL section_add_keyword(section, keyword)
1666 5520 : CALL keyword_release(keyword)
1667 :
1668 : CALL keyword_create(keyword, __LOCATION__, name="OXYGENS_ACID", &
1669 : description="Specifies indexes of atoms building the coordination variable."// &
1670 : " Oxygens of the carboxyl groups.", &
1671 : usage="OXYGENS_ACID {integer} {integer} ..", repeats=.TRUE., &
1672 5520 : n_var=-1, type_of_var=integer_t)
1673 5520 : CALL section_add_keyword(section, keyword)
1674 5520 : CALL keyword_release(keyword)
1675 :
1676 : CALL keyword_create(keyword, __LOCATION__, name="HYDROGENS", &
1677 : description="Specifies indexes of atoms building the coordination variable."// &
1678 : " Hydrogens of the water molecules and of the carboxyl groups.", &
1679 : usage="HYDROGENS {integer} {integer} ..", repeats=.TRUE., &
1680 5520 : n_var=-1, type_of_var=integer_t)
1681 5520 : CALL section_add_keyword(section, keyword)
1682 5520 : CALL keyword_release(keyword)
1683 :
1684 : CALL keyword_create(keyword, __LOCATION__, name="pWOH", &
1685 : description="Sets the value of the numerator of the exponential factor"// &
1686 : " in the coordination function: number of hydrogens per water molecule.", &
1687 : usage="pWOH {integer}", default_i_val=8, &
1688 5520 : n_var=1)
1689 5520 : CALL section_add_keyword(section, keyword)
1690 5520 : CALL keyword_release(keyword)
1691 :
1692 : CALL keyword_create(keyword, __LOCATION__, name="qWOH", &
1693 : description="Sets the value of the denominator of the exponential factor"// &
1694 : " in the coordination function: number of hydrogens per water molecule.", &
1695 : usage="qWOH {integer}", default_i_val=16, &
1696 5520 : n_var=1)
1697 5520 : CALL section_add_keyword(section, keyword)
1698 5520 : CALL keyword_release(keyword)
1699 :
1700 : CALL keyword_create(keyword, __LOCATION__, name="RWOH", &
1701 : description="Specifies the rc parameter in the coordination function:"// &
1702 : " number of hydrogens per water molecule.", &
1703 : usage="RWOH {real}", default_r_val=cp_unit_to_cp2k(value=2.4_dp, &
1704 5520 : unit_str="bohr"), unit_str="bohr", n_var=1)
1705 5520 : CALL section_add_keyword(section, keyword)
1706 5520 : CALL keyword_release(keyword)
1707 :
1708 : CALL keyword_create(keyword, __LOCATION__, name="pAOH", &
1709 : description="Sets the value of the numerator of the exponential factor"// &
1710 : " in the coordination function: number of hydrogens per carboxyl group.", &
1711 : usage="pAOH {integer}", default_i_val=6, &
1712 5520 : n_var=1)
1713 5520 : CALL section_add_keyword(section, keyword)
1714 5520 : CALL keyword_release(keyword)
1715 :
1716 : CALL keyword_create(keyword, __LOCATION__, name="qAOH", &
1717 : description="Sets the value of the denominator of the exponential factor"// &
1718 : " in the coordination function: number of hydrogens per carboxyl group.", &
1719 : usage="qAOH {integer}", default_i_val=14, &
1720 5520 : n_var=1)
1721 5520 : CALL section_add_keyword(section, keyword)
1722 5520 : CALL keyword_release(keyword)
1723 :
1724 : CALL keyword_create(keyword, __LOCATION__, name="RAOH", &
1725 : description="Specifies the rc parameter in the coordination function:"// &
1726 : " number of hydrogens per carboxyl group.", &
1727 : usage="RAOH {real}", default_r_val=cp_unit_to_cp2k(value=2.4_dp, &
1728 5520 : unit_str="bohr"), unit_str="bohr", n_var=1)
1729 5520 : CALL section_add_keyword(section, keyword)
1730 5520 : CALL keyword_release(keyword)
1731 :
1732 : CALL keyword_create(keyword, __LOCATION__, name="pOO", &
1733 : description="Sets the value of the numerator of the exponential factor"// &
1734 : " in the coordination function: number of oxygens per water oxygen.", &
1735 : usage="pOO {integer}", default_i_val=6, &
1736 5520 : n_var=1)
1737 5520 : CALL section_add_keyword(section, keyword)
1738 5520 : CALL keyword_release(keyword)
1739 :
1740 : CALL keyword_create(keyword, __LOCATION__, name="qOO", &
1741 : description="Sets the value of the denominator of the exponential factor"// &
1742 : " in the coordination function: number of oxygens per water oxygen.", &
1743 : usage="qOO {integer}", default_i_val=12, &
1744 5520 : n_var=1)
1745 5520 : CALL section_add_keyword(section, keyword)
1746 5520 : CALL keyword_release(keyword)
1747 :
1748 : CALL keyword_create(keyword, __LOCATION__, name="ROO", &
1749 : description="Specifies the rc parameter in the coordination function:"// &
1750 : " number of oxygens per water oxygen.", &
1751 : usage="ROO {real}", default_r_val=cp_unit_to_cp2k(value=5.5_dp, &
1752 5520 : unit_str="bohr"), unit_str="bohr", n_var=1)
1753 5520 : CALL section_add_keyword(section, keyword)
1754 5520 : CALL keyword_release(keyword)
1755 :
1756 : CALL keyword_create(keyword, __LOCATION__, name="pM", &
1757 : description="Sets the value of the numerator of the exponential factor"// &
1758 : " in the M function.", &
1759 : usage="pM {integer}", default_i_val=8, &
1760 5520 : n_var=1)
1761 5520 : CALL section_add_keyword(section, keyword)
1762 5520 : CALL keyword_release(keyword)
1763 :
1764 : CALL keyword_create(keyword, __LOCATION__, name="qM", &
1765 : description="Sets the value of the denominator of the exponential factor"// &
1766 : " in the M function.", &
1767 : usage="qM {integer}", default_i_val=16, &
1768 5520 : n_var=1)
1769 5520 : CALL section_add_keyword(section, keyword)
1770 5520 : CALL keyword_release(keyword)
1771 :
1772 : CALL keyword_create(keyword, __LOCATION__, name="NH", &
1773 : description="Specifies the NH parameter in the M function.", &
1774 : usage="NH {real}", default_r_val=2.2_dp, &
1775 5520 : n_var=1)
1776 5520 : CALL section_add_keyword(section, keyword)
1777 5520 : CALL keyword_release(keyword)
1778 :
1779 : CALL keyword_create(keyword, __LOCATION__, name="pCUT", &
1780 : description="Sets the value of the numerator of the exponential factor"// &
1781 : " in the cutoff function.", &
1782 : usage="pCUT {integer}", default_i_val=6, &
1783 5520 : n_var=1)
1784 5520 : CALL section_add_keyword(section, keyword)
1785 5520 : CALL keyword_release(keyword)
1786 :
1787 : CALL keyword_create(keyword, __LOCATION__, name="qCUT", &
1788 : description="Sets the value of the denominator of the exponential factor"// &
1789 : " in the cutoff function.", &
1790 : usage="qCUT {integer}", default_i_val=12, &
1791 5520 : n_var=1)
1792 5520 : CALL section_add_keyword(section, keyword)
1793 5520 : CALL keyword_release(keyword)
1794 :
1795 : CALL keyword_create(keyword, __LOCATION__, name="NC", &
1796 : description="Specifies the NC parameter in the cutoff function.", &
1797 : usage="NC {real}", default_r_val=0.9_dp, &
1798 5520 : n_var=1)
1799 5520 : CALL section_add_keyword(section, keyword)
1800 5520 : CALL keyword_release(keyword)
1801 :
1802 : CALL keyword_create(keyword, __LOCATION__, name="LAMBDA", &
1803 : variants=["LAMBDA"], &
1804 : description="Specifies the LAMBDA parameter carboxylic acid function.", &
1805 : usage="LAMBDA {real}", default_r_val=10.0_dp, &
1806 11040 : n_var=1)
1807 5520 : CALL section_add_keyword(section, keyword)
1808 5520 : CALL keyword_release(keyword)
1809 :
1810 5520 : END SUBROUTINE create_colvar_acid_hyd_shell_section
1811 :
1812 : ! **************************************************************************************************
1813 : !> \brief ...
1814 : !> \param section ...
1815 : ! **************************************************************************************************
1816 5520 : SUBROUTINE create_colvar_rmsd_section(section)
1817 : TYPE(section_type), POINTER :: section
1818 :
1819 : TYPE(keyword_type), POINTER :: keyword
1820 : TYPE(section_type), POINTER :: subsection, subsubsection
1821 :
1822 5520 : CPASSERT(.NOT. ASSOCIATED(section))
1823 : CALL section_create(section, __LOCATION__, name="rmsd", &
1824 : description="Section to define a CV as function of RMSD computed with respect to"// &
1825 : " given reference configurations. For 2 configurations the colvar is equal to:"// &
1826 : " ss = (RMSDA-RMSDB)/(RMSDA+RMSDB), while if only 1 configuration is given, then the"// &
1827 : " colvar is just the RMSD from that frame.", &
1828 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1829 :
1830 5520 : NULLIFY (keyword, subsection, subsubsection)
1831 : CALL keyword_create(keyword, __LOCATION__, name="SUBSET_TYPE", &
1832 : description="Define the subsytem used to compute the RMSD. With ALL the displacements"// &
1833 : " are mass-weighted, with LIST all weights are set to 1,"// &
1834 : " with WEIGHT_LIST a list of weights is expected from input.", &
1835 : usage="SUBSET_TYPE ALL", &
1836 : enum_c_vals=s2a("ALL", "LIST", "WEIGHT_LIST"), &
1837 : enum_i_vals=[rmsd_all, rmsd_list, rmsd_weightlist], &
1838 5520 : default_i_val=rmsd_all)
1839 5520 : CALL section_add_keyword(section, keyword)
1840 5520 : CALL keyword_release(keyword)
1841 :
1842 : CALL keyword_create(keyword, __LOCATION__, name="ALIGN_FRAMES", &
1843 : description="Whether the reference frames should be aligned to minimize the RMSD", &
1844 : usage="ALIGN_FRAMES", &
1845 5520 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
1846 5520 : CALL section_add_keyword(section, keyword)
1847 5520 : CALL keyword_release(keyword)
1848 :
1849 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
1850 : description="Specify indexes of atoms building the subset. ", &
1851 : usage="ATOMS {integer} {integer} ..", repeats=.TRUE., &
1852 5520 : n_var=-1, type_of_var=integer_t)
1853 5520 : CALL section_add_keyword(section, keyword)
1854 5520 : CALL keyword_release(keyword)
1855 :
1856 : CALL keyword_create(keyword, __LOCATION__, name="WEIGHTS", &
1857 : description="Specify weights of atoms building the subset. It is used only with WEIGHT_LIST ", &
1858 : usage="weightS {real} {real} ..", repeats=.TRUE., &
1859 5520 : n_var=-1, type_of_var=real_t)
1860 5520 : CALL section_add_keyword(section, keyword)
1861 5520 : CALL keyword_release(keyword)
1862 :
1863 : CALL section_create(subsection, __LOCATION__, name="FRAME", &
1864 : description="Specify coordinates of the frame (number of frames can be either 1 or 2)", &
1865 5520 : repeats=.TRUE.)
1866 :
1867 : CALL keyword_create(keyword, __LOCATION__, name="COORD_FILE_NAME", &
1868 : description="Name of the xyz file with coordinates (alternative to &COORD section)", &
1869 : usage="COORD_FILE_NAME <CHAR>", &
1870 5520 : default_lc_val="")
1871 5520 : CALL section_add_keyword(subsection, keyword)
1872 5520 : CALL keyword_release(keyword)
1873 :
1874 5520 : CALL create_coord_section_cv(subsubsection, "RMSD")
1875 5520 : CALL section_add_subsection(subsection, subsubsection)
1876 5520 : CALL section_release(subsubsection)
1877 :
1878 5520 : CALL section_add_subsection(section, subsection)
1879 5520 : CALL section_release(subsection)
1880 :
1881 5520 : END SUBROUTINE create_colvar_rmsd_section
1882 :
1883 : ! **************************************************************************************************
1884 : !> \brief collective variables specifying the space orthogonal to the reaction path
1885 : !> in the space spanned by the involved collective coordinates
1886 : !> \param section the section to be created
1887 : !> \author fschiff
1888 : ! **************************************************************************************************
1889 1380 : SUBROUTINE create_colvar_rpath_section(section)
1890 : TYPE(section_type), POINTER :: section
1891 :
1892 1380 : CPASSERT(.NOT. ASSOCIATED(section))
1893 : CALL section_create(section, __LOCATION__, name="REACTION_PATH", &
1894 : description="Section defining a one dimensional reaction path in an Q-dimensional space of colvars. "// &
1895 : "Constraining this colvar, allows to sample the space orthogonal to the reaction path, "// &
1896 : "both in the Q-dimensional colvar and 3N-Q remaining coordinates. "// &
1897 : "For the details of the function see cited literature.", &
1898 : n_keywords=1, n_subsections=0, repeats=.FALSE., &
1899 2760 : citations=[Branduardi2007])
1900 :
1901 1380 : CALL keywords_colvar_path(section)
1902 1380 : END SUBROUTINE create_colvar_rpath_section
1903 :
1904 : ! **************************************************************************************************
1905 : !> \brief Distance from reaction path
1906 : !> \param section the section to be created
1907 : !> \author 01.2010
1908 : ! **************************************************************************************************
1909 1380 : SUBROUTINE create_colvar_dpath_section(section)
1910 : TYPE(section_type), POINTER :: section
1911 :
1912 1380 : CPASSERT(.NOT. ASSOCIATED(section))
1913 : CALL section_create(section, __LOCATION__, name="DISTANCE_FROM_PATH", &
1914 : description="Section defining the distance from a one dimensional reaction "// &
1915 : "path in an Q-dimensional space of colvars. "// &
1916 : "Constraining this colvar, allows to sample the space equidistant to the reaction path, "// &
1917 : "both in the Q-dimensional colvar and 3N-Q remaining coordinates. "// &
1918 : "For the details of the function see cited literature.", &
1919 : n_keywords=1, n_subsections=0, repeats=.FALSE., &
1920 2760 : citations=[Branduardi2007])
1921 :
1922 1380 : CALL keywords_colvar_path(section)
1923 1380 : END SUBROUTINE create_colvar_dpath_section
1924 :
1925 : ! **************************************************************************************************
1926 : !> \brief Section describinf keywords for both reaction path and distance from reaction path
1927 : !> \param section the section to be created
1928 : !> \author 01.2010
1929 : ! **************************************************************************************************
1930 2760 : SUBROUTINE keywords_colvar_path(section)
1931 :
1932 : TYPE(section_type), POINTER :: section
1933 :
1934 : TYPE(keyword_type), POINTER :: keyword
1935 : TYPE(section_type), POINTER :: print_key, subsection, subsubsection
1936 :
1937 2760 : NULLIFY (keyword, subsection, subsubsection, print_key)
1938 2760 : CALL create_colvar_section(subsection, skip_recursive_colvar=.TRUE.)
1939 2760 : CALL section_add_subsection(section, subsection)
1940 2760 : CALL section_release(subsection)
1941 :
1942 : CALL keyword_create(keyword, __LOCATION__, name="DISTANCES_RMSD", &
1943 : description=" ", &
1944 : usage="DISTANCES_RMSD T", &
1945 2760 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
1946 2760 : CALL section_add_keyword(section, keyword)
1947 2760 : CALL keyword_release(keyword)
1948 :
1949 : CALL keyword_create(keyword, __LOCATION__, name="RMSD", &
1950 : description=" ", &
1951 : usage="RMSD T", &
1952 2760 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
1953 2760 : CALL section_add_keyword(section, keyword)
1954 2760 : CALL keyword_release(keyword)
1955 :
1956 : CALL keyword_create(keyword, __LOCATION__, name="SUBSET_TYPE", &
1957 : description="Define the subsytem used to compute the RMSD", &
1958 : usage="SUBSET_TYPE ALL", &
1959 : enum_c_vals=s2a("ALL", "LIST"), &
1960 : enum_i_vals=[rmsd_all, rmsd_list], &
1961 2760 : default_i_val=rmsd_all)
1962 2760 : CALL section_add_keyword(section, keyword)
1963 2760 : CALL keyword_release(keyword)
1964 :
1965 : CALL keyword_create(keyword, __LOCATION__, name="ALIGN_FRAMES", &
1966 : description="Whether the reference frames should be aligned to minimize the RMSD", &
1967 : usage="ALIGN_FRAMES", &
1968 2760 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
1969 2760 : CALL section_add_keyword(section, keyword)
1970 2760 : CALL keyword_release(keyword)
1971 :
1972 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
1973 : description="Specify indexes of atoms building the subset. ", &
1974 : usage="ATOMS {integer} {integer} ..", repeats=.TRUE., &
1975 2760 : n_var=-1, type_of_var=integer_t)
1976 2760 : CALL section_add_keyword(section, keyword)
1977 2760 : CALL keyword_release(keyword)
1978 :
1979 : CALL section_create(subsection, __LOCATION__, name="FRAME", &
1980 : description="Specify coordinates of the frame", &
1981 2760 : repeats=.TRUE.)
1982 :
1983 : CALL keyword_create(keyword, __LOCATION__, name="COORD_FILE_NAME", &
1984 : description="Name of the xyz file with coordinates (alternative to &COORD section)", &
1985 : usage="COORD_FILE_NAME <CHAR>", &
1986 2760 : default_lc_val="")
1987 2760 : CALL section_add_keyword(subsection, keyword)
1988 2760 : CALL keyword_release(keyword)
1989 :
1990 2760 : CALL create_coord_section_cv(subsubsection, "RMSD")
1991 2760 : CALL section_add_subsection(subsection, subsubsection)
1992 2760 : CALL section_release(subsubsection)
1993 :
1994 2760 : CALL section_add_subsection(section, subsection)
1995 2760 : CALL section_release(subsection)
1996 :
1997 : CALL keyword_create(keyword, __LOCATION__, name="FUNCTION", &
1998 : description="Specifies the ith element of the vector valued function that defines the reaction path. "// &
1999 : "This keyword needs to repeat exactly Q times, and the order must match the order of the colvars. "// &
2000 : "The VARIABLE (e.g. T) which parametrises the curve can be used as the target of a constraint.", &
2001 : usage="FUNCTION (sin(T+2)+2*T)", type_of_var=lchar_t, &
2002 2760 : n_var=1, default_lc_val="0", repeats=.TRUE.)
2003 2760 : CALL section_add_keyword(section, keyword)
2004 2760 : CALL keyword_release(keyword)
2005 :
2006 : CALL keyword_create(keyword, __LOCATION__, name="VARIABLE", &
2007 : description="Specifies the name of the variable that parametrises the FUNCTION "// &
2008 : "defining the reaction path.", &
2009 : usage="VARIABLE T", type_of_var=char_t, &
2010 2760 : n_var=1, repeats=.FALSE.)
2011 2760 : CALL section_add_keyword(section, keyword)
2012 2760 : CALL keyword_release(keyword)
2013 :
2014 : CALL keyword_create( &
2015 : keyword, __LOCATION__, name="LAMBDA", &
2016 : description="Specifies the exponent of the Gaussian used in the integral representation of the colvar. "// &
2017 : "The shape of the space orthogonal to the reaction path is defined by this choice. "// &
2018 : "In the limit of large values, it is given by the plane orthogonal to the path. "// &
2019 : "In practice, modest values are required for stable numerical integration.", &
2020 : usage="LAMBDA {real}", &
2021 2760 : type_of_var=real_t, default_r_val=5.0_dp)
2022 2760 : CALL section_add_keyword(section, keyword)
2023 2760 : CALL keyword_release(keyword)
2024 :
2025 : CALL keyword_create(keyword, __LOCATION__, name="STEP_SIZE", &
2026 : description="Step size in the numerical integration, "// &
2027 : "a few thousand points are common, and the proper number also depends on LAMBDA.", &
2028 : usage="STEP_SIZE {real}", &
2029 2760 : type_of_var=real_t, default_r_val=0.01_dp)
2030 2760 : CALL section_add_keyword(section, keyword)
2031 2760 : CALL keyword_release(keyword)
2032 :
2033 : CALL keyword_create(keyword, __LOCATION__, name="RANGE", &
2034 : description="The range of VARIABLE used for the parametrisation.", &
2035 : usage="RANGE <REAL> <REAL>", &
2036 2760 : n_var=2, type_of_var=real_t)
2037 2760 : CALL section_add_keyword(section, keyword)
2038 2760 : CALL keyword_release(keyword)
2039 :
2040 : CALL cp_print_key_section_create( &
2041 : print_key, __LOCATION__, name="MAP", &
2042 : description="Activating this print key will print once a file with the values of the FUNCTION on a grid "// &
2043 : "of COLVAR values in a specified range. "// &
2044 : "GRID_SPACING and RANGE for every COLVAR has to be specified again in the same order as they are in the input.", &
2045 2760 : print_level=high_print_level, filename="PATH")
2046 :
2047 : CALL keyword_create(keyword, __LOCATION__, name="RANGE", &
2048 : description="The range of of the grid of the COLVAR.", &
2049 : usage="RANGE <REAL> <REAL>", &
2050 2760 : n_var=2, type_of_var=real_t, repeats=.TRUE.)
2051 2760 : CALL section_add_keyword(print_key, keyword)
2052 2760 : CALL keyword_release(keyword)
2053 :
2054 : CALL keyword_create(keyword, __LOCATION__, name="GRID_SPACING", &
2055 : description="Distance between two gridpoints for the grid on the COLVAR", &
2056 : usage="GRID_SPACING {real}", repeats=.TRUE., &
2057 2760 : type_of_var=real_t, default_r_val=0.01_dp)
2058 2760 : CALL section_add_keyword(print_key, keyword)
2059 2760 : CALL keyword_release(keyword)
2060 :
2061 2760 : CALL section_add_subsection(section, print_key)
2062 2760 : CALL section_release(print_key)
2063 :
2064 2760 : END SUBROUTINE keywords_colvar_path
2065 :
2066 : ! **************************************************************************************************
2067 : !> \brief Colvar allowing a combination of COLVARS
2068 : !> \param section the section to be created
2069 : !> \author Teodoro Laino [tlaino] - 12.2008
2070 : ! **************************************************************************************************
2071 1380 : SUBROUTINE create_colvar_comb_section(section)
2072 : TYPE(section_type), POINTER :: section
2073 :
2074 : TYPE(keyword_type), POINTER :: keyword
2075 : TYPE(section_type), POINTER :: subsection
2076 :
2077 1380 : CPASSERT(.NOT. ASSOCIATED(section))
2078 : CALL section_create(section, __LOCATION__, name="COMBINE_COLVAR", &
2079 : description="Allows the possibility to combine several COLVARs into one COLVAR "// &
2080 : "with a generic function. "//docf(), &
2081 1380 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
2082 :
2083 1380 : NULLIFY (keyword, subsection)
2084 1380 : CALL create_colvar_section(subsection, skip_recursive_colvar=.TRUE.)
2085 1380 : CALL section_add_subsection(section, subsection)
2086 1380 : CALL section_release(subsection)
2087 :
2088 : CALL keyword_create(keyword, __LOCATION__, name="FUNCTION", &
2089 : description="Specifies the function used to combine different COLVARs into one.", &
2090 : ! **************************************************************************************************
2091 : !> \brief ...
2092 : !> \param CV1^2 ...
2093 : !> \param CV2^2 ...
2094 : !> \param " ...
2095 : !> \param type_of_var=lchar_t ...
2096 : !> \param n_var=1 ...
2097 : !> \param error=error ...
2098 : ! **************************************************************************************************
2099 : usage="FUNCTION SQRT(CV1^2+CV2^2)", type_of_var=lchar_t, &
2100 1380 : n_var=1)
2101 1380 : CALL section_add_keyword(section, keyword)
2102 1380 : CALL keyword_release(keyword)
2103 :
2104 : CALL keyword_create(keyword, __LOCATION__, name="VARIABLES", &
2105 : description="Specifies the name of the variable that parametrises the FUNCTION "// &
2106 : "defining how COLVARS should be combined. The matching follows the same order of the "// &
2107 : "COLVARS definition in the input file.", &
2108 1380 : usage="VARIABLES CV1 CV2 CV3", type_of_var=char_t, n_var=-1, repeats=.FALSE.)
2109 1380 : CALL section_add_keyword(section, keyword)
2110 1380 : CALL keyword_release(keyword)
2111 :
2112 : CALL keyword_create(keyword, __LOCATION__, name="PARAMETERS", &
2113 : description="Defines the parameters of the functional form", &
2114 : usage="PARAMETERS a b D", type_of_var=char_t, &
2115 1380 : n_var=-1, repeats=.TRUE.)
2116 1380 : CALL section_add_keyword(section, keyword)
2117 1380 : CALL keyword_release(keyword)
2118 :
2119 : CALL keyword_create(keyword, __LOCATION__, name="VALUES", &
2120 : description="Defines the values of parameter of the functional form", &
2121 : usage="VALUES ", type_of_var=real_t, &
2122 1380 : n_var=-1, repeats=.TRUE., unit_str="internal_cp2k")
2123 1380 : CALL section_add_keyword(section, keyword)
2124 1380 : CALL keyword_release(keyword)
2125 :
2126 : CALL keyword_create(keyword, __LOCATION__, name="DX", &
2127 : description="Parameter used for computing the derivative of the combination "// &
2128 : "of COLVARs with the Ridders' method.", &
2129 1380 : usage="DX <REAL>", default_r_val=0.1_dp, unit_str="bohr")
2130 1380 : CALL section_add_keyword(section, keyword)
2131 1380 : CALL keyword_release(keyword)
2132 :
2133 : CALL keyword_create(keyword, __LOCATION__, name="ERROR_LIMIT", &
2134 : description="Checks that the error in computing the derivative is not larger than "// &
2135 : "the value set; in case error is larger a warning message is printed.", &
2136 1380 : usage="ERROR_LIMIT <REAL>", default_r_val=1.0E-12_dp)
2137 1380 : CALL section_add_keyword(section, keyword)
2138 1380 : CALL keyword_release(keyword)
2139 :
2140 1380 : END SUBROUTINE create_colvar_comb_section
2141 :
2142 : ! **************************************************************************************************
2143 : !> \brief Creates the coord section
2144 : !> \param section the section to create
2145 : !> \param name ...
2146 : !> \author teo
2147 : ! **************************************************************************************************
2148 8280 : SUBROUTINE create_coord_section_cv(section, name)
2149 : TYPE(section_type), POINTER :: section
2150 : CHARACTER(LEN=*), INTENT(IN) :: name
2151 :
2152 : TYPE(keyword_type), POINTER :: keyword
2153 :
2154 8280 : CPASSERT(.NOT. ASSOCIATED(section))
2155 : CALL section_create(section, __LOCATION__, name="coord", &
2156 : description="The positions for "//TRIM(name)//" used for restart", &
2157 8280 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
2158 8280 : NULLIFY (keyword)
2159 :
2160 : CALL keyword_create(keyword, __LOCATION__, name="_DEFAULT_KEYWORD_", &
2161 : description="Specify positions of the system", repeats=.TRUE., &
2162 8280 : usage="{Real} ...", type_of_var=real_t, n_var=-1)
2163 8280 : CALL section_add_keyword(section, keyword)
2164 8280 : CALL keyword_release(keyword)
2165 :
2166 8280 : END SUBROUTINE create_coord_section_cv
2167 :
2168 : ! **************************************************************************************************
2169 : !> \brief collective variables specifying h bonds
2170 : !> \param section the section to be created
2171 : !> \author alin m elena
2172 : ! **************************************************************************************************
2173 5520 : SUBROUTINE create_colvar_wc_section(section)
2174 : TYPE(section_type), POINTER :: section
2175 :
2176 : TYPE(keyword_type), POINTER :: keyword
2177 : TYPE(section_type), POINTER :: subsection
2178 :
2179 5520 : CPASSERT(.NOT. ASSOCIATED(section))
2180 : CALL section_create(section, __LOCATION__, name="wc", &
2181 : description="Section to define the hbond wannier centre as a collective variables.", &
2182 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
2183 5520 : NULLIFY (keyword, subsection)
2184 :
2185 : CALL keyword_create(keyword, __LOCATION__, name="RCUT", &
2186 : description="Parameter used for computing the cutoff radius for searching "// &
2187 : "the wannier centres around an atom", &
2188 : usage="RCUT <REAL>", default_r_val=0.529177208590000_dp, unit_str="angstrom", &
2189 5520 : type_of_var=real_t, repeats=.FALSE.)
2190 5520 : CALL section_add_keyword(section, keyword)
2191 5520 : CALL keyword_release(keyword)
2192 :
2193 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
2194 : variants=["POINTS"], &
2195 : description="Specifies the indexes of atoms/points defining the bond (Od, H, Oa).", &
2196 : usage="ATOMS {integer} {integer} {integer}", &
2197 11040 : n_var=3, type_of_var=integer_t, repeats=.TRUE.)
2198 5520 : CALL section_add_keyword(section, keyword)
2199 5520 : CALL keyword_release(keyword)
2200 :
2201 : ! Must be present in each colvar and handled properly
2202 5520 : CALL create_point_section(subsection)
2203 5520 : CALL section_add_subsection(section, subsection)
2204 5520 : CALL section_release(subsection)
2205 :
2206 5520 : END SUBROUTINE create_colvar_wc_section
2207 :
2208 : ! **************************************************************************************************
2209 : !> \brief collective variables specifying h bonds= wire
2210 : !> \param section the section to be created
2211 : !> \author alin m elena
2212 : ! **************************************************************************************************
2213 5520 : SUBROUTINE create_colvar_hbp_section(section)
2214 : TYPE(section_type), POINTER :: section
2215 :
2216 : TYPE(keyword_type), POINTER :: keyword
2217 : TYPE(section_type), POINTER :: subsection
2218 :
2219 5520 : CPASSERT(.NOT. ASSOCIATED(section))
2220 : CALL section_create(section, __LOCATION__, name="hbp", &
2221 : description="Section to define the hbond wannier centre as a collective variables.", &
2222 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
2223 5520 : NULLIFY (keyword, subsection)
2224 :
2225 : CALL keyword_create(keyword, __LOCATION__, name="RCUT", &
2226 : description="Parameter used for computing the cutoff radius for searching "// &
2227 : "the wannier centres around an atom", &
2228 : usage="RCUT <REAL>", default_r_val=0.529177208590000_dp, unit_str="angstrom", &
2229 5520 : type_of_var=real_t, repeats=.FALSE.)
2230 5520 : CALL section_add_keyword(section, keyword)
2231 5520 : CALL keyword_release(keyword)
2232 :
2233 : CALL keyword_create(keyword, __LOCATION__, name="SHIFT", &
2234 : description="Parameter used for shifting each term in the sum ", &
2235 : usage="SHIFT <REAL>", default_r_val=0.5_dp, &
2236 5520 : type_of_var=real_t, repeats=.FALSE.)
2237 5520 : CALL section_add_keyword(section, keyword)
2238 5520 : CALL keyword_release(keyword)
2239 :
2240 : CALL keyword_create(keyword, __LOCATION__, name="NPOINTS", &
2241 : description="The number of points in the path", &
2242 : usage="NPOINTS {integer}", default_i_val=-1, &
2243 5520 : n_var=1, type_of_var=integer_t, repeats=.FALSE.)
2244 5520 : CALL section_add_keyword(section, keyword)
2245 5520 : CALL keyword_release(keyword)
2246 :
2247 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
2248 : variants=["POINTS"], &
2249 : description="Specifies the indexes of atoms/points defining the bond (Od, H, Oa).", &
2250 : usage="ATOMS {integer} {integer} {integer}", &
2251 11040 : n_var=3, type_of_var=integer_t, repeats=.TRUE.)
2252 5520 : CALL section_add_keyword(section, keyword)
2253 5520 : CALL keyword_release(keyword)
2254 :
2255 : ! Must be present in each colvar and handled properly
2256 5520 : CALL create_point_section(subsection)
2257 5520 : CALL section_add_subsection(section, subsection)
2258 5520 : CALL section_release(subsection)
2259 :
2260 5520 : END SUBROUTINE create_colvar_hbp_section
2261 :
2262 : ! **************************************************************************************************
2263 : !> \brief collective variables specifying ring puckering
2264 : !> \brief D. Cremer and J.A. Pople, JACS 97 1354 (1975)
2265 : !> \param section the section to be created
2266 : !> \author Marcel Baer
2267 : ! **************************************************************************************************
2268 5520 : SUBROUTINE create_colvar_ring_puckering_section(section)
2269 : TYPE(section_type), POINTER :: section
2270 :
2271 : TYPE(keyword_type), POINTER :: keyword
2272 : TYPE(section_type), POINTER :: subsection
2273 :
2274 5520 : CPASSERT(.NOT. ASSOCIATED(section))
2275 : CALL section_create(section, __LOCATION__, name="RING_PUCKERING", &
2276 : description="Section to define general ring puckering collective variables.", &
2277 5520 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
2278 :
2279 5520 : NULLIFY (keyword, subsection)
2280 :
2281 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
2282 : variants=["POINTS"], &
2283 : description="Specifies the indexes of atoms/points defining the ring. "// &
2284 : "At least 4 Atoms are needed.", &
2285 : usage="ATOMS {integer} {integer} {integer} ..", &
2286 11040 : n_var=-1, type_of_var=integer_t)
2287 5520 : CALL section_add_keyword(section, keyword)
2288 5520 : CALL keyword_release(keyword)
2289 :
2290 : CALL keyword_create(keyword, __LOCATION__, name="COORDINATE", &
2291 : description="Indicate the coordinate to be used. Follow the Cremer-Pople definition for a N ring. "// &
2292 : "0 is the total puckering variable Q, "// &
2293 : "2..[N/2] are puckering coordinates. "// &
2294 : "-2..-[N/2-1] are puckering angles.", &
2295 : usage="COORDINATE {integer}", default_i_val=0, &
2296 5520 : n_var=1)
2297 5520 : CALL section_add_keyword(section, keyword)
2298 5520 : CALL keyword_release(keyword)
2299 :
2300 : ! Must be present in each colvar and handled properly
2301 5520 : CALL create_point_section(subsection)
2302 5520 : CALL section_add_subsection(section, subsection)
2303 5520 : CALL section_release(subsection)
2304 :
2305 5520 : END SUBROUTINE create_colvar_ring_puckering_section
2306 :
2307 : ! **************************************************************************************************
2308 : !> \brief Creates the VORONOIIPZ collective variable input section
2309 : !> \param section the section to create
2310 : ! **************************************************************************************************
2311 5520 : SUBROUTINE create_voronoiipz_section(section)
2312 : TYPE(section_type), POINTER :: section
2313 :
2314 : TYPE(keyword_type), POINTER :: keyword
2315 :
2316 5520 : CPASSERT(.NOT. ASSOCIATED(section))
2317 5520 : NULLIFY (keyword)
2318 : CALL section_create(section, __LOCATION__, name="VORONOIIPZ", &
2319 : description="Absolute location of a hydronium ion along a Cartesian axis, "// &
2320 : "based on continuous Voronoi weights.", &
2321 11040 : citations=[Zhang2025], n_subsections=0, repeats=.FALSE.)
2322 :
2323 : CALL keyword_create(keyword, __LOCATION__, name="LAMBDA", &
2324 : description="Exponent in the Voronoi weight exp(LAMBDA*r). "// &
2325 : "Negative values assign each hydrogen predominantly to nearby oxygen atoms.", &
2326 : usage="LAMBDA [angstrom^-1] -8.0", type_of_var=real_t, &
2327 : default_r_val=cp_unit_to_cp2k(value=-8.0_dp, unit_str="angstrom^-1"), &
2328 5520 : unit_str="angstrom^-1", n_var=1)
2329 5520 : CALL section_add_keyword(section, keyword)
2330 5520 : CALL keyword_release(keyword)
2331 :
2332 : CALL keyword_create(keyword, __LOCATION__, name="ZMID", &
2333 : description="Coordinate of the reference plane along the selected axis.", &
2334 : usage="ZMID [angstrom] 0.0", type_of_var=real_t, default_r_val=0.0_dp, &
2335 5520 : unit_str="angstrom", n_var=1)
2336 5520 : CALL section_add_keyword(section, keyword)
2337 5520 : CALL keyword_release(keyword)
2338 :
2339 : CALL keyword_create(keyword, __LOCATION__, name="ZIDX", &
2340 : description="Cartesian direction used for the ion location: 1=X, 2=Y, 3=Z.", &
2341 5520 : usage="ZIDX 3", type_of_var=integer_t, default_i_val=3, n_var=1)
2342 5520 : CALL section_add_keyword(section, keyword)
2343 5520 : CALL keyword_release(keyword)
2344 :
2345 : CALL keyword_create(keyword, __LOCATION__, name="D_0", &
2346 : description="Reference coordination of the non-reactive GROUPA atoms.", &
2347 5520 : usage="D_0 2.0", type_of_var=real_t, default_r_val=2.0_dp, n_var=1)
2348 5520 : CALL section_add_keyword(section, keyword)
2349 5520 : CALL keyword_release(keyword)
2350 :
2351 : CALL keyword_create(keyword, __LOCATION__, name="D_1", &
2352 : description="Reference coordination of the first reactive GROUPA atom.", &
2353 5520 : usage="D_1 2.0", type_of_var=real_t, default_r_val=2.0_dp, n_var=1)
2354 5520 : CALL section_add_keyword(section, keyword)
2355 5520 : CALL keyword_release(keyword)
2356 :
2357 : CALL keyword_create(keyword, __LOCATION__, name="D_2", &
2358 : description="Reference coordination of the second reactive GROUPA atom.", &
2359 5520 : usage="D_2 2.0", type_of_var=real_t, default_r_val=2.0_dp, n_var=1)
2360 5520 : CALL section_add_keyword(section, keyword)
2361 5520 : CALL keyword_release(keyword)
2362 :
2363 : CALL keyword_create(keyword, __LOCATION__, name="D_3", &
2364 : description="Reference coordination of the third reactive GROUPA atom.", &
2365 5520 : usage="D_3 2.0", type_of_var=real_t, default_r_val=2.0_dp, n_var=1)
2366 5520 : CALL section_add_keyword(section, keyword)
2367 5520 : CALL keyword_release(keyword)
2368 :
2369 : CALL keyword_create(keyword, __LOCATION__, name="NL_CUTOFF", &
2370 : description="Maximum GROUPA-GROUPB distance included in the Voronoi weights.", &
2371 : usage="NL_CUTOFF [angstrom] 2.4", &
2372 : default_r_val=cp_unit_to_cp2k(value=2.4_dp, unit_str="angstrom"), &
2373 5520 : unit_str="angstrom", n_var=1)
2374 5520 : CALL section_add_keyword(section, keyword)
2375 5520 : CALL keyword_release(keyword)
2376 :
2377 : CALL keyword_create(keyword, __LOCATION__, name="GROUPA", &
2378 : description="Oxygen atoms used as Voronoi sites. Any reactive sites must "// &
2379 : "be the final NRX entries.", &
2380 5520 : usage="GROUPA 1 4 7", n_var=-1, type_of_var=integer_t)
2381 5520 : CALL section_add_keyword(section, keyword)
2382 5520 : CALL keyword_release(keyword)
2383 :
2384 : CALL keyword_create(keyword, __LOCATION__, name="GROUPB", &
2385 : description="Hydrogen atoms assigned to the GROUPA sites.", &
2386 5520 : usage="GROUPB 2 3 5 6 8 9", n_var=-1, type_of_var=integer_t)
2387 5520 : CALL section_add_keyword(section, keyword)
2388 5520 : CALL keyword_release(keyword)
2389 :
2390 : CALL keyword_create(keyword, __LOCATION__, name="NRX", &
2391 : description="Number of reactive sites at the end of GROUPA (zero to three). "// &
2392 : "Their reference coordinations are D_1 through D_3.", &
2393 5520 : usage="NRX 0", type_of_var=integer_t, default_i_val=0, n_var=1)
2394 5520 : CALL section_add_keyword(section, keyword)
2395 5520 : CALL keyword_release(keyword)
2396 :
2397 5520 : END SUBROUTINE create_voronoiipz_section
2398 :
2399 : END MODULE input_cp2k_colvar
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