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 : USE colvar_types, ONLY: &
16 : do_clv_fix_point, do_clv_geo_center, do_clv_x, do_clv_xy, do_clv_xyz, do_clv_xz, do_clv_y, &
17 : do_clv_yz, do_clv_z, plane_def_atoms, plane_def_vec
18 : USE cp_output_handling, ONLY: add_last_numeric,&
19 : cp_print_key_section_create,&
20 : high_print_level,&
21 : low_print_level
22 : USE cp_units, ONLY: cp_unit_to_cp2k
23 : USE fparser, ONLY: docf
24 : USE input_constants, ONLY: gaussian,&
25 : numerical,&
26 : rmsd_all,&
27 : rmsd_list,&
28 : rmsd_weightlist
29 : USE input_keyword_types, ONLY: keyword_create,&
30 : keyword_release,&
31 : keyword_type
32 : USE input_section_types, ONLY: section_add_keyword,&
33 : section_add_subsection,&
34 : section_create,&
35 : section_release,&
36 : section_type
37 : USE input_val_types, ONLY: char_t,&
38 : integer_t,&
39 : lchar_t,&
40 : real_t
41 : USE kinds, ONLY: dp
42 : USE string_utilities, ONLY: s2a
43 : #include "./base/base_uses.f90"
44 :
45 : IMPLICIT NONE
46 : PRIVATE
47 :
48 : LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .FALSE.
49 : CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'input_cp2k_colvar'
50 :
51 : PUBLIC :: create_colvar_section, &
52 : create_colvar_xyz_d_section, &
53 : create_colvar_xyz_od_section
54 :
55 : CONTAINS
56 :
57 : ! **************************************************************************************************
58 : !> \brief creates the colvar section
59 : !> \param section the section to be created
60 : !> \param skip_recursive_colvar ...
61 : !> \author teo
62 : ! **************************************************************************************************
63 38056 : RECURSIVE SUBROUTINE create_colvar_section(section, skip_recursive_colvar)
64 : TYPE(section_type), POINTER :: section
65 : LOGICAL, OPTIONAL :: skip_recursive_colvar
66 :
67 : LOGICAL :: skip
68 : TYPE(section_type), POINTER :: print_key, subsection
69 :
70 38056 : skip = .FALSE.
71 38056 : IF (PRESENT(skip_recursive_colvar)) skip = skip_recursive_colvar
72 38056 : CPASSERT(.NOT. ASSOCIATED(section))
73 : CALL section_create(section, __LOCATION__, name="COLVAR", &
74 : description="This section specifies the nature of the collective variables.", &
75 38056 : n_keywords=1, n_subsections=1, repeats=.TRUE.)
76 38056 : NULLIFY (subsection, print_key)
77 :
78 : CALL create_colvar_var_section(subsection=subsection, &
79 38056 : section=section, skip_recursive_colvar=skip)
80 :
81 : CALL section_create(subsection, __LOCATION__, name="PRINT", &
82 : description="Controls the printing of the colvar specifications", &
83 38056 : n_keywords=0, n_subsections=1, repeats=.TRUE.)
84 38056 : NULLIFY (print_key)
85 : CALL cp_print_key_section_create(print_key, __LOCATION__, "PROGRAM_RUN_INFO", &
86 : description="Controls the printing of basic information during colvar setup.", &
87 38056 : print_level=low_print_level, add_last=add_last_numeric, filename="__STD_OUT__")
88 38056 : CALL section_add_subsection(subsection, print_key)
89 38056 : CALL section_release(print_key)
90 38056 : CALL section_add_subsection(section, subsection)
91 38056 : CALL section_release(subsection)
92 :
93 38056 : CALL create_clv_info_section(subsection)
94 38056 : CALL section_add_subsection(section, subsection)
95 38056 : CALL section_release(subsection)
96 :
97 38056 : END SUBROUTINE create_colvar_section
98 :
99 : ! **************************************************************************************************
100 : !> \brief Create the restart section for colvar restraints
101 : !> This section will be only used for restraint restarts.
102 : !> Constraints are handled automatically
103 : !> \param section the section to create
104 : !> \author Teodoro Laino 08.2006
105 : ! **************************************************************************************************
106 38056 : SUBROUTINE create_clv_info_section(section)
107 : TYPE(section_type), POINTER :: section
108 :
109 : TYPE(keyword_type), POINTER :: keyword
110 :
111 38056 : CPASSERT(.NOT. ASSOCIATED(section))
112 38056 : NULLIFY (keyword)
113 : CALL section_create(section, __LOCATION__, name="COLVAR_FUNC_INFO", &
114 : description="Specify further data possibly used by colvars, depending "// &
115 : "on the starting geometry, for computing the functions value.", &
116 38056 : n_subsections=0, repeats=.FALSE.)
117 :
118 : CALL keyword_create(keyword, __LOCATION__, name="_DEFAULT_KEYWORD_", &
119 : description="Colvar function data."// &
120 : " The order is an internal order. So if you decide to edit/modify/add these values by hand"// &
121 : " you should know very well what you are doing.!", repeats=.TRUE., &
122 38056 : usage="{Real} ...", type_of_var=real_t, n_var=-1)
123 38056 : CALL section_add_keyword(section, keyword)
124 38056 : CALL keyword_release(keyword)
125 :
126 38056 : END SUBROUTINE create_clv_info_section
127 :
128 : ! **************************************************************************************************
129 : !> \brief creates the collective variables for the colvar section
130 : !> \param subsection ...
131 : !> \param section the section to be created
132 : !> \param skip_recursive_colvar ...
133 : !> \author teo
134 : ! **************************************************************************************************
135 38056 : RECURSIVE SUBROUTINE create_colvar_var_section(subsection, section, skip_recursive_colvar)
136 : TYPE(section_type), POINTER :: subsection, section
137 : LOGICAL, INTENT(IN) :: skip_recursive_colvar
138 :
139 38056 : CPASSERT(.NOT. ASSOCIATED(subsection))
140 38056 : CPASSERT(ASSOCIATED(section))
141 :
142 38056 : CALL create_colvar_dist_section(subsection)
143 38056 : CALL section_add_subsection(section, subsection)
144 38056 : CALL section_release(subsection)
145 :
146 38056 : CALL create_colvar_angle_section(subsection)
147 38056 : CALL section_add_subsection(section, subsection)
148 38056 : CALL section_release(subsection)
149 :
150 38056 : CALL create_colvar_torsion_section(subsection)
151 38056 : CALL section_add_subsection(section, subsection)
152 38056 : CALL section_release(subsection)
153 :
154 38056 : CALL create_colvar_coord_section(subsection)
155 38056 : CALL section_add_subsection(section, subsection)
156 38056 : CALL section_release(subsection)
157 :
158 38056 : CALL create_colvar_pop_section(subsection)
159 38056 : CALL section_add_subsection(section, subsection)
160 38056 : CALL section_release(subsection)
161 :
162 38056 : CALL create_colvar_gyr_section(subsection)
163 38056 : CALL section_add_subsection(section, subsection)
164 38056 : CALL section_release(subsection)
165 :
166 38056 : CALL create_colvar_d_pl_section(subsection)
167 38056 : CALL section_add_subsection(section, subsection)
168 38056 : CALL section_release(subsection)
169 :
170 38056 : CALL create_colvar_a_pl_section(subsection)
171 38056 : CALL section_add_subsection(section, subsection)
172 38056 : CALL section_release(subsection)
173 :
174 38056 : CALL create_colvar_rot_section(subsection)
175 38056 : CALL section_add_subsection(section, subsection)
176 38056 : CALL section_release(subsection)
177 :
178 38056 : CALL create_colvar_dfunct_section(subsection)
179 38056 : CALL section_add_subsection(section, subsection)
180 38056 : CALL section_release(subsection)
181 :
182 38056 : CALL create_colvar_qparm_section(subsection)
183 38056 : CALL section_add_subsection(section, subsection)
184 38056 : CALL section_release(subsection)
185 :
186 38056 : CALL create_colvar_hydronium_shell_section(subsection)
187 38056 : CALL section_add_subsection(section, subsection)
188 38056 : CALL section_release(subsection)
189 :
190 38056 : CALL create_colvar_hydronium_dist_section(subsection)
191 38056 : CALL section_add_subsection(section, subsection)
192 38056 : CALL section_release(subsection)
193 :
194 38056 : CALL create_colvar_acid_hyd_dist_section(subsection)
195 38056 : CALL section_add_subsection(section, subsection)
196 38056 : CALL section_release(subsection)
197 :
198 38056 : CALL create_colvar_acid_hyd_shell_section(subsection)
199 38056 : CALL section_add_subsection(section, subsection)
200 38056 : CALL section_release(subsection)
201 :
202 38056 : CALL create_colvar_rmsd_section(subsection)
203 38056 : CALL section_add_subsection(section, subsection)
204 38056 : CALL section_release(subsection)
205 :
206 38056 : CALL create_colvar_xyz_d_section(subsection)
207 38056 : CALL section_add_subsection(section, subsection)
208 38056 : CALL section_release(subsection)
209 :
210 38056 : CALL create_colvar_xyz_od_section(subsection)
211 38056 : CALL section_add_subsection(section, subsection)
212 38056 : CALL section_release(subsection)
213 :
214 38056 : CALL create_colvar_u_section(subsection)
215 38056 : CALL section_add_subsection(section, subsection)
216 38056 : CALL section_release(subsection)
217 :
218 38056 : CALL create_colvar_wc_section(subsection)
219 38056 : CALL section_add_subsection(section, subsection)
220 38056 : CALL section_release(subsection)
221 :
222 38056 : CALL create_colvar_hbp_section(subsection)
223 38056 : CALL section_add_subsection(section, subsection)
224 38056 : CALL section_release(subsection)
225 :
226 38056 : CALL create_colvar_ring_puckering_section(subsection)
227 38056 : CALL section_add_subsection(section, subsection)
228 38056 : CALL section_release(subsection)
229 :
230 38056 : CALL create_colvar_cond_dist_section(subsection)
231 38056 : CALL section_add_subsection(section, subsection)
232 38056 : CALL section_release(subsection)
233 :
234 38056 : IF (.NOT. skip_recursive_colvar) THEN
235 9514 : CALL create_colvar_rpath_section(subsection)
236 9514 : CALL section_add_subsection(section, subsection)
237 9514 : CALL section_release(subsection)
238 :
239 9514 : CALL create_colvar_dpath_section(subsection)
240 9514 : CALL section_add_subsection(section, subsection)
241 9514 : CALL section_release(subsection)
242 :
243 9514 : CALL create_colvar_comb_section(subsection)
244 9514 : CALL section_add_subsection(section, subsection)
245 9514 : CALL section_release(subsection)
246 : END IF
247 :
248 38056 : END SUBROUTINE create_colvar_var_section
249 :
250 : ! **************************************************************************************************
251 : !> \brief collective variables specifying coordination
252 : !> \param section the section to be created
253 : !> \author teo
254 : ! **************************************************************************************************
255 38056 : SUBROUTINE create_colvar_coord_section(section)
256 : TYPE(section_type), POINTER :: section
257 :
258 : TYPE(keyword_type), POINTER :: keyword
259 : TYPE(section_type), POINTER :: subsection
260 :
261 38056 : CPASSERT(.NOT. ASSOCIATED(section))
262 : CALL section_create(section, __LOCATION__, name="coordination", &
263 : description="Section to define the coordination number as a collective variable.", &
264 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
265 :
266 38056 : NULLIFY (subsection, keyword)
267 :
268 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_FROM", &
269 : variants=["POINTS_FROM"], &
270 : description="Specify indexes of atoms/points building the coordination variable. ", &
271 : usage="ATOMS_FROM {integer} {integer} ..", repeats=.TRUE., &
272 76112 : n_var=-1, type_of_var=integer_t)
273 38056 : CALL section_add_keyword(section, keyword)
274 38056 : CALL keyword_release(keyword)
275 :
276 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_TO", &
277 : variants=["POINTS_TO"], &
278 : description="Specify indexes of atoms/points building the coordination variable. ", &
279 : usage="ATOMS_TO {integer} {integer} ..", repeats=.TRUE., &
280 76112 : n_var=-1, type_of_var=integer_t)
281 38056 : CALL section_add_keyword(section, keyword)
282 38056 : CALL keyword_release(keyword)
283 :
284 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_TO_B", &
285 : variants=["POINTS_TO_B"], &
286 : description="For the CV given by the multiplication of two coorination numbers,"// &
287 : " here specify indexes of the third set of atoms/points. ", &
288 : usage="ATOMS_TO_B {integer} {integer} ..", repeats=.TRUE., &
289 76112 : n_var=-1, type_of_var=integer_t)
290 38056 : CALL section_add_keyword(section, keyword)
291 38056 : CALL keyword_release(keyword)
292 :
293 : CALL keyword_create(keyword, __LOCATION__, name="KINDS_FROM", &
294 : description="Specify alternatively kinds of atoms building the coordination variable.", &
295 : usage="KINDS_FROM {CHAR} {CHAR} ..", repeats=.TRUE., &
296 38056 : n_var=-1, type_of_var=char_t)
297 38056 : CALL section_add_keyword(section, keyword)
298 38056 : CALL keyword_release(keyword)
299 :
300 : CALL keyword_create(keyword, __LOCATION__, name="KINDS_TO", &
301 : description="Specify alternatively kinds of atoms building the coordination variable.", &
302 : usage="KINDS_TO {CHAR} {CHAR} ..", repeats=.TRUE., &
303 38056 : n_var=-1, type_of_var=char_t)
304 38056 : CALL section_add_keyword(section, keyword)
305 38056 : CALL keyword_release(keyword)
306 :
307 : CALL keyword_create(keyword, __LOCATION__, name="KINDS_TO_B", &
308 : description="For the CV given by the multiplication of two coorination numbers,"// &
309 : " here specify alternatively kinds of atoms building the coordination variable.", &
310 : usage="KINDS_TO_B {CHAR} {CHAR} ..", repeats=.TRUE., &
311 38056 : n_var=-1, type_of_var=char_t)
312 38056 : CALL section_add_keyword(section, keyword)
313 38056 : CALL keyword_release(keyword)
314 :
315 : ! Must be present in each colvar and handled properly
316 38056 : CALL create_point_section(subsection)
317 38056 : CALL section_add_subsection(section, subsection)
318 38056 : CALL section_release(subsection)
319 :
320 : CALL keyword_create(keyword, __LOCATION__, name="R0", &
321 : variants=["R_0"], &
322 : description="Specify the R0 parameter in the coordination function.", &
323 : usage="R0 {real}", default_r_val=3.0_dp, &
324 76112 : unit_str="bohr", n_var=1)
325 38056 : CALL section_add_keyword(section, keyword)
326 38056 : CALL keyword_release(keyword)
327 :
328 : CALL keyword_create(keyword, __LOCATION__, name="NN", &
329 : variants=["EXPON_NUMERATOR"], &
330 : description="Sets the value of the numerator of the exponential factor"// &
331 : " in the coordination FUNCTION.", &
332 : usage="NN {integer}", default_i_val=6, &
333 76112 : n_var=1)
334 38056 : CALL section_add_keyword(section, keyword)
335 38056 : CALL keyword_release(keyword)
336 :
337 : CALL keyword_create(keyword, __LOCATION__, name="ND", &
338 : variants=["EXPON_DENOMINATOR"], &
339 : description="Sets the value of the denominator of the exponential factor"// &
340 : " in the coordination FUNCTION.", &
341 : usage="ND {integer}", default_i_val=12, &
342 76112 : n_var=1)
343 38056 : CALL section_add_keyword(section, keyword)
344 38056 : CALL keyword_release(keyword)
345 :
346 : CALL keyword_create(keyword, __LOCATION__, name="R0_B", &
347 : variants=["R_0_B"], &
348 : description="For the CV given by the multiplication of two coorination numbers,"// &
349 : " specify the R0 parameter in the second coordination function.", &
350 : usage="R0_B {real}", default_r_val=3.0_dp, &
351 76112 : unit_str="bohr", n_var=1)
352 38056 : CALL section_add_keyword(section, keyword)
353 38056 : CALL keyword_release(keyword)
354 :
355 : CALL keyword_create(keyword, __LOCATION__, name="NN_B", &
356 : variants=["EXPON_NUMERATOR_B"], &
357 : description="For the CV given by the multiplication of two coorination numbers,"// &
358 : " Sets the value of the numerator of the exponential factor"// &
359 : " in the coordination FUNCTION.", &
360 : usage="NN_B {integer}", default_i_val=6, &
361 76112 : n_var=1)
362 38056 : CALL section_add_keyword(section, keyword)
363 38056 : CALL keyword_release(keyword)
364 :
365 : CALL keyword_create(keyword, __LOCATION__, name="ND_B", &
366 : variants=["EXPON_DENOMINATOR_B"], &
367 : description="For the CV given by the multiplication of two coorination numbers,"// &
368 : " Sets the value of the denominator of the exponential factor"// &
369 : " in the coordination FUNCTION.", &
370 : usage="ND_B {integer}", default_i_val=12, &
371 76112 : n_var=1)
372 38056 : CALL section_add_keyword(section, keyword)
373 38056 : CALL keyword_release(keyword)
374 :
375 38056 : END SUBROUTINE create_colvar_coord_section
376 :
377 : ! **************************************************************************************************
378 : !> \brief ...
379 : !> \param section ...
380 : ! **************************************************************************************************
381 38056 : SUBROUTINE create_colvar_cond_dist_section(section)
382 : TYPE(section_type), POINTER :: section
383 :
384 : TYPE(keyword_type), POINTER :: keyword
385 : TYPE(section_type), POINTER :: subsection
386 :
387 38056 : CPASSERT(.NOT. ASSOCIATED(section))
388 : CALL section_create(section, __LOCATION__, name="CONDITIONED_DISTANCE", &
389 : description="Section to define the conditioned distance as a collective variable.", &
390 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
391 :
392 38056 : NULLIFY (subsection, keyword)
393 :
394 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_DISTANCE", &
395 : description="Specify indexes of atoms/points from which the distance is computed. ", &
396 : usage="ATOMS_DISTANCE {integer} {integer} ..", repeats=.TRUE., &
397 38056 : n_var=-1, type_of_var=integer_t)
398 38056 : CALL section_add_keyword(section, keyword)
399 38056 : CALL keyword_release(keyword)
400 :
401 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_FROM", &
402 : variants=["POINTS_FROM"], &
403 : description="Specify indexes of atoms/points building the coordination variable. ", &
404 : usage="ATOMS_FROM {integer} {integer} ..", repeats=.TRUE., &
405 76112 : n_var=-1, type_of_var=integer_t)
406 38056 : CALL section_add_keyword(section, keyword)
407 38056 : CALL keyword_release(keyword)
408 :
409 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_TO", &
410 : variants=["POINTS_TO"], &
411 : description="Specify indexes of atoms/points building the coordination variable. ", &
412 : usage="ATOMS_TO {integer} {integer} ..", repeats=.TRUE., &
413 76112 : n_var=-1, type_of_var=integer_t)
414 38056 : CALL section_add_keyword(section, keyword)
415 38056 : CALL keyword_release(keyword)
416 :
417 : CALL keyword_create(keyword, __LOCATION__, name="KINDS_FROM", &
418 : description="Specify alternatively kinds of atoms building the coordination variable.", &
419 : usage="KINDS_FROM {CHAR} {CHAR} ..", repeats=.TRUE., &
420 38056 : n_var=-1, type_of_var=char_t)
421 38056 : CALL section_add_keyword(section, keyword)
422 38056 : CALL keyword_release(keyword)
423 :
424 : CALL keyword_create(keyword, __LOCATION__, name="KINDS_TO", &
425 : description="Specify alternatively kinds of atoms building the coordination variable.", &
426 : usage="KINDS_TO {CHAR} {CHAR} ..", repeats=.TRUE., &
427 38056 : n_var=-1, type_of_var=char_t)
428 38056 : CALL section_add_keyword(section, keyword)
429 38056 : CALL keyword_release(keyword)
430 :
431 : ! Must be present in each colvar and handled properly
432 38056 : CALL create_point_section(subsection)
433 38056 : CALL section_add_subsection(section, subsection)
434 38056 : CALL section_release(subsection)
435 :
436 : CALL keyword_create(keyword, __LOCATION__, name="R0", &
437 : variants=["R_0"], &
438 : description="Specify the R0 parameter in the coordination function.", &
439 : usage="R0 {real}", default_r_val=3.0_dp, &
440 76112 : unit_str="bohr", n_var=1)
441 38056 : CALL section_add_keyword(section, keyword)
442 38056 : CALL keyword_release(keyword)
443 :
444 : CALL keyword_create(keyword, __LOCATION__, name="NN", &
445 : variants=["EXPON_NUMERATOR"], &
446 : description="Sets the value of the numerator of the exponential factor"// &
447 : " in the coordination FUNCTION.", &
448 : usage="NN {integer}", default_i_val=6, &
449 76112 : n_var=1)
450 38056 : CALL section_add_keyword(section, keyword)
451 38056 : CALL keyword_release(keyword)
452 :
453 : CALL keyword_create(keyword, __LOCATION__, name="ND", &
454 : variants=["EXPON_DENOMINATOR"], &
455 : description="Sets the value of the denominator of the exponential factor"// &
456 : " in the coordination FUNCTION.", &
457 : usage="ND {integer}", default_i_val=12, &
458 76112 : n_var=1)
459 38056 : CALL section_add_keyword(section, keyword)
460 38056 : CALL keyword_release(keyword)
461 :
462 : CALL keyword_create(keyword, __LOCATION__, name="LAMBDA", &
463 : description="Specify the lambda parameter at the exponent of the conditioned distance function.", &
464 : usage="LAMBDA {real}", default_r_val=3.0_dp, &
465 38056 : unit_str="bohr", n_var=1)
466 38056 : CALL section_add_keyword(section, keyword)
467 38056 : CALL keyword_release(keyword)
468 :
469 38056 : END SUBROUTINE create_colvar_cond_dist_section
470 :
471 : ! **************************************************************************************************
472 : !> \brief collective variables specifying population of a specie based on coordination
473 : !> \param section the section to be created
474 : !> \date 01.2009
475 : !> \author Fabio Sterpone
476 : ! **************************************************************************************************
477 38056 : SUBROUTINE create_colvar_pop_section(section)
478 : TYPE(section_type), POINTER :: section
479 :
480 : TYPE(keyword_type), POINTER :: keyword
481 : TYPE(section_type), POINTER :: subsection
482 :
483 38056 : CPASSERT(.NOT. ASSOCIATED(section))
484 : CALL section_create(section, __LOCATION__, name="population", &
485 : description="Section to define the population of specie as a collective variable. "// &
486 : "See also <https://doi.org/10.1021/jp3019588>.", &
487 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
488 :
489 38056 : NULLIFY (subsection, keyword)
490 :
491 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_FROM", &
492 : variants=["POINTS_FROM"], &
493 : description="Specify indexes of atoms/points building the coordination variable. ", &
494 : usage="ATOMS_FROM {integer} {integer} ..", repeats=.TRUE., &
495 76112 : n_var=-1, type_of_var=integer_t)
496 38056 : CALL section_add_keyword(section, keyword)
497 38056 : CALL keyword_release(keyword)
498 :
499 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_TO", &
500 : variants=["POINTS_TO"], &
501 : description="Specify indexes of atoms/points building the coordination variable. ", &
502 : usage="ATOMS_TO {integer} {integer} ..", repeats=.TRUE., &
503 76112 : n_var=-1, type_of_var=integer_t)
504 38056 : CALL section_add_keyword(section, keyword)
505 38056 : CALL keyword_release(keyword)
506 :
507 : CALL keyword_create(keyword, __LOCATION__, name="KINDS_FROM", &
508 : description="Specify alternatively kinds of atoms building the coordination variable.", &
509 : usage="KINDS_FROM {CHAR} {CHAR} ..", repeats=.TRUE., &
510 38056 : n_var=-1, type_of_var=char_t)
511 38056 : CALL section_add_keyword(section, keyword)
512 38056 : CALL keyword_release(keyword)
513 :
514 : CALL keyword_create(keyword, __LOCATION__, name="KINDS_TO", &
515 : description="Specify alternatively kinds of atoms building the coordination variable.", &
516 : usage="KINDS_TO {CHAR} {CHAR} ..", repeats=.TRUE., &
517 38056 : n_var=-1, type_of_var=char_t)
518 38056 : CALL section_add_keyword(section, keyword)
519 38056 : CALL keyword_release(keyword)
520 :
521 : ! Must be present in each colvar and handled properly
522 38056 : CALL create_point_section(subsection)
523 38056 : CALL section_add_subsection(section, subsection)
524 38056 : CALL section_release(subsection)
525 :
526 : CALL keyword_create(keyword, __LOCATION__, name="R0", &
527 : variants=["R_0"], &
528 : description="Specify the R0 parameter in the coordination function.", &
529 : usage="R0 {real}", default_r_val=3.0_dp, &
530 76112 : n_var=1)
531 38056 : CALL section_add_keyword(section, keyword)
532 38056 : CALL keyword_release(keyword)
533 :
534 : CALL keyword_create(keyword, __LOCATION__, name="NN", &
535 : variants=["EXPON_NUMERATOR"], &
536 : description="Sets the value of the numerator of the exponential factor"// &
537 : " in the coordination FUNCTION.", &
538 : usage="NN {integer}", default_i_val=6, &
539 76112 : n_var=1)
540 38056 : CALL section_add_keyword(section, keyword)
541 38056 : CALL keyword_release(keyword)
542 :
543 : CALL keyword_create(keyword, __LOCATION__, name="ND", &
544 : variants=["EXPON_DENOMINATOR"], &
545 : description="Sets the value of the denominator of the exponential factor"// &
546 : " in the coordination FUNCTION.", &
547 : usage="ND {integer}", default_i_val=12, &
548 76112 : n_var=1)
549 38056 : CALL section_add_keyword(section, keyword)
550 38056 : CALL keyword_release(keyword)
551 :
552 : CALL keyword_create(keyword, __LOCATION__, name="n0", &
553 : variants=["n_0"], &
554 : description="Specify the n0 parameter that sets the coordination of the species.", &
555 : usage="n0 {integer}", default_i_val=4, &
556 76112 : n_var=1)
557 38056 : CALL section_add_keyword(section, keyword)
558 38056 : CALL keyword_release(keyword)
559 :
560 : CALL keyword_create(keyword, __LOCATION__, name="SIGMA", &
561 : description="Specify the gaussian width of used to build the population istogram.", &
562 : usage="SIGMA {real}", default_r_val=0.5_dp, &
563 38056 : n_var=1)
564 38056 : CALL section_add_keyword(section, keyword)
565 38056 : CALL keyword_release(keyword)
566 :
567 38056 : END SUBROUTINE create_colvar_pop_section
568 :
569 : ! **************************************************************************************************
570 : !> \brief ...
571 : !> \param section ...
572 : ! **************************************************************************************************
573 38056 : SUBROUTINE create_colvar_gyr_section(section)
574 : TYPE(section_type), POINTER :: section
575 :
576 : TYPE(keyword_type), POINTER :: keyword
577 : TYPE(section_type), POINTER :: subsection
578 :
579 38056 : CPASSERT(.NOT. ASSOCIATED(section))
580 : CALL section_create(section, __LOCATION__, name="GYRATION_RADIUS", &
581 : description="Section to define the gyration radius as a collective variable.", &
582 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
583 :
584 38056 : NULLIFY (subsection, keyword)
585 :
586 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
587 : variants=["POINTS"], &
588 : description="Specify indexes of atoms/points defyining the gyration radius variable. ", &
589 : usage="ATOMS {integer} {integer} ..", repeats=.TRUE., &
590 76112 : n_var=-1, type_of_var=integer_t)
591 38056 : CALL section_add_keyword(section, keyword)
592 38056 : CALL keyword_release(keyword)
593 :
594 : CALL keyword_create(keyword, __LOCATION__, name="KINDS", &
595 : description="Specify alternatively kinds of atoms defining the gyration radius.", &
596 : usage="KINDS {CHAR} {CHAR} ..", repeats=.TRUE., &
597 38056 : n_var=-1, type_of_var=char_t)
598 38056 : CALL section_add_keyword(section, keyword)
599 38056 : CALL keyword_release(keyword)
600 :
601 : ! Must be present in each colvar and handled properly
602 38056 : CALL create_point_section(subsection)
603 38056 : CALL section_add_subsection(section, subsection)
604 38056 : CALL section_release(subsection)
605 :
606 38056 : END SUBROUTINE create_colvar_gyr_section
607 :
608 : ! **************************************************************************************************
609 : !> \brief collective variables specifying torsion
610 : !> \param section the section to be created
611 : !> \author teo
612 : ! **************************************************************************************************
613 38056 : SUBROUTINE create_colvar_dfunct_section(section)
614 : TYPE(section_type), POINTER :: section
615 :
616 : TYPE(keyword_type), POINTER :: keyword
617 : TYPE(section_type), POINTER :: subsection
618 :
619 38056 : CPASSERT(.NOT. ASSOCIATED(section))
620 : CALL section_create(section, __LOCATION__, name="DISTANCE_FUNCTION", &
621 : description="Section to define functions between two distances as collective variables."// &
622 : " The function is defined as d1+coeff*d2", &
623 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
624 :
625 38056 : NULLIFY (keyword, subsection)
626 :
627 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
628 : variants=["POINTS"], &
629 : description="Specifies the indexes of atoms/points for the two bonds d1=(1-2) d2=(3-4).", &
630 : usage="ATOMS {integer} {integer} {integer} {integer}", &
631 76112 : n_var=4, type_of_var=integer_t)
632 38056 : CALL section_add_keyword(section, keyword)
633 38056 : CALL keyword_release(keyword)
634 :
635 : CALL keyword_create(keyword, __LOCATION__, name="COEFFICIENT", &
636 : description="Specifies the coefficient in the function for the constraint."// &
637 : " -1.0 has to be used for distance difference, 1.0 for distance addition", &
638 : usage="COEFFICIENT {real}", &
639 38056 : type_of_var=real_t)
640 38056 : CALL section_add_keyword(section, keyword)
641 38056 : CALL keyword_release(keyword)
642 :
643 : CALL keyword_create(keyword, __LOCATION__, name="PBC", &
644 : description="Whether periodic boundary conditions should be applied on the "// &
645 : "atomic position before computing the colvar or not.", &
646 : usage="PBC", &
647 38056 : default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
648 38056 : CALL section_add_keyword(section, keyword)
649 38056 : CALL keyword_release(keyword)
650 :
651 : ! Must be present in each colvar and handled properly
652 38056 : CALL create_point_section(subsection)
653 38056 : CALL section_add_subsection(section, subsection)
654 38056 : CALL section_release(subsection)
655 :
656 38056 : END SUBROUTINE create_colvar_dfunct_section
657 :
658 : ! **************************************************************************************************
659 : !> \brief collective variables specifying torsion
660 : !> \param section the section to be created
661 : !> \author teo
662 : ! **************************************************************************************************
663 38056 : SUBROUTINE create_colvar_torsion_section(section)
664 : TYPE(section_type), POINTER :: section
665 :
666 : TYPE(keyword_type), POINTER :: keyword
667 : TYPE(section_type), POINTER :: subsection
668 :
669 38056 : CPASSERT(.NOT. ASSOCIATED(section))
670 : CALL section_create(section, __LOCATION__, name="torsion", &
671 : description="Section to define the torsion as a collective variables.", &
672 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
673 :
674 38056 : NULLIFY (keyword, subsection)
675 :
676 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
677 : variants=["POINTS"], &
678 : description="Specifies the indexes of atoms/points defining the torsion.", &
679 : usage="ATOMS {integer} {integer} {integer} {integer}", &
680 76112 : n_var=4, type_of_var=integer_t)
681 38056 : CALL section_add_keyword(section, keyword)
682 38056 : CALL keyword_release(keyword)
683 :
684 : ! Must be present in each colvar and handled properly
685 38056 : CALL create_point_section(subsection)
686 38056 : CALL section_add_subsection(section, subsection)
687 38056 : CALL section_release(subsection)
688 :
689 38056 : END SUBROUTINE create_colvar_torsion_section
690 :
691 : ! **************************************************************************************************
692 : !> \brief collective variables specifying torsion
693 : !> \param section the section to be created
694 : !> \author teo
695 : ! **************************************************************************************************
696 38056 : SUBROUTINE create_colvar_rot_section(section)
697 : TYPE(section_type), POINTER :: section
698 :
699 : TYPE(keyword_type), POINTER :: keyword
700 : TYPE(section_type), POINTER :: subsection
701 :
702 38056 : CPASSERT(.NOT. ASSOCIATED(section))
703 : CALL section_create(section, __LOCATION__, name="bond_rotation", &
704 : description="Section to define the rotation of a bond/line with respect to"// &
705 : " another bond/line", &
706 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
707 :
708 38056 : NULLIFY (keyword, subsection)
709 :
710 : CALL keyword_create(keyword, __LOCATION__, name="P1_BOND1", &
711 : description="Specifies the index of atom/point defining the first point"// &
712 : " of the first bond/line.", &
713 : usage="P1_BOND1 {integer}", &
714 38056 : n_var=1, type_of_var=integer_t)
715 38056 : CALL section_add_keyword(section, keyword)
716 38056 : CALL keyword_release(keyword)
717 :
718 : CALL keyword_create(keyword, __LOCATION__, name="P2_BOND1", &
719 : description="Specifies the index of atom/point defining the second point"// &
720 : " of the first bond/line.", &
721 : usage="P2_BOND1 {integer}", &
722 38056 : n_var=1, type_of_var=integer_t)
723 38056 : CALL section_add_keyword(section, keyword)
724 38056 : CALL keyword_release(keyword)
725 :
726 : CALL keyword_create(keyword, __LOCATION__, name="P1_BOND2", &
727 : description="Specifies the index of atom/point defining the first point"// &
728 : " of the second bond/line.", &
729 : usage="P1_BOND2 {integer}", &
730 38056 : n_var=1, type_of_var=integer_t)
731 38056 : CALL section_add_keyword(section, keyword)
732 38056 : CALL keyword_release(keyword)
733 :
734 : CALL keyword_create(keyword, __LOCATION__, name="P2_BOND2", &
735 : description="Specifies the index of atom/point defining the second point"// &
736 : " of the second bond/line.", &
737 : usage="P2_BOND2 {integer}", &
738 38056 : n_var=1, type_of_var=integer_t)
739 38056 : CALL section_add_keyword(section, keyword)
740 38056 : CALL keyword_release(keyword)
741 :
742 : ! Must be present in each colvar and handled properly
743 38056 : CALL create_point_section(subsection)
744 38056 : CALL section_add_subsection(section, subsection)
745 38056 : CALL section_release(subsection)
746 :
747 38056 : END SUBROUTINE create_colvar_rot_section
748 :
749 : ! **************************************************************************************************
750 : !> \brief collective variables specifying angles
751 : !> \param section the section to be created
752 : !> \author teo
753 : ! **************************************************************************************************
754 38056 : SUBROUTINE create_colvar_angle_section(section)
755 : TYPE(section_type), POINTER :: section
756 :
757 : TYPE(keyword_type), POINTER :: keyword
758 : TYPE(section_type), POINTER :: subsection
759 :
760 38056 : CPASSERT(.NOT. ASSOCIATED(section))
761 : CALL section_create(section, __LOCATION__, name="angle", &
762 : description="Section to define the angle as a collective variables.", &
763 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
764 38056 : NULLIFY (keyword, subsection)
765 :
766 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
767 : variants=["POINTS"], &
768 : description="Specifies the indexes of atoms/points defining the angle.", &
769 : usage="ATOMS {integer} {integer} {integer}", &
770 76112 : n_var=3, type_of_var=integer_t)
771 38056 : CALL section_add_keyword(section, keyword)
772 38056 : CALL keyword_release(keyword)
773 :
774 : ! Must be present in each colvar and handled properly
775 38056 : CALL create_point_section(subsection)
776 38056 : CALL section_add_subsection(section, subsection)
777 38056 : CALL section_release(subsection)
778 :
779 38056 : END SUBROUTINE create_colvar_angle_section
780 :
781 : ! **************************************************************************************************
782 : !> \brief creates the colvar section regarded to the collective variables dist
783 : !> \param section the section to be created
784 : !> \author teo
785 : ! **************************************************************************************************
786 38056 : SUBROUTINE create_colvar_dist_section(section)
787 : TYPE(section_type), POINTER :: section
788 :
789 : TYPE(keyword_type), POINTER :: keyword
790 : TYPE(section_type), POINTER :: subsection
791 :
792 38056 : CPASSERT(.NOT. ASSOCIATED(section))
793 : CALL section_create(section, __LOCATION__, name="distance", &
794 : description="Section to define the distance as a collective variables.", &
795 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
796 38056 : NULLIFY (keyword, subsection)
797 :
798 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
799 : variants=["POINTS"], &
800 : description="Specifies the indexes of atoms/points defining the distance.", &
801 : usage="ATOMS {integer} {integer}", &
802 76112 : n_var=2, type_of_var=integer_t)
803 38056 : CALL section_add_keyword(section, keyword)
804 38056 : CALL keyword_release(keyword)
805 : CALL keyword_create(keyword, __LOCATION__, name="AXIS", &
806 : description="Define the axes along which the colvar should be evaluated", &
807 : usage="AXIS (XYZ | X | Y | Z | XY| XZ | YZ)", &
808 : enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
809 : enum_i_vals=[do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz], &
810 38056 : default_i_val=do_clv_xyz)
811 38056 : CALL section_add_keyword(section, keyword)
812 38056 : CALL keyword_release(keyword)
813 :
814 : CALL keyword_create(keyword, __LOCATION__, name="SIGN", &
815 : description="Whether the distance along one Cartesian axis has to be considered with sign."// &
816 : " This option is valid if only one dimension is selected.", &
817 : usage="SIGN", &
818 38056 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
819 38056 : CALL section_add_keyword(section, keyword)
820 38056 : CALL keyword_release(keyword)
821 :
822 : ! Must be present in each colvar and handled properly
823 38056 : CALL create_point_section(subsection)
824 38056 : CALL section_add_subsection(section, subsection)
825 38056 : CALL section_release(subsection)
826 :
827 38056 : END SUBROUTINE create_colvar_dist_section
828 :
829 : ! **************************************************************************************************
830 : !> \brief creates the colvar section regarded to the collective variables dist
831 : !> \param section the section to be created
832 : !> \author teo
833 : ! **************************************************************************************************
834 38059 : SUBROUTINE create_colvar_xyz_d_section(section)
835 : TYPE(section_type), POINTER :: section
836 :
837 : TYPE(keyword_type), POINTER :: keyword
838 : TYPE(section_type), POINTER :: subsection
839 :
840 38059 : CPASSERT(.NOT. ASSOCIATED(section))
841 : CALL section_create(section, __LOCATION__, name="XYZ_DIAG", &
842 : description="Section to define the distance of an atom from its starting "// &
843 : "position ((X-X(0))^2+(Y-Y(0))^2+(Z-Z(0))^2) or part of its components as a collective variable. "// &
844 : "If absolute_position is specified, instead the CV is represented by the "// &
845 : "instantaneous position of the atom (only available for X, Y or Z components).", &
846 38059 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
847 38059 : NULLIFY (keyword, subsection)
848 :
849 : CALL keyword_create(keyword, __LOCATION__, name="ATOM", &
850 : variants=["POINT"], &
851 : description="Specifies the index of the atom/point.", &
852 : usage="ATOM {integer}", &
853 76118 : n_var=1, type_of_var=integer_t)
854 38059 : CALL section_add_keyword(section, keyword)
855 38059 : CALL keyword_release(keyword)
856 :
857 : CALL keyword_create(keyword, __LOCATION__, name="COMPONENT", &
858 : description="Define the component of the position vector which will be used "// &
859 : "as a colvar.", &
860 : usage="COMPONENT (XYZ | X | Y | Z | XY| XZ | YZ)", &
861 : enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
862 : enum_i_vals=[do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz], &
863 38059 : default_i_val=do_clv_xyz)
864 38059 : CALL section_add_keyword(section, keyword)
865 38059 : CALL keyword_release(keyword)
866 :
867 : CALL keyword_create(keyword, __LOCATION__, name="PBC", &
868 : description="Whether periodic boundary conditions should be applied on the "// &
869 : "atomic position before computing the colvar or not.", &
870 : usage="PBC", &
871 38059 : default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
872 38059 : CALL section_add_keyword(section, keyword)
873 38059 : CALL keyword_release(keyword)
874 :
875 : CALL keyword_create(keyword, __LOCATION__, name="ABSOLUTE_POSITION", &
876 : description="If enabled, the absolute position of the atoms will be used. ", &
877 : usage="ABSOLUTE_POSITION", &
878 38059 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
879 38059 : CALL section_add_keyword(section, keyword)
880 38059 : CALL keyword_release(keyword)
881 :
882 : ! Must be present in each colvar and handled properly
883 38059 : CALL create_point_section(subsection)
884 38059 : CALL section_add_subsection(section, subsection)
885 38059 : CALL section_release(subsection)
886 :
887 38059 : END SUBROUTINE create_colvar_xyz_d_section
888 :
889 : ! **************************************************************************************************
890 : !> \brief creates the colvar section regarded to the collective variables dist
891 : !> \param section the section to be created
892 : !> \author teo
893 : ! **************************************************************************************************
894 38059 : SUBROUTINE create_colvar_xyz_od_section(section)
895 : TYPE(section_type), POINTER :: section
896 :
897 : TYPE(keyword_type), POINTER :: keyword
898 : TYPE(section_type), POINTER :: subsection
899 :
900 38059 : CPASSERT(.NOT. ASSOCIATED(section))
901 : CALL section_create(section, __LOCATION__, name="XYZ_OUTERDIAG", &
902 : description="Section to define the cross term (XA-XA(0))*(XB-XB(0))+(XA-XA(0))*(YB-YB(0))"// &
903 : " or part of its components as a collective variable. The final term is given by the product"// &
904 : " of the components of A with the components of B.", &
905 38059 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
906 38059 : NULLIFY (keyword, subsection)
907 :
908 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
909 : variants=["POINTS"], &
910 : description="Specifies the index of the atoms/points A and B.", &
911 : usage="ATOMS {integer} {integer}", &
912 76118 : n_var=2, type_of_var=integer_t)
913 38059 : CALL section_add_keyword(section, keyword)
914 38059 : CALL keyword_release(keyword)
915 :
916 : CALL keyword_create(keyword, __LOCATION__, name="COMPONENT_A", &
917 : description="Define the component of the position vector which will be used "// &
918 : "as a colvar for atom A.", &
919 : usage="COMPONENT_A (XYZ | X | Y | Z | XY| XZ | YZ)", &
920 : enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
921 : enum_i_vals=[do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz], &
922 38059 : default_i_val=do_clv_xyz)
923 38059 : CALL section_add_keyword(section, keyword)
924 38059 : CALL keyword_release(keyword)
925 :
926 : CALL keyword_create(keyword, __LOCATION__, name="COMPONENT_B", &
927 : description="Define the component of the position vector which will be used "// &
928 : "as a colvar for atom B.", &
929 : usage="COMPONENT_B (XYZ | X | Y | Z | XY| XZ | YZ)", &
930 : enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
931 : enum_i_vals=[do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz], &
932 38059 : default_i_val=do_clv_xyz)
933 38059 : CALL section_add_keyword(section, keyword)
934 38059 : CALL keyword_release(keyword)
935 :
936 : CALL keyword_create(keyword, __LOCATION__, name="PBC", &
937 : description="Whether periodic boundary conditions should be applied on the "// &
938 : "atomic position before computing the colvar or not.", &
939 : usage="PBC", &
940 38059 : default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
941 38059 : CALL section_add_keyword(section, keyword)
942 38059 : CALL keyword_release(keyword)
943 :
944 : ! Must be present in each colvar and handled properly
945 38059 : CALL create_point_section(subsection)
946 38059 : CALL section_add_subsection(section, subsection)
947 38059 : CALL section_release(subsection)
948 :
949 38059 : END SUBROUTINE create_colvar_xyz_od_section
950 :
951 : ! **************************************************************************************************
952 : !> \brief energy as collective variable
953 : !> \param section the section to be created
954 : !> \author Sebastiano Caravati
955 : ! **************************************************************************************************
956 38056 : SUBROUTINE create_colvar_u_section(section)
957 : TYPE(section_type), POINTER :: section
958 :
959 : TYPE(keyword_type), POINTER :: keyword
960 : TYPE(section_type), POINTER :: subsection
961 :
962 38056 : CPASSERT(.NOT. ASSOCIATED(section))
963 : CALL section_create(section, __LOCATION__, name="u", &
964 : description="Section to define the energy as a generalized collective variable.", &
965 38056 : n_keywords=0, n_subsections=0, repeats=.FALSE.)
966 :
967 38056 : NULLIFY (subsection, keyword)
968 : CALL section_create(subsection, __LOCATION__, name="MIXED", &
969 : description="This section allows to use any function of the energy subsystems"// &
970 : " in a mixed_env calculation as a collective variable.", &
971 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
972 :
973 : CALL keyword_create(keyword, __LOCATION__, name="ENERGY_FUNCTION", &
974 : description="Specifies the functional form of the collective variable in mathematical notation.", &
975 : usage="ENERGY_FUNCTION (E1+E2-LOG(E1/E2))", type_of_var=lchar_t, &
976 38056 : n_var=1)
977 38056 : CALL section_add_keyword(subsection, keyword)
978 38056 : CALL keyword_release(keyword)
979 :
980 : CALL keyword_create(keyword, __LOCATION__, name="VARIABLES", &
981 : description="Defines the variables of the functional form. To allow an efficient"// &
982 : " mapping the order of the energy variables will be considered identical to the"// &
983 : " order of the force_eval in the force_eval_order list.", &
984 : usage="VARIABLES x", type_of_var=char_t, &
985 38056 : n_var=-1)
986 38056 : CALL section_add_keyword(subsection, keyword)
987 38056 : CALL keyword_release(keyword)
988 :
989 : CALL keyword_create(keyword, __LOCATION__, name="PARAMETERS", &
990 : description="Defines the parameters of the functional form", &
991 : usage="PARAMETERS a b D", type_of_var=char_t, &
992 38056 : n_var=-1, repeats=.TRUE.)
993 38056 : CALL section_add_keyword(subsection, keyword)
994 38056 : CALL keyword_release(keyword)
995 :
996 : CALL keyword_create(keyword, __LOCATION__, name="VALUES", &
997 : description="Defines the values of parameter of the functional form", &
998 : usage="VALUES ", type_of_var=real_t, &
999 38056 : n_var=-1, repeats=.TRUE., unit_str="internal_cp2k")
1000 38056 : CALL section_add_keyword(subsection, keyword)
1001 38056 : CALL keyword_release(keyword)
1002 :
1003 : CALL keyword_create(keyword, __LOCATION__, name="UNITS", &
1004 : description="Optionally, allows to define valid CP2K unit strings for each parameter value. "// &
1005 : "It is assumed that the corresponding parameter value is specified in this unit.", &
1006 : usage="UNITS angstrom eV*angstrom^-1 angstrom^1 K", type_of_var=char_t, &
1007 38056 : n_var=-1, repeats=.TRUE.)
1008 38056 : CALL section_add_keyword(subsection, keyword)
1009 38056 : CALL keyword_release(keyword)
1010 :
1011 : CALL keyword_create(keyword, __LOCATION__, name="DX", &
1012 : description="Parameter used for computing the derivative with the Ridders' method.", &
1013 38056 : usage="DX <REAL>", default_r_val=0.1_dp, unit_str="bohr")
1014 38056 : CALL section_add_keyword(subsection, keyword)
1015 38056 : CALL keyword_release(keyword)
1016 :
1017 : CALL keyword_create(keyword, __LOCATION__, name="ERROR_LIMIT", &
1018 : description="Checks that the error in computing the derivative is not larger than "// &
1019 : "the value set; in case error is larger a warning message is printed.", &
1020 38056 : usage="ERROR_LIMIT <REAL>", default_r_val=1.0E-12_dp)
1021 38056 : CALL section_add_keyword(subsection, keyword)
1022 38056 : CALL keyword_release(keyword)
1023 :
1024 38056 : CALL section_add_subsection(section, subsection)
1025 38056 : CALL section_release(subsection)
1026 :
1027 38056 : END SUBROUTINE create_colvar_u_section
1028 :
1029 : ! **************************************************************************************************
1030 : !> \brief creates the colvar section regarded to the collective variables distance
1031 : !> of a point from a plane
1032 : !> \param section the section to be created
1033 : !> \author teo
1034 : ! **************************************************************************************************
1035 38056 : SUBROUTINE create_colvar_d_pl_section(section)
1036 : TYPE(section_type), POINTER :: section
1037 :
1038 : TYPE(keyword_type), POINTER :: keyword
1039 : TYPE(section_type), POINTER :: subsection
1040 :
1041 38056 : CPASSERT(.NOT. ASSOCIATED(section))
1042 : CALL section_create(section, __LOCATION__, name="distance_point_plane", &
1043 : description="Section to define the distance of a point from a plane "// &
1044 : "as a collective variables.", &
1045 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1046 38056 : NULLIFY (keyword, subsection)
1047 :
1048 : CALL keyword_create(keyword, __LOCATION__, name="PBC", &
1049 : description="Whether periodic boundary conditions should be applied on the "// &
1050 : "atomic position before computing the colvar or not.", &
1051 : usage="PBC", &
1052 38056 : default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
1053 38056 : CALL section_add_keyword(section, keyword)
1054 38056 : CALL keyword_release(keyword)
1055 :
1056 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_PLANE", &
1057 : variants=["POINTS_PLANE"], &
1058 : description="Specifies the indexes of atoms/points defining the plane.", &
1059 : usage="ATOMS_PLANE <INTEGER> <INTEGER> <INTEGER>", &
1060 76112 : n_var=3, type_of_var=integer_t)
1061 38056 : CALL section_add_keyword(section, keyword)
1062 38056 : CALL keyword_release(keyword)
1063 :
1064 : CALL keyword_create(keyword, __LOCATION__, name="ATOM_POINT", &
1065 : variants=["POINT_POINT"], &
1066 : description="Specifies the atom/point index defining the point.", &
1067 : usage="ATOM_POINT <INTEGER>", &
1068 76112 : n_var=1, type_of_var=integer_t)
1069 38056 : CALL section_add_keyword(section, keyword)
1070 38056 : CALL keyword_release(keyword)
1071 :
1072 : ! Must be present in each colvar and handled properly
1073 38056 : CALL create_point_section(subsection)
1074 38056 : CALL section_add_subsection(section, subsection)
1075 38056 : CALL section_release(subsection)
1076 :
1077 38056 : END SUBROUTINE create_colvar_d_pl_section
1078 :
1079 : ! **************************************************************************************************
1080 : !> \brief creates the colvar section regarded to the collective variables
1081 : !> angles betweem two planes
1082 : !> \param section the section to be created
1083 : !> \author teo
1084 : ! **************************************************************************************************
1085 38056 : SUBROUTINE create_colvar_a_pl_section(section)
1086 : TYPE(section_type), POINTER :: section
1087 :
1088 : TYPE(keyword_type), POINTER :: keyword
1089 : TYPE(section_type), POINTER :: subsection
1090 :
1091 38056 : CPASSERT(.NOT. ASSOCIATED(section))
1092 : CALL section_create(section, __LOCATION__, name="angle_plane_plane", &
1093 : description="This section defines the angle between two planes "// &
1094 : "as a collective variables.", &
1095 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1096 38056 : NULLIFY (keyword, subsection)
1097 :
1098 : CALL section_create(subsection, __LOCATION__, name="PLANE", &
1099 : description="This section defines the plane. When using this colvar, "// &
1100 : "two plane section must be defined!", &
1101 38056 : n_keywords=1, n_subsections=0, repeats=.TRUE.)
1102 :
1103 : CALL keyword_create(keyword, __LOCATION__, name="DEF_TYPE", &
1104 : description="Specify how the plane is defined: either by 3 atoms or by a fixed normal "// &
1105 : "vector. At least one plane must be defined through atoms.", &
1106 : usage="DEF_TYPE ATOMS", &
1107 : default_i_val=plane_def_atoms, &
1108 : enum_c_vals=s2a("ATOMS", "VECTOR"), &
1109 : enum_desc=s2a("Plane defined by the position of 3 atoms", &
1110 : "Plane defined by a fixed normal vector"), &
1111 38056 : enum_i_vals=[plane_def_atoms, plane_def_vec])
1112 38056 : CALL section_add_keyword(subsection, keyword)
1113 38056 : CALL keyword_release(keyword)
1114 :
1115 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
1116 : description="Specifies the indexes of 3 atoms/points defining the plane.", &
1117 : usage="ATOMS <INTEGER> <INTEGER> <INTEGER>", &
1118 38056 : n_var=3, type_of_var=integer_t)
1119 38056 : CALL section_add_keyword(subsection, keyword)
1120 38056 : CALL keyword_release(keyword)
1121 :
1122 : CALL keyword_create(keyword, __LOCATION__, name="NORMAL_VECTOR", &
1123 : description="Alternatively to 3 atoms/points one can define one of the two, "// &
1124 : "planes by defining its NORMAL vector.", &
1125 : usage="NORMAL_VECTOR 0.0 1.0 0.0", &
1126 38056 : n_var=3, type_of_var=real_t)
1127 38056 : CALL section_add_keyword(subsection, keyword)
1128 38056 : CALL keyword_release(keyword)
1129 38056 : CALL section_add_subsection(section, subsection)
1130 38056 : CALL section_release(subsection)
1131 :
1132 : ! Must be present in each colvar and handled properly
1133 38056 : CALL create_point_section(subsection)
1134 38056 : CALL section_add_subsection(section, subsection)
1135 38056 : CALL section_release(subsection)
1136 38056 : END SUBROUTINE create_colvar_a_pl_section
1137 :
1138 : ! **************************************************************************************************
1139 : !> \brief create a geometrical point as a function of several atom coordinates
1140 : !> \param section the section to be created
1141 : !> \author teo
1142 : ! **************************************************************************************************
1143 646958 : SUBROUTINE create_point_section(section)
1144 : TYPE(section_type), POINTER :: section
1145 :
1146 : TYPE(keyword_type), POINTER :: keyword
1147 :
1148 646958 : CPASSERT(.NOT. ASSOCIATED(section))
1149 : CALL section_create(section, __LOCATION__, name="POINT", &
1150 : description="Enables the possibility to use geometrical centers instead of single atoms"// &
1151 : " to define colvars", &
1152 646958 : n_keywords=1, n_subsections=0, repeats=.TRUE.)
1153 :
1154 646958 : NULLIFY (keyword)
1155 :
1156 : CALL keyword_create(keyword, __LOCATION__, name="TYPE", &
1157 : description="Chooses the type of geometrical point", &
1158 : usage="type (GEO_CENTER|FIX_POINT)", &
1159 : enum_c_vals=s2a("GEO_CENTER", "FIX_POINT"), &
1160 : enum_desc=s2a("Computes the geometrical center of the listed atoms", &
1161 : "Defines a fixed point in space"), &
1162 : enum_i_vals=[do_clv_geo_center, do_clv_fix_point], &
1163 646958 : default_i_val=do_clv_geo_center)
1164 646958 : CALL section_add_keyword(section, keyword)
1165 646958 : CALL keyword_release(keyword)
1166 :
1167 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
1168 : description="Specifies the indexes of atoms defining the geometrical center", &
1169 : usage="ATOMS {integer} {integer} {integer} {integer}", &
1170 646958 : n_var=-1, type_of_var=integer_t, repeats=.TRUE.)
1171 646958 : CALL section_add_keyword(section, keyword)
1172 646958 : CALL keyword_release(keyword)
1173 :
1174 : CALL keyword_create( &
1175 : keyword, __LOCATION__, name="WEIGHTS", &
1176 : description="Specifies the weights for a weighted geometrical center. Default is 1/natoms for every atom", &
1177 : usage="WEIGHTS {real} {real} {real} {real}", &
1178 646958 : n_var=-1, type_of_var=real_t, repeats=.TRUE.)
1179 646958 : CALL section_add_keyword(section, keyword)
1180 646958 : CALL keyword_release(keyword)
1181 :
1182 : CALL keyword_create(keyword, __LOCATION__, name="XYZ", &
1183 : description="Specifies the xyz of the fixed point (if the case)", &
1184 : usage="XYZ {real} {real} {real}", &
1185 : n_var=3, type_of_var=real_t, unit_str="bohr", &
1186 646958 : repeats=.FALSE.)
1187 646958 : CALL section_add_keyword(section, keyword)
1188 646958 : CALL keyword_release(keyword)
1189 :
1190 646958 : END SUBROUTINE create_point_section
1191 :
1192 : ! **************************************************************************************************
1193 : !> \brief collective variables specifying torsion
1194 : !> \param section the section to be created
1195 : !> \author teo
1196 : ! **************************************************************************************************
1197 38056 : SUBROUTINE create_colvar_qparm_section(section)
1198 : TYPE(section_type), POINTER :: section
1199 :
1200 : TYPE(keyword_type), POINTER :: keyword
1201 : TYPE(section_type), POINTER :: subsection
1202 :
1203 38056 : CPASSERT(.NOT. ASSOCIATED(section))
1204 : CALL section_create(section, __LOCATION__, name="qparm", &
1205 : description="Section to define the Q parameter (crystalline order parameter) as a collective variable.", &
1206 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1207 :
1208 38056 : NULLIFY (keyword, subsection)
1209 :
1210 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_FROM", &
1211 : variants=["POINTS_FROM"], &
1212 : description="Specify indexes of atoms/points building the coordination variable. ", &
1213 : usage="ATOMS_FROM {integer} {integer} ..", repeats=.TRUE., &
1214 76112 : n_var=-1, type_of_var=integer_t)
1215 38056 : CALL section_add_keyword(section, keyword)
1216 38056 : CALL keyword_release(keyword)
1217 :
1218 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS_TO", &
1219 : variants=["POINTS_TO"], &
1220 : description="Specify indexes of atoms/points building the coordination variable. ", &
1221 : usage="ATOMS_TO {integer} {integer} ..", repeats=.TRUE., &
1222 76112 : n_var=-1, type_of_var=integer_t)
1223 38056 : CALL section_add_keyword(section, keyword)
1224 38056 : CALL keyword_release(keyword)
1225 :
1226 : CALL keyword_create(keyword, __LOCATION__, name="RCUT", &
1227 : description="Specifies the distance cutoff for neighbors. "// &
1228 : "Cutoff function is exactly zero for all neighbors beyond RCUT.", &
1229 : usage="RCUT {real}", &
1230 38056 : n_var=1, unit_str="angstrom", type_of_var=real_t)
1231 38056 : CALL section_add_keyword(section, keyword)
1232 38056 : CALL keyword_release(keyword)
1233 :
1234 : CALL keyword_create(keyword, __LOCATION__, name="INCLUDE_IMAGES", &
1235 : description="Whether to include periodic images of ATOMS_TO into the neighbor list.", &
1236 : usage="INCLUDE_IMAGES", &
1237 38056 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
1238 38056 : CALL section_add_keyword(section, keyword)
1239 38056 : CALL keyword_release(keyword)
1240 :
1241 : CALL keyword_create(keyword, __LOCATION__, name="RSTART", &
1242 : description="Specifies the distance cutoff for neighbors. "// &
1243 : "Cutoff function is exactly 1 for all neighbors closer than RSTART.", &
1244 : usage="RSTART {real}", &
1245 38056 : n_var=1, unit_str="angstrom", type_of_var=real_t)
1246 38056 : CALL section_add_keyword(section, keyword)
1247 38056 : CALL keyword_release(keyword)
1248 :
1249 : CALL keyword_create(keyword, __LOCATION__, name="L", &
1250 : description="Specifies the L spherical harmonics from Ylm.", &
1251 : usage="L {integer}", &
1252 38056 : n_var=1, type_of_var=integer_t)
1253 38056 : CALL section_add_keyword(section, keyword)
1254 38056 : CALL keyword_release(keyword)
1255 :
1256 : !CALL keyword_create(keyword, __LOCATION__, name="ALPHA", &
1257 : ! description="Specifies the width of the Fermi-Dirac style smearing around RCUT.", &
1258 : ! usage="ALPHA {real}", unit_str="angstrom^-1", default_r_val=0.0_dp)
1259 : !CALL section_add_keyword(section, keyword)
1260 : !CALL keyword_release(keyword)
1261 :
1262 : ! Must be present in each colvar and handled properly
1263 38056 : CALL create_point_section(subsection)
1264 38056 : CALL section_add_subsection(section, subsection)
1265 38056 : CALL section_release(subsection)
1266 :
1267 38056 : END SUBROUTINE create_colvar_qparm_section
1268 :
1269 : ! **************************************************************************************************
1270 : !> \brief collective variables specifying hydronium solvation
1271 : !> \param section the section to be created
1272 : !> \author Marcel Baer
1273 : ! **************************************************************************************************
1274 38056 : SUBROUTINE create_colvar_hydronium_shell_section(section)
1275 : TYPE(section_type), POINTER :: section
1276 :
1277 : TYPE(keyword_type), POINTER :: keyword
1278 :
1279 38056 : CPASSERT(.NOT. ASSOCIATED(section))
1280 : CALL section_create(section, __LOCATION__, name="HYDRONIUM_SHELL", &
1281 : description="Section to define the formation of a hydronium as a"// &
1282 : " collective variable. Number of oxygens in the 1st shell of the"// &
1283 : " hydronium. Adapted from Equation (3) in Supplementary Info of"// &
1284 : " J. Am. Chem. Soc.,128, 2006, 11318, i.e. omitting the cutoff function"// &
1285 : " and summing only over the oxygens of water.", &
1286 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1287 :
1288 38056 : NULLIFY (keyword)
1289 :
1290 : CALL keyword_create(keyword, __LOCATION__, name="OXYGENS", &
1291 : description="Specifies indexes of atoms building the coordination variable."// &
1292 : " Oxygens of the water molecules.", &
1293 : usage="OXYGENS {integer} {integer} ..", repeats=.TRUE., &
1294 38056 : n_var=-1, type_of_var=integer_t)
1295 38056 : CALL section_add_keyword(section, keyword)
1296 38056 : CALL keyword_release(keyword)
1297 :
1298 : CALL keyword_create(keyword, __LOCATION__, name="HYDROGENS", &
1299 : description="Specifies indexes of atoms building the coordination variable."// &
1300 : " Hydrogens of the water molecules.", &
1301 : usage="HYDROGENS {integer} {integer} ..", repeats=.TRUE., &
1302 38056 : n_var=-1, type_of_var=integer_t)
1303 38056 : CALL section_add_keyword(section, keyword)
1304 38056 : CALL keyword_release(keyword)
1305 :
1306 : CALL keyword_create(keyword, __LOCATION__, name="ROO", &
1307 : description="Specifies the rc parameter in the coordination function:"// &
1308 : " number of oxygens per water oxygen.", &
1309 : usage="ROO {real}", default_r_val=cp_unit_to_cp2k(value=3.0_dp, &
1310 38056 : unit_str="bohr"), unit_str="bohr", n_var=1)
1311 38056 : CALL section_add_keyword(section, keyword)
1312 38056 : CALL keyword_release(keyword)
1313 :
1314 : CALL keyword_create(keyword, __LOCATION__, name="pOO", &
1315 : variants=["EXPON_NUMERATORA"], &
1316 : description="Sets the value of the numerator of the exponential factor"// &
1317 : " in the coordination function: number of oxygens per water oxygen.", &
1318 : usage="pOO {integer}", default_i_val=6, &
1319 76112 : n_var=1)
1320 38056 : CALL section_add_keyword(section, keyword)
1321 38056 : CALL keyword_release(keyword)
1322 :
1323 : CALL keyword_create(keyword, __LOCATION__, name="qOO", &
1324 : variants=["EXPON_DENOMINATORA"], &
1325 : description="Sets the value of the denominator of the exponential factor"// &
1326 : " in the coordination function: number of oxygens per water oxygen.", &
1327 : usage="qOO {integer}", default_i_val=12, &
1328 76112 : n_var=1)
1329 38056 : CALL section_add_keyword(section, keyword)
1330 38056 : CALL keyword_release(keyword)
1331 :
1332 : CALL keyword_create(keyword, __LOCATION__, name="ROH", &
1333 : description="Specifies the rc parameter in the coordination function:"// &
1334 : " number of hydrogens per water molecule.", &
1335 : usage="ROH {real}", default_r_val=cp_unit_to_cp2k(value=3.0_dp, &
1336 38056 : unit_str="bohr"), unit_str="bohr", n_var=1)
1337 38056 : CALL section_add_keyword(section, keyword)
1338 38056 : CALL keyword_release(keyword)
1339 :
1340 : CALL keyword_create(keyword, __LOCATION__, name="pOH", &
1341 : variants=["EXPON_NUMERATORB"], &
1342 : description="Sets the value of the numerator of the exponential factor"// &
1343 : " in the coordination function: number of hydrogens per water molecule.", &
1344 : usage="pOH {integer}", default_i_val=6, &
1345 76112 : n_var=1)
1346 38056 : CALL section_add_keyword(section, keyword)
1347 38056 : CALL keyword_release(keyword)
1348 :
1349 : CALL keyword_create(keyword, __LOCATION__, name="qOH", &
1350 : variants=["EXPON_DENOMINATORB"], &
1351 : description="Sets the value of the denominator of the exponential factor"// &
1352 : " in the coordination function: number of hydrogens per water molecule.", &
1353 : usage="qOH {integer}", default_i_val=12, &
1354 76112 : n_var=1)
1355 38056 : CALL section_add_keyword(section, keyword)
1356 38056 : CALL keyword_release(keyword)
1357 :
1358 : CALL keyword_create(keyword, __LOCATION__, name="NH", &
1359 : description="Specifies the NH parameter in the M function.", &
1360 : usage="NH {real}", default_r_val=3.0_dp, &
1361 38056 : n_var=1)
1362 38056 : CALL section_add_keyword(section, keyword)
1363 38056 : CALL keyword_release(keyword)
1364 :
1365 : CALL keyword_create(keyword, __LOCATION__, name="pM", &
1366 : variants=["EXPON_NUMERATOR"], &
1367 : description="Sets the value of the numerator of the exponential factor"// &
1368 : " in the M function.", &
1369 : usage="pM {integer}", default_i_val=8, &
1370 76112 : n_var=1)
1371 38056 : CALL section_add_keyword(section, keyword)
1372 38056 : CALL keyword_release(keyword)
1373 :
1374 : CALL keyword_create(keyword, __LOCATION__, name="qM", &
1375 : variants=["EXPON_DENOMINATOR"], &
1376 : description="Sets the value of the denominator of the exponential factor"// &
1377 : " in the M function.", &
1378 : usage="qM {integer}", default_i_val=16, &
1379 76112 : n_var=1)
1380 38056 : CALL section_add_keyword(section, keyword)
1381 38056 : CALL keyword_release(keyword)
1382 :
1383 : CALL keyword_create(keyword, __LOCATION__, name="LAMBDA", &
1384 : description="Specify the LAMBDA parameter in the hydronium function.", &
1385 : usage="LAMBDA {real}", default_r_val=10.0_dp, &
1386 38056 : n_var=1)
1387 38056 : CALL section_add_keyword(section, keyword)
1388 38056 : CALL keyword_release(keyword)
1389 :
1390 38056 : END SUBROUTINE create_colvar_hydronium_shell_section
1391 :
1392 : ! **************************************************************************************************
1393 : !> \brief collective variables specifying the distance between hydronium and hydroxide ion
1394 : !> \param section the section to be created
1395 : !> \author Dorothea Golze
1396 : ! **************************************************************************************************
1397 38056 : SUBROUTINE create_colvar_hydronium_dist_section(section)
1398 : TYPE(section_type), POINTER :: section
1399 :
1400 : TYPE(keyword_type), POINTER :: keyword
1401 :
1402 38056 : CPASSERT(.NOT. ASSOCIATED(section))
1403 : CALL section_create(section, __LOCATION__, name="HYDRONIUM_DISTANCE", &
1404 : description="Section to define the formation of a hydronium as a"// &
1405 : " collective variable. Distance between hydronium and hydroxide ion"// &
1406 : " Experimental at this point, i.e. not proved to be an effective"// &
1407 : " collective variable.", &
1408 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1409 :
1410 38056 : NULLIFY (keyword)
1411 :
1412 : CALL keyword_create(keyword, __LOCATION__, name="OXYGENS", &
1413 : description="Specifies indexes of atoms building the coordination variable."// &
1414 : " Oxygens of the water molecules.", &
1415 : usage="OXYGENS {integer} {integer} ..", repeats=.TRUE., &
1416 38056 : n_var=-1, type_of_var=integer_t)
1417 38056 : CALL section_add_keyword(section, keyword)
1418 38056 : CALL keyword_release(keyword)
1419 :
1420 : CALL keyword_create(keyword, __LOCATION__, name="HYDROGENS", &
1421 : description="Specifies indexes of atoms building the coordination variable."// &
1422 : " Hydrogens of the water molecules.", &
1423 : usage="HYDROGENS {integer} {integer} ..", repeats=.TRUE., &
1424 38056 : n_var=-1, type_of_var=integer_t)
1425 38056 : CALL section_add_keyword(section, keyword)
1426 38056 : CALL keyword_release(keyword)
1427 :
1428 : CALL keyword_create(keyword, __LOCATION__, name="ROH", &
1429 : description="Specifies the rc parameter in the coordination function:"// &
1430 : " number of hydrogens per water molecule.", &
1431 : usage="ROH {real}", default_r_val=cp_unit_to_cp2k(value=2.4_dp, &
1432 38056 : unit_str="bohr"), unit_str="bohr", n_var=1)
1433 38056 : CALL section_add_keyword(section, keyword)
1434 38056 : CALL keyword_release(keyword)
1435 :
1436 : CALL keyword_create(keyword, __LOCATION__, name="pOH", &
1437 : description="Sets the value of the numerator of the exponential factor"// &
1438 : " in the coordination function: number of hydrogens per water molecule.", &
1439 : usage="pOH {integer}", default_i_val=6, &
1440 38056 : n_var=1)
1441 38056 : CALL section_add_keyword(section, keyword)
1442 38056 : CALL keyword_release(keyword)
1443 :
1444 : CALL keyword_create(keyword, __LOCATION__, name="qOH", &
1445 : description="Sets the value of the denominator of the exponential factor"// &
1446 : " in the coordination function: number of hydrogens per water molecule.", &
1447 : usage="qOH {integer}", default_i_val=12, &
1448 38056 : n_var=1)
1449 38056 : CALL section_add_keyword(section, keyword)
1450 38056 : CALL keyword_release(keyword)
1451 :
1452 : CALL keyword_create(keyword, __LOCATION__, name="NH", &
1453 : description="Specifies the NH parameter in the M function.", &
1454 : usage="NH {real}", default_r_val=2.2_dp, &
1455 38056 : n_var=1)
1456 38056 : CALL section_add_keyword(section, keyword)
1457 38056 : CALL keyword_release(keyword)
1458 :
1459 : CALL keyword_create(keyword, __LOCATION__, name="pM", &
1460 : description="Sets the value of the numerator of the exponential factor"// &
1461 : " in the M function.", &
1462 : usage="pM {integer}", default_i_val=8, &
1463 38056 : n_var=1)
1464 38056 : CALL section_add_keyword(section, keyword)
1465 38056 : CALL keyword_release(keyword)
1466 :
1467 : CALL keyword_create(keyword, __LOCATION__, name="qM", &
1468 : description="Sets the value of the denominator of the exponential factor"// &
1469 : " in the M function.", &
1470 : usage="qM {integer}", default_i_val=16, &
1471 38056 : n_var=1)
1472 38056 : CALL section_add_keyword(section, keyword)
1473 38056 : CALL keyword_release(keyword)
1474 :
1475 : CALL keyword_create(keyword, __LOCATION__, name="NN", &
1476 : description="Specifies the NN parameter in the F function.", &
1477 : usage="NN {real}", default_r_val=1.5_dp, &
1478 38056 : n_var=1)
1479 38056 : CALL section_add_keyword(section, keyword)
1480 38056 : CALL keyword_release(keyword)
1481 :
1482 : CALL keyword_create(keyword, __LOCATION__, name="pF", &
1483 : description="Sets the value of the numerator of the exponential factor"// &
1484 : " in the F function.", &
1485 : usage="pF {integer}", default_i_val=8, &
1486 38056 : n_var=1)
1487 38056 : CALL section_add_keyword(section, keyword)
1488 38056 : CALL keyword_release(keyword)
1489 :
1490 : CALL keyword_create(keyword, __LOCATION__, name="qF", &
1491 : description="Sets the value of the denominator of the exponential factor"// &
1492 : " in the F function.", &
1493 : usage="qF {integer}", default_i_val=16, &
1494 38056 : n_var=1)
1495 38056 : CALL section_add_keyword(section, keyword)
1496 38056 : CALL keyword_release(keyword)
1497 :
1498 : CALL keyword_create(keyword, __LOCATION__, name="LAMBDA", &
1499 : description="Specify the LAMBDA parameter in the hydronium function.", &
1500 : usage="LAMBDA {real}", default_r_val=20.0_dp, &
1501 38056 : n_var=1)
1502 38056 : CALL section_add_keyword(section, keyword)
1503 38056 : CALL keyword_release(keyword)
1504 :
1505 38056 : END SUBROUTINE create_colvar_hydronium_dist_section
1506 :
1507 : ! **************************************************************************************************
1508 : !> \brief collective variables specifying the solvation of carboxylic acid;
1509 : !> distance between hydronium ion and acetate ion; Equation (2) in
1510 : !> Supplementary Information of J. Am. Chem. Soc.,128, 2006, 11318
1511 : !> \param section the section to be created
1512 : !> \author Dorothea Golze
1513 : ! **************************************************************************************************
1514 38056 : SUBROUTINE create_colvar_acid_hyd_dist_section(section)
1515 : TYPE(section_type), POINTER :: section
1516 :
1517 : TYPE(keyword_type), POINTER :: keyword
1518 :
1519 38056 : CPASSERT(.NOT. ASSOCIATED(section))
1520 : CALL section_create(section, __LOCATION__, name="ACID_HYDRONIUM_DISTANCE", &
1521 : description="Section to define the dissociation of a carboxylic acid in"// &
1522 : " water. Distance between hydronium ion and acetate ion. Equation (2)"// &
1523 : " in Supplementary Info of J. Am. Chem. Soc.,128, 2006, 11318.", &
1524 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1525 :
1526 38056 : NULLIFY (keyword)
1527 :
1528 : CALL keyword_create(keyword, __LOCATION__, name="OXYGENS_WATER", &
1529 : description="Specifies indexes of atoms building the coordination variable."// &
1530 : " Oxygens of the water molecules. ", &
1531 : usage="OXYGENS_WATER {integer} {integer} ..", repeats=.TRUE., &
1532 38056 : n_var=-1, type_of_var=integer_t)
1533 38056 : CALL section_add_keyword(section, keyword)
1534 38056 : CALL keyword_release(keyword)
1535 :
1536 : CALL keyword_create(keyword, __LOCATION__, name="OXYGENS_ACID", &
1537 : description="Specifies indexes of atoms building the coordination variable."// &
1538 : " Oxygens of the carboxyl groups.", &
1539 : usage="OXYGENS_ACID {integer} {integer} ..", repeats=.TRUE., &
1540 38056 : n_var=-1, type_of_var=integer_t)
1541 38056 : CALL section_add_keyword(section, keyword)
1542 38056 : CALL keyword_release(keyword)
1543 :
1544 : CALL keyword_create(keyword, __LOCATION__, name="HYDROGENS", &
1545 : description="Specifies indexes of atoms building the coordination variable."// &
1546 : " Hydrogens of the water molecules and of the carboxyl groups.", &
1547 : usage="HYDROGENS {integer} {integer} ..", repeats=.TRUE., &
1548 38056 : n_var=-1, type_of_var=integer_t)
1549 38056 : CALL section_add_keyword(section, keyword)
1550 38056 : CALL keyword_release(keyword)
1551 :
1552 : CALL keyword_create(keyword, __LOCATION__, name="pWOH", &
1553 : description="Sets the value of the numerator of the exponential factor"// &
1554 : " in the coordination function: number of hydrogens per water molecule.", &
1555 : usage="pWOH {integer}", default_i_val=8, &
1556 38056 : n_var=1)
1557 38056 : CALL section_add_keyword(section, keyword)
1558 38056 : CALL keyword_release(keyword)
1559 :
1560 : CALL keyword_create(keyword, __LOCATION__, name="qWOH", &
1561 : description="Sets the value of the denominator of the exponential factor"// &
1562 : " in the coordination function: number of hydrogens per water molecule.", &
1563 : usage="qWOH {integer}", default_i_val=16, &
1564 38056 : n_var=1)
1565 38056 : CALL section_add_keyword(section, keyword)
1566 38056 : CALL keyword_release(keyword)
1567 :
1568 : CALL keyword_create(keyword, __LOCATION__, name="RWOH", &
1569 : description="Specify the rc parameter in the coordination function:"// &
1570 : " number of hydrogens per water molecule.", &
1571 : usage="RWOH {real}", default_r_val=cp_unit_to_cp2k(value=2.4_dp, &
1572 38056 : unit_str="bohr"), unit_str="bohr", n_var=1)
1573 38056 : CALL section_add_keyword(section, keyword)
1574 38056 : CALL keyword_release(keyword)
1575 :
1576 : CALL keyword_create(keyword, __LOCATION__, name="pAOH", &
1577 : description="Sets the value of the numerator of the exponential factor"// &
1578 : " in the coordination function: number of hydrogens per carboxyl group.", &
1579 : usage="pAOH {integer}", default_i_val=6, &
1580 38056 : n_var=1)
1581 38056 : CALL section_add_keyword(section, keyword)
1582 38056 : CALL keyword_release(keyword)
1583 :
1584 : CALL keyword_create(keyword, __LOCATION__, name="qAOH", &
1585 : description="Sets the value of the denominator of the exponential factor"// &
1586 : " in the coordination function: number of hydrogens per carboxyl group.", &
1587 : usage="qAOH {integer}", default_i_val=14, &
1588 38056 : n_var=1)
1589 38056 : CALL section_add_keyword(section, keyword)
1590 38056 : CALL keyword_release(keyword)
1591 :
1592 : CALL keyword_create(keyword, __LOCATION__, name="RAOH", &
1593 : description="Specify the rc parameter in the coordination function:"// &
1594 : " number of hydrogens per carboxyl group.", &
1595 : usage="RAOH {real}", default_r_val=cp_unit_to_cp2k(value=2.4_dp, &
1596 38056 : unit_str="bohr"), unit_str="bohr", n_var=1)
1597 38056 : CALL section_add_keyword(section, keyword)
1598 38056 : CALL keyword_release(keyword)
1599 :
1600 : CALL keyword_create(keyword, __LOCATION__, name="pCUT", &
1601 : description="Sets the value of the numerator of the exponential factor"// &
1602 : " in the cutoff function.", &
1603 : usage="pCUT {integer}", default_i_val=6, &
1604 38056 : n_var=1)
1605 38056 : CALL section_add_keyword(section, keyword)
1606 38056 : CALL keyword_release(keyword)
1607 :
1608 : CALL keyword_create(keyword, __LOCATION__, name="qCUT", &
1609 : description="Sets the value of the denominator of the exponential factor"// &
1610 : " in the cutoff function.", &
1611 : usage="qCUT {integer}", default_i_val=12, &
1612 38056 : n_var=1)
1613 38056 : CALL section_add_keyword(section, keyword)
1614 38056 : CALL keyword_release(keyword)
1615 :
1616 : CALL keyword_create(keyword, __LOCATION__, name="NC", &
1617 : description="Specifies the NC parameter in the cutoff function.", &
1618 : usage="NC {real}", default_r_val=0.56_dp, &
1619 38056 : n_var=1)
1620 38056 : CALL section_add_keyword(section, keyword)
1621 38056 : CALL keyword_release(keyword)
1622 :
1623 : CALL keyword_create(keyword, __LOCATION__, name="LAMBDA", &
1624 : variants=["LAMBDA"], &
1625 : description="Specifies the LAMBDA parameter carboxylic acid function.", &
1626 : usage="LAMBDA {real}", default_r_val=20.0_dp, &
1627 76112 : n_var=1)
1628 38056 : CALL section_add_keyword(section, keyword)
1629 38056 : CALL keyword_release(keyword)
1630 :
1631 38056 : END SUBROUTINE create_colvar_acid_hyd_dist_section
1632 :
1633 : ! **************************************************************************************************
1634 : !> \brief collective variables specifying the solvation of carboxylic acid;
1635 : !> number of oxygens in the 1st shell of the hydronium; Equation (3) in
1636 : !> Supplementary Information of J. Am. Chem. Soc.,128, 2006, 11318
1637 : !> \param section the section to be created
1638 : !> \author Dorothea Golze
1639 : ! **************************************************************************************************
1640 38056 : SUBROUTINE create_colvar_acid_hyd_shell_section(section)
1641 : TYPE(section_type), POINTER :: section
1642 :
1643 : TYPE(keyword_type), POINTER :: keyword
1644 :
1645 38056 : CPASSERT(.NOT. ASSOCIATED(section))
1646 : CALL section_create(section, __LOCATION__, name="ACID_HYDRONIUM_SHELL", &
1647 : description="Section to define the dissociation of a carboxylic acid in"// &
1648 : " water. Number of oxygens in the 1st shell of the hydronium. Equation (3)"// &
1649 : " in Supplementary Info of J. Am. Chem. Soc.,128, 2006, 11318. Similar to"// &
1650 : " the HYDRONIUM colvar, but with modification for the acid.", &
1651 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1652 :
1653 38056 : NULLIFY (keyword)
1654 :
1655 : CALL keyword_create(keyword, __LOCATION__, name="OXYGENS_WATER", &
1656 : description="Specifies indexes of atoms building the coordination variable."// &
1657 : " Oxygens of the water molecules. ", &
1658 : usage="OXYGENS_WATER {integer} {integer} ..", repeats=.TRUE., &
1659 38056 : n_var=-1, type_of_var=integer_t)
1660 38056 : CALL section_add_keyword(section, keyword)
1661 38056 : CALL keyword_release(keyword)
1662 :
1663 : CALL keyword_create(keyword, __LOCATION__, name="OXYGENS_ACID", &
1664 : description="Specifies indexes of atoms building the coordination variable."// &
1665 : " Oxygens of the carboxyl groups.", &
1666 : usage="OXYGENS_ACID {integer} {integer} ..", repeats=.TRUE., &
1667 38056 : n_var=-1, type_of_var=integer_t)
1668 38056 : CALL section_add_keyword(section, keyword)
1669 38056 : CALL keyword_release(keyword)
1670 :
1671 : CALL keyword_create(keyword, __LOCATION__, name="HYDROGENS", &
1672 : description="Specifies indexes of atoms building the coordination variable."// &
1673 : " Hydrogens of the water molecules and of the carboxyl groups.", &
1674 : usage="HYDROGENS {integer} {integer} ..", repeats=.TRUE., &
1675 38056 : n_var=-1, type_of_var=integer_t)
1676 38056 : CALL section_add_keyword(section, keyword)
1677 38056 : CALL keyword_release(keyword)
1678 :
1679 : CALL keyword_create(keyword, __LOCATION__, name="pWOH", &
1680 : description="Sets the value of the numerator of the exponential factor"// &
1681 : " in the coordination function: number of hydrogens per water molecule.", &
1682 : usage="pWOH {integer}", default_i_val=8, &
1683 38056 : n_var=1)
1684 38056 : CALL section_add_keyword(section, keyword)
1685 38056 : CALL keyword_release(keyword)
1686 :
1687 : CALL keyword_create(keyword, __LOCATION__, name="qWOH", &
1688 : description="Sets the value of the denominator of the exponential factor"// &
1689 : " in the coordination function: number of hydrogens per water molecule.", &
1690 : usage="qWOH {integer}", default_i_val=16, &
1691 38056 : n_var=1)
1692 38056 : CALL section_add_keyword(section, keyword)
1693 38056 : CALL keyword_release(keyword)
1694 :
1695 : CALL keyword_create(keyword, __LOCATION__, name="RWOH", &
1696 : description="Specifies the rc parameter in the coordination function:"// &
1697 : " number of hydrogens per water molecule.", &
1698 : usage="RWOH {real}", default_r_val=cp_unit_to_cp2k(value=2.4_dp, &
1699 38056 : unit_str="bohr"), unit_str="bohr", n_var=1)
1700 38056 : CALL section_add_keyword(section, keyword)
1701 38056 : CALL keyword_release(keyword)
1702 :
1703 : CALL keyword_create(keyword, __LOCATION__, name="pAOH", &
1704 : description="Sets the value of the numerator of the exponential factor"// &
1705 : " in the coordination function: number of hydrogens per carboxyl group.", &
1706 : usage="pAOH {integer}", default_i_val=6, &
1707 38056 : n_var=1)
1708 38056 : CALL section_add_keyword(section, keyword)
1709 38056 : CALL keyword_release(keyword)
1710 :
1711 : CALL keyword_create(keyword, __LOCATION__, name="qAOH", &
1712 : description="Sets the value of the denominator of the exponential factor"// &
1713 : " in the coordination function: number of hydrogens per carboxyl group.", &
1714 : usage="qAOH {integer}", default_i_val=14, &
1715 38056 : n_var=1)
1716 38056 : CALL section_add_keyword(section, keyword)
1717 38056 : CALL keyword_release(keyword)
1718 :
1719 : CALL keyword_create(keyword, __LOCATION__, name="RAOH", &
1720 : description="Specifies the rc parameter in the coordination function:"// &
1721 : " number of hydrogens per carboxyl group.", &
1722 : usage="RAOH {real}", default_r_val=cp_unit_to_cp2k(value=2.4_dp, &
1723 38056 : unit_str="bohr"), unit_str="bohr", n_var=1)
1724 38056 : CALL section_add_keyword(section, keyword)
1725 38056 : CALL keyword_release(keyword)
1726 :
1727 : CALL keyword_create(keyword, __LOCATION__, name="pOO", &
1728 : description="Sets the value of the numerator of the exponential factor"// &
1729 : " in the coordination function: number of oxygens per water oxygen.", &
1730 : usage="pOO {integer}", default_i_val=6, &
1731 38056 : n_var=1)
1732 38056 : CALL section_add_keyword(section, keyword)
1733 38056 : CALL keyword_release(keyword)
1734 :
1735 : CALL keyword_create(keyword, __LOCATION__, name="qOO", &
1736 : description="Sets the value of the denominator of the exponential factor"// &
1737 : " in the coordination function: number of oxygens per water oxygen.", &
1738 : usage="qOO {integer}", default_i_val=12, &
1739 38056 : n_var=1)
1740 38056 : CALL section_add_keyword(section, keyword)
1741 38056 : CALL keyword_release(keyword)
1742 :
1743 : CALL keyword_create(keyword, __LOCATION__, name="ROO", &
1744 : description="Specifies the rc parameter in the coordination function:"// &
1745 : " number of oxygens per water oxygen.", &
1746 : usage="ROO {real}", default_r_val=cp_unit_to_cp2k(value=5.5_dp, &
1747 38056 : unit_str="bohr"), unit_str="bohr", n_var=1)
1748 38056 : CALL section_add_keyword(section, keyword)
1749 38056 : CALL keyword_release(keyword)
1750 :
1751 : CALL keyword_create(keyword, __LOCATION__, name="pM", &
1752 : description="Sets the value of the numerator of the exponential factor"// &
1753 : " in the M function.", &
1754 : usage="pM {integer}", default_i_val=8, &
1755 38056 : n_var=1)
1756 38056 : CALL section_add_keyword(section, keyword)
1757 38056 : CALL keyword_release(keyword)
1758 :
1759 : CALL keyword_create(keyword, __LOCATION__, name="qM", &
1760 : description="Sets the value of the denominator of the exponential factor"// &
1761 : " in the M function.", &
1762 : usage="qM {integer}", default_i_val=16, &
1763 38056 : n_var=1)
1764 38056 : CALL section_add_keyword(section, keyword)
1765 38056 : CALL keyword_release(keyword)
1766 :
1767 : CALL keyword_create(keyword, __LOCATION__, name="NH", &
1768 : description="Specifies the NH parameter in the M function.", &
1769 : usage="NH {real}", default_r_val=2.2_dp, &
1770 38056 : n_var=1)
1771 38056 : CALL section_add_keyword(section, keyword)
1772 38056 : CALL keyword_release(keyword)
1773 :
1774 : CALL keyword_create(keyword, __LOCATION__, name="pCUT", &
1775 : description="Sets the value of the numerator of the exponential factor"// &
1776 : " in the cutoff function.", &
1777 : usage="pCUT {integer}", default_i_val=6, &
1778 38056 : n_var=1)
1779 38056 : CALL section_add_keyword(section, keyword)
1780 38056 : CALL keyword_release(keyword)
1781 :
1782 : CALL keyword_create(keyword, __LOCATION__, name="qCUT", &
1783 : description="Sets the value of the denominator of the exponential factor"// &
1784 : " in the cutoff function.", &
1785 : usage="qCUT {integer}", default_i_val=12, &
1786 38056 : n_var=1)
1787 38056 : CALL section_add_keyword(section, keyword)
1788 38056 : CALL keyword_release(keyword)
1789 :
1790 : CALL keyword_create(keyword, __LOCATION__, name="NC", &
1791 : description="Specifies the NC parameter in the cutoff function.", &
1792 : usage="NC {real}", default_r_val=0.9_dp, &
1793 38056 : n_var=1)
1794 38056 : CALL section_add_keyword(section, keyword)
1795 38056 : CALL keyword_release(keyword)
1796 :
1797 : CALL keyword_create(keyword, __LOCATION__, name="LAMBDA", &
1798 : variants=["LAMBDA"], &
1799 : description="Specifies the LAMBDA parameter carboxylic acid function.", &
1800 : usage="LAMBDA {real}", default_r_val=10.0_dp, &
1801 76112 : n_var=1)
1802 38056 : CALL section_add_keyword(section, keyword)
1803 38056 : CALL keyword_release(keyword)
1804 :
1805 38056 : END SUBROUTINE create_colvar_acid_hyd_shell_section
1806 :
1807 : ! **************************************************************************************************
1808 : !> \brief ...
1809 : !> \param section ...
1810 : ! **************************************************************************************************
1811 38056 : SUBROUTINE create_colvar_rmsd_section(section)
1812 : TYPE(section_type), POINTER :: section
1813 :
1814 : TYPE(keyword_type), POINTER :: keyword
1815 : TYPE(section_type), POINTER :: subsection, subsubsection
1816 :
1817 38056 : CPASSERT(.NOT. ASSOCIATED(section))
1818 : CALL section_create(section, __LOCATION__, name="rmsd", &
1819 : description="Section to define a CV as function of RMSD computed with respect to"// &
1820 : " given reference configurations. For 2 configurations the colvar is equal to:"// &
1821 : " ss = (RMSDA-RMSDB)/(RMSDA+RMSDB), while if only 1 configuration is given, then the"// &
1822 : " colvar is just the RMSD from that frame.", &
1823 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1824 :
1825 38056 : NULLIFY (keyword, subsection, subsubsection)
1826 : CALL keyword_create(keyword, __LOCATION__, name="SUBSET_TYPE", &
1827 : description="Define the subsytem used to compute the RMSD. With ALL the displacements"// &
1828 : " are mass-weighted, with LIST all weights are set to 1,"// &
1829 : " with WEIGHT_LIST a list of weights is expected from input.", &
1830 : usage="SUBSET_TYPE ALL", &
1831 : enum_c_vals=s2a("ALL", "LIST", "WEIGHT_LIST"), &
1832 : enum_i_vals=[rmsd_all, rmsd_list, rmsd_weightlist], &
1833 38056 : default_i_val=rmsd_all)
1834 38056 : CALL section_add_keyword(section, keyword)
1835 38056 : CALL keyword_release(keyword)
1836 :
1837 : CALL keyword_create(keyword, __LOCATION__, name="ALIGN_FRAMES", &
1838 : description="Whether the reference frames should be aligned to minimize the RMSD", &
1839 : usage="ALIGN_FRAMES", &
1840 38056 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
1841 38056 : CALL section_add_keyword(section, keyword)
1842 38056 : CALL keyword_release(keyword)
1843 :
1844 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
1845 : description="Specify indexes of atoms building the subset. ", &
1846 : usage="ATOMS {integer} {integer} ..", repeats=.TRUE., &
1847 38056 : n_var=-1, type_of_var=integer_t)
1848 38056 : CALL section_add_keyword(section, keyword)
1849 38056 : CALL keyword_release(keyword)
1850 :
1851 : CALL keyword_create(keyword, __LOCATION__, name="WEIGHTS", &
1852 : description="Specify weights of atoms building the subset. It is used only with WEIGHT_LIST ", &
1853 : usage="weightS {real} {real} ..", repeats=.TRUE., &
1854 38056 : n_var=-1, type_of_var=real_t)
1855 38056 : CALL section_add_keyword(section, keyword)
1856 38056 : CALL keyword_release(keyword)
1857 :
1858 : CALL section_create(subsection, __LOCATION__, name="FRAME", &
1859 : description="Specify coordinates of the frame (number of frames can be either 1 or 2)", &
1860 38056 : repeats=.TRUE.)
1861 :
1862 : CALL keyword_create(keyword, __LOCATION__, name="COORD_FILE_NAME", &
1863 : description="Name of the xyz file with coordinates (alternative to &COORD section)", &
1864 : usage="COORD_FILE_NAME <CHAR>", &
1865 38056 : default_lc_val="")
1866 38056 : CALL section_add_keyword(subsection, keyword)
1867 38056 : CALL keyword_release(keyword)
1868 :
1869 38056 : CALL create_coord_section_cv(subsubsection, "RMSD")
1870 38056 : CALL section_add_subsection(subsection, subsubsection)
1871 38056 : CALL section_release(subsubsection)
1872 :
1873 38056 : CALL section_add_subsection(section, subsection)
1874 38056 : CALL section_release(subsection)
1875 :
1876 38056 : END SUBROUTINE create_colvar_rmsd_section
1877 :
1878 : ! **************************************************************************************************
1879 : !> \brief collective variables specifying the space orthogonal to the reaction path
1880 : !> in the space spanned by the involved collective coordinates
1881 : !> \param section the section to be created
1882 : !> \author fschiff
1883 : ! **************************************************************************************************
1884 9514 : SUBROUTINE create_colvar_rpath_section(section)
1885 : TYPE(section_type), POINTER :: section
1886 :
1887 9514 : CPASSERT(.NOT. ASSOCIATED(section))
1888 : CALL section_create(section, __LOCATION__, name="REACTION_PATH", &
1889 : description="Section defining a one dimensional reaction path in an Q-dimensional space of colvars. "// &
1890 : "Constraining this colvar, allows to sample the space orthogonal to the reaction path, "// &
1891 : "both in the Q-dimensional colvar and 3N-Q remaining coordinates. "// &
1892 : "For the details of the function see cited literature.", &
1893 : n_keywords=1, n_subsections=0, repeats=.FALSE., &
1894 19028 : citations=[Branduardi2007])
1895 :
1896 9514 : CALL keywords_colvar_path(section)
1897 9514 : END SUBROUTINE create_colvar_rpath_section
1898 :
1899 : ! **************************************************************************************************
1900 : !> \brief Distance from reaction path
1901 : !> \param section the section to be created
1902 : !> \author 01.2010
1903 : ! **************************************************************************************************
1904 9514 : SUBROUTINE create_colvar_dpath_section(section)
1905 : TYPE(section_type), POINTER :: section
1906 :
1907 9514 : CPASSERT(.NOT. ASSOCIATED(section))
1908 : CALL section_create(section, __LOCATION__, name="DISTANCE_FROM_PATH", &
1909 : description="Section defining the distance from a one dimensional reaction "// &
1910 : "path in an Q-dimensional space of colvars. "// &
1911 : "Constraining this colvar, allows to sample the space equidistant to the reaction path, "// &
1912 : "both in the Q-dimensional colvar and 3N-Q remaining coordinates. "// &
1913 : "For the details of the function see cited literature.", &
1914 : n_keywords=1, n_subsections=0, repeats=.FALSE., &
1915 19028 : citations=[Branduardi2007])
1916 :
1917 9514 : CALL keywords_colvar_path(section)
1918 9514 : END SUBROUTINE create_colvar_dpath_section
1919 :
1920 : ! **************************************************************************************************
1921 : !> \brief Section describinf keywords for both reaction path and distance from reaction path
1922 : !> \param section the section to be created
1923 : !> \author 01.2010
1924 : ! **************************************************************************************************
1925 19028 : SUBROUTINE keywords_colvar_path(section)
1926 :
1927 : TYPE(section_type), POINTER :: section
1928 :
1929 : TYPE(keyword_type), POINTER :: keyword
1930 : TYPE(section_type), POINTER :: print_key, subsection, subsubsection
1931 :
1932 19028 : NULLIFY (keyword, subsection, subsubsection, print_key)
1933 19028 : CALL create_colvar_section(subsection, skip_recursive_colvar=.TRUE.)
1934 19028 : CALL section_add_subsection(section, subsection)
1935 19028 : CALL section_release(subsection)
1936 :
1937 : CALL keyword_create(keyword, __LOCATION__, name="DISTANCES_RMSD", &
1938 : description=" ", &
1939 : usage="DISTANCES_RMSD T", &
1940 19028 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
1941 19028 : CALL section_add_keyword(section, keyword)
1942 19028 : CALL keyword_release(keyword)
1943 :
1944 : CALL keyword_create(keyword, __LOCATION__, name="RMSD", &
1945 : description=" ", &
1946 : usage="RMSD T", &
1947 19028 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
1948 19028 : CALL section_add_keyword(section, keyword)
1949 19028 : CALL keyword_release(keyword)
1950 :
1951 : CALL keyword_create(keyword, __LOCATION__, name="SUBSET_TYPE", &
1952 : description="Define the subsytem used to compute the RMSD", &
1953 : usage="SUBSET_TYPE ALL", &
1954 : enum_c_vals=s2a("ALL", "LIST"), &
1955 : enum_i_vals=[rmsd_all, rmsd_list], &
1956 19028 : default_i_val=rmsd_all)
1957 19028 : CALL section_add_keyword(section, keyword)
1958 19028 : CALL keyword_release(keyword)
1959 :
1960 : CALL keyword_create(keyword, __LOCATION__, name="ALIGN_FRAMES", &
1961 : description="Whether the reference frames should be aligned to minimize the RMSD", &
1962 : usage="ALIGN_FRAMES", &
1963 19028 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
1964 19028 : CALL section_add_keyword(section, keyword)
1965 19028 : CALL keyword_release(keyword)
1966 :
1967 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
1968 : description="Specify indexes of atoms building the subset. ", &
1969 : usage="ATOMS {integer} {integer} ..", repeats=.TRUE., &
1970 19028 : n_var=-1, type_of_var=integer_t)
1971 19028 : CALL section_add_keyword(section, keyword)
1972 19028 : CALL keyword_release(keyword)
1973 :
1974 : CALL section_create(subsection, __LOCATION__, name="FRAME", &
1975 : description="Specify coordinates of the frame", &
1976 19028 : repeats=.TRUE.)
1977 :
1978 : CALL keyword_create(keyword, __LOCATION__, name="COORD_FILE_NAME", &
1979 : description="Name of the xyz file with coordinates (alternative to &COORD section)", &
1980 : usage="COORD_FILE_NAME <CHAR>", &
1981 19028 : default_lc_val="")
1982 19028 : CALL section_add_keyword(subsection, keyword)
1983 19028 : CALL keyword_release(keyword)
1984 :
1985 19028 : CALL create_coord_section_cv(subsubsection, "RMSD")
1986 19028 : CALL section_add_subsection(subsection, subsubsection)
1987 19028 : CALL section_release(subsubsection)
1988 :
1989 19028 : CALL section_add_subsection(section, subsection)
1990 19028 : CALL section_release(subsection)
1991 :
1992 : CALL keyword_create(keyword, __LOCATION__, name="FUNCTION", &
1993 : description="Specifies the ith element of the vector valued function that defines the reaction path. "// &
1994 : "This keyword needs to repeat exactly Q times, and the order must match the order of the colvars. "// &
1995 : "The VARIABLE (e.g. T) which parametrises the curve can be used as the target of a constraint.", &
1996 : usage="FUNCTION (sin(T+2)+2*T)", type_of_var=lchar_t, &
1997 19028 : n_var=1, default_lc_val="0", repeats=.TRUE.)
1998 19028 : CALL section_add_keyword(section, keyword)
1999 19028 : CALL keyword_release(keyword)
2000 :
2001 : CALL keyword_create(keyword, __LOCATION__, name="VARIABLE", &
2002 : description="Specifies the name of the variable that parametrises the FUNCTION "// &
2003 : "defining the reaction path.", &
2004 : usage="VARIABLE T", type_of_var=char_t, &
2005 19028 : n_var=1, repeats=.FALSE.)
2006 19028 : CALL section_add_keyword(section, keyword)
2007 19028 : CALL keyword_release(keyword)
2008 :
2009 : CALL keyword_create( &
2010 : keyword, __LOCATION__, name="LAMBDA", &
2011 : description="Specifies the exponent of the Gaussian used in the integral representation of the colvar. "// &
2012 : "The shape of the space orthogonal to the reaction path is defined by this choice. "// &
2013 : "In the limit of large values, it is given by the plane orthogonal to the path. "// &
2014 : "In practice, modest values are required for stable numerical integration.", &
2015 : usage="LAMBDA {real}", &
2016 19028 : type_of_var=real_t, default_r_val=5.0_dp)
2017 19028 : CALL section_add_keyword(section, keyword)
2018 19028 : CALL keyword_release(keyword)
2019 :
2020 : CALL keyword_create(keyword, __LOCATION__, name="STEP_SIZE", &
2021 : description="Step size in the numerical integration, "// &
2022 : "a few thousand points are common, and the proper number also depends on LAMBDA.", &
2023 : usage="STEP_SIZE {real}", &
2024 19028 : type_of_var=real_t, default_r_val=0.01_dp)
2025 19028 : CALL section_add_keyword(section, keyword)
2026 19028 : CALL keyword_release(keyword)
2027 :
2028 : CALL keyword_create(keyword, __LOCATION__, name="RANGE", &
2029 : description="The range of VARIABLE used for the parametrisation.", &
2030 : usage="RANGE <REAL> <REAL>", &
2031 19028 : n_var=2, type_of_var=real_t)
2032 19028 : CALL section_add_keyword(section, keyword)
2033 19028 : CALL keyword_release(keyword)
2034 :
2035 : CALL cp_print_key_section_create( &
2036 : print_key, __LOCATION__, name="MAP", &
2037 : description="Activating this print key will print once a file with the values of the FUNCTION on a grid "// &
2038 : "of COLVAR values in a specified range. "// &
2039 : "GRID_SPACING and RANGE for every COLVAR has to be specified again in the same order as they are in the input.", &
2040 19028 : print_level=high_print_level, filename="PATH")
2041 :
2042 : CALL keyword_create(keyword, __LOCATION__, name="RANGE", &
2043 : description="The range of of the grid of the COLVAR.", &
2044 : usage="RANGE <REAL> <REAL>", &
2045 19028 : n_var=2, type_of_var=real_t, repeats=.TRUE.)
2046 19028 : CALL section_add_keyword(print_key, keyword)
2047 19028 : CALL keyword_release(keyword)
2048 :
2049 : CALL keyword_create(keyword, __LOCATION__, name="GRID_SPACING", &
2050 : description="Distance between two gridpoints for the grid on the COLVAR", &
2051 : usage="GRID_SPACING {real}", repeats=.TRUE., &
2052 19028 : type_of_var=real_t, default_r_val=0.01_dp)
2053 19028 : CALL section_add_keyword(print_key, keyword)
2054 19028 : CALL keyword_release(keyword)
2055 :
2056 19028 : CALL section_add_subsection(section, print_key)
2057 19028 : CALL section_release(print_key)
2058 :
2059 19028 : END SUBROUTINE keywords_colvar_path
2060 :
2061 : ! **************************************************************************************************
2062 : !> \brief Colvar allowing a combination of COLVARS
2063 : !> \param section the section to be created
2064 : !> \author Teodoro Laino [tlaino] - 12.2008
2065 : ! **************************************************************************************************
2066 9514 : SUBROUTINE create_colvar_comb_section(section)
2067 : TYPE(section_type), POINTER :: section
2068 :
2069 : TYPE(keyword_type), POINTER :: keyword
2070 : TYPE(section_type), POINTER :: subsection
2071 :
2072 9514 : CPASSERT(.NOT. ASSOCIATED(section))
2073 : CALL section_create(section, __LOCATION__, name="COMBINE_COLVAR", &
2074 : description="Allows the possibility to combine several COLVARs into one COLVAR "// &
2075 : "with a generic function. "//docf(), &
2076 9514 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
2077 :
2078 9514 : NULLIFY (keyword, subsection)
2079 9514 : CALL create_colvar_section(subsection, skip_recursive_colvar=.TRUE.)
2080 9514 : CALL section_add_subsection(section, subsection)
2081 9514 : CALL section_release(subsection)
2082 :
2083 : CALL keyword_create(keyword, __LOCATION__, name="FUNCTION", &
2084 : description="Specifies the function used to combine different COLVARs into one.", &
2085 : ! **************************************************************************************************
2086 : !> \brief ...
2087 : !> \param CV1^2 ...
2088 : !> \param CV2^2 ...
2089 : !> \param " ...
2090 : !> \param type_of_var=lchar_t ...
2091 : !> \param n_var=1 ...
2092 : !> \param error=error ...
2093 : ! **************************************************************************************************
2094 : usage="FUNCTION SQRT(CV1^2+CV2^2)", type_of_var=lchar_t, &
2095 9514 : n_var=1)
2096 9514 : CALL section_add_keyword(section, keyword)
2097 9514 : CALL keyword_release(keyword)
2098 :
2099 : CALL keyword_create(keyword, __LOCATION__, name="VARIABLES", &
2100 : description="Specifies the name of the variable that parametrises the FUNCTION "// &
2101 : "defining how COLVARS should be combined. The matching follows the same order of the "// &
2102 : "COLVARS definition in the input file.", &
2103 9514 : usage="VARIABLES CV1 CV2 CV3", type_of_var=char_t, n_var=-1, repeats=.FALSE.)
2104 9514 : CALL section_add_keyword(section, keyword)
2105 9514 : CALL keyword_release(keyword)
2106 :
2107 : CALL keyword_create(keyword, __LOCATION__, name="PARAMETERS", &
2108 : description="Defines the parameters of the functional form", &
2109 : usage="PARAMETERS a b D", type_of_var=char_t, &
2110 9514 : n_var=-1, repeats=.TRUE.)
2111 9514 : CALL section_add_keyword(section, keyword)
2112 9514 : CALL keyword_release(keyword)
2113 :
2114 : CALL keyword_create(keyword, __LOCATION__, name="VALUES", &
2115 : description="Defines the values of parameter of the functional form", &
2116 : usage="VALUES ", type_of_var=real_t, &
2117 9514 : n_var=-1, repeats=.TRUE., unit_str="internal_cp2k")
2118 9514 : CALL section_add_keyword(section, keyword)
2119 9514 : CALL keyword_release(keyword)
2120 :
2121 : CALL keyword_create(keyword, __LOCATION__, name="DX", &
2122 : description="Parameter used for computing the derivative of the combination "// &
2123 : "of COLVARs with the Ridders' method.", &
2124 9514 : usage="DX <REAL>", default_r_val=0.1_dp, unit_str="bohr")
2125 9514 : CALL section_add_keyword(section, keyword)
2126 9514 : CALL keyword_release(keyword)
2127 :
2128 : CALL keyword_create(keyword, __LOCATION__, name="ERROR_LIMIT", &
2129 : description="Checks that the error in computing the derivative is not larger than "// &
2130 : "the value set; in case error is larger a warning message is printed.", &
2131 9514 : usage="ERROR_LIMIT <REAL>", default_r_val=1.0E-12_dp)
2132 9514 : CALL section_add_keyword(section, keyword)
2133 9514 : CALL keyword_release(keyword)
2134 :
2135 9514 : END SUBROUTINE create_colvar_comb_section
2136 :
2137 : ! **************************************************************************************************
2138 : !> \brief Creates the coord section
2139 : !> \param section the section to create
2140 : !> \param name ...
2141 : !> \author teo
2142 : ! **************************************************************************************************
2143 57084 : SUBROUTINE create_coord_section_cv(section, name)
2144 : TYPE(section_type), POINTER :: section
2145 : CHARACTER(LEN=*), INTENT(IN) :: name
2146 :
2147 : TYPE(keyword_type), POINTER :: keyword
2148 :
2149 57084 : CPASSERT(.NOT. ASSOCIATED(section))
2150 : CALL section_create(section, __LOCATION__, name="coord", &
2151 : description="The positions for "//TRIM(name)//" used for restart", &
2152 57084 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
2153 57084 : NULLIFY (keyword)
2154 :
2155 : CALL keyword_create(keyword, __LOCATION__, name="_DEFAULT_KEYWORD_", &
2156 : description="Specify positions of the system", repeats=.TRUE., &
2157 57084 : usage="{Real} ...", type_of_var=real_t, n_var=-1)
2158 57084 : CALL section_add_keyword(section, keyword)
2159 57084 : CALL keyword_release(keyword)
2160 :
2161 57084 : END SUBROUTINE create_coord_section_cv
2162 :
2163 : ! **************************************************************************************************
2164 : !> \brief collective variables specifying h bonds
2165 : !> \param section the section to be created
2166 : !> \author alin m elena
2167 : ! **************************************************************************************************
2168 38056 : SUBROUTINE create_colvar_wc_section(section)
2169 : TYPE(section_type), POINTER :: section
2170 :
2171 : TYPE(keyword_type), POINTER :: keyword
2172 : TYPE(section_type), POINTER :: subsection
2173 :
2174 38056 : CPASSERT(.NOT. ASSOCIATED(section))
2175 : CALL section_create(section, __LOCATION__, name="wc", &
2176 : description="Section to define the hbond wannier centre as a collective variables.", &
2177 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
2178 38056 : NULLIFY (keyword, subsection)
2179 :
2180 : CALL keyword_create(keyword, __LOCATION__, name="RCUT", &
2181 : description="Parameter used for computing the cutoff radius for searching "// &
2182 : "the wannier centres around an atom", &
2183 : usage="RCUT <REAL>", default_r_val=0.529177208590000_dp, unit_str="angstrom", &
2184 38056 : type_of_var=real_t, repeats=.FALSE.)
2185 38056 : CALL section_add_keyword(section, keyword)
2186 38056 : CALL keyword_release(keyword)
2187 :
2188 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
2189 : variants=["POINTS"], &
2190 : description="Specifies the indexes of atoms/points defining the bond (Od, H, Oa).", &
2191 : usage="ATOMS {integer} {integer} {integer}", &
2192 76112 : n_var=3, type_of_var=integer_t, repeats=.TRUE.)
2193 38056 : CALL section_add_keyword(section, keyword)
2194 38056 : CALL keyword_release(keyword)
2195 :
2196 : ! Must be present in each colvar and handled properly
2197 38056 : CALL create_point_section(subsection)
2198 38056 : CALL section_add_subsection(section, subsection)
2199 38056 : CALL section_release(subsection)
2200 :
2201 38056 : END SUBROUTINE create_colvar_wc_section
2202 :
2203 : ! **************************************************************************************************
2204 : !> \brief collective variables specifying h bonds= wire
2205 : !> \param section the section to be created
2206 : !> \author alin m elena
2207 : ! **************************************************************************************************
2208 38056 : SUBROUTINE create_colvar_hbp_section(section)
2209 : TYPE(section_type), POINTER :: section
2210 :
2211 : TYPE(keyword_type), POINTER :: keyword
2212 : TYPE(section_type), POINTER :: subsection
2213 :
2214 38056 : CPASSERT(.NOT. ASSOCIATED(section))
2215 : CALL section_create(section, __LOCATION__, name="hbp", &
2216 : description="Section to define the hbond wannier centre as a collective variables.", &
2217 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
2218 38056 : NULLIFY (keyword, subsection)
2219 :
2220 : CALL keyword_create(keyword, __LOCATION__, name="RCUT", &
2221 : description="Parameter used for computing the cutoff radius for searching "// &
2222 : "the wannier centres around an atom", &
2223 : usage="RCUT <REAL>", default_r_val=0.529177208590000_dp, unit_str="angstrom", &
2224 38056 : type_of_var=real_t, repeats=.FALSE.)
2225 38056 : CALL section_add_keyword(section, keyword)
2226 38056 : CALL keyword_release(keyword)
2227 :
2228 : CALL keyword_create(keyword, __LOCATION__, name="SHIFT", &
2229 : description="Parameter used for shifting each term in the sum ", &
2230 : usage="SHIFT <REAL>", default_r_val=0.5_dp, &
2231 38056 : type_of_var=real_t, repeats=.FALSE.)
2232 38056 : CALL section_add_keyword(section, keyword)
2233 38056 : CALL keyword_release(keyword)
2234 :
2235 : CALL keyword_create(keyword, __LOCATION__, name="NPOINTS", &
2236 : description="The number of points in the path", &
2237 : usage="NPOINTS {integer}", default_i_val=-1, &
2238 38056 : n_var=1, type_of_var=integer_t, repeats=.FALSE.)
2239 38056 : CALL section_add_keyword(section, keyword)
2240 38056 : CALL keyword_release(keyword)
2241 :
2242 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
2243 : variants=["POINTS"], &
2244 : description="Specifies the indexes of atoms/points defining the bond (Od, H, Oa).", &
2245 : usage="ATOMS {integer} {integer} {integer}", &
2246 76112 : n_var=3, type_of_var=integer_t, repeats=.TRUE.)
2247 38056 : CALL section_add_keyword(section, keyword)
2248 38056 : CALL keyword_release(keyword)
2249 :
2250 : ! Must be present in each colvar and handled properly
2251 38056 : CALL create_point_section(subsection)
2252 38056 : CALL section_add_subsection(section, subsection)
2253 38056 : CALL section_release(subsection)
2254 :
2255 38056 : END SUBROUTINE create_colvar_hbp_section
2256 :
2257 : ! **************************************************************************************************
2258 : !> \brief collective variables specifying ring puckering
2259 : !> \brief D. Cremer and J.A. Pople, JACS 97 1354 (1975)
2260 : !> \param section the section to be created
2261 : !> \author Marcel Baer
2262 : ! **************************************************************************************************
2263 38056 : SUBROUTINE create_colvar_ring_puckering_section(section)
2264 : TYPE(section_type), POINTER :: section
2265 :
2266 : TYPE(keyword_type), POINTER :: keyword
2267 : TYPE(section_type), POINTER :: subsection
2268 :
2269 38056 : CPASSERT(.NOT. ASSOCIATED(section))
2270 : CALL section_create(section, __LOCATION__, name="RING_PUCKERING", &
2271 : description="Section to define general ring puckering collective variables.", &
2272 38056 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
2273 :
2274 38056 : NULLIFY (keyword, subsection)
2275 :
2276 : CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
2277 : variants=["POINTS"], &
2278 : description="Specifies the indexes of atoms/points defining the ring. "// &
2279 : "At least 4 Atoms are needed.", &
2280 : usage="ATOMS {integer} {integer} {integer} ..", &
2281 76112 : n_var=-1, type_of_var=integer_t)
2282 38056 : CALL section_add_keyword(section, keyword)
2283 38056 : CALL keyword_release(keyword)
2284 :
2285 : CALL keyword_create(keyword, __LOCATION__, name="COORDINATE", &
2286 : description="Indicate the coordinate to be used. Follow the Cremer-Pople definition for a N ring. "// &
2287 : "0 is the total puckering variable Q, "// &
2288 : "2..[N/2] are puckering coordinates. "// &
2289 : "-2..-[N/2-1] are puckering angles.", &
2290 : usage="COORDINATE {integer}", default_i_val=0, &
2291 38056 : n_var=1)
2292 38056 : CALL section_add_keyword(section, keyword)
2293 38056 : CALL keyword_release(keyword)
2294 :
2295 : ! Must be present in each colvar and handled properly
2296 38056 : CALL create_point_section(subsection)
2297 38056 : CALL section_add_subsection(section, subsection)
2298 38056 : CALL section_release(subsection)
2299 :
2300 38056 : END SUBROUTINE create_colvar_ring_puckering_section
2301 :
2302 : ! **************************************************************************************************
2303 :
2304 : END MODULE input_cp2k_colvar
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