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input_cp2k_free_energy.F
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1!--------------------------------------------------------------------------------------------------!
2! CP2K: A general program to perform molecular dynamics simulations !
3! Copyright 2000-2024 CP2K developers group <https://cp2k.org> !
4! !
5! SPDX-License-Identifier: GPL-2.0-or-later !
6!--------------------------------------------------------------------------------------------------!
7
8! **************************************************************************************************
9!> \par History
10!> 10.2005 split input_cp2k into smaller modules [fawzi]
11!> \author teo & fawzi
12! **************************************************************************************************
13MODULE input_cp2k_free_energy
14 USE bibliography, ONLY: barducbus2008,&
15 vandencic2006
16 USE cp_output_handling, ONLY: add_last_numeric,&
17 cp_print_key_section_create,&
18 high_print_level,&
19 low_print_level
20 USE cp_units, ONLY: cp_unit_to_cp2k
21 USE input_constants, ONLY: &
22 do_fe_ac, do_fe_meta, do_fe_ui, do_wall_gaussian, do_wall_m, do_wall_none, do_wall_p, &
23 do_wall_quadratic, do_wall_quartic, do_wall_reflective, gaussian
24 USE input_keyword_types, ONLY: keyword_create,&
25 keyword_release,&
26 keyword_type
27 USE input_section_types, ONLY: section_add_keyword,&
28 section_add_subsection,&
29 section_create,&
30 section_release,&
31 section_type
32 USE input_val_types, ONLY: char_t,&
33 integer_t,&
34 lchar_t,&
35 real_t
36 USE kinds, ONLY: dp
37 USE string_utilities, ONLY: s2a
38#include "./base/base_uses.f90"
39
40 IMPLICIT NONE
41 PRIVATE
42
43 LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .true.
44 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'input_cp2k_free_energy'
45
46 PUBLIC :: create_metavar_section, &
47 create_fe_section
48
49!***
50CONTAINS
51
52! **************************************************************************************************
53!> \brief creates the free energy section
54!> \param section the section to be created
55!> \author teo
56! **************************************************************************************************
57 SUBROUTINE create_fe_section(section)
58 TYPE(section_type), POINTER :: section
59
60 TYPE(keyword_type), POINTER :: keyword
61 TYPE(section_type), POINTER :: print_key, subsection
62
63 NULLIFY (subsection, keyword, print_key)
64 cpassert(.NOT. ASSOCIATED(section))
65 CALL section_create(section, __location__, name="free_energy", &
66 description="Controls the calculation of free energy and free energy derivatives"// &
67 " with different possible methods", &
68 n_keywords=0, n_subsections=1, repeats=.false.)
69
70 CALL keyword_create(keyword, __location__, name="METHOD", &
71 description="Defines the method to use to compute free energy.", &
72 usage="METHOD (METADYN|UI|AC)", &
73 enum_c_vals=s2a("METADYN", "UI", "AC"), &
74 enum_i_vals=(/do_fe_meta, do_fe_ui, do_fe_ac/), &
75 enum_desc=s2a("Metadynamics", &
76 "Umbrella Integration", &
77 "Alchemical Change"), &
78 default_i_val=do_fe_meta, repeats=.false.)
79 CALL section_add_keyword(section, keyword)
80 CALL keyword_release(keyword)
81
82 CALL create_metadyn_section(subsection)
83 CALL section_add_subsection(section, subsection)
84 CALL section_release(subsection)
85
86 CALL create_ui_section(subsection)
87 CALL section_add_subsection(section, subsection)
88 CALL section_release(subsection)
89
90 CALL create_ac_section(subsection)
91 CALL section_add_subsection(section, subsection)
92 CALL section_release(subsection)
93
94 CALL cp_print_key_section_create(print_key, __location__, "free_energy_info", &
95 description="Controls the printing of basic and summary information during the"// &
96 " Free Energy calculation", &
97 print_level=low_print_level, each_iter_names=s2a("MD"), &
98 each_iter_values=(/1/), add_last=add_last_numeric, filename="__STD_OUT__")
99 CALL section_add_subsection(section, print_key)
100 CALL section_release(print_key)
101
102 END SUBROUTINE create_fe_section
103
104! **************************************************************************************************
105!> \brief creates the metadynamics section
106!> \param section the section to be created
107!> \author teo
108! **************************************************************************************************
109 SUBROUTINE create_metadyn_section(section)
110 TYPE(section_type), POINTER :: section
111
112 TYPE(keyword_type), POINTER :: keyword
113 TYPE(section_type), POINTER :: print_key, subsection
114
115 cpassert(.NOT. ASSOCIATED(section))
116 CALL section_create(section, __location__, name="metadyn", &
117 description="This section sets parameters to set up a calculation of metadynamics.", &
118 n_keywords=1, n_subsections=1, repeats=.false., &
119 citations=(/vandencic2006/))
120
121 NULLIFY (subsection, keyword, print_key)
122
123 CALL keyword_create(keyword, __location__, name="USE_PLUMED", &
124 description="Specify whether to use plumed as an external metadynamics driver.", &
125 usage="USE_PLUMED .FALSE./.TRUE.", &
126 default_l_val=.false., lone_keyword_l_val=.true.)
127 CALL section_add_keyword(section, keyword)
128 CALL keyword_release(keyword)
129
130 CALL keyword_create(keyword, __location__, name="PLUMED_INPUT_FILE", &
131 description="Specify the file name of the external plumed input file", &
132 usage="PLUMED_INPUT_FILE ./FILENAME", &
133 default_c_val="./plumed.dat")
134 CALL section_add_keyword(section, keyword)
135 CALL keyword_release(keyword)
136
137 CALL keyword_create(keyword, __location__, name="MIN_NT_HILLS", &
138 description="Specify the minimum MD step interval between spawning "// &
139 "two hills. If specified, it must be >= than NT_HILLS. In case MIN_DISP "// &
140 "is used, if MIN_DISP is satisfied before MIN_NT_HILLS MD steps have been "// &
141 "performed, the MD will continue without any spawning until MIN_NT_HILLS is "// &
142 "reached. The default value has the net effect of skipping this check.", &
143 usage="MIN_NT_HILLS {integer}", default_i_val=1)
144 CALL section_add_keyword(section, keyword)
145 CALL keyword_release(keyword)
146
147 CALL keyword_create(keyword, __location__, name="NT_HILLS", &
148 description="Specify the maximum MD step interval between spawning "// &
149 "two hills. When negative, no new hills are spawned and only "// &
150 "the hills read from SPAWNED_HILLS_* are in effect. The latter "// &
151 "is useful when one wants to add a custom constant bias potential.", &
152 usage="NT_HILLS {integer}", default_i_val=30)
153 CALL section_add_keyword(section, keyword)
154 CALL keyword_release(keyword)
155
156 CALL keyword_create(keyword, __location__, name="TEMPERATURE", &
157 description="If a Lagrangian scheme is used the temperature for the collective "// &
158 "variables is specified. ", usage="TEMPERATURE <REAL>", &
159 default_r_val=0.0_dp, unit_str='K')
160 CALL section_add_keyword(section, keyword)
161 CALL keyword_release(keyword)
162
163 !RG Adaptive hills
164 CALL keyword_create(keyword, __location__, name="MIN_DISP", &
165 description="Minimum displacement between hills before placing a new hill.", &
166 usage="MIN_DISP <REAL>", &
167 default_r_val=-1.0_dp)
168 CALL section_add_keyword(section, keyword)
169 CALL keyword_release(keyword)
170
171 CALL keyword_create(keyword, __location__, name="OLD_HILL_NUMBER", &
172 description="Index of the last hill spawned for this walker.Needed to calculate MIN_DISP", &
173 usage="OLD_HILL_NUMBER <INT>", &
174 default_i_val=0)
175 CALL section_add_keyword(section, keyword)
176 CALL keyword_release(keyword)
177 CALL keyword_create(keyword, __location__, name="OLD_HILL_STEP", &
178 description="Timestep of the last hill spawned for this walker.Needed to calculate MIN_DISP", &
179 usage="OLD_HILL_STEP <INT>", &
180 default_i_val=0)
181 CALL section_add_keyword(section, keyword)
182 CALL keyword_release(keyword)
183 !RG Adaptive hills
184
185 !Hills tail damping
186 CALL keyword_create(keyword, __location__, name="HILL_TAIL_CUTOFF", &
187 description="By setting this variable larger than 0 the tail of the Gaussian hill"// &
188 " is damped to zero faster. The Gaussian function is multiplied by a cutoff function"// &
189 " that becomes active at |x-X0|>HILL_TAIL_CUTOFF*SCALE, where X0 is the location of "// &
190 "the Gaussian and SCALE is the width of the Gaussian. For more than one METAVAR"// &
191 " X0 and SCALE are METAVAR-dependent."// &
192 " (1-(|x-X0|/HILL_TAIL_CUTOFF*SCALE)^P_EXP)/(1-(|x-X0|/HILL_TAIL_CUTOFF*SCALE)^Q_EXP)", &
193 usage="HILL_TAIL_CUTOFF <REAL>", &
194 default_r_val=-1.0_dp)
195 CALL section_add_keyword(section, keyword)
196 CALL keyword_release(keyword)
197 CALL keyword_create(keyword, __location__, name="P_EXPONENT", &
198 description="Exponent at the numerator of the cutoff function to damp the tail of the Gaussian.", &
199 usage="P_EXPONENT <INT>", &
200 default_i_val=8)
201 CALL section_add_keyword(section, keyword)
202 CALL keyword_release(keyword)
203 CALL keyword_create(keyword, __location__, name="Q_EXPONENT", &
204 description="Exponent at the denominator of the cutoff function to damp the tail of the Gaussian.", &
205 usage="Q_EXPONENT <INT>", &
206 default_i_val=20)
207 CALL section_add_keyword(section, keyword)
208 CALL keyword_release(keyword)
209
210 CALL keyword_create(keyword, __location__, name="SLOW_GROWTH", &
211 description="Let the last hill grow slowly over NT_HILLS. ", &
212 usage="SLOW_GROWTH {logical}", &
213 default_l_val=.false., lone_keyword_l_val=.true.)
214 CALL section_add_keyword(section, keyword)
215 CALL keyword_release(keyword)
216
217 CALL keyword_create(keyword, __location__, name="TEMP_TOL", &
218 description="If a Lagrangian scheme is used the temperature tolerance for the collective "// &
219 "variables is specified.", usage="TEMP_TOL <REAL>", &
220 unit_str='K', default_r_val=0.0_dp)
221 CALL section_add_keyword(section, keyword)
222 CALL keyword_release(keyword)
223
224 CALL keyword_create(keyword, __location__, name="LANGEVIN", &
225 description="If a Lagrangian scheme is used the eq. motion of the COLVARS are integrated "// &
226 "with a LANGEVIN scheme.", &
227 usage="LANGEVIN {logical}", &
228 citations=(/vandencic2006/), &
229 default_l_val=.false., lone_keyword_l_val=.true.)
230 CALL section_add_keyword(section, keyword)
231 CALL keyword_release(keyword)
232
233 CALL keyword_create(keyword, __location__, name="WW", &
234 description="Specifies the height of the gaussian to spawn. Default 0.1 .", &
235 usage="WW <REAL>", unit_str='hartree', default_r_val=0.1_dp)
236 CALL section_add_keyword(section, keyword)
237 CALL keyword_release(keyword)
238
239 CALL keyword_create(keyword, __location__, name="DO_HILLS", &
240 description="This keyword enables the spawning of the hills. Default .FALSE.", &
241 usage="DO_HILLS", default_l_val=.false., lone_keyword_l_val=.true.)
242 CALL section_add_keyword(section, keyword)
243 CALL keyword_release(keyword)
244
245 CALL keyword_create(keyword, __location__, name="WELL_TEMPERED", &
246 description="This keyword enables Well-tempered metadynamics. Default .FALSE.", &
247 usage="WELL_TEMPERED", citations=(/barducbus2008/), &
248 default_l_val=.false., lone_keyword_l_val=.true.)
249 CALL section_add_keyword(section, keyword)
250 CALL keyword_release(keyword)
251
252 CALL keyword_create(keyword, __location__, name="DELTA_T", &
253 description="If Well-tempered metaD is used, the temperature parameter "// &
254 "must be specified.", usage="DELTA_T <REAL>", &
255 unit_str='K', default_r_val=0.0_dp)
256 CALL section_add_keyword(section, keyword)
257 CALL keyword_release(keyword)
258
259 CALL keyword_create(keyword, __location__, name="WTGAMMA", &
260 description="If Well-tempered metaD is used, the gamma parameter "// &
261 "must be specified if not DELTA_T.", usage="WTGAMMA <REAL>", &
262 default_r_val=0.0_dp)
263 CALL section_add_keyword(section, keyword)
264 CALL keyword_release(keyword)
265
266 CALL keyword_create(keyword, __location__, name="LAGRANGE", &
267 description="Specifies whether an extended-lagrangian should be used. Default .FALSE.", &
268 usage="LAGRANGE", default_l_val=.false., lone_keyword_l_val=.true.)
269 CALL section_add_keyword(section, keyword)
270 CALL keyword_release(keyword)
271
272 CALL keyword_create(keyword, __location__, name="step_start_val", &
273 description="The starting step value for metadynamics", &
274 usage="step_start_val <integer>", default_i_val=0)
275 CALL section_add_keyword(section, keyword)
276 CALL keyword_release(keyword)
277
278 CALL keyword_create(keyword, __location__, name="nhills_start_val", &
279 description="The starting value of previously spawned hills", &
280 usage="nhills_start_val <integer>", default_i_val=0)
281 CALL section_add_keyword(section, keyword)
282 CALL keyword_release(keyword)
283
284 CALL keyword_create(keyword, __location__, name="COLVAR_AVG_TEMPERATURE_RESTART", &
285 description="COLVAR average temperature. Only for restarting purposes.", &
286 usage="COLVAR_AVG_TEMPERATURE_RESTART 0.0", default_r_val=0.0_dp)
287 CALL section_add_keyword(section, keyword)
288 CALL keyword_release(keyword)
289
290 CALL keyword_create(keyword, __location__, name="TAMCSteps", &
291 description="Number of sampling points for z", &
292 usage="TAMCSteps <integer>", default_i_val=1)
293 CALL section_add_keyword(section, keyword)
294 CALL keyword_release(keyword)
295
296 CALL keyword_create(keyword, __location__, name="timestep", &
297 description="The length of an integration step for colvars (TAMC only)", &
298 usage="timestep <real>", default_r_val=cp_unit_to_cp2k(value=0.5_dp, unit_str="fs"), &
299 unit_str="fs")
300
301 CALL section_add_keyword(section, keyword)
302 CALL keyword_release(keyword)
303
304 CALL create_metavar_section(subsection)
305 CALL section_add_subsection(section, subsection)
306 CALL section_release(subsection)
307
308 CALL create_multiple_walkers_section(subsection)
309 CALL section_add_subsection(section, subsection)
310 CALL section_release(subsection)
311
312 CALL section_create(subsection, __location__, name="print", &
313 description="Controls the printing properties during an metadynamics run", &
314 n_keywords=0, n_subsections=1, repeats=.true.)
315 NULLIFY (print_key)
316
317 CALL cp_print_key_section_create(print_key, __location__, "program_run_info", &
318 description="Controls the printing of basic and summary information during"// &
319 " metadynamics.", &
320 print_level=low_print_level, each_iter_names=s2a("MD", "METADYNAMICS"), &
321 each_iter_values=(/1, 1/), add_last=add_last_numeric, filename="__STD_OUT__")
322 CALL section_add_subsection(subsection, print_key)
323 CALL section_release(print_key)
324
325 CALL cp_print_key_section_create(print_key, __location__, "temperature_colvar", &
326 description="Controls the printing of the temperature of COLVARS in an "// &
327 "extended lagrangian scheme.", &
328 print_level=low_print_level, each_iter_names=s2a("MD", "METADYNAMICS"), &
329 each_iter_values=(/1, 1/), add_last=add_last_numeric, filename="__STD_OUT__")
330 CALL section_add_subsection(subsection, print_key)
331 CALL section_release(print_key)
332
333 CALL cp_print_key_section_create(print_key, __location__, "COLVAR", &
334 description="Controls the printing of COLVAR summary information during"// &
335 " metadynamics. When an extended Lagrangian use used, the files"// &
336 " contain (in order): colvar value of the extended Lagrangian,"// &
337 " instantaneous colvar value, force due to the harmonic term of the extended"// &
338 " Lagrangian and the force due to the previously spawned hills,"// &
339 " the force due to the walls, the velocities in the extended"// &
340 " Lagrangian, the potential of the harmonic term of the"// &
341 " Lagrangian, the potential energy of the hills, the potential"// &
342 " energy of the walls and the temperature of the extended"// &
343 " Lagrangian. When the extended Lagrangian is not used, all"// &
344 " related fields are omitted.", &
345 print_level=low_print_level, each_iter_names=s2a("MD", "METADYNAMICS"), &
346 each_iter_values=(/1, 1/), add_last=add_last_numeric, filename="COLVAR")
347 CALL section_add_subsection(subsection, print_key)
348 CALL section_release(print_key)
349
350 CALL cp_print_key_section_create(print_key, __location__, "HILLS", &
351 description="Controls the printing of HILLS summary information during"// &
352 " metadynamics. The file contains: instantaneous colvar value, width of"// &
353 " the spawned gaussian and height of the gaussian. According the value of"// &
354 " the EACH keyword this file may not be synchronized with the COLVAR file.", &
355 print_level=high_print_level, each_iter_names=s2a("MD", "METADYNAMICS"), &
356 each_iter_values=(/1, 1/), add_last=add_last_numeric, filename="HILLS")
357 CALL section_add_subsection(subsection, print_key)
358 CALL section_release(print_key)
359
360 CALL section_add_subsection(section, subsection)
361 CALL section_release(subsection)
362
363 CALL create_metadyn_history(subsection, section)
364 END SUBROUTINE create_metadyn_section
365
366! **************************************************************************************************
367!> \brief creates the multiple walker section
368!> \param section the section to be created
369!> \author teodoro laino [tlaino] 10.2008
370! **************************************************************************************************
371 SUBROUTINE create_multiple_walkers_section(section)
372 TYPE(section_type), POINTER :: section
373
374 TYPE(keyword_type), POINTER :: keyword
375 TYPE(section_type), POINTER :: subsection
376
377 cpassert(.NOT. ASSOCIATED(section))
378 CALL section_create(section, __location__, name="MULTIPLE_WALKERS", &
379 description="Enables and configures the metadynamics using multiple walkers.", &
380 n_keywords=0, n_subsections=0, repeats=.false.)
381
382 NULLIFY (subsection, keyword)
383 CALL keyword_create(keyword, __location__, name="_SECTION_PARAMETERS_", &
384 description="Controls the usage of the multiple walkers in a metadynamics run.", &
385 usage="&MULTIPLE_WALKERS T", default_l_val=.false., lone_keyword_l_val=.true.)
386 CALL section_add_keyword(section, keyword)
387 CALL keyword_release(keyword)
388
389 CALL keyword_create(keyword, __location__, name="WALKER_ID", &
390 description="Sets the walker ID for the local metadynamics run.", &
391 usage="WALKER_ID <INTEGER>", type_of_var=integer_t)
392 CALL section_add_keyword(section, keyword)
393 CALL keyword_release(keyword)
394
395 CALL keyword_create(keyword, __location__, name="NUMBER_OF_WALKERS", &
396 description="Sets the total number of walkers in the metadynamic run.", &
397 usage="NUMBER_OF_WALKERS <INTEGER>", type_of_var=integer_t)
398 CALL section_add_keyword(section, keyword)
399 CALL keyword_release(keyword)
400
401 CALL keyword_create(keyword, __location__, name="WALKER_COMM_FREQUENCY", &
402 description="Sets the frequency (in unit of spawned hills) for the "// &
403 "communication between the several walkers, in order to update the "// &
404 "local list of hills with the ones coming from the other walkers", &
405 usage="WALKER_COMM_FREQUENCY <INTEGER>", default_i_val=1)
406 CALL section_add_keyword(section, keyword)
407 CALL keyword_release(keyword)
408
409 CALL keyword_create(keyword, __location__, name="WALKERS_STATUS", &
410 description="Stores the status of the several walkers in the local run.", &
411 usage="WALKERS_STATUS <INTEGER> .. <INTEGER>", type_of_var=integer_t, n_var=-1)
412 CALL section_add_keyword(section, keyword)
413 CALL keyword_release(keyword)
414
415 CALL section_create(subsection, __location__, name="WALKERS_FILE_NAME", &
416 description="Specify the basename for the NUMBER_OF_WALKERS files used to "// &
417 "communicate between the walkers. Absolute path can be input as well "// &
418 "together with the filename. One file will be created for each spawned hill.", &
419 n_keywords=1, n_subsections=0, repeats=.false.)
420 CALL keyword_create(keyword, __location__, name="_DEFAULT_KEYWORD_", &
421 description="Specified the communication filename for each walker.", repeats=.true., &
422 usage="{String}", type_of_var=lchar_t, n_var=1)
423 CALL section_add_keyword(subsection, keyword)
424 CALL keyword_release(keyword)
425 CALL section_add_subsection(section, subsection)
426 CALL section_release(subsection)
427 END SUBROUTINE create_multiple_walkers_section
428
429! **************************************************************************************************
430!> \brief creates the alchemical section for free energy evaluation
431!> \param section the section to be created
432!> \author teodoro laino [tlaino] 04.2007
433! **************************************************************************************************
434 SUBROUTINE create_ac_section(section)
435 TYPE(section_type), POINTER :: section
436
437 TYPE(keyword_type), POINTER :: keyword
438
439 NULLIFY (keyword)
440 cpassert(.NOT. ASSOCIATED(section))
441 CALL section_create(section, __location__, name="ALCHEMICAL_CHANGE", &
442 description="Controls the calculation of delta free energies"// &
443 " with the alchemical change method.", &
444 n_keywords=0, n_subsections=0, repeats=.false.)
445
446 CALL keyword_create(keyword, __location__, name="PARAMETER", &
447 description="Defines the perturbing parameter of the alchemical change transformation", &
448 usage="PARAMETERS k", type_of_var=char_t, &
449 n_var=1)
450 CALL section_add_keyword(section, keyword)
451 CALL keyword_release(keyword)
452
453 CALL keyword_create(keyword, __location__, name="WEIGHTING_FUNCTION", &
454 description="Specifies the weighting function (umbrella potential, part of the mixing function)", &
455 usage="WEIGHTING_FUNCTION (E1+E2-LOG(E1/E2))", type_of_var=lchar_t, &
456 n_var=1, default_lc_val="0")
457 CALL section_add_keyword(section, keyword)
458 CALL keyword_release(keyword)
459
460 CALL keyword_create(keyword, __location__, name="EPS_CONV", &
461 description="Set the relative tolerance for the convergence of the free energy derivative", &
462 usage="EPS_CONV <REAL>", &
463 default_r_val=1.0e-2_dp)
464 CALL section_add_keyword(section, keyword)
465 CALL keyword_release(keyword)
466
467 CALL keyword_create(keyword, __location__, name="NEQUIL_STEPS", &
468 description="Set the number of equilibration steps, skipped to compute averages", &
469 usage="NEQUIL_STEPS <INTEGER>", &
470 default_i_val=0)
471 CALL section_add_keyword(section, keyword)
472 CALL keyword_release(keyword)
473
474 END SUBROUTINE create_ac_section
475
476! **************************************************************************************************
477!> \brief creates the umbrella integration section
478!> \param section the section to be created
479!> \author teodoro laino [tlaino] 01.2007
480! **************************************************************************************************
481 SUBROUTINE create_ui_section(section)
482 TYPE(section_type), POINTER :: section
483
484 TYPE(section_type), POINTER :: subsection
485
486 cpassert(.NOT. ASSOCIATED(section))
487 CALL section_create(section, __location__, name="umbrella_integration", &
488 description="Controls the calculation of free energy derivatives"// &
489 " with the umbrella integration method.", &
490 n_keywords=0, n_subsections=0, repeats=.false.)
491
492 NULLIFY (subsection)
493 CALL create_uvar_conv_section(subsection)
494 CALL section_add_subsection(section, subsection)
495 CALL section_release(subsection)
496
497 CALL create_uvar_section(subsection)
498 CALL section_add_subsection(section, subsection)
499 CALL section_release(subsection)
500
501 END SUBROUTINE create_ui_section
502
503! **************************************************************************************************
504!> \brief Creates the velocity section
505!> \param section the section to create
506!> \param metadyn_section ...
507!> \author teo
508! **************************************************************************************************
509 SUBROUTINE create_metadyn_history(section, metadyn_section)
510 TYPE(section_type), POINTER :: section, metadyn_section
511
512 TYPE(keyword_type), POINTER :: keyword
513
514 cpassert(.NOT. ASSOCIATED(section))
515 CALL section_create(section, __location__, name="SPAWNED_HILLS_POS", &
516 description="The position of the spawned hills during metadynamics. "// &
517 "Used for RESTART.", &
518 n_keywords=1, n_subsections=0, repeats=.false.)
519 NULLIFY (keyword)
520 CALL keyword_create(keyword, __location__, name="_DEFAULT_KEYWORD_", &
521 description="Specify the spawned hills", repeats=.true., &
522 usage="{Real} ...", type_of_var=real_t, n_var=-1)
523 CALL section_add_keyword(section, keyword)
524 CALL keyword_release(keyword)
525 CALL section_add_subsection(metadyn_section, section)
526 CALL section_release(section)
527
528 CALL section_create(section, __location__, name="SPAWNED_HILLS_SCALE", &
529 description="The scales of the spawned hills during metadynamics. "// &
530 "Used for RESTART. When a scale is zero in one or more "// &
531 "directions, the Gaussian hill is assumed to be infinitely wide "// &
532 "in those directions. The latter can be used to combine spawned "// &
533 "hills from multiple 1D metadynamics runs in one multidimensional "// &
534 "metadynamics run.", &
535 n_keywords=1, n_subsections=0, repeats=.false.)
536 NULLIFY (keyword)
537 CALL keyword_create(keyword, __location__, name="_DEFAULT_KEYWORD_", &
538 description="Specify the spawned hills", repeats=.true., &
539 usage="{Real} ...", type_of_var=real_t, n_var=-1)
540 CALL section_add_keyword(section, keyword)
541 CALL keyword_release(keyword)
542 CALL section_add_subsection(metadyn_section, section)
543 CALL section_release(section)
544
545 CALL section_create(section, __location__, name="SPAWNED_HILLS_HEIGHT", &
546 description="The height of the spawned hills during metadynamics. "// &
547 "Used for RESTART.", &
548 n_keywords=1, n_subsections=0, repeats=.false.)
549 NULLIFY (keyword)
550 CALL keyword_create(keyword, __location__, name="_DEFAULT_KEYWORD_", &
551 description="Specify the spawned hills", repeats=.true., &
552 usage="{Real}", type_of_var=real_t, n_var=1)
553 CALL section_add_keyword(section, keyword)
554 CALL keyword_release(keyword)
555 CALL section_add_subsection(metadyn_section, section)
556 CALL section_release(section)
557
558 CALL section_create(section, __location__, name="SPAWNED_HILLS_INVDT", &
559 description="The inverse of the DELTA_T parameter used for Well-Tempered metadynamics. "// &
560 "Used for RESTART.", &
561 n_keywords=1, n_subsections=0, repeats=.false.)
562 NULLIFY (keyword)
563 CALL keyword_create(keyword, __location__, name="_DEFAULT_KEYWORD_", &
564 description="Specify the spawned hills", repeats=.true., &
565 usage="{Real}", type_of_var=real_t, n_var=1)
566 CALL section_add_keyword(section, keyword)
567 CALL keyword_release(keyword)
568 CALL section_add_subsection(metadyn_section, section)
569 CALL section_release(section)
570 !
571 ! Extended Lagrangian
572 !
573 CALL section_create(section, __location__, name="EXT_LAGRANGE_SS0", &
574 description="Colvar position within an extended Lagrangian formalism. "// &
575 "Used for RESTART.", &
576 n_keywords=1, n_subsections=0, repeats=.false.)
577 NULLIFY (keyword)
578 CALL keyword_create(keyword, __location__, name="_DEFAULT_KEYWORD_", &
579 description="Specified the positions", repeats=.true., &
580 usage="{Real}", type_of_var=real_t, n_var=1)
581 CALL section_add_keyword(section, keyword)
582 CALL keyword_release(keyword)
583 CALL section_add_subsection(metadyn_section, section)
584 CALL section_release(section)
585
586 CALL section_create(section, __location__, name="EXT_LAGRANGE_VVP", &
587 description="Colvar velocities within an extended Lagrangian formalism. "// &
588 "Used for RESTART.", &
589 n_keywords=1, n_subsections=0, repeats=.false.)
590 NULLIFY (keyword)
591 CALL keyword_create(keyword, __location__, name="_DEFAULT_KEYWORD_", &
592 description="Specified the velocities", repeats=.true., &
593 usage="{Real}", type_of_var=real_t, n_var=1)
594 CALL section_add_keyword(section, keyword)
595 CALL keyword_release(keyword)
596 CALL section_add_subsection(metadyn_section, section)
597 CALL section_release(section)
598
599 CALL section_create(section, __location__, name="EXT_LAGRANGE_SS", &
600 description="Colvar Theta within an extended Lagrangian formalism. "// &
601 "Used for RESTART.", &
602 n_keywords=1, n_subsections=0, repeats=.false.)
603 NULLIFY (keyword)
604 CALL keyword_create(keyword, __location__, name="_DEFAULT_KEYWORD_", &
605 description="Specified the theta", repeats=.true., &
606 usage="{Real}", type_of_var=real_t, n_var=1)
607 CALL section_add_keyword(section, keyword)
608 CALL keyword_release(keyword)
609 CALL section_add_subsection(metadyn_section, section)
610 CALL section_release(section)
611
612 CALL section_create(section, __location__, name="EXT_LAGRANGE_FS", &
613 description="Colvar force within an extended Lagrangian formalism. "// &
614 "Used for RESTART.", &
615 n_keywords=1, n_subsections=0, repeats=.false.)
616 NULLIFY (keyword)
617 CALL keyword_create(keyword, __location__, name="_DEFAULT_KEYWORD_", &
618 description="Specified the theta", repeats=.true., &
619 usage="{Real}", type_of_var=real_t, n_var=1)
620 CALL section_add_keyword(section, keyword)
621 CALL keyword_release(keyword)
622 CALL section_add_subsection(metadyn_section, section)
623 CALL section_release(section)
624
625 END SUBROUTINE create_metadyn_history
626
627! **************************************************************************************************
628!> \brief creates the metavar section
629!> \param section the section to be created
630!> \author teo
631! **************************************************************************************************
632 SUBROUTINE create_metavar_section(section)
633 TYPE(section_type), POINTER :: section
634
635 TYPE(keyword_type), POINTER :: keyword
636 TYPE(section_type), POINTER :: subsection, wall_section
637
638 cpassert(.NOT. ASSOCIATED(section))
639 CALL section_create(section, __location__, name="METAVAR", &
640 description="This section specify the nature of the collective variables.", &
641 n_keywords=1, n_subsections=1, repeats=.true.)
642
643 NULLIFY (keyword)
644 CALL keyword_create(keyword, __location__, name="LAMBDA", &
645 description="Specifies the lambda parameter for the coupling of the collective variable with the system coordinates in the"// &
646 " extended lagrangian scheme.", &
647 usage="LAMBDA <REAL>", unit_str='internal_cp2k', type_of_var=real_t)
648 CALL section_add_keyword(section, keyword)
649 CALL keyword_release(keyword)
650
651 CALL keyword_create(keyword, __location__, name="MASS", &
652 description="Specifies the mass parameter of the collective variable in the"// &
653 " extended lagrangian scheme.", usage="MASS <REAL>", unit_str='amu', type_of_var=real_t)
654 CALL section_add_keyword(section, keyword)
655 CALL keyword_release(keyword)
656
657 CALL keyword_create(keyword, __location__, name="GAMMA", &
658 description="Specifies the friction term in Langevin integration of the collective variable in the"// &
659 " extended lagrangian scheme.", &
660 citations=(/vandencic2006/), &
661 usage="GAMMA {real}", type_of_var=real_t, unit_str="fs^-1")
662 CALL section_add_keyword(section, keyword)
663 CALL keyword_release(keyword)
664
665 CALL keyword_create(keyword, __location__, name="SCALE", &
666 variants=(/"WIDTH"/), &
667 description="Specifies the scale factor for the following collective variable. The history "// &
668 "dependent term has the expression: WW * Sum_{j=1}^{nhills} Prod_{k=1}^{ncolvar} "// &
669 "[EXP[-0.5*((ss-ss0(k,j))/SCALE(k))^2]], "// &
670 "where ncolvar is the number of defined METAVAR and nhills is the number of spawned hills. ", &
671 usage="SCALE <REAL>", type_of_var=real_t, unit_str='internal_cp2k')
672 CALL section_add_keyword(section, keyword)
673 CALL keyword_release(keyword)
674
675 CALL keyword_create(keyword, __location__, name="COLVAR", &
676 description="Specifies the colvar on which to apply metadynamics.", &
677 usage="COLVAR {integer}", type_of_var=integer_t)
678 CALL section_add_keyword(section, keyword)
679 CALL keyword_release(keyword)
680
681 ! Wall section
682 NULLIFY (wall_section, subsection)
683 CALL section_create(wall_section, __location__, name="WALL", &
684 description="Controls the activation of walls on COLVAR during a metadynamic run.", &
685 n_keywords=0, n_subsections=1, repeats=.true.)
686
687 CALL keyword_create( &
688 keyword, __location__, name="TYPE", &
689 description="Specify the type of wall", &
690 usage=" TYPE (REFLECTIVE|QUADRATIC|QUARTIC|GAUSSIAN|NONE)", &
691 enum_c_vals=s2a("REFLECTIVE", "QUADRATIC", "QUARTIC", "GAUSSIAN", "NONE"), &
692 enum_desc=s2a("Reflective wall. Colvar velocity is inverted when the colvar is beyond the wall position.", &
693 "Applies a quadratic potential at the wall position.", &
694 "Applies a quartic potential at the wall position.", &
695 "Applies a gaussian potential at the wall position.", &
696 "No walls are applied."), &
697 enum_i_vals=(/do_wall_reflective, do_wall_quadratic, do_wall_quartic, do_wall_gaussian, do_wall_none/), &
698 default_i_val=do_wall_none)
699 CALL section_add_keyword(wall_section, keyword)
700 CALL keyword_release(keyword)
701
702 CALL keyword_create(keyword, __location__, name="POSITION", &
703 description="Specify the value of the colvar for the wall position", &
704 usage="POSITION <REAL>", unit_str='internal_cp2k', &
705 type_of_var=real_t)
706 CALL section_add_keyword(wall_section, keyword)
707 CALL keyword_release(keyword)
708
709 ! Reflective wall
710 CALL section_create(subsection, __location__, name="REFLECTIVE", &
711 description="Parameters controlling the reflective wall", &
712 n_keywords=0, n_subsections=1, repeats=.false.)
713
714 CALL keyword_create(keyword, __location__, name="DIRECTION", &
715 description="Specify the direction of the wall.", &
716 usage=" TYPE (WALL_PLUS|WALL_MINUS)", &
717 enum_c_vals=s2a("WALL_PLUS", "WALL_MINUS"), &
718 enum_desc=s2a("Wall extends from the position towards larger values of COLVAR", &
719 "Wall extends from the position towards smaller values of COLVAR"), &
720 enum_i_vals=(/do_wall_p, do_wall_m/), default_i_val=do_wall_p)
721 CALL section_add_keyword(subsection, keyword)
722 CALL keyword_release(keyword)
723 CALL section_add_subsection(wall_section, subsection)
724 CALL section_release(subsection)
725
726 ! Quadratic wall
727 CALL section_create(subsection, __location__, name="QUADRATIC", &
728 description="Parameters controlling the quadratic wall", &
729 n_keywords=0, n_subsections=1, repeats=.false.)
730
731 CALL keyword_create(keyword, __location__, name="DIRECTION", &
732 description="Specify the direction of the wall.", &
733 usage=" TYPE (WALL_PLUS|WALL_MINUS)", &
734 enum_c_vals=s2a("WALL_PLUS", "WALL_MINUS"), &
735 enum_desc=s2a("Wall extends from the position towards larger values of COLVAR", &
736 "Wall extends from the position towards smaller values of COLVAR"), &
737 enum_i_vals=(/do_wall_p, do_wall_m/), default_i_val=do_wall_p)
738 CALL section_add_keyword(subsection, keyword)
739 CALL keyword_release(keyword)
740
741 CALL keyword_create(keyword, __location__, name="K", &
742 description="Specify the value of the quadratic potential constant: K*(CV-POS)^2", &
743 usage="K <REAL>", unit_str='hartree', &
744 type_of_var=real_t)
745 CALL section_add_keyword(subsection, keyword)
746 CALL keyword_release(keyword)
747
748 CALL section_add_subsection(wall_section, subsection)
749 CALL section_release(subsection)
750
751 ! Quartic wall
752 CALL section_create(subsection, __location__, name="QUARTIC", &
753 description="Parameters controlling the quartic wall", &
754 n_keywords=0, n_subsections=1, repeats=.false.)
755
756 CALL keyword_create(keyword, __location__, name="DIRECTION", &
757 description="Specify the direction of the wall.", &
758 usage=" TYPE (WALL_PLUS|WALL_MINUS)", &
759 enum_c_vals=s2a("WALL_PLUS", "WALL_MINUS"), &
760 enum_desc=s2a("Wall extends from the position towards larger values of COLVAR", &
761 "Wall extends from the position towards smaller values of COLVAR"), &
762 enum_i_vals=(/do_wall_p, do_wall_m/), default_i_val=do_wall_p)
763 CALL section_add_keyword(subsection, keyword)
764 CALL keyword_release(keyword)
765
766 CALL keyword_create(keyword, __location__, name="K", &
767 description="Specify the value of the quartic potential constant: K*(CV-(POS+/-(1/K^(1/4))))^4", &
768 usage="K <REAL>", unit_str='hartree', &
769 type_of_var=real_t)
770 CALL section_add_keyword(subsection, keyword)
771 CALL keyword_release(keyword)
772
773 CALL section_add_subsection(wall_section, subsection)
774 CALL section_release(subsection)
775
776 ! Gaussian wall
777 CALL section_create(subsection, __location__, name="GAUSSIAN", &
778 description="Parameters controlling the gaussian wall.", &
779 n_keywords=0, n_subsections=1, repeats=.false.)
780
781 CALL keyword_create(keyword, __location__, name="WW", &
782 description="Specify the height of the gaussian: WW*e^(-((CV-POS)/sigma)^2)", &
783 usage="K <REAL>", unit_str='hartree', &
784 type_of_var=real_t)
785 CALL section_add_keyword(subsection, keyword)
786 CALL keyword_release(keyword)
787
788 CALL keyword_create(keyword, __location__, name="SIGMA", &
789 description="Specify the width of the gaussian: WW*e^(-((CV-POS)/sigma)^2)", &
790 usage="SIGMA <REAL>", unit_str='internal_cp2k', &
791 type_of_var=real_t)
792 CALL section_add_keyword(subsection, keyword)
793 CALL keyword_release(keyword)
794
795 CALL section_add_subsection(wall_section, subsection)
796 CALL section_release(subsection)
797
798 CALL section_add_subsection(section, wall_section)
799 CALL section_release(wall_section)
800
801 END SUBROUTINE create_metavar_section
802
803! **************************************************************************************************
804!> \brief creates the uvar section
805!> \param section the section to be created
806!> \author teo
807! **************************************************************************************************
808 SUBROUTINE create_uvar_section(section)
809 TYPE(section_type), POINTER :: section
810
811 TYPE(keyword_type), POINTER :: keyword
812
813 cpassert(.NOT. ASSOCIATED(section))
814 CALL section_create(section, __location__, name="UVAR", &
815 description="This section specify the nature of the collective variables"// &
816 " used in computing the free energy.", &
817 n_keywords=1, n_subsections=1, repeats=.true.)
818
819 NULLIFY (keyword)
820
821 CALL keyword_create(keyword, __location__, name="COLVAR", &
822 description="Specifies the colvar used to compute free energy", &
823 usage="COLVAR {integer}", type_of_var=integer_t)
824 CALL section_add_keyword(section, keyword)
825 CALL keyword_release(keyword)
826 END SUBROUTINE create_uvar_section
827
828! **************************************************************************************************
829!> \brief creates the section specifying parameters to control the convergence
830!> of the free energy
831!> \param section the section to be created
832!> \author teodoro laino [tlaino] 01.2007
833! **************************************************************************************************
834 SUBROUTINE create_uvar_conv_section(section)
835 TYPE(section_type), POINTER :: section
836
837 TYPE(keyword_type), POINTER :: keyword
838
839 cpassert(.NOT. ASSOCIATED(section))
840 CALL section_create(section, __location__, name="CONVERGENCE_CONTROL", &
841 description="This section specify parameters controlling the convergence"// &
842 " of the free energy.", &
843 n_keywords=1, n_subsections=1, repeats=.true.)
844
845 NULLIFY (keyword)
846 CALL keyword_create(keyword, __location__, name="COARSE_GRAINED_WIDTH", &
847 variants=(/"CG_WIDTH"/), &
848 description="Width of segments in MD steps to generate the set of"// &
849 " coarse grained data, providing a correlation independent data set.", &
850 usage="COARSE_GRAINED_WIDTH <INTEGER>", default_i_val=50)
851 CALL section_add_keyword(section, keyword)
852 CALL keyword_release(keyword)
853
854 CALL keyword_create(keyword, __location__, name="MAX_COARSE_GRAINED_WIDTH", &
855 variants=(/"MAX_CG_WIDTH"/), &
856 description="Max Width of segments in MD steps to generate the set of"// &
857 " coarse grained data.", &
858 usage="MAX_COARSE_GRAINED_WIDTH <INTEGER>", default_i_val=200)
859 CALL section_add_keyword(section, keyword)
860 CALL keyword_release(keyword)
861
862 CALL keyword_create(keyword, __location__, name="COARSE_GRAINED_POINTS", &
863 variants=(/"CG_POINTS"/), &
864 description="Set the minimum amount of coarse grained points to collect"// &
865 " before starting the statistical analysis", &
866 usage="COARSE_GRAINED_POINTS <INTEGER>", default_i_val=30)
867 CALL section_add_keyword(section, keyword)
868 CALL keyword_release(keyword)
869
870 CALL keyword_create(keyword, __location__, name="EPS_CONV", &
871 description="Set the relative tolerance for the convergence of the collective"// &
872 " variable averages used to compute the free energy.", &
873 usage="EPS_CONV <REAL>", &
874 default_r_val=1.0e-2_dp)
875 CALL section_add_keyword(section, keyword)
876 CALL keyword_release(keyword)
877
878 CALL keyword_create(keyword, __location__, name="K_CONFIDENCE_LIMIT", &
879 description="Set the confidence limit for the Mann-Kendall trend test.", &
880 usage="K_CONFIDENCE_LIMIT <REAL>", &
881 default_r_val=0.90_dp)
882 CALL section_add_keyword(section, keyword)
883 CALL keyword_release(keyword)
884
885 CALL keyword_create(keyword, __location__, name="SW_CONFIDENCE_LIMIT", &
886 description="Set the confidence limit for the Shapiro-Wilks normality test.", &
887 usage="SW_CONFIDENCE_LIMIT <REAL>", &
888 default_r_val=0.90_dp)
889 CALL section_add_keyword(section, keyword)
890 CALL keyword_release(keyword)
891
892 CALL keyword_create(keyword, __location__, name="VN_CONFIDENCE_LIMIT", &
893 description="Set the confidence limit for the Von Neumann serial correlation test.", &
894 usage="VN_CONFIDENCE_LIMIT <REAL>", &
895 default_r_val=0.90_dp)
896 CALL section_add_keyword(section, keyword)
897 CALL keyword_release(keyword)
898 END SUBROUTINE create_uvar_conv_section
899
900END MODULE input_cp2k_free_energy
string_utilities::s2a
Definition string_utilities.F:48
bibliography
collects all references to literature in CP2K as new algorithms / method are included from literature...
Definition bibliography.F:28
bibliography::barducbus2008
integer, save, public barducbus2008
Definition bibliography.F:43
bibliography::vandencic2006
integer, save, public vandencic2006
Definition bibliography.F:43
cp_output_handling
routines to handle the output, The idea is to remove the decision of wheter to output and what to out...
Definition cp_output_handling.F:25
cp_output_handling::low_print_level
integer, parameter, public low_print_level
Definition cp_output_handling.F:73
cp_output_handling::high_print_level
integer, parameter, public high_print_level
Definition cp_output_handling.F:73
cp_output_handling::add_last_numeric
integer, parameter, public add_last_numeric
Definition cp_output_handling.F:70
cp_output_handling::cp_print_key_section_create
subroutine, public cp_print_key_section_create(print_key_section, location, name, description, print_level, each_iter_names, each_iter_values, add_last, filename, common_iter_levels, citations, unit_str)
creates a print_key section
Definition cp_output_handling.F:174
cp_units
unit conversion facility
Definition cp_units.F:30
cp_units::cp_unit_to_cp2k
real(kind=dp) function, public cp_unit_to_cp2k(value, unit_str, defaults, power)
converts to the internal cp2k units to the given unit
Definition cp_units.F:1150
input_constants
collects all constants needed in input so that they can be used without circular dependencies
Definition input_constants.F:17
input_constants::do_wall_p
integer, parameter, public do_wall_p
Definition input_constants.F:372
input_constants::do_wall_m
integer, parameter, public do_wall_m
Definition input_constants.F:372
input_constants::do_fe_ac
integer, parameter, public do_fe_ac
Definition input_constants.F:362
input_constants::do_wall_none
integer, parameter, public do_wall_none
Definition input_constants.F:366
input_constants::do_wall_gaussian
integer, parameter, public do_wall_gaussian
Definition input_constants.F:366
input_constants::do_fe_ui
integer, parameter, public do_fe_ui
Definition input_constants.F:362
input_constants::do_wall_quartic
integer, parameter, public do_wall_quartic
Definition input_constants.F:366
input_constants::do_wall_reflective
integer, parameter, public do_wall_reflective
Definition input_constants.F:366
input_constants::do_wall_quadratic
integer, parameter, public do_wall_quadratic
Definition input_constants.F:366
input_constants::do_fe_meta
integer, parameter, public do_fe_meta
Definition input_constants.F:362
input_constants::gaussian
integer, parameter, public gaussian
Definition input_constants.F:153
input_cp2k_free_energy
Definition input_cp2k_free_energy.F:13
input_cp2k_free_energy::create_metavar_section
subroutine, public create_metavar_section(section)
creates the metavar section
Definition input_cp2k_free_energy.F:633
input_cp2k_free_energy::create_fe_section
subroutine, public create_fe_section(section)
creates the free energy section
Definition input_cp2k_free_energy.F:58
input_keyword_types
represents keywords in an input
Definition input_keyword_types.F:14
input_keyword_types::keyword_release
subroutine, public keyword_release(keyword)
releases the given keyword (see doc/ReferenceCounting.html)
Definition input_keyword_types.F:426
input_keyword_types::keyword_create
subroutine, public keyword_create(keyword, location, name, description, usage, type_of_var, n_var, repeats, variants, default_val, default_l_val, default_r_val, default_lc_val, default_c_val, default_i_val, default_l_vals, default_r_vals, default_c_vals, default_i_vals, lone_keyword_val, lone_keyword_l_val, lone_keyword_r_val, lone_keyword_c_val, lone_keyword_i_val, lone_keyword_l_vals, lone_keyword_r_vals, lone_keyword_c_vals, lone_keyword_i_vals, enum_c_vals, enum_i_vals, enum, enum_strict, enum_desc, unit_str, citations, deprecation_notice, removed)
creates a keyword object
Definition input_keyword_types.F:155
input_section_types
objects that represent the structure of input sections and the data contained in an input section
Definition input_section_types.F:15
input_section_types::section_create
subroutine, public section_create(section, location, name, description, n_keywords, n_subsections, repeats, citations)
creates a list of keywords
Definition input_section_types.F:156
input_section_types::section_add_keyword
subroutine, public section_add_keyword(section, keyword)
adds a keyword to the given section
Definition input_section_types.F:504
input_section_types::section_add_subsection
subroutine, public section_add_subsection(section, subsection)
adds a subsection to the given section
Definition input_section_types.F:560
input_section_types::section_release
recursive subroutine, public section_release(section)
releases the given keyword list (see doc/ReferenceCounting.html)
Definition input_section_types.F:231
input_val_types
a wrapper for basic fortran types.
Definition input_val_types.F:14
input_val_types::real_t
integer, parameter, public real_t
Definition input_val_types.F:41
input_val_types::lchar_t
integer, parameter, public lchar_t
Definition input_val_types.F:41
input_val_types::char_t
integer, parameter, public char_t
Definition input_val_types.F:41
input_val_types::integer_t
integer, parameter, public integer_t
Definition input_val_types.F:41
kinds
Defines the basic variable types.
Definition kinds.F:23
kinds::dp
integer, parameter, public dp
Definition kinds.F:34
string_utilities
Utilities for string manipulations.
Definition string_utilities.F:16
input_keyword_types::keyword_type
represent a keyword in the input
Definition input_keyword_types.F:88
input_section_types::section_type
represent a section of the input file
Definition input_section_types.F:102