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 Ole Schuett
12 : ! **************************************************************************************************
13 :
14 : MODULE input_cp2k_md
15 : USE bibliography, ONLY: &
16 : Evans1983, Guidon2008, Kantorovich2008, Kantorovich2008a, Kuhne2007, Minary2003, &
17 : Rengaraj2020, Ricci2003, Tuckerman1992, VandeVondele2002, West2006
18 : USE cp_output_handling, ONLY: add_last_numeric,&
19 : cp_print_key_section_create,&
20 : debug_print_level,&
21 : high_print_level,&
22 : low_print_level,&
23 : medium_print_level
24 : USE cp_units, ONLY: cp_unit_to_cp2k
25 : USE fparser, ONLY: docf
26 : USE input_constants, ONLY: &
27 : do_constr_atomic, do_constr_molec, do_constr_none, isokin_ensemble, langevin_ensemble, &
28 : md_init_default, md_init_vib, npe_f_ensemble, npe_i_ensemble, nph_ensemble, &
29 : nph_uniaxial_damped_ensemble, nph_uniaxial_ensemble, npt_f_ensemble, npt_i_ensemble, &
30 : npt_ia_ensemble, nve_ensemble, nvt_adiabatic_ensemble, nvt_ensemble, reftraj_ensemble
31 : USE input_cp2k_barostats, ONLY: create_barostat_section
32 : USE input_cp2k_thermostats, ONLY: create_region_section,&
33 : create_thermo_fast_section,&
34 : create_thermo_slow_section,&
35 : create_thermostat_section
36 : USE input_keyword_types, ONLY: keyword_create,&
37 : keyword_release,&
38 : keyword_type
39 : USE input_section_types, ONLY: section_add_keyword,&
40 : section_add_subsection,&
41 : section_create,&
42 : section_release,&
43 : section_type
44 : USE input_val_types, ONLY: char_t,&
45 : integer_t,&
46 : lchar_t,&
47 : real_t
48 : USE kinds, ONLY: dp
49 : USE reftraj_types, ONLY: REFTRAJ_EVAL_ENERGY,&
50 : REFTRAJ_EVAL_ENERGY_FORCES,&
51 : REFTRAJ_EVAL_NONE,&
52 : REFTRAJ_WRAP_CENTRAL,&
53 : REFTRAJ_WRAP_NONE,&
54 : REFTRAJ_WRAP_POSITIVE
55 : USE string_utilities, ONLY: newline,&
56 : s2a
57 : #include "../base/base_uses.f90"
58 :
59 : IMPLICIT NONE
60 : PRIVATE
61 :
62 : LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .TRUE.
63 : CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'input_cp2k_md'
64 :
65 : PUBLIC :: create_md_section
66 :
67 : CONTAINS
68 :
69 : ! **************************************************************************************************
70 : !> \brief ...
71 : !> \param section will contain the md section
72 : !> \author fawzi
73 : ! **************************************************************************************************
74 30706 : SUBROUTINE create_md_section(section)
75 : TYPE(section_type), POINTER :: section
76 :
77 : TYPE(keyword_type), POINTER :: keyword
78 : TYPE(section_type), POINTER :: subsection
79 :
80 30706 : CPASSERT(.NOT. ASSOCIATED(section))
81 : CALL section_create(section, __LOCATION__, name="MD", &
82 : description="This section defines the whole set of parameters needed perform an MD run.", &
83 30706 : n_keywords=13, n_subsections=6, repeats=.FALSE.)
84 :
85 30706 : NULLIFY (keyword, subsection)
86 : CALL keyword_create(keyword, __LOCATION__, name="ensemble", &
87 : description="The ensemble/integrator that you want to use for MD propagation", &
88 : usage="ensemble nve", &
89 : default_i_val=nve_ensemble, &
90 : enum_c_vals=s2a("NVE", "NVT", "NPT_I", "NPT_F", "MSST", "MSST_DAMPED", &
91 : "HYDROSTATICSHOCK", "ISOKIN", "REFTRAJ", "LANGEVIN", "NPE_F", &
92 : "NPE_I", "NVT_ADIABATIC", "NPT_IA"), &
93 : enum_desc=s2a("constant energy (microcanonical)", &
94 : "constant temperature and volume (canonical)", &
95 : "constant temperature and pressure using an isotropic cell", &
96 : "constant temperature and pressure using a flexible cell", &
97 : "simulate steady shock (uniaxial)", &
98 : "simulate steady shock (uniaxial) with extra viscosity", &
99 : "simulate steady shock with hydrostatic pressure", &
100 : "constant kinetic energy", &
101 : "reading frames from a file called reftraj.xyz (e.g. for property calculation)", &
102 : "langevin dynamics (constant temperature)", &
103 : "constant pressure ensemble (no thermostat)", &
104 : "constant pressure ensemble using an isotropic cell (no thermostat)", &
105 : "adiabatic dynamics in constant temperature and volume ensemble (CAFES)", &
106 : "NPT_I ensemble with frozen atoms in absolute coordinate"), &
107 : citations=[Evans1983, VandeVondele2002, Minary2003], &
108 : enum_i_vals=[nve_ensemble, nvt_ensemble, npt_i_ensemble, npt_f_ensemble, &
109 : nph_uniaxial_ensemble, nph_uniaxial_damped_ensemble, nph_ensemble, isokin_ensemble, &
110 : reftraj_ensemble, langevin_ensemble, npe_f_ensemble, npe_i_ensemble, &
111 122824 : nvt_adiabatic_ensemble, npt_ia_ensemble])
112 30706 : CALL section_add_keyword(section, keyword)
113 30706 : CALL keyword_release(keyword)
114 :
115 : CALL keyword_create(keyword, __LOCATION__, name="STEPS", &
116 : description="The number of MD steps to perform, counting from step_start_val. ", &
117 30706 : usage="STEPS 100", default_i_val=3)
118 30706 : CALL section_add_keyword(section, keyword)
119 30706 : CALL keyword_release(keyword)
120 :
121 : CALL keyword_create(keyword, __LOCATION__, name="MAX_STEPS", &
122 : description="The number of MD steps to perform, counting from step 1", &
123 30706 : usage="MAX_STEPS 100", default_i_val=1000000000)
124 30706 : CALL section_add_keyword(section, keyword)
125 30706 : CALL keyword_release(keyword)
126 :
127 : CALL keyword_create(keyword, __LOCATION__, name="TIMESTEP", &
128 : description="The length of an integration step (in case RESPA the large TIMESTEP)", &
129 : usage="TIMESTEP 1.0", default_r_val=cp_unit_to_cp2k(value=0.5_dp, unit_str="fs"), &
130 30706 : unit_str="fs")
131 30706 : CALL section_add_keyword(section, keyword)
132 30706 : CALL keyword_release(keyword)
133 :
134 : CALL keyword_create(keyword, __LOCATION__, name="STEP_START_VAL", &
135 : description="The starting step value for the MD", usage="STEP_START_VAL <integer>", &
136 30706 : default_i_val=0)
137 30706 : CALL section_add_keyword(section, keyword)
138 30706 : CALL keyword_release(keyword)
139 :
140 : CALL keyword_create(keyword, __LOCATION__, name="TIME_START_VAL", &
141 : description="The starting timer value for the MD", &
142 : usage="TIME_START_VAL <real>", default_r_val=cp_unit_to_cp2k(value=0.0_dp, unit_str="fs"), &
143 30706 : unit_str="fs")
144 30706 : CALL section_add_keyword(section, keyword)
145 30706 : CALL keyword_release(keyword)
146 :
147 : CALL keyword_create(keyword, __LOCATION__, name="ECONS_START_VAL", &
148 : description="The starting value of the conserved quantity", &
149 : usage="ECONS_START_VAL <real>", default_r_val=0.0_dp, &
150 30706 : unit_str="hartree")
151 30706 : CALL section_add_keyword(section, keyword)
152 30706 : CALL keyword_release(keyword)
153 :
154 : CALL keyword_create(keyword, __LOCATION__, name="TEMPERATURE", &
155 : description="The temperature in K used to initialize "// &
156 : "the velocities with init and pos restart, and in the NPT/NVT simulations", &
157 : usage="TEMPERATURE 325.0", default_r_val=cp_unit_to_cp2k(value=300.0_dp, unit_str="K"), &
158 30706 : unit_str="K")
159 30706 : CALL section_add_keyword(section, keyword)
160 30706 : CALL keyword_release(keyword)
161 :
162 : CALL keyword_create(keyword, __LOCATION__, name="TEMP_TOL", &
163 : variants=s2a("temp_to", "temperature_tolerance"), &
164 : description="The maximum accepted deviation of the (global) temperature "// &
165 : "from the desired target temperature before a rescaling of the velocities "// &
166 : "is performed. If it is 0 no rescaling is performed. NOTE: This keyword is "// &
167 : "obsolescent; Using a CSVR thermostat with a short timeconstant is "// &
168 : "recommended as a better alternative.", &
169 30706 : usage="TEMP_TOL 0.0", default_r_val=0.0_dp, unit_str='K')
170 30706 : CALL section_add_keyword(section, keyword)
171 30706 : CALL keyword_release(keyword)
172 :
173 : CALL keyword_create(keyword, __LOCATION__, name="TEMP_KIND", &
174 : description="Compute the temperature per each kind separately", &
175 : usage="TEMP_KIND LOGICAL", &
176 30706 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
177 30706 : CALL section_add_keyword(section, keyword)
178 30706 : CALL keyword_release(keyword)
179 :
180 : CALL keyword_create(keyword, __LOCATION__, name="SCALE_TEMP_KIND", &
181 : description="When necessary rescale the temperature per each kind separately", &
182 : usage="SCALE_TEMP_KIND LOGICAL", &
183 30706 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
184 30706 : CALL section_add_keyword(section, keyword)
185 30706 : CALL keyword_release(keyword)
186 :
187 : CALL keyword_create(keyword, __LOCATION__, name="COMVEL_TOL", &
188 : description="The maximum accepted velocity of the center of mass. "// &
189 : "With Shell-Model, comvel may drift if MD%THERMOSTAT%REGION /= GLOBAL ", &
190 30706 : usage="COMVEL_TOL 0.1", type_of_var=real_t, n_var=1, unit_str="bohr*au_t^-1")
191 30706 : CALL section_add_keyword(section, keyword)
192 30706 : CALL keyword_release(keyword)
193 :
194 : CALL keyword_create(keyword, __LOCATION__, name="ANGVEL_TOL", &
195 : description="The maximum accepted angular velocity. This option is ignored "// &
196 : "when the system is periodic. Removes the components of the velocities that "// &
197 : "project on the external rotational degrees of freedom.", &
198 30706 : usage="ANGVEL_TOL 0.1", type_of_var=real_t, n_var=1, unit_str="bohr*au_t^-1")
199 30706 : CALL section_add_keyword(section, keyword)
200 30706 : CALL keyword_release(keyword)
201 :
202 : CALL keyword_create(keyword, __LOCATION__, name="ANGVEL_ZERO", &
203 : description="Set the initial angular velocity to zero. This option is ignored "// &
204 : "when the system is periodic or when initial velocities are defined. Technically, "// &
205 : "the part of the random initial velocities that projects on the external "// &
206 : "rotational degrees of freedom is subtracted.", &
207 : usage="ANGVEL_ZERO LOGICAL", &
208 30706 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
209 30706 : CALL section_add_keyword(section, keyword)
210 30706 : CALL keyword_release(keyword)
211 :
212 : CALL keyword_create(keyword, __LOCATION__, name="ANNEALING", &
213 : description="Specifies the rescaling factor for annealing velocities. "// &
214 : "Automatically enables the annealing procedure. This scheme works only for ensembles "// &
215 : "that do not have thermostats on particles.", &
216 30706 : usage="annealing <REAL>", default_r_val=1.0_dp)
217 30706 : CALL section_add_keyword(section, keyword)
218 30706 : CALL keyword_release(keyword)
219 :
220 : CALL keyword_create(keyword, __LOCATION__, name="ANNEALING_CELL", &
221 : description="Specifies the rescaling factor for annealing velocities of the CELL "// &
222 : "Automatically enables the annealing procedure for the CELL. This scheme works only "// &
223 : "for ensambles that do not have thermostat on CELLS velocities.", &
224 30706 : usage="ANNEALING_CELL <REAL>", default_r_val=1.0_dp)
225 30706 : CALL section_add_keyword(section, keyword)
226 30706 : CALL keyword_release(keyword)
227 :
228 : CALL keyword_create(keyword, __LOCATION__, name="TEMPERATURE_ANNEALING", &
229 : description="Specifies the rescaling factor for the external temperature. "// &
230 : "This scheme works only for the Langevin ensemble.", &
231 30706 : usage="TEMPERATURE_ANNEALING <REAL>", default_r_val=1.0_dp)
232 30706 : CALL section_add_keyword(section, keyword)
233 30706 : CALL keyword_release(keyword)
234 :
235 : CALL keyword_create(keyword, __LOCATION__, name="DISPLACEMENT_TOL", &
236 : description="This keyword sets a maximum atomic displacement "// &
237 : "in each Cartesian direction. "// &
238 : "The maximum velocity is evaluated and if it is too large to remain "// &
239 : "within the assigned limit, the time step is rescaled accordingly, "// &
240 : "and the first half step of the velocity verlet is repeated.", &
241 : usage="DISPLACEMENT_TOL <REAL>", default_r_val=100.0_dp, &
242 30706 : unit_str='angstrom')
243 30706 : CALL section_add_keyword(section, keyword)
244 30706 : CALL keyword_release(keyword)
245 :
246 : CALL keyword_create(keyword, __LOCATION__, name="INITIALIZATION_METHOD", &
247 : description="This keyword selects which method to use to initialize MD. "// &
248 : "If velecities are not set explicitly, DEFAULT optioin will assign "// &
249 : "random velocities and then scale according to TEMPERATURE; VIBRATIONAL "// &
250 : "option will then use previously calculated vibrational modes to "// &
251 : "initialise both the atomic positions and velocities so that the "// &
252 : "starting point for MD is as close to canonical ensemble as possible, "// &
253 : "without the need for lengthy equilibration steps. See PRL 96, 115504 "// &
254 : "(2006). The user input atomic positions in this case are expected to "// &
255 : "be already geometry optimised. Further options for VIBRATIONAL mode "// &
256 : "is can be set in INITIAL_VIBRATION subsection. If unspecified, then "// &
257 : "the DEFAULT mode will be used.", &
258 : usage="INITIALIZATION_METHOD DEFAULT", &
259 : default_i_val=md_init_default, &
260 : enum_c_vals=s2a("DEFAULT", "VIBRATIONAL"), &
261 : enum_desc=s2a("Assign random velocities and then scale according to "// &
262 : "TEMPERATURE", &
263 : "Initialise positions and velocities to give canonical ensemble "// &
264 : "with TEMPERATURE, using the method described in PRL 96, 115504 (2006)"), &
265 30706 : enum_i_vals=[md_init_default, md_init_vib])
266 30706 : CALL section_add_keyword(section, keyword)
267 30706 : CALL keyword_release(keyword)
268 :
269 30706 : CALL create_langevin_section(subsection)
270 30706 : CALL section_add_subsection(section, subsection)
271 30706 : CALL section_release(subsection)
272 :
273 30706 : CALL create_msst_section(subsection)
274 30706 : CALL section_add_subsection(section, subsection)
275 30706 : CALL section_release(subsection)
276 :
277 30706 : CALL create_barostat_section(subsection)
278 30706 : CALL section_add_subsection(section, subsection)
279 30706 : CALL section_release(subsection)
280 :
281 30706 : CALL create_thermostat_section(subsection)
282 30706 : CALL section_add_subsection(section, subsection)
283 30706 : CALL section_release(subsection)
284 :
285 30706 : CALL create_respa_section(subsection)
286 30706 : CALL section_add_subsection(section, subsection)
287 30706 : CALL section_release(subsection)
288 :
289 30706 : CALL create_shell_section(subsection)
290 30706 : CALL section_add_subsection(section, subsection)
291 30706 : CALL section_release(subsection)
292 :
293 30706 : CALL create_adiabatic_section(subsection)
294 30706 : CALL section_add_subsection(section, subsection)
295 30706 : CALL section_release(subsection)
296 :
297 30706 : CALL create_softening_section(subsection)
298 30706 : CALL section_add_subsection(section, subsection)
299 30706 : CALL section_release(subsection)
300 :
301 30706 : CALL create_reftraj_section(subsection)
302 30706 : CALL section_add_subsection(section, subsection)
303 30706 : CALL section_release(subsection)
304 :
305 30706 : CALL create_avgs_section(subsection)
306 30706 : CALL section_add_subsection(section, subsection)
307 30706 : CALL section_release(subsection)
308 :
309 30706 : CALL create_thermal_region_section(subsection)
310 30706 : CALL section_add_subsection(section, subsection)
311 30706 : CALL section_release(subsection)
312 :
313 30706 : CALL create_md_print_section(subsection)
314 30706 : CALL section_add_subsection(section, subsection)
315 30706 : CALL section_release(subsection)
316 :
317 30706 : CALL create_cascade_section(subsection)
318 30706 : CALL section_add_subsection(section, subsection)
319 30706 : CALL section_release(subsection)
320 :
321 30706 : CALL create_vib_init_section(subsection)
322 30706 : CALL section_add_subsection(section, subsection)
323 30706 : CALL section_release(subsection)
324 :
325 30706 : END SUBROUTINE create_md_section
326 :
327 : ! **************************************************************************************************
328 : !> \brief Defines LANGEVIN section
329 : !> \param section ...
330 : !> \author teo
331 : ! **************************************************************************************************
332 30706 : SUBROUTINE create_langevin_section(section)
333 : TYPE(section_type), POINTER :: section
334 :
335 : TYPE(keyword_type), POINTER :: keyword
336 :
337 30706 : CPASSERT(.NOT. ASSOCIATED(section))
338 : CALL section_create(section, __LOCATION__, name="Langevin", &
339 : description="Controls the set of parameters to run a Langevin MD. "// &
340 : "The integrator used follows that given in the article by Ricci et al. "// &
341 : "The user can define regions in the system where the atoms inside "// &
342 : "undergoes Langevin MD, while those outside the regions undergoes "// &
343 : "NVE Born Oppenheimer MD. To define the regions, the user should "// &
344 : "use THERMAL_REGION subsection of MOTION%MD. ", &
345 : citations=[Ricci2003, Kuhne2007, Rengaraj2020], &
346 122824 : n_keywords=0, n_subsections=1, repeats=.FALSE.)
347 30706 : NULLIFY (keyword)
348 :
349 : CALL keyword_create(keyword, __LOCATION__, name="gamma", &
350 : description="Gamma parameter for the Langevin dynamics (LD)", &
351 : usage="gamma 0.001", &
352 30706 : default_r_val=0.0_dp, unit_str='fs^-1')
353 30706 : CALL section_add_keyword(section, keyword)
354 30706 : CALL keyword_release(keyword)
355 :
356 : CALL keyword_create(keyword, __LOCATION__, name="Noisy_Gamma", &
357 : variants=["NoisyGamma"], &
358 : description="Imaginary Langevin Friction term for LD with noisy forces.", &
359 : citations=[Kuhne2007], &
360 92118 : usage="Noisy_Gamma 4.0E-5", default_r_val=0.0_dp, unit_str='fs^-1')
361 30706 : CALL section_add_keyword(section, keyword)
362 30706 : CALL keyword_release(keyword)
363 :
364 : CALL keyword_create(keyword, __LOCATION__, name="Shadow_Gamma", &
365 : variants=["ShadowGamma"], &
366 : description="Shadow Langevin Friction term for LD with noisy forces in order to adjust Noisy_Gamma.", &
367 : citations=[Rengaraj2020], &
368 92118 : usage="Shadow_Gamma 0.001", default_r_val=0.0_dp, unit_str='fs^-1')
369 30706 : CALL section_add_keyword(section, keyword)
370 30706 : CALL keyword_release(keyword)
371 30706 : END SUBROUTINE create_langevin_section
372 :
373 : ! **************************************************************************************************
374 : !> \brief Defines print section for MD
375 : !> \param section ...
376 : !> \author teo
377 : ! **************************************************************************************************
378 30706 : SUBROUTINE create_md_print_section(section)
379 : TYPE(section_type), POINTER :: section
380 :
381 : TYPE(keyword_type), POINTER :: keyword
382 : TYPE(section_type), POINTER :: print_key
383 :
384 30706 : CPASSERT(.NOT. ASSOCIATED(section))
385 : CALL section_create(section, __LOCATION__, name="print", &
386 : description="Controls the printing properties during an MD run", &
387 30706 : n_keywords=0, n_subsections=1, repeats=.FALSE.)
388 30706 : NULLIFY (print_key, keyword)
389 :
390 : CALL keyword_create(keyword, __LOCATION__, name="FORCE_LAST", &
391 : description="Print the output and restart file if walltime is reached or "// &
392 : "if an external EXIT command is given. It still requires the keyword LAST "// &
393 : "to be present for the specific print key (in case the last step should not "// &
394 : "match with the print_key iteration number).", &
395 : usage="FORCE_LAST LOGICAL", &
396 30706 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
397 30706 : CALL section_add_keyword(section, keyword)
398 30706 : CALL keyword_release(keyword)
399 :
400 : CALL cp_print_key_section_create(print_key, __LOCATION__, "ENERGY", &
401 : description="Controls the output the ener file", &
402 : print_level=low_print_level, common_iter_levels=1, &
403 30706 : filename="")
404 30706 : CALL section_add_subsection(section, print_key)
405 30706 : CALL section_release(print_key)
406 :
407 : CALL cp_print_key_section_create(print_key, __LOCATION__, "SHELL_ENERGY", &
408 : description="Controls the output of the shell-energy file (only if shell-model)", &
409 : print_level=medium_print_level, common_iter_levels=1, &
410 30706 : filename="")
411 30706 : CALL section_add_subsection(section, print_key)
412 30706 : CALL section_release(print_key)
413 :
414 : CALL cp_print_key_section_create(print_key, __LOCATION__, "TEMP_KIND", &
415 : description="Controls the output of the temperature"// &
416 : " computed separately for each kind", &
417 : print_level=high_print_level, common_iter_levels=1, &
418 30706 : filename="")
419 30706 : CALL section_add_subsection(section, print_key)
420 30706 : CALL section_release(print_key)
421 :
422 : CALL cp_print_key_section_create(print_key, __LOCATION__, "TEMP_SHELL_KIND", &
423 : description="Controls the output of the temperature of the"// &
424 : " shell-core motion computed separately for each kind", &
425 : print_level=high_print_level, common_iter_levels=1, &
426 30706 : filename="")
427 30706 : CALL section_add_subsection(section, print_key)
428 30706 : CALL section_release(print_key)
429 :
430 : CALL cp_print_key_section_create(print_key, __LOCATION__, "CENTER_OF_MASS", &
431 : description="Controls the printing of COM velocity during an MD", &
432 : print_level=medium_print_level, common_iter_levels=1, &
433 30706 : filename="__STD_OUT__")
434 30706 : CALL section_add_subsection(section, print_key)
435 30706 : CALL section_release(print_key)
436 :
437 : CALL cp_print_key_section_create(print_key, __LOCATION__, "COEFFICIENTS", &
438 : description="Controls the printing of coefficients during an MD run.", &
439 : print_level=medium_print_level, common_iter_levels=1, &
440 30706 : filename="")
441 30706 : CALL section_add_subsection(section, print_key)
442 30706 : CALL section_release(print_key)
443 :
444 : CALL cp_print_key_section_create(print_key, __LOCATION__, "ROTATIONAL_INFO", &
445 : description="Controls the printing basic info during the calculation of the "// &
446 : "translational/rotational degrees of freedom.", print_level=low_print_level, &
447 30706 : add_last=add_last_numeric, filename="__STD_OUT__")
448 : CALL keyword_create(keyword, __LOCATION__, name="COORDINATES", &
449 : description="Prints atomic coordinates in the standard orientation. "// &
450 : "Coordinates are not affected during the calculation.", &
451 30706 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
452 30706 : CALL section_add_keyword(print_key, keyword)
453 30706 : CALL keyword_release(keyword)
454 30706 : CALL section_add_subsection(section, print_key)
455 30706 : CALL section_release(print_key)
456 :
457 : CALL cp_print_key_section_create(print_key, __LOCATION__, "PROGRAM_RUN_INFO", &
458 : description="Controls the printing of basic and summary information during the"// &
459 : " Molecular Dynamics", &
460 30706 : print_level=low_print_level, add_last=add_last_numeric, filename="__STD_OUT__")
461 30706 : CALL section_add_subsection(section, print_key)
462 30706 : CALL section_release(print_key)
463 30706 : END SUBROUTINE create_md_print_section
464 :
465 : ! **************************************************************************************************
466 : !> \brief Defines parameters for RESPA integration scheme
467 : !> \param section will contain the coeff section
468 : !> \author teo
469 : ! **************************************************************************************************
470 30706 : SUBROUTINE create_respa_section(section)
471 : TYPE(section_type), POINTER :: section
472 :
473 : TYPE(keyword_type), POINTER :: keyword
474 :
475 30706 : CPASSERT(.NOT. ASSOCIATED(section))
476 :
477 : CALL section_create(section, __LOCATION__, name="RESPA", &
478 : description="Multiple timestep integration based on RESPA (implemented for NVE only)."// &
479 : " RESPA exploits multiple force_eval."// &
480 : " In this case the order of the force_eval maps"// &
481 : " the order of the respa shells from the slowest to the fastest force evaluation."// &
482 : " If force_evals share the same subsys, it's enough then to specify the"// &
483 : " subsys in the force_eval corresponding at the first index in the multiple_force_eval list."// &
484 : " Can be used to speedup classical and ab initio MD simulations.", &
485 : n_keywords=1, n_subsections=0, repeats=.FALSE., &
486 92118 : citations=[Tuckerman1992, Guidon2008])
487 :
488 30706 : NULLIFY (keyword)
489 : CALL keyword_create(keyword, __LOCATION__, name="FREQUENCY", &
490 : description="The number of reference MD steps between two RESPA corrections.", &
491 30706 : usage="FREQUENCY <INTEGER>", default_i_val=5)
492 30706 : CALL section_add_keyword(section, keyword)
493 30706 : CALL keyword_release(keyword)
494 :
495 30706 : END SUBROUTINE create_respa_section
496 :
497 : ! **************************************************************************************************
498 : !> \brief Defines parameters for REFTRAJ analysis
499 : !> \param section will contain the coeff section
500 : !> \author teo
501 : ! **************************************************************************************************
502 30706 : SUBROUTINE create_reftraj_section(section)
503 : TYPE(section_type), POINTER :: section
504 :
505 : TYPE(keyword_type), POINTER :: keyword
506 : TYPE(section_type), POINTER :: print_key, subsection
507 :
508 30706 : CPASSERT(.NOT. ASSOCIATED(section))
509 :
510 : CALL section_create(section, __LOCATION__, name="REFTRAJ", &
511 : description="Loads an external trajectory file and performs analysis on "// &
512 : "the loaded snapshots; optionally, calculates per-frame potential energy, "// &
513 : "forces and other properties as requested by the keyword `EVAL` below with "// &
514 : "the force method specified in the `&FORCE_EVAL` section. Time integration "// &
515 : "is not performed here, and quantities of velocity, temperature and kinetic "// &
516 : "energy from nuclear motion are therefore irrelevant. Such a REFTRAJ run is "// &
517 : "essentially a series of single-point calculations; the snapshots are not "// &
518 : "necessarily from MD and may be from custom concatenation."//newline//newline// &
519 : "The trajectory should be a multi-frame XYZ file where each frame has the "// &
520 : "same number of atoms and kind specification as the `&FORCE_EVAL/&SUBSYS` "// &
521 : "down to the exact ordering, but cell (box) size and shape can be different. "// &
522 : "The comment line of each frame is parsed for additional information such "// &
523 : "as cell, step, time and energy; currently the parser supports the same "// &
524 : "formats as the XYZ option of `&FORCE_EVAL/&SUBSYS/&CELL/CELL_FILE_FORMAT`, "// &
525 : "corresponding to trajectory files printed from `&MOTION/&PRINT/&TRAJECTORY` "// &
526 : "as XYZ and EXTXYZ and from the external `dumpdcd` tool."//newline//newline// &
527 : "A minimal working example trajectory in the extended XYZ format should have "// &
528 : '`Lattice="<Ax> <Ay> <Az> <Bx> <By> <Bz> <Cx> <Cy> <Cz>"` for the components '// &
529 : "of cell vectors A, B, C, and `Step=<integer>` for the integer timestep. "// &
530 : "`Time=<real>` and `Energy=<real>` for simulation time and potential energy "// &
531 : "respectively are also parsed; if omitted, the default value will be 0.0 . "// &
532 : "Note that the parser is case insensitive, but whitespaces are only used "// &
533 : "between key-value pairs as delimiters and not around the = signs in an "// &
534 : "extended XYZ file. `Properties=species:S:1:pos:R:3` is always assumed for "// &
535 : "backwards compatibility with the primitive XYZ specification: the first "// &
536 : "column is a string for element symbol (or kind alias), followed by three "// &
537 : "columns of real values for Cartesian coordinates in angstrom."//newline//newline// &
538 : "Alternatively, the legacy brief format from `&TRAJECTORY` output where the "// &
539 : "comment line starts with `i = <integer>` for the integer timestep can also "// &
540 : "be used, this time with the = sign surrounded by whitespaces. The cell "// &
541 : "information may come from a separate file requested by `CELL_FILE_NAME` if "// &
542 : "variable, or may be taken as the `&FORCE_EVAL/&SUBSYS/&CELL` if constant.", &
543 30706 : n_keywords=1, n_subsections=1, repeats=.FALSE.)
544 :
545 30706 : NULLIFY (keyword, print_key, subsection)
546 :
547 : CALL keyword_create(keyword, __LOCATION__, name="TRAJ_FILE_NAME", &
548 : description="Specify the filename where the trajectory is stored.", &
549 : repeats=.FALSE., &
550 30706 : usage="TRAJ_FILE_NAME <CHARACTER>", default_lc_val="reftraj.xyz")
551 30706 : CALL section_add_keyword(section, keyword)
552 30706 : CALL keyword_release(keyword)
553 :
554 : CALL keyword_create(keyword, __LOCATION__, name="CELL_FILE_NAME", &
555 : description="Specify the filename where the cell is stored "// &
556 : "(for trajectories generated within variable cell ensembles). "// &
557 : "This file will be parsed only when no cell information is found "// &
558 : "in the trajectory file and VARIABLE_VOLUME is set to .TRUE.", &
559 : repeats=.FALSE., &
560 30706 : usage="CELL_FILE_NAME <CHARACTER>", default_lc_val="reftraj.cell")
561 30706 : CALL section_add_keyword(section, keyword)
562 30706 : CALL keyword_release(keyword)
563 :
564 : CALL keyword_create(keyword, __LOCATION__, name="VARIABLE_VOLUME", &
565 : description="Enables the possibility to read a CELL file with "// &
566 : "information on the CELL size during the MD. This keyword will be "// &
567 : "ignored if cell information is already available in the trajectory file.", &
568 30706 : repeats=.FALSE., default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
569 30706 : CALL section_add_keyword(section, keyword)
570 30706 : CALL keyword_release(keyword)
571 :
572 : CALL keyword_create(keyword, __LOCATION__, name="FIRST_SNAPSHOT", &
573 : description="Index of the snapshot stored in the trajectory file "// &
574 : "from which to start a REFTRAJ run", &
575 30706 : repeats=.FALSE., usage="FIRST_SNAPSHOT <INTEGER>", default_i_val=1)
576 30706 : CALL section_add_keyword(section, keyword)
577 30706 : CALL keyword_release(keyword)
578 :
579 : CALL keyword_create(keyword, __LOCATION__, name="LAST_SNAPSHOT", &
580 : description="Index of the last snapshot stored in the trajectory file "// &
581 : "that is read along a REFTRAJ run. Must be specified as default is 0. "// &
582 : "Must be specified exactly as LAST_SNAPSHOT = FIRST_SNAPSHOT + STRIDE*(number of strides) "// &
583 : "to avoid an error 'Unexpected EOF'. Note that STRIDE*(number of strides) "// &
584 : "is simply the number of steps between the first to last snapshot.", &
585 30706 : repeats=.FALSE., usage="LAST_SNAPSHOT", default_i_val=0)
586 30706 : CALL section_add_keyword(section, keyword)
587 30706 : CALL keyword_release(keyword)
588 :
589 : CALL keyword_create(keyword, __LOCATION__, name="STRIDE", &
590 : description=" Stride in number of snapshot for the reftraj analysis", &
591 30706 : repeats=.FALSE., usage="STRIDE", default_i_val=1)
592 30706 : CALL section_add_keyword(section, keyword)
593 30706 : CALL keyword_release(keyword)
594 :
595 : CALL keyword_create(keyword, __LOCATION__, name="EVAL", &
596 : description="Selects the mode of energy and force evaluation for each "// &
597 : "retrieved snapshot during a REFTRAJ run, which determines availability "// &
598 : "of other properties and the time consumption in the computation. The "// &
599 : "default is NONE, a conservative option useful for analyses concerning "// &
600 : "structure only that are independent of force method, such as MSD and "// &
601 : "`&MOTION/&PRINT/&STRUCTURE_DATA`. This keyword supersedes the logical "// &
602 : "keywords `EVAL_<mode>` in older versions of the program.", &
603 : default_i_val=REFTRAJ_EVAL_NONE, &
604 : enum_i_vals=[REFTRAJ_EVAL_NONE, REFTRAJ_EVAL_ENERGY, REFTRAJ_EVAL_ENERGY_FORCES], &
605 : enum_c_vals=s2a("NONE", "ENERGY", "ENERGY_FORCES"), &
606 : enum_desc=s2a("Do not evaluate energy or force", &
607 : "Evaluate only the energy", &
608 30706 : "Evaluate energy and forces"))
609 30706 : CALL section_add_keyword(section, keyword)
610 30706 : CALL keyword_release(keyword)
611 :
612 : CALL keyword_create(keyword, __LOCATION__, name="WRAP", &
613 : description="Whether and how atoms would be wrapped to inside the "// &
614 : "simulation box according to periodic boundary condition before any "// &
615 : "subsequent analysis. Useful when there is need to convert the raw, "// &
616 : "unwrapped coordinates produced from `MOTION%PRINT%TRAJECTORY` for "// &
617 : "post-processing. This keyword will be ignored when requesting MSD "// &
618 : "calculation because wrapping coordinates makes displacement discontinuous.", &
619 : default_i_val=REFTRAJ_WRAP_NONE, &
620 : enum_i_vals=[REFTRAJ_WRAP_NONE, REFTRAJ_WRAP_POSITIVE, REFTRAJ_WRAP_CENTRAL], &
621 : enum_c_vals=s2a("NONE", "POSITIVE", "CENTRAL"), &
622 : enum_desc=s2a("Do not wrap atoms at all and use coordinates exactly as input", &
623 : "Wrap atoms so that fractional coordinates are within [0, 1]", &
624 30706 : "Wrap atoms so that fractional coordinates are within [-1/2, +1/2]"))
625 30706 : CALL section_add_keyword(section, keyword)
626 30706 : CALL keyword_release(keyword)
627 :
628 30706 : CALL create_msd_section(subsection)
629 30706 : CALL section_add_subsection(section, subsection)
630 30706 : CALL section_release(subsection)
631 :
632 : CALL section_create(subsection, __LOCATION__, name="print", &
633 : description="The section that controls the output of a reftraj run", &
634 30706 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
635 :
636 30706 : NULLIFY (print_key)
637 : CALL cp_print_key_section_create(print_key, __LOCATION__, "msd_kind", &
638 : description="Controls the output of msd per kind", &
639 : print_level=low_print_level, common_iter_levels=1, &
640 30706 : filename="")
641 30706 : CALL section_add_subsection(subsection, print_key)
642 30706 : CALL section_release(print_key)
643 :
644 : CALL cp_print_key_section_create(print_key, __LOCATION__, "msd_molecule", &
645 : description="Controls the output of msd per molecule kind", &
646 : print_level=low_print_level, common_iter_levels=1, &
647 30706 : filename="")
648 30706 : CALL section_add_subsection(subsection, print_key)
649 30706 : CALL section_release(print_key)
650 :
651 : CALL cp_print_key_section_create(print_key, __LOCATION__, "displaced_atom", &
652 : description="Controls the output of index and dislacement of "// &
653 : "atoms that moved away from the initial position of more than a "// &
654 : "given distance (see msd%disp_tol)", &
655 : print_level=low_print_level, common_iter_levels=1, &
656 30706 : filename="")
657 30706 : CALL section_add_subsection(subsection, print_key)
658 30706 : CALL section_release(print_key)
659 :
660 30706 : CALL section_add_subsection(section, subsection)
661 30706 : CALL section_release(subsection)
662 :
663 30706 : END SUBROUTINE create_reftraj_section
664 :
665 : ! **************************************************************************************************
666 : !> \brief Defines parameters for MSD calculation along a REFTRAJ analysis
667 : !> \param section will contain the coeff section
668 : !> \author MI
669 : ! **************************************************************************************************
670 30706 : SUBROUTINE create_msd_section(section)
671 : TYPE(section_type), POINTER :: section
672 :
673 : TYPE(keyword_type), POINTER :: keyword
674 : TYPE(section_type), POINTER :: subsection
675 :
676 30706 : CPASSERT(.NOT. ASSOCIATED(section))
677 :
678 : CALL section_create(section, __LOCATION__, name="MSD", &
679 : description="Loads an external trajectory file and performs analysis on the"// &
680 : " loaded snapshots.", &
681 30706 : n_keywords=3, n_subsections=0, repeats=.FALSE.)
682 :
683 30706 : NULLIFY (keyword, subsection)
684 :
685 : CALL keyword_create(keyword, __LOCATION__, name="_SECTION_PARAMETERS_", &
686 : description="controls the activation of core-level spectroscopy simulations", &
687 : usage="&MSD T", &
688 : default_l_val=.FALSE., &
689 30706 : lone_keyword_l_val=.TRUE.)
690 30706 : CALL section_add_keyword(section, keyword)
691 30706 : CALL keyword_release(keyword)
692 :
693 : CALL keyword_create(keyword, __LOCATION__, name="REF0_FILENAME", &
694 : description="Specify the filename where the initial reference configuration is stored.", &
695 30706 : repeats=.FALSE., usage="REF0_FILENAME <CHARACTER>", default_lc_val="")
696 30706 : CALL section_add_keyword(section, keyword)
697 30706 : CALL keyword_release(keyword)
698 :
699 : CALL keyword_create(keyword, __LOCATION__, name="MSD_PER_KIND", &
700 : description="Set up the calculation of the MSD for each atomic kind", &
701 : usage="MSD_PER_KIND <LOGICAL>", repeats=.FALSE., &
702 30706 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
703 30706 : CALL section_add_keyword(section, keyword)
704 30706 : CALL keyword_release(keyword)
705 :
706 : CALL keyword_create(keyword, __LOCATION__, name="MSD_PER_MOLKIND", &
707 : description="Set up the calculation of the MSD for each molecule kind. "// &
708 : "The position of the center of mass of the molecule is considered.", &
709 : usage="MSD_PER_MOLKIND <LOGICAL>", repeats=.FALSE., &
710 30706 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
711 30706 : CALL section_add_keyword(section, keyword)
712 30706 : CALL keyword_release(keyword)
713 :
714 : CALL keyword_create(keyword, __LOCATION__, name="MSD_PER_REGION", &
715 : description="Set up the calculation of the MSD for each defined region.", &
716 : usage="MSD_PER_REGION <LOGICAL>", repeats=.FALSE., &
717 30706 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
718 30706 : CALL section_add_keyword(section, keyword)
719 30706 : CALL keyword_release(keyword)
720 :
721 30706 : CALL create_region_section(subsection, "MSD calculation")
722 30706 : CALL section_add_subsection(section, subsection)
723 30706 : CALL section_release(subsection)
724 :
725 : CALL keyword_create(keyword, __LOCATION__, name="DISPLACED_ATOM", &
726 : description="Identify the atoms that moved from their initial "// &
727 : "position of a distance larger than a given tolerance (see msd%displacement_tol).", &
728 : usage="DISPLACED_ATOM <LOGICAL>", repeats=.FALSE., &
729 30706 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
730 30706 : CALL section_add_keyword(section, keyword)
731 30706 : CALL keyword_release(keyword)
732 :
733 : CALL keyword_create(keyword, __LOCATION__, name="displacement_tol", &
734 : description="Lower limit to define displaced atoms", &
735 : usage="DISPLACEMENT_TOL real", &
736 30706 : default_r_val=0._dp, n_var=1, unit_str='bohr')
737 30706 : CALL section_add_keyword(section, keyword)
738 30706 : CALL keyword_release(keyword)
739 :
740 30706 : END SUBROUTINE create_msd_section
741 :
742 : ! **************************************************************************************************
743 : !> \brief ...
744 : !> \param section will contain the coeff section
745 : !> \author teo
746 : ! **************************************************************************************************
747 30706 : SUBROUTINE create_msst_section(section)
748 : TYPE(section_type), POINTER :: section
749 :
750 : TYPE(keyword_type), POINTER :: keyword
751 :
752 30706 : CPASSERT(.NOT. ASSOCIATED(section))
753 :
754 : CALL section_create(section, __LOCATION__, name="msst", &
755 : description="Parameters for Multi-Scale Shock Technique (MSST) "// &
756 : "which simulate the effect of a steady planar shock on a unit cell. "// &
757 : "Reed et. al. Physical Review Letters 90, 235503 (2003).", &
758 30706 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
759 :
760 30706 : NULLIFY (keyword)
761 : CALL keyword_create(keyword, __LOCATION__, name="PRESSURE", &
762 : description="Initial pressure", &
763 : usage="PRESSURE real", &
764 30706 : default_r_val=0._dp, n_var=1, unit_str='bar')
765 30706 : CALL section_add_keyword(section, keyword)
766 30706 : CALL keyword_release(keyword)
767 :
768 : CALL keyword_create(keyword, __LOCATION__, name="ENERGY", &
769 : description="Initial energy", &
770 : usage="ENERGY real", &
771 30706 : default_r_val=0._dp, n_var=1, unit_str='hartree')
772 30706 : CALL section_add_keyword(section, keyword)
773 30706 : CALL keyword_release(keyword)
774 :
775 : CALL keyword_create(keyword, __LOCATION__, name="VOLUME", &
776 : description="Initial volume", &
777 : usage="VOLUME real", &
778 30706 : default_r_val=0._dp, n_var=1, unit_str='angstrom^3')
779 30706 : CALL section_add_keyword(section, keyword)
780 30706 : CALL keyword_release(keyword)
781 :
782 : CALL keyword_create(keyword, __LOCATION__, name="CMASS", &
783 : description="Effective cell mass", &
784 : usage="CMASS real", &
785 30706 : default_r_val=0._dp, n_var=1, unit_str='au_m')
786 30706 : CALL section_add_keyword(section, keyword)
787 30706 : CALL keyword_release(keyword)
788 :
789 : CALL keyword_create(keyword, __LOCATION__, name="VSHOCK", variants=["V_SHOCK"], &
790 : description="Velocity shock", &
791 : usage="VSHOCK real", &
792 61412 : default_r_val=0._dp, n_var=1, unit_str='m/s')
793 30706 : CALL section_add_keyword(section, keyword)
794 30706 : CALL keyword_release(keyword)
795 :
796 : CALL keyword_create(keyword, __LOCATION__, name="GAMMA", &
797 : description="Damping coefficient for cell volume", &
798 : usage="GAMMA real", &
799 : unit_str='fs^-1', &
800 30706 : default_r_val=0.0_dp)
801 30706 : CALL section_add_keyword(section, keyword)
802 30706 : CALL keyword_release(keyword)
803 :
804 30706 : END SUBROUTINE create_msst_section
805 :
806 : ! **************************************************************************************************
807 : !> \brief section will contain some parameters for the shells dynamics
808 : !> \param section ...
809 : ! **************************************************************************************************
810 30706 : SUBROUTINE create_shell_section(section)
811 : TYPE(section_type), POINTER :: section
812 :
813 : TYPE(keyword_type), POINTER :: keyword
814 : TYPE(section_type), POINTER :: thermo_section
815 :
816 30706 : CPASSERT(.NOT. ASSOCIATED(section))
817 :
818 : CALL section_create(section, __LOCATION__, name="shell", &
819 : description="Parameters of shell model in adiabatic dynamics.", &
820 30706 : n_keywords=4, n_subsections=1, repeats=.FALSE.)
821 :
822 30706 : NULLIFY (keyword, thermo_section)
823 :
824 : CALL keyword_create(keyword, __LOCATION__, name="temperature", &
825 : description="Temperature in K used to control "// &
826 : "the internal velocities of the core-shell motion ", &
827 : usage="temperature 5.0", &
828 : default_r_val=cp_unit_to_cp2k(value=0.0_dp, unit_str="K"), &
829 30706 : unit_str="K")
830 30706 : CALL section_add_keyword(section, keyword)
831 30706 : CALL keyword_release(keyword)
832 :
833 : CALL keyword_create(keyword, __LOCATION__, name="temp_tol", &
834 : description="Maximum accepted temperature deviation"// &
835 : " from the expected value, for the internal core-shell motion."// &
836 : " If 0, no rescaling is performed", &
837 30706 : usage="temp_tol 0.0", default_r_val=0.0_dp, unit_str='K')
838 30706 : CALL section_add_keyword(section, keyword)
839 30706 : CALL keyword_release(keyword)
840 :
841 : CALL keyword_create(keyword, __LOCATION__, name="nose_particle", &
842 : description="If nvt or npt, the core and shell velocities are controlled "// &
843 : "by the same thermostat used for the particle. This might favour heat exchange "// &
844 : "and additional rescaling of the internal core-shell velocity is needed (TEMP_TOL)", &
845 30706 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
846 30706 : CALL section_add_keyword(section, keyword)
847 30706 : CALL keyword_release(keyword)
848 :
849 : CALL keyword_create(keyword, __LOCATION__, name="DISPLACEMENT_SHELL_TOL", &
850 : description="This keyword sets a maximum variation of the shell"// &
851 : " core distance in each Cartesian direction."// &
852 : " The maximum internal core-shell velocity is evaluated and"// &
853 : " if it is too large to remain"// &
854 : " within the assigned limit, the time step is rescaled accordingly,"// &
855 : " and the first half step of the velocity verlet is repeated.", &
856 : usage="DISPLACEMENT_SHELL_TOL <REAL>", default_r_val=100.0_dp, &
857 30706 : unit_str='angstrom')
858 30706 : CALL section_add_keyword(section, keyword)
859 30706 : CALL keyword_release(keyword)
860 :
861 30706 : CALL create_thermostat_section(thermo_section)
862 30706 : CALL section_add_subsection(section, thermo_section)
863 30706 : CALL section_release(thermo_section)
864 :
865 30706 : END SUBROUTINE create_shell_section
866 :
867 : ! **************************************************************************************************
868 : !> \brief section will contain some parameters for the adiabatic dynamics
869 : !> \param section ...
870 : ! **************************************************************************************************
871 30706 : SUBROUTINE create_adiabatic_section(section)
872 : TYPE(section_type), POINTER :: section
873 :
874 : TYPE(keyword_type), POINTER :: keyword
875 : TYPE(section_type), POINTER :: thermo_fast_section, thermo_slow_section
876 :
877 30706 : CPASSERT(.NOT. ASSOCIATED(section))
878 :
879 : CALL section_create(section, __LOCATION__, name="ADIABATIC_DYNAMICS", &
880 : description="Parameters used in canonical adiabatic free energy sampling (CAFES).", &
881 : n_keywords=5, n_subsections=2, repeats=.FALSE., &
882 61412 : citations=[VandeVondele2002])
883 :
884 30706 : NULLIFY (keyword, thermo_fast_section, thermo_slow_section)
885 :
886 : CALL keyword_create(keyword, __LOCATION__, name="temp_fast", &
887 : description="Temperature in K used to control "// &
888 : "the fast degrees of freedom ", &
889 : usage="temp_fast 5.0", &
890 : default_r_val=cp_unit_to_cp2k(value=0.0_dp, unit_str="K"), &
891 30706 : unit_str="K")
892 30706 : CALL section_add_keyword(section, keyword)
893 30706 : CALL keyword_release(keyword)
894 :
895 : CALL keyword_create(keyword, __LOCATION__, name="temp_slow", &
896 : description="Temperature in K used to control "// &
897 : "the slow degrees of freedom ", &
898 : usage="temp_slow 5.0", &
899 : default_r_val=cp_unit_to_cp2k(value=0.0_dp, unit_str="K"), &
900 30706 : unit_str="K")
901 30706 : CALL section_add_keyword(section, keyword)
902 30706 : CALL keyword_release(keyword)
903 :
904 : CALL keyword_create(keyword, __LOCATION__, name="temp_tol_fast", &
905 : description="Maximum accepted temperature deviation"// &
906 : " from the expected value, for the fast motion."// &
907 : " If 0, no rescaling is performed", &
908 30706 : usage="temp_tol_fast 0.0", default_r_val=0.0_dp, unit_str='K')
909 30706 : CALL section_add_keyword(section, keyword)
910 30706 : CALL keyword_release(keyword)
911 :
912 : CALL keyword_create(keyword, __LOCATION__, name="temp_tol_slow", &
913 : description="Maximum accepted temperature deviation"// &
914 : " from the expected value, for the slow motion."// &
915 : " If 0, no rescaling is performed", &
916 30706 : usage="temp_tol_slow 0.0", default_r_val=0.0_dp, unit_str='K')
917 30706 : CALL section_add_keyword(section, keyword)
918 30706 : CALL keyword_release(keyword)
919 :
920 : CALL keyword_create(keyword, __LOCATION__, name="n_resp_fast", &
921 : description="number of respa steps for fast degrees of freedom", &
922 30706 : repeats=.FALSE., default_i_val=1)
923 30706 : CALL section_add_keyword(section, keyword)
924 30706 : CALL keyword_release(keyword)
925 :
926 30706 : CALL create_thermo_fast_section(thermo_fast_section)
927 30706 : CALL section_add_subsection(section, thermo_fast_section)
928 30706 : CALL section_release(thermo_fast_section)
929 :
930 30706 : CALL create_thermo_slow_section(thermo_slow_section)
931 30706 : CALL section_add_subsection(section, thermo_slow_section)
932 30706 : CALL section_release(thermo_slow_section)
933 :
934 30706 : END SUBROUTINE create_adiabatic_section
935 :
936 : ! **************************************************************************************************
937 : !> \brief section will contain parameters for the velocity softening
938 : !> \param section ...
939 : !> \author Ole Schuett
940 : ! **************************************************************************************************
941 30706 : SUBROUTINE create_softening_section(section)
942 : TYPE(section_type), POINTER :: section
943 :
944 : TYPE(keyword_type), POINTER :: keyword
945 :
946 : CALL section_create(section, __LOCATION__, name="VELOCITY_SOFTENING", &
947 : description="A method to initialize the velocities along low-curvature " &
948 : //"directions in order to favors MD trajectories to cross rapidly over " &
949 : //"small energy barriers into neighboring basins. " &
950 : //"In each iteration the forces are calculated at a point y, which " &
951 : //"is slightly displaced from the current positions x in the direction " &
952 : //"of the original velocities v. The velocities are then updated with " &
953 : //"the force component F_t, which is perpendicular to N. " &
954 : //"N = v / |v|; y = x + delta * N; F_t = F(y) - ⟨ F(y) | N ⟩ * N; " &
955 30706 : //"v' = v + alpha * F_t")
956 :
957 30706 : NULLIFY (keyword)
958 : CALL keyword_create(keyword, __LOCATION__, name="STEPS", &
959 : description="Number of softening iterations performed. " &
960 : //"Typical values are around 40 steps.", &
961 30706 : default_i_val=0)
962 30706 : CALL section_add_keyword(section, keyword)
963 30706 : CALL keyword_release(keyword)
964 :
965 : CALL keyword_create(keyword, __LOCATION__, name="DELTA", &
966 : description="Displacement used to obtain y.", &
967 30706 : default_r_val=0.1_dp)
968 30706 : CALL section_add_keyword(section, keyword)
969 30706 : CALL keyword_release(keyword)
970 :
971 : CALL keyword_create(keyword, __LOCATION__, name="ALPHA", &
972 : description="Mixing factor used for updating velocities.", &
973 30706 : default_r_val=0.15_dp)
974 30706 : CALL section_add_keyword(section, keyword)
975 30706 : CALL keyword_release(keyword)
976 :
977 30706 : END SUBROUTINE create_softening_section
978 :
979 : ! **************************************************************************************************
980 : !> \brief input section used to define regions with different temperature
981 : !> initialization and control
982 : !> \param section ...
983 : !> \par History
984 : !> - Added input for langevin regions in thermal regions section
985 : !> (2014/02/04, LT)
986 : ! **************************************************************************************************
987 30706 : SUBROUTINE create_thermal_region_section(section)
988 : TYPE(section_type), POINTER :: section
989 :
990 : TYPE(keyword_type), POINTER :: keyword
991 : TYPE(section_type), POINTER :: print_key, region_section, subsection, &
992 : tfunc_section
993 :
994 30706 : CPASSERT(.NOT. ASSOCIATED(section))
995 :
996 : CALL section_create(section, __LOCATION__, name="THERMAL_REGION", &
997 : description="Define regions where different initialization and control "// &
998 : "of the temperature is used. When MOTION%MD%ENSEMBLE is set to LANGEVIN, "// &
999 : "this section controls if the atoms defined inside and outside the "// &
1000 : "thermal regions should undergo Langevin MD or NVE Born-Oppenheimer MD. "// &
1001 : "The theory behind Langevin MD using different regions can be found in "// &
1002 : "articles by Kantorovitch et al. listed below.", &
1003 : citations=[Kantorovich2008, Kantorovich2008a], &
1004 92118 : n_keywords=0, n_subsections=1, repeats=.FALSE.)
1005 :
1006 30706 : NULLIFY (region_section)
1007 30706 : NULLIFY (keyword, subsection, tfunc_section)
1008 :
1009 : CALL keyword_create(keyword, __LOCATION__, name="FORCE_RESCALING", &
1010 : description="Control the rescaling ot the velocities in all the regions, "// &
1011 : "according to the temperature assigned to each reagion, when "// &
1012 : "RESTART_VELOCITY in EXT_RESTART is active.", &
1013 30706 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
1014 30706 : CALL section_add_keyword(section, keyword)
1015 30706 : CALL keyword_release(keyword)
1016 :
1017 : CALL keyword_create(keyword, __LOCATION__, name="DO_LANGEVIN_DEFAULT", &
1018 : description="If ENSEMBLE is set to LANGEVIN, controls whether the "// &
1019 : "atoms NOT defined in the thermal regions to undergo langevin MD "// &
1020 : "or not. If not, then the atoms will undergo NVE Born-Oppenheimer MD.", &
1021 : usage="DO_LANGEVIN_DEFAULT .FALSE.", &
1022 30706 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
1023 30706 : CALL section_add_keyword(section, keyword)
1024 30706 : CALL keyword_release(keyword)
1025 :
1026 : CALL section_create(region_section, __LOCATION__, name="DEFINE_REGION", &
1027 : description="Define arbitrary thermal region with distinct "// &
1028 : "temperature controls. For thermostat regions, see section "// &
1029 : "MOTION%MD%THERMOSTAT%DEFINE_REGION; when the keyword "// &
1030 : "MOTION%MD%THERMOSTAT%REGION is set to THERMAL, the "// &
1031 : "definition of thermostat regions will be the same as "// &
1032 : "that of thermal regions.", &
1033 30706 : n_keywords=3, n_subsections=1, repeats=.TRUE.)
1034 :
1035 30706 : NULLIFY (keyword)
1036 : CALL keyword_create(keyword, __LOCATION__, name="LIST", &
1037 : description="Specifies a list of atoms belonging to the region.", &
1038 : usage="LIST {integer} {integer} .. {integer}", &
1039 30706 : repeats=.TRUE., n_var=-1, type_of_var=integer_t)
1040 30706 : CALL section_add_keyword(region_section, keyword)
1041 30706 : CALL keyword_release(keyword)
1042 :
1043 : CALL keyword_create(keyword, __LOCATION__, name="MOLNAME", &
1044 : variants=["SEGNAME"], &
1045 : description="Specifies the name of the molecules belonging to the region.", &
1046 : usage="MOLNAME WAT MEOH", repeats=.TRUE., &
1047 61412 : n_var=-1, type_of_var=char_t)
1048 30706 : CALL section_add_keyword(region_section, keyword)
1049 30706 : CALL keyword_release(keyword)
1050 :
1051 : CALL keyword_create(keyword, __LOCATION__, name="MM_SUBSYS", &
1052 : variants=["PROTEIN"], &
1053 : description="Not yet implemented: In a QM/MM run all "// &
1054 : "MM atoms are specified as a whole region", &
1055 : usage="MM_SUBSYS (NONE|ATOMIC|MOLECULAR)", &
1056 : enum_c_vals=s2a("NONE", "ATOMIC", "MOLECULAR"), &
1057 : enum_i_vals=[do_constr_none, do_constr_atomic, do_constr_molec], &
1058 : enum_desc=s2a("Nothing in the region", &
1059 : "Only the MM atoms itself", &
1060 : "The full molecule/residue that contains a MM atom"), &
1061 61412 : default_i_val=do_constr_none, repeats=.FALSE.)
1062 30706 : CALL section_add_keyword(region_section, keyword)
1063 30706 : CALL keyword_release(keyword)
1064 :
1065 : CALL keyword_create(keyword, __LOCATION__, name="QM_SUBSYS", &
1066 : description="Not yet implemented: In a QM/MM run all "// &
1067 : "QM atoms are specified as a whole region", &
1068 : usage="QM_SUBSYS (NONE|ATOMIC|MOLECULAR)", &
1069 : enum_c_vals=s2a("NONE", "ATOMIC", "MOLECULAR"), &
1070 : enum_desc=s2a("Nothing in the region", &
1071 : "Only the QM atoms itself", &
1072 : "The full molecule/residue that contains a QM atom"), &
1073 : enum_i_vals=[do_constr_none, do_constr_atomic, do_constr_molec], &
1074 30706 : default_i_val=do_constr_none, repeats=.FALSE.)
1075 30706 : CALL section_add_keyword(region_section, keyword)
1076 30706 : CALL keyword_release(keyword)
1077 :
1078 : CALL keyword_create(keyword, __LOCATION__, name="TEMPERATURE", &
1079 : description="The temperature in K used to initialize the velocities "// &
1080 : "of the atoms in this region. It overrides the value evaluated by the "// &
1081 : "function defined in TFUNC section.", &
1082 : usage="TEMPERATURE 5.0", &
1083 : default_r_val=cp_unit_to_cp2k(value=0.0_dp, unit_str="K"), &
1084 30706 : unit_str="K")
1085 30706 : CALL section_add_keyword(region_section, keyword)
1086 30706 : CALL keyword_release(keyword)
1087 :
1088 : CALL keyword_create(keyword, __LOCATION__, name="TEMP_TOL", &
1089 : description="Maximum accepted temperature deviation from the target "// &
1090 : "value for this region, which is defined by TEMPERATURE or evaluated "// &
1091 : "with the function defined in TFUNC section. Default value is 0 that "// &
1092 : "turns off rescaling.", &
1093 : usage="TEMP_TOL 0.0", &
1094 30706 : default_r_val=0.0_dp, unit_str='K')
1095 30706 : CALL section_add_keyword(region_section, keyword)
1096 30706 : CALL keyword_release(keyword)
1097 :
1098 : CALL keyword_create(keyword, __LOCATION__, name="DO_LANGEVIN", &
1099 : description="When ENSEMBLE is set to LANGEVIN, Controls whether "// &
1100 : "the atoms in the thermal region should undergo Langevin MD. If "// &
1101 : "not, then they will undergo NVE Born-Oppenheimer MD.", &
1102 : usage="DO_LANGEVIN .TRUE.", &
1103 30706 : default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
1104 30706 : CALL section_add_keyword(region_section, keyword)
1105 30706 : CALL keyword_release(keyword)
1106 :
1107 : CALL keyword_create(keyword, __LOCATION__, name="NOISY_GAMMA_REGION", &
1108 : description="Special imaginary Langevin Friction term"// &
1109 : " for Langevin Dynamics with noisy forces for the atoms in this region."// &
1110 : " When set, overrides the general value set by NOISY_GAMMA in the MOTION%MD%LANGEVIN section."// &
1111 : " When unset for a defined region, the general NOISY_GAMMA value applies.", &
1112 : citations=[Kuhne2007], usage="NOISY_GAMMA_REGION 4.0E-5", &
1113 : type_of_var=real_t, &
1114 61412 : unit_str="fs^-1")
1115 30706 : CALL section_add_keyword(region_section, keyword)
1116 30706 : CALL keyword_release(keyword)
1117 :
1118 : ! Define temperature function start
1119 : CALL section_create(tfunc_section, __LOCATION__, name="TFUNC", &
1120 : description="This section specifies the target temperature by using "// &
1121 : "the time step and the temperature of the last step, allowing for "// &
1122 : "simple region-wise simulated annealing (heating/cooling) controls. "// &
1123 : "When the absolute difference between target and actual temperature "// &
1124 : "is larger than TEMP_TOL value, the atomic velocities in this region "// &
1125 : "are rescaled to match the target temperature. However, note that "// &
1126 : "the actual temperature is subject to thermostat coupling as well "// &
1127 : "and a small restrictive TEMP_TOL together with a rapidly varying "// &
1128 : "target temperature function leaves little time for the system to "// &
1129 : "adjust itself, possibly showing unphysical relaxation behaviors. "// &
1130 : newline//newline//"Further notes about temperature. "//docf(), &
1131 30706 : n_keywords=4, n_subsections=0, repeats=.FALSE.)
1132 :
1133 30706 : NULLIFY (keyword)
1134 : CALL keyword_create(keyword, __LOCATION__, name="FUNCTION", &
1135 : description="Specifies the functional form of the temperature "// &
1136 : "in Kelvin in mathematical notation. Two variables are available "// &
1137 : "with one denoted S for the integer time step and another denoted "// &
1138 : "T for the temperature of the last step in Kelvin respectively. When "// &
1139 : "DEFINE_REGION%TEMPERATURE is not explicitly set, the function "// &
1140 : "will be evaluated at S set in MD%STEP_START_VAL and T = 0.0 "// &
1141 : "to initialize the velocities of atoms in the region.", &
1142 : usage="FUNCTION A*T+(1-A)*B*(2/(1+EXP(-0.001*S))-1)", &
1143 30706 : type_of_var=lchar_t, n_var=1)
1144 30706 : CALL section_add_keyword(tfunc_section, keyword)
1145 30706 : CALL keyword_release(keyword)
1146 :
1147 : CALL keyword_create(keyword, __LOCATION__, name="PARAMETERS", &
1148 : description="Defines the parameters of the functional form", &
1149 : usage="PARAMETERS A B", type_of_var=char_t, &
1150 30706 : n_var=-1, repeats=.TRUE.)
1151 30706 : CALL section_add_keyword(tfunc_section, keyword)
1152 30706 : CALL keyword_release(keyword)
1153 :
1154 : CALL keyword_create(keyword, __LOCATION__, name="UNITS", &
1155 : description="Optionally, allows to define valid CP2K unit strings for each parameter value. "// &
1156 : "It is assumed that the corresponding parameter value is specified in this unit.", &
1157 : usage="UNITS ", type_of_var=char_t, &
1158 30706 : n_var=-1, repeats=.TRUE.)
1159 30706 : CALL section_add_keyword(tfunc_section, keyword)
1160 30706 : CALL keyword_release(keyword)
1161 :
1162 : CALL keyword_create(keyword, __LOCATION__, name="VALUES", &
1163 : description="Defines the values of the parameter of the functional form", &
1164 : usage="VALUES 0.75 3.00E+2", type_of_var=real_t, &
1165 30706 : n_var=-1, repeats=.TRUE., unit_str="internal_cp2k")
1166 30706 : CALL section_add_keyword(tfunc_section, keyword)
1167 30706 : CALL keyword_release(keyword)
1168 :
1169 30706 : CALL section_add_subsection(region_section, tfunc_section)
1170 30706 : CALL section_release(tfunc_section)
1171 : ! Define temperature function end
1172 :
1173 30706 : CALL section_add_subsection(section, region_section)
1174 30706 : CALL section_release(region_section)
1175 :
1176 30706 : NULLIFY (print_key)
1177 : CALL section_create(subsection, __LOCATION__, name="PRINT", &
1178 : description="Collects all print_keys for thermal_regions", &
1179 30706 : n_keywords=1, n_subsections=0, repeats=.FALSE.)
1180 :
1181 : CALL cp_print_key_section_create(print_key, __LOCATION__, "TEMPERATURE", &
1182 : description="Controls the output of the temperature per "// &
1183 : "region. The first three columns are: step number, time "// &
1184 : "(in fs), and the temperature of atoms not in any temperature "// &
1185 : "region (or zero if all atoms are in some temperature region). "// &
1186 : "Subsequent columns are, in pairs, the target value "// &
1187 : "(calculated by TFUNC or specified by TEMPERATURE) "// &
1188 : "and the actual value of the temperature for each region.", &
1189 : print_level=high_print_level, common_iter_levels=1, &
1190 30706 : filename="")
1191 30706 : CALL section_add_subsection(subsection, print_key)
1192 30706 : CALL section_release(print_key)
1193 :
1194 : CALL cp_print_key_section_create(print_key, __LOCATION__, "LANGEVIN_REGIONS", &
1195 : description="Controls output of information on which atoms "// &
1196 : "underwent Langevin MD and which atoms did not.", &
1197 : print_level=high_print_level, &
1198 30706 : filename="")
1199 30706 : CALL section_add_subsection(subsection, print_key)
1200 30706 : CALL section_release(print_key)
1201 :
1202 30706 : CALL section_add_subsection(section, subsection)
1203 30706 : CALL section_release(subsection)
1204 :
1205 30706 : END SUBROUTINE create_thermal_region_section
1206 :
1207 : ! **************************************************************************************************
1208 : !> \brief Defines the parameters for the setup of a cascade simulation
1209 : !> \param section ...
1210 : !> \date 03.02.2012
1211 : !> \author Matthias Krack (MK)
1212 : !> \version 1.0
1213 : ! **************************************************************************************************
1214 30706 : SUBROUTINE create_cascade_section(section)
1215 :
1216 : TYPE(section_type), POINTER :: section
1217 :
1218 : TYPE(keyword_type), POINTER :: keyword
1219 : TYPE(section_type), POINTER :: subsection
1220 :
1221 30706 : NULLIFY (keyword)
1222 30706 : NULLIFY (subsection)
1223 30706 : CPASSERT(.NOT. ASSOCIATED(section))
1224 :
1225 : CALL section_create(section, __LOCATION__, name="CASCADE", &
1226 : description="Defines the parameters for the setup of a cascade simulation.", &
1227 : n_keywords=1, &
1228 : n_subsections=1, &
1229 30706 : repeats=.FALSE.)
1230 :
1231 : CALL keyword_create(keyword, __LOCATION__, &
1232 : name="_SECTION_PARAMETERS_", &
1233 : description="Controls the activation of the CASCADE section.", &
1234 : usage="&CASCADE on", &
1235 : default_l_val=.FALSE., &
1236 30706 : lone_keyword_l_val=.TRUE.)
1237 30706 : CALL section_add_keyword(section, keyword)
1238 30706 : CALL keyword_release(keyword)
1239 :
1240 : CALL keyword_create(keyword, __LOCATION__, name="ENERGY", &
1241 : description="Total energy transferred to the system during the cascade event.", &
1242 : usage="ENERGY 20.0", &
1243 : default_r_val=0.0_dp, &
1244 30706 : unit_str="keV")
1245 30706 : CALL section_add_keyword(section, keyword)
1246 30706 : CALL keyword_release(keyword)
1247 :
1248 : CALL section_create(subsection, __LOCATION__, name="ATOM_LIST", &
1249 : description="Defines a list of atoms for which the initial velocities are modified", &
1250 : n_keywords=1, &
1251 : n_subsections=0, &
1252 30706 : repeats=.FALSE.)
1253 :
1254 : CALL keyword_create(keyword, __LOCATION__, name="_DEFAULT_KEYWORD_", &
1255 : description="Defines the list of atoms for which the velocities are modified. "// &
1256 : "Each record consists of the atomic index, the velocity vector, and "// &
1257 : "a weight to define which fraction of the total energy is assigned "// &
1258 : "to the current atom: `Atomic_index v_x v_y v_z Weight`", &
1259 : usage="{{Integer} {Real} {Real} {Real} {Real}}", &
1260 : repeats=.TRUE., &
1261 30706 : type_of_var=lchar_t)
1262 30706 : CALL section_add_keyword(subsection, keyword)
1263 30706 : CALL keyword_release(keyword)
1264 :
1265 30706 : CALL section_add_subsection(section, subsection)
1266 30706 : CALL section_release(subsection)
1267 :
1268 30706 : END SUBROUTINE create_cascade_section
1269 :
1270 : ! **************************************************************************************************
1271 : !> \brief Defines AVERAGES section
1272 : !> \param section ...
1273 : !> \author teo
1274 : ! **************************************************************************************************
1275 30706 : SUBROUTINE create_avgs_section(section)
1276 : TYPE(section_type), POINTER :: section
1277 :
1278 : TYPE(keyword_type), POINTER :: keyword
1279 : TYPE(section_type), POINTER :: print_key, subsection
1280 :
1281 30706 : CPASSERT(.NOT. ASSOCIATED(section))
1282 : CALL section_create(section, __LOCATION__, name="Averages", &
1283 : description="Controls the calculation of the averages during an MD run.", &
1284 30706 : n_keywords=1, n_subsections=1, repeats=.FALSE.)
1285 30706 : NULLIFY (keyword, print_key, subsection)
1286 :
1287 : CALL keyword_create(keyword, __LOCATION__, name="_SECTION_PARAMETERS_", &
1288 : description="Controls the calculations of the averages.", &
1289 30706 : usage="&AVERAGES T", default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
1290 30706 : CALL section_add_keyword(section, keyword)
1291 30706 : CALL keyword_release(keyword)
1292 :
1293 : CALL keyword_create(keyword, __LOCATION__, name="ACQUISITION_START_TIME", &
1294 : description="Setup up the simulation time when the acquisition process to compute"// &
1295 : " averages is started.", &
1296 : usage="ACQUISITION_START_TIME <REAL>", &
1297 30706 : default_r_val=0.0_dp, unit_str='fs')
1298 30706 : CALL section_add_keyword(section, keyword)
1299 30706 : CALL keyword_release(keyword)
1300 :
1301 : CALL keyword_create(keyword, __LOCATION__, name="AVERAGE_COLVAR", &
1302 : description="Switch for computing the averages of COLVARs.", &
1303 : usage="AVERAGE_COLVAR <LOGICAL>", default_l_val=.FALSE., &
1304 30706 : lone_keyword_l_val=.TRUE.)
1305 30706 : CALL section_add_keyword(section, keyword)
1306 30706 : CALL keyword_release(keyword)
1307 :
1308 : CALL cp_print_key_section_create(print_key, __LOCATION__, "PRINT_AVERAGES", &
1309 : description="Controls the output the averaged quantities", &
1310 : print_level=debug_print_level + 1, common_iter_levels=1, &
1311 30706 : filename="")
1312 30706 : CALL section_add_subsection(section, print_key)
1313 30706 : CALL section_release(print_key)
1314 :
1315 30706 : CALL create_avgs_restart_section(subsection)
1316 30706 : CALL section_add_subsection(section, subsection)
1317 30706 : CALL section_release(subsection)
1318 30706 : END SUBROUTINE create_avgs_section
1319 :
1320 : ! **************************************************************************************************
1321 : !> \brief Defines the AVERAGES RESTART section
1322 : !> \param section ...
1323 : !> \author teo
1324 : ! **************************************************************************************************
1325 30706 : SUBROUTINE create_avgs_restart_section(section)
1326 : TYPE(section_type), POINTER :: section
1327 :
1328 : TYPE(keyword_type), POINTER :: keyword
1329 :
1330 30706 : CPASSERT(.NOT. ASSOCIATED(section))
1331 : CALL section_create(section, __LOCATION__, name="RESTART_AVERAGES", &
1332 : description="Stores information for restarting averages.", &
1333 30706 : n_keywords=1, n_subsections=1, repeats=.FALSE.)
1334 30706 : NULLIFY (keyword)
1335 :
1336 : CALL keyword_create(keyword, __LOCATION__, name="ITIMES_START", &
1337 : description="TIME STEP starting the evaluation of averages", &
1338 30706 : usage="ITIMES_START <INTEGER>", type_of_var=integer_t, n_var=1)
1339 30706 : CALL section_add_keyword(section, keyword)
1340 30706 : CALL keyword_release(keyword)
1341 :
1342 : CALL keyword_create(keyword, __LOCATION__, name="AVECPU", &
1343 : description="CPU average", usage="AVECPU <REAL>", &
1344 30706 : type_of_var=real_t, n_var=1)
1345 30706 : CALL section_add_keyword(section, keyword)
1346 30706 : CALL keyword_release(keyword)
1347 :
1348 : CALL keyword_create(keyword, __LOCATION__, name="AVEHUGONIOT", &
1349 : description="HUGONIOT average", usage="AVEHUGONIOT <REAL>", &
1350 30706 : type_of_var=real_t, n_var=1)
1351 30706 : CALL section_add_keyword(section, keyword)
1352 30706 : CALL keyword_release(keyword)
1353 :
1354 : CALL keyword_create(keyword, __LOCATION__, name="AVETEMP_BARO", &
1355 : description="BAROSTAT TEMPERATURE average", usage="AVETEMP_BARO <REAL>", &
1356 30706 : type_of_var=real_t, n_var=1)
1357 30706 : CALL section_add_keyword(section, keyword)
1358 30706 : CALL keyword_release(keyword)
1359 :
1360 : CALL keyword_create(keyword, __LOCATION__, name="AVEPOT", &
1361 : description="POTENTIAL ENERGY average", usage="AVEPOT <REAL>", &
1362 30706 : type_of_var=real_t, n_var=1)
1363 30706 : CALL section_add_keyword(section, keyword)
1364 30706 : CALL keyword_release(keyword)
1365 :
1366 : CALL keyword_create(keyword, __LOCATION__, name="AVEKIN", &
1367 : description="KINETIC ENERGY average", usage="AVEKIN <REAL>", &
1368 30706 : type_of_var=real_t, n_var=1)
1369 30706 : CALL section_add_keyword(section, keyword)
1370 30706 : CALL keyword_release(keyword)
1371 :
1372 : CALL keyword_create(keyword, __LOCATION__, name="AVETEMP", &
1373 : description="TEMPERATURE average", usage="AVETEMP <REAL>", &
1374 30706 : type_of_var=real_t, n_var=1)
1375 30706 : CALL section_add_keyword(section, keyword)
1376 30706 : CALL keyword_release(keyword)
1377 :
1378 : CALL keyword_create(keyword, __LOCATION__, name="AVEKIN_QM", &
1379 : description="QM KINETIC ENERGY average in QMMM runs", usage="AVEKIN_QM <REAL>", &
1380 30706 : type_of_var=real_t, n_var=1)
1381 30706 : CALL section_add_keyword(section, keyword)
1382 30706 : CALL keyword_release(keyword)
1383 :
1384 : CALL keyword_create(keyword, __LOCATION__, name="AVETEMP_QM", &
1385 : description="QM TEMPERATURE average in QMMM runs", usage="AVETEMP_QM <REAL>", &
1386 30706 : type_of_var=real_t, n_var=1)
1387 30706 : CALL section_add_keyword(section, keyword)
1388 30706 : CALL keyword_release(keyword)
1389 :
1390 : CALL keyword_create(keyword, __LOCATION__, name="AVEVOL", &
1391 : description="VOLUME average", usage="AVEVOL <REAL>", &
1392 30706 : type_of_var=real_t, n_var=1)
1393 30706 : CALL section_add_keyword(section, keyword)
1394 30706 : CALL keyword_release(keyword)
1395 :
1396 : CALL keyword_create(keyword, __LOCATION__, name="AVECELL_A", &
1397 : description="CELL VECTOR A average", usage="AVECELL_A <REAL>", &
1398 30706 : type_of_var=real_t, n_var=1)
1399 30706 : CALL section_add_keyword(section, keyword)
1400 30706 : CALL keyword_release(keyword)
1401 :
1402 : CALL keyword_create(keyword, __LOCATION__, name="AVECELL_B", &
1403 : description="CELL VECTOR B average", usage="AVECELL_B <REAL>", &
1404 30706 : type_of_var=real_t, n_var=1)
1405 30706 : CALL section_add_keyword(section, keyword)
1406 30706 : CALL keyword_release(keyword)
1407 :
1408 : CALL keyword_create(keyword, __LOCATION__, name="AVECELL_C", &
1409 : description="CELL VECTOR C average", usage="AVECELL_C <REAL>", &
1410 30706 : type_of_var=real_t, n_var=1)
1411 30706 : CALL section_add_keyword(section, keyword)
1412 30706 : CALL keyword_release(keyword)
1413 :
1414 : CALL keyword_create(keyword, __LOCATION__, name="AVEALPHA", &
1415 : description="ALPHA cell angle average", usage="AVEALPHA <REAL>", &
1416 30706 : type_of_var=real_t, n_var=1)
1417 30706 : CALL section_add_keyword(section, keyword)
1418 30706 : CALL keyword_release(keyword)
1419 :
1420 : CALL keyword_create(keyword, __LOCATION__, name="AVEBETA", &
1421 : description="BETA cell angle average", usage="AVEBETA <REAL>", &
1422 30706 : type_of_var=real_t, n_var=1)
1423 30706 : CALL section_add_keyword(section, keyword)
1424 30706 : CALL keyword_release(keyword)
1425 :
1426 : CALL keyword_create(keyword, __LOCATION__, name="AVEGAMMA", &
1427 : description="GAMMA cell angle average", usage="AVEGAMMA <REAL>", &
1428 30706 : type_of_var=real_t, n_var=1)
1429 30706 : CALL section_add_keyword(section, keyword)
1430 30706 : CALL keyword_release(keyword)
1431 :
1432 : CALL keyword_create(keyword, __LOCATION__, name="AVE_ECONS", &
1433 : description="CONSTANT ENERGY average", usage="AVE_ECONS <REAL>", &
1434 30706 : type_of_var=real_t, n_var=1)
1435 30706 : CALL section_add_keyword(section, keyword)
1436 30706 : CALL keyword_release(keyword)
1437 :
1438 : CALL keyword_create(keyword, __LOCATION__, name="AVE_PRESS", &
1439 : description="PRESSURE average", usage="AVE_PRESS <REAL>", &
1440 30706 : type_of_var=real_t, n_var=1)
1441 30706 : CALL section_add_keyword(section, keyword)
1442 30706 : CALL keyword_release(keyword)
1443 :
1444 : CALL keyword_create(keyword, __LOCATION__, name="AVE_PXX", &
1445 : description="P_{XX} average", usage="AVE_PXX <REAL>", &
1446 30706 : type_of_var=real_t, n_var=1)
1447 30706 : CALL section_add_keyword(section, keyword)
1448 30706 : CALL keyword_release(keyword)
1449 :
1450 : CALL keyword_create(keyword, __LOCATION__, name="AVE_PV_VIR", &
1451 : description="PV VIRIAL average", usage="AVE_PV_VIR <REAL> .. <REAL>", &
1452 30706 : type_of_var=real_t, n_var=9)
1453 30706 : CALL section_add_keyword(section, keyword)
1454 30706 : CALL keyword_release(keyword)
1455 :
1456 : CALL keyword_create(keyword, __LOCATION__, name="AVE_PV_TOT", &
1457 : description="PV TOTAL average", usage="AVE_PV_TOT <REAL> .. <REAL>", &
1458 30706 : type_of_var=real_t, n_var=9)
1459 30706 : CALL section_add_keyword(section, keyword)
1460 30706 : CALL keyword_release(keyword)
1461 :
1462 : CALL keyword_create(keyword, __LOCATION__, name="AVE_PV_KIN", &
1463 : description="PV KINETIC average", usage="AVE_PV_KIN <REAL> .. <REAL>", &
1464 30706 : type_of_var=real_t, n_var=9)
1465 30706 : CALL section_add_keyword(section, keyword)
1466 30706 : CALL keyword_release(keyword)
1467 :
1468 : CALL keyword_create(keyword, __LOCATION__, name="AVE_PV_CNSTR", &
1469 : description="PV CONSTRAINTS average", usage="AVE_PV_CNSTR <REAL> .. <REAL>", &
1470 30706 : type_of_var=real_t, n_var=9)
1471 30706 : CALL section_add_keyword(section, keyword)
1472 30706 : CALL keyword_release(keyword)
1473 :
1474 : CALL keyword_create(keyword, __LOCATION__, name="AVE_PV_XC", &
1475 : description="PV XC average", usage="AVE_PV_XC <REAL> .. <REAL>", &
1476 30706 : type_of_var=real_t, n_var=9)
1477 30706 : CALL section_add_keyword(section, keyword)
1478 30706 : CALL keyword_release(keyword)
1479 :
1480 : CALL keyword_create(keyword, __LOCATION__, name="AVE_PV_FOCK_4C", &
1481 : description="PV XC average", usage="AVE_PV_FOCK_4C <REAL> .. <REAL>", &
1482 30706 : type_of_var=real_t, n_var=9)
1483 30706 : CALL section_add_keyword(section, keyword)
1484 30706 : CALL keyword_release(keyword)
1485 :
1486 : CALL keyword_create(keyword, __LOCATION__, name="AVE_COLVARS", &
1487 : description="COLVARS averages", usage="AVE_COLVARS <REAL> .. <REAL>", &
1488 30706 : type_of_var=real_t, n_var=-1)
1489 30706 : CALL section_add_keyword(section, keyword)
1490 30706 : CALL keyword_release(keyword)
1491 :
1492 : CALL keyword_create(keyword, __LOCATION__, name="AVE_MMATRIX", &
1493 : description="METRIC TENSOR averages", usage="AVE_MMATRIX <REAL> .. <REAL>", &
1494 30706 : type_of_var=real_t, n_var=-1)
1495 30706 : CALL section_add_keyword(section, keyword)
1496 30706 : CALL keyword_release(keyword)
1497 30706 : END SUBROUTINE create_avgs_restart_section
1498 :
1499 : ! **************************************************************************************************
1500 : !> \brief Defines the INITIAL_VIBRATION section
1501 : !> \param section ...
1502 : !> \author Lianheng Tong
1503 : ! **************************************************************************************************
1504 30706 : SUBROUTINE create_vib_init_section(section)
1505 : TYPE(section_type), POINTER :: section
1506 :
1507 : TYPE(keyword_type), POINTER :: keyword
1508 :
1509 30706 : CPASSERT(.NOT. ASSOCIATED(section))
1510 : CALL section_create(section, __LOCATION__, name="INITIAL_VIBRATION", &
1511 : description="Controls the set of parameters for MD initialisation "// &
1512 : "based on vibration analysis data. The starting atomic coordinates "// &
1513 : "should be based on the relaxed positions obtained from a previous "// &
1514 : "geometry/cell optimisation calculation, and the vibrational "// &
1515 : "frequencies and displacements data should be obtained from a "// &
1516 : "vibrational analysis calculation done based on the relaxed "// &
1517 : "coordinates. The MD initialisation process expects the user has "// &
1518 : "performed both geometry optimisation and vibrational analysis "// &
1519 : "before hand, and won't perform those calculations automatically ", &
1520 : citations=[West2006], &
1521 61412 : n_keywords=0, n_subsections=1, repeats=.FALSE.)
1522 30706 : NULLIFY (keyword)
1523 : CALL keyword_create(keyword, __LOCATION__, name="VIB_EIGS_FILE_NAME", &
1524 : description="The file name of vibrational frequency (eigenvalue) "// &
1525 : "and displacement (eigenvector) data calculated from the a "// &
1526 : "vibrational analysis calculation done previously. This file must "// &
1527 : "be the same unformatted binary file as referred to by "// &
1528 : "VIBRATIONAL_ANALYSIS%PRINT%CARTESIAN_EIGS keyword. If this keyword "// &
1529 : "is not explicitly defined by the user, then the default file "// &
1530 : "name of: <project_name>-<CARTESIAN_EIGS_FILENAME>.eig will be used", &
1531 : usage="VIB_EIGS_FILE_NAME <FILENAME>", &
1532 30706 : type_of_var=lchar_t)
1533 30706 : CALL section_add_keyword(section, keyword)
1534 30706 : CALL keyword_release(keyword)
1535 30706 : NULLIFY (keyword)
1536 : CALL keyword_create(keyword, __LOCATION__, name="PHASE", &
1537 : description="Controls the initial ratio of potential and kinetic "// &
1538 : "contribution to the total energy. The contribution is determined by "// &
1539 : "COS**2(2*pi*PHASE) for potential energy, and SIN**2(2*pi*PHASE) "// &
1540 : "for kinetic energy. If PHASE is negative, then for each vibration "// &
1541 : "mode the phase is determined randomly. Otherwise, PHASE must be "// &
1542 : "between 0.0 and 1.0 and will be the same for all vibration modes. "// &
1543 : "If value > 1.0 it will just be treated as 1.0. "// &
1544 : "For example, setting PHASE = 0.25 would set all modes to "// &
1545 : "begin with entirely kinetic energy --- in other words, the initial "// &
1546 : "atomic positions will remain at their optimised location", &
1547 : default_r_val=-1.0_dp, &
1548 30706 : usage="PHASE <REAL>")
1549 30706 : CALL section_add_keyword(section, keyword)
1550 30706 : CALL keyword_release(keyword)
1551 30706 : END SUBROUTINE create_vib_init_section
1552 :
1553 : END MODULE input_cp2k_md
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