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tamc_run.F
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1!--------------------------------------------------------------------------------------------------!
2! CP2K: A general program to perform molecular dynamics simulations !
3! Copyright 2000-2025 CP2K developers group <https://cp2k.org> !
4! !
5! SPDX-License-Identifier: GPL-2.0-or-later !
6!--------------------------------------------------------------------------------------------------!
7
8! **************************************************************************************************
9!> \brief Perform a temperature accelarated hybrid monte carlo (TAHMC) run using QUICKSTEP
10!> \par History
11!> none
12!> \author Alin M Elena
13! **************************************************************************************************
14MODULE tamc_run
15
16 USE atomic_kind_list_types, ONLY: atomic_kind_list_type
17 USE atomic_kind_types, ONLY: atomic_kind_type
18 USE averages_types, ONLY: average_quantities_type
19 USE barostat_types, ONLY: barostat_type,&
20 create_barostat_type
21 USE bibliography, ONLY: vandencic2006
22 USE cell_types, ONLY: cell_type
23 USE colvar_methods, ONLY: colvar_eval_glob_f
24 USE colvar_types, ONLY: hbp_colvar_id,&
25 wc_colvar_id,&
26 colvar_p_type
27 USE constraint_fxd, ONLY: fix_atom_control
28 USE cp_external_control, ONLY: external_control
29 USE cp_log_handling, ONLY: cp_get_default_logger,&
30 cp_logger_get_default_io_unit,&
31 cp_logger_type
32 USE cp_output_handling, ONLY: cp_add_iter_level,&
33 cp_iterate,&
34 cp_p_file,&
35 cp_print_key_finished_output,&
36 cp_print_key_should_output,&
37 cp_print_key_unit_nr,&
38 cp_rm_iter_level
39 USE cp_subsys_types, ONLY: cp_subsys_get,&
40 cp_subsys_type
41 USE cp_units, ONLY: cp_unit_from_cp2k
42 USE distribution_1d_types, ONLY: distribution_1d_type
43 USE force_env_methods, ONLY: force_env_calc_energy_force
44 USE force_env_types, ONLY: force_env_get,&
45 force_env_type
46 USE free_energy_types, ONLY: fe_env_create,&
47 free_energy_type
48 USE global_types, ONLY: global_environment_type
49 USE input_constants, ONLY: &
50 langevin_ensemble, npe_f_ensemble, npe_i_ensemble, nph_uniaxial_damped_ensemble, &
51 nph_uniaxial_ensemble, npt_f_ensemble, npt_i_ensemble, npt_ia_ensemble, reftraj_ensemble
52 USE input_cp2k_check, ONLY: remove_restart_info
53 USE input_cp2k_restarts, ONLY: write_restart
54 USE input_section_types, ONLY: section_vals_get,&
55 section_vals_get_subs_vals,&
56 section_vals_remove_values,&
57 section_vals_type,&
58 section_vals_val_get,&
59 section_vals_val_set
60 USE kinds, ONLY: dp
61 USE machine, ONLY: m_walltime
62 USE mc_environment_types, ONLY: get_mc_env,&
63 mc_env_create,&
64 mc_env_release,&
65 mc_environment_type,&
66 set_mc_env
67 USE mc_misc, ONLY: mc_averages_create,&
68 mc_averages_release
69 USE mc_move_control, ONLY: init_mc_moves,&
70 mc_moves_release
71 USE mc_types, ONLY: get_mc_par,&
72 mc_averages_type,&
73 mc_ekin_type,&
74 mc_moves_type,&
75 mc_simpar_type,&
76 set_mc_par
77 USE md_ener_types, ONLY: create_md_ener,&
78 md_ener_type
79 USE md_energies, ONLY: initialize_md_ener,&
80 md_energy
81 USE md_environment_types, ONLY: get_md_env,&
82 md_env_create,&
83 md_env_release,&
84 md_environment_type,&
85 set_md_env
86 USE md_run, ONLY: qs_mol_dyn
87 USE message_passing, ONLY: mp_comm_type,&
88 mp_para_env_type
89 USE metadynamics_types, ONLY: meta_env_type,&
90 metavar_type,&
91 set_meta_env
92 USE molecule_kind_list_types, ONLY: molecule_kind_list_type
93 USE molecule_kind_types, ONLY: molecule_kind_type
94 USE molecule_list_types, ONLY: molecule_list_type
95 USE molecule_types, ONLY: global_constraint_type,&
96 molecule_type
97 USE parallel_rng_types, ONLY: uniform,&
98 rng_stream_type
99 USE particle_list_types, ONLY: particle_list_type
100 USE particle_types, ONLY: particle_type
101 USE physcon, ONLY: boltzmann,&
102 femtoseconds,&
103 joule,&
104 kelvin
105 USE qmmm_util, ONLY: apply_qmmm_walls_reflective
106 USE qs_environment_types, ONLY: get_qs_env
107 USE qs_scf_post_gpw, ONLY: scf_post_calculation_gpw
108 USE reference_manager, ONLY: cite_reference
109 USE reftraj_types, ONLY: create_reftraj,&
110 reftraj_type
111 USE reftraj_util, ONLY: initialize_reftraj
112 USE simpar_methods, ONLY: read_md_section
113 USE simpar_types, ONLY: create_simpar_type,&
114 release_simpar_type,&
115 simpar_type
116 USE string_utilities, ONLY: str_comp
117 USE thermal_region_types, ONLY: thermal_regions_type
118 USE thermal_region_utils, ONLY: create_thermal_regions
119 USE thermostat_methods, ONLY: create_thermostats
120 USE thermostat_types, ONLY: thermostats_type
121 USE virial_methods, ONLY: virial_evaluate
122 USE virial_types, ONLY: virial_type
123 USE wiener_process, ONLY: create_wiener_process,&
124 create_wiener_process_cv
125!!!!! monte carlo part
126#include "../../base/base_uses.f90"
127
128 IMPLICIT NONE
129
130 PRIVATE
131
132 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'tamc_run'
133
134 PUBLIC :: qs_tamc
135
136CONTAINS
137
138! **************************************************************************************************
139!> \brief Driver routine for TAHMC
140!> \param force_env ...
141!> \param globenv ...
142!> \param averages ...
143!> \author Alin M Elena
144!> \note it computes the forces using QuickStep.
145! **************************************************************************************************
146 SUBROUTINE qs_tamc(force_env, globenv, averages)
147
148 TYPE(force_env_type), POINTER :: force_env
149 TYPE(global_environment_type), POINTER :: globenv
150 TYPE(average_quantities_type), OPTIONAL, POINTER :: averages
151
152 CHARACTER(LEN=*), PARAMETER :: routinen = 'qs_tamc'
153
154 CHARACTER(LEN=20) :: ensemble
155 INTEGER :: handle, i, initialstep, iprint, isos, &
156 istep, j, md_stride, nmccycles, &
157 output_unit, rand2skip, run_type_id
158 INTEGER, POINTER :: itimes
159 LOGICAL :: check, explicit, my_rm_restart_info, &
160 save_mem, should_stop
161 REAL(kind=dp) :: auxrandom, inittime, rval, temp, &
162 time_iter_start, time_iter_stop
163 REAL(kind=dp), ALLOCATABLE, DIMENSION(:) :: an, fz, xieta, zbuff
164 REAL(kind=dp), ALLOCATABLE, DIMENSION(:, :) :: r
165 REAL(kind=dp), POINTER :: constant, time, used_time
166 TYPE(atomic_kind_list_type), POINTER :: atomic_kinds
167 TYPE(barostat_type), POINTER :: barostat
168 TYPE(cell_type), POINTER :: cell
169 TYPE(cp_logger_type), POINTER :: logger
170 TYPE(cp_subsys_type), POINTER :: subsys, subsys_i
171 TYPE(distribution_1d_type), POINTER :: local_particles
172 TYPE(free_energy_type), POINTER :: fe_env
173 TYPE(mc_averages_type), POINTER :: mcaverages
174 TYPE(mc_environment_type), POINTER :: mc_env
175 TYPE(mc_moves_type), POINTER :: gmoves, moves
176 TYPE(mc_simpar_type), POINTER :: mc_par
177 TYPE(md_ener_type), POINTER :: md_ener
178 TYPE(md_environment_type), POINTER :: md_env
179 TYPE(meta_env_type), POINTER :: meta_env_saved
180 TYPE(mp_para_env_type), POINTER :: para_env
181 TYPE(particle_list_type), POINTER :: particles
182 TYPE(reftraj_type), POINTER :: reftraj
183 TYPE(rng_stream_type) :: rng_stream_mc
184 TYPE(section_vals_type), POINTER :: constraint_section, force_env_section, &
185 free_energy_section, fs_section, global_section, mc_section, md_section, motion_section, &
186 reftraj_section, subsys_section, work_section
187 TYPE(simpar_type), POINTER :: simpar
188 TYPE(thermal_regions_type), POINTER :: thermal_regions
189 TYPE(thermostats_type), POINTER :: thermostats
190 TYPE(virial_type), POINTER :: virial
191
192 initialstep = 0
193 inittime = 0.0_dp
194
195 CALL timeset(routinen, handle)
196 my_rm_restart_info = .true.
197 NULLIFY (para_env, fs_section, virial)
198 para_env => force_env%para_env
199 motion_section => section_vals_get_subs_vals(force_env%root_section, "MOTION")
200 md_section => section_vals_get_subs_vals(motion_section, "MD")
201
202 ! Real call to MD driver - Low Level
203 ALLOCATE (md_env)
204 CALL md_env_create(md_env, md_section, para_env, force_env=force_env)
205 IF (PRESENT(averages)) CALL set_md_env(md_env, averages=averages)
206
207 cpassert(ASSOCIATED(globenv))
208 cpassert(ASSOCIATED(force_env))
209
210 NULLIFY (particles, cell, simpar, itimes, used_time, subsys, &
211 md_ener, thermostats, barostat, reftraj, force_env_section, &
212 reftraj_section, work_section, atomic_kinds, &
213 local_particles, time, fe_env, free_energy_section, &
214 constraint_section, thermal_regions, subsys_i)
215 logger => cp_get_default_logger()
216 para_env => force_env%para_env
217
218 global_section => section_vals_get_subs_vals(force_env%root_section, "GLOBAL")
219 free_energy_section => section_vals_get_subs_vals(motion_section, "FREE_ENERGY")
220 constraint_section => section_vals_get_subs_vals(motion_section, "CONSTRAINT")
221 CALL section_vals_val_get(global_section, "SAVE_MEM", l_val=save_mem)
222
223 CALL section_vals_val_get(global_section, "RUN_TYPE", i_val=run_type_id)
224
225 CALL create_simpar_type(simpar)
226 force_env_section => force_env%force_env_section
227 subsys_section => section_vals_get_subs_vals(force_env_section, "SUBSYS")
228 CALL cp_add_iter_level(logger%iter_info, "MD")
229 CALL cp_iterate(logger%iter_info, iter_nr=initialstep)
230 ! Read MD section
231 CALL read_md_section(simpar, motion_section, md_section)
232 ! Setup print_keys
233 simpar%info_constraint = cp_print_key_unit_nr(logger, constraint_section, &
234 "CONSTRAINT_INFO", extension=".shakeLog", log_filename=.false.)
235 simpar%lagrange_multipliers = cp_print_key_unit_nr(logger, constraint_section, &
236 "LAGRANGE_MULTIPLIERS", extension=".LagrangeMultLog", log_filename=.false.)
237 simpar%dump_lm = btest(cp_print_key_should_output(logger%iter_info, constraint_section, &
238 "LAGRANGE_MULTIPLIERS"), cp_p_file)
239
240 ! Create the structure for the md energies
241 ALLOCATE (md_ener)
242 CALL create_md_ener(md_ener)
243 CALL set_md_env(md_env, md_ener=md_ener)
244
245 ! If requested setup Thermostats
246 CALL create_thermostats(thermostats, md_section, force_env, simpar, para_env, &
247 globenv, global_section)
248
249 ! If requested setup Barostat
250 CALL create_barostat_type(barostat, md_section, force_env, simpar, globenv)
251
252 ! If requested setup different thermal regions
253 CALL create_thermal_regions(thermal_regions, md_section, simpar, force_env)
254
255 CALL set_md_env(md_env, thermostats=thermostats, barostat=barostat, thermal_regions=thermal_regions)
256
257 IF (simpar%ensemble == reftraj_ensemble) THEN
258 reftraj_section => section_vals_get_subs_vals(md_section, "REFTRAJ")
259 ALLOCATE (reftraj)
260 CALL create_reftraj(reftraj, reftraj_section, para_env)
261 CALL set_md_env(md_env, reftraj=reftraj)
262 END IF
263
264 CALL force_env_get(force_env, subsys=subsys, cell=cell, &
265 force_env_section=force_env_section)
266
267 ! Set V0 if needed
268 IF (simpar%ensemble == nph_uniaxial_ensemble .OR. simpar%ensemble == nph_uniaxial_damped_ensemble) THEN
269 IF (simpar%v0 == 0._dp) simpar%v0 = cell%deth
270 END IF
271
272 ! Initialize velocities possibly applying constraints at the zeroth MD step
273! ! ! CALL section_vals_val_get(motion_section,"PRINT%RESTART%SPLIT_RESTART_FILE",&
274! ! ! l_val=write_binary_restart_file)
275!! let us see if this created all the trouble
276! CALL setup_velocities(force_env,simpar,globenv,md_env,md_section,constraint_section, &
277! write_binary_restart_file)
278
279 ! Setup Free Energy Calculation (if required)
280 CALL fe_env_create(fe_env, free_energy_section)
281 CALL set_md_env(md_env=md_env, simpar=simpar, fe_env=fe_env, cell=cell, &
282 force_env=force_env)
283
284 ! Possibly initialize Wiener processes
285 IF (simpar%ensemble == langevin_ensemble) CALL create_wiener_process(md_env)
286 time_iter_start = m_walltime()
287
288 CALL get_md_env(md_env, force_env=force_env, itimes=itimes, constant=constant, &
289 md_ener=md_ener, t=time, used_time=used_time)
290
291 ! Attach the time counter of the meta_env to the one of the MD
292 CALL set_meta_env(force_env%meta_env, time=time)
293 ! Initialize the md_ener structure
294
295 force_env%meta_env%dt = force_env%meta_env%zdt
296 CALL initialize_md_ener(md_ener, force_env, simpar)
297! force_env%meta_env%dt=force_env%meta_env%zdt
298
299!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! MC setup up
300!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
301
302 NULLIFY (mc_env, mc_par, mcaverages)
303
304 CALL section_vals_get(force_env_section, n_repetition=isos)
305 cpassert(isos == 1)
306! set some values...will use get_globenv if that ever comes around
307
308! initialize the random numbers
309! IF (para_env%is_source()) THEN
310 rng_stream_mc = rng_stream_type(name="Random numbers for monte carlo acc/rej", &
311 distribution_type=uniform)
312! ENDIF
313!!!!! this should go in a routine hmc_read
314
315 NULLIFY (mc_section)
316 ALLOCATE (mc_par)
317
318 mc_section => section_vals_get_subs_vals(force_env%root_section, &
319 "MOTION%MC")
320 CALL section_vals_val_get(mc_section, "ENSEMBLE", &
321 c_val=ensemble)
322 cpassert(str_comp(ensemble, "TRADITIONAL"))
323 CALL section_vals_val_get(mc_section, "NSTEP", &
324 i_val=nmccycles)
325 cpassert(nmccycles > 0)
326 CALL section_vals_val_get(mc_section, "IPRINT", &
327 i_val=iprint)
328 CALL section_vals_val_get(mc_section, "RANDOMTOSKIP", i_val=rand2skip)
329 cpassert(rand2skip >= 0)
330 temp = cp_unit_from_cp2k(simpar%temp_ext, "K")
331!
332
333 CALL set_mc_par(mc_par, ensemble=ensemble, nstep=nmccycles, iprint=iprint, temperature=temp, &
334 beta=1.0_dp/temp/boltzmann*joule, exp_max_val=0.9_dp*log(huge(0.0_dp)), &
335 exp_min_val=0.9_dp*log(tiny(0.0_dp)), max_val=huge(0.0_dp), min_val=0.0_dp, &
336 source=para_env%source, group=para_env, ionode=para_env%is_source(), rand2skip=rand2skip)
337
338 output_unit = cp_logger_get_default_io_unit(logger)
339 IF (output_unit > 0) THEN
340 WRITE (output_unit, '(a,a)') "HMC| Hybrid Monte Carlo Scheme "
341 WRITE (output_unit, '(a,a)') "HMC| Ensemble ", adjustl(ensemble)
342 WRITE (output_unit, '(a,i0)') "HMC| MC Cycles ", nmccycles
343 WRITE (output_unit, '(a,i0,a)') "HMC| Print every ", iprint, " cycles"
344 WRITE (output_unit, '(a,i0)') "HMC| Number of random numbers to skip ", rand2skip
345 WRITE (output_unit, '(a,f16.8,a)') "HMC| Temperature ", temp, "K"
346 END IF
347
348 CALL force_env_get(force_env, subsys=subsys)
349
350 CALL cp_subsys_get(subsys, atomic_kinds=atomic_kinds, local_particles=local_particles, &
351 particles=particles, virial=virial)
352
353 DO i = 1, rand2skip
354 auxrandom = rng_stream_mc%next()
355 DO j = 1, 3*SIZE(particles%els)
356 auxrandom = globenv%gaussian_rng_stream%next()
357 END DO
358 END DO
359
360 ALLOCATE (mc_env)
361 CALL mc_env_create(mc_env)
362 CALL set_mc_env(mc_env, mc_par=mc_par, force_env=force_env)
363!!!!!!!end mc setup
364
365 ! Check for ensembles requiring the stress tensor - takes into account the possibility for
366 ! multiple force_evals
367 IF ((simpar%ensemble == npt_i_ensemble) .OR. &
368 (simpar%ensemble == npt_ia_ensemble) .OR. &
369 (simpar%ensemble == npt_f_ensemble) .OR. &
370 (simpar%ensemble == npe_f_ensemble) .OR. &
371 (simpar%ensemble == npe_i_ensemble) .OR. &
372 (simpar%ensemble == nph_uniaxial_ensemble) .OR. &
373 (simpar%ensemble == nph_uniaxial_damped_ensemble)) THEN
374 check = virial%pv_availability
375 IF (.NOT. check) &
376 CALL cp_abort(__location__, &
377 "Virial evaluation not requested for this run in the input file! "// &
378 "You may consider to switch on the virial evaluation with the keyword: STRESS_TENSOR. "// &
379 "Be sure the method you are using can compute the virial!")
380 IF (ASSOCIATED(force_env%sub_force_env)) THEN
381 DO i = 1, SIZE(force_env%sub_force_env)
382 IF (ASSOCIATED(force_env%sub_force_env(i)%force_env)) THEN
383 CALL force_env_get(force_env%sub_force_env(i)%force_env, subsys=subsys_i)
384 CALL cp_subsys_get(subsys_i, virial=virial)
385 check = check .AND. virial%pv_availability
386 END IF
387 END DO
388 END IF
389 IF (.NOT. check) &
390 CALL cp_abort(__location__, &
391 "Virial evaluation not requested for all the force_eval sections present in"// &
392 " the input file! You have to switch on the virial evaluation with the keyword: STRESS_TENSOR"// &
393 " in each force_eval section. Be sure the method you are using can compute the virial!")
394 END IF
395
396 ! Computing Forces at zero MD step
397 IF (simpar%ensemble /= reftraj_ensemble) THEN
398 CALL section_vals_val_get(md_section, "STEP_START_VAL", i_val=itimes)
399 CALL section_vals_val_get(md_section, "TIME_START_VAL", r_val=time)
400 CALL section_vals_val_get(md_section, "ECONS_START_VAL", r_val=constant)
401 CALL section_vals_val_set(md_section, "STEP_START_VAL", i_val=initialstep)
402 CALL section_vals_val_set(md_section, "TIME_START_VAL", r_val=inittime)
403 initialstep = itimes
404 CALL cp_iterate(logger%iter_info, iter_nr=itimes)
405 IF (save_mem) THEN
406 work_section => section_vals_get_subs_vals(subsys_section, "VELOCITY")
407 CALL section_vals_remove_values(work_section)
408 work_section => section_vals_get_subs_vals(subsys_section, "SHELL_VELOCITY")
409 CALL section_vals_remove_values(work_section)
410 work_section => section_vals_get_subs_vals(subsys_section, "CORE_VELOCITY")
411 CALL section_vals_remove_values(work_section)
412 END IF
413
414! CALL force_env_calc_energy_force (force_env, calc_force=.TRUE.)
415 meta_env_saved => force_env%meta_env
416 NULLIFY (force_env%meta_env)
417 CALL force_env_calc_energy_force(force_env, calc_force=.false.)
418 force_env%meta_env => meta_env_saved
419
420 IF (ASSOCIATED(force_env%qs_env)) THEN
421! force_env%qs_env%sim_time=time
422! force_env%qs_env%sim_step=itimes
423 force_env%qs_env%sim_time = 0.0_dp
424 force_env%qs_env%sim_step = 0
425 END IF
426 ! Warm-up engines for metadynamics
427 IF (ASSOCIATED(force_env%meta_env)) THEN
428 IF (force_env%meta_env%langevin) THEN
429 CALL create_wiener_process_cv(force_env%meta_env)
430 DO j = 1, (rand2skip - 1)/nmccycles
431 DO i = 1, force_env%meta_env%n_colvar
432 auxrandom = force_env%meta_env%rng(i)%next()
433 auxrandom = force_env%meta_env%rng(i)%next()
434 END DO
435 END DO
436 END IF
437! IF (force_env%meta_env%well_tempered) THEN
438! force_env%meta_env%wttemperature = simpar%temp_ext
439! IF (force_env%meta_env%wtgamma>EPSILON(1._dp)) THEN
440! dummy=force_env%meta_env%wttemperature*(force_env%meta_env%wtgamma-1._dp)
441! IF (force_env%meta_env%delta_t>EPSILON(1._dp)) THEN
442! check=ABS(force_env%meta_env%delta_t-dummy)<1.E+3_dp*EPSILON(1._dp)
443! IF(.NOT.check) CALL cp_abort(__LOCATION__,&
444! "Inconsistency between DELTA_T and WTGAMMA (both specified):"//&
445! " please, verify that DELTA_T=(WTGAMMA-1)*TEMPERATURE")
446! ELSE
447! force_env%meta_env%delta_t = dummy
448! ENDIF
449! ELSE
450! force_env%meta_env%wtgamma = 1._dp &
451! + force_env%meta_env%delta_t/force_env%meta_env%wttemperature
452! ENDIF
453! force_env%meta_env%invdt = 1._dp/force_env%meta_env%delta_t
454! ENDIF
455 CALL tamc_force(force_env)
456! CALL metadyn_write_colvar(force_env)
457 END IF
458
459 IF (simpar%do_respa) THEN
460 CALL force_env_calc_energy_force(force_env%sub_force_env(1)%force_env, &
461 calc_force=.true.)
462 END IF
463
464! CALL force_env_get( force_env, subsys=subsys)
465!
466! CALL cp_subsys_get(subsys,atomic_kinds=atomic_kinds,local_particles=local_particles,&
467! particles=particles)
468
469 CALL virial_evaluate(atomic_kinds%els, particles%els, local_particles, &
470 virial, force_env%para_env)
471
472 CALL md_energy(md_env, md_ener)
473! CALL md_write_output(md_env) !inits the print env at itimes == 0 also writes trajectories
474 md_stride = 1
475 ELSE
476 CALL get_md_env(md_env, reftraj=reftraj)
477 CALL initialize_reftraj(reftraj, reftraj_section, md_env)
478 itimes = reftraj%info%first_snapshot - 1
479 md_stride = reftraj%info%stride
480 END IF
481
482 CALL cp_print_key_finished_output(simpar%info_constraint, logger, &
483 constraint_section, "CONSTRAINT_INFO")
484 CALL cp_print_key_finished_output(simpar%lagrange_multipliers, logger, &
485 constraint_section, "LAGRANGE_MULTIPLIERS")
486 CALL init_mc_moves(moves)
487 CALL init_mc_moves(gmoves)
488 ALLOCATE (r(1:3, SIZE(particles%els)))
489! ALLOCATE (r_old(1:3,size(particles%els)))
490 CALL mc_averages_create(mcaverages)
491 !!!!! some more buffers
492 ! Allocate random number for Langevin Thermostat acting on COLVARS
493 ALLOCATE (xieta(2*force_env%meta_env%n_colvar))
494 xieta(:) = 0.0_dp
495 ALLOCATE (an(force_env%meta_env%n_colvar))
496 an(:) = 0.0_dp
497 ALLOCATE (fz(force_env%meta_env%n_colvar))
498 fz(:) = 0.0_dp
499 ALLOCATE (zbuff(2*force_env%meta_env%n_colvar))
500 zbuff(:) = 0.0_dp
501
502 IF (output_unit > 0) THEN
503 WRITE (output_unit, '(a)') "HMC|==== Initial average forces"
504 END IF
505 CALL metadyn_write_colvar_header(force_env)
506 moves%hmc%attempts = 0
507 moves%hmc%successes = 0
508 gmoves%hmc%attempts = 0
509 gmoves%hmc%successes = 0
510 IF (initialstep == 0) THEN
511!!! if we come from a restart we shall properly compute the average force
512!!! read the average force up to now
513 DO i = 1, force_env%meta_env%n_colvar
514 fs_section => section_vals_get_subs_vals(force_env%meta_env%metadyn_section, "EXT_LAGRANGE_FS")
515 CALL section_vals_get(fs_section, explicit=explicit)
516 IF (explicit) THEN
517 CALL section_vals_val_get(fs_section, "_DEFAULT_KEYWORD_", &
518 i_rep_val=i, r_val=rval)
519 fz(i) = rval*rand2skip
520 END IF
521 END DO
522
523 CALL hmcsampler(globenv, force_env, mcaverages, r, mc_par, moves, gmoves, rng_stream_mc, output_unit, &
524 fz, zbuff, nskip=rand2skip)
525 CALL cp_iterate(logger%iter_info, last=.false., iter_nr=0)
526 CALL section_vals_val_set(mc_section, "RANDOMTOSKIP", i_val=rand2skip + nmccycles)
527 CALL write_restart(md_env=md_env, root_section=force_env%root_section)
528 END IF
529 IF (output_unit > 0) THEN
530 WRITE (output_unit, '(a)') "HMC|==== end initial average forces"
531 END IF
532! call set_md_env(md_env, init=.FALSE.)
533
534 CALL metadyn_write_colvar(force_env)
535
536 DO istep = 1, force_env%meta_env%TAMCSteps
537 ! Increase counters
538 itimes = itimes + 1
539 time = time + force_env%meta_env%dt
540 IF (output_unit > 0) THEN
541 WRITE (output_unit, '(a)') "HMC|==================================="
542 WRITE (output_unit, '(a,1x,i0)') "HMC| on z step ", istep
543 END IF
544 !needed when electric field fields are applied
545 IF (ASSOCIATED(force_env%qs_env)) THEN
546 force_env%qs_env%sim_time = time
547 force_env%qs_env%sim_step = itimes
548 force_env%meta_env%time = force_env%qs_env%sim_time
549 END IF
550
551 CALL cp_iterate(logger%iter_info, last=(istep == force_env%meta_env%TAMCSteps), iter_nr=itimes)
552 ! Open possible Shake output units
553 simpar%info_constraint = cp_print_key_unit_nr(logger, constraint_section, "CONSTRAINT_INFO", &
554 extension=".shakeLog", log_filename=.false.)
555 simpar%lagrange_multipliers = cp_print_key_unit_nr( &
556 logger, constraint_section, &
557 "LAGRANGE_MULTIPLIERS", extension=".LagrangeMultLog", log_filename=.false.)
558 simpar%dump_lm = btest(cp_print_key_should_output(logger%iter_info, constraint_section, &
559 "LAGRANGE_MULTIPLIERS"), cp_p_file)
560
561 ! Velocity Verlet Integrator
562
563 moves%hmc%attempts = 0
564 moves%hmc%successes = 0
565 CALL langevinvec(md_env, globenv, mc_env, moves, gmoves, r, &
566 rng_stream_mc, xieta, an, fz, mcaverages, zbuff)
567
568 ! Close Shake output if requested...
569 CALL cp_print_key_finished_output(simpar%info_constraint, logger, &
570 constraint_section, "CONSTRAINT_INFO")
571 CALL cp_print_key_finished_output(simpar%lagrange_multipliers, logger, &
572 constraint_section, "LAGRANGE_MULTIPLIERS")
573 CALL cp_iterate(logger%iter_info, iter_nr=initialstep)
574 CALL metadyn_write_colvar(force_env)
575 ! Free Energy calculation
576! CALL free_energy_evaluate(md_env,should_stop,free_energy_section)
577
578 ![AME:UB] IF (should_stop) EXIT
579
580 ! Test for <PROJECT_NAME>.EXIT_MD or for WALL_TIME to exit
581 ! Default:
582 ! IF so we don't overwrite the restart or append to the trajectory
583 ! because the execution could in principle stop inside the SCF where energy
584 ! and forces are not converged.
585 ! But:
586 ! You can force to print the last step (for example if the method used
587 ! to compute energy and forces is not SCF based) activating the print_key
588 ! MOTION%MD%PRINT%FORCE_LAST.
589 CALL external_control(should_stop, "MD", globenv=globenv)
590 IF (should_stop) THEN
591 CALL cp_iterate(logger%iter_info, last=.true., iter_nr=itimes)
592! CALL md_output(md_env,md_section,force_env%root_section,should_stop)
593 EXIT
594 END IF
595
596! IF(simpar%ensemble /= reftraj_ensemble) THEN
597! CALL md_energy(md_env, md_ener)
598! CALL temperature_control(simpar, md_env, md_ener, force_env, logger)
599! CALL comvel_control(md_ener, force_env, md_section, logger)
600! CALL angvel_control(md_ener, force_env, md_section, logger)
601! ELSE
602! CALL md_ener_reftraj(md_env, md_ener)
603! END IF
604
605 time_iter_stop = m_walltime()
606 used_time = time_iter_stop - time_iter_start
607 time_iter_start = time_iter_stop
608
609!!!!! this writes the restart...
610! CALL md_output(md_env,md_section,force_env%root_section,should_stop)
611
612! IF(simpar%ensemble == reftraj_ensemble ) THEN
613! CALL write_output_reftraj(md_env)
614! END IF
615
616 IF (output_unit > 0) THEN
617 WRITE (output_unit, '(a,1x,i0)') "HMC| end z step ", istep
618 WRITE (output_unit, '(a)') "HMC|==================================="
619 END IF
620 END DO
621 CALL cp_iterate(logger%iter_info, last=.true., iter_nr=itimes)
622 force_env%qs_env%sim_time = 0.0_dp
623 force_env%qs_env%sim_step = 0
624 rand2skip = rand2skip + nmccycles*force_env%meta_env%TAMCSteps
625 IF (initialstep == 0) rand2skip = rand2skip + nmccycles
626 CALL section_vals_val_set(mc_section, "RANDOMTOSKIP", i_val=rand2skip)
627
628 CALL write_restart(md_env=md_env, root_section=force_env%root_section)
629! if we need the final kinetic energy for Hybrid Monte Carlo
630! hmc_ekin%final_ekin=md_ener%ekin
631
632 ! Remove the iteration level
633 CALL cp_rm_iter_level(logger%iter_info, "MD")
634
635 ! Deallocate Thermostats and Barostats
636 CALL release_simpar_type(simpar)
637
638 CALL md_env_release(md_env)
639 DEALLOCATE (md_env)
640 ! Clean restartable sections..
641 IF (my_rm_restart_info) CALL remove_restart_info(force_env%root_section)
642! IF (para_env%is_source()) THEN
643! ENDIF
644 CALL mc_env_release(mc_env)
645 DEALLOCATE (mc_env)
646 DEALLOCATE (mc_par)
647 CALL mc_moves_release(moves)
648 CALL mc_moves_release(gmoves)
649 DEALLOCATE (r)
650! DEALLOCATE(r_old)
651 DEALLOCATE (xieta)
652 DEALLOCATE (an)
653 DEALLOCATE (fz)
654 DEALLOCATE (zbuff)
655 CALL mc_averages_release(mcaverages)
656 CALL timestop(handle)
657
658 END SUBROUTINE qs_tamc
659
660! **************************************************************************************************
661!> \brief Propagates velocities for z half a step
662!> \param force_env ...
663!> \param An ...
664!> \author Alin M Elena
665!> \note Vanden-Eijnden Ciccotti C.Phys.Letter 429 (2006) 310-316
666! **************************************************************************************************
667 SUBROUTINE tamc_velocities_colvar(force_env, An)
668 TYPE(force_env_type), POINTER :: force_env
669 REAL(kind=dp), DIMENSION(:), INTENT(INOUT) :: an
670
671 CHARACTER(len=*), PARAMETER :: routinen = 'tamc_velocities_colvar'
672
673 INTEGER :: handle, i_c
674 REAL(kind=dp) :: dt, fft, sigma
675 TYPE(cp_logger_type), POINTER :: logger
676 TYPE(meta_env_type), POINTER :: meta_env
677 TYPE(metavar_type), POINTER :: cv
678
679 NULLIFY (logger, meta_env, cv)
680 meta_env => force_env%meta_env
681 CALL timeset(routinen, handle)
682 logger => cp_get_default_logger()
683 ! Add citation
684 IF (meta_env%langevin) CALL cite_reference(vandencic2006)
685 dt = meta_env%dt
686
687 ! Evolve Velocities
688 meta_env%epot_walls = 0.0_dp
689 DO i_c = 1, meta_env%n_colvar
690 cv => meta_env%metavar(i_c)
691 fft = cv%ff_s + cv%ff_hills
692 sigma = sqrt((meta_env%temp_wanted*kelvin)*2.0_dp*(boltzmann/joule)*cv%gamma/cv%mass)
693 cv%vvp = cv%vvp + 0.5_dp*dt*(fft/cv%mass - cv%gamma*cv%vvp)*(1.0_dp - 0.25_dp*dt*cv%gamma) + an(i_c)
694 meta_env%epot_walls = meta_env%epot_walls + cv%epot_walls
695 END DO
696 CALL timestop(handle)
697 END SUBROUTINE tamc_velocities_colvar
698
699! **************************************************************************************************
700!> \brief propagates z one step
701!> \param force_env ...
702!> \param xieta ...
703!> \author Alin M Elena
704!> \note Vanden-Eijnden Ciccotti C.Phys.Letter 429 (2006) 310-316
705! **************************************************************************************************
706 SUBROUTINE tamc_position_colvar(force_env, xieta)
707 TYPE(force_env_type), POINTER :: force_env
708 REAL(kind=dp), DIMENSION(:), INTENT(INOUT) :: xieta
709
710 CHARACTER(len=*), PARAMETER :: routinen = 'tamc_position_colvar'
711
712 INTEGER :: handle, i_c
713 REAL(kind=dp) :: dt, sigma
714 TYPE(cp_logger_type), POINTER :: logger
715 TYPE(meta_env_type), POINTER :: meta_env
716 TYPE(metavar_type), POINTER :: cv
717
718 NULLIFY (logger, meta_env, cv)
719 meta_env => force_env%meta_env
720! IF (.NOT.ASSOCIATED(meta_env)) RETURN
721
722 CALL timeset(routinen, handle)
723 logger => cp_get_default_logger()
724
725 ! Add citation
726 IF (meta_env%langevin) CALL cite_reference(vandencic2006)
727 dt = meta_env%dt
728
729 ! Update of ss0
730 DO i_c = 1, meta_env%n_colvar
731 cv => meta_env%metavar(i_c)
732 sigma = sqrt((meta_env%temp_wanted*kelvin)*2.0_dp*(boltzmann/joule)*cv%gamma/cv%mass)
733! cv%ss0 =cv%ss0 +dt*cv%vvp
734 cv%ss0 = cv%ss0 + dt*cv%vvp + dt*sqrt(dt/12.0_dp)*sigma*xieta(i_c + meta_env%n_colvar)
735 IF (cv%periodic) THEN
736 ! A periodic COLVAR is always within [-pi,pi]
737 cv%ss0 = sign(1.0_dp, asin(sin(cv%ss0)))*acos(cos(cv%ss0))
738 END IF
739 END DO
740 CALL timestop(handle)
741
742 END SUBROUTINE tamc_position_colvar
743
744! **************************************************************************************************
745!> \brief Computes forces on z
746!> #details also can be used to get the potenzial evergy of z
747!> \param force_env ...
748!> \param zpot ...
749!> \author Alin M Elena
750! **************************************************************************************************
751 SUBROUTINE tamc_force(force_env, zpot)
752 TYPE(force_env_type), POINTER :: force_env
753 REAL(kind=dp), INTENT(inout), OPTIONAL :: zpot
754
755 CHARACTER(len=*), PARAMETER :: routinen = 'tamc_force'
756
757 INTEGER :: handle, i, i_c, icolvar, ii
758 LOGICAL :: explicit
759 REAL(kind=dp) :: diff_ss, dt, rval
760 TYPE(colvar_p_type), DIMENSION(:), POINTER :: colvar_p
761 TYPE(cp_logger_type), POINTER :: logger
762 TYPE(cp_subsys_type), POINTER :: subsys
763 TYPE(meta_env_type), POINTER :: meta_env
764 TYPE(metavar_type), POINTER :: cv
765 TYPE(particle_list_type), POINTER :: particles
766 TYPE(section_vals_type), POINTER :: ss0_section, ss_section, vvp_section
767
768 NULLIFY (logger, meta_env)
769 meta_env => force_env%meta_env
770! IF (.NOT.ASSOCIATED(meta_env)) RETURN
771
772 CALL timeset(routinen, handle)
773 logger => cp_get_default_logger()
774 NULLIFY (colvar_p, subsys, cv, ss0_section, vvp_section, ss_section)
775 CALL force_env_get(force_env, subsys=subsys)
776
777 dt = meta_env%dt
778 IF (.NOT. meta_env%restart) meta_env%n_steps = meta_env%n_steps + 1
779 ! compute ss and the derivative of ss with respect to the atomic positions
780 DO i_c = 1, meta_env%n_colvar
781 cv => meta_env%metavar(i_c)
782 icolvar = cv%icolvar
783 CALL colvar_eval_glob_f(icolvar, force_env)
784 cv%ss = subsys%colvar_p(icolvar)%colvar%ss
785 ! Restart for Extended Lagrangian Metadynamics
786 IF (meta_env%restart) THEN
787 ! Initialize the position of the collective variable in the extended lagrange
788 ss0_section => section_vals_get_subs_vals(meta_env%metadyn_section, "EXT_LAGRANGE_SS0")
789 CALL section_vals_get(ss0_section, explicit=explicit)
790 IF (explicit) THEN
791 CALL section_vals_val_get(ss0_section, "_DEFAULT_KEYWORD_", &
792 i_rep_val=i_c, r_val=rval)
793 cv%ss0 = rval
794 ELSE
795 cv%ss0 = cv%ss
796 END IF
797 vvp_section => section_vals_get_subs_vals(meta_env%metadyn_section, "EXT_LAGRANGE_VVP")
798 CALL section_vals_get(vvp_section, explicit=explicit)
799 IF (explicit) THEN
800 CALL setup_velocities_z(force_env)
801 CALL section_vals_val_get(vvp_section, "_DEFAULT_KEYWORD_", &
802 i_rep_val=i_c, r_val=rval)
803 cv%vvp = rval
804 ELSE
805 CALL setup_velocities_z(force_env)
806 END IF
807 ss_section => section_vals_get_subs_vals(meta_env%metadyn_section, "EXT_LAGRANGE_SS")
808 CALL section_vals_get(ss_section, explicit=explicit)
809 IF (explicit) THEN
810 CALL section_vals_val_get(ss_section, "_DEFAULT_KEYWORD_", &
811 i_rep_val=i_c, r_val=rval)
812 cv%ss = rval
813 END IF
814 END IF
815 !
816 END DO
817 ! forces on the atoms
818 NULLIFY (particles)
819 CALL cp_subsys_get(subsys, colvar_p=colvar_p, &
820 particles=particles)
821
822 meta_env%restart = .false.
823 meta_env%epot_s = 0.0_dp
824 meta_env%epot_walls = 0.0_dp
825 DO i_c = 1, meta_env%n_colvar
826 cv => meta_env%metavar(i_c)
827 diff_ss = cv%ss - cv%ss0
828 IF (cv%periodic) THEN
829 ! The difference of a periodic COLVAR is always within [-pi,pi]
830 diff_ss = sign(1.0_dp, asin(sin(diff_ss)))*acos(cos(diff_ss))
831 END IF
832 cv%epot_s = 0.5_dp*cv%lambda*diff_ss*diff_ss
833 cv%ff_s = cv%lambda*(diff_ss)
834 meta_env%epot_s = meta_env%epot_s + cv%epot_s
835 icolvar = cv%icolvar
836
837 DO ii = 1, colvar_p(icolvar)%colvar%n_atom_s
838 i = colvar_p(icolvar)%colvar%i_atom(ii)
839 particles%els(i)%f = particles%els(i)%f - cv%ff_s*colvar_p(icolvar)%colvar%dsdr(:, ii)
840 END DO
841
842 END DO
843 IF (PRESENT(zpot)) zpot = meta_env%epot_s
844 CALL fix_atom_control(force_env)
845
846 CALL timestop(handle)
847 END SUBROUTINE tamc_force
848
849! **************************************************************************************************
850!> \brief propagates one time step both z systems and samples the x system
851!> \param md_env ...
852!> \param globenv ...
853!> \param mc_env ...
854!> \param moves ...
855!> \param gmoves ...
856!> \param r ...
857!> \param rng_stream_mc ...
858!> \param xieta ...
859!> \param An ...
860!> \param fz ...
861!> \param averages ...
862!> \param zbuff ...
863!> \author Alin M Elena
864! **************************************************************************************************
865 SUBROUTINE langevinvec(md_env, globenv, mc_env, moves, gmoves, r, &
866 rng_stream_mc, xieta, An, fz, averages, zbuff)
867
868 TYPE(md_environment_type), POINTER :: md_env
869 TYPE(global_environment_type), POINTER :: globenv
870 TYPE(mc_environment_type), POINTER :: mc_env
871 TYPE(mc_moves_type), POINTER :: moves, gmoves
872 REAL(kind=dp), DIMENSION(:, :), INTENT(INOUT) :: r
873 TYPE(rng_stream_type), INTENT(INOUT) :: rng_stream_mc
874 REAL(kind=dp), DIMENSION(:), INTENT(INOUT) :: xieta, an, fz
875 TYPE(mc_averages_type), INTENT(INOUT), POINTER :: averages
876 REAL(kind=dp), DIMENSION(:), INTENT(INOUT) :: zbuff
877
878 INTEGER :: iprint, ivar, nparticle, nparticle_kind, &
879 nstep, output_unit
880 REAL(kind=dp) :: dt, gamma, mass, sigma
881 TYPE(atomic_kind_list_type), POINTER :: atomic_kinds
882 TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
883 TYPE(cell_type), POINTER :: cell
884 TYPE(cp_logger_type), POINTER :: logger
885 TYPE(cp_subsys_type), POINTER :: subsys
886 TYPE(distribution_1d_type), POINTER :: local_molecules, local_particles
887 TYPE(force_env_type), POINTER :: force_env
888 TYPE(global_constraint_type), POINTER :: gci
889 TYPE(mc_simpar_type), POINTER :: mc_par
890 TYPE(molecule_kind_list_type), POINTER :: molecule_kinds
891 TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
892 TYPE(molecule_list_type), POINTER :: molecules
893 TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
894 TYPE(mp_para_env_type), POINTER :: para_env
895 TYPE(particle_list_type), POINTER :: particles
896 TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
897 TYPE(simpar_type), POINTER :: simpar
898 TYPE(virial_type), POINTER :: virial
899
900 NULLIFY (logger, mc_par)
901 logger => cp_get_default_logger()
902 output_unit = cp_logger_get_default_io_unit(logger)
903
904! quantitites to be nullified for the get_md_env
905 NULLIFY (simpar, force_env, para_env)
906! quantities to be nullified for the force_env_get environment
907 NULLIFY (subsys, cell)
908! quantitites to be nullified for the cp_subsys_get
909 NULLIFY (atomic_kinds, local_particles, particles, local_molecules, molecules, molecule_kinds, gci)
910
911 CALL get_md_env(md_env=md_env, simpar=simpar, force_env=force_env, &
912 para_env=para_env)
913 CALL get_mc_env(mc_env, mc_par=mc_par)
914 CALL get_mc_par(mc_par, nstep=nstep, iprint=iprint)
915
916 dt = simpar%dt
917 CALL force_env_get(force_env=force_env, subsys=subsys, cell=cell)
918
919!!!! this bit should vanish once I understand what the hell is with it
920
921! ! Do some checks on coordinates and box
922 CALL apply_qmmm_walls_reflective(force_env)
923
924 CALL cp_subsys_get(subsys=subsys, atomic_kinds=atomic_kinds, local_particles=local_particles, &
925 particles=particles, local_molecules=local_molecules, molecules=molecules, &
926 molecule_kinds=molecule_kinds, gci=gci, virial=virial)
927
928 nparticle_kind = atomic_kinds%n_els
929 atomic_kind_set => atomic_kinds%els
930 molecule_kind_set => molecule_kinds%els
931
932 nparticle = particles%n_els
933 particle_set => particles%els
934 molecule_set => molecules%els
935 cpassert(ASSOCIATED(force_env%meta_env))
936 cpassert(force_env%meta_env%langevin)
937 ! *** Velocity Verlet for Langevin *** v(t)--> v(t+1/2)
938 !!!!!! noise xi is in the first half, eta in the second half
939 DO ivar = 1, force_env%meta_env%n_colvar
940 xieta(ivar) = force_env%meta_env%rng(ivar)%next()
941 xieta(ivar + force_env%meta_env%n_colvar) = force_env%meta_env%rng(ivar)%next()
942 gamma = force_env%meta_env%metavar(ivar)%gamma
943 mass = force_env%meta_env%metavar(ivar)%mass
944 sigma = sqrt((force_env%meta_env%temp_wanted*kelvin)*2.0_dp*(boltzmann/joule)*gamma/mass)
945 an(ivar) = 0.5_dp*sqrt(dt)*sigma*(xieta(ivar)*(1.0_dp - 0.5_dp*dt*gamma) - &
946 dt*gamma*xieta(ivar + force_env%meta_env%n_colvar)/sqrt(12.0_dp))
947 END DO
948! *** Velocity Verlet for Langeving *** v(t)--> v(t+1/2)
949 CALL tamc_velocities_colvar(force_env, an)
950! *** Velocity Verlet for Langevin S(t)->S(t+1)
951 CALL tamc_position_colvar(force_env, xieta)
952!!!!! start zHMC sampler
953 CALL hmcsampler(globenv, force_env, averages, r, mc_par, moves, gmoves, rng_stream_mc, output_unit, fz, zbuff)
954
955! CALL final_mc_write(mc_par,tmp_moves,&
956! output_unit,energy_check,&
957! initial_energy,final_energy,&
958! averages)
959
960!!!!!!!!!!!!!!!!!!!! end zHMC sampler
961 ! *** Velocity Verlet for Langeving *** v(t+1/2)--> v(t+1)
962 CALL tamc_velocities_colvar(force_env, an)
963! CALL virial_evaluate ( atomic_kind_set, particle_set, &
964! local_particles, virial, para_env)
965
966 END SUBROUTINE langevinvec
967
968! **************************************************************************************************
969!> \brief Driver routin for the canonical sampler using modified HMC
970!> \param globenv ...
971!> \param force_env ...
972!> \param averages ...
973!> \param r ...
974!> \param mc_par ...
975!> \param moves ...
976!> \param gmoves ...
977!> \param rng_stream_mc ...
978!> \param output_unit ...
979!> \param fz ...
980!> \param zbuff ...
981!> \param nskip ...
982!> \author Alin M Elena
983!> \note at the end of this routine %ff_s will contain mean force
984! **************************************************************************************************
985
986 SUBROUTINE hmcsampler(globenv, force_env, averages, r, mc_par, moves, gmoves, rng_stream_mc, output_unit, &
987 fz, zbuff, nskip)
988 TYPE(global_environment_type), POINTER :: globenv
989 TYPE(force_env_type), POINTER :: force_env
990 TYPE(mc_averages_type), POINTER :: averages
991 REAL(kind=dp), DIMENSION(:, :), INTENT(INOUT) :: r
992 TYPE(mc_simpar_type), POINTER :: mc_par
993 TYPE(mc_moves_type), POINTER :: moves, gmoves
994 TYPE(rng_stream_type), INTENT(INOUT) :: rng_stream_mc
995 INTEGER, INTENT(IN) :: output_unit
996 REAL(kind=dp), DIMENSION(:), INTENT(INOUT) :: fz, zbuff
997 INTEGER, INTENT(IN), OPTIONAL :: nskip
998
999 INTEGER :: i, iprint, ishift, it1, j, nsamples, &
1000 nstep
1001 REAL(kind=dp) :: energy_check, old_epx, old_epz, t1
1002 TYPE(meta_env_type), POINTER :: meta_env_saved
1003
1004 IF (PRESENT(nskip)) THEN
1005 nsamples = nskip
1006 ishift = nskip
1007 ELSE
1008 nsamples = 0
1009 fz = 0.0_dp
1010 ishift = 0
1011 END IF
1012! lrestart = .false.
1013! if (present(logger) .and. present(iter)) THEN
1014! lrestart=.true.
1015! ENDIF
1016 CALL get_mc_par(mc_par, nstep=nstep, iprint=iprint)
1017 meta_env_saved => force_env%meta_env
1018 NULLIFY (force_env%meta_env)
1019 CALL force_env_get(force_env, potential_energy=old_epx)
1020 force_env%meta_env => meta_env_saved
1021
1022 old_epz = force_env%meta_env%epot_s
1023!!! average energy will be wrong on restarts
1024 averages%ave_energy = 0.0_dp
1025 t1 = force_env%qs_env%sim_time
1026 it1 = force_env%qs_env%sim_step
1027 IF (output_unit > 0) THEN
1028 WRITE (output_unit, '(a,l4)') "HMC|restart? ", force_env%meta_env%restart
1029 WRITE (output_unit, '(a,3(f16.8,1x))') &
1030 "HMC|Ep, Epx, Epz ", old_epx + force_env%meta_env%epot_s, old_epx, force_env%meta_env%epot_s
1031 WRITE (output_unit, '(a)') "#HMC| No | z.. | theta.. | ff_z... | ff_z/n |"
1032 END IF
1033 DO i = 1, nstep
1034 IF (mod(i, iprint) == 0 .AND. (output_unit > 0)) THEN
1035 WRITE (output_unit, '(a,1x,i0)') "HMC|========== On Monte Carlo cycle ", i + ishift
1036 WRITE (output_unit, '(a)') "HMC| Attempting a minitrajectory move"
1037 WRITE (output_unit, '(a,1x,i0)') "HMC| start mini-trajectory", i + ishift
1038 WRITE (output_unit, '(a,1x,i0,1x)', advance="no") "#HMC|0 ", i + ishift
1039 DO j = 1, force_env%meta_env%n_colvar
1040 WRITE (output_unit, '(f16.8,1x,f16.8,1x,f16.8)', advance="no") force_env%meta_env%metavar(j)%ss0, &
1041 force_env%meta_env%metavar(j)%ss, &
1042 force_env%meta_env%metavar(j)%ff_s !,fz(j)/real(i+ishift,dp)
1043 END DO
1044 WRITE (output_unit, *)
1045 END IF
1046
1047 CALL mc_hmc_move(mc_par, force_env, globenv, moves, gmoves, old_epx, old_epz, energy_check, &
1048 r, output_unit, rng_stream_mc, zbuff)
1049 ! check averages...
1050 ! force average for z needed too...
1051 averages%ave_energy = averages%ave_energy*real(i - 1, dp)/real(i, dp) + &
1052 old_epx/real(i, dp)
1053 DO j = 1, force_env%meta_env%n_colvar
1054 fz(j) = fz(j) + force_env%meta_env%metavar(j)%ff_s
1055 END DO
1056 IF (output_unit > 0) THEN
1057 WRITE (output_unit, '(a,1x,i0)') "HMC|end mini-trajectory", i + ishift
1058!!!!!!!! this prints z and theta(x) --ss0,ss-- needed to determine an acceptable k then
1059 ! the instanteneous force and some instanteneous average for force
1060 WRITE (output_unit, '(a,1x,i0,1x)', advance="no") "#HMC|1 ", i + ishift
1061 DO j = 1, force_env%meta_env%n_colvar
1062 WRITE (output_unit, '(f16.8,1x,f16.8,1x,f16.8,1x,f16.8)', advance="no") force_env%meta_env%metavar(j)%ss0, &
1063 force_env%meta_env%metavar(j)%ss, &
1064 force_env%meta_env%metavar(j)%ff_s, fz(j)/real(i + ishift, dp)
1065 END DO
1066 WRITE (output_unit, *)
1067 END IF
1068 nsamples = nsamples + 1
1069 IF (mod(i, iprint) == 0 .AND. (output_unit > 0)) THEN
1070 WRITE (output_unit, '(a,f16.8)') "HMC| Running average for potential energy ", averages%ave_energy
1071 WRITE (output_unit, '(a,1x,i0)') "HMC|======== End Monte Carlo cycle ", i + ishift
1072 END IF
1073! IF (lrestart) THEN
1074! k=nstep/5
1075! IF(MOD(i,k) == 0) THEN
1076! force_env%qs_env%sim_time=t1
1077! force_env%qs_env%sim_step=it1
1078! DO j=1,force_env%meta_env%n_colvar
1079! force_env%meta_env%metavar(j)%ff_s=fz(j)/real(i+ishift,dp)
1080! ENDDO
1081! ! CALL cp_iterate(logger%iter_info,last=.FALSE.,iter_nr=-1)
1082! CALL section_vals_val_set(mcsec,"RANDOMTOSKIP",i_val=i+ishift)
1083! CALL write_restart(md_env=mdenv,root_section=force_env%root_section)
1084! ! CALL cp_iterate(logger%iter_info,last=.FALSE.,iter_nr=iter)
1085! ENDIF
1086! ENDIF
1087 END DO
1088 force_env%qs_env%sim_time = t1
1089 force_env%qs_env%sim_step = it1
1090 IF (output_unit > 0) THEN
1091 WRITE (output_unit, '(a,i0,a,i0,a,f16.8)') "HMC| local acceptance ratio: ", moves%hmc%successes, "/", &
1092 moves%hmc%attempts, "=", real(moves%hmc%successes, dp)/real(moves%hmc%attempts, dp)
1093 WRITE (output_unit, '(a,i0,a,i0,a,f16.8)') "HMC| global acceptance ratio: ", gmoves%hmc%successes, "/", &
1094 gmoves%hmc%attempts, "=", real(gmoves%hmc%successes, dp)/real(gmoves%hmc%attempts, dp)
1095 END IF
1096 !average force
1097 DO j = 1, force_env%meta_env%n_colvar
1098 force_env%meta_env%metavar(j)%ff_s = fz(j)/nsamples
1099 END DO
1100 END SUBROUTINE hmcsampler
1101
1102! **************************************************************************************************
1103!> \brief performs a hybrid Monte Carlo move
1104!> \param mc_par ...
1105!> \param force_env ...
1106!> \param globenv ...
1107!> \param moves ...
1108!> \param gmoves ...
1109!> \param old_epx ...
1110!> \param old_epz ...
1111!> \param energy_check ...
1112!> \param r ...
1113!> \param output_unit ...
1114!> \param rng_stream ...
1115!> \param zbuff ...
1116!> \author Alin M Elena
1117!> \note It runs a NVE trajectory, followed by localisation and accepts rejects
1118!> using the biased Hamiltonian, rather than the traditional guiding Hamiltonian
1119! **************************************************************************************************
1120 SUBROUTINE mc_hmc_move(mc_par, force_env, globenv, moves, gmoves, old_epx, old_epz, &
1121 energy_check, r, output_unit, rng_stream, zbuff)
1122
1123 TYPE(mc_simpar_type), POINTER :: mc_par
1124 TYPE(force_env_type), POINTER :: force_env
1125 TYPE(global_environment_type), POINTER :: globenv
1126 TYPE(mc_moves_type), POINTER :: moves, gmoves
1127 REAL(kind=dp), INTENT(INOUT) :: old_epx, old_epz, energy_check
1128 REAL(kind=dp), DIMENSION(:, :), INTENT(INOUT) :: r
1129 INTEGER, INTENT(IN) :: output_unit
1130 TYPE(rng_stream_type), INTENT(INOUT) :: rng_stream
1131 REAL(kind=dp), DIMENSION(:), INTENT(INOUT) :: zbuff
1132
1133 CHARACTER(LEN=*), PARAMETER :: routinen = 'mc_hmc_move'
1134
1135 INTEGER :: handle, iatom, j, natoms, source
1136 LOGICAL :: ionode, localise
1137 REAL(kind=dp) :: beta, energy_term, exp_max_val, &
1138 exp_min_val, new_energy, new_epx, &
1139 new_epz, rand, value, w
1140 TYPE(cp_subsys_type), POINTER :: oldsys
1141 TYPE(mc_ekin_type), POINTER :: hmc_ekin
1142 TYPE(meta_env_type), POINTER :: meta_env_saved
1143 TYPE(mp_comm_type) :: group
1144 TYPE(particle_list_type), POINTER :: particles_set
1145 TYPE(section_vals_type), POINTER :: dft_section, input
1146
1147! begin the timing of the subroutine
1148
1149 CALL timeset(routinen, handle)
1150
1151 CALL get_qs_env(force_env%qs_env, input=input)
1152 dft_section => section_vals_get_subs_vals(input, "DFT")
1153
1154! get a bunch of stuff from mc_par
1155 CALL get_mc_par(mc_par, ionode=ionode, &
1156 beta=beta, exp_max_val=exp_max_val, &
1157 exp_min_val=exp_min_val, source=source, group=group)
1158
1159! nullify some pointers
1160! NULLIFY(particles_set,oldsys,hmc_ekin)
1161 NULLIFY (particles_set, oldsys, meta_env_saved, hmc_ekin)
1162 ! now let's grab the particle positions
1163 CALL force_env_get(force_env, subsys=oldsys)
1164 CALL cp_subsys_get(oldsys, particles=particles_set)
1165 natoms = SIZE(particles_set%els)
1166! do some allocation
1167
1168 ALLOCATE (hmc_ekin)
1169
1170! record the attempt
1171 moves%hmc%attempts = moves%hmc%attempts + 1
1172 gmoves%hmc%attempts = gmoves%hmc%attempts + 1
1173
1174! save the old coordinates just in case we need to go back
1175 DO iatom = 1, natoms
1176 r(1:3, iatom) = particles_set%els(iatom)%r(1:3)
1177 END DO
1178 localise = .true.
1179! the same for collective variables data should be made,ss first half and ff_s the last half
1180 DO j = 1, force_env%meta_env%n_colvar
1181 zbuff(j) = force_env%meta_env%metavar(j)%ss
1182 zbuff(j + force_env%meta_env%n_colvar) = force_env%meta_env%metavar(j)%ff_s
1183 IF ((oldsys%colvar_p(force_env%meta_env%metavar(j)%icolvar)%colvar%type_id == hbp_colvar_id) .OR. &
1184 (oldsys%colvar_p(force_env%meta_env%metavar(j)%icolvar)%colvar%type_id == wc_colvar_id)) THEN
1185 localise = .false.
1186 END IF
1187 END DO
1188
1189! now run the MD simulation
1190 meta_env_saved => force_env%meta_env
1191 NULLIFY (force_env%meta_env)
1192 force_env%qs_env%sim_time = 0.0_dp
1193 force_env%qs_env%sim_step = 0
1194 IF (.NOT. localise) THEN
1195 CALL section_vals_val_set(dft_section, "LOCALIZE%_SECTION_PARAMETERS_", l_val=.false.)
1196 END IF
1197 CALL qs_mol_dyn(force_env, globenv, hmc_e_initial=hmc_ekin%initial_ekin, hmc_e_final=hmc_ekin%final_ekin)
1198 IF (.NOT. localise) THEN
1199 CALL section_vals_val_set(dft_section, "LOCALIZE%_SECTION_PARAMETERS_", l_val=.true.)
1200 CALL scf_post_calculation_gpw(force_env%qs_env)
1201 END IF
1202
1203 CALL force_env_get(force_env, potential_energy=new_epx)
1204
1205 force_env%meta_env => meta_env_saved
1206 CALL tamc_force(force_env, zpot=new_epz)
1207 new_energy = new_epx + new_epz
1208 IF (output_unit > 0) THEN
1209 WRITE (output_unit, '(a,4(f16.8,1x))') &
1210 "HMC|old Ep, Ekx, Epz, Epx ", old_epx + old_epz, hmc_ekin%initial_ekin, old_epz, old_epx
1211 WRITE (output_unit, '(a,4(f16.8,1x))') "HMC|new Ep, Ekx, Epz, Epx ", new_energy, hmc_ekin%final_ekin, new_epz, new_epx
1212 END IF
1213 energy_term = new_energy - old_epx - old_epz + hmc_ekin%final_ekin - hmc_ekin%initial_ekin
1214
1215 value = -beta*(energy_term)
1216! to prevent overflows
1217 IF (value > exp_max_val) THEN
1218 w = 10.0_dp
1219 ELSEIF (value < exp_min_val) THEN
1220 w = 0.0_dp
1221 ELSE
1222 w = exp(value)
1223 END IF
1224
1225 rand = rng_stream%next()
1226 IF (rand < w) THEN
1227! accept the move
1228 moves%hmc%successes = moves%hmc%successes + 1
1229 gmoves%hmc%successes = gmoves%hmc%successes + 1
1230! update energies
1231 energy_check = energy_check + (new_energy - old_epx - old_epz)
1232 old_epx = new_epx
1233 old_epz = new_epz
1234 ELSE
1235! reset the cell and particle positions
1236 DO iatom = 1, natoms
1237 particles_set%els(iatom)%r(1:3) = r(1:3, iatom)
1238 END DO
1239 DO j = 1, force_env%meta_env%n_colvar
1240 force_env%meta_env%metavar(j)%ss = zbuff(j)
1241 force_env%meta_env%metavar(j)%ff_s = zbuff(j + force_env%meta_env%n_colvar)
1242 END DO
1243
1244 END IF
1245
1246 DEALLOCATE (hmc_ekin)
1247
1248! end the timing
1249 CALL timestop(handle)
1250
1251 END SUBROUTINE mc_hmc_move
1252
1253! **************************************************************************************************
1254!> \brief ...
1255!> \param force_env ...
1256! **************************************************************************************************
1257 SUBROUTINE metadyn_write_colvar_header(force_env)
1258 TYPE(force_env_type), POINTER :: force_env
1259
1260 CHARACTER(len=*), PARAMETER :: routinen = 'metadyn_write_colvar_header'
1261
1262 CHARACTER(len=100) :: aux, fmt
1263 CHARACTER(len=255) :: label1, label2, label3, label4, label5, &
1264 label6
1265 INTEGER :: handle, i, iw, m
1266 TYPE(cp_logger_type), POINTER :: logger
1267 TYPE(meta_env_type), POINTER :: meta_env
1268
1269 NULLIFY (logger, meta_env)
1270 meta_env => force_env%meta_env
1271 IF (.NOT. ASSOCIATED(meta_env)) RETURN
1272
1273 CALL timeset(routinen, handle)
1274 logger => cp_get_default_logger()
1275
1276 iw = cp_print_key_unit_nr(logger, meta_env%metadyn_section, &
1277 "PRINT%COLVAR", extension=".metadynLog")
1278 IF (iw > 0) THEN
1279 label1 = ""
1280 label2 = ""
1281 label3 = ""
1282 label4 = ""
1283 label5 = ""
1284 label6 = ""
1285 DO i = 1, meta_env%n_colvar
1286 WRITE (aux, '(a,i0)') "z_", i
1287 label1 = trim(label1)//trim(aux)
1288 m = 15*i - len_trim(label1) - 1
1289 label1 = trim(label1)//repeat(" ", m)//"|"
1290 WRITE (aux, '(a,i0)') "Theta_", i
1291 label2 = trim(label2)//trim(aux)
1292 m = 15*i - len_trim(label2) - 1
1293 label2 = trim(label2)//repeat(" ", m)//"|"
1294 WRITE (aux, '(a,i0)') "F_z", i
1295 label3 = trim(label3)//trim(aux)
1296 m = 15*i - len_trim(label3) - 1
1297 label3 = trim(label3)//repeat(" ", m)//"|"
1298 WRITE (aux, '(a,i0)') "F_h", i
1299 label4 = trim(label4)//trim(aux)
1300 m = 15*i - len_trim(label4) - 1
1301 label4 = trim(label4)//repeat(" ", m)//"|"
1302 WRITE (aux, '(a,i0)') "F_w", i
1303 label5 = trim(label5)//trim(aux)
1304 m = 15*i - len_trim(label5) - 1
1305 label5 = trim(label5)//repeat(" ", m)//"|"
1306 WRITE (aux, '(a,i0)') "v_z", i
1307 label6 = trim(label6)//trim(aux)
1308 m = 15*i - len_trim(label6) - 1
1309 label6 = trim(label6)//repeat(" ", m)//"|"
1310 END DO
1311 WRITE (fmt, '("(a17,6a",i0 ,",4a15)")') meta_env%n_colvar*15
1312 WRITE (iw, trim(fmt)) "#Time[fs] |", &
1313 trim(label1), &
1314 trim(label2), &
1315 trim(label3), &
1316 trim(label4), &
1317 trim(label5), &
1318 trim(label6), &
1319 "Epot_z |", &
1320 "Ene hills |", &
1321 "Epot walls |", &
1322 "Temperature |"
1323
1324 END IF
1325 CALL cp_print_key_finished_output(iw, logger, meta_env%metadyn_section, &
1326 "PRINT%COLVAR")
1327
1328 CALL timestop(handle)
1329
1330 END SUBROUTINE metadyn_write_colvar_header
1331
1332! **************************************************************************************************
1333!> \brief ...
1334!> \param force_env ...
1335! **************************************************************************************************
1336 SUBROUTINE metadyn_write_colvar(force_env)
1337 TYPE(force_env_type), POINTER :: force_env
1338
1339 CHARACTER(len=*), PARAMETER :: routinen = 'metadyn_write_colvar'
1340
1341 INTEGER :: handle, i, i_c, iw
1342 REAL(kind=dp) :: temp
1343 TYPE(cp_logger_type), POINTER :: logger
1344 TYPE(meta_env_type), POINTER :: meta_env
1345 TYPE(metavar_type), POINTER :: cv
1346
1347 NULLIFY (logger, meta_env, cv)
1348 meta_env => force_env%meta_env
1349 IF (.NOT. ASSOCIATED(meta_env)) RETURN
1350
1351 CALL timeset(routinen, handle)
1352 logger => cp_get_default_logger()
1353
1354 IF (meta_env%langevin) THEN
1355 meta_env%ekin_s = 0.0_dp
1356! meta_env%epot_s = 0.0_dp
1357 DO i_c = 1, meta_env%n_colvar
1358 cv => meta_env%metavar(i_c)
1359 meta_env%ekin_s = meta_env%ekin_s + 0.5_dp*cv%mass*cv%vvp**2
1360 END DO
1361 END IF
1362
1363 ! write COLVAR file
1364 iw = cp_print_key_unit_nr(logger, meta_env%metadyn_section, &
1365 "PRINT%COLVAR", extension=".metadynLog")
1366 IF (iw > 0) THEN
1367 IF (meta_env%extended_lagrange) THEN
1368 WRITE (iw, '(f16.8,70f15.8)') meta_env%time*femtoseconds, &
1369 (meta_env%metavar(i)%ss0, i=1, meta_env%n_colvar), &
1370 (meta_env%metavar(i)%ss, i=1, meta_env%n_colvar), &
1371 (meta_env%metavar(i)%ff_s, i=1, meta_env%n_colvar), &
1372 (meta_env%metavar(i)%ff_hills, i=1, meta_env%n_colvar), &
1373 (meta_env%metavar(i)%ff_walls, i=1, meta_env%n_colvar), &
1374 (meta_env%metavar(i)%vvp, i=1, meta_env%n_colvar), &
1375 meta_env%epot_s, &
1376 meta_env%hills_env%energy, &
1377 meta_env%epot_walls, &
1378 (meta_env%ekin_s)*2.0_dp/(real(meta_env%n_colvar, kind=dp))*kelvin
1379 ELSE
1380 WRITE (iw, '(f16.8,40f13.5)') meta_env%time*femtoseconds, &
1381 (meta_env%metavar(i)%ss0, i=1, meta_env%n_colvar), &
1382 (meta_env%metavar(i)%ff_hills, i=1, meta_env%n_colvar), &
1383 (meta_env%metavar(i)%ff_walls, i=1, meta_env%n_colvar), &
1384 meta_env%hills_env%energy, &
1385 meta_env%epot_walls
1386 END IF
1387 END IF
1388 CALL cp_print_key_finished_output(iw, logger, meta_env%metadyn_section, &
1389 "PRINT%COLVAR")
1390 ! Temperature for COLVAR
1391 IF (meta_env%extended_lagrange) THEN
1392 temp = meta_env%ekin_s*2.0_dp/(real(meta_env%n_colvar, kind=dp))*kelvin
1393 meta_env%avg_temp = (meta_env%avg_temp*real(meta_env%n_steps, kind=dp) + &
1394 temp)/real(meta_env%n_steps + 1, kind=dp)
1395 iw = cp_print_key_unit_nr(logger, meta_env%metadyn_section, &
1396 "PRINT%TEMPERATURE_COLVAR", extension=".metadynLog")
1397 IF (iw > 0) THEN
1398 WRITE (iw, '(T2,79("-"))')
1399 WRITE (iw, '( A,T51,f10.2,T71,f10.2)') ' COLVARS INSTANTANEOUS/AVERAGE TEMPERATURE ', &
1400 temp, meta_env%avg_temp
1401 WRITE (iw, '(T2,79("-"))')
1402 END IF
1403 CALL cp_print_key_finished_output(iw, logger, meta_env%metadyn_section, &
1404 "PRINT%TEMPERATURE_COLVAR")
1405 END IF
1406 CALL timestop(handle)
1407
1408 END SUBROUTINE metadyn_write_colvar
1409
1410! **************************************************************************************************
1411!> \brief ...
1412!> \param force_env ...
1413! **************************************************************************************************
1414 SUBROUTINE setup_velocities_z(force_env)
1415 TYPE(force_env_type), POINTER :: force_env
1416
1417 INTEGER :: i_c
1418 REAL(kind=dp) :: ekin_w, fac_t
1419 TYPE(meta_env_type), POINTER :: meta_env
1420 TYPE(metavar_type), POINTER :: cv
1421
1422 NULLIFY (meta_env)
1423 meta_env => force_env%meta_env
1424 meta_env%ekin_s = 0.0_dp
1425 DO i_c = 1, meta_env%n_colvar
1426 cv => meta_env%metavar(i_c)
1427 cv%vvp = force_env%globenv%gaussian_rng_stream%next()
1428 meta_env%ekin_s = meta_env%ekin_s + 0.5_dp*cv%mass*cv%vvp**2
1429 END DO
1430 ekin_w = 0.5_dp*meta_env%temp_wanted*real(meta_env%n_colvar, kind=dp)
1431 fac_t = sqrt(ekin_w/max(meta_env%ekin_s, 1.0e-8_dp))
1432 DO i_c = 1, meta_env%n_colvar
1433 cv => meta_env%metavar(i_c)
1434 cv%vvp = cv%vvp*fac_t
1435 END DO
1436 END SUBROUTINE setup_velocities_z
1437END MODULE tamc_run
atomic_kind_list_types
represent a simple array based list of the given type
Definition atomic_kind_list_types.F:15
atomic_kind_types
Define the atomic kind types and their sub types.
Definition atomic_kind_types.F:23
averages_types
Handles the type to compute averages during an MD.
Definition averages_types.F:12
barostat_types
Barostat structure: module containing barostat available for MD.
Definition barostat_types.F:12
barostat_types::create_barostat_type
subroutine, public create_barostat_type(barostat, md_section, force_env, simpar, globenv)
...
Definition barostat_types.F:79
bibliography
collects all references to literature in CP2K as new algorithms / method are included from literature...
Definition bibliography.F:21
bibliography::vandencic2006
integer, save, public vandencic2006
Definition bibliography.F:36
cell_types
Handles all functions related to the CELL.
Definition cell_types.F:15
colvar_methods
defines collective variables s({R}) and the derivative of this variable wrt R these can then be used ...
Definition colvar_methods.F:16
colvar_methods::colvar_eval_glob_f
subroutine, public colvar_eval_glob_f(icolvar, force_env)
evaluates the derivatives (dsdr) given and due to the given colvar
Definition colvar_methods.F:1725
colvar_types
Initialize the collective variables types.
Definition colvar_types.F:15
colvar_types::wc_colvar_id
integer, parameter, public wc_colvar_id
Definition colvar_types.F:56
colvar_types::hbp_colvar_id
integer, parameter, public hbp_colvar_id
Definition colvar_types.F:56
constraint_fxd
Definition constraint_fxd.F:12
constraint_fxd::fix_atom_control
subroutine, public fix_atom_control(force_env, w)
allows for fix atom constraints
Definition constraint_fxd.F:65
cp_external_control
Routines to handle the external control of CP2K.
Definition cp_external_control.F:15
cp_external_control::external_control
subroutine, public external_control(should_stop, flag, globenv, target_time, start_time, force_check)
External manipulations during a run : when the <PROJECT_NAME>.EXIT_$runtype command is sent the progr...
Definition cp_external_control.F:90
cp_log_handling
various routines to log and control the output. The idea is that decisions about where to log should ...
Definition cp_log_handling.F:41
cp_log_handling::cp_logger_get_default_io_unit
integer function, public cp_logger_get_default_io_unit(logger)
returns the unit nr for the ionode (-1 on all other processors) skips as well checks if the procs cal...
Definition cp_log_handling.F:515
cp_log_handling::cp_get_default_logger
type(cp_logger_type) function, pointer, public cp_get_default_logger()
returns the default logger
Definition cp_log_handling.F:234
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::cp_print_key_unit_nr
integer function, public cp_print_key_unit_nr(logger, basis_section, print_key_path, extension, middle_name, local, log_filename, ignore_should_output, file_form, file_position, file_action, file_status, do_backup, on_file, is_new_file, mpi_io, fout)
...
Definition cp_output_handling.F:853
cp_output_handling::cp_print_key_finished_output
subroutine, public cp_print_key_finished_output(unit_nr, logger, basis_section, print_key_path, local, ignore_should_output, on_file, mpi_io)
should be called after you finish working with a unit obtained with cp_print_key_unit_nr,...
Definition cp_output_handling.F:1063
cp_output_handling::cp_p_file
integer, parameter, public cp_p_file
Definition cp_output_handling.F:103
cp_output_handling::cp_iterate
subroutine, public cp_iterate(iteration_info, last, iter_nr, increment, iter_nr_out)
adds one to the actual iteration
Definition cp_output_handling.F:574
cp_output_handling::cp_rm_iter_level
subroutine, public cp_rm_iter_level(iteration_info, level_name, n_rlevel_att)
Removes an iteration level.
Definition cp_output_handling.F:705
cp_output_handling::cp_print_key_should_output
integer function, public cp_print_key_should_output(iteration_info, basis_section, print_key_path, used_print_key, first_time)
returns what should be done with the given property if btest(res,cp_p_store) then the property should...
Definition cp_output_handling.F:345
cp_output_handling::cp_add_iter_level
subroutine, public cp_add_iter_level(iteration_info, level_name, n_rlevel_new)
Adds an iteration level.
Definition cp_output_handling.F:662
cp_subsys_types
types that represent a subsys, i.e. a part of the system
Definition cp_subsys_types.F:16
cp_subsys_types::cp_subsys_get
subroutine, public cp_subsys_get(subsys, ref_count, atomic_kinds, atomic_kind_set, particles, particle_set, local_particles, molecules, molecule_set, molecule_kinds, molecule_kind_set, local_molecules, para_env, colvar_p, shell_particles, core_particles, gci, multipoles, natom, nparticle, ncore, nshell, nkind, atprop, virial, results, cell)
returns information about various attributes of the given subsys
Definition cp_subsys_types.F:345
cp_units
unit conversion facility
Definition cp_units.F:30
cp_units::cp_unit_from_cp2k
real(kind=dp) function, public cp_unit_from_cp2k(value, unit_str, defaults, power)
converts from the internal cp2k units to the given unit
Definition cp_units.F:1179
distribution_1d_types
stores a lists of integer that are local to a processor. The idea is that these integers represent ob...
Definition distribution_1d_types.F:24
force_env_methods
Interface for the force calculations.
Definition force_env_methods.F:17
force_env_methods::force_env_calc_energy_force
recursive subroutine, public force_env_calc_energy_force(force_env, calc_force, consistent_energies, skip_external_control, eval_energy_forces, require_consistent_energy_force, linres, calc_stress_tensor)
Interface routine for force and energy calculations.
Definition force_env_methods.F:196
force_env_types
Interface for the force calculations.
Definition force_env_types.F:18
force_env_types::force_env_get
recursive subroutine, public force_env_get(force_env, in_use, fist_env, qs_env, meta_env, fp_env, subsys, para_env, potential_energy, additional_potential, kinetic_energy, harmonic_shell, kinetic_shell, cell, sub_force_env, qmmm_env, qmmmx_env, eip_env, pwdft_env, globenv, input, force_env_section, method_name_id, root_section, mixed_env, nnp_env, embed_env, ipi_env)
returns various attributes about the force environment
Definition force_env_types.F:342
free_energy_types
defines types for metadynamics calculation
Definition free_energy_types.F:13
free_energy_types::fe_env_create
subroutine, public fe_env_create(fe_env, fe_section)
creates the fe_env
Definition free_energy_types.F:88
gamma
Calculation of the incomplete Gamma function F_n(t) for multi-center integrals over Cartesian Gaussia...
Definition gamma.F:15
global_types
Define type storing the global information of a run. Keep the amount of stored data small....
Definition global_types.F:21
input_constants
collects all constants needed in input so that they can be used without circular dependencies
Definition input_constants.F:17
input_constants::nph_uniaxial_ensemble
integer, parameter, public nph_uniaxial_ensemble
Definition input_constants.F:96
input_constants::npt_i_ensemble
integer, parameter, public npt_i_ensemble
Definition input_constants.F:96
input_constants::nph_uniaxial_damped_ensemble
integer, parameter, public nph_uniaxial_damped_ensemble
Definition input_constants.F:96
input_constants::npe_f_ensemble
integer, parameter, public npe_f_ensemble
Definition input_constants.F:96
input_constants::langevin_ensemble
integer, parameter, public langevin_ensemble
Definition input_constants.F:96
input_constants::npe_i_ensemble
integer, parameter, public npe_i_ensemble
Definition input_constants.F:96
input_constants::npt_ia_ensemble
integer, parameter, public npt_ia_ensemble
Definition input_constants.F:96
input_constants::npt_f_ensemble
integer, parameter, public npt_f_ensemble
Definition input_constants.F:96
input_constants::reftraj_ensemble
integer, parameter, public reftraj_ensemble
Definition input_constants.F:96
input_cp2k_check
checks the input and perform some automatic "magic" on it
Definition input_cp2k_check.F:14
input_cp2k_check::remove_restart_info
subroutine, public remove_restart_info(input_file)
Removes section used to restart a calculation from an input file in memory.
Definition input_cp2k_check.F:1002
input_cp2k_restarts
Set of routines to dump the restart file of CP2K.
Definition input_cp2k_restarts.F:13
input_cp2k_restarts::write_restart
subroutine, public write_restart(md_env, force_env, root_section, coords, vels, pint_env, helium_env)
checks if a restart needs to be written and does so, updating all necessary fields in the input file....
Definition input_cp2k_restarts.F:112
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_vals_val_set
subroutine, public section_vals_val_set(section_vals, keyword_name, i_rep_section, i_rep_val, val, l_val, i_val, r_val, c_val, l_vals_ptr, i_vals_ptr, r_vals_ptr, c_vals_ptr)
sets the requested value
Definition input_section_types.F:1223
input_section_types::section_vals_remove_values
subroutine, public section_vals_remove_values(section_vals)
removes the values of a repetition of the section
Definition input_section_types.F:896
input_section_types::section_vals_get_subs_vals
recursive type(section_vals_type) function, pointer, public section_vals_get_subs_vals(section_vals, subsection_name, i_rep_section, can_return_null)
returns the values of the requested subsection
Definition input_section_types.F:731
input_section_types::section_vals_get
subroutine, public section_vals_get(section_vals, ref_count, n_repetition, n_subs_vals_rep, section, explicit)
returns various attributes about the section_vals
Definition input_section_types.F:704
input_section_types::section_vals_val_get
subroutine, public section_vals_val_get(section_vals, keyword_name, i_rep_section, i_rep_val, n_rep_val, val, l_val, i_val, r_val, c_val, l_vals, i_vals, r_vals, c_vals, explicit)
returns the requested value
Definition input_section_types.F:1047
kinds
Defines the basic variable types.
Definition kinds.F:23
kinds::dp
integer, parameter, public dp
Definition kinds.F:34
machine
Machine interface based on Fortran 2003 and POSIX.
Definition machine.F:17
machine::m_walltime
real(kind=dp) function, public m_walltime()
returns time from a real-time clock, protected against rolling early/easily
Definition machine.F:147
mc_environment_types
contains the subroutines for dealing with the mc_env
Definition mc_environment_types.F:12
mc_environment_types::get_mc_env
subroutine, public get_mc_env(mc_env, mc_par, force_env)
provides a method for getting the various structures attached to an mc_env
Definition mc_environment_types.F:95
mc_environment_types::mc_env_create
subroutine, public mc_env_create(mc_env)
creates and initializes an mc_env
Definition mc_environment_types.F:52
mc_environment_types::set_mc_env
subroutine, public set_mc_env(mc_env, mc_par, force_env)
provides a method for attaching various structures to an mc_env
Definition mc_environment_types.F:70
mc_environment_types::mc_env_release
subroutine, public mc_env_release(mc_env)
releases the given mc env
Definition mc_environment_types.F:113
mc_misc
contains miscellaneous subroutines used in the Monte Carlo runs, mostly I/O stuff
Definition mc_misc.F:13
mc_misc::mc_averages_release
subroutine, public mc_averages_release(averages)
deallocates the structure that holds running averages of MC variables
Definition mc_misc.F:77
mc_misc::mc_averages_create
subroutine, public mc_averages_create(averages)
initializes the structure that holds running averages of MC variables
Definition mc_misc.F:46
mc_move_control
control the handling of the move data in Monte Carlo (MC) simulations
Definition mc_move_control.F:14
mc_move_control::mc_moves_release
subroutine, public mc_moves_release(moves)
deallocates all the structures and nullifies the pointer
Definition mc_move_control.F:97
mc_move_control::init_mc_moves
subroutine, public init_mc_moves(moves)
allocates and initializes the structure to record all move attempts/successes
Definition mc_move_control.F:50
mc_types
holds all the structure types needed for Monte Carlo, except the mc_environment_type
Definition mc_types.F:15
mc_types::get_mc_par
subroutine, public get_mc_par(mc_par, nstep, nvirial, iuptrans, iupcltrans, iupvolume, nmoves, nswapmoves, rm, cl, diff, nstart, source, group, lbias, ionode, lrestart, lstop, rmvolume, rmcltrans, rmbond, rmangle, rmrot, rmtrans, temperature, pressure, rclus, beta, pmswap, pmvolume, pmtraion, pmtrans, pmcltrans, ensemble, program, restart_file_name, molecules_file, moves_file, coords_file, energy_file, displacement_file, cell_file, dat_file, data_file, box2_file, fft_lib, iprint, rcut, ldiscrete, discrete_step, pmavbmc, pbias, avbmc_atom, avbmc_rmin, avbmc_rmax, rmdihedral, input_file, mc_molecule_info, pmswap_mol, pmavbmc_mol, pmtrans_mol, pmrot_mol, pmtraion_mol, mc_input_file, mc_bias_file, pmvol_box, pmclus_box, virial_temps, exp_min_val, exp_max_val, min_val, max_val, eta, pmhmc, pmhmc_box, lhmc, rand2skip)
...
Definition mc_types.F:405
mc_types::set_mc_par
subroutine, public set_mc_par(mc_par, rm, cl, diff, nstart, rmvolume, rmcltrans, rmbond, rmangle, rmdihedral, rmrot, rmtrans, program, nmoves, nswapmoves, lstop, temperature, pressure, rclus, iuptrans, iupcltrans, iupvolume, pmswap, pmvolume, pmtraion, pmtrans, pmcltrans, beta, rcut, iprint, lbias, nstep, lrestart, ldiscrete, discrete_step, pmavbmc, mc_molecule_info, pmavbmc_mol, pmtrans_mol, pmrot_mol, pmtraion_mol, pmswap_mol, avbmc_rmin, avbmc_rmax, avbmc_atom, pbias, ensemble, pmvol_box, pmclus_box, eta, mc_input_file, mc_bias_file, exp_max_val, exp_min_val, min_val, max_val, pmhmc, pmhmc_box, lhmc, ionode, source, group, rand2skip)
changes the private elements of the mc_parameters_type
Definition mc_types.F:667
md_ener_types
Split md_ener module from md_environment_type.
Definition md_ener_types.F:12
md_ener_types::create_md_ener
subroutine, public create_md_ener(md_ener)
retains the given md_ener structure
Definition md_ener_types.F:66
md_energies
prints all energy info per timestep to the screen or to user defined output files
Definition md_energies.F:16
md_energies::initialize_md_ener
subroutine, public initialize_md_ener(md_ener, force_env, simpar)
...
Definition md_energies.F:115
md_energies::md_energy
subroutine, public md_energy(md_env, md_ener)
...
Definition md_energies.F:177
md_environment_types
Definition md_environment_types.F:15
md_environment_types::set_md_env
subroutine, public set_md_env(md_env, itimes, constant, cell, simpar, fe_env, force_env, para_env, init, first_time, thermostats, barostat, reftraj, md_ener, averages, thermal_regions, ehrenfest_md)
Set the integrator environment to the correct program.
Definition md_environment_types.F:291
md_environment_types::md_env_create
subroutine, public md_env_create(md_env, md_section, para_env, force_env)
Creates MD environment Purpose: Initialise the integrator environment. retain the para_env for this e...
Definition md_environment_types.F:95
md_environment_types::md_env_release
subroutine, public md_env_release(md_env)
releases the given md env
Definition md_environment_types.F:128
md_environment_types::get_md_env
subroutine, public get_md_env(md_env, itimes, constant, used_time, cell, simpar, npt, force_env, para_env, reftraj, t, init, first_time, fe_env, thermostats, barostat, thermostat_coeff, thermostat_part, thermostat_shell, thermostat_baro, thermostat_fast, thermostat_slow, md_ener, averages, thermal_regions, ehrenfest_md)
get components of MD environment type
Definition md_environment_types.F:195
md_run
Perform a molecular dynamics (MD) run using QUICKSTEP.
Definition md_run.F:14
md_run::qs_mol_dyn
subroutine, public qs_mol_dyn(force_env, globenv, averages, rm_restart_info, hmc_e_initial, hmc_e_final, mdctrl)
Main driver module for Molecular Dynamics.
Definition md_run.F:121
message_passing
Interface to the message passing library MPI.
Definition message_passing.F:23
metadynamics_types
defines types for metadynamics calculation
Definition metadynamics_types.F:13
metadynamics_types::set_meta_env
subroutine, public set_meta_env(meta_env, time)
sets the meta_env
Definition metadynamics_types.F:230
molecule_kind_list_types
represent a simple array based list of the given type
Definition molecule_kind_list_types.F:15
molecule_kind_types
Define the molecule kind structure types and the corresponding functionality.
Definition molecule_kind_types.F:16
molecule_list_types
represent a simple array based list of the given type
Definition molecule_list_types.F:15
molecule_types
Define the data structure for the molecule information.
Definition molecule_types.F:16
parallel_rng_types
Parallel (pseudo)random number generator (RNG) for multiple streams and substreams of random numbers.
Definition parallel_rng_types.F:51
parallel_rng_types::advance
subroutine advance(self, e, c)
Advance the state by n steps, i.e. jump n steps forward, if n > 0, or backward if n < 0.
Definition parallel_rng_types.F:228
parallel_rng_types::uniform
integer, parameter, public uniform
Definition parallel_rng_types.F:73
particle_list_types
represent a simple array based list of the given type
Definition particle_list_types.F:15
particle_types
Define the data structure for the particle information.
Definition particle_types.F:19
physcon
Definition of physical constants:
Definition physcon.F:68
physcon::boltzmann
real(kind=dp), parameter, public boltzmann
Definition physcon.F:129
physcon::femtoseconds
real(kind=dp), parameter, public femtoseconds
Definition physcon.F:153
physcon::joule
real(kind=dp), parameter, public joule
Definition physcon.F:159
physcon::kelvin
real(kind=dp), parameter, public kelvin
Definition physcon.F:165
qmmm_util
Definition qmmm_util.F:13
qmmm_util::apply_qmmm_walls_reflective
subroutine, public apply_qmmm_walls_reflective(force_env)
Apply reflective QM walls in order to avoid QM atoms escaping from the QM Box.
Definition qmmm_util.F:99
qs_environment_types
Definition qs_environment_types.F:14
qs_environment_types::get_qs_env
subroutine, public get_qs_env(qs_env, atomic_kind_set, qs_kind_set, cell, super_cell, cell_ref, use_ref_cell, kpoints, dft_control, mos, sab_orb, sab_all, qmmm, qmmm_periodic, sac_ae, sac_ppl, sac_lri, sap_ppnl, sab_vdw, sab_scp, sap_oce, sab_lrc, sab_se, sab_xtbe, sab_tbe, sab_core, sab_xb, sab_xtb_pp, sab_xtb_nonbond, sab_almo, sab_kp, sab_kp_nosym, particle_set, energy, force, matrix_h, matrix_h_im, matrix_ks, matrix_ks_im, matrix_vxc, run_rtp, rtp, matrix_h_kp, matrix_h_im_kp, matrix_ks_kp, matrix_ks_im_kp, matrix_vxc_kp, kinetic_kp, matrix_s_kp, matrix_w_kp, matrix_s_ri_aux_kp, matrix_s, matrix_s_ri_aux, matrix_w, matrix_p_mp2, matrix_p_mp2_admm, rho, rho_xc, pw_env, ewald_env, ewald_pw, active_space, mpools, input, para_env, blacs_env, scf_control, rel_control, kinetic, qs_charges, vppl, rho_core, rho_nlcc, rho_nlcc_g, ks_env, ks_qmmm_env, wf_history, scf_env, local_particles, local_molecules, distribution_2d, dbcsr_dist, molecule_kind_set, molecule_set, subsys, cp_subsys, oce, local_rho_set, rho_atom_set, task_list, task_list_soft, rho0_atom_set, rho0_mpole, rhoz_set, ecoul_1c, rho0_s_rs, rho0_s_gs, do_kpoints, has_unit_metric, requires_mo_derivs, mo_derivs, mo_loc_history, nkind, natom, nelectron_total, nelectron_spin, efield, neighbor_list_id, linres_control, xas_env, virial, cp_ddapc_env, cp_ddapc_ewald, outer_scf_history, outer_scf_ihistory, x_data, et_coupling, dftb_potential, results, se_taper, se_store_int_env, se_nddo_mpole, se_nonbond_env, admm_env, lri_env, lri_density, exstate_env, ec_env, harris_env, dispersion_env, gcp_env, vee, rho_external, external_vxc, mask, mp2_env, bs_env, kg_env, wanniercentres, atprop, ls_scf_env, do_transport, transport_env, v_hartree_rspace, s_mstruct_changed, rho_changed, potential_changed, forces_up_to_date, mscfg_env, almo_scf_env, gradient_history, variable_history, embed_pot, spin_embed_pot, polar_env, mos_last_converged, eeq, rhs)
Get the QUICKSTEP environment.
Definition qs_environment_types.F:514
qs_scf_post_gpw
Does all kind of post scf calculations for GPW/GAPW.
Definition qs_scf_post_gpw.F:15
qs_scf_post_gpw::scf_post_calculation_gpw
subroutine, public scf_post_calculation_gpw(qs_env, wf_type, do_mp2)
collects possible post - scf calculations and prints info / computes properties.
Definition qs_scf_post_gpw.F:238
reference_manager
provides a uniform framework to add references to CP2K cite and output these
Definition reference_manager.F:25
reference_manager::cite_reference
subroutine, public cite_reference(key)
marks a given reference as cited.
Definition reference_manager.F:85
reftraj_types
initialization of the reftraj structure used to analyse previously generated trajectories
Definition reftraj_types.F:15
reftraj_types::create_reftraj
subroutine, public create_reftraj(reftraj, reftraj_section, para_env)
...
Definition reftraj_types.F:89
reftraj_util
Initialize the analysis of trajectories to be done by activating the REFTRAJ ensemble.
Definition reftraj_util.F:15
reftraj_util::initialize_reftraj
subroutine, public initialize_reftraj(reftraj, reftraj_section, md_env)
...
Definition reftraj_util.F:82
simpar_methods
Methods for storing MD parameters type.
Definition simpar_methods.F:14
simpar_methods::read_md_section
subroutine, public read_md_section(simpar, motion_section, md_section)
Reads the MD section and setup the simulation parameters type.
Definition simpar_methods.F:64
simpar_types
Type for storing MD parameters.
Definition simpar_types.F:14
simpar_types::release_simpar_type
subroutine, public release_simpar_type(simpar)
Releases the simulation parameters type.
Definition simpar_types.F:118
simpar_types::create_simpar_type
subroutine, public create_simpar_type(simpar)
Creates the simulation parameters type.
Definition simpar_types.F:106
string_utilities
Utilities for string manipulations.
Definition string_utilities.F:16
string_utilities::str_comp
elemental logical function, public str_comp(str1, str2)
...
Definition string_utilities.F:3403
tamc_run
Perform a temperature accelarated hybrid monte carlo (TAHMC) run using QUICKSTEP.
Definition tamc_run.F:14
tamc_run::qs_tamc
subroutine, public qs_tamc(force_env, globenv, averages)
Driver routine for TAHMC.
Definition tamc_run.F:147
thermal_region_types
Thermal regions type: to initialize and control the temperature of different regions.
Definition thermal_region_types.F:15
thermal_region_utils
Setup of regions with different temperature.
Definition thermal_region_utils.F:17
thermal_region_utils::create_thermal_regions
subroutine, public create_thermal_regions(thermal_regions, md_section, simpar, force_env)
create thermal_regions
Definition thermal_region_utils.F:78
thermostat_methods
Methods for Thermostats.
Definition thermostat_methods.F:12
thermostat_methods::create_thermostats
subroutine, public create_thermostats(thermostats, md_section, force_env, simpar, para_env, globenv, global_section)
...
Definition thermostat_methods.F:113
thermostat_types
Thermostat structure: module containing thermostat available for MD.
Definition thermostat_types.F:12
virial_methods
Definition virial_methods.F:12
virial_methods::virial_evaluate
subroutine, public virial_evaluate(atomic_kind_set, particle_set, local_particles, virial, igroup)
Computes the kinetic part of the pressure tensor and updates the full VIRIAL (PV)
Definition virial_methods.F:83
virial_types
Definition virial_types.F:13
wiener_process
Handling of the Wiener process currently employed in turn of the Langevin dynamics.
Definition wiener_process.F:15
wiener_process::create_wiener_process
subroutine, public create_wiener_process(md_env)
Create a Wiener process for Langevin dynamics and initialize an independent random number generator f...
Definition wiener_process.F:64
wiener_process::create_wiener_process_cv
subroutine, public create_wiener_process_cv(meta_env)
Create a Wiener process for Langevin dynamics used for metadynamics and initialize an independent ran...
Definition wiener_process.F:209
atomic_kind_list_types::atomic_kind_list_type
represent a list of objects
Definition atomic_kind_list_types.F:45
atomic_kind_types::atomic_kind_type
Provides all information about an atomic kind.
Definition atomic_kind_types.F:45
averages_types::average_quantities_type
Definition averages_types.F:38
barostat_types::barostat_type
Definition barostat_types.F:52
cell_types::cell_type
Type defining parameters related to the simulation cell.
Definition cell_types.F:55
colvar_types::colvar_p_type
Definition colvar_types.F:383
cp_log_handling::cp_logger_type
type of a logger, at the moment it contains just a print level starting at which level it should be l...
Definition cp_log_handling.F:140
cp_subsys_types::cp_subsys_type
represents a system: atoms, molecules, their pos,vel,...
Definition cp_subsys_types.F:89
distribution_1d_types::distribution_1d_type
structure to store local (to a processor) ordered lists of integers.
Definition distribution_1d_types.F:62
force_env_types::force_env_type
wrapper to abstract the force evaluation of the various methods
Definition force_env_types.F:145
free_energy_types::free_energy_type
Definition free_energy_types.F:64
global_types::global_environment_type
contains the initially parsed file and the initial parallel environment
Definition global_types.F:66
input_section_types::section_vals_type
stores the values of a section
Definition input_section_types.F:127
mc_environment_types::mc_environment_type
Definition mc_environment_types.F:23
mc_types::mc_averages_type
Definition mc_types.F:190
mc_types::mc_ekin_type
Definition mc_types.F:150
mc_types::mc_moves_type
Definition mc_types.F:204
mc_types::mc_simpar_type
Definition mc_types.F:81
md_ener_types::md_ener_type
Definition md_ener_types.F:22
md_environment_types::md_environment_type
Definition md_environment_types.F:53
message_passing::mp_comm_type
Definition message_passing.F:189
message_passing::mp_para_env_type
stores all the informations relevant to an mpi environment
Definition message_passing.F:763
metadynamics_types::meta_env_type
defines meta_env type
Definition metadynamics_types.F:95
metadynamics_types::metavar_type
defines types for COLVAR used in the metadynamics
Definition metadynamics_types.F:69
molecule_kind_list_types::molecule_kind_list_type
represent a list of objects
Definition molecule_kind_list_types.F:45
molecule_kind_types::molecule_kind_type
Definition molecule_kind_types.F:161
molecule_list_types::molecule_list_type
represent a list of objects
Definition molecule_list_types.F:46
molecule_types::global_constraint_type
Definition molecule_types.F:93
molecule_types::molecule_type
Definition molecule_types.F:110
parallel_rng_types::rng_stream_type
Definition parallel_rng_types.F:157
particle_list_types::particle_list_type
represent a list of objects
Definition particle_list_types.F:46
particle_types::particle_type
Definition particle_types.F:35
reftraj_types::reftraj_type
Definition reftraj_types.F:67
simpar_types::simpar_type
Simulation parameter type for molecular dynamics.
Definition simpar_types.F:30
thermal_region_types::thermal_regions_type
Definition thermal_region_types.F:29
thermostat_types::thermostats_type
Define thermostat types.
Definition thermostat_types.F:61
virial_types::virial_type
Definition virial_types.F:26