98#include "./base/base_uses.f90"
103 CHARACTER(len=*),
PARAMETER,
PRIVATE :: moduleN =
'colvar_methods'
104 REAL(KIND=
dp),
PRIVATE,
PARAMETER :: tolerance_acos = 1.0e-5_dp
122 RECURSIVE SUBROUTINE colvar_read(colvar, icol, colvar_section, para_env)
124 INTEGER,
INTENT(IN) :: icol
128 CHARACTER(len=*),
PARAMETER :: routinen =
'colvar_read'
130 CHARACTER(LEN=3) :: fmid
131 CHARACTER(LEN=7) :: tag, tag_comp, tag_comp1, tag_comp2
132 CHARACTER(LEN=default_path_length) :: path_function
133 CHARACTER(LEN=default_string_length) :: tmpstr, tmpstr2
134 CHARACTER(LEN=default_string_length), &
135 DIMENSION(:),
POINTER :: c_kinds, my_par
136 INTEGER :: handle, i, iatm, icomponent, iend, &
137 ifunc, ii, isize, istart, iw, iw1, j, &
138 k, kk, n_var, n_var_k, ncol, ndim, &
140 INTEGER,
DIMENSION(:),
POINTER :: iatms
141 INTEGER,
DIMENSION(:, :),
POINTER :: p_bounds
142 LOGICAL :: check, use_mixed_energy
143 LOGICAL,
DIMENSION(26) :: my_subsection
144 REAL(
dp),
DIMENSION(:),
POINTER :: s1, wei, weights
145 REAL(
dp),
DIMENSION(:, :),
POINTER :: p_range, s1v
146 REAL(kind=
dp),
DIMENSION(1) :: my_val
147 REAL(kind=
dp),
DIMENSION(:),
POINTER :: g_range, grid_point, grid_sp, my_vals, &
153 TYPE(
section_vals_type),
POINTER :: acid_hyd_dist_section, acid_hyd_shell_section, &
154 angle_section, colvar_subsection, combine_section, coordination_section, dfunct_section, &
155 distance_from_path_section, distance_section, frame_section, gyration_section, &
156 hbp_section, hydronium_dist_section, hydronium_shell_section, mindist_section, &
157 path_section, plane_dist_section, plane_plane_angle_section, plane_sections, &
158 point_section, population_section, qparm_section, reaction_path_section, &
159 ring_puckering_section, rmsd_section, rotation_section, torsion_section, u_section, &
160 wc_section, wrk_section
163 CALL timeset(routinen, handle)
164 NULLIFY (logger, c_kinds, iatms)
166 my_subsection = .false.
174 plane_plane_angle_section &
181 acid_hyd_shell_section &
184 can_return_null=.true.)
185 distance_from_path_section &
187 i_rep_section=icol, can_return_null=.true.)
189 can_return_null=.true.)
198 ring_puckering_section &
212 IF (
ASSOCIATED(reaction_path_section))
THEN
214 explicit=my_subsection(10))
216 IF (
ASSOCIATED(distance_from_path_section))
THEN
218 explicit=my_subsection(16))
220 IF (
ASSOCIATED(combine_section))
THEN
225 explicit=my_subsection(13))
234 explicit=my_subsection(22))
241 cpassert(count(my_subsection) == 1)
242 cpassert(.NOT.
ASSOCIATED(colvar))
244 IF (my_subsection(1))
THEN
246 wrk_section => distance_section
248 CALL colvar_check_points(colvar, distance_section)
250 colvar%dist_param%i_at = iatms(1)
251 colvar%dist_param%j_at = iatms(2)
254 ELSE IF (my_subsection(2))
THEN
256 wrk_section => angle_section
258 CALL colvar_check_points(colvar, angle_section)
260 colvar%angle_param%i_at_angle = iatms
261 ELSE IF (my_subsection(3))
THEN
263 wrk_section => torsion_section
265 CALL colvar_check_points(colvar, torsion_section)
267 colvar%torsion_param%i_at_tors = iatms
268 colvar%torsion_param%o0 = 0.0_dp
269 ELSE IF (my_subsection(4))
THEN
271 wrk_section => coordination_section
273 CALL colvar_check_points(colvar, coordination_section)
274 NULLIFY (colvar%coord_param%i_at_from, colvar%coord_param%c_kinds_from)
275 NULLIFY (colvar%coord_param%i_at_to, colvar%coord_param%c_kinds_to)
276 NULLIFY (colvar%coord_param%i_at_to_b, colvar%coord_param%c_kinds_to_b)
284 CALL reallocate(colvar%coord_param%i_at_from, 1, ndim +
SIZE(iatms))
285 colvar%coord_param%i_at_from(ndim + 1:ndim +
SIZE(iatms)) = iatms
286 ndim = ndim +
SIZE(iatms)
288 colvar%coord_param%n_atoms_from = ndim
289 colvar%coord_param%use_kinds_from = .false.
296 CALL reallocate(colvar%coord_param%c_kinds_from, 1, ndim +
SIZE(c_kinds))
297 colvar%coord_param%c_kinds_from(ndim + 1:ndim +
SIZE(c_kinds)) = c_kinds
298 ndim = ndim +
SIZE(c_kinds)
300 colvar%coord_param%n_atoms_from = 0
301 colvar%coord_param%use_kinds_from = .true.
304 CALL uppercase(colvar%coord_param%c_kinds_from(k))
314 CALL reallocate(colvar%coord_param%i_at_to, 1, ndim +
SIZE(iatms))
315 colvar%coord_param%i_at_to(ndim + 1:ndim +
SIZE(iatms)) = iatms
316 ndim = ndim +
SIZE(iatms)
318 colvar%coord_param%n_atoms_to = ndim
319 colvar%coord_param%use_kinds_to = .false.
326 CALL reallocate(colvar%coord_param%c_kinds_to, 1, ndim +
SIZE(c_kinds))
327 colvar%coord_param%c_kinds_to(ndim + 1:ndim +
SIZE(c_kinds)) = c_kinds
328 ndim = ndim +
SIZE(c_kinds)
330 colvar%coord_param%n_atoms_to = 0
331 colvar%coord_param%use_kinds_to = .true.
334 CALL uppercase(colvar%coord_param%c_kinds_to(k))
345 IF (n_var /= 0 .OR. n_var_k /= 0)
THEN
346 colvar%coord_param%do_chain = .true.
351 CALL reallocate(colvar%coord_param%i_at_to_b, 1, ndim +
SIZE(iatms))
352 colvar%coord_param%i_at_to_b(ndim + 1:ndim +
SIZE(iatms)) = iatms
353 ndim = ndim +
SIZE(iatms)
355 colvar%coord_param%n_atoms_to_b = ndim
356 colvar%coord_param%use_kinds_to_b = .false.
360 cpassert(n_var_k > 0)
363 CALL reallocate(colvar%coord_param%c_kinds_to_b, 1, ndim +
SIZE(c_kinds))
364 colvar%coord_param%c_kinds_to_b(ndim + 1:ndim +
SIZE(c_kinds)) = c_kinds
365 ndim = ndim +
SIZE(c_kinds)
367 colvar%coord_param%n_atoms_to_b = 0
368 colvar%coord_param%use_kinds_to_b = .true.
371 CALL uppercase(colvar%coord_param%c_kinds_to_b(k))
379 colvar%coord_param%do_chain = .false.
380 colvar%coord_param%n_atoms_to_b = 0
381 colvar%coord_param%use_kinds_to_b = .false.
382 NULLIFY (colvar%coord_param%i_at_to_b)
383 NULLIFY (colvar%coord_param%c_kinds_to_b)
384 colvar%coord_param%nncrd_b = 0
385 colvar%coord_param%ndcrd_b = 0
386 colvar%coord_param%r_0_b = 0._dp
389 ELSE IF (my_subsection(5))
THEN
391 wrk_section => plane_dist_section
393 CALL colvar_check_points(colvar, plane_dist_section)
395 cpassert(
SIZE(iatms) == 3)
396 colvar%plane_distance_param%plane = iatms
398 colvar%plane_distance_param%point = iatm
400 ELSE IF (my_subsection(6))
THEN
402 wrk_section => rotation_section
404 CALL colvar_check_points(colvar, rotation_section)
405 CALL section_vals_val_get(rotation_section,
"P1_BOND1", i_val=colvar%rotation_param%i_at1_bond1)
406 CALL section_vals_val_get(rotation_section,
"P2_BOND1", i_val=colvar%rotation_param%i_at2_bond1)
407 CALL section_vals_val_get(rotation_section,
"P1_BOND2", i_val=colvar%rotation_param%i_at1_bond2)
408 CALL section_vals_val_get(rotation_section,
"P2_BOND2", i_val=colvar%rotation_param%i_at2_bond2)
409 ELSE IF (my_subsection(7))
THEN
411 wrk_section => dfunct_section
413 CALL colvar_check_points(colvar, dfunct_section)
415 colvar%dfunct_param%i_at_dfunct = iatms
418 ELSE IF (my_subsection(8))
THEN
420 wrk_section => qparm_section
422 CALL colvar_check_points(colvar, qparm_section)
425 CALL section_vals_val_get(qparm_section,
"INCLUDE_IMAGES", l_val=colvar%qparm_param%include_images)
428 NULLIFY (colvar%qparm_param%i_at_from)
429 NULLIFY (colvar%qparm_param%i_at_to)
434 CALL reallocate(colvar%qparm_param%i_at_from, 1, ndim +
SIZE(iatms))
435 colvar%qparm_param%i_at_from(ndim + 1:ndim +
SIZE(iatms)) = iatms
436 ndim = ndim +
SIZE(iatms)
438 colvar%qparm_param%n_atoms_from = ndim
444 CALL reallocate(colvar%qparm_param%i_at_to, 1, ndim +
SIZE(iatms))
445 colvar%qparm_param%i_at_to(ndim + 1:ndim +
SIZE(iatms)) = iatms
446 ndim = ndim +
SIZE(iatms)
448 colvar%qparm_param%n_atoms_to = ndim
449 ELSE IF (my_subsection(9))
THEN
452 NULLIFY (colvar%hydronium_shell_param%i_oxygens)
453 NULLIFY (colvar%hydronium_shell_param%i_hydrogens)
455 colvar%hydronium_shell_param%n_oxygens, &
456 colvar%hydronium_shell_param%n_hydrogens, &
457 colvar%hydronium_shell_param%i_oxygens, &
458 colvar%hydronium_shell_param%i_hydrogens)
459 ELSE IF (my_subsection(10) .OR. my_subsection(16))
THEN
461 IF (my_subsection(10))
THEN
462 path_section => reaction_path_section
466 ELSE IF (my_subsection(16))
THEN
467 path_section => distance_from_path_section
472 colvar%use_points = .false.
474 CALL section_vals_val_get(path_section,
"DISTANCES_RMSD", l_val=colvar%reaction_path_param%dist_rmsd)
476 IF (colvar%reaction_path_param%dist_rmsd .AND. colvar%reaction_path_param%rmsd)
THEN
477 cpabort(
"CV REACTION PATH: only one between DISTANCES_RMSD and RMSD can be used ")
479 IF (colvar%reaction_path_param%dist_rmsd .OR. colvar%reaction_path_param%rmsd)
THEN
480 NULLIFY (colvar%reaction_path_param%i_rmsd, colvar%reaction_path_param%r_ref)
484 colvar%reaction_path_param%nr_frames = nr_frame
485 CALL read_frames(frame_section, para_env, nr_frame, colvar%reaction_path_param%r_ref, &
486 colvar%reaction_path_param%n_components)
488 IF (colvar%reaction_path_param%subset ==
rmsd_all)
THEN
489 ALLOCATE (colvar%reaction_path_param%i_rmsd(colvar%reaction_path_param%n_components))
490 DO i = 1, colvar%reaction_path_param%n_components
491 colvar%reaction_path_param%i_rmsd(i) = i
493 ELSE IF (colvar%reaction_path_param%subset ==
rmsd_list)
THEN
501 CALL reallocate(colvar%reaction_path_param%i_rmsd, 1, ndim +
SIZE(iatms))
502 colvar%reaction_path_param%i_rmsd(ndim + 1:ndim +
SIZE(iatms)) = iatms
503 ndim = ndim +
SIZE(iatms)
505 colvar%reaction_path_param%n_components = ndim
507 cpabort(
"CV REACTION PATH: if SUBSET_TYPE=LIST a list of atoms needs to be provided ")
511 CALL section_vals_val_get(path_section,
"ALIGN_FRAMES", l_val=colvar%reaction_path_param%align_frames)
515 ALLOCATE (colvar%reaction_path_param%colvar_p(ncol))
518 NULLIFY (colvar%reaction_path_param%colvar_p(i)%colvar)
519 CALL colvar_read(colvar%reaction_path_param%colvar_p(i)%colvar, i, colvar_subsection, para_env)
522 cpabort(
"CV REACTION PATH: the number of CV to define the path must be >0 ")
524 colvar%reaction_path_param%n_components = ncol
527 CALL section_vals_val_get(path_section,
"STEP_SIZE", r_val=colvar%reaction_path_param%step_size)
528 iend = ceiling(max(range(1), range(2))/colvar%reaction_path_param%step_size)
529 istart = floor(min(range(1), range(2))/colvar%reaction_path_param%step_size)
530 colvar%reaction_path_param%function_bounds(1) = istart
531 colvar%reaction_path_param%function_bounds(2) = iend
532 colvar%reaction_path_param%nr_frames = 2
533 ALLOCATE (colvar%reaction_path_param%f_vals(ncol, istart:iend))
536 check = (ncol ==
SIZE(colvar%reaction_path_param%colvar_p))
541 CALL compress(path_function, full=.true.)
542 CALL parsef(i, trim(path_function), my_par)
544 my_val = real(j, kind=
dp)*colvar%reaction_path_param%step_size
545 colvar%reaction_path_param%f_vals(i, j) =
evalf(i, my_val)
551 "MAP", middle_name=fmid, extension=
".dat", file_status=
"REPLACE")
554 ALLOCATE (grid_sp(ncol))
559 cpassert(ncol ==
SIZE(grid_sp))
560 ALLOCATE (p_range(2, ncol))
561 ALLOCATE (p_bounds(2, ncol))
564 p_range(:, i) = g_range(:)
565 p_bounds(2, i) = ceiling(max(p_range(1, i), p_range(2, i))/grid_sp(i))
566 p_bounds(1, i) = floor(min(p_range(1, i), p_range(2, i))/grid_sp(i))
568 ALLOCATE (s1v(2, istart:iend))
570 ALLOCATE (grid_point(ncol))
572 kk = rec_eval_grid(iw1, ncol, colvar%reaction_path_param%f_vals, v_count, &
573 grid_point, grid_sp, colvar%reaction_path_param%step_size, istart, &
574 iend, s1v, s1, p_bounds, colvar%reaction_path_param%lambda, ifunc=ifunc, &
575 nconf=colvar%reaction_path_param%nr_frames)
578 DEALLOCATE (p_bounds)
581 DEALLOCATE (grid_point)
587 ELSE IF (my_subsection(11))
THEN
590 colvar%use_points = .false.
593 ALLOCATE (colvar%combine_cvs_param%colvar_p(ncol))
596 "PRINT%PROGRAM_RUN_INFO", extension=
".colvarLog")
598 WRITE (iw,
'( A )')
' '// &
599 '**********************************************************************'
600 WRITE (iw,
'( A,I8)')
' COLVARS| COLVAR INPUT INDEX: ', icol
601 WRITE (iw,
'( A,T49,4I8)')
' COLVARS| COMBINATION OF THE FOLLOWING COLVARS:'
604 "PRINT%PROGRAM_RUN_INFO")
607 NULLIFY (colvar%combine_cvs_param%colvar_p(i)%colvar)
608 CALL colvar_read(colvar%combine_cvs_param%colvar_p(i)%colvar, i, colvar_subsection, para_env)
612 CALL compress(colvar%combine_cvs_param%function, full=.true.)
615 ALLOCATE (colvar%combine_cvs_param%variables(
SIZE(my_par)))
616 colvar%combine_cvs_param%variables = my_par
618 IF (
SIZE(my_par) /= ncol) &
619 CALL cp_abort(__location__, &
620 "Number of defined COLVAR for COMBINE_COLVAR is different from the "// &
621 "number of variables! It is not possible to define COLVARs in a COMBINE_COLVAR "// &
622 "and avoid their usage in the combininig function!")
624 ALLOCATE (colvar%combine_cvs_param%c_parameters(0))
627 isize =
SIZE(colvar%combine_cvs_param%c_parameters)
629 CALL reallocate(colvar%combine_cvs_param%c_parameters, 1, isize +
SIZE(my_par))
630 colvar%combine_cvs_param%c_parameters(isize + 1:isize +
SIZE(my_par)) = my_par
632 ALLOCATE (colvar%combine_cvs_param%v_parameters(0))
635 isize =
SIZE(colvar%combine_cvs_param%v_parameters)
637 CALL reallocate(colvar%combine_cvs_param%v_parameters, 1, isize +
SIZE(my_vals))
638 colvar%combine_cvs_param%v_parameters(isize + 1:isize +
SIZE(my_vals)) = my_vals
643 ELSE IF (my_subsection(12))
THEN
645 wrk_section => population_section
647 CALL colvar_check_points(colvar, population_section)
649 NULLIFY (colvar%population_param%i_at_from, colvar%population_param%c_kinds_from)
650 NULLIFY (colvar%population_param%i_at_to, colvar%population_param%c_kinds_to)
659 CALL reallocate(colvar%population_param%i_at_from, 1, ndim +
SIZE(iatms))
660 colvar%population_param%i_at_from(ndim + 1:ndim +
SIZE(iatms)) = iatms
661 ndim = ndim +
SIZE(iatms)
663 colvar%population_param%n_atoms_from = ndim
664 colvar%population_param%use_kinds_from = .false.
671 CALL reallocate(colvar%population_param%c_kinds_from, 1, ndim +
SIZE(c_kinds))
672 colvar%population_param%c_kinds_from(ndim + 1:ndim +
SIZE(c_kinds)) = c_kinds
673 ndim = ndim +
SIZE(c_kinds)
675 colvar%population_param%n_atoms_from = 0
676 colvar%population_param%use_kinds_from = .true.
679 CALL uppercase(colvar%population_param%c_kinds_from(k))
689 CALL reallocate(colvar%population_param%i_at_to, 1, ndim +
SIZE(iatms))
690 colvar%population_param%i_at_to(ndim + 1:ndim +
SIZE(iatms)) = iatms
691 ndim = ndim +
SIZE(iatms)
693 colvar%population_param%n_atoms_to = ndim
694 colvar%population_param%use_kinds_to = .false.
701 CALL reallocate(colvar%population_param%c_kinds_to, 1, ndim +
SIZE(c_kinds))
702 colvar%population_param%c_kinds_to(ndim + 1:ndim +
SIZE(c_kinds)) = c_kinds
703 ndim = ndim +
SIZE(c_kinds)
705 colvar%population_param%n_atoms_to = 0
706 colvar%population_param%use_kinds_to = .true.
709 CALL uppercase(colvar%population_param%c_kinds_to(k))
718 ELSE IF (my_subsection(13))
THEN
720 wrk_section => plane_plane_angle_section
722 CALL colvar_check_points(colvar, plane_plane_angle_section)
727 cpabort(
"PLANE_PLANE_ANGLE Colvar section: Two PLANE sections must be provided!")
730 i_val=colvar%plane_plane_angle_param%plane1%type_of_def)
731 IF (colvar%plane_plane_angle_param%plane1%type_of_def ==
plane_def_vec)
THEN
734 colvar%plane_plane_angle_param%plane1%normal_vec = s1
738 colvar%plane_plane_angle_param%plane1%points = iatms
743 i_val=colvar%plane_plane_angle_param%plane2%type_of_def)
744 IF (colvar%plane_plane_angle_param%plane2%type_of_def ==
plane_def_vec)
THEN
747 colvar%plane_plane_angle_param%plane2%normal_vec = s1
751 colvar%plane_plane_angle_param%plane2%points = iatms
753 ELSE IF (my_subsection(14))
THEN
755 wrk_section => gyration_section
757 CALL colvar_check_points(colvar, gyration_section)
759 NULLIFY (colvar%gyration_param%i_at, colvar%gyration_param%c_kinds)
768 CALL reallocate(colvar%gyration_param%i_at, 1, ndim +
SIZE(iatms))
769 colvar%gyration_param%i_at(ndim + 1:ndim +
SIZE(iatms)) = iatms
770 ndim = ndim +
SIZE(iatms)
772 colvar%gyration_param%n_atoms = ndim
773 colvar%gyration_param%use_kinds = .false.
780 CALL reallocate(colvar%gyration_param%c_kinds, 1, ndim +
SIZE(c_kinds))
781 colvar%gyration_param%c_kinds(ndim + 1:ndim +
SIZE(c_kinds)) = c_kinds
782 ndim = ndim +
SIZE(c_kinds)
784 colvar%gyration_param%n_atoms = 0
785 colvar%gyration_param%use_kinds = .true.
788 CALL uppercase(colvar%gyration_param%c_kinds(k))
791 ELSE IF (my_subsection(15))
THEN
793 wrk_section => rmsd_section
796 NULLIFY (colvar%rmsd_param%i_rmsd, colvar%rmsd_param%r_ref, colvar%rmsd_param%weights)
801 colvar%rmsd_param%nr_frames = nr_frame
803 cpassert(nr_frame >= 1 .AND. nr_frame <= 2)
804 CALL read_frames(frame_section, para_env, nr_frame, colvar%rmsd_param%r_ref, &
805 colvar%rmsd_param%n_atoms)
806 ALLOCATE (colvar%rmsd_param%weights(colvar%rmsd_param%n_atoms))
807 colvar%rmsd_param%weights = 0.0_dp
809 IF (colvar%rmsd_param%subset ==
rmsd_all)
THEN
810 ALLOCATE (colvar%rmsd_param%i_rmsd(colvar%rmsd_param%n_atoms))
811 DO i = 1, colvar%rmsd_param%n_atoms
812 colvar%rmsd_param%i_rmsd(i) = i
814 ELSE IF (colvar%rmsd_param%subset ==
rmsd_list)
THEN
822 CALL reallocate(colvar%rmsd_param%i_rmsd, 1, ndim +
SIZE(iatms))
823 colvar%rmsd_param%i_rmsd(ndim + 1:ndim +
SIZE(iatms)) = iatms
824 ndim = ndim +
SIZE(iatms)
826 colvar%rmsd_param%n_atoms = ndim
828 cpabort(
"CV RMSD: if SUBSET_TYPE=LIST a list of atoms needs to be provided ")
837 CALL reallocate(colvar%rmsd_param%i_rmsd, 1, ndim +
SIZE(iatms))
838 colvar%rmsd_param%i_rmsd(ndim + 1:ndim +
SIZE(iatms)) = iatms
839 ndim = ndim +
SIZE(iatms)
841 colvar%rmsd_param%n_atoms = ndim
843 cpabort(
"CV RMSD: if SUBSET_TYPE=WEIGHT_LIST a list of atoms needs to be provided ")
852 weights(ndim + 1:ndim +
SIZE(wei)) = wei
853 ndim = ndim +
SIZE(wei)
855 IF (ndim /= colvar%rmsd_param%n_atoms) &
856 CALL cp_abort(__location__,
"CV RMSD: list of atoms and list of "// &
857 "weights need to contain same number of entries. ")
859 ii = colvar%rmsd_param%i_rmsd(i)
860 colvar%rmsd_param%weights(ii) = weights(i)
864 cpabort(
"CV RMSD: if SUBSET_TYPE=WEIGHT_LIST a list of weights need to be provided. ")
868 cpabort(
"CV RMSD: unknown SUBSET_TYPE.")
873 ELSE IF (my_subsection(17))
THEN
875 wrk_section => xyz_diag_section
877 CALL colvar_check_points(colvar, wrk_section)
881 CALL section_vals_val_get(wrk_section,
"ABSOLUTE_POSITION", l_val=colvar%xyz_diag_param%use_absolute_position)
882 colvar%xyz_diag_param%i_atom = iatm
883 colvar%xyz_diag_param%component = icomponent
884 ELSE IF (my_subsection(18))
THEN
886 wrk_section => xyz_outerdiag_section
888 CALL colvar_check_points(colvar, wrk_section)
890 colvar%xyz_outerdiag_param%i_atoms = iatms
892 colvar%xyz_outerdiag_param%components(1) = icomponent
894 colvar%xyz_outerdiag_param%components(2) = icomponent
896 ELSE IF (my_subsection(19))
THEN
898 wrk_section => u_section
901 CALL section_vals_get(colvar%u_param%mixed_energy_section, explicit=use_mixed_energy)
902 IF (.NOT. use_mixed_energy)
NULLIFY (colvar%u_param%mixed_energy_section)
903 ELSE IF (my_subsection(20))
THEN
905 wrk_section => wc_section
907 CALL colvar_check_points(colvar, wc_section)
911 colvar%Wc%ids = iatms
912 ELSE IF (my_subsection(21))
THEN
914 wrk_section => hbp_section
916 CALL colvar_check_points(colvar, hbp_section)
922 ALLOCATE (colvar%HBP%ids(colvar%HBP%nPoints, 3))
923 ALLOCATE (colvar%HBP%ewc(colvar%HBP%nPoints))
924 DO i = 1, colvar%HBP%nPoints
926 colvar%HBP%ids(i, :) = iatms
928 ELSE IF (my_subsection(22))
THEN
932 colvar%ring_puckering_param%nring =
SIZE(iatms)
933 ALLOCATE (colvar%ring_puckering_param%atoms(
SIZE(iatms)))
934 colvar%ring_puckering_param%atoms = iatms
936 i_val=colvar%ring_puckering_param%iq)
938 ndim = colvar%ring_puckering_param%nring
940 cpabort(
"CV Ring Puckering: Ring size has to be 4 or larger. ")
941 ii = colvar%ring_puckering_param%iq
942 IF (abs(ii) == 1 .OR. ii < -(ndim - 1)/2 .OR. ii > ndim/2) &
943 cpabort(
"CV Ring Puckering: Invalid coordinate number.")
944 ELSE IF (my_subsection(23))
THEN
946 wrk_section => mindist_section
948 CALL colvar_check_points(colvar, mindist_section)
949 NULLIFY (colvar%mindist_param%i_dist_from, colvar%mindist_param%i_coord_from, &
950 colvar%mindist_param%k_coord_from, colvar%mindist_param%i_coord_to, &
951 colvar%mindist_param%k_coord_to)
953 colvar%mindist_param%n_dist_from =
SIZE(iatms)
954 ALLOCATE (colvar%mindist_param%i_dist_from(
SIZE(iatms)))
955 colvar%mindist_param%i_dist_from = iatms
962 CALL reallocate(colvar%mindist_param%i_coord_from, 1, ndim +
SIZE(iatms))
963 colvar%mindist_param%i_coord_from(ndim + 1:ndim +
SIZE(iatms)) = iatms
964 ndim = ndim +
SIZE(iatms)
966 colvar%mindist_param%n_coord_from = ndim
967 colvar%mindist_param%use_kinds_from = .false.
974 CALL reallocate(colvar%mindist_param%k_coord_from, 1, ndim +
SIZE(c_kinds))
975 colvar%mindist_param%k_coord_from(ndim + 1:ndim +
SIZE(c_kinds)) = c_kinds
976 ndim = ndim +
SIZE(c_kinds)
978 colvar%mindist_param%n_coord_from = 0
979 colvar%mindist_param%use_kinds_from = .true.
982 CALL uppercase(colvar%mindist_param%k_coord_from(k))
992 CALL reallocate(colvar%mindist_param%i_coord_to, 1, ndim +
SIZE(iatms))
993 colvar%mindist_param%i_coord_to(ndim + 1:ndim +
SIZE(iatms)) = iatms
994 ndim = ndim +
SIZE(iatms)
996 colvar%mindist_param%n_coord_to = ndim
997 colvar%mindist_param%use_kinds_to = .false.
1004 CALL reallocate(colvar%mindist_param%k_coord_to, 1, ndim +
SIZE(c_kinds))
1005 colvar%mindist_param%k_coord_to(ndim + 1:ndim +
SIZE(c_kinds)) = c_kinds
1006 ndim = ndim +
SIZE(c_kinds)
1008 colvar%mindist_param%n_coord_to = 0
1009 colvar%mindist_param%use_kinds_to = .true.
1012 CALL uppercase(colvar%mindist_param%k_coord_to(k))
1021 ELSE IF (my_subsection(24))
THEN
1024 NULLIFY (colvar%acid_hyd_dist_param%i_oxygens_water)
1025 NULLIFY (colvar%acid_hyd_dist_param%i_oxygens_acid)
1026 NULLIFY (colvar%acid_hyd_dist_param%i_hydrogens)
1028 colvar%acid_hyd_dist_param%n_oxygens_water, &
1029 colvar%acid_hyd_dist_param%n_oxygens_acid, &
1030 colvar%acid_hyd_dist_param%n_hydrogens, &
1031 colvar%acid_hyd_dist_param%i_oxygens_water, &
1032 colvar%acid_hyd_dist_param%i_oxygens_acid, &
1033 colvar%acid_hyd_dist_param%i_hydrogens)
1034 ELSE IF (my_subsection(25))
THEN
1037 NULLIFY (colvar%acid_hyd_shell_param%i_oxygens_water)
1038 NULLIFY (colvar%acid_hyd_shell_param%i_oxygens_acid)
1039 NULLIFY (colvar%acid_hyd_shell_param%i_hydrogens)
1041 colvar%acid_hyd_shell_param%n_oxygens_water, &
1042 colvar%acid_hyd_shell_param%n_oxygens_acid, &
1043 colvar%acid_hyd_shell_param%n_hydrogens, &
1044 colvar%acid_hyd_shell_param%i_oxygens_water, &
1045 colvar%acid_hyd_shell_param%i_oxygens_acid, &
1046 colvar%acid_hyd_shell_param%i_hydrogens)
1047 ELSE IF (my_subsection(26))
THEN
1050 NULLIFY (colvar%hydronium_dist_param%i_oxygens)
1051 NULLIFY (colvar%hydronium_dist_param%i_hydrogens)
1053 colvar%hydronium_dist_param%n_oxygens, &
1054 colvar%hydronium_dist_param%n_hydrogens, &
1055 colvar%hydronium_dist_param%i_oxygens, &
1056 colvar%hydronium_dist_param%i_hydrogens)
1061 "PRINT%PROGRAM_RUN_INFO", extension=
".colvarLog")
1064 IF (colvar%use_points) tag =
"POINTS:"
1067 WRITE (iw,
'( A )')
' '// &
1068 '----------------------------------------------------------------------'
1069 WRITE (iw,
'( A,I8)')
' COLVARS| COLVAR INPUT INDEX: ', icol
1072 SELECT CASE (colvar%type_id)
1074 WRITE (iw,
'( A,T57,3I8)')
' COLVARS| ANGLE >>> '//tag, &
1075 colvar%angle_param%i_at_angle
1077 WRITE (iw,
'( A,T49,4I8)')
' COLVARS| DISTANCE DIFFERENCE >>> '//tag, &
1078 colvar%dfunct_param%i_at_dfunct
1080 WRITE (iw,
'( A,T57,3I8)')
' COLVARS| PLANE DISTANCE - PLANE >>> '//tag, &
1081 colvar%plane_distance_param%plane
1082 WRITE (iw,
'( A,T73,1I8)')
' COLVARS| PLANE DISTANCE - POINT >>> '//tag, &
1083 colvar%plane_distance_param%point
1085 IF (colvar%plane_plane_angle_param%plane1%type_of_def ==
plane_def_atoms)
THEN
1086 WRITE (iw,
'( A,T57,3I8)')
' COLVARS| PLANE-PLANE ANGLE - PLANE 1 (ATOMS) >>> '//tag, &
1087 colvar%plane_plane_angle_param%plane1%points
1089 WRITE (iw,
'( A,T57,3F8.3)')
' COLVARS| PLANE-PLANE ANGLE - PLANE 1 (VECTOR) >>> '//tag, &
1090 colvar%plane_plane_angle_param%plane1%normal_vec
1093 IF (colvar%plane_plane_angle_param%plane2%type_of_def ==
plane_def_atoms)
THEN
1094 WRITE (iw,
'( A,T57,3I8)')
' COLVARS| PLANE-PLANE ANGLE - PLANE 1 (ATOMS) >>> '//tag, &
1095 colvar%plane_plane_angle_param%plane2%points
1097 WRITE (iw,
'( A,T57,3F8.3)')
' COLVARS| PLANE-PLANE ANGLE - PLANE 1 (VECTOR) >>> '//tag, &
1098 colvar%plane_plane_angle_param%plane2%normal_vec
1101 WRITE (iw,
'( A,T49,4I8)')
' COLVARS| TORSION >>> '//tag, &
1102 colvar%torsion_param%i_at_tors
1104 WRITE (iw,
'( A,T65,2I8)')
' COLVARS| BOND >>> '//tag, &
1105 colvar%dist_param%i_at, colvar%dist_param%j_at
1107 IF (colvar%coord_param%do_chain)
THEN
1108 WRITE (iw,
'( A)')
' COLVARS| COORDINATION CHAIN FC(from->to)*FC(to->to_B)>> '
1110 IF (colvar%coord_param%use_kinds_from)
THEN
1111 WRITE (iw,
'( A,T71,A10)') (
' COLVARS| COORDINATION >>> FROM KINDS', &
1112 adjustr(colvar%coord_param%c_kinds_from(kk) (1:10)), &
1113 kk=1,
SIZE(colvar%coord_param%c_kinds_from))
1115 WRITE (iw,
'( A,T71,I10)') (
' COLVARS| COORDINATION >>> FROM '//tag, &
1116 colvar%coord_param%i_at_from(kk), &
1117 kk=1,
SIZE(colvar%coord_param%i_at_from))
1119 IF (colvar%coord_param%use_kinds_to)
THEN
1120 WRITE (iw,
'( A,T71,A10)') (
' COLVARS| COORDINATION >>> TO KINDS', &
1121 adjustr(colvar%coord_param%c_kinds_to(kk) (1:10)), &
1122 kk=1,
SIZE(colvar%coord_param%c_kinds_to))
1124 WRITE (iw,
'( A,T71,I10)') (
' COLVARS| COORDINATION >>> TO '//tag, &
1125 colvar%coord_param%i_at_to(kk), &
1126 kk=1,
SIZE(colvar%coord_param%i_at_to))
1128 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| R0', colvar%coord_param%r_0
1129 WRITE (iw,
'( A,T71,I10)')
' COLVARS| NN', colvar%coord_param%nncrd
1130 WRITE (iw,
'( A,T71,I10)')
' COLVARS| ND', colvar%coord_param%ndcrd
1131 IF (colvar%coord_param%do_chain)
THEN
1132 IF (colvar%coord_param%use_kinds_to_b)
THEN
1133 WRITE (iw,
'( A,T71,A10)') (
' COLVARS| COORDINATION >>> TO KINDS B', &
1134 adjustr(colvar%coord_param%c_kinds_to_b(kk) (1:10)), &
1135 kk=1,
SIZE(colvar%coord_param%c_kinds_to_b))
1137 WRITE (iw,
'( A,T71,I10)') (
' COLVARS| COORDINATION >>> TO '//tag//
' B', &
1138 colvar%coord_param%i_at_to_b(kk), &
1139 kk=1,
SIZE(colvar%coord_param%i_at_to_b))
1141 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| R0 B', colvar%coord_param%r_0_b
1142 WRITE (iw,
'( A,T71,I10)')
' COLVARS| NN B', colvar%coord_param%nncrd_b
1143 WRITE (iw,
'( A,T71,I10)')
' COLVARS| ND B', colvar%coord_param%ndcrd_b
1146 IF (colvar%population_param%use_kinds_from)
THEN
1147 WRITE (iw,
'( A,T71,A10)') (
' COLVARS| POPULATION based on coordination >>> FROM KINDS', &
1148 adjustr(colvar%population_param%c_kinds_from(kk) (1:10)), &
1149 kk=1,
SIZE(colvar%population_param%c_kinds_from))
1151 WRITE (iw,
'( A,T71,I10)') (
' COLVARS| POPULATION based on coordination >>> FROM '//tag, &
1152 colvar%population_param%i_at_from(kk), &
1153 kk=1,
SIZE(colvar%population_param%i_at_from))
1155 IF (colvar%population_param%use_kinds_to)
THEN
1156 WRITE (iw,
'( A,T71,A10)') (
' COLVARS| POPULATION based on coordination >>> TO KINDS', &
1157 adjustr(colvar%population_param%c_kinds_to(kk) (1:10)), &
1158 kk=1,
SIZE(colvar%population_param%c_kinds_to))
1160 WRITE (iw,
'( A,T71,I10)') (
' COLVARS| POPULATION based on coordination >>> TO '//tag, &
1161 colvar%population_param%i_at_to(kk), &
1162 kk=1,
SIZE(colvar%population_param%i_at_to))
1164 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| R0', colvar%population_param%r_0
1165 WRITE (iw,
'( A,T71,I10)')
' COLVARS| NN', colvar%population_param%nncrd
1166 WRITE (iw,
'( A,T71,I10)')
' COLVARS| ND', colvar%population_param%ndcrd
1167 WRITE (iw,
'( A,T71,I10)')
' COLVARS| N0', colvar%population_param%n0
1168 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| SIGMA', colvar%population_param%sigma
1170 IF (colvar%gyration_param%use_kinds)
THEN
1171 WRITE (iw,
'( A,T71,A10)') (
' COLVARS| Gyration Radius >>> KINDS', &
1172 adjustr(colvar%gyration_param%c_kinds(kk) (1:10)), &
1173 kk=1,
SIZE(colvar%gyration_param%c_kinds))
1175 WRITE (iw,
'( A,T71,I10)') (
' COLVARS| Gyration Radius >>> ATOMS '//tag, &
1176 colvar%gyration_param%i_at(kk), &
1177 kk=1,
SIZE(colvar%gyration_param%i_at))
1180 WRITE (iw,
'( A,T71,I10)')
' COLVARS| BOND_ROTATION - POINT 1 LINE 1 >>> '//tag, &
1181 colvar%rotation_param%i_at1_bond1
1182 WRITE (iw,
'( A,T71,I10)')
' COLVARS| BOND_ROTATION - POINT 2 LINE 1 >>> '//tag, &
1183 colvar%rotation_param%i_at2_bond1
1184 WRITE (iw,
'( A,T71,I10)')
' COLVARS| BOND_ROTATION - POINT 1 LINE 2 >>> '//tag, &
1185 colvar%rotation_param%i_at1_bond2
1186 WRITE (iw,
'( A,T71,I10)')
' COLVARS| BOND_ROTATION - POINT 2 LINE 2 >>> '//tag, &
1187 colvar%rotation_param%i_at2_bond2
1189 WRITE (iw,
'( A,T71,I10)') (
' COLVARS| Q-PARM >>> FROM '//tag, &
1190 colvar%qparm_param%i_at_from(kk), &
1191 kk=1,
SIZE(colvar%qparm_param%i_at_from))
1192 WRITE (iw,
'( A,T71,I10)') (
' COLVARS| Q-PARM >>> TO '//tag, &
1193 colvar%qparm_param%i_at_to(kk), &
1194 kk=1,
SIZE(colvar%qparm_param%i_at_to))
1195 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| RCUT', colvar%qparm_param%rcut
1196 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| RSTART', colvar%qparm_param%rstart
1197 WRITE (iw,
'( A,T71,L10)')
' COLVARS| INCLUDE IMAGES', colvar%qparm_param%include_images
1199 WRITE (iw,
'( A,T71,I10)')
' COLVARS| L', colvar%qparm_param%l
1201 WRITE (iw,
'( A)')
' COLVARS| COMBINING FUNCTION : '// &
1202 trim(colvar%combine_cvs_param%function)
1203 WRITE (iw,
'( A)', advance=
"NO")
' COLVARS| VARIABLES : '
1204 DO i = 1,
SIZE(colvar%combine_cvs_param%variables)
1205 WRITE (iw,
'( A)', advance=
"NO") &
1206 trim(colvar%combine_cvs_param%variables(i))//
" "
1209 WRITE (iw,
'( A)')
' COLVARS| DEFINED PARAMETERS [label] [value]:'
1210 DO i = 1,
SIZE(colvar%combine_cvs_param%c_parameters)
1211 WRITE (iw,
'( A,A7,F9.3)')
' ', &
1212 trim(colvar%combine_cvs_param%c_parameters(i)), colvar%combine_cvs_param%v_parameters(i)
1214 WRITE (iw,
'( A,T71,G10.5)')
' COLVARS| ERROR ON DERIVATIVE EVALUATION', &
1215 colvar%combine_cvs_param%lerr
1216 WRITE (iw,
'( A,T71,G10.5)')
' COLVARS| DX', &
1217 colvar%combine_cvs_param%dx
1219 cpwarn(
"Description header for REACTION_PATH COLVAR missing!")
1221 cpwarn(
"Description header for REACTION_PATH COLVAR missing!")
1223 WRITE (iw,
'( A,T71,I10)')
' COLVARS| POH', colvar%hydronium_shell_param%poh
1224 WRITE (iw,
'( A,T71,I10)')
' COLVARS| QOH', colvar%hydronium_shell_param%qoh
1225 WRITE (iw,
'( A,T71,I10)')
' COLVARS| POO', colvar%hydronium_shell_param%poo
1226 WRITE (iw,
'( A,T71,I10)')
' COLVARS| QOO', colvar%hydronium_shell_param%qoo
1227 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| ROO', colvar%hydronium_shell_param%roo
1228 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| ROH', colvar%hydronium_shell_param%roh
1229 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| NH', colvar%hydronium_shell_param%nh
1230 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| LAMBDA', colvar%hydronium_shell_param%lambda
1232 WRITE (iw,
'( A,T71,I10)')
' COLVARS| POH', colvar%hydronium_dist_param%poh
1233 WRITE (iw,
'( A,T71,I10)')
' COLVARS| QOH', colvar%hydronium_dist_param%qoh
1234 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| ROH', colvar%hydronium_dist_param%roh
1235 WRITE (iw,
'( A,T71,I10)')
' COLVARS| PM', colvar%hydronium_dist_param%pm
1236 WRITE (iw,
'( A,T71,I10)')
' COLVARS| QM', colvar%hydronium_dist_param%qm
1237 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| NH', colvar%hydronium_dist_param%nh
1238 WRITE (iw,
'( A,T71,I10)')
' COLVARS| PF', colvar%hydronium_dist_param%pf
1239 WRITE (iw,
'( A,T71,I10)')
' COLVARS| QF', colvar%hydronium_dist_param%qf
1240 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| NN', colvar%hydronium_dist_param%nn
1242 WRITE (iw,
'( A,T71,I10)')
' COLVARS| PAOH', colvar%acid_hyd_dist_param%paoh
1243 WRITE (iw,
'( A,T71,I10)')
' COLVARS| QAOH', colvar%acid_hyd_dist_param%qaoh
1244 WRITE (iw,
'( A,T71,I10)')
' COLVARS| PWOH', colvar%acid_hyd_dist_param%pwoh
1245 WRITE (iw,
'( A,T71,I10)')
' COLVARS| QWOH', colvar%acid_hyd_dist_param%qwoh
1246 WRITE (iw,
'( A,T71,I10)')
' COLVARS| PCUT', colvar%acid_hyd_dist_param%pcut
1247 WRITE (iw,
'( A,T71,I10)')
' COLVARS| QCUT', colvar%acid_hyd_dist_param%qcut
1248 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| RAOH', colvar%acid_hyd_dist_param%raoh
1249 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| RWOH', colvar%acid_hyd_dist_param%rwoh
1250 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| NC', colvar%acid_hyd_dist_param%nc
1251 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| LAMBDA', colvar%acid_hyd_dist_param%lambda
1253 WRITE (iw,
'( A,T71,I10)')
' COLVARS| PAOH', colvar%acid_hyd_shell_param%paoh
1254 WRITE (iw,
'( A,T71,I10)')
' COLVARS| QAOH', colvar%acid_hyd_shell_param%qaoh
1255 WRITE (iw,
'( A,T71,I10)')
' COLVARS| PWOH', colvar%acid_hyd_shell_param%pwoh
1256 WRITE (iw,
'( A,T71,I10)')
' COLVARS| QWOH', colvar%acid_hyd_shell_param%qwoh
1257 WRITE (iw,
'( A,T71,I10)')
' COLVARS| POO', colvar%acid_hyd_shell_param%poo
1258 WRITE (iw,
'( A,T71,I10)')
' COLVARS| QOO', colvar%acid_hyd_shell_param%qoo
1259 WRITE (iw,
'( A,T71,I10)')
' COLVARS| PM', colvar%acid_hyd_shell_param%pm
1260 WRITE (iw,
'( A,T71,I10)')
' COLVARS| QM', colvar%acid_hyd_shell_param%qm
1261 WRITE (iw,
'( A,T71,I10)')
' COLVARS| PCUT', colvar%acid_hyd_shell_param%pcut
1262 WRITE (iw,
'( A,T71,I10)')
' COLVARS| QCUT', colvar%acid_hyd_shell_param%qcut
1263 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| RAOH', colvar%acid_hyd_shell_param%raoh
1264 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| RWOH', colvar%acid_hyd_shell_param%rwoh
1265 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| ROO', colvar%acid_hyd_shell_param%roo
1266 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| NH', colvar%acid_hyd_shell_param%nh
1267 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| NC', colvar%acid_hyd_shell_param%nc
1268 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| LAMBDA', colvar%acid_hyd_shell_param%lambda
1270 cpwarn(
"Description header for RMSD COLVAR missing!")
1272 NULLIFY (section, keyword, enum)
1276 tag_comp =
enum_i2c(enum, colvar%xyz_diag_param%component)
1279 WRITE (iw,
'( A,T57,3I8)')
' COLVARS| POSITION ('//trim(tag_comp) &
1280 //
') >>> '//tag, colvar%xyz_diag_param%i_atom
1282 NULLIFY (section, keyword, enum)
1286 tag_comp1 =
enum_i2c(enum, colvar%xyz_outerdiag_param%components(1))
1289 tag_comp2 =
enum_i2c(enum, colvar%xyz_outerdiag_param%components(2))
1292 WRITE (iw,
'( A,T57,3I8)')
' COLVARS| CROSS TERM POSITION ('//trim(tag_comp1) &
1293 //
" * "//trim(tag_comp2)//
') >>> '//tag, colvar%xyz_outerdiag_param%i_atoms
1295 WRITE (iw,
'( A,T77,A4)')
' COLVARS| ENERGY >>> '//tag,
'all!'
1297 WRITE (iw,
'( A,T57,F16.8)')
' COLVARS| Wc >>> RCUT: ', &
1299 WRITE (iw,
'( A,T57,3I8)')
' COLVARS| Wc >>> '//tag, &
1302 WRITE (iw,
'( A,T57,I8)')
' COLVARS| HBP >>> NPOINTS', &
1304 WRITE (iw,
'( A,T57,F16.8)')
' COLVARS| HBP >>> RCUT', &
1306 WRITE (iw,
'( A,T57,F16.8)')
' COLVARS| HBP >>> RCUT', &
1308 DO i = 1, colvar%HBP%nPoints
1309 WRITE (iw,
'( A,T57,3I8)')
' COLVARS| HBP >>> '//tag, &
1310 colvar%HBP%ids(i, :)
1313 WRITE (iw,
'( A,T57,I8)')
' COLVARS| Ring Puckering >>> ring size', &
1314 colvar%ring_puckering_param%nring
1315 IF (colvar%ring_puckering_param%iq == 0)
THEN
1316 WRITE (iw,
'( A,T40,A)')
' COLVARS| Ring Puckering >>> coordinate', &
1317 ' Total Puckering Amplitude'
1318 ELSEIF (colvar%ring_puckering_param%iq > 0)
THEN
1319 WRITE (iw,
'( A,T35,A,T57,I8)')
' COLVARS| Ring Puckering >>> coordinate', &
1320 ' Puckering Amplitude', &
1321 colvar%ring_puckering_param%iq
1323 WRITE (iw,
'( A,T35,A,T57,I8)')
' COLVARS| Ring Puckering >>> coordinate', &
1324 ' Puckering Angle', &
1325 colvar%ring_puckering_param%iq
1328 WRITE (iw,
'( A)')
' COLVARS| CONDITIONED DISTANCE>> '
1329 WRITE (iw,
'( A,T71,I10)') (
' COLVARS| COND.DISTANCE >>> DISTANCE FROM '//tag, &
1330 colvar%mindist_param%i_dist_from(kk), &
1331 kk=1,
SIZE(colvar%mindist_param%i_dist_from))
1332 IF (colvar%mindist_param%use_kinds_from)
THEN
1333 WRITE (iw,
'( A,T71,A10)') (
' COLVARS| COND.DIST. >>> COORDINATION FROM KINDS ', &
1334 adjustr(colvar%mindist_param%k_coord_from(kk) (1:10)), &
1335 kk=1,
SIZE(colvar%mindist_param%k_coord_from))
1337 WRITE (iw,
'( A,T71,I10)') (
' COLVARS| COND.DIST. >>> COORDINATION FROM '//tag, &
1338 colvar%mindist_param%i_coord_from(kk), &
1339 kk=1,
SIZE(colvar%mindist_param%i_coord_from))
1341 IF (colvar%mindist_param%use_kinds_to)
THEN
1342 WRITE (iw,
'( A,T71,A10)') (
' COLVARS| COND.DIST. >>> COORDINATION TO KINDS ', &
1343 adjustr(colvar%mindist_param%k_coord_to(kk) (1:10)), &
1344 kk=1,
SIZE(colvar%mindist_param%k_coord_to))
1346 WRITE (iw,
'( A,T71,I10)') (
' COLVARS| COND.DIST. >>> COORDINATION TO '//tag, &
1347 colvar%mindist_param%i_coord_to(kk), &
1348 kk=1,
SIZE(colvar%mindist_param%i_coord_to))
1350 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| R0', colvar%mindist_param%r_cut
1351 WRITE (iw,
'( A,T71,I10)')
' COLVARS| NN', colvar%mindist_param%p_exp
1352 WRITE (iw,
'( A,T71,I10)')
' COLVARS| ND', colvar%mindist_param%q_exp
1353 WRITE (iw,
'( A,T71,F10.5)')
' COLVARS| LAMBDA', colvar%mindist_param%lambda
1356 IF (colvar%use_points)
THEN
1357 WRITE (iw,
'( A)')
' COLVARS| INFORMATION ON DEFINED GEOMETRICAL POINTS'
1358 DO kk = 1,
SIZE(colvar%points)
1362 WRITE (iw,
'( A)')
' COLVARS| POINT Nr.'//trim(tmpstr2)//
' OF TYPE: '//trim(tmpstr)
1363 IF (
ASSOCIATED(colvar%points(kk)%atoms))
THEN
1364 WRITE (iw,
'( A)')
' COLVARS| ATOMS BUILDING THE GEOMETRICAL POINT'
1365 WRITE (iw,
'( A, I10)') (
' COLVARS| ATOM:', colvar%points(kk)%atoms(k), k=1,
SIZE(colvar%points(kk)%atoms))
1367 WRITE (iw,
'( A,4X,3F12.6)')
' COLVARS| XYZ POSITION OF FIXED POINT:', colvar%points(kk)%r
1373 WRITE (iw,
'( A )')
' '// &
1374 '----------------------------------------------------------------------'
1376 WRITE (iw,
'( A )')
' '// &
1377 '**********************************************************************'
1381 "PRINT%PROGRAM_RUN_INFO")
1382 CALL timestop(handle)
122 RECURSIVE SUBROUTINE colvar_read(colvar, icol, colvar_section, para_env)
…
1396 SUBROUTINE read_hydronium_colvars(section, colvar, colvar_id, n_oxygens, n_hydrogens, &
1397 i_oxygens, i_hydrogens)
1400 INTEGER,
INTENT(IN) :: colvar_id
1401 INTEGER,
INTENT(OUT) :: n_oxygens, n_hydrogens
1402 INTEGER,
DIMENSION(:),
POINTER :: i_oxygens, i_hydrogens
1404 INTEGER :: k, n_var, ndim
1405 INTEGER,
DIMENSION(:),
POINTER :: iatms
1413 CALL reallocate(i_oxygens, 1, ndim +
SIZE(iatms))
1414 i_oxygens(ndim + 1:ndim +
SIZE(iatms)) = iatms
1415 ndim = ndim +
SIZE(iatms)
1423 CALL reallocate(i_hydrogens, 1, ndim +
SIZE(iatms))
1424 i_hydrogens(ndim + 1:ndim +
SIZE(iatms)) = iatms
1425 ndim = ndim +
SIZE(iatms)
1429 SELECT CASE (colvar_id)
1454 END SUBROUTINE read_hydronium_colvars
1470 SUBROUTINE read_acid_hydronium_colvars(section, colvar, colvar_id, n_oxygens_water, &
1471 n_oxygens_acid, n_hydrogens, i_oxygens_water, &
1472 i_oxygens_acid, i_hydrogens)
1475 INTEGER,
INTENT(IN) :: colvar_id
1476 INTEGER,
INTENT(OUT) :: n_oxygens_water, n_oxygens_acid, &
1478 INTEGER,
DIMENSION(:),
POINTER :: i_oxygens_water, i_oxygens_acid, &
1481 INTEGER :: k, n_var, ndim
1482 INTEGER,
DIMENSION(:),
POINTER :: iatms
1490 CALL reallocate(i_oxygens_water, 1, ndim +
SIZE(iatms))
1491 i_oxygens_water(ndim + 1:ndim +
SIZE(iatms)) = iatms
1492 ndim = ndim +
SIZE(iatms)
1494 n_oxygens_water = ndim
1500 CALL reallocate(i_oxygens_acid, 1, ndim +
SIZE(iatms))
1501 i_oxygens_acid(ndim + 1:ndim +
SIZE(iatms)) = iatms
1502 ndim = ndim +
SIZE(iatms)
1504 n_oxygens_acid = ndim
1510 CALL reallocate(i_hydrogens, 1, ndim +
SIZE(iatms))
1511 i_hydrogens(ndim + 1:ndim +
SIZE(iatms)) = iatms
1512 ndim = ndim +
SIZE(iatms)
1516 SELECT CASE (colvar_id)
1547 END SUBROUTINE read_acid_hydronium_colvars
1555 SUBROUTINE colvar_check_points(colvar, section)
1559 INTEGER :: i, irep, natoms, npoints, nrep, nweights
1560 INTEGER,
DIMENSION(:),
POINTER :: atoms
1562 REAL(kind=
dp),
DIMENSION(:),
POINTER :: r, weights
1565 NULLIFY (point_sections)
1568 cpassert(
ASSOCIATED(colvar))
1572 colvar%use_points = .true.
1574 ALLOCATE (colvar%points(npoints))
1579 NULLIFY (colvar%points(i)%atoms)
1580 NULLIFY (colvar%points(i)%weights)
1581 CALL section_vals_val_get(point_sections,
"TYPE", i_rep_section=i, i_val=colvar%points(i)%type_id)
1582 SELECT CASE (colvar%points(i)%type_id)
1585 CALL section_vals_val_get(point_sections,
"ATOMS", i_rep_section=i, n_rep_val=nrep, i_vals=atoms)
1587 CALL section_vals_val_get(point_sections,
"ATOMS", i_rep_section=i, i_rep_val=irep, i_vals=atoms)
1588 natoms = natoms +
SIZE(atoms)
1590 ALLOCATE (colvar%points(i)%atoms(natoms))
1593 CALL section_vals_val_get(point_sections,
"ATOMS", i_rep_section=i, i_rep_val=irep, i_vals=atoms)
1594 colvar%points(i)%atoms(natoms + 1:) = atoms(:)
1595 natoms = natoms +
SIZE(atoms)
1598 ALLOCATE (colvar%points(i)%weights(natoms))
1599 colvar%points(i)%weights = 1.0_dp/real(natoms, kind=
dp)
1605 colvar%points(i)%weights(nweights + 1:) = weights(:)
1606 nweights = nweights +
SIZE(weights)
1608 cpassert(natoms == nweights)
1613 colvar%points(i)%r = r
1617 END SUBROUTINE colvar_check_points
1633 REAL(kind=
dp),
DIMENSION(:, :),
INTENT(IN), &
1636 OPTIONAL,
POINTER :: fixd_list
1639 LOGICAL :: colvar_ok
1641 colvar_ok =
ASSOCIATED(colvar)
1644 IF (
PRESENT(pos))
THEN
1645 DO i = 1,
SIZE(colvar%i_atom)
1646 j = colvar%i_atom(i)
1647 particles(j)%r = pos(:, j)
1651 colvar%dsdr = 0.0_dp
1652 SELECT CASE (colvar%type_id)
1654 CALL dist_colvar(colvar, cell, particles=particles)
1656 CALL coord_colvar(colvar, cell, particles=particles)
1658 CALL population_colvar(colvar, cell, particles=particles)
1660 CALL gyration_radius_colvar(colvar, cell, particles=particles)
1662 CALL torsion_colvar(colvar, cell, particles=particles)
1664 CALL angle_colvar(colvar, cell, particles=particles)
1666 CALL dfunct_colvar(colvar, cell, particles=particles)
1668 CALL plane_distance_colvar(colvar, cell, particles=particles)
1670 CALL plane_plane_angle_colvar(colvar, cell, particles=particles)
1672 CALL rotation_colvar(colvar, cell, particles=particles)
1674 CALL qparm_colvar(colvar, cell, particles=particles)
1676 CALL hydronium_shell_colvar(colvar, cell, particles=particles)
1678 CALL hydronium_dist_colvar(colvar, cell, particles=particles)
1680 CALL acid_hyd_dist_colvar(colvar, cell, particles=particles)
1682 CALL acid_hyd_shell_colvar(colvar, cell, particles=particles)
1684 CALL rmsd_colvar(colvar, particles=particles)
1686 CALL reaction_path_colvar(colvar, cell, particles=particles)
1688 CALL distance_from_path_colvar(colvar, cell, particles=particles)
1690 CALL combine_colvar(colvar, cell, particles=particles)
1692 CALL xyz_diag_colvar(colvar, cell, particles=particles)
1694 CALL xyz_outerdiag_colvar(colvar, cell, particles=particles)
1696 CALL ring_puckering_colvar(colvar, cell, particles=particles)
1698 CALL mindist_colvar(colvar, cell, particles=particles)
1700 cpabort(
"need force_env!")
1703 CALL wc_colvar(colvar, cell, particles=particles)
1706 CALL hbp_colvar(colvar, cell, particles=particles)
1728 LOGICAL :: colvar_ok
1734 NULLIFY (subsys, cell, colvar, qs_env)
1735 CALL force_env_get(force_env, subsys=subsys, cell=cell, qs_env=qs_env)
1736 colvar_ok =
ASSOCIATED(subsys%colvar_p)
1739 colvar => subsys%colvar_p(icolvar)%colvar
1741 colvar%dsdr = 0.0_dp
1742 SELECT CASE (colvar%type_id)
1744 CALL dist_colvar(colvar, cell, subsys=subsys)
1746 CALL coord_colvar(colvar, cell, subsys=subsys)
1748 CALL population_colvar(colvar, cell, subsys=subsys)
1750 CALL gyration_radius_colvar(colvar, cell, subsys=subsys)
1752 CALL torsion_colvar(colvar, cell, subsys=subsys, no_riemann_sheet_op=.true.)
1754 CALL angle_colvar(colvar, cell, subsys=subsys)
1756 CALL dfunct_colvar(colvar, cell, subsys=subsys)
1758 CALL plane_distance_colvar(colvar, cell, subsys=subsys)
1760 CALL plane_plane_angle_colvar(colvar, cell, subsys=subsys)
1762 CALL rotation_colvar(colvar, cell, subsys=subsys)
1764 CALL qparm_colvar(colvar, cell, subsys=subsys)
1766 CALL hydronium_shell_colvar(colvar, cell, subsys=subsys)
1768 CALL hydronium_dist_colvar(colvar, cell, subsys=subsys)
1770 CALL acid_hyd_dist_colvar(colvar, cell, subsys=subsys)
1772 CALL acid_hyd_shell_colvar(colvar, cell, subsys=subsys)
1774 CALL rmsd_colvar(colvar, subsys=subsys)
1776 CALL reaction_path_colvar(colvar, cell, subsys=subsys)
1778 CALL distance_from_path_colvar(colvar, cell, subsys=subsys)
1780 CALL combine_colvar(colvar, cell, subsys=subsys)
1782 CALL xyz_diag_colvar(colvar, cell, subsys=subsys)
1784 CALL xyz_outerdiag_colvar(colvar, cell, subsys=subsys)
1786 CALL u_colvar(colvar, force_env=force_env)
1788 CALL wc_colvar(colvar, cell, subsys=subsys, qs_env=qs_env)
1790 CALL hbp_colvar(colvar, cell, subsys=subsys, qs_env=qs_env)
1792 CALL ring_puckering_colvar(colvar, cell, subsys=subsys)
1794 CALL mindist_colvar(colvar, cell, subsys=subsys)
1810 SUBROUTINE colvar_recursive_eval(colvar, cell, particles)
1817 colvar%dsdr = 0.0_dp
1818 SELECT CASE (colvar%type_id)
1820 CALL dist_colvar(colvar, cell, particles=particles)
1822 CALL coord_colvar(colvar, cell, particles=particles)
1824 CALL torsion_colvar(colvar, cell, particles=particles)
1826 CALL angle_colvar(colvar, cell, particles=particles)
1828 CALL dfunct_colvar(colvar, cell, particles=particles)
1830 CALL plane_distance_colvar(colvar, cell, particles=particles)
1832 CALL plane_plane_angle_colvar(colvar, cell, particles=particles)
1834 CALL rotation_colvar(colvar, cell, particles=particles)
1836 CALL qparm_colvar(colvar, cell, particles=particles)
1838 CALL hydronium_shell_colvar(colvar, cell, particles=particles)
1840 CALL hydronium_dist_colvar(colvar, cell, particles=particles)
1842 CALL acid_hyd_dist_colvar(colvar, cell, particles=particles)
1844 CALL acid_hyd_shell_colvar(colvar, cell, particles=particles)
1846 CALL rmsd_colvar(colvar, particles=particles)
1848 CALL reaction_path_colvar(colvar, cell, particles=particles)
1850 CALL distance_from_path_colvar(colvar, cell, particles=particles)
1852 CALL combine_colvar(colvar, cell, particles=particles)
1854 CALL xyz_diag_colvar(colvar, cell, particles=particles)
1856 CALL xyz_outerdiag_colvar(colvar, cell, particles=particles)
1858 CALL ring_puckering_colvar(colvar, cell, particles=particles)
1860 CALL mindist_colvar(colvar, cell, particles=particles)
1862 cpabort(
"need force_env!")
1864 CALL wc_colvar(colvar, cell, particles=particles)
1866 CALL hbp_colvar(colvar, cell, particles=particles)
1870 END SUBROUTINE colvar_recursive_eval
1880 SUBROUTINE get_coordinates(colvar, i, ri, my_particles)
1882 INTEGER,
INTENT(IN) :: i
1883 REAL(kind=
dp),
DIMENSION(3),
INTENT(OUT) :: ri
1886 IF (colvar%use_points)
THEN
1889 ri(:) = my_particles(i)%r(:)
1892 END SUBROUTINE get_coordinates
1902 SUBROUTINE get_mass(colvar, i, mi, my_particles)
1904 INTEGER,
INTENT(IN) :: i
1905 REAL(kind=
dp),
INTENT(OUT) :: mi
1908 IF (colvar%use_points)
THEN
1911 mi = my_particles(i)%atomic_kind%mass
1914 END SUBROUTINE get_mass
1923 SUBROUTINE put_derivative(colvar, i, fi)
1925 INTEGER,
INTENT(IN) :: i
1926 REAL(kind=
dp),
DIMENSION(3),
INTENT(IN) :: fi
1928 IF (colvar%use_points)
THEN
1931 colvar%dsdr(:, i) = colvar%dsdr(:, i) + fi
1934 END SUBROUTINE put_derivative
1944 SUBROUTINE xyz_diag_colvar(colvar, cell, subsys, particles)
1949 POINTER :: particles
1952 REAL(
dp) :: fi(3), r, r0(3), ss(3), xi(3), xpi(3)
1956 NULLIFY (particles_i)
1959 IF (
PRESENT(particles))
THEN
1960 my_particles => particles
1962 cpassert(
PRESENT(subsys))
1964 my_particles => particles_i%els
1966 i = colvar%xyz_diag_param%i_atom
1968 CALL get_coordinates(colvar, i, xpi, my_particles)
1971 IF (.NOT. colvar%xyz_diag_param%use_absolute_position)
THEN
1972 IF (all(colvar%xyz_diag_param%r0 == huge(0.0_dp)))
THEN
1973 colvar%xyz_diag_param%r0 = xpi
1975 r0 = colvar%xyz_diag_param%r0
1980 IF (colvar%xyz_diag_param%use_pbc)
THEN
1981 ss = matmul(cell%h_inv, xpi - r0)
1983 xi = matmul(cell%hmat, ss)
1988 IF (.NOT. colvar%xyz_diag_param%use_absolute_position)
THEN
1989 SELECT CASE (colvar%xyz_diag_param%component)
2009 r = xi(1)**2 + xi(2)**2 + xi(3)**2
2012 SELECT CASE (colvar%xyz_diag_param%component)
2036 CALL put_derivative(colvar, 1, fi)
2038 END SUBROUTINE xyz_diag_colvar
2048 SUBROUTINE xyz_outerdiag_colvar(colvar, cell, subsys, particles)
2053 POINTER :: particles
2056 REAL(
dp) :: fi(3, 2), r, r0(3), ss(3), xi(3, 2), &
2061 NULLIFY (particles_i)
2064 IF (
PRESENT(particles))
THEN
2065 my_particles => particles
2067 cpassert(
PRESENT(subsys))
2069 my_particles => particles_i%els
2072 i = colvar%xyz_outerdiag_param%i_atoms(k)
2074 CALL get_coordinates(colvar, i, xpi, my_particles)
2075 r0 = colvar%xyz_outerdiag_param%r0(:, k)
2076 IF (all(colvar%xyz_outerdiag_param%r0(:, k) == huge(0.0_dp))) r0 = xpi
2078 IF (colvar%xyz_outerdiag_param%use_pbc)
THEN
2079 ss = matmul(cell%h_inv, xpi - r0)
2081 xi(:, k) = matmul(cell%hmat, ss)
2086 SELECT CASE (colvar%xyz_outerdiag_param%components(k))
2111 IF (xi(l, 1) /= 0.0_dp) fi(l, 1) = fi(l, 1) + xi(i, 2)
2112 r = r + xi(l, 1)*xi(i, 2)
2114 IF (xi(i, 2) /= 0.0_dp) fi(i, 2) = sum(xi(:, 1))
2118 CALL put_derivative(colvar, 1, fi(:, 1))
2119 CALL put_derivative(colvar, 2, fi(:, 2))
2121 END SUBROUTINE xyz_outerdiag_colvar
2131 SUBROUTINE u_colvar(colvar, force_env)
2135 CHARACTER(LEN=default_path_length) :: coupling_function
2136 CHARACTER(LEN=default_string_length) :: def_error, this_error
2137 CHARACTER(LEN=default_string_length), &
2138 DIMENSION(:),
POINTER :: parameters
2139 INTEGER :: iatom, iforce_eval, iparticle, &
2140 jparticle, natom, natom_iforce, &
2142 INTEGER,
DIMENSION(:),
POINTER :: glob_natoms, map_index
2143 REAL(
dp) :: dedf, dx, err, fi(3), lerr, &
2145 REAL(kind=
dp),
DIMENSION(:),
POINTER :: values
2154 IF (
PRESENT(force_env))
THEN
2155 NULLIFY (particles_main, subsys_main)
2157 CALL cp_subsys_get(subsys=subsys_main, particles=particles_main)
2158 natom =
SIZE(particles_main%els)
2159 colvar%n_atom_s = natom
2160 colvar%u_param%natom = natom
2164 colvar%i_atom(iatom) = iatom
2167 IF (.NOT.
ASSOCIATED(colvar%u_param%mixed_energy_section))
THEN
2168 CALL force_env_get(force_env, potential_energy=potential_energy)
2169 colvar%ss = potential_energy
2173 fi(:) = -particles_main%els(iatom)%f
2174 CALL put_derivative(colvar, iatom, fi)
2178 CALL cp_abort(__location__, &
2179 'ASSERTION (cond) failed at line '//
cp_to_string(__line__)// &
2180 ' A combination of mixed force_eval energies has been requested as '// &
2181 ' collective variable, but the MIXED env is not in use! Aborting.')
2182 CALL force_env_get(force_env, force_env_section=force_env_section)
2184 NULLIFY (values, parameters, subsystems, particles, global_forces, map_index, glob_natoms)
2185 nforce_eval =
SIZE(force_env%sub_force_env)
2186 ALLOCATE (glob_natoms(nforce_eval))
2187 ALLOCATE (subsystems(nforce_eval))
2188 ALLOCATE (particles(nforce_eval))
2190 ALLOCATE (global_forces(nforce_eval))
2193 DO iforce_eval = 1, nforce_eval
2194 NULLIFY (subsystems(iforce_eval)%subsys, particles(iforce_eval)%list)
2195 IF (.NOT.
ASSOCIATED(force_env%sub_force_env(iforce_eval)%force_env)) cycle
2197 CALL force_env_get(force_env=force_env%sub_force_env(iforce_eval)%force_env, &
2198 subsys=subsystems(iforce_eval)%subsys)
2201 particles=particles(iforce_eval)%list)
2204 natom_iforce =
SIZE(particles(iforce_eval)%list%els)
2207 IF (force_env%sub_force_env(iforce_eval)%force_env%para_env%is_source())
THEN
2208 glob_natoms(iforce_eval) = natom_iforce
2213 CALL force_env%para_env%sync()
2214 CALL force_env%para_env%sum(glob_natoms)
2217 DO iforce_eval = 1, nforce_eval
2218 ALLOCATE (global_forces(iforce_eval)%forces(3, glob_natoms(iforce_eval)))
2219 global_forces(iforce_eval)%forces = 0.0_dp
2220 IF (
ASSOCIATED(force_env%sub_force_env(iforce_eval)%force_env))
THEN
2221 IF (force_env%sub_force_env(iforce_eval)%force_env%para_env%is_source())
THEN
2223 DO iparticle = 1, glob_natoms(iforce_eval)
2224 global_forces(iforce_eval)%forces(:, iparticle) = &
2225 particles(iforce_eval)%list%els(iparticle)%f
2229 CALL force_env%para_env%sum(global_forces(iforce_eval)%forces)
2232 wrk_section => colvar%u_param%mixed_energy_section
2234 CALL get_generic_info(wrk_section,
"ENERGY_FUNCTION", coupling_function, parameters, &
2235 values, force_env%mixed_env%energies)
2237 CALL parsef(1, trim(coupling_function), parameters)
2239 colvar%ss =
evalf(1, values)
2242 DO iforce_eval = 1, nforce_eval
2245 dedf =
evalfd(1, iforce_eval, values, dx, err)
2246 IF (abs(err) > lerr)
THEN
2247 WRITE (this_error,
"(A,G12.6,A)")
"(", err,
")"
2248 WRITE (def_error,
"(A,G12.6,A)")
"(", lerr,
")"
2251 CALL cp_warn(__location__, &
2252 'ASSERTION (cond) failed at line '//
cp_to_string(__line__)// &
2253 ' Error '//trim(this_error)//
' in computing numerical derivatives larger then'// &
2254 trim(def_error)//
' .')
2259 nforce_eval, map_index)
2262 DO iparticle = 1, glob_natoms(iforce_eval)
2263 jparticle = map_index(iparticle)
2264 fi = -dedf*global_forces(iforce_eval)%forces(:, iparticle)
2265 CALL put_derivative(colvar, jparticle, fi)
2268 IF (
ASSOCIATED(map_index))
THEN
2269 DEALLOCATE (map_index)
2273 DO iforce_eval = 1, nforce_eval
2274 DEALLOCATE (global_forces(iforce_eval)%forces)
2276 DEALLOCATE (glob_natoms)
2278 DEALLOCATE (parameters)
2279 DEALLOCATE (global_forces)
2280 DEALLOCATE (subsystems)
2281 DEALLOCATE (particles)
2284 cpabort(
"need force_env!")
2286 END SUBROUTINE u_colvar
2296 SUBROUTINE plane_distance_colvar(colvar, cell, subsys, particles)
2302 POINTER :: particles
2304 INTEGER :: i, j, k, l
2305 REAL(
dp) :: a, b, dsdxpn(3), dxpndxi(3, 3), dxpndxj(3, 3), dxpndxk(3, 3), fi(3), fj(3), &
2306 fk(3), fl(3), r12, ri(3), rj(3), rk(3), rl(3), ss(3), xpij(3), xpkj(3), xpl(3), xpn(3)
2310 NULLIFY (particles_i)
2313 IF (
PRESENT(particles))
THEN
2314 my_particles => particles
2316 cpassert(
PRESENT(subsys))
2318 my_particles => particles_i%els
2320 i = colvar%plane_distance_param%plane(1)
2321 j = colvar%plane_distance_param%plane(2)
2322 k = colvar%plane_distance_param%plane(3)
2323 l = colvar%plane_distance_param%point
2325 CALL get_coordinates(colvar, i, ri, my_particles)
2326 CALL get_coordinates(colvar, j, rj, my_particles)
2327 CALL get_coordinates(colvar, k, rk, my_particles)
2328 CALL get_coordinates(colvar, l, rl, my_particles)
2331 xpl = rl - (ri + rj + rk)/3.0_dp
2332 IF (colvar%plane_distance_param%use_pbc)
THEN
2334 ss = matmul(cell%h_inv, ri - rj)
2336 xpij = matmul(cell%hmat, ss)
2338 ss = matmul(cell%h_inv, rk - rj)
2340 xpkj = matmul(cell%hmat, ss)
2342 ss = matmul(cell%h_inv, rl - (ri + rj + rk)/3.0_dp)
2344 xpl = matmul(cell%hmat, ss)
2347 xpn(1) = xpij(2)*xpkj(3) - xpij(3)*xpkj(2)
2348 xpn(2) = xpij(3)*xpkj(1) - xpij(1)*xpkj(3)
2349 xpn(3) = xpij(1)*xpkj(2) - xpij(2)*xpkj(1)
2350 a = dot_product(xpn, xpn)
2351 b = dot_product(xpl, xpn)
2354 dsdxpn(1) = xpl(1)/r12 - b*xpn(1)/(r12*a)
2355 dsdxpn(2) = xpl(2)/r12 - b*xpn(2)/(r12*a)
2356 dsdxpn(3) = xpl(3)/r12 - b*xpn(3)/(r12*a)
2358 dxpndxi(1, 1) = 0.0_dp
2359 dxpndxi(1, 2) = 1.0_dp*xpkj(3)
2360 dxpndxi(1, 3) = -1.0_dp*xpkj(2)
2361 dxpndxi(2, 1) = -1.0_dp*xpkj(3)
2362 dxpndxi(2, 2) = 0.0_dp
2363 dxpndxi(2, 3) = 1.0_dp*xpkj(1)
2364 dxpndxi(3, 1) = 1.0_dp*xpkj(2)
2365 dxpndxi(3, 2) = -1.0_dp*xpkj(1)
2366 dxpndxi(3, 3) = 0.0_dp
2368 dxpndxj(1, 1) = 0.0_dp
2369 dxpndxj(1, 2) = -1.0_dp*xpkj(3) + xpij(3)
2370 dxpndxj(1, 3) = -1.0_dp*xpij(2) + xpkj(2)
2371 dxpndxj(2, 1) = -1.0_dp*xpij(3) + xpkj(3)
2372 dxpndxj(2, 2) = 0.0_dp
2373 dxpndxj(2, 3) = -1.0_dp*xpkj(1) + xpij(1)
2374 dxpndxj(3, 1) = -1.0_dp*xpkj(2) + xpij(2)
2375 dxpndxj(3, 2) = -1.0_dp*xpij(1) + xpkj(1)
2376 dxpndxj(3, 3) = 0.0_dp
2378 dxpndxk(1, 1) = 0.0_dp
2379 dxpndxk(1, 2) = -1.0_dp*xpij(3)
2380 dxpndxk(1, 3) = 1.0_dp*xpij(2)
2381 dxpndxk(2, 1) = 1.0_dp*xpij(3)
2382 dxpndxk(2, 2) = 0.0_dp
2383 dxpndxk(2, 3) = -1.0_dp*xpij(1)
2384 dxpndxk(3, 1) = -1.0_dp*xpij(2)
2385 dxpndxk(3, 2) = 1.0_dp*xpij(1)
2386 dxpndxk(3, 3) = 0.0_dp
2388 fi(:) = matmul(dsdxpn, dxpndxi) - xpn/(3.0_dp*r12)
2389 fj(:) = matmul(dsdxpn, dxpndxj) - xpn/(3.0_dp*r12)
2390 fk(:) = matmul(dsdxpn, dxpndxk) - xpn/(3.0_dp*r12)
2393 CALL put_derivative(colvar, 1, fi)
2394 CALL put_derivative(colvar, 2, fj)
2395 CALL put_derivative(colvar, 3, fk)
2396 CALL put_derivative(colvar, 4, fl)
2398 END SUBROUTINE plane_distance_colvar
2409 SUBROUTINE plane_plane_angle_colvar(colvar, cell, subsys, particles)
2415 POINTER :: particles
2417 INTEGER :: i1, i2, j1, j2, k1, k2, np
2419 REAL(
dp) :: a1, a2, d, dnorm_dxpn(3), dprod12_dxpn(3), dsdxpn(3), dt_dxpn(3), dxpndxi(3, 3), &
2420 dxpndxj(3, 3), dxpndxk(3, 3), fi(3), fj(3), fk(3), fmod, norm1, norm2, prod_12, ri1(3), &
2421 ri2(3), rj1(3), rj2(3), rk1(3), rk2(3), ss(3), t, xpij1(3), xpij2(3), xpkj1(3), xpkj2(3), &
2426 NULLIFY (particles_i)
2430 IF (
PRESENT(particles))
THEN
2431 my_particles => particles
2433 cpassert(
PRESENT(subsys))
2435 my_particles => particles_i%els
2439 IF (colvar%plane_plane_angle_param%plane1%type_of_def ==
plane_def_atoms)
THEN
2440 i1 = colvar%plane_plane_angle_param%plane1%points(1)
2441 j1 = colvar%plane_plane_angle_param%plane1%points(2)
2442 k1 = colvar%plane_plane_angle_param%plane1%points(3)
2445 CALL get_coordinates(colvar, i1, ri1, my_particles)
2446 CALL get_coordinates(colvar, j1, rj1, my_particles)
2447 CALL get_coordinates(colvar, k1, rk1, my_particles)
2450 ss = matmul(cell%h_inv, ri1 - rj1)
2452 xpij1 = matmul(cell%hmat, ss)
2455 ss = matmul(cell%h_inv, rk1 - rj1)
2457 xpkj1 = matmul(cell%hmat, ss)
2460 xpn1(1) = xpij1(2)*xpkj1(3) - xpij1(3)*xpkj1(2)
2461 xpn1(2) = xpij1(3)*xpkj1(1) - xpij1(1)*xpkj1(3)
2462 xpn1(3) = xpij1(1)*xpkj1(2) - xpij1(2)*xpkj1(1)
2464 xpn1 = colvar%plane_plane_angle_param%plane1%normal_vec
2466 a1 = dot_product(xpn1, xpn1)
2468 cpassert(norm1 /= 0.0_dp)
2471 IF (colvar%plane_plane_angle_param%plane2%type_of_def ==
plane_def_atoms)
THEN
2472 i2 = colvar%plane_plane_angle_param%plane2%points(1)
2473 j2 = colvar%plane_plane_angle_param%plane2%points(2)
2474 k2 = colvar%plane_plane_angle_param%plane2%points(3)
2477 CALL get_coordinates(colvar, i2, ri2, my_particles)
2478 CALL get_coordinates(colvar, j2, rj2, my_particles)
2479 CALL get_coordinates(colvar, k2, rk2, my_particles)
2482 ss = matmul(cell%h_inv, ri2 - rj2)
2484 xpij2 = matmul(cell%hmat, ss)
2487 ss = matmul(cell%h_inv, rk2 - rj2)
2489 xpkj2 = matmul(cell%hmat, ss)
2492 xpn2(1) = xpij2(2)*xpkj2(3) - xpij2(3)*xpkj2(2)
2493 xpn2(2) = xpij2(3)*xpkj2(1) - xpij2(1)*xpkj2(3)
2494 xpn2(3) = xpij2(1)*xpkj2(2) - xpij2(2)*xpkj2(1)
2496 xpn2 = colvar%plane_plane_angle_param%plane2%normal_vec
2498 a2 = dot_product(xpn2, xpn2)
2500 cpassert(norm2 /= 0.0_dp)
2503 prod_12 = dot_product(xpn1, xpn2)
2507 t = min(1.0_dp, abs(t))*sign(1.0_dp, t)
2510 IF ((abs(colvar%ss) .LT. tolerance_acos) .OR. (abs(colvar%ss -
pi) .LT. tolerance_acos))
THEN
2513 fmod = -1.0_dp/sin(colvar%ss)
2518 IF (colvar%plane_plane_angle_param%plane1%type_of_def ==
plane_def_atoms)
THEN
2520 dnorm_dxpn = 1.0_dp/norm1*xpn1
2521 dt_dxpn = (dprod12_dxpn*d - prod_12*dnorm_dxpn*norm2)/d**2
2523 dsdxpn(1) = fmod*dt_dxpn(1)
2524 dsdxpn(2) = fmod*dt_dxpn(2)
2525 dsdxpn(3) = fmod*dt_dxpn(3)
2527 dxpndxi(1, 1) = 0.0_dp
2528 dxpndxi(1, 2) = 1.0_dp*xpkj1(3)
2529 dxpndxi(1, 3) = -1.0_dp*xpkj1(2)
2530 dxpndxi(2, 1) = -1.0_dp*xpkj1(3)
2531 dxpndxi(2, 2) = 0.0_dp
2532 dxpndxi(2, 3) = 1.0_dp*xpkj1(1)
2533 dxpndxi(3, 1) = 1.0_dp*xpkj1(2)
2534 dxpndxi(3, 2) = -1.0_dp*xpkj1(1)
2535 dxpndxi(3, 3) = 0.0_dp
2537 dxpndxj(1, 1) = 0.0_dp
2538 dxpndxj(1, 2) = -1.0_dp*xpkj1(3) + xpij1(3)
2539 dxpndxj(1, 3) = -1.0_dp*xpij1(2) + xpkj1(2)
2540 dxpndxj(2, 1) = -1.0_dp*xpij1(3) + xpkj1(3)
2541 dxpndxj(2, 2) = 0.0_dp
2542 dxpndxj(2, 3) = -1.0_dp*xpkj1(1) + xpij1(1)
2543 dxpndxj(3, 1) = -1.0_dp*xpkj1(2) + xpij1(2)
2544 dxpndxj(3, 2) = -1.0_dp*xpij1(1) + xpkj1(1)
2545 dxpndxj(3, 3) = 0.0_dp
2547 dxpndxk(1, 1) = 0.0_dp
2548 dxpndxk(1, 2) = -1.0_dp*xpij1(3)
2549 dxpndxk(1, 3) = 1.0_dp*xpij1(2)
2550 dxpndxk(2, 1) = 1.0_dp*xpij1(3)
2551 dxpndxk(2, 2) = 0.0_dp
2552 dxpndxk(2, 3) = -1.0_dp*xpij1(1)
2553 dxpndxk(3, 1) = -1.0_dp*xpij1(2)
2554 dxpndxk(3, 2) = 1.0_dp*xpij1(1)
2555 dxpndxk(3, 3) = 0.0_dp
2557 fi = matmul(dsdxpn, dxpndxi)
2558 fj = matmul(dsdxpn, dxpndxj)
2559 fk = matmul(dsdxpn, dxpndxk)
2562 CALL put_derivative(colvar, np + 1, fi)
2563 CALL put_derivative(colvar, np + 2, fj)
2564 CALL put_derivative(colvar, np + 3, fk)
2569 IF (colvar%plane_plane_angle_param%plane2%type_of_def ==
plane_def_atoms)
THEN
2571 dnorm_dxpn = 1.0_dp/norm2*xpn2
2572 dt_dxpn = (dprod12_dxpn*d - prod_12*dnorm_dxpn*norm1)/d**2
2574 dsdxpn(1) = fmod*dt_dxpn(1)
2575 dsdxpn(2) = fmod*dt_dxpn(2)
2576 dsdxpn(3) = fmod*dt_dxpn(3)
2578 dxpndxi(1, 1) = 0.0_dp
2579 dxpndxi(1, 2) = 1.0_dp*xpkj1(3)
2580 dxpndxi(1, 3) = -1.0_dp*xpkj1(2)
2581 dxpndxi(2, 1) = -1.0_dp*xpkj1(3)
2582 dxpndxi(2, 2) = 0.0_dp
2583 dxpndxi(2, 3) = 1.0_dp*xpkj1(1)
2584 dxpndxi(3, 1) = 1.0_dp*xpkj1(2)
2585 dxpndxi(3, 2) = -1.0_dp*xpkj1(1)
2586 dxpndxi(3, 3) = 0.0_dp
2588 dxpndxj(1, 1) = 0.0_dp
2589 dxpndxj(1, 2) = -1.0_dp*xpkj1(3) + xpij1(3)
2590 dxpndxj(1, 3) = -1.0_dp*xpij1(2) + xpkj1(2)
2591 dxpndxj(2, 1) = -1.0_dp*xpij1(3) + xpkj1(3)
2592 dxpndxj(2, 2) = 0.0_dp
2593 dxpndxj(2, 3) = -1.0_dp*xpkj1(1) + xpij1(1)
2594 dxpndxj(3, 1) = -1.0_dp*xpkj1(2) + xpij1(2)
2595 dxpndxj(3, 2) = -1.0_dp*xpij1(1) + xpkj1(1)
2596 dxpndxj(3, 3) = 0.0_dp
2598 dxpndxk(1, 1) = 0.0_dp
2599 dxpndxk(1, 2) = -1.0_dp*xpij1(3)
2600 dxpndxk(1, 3) = 1.0_dp*xpij1(2)
2601 dxpndxk(2, 1) = 1.0_dp*xpij1(3)
2602 dxpndxk(2, 2) = 0.0_dp
2603 dxpndxk(2, 3) = -1.0_dp*xpij1(1)
2604 dxpndxk(3, 1) = -1.0_dp*xpij1(2)
2605 dxpndxk(3, 2) = 1.0_dp*xpij1(1)
2606 dxpndxk(3, 3) = 0.0_dp
2608 fi = matmul(dsdxpn, dxpndxi)
2609 fj = matmul(dsdxpn, dxpndxj)
2610 fk = matmul(dsdxpn, dxpndxk)
2613 CALL put_derivative(colvar, np + 1, fi)
2614 CALL put_derivative(colvar, np + 2, fj)
2615 CALL put_derivative(colvar, np + 3, fk)
2618 END SUBROUTINE plane_plane_angle_colvar
2628 SUBROUTINE rotation_colvar(colvar, cell, subsys, particles)
2633 POINTER :: particles
2636 REAL(
dp) :: a, b, fmod, t0, t1, t2, t3, xdum(3), &
2638 REAL(kind=
dp) :: dp1b1(3), dp1b2(3), dp2b1(3), dp2b2(3), &
2639 ss(3), xp1b1(3), xp1b2(3), xp2b1(3), &
2644 NULLIFY (particles_i)
2647 IF (
PRESENT(particles))
THEN
2648 my_particles => particles
2650 cpassert(
PRESENT(subsys))
2652 my_particles => particles_i%els
2654 i = colvar%rotation_param%i_at1_bond1
2655 CALL get_coordinates(colvar, i, xp1b1, my_particles)
2656 i = colvar%rotation_param%i_at2_bond1
2657 CALL get_coordinates(colvar, i, xp2b1, my_particles)
2658 i = colvar%rotation_param%i_at1_bond2
2659 CALL get_coordinates(colvar, i, xp1b2, my_particles)
2660 i = colvar%rotation_param%i_at2_bond2
2661 CALL get_coordinates(colvar, i, xp2b2, my_particles)
2663 ss = matmul(cell%h_inv, xp1b1 - xp2b1)
2665 xij = matmul(cell%hmat, ss)
2667 ss = matmul(cell%h_inv, xp1b2 - xp2b2)
2669 xkj = matmul(cell%hmat, ss)
2671 a = sqrt(dot_product(xij, xij))
2672 b = sqrt(dot_product(xkj, xkj))
2674 t1 = 1.0_dp/(a**3.0_dp*b)
2675 t2 = 1.0_dp/(a*b**3.0_dp)
2676 t3 = dot_product(xij, xkj)
2677 colvar%ss = acos(t3*t0)
2678 IF ((abs(colvar%ss) .LT. tolerance_acos) .OR. (abs(colvar%ss -
pi) .LT. tolerance_acos))
THEN
2681 fmod = -1.0_dp/sin(colvar%ss)
2683 dp1b1 = xkj(:)*t0 - xij(:)*t1*t3
2684 dp2b1 = -xkj(:)*t0 + xij(:)*t1*t3
2685 dp1b2 = xij(:)*t0 - xkj(:)*t2*t3
2686 dp2b2 = -xij(:)*t0 + xkj(:)*t2*t3
2689 idum = colvar%rotation_param%i_at1_bond1
2690 CALL put_derivative(colvar, idum, xdum)
2692 idum = colvar%rotation_param%i_at2_bond1
2693 CALL put_derivative(colvar, idum, xdum)
2695 idum = colvar%rotation_param%i_at1_bond2
2696 CALL put_derivative(colvar, idum, xdum)
2698 idum = colvar%rotation_param%i_at2_bond2
2699 CALL put_derivative(colvar, idum, xdum)
2701 END SUBROUTINE rotation_colvar
2712 SUBROUTINE dfunct_colvar(colvar, cell, subsys, particles)
2717 POINTER :: particles
2719 INTEGER :: i, j, k, l
2720 REAL(
dp) :: fi(3), fj(3), fk(3), fl(3), r12, r34, &
2721 ss(3), xij(3), xkl(3), xpi(3), xpj(3), &
2726 NULLIFY (particles_i)
2729 IF (
PRESENT(particles))
THEN
2730 my_particles => particles
2732 cpassert(
PRESENT(subsys))
2734 my_particles => particles_i%els
2736 i = colvar%dfunct_param%i_at_dfunct(1)
2737 j = colvar%dfunct_param%i_at_dfunct(2)
2739 CALL get_coordinates(colvar, i, xpi, my_particles)
2740 CALL get_coordinates(colvar, j, xpj, my_particles)
2741 IF (colvar%dfunct_param%use_pbc)
THEN
2742 ss = matmul(cell%h_inv, xpi - xpj)
2744 xij = matmul(cell%hmat, ss)
2748 r12 = sqrt(xij(1)**2 + xij(2)**2 + xij(3)**2)
2750 k = colvar%dfunct_param%i_at_dfunct(3)
2751 l = colvar%dfunct_param%i_at_dfunct(4)
2752 CALL get_coordinates(colvar, k, xpk, my_particles)
2753 CALL get_coordinates(colvar, l, xpl, my_particles)
2754 IF (colvar%dfunct_param%use_pbc)
THEN
2755 ss = matmul(cell%h_inv, xpk - xpl)
2757 xkl = matmul(cell%hmat, ss)
2761 r34 = sqrt(xkl(1)**2 + xkl(2)**2 + xkl(3)**2)
2763 colvar%ss = r12 + colvar%dfunct_param%coeff*r34
2766 fk(:) = colvar%dfunct_param%coeff*xkl/r34
2767 fl(:) = -colvar%dfunct_param%coeff*xkl/r34
2768 CALL put_derivative(colvar, 1, fi)
2769 CALL put_derivative(colvar, 2, fj)
2770 CALL put_derivative(colvar, 3, fk)
2771 CALL put_derivative(colvar, 4, fl)
2773 END SUBROUTINE dfunct_colvar
2783 SUBROUTINE angle_colvar(colvar, cell, subsys, particles)
2788 POINTER :: particles
2791 REAL(
dp) :: a, b, fi(3), fj(3), fk(3), fmod, ri(3), &
2792 rj(3), rk(3), ss(3), t0, t1, t2, t3, &
2797 NULLIFY (particles_i)
2800 IF (
PRESENT(particles))
THEN
2801 my_particles => particles
2803 cpassert(
PRESENT(subsys))
2805 my_particles => particles_i%els
2807 i = colvar%angle_param%i_at_angle(1)
2808 j = colvar%angle_param%i_at_angle(2)
2809 k = colvar%angle_param%i_at_angle(3)
2810 CALL get_coordinates(colvar, i, ri, my_particles)
2811 CALL get_coordinates(colvar, j, rj, my_particles)
2812 CALL get_coordinates(colvar, k, rk, my_particles)
2814 ss = matmul(cell%h_inv, ri - rj)
2816 xij = matmul(cell%hmat, ss)
2818 ss = matmul(cell%h_inv, rk - rj)
2820 xkj = matmul(cell%hmat, ss)
2822 a = sqrt(dot_product(xij, xij))
2823 b = sqrt(dot_product(xkj, xkj))
2825 t1 = 1.0_dp/(a**3.0_dp*b)
2826 t2 = 1.0_dp/(a*b**3.0_dp)
2827 t3 = dot_product(xij, xkj)
2828 colvar%ss = acos(t3*t0)
2829 IF ((abs(colvar%ss) .LT. tolerance_acos) .OR. (abs(colvar%ss -
pi) .LT. tolerance_acos))
THEN
2832 fmod = -1.0_dp/sin(colvar%ss)
2834 fi(:) = xkj(:)*t0 - xij(:)*t1*t3
2835 fj(:) = -xkj(:)*t0 + xij(:)*t1*t3 - xij(:)*t0 + xkj(:)*t2*t3
2836 fk(:) = xij(:)*t0 - xkj(:)*t2*t3
2840 CALL put_derivative(colvar, 1, fi)
2841 CALL put_derivative(colvar, 2, fj)
2842 CALL put_derivative(colvar, 3, fk)
2844 END SUBROUTINE angle_colvar
2854 SUBROUTINE dist_colvar(colvar, cell, subsys, particles)
2859 POINTER :: particles
2862 REAL(
dp) :: fi(3), fj(3), r12, ss(3), xij(3), &
2867 NULLIFY (particles_i)
2870 IF (
PRESENT(particles))
THEN
2871 my_particles => particles
2873 cpassert(
PRESENT(subsys))
2875 my_particles => particles_i%els
2877 i = colvar%dist_param%i_at
2878 j = colvar%dist_param%j_at
2879 CALL get_coordinates(colvar, i, xpi, my_particles)
2880 CALL get_coordinates(colvar, j, xpj, my_particles)
2881 ss = matmul(cell%h_inv, xpi - xpj)
2883 xij = matmul(cell%hmat, ss)
2884 SELECT CASE (colvar%dist_param%axis_id)
2903 r12 = sqrt(xij(1)**2 + xij(2)**2 + xij(3)**2)
2905 IF (colvar%dist_param%sign_d)
THEN
2906 SELECT CASE (colvar%dist_param%axis_id)
2924 CALL put_derivative(colvar, 1, fi)
2925 CALL put_derivative(colvar, 2, fj)
2927 END SUBROUTINE dist_colvar
2938 SUBROUTINE torsion_colvar(colvar, cell, subsys, particles, no_riemann_sheet_op)
2944 POINTER :: particles
2945 LOGICAL,
INTENT(IN),
OPTIONAL :: no_riemann_sheet_op
2948 LOGICAL :: no_riemann_sheet
2949 REAL(
dp) ::
angle, cosine, dedphi, dedxia, dedxib, dedxic, dedxid, dedxt, dedxu, dedyia, &
2950 dedyib, dedyic, dedyid, dedyt, dedyu, dedzia, dedzib, dedzic, dedzid, dedzt, dedzu, dt, &
2951 e, ftmp(3), o0, rcb, rt2, rtmp(3), rtru, ru2, sine, ss(3), xba, xca, xcb, xdb, xdc, xt, &
2952 xtu, xu, yba, yca, ycb, ydb, ydc, yt, ytu, yu, zba, zca, zcb, zdb, zdc, zt, ztu, zu
2953 REAL(
dp),
DIMENSION(3, 4) :: rr
2957 NULLIFY (particles_i)
2959 IF (
PRESENT(particles))
THEN
2960 my_particles => particles
2962 cpassert(
PRESENT(subsys))
2964 my_particles => particles_i%els
2966 no_riemann_sheet = .false.
2967 IF (
PRESENT(no_riemann_sheet_op)) no_riemann_sheet = no_riemann_sheet_op
2969 i = colvar%torsion_param%i_at_tors(ii)
2970 CALL get_coordinates(colvar, i, rtmp, my_particles)
2971 rr(:, ii) = rtmp(1:3)
2973 o0 = colvar%torsion_param%o0
2975 ss = matmul(cell%h_inv, rr(:, 2) - rr(:, 1))
2977 ss = matmul(cell%hmat, ss)
2982 ss = matmul(cell%h_inv, rr(:, 3) - rr(:, 2))
2984 ss = matmul(cell%hmat, ss)
2989 ss = matmul(cell%h_inv, rr(:, 4) - rr(:, 3))
2991 ss = matmul(cell%hmat, ss)
2996 xt = yba*zcb - ycb*zba
2997 yt = zba*xcb - zcb*xba
2998 zt = xba*ycb - xcb*yba
2999 xu = ycb*zdc - ydc*zcb
3000 yu = zcb*xdc - zdc*xcb
3001 zu = xcb*ydc - xdc*ycb
3005 rt2 = xt*xt + yt*yt + zt*zt
3006 ru2 = xu*xu + yu*yu + zu*zu
3007 rtru = sqrt(rt2*ru2)
3008 IF (rtru .NE. 0.0_dp)
THEN
3009 rcb = sqrt(xcb*xcb + ycb*ycb + zcb*zcb)
3010 cosine = (xt*xu + yt*yu + zt*zu)/rtru
3011 sine = (xcb*xtu + ycb*ytu + zcb*ztu)/(rcb*rtru)
3012 cosine = min(1.0_dp, max(-1.0_dp, cosine))
3013 angle = acos(cosine)
3017 dt = mod(2.0e4_dp*
pi + dt - o0, 2.0_dp*
pi)
3018 IF (dt .GT.
pi) dt = dt - 2.0_dp*
pi
3020 colvar%torsion_param%o0 = dt
3030 ss = matmul(cell%h_inv, rr(:, 3) - rr(:, 1))
3032 ss = matmul(cell%hmat, ss)
3037 ss = matmul(cell%h_inv, rr(:, 4) - rr(:, 2))
3039 ss = matmul(cell%hmat, ss)
3044 dedxt = dedphi*(yt*zcb - ycb*zt)/(rt2*rcb)
3045 dedyt = dedphi*(zt*xcb - zcb*xt)/(rt2*rcb)
3046 dedzt = dedphi*(xt*ycb - xcb*yt)/(rt2*rcb)
3047 dedxu = -dedphi*(yu*zcb - ycb*zu)/(ru2*rcb)
3048 dedyu = -dedphi*(zu*xcb - zcb*xu)/(ru2*rcb)
3049 dedzu = -dedphi*(xu*ycb - xcb*yu)/(ru2*rcb)
3053 dedxia = zcb*dedyt - ycb*dedzt
3054 dedyia = xcb*dedzt - zcb*dedxt
3055 dedzia = ycb*dedxt - xcb*dedyt
3056 dedxib = yca*dedzt - zca*dedyt + zdc*dedyu - ydc*dedzu
3057 dedyib = zca*dedxt - xca*dedzt + xdc*dedzu - zdc*dedxu
3058 dedzib = xca*dedyt - yca*dedxt + ydc*dedxu - xdc*dedyu
3059 dedxic = zba*dedyt - yba*dedzt + ydb*dedzu - zdb*dedyu
3060 dedyic = xba*dedzt - zba*dedxt + zdb*dedxu - xdb*dedzu
3061 dedzic = yba*dedxt - xba*dedyt + xdb*dedyu - ydb*dedxu
3062 dedxid = zcb*dedyu - ycb*dedzu
3063 dedyid = xcb*dedzu - zcb*dedxu
3064 dedzid = ycb*dedxu - xcb*dedyu
3081 IF (no_riemann_sheet) colvar%ss = atan2(sin(e), cos(e))
3085 CALL put_derivative(colvar, 1, ftmp)
3089 CALL put_derivative(colvar, 2, ftmp)
3093 CALL put_derivative(colvar, 3, ftmp)
3097 CALL put_derivative(colvar, 4, ftmp)
3098 END SUBROUTINE torsion_colvar
3107 SUBROUTINE qparm_colvar(colvar, cell, subsys, particles)
3112 POINTER :: particles
3114 INTEGER :: aa, bb, cc, i, idim, ii, j, jj, l, mm, &
3115 n_atoms_from, n_atoms_to, ncells(3)
3116 LOGICAL :: include_images
3117 REAL(kind=
dp) :: denominator_tolerance, fact, ftmp(3), im_qlm, inv_n_atoms_from, nbond, &
3118 pre_fac, ql, qparm, r1cut, rcut, re_qlm, rij, rij_shift, shift(3), ss(3), ss0(3), xij(3), &
3120 REAL(kind=
dp),
DIMENSION(3) :: d_im_qlm_dxi, d_nbond_dxi, d_ql_dxi, &
3121 d_re_qlm_dxi, xpi, xpj
3129 n_atoms_to = colvar%qparm_param%n_atoms_to
3130 n_atoms_from = colvar%qparm_param%n_atoms_from
3131 rcut = colvar%qparm_param%rcut
3132 l = colvar%qparm_param%l
3133 r1cut = colvar%qparm_param%rstart
3134 include_images = colvar%qparm_param%include_images
3135 NULLIFY (particles_i)
3137 IF (
PRESENT(particles))
THEN
3138 my_particles => particles
3140 cpassert(
PRESENT(subsys))
3142 my_particles => particles_i%els
3144 cpassert(r1cut .LT. rcut)
3145 denominator_tolerance = 1.0e-8_dp
3152 inv_n_atoms_from = 1.0_dp/real(n_atoms_from, kind=
dp)
3153 DO ii = 1, n_atoms_from
3154 i = colvar%qparm_param%i_at_from(ii)
3155 CALL get_coordinates(colvar, i, xpi, my_particles)
3158 d_ql_dxi(:) = 0.0_dp
3164 d_re_qlm_dxi(:) = 0.0_dp
3165 d_im_qlm_dxi(:) = 0.0_dp
3166 d_nbond_dxi(:) = 0.0_dp
3168 jloop:
DO jj = 1, n_atoms_to
3170 j = colvar%qparm_param%i_at_to(jj)
3171 CALL get_coordinates(colvar, j, xpj, my_particles)
3173 IF (include_images)
THEN
3175 cpassert(cell%orthorhombic)
3179 xij(:) = xpj(:) - xpi(:)
3180 ss = matmul(cell%h_inv, xij)
3186 shift(idim) = 1.0_dp
3187 xij_shift = matmul(cell%hmat, shift)
3188 rij_shift = sqrt(dot_product(xij_shift, xij_shift))
3189 ncells(idim) = floor(rcut/rij_shift - 0.5)
3194 DO aa = -ncells(1), ncells(1)
3195 DO bb = -ncells(2), ncells(2)
3196 DO cc = -ncells(3), ncells(3)
3198 IF (i == j .AND. aa .EQ. 0 .AND. bb .EQ. 0 .AND. cc .EQ. 0) cycle
3199 shift(1) = real(aa, kind=
dp)
3200 shift(2) = real(bb, kind=
dp)
3201 shift(3) = real(cc, kind=
dp)
3202 xij = matmul(cell%hmat, ss0(:) + shift(:))
3203 rij = sqrt(dot_product(xij, xij))
3209 IF (rij > rcut) cycle
3212 CALL accumulate_qlm_over_neigbors(xij, rij, rcut, r1cut, &
3213 denominator_tolerance, l, mm, nbond, re_qlm, im_qlm, &
3214 d_re_qlm_dxi, d_im_qlm_dxi, d_nbond_dxi)
3222 IF (i == j) cycle jloop
3223 xij(:) = xpj(:) - xpi(:)
3224 rij = sqrt(dot_product(xij, xij))
3225 IF (rij > rcut) cycle
3228 CALL accumulate_qlm_over_neigbors(xij, rij, rcut, r1cut, &
3229 denominator_tolerance, l, mm, nbond, re_qlm, im_qlm, &
3230 d_re_qlm_dxi, d_im_qlm_dxi, d_nbond_dxi)
3245 IF (nbond .LT. denominator_tolerance)
THEN
3246 cpwarn(
"QPARM: number of neighbors is very close to zero!")
3249 d_nbond_dxi(:) = d_nbond_dxi(:)/nbond
3250 re_qlm = re_qlm/nbond
3251 d_re_qlm_dxi(:) = d_re_qlm_dxi(:)/nbond - d_nbond_dxi(:)*re_qlm
3252 im_qlm = im_qlm/nbond
3253 d_im_qlm_dxi(:) = d_im_qlm_dxi(:)/nbond - d_nbond_dxi(:)*im_qlm
3255 ql = ql + fact*(re_qlm*re_qlm + im_qlm*im_qlm)
3256 d_ql_dxi(:) = d_ql_dxi(:) &
3257 + fact*2.0_dp*(re_qlm*d_re_qlm_dxi(:) + im_qlm*d_im_qlm_dxi(:))
3261 pre_fac = (4.0_dp*
pi)/(2.0_dp*l + 1)
3263 qparm = qparm + sqrt(pre_fac*ql)
3264 ftmp(:) = 0.5_dp*sqrt(pre_fac/ql)*d_ql_dxi(:)
3266 ftmp(:) = -1.0_dp*ftmp(:)
3268 CALL put_derivative(colvar, ii, ftmp)
3272 colvar%ss = qparm*inv_n_atoms_from
3273 colvar%dsdr(:, :) = colvar%dsdr(:, :)*inv_n_atoms_from
3279 END SUBROUTINE qparm_colvar
3297 SUBROUTINE accumulate_qlm_over_neigbors(xij, rij, rcut, r1cut, &
3298 denominator_tolerance, ll, mm, nbond, re_qlm, im_qlm, &
3299 d_re_qlm_dxi, d_im_qlm_dxi, d_nbond_dxi)
3301 REAL(kind=
dp),
INTENT(IN) :: xij(3), rij, rcut, r1cut, &
3302 denominator_tolerance
3303 INTEGER,
INTENT(IN) :: ll, mm
3304 REAL(kind=
dp),
INTENT(INOUT) :: nbond, re_qlm, im_qlm, d_re_qlm_dxi(3), &
3305 d_im_qlm_dxi(3), d_nbond_dxi(3)
3307 REAL(kind=
dp) :: bond, costheta, dplm, dylm, exp0, &
3308 exp_fac, fi, plm, pre_fac, sqrt_c1
3309 REAL(kind=
dp),
DIMENSION(3) :: dcostheta, dfi
3314 IF (rij .GT. rcut)
THEN
3319 IF (rij .LT. r1cut)
THEN
3323 exp0 = exp((r1cut - rcut)/(rij - rcut) - (r1cut - rcut)/(r1cut - rij))
3324 bond = 1.0_dp/(1.0_dp + exp0)
3325 exp_fac = ((rcut - r1cut)/(rij - rcut)**2 + (rcut - r1cut)/(r1cut - rij)**2)*exp0/(1.0_dp + exp0)**2
3328 IF (bond > 1.0_dp)
THEN
3329 cpabort(
"bond > 1.0_dp")
3332 nbond = nbond + bond
3333 IF (abs(xij(1)) .LT. denominator_tolerance &
3334 .AND. abs(xij(2)) .LT. denominator_tolerance)
THEN
3337 fi = atan2(xij(2), xij(1))
3340 costheta = xij(3)/rij
3341 IF (costheta > 1.0_dp) costheta = 1.0_dp
3342 IF (costheta < -1.0_dp) costheta = -1.0_dp
3347 IF ((ll + abs(mm)) >
maxfac)
THEN
3348 cpabort(
"(l+m) > maxfac")
3351 sqrt_c1 = sqrt(((2*ll + 1)*
fac(ll - abs(mm)))/(4*
pi*
fac(ll + abs(mm))))
3352 pre_fac = bond*sqrt_c1
3360 re_qlm = re_qlm + pre_fac*plm*cos(mm*fi)
3361 im_qlm = im_qlm + pre_fac*plm*sin(mm*fi)
3366 dcostheta(:) = xij(:)*xij(3)/(rij**3)
3367 dcostheta(3) = dcostheta(3) - 1.0_dp/rij
3371 dfi(1) = xij(2)/(xij(1)**2 + xij(2)**2)
3372 dfi(2) = -xij(1)/(xij(1)**2 + xij(2)**2)
3374 d_re_qlm_dxi(:) = d_re_qlm_dxi(:) &
3375 + exp_fac*sqrt_c1*plm*cos(mm*fi)*xij(:)/rij &
3376 + dylm*dcostheta(:)*cos(mm*fi) &
3377 + pre_fac*plm*mm*(-1.0_dp)*sin(mm*fi)*dfi(:)
3378 d_im_qlm_dxi(:) = d_im_qlm_dxi(:) &
3379 + exp_fac*sqrt_c1*plm*sin(mm*fi)*xij(:)/rij &
3380 + dylm*dcostheta(:)*sin(mm*fi) &
3381 + pre_fac*plm*mm*(+1.0_dp)*cos(mm*fi)*dfi(:)
3382 d_nbond_dxi(:) = d_nbond_dxi(:) + exp_fac*xij(:)/rij
3384 END SUBROUTINE accumulate_qlm_over_neigbors
3396 SUBROUTINE hydronium_shell_colvar(colvar, cell, subsys, particles)
3401 POINTER :: particles
3403 INTEGER :: i, ii, j, jj, n_hydrogens, n_oxygens, &
3404 pm, poh, poo, qm, qoh, qoo
3405 REAL(
dp) :: drji, fscalar, invden, lambda, nh, num, &
3406 qtot, rji(3), roh, roo, rrel
3407 REAL(
dp),
ALLOCATABLE,
DIMENSION(:) :: m, noh, noo, qloc
3408 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :, :) :: dm, dnoh, dnoo
3409 REAL(
dp),
DIMENSION(3) :: rpi, rpj
3413 n_oxygens = colvar%hydronium_shell_param%n_oxygens
3414 n_hydrogens = colvar%hydronium_shell_param%n_hydrogens
3415 nh = colvar%hydronium_shell_param%nh
3416 poh = colvar%hydronium_shell_param%poh
3417 qoh = colvar%hydronium_shell_param%qoh
3418 poo = colvar%hydronium_shell_param%poo
3419 qoo = colvar%hydronium_shell_param%qoo
3420 roo = colvar%hydronium_shell_param%roo
3421 roh = colvar%hydronium_shell_param%roh
3422 lambda = colvar%hydronium_shell_param%lambda
3423 pm = colvar%hydronium_shell_param%pm
3424 qm = colvar%hydronium_shell_param%qm
3426 NULLIFY (particles_i)
3428 IF (
PRESENT(particles))
THEN
3429 my_particles => particles
3431 cpassert(
PRESENT(subsys))
3433 my_particles => particles_i%els
3436 ALLOCATE (dnoh(3, n_hydrogens, n_oxygens))
3437 ALLOCATE (noh(n_oxygens))
3438 ALLOCATE (m(n_oxygens))
3439 ALLOCATE (dm(3, n_hydrogens, n_oxygens))
3441 ALLOCATE (dnoo(3, n_oxygens, n_oxygens))
3442 ALLOCATE (noo(n_oxygens))
3444 ALLOCATE (qloc(n_oxygens))
3454 DO ii = 1, n_oxygens
3455 i = colvar%hydronium_shell_param%i_oxygens(ii)
3456 rpi(:) = my_particles(i)%r(1:3)
3458 DO jj = 1, n_hydrogens
3459 j = colvar%hydronium_shell_param%i_hydrogens(jj)
3460 rpj(:) = my_particles(j)%r(1:3)
3461 rji =
pbc(rpj, rpi, cell)
3462 drji = sqrt(sum(rji**2))
3464 num = (1.0_dp - rrel**poh)
3465 invden = 1.0_dp/(1.0_dp - rrel**qoh)
3466 IF (abs(1.0_dp - rrel) > 1.0e-6_dp)
THEN
3467 noh(ii) = noh(ii) + num*invden
3468 fscalar = ((-poh*(rrel**(poh - 1))*invden) &
3469 + num*(invden)**2*qoh*(rrel**(qoh - 1)))/(drji*roh)
3470 dnoh(1:3, jj, ii) = rji(1:3)*fscalar
3473 noh(ii) = noh(ii) + real(poh,
dp)/real(qoh,
dp)
3474 fscalar = real(poh*(poh - qoh),
dp)/(real(2*qoh,
dp)*roh*drji)
3475 dnoh(1:3, jj, ii) = rji(1:3)*fscalar
3478 m(ii) = 1.0_dp - (1.0_dp - (noh(ii)/nh)**pm)/ &
3479 (1.0_dp - (noh(ii)/nh)**qm)
3482 DO jj = 1, n_oxygens
3484 j = colvar%hydronium_shell_param%i_oxygens(jj)
3485 rpj(:) = my_particles(j)%r(1:3)
3486 rji =
pbc(rpj, rpi, cell)
3487 drji = sqrt(sum(rji**2))
3489 num = (1.0_dp - rrel**poo)
3490 invden = 1.0_dp/(1.0_dp - rrel**qoo)
3491 IF (abs(1.0_dp - rrel) > 1.0e-6_dp)
THEN
3492 noo(ii) = noo(ii) + num*invden
3493 fscalar = ((-poo*(rrel**(poo - 1))*invden) &
3494 + num*(invden)**2*qoo*(rrel**(qoo - 1)))/(drji*roo)
3495 dnoo(1:3, jj, ii) = rji(1:3)*fscalar
3498 noo(ii) = noo(ii) + real(poo,
dp)/real(qoo,
dp)
3499 fscalar = real(poo*(poo - qoo),
dp)/(real(2*qoo,
dp)*roo*drji)
3500 dnoo(1:3, jj, ii) = rji(1:3)*fscalar
3507 DO ii = 1, n_oxygens
3508 qloc(ii) = exp(lambda*m(ii)*noo(ii))
3509 qtot = qtot + qloc(ii)
3512 DO ii = 1, n_oxygens
3514 DO jj = 1, n_hydrogens
3515 dm(1:3, jj, ii) = (pm*((noh(ii)/nh)**(pm - 1))*dnoh(1:3, jj, ii))/nh/ &
3516 (1.0_dp - (noh(ii)/nh)**qm) - &
3517 (1.0_dp - (noh(ii)/nh)**pm)/ &
3518 ((1.0_dp - (noh(ii)/nh)**qm)**2)* &
3519 qm*dnoh(1:3, jj, ii)*(noh(ii)/nh)**(qm - 1)/nh
3521 colvar%dsdr(1:3, ii) = colvar%dsdr(1:3, ii) + qloc(ii)*dm(1:3, jj, ii)*noo(ii)/qtot
3522 colvar%dsdr(1:3, n_oxygens + jj) = colvar%dsdr(1:3, n_oxygens + jj) &
3523 - qloc(ii)*dm(1:3, jj, ii)*noo(ii)/qtot
3526 DO jj = 1, n_oxygens
3527 colvar%dsdr(1:3, ii) = colvar%dsdr(1:3, ii) + qloc(ii)*m(ii)*dnoo(1:3, jj, ii)/qtot
3528 colvar%dsdr(1:3, jj) = colvar%dsdr(1:3, jj) &
3529 - qloc(ii)*m(ii)*dnoo(1:3, jj, ii)/qtot
3533 colvar%ss = log(qtot)/lambda
3542 END SUBROUTINE hydronium_shell_colvar
3553 SUBROUTINE hydronium_dist_colvar(colvar, cell, subsys, particles)
3558 POINTER :: particles
3560 INTEGER :: i, ii, j, jj, k, kk, n_hydrogens, &
3561 n_oxygens, offseth, pf, pm, poh, qf, &
3563 REAL(
dp) :: drji, drki, fscalar, invden, lambda, nh, nn, num, rion, rion_den, rion_num, &
3564 rji(3), rki(3), roh, rrel, sum_expfac_f, sum_expfac_noh
3565 REAL(
dp),
ALLOCATABLE,
DIMENSION(:) :: dexpfac_f, dexpfac_noh, df, dm, &
3566 expfac_f, expfac_f_rki, expfac_noh, f, &
3568 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :) :: dexpfac_f_rki
3569 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :, :) :: ddist_rki, dnoh
3570 REAL(
dp),
DIMENSION(3) :: rpi, rpj, rpk
3574 n_oxygens = colvar%hydronium_dist_param%n_oxygens
3575 n_hydrogens = colvar%hydronium_dist_param%n_hydrogens
3576 poh = colvar%hydronium_dist_param%poh
3577 qoh = colvar%hydronium_dist_param%qoh
3578 roh = colvar%hydronium_dist_param%roh
3579 pm = colvar%hydronium_dist_param%pm
3580 qm = colvar%hydronium_dist_param%qm
3581 nh = colvar%hydronium_dist_param%nh
3582 pf = colvar%hydronium_dist_param%pf
3583 qf = colvar%hydronium_dist_param%qf
3584 nn = colvar%hydronium_dist_param%nn
3585 lambda = colvar%hydronium_dist_param%lambda
3587 NULLIFY (particles_i)
3589 IF (
PRESENT(particles))
THEN
3590 my_particles => particles
3592 cpassert(
PRESENT(subsys))
3594 my_particles => particles_i%els
3597 ALLOCATE (dnoh(3, n_hydrogens, n_oxygens))
3598 ALLOCATE (noh(n_oxygens))
3599 ALLOCATE (m(n_oxygens), dm(n_oxygens))
3600 ALLOCATE (f(n_oxygens), df(n_oxygens))
3601 ALLOCATE (expfac_noh(n_oxygens), dexpfac_noh(n_oxygens))
3602 ALLOCATE (expfac_f(n_oxygens), dexpfac_f(n_oxygens))
3603 ALLOCATE (ddist_rki(3, n_oxygens, n_oxygens))
3604 ALLOCATE (expfac_f_rki(n_oxygens))
3605 ALLOCATE (dexpfac_f_rki(n_oxygens, n_oxygens))
3617 sum_expfac_noh = 0._dp
3618 sum_expfac_f = 0._dp
3620 expfac_f_rki = 0._dp
3621 dexpfac_f_rki = 0._dp
3624 DO ii = 1, n_oxygens
3625 i = colvar%hydronium_dist_param%i_oxygens(ii)
3626 rpi(:) = my_particles(i)%r(1:3)
3627 DO jj = 1, n_hydrogens
3628 j = colvar%hydronium_dist_param%i_hydrogens(jj)
3629 rpj(:) = my_particles(j)%r(1:3)
3630 rji =
pbc(rpj, rpi, cell)
3631 drji = sqrt(sum(rji**2))
3633 num = (1.0_dp - rrel**poh)
3634 invden = 1.0_dp/(1.0_dp - rrel**qoh)
3635 IF (abs(1.0_dp - rrel) > 1.0e-6_dp)
THEN
3636 noh(ii) = noh(ii) + num*invden
3637 fscalar = ((-poh*(rrel**(poh - 1))*invden) &
3638 + num*(invden)**2*qoh*(rrel**(qoh - 1)))/(drji*roh)
3639 dnoh(1:3, jj, ii) = rji(1:3)*fscalar
3642 noh(ii) = noh(ii) + real(poh,
dp)/real(qoh,
dp)
3643 fscalar = real(poh*(poh - qoh),
dp)/(real(2*qoh,
dp)*roh*drji)
3644 dnoh(1:3, jj, ii) = rji(1:3)*fscalar
3650 DO ii = 1, n_oxygens
3651 num = 1.0_dp - (noh(ii)/nh)**pm
3652 invden = 1.0_dp/(1.0_dp - (noh(ii)/nh)**qm)
3653 m(ii) = 1.0_dp - num*invden
3654 dm(ii) = (pm*(noh(ii)/nh)**(pm - 1)*invden - qm*num*(invden**2)* &
3655 (noh(ii)/nh)**(qm - 1))/nh
3656 expfac_noh(ii) = exp(lambda*noh(ii))
3657 dexpfac_noh(ii) = lambda*expfac_noh(ii)
3658 sum_expfac_noh = sum_expfac_noh + expfac_noh(ii)
3662 DO ii = 1, n_oxygens
3663 i = colvar%hydronium_dist_param%i_oxygens(ii)
3664 num = 1.0_dp - (noh(ii)/nn)**pf
3665 invden = 1.0_dp/(1.0_dp - (noh(ii)/nn)**qf)
3667 df(ii) = (-pf*(noh(ii)/nn)**(pf - 1)*invden + qf*num*(invden**2)* &
3668 (noh(ii)/nn)**(qf - 1))/nn
3669 expfac_f(ii) = exp(lambda*f(ii))
3670 dexpfac_f(ii) = lambda*expfac_f(ii)
3671 sum_expfac_f = sum_expfac_f + expfac_f(ii)
3675 DO ii = 1, n_oxygens
3676 i = colvar%hydronium_dist_param%i_oxygens(ii)
3677 rpi(:) = my_particles(i)%r(1:3)
3678 DO kk = 1, n_oxygens
3680 k = colvar%hydronium_dist_param%i_oxygens(kk)
3681 rpk(:) = my_particles(k)%r(1:3)
3682 rki =
pbc(rpk, rpi, cell)
3683 drki = sqrt(sum(rki**2))
3684 expfac_f_rki(ii) = expfac_f_rki(ii) + drki*expfac_f(kk)
3685 ddist_rki(1:3, kk, ii) = rki(1:3)/drki
3686 dexpfac_f_rki(kk, ii) = drki*dexpfac_f(kk)
3688 rion_num = rion_num + m(ii)*expfac_noh(ii)*expfac_f_rki(ii)
3692 rion_den = sum_expfac_noh*sum_expfac_f
3693 rion = rion_num/rion_den
3698 DO ii = 1, n_oxygens
3699 DO jj = 1, n_hydrogens
3700 colvar%dsdr(1:3, ii) = colvar%dsdr(1:3, ii) &
3701 + dm(ii)*dnoh(1:3, jj, ii)*expfac_noh(ii) &
3702 *expfac_f_rki(ii)/rion_den
3703 colvar%dsdr(1:3, offseth + jj) = colvar%dsdr(1:3, offseth + jj) &
3704 - dm(ii)*dnoh(1:3, jj, ii)*expfac_noh(ii) &
3705 *expfac_f_rki(ii)/rion_den
3706 colvar%dsdr(1:3, ii) = colvar%dsdr(1:3, ii) &
3707 + m(ii)*dexpfac_noh(ii)*dnoh(1:3, jj, ii) &
3708 *expfac_f_rki(ii)/rion_den
3709 colvar%dsdr(1:3, offseth + jj) = colvar%dsdr(1:3, offseth + jj) &
3710 - m(ii)*dexpfac_noh(ii)*dnoh(1:3, jj, ii) &
3711 *expfac_f_rki(ii)/rion_den
3713 DO kk = 1, n_oxygens
3715 colvar%dsdr(1:3, kk) = colvar%dsdr(1:3, kk) &
3716 - m(ii)*expfac_noh(ii)*ddist_rki(1:3, kk, ii) &
3717 *expfac_f(kk)/rion_den
3718 colvar%dsdr(1:3, ii) = colvar%dsdr(1:3, ii) &
3719 + m(ii)*expfac_noh(ii)*ddist_rki(1:3, kk, ii) &
3720 *expfac_f(kk)/rion_den
3721 DO jj = 1, n_hydrogens
3722 colvar%dsdr(1:3, kk) = colvar%dsdr(1:3, kk) &
3723 + m(ii)*expfac_noh(ii)*dexpfac_f_rki(kk, ii) &
3724 *df(kk)*dnoh(1:3, jj, kk)/rion_den
3725 colvar%dsdr(1:3, offseth + jj) = colvar%dsdr(1:3, offseth + jj) &
3726 - m(ii)*expfac_noh(ii)*dexpfac_f_rki(kk, ii) &
3727 *df(kk)*dnoh(1:3, jj, kk)/rion_den
3732 DO ii = 1, n_oxygens
3733 DO jj = 1, n_hydrogens
3734 colvar%dsdr(1:3, ii) = colvar%dsdr(1:3, ii) &
3735 - rion_num*sum_expfac_f*dexpfac_noh(ii) &
3736 *dnoh(1:3, jj, ii)/(rion_den**2)
3737 colvar%dsdr(1:3, offseth + jj) = colvar%dsdr(1:3, offseth + jj) &
3738 + rion_num*sum_expfac_f*dexpfac_noh(ii) &
3739 *dnoh(1:3, jj, ii)/(rion_den**2)
3740 colvar%dsdr(1:3, ii) = colvar%dsdr(1:3, ii) &
3741 - rion_num*sum_expfac_noh*dexpfac_f(ii)*df(ii) &
3742 *dnoh(1:3, jj, ii)/(rion_den**2)
3743 colvar%dsdr(1:3, offseth + jj) = colvar%dsdr(1:3, offseth + jj) &
3744 + rion_num*sum_expfac_noh*dexpfac_f(ii)*df(ii) &
3745 *dnoh(1:3, jj, ii)/(rion_den**2)
3749 DEALLOCATE (noh, m, f, expfac_noh, expfac_f)
3750 DEALLOCATE (dnoh, dm, df, dexpfac_noh, dexpfac_f)
3751 DEALLOCATE (ddist_rki, expfac_f_rki, dexpfac_f_rki)
3753 END SUBROUTINE hydronium_dist_colvar
3766 SUBROUTINE acid_hyd_dist_colvar(colvar, cell, subsys, particles)
3771 POINTER :: particles
3773 INTEGER :: i, ii, j, jj, k, kk, n_hydrogens, &
3774 n_oxygens_acid, n_oxygens_water, &
3775 offseth, offseto, paoh, pcut, pwoh, &
3777 REAL(
dp),
ALLOCATABLE,
DIMENSION(:) :: dexpfac, expfac, nwoh
3778 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :) :: dexpfac_rik
3779 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :, :) :: ddist_rik, dnaoh, dnwoh
3780 REAL(kind=
dp) :: dfcut, drik, drji, drjk, fbrace, fcut, fscalar, invden, invden_cut, lambda, &
3781 naoh, nc, num, num_cut, raoh, rik(3), rion, rion_den, rion_num, rji(3), rjk(3), rpi(3), &
3782 rpj(3), rpk(3), rrel, rwoh
3786 NULLIFY (my_particles, particles_i)
3788 n_oxygens_water = colvar%acid_hyd_dist_param%n_oxygens_water
3789 n_oxygens_acid = colvar%acid_hyd_dist_param%n_oxygens_acid
3790 n_hydrogens = colvar%acid_hyd_dist_param%n_hydrogens
3791 pwoh = colvar%acid_hyd_dist_param%pwoh
3792 qwoh = colvar%acid_hyd_dist_param%qwoh
3793 paoh = colvar%acid_hyd_dist_param%paoh
3794 qaoh = colvar%acid_hyd_dist_param%qaoh
3795 pcut = colvar%acid_hyd_dist_param%pcut
3796 qcut = colvar%acid_hyd_dist_param%qcut
3797 rwoh = colvar%acid_hyd_dist_param%rwoh
3798 raoh = colvar%acid_hyd_dist_param%raoh
3799 nc = colvar%acid_hyd_dist_param%nc
3800 lambda = colvar%acid_hyd_dist_param%lambda
3801 ALLOCATE (expfac(n_oxygens_water))
3802 ALLOCATE (nwoh(n_oxygens_water))
3803 ALLOCATE (dnwoh(3, n_hydrogens, n_oxygens_water))
3804 ALLOCATE (dnaoh(3, n_hydrogens, n_oxygens_acid))
3805 ALLOCATE (dexpfac(n_oxygens_water))
3806 ALLOCATE (ddist_rik(3, n_oxygens_water, n_oxygens_acid))
3807 ALLOCATE (dexpfac_rik(n_oxygens_water, n_oxygens_acid))
3812 dnaoh(:, :, :) = 0._dp
3813 dnwoh(:, :, :) = 0._dp
3814 ddist_rik(:, :, :) = 0._dp
3816 dexpfac_rik(:, :) = 0._dp
3819 IF (
PRESENT(particles))
THEN
3820 my_particles => particles
3822 cpassert(
PRESENT(subsys))
3824 my_particles => particles_i%els
3828 DO ii = 1, n_oxygens_water
3829 i = colvar%acid_hyd_dist_param%i_oxygens_water(ii)
3830 rpi(:) = my_particles(i)%r(1:3)
3831 DO jj = 1, n_hydrogens
3832 j = colvar%acid_hyd_dist_param%i_hydrogens(jj)
3833 rpj(:) = my_particles(j)%r(1:3)
3834 rji =
pbc(rpj, rpi, cell)
3835 drji = sqrt(sum(rji**2))
3837 num = 1.0_dp - rrel**pwoh
3838 invden = 1.0_dp/(1.0_dp - rrel**qwoh)
3839 IF (abs(1.0_dp - rrel) > 1.0e-6_dp)
THEN
3840 nwoh(ii) = nwoh(ii) + num*invden
3841 fscalar = (-pwoh*(rrel**(pwoh - 1))*invden &
3842 + num*(invden**2)*qwoh*(rrel**(qwoh - 1)))/(drji*rwoh)
3843 dnwoh(1:3, jj, ii) = rji(1:3)*fscalar
3846 nwoh(ii) = nwoh(ii) + real(pwoh,
dp)/real(qwoh,
dp)
3847 fscalar = real(pwoh*(pwoh - qwoh),
dp)/(real(2*qwoh,
dp)*rwoh*drji)
3848 dnwoh(1:3, jj, ii) = rji(1:3)*fscalar
3851 expfac(ii) = exp(lambda*nwoh(ii))
3852 dexpfac(ii) = lambda*expfac(ii)
3853 rion_den = rion_den + expfac(ii)
3857 DO kk = 1, n_oxygens_acid
3858 k = colvar%acid_hyd_dist_param%i_oxygens_acid(kk)
3859 rpk(:) = my_particles(k)%r(1:3)
3860 DO ii = 1, n_oxygens_water
3861 i = colvar%acid_hyd_dist_param%i_oxygens_water(ii)
3862 rpi(:) = my_particles(i)%r(1:3)
3863 rik =
pbc(rpi, rpk, cell)
3864 drik = sqrt(sum(rik**2))
3865 rion_num = rion_num + drik*expfac(ii)
3866 ddist_rik(1:3, ii, kk) = rik(1:3)/drik
3867 dexpfac_rik(ii, kk) = drik*dexpfac(ii)
3872 DO kk = 1, n_oxygens_acid
3873 k = colvar%acid_hyd_dist_param%i_oxygens_acid(kk)
3874 rpk(:) = my_particles(k)%r(1:3)
3875 DO jj = 1, n_hydrogens
3876 j = colvar%acid_hyd_dist_param%i_hydrogens(jj)
3877 rpj(:) = my_particles(j)%r(1:3)
3878 rjk =
pbc(rpj, rpk, cell)
3879 drjk = sqrt(sum(rjk**2))
3881 num = 1.0_dp - rrel**paoh
3882 invden = 1.0_dp/(1.0_dp - rrel**qaoh)
3883 IF (abs(1.0_dp - rrel) > 1.0e-6_dp)
THEN
3884 naoh = naoh + num*invden
3885 fscalar = (-paoh*(rrel**(paoh - 1))*invden &
3886 + num*(invden**2)*qaoh*(rrel**(qaoh - 1)))/(drjk*raoh)
3887 dnaoh(1:3, jj, kk) = rjk(1:3)*fscalar
3890 naoh = naoh + real(paoh,
dp)/real(qaoh,
dp)
3891 fscalar = real(paoh*(paoh - qaoh),
dp)/(real(2*qaoh,
dp)*raoh*drjk)
3892 dnaoh(1:3, jj, kk) = rjk(1:3)*fscalar
3896 num_cut = 1.0_dp - (naoh/nc)**pcut
3897 invden_cut = 1.0_dp/(1.0_dp - (naoh/nc)**qcut)
3898 fcut = num_cut*invden_cut
3902 fbrace = rion_num/rion_den/n_oxygens_acid
3907 dfcut = ((-pcut*(naoh/nc)**(pcut - 1)*invden_cut) &
3908 + num_cut*(invden_cut**2)*qcut*(naoh/nc)**(qcut - 1))/nc
3909 offseto = n_oxygens_water
3910 offseth = n_oxygens_water + n_oxygens_acid
3911 DO kk = 1, n_oxygens_acid
3912 DO jj = 1, n_hydrogens
3913 colvar%dsdr(1:3, offseto + kk) = colvar%dsdr(1:3, offseto + kk) &
3914 + dfcut*dnaoh(1:3, jj, kk)*fbrace
3915 colvar%dsdr(1:3, offseth + jj) = colvar%dsdr(1:3, offseth + jj) &
3916 - dfcut*dnaoh(1:3, jj, kk)*fbrace
3922 DO kk = 1, n_oxygens_acid
3923 DO ii = 1, n_oxygens_water
3924 colvar%dsdr(1:3, offseto + kk) = colvar%dsdr(1:3, offseto + kk) &
3925 + fcut*ddist_rik(1:3, ii, kk)*expfac(ii)/rion_den/n_oxygens_acid
3927 colvar%dsdr(1:3, ii) = colvar%dsdr(1:3, ii) &
3928 - fcut*ddist_rik(1:3, ii, kk)*expfac(ii)/rion_den/n_oxygens_acid
3930 DO jj = 1, n_hydrogens
3931 colvar%dsdr(1:3, ii) = colvar%dsdr(1:3, ii) &
3932 + fcut*dexpfac_rik(ii, kk)*dnwoh(1:3, jj, ii)/rion_den/n_oxygens_acid
3934 colvar%dsdr(1:3, offseth + jj) = colvar%dsdr(1:3, offseth + jj) &
3935 - fcut*dexpfac_rik(ii, kk)*dnwoh(1:3, jj, ii)/rion_den/n_oxygens_acid
3941 DO ii = 1, n_oxygens_water
3942 DO jj = 1, n_hydrogens
3943 colvar%dsdr(1:3, ii) = colvar%dsdr(1:3, ii) &
3944 - fcut*rion_num*dexpfac(ii)*dnwoh(1:3, jj, ii)/2.0_dp/(rion_den**2)
3945 colvar%dsdr(1:3, offseth + jj) = colvar%dsdr(1:3, offseth + jj) &
3946 + fcut*rion_num*dexpfac(ii)*dnwoh(1:3, jj, ii)/2.0_dp/(rion_den**2)
3950 END SUBROUTINE acid_hyd_dist_colvar
3963 SUBROUTINE acid_hyd_shell_colvar(colvar, cell, subsys, particles)
3968 POINTER :: particles
3970 INTEGER :: i, ii, j, jj, k, kk, n_hydrogens, n_oxygens_acid, n_oxygens_water, offseth, &
3971 offseto, paoh, pcut, pm, poo, pwoh, qaoh, qcut, qm, qoo, qwoh, tt
3972 REAL(
dp),
ALLOCATABLE,
DIMENSION(:) :: dm, m, noo, nwoh, qloc
3973 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :, :) :: dnaoh, dnoo, dnwoh
3974 REAL(kind=
dp) :: dfcut, drji, drjk, drki, fcut, fscalar, invden, invden_cut, lambda, naoh, &
3975 nc, nh, num, num_cut, qsol, qtot, raoh, rji(3), rjk(3), rki(3), roo, rpi(3), rpj(3), &
3980 NULLIFY (my_particles, particles_i)
3982 n_oxygens_water = colvar%acid_hyd_shell_param%n_oxygens_water
3983 n_oxygens_acid = colvar%acid_hyd_shell_param%n_oxygens_acid
3984 n_hydrogens = colvar%acid_hyd_shell_param%n_hydrogens
3985 pwoh = colvar%acid_hyd_shell_param%pwoh
3986 qwoh = colvar%acid_hyd_shell_param%qwoh
3987 paoh = colvar%acid_hyd_shell_param%paoh
3988 qaoh = colvar%acid_hyd_shell_param%qaoh
3989 poo = colvar%acid_hyd_shell_param%poo
3990 qoo = colvar%acid_hyd_shell_param%qoo
3991 pm = colvar%acid_hyd_shell_param%pm
3992 qm = colvar%acid_hyd_shell_param%qm
3993 pcut = colvar%acid_hyd_shell_param%pcut
3994 qcut = colvar%acid_hyd_shell_param%qcut
3995 rwoh = colvar%acid_hyd_shell_param%rwoh
3996 raoh = colvar%acid_hyd_shell_param%raoh
3997 roo = colvar%acid_hyd_shell_param%roo
3998 nc = colvar%acid_hyd_shell_param%nc
3999 nh = colvar%acid_hyd_shell_param%nh
4000 lambda = colvar%acid_hyd_shell_param%lambda
4001 ALLOCATE (nwoh(n_oxygens_water))
4002 ALLOCATE (dnwoh(3, n_hydrogens, n_oxygens_water))
4003 ALLOCATE (dnaoh(3, n_hydrogens, n_oxygens_acid))
4004 ALLOCATE (m(n_oxygens_water))
4005 ALLOCATE (dm(n_oxygens_water))
4006 ALLOCATE (noo(n_oxygens_water))
4007 ALLOCATE (dnoo(3, n_oxygens_water + n_oxygens_acid, n_oxygens_water))
4008 ALLOCATE (qloc(n_oxygens_water))
4012 dnaoh(:, :, :) = 0._dp
4013 dnwoh(:, :, :) = 0._dp
4014 dnoo(:, :, :) = 0._dp
4020 IF (
PRESENT(particles))
THEN
4021 my_particles => particles
4023 cpassert(
PRESENT(subsys))
4025 my_particles => particles_i%els
4029 DO ii = 1, n_oxygens_water
4030 i = colvar%acid_hyd_shell_param%i_oxygens_water(ii)
4031 rpi(:) = my_particles(i)%r(1:3)
4032 DO jj = 1, n_hydrogens
4033 j = colvar%acid_hyd_shell_param%i_hydrogens(jj)
4034 rpj(:) = my_particles(j)%r(1:3)
4035 rji =
pbc(rpj, rpi, cell)
4036 drji = sqrt(sum(rji**2))
4038 num = 1.0_dp - rrel**pwoh
4039 invden = 1.0_dp/(1.0_dp - rrel**qwoh)
4040 IF (abs(1.0_dp - rrel) > 1.0e-6_dp)
THEN
4041 nwoh(ii) = nwoh(ii) + num*invden
4042 fscalar = (-pwoh*(rrel**(pwoh - 1))*invden &
4043 + num*(invden**2)*qwoh*(rrel**(qwoh - 1)))/(drji*rwoh)
4044 dnwoh(1:3, jj, ii) = rji(1:3)*fscalar
4047 nwoh(ii) = nwoh(ii) + real(pwoh,
dp)/real(qwoh,
dp)
4048 fscalar = real(pwoh*(pwoh - qwoh),
dp)/(real(2*qwoh,
dp)*rwoh*drji)
4049 dnwoh(1:3, jj, ii) = rji(1:3)*fscalar
4055 DO ii = 1, n_oxygens_water
4056 num = 1.0_dp - (nwoh(ii)/nh)**pm
4057 invden = 1.0_dp/(1.0_dp - (nwoh(ii)/nh)**qm)
4058 m(ii) = 1.0_dp - num*invden
4059 dm(ii) = (pm*(nwoh(ii)/nh)**(pm - 1)*invden - qm*num*(invden**2)* &
4060 (nwoh(ii)/nh)**(qm - 1))/nh
4064 DO ii = 1, n_oxygens_water
4065 i = colvar%acid_hyd_shell_param%i_oxygens_water(ii)
4066 rpi(:) = my_particles(i)%r(1:3)
4067 DO kk = 1, n_oxygens_water + n_oxygens_acid
4069 IF (kk <= n_oxygens_water)
THEN
4070 k = colvar%acid_hyd_shell_param%i_oxygens_water(kk)
4071 rpk(:) = my_particles(k)%r(1:3)
4073 tt = kk - n_oxygens_water
4074 k = colvar%acid_hyd_shell_param%i_oxygens_acid(tt)
4075 rpk(:) = my_particles(k)%r(1:3)
4077 rki =
pbc(rpk, rpi, cell)
4078 drki = sqrt(sum(rki**2))
4080 num = 1.0_dp - rrel**poo
4081 invden = 1.0_dp/(1.0_dp - rrel**qoo)
4082 IF (abs(1.0_dp - rrel) > 1.0e-6_dp)
THEN
4083 noo(ii) = noo(ii) + num*invden
4084 fscalar = (-poo*(rrel**(poo - 1))*invden &
4085 + num*(invden**2)*qoo*(rrel**(qoo - 1)))/(drki*roo)
4086 dnoo(1:3, kk, ii) = rki(1:3)*fscalar
4089 noo(ii) = noo(ii) + real(poo,
dp)/real(qoo,
dp)
4090 fscalar = real(poo*(poo - qoo),
dp)/(real(2*qoo,
dp)*roo*drki)
4091 dnoo(1:3, kk, ii) = rki(1:3)*fscalar
4097 DO kk = 1, n_oxygens_acid
4098 k = colvar%acid_hyd_shell_param%i_oxygens_acid(kk)
4099 rpk(:) = my_particles(k)%r(1:3)
4100 DO jj = 1, n_hydrogens
4101 j = colvar%acid_hyd_shell_param%i_hydrogens(jj)
4102 rpj(:) = my_particles(j)%r(1:3)
4103 rjk =
pbc(rpj, rpk, cell)
4104 drjk = sqrt(sum(rjk**2))
4106 num = 1.0_dp - rrel**paoh
4107 invden = 1.0_dp/(1.0_dp - rrel**qaoh)
4108 IF (abs(1.0_dp - rrel) > 1.0e-6_dp)
THEN
4109 naoh = naoh + num*invden
4110 fscalar = (-paoh*(rrel**(paoh - 1))*invden &
4111 + num*(invden**2)*qaoh*(rrel**(qaoh - 1)))/(drjk*raoh)
4112 dnaoh(1:3, jj, kk) = rjk(1:3)*fscalar
4115 naoh = naoh + real(paoh,
dp)/real(qaoh,
dp)
4116 fscalar = real(paoh*(paoh - qaoh),
dp)/(real(2*qaoh,
dp)*raoh*drjk)
4117 dnaoh(1:3, jj, kk) = rjk(1:3)*fscalar
4121 num_cut = 1.0_dp - (naoh/nc)**pcut
4122 invden_cut = 1.0_dp/(1.0_dp - (naoh/nc)**qcut)
4123 fcut = num_cut*invden_cut
4126 DO ii = 1, n_oxygens_water
4127 qloc(ii) = exp(lambda*m(ii)*noo(ii))
4128 qtot = qtot + qloc(ii)
4130 qsol = log(qtot)/lambda
4131 colvar%ss = fcut*qsol
4134 dfcut = ((-pcut*(naoh/nc)**(pcut - 1)*invden_cut) &
4135 + num_cut*(invden_cut**2)*qcut*(naoh/nc)**(qcut - 1))/nc
4136 offseto = n_oxygens_water
4137 offseth = n_oxygens_water + n_oxygens_acid
4138 DO kk = 1, n_oxygens_acid
4139 DO jj = 1, n_hydrogens
4140 colvar%dsdr(1:3, offseto + kk) = colvar%dsdr(1:3, offseto + kk) &
4141 + dfcut*dnaoh(1:3, jj, kk)*qsol
4142 colvar%dsdr(1:3, offseth + jj) = colvar%dsdr(1:3, offseth + jj) &
4143 - dfcut*dnaoh(1:3, jj, kk)*qsol
4149 DO ii = 1, n_oxygens_water
4150 fscalar = fcut*qloc(ii)*dm(ii)*noo(ii)/qtot
4151 DO jj = 1, n_hydrogens
4152 colvar%dsdr(1:3, ii) = colvar%dsdr(1:3, ii) &
4153 + fscalar*dnwoh(1:3, jj, ii)
4154 colvar%dsdr(1:3, offseth + jj) = colvar%dsdr(1:3, offseth + jj) &
4155 - fscalar*dnwoh(1:3, jj, ii)
4159 DO ii = 1, n_oxygens_water
4160 fscalar = fcut*qloc(ii)*m(ii)/qtot
4161 DO kk = 1, n_oxygens_water + n_oxygens_acid
4163 colvar%dsdr(1:3, ii) = colvar%dsdr(1:3, ii) + fscalar*dnoo(1:3, kk, ii)
4164 colvar%dsdr(1:3, kk) = colvar%dsdr(1:3, kk) - fscalar*dnoo(1:3, kk, ii)
4168 END SUBROUTINE acid_hyd_shell_colvar
4180 SUBROUTINE coord_colvar(colvar, cell, subsys, particles)
4185 POINTER :: particles
4187 INTEGER :: i, ii, j, jj, k, kk, n_atoms_from, &
4188 n_atoms_to_a, n_atoms_to_b, p_a, p_b, &
4190 REAL(
dp) :: dfunc_ij, dfunc_jk, func_ij, func_jk, func_k, inv_n_atoms_from, invden_ij, &
4191 invden_jk, ncoord, num_ij, num_jk, r_0_a, r_0_b, rdist_ij, rdist_jk, rij, rjk
4192 REAL(
dp),
DIMENSION(3) :: ftmp_i, ftmp_j, ftmp_k, ss, xij, xjk, &
4200 NULLIFY (particles_i)
4202 IF (
PRESENT(particles))
THEN
4203 my_particles => particles
4205 cpassert(
PRESENT(subsys))
4207 my_particles => particles_i%els
4209 n_atoms_to_a = colvar%coord_param%n_atoms_to
4210 n_atoms_to_b = colvar%coord_param%n_atoms_to_b
4211 n_atoms_from = colvar%coord_param%n_atoms_from
4212 p_a = colvar%coord_param%nncrd
4213 q_a = colvar%coord_param%ndcrd
4214 r_0_a = colvar%coord_param%r_0
4215 p_b = colvar%coord_param%nncrd_b
4216 q_b = colvar%coord_param%ndcrd_b
4217 r_0_b = colvar%coord_param%r_0_b
4220 inv_n_atoms_from = 1.0_dp/real(n_atoms_from, kind=
dp)
4221 DO ii = 1, n_atoms_from
4222 i = colvar%coord_param%i_at_from(ii)
4223 CALL get_coordinates(colvar, i, xpi, my_particles)
4224 DO jj = 1, n_atoms_to_a
4225 j = colvar%coord_param%i_at_to(jj)
4226 CALL get_coordinates(colvar, j, xpj, my_particles)
4229 ss = matmul(cell%h_inv, xpi(:) - xpj(:))
4231 xij = matmul(cell%hmat, ss)
4232 rij = sqrt(xij(1)**2 + xij(2)**2 + xij(3)**2)
4233 IF (rij < 1.0e-8_dp) cycle
4234 rdist_ij = rij/r_0_a
4235 IF (abs(1.0_dp - rdist_ij) > epsilon(0.0_dp)*1.0e+4_dp)
THEN
4236 num_ij = (1.0_dp - rdist_ij**p_a)
4237 invden_ij = 1.0_dp/(1.0_dp - rdist_ij**q_a)
4238 func_ij = num_ij*invden_ij
4239 IF (rij < 1.0e-8_dp)
THEN
4243 dfunc_ij = (-p_a*rdist_ij**(p_a - 1)*invden_ij &
4244 + num_ij*(invden_ij)**2*q_a*rdist_ij**(q_a - 1))/(rij*r_0_a)
4248 func_ij = real(p_a, kind=
dp)/real(q_a, kind=
dp)
4249 dfunc_ij = real(p_a, kind=
dp)*real((-q_a + p_a), kind=
dp)/(real(2*q_a, kind=
dp)*r_0_a)
4251 IF (n_atoms_to_b /= 0)
THEN
4253 DO kk = 1, n_atoms_to_b
4254 k = colvar%coord_param%i_at_to_b(kk)
4256 CALL get_coordinates(colvar, k, xpk, my_particles)
4257 ss = matmul(cell%h_inv, xpj(:) - xpk(:))
4259 xjk = matmul(cell%hmat, ss)
4260 rjk = sqrt(xjk(1)**2 + xjk(2)**2 + xjk(3)**2)
4261 IF (rjk < 1.0e-8_dp) cycle
4262 rdist_jk = rjk/r_0_b
4263 IF (abs(1.0_dp - rdist_jk) > epsilon(0.0_dp)*1.0e+4_dp)
THEN
4264 num_jk = (1.0_dp - rdist_jk**p_b)
4265 invden_jk = 1.0_dp/(1.0_dp - rdist_jk**q_b)
4266 func_jk = num_jk*invden_jk
4267 IF (rjk < 1.0e-8_dp)
THEN
4271 dfunc_jk = (-p_b*rdist_jk**(p_b - 1)*invden_jk &
4272 + num_jk*(invden_jk)**2*q_b*rdist_jk**(q_b - 1))/(rjk*r_0_b)
4276 func_jk = real(p_b, kind=
dp)/real(q_b, kind=
dp)
4277 dfunc_jk = real(p_b, kind=
dp)*real((-q_b + p_b), kind=
dp)/(real(2*q_b, kind=
dp)*r_0_b)
4279 func_k = func_k + func_jk
4280 ftmp_k = -func_ij*dfunc_jk*xjk
4281 CALL put_derivative(colvar, n_atoms_from + n_atoms_to_a + kk, ftmp_k)
4283 ftmp_j = -dfunc_ij*xij*func_jk + func_ij*dfunc_jk*xjk
4284 CALL put_derivative(colvar, n_atoms_from + jj, ftmp_j)
4289 ftmp_j = -dfunc_ij*xij
4290 CALL put_derivative(colvar, n_atoms_from + jj, ftmp_j)
4292 ncoord = ncoord + func_ij*func_k
4293 ftmp_i = dfunc_ij*xij*func_k
4294 CALL put_derivative(colvar, ii, ftmp_i)
4297 colvar%ss = ncoord*inv_n_atoms_from
4298 colvar%dsdr(:, :) = colvar%dsdr(:, :)*inv_n_atoms_from
4299 END SUBROUTINE coord_colvar
4308 SUBROUTINE mindist_colvar(colvar, cell, subsys, particles)
4314 POINTER :: particles
4316 INTEGER :: i, ii, j, jj, n_coord_from, n_coord_to, &
4318 REAL(
dp) :: den_n, den_q, fscalar, ftemp_i(3), inv_den_n, inv_den_q, lambda, num_n, num_q, &
4319 qfunc, r12, r_cut, rfact, rij(3), rpi(3), rpj(3)
4320 REAL(
dp),
DIMENSION(:),
POINTER :: dqfunc_dnl, expnl, nlcoord, sum_rij
4321 REAL(
dp),
DIMENSION(:, :, :),
POINTER :: dnlcoord, dqfunc_dr
4328 NULLIFY (particles_i)
4330 IF (
PRESENT(particles))
THEN
4331 my_particles => particles
4333 cpassert(
PRESENT(subsys))
4335 my_particles => particles_i%els
4338 n_dist_from = colvar%mindist_param%n_dist_from
4339 n_coord_from = colvar%mindist_param%n_coord_from
4340 n_coord_to = colvar%mindist_param%n_coord_to
4341 p = colvar%mindist_param%p_exp
4342 q = colvar%mindist_param%q_exp
4343 r_cut = colvar%mindist_param%r_cut
4344 lambda = colvar%mindist_param%lambda
4346 NULLIFY (nlcoord, dnlcoord, dqfunc_dr, dqfunc_dnl, expnl, sum_rij)
4347 ALLOCATE (nlcoord(n_coord_from))
4348 ALLOCATE (dnlcoord(3, n_coord_from, n_coord_to))
4349 ALLOCATE (expnl(n_coord_from))
4350 ALLOCATE (sum_rij(n_coord_from))
4351 ALLOCATE (dqfunc_dr(3, n_dist_from, n_coord_from))
4352 ALLOCATE (dqfunc_dnl(n_coord_from))
4359 DO i = 1, n_coord_from
4360 ii = colvar%mindist_param%i_coord_from(i)
4361 rpi = my_particles(ii)%r(1:3)
4362 DO j = 1, n_coord_to
4363 jj = colvar%mindist_param%i_coord_to(j)
4364 rpj = my_particles(jj)%r(1:3)
4365 rij =
pbc(rpj, rpi, cell)
4366 r12 = sqrt(rij(1)*rij(1) + rij(2)*rij(2) + rij(3)*rij(3))
4368 num_n = 1.0_dp - rfact**p
4369 den_n = 1.0_dp - rfact**q
4370 inv_den_n = 1.0_dp/den_n
4371 IF (abs(inv_den_n) < 1.e-10_dp)
THEN
4372 inv_den_n = 1.e-10_dp
4376 fscalar = (-p*rfact**(p - 1) + num_n*q*rfact**(q - 1)*inv_den_n)*inv_den_n/(r_cut*r12)
4378 dnlcoord(1, i, j) = rij(1)*fscalar
4379 dnlcoord(2, i, j) = rij(2)*fscalar
4380 dnlcoord(3, i, j) = rij(3)*fscalar
4382 nlcoord(i) = nlcoord(i) + num_n*inv_den_n
4384 expnl(i) = exp(lambda*nlcoord(i))
4385 den_q = den_q + expnl(i)
4387 inv_den_q = 1.0_dp/den_q
4394 DO i = 1, n_dist_from
4395 ii = colvar%mindist_param%i_dist_from(i)
4396 rpi = my_particles(ii)%r(1:3)
4397 DO j = 1, n_coord_from
4398 jj = colvar%mindist_param%i_coord_from(j)
4399 rpj = my_particles(jj)%r(1:3)
4400 rij =
pbc(rpj, rpi, cell)
4401 r12 = sqrt(rij(1)*rij(1) + rij(2)*rij(2) + rij(3)*rij(3))
4403 num_q = num_q + r12*expnl(j)
4405 sum_rij(j) = sum_rij(j) + r12
4406 dqfunc_dr(1, i, j) = expnl(j)*rij(1)/r12
4407 dqfunc_dr(2, i, j) = expnl(j)*rij(2)/r12
4408 dqfunc_dr(3, i, j) = expnl(j)*rij(3)/r12
4415 qfunc = num_q*inv_den_q
4416 dqfunc_dr = dqfunc_dr*inv_den_q
4419 DO i = 1, n_coord_from
4420 dqfunc_dnl(i) = lambda*expnl(i)*inv_den_q*(sum_rij(i) - num_q*inv_den_q)
4424 DO i = 1, n_dist_from
4425 DO j = 1, n_coord_from
4426 ftemp_i(1) = dqfunc_dr(1, i, j)
4427 ftemp_i(2) = dqfunc_dr(2, i, j)
4428 ftemp_i(3) = dqfunc_dr(3, i, j)
4430 CALL put_derivative(colvar, i, ftemp_i)
4431 CALL put_derivative(colvar, j + n_dist_from, -ftemp_i)
4435 DO i = 1, n_coord_from
4436 DO j = 1, n_coord_to
4437 ftemp_i(1) = dqfunc_dnl(i)*dnlcoord(1, i, j)
4438 ftemp_i(2) = dqfunc_dnl(i)*dnlcoord(2, i, j)
4439 ftemp_i(3) = dqfunc_dnl(i)*dnlcoord(3, i, j)
4441 CALL put_derivative(colvar, i + n_dist_from, ftemp_i)
4442 CALL put_derivative(colvar, j + n_dist_from + n_coord_from, -ftemp_i)
4447 DEALLOCATE (nlcoord)
4448 DEALLOCATE (dnlcoord)
4450 DEALLOCATE (dqfunc_dr)
4451 DEALLOCATE (sum_rij)
4452 DEALLOCATE (dqfunc_dnl)
4454 END SUBROUTINE mindist_colvar
4464 SUBROUTINE combine_colvar(colvar, cell, subsys, particles)
4469 POINTER :: particles
4471 CHARACTER(LEN=default_string_length) :: def_error, this_error
4472 CHARACTER(LEN=default_string_length), &
4473 ALLOCATABLE,
DIMENSION(:) :: my_par
4474 INTEGER :: i, ii, j, ncolv, ndim
4476 REAL(
dp),
ALLOCATABLE,
DIMENSION(:) :: dss_vals, my_val, ss_vals
4477 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :) :: fi
4482 IF (
PRESENT(particles))
THEN
4483 my_particles => particles
4485 cpassert(
PRESENT(subsys))
4487 my_particles => particles_i%els
4490 ncolv =
SIZE(colvar%combine_cvs_param%colvar_p)
4491 ALLOCATE (ss_vals(ncolv))
4492 ALLOCATE (dss_vals(ncolv))
4496 CALL colvar_recursive_eval(colvar%combine_cvs_param%colvar_p(i)%colvar, cell, my_particles)
4497 ss_vals(i) = colvar%combine_cvs_param%colvar_p(i)%colvar%ss
4502 ndim =
SIZE(colvar%combine_cvs_param%c_parameters) + &
4503 SIZE(colvar%combine_cvs_param%variables)
4504 ALLOCATE (my_par(ndim))
4505 my_par(1:
SIZE(colvar%combine_cvs_param%variables)) = colvar%combine_cvs_param%variables
4506 my_par(
SIZE(colvar%combine_cvs_param%variables) + 1:) = colvar%combine_cvs_param%c_parameters
4507 ALLOCATE (my_val(ndim))
4508 my_val(1:
SIZE(colvar%combine_cvs_param%variables)) = ss_vals
4509 my_val(
SIZE(colvar%combine_cvs_param%variables) + 1:) = colvar%combine_cvs_param%v_parameters
4510 CALL parsef(1, trim(colvar%combine_cvs_param%function), my_par)
4511 colvar%ss =
evalf(1, my_val)
4513 dss_vals(i) =
evalfd(1, i, my_val, colvar%combine_cvs_param%dx, err)
4514 IF ((abs(err) > colvar%combine_cvs_param%lerr))
THEN
4515 WRITE (this_error,
"(A,G12.6,A)")
"(", err,
")"
4516 WRITE (def_error,
"(A,G12.6,A)")
"(", colvar%combine_cvs_param%lerr,
")"
4519 CALL cp_warn(__location__, &
4520 'ASSERTION (cond) failed at line '//
cp_to_string(__line__)// &
4521 ' Error '//trim(this_error)//
' in computing numerical derivatives larger then'// &
4522 trim(def_error)//
' . ')
4530 ALLOCATE (fi(3, colvar%n_atom_s))
4533 DO j = 1, colvar%combine_cvs_param%colvar_p(i)%colvar%n_atom_s
4535 fi(:, ii) = colvar%combine_cvs_param%colvar_p(i)%colvar%dsdr(:, j)*dss_vals(i)
4539 DO i = 1, colvar%n_atom_s
4540 CALL put_derivative(colvar, i, fi(:, i))
4544 DEALLOCATE (ss_vals)
4545 DEALLOCATE (dss_vals)
4546 END SUBROUTINE combine_colvar
4562 SUBROUTINE reaction_path_colvar(colvar, cell, subsys, particles)
4567 POINTER :: particles
4573 IF (
PRESENT(particles))
THEN
4574 my_particles => particles
4576 cpassert(
PRESENT(subsys))
4578 my_particles => particles_i%els
4581 IF (colvar%reaction_path_param%dist_rmsd)
THEN
4582 CALL rpath_dist_rmsd(colvar, my_particles)
4583 ELSEIF (colvar%reaction_path_param%rmsd)
THEN
4584 CALL rpath_rmsd(colvar, my_particles)
4586 CALL rpath_colvar(colvar, cell, my_particles)
4589 END SUBROUTINE reaction_path_colvar
4600 SUBROUTINE rpath_colvar(colvar, cell, particles)
4605 INTEGER :: i, iend, ii, istart, j, k, ncolv, nconf
4606 REAL(
dp) :: lambda, step_size
4607 REAL(
dp),
ALLOCATABLE,
DIMENSION(:) :: s1, ss_vals
4608 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :) :: ds1, f_vals, fi, s1v
4609 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :, :) :: ds1v
4611 istart = colvar%reaction_path_param%function_bounds(1)
4612 iend = colvar%reaction_path_param%function_bounds(2)
4614 nconf = colvar%reaction_path_param%nr_frames
4615 step_size = colvar%reaction_path_param%step_size
4616 ncolv = colvar%reaction_path_param%n_components
4617 lambda = colvar%reaction_path_param%lambda
4618 ALLOCATE (f_vals(ncolv, istart:iend))
4619 f_vals(:, :) = colvar%reaction_path_param%f_vals
4620 ALLOCATE (ss_vals(ncolv))
4623 CALL colvar_recursive_eval(colvar%reaction_path_param%colvar_p(i)%colvar, cell, particles)
4624 ss_vals(i) = colvar%reaction_path_param%colvar_p(i)%colvar%ss
4627 ALLOCATE (s1v(2, istart:iend))
4628 ALLOCATE (ds1v(ncolv, 2, istart:iend))
4631 ALLOCATE (ds1(ncolv, 2))
4634 s1v(1, k) = real(k, kind=
dp)*step_size*exp(-lambda*dot_product(ss_vals(:) - f_vals(:, k), ss_vals(:) - f_vals(:, k)))
4635 s1v(2, k) = exp(-lambda*dot_product(ss_vals(:) - f_vals(:, k), ss_vals(:) - f_vals(:, k)))
4637 ds1v(j, 1, k) = f_vals(j, k)*s1v(1, k)
4638 ds1v(j, 2, k) = f_vals(j, k)*s1v(2, k)
4648 colvar%ss = s1(1)/s1(2)/real(nconf - 1,
dp)
4650 ALLOCATE (fi(3, colvar%n_atom_s))
4654 DO j = 1, colvar%reaction_path_param%colvar_p(i)%colvar%n_atom_s
4656 fi(:, ii) = colvar%reaction_path_param%colvar_p(i)%colvar%dsdr(:, j)*lambda* &
4657 (ds1(i, 1)/s1(2)/real(nconf - 1,
dp) - colvar%ss*ds1(i, 2)/s1(2))*2.0_dp
4661 DO i = 1, colvar%n_atom_s
4662 CALL put_derivative(colvar, i, fi(:, i))
4667 DEALLOCATE (ss_vals)
4673 END SUBROUTINE rpath_colvar
4684 SUBROUTINE rpath_dist_rmsd(colvar, particles)
4688 INTEGER :: i, iat, ii, ik, natom, nconf, rmsd_atom
4689 INTEGER,
DIMENSION(:),
POINTER :: iatom
4690 REAL(
dp) :: lambda, my_rmsd, s1(2), sum_exp
4691 REAL(
dp),
ALLOCATABLE,
DIMENSION(:) :: r, r0, vec_dif
4692 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :) :: dvec_dif, fi, riat, s1v
4693 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :, :) :: ds1
4694 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :, :, :) :: ds1v
4695 REAL(
dp),
DIMENSION(:, :),
POINTER :: path_conf
4697 nconf = colvar%reaction_path_param%nr_frames
4698 rmsd_atom = colvar%reaction_path_param%n_components
4699 lambda = colvar%reaction_path_param%lambda
4700 path_conf => colvar%reaction_path_param%r_ref
4701 iatom => colvar%reaction_path_param%i_rmsd
4703 natom =
SIZE(particles)
4705 ALLOCATE (r0(3*natom))
4706 ALLOCATE (r(3*natom))
4707 ALLOCATE (riat(3, rmsd_atom))
4708 ALLOCATE (vec_dif(rmsd_atom))
4709 ALLOCATE (dvec_dif(3, rmsd_atom))
4710 ALLOCATE (s1v(2, nconf))
4711 ALLOCATE (ds1v(3, rmsd_atom, 2, nconf))
4712 ALLOCATE (ds1(3, rmsd_atom, 2))
4715 r0(ii + 1) = particles(i)%r(1)
4716 r0(ii + 2) = particles(i)%r(2)
4717 r0(ii + 3) = particles(i)%r(3)
4720 DO iat = 1, rmsd_atom
4722 riat(:, iat) = particles(ii)%r
4728 r(ii + 1) = path_conf(ii + 1, ik)
4729 r(ii + 2) = path_conf(ii + 2, ik)
4730 r(ii + 3) = path_conf(ii + 3, ik)
4733 CALL rmsd3(particles, r, r0, output_unit=-1, my_val=my_rmsd, rotate=.true.)
4736 DO iat = 1, rmsd_atom
4739 vec_dif(iat) = (riat(1, iat) - r(ii + 1))**2 + (riat(2, iat) - r(ii + 2))**2 &
4740 + (riat(3, iat) - r(ii + 3))**2
4741 sum_exp = sum_exp + vec_dif(iat)
4744 s1v(1, ik) = real(ik - 1,
dp)*exp(-lambda*sum_exp)
4745 s1v(2, ik) = exp(-lambda*sum_exp)
4746 DO iat = 1, rmsd_atom
4749 ds1v(1, iat, 1, ik) = r(ii + 1)*s1v(1, ik)
4750 ds1v(1, iat, 2, ik) = r(ii + 1)*s1v(2, ik)
4751 ds1v(2, iat, 1, ik) = r(ii + 2)*s1v(1, ik)
4752 ds1v(2, iat, 2, ik) = r(ii + 2)*s1v(2, ik)
4753 ds1v(3, iat, 1, ik) = r(ii + 3)*s1v(1, ik)
4754 ds1v(3, iat, 2, ik) = r(ii + 3)*s1v(2, ik)
4761 DO iat = 1, rmsd_atom
4768 colvar%ss = s1(1)/s1(2)/real(nconf - 1,
dp)
4770 ALLOCATE (fi(3, rmsd_atom))
4772 DO iat = 1, rmsd_atom
4773 fi(1, iat) = 2.0_dp*lambda/s1(2)/real(nconf - 1,
dp)*(ds1(1, iat, 1) - ds1(1, iat, 2)*s1(1)/s1(2))
4774 fi(2, iat) = 2.0_dp*lambda/s1(2)/real(nconf - 1,
dp)*(ds1(2, iat, 1) - ds1(2, iat, 2)*s1(1)/s1(2))
4775 fi(3, iat) = 2.0_dp*lambda/s1(2)/real(nconf - 1,
dp)*(ds1(3, iat, 1) - ds1(3, iat, 2)*s1(1)/s1(2))
4776 CALL put_derivative(colvar, iat, fi(:, iat))
4783 DEALLOCATE (vec_dif)
4784 DEALLOCATE (dvec_dif)
4789 END SUBROUTINE rpath_dist_rmsd
4796 SUBROUTINE rpath_rmsd(colvar, particles)
4800 INTEGER :: i, iat, ii, ik, natom, nconf, rmsd_atom
4801 INTEGER,
DIMENSION(:),
POINTER :: iatom
4802 REAL(
dp) :: lambda, my_rmsd, s1(2)
4803 REAL(
dp),
ALLOCATABLE,
DIMENSION(:) :: r, r0
4804 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :) :: fi, riat, s1v
4805 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :, :) :: ds1
4806 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :, :, :) :: ds1v
4807 REAL(
dp),
DIMENSION(:, :),
POINTER :: path_conf
4808 REAL(kind=
dp),
ALLOCATABLE,
DIMENSION(:) :: weight
4809 REAL(kind=
dp),
ALLOCATABLE,
DIMENSION(:, :) :: drmsd
4811 nconf = colvar%reaction_path_param%nr_frames
4812 rmsd_atom = colvar%reaction_path_param%n_components
4813 lambda = colvar%reaction_path_param%lambda
4814 path_conf => colvar%reaction_path_param%r_ref
4815 iatom => colvar%reaction_path_param%i_rmsd
4817 natom =
SIZE(particles)
4819 ALLOCATE (r0(3*natom))
4820 ALLOCATE (r(3*natom))
4821 ALLOCATE (riat(3, rmsd_atom))
4822 ALLOCATE (s1v(2, nconf))
4823 ALLOCATE (ds1v(3, rmsd_atom, 2, nconf))
4824 ALLOCATE (ds1(3, rmsd_atom, 2))
4825 ALLOCATE (drmsd(3, natom))
4827 ALLOCATE (weight(natom))
4831 r0(ii + 1) = particles(i)%r(1)
4832 r0(ii + 2) = particles(i)%r(2)
4833 r0(ii + 3) = particles(i)%r(3)
4836 DO iat = 1, rmsd_atom
4838 riat(:, iat) = particles(ii)%r
4843 DO iat = 1, rmsd_atom
4851 r(ii + 1) = path_conf(ii + 1, ik)
4852 r(ii + 2) = path_conf(ii + 2, ik)
4853 r(ii + 3) = path_conf(ii + 3, ik)
4856 CALL rmsd3(particles, r0, r, output_unit=-1, weights=weight, my_val=my_rmsd, &
4857 rotate=.false., drmsd3=drmsd)
4859 s1v(1, ik) = real(ik - 1,
dp)*exp(-lambda*my_rmsd)
4860 s1v(2, ik) = exp(-lambda*my_rmsd)
4861 DO iat = 1, rmsd_atom
4863 ds1v(1, iat, 1, ik) = drmsd(1, i)*s1v(1, ik)
4864 ds1v(1, iat, 2, ik) = drmsd(1, i)*s1v(2, ik)
4865 ds1v(2, iat, 1, ik) = drmsd(2, i)*s1v(1, ik)
4866 ds1v(2, iat, 2, ik) = drmsd(2, i)*s1v(2, ik)
4867 ds1v(3, iat, 1, ik) = drmsd(3, i)*s1v(1, ik)
4868 ds1v(3, iat, 2, ik) = drmsd(3, i)*s1v(2, ik)
4875 DO iat = 1, rmsd_atom
4882 colvar%ss = s1(1)/s1(2)/real(nconf - 1,
dp)
4884 ALLOCATE (fi(3, rmsd_atom))
4886 DO iat = 1, rmsd_atom
4887 fi(1, iat) = -lambda/s1(2)/real(nconf - 1,
dp)*(ds1(1, iat, 1) - ds1(1, iat, 2)*s1(1)/s1(2))
4888 fi(2, iat) = -lambda/s1(2)/real(nconf - 1,
dp)*(ds1(2, iat, 1) - ds1(2, iat, 2)*s1(1)/s1(2))
4889 fi(3, iat) = -lambda/s1(2)/real(nconf - 1,
dp)*(ds1(3, iat, 1) - ds1(3, iat, 2)*s1(1)/s1(2))
4890 CALL put_derivative(colvar, iat, fi(:, iat))
4903 END SUBROUTINE rpath_rmsd
4915 SUBROUTINE distance_from_path_colvar(colvar, cell, subsys, particles)
4920 POINTER :: particles
4926 IF (
PRESENT(particles))
THEN
4927 my_particles => particles
4929 cpassert(
PRESENT(subsys))
4931 my_particles => particles_i%els
4934 IF (colvar%reaction_path_param%dist_rmsd)
THEN
4935 CALL dpath_dist_rmsd(colvar, my_particles)
4936 ELSEIF (colvar%reaction_path_param%rmsd)
THEN
4937 CALL dpath_rmsd(colvar, my_particles)
4939 CALL dpath_colvar(colvar, cell, my_particles)
4942 END SUBROUTINE distance_from_path_colvar
4954 SUBROUTINE dpath_colvar(colvar, cell, particles)
4959 INTEGER :: i, iend, ii, istart, j, k, ncolv
4960 REAL(
dp) :: lambda, s1
4961 REAL(
dp),
ALLOCATABLE,
DIMENSION(:) :: ds1, s1v, ss_vals
4962 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :) :: ds1v, f_vals, fi
4964 istart = colvar%reaction_path_param%function_bounds(1)
4965 iend = colvar%reaction_path_param%function_bounds(2)
4967 ncolv = colvar%reaction_path_param%n_components
4968 lambda = colvar%reaction_path_param%lambda
4969 ALLOCATE (f_vals(ncolv, istart:iend))
4970 f_vals(:, :) = colvar%reaction_path_param%f_vals
4971 ALLOCATE (ss_vals(ncolv))
4974 CALL colvar_recursive_eval(colvar%reaction_path_param%colvar_p(i)%colvar, cell, particles)
4975 ss_vals(i) = colvar%reaction_path_param%colvar_p(i)%colvar%ss
4978 ALLOCATE (s1v(istart:iend))
4979 ALLOCATE (ds1v(ncolv, istart:iend))
4980 ALLOCATE (ds1(ncolv))
4983 s1v(k) = exp(-lambda*dot_product(ss_vals(:) - f_vals(:, k), ss_vals(:) - f_vals(:, k)))
4985 ds1v(j, k) = f_vals(j, k)*s1v(k)
4993 colvar%ss = -1.0_dp/lambda*log(s1)
4995 ALLOCATE (fi(3, colvar%n_atom_s))
4999 DO j = 1, colvar%reaction_path_param%colvar_p(i)%colvar%n_atom_s
5001 fi(:, ii) = colvar%reaction_path_param%colvar_p(i)%colvar%dsdr(:, j)* &
5002 2.0_dp*(ss_vals(i) - ds1(i)/s1)
5006 DO i = 1, colvar%n_atom_s
5007 CALL put_derivative(colvar, i, fi(:, i))
5012 DEALLOCATE (ss_vals)
5017 END SUBROUTINE dpath_colvar
5028 SUBROUTINE dpath_dist_rmsd(colvar, particles)
5033 INTEGER :: i, iat, ii, ik, natom, nconf, rmsd_atom
5034 INTEGER,
DIMENSION(:),
POINTER :: iatom
5035 REAL(
dp) :: lambda, s1, sum_exp
5036 REAL(
dp),
ALLOCATABLE,
DIMENSION(:) :: r, r0, s1v, vec_dif
5037 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :) :: ds1, dvec_dif, fi, riat
5038 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :, :) :: ds1v
5039 REAL(
dp),
DIMENSION(:, :),
POINTER :: path_conf
5041 nconf = colvar%reaction_path_param%nr_frames
5042 rmsd_atom = colvar%reaction_path_param%n_components
5043 lambda = colvar%reaction_path_param%lambda
5044 path_conf => colvar%reaction_path_param%r_ref
5045 iatom => colvar%reaction_path_param%i_rmsd
5047 natom =
SIZE(particles)
5049 ALLOCATE (r0(3*natom))
5050 ALLOCATE (r(3*natom))
5051 ALLOCATE (riat(3, rmsd_atom))
5052 ALLOCATE (vec_dif(rmsd_atom))
5053 ALLOCATE (dvec_dif(3, rmsd_atom))
5054 ALLOCATE (s1v(nconf))
5055 ALLOCATE (ds1v(3, rmsd_atom, nconf))
5056 ALLOCATE (ds1(3, rmsd_atom))
5059 r0(ii + 1) = particles(i)%r(1)
5060 r0(ii + 2) = particles(i)%r(2)
5061 r0(ii + 3) = particles(i)%r(3)
5064 DO iat = 1, rmsd_atom
5066 riat(:, iat) = particles(ii)%r
5072 r(ii + 1) = path_conf(ii + 1, ik)
5073 r(ii + 2) = path_conf(ii + 2, ik)
5074 r(ii + 3) = path_conf(ii + 3, ik)
5077 CALL rmsd3(particles, r, r0, output_unit=-1, rotate=.true.)
5080 DO iat = 1, rmsd_atom
5083 vec_dif(iat) = (riat(1, iat) - r(ii + 1))**2 + (riat(2, iat) - r(ii + 2))**2 + (riat(3, iat) - r(ii + 3))**2
5084 sum_exp = sum_exp + vec_dif(iat)
5085 dvec_dif(1, iat) = r(ii + 1)
5086 dvec_dif(2, iat) = r(ii + 2)
5087 dvec_dif(3, iat) = r(ii + 3)
5089 s1v(ik) = exp(-lambda*sum_exp)
5090 DO iat = 1, rmsd_atom
5091 ds1v(1, iat, ik) = dvec_dif(1, iat)*s1v(ik)
5092 ds1v(2, iat, ik) = dvec_dif(2, iat)*s1v(ik)
5093 ds1v(3, iat, ik) = dvec_dif(3, iat)*s1v(ik)
5098 DO iat = 1, rmsd_atom
5103 colvar%ss = -1.0_dp/lambda*log(s1)
5105 ALLOCATE (fi(3, rmsd_atom))
5107 DO iat = 1, rmsd_atom
5108 fi(:, iat) = 2.0_dp*(riat(:, iat) - ds1(:, iat)/s1)
5109 CALL put_derivative(colvar, iat, fi(:, iat))
5116 DEALLOCATE (vec_dif)
5117 DEALLOCATE (dvec_dif)
5121 END SUBROUTINE dpath_dist_rmsd
5128 SUBROUTINE dpath_rmsd(colvar, particles)
5133 INTEGER :: i, iat, ii, ik, natom, nconf, rmsd_atom
5134 INTEGER,
DIMENSION(:),
POINTER :: iatom
5135 REAL(
dp) :: lambda, my_rmsd, s1
5136 REAL(
dp),
ALLOCATABLE,
DIMENSION(:) :: r, r0, s1v
5137 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :) :: ds1, fi, riat
5138 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :, :) :: ds1v
5139 REAL(
dp),
DIMENSION(:, :),
POINTER :: path_conf
5140 REAL(kind=
dp),
ALLOCATABLE,
DIMENSION(:) :: weight
5141 REAL(kind=
dp),
ALLOCATABLE,
DIMENSION(:, :) :: drmsd
5143 nconf = colvar%reaction_path_param%nr_frames
5144 rmsd_atom = colvar%reaction_path_param%n_components
5145 lambda = colvar%reaction_path_param%lambda
5146 path_conf => colvar%reaction_path_param%r_ref
5147 iatom => colvar%reaction_path_param%i_rmsd
5149 natom =
SIZE(particles)
5151 ALLOCATE (r0(3*natom))
5152 ALLOCATE (r(3*natom))
5153 ALLOCATE (riat(3, rmsd_atom))
5154 ALLOCATE (s1v(nconf))
5155 ALLOCATE (ds1v(3, rmsd_atom, nconf))
5156 ALLOCATE (ds1(3, rmsd_atom))
5157 ALLOCATE (drmsd(3, natom))
5159 ALLOCATE (weight(natom))
5163 r0(ii + 1) = particles(i)%r(1)
5164 r0(ii + 2) = particles(i)%r(2)
5165 r0(ii + 3) = particles(i)%r(3)
5168 DO iat = 1, rmsd_atom
5170 riat(:, iat) = particles(ii)%r
5175 DO iat = 1, rmsd_atom
5183 r(ii + 1) = path_conf(ii + 1, ik)
5184 r(ii + 2) = path_conf(ii + 2, ik)
5185 r(ii + 3) = path_conf(ii + 3, ik)
5188 CALL rmsd3(particles, r0, r, output_unit=-1, weights=weight, my_val=my_rmsd, &
5189 rotate=.false., drmsd3=drmsd)
5191 s1v(ik) = exp(-lambda*my_rmsd)
5192 DO iat = 1, rmsd_atom
5194 ds1v(1, iat, ik) = drmsd(1, i)*s1v(ik)
5195 ds1v(2, iat, ik) = drmsd(2, i)*s1v(ik)
5196 ds1v(3, iat, ik) = drmsd(3, i)*s1v(ik)
5201 DO iat = 1, rmsd_atom
5206 colvar%ss = -1.0_dp/lambda*log(s1)
5208 ALLOCATE (fi(3, rmsd_atom))
5210 DO iat = 1, rmsd_atom
5211 fi(:, iat) = ds1(:, iat)/s1
5212 CALL put_derivative(colvar, iat, fi(:, iat))
5225 END SUBROUTINE dpath_rmsd
5236 SUBROUTINE population_colvar(colvar, cell, subsys, particles)
5241 POINTER :: particles
5243 INTEGER :: i, ii, jj, n_atoms_from, n_atoms_to, &
5245 REAL(
dp) :: dfunc, dfunc_coord, ftmp(3), func, func_coord, inv_n_atoms_from, invden, n_0, &
5246 ncoord, norm, num, population, r12, r_0, rdist, sigma, ss(3), xij(3)
5247 REAL(
dp),
ALLOCATABLE,
DIMENSION(:, :) :: ftmp_coord
5248 REAL(
dp),
DIMENSION(3) :: xpi, xpj
5255 NULLIFY (particles_i)
5257 IF (
PRESENT(particles))
THEN
5258 my_particles => particles
5260 cpassert(
PRESENT(subsys))
5262 my_particles => particles_i%els
5264 n_atoms_to = colvar%population_param%n_atoms_to
5265 n_atoms_from = colvar%population_param%n_atoms_from
5266 nncrd = colvar%population_param%nncrd
5267 ndcrd = colvar%population_param%ndcrd
5268 r_0 = colvar%population_param%r_0
5269 n_0 = colvar%population_param%n0
5270 sigma = colvar%population_param%sigma
5272 ALLOCATE (ftmp_coord(3, n_atoms_to))
5278 colvar%dsdr = 0.0_dp
5279 inv_n_atoms_from = 1.0_dp/real(n_atoms_from, kind=
dp)
5281 norm = sqrt(
pi*2.0_dp)*sigma
5284 DO ii = 1, n_atoms_from
5285 i = colvar%population_param%i_at_from(ii)
5286 CALL get_coordinates(colvar, i, xpi, my_particles)
5287 DO jj = 1, n_atoms_to
5288 i = colvar%population_param%i_at_to(jj)
5289 CALL get_coordinates(colvar, i, xpj, my_particles)
5290 ss = matmul(cell%h_inv, xpi(:) - xpj(:))
5292 xij = matmul(cell%hmat, ss)
5293 r12 = sqrt(xij(1)**2 + xij(2)**2 + xij(3)**2)
5294 IF (r12 < 1.0e-8_dp) cycle
5296 num = (1.0_dp - rdist**nncrd)
5297 invden = 1.0_dp/(1.0_dp - rdist**ndcrd)
5298 func_coord = num*invden
5299 dfunc_coord = (-nncrd*rdist**(nncrd - 1)*invden &
5300 + num*(invden)**2*ndcrd*rdist**(ndcrd - 1))/(r12*r_0)
5302 ncoord = ncoord + func_coord
5303 ftmp_coord(1, jj) = dfunc_coord*xij(1)
5304 ftmp_coord(2, jj) = dfunc_coord*xij(2)
5305 ftmp_coord(3, jj) = dfunc_coord*xij(3)
5308 func = exp(-(ncoord - n_0)**2/(2.0_dp*sigma*sigma))
5309 dfunc = -func*(ncoord - n_0)/(sigma*sigma)
5311 population = population + norm*func
5312 DO jj = 1, n_atoms_to
5313 ftmp(1) = ftmp_coord(1, jj)*dfunc
5314 ftmp(2) = ftmp_coord(2, jj)*dfunc
5315 ftmp(3) = ftmp_coord(3, jj)*dfunc
5316 CALL put_derivative(colvar, ii, ftmp)
5317 ftmp(1) = -ftmp_coord(1, jj)*dfunc
5318 ftmp(2) = -ftmp_coord(2, jj)*dfunc
5319 ftmp(3) = -ftmp_coord(3, jj)*dfunc
5320 CALL put_derivative(colvar, n_atoms_from + jj, ftmp)
5324 colvar%ss = population
5325 END SUBROUTINE population_colvar
5337 SUBROUTINE gyration_radius_colvar(colvar, cell, subsys, particles)
5343 POINTER :: particles
5345 INTEGER :: i, ii, n_atoms
5346 REAL(
dp) :: dri2, func, gyration, inv_n, mass_tot, mi
5347 REAL(
dp),
DIMENSION(3) :: dfunc, dxi, ftmp, ss, xpcom, xpi
5351 NULLIFY (particles_i, my_particles)
5353 IF (
PRESENT(particles))
THEN
5354 my_particles => particles
5356 cpassert(
PRESENT(subsys))
5358 my_particles => particles_i%els
5360 n_atoms = colvar%gyration_param%n_atoms
5361 inv_n = 1.0_dp/n_atoms
5367 i = colvar%gyration_param%i_at(ii)
5368 CALL get_coordinates(colvar, i, xpi, my_particles)
5369 CALL get_mass(colvar, i, mi, my_particles)
5370 xpcom(:) = xpcom(:) + xpi(:)*mi
5371 mass_tot = mass_tot + mi
5373 xpcom(:) = xpcom(:)/mass_tot
5379 i = colvar%gyration_param%i_at(ii)
5380 CALL get_coordinates(colvar, i, xpi, my_particles)
5381 ss = matmul(cell%h_inv, xpi(:) - xpcom(:))
5383 dxi = matmul(cell%hmat, ss)
5384 dri2 = (dxi(1)**2 + dxi(2)**2 + dxi(3)**2)
5386 dfunc(:) = dfunc(:) + dxi(:)
5388 gyration = sqrt(inv_n*func)
5391 i = colvar%gyration_param%i_at(ii)
5392 CALL get_coordinates(colvar, i, xpi, my_particles)
5393 CALL get_mass(colvar, i, mi, my_particles)
5394 ss = matmul(cell%h_inv, xpi(:) - xpcom(:))
5396 dxi = matmul(cell%hmat, ss)
5397 ftmp(1) = dxi(1) - dfunc(1)*mi/mass_tot
5398 ftmp(2) = dxi(2) - dfunc(2)*mi/mass_tot
5399 ftmp(3) = dxi(3) - dfunc(3)*mi/mass_tot
5400 ftmp(:) = ftmp(:)*inv_n/gyration
5401 CALL put_derivative(colvar, ii, ftmp)
5403 colvar%ss = gyration
5405 END SUBROUTINE gyration_radius_colvar
5416 SUBROUTINE rmsd_colvar(colvar, subsys, particles)
5420 POINTER :: particles
5422 CALL rmsd_colvar_low(colvar, subsys, particles)
5423 END SUBROUTINE rmsd_colvar
5438 SUBROUTINE rmsd_colvar_low(colvar, subsys, particles)
5443 POINTER :: particles
5445 INTEGER :: i, ii, natom, nframes
5446 REAL(kind=
dp) :: cv_val, f1, ftmp(3)
5447 REAL(kind=
dp),
ALLOCATABLE,
DIMENSION(:) :: der, r,
rmsd
5448 REAL(kind=
dp),
ALLOCATABLE,
DIMENSION(:, :) :: r0
5449 REAL(kind=
dp),
ALLOCATABLE,
DIMENSION(:, :, :) :: drmsd
5450 REAL(kind=
dp),
DIMENSION(:),
POINTER :: weights
5454 NULLIFY (my_particles, particles_i, weights)
5456 IF (
PRESENT(particles))
THEN
5457 my_particles => particles
5459 cpassert(
PRESENT(subsys))
5461 my_particles => particles_i%els
5464 natom =
SIZE(my_particles)
5465 nframes = colvar%rmsd_param%nr_frames
5466 ALLOCATE (drmsd(3, natom, nframes))
5469 ALLOCATE (r0(3*natom, nframes))
5470 ALLOCATE (
rmsd(nframes))
5471 ALLOCATE (der(nframes))
5472 ALLOCATE (r(3*natom))
5474 weights => colvar%rmsd_param%weights
5477 r(ii + 1) = my_particles(i)%r(1)
5478 r(ii + 2) = my_particles(i)%r(2)
5479 r(ii + 3) = my_particles(i)%r(3)
5481 r0(:, :) = colvar%rmsd_param%r_ref
5484 CALL rmsd3(my_particles, r, r0(:, 1), output_unit=-1, weights=weights, my_val=
rmsd(1), rotate=.false., drmsd3=drmsd(:, :, 1))
5486 IF (nframes == 2)
THEN
5487 CALL rmsd3(my_particles, r, r0(:, 2), output_unit=-1, weights=weights, &
5488 my_val=
rmsd(2), rotate=.false., drmsd3=drmsd(:, :, 2))
5494 der(1) = f1 - cv_val*f1
5496 der(2) = -f1 - cv_val*f1
5498 DO i = 1, colvar%rmsd_param%n_atoms
5499 ii = colvar%rmsd_param%i_rmsd(i)
5500 IF (weights(ii) > 0.0_dp)
THEN
5501 ftmp(1) = der(1)*drmsd(1, ii, 1) + der(2)*drmsd(1, ii, 2)
5502 ftmp(2) = der(1)*drmsd(2, ii, 1) + der(2)*drmsd(2, ii, 2)
5503 ftmp(3) = der(1)*drmsd(3, ii, 1) + der(2)*drmsd(3, ii, 2)
5504 CALL put_derivative(colvar, i, ftmp)
5507 ELSE IF (nframes == 1)
THEN
5510 cv_val = sqrt(
rmsd(1))
5512 IF (cv_val /= 0.0_dp) f1 = 0.5_dp/cv_val
5513 DO i = 1, colvar%rmsd_param%n_atoms
5514 ii = colvar%rmsd_param%i_rmsd(i)
5515 IF (weights(ii) > 0.0_dp)
THEN
5516 ftmp(1) = f1*drmsd(1, ii, 1)
5517 ftmp(2) = f1*drmsd(2, ii, 1)
5518 ftmp(3) = f1*drmsd(3, ii, 1)
5519 CALL put_derivative(colvar, i, ftmp)
5523 cpabort(
"RMSD implemented only for 1 and 2 reference frames!")
5533 END SUBROUTINE rmsd_colvar_low
5545 SUBROUTINE ring_puckering_colvar(colvar, cell, subsys, particles)
5550 POINTER :: particles
5552 INTEGER :: i, ii, j, jj, m, nring
5553 REAL(kind=
dp) :: a, at, b, da, db, ds, kr, rpxpp, svar
5554 REAL(kind=
dp),
ALLOCATABLE,
DIMENSION(:) :: cosj, sinj, z
5555 REAL(kind=
dp),
ALLOCATABLE,
DIMENSION(:, :) :: r
5556 REAL(kind=
dp),
ALLOCATABLE,
DIMENSION(:, :, :) :: nforce, zforce
5557 REAL(kind=
dp),
DIMENSION(3) :: ftmp, nv, r0, rp, rpp, uv
5558 REAL(kind=
dp),
DIMENSION(3, 3) :: dnvp, dnvpp
5563 IF (
PRESENT(particles))
THEN
5564 my_particles => particles
5566 cpassert(
PRESENT(subsys))
5568 my_particles => particles_i%els
5571 nring = colvar%ring_puckering_param%nring
5572 ALLOCATE (r(3, nring), z(nring), cosj(nring), sinj(nring))
5573 ALLOCATE (nforce(3, 3, nring), zforce(nring, nring, 3))
5575 i = colvar%ring_puckering_param%atoms(ii)
5576 CALL get_coordinates(colvar, i, r(:, ii), my_particles)
5581 r(:, ii) =
pbc(r(:, ii), r0, cell)
5586 r0(:) = r0(:) + r(:, ii)
5588 kr = 1._dp/real(nring, kind=
dp)
5591 r(:, ii) = r(:, ii) - r0(:)
5597 cosj(ii) = cos(
twopi*(ii - 1)*kr)
5598 sinj(ii) = sin(
twopi*(ii - 1)*kr)
5599 rp(:) = rp(:) + r(:, ii)*sinj(ii)
5600 rpp(:) = rpp(:) + r(:, ii)*cosj(ii)
5603 nv = nv/sqrt(sum(nv**2))
5607 rpxpp = sqrt(sum(uv**2))
5612 dnvp(:, i) = uv - nv*sum(uv*nv)
5616 dnvpp(:, i) = uv - nv*sum(uv*nv)
5619 nforce(:, :, ii) = dnvp(:, :)*sinj(ii) + dnvpp(:, :)*cosj(ii)
5624 z(ii) = sum(r(:, ii)*nv(:))
5630 zforce(ii, jj, :) = nv
5632 zforce(ii, jj, :) = 0._dp
5636 zforce(ii, jj, i) = zforce(ii, jj, i) + r(j, ii)*nforce(j, i, jj)
5642 IF (colvar%ring_puckering_param%iq == 0)
THEN
5644 svar = sqrt(sum(z**2))
5648 ftmp(:) = ftmp(:) + zforce(jj, ii, :)*z(jj)
5651 CALL put_derivative(colvar, ii, ftmp)
5654 m = abs(colvar%ring_puckering_param%iq)
5656 IF (mod(nring, 2) == 0 .AND. colvar%ring_puckering_param%iq == nring/2)
THEN
5660 IF (mod(ii, 2) == 0)
THEN
5666 svar = svar*sqrt(kr)
5670 IF (mod(jj, 2) == 0)
THEN
5671 ftmp(:) = ftmp(:) - zforce(jj, ii, :)*sqrt(kr)
5673 ftmp(:) = ftmp(:) + zforce(jj, ii, :)*sqrt(kr)
5676 CALL put_derivative(colvar, ii, -ftmp)
5679 cpassert(m <= (nring - 1)/2)
5683 a = a + z(ii)*cos(
twopi*m*(ii - 1)*kr)
5684 b = b - z(ii)*sin(
twopi*m*(ii - 1)*kr)
5686 a = a*sqrt(2._dp*kr)
5687 b = b*sqrt(2._dp*kr)
5688 IF (colvar%ring_puckering_param%iq > 0)
THEN
5690 svar = sqrt(a*a + b*b)
5696 IF (at >
pi/2._dp)
THEN
5697 svar = 2.5_dp*
pi - at
5699 svar = 0.5_dp*
pi - at
5707 ds = da*cos(
twopi*m*(ii - 1)*kr)
5708 ds = ds - db*sin(
twopi*m*(ii - 1)*kr)
5709 ftmp(:) = ftmp(:) + ds*sqrt(2._dp*kr)*zforce(ii, jj, :)
5711 CALL put_derivative(colvar, jj, ftmp)
5718 DEALLOCATE (r, z, cosj, sinj, nforce, zforce)
5720 END SUBROUTINE ring_puckering_colvar
5742 RECURSIVE FUNCTION rec_eval_grid(iw1, ncol, f_vals, v_count, &
5743 gp, grid_sp, step_size, istart, iend, s1v, s1, p_bounds, lambda, ifunc, nconf)
RESULT(k)
5744 INTEGER :: iw1, ncol
5745 REAL(
dp),
DIMENSION(:, :),
POINTER :: f_vals
5747 REAL(
dp),
DIMENSION(:),
POINTER :: gp, grid_sp
5748 REAL(
dp) :: step_size
5749 INTEGER :: istart, iend
5750 REAL(
dp),
DIMENSION(:, :),
POINTER :: s1v
5751 REAL(
dp),
DIMENSION(:),
POINTER :: s1
5752 INTEGER,
DIMENSION(:, :),
POINTER :: p_bounds
5754 INTEGER :: ifunc, nconf, k
5756 INTEGER :: count1, i
5759 IF (v_count .LT. ncol)
THEN
5760 count1 = v_count + 1
5761 DO i = p_bounds(1, count1), p_bounds(2, count1)
5762 gp(count1) = real(i, kind=
dp)*grid_sp(count1)
5763 k = rec_eval_grid(iw1, ncol, f_vals, count1, gp, grid_sp, step_size, &
5764 istart, iend, s1v, s1, p_bounds, lambda, ifunc, nconf)
5766 ELSE IF (v_count == ncol .AND. ifunc == 1)
THEN
5768 s1v(1, i) = real(i, kind=
dp)*step_size*exp(-lambda*dot_product(gp(:) - f_vals(:, i), &
5769 gp(:) - f_vals(:, i)))
5770 s1v(2, i) = exp(-lambda*dot_product(gp(:) - f_vals(:, i), gp(:) - f_vals(:, i)))
5775 WRITE (iw1,
'(5F10.5)') gp(:), s1(1)/s1(2)/real(nconf - 1,
dp)
5776 ELSE IF (v_count == ncol .AND. ifunc == 2)
THEN
5778 s1v(1, i) = exp(-lambda*dot_product(gp(:) - f_vals(:, i), gp(:) - f_vals(:, i)))
5782 WRITE (iw1,
'(5F10.5)') gp(:), -lambda*log(s1(1))
5784 END FUNCTION rec_eval_grid
5797 SUBROUTINE read_frames(frame_section, para_env, nr_frames, r_ref, n_atoms)
5801 INTEGER,
INTENT(IN) :: nr_frames
5802 REAL(
dp),
DIMENSION(:, :),
POINTER :: r_ref
5803 INTEGER,
INTENT(OUT) :: n_atoms
5805 CHARACTER(LEN=default_path_length) :: filename
5806 CHARACTER(LEN=default_string_length) :: dummy_char
5807 INTEGER :: i, j, natom
5808 LOGICAL :: explicit, my_end
5809 REAL(kind=
dp),
DIMENSION(:),
POINTER :: rptr
5822 ALLOCATE (r_ref(3*natom, nr_frames))
5825 cpassert(3*natom ==
SIZE(r_ref, 1))
5829 i_rep_val=j, r_vals=rptr)
5830 r_ref((j - 1)*3 + 1:(j - 1)*3 + 3, i) = rptr(1:3)
5836 cpassert(trim(filename) /=
"")
5838 CALL parser_create(parser, filename, para_env=para_env, parse_white_lines=.true.)
5844 ALLOCATE (r_ref(3*natom, nr_frames))
5847 cpassert(3*natom ==
SIZE(r_ref, 1))
5853 CALL cp_abort(__location__, &
5854 "Number of lines in XYZ format not equal to the number of atoms."// &
5855 " Error in XYZ format for COORD_A (CV rmsd). Very probably the"// &
5856 " line with title is missing or is empty. Please check the XYZ file and rerun your job!")
5857 READ (parser%input_line, *) dummy_char, rptr(1:3)
5868 END SUBROUTINE read_frames
5879 SUBROUTINE wc_colvar(colvar, cell, subsys, particles, qs_env)
5880 TYPE(colvar_type),
POINTER :: colvar
5881 TYPE(cell_type),
POINTER :: cell
5882 TYPE(cp_subsys_type),
OPTIONAL,
POINTER :: subsys
5883 TYPE(particle_type),
DIMENSION(:), &
5884 OPTIONAL,
POINTER :: particles
5885 TYPE(qs_environment_type),
POINTER,
OPTIONAL :: qs_env
5887 INTEGER :: od, h, oa
5888 REAL(dp) :: rod(3), roa(3), rh(3), &
5889 x, y, s(3), xv(3), dmin, amin
5890 INTEGER :: idmin, iamin, i, j
5891 TYPE(particle_list_type),
POINTER :: particles_i
5892 TYPE(particle_type),
DIMENSION(:), &
5893 POINTER :: my_particles
5894 TYPE(wannier_centres_type),
DIMENSION(:),
POINTER :: wc
5895 INTEGER,
ALLOCATABLE :: wcai(:), wcdi(:)
5896 INTEGER :: nwca, nwcd
5899 NULLIFY (particles_i, wc)
5901 cpassert(colvar%type_id == wc_colvar_id)
5902 IF (
PRESENT(particles))
THEN
5903 my_particles => particles
5905 cpassert(
PRESENT(subsys))
5906 CALL cp_subsys_get(subsys, particles=particles_i)
5907 my_particles => particles_i%els
5909 CALL get_qs_env(qs_env, wanniercentres=wc)
5910 rcut = colvar%Wc%rcut
5911 od = colvar%Wc%ids(1)
5912 h = colvar%Wc%ids(2)
5913 oa = colvar%Wc%ids(3)
5914 CALL get_coordinates(colvar, od, rod, my_particles)
5915 CALL get_coordinates(colvar, h, rh, my_particles)
5916 CALL get_coordinates(colvar, oa, roa, my_particles)
5917 ALLOCATE (wcai(
SIZE(wc(1)%WannierHamDiag)))
5918 ALLOCATE (wcdi(
SIZE(wc(1)%WannierHamDiag)))
5921 DO j = 1,
SIZE(wc(1)%WannierHamDiag)
5922 x = distance(rod - wc(1)%centres(:, j))
5923 y = distance(roa - wc(1)%centres(:, j))
5935 dmin = distance(rh - wc(1)%centres(:, wcdi(1)))
5936 amin = distance(rh - wc(1)%centres(:, wcai(1)))
5941 x = distance(rh - wc(1)%centres(:, wcdi(i)))
5948 x = distance(rh - wc(1)%centres(:, wcai(i)))
5960 colvar%ss = wc(1)%WannierHamDiag(idmin) - wc(1)%WannierHamDiag(iamin)
5970 REAL(dp) function distance(rij)
5971 REAL(dp),
INTENT(in) :: rij(3)
5973 s = matmul(cell%h_inv, rij)
5975 xv = matmul(cell%hmat, s)
5976 distance = sqrt(dot_product(xv, xv))
5977 END FUNCTION distance
5979 END SUBROUTINE wc_colvar
5990 SUBROUTINE hbp_colvar(colvar, cell, subsys, particles, qs_env)
5991 TYPE(colvar_type),
POINTER :: colvar
5992 TYPE(cell_type),
POINTER :: cell
5993 TYPE(cp_subsys_type),
OPTIONAL,
POINTER :: subsys
5994 TYPE(particle_type),
DIMENSION(:), &
5995 OPTIONAL,
POINTER :: particles
5996 TYPE(qs_environment_type),
POINTER,
OPTIONAL :: qs_env
5998 INTEGER :: od, h, oa
5999 REAL(dp) :: rod(3), roa(3), rh(3), &
6000 x, y, s(3), xv(3), dmin, amin
6001 INTEGER :: idmin, iamin, i, j, il, output_unit
6002 TYPE(particle_list_type),
POINTER :: particles_i
6003 TYPE(particle_type),
DIMENSION(:), &
6004 POINTER :: my_particles
6005 TYPE(wannier_centres_type), &
6006 DIMENSION(:),
POINTER :: wc
6007 INTEGER,
ALLOCATABLE :: wcai(:), wcdi(:)
6008 INTEGER :: nwca, nwcd
6011 NULLIFY (particles_i, wc)
6012 output_unit = cp_logger_get_default_io_unit()
6014 cpassert(colvar%type_id == hbp_colvar_id)
6015 IF (
PRESENT(particles))
THEN
6016 my_particles => particles
6018 cpassert(
PRESENT(subsys))
6019 CALL cp_subsys_get(subsys, particles=particles_i)
6020 my_particles => particles_i%els
6022 CALL get_qs_env(qs_env, wanniercentres=wc)
6023 rcut = colvar%HBP%rcut
6024 ALLOCATE (wcai(
SIZE(wc(1)%WannierHamDiag)))
6025 ALLOCATE (wcdi(
SIZE(wc(1)%WannierHamDiag)))
6027 DO il = 1, colvar%HBP%nPoints
6028 od = colvar%HBP%ids(il, 1)
6029 h = colvar%HBP%ids(il, 2)
6030 oa = colvar%HBP%ids(il, 3)
6031 CALL get_coordinates(colvar, od, rod, my_particles)
6032 CALL get_coordinates(colvar, h, rh, my_particles)
6033 CALL get_coordinates(colvar, oa, roa, my_particles)
6036 DO j = 1,
SIZE(wc(1)%WannierHamDiag)
6037 x = distance(rod - wc(1)%centres(:, j))
6038 y = distance(roa - wc(1)%centres(:, j))
6050 dmin = distance(rh - wc(1)%centres(:, wcdi(1)))
6051 amin = distance(rh - wc(1)%centres(:, wcai(1)))
6056 x = distance(rh - wc(1)%centres(:, wcdi(i)))
6063 x = distance(rh - wc(1)%centres(:, wcai(i)))
6069 colvar%HBP%ewc(il) = colvar%HBP%shift + wc(1)%WannierHamDiag(idmin) - wc(1)%WannierHamDiag(iamin)
6070 colvar%ss = colvar%ss + colvar%HBP%shift + wc(1)%WannierHamDiag(idmin) - wc(1)%WannierHamDiag(iamin)
6072 IF (output_unit > 0)
THEN
6073 DO il = 1, colvar%HBP%nPoints
6074 WRITE (output_unit,
'(a,1(f16.8,1x))')
"HBP| = ", colvar%HBP%ewc(il)
6076 WRITE (output_unit,
'(a,1(f16.8,1x))')
"HBP|\theta(x) = ", colvar%ss
6087 REAL(dp) function distance(rij)
6088 REAL(dp),
INTENT(in) :: rij(3)
6090 s = matmul(cell%h_inv, rij)
6092 xv = matmul(cell%hmat, s)
6093 distance = sqrt(dot_product(xv, xv))
6094 END FUNCTION distance
6096 END SUBROUTINE hbp_colvar
Handles all functions related to the CELL.
defines collective variables s({R}) and the derivative of this variable wrt R these can then be used ...
subroutine, public colvar_eval_glob_f(icolvar, force_env)
evaluates the derivatives (dsdr) given and due to the given colvar
recursive subroutine, public colvar_read(colvar, icol, colvar_section, para_env)
reads a colvar from the input
subroutine, public colvar_eval_mol_f(colvar, cell, particles, pos, fixd_list)
evaluates the derivatives (dsdr) given and due to the given colvar variables in a molecular environme...
Initialize the collective variables types.
integer, parameter, public ring_puckering_colvar_id
integer, parameter, public population_colvar_id
integer, parameter, public do_clv_geo_center
integer, parameter, public distance_from_path_colvar_id
integer, parameter, public rmsd_colvar_id
integer, parameter, public mindist_colvar_id
integer, parameter, public wc_colvar_id
integer, parameter, public acid_hyd_dist_colvar_id
integer, parameter, public xyz_outerdiag_colvar_id
integer, parameter, public do_clv_xz
integer, parameter, public plane_plane_angle_colvar_id
subroutine, public colvar_create(colvar, colvar_id)
initializes a colvar_param type
integer, parameter, public plane_distance_colvar_id
integer, parameter, public combine_colvar_id
integer, parameter, public gyration_colvar_id
integer, parameter, public hbp_colvar_id
integer, parameter, public rotation_colvar_id
integer, parameter, public hydronium_dist_colvar_id
integer, parameter, public coord_colvar_id
integer, parameter, public do_clv_fix_point
integer, parameter, public do_clv_z
subroutine, public eval_point_pos(point, particles, r)
Evaluate the position of the geometrical point.
integer, parameter, public plane_def_atoms
integer, parameter, public do_clv_yz
integer, parameter, public dfunct_colvar_id
integer, parameter, public angle_colvar_id
integer, parameter, public qparm_colvar_id
subroutine, public eval_point_der(points, i, dsdr, f)
Evaluate the position of the geometrical point.
subroutine, public eval_point_mass(point, particles, m)
...
integer, parameter, public dist_colvar_id
subroutine, public colvar_setup(colvar)
Finalize the setup of the collective variable.
integer, parameter, public do_clv_xy
integer, parameter, public u_colvar_id
integer, parameter, public hydronium_shell_colvar_id
integer, parameter, public torsion_colvar_id
integer, parameter, public do_clv_y
integer, parameter, public plane_def_vec
integer, parameter, public xyz_diag_colvar_id
integer, parameter, public reaction_path_colvar_id
integer, parameter, public do_clv_x
integer, parameter, public acid_hyd_shell_colvar_id
subroutine, public check_fixed_atom_cns_colv(fixd_list, colvar)
...
various routines to log and control the output. The idea is that decisions about where to log should ...
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...
type(cp_logger_type) function, pointer, public cp_get_default_logger()
returns the default logger
routines to handle the output, The idea is to remove the decision of wheter to output and what to out...
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)
...
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,...
Utility routines to read data from files. Kept as close as possible to the old parser because.
subroutine, public parser_get_next_line(parser, nline, at_end)
Read the next input line and broadcast the input information. Skip (nline-1) lines and skip also all ...
Utility routines to read data from files. Kept as close as possible to the old parser because.
subroutine, public parser_release(parser)
releases the parser
subroutine, public parser_create(parser, file_name, unit_nr, para_env, end_section_label, separator_chars, comment_char, continuation_char, quote_char, section_char, parse_white_lines, initial_variables, apply_preprocessing)
Start a parser run. Initial variables allow to @SET stuff before opening the file.
types that represent a subsys, i.e. a part of the system
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
real(kind=dp) function, public cp_unit_to_cp2k(value, unit_str, defaults, power)
converts to the internal cp2k units to the given unit
Interface for the force calculations.
integer, parameter, public use_mixed_force
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
subroutine, public get_generic_info(gen_section, func_name, xfunction, parameters, values, var_values, size_variables, i_rep_sec, input_variables)
Reads from the input structure all information for generic functions.
This public domain function parser module is intended for applications where a set of mathematical ex...
subroutine, public parsef(i, funcstr, var)
Parse ith function string FuncStr and compile it into bytecode.
real(rn) function, public evalf(i, val)
...
integer, public evalerrtype
real(kind=rn) function, public evalfd(id_fun, ipar, vals, h, err)
Evaluates derivatives.
subroutine, public finalizef()
...
subroutine, public initf(n)
...
sums arrays of real/complex numbers with much reduced round-off as compared to a naive implementation...
Defines the basic variable types.
integer, parameter, public dp
integer, parameter, public default_string_length
integer, parameter, public default_path_length
Definition of mathematical constants and functions.
real(kind=dp), parameter, public pi
real(kind=dp), parameter, public twopi
integer, parameter, public maxfac
real(kind=dp), dimension(0:maxfac), parameter, public fac
Collection of simple mathematical functions and subroutines.
pure real(kind=dp) function, public angle(a, b)
Calculation of the angle between the vectors a and b. The angle is returned in radians.
pure real(kind=dp) function, dimension(3), public vector_product(a, b)
Calculation of the vector product c = a x b.
Utility routines for the memory handling.
Interface to the message passing library MPI.
subroutine, public get_subsys_map_index(mapping_section, natom, iforce_eval, nforce_eval, map_index, force_eval_embed)
performs mapping of the subsystems of different force_eval
Define the molecule kind structure types and the corresponding functionality.
represent a simple array based list of the given type
Define the data structure for the particle information.
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.
Defines functions to perform rmsd in 3D.
subroutine, public rmsd3(particle_set, r, r0, output_unit, weights, my_val, rotate, transl, rot, drmsd3)
Computes the RMSD in 3D. Provides also derivatives.
Calculate spherical harmonics.
real(kind=dp) function, public legendre(x, l, m)
...
real(kind=dp) function, public dlegendre(x, l, m)
...
Utilities for string manipulations.
subroutine, public compress(string, full)
Eliminate multiple space characters in a string. If full is .TRUE., then all spaces are eliminated.
elemental subroutine, public uppercase(string)
Convert all lower case characters in a string to upper case.
defines the type needed for computing wannier states expectations
Type defining parameters related to the simulation cell.
parameters for a collective variable
type of a logger, at the moment it contains just a print level starting at which level it should be l...
represent a pointer to a subsys, to be able to create arrays of pointers
represents a system: atoms, molecules, their pos,vel,...
wrapper to abstract the force evaluation of the various methods
stores all the informations relevant to an mpi environment
represents a pointer to a list
represent a list of objects