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colvar_methods.F
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!--------------------------------------------------------------------------------------------------!
! CP2K: A general program to perform molecular dynamics simulations !
! Copyright 2000-2024 CP2K developers group <https://cp2k.org> !
! !
! SPDX-License-Identifier: GPL-2.0-or-later !
!--------------------------------------------------------------------------------------------------!
! **************************************************************************************************
!> \brief defines collective variables s({R}) and the derivative of this variable wrt R
!> these can then be used in constraints, restraints and metadynamics ...
!> \par History
!> 04.2004 created
!> 01.2006 Refactored [Joost VandeVondele]
!> \author Alessandro Laio,Fawzi Mohamed
! **************************************************************************************************
MODULE colvar_methods
USE cell_types, ONLY: cell_type,&
pbc
USE colvar_types, ONLY: &
HBP_colvar_id, Wc_colvar_id, acid_hyd_dist_colvar_id, acid_hyd_shell_colvar_id, &
angle_colvar_id, colvar_create, colvar_setup, colvar_type, combine_colvar_id, &
coord_colvar_id, dfunct_colvar_id, dist_colvar_id, distance_from_path_colvar_id, &
do_clv_fix_point, do_clv_geo_center, do_clv_x, do_clv_xy, do_clv_xz, do_clv_y, do_clv_yz, &
do_clv_z, eval_point_der, eval_point_mass, eval_point_pos, gyration_colvar_id, &
hydronium_dist_colvar_id, hydronium_shell_colvar_id, mindist_colvar_id, plane_def_atoms, &
plane_def_vec, plane_distance_colvar_id, plane_plane_angle_colvar_id, &
population_colvar_id, qparm_colvar_id, reaction_path_colvar_id, ring_puckering_colvar_id, &
rmsd_colvar_id, rotation_colvar_id, torsion_colvar_id, u_colvar_id, xyz_diag_colvar_id, &
xyz_outerdiag_colvar_id
USE constraint_fxd, ONLY: check_fixed_atom_cns_colv
USE cp_log_handling, ONLY: cp_get_default_logger,&
cp_logger_get_default_io_unit,&
cp_logger_type,&
cp_to_string
USE cp_output_handling, ONLY: cp_print_key_finished_output,&
cp_print_key_unit_nr
USE cp_parser_methods, ONLY: parser_get_next_line,&
parser_get_object
USE cp_parser_types, ONLY: cp_parser_type,&
parser_create,&
parser_release
USE cp_subsys_types, ONLY: cp_subsys_get,&
cp_subsys_p_type,&
cp_subsys_type
USE cp_units, ONLY: cp_unit_to_cp2k
USE force_env_types, ONLY: force_env_get,&
force_env_type,&
use_mixed_force
USE force_fields_util, ONLY: get_generic_info
USE fparser, ONLY: EvalErrType,&
evalf,&
evalfd,&
finalizef,&
initf,&
parsef
USE input_constants, ONLY: rmsd_all,&
rmsd_list,&
rmsd_weightlist
USE input_cp2k_colvar, ONLY: create_colvar_xyz_d_section,&
create_colvar_xyz_od_section
USE input_enumeration_types, ONLY: enum_i2c,&
enumeration_type
USE input_keyword_types, ONLY: keyword_get,&
keyword_type
USE input_section_types, ONLY: section_get_keyword,&
section_release,&
section_type,&
section_vals_get,&
section_vals_get_subs_vals,&
section_vals_type,&
section_vals_val_get
USE kahan_sum, ONLY: accurate_sum
USE kinds, ONLY: default_path_length,&
default_string_length,&
dp
USE mathconstants, ONLY: fac,&
maxfac,&
pi,&
twopi
USE mathlib, ONLY: vector_product
USE memory_utilities, ONLY: reallocate
USE message_passing, ONLY: mp_para_env_type
USE mixed_energy_types, ONLY: mixed_force_type
USE mixed_environment_utils, ONLY: get_subsys_map_index
USE molecule_kind_types, ONLY: fixd_constraint_type
USE particle_list_types, ONLY: particle_list_p_type,&
particle_list_type
USE particle_types, ONLY: particle_type
USE qs_environment_types, ONLY: get_qs_env,&
qs_environment_type
USE rmsd, ONLY: rmsd3
USE spherical_harmonics, ONLY: dlegendre,&
legendre
USE string_utilities, ONLY: compress,&
uppercase
USE wannier_states_types, ONLY: wannier_centres_type
#include "./base/base_uses.f90"
IMPLICIT NONE
PRIVATE
CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'colvar_methods'
REAL(KIND=dp), PRIVATE, PARAMETER :: tolerance_acos = 1.0E-5_dp
PUBLIC :: colvar_read, &
colvar_eval_glob_f, &
colvar_eval_mol_f
CONTAINS
! **************************************************************************************************
!> \brief reads a colvar from the input
!> \param colvar the place where to store what will be read
!> \param icol number of the current colvar (repetition in colvar_section)
!> \param colvar_section the colvar section
!> \param para_env ...
!> \par History
!> 04.2004 created [alessandro laio and fawzi mohamed]
!> \author teo
! **************************************************************************************************
RECURSIVE SUBROUTINE colvar_read(colvar, icol, colvar_section, para_env)
TYPE(colvar_type), POINTER :: colvar
INTEGER, INTENT(IN) :: icol
TYPE(section_vals_type), POINTER :: colvar_section
TYPE(mp_para_env_type), POINTER :: para_env
CHARACTER(len=*), PARAMETER :: routineN = 'colvar_read'
CHARACTER(LEN=3) :: fmid
CHARACTER(LEN=7) :: tag, tag_comp, tag_comp1, tag_comp2
CHARACTER(LEN=default_path_length) :: path_function
CHARACTER(LEN=default_string_length) :: tmpStr, tmpStr2
CHARACTER(LEN=default_string_length), &
DIMENSION(:), POINTER :: c_kinds, my_par
INTEGER :: handle, i, iatm, icomponent, iend, &
ifunc, ii, isize, istart, iw, iw1, j, &
k, kk, n_var, n_var_k, ncol, ndim, &
nr_frame, v_count
INTEGER, DIMENSION(:), POINTER :: iatms
INTEGER, DIMENSION(:, :), POINTER :: p_bounds
LOGICAL :: check, use_mixed_energy
LOGICAL, DIMENSION(26) :: my_subsection
REAL(dp), DIMENSION(:), POINTER :: s1, wei, weights
REAL(dp), DIMENSION(:, :), POINTER :: p_range, s1v
REAL(KIND=dp), DIMENSION(1) :: my_val
REAL(KIND=dp), DIMENSION(:), POINTER :: g_range, grid_point, grid_sp, my_vals, &
range
TYPE(cp_logger_type), POINTER :: logger
TYPE(enumeration_type), POINTER :: enum
TYPE(keyword_type), POINTER :: keyword
TYPE(section_type), POINTER :: section
TYPE(section_vals_type), POINTER :: acid_hyd_dist_section, acid_hyd_shell_section, &
angle_section, colvar_subsection, combine_section, coordination_section, dfunct_section, &
distance_from_path_section, distance_section, frame_section, gyration_section, &
HBP_section, hydronium_dist_section, hydronium_shell_section, mindist_section, &
path_section, plane_dist_section, plane_plane_angle_section, plane_sections, &
point_section, population_section, qparm_section, reaction_path_section, &
ring_puckering_section, rmsd_section, rotation_section, torsion_section, u_section, &
Wc_section, wrk_section
TYPE(section_vals_type), POINTER :: xyz_diag_section, xyz_outerdiag_section
CALL timeset(routineN, handle)
NULLIFY (logger, c_kinds, iatms)
logger => cp_get_default_logger()
my_subsection = .FALSE.
distance_section => section_vals_get_subs_vals(colvar_section, "DISTANCE", i_rep_section=icol)
dfunct_section => section_vals_get_subs_vals(colvar_section, "DISTANCE_FUNCTION", &
i_rep_section=icol)
angle_section => section_vals_get_subs_vals(colvar_section, "ANGLE", i_rep_section=icol)
torsion_section => section_vals_get_subs_vals(colvar_section, "TORSION", i_rep_section=icol)
coordination_section => section_vals_get_subs_vals(colvar_section, "COORDINATION", i_rep_section=icol)
plane_dist_section => section_vals_get_subs_vals(colvar_section, "DISTANCE_POINT_PLANE", i_rep_section=icol)
plane_plane_angle_section &
=> section_vals_get_subs_vals(colvar_section, "ANGLE_PLANE_PLANE", i_rep_section=icol)
rotation_section => section_vals_get_subs_vals(colvar_section, "BOND_ROTATION", i_rep_section=icol)
qparm_section => section_vals_get_subs_vals(colvar_section, "QPARM", i_rep_section=icol)
hydronium_shell_section => section_vals_get_subs_vals(colvar_section, "HYDRONIUM_SHELL", i_rep_section=icol)
hydronium_dist_section => section_vals_get_subs_vals(colvar_section, "HYDRONIUM_DISTANCE", i_rep_section=icol)
acid_hyd_dist_section => section_vals_get_subs_vals(colvar_section, "ACID_HYDRONIUM_DISTANCE", i_rep_section=icol)
acid_hyd_shell_section &
=> section_vals_get_subs_vals(colvar_section, "ACID_HYDRONIUM_SHELL", i_rep_section=icol)
reaction_path_section => section_vals_get_subs_vals(colvar_section, "REACTION_PATH", i_rep_section=icol, &
can_return_null=.TRUE.)
distance_from_path_section &
=> section_vals_get_subs_vals(colvar_section, "DISTANCE_FROM_PATH", &
i_rep_section=icol, can_return_null=.TRUE.)
combine_section => section_vals_get_subs_vals(colvar_section, "COMBINE_COLVAR", i_rep_section=icol, &
can_return_null=.TRUE.)
population_section => section_vals_get_subs_vals(colvar_section, "POPULATION", i_rep_section=icol)
gyration_section => section_vals_get_subs_vals(colvar_section, "GYRATION_RADIUS", i_rep_section=icol)
rmsd_section => section_vals_get_subs_vals(colvar_section, "RMSD", i_rep_section=icol)
xyz_diag_section => section_vals_get_subs_vals(colvar_section, "XYZ_DIAG", i_rep_section=icol)
xyz_outerdiag_section => section_vals_get_subs_vals(colvar_section, "XYZ_OUTERDIAG", i_rep_section=icol)
u_section => section_vals_get_subs_vals(colvar_section, "U", i_rep_section=icol)
Wc_section => section_vals_get_subs_vals(colvar_section, "WC", i_rep_section=icol)
HBP_section => section_vals_get_subs_vals(colvar_section, "HBP", i_rep_section=icol)
ring_puckering_section &
=> section_vals_get_subs_vals(colvar_section, "RING_PUCKERING", i_rep_section=icol)
mindist_section => section_vals_get_subs_vals(colvar_section, "CONDITIONED_DISTANCE", i_rep_section=icol)
CALL section_vals_get(distance_section, explicit=my_subsection(1))
CALL section_vals_get(angle_section, explicit=my_subsection(2))
CALL section_vals_get(torsion_section, explicit=my_subsection(3))
CALL section_vals_get(coordination_section, explicit=my_subsection(4))
CALL section_vals_get(plane_dist_section, explicit=my_subsection(5))
CALL section_vals_get(rotation_section, explicit=my_subsection(6))
CALL section_vals_get(dfunct_section, explicit=my_subsection(7))
CALL section_vals_get(qparm_section, explicit=my_subsection(8))
CALL section_vals_get(hydronium_shell_section, explicit=my_subsection(9))
! These are just special cases since they are not present in their own defition of COLVARS
IF (ASSOCIATED(reaction_path_section)) THEN
CALL section_vals_get(reaction_path_section, &
explicit=my_subsection(10))
END IF
IF (ASSOCIATED(distance_from_path_section)) THEN
CALL section_vals_get(distance_from_path_section, &
explicit=my_subsection(16))
END IF
IF (ASSOCIATED(combine_section)) THEN
CALL section_vals_get(combine_section, explicit=my_subsection(11))
END IF
CALL section_vals_get(population_section, explicit=my_subsection(12))
CALL section_vals_get(plane_plane_angle_section, &
explicit=my_subsection(13))
CALL section_vals_get(gyration_section, explicit=my_subsection(14))
CALL section_vals_get(rmsd_section, explicit=my_subsection(15))
CALL section_vals_get(xyz_diag_section, explicit=my_subsection(17))
CALL section_vals_get(xyz_outerdiag_section, explicit=my_subsection(18))
CALL section_vals_get(u_section, explicit=my_subsection(19))
CALL section_vals_get(Wc_section, explicit=my_subsection(20))
CALL section_vals_get(HBP_section, explicit=my_subsection(21))
CALL section_vals_get(ring_puckering_section, &
explicit=my_subsection(22))
CALL section_vals_get(mindist_section, explicit=my_subsection(23))
CALL section_vals_get(acid_hyd_dist_section, explicit=my_subsection(24))
CALL section_vals_get(acid_hyd_shell_section, explicit=my_subsection(25))
CALL section_vals_get(hydronium_dist_section, explicit=my_subsection(26))
! Only one colvar can be present
CPASSERT(COUNT(my_subsection) == 1)
CPASSERT(.NOT. ASSOCIATED(colvar))
IF (my_subsection(1)) THEN
! Distance
wrk_section => distance_section
CALL colvar_create(colvar, dist_colvar_id)
CALL colvar_check_points(colvar, distance_section)
CALL section_vals_val_get(distance_section, "ATOMS", i_vals=iatms)
colvar%dist_param%i_at = iatms(1)
colvar%dist_param%j_at = iatms(2)
CALL section_vals_val_get(distance_section, "AXIS", i_val=colvar%dist_param%axis_id)
CALL section_vals_val_get(distance_section, "SIGN", l_val=colvar%dist_param%sign_d)
ELSE IF (my_subsection(2)) THEN
! Angle
wrk_section => angle_section
CALL colvar_create(colvar, angle_colvar_id)
CALL colvar_check_points(colvar, angle_section)
CALL section_vals_val_get(angle_section, "ATOMS", i_vals=iatms)
colvar%angle_param%i_at_angle = iatms
ELSE IF (my_subsection(3)) THEN
! Torsion
wrk_section => torsion_section
CALL colvar_create(colvar, torsion_colvar_id)
CALL colvar_check_points(colvar, torsion_section)
CALL section_vals_val_get(torsion_section, "ATOMS", i_vals=iatms)
colvar%torsion_param%i_at_tors = iatms
colvar%torsion_param%o0 = 0.0_dp
ELSE IF (my_subsection(4)) THEN
! Coordination
wrk_section => coordination_section
CALL colvar_create(colvar, coord_colvar_id)
CALL colvar_check_points(colvar, coordination_section)
NULLIFY (colvar%coord_param%i_at_from, colvar%coord_param%c_kinds_from)
NULLIFY (colvar%coord_param%i_at_to, colvar%coord_param%c_kinds_to)
NULLIFY (colvar%coord_param%i_at_to_b, colvar%coord_param%c_kinds_to_b)
! This section can be repeated
CALL section_vals_val_get(coordination_section, "ATOMS_FROM", n_rep_val=n_var)
ndim = 0
IF (n_var /= 0) THEN
! INDEX LIST
DO k = 1, n_var
CALL section_vals_val_get(coordination_section, "ATOMS_FROM", i_rep_val=k, i_vals=iatms)
CALL reallocate(colvar%coord_param%i_at_from, 1, ndim + SIZE(iatms))
colvar%coord_param%i_at_from(ndim + 1:ndim + SIZE(iatms)) = iatms
ndim = ndim + SIZE(iatms)
END DO
colvar%coord_param%n_atoms_from = ndim
colvar%coord_param%use_kinds_from = .FALSE.
ELSE
! KINDS
CALL section_vals_val_get(coordination_section, "KINDS_FROM", n_rep_val=n_var)
CPASSERT(n_var > 0)
DO k = 1, n_var
CALL section_vals_val_get(coordination_section, "KINDS_FROM", i_rep_val=k, c_vals=c_kinds)
CALL reallocate(colvar%coord_param%c_kinds_from, 1, ndim + SIZE(c_kinds))
colvar%coord_param%c_kinds_from(ndim + 1:ndim + SIZE(c_kinds)) = c_kinds
ndim = ndim + SIZE(c_kinds)
END DO
colvar%coord_param%n_atoms_from = 0
colvar%coord_param%use_kinds_from = .TRUE.
! Uppercase the label
DO k = 1, ndim
CALL uppercase(colvar%coord_param%c_kinds_from(k))
END DO
END IF
! This section can be repeated
CALL section_vals_val_get(coordination_section, "ATOMS_TO", n_rep_val=n_var)
ndim = 0
IF (n_var /= 0) THEN
! INDEX LIST
DO k = 1, n_var
CALL section_vals_val_get(coordination_section, "ATOMS_TO", i_rep_val=k, i_vals=iatms)
CALL reallocate(colvar%coord_param%i_at_to, 1, ndim + SIZE(iatms))
colvar%coord_param%i_at_to(ndim + 1:ndim + SIZE(iatms)) = iatms
ndim = ndim + SIZE(iatms)
END DO
colvar%coord_param%n_atoms_to = ndim
colvar%coord_param%use_kinds_to = .FALSE.
ELSE
! KINDS
CALL section_vals_val_get(coordination_section, "KINDS_TO", n_rep_val=n_var)
CPASSERT(n_var > 0)
DO k = 1, n_var
CALL section_vals_val_get(coordination_section, "KINDS_TO", i_rep_val=k, c_vals=c_kinds)
CALL reallocate(colvar%coord_param%c_kinds_to, 1, ndim + SIZE(c_kinds))
colvar%coord_param%c_kinds_to(ndim + 1:ndim + SIZE(c_kinds)) = c_kinds
ndim = ndim + SIZE(c_kinds)
END DO
colvar%coord_param%n_atoms_to = 0
colvar%coord_param%use_kinds_to = .TRUE.
! Uppercase the label
DO k = 1, ndim
CALL uppercase(colvar%coord_param%c_kinds_to(k))
END DO
END IF
! Let's finish reading the other parameters
CALL section_vals_val_get(coordination_section, "R0", r_val=colvar%coord_param%r_0)
CALL section_vals_val_get(coordination_section, "NN", i_val=colvar%coord_param%nncrd)
CALL section_vals_val_get(coordination_section, "ND", i_val=colvar%coord_param%ndcrd)
! This section can be repeated
CALL section_vals_val_get(coordination_section, "ATOMS_TO_B", n_rep_val=n_var)
CALL section_vals_val_get(coordination_section, "KINDS_TO_B", n_rep_val=n_var_k)
ndim = 0
IF (n_var /= 0 .OR. n_var_k /= 0) THEN
colvar%coord_param%do_chain = .TRUE.
IF (n_var /= 0) THEN
! INDEX LIST
DO k = 1, n_var
CALL section_vals_val_get(coordination_section, "ATOMS_TO_B", i_rep_val=k, i_vals=iatms)
CALL reallocate(colvar%coord_param%i_at_to_b, 1, ndim + SIZE(iatms))
colvar%coord_param%i_at_to_b(ndim + 1:ndim + SIZE(iatms)) = iatms
ndim = ndim + SIZE(iatms)
END DO
colvar%coord_param%n_atoms_to_b = ndim
colvar%coord_param%use_kinds_to_b = .FALSE.
ELSE
! KINDS
CALL section_vals_val_get(coordination_section, "KINDS_TO_B", n_rep_val=n_var_k)
CPASSERT(n_var_k > 0)
DO k = 1, n_var_k
CALL section_vals_val_get(coordination_section, "KINDS_TO_B", i_rep_val=k, c_vals=c_kinds)
CALL reallocate(colvar%coord_param%c_kinds_to_b, 1, ndim + SIZE(c_kinds))
colvar%coord_param%c_kinds_to_b(ndim + 1:ndim + SIZE(c_kinds)) = c_kinds
ndim = ndim + SIZE(c_kinds)
END DO
colvar%coord_param%n_atoms_to_b = 0
colvar%coord_param%use_kinds_to_b = .TRUE.
! Uppercase the label
DO k = 1, ndim
CALL uppercase(colvar%coord_param%c_kinds_to_b(k))
END DO
END IF
! Let's finish reading the other parameters
CALL section_vals_val_get(coordination_section, "R0_B", r_val=colvar%coord_param%r_0_b)
CALL section_vals_val_get(coordination_section, "NN_B", i_val=colvar%coord_param%nncrd_b)
CALL section_vals_val_get(coordination_section, "ND_B", i_val=colvar%coord_param%ndcrd_b)
ELSE
colvar%coord_param%do_chain = .FALSE.
colvar%coord_param%n_atoms_to_b = 0
colvar%coord_param%use_kinds_to_b = .FALSE.
NULLIFY (colvar%coord_param%i_at_to_b)
NULLIFY (colvar%coord_param%c_kinds_to_b)
colvar%coord_param%nncrd_b = 0
colvar%coord_param%ndcrd_b = 0
colvar%coord_param%r_0_b = 0._dp
END IF
ELSE IF (my_subsection(5)) THEN
! Distance point from plane
wrk_section => plane_dist_section
CALL colvar_create(colvar, plane_distance_colvar_id)
CALL colvar_check_points(colvar, plane_dist_section)
CALL section_vals_val_get(plane_dist_section, "ATOMS_PLANE", i_vals=iatms)
CPASSERT(SIZE(iatms) == 3)
colvar%plane_distance_param%plane = iatms
CALL section_vals_val_get(plane_dist_section, "ATOM_POINT", i_val=iatm)
colvar%plane_distance_param%point = iatm
CALL section_vals_val_get(plane_dist_section, "PBC", l_val=colvar%plane_distance_param%use_pbc)
ELSE IF (my_subsection(6)) THEN
! Rotation colvar of a segment w.r.t. another segment
wrk_section => rotation_section
CALL colvar_create(colvar, rotation_colvar_id)
CALL colvar_check_points(colvar, rotation_section)
CALL section_vals_val_get(rotation_section, "P1_BOND1", i_val=colvar%rotation_param%i_at1_bond1)
CALL section_vals_val_get(rotation_section, "P2_BOND1", i_val=colvar%rotation_param%i_at2_bond1)
CALL section_vals_val_get(rotation_section, "P1_BOND2", i_val=colvar%rotation_param%i_at1_bond2)
CALL section_vals_val_get(rotation_section, "P2_BOND2", i_val=colvar%rotation_param%i_at2_bond2)
ELSE IF (my_subsection(7)) THEN
! Difference of two distances
wrk_section => dfunct_section
CALL colvar_create(colvar, dfunct_colvar_id)
CALL colvar_check_points(colvar, dfunct_section)
CALL section_vals_val_get(dfunct_section, "ATOMS", i_vals=iatms)
colvar%dfunct_param%i_at_dfunct = iatms
CALL section_vals_val_get(dfunct_section, "COEFFICIENT", r_val=colvar%dfunct_param%coeff)
CALL section_vals_val_get(dfunct_section, "PBC", l_val=colvar%dfunct_param%use_pbc)
ELSE IF (my_subsection(8)) THEN
! Q Parameter
wrk_section => qparm_section
CALL colvar_create(colvar, qparm_colvar_id)
CALL colvar_check_points(colvar, qparm_section)
CALL section_vals_val_get(qparm_section, "RCUT", r_val=colvar%qparm_param%rcut)
CALL section_vals_val_get(qparm_section, "RSTART", r_val=colvar%qparm_param%rstart)
CALL section_vals_val_get(qparm_section, "INCLUDE_IMAGES", l_val=colvar%qparm_param%include_images)
!CALL section_vals_val_get(qparm_section, "ALPHA", r_val=colvar%qparm_param%alpha)
CALL section_vals_val_get(qparm_section, "L", i_val=colvar%qparm_param%l)
NULLIFY (colvar%qparm_param%i_at_from)
NULLIFY (colvar%qparm_param%i_at_to)
CALL section_vals_val_get(qparm_section, "ATOMS_FROM", n_rep_val=n_var)
ndim = 0
DO k = 1, n_var
CALL section_vals_val_get(qparm_section, "ATOMS_FROM", i_rep_val=k, i_vals=iatms)
CALL reallocate(colvar%qparm_param%i_at_from, 1, ndim + SIZE(iatms))
colvar%qparm_param%i_at_from(ndim + 1:ndim + SIZE(iatms)) = iatms
ndim = ndim + SIZE(iatms)
END DO
colvar%qparm_param%n_atoms_from = ndim
! This section can be repeated
CALL section_vals_val_get(qparm_section, "ATOMS_TO", n_rep_val=n_var)
ndim = 0
DO k = 1, n_var
CALL section_vals_val_get(qparm_section, "ATOMS_TO", i_rep_val=k, i_vals=iatms)
CALL reallocate(colvar%qparm_param%i_at_to, 1, ndim + SIZE(iatms))
colvar%qparm_param%i_at_to(ndim + 1:ndim + SIZE(iatms)) = iatms
ndim = ndim + SIZE(iatms)
END DO
colvar%qparm_param%n_atoms_to = ndim
ELSE IF (my_subsection(9)) THEN
! Hydronium
CALL colvar_create(colvar, hydronium_shell_colvar_id)
NULLIFY (colvar%hydronium_shell_param%i_oxygens)
NULLIFY (colvar%hydronium_shell_param%i_hydrogens)
CALL read_hydronium_colvars(hydronium_shell_section, colvar, hydronium_shell_colvar_id, &
colvar%hydronium_shell_param%n_oxygens, &
colvar%hydronium_shell_param%n_hydrogens, &
colvar%hydronium_shell_param%i_oxygens, &
colvar%hydronium_shell_param%i_hydrogens)
ELSE IF (my_subsection(10) .OR. my_subsection(16)) THEN
!reaction path or distance from reaction path
IF (my_subsection(10)) THEN
path_section => reaction_path_section
CALL colvar_create(colvar, reaction_path_colvar_id)
fmid = "POS"
ifunc = 1
ELSE IF (my_subsection(16)) THEN
path_section => distance_from_path_section
CALL colvar_create(colvar, distance_from_path_colvar_id)
fmid = "DIS"
ifunc = 2
END IF
colvar%use_points = .FALSE.
CALL section_vals_val_get(path_section, "LAMBDA", r_val=colvar%reaction_path_param%lambda)
CALL section_vals_val_get(path_section, "DISTANCES_RMSD", l_val=colvar%reaction_path_param%dist_rmsd)
CALL section_vals_val_get(path_section, "RMSD", l_val=colvar%reaction_path_param%rmsd)
IF (colvar%reaction_path_param%dist_rmsd .AND. colvar%reaction_path_param%rmsd) THEN
CPABORT("CV REACTION PATH: only one between DISTANCES_RMSD and RMSD can be used ")
END IF
IF (colvar%reaction_path_param%dist_rmsd .OR. colvar%reaction_path_param%rmsd) THEN
NULLIFY (colvar%reaction_path_param%i_rmsd, colvar%reaction_path_param%r_ref)
frame_section => section_vals_get_subs_vals(path_section, "FRAME")
CALL section_vals_get(frame_section, n_repetition=nr_frame)
colvar%reaction_path_param%nr_frames = nr_frame
CALL read_frames(frame_section, para_env, nr_frame, colvar%reaction_path_param%r_ref, &
colvar%reaction_path_param%n_components)
CALL section_vals_val_get(path_section, "SUBSET_TYPE", i_val=colvar%reaction_path_param%subset)
IF (colvar%reaction_path_param%subset == rmsd_all) THEN
ALLOCATE (colvar%reaction_path_param%i_rmsd(colvar%reaction_path_param%n_components))
DO i = 1, colvar%reaction_path_param%n_components
colvar%reaction_path_param%i_rmsd(i) = i
END DO
ELSE IF (colvar%reaction_path_param%subset == rmsd_list) THEN
! This section can be repeated
CALL section_vals_val_get(path_section, "ATOMS", n_rep_val=n_var)
ndim = 0
IF (n_var /= 0) THEN
! INDEX LIST
DO k = 1, n_var
CALL section_vals_val_get(path_section, "ATOMS", i_rep_val=k, i_vals=iatms)
CALL reallocate(colvar%reaction_path_param%i_rmsd, 1, ndim + SIZE(iatms))
colvar%reaction_path_param%i_rmsd(ndim + 1:ndim + SIZE(iatms)) = iatms
ndim = ndim + SIZE(iatms)
END DO
colvar%reaction_path_param%n_components = ndim
ELSE
CPABORT("CV REACTION PATH: if SUBSET_TYPE=LIST a list of atoms needs to be provided ")
END IF
END IF
CALL section_vals_val_get(path_section, "ALIGN_FRAMES", l_val=colvar%reaction_path_param%align_frames)
ELSE
colvar_subsection => section_vals_get_subs_vals(path_section, "COLVAR")
CALL section_vals_get(colvar_subsection, n_repetition=ncol)
ALLOCATE (colvar%reaction_path_param%colvar_p(ncol))
IF (ncol > 0) THEN
DO i = 1, ncol
NULLIFY (colvar%reaction_path_param%colvar_p(i)%colvar)
CALL colvar_read(colvar%reaction_path_param%colvar_p(i)%colvar, i, colvar_subsection, para_env)
END DO
ELSE
CPABORT("CV REACTION PATH: the number of CV to define the path must be >0 ")
END IF
colvar%reaction_path_param%n_components = ncol
NULLIFY (range)
CALL section_vals_val_get(path_section, "RANGE", r_vals=range)
CALL section_vals_val_get(path_section, "STEP_SIZE", r_val=colvar%reaction_path_param%step_size)
iend = CEILING(MAX(RANGE(1), RANGE(2))/colvar%reaction_path_param%step_size)
istart = FLOOR(MIN(RANGE(1), RANGE(2))/colvar%reaction_path_param%step_size)
colvar%reaction_path_param%function_bounds(1) = istart
colvar%reaction_path_param%function_bounds(2) = iend
colvar%reaction_path_param%nr_frames = 2 !iend - istart + 1
ALLOCATE (colvar%reaction_path_param%f_vals(ncol, istart:iend))
CALL section_vals_val_get(path_section, "VARIABLE", c_vals=my_par, i_rep_val=1)
CALL section_vals_val_get(path_section, "FUNCTION", n_rep_val=ncol)
check = (ncol == SIZE(colvar%reaction_path_param%colvar_p))
CPASSERT(check)
CALL initf(ncol)
DO i = 1, ncol
CALL section_vals_val_get(path_section, "FUNCTION", c_val=path_function, i_rep_val=i)
CALL compress(path_function, full=.TRUE.)
CALL parsef(i, TRIM(path_function), my_par)
DO j = istart, iend
my_val = REAL(j, kind=dp)*colvar%reaction_path_param%step_size
colvar%reaction_path_param%f_vals(i, j) = evalf(i, my_val)
END DO
END DO
CALL finalizef()
iw1 = cp_print_key_unit_nr(logger, path_section, &
"MAP", middle_name=fmid, extension=".dat", file_status="REPLACE")
IF (iw1 > 0) THEN
CALL section_vals_val_get(path_section, "MAP%GRID_SPACING", n_rep_val=ncol)
ALLOCATE (grid_sp(ncol))
DO i = 1, ncol
CALL section_vals_val_get(path_section, "MAP%GRID_SPACING", r_val=grid_sp(i))
END DO
CALL section_vals_val_get(path_section, "MAP%RANGE", n_rep_val=ncol)
CPASSERT(ncol == SIZE(grid_sp))
ALLOCATE (p_range(2, ncol))
ALLOCATE (p_bounds(2, ncol))
DO i = 1, ncol
CALL section_vals_val_get(path_section, "MAP%RANGE", r_vals=g_range)
p_range(:, i) = g_range(:)
p_bounds(2, i) = CEILING(MAX(p_range(1, i), p_range(2, i))/grid_sp(i))
p_bounds(1, i) = FLOOR(MIN(p_range(1, i), p_range(2, i))/grid_sp(i))
END DO
ALLOCATE (s1v(2, istart:iend))
ALLOCATE (s1(2))
ALLOCATE (grid_point(ncol))
v_count = 0
kk = rec_eval_grid(iw1, ncol, colvar%reaction_path_param%f_vals, v_count, &
grid_point, grid_sp, colvar%reaction_path_param%step_size, istart, &
iend, s1v, s1, p_bounds, colvar%reaction_path_param%lambda, ifunc=ifunc, &
nconf=colvar%reaction_path_param%nr_frames)
DEALLOCATE (grid_sp)
DEALLOCATE (p_range)
DEALLOCATE (p_bounds)
DEALLOCATE (s1v)
DEALLOCATE (s1)
DEALLOCATE (grid_point)
END IF
CALL cp_print_key_finished_output(iw1, logger, path_section, &
"MAP")
END IF
ELSE IF (my_subsection(11)) THEN
! combine colvar
CALL colvar_create(colvar, combine_colvar_id)
colvar%use_points = .FALSE.
colvar_subsection => section_vals_get_subs_vals(combine_section, "COLVAR")
CALL section_vals_get(colvar_subsection, n_repetition=ncol)
ALLOCATE (colvar%combine_cvs_param%colvar_p(ncol))
! In case we need to print some information..
iw = cp_print_key_unit_nr(logger, colvar_section, &
"PRINT%PROGRAM_RUN_INFO", extension=".colvarLog")
IF (iw > 0) THEN
WRITE (iw, '( A )') ' '// &
'**********************************************************************'
WRITE (iw, '( A,I8)') ' COLVARS| COLVAR INPUT INDEX: ', icol
WRITE (iw, '( A,T49,4I8)') ' COLVARS| COMBINATION OF THE FOLLOWING COLVARS:'
END IF
CALL cp_print_key_finished_output(iw, logger, colvar_section, &
"PRINT%PROGRAM_RUN_INFO")
! Parsing the real COLVARs
DO i = 1, ncol
NULLIFY (colvar%combine_cvs_param%colvar_p(i)%colvar)
CALL colvar_read(colvar%combine_cvs_param%colvar_p(i)%colvar, i, colvar_subsection, para_env)
END DO
! Function definition
CALL section_vals_val_get(combine_section, "FUNCTION", c_val=colvar%combine_cvs_param%function)
CALL compress(colvar%combine_cvs_param%function, full=.TRUE.)
! Variables
CALL section_vals_val_get(combine_section, "VARIABLES", c_vals=my_par)
ALLOCATE (colvar%combine_cvs_param%variables(SIZE(my_par)))
colvar%combine_cvs_param%variables = my_par
! Check that the number of COLVAR provided is equal to the number of variables..
IF (SIZE(my_par) /= ncol) &
CALL cp_abort(__LOCATION__, &
"Number of defined COLVAR for COMBINE_COLVAR is different from the "// &
"number of variables! It is not possible to define COLVARs in a COMBINE_COLVAR "// &
"and avoid their usage in the combininig function!")
! Parameters
ALLOCATE (colvar%combine_cvs_param%c_parameters(0))
CALL section_vals_val_get(combine_section, "PARAMETERS", n_rep_val=ncol)
DO i = 1, ncol
isize = SIZE(colvar%combine_cvs_param%c_parameters)
CALL section_vals_val_get(combine_section, "PARAMETERS", c_vals=my_par, i_rep_val=i)
CALL reallocate(colvar%combine_cvs_param%c_parameters, 1, isize + SIZE(my_par))
colvar%combine_cvs_param%c_parameters(isize + 1:isize + SIZE(my_par)) = my_par
END DO
ALLOCATE (colvar%combine_cvs_param%v_parameters(0))
CALL section_vals_val_get(combine_section, "VALUES", n_rep_val=ncol)
DO i = 1, ncol
isize = SIZE(colvar%combine_cvs_param%v_parameters)
CALL section_vals_val_get(combine_section, "VALUES", r_vals=my_vals, i_rep_val=i)
CALL reallocate(colvar%combine_cvs_param%v_parameters, 1, isize + SIZE(my_vals))
colvar%combine_cvs_param%v_parameters(isize + 1:isize + SIZE(my_vals)) = my_vals
END DO
! Info on derivative evaluation
CALL section_vals_val_get(combine_section, "DX", r_val=colvar%combine_cvs_param%dx)
CALL section_vals_val_get(combine_section, "ERROR_LIMIT", r_val=colvar%combine_cvs_param%lerr)
ELSE IF (my_subsection(12)) THEN
! Population
wrk_section => population_section
CALL colvar_create(colvar, population_colvar_id)
CALL colvar_check_points(colvar, population_section)
NULLIFY (colvar%population_param%i_at_from, colvar%population_param%c_kinds_from)
NULLIFY (colvar%population_param%i_at_to, colvar%population_param%c_kinds_to)
! This section can be repeated
CALL section_vals_val_get(population_section, "ATOMS_FROM", n_rep_val=n_var)
ndim = 0
IF (n_var /= 0) THEN
! INDEX LIST
DO k = 1, n_var
CALL section_vals_val_get(population_section, "ATOMS_FROM", i_rep_val=k, i_vals=iatms)
CALL reallocate(colvar%population_param%i_at_from, 1, ndim + SIZE(iatms))
colvar%population_param%i_at_from(ndim + 1:ndim + SIZE(iatms)) = iatms
ndim = ndim + SIZE(iatms)
END DO
colvar%population_param%n_atoms_from = ndim
colvar%population_param%use_kinds_from = .FALSE.
ELSE
! KINDS
CALL section_vals_val_get(population_section, "KINDS_FROM", n_rep_val=n_var)
CPASSERT(n_var > 0)
DO k = 1, n_var
CALL section_vals_val_get(population_section, "KINDS_FROM", i_rep_val=k, c_vals=c_kinds)
CALL reallocate(colvar%population_param%c_kinds_from, 1, ndim + SIZE(c_kinds))
colvar%population_param%c_kinds_from(ndim + 1:ndim + SIZE(c_kinds)) = c_kinds
ndim = ndim + SIZE(c_kinds)
END DO
colvar%population_param%n_atoms_from = 0
colvar%population_param%use_kinds_from = .TRUE.
! Uppercase the label
DO k = 1, ndim
CALL uppercase(colvar%population_param%c_kinds_from(k))
END DO
END IF
! This section can be repeated
CALL section_vals_val_get(population_section, "ATOMS_TO", n_rep_val=n_var)
ndim = 0
IF (n_var /= 0) THEN
! INDEX LIST
DO k = 1, n_var
CALL section_vals_val_get(population_section, "ATOMS_TO", i_rep_val=k, i_vals=iatms)
CALL reallocate(colvar%population_param%i_at_to, 1, ndim + SIZE(iatms))
colvar%population_param%i_at_to(ndim + 1:ndim + SIZE(iatms)) = iatms
ndim = ndim + SIZE(iatms)
END DO
colvar%population_param%n_atoms_to = ndim
colvar%population_param%use_kinds_to = .FALSE.
ELSE
! KINDS
CALL section_vals_val_get(population_section, "KINDS_TO", n_rep_val=n_var)
CPASSERT(n_var > 0)
DO k = 1, n_var
CALL section_vals_val_get(population_section, "KINDS_TO", i_rep_val=k, c_vals=c_kinds)
CALL reallocate(colvar%population_param%c_kinds_to, 1, ndim + SIZE(c_kinds))
colvar%population_param%c_kinds_to(ndim + 1:ndim + SIZE(c_kinds)) = c_kinds
ndim = ndim + SIZE(c_kinds)
END DO
colvar%population_param%n_atoms_to = 0
colvar%population_param%use_kinds_to = .TRUE.
! Uppercase the label
DO k = 1, ndim
CALL uppercase(colvar%population_param%c_kinds_to(k))
END DO
END IF
! Let's finish reading the other parameters
CALL section_vals_val_get(population_section, "R0", r_val=colvar%population_param%r_0)
CALL section_vals_val_get(population_section, "NN", i_val=colvar%population_param%nncrd)
CALL section_vals_val_get(population_section, "ND", i_val=colvar%population_param%ndcrd)
CALL section_vals_val_get(population_section, "N0", i_val=colvar%population_param%n0)
CALL section_vals_val_get(population_section, "SIGMA", r_val=colvar%population_param%sigma)
ELSE IF (my_subsection(13)) THEN
! Angle between two planes
wrk_section => plane_plane_angle_section
CALL colvar_create(colvar, plane_plane_angle_colvar_id)
CALL colvar_check_points(colvar, plane_plane_angle_section)
! Read the specification of the two planes
plane_sections => section_vals_get_subs_vals(plane_plane_angle_section, "PLANE")
CALL section_vals_get(plane_sections, n_repetition=n_var)
IF (n_var /= 2) &
CPABORT("PLANE_PLANE_ANGLE Colvar section: Two PLANE sections must be provided!")
! Plane 1
CALL section_vals_val_get(plane_sections, "DEF_TYPE", i_rep_section=1, &
i_val=colvar%plane_plane_angle_param%plane1%type_of_def)
IF (colvar%plane_plane_angle_param%plane1%type_of_def == plane_def_vec) THEN
CALL section_vals_val_get(plane_sections, "NORMAL_VECTOR", i_rep_section=1, &
r_vals=s1)
colvar%plane_plane_angle_param%plane1%normal_vec = s1
ELSE
CALL section_vals_val_get(plane_sections, "ATOMS", i_rep_section=1, &
i_vals=iatms)
colvar%plane_plane_angle_param%plane1%points = iatms
END IF
! Plane 2
CALL section_vals_val_get(plane_sections, "DEF_TYPE", i_rep_section=2, &
i_val=colvar%plane_plane_angle_param%plane2%type_of_def)
IF (colvar%plane_plane_angle_param%plane2%type_of_def == plane_def_vec) THEN
CALL section_vals_val_get(plane_sections, "NORMAL_VECTOR", i_rep_section=2, &
r_vals=s1)
colvar%plane_plane_angle_param%plane2%normal_vec = s1
ELSE
CALL section_vals_val_get(plane_sections, "ATOMS", i_rep_section=2, &
i_vals=iatms)
colvar%plane_plane_angle_param%plane2%points = iatms
END IF
ELSE IF (my_subsection(14)) THEN
! Gyration Radius
wrk_section => gyration_section
CALL colvar_create(colvar, gyration_colvar_id)
CALL colvar_check_points(colvar, gyration_section)
NULLIFY (colvar%gyration_param%i_at, colvar%gyration_param%c_kinds)
! This section can be repeated
CALL section_vals_val_get(gyration_section, "ATOMS", n_rep_val=n_var)
ndim = 0
IF (n_var /= 0) THEN
! INDEX LIST
DO k = 1, n_var
CALL section_vals_val_get(gyration_section, "ATOMS", i_rep_val=k, i_vals=iatms)
CALL reallocate(colvar%gyration_param%i_at, 1, ndim + SIZE(iatms))
colvar%gyration_param%i_at(ndim + 1:ndim + SIZE(iatms)) = iatms
ndim = ndim + SIZE(iatms)
END DO
colvar%gyration_param%n_atoms = ndim
colvar%gyration_param%use_kinds = .FALSE.
ELSE
! KINDS
CALL section_vals_val_get(gyration_section, "KINDS", n_rep_val=n_var)
CPASSERT(n_var > 0)
DO k = 1, n_var
CALL section_vals_val_get(gyration_section, "KINDS", i_rep_val=k, c_vals=c_kinds)
CALL reallocate(colvar%gyration_param%c_kinds, 1, ndim + SIZE(c_kinds))
colvar%gyration_param%c_kinds(ndim + 1:ndim + SIZE(c_kinds)) = c_kinds
ndim = ndim + SIZE(c_kinds)
END DO
colvar%gyration_param%n_atoms = 0
colvar%gyration_param%use_kinds = .TRUE.
! Uppercase the label
DO k = 1, ndim
CALL uppercase(colvar%gyration_param%c_kinds(k))
END DO
END IF
ELSE IF (my_subsection(15)) THEN
! RMSD_AB
wrk_section => rmsd_section
CALL colvar_create(colvar, rmsd_colvar_id)
NULLIFY (colvar%rmsd_param%i_rmsd, colvar%rmsd_param%r_ref, colvar%rmsd_param%weights)
frame_section => section_vals_get_subs_vals(rmsd_section, "FRAME")
CALL section_vals_get(frame_section, n_repetition=nr_frame)
colvar%rmsd_param%nr_frames = nr_frame
! Calculation is aborted if reference frame are less than 2
CPASSERT(nr_frame >= 1 .AND. nr_frame <= 2)
CALL read_frames(frame_section, para_env, nr_frame, colvar%rmsd_param%r_ref, &
colvar%rmsd_param%n_atoms)
ALLOCATE (colvar%rmsd_param%weights(colvar%rmsd_param%n_atoms))
colvar%rmsd_param%weights = 0.0_dp
CALL section_vals_val_get(rmsd_section, "SUBSET_TYPE", i_val=colvar%rmsd_param%subset)
IF (colvar%rmsd_param%subset == rmsd_all) THEN
ALLOCATE (colvar%rmsd_param%i_rmsd(colvar%rmsd_param%n_atoms))
DO i = 1, colvar%rmsd_param%n_atoms
colvar%rmsd_param%i_rmsd(i) = i
END DO
ELSE IF (colvar%rmsd_param%subset == rmsd_list) THEN
! This section can be repeated
CALL section_vals_val_get(rmsd_section, "ATOMS", n_rep_val=n_var)
ndim = 0
IF (n_var /= 0) THEN
! INDEX LIST
DO k = 1, n_var
CALL section_vals_val_get(rmsd_section, "ATOMS", i_rep_val=k, i_vals=iatms)
CALL reallocate(colvar%rmsd_param%i_rmsd, 1, ndim + SIZE(iatms))
colvar%rmsd_param%i_rmsd(ndim + 1:ndim + SIZE(iatms)) = iatms
ndim = ndim + SIZE(iatms)
END DO
colvar%rmsd_param%n_atoms = ndim
ELSE
CPABORT("CV RMSD: if SUBSET_TYPE=LIST a list of atoms needs to be provided ")
END IF
ELSE IF (colvar%rmsd_param%subset == rmsd_weightlist) THEN
CALL section_vals_val_get(rmsd_section, "ATOMS", n_rep_val=n_var)
ndim = 0
IF (n_var /= 0) THEN
! INDEX LIST
DO k = 1, n_var
CALL section_vals_val_get(rmsd_section, "ATOMS", i_rep_val=k, i_vals=iatms)
CALL reallocate(colvar%rmsd_param%i_rmsd, 1, ndim + SIZE(iatms))
colvar%rmsd_param%i_rmsd(ndim + 1:ndim + SIZE(iatms)) = iatms
ndim = ndim + SIZE(iatms)
END DO
colvar%rmsd_param%n_atoms = ndim
ELSE
CPABORT("CV RMSD: if SUBSET_TYPE=WEIGHT_LIST a list of atoms needs to be provided ")
END IF
CALL section_vals_val_get(rmsd_section, "WEIGHTS", n_rep_val=n_var)
ndim = 0
IF (n_var /= 0) THEN
! INDEX LIST
DO k = 1, n_var
CALL section_vals_val_get(rmsd_section, "WEIGHTS", i_rep_val=k, r_vals=wei)
CALL reallocate(weights, 1, ndim + SIZE(wei))
weights(ndim + 1:ndim + SIZE(wei)) = wei
ndim = ndim + SIZE(wei)
END DO
IF (ndim /= colvar%rmsd_param%n_atoms) &
CALL cp_abort(__LOCATION__, "CV RMSD: list of atoms and list of "// &
"weights need to contain same number of entries. ")
DO i = 1, ndim
ii = colvar%rmsd_param%i_rmsd(i)
colvar%rmsd_param%weights(ii) = weights(i)
END DO
DEALLOCATE (weights)
ELSE
CPABORT("CV RMSD: if SUBSET_TYPE=WEIGHT_LIST a list of weights need to be provided. ")
END IF
ELSE
CPABORT("CV RMSD: unknown SUBSET_TYPE.")
END IF
CALL section_vals_val_get(rmsd_section, "ALIGN_FRAMES", l_val=colvar%rmsd_param%align_frames)
ELSE IF (my_subsection(17)) THEN
! Work on XYZ positions of atoms
wrk_section => xyz_diag_section
CALL colvar_create(colvar, xyz_diag_colvar_id)
CALL colvar_check_points(colvar, wrk_section)
CALL section_vals_val_get(wrk_section, "ATOM", i_val=iatm)
CALL section_vals_val_get(wrk_section, "COMPONENT", i_val=icomponent)
CALL section_vals_val_get(wrk_section, "PBC", l_val=colvar%xyz_diag_param%use_pbc)
CALL section_vals_val_get(wrk_section, "ABSOLUTE_POSITION", l_val=colvar%xyz_diag_param%use_absolute_position)
colvar%xyz_diag_param%i_atom = iatm
colvar%xyz_diag_param%component = icomponent
ELSE IF (my_subsection(18)) THEN
! Work on the outer diagonal (two atoms A,B) XYZ positions
wrk_section => xyz_outerdiag_section
CALL colvar_create(colvar, xyz_outerdiag_colvar_id)
CALL colvar_check_points(colvar, wrk_section)
CALL section_vals_val_get(wrk_section, "ATOMS", i_vals=iatms)
colvar%xyz_outerdiag_param%i_atoms = iatms
CALL section_vals_val_get(wrk_section, "COMPONENT_A", i_val=icomponent)
colvar%xyz_outerdiag_param%components(1) = icomponent
CALL section_vals_val_get(wrk_section, "COMPONENT_B", i_val=icomponent)
colvar%xyz_outerdiag_param%components(2) = icomponent
CALL section_vals_val_get(wrk_section, "PBC", l_val=colvar%xyz_outerdiag_param%use_pbc)
ELSE IF (my_subsection(19)) THEN
! Energy
wrk_section => u_section
CALL colvar_create(colvar, u_colvar_id)
colvar%u_param%mixed_energy_section => section_vals_get_subs_vals(wrk_section, "MIXED")
CALL section_vals_get(colvar%u_param%mixed_energy_section, explicit=use_mixed_energy)
IF (.NOT. use_mixed_energy) NULLIFY (colvar%u_param%mixed_energy_section)
ELSE IF (my_subsection(20)) THEN
! Wc hydrogen bond
wrk_section => Wc_section
CALL colvar_create(colvar, Wc_colvar_id)
CALL colvar_check_points(colvar, Wc_section)
CALL section_vals_val_get(Wc_section, "ATOMS", i_vals=iatms)
CALL section_vals_val_get(wrk_section, "RCUT", r_val=my_val(1))
colvar%Wc%rcut = cp_unit_to_cp2k(my_val(1), "angstrom")
colvar%Wc%ids = iatms
ELSE IF (my_subsection(21)) THEN
! HBP colvar
wrk_section => HBP_section
CALL colvar_create(colvar, HBP_colvar_id)
CALL colvar_check_points(colvar, HBP_section)
CALL section_vals_val_get(wrk_section, "NPOINTS", i_val=colvar%HBP%nPoints)
CALL section_vals_val_get(wrk_section, "RCUT", r_val=my_val(1))
colvar%HBP%rcut = cp_unit_to_cp2k(my_val(1), "angstrom")
CALL section_vals_val_get(wrk_section, "RCUT", r_val=colvar%HBP%shift)
ALLOCATE (colvar%HBP%ids(colvar%HBP%nPoints, 3))
ALLOCATE (colvar%HBP%ewc(colvar%HBP%nPoints))
DO i = 1, colvar%HBP%nPoints
CALL section_vals_val_get(wrk_section, "ATOMS", i_rep_val=i, i_vals=iatms)
colvar%HBP%ids(i, :) = iatms
END DO
ELSE IF (my_subsection(22)) THEN
! Ring Puckering
CALL colvar_create(colvar, ring_puckering_colvar_id)
CALL section_vals_val_get(ring_puckering_section, "ATOMS", i_vals=iatms)
colvar%ring_puckering_param%nring = SIZE(iatms)
ALLOCATE (colvar%ring_puckering_param%atoms(SIZE(iatms)))
colvar%ring_puckering_param%atoms = iatms
CALL section_vals_val_get(ring_puckering_section, "COORDINATE", &
i_val=colvar%ring_puckering_param%iq)
! test the validity of the parameters
ndim = colvar%ring_puckering_param%nring
IF (ndim <= 3) &
CPABORT("CV Ring Puckering: Ring size has to be 4 or larger. ")
ii = colvar%ring_puckering_param%iq
IF (ABS(ii) == 1 .OR. ii < -(ndim - 1)/2 .OR. ii > ndim/2) &
CPABORT("CV Ring Puckering: Invalid coordinate number.")
ELSE IF (my_subsection(23)) THEN
! Minimum Distance
wrk_section => mindist_section
CALL colvar_create(colvar, mindist_colvar_id)
CALL colvar_check_points(colvar, mindist_section)
NULLIFY (colvar%mindist_param%i_dist_from, colvar%mindist_param%i_coord_from, &
colvar%mindist_param%k_coord_from, colvar%mindist_param%i_coord_to, &
colvar%mindist_param%k_coord_to)
CALL section_vals_val_get(mindist_section, "ATOMS_DISTANCE", i_vals=iatms)
colvar%mindist_param%n_dist_from = SIZE(iatms)
ALLOCATE (colvar%mindist_param%i_dist_from(SIZE(iatms)))
colvar%mindist_param%i_dist_from = iatms
CALL section_vals_val_get(mindist_section, "ATOMS_FROM", n_rep_val=n_var)
ndim = 0
IF (n_var /= 0) THEN
! INDEX LIST
DO k = 1, n_var
CALL section_vals_val_get(mindist_section, "ATOMS_FROM", i_rep_val=k, i_vals=iatms)
CALL reallocate(colvar%mindist_param%i_coord_from, 1, ndim + SIZE(iatms))
colvar%mindist_param%i_coord_from(ndim + 1:ndim + SIZE(iatms)) = iatms
ndim = ndim + SIZE(iatms)
END DO
colvar%mindist_param%n_coord_from = ndim
colvar%mindist_param%use_kinds_from = .FALSE.
ELSE
!KINDS
CALL section_vals_val_get(mindist_section, "KINDS_FROM", n_rep_val=n_var)
CPASSERT(n_var > 0)
DO k = 1, n_var
CALL section_vals_val_get(mindist_section, "KINDS_FROM", i_rep_val=k, c_vals=c_kinds)
CALL reallocate(colvar%mindist_param%k_coord_from, 1, ndim + SIZE(c_kinds))
colvar%mindist_param%k_coord_from(ndim + 1:ndim + SIZE(c_kinds)) = c_kinds
ndim = ndim + SIZE(c_kinds)
END DO
colvar%mindist_param%n_coord_from = 0
colvar%mindist_param%use_kinds_from = .TRUE.
! Uppercase the label
DO k = 1, ndim
CALL uppercase(colvar%mindist_param%k_coord_from(k))
END DO
END IF
CALL section_vals_val_get(mindist_section, "ATOMS_TO", n_rep_val=n_var)
ndim = 0
IF (n_var /= 0) THEN
! INDEX LIST
DO k = 1, n_var
CALL section_vals_val_get(mindist_section, "ATOMS_TO", i_rep_val=k, i_vals=iatms)
CALL reallocate(colvar%mindist_param%i_coord_to, 1, ndim + SIZE(iatms))
colvar%mindist_param%i_coord_to(ndim + 1:ndim + SIZE(iatms)) = iatms
ndim = ndim + SIZE(iatms)
END DO
colvar%mindist_param%n_coord_to = ndim
colvar%mindist_param%use_kinds_to = .FALSE.
ELSE
!KINDS