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input_cp2k_colvar.F
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input_cp2k_colvar.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 !
!--------------------------------------------------------------------------------------------------!
! **************************************************************************************************
!> \par History
!> - taken out of input_cp2k_motion
!> \author teo & fawzi
! **************************************************************************************************
MODULE input_cp2k_colvar
USE bibliography, ONLY: Branduardi2007
USE colvar_types, ONLY: &
do_clv_fix_point, do_clv_geo_center, do_clv_x, do_clv_xy, do_clv_xyz, do_clv_xz, do_clv_y, &
do_clv_yz, do_clv_z, plane_def_atoms, plane_def_vec
USE cp_output_handling, ONLY: add_last_numeric,&
cp_print_key_section_create,&
high_print_level,&
low_print_level
USE cp_units, ONLY: cp_unit_to_cp2k
USE input_constants, ONLY: gaussian,&
numerical,&
rmsd_all,&
rmsd_list,&
rmsd_weightlist
USE input_keyword_types, ONLY: keyword_create,&
keyword_release,&
keyword_type
USE input_section_types, ONLY: section_add_keyword,&
section_add_subsection,&
section_create,&
section_release,&
section_type
USE input_val_types, ONLY: char_t,&
integer_t,&
lchar_t,&
real_t
USE kinds, ONLY: dp
USE string_utilities, ONLY: s2a
#include "./base/base_uses.f90"
IMPLICIT NONE
PRIVATE
LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .FALSE.
CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'input_cp2k_colvar'
PUBLIC :: create_colvar_section, &
create_colvar_xyz_d_section, &
create_colvar_xyz_od_section
CONTAINS
! **************************************************************************************************
!> \brief creates the colvar section
!> \param section the section to be created
!> \param skip_recursive_colvar ...
!> \author teo
! **************************************************************************************************
RECURSIVE SUBROUTINE create_colvar_section(section, skip_recursive_colvar)
TYPE(section_type), POINTER :: section
LOGICAL, OPTIONAL :: skip_recursive_colvar
LOGICAL :: skip
TYPE(section_type), POINTER :: print_key, subsection
skip = .FALSE.
IF (PRESENT(skip_recursive_colvar)) skip = skip_recursive_colvar
CPASSERT(.NOT. ASSOCIATED(section))
CALL section_create(section, __LOCATION__, name="COLVAR", &
description="This section specifies the nature of the collective variables.", &
n_keywords=1, n_subsections=1, repeats=.TRUE.)
NULLIFY (subsection, print_key)
CALL create_colvar_var_section(subsection=subsection, &
section=section, skip_recursive_colvar=skip)
CALL section_create(subsection, __LOCATION__, name="PRINT", &
description="Controls the printing of the colvar specifications", &
n_keywords=0, n_subsections=1, repeats=.TRUE.)
NULLIFY (print_key)
CALL cp_print_key_section_create(print_key, __LOCATION__, "PROGRAM_RUN_INFO", &
description="Controls the printing of basic information during colvar setup.", &
print_level=low_print_level, add_last=add_last_numeric, filename="__STD_OUT__")
CALL section_add_subsection(subsection, print_key)
CALL section_release(print_key)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_clv_info_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
END SUBROUTINE create_colvar_section
! **************************************************************************************************
!> \brief Create the restart section for colvar restraints
!> This section will be only used for restraint restarts.
!> Constraints are handled automatically
!> \param section the section to create
!> \author Teodoro Laino 08.2006
! **************************************************************************************************
SUBROUTINE create_clv_info_section(section)
TYPE(section_type), POINTER :: section
TYPE(keyword_type), POINTER :: keyword
CPASSERT(.NOT. ASSOCIATED(section))
NULLIFY (keyword)
CALL section_create(section, __LOCATION__, name="COLVAR_FUNC_INFO", &
description="Specify further data possibly used by colvars, depending "// &
"on the starting geometry, for computing the functions value.", &
n_subsections=0, repeats=.FALSE.)
CALL keyword_create(keyword, __LOCATION__, name="_DEFAULT_KEYWORD_", &
description="Colvar function data."// &
" The order is an internal order. So if you decide to edit/modify/add these values by hand"// &
" you should know very well what you are doing.!", repeats=.TRUE., &
usage="{Real} ...", type_of_var=real_t, n_var=-1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
END SUBROUTINE create_clv_info_section
! **************************************************************************************************
!> \brief creates the collective variables for the colvar section
!> \param subsection ...
!> \param section the section to be created
!> \param skip_recursive_colvar ...
!> \author teo
! **************************************************************************************************
RECURSIVE SUBROUTINE create_colvar_var_section(subsection, section, skip_recursive_colvar)
TYPE(section_type), POINTER :: subsection, section
LOGICAL, INTENT(IN) :: skip_recursive_colvar
CPASSERT(.NOT. ASSOCIATED(subsection))
CPASSERT(ASSOCIATED(section))
CALL create_colvar_dist_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_angle_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_torsion_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_coord_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_pop_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_gyr_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_d_pl_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_a_pl_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_rot_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_dfunct_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_qparm_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_hydronium_shell_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_hydronium_dist_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_acid_hyd_dist_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_acid_hyd_shell_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_rmsd_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_xyz_d_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_xyz_od_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_u_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_wc_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_hbp_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_ring_puckering_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_cond_dist_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
IF (.NOT. skip_recursive_colvar) THEN
CALL create_colvar_rpath_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_dpath_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL create_colvar_comb_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
END IF
END SUBROUTINE create_colvar_var_section
! **************************************************************************************************
!> \brief collective variables specifying coordination
!> \param section the section to be created
!> \author teo
! **************************************************************************************************
SUBROUTINE create_colvar_coord_section(section)
TYPE(section_type), POINTER :: section
TYPE(keyword_type), POINTER :: keyword
TYPE(section_type), POINTER :: subsection
CPASSERT(.NOT. ASSOCIATED(section))
CALL section_create(section, __LOCATION__, name="coordination", &
description="Section to define the coordination number as a collective variable.", &
n_keywords=1, n_subsections=0, repeats=.FALSE.)
NULLIFY (subsection, keyword)
CALL keyword_create(keyword, __LOCATION__, name="ATOMS_FROM", &
variants=(/"POINTS_FROM"/), &
description="Specify indexes of atoms/points building the coordination variable. ", &
usage="ATOMS_FROM {integer} {integer} ..", repeats=.TRUE., &
n_var=-1, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="ATOMS_TO", &
variants=(/"POINTS_TO"/), &
description="Specify indexes of atoms/points building the coordination variable. ", &
usage="ATOMS_TO {integer} {integer} ..", repeats=.TRUE., &
n_var=-1, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="ATOMS_TO_B", &
variants=(/"POINTS_TO_B"/), &
description="For the CV given by the multiplication of two coorination numbers,"// &
" here specify indexes of the third set of atoms/points. ", &
usage="ATOMS_TO_B {integer} {integer} ..", repeats=.TRUE., &
n_var=-1, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="KINDS_FROM", &
description="Specify alternatively kinds of atoms building the coordination variable.", &
usage="KINDS_FROM {CHAR} {CHAR} ..", repeats=.TRUE., &
n_var=-1, type_of_var=char_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="KINDS_TO", &
description="Specify alternatively kinds of atoms building the coordination variable.", &
usage="KINDS_TO {CHAR} {CHAR} ..", repeats=.TRUE., &
n_var=-1, type_of_var=char_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="KINDS_TO_B", &
description="For the CV given by the multiplication of two coorination numbers,"// &
" here specify alternatively kinds of atoms building the coordination variable.", &
usage="KINDS_TO_B {CHAR} {CHAR} ..", repeats=.TRUE., &
n_var=-1, type_of_var=char_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
! Must be present in each colvar and handled properly
CALL create_point_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL keyword_create(keyword, __LOCATION__, name="R0", &
variants=(/"R_0"/), &
description="Specify the R0 parameter in the coordination function.", &
usage="R0 {real}", default_r_val=3.0_dp, &
unit_str="bohr", n_var=1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="NN", &
variants=(/"EXPON_NUMERATOR"/), &
description="Sets the value of the numerator of the exponential factor"// &
" in the coordination FUNCTION.", &
usage="NN {integer}", default_i_val=6, &
n_var=1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="ND", &
variants=(/"EXPON_DENOMINATOR"/), &
description="Sets the value of the denominator of the exponential factor"// &
" in the coordination FUNCTION.", &
usage="ND {integer}", default_i_val=12, &
n_var=1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="R0_B", &
variants=(/"R_0_B"/), &
description="For the CV given by the multiplication of two coorination numbers,"// &
" specify the R0 parameter in the second coordination function.", &
usage="R0_B {real}", default_r_val=3.0_dp, &
unit_str="bohr", n_var=1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="NN_B", &
variants=(/"EXPON_NUMERATOR_B"/), &
description="For the CV given by the multiplication of two coorination numbers,"// &
" Sets the value of the numerator of the exponential factor"// &
" in the coordination FUNCTION.", &
usage="NN_B {integer}", default_i_val=6, &
n_var=1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="ND_B", &
variants=(/"EXPON_DENOMINATOR_B"/), &
description="For the CV given by the multiplication of two coorination numbers,"// &
" Sets the value of the denominator of the exponential factor"// &
" in the coordination FUNCTION.", &
usage="ND_B {integer}", default_i_val=12, &
n_var=1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
END SUBROUTINE create_colvar_coord_section
! **************************************************************************************************
!> \brief ...
!> \param section ...
! **************************************************************************************************
SUBROUTINE create_colvar_cond_dist_section(section)
TYPE(section_type), POINTER :: section
TYPE(keyword_type), POINTER :: keyword
TYPE(section_type), POINTER :: subsection
CPASSERT(.NOT. ASSOCIATED(section))
CALL section_create(section, __LOCATION__, name="CONDITIONED_DISTANCE", &
description="Section to define the conditioned distance as a collective variable.", &
n_keywords=1, n_subsections=0, repeats=.FALSE.)
NULLIFY (subsection, keyword)
CALL keyword_create(keyword, __LOCATION__, name="ATOMS_DISTANCE", &
description="Specify indexes of atoms/points from which the distance is computed. ", &
usage="ATOMS_DISTANCE {integer} {integer} ..", repeats=.TRUE., &
n_var=-1, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="ATOMS_FROM", &
variants=(/"POINTS_FROM"/), &
description="Specify indexes of atoms/points building the coordination variable. ", &
usage="ATOMS_FROM {integer} {integer} ..", repeats=.TRUE., &
n_var=-1, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="ATOMS_TO", &
variants=(/"POINTS_TO"/), &
description="Specify indexes of atoms/points building the coordination variable. ", &
usage="ATOMS_TO {integer} {integer} ..", repeats=.TRUE., &
n_var=-1, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="KINDS_FROM", &
description="Specify alternatively kinds of atoms building the coordination variable.", &
usage="KINDS_FROM {CHAR} {CHAR} ..", repeats=.TRUE., &
n_var=-1, type_of_var=char_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="KINDS_TO", &
description="Specify alternatively kinds of atoms building the coordination variable.", &
usage="KINDS_TO {CHAR} {CHAR} ..", repeats=.TRUE., &
n_var=-1, type_of_var=char_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
! Must be present in each colvar and handled properly
CALL create_point_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL keyword_create(keyword, __LOCATION__, name="R0", &
variants=(/"R_0"/), &
description="Specify the R0 parameter in the coordination function.", &
usage="R0 {real}", default_r_val=3.0_dp, &
unit_str="bohr", n_var=1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="NN", &
variants=(/"EXPON_NUMERATOR"/), &
description="Sets the value of the numerator of the exponential factor"// &
" in the coordination FUNCTION.", &
usage="NN {integer}", default_i_val=6, &
n_var=1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="ND", &
variants=(/"EXPON_DENOMINATOR"/), &
description="Sets the value of the denominator of the exponential factor"// &
" in the coordination FUNCTION.", &
usage="ND {integer}", default_i_val=12, &
n_var=1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="LAMBDA", &
description="Specify the lambda parameter at the exponent of the conditioned distance function.", &
usage="R0 {real}", default_r_val=3.0_dp, &
unit_str="bohr", n_var=1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
END SUBROUTINE create_colvar_cond_dist_section
! **************************************************************************************************
!> \brief collective variables specifying population of a specie based on coordination
!> \param section the section to be created
!> \date 01.2009
!> \author Fabio Sterpone
! **************************************************************************************************
SUBROUTINE create_colvar_pop_section(section)
TYPE(section_type), POINTER :: section
TYPE(keyword_type), POINTER :: keyword
TYPE(section_type), POINTER :: subsection
CPASSERT(.NOT. ASSOCIATED(section))
CALL section_create(section, __LOCATION__, name="population", &
description="Section to define the population of specie as a collective variable. "// &
"See also <https://doi.org/10.1021/jp3019588>.", &
n_keywords=1, n_subsections=0, repeats=.FALSE.)
NULLIFY (subsection, keyword)
CALL keyword_create(keyword, __LOCATION__, name="ATOMS_FROM", &
variants=(/"POINTS_FROM"/), &
description="Specify indexes of atoms/points building the coordination variable. ", &
usage="ATOMS_FROM {integer} {integer} ..", repeats=.TRUE., &
n_var=-1, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="ATOMS_TO", &
variants=(/"POINTS_TO"/), &
description="Specify indexes of atoms/points building the coordination variable. ", &
usage="ATOMS_TO {integer} {integer} ..", repeats=.TRUE., &
n_var=-1, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="KINDS_FROM", &
description="Specify alternatively kinds of atoms building the coordination variable.", &
usage="KINDS_FROM {CHAR} {CHAR} ..", repeats=.TRUE., &
n_var=-1, type_of_var=char_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="KINDS_TO", &
description="Specify alternatively kinds of atoms building the coordination variable.", &
usage="KINDS_TO {CHAR} {CHAR} ..", repeats=.TRUE., &
n_var=-1, type_of_var=char_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
! Must be present in each colvar and handled properly
CALL create_point_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
CALL keyword_create(keyword, __LOCATION__, name="R0", &
variants=(/"R_0"/), &
description="Specify the R0 parameter in the coordination function.", &
usage="R0 {real}", default_r_val=3.0_dp, &
n_var=1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="NN", &
variants=(/"EXPON_NUMERATOR"/), &
description="Sets the value of the numerator of the exponential factor"// &
" in the coordination FUNCTION.", &
usage="NN {integer}", default_i_val=6, &
n_var=1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="ND", &
variants=(/"EXPON_DENOMINATOR"/), &
description="Sets the value of the denominator of the exponential factor"// &
" in the coordination FUNCTION.", &
usage="ND {integer}", default_i_val=12, &
n_var=1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="n0", &
variants=(/"n_0"/), &
description="Specify the n0 parameter that sets the coordination of the species.", &
usage="n0 {integer}", default_i_val=4, &
n_var=1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="SIGMA", &
description="Specify the gaussian width of used to build the population istogram.", &
usage="SIGMA {real}", default_r_val=0.5_dp, &
n_var=1)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
END SUBROUTINE create_colvar_pop_section
! **************************************************************************************************
!> \brief ...
!> \param section ...
! **************************************************************************************************
SUBROUTINE create_colvar_gyr_section(section)
TYPE(section_type), POINTER :: section
TYPE(keyword_type), POINTER :: keyword
TYPE(section_type), POINTER :: subsection
CPASSERT(.NOT. ASSOCIATED(section))
CALL section_create(section, __LOCATION__, name="GYRATION_RADIUS", &
description="Section to define the gyration radius as a collective variable.", &
n_keywords=1, n_subsections=0, repeats=.FALSE.)
NULLIFY (subsection, keyword)
CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
variants=(/"POINTS"/), &
description="Specify indexes of atoms/points defyining the gyration radius variable. ", &
usage="ATOMS {integer} {integer} ..", repeats=.TRUE., &
n_var=-1, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="KINDS", &
description="Specify alternatively kinds of atoms defining the gyration radius.", &
usage="KINDS {CHAR} {CHAR} ..", repeats=.TRUE., &
n_var=-1, type_of_var=char_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
! Must be present in each colvar and handled properly
CALL create_point_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
END SUBROUTINE create_colvar_gyr_section
! **************************************************************************************************
!> \brief collective variables specifying torsion
!> \param section the section to be created
!> \author teo
! **************************************************************************************************
SUBROUTINE create_colvar_dfunct_section(section)
TYPE(section_type), POINTER :: section
TYPE(keyword_type), POINTER :: keyword
TYPE(section_type), POINTER :: subsection
CPASSERT(.NOT. ASSOCIATED(section))
CALL section_create(section, __LOCATION__, name="DISTANCE_FUNCTION", &
description="Section to define functions between two distances as collective variables."// &
" The function is defined as d1+coeff*d2", &
n_keywords=1, n_subsections=0, repeats=.FALSE.)
NULLIFY (keyword, subsection)
CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
variants=(/"POINTS"/), &
description="Specifies the indexes of atoms/points for the two bonds d1=(1-2) d2=(3-4).", &
usage="ATOMS {integer} {integer} {integer} {integer}", &
n_var=4, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="COEFFICIENT", &
description="Specifies the coefficient in the function for the constraint."// &
" -1.0 has to be used for distance difference, 1.0 for distance addition", &
usage="COEFFICIENT {real}", &
type_of_var=real_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="PBC", &
description="Whether periodic boundary conditions should be applied on the "// &
"atomic position before computing the colvar or not.", &
usage="PBC", &
default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
! Must be present in each colvar and handled properly
CALL create_point_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
END SUBROUTINE create_colvar_dfunct_section
! **************************************************************************************************
!> \brief collective variables specifying torsion
!> \param section the section to be created
!> \author teo
! **************************************************************************************************
SUBROUTINE create_colvar_torsion_section(section)
TYPE(section_type), POINTER :: section
TYPE(keyword_type), POINTER :: keyword
TYPE(section_type), POINTER :: subsection
CPASSERT(.NOT. ASSOCIATED(section))
CALL section_create(section, __LOCATION__, name="torsion", &
description="Section to define the torsion as a collective variables.", &
n_keywords=1, n_subsections=0, repeats=.FALSE.)
NULLIFY (keyword, subsection)
CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
variants=(/"POINTS"/), &
description="Specifies the indexes of atoms/points defining the torsion.", &
usage="ATOMS {integer} {integer} {integer} {integer}", &
n_var=4, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
! Must be present in each colvar and handled properly
CALL create_point_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
END SUBROUTINE create_colvar_torsion_section
! **************************************************************************************************
!> \brief collective variables specifying torsion
!> \param section the section to be created
!> \author teo
! **************************************************************************************************
SUBROUTINE create_colvar_rot_section(section)
TYPE(section_type), POINTER :: section
TYPE(keyword_type), POINTER :: keyword
TYPE(section_type), POINTER :: subsection
CPASSERT(.NOT. ASSOCIATED(section))
CALL section_create(section, __LOCATION__, name="bond_rotation", &
description="Section to define the rotation of a bond/line with respect to"// &
" another bond/line", &
n_keywords=1, n_subsections=0, repeats=.FALSE.)
NULLIFY (keyword, subsection)
CALL keyword_create(keyword, __LOCATION__, name="P1_BOND1", &
description="Specifies the index of atom/point defining the first point"// &
" of the first bond/line.", &
usage="P1_BOND1 {integer}", &
n_var=1, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="P2_BOND1", &
description="Specifies the index of atom/point defining the second point"// &
" of the first bond/line.", &
usage="P2_BOND1 {integer}", &
n_var=1, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="P1_BOND2", &
description="Specifies the index of atom/point defining the first point"// &
" of the second bond/line.", &
usage="P1_BOND2 {integer}", &
n_var=1, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="P2_BOND2", &
description="Specifies the index of atom/point defining the second point"// &
" of the second bond/line.", &
usage="P2_BOND2 {integer}", &
n_var=1, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
! Must be present in each colvar and handled properly
CALL create_point_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
END SUBROUTINE create_colvar_rot_section
! **************************************************************************************************
!> \brief collective variables specifying angles
!> \param section the section to be created
!> \author teo
! **************************************************************************************************
SUBROUTINE create_colvar_angle_section(section)
TYPE(section_type), POINTER :: section
TYPE(keyword_type), POINTER :: keyword
TYPE(section_type), POINTER :: subsection
CPASSERT(.NOT. ASSOCIATED(section))
CALL section_create(section, __LOCATION__, name="angle", &
description="Section to define the angle as a collective variables.", &
n_keywords=1, n_subsections=0, repeats=.FALSE.)
NULLIFY (keyword, subsection)
CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
variants=(/"POINTS"/), &
description="Specifies the indexes of atoms/points defining the angle.", &
usage="ATOMS {integer} {integer} {integer}", &
n_var=3, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
! Must be present in each colvar and handled properly
CALL create_point_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
END SUBROUTINE create_colvar_angle_section
! **************************************************************************************************
!> \brief creates the colvar section regarded to the collective variables dist
!> \param section the section to be created
!> \author teo
! **************************************************************************************************
SUBROUTINE create_colvar_dist_section(section)
TYPE(section_type), POINTER :: section
TYPE(keyword_type), POINTER :: keyword
TYPE(section_type), POINTER :: subsection
CPASSERT(.NOT. ASSOCIATED(section))
CALL section_create(section, __LOCATION__, name="distance", &
description="Section to define the distance as a collective variables.", &
n_keywords=1, n_subsections=0, repeats=.FALSE.)
NULLIFY (keyword, subsection)
CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
variants=(/"POINTS"/), &
description="Specifies the indexes of atoms/points defining the distance.", &
usage="ATOMS {integer} {integer}", &
n_var=2, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="AXIS", &
description="Define the axes along which the colvar should be evaluated", &
usage="AXIS (XYZ | X | Y | Z | XY| XZ | YZ)", &
enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
enum_i_vals=(/do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz/), &
default_i_val=do_clv_xyz)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="SIGN", &
description="Whether the distance along one Cartesian axis has to be considered with sign."// &
" This option is valid if only one dimension is selected.", &
usage="SIGN", &
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
! Must be present in each colvar and handled properly
CALL create_point_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
END SUBROUTINE create_colvar_dist_section
! **************************************************************************************************
!> \brief creates the colvar section regarded to the collective variables dist
!> \param section the section to be created
!> \author teo
! **************************************************************************************************
SUBROUTINE create_colvar_xyz_d_section(section)
TYPE(section_type), POINTER :: section
TYPE(keyword_type), POINTER :: keyword
TYPE(section_type), POINTER :: subsection
CPASSERT(.NOT. ASSOCIATED(section))
CALL section_create(section, __LOCATION__, name="XYZ_DIAG", &
description="Section to define the distance of an atom from its starting "// &
"position ((X-X(0))^2+(Y-Y(0))^2+(Z-Z(0))^2) or part of its components as a collective variable. "// &
"If absolute_position is specified, instead the CV is represented by the "// &
"instantaneous position of the atom (only available for X, Y or Z components).", &
n_keywords=1, n_subsections=0, repeats=.FALSE.)
NULLIFY (keyword, subsection)
CALL keyword_create(keyword, __LOCATION__, name="ATOM", &
variants=(/"POINT"/), &
description="Specifies the index of the atom/point.", &
usage="ATOM {integer}", &
n_var=1, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="COMPONENT", &
description="Define the component of the position vector which will be used "// &
"as a colvar.", &
usage="AXIS (XYZ | X | Y | Z | XY| XZ | YZ)", &
enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
enum_i_vals=(/do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz/), &
default_i_val=do_clv_xyz)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="PBC", &
description="Whether periodic boundary conditions should be applied on the "// &
"atomic position before computing the colvar or not.", &
usage="PBC", &
default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="ABSOLUTE_POSITION", &
description="If enabled, the absolute position of the atoms will be used. ", &
usage="ABSOLUTE_POSITION", &
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
! Must be present in each colvar and handled properly
CALL create_point_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
END SUBROUTINE create_colvar_xyz_d_section
! **************************************************************************************************
!> \brief creates the colvar section regarded to the collective variables dist
!> \param section the section to be created
!> \author teo
! **************************************************************************************************
SUBROUTINE create_colvar_xyz_od_section(section)
TYPE(section_type), POINTER :: section
TYPE(keyword_type), POINTER :: keyword
TYPE(section_type), POINTER :: subsection
CPASSERT(.NOT. ASSOCIATED(section))
CALL section_create(section, __LOCATION__, name="XYZ_OUTERDIAG", &
description="Section to define the cross term (XA-XA(0))*(XB-XB(0))+(XA-XA(0))*(YB-YB(0))"// &
" or part of its components as a collective variable. The final term is given by the product"// &
" of the components of A with the components of B.", &
n_keywords=1, n_subsections=0, repeats=.FALSE.)
NULLIFY (keyword, subsection)
CALL keyword_create(keyword, __LOCATION__, name="ATOMS", &
variants=(/"POINTS"/), &
description="Specifies the index of the atoms/points A and B.", &
usage="ATOMS {integer} {integer}", &
n_var=2, type_of_var=integer_t)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="COMPONENT_A", &
description="Define the component of the position vector which will be used "// &
"as a colvar for atom A.", &
usage="AXIS (XYZ | X | Y | Z | XY| XZ | YZ)", &
enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
enum_i_vals=(/do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz/), &
default_i_val=do_clv_xyz)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="COMPONENT_B", &
description="Define the component of the position vector which will be used "// &
"as a colvar for atom B.", &
usage="AXIS (XYZ | X | Y | Z | XY| XZ | YZ)", &
enum_c_vals=s2a("XYZ", "X", "Y", "Z", "XY", "XZ", "YZ"), &
enum_i_vals=(/do_clv_xyz, do_clv_x, do_clv_y, do_clv_z, do_clv_xy, do_clv_xz, do_clv_yz/), &
default_i_val=do_clv_xyz)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="PBC", &
description="Whether periodic boundary conditions should be applied on the "// &
"atomic position before computing the colvar or not.", &
usage="PBC", &
default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
! Must be present in each colvar and handled properly
CALL create_point_section(subsection)
CALL section_add_subsection(section, subsection)
CALL section_release(subsection)
END SUBROUTINE create_colvar_xyz_od_section
! **************************************************************************************************
!> \brief energy as collective variable
!> \param section the section to be created
!> \author Sebastiano Caravati
! **************************************************************************************************
SUBROUTINE create_colvar_u_section(section)
TYPE(section_type), POINTER :: section
TYPE(keyword_type), POINTER :: keyword
TYPE(section_type), POINTER :: subsection
CPASSERT(.NOT. ASSOCIATED(section))
CALL section_create(section, __LOCATION__, name="u", &
description="Section to define the energy as a generalized collective variable.", &
n_keywords=0, n_subsections=0, repeats=.FALSE.)
NULLIFY (subsection, keyword)
CALL section_create(subsection, __LOCATION__, name="MIXED", &
description="This section allows to use any function of the energy subsystems"// &
" in a mixed_env calculation as a collective variable.", &
n_keywords=1, n_subsections=0, repeats=.FALSE.)
CALL keyword_create(keyword, __LOCATION__, name="ENERGY_FUNCTION", &
description="Specifies the functional form of the collective variable in mathematical notation.", &
usage="ENERGY_FUNCTION (E1+E2-LOG(E1/E2))", type_of_var=lchar_t, &
n_var=1)
CALL section_add_keyword(subsection, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="VARIABLES", &
description="Defines the variables of the functional form. To allow an efficient"// &
" mapping the order of the energy variables will be considered identical to the"// &
" order of the force_eval in the force_eval_order list.", &
usage="VARIABLES x", type_of_var=char_t, &
n_var=-1)
CALL section_add_keyword(subsection, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="PARAMETERS", &
description="Defines the parameters of the functional form", &
usage="PARAMETERS a b D", type_of_var=char_t, &
n_var=-1, repeats=.TRUE.)
CALL section_add_keyword(subsection, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="VALUES", &
description="Defines the values of parameter of the functional form", &
usage="VALUES ", type_of_var=real_t, &
n_var=-1, repeats=.TRUE., unit_str="internal_cp2k")
CALL section_add_keyword(subsection, keyword)
CALL keyword_release(keyword)