Documentation for module colvar_types

Initialize the collective variables types

source: colvar_types.F
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public Types:

colvar_counters
...
colvar_p_type
...
colvar_type
parameters for a collective variable

public Subroutines/Functions:

Clone a colvar type
initializes a colvar_param type
Change the dimension of a colvar_p_type
Deallocate a set of colvar_p_type
SUBROUTINE RECURSIVE
colvar_release (colvar)
releases the memory that might have been allocated by the colvar
SUBROUTINE
colvar_setup (colvar)
Finalize the setup of the collective variable
FUNCTION
REAL(dp)
diff_colvar (colvar, b)
subtract b from the ss value of a colvar: general function for handling periodic/non-periodic colvar
SUBROUTINE
eval_point_der (points, i, dsdr, f)
Evaluate the position of the geometrical point
...
Evaluate the position of the geometrical point

Parameters:

INTEGER
:: acid_hyd_dist_colvar_id = 24
INTEGER
:: acid_hyd_shell_colvar_id = 25
INTEGER
:: angle_colvar_id = 4
INTEGER
:: combine_colvar_id = 11
INTEGER
:: coord_colvar_id = 2
INTEGER
:: dfunct_colvar_id = 7
INTEGER
:: distance_from_path_colvar_id = 16
INTEGER
:: dist_colvar_id = 1
INTEGER
:: do_clv_fix_point = 1
INTEGER
:: do_clv_geo_center = 0
INTEGER
:: do_clv_x = 1
INTEGER
:: do_clv_xy = 4
INTEGER
:: do_clv_xyz = 0
INTEGER
:: do_clv_xz = 5
INTEGER
:: do_clv_y = 2
INTEGER
:: do_clv_yz = 6
INTEGER
:: do_clv_z = 3
INTEGER
:: gyration_colvar_id = 14
INTEGER
:: hbp_colvar_id = 21
INTEGER
:: hydronium_dist_colvar_id = 26
INTEGER
:: hydronium_shell_colvar_id = 9
INTEGER
:: mindist_colvar_id = 23
INTEGER
:: no_colvar_id = -2
INTEGER
:: plane_def_atoms = 0
INTEGER
:: plane_def_vec = 1
INTEGER
:: plane_distance_colvar_id = 5
INTEGER
:: plane_plane_angle_colvar_id = 13
INTEGER
:: population_colvar_id = 12
INTEGER
:: qparm_colvar_id = 8
INTEGER
:: reaction_path_colvar_id = 10
INTEGER
:: ring_puckering_colvar_id = 22
INTEGER
:: rmsd_colvar_id = 15
INTEGER
:: rotation_colvar_id = 6
INTEGER
:: torsion_colvar_id = 3
INTEGER
:: u_colvar_id = 19
INTEGER
:: wc_colvar_id = 20
INTEGER
:: xyz_diag_colvar_id = 17
INTEGER
:: xyz_outerdiag_colvar_id = 18

public Types:

TYPE :: colvar_counters

...


INTEGER
:: ndist ...
INTEGER
:: nangle ...
INTEGER
:: ntorsion ...
INTEGER
:: ncoord ...
INTEGER
:: nplane_dist ...
INTEGER
:: nplane_angle ...
INTEGER
:: nrot ...
INTEGER
:: ndfunct ...
INTEGER
:: nqparm ...
INTEGER
:: nhydronium_shell ...
INTEGER
:: nhydronium_dist ...
INTEGER
:: nacid_hyd_dist ...
INTEGER
:: nacid_hyd_shell ...
INTEGER
:: nreactionpath ...
INTEGER
:: ncombinecvs ...
INTEGER
:: nrestraint ...
INTEGER
:: npopulation ...
INTEGER
:: ngyration ...
INTEGER
:: nrmsd ...
INTEGER
:: nxyz_diag ...
INTEGER
:: nxyz_outerdiag ...
INTEGER
:: ntot ...
INTEGER
:: nwc ...
INTEGER
:: nhbp ...
INTEGER
:: nring_puckering ...

TYPE :: colvar_p_type

...


POINTER :: colvar ...

TYPE :: colvar_type

parameters for a collective variable


INTEGER
:: type_id ...
LOGICAL
:: use_points ...
REAL(dp)
:: ss ...
REAL(dp),
DIMENSION(:,:), POINTER :: dsdr ...
INTEGER,
DIMENSION(:), POINTER :: i_atom ...
INTEGER
:: n_atom_s ...
POINTER :: dist_param ...
POINTER :: coord_param ...
POINTER :: population_param ...
POINTER :: gyration_param ...
POINTER :: torsion_param ...
POINTER :: angle_param ...
POINTER :: plane_distance_param ...
POINTER :: plane_plane_angle_param ...
POINTER :: rotation_param ...
POINTER :: dfunct_param ...
POINTER :: qparm_param ...
POINTER :: hydronium_shell_param ...
POINTER :: hydronium_dist_param ...
POINTER :: acid_hyd_dist_param ...
POINTER :: acid_hyd_shell_param ...
POINTER :: reaction_path_param ...
POINTER :: combine_cvs_param ...
POINTER :: rmsd_param ...
POINTER :: xyz_diag_param ...
POINTER :: xyz_outerdiag_param ...
POINTER :: u_param ...
TYPE(point_type),
DIMENSION(:), POINTER :: points ...
POINTER :: wc ...
POINTER :: hbp ...
POINTER :: ring_puckering_param ...
POINTER :: mindist_param ...

RECURSIVE SUBROUTINEcolvar_clone(colvar_out, colvar_in, i_atom_offset)

Clone a colvar type

Arguments:
POINTER
:: colvar_out ...
POINTER
:: colvar_in the colvar to deallocate
INTEGER,
INTENT(in),
OPTIONAL
:: i_atom_offset ...

SUBROUTINEcolvar_create(colvar, colvar_id)

initializes a colvar_param type

Arguments:
POINTER
:: colvar the colvat to initialize
INTEGER,
INTENT(in)
:: colvar_id ...

SUBROUTINEcolvar_p_reallocate(colvar_set, lb1_new, ub1_new)

Change the dimension of a colvar_p_type

Arguments:
POINTER
:: colvar_set(:) ...
INTEGER,
INTENT(in)
:: lb1_new ...
INTEGER,
INTENT(in)
:: ub1_new ...

SUBROUTINEcolvar_p_release(colvar_p)

Deallocate a set of colvar_p_type

Arguments:
POINTER
:: colvar_p(:) ...

RECURSIVE SUBROUTINEcolvar_release(colvar)

releases the memory that might have been allocated by the colvar

Arguments:
POINTER
:: colvar the colvar to deallocate

SUBROUTINEcolvar_setup(colvar)

Finalize the setup of the collective variable

Arguments:
POINTER
:: colvar the colvar to initialize

FUNCTIONdiff_colvar(colvar, b)

subtract b from the ss value of a colvar: general function for handling periodic/non-periodic colvar

Return Value ::
REAL(dp)
Arguments:
POINTER
:: colvar ...
REAL(dp),
INTENT(in)
:: b ...

SUBROUTINEeval_point_der(points, i, dsdr, f)

Evaluate the position of the geometrical point

Arguments:
TYPE(point_type),
POINTER
:: points(:) ...
INTEGER,
INTENT(in)
:: i ...
REAL(dp),
POINTER
:: dsdr(:,:) ...
REAL(dp),
INTENT(in)
:: f(3) ...

SUBROUTINEeval_point_mass(point, particles, m)

...

Arguments:
:: point ...
POINTER
:: particles(:) ...
REAL(dp),
INTENT(out)
:: m ...

SUBROUTINEeval_point_pos(point, particles, r)

Evaluate the position of the geometrical point

Arguments:
:: point ...
POINTER
:: particles(:) ...
REAL(dp),
INTENT(out)
:: r(3) ...

private Parameters/Types:

private Types:

TYPE :: acid_hyd_dist_colvar_type

...


INTEGER
:: n_oxygens_water ...
INTEGER
:: n_oxygens_acid ...
INTEGER
:: n_hydrogens ...
INTEGER
:: pwoh ...
INTEGER
:: qwoh ...
INTEGER
:: paoh ...
INTEGER
:: qaoh ...
INTEGER
:: pcut ...
INTEGER
:: qcut ...
INTEGER,
POINTER, DIMENSION(:) :: i_oxygens_water ...
INTEGER,
POINTER, DIMENSION(:) :: i_oxygens_acid ...
INTEGER,
POINTER, DIMENSION(:) :: i_hydrogens ...
REAL(dp)
:: rwoh ...
REAL(dp)
:: raoh ...
REAL(dp)
:: lambda ...
REAL(dp)
:: nc ...

TYPE :: acid_hyd_shell_colvar_type

...


INTEGER
:: n_oxygens_water ...
INTEGER
:: n_oxygens_acid ...
INTEGER
:: n_hydrogens ...
INTEGER
:: pwoh ...
INTEGER
:: qwoh ...
INTEGER
:: paoh ...
INTEGER
:: qaoh ...
INTEGER
:: poo ...
INTEGER
:: qoo ...
INTEGER
:: pcut ...
INTEGER
:: qcut ...
INTEGER
:: pm ...
INTEGER
:: qm ...
INTEGER,
POINTER, DIMENSION(:) :: i_oxygens_water ...
INTEGER,
POINTER, DIMENSION(:) :: i_oxygens_acid ...
INTEGER,
POINTER, DIMENSION(:) :: i_hydrogens ...
REAL(dp)
:: rwoh ...
REAL(dp)
:: raoh ...
REAL(dp)
:: roo ...
REAL(dp)
:: lambda ...
REAL(dp)
:: nc ...
REAL(dp)
:: nh ...

TYPE :: angle_colvar_type

...


INTEGER,
DIMENSION(3) :: i_at_angle ...

TYPE :: combine_colvar_type

...


INTEGER
:: type_id ...
POINTER, DIMENSION(:) :: colvar_p ...
REAL(dp)
:: lerr ...
REAL(dp)
:: dx ...
:: function ...
DIMENSION(:), POINTER :: c_parameters ...
DIMENSION(:), POINTER :: variables ...
REAL(dp),
DIMENSION(:), POINTER :: v_parameters ...

TYPE :: coord_colvar_type

...


LOGICAL
:: do_chain ...
LOGICAL
:: use_kinds_from ...
LOGICAL
:: use_kinds_to ...
LOGICAL
:: use_kinds_to_b ...
INTEGER
:: n_atoms_to ...
INTEGER
:: n_atoms_from ...
INTEGER
:: nncrd ...
INTEGER
:: ndcrd ...
INTEGER
:: n_atoms_to_b ...
INTEGER
:: nncrd_b ...
INTEGER
:: ndcrd_b ...
INTEGER,
POINTER, DIMENSION(:) :: i_at_from ...
INTEGER,
POINTER, DIMENSION(:) :: i_at_to ...
INTEGER,
POINTER, DIMENSION(:) :: i_at_to_b ...
DIMENSION(:), POINTER :: c_kinds_from ...
DIMENSION(:), POINTER :: c_kinds_to ...
DIMENSION(:), POINTER :: c_kinds_to_b ...
REAL(dp)
:: r_0 ...
REAL(dp)
:: r_0_b ...

TYPE :: dfunct_colvar_type

...


INTEGER,
DIMENSION(4) :: i_at_dfunct ...
LOGICAL
:: use_pbc ...
REAL(dp)
:: coeff ...

TYPE :: dist_colvar_type

parameters for the distance collective variable


INTEGER
:: i_at ...
INTEGER
:: j_at ...
INTEGER
:: axis_id ...

TYPE :: gyration_colvar_type

...


LOGICAL
:: use_kinds ...
INTEGER
:: n_atoms ...
INTEGER,
POINTER, DIMENSION(:) :: i_at ...
DIMENSION(:), POINTER :: c_kinds ...

TYPE :: hbp_colvar_type

...


INTEGER
:: npoints ...
INTEGER,
POINTER :: ids ...
REAL(dp),
POINTER :: ewc ...
REAL(dp)
:: rcut ...
REAL(dp)
:: shift ...

TYPE :: hydronium_dist_colvar_type

...


INTEGER
:: n_oxygens ...
INTEGER
:: n_hydrogens ...
INTEGER
:: poh ...
INTEGER
:: qoh ...
INTEGER
:: pf ...
INTEGER
:: qf ...
INTEGER
:: pm ...
INTEGER
:: qm ...
INTEGER,
POINTER, DIMENSION(:) :: i_oxygens ...
INTEGER,
POINTER, DIMENSION(:) :: i_hydrogens ...
REAL(dp)
:: roh ...
REAL(dp)
:: lambda ...
REAL(dp)
:: nh ...
REAL(dp)
:: nn ...

TYPE :: hydronium_shell_colvar_type

...


INTEGER
:: n_oxygens ...
INTEGER
:: n_hydrogens ...
INTEGER
:: poh ...
INTEGER
:: qoh ...
INTEGER
:: poo ...
INTEGER
:: qoo ...
INTEGER
:: pm ...
INTEGER
:: qm ...
INTEGER,
POINTER, DIMENSION(:) :: i_oxygens ...
INTEGER,
POINTER, DIMENSION(:) :: i_hydrogens ...
REAL(dp)
:: roo ...
REAL(dp)
:: roh ...
REAL(dp)
:: lambda ...
REAL(dp)
:: nh ...

TYPE :: mindist_colvar_type

...


LOGICAL
:: use_kinds_from ...
LOGICAL
:: use_kinds_to ...
INTEGER
:: n_coord_to ...
INTEGER
:: n_coord_from ...
INTEGER
:: n_dist_from ...
INTEGER
:: p_exp ...
INTEGER
:: q_exp ...
INTEGER,
POINTER, DIMENSION(:) :: i_coord_from ...
INTEGER,
POINTER, DIMENSION(:) :: i_coord_to ...
INTEGER,
POINTER, DIMENSION(:) :: i_dist_from ...
DIMENSION(:), POINTER :: k_coord_from ...
DIMENSION(:), POINTER :: k_coord_to ...
REAL(dp)
:: lambda ...
REAL(dp)
:: r_cut ...

TYPE :: plane_def_type

...


INTEGER
:: type_of_def ...
INTEGER,
DIMENSION(3) :: points ...
REAL(dp),
DIMENSION(3) :: normal_vec ...

TYPE :: plane_distance_colvar_type

...


LOGICAL
:: use_pbc ...
INTEGER,
DIMENSION(3) :: plane ...
INTEGER
:: point ...

TYPE :: plane_plane_angle_colvar_type

...


:: plane1 ...
:: plane2 ...

TYPE :: point_type

...


INTEGER
:: type_id ...
INTEGER,
DIMENSION(:), POINTER :: atoms ...
REAL(dp),
DIMENSION(:), POINTER :: weights ...
REAL(dp),
DIMENSION(3) :: r ...

TYPE :: population_colvar_type

...


LOGICAL
:: use_kinds_from ...
LOGICAL
:: use_kinds_to ...
INTEGER
:: n_atoms_to ...
INTEGER
:: n_atoms_from ...
INTEGER
:: nncrd ...
INTEGER
:: ndcrd ...
INTEGER
:: n0 ...
INTEGER,
POINTER, DIMENSION(:) :: i_at_from ...
INTEGER,
POINTER, DIMENSION(:) :: i_at_to ...
DIMENSION(:), POINTER :: c_kinds_from ...
DIMENSION(:), POINTER :: c_kinds_to ...
REAL(dp)
:: r_0 ...
REAL(dp)
:: sigma ...

TYPE :: qparm_colvar_type

...


INTEGER
:: l ...
INTEGER
:: n_atoms_to ...
INTEGER
:: n_atoms_from ...
INTEGER,
POINTER, DIMENSION(:) :: i_at_from ...
INTEGER,
POINTER, DIMENSION(:) :: i_at_to ...
REAL(dp)
:: rcut ...
REAL(dp)
:: rstart ...
LOGICAL
:: include_images ...

TYPE :: reaction_path_colvar_type

...


INTEGER
:: type_id ...
INTEGER
:: n_components ...
INTEGER
:: nr_frames ...
INTEGER
:: subset ...
INTEGER,
DIMENSION(2) :: function_bounds ...
INTEGER,
POINTER, DIMENSION(:) :: i_rmsd ...
LOGICAL
:: align_frames ...
LOGICAL
:: dist_rmsd ...
LOGICAL
:: rmsd ...
REAL(dp),
DIMENSION(:,:), POINTER :: f_vals ...
REAL(dp),
DIMENSION(:,:), POINTER :: r_ref ...
REAL(dp)
:: lambda ...
REAL(dp)
:: step_size ...
POINTER, DIMENSION(:) :: colvar_p ...

TYPE :: ring_puckering_colvar_type

...


INTEGER
:: nring ...
INTEGER,
POINTER, DIMENSION(:) :: atoms ...
INTEGER
:: iq ...

TYPE :: rmsd_colvar_type

...


INTEGER
:: n_atoms ...
INTEGER
:: nr_frames ...
INTEGER
:: subset ...
INTEGER,
POINTER, DIMENSION(:) :: i_rmsd ...
LOGICAL
:: align_frames ...
REAL(dp),
DIMENSION(:), POINTER :: weights ...
REAL(dp),
DIMENSION(:,:), POINTER :: r_ref ...

TYPE :: rotation_colvar_type

...


INTEGER
:: i_at1_bond1 ...
INTEGER
:: i_at2_bond1 ...
INTEGER
:: i_at1_bond2 ...
INTEGER
:: i_at2_bond2 ...

TYPE :: torsion_colvar_type

...


REAL(dp)
:: o0 ...
INTEGER,
DIMENSION(4) :: i_at_tors ...

TYPE :: u_colvar_type

...


POINTER :: mixed_energy_section ...
INTEGER
:: natom ...

TYPE :: wc_colvar_type

...


INTEGER
:: ids ...
REAL(dp)
:: ewc ...
REAL(dp)
:: rcut ...

TYPE :: xyz_diag_colvar_type

...


LOGICAL
:: use_pbc ...
LOGICAL
:: use_absolute_position ...
INTEGER
:: i_atom ...
INTEGER
:: component ...
REAL(dp),
DIMENSION(3) :: r0 ...

TYPE :: xyz_outerdiag_colvar_type

...


LOGICAL
:: use_pbc ...
INTEGER,
DIMENSION(2) :: i_atoms ...
INTEGER,
DIMENSION(2) :: components ...
REAL(dp),
DIMENSION(3,2) :: r0 ...