colvar_types Module Reference

Initialize the collective variables types. More...

Functions/Subroutines
subroutine, public	colvar_create (colvar, colvar_id)
	initializes a colvar_param type More...
subroutine, public	colvar_setup (colvar)
	Finalize the setup of the collective variable. More...
recursive subroutine, public	colvar_release (colvar)
	releases the memory that might have been allocated by the colvar More...
recursive subroutine, public	colvar_clone (colvar_out, colvar_in, i_atom_offset)
	Clone a colvar type. More...
subroutine, public	colvar_p_reallocate (colvar_set, lb1_new, ub1_new)
	Change the dimension of a colvar_p_type. More...
subroutine, public	colvar_p_release (colvar_p)
	Deallocate a set of colvar_p_type. More...
subroutine, public	eval_point_pos (point, particles, r)
	Evaluate the position of the geometrical point. More...
subroutine, public	eval_point_mass (point, particles, m)
	... More...
subroutine, public	eval_point_der (points, i, dsdr, f)
	Evaluate the position of the geometrical point. More...
real(kind=dp) function, public	diff_colvar (colvar, b)
	subtract b from the ss value of a colvar: general function for handling periodic/non-periodic colvar More...

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

Detailed Description

Initialize the collective variables types.

History

5.2004 created [fawzi and alessandro] 1.2009 Fabio Sterpone : added the population COLVAR

Author

Teodoro Laino

Function/Subroutine Documentation

colvar_create()

subroutine, public colvar_types::colvar_create	(	type(colvar_type), pointer	colvar,
		integer, intent(in)	colvar_id
	)

initializes a colvar_param type

Parameters

colvar	the colvat to initialize
colvar_id	...

Author

alessandro laio and fawzi mohamed

Definition at line 420 of file colvar_types.F.

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colvar_setup()

subroutine, public colvar_types::colvar_setup

(

type(colvar_type), intent(inout)

colvar

)

Finalize the setup of the collective variable.

Parameters

colvar

the colvar to initialize

Author

Teodoro Laino, [teo] 09.03.2006

Definition at line 501 of file colvar_types.F.

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colvar_release()

recursive subroutine, public colvar_types::colvar_release

(

type(colvar_type), pointer

colvar

)

releases the memory that might have been allocated by the colvar

Parameters

colvar

the colvar to deallocate

Author

alessandro laio and fawzi mohamed

Definition at line 1175 of file colvar_types.F.

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colvar_clone()

recursive subroutine, public colvar_types::colvar_clone	(	type(colvar_type), intent(inout), pointer	colvar_out,
		type(colvar_type), intent(in)	colvar_in,
		integer, intent(in), optional	i_atom_offset
	)

Clone a colvar type.

Parameters

colvar_out	...
colvar_in	the colvar to deallocate
i_atom_offset	...

Author

Teodoro Laino [tlaino] 04.2006

Definition at line 1352 of file colvar_types.F.

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colvar_p_reallocate()

subroutine, public colvar_types::colvar_p_reallocate	(	type(colvar_p_type), dimension(:), pointer	colvar_set,
		integer, intent(in)	lb1_new,
		integer, intent(in)	ub1_new
	)

Change the dimension of a colvar_p_type.

Parameters

colvar_set	...
lb1_new	...
ub1_new	...

Author

Teodoro Laino [tlaino] 04.2006

Definition at line 1790 of file colvar_types.F.

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colvar_p_release()

subroutine, public colvar_types::colvar_p_release

(

type(colvar_p_type), dimension(:), pointer

colvar_p

)

Deallocate a set of colvar_p_type.

Parameters

colvar_p

...

History

07.2003 created [fawzi] 01.2014 moved from cp_subsys_release() into separate routine.

Author

Ole Schuett

Definition at line 1836 of file colvar_types.F.

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eval_point_pos()

subroutine, public colvar_types::eval_point_pos	(	type(point_type), intent(in)	point,
		type(particle_type), dimension(:), intent(in)	particles,
		real(kind=dp), dimension(3), intent(out)	r
	)

Evaluate the position of the geometrical point.

Parameters

point	...
particles	...
r	...

Author

Teodoro Laino - 03.2007

Definition at line 1859 of file colvar_types.F.

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eval_point_mass()

subroutine, public colvar_types::eval_point_mass	(	type(point_type), intent(in)	point,
		type(particle_type), dimension(:), intent(in)	particles,
		real(kind=dp), intent(out)	m
	)

...

Parameters

point	...
particles	...
m	...

Definition at line 1884 of file colvar_types.F.

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eval_point_der()

subroutine, public colvar_types::eval_point_der	(	type(point_type), dimension(:), intent(in)	points,
		integer, intent(in)	i,
		real(kind=dp), dimension(:, :), intent(inout)	dsdr,
		real(kind=dp), dimension(3), intent(in)	f
	)

Evaluate the position of the geometrical point.

Parameters

points	...
i	...
dsdr	...
f	...

Author

Teodoro Laino - 03.2007

Definition at line 1911 of file colvar_types.F.

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diff_colvar()

real(kind=dp) function, public colvar_types::diff_colvar	(	type(colvar_type), intent(in)	colvar,
		real(kind=dp), intent(in)	b
	)

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

Parameters

colvar	...
b	...

Returns

...

Author

Teodoro Laino [tlaino] - University of Zurich 10.2008

Definition at line 1946 of file colvar_types.F.

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Variable Documentation

plane_def_atoms

integer, parameter, public colvar_types::plane_def_atoms = 0

Definition at line 30 of file colvar_types.F.

plane_def_vec

integer, parameter, public colvar_types::plane_def_vec = 1

Definition at line 30 of file colvar_types.F.

do_clv_geo_center

integer, parameter, public colvar_types::do_clv_geo_center = 0

Definition at line 33 of file colvar_types.F.

do_clv_fix_point

integer, parameter, public colvar_types::do_clv_fix_point = 1

Definition at line 33 of file colvar_types.F.

do_clv_xyz

integer, parameter, public colvar_types::do_clv_xyz = 0

Definition at line 33 of file colvar_types.F.

do_clv_x

integer, parameter, public colvar_types::do_clv_x = 1

Definition at line 33 of file colvar_types.F.

do_clv_y

integer, parameter, public colvar_types::do_clv_y = 2

Definition at line 33 of file colvar_types.F.

do_clv_z

integer, parameter, public colvar_types::do_clv_z = 3

Definition at line 33 of file colvar_types.F.

do_clv_xy

integer, parameter, public colvar_types::do_clv_xy = 4

Definition at line 33 of file colvar_types.F.

do_clv_xz

integer, parameter, public colvar_types::do_clv_xz = 5

Definition at line 33 of file colvar_types.F.

do_clv_yz

integer, parameter, public colvar_types::do_clv_yz = 6

Definition at line 33 of file colvar_types.F.

no_colvar_id

integer, parameter, public colvar_types::no_colvar_id = -2

Definition at line 56 of file colvar_types.F.

dist_colvar_id

integer, parameter, public colvar_types::dist_colvar_id = 1

Definition at line 56 of file colvar_types.F.

coord_colvar_id

integer, parameter, public colvar_types::coord_colvar_id = 2

Definition at line 56 of file colvar_types.F.

torsion_colvar_id

integer, parameter, public colvar_types::torsion_colvar_id = 3

Definition at line 56 of file colvar_types.F.

angle_colvar_id

integer, parameter, public colvar_types::angle_colvar_id = 4

Definition at line 56 of file colvar_types.F.

plane_distance_colvar_id

integer, parameter, public colvar_types::plane_distance_colvar_id = 5

Definition at line 56 of file colvar_types.F.

rotation_colvar_id

integer, parameter, public colvar_types::rotation_colvar_id = 6

Definition at line 56 of file colvar_types.F.

dfunct_colvar_id

integer, parameter, public colvar_types::dfunct_colvar_id = 7

Definition at line 56 of file colvar_types.F.

qparm_colvar_id

integer, parameter, public colvar_types::qparm_colvar_id = 8

Definition at line 56 of file colvar_types.F.

hydronium_shell_colvar_id

integer, parameter, public colvar_types::hydronium_shell_colvar_id = 9

Definition at line 56 of file colvar_types.F.

reaction_path_colvar_id

integer, parameter, public colvar_types::reaction_path_colvar_id = 10

Definition at line 56 of file colvar_types.F.

combine_colvar_id

integer, parameter, public colvar_types::combine_colvar_id = 11

Definition at line 56 of file colvar_types.F.

population_colvar_id

integer, parameter, public colvar_types::population_colvar_id = 12

Definition at line 56 of file colvar_types.F.

plane_plane_angle_colvar_id

integer, parameter, public colvar_types::plane_plane_angle_colvar_id = 13

Definition at line 56 of file colvar_types.F.

gyration_colvar_id

integer, parameter, public colvar_types::gyration_colvar_id = 14

Definition at line 56 of file colvar_types.F.

rmsd_colvar_id

integer, parameter, public colvar_types::rmsd_colvar_id = 15

Definition at line 56 of file colvar_types.F.

distance_from_path_colvar_id

integer, parameter, public colvar_types::distance_from_path_colvar_id = 16

Definition at line 56 of file colvar_types.F.

xyz_diag_colvar_id

integer, parameter, public colvar_types::xyz_diag_colvar_id = 17

Definition at line 56 of file colvar_types.F.

xyz_outerdiag_colvar_id

integer, parameter, public colvar_types::xyz_outerdiag_colvar_id = 18

Definition at line 56 of file colvar_types.F.

u_colvar_id

integer, parameter, public colvar_types::u_colvar_id = 19

Definition at line 56 of file colvar_types.F.

wc_colvar_id

integer, parameter, public colvar_types::wc_colvar_id = 20

Definition at line 56 of file colvar_types.F.

hbp_colvar_id

integer, parameter, public colvar_types::hbp_colvar_id = 21

Definition at line 56 of file colvar_types.F.

ring_puckering_colvar_id

integer, parameter, public colvar_types::ring_puckering_colvar_id = 22

Definition at line 56 of file colvar_types.F.

mindist_colvar_id

integer, parameter, public colvar_types::mindist_colvar_id = 23

Definition at line 56 of file colvar_types.F.

acid_hyd_dist_colvar_id

integer, parameter, public colvar_types::acid_hyd_dist_colvar_id = 24

Definition at line 56 of file colvar_types.F.

acid_hyd_shell_colvar_id

integer, parameter, public colvar_types::acid_hyd_shell_colvar_id = 25

Definition at line 56 of file colvar_types.F.

hydronium_dist_colvar_id

integer, parameter, public colvar_types::hydronium_dist_colvar_id = 26

Definition at line 56 of file colvar_types.F.