position.h File Reference

#include "gromacs/math/vectypes.h"
#include "gromacs/selection/indexutil.h"

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Description

API for handling positions.

Author

Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com

Classes
struct	gmx_ana_pos_t
	Stores a set of positions together with their origins. More...

Functions
void	gmx_ana_pos_reserve (gmx_ana_pos_t *pos, int n, int isize)
	Ensures that enough memory has been allocated to store positions. More...
void	gmx_ana_pos_reserve_velocities (gmx_ana_pos_t *pos)
	Request memory allocation for velocities. More...
void	gmx_ana_pos_reserve_forces (gmx_ana_pos_t *pos)
	Request memory allocation for forces. More...
void	gmx_ana_pos_reserve_for_append (gmx_ana_pos_t *pos, int n, int isize, bool bVelocities, bool bForces)
	Reserves memory for use with gmx_ana_pos_append_init(). More...
void	gmx_ana_pos_init_const (gmx_ana_pos_t *pos, const rvec x)
	Initializes a gmx_ana_pos_t to represent a constant position. More...
void	gmx_ana_pos_copy (gmx_ana_pos_t *dest, gmx_ana_pos_t *src, bool bFirst)
	Copies the evaluated positions to a preallocated data structure. More...
void	gmx_ana_pos_set_nr (gmx_ana_pos_t *pos, int n)
	Sets the number of positions in a position structure. More...
void	gmx_ana_pos_empty_init (gmx_ana_pos_t *pos)
	Empties a position data structure with full initialization. More...
void	gmx_ana_pos_empty (gmx_ana_pos_t *pos)
	Empties a position data structure. More...
void	gmx_ana_pos_append_init (gmx_ana_pos_t *dest, gmx_ana_pos_t *src, int i)
	Appends a position to a preallocated data structure with full initialization. More...
void	gmx_ana_pos_append (gmx_ana_pos_t *dest, gmx_ana_pos_t *src, int i, int refid)
	Appends a position to a preallocated data structure. More...
void	gmx_ana_pos_append_finish (gmx_ana_pos_t *pos)
	Updates position data structure state after appends. More...
void	gmx_ana_pos_add_to_group (gmx_ana_index_t *g, gmx_ana_pos_t *src, int i)
	Appends atoms from a position into a preallocated index group. More...

Function Documentation

void gmx_ana_pos_add_to_group	(	gmx_ana_index_t *	g,
		gmx_ana_pos_t *	src,
		int	i
	)

Appends atoms from a position into a preallocated index group.

Parameters

[in,out]	g	Data structure to which the new atoms are appended.
[in]	src	Data structure from which the position is copied.
[in]	i	Index in src to copy.

void gmx_ana_pos_append	(	gmx_ana_pos_t *	dest,
		gmx_ana_pos_t *	src,
		int	i,
		int	refid
	)

Appends a position to a preallocated data structure.

Parameters

[in,out]	dest	Data structure to which the new position is appended.
[in]	src	Data structure from which the position is copied.
[in]	i	Index in src to copy.
[in]	refid	Reference ID in out (all negative values are treated as -1).

void gmx_ana_pos_append_finish

(

gmx_ana_pos_t *

pos

)

Updates position data structure state after appends.

Parameters

[in,out]

pos

Position data structure.

After gmx_ana_pos_empty(), internal state of the position data structure is not consistent before this function is called. This function should be called after any gmx_ana_pos_append() calls have been made.

void gmx_ana_pos_append_init	(	gmx_ana_pos_t *	dest,
		gmx_ana_pos_t *	src,
		int	i
	)

Appends a position to a preallocated data structure with full initialization.

Parameters

[in,out]	dest	Data structure to which the new position is appended.
[in]	src	Data structure from which the position is copied.
[in]	i	Index in from to copy.

void gmx_ana_pos_copy	(	gmx_ana_pos_t *	dest,
		gmx_ana_pos_t *	src,
		bool	bFirst
	)

Copies the evaluated positions to a preallocated data structure.

Parameters

[in,out]	dest	Destination positions.
[in]	src	Source positions.
[in]	bFirst	If true, memory is allocated for dest and a full copy is made; otherwise, only variable parts are copied, and no memory is allocated.

dest should have been initialized somehow (calloc() is enough).

void gmx_ana_pos_empty

(

gmx_ana_pos_t *

pos

)

Empties a position data structure.

Parameters

[in,out]

pos

Position data structure.

Sets the number of positions to 0.

void gmx_ana_pos_empty_init

(

gmx_ana_pos_t *

pos

)

Empties a position data structure with full initialization.

Parameters

[in,out]

pos

Position data structure.

Sets the number of positions to 0.

void gmx_ana_pos_init_const	(	gmx_ana_pos_t *	pos,
		const rvec	x
	)

Initializes a gmx_ana_pos_t to represent a constant position.

Parameters

[out]	pos	Position data structure to initialize.
[in]	x	Position vector to use.

void gmx_ana_pos_reserve	(	gmx_ana_pos_t *	pos,
		int	n,
		int	isize
	)

Ensures that enough memory has been allocated to store positions.

Parameters

[in,out]	pos	Position data structure.
[in]	n	Maximum number of positions.
[in]	isize	Maximum number of atoms.

Ensures that enough memory is allocated in pos to calculate n positions from isize atoms.

void gmx_ana_pos_reserve_for_append	(	gmx_ana_pos_t *	pos,
		int	n,
		int	isize,
		bool	bVelocities,
		bool	bForces
	)

Reserves memory for use with gmx_ana_pos_append_init().

Parameters

[in,out]	pos	Position data structure.
[in]	n	Maximum number of positions.
[in]	isize	Maximum number of atoms.
[in]	bVelocities	Whether to reserve space for velocities.
[in]	bForces	Whether to reserve space for forces.

Ensures that enough memory is allocated in pos to calculate n positions from isize atoms.

This method needs to be called instead of gmx_ana_pos_reserve() if the intent is to use gmx_ana_pos_append_init()/gmx_ana_pos_append().

void gmx_ana_pos_reserve_forces

(

gmx_ana_pos_t *

pos

)

Request memory allocation for forces.

Parameters

[in,out]

pos

Position data structure.

Currently, this function can only be called after gmx_ana_pos_reserve() has been called at least once with a n >= 0.

void gmx_ana_pos_reserve_velocities

(

gmx_ana_pos_t *

pos

)

Request memory allocation for velocities.

Parameters

[in,out]

pos

Position data structure.

Currently, this function can only be called after gmx_ana_pos_reserve() has been called at least once with a n >= 0.

void gmx_ana_pos_set_nr	(	gmx_ana_pos_t *	pos,
		int	nr
	)

Sets the number of positions in a position structure.

Parameters

[in,out]	pos	Position data structure.
[in]	nr	Number of positions.