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/*
*
* This source code is part of
*
* G R O M A C S
*
* GROningen MAchine for Chemical Simulations
*
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2009, The GROMACS development team,
* check out http://www.gromacs.org for more information.
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
*
* For more info, check our website at http://www.gromacs.org
*/
/*! \file
* \brief API for handling positions.
*/
#ifndef POSITION_H
#define POSITION_H
#include "typedefs.h"
#include "indexutil.h"
#ifdef __cplusplus
extern "C" {
#endif
/*! \brief
* Stores a set of positions together with their origins.
*/
typedef struct gmx_ana_pos_t
{
/*! \brief
* Number of positions.
*/
int nr;
/*! \brief
* Array of positions.
*/
rvec *x;
/*! \brief
* Velocities (can be NULL).
*/
rvec *v;
/*! \brief
* Forces (can be NULL).
*/
rvec *f;
/*! \brief
* Mapping of the current positions to the original group.
*
* \see gmx_ana_indexmap_t
*/
gmx_ana_indexmap_t m;
/*! \brief
* Pointer to the current evaluation group.
*/
gmx_ana_index_t *g;
/*! \brief
* Number of elements allocated for \c x.
*/
int nalloc_x;
} gmx_ana_pos_t;
/** Initializes an empty position structure. */
void
gmx_ana_pos_clear(gmx_ana_pos_t *pos);
/** Ensures that enough memory has been allocated to store positions. */
void
gmx_ana_pos_reserve(gmx_ana_pos_t *pos, int n, int isize);
/** Request memory allocation for velocities. */
void
gmx_ana_pos_reserve_velocities(gmx_ana_pos_t *pos);
/** Request memory allocation for forces. */
void
gmx_ana_pos_reserve_forces(gmx_ana_pos_t *pos);
/** Initializes a \c gmx_ana_pos_t to represent a constant position. */
void
gmx_ana_pos_init_const(gmx_ana_pos_t *pos, rvec x);
/** Frees the memory allocated for position storage. */
void
gmx_ana_pos_deinit(gmx_ana_pos_t *pos);
/** Frees the memory allocated for positions. */
void
gmx_ana_pos_free(gmx_ana_pos_t *pos);
/** Copies the evaluated positions to a preallocated data structure. */
void
gmx_ana_pos_copy(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, gmx_bool bFirst);
/** Sets the number of positions in a position structure. */
void
gmx_ana_pos_set_nr(gmx_ana_pos_t *pos, int n);
/** Sets the evaluation group of a position data structure. */
void
gmx_ana_pos_set_evalgrp(gmx_ana_pos_t *pos, gmx_ana_index_t *g);
/** Empties a position data structure with full initialization. */
void
gmx_ana_pos_empty_init(gmx_ana_pos_t *pos);
/** Empties a position data structure. */
void
gmx_ana_pos_empty(gmx_ana_pos_t *pos);
/** Appends a position to a preallocated data structure with full
* initialization. */
void
gmx_ana_pos_append_init(gmx_ana_pos_t *dest, gmx_ana_index_t *g,
gmx_ana_pos_t *src, int i);
/** Appends a position to a preallocated data structure. */
void
gmx_ana_pos_append(gmx_ana_pos_t *dest, gmx_ana_index_t *g,
gmx_ana_pos_t *src, int i, int refid);
/** Updates position data structure state after appends. */
void
gmx_ana_pos_append_finish(gmx_ana_pos_t *pos);
#ifdef __cplusplus
}
#endif
#endif
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