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+ * the research papers on the package. Check out http://www.gromacs.org.
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/*! \file
* \brief API for handling positions.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
#ifndef GMX_SELECTION_POSITION_H
#define GMX_SELECTION_POSITION_H
-#include "../legacyheaders/types/simple.h"
-
-#include "indexutil.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/selection/indexutil.h"
/*! \brief
* Stores a set of positions together with their origins.
*/
-typedef struct gmx_ana_pos_t
+struct gmx_ana_pos_t
{
- /*! \brief
- * Number of positions.
- */
- int nr;
+ //! Initializes an empty position structure.
+ gmx_ana_pos_t();
+ ~gmx_ana_pos_t();
+
+ //! Returns the number of positions.
+ int count() const { return m.mapb.nr; }
+
/*! \brief
* Array of positions.
*/
* \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 forces. */
void
gmx_ana_pos_reserve_forces(gmx_ana_pos_t *pos);
+/** Reserves memory for use with gmx_ana_pos_append_init(). */
+void
+gmx_ana_pos_reserve_for_append(gmx_ana_pos_t *pos, int n, int isize,
+ bool bVelocities, bool bForces);
/** Initializes a \c gmx_ana_pos_t to represent a constant position. */
void
gmx_ana_pos_init_const(gmx_ana_pos_t *pos, const 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, 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);
/** 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);
+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. */
void
-gmx_ana_pos_append(gmx_ana_pos_t *dest, gmx_ana_index_t *g,
- gmx_ana_pos_t *src, int i, int refid);
+gmx_ana_pos_append(gmx_ana_pos_t *dest, 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);
+void
+/** Appends atoms from a position into a preallocated index group. */
+gmx_ana_pos_add_to_group(gmx_ana_index_t *g, gmx_ana_pos_t *src, int i);
#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff