/usr/include/gromacs/fileio/confio.h

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#ifndef GMX_FILEIO_CONFIO_H
#define GMX_FILEIO_CONFIO_H

#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"

/* For reading coordinate files it is assumed that enough memory
 * has been allocated beforehand.
 */
#ifdef __cplusplus
extern "C" {
#endif

struct gmx_mtop_t;
struct t_atoms;
struct t_topology;

void write_sto_conf_indexed(const char *outfile, const char *title,
                            const t_atoms *atoms,
                            const rvec x[], const rvec *v, int ePBC, const matrix box,
                            int nindex, int index[]);
/* like write_sto_conf, but indexed */

void write_sto_conf(const char *outfile, const char *title,
                    const t_atoms *atoms,
                    const rvec x[], const rvec *v, int ePBC, const matrix box);
/* write atoms, x, v (if .gro and not NULL) and box (if not NULL)
 * to an STO (.gro or .pdb) file */

void write_sto_conf_mtop(const char *outfile, const char *title,
                         struct gmx_mtop_t *mtop,
                         const rvec x[], const rvec *v, int ePBC, const matrix box);
/* As write_sto_conf, but uses a gmx_mtop_t struct */

/*! \brief Read a configuration and, when available, a topology from a tpr or structure file.
 *
 * When reading from a tpr file, the complete topology is returned in \p mtop.
 * When reading from a structure file, only the atoms struct in \p mtop contains data.
 *
 * \param[in]     infile        Input file name
 * \param[out]    haveTopology  true when a topology was read and stored in mtop
 * \param[out]    mtop          The topology, either complete or only atom data
 * \param[out]    ePBC          Enum reporting the type of PBC
 * \param[in,out] x             Coordinates will be stored when *x!=NULL
 * \param[in,out] v             Velocities will be stored when *v!=NULL
 * \param[out]    box           Box dimensions
 */
void readConfAndTopology(const char *infile,
                         bool *haveTopology, gmx_mtop_t *mtop,
                         int *ePBC,
                         rvec **x, rvec **v, matrix box);

/*! \brief Read a configuration and, when available, a topology from a tpr or structure file.
 *
 * Deprecated, superseded by readConfAndTopology().
 * When \p requireMasses = TRUE, this routine must return a topology with
 * mass data. Masses are either read from a tpr input file, or otherwise
 * looked up from the mass database, and when such lookup fails a fatal error
 * results.
 * When \p requireMasses = FALSE, masses will still be read from tpr input and
 * their presence is signaled with the \p haveMass flag in t_atoms of \p top.
 *
 * \param[in]     infile        Input file name
 * \param[out]    top           The topology, either complete or only atom data. Caller is responsible for calling done_top().
 * \param[out]    ePBC          Enum reporting the type of PBC
 * \param[in,out] x             Coordinates will be stored when *x!=NULL
 * \param[in,out] v             Velocities will be stored when *v!=NULL
 * \param[out]    box           Box dimensions
 * \param[in]     requireMasses Require masses to be present, either from tpr or from the mass database
 * \returns if a topology is available
 */
gmx_bool read_tps_conf(const char *infile, struct t_topology *top,
                       int *ePBC, rvec **x, rvec **v, matrix box,
                       gmx_bool requireMasses);

#ifdef __cplusplus
}
#endif

#endif
libgromacs-dev 2018.1-1 / usr / include / gromacs / fileio / confio.h
