src/gromacs/fileio/confio.h

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  37 #ifndef GMX_FILEIO_CONFIO_H
  38 #define GMX_FILEIO_CONFIO_H
  39
  40 #include "gromacs/math/vectypes.h"
  41 #include "gromacs/utility/basedefinitions.h"
  42
  43 /* For reading coordinate files it is assumed that enough memory
  44  * has been allocated beforehand.
  45  */
  46 #ifdef __cplusplus
  47 extern "C" {
  48 #endif
  49
  50 struct gmx_mtop_t;
  51 struct t_atoms;
  52 struct t_topology;
  53
  54 void write_sto_conf_indexed(const char *outfile, const char *title,
  55                             const t_atoms *atoms,
  56                             const rvec x[], const rvec *v, int ePBC, const matrix box,
  57                             int nindex, int index[]);
  58 /* like write_sto_conf, but indexed */
  59
  60 void write_sto_conf(const char *outfile, const char *title,
  61                     const t_atoms *atoms,
  62                     const rvec x[], const rvec *v, int ePBC, const matrix box);
  63 /* write atoms, x, v (if .gro and not NULL) and box (if not NULL)
  64  * to an STO (.gro or .pdb) file */
  65
  66 void write_sto_conf_mtop(const char *outfile, const char *title,
  67                          struct gmx_mtop_t *mtop,
  68                          const rvec x[], const rvec *v, int ePBC, const matrix box);
  69 /* As write_sto_conf, but uses a gmx_mtop_t struct */
  70
  71 /*! \brief Read a configuration and, when available, a topology from a tpr or structure file.
  72  *
  73  * When reading from a tpr file, the complete topology is returned in \p mtop.
  74  * When reading from a structure file, only the atoms struct in \p mtop contains data.
  75  *
  76  * \param[in]     infile        Input file name
  77  * \param[out]    haveTopology  true when a topology was read and stored in mtop
  78  * \param[out]    mtop          The topology, either complete or only atom data
  79  * \param[out]    ePBC          Enum reporting the type of PBC
  80  * \param[in,out] x             Coordinates will be stored when *x!=NULL
  81  * \param[in,out] v             Velocities will be stored when *v!=NULL
  82  * \param[out]    box           Box dimensions
  83  */
  84 void readConfAndTopology(const char *infile,
  85                          bool *haveTopology, gmx_mtop_t *mtop,
  86                          int *ePBC,
  87                          rvec **x, rvec **v, matrix box);
  88
  89 /*! \brief Read a configuration and, when available, a topology from a tpr or structure file.
  90  *
  91  * Deprecated, superseded by readConfAndTopology().
  92  * When \p requireMasses = TRUE, this routine must return a topology with
  93  * mass data. Masses are either read from a tpr input file, or otherwise
  94  * looked up from the mass database, and when such lookup fails a fatal error
  95  * results.
  96  * When \p requireMasses = FALSE, masses will still be read from tpr input and
  97  * their presence is signaled with the \p haveMass flag in t_atoms of \p top.
  98  *
  99  * \param[in]     infile        Input file name
 100  * \param[out]    top           The topology, either complete or only atom data. Caller is responsible for calling done_top().
 101  * \param[out]    ePBC          Enum reporting the type of PBC
 102  * \param[in,out] x             Coordinates will be stored when *x!=NULL
 103  * \param[in,out] v             Velocities will be stored when *v!=NULL
 104  * \param[out]    box           Box dimensions
 105  * \param[in]     requireMasses Require masses to be present, either from tpr or from the mass database
 106  * \returns if a topology is available
 107  */
 108 gmx_bool read_tps_conf(const char *infile, struct t_topology *top,
 109                        int *ePBC, rvec **x, rvec **v, matrix box,
 110                        gmx_bool requireMasses);
 111
 112 #ifdef __cplusplus
 113 }
 114 #endif
 115
 116 #endif