include/tpxio.h

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  38
  39 #ifndef _tpxio_h
  40 #define _tpxio_h
  41
  42
  43 /**************************************************************
  44  *
  45  * The routines in the corresponding c-file tpxio.c
  46  * are based on the lower level routines in gmxfio.c
  47  * The integer file pointer returned from open_tpx
  48  * can also be used with the routines in gmxfio.h
  49  *
  50  **************************************************************/
  51 #include "visibility.h"
  52 #include "typedefs.h"
  53 #include "gmxfio.h"
  54
  55 #ifdef __cplusplus
  56 extern "C" {
  57 #endif
  58
  59 typedef struct
  60 {
  61     int   bIr;       /* Non zero if input_rec is present                */
  62     int   bBox;      /* Non zero if a box is present                    */
  63     int   bTop;      /* Non zero if a topology is present               */
  64     int   bX;        /* Non zero if coordinates are present             */
  65     int   bV;        /* Non zero if velocities are present              */
  66     int   bF;        /* Non zero if forces are present          */
  67
  68     int   natoms;    /* The total number of atoms                       */
  69     int   ngtc;      /* The number of temperature coupling groups    */
  70     real  lambda;    /* Current value of lambda                 */
  71     int   fep_state; /* Current value of the alchemical state --
  72                       * not yet printed out.  */
  73     /*a better decision will eventually (5.0 or later) need to be made
  74        on how to treat the alchemical state of the system, which can now
  75        vary through a simulation, and cannot be completely described
  76        though a single lambda variable, or even a single state
  77        index. Eventually, should probably be a vector. MRS*/
  78 } t_tpxheader;
  79
  80 /*
  81  * These routines handle reading and writing of preprocessed
  82  * topology files in any of the following formats:
  83  * TPR : topology in XDR format, portable accross platforms
  84  * TPB : binary topology, not portable accross platforms
  85  * TPA : ascii topology (possibbly huge)
  86  * TRR : trajectory in XDR format (non compressed)
  87  * TRJ : trajectory in binary format
  88  *
  89  * Files are written in the precision with which the source are compiled,
  90  * but double and single precision can be read by either.
  91  */
  92
  93 GMX_LIBGMX_EXPORT
  94 t_fileio *open_tpx(const char *fn, const char *mode);
  95 /* Return an file pointer corresponding to the file you have just opened */
  96
  97 GMX_LIBGMX_EXPORT
  98 void close_tpx(t_fileio *fio);
  99 /*  Close the file corresponding to fio */
 100
 101 GMX_LIBGMX_EXPORT
 102 void read_tpxheader(const char *fn, t_tpxheader *tpx, gmx_bool TopOnlyOK,
 103                     int *version, int *generation);
 104 /* Read the header from a tpx file and then close it again.
 105  * By setting TopOnlyOK to true, it is possible to read future
 106  * versions too (we skip the changed inputrec), provided we havent
 107  * changed the topology description. If it is possible to read
 108  * the inputrec it will still be done even if TopOnlyOK is TRUE.
 109  *
 110  * The version and generation if the topology (see top of tpxio.c)
 111  * are returned in the two last arguments.
 112  */
 113
 114 GMX_LIBGMX_EXPORT
 115 void write_tpx_state(const char *fn,
 116                      t_inputrec *ir, t_state *state, gmx_mtop_t *mtop);
 117 /* Write a file, and close it again.
 118  * If fn == NULL, an efTPA file will be written to stdout (which
 119  * will not be closed afterwards)
 120  */
 121
 122 GMX_LIBGMX_EXPORT
 123 void read_tpx_state(const char *fn,
 124                     t_inputrec *ir, t_state *state, rvec *f,
 125                     gmx_mtop_t *mtop);
 126 GMX_LIBGMX_EXPORT
 127 int read_tpx(const char *fn,
 128              t_inputrec *ir, matrix box, int *natoms,
 129              rvec *x, rvec *v, rvec *f, gmx_mtop_t *mtop);
 130 /* Read a file, and close it again.
 131  * If fn == NULL, an efTPA file will be read from stdin (which
 132  * will not be closed afterwards)
 133  * When step, t or lambda are NULL they will not be stored.
 134  * Returns ir->ePBC, if it could be read from the file.
 135  */
 136
 137 GMX_LIBGMX_EXPORT
 138 int read_tpx_top(const char *fn,
 139                  t_inputrec *ir, matrix box, int *natoms,
 140                  rvec *x, rvec *v, rvec *f, t_topology *top);
 141 /* As read_tpx, but for the old t_topology struct */
 142
 143 GMX_LIBGMX_EXPORT
 144 gmx_bool fn2bTPX(const char *file);
 145 /* return if *file is one of the TPX file types */
 146
 147 GMX_LIBGMX_EXPORT
 148 gmx_bool read_tps_conf(const char *infile, char *title, t_topology *top,
 149                        int *ePBC, rvec **x, rvec **v, matrix box, gmx_bool bMass);
 150 /* Read title, top.atoms, x, v (if not NULL) and box from an STX file,
 151  * memory for atoms, x and v will be allocated.
 152  * Return TRUE if a complete topology was read.
 153  * If infile is a TPX file read the whole top,
 154  * else if bMass=TRUE, read the masses into top.atoms from the mass database.
 155  */
 156
 157 void tpx_make_chain_identifiers(t_atoms *atoms, t_block *mols);
 158
 159 #ifdef __cplusplus
 160 }
 161 #endif
 162
 163 #endif