include/tpxio.h

   1 /*
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   9  *                        VERSION 3.2.0
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  35
  36 #ifndef _tpxio_h
  37 #define _tpxio_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  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 "typedefs.h"
  52 #include "gmxfio.h"
  53
  54 #ifdef __cplusplus
  55 extern "C" {
  56 #endif
  57
  58 typedef struct
  59 {
  60   int   bIr;            /* Non zero if input_rec is present             */
  61   int   bBox;           /* Non zero if a box is present                 */
  62   int   bTop;           /* Non zero if a topology is present            */
  63   int   bX;             /* Non zero if coordinates are present          */
  64   int   bV;             /* Non zero if velocities are present           */
  65   int   bF;             /* Non zero if forces are present               */
  66
  67   int   natoms;         /* The total number of atoms                    */
  68   int   ngtc;           /* The number of temperature coupling groups    */
  69   real  lambda;         /* Current value of lambda                      */
  70 } t_tpxheader;
  71
  72 /*
  73  * These routines handle reading and writing of preprocessed
  74  * topology files in any of the following formats:
  75  * TPR : topology in XDR format, portable accross platforms
  76  * TPB : binary topology, not portable accross platforms
  77  * TPA : ascii topology (possibbly huge)
  78  * TRR : trajectory in XDR format (non compressed)
  79  * TRJ : trajectory in binary format
  80  *
  81  * Files are written in the precision with which the source are compiled,
  82  * but double and single precision can be read by either.
  83  */
  84
  85 extern t_fileio *open_tpx(const char *fn, const char *mode);
  86 /* Return an file pointer corresponding to the file you have just opened */
  87
  88 extern void close_tpx(t_fileio *fio);
  89 /*  Close the file corresponding to fio */
  90
  91 extern void read_tpxheader(const char *fn, t_tpxheader *tpx, bool TopOnlyOK,
  92                            int *version, int *generation);
  93 /* Read the header from a tpx file and then close it again.
  94  * By setting TopOnlyOK to true, it is possible to read future
  95  * versions too (we skip the changed inputrec), provided we havent
  96  * changed the topology description. If it is possible to read
  97  * the inputrec it will still be done even if TopOnlyOK is TRUE.
  98  *
  99  * The version and generation if the topology (see top of tpxio.c)
 100  * are returned in the two last arguments.
 101  */
 102
 103 extern void write_tpx_state(const char *fn,
 104                             t_inputrec *ir,t_state *state,gmx_mtop_t *mtop);
 105 /* Write a file, and close it again.
 106  * If fn == NULL, an efTPA file will be written to stdout (which
 107  * will not be closed afterwards)
 108  */
 109
 110 extern void read_tpx_state(const char *fn,
 111                            t_inputrec *ir,t_state *state,rvec *f,
 112                            gmx_mtop_t *mtop);
 113 extern int read_tpx(const char *fn,
 114                     t_inputrec *ir,matrix box,int *natoms,
 115                     rvec *x,rvec *v,rvec *f,gmx_mtop_t *mtop);
 116 /* Read a file, and close it again.
 117  * If fn == NULL, an efTPA file will be read from stdin (which
 118  * will not be closed afterwards)
 119  * When step, t or lambda are NULL they will not be stored.
 120  * Returns ir->ePBC, if it could be read from the file.
 121  */
 122
 123 extern int read_tpx_top(const char *fn,
 124                         t_inputrec *ir, matrix box,int *natoms,
 125                         rvec *x,rvec *v,rvec *f,t_topology *top);
 126 /* As read_tpx, but for the old t_topology struct */
 127
 128 extern bool fn2bTPX(const char *file);
 129 /* return if *file is one of the TPX file types */
 130
 131 extern bool read_tps_conf(const char *infile,char *title,t_topology *top,
 132                           int *ePBC, rvec **x,rvec **v,matrix box,bool bMass);
 133 /* Read title, top.atoms, x, v (if not NULL) and box from an STX file,
 134  * memory for atoms, x and v will be allocated.
 135  * Return TRUE if a complete topology was read.
 136  * If infile is a TPX file read the whole top,
 137  * else if bMass=TRUE, read the masses into top.atoms from the mass database.
 138  */
 139
 140 void tpx_make_chain_identifiers(t_atoms *atoms,t_block *mols);
 141
 142 #ifdef __cplusplus
 143 }
 144 #endif
 145
 146 #endif