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