include/tpxio.h

   1 /*
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   4  *
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   6  *
   7  *          GROningen MAchine for Chemical Simulations
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   9  *                        VERSION 3.2.0
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  12  * Copyright (c) 2001-2004, The GROMACS development team,
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  15  * This program is free software; you can redistribute it and/or
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  35
  36 #ifndef _tpxio_h
  37 #define _tpxio_h
  38
  39
  40   /**************************************************************
  41    *
  42    * The routines in the corresponding c-file tpxio.c
  43    * are based on the lower level routines in gmxfio.c
  44    * The integer file pointer returned from open_tpx
  45    * can also be used with the routines in gmxfio.h
  46    *
  47    **************************************************************/
  48 #include "typedefs.h"
  49 #include "gmxfio.h"
  50
  51 #ifdef __cplusplus
  52 extern "C" {
  53 #endif
  54
  55 typedef struct
  56 {
  57   int   bIr;            /* Non zero if input_rec is present             */
  58   int   bBox;           /* Non zero if a box is present                 */
  59   int   bTop;           /* Non zero if a topology is present            */
  60   int   bX;             /* Non zero if coordinates are present          */
  61   int   bV;             /* Non zero if velocities are present           */
  62   int   bF;             /* Non zero if forces are present               */
  63
  64   int   natoms;         /* The total number of atoms                    */
  65   int   ngtc;           /* The number of temperature coupling groups    */
  66   real  lambda;         /* Current value of lambda                      */
  67 } t_tpxheader;
  68
  69 /*
  70  * These routines handle reading and writing of preprocessed
  71  * topology files in any of the following formats:
  72  * TPR : topology in XDR format, portable accross platforms
  73  * TPB : binary topology, not portable accross platforms
  74  * TPA : ascii topology (possibbly huge)
  75  * TRR : trajectory in XDR format (non compressed)
  76  * TRJ : trajectory in binary format
  77  *
  78  * Files are written in the precision with which the source are compiled,
  79  * but double and single precision can be read by either.
  80  */
  81
  82 t_fileio *open_tpx(const char *fn, const char *mode);
  83 /* Return an file pointer corresponding to the file you have just opened */
  84
  85 void close_tpx(t_fileio *fio);
  86 /*  Close the file corresponding to fio */
  87
  88 void read_tpxheader(const char *fn, t_tpxheader *tpx, gmx_bool TopOnlyOK,
  89                            int *version, int *generation);
  90 /* Read the header from a tpx file and then close it again.
  91  * By setting TopOnlyOK to true, it is possible to read future
  92  * versions too (we skip the changed inputrec), provided we havent
  93  * changed the topology description. If it is possible to read
  94  * the inputrec it will still be done even if TopOnlyOK is TRUE.
  95  *
  96  * The version and generation if the topology (see top of tpxio.c)
  97  * are returned in the two last arguments.
  98  */
  99
 100 void write_tpx_state(const char *fn,
 101                             t_inputrec *ir,t_state *state,gmx_mtop_t *mtop);
 102 /* Write a file, and close it again.
 103  * If fn == NULL, an efTPA file will be written to stdout (which
 104  * will not be closed afterwards)
 105  */
 106
 107 void read_tpx_state(const char *fn,
 108                            t_inputrec *ir,t_state *state,rvec *f,
 109                            gmx_mtop_t *mtop);
 110 int read_tpx(const char *fn,
 111                     t_inputrec *ir,matrix box,int *natoms,
 112                     rvec *x,rvec *v,rvec *f,gmx_mtop_t *mtop);
 113 /* Read a file, and close it again.
 114  * If fn == NULL, an efTPA file will be read from stdin (which
 115  * will not be closed afterwards)
 116  * When step, t or lambda are NULL they will not be stored.
 117  * Returns ir->ePBC, if it could be read from the file.
 118  */
 119
 120 int read_tpx_top(const char *fn,
 121                         t_inputrec *ir, matrix box,int *natoms,
 122                         rvec *x,rvec *v,rvec *f,t_topology *top);
 123 /* As read_tpx, but for the old t_topology struct */
 124
 125 gmx_bool fn2bTPX(const char *file);
 126 /* return if *file is one of the TPX file types */
 127
 128 gmx_bool read_tps_conf(const char *infile,char *title,t_topology *top,
 129                           int *ePBC, rvec **x,rvec **v,matrix box,gmx_bool bMass);
 130 /* Read title, top.atoms, x, v (if not NULL) and box from an STX file,
 131  * memory for atoms, x and v will be allocated.
 132  * Return TRUE if a complete topology was read.
 133  * If infile is a TPX file read the whole top,
 134  * else if bMass=TRUE, read the masses into top.atoms from the mass database.
 135  */
 136
 137 void tpx_make_chain_identifiers(t_atoms *atoms,t_block *mols);
 138
 139 #ifdef __cplusplus
 140 }
 141 #endif
 142
 143 #endif