include/tpxio.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   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,
  13  * check out http://www.gromacs.org for more information.
  14
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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   int   fep_state;      /* Current value of the alchemical state --
  68                          * not yet printed out.  */
  69   /*a better decision will eventually (5.0 or later) need to be made
  70     on how to treat the alchemical state of the system, which can now
  71     vary through a simulation, and cannot be completely described
  72     though a single lambda variable, or even a single state
  73     index. Eventually, should probably be a vector. MRS*/
  74 } t_tpxheader;
  75
  76 /*
  77  * These routines handle reading and writing of preprocessed
  78  * topology files in any of the following formats:
  79  * TPR : topology in XDR format, portable accross platforms
  80  * TPB : binary topology, not portable accross platforms
  81  * TPA : ascii topology (possibbly huge)
  82  * TRR : trajectory in XDR format (non compressed)
  83  * TRJ : trajectory in binary format
  84  *
  85  * Files are written in the precision with which the source are compiled,
  86  * but double and single precision can be read by either.
  87  */
  88
  89 t_fileio *open_tpx(const char *fn, const char *mode);
  90 /* Return an file pointer corresponding to the file you have just opened */
  91
  92 void close_tpx(t_fileio *fio);
  93 /*  Close the file corresponding to fio */
  94
  95 void read_tpxheader(const char *fn, t_tpxheader *tpx, gmx_bool TopOnlyOK,
  96                            int *version, int *generation);
  97 /* Read the header from a tpx file and then close it again.
  98  * By setting TopOnlyOK to true, it is possible to read future
  99  * versions too (we skip the changed inputrec), provided we havent
 100  * changed the topology description. If it is possible to read
 101  * the inputrec it will still be done even if TopOnlyOK is TRUE.
 102  *
 103  * The version and generation if the topology (see top of tpxio.c)
 104  * are returned in the two last arguments.
 105  */
 106
 107 void write_tpx_state(const char *fn,
 108                             t_inputrec *ir,t_state *state,gmx_mtop_t *mtop);
 109 /* Write a file, and close it again.
 110  * If fn == NULL, an efTPA file will be written to stdout (which
 111  * will not be closed afterwards)
 112  */
 113
 114 void read_tpx_state(const char *fn,
 115                            t_inputrec *ir,t_state *state,rvec *f,
 116                            gmx_mtop_t *mtop);
 117 int read_tpx(const char *fn,
 118                     t_inputrec *ir,matrix box,int *natoms,
 119                     rvec *x,rvec *v,rvec *f,gmx_mtop_t *mtop);
 120 /* Read a file, and close it again.
 121  * If fn == NULL, an efTPA file will be read from stdin (which
 122  * will not be closed afterwards)
 123  * When step, t or lambda are NULL they will not be stored.
 124  * Returns ir->ePBC, if it could be read from the file.
 125  */
 126
 127 int read_tpx_top(const char *fn,
 128                         t_inputrec *ir, matrix box,int *natoms,
 129                         rvec *x,rvec *v,rvec *f,t_topology *top);
 130 /* As read_tpx, but for the old t_topology struct */
 131
 132 gmx_bool fn2bTPX(const char *file);
 133 /* return if *file is one of the TPX file types */
 134
 135 gmx_bool read_tps_conf(const char *infile,char *title,t_topology *top,
 136                           int *ePBC, rvec **x,rvec **v,matrix box,gmx_bool bMass);
 137 /* Read title, top.atoms, x, v (if not NULL) and box from an STX file,
 138  * memory for atoms, x and v will be allocated.
 139  * Return TRUE if a complete topology was read.
 140  * If infile is a TPX file read the whole top,
 141  * else if bMass=TRUE, read the masses into top.atoms from the mass database.
 142  */
 143
 144 void tpx_make_chain_identifiers(t_atoms *atoms,t_block *mols);
 145
 146 #ifdef __cplusplus
 147 }
 148 #endif
 149
 150 #endif