include/statutil.h

   1 /*
   2  * $Id$
   3  *
   4  *       This source code is part of
   5  *
   6  *        G   R   O   M   A   C   S
   7  *
   8  * GROningen MAchine for Chemical Simulations
   9  *
  10  *               VERSION 2.0
  11  *
  12  * Copyright (c) 1991-1999
  13  * BIOSON Research Institute, Dept. of Biophysical Chemistry
  14  * University of Groningen, The Netherlands
  15  *
  16  * Please refer to:
  17  * GROMACS: A message-passing parallel molecular dynamics implementation
  18  * H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  19  * Comp. Phys. Comm. 91, 43-56 (1995)
  20  *
  21  * Also check out our WWW page:
  22  * http://md.chem.rug.nl/~gmx
  23  * or e-mail to:
  24  * gromacs@chem.rug.nl
  25  *
  26  * And Hey:
  27  * Green Red Orange Magenta Azure Cyan Skyblue
  28  */
  29
  30 #ifndef _statutil_h
  31 #define _statutil_h
  32
  33 static char *SRCID_statutil_h = "$Id$";
  34
  35 #ifdef CPLUSPLUS
  36 extern "C" {
  37 #endif
  38
  39 #include <stdio.h>
  40 #include "typedefs.h"
  41 #include "filenm.h"
  42 #include "readinp.h"
  43 #include "wman.h"
  44
  45 typedef int t_first_x(int *status,char *fn,real *t,rvec **x,matrix box);
  46 typedef bool t_next_x(int status,real *t,int natoms,rvec x[],matrix box);
  47
  48 /* I/O function types */
  49
  50 extern char *Program(void);
  51 /* Return the name of the program */
  52 extern char *ShortProgram(void);
  53 /* Id. without leading directory */
  54
  55 /************************************************
  56  *             Trajectory functions
  57  ************************************************/
  58
  59 extern int nframes_read(void);
  60   /* Returns the number of frames read from the trajectory */
  61
  62 int write_trx(int fnum,int nind,atom_id *ind,t_atoms *atoms,
  63               int step,real time,matrix box,rvec x[],rvec *v);
  64 /* write an indexed frame to a TRX file */
  65
  66 int close_trx(int fnum);
  67 /* Close a TRX file */
  68
  69 int open_trx(char *outfile,char *filemode);
  70 /* Open a TRX file and return the file number */
  71
  72 extern int check_times(real t);
  73 /* This routine checkes if the read-in time is correct or not;
  74  * returns -1 if t<tbegin,
  75  *         0  if tbegin <= t <=tend,
  76  *         1  if t>tend
  77  */
  78
  79 extern int read_first_x(int *status,char *fn,
  80                         real *t,rvec **x,matrix box);
  81 /* These routines read first coordinates and box, and allocates
  82  * memory for the coordinates, for a trajectory file.
  83  * The routine returns the number of atoms, or 0 when something is wrong.
  84  * The integer in status should be passed to calls of read_next_x
  85  */
  86
  87 extern bool read_next_x(int status,real *t,int natoms,rvec x[],matrix box);
  88 /* Read coordinates and box from a trajectory file. Return TRUE when all well,
  89  * or FALSE when end of file (or last frame requested by user).
  90  * status is the integer set in read_first_x.
  91  */
  92
  93 extern void close_trj(int status);
  94 /* Close trj file as opened with read_first_x */
  95
  96 extern void rewind_trj(int status);
  97 /* Rewind trj file as opened with read_first_x */
  98
  99 extern int read_first_v(int *status,char *fn,real *t,rvec **v,matrix box);
 100 /* Same as above, but for velocities */
 101
 102 extern  bool read_next_v(int status,real *t,int natoms,rvec v[],matrix box);
 103 /* Idem */
 104
 105 extern int read_first_x_v(int *status,char *fn,real *t,rvec **x,rvec **v,matrix box);
 106 /* Same as above, but for coordinates and velocities */
 107
 108 extern  bool read_next_x_v(int status,real *t,int natoms,rvec x[],rvec v[],matrix box);
 109 /* Idem */
 110
 111 extern  bool read_next_x_or_v(int status,real *t,int natoms,rvec x[],rvec v[],matrix box);
 112 /* Same as above, but for coordinates *AND/OR* velocities */
 113
 114 extern  bool read_first_x_or_v(int *status,char *fn,real *t,rvec **x,rvec **v,matrix box);
 115 /* Idem */
 116
 117 extern bool next_e(FILE *status, real *t, t_energy e[]);
 118 /* Read energy terms from trajectory file */
 119
 120 extern t_topology *read_top(char *fn);
 121 /* Extract a topology data structure from a topology file */
 122
 123 extern void mk_single_top(t_topology *top);
 124 /* Make the topology file single processor ready */
 125
 126 extern char *status_title(FILE *status);
 127 /* Return a title from a topology file */
 128
 129 extern bool bDoView(void);
 130 /* Return TRUE when user requested viewing of the file */
 131
 132 /*****************************************************
 133  *         Some command line parsing routines
 134  *****************************************************/
 135
 136 #define PCA_CAN_VIEW       (1<<5)
 137 /* add option -w to view output files (must be implemented in program) */
 138 #define PCA_CAN_BEGIN      (1<<6)
 139 #define PCA_CAN_END        (1<<7)
 140 #define PCA_CAN_TIME       (PCA_CAN_BEGIN | PCA_CAN_END)
 141 /* adds options -b and -e for begin and end time for reading trajectories */
 142 #define PCA_KEEP_ARGS      (1<<8)
 143 /* keep parsed args in argv (doesn't make sense without NOEXIT_ON_ARGS) */
 144 #define PCA_SILENT         (1<<9)
 145 /* don't print options by default */
 146 #define PCA_CAN_SET_DEFFNM (1<<10)
 147 /* does something for non-master mdrun processes */
 148 #define PCA_NOEXIT_ON_ARGS (1<<11)
 149 /* no fatal_error when invalid options are encountered */
 150 #define PCA_QUIET          (1<<12)
 151 /* does something for non-master mdrun processes */
 152 #define PCA_SET_NPRI       (1<<13)
 153 /* set weightless prioriy by default */
 154
 155 extern int iscan(int argc,char *argv[],int *i);
 156 /* Scan an int from the argument at *i. If the argument length
 157  * is > 2, the int is assumed to be in the remainder of the arg,
 158  * eg: -p32, else the int is assumed to be in the next argument
 159  * eg: -p 32. If neither is the case the routine exits with an error,
 160  * otherwise it returns the value found. If the value is in the next
 161  * argument *i is incremented. You typically would want to pass
 162  * a loop variable to this routine.
 163  */
 164
 165 extern double dscan(int argc,char *argv[],int *i);
 166 /* Routine similar to the above, but working on doubles. */
 167
 168 extern char *sscan(int argc,char *argv[],int *i);
 169 /* Routine similar to the above, but working on strings. The pointer
 170  * returned is a pointer to the argv field.
 171  */
 172
 173 extern void vscan(int argc,char *argv[],int *i,rvec *vec);
 174 /* Routine similar to the above, but working on rvecs. */
 175
 176 #ifdef HAVE_MOTIF
 177 extern void gmx_gui(int *argc,char *argv[],
 178                     int nfile,t_filenm fnm[],int npargs,t_pargs pa[],
 179                     int ndesc,char *desc[],int nbugs,char *bugs[]);
 180 /* This function plops up a Motif dialog box in which the command-line options
 181  * can be changed.
 182  */
 183 #endif
 184
 185 extern void parse_common_args(int *argc,char *argv[],unsigned long Flags,bool bNice,
 186                               int nfile,t_filenm fnm[],int npargs,t_pargs *pa,
 187                               int ndesc,char **desc,int nbugs,char **bugs);
 188 /* Get arguments from the arg-list. The arguments extracted
 189  * are removed from the list. If manual is NULL a default message is displayed
 190  * when errors are encountered. The Flags argument, when non-0 enables
 191  * some input checks. Using this routine also means that the arguments
 192  * -b and -e will be used for begin and end time, whether this is
 193  * appropriate or not!
 194  */
 195
 196 #ifdef CPLUSPLUS
 197 }
 198 #endif
 199
 200 #endif