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 3.2.0
  11  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  12  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  13  * Copyright (c) 2001-2004, The GROMACS development team,
  14  * check out http://www.gromacs.org for more information.
  15
  16  * This program is free software; you can redistribute it and/or
  17  * modify it under the terms of the GNU General Public License
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  19  * of the License, or (at your option) any later version.
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  22  * scientific software is very special. Version control is crucial -
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  26  * files - if they are missing, get the official version at www.gromacs.org.
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  29  * the papers on the package - you can find them in the top README file.
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  35  */
  36
  37 #ifndef _statutil_h
  38 #define _statutil_h
  39
  40 #ifdef HAVE_CONFIG_H
  41 #include <config.h>
  42 #endif
  43
  44 #ifdef CPLUSPLUS
  45 extern "C" {
  46 #endif
  47
  48 #include <stdio.h>
  49 #include "typedefs.h"
  50 #include "filenm.h"
  51 #include "readinp.h"
  52 #include "wman.h"
  53
  54 typedef int t_first_x(int *status,char *fn,real *t,rvec **x,matrix box);
  55 typedef bool t_next_x(int status,real *t,int natoms,rvec x[],matrix box);
  56
  57 /* I/O function types */
  58
  59 extern char *Program(void);
  60 /* Return the name of the program */
  61 extern char *ShortProgram(void);
  62 /* Id. without leading directory */
  63 extern void set_program_name(char *argvzero);
  64 /* set the program name to the provided string, but note
  65  * that it must be a real file - we determine the library
  66  * directory from its location!
  67  */
  68
  69 /************************************************
  70  *             Trajectory functions
  71  ************************************************/
  72
  73 extern int prec2ndec(real prec);
  74 /* Convert precision in 1/(nm) to number of decimal places */
  75
  76 extern void clear_trxframe(t_trxframe *fr,bool bFirst);
  77 /* Set all content booleans to FALSE.
  78  * When bFirst = TRUE, set natoms=-1, all pointers to NULL
  79  *                     and all data to zero.
  80  */
  81
  82 extern int nframes_read(void);
  83 /* Returns the number of frames read from the trajectory */
  84
  85 int write_trxframe_indexed(int status,t_trxframe *fr,int nind,atom_id *ind);
  86 /* Write an indexed frame to a TRX file, see write_trxframe */
  87
  88 int write_trxframe(int status,t_trxframe *fr);
  89 /* Write a frame to a TRX file.
  90  * Only entries for which the boolean is TRUE will be written,
  91  * except for step, time, lambda and/or box, which may not be
  92  * omitted for certain trajectory formats.
  93  * The precision for .xtc and .gro is fr->prec, when fr->bPrec=FALSE,
  94  * the precision is set to 1000.
  95  */
  96
  97 int write_trx(int status,int nind,atom_id *ind,t_atoms *atoms,
  98               int step,real time,matrix box,rvec x[],rvec *v);
  99 /* Write an indexed frame to a TRX file.
 100  * v can be NULL.
 101  * atoms can be NULL for file types which don't need atom names.
 102  */
 103
 104 void close_trx(int status);
 105 /* Close trj file as opened with read_first_x, read_frist_frame
 106  * or open_trx. Identical to close_trj.
 107  */
 108
 109 int open_trx(char *outfile,char *filemode);
 110 /* Open a TRX file and return the file number */
 111
 112 extern bool bRmod(double a, double b, double c);
 113 /* Returns TRUE when (a - b) MOD c = 0, using a margin which is slightly
 114  * larger than the float/double precision.
 115  */
 116
 117 extern int check_times2(real t,real t0,real tp,real tpp);
 118 /* This routine checkes if the read-in time is correct or not;
 119  * returns -1 if t<tbegin or t MOD dt = t0,
 120  *          0 if tbegin <= t <=tend+margin,
 121  *          1 if t>tend
 122  * where margin is 0.1*min(t-tp,tp-tpp), if this positive, 0 otherwise.
 123  * tp and tpp should be the time of the previous frame and the one before.
 124  */
 125
 126 extern int check_times(real t);
 127 /* This routine checkes if the read-in time is correct or not;
 128  * returns -1 if t<tbegin,
 129  *          0 if tbegin <= t <=tend,
 130  *          1 if t>tend
 131  */
 132
 133 extern char *time_unit(void);
 134 /* return time unit (e.g. ps or ns) */
 135
 136 extern char *time_label(void);
 137 /* return time unit label (e.g. "Time (ps)") */
 138
 139 extern char *xvgr_tlabel(void);
 140 /* retrun x-axis time label for xmgr */
 141
 142 extern real time_factor(void);
 143 /* return time conversion factor from ps (i.e. 1e-3 for ps->ns) */
 144
 145 extern real convert_time(real time);
 146 /* return converted time */
 147
 148 extern void convert_times(int n, real *time);
 149 /* convert array of times */
 150
 151 extern void default_time(void);
 152 /* set time conversion to default (i.e. ps) */
 153
 154 /* For trxframe.flags, used in trxframe read routines.
 155  * When a READ flag is set, the field will be read when present,
 156  * but a frame might be returned which does not contain the field.
 157  * When a NEED flag is set, frames not containing the field will be skipped.
 158  */
 159 #define TRX_READ_X    (1<<0)
 160 #define TRX_NEED_X    (1<<1)
 161 #define TRX_READ_V    (1<<2)
 162 #define TRX_NEED_V    (1<<3)
 163 #define TRX_READ_F    (1<<4)
 164 #define TRX_NEED_F    (1<<5)
 165 /* Useful for reading natoms from a trajectory without skipping */
 166 #define TRX_DONT_SKIP (1<<6)
 167
 168 /* For trxframe.not_ok */
 169 #define HEADER_NOT_OK (1<<0)
 170 #define DATA_NOT_OK   (1<<1)
 171 #define FRAME_NOT_OK  (HEADER_NOT_OK | DATA_NOT_OK)
 172
 173 extern bool read_first_frame(int *status,char *fn,t_trxframe *fr,int flags);
 174   /* Read the first frame which is in accordance with flags, which are
 175    * defined further up in this file.
 176    * Returns natoms when succeeded, 0 otherwise.
 177    * Memory will be allocated for flagged entries.
 178    * The flags are copied to fr for subsequent calls to read_next_frame.
 179    * Returns TRUE when succeeded, FALSE otherwise.
 180    */
 181
 182 extern bool read_next_frame(int status,t_trxframe *fr);
 183   /* Reads the next frame which is in accordance with fr->flags.
 184    * Returns TRUE when succeeded, FALSE otherwise.
 185    */
 186
 187 extern int read_first_x(int *status,char *fn,
 188                         real *t,rvec **x,matrix box);
 189 /* These routines read first coordinates and box, and allocates
 190  * memory for the coordinates, for a trajectory file.
 191  * The routine returns the number of atoms, or 0 when something is wrong.
 192  * The integer in status should be passed to calls of read_next_x
 193  */
 194
 195 extern bool read_next_x(int status,real *t,int natoms,rvec x[],matrix box);
 196 /* Read coordinates and box from a trajectory file. Return TRUE when all well,
 197  * or FALSE when end of file (or last frame requested by user).
 198  * status is the integer set in read_first_x.
 199  */
 200
 201 extern void close_trj(int status);
 202 /* Close trj file as opened with read_first_x, read_frist_frame
 203  * or open_trx. Identical to close_trx.
 204  */
 205
 206 extern void rewind_trj(int status);
 207 /* Rewind trj file as opened with read_first_x */
 208
 209 extern t_topology *read_top(char *fn);
 210 /* Extract a topology data structure from a topology file */
 211
 212 extern void mk_single_top(t_topology *top);
 213 /* Make the topology file single node ready */
 214
 215 extern bool bDoView(void);
 216 /* Return TRUE when user requested viewing of the file */
 217
 218 /*****************************************************
 219  *         Some command line parsing routines
 220  *****************************************************/
 221
 222 #define PCA_CAN_VIEW       (1<<5)
 223 /* add option -w to view output files (must be implemented in program) */
 224 #define PCA_CAN_BEGIN      (1<<6)
 225 #define PCA_CAN_END        (1<<7)
 226 #define PCA_CAN_DT         (1<<14)
 227 #define PCA_CAN_TIME       (PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_DT)
 228 /* adds options -b and -e for begin and end time for reading trajectories */
 229 #define PCA_TIME_UNIT      (1<<15)
 230 /* set time unit for output */
 231 #define PCA_KEEP_ARGS      (1<<8)
 232 /* keep parsed args in argv (doesn't make sense without NOEXIT_ON_ARGS) */
 233 #define PCA_SILENT         (1<<9)
 234 /* don't print options by default */
 235 #define PCA_CAN_SET_DEFFNM (1<<10)
 236 /* does something for non-master mdrun nodes */
 237 #define PCA_NOEXIT_ON_ARGS (1<<11)
 238 /* no fatal_error when invalid options are encountered */
 239 #define PCA_QUIET          (1<<12)
 240 /* does something for non-master mdrun nodes */
 241 #define PCA_BE_NICE        (1<<13)
 242 /* Default to low priority, unless configured with --disable-nice */
 243
 244 extern int iscan(int argc,char *argv[],int *i);
 245 /* Scan an int from the argument at *i. If the argument length
 246  * is > 2, the int is assumed to be in the remainder of the arg,
 247  * eg: -p32, else the int is assumed to be in the next argument
 248  * eg: -p 32. If neither is the case the routine exits with an error,
 249  * otherwise it returns the value found. If the value is in the next
 250  * argument *i is incremented. You typically would want to pass
 251  * a loop variable to this routine.
 252  */
 253
 254 extern double dscan(int argc,char *argv[],int *i);
 255 /* Routine similar to the above, but working on doubles. */
 256
 257 extern char *sscan(int argc,char *argv[],int *i);
 258 /* Routine similar to the above, but working on strings. The pointer
 259  * returned is a pointer to the argv field.
 260  */
 261
 262 extern void vscan(int argc,char *argv[],int *i,rvec *vec);
 263 /* Routine similar to the above, but working on rvecs. */
 264
 265 extern int nenum(char *enumc[]);
 266 /* returns ordinal number of selected enum from args
 267  * depends on enumc[0] pointing to one of the other elements
 268  * array must be terminated by a NULL pointer
 269  */
 270
 271 #ifdef HAVE_MOTIF
 272 extern void gmx_gui(int *argc,char *argv[],
 273                     int nfile,t_filenm fnm[],int npargs,t_pargs pa[],
 274                     int ndesc,char *desc[],int nbugs,char *bugs[]);
 275 /* This function plops up a Motif dialog box in which the command-line options
 276  * can be changed.
 277  */
 278 #endif
 279
 280 extern void parse_common_args(int *argc,char *argv[],unsigned long Flags,
 281                               int nfile,t_filenm fnm[],int npargs,t_pargs *pa,
 282                               int ndesc,char **desc,int nbugs,char **bugs);
 283 /* Get arguments from the arg-list. The arguments extracted
 284  * are removed from the list. If manual is NULL a default message is displayed
 285  * when errors are encountered. The Flags argument, when non-0 enables
 286  * some input checks. Using this routine also means that the arguments
 287  * -b and -e will be used for begin and end time, whether this is
 288  * appropriate or not!
 289  */
 290
 291 #ifdef CPLUSPLUS
 292 }
 293 #endif
 294
 295 #endif