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
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  10  *                        VERSION 3.2.0
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  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
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  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   /* The code below is to facilitate controlled begin and end of
  55      trajectory reading. Corresponding routines in
  56      src/gmxlib/tcontrol.c
  57    */
  58   enum { TBEGIN, TEND, TDELTA, TNR };
  59
  60   extern bool bTimeSet(int tcontrol);
  61
  62   extern real rTimeValue(int tcontrol);
  63
  64   extern void setTimeValue(int tcontrol,real value);
  65
  66   /* End trajectory time control */
  67
  68 typedef int t_first_x(int *status,char *fn,real *t,rvec **x,matrix box);
  69
  70 typedef bool t_next_x(int status,real *t,int natoms,rvec x[],matrix box);
  71
  72 /* I/O function types */
  73
  74 extern char *Program(void);
  75 /* Return the name of the program */
  76 extern char *ShortProgram(void);
  77 /* Id. without leading directory */
  78 extern char *command_line(void);
  79 /* Return the command line for this program */
  80 extern void set_program_name(char *argvzero);
  81 /* set the program name to the provided string, but note
  82  * that it must be a real file - we determine the library
  83  * directory from its location!
  84  */
  85
  86 /************************************************
  87  *             Trajectory functions
  88  ************************************************/
  89
  90 extern int prec2ndec(real prec);
  91 /* Convert precision in 1/(nm) to number of decimal places */
  92
  93 extern void clear_trxframe(t_trxframe *fr,bool bFirst);
  94 /* Set all content booleans to FALSE.
  95  * When bFirst = TRUE, set natoms=-1, all pointers to NULL
  96  *                     and all data to zero.
  97  */
  98
  99 extern void set_trxframe_ePBC(t_trxframe *fr,int ePBC);
 100 /* Set the type of periodic boundary conditions, ePBC=-1 is not set */
 101
 102 extern int nframes_read(void);
 103 /* Returns the number of frames read from the trajectory */
 104
 105 int write_trxframe_indexed(int status,t_trxframe *fr,int nind,atom_id *ind);
 106 /* Write an indexed frame to a TRX file, see write_trxframe */
 107
 108 int write_trxframe(int status,t_trxframe *fr);
 109 /* Write a frame to a TRX file.
 110  * Only entries for which the boolean is TRUE will be written,
 111  * except for step, time, lambda and/or box, which may not be
 112  * omitted for certain trajectory formats.
 113  * The precision for .xtc and .gro is fr->prec, when fr->bPrec=FALSE,
 114  * the precision is set to 1000.
 115  */
 116
 117 int write_trx(int status,int nind,atom_id *ind,t_atoms *atoms,
 118               int step,real time,matrix box,rvec x[],rvec *v);
 119 /* Write an indexed frame to a TRX file.
 120  * v can be NULL.
 121  * atoms can be NULL for file types which don't need atom names.
 122  */
 123
 124 void close_trx(int status);
 125 /* Close trj file as opened with read_first_x, read_frist_frame
 126  * or open_trx. Identical to close_trj.
 127  */
 128
 129 int open_trx(char *outfile,char *filemode);
 130 /* Open a TRX file and return the file number */
 131
 132 extern bool bRmod_fd(double a, double b, double c,bool bDouble);
 133 /* Returns TRUE when (a - b) MOD c = 0, using a margin which is slightly
 134  * larger than the float/double precision.
 135  */
 136
 137 #ifdef GMX_DOUBLE
 138 #define bRmod(a,b,c) bRmod_fd(a,b,c,TRUE)
 139 #else
 140 #define bRmod(a,b,c) bRmod_fd(a,b,c,FALSE)
 141 #endif
 142
 143 extern int check_times2(real t,real t0,real tp,real tpp,bool bDouble);
 144 /* This routine checkes if the read-in time is correct or not;
 145  * returns -1 if t<tbegin or t MOD dt = t0,
 146  *          0 if tbegin <= t <=tend+margin,
 147  *          1 if t>tend
 148  * where margin is 0.1*min(t-tp,tp-tpp), if this positive, 0 otherwise.
 149  * tp and tpp should be the time of the previous frame and the one before.
 150  * The mod is done with single or double precision accuracy depending
 151  * on the value of bDouble.
 152  */
 153
 154 extern int check_times(real t);
 155 /* This routine checkes if the read-in time is correct or not;
 156  * returns -1 if t<tbegin,
 157  *          0 if tbegin <= t <=tend,
 158  *          1 if t>tend
 159  */
 160
 161 extern char *time_unit(void);
 162 /* return time unit (e.g. ps or ns) */
 163
 164 extern char *time_label(void);
 165 /* return time unit label (e.g. "Time (ps)") */
 166
 167 extern char *xvgr_tlabel(void);
 168 /* retrun x-axis time label for xmgr */
 169
 170 extern real time_factor(void);
 171 /* return time conversion factor from ps (i.e. 1e-3 for ps->ns) */
 172
 173 extern real time_invfactor(void);
 174 /* return inverse time conversion factor from ps (i.e. 1e3 for ps->ns) */
 175
 176 extern real convert_time(real time);
 177 /* return converted time */
 178
 179 extern void convert_times(int n, real *time);
 180 /* convert array of times */
 181
 182 /* For trxframe.flags, used in trxframe read routines.
 183  * When a READ flag is set, the field will be read when present,
 184  * but a frame might be returned which does not contain the field.
 185  * When a NEED flag is set, frames not containing the field will be skipped.
 186  */
 187 #define TRX_READ_X    (1<<0)
 188 #define TRX_NEED_X    (1<<1)
 189 #define TRX_READ_V    (1<<2)
 190 #define TRX_NEED_V    (1<<3)
 191 #define TRX_READ_F    (1<<4)
 192 #define TRX_NEED_F    (1<<5)
 193 /* Useful for reading natoms from a trajectory without skipping */
 194 #define TRX_DONT_SKIP (1<<6)
 195
 196 /* For trxframe.not_ok */
 197 #define HEADER_NOT_OK (1<<0)
 198 #define DATA_NOT_OK   (1<<1)
 199 #define FRAME_NOT_OK  (HEADER_NOT_OK | DATA_NOT_OK)
 200
 201 extern int read_first_frame(int *status,char *fn,t_trxframe *fr,int flags);
 202   /* Read the first frame which is in accordance with flags, which are
 203    * defined further up in this file.
 204    * Returns natoms when succeeded, 0 otherwise.
 205    * Memory will be allocated for flagged entries.
 206    * The flags are copied to fr for subsequent calls to read_next_frame.
 207    * Returns TRUE when succeeded, FALSE otherwise.
 208    */
 209
 210 extern bool read_next_frame(int status,t_trxframe *fr);
 211   /* Reads the next frame which is in accordance with fr->flags.
 212    * Returns TRUE when succeeded, FALSE otherwise.
 213    */
 214
 215 extern int read_first_x(int *status,char *fn,
 216                         real *t,rvec **x,matrix box);
 217 /* These routines read first coordinates and box, and allocates
 218  * memory for the coordinates, for a trajectory file.
 219  * The routine returns the number of atoms, or 0 when something is wrong.
 220  * The integer in status should be passed to calls of read_next_x
 221  */
 222
 223 extern bool read_next_x(int status,real *t,int natoms,rvec x[],matrix box);
 224 /* Read coordinates and box from a trajectory file. Return TRUE when all well,
 225  * or FALSE when end of file (or last frame requested by user).
 226  * status is the integer set in read_first_x.
 227  */
 228
 229 extern void close_trj(int status);
 230 /* Close trj file as opened with read_first_x, read_frist_frame
 231  * or open_trx. Identical to close_trx.
 232  */
 233
 234 extern void rewind_trj(int status);
 235 /* Rewind trj file as opened with read_first_x */
 236
 237 extern t_topology *read_top(char *fn,int *ePBC);
 238 /* Extract a topology data structure from a topology file.
 239  * If ePBC!=NULL *ePBC gives the pbc type.
 240  */
 241
 242 extern bool bDoView(void);
 243 /* Return TRUE when user requested viewing of the file */
 244
 245 extern bool bPrintXvgrCodes(void);
 246 /* Return TRUE when user wants printing of legends etc. in the file. */
 247
 248 /*****************************************************
 249  *         Some command line parsing routines
 250  *****************************************************/
 251
 252 #define PCA_CAN_VIEW       (1<<5)
 253 /* add option -w to view output files (must be implemented in program) */
 254 #define PCA_CAN_BEGIN      (1<<6)
 255 #define PCA_CAN_END        (1<<7)
 256 #define PCA_CAN_DT         (1<<14)
 257 #define PCA_CAN_TIME       (PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_DT)
 258 /* adds options -b and -e for begin and end time for reading trajectories */
 259 #define PCA_TIME_UNIT      (1<<15)
 260 /* set time unit for output */
 261 #define PCA_KEEP_ARGS      (1<<8)
 262 /* keep parsed args in argv (doesn't make sense without NOEXIT_ON_ARGS) */
 263 #define PCA_SILENT         (1<<9)
 264 /* don't print options by default */
 265 #define PCA_CAN_SET_DEFFNM (1<<10)
 266 /* does something for non-master mdrun nodes */
 267 #define PCA_NOEXIT_ON_ARGS (1<<11)
 268 /* no fatal_error when invalid options are encountered */
 269 #define PCA_QUIET          (1<<12)
 270 /* does something for non-master mdrun nodes */
 271 #define PCA_BE_NICE        (1<<13)
 272 /* Default to low priority, unless configured with --disable-nice */
 273
 274 extern int iscan(int argc,char *argv[],int *i);
 275 /* Scan an int from the argument at *i. If the argument length
 276  * is > 2, the int is assumed to be in the remainder of the arg,
 277  * eg: -p32, else the int is assumed to be in the next argument
 278  * eg: -p 32. If neither is the case the routine exits with an error,
 279  * otherwise it returns the value found. If the value is in the next
 280  * argument *i is incremented. You typically would want to pass
 281  * a loop variable to this routine.
 282  */
 283
 284 extern double dscan(int argc,char *argv[],int *i);
 285 /* Routine similar to the above, but working on doubles. */
 286
 287 extern char *sscan(int argc,char *argv[],int *i);
 288 /* Routine similar to the above, but working on strings. The pointer
 289  * returned is a pointer to the argv field.
 290  */
 291
 292 extern void vscan(int argc,char *argv[],int *i,rvec *vec);
 293 /* Routine similar to the above, but working on rvecs. */
 294
 295 extern int nenum(char *enumc[]);
 296 /* returns ordinal number of selected enum from args
 297  * depends on enumc[0] pointing to one of the other elements
 298  * array must be terminated by a NULL pointer
 299  */
 300
 301 #ifdef HAVE_MOTIF
 302 extern void gmx_gui(int *argc,char *argv[],
 303                     int nfile,t_filenm fnm[],int npargs,t_pargs pa[],
 304                     int ndesc,char *desc[],int nbugs,char *bugs[]);
 305 /* This function plops up a Motif dialog box in which the command-line options
 306  * can be changed.
 307  */
 308 #endif
 309
 310 extern void parse_common_args(int *argc,char *argv[],unsigned long Flags,
 311                               int nfile,t_filenm fnm[],int npargs,t_pargs *pa,
 312                               int ndesc,char **desc,int nbugs,char **bugs);
 313 /* Get arguments from the arg-list. The arguments extracted
 314  * are removed from the list. If manual is NULL a default message is displayed
 315  * when errors are encountered. The Flags argument, when non-0 enables
 316  * some input checks. Using this routine also means that the arguments
 317  * -b and -e will be used for begin and end time, whether this is
 318  * appropriate or not!
 319  */
 320
 321 #ifdef CPLUSPLUS
 322 }
 323 #endif
 324
 325 #endif