1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
4 * This source code is part of
8 * GROningen MAchine for Chemical Simulations
11 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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34 * GROningen Mixture of Alchemy and Childrens' Stories
44 #ifdef HAVE_SYS_TIME_H
59 /* Portable version of ctime_r implemented in src/gmxlib/string2.c, but we do not want it declared in public installed headers */
61 gmx_ctime_r(const time_t *clock,char *buf, int n);
64 gmx_bool output_env_get_print_xvgr_codes(const output_env_t oenv)
68 xvg_format = output_env_get_xvg_format(oenv);
70 return (xvg_format == exvgXMGRACE || xvg_format == exvgXMGR);
73 static char *xvgrstr(const char *gmx,const output_env_t oenv,
76 /* Supported greek letter names and corresponding xmgrace/xmgr symbols */
77 const char *sym[]={ "beta", "chi", "delta", "eta", "lambda", "mu", "omega", "phi", "psi", "rho", "theta", NULL };
78 const char symc[]={ 'b', 'c', 'd', 'h', 'l', 'm', 'w', 'f', 'y', 'r', 'q', '\0' };
84 xvgf = output_env_get_xvg_format(oenv);
85 bXVGR = (xvgf == exvgXMGRACE || xvgf == exvgXMGR);
89 while (gmx[g] != '\0')
91 /* Check with the largest string we have ("lambda"), add one for \0 */
92 if (b + 6 + 1 >= buflen)
94 gmx_fatal(FARGS,"Output buffer length in xvgstr (%d) too small to process xvg input string '%s'",buflen,gmx);
113 else if (gmx[g] == 'S')
127 else if (gmx[g] == 'N')
129 /* End sub/superscript */
144 else if (gmx[g] == '4')
146 /* Backward compatibility for xmgr normal font "\4" */
150 sprintf(buf+b,"%s","\\f{}");
153 sprintf(buf+b,"%s","\\4");
162 else if (gmx[g] == '8')
164 /* Backward compatibility for xmgr symbol font "\8" */
168 sprintf(buf+b,"%s","\\x");
171 sprintf(buf+b,"%s","\\8");
182 /* Check for special symbol */
184 while (sym[i] != NULL &&
185 gmx_strncasecmp(sym[i],gmx+g,strlen(sym[i])) != 0)
199 sprintf(buf+b,"%s%c%s","\\x",c,"\\f{}");
202 sprintf(buf+b,"%s%c%s","\\8",c,"\\4");
205 strncat(buf+b,gmx+g,strlen(sym[i]));
207 if (gmx[g+strlen(sym[i])] != ' ')
219 /* Unknown escape sequence, this should not happen.
220 * We do not generate a fatal error, since that might
221 * stop otherwise functioning code from working.
222 * Copy the backslash to the output and continue processing.
239 void xvgr_header(FILE *fp,const char *title,const char *xaxis,
240 const char *yaxis,int exvg_graph_type,
241 const output_env_t oenv)
243 char pukestr[100],buf[STRLEN];
246 if (output_env_get_print_xvgr_codes(oenv))
249 gmx_ctime_r(&t,buf,STRLEN);
250 fprintf(fp,"# This file was created %s",buf);
251 fprintf(fp,"# by the following command:\n# %s\n#\n",command_line());
252 fprintf(fp,"# %s is part of G R O M A C S:\n#\n",ShortProgram());
254 fprintf(fp,"# %s\n#\n",pukestr);
255 fprintf(fp,"@ title \"%s\"\n",xvgrstr(title,oenv,buf,STRLEN));
256 fprintf(fp,"@ xaxis label \"%s\"\n",
257 xvgrstr(xaxis,oenv,buf,STRLEN));
258 fprintf(fp,"@ yaxis label \"%s\"\n",
259 xvgrstr(yaxis,oenv,buf,STRLEN));
260 switch (exvg_graph_type)
263 if (output_env_get_xvg_format(oenv) == exvgXMGR)
265 fprintf(fp,"@TYPE nxy\n");
269 fprintf(fp,"@TYPE xy\n");
273 fprintf(fp,"@TYPE xydy\n");
276 fprintf(fp,"@TYPE xydydy\n");
282 FILE *xvgropen_type(const char *fn,const char *title,const char *xaxis,
283 const char *yaxis,int exvg_graph_type,
284 const output_env_t oenv)
289 fp = gmx_fio_fopen(fn,"w");
291 xvgr_header(fp,title,xaxis,yaxis,exvg_graph_type,oenv);
296 FILE *xvgropen(const char *fn,const char *title,const char *xaxis,
297 const char *yaxis,const output_env_t oenv)
299 return xvgropen_type(fn,title,xaxis,yaxis,exvggtXNY,oenv);
308 void xvgr_subtitle(FILE *out,const char *subtitle,const output_env_t oenv)
312 if (output_env_get_print_xvgr_codes(oenv))
314 fprintf(out,"@ subtitle \"%s\"\n",xvgrstr(subtitle,oenv,buf,STRLEN));
318 void xvgr_view(FILE *out,real xmin,real ymin,real xmax,real ymax,
319 const output_env_t oenv)
321 if (output_env_get_print_xvgr_codes(oenv))
323 fprintf(out,"@ view %g, %g, %g, %g\n",xmin,ymin,xmax,ymax);
327 void xvgr_world(FILE *out,real xmin,real ymin,real xmax,real ymax,
328 const output_env_t oenv)
330 if (output_env_get_print_xvgr_codes(oenv))
332 fprintf(out,"@ world xmin %g\n"
335 "@ world ymax %g\n",xmin,ymin,xmax,ymax);
339 void xvgr_legend(FILE *out,int nsets,const char** setname,
340 const output_env_t oenv)
345 if (output_env_get_print_xvgr_codes(oenv))
347 xvgr_view(out,0.15,0.15,0.75,0.85,oenv);
348 fprintf(out,"@ legend on\n");
349 fprintf(out,"@ legend box on\n");
350 fprintf(out,"@ legend loctype view\n");
351 fprintf(out,"@ legend %g, %g\n",0.78,0.8);
352 fprintf(out,"@ legend length %d\n",2);
353 for(i=0; (i<nsets); i++)
356 if (output_env_get_xvg_format(oenv) == exvgXMGR)
358 fprintf(out,"@ legend string %d \"%s\"\n",
359 i,xvgrstr(setname[i],oenv,buf,STRLEN));
363 fprintf(out,"@ s%d legend \"%s\"\n",
364 i,xvgrstr(setname[i],oenv,buf,STRLEN));
371 void xvgr_new_dataset(FILE *out, int nr_first, int nsets,
372 const char **setname,
373 const output_env_t oenv)
378 if (output_env_get_print_xvgr_codes(oenv))
381 for(i=0; (i<nsets); i++)
384 if (output_env_get_xvg_format(oenv) == exvgXMGR)
386 fprintf(out,"@ legend string %d \"%s\"\n",
387 i+nr_first,xvgrstr(setname[i],oenv,buf,STRLEN));
391 fprintf(out,"@ s%d legend \"%s\"\n",
392 i+nr_first,xvgrstr(setname[i],oenv,buf,STRLEN));
403 void xvgr_line_props(FILE *out, int NrSet, int LineStyle, int LineColor,
404 const output_env_t oenv)
406 if (output_env_get_print_xvgr_codes(oenv))
408 fprintf(out, "@ with g0\n");
409 fprintf(out, "@ s%d linestyle %d\n", NrSet, LineStyle);
410 fprintf(out, "@ s%d color %d\n", NrSet, LineColor);
414 static const char *LocTypeStr[] = { "view", "world" };
415 static const char *BoxFillStr[] = { "none", "color", "pattern" };
417 void xvgr_box(FILE *out,
419 real xmin,real ymin,real xmax,real ymax,
420 int LineStyle,int LineWidth,int LineColor,
421 int BoxFill,int BoxColor,int BoxPattern,const output_env_t oenv)
423 if (output_env_get_print_xvgr_codes(oenv))
425 fprintf(out,"@with box\n");
426 fprintf(out,"@ box on\n");
427 fprintf(out,"@ box loctype %s\n",LocTypeStr[LocType]);
428 fprintf(out,"@ box %g, %g, %g, %g\n",xmin,ymin,xmax,ymax);
429 fprintf(out,"@ box linestyle %d\n",LineStyle);
430 fprintf(out,"@ box linewidth %d\n",LineWidth);
431 fprintf(out,"@ box color %d\n",LineColor);
432 fprintf(out,"@ box fill %s\n",BoxFillStr[BoxFill]);
433 fprintf(out,"@ box fill color %d\n",BoxColor);
434 fprintf(out,"@ box fill pattern %d\n",BoxPattern);
435 fprintf(out,"@box def\n");
439 /* reads a line into ptr, adjusting len and renewing ptr if neccesary */
440 static char *fgets3(FILE *fp,char **ptr,int *len, int maxlen)
443 int len_remaining=*len; /* remaining amount of allocated bytes in buf */
444 int curp=0; /* current position in buf to read into */
448 if (len_remaining < 2)
450 if ( *len + STRLEN < maxlen)
452 /* This line is longer than len characters, let's increase len! */
454 len_remaining += STRLEN;
459 /*something is wrong, we'll just keep reading and return NULL*/
460 len_remaining = STRLEN;
464 if (fgets(*ptr + curp, len_remaining, fp)==NULL)
466 /* if last line, skip */
469 curp += len_remaining-1; /* overwrite the nul char in next iteration */
472 while ((strchr(*ptr,'\n') == NULL) && (!feof(fp)));
474 if ( *len + STRLEN >= maxlen )
476 return NULL; /* this line was too long */
481 /* We reached EOF before '\n', skip this last line. */
485 /* now remove newline */
486 int slen = strlen(*ptr);
487 if ((*ptr)[slen-1] == '\n')
489 (*ptr)[slen-1] = '\0';
496 static int wordcount(char *ptr)
502 if (strlen(ptr) == 0)
504 /* fprintf(stderr,"ptr='%s'\n",ptr); */
506 for(i=0; (ptr[i] != '\0'); i++) {
507 is[cur] = isspace(ptr[i]);
508 if ((i > 0) && (is[cur] && !is[prev]))
515 static char *read_xvgr_string(const char *line)
517 const char *ptr0,*ptr1;
520 ptr0 = strchr(line,'"');
523 ptr1 = strchr(ptr0,'"');
527 str[ptr1-ptr0] = '\0';
542 int read_xvg_legend(const char *fn,double ***y,int *ny,
543 char **subtitle,char ***legend)
546 char *ptr,*ptr0,*ptr1;
549 int k,line=0,nny,nx,maxx,rval,legend_nalloc,set,nchar;
558 fp = gmx_fio_fopen(fn,"r");
561 if (subtitle != NULL) {
565 if (legend != NULL) {
569 while ((ptr = fgets3(fp,&tmpbuf,&len,10*STRLEN)) != NULL && ptr[0]!='&') {
573 if (legend != NULL) {
577 if (strncmp(ptr,"subtitle",8) == 0) {
579 if (subtitle != NULL)
581 *subtitle = read_xvgr_string(ptr);
583 } else if (strncmp(ptr,"legend string",13) == 0) {
585 sscanf(ptr,"%d%n",&set,&nchar);
587 } else if (ptr[0] == 's') {
589 sscanf(ptr,"%d%n",&set,&nchar);
592 if (strncmp(ptr,"legend",6) == 0) {
599 if (set >= legend_nalloc) {
600 legend_nalloc = set + 1;
601 srenew(*legend,legend_nalloc);
602 (*legend)[set] = read_xvgr_string(ptr);
606 } else if (ptr[0] != '#') {
608 (*ny) = nny = wordcount(ptr);
609 /* fprintf(stderr,"There are %d columns in your file\n",nny);*/
616 /* Allocate column space */
619 for(k=0; (k<nny); k++)
622 /* Initiate format string */
626 /* fprintf(stderr,"ptr='%s'\n",ptr);*/
627 for(k=0; (k<nny); k++) {
630 rval = sscanf(ptr,fmt,&lf);
631 /* fprintf(stderr,"rval = %d\n",rval);*/
632 if ((rval == EOF) || (rval == 0))
635 srenew(fmt,3*(nny+1)+1);
636 srenew(base,3*nny+1);
640 fprintf(stderr,"Only %d columns on line %d in file %s\n",
653 if (legend_nalloc > 0) {
654 if (*ny - 1 > legend_nalloc) {
655 srenew(*legend,*ny-1);
656 for(set=legend_nalloc; set<*ny-1; set++) {
657 (*legend)[set] = NULL;
665 int read_xvg(const char *fn,double ***y,int *ny)
667 return read_xvg_legend(fn,y,ny,NULL,NULL);
670 void write_xvg(const char *fn,const char *title,int nx,int ny,real **y,
671 const char **leg,const output_env_t oenv)
676 fp=xvgropen(fn,title,"X","Y",oenv);
678 xvgr_legend(fp,ny-1,leg,oenv);
679 for(i=0; (i<nx); i++) {
680 for(j=0; (j<ny); j++) {
681 fprintf(fp," %12.5e",y[j][i]);
688 real **read_xvg_time(const char *fn,
689 gmx_bool bHaveT,gmx_bool bTB,real tb,gmx_bool bTE,real te,
690 int nsets_in,int *nset,int *nval,real *dt,real **t)
693 #define MAXLINELEN 16384
694 char line0[MAXLINELEN];
696 int t_nalloc,*val_nalloc,a,narg,n,sin,set,nchar;
698 gmx_bool bEndOfSet,bTimeInRange,bFirstLine=TRUE;
707 fp = gmx_fio_fopen(fn,"r");
708 for(sin=0; sin<nsets_in; sin++) {
712 narg = bHaveT ? 2 : 1;
715 while (!bEndOfSet && fgets(line0,MAXLINELEN,fp)) {
717 /* Remove whitespace */
718 while (line[0]==' ' || line[0]=='\t')
720 bEndOfSet = (line[0] == '&');
721 if (line[0]!='#' && line[0]!='@' && line[0]!='\n' && !bEndOfSet) {
722 if (bFirstLine && bHaveT) {
723 /* Check the first line that should contain data */
724 a = sscanf(line,"%lf%lf",&dbl,&dbl);
726 gmx_fatal(FARGS,"Expected a number in %s on line:\n%s",fn,line0);
728 fprintf(stderr,"Found only 1 number on line, "
729 "assuming no time is present.\n");
738 while ((a<narg || (nsets_in==1 && n==0)) &&
739 sscanf(line,"%lf%n",&dbl,&nchar)==1 && bTimeInRange) {
740 /* Use set=-1 as the time "set" */
742 if (!bHaveT || (a>0))
752 if (set==-1 && ((bTB && dbl<tb) || (bTE && dbl>te)))
753 bTimeInRange = FALSE;
762 srenew(val_nalloc,*nset);
770 t_nalloc = over_alloc_small(n);
775 /* else we should check the time of the next sets with set 0 */
777 if (n >= val_nalloc[set]) {
778 val_nalloc[set] = over_alloc_small(n);
779 srenew(val[set],val_nalloc[set]);
781 val[set][n] = (real)dbl;
787 if (line0[strlen(line0)-1] != '\n') {
788 fprintf(stderr,"File %s does not end with a newline, ignoring the last line\n",fn);
789 } else if (bTimeInRange) {
791 fprintf(stderr,"Ignoring invalid line in %s:\n%s",fn,line0);
794 fprintf(stderr,"Invalid line in %s:\n%s"
795 "Using zeros for the last %d sets\n",
812 *dt = (real)((*t)[n-1]-(*t)[0])/(n-1.0);
817 fprintf(stderr,"Set %d is shorter (%d) than the previous set (%d)\n",
820 fprintf(stderr,"Will use only the first %d points of every set\n",