src/gmxlib/readinp.c

   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
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
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  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * GROningen Mixture of Alchemy and Childrens' Stories
  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <stdio.h>
  40 #include <stdlib.h>
  41 #include "typedefs.h"
  42 #include "string2.h"
  43 #include "futil.h"
  44 #include "smalloc.h"
  45 #include "readinp.h"
  46 #include "macros.h"
  47 #include "statutil.h"
  48 #include "gmxfio.h"
  49 #include "names.h"
  50 #include "warninp.h"
  51 #include "gmx_fatal.h"
  52
  53 /* find an entry; return index, or -1 if not found */
  54 static int search_einp(int ninp, const t_inpfile *inp, const char *name);
  55
  56
  57 t_inpfile *read_inpfile(const char *fn,int *ninp,
  58                         char **cppopts,
  59                         warninp_t wi)
  60 {
  61   FILE      *in;
  62   char      buf[STRLEN],lbuf[STRLEN],rbuf[STRLEN],warn_buf[STRLEN];
  63   char      *ptr,*cptr;
  64   t_inpfile *inp=NULL;
  65   int       nin,lc,i,j,k;
  66   /* setting cppopts from command-line options would be cooler */
  67   gmx_bool allow_override=FALSE;
  68
  69
  70   if (debug)
  71     fprintf(debug,"Reading MDP file %s\n",fn);
  72
  73   in = ffopen(fn, "r");
  74
  75   nin = lc  = 0;
  76   do {
  77     ptr = fgets2(buf,STRLEN-1,in);
  78     lc++;
  79     set_warning_line(wi,fn,lc);
  80     if (ptr) {
  81       /* Strip comment */
  82       if ((cptr=strchr(buf,COMMENTSIGN)) != NULL)
  83         *cptr='\0';
  84       /* Strip spaces */
  85       trim(buf);
  86
  87       for(j=0; (buf[j] != '=') && (buf[j] != '\0'); j++)
  88         ;
  89       if (buf[j] == '\0') {
  90         if (j > 0) {
  91           if (debug)
  92             fprintf(debug,"No = on line %d in file %s, ignored\n",lc,fn);
  93         }
  94       }
  95       else {
  96         for(i=0; (i<j); i++)
  97           lbuf[i]=buf[i];
  98         lbuf[i]='\0';
  99         trim(lbuf);
 100         if (lbuf[0] == '\0') {
 101           if (debug)
 102             fprintf(debug,"Empty left hand side on line %d in file %s, ignored\n",lc,fn);
 103         }
 104         else {
 105           for(i=j+1,k=0; (buf[i] != '\0'); i++,k++)
 106             rbuf[k]=buf[i];
 107           rbuf[k]='\0';
 108           trim(rbuf);
 109           if (rbuf[0] == '\0') {
 110             if (debug)
 111               fprintf(debug,"Empty right hand side on line %d in file %s, ignored\n",lc,fn);
 112           }
 113           else {
 114             /* Now finally something sensible */
 115             int found_index;
 116
 117             /* first check whether we hit the 'multiple_entries' option */
 118             if (gmx_strcasecmp_min(eMultentOpt_names[eMultentOptName], lbuf)==0)
 119             {
 120               /* we now check whether to allow overrides from here or not */
 121               if (gmx_strcasecmp_min(eMultentOpt_names[eMultentOptNo], rbuf)==0)
 122               {
 123                 allow_override=FALSE;
 124               }
 125               else if (gmx_strcasecmp_min(eMultentOpt_names[eMultentOptLast], rbuf)==0)
 126               {
 127                 allow_override=TRUE;
 128               }
 129               else
 130               {
 131                 sprintf(warn_buf,
 132                         "Parameter \"%s\" should either be %s or %s\n",
 133                         lbuf,
 134                         eMultentOpt_names[eMultentOptNo],
 135                         eMultentOpt_names[eMultentOptLast]);
 136                 warning_error(wi,warn_buf);
 137               }
 138             }
 139             else
 140             {
 141               /* it is a regular option; check for duplicates */
 142               found_index=search_einp(nin, inp, lbuf);
 143
 144               if (found_index == -1)
 145               {
 146                 /* add a new item */
 147                 srenew(inp,++nin);
 148                 inp[nin-1].inp_count  = 1;
 149                 inp[nin-1].count      = 0;
 150                 inp[nin-1].bObsolete  = FALSE;
 151                 inp[nin-1].bSet       = FALSE;
 152                 inp[nin-1].name       = strdup(lbuf);
 153                 inp[nin-1].value      = strdup(rbuf);
 154               }
 155               else
 156               {
 157                 if (!allow_override)
 158                 {
 159                   sprintf(warn_buf,
 160                           "Parameter \"%s\" doubly defined (and multiple assignments not allowed)\n",
 161                           lbuf);
 162                   warning_error(wi,warn_buf);
 163                 }
 164                 else
 165                 {
 166                   /* override */
 167                   sfree(inp[found_index].value);
 168                   inp[found_index].value = strdup(rbuf);
 169                   sprintf(warn_buf,
 170                           "Overriding existing parameter \"%s\" with value \"%s\"\n",
 171                           lbuf,rbuf);
 172                   warning_note(wi,warn_buf);
 173                 }
 174               }
 175             }
 176           }
 177         }
 178       }
 179     }
 180   } while (ptr);
 181
 182   fclose(in);
 183
 184   if (debug) {
 185     fprintf(debug,"Done reading MDP file, there were %d entries in there\n",
 186             nin);
 187   }
 188
 189   *ninp = nin;
 190
 191   return inp;
 192 }
 193
 194
 195
 196
 197 static int inp_comp(const void *a,const void *b)
 198 {
 199   return ((t_inpfile *)a)->count - ((t_inpfile *)b)->count;
 200 }
 201
 202 static void sort_inp(int ninp,t_inpfile inp[])
 203 {
 204   int i,mm;
 205
 206   mm=-1;
 207   for(i=0; (i<ninp); i++)
 208     mm=max(mm,inp[i].count);
 209   for(i=0; (i<ninp); i++) {
 210     if (inp[i].count == 0)
 211       inp[i].count = mm++;
 212   }
 213   qsort(inp,ninp,(size_t)sizeof(inp[0]),inp_comp);
 214 }
 215
 216 void write_inpfile(const char *fn,int ninp,t_inpfile inp[],gmx_bool bHaltOnUnknown,
 217                    warninp_t wi)
 218 {
 219   FILE *out;
 220   int  i;
 221   char warn_buf[STRLEN];
 222
 223   sort_inp(ninp,inp);
 224   out=gmx_fio_fopen(fn,"w");
 225   nice_header(out,fn);
 226   for(i=0; (i<ninp); i++) {
 227     if (inp[i].bSet) {
 228       if(inp[i].name[0]==';' || (strlen(inp[i].name)>2 && inp[i].name[1]==';'))
 229         fprintf(out,"%-24s\n",inp[i].name);
 230       else
 231         fprintf(out,"%-24s = %s\n",inp[i].name,inp[i].value ? inp[i].value : "");
 232     } else if (!inp[i].bObsolete) {
 233       sprintf(warn_buf,"Unknown left-hand '%s' in parameter file\n",
 234               inp[i].name);
 235       if (bHaltOnUnknown) {
 236         warning_error(wi,warn_buf);
 237       } else {
 238         warning(wi,warn_buf);
 239       }
 240     }
 241   }
 242   gmx_fio_fclose(out);
 243
 244   check_warning_error(wi,FARGS);
 245 }
 246
 247 void replace_inp_entry(int ninp,t_inpfile *inp,const char *old_entry,const char *new_entry)
 248 {
 249   int  i;
 250
 251   for(i=0; (i<ninp); i++) {
 252     if (gmx_strcasecmp_min(old_entry,inp[i].name) == 0) {
 253       if (new_entry) {
 254         fprintf(stderr,"Replacing old mdp entry '%s' by '%s'\n",
 255                 inp[i].name,new_entry);
 256         sfree(inp[i].name);
 257         inp[i].name = strdup(new_entry);
 258       } else {
 259         fprintf(stderr,"Ignoring obsolete mdp entry '%s'\n",
 260                 inp[i].name);
 261         inp[i].bObsolete = TRUE;
 262       }
 263     }
 264   }
 265 }
 266
 267 static int search_einp(int ninp, const t_inpfile *inp, const char *name)
 268 {
 269   int i;
 270
 271   if (inp==NULL)
 272     return -1;
 273   for(i=0; i<ninp; i++)
 274     if (gmx_strcasecmp_min(name,inp[i].name) == 0)
 275       return i;
 276   return -1;
 277 }
 278
 279 static int get_einp(int *ninp,t_inpfile **inp,const char *name)
 280 {
 281   int    i;
 282   int    notfound=FALSE;
 283   char   warn_buf[STRLEN];
 284
 285 /*  if (inp==NULL)
 286     return -1;
 287   for(i=0; (i<(*ninp)); i++)
 288     if (gmx_strcasecmp_min(name,(*inp)[i].name) == 0)
 289       break;
 290   if (i == (*ninp)) {*/
 291   i=search_einp(*ninp, *inp, name);
 292   if (i == -1)
 293   {
 294     notfound=TRUE;
 295     i=(*ninp)++;
 296     srenew(*inp,(*ninp));
 297     (*inp)[i].name=strdup(name);
 298     (*inp)[i].bSet=TRUE;
 299   }
 300   (*inp)[i].count = (*inp)[0].inp_count++;
 301   (*inp)[i].bSet  = TRUE;
 302   if (debug)
 303     fprintf(debug,"Inp %d = %s\n",(*inp)[i].count,(*inp)[i].name);
 304
 305   /*if (i == (*ninp)-1)*/
 306   if (notfound)
 307     return -1;
 308   else
 309     return i;
 310 }
 311
 312 int get_eint(int *ninp,t_inpfile **inp,const char *name,int def,
 313              warninp_t wi)
 314 {
 315   char buf[32],*ptr,warn_buf[STRLEN];
 316   int  ii;
 317   int  ret;
 318
 319   ii=get_einp(ninp,inp,name);
 320
 321   if (ii == -1) {
 322     sprintf(buf,"%d",def);
 323     (*inp)[(*ninp)-1].value=strdup(buf);
 324
 325     return def;
 326   }
 327   else {
 328     ret = strtol((*inp)[ii].value,&ptr,10);
 329     if (ptr == (*inp)[ii].value) {
 330       sprintf(warn_buf,"Right hand side '%s' for parameter '%s' in parameter file is not an integer value\n",(*inp)[ii].value,(*inp)[ii].name);
 331       warning_error(wi,warn_buf);
 332     }
 333
 334     return ret;
 335   }
 336 }
 337
 338 gmx_large_int_t get_egmx_large_int(int *ninp,t_inpfile **inp,
 339                                    const char *name,gmx_large_int_t def,
 340                                    warninp_t wi)
 341 {
 342   char buf[32],*ptr,warn_buf[STRLEN];
 343   int  ii;
 344   gmx_large_int_t ret;
 345
 346   ii=get_einp(ninp,inp,name);
 347
 348   if (ii == -1) {
 349     sprintf(buf,gmx_large_int_pfmt,def);
 350     (*inp)[(*ninp)-1].value=strdup(buf);
 351
 352     return def;
 353   }
 354   else {
 355     ret = str_to_large_int_t((*inp)[ii].value,&ptr);
 356     if (ptr == (*inp)[ii].value) {
 357       sprintf(warn_buf,"Right hand side '%s' for parameter '%s' in parameter file is not an integer value\n",(*inp)[ii].value,(*inp)[ii].name);
 358       warning_error(wi,warn_buf);
 359     }
 360
 361     return ret;
 362   }
 363 }
 364
 365 double get_ereal(int *ninp,t_inpfile **inp,const char *name,double def,
 366                  warninp_t wi)
 367 {
 368   char buf[32],*ptr,warn_buf[STRLEN];
 369   int  ii;
 370   double ret;
 371
 372   ii=get_einp(ninp,inp,name);
 373
 374   if (ii == -1) {
 375     sprintf(buf,"%g",def);
 376     (*inp)[(*ninp)-1].value=strdup(buf);
 377
 378     return def;
 379   }
 380   else {
 381     ret = strtod((*inp)[ii].value,&ptr);
 382     if (ptr == (*inp)[ii].value) {
 383       sprintf(warn_buf,"Right hand side '%s' for parameter '%s' in parameter file is not a real value\n",(*inp)[ii].value,(*inp)[ii].name);
 384       warning_error(wi,warn_buf);
 385     }
 386
 387     return ret;
 388   }
 389 }
 390
 391 const char *get_estr(int *ninp,t_inpfile **inp,const char *name,const char *def)
 392 {
 393   char buf[32];
 394   int  ii;
 395
 396   ii=get_einp(ninp,inp,name);
 397
 398   if (ii == -1) {
 399     if (def) {
 400       sprintf(buf,"%s",def);
 401       (*inp)[(*ninp)-1].value=strdup(buf);
 402     }
 403     else
 404       (*inp)[(*ninp)-1].value=NULL;
 405
 406     return def;
 407   }
 408   else
 409     return (*inp)[ii].value;
 410 }
 411
 412 int get_eeenum(int *ninp,t_inpfile **inp,const char *name,const char **defs,
 413                warninp_t wi)
 414 {
 415   int  ii,i,j;
 416   int n=0;
 417   char buf[STRLEN];
 418
 419   ii=get_einp(ninp,inp,name);
 420
 421   if (ii == -1) {
 422     (*inp)[(*ninp)-1].value=strdup(defs[0]);
 423
 424     return 0;
 425   }
 426
 427   for(i=0; (defs[i] != NULL); i++)
 428     if (gmx_strcasecmp_min(defs[i],(*inp)[ii].value) == 0)
 429       break;
 430
 431   if (defs[i] == NULL) {
 432     n += sprintf(buf,"Invalid enum '%s' for variable %s, using '%s'\n",
 433                 (*inp)[ii].value,name,defs[0]);
 434     n += sprintf(buf+n,"Next time use one of:");
 435     j=0;
 436     while (defs[j]) {
 437       n += sprintf(buf+n," '%s'",defs[j]);
 438       j++;
 439     }
 440     if (wi != NULL) {
 441       warning_error(wi,buf);
 442     } else {
 443       fprintf(stderr,"%s\n",buf);
 444     }
 445
 446     (*inp)[ii].value = strdup(defs[0]);
 447
 448     return 0;
 449   }
 450
 451   return i;
 452 }
 453
 454 int get_eenum(int *ninp,t_inpfile **inp,const char *name,const char **defs)
 455 {
 456   int dum=0;
 457
 458   return get_eeenum(ninp,inp,name,defs,NULL);
 459 }
 460