src/gmxlib/statutil.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
   2  *
   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
  18  * as published by the Free Software Foundation; either version 2
  19  * of the License, or (at your option) any later version.
  20  *
  21  * If you want to redistribute modifications, please consider that
  22  * scientific software is very special. Version control is crucial -
  23  * bugs must be traceable. We will be happy to consider code for
  24  * inclusion in the official distribution, but derived work must not
  25  * be called official GROMACS. Details are found in the README & COPYING
  26  * files - if they are missing, get the official version at www.gromacs.org.
  27  *
  28  * To help us fund GROMACS development, we humbly ask that you cite
  29  * the papers on the package - you can find them in the top README file.
  30  *
  31  * For more info, check our website at http://www.gromacs.org
  32  *
  33  * And Hey:
  34  * GROningen Mixture of Alchemy and Childrens' Stories
  35  */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40
  41 #include <ctype.h>
  42 #include "copyrite.h"
  43 #include "sysstuff.h"
  44 #include "macros.h"
  45 #include "string2.h"
  46 #include "smalloc.h"
  47 #include "pbc.h"
  48 #include "statutil.h"
  49 #include "names.h"
  50 #include "vec.h"
  51 #include "futil.h"
  52 #include "wman.h"
  53 #include "tpxio.h"
  54 #include "gmx_fatal.h"
  55 #include "network.h"
  56 #include "vec.h"
  57 #include "mtop_util.h"
  58 #include "gmxfio.h"
  59
  60 #ifdef GMX_THREADS
  61 #include "thread_mpi.h"
  62 #endif
  63
  64 /* used for npri */
  65 #ifdef __sgi
  66 #include <sys/schedctl.h>
  67 #include <sys/sysmp.h>
  68 #endif
  69
  70 /* The source code in this file should be thread-safe.
  71       Please keep it that way. */
  72
  73 /******************************************************************
  74  *
  75  *             T R A J E C T O R Y   S T U F F
  76  *
  77  ******************************************************************/
  78
  79 /* inherently globally shared names: */
  80 static const char *program_name=NULL;
  81 static char *cmd_line=NULL;
  82
  83 #ifdef GMX_THREADS
  84 /* For now, some things here are simply not re-entrant, so
  85    we have to actively lock them. */
  86 static tMPI_Thread_mutex_t init_mutex=TMPI_THREAD_MUTEX_INITIALIZER;
  87 #endif
  88
  89
  90 /****************************************************************
  91  *
  92  *            E X P O R T E D   F U N C T I O N S
  93  *
  94  ****************************************************************/
  95
  96
  97 /* progam names, etc. */
  98
  99 const char *ShortProgram(void)
 100 {
 101     const char *pr,*ret;
 102 #ifdef GMX_THREADS
 103     tMPI_Thread_mutex_lock(&init_mutex);
 104 #endif
 105     pr=ret=program_name;
 106 #ifdef GMX_THREADS
 107     tMPI_Thread_mutex_unlock(&init_mutex);
 108 #endif
 109     if ((pr=strrchr(ret,DIR_SEPARATOR)) != NULL)
 110         ret=pr+1;
 111     /* Strip away the libtool prefix if it's still there. */
 112     if(strlen(ret) > 3 && !strncmp(ret, "lt-", 3))
 113         ret = ret + 3;
 114     return ret;
 115 }
 116
 117 const char *Program(void)
 118 {
 119     const char *ret;
 120 #ifdef GMX_THREADS
 121     tMPI_Thread_mutex_lock(&init_mutex);
 122 #endif
 123     ret=program_name;
 124 #ifdef GMX_THREADS
 125     tMPI_Thread_mutex_unlock(&init_mutex);
 126 #endif
 127     return ret;
 128 }
 129
 130 const char *command_line(void)
 131 {
 132     const char *ret;
 133 #ifdef GMX_THREADS
 134     tMPI_Thread_mutex_lock(&init_mutex);
 135 #endif
 136     ret=cmd_line;
 137 #ifdef GMX_THREADS
 138     tMPI_Thread_mutex_unlock(&init_mutex);
 139 #endif
 140     return ret;
 141 }
 142
 143 void set_program_name(const char *argvzero)
 144 {
 145 #ifdef GMX_THREADS
 146     tMPI_Thread_mutex_lock(&init_mutex);
 147 #endif
 148     /* When you run a dynamically linked program before installing
 149      * it, libtool uses wrapper scripts and prefixes the name with "lt-".
 150      * Until libtool is fixed to set argv[0] right, rip away the prefix:
 151      */
 152     if (program_name == NULL)
 153     {
 154         if(strlen(argvzero)>3 && !strncmp(argvzero,"lt-",3))
 155             program_name=strdup(argvzero+3);
 156         else
 157             program_name=strdup(argvzero);
 158     }
 159     if (program_name == NULL)
 160         program_name="GROMACS";
 161 #ifdef GMX_THREADS
 162     tMPI_Thread_mutex_unlock(&init_mutex);
 163 #endif
 164 }
 165
 166
 167 void set_command_line(int argc, char *argv[])
 168 {
 169     int i;
 170     size_t cmdlength;
 171
 172 #ifdef GMX_THREADS
 173     tMPI_Thread_mutex_lock(&init_mutex);
 174 #endif
 175     if (cmd_line==NULL)
 176     {
 177         cmdlength = strlen(argv[0]);
 178         for (i=1; i<argc; i++)
 179         {
 180             cmdlength += strlen(argv[i]);
 181         }
 182
 183         /* Fill the cmdline string */
 184         snew(cmd_line,cmdlength+argc+1);
 185         for (i=0; i<argc; i++)
 186         {
 187             strcat(cmd_line,argv[i]);
 188             strcat(cmd_line," ");
 189         }
 190     }
 191 #ifdef GMX_THREADS
 192     tMPI_Thread_mutex_unlock(&init_mutex);
 193 #endif
 194
 195 }
 196
 197 /* utility functions */
 198
 199 gmx_bool bRmod_fd(double a, double b, double c, gmx_bool bDouble)
 200 {
 201     int iq;
 202     double tol;
 203
 204     tol = 2*(bDouble ? GMX_DOUBLE_EPS : GMX_FLOAT_EPS);
 205
 206     iq = (a - b + tol*a)/c;
 207
 208     if (fabs(a - b - c*iq) <= tol*fabs(a))
 209         return TRUE;
 210     else
 211         return FALSE;
 212 }
 213
 214 int check_times2(real t,real t0,real tp, real tpp, gmx_bool bDouble)
 215 {
 216     int  r;
 217     real margin;
 218
 219 #ifndef GMX_DOUBLE
 220     /* since t is float, we can not use double precision for bRmod */
 221     bDouble = FALSE;
 222 #endif
 223
 224     if (t-tp>0 && tp-tpp>0)
 225         margin = 0.1*min(t-tp,tp-tpp);
 226     else
 227         margin = 0;
 228
 229     r=-1;
 230     if ((!bTimeSet(TBEGIN) || (t >= rTimeValue(TBEGIN)))  &&
 231         (!bTimeSet(TEND)   || (t <= rTimeValue(TEND)))) {
 232         if (bTimeSet(TDELTA) && !bRmod_fd(t,t0,rTimeValue(TDELTA),bDouble))
 233             r = -1;
 234         else
 235             r = 0;
 236     }
 237     else if (bTimeSet(TEND) && (t >= rTimeValue(TEND)))
 238         r = 1;
 239     if (debug)
 240         fprintf(debug,"t=%g, t0=%g, b=%g, e=%g, dt=%g: r=%d\n",
 241                 t,t0,rTimeValue(TBEGIN),rTimeValue(TEND),rTimeValue(TDELTA),r);
 242     return r;
 243 }
 244
 245 int check_times(real t)
 246 {
 247     return check_times2(t,t,t,t,FALSE);
 248 }
 249
 250
 251
 252
 253 static void set_default_time_unit(const char *time_list[], gmx_bool bCanTime)
 254 {
 255     int i,j;
 256     const char *select;
 257
 258     if (bCanTime)
 259     {
 260         select = getenv("GMXTIMEUNIT");
 261         if (select != NULL)
 262         {
 263             i = 1;
 264             while(time_list[i] && strcmp(time_list[i], select) != 0)
 265             {
 266                 i++;
 267             }
 268         }
 269     }
 270     if (!bCanTime || select == NULL || strcmp(time_list[i], select) != 0)
 271     {
 272         /* Set it to the default: ps */
 273         i = 1;
 274         while(time_list[i] && strcmp(time_list[i], "ps") != 0)
 275         {
 276             i++;
 277         }
 278
 279     }
 280     time_list[0] = time_list[i];
 281 }
 282
 283
 284 static void set_default_xvg_format(const char *xvg_list[])
 285 {
 286     int i,j;
 287     const char *select,*tmp;
 288
 289     select = getenv("GMX_VIEW_XVG");
 290     if (select == NULL)
 291     {
 292         /* The default is the first option */
 293         xvg_list[0] = xvg_list[1];
 294     }
 295     else
 296     {
 297         i = 1;
 298         while (xvg_list[i] && strcmp(xvg_list[i], select) != 0)
 299         {
 300             i++;
 301         }
 302         if (xvg_list[i] != NULL)
 303         {
 304             xvg_list[0] = xvg_list[i];
 305         }
 306         else
 307         {
 308             xvg_list[0] = xvg_list[exvgNONE];
 309         }
 310     }
 311 }
 312
 313
 314 /***** T O P O L O G Y   S T U F F ******/
 315
 316 t_topology *read_top(const char *fn,int *ePBC)
 317 {
 318     int        epbc,natoms;
 319     t_topology *top;
 320
 321     snew(top,1);
 322     epbc = read_tpx_top(fn,NULL,NULL,&natoms,NULL,NULL,NULL,top);
 323     if (ePBC)
 324         *ePBC = epbc;
 325
 326     return top;
 327 }
 328
 329 /*************************************************************
 330  *
 331  *           P A R S I N G   S T U F F
 332  *
 333  *************************************************************/
 334
 335 static void usage(const char *type,const char *arg)
 336 {
 337     if (arg != NULL)
 338         gmx_fatal(FARGS,"Expected %s argument for option %s\n",type,arg);
 339 }
 340
 341 int iscan(int argc,char *argv[],int *i)
 342 {
 343     int var;
 344
 345     if (argc > (*i)+1) {
 346         if (!sscanf(argv[++(*i)],"%d",&var))
 347             usage("an integer",argv[(*i)-1]);
 348     } else
 349         usage("an integer",argv[*i]);
 350
 351     return var;
 352 }
 353
 354 gmx_large_int_t istepscan(int argc,char *argv[],int *i)
 355 {
 356     gmx_large_int_t var;
 357
 358     if (argc > (*i)+1) {
 359         if (!sscanf(argv[++(*i)],gmx_large_int_pfmt,&var))
 360             usage("an integer",argv[(*i)-1]);
 361     } else
 362         usage("an integer",argv[*i]);
 363
 364     return var;
 365 }
 366
 367 double dscan(int argc,char *argv[],int *i)
 368 {
 369     double var;
 370
 371     if (argc > (*i)+1) {
 372         if (!sscanf(argv[++(*i)],"%lf",&var))
 373             usage("a real",argv[(*i)-1]);
 374     } else
 375         usage("a real",argv[*i]);
 376
 377     return var;
 378 }
 379
 380 char *sscan(int argc,char *argv[],int *i)
 381 {
 382     if (argc > (*i)+1)
 383     {
 384         if ( (argv[(*i)+1][0]=='-') && (argc > (*i)+2) &&
 385            (argv[(*i)+2][0]!='-') )
 386         {
 387             fprintf(stderr,"Possible missing string argument for option %s\n\n",
 388                     argv[*i]);
 389         }
 390     }
 391     else
 392         usage("a string",argv[*i]);
 393
 394     return argv[++(*i)];
 395 }
 396
 397 int nenum(const char *const enumc[])
 398 {
 399     int i;
 400
 401     i=1;
 402     /* we *can* compare pointers directly here! */
 403     while(enumc[i] && enumc[0]!=enumc[i])
 404         i++;
 405
 406     return i;
 407 }
 408
 409 static void pdesc(char *desc)
 410 {
 411     char *ptr,*nptr;
 412
 413     ptr=desc;
 414     if ((int)strlen(ptr) < 70)
 415         fprintf(stderr,"\t%s\n",ptr);
 416     else {
 417         for(nptr=ptr+70; (nptr != ptr) && (!isspace(*nptr)); nptr--)
 418             ;
 419         if (nptr == ptr)
 420             fprintf(stderr,"\t%s\n",ptr);
 421         else {
 422             *nptr='\0';
 423             nptr++;
 424             fprintf(stderr,"\t%s\n",ptr);
 425             pdesc(nptr);
 426         }
 427     }
 428 }
 429
 430 static FILE *man_file(const output_env_t oenv,const char *mantp)
 431 {
 432     FILE   *fp;
 433     char   buf[256];
 434     const char *pr = output_env_get_short_program_name(oenv);
 435
 436     if (strcmp(mantp,"ascii") != 0)
 437         sprintf(buf,"%s.%s",pr,mantp);
 438     else
 439         sprintf(buf,"%s.txt",pr);
 440     fp = gmx_fio_fopen(buf,"w");
 441
 442     return fp;
 443 }
 444
 445 static int add_parg(int npargs,t_pargs *pa,t_pargs *pa_add)
 446 {
 447     memcpy(&(pa[npargs]),pa_add,sizeof(*pa_add));
 448
 449     return npargs+1;
 450 }
 451
 452 static char *mk_desc(t_pargs *pa, const char *time_unit_str)
 453 {
 454     char *newdesc=NULL,*ndesc=NULL,*nptr=NULL;
 455     const char*ptr=NULL;
 456     int  len,k;
 457
 458     /* First compute length for description */
 459     len = strlen(pa->desc)+1;
 460     if ((ptr = strstr(pa->desc,"HIDDEN")) != NULL)
 461         len += 4;
 462     if (pa->type == etENUM) {
 463         len += 10;
 464         for(k=1; (pa->u.c[k] != NULL); k++) {
 465             len += strlen(pa->u.c[k])+12;
 466         }
 467     }
 468     snew(newdesc,len);
 469
 470     /* add label for hidden options */
 471     if (is_hidden(pa))
 472         sprintf(newdesc,"[hidden] %s",ptr+6);
 473     else
 474         strcpy(newdesc,pa->desc);
 475
 476     /* change '%t' into time_unit */
 477 #define TUNITLABEL "%t"
 478 #define NTUNIT strlen(TUNITLABEL)
 479     if (pa->type == etTIME)
 480         while( (nptr=strstr(newdesc,TUNITLABEL)) != NULL ) {
 481             nptr[0]='\0';
 482             nptr+=NTUNIT;
 483             len+=strlen(time_unit_str)-NTUNIT;
 484             snew(ndesc,len);
 485             strcpy(ndesc,newdesc);
 486             strcat(ndesc,time_unit_str);
 487             strcat(ndesc,nptr);
 488             sfree(newdesc);
 489             newdesc=ndesc;
 490             ndesc=NULL;
 491         }
 492 #undef TUNITLABEL
 493 #undef NTUNIT
 494
 495     /* Add extra comment for enumerateds */
 496     if (pa->type == etENUM) {
 497         strcat(newdesc,": ");
 498         for(k=1; (pa->u.c[k] != NULL); k++) {
 499             strcat(newdesc,"[TT]");
 500             strcat(newdesc,pa->u.c[k]);
 501             strcat(newdesc,"[tt]");
 502             /* Print a comma everywhere but at the last one */
 503             if (pa->u.c[k+1] != NULL) {
 504                 if (pa->u.c[k+2] == NULL)
 505                     strcat(newdesc," or ");
 506                 else
 507                     strcat(newdesc,", ");
 508             }
 509         }
 510     }
 511     return newdesc;
 512 }
 513
 514
 515 void parse_common_args(int *argc,char *argv[],unsigned long Flags,
 516                        int nfile,t_filenm fnm[],int npargs,t_pargs *pa,
 517                        int ndesc,const char **desc,
 518                        int nbugs,const char **bugs,
 519                        output_env_t *oenv)
 520 {
 521     gmx_bool bHelp=FALSE,bHidden=FALSE,bQuiet=FALSE,bVersion=FALSE;
 522     const char *manstr[] = { NULL, "no", "html", "tex", "nroff", "ascii",
 523                             "completion", "py", "xml", "wiki", NULL };
 524     /* This array should match the order of the enum in oenv.h */
 525     const char *xvg_format[] = { NULL, "xmgrace", "xmgr", "none", NULL };
 526     /* This array should match the order of the enum in oenv.h */
 527     const char *time_units[] = { NULL, "fs", "ps", "ns", "us", "ms", "s",
 528                                 NULL };
 529     int  nicelevel=0,mantp=0,npri=0,debug_level=0,verbose_level=0;
 530     char *deffnm=NULL;
 531     real tbegin=0,tend=0,tdelta=0;
 532     gmx_bool bView=FALSE;
 533
 534     t_pargs *all_pa=NULL;
 535
 536     t_pargs npri_pa   = { "-npri", FALSE, etINT,   {&npri},
 537     "HIDDEN Set non blocking priority (try 128)" };
 538     t_pargs nice_pa   = { "-nice", FALSE, etINT,   {&nicelevel},
 539     "Set the nicelevel" };
 540     t_pargs deffnm_pa = { "-deffnm", FALSE, etSTR, {&deffnm},
 541     "Set the default filename for all file options" };
 542     t_pargs begin_pa  = { "-b",    FALSE, etTIME,  {&tbegin},
 543     "First frame (%t) to read from trajectory" };
 544     t_pargs end_pa    = { "-e",    FALSE, etTIME,  {&tend},
 545     "Last frame (%t) to read from trajectory" };
 546     t_pargs dt_pa     = { "-dt",   FALSE, etTIME,  {&tdelta},
 547     "Only use frame when t MOD dt = first time (%t)" };
 548     t_pargs view_pa   = { "-w",    FALSE, etBOOL,  {&bView},
 549     "View output [TT].xvg[tt], [TT].xpm[tt], [TT].eps[tt] and [TT].pdb[tt] files" };
 550     t_pargs xvg_pa    = { "-xvg",  FALSE, etENUM,  {xvg_format},
 551     "xvg plot formatting" };
 552     t_pargs time_pa   = { "-tu",   FALSE, etENUM,  {time_units},
 553     "Time unit" };
 554     /* Maximum number of extra arguments */
 555 #define EXTRA_PA 16
 556
 557     t_pargs pca_pa[] = {
 558       { "-h",    FALSE, etBOOL, {&bHelp},
 559         "Print help info and quit" },
 560       { "-version",  FALSE, etBOOL, {&bVersion},
 561         "Print version info and quit" },
 562       { "-verb",    FALSE,  etINT, {&verbose_level},
 563         "HIDDENLevel of verbosity for this program" },
 564       { "-hidden", FALSE, etBOOL, {&bHidden},
 565           "HIDDENPrint hidden options" },
 566       { "-quiet",FALSE, etBOOL, {&bQuiet},
 567         "HIDDENDo not print help info" },
 568       { "-man",  FALSE, etENUM,  {manstr},
 569         "HIDDENWrite manual and quit" },
 570       { "-debug",FALSE, etINT, {&debug_level},
 571         "HIDDENWrite file with debug information, 1: short, 2: also x and f" },
 572     };
 573 #define NPCA_PA asize(pca_pa)
 574     FILE *fp;
 575     gmx_bool bPrint,bExit,bXvgr;
 576     int  i,j,k,npall,max_pa,cmdlength;
 577     char *ptr,*newdesc;
 578     const char *envstr;
 579
 580 #define FF(arg) ((Flags & arg)==arg)
 581
 582     snew(*oenv, 1);
 583
 584     cmdlength = strlen(argv[0]);
 585     /* Check for double arguments */
 586     for (i=1; (i<*argc); i++)
 587     {
 588         cmdlength += strlen(argv[i]);
 589         if (argv[i] && (strlen(argv[i]) > 1) && (!isdigit(argv[i][1])))
 590         {
 591             for (j=i+1; (j<*argc); j++)
 592             {
 593                 if ( (argv[i][0]=='-') && (argv[j][0]=='-') &&
 594                     (strcmp(argv[i],argv[j])==0) )
 595                 {
 596                     if (FF(PCA_NOEXIT_ON_ARGS))
 597                         fprintf(stderr,"Double command line argument %s\n",
 598                                 argv[i]);
 599                     else
 600                         gmx_fatal(FARGS,"Double command line argument %s\n",
 601                                   argv[i]);
 602                 }
 603             }
 604         }
 605     }
 606     debug_gmx();
 607     set_program_name(argv[0]);
 608     set_command_line(*argc, argv);
 609
 610     /* Handle the flags argument, which is a bit field
 611      * The FF macro returns whether or not the bit is set
 612      */
 613     bPrint        = !FF(PCA_SILENT);
 614
 615     /* Check ALL the flags ... */
 616     max_pa = NPCA_PA + EXTRA_PA + npargs+1;
 617     snew(all_pa,max_pa);
 618
 619     for(i=npall=0; (i<NPCA_PA); i++)
 620         npall = add_parg(npall,all_pa,&(pca_pa[i]));
 621
 622 #ifdef __sgi
 623     envstr = getenv("GMXNPRIALL");
 624     if (envstr)
 625         npri=strtol(envstr,NULL,10);
 626     if (FF(PCA_BE_NICE)) {
 627         envstr = getenv("GMXNPRI");
 628         if (envstr)
 629             npri=strtol(envstr,NULL,10);
 630     }
 631     npall = add_parg(npall,all_pa,&npri_pa);
 632 #endif
 633
 634     if (FF(PCA_BE_NICE))
 635         nicelevel=19;
 636     npall = add_parg(npall,all_pa,&nice_pa);
 637
 638     if (FF(PCA_CAN_SET_DEFFNM))
 639         npall = add_parg(npall,all_pa,&deffnm_pa);
 640     if (FF(PCA_CAN_BEGIN))
 641         npall = add_parg(npall,all_pa,&begin_pa);
 642     if (FF(PCA_CAN_END))
 643         npall = add_parg(npall,all_pa,&end_pa);
 644     if (FF(PCA_CAN_DT))
 645     {
 646         npall = add_parg(npall,all_pa,&dt_pa);
 647     }
 648     if (FF(PCA_TIME_UNIT)) {
 649         npall = add_parg(npall,all_pa,&time_pa);
 650     }
 651     if (FF(PCA_CAN_VIEW))
 652         npall = add_parg(npall,all_pa,&view_pa);
 653
 654     bXvgr = FALSE;
 655     for(i=0; (i<nfile); i++)
 656     {
 657         bXvgr = bXvgr ||  (fnm[i].ftp == efXVG);
 658     }
 659     if (bXvgr)
 660     {
 661         npall = add_parg(npall,all_pa,&xvg_pa);
 662     }
 663
 664     /* Now append the program specific arguments */
 665     for(i=0; (i<npargs); i++)
 666         npall = add_parg(npall,all_pa,&(pa[i]));
 667
 668     /* set etENUM options to default */
 669     for(i=0; (i<npall); i++)
 670     {
 671         if (all_pa[i].type==etENUM)
 672         {
 673             all_pa[i].u.c[0]=all_pa[i].u.c[1];
 674         }
 675     }
 676     set_default_time_unit(time_units,FF(PCA_TIME_UNIT));
 677     set_default_xvg_format(xvg_format);
 678
 679     /* Now parse all the command-line options */
 680     get_pargs(argc,argv,npall,all_pa,FF(PCA_KEEP_ARGS));
 681
 682     /* set program name, command line, and default values for output options */
 683     output_env_init(*oenv, *argc, argv, (time_unit_t)nenum(time_units), bView,
 684                     (xvg_format_t)nenum(xvg_format), verbose_level, debug_level);
 685
 686     if (bVersion) {
 687       printf("Program: %s\n",output_env_get_program_name(*oenv));
 688       gmx_print_version_info(stdout);
 689       exit(0);
 690     }
 691
 692     if (FF(PCA_CAN_SET_DEFFNM) && (deffnm!=NULL))
 693         set_default_file_name(deffnm);
 694
 695     /* Parse the file args */
 696     parse_file_args(argc,argv,nfile,fnm,FF(PCA_KEEP_ARGS),!FF(PCA_NOT_READ_NODE));
 697
 698     /* Open the debug file */
 699     if (debug_level > 0) {
 700         char buf[256];
 701
 702         if (gmx_mpi_initialized())
 703             sprintf(buf,"%s%d.debug",output_env_get_short_program_name(*oenv),
 704                     gmx_node_rank());
 705         else
 706             sprintf(buf,"%s.debug",output_env_get_short_program_name(*oenv));
 707
 708         init_debug(debug_level,buf);
 709         fprintf(stderr,"Opening debug file %s (src code file %s, line %d)\n",
 710                 buf,__FILE__,__LINE__);
 711     }
 712
 713     /* Now copy the results back... */
 714     for(i=0,k=npall-npargs; (i<npargs); i++,k++)
 715         memcpy(&(pa[i]),&(all_pa[k]),(size_t)sizeof(pa[i]));
 716
 717
 718     for(i=0; (i<npall); i++)
 719         all_pa[i].desc = mk_desc(&(all_pa[i]), output_env_get_time_unit(*oenv));
 720
 721     bExit = bHelp || (strcmp(manstr[0],"no") != 0);
 722
 723 #if (defined __sgi && USE_SGI_FPE)
 724     doexceptions();
 725 #endif
 726
 727     /* Set the nice level */
 728 #ifdef __sgi
 729     if (npri != 0 && !bExit) {
 730         schedctl(MPTS_RTPRI,0,npri);
 731     }
 732 #endif
 733
 734 #ifdef HAVE_UNISTD_H
 735
 736 #ifndef GMX_NO_NICE
 737     /* The some system, e.g. the catamount kernel on cray xt3 do not have nice(2). */
 738     if (nicelevel != 0 && !bExit)
 739     {
 740 #ifdef GMX_THREADS
 741         static gmx_bool nice_set=FALSE; /* only set it once */
 742         tMPI_Thread_mutex_lock(&init_mutex);
 743         if (!nice_set)
 744         {
 745 #endif
 746             i=nice(nicelevel); /* assign ret value to avoid warnings */
 747 #ifdef GMX_THREADS
 748             nice_set=TRUE;
 749         }
 750         tMPI_Thread_mutex_unlock(&init_mutex);
 751 #endif
 752     }
 753 #endif
 754 #endif
 755
 756     /* Update oenv for parsed command line options settings. */
 757     (*oenv)->xvg_format = (xvg_format_t)nenum(xvg_format);
 758     (*oenv)->time_unit  = (time_unit_t)nenum(time_units);
 759
 760     if (!(FF(PCA_QUIET) || bQuiet )) {
 761         if (bHelp)
 762             write_man(stderr,"help",output_env_get_program_name(*oenv),
 763                       ndesc,desc,nfile, fnm,npall,all_pa, nbugs,bugs,bHidden);
 764         else if (bPrint) {
 765             pr_fns(stderr,nfile,fnm);
 766             print_pargs(stderr,npall,all_pa,FALSE);
 767         }
 768     }
 769
 770     if (strcmp(manstr[0],"no") != 0) {
 771         if(!strcmp(manstr[0],"completion")) {
 772             /* one file each for csh, bash and zsh if we do completions */
 773             fp=man_file(*oenv,"completion-zsh");
 774
 775             write_man(fp,"completion-zsh",output_env_get_program_name(*oenv),
 776                       ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
 777             gmx_fio_fclose(fp);
 778             fp=man_file(*oenv,"completion-bash");
 779             write_man(fp,"completion-bash",output_env_get_program_name(*oenv),
 780                       ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
 781             gmx_fio_fclose(fp);
 782             fp=man_file(*oenv,"completion-csh");
 783             write_man(fp,"completion-csh",output_env_get_program_name(*oenv),
 784                       ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
 785             gmx_fio_fclose(fp);
 786         } else {
 787             fp=man_file(*oenv,manstr[0]);
 788             write_man(fp,manstr[0],output_env_get_program_name(*oenv),
 789                       ndesc,desc,nfile,fnm, npall, all_pa,nbugs,bugs,bHidden);
 790             gmx_fio_fclose(fp);
 791         }
 792     }
 793
 794     /* convert time options, must be done after printing! */
 795
 796     for(i=0; i<npall; i++) {
 797         if ((all_pa[i].type == etTIME) && (*all_pa[i].u.r >= 0)) {
 798             *all_pa[i].u.r *= output_env_get_time_invfactor(*oenv);
 799         }
 800     }
 801
 802     /* Extract Time info from arguments */
 803     if (FF(PCA_CAN_BEGIN) && opt2parg_bSet("-b",npall,all_pa))
 804         setTimeValue(TBEGIN,opt2parg_real("-b",npall,all_pa));
 805
 806     if (FF(PCA_CAN_END) && opt2parg_bSet("-e",npall,all_pa))
 807         setTimeValue(TEND,opt2parg_real("-e",npall,all_pa));
 808
 809     if (FF(PCA_CAN_DT) && opt2parg_bSet("-dt",npall,all_pa))
 810         setTimeValue(TDELTA,opt2parg_real("-dt",npall,all_pa));
 811
 812     /* clear memory */
 813     for (i = 0; i < npall; ++i)
 814         sfree((void *)all_pa[i].desc);
 815     sfree(all_pa);
 816
 817     if (!FF(PCA_NOEXIT_ON_ARGS)) {
 818         if (*argc > 1) {
 819             gmx_cmd(argv[1]);
 820         }
 821     }
 822     if (bExit) {
 823         if (gmx_parallel_env_initialized())
 824             /*gmx_abort(gmx_node_rank(),gmx_node_num(),0);*/
 825             gmx_finalize();
 826         exit(0);
 827     }
 828 #undef FF
 829 }
 830