src/gmxlib/statutil.c

   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 3.1
  11  * Copyright (c) 1991-2001, University of Groningen, The Netherlands
  12  * This program is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU General Public License
  14  * as published by the Free Software Foundation; either version 2
  15  * of the License, or (at your option) any later version.
  16  *
  17  * If you want to redistribute modifications, please consider that
  18  * scientific software is very special. Version control is crucial -
  19  * bugs must be traceable. We will be happy to consider code for
  20  * inclusion in the official distribution, but derived work must not
  21  * be called official GROMACS. Details are found in the README & COPYING
  22  * files - if they are missing, get the official version at www.gromacs.org.
  23  *
  24  * To help us fund GROMACS development, we humbly ask that you cite
  25  * the papers on the package - you can find them in the top README file.
  26  *
  27  * For more info, check our website at http://www.gromacs.org
  28  *
  29  * And Hey:
  30  * Gnomes, ROck Monsters And Chili Sauce
  31  */
  32
  33 #ifdef HAVE_CONFIG_H
  34 #include <config.h>
  35 #endif
  36
  37
  38 #include <ctype.h>
  39 #include "sysstuff.h"
  40 #include "macros.h"
  41 #include "string2.h"
  42 #include "smalloc.h"
  43 #include "pbc.h"
  44 #include "statutil.h"
  45 #include "names.h"
  46 #include "vec.h"
  47 #include "futil.h"
  48 #include "wman.h"
  49 #include "tpxio.h"
  50 #include "assert.h"
  51 #include "fatal.h"
  52 #include "network.h"
  53
  54 /* used for npri */
  55 #ifdef __sgi
  56 #include <sys/schedctl.h>
  57 #include <sys/sysmp.h>
  58 #endif
  59
  60 /******************************************************************
  61  *
  62  *             T R A J E C T O R Y   S T U F F
  63  *
  64  ******************************************************************/
  65
  66 /* Globals for trajectory input */
  67 real         tbegin = -1;
  68 real         tend   = -1;
  69 real         tdelta = -1;
  70 real         timefactor = NOTSET;
  71 char         *timelabel = NULL;
  72 static char *timestr[] = { NULL, "fs", "ps", "ns", "us", "ms", "s",
  73                            "m",              "h",                NULL };
  74 real timefactors[]     = { 0,    1e3,  1,    1e-3, 1e-6, 1e-9, 1e-12,
  75                            (1.0/60.0)*1e-12, (1.0/3600.0)*1e-12, 0 };
  76 static char *xvgrtimestr[] = { NULL, "fs", "ps", "ns", "\\8m\\4s", "ms", "s",
  77                                "m", "h", NULL };
  78 static bool  bView=FALSE;
  79 static unsigned long uFlags=0;
  80 static char  *program=NULL;
  81
  82 #define FF(arg) ((uFlags & arg)==arg)
  83
  84 char *ShortProgram(void)
  85 {
  86   char *pr;
  87
  88   if (program) {
  89     if ((pr=strrchr(program,'/')) != NULL)
  90       return pr+1;
  91     else
  92       return program;
  93   }
  94   else
  95     return "GROMACS";
  96 }
  97
  98 char *Program(void)
  99 {
 100   if (program)
 101     return program;
 102   else
 103     return "GROMACS";
 104 }
 105
 106 void set_program_name(char *argvzero)
 107 {
 108   /* When you run a dynamically linked program before installing
 109    * it, libtool uses wrapper scripts and prefixes the name with "lt-".
 110    * Until libtool is fixed to set argv[0] right, rip away the prefix:
 111    */
 112   if(program==NULL) {
 113     if(strlen(argvzero)>3 && !strncmp(argvzero,"lt-",3))
 114       program = strdup(argvzero+3);
 115     else
 116       program = strdup(argvzero);
 117   }
 118 }
 119
 120 /****************************************************************
 121  *
 122  *            E X P O R T E D   F U N C T I O N S
 123  *
 124  ****************************************************************/
 125
 126 bool bRmod(double a,double b)
 127 {
 128   int iq;
 129   double tol;
 130
 131   tol = 5*GMX_REAL_EPS;
 132
 133   iq = ((1.0+tol)*a)/b;
 134
 135   if (fabs(a-b*iq) <= tol*fabs(a))
 136     return TRUE;
 137   else
 138     return FALSE;
 139 }
 140
 141 int check_times2(real t,real t0,real tp, real tpp)
 142 {
 143   int  r;
 144   real margin;
 145
 146   if (t-tp>0 && tp-tpp>0)
 147     margin = 0.1*min(t-tp,tp-tpp);
 148   else
 149     margin = 0;
 150
 151   r=-1;
 152   if ((((tbegin >= 0.0) && (t >= tbegin)) || (tbegin == -1.0)) &&
 153       (((tend   >= 0.0) && (t <= tend+margin))   || (tend   == -1.0))) {
 154     if (tdelta > 0 && !bRmod(t-t0,tdelta))
 155       r = -1;
 156     else
 157       r = 0;
 158   }
 159   else if ((tend != -1.0) && (t>=tend))
 160     r = 1;
 161   if (debug) fprintf(debug,"t=%g, t0=%g, b=%g, e=%g, dt=%g: r=%d\n",
 162                      t,t0,tbegin,tend,tdelta,r);
 163   return r;
 164 }
 165
 166 int check_times(real t)
 167 {
 168   return check_times2(t,t,t,t);
 169 }
 170
 171 char *time_unit(void)
 172 {
 173   return timestr[0];
 174 }
 175
 176 char *time_label(void)
 177 {
 178   static char label[20];
 179
 180   sprintf(label,"Time (%s)",timestr[0] ? timestr[0] : "ps");
 181
 182   return label;
 183 }
 184
 185 char *xvgr_tlabel(void)
 186 {
 187   static char label[20];
 188
 189   sprintf(label,"Time (%s)",
 190           nenum(timestr) ? xvgrtimestr[nenum(timestr)] : "ps");
 191
 192   return label;
 193 }
 194
 195 static void init_time_factor()
 196 {
 197   if (timefactor == NOTSET)
 198     timefactor = timefactors[nenum(timestr)];
 199 }
 200
 201 real time_factor(void)
 202 {
 203   init_time_factor();
 204
 205   return timefactor;
 206 }
 207
 208 real convert_time(real time)
 209 {
 210   init_time_factor();
 211
 212   return (time*timefactor);
 213 }
 214
 215
 216 void convert_times(int n, real *time)
 217 {
 218   int i;
 219
 220   init_time_factor();
 221
 222   if (timefactor!=1)
 223     for(i=0; i<n; i++)
 224       time[i] *= timefactor;
 225 }
 226
 227 void default_time(void)
 228 {
 229   timestr[0] = timestr[1];
 230   timefactor = timefactors[1];
 231   xvgrtimestr[0] = xvgrtimestr[1];
 232 }
 233
 234 static void set_default_time_unit(char *select)
 235 {
 236   int i,j;
 237
 238   i=1;
 239   while(timestr[i] && strcmp(timestr[i], select)!=0)
 240     i++;
 241   if (strcmp(timestr[i], select)==0) {
 242     timestr[0] = timestr[i];
 243     timefactors[0] = timefactors[i];
 244     xvgrtimestr[0] = xvgrtimestr[i];
 245     for(j=i; j>1; j--) {
 246       timestr[j]=timestr[j-1];
 247       timefactors[j]=timefactors[j-1];
 248       xvgrtimestr[j]=xvgrtimestr[j-1];
 249     }
 250     timestr[1]=timestr[0];
 251     timefactors[1]=timefactors[0];
 252     xvgrtimestr[1]=xvgrtimestr[0];
 253   }
 254 }
 255
 256 /***** T O P O L O G Y   S T U F F ******/
 257
 258 t_topology *read_top(char *fn)
 259 {
 260   int        step,natoms;
 261   real       t,lambda;
 262   t_topology *top;
 263
 264   snew(top,1);
 265   read_tpx(fn,&step,&t,&lambda,NULL,NULL,
 266            &natoms,NULL,NULL,NULL,top);
 267
 268   return top;
 269 }
 270
 271 void mk_single_top(t_topology *top)
 272 {
 273   int i;
 274
 275   for(i=0; (i<ebNR); i++)
 276     top->blocks[i].multinr[0]=top->blocks[i].multinr[MAXNODES-1];
 277   for(i=0; (i<F_NRE); i++)
 278     top->idef.il[i].multinr[0]=top->idef.il[i].multinr[MAXNODES-1];
 279 }
 280
 281 /*************************************************************
 282  *
 283  *           P A R S I N G   S T U F F
 284  *
 285  *************************************************************/
 286
 287 static void usage(char *type,char *arg)
 288 {
 289   if (arg != NULL)
 290     fatal_error(0,"Expected %s argument for option %s\n",type,arg);
 291 }
 292
 293 int iscan(int argc,char *argv[],int *i)
 294 {
 295   int var;
 296
 297   if (argc > (*i)+1) {
 298     if (!sscanf(argv[++(*i)],"%d",&var))
 299       usage("an integer",argv[(*i)-1]);
 300   } else
 301     usage("an integer",argv[*i]);
 302
 303   return var;
 304 }
 305
 306 double dscan(int argc,char *argv[],int *i)
 307 {
 308   double var;
 309
 310   if (argc > (*i)+1) {
 311     if (!sscanf(argv[++(*i)],"%lf",&var))
 312       usage("a real",argv[(*i)-1]);
 313   } else
 314     usage("a real",argv[*i]);
 315
 316   return var;
 317 }
 318
 319 char *sscan(int argc,char *argv[],int *i)
 320 {
 321   if (argc > (*i)+1) {
 322     if ( (argv[(*i)+1][0]=='-') && (argc > (*i)+2) && (argv[(*i)+2][0]!='-') )
 323       fprintf(stderr,"Possible missing string argument for option %s\n\n",
 324               argv[*i]);
 325   } else
 326     usage("a string",argv[*i]);
 327
 328   return argv[++(*i)];
 329 }
 330
 331 int nenum(char *enumc[])
 332 {
 333   int i;
 334
 335   i=1;
 336   /* we *can* compare pointers directly here! */
 337   while(enumc[i] && enumc[0]!=enumc[i])
 338     i++;
 339
 340   return i;
 341 }
 342
 343 static void pdesc(char *desc)
 344 {
 345   char *ptr,*nptr;
 346
 347   ptr=desc;
 348   if ((int)strlen(ptr) < 70)
 349     fprintf(stderr,"\t%s\n",ptr);
 350   else {
 351     for(nptr=ptr+70; (nptr != ptr) && (!isspace(*nptr)); nptr--)
 352       ;
 353     if (nptr == ptr)
 354       fprintf(stderr,"\t%s\n",ptr);
 355     else {
 356       *nptr='\0';
 357       nptr++;
 358       fprintf(stderr,"\t%s\n",ptr);
 359       pdesc(nptr);
 360     }
 361   }
 362 }
 363
 364 bool bDoView(void)
 365 {
 366   return bView;
 367 }
 368
 369 static FILE *man_file(char *program,char *mantp)
 370 {
 371   FILE   *fp;
 372   char   buf[256],*pr;
 373
 374   if ((pr=strrchr(program,'/')) == NULL)
 375     pr=program;
 376   else
 377     pr+=1;
 378
 379   if (strcmp(mantp,"ascii") != 0)
 380     sprintf(buf,"%s.%s",pr,mantp);
 381   else
 382     sprintf(buf,"%s.txt",pr);
 383   fp = ffopen(buf,"w");
 384
 385   return fp;
 386 }
 387
 388 static int add_parg(int npargs,t_pargs **pa,t_pargs *pa_add)
 389 {
 390   srenew((*pa),npargs+1);
 391   memcpy(&((*pa)[npargs]),pa_add,sizeof(*pa_add));
 392
 393   return npargs+1;
 394 }
 395
 396 static char *mk_desc(t_pargs *pa, char *time_unit_str)
 397 {
 398   char *newdesc=NULL,*ndesc=NULL,*ptr=NULL;
 399   int  len,k;
 400
 401   /* First compute length for description */
 402   len = strlen(pa->desc)+1;
 403   if ((ptr = strstr(pa->desc,"HIDDEN")) != NULL)
 404     len += 4;
 405   if (pa->type == etENUM) {
 406     len += 10;
 407     for(k=1; (pa->u.c[k] != NULL); k++) {
 408       len += strlen(pa->u.c[k])+12;
 409     }
 410   }
 411   snew(newdesc,len);
 412
 413   /* add label for hidden options */
 414   if (is_hidden(pa))
 415     sprintf(newdesc,"[hidden] %s",ptr+6);
 416   else
 417     strcpy(newdesc,pa->desc);
 418
 419   /* change '%t' into time_unit */
 420 #define TUNITLABEL "%t"
 421 #define NTUNIT strlen(TUNITLABEL)
 422   if (pa->type == etTIME)
 423     while( (ptr=strstr(newdesc,TUNITLABEL)) != NULL ) {
 424       ptr[0]='\0';
 425       ptr+=NTUNIT;
 426       len+=strlen(time_unit_str)-NTUNIT;
 427       snew(ndesc,len);
 428       strcpy(ndesc,newdesc);
 429       strcat(ndesc,time_unit_str);
 430       strcat(ndesc,ptr);
 431       sfree(newdesc);
 432       newdesc=ndesc;
 433       ndesc=NULL;
 434     }
 435 #undef TUNITLABEL
 436 #undef NTUNIT
 437
 438   /* Add extra comment for enumerateds */
 439   if (pa->type == etENUM) {
 440     strcat(newdesc,": ");
 441     for(k=1; (pa->u.c[k] != NULL); k++) {
 442       strcat(newdesc,"[TT]");
 443       strcat(newdesc,pa->u.c[k]);
 444       strcat(newdesc,"[tt]");
 445       /* Print a comma everywhere but at the last one */
 446       if (pa->u.c[k+1] != NULL) {
 447         if (pa->u.c[k+2] == NULL)
 448           strcat(newdesc," or ");
 449         else
 450           strcat(newdesc,", ");
 451       }
 452     }
 453   }
 454   return newdesc;
 455 }
 456
 457 void parse_common_args(int *argc,char *argv[],unsigned long Flags,
 458                        int nfile,t_filenm fnm[],int npargs,t_pargs *pa,
 459                        int ndesc,char **desc,int nbugs,char **bugs)
 460 {
 461   static bool bHelp=FALSE,bHidden=FALSE,bQuiet=FALSE;
 462   static char *manstr[]      = { NULL, "no", "html", "tex", "nroff", "ascii", "completion", NULL };
 463   static char *not_nicestr[] = { NULL, "0", "4", "10", "19", NULL };
 464   static char *nicestr[]     = { NULL, "19", "10", "4", "0", NULL };
 465   static char *not_npristr[] = { NULL, "0", "128", "100", "200", "250", NULL };
 466   static char *npristr[]     = { NULL, "128", "250", "200", "100", "0", NULL };
 467   static int  nicelevel=0,mantp=0,npri=0;
 468   static bool bGUI=FALSE,bDebug=FALSE;
 469   static char *deffnm=NULL;
 470
 471   FILE *fp;
 472   bool bPrint,bExit;
 473   int  i,j,k,npall;
 474   char *ptr,*newdesc;
 475   char *envstr;
 476
 477   t_pargs *all_pa=NULL;
 478
 479   t_pargs motif_pa  = { "-X",    FALSE, etBOOL,  {&bGUI},
 480                        "Use dialog box GUI to edit command line options" };
 481   t_pargs npri_paX  = { "-npri", FALSE, etENUM,  {not_npristr},
 482                        "Set non blocking priority" };
 483   t_pargs npri_pa   = { "-npri", FALSE, etINT,   {&npri},
 484                        "HIDDEN Set non blocking priority (try 128)" };
 485   t_pargs nice_paX  = { "-nice", FALSE, etENUM,  {not_nicestr},
 486                        "Set the nicelevel" };
 487   t_pargs nice_pa   = { "-nice", FALSE, etINT,   {&nicelevel},
 488                        "Set the nicelevel" };
 489   t_pargs deffnm_pa = { "-deffnm", FALSE, etSTR, {&deffnm},
 490                        "Set the default filename for all file options" };
 491   t_pargs begin_pa  = { "-b",    FALSE, etTIME,  {&tbegin},
 492                        "First frame (%t) to read from trajectory" };
 493   t_pargs end_pa    = { "-e",    FALSE, etTIME,  {&tend},
 494                        "Last frame (%t) to read from trajectory" };
 495   t_pargs dt_pa     = { "-dt",   FALSE, etTIME,  {&tdelta},
 496                        "Only use frame when t MOD dt = first time (%t)" };
 497   t_pargs view_pa   = { "-w",    FALSE, etBOOL,  {&bView},
 498                        "View output xvg, xpm, eps and pdb files" };
 499   t_pargs time_pa   = { "-tu",   FALSE, etENUM,  {timestr},
 500                         "Time unit" };
 501
 502   t_pargs pca_pa[] = {
 503     { "-h",    FALSE, etBOOL, {&bHelp},
 504       "Print help info and quit" },
 505     { "-hidden", FALSE, etBOOL, {&bHidden},
 506       "HIDDENPrint hidden options" },
 507     { "-quiet",FALSE, etBOOL, {&bQuiet},
 508       "HIDDENDo not print help info" },
 509     { "-man",  FALSE, etENUM,  {manstr},
 510       "HIDDENWrite manual and quit" },
 511     { "-debug",FALSE, etBOOL, {&bDebug},
 512       "HIDDENWrite file with debug information" },
 513   };
 514 #define NPCA_PA asize(pca_pa)
 515
 516   debug_gmx();
 517   if (debug) {
 518     fprintf(debug,"PID=%d, argc = %d\n",gmx_node_id(),*argc);
 519     for(i=0; (i<*argc); i++)
 520       fprintf(debug,"PID=%d, argv[%d] = %s\n",gmx_node_id(),i,argv[i]);
 521   }
 522
 523   /* Check for double arguments */
 524   for (i=1; (i<*argc); i++) {
 525     if (argv[i] && (strlen(argv[i]) > 1) && (!isdigit(argv[i][1]))) {
 526       for (j=i+1; (j<*argc); j++) {
 527         if ( (argv[i][0]=='-') && (argv[j][0]=='-') &&
 528              (strcmp(argv[i],argv[j])==0) ) {
 529           if (FF(PCA_NOEXIT_ON_ARGS))
 530             fprintf(stderr,"Double command line argument %s\n",argv[i]);
 531           else
 532             fatal_error(0,"Double command line argument %s\n",argv[i]);
 533         }
 534       }
 535     }
 536   }
 537   debug_gmx();
 538
 539   /* Handle the flags argument, which is a bit field
 540    * The FF macro returns whether or not the bit is set
 541    */
 542   uFlags        = Flags;
 543   bPrint        = !FF(PCA_SILENT);
 544
 545   /* Check whether we should have GUI or not */
 546 #ifdef HAVE_MOTIF
 547   bGUI = (getenv("GMXMOTIF") != NULL);
 548   for(i=1; (i<*argc); i++) {
 549     if (strcmp(argv[i],"-X") == 0)
 550       bGUI = TRUE;
 551     else if (strcmp(argv[i],"-noX") == 0)
 552       bGUI = FALSE;
 553   }
 554   if (bGUI)
 555     bQuiet = TRUE;
 556 #else
 557   bGUI = FALSE;
 558 #endif
 559
 560   set_program_name(argv[0]);
 561
 562   /* Check ALL the flags ... */
 563   snew(all_pa,NPCA_PA+npargs);
 564   for(i=npall=0; (i<NPCA_PA); i++)
 565     npall = add_parg(npall,&(all_pa),&(pca_pa[i]));
 566
 567   /* Motif options */
 568   npall = add_parg(npall,&(all_pa),&motif_pa);
 569
 570 #ifdef __sgi
 571   envstr = getenv("GMXNPRIALL");
 572   if (envstr)
 573     npri=atoi(envstr);
 574   if (FF(PCA_BE_NICE)) {
 575     envstr = getenv("GMXNPRI");
 576     if (envstr)
 577       npri=atoi(envstr);
 578   }
 579   if (bGUI) {
 580     if (npri)
 581       npri_paX.u.c = npristr;
 582     npall = add_parg(npall,&(all_pa),&npri_paX);
 583   }
 584   else
 585     npall = add_parg(npall,&(all_pa),&npri_pa);
 586 #endif
 587
 588   if (bGUI) {
 589     /* Automatic nice or scheduling options */
 590     if (FF(PCA_BE_NICE))
 591       nice_paX.u.c = nicestr;
 592     npall = add_parg(npall,&(all_pa),&nice_paX);
 593   }
 594   else {
 595     if (FF(PCA_BE_NICE))
 596       nicelevel=19;
 597     npall = add_parg(npall,&(all_pa),&nice_pa);
 598   }
 599
 600   if (FF(PCA_CAN_SET_DEFFNM))
 601     npall = add_parg(npall,&(all_pa),&deffnm_pa);
 602   if (FF(PCA_CAN_BEGIN))
 603     npall = add_parg(npall,&(all_pa),&begin_pa);
 604   if (FF(PCA_CAN_END))
 605     npall = add_parg(npall,&(all_pa),&end_pa);
 606   if (FF(PCA_CAN_DT))
 607     npall = add_parg(npall,&(all_pa),&dt_pa);
 608   if (FF(PCA_TIME_UNIT)) {
 609     envstr = getenv("GMXTIMEUNIT");
 610     if ( envstr == NULL )
 611       envstr="ps";
 612     set_default_time_unit(envstr);
 613     npall = add_parg(npall,&(all_pa),&time_pa);
 614   } else
 615     set_default_time_unit("ps");
 616   if (FF(PCA_CAN_VIEW))
 617     npall = add_parg(npall,&(all_pa),&view_pa);
 618
 619   /* Now append the program specific arguments */
 620   for(i=0; (i<npargs); i++)
 621     npall = add_parg(npall,&(all_pa),&(pa[i]));
 622
 623   /* set etENUM options to default */
 624   for(i=0; (i<npall); i++)
 625     if (all_pa[i].type==etENUM)
 626       all_pa[i].u.c[0]=all_pa[i].u.c[1];
 627
 628   /* Now parse all the command-line options */
 629   get_pargs(argc,argv,npall,all_pa,FF(PCA_KEEP_ARGS));
 630
 631   if (FF(PCA_CAN_SET_DEFFNM) && (deffnm!=NULL))
 632     set_default_file_name(deffnm);
 633
 634   /* Parse the file args */
 635   parse_file_args(argc,argv,nfile,fnm,FF(PCA_KEEP_ARGS));
 636
 637   /* Open the debug file */
 638   if (bDebug) {
 639     char buf[256];
 640
 641     if (gmx_node_num() > 1)
 642       sprintf(buf,"%s%d.log",ShortProgram(),gmx_node_id());
 643     else
 644       sprintf(buf,"%s.log",ShortProgram());
 645
 646     init_debug(buf);
 647     fprintf(debug,"%s (this file) opened in file %s, line %d\n",
 648             buf,__FILE__,__LINE__);
 649   }
 650
 651   /* Now we have parsed the command line arguments. If the user wants it
 652    * we can now plop up a GUI dialog box to edit options.
 653    */
 654   if (bGUI) {
 655 #ifdef HAVE_MOTIF
 656     gmx_gui(argc,argv,nfile,fnm,npall,all_pa,ndesc,desc,nbugs,bugs);
 657 #else
 658     fatal_error(0,"GROMACS compiled without MOTIF support - can't use X interface");
 659 #endif
 660   }
 661
 662   /* Now copy the results back... */
 663   for(i=0,k=npall-npargs; (i<npargs); i++,k++)
 664     memcpy(&(pa[i]),&(all_pa[k]),(size_t)sizeof(pa[i]));
 665
 666   for(i=0; (i<npall); i++)
 667     all_pa[i].desc = mk_desc(&(all_pa[i]), time_unit() );
 668
 669   bExit = bHelp || (strcmp(manstr[0],"no") != 0);
 670
 671 #if (defined __sgi && USE_SGI_FPE)
 672   doexceptions();
 673 #endif
 674
 675   /* Set the nice level */
 676 #ifdef __sgi
 677   if (bGUI)
 678     if (npri)
 679       sscanf(npristr[0],"%d",&npri);
 680     else
 681       sscanf(not_npristr[0],"%d",&npri);
 682   if (npri != 0 && !bExit) {
 683     (void) schedctl(MPTS_RTPRI,0,npri);
 684   }
 685   else
 686 #endif
 687
 688 #ifdef HAVE_UNISTD_H
 689     if (bGUI) {
 690       if (FF(PCA_BE_NICE))
 691         sscanf(nicestr[0],"%d",&nicelevel);
 692       else
 693         sscanf(not_nicestr[0],"%d",&nicelevel);
 694     }
 695   if (nicelevel != 0 && !bExit)
 696     nice(nicelevel);
 697 #endif
 698
 699   if (!(FF(PCA_QUIET) || bQuiet )) {
 700     if (bHelp)
 701       write_man(stderr,"help",program,ndesc,desc,nfile,fnm,npall,all_pa,
 702                 nbugs,bugs,bHidden);
 703     else if (bPrint) {
 704       pr_fns(stderr,nfile,fnm);
 705       print_pargs(stderr,npall,all_pa);
 706     }
 707   }
 708
 709   if (strcmp(manstr[0],"no") != 0) {
 710     if(!strcmp(manstr[0],"completion")) {
 711       /* one file each for csh, bash and zsh if we do completions */
 712       fp=man_file(program,"completion-zsh");
 713       write_man(fp,"completion-zsh",program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
 714       fclose(fp);
 715       fp=man_file(program,"completion-bash");
 716       write_man(fp,"completion-bash",program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
 717       fclose(fp);
 718       fp=man_file(program,"completion-csh");
 719       write_man(fp,"completion-csh",program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
 720       fclose(fp);
 721     } else {
 722       fp=man_file(program,manstr[0]);
 723       write_man(fp,manstr[0],program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
 724       fclose(fp);
 725     }
 726   }
 727
 728   /* convert time options, must be done after printing! */
 729   init_time_factor();
 730   for(i=0; i<npall; i++) {
 731     if ((all_pa[i].type == etTIME) && (*all_pa[i].u.r >= 0)) {
 732       *all_pa[i].u.r /= timefactor;
 733     }
 734   }
 735
 736   /* clear memory */
 737   for(i=0; i<npall; i++)
 738     sfree(all_pa[i].desc);
 739   sfree(all_pa);
 740
 741   if (!FF(PCA_NOEXIT_ON_ARGS)) {
 742     if (*argc > 1) {
 743       for(i=1; (i<*argc); i++)
 744         fprintf(stderr,"Unknown argument: %s\n",argv[i]);
 745       fatal_error(0,"Program %s halted",Program());
 746     }
 747   }
 748   if (bExit) {
 749 #ifdef USE_MPI
 750     if (gmx_parallel)
 751       gmx_abort(gmx_node_id(),gmx_node_num(),0);
 752 #endif
 753     exit(0);
 754   }
 755 }
 756