sys/objects/options.c

/* Define Feature test macros to make sure atoll is available (SVr4, POSIX.1-2001, 4.3BSD, C99), not in (C89 and POSIX.1-1996) */
#define PETSC_DESIRE_FEATURE_TEST_MACROS

/*
   These routines simplify the use of command line, file options, etc., and are used to manipulate the options database.
   This provides the low-level interface, the high level interface is in aoptions.c

   Some routines use regular malloc and free because it cannot know  what malloc is requested with the
   options database until it has already processed the input.
*/

#include <petscsys.h>        /*I  "petscsys.h"   I*/
#include <ctype.h>
#if defined(PETSC_HAVE_STDLIB_H)
#include <stdlib.h>
#endif
#if defined(PETSC_HAVE_MALLOC_H)
#include <malloc.h>
#endif
#if defined(PETSC_HAVE_SYS_PARAM_H)
#include <sys/param.h>
#endif
#if defined(PETSC_HAVE_YAML)
#include <yaml.h>
#endif

/*
    This table holds all the options set by the user. For simplicity, we use a static size database
*/
#define MAXOPTIONS 512
#define MAXALIASES 25
#define MAXOPTIONSMONITORS 5
#define MAXPREFIXES 25

typedef struct {
  int            N,argc,Naliases;
  char           **args,*names[MAXOPTIONS],*values[MAXOPTIONS];
  char           *aliases1[MAXALIASES],*aliases2[MAXALIASES];
  PetscBool      used[MAXOPTIONS];
  PetscBool      namegiven;
  char           programname[PETSC_MAX_PATH_LEN]; /* HP includes entire path in name */

  /* --------User (or default) routines (most return -1 on error) --------*/
  PetscErrorCode (*monitor[MAXOPTIONSMONITORS])(const char[], const char[], void*); /* returns control to user after */
  PetscErrorCode (*monitordestroy[MAXOPTIONSMONITORS])(void**);         /* */
  void           *monitorcontext[MAXOPTIONSMONITORS];                  /* to pass arbitrary user data into monitor */
  PetscInt       numbermonitors;                                       /* to, for instance, detect options being set */

  /* Prefixes */
  PetscInt prefixind,prefixstack[MAXPREFIXES];
  char prefix[2048];
} PetscOptionsTable;


static PetscOptionsTable      *options = 0;
extern PetscOptionsObjectType PetscOptionsObject;

/*
    Options events monitor
*/
#define PetscOptionsMonitor(name,value)                                     \
        { PetscErrorCode _ierr; PetscInt _i,_im = options->numbermonitors; \
          for (_i=0; _i<_im; _i++) {\
            _ierr = (*options->monitor[_i])(name, value, options->monitorcontext[_i]);CHKERRQ(_ierr); \
	  } \
	}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsStringToInt"
/*
   PetscOptionsStringToInt - Converts a string to an integer value. Handles special cases such as "default" and "decide"
*/
PetscErrorCode  PetscOptionsStringToInt(const char name[],PetscInt *a)
{
  PetscErrorCode ierr;
  size_t         i,len;
  PetscBool      decide,tdefault,mouse;

  PetscFunctionBegin;
  ierr = PetscStrlen(name,&len);CHKERRQ(ierr);
  if (!len) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"character string of length zero has no numerical value");

  ierr = PetscStrcasecmp(name,"PETSC_DEFAULT",&tdefault);CHKERRQ(ierr);
  if (!tdefault) {
    ierr = PetscStrcasecmp(name,"DEFAULT",&tdefault);CHKERRQ(ierr);
  }
  ierr = PetscStrcasecmp(name,"PETSC_DECIDE",&decide);CHKERRQ(ierr);
  if (!decide) {
    ierr = PetscStrcasecmp(name,"DECIDE",&decide);CHKERRQ(ierr);
  }
  ierr = PetscStrcasecmp(name,"mouse",&mouse);CHKERRQ(ierr);

  if (tdefault) {
    *a = PETSC_DEFAULT;
  } else if (decide) {
    *a = PETSC_DECIDE;
  } else if (mouse) {
    *a = -1;
  } else {
    if (name[0] != '+' && name[0] != '-' && name[0] < '0' && name[0] > '9') {
      SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Input string %s has no integer value (do not include . in it)",name);
    }
    for (i=1; i<len; i++) {
      if (name[i] < '0' || name[i] > '9') {
        SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Input string %s has no integer value (do not include . in it)",name);
      }
    }

#if defined(PETSC_USE_64BIT_INDICES) && defined(PETSC_HAVE_ATOLL)
    *a = atoll(name);
#else
    *a = (PetscInt)atoi(name);
#endif
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsStringToReal"
/*
   Converts a string to PetscReal value. Handles special cases like "default" and "decide"
*/
PetscErrorCode  PetscOptionsStringToReal(const char name[],PetscReal *a)
{
  PetscErrorCode ierr;
  size_t         len;
  PetscBool      decide,tdefault;

  PetscFunctionBegin;
  ierr = PetscStrlen(name,&len);CHKERRQ(ierr);
  if (!len) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"character string of length zero has no numerical value");

  ierr = PetscStrcasecmp(name,"PETSC_DEFAULT",&tdefault);CHKERRQ(ierr);
  if (!tdefault) {
    ierr = PetscStrcasecmp(name,"DEFAULT",&tdefault);CHKERRQ(ierr);
  }
  ierr = PetscStrcasecmp(name,"PETSC_DECIDE",&decide);CHKERRQ(ierr);
  if (!decide) {
    ierr = PetscStrcasecmp(name,"DECIDE",&decide);CHKERRQ(ierr);
  }

  if (tdefault) {
    *a = PETSC_DEFAULT;
  } else if (decide) {
    *a = PETSC_DECIDE;
  } else {
    if (name[0] != '+' && name[0] != '-' && name[0] != '.' && name[0] < '0' && name[0] > '9') {
      SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Input string %s has no numeric value ",name);
    }
    *a  = atof(name);
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsStringToBool"
/*
   PetscOptionsStringToBool - Converts string to PetscBool , handles cases like "yes", "no", "true", "false", "0", "1"
*/
PetscErrorCode  PetscOptionsStringToBool(const char value[], PetscBool  *a)
{
  PetscBool      istrue, isfalse;
  size_t         len;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscStrlen(value, &len);CHKERRQ(ierr);
  if (!len) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG, "Character string of length zero has no logical value");
  ierr = PetscStrcasecmp(value,"TRUE",&istrue);CHKERRQ(ierr);
  if (istrue) {*a = PETSC_TRUE; PetscFunctionReturn(0);}
  ierr = PetscStrcasecmp(value,"YES",&istrue);CHKERRQ(ierr);
  if (istrue) {*a = PETSC_TRUE; PetscFunctionReturn(0);}
  ierr = PetscStrcasecmp(value,"1",&istrue);CHKERRQ(ierr);
  if (istrue) {*a = PETSC_TRUE; PetscFunctionReturn(0);}
  ierr = PetscStrcasecmp(value,"on",&istrue);CHKERRQ(ierr);
  if (istrue) {*a = PETSC_TRUE; PetscFunctionReturn(0);}
  ierr = PetscStrcasecmp(value,"FALSE",&isfalse);CHKERRQ(ierr);
  if (isfalse) {*a = PETSC_FALSE; PetscFunctionReturn(0);}
  ierr = PetscStrcasecmp(value,"NO",&isfalse);CHKERRQ(ierr);
  if (isfalse) {*a = PETSC_FALSE; PetscFunctionReturn(0);}
  ierr = PetscStrcasecmp(value,"0",&isfalse);CHKERRQ(ierr);
  if (isfalse) {*a = PETSC_FALSE; PetscFunctionReturn(0);}
  ierr = PetscStrcasecmp(value,"off",&isfalse);CHKERRQ(ierr);
  if (isfalse) {*a = PETSC_FALSE; PetscFunctionReturn(0);}
  SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG, "Unknown logical value: %s", value);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscGetProgramName"
/*@C
    PetscGetProgramName - Gets the name of the running program.

    Not Collective

    Input Parameter:
.   len - length of the string name

    Output Parameter:
.   name - the name of the running program

   Level: advanced

    Notes:
    The name of the program is copied into the user-provided character
    array of length len.  On some machines the program name includes
    its entire path, so one should generally set len >= PETSC_MAX_PATH_LEN.
@*/
PetscErrorCode  PetscGetProgramName(char name[],size_t len)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (!options) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call PetscInitialize() first");
  if (!options->namegiven) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Unable to determine program name");
  ierr = PetscStrncpy(name,options->programname,len);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscSetProgramName"
PetscErrorCode  PetscSetProgramName(const char name[])
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  options->namegiven = PETSC_TRUE;
  ierr  = PetscStrncpy(options->programname,name,PETSC_MAX_PATH_LEN);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsValidKey"
/*@
    PetscOptionsValidKey - PETSc Options database keys must begin with a - followed by a letter.

   Input Parameter:
.    in_str - string to check if valid

   Output Parameter:
.    key - PETSC_TRUE if a valid key

  Level: intermediate

@*/
PetscErrorCode  PetscOptionsValidKey(const char in_str[],PetscBool  *key)
{
  PetscFunctionBegin;
  *key = PETSC_FALSE;
  if (!in_str) PetscFunctionReturn(0);
  if (in_str[0] != '-') PetscFunctionReturn(0);
  if (!(isalpha(in_str[1]))) PetscFunctionReturn(0);
  if ((!strncmp(in_str+1,"inf",3) || !strncmp(in_str+1,"INF",3)) && !(in_str[4] == '_' || isalnum(in_str[4]))) PetscFunctionReturn(0);
  *key = PETSC_TRUE;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsInsertString"
/*@C
     PetscOptionsInsertString - Inserts options into the database from a string

     Not collective: but only processes that call this routine will set the options
                     included in the string

  Input Parameter:
.   in_str - string that contains options separated by blanks


  Level: intermediate

  Contributed by Boyana Norris

.seealso: PetscOptionsSetValue(), PetscOptionsView(), PetscOptionsHasName(), PetscOptionsGetInt(),
          PetscOptionsGetReal(), PetscOptionsGetString(), PetscOptionsGetIntArray(), PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList(), PetscOptionsInsertFile()

@*/
PetscErrorCode  PetscOptionsInsertString(const char in_str[])
{
  char           *first,*second;
  PetscErrorCode ierr;
  PetscToken     token;
  PetscBool      key,ispush,ispop;

  PetscFunctionBegin;
  ierr = PetscTokenCreate(in_str,' ',&token);CHKERRQ(ierr);
  ierr = PetscTokenFind(token,&first);CHKERRQ(ierr);
  while (first) {
    ierr = PetscStrcasecmp(first,"-prefix_push",&ispush);CHKERRQ(ierr);
    ierr = PetscStrcasecmp(first,"-prefix_pop",&ispop);CHKERRQ(ierr);
    ierr = PetscOptionsValidKey(first,&key);CHKERRQ(ierr);
    if (ispush) {
      ierr = PetscTokenFind(token,&second);CHKERRQ(ierr);
      ierr = PetscOptionsPrefixPush(second);CHKERRQ(ierr);
      ierr = PetscTokenFind(token,&first);CHKERRQ(ierr);
    } else if (ispop) {
      ierr = PetscOptionsPrefixPop();CHKERRQ(ierr);
      ierr = PetscTokenFind(token,&first);CHKERRQ(ierr);
    } else if (key) {
      ierr = PetscTokenFind(token,&second);CHKERRQ(ierr);
      ierr = PetscOptionsValidKey(second,&key);CHKERRQ(ierr);
      if (!key) {
        ierr = PetscOptionsSetValue(first,second);CHKERRQ(ierr);
        ierr = PetscTokenFind(token,&first);CHKERRQ(ierr);
      } else {
        ierr  = PetscOptionsSetValue(first,PETSC_NULL);CHKERRQ(ierr);
        first = second;
      }
    } else {
      ierr = PetscTokenFind(token,&first);CHKERRQ(ierr);
    }
  }
  ierr = PetscTokenDestroy(token);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*
    Returns a line (ended by a \n, \r or null character of any length. Result should be freed with free()
*/
static char *Petscgetline(FILE * f)
{
  size_t size = 0;
  size_t len  = 0;
  size_t last = 0;
  char * buf  = PETSC_NULL;

  if (feof(f)) return 0;
  do {
    size += 1024; /* BUFSIZ is defined as "the optimal read size for this platform" */
    buf = (char*)realloc((void *)buf,size); /* realloc(NULL,n) is the same as malloc(n) */
    /* Actually do the read. Note that fgets puts a terminal '\0' on the
    end of the string, so we make sure we overwrite this */
    if (!fgets(buf+len,size,f)) buf[len]=0;
    PetscStrlen(buf,&len);
    last = len - 1;
  } while (!feof(f) && buf[last] != '\n' && buf[last] != '\r');
  if (len) return buf;
  free(buf);
  return 0;
}


#undef __FUNCT__
#define __FUNCT__ "PetscOptionsInsertFile"
/*@C
     PetscOptionsInsertFile - Inserts options into the database from a file.

     Collective on MPI_Comm

  Input Parameter:
+   comm - the processes that will share the options (usually PETSC_COMM_WORLD)
.   file - name of file
-   require - if PETSC_TRUE will generate an error if the file does not exist


  Level: developer

.seealso: PetscOptionsSetValue(), PetscOptionsView(), PetscOptionsHasName(), PetscOptionsGetInt(),
          PetscOptionsGetReal(), PetscOptionsGetString(), PetscOptionsGetIntArray(), PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList()

@*/
PetscErrorCode  PetscOptionsInsertFile(MPI_Comm comm,const char file[],PetscBool require)
{
  char           *string,fname[PETSC_MAX_PATH_LEN],*first,*second,*third,*vstring = 0,*astring = 0;
  PetscErrorCode ierr;
  size_t         i,len;
  FILE           *fd;
  PetscToken     token;
  int            err;
  char           cmt[3]={'#','!','%'},*cmatch;
  PetscMPIInt    rank,cnt=0,acnt=0;

  PetscFunctionBegin;
  ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
  if (!rank) {
    /* Warning: assume a maximum size for all options in a string */
    ierr = PetscMalloc(128000*sizeof(char),&vstring);CHKERRQ(ierr);
    vstring[0] = 0;
    ierr = PetscMalloc(64000*sizeof(char),&astring);CHKERRQ(ierr);
    astring[0] = 0;
    cnt     = 0;
    acnt    = 0;

    ierr = PetscFixFilename(file,fname);CHKERRQ(ierr);
    fd   = fopen(fname,"r");
    if (fd) {
      /* the following line will not work when opening initial files (like .petscrc) since info is not yet set */
      ierr = PetscInfo1(0,"Opened options file %s\n",file);CHKERRQ(ierr);
      while ((string = Petscgetline(fd))) {
        /* eliminate comments from each line */
        for (i=0; i<3; i++){
          ierr = PetscStrchr(string,cmt[i],&cmatch);
          if (cmatch) *cmatch = 0;
        }
        ierr = PetscStrlen(string,&len);CHKERRQ(ierr);
        /* replace tabs, ^M, \n with " " */
        for (i=0; i<len; i++) {
          if (string[i] == '\t' || string[i] == '\r' || string[i] == '\n') {
            string[i] = ' ';
          }
        }
        ierr = PetscTokenCreate(string,' ',&token);CHKERRQ(ierr);
        free(string);
        ierr = PetscTokenFind(token,&first);CHKERRQ(ierr);
        if (!first) {
          goto destroy;
        } else if (!first[0]) { /* if first token is empty spaces, redo first token */
          ierr = PetscTokenFind(token,&first);CHKERRQ(ierr);
        }
        ierr = PetscTokenFind(token,&second);CHKERRQ(ierr);
        if (!first) {
          goto destroy;
        } else if (first[0] == '-') {
          /* warning: should be making sure we do not overfill vstring */
          ierr = PetscStrcat(vstring,first);CHKERRQ(ierr);
          ierr = PetscStrcat(vstring," ");CHKERRQ(ierr);
          if (second) {
            /* protect second with quotes in case it contains strings */
            ierr = PetscStrcat(vstring,"\"");CHKERRQ(ierr);
            ierr = PetscStrcat(vstring,second);CHKERRQ(ierr);
            ierr = PetscStrcat(vstring,"\"");CHKERRQ(ierr);
          }
          ierr = PetscStrcat(vstring," ");CHKERRQ(ierr);
        } else {
          PetscBool  match;

          ierr = PetscStrcasecmp(first,"alias",&match);CHKERRQ(ierr);
          if (match) {
            ierr = PetscTokenFind(token,&third);CHKERRQ(ierr);
            if (!third) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Error in options file:alias missing (%s)",second);
            ierr = PetscStrcat(astring,second);CHKERRQ(ierr);
            ierr = PetscStrcat(astring," ");CHKERRQ(ierr);
            ierr = PetscStrcat(astring,third);CHKERRQ(ierr);
            ierr = PetscStrcat(astring," ");CHKERRQ(ierr);
          } else {
            SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Unknown statement in options file: (%s)",string);
          }
        }
        destroy:
        ierr = PetscTokenDestroy(token);CHKERRQ(ierr);
      }
      err = fclose(fd);
      if (err) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SYS,"fclose() failed on file");
      ierr = PetscStrlen(astring,&len);CHKERRQ(ierr);
      acnt = PetscMPIIntCast(len);CHKERRQ(ierr);
      ierr = PetscStrlen(vstring,&len);CHKERRQ(ierr);
      cnt  = PetscMPIIntCast(len);CHKERRQ(ierr);
    } else if (require) {
      SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Unable to open Options File %s",fname);
    }
  }

  ierr = MPI_Bcast(&acnt,1,MPI_INT,0,comm);CHKERRQ(ierr);
  if (acnt) {
    PetscToken token;
    char       *first,*second;

    if (rank) {
      ierr = PetscMalloc((acnt+1)*sizeof(char),&astring);CHKERRQ(ierr);
    }
    ierr = MPI_Bcast(astring,acnt,MPI_CHAR,0,comm);CHKERRQ(ierr);
    astring[acnt] = 0;
    ierr = PetscTokenCreate(astring,' ',&token);CHKERRQ(ierr);
    ierr = PetscTokenFind(token,&first);CHKERRQ(ierr);
    while (first) {
      ierr = PetscTokenFind(token,&second);CHKERRQ(ierr);
      ierr = PetscOptionsSetAlias(first,second);CHKERRQ(ierr);
      ierr = PetscTokenFind(token,&first);CHKERRQ(ierr);
    }
    ierr = PetscTokenDestroy(token);CHKERRQ(ierr);
  }

  ierr = MPI_Bcast(&cnt,1,MPI_INT,0,comm);CHKERRQ(ierr);
  if (cnt) {
    if (rank) {
      ierr = PetscMalloc((cnt+1)*sizeof(char),&vstring);CHKERRQ(ierr);
    }
    ierr = MPI_Bcast(vstring,cnt,MPI_CHAR,0,comm);CHKERRQ(ierr);
    vstring[cnt] = 0;
    ierr = PetscOptionsInsertString(vstring);CHKERRQ(ierr);
  }
  ierr = PetscFree(astring);CHKERRQ(ierr);
  ierr = PetscFree(vstring);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsInsertArgs_Private"
static PetscErrorCode PetscOptionsInsertArgs_Private(int argc,char *args[])
{
  PetscErrorCode ierr;
  int            left    = argc - 1;
  char           **eargs = args + 1;

  PetscFunctionBegin;
  while (left) {
    PetscBool  isoptions_file,isprefixpush,isprefixpop,isp4,tisp4,isp4yourname,isp4rmrank;
    ierr = PetscStrcasecmp(eargs[0],"-options_file",&isoptions_file);CHKERRQ(ierr);
    ierr = PetscStrcasecmp(eargs[0],"-prefix_push",&isprefixpush);CHKERRQ(ierr);
    ierr = PetscStrcasecmp(eargs[0],"-prefix_pop",&isprefixpop);CHKERRQ(ierr);
    ierr = PetscStrcasecmp(eargs[0],"-p4pg",&isp4);CHKERRQ(ierr);
    ierr = PetscStrcasecmp(eargs[0],"-p4yourname",&isp4yourname);CHKERRQ(ierr);
    ierr = PetscStrcasecmp(eargs[0],"-p4rmrank",&isp4rmrank);CHKERRQ(ierr);
    ierr = PetscStrcasecmp(eargs[0],"-p4wd",&tisp4);CHKERRQ(ierr);
    isp4 = (PetscBool) (isp4 || tisp4);
    ierr = PetscStrcasecmp(eargs[0],"-np",&tisp4);CHKERRQ(ierr);
    isp4 = (PetscBool) (isp4 || tisp4);
    ierr = PetscStrcasecmp(eargs[0],"-p4amslave",&tisp4);CHKERRQ(ierr);

    if (eargs[0][0] != '-') {
      eargs++; left--;
    } else if (isoptions_file) {
      if (left <= 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Missing filename for -options_file filename option");
      if (eargs[1][0] == '-') SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Missing filename for -options_file filename option");
      ierr = PetscOptionsInsertFile(PETSC_COMM_WORLD,eargs[1],PETSC_TRUE);CHKERRQ(ierr);
      eargs += 2; left -= 2;
    } else if (isprefixpush) {
      if (left <= 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Missing prefix for -prefix_push option");
      if (eargs[1][0] == '-') SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Missing prefix for -prefix_push option (prefixes cannot start with '-')");
      ierr = PetscOptionsPrefixPush(eargs[1]);CHKERRQ(ierr);
      eargs += 2; left -= 2;
    } else if (isprefixpop) {
      ierr = PetscOptionsPrefixPop();CHKERRQ(ierr);
      eargs++; left--;

      /*
       These are "bad" options that MPICH, etc put on the command line
       we strip them out here.
       */
    } else if (tisp4 || isp4rmrank) {
      eargs += 1; left -= 1;
    } else if (isp4 || isp4yourname) {
      eargs += 2; left -= 2;
    } else {
      PetscBool nextiskey = PETSC_FALSE;
      if (left >= 2) {ierr = PetscOptionsValidKey(eargs[1],&nextiskey);CHKERRQ(ierr);}
      if (left < 2 || nextiskey) {
        ierr = PetscOptionsSetValue(eargs[0],PETSC_NULL);CHKERRQ(ierr);
        eargs++; left--;
      } else {
        ierr = PetscOptionsSetValue(eargs[0],eargs[1]);CHKERRQ(ierr);
        eargs += 2; left -= 2;
      }
    }
  }
  PetscFunctionReturn(0);
}


#undef __FUNCT__
#define __FUNCT__ "PetscOptionsInsert"
/*@C
   PetscOptionsInsert - Inserts into the options database from the command line,
                   the environmental variable and a file.

   Input Parameters:
+  argc - count of number of command line arguments
.  args - the command line arguments
-  file - optional filename, defaults to ~username/.petscrc

   Note:
   Since PetscOptionsInsert() is automatically called by PetscInitialize(),
   the user does not typically need to call this routine. PetscOptionsInsert()
   can be called several times, adding additional entries into the database.

   Options Database Keys:
+   -options_monitor <optional filename> - print options names and values as they are set
.   -options_file <filename> - read options from a file

   Level: advanced

   Concepts: options database^adding

.seealso: PetscOptionsDestroy_Private(), PetscOptionsView(), PetscOptionsInsertString(), PetscOptionsInsertFile(),
          PetscInitialize()
@*/
PetscErrorCode  PetscOptionsInsert(int *argc,char ***args,const char file[])
{
  PetscErrorCode ierr;
  PetscMPIInt    rank;
  char           pfile[PETSC_MAX_PATH_LEN];
  PetscBool      flag = PETSC_FALSE;

  PetscFunctionBegin;
  if (!options) {
    fprintf(stderr, "Options have not been enabled.\nYou might have forgotten to call PetscInitialize().\n");
    MPI_Abort(MPI_COMM_WORLD, PETSC_ERR_SUP);
  }
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);

  options->argc     = (argc) ? *argc : 0;
  options->args     = (args) ? *args : PETSC_NULL;

  if (file && file[0]) {
    ierr = PetscOptionsInsertFile(PETSC_COMM_WORLD,file,PETSC_TRUE);CHKERRQ(ierr);
  }
  /*
     We want to be able to give -skip_petscrc on the command line, but need to parse it first.  Since the command line
     should take precedence, we insert it twice.  It would be sufficient to just scan for -skip_petscrc.
  */
  if (argc && args && *argc) {ierr = PetscOptionsInsertArgs_Private(*argc,*args);CHKERRQ(ierr);}
  ierr = PetscOptionsGetBool(PETSC_NULL,"-skip_petscrc",&flag,PETSC_NULL);CHKERRQ(ierr);
  if (!flag) {
    ierr = PetscGetHomeDirectory(pfile,PETSC_MAX_PATH_LEN-16);CHKERRQ(ierr);
    /* warning: assumes all processes have a home directory or none, but nothing in between */
    if (pfile[0]) {
      ierr = PetscStrcat(pfile,"/.petscrc");CHKERRQ(ierr);
      ierr = PetscOptionsInsertFile(PETSC_COMM_WORLD,pfile,PETSC_FALSE);CHKERRQ(ierr);
    }
    ierr = PetscOptionsInsertFile(PETSC_COMM_WORLD,".petscrc",PETSC_FALSE);CHKERRQ(ierr);
    ierr = PetscOptionsInsertFile(PETSC_COMM_WORLD,"petscrc",PETSC_FALSE);CHKERRQ(ierr);
  }

  /* insert environmental options */
  {
    char   *eoptions = 0;
    size_t len = 0;
    if (!rank) {
      eoptions = (char*)getenv("PETSC_OPTIONS");
      ierr     = PetscStrlen(eoptions,&len);CHKERRQ(ierr);
      ierr     = MPI_Bcast(&len,1,MPIU_SIZE_T,0,PETSC_COMM_WORLD);CHKERRQ(ierr);
    } else {
      ierr = MPI_Bcast(&len,1,MPIU_SIZE_T,0,PETSC_COMM_WORLD);CHKERRQ(ierr);
      if (len) {
        ierr = PetscMalloc((len+1)*sizeof(char*),&eoptions);CHKERRQ(ierr);
      }
    }
    if (len) {
      ierr = MPI_Bcast(eoptions,len,MPI_CHAR,0,PETSC_COMM_WORLD);CHKERRQ(ierr);
      if (rank) eoptions[len] = 0;
      ierr = PetscOptionsInsertString(eoptions);CHKERRQ(ierr);
      if (rank) {ierr = PetscFree(eoptions);CHKERRQ(ierr);}
    }
  }

#if defined(PETSC_HAVE_YAML)
  char yaml_file[PETSC_MAX_PATH_LEN];
  PetscBool yaml_flg = PETSC_FALSE;
  ierr = PetscOptionsGetString(PETSC_NULL,"-options_file_yaml",yaml_file,PETSC_MAX_PATH_LEN,&yaml_flg);CHKERRQ(ierr);
  if (yaml_flg) ierr = PetscOptionsInsertFile_YAML(PETSC_COMM_WORLD,yaml_file,PETSC_TRUE);CHKERRQ(ierr);
#endif

  /* insert command line options again because they take precedence over arguments in petscrc/environment */
  if (argc && args && *argc) {ierr = PetscOptionsInsertArgs_Private(*argc,*args);CHKERRQ(ierr);}

  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsView"
/*@C
   PetscOptionsView - Prints the options that have been loaded. This is
   useful for debugging purposes.

   Logically Collective on PetscViewer

   Input Parameter:
.  viewer - must be an PETSCVIEWERASCII viewer

   Options Database Key:
.  -optionstable - Activates PetscOptionsView() within PetscFinalize()

   Level: advanced

   Concepts: options database^printing

.seealso: PetscOptionsAllUsed()
@*/
PetscErrorCode  PetscOptionsView(PetscViewer viewer)
{
  PetscErrorCode ierr;
  PetscInt       i;
  PetscBool      isascii;

  PetscFunctionBegin;
  if (!viewer) viewer = PETSC_VIEWER_STDOUT_WORLD;
  ierr = PetscTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&isascii);CHKERRQ(ierr);
  if (!isascii) SETERRQ(((PetscObject)viewer)->comm,PETSC_ERR_SUP,"Only supports ASCII viewer");

  if (!options) {ierr = PetscOptionsInsert(0,0,0);CHKERRQ(ierr);}
  if (options->N) {
    ierr = PetscViewerASCIIPrintf(viewer,"#PETSc Option Table entries:\n");CHKERRQ(ierr);
  } else {
    ierr = PetscViewerASCIIPrintf(viewer,"#No PETSc Option Table entries\n");CHKERRQ(ierr);
  }
  for (i=0; i<options->N; i++) {
    if (options->values[i]) {
      ierr = PetscViewerASCIIPrintf(viewer,"-%s %s\n",options->names[i],options->values[i]);CHKERRQ(ierr);
    } else {
      ierr = PetscViewerASCIIPrintf(viewer,"-%s\n",options->names[i]);CHKERRQ(ierr);
    }
  }
  if (options->N) {
    ierr = PetscViewerASCIIPrintf(viewer,"#End of PETSc Option Table entries\n");CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsGetAll"
/*@C
   PetscOptionsGetAll - Lists all the options the program was run with in a single string.

   Not Collective

   Output Parameter:
.  copts - pointer where string pointer is stored

   Notes: the array and each entry in the array should be freed with PetscFree()

   Level: advanced

   Concepts: options database^listing

.seealso: PetscOptionsAllUsed(), PetscOptionsView()
@*/
PetscErrorCode  PetscOptionsGetAll(char *copts[])
{
  PetscErrorCode ierr;
  PetscInt       i;
  size_t         len = 1,lent;
  char           *coptions;

  PetscFunctionBegin;
  if (!options) {ierr = PetscOptionsInsert(0,0,0);CHKERRQ(ierr);}

  /* count the length of the required string */
  for (i=0; i<options->N; i++) {
    ierr = PetscStrlen(options->names[i],&lent);CHKERRQ(ierr);
    len += 2 + lent;
    if (options->values[i]) {
      ierr = PetscStrlen(options->values[i],&lent);CHKERRQ(ierr);
      len += 1 + lent;
    }
  }
  ierr = PetscMalloc(len*sizeof(char),&coptions);CHKERRQ(ierr);
  coptions[0] = 0;
  for (i=0; i<options->N; i++) {
    ierr = PetscStrcat(coptions,"-");CHKERRQ(ierr);
    ierr = PetscStrcat(coptions,options->names[i]);CHKERRQ(ierr);
    ierr = PetscStrcat(coptions," ");CHKERRQ(ierr);
    if (options->values[i]) {
      ierr = PetscStrcat(coptions,options->values[i]);CHKERRQ(ierr);
      ierr = PetscStrcat(coptions," ");CHKERRQ(ierr);
    }
  }
  *copts = coptions;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsPrefixPush"
/*@
   PetscOptionsPrefixPush - Designate a prefix to be used by all options insertions to follow.

   Not Collective, but prefix will only be applied on calling ranks

   Input Parameter:
.  prefix - The string to append to the existing prefix

   Options Database Keys:
 +   -prefix_push <some_prefix_> - push the given prefix
 -   -prefix_pop - pop the last prefix

   Notes:
   It is common to use this in conjunction with -options_file as in

 $ -prefix_push system1_ -options_file system1rc -prefix_pop -prefix_push system2_ -options_file system2rc -prefix_pop

   where the files no longer require all options to be prefixed with -system2_.

Level: advanced

.seealso: PetscOptionsPrefixPop()
@*/
PetscErrorCode  PetscOptionsPrefixPush(const char prefix[])
{
  PetscErrorCode ierr;
  size_t n;
  PetscInt start;
  char buf[2048];
  PetscBool  key;

  PetscFunctionBegin;
  PetscValidCharPointer(prefix,1);
  /* Want to check validity of the key using PetscOptionsValidKey(), which requires that the first character is a '-' */
  buf[0] = '-';
  ierr = PetscStrncpy(buf+1,prefix,sizeof buf - 1);
  buf[sizeof buf - 1] = 0;
  ierr = PetscOptionsValidKey(buf,&key);CHKERRQ(ierr);
  if (!key) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Given prefix \"%s\" not valid (the first character must be a letter, do not include leading '-')",prefix);

  if (!options) {ierr = PetscOptionsInsert(0,0,0);CHKERRQ(ierr);}
  if (options->prefixind >= MAXPREFIXES) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Maximum depth of prefix stack %d exceeded, recompile \n src/sys/objects/options.c with larger value for MAXPREFIXES",MAXPREFIXES);
  start = options->prefixind ? options->prefixstack[options->prefixind-1] : 0;
  ierr = PetscStrlen(prefix,&n);CHKERRQ(ierr);
  if (n+1 > sizeof(options->prefix)-start) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Maximum prefix length %d exceeded",sizeof(options->prefix));
  ierr = PetscMemcpy(options->prefix+start,prefix,n+1);CHKERRQ(ierr);
  options->prefixstack[options->prefixind++] = start+n;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsPrefixPop"
/*@
   PetscOptionsPrefixPop - Remove the latest options prefix, see PetscOptionsPrefixPush() for details

   Not  Collective, but prefix will only be popped on calling ranks

   Level: advanced

.seealso: PetscOptionsPrefixPush()
@*/
PetscErrorCode  PetscOptionsPrefixPop(void)
{
  PetscInt offset;

  PetscFunctionBegin;
  if (options->prefixind < 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"More prefixes popped than pushed");
  options->prefixind--;
  offset = options->prefixind ? options->prefixstack[options->prefixind-1] : 0;
  options->prefix[offset] = 0;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsClear"
/*@C
    PetscOptionsClear - Removes all options form the database leaving it empty.

   Level: developer

.seealso: PetscOptionsInsert()
@*/
PetscErrorCode  PetscOptionsClear(void)
{
  PetscInt i;

  PetscFunctionBegin;
  if (!options) PetscFunctionReturn(0);
  for (i=0; i<options->N; i++) {
    if (options->names[i])  free(options->names[i]);
    if (options->values[i]) free(options->values[i]);
  }
  for (i=0; i<options->Naliases; i++) {
    free(options->aliases1[i]);
    free(options->aliases2[i]);
  }
  options->prefix[0] = 0;
  options->prefixind = 0;
  options->N        = 0;
  options->Naliases = 0;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsDestroy"
/*@C
    PetscOptionsDestroy - Destroys the option database.

    Note:
    Since PetscOptionsDestroy() is called by PetscFinalize(), the user
    typically does not need to call this routine.

   Level: developer

.seealso: PetscOptionsInsert()
@*/
PetscErrorCode  PetscOptionsDestroy(void)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (!options) PetscFunctionReturn(0);
  ierr = PetscOptionsClear();CHKERRQ(ierr);
  free(options);
  options = 0;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsSetValue"
/*@C
   PetscOptionsSetValue - Sets an option name-value pair in the options
   database, overriding whatever is already present.

   Not collective, but setting values on certain processors could cause problems
   for parallel objects looking for options.

   Input Parameters:
+  name - name of option, this SHOULD have the - prepended
-  value - the option value (not used for all options)

   Level: intermediate

   Note:
   Only some options have values associated with them, such as
   -ksp_rtol tol.  Other options stand alone, such as -ksp_monitor.

  Concepts: options database^adding option

.seealso: PetscOptionsInsert()
@*/
PetscErrorCode  PetscOptionsSetValue(const char iname[],const char value[])
{
  size_t         len;
  PetscErrorCode ierr;
  PetscInt       N,n,i;
  char           **names;
  char           fullname[2048];
  const char     *name = iname;
  PetscBool      gt,match;

  PetscFunctionBegin;
  if (!options) {ierr = PetscOptionsInsert(0,0,0);CHKERRQ(ierr);}

  /* this is so that -h and -hel\p are equivalent (p4 does not like -help)*/
  ierr = PetscStrcasecmp(name,"-h",&match);CHKERRQ(ierr);
  if (match) name = "-help";

  name++; /* skip starting hyphen */
  if (options->prefixind > 0) {
    ierr = PetscStrncpy(fullname,options->prefix,sizeof fullname);CHKERRQ(ierr);
    ierr = PetscStrncat(fullname,name,sizeof fullname);CHKERRQ(ierr);
    name = fullname;
  }

  /* check against aliases */
  N = options->Naliases;
  for (i=0; i<N; i++) {
    ierr = PetscStrcasecmp(options->aliases1[i],name,&match);CHKERRQ(ierr);
    if (match) {
      name = options->aliases2[i];
      break;
    }
  }

  N     = options->N;
  n     = N;
  names = options->names;

  for (i=0; i<N; i++) {
    ierr = PetscStrcasecmp(names[i],name,&match);CHKERRQ(ierr);
    ierr  = PetscStrgrt(names[i],name,&gt);CHKERRQ(ierr);
    if (match) {
      if (options->values[i]) free(options->values[i]);
      ierr = PetscStrlen(value,&len);CHKERRQ(ierr);
      if (len) {
        options->values[i] = (char*)malloc((len+1)*sizeof(char));
        ierr = PetscStrcpy(options->values[i],value);CHKERRQ(ierr);
      } else { options->values[i] = 0;}
      PetscOptionsMonitor(name,value);
      PetscFunctionReturn(0);
    } else if (gt) {
      n = i;
      break;
    }
  }
  if (N >= MAXOPTIONS) {
    SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"No more room in option table, limit %d recompile \n src/sys/objects/options.c with larger value for MAXOPTIONS\n",MAXOPTIONS);
  }
  /* shift remaining values down 1 */
  for (i=N; i>n; i--) {
    options->names[i]  = options->names[i-1];
    options->values[i] = options->values[i-1];
    options->used[i]   = options->used[i-1];
  }
  /* insert new name and value */
  ierr = PetscStrlen(name,&len);CHKERRQ(ierr);
  options->names[n] = (char*)malloc((len+1)*sizeof(char));
  ierr = PetscStrcpy(options->names[n],name);CHKERRQ(ierr);
  ierr = PetscStrlen(value,&len);CHKERRQ(ierr);
  if (len) {
    options->values[n] = (char*)malloc((len+1)*sizeof(char));
    ierr = PetscStrcpy(options->values[n],value);CHKERRQ(ierr);
  } else {options->values[n] = 0;}
  options->used[n] = PETSC_FALSE;
  options->N++;
  PetscOptionsMonitor(name,value);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsClearValue"
/*@C
   PetscOptionsClearValue - Clears an option name-value pair in the options
   database, overriding whatever is already present.

   Not Collective, but setting values on certain processors could cause problems
   for parallel objects looking for options.

   Input Parameter:
.  name - name of option, this SHOULD have the - prepended

   Level: intermediate

   Concepts: options database^removing option
.seealso: PetscOptionsInsert()
@*/
PetscErrorCode  PetscOptionsClearValue(const char iname[])
{
  PetscErrorCode ierr;
  PetscInt       N,n,i;
  char           **names,*name=(char*)iname;
  PetscBool      gt,match;

  PetscFunctionBegin;
  if (name[0] != '-') SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Name must begin with -: Instead %s",name);
  if (!options) {ierr = PetscOptionsInsert(0,0,0);CHKERRQ(ierr);}

  name++;

  N     = options->N; n = 0;
  names = options->names;

  for (i=0; i<N; i++) {
    ierr  = PetscStrcasecmp(names[i],name,&match);CHKERRQ(ierr);
    ierr  = PetscStrgrt(names[i],name,&gt);CHKERRQ(ierr);
    if (match) {
      if (options->names[i])  free(options->names[i]);
      if (options->values[i]) free(options->values[i]);
      PetscOptionsMonitor(name,"");
      break;
    } else if (gt) {
      PetscFunctionReturn(0); /* it was not listed */
    }
    n++;
  }
  if (n == N) PetscFunctionReturn(0); /* it was not listed */

  /* shift remaining values down 1 */
  for (i=n; i<N-1; i++) {
    options->names[i]  = options->names[i+1];
    options->values[i] = options->values[i+1];
    options->used[i]   = options->used[i+1];
  }
  options->N--;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsSetAlias"
/*@C
   PetscOptionsSetAlias - Makes a key and alias for another key

   Not Collective, but setting values on certain processors could cause problems
   for parallel objects looking for options.

   Input Parameters:
+  inewname - the alias
-  ioldname - the name that alias will refer to

   Level: advanced

.seealso: PetscOptionsGetInt(), PetscOptionsGetReal(),OptionsHasName(),
           PetscOptionsGetString(), PetscOptionsGetIntArray(), PetscOptionsGetRealArray(),PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList()
@*/
PetscErrorCode  PetscOptionsSetAlias(const char inewname[],const char ioldname[])
{
  PetscErrorCode ierr;
  PetscInt       n = options->Naliases;
  size_t         len;
  char           *newname = (char *)inewname,*oldname = (char*)ioldname;

  PetscFunctionBegin;
  if (newname[0] != '-') SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"aliased must have -: Instead %s",newname);
  if (oldname[0] != '-') SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"aliasee must have -: Instead %s",oldname);
  if (n >= MAXALIASES) {
    SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_MEM,"You have defined to many PETSc options aliases, limit %d recompile \n  src/sys/objects/options.c with larger value for MAXALIASES",MAXALIASES);
  }

  newname++; oldname++;
  ierr = PetscStrlen(newname,&len);CHKERRQ(ierr);
  options->aliases1[n] = (char*)malloc((len+1)*sizeof(char));
  ierr = PetscStrcpy(options->aliases1[n],newname);CHKERRQ(ierr);
  ierr = PetscStrlen(oldname,&len);CHKERRQ(ierr);
  options->aliases2[n] = (char*)malloc((len+1)*sizeof(char));
  ierr = PetscStrcpy(options->aliases2[n],oldname);CHKERRQ(ierr);
  options->Naliases++;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsFindPair_Private"
static PetscErrorCode PetscOptionsFindPair_Private(const char pre[],const char name[],char *value[],PetscBool  *flg)
{
  PetscErrorCode ierr;
  PetscInt       i,N;
  size_t         len;
  char           **names,tmp[256];
  PetscBool      match;

  PetscFunctionBegin;
  if (!options) {ierr = PetscOptionsInsert(0,0,0);CHKERRQ(ierr);}
  N = options->N;
  names = options->names;

  if (name[0] != '-') SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Name must begin with -: Instead %s",name);

  /* append prefix to name */
  if (pre) {
    if (pre[0] == '-') SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Prefix should not begin with a -");
    ierr = PetscStrncpy(tmp,pre,256);CHKERRQ(ierr);
    ierr = PetscStrlen(tmp,&len);CHKERRQ(ierr);
    ierr = PetscStrncat(tmp,name+1,256-len-1);CHKERRQ(ierr);
  } else {
    ierr = PetscStrncpy(tmp,name+1,256);CHKERRQ(ierr);
  }

  /* slow search */
  *flg = PETSC_FALSE;
  for (i=0; i<N; i++) {
    ierr = PetscStrcasecmp(names[i],tmp,&match);CHKERRQ(ierr);
    if (match) {
       *value           = options->values[i];
       options->used[i] = PETSC_TRUE;
       *flg             = PETSC_TRUE;
       break;
     }
  }
  if (!*flg) {
    PetscInt j,cnt = 0,locs[16],loce[16];
    size_t   n;
    ierr = PetscStrlen(tmp,&n);CHKERRQ(ierr);
    /* determine the location and number of all _%d_ in the key */
    for (i=0; i< (PetscInt)n; i++) {
      if (tmp[i] == '_') {
        for (j=i+1; j< (PetscInt)n; j++) {
          if (tmp[j] >= '0' && tmp[j] <= '9') continue;
          if (tmp[j] == '_' && j > i+1) { /* found a number */
            locs[cnt]   = i+1;
            loce[cnt++] = j+1;
          }
          break;
        }
      }
    }
    if (cnt) {
      char tmp2[256];
      for (i=0; i<cnt; i++) {
        ierr = PetscStrcpy(tmp2,"-");CHKERRQ(ierr);
        ierr = PetscStrncat(tmp2,tmp,locs[i]);CHKERRQ(ierr);
        ierr = PetscStrcat(tmp2,tmp+loce[i]);CHKERRQ(ierr);
        ierr = PetscOptionsFindPair_Private(PETSC_NULL,tmp2,value,flg);CHKERRQ(ierr);
        if (*flg) break;
      }
    }
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsReject"
/*@C
   PetscOptionsReject - Generates an error if a certain option is given.

   Not Collective, but setting values on certain processors could cause problems
   for parallel objects looking for options.

   Input Parameters:
+  name - the option one is seeking
-  mess - error message (may be PETSC_NULL)

   Level: advanced

   Concepts: options database^rejecting option

.seealso: PetscOptionsGetInt(), PetscOptionsGetReal(),OptionsHasName(),
           PetscOptionsGetString(), PetscOptionsGetIntArray(), PetscOptionsGetRealArray(), PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList()
@*/
PetscErrorCode  PetscOptionsReject(const char name[],const char mess[])
{
  PetscErrorCode ierr;
  PetscBool      flag = PETSC_FALSE;

  PetscFunctionBegin;
  ierr = PetscOptionsHasName(PETSC_NULL,name,&flag);CHKERRQ(ierr);
  if (flag) {
    if (mess) {
      SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Program has disabled option: %s with %s",name,mess);
    } else {
      SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Program has disabled option: %s",name);
    }
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsHasName"
/*@C
   PetscOptionsHasName - Determines whether a certain option is given in the database. This returns true whether the option is a number, string or boolean, even
                      its value is set to false.

   Not Collective

   Input Parameters:
+  name - the option one is seeking
-  pre - string to prepend to the name or PETSC_NULL

   Output Parameters:
.  set - PETSC_TRUE if found else PETSC_FALSE.

   Level: beginner

   Concepts: options database^has option name

   Notes: Name cannot be simply -h

          In many cases you probably want to use PetscOptionsGetBool() instead of calling this, to allowing toggling values.

.seealso: PetscOptionsGetInt(), PetscOptionsGetReal(),
           PetscOptionsGetString(), PetscOptionsGetIntArray(), PetscOptionsGetRealArray(), PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList()
@*/
PetscErrorCode  PetscOptionsHasName(const char pre[],const char name[],PetscBool  *set)
{
  char           *value;
  PetscErrorCode ierr;
  PetscBool      flag;

  PetscFunctionBegin;
  ierr = PetscOptionsFindPair_Private(pre,name,&value,&flag);CHKERRQ(ierr);
  if (set) *set = flag;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsGetInt"
/*@C
   PetscOptionsGetInt - Gets the integer value for a particular option in the database.

   Not Collective

   Input Parameters:
+  pre - the string to prepend to the name or PETSC_NULL
-  name - the option one is seeking

   Output Parameter:
+  ivalue - the integer value to return
-  set - PETSC_TRUE if found, else PETSC_FALSE

   Level: beginner

   Concepts: options database^has int

.seealso: PetscOptionsGetReal(), PetscOptionsHasName(), PetscOptionsGetString(),
          PetscOptionsGetIntArray(), PetscOptionsGetRealArray(), PetscOptionsBool()
          PetscOptionsInt(), PetscOptionsString(), PetscOptionsReal(), PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList()
@*/
PetscErrorCode  PetscOptionsGetInt(const char pre[],const char name[],PetscInt *ivalue,PetscBool  *set)
{
  char           *value;
  PetscErrorCode ierr;
  PetscBool      flag;

  PetscFunctionBegin;
  PetscValidCharPointer(name,2);
  PetscValidIntPointer(ivalue,3);
  ierr = PetscOptionsFindPair_Private(pre,name,&value,&flag);CHKERRQ(ierr);
  if (flag) {
    if (!value) {if (set) *set = PETSC_FALSE;}
    else {
      if (set) *set = PETSC_TRUE;
      ierr = PetscOptionsStringToInt(value,ivalue);CHKERRQ(ierr);
    }
  } else {
    if (set) *set = PETSC_FALSE;
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsGetEList"
/*@C
     PetscOptionsGetEList - Puts a list of option values that a single one may be selected from

   Not Collective

   Input Parameters:
+  pre - the string to prepend to the name or PETSC_NULL
.  opt - option name
.  list - the possible choices
.  ntext - number of choices

   Output Parameter:
+  value - the index of the value to return (defaults to zero if the option name is given but choice is listed)
-  set - PETSC_TRUE if found, else PETSC_FALSE

   Level: intermediate

   See PetscOptionsList() for when the choices are given in a PetscFList()

   Concepts: options database^list

.seealso: PetscOptionsGetInt(), PetscOptionsGetReal(),
           PetscOptionsHasName(), PetscOptionsGetIntArray(), PetscOptionsGetRealArray(), PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList()
@*/
PetscErrorCode  PetscOptionsGetEList(const char pre[],const char opt[],const char *const*list,PetscInt ntext,PetscInt *value,PetscBool  *set)
{
  PetscErrorCode ierr;
  size_t         alen,len = 0;
  char           *svalue;
  PetscBool      aset,flg = PETSC_FALSE;
  PetscInt       i;

  PetscFunctionBegin;
  for ( i=0; i<ntext; i++) {
    ierr = PetscStrlen(list[i],&alen);CHKERRQ(ierr);
    if (alen > len) len = alen;
  }
  len += 5; /* a little extra space for user mistypes */
  ierr = PetscMalloc(len*sizeof(char),&svalue);CHKERRQ(ierr);
  ierr = PetscOptionsGetString(pre,opt,svalue,len,&aset);CHKERRQ(ierr);
  if (aset) {
    if (set) *set = PETSC_TRUE;
    for (i=0; i<ntext; i++) {
      ierr = PetscStrcasecmp(svalue,list[i],&flg);CHKERRQ(ierr);
      if (flg || !svalue[0]) {
        flg    = PETSC_TRUE;
        *value = i;
        break;
      }
    }
    if (!flg) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_USER,"Unknown option %s for -%s%s",svalue,pre?pre:"",opt+1);
  } else if (set) {
    *set = PETSC_FALSE;
  }
  ierr = PetscFree(svalue);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsGetEnum"
/*@C
   PetscOptionsGetEnum - Gets the enum value for a particular option in the database.

   Not Collective

   Input Parameters:
+  pre - option prefix or PETSC_NULL
.  opt - option name
.  list - array containing the list of choices, followed by the enum name, followed by the enum prefix, followed by a null
-  defaultv - the default (current) value

   Output Parameter:
+  value - the  value to return
-  set - PETSC_TRUE if found, else PETSC_FALSE

   Level: beginner

   Concepts: options database

   Notes: Must be between a PetscOptionsBegin() and a PetscOptionsEnd()

          list is usually something like PCASMTypes or some other predefined list of enum names

.seealso: PetscOptionsGetReal(), PetscOptionsHasName(), PetscOptionsGetString(), PetscOptionsGetInt(),
          PetscOptionsGetIntArray(), PetscOptionsGetRealArray(), PetscOptionsBool()
          PetscOptionsInt(), PetscOptionsString(), PetscOptionsReal(), PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList(), PetscOptionsGetEList(), PetscOptionsEnum()
@*/
PetscErrorCode  PetscOptionsGetEnum(const char pre[],const char opt[],const char *const*list,PetscEnum *value,PetscBool  *set)
{
  PetscErrorCode ierr;
  PetscInt       ntext = 0,tval;
  PetscBool      fset;

  PetscFunctionBegin;
  while (list[ntext++]) {
    if (ntext > 50) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"List argument appears to be wrong or have more than 50 entries");
  }
  if (ntext < 3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"List argument must have at least two entries: typename and type prefix");
  ntext -= 3;
  ierr = PetscOptionsGetEList(pre,opt,list,ntext,&tval,&fset);CHKERRQ(ierr);
  /* with PETSC_USE_64BIT_INDICES sizeof(PetscInt) != sizeof(PetscEnum) */
  if (fset) *value = (PetscEnum)tval;
  if (set) *set = fset;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsGetBool"
/*@C
   PetscOptionsGetBool - Gets the Logical (true or false) value for a particular
            option in the database.

   Not Collective

   Input Parameters:
+  pre - the string to prepend to the name or PETSC_NULL
-  name - the option one is seeking

   Output Parameter:
+  ivalue - the logical value to return
-  set - PETSC_TRUE  if found, else PETSC_FALSE

   Level: beginner

   Notes:
       TRUE, true, YES, yes, nostring, and 1 all translate to PETSC_TRUE
       FALSE, false, NO, no, and 0 all translate to PETSC_FALSE

       If the user does not supply the option (as either true or false) ivalue is NOT changed. Thus
     you NEED TO ALWAYS initialize the ivalue.

   Concepts: options database^has logical

.seealso: PetscOptionsGetReal(), PetscOptionsHasName(), PetscOptionsGetString(),
          PetscOptionsGetIntArray(), PetscOptionsGetRealArray(), PetscOptionsGetInt(), PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList()
@*/
PetscErrorCode  PetscOptionsGetBool(const char pre[],const char name[],PetscBool  *ivalue,PetscBool  *set)
{
  char           *value;
  PetscBool      flag;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidCharPointer(name,2);
  PetscValidIntPointer(ivalue,3);
  ierr = PetscOptionsFindPair_Private(pre,name,&value,&flag);CHKERRQ(ierr);
  if (flag) {
    if (set) *set = PETSC_TRUE;
    if (!value) {
      *ivalue = PETSC_TRUE;
    } else {
      ierr = PetscOptionsStringToBool(value, ivalue);CHKERRQ(ierr);
    }
  } else {
    if (set) *set = PETSC_FALSE;
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsGetBoolArray"
/*@C
   PetscOptionsGetBoolArray - Gets an array of Logical (true or false) values for a particular
   option in the database.  The values must be separated with commas with
   no intervening spaces.

   Not Collective

   Input Parameters:
+  pre - string to prepend to each name or PETSC_NULL
.  name - the option one is seeking
-  nmax - maximum number of values to retrieve

   Output Parameter:
+  dvalue - the integer values to return
.  nmax - actual number of values retreived
-  set - PETSC_TRUE if found, else PETSC_FALSE

   Level: beginner

   Concepts: options database^array of ints

   Notes:
       TRUE, true, YES, yes, nostring, and 1 all translate to PETSC_TRUE
       FALSE, false, NO, no, and 0 all translate to PETSC_FALSE

.seealso: PetscOptionsGetInt(), PetscOptionsHasName(),
           PetscOptionsGetString(), PetscOptionsGetRealArray(), PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList()
@*/
PetscErrorCode  PetscOptionsGetBoolArray(const char pre[],const char name[],PetscBool  dvalue[],PetscInt *nmax,PetscBool  *set)
{
  char           *value;
  PetscErrorCode ierr;
  PetscInt       n = 0;
  PetscBool      flag;
  PetscToken     token;

  PetscFunctionBegin;
  PetscValidCharPointer(name,2);
  PetscValidIntPointer(dvalue,3);
  ierr = PetscOptionsFindPair_Private(pre,name,&value,&flag);CHKERRQ(ierr);
  if (!flag)  {if (set) *set = PETSC_FALSE; *nmax = 0; PetscFunctionReturn(0);}
  if (!value) {if (set) *set = PETSC_TRUE; *nmax = 0; PetscFunctionReturn(0);}

  if (set) *set = PETSC_TRUE;

  ierr = PetscTokenCreate(value,',',&token);CHKERRQ(ierr);
  ierr = PetscTokenFind(token,&value);CHKERRQ(ierr);
  while (n < *nmax) {
    if (!value) break;
    ierr = PetscOptionsStringToBool(value,dvalue);CHKERRQ(ierr);
    ierr = PetscTokenFind(token,&value);CHKERRQ(ierr);
    dvalue++;
    n++;
  }
  ierr  = PetscTokenDestroy(token);CHKERRQ(ierr);
  *nmax = n;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsGetReal"
/*@C
   PetscOptionsGetReal - Gets the double precision value for a particular
   option in the database.

   Not Collective

   Input Parameters:
+  pre - string to prepend to each name or PETSC_NULL
-  name - the option one is seeking

   Output Parameter:
+  dvalue - the double value to return
-  set - PETSC_TRUE if found, PETSC_FALSE if not found

   Note: if the option is given but no value is provided then set is given the value PETSC_FALSE

   Level: beginner

   Concepts: options database^has double

.seealso: PetscOptionsGetInt(), PetscOptionsHasName(),
           PetscOptionsGetString(), PetscOptionsGetIntArray(), PetscOptionsGetRealArray(),PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList()
@*/
PetscErrorCode  PetscOptionsGetReal(const char pre[],const char name[],PetscReal *dvalue,PetscBool  *set)
{
  char           *value;
  PetscErrorCode ierr;
  PetscBool      flag;

  PetscFunctionBegin;
  PetscValidCharPointer(name,2);
  PetscValidDoublePointer(dvalue,3);
  ierr = PetscOptionsFindPair_Private(pre,name,&value,&flag);CHKERRQ(ierr);
  if (flag) {
    if (!value) {if (set) *set = PETSC_FALSE;}
    else        {if (set) *set = PETSC_TRUE; ierr = PetscOptionsStringToReal(value,dvalue);CHKERRQ(ierr);}
  } else {
    if (set) *set = PETSC_FALSE;
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsGetScalar"
/*@C
   PetscOptionsGetScalar - Gets the scalar value for a particular
   option in the database.

   Not Collective

   Input Parameters:
+  pre - string to prepend to each name or PETSC_NULL
-  name - the option one is seeking

   Output Parameter:
+  dvalue - the double value to return
-  set - PETSC_TRUE if found, else PETSC_FALSE

   Level: beginner

   Usage:
   A complex number 2+3i can be specified as 2,3 at the command line.
   or a number 2.0e-10 - 3.3e-20 i  can be specified as 2.0e-10,3.3e-20

   Note: if the option is given but no value is provided then set is given the value PETSC_FALSE

   Concepts: options database^has scalar

.seealso: PetscOptionsGetInt(), PetscOptionsHasName(),
           PetscOptionsGetString(), PetscOptionsGetIntArray(), PetscOptionsGetRealArray(), PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList()
@*/
PetscErrorCode  PetscOptionsGetScalar(const char pre[],const char name[],PetscScalar *dvalue,PetscBool  *set)
{
  char           *value;
  PetscBool      flag;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidCharPointer(name,2);
  PetscValidScalarPointer(dvalue,3);
  ierr = PetscOptionsFindPair_Private(pre,name,&value,&flag);CHKERRQ(ierr);
  if (flag) {
    if (!value) {
      if (set) *set = PETSC_FALSE;
    } else {
#if !defined(PETSC_USE_COMPLEX)
      ierr = PetscOptionsStringToReal(value,dvalue);CHKERRQ(ierr);
#else
      PetscReal  re=0.0,im=0.0;
      PetscToken token;
      char       *tvalue = 0;

      ierr = PetscTokenCreate(value,',',&token);CHKERRQ(ierr);
      ierr = PetscTokenFind(token,&tvalue);CHKERRQ(ierr);
      if (!tvalue) { SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"unknown string specified\n"); }
      ierr    = PetscOptionsStringToReal(tvalue,&re);CHKERRQ(ierr);
      ierr    = PetscTokenFind(token,&tvalue);CHKERRQ(ierr);
      if (!tvalue) { /* Unknown separator used. using only real value */
        *dvalue = re;
      } else {
        ierr    = PetscOptionsStringToReal(tvalue,&im);CHKERRQ(ierr);
        *dvalue = re + PETSC_i*im;
      }
      ierr    = PetscTokenDestroy(token);CHKERRQ(ierr);
#endif
      if (set) *set    = PETSC_TRUE;
    }
  } else { /* flag */
    if (set) *set = PETSC_FALSE;
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsGetRealArray"
/*@C
   PetscOptionsGetRealArray - Gets an array of double precision values for a
   particular option in the database.  The values must be separated with
   commas with no intervening spaces.

   Not Collective

   Input Parameters:
+  pre - string to prepend to each name or PETSC_NULL
.  name - the option one is seeking
-  nmax - maximum number of values to retrieve

   Output Parameters:
+  dvalue - the double value to return
.  nmax - actual number of values retreived
-  set - PETSC_TRUE if found, else PETSC_FALSE

   Level: beginner

   Concepts: options database^array of doubles

.seealso: PetscOptionsGetInt(), PetscOptionsHasName(),
           PetscOptionsGetString(), PetscOptionsGetIntArray(), PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList()
@*/
PetscErrorCode  PetscOptionsGetRealArray(const char pre[],const char name[],PetscReal dvalue[],PetscInt *nmax,PetscBool  *set)
{
  char           *value;
  PetscErrorCode ierr;
  PetscInt       n = 0;
  PetscBool      flag;
  PetscToken     token;

  PetscFunctionBegin;
  PetscValidCharPointer(name,2);
  PetscValidDoublePointer(dvalue,3);
  ierr = PetscOptionsFindPair_Private(pre,name,&value,&flag);CHKERRQ(ierr);
  if (!flag)  {if (set) *set = PETSC_FALSE; *nmax = 0; PetscFunctionReturn(0);}
  if (!value) {if (set) *set = PETSC_TRUE; *nmax = 0; PetscFunctionReturn(0);}

  if (set) *set = PETSC_TRUE;

  ierr = PetscTokenCreate(value,',',&token);CHKERRQ(ierr);
  ierr = PetscTokenFind(token,&value);CHKERRQ(ierr);
  while (n < *nmax) {
    if (!value) break;
    ierr = PetscOptionsStringToReal(value,dvalue++);CHKERRQ(ierr);
    ierr = PetscTokenFind(token,&value);CHKERRQ(ierr);
    n++;
  }
  ierr = PetscTokenDestroy(token);CHKERRQ(ierr);
  *nmax = n;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsGetIntArray"
/*@C
   PetscOptionsGetIntArray - Gets an array of integer values for a particular
   option in the database.  The values must be separated with commas with
   no intervening spaces.

   Not Collective

   Input Parameters:
+  pre - string to prepend to each name or PETSC_NULL
.  name - the option one is seeking
-  nmax - maximum number of values to retrieve, can include d-D to indicate d,d+1,..,D-1

   Output Parameter:
+  dvalue - the integer values to return
.  nmax - actual number of values retreived
-  set - PETSC_TRUE if found, else PETSC_FALSE

   Level: beginner

   Concepts: options database^array of ints

.seealso: PetscOptionsGetInt(), PetscOptionsHasName(),
           PetscOptionsGetString(), PetscOptionsGetRealArray(), PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList()
@*/
PetscErrorCode  PetscOptionsGetIntArray(const char pre[],const char name[],PetscInt dvalue[],PetscInt *nmax,PetscBool  *set)
{
  char           *value;
  PetscErrorCode ierr;
  PetscInt       n = 0,i,start,end;
  size_t         len;
  PetscBool      flag,foundrange;
  PetscToken     token;

  PetscFunctionBegin;
  PetscValidCharPointer(name,2);
  PetscValidIntPointer(dvalue,3);
  ierr = PetscOptionsFindPair_Private(pre,name,&value,&flag);CHKERRQ(ierr);
  if (!flag)  {if (set) *set = PETSC_FALSE; *nmax = 0; PetscFunctionReturn(0);}
  if (!value) {if (set) *set = PETSC_TRUE; *nmax = 0; PetscFunctionReturn(0);}

  if (set) *set = PETSC_TRUE;

  ierr = PetscTokenCreate(value,',',&token);CHKERRQ(ierr);
  ierr = PetscTokenFind(token,&value);CHKERRQ(ierr);
  while (n < *nmax) {
    if (!value) break;

    /* look for form  d-D where d and D are integers */
    foundrange = PETSC_FALSE;
    ierr      = PetscStrlen(value,&len);CHKERRQ(ierr);
    if (value[0] == '-') i=2;
    else i=1;
    for (;i<(int)len; i++) {
      if (value[i] == '-') {
        if (i == (int)len-1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_USER,"Error in %D-th array entry %s\n",n,value);
        value[i] = 0;
        ierr     = PetscOptionsStringToInt(value,&start);CHKERRQ(ierr);
        ierr     = PetscOptionsStringToInt(value+i+1,&end);CHKERRQ(ierr);
        if (end <= start) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_USER,"Error in %D-th array entry, %s-%s cannot have decreasing list",n,value,value+i+1);
        if (n + end - start - 1 >= *nmax) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_USER,"Error in %D-th array entry, not enough space in left in array (%D) to contain entire range from %D to %D",n,*nmax-n,start,end);
        for (;start<end; start++) {
          *dvalue = start; dvalue++;n++;
        }
        foundrange = PETSC_TRUE;
        break;
      }
    }
    if (!foundrange) {
      ierr      = PetscOptionsStringToInt(value,dvalue);CHKERRQ(ierr);
      dvalue++;
      n++;
    }
    ierr      = PetscTokenFind(token,&value);CHKERRQ(ierr);
  }
  ierr      = PetscTokenDestroy(token);CHKERRQ(ierr);
  *nmax = n;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsGetString"
/*@C
   PetscOptionsGetString - Gets the string value for a particular option in
   the database.

   Not Collective

   Input Parameters:
+  pre - string to prepend to name or PETSC_NULL
.  name - the option one is seeking
-  len - maximum length of the string including null termination

   Output Parameters:
+  string - location to copy string
-  set - PETSC_TRUE if found, else PETSC_FALSE

   Level: beginner

   Fortran Note:
   The Fortran interface is slightly different from the C/C++
   interface (len is not used).  Sample usage in Fortran follows
.vb
      character *20 string
      integer   flg, ierr
      call PetscOptionsGetString(PETSC_NULL_CHARACTER,'-s',string,flg,ierr)
.ve

   Notes: if the option is given but no string is provided then an empty string is returned and set is given the value of PETSC_TRUE

   Concepts: options database^string

    Note:
      Even if the user provided no string (for example -optionname -someotheroption) the flag is set to PETSC_TRUE (and the string is fulled with nulls).

.seealso: PetscOptionsGetInt(), PetscOptionsGetReal(),
           PetscOptionsHasName(), PetscOptionsGetIntArray(), PetscOptionsGetRealArray(), PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList()
@*/
PetscErrorCode  PetscOptionsGetString(const char pre[],const char name[],char string[],size_t len,PetscBool  *set)
{
  char           *value;
  PetscErrorCode ierr;
  PetscBool      flag;

  PetscFunctionBegin;
  PetscValidCharPointer(name,2);
  PetscValidCharPointer(string,3);
  ierr = PetscOptionsFindPair_Private(pre,name,&value,&flag);CHKERRQ(ierr);
  if (!flag) {
    if (set) *set = PETSC_FALSE;
  } else {
    if (set) *set = PETSC_TRUE;
    if (value) {
      ierr = PetscStrncpy(string,value,len);CHKERRQ(ierr);
      string[len-1] = 0;        /* Ensure that the string is NULL terminated */
    } else {
      ierr = PetscMemzero(string,len);CHKERRQ(ierr);
    }
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsGetStringMatlab"
char* PetscOptionsGetStringMatlab(const char pre[],const char name[])
{
  char           *value;
  PetscErrorCode ierr;
  PetscBool      flag;

  PetscFunctionBegin;
  ierr = PetscOptionsFindPair_Private(pre,name,&value,&flag);if (ierr) PetscFunctionReturn(0);
  if (flag) PetscFunctionReturn(value);
  else PetscFunctionReturn(0);
}


#undef __FUNCT__
#define __FUNCT__ "PetscOptionsGetStringArray"
/*@C
   PetscOptionsGetStringArray - Gets an array of string values for a particular
   option in the database. The values must be separated with commas with
   no intervening spaces.

   Not Collective

   Input Parameters:
+  pre - string to prepend to name or PETSC_NULL
.  name - the option one is seeking
-  nmax - maximum number of strings

   Output Parameter:
+  strings - location to copy strings
-  set - PETSC_TRUE if found, else PETSC_FALSE

   Level: beginner

   Notes:
   The user should pass in an array of pointers to char, to hold all the
   strings returned by this function.

   The user is responsible for deallocating the strings that are
   returned. The Fortran interface for this routine is not supported.

   Contributed by Matthew Knepley.

   Concepts: options database^array of strings

.seealso: PetscOptionsGetInt(), PetscOptionsGetReal(),
           PetscOptionsHasName(), PetscOptionsGetIntArray(), PetscOptionsGetRealArray(), PetscOptionsBool(),
          PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
          PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
          PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
          PetscOptionsList(), PetscOptionsEList()
@*/
PetscErrorCode  PetscOptionsGetStringArray(const char pre[],const char name[],char *strings[],PetscInt *nmax,PetscBool  *set)
{
  char           *value;
  PetscErrorCode ierr;
  PetscInt       n;
  PetscBool      flag;
  PetscToken     token;

  PetscFunctionBegin;
  PetscValidCharPointer(name,2);
  PetscValidPointer(strings,3);
  ierr = PetscOptionsFindPair_Private(pre,name,&value,&flag);CHKERRQ(ierr);
  if (!flag)  {*nmax = 0; if (set) *set = PETSC_FALSE; PetscFunctionReturn(0);}
  if (!value) {*nmax = 0; if (set) *set = PETSC_FALSE;PetscFunctionReturn(0);}
  if (!*nmax) {if (set) *set = PETSC_FALSE;PetscFunctionReturn(0);}
  if (set) *set = PETSC_TRUE;

  ierr = PetscTokenCreate(value,',',&token);CHKERRQ(ierr);
  ierr = PetscTokenFind(token,&value);CHKERRQ(ierr);
  n = 0;
  while (n < *nmax) {
    if (!value) break;
    ierr = PetscStrallocpy(value,&strings[n]);CHKERRQ(ierr);
    ierr = PetscTokenFind(token,&value);CHKERRQ(ierr);
    n++;
  }
  ierr = PetscTokenDestroy(token);CHKERRQ(ierr);
  *nmax = n;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsAllUsed"
/*@C
   PetscOptionsAllUsed - Returns a count of the number of options in the
   database that have never been selected.

   Not Collective

   Output Parameter:
.   N - count of options not used

   Level: advanced

.seealso: PetscOptionsView()
@*/
PetscErrorCode  PetscOptionsAllUsed(PetscInt *N)
{
  PetscInt i,n = 0;

  PetscFunctionBegin;
  for (i=0; i<options->N; i++) {
    if (!options->used[i]) { n++; }
  }
  *N = n;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsLeft"
/*@
    PetscOptionsLeft - Prints to screen any options that were set and never used.

  Not collective

   Options Database Key:
.  -options_left - Activates OptionsAllUsed() within PetscFinalize()

  Level: advanced

.seealso: PetscOptionsAllUsed()
@*/
PetscErrorCode  PetscOptionsLeft(void)
{
  PetscErrorCode ierr;
  PetscInt       i;

  PetscFunctionBegin;
  for (i=0; i<options->N; i++) {
    if (!options->used[i]) {
      if (options->values[i]) {
        ierr = PetscPrintf(PETSC_COMM_WORLD,"Option left: name:-%s value: %s\n",options->names[i],options->values[i]);CHKERRQ(ierr);
      } else {
        ierr = PetscPrintf(PETSC_COMM_WORLD,"Option left: name:-%s no value \n",options->names[i]);CHKERRQ(ierr);
      }
    }
  }
  PetscFunctionReturn(0);
}


#undef __FUNCT__
#define __FUNCT__ "PetscOptionsCreate"
/*
    PetscOptionsCreate - Creates the empty options database.

*/
PetscErrorCode  PetscOptionsCreate(void)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  options = (PetscOptionsTable*)malloc(sizeof(PetscOptionsTable));
  ierr    = PetscMemzero(options,sizeof(PetscOptionsTable));CHKERRQ(ierr);
  options->namegiven 		= PETSC_FALSE;
  options->N         		= 0;
  options->Naliases  		= 0;
  options->numbermonitors 	= 0;

  PetscOptionsObject.prefix = PETSC_NULL;
  PetscOptionsObject.title  = PETSC_NULL;

  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsSetFromOptions"
/*@
   PetscOptionsSetFromOptions - Sets various SNES and KSP parameters from user options.

   Collective on PETSC_COMM_WORLD

   Options Database Keys:
+  -options_monitor <optional filename> - prints the names and values of all runtime options as they are set. The monitor functionality is not
                available for options set through a file, environment variable, or on
                the command line. Only options set after PetscInitialize completes will
                be monitored.
.  -options_monitor_cancel - cancel all options database monitors

   Notes:
   To see all options, run your program with the -help option or consult
   the <A href="../../docs/manual.pdf">users manual</A>..

   Level: intermediate

.keywords: set, options, database
@*/
PetscErrorCode  PetscOptionsSetFromOptions(void)
{
  PetscBool           flgc,flgm;
  PetscErrorCode      ierr;
  char                monfilename[PETSC_MAX_PATH_LEN];
  PetscViewer         monviewer;

  PetscFunctionBegin;
  ierr = PetscOptionsBegin(PETSC_COMM_WORLD,"","Options database options","PetscOptions");CHKERRQ(ierr);
    ierr = PetscOptionsString("-options_monitor","Monitor options database","PetscOptionsMonitorSet","stdout",monfilename,PETSC_MAX_PATH_LEN,&flgm);CHKERRQ(ierr);
    ierr = PetscOptionsBool("-options_monitor_cancel","Cancel all options database monitors","PetscOptionsMonitorCancel",PETSC_FALSE,&flgc,PETSC_NULL);CHKERRQ(ierr);
  ierr = PetscOptionsEnd();CHKERRQ(ierr);
  if (flgm) {
    ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,monfilename,&monviewer);CHKERRQ(ierr);
    ierr = PetscOptionsMonitorSet(PetscOptionsMonitorDefault,monviewer,(PetscErrorCode (*)(void**))PetscViewerDestroy);CHKERRQ(ierr);
  }
  if (flgc) { ierr = PetscOptionsMonitorCancel();CHKERRQ(ierr); }
  PetscFunctionReturn(0);
}


#undef __FUNCT__
#define __FUNCT__ "PetscOptionsMonitorDefault"
/*@C
   PetscOptionsMonitorDefault - Print all options set value events.

   Logically Collective on PETSC_COMM_WORLD

   Input Parameters:
+  name  - option name string
.  value - option value string
-  dummy - unused monitor context

   Level: intermediate

.keywords: PetscOptions, default, monitor

.seealso: PetscOptionsMonitorSet()
@*/
PetscErrorCode  PetscOptionsMonitorDefault(const char name[], const char value[], void *dummy)
{
  PetscErrorCode ierr;
  PetscViewer    viewer = (PetscViewer) dummy;

  PetscFunctionBegin;
  if (!viewer) {
    ierr = PetscViewerASCIIGetStdout(PETSC_COMM_WORLD,&viewer);CHKERRQ(ierr);
  }
  ierr = PetscViewerASCIIPrintf(viewer,"Setting option: %s = %s\n",name,value);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsMonitorSet"
/*@C
   PetscOptionsMonitorSet - Sets an ADDITIONAL function to be called at every method that
   modified the PETSc options database.

   Not collective

   Input Parameters:
+  monitor - pointer to function (if this is PETSC_NULL, it turns off monitoring
.  mctx    - [optional] context for private data for the
             monitor routine (use PETSC_NULL if no context is desired)
-  monitordestroy - [optional] routine that frees monitor context
          (may be PETSC_NULL)

   Calling Sequence of monitor:
$     monitor (const char name[], const char value[], void *mctx)

+  name - option name string
.  value - option value string
-  mctx  - optional monitoring context, as set by PetscOptionsMonitorSet()

   Options Database Keys:
+    -options_monitor    - sets PetscOptionsMonitorDefault()
-    -options_monitor_cancel - cancels all monitors that have
                          been hardwired into a code by
                          calls to PetscOptionsMonitorSet(), but
                          does not cancel those set via
                          the options database.

   Notes:
   The default is to do nothing.  To print the name and value of options
   being inserted into the database, use PetscOptionsMonitorDefault() as the monitoring routine,
   with a null monitoring context.

   Several different monitoring routines may be set by calling
   PetscOptionsMonitorSet() multiple times; all will be called in the
   order in which they were set.

   Level: beginner

.keywords: PetscOptions, set, monitor

.seealso: PetscOptionsMonitorDefault(), PetscOptionsMonitorCancel()
@*/
PetscErrorCode  PetscOptionsMonitorSet(PetscErrorCode (*monitor)(const char name[], const char value[], void*),void *mctx,PetscErrorCode (*monitordestroy)(void**))
{
  PetscFunctionBegin;
  if (options->numbermonitors >= MAXOPTIONSMONITORS) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Too many PetscOptions monitors set");
  options->monitor[options->numbermonitors]           = monitor;
  options->monitordestroy[options->numbermonitors]    = monitordestroy;
  options->monitorcontext[options->numbermonitors++]  = (void*)mctx;
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "PetscOptionsMonitorCancel"
/*@
   PetscOptionsMonitorCancel - Clears all monitors for a PetscOptions object.

   Not collective

   Options Database Key:
.  -options_monitor_cancel - Cancels all monitors that have
    been hardwired into a code by calls to PetscOptionsMonitorSet(),
    but does not cancel those set via the options database.

   Level: intermediate

.keywords: PetscOptions, set, monitor

.seealso: PetscOptionsMonitorDefault(), PetscOptionsMonitorSet()
@*/
PetscErrorCode  PetscOptionsMonitorCancel(void)
{
  PetscErrorCode ierr;
  PetscInt       i;

  PetscFunctionBegin;
  for (i=0; i<options->numbermonitors; i++) {
    if (options->monitordestroy[i]) {
      ierr = (*options->monitordestroy[i])(&options->monitorcontext[i]);CHKERRQ(ierr);
    }
  }
  options->numbermonitors = 0;
  PetscFunctionReturn(0);
}