/*@C
PetscBagRegisterEnum - add an enum value to the bag
Logically Collective on PetscBag
Input Parameter:
+ bag - the bag of values
. addr - location of enum in struct
. mdefault - the initial value
. list - array of strings containing names of enum values followed by enum name followed by enum prefix
- help - longer string with more information about the value
Level: beginner
.seealso: PetscBag, PetscBagSetName(), PetscBagView(), PetscBagLoad(), PetscBagGetData()
PetscBagRegisterInt(), PetscBagRegisterBool(), PetscBagRegisterScalar()
PetscBagSetFromOptions(), PetscBagCreate(), PetscBagGetName()
@*/
PetscErrorCode PetscBagRegisterEnum(PetscBag bag,void *addr,const char *const *list,PetscEnum mdefault, const char *name, const char *help)
{
PetscErrorCode ierr;
PetscBagItem item;
char nname[PETSC_BAG_NAME_LENGTH+1];
PetscBool printhelp;
PetscInt i = 0;
PetscFunctionBegin;
nname[0] = '-';
nname[1] = 0;
ierr = PetscStrncat(nname,name,PETSC_BAG_NAME_LENGTH-1);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-help",&printhelp);CHKERRQ(ierr);
if (printhelp) {
while (list[i++]) ;
ierr = (*PetscHelpPrintf)(bag->bagcomm," -%s%s <%s>: (%s) %s (choose one of) ",bag->bagprefix ? bag->bagprefix : "",name,list[mdefault],list[i-3],help);CHKERRQ(ierr);
for (i=0; list[i+2]; i++) {
ierr = (*PetscHelpPrintf)(bag->bagcomm," %s",list[i]);CHKERRQ(ierr);
}
ierr = (*PetscHelpPrintf)(bag->bagcomm,"\n");CHKERRQ(ierr);
}
ierr = PetscOptionsGetEnum(bag->bagprefix,nname,list,&mdefault,NULL);CHKERRQ(ierr);
ierr = PetscNew(&item);CHKERRQ(ierr);
item->dtype = PETSC_ENUM;
item->offset = ((char*)addr) - ((char*)bag);
if (item->offset > bag->bagsize) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Registered item %s %s is not in bag memory space",name,help);
item->next = 0;
item->msize = 1;
ierr = PetscStrArrayallocpy(list,(char***)&item->list);CHKERRQ(ierr);
*(PetscEnum*)addr = mdefault;
ierr = PetscBagRegister_Private(bag,item,name,help);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
PetscBagRegisterBool - add a logical value to the bag
Logically Collective on PetscBag
Input Parameter:
+ bag - the bag of values
. addr - location of logical in struct
. mdefault - the initial value
. name - name of the variable
- help - longer string with more information about the value
Level: beginner
.seealso: PetscBag, PetscBagSetName(), PetscBagView(), PetscBagLoad(), PetscBagGetData()
PetscBagRegisterInt(), PetscBagRegisterBool(), PetscBagRegisterScalar()
PetscBagSetFromOptions(), PetscBagCreate(), PetscBagGetName(), PetscBagRegisterEnum()
@*/
PetscErrorCode PetscBagRegisterBool(PetscBag bag,void *addr,PetscBool mdefault,const char *name,const char *help)
{
PetscErrorCode ierr;
PetscBagItem item;
char nname[PETSC_BAG_NAME_LENGTH+1];
PetscBool printhelp;
PetscFunctionBegin;
/* the checks here with != PETSC_FALSE and PETSC_TRUE is a special case; here we truly demand that the value be 0 or 1 */
if (mdefault != PETSC_FALSE && mdefault != PETSC_TRUE) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Boolean %s %s must be boolean; integer value %d",name,help,(int)mdefault);
nname[0] = '-';
nname[1] = 0;
ierr = PetscStrncat(nname,name,PETSC_BAG_NAME_LENGTH-1);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-help",&printhelp);CHKERRQ(ierr);
if (printhelp) {
ierr = (*PetscHelpPrintf)(bag->bagcomm," -%s%s <%s>: %s \n",bag->bagprefix ? bag->bagprefix : "",name,PetscBools[mdefault],help);CHKERRQ(ierr);
}
ierr = PetscOptionsGetBool(bag->bagprefix,nname,&mdefault,NULL);CHKERRQ(ierr);
ierr = PetscNew(&item);CHKERRQ(ierr);
item->dtype = PETSC_BOOL;
item->offset = ((char*)addr) - ((char*)bag);
if (item->offset > bag->bagsize) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Registered item %s %s is not in bag memory space",name,help);
item->next = 0;
item->msize = 1;
*(PetscBool*)addr = mdefault;
ierr = PetscBagRegister_Private(bag,item,name,help);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
PetscBagRegisterScalar - add a real or complex number value to the bag
Logically Collective on PetscBag
Input Parameter:
+ bag - the bag of values
. addr - location of scalar in struct
. mdefault - the initial value
. name - name of the variable
- help - longer string with more information about the value
Level: beginner
.seealso: PetscBag, PetscBagSetName(), PetscBagView(), PetscBagLoad(), PetscBagGetData()
PetscBagRegisterInt(), PetscBagRegisterBool(), PetscBagRegisterScalar()
PetscBagSetFromOptions(), PetscBagCreate(), PetscBagGetName(), PetscBagRegisterEnum()
@*/
PetscErrorCode PetscBagRegisterScalar(PetscBag bag,void *addr,PetscScalar mdefault,const char *name,const char *help)
{
PetscErrorCode ierr;
PetscBagItem item;
char nname[PETSC_BAG_NAME_LENGTH+1];
PetscBool printhelp;
PetscFunctionBegin;
nname[0] = '-';
nname[1] = 0;
ierr = PetscStrncat(nname,name,PETSC_BAG_NAME_LENGTH-1);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-help",&printhelp);CHKERRQ(ierr);
if (printhelp) {
ierr = (*PetscHelpPrintf)(bag->bagcomm," -%s%s <%g + %gi>: %s \n",bag->bagprefix ? bag->bagprefix : "",name,(double)PetscRealPart(mdefault),(double)PetscImaginaryPart(mdefault),help);CHKERRQ(ierr);
}
ierr = PetscOptionsGetScalar(bag->bagprefix,nname,&mdefault,NULL);CHKERRQ(ierr);
ierr = PetscNew(&item);CHKERRQ(ierr);
item->dtype = PETSC_SCALAR;
item->offset = ((char*)addr) - ((char*)bag);
if (item->offset > bag->bagsize) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Registered item %s %s is not in bag memory space",name,help);
item->next = 0;
item->msize = 1;
*(PetscScalar*)addr = mdefault;
ierr = PetscBagRegister_Private(bag,item,name,help);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
PetscBagRegisterString - add a string value to the bag
Logically Collective on PetscBag
Input Parameter:
+ bag - the bag of values
. addr - location of start of string in struct
. msize - length of the string space in the struct
. mdefault - the initial value
. name - name of the string
- help - longer string with more information about the value
Level: beginner
Note: The struct should have the field char mystring[msize]; not char *mystring
.seealso: PetscBag, PetscBagSetName(), PetscBagView(), PetscBagLoad(), PetscBagGetData()
PetscBagRegisterInt(), PetscBagRegisterBool(), PetscBagRegisterScalar()
PetscBagSetFromOptions(),PetscBagCreate(), PetscBagGetName(), PetscBagRegisterEnum()
@*/
PetscErrorCode PetscBagRegisterString(PetscBag bag,void *addr,PetscInt msize,const char* mdefault,const char* name,const char* help)
{
PetscErrorCode ierr;
PetscBagItem item;
char nname[PETSC_BAG_NAME_LENGTH+1];
PetscBool printhelp;
PetscFunctionBegin;
nname[0] = '-';
nname[1] = 0;
ierr = PetscStrncat(nname,name,PETSC_BAG_NAME_LENGTH-1);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-help",&printhelp);CHKERRQ(ierr);
if (printhelp) {
ierr = (*PetscHelpPrintf)(bag->bagcomm," -%s%s <%s>: %s \n",bag->bagprefix ? bag->bagprefix : "",name,mdefault,help);CHKERRQ(ierr);
}
ierr = PetscNew(&item);CHKERRQ(ierr);
item->dtype = PETSC_CHAR;
item->offset = ((char*)addr) - ((char*)bag);
if (item->offset > bag->bagsize) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Registered item %s %s is not in bag memory space",name,help);
item->next = 0;
item->msize = msize;
if (mdefault != (char*)addr) {
ierr = PetscStrncpy((char*)addr,mdefault,msize-1);CHKERRQ(ierr);
}
ierr = PetscOptionsGetString(bag->bagprefix,nname,(char*)addr,msize,NULL);CHKERRQ(ierr);
ierr = PetscBagRegister_Private(bag,item,name,help);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
PetscBagRegisterBoolArray - add a n logical values to the bag
Logically Collective on PetscBag
Input Parameter:
+ bag - the bag of values
. addr - location of boolean array in struct
. msize - number of entries in array
. name - name of the boolean array
- help - longer string with more information about the value
Level: beginner
.seealso: PetscBag, PetscBagSetName(), PetscBagView(), PetscBagLoad(), PetscBagGetData()
PetscBagRegisterInt(), PetscBagRegisterBool(), PetscBagRegisterScalar()
PetscBagSetFromOptions(), PetscBagCreate(), PetscBagGetName(), PetscBagRegisterEnum()
@*/
PetscErrorCode PetscBagRegisterBoolArray(PetscBag bag,void *addr,PetscInt msize, const char* name, const char* help)
{
PetscErrorCode ierr;
PetscBagItem item;
char nname[PETSC_BAG_NAME_LENGTH+1];
PetscBool printhelp;
PetscInt i,tmp = msize;
PetscFunctionBegin;
/* ierr = PetscMemzero(addr,msize*sizeof(PetscInt));CHKERRQ(ierr);*/
nname[0] = '-';
nname[1] = 0;
ierr = PetscStrncat(nname,name,PETSC_BAG_NAME_LENGTH-1);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-help",&printhelp);CHKERRQ(ierr);
if (printhelp) {
ierr = (*PetscHelpPrintf)(bag->bagcomm," -%s%s <",bag->bagprefix?bag->bagprefix:"",name);CHKERRQ(ierr);
for (i=0; i<msize; i++) {
ierr = (*PetscHelpPrintf)(bag->bagcomm,"%D ",*((PetscInt*)addr)+i);CHKERRQ(ierr);
}
ierr = (*PetscHelpPrintf)(bag->bagcomm,">: %s \n",help);CHKERRQ(ierr);
}
ierr = PetscOptionsGetBoolArray(bag->bagprefix,nname,(PetscBool*)addr,&tmp,NULL);CHKERRQ(ierr);
ierr = PetscNew(&item);CHKERRQ(ierr);
item->dtype = PETSC_BOOL;
item->offset = ((char*)addr) - ((char*)bag);
if (item->offset > bag->bagsize) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Registered item %s %s is not in bag memory space",name,help);
item->next = 0;
item->msize = msize;
ierr = PetscBagRegister_Private(bag,item,name,help);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode InitializeProblem(AppCtx *user)
{
PetscErrorCode ierr;
PetscViewer loader;
MPI_Comm comm;
PetscInt nrows,ncols,i;
PetscScalar one=1.0;
char filebase[128];
char filename[128];
PetscFunctionBegin;
comm = PETSC_COMM_WORLD;
ierr = PetscStrncpy(filebase,user->name,128);CHKERRQ(ierr);
ierr = PetscStrncat(filebase,"/",1);CHKERRQ(ierr);
ierr = PetscStrncpy(filename,filebase,128);CHKERRQ(ierr);
ierr = PetscStrncat(filename,"f",3);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(comm,filename,FILE_MODE_READ,&loader);CHKERRQ(ierr);
ierr = VecCreate(comm,&user->d);CHKERRQ(ierr);
ierr = VecLoad(user->d,loader);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&loader);CHKERRQ(ierr);
ierr = VecGetSize(user->d,&nrows);CHKERRQ(ierr);
ierr = VecSetFromOptions(user->d);CHKERRQ(ierr);
user->n = nrows;
ierr = PetscStrncpy(filename,filebase,128);CHKERRQ(ierr);
ierr = PetscStrncat(filename,"H",3);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(comm,filename,FILE_MODE_READ,&loader);CHKERRQ(ierr);
ierr = MatCreate(comm,&user->H);CHKERRQ(ierr);
ierr = MatSetSizes(user->H,PETSC_DECIDE,PETSC_DECIDE,nrows,nrows);CHKERRQ(ierr);
ierr = MatLoad(user->H,loader);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&loader);CHKERRQ(ierr);
ierr = MatGetSize(user->H,&nrows,&ncols);CHKERRQ(ierr);
if (nrows != user->n) SETERRQ(comm,0,"H: nrows != n\n");
if (ncols != user->n) SETERRQ(comm,0,"H: ncols != n\n");
ierr = MatSetFromOptions(user->H);CHKERRQ(ierr);
ierr = PetscStrncpy(filename,filebase,128);CHKERRQ(ierr);
ierr = PetscStrncat(filename,"Aeq",3);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(comm,filename,FILE_MODE_READ,&loader);
if (ierr) {
user->Aeq = NULL;
user->me = 0;
} else {
ierr = MatCreate(comm,&user->Aeq);CHKERRQ(ierr);
ierr = MatLoad(user->Aeq,loader);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&loader);CHKERRQ(ierr);
ierr = MatGetSize(user->Aeq,&nrows,&ncols);CHKERRQ(ierr);
if (ncols != user->n) SETERRQ(comm,0,"Aeq ncols != H nrows\n");
ierr = MatSetFromOptions(user->Aeq);CHKERRQ(ierr);
user->me = nrows;
}
ierr = PetscStrncpy(filename,filebase,128);CHKERRQ(ierr);
ierr = PetscStrncat(filename,"Beq",3);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(comm,filename,FILE_MODE_READ,&loader);CHKERRQ(ierr);
if (ierr) {
user->beq = 0;
} else {
ierr = VecCreate(comm,&user->beq);CHKERRQ(ierr);
ierr = VecLoad(user->beq,loader);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&loader);CHKERRQ(ierr);
ierr = VecGetSize(user->beq,&nrows);CHKERRQ(ierr);
if (nrows != user->me) SETERRQ(comm,0,"Aeq nrows != Beq n\n");
ierr = VecSetFromOptions(user->beq);CHKERRQ(ierr);
}
user->mi = user->n;
/* Ain = eye(n,n) */
ierr = MatCreate(comm,&user->Ain);CHKERRQ(ierr);
ierr = MatSetType(user->Ain,MATAIJ);CHKERRQ(ierr);
ierr = MatSetSizes(user->Ain,PETSC_DECIDE,PETSC_DECIDE,user->mi,user->mi);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(user->Ain,1,NULL,0,NULL);CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(user->Ain,1,NULL);CHKERRQ(ierr);
for (i=0;i<user->mi;i++) {
ierr = MatSetValues(user->Ain,1,&i,1,&i,&one,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(user->Ain,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(user->Ain,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatSetFromOptions(user->Ain);CHKERRQ(ierr);
/* bin = [0,0 ... 0]' */
ierr = VecCreate(comm,&user->bin);CHKERRQ(ierr);
ierr = VecSetType(user->bin,VECMPI);CHKERRQ(ierr);
ierr = VecSetSizes(user->bin,PETSC_DECIDE,user->mi);CHKERRQ(ierr);
ierr = VecSet(user->bin,0.0);CHKERRQ(ierr);
ierr = VecSetFromOptions(user->bin);CHKERRQ(ierr);
user->m = user->me + user->mi;
PetscFunctionReturn(0);
}
/*@C
PetscGetFullPath - Given a filename, returns the fully qualified file name.
Not Collective
Input Parameters:
+ path - pathname to qualify
. fullpath - pointer to buffer to hold full pathname
- flen - size of fullpath
Level: developer
Concepts: full path
Concepts: path^full
.seealso: PetscGetRelativePath()
@*/
PetscErrorCode PetscGetFullPath(const char path[],char fullpath[],size_t flen)
{
PetscErrorCode ierr;
size_t ln;
PetscBool flg;
PetscFunctionBegin;
if (path[0] == '/') {
ierr = PetscStrncmp("/tmp_mnt/",path,9,&flg);CHKERRQ(ierr);
if (flg) {ierr = PetscStrncpy(fullpath,path + 8,flen);CHKERRQ(ierr);}
else {ierr = PetscStrncpy(fullpath,path,flen);CHKERRQ(ierr);}
fullpath[flen-1] = 0;
PetscFunctionReturn(0);
}
ierr = PetscStrncpy(fullpath,path,flen);CHKERRQ(ierr);
fullpath[flen-1] = 0;
/* Remove the various "special" forms (~username/ and ~/) */
if (fullpath[0] == '~') {
char tmppath[PETSC_MAX_PATH_LEN],*rest;
if (fullpath[1] == '/') {
ierr = PetscGetHomeDirectory(tmppath,PETSC_MAX_PATH_LEN);CHKERRQ(ierr);
rest = fullpath + 2;
} else {
#if defined(PETSC_HAVE_PWD_H)
struct passwd *pwde;
char *p,*name;
/* Find username */
name = fullpath + 1;
p = name;
while (*p && *p != '/') p++;
*p = 0;
rest = p + 1;
pwde = getpwnam(name);
if (!pwde) PetscFunctionReturn(0);
ierr = PetscStrcpy(tmppath,pwde->pw_dir);CHKERRQ(ierr);
#else
PetscFunctionReturn(0);
#endif
}
ierr = PetscStrlen(tmppath,&ln);CHKERRQ(ierr);
if (tmppath[ln-1] != '/') {ierr = PetscStrcat(tmppath+ln-1,"/");CHKERRQ(ierr);}
ierr = PetscStrcat(tmppath,rest);CHKERRQ(ierr);
ierr = PetscStrncpy(fullpath,tmppath,flen);CHKERRQ(ierr);
fullpath[flen-1] = 0;
} else {
ierr = PetscGetWorkingDirectory(fullpath,flen);CHKERRQ(ierr);
ierr = PetscStrlen(fullpath,&ln);CHKERRQ(ierr);
ierr = PetscStrncpy(fullpath+ln,"/",flen - ln);CHKERRQ(ierr);
fullpath[flen-1] = 0;
ierr = PetscStrlen(fullpath,&ln);CHKERRQ(ierr);
if (path[0] == '.' && path[1] == '/') {
ierr = PetscStrncat(fullpath,path+2,flen - ln - 1);CHKERRQ(ierr);
} else {
ierr = PetscStrncat(fullpath,path,flen - ln - 1);CHKERRQ(ierr);
}
fullpath[flen-1] = 0;
}
/* Remove the automounter part of the path */
ierr = PetscStrncmp(fullpath,"/tmp_mnt/",9,&flg);CHKERRQ(ierr);
if (flg) {
char tmppath[PETSC_MAX_PATH_LEN];
ierr = PetscStrcpy(tmppath,fullpath + 8);CHKERRQ(ierr);
ierr = PetscStrcpy(fullpath,tmppath);CHKERRQ(ierr);
}
/* We could try to handle things like the removal of .. etc */
PetscFunctionReturn(0);
}
