PetscErrorCode Parameter_settings(AppCtx *user)
{
PetscErrorCode ierr;
PetscBool flg;
PetscFunctionBeginUser;
/* Set default parameters */
user->ws = 1.0;
user->H = 5.0;
user->Pmax = 2.1;
user->PM_min = 1.0;
user->lambda = 0.1;
user->q = 1.0;
user->mux = asin(user->PM_min/user->Pmax);
user->sigmax = 0.1;
user->sigmay = 0.1;
user->rho = 0.0;
user->xmin = -PETSC_PI;
user->xmax = PETSC_PI;
user->bx = DMDA_BOUNDARY_PERIODIC;
user->by = DMDA_BOUNDARY_MIRROR;
user->nonoiseinitial = PETSC_FALSE;
/*
ymin of -3 seems to let the unstable solution move up and leave a zero in its wake
with an ymin of -1 the wake is never exactly zero
*/
user->ymin = -3.0;
user->ymax = 10.0;
user->st_width = 1;
ierr = PetscOptionsGetScalar(NULL,"-ws",&user->ws,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-Inertia",&user->H,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-Pmax",&user->Pmax,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-PM_min",&user->PM_min,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-lambda",&user->lambda,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-q",&user->q,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-mux",&user->mux,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-sigmax",&user->sigmax,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-muy",&user->muy,&flg);CHKERRQ(ierr);
if (flg == 0) {
user->muy = user->ws;
}
ierr = PetscOptionsGetScalar(NULL,"-sigmay",&user->sigmay,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-rho",&user->rho,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-xmin",&user->xmin,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-xmax",&user->xmax,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-ymin",&user->ymin,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-ymax",&user->ymax,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-stencil_width",&user->st_width,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetEnum(NULL,"-bx",DMDABoundaryTypes,(PetscEnum*)&user->bx,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetEnum(NULL,"-by",DMDABoundaryTypes,(PetscEnum*)&user->by,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-nonoiseinitial",&user->nonoiseinitial,&flg);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode Parameter_settings(AppCtx *user)
{
PetscErrorCode ierr;
PetscBool flg;
PetscFunctionBeginUser;
/* Set default parameters */
user->ws = 1.0;
user->H = 5.0;
user->D = 0.0;
user->Pmax = user->Pmax_s = 2.1;
user->PM_min = 1.0;
user->lambda = 0.1;
user->q = 1.0;
user->mux = PetscAsinScalar(user->PM_min/user->Pmax);
user->sigmax = 0.1;
user->sigmay = 0.1;
user->rho = 0.0;
user->xmin = -PETSC_PI;
user->xmax = PETSC_PI;
user->bx = DM_BOUNDARY_PERIODIC;
user->by = DM_BOUNDARY_GHOSTED;
user->tf = user->tcl = -1;
user->ymin = -2.0;
user->ymax = 2.0;
user->st_width = 1;
ierr = PetscOptionsGetScalar(NULL,"-ws",&user->ws,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-Inertia",&user->H,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-D",&user->D,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-Pmax",&user->Pmax,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-PM_min",&user->PM_min,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-lambda",&user->lambda,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-q",&user->q,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-mux",&user->mux,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-muy",&user->muy,&flg);CHKERRQ(ierr);
if (flg == 0) {
user->muy = user->ws;
}
ierr = PetscOptionsGetScalar(NULL,"-xmin",&user->xmin,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-xmax",&user->xmax,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-ymin",&user->ymin,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-ymax",&user->ymax,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-stencil_width",&user->st_width,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetEnum("","-bx",BoundaryTypes,(PetscEnum*)&user->bx,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetEnum("","-by",BoundaryTypes,(PetscEnum*)&user->by,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-tf",&user->tf,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-tcl",&user->tcl,&flg);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode PetscP4estInitialize(void)
{
PetscBool psc_catch_signals = PETSC_FALSE;
PetscBool psc_print_backtrace = PETSC_TRUE;
int psc_log_threshold = SC_LP_DEFAULT;
int pp4est_log_threshold = SC_LP_DEFAULT;
char logList[256], *className;
PetscBool opt;
PetscErrorCode ierr;
PetscFunctionBegin;
if (PetscP4estInitialized) PetscFunctionReturn(0);
PetscP4estInitialized = PETSC_TRUE;
ierr = PetscClassIdRegister("p4est logging",&P4ESTLOGGING_CLASSID);CHKERRQ(ierr);
ierr = PetscOptionsGetString(NULL,NULL, "-info_exclude", logList, 256, &opt);CHKERRQ(ierr);
if (opt) {
ierr = PetscStrstr(logList, "p4est", &className);CHKERRQ(ierr);
if (className) {
ierr = PetscInfoDeactivateClass(P4ESTLOGGING_CLASSID);CHKERRQ(ierr);
}
}
ierr = PetscHeaderCreate(P4estLoggingObject,P4ESTLOGGING_CLASSID,"p4est","p4est logging","DM",PETSC_COMM_WORLD,NULL,PetscObjectView);CHKERRQ(ierr);
if (sc_package_id == -1) {
int log_threshold_shifted = psc_log_threshold + 1;
PetscBool set;
PetscBeganSc = PETSC_TRUE;
ierr = PetscOptionsGetBool(NULL,NULL,"-petsc_sc_catch_signals",&psc_catch_signals,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-petsc_sc_print_backtrace",&psc_print_backtrace,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetEnum(NULL,NULL,"-petsc_sc_log_threshold",SCLogTypes,(PetscEnum*)&log_threshold_shifted,&set);CHKERRQ(ierr);
if (set) psc_log_threshold = log_threshold_shifted - 1;
sc_init(PETSC_COMM_WORLD,(int)psc_catch_signals,(int)psc_print_backtrace,PetscScLogHandler,psc_log_threshold);
if (sc_package_id == -1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_LIB,"Could not initialize libsc package used by p4est");
sc_set_abort_handler(PetscScAbort);
}
if (p4est_package_id == -1) {
int log_threshold_shifted = pp4est_log_threshold + 1;
PetscBool set;
ierr = PetscOptionsGetEnum(NULL,NULL,"-petsc_p4est_log_threshold",SCLogTypes,(PetscEnum*)&log_threshold_shifted,&set);CHKERRQ(ierr);
if (set) pp4est_log_threshold = log_threshold_shifted - 1;
PetscStackCallP4est(p4est_init,(PetscScLogHandler,pp4est_log_threshold));
if (p4est_package_id == -1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_LIB,"Could not initialize p4est");
}
ierr = DMForestRegisterType(DMP4EST);CHKERRQ(ierr);
ierr = DMForestRegisterType(DMP8EST);CHKERRQ(ierr);
ierr = PetscRegisterFinalize(PetscP4estFinalize);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@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);
}
/*@
PetscDrawLGSetFromOptions - Sets options related to the PetscDrawLG
Collective on PetscDrawLG
Options Database:
Level: intermediate
Concepts: line graph^creating
.seealso: PetscDrawLGDestroy(), PetscDrawLGCreate()
@*/
PetscErrorCode PetscDrawLGSetFromOptions(PetscDrawLG lg)
{
PetscErrorCode ierr;
PetscBool usemarkers,set;
PetscDrawMarkerType markertype;
PetscFunctionBegin;
PetscValidHeaderSpecific(lg,PETSC_DRAWLG_CLASSID,1);
ierr = PetscDrawGetMarkerType(lg->win,&markertype);CHKERRQ(ierr);
ierr = PetscOptionsGetEnum(((PetscObject)lg)->options,((PetscObject)lg)->prefix,"-lg_marker_type",PetscDrawMarkerTypes,(PetscEnum*)&markertype,&set);CHKERRQ(ierr);
if (set) {
ierr = PetscDrawLGSetUseMarkers(lg,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscDrawSetMarkerType(lg->win,markertype);CHKERRQ(ierr);
}
usemarkers = lg->use_markers;
ierr = PetscOptionsGetBool(((PetscObject)lg)->options,((PetscObject)lg)->prefix,"-lg_use_markers",&usemarkers,&set);CHKERRQ(ierr);
if (set) {ierr = PetscDrawLGSetUseMarkers(lg,usemarkers);CHKERRQ(ierr);}
PetscFunctionReturn(0);
}
/*@
PetscCommBuildTwoSidedGetType - set algorithm to use when building two-sided communication
Logically Collective
Output Arguments:
+ comm - communicator on which to query algorithm
- twosided - algorithm to use for PetscCommBuildTwoSided()
Level: developer
.seealso: PetscCommBuildTwoSided(), PetscCommBuildTwoSidedSetType()
@*/
PetscErrorCode PetscCommBuildTwoSidedGetType(MPI_Comm comm,PetscBuildTwoSidedType *twosided)
{
PetscErrorCode ierr;
PetscFunctionBegin;
*twosided = PETSC_BUILDTWOSIDED_NOTSET;
if (_twosided_type == PETSC_BUILDTWOSIDED_NOTSET) {
#if defined(PETSC_HAVE_MPI_IBARRIER)
# if defined(PETSC_HAVE_MPICH_CH3_SOCK) && !defined(PETSC_HAVE_MPICH_CH3_SOCK_FIXED_NBC_PROGRESS)
/* Deadlock in Ibarrier: http://trac.mpich.org/projects/mpich/ticket/1785 */
_twosided_type = PETSC_BUILDTWOSIDED_ALLREDUCE;
# else
_twosided_type = PETSC_BUILDTWOSIDED_IBARRIER;
# endif
#else
_twosided_type = PETSC_BUILDTWOSIDED_ALLREDUCE;
#endif
ierr = PetscOptionsGetEnum(NULL,"-build_twosided",PetscBuildTwoSidedTypes,(PetscEnum*)&_twosided_type,NULL);CHKERRQ(ierr);
}
*twosided = _twosided_type;
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscMPIInt rank;
PetscInt M = 13,s=1,dof=1;
DMDABoundaryType bx = DMDA_BOUNDARY_PERIODIC;
PetscErrorCode ierr;
DM da;
PetscViewer viewer;
Vec local,global;
PetscScalar value;
PetscDraw draw;
PetscBool flg = PETSC_FALSE;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
/* Create viewers */
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"",280,480,600,200,&viewer);CHKERRQ(ierr);
ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr);
ierr = PetscDrawSetDoubleBuffer(draw);CHKERRQ(ierr);
/* Readoptions */
ierr = PetscOptionsGetInt(NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetEnum(NULL,"-wrap",DMDABoundaryTypes,(PetscEnum*)&bx,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-dof",&dof,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-s",&s,NULL);CHKERRQ(ierr);
/* Create distributed array and get vectors */
ierr = DMDACreate1d(PETSC_COMM_WORLD,bx,M,dof,s,NULL,&da);CHKERRQ(ierr);
ierr = DMView(da,viewer);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
/* Set global vector; send ghost points to local vectors */
value = 1;
ierr = VecSet(global,value);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
/* Scale local vectors according to processor rank; pass to global vector */
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
value = rank+1;
ierr = VecScale(local,value);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(da,local,INSERT_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da,local,INSERT_VALUES,global);CHKERRQ(ierr);
ierr = VecView(global,viewer);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nGlobal Vector:\n");CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n");CHKERRQ(ierr);
/* Send ghost points to local vectors */
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-local_print",&flg,NULL);CHKERRQ(ierr);
if (flg) {
PetscViewer sviewer;
ISLocalToGlobalMapping is;
ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"\nLocal Vector: processor %d\n",rank);CHKERRQ(ierr);
ierr = PetscViewerGetSingleton(PETSC_VIEWER_STDOUT_WORLD,&sviewer);CHKERRQ(ierr);
ierr = VecView(local,sviewer);CHKERRQ(ierr);
ierr = PetscViewerRestoreSingleton(PETSC_VIEWER_STDOUT_WORLD,&sviewer);CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr);
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"\nLocal to global mapping: processor %d\n",rank);CHKERRQ(ierr);
ierr = PetscViewerGetSingleton(PETSC_VIEWER_STDOUT_WORLD,&sviewer);CHKERRQ(ierr);
ierr = DMGetLocalToGlobalMapping(da,&is);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingView(is,sviewer);CHKERRQ(ierr);
ierr = PetscViewerRestoreSingleton(PETSC_VIEWER_STDOUT_WORLD,&sviewer);CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr);
}
/* Free memory */
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
