/*
MSA_Plate - Calculates an obstacle for surface to stretch over.
*/
PetscErrorCode MSA_Plate(Vec XL,Vec XU,void *ctx)
{
AppCtx *user=(AppCtx *)ctx;
PetscErrorCode info;
PetscInt i,j;
PetscInt xs,ys,xm,ym;
PetscInt mx=user->mx, my=user->my, bmy, bmx;
PetscScalar t1,t2,t3;
PetscScalar **xl;
PetscScalar lb=-SNES_VI_INF, ub=SNES_VI_INF;
PetscBool cylinder;
user->bmy = PetscMax(0,user->bmy);user->bmy = PetscMin(my,user->bmy);
user->bmx = PetscMax(0,user->bmx);user->bmx = PetscMin(mx,user->bmx);
bmy=user->bmy, bmx=user->bmx;
info = DMDAGetCorners(user->da,&xs,&ys,PETSC_NULL,&xm,&ym,PETSC_NULL); CHKERRQ(info);
info = VecSet(XL, lb); CHKERRQ(info);
info = DMDAVecGetArray(user->da,XL,&xl);CHKERRQ(info);
info = VecSet(XU, ub); CHKERRQ(info);
info = PetscOptionsHasName(PETSC_NULL,"-cylinder",&cylinder); CHKERRQ(info);
/* Compute the optional lower box */
if (cylinder){
for (i=xs; i< xs+xm; i++){
for (j=ys; j<ys+ym; j++){
t1=(2.0*i-mx)*bmy;
t2=(2.0*j-my)*bmx;
t3=bmx*bmx*bmy*bmy;
if ( t1*t1 + t2*t2 <= t3 ){
xl[j][i] = user->bheight;
}
}
}
} else {
/* Compute the optional lower box */
for (i=xs; i< xs+xm; i++){
for (j=ys; j<ys+ym; j++){
if (i>=(mx-bmx)/2 && i<mx-(mx-bmx)/2 &&
j>=(my-bmy)/2 && j<my-(my-bmy)/2 ){
xl[j][i] = user->bheight;
}
}
}
}
info = DMDAVecRestoreArray(user->da,XL,&xl); CHKERRQ(info);
PetscFunctionReturn(0);
}
/*@
PetscDrawAxisSetLimits - Sets the limits (in user coords) of the axis
Not Collective (ignored on all processors except processor 0 of PetscDrawAxis)
Input Parameters:
+ axis - the axis
. xmin,xmax - limits in x
- ymin,ymax - limits in y
Options Database:
. -drawaxis_hold - hold the initial set of axis limits for future plotting
Level: advanced
.seealso: PetscDrawAxisSetHoldLimits()
@*/
PetscErrorCode PetscDrawAxisSetLimits(PetscDrawAxis axis,PetscReal xmin,PetscReal xmax,PetscReal ymin,PetscReal ymax)
{
PetscErrorCode ierr;
PetscFunctionBegin;
if (!axis) PetscFunctionReturn(0);
if (axis->hold) PetscFunctionReturn(0);
axis->xlow = xmin;
axis->xhigh= xmax;
axis->ylow = ymin;
axis->yhigh= ymax;
ierr = PetscOptionsHasName(((PetscObject)axis)->prefix,"-drawaxis_hold",&axis->hold);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
PetscDrawBarSetFromOptions - Sets options related to the PetscDrawBar
Collective over PetscDrawBar
Options Database:
. -bar_sort - sort the entries before drawing the bar graph
Level: intermediate
.seealso: PetscDrawBarDestroy(), PetscDrawBarCreate()
@*/
PetscErrorCode PetscDrawBarSetFromOptions(PetscDrawBar bar)
{
PetscErrorCode ierr;
PetscBool set;
PetscReal tol = bar->sorttolerance;
PetscFunctionBegin;
ierr = PetscOptionsHasName(NULL,"-bar_sort",&set);CHKERRQ(ierr);
if (set) {
ierr = PetscOptionsGetReal(NULL,"-bar_sort",&tol,NULL);CHKERRQ(ierr);
ierr = PetscDrawBarSort(bar,PETSC_TRUE,tol);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*
MatMFFDView_MFFD - Views matrix-free parameters.
*/
PetscErrorCode MatView_MFFD(Mat J,PetscViewer viewer)
{
PetscErrorCode ierr;
MatMFFD ctx = (MatMFFD)J->data;
PetscBool iascii, viewbase, viewfunction;
const char *prefix;
PetscFunctionBegin;
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr);
if (iascii) {
ierr = PetscViewerASCIIPrintf(viewer,"Matrix-free approximation:\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"err=%G (relative error in function evaluation)\n",ctx->error_rel);CHKERRQ(ierr);
if (!((PetscObject)ctx)->type_name) {
ierr = PetscViewerASCIIPrintf(viewer,"The compute h routine has not yet been set\n");CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIIPrintf(viewer,"Using %s compute h routine\n",((PetscObject)ctx)->type_name);CHKERRQ(ierr);
}
if (ctx->ops->view) {
ierr = (*ctx->ops->view)(ctx,viewer);CHKERRQ(ierr);
}
ierr = PetscObjectGetOptionsPrefix((PetscObject)J, &prefix);CHKERRQ(ierr);
ierr = PetscOptionsHasName(prefix, "-mat_mffd_view_base", &viewbase);CHKERRQ(ierr);
if (viewbase) {
ierr = PetscViewerASCIIPrintf(viewer, "Base:\n");CHKERRQ(ierr);
ierr = VecView(ctx->current_u, viewer);CHKERRQ(ierr);
}
ierr = PetscOptionsHasName(prefix, "-mat_mffd_view_function", &viewfunction);CHKERRQ(ierr);
if (viewfunction) {
ierr = PetscViewerASCIIPrintf(viewer, "Function:\n");CHKERRQ(ierr);
ierr = VecView(ctx->current_f, viewer);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscDraw draw;
PetscDrawLG lg;
PetscDrawAxis axis;
PetscInt n = 20,i,x = 0,y = 0,width = 300,height = 300,nports = 1;
PetscTruth flg;
const char *xlabel,*ylabel,*toplabel;
PetscReal xd,yd;
PetscDrawViewPorts *ports;
PetscErrorCode ierr;
xlabel = "X-axis Label";toplabel = "Top Label";ylabel = "Y-axis Label";
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-width",&width,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-height",&height,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL,"-nolabels",&flg);CHKERRQ(ierr);
if (flg) {
xlabel = (char *)0; toplabel = (char *)0;
}
ierr = PetscDrawCreate(PETSC_COMM_SELF,0,"Title",x,y,width,height,&draw);CHKERRQ(ierr);
ierr = PetscDrawSetFromOptions(draw);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-nports",&nports,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscDrawViewPortsCreate(draw,nports,&ports);CHKERRQ(ierr);
ierr = PetscDrawViewPortsSet(ports,0);CHKERRQ(ierr);
ierr = PetscDrawLGCreate(draw,1,&lg);CHKERRQ(ierr);
ierr = PetscDrawLGGetAxis(lg,&axis);CHKERRQ(ierr);
ierr = PetscDrawAxisSetColors(axis,PETSC_DRAW_BLACK,PETSC_DRAW_RED,PETSC_DRAW_BLUE);CHKERRQ(ierr);
ierr = PetscDrawAxisSetLabels(axis,toplabel,xlabel,ylabel);CHKERRQ(ierr);
for (i=0; i<n ; i++) {
xd = (PetscReal)(i - 5); yd = xd*xd;
ierr = PetscDrawLGAddPoint(lg,&xd,&yd);CHKERRQ(ierr);
}
ierr = PetscDrawLGIndicateDataPoints(lg);CHKERRQ(ierr);
ierr = PetscDrawLGDraw(lg);CHKERRQ(ierr);
ierr = PetscDrawString(draw,-3.,150.0,PETSC_DRAW_BLUE,"A legend");CHKERRQ(ierr);
ierr = PetscDrawFlush(draw);CHKERRQ(ierr);
ierr = PetscSleep(2);CHKERRQ(ierr);
ierr = PetscDrawViewPortsDestroy(ports);CHKERRQ(ierr);
ierr = PetscDrawLGDestroy(lg);CHKERRQ(ierr);
ierr = PetscDrawDestroy(draw);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
/*@
PetscDrawAxisSetLimits - Sets the limits (in user coords) of the axis
Not Collective (ignored on all processors except processor 0 of PetscDrawAxis)
Input Parameters:
+ axis - the axis
. xmin,xmax - limits in x
- ymin,ymax - limits in y
Options Database:
. -drawaxis_hold - hold the initial set of axis limits for future plotting
Level: advanced
.seealso: PetscDrawAxisSetHoldLimits()
@*/
PetscErrorCode PetscDrawAxisSetLimits(PetscDrawAxis axis,PetscReal xmin,PetscReal xmax,PetscReal ymin,PetscReal ymax)
{
PetscErrorCode ierr;
PetscFunctionBegin;
if (!axis) PetscFunctionReturn(0);
PetscValidHeaderSpecific(axis,PETSC_DRAWAXIS_CLASSID,1);
if (axis->hold) PetscFunctionReturn(0);
axis->xlow = xmin;
axis->xhigh= xmax;
axis->ylow = ymin;
axis->yhigh= ymax;
ierr = PetscOptionsHasName(((PetscObject)axis)->options,((PetscObject)axis)->prefix,"-drawaxis_hold",&axis->hold);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
PetscDrawBarSetFromOptions - Sets options related to the PetscDrawBar
Collective over PetscDrawBar
Options Database:
. -bar_sort - sort the entries before drawing the bar graph
Level: intermediate
.seealso: PetscDrawBarDestroy(), PetscDrawBarCreate(), PetscDrawBarSort()
@*/
PetscErrorCode PetscDrawBarSetFromOptions(PetscDrawBar bar)
{
PetscErrorCode ierr;
PetscBool set;
PetscFunctionBegin;
PetscValidHeaderSpecific(bar,PETSC_DRAWBAR_CLASSID,1);
ierr = PetscOptionsHasName(((PetscObject)bar)->options,((PetscObject)bar)->prefix,"-bar_sort",&set);CHKERRQ(ierr);
if (set) {
PetscReal tol = bar->sorttolerance;
ierr = PetscOptionsGetReal(((PetscObject)bar)->options,((PetscObject)bar)->prefix,"-bar_sort",&tol,NULL);CHKERRQ(ierr);
ierr = PetscDrawBarSort(bar,PETSC_TRUE,tol);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscDraw draw;
PetscDrawHG hist;
PetscDrawAxis axis;
PetscErrorCode ierr;
int n = 20,i,x = 0,y = 0,width = 300,height = 300,bins = 8;
PetscInt w = 300,h = 300,nn = 20,b = 8,c = PETSC_DRAW_GREEN;
int color = PETSC_DRAW_GREEN;
const char *xlabel,*ylabel,*toplabel;
PetscReal xd;
PetscTruth flg;
xlabel = "X-axis Label";toplabel = "Top Label";ylabel = "Y-axis Label";
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-width",&w,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-height",&h,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&nn,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-bins",&b,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-color",&c,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL,"-nolabels",&flg);CHKERRQ(ierr);
width = (int) w; height = (int)h; n = (int)nn; bins = (int) b; color = (int) c;
if (flg) {
xlabel = (char *)0; toplabel = (char *)0;
}
/* ierr = PetscDrawOpenX(PETSC_COMM_SELF,0,"Title",x,y,width,height,&draw);CHKERRQ(ierr);*/
ierr = PetscDrawCreate(PETSC_COMM_SELF,0,"Title",x,y,width,height,&draw);CHKERRQ(ierr);
ierr = PetscDrawSetType(draw,PETSC_DRAW_X);CHKERRQ(ierr);
ierr = PetscDrawHGCreate(draw,bins,&hist);CHKERRQ(ierr);
ierr = PetscDrawHGGetAxis(hist,&axis);CHKERRQ(ierr);
ierr = PetscDrawAxisSetColors(axis,PETSC_DRAW_BLACK,PETSC_DRAW_RED,PETSC_DRAW_BLUE);CHKERRQ(ierr);
ierr = PetscDrawAxisSetLabels(axis,toplabel,xlabel,ylabel);CHKERRQ(ierr);
for (i=0; i<n ; i++) {
xd = (PetscReal)(i - 5);
ierr = PetscDrawHGAddValue(hist,xd*xd);CHKERRQ(ierr);
}
ierr = PetscDrawHGSetColor(hist,color);CHKERRQ(ierr);
ierr = PetscDrawHGDraw(hist);CHKERRQ(ierr);
ierr = PetscDrawFlush(draw);CHKERRQ(ierr);
ierr = PetscDrawHGDestroy(hist);CHKERRQ(ierr);
ierr = PetscDrawDestroy(draw);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
PetscErrorCode PetscOptionsCheckInitial_Components(void)
{
PetscBool flg1;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscOptionsHasName(NULL,"-help",&flg1);CHKERRQ(ierr);
if (flg1) {
#if defined(PETSC_USE_LOG)
MPI_Comm comm = PETSC_COMM_WORLD;
ierr = (*PetscHelpPrintf)(comm,"------Additional PETSc component options--------\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -log_summary_exclude: <vec,mat,pc.ksp,snes>\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -info_exclude: <null,vec,mat,pc,ksp,snes,ts>\n");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm,"-----------------------------------------------\n");CHKERRQ(ierr);
#endif
}
PetscFunctionReturn(0);
}
PetscErrorCode PetscStackCreate(void)
{
PetscStack *petscstack_in;
if (PetscStackActive()) return 0;
petscstack_in = (PetscStack*)malloc(sizeof(PetscStack));
petscstack_in->currentsize = 0;
PetscThreadLocalSetValue((PetscThreadKey*)&petscstack,petscstack_in);
#if defined(PETSC_HAVE_AMS)
{
PetscBool flg = PETSC_FALSE;
PetscOptionsHasName(NULL,"-stack_view",&flg);
if (flg) PetscStackViewAMS();
}
#endif
return 0;
}
int main(int argc,char **args)
{
Mat C;
PetscInt i,j,m = 5,n = 5,Ii,J;
PetscErrorCode ierr;
PetscScalar v,five = 5.0;
IS isrow;
PetscBool keepnonzeropattern;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
/* create the matrix for the five point stencil, YET AGAIN*/
ierr = MatCreate(PETSC_COMM_SELF,&C);CHKERRQ(ierr);
ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,m*n,m*n);CHKERRQ(ierr);
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
for (i=0; i<m; i++) {
for (j=0; j<n; j++) {
v = -1.0; Ii = j + n*i;
if (i>0) {J = Ii - n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (i<m-1) {J = Ii + n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (j>0) {J = Ii - 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (j<n-1) {J = Ii + 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
v = 4.0; ierr = MatSetValues(C,1,&Ii,1,&Ii,&v,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,(m*n)/2,0,2,&isrow);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,NULL,"-keep_nonzero_pattern",&keepnonzeropattern);CHKERRQ(ierr);
if (keepnonzeropattern) {
ierr = MatSetOption(C,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE);CHKERRQ(ierr);
}
ierr = MatZeroRowsIS(C,isrow,five,0,0);CHKERRQ(ierr);
ierr = MatView(C,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = ISDestroy(&isrow);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode TestMatZeroRows_Basic(Mat A,IS is,PetscScalar diag)
{
Mat B;
PetscErrorCode ierr;
PetscBool keepnonzeropattern;
/* Now copy A into B, and test it with MatZeroRows() */
ierr = MatDuplicate(A,MAT_COPY_VALUES,&B);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,NULL,"-keep_nonzero_pattern",&keepnonzeropattern);CHKERRQ(ierr);
if (keepnonzeropattern) {
ierr = MatSetOption(B,MAT_KEEP_NONZERO_PATTERN,PETSC_TRUE);CHKERRQ(ierr);
}
ierr = MatZeroRowsIS(B,is,diag,0,0);CHKERRQ(ierr);
ierr = MatView(B,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
return 0;
}
PetscErrorCode GetListofEdges_Water(WATERDATA *water,PetscInt *edgelist)
{
PetscErrorCode ierr;
PetscInt i,j,node1,node2;
Pipe *pipe;
Pump *pump;
PetscBool netview=PETSC_FALSE;
PetscFunctionBegin;
ierr = PetscOptionsHasName(NULL,NULL, "-water_view",&netview);CHKERRQ(ierr);
for (i=0; i < water->nedge; i++) {
if (water->edge[i].type == EDGE_TYPE_PIPE) {
pipe = &water->edge[i].pipe;
node1 = pipe->node1;
node2 = pipe->node2;
if (netview) {
ierr = PetscPrintf(PETSC_COMM_SELF,"edge %d, pipe v[%d] -> v[%d]\n",i,node1,node2);CHKERRQ(ierr);
}
} else {
pump = &water->edge[i].pump;
node1 = pump->node1;
node2 = pump->node2;
if (netview) {
ierr = PetscPrintf(PETSC_COMM_SELF,"edge %d, pump v[%d] -> v[%d]\n",i,node1,node2);CHKERRQ(ierr);
}
}
for (j=0; j < water->nvertex; j++) {
if (water->vertex[j].id == node1) {
edgelist[2*i] = j;
break;
}
}
for (j=0; j < water->nvertex; j++) {
if (water->vertex[j].id == node2) {
edgelist[2*i+1] = j;
break;
}
}
}
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
PetscErrorCode ierr;
Mat A,AT,B,C;
PetscViewer viewer;
PetscBool flg;
char file[PETSC_MAX_PATH_LEN];
PetscInitialize(&argc,&args,(char *)0,help);
ierr = PetscOptionsGetString(PETSC_NULL,"-fA",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Input fileA not specified");
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetType(A,MATAIJ);CHKERRQ(ierr);
ierr = MatLoad(A,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-fB",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Input fileB not specified");
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&B);CHKERRQ(ierr);
ierr = MatSetType(B,MATDENSE);CHKERRQ(ierr);
ierr = MatLoad(B,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&AT);CHKERRQ(ierr);
ierr = MatMatMult(AT,B,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&C);
ierr = PetscOptionsHasName(PETSC_NULL,"-view_C",&flg);CHKERRQ(ierr);
if (flg){
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"C.dat",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer,PETSC_VIEWER_NATIVE);CHKERRQ(ierr);
ierr = MatView(C,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&AT);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode DMTSCheckFromOptions(TS ts, Vec u, PetscErrorCode (**exactFuncs)(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx), void **ctxs)
{
DM dm;
SNES snes;
Vec sol;
PetscBool check;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscOptionsHasName(((PetscObject)ts)->options,((PetscObject)ts)->prefix, "-dmts_check", &check);CHKERRQ(ierr);
if (!check) PetscFunctionReturn(0);
ierr = VecDuplicate(u, &sol);CHKERRQ(ierr);
ierr = TSSetSolution(ts, sol);CHKERRQ(ierr);
ierr = TSGetDM(ts, &dm);CHKERRQ(ierr);
ierr = TSSetUp(ts);CHKERRQ(ierr);
ierr = TSGetSNES(ts, &snes);CHKERRQ(ierr);
ierr = SNESSetSolution(snes, sol);CHKERRQ(ierr);
ierr = DMSNESCheckFromOptions_Internal(snes, dm, u, sol, exactFuncs, ctxs);CHKERRQ(ierr);
ierr = VecDestroy(&sol);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscDraw draw;
PetscDrawBar bar;
PetscDrawAxis axis;
PetscErrorCode ierr;
int color = PETSC_DRAW_ROTATE;
const char *xlabel,*ylabel,*toplabel;
const PetscReal values[] = {.3, .5, .05, .11};
const char *const labels[] = {"A","B","C","D",NULL};
PetscReal limits[2] = {0,0.55}; PetscInt nlimits = 2;
PetscBool nolabels,setlimits;
xlabel = "X-axis Label"; toplabel = "Top Label"; ylabel = "Y-axis Label";
ierr = PetscInitialize(&argc,&argv,NULL,help);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,NULL,"-nolabels",&nolabels);CHKERRQ(ierr);
if (nolabels) { xlabel = NULL; ylabel = NULL; toplabel = NULL; }
ierr = PetscOptionsGetRealArray(NULL,NULL,"-limits",limits,&nlimits,&setlimits);CHKERRQ(ierr);
ierr = PetscDrawCreate(PETSC_COMM_WORLD,NULL,"Title",PETSC_DECIDE,PETSC_DECIDE,400,300,&draw);CHKERRQ(ierr);
ierr = PetscDrawSetFromOptions(draw);CHKERRQ(ierr);
ierr = PetscDrawBarCreate(draw,&bar);CHKERRQ(ierr);
ierr = PetscDrawBarGetAxis(bar,&axis);CHKERRQ(ierr);
ierr = PetscDrawAxisSetColors(axis,PETSC_DRAW_BLACK,PETSC_DRAW_RED,PETSC_DRAW_BLUE);CHKERRQ(ierr);
ierr = PetscDrawAxisSetLabels(axis,toplabel,xlabel,ylabel);CHKERRQ(ierr);
ierr = PetscDrawBarSetColor(bar,color);CHKERRQ(ierr);
ierr = PetscDrawBarSetFromOptions(bar);CHKERRQ(ierr);
if (setlimits) {ierr = PetscDrawBarSetLimits(bar,limits[0],limits[1]);CHKERRQ(ierr);}
ierr = PetscDrawBarSetData(bar,4,values,labels);CHKERRQ(ierr);
ierr = PetscDrawBarDraw(bar);CHKERRQ(ierr);
ierr = PetscDrawBarSave(bar);CHKERRQ(ierr);
ierr = PetscDrawBarDestroy(&bar);CHKERRQ(ierr);
ierr = PetscDrawDestroy(&draw);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int Argc,char **Args)
{
PetscInt x_mesh = 15,levels = 3,cycles = 1,use_jacobi = 0;
PetscInt i,smooths = 1,*N,its;
PetscErrorCode ierr;
PCMGType am = PC_MG_MULTIPLICATIVE;
Mat cmat,mat[20],fmat;
KSP cksp,ksp[20],kspmg;
PetscReal e[3]; /* l_2 error,max error, residual */
const char *shellname;
Vec x,solution,X[20],R[20],B[20];
PC pcmg,pc;
PetscBool flg;
PetscInitialize(&Argc,&Args,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-x",&x_mesh,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-l",&levels,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-c",&cycles,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-smooths",&smooths,NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-a",&flg);CHKERRQ(ierr);
if (flg) am = PC_MG_ADDITIVE;
ierr = PetscOptionsHasName(NULL,"-f",&flg);CHKERRQ(ierr);
if (flg) am = PC_MG_FULL;
ierr = PetscOptionsHasName(NULL,"-j",&flg);CHKERRQ(ierr);
if (flg) use_jacobi = 1;
ierr = PetscMalloc1(levels,&N);CHKERRQ(ierr);
N[0] = x_mesh;
for (i=1; i<levels; i++) {
N[i] = N[i-1]/2;
if (N[i] < 1) SETERRQ(PETSC_COMM_WORLD,1,"Too many levels");
}
ierr = Create1dLaplacian(N[levels-1],&cmat);CHKERRQ(ierr);
ierr = KSPCreate(PETSC_COMM_WORLD,&kspmg);CHKERRQ(ierr);
ierr = KSPGetPC(kspmg,&pcmg);CHKERRQ(ierr);
ierr = KSPSetFromOptions(kspmg);CHKERRQ(ierr);
ierr = PCSetType(pcmg,PCMG);CHKERRQ(ierr);
ierr = PCMGSetLevels(pcmg,levels,NULL);CHKERRQ(ierr);
ierr = PCMGSetType(pcmg,am);CHKERRQ(ierr);
ierr = PCMGGetCoarseSolve(pcmg,&cksp);CHKERRQ(ierr);
ierr = KSPSetOperators(cksp,cmat,cmat);CHKERRQ(ierr);
ierr = KSPGetPC(cksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCLU);CHKERRQ(ierr);
ierr = KSPSetType(cksp,KSPPREONLY);CHKERRQ(ierr);
/* zero is finest level */
for (i=0; i<levels-1; i++) {
ierr = PCMGSetResidual(pcmg,levels - 1 - i,residual,(Mat)0);CHKERRQ(ierr);
ierr = MatCreateShell(PETSC_COMM_WORLD,N[i+1],N[i],N[i+1],N[i],(void*)0,&mat[i]);CHKERRQ(ierr);
ierr = MatShellSetOperation(mat[i],MATOP_MULT,(void (*)(void))restrct);CHKERRQ(ierr);
ierr = MatShellSetOperation(mat[i],MATOP_MULT_TRANSPOSE_ADD,(void (*)(void))interpolate);CHKERRQ(ierr);
ierr = PCMGSetInterpolation(pcmg,levels - 1 - i,mat[i]);CHKERRQ(ierr);
ierr = PCMGSetRestriction(pcmg,levels - 1 - i,mat[i]);CHKERRQ(ierr);
ierr = PCMGSetCyclesOnLevel(pcmg,levels - 1 - i,cycles);CHKERRQ(ierr);
/* set smoother */
ierr = PCMGGetSmoother(pcmg,levels - 1 - i,&ksp[i]);CHKERRQ(ierr);
ierr = KSPGetPC(ksp[i],&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCSHELL);CHKERRQ(ierr);
ierr = PCShellSetName(pc,"user_precond");CHKERRQ(ierr);
ierr = PCShellGetName(pc,&shellname);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"level=%D, PCShell name is %s\n",i,shellname);CHKERRQ(ierr);
/* this is a dummy! since KSP requires a matrix passed in */
ierr = KSPSetOperators(ksp[i],mat[i],mat[i]);CHKERRQ(ierr);
/*
We override the matrix passed in by forcing it to use Richardson with
a user provided application. This is non-standard and this practice
should be avoided.
*/
ierr = PCShellSetApplyRichardson(pc,gauss_seidel);CHKERRQ(ierr);
if (use_jacobi) {
ierr = PCShellSetApplyRichardson(pc,jacobi);CHKERRQ(ierr);
}
ierr = KSPSetType(ksp[i],KSPRICHARDSON);CHKERRQ(ierr);
ierr = KSPSetInitialGuessNonzero(ksp[i],PETSC_TRUE);CHKERRQ(ierr);
ierr = KSPSetTolerances(ksp[i],PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,smooths);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,N[i],&x);CHKERRQ(ierr);
X[levels - 1 - i] = x;
if (i > 0) {
ierr = PCMGSetX(pcmg,levels - 1 - i,x);CHKERRQ(ierr);
}
ierr = VecCreateSeq(PETSC_COMM_SELF,N[i],&x);CHKERRQ(ierr);
B[levels -1 - i] = x;
if (i > 0) {
ierr = PCMGSetRhs(pcmg,levels - 1 - i,x);CHKERRQ(ierr);
}
ierr = VecCreateSeq(PETSC_COMM_SELF,N[i],&x);CHKERRQ(ierr);
R[levels - 1 - i] = x;
ierr = PCMGSetR(pcmg,levels - 1 - i,x);CHKERRQ(ierr);
}
/* create coarse level vectors */
ierr = VecCreateSeq(PETSC_COMM_SELF,N[levels-1],&x);CHKERRQ(ierr);
ierr = PCMGSetX(pcmg,0,x);CHKERRQ(ierr); X[0] = x;
ierr = VecCreateSeq(PETSC_COMM_SELF,N[levels-1],&x);CHKERRQ(ierr);
ierr = PCMGSetRhs(pcmg,0,x);CHKERRQ(ierr); B[0] = x;
/* create matrix multiply for finest level */
ierr = MatCreateShell(PETSC_COMM_WORLD,N[0],N[0],N[0],N[0],(void*)0,&fmat);CHKERRQ(ierr);
ierr = MatShellSetOperation(fmat,MATOP_MULT,(void (*)(void))amult);CHKERRQ(ierr);
ierr = KSPSetOperators(kspmg,fmat,fmat);CHKERRQ(ierr);
ierr = CalculateSolution(N[0],&solution);CHKERRQ(ierr);
ierr = CalculateRhs(B[levels-1]);CHKERRQ(ierr);
ierr = VecSet(X[levels-1],0.0);CHKERRQ(ierr);
ierr = residual((Mat)0,B[levels-1],X[levels-1],R[levels-1]);CHKERRQ(ierr);
ierr = CalculateError(solution,X[levels-1],R[levels-1],e);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"l_2 error %g max error %g resi %g\n",(double)e[0],(double)e[1],(double)e[2]);CHKERRQ(ierr);
ierr = KSPSolve(kspmg,B[levels-1],X[levels-1]);CHKERRQ(ierr);
ierr = KSPGetIterationNumber(kspmg,&its);CHKERRQ(ierr);
ierr = residual((Mat)0,B[levels-1],X[levels-1],R[levels-1]);CHKERRQ(ierr);
ierr = CalculateError(solution,X[levels-1],R[levels-1],e);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"its %D l_2 error %g max error %g resi %g\n",its,(double)e[0],(double)e[1],(double)e[2]);CHKERRQ(ierr);
ierr = PetscFree(N);CHKERRQ(ierr);
ierr = VecDestroy(&solution);CHKERRQ(ierr);
/* note we have to keep a list of all vectors allocated, this is
not ideal, but putting it in MGDestroy is not so good either*/
for (i=0; i<levels; i++) {
ierr = VecDestroy(&X[i]);CHKERRQ(ierr);
ierr = VecDestroy(&B[i]);CHKERRQ(ierr);
if (i) {ierr = VecDestroy(&R[i]);CHKERRQ(ierr);}
}
for (i=0; i<levels-1; i++) {
ierr = MatDestroy(&mat[i]);CHKERRQ(ierr);
}
ierr = MatDestroy(&cmat);CHKERRQ(ierr);
ierr = MatDestroy(&fmat);CHKERRQ(ierr);
ierr = KSPDestroy(&kspmg);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscMPIInt rank;
PetscInt M=8,dof=1,stencil_width=1,i,start,end,P=5,N = 6,m=PETSC_DECIDE,n=PETSC_DECIDE,p=PETSC_DECIDE,pt = 0,st = 0;
PetscErrorCode ierr;
PetscBool flg = PETSC_FALSE,flg2,flg3;
DMDABoundaryType periodic;
DMDAStencilType stencil_type;
DM da;
Vec local,global,local_copy;
PetscScalar value;
PetscReal norm,work;
PetscViewer viewer;
char filename[64];
FILE *file;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-N",&N,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-dof",&dof,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-stencil_width",&stencil_width,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-periodic",&pt,NULL);CHKERRQ(ierr);
periodic = (DMDABoundaryType) pt;
ierr = PetscOptionsGetInt(NULL,"-stencil_type",&st,NULL);CHKERRQ(ierr);
stencil_type = (DMDAStencilType) st;
ierr = PetscOptionsHasName(NULL,"-2d",&flg2);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-3d",&flg3);CHKERRQ(ierr);
if (flg2) {
ierr = DMDACreate2d(PETSC_COMM_WORLD,periodic,periodic,stencil_type,M,N,m,n,dof,stencil_width,
NULL,NULL,&da);CHKERRQ(ierr);
} else if (flg3) {
ierr = DMDACreate3d(PETSC_COMM_WORLD,periodic,periodic,periodic,stencil_type,M,N,P,m,n,p,dof,stencil_width,
NULL,NULL,NULL,&da);CHKERRQ(ierr);
} else {
ierr = DMDACreate1d(PETSC_COMM_WORLD,periodic,M,dof,stencil_width,NULL,&da);CHKERRQ(ierr);
}
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = VecDuplicate(local,&local_copy);CHKERRQ(ierr);
/* zero out vectors so that ghostpoints are zero */
value = 0;
ierr = VecSet(local,value);CHKERRQ(ierr);
ierr = VecSet(local_copy,value);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(global,&start,&end);CHKERRQ(ierr);
for (i=start; i<end; i++) {
value = i + 1;
ierr = VecSetValues(global,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(global);CHKERRQ(ierr);
ierr = VecAssemblyEnd(global);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMDALocalToLocalBegin(da,local,INSERT_VALUES,local_copy);CHKERRQ(ierr);
ierr = DMDALocalToLocalEnd(da,local,INSERT_VALUES,local_copy);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-save",&flg,NULL);CHKERRQ(ierr);
if (flg) {
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
sprintf(filename,"local.%d",rank);
ierr = PetscViewerASCIIOpen(PETSC_COMM_SELF,filename,&viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIGetPointer(viewer,&file);CHKERRQ(ierr);
ierr = VecView(local,viewer);CHKERRQ(ierr);
fprintf(file,"Vector with correct ghost points\n");
ierr = VecView(local_copy,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = VecAXPY(local_copy,-1.0,local);CHKERRQ(ierr);
ierr = VecNorm(local_copy,NORM_MAX,&work);CHKERRQ(ierr);
ierr = MPI_Allreduce(&work,&norm,1,MPIU_REAL,MPIU_MAX,PETSC_COMM_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Norm of difference %G should be zero\n",norm);CHKERRQ(ierr);
ierr = VecDestroy(&local_copy);CHKERRQ(ierr);
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
DS ds;
SlepcSC sc;
PetscScalar *A,*B,*wr,*wi;
PetscReal re,im;
PetscInt i,j,n=10,ld;
PetscViewer viewer;
PetscBool verbose;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Solve a Dense System of type GNHEP - dimension %D.\n",n);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-verbose",&verbose);CHKERRQ(ierr);
/* Create DS object */
ierr = DSCreate(PETSC_COMM_WORLD,&ds);CHKERRQ(ierr);
ierr = DSSetType(ds,DSGNHEP);CHKERRQ(ierr);
ierr = DSSetFromOptions(ds);CHKERRQ(ierr);
ld = n+2; /* test leading dimension larger than n */
ierr = DSAllocate(ds,ld);CHKERRQ(ierr);
ierr = DSSetDimensions(ds,n,0,0,0);CHKERRQ(ierr);
/* Set up viewer */
ierr = PetscViewerASCIIGetStdout(PETSC_COMM_WORLD,&viewer);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(viewer,PETSC_VIEWER_ASCII_INFO_DETAIL);CHKERRQ(ierr);
ierr = DSView(ds,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
if (verbose) {
ierr = PetscViewerPushFormat(viewer,PETSC_VIEWER_ASCII_MATLAB);CHKERRQ(ierr);
}
/* Fill A with Grcar matrix */
ierr = DSGetArray(ds,DS_MAT_A,&A);CHKERRQ(ierr);
ierr = PetscMemzero(A,sizeof(PetscScalar)*ld*n);CHKERRQ(ierr);
for (i=1;i<n;i++) A[i+(i-1)*ld]=-1.0;
for (j=0;j<4;j++) {
for (i=0;i<n-j;i++) A[i+(i+j)*ld]=1.0;
}
ierr = DSRestoreArray(ds,DS_MAT_A,&A);CHKERRQ(ierr);
/* Fill B with an identity matrix */
ierr = DSGetArray(ds,DS_MAT_B,&B);CHKERRQ(ierr);
ierr = PetscMemzero(B,sizeof(PetscScalar)*ld*n);CHKERRQ(ierr);
for (i=0;i<n;i++) B[i+i*ld]=1.0;
ierr = DSRestoreArray(ds,DS_MAT_B,&B);CHKERRQ(ierr);
if (verbose) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Initial - - - - - - - - -\n");CHKERRQ(ierr);
ierr = DSView(ds,viewer);CHKERRQ(ierr);
}
/* Solve */
ierr = PetscMalloc2(n,&wr,n,&wi);CHKERRQ(ierr);
ierr = DSGetSlepcSC(ds,&sc);CHKERRQ(ierr);
sc->comparison = SlepcCompareLargestMagnitude;
sc->comparisonctx = NULL;
sc->map = NULL;
sc->mapobj = NULL;
ierr = DSSolve(ds,wr,wi);CHKERRQ(ierr);
ierr = DSSort(ds,wr,wi,NULL,NULL,NULL);CHKERRQ(ierr);
if (verbose) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"After solve - - - - - - - - -\n");CHKERRQ(ierr);
ierr = DSView(ds,viewer);CHKERRQ(ierr);
}
/* Print eigenvalues */
ierr = PetscPrintf(PETSC_COMM_WORLD,"Computed eigenvalues =\n",n);CHKERRQ(ierr);
for (i=0;i<n;i++) {
#if defined(PETSC_USE_COMPLEX)
re = PetscRealPart(wr[i]);
im = PetscImaginaryPart(wr[i]);
#else
re = wr[i];
im = wi[i];
#endif
if (PetscAbs(im)<1e-10) {
ierr = PetscViewerASCIIPrintf(viewer," %.5f\n",(double)re);CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIIPrintf(viewer," %.5f%+.5fi\n",(double)re,(double)im);CHKERRQ(ierr);
}
}
ierr = PetscFree2(wr,wi);CHKERRQ(ierr);
ierr = DSDestroy(&ds);CHKERRQ(ierr);
ierr = SlepcFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscMPIInt rank,size;
PetscInt nlocal = 6,nghost = 2,ifrom[2],i,rstart,rend;
PetscErrorCode ierr;
PetscBool flg,flg2;
PetscScalar value,*array,*tarray=0;
Vec lx,gx,gxs;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 2) SETERRQ(PETSC_COMM_SELF,1,"Must run example with two processors\n");
/*
Construct a two dimensional graph connecting nlocal degrees of
freedom per processor. From this we will generate the global
indices of needed ghost values
For simplicity we generate the entire graph on each processor:
in real application the graph would stored in parallel, but this
example is only to demonstrate the management of ghost padding
with VecCreateGhost().
In this example we consider the vector as representing
degrees of freedom in a one dimensional grid with periodic
boundary conditions.
----Processor 1--------- ----Processor 2 --------
0 1 2 3 4 5 6 7 8 9 10 11
|----|
|-------------------------------------------------|
*/
if (!rank) {
ifrom[0] = 11; ifrom[1] = 6;
} else {
ifrom[0] = 0; ifrom[1] = 5;
}
/*
Create the vector with two slots for ghost points. Note that both
the local vector (lx) and the global vector (gx) share the same
array for storing vector values.
*/
ierr = PetscOptionsHasName(PETSC_NULL,"-allocate",&flg);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL,"-vecmpisetghost",&flg2);CHKERRQ(ierr);
if (flg) {
ierr = PetscMalloc((nlocal+nghost)*sizeof(PetscScalar),&tarray);CHKERRQ(ierr);
ierr = VecCreateGhostWithArray(PETSC_COMM_WORLD,nlocal,PETSC_DECIDE,nghost,ifrom,tarray,&gxs);CHKERRQ(ierr);
} else if (flg2) {
ierr = VecCreate(PETSC_COMM_WORLD,&gxs);CHKERRQ(ierr);
ierr = VecSetType(gxs,VECMPI);CHKERRQ(ierr);
ierr = VecSetSizes(gxs,nlocal,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecMPISetGhost(gxs,nghost,ifrom);CHKERRQ(ierr);
} else {
ierr = VecCreateGhost(PETSC_COMM_WORLD,nlocal,PETSC_DECIDE,nghost,ifrom,&gxs);CHKERRQ(ierr);
}
/*
Test VecDuplicate()
*/
ierr = VecDuplicate(gxs,&gx);CHKERRQ(ierr);
ierr = VecDestroy(&gxs);CHKERRQ(ierr);
/*
Access the local representation
*/
ierr = VecGhostGetLocalForm(gx,&lx);CHKERRQ(ierr);
/*
Set the values from 0 to 12 into the "global" vector
*/
ierr = VecGetOwnershipRange(gx,&rstart,&rend);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) {
value = (PetscScalar) i;
ierr = VecSetValues(gx,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(gx);CHKERRQ(ierr);
ierr = VecAssemblyEnd(gx);CHKERRQ(ierr);
ierr = VecGhostUpdateBegin(gx,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecGhostUpdateEnd(gx,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
/*
Print out each vector, including the ghost padding region.
*/
ierr = VecGetArray(lx,&array);CHKERRQ(ierr);
for (i=0; i<nlocal+nghost; i++) {
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"%D %G\n",i,PetscRealPart(array[i]));CHKERRQ(ierr);
}
ierr = VecRestoreArray(lx,&array);CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD);CHKERRQ(ierr);
ierr = VecGhostRestoreLocalForm(gx,&lx);CHKERRQ(ierr);
ierr = VecDestroy(&gx);CHKERRQ(ierr);
if (flg) {ierr = PetscFree(tarray);CHKERRQ(ierr);}
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
DS ds;
FN f1,f2,f3,funs[3];
PetscScalar *Id,*A,*B,*wr,*wi,coeffs[2];
PetscReal tau=0.001,h,a=20,xi,re,im;
PetscInt i,n=10,ld,nev;
PetscViewer viewer;
PetscBool verbose;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-tau",&tau,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Solve a Dense System of type NEP - dimension %D, tau=%g.\n",n,(double)tau);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-verbose",&verbose);CHKERRQ(ierr);
/* Create DS object */
ierr = DSCreate(PETSC_COMM_WORLD,&ds);CHKERRQ(ierr);
ierr = DSSetType(ds,DSNEP);CHKERRQ(ierr);
ierr = DSSetFromOptions(ds);CHKERRQ(ierr);
/* Set functions (prior to DSAllocate) */
ierr = FNCreate(PETSC_COMM_WORLD,&f1);CHKERRQ(ierr);
ierr = FNSetType(f1,FNRATIONAL);CHKERRQ(ierr);
coeffs[0] = -1.0; coeffs[1] = 0.0;
ierr = FNSetParameters(f1,2,coeffs,0,NULL);CHKERRQ(ierr);
ierr = FNCreate(PETSC_COMM_WORLD,&f2);CHKERRQ(ierr);
ierr = FNSetType(f2,FNRATIONAL);CHKERRQ(ierr);
coeffs[0] = 1.0;
ierr = FNSetParameters(f2,1,coeffs,0,NULL);CHKERRQ(ierr);
ierr = FNCreate(PETSC_COMM_WORLD,&f3);CHKERRQ(ierr);
ierr = FNSetType(f3,FNEXP);CHKERRQ(ierr);
coeffs[0] = -tau;
ierr = FNSetParameters(f3,1,coeffs,0,NULL);CHKERRQ(ierr);
funs[0] = f1;
funs[1] = f2;
funs[2] = f3;
ierr = DSSetFN(ds,3,funs);CHKERRQ(ierr);
/* Set dimensions */
ld = n+2; /* test leading dimension larger than n */
ierr = DSAllocate(ds,ld);CHKERRQ(ierr);
ierr = DSSetDimensions(ds,n,0,0,0);CHKERRQ(ierr);
/* Set up viewer */
ierr = PetscViewerASCIIGetStdout(PETSC_COMM_WORLD,&viewer);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(viewer,PETSC_VIEWER_ASCII_INFO_DETAIL);CHKERRQ(ierr);
ierr = DSView(ds,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
if (verbose) {
ierr = PetscViewerPushFormat(viewer,PETSC_VIEWER_ASCII_MATLAB);CHKERRQ(ierr);
}
/* Fill matrices */
ierr = DSGetArray(ds,DS_MAT_E0,&Id);CHKERRQ(ierr);
for (i=0;i<n;i++) Id[i+i*ld]=1.0;
ierr = DSRestoreArray(ds,DS_MAT_E0,&Id);CHKERRQ(ierr);
h = PETSC_PI/(PetscReal)(n+1);
ierr = DSGetArray(ds,DS_MAT_E1,&A);CHKERRQ(ierr);
for (i=0;i<n;i++) A[i+i*ld]=-2.0/(h*h)+a;
for (i=1;i<n;i++) {
A[i+(i-1)*ld]=1.0/(h*h);
A[(i-1)+i*ld]=1.0/(h*h);
}
ierr = DSRestoreArray(ds,DS_MAT_E1,&A);CHKERRQ(ierr);
ierr = DSGetArray(ds,DS_MAT_E2,&B);CHKERRQ(ierr);
for (i=0;i<n;i++) {
xi = (i+1)*h;
B[i+i*ld] = -4.1+xi*(1.0-PetscExpReal(xi-PETSC_PI));
}
ierr = DSRestoreArray(ds,DS_MAT_E2,&B);CHKERRQ(ierr);
if (verbose) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Initial - - - - - - - - -\n");CHKERRQ(ierr);
ierr = DSView(ds,viewer);CHKERRQ(ierr);
}
/* Solve */
ierr = PetscMalloc2(n,&wr,n,&wi);CHKERRQ(ierr);
ierr = DSSolve(ds,wr,wi);CHKERRQ(ierr);
if (verbose) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"After solve - - - - - - - - -\n");CHKERRQ(ierr);
ierr = DSView(ds,viewer);CHKERRQ(ierr);
}
/* Print first eigenvalue */
ierr = PetscPrintf(PETSC_COMM_WORLD,"Computed eigenvalue =\n",n);CHKERRQ(ierr);
nev = 1;
for (i=0;i<nev;i++) {
#if defined(PETSC_USE_COMPLEX)
re = PetscRealPart(wr[i]);
im = PetscImaginaryPart(wr[i]);
#else
re = wr[i];
im = wi[i];
#endif
if (PetscAbs(im)<1e-10) {
ierr = PetscViewerASCIIPrintf(viewer," %.5f\n",(double)re);CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIIPrintf(viewer," %.5f%+.5fi\n",(double)re,(double)im);CHKERRQ(ierr);
}
}
ierr = PetscFree2(wr,wi);CHKERRQ(ierr);
ierr = FNDestroy(&f1);CHKERRQ(ierr);
ierr = FNDestroy(&f2);CHKERRQ(ierr);
ierr = FNDestroy(&f3);CHKERRQ(ierr);
ierr = DSDestroy(&ds);CHKERRQ(ierr);
ierr = SlepcFinalize();
return 0;
}
int main(int argc,char **argv)
{
Mat mat,tmat = 0;
PetscInt m = 7,n,i,j,rstart,rend,rect = 0;
PetscErrorCode ierr;
PetscMPIInt size,rank;
PetscBool flg;
PetscScalar v, alpha;
PetscReal normf,normi,norm1;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_COMMON);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-m",&m,NULL);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
n = m;
ierr = PetscOptionsHasName(NULL,"-rectA",&flg);CHKERRQ(ierr);
if (flg) {n += 2; rect = 1;}
ierr = PetscOptionsHasName(NULL,"-rectB",&flg);CHKERRQ(ierr);
if (flg) {n -= 2; rect = 1;}
/* ------- Assemble matrix, test MatValid() --------- */
ierr = MatCreate(PETSC_COMM_WORLD,&mat);CHKERRQ(ierr);
ierr = MatSetSizes(mat,PETSC_DECIDE,PETSC_DECIDE,m,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(mat);CHKERRQ(ierr);
ierr = MatSetUp(mat);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(mat,&rstart,&rend);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) {
for (j=0; j<n; j++) {
v = 10.0*i+j;
ierr = MatSetValues(mat,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* ----------------- Test MatNorm() ----------------- */
ierr = MatNorm(mat,NORM_FROBENIUS,&normf);CHKERRQ(ierr);
ierr = MatNorm(mat,NORM_1,&norm1);CHKERRQ(ierr);
ierr = MatNorm(mat,NORM_INFINITY,&normi);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"original A: Frobenious norm = %G, one norm = %G, infinity norm = %G\n",
normf,norm1,normi);CHKERRQ(ierr);
ierr = MatView(mat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* --------------- Test MatTranspose() -------------- */
ierr = PetscOptionsHasName(NULL,"-in_place",&flg);CHKERRQ(ierr);
if (!rect && flg) {
ierr = MatTranspose(mat,MAT_REUSE_MATRIX,&mat);CHKERRQ(ierr); /* in-place transpose */
tmat = mat; mat = 0;
} else { /* out-of-place transpose */
ierr = MatTranspose(mat,MAT_INITIAL_MATRIX,&tmat);CHKERRQ(ierr);
}
/* ----------------- Test MatNorm() ----------------- */
/* Print info about transpose matrix */
ierr = MatNorm(tmat,NORM_FROBENIUS,&normf);CHKERRQ(ierr);
ierr = MatNorm(tmat,NORM_1,&norm1);CHKERRQ(ierr);
ierr = MatNorm(tmat,NORM_INFINITY,&normi);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"B = A^T: Frobenious norm = %G, one norm = %G, infinity norm = %G\n",
normf,norm1,normi);CHKERRQ(ierr);
ierr = MatView(tmat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* ----------------- Test MatAXPY(), MatAYPX() ----------------- */
if (mat && !rect) {
alpha = 1.0;
ierr = PetscOptionsGetScalar(NULL,"-alpha",&alpha,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"MatAXPY: B = B + alpha * A\n");CHKERRQ(ierr);
ierr = MatAXPY(tmat,alpha,mat,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatView(tmat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"MatAYPX: B = alpha*B + A\n");CHKERRQ(ierr);
ierr = MatAYPX(tmat,alpha,mat,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatView(tmat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
{
Mat C;
alpha = 1.0;
ierr = PetscPrintf(PETSC_COMM_WORLD,"MatAXPY: C = C + alpha * A, C=A, SAME_NONZERO_PATTERN\n");CHKERRQ(ierr);
ierr = MatDuplicate(mat,MAT_COPY_VALUES,&C);CHKERRQ(ierr);
ierr = MatAXPY(C,alpha,mat,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
}
{
Mat matB;
/* get matB that has nonzeros of mat in all even numbers of row and col */
ierr = MatCreate(PETSC_COMM_WORLD,&matB);CHKERRQ(ierr);
ierr = MatSetSizes(matB,PETSC_DECIDE,PETSC_DECIDE,m,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(matB);CHKERRQ(ierr);
ierr = MatSetUp(matB);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(matB,&rstart,&rend);CHKERRQ(ierr);
if (rstart % 2 != 0) rstart++;
for (i=rstart; i<rend; i += 2) {
for (j=0; j<n; j += 2) {
v = 10.0*i+j;
ierr = MatSetValues(matB,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(matB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(matB,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
PetscPrintf(PETSC_COMM_WORLD," A: original matrix:\n");
ierr = MatView(mat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
PetscPrintf(PETSC_COMM_WORLD," B(a subset of A):\n");
ierr = MatView(matB,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"MatAXPY: B = B + alpha * A, SUBSET_NONZERO_PATTERN\n");CHKERRQ(ierr);
ierr = MatAXPY(mat,alpha,matB,SUBSET_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatView(mat,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&matB);CHKERRQ(ierr);
}
/* Free data structures */
if (mat) {ierr = MatDestroy(&mat);CHKERRQ(ierr);}
if (tmat) {ierr = MatDestroy(&tmat);CHKERRQ(ierr);}
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat A,Asp;
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
PetscErrorCode ierr;
PetscInt m,n,rstart,rend;
PetscBool flg;
PetscInt row,ncols,j,nrows,nnzA=0,nnzAsp=0;
const PetscInt *cols;
const PetscScalar *vals;
PetscReal norm,percent,val,dtol=1.e-16;
PetscMPIInt rank;
MatInfo matinfo;
PetscInt Dnnz,Onnz;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
/* Determine files from which we read the linear systems. */
ierr = PetscOptionsGetString(PETSC_NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
/* Open binary file. Note that we use FILE_MODE_READ to indicate
reading from this file. */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
/* Load the matrix; then destroy the viewer. */
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(A,"a_");CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr);
ierr = MatGetInfo(A,MAT_LOCAL,&matinfo);CHKERRQ(ierr);
//printf("matinfo.nz_used %g\n",matinfo.nz_used);
/* Get a sparse matrix Asp by dumping zero entries of A */
ierr = MatCreate(PETSC_COMM_WORLD,&Asp);CHKERRQ(ierr);
ierr = MatSetSizes(Asp,m,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(Asp,"asp_");CHKERRQ(ierr);
ierr = MatSetFromOptions(Asp);CHKERRQ(ierr);
Dnnz = (PetscInt)matinfo.nz_used/m + 1;
Onnz = Dnnz/2;
printf("Dnnz %d %d\n",Dnnz,Onnz);
ierr = MatSeqAIJSetPreallocation(Asp,Dnnz,PETSC_NULL);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(Asp,Dnnz,PETSC_NULL,Onnz,PETSC_NULL);CHKERRQ(ierr);
/* Check zero rows */
ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
nrows = 0;
for (row=rstart; row<rend; row++){
ierr = MatGetRow(A,row,&ncols,&cols,&vals);CHKERRQ(ierr);
nnzA += ncols;
norm = 0.0;
for (j=0; j<ncols; j++){
val = PetscAbsScalar(vals[j]);
if (norm < val) norm = norm;
if (val > dtol){
ierr = MatSetValues(Asp,1,&row,1,&cols[j],&vals[j],INSERT_VALUES);CHKERRQ(ierr);
nnzAsp++;
}
}
if (!norm) nrows++;
ierr = MatRestoreRow(A,row,&ncols,&cols,&vals);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(Asp,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Asp,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
percent=(PetscReal)nnzA*100/(m*n);
ierr = PetscPrintf(PETSC_COMM_SELF," [%d] Matrix A local size %d,%d; nnzA %d, %g percent; No. of zero rows: %d\n",rank,m,n,nnzA,percent,nrows);
percent=(PetscReal)nnzAsp*100/(m*n);
ierr = PetscPrintf(PETSC_COMM_SELF," [%d] Matrix Asp nnzAsp %d, %g percent\n",rank,nnzAsp,percent);
/* investigate matcoloring for Asp */
PetscBool Asp_coloring = PETSC_FALSE;
ierr = PetscOptionsHasName(PETSC_NULL,"-Asp_color",&Asp_coloring);CHKERRQ(ierr);
if (Asp_coloring){
ISColoring iscoloring;
MatFDColoring matfdcoloring;
ierr = PetscPrintf(PETSC_COMM_WORLD," Create coloring of Asp...\n");
ierr = MatGetColoring(Asp,MATCOLORINGSL,&iscoloring);CHKERRQ(ierr);
ierr = MatFDColoringCreate(Asp,iscoloring,&matfdcoloring);CHKERRQ(ierr);
ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr);
//ierr = MatFDColoringView(matfdcoloring,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
ierr = MatFDColoringDestroy(&matfdcoloring);CHKERRQ(ierr);
}
/* Write Asp in binary for study - see ~petsc/src/mat/examples/tests/ex124.c */
PetscBool Asp_write = PETSC_FALSE;
ierr = PetscOptionsHasName(PETSC_NULL,"-Asp_write",&Asp_write);CHKERRQ(ierr);
if (Asp_write){
PetscViewer viewer;
ierr = PetscPrintf(PETSC_COMM_SELF,"Write Asp into file Asp.dat ...\n");
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Asp.dat",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = MatView(Asp,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&Asp);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
/*@
PetscDrawSetFromOptions - Sets the graphics type from the options database.
Defaults to a PETSc X windows graphics.
Collective on PetscDraw
Input Parameter:
. draw - the graphics context
Options Database Keys:
+ -nox - do not use X graphics (ignore graphics calls, but run program correctly)
. -nox_warning - when X windows support is not installed this prevents the warning message
from being printed
. -draw_pause <pause amount> -- -1 indicates wait for mouse input, -2 indicates pause when window is to be destroyed
. -draw_save [optional filename] - (X windows only) saves each image before it is cleared to a file
. -draw_save_movie - converts image files to a movie at the end of the run. See PetscDrawSetSave()
- -draw_save_on_flush - saves an image on each flush in addition to each clear
Level: intermediate
Notes:
Must be called after PetscDrawCreate() before the PetscDrawtor is used.
Concepts: drawing^setting options
Concepts: graphics^setting options
.seealso: PetscDrawCreate(), PetscDrawSetType(), PetscDrawSetSave()
@*/
PetscErrorCode PetscDrawSetFromOptions(PetscDraw draw)
{
PetscErrorCode ierr;
PetscBool flg,nox;
char vtype[256];
const char *def;
PetscReal dpause;
#if !defined(PETSC_USE_WINDOWS_GRAPHICS) && !defined(PETSC_HAVE_X)
PetscBool warn;
#endif
PetscFunctionBegin;
PetscValidHeaderSpecific(draw,PETSC_DRAW_CLASSID,1);
if (!PetscDrawList) {
ierr = PetscDrawRegisterAll();CHKERRQ(ierr);
}
if (((PetscObject)draw)->type_name) def = ((PetscObject)draw)->type_name;
else {
ierr = PetscOptionsHasName(NULL,"-nox",&nox);CHKERRQ(ierr);
def = PETSC_DRAW_NULL;
#if defined(PETSC_USE_WINDOWS_GRAPHICS)
if (!nox) def = PETSC_DRAW_WIN32;
#elif defined(PETSC_HAVE_X)
if (!nox) def = PETSC_DRAW_X;
#elif defined(PETSC_HAVE_GLUT)
if (!nox) def = PETSC_DRAW_GLUT;
#elif defined(PETSC_HAVE_OPENGLES)
if (!nox) def = PETSC_DRAW_OPENGLES;
#else
ierr = PetscOptionsHasName(NULL,"-nox_warning",&warn);CHKERRQ(ierr);
if (!nox && !warn) (*PetscErrorPrintf)("PETSc installed without X windows, Microsoft Graphics, OpenGL ES, or GLUT/OpenGL on this machine\nproceeding without graphics\n");
#endif
}
ierr = PetscObjectOptionsBegin((PetscObject)draw);CHKERRQ(ierr);
ierr = PetscOptionsList("-draw_type","Type of graphical output","PetscDrawSetType",PetscDrawList,def,vtype,256,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscDrawSetType(draw,vtype);CHKERRQ(ierr);
} else if (!((PetscObject)draw)->type_name) {
ierr = PetscDrawSetType(draw,def);CHKERRQ(ierr);
}
ierr = PetscOptionsName("-nox","Run without graphics","None",&nox);CHKERRQ(ierr);
#if defined(PETSC_HAVE_X)
{
char filename[PETSC_MAX_PATH_LEN];
PetscBool save,movie = PETSC_FALSE;
ierr = PetscOptionsBool("-draw_save_movie","Make a movie from the images saved (X Windows only)","PetscDrawSetSave",movie,&movie,NULL);CHKERRQ(ierr);
ierr = PetscOptionsString("-draw_save","Save graphics to file (X Windows only)","PetscDrawSetSave",filename,filename,PETSC_MAX_PATH_LEN,&save);CHKERRQ(ierr);
if (save) {
ierr = PetscDrawSetSave(draw,filename,movie);CHKERRQ(ierr);
}
ierr = PetscOptionsBool("-draw_save_on_flush","Save graphics to file (X Windows only) on each flush","PetscDrawSetSave",draw->saveonflush,&draw->saveonflush,NULL);CHKERRQ(ierr);
}
#endif
ierr = PetscOptionsGetReal(NULL,"-draw_pause",&dpause,&flg);CHKERRQ(ierr);
if (flg) draw->pause = dpause;
/* process any options handlers added with PetscObjectAddOptionsHandler() */
ierr = PetscObjectProcessOptionsHandlers((PetscObject)draw);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat C;
PetscInt i,j,m = 3,n = 3,Ii,J;
PetscErrorCode ierr;
PetscBool flg;
PetscScalar v;
IS perm,iperm;
Vec x,u,b,y;
PetscReal norm,tol=PETSC_SMALL;
MatFactorInfo info;
PetscMPIInt size;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_WORLD,1,"This is a uniprocessor example only!");
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,m*n,m*n);CHKERRQ(ierr);
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,NULL,"-symmetric",&flg);CHKERRQ(ierr);
if (flg) { /* Treat matrix as symmetric only if we set this flag */
ierr = MatSetOption(C,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatSetOption(C,MAT_SYMMETRY_ETERNAL,PETSC_TRUE);CHKERRQ(ierr);
}
/* Create the matrix for the five point stencil, YET AGAIN */
for (i=0; i<m; i++) {
for (j=0; j<n; j++) {
v = -1.0; Ii = j + n*i;
if (i>0) {J = Ii - n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (i<m-1) {J = Ii + n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (j>0) {J = Ii - 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (j<n-1) {J = Ii + 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
v = 4.0; ierr = MatSetValues(C,1,&Ii,1,&Ii,&v,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatGetOrdering(C,MATORDERINGRCM,&perm,&iperm);CHKERRQ(ierr);
ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISView(perm,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,m*n,&u);CHKERRQ(ierr);
ierr = VecSet(u,1.0);CHKERRQ(ierr);
ierr = VecDuplicate(u,&x);CHKERRQ(ierr);
ierr = VecDuplicate(u,&b);CHKERRQ(ierr);
ierr = VecDuplicate(u,&y);CHKERRQ(ierr);
ierr = MatMult(C,u,b);CHKERRQ(ierr);
ierr = VecCopy(b,y);CHKERRQ(ierr);
ierr = VecScale(y,2.0);CHKERRQ(ierr);
ierr = MatNorm(C,NORM_FROBENIUS,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"Frobenius norm of matrix %g\n",(double)norm);CHKERRQ(ierr);
ierr = MatNorm(C,NORM_1,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"One norm of matrix %g\n",(double)norm);CHKERRQ(ierr);
ierr = MatNorm(C,NORM_INFINITY,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"Infinity norm of matrix %g\n",(double)norm);CHKERRQ(ierr);
ierr = MatFactorInfoInitialize(&info);CHKERRQ(ierr);
info.fill = 2.0;
info.dtcol = 0.0;
info.zeropivot = 1.e-14;
info.pivotinblocks = 1.0;
ierr = MatLUFactor(C,perm,iperm,&info);CHKERRQ(ierr);
/* Test MatSolve */
ierr = MatSolve(C,b,x);CHKERRQ(ierr);
ierr = VecView(b,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = VecView(x,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = VecAXPY(x,-1.0,u);CHKERRQ(ierr);
ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
if (norm > tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"MatSolve: Norm of error %g\n",(double)norm);CHKERRQ(ierr);
}
/* Test MatSolveAdd */
ierr = MatSolveAdd(C,b,y,x);CHKERRQ(ierr);
ierr = VecAXPY(x,-1.0,y);CHKERRQ(ierr);
ierr = VecAXPY(x,-1.0,u);CHKERRQ(ierr);
ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
if (norm > tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"MatSolveAdd(): Norm of error %g\n",(double)norm);CHKERRQ(ierr);
}
ierr = ISDestroy(&perm);CHKERRQ(ierr);
ierr = ISDestroy(&iperm);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
{
AppCtx user; /* user-defined work context */
PetscInt mx,my;
PetscErrorCode ierr;
MPI_Comm comm;
DM da;
Vec x;
Mat J = NULL,Jmf = NULL;
MatShellCtx matshellctx;
PetscInt mlocal,nlocal;
PC pc;
KSP ksp;
PetscBool errorinmatmult = PETSC_FALSE,errorinpcapply = PETSC_FALSE,errorinpcsetup = PETSC_FALSE;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return(1);
PetscFunctionBeginUser;
ierr = PetscOptionsGetBool(NULL,"-error_in_matmult",&errorinmatmult,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-error_in_pcapply",&errorinpcapply,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-error_in_pcsetup",&errorinpcsetup,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-error_in_domain",&user.errorindomain,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-error_in_domainmf",&user.errorindomainmf,NULL);CHKERRQ(ierr);
comm = PETSC_COMM_WORLD;
ierr = SNESCreate(comm,&user.snes);CHKERRQ(ierr);
/*
Create distributed array object to manage parallel grid and vectors
for principal unknowns (x) and governing residuals (f)
*/
ierr = DMDACreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,4,1,0,0,&da);CHKERRQ(ierr);
ierr = SNESSetDM(user.snes,da);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,0,&mx,&my,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,
PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr);
/*
Problem parameters (velocity of lid, prandtl, and grashof numbers)
*/
user.lidvelocity = 1.0/(mx*my);
user.prandtl = 1.0;
user.grashof = 1.0;
ierr = PetscOptionsGetReal(NULL,"-lidvelocity",&user.lidvelocity,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-prandtl",&user.prandtl,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-grashof",&user.grashof,NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-contours",&user.draw_contours);CHKERRQ(ierr);
ierr = DMDASetFieldName(da,0,"x_velocity");CHKERRQ(ierr);
ierr = DMDASetFieldName(da,1,"y_velocity");CHKERRQ(ierr);
ierr = DMDASetFieldName(da,2,"Omega");CHKERRQ(ierr);
ierr = DMDASetFieldName(da,3,"temperature");CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create user context, set problem data, create vector data structures.
Also, compute the initial guess.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create nonlinear solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMSetApplicationContext(da,&user);CHKERRQ(ierr);
ierr = DMDASNESSetFunctionLocal(da,INSERT_VALUES,(PetscErrorCode (*)(DMDALocalInfo*,void*,void*,void*))FormFunctionLocal,&user);CHKERRQ(ierr);
if (errorinmatmult) {
ierr = MatCreateSNESMF(user.snes,&Jmf);CHKERRQ(ierr);
ierr = MatSetFromOptions(Jmf);CHKERRQ(ierr);
ierr = MatGetLocalSize(Jmf,&mlocal,&nlocal);CHKERRQ(ierr);
matshellctx.Jmf = Jmf;
ierr = MatCreateShell(PetscObjectComm((PetscObject)Jmf),mlocal,nlocal,PETSC_DECIDE,PETSC_DECIDE,&matshellctx,&J);CHKERRQ(ierr);
ierr = MatShellSetOperation(J,MATOP_MULT,(void (*)(void))MatMult_MyShell);CHKERRQ(ierr);
ierr = MatShellSetOperation(J,MATOP_ASSEMBLY_END,(void (*)(void))MatAssemblyEnd_MyShell);CHKERRQ(ierr);
ierr = SNESSetJacobian(user.snes,J,J,MatMFFDComputeJacobian,NULL);CHKERRQ(ierr);
}
ierr = SNESSetFromOptions(user.snes);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"lid velocity = %g, prandtl # = %g, grashof # = %g\n",(double)user.lidvelocity,(double)user.prandtl,(double)user.grashof);CHKERRQ(ierr);
if (errorinpcapply) {
ierr = SNESGetKSP(user.snes,&ksp);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCSHELL);CHKERRQ(ierr);
ierr = PCShellSetApply(pc,PCApply_MyShell);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve the nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr);
ierr = FormInitialGuess(&user,da,x);CHKERRQ(ierr);
if (errorinpcsetup) {
ierr = SNESSetUp(user.snes);CHKERRQ(ierr);
ierr = SNESSetJacobian(user.snes,NULL,NULL,SNESComputeJacobian_MyShell,NULL);CHKERRQ(ierr);
}
ierr = SNESSolve(user.snes,NULL,x);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = MatDestroy(&Jmf);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = SNESDestroy(&user.snes);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat C,A;
PetscInt i,j,m = 3,n = 2,rstart,rend;
PetscMPIInt size,rank;
PetscErrorCode ierr;
PetscScalar v;
IS isrow;
PetscBool detect_bug = PETSC_FALSE;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = PetscOptionsHasName(NULL,NULL,"-detect_bug",&detect_bug);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
n = 2*size;
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,m*n,m*n);CHKERRQ(ierr);
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
/*
This is JUST to generate a nice test matrix, all processors fill up
the entire matrix. This is not something one would ever do in practice.
*/
ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) {
for (j=0; j<m*n; j++) {
v = i + j + 1;
ierr = MatSetValues(C,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_COMMON);CHKERRQ(ierr);
ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/*
Generate a new matrix consisting every row and column of the original matrix
*/
ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr);
/* Create parallel IS with the rows we want on THIS processor */
if (detect_bug && !rank) {
ierr = ISCreateStride(PETSC_COMM_WORLD,1,rstart,1,&isrow);CHKERRQ(ierr);
} else {
ierr = ISCreateStride(PETSC_COMM_WORLD,rend-rstart,rstart,1,&isrow);CHKERRQ(ierr);
}
ierr = MatGetSubMatrix(C,isrow,NULL,MAT_INITIAL_MATRIX,&A);CHKERRQ(ierr);
/* Change C to test the case MAT_REUSE_MATRIX */
if (!rank ) {
i = 0; j = 0; v = 100;
ierr = MatSetValues(C,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatGetSubMatrix(C,isrow,NULL,MAT_REUSE_MATRIX,&A);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_COMMON);CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = ISDestroy(&isrow);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
/*@C
PetscTraceBackErrorHandler - Default error handler routine that generates
a traceback on error detection.
Not Collective
Input Parameters:
+ comm - communicator over which error occurred
. line - the line number of the error (indicated by __LINE__)
. func - the function where error is detected (indicated by __FUNCT__)
. file - the file in which the error was detected (indicated by __FILE__)
. dir - the directory of the file (indicated by __SDIR__)
. mess - an error text string, usually just printed to the screen
. n - the generic error number
. p - PETSC_ERROR_INITIAL if this is the first call the the error handler, otherwise PETSC_ERROR_REPEAT
- ctx - error handler context
Level: developer
Notes:
Most users need not directly employ this routine and the other error
handlers, but can instead use the simplified interface SETERRQ, which has
the calling sequence
$ SETERRQ(comm,number,n,mess)
Notes for experienced users:
Use PetscPushErrorHandler() to set the desired error handler. The
currently available PETSc error handlers include PetscTraceBackErrorHandler(),
PetscAttachDebuggerErrorHandler(), PetscAbortErrorHandler(), and PetscMPIAbortErrorHandler()
Concepts: error handler^traceback
Concepts: traceback^generating
.seealso: PetscPushErrorHandler(), PetscAttachDebuggerErrorHandler(),
PetscAbortErrorHandler()
@*/
PetscErrorCode PetscTraceBackErrorHandler(MPI_Comm comm,int line,const char *fun,const char* file,const char *dir,PetscErrorCode n,PetscErrorType p,const char *mess,void *ctx)
{
PetscLogDouble mem,rss;
PetscBool flg1 = PETSC_FALSE,flg2 = PETSC_FALSE,flg3 = PETSC_FALSE;
PetscMPIInt rank = 0;
PetscFunctionBegin;
if (comm != PETSC_COMM_SELF) {
MPI_Comm_rank(comm,&rank);
}
if (!rank) {
if (p == PETSC_ERROR_INITIAL) {
(*PetscErrorPrintf)("--------------------- Error Message ------------------------------------\n");
if (n == PETSC_ERR_MEM) {
(*PetscErrorPrintf)("Out of memory. This could be due to allocating\n");
(*PetscErrorPrintf)("too large an object or bleeding by not properly\n");
(*PetscErrorPrintf)("destroying unneeded objects.\n");
PetscMallocGetCurrentUsage(&mem);
PetscMemoryGetCurrentUsage(&rss);
PetscOptionsGetBool(PETSC_NULL,"-malloc_dump",&flg1,PETSC_NULL);
PetscOptionsGetBool(PETSC_NULL,"-malloc_log",&flg2,PETSC_NULL);
PetscOptionsHasName(PETSC_NULL,"-malloc_log_threshold",&flg3);
if (flg2 || flg3) {
PetscMallocDumpLog(stdout);
} else {
(*PetscErrorPrintf)("Memory allocated %.0f Memory used by process %.0f\n",mem,rss);
if (flg1) {
PetscMallocDump(stdout);
} else {
(*PetscErrorPrintf)("Try running with -malloc_dump or -malloc_log for info.\n");
}
}
} else {
const char *text;
PetscErrorMessage(n,&text,PETSC_NULL);
if (text) (*PetscErrorPrintf)("%s!\n",text);
}
if (mess) {
(*PetscErrorPrintf)("%s!\n",mess);
}
(*PetscErrorPrintf)("------------------------------------------------------------------------\n");
(*PetscErrorPrintf)("%s\n",version);
(*PetscErrorPrintf)("See docs/changes/index.html for recent updates.\n");
(*PetscErrorPrintf)("See docs/faq.html for hints about trouble shooting.\n");
(*PetscErrorPrintf)("See docs/index.html for manual pages.\n");
(*PetscErrorPrintf)("------------------------------------------------------------------------\n");
if (PetscErrorPrintfInitializeCalled) {
(*PetscErrorPrintf)("%s on a %s named %s by %s %s\n",pname,arch,hostname,username,date);
}
(*PetscErrorPrintf)("Libraries linked from %s\n",PETSC_LIB_DIR);
(*PetscErrorPrintf)("Configure run at %s\n",petscconfigureruntime);
(*PetscErrorPrintf)("Configure options %s\n",petscconfigureoptions);
(*PetscErrorPrintf)("------------------------------------------------------------------------\n");
}
/* print line of stack trace */
(*PetscErrorPrintf)("%s() line %d in %s%s\n",fun,line,dir,file);
} else {
/* do not print error messages since process 0 will print them, sleep before aborting so will not accidently kill process 0*/
PetscSleep(10.0);
abort();
}
PetscFunctionReturn(n);
}
int main(int argc,char **args)
{
Mat C,A,B,D;
PetscErrorCode ierr;
PetscInt i,j,ntypes,bs,mbs,m,block,d_nz=6, o_nz=3,col[3],row,verbose=0;
PetscMPIInt size,rank;
const MatType type[9];
char file[PETSC_MAX_PATH_LEN];
PetscViewer fd;
PetscBool equal,flg_loadmat,flg;
PetscScalar value[3];
PetscInitialize(&argc,&args,(char *)0,help);
ierr = PetscOptionsGetInt(PETSC_NULL,"-verbose",&verbose,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg_loadmat);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL,"-testseqaij",&flg);CHKERRQ(ierr);
if (flg){
if (size == 1){
type[0] = MATSEQAIJ;
} else {
type[0] = MATMPIAIJ;
}
} else {
type[0] = MATAIJ;
}
if (size == 1){
ntypes = 3;
type[1] = MATSEQBAIJ;
type[2] = MATSEQSBAIJ;
} else {
ntypes = 3;
type[1] = MATMPIBAIJ;
type[2] = MATMPISBAIJ;
}
/* input matrix C */
if (flg_loadmat){
/* Open binary file. */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
/* Load a baij matrix, then destroy the viewer. */
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
if (size == 1){
ierr = MatSetType(C,MATSEQBAIJ);CHKERRQ(ierr);
} else {
ierr = MatSetType(C,MATMPIBAIJ);CHKERRQ(ierr);
}
ierr = MatLoad(C,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
} else { /* Create a baij mat with bs>1 */
bs = 2; mbs=8;
ierr = PetscOptionsGetInt(PETSC_NULL,"-mbs",&mbs,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-bs",&bs,PETSC_NULL);CHKERRQ(ierr);
if (bs <= 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG," bs must be >1 in this case");
m = mbs*bs;
ierr = MatCreateBAIJ(PETSC_COMM_WORLD,bs,PETSC_DECIDE,PETSC_DECIDE,m,m,d_nz,PETSC_NULL,o_nz,PETSC_NULL,&C);CHKERRQ(ierr);
for (block=0; block<mbs; block++){
/* diagonal blocks */
value[0] = -1.0; value[1] = 4.0; value[2] = -1.0;
for (i=1+block*bs; i<bs-1+block*bs; i++) {
col[0] = i-1; col[1] = i; col[2] = i+1;
ierr = MatSetValues(C,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
i = bs - 1+block*bs; col[0] = bs - 2+block*bs; col[1] = bs - 1+block*bs;
value[0]=-1.0; value[1]=4.0;
ierr = MatSetValues(C,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
i = 0+block*bs; col[0] = 0+block*bs; col[1] = 1+block*bs;
value[0]=4.0; value[1] = -1.0;
ierr = MatSetValues(C,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
/* off-diagonal blocks */
value[0]=-1.0;
for (i=0; i<(mbs-1)*bs; i++){
col[0]=i+bs;
ierr = MatSetValues(C,1,&i,1,col,value,INSERT_VALUES);CHKERRQ(ierr);
col[0]=i; row=i+bs;
ierr = MatSetValues(C,1,&row,1,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
{
/* Check the symmetry of C because it will be converted to a sbaij matrix */
Mat Ctrans;
ierr = MatTranspose(C, MAT_INITIAL_MATRIX,&Ctrans);
ierr = MatEqual(C, Ctrans, &flg);CHKERRQ(ierr);
if (flg) {
ierr = MatSetOption(C,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
} else {
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"C must be symmetric for this example");
}
ierr = MatDestroy(&Ctrans);CHKERRQ(ierr);
}
//ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* convert C to other formats */
for (i=0; i<ntypes; i++) {
ierr = MatConvert(C,type[i],MAT_INITIAL_MATRIX,&A);CHKERRQ(ierr);
ierr = MatMultEqual(A,C,10,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMETYPE,"Error in conversion from BAIJ to %s",type[i]);
for (j=i+1; j<ntypes; j++) {
if (verbose>0) {
ierr = PetscPrintf(PETSC_COMM_WORLD," \n[%d] test conversion between %s and %s\n",rank,type[i],type[j]);CHKERRQ(ierr);
}
if (!rank && verbose) printf("Convert %s A to %s B\n",type[i],type[j]);
ierr = MatConvert(A,type[j],MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr);
/*
if (j == 2){
ierr = PetscPrintf(PETSC_COMM_SELF," A: %s\n",type[i]);CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF," B: %s\n",type[j]);CHKERRQ(ierr);
ierr = MatView(B,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
*/
ierr = MatMultEqual(A,B,10,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMETYPE,"Error in conversion from %s to %s",type[i],type[j]);
if (size == 1 || j != 2){ /* Matconvert from mpisbaij mat to other formats are not supported */
if (!rank && verbose) printf("Convert %s B to %s D\n",type[j],type[i]);
ierr = MatConvert(B,type[i],MAT_INITIAL_MATRIX,&D);CHKERRQ(ierr);
ierr = MatMultEqual(B,D,10,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMETYPE,"Error in conversion from %s to %s",type[j],type[i]);
ierr = MatDestroy(&D);CHKERRQ(ierr);
}
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&D);CHKERRQ(ierr);
}
/* Test in-place convert */
if (size == 1){ /* size > 1 is not working yet! */
j = (i+1)%ntypes;
/* printf("[%d] i: %d, j: %d\n",rank,i,j); */
ierr = MatConvert(A,type[j],MAT_REUSE_MATRIX,&A);CHKERRQ(ierr);
}
ierr = MatDestroy(&A);CHKERRQ(ierr);
}
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
TS ts; /* nonlinear solver */
Vec u,r; /* solution, residual vectors */
Mat J,Jmf = PETSC_NULL; /* Jacobian matrices */
PetscInt maxsteps = 1000; /* iterations for convergence */
PetscErrorCode ierr;
DM da;
PetscReal dt;
AppCtx user; /* user-defined work context */
SNES snes;
PetscInt Jtype; /* Jacobian type
0: user provide Jacobian;
1: slow finite difference;
2: fd with coloring; */
PetscInitialize(&argc,&argv,(char *)0,help);
/* Initialize user application context */
user.da = PETSC_NULL;
user.nstencilpts = 5;
user.c = -30.0;
user.boundary = 0; /* 0: Drichlet BC; 1: Neumann BC */
user.viewJacobian = PETSC_FALSE;
ierr = PetscOptionsGetInt(PETSC_NULL,"-nstencilpts",&user.nstencilpts,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-boundary",&user.boundary,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL,"-viewJacobian",&user.viewJacobian);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create distributed array (DMDA) to manage parallel grid and vectors
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
if (user.nstencilpts == 5){
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-11,-11,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr);
} else if (user.nstencilpts == 9){
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,-11,-11,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr);
} else {
SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"nstencilpts %d is not supported",user.nstencilpts);
}
user.da = da;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Extract global vectors from DMDA;
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMCreateGlobalVector(da,&u);CHKERRQ(ierr);
ierr = VecDuplicate(u,&r);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create timestepping solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr);
ierr = TSSetDM(ts,da);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,r,FormIFunction,&user);CHKERRQ(ierr);
ierr = TSSetDuration(ts,maxsteps,1.0);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set initial conditions
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = FormInitialSolution(u,&user);CHKERRQ(ierr);
ierr = TSSetSolution(ts,u);CHKERRQ(ierr);
dt = .01;
ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set Jacobian evaluation routine
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMCreateMatrix(da,MATAIJ,&J);CHKERRQ(ierr);
Jtype = 0;
ierr = PetscOptionsGetInt(PETSC_NULL, "-Jtype",&Jtype,PETSC_NULL);CHKERRQ(ierr);
if (Jtype == 0){ /* use user provided Jacobian evaluation routine */
if (user.nstencilpts != 5) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"user Jacobian routine FormIJacobian() does not support nstencilpts=%D",user.nstencilpts);
ierr = TSSetIJacobian(ts,J,J,FormIJacobian,&user);CHKERRQ(ierr);
} else { /* use finite difference Jacobian J as preconditioner and '-snes_mf_operator' for Mat*vec */
ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr);
ierr = MatCreateSNESMF(snes,&Jmf);CHKERRQ(ierr);
if (Jtype == 1){ /* slow finite difference J; */
ierr = SNESSetJacobian(snes,Jmf,J,SNESDefaultComputeJacobian,PETSC_NULL);CHKERRQ(ierr);
} else if (Jtype == 2){ /* Use coloring to compute finite difference J efficiently */
ierr = SNESSetJacobian(snes,Jmf,J,SNESDefaultComputeJacobianColor,0);CHKERRQ(ierr);
} else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Jtype is not supported");
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Sets various TS parameters from user options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSolve(ts,u);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = MatDestroy(&Jmf);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
PetscFunctionReturn(0);
}
