/*
This routine is not parallel
*/
PetscErrorCode MyMonitor(TS ts,PetscInt step,PetscReal time,Vec U,void *ptr)
{
UserCtx *ctx = (UserCtx*)ptr;
PetscDrawLG lg;
PetscErrorCode ierr;
PetscScalar *u;
PetscInt Mx,i,xs,xm,cnt;
PetscReal x,y,hx,pause,sx,len,max,xx[2],yy[2];
PetscDraw draw;
Vec localU;
DM da;
int colors[] = {PETSC_DRAW_YELLOW,PETSC_DRAW_RED,PETSC_DRAW_BLUE};
const char*const legend[] = {"-kappa (\\grad u,\\grad u)","(1 - u^2)^2"};
PetscDrawAxis axis;
PetscDrawViewPorts *ports;
PetscReal vbounds[] = {-1.1,1.1};
PetscFunctionBegin;
ierr = PetscViewerDrawSetBounds(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),1,vbounds);CHKERRQ(ierr);
ierr = PetscViewerDrawResize(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),1200,800);CHKERRQ(ierr);
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMGetLocalVector(da,&localU);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
hx = 1.0/(PetscReal)Mx; sx = 1.0/(hx*hx);
ierr = DMGlobalToLocalBegin(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(da,localU,&u);CHKERRQ(ierr);
ierr = PetscViewerDrawGetDrawLG(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),1,&lg);CHKERRQ(ierr);
ierr = PetscDrawLGGetDraw(lg,&draw);CHKERRQ(ierr);
ierr = PetscDrawCheckResizedWindow(draw);CHKERRQ(ierr);
if (!ctx->ports) {
ierr = PetscDrawViewPortsCreateRect(draw,1,3,&ctx->ports);CHKERRQ(ierr);
}
ports = ctx->ports;
ierr = PetscDrawLGGetAxis(lg,&axis);CHKERRQ(ierr);
ierr = PetscDrawLGReset(lg);CHKERRQ(ierr);
xx[0] = 0.0; xx[1] = 1.0; cnt = 2;
ierr = PetscOptionsGetRealArray(NULL,NULL,"-zoom",xx,&cnt,NULL);CHKERRQ(ierr);
xs = xx[0]/hx; xm = (xx[1] - xx[0])/hx;
/*
Plot the energies
*/
ierr = PetscDrawLGSetDimension(lg,1 + (ctx->allencahn ? 1 : 0));CHKERRQ(ierr);
ierr = PetscDrawLGSetColors(lg,colors+1);CHKERRQ(ierr);
ierr = PetscDrawViewPortsSet(ports,2);CHKERRQ(ierr);
x = hx*xs;
for (i=xs; i<xs+xm; i++) {
xx[0] = xx[1] = x;
yy[0] = PetscRealPart(.25*ctx->kappa*(u[i-1] - u[i+1])*(u[i-1] - u[i+1])*sx);
if (ctx->allencahn) yy[1] = .25*PetscRealPart((1. - u[i]*u[i])*(1. - u[i]*u[i]));
ierr = PetscDrawLGAddPoint(lg,xx,yy);CHKERRQ(ierr);
x += hx;
}
ierr = PetscDrawGetPause(draw,&pause);CHKERRQ(ierr);
ierr = PetscDrawSetPause(draw,0.0);CHKERRQ(ierr);
ierr = PetscDrawAxisSetLabels(axis,"Energy","","");CHKERRQ(ierr);
ierr = PetscDrawLGSetLegend(lg,legend);CHKERRQ(ierr);
ierr = PetscDrawLGDraw(lg);CHKERRQ(ierr);
/*
Plot the forces
*/
ierr = PetscDrawViewPortsSet(ports,1);CHKERRQ(ierr);
ierr = PetscDrawLGReset(lg);CHKERRQ(ierr);
x = xs*hx;;
max = 0.;
for (i=xs; i<xs+xm; i++) {
xx[0] = xx[1] = x;
yy[0] = PetscRealPart(ctx->kappa*(u[i-1] + u[i+1] - 2.0*u[i])*sx);
max = PetscMax(max,PetscAbs(yy[0]));
if (ctx->allencahn) {
yy[1] = PetscRealPart(u[i] - u[i]*u[i]*u[i]);
max = PetscMax(max,PetscAbs(yy[1]));
}
ierr = PetscDrawLGAddPoint(lg,xx,yy);CHKERRQ(ierr);
x += hx;
}
ierr = PetscDrawAxisSetLabels(axis,"Right hand side","","");CHKERRQ(ierr);
ierr = PetscDrawLGSetLegend(lg,NULL);CHKERRQ(ierr);
ierr = PetscDrawLGDraw(lg);CHKERRQ(ierr);
/*
Plot the solution
*/
ierr = PetscDrawLGSetDimension(lg,1);CHKERRQ(ierr);
ierr = PetscDrawViewPortsSet(ports,0);CHKERRQ(ierr);
ierr = PetscDrawLGReset(lg);CHKERRQ(ierr);
x = hx*xs;
ierr = PetscDrawLGSetLimits(lg,x,x+(xm-1)*hx,-1.1,1.1);CHKERRQ(ierr);
ierr = PetscDrawLGSetColors(lg,colors);CHKERRQ(ierr);
for (i=xs; i<xs+xm; i++) {
xx[0] = x;
yy[0] = PetscRealPart(u[i]);
ierr = PetscDrawLGAddPoint(lg,xx,yy);CHKERRQ(ierr);
x += hx;
}
ierr = PetscDrawAxisSetLabels(axis,"Solution","","");CHKERRQ(ierr);
ierr = PetscDrawLGDraw(lg);CHKERRQ(ierr);
/*
Print the forces as arrows on the solution
*/
x = hx*xs;
cnt = xm/60;
cnt = (!cnt) ? 1 : cnt;
for (i=xs; i<xs+xm; i += cnt) {
y = PetscRealPart(u[i]);
len = .5*PetscRealPart(ctx->kappa*(u[i-1] + u[i+1] - 2.0*u[i])*sx)/max;
ierr = PetscDrawArrow(draw,x,y,x,y+len,PETSC_DRAW_RED);CHKERRQ(ierr);
if (ctx->allencahn) {
len = .5*PetscRealPart(u[i] - u[i]*u[i]*u[i])/max;
ierr = PetscDrawArrow(draw,x,y,x,y+len,PETSC_DRAW_BLUE);CHKERRQ(ierr);
}
x += cnt*hx;
}
ierr = DMDAVecRestoreArrayRead(da,localU,&x);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&localU);CHKERRQ(ierr);
ierr = PetscDrawStringSetSize(draw,.2,.2);CHKERRQ(ierr);
ierr = PetscDrawFlush(draw);CHKERRQ(ierr);
ierr = PetscDrawSetPause(draw,pause);CHKERRQ(ierr);
ierr = PetscDrawPause(draw);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscDrawLG lg;
PetscErrorCode ierr;
PetscInt Mx = 100,i;
PetscReal x,hx = .1/Mx,pause,xx[3],yy[3];
PetscDraw draw;
const char *const legend[] = {"(1 - u^2)^2","1 - u^2","-(1 - u)log(1 - u)"};
PetscDrawAxis axis;
static PetscDrawViewPorts *ports = 0;
PetscFunctionBegin;
PetscInitialize(&argc,&argv,0,help);
ierr = PetscViewerDrawResize(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),1200,800);CHKERRQ(ierr);
ierr = PetscViewerDrawGetDrawLG(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),0,&lg);CHKERRQ(ierr);
ierr = PetscDrawLGGetDraw(lg,&draw);CHKERRQ(ierr);
ierr = PetscDrawCheckResizedWindow(draw);CHKERRQ(ierr);
if (!ports) {
ierr = PetscDrawViewPortsCreateRect(draw,1,2,&ports);CHKERRQ(ierr);
}
ierr = PetscDrawLGGetAxis(lg,&axis);CHKERRQ(ierr);
ierr = PetscDrawLGReset(lg);CHKERRQ(ierr);
/*
Plot the energies
*/
ierr = PetscDrawLGSetDimension(lg,3);CHKERRQ(ierr);
ierr = PetscDrawViewPortsSet(ports,1);CHKERRQ(ierr);
x = .9;
for (i=0; i<Mx; i++) {
xx[0] = xx[1] = xx[2] = x;
yy[0] = (1.-x*x)*(1. - x*x);
yy[1] = (1. - x*x);
yy[2] = -(1.-x)*PetscLogScalar(1.-x);
ierr = PetscDrawLGAddPoint(lg,xx,yy);CHKERRQ(ierr);
x += hx;
}
ierr = PetscDrawGetPause(draw,&pause);CHKERRQ(ierr);
ierr = PetscDrawSetPause(draw,0.0);CHKERRQ(ierr);
ierr = PetscDrawAxisSetLabels(axis,"Energy","","");CHKERRQ(ierr);
ierr = PetscDrawLGSetLegend(lg,legend);CHKERRQ(ierr);
ierr = PetscDrawLGDraw(lg);CHKERRQ(ierr);
/*
Plot the forces
*/
ierr = PetscDrawViewPortsSet(ports,0);CHKERRQ(ierr);
ierr = PetscDrawLGReset(lg);CHKERRQ(ierr);
x = .9;
for (i=0; i<Mx; i++) {
xx[0] = xx[1] = xx[2] = x;
yy[0] = x*x*x - x;
yy[1] = -x;
yy[2] = 1.0 + PetscLogScalar(1. - x);
ierr = PetscDrawLGAddPoint(lg,xx,yy);CHKERRQ(ierr);
x += hx;
}
ierr = PetscDrawAxisSetLabels(axis,"Derivative","","");CHKERRQ(ierr);
ierr = PetscDrawLGSetLegend(lg,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscDrawLGDraw(lg);CHKERRQ(ierr);
ierr = PetscDrawSetPause(draw,pause);CHKERRQ(ierr);
ierr = PetscDrawPause(draw);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
TS ts; /* nonlinear solver */
Vec x,r; /* solution, residual vectors */
Mat J; /* Jacobian matrix */
PetscInt steps,Mx,maxsteps = 10000000;
PetscErrorCode ierr;
DM da;
MatFDColoring matfdcoloring;
ISColoring iscoloring;
PetscReal dt;
PetscReal vbounds[] = {-100000,100000,-1.1,1.1};
PetscBool wait;
Vec ul,uh;
SNES snes;
UserCtx ctx;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Initialize program
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ctx.kappa = 1.0;
ierr = PetscOptionsGetReal(NULL,"-kappa",&ctx.kappa,NULL);CHKERRQ(ierr);
ctx.cahnhillard = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-cahn-hillard",&ctx.cahnhillard,NULL);CHKERRQ(ierr);
ierr = PetscViewerDrawSetBounds(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),2,vbounds);CHKERRQ(ierr);
ierr = PetscViewerDrawResize(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),600,600);CHKERRQ(ierr);
ctx.energy = 1;
/* ierr = PetscOptionsGetInt(NULL,NULL,"-energy",&ctx.energy,NULL);CHKERRQ(ierr); */
ierr = PetscOptionsGetInt(NULL,NULL,"-energy",&ctx.energy,NULL);CHKERRQ(ierr);
ctx.tol = 1.0e-8;
ierr = PetscOptionsGetReal(NULL,"-tol",&ctx.tol,NULL);CHKERRQ(ierr);
ctx.theta = .001;
ctx.theta_c = 1.0;
ierr = PetscOptionsGetReal(NULL,"-theta",&ctx.theta,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-theta_c",&ctx.theta_c,NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create distributed array (DMDA) to manage parallel grid and vectors
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_PERIODIC, -10,2,2,NULL,&da);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMDASetFieldName(da,0,"Biharmonic heat equation: w = -kappa*u_xx");CHKERRQ(ierr);
ierr = DMDASetFieldName(da,1,"Biharmonic heat equation: u");CHKERRQ(ierr);
ierr = DMDAGetInfo(da,0,&Mx,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
dt = 1.0/(10.*ctx.kappa*Mx*Mx*Mx*Mx);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Extract global vectors from DMDA; then duplicate for remaining
vectors that are the same types
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&r);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create timestepping solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetDM(ts,da);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,NULL,FormFunction,&ctx);CHKERRQ(ierr);
ierr = TSSetDuration(ts,maxsteps,.02);CHKERRQ(ierr);
ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create matrix data structure; set Jacobian evaluation routine
< Set Jacobian matrix data structure and default Jacobian evaluation
routine. User can override with:
-snes_mf : matrix-free Newton-Krylov method with no preconditioning
(unless user explicitly sets preconditioner)
-snes_mf_operator : form preconditioning matrix as set by the user,
but use matrix-free approx for Jacobian-vector
products within Newton-Krylov method
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr);
ierr = DMCreateColoring(da,IS_COLORING_GLOBAL,&iscoloring);CHKERRQ(ierr);
ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr);
ierr = DMCreateMatrix(da,&J);CHKERRQ(ierr);
ierr = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr);
ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
ierr = MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode (*)(void))SNESTSFormFunction,ts);CHKERRQ(ierr);
ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr);
ierr = MatFDColoringSetUp(J,iscoloring,matfdcoloring);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,matfdcoloring);CHKERRQ(ierr);
{
ierr = VecDuplicate(x,&ul);CHKERRQ(ierr);
ierr = VecDuplicate(x,&uh);CHKERRQ(ierr);
ierr = VecStrideSet(ul,0,PETSC_NINFINITY);CHKERRQ(ierr);
ierr = VecStrideSet(ul,1,-1.0);CHKERRQ(ierr);
ierr = VecStrideSet(uh,0,PETSC_INFINITY);CHKERRQ(ierr);
ierr = VecStrideSet(uh,1,1.0);CHKERRQ(ierr);
ierr = TSVISetVariableBounds(ts,ul,uh);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Customize nonlinear solver
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set initial conditions
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = FormInitialSolution(da,x,ctx.kappa);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr);
ierr = TSSetSolution(ts,x);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set runtime options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSolve(ts,x);CHKERRQ(ierr);
wait = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-wait",&wait,NULL);CHKERRQ(ierr);
if (wait) {
ierr = PetscSleep(-1);CHKERRQ(ierr);
}
ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
{
ierr = VecDestroy(&ul);CHKERRQ(ierr);
ierr = VecDestroy(&uh);CHKERRQ(ierr);
}
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = MatFDColoringDestroy(&matfdcoloring);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
PetscFunctionReturn(0);
}
