/*@C
PetscBagRegisterRealArray - add an real array to the bag
Logically Collective on PetscBag
Input Parameter:
+ bag - the bag of values
. addr - location of real array in struct
. msize - number of entries in array
. name - name of the integer array
- help - longer string with more information about the value
Level: beginner
.seealso: PetscBag, PetscBagSetName(), PetscBagView(), PetscBagLoad(), PetscBagGetData()
PetscBagRegisterInt(), PetscBagRegisterBool(), PetscBagRegisterScalar()
PetscBagSetFromOptions(), PetscBagCreate(), PetscBagGetName(), PetscBagRegisterEnum()
@*/
PetscErrorCode PetscBagRegisterRealArray(PetscBag bag,void *addr,PetscInt msize, const char *name, const char *help)
{
PetscErrorCode ierr;
PetscBagItem item;
char nname[PETSC_BAG_NAME_LENGTH+1];
PetscBool printhelp;
PetscInt i,tmp = msize;
PetscFunctionBegin;
/* ierr = PetscMemzero(addr,msize*sizeof(PetscInt));CHKERRQ(ierr);*/
nname[0] = '-';
nname[1] = 0;
ierr = PetscStrncat(nname,name,PETSC_BAG_NAME_LENGTH-1);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-help",&printhelp);CHKERRQ(ierr);
if (printhelp) {
ierr = (*PetscHelpPrintf)(bag->bagcomm," -%s%s <",bag->bagprefix ? bag->bagprefix : "",name);CHKERRQ(ierr);
for (i=0; i<msize; i++) {
ierr = (*PetscHelpPrintf)(bag->bagcomm,"%g ",(double)*((PetscReal*)addr)+i);CHKERRQ(ierr);
}
ierr = (*PetscHelpPrintf)(bag->bagcomm,">: %s \n",help);CHKERRQ(ierr);
}
ierr = PetscOptionsGetRealArray(bag->bagprefix,nname,(PetscReal*)addr,&tmp,NULL);CHKERRQ(ierr);
ierr = PetscNew(&item);CHKERRQ(ierr);
item->dtype = PETSC_REAL;
item->offset = ((char*)addr) - ((char*)bag);
if (item->offset > bag->bagsize) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Registered item %s %s is not in bag memory space",name,help);
item->next = 0;
item->msize = msize;
ierr = PetscBagRegister_Private(bag,item,name,help);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SetFromOptions(AppCtx * ctx)
{
PetscErrorCode ierr;
PetscInt i,j;
PetscFunctionBeginUser;
ctx->dispersivity = 0.5;
ctx->porosity = 0.25;
ctx->saturation = 1.0;
ctx->gradq_inflow = 1.0;
ctx->rate_constant[0] = 0.5;
ctx->length[0] = 100.0;
ctx->length[1] = 100.0;
ctx->x_0.sp[0] = 0.0;
ctx->x_0.sp[1] = 0.0;
ctx->x_0.sp[2] = 0.0;
ctx->x_inflow.sp[0] = 0.05;
ctx->x_inflow.sp[1] = 0.05;
ctx->x_inflow.sp[2] = 0.0;
for (i = 0; i < N_REACTIONS; i++) {
for (j = 0; j < N_SPECIES; j++) stoich(i, j) = 0.;
}
/* set up a pretty easy example */
stoich(0, 0) = -1.;
stoich(0, 1) = -2.;
stoich(0, 2) = 1.;
PetscInt as = N_SPECIES;
ierr = PetscOptionsGetReal(NULL,"-length_x",&ctx->length[0],NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-length_y",&ctx->length[1],NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-porosity",&ctx->porosity,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-saturation",&ctx->saturation,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-dispersivity",&ctx->dispersivity,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-gradq_inflow",&ctx->gradq_inflow,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-rate_constant",&ctx->rate_constant[0],NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetRealArray(NULL,"-sp_inflow",ctx->x_inflow.sp,&as,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetRealArray(NULL,"-sp_0",ctx->x_0.sp,&as,NULL);CHKERRQ(ierr);
as = N_SPECIES;
ierr = PetscOptionsGetRealArray(NULL,"-stoich",ctx->stoichiometry,&as,NULL);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FluidFieldCreate(MPI_Comm comm, FluidField *fluid)
{
FluidField f;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscNew(struct _FluidField, &f); CHKERRQ(ierr);
// Default values
f->comm = comm;
f->mu = 1e-3; // pN s / um^2
ierr = PetscOptionsGetReal(0,"-fluid_viscosity",&f->mu,0); CHKERRQ(ierr);
int nmax = 3;
f->lens.x = 7;
f->lens.y = 7;
f->lens.z = 0;
ierr = PetscOptionsGetRealArray(0,"-fluid_lens", &f->lens.x, &nmax, 0); CHKERRQ(ierr);
f->is3D = (nmax == 3);
PetscReal dx = 1;
ierr = PetscOptionsGetReal(0,"-fluid_dx",&dx,0); CHKERRQ(ierr);
f->dh.x = dx;
f->dh.y = dx;
f->dh.z = dx;
nmax = 3;
f->dims.x = f->lens.x / f->dh.x;
f->dims.y = f->lens.y / f->dh.y;
f->dims.z = f->lens.z / f->dh.z;
ierr = PetscOptionsGetIntArray(0,"-fluid_dims", &f->dims.x, &nmax, 0); CHKERRQ(ierr);
if( !f->is3D ) {
f->lens.z = 0;
f->dims.z = 0;
f->dh.z = 0;
}
// Create BC index set
ierr = ArrayCreate("dirichletBC",sizeof(MatStencil),&f->dirichletBC); CHKERRQ(ierr);
ierr = FluidFieldRegisterEvents(); CHKERRQ(ierr);
*fluid = f;
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 **argv)
{
Mat A[NMAT]; /* problem matrices */
PEP pep; /* polynomial eigenproblem solver context */
PetscInt m=15,n,II,Istart,Iend,i,j,k;
PetscReal h,xi,xj,c[7] = { 2, .3, -2, .2, -2, -.3, -PETSC_PI/2 };
PetscScalar alpha,beta,gamma;
PetscBool flg;
PetscErrorCode ierr;
SlepcInitialize(&argc,&argv,(char*)0,help);
#if !defined(PETSC_USE_COMPLEX)
SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP, "This example requires complex scalars");
#endif
ierr = PetscOptionsGetInt(NULL,"-m",&m,NULL);CHKERRQ(ierr);
n = m*m;
h = PETSC_PI/(m+1);
gamma = PetscExpScalar(PETSC_i*c[6]);
gamma = gamma/PetscAbsScalar(gamma);
k = 7;
ierr = PetscOptionsGetRealArray(NULL,"-c",c,&k,&flg);CHKERRQ(ierr);
if (flg && k!=7) SETERRQ1(PETSC_COMM_WORLD,1,"The number of parameters -c should be 7, you provided %D",k);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nPDDE stability, n=%D (m=%D)\n\n",n,m);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Compute the polynomial matrices
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* initialize matrices */
for (i=0;i<NMAT;i++) {
ierr = MatCreate(PETSC_COMM_WORLD,&A[i]);CHKERRQ(ierr);
ierr = MatSetSizes(A[i],PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(A[i]);CHKERRQ(ierr);
ierr = MatSetUp(A[i]);CHKERRQ(ierr);
}
ierr = MatGetOwnershipRange(A[0],&Istart,&Iend);CHKERRQ(ierr);
/* A[1] has a pattern similar to the 2D Laplacian */
for (II=Istart;II<Iend;II++) {
i = II/m; j = II-i*m;
xi = (i+1)*h; xj = (j+1)*h;
alpha = c[0]+c[1]*PetscSinReal(xi)+gamma*(c[2]+c[3]*xi*(1.0-PetscExpReal(xi-PETSC_PI)));
beta = c[0]+c[1]*PetscSinReal(xj)-gamma*(c[2]+c[3]*xj*(1.0-PetscExpReal(xj-PETSC_PI)));
ierr = MatSetValue(A[1],II,II,alpha+beta-4.0/(h*h),INSERT_VALUES);CHKERRQ(ierr);
if (j>0) { ierr = MatSetValue(A[1],II,II-1,1.0/(h*h),INSERT_VALUES);CHKERRQ(ierr); }
if (j<m-1) { ierr = MatSetValue(A[1],II,II+1,1.0/(h*h),INSERT_VALUES);CHKERRQ(ierr); }
if (i>0) { ierr = MatSetValue(A[1],II,II-m,1.0/(h*h),INSERT_VALUES);CHKERRQ(ierr); }
if (i<m-1) { ierr = MatSetValue(A[1],II,II+m,1.0/(h*h),INSERT_VALUES);CHKERRQ(ierr); }
}
/* A[0] and A[2] are diagonal */
for (II=Istart;II<Iend;II++) {
i = II/m; j = II-i*m;
xi = (i+1)*h; xj = (j+1)*h;
alpha = c[4]+c[5]*xi*(PETSC_PI-xi);
beta = c[4]+c[5]*xj*(PETSC_PI-xj);
ierr = MatSetValue(A[0],II,II,alpha,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValue(A[2],II,II,beta,INSERT_VALUES);CHKERRQ(ierr);
}
/* assemble matrices */
for (i=0;i<NMAT;i++) {
ierr = MatAssemblyBegin(A[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
for (i=0;i<NMAT;i++) {
ierr = MatAssemblyEnd(A[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the eigensolver and solve the problem
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PEPCreate(PETSC_COMM_WORLD,&pep);CHKERRQ(ierr);
ierr = PEPSetOperators(pep,NMAT,A);CHKERRQ(ierr);
ierr = PEPSetFromOptions(pep);CHKERRQ(ierr);
ierr = PEPSolve(pep);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Display solution and clean up
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PEPPrintSolution(pep,NULL);CHKERRQ(ierr);
ierr = PEPDestroy(&pep);CHKERRQ(ierr);
for (i=0;i<NMAT;i++) {
ierr = MatDestroy(&A[i]);CHKERRQ(ierr);
}
ierr = SlepcFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **argv)
{
Mat A[NMAT]; /* problem matrices */
PEP pep; /* polynomial eigenproblem solver context */
PetscInt n,m=8,k,II,Istart,Iend,i,j;
PetscReal c[10] = { 0.6, 1.3, 1.3, 0.1, 0.1, 1.2, 1.0, 1.0, 1.2, 1.0 };
PetscBool flg;
PetscErrorCode ierr;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-m",&m,NULL);CHKERRQ(ierr);
n = m*m;
k = 10;
ierr = PetscOptionsGetRealArray(NULL,"-c",c,&k,&flg);CHKERRQ(ierr);
if (flg && k!=10) SETERRQ1(PETSC_COMM_WORLD,1,"The number of parameters -c should be 10, you provided %D",k);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nButterfly problem, n=%D (m=%D)\n\n",n,m);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Compute the polynomial matrices
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* initialize matrices */
for (i=0;i<NMAT;i++) {
ierr = MatCreate(PETSC_COMM_WORLD,&A[i]);CHKERRQ(ierr);
ierr = MatSetSizes(A[i],PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(A[i]);CHKERRQ(ierr);
ierr = MatSetUp(A[i]);CHKERRQ(ierr);
}
ierr = MatGetOwnershipRange(A[0],&Istart,&Iend);CHKERRQ(ierr);
/* A0 */
for (II=Istart;II<Iend;II++) {
i = II/m; j = II-i*m;
ierr = MatSetValue(A[0],II,II,4.0*c[0]/6.0+4.0*c[1]/6.0,INSERT_VALUES);CHKERRQ(ierr);
if (j>0) { ierr = MatSetValue(A[0],II,II-1,c[0]/6.0,INSERT_VALUES);CHKERRQ(ierr); }
if (j<m-1) { ierr = MatSetValue(A[0],II,II+1,c[0]/6.0,INSERT_VALUES);CHKERRQ(ierr); }
if (i>0) { ierr = MatSetValue(A[0],II,II-m,c[1]/6.0,INSERT_VALUES);CHKERRQ(ierr); }
if (i<m-1) { ierr = MatSetValue(A[0],II,II+m,c[1]/6.0,INSERT_VALUES);CHKERRQ(ierr); }
}
/* A1 */
for (II=Istart;II<Iend;II++) {
i = II/m; j = II-i*m;
if (j>0) { ierr = MatSetValue(A[1],II,II-1,c[2],INSERT_VALUES);CHKERRQ(ierr); }
if (j<m-1) { ierr = MatSetValue(A[1],II,II+1,-c[2],INSERT_VALUES);CHKERRQ(ierr); }
if (i>0) { ierr = MatSetValue(A[1],II,II-m,c[3],INSERT_VALUES);CHKERRQ(ierr); }
if (i<m-1) { ierr = MatSetValue(A[1],II,II+m,-c[3],INSERT_VALUES);CHKERRQ(ierr); }
}
/* A2 */
for (II=Istart;II<Iend;II++) {
i = II/m; j = II-i*m;
ierr = MatSetValue(A[2],II,II,-2.0*c[4]-2.0*c[5],INSERT_VALUES);CHKERRQ(ierr);
if (j>0) { ierr = MatSetValue(A[2],II,II-1,c[4],INSERT_VALUES);CHKERRQ(ierr); }
if (j<m-1) { ierr = MatSetValue(A[2],II,II+1,c[4],INSERT_VALUES);CHKERRQ(ierr); }
if (i>0) { ierr = MatSetValue(A[2],II,II-m,c[5],INSERT_VALUES);CHKERRQ(ierr); }
if (i<m-1) { ierr = MatSetValue(A[2],II,II+m,c[5],INSERT_VALUES);CHKERRQ(ierr); }
}
/* A3 */
for (II=Istart;II<Iend;II++) {
i = II/m; j = II-i*m;
if (j>0) { ierr = MatSetValue(A[3],II,II-1,c[6],INSERT_VALUES);CHKERRQ(ierr); }
if (j<m-1) { ierr = MatSetValue(A[3],II,II+1,-c[6],INSERT_VALUES);CHKERRQ(ierr); }
if (i>0) { ierr = MatSetValue(A[3],II,II-m,c[7],INSERT_VALUES);CHKERRQ(ierr); }
if (i<m-1) { ierr = MatSetValue(A[3],II,II+m,-c[7],INSERT_VALUES);CHKERRQ(ierr); }
}
/* A4 */
for (II=Istart;II<Iend;II++) {
i = II/m; j = II-i*m;
ierr = MatSetValue(A[4],II,II,2.0*c[8]+2.0*c[9],INSERT_VALUES);CHKERRQ(ierr);
if (j>0) { ierr = MatSetValue(A[4],II,II-1,-c[8],INSERT_VALUES);CHKERRQ(ierr); }
if (j<m-1) { ierr = MatSetValue(A[4],II,II+1,-c[8],INSERT_VALUES);CHKERRQ(ierr); }
if (i>0) { ierr = MatSetValue(A[4],II,II-m,-c[9],INSERT_VALUES);CHKERRQ(ierr); }
if (i<m-1) { ierr = MatSetValue(A[4],II,II+m,-c[9],INSERT_VALUES);CHKERRQ(ierr); }
}
/* assemble matrices */
for (i=0;i<NMAT;i++) {
ierr = MatAssemblyBegin(A[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
for (i=0;i<NMAT;i++) {
ierr = MatAssemblyEnd(A[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the eigensolver and solve the problem
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PEPCreate(PETSC_COMM_WORLD,&pep);CHKERRQ(ierr);
ierr = PEPSetOperators(pep,NMAT,A);CHKERRQ(ierr);
ierr = PEPSetFromOptions(pep);CHKERRQ(ierr);
ierr = PEPSolve(pep);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Display solution and clean up
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PEPPrintSolution(pep,NULL);CHKERRQ(ierr);
ierr = PEPDestroy(&pep);CHKERRQ(ierr);
for (i=0;i<NMAT;i++) {
ierr = MatDestroy(&A[i]);CHKERRQ(ierr);
}
ierr = SlepcFinalize();CHKERRQ(ierr);
return 0;
}
/*
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);
}