static PetscErrorCode FormFunction_All(SNES snes,Vec X,Vec F,void *ctx)
{
User user = (User)ctx;
DM dau,dak;
DMDALocalInfo infou,infok;
PetscScalar *u,*k;
PetscScalar *fu,*fk;
PetscErrorCode ierr;
Vec Uloc,Kloc,Fu,Fk;
PetscFunctionBeginUser;
ierr = DMCompositeGetEntries(user->pack,&dau,&dak);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dau,&infou);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dak,&infok);CHKERRQ(ierr);
ierr = DMCompositeGetLocalVectors(user->pack,&Uloc,&Kloc);CHKERRQ(ierr);
switch (user->ptype) {
case 0:
ierr = DMGlobalToLocalBegin(dau,X,INSERT_VALUES,Uloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd (dau,X,INSERT_VALUES,Uloc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dau,Uloc,&u);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dak,user->Kloc,&k);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dau,F,&fu);CHKERRQ(ierr);
ierr = FormFunctionLocal_U(user,&infou,u,k,fu);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dau,F,&fu);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dau,Uloc,&u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dak,user->Kloc,&k);CHKERRQ(ierr);
break;
case 1:
ierr = DMGlobalToLocalBegin(dak,X,INSERT_VALUES,Kloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd (dak,X,INSERT_VALUES,Kloc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dau,user->Uloc,&u);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dak,Kloc,&k);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dak,F,&fk);CHKERRQ(ierr);
ierr = FormFunctionLocal_K(user,&infok,u,k,fk);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dak,F,&fk);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dau,user->Uloc,&u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dak,Kloc,&k);CHKERRQ(ierr);
break;
case 2:
ierr = DMCompositeScatter(user->pack,X,Uloc,Kloc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dau,Uloc,&u);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dak,Kloc,&k);CHKERRQ(ierr);
ierr = DMCompositeGetAccess(user->pack,F,&Fu,&Fk);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dau,Fu,&fu);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dak,Fk,&fk);CHKERRQ(ierr);
ierr = FormFunctionLocal_U(user,&infou,u,k,fu);CHKERRQ(ierr);
ierr = FormFunctionLocal_K(user,&infok,u,k,fk);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dau,Fu,&fu);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dak,Fk,&fk);CHKERRQ(ierr);
ierr = DMCompositeRestoreAccess(user->pack,F,&Fu,&Fk);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dau,Uloc,&u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dak,Kloc,&k);CHKERRQ(ierr);
break;
}
ierr = DMCompositeRestoreLocalVectors(user->pack,&Uloc,&Kloc);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode TcSolver::generateBC2()
{
PetscErrorCode ierr;
PetscInt mstart, nstart, m, n, i, j;
PetscReal **qx, **qy;
PetscReal **bc22;
Vec bc2Global;
ierr = VecSet(bc2, 0.0); CHKERRQ(ierr);
ierr = DMCompositeGetAccess(lambdaPack, bc2, &bc2Global, NULL); CHKERRQ(ierr);
ierr = DMDAVecGetArray(uda, qxLocal, &qx); CHKERRQ(ierr);
ierr = DMDAVecGetArray(vda, qyLocal, &qy); CHKERRQ(ierr);
ierr = DMDAVecGetArray(pda, bc2Global, &bc22); CHKERRQ(ierr);
ierr = DMDAGetCorners(pda, &mstart, &nstart, NULL, &m, &n, NULL); CHKERRQ(ierr);
//x-faces
for(j=nstart; j<nstart+n; j++)
{
//-X
if(mstart == 0) //if -X is current process
{
bc22[j][0] -= qx[j][-1];
}
//+X
if(mstart+m-1 == fluid.nx-1)
{
bc22[j][fluid.nx-1] += qx[j][fluid.nx-1];
}
}
//y-faces
for(i=mstart; i<mstart+m; i++)
{
//-Y
if(nstart ==0)
{
bc22[0][i] -= qy[-1][i];
}
//+Y
if(nstart+n-1 == fluid.ny-1)
{
bc22[fluid.ny-1][i] += qy[fluid.ny-1][i];
}
}
ierr = DMDAVecRestoreArray(pda, bc2Global, &bc22); CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(uda, qxLocal, &qx); CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(vda, qyLocal, &qy); CHKERRQ(ierr);
ierr = DMCompositeRestoreAccess(lambdaPack, bc2, &bc2Global, NULL); CHKERRQ(ierr);
return 0;
}
PetscErrorCode ini_bou(Vec X,AppCtx* user)
{
PetscErrorCode ierr;
DM cda;
DMDACoor2d **coors;
PetscScalar **p;
Vec gc;
PetscInt i,j;
PetscInt xs,ys,xm,ym,M,N;
PetscScalar xi,yi;
PetscScalar sigmax=user->sigmax,sigmay=user->sigmay;
PetscScalar rho =user->rho;
PetscScalar mux =user->mux,muy=user->muy;
PetscMPIInt rank;
PetscScalar sum;
PetscFunctionBeginUser;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = DMDAGetInfo(user->da,NULL,&M,&N,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
user->dx = (user->xmax - user->xmin)/(M-1); user->dy = (user->ymax - user->ymin)/(N-1);
ierr = DMGetCoordinateDM(user->da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinates(user->da,&gc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->da,X,&p);CHKERRQ(ierr);
ierr = DMDAGetCorners(cda,&xs,&ys,0,&xm,&ym,0);CHKERRQ(ierr);
/* mux and muy need to be grid points in the x and y-direction otherwise the solution goes unstable
muy is set by choosing the y domain, no. of grid points along y-direction so that muy is a grid point
in the y-direction. We only modify mux here
*/
mux = user->mux = coors[0][M/2+10].x; /* For -pi < x < pi, this should be some angle between 0 and pi/2 */
if (user->nonoiseinitial) {
for (i=xs; i < xs+xm; i++) {
for (j=ys; j < ys+ym; j++) {
xi = coors[j][i].x; yi = coors[j][i].y;
if ((xi == mux) && (yi == muy)) {
p[j][i] = 1.0;
}
}
}
} else {
/* Change PM_min accordingly */
user->PM_min = user->Pmax*sin(mux);
for (i=xs; i < xs+xm; i++) {
for (j=ys; j < ys+ym; j++) {
xi = coors[j][i].x; yi = coors[j][i].y;
p[j][i] = (0.5/(PETSC_PI*sigmax*sigmay*PetscSqrtScalar(1.0-rho*rho)))*PetscExpScalar(-0.5/(1-rho*rho)*(PetscPowScalar((xi-mux)/sigmax,2) + PetscPowScalar((yi-muy)/sigmay,2) - 2*rho*(xi-mux)*(yi-muy)/(sigmax*sigmay)));
}
}
}
ierr = DMDAVecRestoreArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(user->da,X,&p);CHKERRQ(ierr);
ierr = VecSum(X,&sum);CHKERRQ(ierr);
ierr = VecScale(X,1.0/sum);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
RHSFunction - Evaluates nonlinear function, F(u).
Input Parameters:
. ts - the TS context
. U - input vector
. ptr - optional user-defined context, as set by TSSetFunction()
Output Parameter:
. F - function vector
*/
PetscErrorCode RHSFunction(TS ts,PetscReal ftime,Vec U,Vec F,void *ptr)
{
/* PETSC_UNUSED AppCtx *user=(AppCtx*)ptr; */
DM da;
PetscErrorCode ierr;
PetscInt i,j,Mx,My,xs,ys,xm,ym;
PetscReal two = 2.0,hx,hy,sx,sy;
PetscScalar u,uxx,uyy,**uarray,**f;
Vec localU;
PetscFunctionBeginUser;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMGetLocalVector(da,&localU);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,&My,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,
PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);
hx = 1.0/(PetscReal)(Mx-1); sx = 1.0/(hx*hx);
hy = 1.0/(PetscReal)(My-1); sy = 1.0/(hy*hy);
/*
Scatter ghost points to local vector,using the 2-step process
DMGlobalToLocalBegin(),DMGlobalToLocalEnd().
By placing code between these two statements, computations can be
done while messages are in transition.
*/
ierr = DMGlobalToLocalBegin(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,U,INSERT_VALUES,localU);CHKERRQ(ierr);
/* Get pointers to vector data */
ierr = DMDAVecGetArray(da,localU,&uarray);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,F,&f);CHKERRQ(ierr);
/* Get local grid boundaries */
ierr = DMDAGetCorners(da,&xs,&ys,NULL,&xm,&ym,NULL);CHKERRQ(ierr);
/* Compute function over the locally owned part of the grid */
for (j=ys; j<ys+ym; j++) {
for (i=xs; i<xs+xm; i++) {
if (i == 0 || j == 0 || i == Mx-1 || j == My-1) {
f[j][i] = uarray[j][i];
continue;
}
u = uarray[j][i];
uxx = (-two*u + uarray[j][i-1] + uarray[j][i+1])*sx;
uyy = (-two*u + uarray[j-1][i] + uarray[j+1][i])*sy;
f[j][i] = uxx + uyy;
}
}
/* Restore vectors */
ierr = DMDAVecRestoreArray(da,localU,&uarray);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,F,&f);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&localU);CHKERRQ(ierr);
ierr = PetscLogFlops(11.0*ym*xm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Evaluates FU = Gradiant(L(w,u,lambda))
This local function acts on the ghosted version of U (accessed via DMCompositeGetLocalVectors() and
DMCompositeScatter()) BUT the global, nonghosted version of FU (via DMCompositeGetAccess()).
*/
PetscErrorCode ComputeFunction(SNES snes,Vec U,Vec FU,void *ctx)
{
PetscErrorCode ierr;
PetscInt xs,xm,i,N;
ULambda *u_lambda,*fu_lambda;
PetscScalar d,h,*w,*fw;
Vec vw,vfw,vu_lambda,vfu_lambda;
DM packer,red,da;
PetscFunctionBeginUser;
ierr = VecGetDM(U, &packer);CHKERRQ(ierr);
ierr = DMCompositeGetEntries(packer,&red,&da);CHKERRQ(ierr);
ierr = DMCompositeGetLocalVectors(packer,&vw,&vu_lambda);CHKERRQ(ierr);
ierr = DMCompositeScatter(packer,U,vw,vu_lambda);CHKERRQ(ierr);
ierr = DMCompositeGetAccess(packer,FU,&vfw,&vfu_lambda);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,0,&N,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
ierr = VecGetArray(vw,&w);CHKERRQ(ierr);
ierr = VecGetArray(vfw,&fw);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,vu_lambda,&u_lambda);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,vfu_lambda,&fu_lambda);CHKERRQ(ierr);
d = N-1.0;
h = 1.0/d;
/* derivative of L() w.r.t. w */
if (xs == 0) { /* only first processor computes this */
fw[0] = -2.0*d*u_lambda[0].lambda;
}
/* derivative of L() w.r.t. u */
for (i=xs; i<xs+xm; i++) {
if (i == 0) fu_lambda[0].lambda = h*u_lambda[0].u + 2.*d*u_lambda[0].lambda - d*u_lambda[1].lambda;
else if (i == 1) fu_lambda[1].lambda = 2.*h*u_lambda[1].u + 2.*d*u_lambda[1].lambda - d*u_lambda[2].lambda;
else if (i == N-1) fu_lambda[N-1].lambda = h*u_lambda[N-1].u + 2.*d*u_lambda[N-1].lambda - d*u_lambda[N-2].lambda;
else if (i == N-2) fu_lambda[N-2].lambda = 2.*h*u_lambda[N-2].u + 2.*d*u_lambda[N-2].lambda - d*u_lambda[N-3].lambda;
else fu_lambda[i].lambda = 2.*h*u_lambda[i].u - d*(u_lambda[i+1].lambda - 2.0*u_lambda[i].lambda + u_lambda[i-1].lambda);
}
/* derivative of L() w.r.t. lambda */
for (i=xs; i<xs+xm; i++) {
if (i == 0) fu_lambda[0].u = 2.0*d*(u_lambda[0].u - w[0]);
else if (i == N-1) fu_lambda[N-1].u = 2.0*d*u_lambda[N-1].u;
else fu_lambda[i].u = -(d*(u_lambda[i+1].u - 2.0*u_lambda[i].u + u_lambda[i-1].u) - 2.0*h);
}
ierr = VecRestoreArray(vw,&w);CHKERRQ(ierr);
ierr = VecRestoreArray(vfw,&fw);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,vu_lambda,&u_lambda);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,vfu_lambda,&fu_lambda);CHKERRQ(ierr);
ierr = DMCompositeRestoreLocalVectors(packer,&vw,&vu_lambda);CHKERRQ(ierr);
ierr = DMCompositeRestoreAccess(packer,FU,&vfw,&vfu_lambda);CHKERRQ(ierr);
ierr = PetscLogFlops(13.0*N);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode SNESComputeFunction_DMDA(SNES snes,Vec X,Vec F,void *ctx)
{
PetscErrorCode ierr;
DM dm;
DMSNES_DA *dmdasnes = (DMSNES_DA*)ctx;
DMDALocalInfo info;
Vec Xloc;
void *x,*f;
PetscFunctionBegin;
PetscValidHeaderSpecific(snes,SNES_CLASSID,1);
PetscValidHeaderSpecific(X,VEC_CLASSID,2);
PetscValidHeaderSpecific(F,VEC_CLASSID,3);
if (!dmdasnes->residuallocal) SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_PLIB,"Corrupt context");
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm,&info);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,Xloc,&x);CHKERRQ(ierr);
switch (dmdasnes->residuallocalimode) {
case INSERT_VALUES: {
ierr = DMDAVecGetArray(dm,F,&f);CHKERRQ(ierr);
ierr = PetscLogEventBegin(SNES_FunctionEval,snes,X,F,0);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmdasnes->residuallocal)(&info,x,f,dmdasnes->residuallocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = PetscLogEventEnd(SNES_FunctionEval,snes,X,F,0);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dm,F,&f);CHKERRQ(ierr);
} break;
case ADD_VALUES: {
Vec Floc;
ierr = DMGetLocalVector(dm,&Floc);CHKERRQ(ierr);
ierr = VecZeroEntries(Floc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,Floc,&f);CHKERRQ(ierr);
ierr = PetscLogEventBegin(SNES_FunctionEval,snes,X,F,0);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmdasnes->residuallocal)(&info,x,f,dmdasnes->residuallocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = PetscLogEventEnd(SNES_FunctionEval,snes,X,F,0);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dm,Floc,&f);CHKERRQ(ierr);
ierr = VecZeroEntries(F);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dm,Floc,ADD_VALUES,F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm,Floc,ADD_VALUES,F);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Floc);CHKERRQ(ierr);
} break;
default: SETERRQ1(PetscObjectComm((PetscObject)snes),PETSC_ERR_ARG_INCOMP,"Cannot use imode=%d",(int)dmdasnes->residuallocalimode);
}
ierr = DMDAVecRestoreArray(dm,Xloc,&x);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr);
if (snes->domainerror) {
ierr = VecSetInf(F);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode IFunction(TS ts,PetscReal t,Vec X,Vec Xdot,Vec F,void *ctx)
{
PetscErrorCode ierr;
AppCtx *user=(AppCtx*)ctx;
DM cda;
DMDACoor2d **coors;
PetscScalar **p,**f,**pdot;
PetscInt i,j;
PetscInt xs,ys,xm,ym,M,N;
Vec localX,gc,localXdot;
PetscScalar p_adv1,p_adv2,p_diff;
PetscFunctionBeginUser;
ierr = DMDAGetInfo(user->da,NULL,&M,&N,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
ierr = DMGetCoordinateDM(user->da,&cda);CHKERRQ(ierr);
ierr = DMDAGetCorners(cda,&xs,&ys,0,&xm,&ym,0);CHKERRQ(ierr);
ierr = DMGetLocalVector(user->da,&localX);CHKERRQ(ierr);
ierr = DMGetLocalVector(user->da,&localXdot);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(user->da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(user->da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(user->da,Xdot,INSERT_VALUES,localXdot);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(user->da,Xdot,INSERT_VALUES,localXdot);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(user->da,&gc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->da,localX,&p);CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->da,localXdot,&pdot);CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->da,F,&f);CHKERRQ(ierr);
user->disper_coe = PetscPowScalar((user->lambda*user->ws)/(2*user->H),2)*user->q*(1.0-PetscExpScalar(-t/user->lambda));
for (i=xs; i < xs+xm; i++) {
for (j=ys; j < ys+ym; j++) {
if (i == 0 || j == 0 || i == M-1 || j == N-1) {
ierr = BoundaryConditions(p,coors,i,j,M,N,f,user);CHKERRQ(ierr);
} else {
ierr = adv1(p,coors[j][i].y,i,j,M,&p_adv1,user);CHKERRQ(ierr);
ierr = adv2(p,coors[j][i].x,i,j,N,&p_adv2,user);CHKERRQ(ierr);
ierr = diffuse(p,i,j,t,&p_diff,user);CHKERRQ(ierr);
f[j][i] = -p_adv1 - p_adv2 + p_diff - pdot[j][i];
}
}
}
ierr = DMDAVecRestoreArray(user->da,localX,&p);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(user->da,localX,&pdot);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(user->da,&localX);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(user->da,&localXdot);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(user->da,F,&f);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(cda,gc,&coors);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
PostCheck - Optional user-defined routine that checks the validity of
candidate steps of a line search method. Set by SNESLineSearchSetPostCheck().
Input Parameters:
snes - the SNES context
ctx - optional user-defined context for private data for the
monitor routine, as set by SNESLineSearchSetPostCheck()
xcurrent - current solution
y - search direction and length
x - the new candidate iterate
Output Parameters:
y - proposed step (search direction and length) (possibly changed)
x - current iterate (possibly modified)
*/
PetscErrorCode PostCheck(SNESLineSearch linesearch,Vec xcurrent,Vec y,Vec x,PetscBool *changed_y,PetscBool *changed_x, void * ctx)
{
PetscErrorCode ierr;
PetscInt i,iter,xs,xm;
StepCheckCtx *check;
ApplicationCtx *user;
PetscScalar *xa,*xa_last,tmp;
PetscReal rdiff;
DM da;
SNES snes;
PetscFunctionBeginUser;
*changed_x = PETSC_FALSE;
*changed_y = PETSC_FALSE;
ierr = SNESLineSearchGetSNES(linesearch, &snes);CHKERRQ(ierr);
check = (StepCheckCtx*)ctx;
user = check->user;
ierr = SNESGetIterationNumber(snes,&iter);CHKERRQ(ierr);
ierr = SNESLineSearchGetPreCheck(linesearch, NULL, (void**)&check);CHKERRQ(ierr);
/* iteration 1 indicates we are working on the second iteration */
if (iter > 0) {
da = user->da;
ierr = PetscPrintf(PETSC_COMM_WORLD,"Checking candidate step at iteration %D with tolerance %G\n",iter,check->tolerance);CHKERRQ(ierr);
/* Access local array data */
ierr = DMDAVecGetArray(da,check->last_step,&xa_last);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,x,&xa);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
/*
If we fail the user-defined check for validity of the candidate iterate,
then modify the iterate as we like. (Note that the particular modification
below is intended simply to demonstrate how to manipulate this data, not
as a meaningful or appropriate choice.)
*/
for (i=xs; i<xs+xm; i++) {
if (!PetscAbsScalar(xa[i])) rdiff = 2*check->tolerance;
else rdiff = PetscAbsScalar((xa[i] - xa_last[i])/xa[i]);
if (rdiff > check->tolerance) {
tmp = xa[i];
xa[i] = .5*(xa[i] + xa_last[i]);
*changed_x = PETSC_TRUE;
ierr = PetscPrintf(PETSC_COMM_WORLD," Altering entry %D: x=%G, x_last=%G, diff=%G, x_new=%G\n",
i,PetscAbsScalar(tmp),PetscAbsScalar(xa_last[i]),rdiff,PetscAbsScalar(xa[i]));CHKERRQ(ierr);
}
}
ierr = DMDAVecRestoreArray(da,check->last_step,&xa_last);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,x,&xa);CHKERRQ(ierr);
}
ierr = VecCopy(x,check->last_step);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
FormFunction - Evaluates nonlinear function, F(x).
Input Parameters:
. snes - the SNES context
. x - input vector
. ctx - optional user-defined context, as set by SNESSetFunction()
Output Parameter:
. f - function vector
Note:
The user-defined context can contain any application-specific
data needed for the function evaluation.
*/
PetscErrorCode FormFunction(SNES snes,Vec x,Vec f,void *ctx)
{
DM da = (DM) ctx;
PetscScalar *xx,*ff;
PetscReal h;
PetscErrorCode ierr;
PetscInt i,M,xs,xm;
Vec xlocal;
PetscFunctionBeginUser;
/* Get local work vector */
ierr = DMGetLocalVector(da,&xlocal);CHKERRQ(ierr);
/*
Scatter ghost points to local vector, using the 2-step process
DMGlobalToLocalBegin(), DMGlobalToLocalEnd().
By placing code between these two statements, computations can
be done while messages are in transition.
*/
ierr = DMGlobalToLocalBegin(da,x,INSERT_VALUES,xlocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,x,INSERT_VALUES,xlocal);CHKERRQ(ierr);
/*
Get pointers to vector data.
- The vector xlocal includes ghost point; the vectors x and f do
NOT include ghost points.
- Using DMDAVecGetArray() allows accessing the values using global ordering
*/
ierr = DMDAVecGetArray(da,xlocal,&xx);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,f,&ff);CHKERRQ(ierr);
/*
Get local grid boundaries (for 1-dimensional DMDA):
xs, xm - starting grid index, width of local grid (no ghost points)
*/
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,NULL,&M,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);CHKERRQ(ierr);
/*
Compute function over locally owned part of the grid
Note the [i-1] and [i+1] will automatically access the ghost points from other processes or the periodic points.
*/
h = 1.0/M;
for (i=xs; i<xs+xm; i++) ff[i] = (xx[i-1] - 2.0*xx[i] + xx[i+1])/(h*h) - PetscSinReal(2.0*PETSC_PI*i*h);
/*
Restore vectors
*/
ierr = DMDAVecRestoreArray(da,xlocal,&xx);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,f,&ff);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&xlocal);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode FormIFunction(TS ts,PetscReal t,Vec X,Vec Xdot,Vec F,void *ptr)
{
User user = (User)ptr;
DM da;
DMDALocalInfo info;
PetscInt i;
Field *x,*xdot,*f;
PetscReal hx;
Vec Xloc;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
hx = 1.0/(PetscReal)(info.mx-1);
/*
Scatter ghost points to local vector,using the 2-step process
DMGlobalToLocalBegin(),DMGlobalToLocalEnd().
By placing code between these two statements, computations can be
done while messages are in transition.
*/
ierr = DMGetLocalVector(da,&Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
/* Get pointers to vector data */
ierr = DMDAVecGetArray(da,Xloc,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,Xdot,&xdot);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,F,&f);CHKERRQ(ierr);
/* Compute function over the locally owned part of the grid */
for (i=info.xs; i<info.xs+info.xm; i++) {
if (i == 0) {
f[i].u = hx * (x[i].u - user->uleft);
f[i].v = hx * (x[i].v - user->vleft);
} else if (i == info.mx-1) {
f[i].u = hx * (x[i].u - user->uright);
f[i].v = hx * (x[i].v - user->vright);
} else {
f[i].u = hx * xdot[i].u - user->alpha * (x[i-1].u - 2.*x[i].u + x[i+1].u) / hx;
f[i].v = hx * xdot[i].v - user->alpha * (x[i-1].v - 2.*x[i].v + x[i+1].v) / hx;
}
}
/* Restore vectors */
ierr = DMDAVecRestoreArray(da,Xloc,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,Xdot,&xdot);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,F,&f);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&Xloc);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DiffusiveTerm<2>::initializeFluxes()
{
PetscErrorCode ierr;
PetscInt i, j, // loop indices
m, n, // local number of nodes along each direction
mstart, nstart; // starting indices
PetscReal x, y; // coordinates of a node
Vec qxGlobal, qyGlobal;
ierr = DMCompositeGetAccess(qPack, q, &qxGlobal, &qyGlobal); CHKERRQ(ierr);
// fluxes in x-direction
PetscReal **qx;
ierr = DMDAVecGetArray(uda, qxGlobal, &qx); CHKERRQ(ierr);
ierr = DMDAGetCorners(uda, &mstart, &nstart, NULL, &m, &n, NULL); CHKERRQ(ierr);
PetscReal u; // value of u-velocity
for (j=nstart; j<nstart+n; j++)
{
for (i=mstart; i<mstart+m; i++)
{
x = mesh->x[i+1];
y = 0.5*(mesh->y[j]+mesh->y[j+1]);
u = sin(PETSC_PI*x)*sin(PETSC_PI*y) + 1.0;
qx[j][i] = u*mesh->dy[j];
}
}
ierr = DMDAVecRestoreArray(uda, qxGlobal, &qx); CHKERRQ(ierr);
// fluxes in y-direction
PetscReal **qy;
ierr = DMDAVecGetArray(vda, qyGlobal, &qy); CHKERRQ(ierr);
ierr = DMDAGetCorners(vda, &mstart, &nstart, NULL, &m, &n, NULL); CHKERRQ(ierr);
PetscReal v; // value of v-velocity
for (j=nstart; j<nstart+n; j++)
{
for (i=mstart; i<mstart+m; i++)
{
x = 0.5*(mesh->x[i]+mesh->x[i+1]);
y = mesh->y[j+1];
v = sin(PETSC_PI*x)*sin(PETSC_PI*y);
qy[j][i] = v*mesh->dx[i];
}
}
ierr = DMDAVecRestoreArray(vda, qyGlobal, &qy); CHKERRQ(ierr);
ierr = DMCompositeRestoreAccess(qPack, q, &qxGlobal, &qyGlobal); CHKERRQ(ierr);
return ierr;
} // initializeFluxes
PetscErrorCode FormTangent(TS ts,PetscReal t,Vec U,Vec Udot,PetscReal shift,Mat *A,Mat *B,MatStructure *flag,void *ctx)
{
PetscFunctionBegin;
PetscErrorCode ierr;
SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "FormTangent not implemented, use -snes_mf");
DMDALocalInfo info;
DM da_dof;
Vec localU,localUdot; // local versions
Field **h,**hdot;
/* get the da from the snes */
ierr = TSGetDM(ts,(DM*)&da_dof);CHKERRQ(ierr);
/* handle the vec U */
ierr = DMGetLocalVector(da_dof,&localU);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da_dof,U,INSERT_VALUES,localU);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da_dof,U,INSERT_VALUES,localU);CHKERRQ(ierr);
/* handle the vec Udot */
ierr = DMGetLocalVector(da_dof,&localUdot);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da_dof,Udot,INSERT_VALUES,localUdot);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da_dof,Udot,INSERT_VALUES,localUdot);CHKERRQ(ierr);
/* Get the arrays from the vectors */
ierr = DMDAVecGetArray(da_dof,localU,&h);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da_dof,localUdot,&hdot);CHKERRQ(ierr);
/* Grab the local info and call the local tangent routine */
ierr = DMDAGetLocalInfo(da_dof,&info);CHKERRQ(ierr);CHKERRQ(ierr);
ierr = MatZeroEntries(*B);CHKERRQ(ierr); // pre-zero the matrix
ierr = FormTangentLocal(&info,t,h,hdot,shift,B,(AppCtx *) ctx);CHKERRQ(ierr);
ierr = MatAssemblyBegin(*B,MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = MatAssemblyEnd(*B,MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
if (*A != *B) { // then we could be matrix free
ierr = MatAssemblyBegin(*A,MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = MatAssemblyEnd(*A,MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
}
*flag = SAME_NONZERO_PATTERN; /* the sparsity pattern does not change */
ierr = DMDAVecRestoreArray(da_dof,localUdot,&hdot);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da_dof,localU,&h);CHKERRQ(ierr);
/* Restore the arrays and local vectors */
ierr = DMRestoreLocalVector(da_dof,&localU);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da_dof,&localUdot);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
This function should eventually replace:
DMDAComputeFunction() and DMDAComputeFunction1()
*/
static PetscErrorCode TSComputeIFunction_DMDA(TS ts,PetscReal ptime,Vec X,Vec Xdot,Vec F,void *ctx)
{
PetscErrorCode ierr;
DM dm;
DMTS_DA *dmdats = (DMTS_DA*)ctx;
DMDALocalInfo info;
Vec Xloc;
void *x,*f,*xdot;
PetscFunctionBegin;
PetscValidHeaderSpecific(ts,TS_CLASSID,1);
PetscValidHeaderSpecific(X,VEC_CLASSID,2);
PetscValidHeaderSpecific(F,VEC_CLASSID,3);
if (!dmdats->ifunctionlocal) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_PLIB,"Corrupt context");
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm,&info);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,Xloc,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,Xdot,&xdot);CHKERRQ(ierr);
switch (dmdats->ifunctionlocalimode) {
case INSERT_VALUES: {
ierr = DMDAVecGetArray(dm,F,&f);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmdats->ifunctionlocal)(&info,ptime,x,xdot,f,dmdats->ifunctionlocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = DMDAVecRestoreArray(dm,F,&f);CHKERRQ(ierr);
} break;
case ADD_VALUES: {
Vec Floc;
ierr = DMGetLocalVector(dm,&Floc);CHKERRQ(ierr);
ierr = VecZeroEntries(Floc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,Floc,&f);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmdats->ifunctionlocal)(&info,ptime,x,xdot,f,dmdats->ifunctionlocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = DMDAVecRestoreArray(dm,Floc,&f);CHKERRQ(ierr);
ierr = VecZeroEntries(F);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dm,Floc,ADD_VALUES,F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm,Floc,ADD_VALUES,F);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Floc);CHKERRQ(ierr);
} break;
default: SETERRQ1(PetscObjectComm((PetscObject)ts),PETSC_ERR_ARG_INCOMP,"Cannot use imode=%d",(int)dmdats->ifunctionlocalimode);
}
ierr = DMDAVecRestoreArray(dm,Xloc,&x);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dm,Xdot,&xdot);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode FormRHSFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr)
{
User user = (User)ptr;
DM da;
Vec Xloc;
DMDALocalInfo info;
PetscInt i,j;
PetscReal hx;
Field *x,*f;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
hx = 1.0/(PetscReal)info.mx;
/*
Scatter ghost points to local vector,using the 2-step process
DMGlobalToLocalBegin(),DMGlobalToLocalEnd().
By placing code between these two statements, computations can be
done while messages are in transition.
*/
ierr = DMGetLocalVector(da,&Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
/* Get pointers to vector data */
ierr = DMDAVecGetArray(da,Xloc,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,F,&f);CHKERRQ(ierr);
/* Compute function over the locally owned part of the grid */
for (i=info.xs; i<info.xs+info.xm; i++) {
const PetscReal *a = user->a;
PetscReal u0t[2] = {1. - PetscPowScalar(sin(12*t),4.),0};
for (j=0; j<2; j++) {
if (i == 0) f[i][j] = a[j]/hx*(1./3*u0t[j] + 0.5*x[i][j] - x[i+1][j] + 1./6*x[i+2][j]);
else if (i == 1) f[i][j] = a[j]/hx*(-1./12*u0t[j] + 2./3*x[i-1][j] - 2./3*x[i+1][j] + 1./12*x[i+2][j]);
else if (i == info.mx-2) f[i][j] = a[j]/hx*(-1./6*x[i-2][j] + x[i-1][j] - 0.5*x[i][j] - 1./3*x[i+1][j]);
else if (i == info.mx-1) f[i][j] = a[j]/hx*(-x[i][j] + x[i-1][j]);
else f[i][j] = a[j]/hx*(-1./12*x[i-2][j] + 2./3*x[i-1][j] - 2./3*x[i+1][j] + 1./12*x[i+2][j]);
}
}
/* Restore vectors */
ierr = DMDAVecRestoreArray(da,Xloc,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,F,&f);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&Xloc);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode efs_set_state(efs *slv, double rhs[], double phi[], double eps[],
double debye[])
{
PetscErrorCode ierr;
slv->state.phi = phi;
slv->state.eps = eps;
slv->state.debye = debye;
slv->state.rhs = rhs;
slv->state.sol = NULL;
if (slv->grid.nd == 2) {
PetscScalar **epsvec;
double **eps_state;
PetscInt i, j;
PetscInt xs, ys, xm, ym;
ierr = DMDAGetCorners(slv->dm, &xs, &ys, 0, &xm, &ym, 0);CHKERRQ(ierr);
ierr = ef_dmap_get(slv->dmap, slv->state.eps, &eps_state);CHKERRQ(ierr);
ierr = DMDAVecGetArray(slv->dm, slv->levels[0].eps, &epsvec);CHKERRQ(ierr);
for (j = ys; j < ys + ym; j++) {
for (i = xs; i < xs + xm; i++) {
epsvec[j][i] = eps_state[j][i];
}
}
ierr = ef_dmap_restore(slv->dmap, &eps_state);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(slv->dm, slv->levels[0].eps, &epsvec);CHKERRQ(ierr);
} else if (slv->grid.nd == 3) {
PetscScalar ***epsvec;
double ***eps_state;
PetscInt i, j, k;
PetscInt xs, ys, zs, xm, ym, zm;
ierr = DMDAGetCorners(slv->dm, &xs, &ys, &zs, &xm, &ym, &zm);CHKERRQ(ierr);
ierr = ef_dmap_get(slv->dmap, slv->state.eps, &eps_state);CHKERRQ(ierr);
ierr = DMDAVecGetArray(slv->dm, slv->levels[0].eps, &epsvec);CHKERRQ(ierr);
for (k = zs; k < zs + zm; k++) {
for (j = ys; j < ys + ym; j++) {
for (i = xs; i < xs + xm; i++) {
epsvec[k][j][i] = eps_state[k][j][i];
}
}
}
ierr = ef_dmap_restore(slv->dmap, &eps_state);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(slv->dm, slv->levels[0].eps, &epsvec);CHKERRQ(ierr);
}
return 0;
}
/*
FormFunctionLocal - Evaluates nonlinear residual, F(x) on local process patch
*/
PetscErrorCode FormFunctionLocal(DMDALocalInfo *info, Field *u, Field *f, AppCtx *user)
{
Vec L;
PetscReal phi = user->phi;
PetscReal dt = user->dt;
PetscReal dx = 1.0/(PetscReal)(info->mx-1);
PetscReal alpha = 2.0;
PetscReal beta = 2.0;
PetscReal kappaWet = user->kappaWet;
PetscReal kappaNoWet = user->kappaNoWet;
Field *uold;
PetscScalar *Kappa;
PetscInt i;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMGetGlobalVector(user->cda, &L);CHKERRQ(ierr);
ierr = DMDAVecGetArray(info->da, user->uold, &uold);CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->cda, user->Kappa, &Kappa);CHKERRQ(ierr);
/* Compute residual over the locally owned part of the grid */
for(i = info->xs; i < info->xs+info->xm; ++i) {
if (i == 0) {
f[i].s = u[i].s - user->sl;
f[i].v = u[i].v - user->vl;
f[i].p = u[i].p - user->pl;
} else {
PetscScalar K = 2*dx/(dx/Kappa[i] + dx/Kappa[i-1]);
PetscReal lambdaWet = kappaWet*pow(u[i].s, alpha);
PetscReal lambda = lambdaWet + kappaNoWet*pow(1-u[i].s, beta);
PetscReal lambdaWetL = kappaWet*pow(u[i-1].s, alpha);
PetscReal lambdaL = lambdaWetL + kappaNoWet*pow(1-u[i-1].s, beta);
f[i].s = phi*(u[i].s - uold[i].s) + (dt/dx)*((lambdaWet/lambda)*u[i].v - (lambdaWetL/lambdaL)*u[i-1].v);
f[i].v = u[i].v + K*lambda*(u[i].p - u[i-1].p)/dx;
//pxx = (2.0*u[i].p - u[i-1].p - u[i+1].p)/dx;
f[i].p = u[i].v - u[i-1].v;
}
}
ierr = DMDAVecRestoreArray(info->da, user->uold, &uold);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(user->cda, user->Kappa, &Kappa);CHKERRQ(ierr);
/* ierr = PetscLogFlops(11.0*info->ym*info->xm);CHKERRQ(ierr); */
ierr = DMRestoreGlobalVector(user->cda, &L);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SetCoordinates1d(DM da)
{
PetscErrorCode ierr;
PetscInt i,start,m;
Vec gc,global;
PetscScalar *coors;
DM cda;
PetscFunctionBeginUser;
ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(da,&gc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAGetCorners(cda,&start,0,0,&m,0,0);CHKERRQ(ierr);
for (i=start; i<start+m; i++) {
if (i % 2) {
coors[i] = coors[i-1] + .1*(coors[i+1] - coors[i-1]);
}
}
ierr = DMDAVecRestoreArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&global);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(cda,gc,INSERT_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(cda,gc,INSERT_VALUES,global);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SetCoordinates3d(DM da)
{
PetscErrorCode ierr;
PetscInt i,j,mstart,m,nstart,n,pstart,p,k;
Vec gc,global;
DMDACoor3d ***coors;
DM cda;
PetscFunctionBeginUser;
ierr = DMDASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(da,&gc);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAGetCorners(cda,&mstart,&nstart,&pstart,&m,&n,&p);CHKERRQ(ierr);
for (i=mstart; i<mstart+m; i++) {
for (j=nstart; j<nstart+n; j++) {
for (k=pstart; k<pstart+p; k++) {
if (i % 2) {
coors[k][j][i].x = coors[k][j][i-1].x + .1*(coors[k][j][i+1].x - coors[k][j][i-1].x);
}
if (j % 2) {
coors[k][j][i].y = coors[k][j-1][i].y + .3*(coors[k][j+1][i].y - coors[k][j-1][i].y);
}
if (k % 2) {
coors[k][j][i].z = coors[k-1][j][i].z + .4*(coors[k+1][j][i].z - coors[k-1][j][i].z);
}
}
}
}
ierr = DMDAVecRestoreArray(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMGetCoordinates(da,&global);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(cda,gc,INSERT_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(cda,gc,INSERT_VALUES,global);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode checkPositivity(PorousCtx *user,Vec X) {
PetscErrorCode ierr;
PetscInt i,j,xs,ys,xm,ym;
DM da = user->da;
WPnode **wp;
PetscFunctionBegin;
ierr = DMDAGetCorners(da,&xs,&ys,PETSC_NULL,&xm,&ym,PETSC_NULL);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,X,&wp);CHKERRQ(ierr);
for (j=ys; j<ys+ym; j++) {
for (i=xs; i<xs+xm; i++) {
if (wp[j][i].W < 0) {
SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE,
"negative water thickness W at (i,j)=(%d,%d) during function eval %d",
i,j,user->fcncount);
}
if (wp[j][i].P < 0) {
SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE,
"negative water pressure P at (i,j)=(%d,%d) during function eval %d",
i,j,user->fcncount);
}
}
}
ierr = DMDAVecRestoreArray(da,X,&wp);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FormInitialGuess(SNES snes,Vec X,void *ctx)
{
AppCtx *user;
PetscInt i,j,xs,ys,xm,ym;
PetscErrorCode ierr;
PetscReal tleft;
PetscScalar **x;
DM da;
PetscFunctionBeginUser;
ierr = SNESGetDM(snes,&da);CHKERRQ(ierr);
ierr = DMGetApplicationContext(da,&user);CHKERRQ(ierr);
tleft = user->tleft;
/* Get ghost points */
ierr = DMDAGetCorners(da,&xs,&ys,0,&xm,&ym,0);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,X,&x);CHKERRQ(ierr);
/* Compute initial guess */
for (j=ys; j<ys+ym; j++) {
for (i=xs; i<xs+xm; i++) {
x[j][i] = tleft;
}
}
ierr = DMDAVecRestoreArray(da,X,&x);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Solution - Computes the exact solution at a given time.
Input Parameters:
t - current time
solution - vector in which exact solution will be computed
appctx - user-defined application context
Output Parameter:
solution - vector with the newly computed exact solution
*/
PetscErrorCode Solution(TS ts,PetscReal t,Vec U,AppCtx *appctx)
{
PetscScalar *u,ex1,ex2,sc1,sc2,h;
PetscErrorCode ierr;
PetscInt i,mstart,mend,xm,M;
DM da;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&mstart,0,0,&xm,0,0);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,PETSC_IGNORE,&M,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
h = 1.0/M;
mend = mstart + xm;
/*
Get a pointer to vector data.
*/
ierr = DMDAVecGetArray(da,U,&u);CHKERRQ(ierr);
/*
Simply write the solution directly into the array locations.
Alternatively, we culd use VecSetValues() or VecSetValuesLocal().
*/
ex1 = PetscExpScalar(-36.*PETSC_PI*PETSC_PI*appctx->d*t);
ex2 = PetscExpScalar(-4.*PETSC_PI*PETSC_PI*appctx->d*t);
sc1 = PETSC_PI*6.*h; sc2 = PETSC_PI*2.*h;
for (i=mstart; i<mend; i++) u[i] = PetscSinScalar(sc1*(PetscReal)i + appctx->a*PETSC_PI*6.*t)*ex1 + 3.*PetscSinScalar(sc2*(PetscReal)i + appctx->a*PETSC_PI*2.*t)*ex2;
/*
Restore vector
*/
ierr = DMDAVecRestoreArray(da,U,&u);CHKERRQ(ierr);
return 0;
}
PetscErrorCode FormInitialGuess(DM da,void *ctx,Vec X)
{
PetscInt i,j,Mx,My,xs,ys,xm,ym;
PetscErrorCode ierr;
PetscScalar **x;
PetscReal x0,x1;
PetscFunctionBeginUser;
ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,&My,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,
PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);
ierr = DMDAVecGetArray(da,X,&x);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,&ys,PETSC_NULL,&xm,&ym,PETSC_NULL);CHKERRQ(ierr);
for (j=ys; j<ys+ym; j++) {
for (i=xs; i<xs+xm; i++) {
x0 = 10.0*(i - 0.5*(Mx-1)) / (Mx-1);
x1 = 10.0*(j - 0.5*(Mx-1)) / (My-1);
if (PetscAbsScalar(x0) < 0.5 && PetscAbsScalar(x1) < 0.5) {
x[j][i] = 1.;
} else {
x[j][i] = 0.0;
}
}
}
ierr = DMDAVecRestoreArray(da,X,&x);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/* FormFunctionLocal - Evaluates nonlinear function, F(x) on local process patch */
PetscErrorCode FormFunctionLocal(DMDALocalInfo *info,PetscScalar **x,PetscScalar **f,ObsCtx *user) {
PetscErrorCode ierr;
PetscInt i,j;
PetscReal dx,dy,uxx,uyy;
PetscReal **uexact; /* used for boundary values only */
PetscFunctionBeginUser;
dx = 4.0 / (PetscReal)(info->mx-1);
dy = 4.0 / (PetscReal)(info->my-1);
ierr = DMDAVecGetArray(info->da, user->uexact, &uexact);CHKERRQ(ierr);
for (j=info->ys; j<info->ys+info->ym; j++) {
for (i=info->xs; i<info->xs+info->xm; i++) {
if (i == 0 || j == 0 || i == info->mx-1 || j == info->my-1) {
f[j][i] = 4.0*(x[j][i] - uexact[j][i]);
} else {
uxx = dy*(x[j][i-1] - 2.0 * x[j][i] + x[j][i+1]) / dx;
uyy = dx*(x[j-1][i] - 2.0 * x[j][i] + x[j+1][i]) / dy;
f[j][i] = -uxx - uyy;
}
}
}
ierr = DMDAVecRestoreArray(info->da, user->uexact, &uexact);CHKERRQ(ierr);
ierr = PetscLogFlops(10.0*info->ym*info->xm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode TSComputeRHSJacobian_DMDA(TS ts,PetscReal ptime,Vec X,Mat *A,Mat *B,MatStructure *mstr,void *ctx)
{
PetscErrorCode ierr;
DM dm;
DMTS_DA *dmdats = (DMTS_DA*)ctx;
DMDALocalInfo info;
Vec Xloc;
void *x;
PetscFunctionBegin;
if (!dmdats->rhsfunctionlocal) SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_PLIB,"Corrupt context");
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
if (dmdats->rhsjacobianlocal) {
ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm,&info);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,Xloc,&x);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmdats->rhsjacobianlocal)(&info,ptime,x,*A,*B,mstr,dmdats->rhsjacobianlocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = DMDAVecRestoreArray(dm,Xloc,&x);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr);
} else SETERRQ(PetscObjectComm((PetscObject)ts),PETSC_ERR_PLIB,"TSComputeRHSJacobian_DMDA() called without calling DMDATSSetRHSJacobian()");
/* This will be redundant if the user called both, but it's too common to forget. */
if (*A != *B) {
ierr = MatAssemblyBegin(*A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*
ComputeInitialGuess - Calculates the initial guess
Input Parameters:
. user - user-defined application context
. X - vector for initial guess
Output Parameters:
. X - newly computed initial guess
*/
PetscErrorCode ComputeInitialGuess(SNES snes, Vec X,void *dummy)
{
PetscErrorCode ierr;
PetscInt i,j,mx,my;
DM da;
AppCtx *user;
PetscScalar **x;
PetscInt xs,xm,ys,ym;
PetscFunctionBeginUser;
ierr = SNESGetDM(snes,&da);CHKERRQ(ierr);
ierr = SNESGetApplicationContext(snes,(void**)&user);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,&ys,NULL,&xm,&ym,NULL);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,PETSC_IGNORE,&mx,&my,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);CHKERRQ(ierr);
/* Get pointers to vector data */
ierr = DMDAVecGetArray(da,X,&x);CHKERRQ(ierr);
/* Perform local computations */
for (j=ys; j<ys+ym; j++) {
for (i=xs; i< xs+xm; i++) {
x[j][i] = (((j+1.0)*user->bottom[i+1]+(my-j+1.0)*user->top[i+1])/(my+2.0)+((i+1.0)*user->left[j+1]+(mx-i+1.0)*user->right[j+1])/(mx+2.0))/2.0;
}
}
/* Restore vectors */
ierr = DMDAVecRestoreArray(da,X,&x);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FormDiffusionCoefficient(DM da,void *ctx,Vec X)
{
PetscInt i,j,Mx,My,xs,ys,xm,ym;
PetscErrorCode ierr;
PetscScalar **x;
PetscReal x1,min=0.1;
PetscFunctionBeginUser;
ierr = DMDAGetInfo(da,PETSC_IGNORE,&Mx,&My,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,
PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE,PETSC_IGNORE);
/*
ierr = VecSetRandom(X,PETSC_NULL);
ierr = VecMin(X,PETSC_NULL,&min);CHKERRQ(ierr);
*/
ierr = DMDAVecGetArray(da,X,&x);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,&ys,PETSC_NULL,&xm,&ym,PETSC_NULL);CHKERRQ(ierr);
for (j=ys; j<ys+ym; j++) {
for (i=xs; i<xs+xm; i++) {
x1 = 10.0*(j - 0.5*(Mx-1)) / (My-1);
x[j][i] += min + (1. - min)*PetscSqr(sin(2.*PETSC_PI*x1));
}
}
ierr = DMDAVecRestoreArray(da,X,&x);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FormInitialSolution(TS ts,Vec X,void *ctx)
{
User user = (User)ctx;
DM da;
PetscInt i;
DMDALocalInfo info;
Field *x;
PetscReal hx;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = TSGetDM(ts,&da);
ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
hx = 1.0/(PetscReal)info.mx;
/* Get pointers to vector data */
ierr = DMDAVecGetArray(da,X,&x);CHKERRQ(ierr);
/* Compute function over the locally owned part of the grid */
for (i=info.xs; i<info.xs+info.xm; i++) {
PetscReal r = (i+1)*hx,ik = user->k[1] != 0.0 ? 1.0/user->k[1] : 1.0;
x[i][0] = 1 + user->s[1]*r;
x[i][1] = user->k[0]*ik*x[i][0] + user->s[1]*ik;
}
ierr = DMDAVecRestoreArray(da,X,&x);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode ini_bou(Vec X,AppCtx* user)
{
PetscErrorCode ierr;
DM cda;
DMDACoor2d **coors;
PetscScalar **p;
Vec gc;
PetscInt M,N,I,J;
PetscMPIInt rank;
PetscFunctionBeginUser;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = DMDAGetInfo(user->da,NULL,&M,&N,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);
user->dx = (user->xmax - user->xmin)/(M-1); user->dy = (user->ymax - user->ymin)/(N-1);
ierr = DMGetCoordinateDM(user->da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinates(user->da,&gc);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->da,X,&p);CHKERRQ(ierr);
/* Point mass at (mux,muy) */
ierr = PetscPrintf(PETSC_COMM_WORLD,"Original user->mux = %f, user->muy = %f\n",user->mux,user->muy);CHKERRQ(ierr);
ierr = DMDAGetLogicalCoordinate(user->da,user->mux,user->muy,0.0,&I,&J,NULL,&user->mux,&user->muy,NULL);CHKERRQ(ierr);
user->PM_min = user->Pmax*PetscSinScalar(user->mux);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Corrected user->mux = %f, user->muy = %f user->PM_min = %f,user->dx = %f\n",user->mux,user->muy,user->PM_min,user->dx);CHKERRQ(ierr);
if (I > -1 && J > -1) {
p[J][I] = 1.0;
}
ierr = DMDAVecRestoreArrayRead(cda,gc,&coors);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(user->da,X,&p);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode ComputeRHS(KSP ksp,Vec b,void *ctx)
{
PetscErrorCode ierr;
PetscInt i,j,k,mx,my,mz,xm,ym,zm,xs,ys,zs;
DM dm;
PetscScalar Hx,Hy,Hz,HxHydHz,HyHzdHx,HxHzdHy;
PetscScalar ***barray;
PetscFunctionBeginUser;
ierr = KSPGetDM(ksp,&dm);CHKERRQ(ierr);
ierr = DMDAGetInfo(dm,0,&mx,&my,&mz,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
Hx = 1.0 / (PetscReal)(mx-1); Hy = 1.0 / (PetscReal)(my-1); Hz = 1.0 / (PetscReal)(mz-1);
HxHydHz = Hx*Hy/Hz; HxHzdHy = Hx*Hz/Hy; HyHzdHx = Hy*Hz/Hx;
ierr = DMDAGetCorners(dm,&xs,&ys,&zs,&xm,&ym,&zm);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,b,&barray);CHKERRQ(ierr);
for (k=zs; k<zs+zm; k++) {
for (j=ys; j<ys+ym; j++) {
for (i=xs; i<xs+xm; i++) {
if (i==0 || j==0 || k==0 || i==mx-1 || j==my-1 || k==mz-1) {
barray[k][j][i] = 2.0*(HxHydHz + HxHzdHy + HyHzdHx);
} else {
barray[k][j][i] = Hx*Hy*Hz;
}
}
}
}
ierr = DMDAVecRestoreArray(dm,b,&barray);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
// Formulas from page 22 of Hundsdorfer & Verwer (2003). Interpretation here is
// to always generate 0.5 x 0.5 non-trivial patch in (0,L) x (0,L) domain.
PetscErrorCode InitialState(Vec Y, double noiselevel, PatternCtx* user) {
PetscErrorCode ierr;
DMDALocalInfo info;
int i,j;
double sx,sy;
const double ledge = (user->L - 0.5) / 2.0, // nontrivial initial values on
redge = user->L - ledge; // ledge < x,y < redge
DMDACoor2d **aC;
Field **aY;
ierr = VecSet(Y,0.0); CHKERRQ(ierr);
if (noiselevel > 0.0) {
// noise added to usual initial condition is uniform on [0,noiselevel],
// independently for each location and component
ierr = VecSetRandom(Y,NULL); CHKERRQ(ierr);
ierr = VecScale(Y,noiselevel); CHKERRQ(ierr);
}
ierr = DMDAGetLocalInfo(user->da,&info); CHKERRQ(ierr);
ierr = DMDAGetCoordinateArray(user->da,&aC); CHKERRQ(ierr);
ierr = DMDAVecGetArray(user->da,Y,&aY); CHKERRQ(ierr);
for (j = info.ys; j < info.ys+info.ym; j++) {
for (i = info.xs; i < info.xs+info.xm; i++) {
if ((aC[j][i].x >= ledge) && (aC[j][i].x <= redge)
&& (aC[j][i].y >= ledge) && (aC[j][i].y <= redge)) {
sx = sin(4.0 * PETSC_PI * aC[j][i].x);
sy = sin(4.0 * PETSC_PI * aC[j][i].y);
aY[j][i].v += 0.5 * sx * sx * sy * sy;
}
aY[j][i].u += 1.0 - 2.0 * aY[j][i].v;
}
}
ierr = DMDAVecRestoreArray(user->da,Y,&aY); CHKERRQ(ierr);
ierr = DMDARestoreCoordinateArray(user->da,&aC); CHKERRQ(ierr);
return 0;
}
