static PetscErrorCode FormRHSFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr)
{
User user = (User)ptr;
PetscErrorCode ierr;
PetscScalar **f;
const PetscScalar **x;
DM dm;
PetscInt i,xs,xm;
PetscFunctionBeginUser;
if (user->reactions) {
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOFRead(dm,X,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(dm,F,&f);CHKERRQ(ierr);
ierr = DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
for (i=xs; i<xs+xm; i++) {
ierr = PetscMemcpy(user->tchemwork,x[i],(user->Nspec+1)*sizeof(x[xs][0]));CHKERRQ(ierr);
user->tchemwork[0] *= user->Tini; /* Dimensionalize */
ierr = TC_getSrc(user->tchemwork,user->Nspec+1,f[i]);TCCHKERRQ(ierr);
f[i][0] /= user->Tini; /* Non-dimensionalize */
}
ierr = DMDAVecRestoreArrayDOFRead(dm,X,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(dm,F,&f);CHKERRQ(ierr);
} else {
ierr = VecZeroEntries(F);CHKERRQ(ierr);
}
if (user->diffusion) {
ierr = FormDiffusionFunction(ts,t,X,F,ptr);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode FormInitialSolution(TS ts, Vec U, void *ctx)
{
/* User user = (User) ctx; */
DM dm, cdm;
DMDALocalInfo info;
Vec C;
Field *u;
PetscScalar *x;
const PetscReal sigma = 1.0;
PetscInt i;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = TSGetDM(ts, &dm);
ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &C);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm, &info);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm, U, &u);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(cdm, C, &x);CHKERRQ(ierr);
for (i = info.xs; i < info.xs+info.xm; ++i) {
u[i].u = 1.5 * PetscExpScalar(-PetscSqr(x[i] - 10)/PetscSqr(sigma));
u[i].v = 0.0;
u[i].th = 0.0;
}
ierr = DMDAVecRestoreArray(dm, U, &u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(cdm, C, &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 FormInitialSolution(TS ts,Vec X,void *ctx)
{
PetscScalar **x,*xc;
PetscErrorCode ierr;
struct {const char *name; PetscReal massfrac;} initial[] = {
{"CH4", 0.0948178320887},
{"O2", 0.189635664177},
{"N2", 0.706766236705},
{"AR", 0.00878026702874}
};
PetscInt i,j,xs,xm;
DM dm;
PetscFunctionBeginUser;
ierr = VecZeroEntries(X);CHKERRQ(ierr);
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
ierr = DMDAGetCoordinateArray(dm,&xc);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(dm,X,&x);CHKERRQ(ierr);
for (i=xs; i<xs+xm; i++) {
x[i][0] = 1.0 + .05*PetscSinScalar(2.*PETSC_PI*xc[i]); /* Non-dimensionalized by user->Tini */
for (j=0; j<sizeof(initial)/sizeof(initial[0]); j++) {
int ispec = TC_getSpos(initial[j].name, strlen(initial[j].name));
if (ispec < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Could not find species %s",initial[j].name);
ierr = PetscPrintf(PETSC_COMM_SELF,"Species %d: %s %g\n",j,initial[j].name,initial[j].massfrac);CHKERRQ(ierr);
x[i][1+ispec] = initial[j].massfrac;
}
}
ierr = DMDAVecRestoreArrayDOF(dm,X,&x);CHKERRQ(ierr);
ierr = DMDARestoreCoordinateArray(dm,&xc);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/* IJacobian - Compute IJacobian = dF/dU + a dF/dUdot */
PetscErrorCode FormIJacobian(TS ts, PetscReal t, Vec U, Vec Udot, PetscReal a, Mat J, Mat Jpre, void *ctx)
{
User user = (User) ctx;
DM dm, cdm;
DMDALocalInfo info;
Vec C;
Field *u, *udot;
PetscScalar *x;
PetscInt i;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = TSGetDM(ts, &dm);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm, &info);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &C);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(dm, U, &u);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(dm, Udot, &udot);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(cdm, C, &x);CHKERRQ(ierr);
for (i = info.xs; i < info.xs+info.xm; ++i) {
if (i == 0) {
const PetscScalar hx = x[i+1] - x[i];
const PetscInt row = i, col[] = {i,i+1};
const PetscScalar dxx0 = PetscSqr(user->c)/hx,dxxR = -PetscSqr(user->c)/hx;
const PetscScalar vals[3][2][3] = {{{a*hx, 0,0},{0,0, 0}},
{{0,a*hx+dxx0,0},{0,dxxR,0}},
{{0,0, a*hx},{0,0, 0}}};
ierr = MatSetValuesBlocked(Jpre, 1, &row, 2, col, &vals[0][0][0], INSERT_VALUES);CHKERRQ(ierr);
} else if (i == info.mx-1) {
const PetscScalar hx = x[i+1] - x[i];
const PetscInt row = i, col[] = {i-1,i};
const PetscScalar dxxL = -PetscSqr(user->c)/hx, dxx0 = PetscSqr(user->c)/hx;
const PetscScalar vals[3][2][3] = {{{0,0, 0},{a*hx, 0,0}},
{{0,dxxL,0},{0,a*hx+dxx0,0}},
{{0,0, 0},{0,0, a*hx}}};
ierr = MatSetValuesBlocked(Jpre, 1, &row, 2, col, &vals[0][0][0], INSERT_VALUES);CHKERRQ(ierr);
} else {
const PetscScalar hx = x[i+1] - x[i];
const PetscInt row = i, col[] = {i-1,i,i+1};
const PetscScalar dxxL = -PetscSqr(user->c)/hx, dxx0 = 2.*PetscSqr(user->c)/hx,dxxR = -PetscSqr(user->c)/hx;
const PetscScalar vals[3][3][3] = {{{0,0, 0},{a*hx, 0,0},{0,0, 0}},
{{0,dxxL,0},{0,a*hx+dxx0,0},{0,dxxR,0}},
{{0,0, 0},{0,0, a*hx},{0,0, 0}}};
ierr = MatSetValuesBlocked(Jpre, 1, &row, 3, col, &vals[0][0][0], INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = DMDAVecRestoreArrayRead(dm, U, &u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(dm, Udot, &udot);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(cdm, C, &x);CHKERRQ(ierr);
ierr = MatAssemblyBegin(Jpre, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Jpre, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (J != Jpre) {
ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*
InitialConditions - Computes the solution at the initial time.
Input Parameter:
u - uninitialized solution vector (global)
appctx - user-defined application context
Output Parameter:
u - vector with solution at initial time (global)
*/
PetscErrorCode InitialConditions(TS ts,Vec U,AppCtx *appctx)
{
PetscScalar *u;
PetscErrorCode ierr;
PetscInt i,mstart,mend,um,M;
DM da;
PetscReal h;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&mstart,0,0,&um,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 + um;
/*
Get a pointer to vector data.
- For default PETSc vectors, VecGetArray() returns a pointer to
the data array. Otherwise, the routine is implementation dependent.
- You MUST call VecRestoreArray() when you no longer need access to
the array.
- Note that the Fortran interface to VecGetArray() differs from the
C version. See the users manual for details.
*/
ierr = DMDAVecGetArray(da,U,&u);CHKERRQ(ierr);
/*
We initialize the solution array by simply writing the solution
directly into the array locations. Alternatively, we could use
VecSetValues() or VecSetValuesLocal().
*/
for (i=mstart; i<mend; i++) u[i] = PetscSinReal(PETSC_PI*i*6.*h) + 3.*PetscSinReal(PETSC_PI*i*2.*h);
/* Restore vector */
ierr = DMDAVecRestoreArray(da,U,&u);CHKERRQ(ierr);
return 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
u(x,t) = sin(6*PI*(x - a*t)) + 3 * sin(2*PI*(x - a*t))
*/
PetscErrorCode Solution(TS ts,PetscReal t,Vec U,AppCtx *appctx)
{
PetscScalar *u;
PetscReal a=appctx->a,h,PI6,PI2;
PetscErrorCode ierr;
PetscInt i,mstart,mend,um,M;
DM da;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&mstart,0,0,&um,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 + um;
/* Get a pointer to vector data. */
ierr = DMDAVecGetArray(da,U,&u);CHKERRQ(ierr);
/* u[i] = sin(6*PI*(x[i] - a*t)) + 3 * sin(2*PI*(x[i] - a*t)) */
PI6 = PETSC_PI*6.;
PI2 = PETSC_PI*2.;
for (i=mstart; i<mend; i++) {
u[i] = PetscSinReal(PI6*(i*h - a*t)) + 3.*PetscSinReal(PI2*(i*h - a*t));
}
/* Restore vector */
ierr = DMDAVecRestoreArray(da,U,&u);CHKERRQ(ierr);
return 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;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
/* Get pointers to vector data */
ierr = DMDAVecGetArray(da,X,&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++) {
f[i][0] = xdot[i][0] + user->k[0]*x[i][0] - user->k[1]*x[i][1] - user->s[0];
f[i][1] = xdot[i][1] - user->k[0]*x[i][0] + user->k[1]*x[i][1] - user->s[1];
}
/* Restore vectors */
ierr = DMDAVecRestoreArray(da,X,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,Xdot,&xdot);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,F,&f);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);
}
int TSFunction_Sundials(realtype t,N_Vector y,N_Vector ydot,void *ctx)
{
TS ts = (TS) ctx;
DM dm;
DMTS tsdm;
TSIFunction ifunction;
MPI_Comm comm;
TS_Sundials *cvode = (TS_Sundials*)ts->data;
Vec yy = cvode->w1,yyd = cvode->w2,yydot = cvode->ydot;
PetscScalar *y_data,*ydot_data;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)ts,&comm);CHKERRQ(ierr);
/* Make the PETSc work vectors yy and yyd point to the arrays in the SUNDIALS vectors y and ydot respectively*/
y_data = (PetscScalar*) N_VGetArrayPointer(y);
ydot_data = (PetscScalar*) N_VGetArrayPointer(ydot);
ierr = VecPlaceArray(yy,y_data);CHKERRABORT(comm,ierr);
ierr = VecPlaceArray(yyd,ydot_data);CHKERRABORT(comm,ierr);
/* Now compute the right hand side function, via IFunction unless only the more efficient RHSFunction is set */
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = DMGetDMTS(dm,&tsdm);CHKERRQ(ierr);
ierr = DMTSGetIFunction(dm,&ifunction,NULL);CHKERRQ(ierr);
if (!ifunction) {
ierr = TSComputeRHSFunction(ts,t,yy,yyd);CHKERRQ(ierr);
} else { /* If rhsfunction is also set, this computes both parts and shifts them to the right */
ierr = VecZeroEntries(yydot);CHKERRQ(ierr);
ierr = TSComputeIFunction(ts,t,yy,yydot,yyd,PETSC_FALSE);CHKERRABORT(comm,ierr);
ierr = VecScale(yyd,-1.);CHKERRQ(ierr);
}
ierr = VecResetArray(yy);CHKERRABORT(comm,ierr);
ierr = VecResetArray(yyd);CHKERRABORT(comm,ierr);
PetscFunctionReturn(0);
}
/* ------------------------------------------------------------------- */
PetscErrorCode
FormInitialSolution(TS ts, Vec U, void * /*ptr*/)
{
DM da;
PetscReal c = -30.0;
PetscErrorCode ierr;
PetscInt i, j, xs, ys, xm, ym, Mx, My;
PetscScalar ** u;
PetscReal hx, hy, x, y, r;
PetscFunctionBeginUser;
ierr = TSGetDM(ts, &da);
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);
hx = 1.0 / (PetscReal)(Mx - 1);
hy = 1.0 / (PetscReal)(My - 1);
/* Get pointers to vector data */
ierr = DMDAVecGetArray(da, U, &u);
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++)
{
y = j * hy;
for (i = xs; i < xs + xm; i++)
{
x = i * hx;
r = PetscSqrtReal((x - .5) * (x - .5) + (y - .5) * (y - .5));
if (r < .125)
u[j][i] = PetscExpReal(c * r * r * r);
else
u[j][i] = 0.0;
}
}
/* Restore vectors */
ierr = DMDAVecRestoreArray(da, U, &u);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode FormRHSFunction(TS ts, PetscReal t, Vec U, Vec F, void *ctx)
{
User user = (User) ctx;
DM dm, cdm;
DMDALocalInfo info;
Vec C;
Field *f;
const Field *u;
const PetscScalar *x;
PetscInt i;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = TSGetDM(ts, &dm);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &C);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm, &info);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(dm, U, &u);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm, F, &f);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cdm, C, &x);CHKERRQ(ierr);
for (i = info.xs; i < info.xs+info.xm; ++i) {
const PetscScalar hx = i+1 == info.xs+info.xm ? x[i] - x[i-1] : x[i+1] - x[i];
f[i].u = hx*(u[i].v);
f[i].v = -hx*(PetscSqr(user->gammaTilde)*u[i].u + (PetscSqr(user->gamma) / user->xi)*(u[i].th + log(u[i].v + 1)));
f[i].th = -hx*(u[i].v + 1)*(u[i].th + (1 + user->epsilon)*log(u[i].v + 1));
}
ierr = DMDAVecRestoreArrayRead(dm, U, &u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dm, F, &f);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(cdm, C, &x);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);
}
static PetscErrorCode TSSetUp_Theta(TS ts)
{
TS_Theta *th = (TS_Theta*)ts->data;
PetscErrorCode ierr;
SNES snes;
TSAdapt adapt;
DM dm;
PetscFunctionBegin;
ierr = VecDuplicate(ts->vec_sol,&th->X);CHKERRQ(ierr);
ierr = VecDuplicate(ts->vec_sol,&th->Xdot);CHKERRQ(ierr);
ierr = VecDuplicate(ts->vec_sol,&th->X0);CHKERRQ(ierr);
ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr);
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
if (dm) {
ierr = DMCoarsenHookAdd(dm,DMCoarsenHook_TSTheta,DMRestrictHook_TSTheta,ts);CHKERRQ(ierr);
ierr = DMSubDomainHookAdd(dm,DMSubDomainHook_TSTheta,DMSubDomainRestrictHook_TSTheta,ts);CHKERRQ(ierr);
}
if (th->Theta == 0.5 && th->endpoint) th->order = 2;
else th->order = 1;
ierr = TSGetAdapt(ts,&adapt);CHKERRQ(ierr);
if (!th->adapt) {
ierr = TSAdaptSetType(adapt,TSADAPTNONE);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-1);
/* 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 xi = i*hx;
x[i].u = user->uleft*(1.-xi) + user->uright*xi + sin(2.*PETSC_PI*xi);
x[i].v = user->vleft*(1.-xi) + user->vright*xi;
}
ierr = DMDAVecRestoreArray(da,X,&x);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode FormRHSFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr)
{
User user = (User)ptr;
DM da;
DMDALocalInfo info;
PetscInt i;
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-1);
/* Get pointers to vector data */
ierr = DMDAVecGetArray(da,X,&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++) {
PetscScalar u = x[i].u,v = x[i].v;
f[i].u = hx*(user->A + u*u*v - (user->B+1)*u);
f[i].v = hx*(user->B*u - u*u*v);
}
/* Restore vectors */
ierr = DMDAVecRestoreArray(da,X,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,F,&f);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Applies the second order centered difference diffusion operator on a one dimensional periodic domain
*/
static PetscErrorCode FormDiffusionFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr)
{
User user = (User)ptr;
PetscErrorCode ierr;
PetscScalar **f;
const PetscScalar **x;
DM dm;
PetscInt i,xs,xm,j,dof;
Vec Xlocal;
PetscReal idx;
PetscFunctionBeginUser;
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = DMDAGetInfo(dm,NULL,NULL,NULL,NULL,NULL,NULL,NULL,&dof,NULL,NULL,NULL,NULL,NULL);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm,&Xlocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xlocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xlocal);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOFRead(dm,Xlocal,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArrayDOF(dm,F,&f);CHKERRQ(ierr);
ierr = DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
idx = 1.0*user->diffus/user->dx;
for (i=xs; i<xs+xm; i++) {
for (j=0; j<dof; j++) {
f[i][j] += idx*(x[i+1][j] - 2.0*x[i][j] + x[i-1][j]);
}
}
ierr = DMDAVecRestoreArrayDOFRead(dm,Xlocal,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayDOF(dm,F,&f);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Xlocal);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Produces the second order centered difference diffusion operator on a one dimensional periodic domain
*/
static PetscErrorCode FormDiffusionJacobian(TS ts,PetscReal t,Vec X,Mat Amat,Mat Pmat,void *ptr)
{
User user = (User)ptr;
PetscErrorCode ierr;
DM dm;
PetscInt i,xs,xm,j,dof;
PetscReal idx,values[3];
MatStencil row,col[3];
PetscFunctionBeginUser;
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = DMDAGetInfo(dm,NULL,NULL,NULL,NULL,NULL,NULL,NULL,&dof,NULL,NULL,NULL,NULL,NULL);CHKERRQ(ierr);
ierr = DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
idx = 1.0*user->diffus/user->dx;
values[0] = idx;
values[1] = -2.0*idx;
values[2] = idx;
for (i=xs; i<xs+xm; i++) {
for (j=0; j<dof; j++) {
row.i = i; row.c = j;
col[0].i = i-1; col[0].c = j;
col[1].i = i; col[1].c = j;
col[2].i = i+1; col[2].c = j;
ierr = MatSetValuesStencil(Pmat,1,&row,3,col,values,ADD_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(Pmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Pmat,MAT_FINAL_ASSEMBLY);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);
}
/*
* This is a modified version of PETSc/src/ts/examples/tutorials/ex15.c
* to demonstrate how MOOSE interact with an external solver package
*/
PetscErrorCode
externalPETScDiffusionFDMSolve(TS ts, Vec u, PetscReal dt, PetscReal time)
{
PetscErrorCode ierr;
#if !PETSC_VERSION_LESS_THAN(3, 8, 0)
PetscInt current_step;
#endif
DM da;
PetscFunctionBeginUser;
ierr = TSGetDM(ts, &da);
CHKERRQ(ierr);
#if !PETSC_VERSION_LESS_THAN(3, 7, 0)
PetscOptionsSetValue(NULL, "-ts_monitor", NULL);
PetscOptionsSetValue(NULL, "-snes_monitor", NULL);
PetscOptionsSetValue(NULL, "-ksp_monitor", NULL);
#else
PetscOptionsSetValue("-ts_monitor", NULL);
PetscOptionsSetValue("-snes_monitor", NULL);
PetscOptionsSetValue("-ksp_monitor", NULL);
#endif
/*ierr = TSSetMaxTime(ts,1.0);CHKERRQ(ierr);*/
ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER);
CHKERRQ(ierr);
ierr = TSSetSolution(ts, u);
CHKERRQ(ierr);
ierr = TSSetTimeStep(ts, dt);
CHKERRQ(ierr);
ierr = TSSetTime(ts, time - dt);
CHKERRQ(ierr);
#if !PETSC_VERSION_LESS_THAN(3, 8, 0)
ierr = TSGetStepNumber(ts, ¤t_step);
CHKERRQ(ierr);
ierr = TSSetMaxSteps(ts, current_step + 1);
CHKERRQ(ierr);
#else
SETERRQ(PetscObjectComm((PetscObject)ts), PETSC_ERR_SUP, "Require PETSc-3.8.x or higher ");
#endif
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Sets various TS parameters from user options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetFromOptions(ts);
CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSolve(ts, u);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FormResidual(TS ts,PetscReal t,Vec U,Vec Udot,Vec R,void *user)
{
PetscFunctionBegin;
PetscErrorCode ierr;
DMDALocalInfo info;
DM dm;
Vec localU,localUdot,localR; // local versions
Field **h,**hdot,**r;
/* get the da from the snes */
ierr = TSGetDM(ts, &dm);CHKERRQ(ierr);
/* handle the vec U */
ierr = DMGetLocalVector(dm,&localU);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,U,INSERT_VALUES,localU);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,U,INSERT_VALUES,localU);CHKERRQ(ierr);
/* handle the vec Udot */
ierr = DMGetLocalVector(dm,&localUdot);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,Udot,INSERT_VALUES,localUdot);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,Udot,INSERT_VALUES,localUdot);CHKERRQ(ierr);
/* handle the vec R */
ierr = DMGetLocalVector(dm,&localR);CHKERRQ(ierr);
ierr = VecZeroEntries(localR);CHKERRQ(ierr);
/* Get the arrays from the vectors */
ierr = DMIGAVecGetArray(dm,localU,&h);CHKERRQ(ierr);
ierr = DMIGAVecGetArray(dm,localUdot,&hdot);CHKERRQ(ierr);
ierr = DMIGAVecGetArray(dm,localR,&r);CHKERRQ(ierr);
/* Grab the local info and call the local residual routine */
ierr = DMIGAGetLocalInfo(dm,&info);CHKERRQ(ierr);CHKERRQ(ierr);
ierr = FormResidualLocal(&info,t,h,hdot,r,(AppCtx *) user);CHKERRQ(ierr);
/* Restore the arrays */
ierr = DMIGAVecRestoreArray(dm,localR,&r);CHKERRQ(ierr);
ierr = DMIGAVecRestoreArray(dm,localUdot,&hdot);CHKERRQ(ierr);
ierr = DMIGAVecRestoreArray(dm,localU,&h);CHKERRQ(ierr);
/* Add contributions back to global R */
ierr = VecZeroEntries(R);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dm,localR,ADD_VALUES,R);CHKERRQ(ierr); // this one adds the values
ierr = DMLocalToGlobalEnd(dm,localR,ADD_VALUES,R);CHKERRQ(ierr);
/* Restore the local vectors */
ierr = DMRestoreLocalVector(dm,&localU);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&localUdot);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&localR);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
FormFunction - Evaluates nonlinear function, F(x).
Input Parameters:
. ts - the TS context
. X - input vector
. ptr - optional user-defined context, as set by SNESSetFunction()
Output Parameter:
. F - function vector
*/
PetscErrorCode FormFunction(TS ts,PetscReal ftime,Vec X,Vec F,void *ptr)
{
DM da;
PetscErrorCode ierr;
PetscInt i,Mx,xs,xm;
PetscReal hx,sx;
PetscScalar *x,*f;
Vec localX;
UserCtx *ctx = (UserCtx*)ptr;
PetscFunctionBegin;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMGetLocalVector(da,&localX);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);
hx = 1.0/(PetscReal)Mx; sx = 1.0/(hx*hx);
/*
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,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
/*
Get pointers to vector data
*/
ierr = DMDAVecGetArrayRead(da,localX,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,F,&f);CHKERRQ(ierr);
/*
Get local grid boundaries
*/
ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr);
/*
Compute function over the locally owned part of the grid
*/
for (i=xs; i<xs+xm; i++) {
f[i] = ctx->kappa*(x[i-1] + x[i+1] - 2.0*x[i])*sx;
if (ctx->allencahn) f[i] += (x[i] - x[i]*x[i]*x[i]);
}
/*
Restore vectors
*/
ierr = DMDAVecRestoreArrayRead(da,localX,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,F,&f);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&localX);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);
}
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 *f;
const Field *x;
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 = DMDAVecGetArrayRead(da,Xloc,(void*)&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];
u0t[0] = 1.0 - PetscPowRealInt(PetscSinReal(12*t),4);
u0t[1] = 0.0;
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 = DMDAVecRestoreArrayRead(da,Xloc,(void*)&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,F,&f);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&Xloc);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Sets up a monitor that will display He as a function of space and cluster size for each time step
*/
PetscErrorCode MyMonitorSetUp(TS ts)
{
DM da;
PetscErrorCode ierr;
PetscInt xi,xs,xm,*idx,M,xj,cnt = 0,dof = 3*N + N*N;
const PetscInt *lx;
Vec C;
MyMonitorCtx *ctx;
PetscBool flg;
IS is;
char ycoor[32];
PetscReal valuebounds[4] = {0, 1.2, 0, 1.2};
PetscFunctionBeginUser;
ierr = PetscOptionsHasName(PETSC_NULL,"-mymonitor",&flg);CHKERRQ(ierr);
if (!flg) PetscFunctionReturn(0);
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = PetscNew(MyMonitorCtx,&ctx);CHKERRQ(ierr);
ierr = PetscViewerDrawOpen(((PetscObject)da)->comm,PETSC_NULL,"",PETSC_DECIDE,PETSC_DECIDE,600,400,&ctx->viewer);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,PETSC_NULL,PETSC_NULL,&xm,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,PETSC_IGNORE,&M,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 = DMDAGetOwnershipRanges(da,&lx,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
ierr = DMDACreate2d(((PetscObject)da)->comm,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,M,N,PETSC_DETERMINE,1,2,1,lx,PETSC_NULL,&ctx->da);CHKERRQ(ierr);
ierr = DMDASetFieldName(ctx->da,0,"He");CHKERRQ(ierr);
ierr = DMDASetFieldName(ctx->da,1,"V");CHKERRQ(ierr);
ierr = DMDASetCoordinateName(ctx->da,0,"X coordinate direction");CHKERRQ(ierr);
ierr = PetscSNPrintf(ycoor,32,"%D ... Cluster size ... 1",N);CHKERRQ(ierr);
ierr = DMDASetCoordinateName(ctx->da,1,ycoor);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(ctx->da,&ctx->He);CHKERRQ(ierr);
ierr = PetscMalloc(2*N*xm*sizeof(PetscInt),&idx);CHKERRQ(ierr);
cnt = 0;
for (xj=0; xj<N; xj++) {
for (xi=xs; xi<xs+xm; xi++) {
idx[cnt++] = dof*xi + xj;
idx[cnt++] = dof*xi + xj + N;
}
}
ierr = ISCreateGeneral(((PetscObject)ts)->comm,2*N*xm,idx,PETSC_OWN_POINTER,&is);CHKERRQ(ierr);
ierr = TSGetSolution(ts,&C);CHKERRQ(ierr);
ierr = VecScatterCreate(C,is,ctx->He,PETSC_NULL,&ctx->scatter);CHKERRQ(ierr);
ierr = ISDestroy(&is);CHKERRQ(ierr);
/* sets the bounds on the contour plot values so the colors mean the same thing for different timesteps */
ierr = PetscViewerDrawSetBounds(ctx->viewer,2,valuebounds);CHKERRQ(ierr);
ierr = TSMonitorSet(ts,MyMonitorMonitor,ctx,MyMonitorDestroy);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
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);
}
PetscErrorCode FormIJacobian(TS ts,PetscReal t,Vec U,Vec Udot,PetscReal a,Mat *J,Mat *Jpre,MatStructure *str,void *ctx)
{
PetscErrorCode ierr;
PetscInt i,rstart,rend,Mx;
PetscReal hx,sx;
AppCtx *user = (AppCtx*)ctx;
DM da;
MatStencil col[3],row;
PetscInt nc;
PetscScalar vals[3];
PetscFunctionBegin;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(*Jpre,&rstart,&rend);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);
hx = 1.0/(PetscReal)(Mx-1); sx = 1.0/(hx*hx);
for (i=rstart; i<rend; i++) {
nc = 0;
row.i = i;
if (user->boundary == 0 && (i == 0 || i == Mx-1)) {
col[nc].i = i; vals[nc++] = 1.0;
} else if (user->boundary > 0 && i == 0) { /* Left Neumann */
col[nc].i = i; vals[nc++] = 1.0;
col[nc].i = i+1; vals[nc++] = -1.0;
} else if (user->boundary > 0 && i == Mx-1) { /* Right Neumann */
col[nc].i = i-1; vals[nc++] = -1.0;
col[nc].i = i; vals[nc++] = 1.0;
} else { /* Interior */
col[nc].i = i-1; vals[nc++] = -1.0*sx;
col[nc].i = i; vals[nc++] = 2.0*sx + a;
col[nc].i = i+1; vals[nc++] = -1.0*sx;
}
ierr = MatSetValuesStencil(*Jpre,1,&row,nc,col,vals,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(*Jpre,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*Jpre,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (*J != *Jpre) {
ierr = MatAssemblyBegin(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
if (user->viewJacobian){
ierr = PetscPrintf(((PetscObject)*Jpre)->comm,"Jpre:\n");CHKERRQ(ierr);
ierr = MatView(*Jpre,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
static PetscErrorCode FormIFunction(TS ts, PetscReal t, Vec U, Vec Udot, Vec F, void *ctx)
{
User user = (User) ctx;
DM dm, cdm;
DMDALocalInfo info;
Vec Uloc, C;
Field *u, *udot, *f;
PetscScalar *x;
PetscInt i;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = TSGetDM(ts, &dm);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm, &info);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &C);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &Uloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm, U, INSERT_VALUES, Uloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm, U, INSERT_VALUES, Uloc);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(dm, Uloc, &u);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(dm, Udot, &udot);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm, F, &f);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(cdm, C, &x);CHKERRQ(ierr);
for (i = info.xs; i < info.xs+info.xm; ++i) {
if (i == 0) {
const PetscScalar hx = x[i+1] - x[i];
f[i].u = hx * udot[i].u;
f[i].v = hx * udot[i].v - PetscSqr(user->c) * (u[i+1].u - u[i].u) / hx;
f[i].th = hx * udot[i].th;
} else if (i == info.mx-1) {
const PetscScalar hx = x[i] - x[i-1];
f[i].u = hx * udot[i].u;
f[i].v = hx * udot[i].v - PetscSqr(user->c) * (u[i-1].u - u[i].u) / hx;
f[i].th = hx * udot[i].th;
} else {
const PetscScalar hx = x[i+1] - x[i];
f[i].u = hx * udot[i].u;
f[i].v = hx * udot[i].v - PetscSqr(user->c) * (u[i-1].u - 2.*u[i].u + u[i+1].u) / hx;
f[i].th = hx * udot[i].th;
}
}
ierr = DMDAVecRestoreArrayRead(dm, Uloc, &u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(dm, Udot, &udot);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(dm, F, &f);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(cdm, C, &x);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &Uloc);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Use Lax-Wendroff method to evaluate F(u,t) = du/dt + a * du/dx
*/
PetscErrorCode IFunction_LaxWendroff(TS ts,PetscReal t,Vec U,Vec Udot,Vec F,void* ctx)
{
PetscErrorCode ierr;
AppCtx *appctx=(AppCtx*)ctx;
PetscInt mstart,mend,M,i,um;
DM da;
Vec Uold,localUold;
PetscScalar *uarray,*f,*uoldarray,h,RFlux,LFlux,lambda;
PetscReal dt,a;
PetscFunctionBegin;
ierr = TSGetTimeStep(ts,&dt);CHKERRQ(ierr);
ierr = TSGetSolution(ts,&Uold);CHKERRQ(ierr);
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,0,&M,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&mstart,0,0,&um,0,0);CHKERRQ(ierr);
h = 1.0/M;
mend = mstart + um;
/* printf(" mstart %d, um %d\n",mstart,um); */
ierr = DMGetLocalVector(da,&localUold);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,Uold,INSERT_VALUES,localUold);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,Uold,INSERT_VALUES,localUold);CHKERRQ(ierr);
/* Get pointers to vector data */
ierr = DMDAVecGetArrayRead(da,U,&uarray);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(da,localUold,&uoldarray);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,F,&f);CHKERRQ(ierr);
/* advection -- finite volume (appctx->a < 0 -- can be relaxed?) */
lambda = dt/h;
a = appctx->a;
for (i=mstart; i<mend; i++) {
RFlux = 0.5 * a * (uoldarray[i+1] + uoldarray[i]) - a*a*0.5*lambda * (uoldarray[i+1] - uoldarray[i]);
LFlux = 0.5 * a * (uoldarray[i-1] + uoldarray[i]) - a*a*0.5*lambda * (uoldarray[i] - uoldarray[i-1]);
f[i] = uarray[i] - uoldarray[i] + lambda * (RFlux - LFlux);
}
/* Restore vectors */
ierr = DMDAVecRestoreArrayRead(da,U,&uarray);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(da,localUold,&uoldarray);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,F,&f);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&localUold);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
