/*
Matrix free operation of 1d Laplacian and Grad for GLL spectral elements
*/
PetscErrorCode MatMult_Laplacian(Mat A,Vec x,Vec y)
{
AppCtx *appctx;
PetscErrorCode ierr;
PetscReal **temp,vv;
PetscInt i,j,xs,xn;
Vec xlocal,ylocal;
const PetscScalar *xl;
PetscScalar *yl;
PetscBLASInt _One = 1,n;
PetscScalar _DOne = 1;
ierr = MatShellGetContext(A,&appctx);CHKERRQ(ierr);
ierr = DMGetLocalVector(appctx->da,&xlocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(appctx->da,x,INSERT_VALUES,xlocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(appctx->da,x,INSERT_VALUES,xlocal);CHKERRQ(ierr);
ierr = DMGetLocalVector(appctx->da,&ylocal);CHKERRQ(ierr);
ierr = VecSet(ylocal,0.0);CHKERRQ(ierr);
ierr = PetscGLLElementLaplacianCreate(&appctx->SEMop.gll,&temp);CHKERRQ(ierr);
for (i=0; i<appctx->param.N; i++) {
vv =-appctx->param.mu*2.0/appctx->param.Le;
for (j=0; j<appctx->param.N; j++) temp[i][j]=temp[i][j]*vv;
}
ierr = DMDAVecGetArrayRead(appctx->da,xlocal,(void*)&xl);CHKERRQ(ierr);
ierr = DMDAVecGetArray(appctx->da,ylocal,&yl);CHKERRQ(ierr);
ierr = DMDAGetCorners(appctx->da,&xs,NULL,NULL,&xn,NULL,NULL);CHKERRQ(ierr);
ierr = PetscBLASIntCast(appctx->param.N,&n);CHKERRQ(ierr);
for (j=xs; j<xs+xn; j += appctx->param.N-1) {
PetscStackCallBLAS("BLASgemv",BLASgemv_("N",&n,&n,&_DOne,&temp[0][0],&n,&xl[j],&_One,&_DOne,&yl[j],&_One));
}
ierr = DMDAVecRestoreArrayRead(appctx->da,xlocal,(void*)&xl);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(appctx->da,ylocal,&yl);CHKERRQ(ierr);
ierr = PetscGLLElementLaplacianDestroy(&appctx->SEMop.gll,&temp);CHKERRQ(ierr);
ierr = VecSet(y,0.0);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(appctx->da,ylocal,ADD_VALUES,y);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(appctx->da,ylocal,ADD_VALUES,y);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(appctx->da,&xlocal);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(appctx->da,&ylocal);CHKERRQ(ierr);
ierr = VecPointwiseDivide(y,y,appctx->SEMop.mass);CHKERRQ(ierr);
return 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);
}
/*
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);
}
/* no discretization is given so DMGetNumFields and PetscDSGetTotalDimension yield 0 */
static PetscErrorCode test2(DM dm, AppCtx *options)
{
IS cells;
Vec locX, locX_t, locA;
PetscScalar *u, *u_t, *a;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF, rank ? 0 : 1, 0, 1, &cells);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &locX);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &locX_t);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &locA);CHKERRQ(ierr);
ierr = DMPlexGetCellFields( dm, cells, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr);
ierr = DMPlexRestoreCellFields(dm, cells, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &locX);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &locX_t);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &locA);CHKERRQ(ierr);
ierr = ISDestroy(&cells);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PETSC_INTERN PetscErrorCode DMStagSetUniformCoordinatesExplicit_1d(DM dm,PetscReal xmin,PetscReal xmax)
{
PetscErrorCode ierr;
DM_Stag *stagCoord;
DM dmCoord;
Vec coordLocal,coord;
PetscReal h,min;
PetscScalar **arr;
PetscInt ind,start,n,nExtra,s;
PetscInt ileft,ielement;
PetscFunctionBegin;
ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr);
stagCoord = (DM_Stag*) dmCoord->data;
for (s=0; s<2; ++s) {
if (stagCoord->dof[s] !=0 && stagCoord->dof[s] != 1) SETERRQ2(PetscObjectComm((PetscObject)dm),PETSC_ERR_PLIB,"Coordinate DM in 1 dimensions must have 0 or 1 dof on each stratum, but stratum %d has %d dof",s,stagCoord->dof[s]);
}
ierr = DMGetLocalVector(dmCoord,&coordLocal);CHKERRQ(ierr);
ierr = DMStagVecGetArrayDOF(dmCoord,coordLocal,&arr);CHKERRQ(ierr);
if (stagCoord->dof[0]) {
ierr = DMStagGetLocationSlot(dmCoord,DMSTAG_LEFT,0,&ileft);CHKERRQ(ierr);
}
if (stagCoord->dof[1]) {
ierr = DMStagGetLocationSlot(dmCoord,DMSTAG_ELEMENT,0,&ielement);CHKERRQ(ierr);
}
ierr = DMStagGetCorners(dmCoord,&start,NULL,NULL,&n,NULL,NULL,&nExtra,NULL,NULL);CHKERRQ(ierr);
min = xmin;
h = (xmax-xmin)/stagCoord->N[0];
for(ind=start; ind<start + n + nExtra; ++ind) {
if (stagCoord->dof[0]) {
const PetscReal off = 0.0;
arr[ind][ileft] = min + ((PetscReal)ind + off) * h;
}
if (stagCoord->dof[1]) {
const PetscReal off = 0.5;
arr[ind][ielement] = min + ((PetscReal)ind + off) * h;
}
}
ierr = DMStagVecRestoreArrayDOF(dmCoord,coordLocal,&arr);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dmCoord,&coord);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dmCoord,coordLocal,INSERT_VALUES,coord);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dmCoord,coordLocal,INSERT_VALUES,coord);CHKERRQ(ierr);
ierr = DMSetCoordinates(dm,coord);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)dm,(PetscObject)coord);CHKERRQ(ierr);
ierr = VecDestroy(&coord);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dmCoord,&coordLocal);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode ComputePredictor(DM da, UserContext *user)
{
Vec uOldLocal, uLocal,uOld;
PetscScalar *pOld;
PetscScalar *p;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMGetGlobalVector(da, &uOld);CHKERRQ(ierr);
ierr = DMGetLocalVector(da, &uOldLocal);CHKERRQ(ierr);
ierr = DMGetLocalVector(da, &uLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da, uOld, INSERT_VALUES, uOldLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da, uOld, INSERT_VALUES, uOldLocal);CHKERRQ(ierr);
ierr = VecGetArray(uOldLocal, &pOld);CHKERRQ(ierr);
ierr = VecGetArray(uLocal, &p);CHKERRQ(ierr);
/* Source terms are all zero right now */
ierr = CalculateElementVelocity(da, user);CHKERRQ(ierr);
ierr = TaylorGalerkinStepI(da, user);CHKERRQ(ierr);
ierr = TaylorGalerkinStepIIMomentum(da, user);CHKERRQ(ierr);
ierr = TaylorGalerkinStepIIMassEnergy(da, user);CHKERRQ(ierr);
/* Solve equation (9) for \delta(\rho\vu) and (\rho\vu)^* */
/* Solve equation (13) for \delta\rho and \rho^* */
/* Solve equation (15) for \delta(\rho e_t) and (\rho e_t)^* */
/* Apply artifical dissipation */
/* Determine the smoothed explicit pressure, \tilde P and temperature \tilde T using the equation of state */
ierr = VecRestoreArray(uOldLocal, &pOld);CHKERRQ(ierr);
ierr = VecRestoreArray(uLocal, &p);CHKERRQ(ierr);
#if 0
ierr = DMLocalToGlobalBegin(da, uLocal, ADD_VALUES,u);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da, uLocal, ADD_VALUES,u);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da, &uOldLocal);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da, &uLocal);CHKERRQ(ierr);
#endif
PetscFunctionReturn(0);
}
PetscErrorCode CreatePressureNullSpace(DM dm, AppCtx *user, MatNullSpace *nullSpace)
{
Vec vec, localVec;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMGetGlobalVector(dm, &vec);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &localVec);CHKERRQ(ierr);
ierr = VecSet(vec, 0.0);CHKERRQ(ierr);
/* Put a constant in for all pressures
Could change this to project the constant function onto the pressure space (when that is finished) */
{
PetscSection section;
PetscInt pStart, pEnd, p;
PetscScalar *a;
ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);
ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr);
ierr = VecGetArray(localVec, &a);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt fDim, off, d;
ierr = PetscSectionGetFieldDof(section, p, 1, &fDim);CHKERRQ(ierr);
ierr = PetscSectionGetFieldOffset(section, p, 1, &off);CHKERRQ(ierr);
for (d = 0; d < fDim; ++d) a[off+d] = 1.0;
}
ierr = VecRestoreArray(localVec, &a);CHKERRQ(ierr);
}
ierr = DMLocalToGlobalBegin(dm, localVec, INSERT_VALUES, vec);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm, localVec, INSERT_VALUES, vec);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &localVec);CHKERRQ(ierr);
ierr = VecNormalize(vec, NULL);CHKERRQ(ierr);
if (user->debug) {
ierr = PetscPrintf(PetscObjectComm((PetscObject)dm), "Pressure Null Space\n");CHKERRQ(ierr);
ierr = VecView(vec, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = MatNullSpaceCreate(PetscObjectComm((PetscObject)dm), PETSC_FALSE, 1, &vec, nullSpace);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dm, &vec);CHKERRQ(ierr);
/* New style for field null spaces */
{
PetscObject pressure;
MatNullSpace nullSpacePres;
ierr = DMGetField(dm, 1, &pressure);CHKERRQ(ierr);
ierr = MatNullSpaceCreate(PetscObjectComm(pressure), PETSC_TRUE, 0, NULL, &nullSpacePres);CHKERRQ(ierr);
ierr = PetscObjectCompose(pressure, "nullspace", (PetscObject) nullSpacePres);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullSpacePres);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode TestVecClosure(DM dm, AppCtx *user)
{
PetscSection s;
Vec v;
PetscInt numRuns, cStart, cEnd, c, i;
PetscScalar tmpArray[64];
PetscScalar *userArray = user->reuseArray ? tmpArray : NULL;
PetscReal maxTimePerRun = user->maxVecClosureTime;
PetscStageLog stageLog;
PetscEventPerfLog eventLog;
PetscInt stage;
PetscLogEvent event;
PetscEventPerfInfo eventInfo;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscLogStageRegister("DMPlex Vector Closure Test", &stage);CHKERRQ(ierr);
ierr = PetscLogEventRegister("VecClosure", PETSC_OBJECT_CLASSID, &event);CHKERRQ(ierr);
ierr = PetscLogStagePush(stage);CHKERRQ(ierr);
ierr = DMPlexCreateSection(dm, user->dim, user->numFields, user->numComponents, user->numDof, 0, NULL, NULL, &s);CHKERRQ(ierr);
ierr = DMSetDefaultSection(dm, s);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&s);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &v);CHKERRQ(ierr);
ierr = PetscLogEventBegin(event,0,0,0,0);CHKERRQ(ierr);
for (i = 0; i < user->iterations; ++i) {
for (c = cStart; c < cEnd; ++c) {
PetscScalar *closure = userArray;
PetscInt closureSize = 64;;
ierr = DMPlexVecGetClosure(dm, s, v, c, &closureSize, &closure);CHKERRQ(ierr);
if (!user->reuseArray) {ierr = DMPlexVecRestoreClosure(dm, s, v, c, &closureSize, &closure);CHKERRQ(ierr);}
}
}
ierr = PetscLogEventEnd(event,0,0,0,0);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &v);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = PetscLogGetStageLog(&stageLog);
ierr = PetscStageLogGetEventPerfLog(stageLog, stage, &eventLog);
numRuns = (cEnd-cStart) * user->iterations;
eventInfo = eventLog->eventInfo[event];
if (eventInfo.count != 1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of event calls %d should be %d", eventInfo.count, 1);
if ((PetscInt) eventInfo.flops != 0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of event flops %d should be %d", (PetscInt) eventInfo.flops, 0);
if (eventInfo.time > maxTimePerRun * numRuns) {
ierr = PetscPrintf(PETSC_COMM_SELF, "VecClosures: %d Average time per cone: %gs standard: %gs\n", numRuns, eventInfo.time/numRuns, maxTimePerRun);
if (user->errors) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Average time for vector closure %g > standard %g", eventInfo.time/numRuns, maxTimePerRun);
}
PetscFunctionReturn(0);
}
PetscErrorCode ComputeCorrector(DM da, Vec uOld, Vec u)
{
Vec uOldLocal, uLocal;
PetscScalar *cOld;
PetscScalar *c;
PetscInt i,ne,nc;
const PetscInt *e;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = VecSet(u,0.0);CHKERRQ(ierr);
ierr = DMGetLocalVector(da, &uOldLocal);CHKERRQ(ierr);
ierr = DMGetLocalVector(da, &uLocal);CHKERRQ(ierr);
ierr = VecSet(uLocal,0.0);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da, uOld, INSERT_VALUES, uOldLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da, uOld, INSERT_VALUES, uOldLocal);CHKERRQ(ierr);
ierr = VecGetArray(uOldLocal, &cOld);CHKERRQ(ierr);
ierr = VecGetArray(uLocal, &c);CHKERRQ(ierr);
/* access the list of elements on this processor and loop over them */
ierr = DMDAGetElements(da,&ne,&nc,&e);CHKERRQ(ierr);
for (i=0; i<ne; i++) {
/* this is nonsense, but copy each nodal value*/
c[e[3*i]] = cOld[e[3*i]];
c[e[3*i+1]] = cOld[e[3*i+1]];
c[e[3*i+2]] = cOld[e[3*i+2]];
}
ierr = DMDARestoreElements(da,&ne,&nc,&e);CHKERRQ(ierr);
ierr = VecRestoreArray(uOldLocal, &cOld);CHKERRQ(ierr);
ierr = VecRestoreArray(uLocal, &c);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(da, uLocal, ADD_VALUES,u);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da, uLocal, ADD_VALUES,u);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da, &uOldLocal);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da, &uLocal);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SetInitialValues(DM networkdm,Vec X,void* appctx)
{
PetscErrorCode ierr;
VERTEXDATA bus;
GEN gen;
PetscInt v, vStart, vEnd, offset;
PetscBool ghostvtex;
Vec localX;
PetscScalar *xarr;
PetscInt key,numComps,j,offsetd;
DMNetworkComponentGenericDataType *arr;
PetscFunctionBegin;
ierr = DMNetworkGetVertexRange(networkdm,&vStart, &vEnd);CHKERRQ(ierr);
ierr = DMGetLocalVector(networkdm,&localX);CHKERRQ(ierr);
ierr = VecSet(X,0.0);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(networkdm,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(networkdm,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = VecGetArray(localX,&xarr);CHKERRQ(ierr);
ierr = DMNetworkGetComponentDataArray(networkdm,&arr);CHKERRQ(ierr);
for (v = vStart; v < vEnd; v++) {
ierr = DMNetworkIsGhostVertex(networkdm,v,&ghostvtex);CHKERRQ(ierr);
if (ghostvtex) continue;
ierr = DMNetworkGetVariableOffset(networkdm,v,&offset);CHKERRQ(ierr);
ierr = DMNetworkGetNumComponents(networkdm,v,&numComps);CHKERRQ(ierr);
for (j=0; j < numComps; j++) {
ierr = DMNetworkGetComponentTypeOffset(networkdm,v,j,&key,&offsetd);CHKERRQ(ierr);
if (key == 1) {
bus = (VERTEXDATA)(arr+offsetd);
xarr[offset] = bus->va*PETSC_PI/180.0;
xarr[offset+1] = bus->vm;
} else if(key == 2) {
gen = (GEN)(arr+offsetd);
if (!gen->status) continue;
xarr[offset+1] = gen->vs;
break;
}
}
}
ierr = VecRestoreArray(localX,&xarr);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(networkdm,localX,ADD_VALUES,X);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(networkdm,localX,ADD_VALUES,X);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(networkdm,&localX);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode WaterFormFunction(SNES snes,Vec X, Vec F, void *user)
{
PetscErrorCode ierr;
DM networkdm;
Vec localX,localF;
const PetscInt *v,*e;
PetscInt nv,ne;
PetscFunctionBegin;
/* Get the DM attached with the SNES */
ierr = SNESGetDM(snes,&networkdm);CHKERRQ(ierr);
/* Get local vertices and edges */
ierr = DMNetworkGetSubnetworkInfo(networkdm,0,&nv,&ne,&v,&e);CHKERRQ(ierr);
/* Get local vectors */
ierr = DMGetLocalVector(networkdm,&localX);CHKERRQ(ierr);
ierr = DMGetLocalVector(networkdm,&localF);CHKERRQ(ierr);
/* Scatter values from global to local vector */
ierr = DMGlobalToLocalBegin(networkdm,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(networkdm,X,INSERT_VALUES,localX);CHKERRQ(ierr);
/* Initialize residual */
ierr = VecSet(F,0.0);CHKERRQ(ierr);
ierr = VecSet(localF,0.0);CHKERRQ(ierr);
ierr = FormFunction_Water(networkdm,localX,localF,nv,ne,v,e,NULL);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(networkdm,&localX);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(networkdm,localF,ADD_VALUES,F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(networkdm,localF,ADD_VALUES,F);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(networkdm,&localF);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);
}
/* Compute pointwise residual f(x) over the locally-owned part of the grid
This is a finite difference method. In TeX, the formula we compute is
f_i = \eta_{i+1/2} H_{i+1/2} (u_{i+1}-u_i) - \eta_{i-1/2} H_{i-1/2} (u_i-u_{i-1})
- dx K (H_{i+1/2}^2 - H_{i-1/2}^2)
where
\eta_{i+1/2} = \left|\frac{u_{i+1}-u_i}{dx}\right|^{p-2}
with some regularization using user.epsilon, and
dx = L / Mx
p = 1+1/n
K = rho * g * (1-r) / (4 * B)
r = rho / rhow
B = A^{1/n}
*/
PetscErrorCode FormFunctionLocal(DMDALocalInfo *info,PetscScalar *u,PetscScalar *f,AppCtx *user)
{
PetscErrorCode ierr;
PetscReal hx, p, K, B, duL, duR, sL, sR;
PetscScalar *H;
PetscInt i, Mx;
Vec localH;
PetscFunctionBegin;
ierr = DMGetLocalVector(info->da,&localH);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(info->da,user->H,INSERT_VALUES,localH); CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(info->da,user->H,INSERT_VALUES,localH); CHKERRQ(ierr);
p = 1.0 + 1.0 / user->n;
B = PetscPowScalar(user->A,-1.0/user->n);
K = user->rho * user->g * (1.0 - user->rho/user->rhow) / (4.0 * B);
Mx = info->mx;
hx = user->L / ((PetscReal)Mx - 1.0);
ierr = DMDAVecGetArray(info->da,localH,&H);CHKERRQ(ierr);
for (i=info->xs; i<info->xs+info->xm; i++) {
if (i == 0) {
f[0] = u[0] - user->ug; /* Dirichlet condition */
} else {
if (i == 1) { /* use Dirichlet condition as value for neighbor, which symmetrizes */
duL = u[i] - user->ug;
} else {
duL = u[i] - u[i-1];
}
sL = GetEta(duL, hx, p, user->epsilon) * H[i-1] * duL;
if (i == Mx-1) { /* Neumann: calving front stress boundary condition */
duR = u[Mx-2] + 2.0 * hx * user->gamma - u[Mx-1];
} else {
duR = u[i+1] - u[i];
}
sR = GetEta(duR, hx, p, user->epsilon) * H[i] * duR;
f[i] = sR - sL - hx * K * (H[i]*H[i] - H[i-1]*H[i-1]);
}
}
ierr = DMDAVecRestoreArray(info->da,localH,&H);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(info->da,&localH);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Use Lax-Friedrichs method to evaluate F(u,t) = du/dt + a * du/dx
See https://en.wikipedia.org/wiki/Lax%E2%80%93Friedrichs_method
*/
PetscErrorCode IFunction_LaxFriedrichs(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,uave,c;
PetscReal dt;
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 */
c = appctx->a*dt/h; /* Courant-Friedrichs-Lewy number (CFL number) */
for (i=mstart; i<mend; i++) {
uave = 0.5*(uoldarray[i-1] + uoldarray[i+1]);
f[i] = uarray[i] - uave + c*0.5*(uoldarray[i+1] - uoldarray[i-1]);
}
/* 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);
}
static PetscErrorCode test5(DM dm, AppCtx *options)
{
IS cells;
Vec locX, locX_t, locA;
PetscScalar *u, *u_t, *a;
PetscErrorCode ierr;
PetscFunctionBegin;
locX_t = NULL;
locA = NULL;
ierr = ISCreateStride(PETSC_COMM_SELF, 0, 0, 1, &cells);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &locX);CHKERRQ(ierr);
ierr = DMPlexGetCellFields( dm, cells, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr);
ierr = DMPlexRestoreCellFields(dm, cells, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &locX);CHKERRQ(ierr);
ierr = ISDestroy(&cells);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexTSComputeRHSFunctionFVM - Form the local forcing F from the local input X using pointwise functions specified by the user
Input Parameters:
+ dm - The mesh
. t - The time
. locX - Local solution
- user - The user context
Output Parameter:
. F - Global output vector
Level: developer
.seealso: DMPlexComputeJacobianActionFEM()
@*/
PetscErrorCode DMPlexTSComputeRHSFunctionFVM(DM dm, PetscReal time, Vec locX, Vec F, void *user)
{
Vec locF;
PetscInt cStart, cEnd, cEndInterior;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
ierr = DMGetLocalVector(dm, &locF);CHKERRQ(ierr);
ierr = VecZeroEntries(locF);CHKERRQ(ierr);
ierr = DMPlexComputeResidual_Internal(dm, cStart, cEnd, time, locX, NULL, locF, user);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dm, locF, INSERT_VALUES, F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm, locF, INSERT_VALUES, F);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &locF);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatMult_DAAD(Mat A,Vec xx,Vec yy)
{
Mat_DAAD *a = (Mat_DAAD*)A->data;
Vec localxx;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMGetLocalVector(a->da,&localxx);
CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(a->da,xx,INSERT_VALUES,localxx);
CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(a->da,xx,INSERT_VALUES,localxx);
CHKERRQ(ierr);
ierr = DMDAMultiplyByJacobian1WithAD(a->da,a->localu,localxx,yy,a->ctx);
CHKERRQ(ierr);
ierr = DMRestoreLocalVector(a->da,&localxx);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/**
This function is for the explicit method, that is the right hand side
of the system: du/dt = F(u)
*/
PetscErrorCode MyRHSFunction(TS ts,PetscReal time,Vec in,Vec out,void *ctx)
{
User user = (User)ctx;
DM dm, dmFace, dmCell;
PetscSection section;
Vec inLocal;
PetscErrorCode ierr;
PetscFunctionBeginUser;
{
PetscReal norm;
PetscInt size;
ierr = VecNorm(in,NORM_INFINITY,&norm);CHKERRQ(ierr);
ierr = VecGetSize(in, &size);CHKERRQ(ierr);
norm = norm/size;
if (norm>1.e5) {
SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_LIB,
"The norm of the solution is: %f (current time: %f). The explicit method is going to DIVERGE!!!", norm, time);
}
}
ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
ierr = VecGetDM(user->facegeom,&dmFace);CHKERRQ(ierr);
ierr = VecGetDM(user->cellgeom,&dmCell);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm,&inLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm, in, INSERT_VALUES, inLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm, in, INSERT_VALUES, inLocal);CHKERRQ(ierr);
ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);
ierr = ApplyBC(dm, time, inLocal, user);CHKERRQ(ierr);
ierr = ConstructCellCentriodGradient(user->dm, dmFace, dmCell, time, inLocal, out, user);CHKERRQ(ierr);
ierr = VecZeroEntries(out);CHKERRQ(ierr);
if (user->second_order){
ierr = CaculateLocalFunction_LS(user->dm, dmFace, dmCell, time, inLocal, out, user);CHKERRQ(ierr);
}else{
ierr = CaculateLocalFunction_Upwind(user->dm, dmFace, dmCell, time, inLocal, out, user);CHKERRQ(ierr);
}
ierr = DMRestoreLocalVector(dm,&inLocal);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatMult_GlobalToLocalNormal(Mat CtC, Vec x, Vec y)
{
DM dm;
Vec local, mask;
projectConstraintsCtx *ctx;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MatShellGetContext(CtC,&ctx);CHKERRQ(ierr);
dm = ctx->dm;
mask = ctx->mask;
ierr = DMGetLocalVector(dm,&local);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,x,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,x,INSERT_VALUES,local);CHKERRQ(ierr);
if (mask) {ierr = VecPointwiseMult(local,mask,local);CHKERRQ(ierr);}
ierr = VecSet(y,0.);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dm,local,ADD_VALUES,y);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm,local,ADD_VALUES,y);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&local);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexTSComputeRHSFunctionFVM - Form the local forcing F from the local input X using pointwise functions specified by the user
Input Parameters:
+ dm - The mesh
. t - The time
. locX - Local solution
- user - The user context
Output Parameter:
. F - Global output vector
Level: developer
.seealso: DMPlexComputeJacobianActionFEM()
@*/
PetscErrorCode DMPlexTSComputeRHSFunctionFVM(DM dm, PetscReal time, Vec locX, Vec F, void *user)
{
Vec locF;
PetscInt cStart, cEnd, cEndInterior;
DM plex;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMTSConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(plex, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
ierr = DMGetLocalVector(plex, &locF);CHKERRQ(ierr);
ierr = VecZeroEntries(locF);CHKERRQ(ierr);
ierr = DMPlexComputeResidual_Internal(plex, cStart, cEnd, time, locX, NULL, time, locF, user);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(plex, locF, ADD_VALUES, F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(plex, locF, ADD_VALUES, F);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(plex, &locF);CHKERRQ(ierr);
ierr = DMDestroy(&plex);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMVecViewLocal(DM dm, Vec v, PetscViewer viewer)
{
Vec lv;
PetscInt p;
PetscMPIInt rank, numProcs;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &numProcs);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &lv);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm, v, INSERT_VALUES, lv);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm, v, INSERT_VALUES, lv);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Local function\n");CHKERRQ(ierr);
for (p = 0; p < numProcs; ++p) {
if (p == rank) {ierr = VecView(lv, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
ierr = PetscBarrier((PetscObject) dm);CHKERRQ(ierr);
}
ierr = DMRestoreLocalVector(dm, &lv);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
DMCompositeRestoreLocalVectors - Restores local vectors for each part of a DMComposite.
Not Collective
Input Parameter:
. dm - the packer object
Output Parameter:
. Vec ... - the individual sequential Vecs
Level: advanced
.seealso DMDestroy(), DMCompositeAddDM(), DMCreateGlobalVector(),
DMCompositeGather(), DMCompositeCreate(), DMCompositeGetISLocalToGlobalMappings(), DMCompositeGetAccess(),
DMCompositeGetLocalVectors(), DMCompositeScatter(), DMCompositeGetEntries()
@*/
PetscErrorCode DMCompositeRestoreLocalVectors(DM dm,...)
{
va_list Argp;
PetscErrorCode ierr;
struct DMCompositeLink *next;
DM_Composite *com = (DM_Composite*)dm->data;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
next = com->next;
/* loop over packed objects, handling one at at time */
va_start(Argp,dm);
while (next) {
Vec *vec;
vec = va_arg(Argp, Vec*);
if (vec) {ierr = DMRestoreLocalVector(next->dm,vec);CHKERRQ(ierr);}
next = next->next;
}
va_end(Argp);
PetscFunctionReturn(0);
}
static PetscErrorCode TestFunctionProjection(DM dm, DM auxdm, DMLabel label, Vec la, const char name[], AppCtx *user)
{
PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *);
Vec x, lx;
PetscInt Nf, f;
PetscInt val[1] = {1};
char lname[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscFunctionBeginUser;
if (auxdm) {
ierr = PetscObjectCompose((PetscObject) dm, "dmAux", (PetscObject) auxdm);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject) dm, "A", (PetscObject) la);CHKERRQ(ierr);
}
ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr);
ierr = PetscMalloc1(Nf, &funcs);CHKERRQ(ierr);
for (f = 0; f < Nf; ++f) funcs[f] = linear;
ierr = DMGetGlobalVector(dm, &x);CHKERRQ(ierr);
ierr = PetscStrcpy(lname, "Function ");CHKERRQ(ierr);
ierr = PetscStrcat(lname, name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) x, lname);CHKERRQ(ierr);
if (!label) {ierr = DMProjectFunction(dm, 0.0, funcs, NULL, INSERT_VALUES, x);CHKERRQ(ierr);}
else {ierr = DMProjectFunctionLabel(dm, 0.0, label, 1, val, 0, NULL, funcs, NULL, INSERT_VALUES, x);CHKERRQ(ierr);}
ierr = VecViewFromOptions(x, NULL, "-func_view");CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dm, &x);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &lx);CHKERRQ(ierr);
ierr = PetscStrcpy(lname, "Local Function ");CHKERRQ(ierr);
ierr = PetscStrcat(lname, name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) lx, lname);CHKERRQ(ierr);
if (!label) {ierr = DMProjectFunctionLocal(dm, 0.0, funcs, NULL, INSERT_VALUES, lx);CHKERRQ(ierr);}
else {ierr = DMProjectFunctionLabelLocal(dm, 0.0, label, 1, val, 0, NULL, funcs, NULL, INSERT_VALUES, lx);CHKERRQ(ierr);}
ierr = VecViewFromOptions(lx, NULL, "-local_func_view");CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &lx);CHKERRQ(ierr);
ierr = PetscFree(funcs);CHKERRQ(ierr);
if (auxdm) {
ierr = PetscObjectCompose((PetscObject) dm, "dmAux", NULL);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject) dm, "A", NULL);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*@C
DMCompositeAddDM - adds a DM vector to a DMComposite
Collective on DMComposite
Input Parameter:
+ dm - the packer object
- dm - the DM object, if the DM is a da you will need to caste it with a (DM)
Level: advanced
.seealso DMDestroy(), DMCompositeGather(), DMCompositeAddDM(), DMCreateGlobalVector(),
DMCompositeScatter(), DMCompositeCreate(), DMCompositeGetISLocalToGlobalMappings(), DMCompositeGetAccess(),
DMCompositeGetLocalVectors(), DMCompositeRestoreLocalVectors(), DMCompositeGetEntries()
@*/
PetscErrorCode DMCompositeAddDM(DM dmc,DM dm)
{
PetscErrorCode ierr;
PetscInt n,nlocal;
struct DMCompositeLink *mine,*next;
Vec global,local;
DM_Composite *com = (DM_Composite*)dmc->data;
PetscFunctionBegin;
PetscValidHeaderSpecific(dmc,DM_CLASSID,1);
PetscValidHeaderSpecific(dm,DM_CLASSID,2);
next = com->next;
if (com->setup) SETERRQ(((PetscObject)dmc)->comm,PETSC_ERR_ARG_WRONGSTATE,"Cannot add a DM once you have used the DMComposite");
/* create new link */
ierr = PetscNew(struct DMCompositeLink,&mine);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)dm);CHKERRQ(ierr);
ierr = DMGetGlobalVector(dm,&global);CHKERRQ(ierr);
ierr = VecGetLocalSize(global,&n);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dm,&global);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm,&local);CHKERRQ(ierr);
ierr = VecGetSize(local,&nlocal);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&local);CHKERRQ(ierr);
mine->n = n;
mine->nlocal = nlocal;
mine->dm = dm;
mine->next = PETSC_NULL;
com->n += n;
/* add to end of list */
if (!next) {
com->next = mine;
} else {
while (next->next) next = next->next;
next->next = mine;
}
com->nDM++;
com->nmine++;
PetscFunctionReturn(0);
}
static PetscErrorCode TestQ2Q1DA( void )
{
DM Q2_da,Q1_da,cda;
PetscInt mx,my,mz;
Vec coords,gcoords,gcoords2;
PetscErrorCode ierr;
mx=7;
my=11;
mz=13;
ierr=DMDACreate3d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,mx,my,mz,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,3,2,0,0,0,&Q2_da);CHKERRQ(ierr);
ierr = DMDASetUniformCoordinates(Q2_da,-1.0,1.0,-2.0,2.0,-3.0,3.0);CHKERRQ(ierr);
ierr = DMDAGetCoordinates(Q2_da,&coords);CHKERRQ(ierr);
ierr = DMDACreate3d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,mx,my,mz,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,3,1,0,0,0,&Q1_da);CHKERRQ(ierr);
ierr = DMDASetCoordinates(Q1_da,coords);CHKERRQ(ierr);
/* Get ghost coordinates one way */
ierr = DMDAGetGhostedCoordinates(Q1_da,&gcoords);CHKERRQ(ierr);
/* And another */
ierr = DMDAGetCoordinates(Q1_da,&coords);CHKERRQ(ierr);
ierr = DMDAGetCoordinateDA(Q1_da,&cda);CHKERRQ(ierr);
ierr = DMGetLocalVector(cda,&gcoords2);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(cda,coords,INSERT_VALUES,gcoords2);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(cda,coords,INSERT_VALUES,gcoords2);CHKERRQ(ierr);
ierr = CompareGhostedCoords(gcoords,gcoords2);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(cda,&gcoords2);CHKERRQ(ierr);
ierr = VecScale(coords,10.0);CHKERRQ(ierr);
ierr = VecScale(gcoords,10.0);CHKERRQ(ierr);
ierr = DMDAGetGhostedCoordinates(Q1_da,&gcoords2);CHKERRQ(ierr);
ierr = CompareGhostedCoords(gcoords,gcoords2);CHKERRQ(ierr);
ierr = DMDestroy(&Q2_da);CHKERRQ(ierr);
ierr = DMDestroy(&Q1_da);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode WaterSetInitialGuess(DM networkdm,Vec X)
{
PetscErrorCode ierr;
PetscInt nv,ne;
const PetscInt *vtx,*edges;
Vec localX;
PetscFunctionBegin;
ierr = DMGetLocalVector(networkdm,&localX);CHKERRQ(ierr);
ierr = VecSet(X,0.0);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(networkdm,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(networkdm,X,INSERT_VALUES,localX);CHKERRQ(ierr);
/* Get subnetwork info */
ierr = DMNetworkGetSubnetworkInfo(networkdm,0,&nv,&ne,&vtx,&edges);CHKERRQ(ierr);
ierr = SetInitialGuess_Water(networkdm,localX,nv,ne,vtx,edges,NULL);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(networkdm,localX,ADD_VALUES,X);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(networkdm,localX,ADD_VALUES,X);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(networkdm,&localX);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FormIFunction(TS ts,PetscReal ptime,Vec X,Vec Xdot,Vec F,void *user)
{
DMDALocalInfo info;
Field **u,**udot,**fu;
PetscErrorCode ierr;
Vec localX;
DM da;
PetscFunctionBeginUser;
ierr = TSGetDM(ts,(DM*)&da);CHKERRQ(ierr);
ierr = DMGetLocalVector(da,&localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,X,INSERT_VALUES,localX);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(da,localX,&u);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(da,Xdot,&udot);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,F,&fu);CHKERRQ(ierr);
ierr = FormIFunctionLocal(&info,ptime,u,udot,fu,(AppCtx*)user);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(da,localX,&u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(da,Xdot,&udot);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,F,&fu);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&localX);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
