/*@C DMPlexProjectField - This projects the given function of the fields into the function space provided. Input Parameters: + dm - The DM . U - The input field vector . funcs - The functions to evaluate, one per field - mode - The insertion mode for values Output Parameter: . X - The output vector Level: developer .seealso: DMPlexProjectFunction(), DMPlexComputeL2Diff() @*/ PetscErrorCode DMPlexProjectField(DM dm, Vec U, void (**funcs)(const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscReal [], PetscScalar []), InsertMode mode, Vec X) { Vec localX, localU; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); ierr = DMGetLocalVector(dm, &localU);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, U, INSERT_VALUES, localU);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, U, INSERT_VALUES, localU);CHKERRQ(ierr); ierr = DMPlexProjectFieldLocal(dm, localU, funcs, mode, localX);CHKERRQ(ierr); ierr = DMLocalToGlobalBegin(dm, localX, mode, X);CHKERRQ(ierr); ierr = DMLocalToGlobalEnd(dm, localX, mode, X);CHKERRQ(ierr); if (mode == INSERT_VALUES || mode == INSERT_ALL_VALUES || mode == INSERT_BC_VALUES) { Mat cMat; ierr = DMGetDefaultConstraints(dm, NULL, &cMat);CHKERRQ(ierr); if (cMat) { ierr = DMGlobalToLocalSolve(dm, localX, X);CHKERRQ(ierr); } } ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &localU);CHKERRQ(ierr); PetscFunctionReturn(0); }
static PetscErrorCode SNESComputeFunction_DMLocal(SNES snes,Vec X,Vec F,void *ctx) { PetscErrorCode ierr; DM dm; DMSNES_Local *dmlocalsnes = (DMSNES_Local*)ctx; Vec Xloc,Floc; PetscFunctionBegin; PetscValidHeaderSpecific(snes,SNES_CLASSID,1); PetscValidHeaderSpecific(X,VEC_CLASSID,2); PetscValidHeaderSpecific(F,VEC_CLASSID,3); ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr); ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr); ierr = DMGetLocalVector(dm,&Floc);CHKERRQ(ierr); ierr = VecZeroEntries(Xloc);CHKERRQ(ierr); ierr = VecZeroEntries(Floc);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr); CHKMEMQ; ierr = (*dmlocalsnes->residuallocal)(dm,Xloc,Floc,dmlocalsnes->residuallocalctx);CHKERRQ(ierr); CHKMEMQ; 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); ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr); PetscFunctionReturn(0); }
/*@C DMProjectField - This projects the given function of the fields into the function space provided. Input Parameters: + dm - The DM . time - The time . U - The input field vector . funcs - The functions to evaluate, one per field - mode - The insertion mode for values Output Parameter: . X - The output vector Level: developer .seealso: DMProjectFunction(), DMComputeL2Diff() @*/ PetscErrorCode DMProjectField(DM dm, PetscReal time, Vec U, void (**funcs)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], PetscReal, const PetscReal[], PetscScalar[]), InsertMode mode, Vec X) { Vec localX, localU; PetscErrorCode ierr; PetscFunctionBegin; PetscValidHeaderSpecific(dm, DM_CLASSID, 1); ierr = DMGetLocalVector(dm, &localX);CHKERRQ(ierr); /* We currently check whether locU == locX to see if we need to apply BC */ if (U != X) {ierr = DMGetLocalVector(dm, &localU);CHKERRQ(ierr);} else {localU = localX;} ierr = DMGlobalToLocalBegin(dm, U, INSERT_VALUES, localU);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, U, INSERT_VALUES, localU);CHKERRQ(ierr); ierr = DMProjectFieldLocal(dm, time, localU, funcs, mode, localX);CHKERRQ(ierr); ierr = DMLocalToGlobalBegin(dm, localX, mode, X);CHKERRQ(ierr); ierr = DMLocalToGlobalEnd(dm, localX, mode, X);CHKERRQ(ierr); if (mode == INSERT_VALUES || mode == INSERT_ALL_VALUES || mode == INSERT_BC_VALUES) { Mat cMat; ierr = DMGetDefaultConstraints(dm, NULL, &cMat);CHKERRQ(ierr); if (cMat) { ierr = DMGlobalToLocalSolve(dm, localX, X);CHKERRQ(ierr); } } ierr = DMRestoreLocalVector(dm, &localX);CHKERRQ(ierr); if (U != X) {ierr = DMRestoreLocalVector(dm, &localU);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 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); }
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 = DMDAVecGetArrayRead(cda,gc,&coors);CHKERRQ(ierr); ierr = DMDAVecGetArrayRead(user->da,localX,&p);CHKERRQ(ierr); ierr = DMDAVecGetArrayRead(user->da,localXdot,&pdot);CHKERRQ(ierr); ierr = DMDAVecGetArray(user->da,F,&f);CHKERRQ(ierr); PetscScalar diffuse1,gamma; gamma = user->D*user->ws/(2*user->H); diffuse1 = user->lambda*user->lambda*user->q/(user->lambda*gamma+1)*(1.0 - PetscExpScalar(-t*(gamma+1.0)/user->lambda)); user->disper_coe = user->ws*user->ws/(4*user->H*user->H)*diffuse1; for (i=xs; i < xs+xm; i++) { for (j=ys; j < ys+ym; j++) { ierr = adv1(p,coors[j][i].y,i,j,M,&p_adv1,user);CHKERRQ(ierr); ierr = adv2(p,coors[j][i].x,coors[j][i].y,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 = DMDAVecRestoreArrayRead(user->da,localX,&p);CHKERRQ(ierr); ierr = DMDAVecRestoreArrayRead(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 = DMDAVecRestoreArrayRead(cda,gc,&coors);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 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); }
/* Evaluates \integral_{-1}^{1} f*v_i where v_i is the ith basis polynomial via the GLL nodes and weights, since the v_i basis function is zero at all nodes except the ith one the integral is simply the weight_i * f(node_i) */ PetscErrorCode ComputeRhs(DM da,PetscGLL *gll,Vec b) { PetscErrorCode ierr; PetscInt i,j,xs,xn,n = gll->n; PetscScalar *bb,*xx; PetscReal xd; Vec blocal,xlocal; PetscFunctionBegin; ierr = DMDAGetCorners(da,&xs,NULL,NULL,&xn,NULL,NULL);CHKERRQ(ierr); xs = xs/(n-1); xn = xn/(n-1); ierr = DMGetLocalVector(da,&blocal);CHKERRQ(ierr); ierr = VecZeroEntries(blocal);CHKERRQ(ierr); ierr = DMDAVecGetArray(da,blocal,&bb);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(da,&xlocal);CHKERRQ(ierr); ierr = DMDAVecGetArray(da,xlocal,&xx);CHKERRQ(ierr); /* loop over local spectral elements */ for (j=xs; j<xs+xn; j++) { /* loop over GLL points in each element */ for (i=0; i<n; i++) { xd = xx[j*(n-1) + i]; bb[j*(n-1) + i] += -gll->weights[i]*(-20.*PETSC_PI*xd*PetscSinReal(5.*PETSC_PI*xd) + (2. - (5.*PETSC_PI)*(5.*PETSC_PI)*(xd*xd - 1.))*PetscCosReal(5.*PETSC_PI*xd)); } } ierr = DMDAVecRestoreArray(da,xlocal,&xx);CHKERRQ(ierr); ierr = DMDAVecRestoreArray(da,blocal,&bb);CHKERRQ(ierr); ierr = VecZeroEntries(b);CHKERRQ(ierr); ierr = DMLocalToGlobalBegin(da,blocal,ADD_VALUES,b);CHKERRQ(ierr); ierr = DMLocalToGlobalEnd(da,blocal,ADD_VALUES,b);CHKERRQ(ierr); ierr = DMRestoreLocalVector(da,&blocal);CHKERRQ(ierr); PetscFunctionReturn(0); }
static PetscErrorCode SNESComputePicardJacobian_DMDA(SNES snes,Vec X,Mat *A,Mat *B,MatStructure *mstr,void *ctx) { PetscErrorCode ierr; DM dm; DMSNES_DA *dmdasnes = (DMSNES_DA*)ctx; DMDALocalInfo info; Vec Xloc; void *x; PetscFunctionBegin; if (!dmdasnes->jacobianplocal) 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); CHKMEMQ; ierr = (*dmdasnes->jacobianplocal)(&info,x,*A,*B,mstr,dmdasnes->picardlocalctx);CHKERRQ(ierr); CHKMEMQ; ierr = DMDAVecRestoreArray(dm,Xloc,&x);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr); *mstr = SAME_NONZERO_PATTERN; if (*A != *B) { ierr = MatAssemblyBegin(*A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(*A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); } PetscFunctionReturn(0); }
/* This function should eventually replace: DMDAComputeFunction() and DMDAComputeFunction1() */ static PetscErrorCode SNESComputeObjective_DMDA(SNES snes,Vec X,PetscReal *ob,void *ctx) { PetscErrorCode ierr; DM dm; DMSNES_DA *dmdasnes = (DMSNES_DA*)ctx; DMDALocalInfo info; Vec Xloc; void *x; PetscFunctionBegin; PetscValidHeaderSpecific(snes,SNES_CLASSID,1); PetscValidHeaderSpecific(X,VEC_CLASSID,2); PetscValidPointer(ob,3); if (!dmdasnes->objectivelocal) 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); CHKMEMQ; ierr = (*dmdasnes->objectivelocal)(&info,x,ob,dmdasnes->objectivelocalctx);CHKERRQ(ierr); CHKMEMQ; ierr = DMDAVecRestoreArray(dm,Xloc,&x);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr); PetscFunctionReturn(0); }
/* Caculate the source term of the equations, which includes all terms except convetion term, diffusion term, and timedependent term. */ PetscErrorCode CaculateLocalSourceTerm(DM dm, Vec locX, Vec F, User user) { PetscErrorCode ierr; DM dmGrad = user->dmGrad; const PetscScalar *x; PetscScalar *f; PetscInt cStart, cell; const PetscScalar *cellgeom; const CellGeom *cg; Vec locGrad, Grad; const PetscScalar *grad; DM dmCell; PetscFunctionBeginUser; ierr = VecGetDM(user->cellgeom,&dmCell);CHKERRQ(ierr); ierr = VecGetArrayRead(locX,&x);CHKERRQ(ierr); ierr = VecGetArray(F,&f);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, &cStart, NULL);CHKERRQ(ierr); ierr = VecGetArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr); ierr = DMGetGlobalVector(dmGrad,&Grad);CHKERRQ(ierr); ierr = DMGetLocalVector(dmGrad,&locGrad);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dmGrad,Grad,INSERT_VALUES,locGrad);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dmGrad,Grad,INSERT_VALUES,locGrad);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(dmGrad,&Grad);CHKERRQ(ierr); ierr = VecGetArrayRead(locGrad,&grad);CHKERRQ(ierr); for (cell = cStart; cell < user->cEndInterior; cell++) { PetscScalar *fref; const PetscScalar *xref; PetscScalar *cgrad; ierr = DMPlexPointLocalRead(dmCell,cell,cellgeom,&cg);CHKERRQ(ierr); ierr = DMPlexPointLocalRead(dm,cell,x,&xref);CHKERRQ(ierr); /*For the unkown variables*/ ierr = DMPlexPointGlobalRef(dm,cell,f,&fref);CHKERRQ(ierr); ierr = DMPlexPointLocalRead(dmGrad,cell,grad,&cgrad);CHKERRQ(ierr); // if (!fref){ PetscPrintf(PETSC_COMM_WORLD,"%d, %d\n", cell, user->cEndInterior);} if (fref){ fref[0] += SourceRho(user, cgrad, xref, cg->centroid);/*the continuity equation*/ fref[1] += SourceU(user, cgrad, xref, cg->centroid); /*Momentum U*/ fref[2] += SourceV(user, cgrad, xref, cg->centroid); /*Momentum V*/ fref[3] += SourceW(user, cgrad, xref, cg->centroid); /*Momentum W*/ fref[4] += SourceE(user, cgrad, xref, cg->centroid);/*Energy*/ } } ierr = VecRestoreArrayRead(locX,&x);CHKERRQ(ierr); ierr = VecRestoreArray(F,&f);CHKERRQ(ierr); ierr = VecRestoreArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr); ierr = VecRestoreArrayRead(locGrad,&grad);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dmGrad,&locGrad);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); }
/* We integrate over each cell (i, j+1)----(i+1, j+1) | \ | | \ | | \ | | \ | | \ | | \ | | \ | (i, j)----(i+1, j) */ PetscErrorCode ComputeRHS(KSP ksp, Vec b, void *ctx) { UserContext *user = (UserContext*)ctx; PetscScalar phi = user->phi; PetscScalar *array; PetscInt ne,nc,i; const PetscInt *e; PetscErrorCode ierr; Vec blocal; DM da; PetscFunctionBeginUser; ierr = KSPGetDM(ksp,&da);CHKERRQ(ierr); /* access a local vector with room for the ghost points */ ierr = DMGetLocalVector(da,&blocal);CHKERRQ(ierr); ierr = VecGetArray(blocal, (PetscScalar**) &array);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 set each nodal value to phi (will actually do integration over element */ array[e[3*i]] = phi; array[e[3*i+1]] = phi; array[e[3*i+2]] = phi; } ierr = VecRestoreArray(blocal, (PetscScalar**) &array);CHKERRQ(ierr); ierr = DMDARestoreElements(da,&ne,&nc,&e);CHKERRQ(ierr); /* add our partial sums over all processors into b */ ierr = DMLocalToGlobalBegin(da,blocal,ADD_VALUES,b);CHKERRQ(ierr); ierr = DMLocalToGlobalEnd(da,blocal, ADD_VALUES,b);CHKERRQ(ierr); ierr = DMRestoreLocalVector(da,&blocal);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); }
/** Form the time step function for the mass term @param Vec in: (y^(n+1)) out @param Vec out: My^(n+1) - M y^(n) if timestep = 1, backward euler will do the BDF2 **/ PetscErrorCode FormMassTimeStepFunction(User user, Algebra algebra, Vec in, Vec out, PetscBool rebuild) { PetscErrorCode ierr; PetscMPIInt rank; Vec inLocal; PetscFunctionBegin; ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = VecSet(out, 0.0);CHKERRQ(ierr); ierr = DMGetLocalVector(user->dm, &inLocal);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(user->dm, in, INSERT_VALUES, inLocal);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(user->dm, in, INSERT_VALUES, inLocal);CHKERRQ(ierr); ierr = ApplyBC(user->dm, user->current_time, inLocal, user);CHKERRQ(ierr); ierr = CaculateLocalMassFunction(user->dm, inLocal, out, user);CHKERRQ(ierr); ierr = DMLocalToGlobalBegin(user->dm, inLocal, INSERT_VALUES, in);CHKERRQ(ierr); ierr = DMLocalToGlobalEnd(user->dm, inLocal, INSERT_VALUES, in);CHKERRQ(ierr); ierr = DMRestoreLocalVector(user->dm, &inLocal);CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode FormFunction(SNES snes, Vec X, Vec F, void *user) { DMDALocalInfo info; Field **u,**fu; PetscErrorCode ierr; Vec localX; DM da; PetscFunctionBegin; ierr = SNESGetDM(snes,(DM*)&da);CHKERRQ(ierr); ierr = DMGetLocalVector(da,&localX);CHKERRQ(ierr); /* Scatter ghost points to local vector, using the 2-step process DMGlobalToLocalBegin(), DMGlobalToLocalEnd(). */ 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 = DMDAVecGetArray(da,localX,&u);CHKERRQ(ierr); ierr = DMDAVecGetArray(da,F,&fu);CHKERRQ(ierr); ierr = FormFunctionLocal(&info,u,fu,user);CHKERRQ(ierr); ierr = DMDAVecRestoreArray(da,localX,&u);CHKERRQ(ierr); ierr = DMDAVecRestoreArray(da,F,&fu);CHKERRQ(ierr); ierr = DMRestoreLocalVector(da,&localX);CHKERRQ(ierr); PetscFunctionReturn(0); }
static PetscErrorCode TestFieldProjection(DM dm, DM auxdm, DMLabel label, Vec la, const char name[], AppCtx *user) { PetscErrorCode (**afuncs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *); void (**funcs)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]); Vec lx, lu; 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 = PetscMalloc2(Nf, &funcs, Nf, &afuncs);CHKERRQ(ierr); for (f = 0; f < Nf; ++f) afuncs[f] = linear; funcs[0] = linear_vector; funcs[1] = linear_scalar; ierr = DMGetLocalVector(dm, &lu);CHKERRQ(ierr); ierr = PetscStrcpy(lname, "Local Field Input ");CHKERRQ(ierr); ierr = PetscStrcat(lname, name);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) lu, lname);CHKERRQ(ierr); if (!label) {ierr = DMProjectFunctionLocal(dm, 0.0, afuncs, NULL, INSERT_VALUES, lu);CHKERRQ(ierr);} else {ierr = DMProjectFunctionLabelLocal(dm, 0.0, label, 1, val, 0, NULL, afuncs, NULL, INSERT_VALUES, lu);CHKERRQ(ierr);} ierr = VecViewFromOptions(lu, NULL, "-local_input_view");CHKERRQ(ierr); ierr = DMGetLocalVector(dm, &lx);CHKERRQ(ierr); ierr = PetscStrcpy(lname, "Local Field ");CHKERRQ(ierr); ierr = PetscStrcat(lname, name);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) lx, lname);CHKERRQ(ierr); if (!label) {ierr = DMProjectFieldLocal(dm, 0.0, lu, funcs, INSERT_VALUES, lx);CHKERRQ(ierr);} else {ierr = DMProjectFieldLabelLocal(dm, 0.0, label, 1, val, 0, NULL, lu, funcs, INSERT_VALUES, lx);CHKERRQ(ierr);} ierr = VecViewFromOptions(lx, NULL, "-local_field_view");CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &lx);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &lu);CHKERRQ(ierr); ierr = PetscFree2(funcs, afuncs);CHKERRQ(ierr); if (auxdm) { ierr = PetscObjectCompose((PetscObject) dm, "dmAux", NULL);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "A", NULL);CHKERRQ(ierr); } PetscFunctionReturn(0); }
PetscErrorCode OpForcing(Op op,DM dm,Vec F) { PetscErrorCode ierr; Vec X,Floc; DM dmx; const PetscScalar *x; PetscScalar *f; const PetscReal *B,*D,*w3; PetscReal L[3]; PetscInt nelem,ne = op->ne,P,Q,P3,Q3; PetscFunctionBegin; ierr = PetscLogEventBegin(OP_Forcing,dm,F,0,0);CHKERRQ(ierr); ierr = DMFEGetTensorEval(dm,&P,&Q,&B,&D,NULL,NULL,&w3);CHKERRQ(ierr); P3 = P*P*P; Q3 = Q*Q*Q; ierr = DMFEGetUniformCoordinates(dm,L);CHKERRQ(ierr); ierr = DMGetLocalVector(dm,&Floc);CHKERRQ(ierr); ierr = DMGetCoordinateDM(dm,&dmx);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm,&X);CHKERRQ(ierr); ierr = DMFEGetNumElements(dm,&nelem);CHKERRQ(ierr); ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr); ierr = VecZeroEntries(Floc);CHKERRQ(ierr); ierr = VecGetArray(Floc,&f);CHKERRQ(ierr); for (PetscInt e=0; e<nelem; e+=ne) { PetscScalar fe[op->dof*P3*ne]_align,fq[op->dof][Q3][ne]_align,xe[3*P3*ne]_align,xq[3][Q3][ne]_align,dx[3][3][Q3][ne]_align,wdxdet[Q3][ne]_align; ierr = DMFEExtractElements(dmx,x,e,ne,xe);CHKERRQ(ierr); ierr = PetscMemzero(xq,sizeof xq);CHKERRQ(ierr); ierr = TensorContract(op->Tensor3,B,B,B,TENSOR_EVAL,xe,xq[0][0]);CHKERRQ(ierr); ierr = PetscMemzero(dx,sizeof dx);CHKERRQ(ierr); ierr = TensorContract(op->Tensor3,D,B,B,TENSOR_EVAL,xe,dx[0][0][0]);CHKERRQ(ierr); ierr = TensorContract(op->Tensor3,B,D,B,TENSOR_EVAL,xe,dx[1][0][0]);CHKERRQ(ierr); ierr = TensorContract(op->Tensor3,B,B,D,TENSOR_EVAL,xe,dx[2][0][0]);CHKERRQ(ierr); ierr = PointwiseJacobianInvert(ne,Q*Q*Q,w3,dx,wdxdet);CHKERRQ(ierr); for (PetscInt i=0; i<Q3; i++) { for (PetscInt l=0; l<ne; l++) { PetscReal xx[] = {xq[0][i][l],xq[1][i][l],xq[2][i][l]}; PetscScalar fql[op->dof]; ierr = (op->PointwiseForcing)(op,xx,L,fql);CHKERRQ(ierr); for (PetscInt d=0; d<op->dof; d++) fq[d][i][l] = wdxdet[i][l] * fql[d]; } } ierr = PetscMemzero(fe,sizeof fe);CHKERRQ(ierr); ierr = TensorContract(op->TensorDOF,B,B,B,TENSOR_TRANSPOSE,fq[0][0],fe);CHKERRQ(ierr); ierr = DMFESetElements(dm,f,e,ne,ADD_VALUES,DOMAIN_INTERIOR,fe);CHKERRQ(ierr); } ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr); ierr = VecRestoreArray(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); ierr = PetscLogEventEnd(OP_Forcing,dm,F,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); }
static PetscErrorCode SNESComputeJacobian_DMLocal(SNES snes,Vec X,Mat A,Mat B,void *ctx) { PetscErrorCode ierr; DM dm; DMSNES_Local *dmlocalsnes = (DMSNES_Local*)ctx; Vec Xloc; PetscFunctionBegin; ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr); if (dmlocalsnes->jacobianlocal) { ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr); ierr = VecZeroEntries(Xloc);CHKERRQ(ierr); if (dmlocalsnes->boundarylocal) {ierr = (*dmlocalsnes->boundarylocal)(dm,Xloc,dmlocalsnes->boundarylocalctx);CHKERRQ(ierr);} ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr); CHKMEMQ; ierr = (*dmlocalsnes->jacobianlocal)(dm,Xloc,A,B,dmlocalsnes->jacobianlocalctx);CHKERRQ(ierr); CHKMEMQ; ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr); } else { MatFDColoring fdcoloring; ierr = PetscObjectQuery((PetscObject)dm,"DMDASNES_FDCOLORING",(PetscObject*)&fdcoloring);CHKERRQ(ierr); if (!fdcoloring) { ISColoring coloring; ierr = DMCreateColoring(dm,dm->coloringtype,&coloring);CHKERRQ(ierr); ierr = MatFDColoringCreate(B,coloring,&fdcoloring);CHKERRQ(ierr); ierr = ISColoringDestroy(&coloring);CHKERRQ(ierr); switch (dm->coloringtype) { case IS_COLORING_GLOBAL: ierr = MatFDColoringSetFunction(fdcoloring,(PetscErrorCode (*)(void))SNESComputeFunction_DMLocal,dmlocalsnes);CHKERRQ(ierr); break; default: SETERRQ1(PetscObjectComm((PetscObject)snes),PETSC_ERR_SUP,"No support for coloring type '%s'",ISColoringTypes[dm->coloringtype]); } ierr = PetscObjectSetOptionsPrefix((PetscObject)fdcoloring,((PetscObject)dm)->prefix);CHKERRQ(ierr); ierr = MatFDColoringSetFromOptions(fdcoloring);CHKERRQ(ierr); ierr = MatFDColoringSetUp(B,coloring,fdcoloring);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject)dm,"DMDASNES_FDCOLORING",(PetscObject)fdcoloring);CHKERRQ(ierr); ierr = PetscObjectDereference((PetscObject)fdcoloring);CHKERRQ(ierr); /* The following breaks an ugly reference counting loop that deserves a paragraph. MatFDColoringApply() will call * VecDuplicate() with the state Vec and store inside the MatFDColoring. This Vec will duplicate the Vec, but the * MatFDColoring is composed with the DM. We dereference the DM here so that the reference count will eventually * drop to 0. Note the code in DMDestroy() that exits early for a negative reference count. That code path will be * taken when the PetscObjectList for the Vec inside MatFDColoring is destroyed. */ ierr = PetscObjectDereference((PetscObject)dm);CHKERRQ(ierr); } ierr = MatFDColoringApply(B,fdcoloring,X,snes);CHKERRQ(ierr); } /* 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); }
PetscErrorCode FormFunctionMatlab(SNES snes,Vec X,Vec F,void *ptr) { AppCtx *user = (AppCtx*)ptr; PetscErrorCode ierr; PetscInt Mx,My; PetscReal lambda,hx,hy; Vec localX,localF; MPI_Comm comm; DM da; PetscFunctionBeginUser; ierr = SNESGetDM(snes,&da);CHKERRQ(ierr); ierr = DMGetLocalVector(da,&localX);CHKERRQ(ierr); ierr = DMGetLocalVector(da,&localF);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)localX,"localX");CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)localF,"localF");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); lambda = user->param; hx = 1.0/(PetscReal)(Mx-1); hy = 1.0/(PetscReal)(My-1); ierr = PetscObjectGetComm((PetscObject)snes,&comm);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,localX);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(da,X,INSERT_VALUES,localX);CHKERRQ(ierr); ierr = PetscMatlabEnginePut(PETSC_MATLAB_ENGINE_(comm),(PetscObject)localX);CHKERRQ(ierr); ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_(comm),"localF=ex5m(localX,%18.16e,%18.16e,%18.16e)",hx,hy,lambda);CHKERRQ(ierr); ierr = PetscMatlabEngineGet(PETSC_MATLAB_ENGINE_(comm),(PetscObject)localF);CHKERRQ(ierr); /* Insert values into global vector */ ierr = DMLocalToGlobalBegin(da,localF,INSERT_VALUES,F);CHKERRQ(ierr); ierr = DMLocalToGlobalEnd(da,localF,INSERT_VALUES,F);CHKERRQ(ierr); ierr = DMRestoreLocalVector(da,&localX);CHKERRQ(ierr); ierr = DMRestoreLocalVector(da,&localF);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); }
/* no discretization is given so DMGetNumFields yields 0 */ static PetscErrorCode test0(DM dm, AppCtx *options) { Vec locX; PetscErrorCode ierr; PetscFunctionBegin; ierr = DMGetLocalVector(dm, &locX);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &locX);CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc, char **argv) { DM dm, subdm, auxdm; Vec la; AppCtx user; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; ierr = ProcessOptions(&user);CHKERRQ(ierr); ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr); ierr = SetupDiscretization(dm, user.dim, user.cellSimplex, &user);CHKERRQ(ierr); /* Volumetric Mesh Projection */ ierr = TestFunctionProjection(dm, NULL, NULL, NULL, "Volumetric Primary", &user);CHKERRQ(ierr); ierr = TestFieldProjection(dm, NULL, NULL, NULL, "Volumetric Primary", &user);CHKERRQ(ierr); if (user.auxfield) { /* Volumetric Mesh Projection with Volumetric Data */ ierr = CreateAuxiliaryData(dm, &auxdm, &la, &user);CHKERRQ(ierr); ierr = TestFunctionProjection(dm, auxdm, NULL, la, "Volumetric Primary and Volumetric Auxiliary", &user);CHKERRQ(ierr); ierr = TestFieldProjection(dm, auxdm, NULL, la, "Volumetric Primary and Volumetric Auxiliary", &user);CHKERRQ(ierr); ierr = VecDestroy(&la);CHKERRQ(ierr); /* Update of Volumetric Auxiliary Data with primary Volumetric Data */ ierr = DMGetLocalVector(dm, &la);CHKERRQ(ierr); ierr = VecSet(la, 1.0);CHKERRQ(ierr); ierr = TestFieldProjection(auxdm, dm, NULL, la, "Volumetric Auxiliary Update with Volumetric Primary", &user);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &la);CHKERRQ(ierr); ierr = DMDestroy(&auxdm);CHKERRQ(ierr); } if (user.submesh) { DMLabel bdLabel; /* Boundary Mesh Projection */ ierr = CreateBoundaryMesh(dm, &bdLabel, &subdm, &user);CHKERRQ(ierr); ierr = TestFunctionProjection(subdm, NULL, NULL, NULL, "Boundary Primary", &user);CHKERRQ(ierr); ierr = TestFieldProjection(subdm, NULL, NULL, NULL, "Boundary Primary", &user);CHKERRQ(ierr); if (user.auxfield) { /* Boundary Mesh Projection with Boundary Data */ ierr = CreateAuxiliaryData(subdm, &auxdm, &la, &user);CHKERRQ(ierr); ierr = TestFunctionProjection(subdm, auxdm, NULL, la, "Boundary Primary and Boundary Auxiliary", &user);CHKERRQ(ierr); ierr = TestFieldProjection(subdm, auxdm, NULL, la, "Boundary Primary and Boundary Auxiliary", &user);CHKERRQ(ierr); ierr = VecDestroy(&la);CHKERRQ(ierr); ierr = DMDestroy(&auxdm);CHKERRQ(ierr); /* Volumetric Mesh Projection with Boundary Data */ ierr = CreateAuxiliaryData(subdm, &auxdm, &la, &user);CHKERRQ(ierr); ierr = TestFunctionProjection(dm, auxdm, bdLabel, la, "Volumetric Primary and Boundary Auxiliary", &user);CHKERRQ(ierr); ierr = TestFieldProjection(dm, auxdm, bdLabel, la, "Volumetric Primary and Boundary Auxiliary", &user);CHKERRQ(ierr); ierr = VecDestroy(&la);CHKERRQ(ierr); ierr = DMDestroy(&auxdm);CHKERRQ(ierr); } ierr = DMLabelDestroy(&bdLabel);CHKERRQ(ierr); ierr = DMDestroy(&subdm);CHKERRQ(ierr); } ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
/* no discretization is given so DMGetNumFields and PetscDSGetTotalDimension yield 0 */ static PetscErrorCode test1(DM dm, AppCtx *options) { IS cells; Vec locX, locX_t, locA; PetscScalar *u, *u_t, *a; PetscErrorCode ierr; PetscFunctionBegin; ierr = ISCreateStride(PETSC_COMM_SELF, 0, 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); }
/* 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 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); }
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); }