static char help[] = "Second Order TVD Finite Volume Example.\n"; /*F We use a second order TVD finite volume method to evolve a system of PDEs. Our simple upwinded residual evaluation loops over all mesh faces and uses a Riemann solver to produce the flux given the face geometry and cell values, $$f_i = \mathrm{riemann}(\mathrm{phys}, p_\mathrm{centroid}, \hat n, x^L, x^R)$$ and then update the cell values given the cell volume. \begin{eqnarray} f^L_i &-=& \frac{f_i}{vol^L} \\ f^R_i &+=& \frac{f_i}{vol^R} \end{eqnarray} As an example, we can consider the shallow water wave equation, \begin{eqnarray} h_t + \nabla\cdot \left( uh \right) &=& 0 \\ (uh)_t + \nabla\cdot \left( u\otimes uh + \frac{g h^2}{2} I \right) &=& 0 \end{eqnarray} where $h$ is wave height, $u$ is wave velocity, and $g$ is the acceleration due to gravity. A representative Riemann solver for the shallow water equations is given in the PhysicsRiemann_SW() function, \begin{eqnarray} f^{L,R}_h &=& uh^{L,R} \cdot \hat n \\ f^{L,R}_{uh} &=& \frac{f^{L,R}_h}{h^{L,R}} uh^{L,R} + g (h^{L,R})^2 \hat n \\ c^{L,R} &=& \sqrt{g h^{L,R}} \\ s &=& \max\left( \left|\frac{uh^L \cdot \hat n}{h^L}\right| + c^L, \left|\frac{uh^R \cdot \hat n}{h^R}\right| + c^R \right) \\ f_i &=& \frac{A_\mathrm{face}}{2} \left( f^L_i + f^R_i + s \left( x^L_i - x^R_i \right) \right) \end{eqnarray} where $c$ is the local gravity wave speed and $f_i$ is a Rusanov flux. The more sophisticated residual evaluation in RHSFunctionLocal_LS() uses a least-squares fit to a quadratic polynomial over a neighborhood of the given element. The mesh is read in from an ExodusII file, usually generated by Cubit. F*/ #include #include #include #include #include /* For SplitFaces() */ #define DIM 2 /* Geometric dimension */ #define ALEN(a) (sizeof(a)/sizeof((a)[0])) static PetscFunctionList PhysicsList, PhysicsRiemannList_SW; /* Represents continuum physical equations. */ typedef struct _n_Physics *Physics; /* Physical model includes boundary conditions, initial conditions, and functionals of interest. It is * discretization-independent, but its members depend on the scenario being solved. */ typedef struct _n_Model *Model; /* 'User' implements a discretization of a continuous model. */ typedef struct _n_User *User; typedef PetscErrorCode (*SolutionFunction)(Model,PetscReal,const PetscReal*,PetscScalar*,void*); typedef PetscErrorCode (*SetUpBCFunction)(DM,PetscDS,Physics); typedef PetscErrorCode (*FunctionalFunction)(Model,PetscReal,const PetscReal*,const PetscScalar*,PetscReal*,void*); typedef PetscErrorCode (*SetupFields)(Physics,PetscSection); static PetscErrorCode ModelSolutionSetDefault(Model,SolutionFunction,void*); static PetscErrorCode ModelFunctionalRegister(Model,const char*,PetscInt*,FunctionalFunction,void*); static PetscErrorCode OutputVTK(DM,const char*,PetscViewer*); struct FieldDescription { const char *name; PetscInt dof; }; typedef struct _n_FunctionalLink *FunctionalLink; struct _n_FunctionalLink { char *name; FunctionalFunction func; void *ctx; PetscInt offset; FunctionalLink next; }; struct _n_Physics { PetscRiemannFunc riemann; PetscInt dof; /* number of degrees of freedom per cell */ PetscReal maxspeed; /* kludge to pick initial time step, need to add monitoring and step control */ void *data; PetscInt nfields; const struct FieldDescription *field_desc; }; struct _n_Model { MPI_Comm comm; /* Does not do collective communicaton, but some error conditions can be collective */ Physics physics; FunctionalLink functionalRegistry; PetscInt maxComputed; PetscInt numMonitored; FunctionalLink *functionalMonitored; PetscInt numCall; FunctionalLink *functionalCall; SolutionFunction solution; SetUpBCFunction setupbc; void *solutionctx; PetscReal maxspeed; /* estimate of global maximum speed (for CFL calculation) */ PetscReal bounds[2*DIM]; DMBoundaryType bcs[3]; PetscErrorCode (*errorIndicator)(PetscInt, PetscReal, PetscInt, const PetscScalar[], const PetscScalar[], PetscReal *, void *); void *errorCtx; }; struct _n_User { PetscInt numSplitFaces; PetscInt vtkInterval; /* For monitor */ char outputBasename[PETSC_MAX_PATH_LEN]; /* Basename for output files */ PetscInt monitorStepOffset; Model model; PetscBool vtkmon; }; PETSC_STATIC_INLINE PetscReal DotDIMReal(const PetscReal *x,const PetscReal *y) { PetscInt i; PetscReal prod=0.0; for (i=0; idata; PetscFunctionBeginUser; xG[0] = advect->inflowState; PetscFunctionReturn(0); } static PetscErrorCode PhysicsBoundary_Advect_Outflow(PetscReal time, const PetscReal *c, const PetscReal *n, const PetscScalar *xI, PetscScalar *xG, void *ctx) { PetscFunctionBeginUser; xG[0] = xI[0]; PetscFunctionReturn(0); } static void PhysicsRiemann_Advect(PetscInt dim, PetscInt Nf, const PetscReal *qp, const PetscReal *n, const PetscScalar *xL, const PetscScalar *xR, PetscInt numConstants, const PetscScalar constants[], PetscScalar *flux, Physics phys) { Physics_Advect *advect = (Physics_Advect*)phys->data; PetscReal wind[DIM],wn; switch (advect->soltype) { case ADVECT_SOL_TILTED: { Physics_Advect_Tilted *tilted = &advect->sol.tilted; wind[0] = tilted->wind[0]; wind[1] = tilted->wind[1]; } break; case ADVECT_SOL_BUMP: wind[0] = -qp[1]; wind[1] = qp[0]; break; case ADVECT_SOL_BUMP_CAVITY: { PetscInt i; PetscReal comp2[3] = {0.,0.,0.}, rad2; rad2 = 0.; for (i = 0; i < dim; i++) { comp2[i] = qp[i] * qp[i]; rad2 += comp2[i]; } wind[0] = -qp[1]; wind[1] = qp[0]; if (rad2 > 1.) { PetscInt maxI = 0; PetscReal maxComp2 = comp2[0]; for (i = 1; i < dim; i++) { if (comp2[i] > maxComp2) { maxI = i; maxComp2 = comp2[i]; } } wind[maxI] = 0.; } } break; default: { PetscInt i; for (i = 0; i < DIM; ++i) wind[i] = 0.0; } /* default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for solution type %s",AdvectSolBumpTypes[advect->soltype]); */ } wn = Dot2Real(wind, n); flux[0] = (wn > 0 ? xL[0] : xR[0]) * wn; } static PetscErrorCode PhysicsSolution_Advect(Model mod,PetscReal time,const PetscReal *x,PetscScalar *u,void *ctx) { Physics phys = (Physics)ctx; Physics_Advect *advect = (Physics_Advect*)phys->data; PetscFunctionBeginUser; switch (advect->soltype) { case ADVECT_SOL_TILTED: { PetscReal x0[DIM]; Physics_Advect_Tilted *tilted = &advect->sol.tilted; Waxpy2Real(-time,tilted->wind,x,x0); if (x0[1] > 0) u[0] = 1.*x[0] + 3.*x[1]; else u[0] = advect->inflowState; } break; case ADVECT_SOL_BUMP_CAVITY: case ADVECT_SOL_BUMP: { Physics_Advect_Bump *bump = &advect->sol.bump; PetscReal x0[DIM],v[DIM],r,cost,sint; cost = PetscCosReal(time); sint = PetscSinReal(time); x0[0] = cost*x[0] + sint*x[1]; x0[1] = -sint*x[0] + cost*x[1]; Waxpy2Real(-1,bump->center,x0,v); r = Norm2Real(v); switch (bump->type) { case ADVECT_SOL_BUMP_CONE: u[0] = PetscMax(1 - r/bump->radius,0); break; case ADVECT_SOL_BUMP_COS: u[0] = 0.5 + 0.5*PetscCosReal(PetscMin(r/bump->radius,1)*PETSC_PI); break; } } break; default: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unknown solution type"); } PetscFunctionReturn(0); } static PetscErrorCode PhysicsFunctional_Advect(Model mod,PetscReal time,const PetscReal *x,const PetscScalar *y,PetscReal *f,void *ctx) { Physics phys = (Physics)ctx; Physics_Advect *advect = (Physics_Advect*)phys->data; PetscScalar yexact[1] = {0.0}; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = PhysicsSolution_Advect(mod,time,x,yexact,phys);CHKERRQ(ierr); f[advect->functional.Solution] = PetscRealPart(y[0]); f[advect->functional.Error] = PetscAbsScalar(y[0]-yexact[0]); PetscFunctionReturn(0); } static PetscErrorCode SetUpBC_Advect(DM dm, PetscDS prob, Physics phys) { PetscErrorCode ierr; const PetscInt inflowids[] = {100,200,300},outflowids[] = {101}; DMLabel label; PetscFunctionBeginUser; /* Register "canned" boundary conditions and defaults for where to apply. */ ierr = DMGetLabel(dm, "Face Sets", &label);CHKERRQ(ierr); ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "inflow", label, ALEN(inflowids), inflowids, 0, 0, NULL, (void (*)(void)) PhysicsBoundary_Advect_Inflow, NULL, phys, NULL);CHKERRQ(ierr); ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "outflow", label, ALEN(outflowids), outflowids, 0, 0, NULL, (void (*)(void)) PhysicsBoundary_Advect_Outflow, NULL, phys, NULL);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode PhysicsCreate_Advect(Model mod,Physics phys,PetscOptionItems *PetscOptionsObject) { Physics_Advect *advect; PetscErrorCode ierr; PetscFunctionBeginUser; phys->field_desc = PhysicsFields_Advect; phys->riemann = (PetscRiemannFunc)PhysicsRiemann_Advect; ierr = PetscNew(&advect);CHKERRQ(ierr); phys->data = advect; mod->setupbc = SetUpBC_Advect; ierr = PetscOptionsHead(PetscOptionsObject,"Advect options");CHKERRQ(ierr); { PetscInt two = 2,dof = 1; advect->soltype = ADVECT_SOL_TILTED; ierr = PetscOptionsEnum("-advect_sol_type","solution type","",AdvectSolTypes,(PetscEnum)advect->soltype,(PetscEnum*)&advect->soltype,NULL);CHKERRQ(ierr); switch (advect->soltype) { case ADVECT_SOL_TILTED: { Physics_Advect_Tilted *tilted = &advect->sol.tilted; two = 2; tilted->wind[0] = 0.0; tilted->wind[1] = 1.0; ierr = PetscOptionsRealArray("-advect_tilted_wind","background wind vx,vy","",tilted->wind,&two,NULL);CHKERRQ(ierr); advect->inflowState = -2.0; ierr = PetscOptionsRealArray("-advect_tilted_inflow","Inflow state","",&advect->inflowState,&dof,NULL);CHKERRQ(ierr); phys->maxspeed = Norm2Real(tilted->wind); } break; case ADVECT_SOL_BUMP_CAVITY: case ADVECT_SOL_BUMP: { Physics_Advect_Bump *bump = &advect->sol.bump; two = 2; bump->center[0] = 2.; bump->center[1] = 0.; ierr = PetscOptionsRealArray("-advect_bump_center","location of center of bump x,y","",bump->center,&two,NULL);CHKERRQ(ierr); bump->radius = 0.9; ierr = PetscOptionsReal("-advect_bump_radius","radius of bump","",bump->radius,&bump->radius,NULL);CHKERRQ(ierr); bump->type = ADVECT_SOL_BUMP_CONE; ierr = PetscOptionsEnum("-advect_bump_type","type of bump","",AdvectSolBumpTypes,(PetscEnum)bump->type,(PetscEnum*)&bump->type,NULL);CHKERRQ(ierr); phys->maxspeed = 3.; /* radius of mesh, kludge */ } break; } } ierr = PetscOptionsTail();CHKERRQ(ierr); /* Initial/transient solution with default boundary conditions */ ierr = ModelSolutionSetDefault(mod,PhysicsSolution_Advect,phys);CHKERRQ(ierr); /* Register "canned" functionals */ ierr = ModelFunctionalRegister(mod,"Solution",&advect->functional.Solution,PhysicsFunctional_Advect,phys);CHKERRQ(ierr); ierr = ModelFunctionalRegister(mod,"Error",&advect->functional.Error,PhysicsFunctional_Advect,phys);CHKERRQ(ierr); mod->bcs[0] = mod->bcs[1] = mod->bcs[2] = DM_BOUNDARY_GHOSTED; PetscFunctionReturn(0); } /******************* Shallow Water ********************/ typedef struct { PetscReal gravity; PetscReal boundaryHeight; struct { PetscInt Height; PetscInt Speed; PetscInt Energy; } functional; } Physics_SW; typedef struct { PetscReal h; PetscReal uh[DIM]; } SWNode; typedef union { SWNode swnode; PetscReal vals[DIM+1]; } SWNodeUnion; static const struct FieldDescription PhysicsFields_SW[] = {{"Height",1},{"Momentum",DIM},{NULL,0}}; /* * h_t + div(uh) = 0 * (uh)_t + div (u\otimes uh + g h^2 / 2 I) = 0 * * */ static PetscErrorCode SWFlux(Physics phys,const PetscReal *n,const SWNode *x,SWNode *f) { Physics_SW *sw = (Physics_SW*)phys->data; PetscReal uhn,u[DIM]; PetscInt i; PetscFunctionBeginUser; Scale2Real(1./x->h,x->uh,u); uhn = x->uh[0] * n[0] + x->uh[1] * n[1]; f->h = uhn; for (i=0; iuh[i] = u[i] * uhn + sw->gravity * PetscSqr(x->h) * n[i]; PetscFunctionReturn(0); } static PetscErrorCode PhysicsBoundary_SW_Wall(PetscReal time, const PetscReal *c, const PetscReal *n, const PetscScalar *xI, PetscScalar *xG, void *ctx) { PetscFunctionBeginUser; xG[0] = xI[0]; xG[1] = -xI[1]; xG[2] = -xI[2]; PetscFunctionReturn(0); } static void PhysicsRiemann_SW_HLL(PetscInt dim, PetscInt Nf, const PetscReal *qp, const PetscReal *n, const PetscScalar *xL, const PetscScalar *xR, PetscInt numConstants, const PetscScalar constants[], PetscScalar *flux, Physics phys) { Physics_SW *sw = (Physics_SW *) phys->data; PetscReal aL, aR; PetscReal nn[DIM]; #if !defined(PETSC_USE_COMPLEX) const SWNode *uL = (const SWNode *) xL, *uR = (const SWNode *) xR; #else SWNodeUnion uLreal, uRreal; const SWNode *uL = &uLreal.swnode; const SWNode *uR = &uRreal.swnode; #endif SWNodeUnion fL, fR; PetscInt i; PetscReal zero = 0.; #if defined(PETSC_USE_COMPLEX) uLreal.swnode.h = 0; uRreal.swnode.h = 0; for (i = 0; i < 1+dim; i++) uLreal.vals[i] = PetscRealPart(xL[i]); for (i = 0; i < 1+dim; i++) uRreal.vals[i] = PetscRealPart(xR[i]); #endif if (uL->h <= 0 || uR->h <= 0) { for (i = 0; i < 1 + dim; i++) flux[i] = zero; return; } /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */ nn[0] = n[0]; nn[1] = n[1]; Normalize2Real(nn); SWFlux(phys, nn, uL, &(fL.swnode)); SWFlux(phys, nn, uR, &(fR.swnode)); /* gravity wave speed */ aL = PetscSqrtReal(sw->gravity * uL->h); aR = PetscSqrtReal(sw->gravity * uR->h); // Defining u_tilda and v_tilda as u and v PetscReal u_L, u_R; u_L = Dot2Real(uL->uh,nn)/uL->h; u_R = Dot2Real(uR->uh,nn)/uR->h; PetscReal sL, sR; sL = PetscMin(u_L - aL, u_R - aR); sR = PetscMax(u_L + aL, u_R + aR); if (sL > zero) { for (i = 0; i < dim + 1; i++) { flux[i] = fL.vals[i] * Norm2Real(n); } } else if (sR < zero) { for (i = 0; i < dim + 1; i++) { flux[i] = fR.vals[i] * Norm2Real(n); } } else { for (i = 0; i < dim + 1; i++) { flux[i] = ((sR * fL.vals[i] - sL * fR.vals[i] + sR * sL * (xR[i] - xL[i])) / (sR - sL)) * Norm2Real(n); } } } static void PhysicsRiemann_SW_Rusanov(PetscInt dim, PetscInt Nf, const PetscReal *qp, const PetscReal *n, const PetscScalar *xL, const PetscScalar *xR, PetscInt numConstants, const PetscScalar constants[], PetscScalar *flux, Physics phys) { Physics_SW *sw = (Physics_SW*)phys->data; PetscReal cL,cR,speed; PetscReal nn[DIM]; #if !defined(PETSC_USE_COMPLEX) const SWNode *uL = (const SWNode*)xL,*uR = (const SWNode*)xR; #else SWNodeUnion uLreal, uRreal; const SWNode *uL = &uLreal.swnode; const SWNode *uR = &uRreal.swnode; #endif SWNodeUnion fL,fR; PetscInt i; PetscReal zero=0.; #if defined(PETSC_USE_COMPLEX) uLreal.swnode.h = 0; uRreal.swnode.h = 0; for (i = 0; i < 1+dim; i++) uLreal.vals[i] = PetscRealPart(xL[i]); for (i = 0; i < 1+dim; i++) uRreal.vals[i] = PetscRealPart(xR[i]); #endif if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = zero/zero; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */ nn[0] = n[0]; nn[1] = n[1]; Normalize2Real(nn); SWFlux(phys,nn,uL,&(fL.swnode)); SWFlux(phys,nn,uR,&(fR.swnode)); cL = PetscSqrtReal(sw->gravity*uL->h); cR = PetscSqrtReal(sw->gravity*uR->h); /* gravity wave speed */ speed = PetscMax(PetscAbsReal(Dot2Real(uL->uh,nn)/uL->h) + cL,PetscAbsReal(Dot2Real(uR->uh,nn)/uR->h) + cR); for (i=0; i<1+dim; i++) flux[i] = (0.5*(fL.vals[i] + fR.vals[i]) + 0.5*speed*(xL[i] - xR[i])) * Norm2Real(n); } static PetscErrorCode PhysicsSolution_SW(Model mod,PetscReal time,const PetscReal *x,PetscScalar *u,void *ctx) { PetscReal dx[2],r,sigma; PetscFunctionBeginUser; if (time != 0.0) SETERRQ1(mod->comm,PETSC_ERR_SUP,"No solution known for time %g",(double)time); dx[0] = x[0] - 1.5; dx[1] = x[1] - 1.0; r = Norm2Real(dx); sigma = 0.5; u[0] = 1 + 2*PetscExpReal(-PetscSqr(r)/(2*PetscSqr(sigma))); u[1] = 0.0; u[2] = 0.0; PetscFunctionReturn(0); } static PetscErrorCode PhysicsFunctional_SW(Model mod,PetscReal time,const PetscReal *coord,const PetscScalar *xx,PetscReal *f,void *ctx) { Physics phys = (Physics)ctx; Physics_SW *sw = (Physics_SW*)phys->data; const SWNode *x = (const SWNode*)xx; PetscReal u[2]; PetscReal h; PetscFunctionBeginUser; h = x->h; Scale2Real(1./x->h,x->uh,u); f[sw->functional.Height] = h; f[sw->functional.Speed] = Norm2Real(u) + PetscSqrtReal(sw->gravity*h); f[sw->functional.Energy] = 0.5*(Dot2Real(x->uh,u) + sw->gravity*PetscSqr(h)); PetscFunctionReturn(0); } static PetscErrorCode SetUpBC_SW(DM dm, PetscDS prob,Physics phys) { PetscErrorCode ierr; const PetscInt wallids[] = {100,101,200,300}; DMLabel label; PetscFunctionBeginUser; ierr = DMGetLabel(dm, "Face Sets", &label);CHKERRQ(ierr); ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "wall", label, ALEN(wallids), wallids, 0, 0, NULL, (void (*)(void)) PhysicsBoundary_SW_Wall, NULL, phys, NULL);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode PhysicsCreate_SW(Model mod,Physics phys,PetscOptionItems *PetscOptionsObject) { Physics_SW *sw; char sw_riemann[64] = "rusanov"; PetscErrorCode ierr; PetscFunctionBeginUser; phys->field_desc = PhysicsFields_SW; ierr = PetscNew(&sw);CHKERRQ(ierr); phys->data = sw; mod->setupbc = SetUpBC_SW; PetscFunctionListAdd(&PhysicsRiemannList_SW, "rusanov", PhysicsRiemann_SW_Rusanov); PetscFunctionListAdd(&PhysicsRiemannList_SW, "hll", PhysicsRiemann_SW_HLL); ierr = PetscOptionsHead(PetscOptionsObject,"SW options");CHKERRQ(ierr); { void (*PhysicsRiemann_SW)(PetscInt, PetscInt, const PetscReal *, const PetscReal *, const PetscScalar *, const PetscScalar *, PetscInt, const PetscScalar, PetscScalar *, Physics); sw->gravity = 1.0; ierr = PetscOptionsReal("-sw_gravity","Gravitational constant","",sw->gravity,&sw->gravity,NULL);CHKERRQ(ierr); ierr = PetscOptionsFList("-sw_riemann","Riemann solver","",PhysicsRiemannList_SW,sw_riemann,sw_riemann,sizeof sw_riemann,NULL);CHKERRQ(ierr); ierr = PetscFunctionListFind(PhysicsRiemannList_SW,sw_riemann,&PhysicsRiemann_SW);CHKERRQ(ierr); phys->riemann = (PetscRiemannFunc) PhysicsRiemann_SW; } ierr = PetscOptionsTail();CHKERRQ(ierr); phys->maxspeed = PetscSqrtReal(2.0*sw->gravity); /* Mach 1 for depth of 2 */ ierr = ModelSolutionSetDefault(mod,PhysicsSolution_SW,phys);CHKERRQ(ierr); ierr = ModelFunctionalRegister(mod,"Height",&sw->functional.Height,PhysicsFunctional_SW,phys);CHKERRQ(ierr); ierr = ModelFunctionalRegister(mod,"Speed",&sw->functional.Speed,PhysicsFunctional_SW,phys);CHKERRQ(ierr); ierr = ModelFunctionalRegister(mod,"Energy",&sw->functional.Energy,PhysicsFunctional_SW,phys);CHKERRQ(ierr); mod->bcs[0] = mod->bcs[1] = mod->bcs[2] = DM_BOUNDARY_GHOSTED; PetscFunctionReturn(0); } /******************* Euler Density Shock (EULER_IV_SHOCK,EULER_SS_SHOCK) ********************/ /* An initial-value and self-similar solutions of the compressible Euler equations */ /* Ravi Samtaney and D. I. Pullin */ /* Phys. Fluids 8, 2650 (1996); http://dx.doi.org/10.1063/1.869050 */ typedef enum {EULER_PAR_GAMMA,EULER_PAR_RHOR,EULER_PAR_AMACH,EULER_PAR_ITANA,EULER_PAR_SIZE} EulerParamIdx; typedef enum {EULER_IV_SHOCK,EULER_SS_SHOCK,EULER_SHOCK_TUBE,EULER_LINEAR_WAVE} EulerType; typedef struct { PetscReal r; PetscReal ru[DIM]; PetscReal E; } EulerNode; typedef union { EulerNode eulernode; PetscReal vals[DIM+2]; } EulerNodeUnion; typedef PetscErrorCode (*EquationOfState)(const PetscReal*, const EulerNode*, PetscReal*); typedef struct { EulerType type; PetscReal pars[EULER_PAR_SIZE]; EquationOfState sound; struct { PetscInt Density; PetscInt Momentum; PetscInt Energy; PetscInt Pressure; PetscInt Speed; } monitor; } Physics_Euler; static const struct FieldDescription PhysicsFields_Euler[] = {{"Density",1},{"Momentum",DIM},{"Energy",1},{NULL,0}}; /* initial condition */ int initLinearWave(EulerNode *ux, const PetscReal gamma, const PetscReal coord[], const PetscReal Lx); static PetscErrorCode PhysicsSolution_Euler(Model mod, PetscReal time, const PetscReal *x, PetscScalar *u, void *ctx) { PetscInt i; Physics phys = (Physics)ctx; Physics_Euler *eu = (Physics_Euler*)phys->data; EulerNode *uu = (EulerNode*)u; PetscReal p0,gamma,c; PetscFunctionBeginUser; if (time != 0.0) SETERRQ1(mod->comm,PETSC_ERR_SUP,"No solution known for time %g",(double)time); for (i=0; iru[i] = 0.0; /* zero out initial velocity */ /* set E and rho */ gamma = eu->pars[EULER_PAR_GAMMA]; if (eu->type==EULER_IV_SHOCK || eu->type==EULER_SS_SHOCK) { /******************* Euler Density Shock ********************/ /* On initial-value and self-similar solutions of the compressible Euler equations */ /* Ravi Samtaney and D. I. Pullin */ /* Phys. Fluids 8, 2650 (1996); http://dx.doi.org/10.1063/1.869050 */ /* initial conditions 1: left of shock, 0: left of discontinuity 2: right of discontinuity, */ p0 = 1.; if (x[0] < 0.0 + x[1]*eu->pars[EULER_PAR_ITANA]) { if (x[0] < mod->bounds[0]*0.5) { /* left of shock (1) */ PetscReal amach,rho,press,gas1,p1; amach = eu->pars[EULER_PAR_AMACH]; rho = 1.; press = p0; p1 = press*(1.0+2.0*gamma/(gamma+1.0)*(amach*amach-1.0)); gas1 = (gamma-1.0)/(gamma+1.0); uu->r = rho*(p1/press+gas1)/(gas1*p1/press+1.0); uu->ru[0] = ((uu->r - rho)*PetscSqrtReal(gamma*press/rho)*amach); uu->E = p1/(gamma-1.0) + .5/uu->r*uu->ru[0]*uu->ru[0]; } else { /* left of discontinuity (0) */ uu->r = 1.; /* rho = 1 */ uu->E = p0/(gamma-1.0); } } else { /* right of discontinuity (2) */ uu->r = eu->pars[EULER_PAR_RHOR]; uu->E = p0/(gamma-1.0); } } else if (eu->type==EULER_SHOCK_TUBE) { /* For (xx0) set (rho,u,p)=(1,0,1). Choose x0 to the midpoint of the domain in the x-direction. */ if (x[0] < 0.0) { uu->r = 8.; uu->E = 10./(gamma-1.); } else { uu->r = 1.; uu->E = 1./(gamma-1.); } } else if (eu->type==EULER_LINEAR_WAVE) { initLinearWave( uu, gamma, x, mod->bounds[1] - mod->bounds[0]); } else SETERRQ1(mod->comm,PETSC_ERR_SUP,"Unknown type %d",eu->type); /* set phys->maxspeed: (mod->maxspeed = phys->maxspeed) in main; */ eu->sound(&gamma,uu,&c); c = (uu->ru[0]/uu->r) + c; if (c > phys->maxspeed) phys->maxspeed = c; PetscFunctionReturn(0); } static PetscErrorCode Pressure_PG(const PetscReal gamma,const EulerNode *x,PetscReal *p) { PetscReal ru2; PetscFunctionBeginUser; ru2 = DotDIMReal(x->ru,x->ru); (*p)=(x->E - 0.5*ru2/x->r)*(gamma - 1.0); /* (E - rho V^2/2)(gamma-1) = e rho (gamma-1) */ PetscFunctionReturn(0); } static PetscErrorCode SpeedOfSound_PG(const PetscReal *gamma, const EulerNode *x, PetscReal *c) { PetscReal p; PetscFunctionBeginUser; Pressure_PG(*gamma,x,&p); if (p<0.) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"negative pressure time %g -- NEED TO FIX!!!!!!",(double) p); /* pars[EULER_PAR_GAMMA] = heat capacity ratio */ (*c)=PetscSqrtReal(*gamma * p / x->r); PetscFunctionReturn(0); } /* * x = (rho,rho*(u_1),...,rho*e)^T * x_t+div(f_1(x))+...+div(f_DIM(x)) = 0 * * f_i(x) = u_i*x+(0,0,...,p,...,p*u_i)^T * */ static PetscErrorCode EulerFlux(Physics phys,const PetscReal *n,const EulerNode *x,EulerNode *f) { Physics_Euler *eu = (Physics_Euler*)phys->data; PetscReal nu,p; PetscInt i; PetscFunctionBeginUser; Pressure_PG(eu->pars[EULER_PAR_GAMMA],x,&p); nu = DotDIMReal(x->ru,n); f->r = nu; /* A rho u */ nu /= x->r; /* A u */ for (i=0; iru[i] = nu * x->ru[i] + n[i]*p; /* r u^2 + p */ f->E = nu * (x->E + p); /* u(e+p) */ PetscFunctionReturn(0); } /* PetscReal* => EulerNode* conversion */ static PetscErrorCode PhysicsBoundary_Euler_Wall(PetscReal time, const PetscReal *c, const PetscReal *n, const PetscScalar *a_xI, PetscScalar *a_xG, void *ctx) { PetscInt i; const EulerNode *xI = (const EulerNode*)a_xI; EulerNode *xG = (EulerNode*)a_xG; Physics phys = (Physics)ctx; Physics_Euler *eu = (Physics_Euler*)phys->data; PetscFunctionBeginUser; xG->r = xI->r; /* ghost cell density - same */ xG->E = xI->E; /* ghost cell energy - same */ if (n[1] != 0.) { /* top and bottom */ xG->ru[0] = xI->ru[0]; /* copy tang to wall */ xG->ru[1] = -xI->ru[1]; /* reflect perp to t/b wall */ } else { /* sides */ for (i=0; iru[i] = xI->ru[i]; /* copy */ } if (eu->type == EULER_LINEAR_WAVE) { /* debug */ #if 0 PetscPrintf(PETSC_COMM_WORLD,"%s coord=%g,%g\n",PETSC_FUNCTION_NAME,c[0],c[1]); #endif } PetscFunctionReturn(0); } int godunovflux( const PetscScalar *ul, const PetscScalar *ur, PetscScalar *flux, const PetscReal *nn, const int *ndim, const PetscReal *gamma); /* PetscReal* => EulerNode* conversion */ static void PhysicsRiemann_Euler_Godunov( PetscInt dim, PetscInt Nf, const PetscReal *qp, const PetscReal *n, const PetscScalar *xL, const PetscScalar *xR, PetscInt numConstants, const PetscScalar constants[], PetscScalar *flux, Physics phys) { Physics_Euler *eu = (Physics_Euler*)phys->data; PetscReal cL,cR,speed,velL,velR,nn[DIM],s2; PetscInt i; PetscErrorCode ierr; PetscFunctionBeginUser; for (i=0,s2=0.; isound(&eu->pars[EULER_PAR_GAMMA],uL,&cL);if (ierr) exit(13); ierr = eu->sound(&eu->pars[EULER_PAR_GAMMA],uR,&cR);if (ierr) exit(14); velL = DotDIMReal(uL->ru,nn)/uL->r; velR = DotDIMReal(uR->ru,nn)/uR->r; speed = PetscMax(velR + cR, velL + cL); for (i=0; i<2+dim; i++) flux[i] = 0.5*((fL.vals[i]+fR.vals[i]) + speed*(xL[i] - xR[i]))*s2; } else { int dim = DIM; /* int iwave = */ godunovflux(xL, xR, flux, nn, &dim, &eu->pars[EULER_PAR_GAMMA]); for (i=0; i<2+dim; i++) flux[i] *= s2; } PetscFunctionReturnVoid(); } static PetscErrorCode PhysicsFunctional_Euler(Model mod,PetscReal time,const PetscReal *coord,const PetscScalar *xx,PetscReal *f,void *ctx) { Physics phys = (Physics)ctx; Physics_Euler *eu = (Physics_Euler*)phys->data; const EulerNode *x = (const EulerNode*)xx; PetscReal p; PetscFunctionBeginUser; f[eu->monitor.Density] = x->r; f[eu->monitor.Momentum] = NormDIM(x->ru); f[eu->monitor.Energy] = x->E; f[eu->monitor.Speed] = NormDIM(x->ru)/x->r; Pressure_PG(eu->pars[EULER_PAR_GAMMA], x, &p); f[eu->monitor.Pressure] = p; PetscFunctionReturn(0); } static PetscErrorCode SetUpBC_Euler(DM dm, PetscDS prob,Physics phys) { PetscErrorCode ierr; Physics_Euler *eu = (Physics_Euler *) phys->data; DMLabel label; ierr = DMGetLabel(dm, "Face Sets", &label);CHKERRQ(ierr); if (eu->type == EULER_LINEAR_WAVE) { const PetscInt wallids[] = {100,101}; ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "wall", label, ALEN(wallids), wallids, 0, 0, NULL, (void (*)(void)) PhysicsBoundary_Euler_Wall, NULL, phys, NULL);CHKERRQ(ierr); } else { const PetscInt wallids[] = {100,101,200,300}; ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "wall", label, ALEN(wallids), wallids, 0, 0, NULL, (void (*)(void)) PhysicsBoundary_Euler_Wall, NULL, phys, NULL);CHKERRQ(ierr); } PetscFunctionReturn(0); } static PetscErrorCode PhysicsCreate_Euler(Model mod,Physics phys,PetscOptionItems *PetscOptionsObject) { Physics_Euler *eu; PetscErrorCode ierr; PetscFunctionBeginUser; phys->field_desc = PhysicsFields_Euler; phys->riemann = (PetscRiemannFunc) PhysicsRiemann_Euler_Godunov; ierr = PetscNew(&eu);CHKERRQ(ierr); phys->data = eu; mod->setupbc = SetUpBC_Euler; ierr = PetscOptionsHead(PetscOptionsObject,"Euler options");CHKERRQ(ierr); { PetscReal alpha; char type[64] = "linear_wave"; PetscBool is; mod->bcs[0] = mod->bcs[1] = mod->bcs[2] = DM_BOUNDARY_GHOSTED; eu->pars[EULER_PAR_GAMMA] = 1.4; eu->pars[EULER_PAR_AMACH] = 2.02; eu->pars[EULER_PAR_RHOR] = 3.0; eu->pars[EULER_PAR_ITANA] = 0.57735026918963; /* angle of Euler self similar (SS) shock */ ierr = PetscOptionsReal("-eu_gamma","Heat capacity ratio","",eu->pars[EULER_PAR_GAMMA],&eu->pars[EULER_PAR_GAMMA],NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-eu_amach","Shock speed (Mach)","",eu->pars[EULER_PAR_AMACH],&eu->pars[EULER_PAR_AMACH],NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-eu_rho2","Density right of discontinuity","",eu->pars[EULER_PAR_RHOR],&eu->pars[EULER_PAR_RHOR],NULL);CHKERRQ(ierr); alpha = 60.; ierr = PetscOptionsReal("-eu_alpha","Angle of discontinuity","",alpha,&alpha,NULL);CHKERRQ(ierr); if (alpha<=0. || alpha>90.) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Alpha bust be > 0 and <= 90 (%g)",alpha); eu->pars[EULER_PAR_ITANA] = 1./PetscTanReal( alpha * PETSC_PI / 180.0); ierr = PetscOptionsString("-eu_type","Type of Euler test","",type,type,sizeof(type),NULL);CHKERRQ(ierr); ierr = PetscStrcmp(type,"linear_wave", &is);CHKERRQ(ierr); if (is) { eu->type = EULER_LINEAR_WAVE; mod->bcs[0] = mod->bcs[1] = mod->bcs[2] = DM_BOUNDARY_PERIODIC; mod->bcs[1] = DM_BOUNDARY_GHOSTED; /* debug */ ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"linear_wave");CHKERRQ(ierr); } else { if (DIM != 2) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"DIM must be 2 unless linear wave test %s",type); ierr = PetscStrcmp(type,"iv_shock", &is);CHKERRQ(ierr); if (is) { eu->type = EULER_IV_SHOCK; ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"iv_shock");CHKERRQ(ierr); } else { ierr = PetscStrcmp(type,"ss_shock", &is);CHKERRQ(ierr); if (is) { eu->type = EULER_SS_SHOCK; ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"ss_shock");CHKERRQ(ierr); } else { ierr = PetscStrcmp(type,"shock_tube", &is);CHKERRQ(ierr); if (is) eu->type = EULER_SHOCK_TUBE; else SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Unknown Euler type %s",type); ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"shock_tube");CHKERRQ(ierr); } } } } ierr = PetscOptionsTail();CHKERRQ(ierr); eu->sound = SpeedOfSound_PG; phys->maxspeed = 0.; /* will get set in solution */ ierr = ModelSolutionSetDefault(mod,PhysicsSolution_Euler,phys);CHKERRQ(ierr); ierr = ModelFunctionalRegister(mod,"Speed",&eu->monitor.Speed,PhysicsFunctional_Euler,phys);CHKERRQ(ierr); ierr = ModelFunctionalRegister(mod,"Energy",&eu->monitor.Energy,PhysicsFunctional_Euler,phys);CHKERRQ(ierr); ierr = ModelFunctionalRegister(mod,"Density",&eu->monitor.Density,PhysicsFunctional_Euler,phys);CHKERRQ(ierr); ierr = ModelFunctionalRegister(mod,"Momentum",&eu->monitor.Momentum,PhysicsFunctional_Euler,phys);CHKERRQ(ierr); ierr = ModelFunctionalRegister(mod,"Pressure",&eu->monitor.Pressure,PhysicsFunctional_Euler,phys);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode ErrorIndicator_Simple(PetscInt dim, PetscReal volume, PetscInt numComps, const PetscScalar u[], const PetscScalar grad[], PetscReal *error, void *ctx) { PetscReal err = 0.; PetscInt i, j; PetscFunctionBeginUser; for (i = 0; i < numComps; i++) { for (j = 0; j < dim; j++) { err += PetscSqr(PetscRealPart(grad[i * dim + j])); } } *error = volume * err; PetscFunctionReturn(0); } PetscErrorCode ConstructCellBoundary(DM dm, User user) { const char *name = "Cell Sets"; const char *bdname = "split faces"; IS regionIS, innerIS; const PetscInt *regions, *cells; PetscInt numRegions, innerRegion, numCells, c; PetscInt cStart, cEnd, cEndInterior, fStart, fEnd; PetscBool hasLabel; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); ierr = DMPlexGetGhostCellStratum(dm, &cEndInterior, NULL);CHKERRQ(ierr); ierr = DMHasLabel(dm, name, &hasLabel);CHKERRQ(ierr); if (!hasLabel) PetscFunctionReturn(0); ierr = DMGetLabelSize(dm, name, &numRegions);CHKERRQ(ierr); if (numRegions != 2) PetscFunctionReturn(0); /* Get the inner id */ ierr = DMGetLabelIdIS(dm, name, ®ionIS);CHKERRQ(ierr); ierr = ISGetIndices(regionIS, ®ions);CHKERRQ(ierr); innerRegion = regions[0]; ierr = ISRestoreIndices(regionIS, ®ions);CHKERRQ(ierr); ierr = ISDestroy(®ionIS);CHKERRQ(ierr); /* Find the faces between cells in different regions, could call DMPlexCreateNeighborCSR() */ ierr = DMGetStratumIS(dm, name, innerRegion, &innerIS);CHKERRQ(ierr); ierr = ISGetLocalSize(innerIS, &numCells);CHKERRQ(ierr); ierr = ISGetIndices(innerIS, &cells);CHKERRQ(ierr); ierr = DMCreateLabel(dm, bdname);CHKERRQ(ierr); for (c = 0; c < numCells; ++c) { const PetscInt cell = cells[c]; const PetscInt *faces; PetscInt numFaces, f; if ((cell < cStart) || (cell >= cEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Got invalid point %d which is not a cell", cell); ierr = DMPlexGetConeSize(dm, cell, &numFaces);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr); for (f = 0; f < numFaces; ++f) { const PetscInt face = faces[f]; const PetscInt *neighbors; PetscInt nC, regionA, regionB; if ((face < fStart) || (face >= fEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Got invalid point %d which is not a face", face); ierr = DMPlexGetSupportSize(dm, face, &nC);CHKERRQ(ierr); if (nC != 2) continue; ierr = DMPlexGetSupport(dm, face, &neighbors);CHKERRQ(ierr); if ((neighbors[0] >= cEndInterior) || (neighbors[1] >= cEndInterior)) continue; if ((neighbors[0] < cStart) || (neighbors[0] >= cEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Got invalid point %d which is not a cell", neighbors[0]); if ((neighbors[1] < cStart) || (neighbors[1] >= cEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Got invalid point %d which is not a cell", neighbors[1]); ierr = DMGetLabelValue(dm, name, neighbors[0], ®ionA);CHKERRQ(ierr); ierr = DMGetLabelValue(dm, name, neighbors[1], ®ionB);CHKERRQ(ierr); if (regionA < 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid label %s: Cell %d has no value", name, neighbors[0]); if (regionB < 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid label %s: Cell %d has no value", name, neighbors[1]); if (regionA != regionB) { ierr = DMSetLabelValue(dm, bdname, faces[f], 1);CHKERRQ(ierr); } } } ierr = ISRestoreIndices(innerIS, &cells);CHKERRQ(ierr); ierr = ISDestroy(&innerIS);CHKERRQ(ierr); { DMLabel label; ierr = DMGetLabel(dm, bdname, &label);CHKERRQ(ierr); ierr = DMLabelView(label, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } PetscFunctionReturn(0); } /* Right now, I have just added duplicate faces, which see both cells. We can - Add duplicate vertices and decouple the face cones - Disconnect faces from cells across the rotation gap */ PetscErrorCode SplitFaces(DM *dmSplit, const char labelName[], User user) { DM dm = *dmSplit, sdm; PetscSF sfPoint, gsfPoint; PetscSection coordSection, newCoordSection; Vec coordinates; IS idIS; const PetscInt *ids; PetscInt *newpoints; PetscInt dim, depth, maxConeSize, maxSupportSize, numLabels, numGhostCells; PetscInt numFS, fs, pStart, pEnd, p, cEnd, cEndInterior, vStart, vEnd, v, fStart, fEnd, newf, d, l; PetscBool hasLabel; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = DMHasLabel(dm, labelName, &hasLabel);CHKERRQ(ierr); if (!hasLabel) PetscFunctionReturn(0); ierr = DMCreate(PetscObjectComm((PetscObject)dm), &sdm);CHKERRQ(ierr); ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMSetDimension(sdm, dim);CHKERRQ(ierr); ierr = DMGetLabelIdIS(dm, labelName, &idIS);CHKERRQ(ierr); ierr = ISGetLocalSize(idIS, &numFS);CHKERRQ(ierr); ierr = ISGetIndices(idIS, &ids);CHKERRQ(ierr); user->numSplitFaces = 0; for (fs = 0; fs < numFS; ++fs) { PetscInt numBdFaces; ierr = DMGetStratumSize(dm, labelName, ids[fs], &numBdFaces);CHKERRQ(ierr); user->numSplitFaces += numBdFaces; } ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); pEnd += user->numSplitFaces; ierr = DMPlexSetChart(sdm, pStart, pEnd);CHKERRQ(ierr); ierr = DMPlexGetGhostCellStratum(dm, &cEndInterior, NULL);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); numGhostCells = cEnd - cEndInterior; /* Set cone and support sizes */ ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); for (d = 0; d <= depth; ++d) { ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { PetscInt newp = p; PetscInt size; ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); ierr = DMPlexSetConeSize(sdm, newp, size);CHKERRQ(ierr); ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(sdm, newp, size);CHKERRQ(ierr); } } ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); for (fs = 0, newf = fEnd; fs < numFS; ++fs) { IS faceIS; const PetscInt *faces; PetscInt numFaces, f; ierr = DMGetStratumIS(dm, labelName, ids[fs], &faceIS);CHKERRQ(ierr); ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); for (f = 0; f < numFaces; ++f, ++newf) { PetscInt size; /* Right now I think that both faces should see both cells */ ierr = DMPlexGetConeSize(dm, faces[f], &size);CHKERRQ(ierr); ierr = DMPlexSetConeSize(sdm, newf, size);CHKERRQ(ierr); ierr = DMPlexGetSupportSize(dm, faces[f], &size);CHKERRQ(ierr); ierr = DMPlexSetSupportSize(sdm, newf, size);CHKERRQ(ierr); } ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); ierr = ISDestroy(&faceIS);CHKERRQ(ierr); } ierr = DMSetUp(sdm);CHKERRQ(ierr); /* Set cones and supports */ ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); ierr = PetscMalloc1(PetscMax(maxConeSize, maxSupportSize), &newpoints);CHKERRQ(ierr); ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); for (p = pStart; p < pEnd; ++p) { const PetscInt *points, *orientations; PetscInt size, i, newp = p; ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); ierr = DMPlexGetCone(dm, p, &points);CHKERRQ(ierr); ierr = DMPlexGetConeOrientation(dm, p, &orientations);CHKERRQ(ierr); for (i = 0; i < size; ++i) newpoints[i] = points[i]; ierr = DMPlexSetCone(sdm, newp, newpoints);CHKERRQ(ierr); ierr = DMPlexSetConeOrientation(sdm, newp, orientations);CHKERRQ(ierr); ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, p, &points);CHKERRQ(ierr); for (i = 0; i < size; ++i) newpoints[i] = points[i]; ierr = DMPlexSetSupport(sdm, newp, newpoints);CHKERRQ(ierr); } ierr = PetscFree(newpoints);CHKERRQ(ierr); for (fs = 0, newf = fEnd; fs < numFS; ++fs) { IS faceIS; const PetscInt *faces; PetscInt numFaces, f; ierr = DMGetStratumIS(dm, labelName, ids[fs], &faceIS);CHKERRQ(ierr); ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); for (f = 0; f < numFaces; ++f, ++newf) { const PetscInt *points; ierr = DMPlexGetCone(dm, faces[f], &points);CHKERRQ(ierr); ierr = DMPlexSetCone(sdm, newf, points);CHKERRQ(ierr); ierr = DMPlexGetSupport(dm, faces[f], &points);CHKERRQ(ierr); ierr = DMPlexSetSupport(sdm, newf, points);CHKERRQ(ierr); } ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); ierr = ISDestroy(&faceIS);CHKERRQ(ierr); } ierr = ISRestoreIndices(idIS, &ids);CHKERRQ(ierr); ierr = ISDestroy(&idIS);CHKERRQ(ierr); ierr = DMPlexStratify(sdm);CHKERRQ(ierr); /* Convert coordinates */ ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &newCoordSection);CHKERRQ(ierr); ierr = PetscSectionSetNumFields(newCoordSection, 1);CHKERRQ(ierr); ierr = PetscSectionSetFieldComponents(newCoordSection, 0, dim);CHKERRQ(ierr); ierr = PetscSectionSetChart(newCoordSection, vStart, vEnd);CHKERRQ(ierr); for (v = vStart; v < vEnd; ++v) { ierr = PetscSectionSetDof(newCoordSection, v, dim);CHKERRQ(ierr); ierr = PetscSectionSetFieldDof(newCoordSection, v, 0, dim);CHKERRQ(ierr); } ierr = PetscSectionSetUp(newCoordSection);CHKERRQ(ierr); ierr = DMSetCoordinateSection(sdm, PETSC_DETERMINE, newCoordSection);CHKERRQ(ierr); ierr = PetscSectionDestroy(&newCoordSection);CHKERRQ(ierr); /* relinquish our reference */ ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(sdm, coordinates);CHKERRQ(ierr); /* Convert labels */ ierr = DMGetNumLabels(dm, &numLabels);CHKERRQ(ierr); for (l = 0; l < numLabels; ++l) { const char *lname; PetscBool isDepth, isDim; ierr = DMGetLabelName(dm, l, &lname);CHKERRQ(ierr); ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); if (isDepth) continue; ierr = PetscStrcmp(lname, "dim", &isDim);CHKERRQ(ierr); if (isDim) continue; ierr = DMCreateLabel(sdm, lname);CHKERRQ(ierr); ierr = DMGetLabelIdIS(dm, lname, &idIS);CHKERRQ(ierr); ierr = ISGetLocalSize(idIS, &numFS);CHKERRQ(ierr); ierr = ISGetIndices(idIS, &ids);CHKERRQ(ierr); for (fs = 0; fs < numFS; ++fs) { IS pointIS; const PetscInt *points; PetscInt numPoints; ierr = DMGetStratumIS(dm, lname, ids[fs], &pointIS);CHKERRQ(ierr); ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr); ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); for (p = 0; p < numPoints; ++p) { PetscInt newpoint = points[p]; ierr = DMSetLabelValue(sdm, lname, newpoint, ids[fs]);CHKERRQ(ierr); } ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); ierr = ISDestroy(&pointIS);CHKERRQ(ierr); } ierr = ISRestoreIndices(idIS, &ids);CHKERRQ(ierr); ierr = ISDestroy(&idIS);CHKERRQ(ierr); } { /* Convert pointSF */ const PetscSFNode *remotePoints; PetscSFNode *gremotePoints; const PetscInt *localPoints; PetscInt *glocalPoints,*newLocation,*newRemoteLocation; PetscInt numRoots, numLeaves; PetscMPIInt size; ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size);CHKERRMPI(ierr); ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); ierr = DMGetPointSF(sdm, &gsfPoint);CHKERRQ(ierr); ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); if (numRoots >= 0) { ierr = PetscMalloc2(numRoots,&newLocation,pEnd-pStart,&newRemoteLocation);CHKERRQ(ierr); for (l=0; l= cEnd ? numGhostCells : 0); */ ierr = PetscSFBcastBegin(sfPoint, MPIU_INT, newLocation, newRemoteLocation,MPI_REPLACE);CHKERRQ(ierr); ierr = PetscSFBcastEnd(sfPoint, MPIU_INT, newLocation, newRemoteLocation,MPI_REPLACE);CHKERRQ(ierr); ierr = PetscMalloc1(numLeaves, &glocalPoints);CHKERRQ(ierr); ierr = PetscMalloc1(numLeaves, &gremotePoints);CHKERRQ(ierr); for (l = 0; l < numLeaves; ++l) { glocalPoints[l] = localPoints[l]; /* localPoints[l] >= cEnd ? localPoints[l] + numGhostCells : localPoints[l]; */ gremotePoints[l].rank = remotePoints[l].rank; gremotePoints[l].index = newRemoteLocation[localPoints[l]]; } ierr = PetscFree2(newLocation,newRemoteLocation);CHKERRQ(ierr); ierr = PetscSFSetGraph(gsfPoint, numRoots+numGhostCells, numLeaves, glocalPoints, PETSC_OWN_POINTER, gremotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); } ierr = DMDestroy(dmSplit);CHKERRQ(ierr); *dmSplit = sdm; } PetscFunctionReturn(0); } PetscErrorCode CreatePartitionVec(DM dm, DM *dmCell, Vec *partition) { PetscSF sfPoint; PetscSection coordSection; Vec coordinates; PetscSection sectionCell; PetscScalar *part; PetscInt cStart, cEnd, c; PetscMPIInt rank; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMClone(dm, dmCell);CHKERRQ(ierr); ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); ierr = DMSetPointSF(*dmCell, sfPoint);CHKERRQ(ierr); ierr = DMSetCoordinateSection(*dmCell, PETSC_DETERMINE, coordSection);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(*dmCell, coordinates);CHKERRQ(ierr); ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRMPI(ierr); ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ionCell);CHKERRQ(ierr); ierr = DMPlexGetHeightStratum(*dmCell, 0, &cStart, &cEnd);CHKERRQ(ierr); ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr); for (c = cStart; c < cEnd; ++c) { ierr = PetscSectionSetDof(sectionCell, c, 1);CHKERRQ(ierr); } ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr); ierr = DMSetLocalSection(*dmCell, sectionCell);CHKERRQ(ierr); ierr = PetscSectionDestroy(§ionCell);CHKERRQ(ierr); ierr = DMCreateLocalVector(*dmCell, partition);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)*partition, "partition");CHKERRQ(ierr); ierr = VecGetArray(*partition, &part);CHKERRQ(ierr); for (c = cStart; c < cEnd; ++c) { PetscScalar *p; ierr = DMPlexPointLocalRef(*dmCell, c, part, &p);CHKERRQ(ierr); p[0] = rank; } ierr = VecRestoreArray(*partition, &part);CHKERRQ(ierr); PetscFunctionReturn(0); } PetscErrorCode CreateMassMatrix(DM dm, Vec *massMatrix, User user) { DM plex, dmMass, dmFace, dmCell, dmCoord; PetscSection coordSection; Vec coordinates, facegeom, cellgeom; PetscSection sectionMass; PetscScalar *m; const PetscScalar *fgeom, *cgeom, *coords; PetscInt vStart, vEnd, v; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMClone(dm, &dmMass);CHKERRQ(ierr); ierr = DMSetCoordinateSection(dmMass, PETSC_DETERMINE, coordSection);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(dmMass, coordinates);CHKERRQ(ierr); ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ionMass);CHKERRQ(ierr); ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); ierr = PetscSectionSetChart(sectionMass, vStart, vEnd);CHKERRQ(ierr); for (v = vStart; v < vEnd; ++v) { PetscInt numFaces; ierr = DMPlexGetSupportSize(dmMass, v, &numFaces);CHKERRQ(ierr); ierr = PetscSectionSetDof(sectionMass, v, numFaces*numFaces);CHKERRQ(ierr); } ierr = PetscSectionSetUp(sectionMass);CHKERRQ(ierr); ierr = DMSetLocalSection(dmMass, sectionMass);CHKERRQ(ierr); ierr = PetscSectionDestroy(§ionMass);CHKERRQ(ierr); ierr = DMGetLocalVector(dmMass, massMatrix);CHKERRQ(ierr); ierr = VecGetArray(*massMatrix, &m);CHKERRQ(ierr); ierr = DMPlexGetGeometryFVM(plex, &facegeom, &cellgeom, NULL);CHKERRQ(ierr); ierr = VecGetDM(facegeom, &dmFace);CHKERRQ(ierr); ierr = VecGetArrayRead(facegeom, &fgeom);CHKERRQ(ierr); ierr = VecGetDM(cellgeom, &dmCell);CHKERRQ(ierr); ierr = VecGetArrayRead(cellgeom, &cgeom);CHKERRQ(ierr); ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr); for (v = vStart; v < vEnd; ++v) { const PetscInt *faces; PetscFVFaceGeom *fgA, *fgB, *cg; PetscScalar *vertex; PetscInt numFaces, sides[2], f, g; ierr = DMPlexPointLocalRead(dmCoord, v, coords, &vertex);CHKERRQ(ierr); ierr = DMPlexGetSupportSize(dmMass, v, &numFaces);CHKERRQ(ierr); ierr = DMPlexGetSupport(dmMass, v, &faces);CHKERRQ(ierr); for (f = 0; f < numFaces; ++f) { sides[0] = faces[f]; ierr = DMPlexPointLocalRead(dmFace, faces[f], fgeom, &fgA);CHKERRQ(ierr); for (g = 0; g < numFaces; ++g) { const PetscInt *cells = NULL; PetscReal area = 0.0; PetscInt numCells; sides[1] = faces[g]; ierr = DMPlexPointLocalRead(dmFace, faces[g], fgeom, &fgB);CHKERRQ(ierr); ierr = DMPlexGetJoin(dmMass, 2, sides, &numCells, &cells);CHKERRQ(ierr); if (numCells != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Invalid join for faces"); ierr = DMPlexPointLocalRead(dmCell, cells[0], cgeom, &cg);CHKERRQ(ierr); area += PetscAbsScalar((vertex[0] - cg->centroid[0])*(fgA->centroid[1] - cg->centroid[1]) - (vertex[1] - cg->centroid[1])*(fgA->centroid[0] - cg->centroid[0])); area += PetscAbsScalar((vertex[0] - cg->centroid[0])*(fgB->centroid[1] - cg->centroid[1]) - (vertex[1] - cg->centroid[1])*(fgB->centroid[0] - cg->centroid[0])); m[f*numFaces+g] = Dot2Real(fgA->normal, fgB->normal)*area*0.5; ierr = DMPlexRestoreJoin(dmMass, 2, sides, &numCells, &cells);CHKERRQ(ierr); } } } ierr = VecRestoreArrayRead(facegeom, &fgeom);CHKERRQ(ierr); ierr = VecRestoreArrayRead(cellgeom, &cgeom);CHKERRQ(ierr); ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr); ierr = VecRestoreArray(*massMatrix, &m);CHKERRQ(ierr); ierr = DMDestroy(&dmMass);CHKERRQ(ierr); ierr = DMDestroy(&plex);CHKERRQ(ierr); PetscFunctionReturn(0); } /* Behavior will be different for multi-physics or when using non-default boundary conditions */ static PetscErrorCode ModelSolutionSetDefault(Model mod,SolutionFunction func,void *ctx) { PetscFunctionBeginUser; mod->solution = func; mod->solutionctx = ctx; PetscFunctionReturn(0); } static PetscErrorCode ModelFunctionalRegister(Model mod,const char *name,PetscInt *offset,FunctionalFunction func,void *ctx) { PetscErrorCode ierr; FunctionalLink link,*ptr; PetscInt lastoffset = -1; PetscFunctionBeginUser; for (ptr=&mod->functionalRegistry; *ptr; ptr = &(*ptr)->next) lastoffset = (*ptr)->offset; ierr = PetscNew(&link);CHKERRQ(ierr); ierr = PetscStrallocpy(name,&link->name);CHKERRQ(ierr); link->offset = lastoffset + 1; link->func = func; link->ctx = ctx; link->next = NULL; *ptr = link; *offset = link->offset; PetscFunctionReturn(0); } static PetscErrorCode ModelFunctionalSetFromOptions(Model mod,PetscOptionItems *PetscOptionsObject) { PetscErrorCode ierr; PetscInt i,j; FunctionalLink link; char *names[256]; PetscFunctionBeginUser; mod->numMonitored = ALEN(names); ierr = PetscOptionsStringArray("-monitor","list of functionals to monitor","",names,&mod->numMonitored,NULL);CHKERRQ(ierr); /* Create list of functionals that will be computed somehow */ ierr = PetscMalloc1(mod->numMonitored,&mod->functionalMonitored);CHKERRQ(ierr); /* Create index of calls that we will have to make to compute these functionals (over-allocation in general). */ ierr = PetscMalloc1(mod->numMonitored,&mod->functionalCall);CHKERRQ(ierr); mod->numCall = 0; for (i=0; inumMonitored; i++) { for (link=mod->functionalRegistry; link; link=link->next) { PetscBool match; ierr = PetscStrcasecmp(names[i],link->name,&match);CHKERRQ(ierr); if (match) break; } if (!link) SETERRQ1(mod->comm,PETSC_ERR_USER,"No known functional '%s'",names[i]); mod->functionalMonitored[i] = link; for (j=0; jfunctionalCall[j]->func == link->func && mod->functionalCall[j]->ctx == link->ctx) goto next_name; } mod->functionalCall[mod->numCall++] = link; /* Just points to the first link using the result. There may be more results. */ next_name: ierr = PetscFree(names[i]);CHKERRQ(ierr); } /* Find out the maximum index of any functional computed by a function we will be calling (even if we are not using it) */ mod->maxComputed = -1; for (link=mod->functionalRegistry; link; link=link->next) { for (i=0; inumCall; i++) { FunctionalLink call = mod->functionalCall[i]; if (link->func == call->func && link->ctx == call->ctx) { mod->maxComputed = PetscMax(mod->maxComputed,link->offset); } } } PetscFunctionReturn(0); } static PetscErrorCode FunctionalLinkDestroy(FunctionalLink *link) { PetscErrorCode ierr; FunctionalLink l,next; PetscFunctionBeginUser; if (!link) PetscFunctionReturn(0); l = *link; *link = NULL; for (; l; l=next) { next = l->next; ierr = PetscFree(l->name);CHKERRQ(ierr); ierr = PetscFree(l);CHKERRQ(ierr); } PetscFunctionReturn(0); } /* put the solution callback into a functional callback */ static PetscErrorCode SolutionFunctional(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *modctx) { Model mod; PetscErrorCode ierr; PetscFunctionBegin; mod = (Model) modctx; ierr = (*mod->solution)(mod, time, x, u, mod->solutionctx);CHKERRQ(ierr); PetscFunctionReturn(0); } PetscErrorCode SetInitialCondition(DM dm, Vec X, User user) { PetscErrorCode (*func[1]) (PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx); void *ctx[1]; Model mod = user->model; PetscErrorCode ierr; PetscFunctionBeginUser; func[0] = SolutionFunctional; ctx[0] = (void *) mod; ierr = DMProjectFunction(dm,0.0,func,ctx,INSERT_ALL_VALUES,X);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode OutputVTK(DM dm, const char *filename, PetscViewer *viewer) { PetscErrorCode ierr; PetscFunctionBeginUser; ierr = PetscViewerCreate(PetscObjectComm((PetscObject)dm), viewer);CHKERRQ(ierr); ierr = PetscViewerSetType(*viewer, PETSCVIEWERVTK);CHKERRQ(ierr); ierr = PetscViewerFileSetName(*viewer, filename);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode MonitorVTK(TS ts,PetscInt stepnum,PetscReal time,Vec X,void *ctx) { User user = (User)ctx; DM dm, plex; PetscViewer viewer; char filename[PETSC_MAX_PATH_LEN],*ftable = NULL; PetscReal xnorm; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = PetscObjectSetName((PetscObject) X, "u");CHKERRQ(ierr); ierr = VecGetDM(X,&dm);CHKERRQ(ierr); ierr = VecNorm(X,NORM_INFINITY,&xnorm);CHKERRQ(ierr); if (stepnum >= 0) { stepnum += user->monitorStepOffset; } if (stepnum >= 0) { /* No summary for final time */ Model mod = user->model; Vec cellgeom; PetscInt c,cStart,cEnd,fcount,i; size_t ftableused,ftablealloc; const PetscScalar *cgeom,*x; DM dmCell; DMLabel vtkLabel; PetscReal *fmin,*fmax,*fintegral,*ftmp; ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); ierr = DMPlexGetGeometryFVM(plex, NULL, &cellgeom, NULL);CHKERRQ(ierr); fcount = mod->maxComputed+1; ierr = PetscMalloc4(fcount,&fmin,fcount,&fmax,fcount,&fintegral,fcount,&ftmp);CHKERRQ(ierr); for (i=0; inumCall; i++) { FunctionalLink flink = mod->functionalCall[i]; ierr = (*flink->func)(mod,time,cg->centroid,cx,ftmp,flink->ctx);CHKERRQ(ierr); } for (i=0; ivolume * ftmp[i]; } } ierr = VecRestoreArrayRead(cellgeom,&cgeom);CHKERRQ(ierr); ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr); ierr = DMDestroy(&plex);CHKERRQ(ierr); ierr = MPI_Allreduce(MPI_IN_PLACE,fmin,fcount,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)ts));CHKERRMPI(ierr); ierr = MPI_Allreduce(MPI_IN_PLACE,fmax,fcount,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)ts));CHKERRMPI(ierr); ierr = MPI_Allreduce(MPI_IN_PLACE,fintegral,fcount,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)ts));CHKERRMPI(ierr); ftablealloc = fcount * 100; ftableused = 0; ierr = PetscMalloc1(ftablealloc,&ftable);CHKERRQ(ierr); for (i=0; inumMonitored; i++) { size_t countused; char buffer[256],*p; FunctionalLink flink = mod->functionalMonitored[i]; PetscInt id = flink->offset; if (i % 3) { ierr = PetscArraycpy(buffer," ",2);CHKERRQ(ierr); p = buffer + 2; } else if (i) { char newline[] = "\n"; ierr = PetscMemcpy(buffer,newline,sizeof(newline)-1);CHKERRQ(ierr); p = buffer + sizeof(newline) - 1; } else { p = buffer; } ierr = PetscSNPrintfCount(p,sizeof buffer-(p-buffer),"%12s [%10.7g,%10.7g] int %10.7g",&countused,flink->name,(double)fmin[id],(double)fmax[id],(double)fintegral[id]);CHKERRQ(ierr); countused--; countused += p - buffer; if (countused > ftablealloc-ftableused-1) { /* reallocate */ char *ftablenew; ftablealloc = 2*ftablealloc + countused; ierr = PetscMalloc(ftablealloc,&ftablenew);CHKERRQ(ierr); ierr = PetscArraycpy(ftablenew,ftable,ftableused);CHKERRQ(ierr); ierr = PetscFree(ftable);CHKERRQ(ierr); ftable = ftablenew; } ierr = PetscArraycpy(ftable+ftableused,buffer,countused);CHKERRQ(ierr); ftableused += countused; ftable[ftableused] = 0; } ierr = PetscFree4(fmin,fmax,fintegral,ftmp);CHKERRQ(ierr); ierr = PetscPrintf(PetscObjectComm((PetscObject)ts),"% 3D time %8.4g |x| %8.4g %s\n",stepnum,(double)time,(double)xnorm,ftable ? ftable : "");CHKERRQ(ierr); ierr = PetscFree(ftable);CHKERRQ(ierr); } if (user->vtkInterval < 1) PetscFunctionReturn(0); if ((stepnum == -1) ^ (stepnum % user->vtkInterval == 0)) { if (stepnum == -1) { /* Final time is not multiple of normal time interval, write it anyway */ ierr = TSGetStepNumber(ts,&stepnum);CHKERRQ(ierr); } ierr = PetscSNPrintf(filename,sizeof filename,"%s-%03D.vtu",user->outputBasename,stepnum);CHKERRQ(ierr); ierr = OutputVTK(dm,filename,&viewer);CHKERRQ(ierr); ierr = VecView(X,viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } PetscFunctionReturn(0); } static PetscErrorCode initializeTS(DM dm, User user, TS *ts) { PetscErrorCode ierr; PetscFunctionBegin; ierr = TSCreate(PetscObjectComm((PetscObject)dm), ts);CHKERRQ(ierr); ierr = TSSetType(*ts, TSSSP);CHKERRQ(ierr); ierr = TSSetDM(*ts, dm);CHKERRQ(ierr); if (user->vtkmon) { ierr = TSMonitorSet(*ts,MonitorVTK,user,NULL);CHKERRQ(ierr); } ierr = DMTSSetBoundaryLocal(dm, DMPlexTSComputeBoundary, user);CHKERRQ(ierr); ierr = DMTSSetRHSFunctionLocal(dm, DMPlexTSComputeRHSFunctionFVM, user);CHKERRQ(ierr); ierr = TSSetMaxTime(*ts,2.0);CHKERRQ(ierr); ierr = TSSetExactFinalTime(*ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); PetscFunctionReturn(0); } static PetscErrorCode adaptToleranceFVM(PetscFV fvm, TS ts, Vec sol, VecTagger refineTag, VecTagger coarsenTag, User user, TS *tsNew, Vec *solNew) { DM dm, gradDM, plex, cellDM, adaptedDM = NULL; Vec cellGeom, faceGeom; PetscBool isForest, computeGradient; Vec grad, locGrad, locX, errVec; PetscInt cStart, cEnd, c, dim, nRefine, nCoarsen; PetscReal minMaxInd[2] = {PETSC_MAX_REAL, PETSC_MIN_REAL}, minMaxIndGlobal[2], minInd, maxInd, time; PetscScalar *errArray; const PetscScalar *pointVals; const PetscScalar *pointGrads; const PetscScalar *pointGeom; DMLabel adaptLabel = NULL; IS refineIS, coarsenIS; PetscErrorCode ierr; PetscFunctionBegin; ierr = TSGetTime(ts,&time);CHKERRQ(ierr); ierr = VecGetDM(sol, &dm);CHKERRQ(ierr); ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); ierr = PetscFVGetComputeGradients(fvm,&computeGradient);CHKERRQ(ierr); ierr = PetscFVSetComputeGradients(fvm,PETSC_TRUE);CHKERRQ(ierr); ierr = DMIsForest(dm, &isForest);CHKERRQ(ierr); ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); ierr = DMPlexGetDataFVM(plex, fvm, &cellGeom, &faceGeom, &gradDM);CHKERRQ(ierr); ierr = DMCreateLocalVector(plex,&locX);CHKERRQ(ierr); ierr = DMPlexInsertBoundaryValues(plex, PETSC_TRUE, locX, 0.0, faceGeom, cellGeom, NULL);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(plex, sol, INSERT_VALUES, locX);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd (plex, sol, INSERT_VALUES, locX);CHKERRQ(ierr); ierr = DMCreateGlobalVector(gradDM, &grad);CHKERRQ(ierr); ierr = DMPlexReconstructGradientsFVM(plex, locX, grad);CHKERRQ(ierr); ierr = DMCreateLocalVector(gradDM, &locGrad);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(gradDM, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(gradDM, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); ierr = VecDestroy(&grad);CHKERRQ(ierr); ierr = DMPlexGetSimplexOrBoxCells(plex,0,&cStart,&cEnd);CHKERRQ(ierr); ierr = VecGetArrayRead(locGrad,&pointGrads);CHKERRQ(ierr); ierr = VecGetArrayRead(cellGeom,&pointGeom);CHKERRQ(ierr); ierr = VecGetArrayRead(locX,&pointVals);CHKERRQ(ierr); ierr = VecGetDM(cellGeom,&cellDM);CHKERRQ(ierr); ierr = DMLabelCreate(PETSC_COMM_SELF,"adapt",&adaptLabel);CHKERRQ(ierr); ierr = VecCreateMPI(PetscObjectComm((PetscObject)plex),cEnd-cStart,PETSC_DETERMINE,&errVec);CHKERRQ(ierr); ierr = VecSetUp(errVec);CHKERRQ(ierr); ierr = VecGetArray(errVec,&errArray);CHKERRQ(ierr); for (c = cStart; c < cEnd; c++) { PetscReal errInd = 0.; PetscScalar *pointGrad; PetscScalar *pointVal; PetscFVCellGeom *cg; ierr = DMPlexPointLocalRead(gradDM,c,pointGrads,&pointGrad);CHKERRQ(ierr); ierr = DMPlexPointLocalRead(cellDM,c,pointGeom,&cg);CHKERRQ(ierr); ierr = DMPlexPointLocalRead(plex,c,pointVals,&pointVal);CHKERRQ(ierr); ierr = (user->model->errorIndicator)(dim,cg->volume,user->model->physics->dof,pointVal,pointGrad,&errInd,user->model->errorCtx);CHKERRQ(ierr); errArray[c-cStart] = errInd; minMaxInd[0] = PetscMin(minMaxInd[0],errInd); minMaxInd[1] = PetscMax(minMaxInd[1],errInd); } ierr = VecRestoreArray(errVec,&errArray);CHKERRQ(ierr); ierr = VecRestoreArrayRead(locX,&pointVals);CHKERRQ(ierr); ierr = VecRestoreArrayRead(cellGeom,&pointGeom);CHKERRQ(ierr); ierr = VecRestoreArrayRead(locGrad,&pointGrads);CHKERRQ(ierr); ierr = VecDestroy(&locGrad);CHKERRQ(ierr); ierr = VecDestroy(&locX);CHKERRQ(ierr); ierr = DMDestroy(&plex);CHKERRQ(ierr); ierr = VecTaggerComputeIS(refineTag,errVec,&refineIS);CHKERRQ(ierr); ierr = VecTaggerComputeIS(coarsenTag,errVec,&coarsenIS);CHKERRQ(ierr); ierr = ISGetSize(refineIS,&nRefine);CHKERRQ(ierr); ierr = ISGetSize(coarsenIS,&nCoarsen);CHKERRQ(ierr); if (nRefine) {ierr = DMLabelSetStratumIS(adaptLabel,DM_ADAPT_REFINE,refineIS);CHKERRQ(ierr);} if (nCoarsen) {ierr = DMLabelSetStratumIS(adaptLabel,DM_ADAPT_COARSEN,coarsenIS);CHKERRQ(ierr);} ierr = ISDestroy(&coarsenIS);CHKERRQ(ierr); ierr = ISDestroy(&refineIS);CHKERRQ(ierr); ierr = VecDestroy(&errVec);CHKERRQ(ierr); ierr = PetscFVSetComputeGradients(fvm,computeGradient);CHKERRQ(ierr); minMaxInd[1] = -minMaxInd[1]; ierr = MPI_Allreduce(minMaxInd,minMaxIndGlobal,2,MPIU_REAL,MPI_MIN,PetscObjectComm((PetscObject)dm));CHKERRMPI(ierr); minInd = minMaxIndGlobal[0]; maxInd = -minMaxIndGlobal[1]; ierr = PetscInfo2(ts, "error indicator range (%E, %E)\n", minInd, maxInd);CHKERRQ(ierr); if (nRefine || nCoarsen) { /* at least one cell is over the refinement threshold */ ierr = DMAdaptLabel(dm,adaptLabel,&adaptedDM);CHKERRQ(ierr); } ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr); if (adaptedDM) { ierr = PetscInfo2(ts, "Adapted mesh, marking %D cells for refinement, and %D cells for coarsening\n", nRefine, nCoarsen);CHKERRQ(ierr); if (tsNew) {ierr = initializeTS(adaptedDM, user, tsNew);CHKERRQ(ierr);} if (solNew) { ierr = DMCreateGlobalVector(adaptedDM, solNew);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) *solNew, "solution");CHKERRQ(ierr); ierr = DMForestTransferVec(dm, sol, adaptedDM, *solNew, PETSC_TRUE, time);CHKERRQ(ierr); } if (isForest) {ierr = DMForestSetAdaptivityForest(adaptedDM,NULL);CHKERRQ(ierr);} /* clear internal references to the previous dm */ ierr = DMDestroy(&adaptedDM);CHKERRQ(ierr); } else { if (tsNew) *tsNew = NULL; if (solNew) *solNew = NULL; } PetscFunctionReturn(0); } int main(int argc, char **argv) { MPI_Comm comm; PetscDS prob; PetscFV fvm; PetscLimiter limiter = NULL, noneLimiter = NULL; User user; Model mod; Physics phys; DM dm, plex; PetscReal ftime, cfl, dt, minRadius; PetscInt dim, nsteps; TS ts; TSConvergedReason reason; Vec X; PetscViewer viewer; PetscBool simplex = PETSC_FALSE, vtkCellGeom, splitFaces, useAMR; PetscInt overlap, adaptInterval; char filename[PETSC_MAX_PATH_LEN] = ""; char physname[256] = "advect"; VecTagger refineTag = NULL, coarsenTag = NULL; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, (char*) 0, help);if (ierr) return ierr; comm = PETSC_COMM_WORLD; ierr = PetscNew(&user);CHKERRQ(ierr); ierr = PetscNew(&user->model);CHKERRQ(ierr); ierr = PetscNew(&user->model->physics);CHKERRQ(ierr); mod = user->model; phys = mod->physics; mod->comm = comm; useAMR = PETSC_FALSE; adaptInterval = 1; /* Register physical models to be available on the command line */ ierr = PetscFunctionListAdd(&PhysicsList,"advect" ,PhysicsCreate_Advect);CHKERRQ(ierr); ierr = PetscFunctionListAdd(&PhysicsList,"sw" ,PhysicsCreate_SW);CHKERRQ(ierr); ierr = PetscFunctionListAdd(&PhysicsList,"euler" ,PhysicsCreate_Euler);CHKERRQ(ierr); ierr = PetscOptionsBegin(comm,NULL,"Unstructured Finite Volume Mesh Options","");CHKERRQ(ierr); { cfl = 0.9 * 4; /* default SSPRKS2 with s=5 stages is stable for CFL number s-1 */ ierr = PetscOptionsReal("-ufv_cfl","CFL number per step","",cfl,&cfl,NULL);CHKERRQ(ierr); ierr = PetscOptionsString("-f","Exodus.II filename to read","",filename,filename,sizeof(filename),NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-simplex","Flag to use a simplex mesh","",simplex,&simplex,NULL);CHKERRQ(ierr); splitFaces = PETSC_FALSE; ierr = PetscOptionsBool("-ufv_split_faces","Split faces between cell sets","",splitFaces,&splitFaces,NULL);CHKERRQ(ierr); overlap = 1; ierr = PetscOptionsInt("-ufv_mesh_overlap","Number of cells to overlap partitions","",overlap,&overlap,NULL);CHKERRQ(ierr); user->vtkInterval = 1; ierr = PetscOptionsInt("-ufv_vtk_interval","VTK output interval (0 to disable)","",user->vtkInterval,&user->vtkInterval,NULL);CHKERRQ(ierr); user->vtkmon = PETSC_TRUE; ierr = PetscOptionsBool("-ufv_vtk_monitor","Use VTKMonitor routine","",user->vtkmon,&user->vtkmon,NULL);CHKERRQ(ierr); vtkCellGeom = PETSC_FALSE; ierr = PetscStrcpy(user->outputBasename, "ex11");CHKERRQ(ierr); ierr = PetscOptionsString("-ufv_vtk_basename","VTK output basename","",user->outputBasename,user->outputBasename,sizeof(user->outputBasename),NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-ufv_vtk_cellgeom","Write cell geometry (for debugging)","",vtkCellGeom,&vtkCellGeom,NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-ufv_use_amr","use local adaptive mesh refinement","",useAMR,&useAMR,NULL);CHKERRQ(ierr); ierr = PetscOptionsInt("-ufv_adapt_interval","time steps between AMR","",adaptInterval,&adaptInterval,NULL);CHKERRQ(ierr); } ierr = PetscOptionsEnd();CHKERRQ(ierr); if (useAMR) { VecTaggerBox refineBox, coarsenBox; refineBox.min = refineBox.max = PETSC_MAX_REAL; coarsenBox.min = coarsenBox.max = PETSC_MIN_REAL; ierr = VecTaggerCreate(comm,&refineTag);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject)refineTag,"refine_");CHKERRQ(ierr); ierr = VecTaggerSetType(refineTag,VECTAGGERABSOLUTE);CHKERRQ(ierr); ierr = VecTaggerAbsoluteSetBox(refineTag,&refineBox);CHKERRQ(ierr); ierr = VecTaggerSetFromOptions(refineTag);CHKERRQ(ierr); ierr = VecTaggerSetUp(refineTag);CHKERRQ(ierr); ierr = PetscObjectViewFromOptions((PetscObject)refineTag,NULL,"-tag_view");CHKERRQ(ierr); ierr = VecTaggerCreate(comm,&coarsenTag);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject)coarsenTag,"coarsen_");CHKERRQ(ierr); ierr = VecTaggerSetType(coarsenTag,VECTAGGERABSOLUTE);CHKERRQ(ierr); ierr = VecTaggerAbsoluteSetBox(coarsenTag,&coarsenBox);CHKERRQ(ierr); ierr = VecTaggerSetFromOptions(coarsenTag);CHKERRQ(ierr); ierr = VecTaggerSetUp(coarsenTag);CHKERRQ(ierr); ierr = PetscObjectViewFromOptions((PetscObject)coarsenTag,NULL,"-tag_view");CHKERRQ(ierr); } ierr = PetscOptionsBegin(comm,NULL,"Unstructured Finite Volume Physics Options","");CHKERRQ(ierr); { PetscErrorCode (*physcreate)(Model,Physics,PetscOptionItems*); ierr = PetscOptionsFList("-physics","Physics module to solve","",PhysicsList,physname,physname,sizeof physname,NULL);CHKERRQ(ierr); ierr = PetscFunctionListFind(PhysicsList,physname,&physcreate);CHKERRQ(ierr); ierr = PetscMemzero(phys,sizeof(struct _n_Physics));CHKERRQ(ierr); ierr = (*physcreate)(mod,phys,PetscOptionsObject);CHKERRQ(ierr); /* Count number of fields and dofs */ for (phys->nfields=0,phys->dof=0; phys->field_desc[phys->nfields].name; phys->nfields++) phys->dof += phys->field_desc[phys->nfields].dof; if (phys->dof <= 0) SETERRQ1(comm,PETSC_ERR_ARG_WRONGSTATE,"Physics '%s' did not set dof",physname); ierr = ModelFunctionalSetFromOptions(mod,PetscOptionsObject);CHKERRQ(ierr); } ierr = PetscOptionsEnd();CHKERRQ(ierr); /* Create mesh */ { size_t len,i; for (i = 0; i < DIM; i++) { mod->bounds[2*i] = 0.; mod->bounds[2*i+1] = 1.;}; ierr = PetscStrlen(filename,&len);CHKERRQ(ierr); dim = DIM; if (!len) { /* a null name means just do a hex box */ PetscInt cells[3] = {1, 1, 1}; /* coarse mesh is one cell; refine from there */ PetscBool flg1, flg2, skew = PETSC_FALSE; PetscInt nret1 = DIM; PetscInt nret2 = 2*DIM; ierr = PetscOptionsBegin(comm,NULL,"Rectangular mesh options","");CHKERRQ(ierr); ierr = PetscOptionsIntArray("-grid_size","number of cells in each direction","",cells,&nret1,&flg1);CHKERRQ(ierr); ierr = PetscOptionsRealArray("-grid_bounds","bounds of the mesh in each direction (i.e., x_min,x_max,y_min,y_max","",mod->bounds,&nret2,&flg2);CHKERRQ(ierr); ierr = PetscOptionsBool("-grid_skew_60","Skew grid for 60 degree shock mesh","",skew,&skew,NULL);CHKERRQ(ierr); ierr = PetscOptionsEnd();CHKERRQ(ierr); if (flg1) { dim = nret1; if (dim != DIM) SETERRQ1(comm,PETSC_ERR_ARG_SIZ,"Dim wrong size %D in -grid_size",dim); } ierr = DMPlexCreateBoxMesh(comm, dim, simplex, cells, NULL, NULL, mod->bcs, PETSC_TRUE, &dm);CHKERRQ(ierr); if (flg2) { PetscInt dimEmbed, i; PetscInt nCoords; PetscScalar *coords; Vec coordinates; ierr = DMGetCoordinatesLocal(dm,&coordinates);CHKERRQ(ierr); ierr = DMGetCoordinateDim(dm,&dimEmbed);CHKERRQ(ierr); ierr = VecGetLocalSize(coordinates,&nCoords);CHKERRQ(ierr); if (nCoords % dimEmbed) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Coordinate vector the wrong size"); ierr = VecGetArray(coordinates,&coords);CHKERRQ(ierr); for (i = 0; i < nCoords; i += dimEmbed) { PetscInt j; PetscScalar *coord = &coords[i]; for (j = 0; j < dimEmbed; j++) { coord[j] = mod->bounds[2 * j] + coord[j] * (mod->bounds[2 * j + 1] - mod->bounds[2 * j]); if (dim==2 && cells[1]==1 && j==0 && skew) { if (cells[0]==2 && i==8) { coord[j] = .57735026918963; /* hack to get 60 deg skewed mesh */ } else if (cells[0]==3) { if (i==2 || i==10) coord[j] = mod->bounds[1]/4.; else if (i==4) coord[j] = mod->bounds[1]/2.; else if (i==12) coord[j] = 1.57735026918963*mod->bounds[1]/2.; } } } } ierr = VecRestoreArray(coordinates,&coords);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(dm,coordinates);CHKERRQ(ierr); } } else { ierr = DMPlexCreateFromFile(comm, filename, PETSC_TRUE, &dm);CHKERRQ(ierr); } } ierr = DMViewFromOptions(dm, NULL, "-orig_dm_view");CHKERRQ(ierr); ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); /* set up BCs, functions, tags */ ierr = DMCreateLabel(dm, "Face Sets");CHKERRQ(ierr); mod->errorIndicator = ErrorIndicator_Simple; { DM dmDist; ierr = DMSetBasicAdjacency(dm, PETSC_TRUE, PETSC_FALSE);CHKERRQ(ierr); ierr = DMPlexDistribute(dm, overlap, NULL, &dmDist);CHKERRQ(ierr); if (dmDist) { ierr = DMDestroy(&dm);CHKERRQ(ierr); dm = dmDist; } } ierr = DMSetFromOptions(dm);CHKERRQ(ierr); { DM gdm; ierr = DMPlexConstructGhostCells(dm, NULL, NULL, &gdm);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); dm = gdm; ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr); } if (splitFaces) {ierr = ConstructCellBoundary(dm, user);CHKERRQ(ierr);} ierr = SplitFaces(&dm, "split faces", user);CHKERRQ(ierr); ierr = PetscFVCreate(comm, &fvm);CHKERRQ(ierr); ierr = PetscFVSetFromOptions(fvm);CHKERRQ(ierr); ierr = PetscFVSetNumComponents(fvm, phys->dof);CHKERRQ(ierr); ierr = PetscFVSetSpatialDimension(fvm, dim);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) fvm,"");CHKERRQ(ierr); { PetscInt f, dof; for (f=0,dof=0; f < phys->nfields; f++) { PetscInt newDof = phys->field_desc[f].dof; if (newDof == 1) { ierr = PetscFVSetComponentName(fvm,dof,phys->field_desc[f].name);CHKERRQ(ierr); } else { PetscInt j; for (j = 0; j < newDof; j++) { char compName[256] = "Unknown"; ierr = PetscSNPrintf(compName,sizeof(compName),"%s_%d",phys->field_desc[f].name,j);CHKERRQ(ierr); ierr = PetscFVSetComponentName(fvm,dof+j,compName);CHKERRQ(ierr); } } dof += newDof; } } /* FV is now structured with one field having all physics as components */ ierr = DMAddField(dm, NULL, (PetscObject) fvm);CHKERRQ(ierr); ierr = DMCreateDS(dm);CHKERRQ(ierr); ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); ierr = PetscDSSetRiemannSolver(prob, 0, user->model->physics->riemann);CHKERRQ(ierr); ierr = PetscDSSetContext(prob, 0, user->model->physics);CHKERRQ(ierr); ierr = (*mod->setupbc)(dm, prob,phys);CHKERRQ(ierr); ierr = PetscDSSetFromOptions(prob);CHKERRQ(ierr); { char convType[256]; PetscBool flg; ierr = PetscOptionsBegin(comm, "", "Mesh conversion options", "DMPLEX");CHKERRQ(ierr); ierr = PetscOptionsFList("-dm_type","Convert DMPlex to another format","ex12",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr); ierr = PetscOptionsEnd();CHKERRQ(ierr); if (flg) { DM dmConv; ierr = DMConvert(dm,convType,&dmConv);CHKERRQ(ierr); if (dmConv) { ierr = DMViewFromOptions(dmConv, NULL, "-dm_conv_view");CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); dm = dmConv; ierr = DMSetFromOptions(dm);CHKERRQ(ierr); } } } ierr = initializeTS(dm, user, &ts);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dm, &X);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) X, "solution");CHKERRQ(ierr); ierr = SetInitialCondition(dm, X, user);CHKERRQ(ierr); if (useAMR) { PetscInt adaptIter; /* use no limiting when reconstructing gradients for adaptivity */ ierr = PetscFVGetLimiter(fvm, &limiter);CHKERRQ(ierr); ierr = PetscObjectReference((PetscObject) limiter);CHKERRQ(ierr); ierr = PetscLimiterCreate(PetscObjectComm((PetscObject) fvm), &noneLimiter);CHKERRQ(ierr); ierr = PetscLimiterSetType(noneLimiter, PETSCLIMITERNONE);CHKERRQ(ierr); ierr = PetscFVSetLimiter(fvm, noneLimiter);CHKERRQ(ierr); for (adaptIter = 0; ; ++adaptIter) { PetscLogDouble bytes; TS tsNew = NULL; ierr = PetscMemoryGetCurrentUsage(&bytes);CHKERRQ(ierr); ierr = PetscInfo2(ts, "refinement loop %D: memory used %g\n", adaptIter, bytes);CHKERRQ(ierr); ierr = DMViewFromOptions(dm, NULL, "-initial_dm_view");CHKERRQ(ierr); ierr = VecViewFromOptions(X, NULL, "-initial_vec_view");CHKERRQ(ierr); #if 0 if (viewInitial) { PetscViewer viewer; char buf[256]; PetscBool isHDF5, isVTK; ierr = PetscViewerCreate(comm,&viewer);CHKERRQ(ierr); ierr = PetscViewerSetType(viewer,PETSCVIEWERVTK);CHKERRQ(ierr); ierr = PetscViewerSetOptionsPrefix(viewer,"initial_");CHKERRQ(ierr); ierr = PetscViewerSetFromOptions(viewer);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&isHDF5);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERVTK,&isVTK);CHKERRQ(ierr); if (isHDF5) { ierr = PetscSNPrintf(buf, 256, "ex11-initial-%d.h5", adaptIter);CHKERRQ(ierr); } else if (isVTK) { ierr = PetscSNPrintf(buf, 256, "ex11-initial-%d.vtu", adaptIter);CHKERRQ(ierr); ierr = PetscViewerPushFormat(viewer,PETSC_VIEWER_VTK_VTU);CHKERRQ(ierr); } ierr = PetscViewerFileSetMode(viewer,FILE_MODE_WRITE);CHKERRQ(ierr); ierr = PetscViewerFileSetName(viewer,buf);CHKERRQ(ierr); if (isHDF5) { ierr = DMView(dm,viewer);CHKERRQ(ierr); ierr = PetscViewerFileSetMode(viewer,FILE_MODE_UPDATE);CHKERRQ(ierr); } ierr = VecView(X,viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } #endif ierr = adaptToleranceFVM(fvm, ts, X, refineTag, coarsenTag, user, &tsNew, NULL);CHKERRQ(ierr); if (!tsNew) { break; } else { ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = VecDestroy(&X);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ts = tsNew; ierr = TSGetDM(ts,&dm);CHKERRQ(ierr); ierr = PetscObjectReference((PetscObject)dm);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dm,&X);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) X, "solution");CHKERRQ(ierr); ierr = SetInitialCondition(dm, X, user);CHKERRQ(ierr); } } /* restore original limiter */ ierr = PetscFVSetLimiter(fvm, limiter);CHKERRQ(ierr); } ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); if (vtkCellGeom) { DM dmCell; Vec cellgeom, partition; ierr = DMPlexGetGeometryFVM(plex, NULL, &cellgeom, NULL);CHKERRQ(ierr); ierr = OutputVTK(dm, "ex11-cellgeom.vtk", &viewer);CHKERRQ(ierr); ierr = VecView(cellgeom, viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = CreatePartitionVec(dm, &dmCell, &partition);CHKERRQ(ierr); ierr = OutputVTK(dmCell, "ex11-partition.vtk", &viewer);CHKERRQ(ierr); ierr = VecView(partition, viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = VecDestroy(&partition);CHKERRQ(ierr); ierr = DMDestroy(&dmCell);CHKERRQ(ierr); } /* collect max maxspeed from all processes -- todo */ ierr = DMPlexGetGeometryFVM(plex, NULL, NULL, &minRadius);CHKERRQ(ierr); ierr = DMDestroy(&plex);CHKERRQ(ierr); ierr = MPI_Allreduce(&phys->maxspeed,&mod->maxspeed,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)ts));CHKERRMPI(ierr); if (mod->maxspeed <= 0) SETERRQ1(comm,PETSC_ERR_ARG_WRONGSTATE,"Physics '%s' did not set maxspeed",physname); dt = cfl * minRadius / mod->maxspeed; ierr = TSSetTimeStep(ts,dt);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); if (!useAMR) { ierr = TSSolve(ts,X);CHKERRQ(ierr); ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); ierr = TSGetStepNumber(ts,&nsteps);CHKERRQ(ierr); } else { PetscReal finalTime; PetscInt adaptIter; TS tsNew = NULL; Vec solNew = NULL; ierr = TSGetMaxTime(ts,&finalTime);CHKERRQ(ierr); ierr = TSSetMaxSteps(ts,adaptInterval);CHKERRQ(ierr); ierr = TSSolve(ts,X);CHKERRQ(ierr); ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); ierr = TSGetStepNumber(ts,&nsteps);CHKERRQ(ierr); for (adaptIter = 0;ftime < finalTime;adaptIter++) { PetscLogDouble bytes; ierr = PetscMemoryGetCurrentUsage(&bytes);CHKERRQ(ierr); ierr = PetscInfo2(ts, "AMR time step loop %D: memory used %g\n", adaptIter, bytes);CHKERRQ(ierr); ierr = PetscFVSetLimiter(fvm,noneLimiter);CHKERRQ(ierr); ierr = adaptToleranceFVM(fvm,ts,X,refineTag,coarsenTag,user,&tsNew,&solNew);CHKERRQ(ierr); ierr = PetscFVSetLimiter(fvm,limiter);CHKERRQ(ierr); if (tsNew) { ierr = PetscInfo(ts, "AMR used\n");CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = VecDestroy(&X);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ts = tsNew; X = solNew; ierr = TSSetFromOptions(ts);CHKERRQ(ierr); ierr = VecGetDM(X,&dm);CHKERRQ(ierr); ierr = PetscObjectReference((PetscObject)dm);CHKERRQ(ierr); ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); ierr = DMPlexGetGeometryFVM(dm, NULL, NULL, &minRadius);CHKERRQ(ierr); ierr = DMDestroy(&plex);CHKERRQ(ierr); ierr = MPI_Allreduce(&phys->maxspeed,&mod->maxspeed,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)ts));CHKERRMPI(ierr); if (mod->maxspeed <= 0) SETERRQ1(comm,PETSC_ERR_ARG_WRONGSTATE,"Physics '%s' did not set maxspeed",physname); dt = cfl * minRadius / mod->maxspeed; ierr = TSSetStepNumber(ts,nsteps);CHKERRQ(ierr); ierr = TSSetTime(ts,ftime);CHKERRQ(ierr); ierr = TSSetTimeStep(ts,dt);CHKERRQ(ierr); } else { ierr = PetscInfo(ts, "AMR not used\n");CHKERRQ(ierr); } user->monitorStepOffset = nsteps; ierr = TSSetMaxSteps(ts,nsteps+adaptInterval);CHKERRQ(ierr); ierr = TSSolve(ts,X);CHKERRQ(ierr); ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); ierr = TSGetStepNumber(ts,&nsteps);CHKERRQ(ierr); } } ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],(double)ftime,nsteps);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = VecTaggerDestroy(&refineTag);CHKERRQ(ierr); ierr = VecTaggerDestroy(&coarsenTag);CHKERRQ(ierr); ierr = PetscFunctionListDestroy(&PhysicsList);CHKERRQ(ierr); ierr = PetscFunctionListDestroy(&PhysicsRiemannList_SW);CHKERRQ(ierr); ierr = FunctionalLinkDestroy(&user->model->functionalRegistry);CHKERRQ(ierr); ierr = PetscFree(user->model->functionalMonitored);CHKERRQ(ierr); ierr = PetscFree(user->model->functionalCall);CHKERRQ(ierr); ierr = PetscFree(user->model->physics->data);CHKERRQ(ierr); ierr = PetscFree(user->model->physics);CHKERRQ(ierr); ierr = PetscFree(user->model);CHKERRQ(ierr); ierr = PetscFree(user);CHKERRQ(ierr); ierr = VecDestroy(&X);CHKERRQ(ierr); ierr = PetscLimiterDestroy(&limiter);CHKERRQ(ierr); ierr = PetscLimiterDestroy(&noneLimiter);CHKERRQ(ierr); ierr = PetscFVDestroy(&fvm);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; } /* Godunov fluxs */ PetscScalar cvmgp_(PetscScalar *a, PetscScalar *b, PetscScalar *test) { /* System generated locals */ PetscScalar ret_val; if (PetscRealPart(*test) > 0.) { goto L10; } ret_val = *b; return ret_val; L10: ret_val = *a; return ret_val; } /* cvmgp_ */ PetscScalar cvmgm_(PetscScalar *a, PetscScalar *b, PetscScalar *test) { /* System generated locals */ PetscScalar ret_val; if (PetscRealPart(*test) < 0.) { goto L10; } ret_val = *b; return ret_val; L10: ret_val = *a; return ret_val; } /* cvmgm_ */ int riem1mdt( PetscScalar *gaml, PetscScalar *gamr, PetscScalar *rl, PetscScalar *pl, PetscScalar *uxl, PetscScalar *rr, PetscScalar *pr, PetscScalar *uxr, PetscScalar *rstarl, PetscScalar *rstarr, PetscScalar * pstar, PetscScalar *ustar) { /* Initialized data */ static PetscScalar smallp = 1e-8; /* System generated locals */ int i__1; PetscScalar d__1, d__2; /* Local variables */ static int i0; static PetscScalar cl, cr, wl, zl, wr, zr, pst, durl, skpr1, skpr2; static int iwave; static PetscScalar gascl4, gascr4, cstarl, dpstar, cstarr; /* static PetscScalar csqrl, csqrr, gascl1, gascl2, gascl3, gascr1, gascr2, gascr3; */ static int iterno; static PetscScalar ustarl, ustarr, rarepr1, rarepr2; /* gascl1 = *gaml - 1.; */ /* gascl2 = (*gaml + 1.) * .5; */ /* gascl3 = gascl2 / *gaml; */ gascl4 = 1. / (*gaml - 1.); /* gascr1 = *gamr - 1.; */ /* gascr2 = (*gamr + 1.) * .5; */ /* gascr3 = gascr2 / *gamr; */ gascr4 = 1. / (*gamr - 1.); iterno = 10; /* find pstar: */ cl = PetscSqrtScalar(*gaml * *pl / *rl); cr = PetscSqrtScalar(*gamr * *pr / *rr); wl = *rl * cl; wr = *rr * cr; /* csqrl = wl * wl; */ /* csqrr = wr * wr; */ *pstar = (wl * *pr + wr * *pl) / (wl + wr); *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp)); pst = *pl / *pr; skpr1 = cr * (pst - 1.) * PetscSqrtScalar(2. / (*gamr * (*gamr - 1. + (*gamr + 1.) * pst))); d__1 = (*gamr - 1.) / (*gamr * 2.); rarepr2 = gascr4 * 2. * cr * (1. - PetscPowScalar(pst, d__1)); pst = *pr / *pl; skpr2 = cl * (pst - 1.) * PetscSqrtScalar(2. / (*gaml * (*gaml - 1. + (*gaml + 1.) * pst))); d__1 = (*gaml - 1.) / (*gaml * 2.); rarepr1 = gascl4 * 2. * cl * (1. - PetscPowScalar(pst, d__1)); durl = *uxr - *uxl; if (PetscRealPart(*pr) < PetscRealPart(*pl)) { if (PetscRealPart(durl) >= PetscRealPart(rarepr1)) { iwave = 100; } else if (PetscRealPart(durl) <= PetscRealPart(-skpr1)) { iwave = 300; } else { iwave = 400; } } else { if (PetscRealPart(durl) >= PetscRealPart(rarepr2)) { iwave = 100; } else if (PetscRealPart(durl) <= PetscRealPart(-skpr2)) { iwave = 300; } else { iwave = 200; } } if (iwave == 100) { /* 1-wave: rarefaction wave, 3-wave: rarefaction wave */ /* case (100) */ i__1 = iterno; for (i0 = 1; i0 <= i__1; ++i0) { d__1 = *pstar / *pl; d__2 = 1. / *gaml; *rstarl = *rl * PetscPowScalar(d__1, d__2); cstarl = PetscSqrtScalar(*gaml * *pstar / *rstarl); ustarl = *uxl - gascl4 * 2. * (cstarl - cl); zl = *rstarl * cstarl; d__1 = *pstar / *pr; d__2 = 1. / *gamr; *rstarr = *rr * PetscPowScalar(d__1, d__2); cstarr = PetscSqrtScalar(*gamr * *pstar / *rstarr); ustarr = *uxr + gascr4 * 2. * (cstarr - cr); zr = *rstarr * cstarr; dpstar = zl * zr * (ustarr - ustarl) / (zl + zr); *pstar -= dpstar; *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp)); if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) { #if 0 break; #endif } } /* 1-wave: shock wave, 3-wave: rarefaction wave */ } else if (iwave == 200) { /* case (200) */ i__1 = iterno; for (i0 = 1; i0 <= i__1; ++i0) { pst = *pstar / *pl; ustarl = *uxl - (pst - 1.) * cl * PetscSqrtScalar(2. / (*gaml * (*gaml - 1. + (*gaml + 1.) * pst))); zl = *pl / cl * PetscSqrtScalar(*gaml * 2. * (*gaml - 1. + (*gaml + 1.) * pst)) * (*gaml - 1. + (*gaml + 1.) * pst) / (*gaml * 3. - 1. + (*gaml + 1.) * pst); d__1 = *pstar / *pr; d__2 = 1. / *gamr; *rstarr = *rr * PetscPowScalar(d__1, d__2); cstarr = PetscSqrtScalar(*gamr * *pstar / *rstarr); zr = *rstarr * cstarr; ustarr = *uxr + gascr4 * 2. * (cstarr - cr); dpstar = zl * zr * (ustarr - ustarl) / (zl + zr); *pstar -= dpstar; *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp)); if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) { #if 0 break; #endif } } /* 1-wave: shock wave, 3-wave: shock */ } else if (iwave == 300) { /* case (300) */ i__1 = iterno; for (i0 = 1; i0 <= i__1; ++i0) { pst = *pstar / *pl; ustarl = *uxl - (pst - 1.) * cl * PetscSqrtScalar(2. / (*gaml * (*gaml - 1. + (*gaml + 1.) * pst))); zl = *pl / cl * PetscSqrtScalar(*gaml * 2. * (*gaml - 1. + (*gaml + 1.) * pst)) * (*gaml - 1. + (*gaml + 1.) * pst) / (*gaml * 3. - 1. + (*gaml + 1.) * pst); pst = *pstar / *pr; ustarr = *uxr + (pst - 1.) * cr * PetscSqrtScalar(2. / (*gamr * (*gamr - 1. + (*gamr + 1.) * pst))); zr = *pr / cr * PetscSqrtScalar(*gamr * 2. * (*gamr - 1. + (*gamr + 1.) * pst)) * (*gamr - 1. + (*gamr + 1.) * pst) / (*gamr * 3. - 1. + (*gamr + 1.) * pst); dpstar = zl * zr * (ustarr - ustarl) / (zl + zr); *pstar -= dpstar; *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp)); if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) { #if 0 break; #endif } } /* 1-wave: rarefaction wave, 3-wave: shock */ } else if (iwave == 400) { /* case (400) */ i__1 = iterno; for (i0 = 1; i0 <= i__1; ++i0) { d__1 = *pstar / *pl; d__2 = 1. / *gaml; *rstarl = *rl * PetscPowScalar(d__1, d__2); cstarl = PetscSqrtScalar(*gaml * *pstar / *rstarl); ustarl = *uxl - gascl4 * 2. * (cstarl - cl); zl = *rstarl * cstarl; pst = *pstar / *pr; ustarr = *uxr + (pst - 1.) * cr * PetscSqrtScalar(2. / (*gamr * (*gamr - 1. + (*gamr + 1.) * pst))); zr = *pr / cr * PetscSqrtScalar(*gamr * 2. * (*gamr - 1. + (*gamr + 1.) * pst)) * (*gamr - 1. + (*gamr + 1.) * pst) / (*gamr * 3. - 1. + (*gamr + 1.) * pst); dpstar = zl * zr * (ustarr - ustarl) / (zl + zr); *pstar -= dpstar; *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp)); if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) { #if 0 break; #endif } } } *ustar = (zl * ustarr + zr * ustarl) / (zl + zr); if (PetscRealPart(*pstar) > PetscRealPart(*pl)) { pst = *pstar / *pl; *rstarl = ((*gaml + 1.) * pst + *gaml - 1.) / ((*gaml - 1.) * pst + * gaml + 1.) * *rl; } if (PetscRealPart(*pstar) > PetscRealPart(*pr)) { pst = *pstar / *pr; *rstarr = ((*gamr + 1.) * pst + *gamr - 1.) / ((*gamr - 1.) * pst + * gamr + 1.) * *rr; } return iwave; } PetscScalar sign(PetscScalar x) { if (PetscRealPart(x) > 0) return 1.0; if (PetscRealPart(x) < 0) return -1.0; return 0.0; } /* Riemann Solver */ /* -------------------------------------------------------------------- */ int riemannsolver(PetscScalar *xcen, PetscScalar *xp, PetscScalar *dtt, PetscScalar *rl, PetscScalar *uxl, PetscScalar *pl, PetscScalar *utl, PetscScalar *ubl, PetscScalar *gaml, PetscScalar *rho1l, PetscScalar *rr, PetscScalar *uxr, PetscScalar *pr, PetscScalar *utr, PetscScalar *ubr, PetscScalar *gamr, PetscScalar *rho1r, PetscScalar *rx, PetscScalar *uxm, PetscScalar *px, PetscScalar *utx, PetscScalar *ubx, PetscScalar *gam, PetscScalar *rho1) { /* System generated locals */ PetscScalar d__1, d__2; /* Local variables */ static PetscScalar s, c0, p0, r0, u0, w0, x0, x2, ri, cx, sgn0, wsp0, gasc1, gasc2, gasc3, gasc4; static PetscScalar cstar, pstar, rstar, ustar, xstar, wspst, ushock, streng, rstarl, rstarr, rstars; int iwave; if (*rl == *rr && *pr == *pl && *uxl == *uxr && *gaml == *gamr) { *rx = *rl; *px = *pl; *uxm = *uxl; *gam = *gaml; x2 = *xcen + *uxm * *dtt; if (PetscRealPart(*xp) >= PetscRealPart(x2)) { *utx = *utr; *ubx = *ubr; *rho1 = *rho1r; } else { *utx = *utl; *ubx = *ubl; *rho1 = *rho1l; } return 0; } iwave = riem1mdt(gaml, gamr, rl, pl, uxl, rr, pr, uxr, &rstarl, &rstarr, &pstar, &ustar); x2 = *xcen + ustar * *dtt; d__1 = *xp - x2; sgn0 = sign(d__1); /* x is in 3-wave if sgn0 = 1 */ /* x is in 1-wave if sgn0 = -1 */ r0 = cvmgm_(rl, rr, &sgn0); p0 = cvmgm_(pl, pr, &sgn0); u0 = cvmgm_(uxl, uxr, &sgn0); *gam = cvmgm_(gaml, gamr, &sgn0); gasc1 = *gam - 1.; gasc2 = (*gam + 1.) * .5; gasc3 = gasc2 / *gam; gasc4 = 1. / (*gam - 1.); c0 = PetscSqrtScalar(*gam * p0 / r0); streng = pstar - p0; w0 = *gam * r0 * p0 * (gasc3 * streng / p0 + 1.); rstars = r0 / (1. - r0 * streng / w0); d__1 = p0 / pstar; d__2 = -1. / *gam; rstarr = r0 * PetscPowScalar(d__1, d__2); rstar = cvmgm_(&rstarr, &rstars, &streng); w0 = PetscSqrtScalar(w0); cstar = PetscSqrtScalar(*gam * pstar / rstar); wsp0 = u0 + sgn0 * c0; wspst = ustar + sgn0 * cstar; ushock = ustar + sgn0 * w0 / rstar; wspst = cvmgp_(&ushock, &wspst, &streng); wsp0 = cvmgp_(&ushock, &wsp0, &streng); x0 = *xcen + wsp0 * *dtt; xstar = *xcen + wspst * *dtt; /* using gas formula to evaluate rarefaction wave */ /* ri : reiman invariant */ ri = u0 - sgn0 * 2. * gasc4 * c0; cx = sgn0 * .5 * gasc1 / gasc2 * ((*xp - *xcen) / *dtt - ri); *uxm = ri + sgn0 * 2. * gasc4 * cx; s = p0 / PetscPowScalar(r0, *gam); d__1 = cx * cx / (*gam * s); *rx = PetscPowScalar(d__1, gasc4); *px = cx * cx * *rx / *gam; d__1 = sgn0 * (x0 - *xp); *rx = cvmgp_(rx, &r0, &d__1); d__1 = sgn0 * (x0 - *xp); *px = cvmgp_(px, &p0, &d__1); d__1 = sgn0 * (x0 - *xp); *uxm = cvmgp_(uxm, &u0, &d__1); d__1 = sgn0 * (xstar - *xp); *rx = cvmgm_(rx, &rstar, &d__1); d__1 = sgn0 * (xstar - *xp); *px = cvmgm_(px, &pstar, &d__1); d__1 = sgn0 * (xstar - *xp); *uxm = cvmgm_(uxm, &ustar, &d__1); if (PetscRealPart(*xp) >= PetscRealPart(x2)) { *utx = *utr; *ubx = *ubr; *rho1 = *rho1r; } else { *utx = *utl; *ubx = *ubl; *rho1 = *rho1l; } return iwave; } int godunovflux( const PetscScalar *ul, const PetscScalar *ur, PetscScalar *flux, const PetscReal *nn, const int *ndim, const PetscReal *gamma) { /* System generated locals */ int i__1,iwave; PetscScalar d__1, d__2, d__3; /* Local variables */ static int k; static PetscScalar bn[3], fn, ft, tg[3], pl, rl, pm, pr, rr, xp, ubl, ubm, ubr, dtt, unm, tmp, utl, utm, uxl, utr, uxr, gaml, gamm, gamr, xcen, rhom, rho1l, rho1m, rho1r; /* Function Body */ xcen = 0.; xp = 0.; i__1 = *ndim; for (k = 1; k <= i__1; ++k) { tg[k - 1] = 0.; bn[k - 1] = 0.; } dtt = 1.; if (*ndim == 3) { if (nn[0] == 0. && nn[1] == 0.) { tg[0] = 1.; } else { tg[0] = -nn[1]; tg[1] = nn[0]; } /* tmp=dsqrt(tg(1)**2+tg(2)**2) */ /* tg=tg/tmp */ bn[0] = -nn[2] * tg[1]; bn[1] = nn[2] * tg[0]; bn[2] = nn[0] * tg[1] - nn[1] * tg[0]; /* Computing 2nd power */ d__1 = bn[0]; /* Computing 2nd power */ d__2 = bn[1]; /* Computing 2nd power */ d__3 = bn[2]; tmp = PetscSqrtScalar(d__1 * d__1 + d__2 * d__2 + d__3 * d__3); i__1 = *ndim; for (k = 1; k <= i__1; ++k) { bn[k - 1] /= tmp; } } else if (*ndim == 2) { tg[0] = -nn[1]; tg[1] = nn[0]; /* tmp=dsqrt(tg(1)**2+tg(2)**2) */ /* tg=tg/tmp */ bn[0] = 0.; bn[1] = 0.; bn[2] = 1.; } rl = ul[0]; rr = ur[0]; uxl = 0.; uxr = 0.; utl = 0.; utr = 0.; ubl = 0.; ubr = 0.; i__1 = *ndim; for (k = 1; k <= i__1; ++k) { uxl += ul[k] * nn[k-1]; uxr += ur[k] * nn[k-1]; utl += ul[k] * tg[k - 1]; utr += ur[k] * tg[k - 1]; ubl += ul[k] * bn[k - 1]; ubr += ur[k] * bn[k - 1]; } uxl /= rl; uxr /= rr; utl /= rl; utr /= rr; ubl /= rl; ubr /= rr; gaml = *gamma; gamr = *gamma; /* Computing 2nd power */ d__1 = uxl; /* Computing 2nd power */ d__2 = utl; /* Computing 2nd power */ d__3 = ubl; pl = (*gamma - 1.) * (ul[*ndim + 1] - rl * .5 * (d__1 * d__1 + d__2 * d__2 + d__3 * d__3)); /* Computing 2nd power */ d__1 = uxr; /* Computing 2nd power */ d__2 = utr; /* Computing 2nd power */ d__3 = ubr; pr = (*gamma - 1.) * (ur[*ndim + 1] - rr * .5 * (d__1 * d__1 + d__2 * d__2 + d__3 * d__3)); rho1l = rl; rho1r = rr; iwave = riemannsolver(&xcen, &xp, &dtt, &rl, &uxl, &pl, &utl, &ubl, &gaml, & rho1l, &rr, &uxr, &pr, &utr, &ubr, &gamr, &rho1r, &rhom, &unm, & pm, &utm, &ubm, &gamm, &rho1m); flux[0] = rhom * unm; fn = rhom * unm * unm + pm; ft = rhom * unm * utm; /* flux(2)=fn*nn(1)+ft*nn(2) */ /* flux(3)=fn*tg(1)+ft*tg(2) */ flux[1] = fn * nn[0] + ft * tg[0]; flux[2] = fn * nn[1] + ft * tg[1]; /* flux(2)=rhom*unm*(unm)+pm */ /* flux(3)=rhom*(unm)*utm */ if (*ndim == 3) { flux[3] = rhom * unm * ubm; } flux[*ndim + 1] = (rhom * .5 * (unm * unm + utm * utm + ubm * ubm) + gamm / (gamm - 1.) * pm) * unm; return iwave; } /* godunovflux_ */ /* Subroutine to set up the initial conditions for the */ /* Shock Interface interaction or linear wave (Ravi Samtaney,Mark Adams). */ /* ----------------------------------------------------------------------- */ int projecteqstate(PetscReal wc[], const PetscReal ueq[], PetscReal lv[][3]) { int j,k; /* Wc=matmul(lv,Ueq) 3 vars */ for (k = 0; k < 3; ++k) { wc[k] = 0.; for (j = 0; j < 3; ++j) { wc[k] += lv[k][j]*ueq[j]; } } return 0; } /* ----------------------------------------------------------------------- */ int projecttoprim(PetscReal v[], const PetscReal wc[], PetscReal rv[][3]) { int k,j; /* V=matmul(rv,WC) 3 vars */ for (k = 0; k < 3; ++k) { v[k] = 0.; for (j = 0; j < 3; ++j) { v[k] += rv[k][j]*wc[j]; } } return 0; } /* ---------------------------------------------------------------------- */ int eigenvectors(PetscReal rv[][3], PetscReal lv[][3], const PetscReal ueq[], PetscReal gamma) { int j,k; PetscReal rho,csnd,p0; /* PetscScalar u; */ for (k = 0; k < 3; ++k) for (j = 0; j < 3; ++j) { lv[k][j] = 0.; rv[k][j] = 0.; } rho = ueq[0]; /* u = ueq[1]; */ p0 = ueq[2]; csnd = PetscSqrtReal(gamma * p0 / rho); lv[0][1] = rho * .5; lv[0][2] = -.5 / csnd; lv[1][0] = csnd; lv[1][2] = -1. / csnd; lv[2][1] = rho * .5; lv[2][2] = .5 / csnd; rv[0][0] = -1. / csnd; rv[1][0] = 1. / rho; rv[2][0] = -csnd; rv[0][1] = 1. / csnd; rv[0][2] = 1. / csnd; rv[1][2] = 1. / rho; rv[2][2] = csnd; return 0; } int initLinearWave(EulerNode *ux, const PetscReal gamma, const PetscReal coord[], const PetscReal Lx) { PetscReal p0,u0,wcp[3],wc[3]; PetscReal lv[3][3]; PetscReal vp[3]; PetscReal rv[3][3]; PetscReal eps, ueq[3], rho0, twopi; /* Function Body */ twopi = 2.*PETSC_PI; eps = 1e-4; /* perturbation */ rho0 = 1e3; /* density of water */ p0 = 101325.; /* init pressure of 1 atm (?) */ u0 = 0.; ueq[0] = rho0; ueq[1] = u0; ueq[2] = p0; /* Project initial state to characteristic variables */ eigenvectors(rv, lv, ueq, gamma); projecteqstate(wc, ueq, lv); wcp[0] = wc[0]; wcp[1] = wc[1]; wcp[2] = wc[2] + eps * PetscCosReal(coord[0] * 2. * twopi / Lx); projecttoprim(vp, wcp, rv); ux->r = vp[0]; /* density */ ux->ru[0] = vp[0] * vp[1]; /* x momentum */ ux->ru[1] = 0.; #if defined DIM > 2 if (dim>2) ux->ru[2] = 0.; #endif /* E = rho * e + rho * v^2/2 = p/(gam-1) + rho*v^2/2 */ ux->E = vp[2]/(gamma - 1.) + 0.5*vp[0]*vp[1]*vp[1]; return 0; } /*TEST # 2D Advection 0-10 test: suffix: 0 requires: exodusii args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo test: suffix: 1 requires: exodusii args: -ufv_vtk_interval 0 -f${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo test: suffix: 2 requires: exodusii nsize: 2 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo test: suffix: 3 requires: exodusii nsize: 2 args: -ufv_vtk_interval 0 -f${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo test: suffix: 4 requires: exodusii nsize: 8 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad.exo test: suffix: 5 requires: exodusii args: -ufv_vtk_interval 0 -f${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo -ts_type rosw -ts_adapt_reject_safety 1 test: suffix: 6 requires: exodusii args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/squaremotor-30.exo -ufv_split_faces test: suffix: 7 requires: exodusii args: -ufv_vtk_interval 0 -f${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo -dm_refine 1 test: suffix: 8 requires: exodusii nsize: 2 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo -dm_refine 1 test: suffix: 9 requires: exodusii nsize: 8 args: -ufv_vtk_interval 0 -f${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo -dm_refine 1 test: suffix: 10 requires: exodusii args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad.exo # 2D Shallow water test: suffix: sw_0 requires: exodusii args: -ufv_vtk_interval 0 -f${wPETSC_DIR}/share/petsc/datafiles/meshes/annulus-20.exo -bc_wall 100,101 -physics sw -ufv_cfl 5 -petscfv_type leastsquares -petsclimiter_type sin -ts_max_time 1 -ts_ssp_type rks2 -ts_ssp_nstages 10 -monitor height,energy test: suffix: sw_hll args: -ufv_vtk_interval 0 -bc_wall 1,2,3,4 -physics sw -ufv_cfl 3 -petscfv_type leastsquares -petsclimiter_type sin -ts_max_steps 5 -ts_ssp_type rks2 -ts_ssp_nstages 10 -monitor height,energy -grid_bounds 0,5,0,5 -grid_size 25,25 -sw_riemann hll # 2D Advection: p4est test: suffix: p4est_advec_2d requires: p4est args: -ufv_vtk_interval 0 -f -dm_type p4est -dm_forest_minimum_refinement 1 -dm_forest_initial_refinement 2 -dm_p4est_refine_pattern hash -dm_forest_maximum_refinement 5 # Advection in a box test: suffix: adv_2d_quad_0 args: -ufv_vtk_interval 0 -dm_refine 3 -dm_plex_separate_marker -bc_inflow 1,2,4 -bc_outflow 3 test: suffix: adv_2d_quad_1 args: -ufv_vtk_interval 0 -dm_refine 3 -dm_plex_separate_marker -grid_bounds -0.5,0.5,-0.5,0.5 -bc_inflow 1,2,4 -bc_outflow 3 -advect_sol_type bump -advect_bump_center 0.25,0 -advect_bump_radius 0.1 timeoutfactor: 3 test: suffix: adv_2d_quad_p4est_0 requires: p4est args: -ufv_vtk_interval 0 -dm_refine 5 -dm_type p4est -dm_plex_separate_marker -bc_inflow 1,2,4 -bc_outflow 3 test: suffix: adv_2d_quad_p4est_1 requires: p4est args: -ufv_vtk_interval 0 -dm_refine 5 -dm_type p4est -dm_plex_separate_marker -grid_bounds -0.5,0.5,-0.5,0.5 -bc_inflow 1,2,4 -bc_outflow 3 -advect_sol_type bump -advect_bump_center 0.25,0 -advect_bump_radius 0.1 timeoutfactor: 3 test: suffix: adv_2d_quad_p4est_adapt_0 requires: p4est !__float128 #broken for quad precision args: -ufv_vtk_interval 0 -dm_refine 3 -dm_type p4est -dm_plex_separate_marker -grid_bounds -0.5,0.5,-0.5,0.5 -bc_inflow 1,2,4 -bc_outflow 3 -advect_sol_type bump -advect_bump_center 0.25,0 -advect_bump_radius 0.1 -ufv_use_amr -refine_vec_tagger_box 0.005,inf -coarsen_vec_tagger_box 0,1.e-5 -petscfv_type leastsquares -ts_max_time 0.01 timeoutfactor: 3 test: suffix: adv_2d_tri_0 requires: triangle TODO: how did this ever get in main when there is no support for this args: -ufv_vtk_interval 0 -simplex -dm_refine 3 -dm_plex_separate_marker -bc_inflow 1,2,4 -bc_outflow 3 test: suffix: adv_2d_tri_1 requires: triangle TODO: how did this ever get in main when there is no support for this args: -ufv_vtk_interval 0 -simplex -dm_refine 5 -dm_plex_separate_marker -grid_bounds -0.5,0.5,-0.5,0.5 -bc_inflow 1,2,4 -bc_outflow 3 -advect_sol_type bump -advect_bump_center 0.25,0 -advect_bump_radius 0.1 test: suffix: adv_0 requires: exodusii args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo -bc_inflow 100,101,200 -bc_outflow 201 test: suffix: shock_0 requires: p4est !single !complex args: -ufv_vtk_interval 0 -monitor density,energy -f -grid_size 2,1 -grid_bounds -1,1.,0.,1 -bc_wall 1,2,3,4 -dm_type p4est -dm_forest_partition_overlap 1 -dm_forest_maximum_refinement 6 -dm_forest_minimum_refinement 2 -dm_forest_initial_refinement 2 -ufv_use_amr -refine_vec_tagger_box 0.5,inf -coarsen_vec_tagger_box 0,1.e-2 -refine_tag_view -coarsen_tag_view -physics euler -eu_type iv_shock -ufv_cfl 10 -eu_alpha 60. -grid_skew_60 -eu_gamma 1.4 -eu_amach 2.02 -eu_rho2 3. -petscfv_type leastsquares -petsclimiter_type minmod -petscfv_compute_gradients 0 -ts_max_time 0.5 -ts_ssp_type rks2 -ts_ssp_nstages 10 -ufv_vtk_basename${wPETSC_DIR}/ex11 timeoutfactor: 3 # Test GLVis visualization of PetscFV fields test: suffix: glvis_adv_2d_tet args: -ufv_vtk_interval 0 -ts_monitor_solution glvis: -ts_max_steps 0 -ufv_vtk_monitor 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/square_periodic.msh -dm_plex_gmsh_periodic 0 test: suffix: glvis_adv_2d_quad args: -ufv_vtk_interval 0 -ts_monitor_solution glvis: -ts_max_steps 0 -ufv_vtk_monitor 0 -dm_refine 5 -dm_plex_separate_marker -bc_inflow 1,2,4 -bc_outflow 3 test: suffix: tut_1 requires: exodusii nsize: 1 args: -f${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo test: suffix: tut_2 requires: exodusii nsize: 1 args: -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo -ts_type rosw test: suffix: tut_3 requires: exodusii nsize: 4 args: -f${wPETSC_DIR}/share/petsc/datafiles/meshes/annulus-20.exo -monitor Error -advect_sol_type bump -petscfv_type leastsquares -petsclimiter_type sin test: suffix: tut_4 requires: exodusii nsize: 4 args: -f \${wPETSC_DIR}/share/petsc/datafiles/meshes/annulus-20.exo -physics sw -monitor Height,Energy -petscfv_type leastsquares -petsclimiter_type minmod TEST*/