xref: /petsc/src/ts/tutorials/ex11.c (revision 3e9753d60b406ac2fec1249fa8fb9cfa31a5ff24) 
1c4762a1bSJed Brown static char help[] = "Second Order TVD Finite Volume Example.\n";
2c4762a1bSJed Brown /*F
3c4762a1bSJed Brown 
4c4762a1bSJed Brown We use a second order TVD finite volume method to evolve a system of PDEs. Our simple upwinded residual evaluation loops
5c4762a1bSJed Brown over all mesh faces and uses a Riemann solver to produce the flux given the face geometry and cell values,
6c4762a1bSJed Brown \begin{equation}
7c4762a1bSJed Brown   f_i = \mathrm{riemann}(\mathrm{phys}, p_\mathrm{centroid}, \hat n, x^L, x^R)
8c4762a1bSJed Brown \end{equation}
9c4762a1bSJed Brown and then update the cell values given the cell volume.
10c4762a1bSJed Brown \begin{eqnarray}
11c4762a1bSJed Brown     f^L_i &-=& \frac{f_i}{vol^L} \\
12c4762a1bSJed Brown     f^R_i &+=& \frac{f_i}{vol^R}
13c4762a1bSJed Brown \end{eqnarray}
14c4762a1bSJed Brown 
15c4762a1bSJed Brown As an example, we can consider the shallow water wave equation,
16c4762a1bSJed Brown \begin{eqnarray}
17c4762a1bSJed Brown      h_t + \nabla\cdot \left( uh                              \right) &=& 0 \\
18c4762a1bSJed Brown   (uh)_t + \nabla\cdot \left( u\otimes uh + \frac{g h^2}{2} I \right) &=& 0
19c4762a1bSJed Brown \end{eqnarray}
20c4762a1bSJed Brown where $h$ is wave height, $u$ is wave velocity, and $g$ is the acceleration due to gravity.
21c4762a1bSJed Brown 
22c4762a1bSJed Brown A representative Riemann solver for the shallow water equations is given in the PhysicsRiemann_SW() function,
23c4762a1bSJed Brown \begin{eqnarray}
24c4762a1bSJed Brown   f^{L,R}_h    &=& uh^{L,R} \cdot \hat n \\
25c4762a1bSJed Brown   f^{L,R}_{uh} &=& \frac{f^{L,R}_h}{h^{L,R}} uh^{L,R} + g (h^{L,R})^2 \hat n \\
26c4762a1bSJed Brown   c^{L,R}      &=& \sqrt{g h^{L,R}} \\
27c4762a1bSJed Brown   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) \\
28c4762a1bSJed Brown   f_i          &=& \frac{A_\mathrm{face}}{2} \left( f^L_i + f^R_i + s \left( x^L_i - x^R_i \right) \right)
29c4762a1bSJed Brown \end{eqnarray}
30c4762a1bSJed Brown where $c$ is the local gravity wave speed and $f_i$ is a Rusanov flux.
31c4762a1bSJed Brown 
32c4762a1bSJed Brown The more sophisticated residual evaluation in RHSFunctionLocal_LS() uses a least-squares fit to a quadratic polynomial
33c4762a1bSJed Brown over a neighborhood of the given element.
34c4762a1bSJed Brown 
35c4762a1bSJed Brown The mesh is read in from an ExodusII file, usually generated by Cubit.
36c4762a1bSJed Brown F*/
37c4762a1bSJed Brown #include <petscdmplex.h>
38c4762a1bSJed Brown #include <petscdmforest.h>
39c4762a1bSJed Brown #include <petscds.h>
40c4762a1bSJed Brown #include <petscts.h>
41c4762a1bSJed Brown #include <petscsf.h> /* For SplitFaces() */
42c4762a1bSJed Brown 
43c4762a1bSJed Brown #define DIM 2                   /* Geometric dimension */
44c4762a1bSJed Brown #define ALEN(a) (sizeof(a)/sizeof((a)[0]))
45c4762a1bSJed Brown 
46c4762a1bSJed Brown static PetscFunctionList PhysicsList;
47c4762a1bSJed Brown 
48c4762a1bSJed Brown /* Represents continuum physical equations. */
49c4762a1bSJed Brown typedef struct _n_Physics *Physics;
50c4762a1bSJed Brown 
51c4762a1bSJed Brown /* Physical model includes boundary conditions, initial conditions, and functionals of interest. It is
52c4762a1bSJed Brown  * discretization-independent, but its members depend on the scenario being solved. */
53c4762a1bSJed Brown typedef struct _n_Model *Model;
54c4762a1bSJed Brown 
55c4762a1bSJed Brown /* 'User' implements a discretization of a continuous model. */
56c4762a1bSJed Brown typedef struct _n_User *User;
57c4762a1bSJed Brown typedef PetscErrorCode (*SolutionFunction)(Model,PetscReal,const PetscReal*,PetscScalar*,void*);
58c4762a1bSJed Brown typedef PetscErrorCode (*SetUpBCFunction)(PetscDS,Physics);
59c4762a1bSJed Brown typedef PetscErrorCode (*FunctionalFunction)(Model,PetscReal,const PetscReal*,const PetscScalar*,PetscReal*,void*);
60c4762a1bSJed Brown typedef PetscErrorCode (*SetupFields)(Physics,PetscSection);
61c4762a1bSJed Brown static PetscErrorCode ModelSolutionSetDefault(Model,SolutionFunction,void*);
62c4762a1bSJed Brown static PetscErrorCode ModelFunctionalRegister(Model,const char*,PetscInt*,FunctionalFunction,void*);
63c4762a1bSJed Brown static PetscErrorCode OutputVTK(DM,const char*,PetscViewer*);
64c4762a1bSJed Brown 
65c4762a1bSJed Brown struct FieldDescription {
66c4762a1bSJed Brown   const char *name;
67c4762a1bSJed Brown   PetscInt dof;
68c4762a1bSJed Brown };
69c4762a1bSJed Brown 
70c4762a1bSJed Brown typedef struct _n_FunctionalLink *FunctionalLink;
71c4762a1bSJed Brown struct _n_FunctionalLink {
72c4762a1bSJed Brown   char               *name;
73c4762a1bSJed Brown   FunctionalFunction func;
74c4762a1bSJed Brown   void               *ctx;
75c4762a1bSJed Brown   PetscInt           offset;
76c4762a1bSJed Brown   FunctionalLink     next;
77c4762a1bSJed Brown };
78c4762a1bSJed Brown 
79c4762a1bSJed Brown struct _n_Physics {
80c4762a1bSJed Brown   PetscRiemannFunc riemann;
81c4762a1bSJed Brown   PetscInt         dof;          /* number of degrees of freedom per cell */
82c4762a1bSJed Brown   PetscReal        maxspeed;     /* kludge to pick initial time step, need to add monitoring and step control */
83c4762a1bSJed Brown   void             *data;
84c4762a1bSJed Brown   PetscInt         nfields;
85c4762a1bSJed Brown   const struct FieldDescription *field_desc;
86c4762a1bSJed Brown };
87c4762a1bSJed Brown 
88c4762a1bSJed Brown struct _n_Model {
89c4762a1bSJed Brown   MPI_Comm         comm;        /* Does not do collective communicaton, but some error conditions can be collective */
90c4762a1bSJed Brown   Physics          physics;
91c4762a1bSJed Brown   FunctionalLink   functionalRegistry;
92c4762a1bSJed Brown   PetscInt         maxComputed;
93c4762a1bSJed Brown   PetscInt         numMonitored;
94c4762a1bSJed Brown   FunctionalLink   *functionalMonitored;
95c4762a1bSJed Brown   PetscInt         numCall;
96c4762a1bSJed Brown   FunctionalLink   *functionalCall;
97c4762a1bSJed Brown   SolutionFunction solution;
98c4762a1bSJed Brown   SetUpBCFunction  setupbc;
99c4762a1bSJed Brown   void             *solutionctx;
100c4762a1bSJed Brown   PetscReal        maxspeed;    /* estimate of global maximum speed (for CFL calculation) */
101c4762a1bSJed Brown   PetscReal        bounds[2*DIM];
102c4762a1bSJed Brown   DMBoundaryType   bcs[3];
103c4762a1bSJed Brown   PetscErrorCode   (*errorIndicator)(PetscInt, PetscReal, PetscInt, const PetscScalar[], const PetscScalar[], PetscReal *, void *);
104c4762a1bSJed Brown   void             *errorCtx;
105c4762a1bSJed Brown };
106c4762a1bSJed Brown 
107c4762a1bSJed Brown struct _n_User {
108c4762a1bSJed Brown   PetscInt numSplitFaces;
109c4762a1bSJed Brown   PetscInt vtkInterval;   /* For monitor */
110c4762a1bSJed Brown   char outputBasename[PETSC_MAX_PATH_LEN]; /* Basename for output files */
111c4762a1bSJed Brown   PetscInt monitorStepOffset;
112c4762a1bSJed Brown   Model    model;
113c4762a1bSJed Brown   PetscBool vtkmon;
114c4762a1bSJed Brown };
115c4762a1bSJed Brown 
116c4762a1bSJed Brown PETSC_STATIC_INLINE PetscReal DotDIMReal(const PetscReal *x,const PetscReal *y)
117c4762a1bSJed Brown {
118c4762a1bSJed Brown   PetscInt  i;
119c4762a1bSJed Brown   PetscReal prod=0.0;
120c4762a1bSJed Brown 
121c4762a1bSJed Brown   for (i=0; i<DIM; i++) prod += x[i]*y[i];
122c4762a1bSJed Brown   return prod;
123c4762a1bSJed Brown }
124c4762a1bSJed Brown PETSC_STATIC_INLINE PetscReal NormDIM(const PetscReal *x) { return PetscSqrtReal(PetscAbsReal(DotDIMReal(x,x))); }
125c4762a1bSJed Brown 
126c4762a1bSJed Brown PETSC_STATIC_INLINE PetscReal Dot2Real(const PetscReal *x,const PetscReal *y) { return x[0]*y[0] + x[1]*y[1];}
127c4762a1bSJed Brown PETSC_STATIC_INLINE PetscReal Norm2Real(const PetscReal *x) { return PetscSqrtReal(PetscAbsReal(Dot2Real(x,x)));}
128c4762a1bSJed Brown PETSC_STATIC_INLINE void Normalize2Real(PetscReal *x) { PetscReal a = 1./Norm2Real(x); x[0] *= a; x[1] *= a; }
129c4762a1bSJed Brown PETSC_STATIC_INLINE void Waxpy2Real(PetscReal a,const PetscReal *x,const PetscReal *y,PetscReal *w) { w[0] = a*x[0] + y[0]; w[1] = a*x[1] + y[1]; }
130c4762a1bSJed Brown PETSC_STATIC_INLINE void Scale2Real(PetscReal a,const PetscReal *x,PetscReal *y) { y[0] = a*x[0]; y[1] = a*x[1]; }
131c4762a1bSJed Brown 
132c4762a1bSJed Brown /******************* Advect ********************/
133c4762a1bSJed Brown typedef enum {ADVECT_SOL_TILTED,ADVECT_SOL_BUMP,ADVECT_SOL_BUMP_CAVITY} AdvectSolType;
134c4762a1bSJed Brown static const char *const AdvectSolTypes[] = {"TILTED","BUMP","BUMP_CAVITY","AdvectSolType","ADVECT_SOL_",0};
135c4762a1bSJed Brown typedef enum {ADVECT_SOL_BUMP_CONE,ADVECT_SOL_BUMP_COS} AdvectSolBumpType;
136c4762a1bSJed Brown static const char *const AdvectSolBumpTypes[] = {"CONE","COS","AdvectSolBumpType","ADVECT_SOL_BUMP_",0};
137c4762a1bSJed Brown 
138c4762a1bSJed Brown typedef struct {
139c4762a1bSJed Brown   PetscReal wind[DIM];
140c4762a1bSJed Brown } Physics_Advect_Tilted;
141c4762a1bSJed Brown typedef struct {
142c4762a1bSJed Brown   PetscReal         center[DIM];
143c4762a1bSJed Brown   PetscReal         radius;
144c4762a1bSJed Brown   AdvectSolBumpType type;
145c4762a1bSJed Brown } Physics_Advect_Bump;
146c4762a1bSJed Brown 
147c4762a1bSJed Brown typedef struct {
148c4762a1bSJed Brown   PetscReal     inflowState;
149c4762a1bSJed Brown   AdvectSolType soltype;
150c4762a1bSJed Brown   union {
151c4762a1bSJed Brown     Physics_Advect_Tilted tilted;
152c4762a1bSJed Brown     Physics_Advect_Bump   bump;
153c4762a1bSJed Brown   } sol;
154c4762a1bSJed Brown   struct {
155c4762a1bSJed Brown     PetscInt Solution;
156c4762a1bSJed Brown     PetscInt Error;
157c4762a1bSJed Brown   } functional;
158c4762a1bSJed Brown } Physics_Advect;
159c4762a1bSJed Brown 
160c4762a1bSJed Brown static const struct FieldDescription PhysicsFields_Advect[] = {{"U",1},{NULL,0}};
161c4762a1bSJed Brown 
162c4762a1bSJed Brown static PetscErrorCode PhysicsBoundary_Advect_Inflow(PetscReal time, const PetscReal *c, const PetscReal *n, const PetscScalar *xI, PetscScalar *xG, void *ctx)
163c4762a1bSJed Brown {
164c4762a1bSJed Brown   Physics        phys    = (Physics)ctx;
165c4762a1bSJed Brown   Physics_Advect *advect = (Physics_Advect*)phys->data;
166c4762a1bSJed Brown 
167c4762a1bSJed Brown   PetscFunctionBeginUser;
168c4762a1bSJed Brown   xG[0] = advect->inflowState;
169c4762a1bSJed Brown   PetscFunctionReturn(0);
170c4762a1bSJed Brown }
171c4762a1bSJed Brown 
172c4762a1bSJed Brown static PetscErrorCode PhysicsBoundary_Advect_Outflow(PetscReal time, const PetscReal *c, const PetscReal *n, const PetscScalar *xI, PetscScalar *xG, void *ctx)
173c4762a1bSJed Brown {
174c4762a1bSJed Brown   PetscFunctionBeginUser;
175c4762a1bSJed Brown   xG[0] = xI[0];
176c4762a1bSJed Brown   PetscFunctionReturn(0);
177c4762a1bSJed Brown }
178c4762a1bSJed Brown 
179c4762a1bSJed Brown 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)
180c4762a1bSJed Brown {
181c4762a1bSJed Brown   Physics_Advect *advect = (Physics_Advect*)phys->data;
182c4762a1bSJed Brown   PetscReal      wind[DIM],wn;
183c4762a1bSJed Brown 
184c4762a1bSJed Brown   switch (advect->soltype) {
185c4762a1bSJed Brown   case ADVECT_SOL_TILTED: {
186c4762a1bSJed Brown     Physics_Advect_Tilted *tilted = &advect->sol.tilted;
187c4762a1bSJed Brown     wind[0] = tilted->wind[0];
188c4762a1bSJed Brown     wind[1] = tilted->wind[1];
189c4762a1bSJed Brown   } break;
190c4762a1bSJed Brown   case ADVECT_SOL_BUMP:
191c4762a1bSJed Brown     wind[0] = -qp[1];
192c4762a1bSJed Brown     wind[1] = qp[0];
193c4762a1bSJed Brown     break;
194c4762a1bSJed Brown   case ADVECT_SOL_BUMP_CAVITY:
195c4762a1bSJed Brown     {
196c4762a1bSJed Brown       PetscInt  i;
197c4762a1bSJed Brown       PetscReal comp2[3] = {0.,0.,0.}, rad2;
198c4762a1bSJed Brown 
199c4762a1bSJed Brown       rad2 = 0.;
200c4762a1bSJed Brown       for (i = 0; i < dim; i++) {
201c4762a1bSJed Brown         comp2[i] = qp[i] * qp[i];
202c4762a1bSJed Brown         rad2    += comp2[i];
203c4762a1bSJed Brown       }
204c4762a1bSJed Brown 
205c4762a1bSJed Brown       wind[0] = -qp[1];
206c4762a1bSJed Brown       wind[1] = qp[0];
207c4762a1bSJed Brown       if (rad2 > 1.) {
208c4762a1bSJed Brown         PetscInt  maxI = 0;
209c4762a1bSJed Brown         PetscReal maxComp2 = comp2[0];
210c4762a1bSJed Brown 
211c4762a1bSJed Brown         for (i = 1; i < dim; i++) {
212c4762a1bSJed Brown           if (comp2[i] > maxComp2) {
213c4762a1bSJed Brown             maxI     = i;
214c4762a1bSJed Brown             maxComp2 = comp2[i];
215c4762a1bSJed Brown           }
216c4762a1bSJed Brown         }
217c4762a1bSJed Brown         wind[maxI] = 0.;
218c4762a1bSJed Brown       }
219c4762a1bSJed Brown     }
220c4762a1bSJed Brown     break;
221c4762a1bSJed Brown   default:
222c4762a1bSJed Brown   {
223c4762a1bSJed Brown     PetscInt i;
224c4762a1bSJed Brown     for (i = 0; i < DIM; ++i) wind[i] = 0.0;
225c4762a1bSJed Brown   }
226c4762a1bSJed Brown   /* default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for solution type %s",AdvectSolBumpTypes[advect->soltype]); */
227c4762a1bSJed Brown   }
228c4762a1bSJed Brown   wn      = Dot2Real(wind, n);
229c4762a1bSJed Brown   flux[0] = (wn > 0 ? xL[0] : xR[0]) * wn;
230c4762a1bSJed Brown }
231c4762a1bSJed Brown 
232c4762a1bSJed Brown static PetscErrorCode PhysicsSolution_Advect(Model mod,PetscReal time,const PetscReal *x,PetscScalar *u,void *ctx)
233c4762a1bSJed Brown {
234c4762a1bSJed Brown   Physics        phys    = (Physics)ctx;
235c4762a1bSJed Brown   Physics_Advect *advect = (Physics_Advect*)phys->data;
236c4762a1bSJed Brown 
237c4762a1bSJed Brown   PetscFunctionBeginUser;
238c4762a1bSJed Brown   switch (advect->soltype) {
239c4762a1bSJed Brown   case ADVECT_SOL_TILTED: {
240c4762a1bSJed Brown     PetscReal             x0[DIM];
241c4762a1bSJed Brown     Physics_Advect_Tilted *tilted = &advect->sol.tilted;
242c4762a1bSJed Brown     Waxpy2Real(-time,tilted->wind,x,x0);
243c4762a1bSJed Brown     if (x0[1] > 0) u[0] = 1.*x[0] + 3.*x[1];
244c4762a1bSJed Brown     else u[0] = advect->inflowState;
245c4762a1bSJed Brown   } break;
246c4762a1bSJed Brown   case ADVECT_SOL_BUMP_CAVITY:
247c4762a1bSJed Brown   case ADVECT_SOL_BUMP: {
248c4762a1bSJed Brown     Physics_Advect_Bump *bump = &advect->sol.bump;
249c4762a1bSJed Brown     PetscReal           x0[DIM],v[DIM],r,cost,sint;
250c4762a1bSJed Brown     cost  = PetscCosReal(time);
251c4762a1bSJed Brown     sint  = PetscSinReal(time);
252c4762a1bSJed Brown     x0[0] = cost*x[0] + sint*x[1];
253c4762a1bSJed Brown     x0[1] = -sint*x[0] + cost*x[1];
254c4762a1bSJed Brown     Waxpy2Real(-1,bump->center,x0,v);
255c4762a1bSJed Brown     r = Norm2Real(v);
256c4762a1bSJed Brown     switch (bump->type) {
257c4762a1bSJed Brown     case ADVECT_SOL_BUMP_CONE:
258c4762a1bSJed Brown       u[0] = PetscMax(1 - r/bump->radius,0);
259c4762a1bSJed Brown       break;
260c4762a1bSJed Brown     case ADVECT_SOL_BUMP_COS:
261c4762a1bSJed Brown       u[0] = 0.5 + 0.5*PetscCosReal(PetscMin(r/bump->radius,1)*PETSC_PI);
262c4762a1bSJed Brown       break;
263c4762a1bSJed Brown     }
264c4762a1bSJed Brown   } break;
265c4762a1bSJed Brown   default: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unknown solution type");
266c4762a1bSJed Brown   }
267c4762a1bSJed Brown   PetscFunctionReturn(0);
268c4762a1bSJed Brown }
269c4762a1bSJed Brown 
270c4762a1bSJed Brown static PetscErrorCode PhysicsFunctional_Advect(Model mod,PetscReal time,const PetscReal *x,const PetscScalar *y,PetscReal *f,void *ctx)
271c4762a1bSJed Brown {
272c4762a1bSJed Brown   Physics        phys    = (Physics)ctx;
273c4762a1bSJed Brown   Physics_Advect *advect = (Physics_Advect*)phys->data;
274c4762a1bSJed Brown   PetscScalar    yexact[1];
275c4762a1bSJed Brown   PetscErrorCode ierr;
276c4762a1bSJed Brown 
277c4762a1bSJed Brown   PetscFunctionBeginUser;
278c4762a1bSJed Brown   ierr = PhysicsSolution_Advect(mod,time,x,yexact,phys);CHKERRQ(ierr);
279c4762a1bSJed Brown   f[advect->functional.Solution] = PetscRealPart(y[0]);
280c4762a1bSJed Brown   f[advect->functional.Error] = PetscAbsScalar(y[0]-yexact[0]);
281c4762a1bSJed Brown   PetscFunctionReturn(0);
282c4762a1bSJed Brown }
283c4762a1bSJed Brown 
284c4762a1bSJed Brown static PetscErrorCode SetUpBC_Advect(PetscDS prob, Physics phys)
285c4762a1bSJed Brown {
286c4762a1bSJed Brown   PetscErrorCode ierr;
287c4762a1bSJed Brown   const PetscInt inflowids[] = {100,200,300},outflowids[] = {101};
288c4762a1bSJed Brown 
289c4762a1bSJed Brown   PetscFunctionBeginUser;
290c4762a1bSJed Brown   /* Register "canned" boundary conditions and defaults for where to apply. */
291c4762a1bSJed Brown   ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "inflow",  "Face Sets", 0, 0, NULL, (void (*)(void)) PhysicsBoundary_Advect_Inflow,  ALEN(inflowids),  inflowids,  phys);CHKERRQ(ierr);
292c4762a1bSJed Brown   ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "outflow", "Face Sets", 0, 0, NULL, (void (*)(void)) PhysicsBoundary_Advect_Outflow, ALEN(outflowids), outflowids, phys);CHKERRQ(ierr);
293c4762a1bSJed Brown   PetscFunctionReturn(0);
294c4762a1bSJed Brown }
295c4762a1bSJed Brown 
296c4762a1bSJed Brown static PetscErrorCode PhysicsCreate_Advect(Model mod,Physics phys,PetscOptionItems *PetscOptionsObject)
297c4762a1bSJed Brown {
298c4762a1bSJed Brown   Physics_Advect *advect;
299c4762a1bSJed Brown   PetscErrorCode ierr;
300c4762a1bSJed Brown 
301c4762a1bSJed Brown   PetscFunctionBeginUser;
302c4762a1bSJed Brown   phys->field_desc = PhysicsFields_Advect;
303c4762a1bSJed Brown   phys->riemann    = (PetscRiemannFunc)PhysicsRiemann_Advect;
304c4762a1bSJed Brown   ierr = PetscNew(&advect);CHKERRQ(ierr);
305c4762a1bSJed Brown   phys->data       = advect;
306c4762a1bSJed Brown   mod->setupbc = SetUpBC_Advect;
307c4762a1bSJed Brown 
308c4762a1bSJed Brown   ierr = PetscOptionsHead(PetscOptionsObject,"Advect options");CHKERRQ(ierr);
309c4762a1bSJed Brown   {
310c4762a1bSJed Brown     PetscInt two = 2,dof = 1;
311c4762a1bSJed Brown     advect->soltype = ADVECT_SOL_TILTED;
312c4762a1bSJed Brown     ierr = PetscOptionsEnum("-advect_sol_type","solution type","",AdvectSolTypes,(PetscEnum)advect->soltype,(PetscEnum*)&advect->soltype,NULL);CHKERRQ(ierr);
313c4762a1bSJed Brown     switch (advect->soltype) {
314c4762a1bSJed Brown     case ADVECT_SOL_TILTED: {
315c4762a1bSJed Brown       Physics_Advect_Tilted *tilted = &advect->sol.tilted;
316c4762a1bSJed Brown       two = 2;
317c4762a1bSJed Brown       tilted->wind[0] = 0.0;
318c4762a1bSJed Brown       tilted->wind[1] = 1.0;
319c4762a1bSJed Brown       ierr = PetscOptionsRealArray("-advect_tilted_wind","background wind vx,vy","",tilted->wind,&two,NULL);CHKERRQ(ierr);
320c4762a1bSJed Brown       advect->inflowState = -2.0;
321c4762a1bSJed Brown       ierr = PetscOptionsRealArray("-advect_tilted_inflow","Inflow state","",&advect->inflowState,&dof,NULL);CHKERRQ(ierr);
322c4762a1bSJed Brown       phys->maxspeed = Norm2Real(tilted->wind);
323c4762a1bSJed Brown     } break;
324c4762a1bSJed Brown     case ADVECT_SOL_BUMP_CAVITY:
325c4762a1bSJed Brown     case ADVECT_SOL_BUMP: {
326c4762a1bSJed Brown       Physics_Advect_Bump *bump = &advect->sol.bump;
327c4762a1bSJed Brown       two = 2;
328c4762a1bSJed Brown       bump->center[0] = 2.;
329c4762a1bSJed Brown       bump->center[1] = 0.;
330c4762a1bSJed Brown       ierr = PetscOptionsRealArray("-advect_bump_center","location of center of bump x,y","",bump->center,&two,NULL);CHKERRQ(ierr);
331c4762a1bSJed Brown       bump->radius = 0.9;
332c4762a1bSJed Brown       ierr = PetscOptionsReal("-advect_bump_radius","radius of bump","",bump->radius,&bump->radius,NULL);CHKERRQ(ierr);
333c4762a1bSJed Brown       bump->type = ADVECT_SOL_BUMP_CONE;
334c4762a1bSJed Brown       ierr = PetscOptionsEnum("-advect_bump_type","type of bump","",AdvectSolBumpTypes,(PetscEnum)bump->type,(PetscEnum*)&bump->type,NULL);CHKERRQ(ierr);
335c4762a1bSJed Brown       phys->maxspeed = 3.;       /* radius of mesh, kludge */
336c4762a1bSJed Brown     } break;
337c4762a1bSJed Brown     }
338c4762a1bSJed Brown   }
339c4762a1bSJed Brown   ierr = PetscOptionsTail();CHKERRQ(ierr);
340c4762a1bSJed Brown   /* Initial/transient solution with default boundary conditions */
341c4762a1bSJed Brown   ierr = ModelSolutionSetDefault(mod,PhysicsSolution_Advect,phys);CHKERRQ(ierr);
342c4762a1bSJed Brown   /* Register "canned" functionals */
343c4762a1bSJed Brown   ierr = ModelFunctionalRegister(mod,"Solution",&advect->functional.Solution,PhysicsFunctional_Advect,phys);CHKERRQ(ierr);
344c4762a1bSJed Brown   ierr = ModelFunctionalRegister(mod,"Error",&advect->functional.Error,PhysicsFunctional_Advect,phys);CHKERRQ(ierr);
345c4762a1bSJed Brown   mod->bcs[0] = mod->bcs[1] = mod->bcs[2] = DM_BOUNDARY_GHOSTED;
346c4762a1bSJed Brown   PetscFunctionReturn(0);
347c4762a1bSJed Brown }
348c4762a1bSJed Brown 
349c4762a1bSJed Brown /******************* Shallow Water ********************/
350c4762a1bSJed Brown typedef struct {
351c4762a1bSJed Brown   PetscReal gravity;
352c4762a1bSJed Brown   PetscReal boundaryHeight;
353c4762a1bSJed Brown   struct {
354c4762a1bSJed Brown     PetscInt Height;
355c4762a1bSJed Brown     PetscInt Speed;
356c4762a1bSJed Brown     PetscInt Energy;
357c4762a1bSJed Brown   } functional;
358c4762a1bSJed Brown } Physics_SW;
359c4762a1bSJed Brown typedef struct {
360c4762a1bSJed Brown   PetscReal h;
361c4762a1bSJed Brown   PetscReal uh[DIM];
362c4762a1bSJed Brown } SWNode;
363c4762a1bSJed Brown typedef union {
364c4762a1bSJed Brown   SWNode    swnode;
365c4762a1bSJed Brown   PetscReal vals[DIM+1];
366c4762a1bSJed Brown } SWNodeUnion;
367c4762a1bSJed Brown 
368c4762a1bSJed Brown static const struct FieldDescription PhysicsFields_SW[] = {{"Height",1},{"Momentum",DIM},{NULL,0}};
369c4762a1bSJed Brown 
370c4762a1bSJed Brown /*
371c4762a1bSJed Brown  * h_t + div(uh) = 0
372c4762a1bSJed Brown  * (uh)_t + div (u\otimes uh + g h^2 / 2 I) = 0
373c4762a1bSJed Brown  *
374c4762a1bSJed Brown  * */
375c4762a1bSJed Brown static PetscErrorCode SWFlux(Physics phys,const PetscReal *n,const SWNode *x,SWNode *f)
376c4762a1bSJed Brown {
377c4762a1bSJed Brown   Physics_SW  *sw = (Physics_SW*)phys->data;
378c4762a1bSJed Brown   PetscReal   uhn,u[DIM];
379c4762a1bSJed Brown   PetscInt     i;
380c4762a1bSJed Brown 
381c4762a1bSJed Brown   PetscFunctionBeginUser;
382c4762a1bSJed Brown   Scale2Real(1./x->h,x->uh,u);
383c4762a1bSJed Brown   uhn  = x->uh[0] * n[0] + x->uh[1] * n[1];
384c4762a1bSJed Brown   f->h = uhn;
385c4762a1bSJed Brown   for (i=0; i<DIM; i++) f->uh[i] = u[i] * uhn + sw->gravity * PetscSqr(x->h) * n[i];
386c4762a1bSJed Brown   PetscFunctionReturn(0);
387c4762a1bSJed Brown }
388c4762a1bSJed Brown 
389c4762a1bSJed Brown static PetscErrorCode PhysicsBoundary_SW_Wall(PetscReal time, const PetscReal *c, const PetscReal *n, const PetscScalar *xI, PetscScalar *xG, void *ctx)
390c4762a1bSJed Brown {
391c4762a1bSJed Brown   PetscFunctionBeginUser;
392c4762a1bSJed Brown   xG[0] = xI[0];
393c4762a1bSJed Brown   xG[1] = -xI[1];
394c4762a1bSJed Brown   xG[2] = -xI[2];
395c4762a1bSJed Brown   PetscFunctionReturn(0);
396c4762a1bSJed Brown }
397c4762a1bSJed Brown 
398c4762a1bSJed Brown static void PhysicsRiemann_SW(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)
399c4762a1bSJed Brown {
400c4762a1bSJed Brown   Physics_SW   *sw = (Physics_SW*)phys->data;
401c4762a1bSJed Brown   PetscReal    cL,cR,speed;
402c4762a1bSJed Brown   PetscReal    nn[DIM];
403c4762a1bSJed Brown #if !defined(PETSC_USE_COMPLEX)
404c4762a1bSJed Brown   const SWNode *uL = (const SWNode*)xL,*uR = (const SWNode*)xR;
405c4762a1bSJed Brown #else
406c4762a1bSJed Brown   SWNodeUnion  uLreal, uRreal;
407c4762a1bSJed Brown   const SWNode *uL = &uLreal.swnode;
408c4762a1bSJed Brown   const SWNode *uR = &uRreal.swnode;
409c4762a1bSJed Brown #endif
410c4762a1bSJed Brown   SWNodeUnion  fL,fR;
411c4762a1bSJed Brown   PetscInt     i;
412c4762a1bSJed Brown   PetscReal    zero=0.;
413c4762a1bSJed Brown 
414c4762a1bSJed Brown #if defined(PETSC_USE_COMPLEX)
415c4762a1bSJed Brown   uLreal.swnode.h = 0; uRreal.swnode.h = 0;
416c4762a1bSJed Brown   for (i = 0; i < 1+dim; i++) uLreal.vals[i] = PetscRealPart(xL[i]);
417c4762a1bSJed Brown   for (i = 0; i < 1+dim; i++) uRreal.vals[i] = PetscRealPart(xR[i]);
418c4762a1bSJed Brown #endif
419c4762a1bSJed Brown   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"); */
420c4762a1bSJed Brown   nn[0] = n[0];
421c4762a1bSJed Brown   nn[1] = n[1];
422c4762a1bSJed Brown   Normalize2Real(nn);
423c4762a1bSJed Brown   SWFlux(phys,nn,uL,&(fL.swnode));
424c4762a1bSJed Brown   SWFlux(phys,nn,uR,&(fR.swnode));
425c4762a1bSJed Brown   cL    = PetscSqrtReal(sw->gravity*uL->h);
426c4762a1bSJed Brown   cR    = PetscSqrtReal(sw->gravity*uR->h); /* gravity wave speed */
427c4762a1bSJed Brown   speed = PetscMax(PetscAbsReal(Dot2Real(uL->uh,nn)/uL->h) + cL,PetscAbsReal(Dot2Real(uR->uh,nn)/uR->h) + cR);
428c4762a1bSJed Brown   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);
429c4762a1bSJed Brown }
430c4762a1bSJed Brown 
431c4762a1bSJed Brown static PetscErrorCode PhysicsSolution_SW(Model mod,PetscReal time,const PetscReal *x,PetscScalar *u,void *ctx)
432c4762a1bSJed Brown {
433c4762a1bSJed Brown   PetscReal dx[2],r,sigma;
434c4762a1bSJed Brown 
435c4762a1bSJed Brown   PetscFunctionBeginUser;
436c4762a1bSJed Brown   if (time != 0.0) SETERRQ1(mod->comm,PETSC_ERR_SUP,"No solution known for time %g",(double)time);
437c4762a1bSJed Brown   dx[0] = x[0] - 1.5;
438c4762a1bSJed Brown   dx[1] = x[1] - 1.0;
439c4762a1bSJed Brown   r     = Norm2Real(dx);
440c4762a1bSJed Brown   sigma = 0.5;
441c4762a1bSJed Brown   u[0]  = 1 + 2*PetscExpReal(-PetscSqr(r)/(2*PetscSqr(sigma)));
442c4762a1bSJed Brown   u[1]  = 0.0;
443c4762a1bSJed Brown   u[2]  = 0.0;
444c4762a1bSJed Brown   PetscFunctionReturn(0);
445c4762a1bSJed Brown }
446c4762a1bSJed Brown 
447c4762a1bSJed Brown static PetscErrorCode PhysicsFunctional_SW(Model mod,PetscReal time,const PetscReal *coord,const PetscScalar *xx,PetscReal *f,void *ctx)
448c4762a1bSJed Brown {
449c4762a1bSJed Brown   Physics      phys = (Physics)ctx;
450c4762a1bSJed Brown   Physics_SW   *sw  = (Physics_SW*)phys->data;
451c4762a1bSJed Brown   const SWNode *x   = (const SWNode*)xx;
452c4762a1bSJed Brown   PetscReal  u[2];
453c4762a1bSJed Brown   PetscReal    h;
454c4762a1bSJed Brown 
455c4762a1bSJed Brown   PetscFunctionBeginUser;
456c4762a1bSJed Brown   h = x->h;
457c4762a1bSJed Brown   Scale2Real(1./x->h,x->uh,u);
458c4762a1bSJed Brown   f[sw->functional.Height] = h;
459c4762a1bSJed Brown   f[sw->functional.Speed]  = Norm2Real(u) + PetscSqrtReal(sw->gravity*h);
460c4762a1bSJed Brown   f[sw->functional.Energy] = 0.5*(Dot2Real(x->uh,u) + sw->gravity*PetscSqr(h));
461c4762a1bSJed Brown   PetscFunctionReturn(0);
462c4762a1bSJed Brown }
463c4762a1bSJed Brown 
464c4762a1bSJed Brown static PetscErrorCode SetUpBC_SW(PetscDS prob,Physics phys)
465c4762a1bSJed Brown {
466c4762a1bSJed Brown   PetscErrorCode ierr;
467c4762a1bSJed Brown   const PetscInt wallids[] = {100,101,200,300};
468c4762a1bSJed Brown   PetscFunctionBeginUser;
469c4762a1bSJed Brown   ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "wall", "Face Sets", 0, 0, NULL, (void (*)(void)) PhysicsBoundary_SW_Wall, ALEN(wallids), wallids, phys);CHKERRQ(ierr);
470c4762a1bSJed Brown   PetscFunctionReturn(0);
471c4762a1bSJed Brown }
472c4762a1bSJed Brown 
473c4762a1bSJed Brown static PetscErrorCode PhysicsCreate_SW(Model mod,Physics phys,PetscOptionItems *PetscOptionsObject)
474c4762a1bSJed Brown {
475c4762a1bSJed Brown   Physics_SW     *sw;
476c4762a1bSJed Brown   PetscErrorCode ierr;
477c4762a1bSJed Brown 
478c4762a1bSJed Brown   PetscFunctionBeginUser;
479c4762a1bSJed Brown   phys->field_desc = PhysicsFields_SW;
480c4762a1bSJed Brown   phys->riemann = (PetscRiemannFunc) PhysicsRiemann_SW;
481c4762a1bSJed Brown   ierr          = PetscNew(&sw);CHKERRQ(ierr);
482c4762a1bSJed Brown   phys->data    = sw;
483c4762a1bSJed Brown   mod->setupbc  = SetUpBC_SW;
484c4762a1bSJed Brown 
485c4762a1bSJed Brown   ierr          = PetscOptionsHead(PetscOptionsObject,"SW options");CHKERRQ(ierr);
486c4762a1bSJed Brown   {
487c4762a1bSJed Brown     sw->gravity = 1.0;
488c4762a1bSJed Brown     ierr = PetscOptionsReal("-sw_gravity","Gravitational constant","",sw->gravity,&sw->gravity,NULL);CHKERRQ(ierr);
489c4762a1bSJed Brown   }
490c4762a1bSJed Brown   ierr = PetscOptionsTail();CHKERRQ(ierr);
491c4762a1bSJed Brown   phys->maxspeed = PetscSqrtReal(2.0*sw->gravity); /* Mach 1 for depth of 2 */
492c4762a1bSJed Brown 
493c4762a1bSJed Brown   ierr = ModelSolutionSetDefault(mod,PhysicsSolution_SW,phys);CHKERRQ(ierr);
494c4762a1bSJed Brown   ierr = ModelFunctionalRegister(mod,"Height",&sw->functional.Height,PhysicsFunctional_SW,phys);CHKERRQ(ierr);
495c4762a1bSJed Brown   ierr = ModelFunctionalRegister(mod,"Speed",&sw->functional.Speed,PhysicsFunctional_SW,phys);CHKERRQ(ierr);
496c4762a1bSJed Brown   ierr = ModelFunctionalRegister(mod,"Energy",&sw->functional.Energy,PhysicsFunctional_SW,phys);CHKERRQ(ierr);
497c4762a1bSJed Brown 
498c4762a1bSJed Brown   mod->bcs[0] = mod->bcs[1] = mod->bcs[2] = DM_BOUNDARY_GHOSTED;
499c4762a1bSJed Brown 
500c4762a1bSJed Brown   PetscFunctionReturn(0);
501c4762a1bSJed Brown }
502c4762a1bSJed Brown 
503c4762a1bSJed Brown /******************* Euler Density Shock (EULER_IV_SHOCK,EULER_SS_SHOCK) ********************/
504c4762a1bSJed Brown /* An initial-value and self-similar solutions of the compressible Euler equations */
505c4762a1bSJed Brown /* Ravi Samtaney and D. I. Pullin */
506c4762a1bSJed Brown /* Phys. Fluids 8, 2650 (1996); http://dx.doi.org/10.1063/1.869050 */
507c4762a1bSJed Brown typedef enum {EULER_PAR_GAMMA,EULER_PAR_RHOR,EULER_PAR_AMACH,EULER_PAR_ITANA,EULER_PAR_SIZE} EulerParamIdx;
508c4762a1bSJed Brown typedef enum {EULER_IV_SHOCK,EULER_SS_SHOCK,EULER_SHOCK_TUBE,EULER_LINEAR_WAVE} EulerType;
509c4762a1bSJed Brown typedef struct {
510c4762a1bSJed Brown   PetscReal r;
511c4762a1bSJed Brown   PetscReal ru[DIM];
512c4762a1bSJed Brown   PetscReal E;
513c4762a1bSJed Brown } EulerNode;
514c4762a1bSJed Brown typedef union {
515c4762a1bSJed Brown   EulerNode eulernode;
516c4762a1bSJed Brown   PetscReal vals[DIM+2];
517c4762a1bSJed Brown } EulerNodeUnion;
518c4762a1bSJed Brown typedef PetscErrorCode (*EquationOfState)(const PetscReal*, const EulerNode*, PetscReal*);
519c4762a1bSJed Brown typedef struct {
520c4762a1bSJed Brown   EulerType       type;
521c4762a1bSJed Brown   PetscReal       pars[EULER_PAR_SIZE];
522c4762a1bSJed Brown   EquationOfState sound;
523c4762a1bSJed Brown   struct {
524c4762a1bSJed Brown     PetscInt Density;
525c4762a1bSJed Brown     PetscInt Momentum;
526c4762a1bSJed Brown     PetscInt Energy;
527c4762a1bSJed Brown     PetscInt Pressure;
528c4762a1bSJed Brown     PetscInt Speed;
529c4762a1bSJed Brown   } monitor;
530c4762a1bSJed Brown } Physics_Euler;
531c4762a1bSJed Brown 
532c4762a1bSJed Brown static const struct FieldDescription PhysicsFields_Euler[] = {{"Density",1},{"Momentum",DIM},{"Energy",1},{NULL,0}};
533c4762a1bSJed Brown 
534c4762a1bSJed Brown /* initial condition */
535c4762a1bSJed Brown int initLinearWave(EulerNode *ux, const PetscReal gamma, const PetscReal coord[], const PetscReal Lx);
536c4762a1bSJed Brown static PetscErrorCode PhysicsSolution_Euler(Model mod, PetscReal time, const PetscReal *x, PetscScalar *u, void *ctx)
537c4762a1bSJed Brown {
538c4762a1bSJed Brown   PetscInt i;
539c4762a1bSJed Brown   Physics         phys = (Physics)ctx;
540c4762a1bSJed Brown   Physics_Euler   *eu  = (Physics_Euler*)phys->data;
541c4762a1bSJed Brown   EulerNode       *uu  = (EulerNode*)u;
542c4762a1bSJed Brown   PetscReal        p0,gamma,c;
543c4762a1bSJed Brown   PetscFunctionBeginUser;
544c4762a1bSJed Brown   if (time != 0.0) SETERRQ1(mod->comm,PETSC_ERR_SUP,"No solution known for time %g",(double)time);
545c4762a1bSJed Brown 
546c4762a1bSJed Brown   for (i=0; i<DIM; i++) uu->ru[i] = 0.0; /* zero out initial velocity */
547c4762a1bSJed Brown   /* set E and rho */
548c4762a1bSJed Brown   gamma = eu->pars[EULER_PAR_GAMMA];
549c4762a1bSJed Brown 
550c4762a1bSJed Brown   if (eu->type==EULER_IV_SHOCK || eu->type==EULER_SS_SHOCK) {
551c4762a1bSJed Brown     /******************* Euler Density Shock ********************/
552c4762a1bSJed Brown     /* On initial-value and self-similar solutions of the compressible Euler equations */
553c4762a1bSJed Brown     /* Ravi Samtaney and D. I. Pullin */
554c4762a1bSJed Brown     /* Phys. Fluids 8, 2650 (1996); http://dx.doi.org/10.1063/1.869050 */
555c4762a1bSJed Brown     /* initial conditions 1: left of shock, 0: left of discontinuity 2: right of discontinuity,  */
556c4762a1bSJed Brown     p0 = 1.;
557c4762a1bSJed Brown     if (x[0] < 0.0 + x[1]*eu->pars[EULER_PAR_ITANA]) {
558c4762a1bSJed Brown       if (x[0] < mod->bounds[0]*0.5) { /* left of shock (1) */
559c4762a1bSJed Brown         PetscReal amach,rho,press,gas1,p1;
560c4762a1bSJed Brown         amach = eu->pars[EULER_PAR_AMACH];
561c4762a1bSJed Brown         rho = 1.;
562c4762a1bSJed Brown         press = p0;
563c4762a1bSJed Brown         p1 = press*(1.0+2.0*gamma/(gamma+1.0)*(amach*amach-1.0));
564c4762a1bSJed Brown         gas1 = (gamma-1.0)/(gamma+1.0);
565c4762a1bSJed Brown         uu->r = rho*(p1/press+gas1)/(gas1*p1/press+1.0);
566c4762a1bSJed Brown         uu->ru[0]   = ((uu->r - rho)*PetscSqrtReal(gamma*press/rho)*amach);
567c4762a1bSJed Brown         uu->E = p1/(gamma-1.0) + .5/uu->r*uu->ru[0]*uu->ru[0];
568c4762a1bSJed Brown       }
569c4762a1bSJed Brown       else { /* left of discontinuity (0) */
570c4762a1bSJed Brown         uu->r = 1.; /* rho = 1 */
571c4762a1bSJed Brown         uu->E = p0/(gamma-1.0);
572c4762a1bSJed Brown       }
573c4762a1bSJed Brown     }
574c4762a1bSJed Brown     else { /* right of discontinuity (2) */
575c4762a1bSJed Brown       uu->r = eu->pars[EULER_PAR_RHOR];
576c4762a1bSJed Brown       uu->E = p0/(gamma-1.0);
577c4762a1bSJed Brown     }
578c4762a1bSJed Brown   }
579c4762a1bSJed Brown   else if (eu->type==EULER_SHOCK_TUBE) {
580c4762a1bSJed Brown     /* For (x<x0) set (rho,u,p)=(8,0,10) and for (x>x0) set (rho,u,p)=(1,0,1). Choose x0 to the midpoint of the domain in the x-direction. */
581c4762a1bSJed Brown     if (x[0] < 0.0 ) {
582c4762a1bSJed Brown       uu->r = 8.;
583c4762a1bSJed Brown       uu->E = 10./(gamma-1.);
584c4762a1bSJed Brown     }
585c4762a1bSJed Brown     else {
586c4762a1bSJed Brown       uu->r = 1.;
587c4762a1bSJed Brown       uu->E = 1./(gamma-1.);
588c4762a1bSJed Brown     }
589c4762a1bSJed Brown   }
590c4762a1bSJed Brown   else if (eu->type==EULER_LINEAR_WAVE) {
591c4762a1bSJed Brown     initLinearWave( uu, gamma, x, mod->bounds[1] - mod->bounds[0]);
592c4762a1bSJed Brown   }
593c4762a1bSJed Brown   else SETERRQ1(mod->comm,PETSC_ERR_SUP,"Unknown type %d",eu->type);
594c4762a1bSJed Brown 
595c4762a1bSJed Brown   /* set phys->maxspeed: (mod->maxspeed = phys->maxspeed) in main; */
596c4762a1bSJed Brown   eu->sound(&gamma,uu,&c);
597c4762a1bSJed Brown   c = (uu->ru[0]/uu->r) + c;
598c4762a1bSJed Brown   if (c > phys->maxspeed) phys->maxspeed = c;
599c4762a1bSJed Brown 
600c4762a1bSJed Brown   PetscFunctionReturn(0);
601c4762a1bSJed Brown }
602c4762a1bSJed Brown 
603c4762a1bSJed Brown static PetscErrorCode Pressure_PG(const PetscReal gamma,const EulerNode *x,PetscReal *p)
604c4762a1bSJed Brown {
605c4762a1bSJed Brown   PetscReal ru2;
606c4762a1bSJed Brown 
607c4762a1bSJed Brown   PetscFunctionBeginUser;
608c4762a1bSJed Brown   ru2  = DotDIMReal(x->ru,x->ru);
609c4762a1bSJed Brown   (*p)=(x->E - 0.5*ru2/x->r)*(gamma - 1.0); /* (E - rho V^2/2)(gamma-1) = e rho (gamma-1) */
610c4762a1bSJed Brown   PetscFunctionReturn(0);
611c4762a1bSJed Brown }
612c4762a1bSJed Brown 
613c4762a1bSJed Brown static PetscErrorCode SpeedOfSound_PG(const PetscReal *gamma, const EulerNode *x, PetscReal *c)
614c4762a1bSJed Brown {
615c4762a1bSJed Brown   PetscReal p;
616c4762a1bSJed Brown 
617c4762a1bSJed Brown   PetscFunctionBeginUser;
618c4762a1bSJed Brown   Pressure_PG(*gamma,x,&p);
619c4762a1bSJed Brown   if (p<0.) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"negative pressure time %g -- NEED TO FIX!!!!!!",(double) p);
620c4762a1bSJed Brown   /* pars[EULER_PAR_GAMMA] = heat capacity ratio */
621c4762a1bSJed Brown   (*c)=PetscSqrtReal(*gamma * p / x->r);
622c4762a1bSJed Brown   PetscFunctionReturn(0);
623c4762a1bSJed Brown }
624c4762a1bSJed Brown 
625c4762a1bSJed Brown /*
626c4762a1bSJed Brown  * x = (rho,rho*(u_1),...,rho*e)^T
627c4762a1bSJed Brown  * x_t+div(f_1(x))+...+div(f_DIM(x)) = 0
628c4762a1bSJed Brown  *
629c4762a1bSJed Brown  * f_i(x) = u_i*x+(0,0,...,p,...,p*u_i)^T
630c4762a1bSJed Brown  *
631c4762a1bSJed Brown  */
632c4762a1bSJed Brown static PetscErrorCode EulerFlux(Physics phys,const PetscReal *n,const EulerNode *x,EulerNode *f)
633c4762a1bSJed Brown {
634c4762a1bSJed Brown   Physics_Euler *eu = (Physics_Euler*)phys->data;
635c4762a1bSJed Brown   PetscReal     nu,p;
636c4762a1bSJed Brown   PetscInt      i;
637c4762a1bSJed Brown 
638c4762a1bSJed Brown   PetscFunctionBeginUser;
639c4762a1bSJed Brown   Pressure_PG(eu->pars[EULER_PAR_GAMMA],x,&p);
640c4762a1bSJed Brown   nu = DotDIMReal(x->ru,n);
641c4762a1bSJed Brown   f->r = nu;   /* A rho u */
642c4762a1bSJed Brown   nu /= x->r;  /* A u */
643c4762a1bSJed Brown   for (i=0; i<DIM; i++) f->ru[i] = nu * x->ru[i] + n[i]*p;  /* r u^2 + p */
644c4762a1bSJed Brown   f->E = nu * (x->E + p); /* u(e+p) */
645c4762a1bSJed Brown   PetscFunctionReturn(0);
646c4762a1bSJed Brown }
647c4762a1bSJed Brown 
648c4762a1bSJed Brown /* PetscReal* => EulerNode* conversion */
649c4762a1bSJed Brown static PetscErrorCode PhysicsBoundary_Euler_Wall(PetscReal time, const PetscReal *c, const PetscReal *n, const PetscScalar *a_xI, PetscScalar *a_xG, void *ctx)
650c4762a1bSJed Brown {
651c4762a1bSJed Brown   PetscInt    i;
652c4762a1bSJed Brown   const EulerNode *xI = (const EulerNode*)a_xI;
653c4762a1bSJed Brown   EulerNode       *xG = (EulerNode*)a_xG;
654c4762a1bSJed Brown   Physics         phys = (Physics)ctx;
655c4762a1bSJed Brown   Physics_Euler   *eu  = (Physics_Euler*)phys->data;
656c4762a1bSJed Brown   PetscFunctionBeginUser;
657c4762a1bSJed Brown   xG->r = xI->r;           /* ghost cell density - same */
658c4762a1bSJed Brown   xG->E = xI->E;           /* ghost cell energy - same */
659c4762a1bSJed Brown   if (n[1] != 0.) {        /* top and bottom */
660c4762a1bSJed Brown     xG->ru[0] =  xI->ru[0]; /* copy tang to wall */
661c4762a1bSJed Brown     xG->ru[1] = -xI->ru[1]; /* reflect perp to t/b wall */
662c4762a1bSJed Brown   }
663c4762a1bSJed Brown   else { /* sides */
664c4762a1bSJed Brown     for (i=0; i<DIM; i++) xG->ru[i] = xI->ru[i]; /* copy */
665c4762a1bSJed Brown   }
666c4762a1bSJed Brown   if (eu->type == EULER_LINEAR_WAVE) { /* debug */
667c4762a1bSJed Brown #if 0
668c4762a1bSJed Brown     PetscPrintf(PETSC_COMM_WORLD,"%s coord=%g,%g\n",PETSC_FUNCTION_NAME,c[0],c[1]);
669c4762a1bSJed Brown #endif
670c4762a1bSJed Brown   }
671c4762a1bSJed Brown   PetscFunctionReturn(0);
672c4762a1bSJed Brown }
673c4762a1bSJed Brown int godunovflux( const PetscScalar *ul, const PetscScalar *ur, PetscScalar *flux, const PetscReal *nn, const int *ndim, const PetscReal *gamma);
674c4762a1bSJed Brown /* PetscReal* => EulerNode* conversion */
675c4762a1bSJed Brown static void PhysicsRiemann_Euler_Godunov( PetscInt dim, PetscInt Nf, const PetscReal *qp, const PetscReal *n,
676c4762a1bSJed Brown                                           const PetscScalar *xL, const PetscScalar *xR, PetscInt numConstants, const PetscScalar constants[], PetscScalar *flux, Physics phys)
677c4762a1bSJed Brown {
678c4762a1bSJed Brown   Physics_Euler   *eu = (Physics_Euler*)phys->data;
679c4762a1bSJed Brown   PetscReal       cL,cR,speed,velL,velR,nn[DIM],s2;
680c4762a1bSJed Brown   PetscInt        i;
681c4762a1bSJed Brown   PetscErrorCode  ierr;
682c4762a1bSJed Brown   PetscFunctionBeginUser;
683c4762a1bSJed Brown 
684c4762a1bSJed Brown   for (i=0,s2=0.; i<DIM; i++) {
685c4762a1bSJed Brown     nn[i] = n[i];
686c4762a1bSJed Brown     s2 += nn[i]*nn[i];
687c4762a1bSJed Brown   }
688c4762a1bSJed Brown   s2 = PetscSqrtReal(s2); /* |n|_2 = sum(n^2)^1/2 */
689c4762a1bSJed Brown   for (i=0.; i<DIM; i++) nn[i] /= s2;
690c4762a1bSJed Brown   if (0) { /* Rusanov */
691c4762a1bSJed Brown     const EulerNode *uL = (const EulerNode*)xL,*uR = (const EulerNode*)xR;
692c4762a1bSJed Brown     EulerNodeUnion  fL,fR;
693c4762a1bSJed Brown     EulerFlux(phys,nn,uL,&(fL.eulernode));
694c4762a1bSJed Brown     EulerFlux(phys,nn,uR,&(fR.eulernode));
695c4762a1bSJed Brown     ierr = eu->sound(&eu->pars[EULER_PAR_GAMMA],uL,&cL);if (ierr) exit(13);
696c4762a1bSJed Brown     ierr = eu->sound(&eu->pars[EULER_PAR_GAMMA],uR,&cR);if (ierr) exit(14);
697c4762a1bSJed Brown     velL = DotDIMReal(uL->ru,nn)/uL->r;
698c4762a1bSJed Brown     velR = DotDIMReal(uR->ru,nn)/uR->r;
699c4762a1bSJed Brown     speed = PetscMax(velR + cR, velL + cL);
700c4762a1bSJed Brown     for (i=0; i<2+dim; i++) flux[i] = 0.5*((fL.vals[i]+fR.vals[i]) + speed*(xL[i] - xR[i]))*s2;
701c4762a1bSJed Brown   }
702c4762a1bSJed Brown   else {
703c4762a1bSJed Brown     int dim = DIM;
704c4762a1bSJed Brown     /* int iwave =  */
705c4762a1bSJed Brown     godunovflux(xL, xR, flux, nn, &dim, &eu->pars[EULER_PAR_GAMMA]);
706c4762a1bSJed Brown     for (i=0; i<2+dim; i++) flux[i] *= s2;
707c4762a1bSJed Brown   }
708c4762a1bSJed Brown   PetscFunctionReturnVoid();
709c4762a1bSJed Brown }
710c4762a1bSJed Brown 
711c4762a1bSJed Brown static PetscErrorCode PhysicsFunctional_Euler(Model mod,PetscReal time,const PetscReal *coord,const PetscScalar *xx,PetscReal *f,void *ctx)
712c4762a1bSJed Brown {
713c4762a1bSJed Brown   Physics         phys = (Physics)ctx;
714c4762a1bSJed Brown   Physics_Euler   *eu  = (Physics_Euler*)phys->data;
715c4762a1bSJed Brown   const EulerNode *x   = (const EulerNode*)xx;
716c4762a1bSJed Brown   PetscReal       p;
717c4762a1bSJed Brown 
718c4762a1bSJed Brown   PetscFunctionBeginUser;
719c4762a1bSJed Brown   f[eu->monitor.Density]  = x->r;
720c4762a1bSJed Brown   f[eu->monitor.Momentum] = NormDIM(x->ru);
721c4762a1bSJed Brown   f[eu->monitor.Energy]   = x->E;
722c4762a1bSJed Brown   f[eu->monitor.Speed]    = NormDIM(x->ru)/x->r;
723c4762a1bSJed Brown   Pressure_PG(eu->pars[EULER_PAR_GAMMA], x, &p);
724c4762a1bSJed Brown   f[eu->monitor.Pressure] = p;
725c4762a1bSJed Brown   PetscFunctionReturn(0);
726c4762a1bSJed Brown }
727c4762a1bSJed Brown 
728c4762a1bSJed Brown static PetscErrorCode SetUpBC_Euler(PetscDS prob,Physics phys)
729c4762a1bSJed Brown {
730c4762a1bSJed Brown   PetscErrorCode  ierr;
731c4762a1bSJed Brown   Physics_Euler   *eu = (Physics_Euler *) phys->data;
732c4762a1bSJed Brown   if (eu->type == EULER_LINEAR_WAVE) {
733c4762a1bSJed Brown     const PetscInt wallids[] = {100,101};
734c4762a1bSJed Brown     ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "wall", "Face Sets", 0, 0, NULL, (void (*)(void)) PhysicsBoundary_Euler_Wall, ALEN(wallids), wallids, phys);CHKERRQ(ierr);
735c4762a1bSJed Brown   }
736c4762a1bSJed Brown   else {
737c4762a1bSJed Brown     const PetscInt wallids[] = {100,101,200,300};
738c4762a1bSJed Brown     ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "wall", "Face Sets", 0, 0, NULL, (void (*)(void)) PhysicsBoundary_Euler_Wall, ALEN(wallids), wallids, phys);CHKERRQ(ierr);
739c4762a1bSJed Brown   }
740c4762a1bSJed Brown   PetscFunctionReturn(0);
741c4762a1bSJed Brown }
742c4762a1bSJed Brown 
743c4762a1bSJed Brown static PetscErrorCode PhysicsCreate_Euler(Model mod,Physics phys,PetscOptionItems *PetscOptionsObject)
744c4762a1bSJed Brown {
745c4762a1bSJed Brown   Physics_Euler   *eu;
746c4762a1bSJed Brown   PetscErrorCode  ierr;
747c4762a1bSJed Brown 
748c4762a1bSJed Brown   PetscFunctionBeginUser;
749c4762a1bSJed Brown   phys->field_desc = PhysicsFields_Euler;
750c4762a1bSJed Brown   phys->riemann = (PetscRiemannFunc) PhysicsRiemann_Euler_Godunov;
751c4762a1bSJed Brown   ierr = PetscNew(&eu);CHKERRQ(ierr);
752c4762a1bSJed Brown   phys->data    = eu;
753c4762a1bSJed Brown   mod->setupbc = SetUpBC_Euler;
754c4762a1bSJed Brown   ierr = PetscOptionsHead(PetscOptionsObject,"Euler options");CHKERRQ(ierr);
755c4762a1bSJed Brown   {
756c4762a1bSJed Brown     PetscReal alpha;
757c4762a1bSJed Brown     char type[64] = "linear_wave";
758c4762a1bSJed Brown     PetscBool  is;
759c4762a1bSJed Brown     mod->bcs[0] = mod->bcs[1] = mod->bcs[2] = DM_BOUNDARY_GHOSTED;
760c4762a1bSJed Brown     eu->pars[EULER_PAR_GAMMA] = 1.4;
761c4762a1bSJed Brown     eu->pars[EULER_PAR_AMACH] = 2.02;
762c4762a1bSJed Brown     eu->pars[EULER_PAR_RHOR] = 3.0;
763c4762a1bSJed Brown     eu->pars[EULER_PAR_ITANA] = 0.57735026918963; /* angle of Euler self similar (SS) shock */
764c4762a1bSJed Brown     ierr = PetscOptionsReal("-eu_gamma","Heat capacity ratio","",eu->pars[EULER_PAR_GAMMA],&eu->pars[EULER_PAR_GAMMA],NULL);CHKERRQ(ierr);
765c4762a1bSJed Brown     ierr = PetscOptionsReal("-eu_amach","Shock speed (Mach)","",eu->pars[EULER_PAR_AMACH],&eu->pars[EULER_PAR_AMACH],NULL);CHKERRQ(ierr);
766c4762a1bSJed Brown     ierr = PetscOptionsReal("-eu_rho2","Density right of discontinuity","",eu->pars[EULER_PAR_RHOR],&eu->pars[EULER_PAR_RHOR],NULL);CHKERRQ(ierr);
767c4762a1bSJed Brown     alpha = 60.;
768c4762a1bSJed Brown     ierr = PetscOptionsReal("-eu_alpha","Angle of discontinuity","",alpha,&alpha,NULL);CHKERRQ(ierr);
769c4762a1bSJed Brown     if (alpha<=0. || alpha>90.) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Alpha bust be > 0 and <= 90 (%g)",alpha);
770c4762a1bSJed Brown     eu->pars[EULER_PAR_ITANA] = 1./PetscTanReal( alpha * PETSC_PI / 180.0 );
771c4762a1bSJed Brown     ierr = PetscOptionsString("-eu_type","Type of Euler test","",type,type,sizeof(type),NULL);CHKERRQ(ierr);
772c4762a1bSJed Brown     ierr = PetscStrcmp(type,"linear_wave", &is);CHKERRQ(ierr);
773c4762a1bSJed Brown     if (is) {
774c4762a1bSJed Brown       eu->type = EULER_LINEAR_WAVE;
775c4762a1bSJed Brown       mod->bcs[0] = mod->bcs[1] = mod->bcs[2] = DM_BOUNDARY_PERIODIC;
776c4762a1bSJed Brown       mod->bcs[1] = DM_BOUNDARY_GHOSTED; /* debug */
777c4762a1bSJed Brown       ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"linear_wave");CHKERRQ(ierr);
778c4762a1bSJed Brown     }
779c4762a1bSJed Brown     else {
780c4762a1bSJed Brown       if (DIM != 2) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"DIM must be 2 unless linear wave test %s",type);
781c4762a1bSJed Brown       ierr = PetscStrcmp(type,"iv_shock", &is);CHKERRQ(ierr);
782c4762a1bSJed Brown       if (is) {
783c4762a1bSJed Brown         eu->type = EULER_IV_SHOCK;
784c4762a1bSJed Brown         ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"iv_shock");CHKERRQ(ierr);
785c4762a1bSJed Brown       }
786c4762a1bSJed Brown       else {
787c4762a1bSJed Brown         ierr = PetscStrcmp(type,"ss_shock", &is);CHKERRQ(ierr);
788c4762a1bSJed Brown         if (is) {
789c4762a1bSJed Brown           eu->type = EULER_SS_SHOCK;
790c4762a1bSJed Brown           ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"ss_shock");CHKERRQ(ierr);
791c4762a1bSJed Brown         }
792c4762a1bSJed Brown         else {
793c4762a1bSJed Brown           ierr = PetscStrcmp(type,"shock_tube", &is);CHKERRQ(ierr);
794c4762a1bSJed Brown           if (is) eu->type = EULER_SHOCK_TUBE;
795c4762a1bSJed Brown           else SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Unknown Euler type %s",type);
796c4762a1bSJed Brown           ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"shock_tube");CHKERRQ(ierr);
797c4762a1bSJed Brown         }
798c4762a1bSJed Brown       }
799c4762a1bSJed Brown     }
800c4762a1bSJed Brown   }
801c4762a1bSJed Brown   ierr = PetscOptionsTail();CHKERRQ(ierr);
802c4762a1bSJed Brown   eu->sound = SpeedOfSound_PG;
803c4762a1bSJed Brown   phys->maxspeed = 0.; /* will get set in solution */
804c4762a1bSJed Brown   ierr = ModelSolutionSetDefault(mod,PhysicsSolution_Euler,phys);CHKERRQ(ierr);
805c4762a1bSJed Brown   ierr = ModelFunctionalRegister(mod,"Speed",&eu->monitor.Speed,PhysicsFunctional_Euler,phys);CHKERRQ(ierr);
806c4762a1bSJed Brown   ierr = ModelFunctionalRegister(mod,"Energy",&eu->monitor.Energy,PhysicsFunctional_Euler,phys);CHKERRQ(ierr);
807c4762a1bSJed Brown   ierr = ModelFunctionalRegister(mod,"Density",&eu->monitor.Density,PhysicsFunctional_Euler,phys);CHKERRQ(ierr);
808c4762a1bSJed Brown   ierr = ModelFunctionalRegister(mod,"Momentum",&eu->monitor.Momentum,PhysicsFunctional_Euler,phys);CHKERRQ(ierr);
809c4762a1bSJed Brown   ierr = ModelFunctionalRegister(mod,"Pressure",&eu->monitor.Pressure,PhysicsFunctional_Euler,phys);CHKERRQ(ierr);
810c4762a1bSJed Brown 
811c4762a1bSJed Brown   PetscFunctionReturn(0);
812c4762a1bSJed Brown }
813c4762a1bSJed Brown 
814c4762a1bSJed Brown static PetscErrorCode ErrorIndicator_Simple(PetscInt dim, PetscReal volume, PetscInt numComps, const PetscScalar u[], const PetscScalar grad[], PetscReal *error, void *ctx)
815c4762a1bSJed Brown {
816c4762a1bSJed Brown   PetscReal      err = 0.;
817c4762a1bSJed Brown   PetscInt       i, j;
818c4762a1bSJed Brown 
819c4762a1bSJed Brown   PetscFunctionBeginUser;
820c4762a1bSJed Brown   for (i = 0; i < numComps; i++) {
821c4762a1bSJed Brown     for (j = 0; j < dim; j++) {
822c4762a1bSJed Brown       err += PetscSqr(PetscRealPart(grad[i * dim + j]));
823c4762a1bSJed Brown     }
824c4762a1bSJed Brown   }
825c4762a1bSJed Brown   *error = volume * err;
826c4762a1bSJed Brown   PetscFunctionReturn(0);
827c4762a1bSJed Brown }
828c4762a1bSJed Brown 
829c4762a1bSJed Brown PetscErrorCode ConstructCellBoundary(DM dm, User user)
830c4762a1bSJed Brown {
831c4762a1bSJed Brown   const char     *name   = "Cell Sets";
832c4762a1bSJed Brown   const char     *bdname = "split faces";
833c4762a1bSJed Brown   IS             regionIS, innerIS;
834c4762a1bSJed Brown   const PetscInt *regions, *cells;
835c4762a1bSJed Brown   PetscInt       numRegions, innerRegion, numCells, c;
836c4762a1bSJed Brown   PetscInt       cStart, cEnd, cEndInterior, fStart, fEnd;
837c4762a1bSJed Brown   PetscBool      hasLabel;
838c4762a1bSJed Brown   PetscErrorCode ierr;
839c4762a1bSJed Brown 
840c4762a1bSJed Brown   PetscFunctionBeginUser;
841c4762a1bSJed Brown   ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
842c4762a1bSJed Brown   ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
843c4762a1bSJed Brown   ierr = DMPlexGetGhostCellStratum(dm, &cEndInterior, NULL);CHKERRQ(ierr);
844c4762a1bSJed Brown 
845c4762a1bSJed Brown   ierr = DMHasLabel(dm, name, &hasLabel);CHKERRQ(ierr);
846c4762a1bSJed Brown   if (!hasLabel) PetscFunctionReturn(0);
847c4762a1bSJed Brown   ierr = DMGetLabelSize(dm, name, &numRegions);CHKERRQ(ierr);
848c4762a1bSJed Brown   if (numRegions != 2) PetscFunctionReturn(0);
849c4762a1bSJed Brown   /* Get the inner id */
850c4762a1bSJed Brown   ierr = DMGetLabelIdIS(dm, name, &regionIS);CHKERRQ(ierr);
851c4762a1bSJed Brown   ierr = ISGetIndices(regionIS, &regions);CHKERRQ(ierr);
852c4762a1bSJed Brown   innerRegion = regions[0];
853c4762a1bSJed Brown   ierr = ISRestoreIndices(regionIS, &regions);CHKERRQ(ierr);
854c4762a1bSJed Brown   ierr = ISDestroy(&regionIS);CHKERRQ(ierr);
855c4762a1bSJed Brown   /* Find the faces between cells in different regions, could call DMPlexCreateNeighborCSR() */
856c4762a1bSJed Brown   ierr = DMGetStratumIS(dm, name, innerRegion, &innerIS);CHKERRQ(ierr);
857c4762a1bSJed Brown   ierr = ISGetLocalSize(innerIS, &numCells);CHKERRQ(ierr);
858c4762a1bSJed Brown   ierr = ISGetIndices(innerIS, &cells);CHKERRQ(ierr);
859c4762a1bSJed Brown   ierr = DMCreateLabel(dm, bdname);CHKERRQ(ierr);
860c4762a1bSJed Brown   for (c = 0; c < numCells; ++c) {
861c4762a1bSJed Brown     const PetscInt cell = cells[c];
862c4762a1bSJed Brown     const PetscInt *faces;
863c4762a1bSJed Brown     PetscInt       numFaces, f;
864c4762a1bSJed Brown 
865c4762a1bSJed Brown     if ((cell < cStart) || (cell >= cEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Got invalid point %d which is not a cell", cell);
866c4762a1bSJed Brown     ierr = DMPlexGetConeSize(dm, cell, &numFaces);CHKERRQ(ierr);
867c4762a1bSJed Brown     ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr);
868c4762a1bSJed Brown     for (f = 0; f < numFaces; ++f) {
869c4762a1bSJed Brown       const PetscInt face = faces[f];
870c4762a1bSJed Brown       const PetscInt *neighbors;
871c4762a1bSJed Brown       PetscInt       nC, regionA, regionB;
872c4762a1bSJed Brown 
873c4762a1bSJed Brown       if ((face < fStart) || (face >= fEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Got invalid point %d which is not a face", face);
874c4762a1bSJed Brown       ierr = DMPlexGetSupportSize(dm, face, &nC);CHKERRQ(ierr);
875c4762a1bSJed Brown       if (nC != 2) continue;
876c4762a1bSJed Brown       ierr = DMPlexGetSupport(dm, face, &neighbors);CHKERRQ(ierr);
877c4762a1bSJed Brown       if ((neighbors[0] >= cEndInterior) || (neighbors[1] >= cEndInterior)) continue;
878c4762a1bSJed Brown       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]);
879c4762a1bSJed Brown       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]);
880c4762a1bSJed Brown       ierr = DMGetLabelValue(dm, name, neighbors[0], &regionA);CHKERRQ(ierr);
881c4762a1bSJed Brown       ierr = DMGetLabelValue(dm, name, neighbors[1], &regionB);CHKERRQ(ierr);
882c4762a1bSJed Brown       if (regionA < 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid label %s: Cell %d has no value", name, neighbors[0]);
883c4762a1bSJed Brown       if (regionB < 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid label %s: Cell %d has no value", name, neighbors[1]);
884c4762a1bSJed Brown       if (regionA != regionB) {
885c4762a1bSJed Brown         ierr = DMSetLabelValue(dm, bdname, faces[f], 1);CHKERRQ(ierr);
886c4762a1bSJed Brown       }
887c4762a1bSJed Brown     }
888c4762a1bSJed Brown   }
889c4762a1bSJed Brown   ierr = ISRestoreIndices(innerIS, &cells);CHKERRQ(ierr);
890c4762a1bSJed Brown   ierr = ISDestroy(&innerIS);CHKERRQ(ierr);
891c4762a1bSJed Brown   {
892c4762a1bSJed Brown     DMLabel label;
893c4762a1bSJed Brown 
894c4762a1bSJed Brown     ierr = DMGetLabel(dm, bdname, &label);CHKERRQ(ierr);
895c4762a1bSJed Brown     ierr = DMLabelView(label, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
896c4762a1bSJed Brown   }
897c4762a1bSJed Brown   PetscFunctionReturn(0);
898c4762a1bSJed Brown }
899c4762a1bSJed Brown 
900c4762a1bSJed Brown /* Right now, I have just added duplicate faces, which see both cells. We can
901c4762a1bSJed Brown - Add duplicate vertices and decouple the face cones
902c4762a1bSJed Brown - Disconnect faces from cells across the rotation gap
903c4762a1bSJed Brown */
904c4762a1bSJed Brown PetscErrorCode SplitFaces(DM *dmSplit, const char labelName[], User user)
905c4762a1bSJed Brown {
906c4762a1bSJed Brown   DM             dm = *dmSplit, sdm;
907c4762a1bSJed Brown   PetscSF        sfPoint, gsfPoint;
908c4762a1bSJed Brown   PetscSection   coordSection, newCoordSection;
909c4762a1bSJed Brown   Vec            coordinates;
910c4762a1bSJed Brown   IS             idIS;
911c4762a1bSJed Brown   const PetscInt *ids;
912c4762a1bSJed Brown   PetscInt       *newpoints;
913c4762a1bSJed Brown   PetscInt       dim, depth, maxConeSize, maxSupportSize, numLabels, numGhostCells;
914c4762a1bSJed Brown   PetscInt       numFS, fs, pStart, pEnd, p, cEnd, cEndInterior, vStart, vEnd, v, fStart, fEnd, newf, d, l;
915c4762a1bSJed Brown   PetscBool      hasLabel;
916c4762a1bSJed Brown   PetscErrorCode ierr;
917c4762a1bSJed Brown 
918c4762a1bSJed Brown   PetscFunctionBeginUser;
919c4762a1bSJed Brown   ierr = DMHasLabel(dm, labelName, &hasLabel);CHKERRQ(ierr);
920c4762a1bSJed Brown   if (!hasLabel) PetscFunctionReturn(0);
921c4762a1bSJed Brown   ierr = DMCreate(PetscObjectComm((PetscObject)dm), &sdm);CHKERRQ(ierr);
922c4762a1bSJed Brown   ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr);
923c4762a1bSJed Brown   ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
924c4762a1bSJed Brown   ierr = DMSetDimension(sdm, dim);CHKERRQ(ierr);
925c4762a1bSJed Brown 
926c4762a1bSJed Brown   ierr = DMGetLabelIdIS(dm, labelName, &idIS);CHKERRQ(ierr);
927c4762a1bSJed Brown   ierr = ISGetLocalSize(idIS, &numFS);CHKERRQ(ierr);
928c4762a1bSJed Brown   ierr = ISGetIndices(idIS, &ids);CHKERRQ(ierr);
929c4762a1bSJed Brown 
930c4762a1bSJed Brown   user->numSplitFaces = 0;
931c4762a1bSJed Brown   for (fs = 0; fs < numFS; ++fs) {
932c4762a1bSJed Brown     PetscInt numBdFaces;
933c4762a1bSJed Brown 
934c4762a1bSJed Brown     ierr = DMGetStratumSize(dm, labelName, ids[fs], &numBdFaces);CHKERRQ(ierr);
935c4762a1bSJed Brown     user->numSplitFaces += numBdFaces;
936c4762a1bSJed Brown   }
937c4762a1bSJed Brown   ierr  = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr);
938c4762a1bSJed Brown   pEnd += user->numSplitFaces;
939c4762a1bSJed Brown   ierr  = DMPlexSetChart(sdm, pStart, pEnd);CHKERRQ(ierr);
940c4762a1bSJed Brown   ierr  = DMPlexGetGhostCellStratum(dm, &cEndInterior, NULL);CHKERRQ(ierr);
941c4762a1bSJed Brown   ierr  = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr);
942c4762a1bSJed Brown   numGhostCells = cEnd - cEndInterior;
943c4762a1bSJed Brown   /* Set cone and support sizes */
944c4762a1bSJed Brown   ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
945c4762a1bSJed Brown   for (d = 0; d <= depth; ++d) {
946c4762a1bSJed Brown     ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr);
947c4762a1bSJed Brown     for (p = pStart; p < pEnd; ++p) {
948c4762a1bSJed Brown       PetscInt newp = p;
949c4762a1bSJed Brown       PetscInt size;
950c4762a1bSJed Brown 
951c4762a1bSJed Brown       ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr);
952c4762a1bSJed Brown       ierr = DMPlexSetConeSize(sdm, newp, size);CHKERRQ(ierr);
953c4762a1bSJed Brown       ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr);
954c4762a1bSJed Brown       ierr = DMPlexSetSupportSize(sdm, newp, size);CHKERRQ(ierr);
955c4762a1bSJed Brown     }
956c4762a1bSJed Brown   }
957c4762a1bSJed Brown   ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
958c4762a1bSJed Brown   for (fs = 0, newf = fEnd; fs < numFS; ++fs) {
959c4762a1bSJed Brown     IS             faceIS;
960c4762a1bSJed Brown     const PetscInt *faces;
961c4762a1bSJed Brown     PetscInt       numFaces, f;
962c4762a1bSJed Brown 
963c4762a1bSJed Brown     ierr = DMGetStratumIS(dm, labelName, ids[fs], &faceIS);CHKERRQ(ierr);
964c4762a1bSJed Brown     ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr);
965c4762a1bSJed Brown     ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr);
966c4762a1bSJed Brown     for (f = 0; f < numFaces; ++f, ++newf) {
967c4762a1bSJed Brown       PetscInt size;
968c4762a1bSJed Brown 
969c4762a1bSJed Brown       /* Right now I think that both faces should see both cells */
970c4762a1bSJed Brown       ierr = DMPlexGetConeSize(dm, faces[f], &size);CHKERRQ(ierr);
971c4762a1bSJed Brown       ierr = DMPlexSetConeSize(sdm, newf, size);CHKERRQ(ierr);
972c4762a1bSJed Brown       ierr = DMPlexGetSupportSize(dm, faces[f], &size);CHKERRQ(ierr);
973c4762a1bSJed Brown       ierr = DMPlexSetSupportSize(sdm, newf, size);CHKERRQ(ierr);
974c4762a1bSJed Brown     }
975c4762a1bSJed Brown     ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr);
976c4762a1bSJed Brown     ierr = ISDestroy(&faceIS);CHKERRQ(ierr);
977c4762a1bSJed Brown   }
978c4762a1bSJed Brown   ierr = DMSetUp(sdm);CHKERRQ(ierr);
979c4762a1bSJed Brown   /* Set cones and supports */
980c4762a1bSJed Brown   ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr);
981c4762a1bSJed Brown   ierr = PetscMalloc1(PetscMax(maxConeSize, maxSupportSize), &newpoints);CHKERRQ(ierr);
982c4762a1bSJed Brown   ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr);
983c4762a1bSJed Brown   for (p = pStart; p < pEnd; ++p) {
984c4762a1bSJed Brown     const PetscInt *points, *orientations;
985c4762a1bSJed Brown     PetscInt       size, i, newp = p;
986c4762a1bSJed Brown 
987c4762a1bSJed Brown     ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr);
988c4762a1bSJed Brown     ierr = DMPlexGetCone(dm, p, &points);CHKERRQ(ierr);
989c4762a1bSJed Brown     ierr = DMPlexGetConeOrientation(dm, p, &orientations);CHKERRQ(ierr);
990c4762a1bSJed Brown     for (i = 0; i < size; ++i) newpoints[i] = points[i];
991c4762a1bSJed Brown     ierr = DMPlexSetCone(sdm, newp, newpoints);CHKERRQ(ierr);
992c4762a1bSJed Brown     ierr = DMPlexSetConeOrientation(sdm, newp, orientations);CHKERRQ(ierr);
993c4762a1bSJed Brown     ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr);
994c4762a1bSJed Brown     ierr = DMPlexGetSupport(dm, p, &points);CHKERRQ(ierr);
995c4762a1bSJed Brown     for (i = 0; i < size; ++i) newpoints[i] = points[i];
996c4762a1bSJed Brown     ierr = DMPlexSetSupport(sdm, newp, newpoints);CHKERRQ(ierr);
997c4762a1bSJed Brown   }
998c4762a1bSJed Brown   ierr = PetscFree(newpoints);CHKERRQ(ierr);
999c4762a1bSJed Brown   for (fs = 0, newf = fEnd; fs < numFS; ++fs) {
1000c4762a1bSJed Brown     IS             faceIS;
1001c4762a1bSJed Brown     const PetscInt *faces;
1002c4762a1bSJed Brown     PetscInt       numFaces, f;
1003c4762a1bSJed Brown 
1004c4762a1bSJed Brown     ierr = DMGetStratumIS(dm, labelName, ids[fs], &faceIS);CHKERRQ(ierr);
1005c4762a1bSJed Brown     ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr);
1006c4762a1bSJed Brown     ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr);
1007c4762a1bSJed Brown     for (f = 0; f < numFaces; ++f, ++newf) {
1008c4762a1bSJed Brown       const PetscInt *points;
1009c4762a1bSJed Brown 
1010c4762a1bSJed Brown       ierr = DMPlexGetCone(dm, faces[f], &points);CHKERRQ(ierr);
1011c4762a1bSJed Brown       ierr = DMPlexSetCone(sdm, newf, points);CHKERRQ(ierr);
1012c4762a1bSJed Brown       ierr = DMPlexGetSupport(dm, faces[f], &points);CHKERRQ(ierr);
1013c4762a1bSJed Brown       ierr = DMPlexSetSupport(sdm, newf, points);CHKERRQ(ierr);
1014c4762a1bSJed Brown     }
1015c4762a1bSJed Brown     ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr);
1016c4762a1bSJed Brown     ierr = ISDestroy(&faceIS);CHKERRQ(ierr);
1017c4762a1bSJed Brown   }
1018c4762a1bSJed Brown   ierr = ISRestoreIndices(idIS, &ids);CHKERRQ(ierr);
1019c4762a1bSJed Brown   ierr = ISDestroy(&idIS);CHKERRQ(ierr);
1020c4762a1bSJed Brown   ierr = DMPlexStratify(sdm);CHKERRQ(ierr);
1021c4762a1bSJed Brown   /* Convert coordinates */
1022c4762a1bSJed Brown   ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
1023c4762a1bSJed Brown   ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
1024c4762a1bSJed Brown   ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &newCoordSection);CHKERRQ(ierr);
1025c4762a1bSJed Brown   ierr = PetscSectionSetNumFields(newCoordSection, 1);CHKERRQ(ierr);
1026c4762a1bSJed Brown   ierr = PetscSectionSetFieldComponents(newCoordSection, 0, dim);CHKERRQ(ierr);
1027c4762a1bSJed Brown   ierr = PetscSectionSetChart(newCoordSection, vStart, vEnd);CHKERRQ(ierr);
1028c4762a1bSJed Brown   for (v = vStart; v < vEnd; ++v) {
1029c4762a1bSJed Brown     ierr = PetscSectionSetDof(newCoordSection, v, dim);CHKERRQ(ierr);
1030c4762a1bSJed Brown     ierr = PetscSectionSetFieldDof(newCoordSection, v, 0, dim);CHKERRQ(ierr);
1031c4762a1bSJed Brown   }
1032c4762a1bSJed Brown   ierr = PetscSectionSetUp(newCoordSection);CHKERRQ(ierr);
1033c4762a1bSJed Brown   ierr = DMSetCoordinateSection(sdm, PETSC_DETERMINE, newCoordSection);CHKERRQ(ierr);
1034c4762a1bSJed Brown   ierr = PetscSectionDestroy(&newCoordSection);CHKERRQ(ierr); /* relinquish our reference */
1035c4762a1bSJed Brown   ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
1036c4762a1bSJed Brown   ierr = DMSetCoordinatesLocal(sdm, coordinates);CHKERRQ(ierr);
1037c4762a1bSJed Brown   /* Convert labels */
1038c4762a1bSJed Brown   ierr = DMGetNumLabels(dm, &numLabels);CHKERRQ(ierr);
1039c4762a1bSJed Brown   for (l = 0; l < numLabels; ++l) {
1040c4762a1bSJed Brown     const char *lname;
1041c4762a1bSJed Brown     PetscBool  isDepth, isDim;
1042c4762a1bSJed Brown 
1043c4762a1bSJed Brown     ierr = DMGetLabelName(dm, l, &lname);CHKERRQ(ierr);
1044c4762a1bSJed Brown     ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr);
1045c4762a1bSJed Brown     if (isDepth) continue;
1046c4762a1bSJed Brown     ierr = PetscStrcmp(lname, "dim", &isDim);CHKERRQ(ierr);
1047c4762a1bSJed Brown     if (isDim) continue;
1048c4762a1bSJed Brown     ierr = DMCreateLabel(sdm, lname);CHKERRQ(ierr);
1049c4762a1bSJed Brown     ierr = DMGetLabelIdIS(dm, lname, &idIS);CHKERRQ(ierr);
1050c4762a1bSJed Brown     ierr = ISGetLocalSize(idIS, &numFS);CHKERRQ(ierr);
1051c4762a1bSJed Brown     ierr = ISGetIndices(idIS, &ids);CHKERRQ(ierr);
1052c4762a1bSJed Brown     for (fs = 0; fs < numFS; ++fs) {
1053c4762a1bSJed Brown       IS             pointIS;
1054c4762a1bSJed Brown       const PetscInt *points;
1055c4762a1bSJed Brown       PetscInt       numPoints;
1056c4762a1bSJed Brown 
1057c4762a1bSJed Brown       ierr = DMGetStratumIS(dm, lname, ids[fs], &pointIS);CHKERRQ(ierr);
1058c4762a1bSJed Brown       ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr);
1059c4762a1bSJed Brown       ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr);
1060c4762a1bSJed Brown       for (p = 0; p < numPoints; ++p) {
1061c4762a1bSJed Brown         PetscInt newpoint = points[p];
1062c4762a1bSJed Brown 
1063c4762a1bSJed Brown         ierr = DMSetLabelValue(sdm, lname, newpoint, ids[fs]);CHKERRQ(ierr);
1064c4762a1bSJed Brown       }
1065c4762a1bSJed Brown       ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr);
1066c4762a1bSJed Brown       ierr = ISDestroy(&pointIS);CHKERRQ(ierr);
1067c4762a1bSJed Brown     }
1068c4762a1bSJed Brown     ierr = ISRestoreIndices(idIS, &ids);CHKERRQ(ierr);
1069c4762a1bSJed Brown     ierr = ISDestroy(&idIS);CHKERRQ(ierr);
1070c4762a1bSJed Brown   }
1071c4762a1bSJed Brown   {
1072c4762a1bSJed Brown     /* Convert pointSF */
1073c4762a1bSJed Brown     const PetscSFNode *remotePoints;
1074c4762a1bSJed Brown     PetscSFNode       *gremotePoints;
1075c4762a1bSJed Brown     const PetscInt    *localPoints;
1076c4762a1bSJed Brown     PetscInt          *glocalPoints,*newLocation,*newRemoteLocation;
1077c4762a1bSJed Brown     PetscInt          numRoots, numLeaves;
1078c4762a1bSJed Brown     PetscMPIInt       size;
1079c4762a1bSJed Brown 
1080c4762a1bSJed Brown     ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size);CHKERRQ(ierr);
1081c4762a1bSJed Brown     ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr);
1082c4762a1bSJed Brown     ierr = DMGetPointSF(sdm, &gsfPoint);CHKERRQ(ierr);
1083c4762a1bSJed Brown     ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr);
1084c4762a1bSJed Brown     ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr);
1085c4762a1bSJed Brown     if (numRoots >= 0) {
1086c4762a1bSJed Brown       ierr = PetscMalloc2(numRoots,&newLocation,pEnd-pStart,&newRemoteLocation);CHKERRQ(ierr);
1087c4762a1bSJed Brown       for (l=0; l<numRoots; l++) newLocation[l] = l; /* + (l >= cEnd ? numGhostCells : 0); */
1088c4762a1bSJed Brown       ierr = PetscSFBcastBegin(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr);
1089c4762a1bSJed Brown       ierr = PetscSFBcastEnd(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr);
1090c4762a1bSJed Brown       ierr = PetscMalloc1(numLeaves,    &glocalPoints);CHKERRQ(ierr);
1091c4762a1bSJed Brown       ierr = PetscMalloc1(numLeaves, &gremotePoints);CHKERRQ(ierr);
1092c4762a1bSJed Brown       for (l = 0; l < numLeaves; ++l) {
1093c4762a1bSJed Brown         glocalPoints[l]        = localPoints[l]; /* localPoints[l] >= cEnd ? localPoints[l] + numGhostCells : localPoints[l]; */
1094c4762a1bSJed Brown         gremotePoints[l].rank  = remotePoints[l].rank;
1095c4762a1bSJed Brown         gremotePoints[l].index = newRemoteLocation[localPoints[l]];
1096c4762a1bSJed Brown       }
1097c4762a1bSJed Brown       ierr = PetscFree2(newLocation,newRemoteLocation);CHKERRQ(ierr);
1098c4762a1bSJed Brown       ierr = PetscSFSetGraph(gsfPoint, numRoots+numGhostCells, numLeaves, glocalPoints, PETSC_OWN_POINTER, gremotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr);
1099c4762a1bSJed Brown     }
1100c4762a1bSJed Brown     ierr     = DMDestroy(dmSplit);CHKERRQ(ierr);
1101c4762a1bSJed Brown     *dmSplit = sdm;
1102c4762a1bSJed Brown   }
1103c4762a1bSJed Brown   PetscFunctionReturn(0);
1104c4762a1bSJed Brown }
1105c4762a1bSJed Brown 
1106c4762a1bSJed Brown PetscErrorCode CreatePartitionVec(DM dm, DM *dmCell, Vec *partition)
1107c4762a1bSJed Brown {
1108c4762a1bSJed Brown   PetscSF        sfPoint;
1109c4762a1bSJed Brown   PetscSection   coordSection;
1110c4762a1bSJed Brown   Vec            coordinates;
1111c4762a1bSJed Brown   PetscSection   sectionCell;
1112c4762a1bSJed Brown   PetscScalar    *part;
1113c4762a1bSJed Brown   PetscInt       cStart, cEnd, c;
1114c4762a1bSJed Brown   PetscMPIInt    rank;
1115c4762a1bSJed Brown   PetscErrorCode ierr;
1116c4762a1bSJed Brown 
1117c4762a1bSJed Brown   PetscFunctionBeginUser;
1118c4762a1bSJed Brown   ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
1119c4762a1bSJed Brown   ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
1120c4762a1bSJed Brown   ierr = DMClone(dm, dmCell);CHKERRQ(ierr);
1121c4762a1bSJed Brown   ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr);
1122c4762a1bSJed Brown   ierr = DMSetPointSF(*dmCell, sfPoint);CHKERRQ(ierr);
1123c4762a1bSJed Brown   ierr = DMSetCoordinateSection(*dmCell, PETSC_DETERMINE, coordSection);CHKERRQ(ierr);
1124c4762a1bSJed Brown   ierr = DMSetCoordinatesLocal(*dmCell, coordinates);CHKERRQ(ierr);
1125c4762a1bSJed Brown   ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr);
1126c4762a1bSJed Brown   ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &sectionCell);CHKERRQ(ierr);
1127c4762a1bSJed Brown   ierr = DMPlexGetHeightStratum(*dmCell, 0, &cStart, &cEnd);CHKERRQ(ierr);
1128c4762a1bSJed Brown   ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr);
1129c4762a1bSJed Brown   for (c = cStart; c < cEnd; ++c) {
1130c4762a1bSJed Brown     ierr = PetscSectionSetDof(sectionCell, c, 1);CHKERRQ(ierr);
1131c4762a1bSJed Brown   }
1132c4762a1bSJed Brown   ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr);
1133c4762a1bSJed Brown   ierr = DMSetLocalSection(*dmCell, sectionCell);CHKERRQ(ierr);
1134c4762a1bSJed Brown   ierr = PetscSectionDestroy(&sectionCell);CHKERRQ(ierr);
1135c4762a1bSJed Brown   ierr = DMCreateLocalVector(*dmCell, partition);CHKERRQ(ierr);
1136c4762a1bSJed Brown   ierr = PetscObjectSetName((PetscObject)*partition, "partition");CHKERRQ(ierr);
1137c4762a1bSJed Brown   ierr = VecGetArray(*partition, &part);CHKERRQ(ierr);
1138c4762a1bSJed Brown   for (c = cStart; c < cEnd; ++c) {
1139c4762a1bSJed Brown     PetscScalar *p;
1140c4762a1bSJed Brown 
1141c4762a1bSJed Brown     ierr = DMPlexPointLocalRef(*dmCell, c, part, &p);CHKERRQ(ierr);
1142c4762a1bSJed Brown     p[0] = rank;
1143c4762a1bSJed Brown   }
1144c4762a1bSJed Brown   ierr = VecRestoreArray(*partition, &part);CHKERRQ(ierr);
1145c4762a1bSJed Brown   PetscFunctionReturn(0);
1146c4762a1bSJed Brown }
1147c4762a1bSJed Brown 
1148c4762a1bSJed Brown PetscErrorCode CreateMassMatrix(DM dm, Vec *massMatrix, User user)
1149c4762a1bSJed Brown {
1150*3e9753d6SMatthew G. Knepley   DM                plex, dmMass, dmFace, dmCell, dmCoord;
1151c4762a1bSJed Brown   PetscSection      coordSection;
1152c4762a1bSJed Brown   Vec               coordinates, facegeom, cellgeom;
1153c4762a1bSJed Brown   PetscSection      sectionMass;
1154c4762a1bSJed Brown   PetscScalar       *m;
1155c4762a1bSJed Brown   const PetscScalar *fgeom, *cgeom, *coords;
1156c4762a1bSJed Brown   PetscInt          vStart, vEnd, v;
1157c4762a1bSJed Brown   PetscErrorCode    ierr;
1158c4762a1bSJed Brown 
1159c4762a1bSJed Brown   PetscFunctionBeginUser;
1160*3e9753d6SMatthew G. Knepley   ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr);
1161c4762a1bSJed Brown   ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
1162c4762a1bSJed Brown   ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
1163c4762a1bSJed Brown   ierr = DMClone(dm, &dmMass);CHKERRQ(ierr);
1164c4762a1bSJed Brown   ierr = DMSetCoordinateSection(dmMass, PETSC_DETERMINE, coordSection);CHKERRQ(ierr);
1165c4762a1bSJed Brown   ierr = DMSetCoordinatesLocal(dmMass, coordinates);CHKERRQ(ierr);
1166c4762a1bSJed Brown   ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &sectionMass);CHKERRQ(ierr);
1167c4762a1bSJed Brown   ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
1168c4762a1bSJed Brown   ierr = PetscSectionSetChart(sectionMass, vStart, vEnd);CHKERRQ(ierr);
1169c4762a1bSJed Brown   for (v = vStart; v < vEnd; ++v) {
1170c4762a1bSJed Brown     PetscInt numFaces;
1171c4762a1bSJed Brown 
1172c4762a1bSJed Brown     ierr = DMPlexGetSupportSize(dmMass, v, &numFaces);CHKERRQ(ierr);
1173c4762a1bSJed Brown     ierr = PetscSectionSetDof(sectionMass, v, numFaces*numFaces);CHKERRQ(ierr);
1174c4762a1bSJed Brown   }
1175c4762a1bSJed Brown   ierr = PetscSectionSetUp(sectionMass);CHKERRQ(ierr);
1176c4762a1bSJed Brown   ierr = DMSetLocalSection(dmMass, sectionMass);CHKERRQ(ierr);
1177c4762a1bSJed Brown   ierr = PetscSectionDestroy(&sectionMass);CHKERRQ(ierr);
1178c4762a1bSJed Brown   ierr = DMGetLocalVector(dmMass, massMatrix);CHKERRQ(ierr);
1179c4762a1bSJed Brown   ierr = VecGetArray(*massMatrix, &m);CHKERRQ(ierr);
1180*3e9753d6SMatthew G. Knepley   ierr = DMPlexGetGeometryFVM(plex, &facegeom, &cellgeom, NULL);CHKERRQ(ierr);
1181c4762a1bSJed Brown   ierr = VecGetDM(facegeom, &dmFace);CHKERRQ(ierr);
1182c4762a1bSJed Brown   ierr = VecGetArrayRead(facegeom, &fgeom);CHKERRQ(ierr);
1183c4762a1bSJed Brown   ierr = VecGetDM(cellgeom, &dmCell);CHKERRQ(ierr);
1184c4762a1bSJed Brown   ierr = VecGetArrayRead(cellgeom, &cgeom);CHKERRQ(ierr);
1185c4762a1bSJed Brown   ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr);
1186c4762a1bSJed Brown   ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr);
1187c4762a1bSJed Brown   for (v = vStart; v < vEnd; ++v) {
1188c4762a1bSJed Brown     const PetscInt        *faces;
1189c4762a1bSJed Brown     PetscFVFaceGeom       *fgA, *fgB, *cg;
1190c4762a1bSJed Brown     PetscScalar           *vertex;
1191c4762a1bSJed Brown     PetscInt               numFaces, sides[2], f, g;
1192c4762a1bSJed Brown 
1193c4762a1bSJed Brown     ierr = DMPlexPointLocalRead(dmCoord, v, coords, &vertex);CHKERRQ(ierr);
1194c4762a1bSJed Brown     ierr = DMPlexGetSupportSize(dmMass, v, &numFaces);CHKERRQ(ierr);
1195c4762a1bSJed Brown     ierr = DMPlexGetSupport(dmMass, v, &faces);CHKERRQ(ierr);
1196c4762a1bSJed Brown     for (f = 0; f < numFaces; ++f) {
1197c4762a1bSJed Brown       sides[0] = faces[f];
1198c4762a1bSJed Brown       ierr = DMPlexPointLocalRead(dmFace, faces[f], fgeom, &fgA);CHKERRQ(ierr);
1199c4762a1bSJed Brown       for (g = 0; g < numFaces; ++g) {
1200c4762a1bSJed Brown         const PetscInt *cells = NULL;
1201c4762a1bSJed Brown         PetscReal      area   = 0.0;
1202c4762a1bSJed Brown         PetscInt       numCells;
1203c4762a1bSJed Brown 
1204c4762a1bSJed Brown         sides[1] = faces[g];
1205c4762a1bSJed Brown         ierr = DMPlexPointLocalRead(dmFace, faces[g], fgeom, &fgB);CHKERRQ(ierr);
1206c4762a1bSJed Brown         ierr = DMPlexGetJoin(dmMass, 2, sides, &numCells, &cells);CHKERRQ(ierr);
1207c4762a1bSJed Brown         if (numCells != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Invalid join for faces");
1208c4762a1bSJed Brown         ierr = DMPlexPointLocalRead(dmCell, cells[0], cgeom, &cg);CHKERRQ(ierr);
1209c4762a1bSJed Brown         area += PetscAbsScalar((vertex[0] - cg->centroid[0])*(fgA->centroid[1] - cg->centroid[1]) - (vertex[1] - cg->centroid[1])*(fgA->centroid[0] - cg->centroid[0]));
1210c4762a1bSJed Brown         area += PetscAbsScalar((vertex[0] - cg->centroid[0])*(fgB->centroid[1] - cg->centroid[1]) - (vertex[1] - cg->centroid[1])*(fgB->centroid[0] - cg->centroid[0]));
1211c4762a1bSJed Brown         m[f*numFaces+g] = Dot2Real(fgA->normal, fgB->normal)*area*0.5;
1212c4762a1bSJed Brown         ierr = DMPlexRestoreJoin(dmMass, 2, sides, &numCells, &cells);CHKERRQ(ierr);
1213c4762a1bSJed Brown       }
1214c4762a1bSJed Brown     }
1215c4762a1bSJed Brown   }
1216c4762a1bSJed Brown   ierr = VecRestoreArrayRead(facegeom, &fgeom);CHKERRQ(ierr);
1217c4762a1bSJed Brown   ierr = VecRestoreArrayRead(cellgeom, &cgeom);CHKERRQ(ierr);
1218c4762a1bSJed Brown   ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr);
1219c4762a1bSJed Brown   ierr = VecRestoreArray(*massMatrix, &m);CHKERRQ(ierr);
1220c4762a1bSJed Brown   ierr = DMDestroy(&dmMass);CHKERRQ(ierr);
1221*3e9753d6SMatthew G. Knepley   ierr = DMDestroy(&plex);CHKERRQ(ierr);
1222c4762a1bSJed Brown   PetscFunctionReturn(0);
1223c4762a1bSJed Brown }
1224c4762a1bSJed Brown 
1225c4762a1bSJed Brown /* Behavior will be different for multi-physics or when using non-default boundary conditions */
1226c4762a1bSJed Brown static PetscErrorCode ModelSolutionSetDefault(Model mod,SolutionFunction func,void *ctx)
1227c4762a1bSJed Brown {
1228c4762a1bSJed Brown   PetscFunctionBeginUser;
1229c4762a1bSJed Brown   mod->solution    = func;
1230c4762a1bSJed Brown   mod->solutionctx = ctx;
1231c4762a1bSJed Brown   PetscFunctionReturn(0);
1232c4762a1bSJed Brown }
1233c4762a1bSJed Brown 
1234c4762a1bSJed Brown static PetscErrorCode ModelFunctionalRegister(Model mod,const char *name,PetscInt *offset,FunctionalFunction func,void *ctx)
1235c4762a1bSJed Brown {
1236c4762a1bSJed Brown   PetscErrorCode ierr;
1237c4762a1bSJed Brown   FunctionalLink link,*ptr;
1238c4762a1bSJed Brown   PetscInt       lastoffset = -1;
1239c4762a1bSJed Brown 
1240c4762a1bSJed Brown   PetscFunctionBeginUser;
1241c4762a1bSJed Brown   for (ptr=&mod->functionalRegistry; *ptr; ptr = &(*ptr)->next) lastoffset = (*ptr)->offset;
1242c4762a1bSJed Brown   ierr         = PetscNew(&link);CHKERRQ(ierr);
1243c4762a1bSJed Brown   ierr         = PetscStrallocpy(name,&link->name);CHKERRQ(ierr);
1244c4762a1bSJed Brown   link->offset = lastoffset + 1;
1245c4762a1bSJed Brown   link->func   = func;
1246c4762a1bSJed Brown   link->ctx    = ctx;
1247c4762a1bSJed Brown   link->next   = NULL;
1248c4762a1bSJed Brown   *ptr         = link;
1249c4762a1bSJed Brown   *offset      = link->offset;
1250c4762a1bSJed Brown   PetscFunctionReturn(0);
1251c4762a1bSJed Brown }
1252c4762a1bSJed Brown 
1253c4762a1bSJed Brown static PetscErrorCode ModelFunctionalSetFromOptions(Model mod,PetscOptionItems *PetscOptionsObject)
1254c4762a1bSJed Brown {
1255c4762a1bSJed Brown   PetscErrorCode ierr;
1256c4762a1bSJed Brown   PetscInt       i,j;
1257c4762a1bSJed Brown   FunctionalLink link;
1258c4762a1bSJed Brown   char           *names[256];
1259c4762a1bSJed Brown 
1260c4762a1bSJed Brown   PetscFunctionBeginUser;
1261c4762a1bSJed Brown   mod->numMonitored = ALEN(names);
1262c4762a1bSJed Brown   ierr = PetscOptionsStringArray("-monitor","list of functionals to monitor","",names,&mod->numMonitored,NULL);CHKERRQ(ierr);
1263c4762a1bSJed Brown   /* Create list of functionals that will be computed somehow */
1264c4762a1bSJed Brown   ierr = PetscMalloc1(mod->numMonitored,&mod->functionalMonitored);CHKERRQ(ierr);
1265c4762a1bSJed Brown   /* Create index of calls that we will have to make to compute these functionals (over-allocation in general). */
1266c4762a1bSJed Brown   ierr = PetscMalloc1(mod->numMonitored,&mod->functionalCall);CHKERRQ(ierr);
1267c4762a1bSJed Brown   mod->numCall = 0;
1268c4762a1bSJed Brown   for (i=0; i<mod->numMonitored; i++) {
1269c4762a1bSJed Brown     for (link=mod->functionalRegistry; link; link=link->next) {
1270c4762a1bSJed Brown       PetscBool match;
1271c4762a1bSJed Brown       ierr = PetscStrcasecmp(names[i],link->name,&match);CHKERRQ(ierr);
1272c4762a1bSJed Brown       if (match) break;
1273c4762a1bSJed Brown     }
1274c4762a1bSJed Brown     if (!link) SETERRQ1(mod->comm,PETSC_ERR_USER,"No known functional '%s'",names[i]);
1275c4762a1bSJed Brown     mod->functionalMonitored[i] = link;
1276c4762a1bSJed Brown     for (j=0; j<i; j++) {
1277c4762a1bSJed Brown       if (mod->functionalCall[j]->func == link->func && mod->functionalCall[j]->ctx == link->ctx) goto next_name;
1278c4762a1bSJed Brown     }
1279c4762a1bSJed Brown     mod->functionalCall[mod->numCall++] = link; /* Just points to the first link using the result. There may be more results. */
1280c4762a1bSJed Brown next_name:
1281c4762a1bSJed Brown     ierr = PetscFree(names[i]);CHKERRQ(ierr);
1282c4762a1bSJed Brown   }
1283c4762a1bSJed Brown 
1284c4762a1bSJed Brown   /* Find out the maximum index of any functional computed by a function we will be calling (even if we are not using it) */
1285c4762a1bSJed Brown   mod->maxComputed = -1;
1286c4762a1bSJed Brown   for (link=mod->functionalRegistry; link; link=link->next) {
1287c4762a1bSJed Brown     for (i=0; i<mod->numCall; i++) {
1288c4762a1bSJed Brown       FunctionalLink call = mod->functionalCall[i];
1289c4762a1bSJed Brown       if (link->func == call->func && link->ctx == call->ctx) {
1290c4762a1bSJed Brown         mod->maxComputed = PetscMax(mod->maxComputed,link->offset);
1291c4762a1bSJed Brown       }
1292c4762a1bSJed Brown     }
1293c4762a1bSJed Brown   }
1294c4762a1bSJed Brown   PetscFunctionReturn(0);
1295c4762a1bSJed Brown }
1296c4762a1bSJed Brown 
1297c4762a1bSJed Brown static PetscErrorCode FunctionalLinkDestroy(FunctionalLink *link)
1298c4762a1bSJed Brown {
1299c4762a1bSJed Brown   PetscErrorCode ierr;
1300c4762a1bSJed Brown   FunctionalLink l,next;
1301c4762a1bSJed Brown 
1302c4762a1bSJed Brown   PetscFunctionBeginUser;
1303c4762a1bSJed Brown   if (!link) PetscFunctionReturn(0);
1304c4762a1bSJed Brown   l     = *link;
1305c4762a1bSJed Brown   *link = NULL;
1306c4762a1bSJed Brown   for (; l; l=next) {
1307c4762a1bSJed Brown     next = l->next;
1308c4762a1bSJed Brown     ierr = PetscFree(l->name);CHKERRQ(ierr);
1309c4762a1bSJed Brown     ierr = PetscFree(l);CHKERRQ(ierr);
1310c4762a1bSJed Brown   }
1311c4762a1bSJed Brown   PetscFunctionReturn(0);
1312c4762a1bSJed Brown }
1313c4762a1bSJed Brown 
1314c4762a1bSJed Brown /* put the solution callback into a functional callback */
1315c4762a1bSJed Brown static PetscErrorCode SolutionFunctional(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *modctx)
1316c4762a1bSJed Brown {
1317c4762a1bSJed Brown   Model          mod;
1318c4762a1bSJed Brown   PetscErrorCode ierr;
1319c4762a1bSJed Brown   PetscFunctionBegin;
1320c4762a1bSJed Brown   mod  = (Model) modctx;
1321c4762a1bSJed Brown   ierr = (*mod->solution)(mod, time, x, u, mod->solutionctx);CHKERRQ(ierr);
1322c4762a1bSJed Brown   PetscFunctionReturn(0);
1323c4762a1bSJed Brown }
1324c4762a1bSJed Brown 
1325c4762a1bSJed Brown PetscErrorCode SetInitialCondition(DM dm, Vec X, User user)
1326c4762a1bSJed Brown {
1327c4762a1bSJed Brown   PetscErrorCode     (*func[1]) (PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx);
1328c4762a1bSJed Brown   void               *ctx[1];
1329c4762a1bSJed Brown   Model              mod = user->model;
1330c4762a1bSJed Brown   PetscErrorCode     ierr;
1331c4762a1bSJed Brown 
1332c4762a1bSJed Brown   PetscFunctionBeginUser;
1333c4762a1bSJed Brown   func[0] = SolutionFunctional;
1334c4762a1bSJed Brown   ctx[0]  = (void *) mod;
1335c4762a1bSJed Brown   ierr    = DMProjectFunction(dm,0.0,func,ctx,INSERT_ALL_VALUES,X);CHKERRQ(ierr);
1336c4762a1bSJed Brown   PetscFunctionReturn(0);
1337c4762a1bSJed Brown }
1338c4762a1bSJed Brown 
1339c4762a1bSJed Brown static PetscErrorCode OutputVTK(DM dm, const char *filename, PetscViewer *viewer)
1340c4762a1bSJed Brown {
1341c4762a1bSJed Brown   PetscErrorCode ierr;
1342c4762a1bSJed Brown 
1343c4762a1bSJed Brown   PetscFunctionBeginUser;
1344c4762a1bSJed Brown   ierr = PetscViewerCreate(PetscObjectComm((PetscObject)dm), viewer);CHKERRQ(ierr);
1345c4762a1bSJed Brown   ierr = PetscViewerSetType(*viewer, PETSCVIEWERVTK);CHKERRQ(ierr);
1346c4762a1bSJed Brown   ierr = PetscViewerFileSetName(*viewer, filename);CHKERRQ(ierr);
1347c4762a1bSJed Brown   PetscFunctionReturn(0);
1348c4762a1bSJed Brown }
1349c4762a1bSJed Brown 
1350c4762a1bSJed Brown static PetscErrorCode MonitorVTK(TS ts,PetscInt stepnum,PetscReal time,Vec X,void *ctx)
1351c4762a1bSJed Brown {
1352c4762a1bSJed Brown   User           user = (User)ctx;
1353*3e9753d6SMatthew G. Knepley   DM             dm, plex;
1354c4762a1bSJed Brown   PetscViewer    viewer;
1355c4762a1bSJed Brown   char           filename[PETSC_MAX_PATH_LEN],*ftable = NULL;
1356c4762a1bSJed Brown   PetscReal      xnorm;
1357c4762a1bSJed Brown   PetscErrorCode ierr;
1358c4762a1bSJed Brown 
1359c4762a1bSJed Brown   PetscFunctionBeginUser;
1360c4762a1bSJed Brown   ierr = PetscObjectSetName((PetscObject) X, "u");CHKERRQ(ierr);
1361c4762a1bSJed Brown   ierr = VecGetDM(X,&dm);CHKERRQ(ierr);
1362c4762a1bSJed Brown   ierr = VecNorm(X,NORM_INFINITY,&xnorm);CHKERRQ(ierr);
1363c4762a1bSJed Brown 
1364c4762a1bSJed Brown   if (stepnum >= 0) {
1365c4762a1bSJed Brown     stepnum += user->monitorStepOffset;
1366c4762a1bSJed Brown   }
1367c4762a1bSJed Brown   if (stepnum >= 0) {           /* No summary for final time */
1368c4762a1bSJed Brown     Model             mod = user->model;
1369*3e9753d6SMatthew G. Knepley     Vec               cellgeom;
1370c4762a1bSJed Brown     PetscInt          c,cStart,cEnd,fcount,i;
1371c4762a1bSJed Brown     size_t            ftableused,ftablealloc;
1372c4762a1bSJed Brown     const PetscScalar *cgeom,*x;
1373c4762a1bSJed Brown     DM                dmCell;
1374c4762a1bSJed Brown     DMLabel           vtkLabel;
1375c4762a1bSJed Brown     PetscReal         *fmin,*fmax,*fintegral,*ftmp;
1376*3e9753d6SMatthew G. Knepley 
1377*3e9753d6SMatthew G. Knepley     ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr);
1378*3e9753d6SMatthew G. Knepley     ierr = DMPlexGetGeometryFVM(plex, NULL, &cellgeom, NULL);CHKERRQ(ierr);
1379c4762a1bSJed Brown     fcount = mod->maxComputed+1;
1380c4762a1bSJed Brown     ierr   = PetscMalloc4(fcount,&fmin,fcount,&fmax,fcount,&fintegral,fcount,&ftmp);CHKERRQ(ierr);
1381c4762a1bSJed Brown     for (i=0; i<fcount; i++) {
1382c4762a1bSJed Brown       fmin[i]      = PETSC_MAX_REAL;
1383c4762a1bSJed Brown       fmax[i]      = PETSC_MIN_REAL;
1384c4762a1bSJed Brown       fintegral[i] = 0;
1385c4762a1bSJed Brown     }
1386c4762a1bSJed Brown     ierr = VecGetDM(cellgeom,&dmCell);CHKERRQ(ierr);
138754fcfd0cSMatthew G. Knepley     ierr = DMPlexGetSimplexOrBoxCells(dmCell,0,&cStart,&cEnd);CHKERRQ(ierr);
1388c4762a1bSJed Brown     ierr = VecGetArrayRead(cellgeom,&cgeom);CHKERRQ(ierr);
1389c4762a1bSJed Brown     ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr);
1390c4762a1bSJed Brown     ierr = DMGetLabel(dm,"vtk",&vtkLabel);CHKERRQ(ierr);
1391c4762a1bSJed Brown     for (c = cStart; c < cEnd; ++c) {
1392c4762a1bSJed Brown       PetscFVCellGeom       *cg;
1393c4762a1bSJed Brown       const PetscScalar     *cx    = NULL;
1394c4762a1bSJed Brown       PetscInt              vtkVal = 0;
1395c4762a1bSJed Brown 
1396c4762a1bSJed Brown       /* not that these two routines as currently implemented work for any dm with a
1397c4762a1bSJed Brown        * localSection/globalSection */
1398c4762a1bSJed Brown       ierr = DMPlexPointLocalRead(dmCell,c,cgeom,&cg);CHKERRQ(ierr);
1399c4762a1bSJed Brown       ierr = DMPlexPointGlobalRead(dm,c,x,&cx);CHKERRQ(ierr);
1400c4762a1bSJed Brown       if (vtkLabel) {ierr = DMLabelGetValue(vtkLabel,c,&vtkVal);CHKERRQ(ierr);}
1401c4762a1bSJed Brown       if (!vtkVal || !cx) continue;        /* ghost, or not a global cell */
1402c4762a1bSJed Brown       for (i=0; i<mod->numCall; i++) {
1403c4762a1bSJed Brown         FunctionalLink flink = mod->functionalCall[i];
1404c4762a1bSJed Brown         ierr = (*flink->func)(mod,time,cg->centroid,cx,ftmp,flink->ctx);CHKERRQ(ierr);
1405c4762a1bSJed Brown       }
1406c4762a1bSJed Brown       for (i=0; i<fcount; i++) {
1407c4762a1bSJed Brown         fmin[i]       = PetscMin(fmin[i],ftmp[i]);
1408c4762a1bSJed Brown         fmax[i]       = PetscMax(fmax[i],ftmp[i]);
1409c4762a1bSJed Brown         fintegral[i] += cg->volume * ftmp[i];
1410c4762a1bSJed Brown       }
1411c4762a1bSJed Brown     }
1412c4762a1bSJed Brown     ierr = VecRestoreArrayRead(cellgeom,&cgeom);CHKERRQ(ierr);
1413c4762a1bSJed Brown     ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr);
1414*3e9753d6SMatthew G. Knepley     ierr = DMDestroy(&plex);CHKERRQ(ierr);
1415c4762a1bSJed Brown     ierr = MPI_Allreduce(MPI_IN_PLACE,fmin,fcount,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr);
1416c4762a1bSJed Brown     ierr = MPI_Allreduce(MPI_IN_PLACE,fmax,fcount,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr);
1417c4762a1bSJed Brown     ierr = MPI_Allreduce(MPI_IN_PLACE,fintegral,fcount,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr);
1418c4762a1bSJed Brown 
1419c4762a1bSJed Brown     ftablealloc = fcount * 100;
1420c4762a1bSJed Brown     ftableused  = 0;
1421c4762a1bSJed Brown     ierr        = PetscMalloc1(ftablealloc,&ftable);CHKERRQ(ierr);
1422c4762a1bSJed Brown     for (i=0; i<mod->numMonitored; i++) {
1423c4762a1bSJed Brown       size_t         countused;
1424c4762a1bSJed Brown       char           buffer[256],*p;
1425c4762a1bSJed Brown       FunctionalLink flink = mod->functionalMonitored[i];
1426c4762a1bSJed Brown       PetscInt       id    = flink->offset;
1427c4762a1bSJed Brown       if (i % 3) {
1428c4762a1bSJed Brown         ierr = PetscArraycpy(buffer,"  ",2);CHKERRQ(ierr);
1429c4762a1bSJed Brown         p    = buffer + 2;
1430c4762a1bSJed Brown       } else if (i) {
1431c4762a1bSJed Brown         char newline[] = "\n";
1432c4762a1bSJed Brown         ierr = PetscMemcpy(buffer,newline,sizeof(newline)-1);CHKERRQ(ierr);
1433c4762a1bSJed Brown         p    = buffer + sizeof(newline) - 1;
1434c4762a1bSJed Brown       } else {
1435c4762a1bSJed Brown         p = buffer;
1436c4762a1bSJed Brown       }
1437c4762a1bSJed Brown       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);
1438c4762a1bSJed Brown       countused--;
1439c4762a1bSJed Brown       countused += p - buffer;
1440c4762a1bSJed Brown       if (countused > ftablealloc-ftableused-1) { /* reallocate */
1441c4762a1bSJed Brown         char *ftablenew;
1442c4762a1bSJed Brown         ftablealloc = 2*ftablealloc + countused;
1443c4762a1bSJed Brown         ierr = PetscMalloc(ftablealloc,&ftablenew);CHKERRQ(ierr);
1444c4762a1bSJed Brown         ierr = PetscArraycpy(ftablenew,ftable,ftableused);CHKERRQ(ierr);
1445c4762a1bSJed Brown         ierr = PetscFree(ftable);CHKERRQ(ierr);
1446c4762a1bSJed Brown         ftable = ftablenew;
1447c4762a1bSJed Brown       }
1448c4762a1bSJed Brown       ierr = PetscArraycpy(ftable+ftableused,buffer,countused);CHKERRQ(ierr);
1449c4762a1bSJed Brown       ftableused += countused;
1450c4762a1bSJed Brown       ftable[ftableused] = 0;
1451c4762a1bSJed Brown     }
1452c4762a1bSJed Brown     ierr = PetscFree4(fmin,fmax,fintegral,ftmp);CHKERRQ(ierr);
1453c4762a1bSJed Brown 
1454c4762a1bSJed Brown     ierr = PetscPrintf(PetscObjectComm((PetscObject)ts),"% 3D  time %8.4g  |x| %8.4g  %s\n",stepnum,(double)time,(double)xnorm,ftable ? ftable : "");CHKERRQ(ierr);
1455c4762a1bSJed Brown     ierr = PetscFree(ftable);CHKERRQ(ierr);
1456c4762a1bSJed Brown   }
1457c4762a1bSJed Brown   if (user->vtkInterval < 1) PetscFunctionReturn(0);
1458c4762a1bSJed Brown   if ((stepnum == -1) ^ (stepnum % user->vtkInterval == 0)) {
1459c4762a1bSJed Brown     if (stepnum == -1) {        /* Final time is not multiple of normal time interval, write it anyway */
1460c4762a1bSJed Brown       ierr = TSGetStepNumber(ts,&stepnum);CHKERRQ(ierr);
1461c4762a1bSJed Brown     }
1462c4762a1bSJed Brown     ierr = PetscSNPrintf(filename,sizeof filename,"%s-%03D.vtu",user->outputBasename,stepnum);CHKERRQ(ierr);
1463c4762a1bSJed Brown     ierr = OutputVTK(dm,filename,&viewer);CHKERRQ(ierr);
1464c4762a1bSJed Brown     ierr = VecView(X,viewer);CHKERRQ(ierr);
1465c4762a1bSJed Brown     ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
1466c4762a1bSJed Brown   }
1467c4762a1bSJed Brown   PetscFunctionReturn(0);
1468c4762a1bSJed Brown }
1469c4762a1bSJed Brown 
1470c4762a1bSJed Brown static PetscErrorCode initializeTS(DM dm, User user, TS *ts)
1471c4762a1bSJed Brown {
1472c4762a1bSJed Brown   PetscErrorCode ierr;
1473c4762a1bSJed Brown 
1474c4762a1bSJed Brown   PetscFunctionBegin;
1475c4762a1bSJed Brown   ierr = TSCreate(PetscObjectComm((PetscObject)dm), ts);CHKERRQ(ierr);
1476c4762a1bSJed Brown   ierr = TSSetType(*ts, TSSSP);CHKERRQ(ierr);
1477c4762a1bSJed Brown   ierr = TSSetDM(*ts, dm);CHKERRQ(ierr);
1478c4762a1bSJed Brown   if (user->vtkmon) {
1479c4762a1bSJed Brown     ierr = TSMonitorSet(*ts,MonitorVTK,user,NULL);CHKERRQ(ierr);
1480c4762a1bSJed Brown   }
1481c4762a1bSJed Brown   ierr = DMTSSetBoundaryLocal(dm, DMPlexTSComputeBoundary, user);CHKERRQ(ierr);
1482c4762a1bSJed Brown   ierr = DMTSSetRHSFunctionLocal(dm, DMPlexTSComputeRHSFunctionFVM, user);CHKERRQ(ierr);
1483c4762a1bSJed Brown   ierr = TSSetMaxTime(*ts,2.0);CHKERRQ(ierr);
1484c4762a1bSJed Brown   ierr = TSSetExactFinalTime(*ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);
1485c4762a1bSJed Brown   PetscFunctionReturn(0);
1486c4762a1bSJed Brown }
1487c4762a1bSJed Brown 
1488c4762a1bSJed Brown static PetscErrorCode adaptToleranceFVM(PetscFV fvm, TS ts, Vec sol, VecTagger refineTag, VecTagger coarsenTag, User user, TS *tsNew, Vec *solNew)
1489c4762a1bSJed Brown {
1490c4762a1bSJed Brown   DM                dm, gradDM, plex, cellDM, adaptedDM = NULL;
1491c4762a1bSJed Brown   Vec               cellGeom, faceGeom;
1492c4762a1bSJed Brown   PetscBool         isForest, computeGradient;
1493c4762a1bSJed Brown   Vec               grad, locGrad, locX, errVec;
1494c4762a1bSJed Brown   PetscInt          cStart, cEnd, c, dim, nRefine, nCoarsen;
1495c4762a1bSJed Brown   PetscReal         minMaxInd[2] = {PETSC_MAX_REAL, PETSC_MIN_REAL}, minMaxIndGlobal[2], minInd, maxInd, time;
1496c4762a1bSJed Brown   PetscScalar       *errArray;
1497c4762a1bSJed Brown   const PetscScalar *pointVals;
1498c4762a1bSJed Brown   const PetscScalar *pointGrads;
1499c4762a1bSJed Brown   const PetscScalar *pointGeom;
1500c4762a1bSJed Brown   DMLabel           adaptLabel = NULL;
1501c4762a1bSJed Brown   IS                refineIS, coarsenIS;
1502c4762a1bSJed Brown   PetscErrorCode    ierr;
1503c4762a1bSJed Brown 
1504c4762a1bSJed Brown   PetscFunctionBegin;
1505c4762a1bSJed Brown   ierr = TSGetTime(ts,&time);CHKERRQ(ierr);
1506c4762a1bSJed Brown   ierr = VecGetDM(sol, &dm);CHKERRQ(ierr);
1507c4762a1bSJed Brown   ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr);
1508c4762a1bSJed Brown   ierr = PetscFVGetComputeGradients(fvm,&computeGradient);CHKERRQ(ierr);
1509c4762a1bSJed Brown   ierr = PetscFVSetComputeGradients(fvm,PETSC_TRUE);CHKERRQ(ierr);
1510c4762a1bSJed Brown   ierr = DMIsForest(dm, &isForest);CHKERRQ(ierr);
1511c4762a1bSJed Brown   ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr);
1512c4762a1bSJed Brown   ierr = DMPlexGetDataFVM(plex, fvm, &cellGeom, &faceGeom, &gradDM);CHKERRQ(ierr);
1513c4762a1bSJed Brown   ierr = DMCreateLocalVector(plex,&locX);CHKERRQ(ierr);
1514c4762a1bSJed Brown   ierr = DMPlexInsertBoundaryValues(plex, PETSC_TRUE, locX, 0.0, faceGeom, cellGeom, NULL);CHKERRQ(ierr);
1515c4762a1bSJed Brown   ierr = DMGlobalToLocalBegin(plex, sol, INSERT_VALUES, locX);CHKERRQ(ierr);
1516c4762a1bSJed Brown   ierr = DMGlobalToLocalEnd  (plex, sol, INSERT_VALUES, locX);CHKERRQ(ierr);
1517c4762a1bSJed Brown   ierr = DMCreateGlobalVector(gradDM, &grad);CHKERRQ(ierr);
1518c4762a1bSJed Brown   ierr = DMPlexReconstructGradientsFVM(plex, locX, grad);CHKERRQ(ierr);
1519c4762a1bSJed Brown   ierr = DMCreateLocalVector(gradDM, &locGrad);CHKERRQ(ierr);
1520c4762a1bSJed Brown   ierr = DMGlobalToLocalBegin(gradDM, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr);
1521c4762a1bSJed Brown   ierr = DMGlobalToLocalEnd(gradDM, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr);
1522c4762a1bSJed Brown   ierr = VecDestroy(&grad);CHKERRQ(ierr);
152354fcfd0cSMatthew G. Knepley   ierr = DMPlexGetSimplexOrBoxCells(plex,0,&cStart,&cEnd);CHKERRQ(ierr);
1524c4762a1bSJed Brown   ierr = VecGetArrayRead(locGrad,&pointGrads);CHKERRQ(ierr);
1525c4762a1bSJed Brown   ierr = VecGetArrayRead(cellGeom,&pointGeom);CHKERRQ(ierr);
1526c4762a1bSJed Brown   ierr = VecGetArrayRead(locX,&pointVals);CHKERRQ(ierr);
1527c4762a1bSJed Brown   ierr = VecGetDM(cellGeom,&cellDM);CHKERRQ(ierr);
1528c4762a1bSJed Brown   ierr = DMLabelCreate(PETSC_COMM_SELF,"adapt",&adaptLabel);CHKERRQ(ierr);
1529c4762a1bSJed Brown   ierr = VecCreateMPI(PetscObjectComm((PetscObject)plex),cEnd-cStart,PETSC_DETERMINE,&errVec);CHKERRQ(ierr);
1530c4762a1bSJed Brown   ierr = VecSetUp(errVec);CHKERRQ(ierr);
1531c4762a1bSJed Brown   ierr = VecGetArray(errVec,&errArray);CHKERRQ(ierr);
1532c4762a1bSJed Brown   for (c = cStart; c < cEnd; c++) {
1533c4762a1bSJed Brown     PetscReal             errInd = 0.;
1534c4762a1bSJed Brown     PetscScalar           *pointGrad;
1535c4762a1bSJed Brown     PetscScalar           *pointVal;
1536c4762a1bSJed Brown     PetscFVCellGeom       *cg;
1537c4762a1bSJed Brown 
1538c4762a1bSJed Brown     ierr = DMPlexPointLocalRead(gradDM,c,pointGrads,&pointGrad);CHKERRQ(ierr);
1539c4762a1bSJed Brown     ierr = DMPlexPointLocalRead(cellDM,c,pointGeom,&cg);CHKERRQ(ierr);
1540c4762a1bSJed Brown     ierr = DMPlexPointLocalRead(plex,c,pointVals,&pointVal);CHKERRQ(ierr);
1541c4762a1bSJed Brown 
1542c4762a1bSJed Brown     ierr = (user->model->errorIndicator)(dim,cg->volume,user->model->physics->dof,pointVal,pointGrad,&errInd,user->model->errorCtx);CHKERRQ(ierr);
1543c4762a1bSJed Brown     errArray[c-cStart] = errInd;
1544c4762a1bSJed Brown     minMaxInd[0] = PetscMin(minMaxInd[0],errInd);
1545c4762a1bSJed Brown     minMaxInd[1] = PetscMax(minMaxInd[1],errInd);
1546c4762a1bSJed Brown   }
1547c4762a1bSJed Brown   ierr = VecRestoreArray(errVec,&errArray);CHKERRQ(ierr);
1548c4762a1bSJed Brown   ierr = VecRestoreArrayRead(locX,&pointVals);CHKERRQ(ierr);
1549c4762a1bSJed Brown   ierr = VecRestoreArrayRead(cellGeom,&pointGeom);CHKERRQ(ierr);
1550c4762a1bSJed Brown   ierr = VecRestoreArrayRead(locGrad,&pointGrads);CHKERRQ(ierr);
1551c4762a1bSJed Brown   ierr = VecDestroy(&locGrad);CHKERRQ(ierr);
1552c4762a1bSJed Brown   ierr = VecDestroy(&locX);CHKERRQ(ierr);
1553c4762a1bSJed Brown   ierr = DMDestroy(&plex);CHKERRQ(ierr);
1554c4762a1bSJed Brown 
1555c4762a1bSJed Brown   ierr = VecTaggerComputeIS(refineTag,errVec,&refineIS);CHKERRQ(ierr);
1556c4762a1bSJed Brown   ierr = VecTaggerComputeIS(coarsenTag,errVec,&coarsenIS);CHKERRQ(ierr);
1557c4762a1bSJed Brown   ierr = ISGetSize(refineIS,&nRefine);CHKERRQ(ierr);
1558c4762a1bSJed Brown   ierr = ISGetSize(coarsenIS,&nCoarsen);CHKERRQ(ierr);
1559c4762a1bSJed Brown   if (nRefine) {ierr = DMLabelSetStratumIS(adaptLabel,DM_ADAPT_REFINE,refineIS);CHKERRQ(ierr);}
1560c4762a1bSJed Brown   if (nCoarsen) {ierr = DMLabelSetStratumIS(adaptLabel,DM_ADAPT_COARSEN,coarsenIS);CHKERRQ(ierr);}
1561c4762a1bSJed Brown   ierr = ISDestroy(&coarsenIS);CHKERRQ(ierr);
1562c4762a1bSJed Brown   ierr = ISDestroy(&refineIS);CHKERRQ(ierr);
1563c4762a1bSJed Brown   ierr = VecDestroy(&errVec);CHKERRQ(ierr);
1564c4762a1bSJed Brown 
1565c4762a1bSJed Brown   ierr = PetscFVSetComputeGradients(fvm,computeGradient);CHKERRQ(ierr);
1566c4762a1bSJed Brown   minMaxInd[1] = -minMaxInd[1];
1567c4762a1bSJed Brown   ierr = MPI_Allreduce(minMaxInd,minMaxIndGlobal,2,MPIU_REAL,MPI_MIN,PetscObjectComm((PetscObject)dm));CHKERRQ(ierr);
1568c4762a1bSJed Brown   minInd = minMaxIndGlobal[0];
1569c4762a1bSJed Brown   maxInd = -minMaxIndGlobal[1];
1570c4762a1bSJed Brown   ierr = PetscInfo2(ts, "error indicator range (%E, %E)\n", minInd, maxInd);CHKERRQ(ierr);
1571c4762a1bSJed Brown   if (nRefine || nCoarsen) { /* at least one cell is over the refinement threshold */
1572c4762a1bSJed Brown     ierr = DMAdaptLabel(dm,adaptLabel,&adaptedDM);CHKERRQ(ierr);
1573c4762a1bSJed Brown   }
1574c4762a1bSJed Brown   ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr);
1575c4762a1bSJed Brown   if (adaptedDM) {
1576c4762a1bSJed Brown     ierr = PetscInfo2(ts, "Adapted mesh, marking %D cells for refinement, and %D cells for coarsening\n", nRefine, nCoarsen);CHKERRQ(ierr);
1577c4762a1bSJed Brown     if (tsNew) {ierr = initializeTS(adaptedDM, user, tsNew);CHKERRQ(ierr);}
1578c4762a1bSJed Brown     if (solNew) {
1579c4762a1bSJed Brown       ierr = DMCreateGlobalVector(adaptedDM, solNew);CHKERRQ(ierr);
1580c4762a1bSJed Brown       ierr = PetscObjectSetName((PetscObject) *solNew, "solution");CHKERRQ(ierr);
1581c4762a1bSJed Brown       ierr = DMForestTransferVec(dm, sol, adaptedDM, *solNew, PETSC_TRUE, time);CHKERRQ(ierr);
1582c4762a1bSJed Brown     }
1583c4762a1bSJed Brown     if (isForest) {ierr = DMForestSetAdaptivityForest(adaptedDM,NULL);CHKERRQ(ierr);} /* clear internal references to the previous dm */
1584c4762a1bSJed Brown     ierr = DMDestroy(&adaptedDM);CHKERRQ(ierr);
1585c4762a1bSJed Brown   } else {
1586c4762a1bSJed Brown     if (tsNew)  *tsNew  = NULL;
1587c4762a1bSJed Brown     if (solNew) *solNew = NULL;
1588c4762a1bSJed Brown   }
1589c4762a1bSJed Brown   PetscFunctionReturn(0);
1590c4762a1bSJed Brown }
1591c4762a1bSJed Brown 
1592c4762a1bSJed Brown int main(int argc, char **argv)
1593c4762a1bSJed Brown {
1594c4762a1bSJed Brown   MPI_Comm          comm;
1595c4762a1bSJed Brown   PetscDS           prob;
1596c4762a1bSJed Brown   PetscFV           fvm;
1597c4762a1bSJed Brown   PetscLimiter      limiter = NULL, noneLimiter = NULL;
1598c4762a1bSJed Brown   User              user;
1599c4762a1bSJed Brown   Model             mod;
1600c4762a1bSJed Brown   Physics           phys;
1601*3e9753d6SMatthew G. Knepley   DM                dm, plex;
1602c4762a1bSJed Brown   PetscReal         ftime, cfl, dt, minRadius;
1603c4762a1bSJed Brown   PetscInt          dim, nsteps;
1604c4762a1bSJed Brown   TS                ts;
1605c4762a1bSJed Brown   TSConvergedReason reason;
1606c4762a1bSJed Brown   Vec               X;
1607c4762a1bSJed Brown   PetscViewer       viewer;
1608c4762a1bSJed Brown   PetscBool         simplex = PETSC_FALSE, vtkCellGeom, splitFaces, useAMR;
1609c4762a1bSJed Brown   PetscInt          overlap, adaptInterval;
1610c4762a1bSJed Brown   char              filename[PETSC_MAX_PATH_LEN] = "";
1611c4762a1bSJed Brown   char              physname[256]  = "advect";
1612c4762a1bSJed Brown   VecTagger         refineTag = NULL, coarsenTag = NULL;
1613c4762a1bSJed Brown   PetscErrorCode    ierr;
1614c4762a1bSJed Brown 
1615c4762a1bSJed Brown   ierr = PetscInitialize(&argc, &argv, (char*) 0, help);if (ierr) return ierr;
1616c4762a1bSJed Brown   comm = PETSC_COMM_WORLD;
1617c4762a1bSJed Brown 
1618c4762a1bSJed Brown   ierr          = PetscNew(&user);CHKERRQ(ierr);
1619c4762a1bSJed Brown   ierr          = PetscNew(&user->model);CHKERRQ(ierr);
1620c4762a1bSJed Brown   ierr          = PetscNew(&user->model->physics);CHKERRQ(ierr);
1621c4762a1bSJed Brown   mod           = user->model;
1622c4762a1bSJed Brown   phys          = mod->physics;
1623c4762a1bSJed Brown   mod->comm     = comm;
1624c4762a1bSJed Brown   useAMR        = PETSC_FALSE;
1625c4762a1bSJed Brown   adaptInterval = 1;
1626c4762a1bSJed Brown 
1627c4762a1bSJed Brown   /* Register physical models to be available on the command line */
1628c4762a1bSJed Brown   ierr = PetscFunctionListAdd(&PhysicsList,"advect"          ,PhysicsCreate_Advect);CHKERRQ(ierr);
1629c4762a1bSJed Brown   ierr = PetscFunctionListAdd(&PhysicsList,"sw"              ,PhysicsCreate_SW);CHKERRQ(ierr);
1630c4762a1bSJed Brown   ierr = PetscFunctionListAdd(&PhysicsList,"euler"           ,PhysicsCreate_Euler);CHKERRQ(ierr);
1631c4762a1bSJed Brown 
1632c4762a1bSJed Brown   ierr = PetscOptionsBegin(comm,NULL,"Unstructured Finite Volume Mesh Options","");CHKERRQ(ierr);
1633c4762a1bSJed Brown   {
1634c4762a1bSJed Brown     cfl  = 0.9 * 4; /* default SSPRKS2 with s=5 stages is stable for CFL number s-1 */
1635c4762a1bSJed Brown     ierr = PetscOptionsReal("-ufv_cfl","CFL number per step","",cfl,&cfl,NULL);CHKERRQ(ierr);
1636c4762a1bSJed Brown     ierr = PetscOptionsString("-f","Exodus.II filename to read","",filename,filename,sizeof(filename),NULL);CHKERRQ(ierr);
1637c4762a1bSJed Brown     ierr = PetscOptionsBool("-simplex","Flag to use a simplex mesh","",simplex,&simplex,NULL);CHKERRQ(ierr);
1638c4762a1bSJed Brown     splitFaces = PETSC_FALSE;
1639c4762a1bSJed Brown     ierr = PetscOptionsBool("-ufv_split_faces","Split faces between cell sets","",splitFaces,&splitFaces,NULL);CHKERRQ(ierr);
1640c4762a1bSJed Brown     overlap = 1;
1641c4762a1bSJed Brown     ierr = PetscOptionsInt("-ufv_mesh_overlap","Number of cells to overlap partitions","",overlap,&overlap,NULL);CHKERRQ(ierr);
1642c4762a1bSJed Brown     user->vtkInterval = 1;
1643c4762a1bSJed Brown     ierr = PetscOptionsInt("-ufv_vtk_interval","VTK output interval (0 to disable)","",user->vtkInterval,&user->vtkInterval,NULL);CHKERRQ(ierr);
1644c4762a1bSJed Brown     user->vtkmon = PETSC_TRUE;
1645c4762a1bSJed Brown     ierr = PetscOptionsBool("-ufv_vtk_monitor","Use VTKMonitor routine","",user->vtkmon,&user->vtkmon,NULL);CHKERRQ(ierr);
1646c4762a1bSJed Brown     vtkCellGeom = PETSC_FALSE;
1647c4762a1bSJed Brown     ierr = PetscStrcpy(user->outputBasename, "ex11");CHKERRQ(ierr);
1648589a23caSBarry Smith     ierr = PetscOptionsString("-ufv_vtk_basename","VTK output basename","",user->outputBasename,user->outputBasename,sizeof(user->outputBasename),NULL);CHKERRQ(ierr);
1649c4762a1bSJed Brown     ierr = PetscOptionsBool("-ufv_vtk_cellgeom","Write cell geometry (for debugging)","",vtkCellGeom,&vtkCellGeom,NULL);CHKERRQ(ierr);
1650c4762a1bSJed Brown     ierr = PetscOptionsBool("-ufv_use_amr","use local adaptive mesh refinement","",useAMR,&useAMR,NULL);CHKERRQ(ierr);
1651c4762a1bSJed Brown     ierr = PetscOptionsInt("-ufv_adapt_interval","time steps between AMR","",adaptInterval,&adaptInterval,NULL);CHKERRQ(ierr);
1652c4762a1bSJed Brown   }
1653c4762a1bSJed Brown   ierr = PetscOptionsEnd();CHKERRQ(ierr);
1654c4762a1bSJed Brown 
1655c4762a1bSJed Brown   if (useAMR) {
1656c4762a1bSJed Brown     VecTaggerBox refineBox, coarsenBox;
1657c4762a1bSJed Brown 
1658c4762a1bSJed Brown     refineBox.min  = refineBox.max  = PETSC_MAX_REAL;
1659c4762a1bSJed Brown     coarsenBox.min = coarsenBox.max = PETSC_MIN_REAL;
1660c4762a1bSJed Brown 
1661c4762a1bSJed Brown     ierr = VecTaggerCreate(comm,&refineTag);CHKERRQ(ierr);
1662c4762a1bSJed Brown     ierr = PetscObjectSetOptionsPrefix((PetscObject)refineTag,"refine_");CHKERRQ(ierr);
1663c4762a1bSJed Brown     ierr = VecTaggerSetType(refineTag,VECTAGGERABSOLUTE);CHKERRQ(ierr);
1664c4762a1bSJed Brown     ierr = VecTaggerAbsoluteSetBox(refineTag,&refineBox);CHKERRQ(ierr);
1665c4762a1bSJed Brown     ierr = VecTaggerSetFromOptions(refineTag);CHKERRQ(ierr);
1666c4762a1bSJed Brown     ierr = VecTaggerSetUp(refineTag);CHKERRQ(ierr);
1667c4762a1bSJed Brown     ierr = PetscObjectViewFromOptions((PetscObject)refineTag,NULL,"-tag_view");CHKERRQ(ierr);
1668c4762a1bSJed Brown 
1669c4762a1bSJed Brown     ierr = VecTaggerCreate(comm,&coarsenTag);CHKERRQ(ierr);
1670c4762a1bSJed Brown     ierr = PetscObjectSetOptionsPrefix((PetscObject)coarsenTag,"coarsen_");CHKERRQ(ierr);
1671c4762a1bSJed Brown     ierr = VecTaggerSetType(coarsenTag,VECTAGGERABSOLUTE);CHKERRQ(ierr);
1672c4762a1bSJed Brown     ierr = VecTaggerAbsoluteSetBox(coarsenTag,&coarsenBox);CHKERRQ(ierr);
1673c4762a1bSJed Brown     ierr = VecTaggerSetFromOptions(coarsenTag);CHKERRQ(ierr);
1674c4762a1bSJed Brown     ierr = VecTaggerSetUp(coarsenTag);CHKERRQ(ierr);
1675c4762a1bSJed Brown     ierr = PetscObjectViewFromOptions((PetscObject)coarsenTag,NULL,"-tag_view");CHKERRQ(ierr);
1676c4762a1bSJed Brown   }
1677c4762a1bSJed Brown 
1678c4762a1bSJed Brown   ierr = PetscOptionsBegin(comm,NULL,"Unstructured Finite Volume Physics Options","");CHKERRQ(ierr);
1679c4762a1bSJed Brown   {
1680c4762a1bSJed Brown     PetscErrorCode (*physcreate)(Model,Physics,PetscOptionItems*);
1681c4762a1bSJed Brown     ierr = PetscOptionsFList("-physics","Physics module to solve","",PhysicsList,physname,physname,sizeof physname,NULL);CHKERRQ(ierr);
1682c4762a1bSJed Brown     ierr = PetscFunctionListFind(PhysicsList,physname,&physcreate);CHKERRQ(ierr);
1683c4762a1bSJed Brown     ierr = PetscMemzero(phys,sizeof(struct _n_Physics));CHKERRQ(ierr);
1684c4762a1bSJed Brown     ierr = (*physcreate)(mod,phys,PetscOptionsObject);CHKERRQ(ierr);
1685c4762a1bSJed Brown     /* Count number of fields and dofs */
1686c4762a1bSJed Brown     for (phys->nfields=0,phys->dof=0; phys->field_desc[phys->nfields].name; phys->nfields++) phys->dof += phys->field_desc[phys->nfields].dof;
1687c4762a1bSJed Brown     if (phys->dof <= 0) SETERRQ1(comm,PETSC_ERR_ARG_WRONGSTATE,"Physics '%s' did not set dof",physname);
1688c4762a1bSJed Brown     ierr = ModelFunctionalSetFromOptions(mod,PetscOptionsObject);CHKERRQ(ierr);
1689c4762a1bSJed Brown   }
1690c4762a1bSJed Brown   ierr = PetscOptionsEnd();CHKERRQ(ierr);
1691c4762a1bSJed Brown 
1692c4762a1bSJed Brown   /* Create mesh */
1693c4762a1bSJed Brown   {
1694c4762a1bSJed Brown     size_t len,i;
1695c4762a1bSJed Brown     for (i = 0; i < DIM; i++) { mod->bounds[2*i] = 0.; mod->bounds[2*i+1] = 1.;};
1696c4762a1bSJed Brown     ierr = PetscStrlen(filename,&len);CHKERRQ(ierr);
1697c4762a1bSJed Brown     dim = DIM;
1698c4762a1bSJed Brown     if (!len) { /* a null name means just do a hex box */
1699c4762a1bSJed Brown       PetscInt cells[3] = {1, 1, 1}; /* coarse mesh is one cell; refine from there */
1700c4762a1bSJed Brown       PetscBool flg1, flg2, skew = PETSC_FALSE;
1701c4762a1bSJed Brown       PetscInt nret1 = DIM;
1702c4762a1bSJed Brown       PetscInt nret2 = 2*DIM;
1703c4762a1bSJed Brown       ierr = PetscOptionsBegin(comm,NULL,"Rectangular mesh options","");CHKERRQ(ierr);
1704c4762a1bSJed Brown       ierr = PetscOptionsIntArray("-grid_size","number of cells in each direction","",cells,&nret1,&flg1);CHKERRQ(ierr);
1705c4762a1bSJed Brown       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);
1706c4762a1bSJed Brown       ierr = PetscOptionsBool("-grid_skew_60","Skew grid for 60 degree shock mesh","",skew,&skew,NULL);CHKERRQ(ierr);
1707c4762a1bSJed Brown       ierr = PetscOptionsEnd();CHKERRQ(ierr);
1708c4762a1bSJed Brown       if (flg1) {
1709c4762a1bSJed Brown         dim = nret1;
1710c4762a1bSJed Brown         if (dim != DIM) SETERRQ1(comm,PETSC_ERR_ARG_SIZ,"Dim wrong size %D in -grid_size",dim);
1711c4762a1bSJed Brown       }
1712c4762a1bSJed Brown       ierr = DMPlexCreateBoxMesh(comm, dim, simplex, cells, NULL, NULL, mod->bcs, PETSC_TRUE, &dm);CHKERRQ(ierr);
1713c4762a1bSJed Brown       if (flg2) {
1714c4762a1bSJed Brown         PetscInt dimEmbed, i;
1715c4762a1bSJed Brown         PetscInt nCoords;
1716c4762a1bSJed Brown         PetscScalar *coords;
1717c4762a1bSJed Brown         Vec coordinates;
1718c4762a1bSJed Brown 
1719c4762a1bSJed Brown         ierr = DMGetCoordinatesLocal(dm,&coordinates);CHKERRQ(ierr);
1720c4762a1bSJed Brown         ierr = DMGetCoordinateDim(dm,&dimEmbed);CHKERRQ(ierr);
1721c4762a1bSJed Brown         ierr = VecGetLocalSize(coordinates,&nCoords);CHKERRQ(ierr);
1722c4762a1bSJed Brown         if (nCoords % dimEmbed) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Coordinate vector the wrong size");
1723c4762a1bSJed Brown         ierr = VecGetArray(coordinates,&coords);CHKERRQ(ierr);
1724c4762a1bSJed Brown         for (i = 0; i < nCoords; i += dimEmbed) {
1725c4762a1bSJed Brown           PetscInt j;
1726c4762a1bSJed Brown 
1727c4762a1bSJed Brown           PetscScalar *coord = &coords[i];
1728c4762a1bSJed Brown           for (j = 0; j < dimEmbed; j++) {
1729c4762a1bSJed Brown             coord[j] = mod->bounds[2 * j] + coord[j] * (mod->bounds[2 * j + 1] - mod->bounds[2 * j]);
1730c4762a1bSJed Brown             if (dim==2 && cells[1]==1 && j==0 && skew) {
1731c4762a1bSJed Brown               if (cells[0]==2 && i==8) {
1732c4762a1bSJed Brown                 coord[j] = .57735026918963; /* hack to get 60 deg skewed mesh */
1733c4762a1bSJed Brown               }
1734c4762a1bSJed Brown               else if (cells[0]==3) {
1735c4762a1bSJed Brown                 if(i==2 || i==10) coord[j] = mod->bounds[1]/4.;
1736c4762a1bSJed Brown                 else if (i==4) coord[j] = mod->bounds[1]/2.;
1737c4762a1bSJed Brown                 else if (i==12) coord[j] = 1.57735026918963*mod->bounds[1]/2.;
1738c4762a1bSJed Brown               }
1739c4762a1bSJed Brown             }
1740c4762a1bSJed Brown           }
1741c4762a1bSJed Brown         }
1742c4762a1bSJed Brown         ierr = VecRestoreArray(coordinates,&coords);CHKERRQ(ierr);
1743c4762a1bSJed Brown         ierr = DMSetCoordinatesLocal(dm,coordinates);CHKERRQ(ierr);
1744c4762a1bSJed Brown       }
1745c4762a1bSJed Brown     } else {
1746c4762a1bSJed Brown       ierr = DMPlexCreateFromFile(comm, filename, PETSC_TRUE, &dm);CHKERRQ(ierr);
1747c4762a1bSJed Brown     }
1748c4762a1bSJed Brown   }
1749c4762a1bSJed Brown   ierr = DMViewFromOptions(dm, NULL, "-orig_dm_view");CHKERRQ(ierr);
1750c4762a1bSJed Brown   ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
1751c4762a1bSJed Brown 
1752c4762a1bSJed Brown   /* set up BCs, functions, tags */
1753c4762a1bSJed Brown   ierr = DMCreateLabel(dm, "Face Sets");CHKERRQ(ierr);
1754c4762a1bSJed Brown 
1755c4762a1bSJed Brown   mod->errorIndicator = ErrorIndicator_Simple;
1756c4762a1bSJed Brown 
1757c4762a1bSJed Brown   {
1758c4762a1bSJed Brown     DM dmDist;
1759c4762a1bSJed Brown 
1760c4762a1bSJed Brown     ierr = DMSetBasicAdjacency(dm, PETSC_TRUE, PETSC_FALSE);CHKERRQ(ierr);
1761c4762a1bSJed Brown     ierr = DMPlexDistribute(dm, overlap, NULL, &dmDist);CHKERRQ(ierr);
1762c4762a1bSJed Brown     if (dmDist) {
1763c4762a1bSJed Brown       ierr = DMDestroy(&dm);CHKERRQ(ierr);
1764c4762a1bSJed Brown       dm   = dmDist;
1765c4762a1bSJed Brown     }
1766c4762a1bSJed Brown   }
1767c4762a1bSJed Brown 
1768c4762a1bSJed Brown   ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
1769c4762a1bSJed Brown 
1770c4762a1bSJed Brown   {
1771c4762a1bSJed Brown     DM gdm;
1772c4762a1bSJed Brown 
1773c4762a1bSJed Brown     ierr = DMPlexConstructGhostCells(dm, NULL, NULL, &gdm);CHKERRQ(ierr);
1774c4762a1bSJed Brown     ierr = DMDestroy(&dm);CHKERRQ(ierr);
1775c4762a1bSJed Brown     dm   = gdm;
1776c4762a1bSJed Brown     ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr);
1777c4762a1bSJed Brown   }
1778c4762a1bSJed Brown   if (splitFaces) {ierr = ConstructCellBoundary(dm, user);CHKERRQ(ierr);}
1779c4762a1bSJed Brown   ierr = SplitFaces(&dm, "split faces", user);CHKERRQ(ierr);
1780c4762a1bSJed Brown 
1781c4762a1bSJed Brown   ierr = PetscFVCreate(comm, &fvm);CHKERRQ(ierr);
1782c4762a1bSJed Brown   ierr = PetscFVSetFromOptions(fvm);CHKERRQ(ierr);
1783c4762a1bSJed Brown   ierr = PetscFVSetNumComponents(fvm, phys->dof);CHKERRQ(ierr);
1784c4762a1bSJed Brown   ierr = PetscFVSetSpatialDimension(fvm, dim);CHKERRQ(ierr);
1785c4762a1bSJed Brown   ierr = PetscObjectSetName((PetscObject) fvm,"");CHKERRQ(ierr);
1786c4762a1bSJed Brown   {
1787c4762a1bSJed Brown     PetscInt f, dof;
1788c4762a1bSJed Brown     for (f=0,dof=0; f < phys->nfields; f++) {
1789c4762a1bSJed Brown       PetscInt newDof = phys->field_desc[f].dof;
1790c4762a1bSJed Brown 
1791c4762a1bSJed Brown       if (newDof == 1) {
1792c4762a1bSJed Brown         ierr = PetscFVSetComponentName(fvm,dof,phys->field_desc[f].name);CHKERRQ(ierr);
1793c4762a1bSJed Brown       }
1794c4762a1bSJed Brown       else {
1795c4762a1bSJed Brown         PetscInt j;
1796c4762a1bSJed Brown 
1797c4762a1bSJed Brown         for (j = 0; j < newDof; j++) {
1798c4762a1bSJed Brown           char     compName[256]  = "Unknown";
1799c4762a1bSJed Brown 
1800c4762a1bSJed Brown           ierr = PetscSNPrintf(compName,sizeof(compName),"%s_%d",phys->field_desc[f].name,j);CHKERRQ(ierr);
1801c4762a1bSJed Brown           ierr = PetscFVSetComponentName(fvm,dof+j,compName);CHKERRQ(ierr);
1802c4762a1bSJed Brown         }
1803c4762a1bSJed Brown       }
1804c4762a1bSJed Brown       dof += newDof;
1805c4762a1bSJed Brown     }
1806c4762a1bSJed Brown   }
1807c4762a1bSJed Brown   /* FV is now structured with one field having all physics as components */
1808c4762a1bSJed Brown   ierr = DMAddField(dm, NULL, (PetscObject) fvm);CHKERRQ(ierr);
1809c4762a1bSJed Brown   ierr = DMCreateDS(dm);CHKERRQ(ierr);
1810c4762a1bSJed Brown   ierr = DMGetDS(dm, &prob);CHKERRQ(ierr);
1811c4762a1bSJed Brown   ierr = PetscDSSetRiemannSolver(prob, 0, user->model->physics->riemann);CHKERRQ(ierr);
1812c4762a1bSJed Brown   ierr = PetscDSSetContext(prob, 0, user->model->physics);CHKERRQ(ierr);
1813c4762a1bSJed Brown   ierr = (*mod->setupbc)(prob,phys);CHKERRQ(ierr);
1814c4762a1bSJed Brown   ierr = PetscDSSetFromOptions(prob);CHKERRQ(ierr);
1815c4762a1bSJed Brown   {
1816c4762a1bSJed Brown     char      convType[256];
1817c4762a1bSJed Brown     PetscBool flg;
1818c4762a1bSJed Brown 
1819c4762a1bSJed Brown     ierr = PetscOptionsBegin(comm, "", "Mesh conversion options", "DMPLEX");CHKERRQ(ierr);
1820c4762a1bSJed Brown     ierr = PetscOptionsFList("-dm_type","Convert DMPlex to another format","ex12",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr);
1821c4762a1bSJed Brown     ierr = PetscOptionsEnd();CHKERRQ(ierr);
1822c4762a1bSJed Brown     if (flg) {
1823c4762a1bSJed Brown       DM dmConv;
1824c4762a1bSJed Brown 
1825c4762a1bSJed Brown       ierr = DMConvert(dm,convType,&dmConv);CHKERRQ(ierr);
1826c4762a1bSJed Brown       if (dmConv) {
1827c4762a1bSJed Brown         ierr = DMViewFromOptions(dmConv, NULL, "-dm_conv_view");CHKERRQ(ierr);
1828c4762a1bSJed Brown         ierr = DMDestroy(&dm);CHKERRQ(ierr);
1829c4762a1bSJed Brown         dm   = dmConv;
1830c4762a1bSJed Brown         ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
1831c4762a1bSJed Brown       }
1832c4762a1bSJed Brown     }
1833c4762a1bSJed Brown   }
1834c4762a1bSJed Brown 
1835c4762a1bSJed Brown   ierr = initializeTS(dm, user, &ts);CHKERRQ(ierr);
1836c4762a1bSJed Brown 
1837c4762a1bSJed Brown   ierr = DMCreateGlobalVector(dm, &X);CHKERRQ(ierr);
1838c4762a1bSJed Brown   ierr = PetscObjectSetName((PetscObject) X, "solution");CHKERRQ(ierr);
1839c4762a1bSJed Brown   ierr = SetInitialCondition(dm, X, user);CHKERRQ(ierr);
1840c4762a1bSJed Brown   if (useAMR) {
1841c4762a1bSJed Brown     PetscInt adaptIter;
1842c4762a1bSJed Brown 
1843c4762a1bSJed Brown     /* use no limiting when reconstructing gradients for adaptivity */
1844c4762a1bSJed Brown     ierr = PetscFVGetLimiter(fvm, &limiter);CHKERRQ(ierr);
1845c4762a1bSJed Brown     ierr = PetscObjectReference((PetscObject) limiter);CHKERRQ(ierr);
1846c4762a1bSJed Brown     ierr = PetscLimiterCreate(PetscObjectComm((PetscObject) fvm), &noneLimiter);CHKERRQ(ierr);
1847c4762a1bSJed Brown     ierr = PetscLimiterSetType(noneLimiter, PETSCLIMITERNONE);CHKERRQ(ierr);
1848c4762a1bSJed Brown 
1849c4762a1bSJed Brown     ierr = PetscFVSetLimiter(fvm, noneLimiter);CHKERRQ(ierr);
1850c4762a1bSJed Brown     for (adaptIter = 0; ; ++adaptIter) {
1851c4762a1bSJed Brown       PetscLogDouble bytes;
1852c4762a1bSJed Brown       TS             tsNew = NULL;
1853c4762a1bSJed Brown 
1854c4762a1bSJed Brown       ierr = PetscMemoryGetCurrentUsage(&bytes);CHKERRQ(ierr);
1855c4762a1bSJed Brown       ierr = PetscInfo2(ts, "refinement loop %D: memory used %g\n", adaptIter, bytes);CHKERRQ(ierr);
1856c4762a1bSJed Brown       ierr = DMViewFromOptions(dm, NULL, "-initial_dm_view");CHKERRQ(ierr);
1857c4762a1bSJed Brown       ierr = VecViewFromOptions(X, NULL, "-initial_vec_view");CHKERRQ(ierr);
1858c4762a1bSJed Brown #if 0
1859c4762a1bSJed Brown       if (viewInitial) {
1860c4762a1bSJed Brown         PetscViewer viewer;
1861c4762a1bSJed Brown         char        buf[256];
1862c4762a1bSJed Brown         PetscBool   isHDF5, isVTK;
1863c4762a1bSJed Brown 
1864c4762a1bSJed Brown         ierr = PetscViewerCreate(comm,&viewer);CHKERRQ(ierr);
1865c4762a1bSJed Brown         ierr = PetscViewerSetType(viewer,PETSCVIEWERVTK);CHKERRQ(ierr);
1866c4762a1bSJed Brown         ierr = PetscViewerSetOptionsPrefix(viewer,"initial_");CHKERRQ(ierr);
1867c4762a1bSJed Brown         ierr = PetscViewerSetFromOptions(viewer);CHKERRQ(ierr);
1868c4762a1bSJed Brown         ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&isHDF5);CHKERRQ(ierr);
1869c4762a1bSJed Brown         ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERVTK,&isVTK);CHKERRQ(ierr);
1870c4762a1bSJed Brown         if (isHDF5) {
1871c4762a1bSJed Brown           ierr = PetscSNPrintf(buf, 256, "ex11-initial-%d.h5", adaptIter);CHKERRQ(ierr);
1872c4762a1bSJed Brown         } else if (isVTK) {
1873c4762a1bSJed Brown           ierr = PetscSNPrintf(buf, 256, "ex11-initial-%d.vtu", adaptIter);CHKERRQ(ierr);
1874c4762a1bSJed Brown           ierr = PetscViewerPushFormat(viewer,PETSC_VIEWER_VTK_VTU);CHKERRQ(ierr);
1875c4762a1bSJed Brown         }
1876c4762a1bSJed Brown         ierr = PetscViewerFileSetMode(viewer,FILE_MODE_WRITE);CHKERRQ(ierr);
1877c4762a1bSJed Brown         ierr = PetscViewerFileSetName(viewer,buf);CHKERRQ(ierr);
1878c4762a1bSJed Brown         if (isHDF5) {
1879c4762a1bSJed Brown           ierr = DMView(dm,viewer);CHKERRQ(ierr);
1880c4762a1bSJed Brown           ierr = PetscViewerFileSetMode(viewer,FILE_MODE_UPDATE);CHKERRQ(ierr);
1881c4762a1bSJed Brown         }
1882c4762a1bSJed Brown         ierr = VecView(X,viewer);CHKERRQ(ierr);
1883c4762a1bSJed Brown         ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
1884c4762a1bSJed Brown       }
1885c4762a1bSJed Brown #endif
1886c4762a1bSJed Brown 
1887c4762a1bSJed Brown       ierr = adaptToleranceFVM(fvm, ts, X, refineTag, coarsenTag, user, &tsNew, NULL);CHKERRQ(ierr);
1888c4762a1bSJed Brown       if (!tsNew) {
1889c4762a1bSJed Brown         break;
1890c4762a1bSJed Brown       } else {
1891c4762a1bSJed Brown         ierr = DMDestroy(&dm);CHKERRQ(ierr);
1892c4762a1bSJed Brown         ierr = VecDestroy(&X);CHKERRQ(ierr);
1893c4762a1bSJed Brown         ierr = TSDestroy(&ts);CHKERRQ(ierr);
1894c4762a1bSJed Brown         ts   = tsNew;
1895c4762a1bSJed Brown         ierr = TSGetDM(ts,&dm);CHKERRQ(ierr);
1896c4762a1bSJed Brown         ierr = PetscObjectReference((PetscObject)dm);CHKERRQ(ierr);
1897c4762a1bSJed Brown         ierr = DMCreateGlobalVector(dm,&X);CHKERRQ(ierr);
1898c4762a1bSJed Brown         ierr = PetscObjectSetName((PetscObject) X, "solution");CHKERRQ(ierr);
1899c4762a1bSJed Brown         ierr = SetInitialCondition(dm, X, user);CHKERRQ(ierr);
1900c4762a1bSJed Brown       }
1901c4762a1bSJed Brown     }
1902c4762a1bSJed Brown     /* restore original limiter */
1903c4762a1bSJed Brown     ierr = PetscFVSetLimiter(fvm, limiter);CHKERRQ(ierr);
1904c4762a1bSJed Brown   }
1905c4762a1bSJed Brown 
1906*3e9753d6SMatthew G. Knepley   ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr);
1907c4762a1bSJed Brown   if (vtkCellGeom) {
1908c4762a1bSJed Brown     DM  dmCell;
1909c4762a1bSJed Brown     Vec cellgeom, partition;
1910c4762a1bSJed Brown 
1911*3e9753d6SMatthew G. Knepley     ierr = DMPlexGetGeometryFVM(plex, NULL, &cellgeom, NULL);CHKERRQ(ierr);
1912c4762a1bSJed Brown     ierr = OutputVTK(dm, "ex11-cellgeom.vtk", &viewer);CHKERRQ(ierr);
1913c4762a1bSJed Brown     ierr = VecView(cellgeom, viewer);CHKERRQ(ierr);
1914c4762a1bSJed Brown     ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
1915c4762a1bSJed Brown     ierr = CreatePartitionVec(dm, &dmCell, &partition);CHKERRQ(ierr);
1916c4762a1bSJed Brown     ierr = OutputVTK(dmCell, "ex11-partition.vtk", &viewer);CHKERRQ(ierr);
1917c4762a1bSJed Brown     ierr = VecView(partition, viewer);CHKERRQ(ierr);
1918c4762a1bSJed Brown     ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
1919c4762a1bSJed Brown     ierr = VecDestroy(&partition);CHKERRQ(ierr);
1920c4762a1bSJed Brown     ierr = DMDestroy(&dmCell);CHKERRQ(ierr);
1921c4762a1bSJed Brown   }
1922c4762a1bSJed Brown   /* collect max maxspeed from all processes -- todo */
1923*3e9753d6SMatthew G. Knepley   ierr = DMPlexGetGeometryFVM(plex, NULL, NULL, &minRadius);CHKERRQ(ierr);
1924*3e9753d6SMatthew G. Knepley   ierr = DMDestroy(&plex);CHKERRQ(ierr);
1925c4762a1bSJed Brown   ierr = MPI_Allreduce(&phys->maxspeed,&mod->maxspeed,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr);
1926c4762a1bSJed Brown   if (mod->maxspeed <= 0) SETERRQ1(comm,PETSC_ERR_ARG_WRONGSTATE,"Physics '%s' did not set maxspeed",physname);
1927c4762a1bSJed Brown   dt   = cfl * minRadius / mod->maxspeed;
1928c4762a1bSJed Brown   ierr = TSSetTimeStep(ts,dt);CHKERRQ(ierr);
1929c4762a1bSJed Brown   ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
1930c4762a1bSJed Brown   if (!useAMR) {
1931c4762a1bSJed Brown     ierr = TSSolve(ts,X);CHKERRQ(ierr);
1932c4762a1bSJed Brown     ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
1933c4762a1bSJed Brown     ierr = TSGetStepNumber(ts,&nsteps);CHKERRQ(ierr);
1934c4762a1bSJed Brown   } else {
1935c4762a1bSJed Brown     PetscReal finalTime;
1936c4762a1bSJed Brown     PetscInt  adaptIter;
1937c4762a1bSJed Brown     TS        tsNew = NULL;
1938c4762a1bSJed Brown     Vec       solNew = NULL;
1939c4762a1bSJed Brown 
1940c4762a1bSJed Brown     ierr   = TSGetMaxTime(ts,&finalTime);CHKERRQ(ierr);
1941c4762a1bSJed Brown     ierr   = TSSetMaxSteps(ts,adaptInterval);CHKERRQ(ierr);
1942c4762a1bSJed Brown     ierr   = TSSolve(ts,X);CHKERRQ(ierr);
1943c4762a1bSJed Brown     ierr   = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
1944c4762a1bSJed Brown     ierr   = TSGetStepNumber(ts,&nsteps);CHKERRQ(ierr);
1945c4762a1bSJed Brown     for (adaptIter = 0;ftime < finalTime;adaptIter++) {
1946c4762a1bSJed Brown       PetscLogDouble bytes;
1947c4762a1bSJed Brown 
1948c4762a1bSJed Brown       ierr = PetscMemoryGetCurrentUsage(&bytes);CHKERRQ(ierr);
1949c4762a1bSJed Brown       ierr = PetscInfo2(ts, "AMR time step loop %D: memory used %g\n", adaptIter, bytes);CHKERRQ(ierr);
1950c4762a1bSJed Brown       ierr = PetscFVSetLimiter(fvm,noneLimiter);CHKERRQ(ierr);
1951c4762a1bSJed Brown       ierr = adaptToleranceFVM(fvm,ts,X,refineTag,coarsenTag,user,&tsNew,&solNew);CHKERRQ(ierr);
1952c4762a1bSJed Brown       ierr = PetscFVSetLimiter(fvm,limiter);CHKERRQ(ierr);
1953c4762a1bSJed Brown       if (tsNew) {
1954c4762a1bSJed Brown         ierr = PetscInfo(ts, "AMR used\n");CHKERRQ(ierr);
1955c4762a1bSJed Brown         ierr = DMDestroy(&dm);CHKERRQ(ierr);
1956c4762a1bSJed Brown         ierr = VecDestroy(&X);CHKERRQ(ierr);
1957c4762a1bSJed Brown         ierr = TSDestroy(&ts);CHKERRQ(ierr);
1958c4762a1bSJed Brown         ts   = tsNew;
1959c4762a1bSJed Brown         X    = solNew;
1960c4762a1bSJed Brown         ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
1961c4762a1bSJed Brown         ierr = VecGetDM(X,&dm);CHKERRQ(ierr);
1962c4762a1bSJed Brown         ierr = PetscObjectReference((PetscObject)dm);CHKERRQ(ierr);
1963*3e9753d6SMatthew G. Knepley         ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr);
1964*3e9753d6SMatthew G. Knepley         ierr = DMPlexGetGeometryFVM(dm, NULL, NULL, &minRadius);CHKERRQ(ierr);
1965*3e9753d6SMatthew G. Knepley         ierr = DMDestroy(&plex);CHKERRQ(ierr);
1966c4762a1bSJed Brown         ierr = MPI_Allreduce(&phys->maxspeed,&mod->maxspeed,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr);
1967c4762a1bSJed Brown         if (mod->maxspeed <= 0) SETERRQ1(comm,PETSC_ERR_ARG_WRONGSTATE,"Physics '%s' did not set maxspeed",physname);
1968c4762a1bSJed Brown         dt   = cfl * minRadius / mod->maxspeed;
1969c4762a1bSJed Brown         ierr = TSSetStepNumber(ts,nsteps);CHKERRQ(ierr);
1970c4762a1bSJed Brown         ierr = TSSetTime(ts,ftime);CHKERRQ(ierr);
1971c4762a1bSJed Brown         ierr = TSSetTimeStep(ts,dt);CHKERRQ(ierr);
1972c4762a1bSJed Brown       } else {
1973c4762a1bSJed Brown         ierr = PetscInfo(ts, "AMR not used\n");CHKERRQ(ierr);
1974c4762a1bSJed Brown       }
1975c4762a1bSJed Brown       user->monitorStepOffset = nsteps;
1976c4762a1bSJed Brown       ierr = TSSetMaxSteps(ts,nsteps+adaptInterval);CHKERRQ(ierr);
1977c4762a1bSJed Brown       ierr = TSSolve(ts,X);CHKERRQ(ierr);
1978c4762a1bSJed Brown       ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
1979c4762a1bSJed Brown       ierr = TSGetStepNumber(ts,&nsteps);CHKERRQ(ierr);
1980c4762a1bSJed Brown     }
1981c4762a1bSJed Brown   }
1982c4762a1bSJed Brown   ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr);
1983c4762a1bSJed Brown   ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],(double)ftime,nsteps);CHKERRQ(ierr);
1984c4762a1bSJed Brown   ierr = TSDestroy(&ts);CHKERRQ(ierr);
1985c4762a1bSJed Brown 
1986c4762a1bSJed Brown   ierr = VecTaggerDestroy(&refineTag);CHKERRQ(ierr);
1987c4762a1bSJed Brown   ierr = VecTaggerDestroy(&coarsenTag);CHKERRQ(ierr);
1988c4762a1bSJed Brown   ierr = PetscFunctionListDestroy(&PhysicsList);CHKERRQ(ierr);
1989c4762a1bSJed Brown   ierr = FunctionalLinkDestroy(&user->model->functionalRegistry);CHKERRQ(ierr);
1990c4762a1bSJed Brown   ierr = PetscFree(user->model->functionalMonitored);CHKERRQ(ierr);
1991c4762a1bSJed Brown   ierr = PetscFree(user->model->functionalCall);CHKERRQ(ierr);
1992c4762a1bSJed Brown   ierr = PetscFree(user->model->physics->data);CHKERRQ(ierr);
1993c4762a1bSJed Brown   ierr = PetscFree(user->model->physics);CHKERRQ(ierr);
1994c4762a1bSJed Brown   ierr = PetscFree(user->model);CHKERRQ(ierr);
1995c4762a1bSJed Brown   ierr = PetscFree(user);CHKERRQ(ierr);
1996c4762a1bSJed Brown   ierr = VecDestroy(&X);CHKERRQ(ierr);
1997c4762a1bSJed Brown   ierr = PetscLimiterDestroy(&limiter);CHKERRQ(ierr);
1998c4762a1bSJed Brown   ierr = PetscLimiterDestroy(&noneLimiter);CHKERRQ(ierr);
1999c4762a1bSJed Brown   ierr = PetscFVDestroy(&fvm);CHKERRQ(ierr);
2000c4762a1bSJed Brown   ierr = DMDestroy(&dm);CHKERRQ(ierr);
2001c4762a1bSJed Brown   ierr = PetscFinalize();
2002c4762a1bSJed Brown   return ierr;
2003c4762a1bSJed Brown }
2004c4762a1bSJed Brown 
2005c4762a1bSJed Brown /* Godunov fluxs */
2006c4762a1bSJed Brown PetscScalar cvmgp_(PetscScalar *a, PetscScalar *b, PetscScalar *test)
2007c4762a1bSJed Brown {
2008c4762a1bSJed Brown     /* System generated locals */
2009c4762a1bSJed Brown     PetscScalar ret_val;
2010c4762a1bSJed Brown 
2011c4762a1bSJed Brown     if (PetscRealPart(*test) > 0.) {
2012c4762a1bSJed Brown 	goto L10;
2013c4762a1bSJed Brown     }
2014c4762a1bSJed Brown     ret_val = *b;
2015c4762a1bSJed Brown     return ret_val;
2016c4762a1bSJed Brown L10:
2017c4762a1bSJed Brown     ret_val = *a;
2018c4762a1bSJed Brown     return ret_val;
2019c4762a1bSJed Brown } /* cvmgp_ */
2020c4762a1bSJed Brown 
2021c4762a1bSJed Brown PetscScalar cvmgm_(PetscScalar *a, PetscScalar *b, PetscScalar *test)
2022c4762a1bSJed Brown {
2023c4762a1bSJed Brown     /* System generated locals */
2024c4762a1bSJed Brown     PetscScalar ret_val;
2025c4762a1bSJed Brown 
2026c4762a1bSJed Brown     if (PetscRealPart(*test) < 0.) {
2027c4762a1bSJed Brown 	goto L10;
2028c4762a1bSJed Brown     }
2029c4762a1bSJed Brown     ret_val = *b;
2030c4762a1bSJed Brown     return ret_val;
2031c4762a1bSJed Brown L10:
2032c4762a1bSJed Brown     ret_val = *a;
2033c4762a1bSJed Brown     return ret_val;
2034c4762a1bSJed Brown } /* cvmgm_ */
2035c4762a1bSJed Brown 
2036c4762a1bSJed Brown int riem1mdt( PetscScalar *gaml, PetscScalar *gamr, PetscScalar *rl, PetscScalar *pl,
2037c4762a1bSJed Brown               PetscScalar *uxl, PetscScalar *rr, PetscScalar *pr,
2038c4762a1bSJed Brown               PetscScalar *uxr, PetscScalar *rstarl, PetscScalar *rstarr, PetscScalar *
2039c4762a1bSJed Brown               pstar, PetscScalar *ustar)
2040c4762a1bSJed Brown {
2041c4762a1bSJed Brown     /* Initialized data */
2042c4762a1bSJed Brown 
2043c4762a1bSJed Brown     static PetscScalar smallp = 1e-8;
2044c4762a1bSJed Brown 
2045c4762a1bSJed Brown     /* System generated locals */
2046c4762a1bSJed Brown     int i__1;
2047c4762a1bSJed Brown     PetscScalar d__1, d__2;
2048c4762a1bSJed Brown 
2049c4762a1bSJed Brown     /* Local variables */
2050c4762a1bSJed Brown     static int i0;
2051c4762a1bSJed Brown     static PetscScalar cl, cr, wl, zl, wr, zr, pst, durl, skpr1, skpr2;
2052c4762a1bSJed Brown     static int iwave;
2053c4762a1bSJed Brown     static PetscScalar gascl4, gascr4, cstarl, dpstar, cstarr;
2054c4762a1bSJed Brown     /* static PetscScalar csqrl, csqrr, gascl1, gascl2, gascl3, gascr1, gascr2, gascr3; */
2055c4762a1bSJed Brown     static int iterno;
2056c4762a1bSJed Brown     static PetscScalar ustarl, ustarr, rarepr1, rarepr2;
2057c4762a1bSJed Brown 
2058c4762a1bSJed Brown 
2059c4762a1bSJed Brown 
2060c4762a1bSJed Brown     /* gascl1 = *gaml - 1.; */
2061c4762a1bSJed Brown     /* gascl2 = (*gaml + 1.) * .5; */
2062c4762a1bSJed Brown     /* gascl3 = gascl2 / *gaml; */
2063c4762a1bSJed Brown     gascl4 = 1. / (*gaml - 1.);
2064c4762a1bSJed Brown 
2065c4762a1bSJed Brown     /* gascr1 = *gamr - 1.; */
2066c4762a1bSJed Brown     /* gascr2 = (*gamr + 1.) * .5; */
2067c4762a1bSJed Brown     /* gascr3 = gascr2 / *gamr; */
2068c4762a1bSJed Brown     gascr4 = 1. / (*gamr - 1.);
2069c4762a1bSJed Brown     iterno = 10;
2070c4762a1bSJed Brown /*        find pstar: */
2071c4762a1bSJed Brown     cl = PetscSqrtScalar(*gaml * *pl / *rl);
2072c4762a1bSJed Brown     cr = PetscSqrtScalar(*gamr * *pr / *rr);
2073c4762a1bSJed Brown     wl = *rl * cl;
2074c4762a1bSJed Brown     wr = *rr * cr;
2075c4762a1bSJed Brown     /* csqrl = wl * wl; */
2076c4762a1bSJed Brown     /* csqrr = wr * wr; */
2077c4762a1bSJed Brown     *pstar = (wl * *pr + wr * *pl) / (wl + wr);
2078c4762a1bSJed Brown     *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp));
2079c4762a1bSJed Brown     pst = *pl / *pr;
2080c4762a1bSJed Brown     skpr1 = cr * (pst - 1.) * PetscSqrtScalar(2. / (*gamr * (*gamr - 1. + (*gamr + 1.) * pst)));
2081c4762a1bSJed Brown     d__1 = (*gamr - 1.) / (*gamr * 2.);
2082c4762a1bSJed Brown     rarepr2 = gascr4 * 2. * cr * (1. - PetscPowScalar(pst, d__1));
2083c4762a1bSJed Brown     pst = *pr / *pl;
2084c4762a1bSJed Brown     skpr2 = cl * (pst - 1.) * PetscSqrtScalar(2. / (*gaml * (*gaml - 1. + (*gaml + 1.) * pst)));
2085c4762a1bSJed Brown     d__1 = (*gaml - 1.) / (*gaml * 2.);
2086c4762a1bSJed Brown     rarepr1 = gascl4 * 2. * cl * (1. - PetscPowScalar(pst, d__1));
2087c4762a1bSJed Brown     durl = *uxr - *uxl;
2088c4762a1bSJed Brown     if (PetscRealPart(*pr) < PetscRealPart(*pl)) {
2089c4762a1bSJed Brown 	if (PetscRealPart(durl) >= PetscRealPart(rarepr1)) {
2090c4762a1bSJed Brown 	    iwave = 100;
2091c4762a1bSJed Brown 	} else if (PetscRealPart(durl) <= PetscRealPart(-skpr1)) {
2092c4762a1bSJed Brown 	    iwave = 300;
2093c4762a1bSJed Brown 	} else {
2094c4762a1bSJed Brown 	    iwave = 400;
2095c4762a1bSJed Brown 	}
2096c4762a1bSJed Brown     } else {
2097c4762a1bSJed Brown 	if (PetscRealPart(durl) >= PetscRealPart(rarepr2)) {
2098c4762a1bSJed Brown 	    iwave = 100;
2099c4762a1bSJed Brown 	} else if (PetscRealPart(durl) <= PetscRealPart(-skpr2)) {
2100c4762a1bSJed Brown 	    iwave = 300;
2101c4762a1bSJed Brown 	} else {
2102c4762a1bSJed Brown 	    iwave = 200;
2103c4762a1bSJed Brown 	}
2104c4762a1bSJed Brown     }
2105c4762a1bSJed Brown     if (iwave == 100) {
2106c4762a1bSJed Brown /*     1-wave: rarefaction wave, 3-wave: rarefaction wave */
2107c4762a1bSJed Brown /*     case (100) */
2108c4762a1bSJed Brown 	i__1 = iterno;
2109c4762a1bSJed Brown 	for (i0 = 1; i0 <= i__1; ++i0) {
2110c4762a1bSJed Brown 	    d__1 = *pstar / *pl;
2111c4762a1bSJed Brown 	    d__2 = 1. / *gaml;
2112c4762a1bSJed Brown 	    *rstarl = *rl * PetscPowScalar(d__1, d__2);
2113c4762a1bSJed Brown 	    cstarl = PetscSqrtScalar(*gaml * *pstar / *rstarl);
2114c4762a1bSJed Brown 	    ustarl = *uxl - gascl4 * 2. * (cstarl - cl);
2115c4762a1bSJed Brown 	    zl = *rstarl * cstarl;
2116c4762a1bSJed Brown 	    d__1 = *pstar / *pr;
2117c4762a1bSJed Brown 	    d__2 = 1. / *gamr;
2118c4762a1bSJed Brown 	    *rstarr = *rr * PetscPowScalar(d__1, d__2);
2119c4762a1bSJed Brown 	    cstarr = PetscSqrtScalar(*gamr * *pstar / *rstarr);
2120c4762a1bSJed Brown 	    ustarr = *uxr + gascr4 * 2. * (cstarr - cr);
2121c4762a1bSJed Brown 	    zr = *rstarr * cstarr;
2122c4762a1bSJed Brown 	    dpstar = zl * zr * (ustarr - ustarl) / (zl + zr);
2123c4762a1bSJed Brown 	    *pstar -= dpstar;
2124c4762a1bSJed Brown 	    *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp));
2125c4762a1bSJed Brown 	    if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) {
2126c4762a1bSJed Brown #if 0
2127c4762a1bSJed Brown         break;
2128c4762a1bSJed Brown #endif
2129c4762a1bSJed Brown 	    }
2130c4762a1bSJed Brown 	}
2131c4762a1bSJed Brown /*     1-wave: shock wave, 3-wave: rarefaction wave */
2132c4762a1bSJed Brown     } else if (iwave == 200) {
2133c4762a1bSJed Brown /*     case (200) */
2134c4762a1bSJed Brown 	i__1 = iterno;
2135c4762a1bSJed Brown 	for (i0 = 1; i0 <= i__1; ++i0) {
2136c4762a1bSJed Brown 	    pst = *pstar / *pl;
2137c4762a1bSJed Brown 	    ustarl = *uxl - (pst - 1.) * cl * PetscSqrtScalar(2. / (*gaml * (*gaml - 1. + (*gaml + 1.) * pst)));
2138c4762a1bSJed Brown 	    zl = *pl / cl * PetscSqrtScalar(*gaml * 2. * (*gaml - 1. + (*gaml + 1.) * pst)) * (*gaml - 1. + (*gaml + 1.) * pst) / (*gaml * 3. - 1. + (*gaml + 1.) * pst);
2139c4762a1bSJed Brown 	    d__1 = *pstar / *pr;
2140c4762a1bSJed Brown 	    d__2 = 1. / *gamr;
2141c4762a1bSJed Brown 	    *rstarr = *rr * PetscPowScalar(d__1, d__2);
2142c4762a1bSJed Brown 	    cstarr = PetscSqrtScalar(*gamr * *pstar / *rstarr);
2143c4762a1bSJed Brown 	    zr = *rstarr * cstarr;
2144c4762a1bSJed Brown 	    ustarr = *uxr + gascr4 * 2. * (cstarr - cr);
2145c4762a1bSJed Brown 	    dpstar = zl * zr * (ustarr - ustarl) / (zl + zr);
2146c4762a1bSJed Brown 	    *pstar -= dpstar;
2147c4762a1bSJed Brown 	    *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp));
2148c4762a1bSJed Brown 	    if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) {
2149c4762a1bSJed Brown #if 0
2150c4762a1bSJed Brown         break;
2151c4762a1bSJed Brown #endif
2152c4762a1bSJed Brown 	    }
2153c4762a1bSJed Brown 	}
2154c4762a1bSJed Brown /*     1-wave: shock wave, 3-wave: shock */
2155c4762a1bSJed Brown     } else if (iwave == 300) {
2156c4762a1bSJed Brown /*     case (300) */
2157c4762a1bSJed Brown 	i__1 = iterno;
2158c4762a1bSJed Brown 	for (i0 = 1; i0 <= i__1; ++i0) {
2159c4762a1bSJed Brown 	    pst = *pstar / *pl;
2160c4762a1bSJed Brown 	    ustarl = *uxl - (pst - 1.) * cl * PetscSqrtScalar(2. / (*gaml * (*gaml - 1. + (*gaml + 1.) * pst)));
2161c4762a1bSJed Brown 	    zl = *pl / cl * PetscSqrtScalar(*gaml * 2. * (*gaml - 1. + (*gaml + 1.) * pst)) * (*gaml - 1. + (*gaml + 1.) * pst) / (*gaml * 3. - 1. + (*gaml + 1.) * pst);
2162c4762a1bSJed Brown 	    pst = *pstar / *pr;
2163c4762a1bSJed Brown 	    ustarr = *uxr + (pst - 1.) * cr * PetscSqrtScalar(2. / (*gamr * (*gamr - 1. + (*gamr + 1.) * pst)));
2164c4762a1bSJed Brown 	    zr = *pr / cr * PetscSqrtScalar(*gamr * 2. * (*gamr - 1. + (*gamr + 1.) * pst)) * (*gamr - 1. + (*gamr + 1.) * pst) / (*gamr * 3. - 1. + (*gamr + 1.) * pst);
2165c4762a1bSJed Brown 	    dpstar = zl * zr * (ustarr - ustarl) / (zl + zr);
2166c4762a1bSJed Brown 	    *pstar -= dpstar;
2167c4762a1bSJed Brown 	    *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp));
2168c4762a1bSJed Brown 	    if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) {
2169c4762a1bSJed Brown #if 0
2170c4762a1bSJed Brown         break;
2171c4762a1bSJed Brown #endif
2172c4762a1bSJed Brown 	    }
2173c4762a1bSJed Brown 	}
2174c4762a1bSJed Brown /*     1-wave: rarefaction wave, 3-wave: shock */
2175c4762a1bSJed Brown     } else if (iwave == 400) {
2176c4762a1bSJed Brown /*     case (400) */
2177c4762a1bSJed Brown 	i__1 = iterno;
2178c4762a1bSJed Brown 	for (i0 = 1; i0 <= i__1; ++i0) {
2179c4762a1bSJed Brown 	    d__1 = *pstar / *pl;
2180c4762a1bSJed Brown 	    d__2 = 1. / *gaml;
2181c4762a1bSJed Brown 	    *rstarl = *rl * PetscPowScalar(d__1, d__2);
2182c4762a1bSJed Brown 	    cstarl = PetscSqrtScalar(*gaml * *pstar / *rstarl);
2183c4762a1bSJed Brown 	    ustarl = *uxl - gascl4 * 2. * (cstarl - cl);
2184c4762a1bSJed Brown 	    zl = *rstarl * cstarl;
2185c4762a1bSJed Brown 	    pst = *pstar / *pr;
2186c4762a1bSJed Brown 	    ustarr = *uxr + (pst - 1.) * cr * PetscSqrtScalar(2. / (*gamr * (*gamr - 1. + (*gamr + 1.) * pst)));
2187c4762a1bSJed Brown 	    zr = *pr / cr * PetscSqrtScalar(*gamr * 2. * (*gamr - 1. + (*gamr + 1.) * pst)) * (*gamr - 1. + (*gamr + 1.) * pst) / (*gamr * 3. - 1. + (*gamr + 1.) * pst);
2188c4762a1bSJed Brown 	    dpstar = zl * zr * (ustarr - ustarl) / (zl + zr);
2189c4762a1bSJed Brown 	    *pstar -= dpstar;
2190c4762a1bSJed Brown 	    *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp));
2191c4762a1bSJed Brown 	    if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) {
2192c4762a1bSJed Brown #if 0
2193c4762a1bSJed Brown 	      break;
2194c4762a1bSJed Brown #endif
2195c4762a1bSJed Brown 	    }
2196c4762a1bSJed Brown 	}
2197c4762a1bSJed Brown     }
2198c4762a1bSJed Brown 
2199c4762a1bSJed Brown     *ustar = (zl * ustarr + zr * ustarl) / (zl + zr);
2200c4762a1bSJed Brown     if (PetscRealPart(*pstar) > PetscRealPart(*pl)) {
2201c4762a1bSJed Brown 	pst = *pstar / *pl;
2202c4762a1bSJed Brown 	*rstarl = ((*gaml + 1.) * pst + *gaml - 1.) / ((*gaml - 1.) * pst + *
2203c4762a1bSJed Brown 		gaml + 1.) * *rl;
2204c4762a1bSJed Brown     }
2205c4762a1bSJed Brown     if (PetscRealPart(*pstar) > PetscRealPart(*pr)) {
2206c4762a1bSJed Brown 	pst = *pstar / *pr;
2207c4762a1bSJed Brown 	*rstarr = ((*gamr + 1.) * pst + *gamr - 1.) / ((*gamr - 1.) * pst + *
2208c4762a1bSJed Brown 		gamr + 1.) * *rr;
2209c4762a1bSJed Brown     }
2210c4762a1bSJed Brown     return iwave;
2211c4762a1bSJed Brown }
2212c4762a1bSJed Brown 
2213c4762a1bSJed Brown PetscScalar sign(PetscScalar x)
2214c4762a1bSJed Brown {
2215c4762a1bSJed Brown     if(PetscRealPart(x) > 0) return 1.0;
2216c4762a1bSJed Brown     if(PetscRealPart(x) < 0) return -1.0;
2217c4762a1bSJed Brown     return 0.0;
2218c4762a1bSJed Brown }
2219c4762a1bSJed Brown /*        Riemann Solver */
2220c4762a1bSJed Brown /* -------------------------------------------------------------------- */
2221c4762a1bSJed Brown int riemannsolver(PetscScalar *xcen, PetscScalar *xp,
2222c4762a1bSJed Brown                    PetscScalar *dtt, PetscScalar *rl, PetscScalar *uxl, PetscScalar *pl,
2223c4762a1bSJed Brown                    PetscScalar *utl, PetscScalar *ubl, PetscScalar *gaml, PetscScalar *rho1l,
2224c4762a1bSJed Brown                    PetscScalar *rr, PetscScalar *uxr, PetscScalar *pr, PetscScalar *utr,
2225c4762a1bSJed Brown                    PetscScalar *ubr, PetscScalar *gamr, PetscScalar *rho1r, PetscScalar *rx,
2226c4762a1bSJed Brown                    PetscScalar *uxm, PetscScalar *px, PetscScalar *utx, PetscScalar *ubx,
2227c4762a1bSJed Brown                    PetscScalar *gam, PetscScalar *rho1)
2228c4762a1bSJed Brown {
2229c4762a1bSJed Brown     /* System generated locals */
2230c4762a1bSJed Brown     PetscScalar d__1, d__2;
2231c4762a1bSJed Brown 
2232c4762a1bSJed Brown     /* Local variables */
2233c4762a1bSJed Brown     static PetscScalar s, c0, p0, r0, u0, w0, x0, x2, ri, cx, sgn0, wsp0, gasc1, gasc2, gasc3, gasc4;
2234c4762a1bSJed Brown     static PetscScalar cstar, pstar, rstar, ustar, xstar, wspst, ushock, streng, rstarl, rstarr, rstars;
2235c4762a1bSJed Brown     int iwave;
2236c4762a1bSJed Brown 
2237c4762a1bSJed Brown     if (*rl == *rr && *pr == *pl && *uxl == *uxr && *gaml == *gamr) {
2238c4762a1bSJed Brown 	*rx = *rl;
2239c4762a1bSJed Brown 	*px = *pl;
2240c4762a1bSJed Brown 	*uxm = *uxl;
2241c4762a1bSJed Brown 	*gam = *gaml;
2242c4762a1bSJed Brown 	x2 = *xcen + *uxm * *dtt;
2243c4762a1bSJed Brown 
2244c4762a1bSJed Brown 	if (PetscRealPart(*xp) >= PetscRealPart(x2)) {
2245c4762a1bSJed Brown 	    *utx = *utr;
2246c4762a1bSJed Brown 	    *ubx = *ubr;
2247c4762a1bSJed Brown 	    *rho1 = *rho1r;
2248c4762a1bSJed Brown 	} else {
2249c4762a1bSJed Brown 	    *utx = *utl;
2250c4762a1bSJed Brown 	    *ubx = *ubl;
2251c4762a1bSJed Brown 	    *rho1 = *rho1l;
2252c4762a1bSJed Brown 	}
2253c4762a1bSJed Brown 	return 0;
2254c4762a1bSJed Brown     }
2255c4762a1bSJed Brown     iwave = riem1mdt(gaml, gamr, rl, pl, uxl, rr, pr, uxr, &rstarl, &rstarr, &pstar, &ustar);
2256c4762a1bSJed Brown 
2257c4762a1bSJed Brown     x2 = *xcen + ustar * *dtt;
2258c4762a1bSJed Brown     d__1 = *xp - x2;
2259c4762a1bSJed Brown     sgn0 = sign(d__1);
2260c4762a1bSJed Brown /*            x is in 3-wave if sgn0 = 1 */
2261c4762a1bSJed Brown /*            x is in 1-wave if sgn0 = -1 */
2262c4762a1bSJed Brown     r0 = cvmgm_(rl, rr, &sgn0);
2263c4762a1bSJed Brown     p0 = cvmgm_(pl, pr, &sgn0);
2264c4762a1bSJed Brown     u0 = cvmgm_(uxl, uxr, &sgn0);
2265c4762a1bSJed Brown     *gam = cvmgm_(gaml, gamr, &sgn0);
2266c4762a1bSJed Brown     gasc1 = *gam - 1.;
2267c4762a1bSJed Brown     gasc2 = (*gam + 1.) * .5;
2268c4762a1bSJed Brown     gasc3 = gasc2 / *gam;
2269c4762a1bSJed Brown     gasc4 = 1. / (*gam - 1.);
2270c4762a1bSJed Brown     c0 = PetscSqrtScalar(*gam * p0 / r0);
2271c4762a1bSJed Brown     streng = pstar - p0;
2272c4762a1bSJed Brown     w0 = *gam * r0 * p0 * (gasc3 * streng / p0 + 1.);
2273c4762a1bSJed Brown     rstars = r0 / (1. - r0 * streng / w0);
2274c4762a1bSJed Brown     d__1 = p0 / pstar;
2275c4762a1bSJed Brown     d__2 = -1. / *gam;
2276c4762a1bSJed Brown     rstarr = r0 * PetscPowScalar(d__1, d__2);
2277c4762a1bSJed Brown     rstar = cvmgm_(&rstarr, &rstars, &streng);
2278c4762a1bSJed Brown     w0 = PetscSqrtScalar(w0);
2279c4762a1bSJed Brown     cstar = PetscSqrtScalar(*gam * pstar / rstar);
2280c4762a1bSJed Brown     wsp0 = u0 + sgn0 * c0;
2281c4762a1bSJed Brown     wspst = ustar + sgn0 * cstar;
2282c4762a1bSJed Brown     ushock = ustar + sgn0 * w0 / rstar;
2283c4762a1bSJed Brown     wspst = cvmgp_(&ushock, &wspst, &streng);
2284c4762a1bSJed Brown     wsp0 = cvmgp_(&ushock, &wsp0, &streng);
2285c4762a1bSJed Brown     x0 = *xcen + wsp0 * *dtt;
2286c4762a1bSJed Brown     xstar = *xcen + wspst * *dtt;
2287c4762a1bSJed Brown /*           using gas formula to evaluate rarefaction wave */
2288c4762a1bSJed Brown /*            ri : reiman invariant */
2289c4762a1bSJed Brown     ri = u0 - sgn0 * 2. * gasc4 * c0;
2290c4762a1bSJed Brown     cx = sgn0 * .5 * gasc1 / gasc2 * ((*xp - *xcen) / *dtt - ri);
2291c4762a1bSJed Brown     *uxm = ri + sgn0 * 2. * gasc4 * cx;
2292c4762a1bSJed Brown     s = p0 / PetscPowScalar(r0, *gam);
2293c4762a1bSJed Brown     d__1 = cx * cx / (*gam * s);
2294c4762a1bSJed Brown     *rx = PetscPowScalar(d__1, gasc4);
2295c4762a1bSJed Brown     *px = cx * cx * *rx / *gam;
2296c4762a1bSJed Brown     d__1 = sgn0 * (x0 - *xp);
2297c4762a1bSJed Brown     *rx = cvmgp_(rx, &r0, &d__1);
2298c4762a1bSJed Brown     d__1 = sgn0 * (x0 - *xp);
2299c4762a1bSJed Brown     *px = cvmgp_(px, &p0, &d__1);
2300c4762a1bSJed Brown     d__1 = sgn0 * (x0 - *xp);
2301c4762a1bSJed Brown     *uxm = cvmgp_(uxm, &u0, &d__1);
2302c4762a1bSJed Brown     d__1 = sgn0 * (xstar - *xp);
2303c4762a1bSJed Brown     *rx = cvmgm_(rx, &rstar, &d__1);
2304c4762a1bSJed Brown     d__1 = sgn0 * (xstar - *xp);
2305c4762a1bSJed Brown     *px = cvmgm_(px, &pstar, &d__1);
2306c4762a1bSJed Brown     d__1 = sgn0 * (xstar - *xp);
2307c4762a1bSJed Brown     *uxm = cvmgm_(uxm, &ustar, &d__1);
2308c4762a1bSJed Brown     if (PetscRealPart(*xp) >= PetscRealPart(x2)) {
2309c4762a1bSJed Brown 	*utx = *utr;
2310c4762a1bSJed Brown 	*ubx = *ubr;
2311c4762a1bSJed Brown 	*rho1 = *rho1r;
2312c4762a1bSJed Brown     } else {
2313c4762a1bSJed Brown 	*utx = *utl;
2314c4762a1bSJed Brown 	*ubx = *ubl;
2315c4762a1bSJed Brown 	*rho1 = *rho1l;
2316c4762a1bSJed Brown     }
2317c4762a1bSJed Brown     return iwave;
2318c4762a1bSJed Brown }
2319c4762a1bSJed Brown int godunovflux( const PetscScalar *ul, const PetscScalar *ur,
2320c4762a1bSJed Brown                  PetscScalar *flux, const PetscReal *nn, const int *ndim,
2321c4762a1bSJed Brown                  const PetscReal *gamma)
2322c4762a1bSJed Brown {
2323c4762a1bSJed Brown     /* System generated locals */
2324c4762a1bSJed Brown   int i__1,iwave;
2325c4762a1bSJed Brown     PetscScalar d__1, d__2, d__3;
2326c4762a1bSJed Brown 
2327c4762a1bSJed Brown     /* Local variables */
2328c4762a1bSJed Brown     static int k;
2329c4762a1bSJed Brown     static PetscScalar bn[3], fn, ft, tg[3], pl, rl, pm, pr, rr, xp, ubl, ubm,
2330c4762a1bSJed Brown 	    ubr, dtt, unm, tmp, utl, utm, uxl, utr, uxr, gaml, gamm, gamr,
2331c4762a1bSJed Brown 	    xcen, rhom, rho1l, rho1m, rho1r;
2332c4762a1bSJed Brown     /* Parameter adjustments */
2333c4762a1bSJed Brown     --nn;
2334c4762a1bSJed Brown     --flux;
2335c4762a1bSJed Brown     --ur;
2336c4762a1bSJed Brown     --ul;
2337c4762a1bSJed Brown 
2338c4762a1bSJed Brown     /* Function Body */
2339c4762a1bSJed Brown     xcen = 0.;
2340c4762a1bSJed Brown     xp = 0.;
2341c4762a1bSJed Brown     i__1 = *ndim;
2342c4762a1bSJed Brown     for (k = 1; k <= i__1; ++k) {
2343c4762a1bSJed Brown 	tg[k - 1] = 0.;
2344c4762a1bSJed Brown 	bn[k - 1] = 0.;
2345c4762a1bSJed Brown     }
2346c4762a1bSJed Brown     dtt = 1.;
2347c4762a1bSJed Brown     if (*ndim == 3) {
2348c4762a1bSJed Brown 	if (nn[1] == 0. && nn[2] == 0.) {
2349c4762a1bSJed Brown 	    tg[0] = 1.;
2350c4762a1bSJed Brown 	} else {
2351c4762a1bSJed Brown 	    tg[0] = -nn[2];
2352c4762a1bSJed Brown 	    tg[1] = nn[1];
2353c4762a1bSJed Brown 	}
2354c4762a1bSJed Brown /*           tmp=dsqrt(tg(1)**2+tg(2)**2) */
2355c4762a1bSJed Brown /*           tg=tg/tmp */
2356c4762a1bSJed Brown 	bn[0] = -nn[3] * tg[1];
2357c4762a1bSJed Brown 	bn[1] = nn[3] * tg[0];
2358c4762a1bSJed Brown 	bn[2] = nn[1] * tg[1] - nn[2] * tg[0];
2359c4762a1bSJed Brown /* Computing 2nd power */
2360c4762a1bSJed Brown 	d__1 = bn[0];
2361c4762a1bSJed Brown /* Computing 2nd power */
2362c4762a1bSJed Brown 	d__2 = bn[1];
2363c4762a1bSJed Brown /* Computing 2nd power */
2364c4762a1bSJed Brown 	d__3 = bn[2];
2365c4762a1bSJed Brown 	tmp = PetscSqrtScalar(d__1 * d__1 + d__2 * d__2 + d__3 * d__3);
2366c4762a1bSJed Brown 	i__1 = *ndim;
2367c4762a1bSJed Brown 	for (k = 1; k <= i__1; ++k) {
2368c4762a1bSJed Brown 	    bn[k - 1] /= tmp;
2369c4762a1bSJed Brown 	}
2370c4762a1bSJed Brown     } else if (*ndim == 2) {
2371c4762a1bSJed Brown 	tg[0] = -nn[2];
2372c4762a1bSJed Brown 	tg[1] = nn[1];
2373c4762a1bSJed Brown /*           tmp=dsqrt(tg(1)**2+tg(2)**2) */
2374c4762a1bSJed Brown /*           tg=tg/tmp */
2375c4762a1bSJed Brown 	bn[0] = 0.;
2376c4762a1bSJed Brown 	bn[1] = 0.;
2377c4762a1bSJed Brown 	bn[2] = 1.;
2378c4762a1bSJed Brown     }
2379c4762a1bSJed Brown     rl = ul[1];
2380c4762a1bSJed Brown     rr = ur[1];
2381c4762a1bSJed Brown     uxl = 0.;
2382c4762a1bSJed Brown     uxr = 0.;
2383c4762a1bSJed Brown     utl = 0.;
2384c4762a1bSJed Brown     utr = 0.;
2385c4762a1bSJed Brown     ubl = 0.;
2386c4762a1bSJed Brown     ubr = 0.;
2387c4762a1bSJed Brown     i__1 = *ndim;
2388c4762a1bSJed Brown     for (k = 1; k <= i__1; ++k) {
2389c4762a1bSJed Brown 	uxl += ul[k + 1] * nn[k];
2390c4762a1bSJed Brown 	uxr += ur[k + 1] * nn[k];
2391c4762a1bSJed Brown 	utl += ul[k + 1] * tg[k - 1];
2392c4762a1bSJed Brown 	utr += ur[k + 1] * tg[k - 1];
2393c4762a1bSJed Brown 	ubl += ul[k + 1] * bn[k - 1];
2394c4762a1bSJed Brown 	ubr += ur[k + 1] * bn[k - 1];
2395c4762a1bSJed Brown     }
2396c4762a1bSJed Brown     uxl /= rl;
2397c4762a1bSJed Brown     uxr /= rr;
2398c4762a1bSJed Brown     utl /= rl;
2399c4762a1bSJed Brown     utr /= rr;
2400c4762a1bSJed Brown     ubl /= rl;
2401c4762a1bSJed Brown     ubr /= rr;
2402c4762a1bSJed Brown 
2403c4762a1bSJed Brown     gaml = *gamma;
2404c4762a1bSJed Brown     gamr = *gamma;
2405c4762a1bSJed Brown /* Computing 2nd power */
2406c4762a1bSJed Brown     d__1 = uxl;
2407c4762a1bSJed Brown /* Computing 2nd power */
2408c4762a1bSJed Brown     d__2 = utl;
2409c4762a1bSJed Brown /* Computing 2nd power */
2410c4762a1bSJed Brown     d__3 = ubl;
2411c4762a1bSJed Brown     pl = (*gamma - 1.) * (ul[*ndim + 2] - rl * .5 * (d__1 * d__1 + d__2 * d__2 + d__3 * d__3));
2412c4762a1bSJed Brown /* Computing 2nd power */
2413c4762a1bSJed Brown     d__1 = uxr;
2414c4762a1bSJed Brown /* Computing 2nd power */
2415c4762a1bSJed Brown     d__2 = utr;
2416c4762a1bSJed Brown /* Computing 2nd power */
2417c4762a1bSJed Brown     d__3 = ubr;
2418c4762a1bSJed Brown     pr = (*gamma - 1.) * (ur[*ndim + 2] - rr * .5 * (d__1 * d__1 + d__2 * d__2 + d__3 * d__3));
2419c4762a1bSJed Brown     rho1l = rl;
2420c4762a1bSJed Brown     rho1r = rr;
2421c4762a1bSJed Brown 
2422c4762a1bSJed Brown     iwave = riemannsolver(&xcen, &xp, &dtt, &rl, &uxl, &pl, &utl, &ubl, &gaml, &
2423c4762a1bSJed Brown                           rho1l, &rr, &uxr, &pr, &utr, &ubr, &gamr, &rho1r, &rhom, &unm, &
2424c4762a1bSJed Brown                           pm, &utm, &ubm, &gamm, &rho1m);
2425c4762a1bSJed Brown 
2426c4762a1bSJed Brown     flux[1] = rhom * unm;
2427c4762a1bSJed Brown     fn = rhom * unm * unm + pm;
2428c4762a1bSJed Brown     ft = rhom * unm * utm;
2429c4762a1bSJed Brown /*           flux(2)=fn*nn(1)+ft*nn(2) */
2430c4762a1bSJed Brown /*           flux(3)=fn*tg(1)+ft*tg(2) */
2431c4762a1bSJed Brown     flux[2] = fn * nn[1] + ft * tg[0];
2432c4762a1bSJed Brown     flux[3] = fn * nn[2] + ft * tg[1];
2433c4762a1bSJed Brown /*           flux(2)=rhom*unm*(unm)+pm */
2434c4762a1bSJed Brown /*           flux(3)=rhom*(unm)*utm */
2435c4762a1bSJed Brown     if (*ndim == 3) {
2436c4762a1bSJed Brown 	flux[4] = rhom * unm * ubm;
2437c4762a1bSJed Brown     }
2438c4762a1bSJed Brown     flux[*ndim + 2] = (rhom * .5 * (unm * unm + utm * utm + ubm * ubm) + gamm / (gamm - 1.) * pm) * unm;
2439c4762a1bSJed Brown     return iwave;
2440c4762a1bSJed Brown } /* godunovflux_ */
2441c4762a1bSJed Brown 
2442c4762a1bSJed Brown /* Subroutine to set up the initial conditions for the */
2443c4762a1bSJed Brown /* Shock Interface interaction or linear wave (Ravi Samtaney,Mark Adams). */
2444c4762a1bSJed Brown /* ----------------------------------------------------------------------- */
2445c4762a1bSJed Brown int projecteqstate(PetscReal wc[], const PetscReal ueq[], PetscReal lv[][3])
2446c4762a1bSJed Brown {
2447c4762a1bSJed Brown   int j,k;
2448c4762a1bSJed Brown /*      Wc=matmul(lv,Ueq) 3 vars */
2449c4762a1bSJed Brown   for (k = 0; k < 3; ++k) {
2450c4762a1bSJed Brown     wc[k] = 0.;
2451c4762a1bSJed Brown     for (j = 0; j < 3; ++j) {
2452c4762a1bSJed Brown       wc[k] += lv[k][j]*ueq[j];
2453c4762a1bSJed Brown     }
2454c4762a1bSJed Brown   }
2455c4762a1bSJed Brown   return 0;
2456c4762a1bSJed Brown }
2457c4762a1bSJed Brown /* ----------------------------------------------------------------------- */
2458c4762a1bSJed Brown int projecttoprim(PetscReal v[], const PetscReal wc[], PetscReal rv[][3])
2459c4762a1bSJed Brown {
2460c4762a1bSJed Brown   int k,j;
2461c4762a1bSJed Brown   /*      V=matmul(rv,WC) 3 vars */
2462c4762a1bSJed Brown   for (k = 0; k < 3; ++k) {
2463c4762a1bSJed Brown     v[k] = 0.;
2464c4762a1bSJed Brown     for (j = 0; j < 3; ++j) {
2465c4762a1bSJed Brown       v[k] += rv[k][j]*wc[j];
2466c4762a1bSJed Brown     }
2467c4762a1bSJed Brown   }
2468c4762a1bSJed Brown   return 0;
2469c4762a1bSJed Brown }
2470c4762a1bSJed Brown /* ---------------------------------------------------------------------- */
2471c4762a1bSJed Brown int eigenvectors(PetscReal rv[][3], PetscReal lv[][3], const PetscReal ueq[], PetscReal gamma)
2472c4762a1bSJed Brown {
2473c4762a1bSJed Brown   int j,k;
2474c4762a1bSJed Brown   PetscReal rho,csnd,p0;
2475c4762a1bSJed Brown   /* PetscScalar u; */
2476c4762a1bSJed Brown 
2477c4762a1bSJed Brown   for (k = 0; k < 3; ++k) for (j = 0; j < 3; ++j) { lv[k][j] = 0.; rv[k][j] = 0.; }
2478c4762a1bSJed Brown   rho = ueq[0];
2479c4762a1bSJed Brown   /* u = ueq[1]; */
2480c4762a1bSJed Brown   p0 = ueq[2];
2481c4762a1bSJed Brown   csnd = PetscSqrtReal(gamma * p0 / rho);
2482c4762a1bSJed Brown   lv[0][1] = rho * .5;
2483c4762a1bSJed Brown   lv[0][2] = -.5 / csnd;
2484c4762a1bSJed Brown   lv[1][0] = csnd;
2485c4762a1bSJed Brown   lv[1][2] = -1. / csnd;
2486c4762a1bSJed Brown   lv[2][1] = rho * .5;
2487c4762a1bSJed Brown   lv[2][2] = .5 / csnd;
2488c4762a1bSJed Brown   rv[0][0] = -1. / csnd;
2489c4762a1bSJed Brown   rv[1][0] = 1. / rho;
2490c4762a1bSJed Brown   rv[2][0] = -csnd;
2491c4762a1bSJed Brown   rv[0][1] = 1. / csnd;
2492c4762a1bSJed Brown   rv[0][2] = 1. / csnd;
2493c4762a1bSJed Brown   rv[1][2] = 1. / rho;
2494c4762a1bSJed Brown   rv[2][2] = csnd;
2495c4762a1bSJed Brown   return 0;
2496c4762a1bSJed Brown }
2497c4762a1bSJed Brown 
2498c4762a1bSJed Brown int initLinearWave(EulerNode *ux, const PetscReal gamma, const PetscReal coord[], const PetscReal Lx)
2499c4762a1bSJed Brown {
2500c4762a1bSJed Brown   PetscReal p0,u0,wcp[3],wc[3];
2501c4762a1bSJed Brown   PetscReal lv[3][3];
2502c4762a1bSJed Brown   PetscReal vp[3];
2503c4762a1bSJed Brown   PetscReal rv[3][3];
2504c4762a1bSJed Brown   PetscReal eps, ueq[3], rho0, twopi;
2505c4762a1bSJed Brown 
2506c4762a1bSJed Brown   /* Function Body */
2507c4762a1bSJed Brown   twopi = 2.*PETSC_PI;
2508c4762a1bSJed Brown   eps = 1e-4; /* perturbation */
2509c4762a1bSJed Brown   rho0 = 1e3;   /* density of water */
2510c4762a1bSJed Brown   p0 = 101325.; /* init pressure of 1 atm (?) */
2511c4762a1bSJed Brown   u0 = 0.;
2512c4762a1bSJed Brown   ueq[0] = rho0;
2513c4762a1bSJed Brown   ueq[1] = u0;
2514c4762a1bSJed Brown   ueq[2] = p0;
2515c4762a1bSJed Brown   /* Project initial state to characteristic variables */
2516c4762a1bSJed Brown   eigenvectors(rv, lv, ueq, gamma);
2517c4762a1bSJed Brown   projecteqstate(wc, ueq, lv);
2518c4762a1bSJed Brown   wcp[0] = wc[0];
2519c4762a1bSJed Brown   wcp[1] = wc[1];
2520c4762a1bSJed Brown   wcp[2] = wc[2] + eps * PetscCosReal(coord[0] * 2. * twopi / Lx);
2521c4762a1bSJed Brown   projecttoprim(vp, wcp, rv);
2522c4762a1bSJed Brown   ux->r = vp[0]; /* density */
2523c4762a1bSJed Brown   ux->ru[0] = vp[0] * vp[1]; /* x momentum */
2524c4762a1bSJed Brown   ux->ru[1] = 0.;
2525c4762a1bSJed Brown #if defined DIM > 2
2526c4762a1bSJed Brown   if (dim>2) ux->ru[2] = 0.;
2527c4762a1bSJed Brown #endif
2528c4762a1bSJed Brown   /* E = rho * e + rho * v^2/2 = p/(gam-1) + rho*v^2/2 */
2529c4762a1bSJed Brown   ux->E = vp[2]/(gamma - 1.) + 0.5*vp[0]*vp[1]*vp[1];
2530c4762a1bSJed Brown   return 0;
2531c4762a1bSJed Brown }
2532c4762a1bSJed Brown 
2533c4762a1bSJed Brown /*TEST
2534c4762a1bSJed Brown 
2535c4762a1bSJed Brown   # 2D Advection 0-10
2536c4762a1bSJed Brown   test:
2537c4762a1bSJed Brown     suffix: 0
2538c4762a1bSJed Brown     requires: exodusii
2539c4762a1bSJed Brown     args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo
2540c4762a1bSJed Brown 
2541c4762a1bSJed Brown   test:
2542c4762a1bSJed Brown     suffix: 1
2543c4762a1bSJed Brown     requires: exodusii
2544c4762a1bSJed Brown     args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo
2545c4762a1bSJed Brown 
2546c4762a1bSJed Brown   test:
2547c4762a1bSJed Brown     suffix: 2
2548c4762a1bSJed Brown     requires: exodusii
2549c4762a1bSJed Brown     nsize: 2
2550c4762a1bSJed Brown     args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo
2551c4762a1bSJed Brown 
2552c4762a1bSJed Brown   test:
2553c4762a1bSJed Brown     suffix: 3
2554c4762a1bSJed Brown     requires: exodusii
2555c4762a1bSJed Brown     nsize: 2
2556c4762a1bSJed Brown     args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo
2557c4762a1bSJed Brown 
2558c4762a1bSJed Brown   test:
2559c4762a1bSJed Brown     suffix: 4
2560c4762a1bSJed Brown     requires: exodusii
2561c4762a1bSJed Brown     nsize: 8
2562c4762a1bSJed Brown     args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad.exo
2563c4762a1bSJed Brown 
2564c4762a1bSJed Brown   test:
2565c4762a1bSJed Brown     suffix: 5
2566c4762a1bSJed Brown     requires: exodusii
2567c4762a1bSJed Brown     args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo -ts_type rosw -ts_adapt_reject_safety 1
2568c4762a1bSJed Brown 
2569c4762a1bSJed Brown   test:
2570c4762a1bSJed Brown     suffix: 6
2571c4762a1bSJed Brown     requires: exodusii
2572c4762a1bSJed Brown     args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/squaremotor-30.exo -ufv_split_faces
2573c4762a1bSJed Brown 
2574c4762a1bSJed Brown   test:
2575c4762a1bSJed Brown     suffix: 7
2576c4762a1bSJed Brown     requires: exodusii
2577c4762a1bSJed Brown     args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo -dm_refine 1
2578c4762a1bSJed Brown 
2579c4762a1bSJed Brown   test:
2580c4762a1bSJed Brown     suffix: 8
2581c4762a1bSJed Brown     requires: exodusii
2582c4762a1bSJed Brown     nsize: 2
2583c4762a1bSJed Brown     args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo -dm_refine 1
2584c4762a1bSJed Brown 
2585c4762a1bSJed Brown   test:
2586c4762a1bSJed Brown     suffix: 9
2587c4762a1bSJed Brown     requires: exodusii
2588c4762a1bSJed Brown     nsize: 8
2589c4762a1bSJed Brown     args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo -dm_refine 1
2590c4762a1bSJed Brown 
2591c4762a1bSJed Brown   test:
2592c4762a1bSJed Brown     suffix: 10
2593c4762a1bSJed Brown     requires: exodusii
2594c4762a1bSJed Brown     args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad.exo
2595c4762a1bSJed Brown 
2596c4762a1bSJed Brown   # 2D Shallow water
2597c4762a1bSJed Brown   test:
2598c4762a1bSJed Brown     suffix: sw_0
2599c4762a1bSJed Brown     requires: exodusii
2600c4762a1bSJed Brown     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
2601c4762a1bSJed Brown 
2602c4762a1bSJed Brown   # 2D Advection: p4est
2603c4762a1bSJed Brown   test:
2604c4762a1bSJed Brown     suffix: p4est_advec_2d
2605c4762a1bSJed Brown     requires: p4est
2606c4762a1bSJed Brown     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
2607c4762a1bSJed Brown 
2608c4762a1bSJed Brown   # Advection in a box
2609c4762a1bSJed Brown   test:
2610c4762a1bSJed Brown     suffix: adv_2d_quad_0
2611c4762a1bSJed Brown     args: -ufv_vtk_interval 0 -dm_refine 3 -dm_plex_separate_marker -bc_inflow 1,2,4 -bc_outflow 3
2612c4762a1bSJed Brown 
2613c4762a1bSJed Brown   test:
2614c4762a1bSJed Brown     suffix: adv_2d_quad_1
2615c4762a1bSJed Brown     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
2616c4762a1bSJed Brown     timeoutfactor: 3
2617c4762a1bSJed Brown 
2618c4762a1bSJed Brown   test:
2619c4762a1bSJed Brown     suffix: adv_2d_quad_p4est_0
2620c4762a1bSJed Brown     requires: p4est
2621c4762a1bSJed Brown     args: -ufv_vtk_interval 0 -dm_refine 5 -dm_type p4est -dm_plex_separate_marker -bc_inflow 1,2,4 -bc_outflow 3
2622c4762a1bSJed Brown 
2623c4762a1bSJed Brown   test:
2624c4762a1bSJed Brown     suffix: adv_2d_quad_p4est_1
2625c4762a1bSJed Brown     requires: p4est
2626c4762a1bSJed Brown     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
2627c4762a1bSJed Brown     timeoutfactor: 3
2628c4762a1bSJed Brown 
2629c4762a1bSJed Brown   test:
2630c4762a1bSJed Brown     suffix: adv_2d_quad_p4est_adapt_0
2631c4762a1bSJed Brown     requires: p4est !__float128 #broken for quad precision
2632c4762a1bSJed Brown     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
2633c4762a1bSJed Brown     timeoutfactor: 3
2634c4762a1bSJed Brown 
2635c4762a1bSJed Brown   test:
2636c4762a1bSJed Brown     suffix: adv_2d_tri_0
2637c4762a1bSJed Brown     requires: triangle
2638c4762a1bSJed Brown     TODO: how did this ever get in master when there is no support for this
2639c4762a1bSJed Brown     args: -ufv_vtk_interval 0 -simplex -dm_refine 3 -dm_plex_separate_marker -bc_inflow 1,2,4 -bc_outflow 3
2640c4762a1bSJed Brown 
2641c4762a1bSJed Brown   test:
2642c4762a1bSJed Brown     suffix: adv_2d_tri_1
2643c4762a1bSJed Brown     requires: triangle
2644c4762a1bSJed Brown     TODO: how did this ever get in master when there is no support for this
2645c4762a1bSJed Brown     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
2646c4762a1bSJed Brown 
2647c4762a1bSJed Brown   test:
2648c4762a1bSJed Brown     suffix: adv_0
2649c4762a1bSJed Brown     requires: exodusii
2650c4762a1bSJed Brown     args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo -bc_inflow 100,101,200 -bc_outflow 201
2651c4762a1bSJed Brown 
2652c4762a1bSJed Brown   test:
2653c4762a1bSJed Brown     suffix: shock_0
2654c4762a1bSJed Brown     requires: p4est !single !complex
2655c4762a1bSJed Brown     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
2656c4762a1bSJed Brown     timeoutfactor: 3
2657c4762a1bSJed Brown 
2658c4762a1bSJed Brown   # Test GLVis visualization of PetscFV fields
2659c4762a1bSJed Brown   test:
2660c4762a1bSJed Brown     suffix: glvis_adv_2d_tet
2661c4762a1bSJed Brown     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
2662c4762a1bSJed Brown 
2663c4762a1bSJed Brown   test:
2664c4762a1bSJed Brown     suffix: glvis_adv_2d_quad
2665c4762a1bSJed Brown     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
2666c4762a1bSJed Brown 
2667c4762a1bSJed Brown   test:
2668c4762a1bSJed Brown     suffix: tut_1
2669c4762a1bSJed Brown     requires: exodusii
2670c4762a1bSJed Brown     nsize: 1
2671c4762a1bSJed Brown     args: -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo
2672c4762a1bSJed Brown 
2673c4762a1bSJed Brown   test:
2674c4762a1bSJed Brown     suffix: tut_2
2675c4762a1bSJed Brown     requires: exodusii
2676c4762a1bSJed Brown     nsize: 1
2677c4762a1bSJed Brown     args: -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo -ts_type rosw
2678c4762a1bSJed Brown 
2679c4762a1bSJed Brown   test:
2680c4762a1bSJed Brown     suffix: tut_3
2681c4762a1bSJed Brown     requires: exodusii
2682c4762a1bSJed Brown     nsize: 4
2683c4762a1bSJed Brown     args: -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/annulus-20.exo -monitor Error -advect_sol_type bump -petscfv_type leastsquares -petsclimiter_type sin
2684c4762a1bSJed Brown 
2685c4762a1bSJed Brown   test:
2686c4762a1bSJed Brown     suffix: tut_4
2687c4762a1bSJed Brown     requires: exodusii
2688c4762a1bSJed Brown     nsize: 4
2689c4762a1bSJed Brown     args: -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/annulus-20.exo -physics sw -monitor Height,Energy -petscfv_type leastsquares -petsclimiter_type minmod
2690c4762a1bSJed Brown 
2691c4762a1bSJed Brown TEST*/
2692