1 static char help[] = "Second Order TVD Finite Volume Example.\n"; 2 /*F 3 4 We use a second order TVD finite volume method to evolve a system of PDEs. Our simple upwinded residual evaluation loops 5 over all mesh faces and uses a Riemann solver to produce the flux given the face geometry and cell values, 6 \begin{equation} 7 f_i = \mathrm{riemann}(\mathrm{phys}, p_\mathrm{centroid}, \hat n, x^L, x^R) 8 \end{equation} 9 and then update the cell values given the cell volume. 10 \begin{eqnarray} 11 f^L_i &-=& \frac{f_i}{vol^L} \\ 12 f^R_i &+=& \frac{f_i}{vol^R} 13 \end{eqnarray} 14 15 As an example, we can consider the shallow water wave equation, 16 \begin{eqnarray} 17 h_t + \nabla\cdot \left( uh \right) &=& 0 \\ 18 (uh)_t + \nabla\cdot \left( u\otimes uh + \frac{g h^2}{2} I \right) &=& 0 19 \end{eqnarray} 20 where $h$ is wave height, $u$ is wave velocity, and $g$ is the acceleration due to gravity. 21 22 A representative Riemann solver for the shallow water equations is given in the PhysicsRiemann_SW() function, 23 \begin{eqnarray} 24 f^{L,R}_h &=& uh^{L,R} \cdot \hat n \\ 25 f^{L,R}_{uh} &=& \frac{f^{L,R}_h}{h^{L,R}} uh^{L,R} + g (h^{L,R})^2 \hat n \\ 26 c^{L,R} &=& \sqrt{g h^{L,R}} \\ 27 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) \\ 28 f_i &=& \frac{A_\mathrm{face}}{2} \left( f^L_i + f^R_i + s \left( x^L_i - x^R_i \right) \right) 29 \end{eqnarray} 30 where $c$ is the local gravity wave speed and $f_i$ is a Rusanov flux. 31 32 The more sophisticated residual evaluation in RHSFunctionLocal_LS() uses a least-squares fit to a quadratic polynomial 33 over a neighborhood of the given element. 34 35 The mesh is read in from an ExodusII file, usually generated by Cubit. 36 F*/ 37 #include <petscdmplex.h> 38 #include <petscdmforest.h> 39 #include <petscds.h> 40 #include <petscts.h> 41 #include <petscsf.h> /* For SplitFaces() */ 42 43 #define DIM 2 /* Geometric dimension */ 44 #define ALEN(a) (sizeof(a)/sizeof((a)[0])) 45 46 static PetscFunctionList PhysicsList; 47 48 /* Represents continuum physical equations. */ 49 typedef struct _n_Physics *Physics; 50 51 /* Physical model includes boundary conditions, initial conditions, and functionals of interest. It is 52 * discretization-independent, but its members depend on the scenario being solved. */ 53 typedef struct _n_Model *Model; 54 55 /* 'User' implements a discretization of a continuous model. */ 56 typedef struct _n_User *User; 57 typedef PetscErrorCode (*SolutionFunction)(Model,PetscReal,const PetscReal*,PetscScalar*,void*); 58 typedef PetscErrorCode (*SetUpBCFunction)(PetscDS,Physics); 59 typedef PetscErrorCode (*FunctionalFunction)(Model,PetscReal,const PetscReal*,const PetscScalar*,PetscReal*,void*); 60 typedef PetscErrorCode (*SetupFields)(Physics,PetscSection); 61 static PetscErrorCode ModelSolutionSetDefault(Model,SolutionFunction,void*); 62 static PetscErrorCode ModelFunctionalRegister(Model,const char*,PetscInt*,FunctionalFunction,void*); 63 static PetscErrorCode OutputVTK(DM,const char*,PetscViewer*); 64 65 struct FieldDescription { 66 const char *name; 67 PetscInt dof; 68 }; 69 70 typedef struct _n_FunctionalLink *FunctionalLink; 71 struct _n_FunctionalLink { 72 char *name; 73 FunctionalFunction func; 74 void *ctx; 75 PetscInt offset; 76 FunctionalLink next; 77 }; 78 79 struct _n_Physics { 80 PetscRiemannFunc riemann; 81 PetscInt dof; /* number of degrees of freedom per cell */ 82 PetscReal maxspeed; /* kludge to pick initial time step, need to add monitoring and step control */ 83 void *data; 84 PetscInt nfields; 85 const struct FieldDescription *field_desc; 86 }; 87 88 struct _n_Model { 89 MPI_Comm comm; /* Does not do collective communicaton, but some error conditions can be collective */ 90 Physics physics; 91 FunctionalLink functionalRegistry; 92 PetscInt maxComputed; 93 PetscInt numMonitored; 94 FunctionalLink *functionalMonitored; 95 PetscInt numCall; 96 FunctionalLink *functionalCall; 97 SolutionFunction solution; 98 SetUpBCFunction setupbc; 99 void *solutionctx; 100 PetscReal maxspeed; /* estimate of global maximum speed (for CFL calculation) */ 101 PetscReal bounds[2*DIM]; 102 DMBoundaryType bcs[3]; 103 PetscErrorCode (*errorIndicator)(PetscInt, PetscReal, PetscInt, const PetscScalar[], const PetscScalar[], PetscReal *, void *); 104 void *errorCtx; 105 }; 106 107 struct _n_User { 108 PetscInt numSplitFaces; 109 PetscInt vtkInterval; /* For monitor */ 110 char outputBasename[PETSC_MAX_PATH_LEN]; /* Basename for output files */ 111 PetscInt monitorStepOffset; 112 Model model; 113 PetscBool vtkmon; 114 }; 115 116 PETSC_STATIC_INLINE PetscReal DotDIMReal(const PetscReal *x,const PetscReal *y) 117 { 118 PetscInt i; 119 PetscReal prod=0.0; 120 121 for (i=0; i<DIM; i++) prod += x[i]*y[i]; 122 return prod; 123 } 124 PETSC_STATIC_INLINE PetscReal NormDIM(const PetscReal *x) { return PetscSqrtReal(PetscAbsReal(DotDIMReal(x,x))); } 125 126 PETSC_STATIC_INLINE PetscReal Dot2Real(const PetscReal *x,const PetscReal *y) { return x[0]*y[0] + x[1]*y[1];} 127 PETSC_STATIC_INLINE PetscReal Norm2Real(const PetscReal *x) { return PetscSqrtReal(PetscAbsReal(Dot2Real(x,x)));} 128 PETSC_STATIC_INLINE void Normalize2Real(PetscReal *x) { PetscReal a = 1./Norm2Real(x); x[0] *= a; x[1] *= a; } 129 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]; } 130 PETSC_STATIC_INLINE void Scale2Real(PetscReal a,const PetscReal *x,PetscReal *y) { y[0] = a*x[0]; y[1] = a*x[1]; } 131 132 /******************* Advect ********************/ 133 typedef enum {ADVECT_SOL_TILTED,ADVECT_SOL_BUMP,ADVECT_SOL_BUMP_CAVITY} AdvectSolType; 134 static const char *const AdvectSolTypes[] = {"TILTED","BUMP","BUMP_CAVITY","AdvectSolType","ADVECT_SOL_",0}; 135 typedef enum {ADVECT_SOL_BUMP_CONE,ADVECT_SOL_BUMP_COS} AdvectSolBumpType; 136 static const char *const AdvectSolBumpTypes[] = {"CONE","COS","AdvectSolBumpType","ADVECT_SOL_BUMP_",0}; 137 138 typedef struct { 139 PetscReal wind[DIM]; 140 } Physics_Advect_Tilted; 141 typedef struct { 142 PetscReal center[DIM]; 143 PetscReal radius; 144 AdvectSolBumpType type; 145 } Physics_Advect_Bump; 146 147 typedef struct { 148 PetscReal inflowState; 149 AdvectSolType soltype; 150 union { 151 Physics_Advect_Tilted tilted; 152 Physics_Advect_Bump bump; 153 } sol; 154 struct { 155 PetscInt Solution; 156 PetscInt Error; 157 } functional; 158 } Physics_Advect; 159 160 static const struct FieldDescription PhysicsFields_Advect[] = {{"U",1},{NULL,0}}; 161 162 static PetscErrorCode PhysicsBoundary_Advect_Inflow(PetscReal time, const PetscReal *c, const PetscReal *n, const PetscScalar *xI, PetscScalar *xG, void *ctx) 163 { 164 Physics phys = (Physics)ctx; 165 Physics_Advect *advect = (Physics_Advect*)phys->data; 166 167 PetscFunctionBeginUser; 168 xG[0] = advect->inflowState; 169 PetscFunctionReturn(0); 170 } 171 172 static PetscErrorCode PhysicsBoundary_Advect_Outflow(PetscReal time, const PetscReal *c, const PetscReal *n, const PetscScalar *xI, PetscScalar *xG, void *ctx) 173 { 174 PetscFunctionBeginUser; 175 xG[0] = xI[0]; 176 PetscFunctionReturn(0); 177 } 178 179 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) 180 { 181 Physics_Advect *advect = (Physics_Advect*)phys->data; 182 PetscReal wind[DIM],wn; 183 184 switch (advect->soltype) { 185 case ADVECT_SOL_TILTED: { 186 Physics_Advect_Tilted *tilted = &advect->sol.tilted; 187 wind[0] = tilted->wind[0]; 188 wind[1] = tilted->wind[1]; 189 } break; 190 case ADVECT_SOL_BUMP: 191 wind[0] = -qp[1]; 192 wind[1] = qp[0]; 193 break; 194 case ADVECT_SOL_BUMP_CAVITY: 195 { 196 PetscInt i; 197 PetscReal comp2[3] = {0.,0.,0.}, rad2; 198 199 rad2 = 0.; 200 for (i = 0; i < dim; i++) { 201 comp2[i] = qp[i] * qp[i]; 202 rad2 += comp2[i]; 203 } 204 205 wind[0] = -qp[1]; 206 wind[1] = qp[0]; 207 if (rad2 > 1.) { 208 PetscInt maxI = 0; 209 PetscReal maxComp2 = comp2[0]; 210 211 for (i = 1; i < dim; i++) { 212 if (comp2[i] > maxComp2) { 213 maxI = i; 214 maxComp2 = comp2[i]; 215 } 216 } 217 wind[maxI] = 0.; 218 } 219 } 220 break; 221 default: 222 { 223 PetscInt i; 224 for (i = 0; i < DIM; ++i) wind[i] = 0.0; 225 } 226 /* default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for solution type %s",AdvectSolBumpTypes[advect->soltype]); */ 227 } 228 wn = Dot2Real(wind, n); 229 flux[0] = (wn > 0 ? xL[0] : xR[0]) * wn; 230 } 231 232 static PetscErrorCode PhysicsSolution_Advect(Model mod,PetscReal time,const PetscReal *x,PetscScalar *u,void *ctx) 233 { 234 Physics phys = (Physics)ctx; 235 Physics_Advect *advect = (Physics_Advect*)phys->data; 236 237 PetscFunctionBeginUser; 238 switch (advect->soltype) { 239 case ADVECT_SOL_TILTED: { 240 PetscReal x0[DIM]; 241 Physics_Advect_Tilted *tilted = &advect->sol.tilted; 242 Waxpy2Real(-time,tilted->wind,x,x0); 243 if (x0[1] > 0) u[0] = 1.*x[0] + 3.*x[1]; 244 else u[0] = advect->inflowState; 245 } break; 246 case ADVECT_SOL_BUMP_CAVITY: 247 case ADVECT_SOL_BUMP: { 248 Physics_Advect_Bump *bump = &advect->sol.bump; 249 PetscReal x0[DIM],v[DIM],r,cost,sint; 250 cost = PetscCosReal(time); 251 sint = PetscSinReal(time); 252 x0[0] = cost*x[0] + sint*x[1]; 253 x0[1] = -sint*x[0] + cost*x[1]; 254 Waxpy2Real(-1,bump->center,x0,v); 255 r = Norm2Real(v); 256 switch (bump->type) { 257 case ADVECT_SOL_BUMP_CONE: 258 u[0] = PetscMax(1 - r/bump->radius,0); 259 break; 260 case ADVECT_SOL_BUMP_COS: 261 u[0] = 0.5 + 0.5*PetscCosReal(PetscMin(r/bump->radius,1)*PETSC_PI); 262 break; 263 } 264 } break; 265 default: SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unknown solution type"); 266 } 267 PetscFunctionReturn(0); 268 } 269 270 static PetscErrorCode PhysicsFunctional_Advect(Model mod,PetscReal time,const PetscReal *x,const PetscScalar *y,PetscReal *f,void *ctx) 271 { 272 Physics phys = (Physics)ctx; 273 Physics_Advect *advect = (Physics_Advect*)phys->data; 274 PetscScalar yexact[1]; 275 PetscErrorCode ierr; 276 277 PetscFunctionBeginUser; 278 ierr = PhysicsSolution_Advect(mod,time,x,yexact,phys);CHKERRQ(ierr); 279 f[advect->functional.Solution] = PetscRealPart(y[0]); 280 f[advect->functional.Error] = PetscAbsScalar(y[0]-yexact[0]); 281 PetscFunctionReturn(0); 282 } 283 284 static PetscErrorCode SetUpBC_Advect(PetscDS prob, Physics phys) 285 { 286 PetscErrorCode ierr; 287 const PetscInt inflowids[] = {100,200,300},outflowids[] = {101}; 288 289 PetscFunctionBeginUser; 290 /* Register "canned" boundary conditions and defaults for where to apply. */ 291 ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "inflow", "Face Sets", 0, 0, NULL, (void (*)(void)) PhysicsBoundary_Advect_Inflow, ALEN(inflowids), inflowids, phys);CHKERRQ(ierr); 292 ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "outflow", "Face Sets", 0, 0, NULL, (void (*)(void)) PhysicsBoundary_Advect_Outflow, ALEN(outflowids), outflowids, phys);CHKERRQ(ierr); 293 PetscFunctionReturn(0); 294 } 295 296 static PetscErrorCode PhysicsCreate_Advect(Model mod,Physics phys,PetscOptionItems *PetscOptionsObject) 297 { 298 Physics_Advect *advect; 299 PetscErrorCode ierr; 300 301 PetscFunctionBeginUser; 302 phys->field_desc = PhysicsFields_Advect; 303 phys->riemann = (PetscRiemannFunc)PhysicsRiemann_Advect; 304 ierr = PetscNew(&advect);CHKERRQ(ierr); 305 phys->data = advect; 306 mod->setupbc = SetUpBC_Advect; 307 308 ierr = PetscOptionsHead(PetscOptionsObject,"Advect options");CHKERRQ(ierr); 309 { 310 PetscInt two = 2,dof = 1; 311 advect->soltype = ADVECT_SOL_TILTED; 312 ierr = PetscOptionsEnum("-advect_sol_type","solution type","",AdvectSolTypes,(PetscEnum)advect->soltype,(PetscEnum*)&advect->soltype,NULL);CHKERRQ(ierr); 313 switch (advect->soltype) { 314 case ADVECT_SOL_TILTED: { 315 Physics_Advect_Tilted *tilted = &advect->sol.tilted; 316 two = 2; 317 tilted->wind[0] = 0.0; 318 tilted->wind[1] = 1.0; 319 ierr = PetscOptionsRealArray("-advect_tilted_wind","background wind vx,vy","",tilted->wind,&two,NULL);CHKERRQ(ierr); 320 advect->inflowState = -2.0; 321 ierr = PetscOptionsRealArray("-advect_tilted_inflow","Inflow state","",&advect->inflowState,&dof,NULL);CHKERRQ(ierr); 322 phys->maxspeed = Norm2Real(tilted->wind); 323 } break; 324 case ADVECT_SOL_BUMP_CAVITY: 325 case ADVECT_SOL_BUMP: { 326 Physics_Advect_Bump *bump = &advect->sol.bump; 327 two = 2; 328 bump->center[0] = 2.; 329 bump->center[1] = 0.; 330 ierr = PetscOptionsRealArray("-advect_bump_center","location of center of bump x,y","",bump->center,&two,NULL);CHKERRQ(ierr); 331 bump->radius = 0.9; 332 ierr = PetscOptionsReal("-advect_bump_radius","radius of bump","",bump->radius,&bump->radius,NULL);CHKERRQ(ierr); 333 bump->type = ADVECT_SOL_BUMP_CONE; 334 ierr = PetscOptionsEnum("-advect_bump_type","type of bump","",AdvectSolBumpTypes,(PetscEnum)bump->type,(PetscEnum*)&bump->type,NULL);CHKERRQ(ierr); 335 phys->maxspeed = 3.; /* radius of mesh, kludge */ 336 } break; 337 } 338 } 339 ierr = PetscOptionsTail();CHKERRQ(ierr); 340 /* Initial/transient solution with default boundary conditions */ 341 ierr = ModelSolutionSetDefault(mod,PhysicsSolution_Advect,phys);CHKERRQ(ierr); 342 /* Register "canned" functionals */ 343 ierr = ModelFunctionalRegister(mod,"Solution",&advect->functional.Solution,PhysicsFunctional_Advect,phys);CHKERRQ(ierr); 344 ierr = ModelFunctionalRegister(mod,"Error",&advect->functional.Error,PhysicsFunctional_Advect,phys);CHKERRQ(ierr); 345 mod->bcs[0] = mod->bcs[1] = mod->bcs[2] = DM_BOUNDARY_GHOSTED; 346 PetscFunctionReturn(0); 347 } 348 349 /******************* Shallow Water ********************/ 350 typedef struct { 351 PetscReal gravity; 352 PetscReal boundaryHeight; 353 struct { 354 PetscInt Height; 355 PetscInt Speed; 356 PetscInt Energy; 357 } functional; 358 } Physics_SW; 359 typedef struct { 360 PetscReal h; 361 PetscReal uh[DIM]; 362 } SWNode; 363 typedef union { 364 SWNode swnode; 365 PetscReal vals[DIM+1]; 366 } SWNodeUnion; 367 368 static const struct FieldDescription PhysicsFields_SW[] = {{"Height",1},{"Momentum",DIM},{NULL,0}}; 369 370 /* 371 * h_t + div(uh) = 0 372 * (uh)_t + div (u\otimes uh + g h^2 / 2 I) = 0 373 * 374 * */ 375 static PetscErrorCode SWFlux(Physics phys,const PetscReal *n,const SWNode *x,SWNode *f) 376 { 377 Physics_SW *sw = (Physics_SW*)phys->data; 378 PetscReal uhn,u[DIM]; 379 PetscInt i; 380 381 PetscFunctionBeginUser; 382 Scale2Real(1./x->h,x->uh,u); 383 uhn = x->uh[0] * n[0] + x->uh[1] * n[1]; 384 f->h = uhn; 385 for (i=0; i<DIM; i++) f->uh[i] = u[i] * uhn + sw->gravity * PetscSqr(x->h) * n[i]; 386 PetscFunctionReturn(0); 387 } 388 389 static PetscErrorCode PhysicsBoundary_SW_Wall(PetscReal time, const PetscReal *c, const PetscReal *n, const PetscScalar *xI, PetscScalar *xG, void *ctx) 390 { 391 PetscFunctionBeginUser; 392 xG[0] = xI[0]; 393 xG[1] = -xI[1]; 394 xG[2] = -xI[2]; 395 PetscFunctionReturn(0); 396 } 397 398 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) 399 { 400 Physics_SW *sw = (Physics_SW*)phys->data; 401 PetscReal cL,cR,speed; 402 PetscReal nn[DIM]; 403 #if !defined(PETSC_USE_COMPLEX) 404 const SWNode *uL = (const SWNode*)xL,*uR = (const SWNode*)xR; 405 #else 406 SWNodeUnion uLreal, uRreal; 407 const SWNode *uL = &uLreal.swnode; 408 const SWNode *uR = &uRreal.swnode; 409 #endif 410 SWNodeUnion fL,fR; 411 PetscInt i; 412 PetscReal zero=0.; 413 414 #if defined(PETSC_USE_COMPLEX) 415 uLreal.swnode.h = 0; uRreal.swnode.h = 0; 416 for (i = 0; i < 1+dim; i++) uLreal.vals[i] = PetscRealPart(xL[i]); 417 for (i = 0; i < 1+dim; i++) uRreal.vals[i] = PetscRealPart(xR[i]); 418 #endif 419 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"); */ 420 nn[0] = n[0]; 421 nn[1] = n[1]; 422 Normalize2Real(nn); 423 SWFlux(phys,nn,uL,&(fL.swnode)); 424 SWFlux(phys,nn,uR,&(fR.swnode)); 425 cL = PetscSqrtReal(sw->gravity*uL->h); 426 cR = PetscSqrtReal(sw->gravity*uR->h); /* gravity wave speed */ 427 speed = PetscMax(PetscAbsReal(Dot2Real(uL->uh,nn)/uL->h) + cL,PetscAbsReal(Dot2Real(uR->uh,nn)/uR->h) + cR); 428 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); 429 } 430 431 static PetscErrorCode PhysicsSolution_SW(Model mod,PetscReal time,const PetscReal *x,PetscScalar *u,void *ctx) 432 { 433 PetscReal dx[2],r,sigma; 434 435 PetscFunctionBeginUser; 436 if (time != 0.0) SETERRQ1(mod->comm,PETSC_ERR_SUP,"No solution known for time %g",(double)time); 437 dx[0] = x[0] - 1.5; 438 dx[1] = x[1] - 1.0; 439 r = Norm2Real(dx); 440 sigma = 0.5; 441 u[0] = 1 + 2*PetscExpReal(-PetscSqr(r)/(2*PetscSqr(sigma))); 442 u[1] = 0.0; 443 u[2] = 0.0; 444 PetscFunctionReturn(0); 445 } 446 447 static PetscErrorCode PhysicsFunctional_SW(Model mod,PetscReal time,const PetscReal *coord,const PetscScalar *xx,PetscReal *f,void *ctx) 448 { 449 Physics phys = (Physics)ctx; 450 Physics_SW *sw = (Physics_SW*)phys->data; 451 const SWNode *x = (const SWNode*)xx; 452 PetscReal u[2]; 453 PetscReal h; 454 455 PetscFunctionBeginUser; 456 h = x->h; 457 Scale2Real(1./x->h,x->uh,u); 458 f[sw->functional.Height] = h; 459 f[sw->functional.Speed] = Norm2Real(u) + PetscSqrtReal(sw->gravity*h); 460 f[sw->functional.Energy] = 0.5*(Dot2Real(x->uh,u) + sw->gravity*PetscSqr(h)); 461 PetscFunctionReturn(0); 462 } 463 464 static PetscErrorCode SetUpBC_SW(PetscDS prob,Physics phys) 465 { 466 PetscErrorCode ierr; 467 const PetscInt wallids[] = {100,101,200,300}; 468 PetscFunctionBeginUser; 469 ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "wall", "Face Sets", 0, 0, NULL, (void (*)(void)) PhysicsBoundary_SW_Wall, ALEN(wallids), wallids, phys);CHKERRQ(ierr); 470 PetscFunctionReturn(0); 471 } 472 473 static PetscErrorCode PhysicsCreate_SW(Model mod,Physics phys,PetscOptionItems *PetscOptionsObject) 474 { 475 Physics_SW *sw; 476 PetscErrorCode ierr; 477 478 PetscFunctionBeginUser; 479 phys->field_desc = PhysicsFields_SW; 480 phys->riemann = (PetscRiemannFunc) PhysicsRiemann_SW; 481 ierr = PetscNew(&sw);CHKERRQ(ierr); 482 phys->data = sw; 483 mod->setupbc = SetUpBC_SW; 484 485 ierr = PetscOptionsHead(PetscOptionsObject,"SW options");CHKERRQ(ierr); 486 { 487 sw->gravity = 1.0; 488 ierr = PetscOptionsReal("-sw_gravity","Gravitational constant","",sw->gravity,&sw->gravity,NULL);CHKERRQ(ierr); 489 } 490 ierr = PetscOptionsTail();CHKERRQ(ierr); 491 phys->maxspeed = PetscSqrtReal(2.0*sw->gravity); /* Mach 1 for depth of 2 */ 492 493 ierr = ModelSolutionSetDefault(mod,PhysicsSolution_SW,phys);CHKERRQ(ierr); 494 ierr = ModelFunctionalRegister(mod,"Height",&sw->functional.Height,PhysicsFunctional_SW,phys);CHKERRQ(ierr); 495 ierr = ModelFunctionalRegister(mod,"Speed",&sw->functional.Speed,PhysicsFunctional_SW,phys);CHKERRQ(ierr); 496 ierr = ModelFunctionalRegister(mod,"Energy",&sw->functional.Energy,PhysicsFunctional_SW,phys);CHKERRQ(ierr); 497 498 mod->bcs[0] = mod->bcs[1] = mod->bcs[2] = DM_BOUNDARY_GHOSTED; 499 500 PetscFunctionReturn(0); 501 } 502 503 /******************* Euler Density Shock (EULER_IV_SHOCK,EULER_SS_SHOCK) ********************/ 504 /* An initial-value and self-similar solutions of the compressible Euler equations */ 505 /* Ravi Samtaney and D. I. Pullin */ 506 /* Phys. Fluids 8, 2650 (1996); http://dx.doi.org/10.1063/1.869050 */ 507 typedef enum {EULER_PAR_GAMMA,EULER_PAR_RHOR,EULER_PAR_AMACH,EULER_PAR_ITANA,EULER_PAR_SIZE} EulerParamIdx; 508 typedef enum {EULER_IV_SHOCK,EULER_SS_SHOCK,EULER_SHOCK_TUBE,EULER_LINEAR_WAVE} EulerType; 509 typedef struct { 510 PetscReal r; 511 PetscReal ru[DIM]; 512 PetscReal E; 513 } EulerNode; 514 typedef union { 515 EulerNode eulernode; 516 PetscReal vals[DIM+2]; 517 } EulerNodeUnion; 518 typedef PetscErrorCode (*EquationOfState)(const PetscReal*, const EulerNode*, PetscReal*); 519 typedef struct { 520 EulerType type; 521 PetscReal pars[EULER_PAR_SIZE]; 522 EquationOfState sound; 523 struct { 524 PetscInt Density; 525 PetscInt Momentum; 526 PetscInt Energy; 527 PetscInt Pressure; 528 PetscInt Speed; 529 } monitor; 530 } Physics_Euler; 531 532 static const struct FieldDescription PhysicsFields_Euler[] = {{"Density",1},{"Momentum",DIM},{"Energy",1},{NULL,0}}; 533 534 /* initial condition */ 535 int initLinearWave(EulerNode *ux, const PetscReal gamma, const PetscReal coord[], const PetscReal Lx); 536 static PetscErrorCode PhysicsSolution_Euler(Model mod, PetscReal time, const PetscReal *x, PetscScalar *u, void *ctx) 537 { 538 PetscInt i; 539 Physics phys = (Physics)ctx; 540 Physics_Euler *eu = (Physics_Euler*)phys->data; 541 EulerNode *uu = (EulerNode*)u; 542 PetscReal p0,gamma,c; 543 PetscFunctionBeginUser; 544 if (time != 0.0) SETERRQ1(mod->comm,PETSC_ERR_SUP,"No solution known for time %g",(double)time); 545 546 for (i=0; i<DIM; i++) uu->ru[i] = 0.0; /* zero out initial velocity */ 547 /* set E and rho */ 548 gamma = eu->pars[EULER_PAR_GAMMA]; 549 550 if (eu->type==EULER_IV_SHOCK || eu->type==EULER_SS_SHOCK) { 551 /******************* Euler Density Shock ********************/ 552 /* On initial-value and self-similar solutions of the compressible Euler equations */ 553 /* Ravi Samtaney and D. I. Pullin */ 554 /* Phys. Fluids 8, 2650 (1996); http://dx.doi.org/10.1063/1.869050 */ 555 /* initial conditions 1: left of shock, 0: left of discontinuity 2: right of discontinuity, */ 556 p0 = 1.; 557 if (x[0] < 0.0 + x[1]*eu->pars[EULER_PAR_ITANA]) { 558 if (x[0] < mod->bounds[0]*0.5) { /* left of shock (1) */ 559 PetscReal amach,rho,press,gas1,p1; 560 amach = eu->pars[EULER_PAR_AMACH]; 561 rho = 1.; 562 press = p0; 563 p1 = press*(1.0+2.0*gamma/(gamma+1.0)*(amach*amach-1.0)); 564 gas1 = (gamma-1.0)/(gamma+1.0); 565 uu->r = rho*(p1/press+gas1)/(gas1*p1/press+1.0); 566 uu->ru[0] = ((uu->r - rho)*PetscSqrtReal(gamma*press/rho)*amach); 567 uu->E = p1/(gamma-1.0) + .5/uu->r*uu->ru[0]*uu->ru[0]; 568 } 569 else { /* left of discontinuity (0) */ 570 uu->r = 1.; /* rho = 1 */ 571 uu->E = p0/(gamma-1.0); 572 } 573 } 574 else { /* right of discontinuity (2) */ 575 uu->r = eu->pars[EULER_PAR_RHOR]; 576 uu->E = p0/(gamma-1.0); 577 } 578 } 579 else if (eu->type==EULER_SHOCK_TUBE) { 580 /* 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. */ 581 if (x[0] < 0.0 ) { 582 uu->r = 8.; 583 uu->E = 10./(gamma-1.); 584 } 585 else { 586 uu->r = 1.; 587 uu->E = 1./(gamma-1.); 588 } 589 } 590 else if (eu->type==EULER_LINEAR_WAVE) { 591 initLinearWave( uu, gamma, x, mod->bounds[1] - mod->bounds[0]); 592 } 593 else SETERRQ1(mod->comm,PETSC_ERR_SUP,"Unknown type %d",eu->type); 594 595 /* set phys->maxspeed: (mod->maxspeed = phys->maxspeed) in main; */ 596 eu->sound(&gamma,uu,&c); 597 c = (uu->ru[0]/uu->r) + c; 598 if (c > phys->maxspeed) phys->maxspeed = c; 599 600 PetscFunctionReturn(0); 601 } 602 603 static PetscErrorCode Pressure_PG(const PetscReal gamma,const EulerNode *x,PetscReal *p) 604 { 605 PetscReal ru2; 606 607 PetscFunctionBeginUser; 608 ru2 = DotDIMReal(x->ru,x->ru); 609 (*p)=(x->E - 0.5*ru2/x->r)*(gamma - 1.0); /* (E - rho V^2/2)(gamma-1) = e rho (gamma-1) */ 610 PetscFunctionReturn(0); 611 } 612 613 static PetscErrorCode SpeedOfSound_PG(const PetscReal *gamma, const EulerNode *x, PetscReal *c) 614 { 615 PetscReal p; 616 617 PetscFunctionBeginUser; 618 Pressure_PG(*gamma,x,&p); 619 if (p<0.) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"negative pressure time %g -- NEED TO FIX!!!!!!",(double) p); 620 /* pars[EULER_PAR_GAMMA] = heat capacity ratio */ 621 (*c)=PetscSqrtReal(*gamma * p / x->r); 622 PetscFunctionReturn(0); 623 } 624 625 /* 626 * x = (rho,rho*(u_1),...,rho*e)^T 627 * x_t+div(f_1(x))+...+div(f_DIM(x)) = 0 628 * 629 * f_i(x) = u_i*x+(0,0,...,p,...,p*u_i)^T 630 * 631 */ 632 static PetscErrorCode EulerFlux(Physics phys,const PetscReal *n,const EulerNode *x,EulerNode *f) 633 { 634 Physics_Euler *eu = (Physics_Euler*)phys->data; 635 PetscReal nu,p; 636 PetscInt i; 637 638 PetscFunctionBeginUser; 639 Pressure_PG(eu->pars[EULER_PAR_GAMMA],x,&p); 640 nu = DotDIMReal(x->ru,n); 641 f->r = nu; /* A rho u */ 642 nu /= x->r; /* A u */ 643 for (i=0; i<DIM; i++) f->ru[i] = nu * x->ru[i] + n[i]*p; /* r u^2 + p */ 644 f->E = nu * (x->E + p); /* u(e+p) */ 645 PetscFunctionReturn(0); 646 } 647 648 /* PetscReal* => EulerNode* conversion */ 649 static PetscErrorCode PhysicsBoundary_Euler_Wall(PetscReal time, const PetscReal *c, const PetscReal *n, const PetscScalar *a_xI, PetscScalar *a_xG, void *ctx) 650 { 651 PetscInt i; 652 const EulerNode *xI = (const EulerNode*)a_xI; 653 EulerNode *xG = (EulerNode*)a_xG; 654 Physics phys = (Physics)ctx; 655 Physics_Euler *eu = (Physics_Euler*)phys->data; 656 PetscFunctionBeginUser; 657 xG->r = xI->r; /* ghost cell density - same */ 658 xG->E = xI->E; /* ghost cell energy - same */ 659 if (n[1] != 0.) { /* top and bottom */ 660 xG->ru[0] = xI->ru[0]; /* copy tang to wall */ 661 xG->ru[1] = -xI->ru[1]; /* reflect perp to t/b wall */ 662 } 663 else { /* sides */ 664 for (i=0; i<DIM; i++) xG->ru[i] = xI->ru[i]; /* copy */ 665 } 666 if (eu->type == EULER_LINEAR_WAVE) { /* debug */ 667 #if 0 668 PetscPrintf(PETSC_COMM_WORLD,"%s coord=%g,%g\n",PETSC_FUNCTION_NAME,c[0],c[1]); 669 #endif 670 } 671 PetscFunctionReturn(0); 672 } 673 int godunovflux( const PetscScalar *ul, const PetscScalar *ur, PetscScalar *flux, const PetscReal *nn, const int *ndim, const PetscReal *gamma); 674 /* PetscReal* => EulerNode* conversion */ 675 static void PhysicsRiemann_Euler_Godunov( PetscInt dim, PetscInt Nf, const PetscReal *qp, const PetscReal *n, 676 const PetscScalar *xL, const PetscScalar *xR, PetscInt numConstants, const PetscScalar constants[], PetscScalar *flux, Physics phys) 677 { 678 Physics_Euler *eu = (Physics_Euler*)phys->data; 679 PetscReal cL,cR,speed,velL,velR,nn[DIM],s2; 680 PetscInt i; 681 PetscErrorCode ierr; 682 PetscFunctionBeginUser; 683 684 for (i=0,s2=0.; i<DIM; i++) { 685 nn[i] = n[i]; 686 s2 += nn[i]*nn[i]; 687 } 688 s2 = PetscSqrtReal(s2); /* |n|_2 = sum(n^2)^1/2 */ 689 for (i=0.; i<DIM; i++) nn[i] /= s2; 690 if (0) { /* Rusanov */ 691 const EulerNode *uL = (const EulerNode*)xL,*uR = (const EulerNode*)xR; 692 EulerNodeUnion fL,fR; 693 EulerFlux(phys,nn,uL,&(fL.eulernode)); 694 EulerFlux(phys,nn,uR,&(fR.eulernode)); 695 ierr = eu->sound(&eu->pars[EULER_PAR_GAMMA],uL,&cL);if (ierr) exit(13); 696 ierr = eu->sound(&eu->pars[EULER_PAR_GAMMA],uR,&cR);if (ierr) exit(14); 697 velL = DotDIMReal(uL->ru,nn)/uL->r; 698 velR = DotDIMReal(uR->ru,nn)/uR->r; 699 speed = PetscMax(velR + cR, velL + cL); 700 for (i=0; i<2+dim; i++) flux[i] = 0.5*((fL.vals[i]+fR.vals[i]) + speed*(xL[i] - xR[i]))*s2; 701 } 702 else { 703 int dim = DIM; 704 /* int iwave = */ 705 godunovflux(xL, xR, flux, nn, &dim, &eu->pars[EULER_PAR_GAMMA]); 706 for (i=0; i<2+dim; i++) flux[i] *= s2; 707 } 708 PetscFunctionReturnVoid(); 709 } 710 711 static PetscErrorCode PhysicsFunctional_Euler(Model mod,PetscReal time,const PetscReal *coord,const PetscScalar *xx,PetscReal *f,void *ctx) 712 { 713 Physics phys = (Physics)ctx; 714 Physics_Euler *eu = (Physics_Euler*)phys->data; 715 const EulerNode *x = (const EulerNode*)xx; 716 PetscReal p; 717 718 PetscFunctionBeginUser; 719 f[eu->monitor.Density] = x->r; 720 f[eu->monitor.Momentum] = NormDIM(x->ru); 721 f[eu->monitor.Energy] = x->E; 722 f[eu->monitor.Speed] = NormDIM(x->ru)/x->r; 723 Pressure_PG(eu->pars[EULER_PAR_GAMMA], x, &p); 724 f[eu->monitor.Pressure] = p; 725 PetscFunctionReturn(0); 726 } 727 728 static PetscErrorCode SetUpBC_Euler(PetscDS prob,Physics phys) 729 { 730 PetscErrorCode ierr; 731 Physics_Euler *eu = (Physics_Euler *) phys->data; 732 if (eu->type == EULER_LINEAR_WAVE) { 733 const PetscInt wallids[] = {100,101}; 734 ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "wall", "Face Sets", 0, 0, NULL, (void (*)(void)) PhysicsBoundary_Euler_Wall, ALEN(wallids), wallids, phys);CHKERRQ(ierr); 735 } 736 else { 737 const PetscInt wallids[] = {100,101,200,300}; 738 ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "wall", "Face Sets", 0, 0, NULL, (void (*)(void)) PhysicsBoundary_Euler_Wall, ALEN(wallids), wallids, phys);CHKERRQ(ierr); 739 } 740 PetscFunctionReturn(0); 741 } 742 743 static PetscErrorCode PhysicsCreate_Euler(Model mod,Physics phys,PetscOptionItems *PetscOptionsObject) 744 { 745 Physics_Euler *eu; 746 PetscErrorCode ierr; 747 748 PetscFunctionBeginUser; 749 phys->field_desc = PhysicsFields_Euler; 750 phys->riemann = (PetscRiemannFunc) PhysicsRiemann_Euler_Godunov; 751 ierr = PetscNew(&eu);CHKERRQ(ierr); 752 phys->data = eu; 753 mod->setupbc = SetUpBC_Euler; 754 ierr = PetscOptionsHead(PetscOptionsObject,"Euler options");CHKERRQ(ierr); 755 { 756 PetscReal alpha; 757 char type[64] = "linear_wave"; 758 PetscBool is; 759 mod->bcs[0] = mod->bcs[1] = mod->bcs[2] = DM_BOUNDARY_GHOSTED; 760 eu->pars[EULER_PAR_GAMMA] = 1.4; 761 eu->pars[EULER_PAR_AMACH] = 2.02; 762 eu->pars[EULER_PAR_RHOR] = 3.0; 763 eu->pars[EULER_PAR_ITANA] = 0.57735026918963; /* angle of Euler self similar (SS) shock */ 764 ierr = PetscOptionsReal("-eu_gamma","Heat capacity ratio","",eu->pars[EULER_PAR_GAMMA],&eu->pars[EULER_PAR_GAMMA],NULL);CHKERRQ(ierr); 765 ierr = PetscOptionsReal("-eu_amach","Shock speed (Mach)","",eu->pars[EULER_PAR_AMACH],&eu->pars[EULER_PAR_AMACH],NULL);CHKERRQ(ierr); 766 ierr = PetscOptionsReal("-eu_rho2","Density right of discontinuity","",eu->pars[EULER_PAR_RHOR],&eu->pars[EULER_PAR_RHOR],NULL);CHKERRQ(ierr); 767 alpha = 60.; 768 ierr = PetscOptionsReal("-eu_alpha","Angle of discontinuity","",alpha,&alpha,NULL);CHKERRQ(ierr); 769 if (alpha<=0. || alpha>90.) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Alpha bust be > 0 and <= 90 (%g)",alpha); 770 eu->pars[EULER_PAR_ITANA] = 1./PetscTanReal( alpha * PETSC_PI / 180.0 ); 771 ierr = PetscOptionsString("-eu_type","Type of Euler test","",type,type,sizeof(type),NULL);CHKERRQ(ierr); 772 ierr = PetscStrcmp(type,"linear_wave", &is);CHKERRQ(ierr); 773 if (is) { 774 eu->type = EULER_LINEAR_WAVE; 775 mod->bcs[0] = mod->bcs[1] = mod->bcs[2] = DM_BOUNDARY_PERIODIC; 776 mod->bcs[1] = DM_BOUNDARY_GHOSTED; /* debug */ 777 ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"linear_wave");CHKERRQ(ierr); 778 } 779 else { 780 if (DIM != 2) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"DIM must be 2 unless linear wave test %s",type); 781 ierr = PetscStrcmp(type,"iv_shock", &is);CHKERRQ(ierr); 782 if (is) { 783 eu->type = EULER_IV_SHOCK; 784 ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"iv_shock");CHKERRQ(ierr); 785 } 786 else { 787 ierr = PetscStrcmp(type,"ss_shock", &is);CHKERRQ(ierr); 788 if (is) { 789 eu->type = EULER_SS_SHOCK; 790 ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"ss_shock");CHKERRQ(ierr); 791 } 792 else { 793 ierr = PetscStrcmp(type,"shock_tube", &is);CHKERRQ(ierr); 794 if (is) eu->type = EULER_SHOCK_TUBE; 795 else SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Unknown Euler type %s",type); 796 ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"shock_tube");CHKERRQ(ierr); 797 } 798 } 799 } 800 } 801 ierr = PetscOptionsTail();CHKERRQ(ierr); 802 eu->sound = SpeedOfSound_PG; 803 phys->maxspeed = 0.; /* will get set in solution */ 804 ierr = ModelSolutionSetDefault(mod,PhysicsSolution_Euler,phys);CHKERRQ(ierr); 805 ierr = ModelFunctionalRegister(mod,"Speed",&eu->monitor.Speed,PhysicsFunctional_Euler,phys);CHKERRQ(ierr); 806 ierr = ModelFunctionalRegister(mod,"Energy",&eu->monitor.Energy,PhysicsFunctional_Euler,phys);CHKERRQ(ierr); 807 ierr = ModelFunctionalRegister(mod,"Density",&eu->monitor.Density,PhysicsFunctional_Euler,phys);CHKERRQ(ierr); 808 ierr = ModelFunctionalRegister(mod,"Momentum",&eu->monitor.Momentum,PhysicsFunctional_Euler,phys);CHKERRQ(ierr); 809 ierr = ModelFunctionalRegister(mod,"Pressure",&eu->monitor.Pressure,PhysicsFunctional_Euler,phys);CHKERRQ(ierr); 810 811 PetscFunctionReturn(0); 812 } 813 814 static PetscErrorCode ErrorIndicator_Simple(PetscInt dim, PetscReal volume, PetscInt numComps, const PetscScalar u[], const PetscScalar grad[], PetscReal *error, void *ctx) 815 { 816 PetscReal err = 0.; 817 PetscInt i, j; 818 819 PetscFunctionBeginUser; 820 for (i = 0; i < numComps; i++) { 821 for (j = 0; j < dim; j++) { 822 err += PetscSqr(PetscRealPart(grad[i * dim + j])); 823 } 824 } 825 *error = volume * err; 826 PetscFunctionReturn(0); 827 } 828 829 PetscErrorCode ConstructCellBoundary(DM dm, User user) 830 { 831 const char *name = "Cell Sets"; 832 const char *bdname = "split faces"; 833 IS regionIS, innerIS; 834 const PetscInt *regions, *cells; 835 PetscInt numRegions, innerRegion, numCells, c; 836 PetscInt cStart, cEnd, cEndInterior, fStart, fEnd; 837 PetscBool hasLabel; 838 PetscErrorCode ierr; 839 840 PetscFunctionBeginUser; 841 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 842 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 843 ierr = DMPlexGetGhostCellStratum(dm, &cEndInterior, NULL);CHKERRQ(ierr); 844 845 ierr = DMHasLabel(dm, name, &hasLabel);CHKERRQ(ierr); 846 if (!hasLabel) PetscFunctionReturn(0); 847 ierr = DMGetLabelSize(dm, name, &numRegions);CHKERRQ(ierr); 848 if (numRegions != 2) PetscFunctionReturn(0); 849 /* Get the inner id */ 850 ierr = DMGetLabelIdIS(dm, name, ®ionIS);CHKERRQ(ierr); 851 ierr = ISGetIndices(regionIS, ®ions);CHKERRQ(ierr); 852 innerRegion = regions[0]; 853 ierr = ISRestoreIndices(regionIS, ®ions);CHKERRQ(ierr); 854 ierr = ISDestroy(®ionIS);CHKERRQ(ierr); 855 /* Find the faces between cells in different regions, could call DMPlexCreateNeighborCSR() */ 856 ierr = DMGetStratumIS(dm, name, innerRegion, &innerIS);CHKERRQ(ierr); 857 ierr = ISGetLocalSize(innerIS, &numCells);CHKERRQ(ierr); 858 ierr = ISGetIndices(innerIS, &cells);CHKERRQ(ierr); 859 ierr = DMCreateLabel(dm, bdname);CHKERRQ(ierr); 860 for (c = 0; c < numCells; ++c) { 861 const PetscInt cell = cells[c]; 862 const PetscInt *faces; 863 PetscInt numFaces, f; 864 865 if ((cell < cStart) || (cell >= cEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Got invalid point %d which is not a cell", cell); 866 ierr = DMPlexGetConeSize(dm, cell, &numFaces);CHKERRQ(ierr); 867 ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr); 868 for (f = 0; f < numFaces; ++f) { 869 const PetscInt face = faces[f]; 870 const PetscInt *neighbors; 871 PetscInt nC, regionA, regionB; 872 873 if ((face < fStart) || (face >= fEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Got invalid point %d which is not a face", face); 874 ierr = DMPlexGetSupportSize(dm, face, &nC);CHKERRQ(ierr); 875 if (nC != 2) continue; 876 ierr = DMPlexGetSupport(dm, face, &neighbors);CHKERRQ(ierr); 877 if ((neighbors[0] >= cEndInterior) || (neighbors[1] >= cEndInterior)) continue; 878 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]); 879 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]); 880 ierr = DMGetLabelValue(dm, name, neighbors[0], ®ionA);CHKERRQ(ierr); 881 ierr = DMGetLabelValue(dm, name, neighbors[1], ®ionB);CHKERRQ(ierr); 882 if (regionA < 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid label %s: Cell %d has no value", name, neighbors[0]); 883 if (regionB < 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid label %s: Cell %d has no value", name, neighbors[1]); 884 if (regionA != regionB) { 885 ierr = DMSetLabelValue(dm, bdname, faces[f], 1);CHKERRQ(ierr); 886 } 887 } 888 } 889 ierr = ISRestoreIndices(innerIS, &cells);CHKERRQ(ierr); 890 ierr = ISDestroy(&innerIS);CHKERRQ(ierr); 891 { 892 DMLabel label; 893 894 ierr = DMGetLabel(dm, bdname, &label);CHKERRQ(ierr); 895 ierr = DMLabelView(label, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 896 } 897 PetscFunctionReturn(0); 898 } 899 900 /* Right now, I have just added duplicate faces, which see both cells. We can 901 - Add duplicate vertices and decouple the face cones 902 - Disconnect faces from cells across the rotation gap 903 */ 904 PetscErrorCode SplitFaces(DM *dmSplit, const char labelName[], User user) 905 { 906 DM dm = *dmSplit, sdm; 907 PetscSF sfPoint, gsfPoint; 908 PetscSection coordSection, newCoordSection; 909 Vec coordinates; 910 IS idIS; 911 const PetscInt *ids; 912 PetscInt *newpoints; 913 PetscInt dim, depth, maxConeSize, maxSupportSize, numLabels, numGhostCells; 914 PetscInt numFS, fs, pStart, pEnd, p, cEnd, cEndInterior, vStart, vEnd, v, fStart, fEnd, newf, d, l; 915 PetscBool hasLabel; 916 PetscErrorCode ierr; 917 918 PetscFunctionBeginUser; 919 ierr = DMHasLabel(dm, labelName, &hasLabel);CHKERRQ(ierr); 920 if (!hasLabel) PetscFunctionReturn(0); 921 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &sdm);CHKERRQ(ierr); 922 ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); 923 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 924 ierr = DMSetDimension(sdm, dim);CHKERRQ(ierr); 925 926 ierr = DMGetLabelIdIS(dm, labelName, &idIS);CHKERRQ(ierr); 927 ierr = ISGetLocalSize(idIS, &numFS);CHKERRQ(ierr); 928 ierr = ISGetIndices(idIS, &ids);CHKERRQ(ierr); 929 930 user->numSplitFaces = 0; 931 for (fs = 0; fs < numFS; ++fs) { 932 PetscInt numBdFaces; 933 934 ierr = DMGetStratumSize(dm, labelName, ids[fs], &numBdFaces);CHKERRQ(ierr); 935 user->numSplitFaces += numBdFaces; 936 } 937 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 938 pEnd += user->numSplitFaces; 939 ierr = DMPlexSetChart(sdm, pStart, pEnd);CHKERRQ(ierr); 940 ierr = DMPlexGetGhostCellStratum(dm, &cEndInterior, NULL);CHKERRQ(ierr); 941 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 942 numGhostCells = cEnd - cEndInterior; 943 /* Set cone and support sizes */ 944 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 945 for (d = 0; d <= depth; ++d) { 946 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 947 for (p = pStart; p < pEnd; ++p) { 948 PetscInt newp = p; 949 PetscInt size; 950 951 ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); 952 ierr = DMPlexSetConeSize(sdm, newp, size);CHKERRQ(ierr); 953 ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); 954 ierr = DMPlexSetSupportSize(sdm, newp, size);CHKERRQ(ierr); 955 } 956 } 957 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 958 for (fs = 0, newf = fEnd; fs < numFS; ++fs) { 959 IS faceIS; 960 const PetscInt *faces; 961 PetscInt numFaces, f; 962 963 ierr = DMGetStratumIS(dm, labelName, ids[fs], &faceIS);CHKERRQ(ierr); 964 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 965 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 966 for (f = 0; f < numFaces; ++f, ++newf) { 967 PetscInt size; 968 969 /* Right now I think that both faces should see both cells */ 970 ierr = DMPlexGetConeSize(dm, faces[f], &size);CHKERRQ(ierr); 971 ierr = DMPlexSetConeSize(sdm, newf, size);CHKERRQ(ierr); 972 ierr = DMPlexGetSupportSize(dm, faces[f], &size);CHKERRQ(ierr); 973 ierr = DMPlexSetSupportSize(sdm, newf, size);CHKERRQ(ierr); 974 } 975 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 976 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 977 } 978 ierr = DMSetUp(sdm);CHKERRQ(ierr); 979 /* Set cones and supports */ 980 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 981 ierr = PetscMalloc1(PetscMax(maxConeSize, maxSupportSize), &newpoints);CHKERRQ(ierr); 982 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 983 for (p = pStart; p < pEnd; ++p) { 984 const PetscInt *points, *orientations; 985 PetscInt size, i, newp = p; 986 987 ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); 988 ierr = DMPlexGetCone(dm, p, &points);CHKERRQ(ierr); 989 ierr = DMPlexGetConeOrientation(dm, p, &orientations);CHKERRQ(ierr); 990 for (i = 0; i < size; ++i) newpoints[i] = points[i]; 991 ierr = DMPlexSetCone(sdm, newp, newpoints);CHKERRQ(ierr); 992 ierr = DMPlexSetConeOrientation(sdm, newp, orientations);CHKERRQ(ierr); 993 ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); 994 ierr = DMPlexGetSupport(dm, p, &points);CHKERRQ(ierr); 995 for (i = 0; i < size; ++i) newpoints[i] = points[i]; 996 ierr = DMPlexSetSupport(sdm, newp, newpoints);CHKERRQ(ierr); 997 } 998 ierr = PetscFree(newpoints);CHKERRQ(ierr); 999 for (fs = 0, newf = fEnd; fs < numFS; ++fs) { 1000 IS faceIS; 1001 const PetscInt *faces; 1002 PetscInt numFaces, f; 1003 1004 ierr = DMGetStratumIS(dm, labelName, ids[fs], &faceIS);CHKERRQ(ierr); 1005 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 1006 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 1007 for (f = 0; f < numFaces; ++f, ++newf) { 1008 const PetscInt *points; 1009 1010 ierr = DMPlexGetCone(dm, faces[f], &points);CHKERRQ(ierr); 1011 ierr = DMPlexSetCone(sdm, newf, points);CHKERRQ(ierr); 1012 ierr = DMPlexGetSupport(dm, faces[f], &points);CHKERRQ(ierr); 1013 ierr = DMPlexSetSupport(sdm, newf, points);CHKERRQ(ierr); 1014 } 1015 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 1016 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 1017 } 1018 ierr = ISRestoreIndices(idIS, &ids);CHKERRQ(ierr); 1019 ierr = ISDestroy(&idIS);CHKERRQ(ierr); 1020 ierr = DMPlexStratify(sdm);CHKERRQ(ierr); 1021 /* Convert coordinates */ 1022 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1023 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1024 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &newCoordSection);CHKERRQ(ierr); 1025 ierr = PetscSectionSetNumFields(newCoordSection, 1);CHKERRQ(ierr); 1026 ierr = PetscSectionSetFieldComponents(newCoordSection, 0, dim);CHKERRQ(ierr); 1027 ierr = PetscSectionSetChart(newCoordSection, vStart, vEnd);CHKERRQ(ierr); 1028 for (v = vStart; v < vEnd; ++v) { 1029 ierr = PetscSectionSetDof(newCoordSection, v, dim);CHKERRQ(ierr); 1030 ierr = PetscSectionSetFieldDof(newCoordSection, v, 0, dim);CHKERRQ(ierr); 1031 } 1032 ierr = PetscSectionSetUp(newCoordSection);CHKERRQ(ierr); 1033 ierr = DMSetCoordinateSection(sdm, PETSC_DETERMINE, newCoordSection);CHKERRQ(ierr); 1034 ierr = PetscSectionDestroy(&newCoordSection);CHKERRQ(ierr); /* relinquish our reference */ 1035 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1036 ierr = DMSetCoordinatesLocal(sdm, coordinates);CHKERRQ(ierr); 1037 /* Convert labels */ 1038 ierr = DMGetNumLabels(dm, &numLabels);CHKERRQ(ierr); 1039 for (l = 0; l < numLabels; ++l) { 1040 const char *lname; 1041 PetscBool isDepth, isDim; 1042 1043 ierr = DMGetLabelName(dm, l, &lname);CHKERRQ(ierr); 1044 ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); 1045 if (isDepth) continue; 1046 ierr = PetscStrcmp(lname, "dim", &isDim);CHKERRQ(ierr); 1047 if (isDim) continue; 1048 ierr = DMCreateLabel(sdm, lname);CHKERRQ(ierr); 1049 ierr = DMGetLabelIdIS(dm, lname, &idIS);CHKERRQ(ierr); 1050 ierr = ISGetLocalSize(idIS, &numFS);CHKERRQ(ierr); 1051 ierr = ISGetIndices(idIS, &ids);CHKERRQ(ierr); 1052 for (fs = 0; fs < numFS; ++fs) { 1053 IS pointIS; 1054 const PetscInt *points; 1055 PetscInt numPoints; 1056 1057 ierr = DMGetStratumIS(dm, lname, ids[fs], &pointIS);CHKERRQ(ierr); 1058 ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr); 1059 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1060 for (p = 0; p < numPoints; ++p) { 1061 PetscInt newpoint = points[p]; 1062 1063 ierr = DMSetLabelValue(sdm, lname, newpoint, ids[fs]);CHKERRQ(ierr); 1064 } 1065 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1066 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1067 } 1068 ierr = ISRestoreIndices(idIS, &ids);CHKERRQ(ierr); 1069 ierr = ISDestroy(&idIS);CHKERRQ(ierr); 1070 } 1071 { 1072 /* Convert pointSF */ 1073 const PetscSFNode *remotePoints; 1074 PetscSFNode *gremotePoints; 1075 const PetscInt *localPoints; 1076 PetscInt *glocalPoints,*newLocation,*newRemoteLocation; 1077 PetscInt numRoots, numLeaves; 1078 PetscMPIInt size; 1079 1080 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size);CHKERRQ(ierr); 1081 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 1082 ierr = DMGetPointSF(sdm, &gsfPoint);CHKERRQ(ierr); 1083 ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); 1084 ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); 1085 if (numRoots >= 0) { 1086 ierr = PetscMalloc2(numRoots,&newLocation,pEnd-pStart,&newRemoteLocation);CHKERRQ(ierr); 1087 for (l=0; l<numRoots; l++) newLocation[l] = l; /* + (l >= cEnd ? numGhostCells : 0); */ 1088 ierr = PetscSFBcastBegin(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 1089 ierr = PetscSFBcastEnd(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 1090 ierr = PetscMalloc1(numLeaves, &glocalPoints);CHKERRQ(ierr); 1091 ierr = PetscMalloc1(numLeaves, &gremotePoints);CHKERRQ(ierr); 1092 for (l = 0; l < numLeaves; ++l) { 1093 glocalPoints[l] = localPoints[l]; /* localPoints[l] >= cEnd ? localPoints[l] + numGhostCells : localPoints[l]; */ 1094 gremotePoints[l].rank = remotePoints[l].rank; 1095 gremotePoints[l].index = newRemoteLocation[localPoints[l]]; 1096 } 1097 ierr = PetscFree2(newLocation,newRemoteLocation);CHKERRQ(ierr); 1098 ierr = PetscSFSetGraph(gsfPoint, numRoots+numGhostCells, numLeaves, glocalPoints, PETSC_OWN_POINTER, gremotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 1099 } 1100 ierr = DMDestroy(dmSplit);CHKERRQ(ierr); 1101 *dmSplit = sdm; 1102 } 1103 PetscFunctionReturn(0); 1104 } 1105 1106 PetscErrorCode CreatePartitionVec(DM dm, DM *dmCell, Vec *partition) 1107 { 1108 PetscSF sfPoint; 1109 PetscSection coordSection; 1110 Vec coordinates; 1111 PetscSection sectionCell; 1112 PetscScalar *part; 1113 PetscInt cStart, cEnd, c; 1114 PetscMPIInt rank; 1115 PetscErrorCode ierr; 1116 1117 PetscFunctionBeginUser; 1118 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1119 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1120 ierr = DMClone(dm, dmCell);CHKERRQ(ierr); 1121 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 1122 ierr = DMSetPointSF(*dmCell, sfPoint);CHKERRQ(ierr); 1123 ierr = DMSetCoordinateSection(*dmCell, PETSC_DETERMINE, coordSection);CHKERRQ(ierr); 1124 ierr = DMSetCoordinatesLocal(*dmCell, coordinates);CHKERRQ(ierr); 1125 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 1126 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ionCell);CHKERRQ(ierr); 1127 ierr = DMPlexGetHeightStratum(*dmCell, 0, &cStart, &cEnd);CHKERRQ(ierr); 1128 ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr); 1129 for (c = cStart; c < cEnd; ++c) { 1130 ierr = PetscSectionSetDof(sectionCell, c, 1);CHKERRQ(ierr); 1131 } 1132 ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr); 1133 ierr = DMSetLocalSection(*dmCell, sectionCell);CHKERRQ(ierr); 1134 ierr = PetscSectionDestroy(§ionCell);CHKERRQ(ierr); 1135 ierr = DMCreateLocalVector(*dmCell, partition);CHKERRQ(ierr); 1136 ierr = PetscObjectSetName((PetscObject)*partition, "partition");CHKERRQ(ierr); 1137 ierr = VecGetArray(*partition, &part);CHKERRQ(ierr); 1138 for (c = cStart; c < cEnd; ++c) { 1139 PetscScalar *p; 1140 1141 ierr = DMPlexPointLocalRef(*dmCell, c, part, &p);CHKERRQ(ierr); 1142 p[0] = rank; 1143 } 1144 ierr = VecRestoreArray(*partition, &part);CHKERRQ(ierr); 1145 PetscFunctionReturn(0); 1146 } 1147 1148 PetscErrorCode CreateMassMatrix(DM dm, Vec *massMatrix, User user) 1149 { 1150 DM plex, dmMass, dmFace, dmCell, dmCoord; 1151 PetscSection coordSection; 1152 Vec coordinates, facegeom, cellgeom; 1153 PetscSection sectionMass; 1154 PetscScalar *m; 1155 const PetscScalar *fgeom, *cgeom, *coords; 1156 PetscInt vStart, vEnd, v; 1157 PetscErrorCode ierr; 1158 1159 PetscFunctionBeginUser; 1160 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1161 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1162 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1163 ierr = DMClone(dm, &dmMass);CHKERRQ(ierr); 1164 ierr = DMSetCoordinateSection(dmMass, PETSC_DETERMINE, coordSection);CHKERRQ(ierr); 1165 ierr = DMSetCoordinatesLocal(dmMass, coordinates);CHKERRQ(ierr); 1166 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ionMass);CHKERRQ(ierr); 1167 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1168 ierr = PetscSectionSetChart(sectionMass, vStart, vEnd);CHKERRQ(ierr); 1169 for (v = vStart; v < vEnd; ++v) { 1170 PetscInt numFaces; 1171 1172 ierr = DMPlexGetSupportSize(dmMass, v, &numFaces);CHKERRQ(ierr); 1173 ierr = PetscSectionSetDof(sectionMass, v, numFaces*numFaces);CHKERRQ(ierr); 1174 } 1175 ierr = PetscSectionSetUp(sectionMass);CHKERRQ(ierr); 1176 ierr = DMSetLocalSection(dmMass, sectionMass);CHKERRQ(ierr); 1177 ierr = PetscSectionDestroy(§ionMass);CHKERRQ(ierr); 1178 ierr = DMGetLocalVector(dmMass, massMatrix);CHKERRQ(ierr); 1179 ierr = VecGetArray(*massMatrix, &m);CHKERRQ(ierr); 1180 ierr = DMPlexGetGeometryFVM(plex, &facegeom, &cellgeom, NULL);CHKERRQ(ierr); 1181 ierr = VecGetDM(facegeom, &dmFace);CHKERRQ(ierr); 1182 ierr = VecGetArrayRead(facegeom, &fgeom);CHKERRQ(ierr); 1183 ierr = VecGetDM(cellgeom, &dmCell);CHKERRQ(ierr); 1184 ierr = VecGetArrayRead(cellgeom, &cgeom);CHKERRQ(ierr); 1185 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 1186 ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr); 1187 for (v = vStart; v < vEnd; ++v) { 1188 const PetscInt *faces; 1189 PetscFVFaceGeom *fgA, *fgB, *cg; 1190 PetscScalar *vertex; 1191 PetscInt numFaces, sides[2], f, g; 1192 1193 ierr = DMPlexPointLocalRead(dmCoord, v, coords, &vertex);CHKERRQ(ierr); 1194 ierr = DMPlexGetSupportSize(dmMass, v, &numFaces);CHKERRQ(ierr); 1195 ierr = DMPlexGetSupport(dmMass, v, &faces);CHKERRQ(ierr); 1196 for (f = 0; f < numFaces; ++f) { 1197 sides[0] = faces[f]; 1198 ierr = DMPlexPointLocalRead(dmFace, faces[f], fgeom, &fgA);CHKERRQ(ierr); 1199 for (g = 0; g < numFaces; ++g) { 1200 const PetscInt *cells = NULL; 1201 PetscReal area = 0.0; 1202 PetscInt numCells; 1203 1204 sides[1] = faces[g]; 1205 ierr = DMPlexPointLocalRead(dmFace, faces[g], fgeom, &fgB);CHKERRQ(ierr); 1206 ierr = DMPlexGetJoin(dmMass, 2, sides, &numCells, &cells);CHKERRQ(ierr); 1207 if (numCells != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Invalid join for faces"); 1208 ierr = DMPlexPointLocalRead(dmCell, cells[0], cgeom, &cg);CHKERRQ(ierr); 1209 area += PetscAbsScalar((vertex[0] - cg->centroid[0])*(fgA->centroid[1] - cg->centroid[1]) - (vertex[1] - cg->centroid[1])*(fgA->centroid[0] - cg->centroid[0])); 1210 area += PetscAbsScalar((vertex[0] - cg->centroid[0])*(fgB->centroid[1] - cg->centroid[1]) - (vertex[1] - cg->centroid[1])*(fgB->centroid[0] - cg->centroid[0])); 1211 m[f*numFaces+g] = Dot2Real(fgA->normal, fgB->normal)*area*0.5; 1212 ierr = DMPlexRestoreJoin(dmMass, 2, sides, &numCells, &cells);CHKERRQ(ierr); 1213 } 1214 } 1215 } 1216 ierr = VecRestoreArrayRead(facegeom, &fgeom);CHKERRQ(ierr); 1217 ierr = VecRestoreArrayRead(cellgeom, &cgeom);CHKERRQ(ierr); 1218 ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr); 1219 ierr = VecRestoreArray(*massMatrix, &m);CHKERRQ(ierr); 1220 ierr = DMDestroy(&dmMass);CHKERRQ(ierr); 1221 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1222 PetscFunctionReturn(0); 1223 } 1224 1225 /* Behavior will be different for multi-physics or when using non-default boundary conditions */ 1226 static PetscErrorCode ModelSolutionSetDefault(Model mod,SolutionFunction func,void *ctx) 1227 { 1228 PetscFunctionBeginUser; 1229 mod->solution = func; 1230 mod->solutionctx = ctx; 1231 PetscFunctionReturn(0); 1232 } 1233 1234 static PetscErrorCode ModelFunctionalRegister(Model mod,const char *name,PetscInt *offset,FunctionalFunction func,void *ctx) 1235 { 1236 PetscErrorCode ierr; 1237 FunctionalLink link,*ptr; 1238 PetscInt lastoffset = -1; 1239 1240 PetscFunctionBeginUser; 1241 for (ptr=&mod->functionalRegistry; *ptr; ptr = &(*ptr)->next) lastoffset = (*ptr)->offset; 1242 ierr = PetscNew(&link);CHKERRQ(ierr); 1243 ierr = PetscStrallocpy(name,&link->name);CHKERRQ(ierr); 1244 link->offset = lastoffset + 1; 1245 link->func = func; 1246 link->ctx = ctx; 1247 link->next = NULL; 1248 *ptr = link; 1249 *offset = link->offset; 1250 PetscFunctionReturn(0); 1251 } 1252 1253 static PetscErrorCode ModelFunctionalSetFromOptions(Model mod,PetscOptionItems *PetscOptionsObject) 1254 { 1255 PetscErrorCode ierr; 1256 PetscInt i,j; 1257 FunctionalLink link; 1258 char *names[256]; 1259 1260 PetscFunctionBeginUser; 1261 mod->numMonitored = ALEN(names); 1262 ierr = PetscOptionsStringArray("-monitor","list of functionals to monitor","",names,&mod->numMonitored,NULL);CHKERRQ(ierr); 1263 /* Create list of functionals that will be computed somehow */ 1264 ierr = PetscMalloc1(mod->numMonitored,&mod->functionalMonitored);CHKERRQ(ierr); 1265 /* Create index of calls that we will have to make to compute these functionals (over-allocation in general). */ 1266 ierr = PetscMalloc1(mod->numMonitored,&mod->functionalCall);CHKERRQ(ierr); 1267 mod->numCall = 0; 1268 for (i=0; i<mod->numMonitored; i++) { 1269 for (link=mod->functionalRegistry; link; link=link->next) { 1270 PetscBool match; 1271 ierr = PetscStrcasecmp(names[i],link->name,&match);CHKERRQ(ierr); 1272 if (match) break; 1273 } 1274 if (!link) SETERRQ1(mod->comm,PETSC_ERR_USER,"No known functional '%s'",names[i]); 1275 mod->functionalMonitored[i] = link; 1276 for (j=0; j<i; j++) { 1277 if (mod->functionalCall[j]->func == link->func && mod->functionalCall[j]->ctx == link->ctx) goto next_name; 1278 } 1279 mod->functionalCall[mod->numCall++] = link; /* Just points to the first link using the result. There may be more results. */ 1280 next_name: 1281 ierr = PetscFree(names[i]);CHKERRQ(ierr); 1282 } 1283 1284 /* Find out the maximum index of any functional computed by a function we will be calling (even if we are not using it) */ 1285 mod->maxComputed = -1; 1286 for (link=mod->functionalRegistry; link; link=link->next) { 1287 for (i=0; i<mod->numCall; i++) { 1288 FunctionalLink call = mod->functionalCall[i]; 1289 if (link->func == call->func && link->ctx == call->ctx) { 1290 mod->maxComputed = PetscMax(mod->maxComputed,link->offset); 1291 } 1292 } 1293 } 1294 PetscFunctionReturn(0); 1295 } 1296 1297 static PetscErrorCode FunctionalLinkDestroy(FunctionalLink *link) 1298 { 1299 PetscErrorCode ierr; 1300 FunctionalLink l,next; 1301 1302 PetscFunctionBeginUser; 1303 if (!link) PetscFunctionReturn(0); 1304 l = *link; 1305 *link = NULL; 1306 for (; l; l=next) { 1307 next = l->next; 1308 ierr = PetscFree(l->name);CHKERRQ(ierr); 1309 ierr = PetscFree(l);CHKERRQ(ierr); 1310 } 1311 PetscFunctionReturn(0); 1312 } 1313 1314 /* put the solution callback into a functional callback */ 1315 static PetscErrorCode SolutionFunctional(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *modctx) 1316 { 1317 Model mod; 1318 PetscErrorCode ierr; 1319 PetscFunctionBegin; 1320 mod = (Model) modctx; 1321 ierr = (*mod->solution)(mod, time, x, u, mod->solutionctx);CHKERRQ(ierr); 1322 PetscFunctionReturn(0); 1323 } 1324 1325 PetscErrorCode SetInitialCondition(DM dm, Vec X, User user) 1326 { 1327 PetscErrorCode (*func[1]) (PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx); 1328 void *ctx[1]; 1329 Model mod = user->model; 1330 PetscErrorCode ierr; 1331 1332 PetscFunctionBeginUser; 1333 func[0] = SolutionFunctional; 1334 ctx[0] = (void *) mod; 1335 ierr = DMProjectFunction(dm,0.0,func,ctx,INSERT_ALL_VALUES,X);CHKERRQ(ierr); 1336 PetscFunctionReturn(0); 1337 } 1338 1339 static PetscErrorCode OutputVTK(DM dm, const char *filename, PetscViewer *viewer) 1340 { 1341 PetscErrorCode ierr; 1342 1343 PetscFunctionBeginUser; 1344 ierr = PetscViewerCreate(PetscObjectComm((PetscObject)dm), viewer);CHKERRQ(ierr); 1345 ierr = PetscViewerSetType(*viewer, PETSCVIEWERVTK);CHKERRQ(ierr); 1346 ierr = PetscViewerFileSetName(*viewer, filename);CHKERRQ(ierr); 1347 PetscFunctionReturn(0); 1348 } 1349 1350 static PetscErrorCode MonitorVTK(TS ts,PetscInt stepnum,PetscReal time,Vec X,void *ctx) 1351 { 1352 User user = (User)ctx; 1353 DM dm, plex; 1354 PetscViewer viewer; 1355 char filename[PETSC_MAX_PATH_LEN],*ftable = NULL; 1356 PetscReal xnorm; 1357 PetscErrorCode ierr; 1358 1359 PetscFunctionBeginUser; 1360 ierr = PetscObjectSetName((PetscObject) X, "u");CHKERRQ(ierr); 1361 ierr = VecGetDM(X,&dm);CHKERRQ(ierr); 1362 ierr = VecNorm(X,NORM_INFINITY,&xnorm);CHKERRQ(ierr); 1363 1364 if (stepnum >= 0) { 1365 stepnum += user->monitorStepOffset; 1366 } 1367 if (stepnum >= 0) { /* No summary for final time */ 1368 Model mod = user->model; 1369 Vec cellgeom; 1370 PetscInt c,cStart,cEnd,fcount,i; 1371 size_t ftableused,ftablealloc; 1372 const PetscScalar *cgeom,*x; 1373 DM dmCell; 1374 DMLabel vtkLabel; 1375 PetscReal *fmin,*fmax,*fintegral,*ftmp; 1376 1377 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1378 ierr = DMPlexGetGeometryFVM(plex, NULL, &cellgeom, NULL);CHKERRQ(ierr); 1379 fcount = mod->maxComputed+1; 1380 ierr = PetscMalloc4(fcount,&fmin,fcount,&fmax,fcount,&fintegral,fcount,&ftmp);CHKERRQ(ierr); 1381 for (i=0; i<fcount; i++) { 1382 fmin[i] = PETSC_MAX_REAL; 1383 fmax[i] = PETSC_MIN_REAL; 1384 fintegral[i] = 0; 1385 } 1386 ierr = VecGetDM(cellgeom,&dmCell);CHKERRQ(ierr); 1387 ierr = DMPlexGetSimplexOrBoxCells(dmCell,0,&cStart,&cEnd);CHKERRQ(ierr); 1388 ierr = VecGetArrayRead(cellgeom,&cgeom);CHKERRQ(ierr); 1389 ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr); 1390 ierr = DMGetLabel(dm,"vtk",&vtkLabel);CHKERRQ(ierr); 1391 for (c = cStart; c < cEnd; ++c) { 1392 PetscFVCellGeom *cg; 1393 const PetscScalar *cx = NULL; 1394 PetscInt vtkVal = 0; 1395 1396 /* not that these two routines as currently implemented work for any dm with a 1397 * localSection/globalSection */ 1398 ierr = DMPlexPointLocalRead(dmCell,c,cgeom,&cg);CHKERRQ(ierr); 1399 ierr = DMPlexPointGlobalRead(dm,c,x,&cx);CHKERRQ(ierr); 1400 if (vtkLabel) {ierr = DMLabelGetValue(vtkLabel,c,&vtkVal);CHKERRQ(ierr);} 1401 if (!vtkVal || !cx) continue; /* ghost, or not a global cell */ 1402 for (i=0; i<mod->numCall; i++) { 1403 FunctionalLink flink = mod->functionalCall[i]; 1404 ierr = (*flink->func)(mod,time,cg->centroid,cx,ftmp,flink->ctx);CHKERRQ(ierr); 1405 } 1406 for (i=0; i<fcount; i++) { 1407 fmin[i] = PetscMin(fmin[i],ftmp[i]); 1408 fmax[i] = PetscMax(fmax[i],ftmp[i]); 1409 fintegral[i] += cg->volume * ftmp[i]; 1410 } 1411 } 1412 ierr = VecRestoreArrayRead(cellgeom,&cgeom);CHKERRQ(ierr); 1413 ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr); 1414 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1415 ierr = MPI_Allreduce(MPI_IN_PLACE,fmin,fcount,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr); 1416 ierr = MPI_Allreduce(MPI_IN_PLACE,fmax,fcount,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr); 1417 ierr = MPI_Allreduce(MPI_IN_PLACE,fintegral,fcount,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr); 1418 1419 ftablealloc = fcount * 100; 1420 ftableused = 0; 1421 ierr = PetscMalloc1(ftablealloc,&ftable);CHKERRQ(ierr); 1422 for (i=0; i<mod->numMonitored; i++) { 1423 size_t countused; 1424 char buffer[256],*p; 1425 FunctionalLink flink = mod->functionalMonitored[i]; 1426 PetscInt id = flink->offset; 1427 if (i % 3) { 1428 ierr = PetscArraycpy(buffer," ",2);CHKERRQ(ierr); 1429 p = buffer + 2; 1430 } else if (i) { 1431 char newline[] = "\n"; 1432 ierr = PetscMemcpy(buffer,newline,sizeof(newline)-1);CHKERRQ(ierr); 1433 p = buffer + sizeof(newline) - 1; 1434 } else { 1435 p = buffer; 1436 } 1437 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); 1438 countused--; 1439 countused += p - buffer; 1440 if (countused > ftablealloc-ftableused-1) { /* reallocate */ 1441 char *ftablenew; 1442 ftablealloc = 2*ftablealloc + countused; 1443 ierr = PetscMalloc(ftablealloc,&ftablenew);CHKERRQ(ierr); 1444 ierr = PetscArraycpy(ftablenew,ftable,ftableused);CHKERRQ(ierr); 1445 ierr = PetscFree(ftable);CHKERRQ(ierr); 1446 ftable = ftablenew; 1447 } 1448 ierr = PetscArraycpy(ftable+ftableused,buffer,countused);CHKERRQ(ierr); 1449 ftableused += countused; 1450 ftable[ftableused] = 0; 1451 } 1452 ierr = PetscFree4(fmin,fmax,fintegral,ftmp);CHKERRQ(ierr); 1453 1454 ierr = PetscPrintf(PetscObjectComm((PetscObject)ts),"% 3D time %8.4g |x| %8.4g %s\n",stepnum,(double)time,(double)xnorm,ftable ? ftable : "");CHKERRQ(ierr); 1455 ierr = PetscFree(ftable);CHKERRQ(ierr); 1456 } 1457 if (user->vtkInterval < 1) PetscFunctionReturn(0); 1458 if ((stepnum == -1) ^ (stepnum % user->vtkInterval == 0)) { 1459 if (stepnum == -1) { /* Final time is not multiple of normal time interval, write it anyway */ 1460 ierr = TSGetStepNumber(ts,&stepnum);CHKERRQ(ierr); 1461 } 1462 ierr = PetscSNPrintf(filename,sizeof filename,"%s-%03D.vtu",user->outputBasename,stepnum);CHKERRQ(ierr); 1463 ierr = OutputVTK(dm,filename,&viewer);CHKERRQ(ierr); 1464 ierr = VecView(X,viewer);CHKERRQ(ierr); 1465 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1466 } 1467 PetscFunctionReturn(0); 1468 } 1469 1470 static PetscErrorCode initializeTS(DM dm, User user, TS *ts) 1471 { 1472 PetscErrorCode ierr; 1473 1474 PetscFunctionBegin; 1475 ierr = TSCreate(PetscObjectComm((PetscObject)dm), ts);CHKERRQ(ierr); 1476 ierr = TSSetType(*ts, TSSSP);CHKERRQ(ierr); 1477 ierr = TSSetDM(*ts, dm);CHKERRQ(ierr); 1478 if (user->vtkmon) { 1479 ierr = TSMonitorSet(*ts,MonitorVTK,user,NULL);CHKERRQ(ierr); 1480 } 1481 ierr = DMTSSetBoundaryLocal(dm, DMPlexTSComputeBoundary, user);CHKERRQ(ierr); 1482 ierr = DMTSSetRHSFunctionLocal(dm, DMPlexTSComputeRHSFunctionFVM, user);CHKERRQ(ierr); 1483 ierr = TSSetMaxTime(*ts,2.0);CHKERRQ(ierr); 1484 ierr = TSSetExactFinalTime(*ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); 1485 PetscFunctionReturn(0); 1486 } 1487 1488 static PetscErrorCode adaptToleranceFVM(PetscFV fvm, TS ts, Vec sol, VecTagger refineTag, VecTagger coarsenTag, User user, TS *tsNew, Vec *solNew) 1489 { 1490 DM dm, gradDM, plex, cellDM, adaptedDM = NULL; 1491 Vec cellGeom, faceGeom; 1492 PetscBool isForest, computeGradient; 1493 Vec grad, locGrad, locX, errVec; 1494 PetscInt cStart, cEnd, c, dim, nRefine, nCoarsen; 1495 PetscReal minMaxInd[2] = {PETSC_MAX_REAL, PETSC_MIN_REAL}, minMaxIndGlobal[2], minInd, maxInd, time; 1496 PetscScalar *errArray; 1497 const PetscScalar *pointVals; 1498 const PetscScalar *pointGrads; 1499 const PetscScalar *pointGeom; 1500 DMLabel adaptLabel = NULL; 1501 IS refineIS, coarsenIS; 1502 PetscErrorCode ierr; 1503 1504 PetscFunctionBegin; 1505 ierr = TSGetTime(ts,&time);CHKERRQ(ierr); 1506 ierr = VecGetDM(sol, &dm);CHKERRQ(ierr); 1507 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 1508 ierr = PetscFVGetComputeGradients(fvm,&computeGradient);CHKERRQ(ierr); 1509 ierr = PetscFVSetComputeGradients(fvm,PETSC_TRUE);CHKERRQ(ierr); 1510 ierr = DMIsForest(dm, &isForest);CHKERRQ(ierr); 1511 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1512 ierr = DMPlexGetDataFVM(plex, fvm, &cellGeom, &faceGeom, &gradDM);CHKERRQ(ierr); 1513 ierr = DMCreateLocalVector(plex,&locX);CHKERRQ(ierr); 1514 ierr = DMPlexInsertBoundaryValues(plex, PETSC_TRUE, locX, 0.0, faceGeom, cellGeom, NULL);CHKERRQ(ierr); 1515 ierr = DMGlobalToLocalBegin(plex, sol, INSERT_VALUES, locX);CHKERRQ(ierr); 1516 ierr = DMGlobalToLocalEnd (plex, sol, INSERT_VALUES, locX);CHKERRQ(ierr); 1517 ierr = DMCreateGlobalVector(gradDM, &grad);CHKERRQ(ierr); 1518 ierr = DMPlexReconstructGradientsFVM(plex, locX, grad);CHKERRQ(ierr); 1519 ierr = DMCreateLocalVector(gradDM, &locGrad);CHKERRQ(ierr); 1520 ierr = DMGlobalToLocalBegin(gradDM, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1521 ierr = DMGlobalToLocalEnd(gradDM, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1522 ierr = VecDestroy(&grad);CHKERRQ(ierr); 1523 ierr = DMPlexGetSimplexOrBoxCells(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1524 ierr = VecGetArrayRead(locGrad,&pointGrads);CHKERRQ(ierr); 1525 ierr = VecGetArrayRead(cellGeom,&pointGeom);CHKERRQ(ierr); 1526 ierr = VecGetArrayRead(locX,&pointVals);CHKERRQ(ierr); 1527 ierr = VecGetDM(cellGeom,&cellDM);CHKERRQ(ierr); 1528 ierr = DMLabelCreate(PETSC_COMM_SELF,"adapt",&adaptLabel);CHKERRQ(ierr); 1529 ierr = VecCreateMPI(PetscObjectComm((PetscObject)plex),cEnd-cStart,PETSC_DETERMINE,&errVec);CHKERRQ(ierr); 1530 ierr = VecSetUp(errVec);CHKERRQ(ierr); 1531 ierr = VecGetArray(errVec,&errArray);CHKERRQ(ierr); 1532 for (c = cStart; c < cEnd; c++) { 1533 PetscReal errInd = 0.; 1534 PetscScalar *pointGrad; 1535 PetscScalar *pointVal; 1536 PetscFVCellGeom *cg; 1537 1538 ierr = DMPlexPointLocalRead(gradDM,c,pointGrads,&pointGrad);CHKERRQ(ierr); 1539 ierr = DMPlexPointLocalRead(cellDM,c,pointGeom,&cg);CHKERRQ(ierr); 1540 ierr = DMPlexPointLocalRead(plex,c,pointVals,&pointVal);CHKERRQ(ierr); 1541 1542 ierr = (user->model->errorIndicator)(dim,cg->volume,user->model->physics->dof,pointVal,pointGrad,&errInd,user->model->errorCtx);CHKERRQ(ierr); 1543 errArray[c-cStart] = errInd; 1544 minMaxInd[0] = PetscMin(minMaxInd[0],errInd); 1545 minMaxInd[1] = PetscMax(minMaxInd[1],errInd); 1546 } 1547 ierr = VecRestoreArray(errVec,&errArray);CHKERRQ(ierr); 1548 ierr = VecRestoreArrayRead(locX,&pointVals);CHKERRQ(ierr); 1549 ierr = VecRestoreArrayRead(cellGeom,&pointGeom);CHKERRQ(ierr); 1550 ierr = VecRestoreArrayRead(locGrad,&pointGrads);CHKERRQ(ierr); 1551 ierr = VecDestroy(&locGrad);CHKERRQ(ierr); 1552 ierr = VecDestroy(&locX);CHKERRQ(ierr); 1553 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1554 1555 ierr = VecTaggerComputeIS(refineTag,errVec,&refineIS);CHKERRQ(ierr); 1556 ierr = VecTaggerComputeIS(coarsenTag,errVec,&coarsenIS);CHKERRQ(ierr); 1557 ierr = ISGetSize(refineIS,&nRefine);CHKERRQ(ierr); 1558 ierr = ISGetSize(coarsenIS,&nCoarsen);CHKERRQ(ierr); 1559 if (nRefine) {ierr = DMLabelSetStratumIS(adaptLabel,DM_ADAPT_REFINE,refineIS);CHKERRQ(ierr);} 1560 if (nCoarsen) {ierr = DMLabelSetStratumIS(adaptLabel,DM_ADAPT_COARSEN,coarsenIS);CHKERRQ(ierr);} 1561 ierr = ISDestroy(&coarsenIS);CHKERRQ(ierr); 1562 ierr = ISDestroy(&refineIS);CHKERRQ(ierr); 1563 ierr = VecDestroy(&errVec);CHKERRQ(ierr); 1564 1565 ierr = PetscFVSetComputeGradients(fvm,computeGradient);CHKERRQ(ierr); 1566 minMaxInd[1] = -minMaxInd[1]; 1567 ierr = MPI_Allreduce(minMaxInd,minMaxIndGlobal,2,MPIU_REAL,MPI_MIN,PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 1568 minInd = minMaxIndGlobal[0]; 1569 maxInd = -minMaxIndGlobal[1]; 1570 ierr = PetscInfo2(ts, "error indicator range (%E, %E)\n", minInd, maxInd);CHKERRQ(ierr); 1571 if (nRefine || nCoarsen) { /* at least one cell is over the refinement threshold */ 1572 ierr = DMAdaptLabel(dm,adaptLabel,&adaptedDM);CHKERRQ(ierr); 1573 } 1574 ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr); 1575 if (adaptedDM) { 1576 ierr = PetscInfo2(ts, "Adapted mesh, marking %D cells for refinement, and %D cells for coarsening\n", nRefine, nCoarsen);CHKERRQ(ierr); 1577 if (tsNew) {ierr = initializeTS(adaptedDM, user, tsNew);CHKERRQ(ierr);} 1578 if (solNew) { 1579 ierr = DMCreateGlobalVector(adaptedDM, solNew);CHKERRQ(ierr); 1580 ierr = PetscObjectSetName((PetscObject) *solNew, "solution");CHKERRQ(ierr); 1581 ierr = DMForestTransferVec(dm, sol, adaptedDM, *solNew, PETSC_TRUE, time);CHKERRQ(ierr); 1582 } 1583 if (isForest) {ierr = DMForestSetAdaptivityForest(adaptedDM,NULL);CHKERRQ(ierr);} /* clear internal references to the previous dm */ 1584 ierr = DMDestroy(&adaptedDM);CHKERRQ(ierr); 1585 } else { 1586 if (tsNew) *tsNew = NULL; 1587 if (solNew) *solNew = NULL; 1588 } 1589 PetscFunctionReturn(0); 1590 } 1591 1592 int main(int argc, char **argv) 1593 { 1594 MPI_Comm comm; 1595 PetscDS prob; 1596 PetscFV fvm; 1597 PetscLimiter limiter = NULL, noneLimiter = NULL; 1598 User user; 1599 Model mod; 1600 Physics phys; 1601 DM dm, plex; 1602 PetscReal ftime, cfl, dt, minRadius; 1603 PetscInt dim, nsteps; 1604 TS ts; 1605 TSConvergedReason reason; 1606 Vec X; 1607 PetscViewer viewer; 1608 PetscBool simplex = PETSC_FALSE, vtkCellGeom, splitFaces, useAMR; 1609 PetscInt overlap, adaptInterval; 1610 char filename[PETSC_MAX_PATH_LEN] = ""; 1611 char physname[256] = "advect"; 1612 VecTagger refineTag = NULL, coarsenTag = NULL; 1613 PetscErrorCode ierr; 1614 1615 ierr = PetscInitialize(&argc, &argv, (char*) 0, help);if (ierr) return ierr; 1616 comm = PETSC_COMM_WORLD; 1617 1618 ierr = PetscNew(&user);CHKERRQ(ierr); 1619 ierr = PetscNew(&user->model);CHKERRQ(ierr); 1620 ierr = PetscNew(&user->model->physics);CHKERRQ(ierr); 1621 mod = user->model; 1622 phys = mod->physics; 1623 mod->comm = comm; 1624 useAMR = PETSC_FALSE; 1625 adaptInterval = 1; 1626 1627 /* Register physical models to be available on the command line */ 1628 ierr = PetscFunctionListAdd(&PhysicsList,"advect" ,PhysicsCreate_Advect);CHKERRQ(ierr); 1629 ierr = PetscFunctionListAdd(&PhysicsList,"sw" ,PhysicsCreate_SW);CHKERRQ(ierr); 1630 ierr = PetscFunctionListAdd(&PhysicsList,"euler" ,PhysicsCreate_Euler);CHKERRQ(ierr); 1631 1632 ierr = PetscOptionsBegin(comm,NULL,"Unstructured Finite Volume Mesh Options","");CHKERRQ(ierr); 1633 { 1634 cfl = 0.9 * 4; /* default SSPRKS2 with s=5 stages is stable for CFL number s-1 */ 1635 ierr = PetscOptionsReal("-ufv_cfl","CFL number per step","",cfl,&cfl,NULL);CHKERRQ(ierr); 1636 ierr = PetscOptionsString("-f","Exodus.II filename to read","",filename,filename,sizeof(filename),NULL);CHKERRQ(ierr); 1637 ierr = PetscOptionsBool("-simplex","Flag to use a simplex mesh","",simplex,&simplex,NULL);CHKERRQ(ierr); 1638 splitFaces = PETSC_FALSE; 1639 ierr = PetscOptionsBool("-ufv_split_faces","Split faces between cell sets","",splitFaces,&splitFaces,NULL);CHKERRQ(ierr); 1640 overlap = 1; 1641 ierr = PetscOptionsInt("-ufv_mesh_overlap","Number of cells to overlap partitions","",overlap,&overlap,NULL);CHKERRQ(ierr); 1642 user->vtkInterval = 1; 1643 ierr = PetscOptionsInt("-ufv_vtk_interval","VTK output interval (0 to disable)","",user->vtkInterval,&user->vtkInterval,NULL);CHKERRQ(ierr); 1644 user->vtkmon = PETSC_TRUE; 1645 ierr = PetscOptionsBool("-ufv_vtk_monitor","Use VTKMonitor routine","",user->vtkmon,&user->vtkmon,NULL);CHKERRQ(ierr); 1646 vtkCellGeom = PETSC_FALSE; 1647 ierr = PetscStrcpy(user->outputBasename, "ex11");CHKERRQ(ierr); 1648 ierr = PetscOptionsString("-ufv_vtk_basename","VTK output basename","",user->outputBasename,user->outputBasename,sizeof(user->outputBasename),NULL);CHKERRQ(ierr); 1649 ierr = PetscOptionsBool("-ufv_vtk_cellgeom","Write cell geometry (for debugging)","",vtkCellGeom,&vtkCellGeom,NULL);CHKERRQ(ierr); 1650 ierr = PetscOptionsBool("-ufv_use_amr","use local adaptive mesh refinement","",useAMR,&useAMR,NULL);CHKERRQ(ierr); 1651 ierr = PetscOptionsInt("-ufv_adapt_interval","time steps between AMR","",adaptInterval,&adaptInterval,NULL);CHKERRQ(ierr); 1652 } 1653 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1654 1655 if (useAMR) { 1656 VecTaggerBox refineBox, coarsenBox; 1657 1658 refineBox.min = refineBox.max = PETSC_MAX_REAL; 1659 coarsenBox.min = coarsenBox.max = PETSC_MIN_REAL; 1660 1661 ierr = VecTaggerCreate(comm,&refineTag);CHKERRQ(ierr); 1662 ierr = PetscObjectSetOptionsPrefix((PetscObject)refineTag,"refine_");CHKERRQ(ierr); 1663 ierr = VecTaggerSetType(refineTag,VECTAGGERABSOLUTE);CHKERRQ(ierr); 1664 ierr = VecTaggerAbsoluteSetBox(refineTag,&refineBox);CHKERRQ(ierr); 1665 ierr = VecTaggerSetFromOptions(refineTag);CHKERRQ(ierr); 1666 ierr = VecTaggerSetUp(refineTag);CHKERRQ(ierr); 1667 ierr = PetscObjectViewFromOptions((PetscObject)refineTag,NULL,"-tag_view");CHKERRQ(ierr); 1668 1669 ierr = VecTaggerCreate(comm,&coarsenTag);CHKERRQ(ierr); 1670 ierr = PetscObjectSetOptionsPrefix((PetscObject)coarsenTag,"coarsen_");CHKERRQ(ierr); 1671 ierr = VecTaggerSetType(coarsenTag,VECTAGGERABSOLUTE);CHKERRQ(ierr); 1672 ierr = VecTaggerAbsoluteSetBox(coarsenTag,&coarsenBox);CHKERRQ(ierr); 1673 ierr = VecTaggerSetFromOptions(coarsenTag);CHKERRQ(ierr); 1674 ierr = VecTaggerSetUp(coarsenTag);CHKERRQ(ierr); 1675 ierr = PetscObjectViewFromOptions((PetscObject)coarsenTag,NULL,"-tag_view");CHKERRQ(ierr); 1676 } 1677 1678 ierr = PetscOptionsBegin(comm,NULL,"Unstructured Finite Volume Physics Options","");CHKERRQ(ierr); 1679 { 1680 PetscErrorCode (*physcreate)(Model,Physics,PetscOptionItems*); 1681 ierr = PetscOptionsFList("-physics","Physics module to solve","",PhysicsList,physname,physname,sizeof physname,NULL);CHKERRQ(ierr); 1682 ierr = PetscFunctionListFind(PhysicsList,physname,&physcreate);CHKERRQ(ierr); 1683 ierr = PetscMemzero(phys,sizeof(struct _n_Physics));CHKERRQ(ierr); 1684 ierr = (*physcreate)(mod,phys,PetscOptionsObject);CHKERRQ(ierr); 1685 /* Count number of fields and dofs */ 1686 for (phys->nfields=0,phys->dof=0; phys->field_desc[phys->nfields].name; phys->nfields++) phys->dof += phys->field_desc[phys->nfields].dof; 1687 if (phys->dof <= 0) SETERRQ1(comm,PETSC_ERR_ARG_WRONGSTATE,"Physics '%s' did not set dof",physname); 1688 ierr = ModelFunctionalSetFromOptions(mod,PetscOptionsObject);CHKERRQ(ierr); 1689 } 1690 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1691 1692 /* Create mesh */ 1693 { 1694 size_t len,i; 1695 for (i = 0; i < DIM; i++) { mod->bounds[2*i] = 0.; mod->bounds[2*i+1] = 1.;}; 1696 ierr = PetscStrlen(filename,&len);CHKERRQ(ierr); 1697 dim = DIM; 1698 if (!len) { /* a null name means just do a hex box */ 1699 PetscInt cells[3] = {1, 1, 1}; /* coarse mesh is one cell; refine from there */ 1700 PetscBool flg1, flg2, skew = PETSC_FALSE; 1701 PetscInt nret1 = DIM; 1702 PetscInt nret2 = 2*DIM; 1703 ierr = PetscOptionsBegin(comm,NULL,"Rectangular mesh options","");CHKERRQ(ierr); 1704 ierr = PetscOptionsIntArray("-grid_size","number of cells in each direction","",cells,&nret1,&flg1);CHKERRQ(ierr); 1705 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); 1706 ierr = PetscOptionsBool("-grid_skew_60","Skew grid for 60 degree shock mesh","",skew,&skew,NULL);CHKERRQ(ierr); 1707 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1708 if (flg1) { 1709 dim = nret1; 1710 if (dim != DIM) SETERRQ1(comm,PETSC_ERR_ARG_SIZ,"Dim wrong size %D in -grid_size",dim); 1711 } 1712 ierr = DMPlexCreateBoxMesh(comm, dim, simplex, cells, NULL, NULL, mod->bcs, PETSC_TRUE, &dm);CHKERRQ(ierr); 1713 if (flg2) { 1714 PetscInt dimEmbed, i; 1715 PetscInt nCoords; 1716 PetscScalar *coords; 1717 Vec coordinates; 1718 1719 ierr = DMGetCoordinatesLocal(dm,&coordinates);CHKERRQ(ierr); 1720 ierr = DMGetCoordinateDim(dm,&dimEmbed);CHKERRQ(ierr); 1721 ierr = VecGetLocalSize(coordinates,&nCoords);CHKERRQ(ierr); 1722 if (nCoords % dimEmbed) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Coordinate vector the wrong size"); 1723 ierr = VecGetArray(coordinates,&coords);CHKERRQ(ierr); 1724 for (i = 0; i < nCoords; i += dimEmbed) { 1725 PetscInt j; 1726 1727 PetscScalar *coord = &coords[i]; 1728 for (j = 0; j < dimEmbed; j++) { 1729 coord[j] = mod->bounds[2 * j] + coord[j] * (mod->bounds[2 * j + 1] - mod->bounds[2 * j]); 1730 if (dim==2 && cells[1]==1 && j==0 && skew) { 1731 if (cells[0]==2 && i==8) { 1732 coord[j] = .57735026918963; /* hack to get 60 deg skewed mesh */ 1733 } 1734 else if (cells[0]==3) { 1735 if(i==2 || i==10) coord[j] = mod->bounds[1]/4.; 1736 else if (i==4) coord[j] = mod->bounds[1]/2.; 1737 else if (i==12) coord[j] = 1.57735026918963*mod->bounds[1]/2.; 1738 } 1739 } 1740 } 1741 } 1742 ierr = VecRestoreArray(coordinates,&coords);CHKERRQ(ierr); 1743 ierr = DMSetCoordinatesLocal(dm,coordinates);CHKERRQ(ierr); 1744 } 1745 } else { 1746 ierr = DMPlexCreateFromFile(comm, filename, PETSC_TRUE, &dm);CHKERRQ(ierr); 1747 } 1748 } 1749 ierr = DMViewFromOptions(dm, NULL, "-orig_dm_view");CHKERRQ(ierr); 1750 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1751 1752 /* set up BCs, functions, tags */ 1753 ierr = DMCreateLabel(dm, "Face Sets");CHKERRQ(ierr); 1754 1755 mod->errorIndicator = ErrorIndicator_Simple; 1756 1757 { 1758 DM dmDist; 1759 1760 ierr = DMSetBasicAdjacency(dm, PETSC_TRUE, PETSC_FALSE);CHKERRQ(ierr); 1761 ierr = DMPlexDistribute(dm, overlap, NULL, &dmDist);CHKERRQ(ierr); 1762 if (dmDist) { 1763 ierr = DMDestroy(&dm);CHKERRQ(ierr); 1764 dm = dmDist; 1765 } 1766 } 1767 1768 ierr = DMSetFromOptions(dm);CHKERRQ(ierr); 1769 1770 { 1771 DM gdm; 1772 1773 ierr = DMPlexConstructGhostCells(dm, NULL, NULL, &gdm);CHKERRQ(ierr); 1774 ierr = DMDestroy(&dm);CHKERRQ(ierr); 1775 dm = gdm; 1776 ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr); 1777 } 1778 if (splitFaces) {ierr = ConstructCellBoundary(dm, user);CHKERRQ(ierr);} 1779 ierr = SplitFaces(&dm, "split faces", user);CHKERRQ(ierr); 1780 1781 ierr = PetscFVCreate(comm, &fvm);CHKERRQ(ierr); 1782 ierr = PetscFVSetFromOptions(fvm);CHKERRQ(ierr); 1783 ierr = PetscFVSetNumComponents(fvm, phys->dof);CHKERRQ(ierr); 1784 ierr = PetscFVSetSpatialDimension(fvm, dim);CHKERRQ(ierr); 1785 ierr = PetscObjectSetName((PetscObject) fvm,"");CHKERRQ(ierr); 1786 { 1787 PetscInt f, dof; 1788 for (f=0,dof=0; f < phys->nfields; f++) { 1789 PetscInt newDof = phys->field_desc[f].dof; 1790 1791 if (newDof == 1) { 1792 ierr = PetscFVSetComponentName(fvm,dof,phys->field_desc[f].name);CHKERRQ(ierr); 1793 } 1794 else { 1795 PetscInt j; 1796 1797 for (j = 0; j < newDof; j++) { 1798 char compName[256] = "Unknown"; 1799 1800 ierr = PetscSNPrintf(compName,sizeof(compName),"%s_%d",phys->field_desc[f].name,j);CHKERRQ(ierr); 1801 ierr = PetscFVSetComponentName(fvm,dof+j,compName);CHKERRQ(ierr); 1802 } 1803 } 1804 dof += newDof; 1805 } 1806 } 1807 /* FV is now structured with one field having all physics as components */ 1808 ierr = DMAddField(dm, NULL, (PetscObject) fvm);CHKERRQ(ierr); 1809 ierr = DMCreateDS(dm);CHKERRQ(ierr); 1810 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1811 ierr = PetscDSSetRiemannSolver(prob, 0, user->model->physics->riemann);CHKERRQ(ierr); 1812 ierr = PetscDSSetContext(prob, 0, user->model->physics);CHKERRQ(ierr); 1813 ierr = (*mod->setupbc)(prob,phys);CHKERRQ(ierr); 1814 ierr = PetscDSSetFromOptions(prob);CHKERRQ(ierr); 1815 { 1816 char convType[256]; 1817 PetscBool flg; 1818 1819 ierr = PetscOptionsBegin(comm, "", "Mesh conversion options", "DMPLEX");CHKERRQ(ierr); 1820 ierr = PetscOptionsFList("-dm_type","Convert DMPlex to another format","ex12",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr); 1821 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1822 if (flg) { 1823 DM dmConv; 1824 1825 ierr = DMConvert(dm,convType,&dmConv);CHKERRQ(ierr); 1826 if (dmConv) { 1827 ierr = DMViewFromOptions(dmConv, NULL, "-dm_conv_view");CHKERRQ(ierr); 1828 ierr = DMDestroy(&dm);CHKERRQ(ierr); 1829 dm = dmConv; 1830 ierr = DMSetFromOptions(dm);CHKERRQ(ierr); 1831 } 1832 } 1833 } 1834 1835 ierr = initializeTS(dm, user, &ts);CHKERRQ(ierr); 1836 1837 ierr = DMCreateGlobalVector(dm, &X);CHKERRQ(ierr); 1838 ierr = PetscObjectSetName((PetscObject) X, "solution");CHKERRQ(ierr); 1839 ierr = SetInitialCondition(dm, X, user);CHKERRQ(ierr); 1840 if (useAMR) { 1841 PetscInt adaptIter; 1842 1843 /* use no limiting when reconstructing gradients for adaptivity */ 1844 ierr = PetscFVGetLimiter(fvm, &limiter);CHKERRQ(ierr); 1845 ierr = PetscObjectReference((PetscObject) limiter);CHKERRQ(ierr); 1846 ierr = PetscLimiterCreate(PetscObjectComm((PetscObject) fvm), &noneLimiter);CHKERRQ(ierr); 1847 ierr = PetscLimiterSetType(noneLimiter, PETSCLIMITERNONE);CHKERRQ(ierr); 1848 1849 ierr = PetscFVSetLimiter(fvm, noneLimiter);CHKERRQ(ierr); 1850 for (adaptIter = 0; ; ++adaptIter) { 1851 PetscLogDouble bytes; 1852 TS tsNew = NULL; 1853 1854 ierr = PetscMemoryGetCurrentUsage(&bytes);CHKERRQ(ierr); 1855 ierr = PetscInfo2(ts, "refinement loop %D: memory used %g\n", adaptIter, bytes);CHKERRQ(ierr); 1856 ierr = DMViewFromOptions(dm, NULL, "-initial_dm_view");CHKERRQ(ierr); 1857 ierr = VecViewFromOptions(X, NULL, "-initial_vec_view");CHKERRQ(ierr); 1858 #if 0 1859 if (viewInitial) { 1860 PetscViewer viewer; 1861 char buf[256]; 1862 PetscBool isHDF5, isVTK; 1863 1864 ierr = PetscViewerCreate(comm,&viewer);CHKERRQ(ierr); 1865 ierr = PetscViewerSetType(viewer,PETSCVIEWERVTK);CHKERRQ(ierr); 1866 ierr = PetscViewerSetOptionsPrefix(viewer,"initial_");CHKERRQ(ierr); 1867 ierr = PetscViewerSetFromOptions(viewer);CHKERRQ(ierr); 1868 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&isHDF5);CHKERRQ(ierr); 1869 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERVTK,&isVTK);CHKERRQ(ierr); 1870 if (isHDF5) { 1871 ierr = PetscSNPrintf(buf, 256, "ex11-initial-%d.h5", adaptIter);CHKERRQ(ierr); 1872 } else if (isVTK) { 1873 ierr = PetscSNPrintf(buf, 256, "ex11-initial-%d.vtu", adaptIter);CHKERRQ(ierr); 1874 ierr = PetscViewerPushFormat(viewer,PETSC_VIEWER_VTK_VTU);CHKERRQ(ierr); 1875 } 1876 ierr = PetscViewerFileSetMode(viewer,FILE_MODE_WRITE);CHKERRQ(ierr); 1877 ierr = PetscViewerFileSetName(viewer,buf);CHKERRQ(ierr); 1878 if (isHDF5) { 1879 ierr = DMView(dm,viewer);CHKERRQ(ierr); 1880 ierr = PetscViewerFileSetMode(viewer,FILE_MODE_UPDATE);CHKERRQ(ierr); 1881 } 1882 ierr = VecView(X,viewer);CHKERRQ(ierr); 1883 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1884 } 1885 #endif 1886 1887 ierr = adaptToleranceFVM(fvm, ts, X, refineTag, coarsenTag, user, &tsNew, NULL);CHKERRQ(ierr); 1888 if (!tsNew) { 1889 break; 1890 } else { 1891 ierr = DMDestroy(&dm);CHKERRQ(ierr); 1892 ierr = VecDestroy(&X);CHKERRQ(ierr); 1893 ierr = TSDestroy(&ts);CHKERRQ(ierr); 1894 ts = tsNew; 1895 ierr = TSGetDM(ts,&dm);CHKERRQ(ierr); 1896 ierr = PetscObjectReference((PetscObject)dm);CHKERRQ(ierr); 1897 ierr = DMCreateGlobalVector(dm,&X);CHKERRQ(ierr); 1898 ierr = PetscObjectSetName((PetscObject) X, "solution");CHKERRQ(ierr); 1899 ierr = SetInitialCondition(dm, X, user);CHKERRQ(ierr); 1900 } 1901 } 1902 /* restore original limiter */ 1903 ierr = PetscFVSetLimiter(fvm, limiter);CHKERRQ(ierr); 1904 } 1905 1906 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1907 if (vtkCellGeom) { 1908 DM dmCell; 1909 Vec cellgeom, partition; 1910 1911 ierr = DMPlexGetGeometryFVM(plex, NULL, &cellgeom, NULL);CHKERRQ(ierr); 1912 ierr = OutputVTK(dm, "ex11-cellgeom.vtk", &viewer);CHKERRQ(ierr); 1913 ierr = VecView(cellgeom, viewer);CHKERRQ(ierr); 1914 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1915 ierr = CreatePartitionVec(dm, &dmCell, &partition);CHKERRQ(ierr); 1916 ierr = OutputVTK(dmCell, "ex11-partition.vtk", &viewer);CHKERRQ(ierr); 1917 ierr = VecView(partition, viewer);CHKERRQ(ierr); 1918 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1919 ierr = VecDestroy(&partition);CHKERRQ(ierr); 1920 ierr = DMDestroy(&dmCell);CHKERRQ(ierr); 1921 } 1922 /* collect max maxspeed from all processes -- todo */ 1923 ierr = DMPlexGetGeometryFVM(plex, NULL, NULL, &minRadius);CHKERRQ(ierr); 1924 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1925 ierr = MPI_Allreduce(&phys->maxspeed,&mod->maxspeed,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr); 1926 if (mod->maxspeed <= 0) SETERRQ1(comm,PETSC_ERR_ARG_WRONGSTATE,"Physics '%s' did not set maxspeed",physname); 1927 dt = cfl * minRadius / mod->maxspeed; 1928 ierr = TSSetTimeStep(ts,dt);CHKERRQ(ierr); 1929 ierr = TSSetFromOptions(ts);CHKERRQ(ierr); 1930 if (!useAMR) { 1931 ierr = TSSolve(ts,X);CHKERRQ(ierr); 1932 ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); 1933 ierr = TSGetStepNumber(ts,&nsteps);CHKERRQ(ierr); 1934 } else { 1935 PetscReal finalTime; 1936 PetscInt adaptIter; 1937 TS tsNew = NULL; 1938 Vec solNew = NULL; 1939 1940 ierr = TSGetMaxTime(ts,&finalTime);CHKERRQ(ierr); 1941 ierr = TSSetMaxSteps(ts,adaptInterval);CHKERRQ(ierr); 1942 ierr = TSSolve(ts,X);CHKERRQ(ierr); 1943 ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); 1944 ierr = TSGetStepNumber(ts,&nsteps);CHKERRQ(ierr); 1945 for (adaptIter = 0;ftime < finalTime;adaptIter++) { 1946 PetscLogDouble bytes; 1947 1948 ierr = PetscMemoryGetCurrentUsage(&bytes);CHKERRQ(ierr); 1949 ierr = PetscInfo2(ts, "AMR time step loop %D: memory used %g\n", adaptIter, bytes);CHKERRQ(ierr); 1950 ierr = PetscFVSetLimiter(fvm,noneLimiter);CHKERRQ(ierr); 1951 ierr = adaptToleranceFVM(fvm,ts,X,refineTag,coarsenTag,user,&tsNew,&solNew);CHKERRQ(ierr); 1952 ierr = PetscFVSetLimiter(fvm,limiter);CHKERRQ(ierr); 1953 if (tsNew) { 1954 ierr = PetscInfo(ts, "AMR used\n");CHKERRQ(ierr); 1955 ierr = DMDestroy(&dm);CHKERRQ(ierr); 1956 ierr = VecDestroy(&X);CHKERRQ(ierr); 1957 ierr = TSDestroy(&ts);CHKERRQ(ierr); 1958 ts = tsNew; 1959 X = solNew; 1960 ierr = TSSetFromOptions(ts);CHKERRQ(ierr); 1961 ierr = VecGetDM(X,&dm);CHKERRQ(ierr); 1962 ierr = PetscObjectReference((PetscObject)dm);CHKERRQ(ierr); 1963 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1964 ierr = DMPlexGetGeometryFVM(dm, NULL, NULL, &minRadius);CHKERRQ(ierr); 1965 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1966 ierr = MPI_Allreduce(&phys->maxspeed,&mod->maxspeed,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr); 1967 if (mod->maxspeed <= 0) SETERRQ1(comm,PETSC_ERR_ARG_WRONGSTATE,"Physics '%s' did not set maxspeed",physname); 1968 dt = cfl * minRadius / mod->maxspeed; 1969 ierr = TSSetStepNumber(ts,nsteps);CHKERRQ(ierr); 1970 ierr = TSSetTime(ts,ftime);CHKERRQ(ierr); 1971 ierr = TSSetTimeStep(ts,dt);CHKERRQ(ierr); 1972 } else { 1973 ierr = PetscInfo(ts, "AMR not used\n");CHKERRQ(ierr); 1974 } 1975 user->monitorStepOffset = nsteps; 1976 ierr = TSSetMaxSteps(ts,nsteps+adaptInterval);CHKERRQ(ierr); 1977 ierr = TSSolve(ts,X);CHKERRQ(ierr); 1978 ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); 1979 ierr = TSGetStepNumber(ts,&nsteps);CHKERRQ(ierr); 1980 } 1981 } 1982 ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr); 1983 ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],(double)ftime,nsteps);CHKERRQ(ierr); 1984 ierr = TSDestroy(&ts);CHKERRQ(ierr); 1985 1986 ierr = VecTaggerDestroy(&refineTag);CHKERRQ(ierr); 1987 ierr = VecTaggerDestroy(&coarsenTag);CHKERRQ(ierr); 1988 ierr = PetscFunctionListDestroy(&PhysicsList);CHKERRQ(ierr); 1989 ierr = FunctionalLinkDestroy(&user->model->functionalRegistry);CHKERRQ(ierr); 1990 ierr = PetscFree(user->model->functionalMonitored);CHKERRQ(ierr); 1991 ierr = PetscFree(user->model->functionalCall);CHKERRQ(ierr); 1992 ierr = PetscFree(user->model->physics->data);CHKERRQ(ierr); 1993 ierr = PetscFree(user->model->physics);CHKERRQ(ierr); 1994 ierr = PetscFree(user->model);CHKERRQ(ierr); 1995 ierr = PetscFree(user);CHKERRQ(ierr); 1996 ierr = VecDestroy(&X);CHKERRQ(ierr); 1997 ierr = PetscLimiterDestroy(&limiter);CHKERRQ(ierr); 1998 ierr = PetscLimiterDestroy(&noneLimiter);CHKERRQ(ierr); 1999 ierr = PetscFVDestroy(&fvm);CHKERRQ(ierr); 2000 ierr = DMDestroy(&dm);CHKERRQ(ierr); 2001 ierr = PetscFinalize(); 2002 return ierr; 2003 } 2004 2005 /* Godunov fluxs */ 2006 PetscScalar cvmgp_(PetscScalar *a, PetscScalar *b, PetscScalar *test) 2007 { 2008 /* System generated locals */ 2009 PetscScalar ret_val; 2010 2011 if (PetscRealPart(*test) > 0.) { 2012 goto L10; 2013 } 2014 ret_val = *b; 2015 return ret_val; 2016 L10: 2017 ret_val = *a; 2018 return ret_val; 2019 } /* cvmgp_ */ 2020 2021 PetscScalar cvmgm_(PetscScalar *a, PetscScalar *b, PetscScalar *test) 2022 { 2023 /* System generated locals */ 2024 PetscScalar ret_val; 2025 2026 if (PetscRealPart(*test) < 0.) { 2027 goto L10; 2028 } 2029 ret_val = *b; 2030 return ret_val; 2031 L10: 2032 ret_val = *a; 2033 return ret_val; 2034 } /* cvmgm_ */ 2035 2036 int riem1mdt( PetscScalar *gaml, PetscScalar *gamr, PetscScalar *rl, PetscScalar *pl, 2037 PetscScalar *uxl, PetscScalar *rr, PetscScalar *pr, 2038 PetscScalar *uxr, PetscScalar *rstarl, PetscScalar *rstarr, PetscScalar * 2039 pstar, PetscScalar *ustar) 2040 { 2041 /* Initialized data */ 2042 2043 static PetscScalar smallp = 1e-8; 2044 2045 /* System generated locals */ 2046 int i__1; 2047 PetscScalar d__1, d__2; 2048 2049 /* Local variables */ 2050 static int i0; 2051 static PetscScalar cl, cr, wl, zl, wr, zr, pst, durl, skpr1, skpr2; 2052 static int iwave; 2053 static PetscScalar gascl4, gascr4, cstarl, dpstar, cstarr; 2054 /* static PetscScalar csqrl, csqrr, gascl1, gascl2, gascl3, gascr1, gascr2, gascr3; */ 2055 static int iterno; 2056 static PetscScalar ustarl, ustarr, rarepr1, rarepr2; 2057 2058 2059 2060 /* gascl1 = *gaml - 1.; */ 2061 /* gascl2 = (*gaml + 1.) * .5; */ 2062 /* gascl3 = gascl2 / *gaml; */ 2063 gascl4 = 1. / (*gaml - 1.); 2064 2065 /* gascr1 = *gamr - 1.; */ 2066 /* gascr2 = (*gamr + 1.) * .5; */ 2067 /* gascr3 = gascr2 / *gamr; */ 2068 gascr4 = 1. / (*gamr - 1.); 2069 iterno = 10; 2070 /* find pstar: */ 2071 cl = PetscSqrtScalar(*gaml * *pl / *rl); 2072 cr = PetscSqrtScalar(*gamr * *pr / *rr); 2073 wl = *rl * cl; 2074 wr = *rr * cr; 2075 /* csqrl = wl * wl; */ 2076 /* csqrr = wr * wr; */ 2077 *pstar = (wl * *pr + wr * *pl) / (wl + wr); 2078 *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp)); 2079 pst = *pl / *pr; 2080 skpr1 = cr * (pst - 1.) * PetscSqrtScalar(2. / (*gamr * (*gamr - 1. + (*gamr + 1.) * pst))); 2081 d__1 = (*gamr - 1.) / (*gamr * 2.); 2082 rarepr2 = gascr4 * 2. * cr * (1. - PetscPowScalar(pst, d__1)); 2083 pst = *pr / *pl; 2084 skpr2 = cl * (pst - 1.) * PetscSqrtScalar(2. / (*gaml * (*gaml - 1. + (*gaml + 1.) * pst))); 2085 d__1 = (*gaml - 1.) / (*gaml * 2.); 2086 rarepr1 = gascl4 * 2. * cl * (1. - PetscPowScalar(pst, d__1)); 2087 durl = *uxr - *uxl; 2088 if (PetscRealPart(*pr) < PetscRealPart(*pl)) { 2089 if (PetscRealPart(durl) >= PetscRealPart(rarepr1)) { 2090 iwave = 100; 2091 } else if (PetscRealPart(durl) <= PetscRealPart(-skpr1)) { 2092 iwave = 300; 2093 } else { 2094 iwave = 400; 2095 } 2096 } else { 2097 if (PetscRealPart(durl) >= PetscRealPart(rarepr2)) { 2098 iwave = 100; 2099 } else if (PetscRealPart(durl) <= PetscRealPart(-skpr2)) { 2100 iwave = 300; 2101 } else { 2102 iwave = 200; 2103 } 2104 } 2105 if (iwave == 100) { 2106 /* 1-wave: rarefaction wave, 3-wave: rarefaction wave */ 2107 /* case (100) */ 2108 i__1 = iterno; 2109 for (i0 = 1; i0 <= i__1; ++i0) { 2110 d__1 = *pstar / *pl; 2111 d__2 = 1. / *gaml; 2112 *rstarl = *rl * PetscPowScalar(d__1, d__2); 2113 cstarl = PetscSqrtScalar(*gaml * *pstar / *rstarl); 2114 ustarl = *uxl - gascl4 * 2. * (cstarl - cl); 2115 zl = *rstarl * cstarl; 2116 d__1 = *pstar / *pr; 2117 d__2 = 1. / *gamr; 2118 *rstarr = *rr * PetscPowScalar(d__1, d__2); 2119 cstarr = PetscSqrtScalar(*gamr * *pstar / *rstarr); 2120 ustarr = *uxr + gascr4 * 2. * (cstarr - cr); 2121 zr = *rstarr * cstarr; 2122 dpstar = zl * zr * (ustarr - ustarl) / (zl + zr); 2123 *pstar -= dpstar; 2124 *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp)); 2125 if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) { 2126 #if 0 2127 break; 2128 #endif 2129 } 2130 } 2131 /* 1-wave: shock wave, 3-wave: rarefaction wave */ 2132 } else if (iwave == 200) { 2133 /* case (200) */ 2134 i__1 = iterno; 2135 for (i0 = 1; i0 <= i__1; ++i0) { 2136 pst = *pstar / *pl; 2137 ustarl = *uxl - (pst - 1.) * cl * PetscSqrtScalar(2. / (*gaml * (*gaml - 1. + (*gaml + 1.) * pst))); 2138 zl = *pl / cl * PetscSqrtScalar(*gaml * 2. * (*gaml - 1. + (*gaml + 1.) * pst)) * (*gaml - 1. + (*gaml + 1.) * pst) / (*gaml * 3. - 1. + (*gaml + 1.) * pst); 2139 d__1 = *pstar / *pr; 2140 d__2 = 1. / *gamr; 2141 *rstarr = *rr * PetscPowScalar(d__1, d__2); 2142 cstarr = PetscSqrtScalar(*gamr * *pstar / *rstarr); 2143 zr = *rstarr * cstarr; 2144 ustarr = *uxr + gascr4 * 2. * (cstarr - cr); 2145 dpstar = zl * zr * (ustarr - ustarl) / (zl + zr); 2146 *pstar -= dpstar; 2147 *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp)); 2148 if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) { 2149 #if 0 2150 break; 2151 #endif 2152 } 2153 } 2154 /* 1-wave: shock wave, 3-wave: shock */ 2155 } else if (iwave == 300) { 2156 /* case (300) */ 2157 i__1 = iterno; 2158 for (i0 = 1; i0 <= i__1; ++i0) { 2159 pst = *pstar / *pl; 2160 ustarl = *uxl - (pst - 1.) * cl * PetscSqrtScalar(2. / (*gaml * (*gaml - 1. + (*gaml + 1.) * pst))); 2161 zl = *pl / cl * PetscSqrtScalar(*gaml * 2. * (*gaml - 1. + (*gaml + 1.) * pst)) * (*gaml - 1. + (*gaml + 1.) * pst) / (*gaml * 3. - 1. + (*gaml + 1.) * pst); 2162 pst = *pstar / *pr; 2163 ustarr = *uxr + (pst - 1.) * cr * PetscSqrtScalar(2. / (*gamr * (*gamr - 1. + (*gamr + 1.) * pst))); 2164 zr = *pr / cr * PetscSqrtScalar(*gamr * 2. * (*gamr - 1. + (*gamr + 1.) * pst)) * (*gamr - 1. + (*gamr + 1.) * pst) / (*gamr * 3. - 1. + (*gamr + 1.) * pst); 2165 dpstar = zl * zr * (ustarr - ustarl) / (zl + zr); 2166 *pstar -= dpstar; 2167 *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp)); 2168 if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) { 2169 #if 0 2170 break; 2171 #endif 2172 } 2173 } 2174 /* 1-wave: rarefaction wave, 3-wave: shock */ 2175 } else if (iwave == 400) { 2176 /* case (400) */ 2177 i__1 = iterno; 2178 for (i0 = 1; i0 <= i__1; ++i0) { 2179 d__1 = *pstar / *pl; 2180 d__2 = 1. / *gaml; 2181 *rstarl = *rl * PetscPowScalar(d__1, d__2); 2182 cstarl = PetscSqrtScalar(*gaml * *pstar / *rstarl); 2183 ustarl = *uxl - gascl4 * 2. * (cstarl - cl); 2184 zl = *rstarl * cstarl; 2185 pst = *pstar / *pr; 2186 ustarr = *uxr + (pst - 1.) * cr * PetscSqrtScalar(2. / (*gamr * (*gamr - 1. + (*gamr + 1.) * pst))); 2187 zr = *pr / cr * PetscSqrtScalar(*gamr * 2. * (*gamr - 1. + (*gamr + 1.) * pst)) * (*gamr - 1. + (*gamr + 1.) * pst) / (*gamr * 3. - 1. + (*gamr + 1.) * pst); 2188 dpstar = zl * zr * (ustarr - ustarl) / (zl + zr); 2189 *pstar -= dpstar; 2190 *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp)); 2191 if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) { 2192 #if 0 2193 break; 2194 #endif 2195 } 2196 } 2197 } 2198 2199 *ustar = (zl * ustarr + zr * ustarl) / (zl + zr); 2200 if (PetscRealPart(*pstar) > PetscRealPart(*pl)) { 2201 pst = *pstar / *pl; 2202 *rstarl = ((*gaml + 1.) * pst + *gaml - 1.) / ((*gaml - 1.) * pst + * 2203 gaml + 1.) * *rl; 2204 } 2205 if (PetscRealPart(*pstar) > PetscRealPart(*pr)) { 2206 pst = *pstar / *pr; 2207 *rstarr = ((*gamr + 1.) * pst + *gamr - 1.) / ((*gamr - 1.) * pst + * 2208 gamr + 1.) * *rr; 2209 } 2210 return iwave; 2211 } 2212 2213 PetscScalar sign(PetscScalar x) 2214 { 2215 if(PetscRealPart(x) > 0) return 1.0; 2216 if(PetscRealPart(x) < 0) return -1.0; 2217 return 0.0; 2218 } 2219 /* Riemann Solver */ 2220 /* -------------------------------------------------------------------- */ 2221 int riemannsolver(PetscScalar *xcen, PetscScalar *xp, 2222 PetscScalar *dtt, PetscScalar *rl, PetscScalar *uxl, PetscScalar *pl, 2223 PetscScalar *utl, PetscScalar *ubl, PetscScalar *gaml, PetscScalar *rho1l, 2224 PetscScalar *rr, PetscScalar *uxr, PetscScalar *pr, PetscScalar *utr, 2225 PetscScalar *ubr, PetscScalar *gamr, PetscScalar *rho1r, PetscScalar *rx, 2226 PetscScalar *uxm, PetscScalar *px, PetscScalar *utx, PetscScalar *ubx, 2227 PetscScalar *gam, PetscScalar *rho1) 2228 { 2229 /* System generated locals */ 2230 PetscScalar d__1, d__2; 2231 2232 /* Local variables */ 2233 static PetscScalar s, c0, p0, r0, u0, w0, x0, x2, ri, cx, sgn0, wsp0, gasc1, gasc2, gasc3, gasc4; 2234 static PetscScalar cstar, pstar, rstar, ustar, xstar, wspst, ushock, streng, rstarl, rstarr, rstars; 2235 int iwave; 2236 2237 if (*rl == *rr && *pr == *pl && *uxl == *uxr && *gaml == *gamr) { 2238 *rx = *rl; 2239 *px = *pl; 2240 *uxm = *uxl; 2241 *gam = *gaml; 2242 x2 = *xcen + *uxm * *dtt; 2243 2244 if (PetscRealPart(*xp) >= PetscRealPart(x2)) { 2245 *utx = *utr; 2246 *ubx = *ubr; 2247 *rho1 = *rho1r; 2248 } else { 2249 *utx = *utl; 2250 *ubx = *ubl; 2251 *rho1 = *rho1l; 2252 } 2253 return 0; 2254 } 2255 iwave = riem1mdt(gaml, gamr, rl, pl, uxl, rr, pr, uxr, &rstarl, &rstarr, &pstar, &ustar); 2256 2257 x2 = *xcen + ustar * *dtt; 2258 d__1 = *xp - x2; 2259 sgn0 = sign(d__1); 2260 /* x is in 3-wave if sgn0 = 1 */ 2261 /* x is in 1-wave if sgn0 = -1 */ 2262 r0 = cvmgm_(rl, rr, &sgn0); 2263 p0 = cvmgm_(pl, pr, &sgn0); 2264 u0 = cvmgm_(uxl, uxr, &sgn0); 2265 *gam = cvmgm_(gaml, gamr, &sgn0); 2266 gasc1 = *gam - 1.; 2267 gasc2 = (*gam + 1.) * .5; 2268 gasc3 = gasc2 / *gam; 2269 gasc4 = 1. / (*gam - 1.); 2270 c0 = PetscSqrtScalar(*gam * p0 / r0); 2271 streng = pstar - p0; 2272 w0 = *gam * r0 * p0 * (gasc3 * streng / p0 + 1.); 2273 rstars = r0 / (1. - r0 * streng / w0); 2274 d__1 = p0 / pstar; 2275 d__2 = -1. / *gam; 2276 rstarr = r0 * PetscPowScalar(d__1, d__2); 2277 rstar = cvmgm_(&rstarr, &rstars, &streng); 2278 w0 = PetscSqrtScalar(w0); 2279 cstar = PetscSqrtScalar(*gam * pstar / rstar); 2280 wsp0 = u0 + sgn0 * c0; 2281 wspst = ustar + sgn0 * cstar; 2282 ushock = ustar + sgn0 * w0 / rstar; 2283 wspst = cvmgp_(&ushock, &wspst, &streng); 2284 wsp0 = cvmgp_(&ushock, &wsp0, &streng); 2285 x0 = *xcen + wsp0 * *dtt; 2286 xstar = *xcen + wspst * *dtt; 2287 /* using gas formula to evaluate rarefaction wave */ 2288 /* ri : reiman invariant */ 2289 ri = u0 - sgn0 * 2. * gasc4 * c0; 2290 cx = sgn0 * .5 * gasc1 / gasc2 * ((*xp - *xcen) / *dtt - ri); 2291 *uxm = ri + sgn0 * 2. * gasc4 * cx; 2292 s = p0 / PetscPowScalar(r0, *gam); 2293 d__1 = cx * cx / (*gam * s); 2294 *rx = PetscPowScalar(d__1, gasc4); 2295 *px = cx * cx * *rx / *gam; 2296 d__1 = sgn0 * (x0 - *xp); 2297 *rx = cvmgp_(rx, &r0, &d__1); 2298 d__1 = sgn0 * (x0 - *xp); 2299 *px = cvmgp_(px, &p0, &d__1); 2300 d__1 = sgn0 * (x0 - *xp); 2301 *uxm = cvmgp_(uxm, &u0, &d__1); 2302 d__1 = sgn0 * (xstar - *xp); 2303 *rx = cvmgm_(rx, &rstar, &d__1); 2304 d__1 = sgn0 * (xstar - *xp); 2305 *px = cvmgm_(px, &pstar, &d__1); 2306 d__1 = sgn0 * (xstar - *xp); 2307 *uxm = cvmgm_(uxm, &ustar, &d__1); 2308 if (PetscRealPart(*xp) >= PetscRealPart(x2)) { 2309 *utx = *utr; 2310 *ubx = *ubr; 2311 *rho1 = *rho1r; 2312 } else { 2313 *utx = *utl; 2314 *ubx = *ubl; 2315 *rho1 = *rho1l; 2316 } 2317 return iwave; 2318 } 2319 int godunovflux( const PetscScalar *ul, const PetscScalar *ur, 2320 PetscScalar *flux, const PetscReal *nn, const int *ndim, 2321 const PetscReal *gamma) 2322 { 2323 /* System generated locals */ 2324 int i__1,iwave; 2325 PetscScalar d__1, d__2, d__3; 2326 2327 /* Local variables */ 2328 static int k; 2329 static PetscScalar bn[3], fn, ft, tg[3], pl, rl, pm, pr, rr, xp, ubl, ubm, 2330 ubr, dtt, unm, tmp, utl, utm, uxl, utr, uxr, gaml, gamm, gamr, 2331 xcen, rhom, rho1l, rho1m, rho1r; 2332 /* Parameter adjustments */ 2333 --nn; 2334 --flux; 2335 --ur; 2336 --ul; 2337 2338 /* Function Body */ 2339 xcen = 0.; 2340 xp = 0.; 2341 i__1 = *ndim; 2342 for (k = 1; k <= i__1; ++k) { 2343 tg[k - 1] = 0.; 2344 bn[k - 1] = 0.; 2345 } 2346 dtt = 1.; 2347 if (*ndim == 3) { 2348 if (nn[1] == 0. && nn[2] == 0.) { 2349 tg[0] = 1.; 2350 } else { 2351 tg[0] = -nn[2]; 2352 tg[1] = nn[1]; 2353 } 2354 /* tmp=dsqrt(tg(1)**2+tg(2)**2) */ 2355 /* tg=tg/tmp */ 2356 bn[0] = -nn[3] * tg[1]; 2357 bn[1] = nn[3] * tg[0]; 2358 bn[2] = nn[1] * tg[1] - nn[2] * tg[0]; 2359 /* Computing 2nd power */ 2360 d__1 = bn[0]; 2361 /* Computing 2nd power */ 2362 d__2 = bn[1]; 2363 /* Computing 2nd power */ 2364 d__3 = bn[2]; 2365 tmp = PetscSqrtScalar(d__1 * d__1 + d__2 * d__2 + d__3 * d__3); 2366 i__1 = *ndim; 2367 for (k = 1; k <= i__1; ++k) { 2368 bn[k - 1] /= tmp; 2369 } 2370 } else if (*ndim == 2) { 2371 tg[0] = -nn[2]; 2372 tg[1] = nn[1]; 2373 /* tmp=dsqrt(tg(1)**2+tg(2)**2) */ 2374 /* tg=tg/tmp */ 2375 bn[0] = 0.; 2376 bn[1] = 0.; 2377 bn[2] = 1.; 2378 } 2379 rl = ul[1]; 2380 rr = ur[1]; 2381 uxl = 0.; 2382 uxr = 0.; 2383 utl = 0.; 2384 utr = 0.; 2385 ubl = 0.; 2386 ubr = 0.; 2387 i__1 = *ndim; 2388 for (k = 1; k <= i__1; ++k) { 2389 uxl += ul[k + 1] * nn[k]; 2390 uxr += ur[k + 1] * nn[k]; 2391 utl += ul[k + 1] * tg[k - 1]; 2392 utr += ur[k + 1] * tg[k - 1]; 2393 ubl += ul[k + 1] * bn[k - 1]; 2394 ubr += ur[k + 1] * bn[k - 1]; 2395 } 2396 uxl /= rl; 2397 uxr /= rr; 2398 utl /= rl; 2399 utr /= rr; 2400 ubl /= rl; 2401 ubr /= rr; 2402 2403 gaml = *gamma; 2404 gamr = *gamma; 2405 /* Computing 2nd power */ 2406 d__1 = uxl; 2407 /* Computing 2nd power */ 2408 d__2 = utl; 2409 /* Computing 2nd power */ 2410 d__3 = ubl; 2411 pl = (*gamma - 1.) * (ul[*ndim + 2] - rl * .5 * (d__1 * d__1 + d__2 * d__2 + d__3 * d__3)); 2412 /* Computing 2nd power */ 2413 d__1 = uxr; 2414 /* Computing 2nd power */ 2415 d__2 = utr; 2416 /* Computing 2nd power */ 2417 d__3 = ubr; 2418 pr = (*gamma - 1.) * (ur[*ndim + 2] - rr * .5 * (d__1 * d__1 + d__2 * d__2 + d__3 * d__3)); 2419 rho1l = rl; 2420 rho1r = rr; 2421 2422 iwave = riemannsolver(&xcen, &xp, &dtt, &rl, &uxl, &pl, &utl, &ubl, &gaml, & 2423 rho1l, &rr, &uxr, &pr, &utr, &ubr, &gamr, &rho1r, &rhom, &unm, & 2424 pm, &utm, &ubm, &gamm, &rho1m); 2425 2426 flux[1] = rhom * unm; 2427 fn = rhom * unm * unm + pm; 2428 ft = rhom * unm * utm; 2429 /* flux(2)=fn*nn(1)+ft*nn(2) */ 2430 /* flux(3)=fn*tg(1)+ft*tg(2) */ 2431 flux[2] = fn * nn[1] + ft * tg[0]; 2432 flux[3] = fn * nn[2] + ft * tg[1]; 2433 /* flux(2)=rhom*unm*(unm)+pm */ 2434 /* flux(3)=rhom*(unm)*utm */ 2435 if (*ndim == 3) { 2436 flux[4] = rhom * unm * ubm; 2437 } 2438 flux[*ndim + 2] = (rhom * .5 * (unm * unm + utm * utm + ubm * ubm) + gamm / (gamm - 1.) * pm) * unm; 2439 return iwave; 2440 } /* godunovflux_ */ 2441 2442 /* Subroutine to set up the initial conditions for the */ 2443 /* Shock Interface interaction or linear wave (Ravi Samtaney,Mark Adams). */ 2444 /* ----------------------------------------------------------------------- */ 2445 int projecteqstate(PetscReal wc[], const PetscReal ueq[], PetscReal lv[][3]) 2446 { 2447 int j,k; 2448 /* Wc=matmul(lv,Ueq) 3 vars */ 2449 for (k = 0; k < 3; ++k) { 2450 wc[k] = 0.; 2451 for (j = 0; j < 3; ++j) { 2452 wc[k] += lv[k][j]*ueq[j]; 2453 } 2454 } 2455 return 0; 2456 } 2457 /* ----------------------------------------------------------------------- */ 2458 int projecttoprim(PetscReal v[], const PetscReal wc[], PetscReal rv[][3]) 2459 { 2460 int k,j; 2461 /* V=matmul(rv,WC) 3 vars */ 2462 for (k = 0; k < 3; ++k) { 2463 v[k] = 0.; 2464 for (j = 0; j < 3; ++j) { 2465 v[k] += rv[k][j]*wc[j]; 2466 } 2467 } 2468 return 0; 2469 } 2470 /* ---------------------------------------------------------------------- */ 2471 int eigenvectors(PetscReal rv[][3], PetscReal lv[][3], const PetscReal ueq[], PetscReal gamma) 2472 { 2473 int j,k; 2474 PetscReal rho,csnd,p0; 2475 /* PetscScalar u; */ 2476 2477 for (k = 0; k < 3; ++k) for (j = 0; j < 3; ++j) { lv[k][j] = 0.; rv[k][j] = 0.; } 2478 rho = ueq[0]; 2479 /* u = ueq[1]; */ 2480 p0 = ueq[2]; 2481 csnd = PetscSqrtReal(gamma * p0 / rho); 2482 lv[0][1] = rho * .5; 2483 lv[0][2] = -.5 / csnd; 2484 lv[1][0] = csnd; 2485 lv[1][2] = -1. / csnd; 2486 lv[2][1] = rho * .5; 2487 lv[2][2] = .5 / csnd; 2488 rv[0][0] = -1. / csnd; 2489 rv[1][0] = 1. / rho; 2490 rv[2][0] = -csnd; 2491 rv[0][1] = 1. / csnd; 2492 rv[0][2] = 1. / csnd; 2493 rv[1][2] = 1. / rho; 2494 rv[2][2] = csnd; 2495 return 0; 2496 } 2497 2498 int initLinearWave(EulerNode *ux, const PetscReal gamma, const PetscReal coord[], const PetscReal Lx) 2499 { 2500 PetscReal p0,u0,wcp[3],wc[3]; 2501 PetscReal lv[3][3]; 2502 PetscReal vp[3]; 2503 PetscReal rv[3][3]; 2504 PetscReal eps, ueq[3], rho0, twopi; 2505 2506 /* Function Body */ 2507 twopi = 2.*PETSC_PI; 2508 eps = 1e-4; /* perturbation */ 2509 rho0 = 1e3; /* density of water */ 2510 p0 = 101325.; /* init pressure of 1 atm (?) */ 2511 u0 = 0.; 2512 ueq[0] = rho0; 2513 ueq[1] = u0; 2514 ueq[2] = p0; 2515 /* Project initial state to characteristic variables */ 2516 eigenvectors(rv, lv, ueq, gamma); 2517 projecteqstate(wc, ueq, lv); 2518 wcp[0] = wc[0]; 2519 wcp[1] = wc[1]; 2520 wcp[2] = wc[2] + eps * PetscCosReal(coord[0] * 2. * twopi / Lx); 2521 projecttoprim(vp, wcp, rv); 2522 ux->r = vp[0]; /* density */ 2523 ux->ru[0] = vp[0] * vp[1]; /* x momentum */ 2524 ux->ru[1] = 0.; 2525 #if defined DIM > 2 2526 if (dim>2) ux->ru[2] = 0.; 2527 #endif 2528 /* E = rho * e + rho * v^2/2 = p/(gam-1) + rho*v^2/2 */ 2529 ux->E = vp[2]/(gamma - 1.) + 0.5*vp[0]*vp[1]*vp[1]; 2530 return 0; 2531 } 2532 2533 /*TEST 2534 2535 # 2D Advection 0-10 2536 test: 2537 suffix: 0 2538 requires: exodusii 2539 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo 2540 2541 test: 2542 suffix: 1 2543 requires: exodusii 2544 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo 2545 2546 test: 2547 suffix: 2 2548 requires: exodusii 2549 nsize: 2 2550 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo 2551 2552 test: 2553 suffix: 3 2554 requires: exodusii 2555 nsize: 2 2556 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo 2557 2558 test: 2559 suffix: 4 2560 requires: exodusii 2561 nsize: 8 2562 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad.exo 2563 2564 test: 2565 suffix: 5 2566 requires: exodusii 2567 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo -ts_type rosw -ts_adapt_reject_safety 1 2568 2569 test: 2570 suffix: 6 2571 requires: exodusii 2572 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/squaremotor-30.exo -ufv_split_faces 2573 2574 test: 2575 suffix: 7 2576 requires: exodusii 2577 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo -dm_refine 1 2578 2579 test: 2580 suffix: 8 2581 requires: exodusii 2582 nsize: 2 2583 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo -dm_refine 1 2584 2585 test: 2586 suffix: 9 2587 requires: exodusii 2588 nsize: 8 2589 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo -dm_refine 1 2590 2591 test: 2592 suffix: 10 2593 requires: exodusii 2594 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad.exo 2595 2596 # 2D Shallow water 2597 test: 2598 suffix: sw_0 2599 requires: exodusii 2600 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 2601 2602 # 2D Advection: p4est 2603 test: 2604 suffix: p4est_advec_2d 2605 requires: p4est 2606 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 2607 2608 # Advection in a box 2609 test: 2610 suffix: adv_2d_quad_0 2611 args: -ufv_vtk_interval 0 -dm_refine 3 -dm_plex_separate_marker -bc_inflow 1,2,4 -bc_outflow 3 2612 2613 test: 2614 suffix: adv_2d_quad_1 2615 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 2616 timeoutfactor: 3 2617 2618 test: 2619 suffix: adv_2d_quad_p4est_0 2620 requires: p4est 2621 args: -ufv_vtk_interval 0 -dm_refine 5 -dm_type p4est -dm_plex_separate_marker -bc_inflow 1,2,4 -bc_outflow 3 2622 2623 test: 2624 suffix: adv_2d_quad_p4est_1 2625 requires: p4est 2626 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 2627 timeoutfactor: 3 2628 2629 test: 2630 suffix: adv_2d_quad_p4est_adapt_0 2631 requires: p4est !__float128 #broken for quad precision 2632 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 2633 timeoutfactor: 3 2634 2635 test: 2636 suffix: adv_2d_tri_0 2637 requires: triangle 2638 TODO: how did this ever get in master when there is no support for this 2639 args: -ufv_vtk_interval 0 -simplex -dm_refine 3 -dm_plex_separate_marker -bc_inflow 1,2,4 -bc_outflow 3 2640 2641 test: 2642 suffix: adv_2d_tri_1 2643 requires: triangle 2644 TODO: how did this ever get in master when there is no support for this 2645 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 2646 2647 test: 2648 suffix: adv_0 2649 requires: exodusii 2650 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo -bc_inflow 100,101,200 -bc_outflow 201 2651 2652 test: 2653 suffix: shock_0 2654 requires: p4est !single !complex 2655 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 2656 timeoutfactor: 3 2657 2658 # Test GLVis visualization of PetscFV fields 2659 test: 2660 suffix: glvis_adv_2d_tet 2661 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 2662 2663 test: 2664 suffix: glvis_adv_2d_quad 2665 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 2666 2667 test: 2668 suffix: tut_1 2669 requires: exodusii 2670 nsize: 1 2671 args: -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo 2672 2673 test: 2674 suffix: tut_2 2675 requires: exodusii 2676 nsize: 1 2677 args: -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo -ts_type rosw 2678 2679 test: 2680 suffix: tut_3 2681 requires: exodusii 2682 nsize: 4 2683 args: -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/annulus-20.exo -monitor Error -advect_sol_type bump -petscfv_type leastsquares -petsclimiter_type sin 2684 2685 test: 2686 suffix: tut_4 2687 requires: exodusii 2688 nsize: 4 2689 args: -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/annulus-20.exo -physics sw -monitor Height,Energy -petscfv_type leastsquares -petsclimiter_type minmod 2690 2691 TEST*/ 2692