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, PhysicsRiemannList_SW; 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, NULL, 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, NULL, 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_HLL(PetscInt dim, PetscInt Nf, const PetscReal *qp, const PetscReal *n, const PetscScalar *xL, const PetscScalar *xR, PetscInt numConstants, const PetscScalar constants[], PetscScalar *flux, Physics phys) 399 { 400 Physics_SW *sw = (Physics_SW *) phys->data; 401 PetscReal aL, aR; 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) { 420 for (i = 0; i < 1 + dim; i++) flux[i] = zero; 421 return; 422 } /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */ 423 nn[0] = n[0]; 424 nn[1] = n[1]; 425 Normalize2Real(nn); 426 SWFlux(phys, nn, uL, &(fL.swnode)); 427 SWFlux(phys, nn, uR, &(fR.swnode)); 428 /* gravity wave speed */ 429 aL = PetscSqrtReal(sw->gravity * uL->h); 430 aR = PetscSqrtReal(sw->gravity * uR->h); 431 // Defining u_tilda and v_tilda as u and v 432 PetscReal u_L, u_R; 433 u_L = Dot2Real(uL->uh,nn)/uL->h; 434 u_R = Dot2Real(uR->uh,nn)/uR->h; 435 PetscReal sL, sR; 436 sL = PetscMin(u_L - aL, u_R - aR); 437 sR = PetscMax(u_L + aL, u_R + aR); 438 if (sL > zero) { 439 for (i = 0; i < dim + 1; i++) { 440 flux[i] = fL.vals[i] * Norm2Real(n); 441 } 442 } else if (sR < zero) { 443 for (i = 0; i < dim + 1; i++) { 444 flux[i] = fR.vals[i] * Norm2Real(n); 445 } 446 } else { 447 for (i = 0; i < dim + 1; i++) { 448 flux[i] = ((sR * fL.vals[i] - sL * fR.vals[i] + sR * sL * (xR[i] - xL[i])) / (sR - sL)) * Norm2Real(n); 449 } 450 } 451 } 452 453 static void PhysicsRiemann_SW_Rusanov(PetscInt dim, PetscInt Nf, const PetscReal *qp, const PetscReal *n, const PetscScalar *xL, const PetscScalar *xR, PetscInt numConstants, const PetscScalar constants[], PetscScalar *flux, Physics phys) 454 { 455 Physics_SW *sw = (Physics_SW*)phys->data; 456 PetscReal cL,cR,speed; 457 PetscReal nn[DIM]; 458 #if !defined(PETSC_USE_COMPLEX) 459 const SWNode *uL = (const SWNode*)xL,*uR = (const SWNode*)xR; 460 #else 461 SWNodeUnion uLreal, uRreal; 462 const SWNode *uL = &uLreal.swnode; 463 const SWNode *uR = &uRreal.swnode; 464 #endif 465 SWNodeUnion fL,fR; 466 PetscInt i; 467 PetscReal zero=0.; 468 469 #if defined(PETSC_USE_COMPLEX) 470 uLreal.swnode.h = 0; uRreal.swnode.h = 0; 471 for (i = 0; i < 1+dim; i++) uLreal.vals[i] = PetscRealPart(xL[i]); 472 for (i = 0; i < 1+dim; i++) uRreal.vals[i] = PetscRealPart(xR[i]); 473 #endif 474 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"); */ 475 nn[0] = n[0]; 476 nn[1] = n[1]; 477 Normalize2Real(nn); 478 SWFlux(phys,nn,uL,&(fL.swnode)); 479 SWFlux(phys,nn,uR,&(fR.swnode)); 480 cL = PetscSqrtReal(sw->gravity*uL->h); 481 cR = PetscSqrtReal(sw->gravity*uR->h); /* gravity wave speed */ 482 speed = PetscMax(PetscAbsReal(Dot2Real(uL->uh,nn)/uL->h) + cL,PetscAbsReal(Dot2Real(uR->uh,nn)/uR->h) + cR); 483 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); 484 } 485 486 static PetscErrorCode PhysicsSolution_SW(Model mod,PetscReal time,const PetscReal *x,PetscScalar *u,void *ctx) 487 { 488 PetscReal dx[2],r,sigma; 489 490 PetscFunctionBeginUser; 491 if (time != 0.0) SETERRQ1(mod->comm,PETSC_ERR_SUP,"No solution known for time %g",(double)time); 492 dx[0] = x[0] - 1.5; 493 dx[1] = x[1] - 1.0; 494 r = Norm2Real(dx); 495 sigma = 0.5; 496 u[0] = 1 + 2*PetscExpReal(-PetscSqr(r)/(2*PetscSqr(sigma))); 497 u[1] = 0.0; 498 u[2] = 0.0; 499 PetscFunctionReturn(0); 500 } 501 502 static PetscErrorCode PhysicsFunctional_SW(Model mod,PetscReal time,const PetscReal *coord,const PetscScalar *xx,PetscReal *f,void *ctx) 503 { 504 Physics phys = (Physics)ctx; 505 Physics_SW *sw = (Physics_SW*)phys->data; 506 const SWNode *x = (const SWNode*)xx; 507 PetscReal u[2]; 508 PetscReal h; 509 510 PetscFunctionBeginUser; 511 h = x->h; 512 Scale2Real(1./x->h,x->uh,u); 513 f[sw->functional.Height] = h; 514 f[sw->functional.Speed] = Norm2Real(u) + PetscSqrtReal(sw->gravity*h); 515 f[sw->functional.Energy] = 0.5*(Dot2Real(x->uh,u) + sw->gravity*PetscSqr(h)); 516 PetscFunctionReturn(0); 517 } 518 519 static PetscErrorCode SetUpBC_SW(PetscDS prob,Physics phys) 520 { 521 PetscErrorCode ierr; 522 const PetscInt wallids[] = {100,101,200,300}; 523 PetscFunctionBeginUser; 524 ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "wall", "Face Sets", 0, 0, NULL, (void (*)(void)) PhysicsBoundary_SW_Wall, NULL, ALEN(wallids), wallids, phys);CHKERRQ(ierr); 525 PetscFunctionReturn(0); 526 } 527 528 static PetscErrorCode PhysicsCreate_SW(Model mod,Physics phys,PetscOptionItems *PetscOptionsObject) 529 { 530 Physics_SW *sw; 531 char sw_riemann[64] = "rusanov"; 532 PetscErrorCode ierr; 533 534 PetscFunctionBeginUser; 535 phys->field_desc = PhysicsFields_SW; 536 ierr = PetscNew(&sw);CHKERRQ(ierr); 537 phys->data = sw; 538 mod->setupbc = SetUpBC_SW; 539 540 PetscFunctionListAdd(&PhysicsRiemannList_SW, "rusanov", PhysicsRiemann_SW_Rusanov); 541 PetscFunctionListAdd(&PhysicsRiemannList_SW, "hll", PhysicsRiemann_SW_HLL); 542 543 ierr = PetscOptionsHead(PetscOptionsObject,"SW options");CHKERRQ(ierr); 544 { 545 void (*PhysicsRiemann_SW)(PetscInt, PetscInt, const PetscReal *, const PetscReal *, const PetscScalar *, const PetscScalar *, PetscInt, const PetscScalar, PetscScalar *, Physics); 546 sw->gravity = 1.0; 547 ierr = PetscOptionsReal("-sw_gravity","Gravitational constant","",sw->gravity,&sw->gravity,NULL);CHKERRQ(ierr); 548 ierr = PetscOptionsFList("-sw_riemann","Riemann solver","",PhysicsRiemannList_SW,sw_riemann,sw_riemann,sizeof sw_riemann,NULL);CHKERRQ(ierr); 549 ierr = PetscFunctionListFind(PhysicsRiemannList_SW,sw_riemann,&PhysicsRiemann_SW);CHKERRQ(ierr); 550 phys->riemann = (PetscRiemannFunc) PhysicsRiemann_SW; 551 } 552 ierr = PetscOptionsTail();CHKERRQ(ierr); 553 phys->maxspeed = PetscSqrtReal(2.0*sw->gravity); /* Mach 1 for depth of 2 */ 554 555 ierr = ModelSolutionSetDefault(mod,PhysicsSolution_SW,phys);CHKERRQ(ierr); 556 ierr = ModelFunctionalRegister(mod,"Height",&sw->functional.Height,PhysicsFunctional_SW,phys);CHKERRQ(ierr); 557 ierr = ModelFunctionalRegister(mod,"Speed",&sw->functional.Speed,PhysicsFunctional_SW,phys);CHKERRQ(ierr); 558 ierr = ModelFunctionalRegister(mod,"Energy",&sw->functional.Energy,PhysicsFunctional_SW,phys);CHKERRQ(ierr); 559 560 mod->bcs[0] = mod->bcs[1] = mod->bcs[2] = DM_BOUNDARY_GHOSTED; 561 562 PetscFunctionReturn(0); 563 } 564 565 /******************* Euler Density Shock (EULER_IV_SHOCK,EULER_SS_SHOCK) ********************/ 566 /* An initial-value and self-similar solutions of the compressible Euler equations */ 567 /* Ravi Samtaney and D. I. Pullin */ 568 /* Phys. Fluids 8, 2650 (1996); http://dx.doi.org/10.1063/1.869050 */ 569 typedef enum {EULER_PAR_GAMMA,EULER_PAR_RHOR,EULER_PAR_AMACH,EULER_PAR_ITANA,EULER_PAR_SIZE} EulerParamIdx; 570 typedef enum {EULER_IV_SHOCK,EULER_SS_SHOCK,EULER_SHOCK_TUBE,EULER_LINEAR_WAVE} EulerType; 571 typedef struct { 572 PetscReal r; 573 PetscReal ru[DIM]; 574 PetscReal E; 575 } EulerNode; 576 typedef union { 577 EulerNode eulernode; 578 PetscReal vals[DIM+2]; 579 } EulerNodeUnion; 580 typedef PetscErrorCode (*EquationOfState)(const PetscReal*, const EulerNode*, PetscReal*); 581 typedef struct { 582 EulerType type; 583 PetscReal pars[EULER_PAR_SIZE]; 584 EquationOfState sound; 585 struct { 586 PetscInt Density; 587 PetscInt Momentum; 588 PetscInt Energy; 589 PetscInt Pressure; 590 PetscInt Speed; 591 } monitor; 592 } Physics_Euler; 593 594 static const struct FieldDescription PhysicsFields_Euler[] = {{"Density",1},{"Momentum",DIM},{"Energy",1},{NULL,0}}; 595 596 /* initial condition */ 597 int initLinearWave(EulerNode *ux, const PetscReal gamma, const PetscReal coord[], const PetscReal Lx); 598 static PetscErrorCode PhysicsSolution_Euler(Model mod, PetscReal time, const PetscReal *x, PetscScalar *u, void *ctx) 599 { 600 PetscInt i; 601 Physics phys = (Physics)ctx; 602 Physics_Euler *eu = (Physics_Euler*)phys->data; 603 EulerNode *uu = (EulerNode*)u; 604 PetscReal p0,gamma,c; 605 PetscFunctionBeginUser; 606 if (time != 0.0) SETERRQ1(mod->comm,PETSC_ERR_SUP,"No solution known for time %g",(double)time); 607 608 for (i=0; i<DIM; i++) uu->ru[i] = 0.0; /* zero out initial velocity */ 609 /* set E and rho */ 610 gamma = eu->pars[EULER_PAR_GAMMA]; 611 612 if (eu->type==EULER_IV_SHOCK || eu->type==EULER_SS_SHOCK) { 613 /******************* Euler Density Shock ********************/ 614 /* On initial-value and self-similar solutions of the compressible Euler equations */ 615 /* Ravi Samtaney and D. I. Pullin */ 616 /* Phys. Fluids 8, 2650 (1996); http://dx.doi.org/10.1063/1.869050 */ 617 /* initial conditions 1: left of shock, 0: left of discontinuity 2: right of discontinuity, */ 618 p0 = 1.; 619 if (x[0] < 0.0 + x[1]*eu->pars[EULER_PAR_ITANA]) { 620 if (x[0] < mod->bounds[0]*0.5) { /* left of shock (1) */ 621 PetscReal amach,rho,press,gas1,p1; 622 amach = eu->pars[EULER_PAR_AMACH]; 623 rho = 1.; 624 press = p0; 625 p1 = press*(1.0+2.0*gamma/(gamma+1.0)*(amach*amach-1.0)); 626 gas1 = (gamma-1.0)/(gamma+1.0); 627 uu->r = rho*(p1/press+gas1)/(gas1*p1/press+1.0); 628 uu->ru[0] = ((uu->r - rho)*PetscSqrtReal(gamma*press/rho)*amach); 629 uu->E = p1/(gamma-1.0) + .5/uu->r*uu->ru[0]*uu->ru[0]; 630 } 631 else { /* left of discontinuity (0) */ 632 uu->r = 1.; /* rho = 1 */ 633 uu->E = p0/(gamma-1.0); 634 } 635 } 636 else { /* right of discontinuity (2) */ 637 uu->r = eu->pars[EULER_PAR_RHOR]; 638 uu->E = p0/(gamma-1.0); 639 } 640 } 641 else if (eu->type==EULER_SHOCK_TUBE) { 642 /* 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. */ 643 if (x[0] < 0.0) { 644 uu->r = 8.; 645 uu->E = 10./(gamma-1.); 646 } 647 else { 648 uu->r = 1.; 649 uu->E = 1./(gamma-1.); 650 } 651 } 652 else if (eu->type==EULER_LINEAR_WAVE) { 653 initLinearWave( uu, gamma, x, mod->bounds[1] - mod->bounds[0]); 654 } 655 else SETERRQ1(mod->comm,PETSC_ERR_SUP,"Unknown type %d",eu->type); 656 657 /* set phys->maxspeed: (mod->maxspeed = phys->maxspeed) in main; */ 658 eu->sound(&gamma,uu,&c); 659 c = (uu->ru[0]/uu->r) + c; 660 if (c > phys->maxspeed) phys->maxspeed = c; 661 662 PetscFunctionReturn(0); 663 } 664 665 static PetscErrorCode Pressure_PG(const PetscReal gamma,const EulerNode *x,PetscReal *p) 666 { 667 PetscReal ru2; 668 669 PetscFunctionBeginUser; 670 ru2 = DotDIMReal(x->ru,x->ru); 671 (*p)=(x->E - 0.5*ru2/x->r)*(gamma - 1.0); /* (E - rho V^2/2)(gamma-1) = e rho (gamma-1) */ 672 PetscFunctionReturn(0); 673 } 674 675 static PetscErrorCode SpeedOfSound_PG(const PetscReal *gamma, const EulerNode *x, PetscReal *c) 676 { 677 PetscReal p; 678 679 PetscFunctionBeginUser; 680 Pressure_PG(*gamma,x,&p); 681 if (p<0.) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"negative pressure time %g -- NEED TO FIX!!!!!!",(double) p); 682 /* pars[EULER_PAR_GAMMA] = heat capacity ratio */ 683 (*c)=PetscSqrtReal(*gamma * p / x->r); 684 PetscFunctionReturn(0); 685 } 686 687 /* 688 * x = (rho,rho*(u_1),...,rho*e)^T 689 * x_t+div(f_1(x))+...+div(f_DIM(x)) = 0 690 * 691 * f_i(x) = u_i*x+(0,0,...,p,...,p*u_i)^T 692 * 693 */ 694 static PetscErrorCode EulerFlux(Physics phys,const PetscReal *n,const EulerNode *x,EulerNode *f) 695 { 696 Physics_Euler *eu = (Physics_Euler*)phys->data; 697 PetscReal nu,p; 698 PetscInt i; 699 700 PetscFunctionBeginUser; 701 Pressure_PG(eu->pars[EULER_PAR_GAMMA],x,&p); 702 nu = DotDIMReal(x->ru,n); 703 f->r = nu; /* A rho u */ 704 nu /= x->r; /* A u */ 705 for (i=0; i<DIM; i++) f->ru[i] = nu * x->ru[i] + n[i]*p; /* r u^2 + p */ 706 f->E = nu * (x->E + p); /* u(e+p) */ 707 PetscFunctionReturn(0); 708 } 709 710 /* PetscReal* => EulerNode* conversion */ 711 static PetscErrorCode PhysicsBoundary_Euler_Wall(PetscReal time, const PetscReal *c, const PetscReal *n, const PetscScalar *a_xI, PetscScalar *a_xG, void *ctx) 712 { 713 PetscInt i; 714 const EulerNode *xI = (const EulerNode*)a_xI; 715 EulerNode *xG = (EulerNode*)a_xG; 716 Physics phys = (Physics)ctx; 717 Physics_Euler *eu = (Physics_Euler*)phys->data; 718 PetscFunctionBeginUser; 719 xG->r = xI->r; /* ghost cell density - same */ 720 xG->E = xI->E; /* ghost cell energy - same */ 721 if (n[1] != 0.) { /* top and bottom */ 722 xG->ru[0] = xI->ru[0]; /* copy tang to wall */ 723 xG->ru[1] = -xI->ru[1]; /* reflect perp to t/b wall */ 724 } 725 else { /* sides */ 726 for (i=0; i<DIM; i++) xG->ru[i] = xI->ru[i]; /* copy */ 727 } 728 if (eu->type == EULER_LINEAR_WAVE) { /* debug */ 729 #if 0 730 PetscPrintf(PETSC_COMM_WORLD,"%s coord=%g,%g\n",PETSC_FUNCTION_NAME,c[0],c[1]); 731 #endif 732 } 733 PetscFunctionReturn(0); 734 } 735 int godunovflux( const PetscScalar *ul, const PetscScalar *ur, PetscScalar *flux, const PetscReal *nn, const int *ndim, const PetscReal *gamma); 736 /* PetscReal* => EulerNode* conversion */ 737 static void PhysicsRiemann_Euler_Godunov( PetscInt dim, PetscInt Nf, const PetscReal *qp, const PetscReal *n, 738 const PetscScalar *xL, const PetscScalar *xR, PetscInt numConstants, const PetscScalar constants[], PetscScalar *flux, Physics phys) 739 { 740 Physics_Euler *eu = (Physics_Euler*)phys->data; 741 PetscReal cL,cR,speed,velL,velR,nn[DIM],s2; 742 PetscInt i; 743 PetscErrorCode ierr; 744 PetscFunctionBeginUser; 745 746 for (i=0,s2=0.; i<DIM; i++) { 747 nn[i] = n[i]; 748 s2 += nn[i]*nn[i]; 749 } 750 s2 = PetscSqrtReal(s2); /* |n|_2 = sum(n^2)^1/2 */ 751 for (i=0.; i<DIM; i++) nn[i] /= s2; 752 if (0) { /* Rusanov */ 753 const EulerNode *uL = (const EulerNode*)xL,*uR = (const EulerNode*)xR; 754 EulerNodeUnion fL,fR; 755 EulerFlux(phys,nn,uL,&(fL.eulernode)); 756 EulerFlux(phys,nn,uR,&(fR.eulernode)); 757 ierr = eu->sound(&eu->pars[EULER_PAR_GAMMA],uL,&cL);if (ierr) exit(13); 758 ierr = eu->sound(&eu->pars[EULER_PAR_GAMMA],uR,&cR);if (ierr) exit(14); 759 velL = DotDIMReal(uL->ru,nn)/uL->r; 760 velR = DotDIMReal(uR->ru,nn)/uR->r; 761 speed = PetscMax(velR + cR, velL + cL); 762 for (i=0; i<2+dim; i++) flux[i] = 0.5*((fL.vals[i]+fR.vals[i]) + speed*(xL[i] - xR[i]))*s2; 763 } 764 else { 765 int dim = DIM; 766 /* int iwave = */ 767 godunovflux(xL, xR, flux, nn, &dim, &eu->pars[EULER_PAR_GAMMA]); 768 for (i=0; i<2+dim; i++) flux[i] *= s2; 769 } 770 PetscFunctionReturnVoid(); 771 } 772 773 static PetscErrorCode PhysicsFunctional_Euler(Model mod,PetscReal time,const PetscReal *coord,const PetscScalar *xx,PetscReal *f,void *ctx) 774 { 775 Physics phys = (Physics)ctx; 776 Physics_Euler *eu = (Physics_Euler*)phys->data; 777 const EulerNode *x = (const EulerNode*)xx; 778 PetscReal p; 779 780 PetscFunctionBeginUser; 781 f[eu->monitor.Density] = x->r; 782 f[eu->monitor.Momentum] = NormDIM(x->ru); 783 f[eu->monitor.Energy] = x->E; 784 f[eu->monitor.Speed] = NormDIM(x->ru)/x->r; 785 Pressure_PG(eu->pars[EULER_PAR_GAMMA], x, &p); 786 f[eu->monitor.Pressure] = p; 787 PetscFunctionReturn(0); 788 } 789 790 static PetscErrorCode SetUpBC_Euler(PetscDS prob,Physics phys) 791 { 792 PetscErrorCode ierr; 793 Physics_Euler *eu = (Physics_Euler *) phys->data; 794 if (eu->type == EULER_LINEAR_WAVE) { 795 const PetscInt wallids[] = {100,101}; 796 ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "wall", "Face Sets", 0, 0, NULL, (void (*)(void)) PhysicsBoundary_Euler_Wall, NULL, ALEN(wallids), wallids, phys);CHKERRQ(ierr); 797 } 798 else { 799 const PetscInt wallids[] = {100,101,200,300}; 800 ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL_RIEMANN, "wall", "Face Sets", 0, 0, NULL, (void (*)(void)) PhysicsBoundary_Euler_Wall, NULL, ALEN(wallids), wallids, phys);CHKERRQ(ierr); 801 } 802 PetscFunctionReturn(0); 803 } 804 805 static PetscErrorCode PhysicsCreate_Euler(Model mod,Physics phys,PetscOptionItems *PetscOptionsObject) 806 { 807 Physics_Euler *eu; 808 PetscErrorCode ierr; 809 810 PetscFunctionBeginUser; 811 phys->field_desc = PhysicsFields_Euler; 812 phys->riemann = (PetscRiemannFunc) PhysicsRiemann_Euler_Godunov; 813 ierr = PetscNew(&eu);CHKERRQ(ierr); 814 phys->data = eu; 815 mod->setupbc = SetUpBC_Euler; 816 ierr = PetscOptionsHead(PetscOptionsObject,"Euler options");CHKERRQ(ierr); 817 { 818 PetscReal alpha; 819 char type[64] = "linear_wave"; 820 PetscBool is; 821 mod->bcs[0] = mod->bcs[1] = mod->bcs[2] = DM_BOUNDARY_GHOSTED; 822 eu->pars[EULER_PAR_GAMMA] = 1.4; 823 eu->pars[EULER_PAR_AMACH] = 2.02; 824 eu->pars[EULER_PAR_RHOR] = 3.0; 825 eu->pars[EULER_PAR_ITANA] = 0.57735026918963; /* angle of Euler self similar (SS) shock */ 826 ierr = PetscOptionsReal("-eu_gamma","Heat capacity ratio","",eu->pars[EULER_PAR_GAMMA],&eu->pars[EULER_PAR_GAMMA],NULL);CHKERRQ(ierr); 827 ierr = PetscOptionsReal("-eu_amach","Shock speed (Mach)","",eu->pars[EULER_PAR_AMACH],&eu->pars[EULER_PAR_AMACH],NULL);CHKERRQ(ierr); 828 ierr = PetscOptionsReal("-eu_rho2","Density right of discontinuity","",eu->pars[EULER_PAR_RHOR],&eu->pars[EULER_PAR_RHOR],NULL);CHKERRQ(ierr); 829 alpha = 60.; 830 ierr = PetscOptionsReal("-eu_alpha","Angle of discontinuity","",alpha,&alpha,NULL);CHKERRQ(ierr); 831 if (alpha<=0. || alpha>90.) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Alpha bust be > 0 and <= 90 (%g)",alpha); 832 eu->pars[EULER_PAR_ITANA] = 1./PetscTanReal( alpha * PETSC_PI / 180.0); 833 ierr = PetscOptionsString("-eu_type","Type of Euler test","",type,type,sizeof(type),NULL);CHKERRQ(ierr); 834 ierr = PetscStrcmp(type,"linear_wave", &is);CHKERRQ(ierr); 835 if (is) { 836 eu->type = EULER_LINEAR_WAVE; 837 mod->bcs[0] = mod->bcs[1] = mod->bcs[2] = DM_BOUNDARY_PERIODIC; 838 mod->bcs[1] = DM_BOUNDARY_GHOSTED; /* debug */ 839 ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"linear_wave");CHKERRQ(ierr); 840 } 841 else { 842 if (DIM != 2) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"DIM must be 2 unless linear wave test %s",type); 843 ierr = PetscStrcmp(type,"iv_shock", &is);CHKERRQ(ierr); 844 if (is) { 845 eu->type = EULER_IV_SHOCK; 846 ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"iv_shock");CHKERRQ(ierr); 847 } 848 else { 849 ierr = PetscStrcmp(type,"ss_shock", &is);CHKERRQ(ierr); 850 if (is) { 851 eu->type = EULER_SS_SHOCK; 852 ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"ss_shock");CHKERRQ(ierr); 853 } 854 else { 855 ierr = PetscStrcmp(type,"shock_tube", &is);CHKERRQ(ierr); 856 if (is) eu->type = EULER_SHOCK_TUBE; 857 else SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Unknown Euler type %s",type); 858 ierr = PetscPrintf(PETSC_COMM_WORLD,"%s set Euler type: %s\n",PETSC_FUNCTION_NAME,"shock_tube");CHKERRQ(ierr); 859 } 860 } 861 } 862 } 863 ierr = PetscOptionsTail();CHKERRQ(ierr); 864 eu->sound = SpeedOfSound_PG; 865 phys->maxspeed = 0.; /* will get set in solution */ 866 ierr = ModelSolutionSetDefault(mod,PhysicsSolution_Euler,phys);CHKERRQ(ierr); 867 ierr = ModelFunctionalRegister(mod,"Speed",&eu->monitor.Speed,PhysicsFunctional_Euler,phys);CHKERRQ(ierr); 868 ierr = ModelFunctionalRegister(mod,"Energy",&eu->monitor.Energy,PhysicsFunctional_Euler,phys);CHKERRQ(ierr); 869 ierr = ModelFunctionalRegister(mod,"Density",&eu->monitor.Density,PhysicsFunctional_Euler,phys);CHKERRQ(ierr); 870 ierr = ModelFunctionalRegister(mod,"Momentum",&eu->monitor.Momentum,PhysicsFunctional_Euler,phys);CHKERRQ(ierr); 871 ierr = ModelFunctionalRegister(mod,"Pressure",&eu->monitor.Pressure,PhysicsFunctional_Euler,phys);CHKERRQ(ierr); 872 873 PetscFunctionReturn(0); 874 } 875 876 static PetscErrorCode ErrorIndicator_Simple(PetscInt dim, PetscReal volume, PetscInt numComps, const PetscScalar u[], const PetscScalar grad[], PetscReal *error, void *ctx) 877 { 878 PetscReal err = 0.; 879 PetscInt i, j; 880 881 PetscFunctionBeginUser; 882 for (i = 0; i < numComps; i++) { 883 for (j = 0; j < dim; j++) { 884 err += PetscSqr(PetscRealPart(grad[i * dim + j])); 885 } 886 } 887 *error = volume * err; 888 PetscFunctionReturn(0); 889 } 890 891 PetscErrorCode ConstructCellBoundary(DM dm, User user) 892 { 893 const char *name = "Cell Sets"; 894 const char *bdname = "split faces"; 895 IS regionIS, innerIS; 896 const PetscInt *regions, *cells; 897 PetscInt numRegions, innerRegion, numCells, c; 898 PetscInt cStart, cEnd, cEndInterior, fStart, fEnd; 899 PetscBool hasLabel; 900 PetscErrorCode ierr; 901 902 PetscFunctionBeginUser; 903 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 904 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 905 ierr = DMPlexGetGhostCellStratum(dm, &cEndInterior, NULL);CHKERRQ(ierr); 906 907 ierr = DMHasLabel(dm, name, &hasLabel);CHKERRQ(ierr); 908 if (!hasLabel) PetscFunctionReturn(0); 909 ierr = DMGetLabelSize(dm, name, &numRegions);CHKERRQ(ierr); 910 if (numRegions != 2) PetscFunctionReturn(0); 911 /* Get the inner id */ 912 ierr = DMGetLabelIdIS(dm, name, ®ionIS);CHKERRQ(ierr); 913 ierr = ISGetIndices(regionIS, ®ions);CHKERRQ(ierr); 914 innerRegion = regions[0]; 915 ierr = ISRestoreIndices(regionIS, ®ions);CHKERRQ(ierr); 916 ierr = ISDestroy(®ionIS);CHKERRQ(ierr); 917 /* Find the faces between cells in different regions, could call DMPlexCreateNeighborCSR() */ 918 ierr = DMGetStratumIS(dm, name, innerRegion, &innerIS);CHKERRQ(ierr); 919 ierr = ISGetLocalSize(innerIS, &numCells);CHKERRQ(ierr); 920 ierr = ISGetIndices(innerIS, &cells);CHKERRQ(ierr); 921 ierr = DMCreateLabel(dm, bdname);CHKERRQ(ierr); 922 for (c = 0; c < numCells; ++c) { 923 const PetscInt cell = cells[c]; 924 const PetscInt *faces; 925 PetscInt numFaces, f; 926 927 if ((cell < cStart) || (cell >= cEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Got invalid point %d which is not a cell", cell); 928 ierr = DMPlexGetConeSize(dm, cell, &numFaces);CHKERRQ(ierr); 929 ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr); 930 for (f = 0; f < numFaces; ++f) { 931 const PetscInt face = faces[f]; 932 const PetscInt *neighbors; 933 PetscInt nC, regionA, regionB; 934 935 if ((face < fStart) || (face >= fEnd)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "Got invalid point %d which is not a face", face); 936 ierr = DMPlexGetSupportSize(dm, face, &nC);CHKERRQ(ierr); 937 if (nC != 2) continue; 938 ierr = DMPlexGetSupport(dm, face, &neighbors);CHKERRQ(ierr); 939 if ((neighbors[0] >= cEndInterior) || (neighbors[1] >= cEndInterior)) continue; 940 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]); 941 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]); 942 ierr = DMGetLabelValue(dm, name, neighbors[0], ®ionA);CHKERRQ(ierr); 943 ierr = DMGetLabelValue(dm, name, neighbors[1], ®ionB);CHKERRQ(ierr); 944 if (regionA < 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid label %s: Cell %d has no value", name, neighbors[0]); 945 if (regionB < 0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Invalid label %s: Cell %d has no value", name, neighbors[1]); 946 if (regionA != regionB) { 947 ierr = DMSetLabelValue(dm, bdname, faces[f], 1);CHKERRQ(ierr); 948 } 949 } 950 } 951 ierr = ISRestoreIndices(innerIS, &cells);CHKERRQ(ierr); 952 ierr = ISDestroy(&innerIS);CHKERRQ(ierr); 953 { 954 DMLabel label; 955 956 ierr = DMGetLabel(dm, bdname, &label);CHKERRQ(ierr); 957 ierr = DMLabelView(label, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 958 } 959 PetscFunctionReturn(0); 960 } 961 962 /* Right now, I have just added duplicate faces, which see both cells. We can 963 - Add duplicate vertices and decouple the face cones 964 - Disconnect faces from cells across the rotation gap 965 */ 966 PetscErrorCode SplitFaces(DM *dmSplit, const char labelName[], User user) 967 { 968 DM dm = *dmSplit, sdm; 969 PetscSF sfPoint, gsfPoint; 970 PetscSection coordSection, newCoordSection; 971 Vec coordinates; 972 IS idIS; 973 const PetscInt *ids; 974 PetscInt *newpoints; 975 PetscInt dim, depth, maxConeSize, maxSupportSize, numLabels, numGhostCells; 976 PetscInt numFS, fs, pStart, pEnd, p, cEnd, cEndInterior, vStart, vEnd, v, fStart, fEnd, newf, d, l; 977 PetscBool hasLabel; 978 PetscErrorCode ierr; 979 980 PetscFunctionBeginUser; 981 ierr = DMHasLabel(dm, labelName, &hasLabel);CHKERRQ(ierr); 982 if (!hasLabel) PetscFunctionReturn(0); 983 ierr = DMCreate(PetscObjectComm((PetscObject)dm), &sdm);CHKERRQ(ierr); 984 ierr = DMSetType(sdm, DMPLEX);CHKERRQ(ierr); 985 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 986 ierr = DMSetDimension(sdm, dim);CHKERRQ(ierr); 987 988 ierr = DMGetLabelIdIS(dm, labelName, &idIS);CHKERRQ(ierr); 989 ierr = ISGetLocalSize(idIS, &numFS);CHKERRQ(ierr); 990 ierr = ISGetIndices(idIS, &ids);CHKERRQ(ierr); 991 992 user->numSplitFaces = 0; 993 for (fs = 0; fs < numFS; ++fs) { 994 PetscInt numBdFaces; 995 996 ierr = DMGetStratumSize(dm, labelName, ids[fs], &numBdFaces);CHKERRQ(ierr); 997 user->numSplitFaces += numBdFaces; 998 } 999 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 1000 pEnd += user->numSplitFaces; 1001 ierr = DMPlexSetChart(sdm, pStart, pEnd);CHKERRQ(ierr); 1002 ierr = DMPlexGetGhostCellStratum(dm, &cEndInterior, NULL);CHKERRQ(ierr); 1003 ierr = DMPlexGetHeightStratum(dm, 0, NULL, &cEnd);CHKERRQ(ierr); 1004 numGhostCells = cEnd - cEndInterior; 1005 /* Set cone and support sizes */ 1006 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1007 for (d = 0; d <= depth; ++d) { 1008 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 1009 for (p = pStart; p < pEnd; ++p) { 1010 PetscInt newp = p; 1011 PetscInt size; 1012 1013 ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); 1014 ierr = DMPlexSetConeSize(sdm, newp, size);CHKERRQ(ierr); 1015 ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); 1016 ierr = DMPlexSetSupportSize(sdm, newp, size);CHKERRQ(ierr); 1017 } 1018 } 1019 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1020 for (fs = 0, newf = fEnd; fs < numFS; ++fs) { 1021 IS faceIS; 1022 const PetscInt *faces; 1023 PetscInt numFaces, f; 1024 1025 ierr = DMGetStratumIS(dm, labelName, ids[fs], &faceIS);CHKERRQ(ierr); 1026 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 1027 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 1028 for (f = 0; f < numFaces; ++f, ++newf) { 1029 PetscInt size; 1030 1031 /* Right now I think that both faces should see both cells */ 1032 ierr = DMPlexGetConeSize(dm, faces[f], &size);CHKERRQ(ierr); 1033 ierr = DMPlexSetConeSize(sdm, newf, size);CHKERRQ(ierr); 1034 ierr = DMPlexGetSupportSize(dm, faces[f], &size);CHKERRQ(ierr); 1035 ierr = DMPlexSetSupportSize(sdm, newf, size);CHKERRQ(ierr); 1036 } 1037 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 1038 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 1039 } 1040 ierr = DMSetUp(sdm);CHKERRQ(ierr); 1041 /* Set cones and supports */ 1042 ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr); 1043 ierr = PetscMalloc1(PetscMax(maxConeSize, maxSupportSize), &newpoints);CHKERRQ(ierr); 1044 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 1045 for (p = pStart; p < pEnd; ++p) { 1046 const PetscInt *points, *orientations; 1047 PetscInt size, i, newp = p; 1048 1049 ierr = DMPlexGetConeSize(dm, p, &size);CHKERRQ(ierr); 1050 ierr = DMPlexGetCone(dm, p, &points);CHKERRQ(ierr); 1051 ierr = DMPlexGetConeOrientation(dm, p, &orientations);CHKERRQ(ierr); 1052 for (i = 0; i < size; ++i) newpoints[i] = points[i]; 1053 ierr = DMPlexSetCone(sdm, newp, newpoints);CHKERRQ(ierr); 1054 ierr = DMPlexSetConeOrientation(sdm, newp, orientations);CHKERRQ(ierr); 1055 ierr = DMPlexGetSupportSize(dm, p, &size);CHKERRQ(ierr); 1056 ierr = DMPlexGetSupport(dm, p, &points);CHKERRQ(ierr); 1057 for (i = 0; i < size; ++i) newpoints[i] = points[i]; 1058 ierr = DMPlexSetSupport(sdm, newp, newpoints);CHKERRQ(ierr); 1059 } 1060 ierr = PetscFree(newpoints);CHKERRQ(ierr); 1061 for (fs = 0, newf = fEnd; fs < numFS; ++fs) { 1062 IS faceIS; 1063 const PetscInt *faces; 1064 PetscInt numFaces, f; 1065 1066 ierr = DMGetStratumIS(dm, labelName, ids[fs], &faceIS);CHKERRQ(ierr); 1067 ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr); 1068 ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr); 1069 for (f = 0; f < numFaces; ++f, ++newf) { 1070 const PetscInt *points; 1071 1072 ierr = DMPlexGetCone(dm, faces[f], &points);CHKERRQ(ierr); 1073 ierr = DMPlexSetCone(sdm, newf, points);CHKERRQ(ierr); 1074 ierr = DMPlexGetSupport(dm, faces[f], &points);CHKERRQ(ierr); 1075 ierr = DMPlexSetSupport(sdm, newf, points);CHKERRQ(ierr); 1076 } 1077 ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr); 1078 ierr = ISDestroy(&faceIS);CHKERRQ(ierr); 1079 } 1080 ierr = ISRestoreIndices(idIS, &ids);CHKERRQ(ierr); 1081 ierr = ISDestroy(&idIS);CHKERRQ(ierr); 1082 ierr = DMPlexStratify(sdm);CHKERRQ(ierr); 1083 /* Convert coordinates */ 1084 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1085 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1086 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &newCoordSection);CHKERRQ(ierr); 1087 ierr = PetscSectionSetNumFields(newCoordSection, 1);CHKERRQ(ierr); 1088 ierr = PetscSectionSetFieldComponents(newCoordSection, 0, dim);CHKERRQ(ierr); 1089 ierr = PetscSectionSetChart(newCoordSection, vStart, vEnd);CHKERRQ(ierr); 1090 for (v = vStart; v < vEnd; ++v) { 1091 ierr = PetscSectionSetDof(newCoordSection, v, dim);CHKERRQ(ierr); 1092 ierr = PetscSectionSetFieldDof(newCoordSection, v, 0, dim);CHKERRQ(ierr); 1093 } 1094 ierr = PetscSectionSetUp(newCoordSection);CHKERRQ(ierr); 1095 ierr = DMSetCoordinateSection(sdm, PETSC_DETERMINE, newCoordSection);CHKERRQ(ierr); 1096 ierr = PetscSectionDestroy(&newCoordSection);CHKERRQ(ierr); /* relinquish our reference */ 1097 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1098 ierr = DMSetCoordinatesLocal(sdm, coordinates);CHKERRQ(ierr); 1099 /* Convert labels */ 1100 ierr = DMGetNumLabels(dm, &numLabels);CHKERRQ(ierr); 1101 for (l = 0; l < numLabels; ++l) { 1102 const char *lname; 1103 PetscBool isDepth, isDim; 1104 1105 ierr = DMGetLabelName(dm, l, &lname);CHKERRQ(ierr); 1106 ierr = PetscStrcmp(lname, "depth", &isDepth);CHKERRQ(ierr); 1107 if (isDepth) continue; 1108 ierr = PetscStrcmp(lname, "dim", &isDim);CHKERRQ(ierr); 1109 if (isDim) continue; 1110 ierr = DMCreateLabel(sdm, lname);CHKERRQ(ierr); 1111 ierr = DMGetLabelIdIS(dm, lname, &idIS);CHKERRQ(ierr); 1112 ierr = ISGetLocalSize(idIS, &numFS);CHKERRQ(ierr); 1113 ierr = ISGetIndices(idIS, &ids);CHKERRQ(ierr); 1114 for (fs = 0; fs < numFS; ++fs) { 1115 IS pointIS; 1116 const PetscInt *points; 1117 PetscInt numPoints; 1118 1119 ierr = DMGetStratumIS(dm, lname, ids[fs], &pointIS);CHKERRQ(ierr); 1120 ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr); 1121 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1122 for (p = 0; p < numPoints; ++p) { 1123 PetscInt newpoint = points[p]; 1124 1125 ierr = DMSetLabelValue(sdm, lname, newpoint, ids[fs]);CHKERRQ(ierr); 1126 } 1127 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1128 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1129 } 1130 ierr = ISRestoreIndices(idIS, &ids);CHKERRQ(ierr); 1131 ierr = ISDestroy(&idIS);CHKERRQ(ierr); 1132 } 1133 { 1134 /* Convert pointSF */ 1135 const PetscSFNode *remotePoints; 1136 PetscSFNode *gremotePoints; 1137 const PetscInt *localPoints; 1138 PetscInt *glocalPoints,*newLocation,*newRemoteLocation; 1139 PetscInt numRoots, numLeaves; 1140 PetscMPIInt size; 1141 1142 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm), &size);CHKERRQ(ierr); 1143 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 1144 ierr = DMGetPointSF(sdm, &gsfPoint);CHKERRQ(ierr); 1145 ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); 1146 ierr = PetscSFGetGraph(sfPoint, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr); 1147 if (numRoots >= 0) { 1148 ierr = PetscMalloc2(numRoots,&newLocation,pEnd-pStart,&newRemoteLocation);CHKERRQ(ierr); 1149 for (l=0; l<numRoots; l++) newLocation[l] = l; /* + (l >= cEnd ? numGhostCells : 0); */ 1150 ierr = PetscSFBcastBegin(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 1151 ierr = PetscSFBcastEnd(sfPoint, MPIU_INT, newLocation, newRemoteLocation);CHKERRQ(ierr); 1152 ierr = PetscMalloc1(numLeaves, &glocalPoints);CHKERRQ(ierr); 1153 ierr = PetscMalloc1(numLeaves, &gremotePoints);CHKERRQ(ierr); 1154 for (l = 0; l < numLeaves; ++l) { 1155 glocalPoints[l] = localPoints[l]; /* localPoints[l] >= cEnd ? localPoints[l] + numGhostCells : localPoints[l]; */ 1156 gremotePoints[l].rank = remotePoints[l].rank; 1157 gremotePoints[l].index = newRemoteLocation[localPoints[l]]; 1158 } 1159 ierr = PetscFree2(newLocation,newRemoteLocation);CHKERRQ(ierr); 1160 ierr = PetscSFSetGraph(gsfPoint, numRoots+numGhostCells, numLeaves, glocalPoints, PETSC_OWN_POINTER, gremotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 1161 } 1162 ierr = DMDestroy(dmSplit);CHKERRQ(ierr); 1163 *dmSplit = sdm; 1164 } 1165 PetscFunctionReturn(0); 1166 } 1167 1168 PetscErrorCode CreatePartitionVec(DM dm, DM *dmCell, Vec *partition) 1169 { 1170 PetscSF sfPoint; 1171 PetscSection coordSection; 1172 Vec coordinates; 1173 PetscSection sectionCell; 1174 PetscScalar *part; 1175 PetscInt cStart, cEnd, c; 1176 PetscMPIInt rank; 1177 PetscErrorCode ierr; 1178 1179 PetscFunctionBeginUser; 1180 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1181 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1182 ierr = DMClone(dm, dmCell);CHKERRQ(ierr); 1183 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 1184 ierr = DMSetPointSF(*dmCell, sfPoint);CHKERRQ(ierr); 1185 ierr = DMSetCoordinateSection(*dmCell, PETSC_DETERMINE, coordSection);CHKERRQ(ierr); 1186 ierr = DMSetCoordinatesLocal(*dmCell, coordinates);CHKERRQ(ierr); 1187 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 1188 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ionCell);CHKERRQ(ierr); 1189 ierr = DMPlexGetHeightStratum(*dmCell, 0, &cStart, &cEnd);CHKERRQ(ierr); 1190 ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr); 1191 for (c = cStart; c < cEnd; ++c) { 1192 ierr = PetscSectionSetDof(sectionCell, c, 1);CHKERRQ(ierr); 1193 } 1194 ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr); 1195 ierr = DMSetLocalSection(*dmCell, sectionCell);CHKERRQ(ierr); 1196 ierr = PetscSectionDestroy(§ionCell);CHKERRQ(ierr); 1197 ierr = DMCreateLocalVector(*dmCell, partition);CHKERRQ(ierr); 1198 ierr = PetscObjectSetName((PetscObject)*partition, "partition");CHKERRQ(ierr); 1199 ierr = VecGetArray(*partition, &part);CHKERRQ(ierr); 1200 for (c = cStart; c < cEnd; ++c) { 1201 PetscScalar *p; 1202 1203 ierr = DMPlexPointLocalRef(*dmCell, c, part, &p);CHKERRQ(ierr); 1204 p[0] = rank; 1205 } 1206 ierr = VecRestoreArray(*partition, &part);CHKERRQ(ierr); 1207 PetscFunctionReturn(0); 1208 } 1209 1210 PetscErrorCode CreateMassMatrix(DM dm, Vec *massMatrix, User user) 1211 { 1212 DM plex, dmMass, dmFace, dmCell, dmCoord; 1213 PetscSection coordSection; 1214 Vec coordinates, facegeom, cellgeom; 1215 PetscSection sectionMass; 1216 PetscScalar *m; 1217 const PetscScalar *fgeom, *cgeom, *coords; 1218 PetscInt vStart, vEnd, v; 1219 PetscErrorCode ierr; 1220 1221 PetscFunctionBeginUser; 1222 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1223 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1224 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1225 ierr = DMClone(dm, &dmMass);CHKERRQ(ierr); 1226 ierr = DMSetCoordinateSection(dmMass, PETSC_DETERMINE, coordSection);CHKERRQ(ierr); 1227 ierr = DMSetCoordinatesLocal(dmMass, coordinates);CHKERRQ(ierr); 1228 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), §ionMass);CHKERRQ(ierr); 1229 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1230 ierr = PetscSectionSetChart(sectionMass, vStart, vEnd);CHKERRQ(ierr); 1231 for (v = vStart; v < vEnd; ++v) { 1232 PetscInt numFaces; 1233 1234 ierr = DMPlexGetSupportSize(dmMass, v, &numFaces);CHKERRQ(ierr); 1235 ierr = PetscSectionSetDof(sectionMass, v, numFaces*numFaces);CHKERRQ(ierr); 1236 } 1237 ierr = PetscSectionSetUp(sectionMass);CHKERRQ(ierr); 1238 ierr = DMSetLocalSection(dmMass, sectionMass);CHKERRQ(ierr); 1239 ierr = PetscSectionDestroy(§ionMass);CHKERRQ(ierr); 1240 ierr = DMGetLocalVector(dmMass, massMatrix);CHKERRQ(ierr); 1241 ierr = VecGetArray(*massMatrix, &m);CHKERRQ(ierr); 1242 ierr = DMPlexGetGeometryFVM(plex, &facegeom, &cellgeom, NULL);CHKERRQ(ierr); 1243 ierr = VecGetDM(facegeom, &dmFace);CHKERRQ(ierr); 1244 ierr = VecGetArrayRead(facegeom, &fgeom);CHKERRQ(ierr); 1245 ierr = VecGetDM(cellgeom, &dmCell);CHKERRQ(ierr); 1246 ierr = VecGetArrayRead(cellgeom, &cgeom);CHKERRQ(ierr); 1247 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 1248 ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr); 1249 for (v = vStart; v < vEnd; ++v) { 1250 const PetscInt *faces; 1251 PetscFVFaceGeom *fgA, *fgB, *cg; 1252 PetscScalar *vertex; 1253 PetscInt numFaces, sides[2], f, g; 1254 1255 ierr = DMPlexPointLocalRead(dmCoord, v, coords, &vertex);CHKERRQ(ierr); 1256 ierr = DMPlexGetSupportSize(dmMass, v, &numFaces);CHKERRQ(ierr); 1257 ierr = DMPlexGetSupport(dmMass, v, &faces);CHKERRQ(ierr); 1258 for (f = 0; f < numFaces; ++f) { 1259 sides[0] = faces[f]; 1260 ierr = DMPlexPointLocalRead(dmFace, faces[f], fgeom, &fgA);CHKERRQ(ierr); 1261 for (g = 0; g < numFaces; ++g) { 1262 const PetscInt *cells = NULL; 1263 PetscReal area = 0.0; 1264 PetscInt numCells; 1265 1266 sides[1] = faces[g]; 1267 ierr = DMPlexPointLocalRead(dmFace, faces[g], fgeom, &fgB);CHKERRQ(ierr); 1268 ierr = DMPlexGetJoin(dmMass, 2, sides, &numCells, &cells);CHKERRQ(ierr); 1269 if (numCells != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Invalid join for faces"); 1270 ierr = DMPlexPointLocalRead(dmCell, cells[0], cgeom, &cg);CHKERRQ(ierr); 1271 area += PetscAbsScalar((vertex[0] - cg->centroid[0])*(fgA->centroid[1] - cg->centroid[1]) - (vertex[1] - cg->centroid[1])*(fgA->centroid[0] - cg->centroid[0])); 1272 area += PetscAbsScalar((vertex[0] - cg->centroid[0])*(fgB->centroid[1] - cg->centroid[1]) - (vertex[1] - cg->centroid[1])*(fgB->centroid[0] - cg->centroid[0])); 1273 m[f*numFaces+g] = Dot2Real(fgA->normal, fgB->normal)*area*0.5; 1274 ierr = DMPlexRestoreJoin(dmMass, 2, sides, &numCells, &cells);CHKERRQ(ierr); 1275 } 1276 } 1277 } 1278 ierr = VecRestoreArrayRead(facegeom, &fgeom);CHKERRQ(ierr); 1279 ierr = VecRestoreArrayRead(cellgeom, &cgeom);CHKERRQ(ierr); 1280 ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr); 1281 ierr = VecRestoreArray(*massMatrix, &m);CHKERRQ(ierr); 1282 ierr = DMDestroy(&dmMass);CHKERRQ(ierr); 1283 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1284 PetscFunctionReturn(0); 1285 } 1286 1287 /* Behavior will be different for multi-physics or when using non-default boundary conditions */ 1288 static PetscErrorCode ModelSolutionSetDefault(Model mod,SolutionFunction func,void *ctx) 1289 { 1290 PetscFunctionBeginUser; 1291 mod->solution = func; 1292 mod->solutionctx = ctx; 1293 PetscFunctionReturn(0); 1294 } 1295 1296 static PetscErrorCode ModelFunctionalRegister(Model mod,const char *name,PetscInt *offset,FunctionalFunction func,void *ctx) 1297 { 1298 PetscErrorCode ierr; 1299 FunctionalLink link,*ptr; 1300 PetscInt lastoffset = -1; 1301 1302 PetscFunctionBeginUser; 1303 for (ptr=&mod->functionalRegistry; *ptr; ptr = &(*ptr)->next) lastoffset = (*ptr)->offset; 1304 ierr = PetscNew(&link);CHKERRQ(ierr); 1305 ierr = PetscStrallocpy(name,&link->name);CHKERRQ(ierr); 1306 link->offset = lastoffset + 1; 1307 link->func = func; 1308 link->ctx = ctx; 1309 link->next = NULL; 1310 *ptr = link; 1311 *offset = link->offset; 1312 PetscFunctionReturn(0); 1313 } 1314 1315 static PetscErrorCode ModelFunctionalSetFromOptions(Model mod,PetscOptionItems *PetscOptionsObject) 1316 { 1317 PetscErrorCode ierr; 1318 PetscInt i,j; 1319 FunctionalLink link; 1320 char *names[256]; 1321 1322 PetscFunctionBeginUser; 1323 mod->numMonitored = ALEN(names); 1324 ierr = PetscOptionsStringArray("-monitor","list of functionals to monitor","",names,&mod->numMonitored,NULL);CHKERRQ(ierr); 1325 /* Create list of functionals that will be computed somehow */ 1326 ierr = PetscMalloc1(mod->numMonitored,&mod->functionalMonitored);CHKERRQ(ierr); 1327 /* Create index of calls that we will have to make to compute these functionals (over-allocation in general). */ 1328 ierr = PetscMalloc1(mod->numMonitored,&mod->functionalCall);CHKERRQ(ierr); 1329 mod->numCall = 0; 1330 for (i=0; i<mod->numMonitored; i++) { 1331 for (link=mod->functionalRegistry; link; link=link->next) { 1332 PetscBool match; 1333 ierr = PetscStrcasecmp(names[i],link->name,&match);CHKERRQ(ierr); 1334 if (match) break; 1335 } 1336 if (!link) SETERRQ1(mod->comm,PETSC_ERR_USER,"No known functional '%s'",names[i]); 1337 mod->functionalMonitored[i] = link; 1338 for (j=0; j<i; j++) { 1339 if (mod->functionalCall[j]->func == link->func && mod->functionalCall[j]->ctx == link->ctx) goto next_name; 1340 } 1341 mod->functionalCall[mod->numCall++] = link; /* Just points to the first link using the result. There may be more results. */ 1342 next_name: 1343 ierr = PetscFree(names[i]);CHKERRQ(ierr); 1344 } 1345 1346 /* Find out the maximum index of any functional computed by a function we will be calling (even if we are not using it) */ 1347 mod->maxComputed = -1; 1348 for (link=mod->functionalRegistry; link; link=link->next) { 1349 for (i=0; i<mod->numCall; i++) { 1350 FunctionalLink call = mod->functionalCall[i]; 1351 if (link->func == call->func && link->ctx == call->ctx) { 1352 mod->maxComputed = PetscMax(mod->maxComputed,link->offset); 1353 } 1354 } 1355 } 1356 PetscFunctionReturn(0); 1357 } 1358 1359 static PetscErrorCode FunctionalLinkDestroy(FunctionalLink *link) 1360 { 1361 PetscErrorCode ierr; 1362 FunctionalLink l,next; 1363 1364 PetscFunctionBeginUser; 1365 if (!link) PetscFunctionReturn(0); 1366 l = *link; 1367 *link = NULL; 1368 for (; l; l=next) { 1369 next = l->next; 1370 ierr = PetscFree(l->name);CHKERRQ(ierr); 1371 ierr = PetscFree(l);CHKERRQ(ierr); 1372 } 1373 PetscFunctionReturn(0); 1374 } 1375 1376 /* put the solution callback into a functional callback */ 1377 static PetscErrorCode SolutionFunctional(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *modctx) 1378 { 1379 Model mod; 1380 PetscErrorCode ierr; 1381 PetscFunctionBegin; 1382 mod = (Model) modctx; 1383 ierr = (*mod->solution)(mod, time, x, u, mod->solutionctx);CHKERRQ(ierr); 1384 PetscFunctionReturn(0); 1385 } 1386 1387 PetscErrorCode SetInitialCondition(DM dm, Vec X, User user) 1388 { 1389 PetscErrorCode (*func[1]) (PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx); 1390 void *ctx[1]; 1391 Model mod = user->model; 1392 PetscErrorCode ierr; 1393 1394 PetscFunctionBeginUser; 1395 func[0] = SolutionFunctional; 1396 ctx[0] = (void *) mod; 1397 ierr = DMProjectFunction(dm,0.0,func,ctx,INSERT_ALL_VALUES,X);CHKERRQ(ierr); 1398 PetscFunctionReturn(0); 1399 } 1400 1401 static PetscErrorCode OutputVTK(DM dm, const char *filename, PetscViewer *viewer) 1402 { 1403 PetscErrorCode ierr; 1404 1405 PetscFunctionBeginUser; 1406 ierr = PetscViewerCreate(PetscObjectComm((PetscObject)dm), viewer);CHKERRQ(ierr); 1407 ierr = PetscViewerSetType(*viewer, PETSCVIEWERVTK);CHKERRQ(ierr); 1408 ierr = PetscViewerFileSetName(*viewer, filename);CHKERRQ(ierr); 1409 PetscFunctionReturn(0); 1410 } 1411 1412 static PetscErrorCode MonitorVTK(TS ts,PetscInt stepnum,PetscReal time,Vec X,void *ctx) 1413 { 1414 User user = (User)ctx; 1415 DM dm, plex; 1416 PetscViewer viewer; 1417 char filename[PETSC_MAX_PATH_LEN],*ftable = NULL; 1418 PetscReal xnorm; 1419 PetscErrorCode ierr; 1420 1421 PetscFunctionBeginUser; 1422 ierr = PetscObjectSetName((PetscObject) X, "u");CHKERRQ(ierr); 1423 ierr = VecGetDM(X,&dm);CHKERRQ(ierr); 1424 ierr = VecNorm(X,NORM_INFINITY,&xnorm);CHKERRQ(ierr); 1425 1426 if (stepnum >= 0) { 1427 stepnum += user->monitorStepOffset; 1428 } 1429 if (stepnum >= 0) { /* No summary for final time */ 1430 Model mod = user->model; 1431 Vec cellgeom; 1432 PetscInt c,cStart,cEnd,fcount,i; 1433 size_t ftableused,ftablealloc; 1434 const PetscScalar *cgeom,*x; 1435 DM dmCell; 1436 DMLabel vtkLabel; 1437 PetscReal *fmin,*fmax,*fintegral,*ftmp; 1438 1439 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1440 ierr = DMPlexGetGeometryFVM(plex, NULL, &cellgeom, NULL);CHKERRQ(ierr); 1441 fcount = mod->maxComputed+1; 1442 ierr = PetscMalloc4(fcount,&fmin,fcount,&fmax,fcount,&fintegral,fcount,&ftmp);CHKERRQ(ierr); 1443 for (i=0; i<fcount; i++) { 1444 fmin[i] = PETSC_MAX_REAL; 1445 fmax[i] = PETSC_MIN_REAL; 1446 fintegral[i] = 0; 1447 } 1448 ierr = VecGetDM(cellgeom,&dmCell);CHKERRQ(ierr); 1449 ierr = DMPlexGetSimplexOrBoxCells(dmCell,0,&cStart,&cEnd);CHKERRQ(ierr); 1450 ierr = VecGetArrayRead(cellgeom,&cgeom);CHKERRQ(ierr); 1451 ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr); 1452 ierr = DMGetLabel(dm,"vtk",&vtkLabel);CHKERRQ(ierr); 1453 for (c = cStart; c < cEnd; ++c) { 1454 PetscFVCellGeom *cg; 1455 const PetscScalar *cx = NULL; 1456 PetscInt vtkVal = 0; 1457 1458 /* not that these two routines as currently implemented work for any dm with a 1459 * localSection/globalSection */ 1460 ierr = DMPlexPointLocalRead(dmCell,c,cgeom,&cg);CHKERRQ(ierr); 1461 ierr = DMPlexPointGlobalRead(dm,c,x,&cx);CHKERRQ(ierr); 1462 if (vtkLabel) {ierr = DMLabelGetValue(vtkLabel,c,&vtkVal);CHKERRQ(ierr);} 1463 if (!vtkVal || !cx) continue; /* ghost, or not a global cell */ 1464 for (i=0; i<mod->numCall; i++) { 1465 FunctionalLink flink = mod->functionalCall[i]; 1466 ierr = (*flink->func)(mod,time,cg->centroid,cx,ftmp,flink->ctx);CHKERRQ(ierr); 1467 } 1468 for (i=0; i<fcount; i++) { 1469 fmin[i] = PetscMin(fmin[i],ftmp[i]); 1470 fmax[i] = PetscMax(fmax[i],ftmp[i]); 1471 fintegral[i] += cg->volume * ftmp[i]; 1472 } 1473 } 1474 ierr = VecRestoreArrayRead(cellgeom,&cgeom);CHKERRQ(ierr); 1475 ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr); 1476 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1477 ierr = MPI_Allreduce(MPI_IN_PLACE,fmin,fcount,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr); 1478 ierr = MPI_Allreduce(MPI_IN_PLACE,fmax,fcount,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr); 1479 ierr = MPI_Allreduce(MPI_IN_PLACE,fintegral,fcount,MPIU_REAL,MPIU_SUM,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr); 1480 1481 ftablealloc = fcount * 100; 1482 ftableused = 0; 1483 ierr = PetscMalloc1(ftablealloc,&ftable);CHKERRQ(ierr); 1484 for (i=0; i<mod->numMonitored; i++) { 1485 size_t countused; 1486 char buffer[256],*p; 1487 FunctionalLink flink = mod->functionalMonitored[i]; 1488 PetscInt id = flink->offset; 1489 if (i % 3) { 1490 ierr = PetscArraycpy(buffer," ",2);CHKERRQ(ierr); 1491 p = buffer + 2; 1492 } else if (i) { 1493 char newline[] = "\n"; 1494 ierr = PetscMemcpy(buffer,newline,sizeof(newline)-1);CHKERRQ(ierr); 1495 p = buffer + sizeof(newline) - 1; 1496 } else { 1497 p = buffer; 1498 } 1499 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); 1500 countused--; 1501 countused += p - buffer; 1502 if (countused > ftablealloc-ftableused-1) { /* reallocate */ 1503 char *ftablenew; 1504 ftablealloc = 2*ftablealloc + countused; 1505 ierr = PetscMalloc(ftablealloc,&ftablenew);CHKERRQ(ierr); 1506 ierr = PetscArraycpy(ftablenew,ftable,ftableused);CHKERRQ(ierr); 1507 ierr = PetscFree(ftable);CHKERRQ(ierr); 1508 ftable = ftablenew; 1509 } 1510 ierr = PetscArraycpy(ftable+ftableused,buffer,countused);CHKERRQ(ierr); 1511 ftableused += countused; 1512 ftable[ftableused] = 0; 1513 } 1514 ierr = PetscFree4(fmin,fmax,fintegral,ftmp);CHKERRQ(ierr); 1515 1516 ierr = PetscPrintf(PetscObjectComm((PetscObject)ts),"% 3D time %8.4g |x| %8.4g %s\n",stepnum,(double)time,(double)xnorm,ftable ? ftable : "");CHKERRQ(ierr); 1517 ierr = PetscFree(ftable);CHKERRQ(ierr); 1518 } 1519 if (user->vtkInterval < 1) PetscFunctionReturn(0); 1520 if ((stepnum == -1) ^ (stepnum % user->vtkInterval == 0)) { 1521 if (stepnum == -1) { /* Final time is not multiple of normal time interval, write it anyway */ 1522 ierr = TSGetStepNumber(ts,&stepnum);CHKERRQ(ierr); 1523 } 1524 ierr = PetscSNPrintf(filename,sizeof filename,"%s-%03D.vtu",user->outputBasename,stepnum);CHKERRQ(ierr); 1525 ierr = OutputVTK(dm,filename,&viewer);CHKERRQ(ierr); 1526 ierr = VecView(X,viewer);CHKERRQ(ierr); 1527 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1528 } 1529 PetscFunctionReturn(0); 1530 } 1531 1532 static PetscErrorCode initializeTS(DM dm, User user, TS *ts) 1533 { 1534 PetscErrorCode ierr; 1535 1536 PetscFunctionBegin; 1537 ierr = TSCreate(PetscObjectComm((PetscObject)dm), ts);CHKERRQ(ierr); 1538 ierr = TSSetType(*ts, TSSSP);CHKERRQ(ierr); 1539 ierr = TSSetDM(*ts, dm);CHKERRQ(ierr); 1540 if (user->vtkmon) { 1541 ierr = TSMonitorSet(*ts,MonitorVTK,user,NULL);CHKERRQ(ierr); 1542 } 1543 ierr = DMTSSetBoundaryLocal(dm, DMPlexTSComputeBoundary, user);CHKERRQ(ierr); 1544 ierr = DMTSSetRHSFunctionLocal(dm, DMPlexTSComputeRHSFunctionFVM, user);CHKERRQ(ierr); 1545 ierr = TSSetMaxTime(*ts,2.0);CHKERRQ(ierr); 1546 ierr = TSSetExactFinalTime(*ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); 1547 PetscFunctionReturn(0); 1548 } 1549 1550 static PetscErrorCode adaptToleranceFVM(PetscFV fvm, TS ts, Vec sol, VecTagger refineTag, VecTagger coarsenTag, User user, TS *tsNew, Vec *solNew) 1551 { 1552 DM dm, gradDM, plex, cellDM, adaptedDM = NULL; 1553 Vec cellGeom, faceGeom; 1554 PetscBool isForest, computeGradient; 1555 Vec grad, locGrad, locX, errVec; 1556 PetscInt cStart, cEnd, c, dim, nRefine, nCoarsen; 1557 PetscReal minMaxInd[2] = {PETSC_MAX_REAL, PETSC_MIN_REAL}, minMaxIndGlobal[2], minInd, maxInd, time; 1558 PetscScalar *errArray; 1559 const PetscScalar *pointVals; 1560 const PetscScalar *pointGrads; 1561 const PetscScalar *pointGeom; 1562 DMLabel adaptLabel = NULL; 1563 IS refineIS, coarsenIS; 1564 PetscErrorCode ierr; 1565 1566 PetscFunctionBegin; 1567 ierr = TSGetTime(ts,&time);CHKERRQ(ierr); 1568 ierr = VecGetDM(sol, &dm);CHKERRQ(ierr); 1569 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 1570 ierr = PetscFVGetComputeGradients(fvm,&computeGradient);CHKERRQ(ierr); 1571 ierr = PetscFVSetComputeGradients(fvm,PETSC_TRUE);CHKERRQ(ierr); 1572 ierr = DMIsForest(dm, &isForest);CHKERRQ(ierr); 1573 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1574 ierr = DMPlexGetDataFVM(plex, fvm, &cellGeom, &faceGeom, &gradDM);CHKERRQ(ierr); 1575 ierr = DMCreateLocalVector(plex,&locX);CHKERRQ(ierr); 1576 ierr = DMPlexInsertBoundaryValues(plex, PETSC_TRUE, locX, 0.0, faceGeom, cellGeom, NULL);CHKERRQ(ierr); 1577 ierr = DMGlobalToLocalBegin(plex, sol, INSERT_VALUES, locX);CHKERRQ(ierr); 1578 ierr = DMGlobalToLocalEnd (plex, sol, INSERT_VALUES, locX);CHKERRQ(ierr); 1579 ierr = DMCreateGlobalVector(gradDM, &grad);CHKERRQ(ierr); 1580 ierr = DMPlexReconstructGradientsFVM(plex, locX, grad);CHKERRQ(ierr); 1581 ierr = DMCreateLocalVector(gradDM, &locGrad);CHKERRQ(ierr); 1582 ierr = DMGlobalToLocalBegin(gradDM, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1583 ierr = DMGlobalToLocalEnd(gradDM, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1584 ierr = VecDestroy(&grad);CHKERRQ(ierr); 1585 ierr = DMPlexGetSimplexOrBoxCells(plex,0,&cStart,&cEnd);CHKERRQ(ierr); 1586 ierr = VecGetArrayRead(locGrad,&pointGrads);CHKERRQ(ierr); 1587 ierr = VecGetArrayRead(cellGeom,&pointGeom);CHKERRQ(ierr); 1588 ierr = VecGetArrayRead(locX,&pointVals);CHKERRQ(ierr); 1589 ierr = VecGetDM(cellGeom,&cellDM);CHKERRQ(ierr); 1590 ierr = DMLabelCreate(PETSC_COMM_SELF,"adapt",&adaptLabel);CHKERRQ(ierr); 1591 ierr = VecCreateMPI(PetscObjectComm((PetscObject)plex),cEnd-cStart,PETSC_DETERMINE,&errVec);CHKERRQ(ierr); 1592 ierr = VecSetUp(errVec);CHKERRQ(ierr); 1593 ierr = VecGetArray(errVec,&errArray);CHKERRQ(ierr); 1594 for (c = cStart; c < cEnd; c++) { 1595 PetscReal errInd = 0.; 1596 PetscScalar *pointGrad; 1597 PetscScalar *pointVal; 1598 PetscFVCellGeom *cg; 1599 1600 ierr = DMPlexPointLocalRead(gradDM,c,pointGrads,&pointGrad);CHKERRQ(ierr); 1601 ierr = DMPlexPointLocalRead(cellDM,c,pointGeom,&cg);CHKERRQ(ierr); 1602 ierr = DMPlexPointLocalRead(plex,c,pointVals,&pointVal);CHKERRQ(ierr); 1603 1604 ierr = (user->model->errorIndicator)(dim,cg->volume,user->model->physics->dof,pointVal,pointGrad,&errInd,user->model->errorCtx);CHKERRQ(ierr); 1605 errArray[c-cStart] = errInd; 1606 minMaxInd[0] = PetscMin(minMaxInd[0],errInd); 1607 minMaxInd[1] = PetscMax(minMaxInd[1],errInd); 1608 } 1609 ierr = VecRestoreArray(errVec,&errArray);CHKERRQ(ierr); 1610 ierr = VecRestoreArrayRead(locX,&pointVals);CHKERRQ(ierr); 1611 ierr = VecRestoreArrayRead(cellGeom,&pointGeom);CHKERRQ(ierr); 1612 ierr = VecRestoreArrayRead(locGrad,&pointGrads);CHKERRQ(ierr); 1613 ierr = VecDestroy(&locGrad);CHKERRQ(ierr); 1614 ierr = VecDestroy(&locX);CHKERRQ(ierr); 1615 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1616 1617 ierr = VecTaggerComputeIS(refineTag,errVec,&refineIS);CHKERRQ(ierr); 1618 ierr = VecTaggerComputeIS(coarsenTag,errVec,&coarsenIS);CHKERRQ(ierr); 1619 ierr = ISGetSize(refineIS,&nRefine);CHKERRQ(ierr); 1620 ierr = ISGetSize(coarsenIS,&nCoarsen);CHKERRQ(ierr); 1621 if (nRefine) {ierr = DMLabelSetStratumIS(adaptLabel,DM_ADAPT_REFINE,refineIS);CHKERRQ(ierr);} 1622 if (nCoarsen) {ierr = DMLabelSetStratumIS(adaptLabel,DM_ADAPT_COARSEN,coarsenIS);CHKERRQ(ierr);} 1623 ierr = ISDestroy(&coarsenIS);CHKERRQ(ierr); 1624 ierr = ISDestroy(&refineIS);CHKERRQ(ierr); 1625 ierr = VecDestroy(&errVec);CHKERRQ(ierr); 1626 1627 ierr = PetscFVSetComputeGradients(fvm,computeGradient);CHKERRQ(ierr); 1628 minMaxInd[1] = -minMaxInd[1]; 1629 ierr = MPI_Allreduce(minMaxInd,minMaxIndGlobal,2,MPIU_REAL,MPI_MIN,PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 1630 minInd = minMaxIndGlobal[0]; 1631 maxInd = -minMaxIndGlobal[1]; 1632 ierr = PetscInfo2(ts, "error indicator range (%E, %E)\n", minInd, maxInd);CHKERRQ(ierr); 1633 if (nRefine || nCoarsen) { /* at least one cell is over the refinement threshold */ 1634 ierr = DMAdaptLabel(dm,adaptLabel,&adaptedDM);CHKERRQ(ierr); 1635 } 1636 ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr); 1637 if (adaptedDM) { 1638 ierr = PetscInfo2(ts, "Adapted mesh, marking %D cells for refinement, and %D cells for coarsening\n", nRefine, nCoarsen);CHKERRQ(ierr); 1639 if (tsNew) {ierr = initializeTS(adaptedDM, user, tsNew);CHKERRQ(ierr);} 1640 if (solNew) { 1641 ierr = DMCreateGlobalVector(adaptedDM, solNew);CHKERRQ(ierr); 1642 ierr = PetscObjectSetName((PetscObject) *solNew, "solution");CHKERRQ(ierr); 1643 ierr = DMForestTransferVec(dm, sol, adaptedDM, *solNew, PETSC_TRUE, time);CHKERRQ(ierr); 1644 } 1645 if (isForest) {ierr = DMForestSetAdaptivityForest(adaptedDM,NULL);CHKERRQ(ierr);} /* clear internal references to the previous dm */ 1646 ierr = DMDestroy(&adaptedDM);CHKERRQ(ierr); 1647 } else { 1648 if (tsNew) *tsNew = NULL; 1649 if (solNew) *solNew = NULL; 1650 } 1651 PetscFunctionReturn(0); 1652 } 1653 1654 int main(int argc, char **argv) 1655 { 1656 MPI_Comm comm; 1657 PetscDS prob; 1658 PetscFV fvm; 1659 PetscLimiter limiter = NULL, noneLimiter = NULL; 1660 User user; 1661 Model mod; 1662 Physics phys; 1663 DM dm, plex; 1664 PetscReal ftime, cfl, dt, minRadius; 1665 PetscInt dim, nsteps; 1666 TS ts; 1667 TSConvergedReason reason; 1668 Vec X; 1669 PetscViewer viewer; 1670 PetscBool simplex = PETSC_FALSE, vtkCellGeom, splitFaces, useAMR; 1671 PetscInt overlap, adaptInterval; 1672 char filename[PETSC_MAX_PATH_LEN] = ""; 1673 char physname[256] = "advect"; 1674 VecTagger refineTag = NULL, coarsenTag = NULL; 1675 PetscErrorCode ierr; 1676 1677 ierr = PetscInitialize(&argc, &argv, (char*) 0, help);if (ierr) return ierr; 1678 comm = PETSC_COMM_WORLD; 1679 1680 ierr = PetscNew(&user);CHKERRQ(ierr); 1681 ierr = PetscNew(&user->model);CHKERRQ(ierr); 1682 ierr = PetscNew(&user->model->physics);CHKERRQ(ierr); 1683 mod = user->model; 1684 phys = mod->physics; 1685 mod->comm = comm; 1686 useAMR = PETSC_FALSE; 1687 adaptInterval = 1; 1688 1689 /* Register physical models to be available on the command line */ 1690 ierr = PetscFunctionListAdd(&PhysicsList,"advect" ,PhysicsCreate_Advect);CHKERRQ(ierr); 1691 ierr = PetscFunctionListAdd(&PhysicsList,"sw" ,PhysicsCreate_SW);CHKERRQ(ierr); 1692 ierr = PetscFunctionListAdd(&PhysicsList,"euler" ,PhysicsCreate_Euler);CHKERRQ(ierr); 1693 1694 1695 ierr = PetscOptionsBegin(comm,NULL,"Unstructured Finite Volume Mesh Options","");CHKERRQ(ierr); 1696 { 1697 cfl = 0.9 * 4; /* default SSPRKS2 with s=5 stages is stable for CFL number s-1 */ 1698 ierr = PetscOptionsReal("-ufv_cfl","CFL number per step","",cfl,&cfl,NULL);CHKERRQ(ierr); 1699 ierr = PetscOptionsString("-f","Exodus.II filename to read","",filename,filename,sizeof(filename),NULL);CHKERRQ(ierr); 1700 ierr = PetscOptionsBool("-simplex","Flag to use a simplex mesh","",simplex,&simplex,NULL);CHKERRQ(ierr); 1701 splitFaces = PETSC_FALSE; 1702 ierr = PetscOptionsBool("-ufv_split_faces","Split faces between cell sets","",splitFaces,&splitFaces,NULL);CHKERRQ(ierr); 1703 overlap = 1; 1704 ierr = PetscOptionsInt("-ufv_mesh_overlap","Number of cells to overlap partitions","",overlap,&overlap,NULL);CHKERRQ(ierr); 1705 user->vtkInterval = 1; 1706 ierr = PetscOptionsInt("-ufv_vtk_interval","VTK output interval (0 to disable)","",user->vtkInterval,&user->vtkInterval,NULL);CHKERRQ(ierr); 1707 user->vtkmon = PETSC_TRUE; 1708 ierr = PetscOptionsBool("-ufv_vtk_monitor","Use VTKMonitor routine","",user->vtkmon,&user->vtkmon,NULL);CHKERRQ(ierr); 1709 vtkCellGeom = PETSC_FALSE; 1710 ierr = PetscStrcpy(user->outputBasename, "ex11");CHKERRQ(ierr); 1711 ierr = PetscOptionsString("-ufv_vtk_basename","VTK output basename","",user->outputBasename,user->outputBasename,sizeof(user->outputBasename),NULL);CHKERRQ(ierr); 1712 ierr = PetscOptionsBool("-ufv_vtk_cellgeom","Write cell geometry (for debugging)","",vtkCellGeom,&vtkCellGeom,NULL);CHKERRQ(ierr); 1713 ierr = PetscOptionsBool("-ufv_use_amr","use local adaptive mesh refinement","",useAMR,&useAMR,NULL);CHKERRQ(ierr); 1714 ierr = PetscOptionsInt("-ufv_adapt_interval","time steps between AMR","",adaptInterval,&adaptInterval,NULL);CHKERRQ(ierr); 1715 } 1716 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1717 1718 if (useAMR) { 1719 VecTaggerBox refineBox, coarsenBox; 1720 1721 refineBox.min = refineBox.max = PETSC_MAX_REAL; 1722 coarsenBox.min = coarsenBox.max = PETSC_MIN_REAL; 1723 1724 ierr = VecTaggerCreate(comm,&refineTag);CHKERRQ(ierr); 1725 ierr = PetscObjectSetOptionsPrefix((PetscObject)refineTag,"refine_");CHKERRQ(ierr); 1726 ierr = VecTaggerSetType(refineTag,VECTAGGERABSOLUTE);CHKERRQ(ierr); 1727 ierr = VecTaggerAbsoluteSetBox(refineTag,&refineBox);CHKERRQ(ierr); 1728 ierr = VecTaggerSetFromOptions(refineTag);CHKERRQ(ierr); 1729 ierr = VecTaggerSetUp(refineTag);CHKERRQ(ierr); 1730 ierr = PetscObjectViewFromOptions((PetscObject)refineTag,NULL,"-tag_view");CHKERRQ(ierr); 1731 1732 ierr = VecTaggerCreate(comm,&coarsenTag);CHKERRQ(ierr); 1733 ierr = PetscObjectSetOptionsPrefix((PetscObject)coarsenTag,"coarsen_");CHKERRQ(ierr); 1734 ierr = VecTaggerSetType(coarsenTag,VECTAGGERABSOLUTE);CHKERRQ(ierr); 1735 ierr = VecTaggerAbsoluteSetBox(coarsenTag,&coarsenBox);CHKERRQ(ierr); 1736 ierr = VecTaggerSetFromOptions(coarsenTag);CHKERRQ(ierr); 1737 ierr = VecTaggerSetUp(coarsenTag);CHKERRQ(ierr); 1738 ierr = PetscObjectViewFromOptions((PetscObject)coarsenTag,NULL,"-tag_view");CHKERRQ(ierr); 1739 } 1740 1741 ierr = PetscOptionsBegin(comm,NULL,"Unstructured Finite Volume Physics Options","");CHKERRQ(ierr); 1742 { 1743 PetscErrorCode (*physcreate)(Model,Physics,PetscOptionItems*); 1744 ierr = PetscOptionsFList("-physics","Physics module to solve","",PhysicsList,physname,physname,sizeof physname,NULL);CHKERRQ(ierr); 1745 ierr = PetscFunctionListFind(PhysicsList,physname,&physcreate);CHKERRQ(ierr); 1746 ierr = PetscMemzero(phys,sizeof(struct _n_Physics));CHKERRQ(ierr); 1747 ierr = (*physcreate)(mod,phys,PetscOptionsObject);CHKERRQ(ierr); 1748 /* Count number of fields and dofs */ 1749 for (phys->nfields=0,phys->dof=0; phys->field_desc[phys->nfields].name; phys->nfields++) phys->dof += phys->field_desc[phys->nfields].dof; 1750 if (phys->dof <= 0) SETERRQ1(comm,PETSC_ERR_ARG_WRONGSTATE,"Physics '%s' did not set dof",physname); 1751 ierr = ModelFunctionalSetFromOptions(mod,PetscOptionsObject);CHKERRQ(ierr); 1752 } 1753 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1754 1755 /* Create mesh */ 1756 { 1757 size_t len,i; 1758 for (i = 0; i < DIM; i++) { mod->bounds[2*i] = 0.; mod->bounds[2*i+1] = 1.;}; 1759 ierr = PetscStrlen(filename,&len);CHKERRQ(ierr); 1760 dim = DIM; 1761 if (!len) { /* a null name means just do a hex box */ 1762 PetscInt cells[3] = {1, 1, 1}; /* coarse mesh is one cell; refine from there */ 1763 PetscBool flg1, flg2, skew = PETSC_FALSE; 1764 PetscInt nret1 = DIM; 1765 PetscInt nret2 = 2*DIM; 1766 ierr = PetscOptionsBegin(comm,NULL,"Rectangular mesh options","");CHKERRQ(ierr); 1767 ierr = PetscOptionsIntArray("-grid_size","number of cells in each direction","",cells,&nret1,&flg1);CHKERRQ(ierr); 1768 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); 1769 ierr = PetscOptionsBool("-grid_skew_60","Skew grid for 60 degree shock mesh","",skew,&skew,NULL);CHKERRQ(ierr); 1770 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1771 if (flg1) { 1772 dim = nret1; 1773 if (dim != DIM) SETERRQ1(comm,PETSC_ERR_ARG_SIZ,"Dim wrong size %D in -grid_size",dim); 1774 } 1775 ierr = DMPlexCreateBoxMesh(comm, dim, simplex, cells, NULL, NULL, mod->bcs, PETSC_TRUE, &dm);CHKERRQ(ierr); 1776 if (flg2) { 1777 PetscInt dimEmbed, i; 1778 PetscInt nCoords; 1779 PetscScalar *coords; 1780 Vec coordinates; 1781 1782 ierr = DMGetCoordinatesLocal(dm,&coordinates);CHKERRQ(ierr); 1783 ierr = DMGetCoordinateDim(dm,&dimEmbed);CHKERRQ(ierr); 1784 ierr = VecGetLocalSize(coordinates,&nCoords);CHKERRQ(ierr); 1785 if (nCoords % dimEmbed) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Coordinate vector the wrong size"); 1786 ierr = VecGetArray(coordinates,&coords);CHKERRQ(ierr); 1787 for (i = 0; i < nCoords; i += dimEmbed) { 1788 PetscInt j; 1789 1790 PetscScalar *coord = &coords[i]; 1791 for (j = 0; j < dimEmbed; j++) { 1792 coord[j] = mod->bounds[2 * j] + coord[j] * (mod->bounds[2 * j + 1] - mod->bounds[2 * j]); 1793 if (dim==2 && cells[1]==1 && j==0 && skew) { 1794 if (cells[0]==2 && i==8) { 1795 coord[j] = .57735026918963; /* hack to get 60 deg skewed mesh */ 1796 } 1797 else if (cells[0]==3) { 1798 if (i==2 || i==10) coord[j] = mod->bounds[1]/4.; 1799 else if (i==4) coord[j] = mod->bounds[1]/2.; 1800 else if (i==12) coord[j] = 1.57735026918963*mod->bounds[1]/2.; 1801 } 1802 } 1803 } 1804 } 1805 ierr = VecRestoreArray(coordinates,&coords);CHKERRQ(ierr); 1806 ierr = DMSetCoordinatesLocal(dm,coordinates);CHKERRQ(ierr); 1807 } 1808 } else { 1809 ierr = DMPlexCreateFromFile(comm, filename, PETSC_TRUE, &dm);CHKERRQ(ierr); 1810 } 1811 } 1812 ierr = DMViewFromOptions(dm, NULL, "-orig_dm_view");CHKERRQ(ierr); 1813 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1814 1815 /* set up BCs, functions, tags */ 1816 ierr = DMCreateLabel(dm, "Face Sets");CHKERRQ(ierr); 1817 1818 mod->errorIndicator = ErrorIndicator_Simple; 1819 1820 { 1821 DM dmDist; 1822 1823 ierr = DMSetBasicAdjacency(dm, PETSC_TRUE, PETSC_FALSE);CHKERRQ(ierr); 1824 ierr = DMPlexDistribute(dm, overlap, NULL, &dmDist);CHKERRQ(ierr); 1825 if (dmDist) { 1826 ierr = DMDestroy(&dm);CHKERRQ(ierr); 1827 dm = dmDist; 1828 } 1829 } 1830 1831 ierr = DMSetFromOptions(dm);CHKERRQ(ierr); 1832 1833 { 1834 DM gdm; 1835 1836 ierr = DMPlexConstructGhostCells(dm, NULL, NULL, &gdm);CHKERRQ(ierr); 1837 ierr = DMDestroy(&dm);CHKERRQ(ierr); 1838 dm = gdm; 1839 ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr); 1840 } 1841 if (splitFaces) {ierr = ConstructCellBoundary(dm, user);CHKERRQ(ierr);} 1842 ierr = SplitFaces(&dm, "split faces", user);CHKERRQ(ierr); 1843 1844 ierr = PetscFVCreate(comm, &fvm);CHKERRQ(ierr); 1845 ierr = PetscFVSetFromOptions(fvm);CHKERRQ(ierr); 1846 ierr = PetscFVSetNumComponents(fvm, phys->dof);CHKERRQ(ierr); 1847 ierr = PetscFVSetSpatialDimension(fvm, dim);CHKERRQ(ierr); 1848 ierr = PetscObjectSetName((PetscObject) fvm,"");CHKERRQ(ierr); 1849 { 1850 PetscInt f, dof; 1851 for (f=0,dof=0; f < phys->nfields; f++) { 1852 PetscInt newDof = phys->field_desc[f].dof; 1853 1854 if (newDof == 1) { 1855 ierr = PetscFVSetComponentName(fvm,dof,phys->field_desc[f].name);CHKERRQ(ierr); 1856 } 1857 else { 1858 PetscInt j; 1859 1860 for (j = 0; j < newDof; j++) { 1861 char compName[256] = "Unknown"; 1862 1863 ierr = PetscSNPrintf(compName,sizeof(compName),"%s_%d",phys->field_desc[f].name,j);CHKERRQ(ierr); 1864 ierr = PetscFVSetComponentName(fvm,dof+j,compName);CHKERRQ(ierr); 1865 } 1866 } 1867 dof += newDof; 1868 } 1869 } 1870 /* FV is now structured with one field having all physics as components */ 1871 ierr = DMAddField(dm, NULL, (PetscObject) fvm);CHKERRQ(ierr); 1872 ierr = DMCreateDS(dm);CHKERRQ(ierr); 1873 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1874 ierr = PetscDSSetRiemannSolver(prob, 0, user->model->physics->riemann);CHKERRQ(ierr); 1875 ierr = PetscDSSetContext(prob, 0, user->model->physics);CHKERRQ(ierr); 1876 ierr = (*mod->setupbc)(prob,phys);CHKERRQ(ierr); 1877 ierr = PetscDSSetFromOptions(prob);CHKERRQ(ierr); 1878 { 1879 char convType[256]; 1880 PetscBool flg; 1881 1882 ierr = PetscOptionsBegin(comm, "", "Mesh conversion options", "DMPLEX");CHKERRQ(ierr); 1883 ierr = PetscOptionsFList("-dm_type","Convert DMPlex to another format","ex12",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr); 1884 ierr = PetscOptionsEnd();CHKERRQ(ierr); 1885 if (flg) { 1886 DM dmConv; 1887 1888 ierr = DMConvert(dm,convType,&dmConv);CHKERRQ(ierr); 1889 if (dmConv) { 1890 ierr = DMViewFromOptions(dmConv, NULL, "-dm_conv_view");CHKERRQ(ierr); 1891 ierr = DMDestroy(&dm);CHKERRQ(ierr); 1892 dm = dmConv; 1893 ierr = DMSetFromOptions(dm);CHKERRQ(ierr); 1894 } 1895 } 1896 } 1897 1898 ierr = initializeTS(dm, user, &ts);CHKERRQ(ierr); 1899 1900 ierr = DMCreateGlobalVector(dm, &X);CHKERRQ(ierr); 1901 ierr = PetscObjectSetName((PetscObject) X, "solution");CHKERRQ(ierr); 1902 ierr = SetInitialCondition(dm, X, user);CHKERRQ(ierr); 1903 if (useAMR) { 1904 PetscInt adaptIter; 1905 1906 /* use no limiting when reconstructing gradients for adaptivity */ 1907 ierr = PetscFVGetLimiter(fvm, &limiter);CHKERRQ(ierr); 1908 ierr = PetscObjectReference((PetscObject) limiter);CHKERRQ(ierr); 1909 ierr = PetscLimiterCreate(PetscObjectComm((PetscObject) fvm), &noneLimiter);CHKERRQ(ierr); 1910 ierr = PetscLimiterSetType(noneLimiter, PETSCLIMITERNONE);CHKERRQ(ierr); 1911 1912 ierr = PetscFVSetLimiter(fvm, noneLimiter);CHKERRQ(ierr); 1913 for (adaptIter = 0; ; ++adaptIter) { 1914 PetscLogDouble bytes; 1915 TS tsNew = NULL; 1916 1917 ierr = PetscMemoryGetCurrentUsage(&bytes);CHKERRQ(ierr); 1918 ierr = PetscInfo2(ts, "refinement loop %D: memory used %g\n", adaptIter, bytes);CHKERRQ(ierr); 1919 ierr = DMViewFromOptions(dm, NULL, "-initial_dm_view");CHKERRQ(ierr); 1920 ierr = VecViewFromOptions(X, NULL, "-initial_vec_view");CHKERRQ(ierr); 1921 #if 0 1922 if (viewInitial) { 1923 PetscViewer viewer; 1924 char buf[256]; 1925 PetscBool isHDF5, isVTK; 1926 1927 ierr = PetscViewerCreate(comm,&viewer);CHKERRQ(ierr); 1928 ierr = PetscViewerSetType(viewer,PETSCVIEWERVTK);CHKERRQ(ierr); 1929 ierr = PetscViewerSetOptionsPrefix(viewer,"initial_");CHKERRQ(ierr); 1930 ierr = PetscViewerSetFromOptions(viewer);CHKERRQ(ierr); 1931 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&isHDF5);CHKERRQ(ierr); 1932 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERVTK,&isVTK);CHKERRQ(ierr); 1933 if (isHDF5) { 1934 ierr = PetscSNPrintf(buf, 256, "ex11-initial-%d.h5", adaptIter);CHKERRQ(ierr); 1935 } else if (isVTK) { 1936 ierr = PetscSNPrintf(buf, 256, "ex11-initial-%d.vtu", adaptIter);CHKERRQ(ierr); 1937 ierr = PetscViewerPushFormat(viewer,PETSC_VIEWER_VTK_VTU);CHKERRQ(ierr); 1938 } 1939 ierr = PetscViewerFileSetMode(viewer,FILE_MODE_WRITE);CHKERRQ(ierr); 1940 ierr = PetscViewerFileSetName(viewer,buf);CHKERRQ(ierr); 1941 if (isHDF5) { 1942 ierr = DMView(dm,viewer);CHKERRQ(ierr); 1943 ierr = PetscViewerFileSetMode(viewer,FILE_MODE_UPDATE);CHKERRQ(ierr); 1944 } 1945 ierr = VecView(X,viewer);CHKERRQ(ierr); 1946 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1947 } 1948 #endif 1949 1950 ierr = adaptToleranceFVM(fvm, ts, X, refineTag, coarsenTag, user, &tsNew, NULL);CHKERRQ(ierr); 1951 if (!tsNew) { 1952 break; 1953 } else { 1954 ierr = DMDestroy(&dm);CHKERRQ(ierr); 1955 ierr = VecDestroy(&X);CHKERRQ(ierr); 1956 ierr = TSDestroy(&ts);CHKERRQ(ierr); 1957 ts = tsNew; 1958 ierr = TSGetDM(ts,&dm);CHKERRQ(ierr); 1959 ierr = PetscObjectReference((PetscObject)dm);CHKERRQ(ierr); 1960 ierr = DMCreateGlobalVector(dm,&X);CHKERRQ(ierr); 1961 ierr = PetscObjectSetName((PetscObject) X, "solution");CHKERRQ(ierr); 1962 ierr = SetInitialCondition(dm, X, user);CHKERRQ(ierr); 1963 } 1964 } 1965 /* restore original limiter */ 1966 ierr = PetscFVSetLimiter(fvm, limiter);CHKERRQ(ierr); 1967 } 1968 1969 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1970 if (vtkCellGeom) { 1971 DM dmCell; 1972 Vec cellgeom, partition; 1973 1974 ierr = DMPlexGetGeometryFVM(plex, NULL, &cellgeom, NULL);CHKERRQ(ierr); 1975 ierr = OutputVTK(dm, "ex11-cellgeom.vtk", &viewer);CHKERRQ(ierr); 1976 ierr = VecView(cellgeom, viewer);CHKERRQ(ierr); 1977 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1978 ierr = CreatePartitionVec(dm, &dmCell, &partition);CHKERRQ(ierr); 1979 ierr = OutputVTK(dmCell, "ex11-partition.vtk", &viewer);CHKERRQ(ierr); 1980 ierr = VecView(partition, viewer);CHKERRQ(ierr); 1981 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 1982 ierr = VecDestroy(&partition);CHKERRQ(ierr); 1983 ierr = DMDestroy(&dmCell);CHKERRQ(ierr); 1984 } 1985 /* collect max maxspeed from all processes -- todo */ 1986 ierr = DMPlexGetGeometryFVM(plex, NULL, NULL, &minRadius);CHKERRQ(ierr); 1987 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1988 ierr = MPI_Allreduce(&phys->maxspeed,&mod->maxspeed,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr); 1989 if (mod->maxspeed <= 0) SETERRQ1(comm,PETSC_ERR_ARG_WRONGSTATE,"Physics '%s' did not set maxspeed",physname); 1990 dt = cfl * minRadius / mod->maxspeed; 1991 ierr = TSSetTimeStep(ts,dt);CHKERRQ(ierr); 1992 ierr = TSSetFromOptions(ts);CHKERRQ(ierr); 1993 if (!useAMR) { 1994 ierr = TSSolve(ts,X);CHKERRQ(ierr); 1995 ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); 1996 ierr = TSGetStepNumber(ts,&nsteps);CHKERRQ(ierr); 1997 } else { 1998 PetscReal finalTime; 1999 PetscInt adaptIter; 2000 TS tsNew = NULL; 2001 Vec solNew = NULL; 2002 2003 ierr = TSGetMaxTime(ts,&finalTime);CHKERRQ(ierr); 2004 ierr = TSSetMaxSteps(ts,adaptInterval);CHKERRQ(ierr); 2005 ierr = TSSolve(ts,X);CHKERRQ(ierr); 2006 ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); 2007 ierr = TSGetStepNumber(ts,&nsteps);CHKERRQ(ierr); 2008 for (adaptIter = 0;ftime < finalTime;adaptIter++) { 2009 PetscLogDouble bytes; 2010 2011 ierr = PetscMemoryGetCurrentUsage(&bytes);CHKERRQ(ierr); 2012 ierr = PetscInfo2(ts, "AMR time step loop %D: memory used %g\n", adaptIter, bytes);CHKERRQ(ierr); 2013 ierr = PetscFVSetLimiter(fvm,noneLimiter);CHKERRQ(ierr); 2014 ierr = adaptToleranceFVM(fvm,ts,X,refineTag,coarsenTag,user,&tsNew,&solNew);CHKERRQ(ierr); 2015 ierr = PetscFVSetLimiter(fvm,limiter);CHKERRQ(ierr); 2016 if (tsNew) { 2017 ierr = PetscInfo(ts, "AMR used\n");CHKERRQ(ierr); 2018 ierr = DMDestroy(&dm);CHKERRQ(ierr); 2019 ierr = VecDestroy(&X);CHKERRQ(ierr); 2020 ierr = TSDestroy(&ts);CHKERRQ(ierr); 2021 ts = tsNew; 2022 X = solNew; 2023 ierr = TSSetFromOptions(ts);CHKERRQ(ierr); 2024 ierr = VecGetDM(X,&dm);CHKERRQ(ierr); 2025 ierr = PetscObjectReference((PetscObject)dm);CHKERRQ(ierr); 2026 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 2027 ierr = DMPlexGetGeometryFVM(dm, NULL, NULL, &minRadius);CHKERRQ(ierr); 2028 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2029 ierr = MPI_Allreduce(&phys->maxspeed,&mod->maxspeed,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)ts));CHKERRQ(ierr); 2030 if (mod->maxspeed <= 0) SETERRQ1(comm,PETSC_ERR_ARG_WRONGSTATE,"Physics '%s' did not set maxspeed",physname); 2031 dt = cfl * minRadius / mod->maxspeed; 2032 ierr = TSSetStepNumber(ts,nsteps);CHKERRQ(ierr); 2033 ierr = TSSetTime(ts,ftime);CHKERRQ(ierr); 2034 ierr = TSSetTimeStep(ts,dt);CHKERRQ(ierr); 2035 } else { 2036 ierr = PetscInfo(ts, "AMR not used\n");CHKERRQ(ierr); 2037 } 2038 user->monitorStepOffset = nsteps; 2039 ierr = TSSetMaxSteps(ts,nsteps+adaptInterval);CHKERRQ(ierr); 2040 ierr = TSSolve(ts,X);CHKERRQ(ierr); 2041 ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); 2042 ierr = TSGetStepNumber(ts,&nsteps);CHKERRQ(ierr); 2043 } 2044 } 2045 ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr); 2046 ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],(double)ftime,nsteps);CHKERRQ(ierr); 2047 ierr = TSDestroy(&ts);CHKERRQ(ierr); 2048 2049 ierr = VecTaggerDestroy(&refineTag);CHKERRQ(ierr); 2050 ierr = VecTaggerDestroy(&coarsenTag);CHKERRQ(ierr); 2051 ierr = PetscFunctionListDestroy(&PhysicsList);CHKERRQ(ierr); 2052 ierr = PetscFunctionListDestroy(&PhysicsRiemannList_SW);CHKERRQ(ierr); 2053 ierr = FunctionalLinkDestroy(&user->model->functionalRegistry);CHKERRQ(ierr); 2054 ierr = PetscFree(user->model->functionalMonitored);CHKERRQ(ierr); 2055 ierr = PetscFree(user->model->functionalCall);CHKERRQ(ierr); 2056 ierr = PetscFree(user->model->physics->data);CHKERRQ(ierr); 2057 ierr = PetscFree(user->model->physics);CHKERRQ(ierr); 2058 ierr = PetscFree(user->model);CHKERRQ(ierr); 2059 ierr = PetscFree(user);CHKERRQ(ierr); 2060 ierr = VecDestroy(&X);CHKERRQ(ierr); 2061 ierr = PetscLimiterDestroy(&limiter);CHKERRQ(ierr); 2062 ierr = PetscLimiterDestroy(&noneLimiter);CHKERRQ(ierr); 2063 ierr = PetscFVDestroy(&fvm);CHKERRQ(ierr); 2064 ierr = DMDestroy(&dm);CHKERRQ(ierr); 2065 ierr = PetscFinalize(); 2066 return ierr; 2067 } 2068 2069 /* Godunov fluxs */ 2070 PetscScalar cvmgp_(PetscScalar *a, PetscScalar *b, PetscScalar *test) 2071 { 2072 /* System generated locals */ 2073 PetscScalar ret_val; 2074 2075 if (PetscRealPart(*test) > 0.) { 2076 goto L10; 2077 } 2078 ret_val = *b; 2079 return ret_val; 2080 L10: 2081 ret_val = *a; 2082 return ret_val; 2083 } /* cvmgp_ */ 2084 2085 PetscScalar cvmgm_(PetscScalar *a, PetscScalar *b, PetscScalar *test) 2086 { 2087 /* System generated locals */ 2088 PetscScalar ret_val; 2089 2090 if (PetscRealPart(*test) < 0.) { 2091 goto L10; 2092 } 2093 ret_val = *b; 2094 return ret_val; 2095 L10: 2096 ret_val = *a; 2097 return ret_val; 2098 } /* cvmgm_ */ 2099 2100 int riem1mdt( PetscScalar *gaml, PetscScalar *gamr, PetscScalar *rl, PetscScalar *pl, 2101 PetscScalar *uxl, PetscScalar *rr, PetscScalar *pr, 2102 PetscScalar *uxr, PetscScalar *rstarl, PetscScalar *rstarr, PetscScalar * 2103 pstar, PetscScalar *ustar) 2104 { 2105 /* Initialized data */ 2106 2107 static PetscScalar smallp = 1e-8; 2108 2109 /* System generated locals */ 2110 int i__1; 2111 PetscScalar d__1, d__2; 2112 2113 /* Local variables */ 2114 static int i0; 2115 static PetscScalar cl, cr, wl, zl, wr, zr, pst, durl, skpr1, skpr2; 2116 static int iwave; 2117 static PetscScalar gascl4, gascr4, cstarl, dpstar, cstarr; 2118 /* static PetscScalar csqrl, csqrr, gascl1, gascl2, gascl3, gascr1, gascr2, gascr3; */ 2119 static int iterno; 2120 static PetscScalar ustarl, ustarr, rarepr1, rarepr2; 2121 2122 2123 2124 /* gascl1 = *gaml - 1.; */ 2125 /* gascl2 = (*gaml + 1.) * .5; */ 2126 /* gascl3 = gascl2 / *gaml; */ 2127 gascl4 = 1. / (*gaml - 1.); 2128 2129 /* gascr1 = *gamr - 1.; */ 2130 /* gascr2 = (*gamr + 1.) * .5; */ 2131 /* gascr3 = gascr2 / *gamr; */ 2132 gascr4 = 1. / (*gamr - 1.); 2133 iterno = 10; 2134 /* find pstar: */ 2135 cl = PetscSqrtScalar(*gaml * *pl / *rl); 2136 cr = PetscSqrtScalar(*gamr * *pr / *rr); 2137 wl = *rl * cl; 2138 wr = *rr * cr; 2139 /* csqrl = wl * wl; */ 2140 /* csqrr = wr * wr; */ 2141 *pstar = (wl * *pr + wr * *pl) / (wl + wr); 2142 *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp)); 2143 pst = *pl / *pr; 2144 skpr1 = cr * (pst - 1.) * PetscSqrtScalar(2. / (*gamr * (*gamr - 1. + (*gamr + 1.) * pst))); 2145 d__1 = (*gamr - 1.) / (*gamr * 2.); 2146 rarepr2 = gascr4 * 2. * cr * (1. - PetscPowScalar(pst, d__1)); 2147 pst = *pr / *pl; 2148 skpr2 = cl * (pst - 1.) * PetscSqrtScalar(2. / (*gaml * (*gaml - 1. + (*gaml + 1.) * pst))); 2149 d__1 = (*gaml - 1.) / (*gaml * 2.); 2150 rarepr1 = gascl4 * 2. * cl * (1. - PetscPowScalar(pst, d__1)); 2151 durl = *uxr - *uxl; 2152 if (PetscRealPart(*pr) < PetscRealPart(*pl)) { 2153 if (PetscRealPart(durl) >= PetscRealPart(rarepr1)) { 2154 iwave = 100; 2155 } else if (PetscRealPart(durl) <= PetscRealPart(-skpr1)) { 2156 iwave = 300; 2157 } else { 2158 iwave = 400; 2159 } 2160 } else { 2161 if (PetscRealPart(durl) >= PetscRealPart(rarepr2)) { 2162 iwave = 100; 2163 } else if (PetscRealPart(durl) <= PetscRealPart(-skpr2)) { 2164 iwave = 300; 2165 } else { 2166 iwave = 200; 2167 } 2168 } 2169 if (iwave == 100) { 2170 /* 1-wave: rarefaction wave, 3-wave: rarefaction wave */ 2171 /* case (100) */ 2172 i__1 = iterno; 2173 for (i0 = 1; i0 <= i__1; ++i0) { 2174 d__1 = *pstar / *pl; 2175 d__2 = 1. / *gaml; 2176 *rstarl = *rl * PetscPowScalar(d__1, d__2); 2177 cstarl = PetscSqrtScalar(*gaml * *pstar / *rstarl); 2178 ustarl = *uxl - gascl4 * 2. * (cstarl - cl); 2179 zl = *rstarl * cstarl; 2180 d__1 = *pstar / *pr; 2181 d__2 = 1. / *gamr; 2182 *rstarr = *rr * PetscPowScalar(d__1, d__2); 2183 cstarr = PetscSqrtScalar(*gamr * *pstar / *rstarr); 2184 ustarr = *uxr + gascr4 * 2. * (cstarr - cr); 2185 zr = *rstarr * cstarr; 2186 dpstar = zl * zr * (ustarr - ustarl) / (zl + zr); 2187 *pstar -= dpstar; 2188 *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp)); 2189 if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) { 2190 #if 0 2191 break; 2192 #endif 2193 } 2194 } 2195 /* 1-wave: shock wave, 3-wave: rarefaction wave */ 2196 } else if (iwave == 200) { 2197 /* case (200) */ 2198 i__1 = iterno; 2199 for (i0 = 1; i0 <= i__1; ++i0) { 2200 pst = *pstar / *pl; 2201 ustarl = *uxl - (pst - 1.) * cl * PetscSqrtScalar(2. / (*gaml * (*gaml - 1. + (*gaml + 1.) * pst))); 2202 zl = *pl / cl * PetscSqrtScalar(*gaml * 2. * (*gaml - 1. + (*gaml + 1.) * pst)) * (*gaml - 1. + (*gaml + 1.) * pst) / (*gaml * 3. - 1. + (*gaml + 1.) * pst); 2203 d__1 = *pstar / *pr; 2204 d__2 = 1. / *gamr; 2205 *rstarr = *rr * PetscPowScalar(d__1, d__2); 2206 cstarr = PetscSqrtScalar(*gamr * *pstar / *rstarr); 2207 zr = *rstarr * cstarr; 2208 ustarr = *uxr + gascr4 * 2. * (cstarr - cr); 2209 dpstar = zl * zr * (ustarr - ustarl) / (zl + zr); 2210 *pstar -= dpstar; 2211 *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp)); 2212 if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) { 2213 #if 0 2214 break; 2215 #endif 2216 } 2217 } 2218 /* 1-wave: shock wave, 3-wave: shock */ 2219 } else if (iwave == 300) { 2220 /* case (300) */ 2221 i__1 = iterno; 2222 for (i0 = 1; i0 <= i__1; ++i0) { 2223 pst = *pstar / *pl; 2224 ustarl = *uxl - (pst - 1.) * cl * PetscSqrtScalar(2. / (*gaml * (*gaml - 1. + (*gaml + 1.) * pst))); 2225 zl = *pl / cl * PetscSqrtScalar(*gaml * 2. * (*gaml - 1. + (*gaml + 1.) * pst)) * (*gaml - 1. + (*gaml + 1.) * pst) / (*gaml * 3. - 1. + (*gaml + 1.) * pst); 2226 pst = *pstar / *pr; 2227 ustarr = *uxr + (pst - 1.) * cr * PetscSqrtScalar(2. / (*gamr * (*gamr - 1. + (*gamr + 1.) * pst))); 2228 zr = *pr / cr * PetscSqrtScalar(*gamr * 2. * (*gamr - 1. + (*gamr + 1.) * pst)) * (*gamr - 1. + (*gamr + 1.) * pst) / (*gamr * 3. - 1. + (*gamr + 1.) * pst); 2229 dpstar = zl * zr * (ustarr - ustarl) / (zl + zr); 2230 *pstar -= dpstar; 2231 *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp)); 2232 if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) { 2233 #if 0 2234 break; 2235 #endif 2236 } 2237 } 2238 /* 1-wave: rarefaction wave, 3-wave: shock */ 2239 } else if (iwave == 400) { 2240 /* case (400) */ 2241 i__1 = iterno; 2242 for (i0 = 1; i0 <= i__1; ++i0) { 2243 d__1 = *pstar / *pl; 2244 d__2 = 1. / *gaml; 2245 *rstarl = *rl * PetscPowScalar(d__1, d__2); 2246 cstarl = PetscSqrtScalar(*gaml * *pstar / *rstarl); 2247 ustarl = *uxl - gascl4 * 2. * (cstarl - cl); 2248 zl = *rstarl * cstarl; 2249 pst = *pstar / *pr; 2250 ustarr = *uxr + (pst - 1.) * cr * PetscSqrtScalar(2. / (*gamr * (*gamr - 1. + (*gamr + 1.) * pst))); 2251 zr = *pr / cr * PetscSqrtScalar(*gamr * 2. * (*gamr - 1. + (*gamr + 1.) * pst)) * (*gamr - 1. + (*gamr + 1.) * pst) / (*gamr * 3. - 1. + (*gamr + 1.) * pst); 2252 dpstar = zl * zr * (ustarr - ustarl) / (zl + zr); 2253 *pstar -= dpstar; 2254 *pstar = PetscMax(PetscRealPart(*pstar),PetscRealPart(smallp)); 2255 if (PetscAbsScalar(dpstar) / PetscRealPart(*pstar) <= 1e-8) { 2256 #if 0 2257 break; 2258 #endif 2259 } 2260 } 2261 } 2262 2263 *ustar = (zl * ustarr + zr * ustarl) / (zl + zr); 2264 if (PetscRealPart(*pstar) > PetscRealPart(*pl)) { 2265 pst = *pstar / *pl; 2266 *rstarl = ((*gaml + 1.) * pst + *gaml - 1.) / ((*gaml - 1.) * pst + * 2267 gaml + 1.) * *rl; 2268 } 2269 if (PetscRealPart(*pstar) > PetscRealPart(*pr)) { 2270 pst = *pstar / *pr; 2271 *rstarr = ((*gamr + 1.) * pst + *gamr - 1.) / ((*gamr - 1.) * pst + * 2272 gamr + 1.) * *rr; 2273 } 2274 return iwave; 2275 } 2276 2277 PetscScalar sign(PetscScalar x) 2278 { 2279 if (PetscRealPart(x) > 0) return 1.0; 2280 if (PetscRealPart(x) < 0) return -1.0; 2281 return 0.0; 2282 } 2283 /* Riemann Solver */ 2284 /* -------------------------------------------------------------------- */ 2285 int riemannsolver(PetscScalar *xcen, PetscScalar *xp, 2286 PetscScalar *dtt, PetscScalar *rl, PetscScalar *uxl, PetscScalar *pl, 2287 PetscScalar *utl, PetscScalar *ubl, PetscScalar *gaml, PetscScalar *rho1l, 2288 PetscScalar *rr, PetscScalar *uxr, PetscScalar *pr, PetscScalar *utr, 2289 PetscScalar *ubr, PetscScalar *gamr, PetscScalar *rho1r, PetscScalar *rx, 2290 PetscScalar *uxm, PetscScalar *px, PetscScalar *utx, PetscScalar *ubx, 2291 PetscScalar *gam, PetscScalar *rho1) 2292 { 2293 /* System generated locals */ 2294 PetscScalar d__1, d__2; 2295 2296 /* Local variables */ 2297 static PetscScalar s, c0, p0, r0, u0, w0, x0, x2, ri, cx, sgn0, wsp0, gasc1, gasc2, gasc3, gasc4; 2298 static PetscScalar cstar, pstar, rstar, ustar, xstar, wspst, ushock, streng, rstarl, rstarr, rstars; 2299 int iwave; 2300 2301 if (*rl == *rr && *pr == *pl && *uxl == *uxr && *gaml == *gamr) { 2302 *rx = *rl; 2303 *px = *pl; 2304 *uxm = *uxl; 2305 *gam = *gaml; 2306 x2 = *xcen + *uxm * *dtt; 2307 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 0; 2318 } 2319 iwave = riem1mdt(gaml, gamr, rl, pl, uxl, rr, pr, uxr, &rstarl, &rstarr, &pstar, &ustar); 2320 2321 x2 = *xcen + ustar * *dtt; 2322 d__1 = *xp - x2; 2323 sgn0 = sign(d__1); 2324 /* x is in 3-wave if sgn0 = 1 */ 2325 /* x is in 1-wave if sgn0 = -1 */ 2326 r0 = cvmgm_(rl, rr, &sgn0); 2327 p0 = cvmgm_(pl, pr, &sgn0); 2328 u0 = cvmgm_(uxl, uxr, &sgn0); 2329 *gam = cvmgm_(gaml, gamr, &sgn0); 2330 gasc1 = *gam - 1.; 2331 gasc2 = (*gam + 1.) * .5; 2332 gasc3 = gasc2 / *gam; 2333 gasc4 = 1. / (*gam - 1.); 2334 c0 = PetscSqrtScalar(*gam * p0 / r0); 2335 streng = pstar - p0; 2336 w0 = *gam * r0 * p0 * (gasc3 * streng / p0 + 1.); 2337 rstars = r0 / (1. - r0 * streng / w0); 2338 d__1 = p0 / pstar; 2339 d__2 = -1. / *gam; 2340 rstarr = r0 * PetscPowScalar(d__1, d__2); 2341 rstar = cvmgm_(&rstarr, &rstars, &streng); 2342 w0 = PetscSqrtScalar(w0); 2343 cstar = PetscSqrtScalar(*gam * pstar / rstar); 2344 wsp0 = u0 + sgn0 * c0; 2345 wspst = ustar + sgn0 * cstar; 2346 ushock = ustar + sgn0 * w0 / rstar; 2347 wspst = cvmgp_(&ushock, &wspst, &streng); 2348 wsp0 = cvmgp_(&ushock, &wsp0, &streng); 2349 x0 = *xcen + wsp0 * *dtt; 2350 xstar = *xcen + wspst * *dtt; 2351 /* using gas formula to evaluate rarefaction wave */ 2352 /* ri : reiman invariant */ 2353 ri = u0 - sgn0 * 2. * gasc4 * c0; 2354 cx = sgn0 * .5 * gasc1 / gasc2 * ((*xp - *xcen) / *dtt - ri); 2355 *uxm = ri + sgn0 * 2. * gasc4 * cx; 2356 s = p0 / PetscPowScalar(r0, *gam); 2357 d__1 = cx * cx / (*gam * s); 2358 *rx = PetscPowScalar(d__1, gasc4); 2359 *px = cx * cx * *rx / *gam; 2360 d__1 = sgn0 * (x0 - *xp); 2361 *rx = cvmgp_(rx, &r0, &d__1); 2362 d__1 = sgn0 * (x0 - *xp); 2363 *px = cvmgp_(px, &p0, &d__1); 2364 d__1 = sgn0 * (x0 - *xp); 2365 *uxm = cvmgp_(uxm, &u0, &d__1); 2366 d__1 = sgn0 * (xstar - *xp); 2367 *rx = cvmgm_(rx, &rstar, &d__1); 2368 d__1 = sgn0 * (xstar - *xp); 2369 *px = cvmgm_(px, &pstar, &d__1); 2370 d__1 = sgn0 * (xstar - *xp); 2371 *uxm = cvmgm_(uxm, &ustar, &d__1); 2372 if (PetscRealPart(*xp) >= PetscRealPart(x2)) { 2373 *utx = *utr; 2374 *ubx = *ubr; 2375 *rho1 = *rho1r; 2376 } else { 2377 *utx = *utl; 2378 *ubx = *ubl; 2379 *rho1 = *rho1l; 2380 } 2381 return iwave; 2382 } 2383 int godunovflux( const PetscScalar *ul, const PetscScalar *ur, 2384 PetscScalar *flux, const PetscReal *nn, const int *ndim, 2385 const PetscReal *gamma) 2386 { 2387 /* System generated locals */ 2388 int i__1,iwave; 2389 PetscScalar d__1, d__2, d__3; 2390 2391 /* Local variables */ 2392 static int k; 2393 static PetscScalar bn[3], fn, ft, tg[3], pl, rl, pm, pr, rr, xp, ubl, ubm, 2394 ubr, dtt, unm, tmp, utl, utm, uxl, utr, uxr, gaml, gamm, gamr, 2395 xcen, rhom, rho1l, rho1m, rho1r; 2396 /* Parameter adjustments */ 2397 --nn; 2398 --flux; 2399 --ur; 2400 --ul; 2401 2402 /* Function Body */ 2403 xcen = 0.; 2404 xp = 0.; 2405 i__1 = *ndim; 2406 for (k = 1; k <= i__1; ++k) { 2407 tg[k - 1] = 0.; 2408 bn[k - 1] = 0.; 2409 } 2410 dtt = 1.; 2411 if (*ndim == 3) { 2412 if (nn[1] == 0. && nn[2] == 0.) { 2413 tg[0] = 1.; 2414 } else { 2415 tg[0] = -nn[2]; 2416 tg[1] = nn[1]; 2417 } 2418 /* tmp=dsqrt(tg(1)**2+tg(2)**2) */ 2419 /* tg=tg/tmp */ 2420 bn[0] = -nn[3] * tg[1]; 2421 bn[1] = nn[3] * tg[0]; 2422 bn[2] = nn[1] * tg[1] - nn[2] * tg[0]; 2423 /* Computing 2nd power */ 2424 d__1 = bn[0]; 2425 /* Computing 2nd power */ 2426 d__2 = bn[1]; 2427 /* Computing 2nd power */ 2428 d__3 = bn[2]; 2429 tmp = PetscSqrtScalar(d__1 * d__1 + d__2 * d__2 + d__3 * d__3); 2430 i__1 = *ndim; 2431 for (k = 1; k <= i__1; ++k) { 2432 bn[k - 1] /= tmp; 2433 } 2434 } else if (*ndim == 2) { 2435 tg[0] = -nn[2]; 2436 tg[1] = nn[1]; 2437 /* tmp=dsqrt(tg(1)**2+tg(2)**2) */ 2438 /* tg=tg/tmp */ 2439 bn[0] = 0.; 2440 bn[1] = 0.; 2441 bn[2] = 1.; 2442 } 2443 rl = ul[1]; 2444 rr = ur[1]; 2445 uxl = 0.; 2446 uxr = 0.; 2447 utl = 0.; 2448 utr = 0.; 2449 ubl = 0.; 2450 ubr = 0.; 2451 i__1 = *ndim; 2452 for (k = 1; k <= i__1; ++k) { 2453 uxl += ul[k + 1] * nn[k]; 2454 uxr += ur[k + 1] * nn[k]; 2455 utl += ul[k + 1] * tg[k - 1]; 2456 utr += ur[k + 1] * tg[k - 1]; 2457 ubl += ul[k + 1] * bn[k - 1]; 2458 ubr += ur[k + 1] * bn[k - 1]; 2459 } 2460 uxl /= rl; 2461 uxr /= rr; 2462 utl /= rl; 2463 utr /= rr; 2464 ubl /= rl; 2465 ubr /= rr; 2466 2467 gaml = *gamma; 2468 gamr = *gamma; 2469 /* Computing 2nd power */ 2470 d__1 = uxl; 2471 /* Computing 2nd power */ 2472 d__2 = utl; 2473 /* Computing 2nd power */ 2474 d__3 = ubl; 2475 pl = (*gamma - 1.) * (ul[*ndim + 2] - rl * .5 * (d__1 * d__1 + d__2 * d__2 + d__3 * d__3)); 2476 /* Computing 2nd power */ 2477 d__1 = uxr; 2478 /* Computing 2nd power */ 2479 d__2 = utr; 2480 /* Computing 2nd power */ 2481 d__3 = ubr; 2482 pr = (*gamma - 1.) * (ur[*ndim + 2] - rr * .5 * (d__1 * d__1 + d__2 * d__2 + d__3 * d__3)); 2483 rho1l = rl; 2484 rho1r = rr; 2485 2486 iwave = riemannsolver(&xcen, &xp, &dtt, &rl, &uxl, &pl, &utl, &ubl, &gaml, & 2487 rho1l, &rr, &uxr, &pr, &utr, &ubr, &gamr, &rho1r, &rhom, &unm, & 2488 pm, &utm, &ubm, &gamm, &rho1m); 2489 2490 flux[1] = rhom * unm; 2491 fn = rhom * unm * unm + pm; 2492 ft = rhom * unm * utm; 2493 /* flux(2)=fn*nn(1)+ft*nn(2) */ 2494 /* flux(3)=fn*tg(1)+ft*tg(2) */ 2495 flux[2] = fn * nn[1] + ft * tg[0]; 2496 flux[3] = fn * nn[2] + ft * tg[1]; 2497 /* flux(2)=rhom*unm*(unm)+pm */ 2498 /* flux(3)=rhom*(unm)*utm */ 2499 if (*ndim == 3) { 2500 flux[4] = rhom * unm * ubm; 2501 } 2502 flux[*ndim + 2] = (rhom * .5 * (unm * unm + utm * utm + ubm * ubm) + gamm / (gamm - 1.) * pm) * unm; 2503 return iwave; 2504 } /* godunovflux_ */ 2505 2506 /* Subroutine to set up the initial conditions for the */ 2507 /* Shock Interface interaction or linear wave (Ravi Samtaney,Mark Adams). */ 2508 /* ----------------------------------------------------------------------- */ 2509 int projecteqstate(PetscReal wc[], const PetscReal ueq[], PetscReal lv[][3]) 2510 { 2511 int j,k; 2512 /* Wc=matmul(lv,Ueq) 3 vars */ 2513 for (k = 0; k < 3; ++k) { 2514 wc[k] = 0.; 2515 for (j = 0; j < 3; ++j) { 2516 wc[k] += lv[k][j]*ueq[j]; 2517 } 2518 } 2519 return 0; 2520 } 2521 /* ----------------------------------------------------------------------- */ 2522 int projecttoprim(PetscReal v[], const PetscReal wc[], PetscReal rv[][3]) 2523 { 2524 int k,j; 2525 /* V=matmul(rv,WC) 3 vars */ 2526 for (k = 0; k < 3; ++k) { 2527 v[k] = 0.; 2528 for (j = 0; j < 3; ++j) { 2529 v[k] += rv[k][j]*wc[j]; 2530 } 2531 } 2532 return 0; 2533 } 2534 /* ---------------------------------------------------------------------- */ 2535 int eigenvectors(PetscReal rv[][3], PetscReal lv[][3], const PetscReal ueq[], PetscReal gamma) 2536 { 2537 int j,k; 2538 PetscReal rho,csnd,p0; 2539 /* PetscScalar u; */ 2540 2541 for (k = 0; k < 3; ++k) for (j = 0; j < 3; ++j) { lv[k][j] = 0.; rv[k][j] = 0.; } 2542 rho = ueq[0]; 2543 /* u = ueq[1]; */ 2544 p0 = ueq[2]; 2545 csnd = PetscSqrtReal(gamma * p0 / rho); 2546 lv[0][1] = rho * .5; 2547 lv[0][2] = -.5 / csnd; 2548 lv[1][0] = csnd; 2549 lv[1][2] = -1. / csnd; 2550 lv[2][1] = rho * .5; 2551 lv[2][2] = .5 / csnd; 2552 rv[0][0] = -1. / csnd; 2553 rv[1][0] = 1. / rho; 2554 rv[2][0] = -csnd; 2555 rv[0][1] = 1. / csnd; 2556 rv[0][2] = 1. / csnd; 2557 rv[1][2] = 1. / rho; 2558 rv[2][2] = csnd; 2559 return 0; 2560 } 2561 2562 int initLinearWave(EulerNode *ux, const PetscReal gamma, const PetscReal coord[], const PetscReal Lx) 2563 { 2564 PetscReal p0,u0,wcp[3],wc[3]; 2565 PetscReal lv[3][3]; 2566 PetscReal vp[3]; 2567 PetscReal rv[3][3]; 2568 PetscReal eps, ueq[3], rho0, twopi; 2569 2570 /* Function Body */ 2571 twopi = 2.*PETSC_PI; 2572 eps = 1e-4; /* perturbation */ 2573 rho0 = 1e3; /* density of water */ 2574 p0 = 101325.; /* init pressure of 1 atm (?) */ 2575 u0 = 0.; 2576 ueq[0] = rho0; 2577 ueq[1] = u0; 2578 ueq[2] = p0; 2579 /* Project initial state to characteristic variables */ 2580 eigenvectors(rv, lv, ueq, gamma); 2581 projecteqstate(wc, ueq, lv); 2582 wcp[0] = wc[0]; 2583 wcp[1] = wc[1]; 2584 wcp[2] = wc[2] + eps * PetscCosReal(coord[0] * 2. * twopi / Lx); 2585 projecttoprim(vp, wcp, rv); 2586 ux->r = vp[0]; /* density */ 2587 ux->ru[0] = vp[0] * vp[1]; /* x momentum */ 2588 ux->ru[1] = 0.; 2589 #if defined DIM > 2 2590 if (dim>2) ux->ru[2] = 0.; 2591 #endif 2592 /* E = rho * e + rho * v^2/2 = p/(gam-1) + rho*v^2/2 */ 2593 ux->E = vp[2]/(gamma - 1.) + 0.5*vp[0]*vp[1]*vp[1]; 2594 return 0; 2595 } 2596 2597 /*TEST 2598 2599 # 2D Advection 0-10 2600 test: 2601 suffix: 0 2602 requires: exodusii 2603 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo 2604 2605 test: 2606 suffix: 1 2607 requires: exodusii 2608 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo 2609 2610 test: 2611 suffix: 2 2612 requires: exodusii 2613 nsize: 2 2614 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo 2615 2616 test: 2617 suffix: 3 2618 requires: exodusii 2619 nsize: 2 2620 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo 2621 2622 test: 2623 suffix: 4 2624 requires: exodusii 2625 nsize: 8 2626 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad.exo 2627 2628 test: 2629 suffix: 5 2630 requires: exodusii 2631 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo -ts_type rosw -ts_adapt_reject_safety 1 2632 2633 test: 2634 suffix: 6 2635 requires: exodusii 2636 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/squaremotor-30.exo -ufv_split_faces 2637 2638 test: 2639 suffix: 7 2640 requires: exodusii 2641 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo -dm_refine 1 2642 2643 test: 2644 suffix: 8 2645 requires: exodusii 2646 nsize: 2 2647 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo -dm_refine 1 2648 2649 test: 2650 suffix: 9 2651 requires: exodusii 2652 nsize: 8 2653 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad-15.exo -dm_refine 1 2654 2655 test: 2656 suffix: 10 2657 requires: exodusii 2658 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside-quad.exo 2659 2660 # 2D Shallow water 2661 test: 2662 suffix: sw_0 2663 requires: exodusii 2664 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 2665 2666 test: 2667 suffix: sw_hll 2668 args: -ufv_vtk_interval 0 -bc_wall 1,2,3,4 -physics sw -ufv_cfl 3 -petscfv_type leastsquares -petsclimiter_type sin -ts_max_steps 5 -ts_ssp_type rks2 -ts_ssp_nstages 10 -monitor height,energy -grid_bounds 0,5,0,5 -grid_size 25,25 -sw_riemann hll 2669 2670 # 2D Advection: p4est 2671 test: 2672 suffix: p4est_advec_2d 2673 requires: p4est 2674 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 2675 2676 # Advection in a box 2677 test: 2678 suffix: adv_2d_quad_0 2679 args: -ufv_vtk_interval 0 -dm_refine 3 -dm_plex_separate_marker -bc_inflow 1,2,4 -bc_outflow 3 2680 2681 test: 2682 suffix: adv_2d_quad_1 2683 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 2684 timeoutfactor: 3 2685 2686 test: 2687 suffix: adv_2d_quad_p4est_0 2688 requires: p4est 2689 args: -ufv_vtk_interval 0 -dm_refine 5 -dm_type p4est -dm_plex_separate_marker -bc_inflow 1,2,4 -bc_outflow 3 2690 2691 test: 2692 suffix: adv_2d_quad_p4est_1 2693 requires: p4est 2694 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 2695 timeoutfactor: 3 2696 2697 test: 2698 suffix: adv_2d_quad_p4est_adapt_0 2699 requires: p4est !__float128 #broken for quad precision 2700 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 2701 timeoutfactor: 3 2702 2703 test: 2704 suffix: adv_2d_tri_0 2705 requires: triangle 2706 TODO: how did this ever get in master when there is no support for this 2707 args: -ufv_vtk_interval 0 -simplex -dm_refine 3 -dm_plex_separate_marker -bc_inflow 1,2,4 -bc_outflow 3 2708 2709 test: 2710 suffix: adv_2d_tri_1 2711 requires: triangle 2712 TODO: how did this ever get in master when there is no support for this 2713 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 2714 2715 test: 2716 suffix: adv_0 2717 requires: exodusii 2718 args: -ufv_vtk_interval 0 -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/blockcylinder-50.exo -bc_inflow 100,101,200 -bc_outflow 201 2719 2720 test: 2721 suffix: shock_0 2722 requires: p4est !single !complex 2723 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 2724 timeoutfactor: 3 2725 2726 # Test GLVis visualization of PetscFV fields 2727 test: 2728 suffix: glvis_adv_2d_tet 2729 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 2730 2731 test: 2732 suffix: glvis_adv_2d_quad 2733 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 2734 2735 test: 2736 suffix: tut_1 2737 requires: exodusii 2738 nsize: 1 2739 args: -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo 2740 2741 test: 2742 suffix: tut_2 2743 requires: exodusii 2744 nsize: 1 2745 args: -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/sevenside.exo -ts_type rosw 2746 2747 test: 2748 suffix: tut_3 2749 requires: exodusii 2750 nsize: 4 2751 args: -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/annulus-20.exo -monitor Error -advect_sol_type bump -petscfv_type leastsquares -petsclimiter_type sin 2752 2753 test: 2754 suffix: tut_4 2755 requires: exodusii 2756 nsize: 4 2757 args: -f ${wPETSC_DIR}/share/petsc/datafiles/meshes/annulus-20.exo -physics sw -monitor Height,Energy -petscfv_type leastsquares -petsclimiter_type minmod 2758 2759 TEST*/ 2760