1 static char help[] = "Time-dependent reactive low Mach Flow in 2d and 3d channels with finite elements.\n\ 2 We solve the reactive low Mach flow problem in a rectangular domain\n\ 3 using a parallel unstructured mesh (DMPLEX) to discretize the flow\n\ 4 and particles (DWSWARM) to discretize the chemical species.\n\n\n"; 5 6 /*F 7 This low Mach flow is time-dependent isoviscous Navier-Stokes flow. We discretize using the 8 finite element method on an unstructured mesh. The weak form equations are 9 10 \begin{align*} 11 < q, \nabla\cdot u > = 0 12 <v, du/dt> + <v, u \cdot \nabla u> + < \nabla v, \nu (\nabla u + {\nabla u}^T) > - < \nabla\cdot v, p > - < v, f > = 0 13 < w, u \cdot \nabla T > + < \nabla w, \alpha \nabla T > - < w, Q > = 0 14 \end{align*} 15 16 where $\nu$ is the kinematic viscosity and $\alpha$ is thermal diffusivity. 17 18 For visualization, use 19 20 -dm_view hdf5:$PWD/sol.h5 -sol_vec_view hdf5:$PWD/sol.h5::append -exact_vec_view hdf5:$PWD/sol.h5::append 21 22 The particles can be visualized using 23 24 -part_dm_view draw -part_dm_view_swarm_radius 0.03 25 26 F*/ 27 28 #include <petscdmplex.h> 29 #include <petscdmswarm.h> 30 #include <petscts.h> 31 #include <petscds.h> 32 #include <petscbag.h> 33 34 typedef enum {SOL_TRIG_TRIG, NUM_SOL_TYPES} SolType; 35 const char *solTypes[NUM_SOL_TYPES+1] = {"trig_trig", "unknown"}; 36 37 typedef enum {PART_LAYOUT_CELL, PART_LAYOUT_BOX, NUM_PART_LAYOUT_TYPES} PartLayoutType; 38 const char *partLayoutTypes[NUM_PART_LAYOUT_TYPES+1] = {"cell", "box", "unknown"}; 39 40 typedef struct { 41 PetscReal nu; /* Kinematic viscosity */ 42 PetscReal alpha; /* Thermal diffusivity */ 43 PetscReal T_in; /* Inlet temperature*/ 44 PetscReal omega; /* Rotation speed in MMS benchmark */ 45 } Parameter; 46 47 typedef struct { 48 /* Problem definition */ 49 PetscBag bag; /* Holds problem parameters */ 50 SolType solType; /* MMS solution type */ 51 PartLayoutType partLayout; /* Type of particle distribution */ 52 PetscInt Npc; /* The initial number of particles per cell */ 53 PetscReal partLower[3]; /* Lower left corner of particle box */ 54 PetscReal partUpper[3]; /* Upper right corner of particle box */ 55 PetscInt Npb; /* The initial number of particles per box dimension */ 56 } AppCtx; 57 58 typedef struct { 59 PetscReal ti; /* The time for ui, at the beginning of the advection solve */ 60 PetscReal tf; /* The time for uf, at the end of the advection solve */ 61 Vec ui; /* The PDE solution field at ti */ 62 Vec uf; /* The PDE solution field at tf */ 63 Vec x0; /* The initial particle positions at t = 0 */ 64 PetscErrorCode (*exact)(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar *, void *); 65 AppCtx *ctx; /* Context for exact solution */ 66 } AdvCtx; 67 68 static PetscErrorCode zero(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nc, PetscScalar *u, void *ctx) 69 { 70 PetscInt d; 71 for (d = 0; d < Nc; ++d) u[d] = 0.0; 72 return 0; 73 } 74 75 static PetscErrorCode constant(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nc, PetscScalar *u, void *ctx) 76 { 77 PetscInt d; 78 for (d = 0; d < Nc; ++d) u[d] = 1.0; 79 return 0; 80 } 81 82 /* 83 CASE: trigonometric-trigonometric 84 In 2D we use exact solution: 85 86 x = r0 cos(w t + theta0) r0 = sqrt(x0^2 + y0^2) 87 y = r0 sin(w t + theta0) theta0 = arctan(y0/x0) 88 u = -w r0 sin(theta0) = -w y 89 v = w r0 cos(theta0) = w x 90 p = x + y - 1 91 T = t + x + y 92 f = <1, 1> 93 Q = 1 + w (x - y)/r 94 95 so that 96 97 \nabla \cdot u = 0 + 0 = 0 98 99 f = du/dt + u \cdot \nabla u - \nu \Delta u + \nabla p 100 = <0, 0> + u_i d_i u_j - \nu 0 + <1, 1> 101 = <1, 1> + w^2 <-y, x> . <<0, 1>, <-1, 0>> 102 = <1, 1> + w^2 <-x, -y> 103 = <1, 1> - w^2 <x, y> 104 105 Q = dT/dt + u \cdot \nabla T - \alpha \Delta T 106 = 1 + <u, v> . <1, 1> - \alpha 0 107 = 1 + u + v 108 */ 109 static PetscErrorCode trig_trig_x(PetscInt dim, PetscReal time, const PetscReal X[], PetscInt Nf, PetscScalar *x, void *ctx) 110 { 111 const PetscReal x0 = X[0]; 112 const PetscReal y0 = X[1]; 113 const PetscReal R0 = PetscSqrtReal(x0*x0 + y0*y0); 114 const PetscReal theta0 = PetscAtan2Real(y0, x0); 115 Parameter *p = (Parameter *) ctx; 116 117 x[0] = R0*PetscCosReal(p->omega*time + theta0); 118 x[1] = R0*PetscSinReal(p->omega*time + theta0); 119 return 0; 120 } 121 static PetscErrorCode trig_trig_u(PetscInt dim, PetscReal time, const PetscReal X[], PetscInt Nf, PetscScalar *u, void *ctx) 122 { 123 Parameter *p = (Parameter *) ctx; 124 125 u[0] = -p->omega*X[1]; 126 u[1] = p->omega*X[0]; 127 return 0; 128 } 129 static PetscErrorCode trig_trig_u_t(PetscInt dim, PetscReal time, const PetscReal X[], PetscInt Nf, PetscScalar *u, void *ctx) 130 { 131 u[0] = 0.0; 132 u[1] = 0.0; 133 return 0; 134 } 135 136 static PetscErrorCode trig_trig_p(PetscInt dim, PetscReal time, const PetscReal X[], PetscInt Nf, PetscScalar *p, void *ctx) 137 { 138 p[0] = X[0] + X[1] - 1.0; 139 return 0; 140 } 141 142 static PetscErrorCode trig_trig_T(PetscInt dim, PetscReal time, const PetscReal X[], PetscInt Nf, PetscScalar *T, void *ctx) 143 { 144 T[0] = time + X[0] + X[1]; 145 return 0; 146 } 147 static PetscErrorCode trig_trig_T_t(PetscInt dim, PetscReal time, const PetscReal X[], PetscInt Nf, PetscScalar *T, void *ctx) 148 { 149 T[0] = 1.0; 150 return 0; 151 } 152 153 static void f0_trig_trig_v(PetscInt dim, PetscInt Nf, PetscInt NfAux, 154 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 155 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 156 PetscReal t, const PetscReal X[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 157 { 158 const PetscReal omega = PetscRealPart(constants[3]); 159 PetscInt Nc = dim; 160 PetscInt c, d; 161 162 for (d = 0; d < dim; ++d) f0[d] = u_t[uOff[0]+d]; 163 164 for (c = 0; c < Nc; ++c) { 165 for (d = 0; d < dim; ++d) f0[c] += u[d]*u_x[c*dim+d]; 166 } 167 f0[0] -= 1.0 - omega*omega*X[0]; 168 f0[1] -= 1.0 - omega*omega*X[1]; 169 } 170 171 static void f0_trig_trig_w(PetscInt dim, PetscInt Nf, PetscInt NfAux, 172 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 173 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 174 PetscReal t, const PetscReal X[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 175 { 176 const PetscReal omega = PetscRealPart(constants[3]); 177 PetscInt d; 178 179 for (d = 0, f0[0] = 0; d < dim; ++d) f0[0] += u[uOff[0]+d]*u_x[uOff_x[2]+d]; 180 f0[0] += u_t[uOff[2]] - (1.0 + omega*(X[0] - X[1])); 181 } 182 183 static void f0_q(PetscInt dim, PetscInt Nf, PetscInt NfAux, 184 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 185 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 186 PetscReal t, const PetscReal X[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 187 { 188 PetscInt d; 189 for (d = 0, f0[0] = 0.0; d < dim; ++d) f0[0] += u_x[d*dim+d]; 190 } 191 192 /*f1_v = \nu[grad(u) + grad(u)^T] - pI */ 193 static void f1_v(PetscInt dim, PetscInt Nf, PetscInt NfAux, 194 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 195 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 196 PetscReal t, const PetscReal X[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f1[]) 197 { 198 const PetscReal nu = PetscRealPart(constants[0]); 199 const PetscInt Nc = dim; 200 PetscInt c, d; 201 202 for (c = 0; c < Nc; ++c) { 203 for (d = 0; d < dim; ++d) { 204 f1[c*dim+d] = nu*(u_x[c*dim+d] + u_x[d*dim+c]); 205 //f1[c*dim+d] = nu*u_x[c*dim+d]; 206 } 207 f1[c*dim+c] -= u[uOff[1]]; 208 } 209 } 210 211 static void f1_w(PetscInt dim, PetscInt Nf, PetscInt NfAux, 212 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 213 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 214 PetscReal t, const PetscReal X[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f1[]) 215 { 216 const PetscReal alpha = PetscRealPart(constants[1]); 217 PetscInt d; 218 for (d = 0; d < dim; ++d) f1[d] = alpha*u_x[uOff_x[2]+d]; 219 } 220 221 /*Jacobians*/ 222 static void g1_qu(PetscInt dim, PetscInt Nf, PetscInt NfAux, 223 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 224 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 225 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g1[]) 226 { 227 PetscInt d; 228 for (d = 0; d < dim; ++d) g1[d*dim+d] = 1.0; 229 } 230 231 static void g0_vu(PetscInt dim, PetscInt Nf, PetscInt NfAux, 232 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 233 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 234 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[]) 235 { 236 PetscInt c, d; 237 const PetscInt Nc = dim; 238 239 for (d = 0; d < dim; ++d) g0[d*dim+d] = u_tShift; 240 241 for (c = 0; c < Nc; ++c) { 242 for (d = 0; d < dim; ++d) { 243 g0[c*Nc+d] += u_x[c*Nc+d]; 244 } 245 } 246 } 247 248 static void g1_vu(PetscInt dim, PetscInt Nf, PetscInt NfAux, 249 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 250 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 251 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g1[]) 252 { 253 PetscInt NcI = dim; 254 PetscInt NcJ = dim; 255 PetscInt c, d, e; 256 257 for (c = 0; c < NcI; ++c) { 258 for (d = 0; d < NcJ; ++d) { 259 for (e = 0; e < dim; ++e) { 260 if (c == d) { 261 g1[(c*NcJ+d)*dim+e] += u[e]; 262 } 263 } 264 } 265 } 266 } 267 268 269 static void g2_vp(PetscInt dim, PetscInt Nf, PetscInt NfAux, 270 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 271 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 272 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g2[]) 273 { 274 PetscInt d; 275 for (d = 0; d < dim; ++d) g2[d*dim+d] = -1.0; 276 } 277 278 static void g3_vu(PetscInt dim, PetscInt Nf, PetscInt NfAux, 279 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 280 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 281 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g3[]) 282 { 283 const PetscReal nu = PetscRealPart(constants[0]); 284 const PetscInt Nc = dim; 285 PetscInt c, d; 286 287 for (c = 0; c < Nc; ++c) { 288 for (d = 0; d < dim; ++d) { 289 g3[((c*Nc+c)*dim+d)*dim+d] += nu; // gradU 290 g3[((c*Nc+d)*dim+d)*dim+c] += nu; // gradU transpose 291 } 292 } 293 } 294 295 static void g0_wT(PetscInt dim, PetscInt Nf, PetscInt NfAux, 296 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 297 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 298 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[]) 299 { 300 PetscInt d; 301 for (d = 0; d < dim; ++d) g0[d] = u_tShift; 302 } 303 304 static void g0_wu(PetscInt dim, PetscInt Nf, PetscInt NfAux, 305 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 306 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 307 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g0[]) 308 { 309 PetscInt d; 310 for (d = 0; d < dim; ++d) g0[d] = u_x[uOff_x[2]+d]; 311 } 312 313 static void g1_wT(PetscInt dim, PetscInt Nf, PetscInt NfAux, 314 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 315 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 316 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g1[]) 317 { 318 PetscInt d; 319 for (d = 0; d < dim; ++d) g1[d] = u[uOff[0]+d]; 320 } 321 322 static void g3_wT(PetscInt dim, PetscInt Nf, PetscInt NfAux, 323 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 324 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 325 PetscReal t, PetscReal u_tShift, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar g3[]) 326 { 327 const PetscReal alpha = PetscRealPart(constants[1]); 328 PetscInt d; 329 330 for (d = 0; d < dim; ++d) g3[d*dim+d] = alpha; 331 } 332 333 static PetscErrorCode ProcessOptions(MPI_Comm comm, AppCtx *options) 334 { 335 PetscInt sol, pl, n; 336 PetscErrorCode ierr; 337 338 PetscFunctionBeginUser; 339 options->solType = SOL_TRIG_TRIG; 340 options->partLayout = PART_LAYOUT_CELL; 341 options->Npc = 1; 342 options->Npb = 1; 343 344 options->partLower[0] = options->partLower[1] = options->partLower[2] = 0.; 345 options->partUpper[0] = options->partUpper[1] = options->partUpper[2] = 1.; 346 ierr = PetscOptionsBegin(comm, "", "Low Mach flow Problem Options", "DMPLEX");CHKERRQ(ierr); 347 sol = options->solType; 348 ierr = PetscOptionsEList("-sol_type", "The solution type", "ex77.c", solTypes, NUM_SOL_TYPES, solTypes[options->solType], &sol, NULL);CHKERRQ(ierr); 349 options->solType = (SolType) sol; 350 pl = options->partLayout; 351 ierr = PetscOptionsEList("-part_layout_type", "The particle layout type", "ex77.c", partLayoutTypes, NUM_PART_LAYOUT_TYPES, partLayoutTypes[options->partLayout], &pl, NULL);CHKERRQ(ierr); 352 options->partLayout = (PartLayoutType) pl; 353 ierr = PetscOptionsInt("-Npc", "The initial number of particles per cell", "ex77.c", options->Npc, &options->Npc, NULL);CHKERRQ(ierr); 354 n = 3; 355 ierr = PetscOptionsRealArray("-part_lower", "The lower left corner of the particle box", "ex77.c", options->partLower, &n, NULL);CHKERRQ(ierr); 356 n = 3; 357 ierr = PetscOptionsRealArray("-part_upper", "The upper right corner of the particle box", "ex77.c", options->partUpper, &n, NULL);CHKERRQ(ierr); 358 ierr = PetscOptionsInt("-Npb", "The initial number of particles per box dimension", "ex77.c", options->Npb, &options->Npb, NULL);CHKERRQ(ierr); 359 ierr = PetscOptionsEnd(); 360 PetscFunctionReturn(0); 361 } 362 363 static PetscErrorCode SetupParameters(AppCtx *user) 364 { 365 PetscBag bag; 366 Parameter *p; 367 PetscErrorCode ierr; 368 369 PetscFunctionBeginUser; 370 /* setup PETSc parameter bag */ 371 ierr = PetscBagGetData(user->bag, (void **) &p);CHKERRQ(ierr); 372 ierr = PetscBagSetName(user->bag, "par", "Low Mach flow parameters");CHKERRQ(ierr); 373 bag = user->bag; 374 ierr = PetscBagRegisterReal(bag, &p->nu, 1.0, "nu", "Kinematic viscosity");CHKERRQ(ierr); 375 ierr = PetscBagRegisterReal(bag, &p->alpha, 1.0, "alpha", "Thermal diffusivity");CHKERRQ(ierr); 376 ierr = PetscBagRegisterReal(bag, &p->T_in, 1.0, "T_in", "Inlet temperature");CHKERRQ(ierr); 377 ierr = PetscBagRegisterReal(bag, &p->omega, 1.0, "omega", "Rotation speed in MMS benchmark");CHKERRQ(ierr); 378 PetscFunctionReturn(0); 379 } 380 381 static PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm) 382 { 383 PetscErrorCode ierr; 384 385 PetscFunctionBeginUser; 386 ierr = DMPlexCreateBoxMesh(comm, 2, PETSC_TRUE, NULL, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr); 387 ierr = DMSetFromOptions(*dm);CHKERRQ(ierr); 388 ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr); 389 PetscFunctionReturn(0); 390 } 391 392 static PetscErrorCode SetupProblem(DM dm, AppCtx *user) 393 { 394 PetscErrorCode (*exactFuncs[3])(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx); 395 PetscErrorCode (*exactFuncs_t[3])(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx); 396 PetscDS prob; 397 Parameter *ctx; 398 PetscInt id; 399 PetscErrorCode ierr; 400 401 PetscFunctionBeginUser; 402 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 403 switch(user->solType){ 404 case SOL_TRIG_TRIG: 405 ierr = PetscDSSetResidual(prob, 0, f0_trig_trig_v, f1_v);CHKERRQ(ierr); 406 ierr = PetscDSSetResidual(prob, 2, f0_trig_trig_w, f1_w);CHKERRQ(ierr); 407 408 exactFuncs[0] = trig_trig_u; 409 exactFuncs[1] = trig_trig_p; 410 exactFuncs[2] = trig_trig_T; 411 exactFuncs_t[0] = trig_trig_u_t; 412 exactFuncs_t[1] = NULL; 413 exactFuncs_t[2] = trig_trig_T_t; 414 break; 415 default: SETERRQ2(PetscObjectComm((PetscObject) prob), PETSC_ERR_ARG_WRONG, "Unsupported solution type: %s (%D)", solTypes[PetscMin(user->solType, NUM_SOL_TYPES)], user->solType); 416 } 417 418 ierr = PetscDSSetResidual(prob, 1, f0_q, NULL);CHKERRQ(ierr); 419 420 ierr = PetscDSSetJacobian(prob, 0, 0, g0_vu, g1_vu, NULL, g3_vu);CHKERRQ(ierr); 421 ierr = PetscDSSetJacobian(prob, 0, 1, NULL, NULL, g2_vp, NULL);CHKERRQ(ierr); 422 ierr = PetscDSSetJacobian(prob, 1, 0, NULL, g1_qu, NULL, NULL);CHKERRQ(ierr); 423 ierr = PetscDSSetJacobian(prob, 2, 0, g0_wu, NULL, NULL, NULL);CHKERRQ(ierr); 424 ierr = PetscDSSetJacobian(prob, 2, 2, g0_wT, g1_wT, NULL, g3_wT);CHKERRQ(ierr); 425 /* Setup constants */ 426 { 427 Parameter *param; 428 PetscScalar constants[4]; 429 430 ierr = PetscBagGetData(user->bag, (void **) ¶m);CHKERRQ(ierr); 431 432 constants[0] = param->nu; 433 constants[1] = param->alpha; 434 constants[2] = param->T_in; 435 constants[3] = param->omega; 436 ierr = PetscDSSetConstants(prob, 4, constants);CHKERRQ(ierr); 437 } 438 /* Setup Boundary Conditions */ 439 ierr = PetscBagGetData(user->bag, (void **) &ctx);CHKERRQ(ierr); 440 id = 3; 441 ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "top wall velocity", "marker", 0, 0, NULL, (void (*)(void)) exactFuncs[0], (void (*)(void)) exactFuncs_t[0], 1, &id, ctx);CHKERRQ(ierr); 442 id = 1; 443 ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "bottom wall velocity", "marker", 0, 0, NULL, (void (*)(void)) exactFuncs[0], (void (*)(void)) exactFuncs_t[0], 1, &id, ctx);CHKERRQ(ierr); 444 id = 2; 445 ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "right wall velocity", "marker", 0, 0, NULL, (void (*)(void)) exactFuncs[0], (void (*)(void)) exactFuncs_t[0], 1, &id, ctx);CHKERRQ(ierr); 446 id = 4; 447 ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "left wall velocity", "marker", 0, 0, NULL, (void (*)(void)) exactFuncs[0], (void (*)(void)) exactFuncs_t[0], 1, &id, ctx);CHKERRQ(ierr); 448 id = 3; 449 ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "top wall temp", "marker", 2, 0, NULL, (void (*)(void)) exactFuncs[2], (void (*)(void)) exactFuncs_t[2], 1, &id, ctx);CHKERRQ(ierr); 450 id = 1; 451 ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "bottom wall temp", "marker", 2, 0, NULL, (void (*)(void)) exactFuncs[2], (void (*)(void)) exactFuncs_t[2], 1, &id, ctx);CHKERRQ(ierr); 452 id = 2; 453 ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "right wall temp", "marker", 2, 0, NULL, (void (*)(void)) exactFuncs[2], (void (*)(void)) exactFuncs_t[2], 1, &id, ctx);CHKERRQ(ierr); 454 id = 4; 455 ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "left wall temp", "marker", 2, 0, NULL, (void (*)(void)) exactFuncs[2], (void (*)(void)) exactFuncs_t[2], 1, &id, ctx);CHKERRQ(ierr); 456 457 /*setup exact solution.*/ 458 ierr = PetscDSSetExactSolution(prob, 0, exactFuncs[0], ctx);CHKERRQ(ierr); 459 ierr = PetscDSSetExactSolution(prob, 1, exactFuncs[1], ctx);CHKERRQ(ierr); 460 ierr = PetscDSSetExactSolution(prob, 2, exactFuncs[2], ctx);CHKERRQ(ierr); 461 ierr = PetscDSSetExactSolutionTimeDerivative(prob, 0, exactFuncs_t[0], ctx);CHKERRQ(ierr); 462 ierr = PetscDSSetExactSolutionTimeDerivative(prob, 1, exactFuncs_t[1], ctx);CHKERRQ(ierr); 463 ierr = PetscDSSetExactSolutionTimeDerivative(prob, 2, exactFuncs_t[2], ctx);CHKERRQ(ierr); 464 PetscFunctionReturn(0); 465 } 466 467 /* x_t = v 468 469 Note that here we use the velocity field at t_{n+1} to advect the particles from 470 t_n to t_{n+1}. If we use both of these fields, we could use Crank-Nicholson or 471 the method of characteristics. 472 */ 473 static PetscErrorCode FreeStreaming(TS ts, PetscReal t, Vec X, Vec F, void *ctx) 474 { 475 AdvCtx *adv = (AdvCtx *) ctx; 476 Vec u = adv->ui; 477 DM sdm, dm, vdm; 478 Vec vel, locvel, pvel; 479 IS vis; 480 DMInterpolationInfo ictx; 481 const PetscScalar *coords, *v; 482 PetscScalar *f; 483 PetscInt vf[1] = {0}; 484 PetscInt dim, Np; 485 PetscErrorCode ierr; 486 487 PetscFunctionBeginUser; 488 ierr = TSGetDM(ts, &sdm);CHKERRQ(ierr); 489 ierr = DMSwarmGetCellDM(sdm, &dm);CHKERRQ(ierr); 490 ierr = DMSwarmVectorDefineField(sdm, DMSwarmPICField_coor);CHKERRQ(ierr); 491 ierr = DMGetGlobalVector(sdm, &pvel);CHKERRQ(ierr); 492 ierr = DMSwarmGetLocalSize(sdm, &Np);CHKERRQ(ierr); 493 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 494 /* Get local velocity */ 495 ierr = DMCreateSubDM(dm, 1, vf, &vis, &vdm);CHKERRQ(ierr); 496 ierr = VecGetSubVector(u, vis, &vel);CHKERRQ(ierr); 497 ierr = DMGetLocalVector(vdm, &locvel);CHKERRQ(ierr); 498 ierr = DMPlexInsertBoundaryValues(vdm, PETSC_TRUE, locvel, adv->ti, NULL, NULL, NULL);CHKERRQ(ierr); 499 ierr = DMGlobalToLocalBegin(vdm, vel, INSERT_VALUES, locvel);CHKERRQ(ierr); 500 ierr = DMGlobalToLocalEnd(vdm, vel, INSERT_VALUES, locvel);CHKERRQ(ierr); 501 ierr = VecRestoreSubVector(u, vis, &vel);CHKERRQ(ierr); 502 ierr = ISDestroy(&vis);CHKERRQ(ierr); 503 /* Interpolate velocity */ 504 ierr = DMInterpolationCreate(PETSC_COMM_SELF, &ictx);CHKERRQ(ierr); 505 ierr = DMInterpolationSetDim(ictx, dim);CHKERRQ(ierr); 506 ierr = DMInterpolationSetDof(ictx, dim);CHKERRQ(ierr); 507 ierr = VecGetArrayRead(X, &coords);CHKERRQ(ierr); 508 ierr = DMInterpolationAddPoints(ictx, Np, (PetscReal *) coords);CHKERRQ(ierr); 509 ierr = VecRestoreArrayRead(X, &coords);CHKERRQ(ierr); 510 ierr = DMInterpolationSetUp(ictx, vdm, PETSC_FALSE);CHKERRQ(ierr); 511 ierr = DMInterpolationEvaluate(ictx, vdm, locvel, pvel);CHKERRQ(ierr); 512 ierr = DMInterpolationDestroy(&ictx);CHKERRQ(ierr); 513 ierr = DMRestoreLocalVector(vdm, &locvel);CHKERRQ(ierr); 514 ierr = DMDestroy(&vdm);CHKERRQ(ierr); 515 516 ierr = VecGetArray(F, &f);CHKERRQ(ierr); 517 ierr = VecGetArrayRead(pvel, &v);CHKERRQ(ierr); 518 ierr = PetscArraycpy(f, v, Np*dim);CHKERRQ(ierr); 519 ierr = VecRestoreArrayRead(pvel, &v);CHKERRQ(ierr); 520 ierr = VecRestoreArray(F, &f);CHKERRQ(ierr); 521 ierr = DMRestoreGlobalVector(sdm, &pvel);CHKERRQ(ierr); 522 PetscFunctionReturn(0); 523 } 524 525 static PetscErrorCode SetInitialParticleConditions(TS ts, Vec u) 526 { 527 AppCtx *user; 528 void *ctx; 529 DM dm; 530 PetscScalar *coords; 531 PetscReal x[3], dx[3]; 532 PetscInt n[3]; 533 PetscInt Np, dim, d, i, j, k; 534 PetscErrorCode ierr; 535 536 PetscFunctionBegin; 537 ierr = TSGetApplicationContext(ts, &ctx);CHKERRQ(ierr); 538 user = ((AdvCtx *) ctx)->ctx; 539 ierr = TSGetDM(ts, &dm);CHKERRQ(ierr); 540 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 541 switch (user->partLayout) { 542 case PART_LAYOUT_CELL: 543 ierr = DMSwarmSetPointCoordinatesRandom(dm, user->Npc);CHKERRQ(ierr); 544 break; 545 case PART_LAYOUT_BOX: 546 Np = 1; 547 for (d = 0; d < dim; ++d) { 548 n[d] = user->Npb; 549 dx[d] = (user->partUpper[d] - user->partLower[d])/PetscMax(1, n[d] - 1); 550 Np *= n[d]; 551 } 552 ierr = VecGetArray(u, &coords);CHKERRQ(ierr); 553 switch (dim) { 554 case 2: 555 x[0] = user->partLower[0]; 556 for (i = 0; i < n[0]; ++i, x[0] += dx[0]) { 557 x[1] = user->partLower[1]; 558 for (j = 0; j < n[1]; ++j, x[1] += dx[1]) { 559 const PetscInt p = j*n[0] + i; 560 for (d = 0; d < dim; ++d) coords[p*dim + d] = x[d]; 561 } 562 } 563 break; 564 case 3: 565 x[0] = user->partLower[0]; 566 for (i = 0; i < n[0]; ++i, x[0] += dx[0]) { 567 x[1] = user->partLower[1]; 568 for (j = 0; j < n[1]; ++j, x[1] += dx[1]) { 569 x[2] = user->partLower[2]; 570 for (k = 0; k < n[2]; ++k, x[2] += dx[2]) { 571 const PetscInt p = (k*n[1] + j)*n[0] + i; 572 for (d = 0; d < dim; ++d) coords[p*dim + d] = x[d]; 573 } 574 } 575 } 576 break; 577 default: SETERRQ1(PetscObjectComm((PetscObject) ts), PETSC_ERR_SUP, "Do not support particle layout in dimension %D", dim); 578 } 579 ierr = VecRestoreArray(u, &coords);CHKERRQ(ierr); 580 break; 581 default: SETERRQ1(PetscObjectComm((PetscObject) ts), PETSC_ERR_ARG_WRONG, "Invalid particle layout type %s", partLayoutTypes[PetscMin(user->partLayout, NUM_PART_LAYOUT_TYPES)]); 582 } 583 PetscFunctionReturn(0); 584 } 585 586 static PetscErrorCode SetupDiscretization(DM dm, DM sdm, AppCtx *user) 587 { 588 DM cdm = dm; 589 PetscFE fe[3]; 590 Parameter *param; 591 PetscInt *cellid, n[3]; 592 PetscReal x[3], dx[3]; 593 PetscScalar *coords; 594 DMPolytopeType ct; 595 PetscInt dim, d, cStart, cEnd, c, Np, p, i, j, k; 596 PetscBool simplex; 597 MPI_Comm comm; 598 PetscErrorCode ierr; 599 600 PetscFunctionBeginUser; 601 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 602 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 603 ierr = DMPlexGetCellType(dm, cStart, &ct);CHKERRQ(ierr); 604 simplex = DMPolytopeTypeGetNumVertices(ct) == DMPolytopeTypeGetDim(ct)+1 ? PETSC_TRUE : PETSC_FALSE; 605 /* Create finite element */ 606 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 607 ierr = PetscFECreateDefault(comm, dim, dim, simplex, "vel_", PETSC_DEFAULT, &fe[0]);CHKERRQ(ierr); 608 ierr = PetscObjectSetName((PetscObject) fe[0], "velocity");CHKERRQ(ierr); 609 610 ierr = PetscFECreateDefault(comm, dim, 1, simplex, "pres_", PETSC_DEFAULT, &fe[1]);CHKERRQ(ierr); 611 ierr = PetscFECopyQuadrature(fe[0], fe[1]);CHKERRQ(ierr); 612 ierr = PetscObjectSetName((PetscObject) fe[1], "pressure");CHKERRQ(ierr); 613 614 ierr = PetscFECreateDefault(comm, dim, 1, simplex, "temp_", PETSC_DEFAULT, &fe[2]);CHKERRQ(ierr); 615 ierr = PetscFECopyQuadrature(fe[0], fe[2]);CHKERRQ(ierr); 616 ierr = PetscObjectSetName((PetscObject) fe[2], "temperature");CHKERRQ(ierr); 617 618 /* Set discretization and boundary conditions for each mesh */ 619 ierr = DMSetField(dm, 0, NULL, (PetscObject) fe[0]);CHKERRQ(ierr); 620 ierr = DMSetField(dm, 1, NULL, (PetscObject) fe[1]);CHKERRQ(ierr); 621 ierr = DMSetField(dm, 2, NULL, (PetscObject) fe[2]);CHKERRQ(ierr); 622 ierr = DMCreateDS(dm);CHKERRQ(ierr); 623 ierr = SetupProblem(dm, user);CHKERRQ(ierr); 624 ierr = PetscBagGetData(user->bag, (void **) ¶m);CHKERRQ(ierr); 625 while (cdm) { 626 ierr = DMCopyDisc(dm, cdm);CHKERRQ(ierr); 627 ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr); 628 } 629 ierr = PetscFEDestroy(&fe[0]);CHKERRQ(ierr); 630 ierr = PetscFEDestroy(&fe[1]);CHKERRQ(ierr); 631 ierr = PetscFEDestroy(&fe[2]);CHKERRQ(ierr); 632 633 { 634 PetscObject pressure; 635 MatNullSpace nullspacePres; 636 637 ierr = DMGetField(dm, 1, NULL, &pressure);CHKERRQ(ierr); 638 ierr = MatNullSpaceCreate(PetscObjectComm(pressure), PETSC_TRUE, 0, NULL, &nullspacePres);CHKERRQ(ierr); 639 ierr = PetscObjectCompose(pressure, "nullspace", (PetscObject) nullspacePres);CHKERRQ(ierr); 640 ierr = MatNullSpaceDestroy(&nullspacePres);CHKERRQ(ierr); 641 } 642 643 /* Setup particle information */ 644 ierr = DMSwarmSetType(sdm, DMSWARM_PIC);CHKERRQ(ierr); 645 ierr = DMSwarmRegisterPetscDatatypeField(sdm, "mass", 1, PETSC_REAL);CHKERRQ(ierr); 646 ierr = DMSwarmFinalizeFieldRegister(sdm);CHKERRQ(ierr); 647 switch (user->partLayout) { 648 case PART_LAYOUT_CELL: 649 ierr = DMSwarmSetLocalSizes(sdm, (cEnd - cStart) * user->Npc, 0);CHKERRQ(ierr); 650 ierr = DMSetFromOptions(sdm);CHKERRQ(ierr); 651 ierr = DMSwarmGetField(sdm, DMSwarmPICField_cellid, NULL, NULL, (void **) &cellid);CHKERRQ(ierr); 652 for (c = cStart; c < cEnd; ++c) { 653 for (p = 0; p < user->Npc; ++p) { 654 const PetscInt n = c*user->Npc + p; 655 656 cellid[n] = c; 657 } 658 } 659 ierr = DMSwarmRestoreField(sdm, DMSwarmPICField_cellid, NULL, NULL, (void **) &cellid);CHKERRQ(ierr); 660 ierr = DMSwarmSetPointCoordinatesRandom(sdm, user->Npc);CHKERRQ(ierr); 661 break; 662 case PART_LAYOUT_BOX: 663 Np = 1; 664 for (d = 0; d < dim; ++d) { 665 n[d] = user->Npb; 666 dx[d] = (user->partUpper[d] - user->partLower[d])/PetscMax(1, n[d] - 1); 667 Np *= n[d]; 668 } 669 ierr = DMSwarmSetLocalSizes(sdm, Np, 0);CHKERRQ(ierr); 670 ierr = DMSetFromOptions(sdm);CHKERRQ(ierr); 671 ierr = DMSwarmGetField(sdm, DMSwarmPICField_coor, NULL, NULL, (void **) &coords);CHKERRQ(ierr); 672 switch (dim) { 673 case 2: 674 x[0] = user->partLower[0]; 675 for (i = 0; i < n[0]; ++i, x[0] += dx[0]) { 676 x[1] = user->partLower[1]; 677 for (j = 0; j < n[1]; ++j, x[1] += dx[1]) { 678 const PetscInt p = j*n[0] + i; 679 for (d = 0; d < dim; ++d) coords[p*dim + d] = x[d]; 680 } 681 } 682 break; 683 case 3: 684 x[0] = user->partLower[0]; 685 for (i = 0; i < n[0]; ++i, x[0] += dx[0]) { 686 x[1] = user->partLower[1]; 687 for (j = 0; j < n[1]; ++j, x[1] += dx[1]) { 688 x[2] = user->partLower[2]; 689 for (k = 0; k < n[2]; ++k, x[2] += dx[2]) { 690 const PetscInt p = (k*n[1] + j)*n[0] + i; 691 for (d = 0; d < dim; ++d) coords[p*dim + d] = x[d]; 692 } 693 } 694 } 695 break; 696 default: SETERRQ1(comm, PETSC_ERR_SUP, "Do not support particle layout in dimension %D", dim); 697 } 698 ierr = DMSwarmRestoreField(sdm, DMSwarmPICField_coor, NULL, NULL, (void **) &coords);CHKERRQ(ierr); 699 ierr = DMSwarmGetField(sdm, DMSwarmPICField_cellid, NULL, NULL, (void **) &cellid);CHKERRQ(ierr); 700 for (p = 0; p < Np; ++p) cellid[p] = 0; 701 ierr = DMSwarmRestoreField(sdm, DMSwarmPICField_cellid, NULL, NULL, (void **) &cellid);CHKERRQ(ierr); 702 ierr = DMSwarmMigrate(sdm, PETSC_TRUE);CHKERRQ(ierr); 703 break; 704 default: SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Invalid particle layout type %s", partLayoutTypes[PetscMin(user->partLayout, NUM_PART_LAYOUT_TYPES)]); 705 } 706 ierr = PetscObjectSetName((PetscObject) sdm, "Particles");CHKERRQ(ierr); 707 ierr = DMViewFromOptions(sdm, NULL, "-dm_view");CHKERRQ(ierr); 708 PetscFunctionReturn(0); 709 } 710 711 static PetscErrorCode CreatePressureNullSpace(DM dm, PetscInt ofield, PetscInt nfield, MatNullSpace *nullSpace) 712 { 713 Vec vec; 714 PetscErrorCode (*funcs[3])(PetscInt, PetscReal, const PetscReal[], PetscInt, PetscScalar *, void *) = {zero, zero, zero}; 715 PetscErrorCode ierr; 716 717 PetscFunctionBeginUser; 718 if (ofield != 1) SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Nullspace must be for pressure field at index 1, not %D", ofield); 719 funcs[nfield] = constant; 720 ierr = DMCreateGlobalVector(dm, &vec);CHKERRQ(ierr); 721 ierr = DMProjectFunction(dm, 0.0, funcs, NULL, INSERT_ALL_VALUES, vec);CHKERRQ(ierr); 722 ierr = VecNormalize(vec, NULL);CHKERRQ(ierr); 723 ierr = PetscObjectSetName((PetscObject) vec, "Pressure Null Space");CHKERRQ(ierr); 724 ierr = VecViewFromOptions(vec, NULL, "-pressure_nullspace_view");CHKERRQ(ierr); 725 ierr = MatNullSpaceCreate(PetscObjectComm((PetscObject) dm), PETSC_FALSE, 1, &vec, nullSpace);CHKERRQ(ierr); 726 ierr = VecDestroy(&vec);CHKERRQ(ierr); 727 PetscFunctionReturn(0); 728 } 729 730 static PetscErrorCode RemoveDiscretePressureNullspace_Private(TS ts, Vec u) 731 { 732 DM dm; 733 MatNullSpace nullsp; 734 PetscErrorCode ierr; 735 736 PetscFunctionBegin; 737 ierr = TSGetDM(ts, &dm);CHKERRQ(ierr); 738 ierr = CreatePressureNullSpace(dm, 1, 1, &nullsp);CHKERRQ(ierr); 739 ierr = MatNullSpaceRemove(nullsp, u);CHKERRQ(ierr); 740 ierr = MatNullSpaceDestroy(&nullsp);CHKERRQ(ierr); 741 PetscFunctionReturn(0); 742 } 743 744 /* Make the discrete pressure discretely divergence free */ 745 static PetscErrorCode RemoveDiscretePressureNullspace(TS ts) 746 { 747 Vec u; 748 PetscErrorCode ierr; 749 750 PetscFunctionBegin; 751 ierr = TSGetSolution(ts, &u);CHKERRQ(ierr); 752 ierr = RemoveDiscretePressureNullspace_Private(ts, u);CHKERRQ(ierr); 753 PetscFunctionReturn(0); 754 } 755 756 static PetscErrorCode SetInitialConditions(TS ts, Vec u) 757 { 758 DM dm; 759 PetscReal t; 760 PetscErrorCode ierr; 761 762 PetscFunctionBegin; 763 ierr = TSGetDM(ts, &dm);CHKERRQ(ierr); 764 ierr = TSGetTime(ts, &t);CHKERRQ(ierr); 765 ierr = DMComputeExactSolution(dm, t, u, NULL);CHKERRQ(ierr); 766 ierr = RemoveDiscretePressureNullspace_Private(ts, u);CHKERRQ(ierr); 767 PetscFunctionReturn(0); 768 } 769 770 static PetscErrorCode MonitorError(TS ts, PetscInt step, PetscReal crtime, Vec u, void *ctx) 771 { 772 PetscErrorCode (*exactFuncs[3])(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx); 773 void *ctxs[3]; 774 DM dm; 775 PetscDS ds; 776 Vec v; 777 PetscReal ferrors[3]; 778 PetscInt f; 779 PetscErrorCode ierr; 780 781 PetscFunctionBeginUser; 782 ierr = TSGetDM(ts, &dm);CHKERRQ(ierr); 783 ierr = DMGetDS(dm, &ds);CHKERRQ(ierr); 784 785 for (f = 0; f < 3; ++f) {ierr = PetscDSGetExactSolution(ds, f, &exactFuncs[f], &ctxs[f]);CHKERRQ(ierr);} 786 ierr = DMComputeL2FieldDiff(dm, crtime, exactFuncs, ctxs, u, ferrors);CHKERRQ(ierr); 787 ierr = PetscPrintf(PETSC_COMM_WORLD, "Timestep: %04d time = %-8.4g \t L_2 Error: [%2.3g, %2.3g, %2.3g]\n", (int) step, (double) crtime, (double) ferrors[0], (double) ferrors[1], (double) ferrors[2]);CHKERRQ(ierr); 788 789 ierr = DMGetGlobalVector(dm, &u);CHKERRQ(ierr); 790 //ierr = TSGetSolution(ts, &u);CHKERRQ(ierr); 791 ierr = PetscObjectSetName((PetscObject) u, "Numerical Solution");CHKERRQ(ierr); 792 ierr = VecViewFromOptions(u, NULL, "-sol_vec_view");CHKERRQ(ierr); 793 ierr = DMRestoreGlobalVector(dm, &u);CHKERRQ(ierr); 794 795 ierr = DMGetGlobalVector(dm, &v);CHKERRQ(ierr); 796 // ierr = VecSet(v, 0.0);CHKERRQ(ierr); 797 ierr = DMProjectFunction(dm, 0.0, exactFuncs, ctxs, INSERT_ALL_VALUES, v);CHKERRQ(ierr); 798 ierr = PetscObjectSetName((PetscObject) v, "Exact Solution");CHKERRQ(ierr); 799 ierr = VecViewFromOptions(v, NULL, "-exact_vec_view");CHKERRQ(ierr); 800 ierr = DMRestoreGlobalVector(dm, &v);CHKERRQ(ierr); 801 802 PetscFunctionReturn(0); 803 } 804 805 static PetscErrorCode ComputeParticleError(TS ts, Vec u, Vec e) 806 { 807 AdvCtx *adv; 808 DM sdm; 809 Parameter *param; 810 const PetscScalar *xp0, *xp; 811 PetscScalar *ep; 812 PetscReal time; 813 PetscInt dim, Np, p; 814 MPI_Comm comm; 815 PetscErrorCode ierr; 816 817 PetscFunctionBeginUser; 818 ierr = TSGetTime(ts, &time);CHKERRQ(ierr); 819 ierr = TSGetApplicationContext(ts, (void **) &adv);CHKERRQ(ierr); 820 ierr = PetscBagGetData(adv->ctx->bag, (void **) ¶m);CHKERRQ(ierr); 821 ierr = PetscObjectGetComm((PetscObject) ts, &comm);CHKERRQ(ierr); 822 ierr = TSGetDM(ts, &sdm);CHKERRQ(ierr); 823 ierr = DMGetDimension(sdm, &dim);CHKERRQ(ierr); 824 ierr = DMSwarmGetLocalSize(sdm, &Np);CHKERRQ(ierr); 825 ierr = VecGetArrayRead(adv->x0, &xp0);CHKERRQ(ierr); 826 ierr = VecGetArrayRead(u, &xp);CHKERRQ(ierr); 827 ierr = VecGetArrayWrite(e, &ep);CHKERRQ(ierr); 828 for (p = 0; p < Np; ++p) { 829 PetscScalar x[3]; 830 PetscReal x0[3]; 831 PetscInt d; 832 833 for (d = 0; d < dim; ++d) x0[d] = PetscRealPart(xp0[p*dim+d]); 834 ierr = adv->exact(dim, time, x0, 1, x, param);CHKERRQ(ierr); 835 for (d = 0; d < dim; ++d) ep[p*dim+d] += x[d] - xp[p*dim+d]; 836 } 837 ierr = VecRestoreArrayRead(adv->x0, &xp0);CHKERRQ(ierr); 838 ierr = VecRestoreArrayRead(u, &xp);CHKERRQ(ierr); 839 ierr = VecRestoreArrayWrite(e, &ep);CHKERRQ(ierr); 840 PetscFunctionReturn(0); 841 } 842 843 static PetscErrorCode MonitorParticleError(TS ts, PetscInt step, PetscReal time, Vec u, void *ctx) 844 { 845 AdvCtx *adv = (AdvCtx *) ctx; 846 DM sdm; 847 Parameter *param; 848 const PetscScalar *xp0, *xp; 849 PetscReal error = 0.0; 850 PetscInt dim, Np, p; 851 MPI_Comm comm; 852 PetscErrorCode ierr; 853 854 PetscFunctionBeginUser; 855 ierr = PetscBagGetData(adv->ctx->bag, (void **) ¶m);CHKERRQ(ierr); 856 ierr = PetscObjectGetComm((PetscObject) ts, &comm);CHKERRQ(ierr); 857 ierr = TSGetDM(ts, &sdm);CHKERRQ(ierr); 858 ierr = DMGetDimension(sdm, &dim);CHKERRQ(ierr); 859 ierr = DMSwarmGetLocalSize(sdm, &Np);CHKERRQ(ierr); 860 ierr = VecGetArrayRead(adv->x0, &xp0);CHKERRQ(ierr); 861 ierr = VecGetArrayRead(u, &xp);CHKERRQ(ierr); 862 for (p = 0; p < Np; ++p) { 863 PetscScalar x[3]; 864 PetscReal x0[3]; 865 PetscReal perror = 0.0; 866 PetscInt d; 867 868 for (d = 0; d < dim; ++d) x0[d] = PetscRealPart(xp0[p*dim+d]); 869 ierr = adv->exact(dim, time, x0, 1, x, param);CHKERRQ(ierr); 870 for (d = 0; d < dim; ++d) perror += PetscSqr(PetscRealPart(x[d] - xp[p*dim+d])); 871 error += perror; 872 } 873 ierr = VecRestoreArrayRead(adv->x0, &xp0);CHKERRQ(ierr); 874 ierr = VecRestoreArrayRead(u, &xp);CHKERRQ(ierr); 875 ierr = PetscPrintf(comm, "Timestep: %04d time = %-8.4g \t L_2 Particle Error: [%2.3g]\n", (int) step, (double) time, (double) error);CHKERRQ(ierr); 876 PetscFunctionReturn(0); 877 } 878 879 static PetscErrorCode AdvectParticles(TS ts) 880 { 881 TS sts; 882 DM sdm; 883 Vec p; 884 AdvCtx *adv; 885 PetscScalar *coord, *a; 886 const PetscScalar *ca; 887 PetscReal time; 888 PetscInt n; 889 PetscErrorCode ierr; 890 891 PetscFunctionBeginUser; 892 ierr = PetscObjectQuery((PetscObject) ts, "_SwarmTS", (PetscObject *) &sts);CHKERRQ(ierr); 893 ierr = PetscObjectQuery((PetscObject) ts, "_SwarmSol", (PetscObject *) &p);CHKERRQ(ierr); 894 ierr = TSGetDM(sts, &sdm);CHKERRQ(ierr); 895 ierr = TSGetRHSFunction(sts, NULL, NULL, (void **) &adv);CHKERRQ(ierr); 896 ierr = DMSwarmGetField(sdm, DMSwarmPICField_coor, NULL, NULL, (void **) &coord);CHKERRQ(ierr); 897 ierr = VecGetLocalSize(p, &n);CHKERRQ(ierr); 898 ierr = VecGetArray(p, &a);CHKERRQ(ierr); 899 ierr = PetscArraycpy(a, coord, n);CHKERRQ(ierr); 900 ierr = VecRestoreArray(p, &a);CHKERRQ(ierr); 901 ierr = DMSwarmRestoreField(sdm, DMSwarmPICField_coor, NULL, NULL, (void **) &coord);CHKERRQ(ierr); 902 ierr = TSGetTime(ts, &time);CHKERRQ(ierr); 903 ierr = TSSetMaxTime(sts, time);CHKERRQ(ierr); 904 adv->tf = time; 905 ierr = TSSolve(sts, p);CHKERRQ(ierr); 906 ierr = DMSwarmGetField(sdm, DMSwarmPICField_coor, NULL, NULL, (void **) &coord);CHKERRQ(ierr); 907 ierr = VecGetLocalSize(p, &n);CHKERRQ(ierr); 908 ierr = VecGetArrayRead(p, &ca);CHKERRQ(ierr); 909 ierr = PetscArraycpy(coord, ca, n);CHKERRQ(ierr); 910 ierr = VecRestoreArrayRead(p, &ca);CHKERRQ(ierr); 911 ierr = DMSwarmRestoreField(sdm, DMSwarmPICField_coor, NULL, NULL, (void **) &coord);CHKERRQ(ierr); 912 913 ierr = VecCopy(adv->uf, adv->ui);CHKERRQ(ierr); 914 adv->ti = adv->tf; 915 916 ierr = DMSwarmMigrate(sdm, PETSC_TRUE);CHKERRQ(ierr); 917 ierr = DMViewFromOptions(sdm, NULL, "-dm_view");CHKERRQ(ierr); 918 PetscFunctionReturn(0); 919 } 920 921 int main(int argc, char **argv) 922 { 923 DM dm, sdm; 924 TS ts, sts; 925 Vec u, p, xtmp; 926 AppCtx user; 927 AdvCtx adv; 928 PetscReal t; 929 PetscInt dim; 930 PetscErrorCode ierr; 931 932 ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; 933 ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); 934 ierr = PetscBagCreate(PETSC_COMM_WORLD, sizeof(Parameter), &user.bag);CHKERRQ(ierr); 935 ierr = SetupParameters(&user);CHKERRQ(ierr); 936 ierr = TSCreate(PETSC_COMM_WORLD, &ts);CHKERRQ(ierr); 937 ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr); 938 ierr = TSSetDM(ts, dm);CHKERRQ(ierr); 939 ierr = DMSetApplicationContext(dm, &user);CHKERRQ(ierr); 940 /* Discretize chemical species */ 941 ierr = DMCreate(PETSC_COMM_WORLD, &sdm);CHKERRQ(ierr); 942 ierr = PetscObjectSetOptionsPrefix((PetscObject) sdm, "part_");CHKERRQ(ierr); 943 ierr = DMSetType(sdm, DMSWARM);CHKERRQ(ierr); 944 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 945 ierr = DMSetDimension(sdm, dim);CHKERRQ(ierr); 946 ierr = DMSwarmSetCellDM(sdm, dm);CHKERRQ(ierr); 947 /* Setup problem */ 948 ierr = SetupDiscretization(dm, sdm, &user);CHKERRQ(ierr); 949 ierr = DMPlexCreateClosureIndex(dm, NULL);CHKERRQ(ierr); 950 951 ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr); 952 ierr = DMSetNullSpaceConstructor(dm, 1, CreatePressureNullSpace);CHKERRQ(ierr); 953 954 ierr = DMTSSetBoundaryLocal(dm, DMPlexTSComputeBoundary, &user);CHKERRQ(ierr); 955 ierr = DMTSSetIFunctionLocal(dm, DMPlexTSComputeIFunctionFEM, &user);CHKERRQ(ierr); 956 ierr = DMTSSetIJacobianLocal(dm, DMPlexTSComputeIJacobianFEM, &user);CHKERRQ(ierr); 957 ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_MATCHSTEP);CHKERRQ(ierr); 958 ierr = TSSetPreStep(ts, RemoveDiscretePressureNullspace);CHKERRQ(ierr); 959 ierr = TSMonitorSet(ts, MonitorError, &user, NULL);CHKERRQ(ierr);CHKERRQ(ierr); 960 ierr = TSSetFromOptions(ts);CHKERRQ(ierr); 961 962 ierr = TSSetComputeInitialCondition(ts, SetInitialConditions);CHKERRQ(ierr); /* Must come after SetFromOptions() */ 963 ierr = SetInitialConditions(ts, u);CHKERRQ(ierr); 964 ierr = TSGetTime(ts, &t);CHKERRQ(ierr); 965 ierr = DMSetOutputSequenceNumber(dm, 0, t);CHKERRQ(ierr); 966 ierr = DMTSCheckFromOptions(ts, u);CHKERRQ(ierr); 967 968 /* Setup particle position integrator */ 969 ierr = TSCreate(PETSC_COMM_WORLD, &sts);CHKERRQ(ierr); 970 ierr = PetscObjectSetOptionsPrefix((PetscObject) sts, "part_");CHKERRQ(ierr); 971 ierr = TSSetDM(sts, sdm);CHKERRQ(ierr); 972 ierr = TSSetProblemType(sts, TS_NONLINEAR);CHKERRQ(ierr); 973 ierr = TSSetExactFinalTime(sts, TS_EXACTFINALTIME_MATCHSTEP);CHKERRQ(ierr); 974 ierr = TSMonitorSet(sts, MonitorParticleError, &adv, NULL);CHKERRQ(ierr);CHKERRQ(ierr); 975 ierr = TSSetFromOptions(sts);CHKERRQ(ierr); 976 ierr = TSSetApplicationContext(sts, &adv);CHKERRQ(ierr); 977 ierr = TSSetComputeExactError(sts, ComputeParticleError);CHKERRQ(ierr); 978 ierr = TSSetComputeInitialCondition(sts, SetInitialParticleConditions);CHKERRQ(ierr); 979 adv.ti = t; 980 adv.uf = u; 981 ierr = VecDuplicate(adv.uf, &adv.ui); 982 ierr = VecCopy(u, adv.ui);CHKERRQ(ierr); 983 ierr = TSSetRHSFunction(sts, NULL, FreeStreaming, &adv);CHKERRQ(ierr); 984 ierr = TSSetPostStep(ts, AdvectParticles);CHKERRQ(ierr); 985 ierr = PetscObjectCompose((PetscObject) ts, "_SwarmTS", (PetscObject) sts);CHKERRQ(ierr); 986 ierr = DMSwarmVectorDefineField(sdm, DMSwarmPICField_coor);CHKERRQ(ierr); 987 ierr = DMCreateGlobalVector(sdm, &p);CHKERRQ(ierr); 988 ierr = PetscObjectCompose((PetscObject) ts, "_SwarmSol", (PetscObject) p);CHKERRQ(ierr); 989 ierr = DMCreateGlobalVector(sdm, &adv.x0);CHKERRQ(ierr); 990 ierr = DMSwarmCreateGlobalVectorFromField(sdm, DMSwarmPICField_coor, &xtmp);CHKERRQ(ierr); 991 ierr = VecCopy(xtmp, adv.x0);CHKERRQ(ierr); 992 ierr = DMSwarmDestroyGlobalVectorFromField(sdm, DMSwarmPICField_coor, &xtmp);CHKERRQ(ierr); 993 switch(user.solType){ 994 case SOL_TRIG_TRIG: adv.exact = trig_trig_x;break; 995 default: SETERRQ2(PetscObjectComm((PetscObject) sdm), PETSC_ERR_ARG_WRONG, "Unsupported solution type: %s (%D)", solTypes[PetscMin(user.solType, NUM_SOL_TYPES)], user.solType); 996 } 997 adv.ctx = &user; 998 999 ierr = TSSolve(ts, u);CHKERRQ(ierr); 1000 ierr = DMTSCheckFromOptions(ts, u);CHKERRQ(ierr); 1001 ierr = PetscObjectSetName((PetscObject) u, "Numerical Solution");CHKERRQ(ierr); 1002 1003 ierr = VecDestroy(&u);CHKERRQ(ierr); 1004 ierr = VecDestroy(&p);CHKERRQ(ierr); 1005 ierr = VecDestroy(&adv.x0);CHKERRQ(ierr); 1006 ierr = VecDestroy(&adv.ui);CHKERRQ(ierr); 1007 ierr = DMDestroy(&dm);CHKERRQ(ierr); 1008 ierr = DMDestroy(&sdm);CHKERRQ(ierr); 1009 ierr = TSDestroy(&ts);CHKERRQ(ierr); 1010 ierr = TSDestroy(&sts);CHKERRQ(ierr); 1011 ierr = PetscBagDestroy(&user.bag);CHKERRQ(ierr); 1012 ierr = PetscFinalize(); 1013 return ierr; 1014 } 1015 1016 /*TEST 1017 1018 # Swarm does not work with complex 1019 test: 1020 suffix: 2d_tri_p2_p1_p1_tconvp 1021 requires: triangle !single !complex 1022 args: -dm_plex_separate_marker -sol_type trig_trig -dm_refine 2 \ 1023 -vel_petscspace_degree 2 -pres_petscspace_degree 1 -temp_petscspace_degree 1 \ 1024 -dmts_check .001 -ts_max_steps 4 -ts_dt 0.1 -ts_monitor_cancel \ 1025 -ksp_type fgmres -ksp_gmres_restart 10 -ksp_rtol 1.0e-9 -ksp_error_if_not_converged \ 1026 -pc_type fieldsplit -pc_fieldsplit_0_fields 0,2 -pc_fieldsplit_1_fields 1 -pc_fieldsplit_type schur -pc_fieldsplit_schur_factorization_type full \ 1027 -fieldsplit_0_pc_type lu \ 1028 -fieldsplit_pressure_ksp_rtol 1e-10 -fieldsplit_pressure_pc_type jacobi \ 1029 -omega 0.5 -part_layout_type box -part_lower 0.25,0.25 -part_upper 0.75,0.75 -Npb 5 \ 1030 -part_ts_max_steps 2 -part_ts_dt 0.05 -part_ts_convergence_estimate -convest_num_refine 1 -part_ts_monitor_cancel 1031 1032 TEST*/ 1033