1 2 static char help[] = "Chemo-taxis Problems from Mathematical Biology.\n"; 3 4 /* 5 Page 18, Chemo-taxis Problems from Mathematical Biology 6 7 rho_t = 8 c_t = 9 10 Further discusson on Page 134 and in 2d on Page 409 11 */ 12 13 /* 14 15 Include "petscdmda.h" so that we can use distributed arrays (DMDAs). 16 Include "petscts.h" so that we can use SNES solvers. Note that this 17 file automatically includes: 18 petscsys.h - base PETSc routines petscvec.h - vectors 19 petscmat.h - matrices 20 petscis.h - index sets petscksp.h - Krylov subspace methods 21 petscviewer.h - viewers petscpc.h - preconditioners 22 petscksp.h - linear solvers 23 */ 24 25 #include <petscdm.h> 26 #include <petscdmda.h> 27 #include <petscts.h> 28 29 typedef struct { 30 PetscScalar rho, c; 31 } Field; 32 33 typedef struct { 34 PetscScalar epsilon, delta, alpha, beta, gamma, kappa, lambda, mu, cstar; 35 PetscBool upwind; 36 } AppCtx; 37 38 /* 39 User-defined routines 40 */ 41 extern PetscErrorCode IFunction(TS, PetscReal, Vec, Vec, Vec, void *), InitialConditions(DM, Vec); 42 43 int main(int argc, char **argv) { 44 TS ts; /* nonlinear solver */ 45 Vec U; /* solution, residual vectors */ 46 DM da; 47 AppCtx appctx; 48 49 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 50 Initialize program 51 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 52 PetscFunctionBeginUser; 53 PetscCall(PetscInitialize(&argc, &argv, (char *)0, help)); 54 55 appctx.epsilon = 1.0e-3; 56 appctx.delta = 1.0; 57 appctx.alpha = 10.0; 58 appctx.beta = 4.0; 59 appctx.gamma = 1.0; 60 appctx.kappa = .75; 61 appctx.lambda = 1.0; 62 appctx.mu = 100.; 63 appctx.cstar = .2; 64 appctx.upwind = PETSC_TRUE; 65 66 PetscCall(PetscOptionsGetScalar(NULL, NULL, "-delta", &appctx.delta, NULL)); 67 PetscCall(PetscOptionsGetBool(NULL, NULL, "-upwind", &appctx.upwind, NULL)); 68 69 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 70 Create distributed array (DMDA) to manage parallel grid and vectors 71 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 72 PetscCall(DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, 8, 2, 1, NULL, &da)); 73 PetscCall(DMSetFromOptions(da)); 74 PetscCall(DMSetUp(da)); 75 PetscCall(DMDASetFieldName(da, 0, "rho")); 76 PetscCall(DMDASetFieldName(da, 1, "c")); 77 78 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 79 Extract global vectors from DMDA; then duplicate for remaining 80 vectors that are the same types 81 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 82 PetscCall(DMCreateGlobalVector(da, &U)); 83 84 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 85 Create timestepping solver context 86 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 87 PetscCall(TSCreate(PETSC_COMM_WORLD, &ts)); 88 PetscCall(TSSetType(ts, TSROSW)); 89 PetscCall(TSSetDM(ts, da)); 90 PetscCall(TSSetProblemType(ts, TS_NONLINEAR)); 91 PetscCall(TSSetIFunction(ts, NULL, IFunction, &appctx)); 92 93 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 94 Set initial conditions 95 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 96 PetscCall(InitialConditions(da, U)); 97 PetscCall(TSSetSolution(ts, U)); 98 99 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 100 Set solver options 101 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 102 PetscCall(TSSetTimeStep(ts, .0001)); 103 PetscCall(TSSetMaxTime(ts, 1.0)); 104 PetscCall(TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER)); 105 PetscCall(TSSetFromOptions(ts)); 106 107 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 108 Solve nonlinear system 109 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 110 PetscCall(TSSolve(ts, U)); 111 112 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 113 Free work space. All PETSc objects should be destroyed when they 114 are no longer needed. 115 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 116 PetscCall(VecDestroy(&U)); 117 PetscCall(TSDestroy(&ts)); 118 PetscCall(DMDestroy(&da)); 119 120 PetscCall(PetscFinalize()); 121 return 0; 122 } 123 /* ------------------------------------------------------------------- */ 124 /* 125 IFunction - Evaluates nonlinear function, F(U). 126 127 Input Parameters: 128 . ts - the TS context 129 . U - input vector 130 . ptr - optional user-defined context, as set by SNESSetFunction() 131 132 Output Parameter: 133 . F - function vector 134 */ 135 PetscErrorCode IFunction(TS ts, PetscReal ftime, Vec U, Vec Udot, Vec F, void *ptr) { 136 AppCtx *appctx = (AppCtx *)ptr; 137 DM da; 138 PetscInt i, Mx, xs, xm; 139 PetscReal hx, sx; 140 PetscScalar rho, c, rhoxx, cxx, cx, rhox, kcxrhox; 141 Field *u, *f, *udot; 142 Vec localU; 143 144 PetscFunctionBegin; 145 PetscCall(TSGetDM(ts, &da)); 146 PetscCall(DMGetLocalVector(da, &localU)); 147 PetscCall(DMDAGetInfo(da, PETSC_IGNORE, &Mx, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE)); 148 149 hx = 1.0 / (PetscReal)(Mx - 1); 150 sx = 1.0 / (hx * hx); 151 152 /* 153 Scatter ghost points to local vector,using the 2-step process 154 DMGlobalToLocalBegin(),DMGlobalToLocalEnd(). 155 By placing code between these two statements, computations can be 156 done while messages are in transition. 157 */ 158 PetscCall(DMGlobalToLocalBegin(da, U, INSERT_VALUES, localU)); 159 PetscCall(DMGlobalToLocalEnd(da, U, INSERT_VALUES, localU)); 160 161 /* 162 Get pointers to vector data 163 */ 164 PetscCall(DMDAVecGetArrayRead(da, localU, &u)); 165 PetscCall(DMDAVecGetArrayRead(da, Udot, &udot)); 166 PetscCall(DMDAVecGetArrayWrite(da, F, &f)); 167 168 /* 169 Get local grid boundaries 170 */ 171 PetscCall(DMDAGetCorners(da, &xs, NULL, NULL, &xm, NULL, NULL)); 172 173 if (!xs) { 174 f[0].rho = udot[0].rho; /* u[0].rho - 0.0; */ 175 f[0].c = udot[0].c; /* u[0].c - 1.0; */ 176 xs++; 177 xm--; 178 } 179 if (xs + xm == Mx) { 180 f[Mx - 1].rho = udot[Mx - 1].rho; /* u[Mx-1].rho - 1.0; */ 181 f[Mx - 1].c = udot[Mx - 1].c; /* u[Mx-1].c - 0.0; */ 182 xm--; 183 } 184 185 /* 186 Compute function over the locally owned part of the grid 187 */ 188 for (i = xs; i < xs + xm; i++) { 189 rho = u[i].rho; 190 rhoxx = (-2.0 * rho + u[i - 1].rho + u[i + 1].rho) * sx; 191 c = u[i].c; 192 cxx = (-2.0 * c + u[i - 1].c + u[i + 1].c) * sx; 193 194 if (!appctx->upwind) { 195 rhox = .5 * (u[i + 1].rho - u[i - 1].rho) / hx; 196 cx = .5 * (u[i + 1].c - u[i - 1].c) / hx; 197 kcxrhox = appctx->kappa * (cxx * rho + cx * rhox); 198 } else { 199 kcxrhox = appctx->kappa * ((u[i + 1].c - u[i].c) * u[i + 1].rho - (u[i].c - u[i - 1].c) * u[i].rho) * sx; 200 } 201 202 f[i].rho = udot[i].rho - appctx->epsilon * rhoxx + kcxrhox - appctx->mu * PetscAbsScalar(rho) * (1.0 - rho) * PetscMax(0, PetscRealPart(c - appctx->cstar)) + appctx->beta * rho; 203 f[i].c = udot[i].c - appctx->delta * cxx + appctx->lambda * c + appctx->alpha * rho * c / (appctx->gamma + c); 204 } 205 206 /* 207 Restore vectors 208 */ 209 PetscCall(DMDAVecRestoreArrayRead(da, localU, &u)); 210 PetscCall(DMDAVecRestoreArrayRead(da, Udot, &udot)); 211 PetscCall(DMDAVecRestoreArrayWrite(da, F, &f)); 212 PetscCall(DMRestoreLocalVector(da, &localU)); 213 PetscFunctionReturn(0); 214 } 215 216 /* ------------------------------------------------------------------- */ 217 PetscErrorCode InitialConditions(DM da, Vec U) { 218 PetscInt i, xs, xm, Mx; 219 Field *u; 220 PetscReal hx, x; 221 222 PetscFunctionBegin; 223 PetscCall(DMDAGetInfo(da, PETSC_IGNORE, &Mx, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE)); 224 225 hx = 1.0 / (PetscReal)(Mx - 1); 226 227 /* 228 Get pointers to vector data 229 */ 230 PetscCall(DMDAVecGetArrayWrite(da, U, &u)); 231 232 /* 233 Get local grid boundaries 234 */ 235 PetscCall(DMDAGetCorners(da, &xs, NULL, NULL, &xm, NULL, NULL)); 236 237 /* 238 Compute function over the locally owned part of the grid 239 */ 240 for (i = xs; i < xs + xm; i++) { 241 x = i * hx; 242 if (i < Mx - 1) u[i].rho = 0.0; 243 else u[i].rho = 1.0; 244 u[i].c = PetscCosReal(.5 * PETSC_PI * x); 245 } 246 247 /* 248 Restore vectors 249 */ 250 PetscCall(DMDAVecRestoreArrayWrite(da, U, &u)); 251 PetscFunctionReturn(0); 252 } 253 254 /*TEST 255 256 test: 257 args: -pc_type lu -da_refine 2 -ts_view -ts_monitor -ts_max_time 1 258 requires: double 259 260 test: 261 suffix: 2 262 args: -pc_type lu -da_refine 2 -ts_view -ts_monitor_draw_solution -ts_monitor -ts_max_time 1 263 requires: x double 264 output_file: output/ex4_1.out 265 266 TEST*/ 267