Actual source code: ex5.c

      1: static char help[] = "Demonstrates Pattern Formation with Reaction-Diffusion Equations.\n";

      3: /*F
      4:      This example is taken from the book, Numerical Solution of Time-Dependent Advection-Diffusion-Reaction Equations by
      5:       W. Hundsdorf and J.G. Verwer,  Page 21, Pattern Formation with Reaction-Diffusion Equations
      6: \begin{eqnarray*}
      7:         u_t = D_1 (u_{xx} + u_{yy})  - u*v^2 + \gamma(1 -u)           \\
      8:         v_t = D_2 (v_{xx} + v_{yy})  + u*v^2 - (\gamma + \kappa)v
      9: \end{eqnarray*}
     10:     Unlike in the book this uses periodic boundary conditions instead of Neumann
     11:     (since they are easier for finite differences).
     12: F*/

     14: /*
     15:       Helpful runtime monitor options:
     16:            -ts_monitor_draw_solution
     17:            -draw_save -draw_save_movie

     19:       Helpful runtime linear solver options:
     20:            -pc_type mg -pc_mg_galerkin pmat -da_refine 1 -snes_monitor -ksp_monitor -ts_view  (note that these Jacobians are so well-conditioned multigrid may not be the best solver)

     22:       Point your browser to localhost:8080 to monitor the simulation
     23:            ./ex5  -ts_view_pre saws  -stack_view saws -draw_save -draw_save_single_file -x_virtual -ts_monitor_draw_solution -saws_root .

     25: */

     27: /*

     29:    Include "petscdmda.h" so that we can use distributed arrays (DMDAs).
     30:    Include "petscts.h" so that we can use SNES numerical (ODE) integrators.  Note that this
     31:    file automatically includes:
     32:      petscsys.h       - base PETSc routines   petscvec.h  - vectors
     33:      petscmat.h - matrices                    petscis.h   - index sets
     34:      petscksp.h - Krylov subspace methods     petscpc.h   - preconditioners
     35:      petscviewer.h - viewers                  petscsnes.h - nonlinear solvers
     36: */
     37: #include "reaction_diffusion.h"
     38: #include <petscdm.h>
     39: #include <petscdmda.h>

     41: /* ------------------------------------------------------------------- */
     42: PetscErrorCode InitialConditions(DM da, Vec U)
     43: {
     44:   PetscInt  i, j, xs, ys, xm, ym, Mx, My;
     45:   Field   **u;
     46:   PetscReal hx, hy, x, y;

     48:   PetscFunctionBegin;
     49:   PetscCall(DMDAGetInfo(da, PETSC_IGNORE, &Mx, &My, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE, PETSC_IGNORE));

     51:   hx = 2.5 / (PetscReal)Mx;
     52:   hy = 2.5 / (PetscReal)My;

     54:   /*
     55:      Get pointers to actual vector data
     56:   */
     57:   PetscCall(DMDAVecGetArray(da, U, &u));

     59:   /*
     60:      Get local grid boundaries
     61:   */
     62:   PetscCall(DMDAGetCorners(da, &xs, &ys, NULL, &xm, &ym, NULL));

     64:   /*
     65:      Compute function over the locally owned part of the grid
     66:   */
     67:   for (j = ys; j < ys + ym; j++) {
     68:     y = j * hy;
     69:     for (i = xs; i < xs + xm; i++) {
     70:       x = i * hx;
     71:       if (PetscApproximateGTE(x, 1.0) && PetscApproximateLTE(x, 1.5) && PetscApproximateGTE(y, 1.0) && PetscApproximateLTE(y, 1.5))
     72:         u[j][i].v = PetscPowReal(PetscSinReal(4.0 * PETSC_PI * x), 2.0) * PetscPowReal(PetscSinReal(4.0 * PETSC_PI * y), 2.0) / 4.0;
     73:       else u[j][i].v = 0.0;

     75:       u[j][i].u = 1.0 - 2.0 * u[j][i].v;
     76:     }
     77:   }

     79:   /*
     80:      Restore access to vector
     81:   */
     82:   PetscCall(DMDAVecRestoreArray(da, U, &u));
     83:   PetscFunctionReturn(PETSC_SUCCESS);
     84: }

     86: int main(int argc, char **argv)
     87: {
     88:   TS     ts; /* ODE integrator */
     89:   Vec    x;  /* solution */
     90:   DM     da;
     91:   AppCtx appctx;

     93:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     94:      Initialize program
     95:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
     96:   PetscFunctionBeginUser;
     97:   PetscCall(PetscInitialize(&argc, &argv, NULL, help));
     98:   appctx.D1    = 8.0e-5;
     99:   appctx.D2    = 4.0e-5;
    100:   appctx.gamma = .024;
    101:   appctx.kappa = .06;
    102:   appctx.aijpc = PETSC_FALSE;

    104:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    105:      Create distributed array (DMDA) to manage parallel grid and vectors
    106:   - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    107:   PetscCall(DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_PERIODIC, DM_BOUNDARY_PERIODIC, DMDA_STENCIL_STAR, 65, 65, PETSC_DECIDE, PETSC_DECIDE, 2, 1, NULL, NULL, &da));
    108:   PetscCall(DMSetFromOptions(da));
    109:   PetscCall(DMSetUp(da));
    110:   PetscCall(DMDASetFieldName(da, 0, "u"));
    111:   PetscCall(DMDASetFieldName(da, 1, "v"));

    113:   /*  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    114:      Create global vector from DMDA; this will be used to store the solution
    115:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    116:   PetscCall(DMCreateGlobalVector(da, &x));

    118:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    119:      Create timestepping solver context
    120:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    121:   PetscCall(TSCreate(PETSC_COMM_WORLD, &ts));
    122:   PetscCall(TSSetType(ts, TSARKIMEX));
    123:   PetscCall(TSARKIMEXSetFullyImplicit(ts, PETSC_TRUE));
    124:   PetscCall(TSSetDM(ts, da));
    125:   PetscCall(TSSetProblemType(ts, TS_NONLINEAR));
    126:   PetscCall(TSSetRHSFunction(ts, NULL, RHSFunction, &appctx));
    127:   PetscCall(TSSetRHSJacobian(ts, NULL, NULL, RHSJacobian, &appctx));

    129:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    130:      Set initial conditions
    131:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    132:   PetscCall(InitialConditions(da, x));
    133:   PetscCall(TSSetSolution(ts, x));

    135:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    136:      Set solver options
    137:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    138:   PetscCall(TSSetMaxTime(ts, 2000.0));
    139:   PetscCall(TSSetTimeStep(ts, .0001));
    140:   PetscCall(TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER));
    141:   PetscCall(TSSetFromOptions(ts));

    143:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    144:      Solve ODE system
    145:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    146:   PetscCall(TSSolve(ts, x));

    148:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    149:      Free work space.
    150:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    151:   PetscCall(VecDestroy(&x));
    152:   PetscCall(TSDestroy(&ts));
    153:   PetscCall(DMDestroy(&da));

    155:   PetscCall(PetscFinalize());
    156:   return 0;
    157: }

    159: /*TEST

    161:    build:
    162:      depends: reaction_diffusion.c

    164:    test:
    165:       args: -ts_view -ts_monitor -ts_max_time 500
    166:       requires: double
    167:       timeoutfactor: 3

    169:    test:
    170:       suffix: 2
    171:       args: -ts_view -ts_monitor -ts_max_time 500 -ts_monitor_draw_solution
    172:       requires: x double
    173:       output_file: output/ex5_1.out
    174:       timeoutfactor: 3

    176: TEST*/