PETSc Example -- Nonlinear Reaction Problem from Chemistry

static char help[] = "Nonlinear Reaction Problem from Chemistry.\n"; /*F This directory contains examples based on the PDES/ODES given in the book Numerical Solution of Time-Dependent Advection-Diffusion-Reaction Equations by W. Hundsdorf and J.G. Verwer Page 3, Section 1.1 Nonlinear Reaction Problems from Chemistry \begin{eqnarray} {U_1}_t - k U_1 U_2 & = & 0 \\ {U_2}_t - k U_1 U_2 & = & 0 \\ {U_3}_t - k U_1 U_2 & = & 0 \end{eqnarray} Helpful runtime monitoring options: -ts_view - prints information about the solver being used -ts_monitor - prints the progess of the solver -ts_adapt_monitor - prints the progress of the time-step adaptor -ts_monitor_lg_timestep - plots the size of each timestep (at each time-step) -ts_monitor_lg_solution - plots each component of the solution as a function of time (at each timestep) -ts_monitor_lg_error - plots each component of the error in the solution as a function of time (at each timestep) -draw_pause -2 - hold the plots a the end of the solution process, enter a mouse press in each window to end the process -ts_monitor_lg_timestep -1 - plots the size of each timestep (at the end of the solution process) -ts_monitor_lg_solution -1 - plots each component of the solution as a function of time (at the end of the solution process) -ts_monitor_lg_error -1 - plots each component of the error in the solution as a function of time (at the end of the solution process) -lg_use_markers false - do NOT show the data points on the plots -draw_save - save the timestep and solution plot as a .Gif image file F*/ /* Project: Generate a nicely formated HTML page using 1) the HTML version of the source code and text in this file, use make html to generate the file ex1.c.html 2) the images (Draw_XXX_0_0.Gif Draw_YYY_0_0.Gif Draw_ZZZ_1_0.Gif) and 3) the text output (output.txt) generated by running the following commands. 4) rm -rf *.Gif ./ex1 -ts_monitor_lg_error -1 -ts_monitor_lg_solution -1 -draw_pause -2 -ts_max_steps 100 -ts_monitor_lg_timestep -1 -draw_save -draw_virtual -ts_monitor -ts_adapt_monitor -ts_view > output.txt For example something like PETSc Example -- Nonlinear Reaction Problem from Chemistry

*/ /* Include "petscts.h" so that we can use TS solvers. Note that this file automatically includes: petscsys.h - base PETSc routines petscvec.h - vectors petscmat.h - matrices petscis.h - index sets petscksp.h - Krylov subspace methods petscviewer.h - viewers petscpc.h - preconditioners petscksp.h - linear solvers */ #include typedef struct { PetscScalar k; Vec initialsolution; } AppCtx; PetscErrorCode IFunctionView(AppCtx *ctx,PetscViewer v) { PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscViewerBinaryWrite(v,&ctx->k,1,PETSC_SCALAR);CHKERRQ(ierr); PetscFunctionReturn(0); } PetscErrorCode IFunctionLoad(AppCtx **ctx,PetscViewer v) { PetscErrorCode ierr; PetscFunctionBegin; ierr = PetscNew(ctx);CHKERRQ(ierr); ierr = PetscViewerBinaryRead(v,&(*ctx)->k,1,NULL,PETSC_SCALAR);CHKERRQ(ierr); PetscFunctionReturn(0); } /* Defines the ODE passed to the ODE solver */ PetscErrorCode IFunction(TS ts,PetscReal t,Vec U,Vec Udot,Vec F,AppCtx *ctx) { PetscErrorCode ierr; PetscScalar *f; const PetscScalar *u,*udot; PetscFunctionBegin; /* The next three lines allow us to access the entries of the vectors directly */ ierr = VecGetArrayRead(U,&u);CHKERRQ(ierr); ierr = VecGetArrayRead(Udot,&udot);CHKERRQ(ierr); ierr = VecGetArrayWrite(F,&f);CHKERRQ(ierr); f[0] = udot[0] + ctx->k*u[0]*u[1]; f[1] = udot[1] + ctx->k*u[0]*u[1]; f[2] = udot[2] - ctx->k*u[0]*u[1]; ierr = VecRestoreArrayRead(U,&u);CHKERRQ(ierr); ierr = VecRestoreArrayRead(Udot,&udot);CHKERRQ(ierr); ierr = VecRestoreArrayWrite(F,&f);CHKERRQ(ierr); PetscFunctionReturn(0); } /* Defines the Jacobian of the ODE passed to the ODE solver. See TSSetIJacobian() for the meaning of a and the Jacobian. */ PetscErrorCode IJacobian(TS ts,PetscReal t,Vec U,Vec Udot,PetscReal a,Mat A,Mat B,AppCtx *ctx) { PetscErrorCode ierr; PetscInt rowcol[] = {0,1,2}; PetscScalar J[3][3]; const PetscScalar *u,*udot; PetscFunctionBegin; ierr = VecGetArrayRead(U,&u);CHKERRQ(ierr); ierr = VecGetArrayRead(Udot,&udot);CHKERRQ(ierr); J[0][0] = a + ctx->k*u[1]; J[0][1] = ctx->k*u[0]; J[0][2] = 0.0; J[1][0] = ctx->k*u[1]; J[1][1] = a + ctx->k*u[0]; J[1][2] = 0.0; J[2][0] = -ctx->k*u[1]; J[2][1] = -ctx->k*u[0]; J[2][2] = a; ierr = MatSetValues(B,3,rowcol,3,rowcol,&J[0][0],INSERT_VALUES);CHKERRQ(ierr); ierr = VecRestoreArrayRead(U,&u);CHKERRQ(ierr); ierr = VecRestoreArrayRead(Udot,&udot);CHKERRQ(ierr); ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); if (A != B) { ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); } PetscFunctionReturn(0); } /* Defines the exact (analytic) solution to the ODE */ static PetscErrorCode Solution(TS ts,PetscReal t,Vec U,AppCtx *ctx) { PetscErrorCode ierr; const PetscScalar *uinit; PetscScalar *u,d0,q; PetscFunctionBegin; ierr = VecGetArrayRead(ctx->initialsolution,&uinit);CHKERRQ(ierr); ierr = VecGetArrayWrite(U,&u);CHKERRQ(ierr); d0 = uinit[0] - uinit[1]; if (d0 == 0.0) q = ctx->k*t; else q = (1.0 - PetscExpScalar(-ctx->k*t*d0))/d0; u[0] = uinit[0]/(1.0 + uinit[1]*q); u[1] = u[0] - d0; u[2] = uinit[1] + uinit[2] - u[1]; ierr = VecRestoreArrayWrite(U,&u);CHKERRQ(ierr); ierr = VecRestoreArrayRead(ctx->initialsolution,&uinit);CHKERRQ(ierr); PetscFunctionReturn(0); } int main(int argc,char **argv) { TS ts; /* ODE integrator */ Vec U; /* solution will be stored here */ Mat A; /* Jacobian matrix */ PetscErrorCode ierr; PetscMPIInt size; PetscInt n = 3; AppCtx ctx; PetscScalar *u; const char * const names[] = {"U1","U2","U3",NULL}; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRMPI(ierr); if (size > 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Only for sequential runs"); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create necessary matrix and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); ierr = MatSetSizes(A,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); ierr = MatSetFromOptions(A);CHKERRQ(ierr); ierr = MatSetUp(A);CHKERRQ(ierr); ierr = MatCreateVecs(A,&U,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ctx.k = .9; ierr = PetscOptionsGetScalar(NULL,NULL,"-k",&ctx.k,NULL);CHKERRQ(ierr); ierr = VecDuplicate(U,&ctx.initialsolution);CHKERRQ(ierr); ierr = VecGetArrayWrite(ctx.initialsolution,&u);CHKERRQ(ierr); u[0] = 1; u[1] = .7; u[2] = 0; ierr = VecRestoreArrayWrite(ctx.initialsolution,&u);CHKERRQ(ierr); ierr = PetscOptionsGetVec(NULL,NULL,"-initial",ctx.initialsolution,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetType(ts,TSROSW);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,(TSIFunction) IFunction,&ctx);CHKERRQ(ierr); ierr = TSSetIJacobian(ts,A,A,(TSIJacobian)IJacobian,&ctx);CHKERRQ(ierr); ierr = TSSetSolutionFunction(ts,(TSSolutionFunction)Solution,&ctx);CHKERRQ(ierr); { DM dm; void *ptr; ierr = TSGetDM(ts,&dm);CHKERRQ(ierr); ierr = PetscDLSym(NULL,"IFunctionView",&ptr);CHKERRQ(ierr); ierr = PetscDLSym(NULL,"IFunctionLoad",&ptr);CHKERRQ(ierr); ierr = DMTSSetIFunctionSerialize(dm,(PetscErrorCode (*)(void*,PetscViewer))IFunctionView,(PetscErrorCode (*)(void**,PetscViewer))IFunctionLoad);CHKERRQ(ierr); ierr = DMTSSetIJacobianSerialize(dm,(PetscErrorCode (*)(void*,PetscViewer))IFunctionView,(PetscErrorCode (*)(void**,PetscViewer))IFunctionLoad);CHKERRQ(ierr); } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = Solution(ts,0,U,&ctx);CHKERRQ(ierr); ierr = TSSetSolution(ts,U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set solver options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetTimeStep(ts,.001);CHKERRQ(ierr); ierr = TSSetMaxSteps(ts,1000);CHKERRQ(ierr); ierr = TSSetMaxTime(ts,20.0);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); ierr = TSMonitorLGSetVariableNames(ts,names);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,U);CHKERRQ(ierr); ierr = TSView(ts,PETSC_VIEWER_BINARY_WORLD);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDestroy(&ctx.initialsolution);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = VecDestroy(&U);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; } /*TEST test: args: -ts_view requires: dlsym defined(PETSC_HAVE_DYNAMIC_LIBRARIES) test: suffix: 2 args: -ts_monitor_lg_error -ts_monitor_lg_solution -ts_view requires: x dlsym defined(PETSC_HAVE_DYNAMIC_LIBRARIES) output_file: output/ex1_1.out TEST*/