Actual source code: extchemfield.c

  1: static const char help[] = "Integrate chemistry using TChem.\n";

  3: #include <petscts.h>
  4: #include <petscdmda.h>

  6: #if defined(PETSC_HAVE_TCHEM)
  7:   #if defined(MAX)
  8:     #undef MAX
  9:   #endif
 10:   #if defined(MIN)
 11:     #undef MIN
 12:   #endif
 13:   #include <TC_params.h>
 14:   #include <TC_interface.h>
 15: #else
 16:   #error TChem is required for this example.  Reconfigure PETSc using --download-tchem.
 17: #endif
 18: /*

 20:     This is an extension of extchem.c to solve the reaction equations independently in each cell of a one dimensional field

 22:     Obtain the three files into this directory

 24:        curl http://combustion.berkeley.edu/gri_mech/version30/files30/grimech30.dat > chem.inp
 25:        curl http://combustion.berkeley.edu/gri_mech/version30/files30/thermo30.dat > therm.dat
 26:        cp $PETSC_DIR/$PETSC_ARCH/externalpackages/tchem/data/periodictable.dat .

 28:     Run with
 29:      ./extchemfield  -ts_arkimex_fully_implicit -ts_max_snes_failures unlimited -ts_adapt_monitor -ts_adapt_dt_max 1e-4 -ts_arkimex_type 4 -ts_max_time .005

 31:      Options for visualizing the solution:
 32:         Watch certain variables in each cell evolve with time
 33:         -draw_solution 1 -ts_monitor_lg_solution_variables Temp,H2,O2,H2O,CH4,CO,CO2,C2H2,N2 -lg_use_markers false  -draw_pause -2

 35:         Watch certain variables in all cells evolve with time
 36:         -da_refine 4 -ts_monitor_draw_solution -draw_fields_by_name Temp,H2 -draw_vec_mark_points  -draw_pause -2

 38:         Keep the initial temperature distribution as one monitors the current temperature distribution
 39:         -ts_monitor_draw_solution_initial -draw_bounds .9,1.7 -draw_fields_by_name Temp

 41:         Save the images in a .gif (movie) file
 42:         -draw_save -draw_save_single_file

 44:         Compute the sensitivities of the solution of the first temperature on the initial conditions
 45:         -ts_adjoint_solve  -ts_dt 1.e-5 -ts_type cn -ts_adjoint_view_solution draw

 47:         Turn off diffusion
 48:         -diffusion no

 50:         Turn off reactions
 51:         -reactions no

 53:     The solution for component i = 0 is the temperature.

 55:     The solution, i > 0, is the mass fraction, massf[i], of species i, i.e. mass of species i/ total mass of all species

 57:     The mole fraction molef[i], i > 0, is the number of moles of a species/ total number of moles of all species
 58:         Define M[i] = mass per mole of species i then
 59:         molef[i] = massf[i]/(M[i]*(sum_j massf[j]/M[j]))

 61:     FormMoleFraction(User,massf,molef) converts the mass fraction solution of each species to the mole fraction of each species.

 63: */
 64: typedef struct _User *User;
 65: struct _User {
 66:   PetscReal pressure;
 67:   int       Nspec;
 68:   int       Nreac;
 69:   PetscReal Tini, dx;
 70:   PetscReal diffus;
 71:   DM        dm;
 72:   PetscBool diffusion, reactions;
 73:   double   *tchemwork;
 74:   double   *Jdense; /* Dense array workspace where Tchem computes the Jacobian */
 75:   PetscInt *rows;
 76: };

 78: static PetscErrorCode MonitorCell(TS, User, PetscInt);
 79: static PetscErrorCode FormRHSFunction(TS, PetscReal, Vec, Vec, void *);
 80: static PetscErrorCode FormRHSJacobian(TS, PetscReal, Vec, Mat, Mat, void *);
 81: static PetscErrorCode FormInitialSolution(TS, Vec, void *);

 83: #define PetscCallTC(ierr) \
 84:   do { \
 85:     PetscCheck(!ierr, PETSC_COMM_SELF, PETSC_ERR_LIB, "Error in TChem library, return code %d", ierr); \
 86:   } while (0)

 88: int main(int argc, char **argv)
 89: {
 90:   TS                ts; /* time integrator */
 91:   TSAdapt           adapt;
 92:   Vec               X; /* solution vector */
 93:   Mat               J; /* Jacobian matrix */
 94:   PetscInt          steps, ncells, xs, xm, i;
 95:   PetscReal         ftime, dt;
 96:   char              chemfile[PETSC_MAX_PATH_LEN] = "chem.inp", thermofile[PETSC_MAX_PATH_LEN] = "therm.dat";
 97:   struct _User      user;
 98:   TSConvergedReason reason;
 99:   PetscBool         showsolutions = PETSC_FALSE;
100:   char            **snames, *names;
101:   Vec               lambda; /* used with TSAdjoint for sensitivities */

103:   PetscFunctionBeginUser;
104:   PetscCall(PetscInitialize(&argc, &argv, NULL, help));
105:   PetscOptionsBegin(PETSC_COMM_WORLD, NULL, "Chemistry solver options", "");
106:   PetscCall(PetscOptionsString("-chem", "CHEMKIN input file", "", chemfile, chemfile, sizeof(chemfile), NULL));
107:   PetscCall(PetscOptionsString("-thermo", "NASA thermo input file", "", thermofile, thermofile, sizeof(thermofile), NULL));
108:   user.pressure = 1.01325e5; /* Pascal */
109:   PetscCall(PetscOptionsReal("-pressure", "Pressure of reaction [Pa]", "", user.pressure, &user.pressure, NULL));
110:   user.Tini = 1550;
111:   PetscCall(PetscOptionsReal("-Tini", "Initial temperature [K]", "", user.Tini, &user.Tini, NULL));
112:   user.diffus = 100;
113:   PetscCall(PetscOptionsReal("-diffus", "Diffusion constant", "", user.diffus, &user.diffus, NULL));
114:   PetscCall(PetscOptionsBool("-draw_solution", "Plot the solution for each cell", "", showsolutions, &showsolutions, NULL));
115:   user.diffusion = PETSC_TRUE;
116:   PetscCall(PetscOptionsBool("-diffusion", "Have diffusion", "", user.diffusion, &user.diffusion, NULL));
117:   user.reactions = PETSC_TRUE;
118:   PetscCall(PetscOptionsBool("-reactions", "Have reactions", "", user.reactions, &user.reactions, NULL));
119:   PetscOptionsEnd();

121:   PetscCallTC(TC_initChem(chemfile, thermofile, 0, 1.0));
122:   user.Nspec = TC_getNspec();
123:   user.Nreac = TC_getNreac();

125:   PetscCall(DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_PERIODIC, 10, user.Nspec + 1, 1, NULL, &user.dm));
126:   PetscCall(DMSetFromOptions(user.dm));
127:   PetscCall(DMSetUp(user.dm));
128:   PetscCall(DMDAGetInfo(user.dm, NULL, &ncells, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL));
129:   user.dx = 1.0 / ncells; /* Set the coordinates of the cell centers; note final ghost cell is at x coordinate 1.0 */
130:   PetscCall(DMDASetUniformCoordinates(user.dm, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0));

132:   /* set the names of each field in the DMDA based on the species name */
133:   PetscCall(PetscMalloc1((user.Nspec + 1) * LENGTHOFSPECNAME, &names));
134:   PetscCall(PetscStrncpy(names, "Temp", (user.Nspec + 1) * LENGTHOFSPECNAME);
135:   TC_getSnames(user.Nspec, names + LENGTHOFSPECNAME);
136:   PetscCall(PetscMalloc1( user.Nspec + 2 , &snames));
137:   for (i = 0; i < user.Nspec + 1; i++) snames[i] = names + i * LENGTHOFSPECNAME;
138:   snames[user.Nspec + 1] = NULL;
139:   PetscCall(DMDASetFieldNames(user.dm, (const char *const *)snames));
140:   PetscCall(PetscFree(snames));
141:   PetscCall(PetscFree(names));

143:   PetscCall(DMCreateMatrix(user.dm, &J));
144:   PetscCall(DMCreateGlobalVector(user.dm, &X));

146:   PetscCall(PetscMalloc3(user.Nspec + 1, &user.tchemwork, PetscSqr(user.Nspec + 1), &user.Jdense, user.Nspec + 1, &user.rows));

148:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
149:      Create timestepping solver context
150:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
151:   PetscCall(TSCreate(PETSC_COMM_WORLD, &ts));
152:   PetscCall(TSSetDM(ts, user.dm));
153:   PetscCall(TSSetType(ts, TSARKIMEX));
154:   PetscCall(TSARKIMEXSetFullyImplicit(ts, PETSC_TRUE));
155:   PetscCall(TSARKIMEXSetType(ts, TSARKIMEX4));
156:   PetscCall(TSSetRHSFunction(ts, NULL, FormRHSFunction, &user));
157:   PetscCall(TSSetRHSJacobian(ts, J, J, FormRHSJacobian, &user));

159:   ftime = 1.0;
160:   PetscCall(TSSetMaxTime(ts, ftime));
161:   PetscCall(TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER));

163:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
164:      Set initial conditions
165:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
166:   PetscCall(FormInitialSolution(ts, X, &user));
167:   PetscCall(TSSetSolution(ts, X));
168:   dt = 1e-10; /* Initial time step */
169:   PetscCall(TSSetTimeStep(ts, dt));
170:   PetscCall(TSGetAdapt(ts, &adapt));
171:   PetscCall(TSAdaptSetStepLimits(adapt, 1e-12, 1e-4)); /* Also available with -ts_adapt_dt_min/-ts_adapt_dt_max */
172:   PetscCall(TSSetMaxSNESFailures(ts, -1));             /* Retry step an unlimited number of times */

174:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
175:      Pass information to graphical monitoring routine
176:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
177:   if (showsolutions) {
178:     PetscCall(DMDAGetCorners(user.dm, &xs, NULL, NULL, &xm, NULL, NULL));
179:     for (i = xs; i < xs + xm; i++) PetscCall(MonitorCell(ts, &user, i));
180:   }

182:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
183:      Set runtime options
184:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
185:   PetscCall(TSSetFromOptions(ts));

187:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
188:      Set final conditions for sensitivities
189:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
190:   PetscCall(DMCreateGlobalVector(user.dm, &lambda));
191:   PetscCall(TSSetCostGradients(ts, 1, &lambda, NULL));
192:   PetscCall(VecSetValue(lambda, 0, 1.0, INSERT_VALUES));
193:   PetscCall(VecAssemblyBegin(lambda));
194:   PetscCall(VecAssemblyEnd(lambda));

196:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
197:      Solve ODE
198:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
199:   PetscCall(TSSolve(ts, X));
200:   PetscCall(TSGetSolveTime(ts, &ftime));
201:   PetscCall(TSGetStepNumber(ts, &steps));
202:   PetscCall(TSGetConvergedReason(ts, &reason));
203:   PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%s at time %g after %" PetscInt_FMT " steps\n", TSConvergedReasons[reason], (double)ftime, steps));

205:   {
206:     Vec                max;
207:     const char *const *names;
208:     PetscInt           i;
209:     const PetscReal   *bmax;

211:     PetscCall(TSMonitorEnvelopeGetBounds(ts, &max, NULL));
212:     if (max) {
213:       PetscCall(TSMonitorLGGetVariableNames(ts, &names));
214:       if (names) {
215:         PetscCall(VecGetArrayRead(max, &bmax));
216:         PetscCall(PetscPrintf(PETSC_COMM_SELF, "Species - maximum mass fraction\n"));
217:         for (i = 1; i < user.Nspec; i++) {
218:           if (bmax[i] > .01) PetscCall(PetscPrintf(PETSC_COMM_SELF, "%s %g\n", names[i], (double)bmax[i]));
219:         }
220:         PetscCall(VecRestoreArrayRead(max, &bmax));
221:       }
222:     }
223:   }

225:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
226:      Free work space.
227:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
228:   TC_reset();
229:   PetscCall(DMDestroy(&user.dm));
230:   PetscCall(MatDestroy(&J));
231:   PetscCall(VecDestroy(&X));
232:   PetscCall(VecDestroy(&lambda));
233:   PetscCall(TSDestroy(&ts));
234:   PetscCall(PetscFree3(user.tchemwork, user.Jdense, user.rows));
235:   PetscCall(PetscFinalize());
236:   return 0;
237: }

239: /*
240:    Applies the second order centered difference diffusion operator on a one dimensional periodic domain
241: */
242: static PetscErrorCode FormDiffusionFunction(TS ts, PetscReal t, Vec X, Vec F, void *ptr)
243: {
244:   User                user = (User)ptr;
245:   PetscScalar       **f;
246:   const PetscScalar **x;
247:   DM                  dm;
248:   PetscInt            i, xs, xm, j, dof;
249:   Vec                 Xlocal;
250:   PetscReal           idx;

252:   PetscFunctionBeginUser;
253:   PetscCall(TSGetDM(ts, &dm));
254:   PetscCall(DMDAGetInfo(dm, NULL, NULL, NULL, NULL, NULL, NULL, NULL, &dof, NULL, NULL, NULL, NULL, NULL));
255:   PetscCall(DMGetLocalVector(dm, &Xlocal));
256:   PetscCall(DMGlobalToLocalBegin(dm, X, INSERT_VALUES, Xlocal));
257:   PetscCall(DMGlobalToLocalEnd(dm, X, INSERT_VALUES, Xlocal));
258:   PetscCall(DMDAVecGetArrayDOFRead(dm, Xlocal, &x));
259:   PetscCall(DMDAVecGetArrayDOF(dm, F, &f));
260:   PetscCall(DMDAGetCorners(dm, &xs, NULL, NULL, &xm, NULL, NULL));

262:   idx = 1.0 * user->diffus / user->dx;
263:   for (i = xs; i < xs + xm; i++) {
264:     for (j = 0; j < dof; j++) f[i][j] += idx * (x[i + 1][j] - 2.0 * x[i][j] + x[i - 1][j]);
265:   }
266:   PetscCall(DMDAVecRestoreArrayDOFRead(dm, Xlocal, &x));
267:   PetscCall(DMDAVecRestoreArrayDOF(dm, F, &f));
268:   PetscCall(DMRestoreLocalVector(dm, &Xlocal));
269:   PetscFunctionReturn(PETSC_SUCCESS);
270: }

272: /*
273:    Produces the second order centered difference diffusion operator on a one dimensional periodic domain
274: */
275: static PetscErrorCode FormDiffusionJacobian(TS ts, PetscReal t, Vec X, Mat Amat, Mat Pmat, void *ptr)
276: {
277:   User       user = (User)ptr;
278:   DM         dm;
279:   PetscInt   i, xs, xm, j, dof;
280:   PetscReal  idx, values[3];
281:   MatStencil row, col[3];

283:   PetscFunctionBeginUser;
284:   PetscCall(TSGetDM(ts, &dm));
285:   PetscCall(DMDAGetInfo(dm, NULL, NULL, NULL, NULL, NULL, NULL, NULL, &dof, NULL, NULL, NULL, NULL, NULL));
286:   PetscCall(DMDAGetCorners(dm, &xs, NULL, NULL, &xm, NULL, NULL));

288:   idx       = 1.0 * user->diffus / user->dx;
289:   values[0] = idx;
290:   values[1] = -2.0 * idx;
291:   values[2] = idx;
292:   for (i = xs; i < xs + xm; i++) {
293:     for (j = 0; j < dof; j++) {
294:       row.i    = i;
295:       row.c    = j;
296:       col[0].i = i - 1;
297:       col[0].c = j;
298:       col[1].i = i;
299:       col[1].c = j;
300:       col[2].i = i + 1;
301:       col[2].c = j;
302:       PetscCall(MatSetValuesStencil(Pmat, 1, &row, 3, col, values, ADD_VALUES));
303:     }
304:   }
305:   PetscCall(MatAssemblyBegin(Pmat, MAT_FINAL_ASSEMBLY));
306:   PetscCall(MatAssemblyEnd(Pmat, MAT_FINAL_ASSEMBLY));
307:   PetscFunctionReturn(PETSC_SUCCESS);
308: }

310: static PetscErrorCode FormRHSFunction(TS ts, PetscReal t, Vec X, Vec F, void *ptr)
311: {
312:   User                user = (User)ptr;
313:   PetscScalar       **f;
314:   const PetscScalar **x;
315:   DM                  dm;
316:   PetscInt            i, xs, xm;

318:   PetscFunctionBeginUser;
319:   if (user->reactions) {
320:     PetscCall(TSGetDM(ts, &dm));
321:     PetscCall(DMDAVecGetArrayDOFRead(dm, X, &x));
322:     PetscCall(DMDAVecGetArrayDOF(dm, F, &f));
323:     PetscCall(DMDAGetCorners(dm, &xs, NULL, NULL, &xm, NULL, NULL));

325:     for (i = xs; i < xs + xm; i++) {
326:       PetscCall(PetscArraycpy(user->tchemwork, x[i], user->Nspec + 1));
327:       user->tchemwork[0] *= user->Tini; /* Dimensionalize */
328:       PetscCallTC(TC_getSrc(user->tchemwork, user->Nspec + 1, f[i]));
329:       f[i][0] /= user->Tini; /* Non-dimensionalize */
330:     }

332:     PetscCall(DMDAVecRestoreArrayDOFRead(dm, X, &x));
333:     PetscCall(DMDAVecRestoreArrayDOF(dm, F, &f));
334:   } else {
335:     PetscCall(VecZeroEntries(F));
336:   }
337:   if (user->diffusion) PetscCall(FormDiffusionFunction(ts, t, X, F, ptr));
338:   PetscFunctionReturn(PETSC_SUCCESS);
339: }

341: static PetscErrorCode FormRHSJacobian(TS ts, PetscReal t, Vec X, Mat Amat, Mat Pmat, void *ptr)
342: {
343:   User                user = (User)ptr;
344:   const PetscScalar **x;
345:   PetscInt            M = user->Nspec + 1, i, j, xs, xm;
346:   DM                  dm;

348:   PetscFunctionBeginUser;
349:   if (user->reactions) {
350:     PetscCall(TSGetDM(ts, &dm));
351:     PetscCall(MatZeroEntries(Pmat));
352:     PetscCall(MatSetOption(Pmat, MAT_ROW_ORIENTED, PETSC_FALSE));
353:     PetscCall(MatSetOption(Pmat, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE));
354:     PetscCall(DMDAVecGetArrayDOFRead(dm, X, &x));
355:     PetscCall(DMDAGetCorners(dm, &xs, NULL, NULL, &xm, NULL, NULL));

357:     for (i = xs; i < xs + xm; i++) {
358:       PetscCall(PetscArraycpy(user->tchemwork, x[i], user->Nspec + 1));
359:       user->tchemwork[0] *= user->Tini; /* Dimensionalize temperature (first row) because that is what Tchem wants */
360:       PetscCall(TC_getJacTYN(user->tchemwork, user->Nspec, user->Jdense, 1));

362:       for (j = 0; j < M; j++) user->Jdense[j + 0 * M] /= user->Tini; /* Non-dimensionalize first column */
363:       for (j = 0; j < M; j++) user->Jdense[0 + j * M] /= user->Tini; /* Non-dimensionalize first row */
364:       for (j = 0; j < M; j++) user->rows[j] = i * M + j;
365:       PetscCall(MatSetValues(Pmat, M, user->rows, M, user->rows, user->Jdense, INSERT_VALUES));
366:     }
367:     PetscCall(DMDAVecRestoreArrayDOFRead(dm, X, &x));
368:     PetscCall(MatAssemblyBegin(Pmat, MAT_FINAL_ASSEMBLY));
369:     PetscCall(MatAssemblyEnd(Pmat, MAT_FINAL_ASSEMBLY));
370:   } else {
371:     PetscCall(MatZeroEntries(Pmat));
372:   }
373:   if (user->diffusion) PetscCall(FormDiffusionJacobian(ts, t, X, Amat, Pmat, ptr));
374:   if (Amat != Pmat) {
375:     PetscCall(MatAssemblyBegin(Amat, MAT_FINAL_ASSEMBLY));
376:     PetscCall(MatAssemblyEnd(Amat, MAT_FINAL_ASSEMBLY));
377:   }
378:   PetscFunctionReturn(PETSC_SUCCESS);
379: }

381: PetscErrorCode FormInitialSolution(TS ts, Vec X, void *ctx)
382: {
383:   PetscScalar **x, *xc;
384:   struct {
385:     const char *name;
386:     PetscReal   massfrac;
387:   } initial[] = {
388:     {"CH4", 0.0948178320887 },
389:     {"O2",  0.189635664177  },
390:     {"N2",  0.706766236705  },
391:     {"AR",  0.00878026702874}
392:   };
393:   PetscInt i, j, xs, xm;
394:   DM       dm;

396:   PetscFunctionBeginUser;
397:   PetscCall(VecZeroEntries(X));
398:   PetscCall(TSGetDM(ts, &dm));
399:   PetscCall(DMDAGetCorners(dm, &xs, NULL, NULL, &xm, NULL, NULL));

401:   PetscCall(DMDAGetCoordinateArray(dm, &xc));
402:   PetscCall(DMDAVecGetArrayDOF(dm, X, &x));
403:   for (i = xs; i < xs + xm; i++) {
404:     x[i][0] = 1.0 + .05 * PetscSinScalar(2. * PETSC_PI * xc[i]); /* Non-dimensionalized by user->Tini */
405:     for (j = 0; j < PETSC_STATIC_ARRAY_LENGTH(initial); j++) {
406:       int ispec = TC_getSpos(initial[j].name, strlen(initial[j].name));
407:       PetscCheck(ispec >= 0, PETSC_COMM_SELF, PETSC_ERR_USER, "Could not find species %s", initial[j].name);
408:       PetscCall(PetscPrintf(PETSC_COMM_SELF, "Species %d: %s %g\n", j, initial[j].name, (double)initial[j].massfrac));
409:       x[i][1 + ispec] = initial[j].massfrac;
410:     }
411:   }
412:   PetscCall(DMDAVecRestoreArrayDOF(dm, X, &x));
413:   PetscCall(DMDARestoreCoordinateArray(dm, &xc));
414:   PetscFunctionReturn(PETSC_SUCCESS);
415: }

417: /*
418:     Routines for displaying the solutions
419: */
420: typedef struct {
421:   PetscInt cell;
422:   User     user;
423: } UserLGCtx;

425: static PetscErrorCode FormMoleFraction(UserLGCtx *ctx, Vec massf, Vec *molef)
426: {
427:   User                user = ctx->user;
428:   PetscReal          *M, tM = 0;
429:   PetscInt            i, n  = user->Nspec + 1;
430:   PetscScalar        *mof;
431:   const PetscScalar **maf;

433:   PetscFunctionBeginUser;
434:   PetscCall(VecCreateSeq(PETSC_COMM_SELF, n, molef));
435:   PetscCall(PetscMalloc1(user->Nspec, &M));
436:   TC_getSmass(user->Nspec, M);
437:   PetscCall(DMDAVecGetArrayDOFRead(user->dm, massf, &maf));
438:   PetscCall(VecGetArray(*molef, &mof));
439:   mof[0] = maf[ctx->cell][0]; /* copy over temperature */
440:   for (i = 1; i < n; i++) tM += maf[ctx->cell][i] / M[i - 1];
441:   for (i = 1; i < n; i++) mof[i] = maf[ctx->cell][i] / (M[i - 1] * tM);
442:   PetscCall(DMDAVecRestoreArrayDOFRead(user->dm, massf, &maf));
443:   PetscCall(VecRestoreArray(*molef, &mof));
444:   PetscCall(PetscFree(M));
445:   PetscFunctionReturn(PETSC_SUCCESS);
446: }

448: static PetscErrorCode MonitorCellDestroy(UserLGCtx *uctx)
449: {
450:   PetscFunctionBeginUser;
451:   PetscCall(PetscFree(uctx));
452:   PetscFunctionReturn(PETSC_SUCCESS);
453: }

455: /*
456:    Use TSMonitorLG to monitor the reactions in a particular cell
457: */
458: static PetscErrorCode MonitorCell(TS ts, User user, PetscInt cell)
459: {
460:   TSMonitorLGCtx ctx;
461:   char         **snames;
462:   UserLGCtx     *uctx;
463:   char           label[128];
464:   PetscReal      temp, *xc;
465:   PetscMPIInt    rank;

467:   PetscFunctionBeginUser;
468:   PetscCall(DMDAGetCoordinateArray(user->dm, &xc));
469:   temp = 1.0 + .05 * PetscSinScalar(2. * PETSC_PI * xc[cell]); /* Non-dimensionalized by user->Tini */
470:   PetscCall(DMDARestoreCoordinateArray(user->dm, &xc));
471:   PetscCallMPI(MPI_Comm_rank(PETSC_COMM_WORLD, &rank));
472:   PetscCall(PetscSNPrintf(label, sizeof(label), "Initial Temperature %g Cell %d Rank %d", (double)user->Tini * temp, (int)cell, rank));
473:   PetscCall(TSMonitorLGCtxCreate(PETSC_COMM_SELF, NULL, label, PETSC_DECIDE, PETSC_DECIDE, 600, 400, 1, &ctx));
474:   PetscCall(DMDAGetFieldNames(user->dm, (const char *const **)&snames));
475:   PetscCall(TSMonitorLGCtxSetVariableNames(ctx, (const char *const *)snames));
476:   PetscCall(PetscNew(&uctx));
477:   uctx->cell = cell;
478:   uctx->user = user;
479:   PetscCall(TSMonitorLGCtxSetTransform(ctx, (PetscErrorCode (*)(void *, Vec, Vec *))FormMoleFraction, (PetscErrorCode (*)(void *))MonitorCellDestroy, uctx));
480:   PetscCall(TSMonitorSet(ts, TSMonitorLGSolution, ctx, (PetscErrorCode (*)(void **))TSMonitorLGCtxDestroy));
481:   PetscFunctionReturn(PETSC_SUCCESS);
482: }