1 static const char help[] = "Integrate chemistry using TChem.\n"; 2 3 #include <petscts.h> 4 #include <petscdmda.h> 5 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 /* 19 20 This is an extension of extchem.c to solve the reaction equations independently in each cell of a one dimensional field 21 22 Obtain the three files into this directory 23 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 . 27 28 Run with 29 ./extchemfield -ts_arkimex_fully_implicit -ts_max_snes_failures -1 -ts_adapt_monitor -ts_adapt_dt_max 1e-4 -ts_arkimex_type 4 -ts_max_time .005 30 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 34 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 37 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 40 41 Save the images in a .gif (movie) file 42 -draw_save -draw_save_single_file 43 44 Compute the sensitivies 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 46 47 Turn off diffusion 48 -diffusion no 49 50 Turn off reactions 51 -reactions no 52 53 The solution for component i = 0 is the temperature. 54 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 56 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])) 60 61 FormMoleFraction(User,massf,molef) converts the mass fraction solution of each species to the mole fraction of each species. 62 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 }; 77 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*); 82 83 #define CHKERRTC(ierr) do {PetscCheck(!ierr,PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in TChem library, return code %d",ierr);} while (0) 84 85 int main(int argc,char **argv) 86 { 87 TS ts; /* time integrator */ 88 TSAdapt adapt; 89 Vec X; /* solution vector */ 90 Mat J; /* Jacobian matrix */ 91 PetscInt steps,ncells,xs,xm,i; 92 PetscErrorCode ierr; 93 PetscReal ftime,dt; 94 char chemfile[PETSC_MAX_PATH_LEN] = "chem.inp",thermofile[PETSC_MAX_PATH_LEN] = "therm.dat"; 95 struct _User user; 96 TSConvergedReason reason; 97 PetscBool showsolutions = PETSC_FALSE; 98 char **snames,*names; 99 Vec lambda; /* used with TSAdjoint for sensitivities */ 100 101 CHKERRQ(PetscInitialize(&argc,&argv,(char*)0,help)); 102 ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Chemistry solver options","");CHKERRQ(ierr); 103 CHKERRQ(PetscOptionsString("-chem","CHEMKIN input file","",chemfile,chemfile,sizeof(chemfile),NULL)); 104 CHKERRQ(PetscOptionsString("-thermo","NASA thermo input file","",thermofile,thermofile,sizeof(thermofile),NULL)); 105 user.pressure = 1.01325e5; /* Pascal */ 106 CHKERRQ(PetscOptionsReal("-pressure","Pressure of reaction [Pa]","",user.pressure,&user.pressure,NULL)); 107 user.Tini = 1550; 108 CHKERRQ(PetscOptionsReal("-Tini","Initial temperature [K]","",user.Tini,&user.Tini,NULL)); 109 user.diffus = 100; 110 CHKERRQ(PetscOptionsReal("-diffus","Diffusion constant","",user.diffus,&user.diffus,NULL)); 111 CHKERRQ(PetscOptionsBool("-draw_solution","Plot the solution for each cell","",showsolutions,&showsolutions,NULL)); 112 user.diffusion = PETSC_TRUE; 113 CHKERRQ(PetscOptionsBool("-diffusion","Have diffusion","",user.diffusion,&user.diffusion,NULL)); 114 user.reactions = PETSC_TRUE; 115 CHKERRQ(PetscOptionsBool("-reactions","Have reactions","",user.reactions,&user.reactions,NULL)); 116 ierr = PetscOptionsEnd();CHKERRQ(ierr); 117 118 CHKERRTC(TC_initChem(chemfile, thermofile, 0, 1.0)); 119 user.Nspec = TC_getNspec(); 120 user.Nreac = TC_getNreac(); 121 122 CHKERRQ(DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_PERIODIC,10,user.Nspec+1,1,NULL,&user.dm)); 123 CHKERRQ(DMSetFromOptions(user.dm)); 124 CHKERRQ(DMSetUp(user.dm)); 125 CHKERRQ(DMDAGetInfo(user.dm,NULL,&ncells,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL)); 126 user.dx = 1.0/ncells; /* Set the coordinates of the cell centers; note final ghost cell is at x coordinate 1.0 */ 127 CHKERRQ(DMDASetUniformCoordinates(user.dm,0.0,1.0,0.0,1.0,0.0,1.0)); 128 129 /* set the names of each field in the DMDA based on the species name */ 130 CHKERRQ(PetscMalloc1((user.Nspec+1)*LENGTHOFSPECNAME,&names)); 131 CHKERRQ(PetscStrcpy(names,"Temp")); 132 TC_getSnames(user.Nspec,names+LENGTHOFSPECNAME); 133 CHKERRQ(PetscMalloc1((user.Nspec+2),&snames)); 134 for (i=0; i<user.Nspec+1; i++) snames[i] = names+i*LENGTHOFSPECNAME; 135 snames[user.Nspec+1] = NULL; 136 CHKERRQ(DMDASetFieldNames(user.dm,(const char * const *)snames)); 137 CHKERRQ(PetscFree(snames)); 138 CHKERRQ(PetscFree(names)); 139 140 CHKERRQ(DMCreateMatrix(user.dm,&J)); 141 CHKERRQ(DMCreateGlobalVector(user.dm,&X)); 142 143 CHKERRQ(PetscMalloc3(user.Nspec+1,&user.tchemwork,PetscSqr(user.Nspec+1),&user.Jdense,user.Nspec+1,&user.rows)); 144 145 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 146 Create timestepping solver context 147 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 148 CHKERRQ(TSCreate(PETSC_COMM_WORLD,&ts)); 149 CHKERRQ(TSSetDM(ts,user.dm)); 150 CHKERRQ(TSSetType(ts,TSARKIMEX)); 151 CHKERRQ(TSARKIMEXSetFullyImplicit(ts,PETSC_TRUE)); 152 CHKERRQ(TSARKIMEXSetType(ts,TSARKIMEX4)); 153 CHKERRQ(TSSetRHSFunction(ts,NULL,FormRHSFunction,&user)); 154 CHKERRQ(TSSetRHSJacobian(ts,J,J,FormRHSJacobian,&user)); 155 156 ftime = 1.0; 157 CHKERRQ(TSSetMaxTime(ts,ftime)); 158 CHKERRQ(TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER)); 159 160 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 161 Set initial conditions 162 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 163 CHKERRQ(FormInitialSolution(ts,X,&user)); 164 CHKERRQ(TSSetSolution(ts,X)); 165 dt = 1e-10; /* Initial time step */ 166 CHKERRQ(TSSetTimeStep(ts,dt)); 167 CHKERRQ(TSGetAdapt(ts,&adapt)); 168 CHKERRQ(TSAdaptSetStepLimits(adapt,1e-12,1e-4)); /* Also available with -ts_adapt_dt_min/-ts_adapt_dt_max */ 169 CHKERRQ(TSSetMaxSNESFailures(ts,-1)); /* Retry step an unlimited number of times */ 170 171 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 172 Pass information to graphical monitoring routine 173 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 174 if (showsolutions) { 175 CHKERRQ(DMDAGetCorners(user.dm,&xs,NULL,NULL,&xm,NULL,NULL)); 176 for (i=xs;i<xs+xm;i++) { 177 CHKERRQ(MonitorCell(ts,&user,i)); 178 } 179 } 180 181 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 182 Set runtime options 183 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 184 CHKERRQ(TSSetFromOptions(ts)); 185 186 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 187 Set final conditions for sensitivities 188 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 189 CHKERRQ(DMCreateGlobalVector(user.dm,&lambda)); 190 CHKERRQ(TSSetCostGradients(ts,1,&lambda,NULL)); 191 CHKERRQ(VecSetValue(lambda,0,1.0,INSERT_VALUES)); 192 CHKERRQ(VecAssemblyBegin(lambda)); 193 CHKERRQ(VecAssemblyEnd(lambda)); 194 195 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 196 Solve ODE 197 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 198 CHKERRQ(TSSolve(ts,X)); 199 CHKERRQ(TSGetSolveTime(ts,&ftime)); 200 CHKERRQ(TSGetStepNumber(ts,&steps)); 201 CHKERRQ(TSGetConvergedReason(ts,&reason)); 202 CHKERRQ(PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],(double)ftime,steps)); 203 204 { 205 Vec max; 206 const char * const *names; 207 PetscInt i; 208 const PetscReal *bmax; 209 210 CHKERRQ(TSMonitorEnvelopeGetBounds(ts,&max,NULL)); 211 if (max) { 212 CHKERRQ(TSMonitorLGGetVariableNames(ts,&names)); 213 if (names) { 214 CHKERRQ(VecGetArrayRead(max,&bmax)); 215 CHKERRQ(PetscPrintf(PETSC_COMM_SELF,"Species - maximum mass fraction\n")); 216 for (i=1; i<user.Nspec; i++) { 217 if (bmax[i] > .01) CHKERRQ(PetscPrintf(PETSC_COMM_SELF,"%s %g\n",names[i],bmax[i])); 218 } 219 CHKERRQ(VecRestoreArrayRead(max,&bmax)); 220 } 221 } 222 } 223 224 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 225 Free work space. 226 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 227 TC_reset(); 228 CHKERRQ(DMDestroy(&user.dm)); 229 CHKERRQ(MatDestroy(&J)); 230 CHKERRQ(VecDestroy(&X)); 231 CHKERRQ(VecDestroy(&lambda)); 232 CHKERRQ(TSDestroy(&ts)); 233 CHKERRQ(PetscFree3(user.tchemwork,user.Jdense,user.rows)); 234 CHKERRQ(PetscFinalize()); 235 return 0; 236 } 237 238 /* 239 Applies the second order centered difference diffusion operator on a one dimensional periodic domain 240 */ 241 static PetscErrorCode FormDiffusionFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr) 242 { 243 User user = (User)ptr; 244 PetscErrorCode ierr; 245 PetscScalar **f; 246 const PetscScalar **x; 247 DM dm; 248 PetscInt i,xs,xm,j,dof; 249 Vec Xlocal; 250 PetscReal idx; 251 252 PetscFunctionBeginUser; 253 CHKERRQ(TSGetDM(ts,&dm)); 254 CHKERRQ(DMDAGetInfo(dm,NULL,NULL,NULL,NULL,NULL,NULL,NULL,&dof,NULL,NULL,NULL,NULL,NULL)); 255 CHKERRQ(DMGetLocalVector(dm,&Xlocal)); 256 CHKERRQ(DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xlocal)); 257 CHKERRQ(DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xlocal)); 258 CHKERRQ(DMDAVecGetArrayDOFRead(dm,Xlocal,&x)); 259 CHKERRQ(DMDAVecGetArrayDOF(dm,F,&f)); 260 CHKERRQ(DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL)); 261 262 idx = 1.0*user->diffus/user->dx; 263 for (i=xs; i<xs+xm; i++) { 264 for (j=0; j<dof; j++) { 265 f[i][j] += idx*(x[i+1][j] - 2.0*x[i][j] + x[i-1][j]); 266 } 267 } 268 CHKERRQ(DMDAVecRestoreArrayDOFRead(dm,Xlocal,&x)); 269 CHKERRQ(DMDAVecRestoreArrayDOF(dm,F,&f)); 270 CHKERRQ(DMRestoreLocalVector(dm,&Xlocal)); 271 PetscFunctionReturn(0); 272 } 273 274 /* 275 Produces the second order centered difference diffusion operator on a one dimensional periodic domain 276 */ 277 static PetscErrorCode FormDiffusionJacobian(TS ts,PetscReal t,Vec X,Mat Amat,Mat Pmat,void *ptr) 278 { 279 User user = (User)ptr; 280 PetscErrorCode ierr; 281 DM dm; 282 PetscInt i,xs,xm,j,dof; 283 PetscReal idx,values[3]; 284 MatStencil row,col[3]; 285 286 PetscFunctionBeginUser; 287 CHKERRQ(TSGetDM(ts,&dm)); 288 CHKERRQ(DMDAGetInfo(dm,NULL,NULL,NULL,NULL,NULL,NULL,NULL,&dof,NULL,NULL,NULL,NULL,NULL)); 289 CHKERRQ(DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL)); 290 291 idx = 1.0*user->diffus/user->dx; 292 values[0] = idx; 293 values[1] = -2.0*idx; 294 values[2] = idx; 295 for (i=xs; i<xs+xm; i++) { 296 for (j=0; j<dof; j++) { 297 row.i = i; row.c = j; 298 col[0].i = i-1; col[0].c = j; 299 col[1].i = i; col[1].c = j; 300 col[2].i = i+1; col[2].c = j; 301 CHKERRQ(MatSetValuesStencil(Pmat,1,&row,3,col,values,ADD_VALUES)); 302 } 303 } 304 CHKERRQ(MatAssemblyBegin(Pmat,MAT_FINAL_ASSEMBLY)); 305 CHKERRQ(MatAssemblyEnd(Pmat,MAT_FINAL_ASSEMBLY)); 306 PetscFunctionReturn(0); 307 } 308 309 static PetscErrorCode FormRHSFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr) 310 { 311 User user = (User)ptr; 312 PetscErrorCode ierr; 313 PetscScalar **f; 314 const PetscScalar **x; 315 DM dm; 316 PetscInt i,xs,xm; 317 318 PetscFunctionBeginUser; 319 if (user->reactions) { 320 CHKERRQ(TSGetDM(ts,&dm)); 321 CHKERRQ(DMDAVecGetArrayDOFRead(dm,X,&x)); 322 CHKERRQ(DMDAVecGetArrayDOF(dm,F,&f)); 323 CHKERRQ(DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL)); 324 325 for (i=xs; i<xs+xm; i++) { 326 CHKERRQ(PetscArraycpy(user->tchemwork,x[i],user->Nspec+1)); 327 user->tchemwork[0] *= user->Tini; /* Dimensionalize */ 328 CHKERRTC(TC_getSrc(user->tchemwork,user->Nspec+1,f[i])); 329 f[i][0] /= user->Tini; /* Non-dimensionalize */ 330 } 331 332 CHKERRQ(DMDAVecRestoreArrayDOFRead(dm,X,&x)); 333 CHKERRQ(DMDAVecRestoreArrayDOF(dm,F,&f)); 334 } else { 335 CHKERRQ(VecZeroEntries(F)); 336 } 337 if (user->diffusion) { 338 CHKERRQ(FormDiffusionFunction(ts,t,X,F,ptr)); 339 } 340 PetscFunctionReturn(0); 341 } 342 343 static PetscErrorCode FormRHSJacobian(TS ts,PetscReal t,Vec X,Mat Amat,Mat Pmat,void *ptr) 344 { 345 User user = (User)ptr; 346 PetscErrorCode ierr; 347 const PetscScalar **x; 348 PetscInt M = user->Nspec+1,i,j,xs,xm; 349 DM dm; 350 351 PetscFunctionBeginUser; 352 if (user->reactions) { 353 CHKERRQ(TSGetDM(ts,&dm)); 354 CHKERRQ(MatZeroEntries(Pmat)); 355 CHKERRQ(MatSetOption(Pmat,MAT_ROW_ORIENTED,PETSC_FALSE)); 356 CHKERRQ(MatSetOption(Pmat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE)); 357 CHKERRQ(DMDAVecGetArrayDOFRead(dm,X,&x)); 358 CHKERRQ(DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL)); 359 360 for (i=xs; i<xs+xm; i++) { 361 CHKERRQ(PetscArraycpy(user->tchemwork,x[i],user->Nspec+1)); 362 user->tchemwork[0] *= user->Tini; /* Dimensionalize temperature (first row) because that is what Tchem wants */ 363 CHKERRQ(TC_getJacTYN(user->tchemwork,user->Nspec,user->Jdense,1)); 364 365 for (j=0; j<M; j++) user->Jdense[j + 0*M] /= user->Tini; /* Non-dimensionalize first column */ 366 for (j=0; j<M; j++) user->Jdense[0 + j*M] /= user->Tini; /* Non-dimensionalize first row */ 367 for (j=0; j<M; j++) user->rows[j] = i*M+j; 368 CHKERRQ(MatSetValues(Pmat,M,user->rows,M,user->rows,user->Jdense,INSERT_VALUES)); 369 } 370 CHKERRQ(DMDAVecRestoreArrayDOFRead(dm,X,&x)); 371 CHKERRQ(MatAssemblyBegin(Pmat,MAT_FINAL_ASSEMBLY)); 372 CHKERRQ(MatAssemblyEnd(Pmat,MAT_FINAL_ASSEMBLY)); 373 } else { 374 CHKERRQ(MatZeroEntries(Pmat)); 375 } 376 if (user->diffusion) { 377 CHKERRQ(FormDiffusionJacobian(ts,t,X,Amat,Pmat,ptr)); 378 } 379 if (Amat != Pmat) { 380 CHKERRQ(MatAssemblyBegin(Amat,MAT_FINAL_ASSEMBLY)); 381 CHKERRQ(MatAssemblyEnd(Amat,MAT_FINAL_ASSEMBLY)); 382 } 383 PetscFunctionReturn(0); 384 } 385 386 PetscErrorCode FormInitialSolution(TS ts,Vec X,void *ctx) 387 { 388 PetscScalar **x,*xc; 389 PetscErrorCode ierr; 390 struct {const char *name; PetscReal massfrac;} initial[] = { 391 {"CH4", 0.0948178320887}, 392 {"O2", 0.189635664177}, 393 {"N2", 0.706766236705}, 394 {"AR", 0.00878026702874} 395 }; 396 PetscInt i,j,xs,xm; 397 DM dm; 398 399 PetscFunctionBeginUser; 400 CHKERRQ(VecZeroEntries(X)); 401 CHKERRQ(TSGetDM(ts,&dm)); 402 CHKERRQ(DMDAGetCorners(dm,&xs,NULL,NULL,&xm,NULL,NULL)); 403 404 CHKERRQ(DMDAGetCoordinateArray(dm,&xc)); 405 CHKERRQ(DMDAVecGetArrayDOF(dm,X,&x)); 406 for (i=xs; i<xs+xm; i++) { 407 x[i][0] = 1.0 + .05*PetscSinScalar(2.*PETSC_PI*xc[i]); /* Non-dimensionalized by user->Tini */ 408 for (j=0; j<sizeof(initial)/sizeof(initial[0]); j++) { 409 int ispec = TC_getSpos(initial[j].name, strlen(initial[j].name)); 410 PetscCheck(ispec >= 0,PETSC_COMM_SELF,PETSC_ERR_USER,"Could not find species %s",initial[j].name); 411 CHKERRQ(PetscPrintf(PETSC_COMM_SELF,"Species %d: %s %g\n",j,initial[j].name,initial[j].massfrac)); 412 x[i][1+ispec] = initial[j].massfrac; 413 } 414 } 415 CHKERRQ(DMDAVecRestoreArrayDOF(dm,X,&x)); 416 CHKERRQ(DMDARestoreCoordinateArray(dm,&xc)); 417 PetscFunctionReturn(0); 418 } 419 420 /* 421 Routines for displaying the solutions 422 */ 423 typedef struct { 424 PetscInt cell; 425 User user; 426 } UserLGCtx; 427 428 static PetscErrorCode FormMoleFraction(UserLGCtx *ctx,Vec massf,Vec *molef) 429 { 430 User user = ctx->user; 431 PetscErrorCode ierr; 432 PetscReal *M,tM=0; 433 PetscInt i,n = user->Nspec+1; 434 PetscScalar *mof; 435 const PetscScalar **maf; 436 437 PetscFunctionBegin; 438 CHKERRQ(VecCreateSeq(PETSC_COMM_SELF,n,molef)); 439 CHKERRQ(PetscMalloc1(user->Nspec,&M)); 440 TC_getSmass(user->Nspec, M); 441 CHKERRQ(DMDAVecGetArrayDOFRead(user->dm,massf,&maf)); 442 CHKERRQ(VecGetArray(*molef,&mof)); 443 mof[0] = maf[ctx->cell][0]; /* copy over temperature */ 444 for (i=1; i<n; i++) tM += maf[ctx->cell][i]/M[i-1]; 445 for (i=1; i<n; i++) { 446 mof[i] = maf[ctx->cell][i]/(M[i-1]*tM); 447 } 448 CHKERRQ(DMDAVecRestoreArrayDOFRead(user->dm,massf,&maf)); 449 CHKERRQ(VecRestoreArray(*molef,&mof)); 450 CHKERRQ(PetscFree(M)); 451 PetscFunctionReturn(0); 452 } 453 454 static PetscErrorCode MonitorCellDestroy(UserLGCtx *uctx) 455 { 456 PetscErrorCode ierr; 457 458 PetscFunctionBegin; 459 CHKERRQ(PetscFree(uctx)); 460 PetscFunctionReturn(0); 461 } 462 463 /* 464 Use TSMonitorLG to monitor the reactions in a particular cell 465 */ 466 static PetscErrorCode MonitorCell(TS ts,User user,PetscInt cell) 467 { 468 PetscErrorCode ierr; 469 TSMonitorLGCtx ctx; 470 char **snames; 471 UserLGCtx *uctx; 472 char label[128]; 473 PetscReal temp,*xc; 474 PetscMPIInt rank; 475 476 PetscFunctionBegin; 477 CHKERRQ(DMDAGetCoordinateArray(user->dm,&xc)); 478 temp = 1.0 + .05*PetscSinScalar(2.*PETSC_PI*xc[cell]); /* Non-dimensionalized by user->Tini */ 479 CHKERRQ(DMDARestoreCoordinateArray(user->dm,&xc)); 480 CHKERRMPI(MPI_Comm_rank(PETSC_COMM_WORLD,&rank)); 481 CHKERRQ(PetscSNPrintf(label,sizeof(label),"Initial Temperature %g Cell %d Rank %d",(double)user->Tini*temp,(int)cell,rank)); 482 CHKERRQ(TSMonitorLGCtxCreate(PETSC_COMM_SELF,NULL,label,PETSC_DECIDE,PETSC_DECIDE,600,400,1,&ctx)); 483 CHKERRQ(DMDAGetFieldNames(user->dm,(const char * const **)&snames)); 484 CHKERRQ(TSMonitorLGCtxSetVariableNames(ctx,(const char * const *)snames)); 485 CHKERRQ(PetscNew(&uctx)); 486 uctx->cell = cell; 487 uctx->user = user; 488 CHKERRQ(TSMonitorLGCtxSetTransform(ctx,(PetscErrorCode (*)(void*,Vec,Vec*))FormMoleFraction,(PetscErrorCode (*)(void*))MonitorCellDestroy,uctx)); 489 CHKERRQ(TSMonitorSet(ts,TSMonitorLGSolution,ctx,(PetscErrorCode (*)(void**))TSMonitorLGCtxDestroy)); 490 PetscFunctionReturn(0); 491 } 492