Actual source code: extchem.c

petsc-3.6.4 2016-04-12
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  1: static const char help[] = "Integrate chemistry using TChem.\n";

  3: #include <petscts.h>

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

 20:        curl http://combustion.berkeley.edu/gri_mech/version30/files30/grimech30.dat > chem.inp
 21:        curl http://combustion.berkeley.edu/gri_mech/version30/files30/thermo30.dat > therm.dat

 23:        https://www-pls.llnl.gov/data/docs/science_and_technology/chemistry/combustion/n_heptane_v3.1_therm.dat
 24:        https://www-pls.llnl.gov/data/docs/science_and_technology/chemistry/combustion/nc7_ver3.1_mech.txt

 26:        cp $PETSC_DIR/$PETSC_ARCH/externalpackages/tchem/data/periodictable.dat .

 28:     Run with
 29:    ./extchem -Tini 1500 -ts_arkimex_fully_implicit -ts_max_snes_failures -1 -ts_adapt_monitor -ts_adapt_dt_max 1e-4 -ts_arkimex_type 4 -ts_monitor_lg_solution -ts_final_time .005 -draw_pause -2 -lg_use_markers false -ts_monitor_lg_solution_variables H2,O2,H2O,CH4,CO,CO2,C2H2,N2  -ts_monitor_envelope

 31:     Determine sensitivity of final tempature on each variables initial conditions
 32:     -ts_dt 1.e-5 -ts_type cn -ts_adjoint_solve -ts_adjoint_view_solution draw

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

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

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

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

 44: */
 45: typedef struct _User *User;
 46: struct _User {
 47:   PetscReal pressure;
 48:   int       Nspec;
 49:   int       Nreac;
 50:   PetscReal Tini;
 51:   double    *tchemwork;
 52:   double    *Jdense;        /* Dense array workspace where Tchem computes the Jacobian */
 53:   PetscInt  *rows;
 54:   char      **snames;
 55: };


 58: static PetscErrorCode PrintSpecies(User,Vec);
 59: static PetscErrorCode MassFractionToMoleFraction(User,Vec,Vec*);
 60: static PetscErrorCode MoleFractionToMassFraction(User,Vec,Vec*);
 61: static PetscErrorCode FormRHSFunction(TS,PetscReal,Vec,Vec,void*);
 62: static PetscErrorCode FormRHSJacobian(TS,PetscReal,Vec,Mat,Mat,void*);
 63: static PetscErrorCode FormInitialSolution(TS,Vec,void*);

 65: #define TCCHKERRQ(ierr) do {if (ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in TChem library, return code %d",ierr);} while (0)

 69: int main(int argc,char **argv)
 70: {
 71:   TS                ts;         /* time integrator */
 72:   TSAdapt           adapt;
 73:   Vec               X,lambda;          /* solution vector */
 74:   Mat               J;          /* Jacobian matrix */
 75:   PetscInt          steps,maxsteps;
 76:   PetscErrorCode    ierr;
 77:   PetscReal         ftime,dt;
 78:   char              chemfile[PETSC_MAX_PATH_LEN] = "chem.inp",thermofile[PETSC_MAX_PATH_LEN] = "therm.dat";
 79:   struct _User      user;       /* user-defined work context */
 80:   TSConvergedReason reason;
 81:   char              **snames,*names;
 82:   PetscInt          i;

 84:   PetscInitialize(&argc,&argv,(char*)0,help);
 85:   PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Chemistry solver options","");
 86:   PetscOptionsString("-chem","CHEMKIN input file","",chemfile,chemfile,sizeof(chemfile),NULL);
 87:   PetscOptionsString("-thermo","NASA thermo input file","",thermofile,thermofile,sizeof(thermofile),NULL);
 88:   user.pressure = 1.01325e5;    /* Pascal */
 89:   PetscOptionsReal("-pressure","Pressure of reaction [Pa]","",user.pressure,&user.pressure,NULL);
 90:   user.Tini = 1000;             /* Kelvin */
 91:   PetscOptionsReal("-Tini","Initial temperature [K]","",user.Tini,&user.Tini,NULL);
 92:   PetscOptionsEnd();

 94:   TC_initChem(chemfile, thermofile, 0, 1.0);TC
 95:   user.Nspec = TC_getNspec();
 96:   user.Nreac = TC_getNreac();
 97:   /*
 98:       Get names of all species in easy to use array
 99:   */
100:   PetscMalloc1((user.Nspec+1)*LENGTHOFSPECNAME,&names);
101:   PetscStrcpy(names,"Temp");
102:   TC_getSnames(user.Nspec,names+LENGTHOFSPECNAME);
103:   PetscMalloc1((user.Nspec+2),&snames);
104:   for (i=0; i<user.Nspec+1; i++) snames[i] = names+i*LENGTHOFSPECNAME;
105:   snames[user.Nspec+1] = NULL;
106:   PetscStrArrayallocpy((const char *const *)snames,&user.snames);
107:   PetscFree(snames);
108:   PetscFree(names);

110:   PetscMalloc3(user.Nspec+1,&user.tchemwork,PetscSqr(user.Nspec+1),&user.Jdense,user.Nspec+1,&user.rows);
111:   VecCreateSeq(PETSC_COMM_SELF,user.Nspec+1,&X);

113:   MatCreateSeqAIJ(PETSC_COMM_SELF,user.Nspec+1,user.Nspec+1,PETSC_DECIDE,NULL,&J);
114:   /*MatCreateSeqDense(PETSC_COMM_SELF,user.Nspec+1,user.Nspec+1,NULL,&J);*/
115:   MatSetFromOptions(J);

117:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
118:      Create timestepping solver context
119:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
120:   TSCreate(PETSC_COMM_WORLD,&ts);
121:   TSSetType(ts,TSARKIMEX);
122:   TSARKIMEXSetFullyImplicit(ts,PETSC_TRUE);
123:   TSARKIMEXSetType(ts,TSARKIMEX4);
124:   TSSetRHSFunction(ts,NULL,FormRHSFunction,&user);
125:   TSSetRHSJacobian(ts,J,J,FormRHSJacobian,&user);

127:   ftime    = 1.0;
128:   maxsteps = 10000;
129:   TSSetDuration(ts,maxsteps,ftime);

131:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
132:      Set initial conditions
133:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
134:   FormInitialSolution(ts,X,&user);
135:   TSSetSolution(ts,X);
136:   dt   = 1e-10;                 /* Initial time step */
137:   TSSetInitialTimeStep(ts,0.0,dt);
138:   TSGetAdapt(ts,&adapt);
139:   TSAdaptSetStepLimits(adapt,1e-12,1e-4); /* Also available with -ts_adapt_dt_min/-ts_adapt_dt_max */
140:   TSSetMaxSNESFailures(ts,-1);            /* Retry step an unlimited number of times */

142:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
143:      Set runtime options
144:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
145:   TSSetFromOptions(ts);

147:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
148:      Set final conditions for sensitivities
149:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
150:   VecDuplicate(X,&lambda);
151:   TSSetCostGradients(ts,1,&lambda,NULL);
152:   VecSetValue(lambda,0,1.0,INSERT_VALUES);
153:   VecAssemblyBegin(lambda);
154:   VecAssemblyEnd(lambda);



158:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
159:      Pass information to graphical monitoring routine
160:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
161:   TSMonitorLGSetVariableNames(ts,(const char * const *)user.snames);
162:   TSMonitorLGSetTransform(ts,(PetscErrorCode (*)(void*,Vec,Vec*))MassFractionToMoleFraction,NULL,&user);

164:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
165:      Solve ODE
166:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
167:   TSSolve(ts,X);
168:   TSGetSolveTime(ts,&ftime);
169:   TSGetTimeStepNumber(ts,&steps);
170:   TSGetConvergedReason(ts,&reason);
171:   PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],(double)ftime,steps);

173:   {
174:     Vec                max;
175:     const char * const *names;
176:     PetscInt           i;
177:     const PetscReal    *bmax;

179:     TSMonitorEnvelopeGetBounds(ts,&max,NULL);
180:     if (max) {
181:       TSMonitorLGGetVariableNames(ts,&names);
182:       VecGetArrayRead(max,&bmax);
183:       PetscPrintf(PETSC_COMM_SELF,"Species - maximum mass fraction\n");
184:       for (i=1; i<user.Nspec; i++) {
185:         if (bmax[i] > .01) {PetscPrintf(PETSC_COMM_SELF,"%s %g\n",names[i],bmax[i]);}
186:       }
187:       VecRestoreArrayRead(max,&bmax);
188:     }
189:   }

191:   Vec y;
192:   MassFractionToMoleFraction(&user,X,&y);
193:   PrintSpecies(&user,y);
194:   VecDestroy(&y);
195: 
196:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
197:      Free work space.
198:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
199:   TC_reset();
200:   PetscStrArrayDestroy(&user.snames);
201:   MatDestroy(&J);
202:   VecDestroy(&X);
203:   VecDestroy(&lambda);
204:   TSDestroy(&ts);
205:   PetscFree3(user.tchemwork,user.Jdense,user.rows);
206:   PetscFinalize();
207:   return 0;
208: }

212: static PetscErrorCode FormRHSFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr)
213: {
214:   User              user = (User)ptr;
215:   PetscErrorCode    ierr;
216:   PetscScalar       *f;
217:   const PetscScalar *x;

220:   VecGetArrayRead(X,&x);
221:   VecGetArray(F,&f);

223:   PetscMemcpy(user->tchemwork,x,(user->Nspec+1)*sizeof(x[0]));
224:   user->tchemwork[0] *= user->Tini; /* Dimensionalize */
225:   TC_getSrc(user->tchemwork,user->Nspec+1,f);TC
226:   f[0] /= user->Tini;           /* Non-dimensionalize */

228:   VecRestoreArrayRead(X,&x);
229:   VecRestoreArray(F,&f);
230:   return(0);
231: }

235: static PetscErrorCode FormRHSJacobian(TS ts,PetscReal t,Vec X,Mat Amat,Mat Pmat,void *ptr)
236: {
237:   User              user = (User)ptr;
238:   PetscErrorCode    ierr;
239:   const PetscScalar *x;
240:   PetscInt          M = user->Nspec+1,i;

243:   VecGetArrayRead(X,&x);
244:   PetscMemcpy(user->tchemwork,x,(user->Nspec+1)*sizeof(x[0]));
245:   VecRestoreArrayRead(X,&x);
246:   user->tchemwork[0] *= user->Tini;  /* Dimensionalize temperature (first row) because that is what Tchem wants */
247:   TC_getJacTYN(user->tchemwork,user->Nspec,user->Jdense,1);

249:   for (i=0; i<M; i++) user->Jdense[i + 0*M] /= user->Tini; /* Non-dimensionalize first column */
250:   for (i=0; i<M; i++) user->Jdense[0 + i*M] /= user->Tini; /* Non-dimensionalize first row */
251:   for (i=0; i<M; i++) user->rows[i] = i;
252:   MatSetOption(Pmat,MAT_ROW_ORIENTED,PETSC_FALSE);
253:   MatSetOption(Pmat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE);
254:   MatZeroEntries(Pmat);
255:   MatSetValues(Pmat,M,user->rows,M,user->rows,user->Jdense,INSERT_VALUES);

257:   MatAssemblyBegin(Pmat,MAT_FINAL_ASSEMBLY);
258:   MatAssemblyEnd(Pmat,MAT_FINAL_ASSEMBLY);
259:   if (Amat != Pmat) {
260:     MatAssemblyBegin(Amat,MAT_FINAL_ASSEMBLY);
261:     MatAssemblyEnd(Amat,MAT_FINAL_ASSEMBLY);
262:   }
263:   return(0);
264: }

268: PetscErrorCode FormInitialSolution(TS ts,Vec X,void *ctx)
269: {
270:   PetscScalar    *x;
272:   struct {const char *name; PetscReal molefrac;} initial[] = {
273:     {"CH4", 0.0948178320887},
274:     {"O2", 0.189635664177},
275:     {"N2", 0.706766236705},
276:     {"AR", 0.00878026702874}
277:   };
278:   PetscInt i;
279:   Vec      y;

282:   VecZeroEntries(X);
283:   VecGetArray(X,&x);
284:   x[0] = 1.0;  /* Non-dimensionalized by user->Tini */

286:   for (i=0; i<sizeof(initial)/sizeof(initial[0]); i++) {
287:     int ispec = TC_getSpos(initial[i].name, strlen(initial[i].name));
288:     if (ispec < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Could not find species %s",initial[i].name);
289:     PetscPrintf(PETSC_COMM_SELF,"Species %d: %s %g\n",i,initial[i].name,initial[i].molefrac);
290:     x[1+ispec] = initial[i].molefrac;
291:   }
292:   VecRestoreArray(X,&x);
293:   PrintSpecies((User)ctx,X);
294:   MoleFractionToMassFraction((User)ctx,X,&y);
295:   VecCopy(y,X);
296:   VecDestroy(&y);
297:   return(0);
298: }

302: /*
303:    Converts the input vector which is in mass fractions (used by tchem) to mole fractions
304: */
305: PetscErrorCode MassFractionToMoleFraction(User user,Vec massf,Vec *molef)
306: {
307:   PetscErrorCode    ierr;
308:   PetscScalar       *mof;
309:   const PetscScalar *maf;

312:   VecDuplicate(massf,molef);
313:   VecGetArrayRead(massf,&maf);
314:   VecGetArray(*molef,&mof);
315:   mof[0] = maf[0]; /* copy over temperature */
316:   TC_getMs2Ml((double*)maf+1,user->Nspec,mof+1);
317:   VecRestoreArray(*molef,&mof);
318:   VecRestoreArrayRead(massf,&maf);
319:   return(0);
320: }

324: /*
325:    Converts the input vector which is in mole fractions to mass fractions (used by tchem)
326: */
327: PetscErrorCode MoleFractionToMassFraction(User user,Vec molef,Vec *massf)
328: {
329:   PetscErrorCode    ierr;
330:   const PetscScalar *mof;
331:   PetscScalar       *maf;

334:   VecDuplicate(molef,massf);
335:   VecGetArrayRead(molef,&mof);
336:   VecGetArray(*massf,&maf);
337:   maf[0] = mof[0]; /* copy over temperature */
338:   TC_getMl2Ms((double*)mof+1,user->Nspec,maf+1);
339:   VecRestoreArrayRead(molef,&mof);
340:   VecRestoreArray(*massf,&maf);
341:   return(0);
342: }

346: /*
347:    Prints out each species with its name
348: */
349: PetscErrorCode PrintSpecies(User user,Vec molef)
350: {
351:   PetscErrorCode    ierr;
352:   const PetscScalar *mof;
353:   PetscInt          i,*idx,n = user->Nspec+1;

356:   PetscMalloc1(n,&idx);
357:   for (i=0; i<n;i++) idx[i] = i;
358:   VecGetArrayRead(molef,&mof);
359:   PetscSortRealWithPermutation(n,mof,idx);
360:   for (i=0; i<n; i++) {
361:     PetscPrintf(PETSC_COMM_SELF,"%6s %g\n",user->snames[idx[n-i-1]],mof[idx[n-i-1]]);
362:   }
363:   PetscFree(idx);
364:   VecRestoreArrayRead(molef,&mof);
365:   return(0);
366: }