Actual source code: extchem.c

      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:     See extchem.example.1 for how to run an example

     20:     See also h2_10sp.inp for another example

     22:     Determine sensitivity of final temperature on each variables initial conditions
     23:     -ts_dt 1.e-5 -ts_type cn -ts_adjoint_solve -ts_adjoint_view_solution draw

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

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

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

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

     35:     These are other data sets for other possible runs
     36:        https://www-pls.llnl.gov/data/docs/science_and_technology/chemistry/combustion/n_heptane_v3.1_therm.dat
     37:        https://www-pls.llnl.gov/data/docs/science_and_technology/chemistry/combustion/nc7_ver3.1_mech.txt

     39: */
     40: typedef struct _User *User;
     41: struct _User {
     42:   PetscReal pressure;
     43:   int       Nspec;
     44:   int       Nreac;
     45:   PetscReal Tini;
     46:   double    *tchemwork;
     47:   double    *Jdense;        /* Dense array workspace where Tchem computes the Jacobian */
     48:   PetscInt  *rows;
     49:   char      **snames;
     50: };

     52: static PetscErrorCode PrintSpecies(User,Vec);
     53: static PetscErrorCode MassFractionToMoleFraction(User,Vec,Vec*);
     54: static PetscErrorCode MoleFractionToMassFraction(User,Vec,Vec*);
     55: static PetscErrorCode FormRHSFunction(TS,PetscReal,Vec,Vec,void*);
     56: static PetscErrorCode FormRHSJacobian(TS,PetscReal,Vec,Mat,Mat,void*);
     57: static PetscErrorCode FormInitialSolution(TS,Vec,void*);
     58: static PetscErrorCode ComputeMassConservation(Vec,PetscReal*,void*);
     59: static PetscErrorCode MonitorMassConservation(TS,PetscInt,PetscReal,Vec,void*);
     60: static PetscErrorCode MonitorTempature(TS,PetscInt,PetscReal,Vec,void*);

     64: int main(int argc,char **argv)
     65: {
     66:   TS                ts;         /* time integrator */
     67:   TSAdapt           adapt;
     68:   Vec               X,lambda;          /* solution vector */
     69:   Mat               J;          /* Jacobian matrix */
     70:   PetscInt          steps;
     71:   PetscErrorCode    ierr;
     72:   PetscReal         ftime,dt;
     73:   char              chemfile[PETSC_MAX_PATH_LEN],thermofile[PETSC_MAX_PATH_LEN],lchemfile[PETSC_MAX_PATH_LEN],lthermofile[PETSC_MAX_PATH_LEN],lperiodic[PETSC_MAX_PATH_LEN];
     74:   const char        *periodic = "file://${PETSC_DIR}/${PETSC_ARCH}/share/periodictable.dat";
     75:   struct _User      user;       /* user-defined work context */
     76:   TSConvergedReason reason;
     77:   char              **snames,*names;
     78:   PetscInt          i;
     79:   TSTrajectory      tj;
     80:   PetscBool         flg = PETSC_FALSE,tflg = PETSC_FALSE,found;

     82:   PetscInitialize(&argc,&argv,(char*)0,help);
     83:   PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Chemistry solver options","");
     84:   PetscOptionsString("-chem","CHEMKIN input file","",chemfile,chemfile,sizeof(chemfile),NULL);
     85:   PetscFileRetrieve(PETSC_COMM_WORLD,chemfile,lchemfile,PETSC_MAX_PATH_LEN,&found);
     87:   PetscOptionsString("-thermo","NASA thermo input file","",thermofile,thermofile,sizeof(thermofile),NULL);
     88:   PetscFileRetrieve(PETSC_COMM_WORLD,thermofile,lthermofile,PETSC_MAX_PATH_LEN,&found);
     90:   user.pressure = 1.01325e5;    /* Pascal */
     91:   PetscOptionsReal("-pressure","Pressure of reaction [Pa]","",user.pressure,&user.pressure,NULL);
     92:   user.Tini = 1000;             /* Kelvin */
     93:   PetscOptionsReal("-Tini","Initial temperature [K]","",user.Tini,&user.Tini,NULL);
     94:   PetscOptionsBool("-monitor_mass","Monitor the total mass at each timestep","",flg,&flg,NULL);
     95:   PetscOptionsBool("-monitor_temp","Monitor the temperature each timestep","",tflg,&tflg,NULL);
     96:   PetscOptionsEnd();

     98:   /* tchem requires periodic table in current directory */
     99:   PetscFileRetrieve(PETSC_COMM_WORLD,periodic,lperiodic,PETSC_MAX_PATH_LEN,&found);

    102:   TC_initChem(lchemfile, lthermofile, 0, 1.0);
    103:   TC_setThermoPres(user.pressure);
    104:   user.Nspec = TC_getNspec();
    105:   user.Nreac = TC_getNreac();
    106:   /*
    107:       Get names of all species in easy to use array
    108:   */
    109:   PetscMalloc1((user.Nspec+1)*LENGTHOFSPECNAME,&names);
    110:   PetscStrcpy(names,"Temp");
    111:   TC_getSnames(user.Nspec,names+LENGTHOFSPECNAME);
    112:   PetscMalloc1((user.Nspec+2),&snames);
    113:   for (i=0; i<user.Nspec+1; i++) snames[i] = names+i*LENGTHOFSPECNAME;
    114:   snames[user.Nspec+1] = NULL;
    115:   PetscStrArrayallocpy((const char *const *)snames,&user.snames);
    116:   PetscFree(snames);
    117:   PetscFree(names);

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

    122:   /* MatCreateSeqAIJ(PETSC_COMM_SELF,user.Nspec+1,user.Nspec+1,PETSC_DECIDE,NULL,&J); */
    123:   MatCreateSeqDense(PETSC_COMM_SELF,user.Nspec+1,user.Nspec+1,NULL,&J);
    124:   MatSetFromOptions(J);

    126:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    127:      Create timestepping solver context
    128:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    129:   TSCreate(PETSC_COMM_WORLD,&ts);
    130:   TSSetType(ts,TSARKIMEX);
    131:   TSARKIMEXSetFullyImplicit(ts,PETSC_TRUE);
    132:   TSARKIMEXSetType(ts,TSARKIMEX4);
    133:   TSSetRHSFunction(ts,NULL,FormRHSFunction,&user);
    134:   TSSetRHSJacobian(ts,J,J,FormRHSJacobian,&user);

    136:   if (flg) {
    137:     TSMonitorSet(ts,MonitorMassConservation,NULL,NULL);
    138:   }
    139:   if (tflg) {
    140:     TSMonitorSet(ts,MonitorTempature,&user,NULL);
    141:   }

    143:   ftime = 1.0;
    144:   TSSetMaxTime(ts,ftime);
    145:   TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);

    147:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    148:      Set initial conditions
    149:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    150:   FormInitialSolution(ts,X,&user);
    151:   TSSetSolution(ts,X);
    152:   dt   = 1e-10;                 /* Initial time step */
    153:   TSSetTimeStep(ts,dt);
    154:   TSGetAdapt(ts,&adapt);
    155:   TSAdaptSetStepLimits(adapt,1e-12,1e-4); /* Also available with -ts_adapt_dt_min/-ts_adapt_dt_max */
    156:   TSSetMaxSNESFailures(ts,-1);            /* Retry step an unlimited number of times */

    158:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    159:      Set runtime options
    160:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    161:   TSSetFromOptions(ts);

    163:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    164:      Set final conditions for sensitivities
    165:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    166:   VecDuplicate(X,&lambda);
    167:   TSSetCostGradients(ts,1,&lambda,NULL);
    168:   VecSetValue(lambda,0,1.0,INSERT_VALUES);
    169:   VecAssemblyBegin(lambda);
    170:   VecAssemblyEnd(lambda);

    172:   TSGetTrajectory(ts,&tj);
    173:   if (tj) {
    174:     TSTrajectorySetVariableNames(tj,(const char * const *)user.snames);
    175:     TSTrajectorySetTransform(tj,(PetscErrorCode (*)(void*,Vec,Vec*))MassFractionToMoleFraction,NULL,&user);
    176:   }

    178:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    179:      Pass information to graphical monitoring routine
    180:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    181:   TSMonitorLGSetVariableNames(ts,(const char * const *)user.snames);
    182:   TSMonitorLGSetTransform(ts,(PetscErrorCode (*)(void*,Vec,Vec*))MassFractionToMoleFraction,NULL,&user);

    184:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    185:      Solve ODE
    186:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    187:   TSSolve(ts,X);
    188:   TSGetSolveTime(ts,&ftime);
    189:   TSGetStepNumber(ts,&steps);
    190:   TSGetConvergedReason(ts,&reason);
    191:   PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],(double)ftime,steps);

    193:   /* {
    194:     Vec                max;
    195:     PetscInt           i;
    196:     const PetscReal    *bmax;

    198:     TSMonitorEnvelopeGetBounds(ts,&max,NULL);
    199:     if (max) {
    200:       VecGetArrayRead(max,&bmax);
    201:       PetscPrintf(PETSC_COMM_SELF,"Species - maximum mass fraction\n");
    202:       for (i=1; i<user.Nspec; i++) {
    203:         if (bmax[i] > .01) PetscPrintf(PETSC_COMM_SELF,"%s %g\n",user.snames[i],(double)bmax[i]);
    204:       }
    205:       VecRestoreArrayRead(max,&bmax);
    206:     }
    207:   }

    209:   Vec y;
    210:   MassFractionToMoleFraction(&user,X,&y);
    211:   PrintSpecies(&user,y);
    212:   VecDestroy(&y); */

    214:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    215:      Free work space.
    216:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    217:   TC_reset();
    218:   PetscStrArrayDestroy(&user.snames);
    219:   MatDestroy(&J);
    220:   VecDestroy(&X);
    221:   VecDestroy(&lambda);
    222:   TSDestroy(&ts);
    223:   PetscFree3(user.tchemwork,user.Jdense,user.rows);
    224:   PetscFinalize();
    225:   return 0;
    226: }

    228: static PetscErrorCode FormRHSFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr)
    229: {
    230:   User              user = (User)ptr;
    231:   PetscScalar       *f;
    232:   const PetscScalar *x;

    235:   VecGetArrayRead(X,&x);
    236:   VecGetArray(F,&f);

    238:   PetscArraycpy(user->tchemwork,x,user->Nspec+1);
    239:   user->tchemwork[0] *= user->Tini; /* Dimensionalize */
    240:   TC_getSrc(user->tchemwork,user->Nspec+1,f);
    241:   f[0] /= user->Tini;           /* Non-dimensionalize */

    243:   VecRestoreArrayRead(X,&x);
    244:   VecRestoreArray(F,&f);
    245:   return 0;
    246: }

    248: static PetscErrorCode FormRHSJacobian(TS ts,PetscReal t,Vec X,Mat Amat,Mat Pmat,void *ptr)
    249: {
    250:   User              user = (User)ptr;
    251:   const PetscScalar *x;
    252:   PetscInt          M = user->Nspec+1,i;

    255:   VecGetArrayRead(X,&x);
    256:   PetscArraycpy(user->tchemwork,x,user->Nspec+1);
    257:   VecRestoreArrayRead(X,&x);
    258:   user->tchemwork[0] *= user->Tini;  /* Dimensionalize temperature (first row) because that is what Tchem wants */
    259:   TC_getJacTYN(user->tchemwork,user->Nspec,user->Jdense,1);

    261:   for (i=0; i<M; i++) user->Jdense[i + 0*M] /= user->Tini; /* Non-dimensionalize first column */
    262:   for (i=0; i<M; i++) user->Jdense[0 + i*M] /= user->Tini; /* Non-dimensionalize first row */
    263:   for (i=0; i<M; i++) user->rows[i] = i;
    264:   MatSetOption(Pmat,MAT_ROW_ORIENTED,PETSC_FALSE);
    265:   MatSetOption(Pmat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE);
    266:   MatZeroEntries(Pmat);
    267:   MatSetValues(Pmat,M,user->rows,M,user->rows,user->Jdense,INSERT_VALUES);

    269:   MatAssemblyBegin(Pmat,MAT_FINAL_ASSEMBLY);
    270:   MatAssemblyEnd(Pmat,MAT_FINAL_ASSEMBLY);
    271:   if (Amat != Pmat) {
    272:     MatAssemblyBegin(Amat,MAT_FINAL_ASSEMBLY);
    273:     MatAssemblyEnd(Amat,MAT_FINAL_ASSEMBLY);
    274:   }
    275:   return 0;
    276: }

    278: PetscErrorCode FormInitialSolution(TS ts,Vec X,void *ctx)
    279: {
    280:   PetscScalar    *x;
    281:   PetscInt       i;
    282:   Vec            y;
    283:   const PetscInt maxspecies = 10;
    284:   PetscInt       smax = maxspecies,mmax = maxspecies;
    285:   char           *names[maxspecies];
    286:   PetscReal      molefracs[maxspecies],sum;
    287:   PetscBool      flg;

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

    294:   PetscOptionsGetStringArray(NULL,NULL,"-initial_species",names,&smax,&flg);
    296:   PetscOptionsGetRealArray(NULL,NULL,"-initial_mole",molefracs,&mmax,&flg);
    298:   sum = 0;
    299:   for (i=0; i<smax; i++) sum += molefracs[i];
    300:   for (i=0; i<smax; i++) molefracs[i] = molefracs[i]/sum;
    301:   for (i=0; i<smax; i++) {
    302:     int ispec = TC_getSpos(names[i], strlen(names[i]));
    304:     PetscPrintf(PETSC_COMM_SELF,"Species %d: %s %g\n",i,names[i],molefracs[i]);
    305:     x[1+ispec] = molefracs[i];
    306:   }
    307:   for (i=0; i<smax; i++) {
    308:     PetscFree(names[i]);
    309:   }
    310:   VecRestoreArray(X,&x);
    311:   /* PrintSpecies((User)ctx,X); */
    312:   MoleFractionToMassFraction((User)ctx,X,&y);
    313:   VecCopy(y,X);
    314:   VecDestroy(&y);
    315:   return 0;
    316: }

    318: /*
    319:    Converts the input vector which is in mass fractions (used by tchem) to mole fractions
    320: */
    321: PetscErrorCode MassFractionToMoleFraction(User user,Vec massf,Vec *molef)
    322: {
    323:   PetscScalar       *mof;
    324:   const PetscScalar *maf;

    326:   VecDuplicate(massf,molef);
    327:   VecGetArrayRead(massf,&maf);
    328:   VecGetArray(*molef,&mof);
    329:   mof[0] = maf[0]; /* copy over temperature */
    330:   TC_getMs2Ml((double*)maf+1,user->Nspec,mof+1);
    331:   VecRestoreArray(*molef,&mof);
    332:   VecRestoreArrayRead(massf,&maf);
    333:   return 0;
    334: }

    336: /*
    337:    Converts the input vector which is in mole fractions to mass fractions (used by tchem)
    338: */
    339: PetscErrorCode MoleFractionToMassFraction(User user,Vec molef,Vec *massf)
    340: {
    341:   const PetscScalar *mof;
    342:   PetscScalar       *maf;

    344:   VecDuplicate(molef,massf);
    345:   VecGetArrayRead(molef,&mof);
    346:   VecGetArray(*massf,&maf);
    347:   maf[0] = mof[0]; /* copy over temperature */
    348:   TC_getMl2Ms((double*)mof+1,user->Nspec,maf+1);
    349:   VecRestoreArrayRead(molef,&mof);
    350:   VecRestoreArray(*massf,&maf);
    351:   return 0;
    352: }

    354: PetscErrorCode ComputeMassConservation(Vec x,PetscReal *mass,void* ctx)
    355: {
    356:   VecSum(x,mass);
    357:   return 0;
    358: }

    360: PetscErrorCode MonitorMassConservation(TS ts,PetscInt step,PetscReal time,Vec x,void* ctx)
    361: {
    362:   const PetscScalar  *T;
    363:   PetscReal          mass;

    365:   ComputeMassConservation(x,&mass,ctx);
    366:   VecGetArrayRead(x,&T);
    367:   mass -= PetscAbsScalar(T[0]);
    368:   VecRestoreArrayRead(x,&T);
    369:   PetscPrintf(PETSC_COMM_WORLD,"Timestep %D time %g percent mass lost or gained %g\n",step,(double)time,(double)100.*(1.0 - mass));
    370:   return 0;
    371: }

    373: PetscErrorCode MonitorTempature(TS ts,PetscInt step,PetscReal time,Vec x,void* ctx)
    374: {
    375:   User               user = (User) ctx;
    376:   const PetscScalar  *T;

    378:   VecGetArrayRead(x,&T);
    379:   PetscPrintf(PETSC_COMM_WORLD,"Timestep %D time %g temperature %g\n",step,(double)time,(double)T[0]*user->Tini);
    380:   VecRestoreArrayRead(x,&T);
    381:   return 0;
    382: }

    384: /*
    385:    Prints out each species with its name
    386: */
    387: PETSC_UNUSED PetscErrorCode PrintSpecies(User user,Vec molef)
    388: {
    389:   const PetscScalar *mof;
    390:   PetscInt          i,*idx,n = user->Nspec+1;

    392:   PetscMalloc1(n,&idx);
    393:   for (i=0; i<n;i++) idx[i] = i;
    394:   VecGetArrayRead(molef,&mof);
    395:   PetscSortRealWithPermutation(n,mof,idx);
    396:   for (i=0; i<n; i++) {
    397:     PetscPrintf(PETSC_COMM_SELF,"%6s %g\n",user->snames[idx[n-i-1]],mof[idx[n-i-1]]);
    398:   }
    399:   PetscFree(idx);
    400:   VecRestoreArrayRead(molef,&mof);
    401:   return 0;
    402: }

    404: /*TEST
    405:     build:
    406:       requires: tchem

    408:     test:
    409:       args: -chem http://combustion.berkeley.edu/gri_mech/version30/files30/grimech30.dat -thermo http://combustion.berkeley.edu/gri_mech/version30/files30/thermo30.dat -initial_species CH4,O2,N2,AR -initial_mole 0.0948178320887,0.189635664177,0.706766236705,0.00878026702874 -Tini 1500 -Tini 1500 -ts_arkimex_fully_implicit -ts_max_snes_failures -1  -ts_adapt_dt_max 1e-4 -ts_arkimex_type 4 -ts_max_time .005
    410:       requires: !single
    411:       filter: grep -v iterations

    413: TEST*/