Actual source code: extchem.c
petsc-3.12.4 2020-02-04
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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:     See extchem.example.1 for how to run an example

     20:     See also h2_10sp.inp for another example

     22:     Determine sensitivity of final tempature 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.

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

     41: */
     42: typedef struct _User *User;
     43: struct _User {
     44:   PetscReal pressure;
     45:   int       Nspec;
     46:   int       Nreac;
     47:   PetscReal Tini;
     48:   double    *tchemwork;
     49:   double    *Jdense;        /* Dense array workspace where Tchem computes the Jacobian */
     50:   PetscInt  *rows;
     51:   char      **snames;
     52: };

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

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

     85:   PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
     86:   PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Chemistry solver options","");
     87:   PetscOptionsString("-chem","CHEMKIN input file","",chemfile,chemfile,sizeof(chemfile),NULL);
     88:   PetscFileRetrieve(PETSC_COMM_WORLD,chemfile,lchemfile,PETSC_MAX_PATH_LEN,&found);
     89:   if (!found) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_FILE_OPEN,"Cannot download %s and no local version %s",chemfile,lchemfile);
     90:   PetscOptionsString("-thermo","NASA thermo input file","",thermofile,thermofile,sizeof(thermofile),NULL);
     91:   PetscFileRetrieve(PETSC_COMM_WORLD,thermofile,lthermofile,PETSC_MAX_PATH_LEN,&found);
     92:   if (!found) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_FILE_OPEN,"Cannot download %s and no local version %s",thermofile,lthermofile);
     93:   user.pressure = 1.01325e5;    /* Pascal */
     94:   PetscOptionsReal("-pressure","Pressure of reaction [Pa]","",user.pressure,&user.pressure,NULL);
     95:   user.Tini = 1000;             /* Kelvin */
     96:   PetscOptionsReal("-Tini","Initial temperature [K]","",user.Tini,&user.Tini,NULL);
     97:   PetscOptionsBool("-monitor_mass","Monitor the total mass at each timestep","",flg,&flg,NULL);
     98:   PetscOptionsBool("-monitor_temp","Monitor the tempature each timestep","",tflg,&tflg,NULL);
     99:   PetscOptionsEnd();

    101:   /* tchem requires periodic table in current directory */
    102:   PetscFileRetrieve(PETSC_COMM_WORLD,periodic,lperiodic,PETSC_MAX_PATH_LEN,&found);
    103:   if (!found) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_FILE_OPEN,"Cannot located required periodic table %s or local version %s",periodic,lperiodic);

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

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

    125:   /* MatCreateSeqAIJ(PETSC_COMM_SELF,user.Nspec+1,user.Nspec+1,PETSC_DECIDE,NULL,&J); */
    126:   MatCreateSeqDense(PETSC_COMM_SELF,user.Nspec+1,user.Nspec+1,NULL,&J);
    127:   MatSetFromOptions(J);

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

    139:   if (flg) {
    140:     TSMonitorSet(ts,MonitorMassConservation,NULL,NULL);
    141:   }
    142:   if (tflg) {
    143:     TSMonitorSet(ts,MonitorTempature,&user,NULL);
    144:   }

    146:   ftime = 1.0;
    147:   TSSetMaxTime(ts,ftime);
    148:   TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);

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

    161:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    162:      Set runtime options
    163:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    164:   TSSetFromOptions(ts);

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

    175:   TSGetTrajectory(ts,&tj);
    176:   if (tj) {
    177:     TSTrajectorySetVariableNames(tj,(const char * const *)user.snames);
    178:     TSTrajectorySetTransform(tj,(PetscErrorCode (*)(void*,Vec,Vec*))MassFractionToMoleFraction,NULL,&user);
    179:   }

    182:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    183:      Pass information to graphical monitoring routine
    184:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    185:   TSMonitorLGSetVariableNames(ts,(const char * const *)user.snames);
    186:   TSMonitorLGSetTransform(ts,(PetscErrorCode (*)(void*,Vec,Vec*))MassFractionToMoleFraction,NULL,&user);

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

    197:   /* {
    198:     Vec                max;
    199:     PetscInt           i;
    200:     const PetscReal    *bmax;

    202:     TSMonitorEnvelopeGetBounds(ts,&max,NULL);
    203:     if (max) {
    204:       VecGetArrayRead(max,&bmax);
    205:       PetscPrintf(PETSC_COMM_SELF,"Species - maximum mass fraction\n");
    206:       for (i=1; i<user.Nspec; i++) {
    207:         if (bmax[i] > .01) {PetscPrintf(PETSC_COMM_SELF,"%s %g\n",user.snames[i],(double)bmax[i]);}
    208:       }
    209:       VecRestoreArrayRead(max,&bmax);
    210:     }
    211:   }

    213:   Vec y;
    214:   MassFractionToMoleFraction(&user,X,&y);
    215:   PrintSpecies(&user,y);
    216:   VecDestroy(&y); */

    218:   /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    219:      Free work space.
    220:    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    221:   TC_reset();
    222:   PetscStrArrayDestroy(&user.snames);
    223:   MatDestroy(&J);
    224:   VecDestroy(&X);
    225:   VecDestroy(&lambda);
    226:   TSDestroy(&ts);
    227:   PetscFree3(user.tchemwork,user.Jdense,user.rows);
    228:   PetscFinalize();
    229:   return ierr;
    230: }

    232: static PetscErrorCode FormRHSFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr)
    233: {
    234:   User              user = (User)ptr;
    235:   PetscErrorCode    ierr;
    236:   PetscScalar       *f;
    237:   const PetscScalar *x;

    240:   VecGetArrayRead(X,&x);
    241:   VecGetArray(F,&f);

    243:   PetscArraycpy(user->tchemwork,x,user->Nspec+1);
    244:   user->tchemwork[0] *= user->Tini; /* Dimensionalize */
    245:   TC_getSrc(user->tchemwork,user->Nspec+1,f);TC
    246:   f[0] /= user->Tini;           /* Non-dimensionalize */

    248:   VecRestoreArrayRead(X,&x);
    249:   VecRestoreArray(F,&f);
    250:   return(0);
    251: }

    253: static PetscErrorCode FormRHSJacobian(TS ts,PetscReal t,Vec X,Mat Amat,Mat Pmat,void *ptr)
    254: {
    255:   User              user = (User)ptr;
    256:   PetscErrorCode    ierr;
    257:   const PetscScalar *x;
    258:   PetscInt          M = user->Nspec+1,i;

    261:   VecGetArrayRead(X,&x);
    262:   PetscArraycpy(user->tchemwork,x,user->Nspec+1);
    263:   VecRestoreArrayRead(X,&x);
    264:   user->tchemwork[0] *= user->Tini;  /* Dimensionalize temperature (first row) because that is what Tchem wants */
    265:   TC_getJacTYN(user->tchemwork,user->Nspec,user->Jdense,1);

    267:   for (i=0; i<M; i++) user->Jdense[i + 0*M] /= user->Tini; /* Non-dimensionalize first column */
    268:   for (i=0; i<M; i++) user->Jdense[0 + i*M] /= user->Tini; /* Non-dimensionalize first row */
    269:   for (i=0; i<M; i++) user->rows[i] = i;
    270:   MatSetOption(Pmat,MAT_ROW_ORIENTED,PETSC_FALSE);
    271:   MatSetOption(Pmat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE);
    272:   MatZeroEntries(Pmat);
    273:   MatSetValues(Pmat,M,user->rows,M,user->rows,user->Jdense,INSERT_VALUES);

    275:   MatAssemblyBegin(Pmat,MAT_FINAL_ASSEMBLY);
    276:   MatAssemblyEnd(Pmat,MAT_FINAL_ASSEMBLY);
    277:   if (Amat != Pmat) {
    278:     MatAssemblyBegin(Amat,MAT_FINAL_ASSEMBLY);
    279:     MatAssemblyEnd(Amat,MAT_FINAL_ASSEMBLY);
    280:   }
    281:   return(0);
    282: }

    284: PetscErrorCode FormInitialSolution(TS ts,Vec X,void *ctx)
    285: {
    286:   PetscScalar    *x;
    288:   PetscInt       i;
    289:   Vec            y;
    290:   const PetscInt maxspecies = 10;
    291:   PetscInt       smax = maxspecies,mmax = maxspecies;
    292:   char           *names[maxspecies];
    293:   PetscReal      molefracs[maxspecies],sum;
    294:   PetscBool      flg;

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

    301:   PetscOptionsGetStringArray(NULL,NULL,"-initial_species",names,&smax,&flg);
    302:   if (smax < 2) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Must provide at least two initial species");
    303:   PetscOptionsGetRealArray(NULL,NULL,"-initial_mole",molefracs,&mmax,&flg);
    304:   if (smax != mmax) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_USER,"Must provide same number of initial species %D as initial moles %D",smax,mmax);
    305:   sum = 0;
    306:   for (i=0; i<smax; i++) sum += molefracs[i];
    307:   for (i=0; i<smax; i++) molefracs[i] = molefracs[i]/sum;
    308:   for (i=0; i<smax; i++) {
    309:     int ispec = TC_getSpos(names[i], strlen(names[i]));
    310:     if (ispec < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_USER,"Could not find species %s",names[i]);
    311:     PetscPrintf(PETSC_COMM_SELF,"Species %d: %s %g\n",i,names[i],molefracs[i]);
    312:     x[1+ispec] = molefracs[i];
    313:   }
    314:   for (i=0; i<smax; i++) {
    315:     PetscFree(names[i]);
    316:   }
    317:   VecRestoreArray(X,&x);
    318:   /* PrintSpecies((User)ctx,X); */
    319:   MoleFractionToMassFraction((User)ctx,X,&y);
    320:   VecCopy(y,X);
    321:   VecDestroy(&y);
    322:   return(0);
    323: }

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

    335:   VecDuplicate(massf,molef);
    336:   VecGetArrayRead(massf,&maf);
    337:   VecGetArray(*molef,&mof);
    338:   mof[0] = maf[0]; /* copy over temperature */
    339:   TC_getMs2Ml((double*)maf+1,user->Nspec,mof+1);
    340:   VecRestoreArray(*molef,&mof);
    341:   VecRestoreArrayRead(massf,&maf);
    342:   return(0);
    343: }

    345: /*
    346:    Converts the input vector which is in mole fractions to mass fractions (used by tchem)
    347: */
    348: PetscErrorCode MoleFractionToMassFraction(User user,Vec molef,Vec *massf)
    349: {
    350:   PetscErrorCode    ierr;
    351:   const PetscScalar *mof;
    352:   PetscScalar       *maf;

    355:   VecDuplicate(molef,massf);
    356:   VecGetArrayRead(molef,&mof);
    357:   VecGetArray(*massf,&maf);
    358:   maf[0] = mof[0]; /* copy over temperature */
    359:   TC_getMl2Ms((double*)mof+1,user->Nspec,maf+1);
    360:   VecRestoreArrayRead(molef,&mof);
    361:   VecRestoreArray(*massf,&maf);
    362:   return(0);
    363: }

    365: PetscErrorCode ComputeMassConservation(Vec x,PetscReal *mass,void* ctx)
    366: {

    370:   VecSum(x,mass);
    371:   return(0);
    372: }

    374: PetscErrorCode MonitorMassConservation(TS ts,PetscInt step,PetscReal time,Vec x,void* ctx)
    375: {
    376:   const PetscScalar  *T;
    377:   PetscReal          mass;
    378:   PetscErrorCode     ierr;

    381:   ComputeMassConservation(x,&mass,ctx);
    382:   VecGetArrayRead(x,&T);
    383:   mass -= PetscAbsScalar(T[0]);
    384:   VecRestoreArrayRead(x,&T);
    385:   PetscPrintf(PETSC_COMM_WORLD,"Timestep %D time %g percent mass lost or gained %g\n",step,(double)time,(double)100.*(1.0 - mass));
    386:   return(0);
    387: }

    389: PetscErrorCode MonitorTempature(TS ts,PetscInt step,PetscReal time,Vec x,void* ctx)
    390: {
    391:   User               user = (User) ctx;
    392:   const PetscScalar  *T;
    393:   PetscErrorCode     ierr;

    396:   VecGetArrayRead(x,&T);
    397:   PetscPrintf(PETSC_COMM_WORLD,"Timestep %D time %g tempature %g\n",step,(double)time,(double)T[0]*user->Tini);
    398:   VecRestoreArrayRead(x,&T);
    399:   return(0);
    400: }

    402: /*
    403:    Prints out each species with its name
    404: */
    405: PETSC_UNUSED PetscErrorCode PrintSpecies(User user,Vec molef)
    406: {
    407:   PetscErrorCode    ierr;
    408:   const PetscScalar *mof;
    409:   PetscInt          i,*idx,n = user->Nspec+1;

    412:   PetscMalloc1(n,&idx);
    413:   for (i=0; i<n;i++) idx[i] = i;
    414:   VecGetArrayRead(molef,&mof);
    415:   PetscSortRealWithPermutation(n,mof,idx);
    416:   for (i=0; i<n; i++) {
    417:     PetscPrintf(PETSC_COMM_SELF,"%6s %g\n",user->snames[idx[n-i-1]],mof[idx[n-i-1]]);
    418:   }
    419:   PetscFree(idx);
    420:   VecRestoreArrayRead(molef,&mof);
    421:   return(0);
    422: }

    424: /*TEST
    425:     build:
    426:       requires: tchem

    428:     test:
    429:       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
    430:       requires: !single
    431:       filter: grep -v iterations

    433: TEST*/