1 static const char help[] = "Integrate chemistry using TChem.\n"; 2 3 #include <petscts.h> 4 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 19 20 See also h2_10sp.inp for another example 21 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 24 25 The solution for component i = 0 is the temperature. 26 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 28 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])) 32 33 FormMoleFraction(User,massf,molef) converts the mass fraction solution of each species to the mole fraction of each species. 34 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 38 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 }; 51 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*); 61 62 #define PetscCallTC(ierr) do {PetscCheck(!ierr,PETSC_COMM_SELF,PETSC_ERR_LIB,"Error in TChem library, return code %d",ierr);} while (0) 63 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 PetscReal ftime,dt; 72 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]; 73 const char *periodic = "file://${PETSC_DIR}/${PETSC_ARCH}/share/periodictable.dat"; 74 struct _User user; /* user-defined work context */ 75 TSConvergedReason reason; 76 char **snames,*names; 77 PetscInt i; 78 TSTrajectory tj; 79 PetscBool flg = PETSC_FALSE,tflg = PETSC_FALSE,found; 80 81 PetscCall(PetscInitialize(&argc,&argv,(char*)0,help)); 82 PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Chemistry solver options",""); 83 PetscCall(PetscOptionsString("-chem","CHEMKIN input file","",chemfile,chemfile,sizeof(chemfile),NULL)); 84 PetscCall(PetscFileRetrieve(PETSC_COMM_WORLD,chemfile,lchemfile,PETSC_MAX_PATH_LEN,&found)); 85 PetscCheck(found,PETSC_COMM_WORLD,PETSC_ERR_FILE_OPEN,"Cannot download %s and no local version %s",chemfile,lchemfile); 86 PetscCall(PetscOptionsString("-thermo","NASA thermo input file","",thermofile,thermofile,sizeof(thermofile),NULL)); 87 PetscCall(PetscFileRetrieve(PETSC_COMM_WORLD,thermofile,lthermofile,PETSC_MAX_PATH_LEN,&found)); 88 PetscCheck(found,PETSC_COMM_WORLD,PETSC_ERR_FILE_OPEN,"Cannot download %s and no local version %s",thermofile,lthermofile); 89 user.pressure = 1.01325e5; /* Pascal */ 90 PetscCall(PetscOptionsReal("-pressure","Pressure of reaction [Pa]","",user.pressure,&user.pressure,NULL)); 91 user.Tini = 1000; /* Kelvin */ 92 PetscCall(PetscOptionsReal("-Tini","Initial temperature [K]","",user.Tini,&user.Tini,NULL)); 93 PetscCall(PetscOptionsBool("-monitor_mass","Monitor the total mass at each timestep","",flg,&flg,NULL)); 94 PetscCall(PetscOptionsBool("-monitor_temp","Monitor the temperature each timestep","",tflg,&tflg,NULL)); 95 PetscOptionsEnd(); 96 97 /* tchem requires periodic table in current directory */ 98 PetscCall(PetscFileRetrieve(PETSC_COMM_WORLD,periodic,lperiodic,PETSC_MAX_PATH_LEN,&found)); 99 PetscCheck(found,PETSC_COMM_WORLD,PETSC_ERR_FILE_OPEN,"Cannot located required periodic table %s or local version %s",periodic,lperiodic); 100 101 PetscCallTC(TC_initChem(lchemfile, lthermofile, 0, 1.0)); 102 TC_setThermoPres(user.pressure); 103 user.Nspec = TC_getNspec(); 104 user.Nreac = TC_getNreac(); 105 /* 106 Get names of all species in easy to use array 107 */ 108 PetscCall(PetscMalloc1((user.Nspec+1)*LENGTHOFSPECNAME,&names)); 109 PetscCall(PetscStrcpy(names,"Temp")); 110 TC_getSnames(user.Nspec,names+LENGTHOFSPECNAME); 111 PetscCall(PetscMalloc1((user.Nspec+2),&snames)); 112 for (i=0; i<user.Nspec+1; i++) snames[i] = names+i*LENGTHOFSPECNAME; 113 snames[user.Nspec+1] = NULL; 114 PetscCall(PetscStrArrayallocpy((const char *const *)snames,&user.snames)); 115 PetscCall(PetscFree(snames)); 116 PetscCall(PetscFree(names)); 117 118 PetscCall(PetscMalloc3(user.Nspec+1,&user.tchemwork,PetscSqr(user.Nspec+1),&user.Jdense,user.Nspec+1,&user.rows)); 119 PetscCall(VecCreateSeq(PETSC_COMM_SELF,user.Nspec+1,&X)); 120 121 /* PetscCall(MatCreateSeqAIJ(PETSC_COMM_SELF,user.Nspec+1,user.Nspec+1,PETSC_DECIDE,NULL,&J)); */ 122 PetscCall(MatCreateSeqDense(PETSC_COMM_SELF,user.Nspec+1,user.Nspec+1,NULL,&J)); 123 PetscCall(MatSetFromOptions(J)); 124 125 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 126 Create timestepping solver context 127 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 128 PetscCall(TSCreate(PETSC_COMM_WORLD,&ts)); 129 PetscCall(TSSetType(ts,TSARKIMEX)); 130 PetscCall(TSARKIMEXSetFullyImplicit(ts,PETSC_TRUE)); 131 PetscCall(TSARKIMEXSetType(ts,TSARKIMEX4)); 132 PetscCall(TSSetRHSFunction(ts,NULL,FormRHSFunction,&user)); 133 PetscCall(TSSetRHSJacobian(ts,J,J,FormRHSJacobian,&user)); 134 135 if (flg) { 136 PetscCall(TSMonitorSet(ts,MonitorMassConservation,NULL,NULL)); 137 } 138 if (tflg) { 139 PetscCall(TSMonitorSet(ts,MonitorTempature,&user,NULL)); 140 } 141 142 ftime = 1.0; 143 PetscCall(TSSetMaxTime(ts,ftime)); 144 PetscCall(TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER)); 145 146 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 147 Set initial conditions 148 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 149 PetscCall(FormInitialSolution(ts,X,&user)); 150 PetscCall(TSSetSolution(ts,X)); 151 dt = 1e-10; /* Initial time step */ 152 PetscCall(TSSetTimeStep(ts,dt)); 153 PetscCall(TSGetAdapt(ts,&adapt)); 154 PetscCall(TSAdaptSetStepLimits(adapt,1e-12,1e-4)); /* Also available with -ts_adapt_dt_min/-ts_adapt_dt_max */ 155 PetscCall(TSSetMaxSNESFailures(ts,-1)); /* Retry step an unlimited number of times */ 156 157 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 158 Set runtime options 159 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 160 PetscCall(TSSetFromOptions(ts)); 161 162 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 163 Set final conditions for sensitivities 164 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 165 PetscCall(VecDuplicate(X,&lambda)); 166 PetscCall(TSSetCostGradients(ts,1,&lambda,NULL)); 167 PetscCall(VecSetValue(lambda,0,1.0,INSERT_VALUES)); 168 PetscCall(VecAssemblyBegin(lambda)); 169 PetscCall(VecAssemblyEnd(lambda)); 170 171 PetscCall(TSGetTrajectory(ts,&tj)); 172 if (tj) { 173 PetscCall(TSTrajectorySetVariableNames(tj,(const char * const *)user.snames)); 174 PetscCall(TSTrajectorySetTransform(tj,(PetscErrorCode (*)(void*,Vec,Vec*))MassFractionToMoleFraction,NULL,&user)); 175 } 176 177 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 178 Pass information to graphical monitoring routine 179 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 180 PetscCall(TSMonitorLGSetVariableNames(ts,(const char * const *)user.snames)); 181 PetscCall(TSMonitorLGSetTransform(ts,(PetscErrorCode (*)(void*,Vec,Vec*))MassFractionToMoleFraction,NULL,&user)); 182 183 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 184 Solve ODE 185 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 186 PetscCall(TSSolve(ts,X)); 187 PetscCall(TSGetSolveTime(ts,&ftime)); 188 PetscCall(TSGetStepNumber(ts,&steps)); 189 PetscCall(TSGetConvergedReason(ts,&reason)); 190 PetscCall(PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],(double)ftime,steps)); 191 192 /* { 193 Vec max; 194 PetscInt i; 195 const PetscReal *bmax; 196 197 PetscCall(TSMonitorEnvelopeGetBounds(ts,&max,NULL)); 198 if (max) { 199 PetscCall(VecGetArrayRead(max,&bmax)); 200 PetscCall(PetscPrintf(PETSC_COMM_SELF,"Species - maximum mass fraction\n")); 201 for (i=1; i<user.Nspec; i++) { 202 if (bmax[i] > .01) PetscCall(PetscPrintf(PETSC_COMM_SELF,"%s %g\n",user.snames[i],(double)bmax[i])); 203 } 204 PetscCall(VecRestoreArrayRead(max,&bmax)); 205 } 206 } 207 208 Vec y; 209 PetscCall(MassFractionToMoleFraction(&user,X,&y)); 210 PetscCall(PrintSpecies(&user,y)); 211 PetscCall(VecDestroy(&y)); */ 212 213 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 214 Free work space. 215 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 216 TC_reset(); 217 PetscCall(PetscStrArrayDestroy(&user.snames)); 218 PetscCall(MatDestroy(&J)); 219 PetscCall(VecDestroy(&X)); 220 PetscCall(VecDestroy(&lambda)); 221 PetscCall(TSDestroy(&ts)); 222 PetscCall(PetscFree3(user.tchemwork,user.Jdense,user.rows)); 223 PetscCall(PetscFinalize()); 224 return 0; 225 } 226 227 static PetscErrorCode FormRHSFunction(TS ts,PetscReal t,Vec X,Vec F,void *ptr) 228 { 229 User user = (User)ptr; 230 PetscScalar *f; 231 const PetscScalar *x; 232 233 PetscFunctionBeginUser; 234 PetscCall(VecGetArrayRead(X,&x)); 235 PetscCall(VecGetArray(F,&f)); 236 237 PetscCall(PetscArraycpy(user->tchemwork,x,user->Nspec+1)); 238 user->tchemwork[0] *= user->Tini; /* Dimensionalize */ 239 PetscCallTC(TC_getSrc(user->tchemwork,user->Nspec+1,f)); 240 f[0] /= user->Tini; /* Non-dimensionalize */ 241 242 PetscCall(VecRestoreArrayRead(X,&x)); 243 PetscCall(VecRestoreArray(F,&f)); 244 PetscFunctionReturn(0); 245 } 246 247 static PetscErrorCode FormRHSJacobian(TS ts,PetscReal t,Vec X,Mat Amat,Mat Pmat,void *ptr) 248 { 249 User user = (User)ptr; 250 const PetscScalar *x; 251 PetscInt M = user->Nspec+1,i; 252 253 PetscFunctionBeginUser; 254 PetscCall(VecGetArrayRead(X,&x)); 255 PetscCall(PetscArraycpy(user->tchemwork,x,user->Nspec+1)); 256 PetscCall(VecRestoreArrayRead(X,&x)); 257 user->tchemwork[0] *= user->Tini; /* Dimensionalize temperature (first row) because that is what Tchem wants */ 258 PetscCall(TC_getJacTYN(user->tchemwork,user->Nspec,user->Jdense,1)); 259 260 for (i=0; i<M; i++) user->Jdense[i + 0*M] /= user->Tini; /* Non-dimensionalize first column */ 261 for (i=0; i<M; i++) user->Jdense[0 + i*M] /= user->Tini; /* Non-dimensionalize first row */ 262 for (i=0; i<M; i++) user->rows[i] = i; 263 PetscCall(MatSetOption(Pmat,MAT_ROW_ORIENTED,PETSC_FALSE)); 264 PetscCall(MatSetOption(Pmat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE)); 265 PetscCall(MatZeroEntries(Pmat)); 266 PetscCall(MatSetValues(Pmat,M,user->rows,M,user->rows,user->Jdense,INSERT_VALUES)); 267 268 PetscCall(MatAssemblyBegin(Pmat,MAT_FINAL_ASSEMBLY)); 269 PetscCall(MatAssemblyEnd(Pmat,MAT_FINAL_ASSEMBLY)); 270 if (Amat != Pmat) { 271 PetscCall(MatAssemblyBegin(Amat,MAT_FINAL_ASSEMBLY)); 272 PetscCall(MatAssemblyEnd(Amat,MAT_FINAL_ASSEMBLY)); 273 } 274 PetscFunctionReturn(0); 275 } 276 277 PetscErrorCode FormInitialSolution(TS ts,Vec X,void *ctx) 278 { 279 PetscScalar *x; 280 PetscInt i; 281 Vec y; 282 const PetscInt maxspecies = 10; 283 PetscInt smax = maxspecies,mmax = maxspecies; 284 char *names[maxspecies]; 285 PetscReal molefracs[maxspecies],sum; 286 PetscBool flg; 287 288 PetscFunctionBeginUser; 289 PetscCall(VecZeroEntries(X)); 290 PetscCall(VecGetArray(X,&x)); 291 x[0] = 1.0; /* Non-dimensionalized by user->Tini */ 292 293 PetscCall(PetscOptionsGetStringArray(NULL,NULL,"-initial_species",names,&smax,&flg)); 294 PetscCheck(smax >= 2,PETSC_COMM_SELF,PETSC_ERR_USER,"Must provide at least two initial species"); 295 PetscCall(PetscOptionsGetRealArray(NULL,NULL,"-initial_mole",molefracs,&mmax,&flg)); 296 PetscCheck(smax == mmax,PETSC_COMM_SELF,PETSC_ERR_USER,"Must provide same number of initial species %D as initial moles %D",smax,mmax); 297 sum = 0; 298 for (i=0; i<smax; i++) sum += molefracs[i]; 299 for (i=0; i<smax; i++) molefracs[i] = molefracs[i]/sum; 300 for (i=0; i<smax; i++) { 301 int ispec = TC_getSpos(names[i], strlen(names[i])); 302 PetscCheck(ispec >= 0,PETSC_COMM_SELF,PETSC_ERR_USER,"Could not find species %s",names[i]); 303 PetscCall(PetscPrintf(PETSC_COMM_SELF,"Species %d: %s %g\n",i,names[i],molefracs[i])); 304 x[1+ispec] = molefracs[i]; 305 } 306 for (i=0; i<smax; i++) { 307 PetscCall(PetscFree(names[i])); 308 } 309 PetscCall(VecRestoreArray(X,&x)); 310 /* PetscCall(PrintSpecies((User)ctx,X)); */ 311 PetscCall(MoleFractionToMassFraction((User)ctx,X,&y)); 312 PetscCall(VecCopy(y,X)); 313 PetscCall(VecDestroy(&y)); 314 PetscFunctionReturn(0); 315 } 316 317 /* 318 Converts the input vector which is in mass fractions (used by tchem) to mole fractions 319 */ 320 PetscErrorCode MassFractionToMoleFraction(User user,Vec massf,Vec *molef) 321 { 322 PetscScalar *mof; 323 const PetscScalar *maf; 324 325 PetscFunctionBegin; 326 PetscCall(VecDuplicate(massf,molef)); 327 PetscCall(VecGetArrayRead(massf,&maf)); 328 PetscCall(VecGetArray(*molef,&mof)); 329 mof[0] = maf[0]; /* copy over temperature */ 330 TC_getMs2Ml((double*)maf+1,user->Nspec,mof+1); 331 PetscCall(VecRestoreArray(*molef,&mof)); 332 PetscCall(VecRestoreArrayRead(massf,&maf)); 333 PetscFunctionReturn(0); 334 } 335 336 /* 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; 343 344 PetscFunctionBegin; 345 PetscCall(VecDuplicate(molef,massf)); 346 PetscCall(VecGetArrayRead(molef,&mof)); 347 PetscCall(VecGetArray(*massf,&maf)); 348 maf[0] = mof[0]; /* copy over temperature */ 349 TC_getMl2Ms((double*)mof+1,user->Nspec,maf+1); 350 PetscCall(VecRestoreArrayRead(molef,&mof)); 351 PetscCall(VecRestoreArray(*massf,&maf)); 352 PetscFunctionReturn(0); 353 } 354 355 PetscErrorCode ComputeMassConservation(Vec x,PetscReal *mass,void* ctx) 356 { 357 PetscFunctionBegin; 358 PetscCall(VecSum(x,mass)); 359 PetscFunctionReturn(0); 360 } 361 362 PetscErrorCode MonitorMassConservation(TS ts,PetscInt step,PetscReal time,Vec x,void* ctx) 363 { 364 const PetscScalar *T; 365 PetscReal mass; 366 367 PetscFunctionBegin; 368 PetscCall(ComputeMassConservation(x,&mass,ctx)); 369 PetscCall(VecGetArrayRead(x,&T)); 370 mass -= PetscAbsScalar(T[0]); 371 PetscCall(VecRestoreArrayRead(x,&T)); 372 PetscCall(PetscPrintf(PETSC_COMM_WORLD,"Timestep %D time %g percent mass lost or gained %g\n",step,(double)time,(double)100.*(1.0 - mass))); 373 PetscFunctionReturn(0); 374 } 375 376 PetscErrorCode MonitorTempature(TS ts,PetscInt step,PetscReal time,Vec x,void* ctx) 377 { 378 User user = (User) ctx; 379 const PetscScalar *T; 380 381 PetscFunctionBegin; 382 PetscCall(VecGetArrayRead(x,&T)); 383 PetscCall(PetscPrintf(PETSC_COMM_WORLD,"Timestep %D time %g temperature %g\n",step,(double)time,(double)T[0]*user->Tini)); 384 PetscCall(VecRestoreArrayRead(x,&T)); 385 PetscFunctionReturn(0); 386 } 387 388 /* 389 Prints out each species with its name 390 */ 391 PETSC_UNUSED PetscErrorCode PrintSpecies(User user,Vec molef) 392 { 393 const PetscScalar *mof; 394 PetscInt i,*idx,n = user->Nspec+1; 395 396 PetscFunctionBegin; 397 PetscCall(PetscMalloc1(n,&idx)); 398 for (i=0; i<n;i++) idx[i] = i; 399 PetscCall(VecGetArrayRead(molef,&mof)); 400 PetscCall(PetscSortRealWithPermutation(n,mof,idx)); 401 for (i=0; i<n; i++) { 402 PetscCall(PetscPrintf(PETSC_COMM_SELF,"%6s %g\n",user->snames[idx[n-i-1]],mof[idx[n-i-1]])); 403 } 404 PetscCall(PetscFree(idx)); 405 PetscCall(VecRestoreArrayRead(molef,&mof)); 406 PetscFunctionReturn(0); 407 } 408 409 /*TEST 410 build: 411 requires: tchem 412 413 test: 414 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 .005 415 requires: !single 416 filter: grep -v iterations 417 418 TEST*/ 419