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) \ 63 do { PetscCheck(!ierr, PETSC_COMM_SELF, PETSC_ERR_LIB, "Error in TChem library, return code %d", ierr); } while (0) 64 65 int main(int argc, char **argv) { 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 PetscFunctionBeginUser; 82 PetscCall(PetscInitialize(&argc, &argv, (char *)0, help)); 83 PetscOptionsBegin(PETSC_COMM_WORLD, NULL, "Chemistry solver options", ""); 84 PetscCall(PetscOptionsString("-chem", "CHEMKIN input file", "", chemfile, chemfile, sizeof(chemfile), NULL)); 85 PetscCall(PetscFileRetrieve(PETSC_COMM_WORLD, chemfile, lchemfile, PETSC_MAX_PATH_LEN, &found)); 86 PetscCheck(found, PETSC_COMM_WORLD, PETSC_ERR_FILE_OPEN, "Cannot download %s and no local version %s", chemfile, lchemfile); 87 PetscCall(PetscOptionsString("-thermo", "NASA thermo input file", "", thermofile, thermofile, sizeof(thermofile), NULL)); 88 PetscCall(PetscFileRetrieve(PETSC_COMM_WORLD, thermofile, lthermofile, PETSC_MAX_PATH_LEN, &found)); 89 PetscCheck(found, PETSC_COMM_WORLD, PETSC_ERR_FILE_OPEN, "Cannot download %s and no local version %s", thermofile, lthermofile); 90 user.pressure = 1.01325e5; /* Pascal */ 91 PetscCall(PetscOptionsReal("-pressure", "Pressure of reaction [Pa]", "", user.pressure, &user.pressure, NULL)); 92 user.Tini = 1000; /* Kelvin */ 93 PetscCall(PetscOptionsReal("-Tini", "Initial temperature [K]", "", user.Tini, &user.Tini, NULL)); 94 PetscCall(PetscOptionsBool("-monitor_mass", "Monitor the total mass at each timestep", "", flg, &flg, NULL)); 95 PetscCall(PetscOptionsBool("-monitor_temp", "Monitor the temperature each timestep", "", tflg, &tflg, NULL)); 96 PetscOptionsEnd(); 97 98 /* tchem requires periodic table in current directory */ 99 PetscCall(PetscFileRetrieve(PETSC_COMM_WORLD, periodic, lperiodic, PETSC_MAX_PATH_LEN, &found)); 100 PetscCheck(found, PETSC_COMM_WORLD, PETSC_ERR_FILE_OPEN, "Cannot located required periodic table %s or local version %s", periodic, lperiodic); 101 102 PetscCallTC(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 PetscCall(PetscMalloc1((user.Nspec + 1) * LENGTHOFSPECNAME, &names)); 110 PetscCall(PetscStrcpy(names, "Temp")); 111 TC_getSnames(user.Nspec, names + LENGTHOFSPECNAME); 112 PetscCall(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 PetscCall(PetscStrArrayallocpy((const char *const *)snames, &user.snames)); 116 PetscCall(PetscFree(snames)); 117 PetscCall(PetscFree(names)); 118 119 PetscCall(PetscMalloc3(user.Nspec + 1, &user.tchemwork, PetscSqr(user.Nspec + 1), &user.Jdense, user.Nspec + 1, &user.rows)); 120 PetscCall(VecCreateSeq(PETSC_COMM_SELF, user.Nspec + 1, &X)); 121 122 /* PetscCall(MatCreateSeqAIJ(PETSC_COMM_SELF,user.Nspec+1,user.Nspec+1,PETSC_DECIDE,NULL,&J)); */ 123 PetscCall(MatCreateSeqDense(PETSC_COMM_SELF, user.Nspec + 1, user.Nspec + 1, NULL, &J)); 124 PetscCall(MatSetFromOptions(J)); 125 126 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 127 Create timestepping solver context 128 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 129 PetscCall(TSCreate(PETSC_COMM_WORLD, &ts)); 130 PetscCall(TSSetType(ts, TSARKIMEX)); 131 PetscCall(TSARKIMEXSetFullyImplicit(ts, PETSC_TRUE)); 132 PetscCall(TSARKIMEXSetType(ts, TSARKIMEX4)); 133 PetscCall(TSSetRHSFunction(ts, NULL, FormRHSFunction, &user)); 134 PetscCall(TSSetRHSJacobian(ts, J, J, FormRHSJacobian, &user)); 135 136 if (flg) PetscCall(TSMonitorSet(ts, MonitorMassConservation, NULL, NULL)); 137 if (tflg) PetscCall(TSMonitorSet(ts, MonitorTempature, &user, NULL)); 138 139 ftime = 1.0; 140 PetscCall(TSSetMaxTime(ts, ftime)); 141 PetscCall(TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER)); 142 143 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 144 Set initial conditions 145 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 146 PetscCall(FormInitialSolution(ts, X, &user)); 147 PetscCall(TSSetSolution(ts, X)); 148 dt = 1e-10; /* Initial time step */ 149 PetscCall(TSSetTimeStep(ts, dt)); 150 PetscCall(TSGetAdapt(ts, &adapt)); 151 PetscCall(TSAdaptSetStepLimits(adapt, 1e-12, 1e-4)); /* Also available with -ts_adapt_dt_min/-ts_adapt_dt_max */ 152 PetscCall(TSSetMaxSNESFailures(ts, -1)); /* Retry step an unlimited number of times */ 153 154 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 155 Set runtime options 156 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 157 PetscCall(TSSetFromOptions(ts)); 158 159 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 160 Set final conditions for sensitivities 161 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 162 PetscCall(VecDuplicate(X, &lambda)); 163 PetscCall(TSSetCostGradients(ts, 1, &lambda, NULL)); 164 PetscCall(VecSetValue(lambda, 0, 1.0, INSERT_VALUES)); 165 PetscCall(VecAssemblyBegin(lambda)); 166 PetscCall(VecAssemblyEnd(lambda)); 167 168 PetscCall(TSGetTrajectory(ts, &tj)); 169 if (tj) { 170 PetscCall(TSTrajectorySetVariableNames(tj, (const char *const *)user.snames)); 171 PetscCall(TSTrajectorySetTransform(tj, (PetscErrorCode(*)(void *, Vec, Vec *))MassFractionToMoleFraction, NULL, &user)); 172 } 173 174 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 175 Pass information to graphical monitoring routine 176 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 177 PetscCall(TSMonitorLGSetVariableNames(ts, (const char *const *)user.snames)); 178 PetscCall(TSMonitorLGSetTransform(ts, (PetscErrorCode(*)(void *, Vec, Vec *))MassFractionToMoleFraction, NULL, &user)); 179 180 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 181 Solve ODE 182 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 183 PetscCall(TSSolve(ts, X)); 184 PetscCall(TSGetSolveTime(ts, &ftime)); 185 PetscCall(TSGetStepNumber(ts, &steps)); 186 PetscCall(TSGetConvergedReason(ts, &reason)); 187 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%s at time %g after %" PetscInt_FMT " steps\n", TSConvergedReasons[reason], (double)ftime, steps)); 188 189 /* { 190 Vec max; 191 PetscInt i; 192 const PetscReal *bmax; 193 194 PetscCall(TSMonitorEnvelopeGetBounds(ts,&max,NULL)); 195 if (max) { 196 PetscCall(VecGetArrayRead(max,&bmax)); 197 PetscCall(PetscPrintf(PETSC_COMM_SELF,"Species - maximum mass fraction\n")); 198 for (i=1; i<user.Nspec; i++) { 199 if (bmax[i] > .01) PetscCall(PetscPrintf(PETSC_COMM_SELF,"%s %g\n",user.snames[i],(double)bmax[i])); 200 } 201 PetscCall(VecRestoreArrayRead(max,&bmax)); 202 } 203 } 204 205 Vec y; 206 PetscCall(MassFractionToMoleFraction(&user,X,&y)); 207 PetscCall(PrintSpecies(&user,y)); 208 PetscCall(VecDestroy(&y)); */ 209 210 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 211 Free work space. 212 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ 213 TC_reset(); 214 PetscCall(PetscStrArrayDestroy(&user.snames)); 215 PetscCall(MatDestroy(&J)); 216 PetscCall(VecDestroy(&X)); 217 PetscCall(VecDestroy(&lambda)); 218 PetscCall(TSDestroy(&ts)); 219 PetscCall(PetscFree3(user.tchemwork, user.Jdense, user.rows)); 220 PetscCall(PetscFinalize()); 221 return 0; 222 } 223 224 static PetscErrorCode FormRHSFunction(TS ts, PetscReal t, Vec X, Vec F, void *ptr) { 225 User user = (User)ptr; 226 PetscScalar *f; 227 const PetscScalar *x; 228 229 PetscFunctionBeginUser; 230 PetscCall(VecGetArrayRead(X, &x)); 231 PetscCall(VecGetArray(F, &f)); 232 233 PetscCall(PetscArraycpy(user->tchemwork, x, user->Nspec + 1)); 234 user->tchemwork[0] *= user->Tini; /* Dimensionalize */ 235 PetscCallTC(TC_getSrc(user->tchemwork, user->Nspec + 1, f)); 236 f[0] /= user->Tini; /* Non-dimensionalize */ 237 238 PetscCall(VecRestoreArrayRead(X, &x)); 239 PetscCall(VecRestoreArray(F, &f)); 240 PetscFunctionReturn(0); 241 } 242 243 static PetscErrorCode FormRHSJacobian(TS ts, PetscReal t, Vec X, Mat Amat, Mat Pmat, void *ptr) { 244 User user = (User)ptr; 245 const PetscScalar *x; 246 PetscInt M = user->Nspec + 1, i; 247 248 PetscFunctionBeginUser; 249 PetscCall(VecGetArrayRead(X, &x)); 250 PetscCall(PetscArraycpy(user->tchemwork, x, user->Nspec + 1)); 251 PetscCall(VecRestoreArrayRead(X, &x)); 252 user->tchemwork[0] *= user->Tini; /* Dimensionalize temperature (first row) because that is what Tchem wants */ 253 PetscCall(TC_getJacTYN(user->tchemwork, user->Nspec, user->Jdense, 1)); 254 255 for (i = 0; i < M; i++) user->Jdense[i + 0 * M] /= user->Tini; /* Non-dimensionalize first column */ 256 for (i = 0; i < M; i++) user->Jdense[0 + i * M] /= user->Tini; /* Non-dimensionalize first row */ 257 for (i = 0; i < M; i++) user->rows[i] = i; 258 PetscCall(MatSetOption(Pmat, MAT_ROW_ORIENTED, PETSC_FALSE)); 259 PetscCall(MatSetOption(Pmat, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE)); 260 PetscCall(MatZeroEntries(Pmat)); 261 PetscCall(MatSetValues(Pmat, M, user->rows, M, user->rows, user->Jdense, INSERT_VALUES)); 262 263 PetscCall(MatAssemblyBegin(Pmat, MAT_FINAL_ASSEMBLY)); 264 PetscCall(MatAssemblyEnd(Pmat, MAT_FINAL_ASSEMBLY)); 265 if (Amat != Pmat) { 266 PetscCall(MatAssemblyBegin(Amat, MAT_FINAL_ASSEMBLY)); 267 PetscCall(MatAssemblyEnd(Amat, MAT_FINAL_ASSEMBLY)); 268 } 269 PetscFunctionReturn(0); 270 } 271 272 PetscErrorCode FormInitialSolution(TS ts, Vec X, void *ctx) { 273 PetscScalar *x; 274 PetscInt i; 275 Vec y; 276 const PetscInt maxspecies = 10; 277 PetscInt smax = maxspecies, mmax = maxspecies; 278 char *names[maxspecies]; 279 PetscReal molefracs[maxspecies], sum; 280 PetscBool flg; 281 282 PetscFunctionBeginUser; 283 PetscCall(VecZeroEntries(X)); 284 PetscCall(VecGetArray(X, &x)); 285 x[0] = 1.0; /* Non-dimensionalized by user->Tini */ 286 287 PetscCall(PetscOptionsGetStringArray(NULL, NULL, "-initial_species", names, &smax, &flg)); 288 PetscCheck(smax >= 2, PETSC_COMM_SELF, PETSC_ERR_USER, "Must provide at least two initial species"); 289 PetscCall(PetscOptionsGetRealArray(NULL, NULL, "-initial_mole", molefracs, &mmax, &flg)); 290 PetscCheck(smax == mmax, PETSC_COMM_SELF, PETSC_ERR_USER, "Must provide same number of initial species %" PetscInt_FMT " as initial moles %" PetscInt_FMT, smax, mmax); 291 sum = 0; 292 for (i = 0; i < smax; i++) sum += molefracs[i]; 293 for (i = 0; i < smax; i++) molefracs[i] = molefracs[i] / sum; 294 for (i = 0; i < smax; i++) { 295 int ispec = TC_getSpos(names[i], strlen(names[i])); 296 PetscCheck(ispec >= 0, PETSC_COMM_SELF, PETSC_ERR_USER, "Could not find species %s", names[i]); 297 PetscCall(PetscPrintf(PETSC_COMM_SELF, "Species %" PetscInt_FMT ": %s %g\n", i, names[i], (double)molefracs[i])); 298 x[1 + ispec] = molefracs[i]; 299 } 300 for (i = 0; i < smax; i++) PetscCall(PetscFree(names[i])); 301 PetscCall(VecRestoreArray(X, &x)); 302 /* PetscCall(PrintSpecies((User)ctx,X)); */ 303 PetscCall(MoleFractionToMassFraction((User)ctx, X, &y)); 304 PetscCall(VecCopy(y, X)); 305 PetscCall(VecDestroy(&y)); 306 PetscFunctionReturn(0); 307 } 308 309 /* 310 Converts the input vector which is in mass fractions (used by tchem) to mole fractions 311 */ 312 PetscErrorCode MassFractionToMoleFraction(User user, Vec massf, Vec *molef) { 313 PetscScalar *mof; 314 const PetscScalar *maf; 315 316 PetscFunctionBeginUser; 317 PetscCall(VecDuplicate(massf, molef)); 318 PetscCall(VecGetArrayRead(massf, &maf)); 319 PetscCall(VecGetArray(*molef, &mof)); 320 mof[0] = maf[0]; /* copy over temperature */ 321 TC_getMs2Ml((double *)maf + 1, user->Nspec, mof + 1); 322 PetscCall(VecRestoreArray(*molef, &mof)); 323 PetscCall(VecRestoreArrayRead(massf, &maf)); 324 PetscFunctionReturn(0); 325 } 326 327 /* 328 Converts the input vector which is in mole fractions to mass fractions (used by tchem) 329 */ 330 PetscErrorCode MoleFractionToMassFraction(User user, Vec molef, Vec *massf) { 331 const PetscScalar *mof; 332 PetscScalar *maf; 333 334 PetscFunctionBeginUser; 335 PetscCall(VecDuplicate(molef, massf)); 336 PetscCall(VecGetArrayRead(molef, &mof)); 337 PetscCall(VecGetArray(*massf, &maf)); 338 maf[0] = mof[0]; /* copy over temperature */ 339 TC_getMl2Ms((double *)mof + 1, user->Nspec, maf + 1); 340 PetscCall(VecRestoreArrayRead(molef, &mof)); 341 PetscCall(VecRestoreArray(*massf, &maf)); 342 PetscFunctionReturn(0); 343 } 344 345 PetscErrorCode ComputeMassConservation(Vec x, PetscReal *mass, void *ctx) { 346 PetscFunctionBeginUser; 347 PetscCall(VecSum(x, mass)); 348 PetscFunctionReturn(0); 349 } 350 351 PetscErrorCode MonitorMassConservation(TS ts, PetscInt step, PetscReal time, Vec x, void *ctx) { 352 const PetscScalar *T; 353 PetscReal mass; 354 355 PetscFunctionBeginUser; 356 PetscCall(ComputeMassConservation(x, &mass, ctx)); 357 PetscCall(VecGetArrayRead(x, &T)); 358 mass -= PetscAbsScalar(T[0]); 359 PetscCall(VecRestoreArrayRead(x, &T)); 360 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Timestep %" PetscInt_FMT " time %g percent mass lost or gained %g\n", step, (double)time, (double)(100. * (1.0 - mass)))); 361 PetscFunctionReturn(0); 362 } 363 364 PetscErrorCode MonitorTempature(TS ts, PetscInt step, PetscReal time, Vec x, void *ctx) { 365 User user = (User)ctx; 366 const PetscScalar *T; 367 368 PetscFunctionBeginUser; 369 PetscCall(VecGetArrayRead(x, &T)); 370 PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Timestep %" PetscInt_FMT " time %g temperature %g\n", step, (double)time, (double)(T[0] * user->Tini))); 371 PetscCall(VecRestoreArrayRead(x, &T)); 372 PetscFunctionReturn(0); 373 } 374 375 /* 376 Prints out each species with its name 377 */ 378 PETSC_UNUSED PetscErrorCode PrintSpecies(User user, Vec molef) { 379 const PetscScalar *mof; 380 PetscInt i, *idx, n = user->Nspec + 1; 381 382 PetscFunctionBeginUser; 383 PetscCall(PetscMalloc1(n, &idx)); 384 for (i = 0; i < n; i++) idx[i] = i; 385 PetscCall(VecGetArrayRead(molef, &mof)); 386 PetscCall(PetscSortRealWithPermutation(n, mof, idx)); 387 for (i = 0; i < n; i++) PetscCall(PetscPrintf(PETSC_COMM_SELF, "%6s %g\n", user->snames[idx[n - i - 1]], (double)PetscRealPart(mof[idx[n - i - 1]]))); 388 PetscCall(PetscFree(idx)); 389 PetscCall(VecRestoreArrayRead(molef, &mof)); 390 PetscFunctionReturn(0); 391 } 392 393 /*TEST 394 build: 395 requires: tchem 396 397 test: 398 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 .005 399 requires: !single 400 filter: grep -v iterations 401 402 TEST*/ 403