Actual source code: ex10.c

      1: /*
      2:   This example implements the model described in

      4:     Rauenzahn, Mousseau, Knoll. "Temporal accuracy of the nonequilibrium radiation diffusion
      5:     equations employing a Saha ionization model" 2005.

      7:   The paper discusses three examples, the first two are nondimensional with a simple
      8:   ionization model.  The third example is fully dimensional and uses the Saha ionization
      9:   model with realistic parameters.
     10: */

     12: #include <petscts.h>
     13: #include <petscdm.h>
     14: #include <petscdmda.h>

     16: typedef enum {
     17:   BC_DIRICHLET,
     18:   BC_NEUMANN,
     19:   BC_ROBIN
     20: } BCType;
     21: static const char *const BCTypes[] = {"DIRICHLET", "NEUMANN", "ROBIN", "BCType", "BC_", 0};
     22: typedef enum {
     23:   JACOBIAN_ANALYTIC,
     24:   JACOBIAN_MATRIXFREE,
     25:   JACOBIAN_FD_COLORING,
     26:   JACOBIAN_FD_FULL
     27: } JacobianType;
     28: static const char *const JacobianTypes[] = {"ANALYTIC", "MATRIXFREE", "FD_COLORING", "FD_FULL", "JacobianType", "FD_", 0};
     29: typedef enum {
     30:   DISCRETIZATION_FD,
     31:   DISCRETIZATION_FE
     32: } DiscretizationType;
     33: static const char *const DiscretizationTypes[] = {"FD", "FE", "DiscretizationType", "DISCRETIZATION_", 0};
     34: typedef enum {
     35:   QUADRATURE_GAUSS1,
     36:   QUADRATURE_GAUSS2,
     37:   QUADRATURE_GAUSS3,
     38:   QUADRATURE_GAUSS4,
     39:   QUADRATURE_LOBATTO2,
     40:   QUADRATURE_LOBATTO3
     41: } QuadratureType;
     42: static const char *const QuadratureTypes[] = {"GAUSS1", "GAUSS2", "GAUSS3", "GAUSS4", "LOBATTO2", "LOBATTO3", "QuadratureType", "QUADRATURE_", 0};

     44: typedef struct {
     45:   PetscScalar E; /* radiation energy */
     46:   PetscScalar T; /* material temperature */
     47: } RDNode;

     49: typedef struct {
     50:   PetscReal meter, kilogram, second, Kelvin; /* Fundamental units */
     51:   PetscReal Joule, Watt;                     /* Derived units */
     52: } RDUnit;

     54: typedef struct _n_RD *RD;

     56: struct _n_RD {
     57:   void (*MaterialEnergy)(RD, const RDNode *, PetscScalar *, RDNode *);
     58:   DM                 da;
     59:   PetscBool          monitor_residual;
     60:   DiscretizationType discretization;
     61:   QuadratureType     quadrature;
     62:   JacobianType       jacobian;
     63:   PetscInt           initial;
     64:   BCType             leftbc;
     65:   PetscBool          view_draw;
     66:   char               view_binary[PETSC_MAX_PATH_LEN];
     67:   PetscBool          test_diff;
     68:   PetscBool          endpoint;
     69:   PetscBool          bclimit;
     70:   PetscBool          bcmidpoint;
     71:   RDUnit             unit;

     73:   /* model constants, see Table 2 and RDCreate() */
     74:   PetscReal rho, K_R, K_p, I_H, m_p, m_e, h, k, c, sigma_b, beta, gamma;

     76:   /* Domain and boundary conditions */
     77:   PetscReal Eapplied; /* Radiation flux from the left */
     78:   PetscReal L;        /* Length of domain */
     79:   PetscReal final_time;
     80: };

     82: static PetscErrorCode RDDestroy(RD *rd)
     83: {
     84:   PetscFunctionBeginUser;
     85:   PetscCall(DMDestroy(&(*rd)->da));
     86:   PetscCall(PetscFree(*rd));
     87:   PetscFunctionReturn(PETSC_SUCCESS);
     88: }

     90: /* The paper has a time derivative for material energy (Eq 2) which is a dependent variable (computable from temperature
     91:  * and density through an uninvertible relation).  Computing this derivative is trivial for trapezoid rule (used in the
     92:  * paper), but does not generalize nicely to higher order integrators.  Here we use the implicit form which provides
     93:  * time derivatives of the independent variables (radiation energy and temperature), so we must compute the time
     94:  * derivative of material energy ourselves (could be done using AD).
     95:  *
     96:  * There are multiple ionization models, this interface dispatches to the one currently in use.
     97:  */
     98: static void RDMaterialEnergy(RD rd, const RDNode *n, PetscScalar *Em, RDNode *dEm)
     99: {
    100:   rd->MaterialEnergy(rd, n, Em, dEm);
    101: }

    103: /* Solves a quadratic equation while propagating tangents */
    104: static void QuadraticSolve(PetscScalar a, PetscScalar a_t, PetscScalar b, PetscScalar b_t, PetscScalar c, PetscScalar c_t, PetscScalar *x, PetscScalar *x_t)
    105: {
    106:   PetscScalar disc = b * b - 4. * a * c, disc_t = 2. * b * b_t - 4. * a_t * c - 4. * a * c_t, num = -b + PetscSqrtScalar(disc), /* choose positive sign */
    107:     num_t = -b_t + 0.5 / PetscSqrtScalar(disc) * disc_t, den = 2. * a, den_t = 2. * a_t;
    108:   *x   = num / den;
    109:   *x_t = (num_t * den - num * den_t) / PetscSqr(den);
    110: }

    112: /* The primary model presented in the paper */
    113: static void RDMaterialEnergy_Saha(RD rd, const RDNode *n, PetscScalar *inEm, RDNode *dEm)
    114: {
    115:   PetscScalar Em, alpha, alpha_t, T = n->T, T_t = 1., chi = rd->I_H / (rd->k * T), chi_t = -chi / T * T_t, a = 1., a_t = 0, b = 4. * rd->m_p / rd->rho * PetscPowScalarReal(2. * PETSC_PI * rd->m_e * rd->I_H / PetscSqr(rd->h), 1.5) * PetscExpScalar(-chi) * PetscPowScalarReal(chi, 1.5), /* Eq 7 */
    116:     b_t = -b * chi_t + 1.5 * b / chi * chi_t, c = -b, c_t = -b_t;
    117:   QuadraticSolve(a, a_t, b, b_t, c, c_t, &alpha, &alpha_t);      /* Solve Eq 7 for alpha */
    118:   Em = rd->k * T / rd->m_p * (1.5 * (1. + alpha) + alpha * chi); /* Eq 6 */
    119:   if (inEm) *inEm = Em;
    120:   if (dEm) {
    121:     dEm->E = 0;
    122:     dEm->T = Em / T * T_t + rd->k * T / rd->m_p * (1.5 * alpha_t + alpha_t * chi + alpha * chi_t);
    123:   }
    124: }
    125: /* Reduced ionization model, Eq 30 */
    126: static void RDMaterialEnergy_Reduced(RD rd, const RDNode *n, PetscScalar *Em, RDNode *dEm)
    127: {
    128:   PetscScalar alpha, alpha_t, T = n->T, T_t = 1., chi = -0.3 / T, chi_t = -chi / T * T_t, a = 1., a_t = 0., b = PetscExpScalar(chi), b_t = b * chi_t, c = -b, c_t = -b_t;
    129:   QuadraticSolve(a, a_t, b, b_t, c, c_t, &alpha, &alpha_t);
    130:   if (Em) *Em = (1. + alpha) * T + 0.3 * alpha;
    131:   if (dEm) {
    132:     dEm->E = 0;
    133:     dEm->T = alpha_t * T + (1. + alpha) * T_t + 0.3 * alpha_t;
    134:   }
    135: }

    137: /* Eq 5 */
    138: static void RDSigma_R(RD rd, RDNode *n, PetscScalar *sigma_R, RDNode *dsigma_R)
    139: {
    140:   *sigma_R    = rd->K_R * rd->rho * PetscPowScalar(n->T, -rd->gamma);
    141:   dsigma_R->E = 0;
    142:   dsigma_R->T = -rd->gamma * (*sigma_R) / n->T;
    143: }

    145: /* Eq 4 */
    146: static void RDDiffusionCoefficient(RD rd, PetscBool limit, RDNode *n, RDNode *nx, PetscScalar *D_R, RDNode *dD_R, RDNode *dxD_R)
    147: {
    148:   PetscScalar sigma_R, denom;
    149:   RDNode      dsigma_R, ddenom, dxdenom;

    151:   RDSigma_R(rd, n, &sigma_R, &dsigma_R);
    152:   denom     = 3. * rd->rho * sigma_R + (int)limit * PetscAbsScalar(nx->E) / n->E;
    153:   ddenom.E  = -(int)limit * PetscAbsScalar(nx->E) / PetscSqr(n->E);
    154:   ddenom.T  = 3. * rd->rho * dsigma_R.T;
    155:   dxdenom.E = (int)limit * (PetscRealPart(nx->E) < 0 ? -1. : 1.) / n->E;
    156:   dxdenom.T = 0;
    157:   *D_R      = rd->c / denom;
    158:   if (dD_R) {
    159:     dD_R->E = -rd->c / PetscSqr(denom) * ddenom.E;
    160:     dD_R->T = -rd->c / PetscSqr(denom) * ddenom.T;
    161:   }
    162:   if (dxD_R) {
    163:     dxD_R->E = -rd->c / PetscSqr(denom) * dxdenom.E;
    164:     dxD_R->T = -rd->c / PetscSqr(denom) * dxdenom.T;
    165:   }
    166: }

    168: static PetscErrorCode RDStateView(RD rd, Vec X, Vec Xdot, Vec F)
    169: {
    170:   DMDALocalInfo info;
    171:   PetscInt      i;
    172:   const RDNode *x, *xdot, *f;
    173:   MPI_Comm      comm;

    175:   PetscFunctionBeginUser;
    176:   PetscCall(PetscObjectGetComm((PetscObject)rd->da, &comm));
    177:   PetscCall(DMDAGetLocalInfo(rd->da, &info));
    178:   PetscCall(DMDAVecGetArrayRead(rd->da, X, (void *)&x));
    179:   PetscCall(DMDAVecGetArrayRead(rd->da, Xdot, (void *)&xdot));
    180:   PetscCall(DMDAVecGetArrayRead(rd->da, F, (void *)&f));
    181:   for (i = info.xs; i < info.xs + info.xm; i++) {
    182:     PetscCall(PetscSynchronizedPrintf(comm, "x[%" PetscInt_FMT "] (%10.2G,%10.2G) (%10.2G,%10.2G) (%10.2G,%10.2G)\n", i, (double)PetscRealPart(x[i].E), (double)PetscRealPart(x[i].T), (double)PetscRealPart(xdot[i].E), (double)PetscRealPart(xdot[i].T),
    183:                                       (double)PetscRealPart(f[i].E), (double)PetscRealPart(f[i].T)));
    184:   }
    185:   PetscCall(DMDAVecRestoreArrayRead(rd->da, X, (void *)&x));
    186:   PetscCall(DMDAVecRestoreArrayRead(rd->da, Xdot, (void *)&xdot));
    187:   PetscCall(DMDAVecRestoreArrayRead(rd->da, F, (void *)&f));
    188:   PetscCall(PetscSynchronizedFlush(comm, PETSC_STDOUT));
    189:   PetscFunctionReturn(PETSC_SUCCESS);
    190: }

    192: static PetscScalar RDRadiation(RD rd, const RDNode *n, RDNode *dn)
    193: {
    194:   PetscScalar sigma_p = rd->K_p * rd->rho * PetscPowScalar(n->T, -rd->beta), sigma_p_T = -rd->beta * sigma_p / n->T, tmp = 4. * rd->sigma_b * PetscSqr(PetscSqr(n->T)) / rd->c - n->E, tmp_E = -1., tmp_T = 4. * rd->sigma_b * 4 * n->T * (PetscSqr(n->T)) / rd->c, rad = sigma_p * rd->c * rd->rho * tmp, rad_E = sigma_p * rd->c * rd->rho * tmp_E, rad_T = rd->c * rd->rho * (sigma_p_T * tmp + sigma_p * tmp_T);
    195:   if (dn) {
    196:     dn->E = rad_E;
    197:     dn->T = rad_T;
    198:   }
    199:   return rad;
    200: }

    202: static PetscScalar RDDiffusion(RD rd, PetscReal hx, const RDNode x[], PetscInt i, RDNode d[])
    203: {
    204:   PetscReal   ihx = 1. / hx;
    205:   RDNode      n_L, nx_L, n_R, nx_R, dD_L, dxD_L, dD_R, dxD_R, dfluxL[2], dfluxR[2];
    206:   PetscScalar D_L, D_R, fluxL, fluxR;

    208:   n_L.E  = 0.5 * (x[i - 1].E + x[i].E);
    209:   n_L.T  = 0.5 * (x[i - 1].T + x[i].T);
    210:   nx_L.E = (x[i].E - x[i - 1].E) / hx;
    211:   nx_L.T = (x[i].T - x[i - 1].T) / hx;
    212:   RDDiffusionCoefficient(rd, PETSC_TRUE, &n_L, &nx_L, &D_L, &dD_L, &dxD_L);
    213:   fluxL       = D_L * nx_L.E;
    214:   dfluxL[0].E = -ihx * D_L + (0.5 * dD_L.E - ihx * dxD_L.E) * nx_L.E;
    215:   dfluxL[1].E = +ihx * D_L + (0.5 * dD_L.E + ihx * dxD_L.E) * nx_L.E;
    216:   dfluxL[0].T = (0.5 * dD_L.T - ihx * dxD_L.T) * nx_L.E;
    217:   dfluxL[1].T = (0.5 * dD_L.T + ihx * dxD_L.T) * nx_L.E;

    219:   n_R.E  = 0.5 * (x[i].E + x[i + 1].E);
    220:   n_R.T  = 0.5 * (x[i].T + x[i + 1].T);
    221:   nx_R.E = (x[i + 1].E - x[i].E) / hx;
    222:   nx_R.T = (x[i + 1].T - x[i].T) / hx;
    223:   RDDiffusionCoefficient(rd, PETSC_TRUE, &n_R, &nx_R, &D_R, &dD_R, &dxD_R);
    224:   fluxR       = D_R * nx_R.E;
    225:   dfluxR[0].E = -ihx * D_R + (0.5 * dD_R.E - ihx * dxD_R.E) * nx_R.E;
    226:   dfluxR[1].E = +ihx * D_R + (0.5 * dD_R.E + ihx * dxD_R.E) * nx_R.E;
    227:   dfluxR[0].T = (0.5 * dD_R.T - ihx * dxD_R.T) * nx_R.E;
    228:   dfluxR[1].T = (0.5 * dD_R.T + ihx * dxD_R.T) * nx_R.E;

    230:   if (d) {
    231:     d[0].E = -ihx * dfluxL[0].E;
    232:     d[0].T = -ihx * dfluxL[0].T;
    233:     d[1].E = ihx * (dfluxR[0].E - dfluxL[1].E);
    234:     d[1].T = ihx * (dfluxR[0].T - dfluxL[1].T);
    235:     d[2].E = ihx * dfluxR[1].E;
    236:     d[2].T = ihx * dfluxR[1].T;
    237:   }
    238:   return ihx * (fluxR - fluxL);
    239: }

    241: static PetscErrorCode RDGetLocalArrays(RD rd, TS ts, Vec X, Vec Xdot, PetscReal *Theta, PetscReal *dt, Vec *X0loc, RDNode **x0, Vec *Xloc, RDNode **x, Vec *Xloc_t, RDNode **xdot)
    242: {
    243:   PetscBool istheta;

    245:   PetscFunctionBeginUser;
    246:   PetscCall(DMGetLocalVector(rd->da, X0loc));
    247:   PetscCall(DMGetLocalVector(rd->da, Xloc));
    248:   PetscCall(DMGetLocalVector(rd->da, Xloc_t));

    250:   PetscCall(DMGlobalToLocalBegin(rd->da, X, INSERT_VALUES, *Xloc));
    251:   PetscCall(DMGlobalToLocalEnd(rd->da, X, INSERT_VALUES, *Xloc));
    252:   PetscCall(DMGlobalToLocalBegin(rd->da, Xdot, INSERT_VALUES, *Xloc_t));
    253:   PetscCall(DMGlobalToLocalEnd(rd->da, Xdot, INSERT_VALUES, *Xloc_t));

    255:   /*
    256:     The following is a hack to subvert TSTHETA which is like an implicit midpoint method to behave more like a trapezoid
    257:     rule.  These methods have equivalent linear stability, but the nonlinear stability is somewhat different.  The
    258:     radiation system is inconvenient to write in explicit form because the ionization model is "on the left".
    259:    */
    260:   PetscCall(PetscObjectTypeCompare((PetscObject)ts, TSTHETA, &istheta));
    261:   if (istheta && rd->endpoint) PetscCall(TSThetaGetTheta(ts, Theta));
    262:   else *Theta = 1.;

    264:   PetscCall(TSGetTimeStep(ts, dt));
    265:   PetscCall(VecWAXPY(*X0loc, -(*Theta) * (*dt), *Xloc_t, *Xloc));     /* back out the value at the start of this step */
    266:   if (rd->endpoint) PetscCall(VecWAXPY(*Xloc, *dt, *Xloc_t, *X0loc)); /* move the abscissa to the end of the step */

    268:   PetscCall(DMDAVecGetArray(rd->da, *X0loc, x0));
    269:   PetscCall(DMDAVecGetArray(rd->da, *Xloc, x));
    270:   PetscCall(DMDAVecGetArray(rd->da, *Xloc_t, xdot));
    271:   PetscFunctionReturn(PETSC_SUCCESS);
    272: }

    274: static PetscErrorCode RDRestoreLocalArrays(RD rd, Vec *X0loc, RDNode **x0, Vec *Xloc, RDNode **x, Vec *Xloc_t, RDNode **xdot)
    275: {
    276:   PetscFunctionBeginUser;
    277:   PetscCall(DMDAVecRestoreArray(rd->da, *X0loc, x0));
    278:   PetscCall(DMDAVecRestoreArray(rd->da, *Xloc, x));
    279:   PetscCall(DMDAVecRestoreArray(rd->da, *Xloc_t, xdot));
    280:   PetscCall(DMRestoreLocalVector(rd->da, X0loc));
    281:   PetscCall(DMRestoreLocalVector(rd->da, Xloc));
    282:   PetscCall(DMRestoreLocalVector(rd->da, Xloc_t));
    283:   PetscFunctionReturn(PETSC_SUCCESS);
    284: }

    286: static PetscErrorCode PETSC_UNUSED RDCheckDomain_Private(RD rd, TS ts, Vec X, PetscBool *in)
    287: {
    288:   PetscInt  minloc;
    289:   PetscReal min;

    291:   PetscFunctionBeginUser;
    292:   PetscCall(VecMin(X, &minloc, &min));
    293:   if (min < 0) {
    294:     SNES snes;
    295:     *in = PETSC_FALSE;
    296:     PetscCall(TSGetSNES(ts, &snes));
    297:     PetscCall(SNESSetFunctionDomainError(snes));
    298:     PetscCall(PetscInfo(ts, "Domain violation at %" PetscInt_FMT " field %" PetscInt_FMT " value %g\n", minloc / 2, minloc % 2, (double)min));
    299:   } else *in = PETSC_TRUE;
    300:   PetscFunctionReturn(PETSC_SUCCESS);
    301: }

    303: /* Energy and temperature must remain positive */
    304: #define RDCheckDomain(rd, ts, X) \
    305:   do { \
    306:     PetscBool _in; \
    307:     PetscCall(RDCheckDomain_Private(rd, ts, X, &_in)); \
    308:     if (!_in) PetscFunctionReturn(PETSC_SUCCESS); \
    309:   } while (0)

    311: static PetscErrorCode RDIFunction_FD(TS ts, PetscReal t, Vec X, Vec Xdot, Vec F, PetscCtx ctx)
    312: {
    313:   RD            rd = (RD)ctx;
    314:   RDNode       *x, *x0, *xdot, *f;
    315:   Vec           X0loc, Xloc, Xloc_t;
    316:   PetscReal     hx, Theta, dt;
    317:   DMDALocalInfo info;
    318:   PetscInt      i;

    320:   PetscFunctionBeginUser;
    321:   PetscCall(RDGetLocalArrays(rd, ts, X, Xdot, &Theta, &dt, &X0loc, &x0, &Xloc, &x, &Xloc_t, &xdot));
    322:   PetscCall(DMDAVecGetArray(rd->da, F, &f));
    323:   PetscCall(DMDAGetLocalInfo(rd->da, &info));
    324:   PetscCall(VecZeroEntries(F));

    326:   hx = rd->L / (info.mx - 1);

    328:   for (i = info.xs; i < info.xs + info.xm; i++) {
    329:     PetscReal   rho = rd->rho;
    330:     PetscScalar Em_t, rad;

    332:     rad = (1. - Theta) * RDRadiation(rd, &x0[i], 0) + Theta * RDRadiation(rd, &x[i], 0);
    333:     if (rd->endpoint) {
    334:       PetscScalar Em0, Em1;
    335:       RDMaterialEnergy(rd, &x0[i], &Em0, NULL);
    336:       RDMaterialEnergy(rd, &x[i], &Em1, NULL);
    337:       Em_t = (Em1 - Em0) / dt;
    338:     } else {
    339:       RDNode dEm;
    340:       RDMaterialEnergy(rd, &x[i], NULL, &dEm);
    341:       Em_t = dEm.E * xdot[i].E + dEm.T * xdot[i].T;
    342:     }
    343:     /* Residuals are multiplied by the volume element (hx).  */
    344:     /* The temperature equation does not have boundary conditions */
    345:     f[i].T = hx * (rho * Em_t + rad);

    347:     if (i == 0) { /* Left boundary condition */
    348:       PetscScalar D_R, bcTheta = rd->bcmidpoint ? Theta : 1.;
    349:       RDNode      n, nx;

    351:       n.E  = (1. - bcTheta) * x0[0].E + bcTheta * x[0].E;
    352:       n.T  = (1. - bcTheta) * x0[0].T + bcTheta * x[0].T;
    353:       nx.E = ((1. - bcTheta) * (x0[1].E - x0[0].E) + bcTheta * (x[1].E - x[0].E)) / hx;
    354:       nx.T = ((1. - bcTheta) * (x0[1].T - x0[0].T) + bcTheta * (x[1].T - x[0].T)) / hx;
    355:       switch (rd->leftbc) {
    356:       case BC_ROBIN:
    357:         RDDiffusionCoefficient(rd, rd->bclimit, &n, &nx, &D_R, 0, 0);
    358:         f[0].E = hx * (n.E - 2. * D_R * nx.E - rd->Eapplied);
    359:         break;
    360:       case BC_NEUMANN:
    361:         f[0].E = x[1].E - x[0].E;
    362:         break;
    363:       default:
    364:         SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Case %" PetscInt_FMT, rd->initial);
    365:       }
    366:     } else if (i == info.mx - 1) {  /* Right boundary */
    367:       f[i].E = x[i].E - x[i - 1].E; /* Homogeneous Neumann */
    368:     } else {
    369:       PetscScalar diff = (1. - Theta) * RDDiffusion(rd, hx, x0, i, 0) + Theta * RDDiffusion(rd, hx, x, i, 0);
    370:       f[i].E           = hx * (xdot[i].E - diff - rad);
    371:     }
    372:   }
    373:   PetscCall(RDRestoreLocalArrays(rd, &X0loc, &x0, &Xloc, &x, &Xloc_t, &xdot));
    374:   PetscCall(DMDAVecRestoreArray(rd->da, F, &f));
    375:   if (rd->monitor_residual) PetscCall(RDStateView(rd, X, Xdot, F));
    376:   PetscFunctionReturn(PETSC_SUCCESS);
    377: }

    379: static PetscErrorCode RDIJacobian_FD(TS ts, PetscReal t, Vec X, Vec Xdot, PetscReal a, Mat A, Mat B, PetscCtx ctx)
    380: {
    381:   RD            rd = (RD)ctx;
    382:   RDNode       *x, *x0, *xdot;
    383:   Vec           X0loc, Xloc, Xloc_t;
    384:   PetscReal     hx, Theta, dt;
    385:   DMDALocalInfo info;
    386:   PetscInt      i;

    388:   PetscFunctionBeginUser;
    389:   PetscCall(RDGetLocalArrays(rd, ts, X, Xdot, &Theta, &dt, &X0loc, &x0, &Xloc, &x, &Xloc_t, &xdot));
    390:   PetscCall(DMDAGetLocalInfo(rd->da, &info));
    391:   hx = rd->L / (info.mx - 1);
    392:   PetscCall(MatZeroEntries(B));

    394:   for (i = info.xs; i < info.xs + info.xm; i++) {
    395:     PetscInt                  col[3];
    396:     PetscReal                 rho = rd->rho;
    397:     PetscScalar /*Em_t,rad,*/ K[2][6];
    398:     RDNode                    dEm_t, drad;

    400:     /*rad = (1.-Theta)* */ RDRadiation(rd, &x0[i], 0); /* + Theta* */
    401:     RDRadiation(rd, &x[i], &drad);

    403:     if (rd->endpoint) {
    404:       PetscScalar Em0, Em1;
    405:       RDNode      dEm1;
    406:       RDMaterialEnergy(rd, &x0[i], &Em0, NULL);
    407:       RDMaterialEnergy(rd, &x[i], &Em1, &dEm1);
    408:       /*Em_t = (Em1 - Em0) / (Theta*dt);*/
    409:       dEm_t.E = dEm1.E / (Theta * dt);
    410:       dEm_t.T = dEm1.T / (Theta * dt);
    411:     } else {
    412:       const PetscScalar epsilon = x[i].T * PETSC_SQRT_MACHINE_EPSILON;
    413:       RDNode            n1;
    414:       RDNode            dEm, dEm1;
    415:       PetscScalar       Em_TT;

    417:       n1.E = x[i].E;
    418:       n1.T = x[i].T + epsilon;
    419:       RDMaterialEnergy(rd, &x[i], NULL, &dEm);
    420:       RDMaterialEnergy(rd, &n1, NULL, &dEm1);
    421:       /* The Jacobian needs another derivative.  We finite difference here instead of
    422:        * propagating second derivatives through the ionization model. */
    423:       Em_TT = (dEm1.T - dEm.T) / epsilon;
    424:       /*Em_t = dEm.E * xdot[i].E + dEm.T * xdot[i].T;*/
    425:       dEm_t.E = dEm.E * a;
    426:       dEm_t.T = dEm.T * a + Em_TT * xdot[i].T;
    427:     }

    429:     PetscCall(PetscMemzero(K, sizeof(K)));
    430:     /* Residuals are multiplied by the volume element (hx).  */
    431:     if (i == 0) {
    432:       PetscScalar D, bcTheta = rd->bcmidpoint ? Theta : 1.;
    433:       RDNode      n, nx;
    434:       RDNode      dD, dxD;

    436:       n.E  = (1. - bcTheta) * x0[0].E + bcTheta * x[0].E;
    437:       n.T  = (1. - bcTheta) * x0[0].T + bcTheta * x[0].T;
    438:       nx.E = ((1. - bcTheta) * (x0[1].E - x0[0].E) + bcTheta * (x[1].E - x[0].E)) / hx;
    439:       nx.T = ((1. - bcTheta) * (x0[1].T - x0[0].T) + bcTheta * (x[1].T - x[0].T)) / hx;
    440:       switch (rd->leftbc) {
    441:       case BC_ROBIN:
    442:         RDDiffusionCoefficient(rd, rd->bclimit, &n, &nx, &D, &dD, &dxD);
    443:         K[0][1 * 2 + 0] = (bcTheta / Theta) * hx * (1. - 2. * D * (-1. / hx) - 2. * nx.E * dD.E + 2. * nx.E * dxD.E / hx);
    444:         K[0][1 * 2 + 1] = (bcTheta / Theta) * hx * (-2. * nx.E * dD.T);
    445:         K[0][2 * 2 + 0] = (bcTheta / Theta) * hx * (-2. * D * (1. / hx) - 2. * nx.E * dD.E - 2. * nx.E * dxD.E / hx);
    446:         break;
    447:       case BC_NEUMANN:
    448:         K[0][1 * 2 + 0] = -1. / Theta;
    449:         K[0][2 * 2 + 0] = 1. / Theta;
    450:         break;
    451:       default:
    452:         SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Case %" PetscInt_FMT, rd->initial);
    453:       }
    454:     } else if (i == info.mx - 1) {
    455:       K[0][0 * 2 + 0] = -1. / Theta;
    456:       K[0][1 * 2 + 0] = 1. / Theta;
    457:     } else {
    458:       /*PetscScalar diff;*/
    459:       RDNode ddiff[3];
    460:       /*diff = (1.-Theta)*RDDiffusion(rd,hx,x0,i,0) + Theta* */ RDDiffusion(rd, hx, x, i, ddiff);
    461:       K[0][0 * 2 + 0] = -hx * ddiff[0].E;
    462:       K[0][0 * 2 + 1] = -hx * ddiff[0].T;
    463:       K[0][1 * 2 + 0] = hx * (a - ddiff[1].E - drad.E);
    464:       K[0][1 * 2 + 1] = hx * (-ddiff[1].T - drad.T);
    465:       K[0][2 * 2 + 0] = -hx * ddiff[2].E;
    466:       K[0][2 * 2 + 1] = -hx * ddiff[2].T;
    467:     }

    469:     K[1][1 * 2 + 0] = hx * (rho * dEm_t.E + drad.E);
    470:     K[1][1 * 2 + 1] = hx * (rho * dEm_t.T + drad.T);

    472:     col[0] = i - 1;
    473:     col[1] = i;
    474:     col[2] = i + 1 < info.mx ? i + 1 : -1;
    475:     PetscCall(MatSetValuesBlocked(B, 1, &i, 3, col, &K[0][0], INSERT_VALUES));
    476:   }
    477:   PetscCall(RDRestoreLocalArrays(rd, &X0loc, &x0, &Xloc, &x, &Xloc_t, &xdot));
    478:   PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY));
    479:   PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY));
    480:   if (A != B) {
    481:     PetscCall(MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY));
    482:     PetscCall(MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY));
    483:   }
    484:   PetscFunctionReturn(PETSC_SUCCESS);
    485: }

    487: /* Evaluate interpolants and derivatives at a select quadrature point */
    488: static void RDEvaluate(PetscReal interp[][2], PetscReal deriv[][2], PetscInt q, const RDNode x[], PetscInt i, RDNode *n, RDNode *nx)
    489: {
    490:   PetscInt j;
    491:   n->E  = 0;
    492:   n->T  = 0;
    493:   nx->E = 0;
    494:   nx->T = 0;
    495:   for (j = 0; j < 2; j++) {
    496:     n->E += interp[q][j] * x[i + j].E;
    497:     n->T += interp[q][j] * x[i + j].T;
    498:     nx->E += deriv[q][j] * x[i + j].E;
    499:     nx->T += deriv[q][j] * x[i + j].T;
    500:   }
    501: }

    503: /*
    504:  Various quadrature rules.  The nonlinear terms are non-polynomial so no standard quadrature will be exact.
    505: */
    506: static PetscErrorCode RDGetQuadrature(RD rd, PetscReal hx, PetscInt *nq, PetscReal weight[], PetscReal interp[][2], PetscReal deriv[][2])
    507: {
    508:   PetscInt         q, j;
    509:   const PetscReal *refweight, (*refinterp)[2], (*refderiv)[2];

    511:   PetscFunctionBeginUser;
    512:   switch (rd->quadrature) {
    513:   case QUADRATURE_GAUSS1: {
    514:     static const PetscReal ww[1]    = {1.};
    515:     static const PetscReal ii[1][2] = {
    516:       {0.5, 0.5}
    517:     };
    518:     static const PetscReal dd[1][2] = {
    519:       {-1., 1.}
    520:     };
    521:     *nq       = 1;
    522:     refweight = ww;
    523:     refinterp = ii;
    524:     refderiv  = dd;
    525:   } break;
    526:   case QUADRATURE_GAUSS2: {
    527:     static const PetscReal ii[2][2] = {
    528:       {0.78867513459481287, 0.21132486540518713},
    529:       {0.21132486540518713, 0.78867513459481287}
    530:     };
    531:     static const PetscReal dd[2][2] = {
    532:       {-1., 1.},
    533:       {-1., 1.}
    534:     };
    535:     static const PetscReal ww[2] = {0.5, 0.5};
    536:     *nq                          = 2;
    537:     refweight                    = ww;
    538:     refinterp                    = ii;
    539:     refderiv                     = dd;
    540:   } break;
    541:   case QUADRATURE_GAUSS3: {
    542:     static const PetscReal ii[3][2] = {
    543:       {0.8872983346207417, 0.1127016653792583},
    544:       {0.5,                0.5               },
    545:       {0.1127016653792583, 0.8872983346207417}
    546:     };
    547:     static const PetscReal dd[3][2] = {
    548:       {-1, 1},
    549:       {-1, 1},
    550:       {-1, 1}
    551:     };
    552:     static const PetscReal ww[3] = {5. / 18, 8. / 18, 5. / 18};
    553:     *nq                          = 3;
    554:     refweight                    = ww;
    555:     refinterp                    = ii;
    556:     refderiv                     = dd;
    557:   } break;
    558:   case QUADRATURE_GAUSS4: {
    559:     static const PetscReal ii[][2] = {
    560:       {0.93056815579702623,  0.069431844202973658},
    561:       {0.66999052179242813,  0.33000947820757187 },
    562:       {0.33000947820757187,  0.66999052179242813 },
    563:       {0.069431844202973658, 0.93056815579702623 }
    564:     };
    565:     static const PetscReal dd[][2] = {
    566:       {-1, 1},
    567:       {-1, 1},
    568:       {-1, 1},
    569:       {-1, 1}
    570:     };
    571:     static const PetscReal ww[] = {0.17392742256872692, 0.3260725774312731, 0.3260725774312731, 0.17392742256872692};

    573:     *nq       = 4;
    574:     refweight = ww;
    575:     refinterp = ii;
    576:     refderiv  = dd;
    577:   } break;
    578:   case QUADRATURE_LOBATTO2: {
    579:     static const PetscReal ii[2][2] = {
    580:       {1., 0.},
    581:       {0., 1.}
    582:     };
    583:     static const PetscReal dd[2][2] = {
    584:       {-1., 1.},
    585:       {-1., 1.}
    586:     };
    587:     static const PetscReal ww[2] = {0.5, 0.5};
    588:     *nq                          = 2;
    589:     refweight                    = ww;
    590:     refinterp                    = ii;
    591:     refderiv                     = dd;
    592:   } break;
    593:   case QUADRATURE_LOBATTO3: {
    594:     static const PetscReal ii[3][2] = {
    595:       {1,   0  },
    596:       {0.5, 0.5},
    597:       {0,   1  }
    598:     };
    599:     static const PetscReal dd[3][2] = {
    600:       {-1, 1},
    601:       {-1, 1},
    602:       {-1, 1}
    603:     };
    604:     static const PetscReal ww[3] = {1. / 6, 4. / 6, 1. / 6};
    605:     *nq                          = 3;
    606:     refweight                    = ww;
    607:     refinterp                    = ii;
    608:     refderiv                     = dd;
    609:   } break;
    610:   default:
    611:     SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Unknown quadrature %d", (int)rd->quadrature);
    612:   }

    614:   for (q = 0; q < *nq; q++) {
    615:     weight[q] = refweight[q] * hx;
    616:     for (j = 0; j < 2; j++) {
    617:       interp[q][j] = refinterp[q][j];
    618:       deriv[q][j]  = refderiv[q][j] / hx;
    619:     }
    620:   }
    621:   PetscFunctionReturn(PETSC_SUCCESS);
    622: }

    624: /*
    625:  Finite element version
    626: */
    627: static PetscErrorCode RDIFunction_FE(TS ts, PetscReal t, Vec X, Vec Xdot, Vec F, PetscCtx ctx)
    628: {
    629:   RD            rd = (RD)ctx;
    630:   RDNode       *x, *x0, *xdot, *f;
    631:   Vec           X0loc, Xloc, Xloc_t, Floc;
    632:   PetscReal     hx, Theta, dt, weight[5], interp[5][2], deriv[5][2];
    633:   DMDALocalInfo info;
    634:   PetscInt      i, j, q, nq;

    636:   PetscFunctionBeginUser;
    637:   PetscCall(RDGetLocalArrays(rd, ts, X, Xdot, &Theta, &dt, &X0loc, &x0, &Xloc, &x, &Xloc_t, &xdot));

    639:   PetscCall(DMGetLocalVector(rd->da, &Floc));
    640:   PetscCall(VecZeroEntries(Floc));
    641:   PetscCall(DMDAVecGetArray(rd->da, Floc, &f));
    642:   PetscCall(DMDAGetLocalInfo(rd->da, &info));

    644:   /* Set up shape functions and quadrature for elements (assumes a uniform grid) */
    645:   hx = rd->L / (info.mx - 1);
    646:   PetscCall(RDGetQuadrature(rd, hx, &nq, weight, interp, deriv));

    648:   for (i = info.xs; i < PetscMin(info.xs + info.xm, info.mx - 1); i++) {
    649:     for (q = 0; q < nq; q++) {
    650:       PetscReal   rho = rd->rho;
    651:       PetscScalar Em_t, rad, D_R, D0_R;
    652:       RDNode      n, n0, nx, n0x, nt, ntx;
    653:       RDEvaluate(interp, deriv, q, x, i, &n, &nx);
    654:       RDEvaluate(interp, deriv, q, x0, i, &n0, &n0x);
    655:       RDEvaluate(interp, deriv, q, xdot, i, &nt, &ntx);

    657:       rad = (1. - Theta) * RDRadiation(rd, &n0, 0) + Theta * RDRadiation(rd, &n, 0);
    658:       if (rd->endpoint) {
    659:         PetscScalar Em0, Em1;
    660:         RDMaterialEnergy(rd, &n0, &Em0, NULL);
    661:         RDMaterialEnergy(rd, &n, &Em1, NULL);
    662:         Em_t = (Em1 - Em0) / dt;
    663:       } else {
    664:         RDNode dEm;
    665:         RDMaterialEnergy(rd, &n, NULL, &dEm);
    666:         Em_t = dEm.E * nt.E + dEm.T * nt.T;
    667:       }
    668:       RDDiffusionCoefficient(rd, PETSC_TRUE, &n0, &n0x, &D0_R, 0, 0);
    669:       RDDiffusionCoefficient(rd, PETSC_TRUE, &n, &nx, &D_R, 0, 0);
    670:       for (j = 0; j < 2; j++) {
    671:         f[i + j].E += (deriv[q][j] * weight[q] * ((1. - Theta) * D0_R * n0x.E + Theta * D_R * nx.E) + interp[q][j] * weight[q] * (nt.E - rad));
    672:         f[i + j].T += interp[q][j] * weight[q] * (rho * Em_t + rad);
    673:       }
    674:     }
    675:   }
    676:   if (info.xs == 0) {
    677:     switch (rd->leftbc) {
    678:     case BC_ROBIN: {
    679:       PetscScalar D_R, D_R_bc;
    680:       PetscReal   ratio, bcTheta = rd->bcmidpoint ? Theta : 1.;
    681:       RDNode      n, nx;

    683:       n.E  = (1 - bcTheta) * x0[0].E + bcTheta * x[0].E;
    684:       n.T  = (1 - bcTheta) * x0[0].T + bcTheta * x[0].T;
    685:       nx.E = (x[1].E - x[0].E) / hx;
    686:       nx.T = (x[1].T - x[0].T) / hx;
    687:       RDDiffusionCoefficient(rd, PETSC_TRUE, &n, &nx, &D_R, 0, 0);
    688:       RDDiffusionCoefficient(rd, rd->bclimit, &n, &nx, &D_R_bc, 0, 0);
    689:       ratio = PetscRealPart(D_R / D_R_bc);
    690:       PetscCheck(ratio <= 1., PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Limited diffusivity is greater than unlimited");
    691:       PetscCheck(ratio >= 1e-3, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Heavily limited diffusivity");
    692:       f[0].E += -ratio * 0.5 * (rd->Eapplied - n.E);
    693:     } break;
    694:     case BC_NEUMANN:
    695:       /* homogeneous Neumann is the natural condition */
    696:       break;
    697:     default:
    698:       SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Case %" PetscInt_FMT, rd->initial);
    699:     }
    700:   }

    702:   PetscCall(RDRestoreLocalArrays(rd, &X0loc, &x0, &Xloc, &x, &Xloc_t, &xdot));
    703:   PetscCall(DMDAVecRestoreArray(rd->da, Floc, &f));
    704:   PetscCall(VecZeroEntries(F));
    705:   PetscCall(DMLocalToGlobalBegin(rd->da, Floc, ADD_VALUES, F));
    706:   PetscCall(DMLocalToGlobalEnd(rd->da, Floc, ADD_VALUES, F));
    707:   PetscCall(DMRestoreLocalVector(rd->da, &Floc));

    709:   if (rd->monitor_residual) PetscCall(RDStateView(rd, X, Xdot, F));
    710:   PetscFunctionReturn(PETSC_SUCCESS);
    711: }

    713: static PetscErrorCode RDIJacobian_FE(TS ts, PetscReal t, Vec X, Vec Xdot, PetscReal a, Mat A, Mat B, PetscCtx ctx)
    714: {
    715:   RD            rd = (RD)ctx;
    716:   RDNode       *x, *x0, *xdot;
    717:   Vec           X0loc, Xloc, Xloc_t;
    718:   PetscReal     hx, Theta, dt, weight[5], interp[5][2], deriv[5][2];
    719:   DMDALocalInfo info;
    720:   PetscInt      i, j, k, q, nq;
    721:   PetscScalar   K[4][4];

    723:   PetscFunctionBeginUser;
    724:   PetscCall(RDGetLocalArrays(rd, ts, X, Xdot, &Theta, &dt, &X0loc, &x0, &Xloc, &x, &Xloc_t, &xdot));
    725:   PetscCall(DMDAGetLocalInfo(rd->da, &info));
    726:   hx = rd->L / (info.mx - 1);
    727:   PetscCall(RDGetQuadrature(rd, hx, &nq, weight, interp, deriv));
    728:   PetscCall(MatZeroEntries(B));
    729:   for (i = info.xs; i < PetscMin(info.xs + info.xm, info.mx - 1); i++) {
    730:     PetscInt rc[2];

    732:     rc[0] = i;
    733:     rc[1] = i + 1;
    734:     PetscCall(PetscMemzero(K, sizeof(K)));
    735:     for (q = 0; q < nq; q++) {
    736:       PetscScalar              D_R;
    737:       PETSC_UNUSED PetscScalar rad;
    738:       RDNode                   n, nx, nt, ntx, drad, dD_R, dxD_R, dEm;
    739:       RDEvaluate(interp, deriv, q, x, i, &n, &nx);
    740:       RDEvaluate(interp, deriv, q, xdot, i, &nt, &ntx);
    741:       rad = RDRadiation(rd, &n, &drad);
    742:       RDDiffusionCoefficient(rd, PETSC_TRUE, &n, &nx, &D_R, &dD_R, &dxD_R);
    743:       RDMaterialEnergy(rd, &n, NULL, &dEm);
    744:       for (j = 0; j < 2; j++) {
    745:         for (k = 0; k < 2; k++) {
    746:           K[j * 2 + 0][k * 2 + 0] += (+interp[q][j] * weight[q] * (a - drad.E) * interp[q][k] + deriv[q][j] * weight[q] * ((D_R + dxD_R.E * nx.E) * deriv[q][k] + dD_R.E * nx.E * interp[q][k]));
    747:           K[j * 2 + 0][k * 2 + 1] += (+interp[q][j] * weight[q] * (-drad.T * interp[q][k]) + deriv[q][j] * weight[q] * (dxD_R.T * deriv[q][k] + dD_R.T * interp[q][k]) * nx.E);
    748:           K[j * 2 + 1][k * 2 + 0] += interp[q][j] * weight[q] * drad.E * interp[q][k];
    749:           K[j * 2 + 1][k * 2 + 1] += interp[q][j] * weight[q] * (a * rd->rho * dEm.T + drad.T) * interp[q][k];
    750:         }
    751:       }
    752:     }
    753:     PetscCall(MatSetValuesBlocked(B, 2, rc, 2, rc, &K[0][0], ADD_VALUES));
    754:   }
    755:   if (info.xs == 0) {
    756:     switch (rd->leftbc) {
    757:     case BC_ROBIN: {
    758:       PetscScalar D_R, D_R_bc;
    759:       PetscReal   ratio;
    760:       RDNode      n, nx;

    762:       n.E  = (1 - Theta) * x0[0].E + Theta * x[0].E;
    763:       n.T  = (1 - Theta) * x0[0].T + Theta * x[0].T;
    764:       nx.E = (x[1].E - x[0].E) / hx;
    765:       nx.T = (x[1].T - x[0].T) / hx;
    766:       RDDiffusionCoefficient(rd, PETSC_TRUE, &n, &nx, &D_R, 0, 0);
    767:       RDDiffusionCoefficient(rd, rd->bclimit, &n, &nx, &D_R_bc, 0, 0);
    768:       ratio = PetscRealPart(D_R / D_R_bc);
    769:       PetscCall(MatSetValue(B, 0, 0, ratio * 0.5, ADD_VALUES));
    770:     } break;
    771:     case BC_NEUMANN:
    772:       /* homogeneous Neumann is the natural condition */
    773:       break;
    774:     default:
    775:       SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Case %" PetscInt_FMT, rd->initial);
    776:     }
    777:   }

    779:   PetscCall(RDRestoreLocalArrays(rd, &X0loc, &x0, &Xloc, &x, &Xloc_t, &xdot));
    780:   PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY));
    781:   PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY));
    782:   if (A != B) {
    783:     PetscCall(MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY));
    784:     PetscCall(MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY));
    785:   }
    786:   PetscFunctionReturn(PETSC_SUCCESS);
    787: }

    789: /* Temperature that is in equilibrium with the radiation density */
    790: static PetscScalar RDRadiationTemperature(RD rd, PetscScalar E)
    791: {
    792:   return PetscPowScalar(E * rd->c / (4. * rd->sigma_b), 0.25);
    793: }

    795: static PetscErrorCode RDInitialState(RD rd, Vec X)
    796: {
    797:   DMDALocalInfo info;
    798:   PetscInt      i;
    799:   RDNode       *x;

    801:   PetscFunctionBeginUser;
    802:   PetscCall(DMDAGetLocalInfo(rd->da, &info));
    803:   PetscCall(DMDAVecGetArray(rd->da, X, &x));
    804:   for (i = info.xs; i < info.xs + info.xm; i++) {
    805:     PetscReal coord = i * rd->L / (info.mx - 1);
    806:     switch (rd->initial) {
    807:     case 1:
    808:       x[i].E = 0.001;
    809:       x[i].T = RDRadiationTemperature(rd, x[i].E);
    810:       break;
    811:     case 2:
    812:       x[i].E = 0.001 + 100. * PetscExpReal(-PetscSqr(coord / 0.1));
    813:       x[i].T = RDRadiationTemperature(rd, x[i].E);
    814:       break;
    815:     case 3:
    816:       x[i].E = 7.56e-2 * rd->unit.Joule / PetscPowScalarInt(rd->unit.meter, 3);
    817:       x[i].T = RDRadiationTemperature(rd, x[i].E);
    818:       break;
    819:     default:
    820:       SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "No initial state %" PetscInt_FMT, rd->initial);
    821:     }
    822:   }
    823:   PetscCall(DMDAVecRestoreArray(rd->da, X, &x));
    824:   PetscFunctionReturn(PETSC_SUCCESS);
    825: }

    827: static PetscErrorCode RDView(RD rd, Vec X, PetscViewer viewer)
    828: {
    829:   Vec             Y;
    830:   const RDNode   *x;
    831:   PetscScalar    *y;
    832:   PetscInt        i, m, M;
    833:   const PetscInt *lx;
    834:   DM              da;
    835:   MPI_Comm        comm;

    837:   PetscFunctionBeginUser;
    838:   /*
    839:     Create a DMDA (one dof per node, zero stencil width, same layout) to hold Trad
    840:     (radiation temperature).  It is not necessary to create a DMDA for this, but this way
    841:     output and visualization will have meaningful variable names and correct scales.
    842:   */
    843:   PetscCall(DMDAGetInfo(rd->da, 0, &M, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0));
    844:   PetscCall(DMDAGetOwnershipRanges(rd->da, &lx, 0, 0));
    845:   PetscCall(PetscObjectGetComm((PetscObject)rd->da, &comm));
    846:   PetscCall(DMDACreate1d(comm, DM_BOUNDARY_NONE, M, 1, 0, lx, &da));
    847:   PetscCall(DMSetFromOptions(da));
    848:   PetscCall(DMSetUp(da));
    849:   PetscCall(DMDASetUniformCoordinates(da, 0., rd->L, 0., 0., 0., 0.));
    850:   PetscCall(DMDASetFieldName(da, 0, "T_rad"));
    851:   PetscCall(DMCreateGlobalVector(da, &Y));

    853:   /* Compute the radiation temperature from the solution at each node */
    854:   PetscCall(VecGetLocalSize(Y, &m));
    855:   PetscCall(VecGetArrayRead(X, (const PetscScalar **)&x));
    856:   PetscCall(VecGetArray(Y, &y));
    857:   for (i = 0; i < m; i++) y[i] = RDRadiationTemperature(rd, x[i].E);
    858:   PetscCall(VecRestoreArrayRead(X, (const PetscScalar **)&x));
    859:   PetscCall(VecRestoreArray(Y, &y));

    861:   PetscCall(VecView(Y, viewer));
    862:   PetscCall(VecDestroy(&Y));
    863:   PetscCall(DMDestroy(&da));
    864:   PetscFunctionReturn(PETSC_SUCCESS);
    865: }

    867: static PetscErrorCode RDTestDifferentiation(RD rd)
    868: {
    869:   MPI_Comm    comm;
    870:   RDNode      n, nx;
    871:   PetscScalar epsilon;

    873:   PetscFunctionBeginUser;
    874:   PetscCall(PetscObjectGetComm((PetscObject)rd->da, &comm));
    875:   epsilon = 1e-8;
    876:   {
    877:     RDNode      dEm, fdEm;
    878:     PetscScalar T0 = 1000., T1 = T0 * (1. + epsilon), Em0, Em1;
    879:     n.E = 1.;
    880:     n.T = T0;
    881:     rd->MaterialEnergy(rd, &n, &Em0, &dEm);
    882:     n.E = 1. + epsilon;
    883:     n.T = T0;
    884:     rd->MaterialEnergy(rd, &n, &Em1, 0);
    885:     fdEm.E = (Em1 - Em0) / epsilon;
    886:     n.E    = 1.;
    887:     n.T    = T1;
    888:     rd->MaterialEnergy(rd, &n, &Em1, 0);
    889:     fdEm.T = (Em1 - Em0) / (T0 * epsilon);
    890:     PetscCall(PetscPrintf(comm, "dEm {%g,%g}, fdEm {%g,%g}, diff {%g,%g}\n", (double)PetscRealPart(dEm.E), (double)PetscRealPart(dEm.T), (double)PetscRealPart(fdEm.E), (double)PetscRealPart(fdEm.T), (double)PetscRealPart(dEm.E - fdEm.E),
    891:                           (double)PetscRealPart(dEm.T - fdEm.T)));
    892:   }
    893:   {
    894:     PetscScalar D0, D;
    895:     RDNode      dD, dxD, fdD, fdxD;
    896:     n.E  = 1.;
    897:     n.T  = 1.;
    898:     nx.E = 1.;
    899:     n.T  = 1.;
    900:     RDDiffusionCoefficient(rd, rd->bclimit, &n, &nx, &D0, &dD, &dxD);
    901:     n.E  = 1. + epsilon;
    902:     n.T  = 1.;
    903:     nx.E = 1.;
    904:     n.T  = 1.;
    905:     RDDiffusionCoefficient(rd, rd->bclimit, &n, &nx, &D, 0, 0);
    906:     fdD.E = (D - D0) / epsilon;
    907:     n.E   = 1;
    908:     n.T   = 1. + epsilon;
    909:     nx.E  = 1.;
    910:     n.T   = 1.;
    911:     RDDiffusionCoefficient(rd, rd->bclimit, &n, &nx, &D, 0, 0);
    912:     fdD.T = (D - D0) / epsilon;
    913:     n.E   = 1;
    914:     n.T   = 1.;
    915:     nx.E  = 1. + epsilon;
    916:     n.T   = 1.;
    917:     RDDiffusionCoefficient(rd, rd->bclimit, &n, &nx, &D, 0, 0);
    918:     fdxD.E = (D - D0) / epsilon;
    919:     n.E    = 1;
    920:     n.T    = 1.;
    921:     nx.E   = 1.;
    922:     n.T    = 1. + epsilon;
    923:     RDDiffusionCoefficient(rd, rd->bclimit, &n, &nx, &D, 0, 0);
    924:     fdxD.T = (D - D0) / epsilon;
    925:     PetscCall(PetscPrintf(comm, "dD {%g,%g}, fdD {%g,%g}, diff {%g,%g}\n", (double)PetscRealPart(dD.E), (double)PetscRealPart(dD.T), (double)PetscRealPart(fdD.E), (double)PetscRealPart(fdD.T), (double)PetscRealPart(dD.E - fdD.E),
    926:                           (double)PetscRealPart(dD.T - fdD.T)));
    927:     PetscCall(PetscPrintf(comm, "dxD {%g,%g}, fdxD {%g,%g}, diffx {%g,%g}\n", (double)PetscRealPart(dxD.E), (double)PetscRealPart(dxD.T), (double)PetscRealPart(fdxD.E), (double)PetscRealPart(fdxD.T), (double)PetscRealPart(dxD.E - fdxD.E),
    928:                           (double)PetscRealPart(dxD.T - fdxD.T)));
    929:   }
    930:   {
    931:     PetscInt    i;
    932:     PetscReal   hx = 1.;
    933:     PetscScalar a0;
    934:     RDNode      n0[3], n1[3], d[3], fd[3];

    936:     n0[0].E = 1.;
    937:     n0[0].T = 1.;
    938:     n0[1].E = 5.;
    939:     n0[1].T = 3.;
    940:     n0[2].E = 4.;
    941:     n0[2].T = 2.;
    942:     a0      = RDDiffusion(rd, hx, n0, 1, d);
    943:     for (i = 0; i < 3; i++) {
    944:       PetscCall(PetscMemcpy(n1, n0, sizeof(n0)));
    945:       n1[i].E += epsilon;
    946:       fd[i].E = (RDDiffusion(rd, hx, n1, 1, 0) - a0) / epsilon;
    947:       PetscCall(PetscMemcpy(n1, n0, sizeof(n0)));
    948:       n1[i].T += epsilon;
    949:       fd[i].T = (RDDiffusion(rd, hx, n1, 1, 0) - a0) / epsilon;
    950:       PetscCall(PetscPrintf(comm, "ddiff[%" PetscInt_FMT "] {%g,%g}, fd {%g %g}, diff {%g,%g}\n", i, (double)PetscRealPart(d[i].E), (double)PetscRealPart(d[i].T), (double)PetscRealPart(fd[i].E), (double)PetscRealPart(fd[i].T),
    951:                             (double)PetscRealPart(d[i].E - fd[i].E), (double)PetscRealPart(d[i].T - fd[i].T)));
    952:     }
    953:   }
    954:   {
    955:     PetscScalar rad0, rad;
    956:     RDNode      drad, fdrad;
    957:     n.E     = 1.;
    958:     n.T     = 1.;
    959:     rad0    = RDRadiation(rd, &n, &drad);
    960:     n.E     = 1. + epsilon;
    961:     n.T     = 1.;
    962:     rad     = RDRadiation(rd, &n, 0);
    963:     fdrad.E = (rad - rad0) / epsilon;
    964:     n.E     = 1.;
    965:     n.T     = 1. + epsilon;
    966:     rad     = RDRadiation(rd, &n, 0);
    967:     fdrad.T = (rad - rad0) / epsilon;
    968:     PetscCall(PetscPrintf(comm, "drad {%g,%g}, fdrad {%g,%g}, diff {%g,%g}\n", (double)PetscRealPart(drad.E), (double)PetscRealPart(drad.T), (double)PetscRealPart(fdrad.E), (double)PetscRealPart(fdrad.T), (double)PetscRealPart(drad.E - drad.E),
    969:                           (double)PetscRealPart(drad.T - fdrad.T)));
    970:   }
    971:   PetscFunctionReturn(PETSC_SUCCESS);
    972: }

    974: static PetscErrorCode RDCreate(MPI_Comm comm, RD *inrd)
    975: {
    976:   RD        rd;
    977:   PetscReal meter = 0, kilogram = 0, second = 0, Kelvin = 0, Joule = 0, Watt = 0;

    979:   PetscFunctionBeginUser;
    980:   *inrd = 0;
    981:   PetscCall(PetscNew(&rd));

    983:   PetscOptionsBegin(comm, NULL, "Options for nonequilibrium radiation-diffusion with RD ionization", NULL);
    984:   {
    985:     rd->initial = 1;
    986:     PetscCall(PetscOptionsInt("-rd_initial", "Initial condition (1=Marshak, 2=Blast, 3=Marshak+)", "", rd->initial, &rd->initial, 0));
    987:     switch (rd->initial) {
    988:     case 1:
    989:     case 2:
    990:       rd->unit.kilogram = 1.;
    991:       rd->unit.meter    = 1.;
    992:       rd->unit.second   = 1.;
    993:       rd->unit.Kelvin   = 1.;
    994:       break;
    995:     case 3:
    996:       rd->unit.kilogram = 1.e12;
    997:       rd->unit.meter    = 1.;
    998:       rd->unit.second   = 1.e9;
    999:       rd->unit.Kelvin   = 1.;
    1000:       break;
    1001:     default:
    1002:       SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Unknown initial condition %" PetscInt_FMT, rd->initial);
    1003:     }
    1004:     /* Fundamental units */
    1005:     PetscCall(PetscOptionsReal("-rd_unit_meter", "Length of 1 meter in nondimensional units", "", rd->unit.meter, &rd->unit.meter, 0));
    1006:     PetscCall(PetscOptionsReal("-rd_unit_kilogram", "Mass of 1 kilogram in nondimensional units", "", rd->unit.kilogram, &rd->unit.kilogram, 0));
    1007:     PetscCall(PetscOptionsReal("-rd_unit_second", "Time of a second in nondimensional units", "", rd->unit.second, &rd->unit.second, 0));
    1008:     PetscCall(PetscOptionsReal("-rd_unit_Kelvin", "Temperature of a Kelvin in nondimensional units", "", rd->unit.Kelvin, &rd->unit.Kelvin, 0));
    1009:     /* Derived units */
    1010:     rd->unit.Joule = rd->unit.kilogram * PetscSqr(rd->unit.meter / rd->unit.second);
    1011:     rd->unit.Watt  = rd->unit.Joule / rd->unit.second;
    1012:     /* Local aliases */
    1013:     meter    = rd->unit.meter;
    1014:     kilogram = rd->unit.kilogram;
    1015:     second   = rd->unit.second;
    1016:     Kelvin   = rd->unit.Kelvin;
    1017:     Joule    = rd->unit.Joule;
    1018:     Watt     = rd->unit.Watt;

    1020:     PetscCall(PetscOptionsBool("-rd_monitor_residual", "Display residuals every time they are evaluated", "", rd->monitor_residual, &rd->monitor_residual, NULL));
    1021:     PetscCall(PetscOptionsEnum("-rd_discretization", "Discretization type", "", DiscretizationTypes, (PetscEnum)rd->discretization, (PetscEnum *)&rd->discretization, NULL));
    1022:     if (rd->discretization == DISCRETIZATION_FE) {
    1023:       rd->quadrature = QUADRATURE_GAUSS2;
    1024:       PetscCall(PetscOptionsEnum("-rd_quadrature", "Finite element quadrature", "", QuadratureTypes, (PetscEnum)rd->quadrature, (PetscEnum *)&rd->quadrature, NULL));
    1025:     }
    1026:     PetscCall(PetscOptionsEnum("-rd_jacobian", "Type of finite difference Jacobian", "", JacobianTypes, (PetscEnum)rd->jacobian, (PetscEnum *)&rd->jacobian, NULL));
    1027:     switch (rd->initial) {
    1028:     case 1:
    1029:       rd->leftbc     = BC_ROBIN;
    1030:       rd->Eapplied   = 4 * rd->unit.Joule / PetscPowRealInt(rd->unit.meter, 3);
    1031:       rd->L          = 1. * rd->unit.meter;
    1032:       rd->beta       = 3.0;
    1033:       rd->gamma      = 3.0;
    1034:       rd->final_time = 3 * second;
    1035:       break;
    1036:     case 2:
    1037:       rd->leftbc     = BC_NEUMANN;
    1038:       rd->Eapplied   = 0.;
    1039:       rd->L          = 1. * rd->unit.meter;
    1040:       rd->beta       = 3.0;
    1041:       rd->gamma      = 3.0;
    1042:       rd->final_time = 1 * second;
    1043:       break;
    1044:     case 3:
    1045:       rd->leftbc     = BC_ROBIN;
    1046:       rd->Eapplied   = 7.503e6 * rd->unit.Joule / PetscPowRealInt(rd->unit.meter, 3);
    1047:       rd->L          = 5. * rd->unit.meter;
    1048:       rd->beta       = 3.5;
    1049:       rd->gamma      = 3.5;
    1050:       rd->final_time = 20e-9 * second;
    1051:       break;
    1052:     default:
    1053:       SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Initial %" PetscInt_FMT, rd->initial);
    1054:     }
    1055:     PetscCall(PetscOptionsEnum("-rd_leftbc", "Left boundary condition", "", BCTypes, (PetscEnum)rd->leftbc, (PetscEnum *)&rd->leftbc, NULL));
    1056:     PetscCall(PetscOptionsReal("-rd_E_applied", "Radiation flux at left end of domain", "", rd->Eapplied, &rd->Eapplied, NULL));
    1057:     PetscCall(PetscOptionsReal("-rd_beta", "Thermal exponent for photon absorption", "", rd->beta, &rd->beta, NULL));
    1058:     PetscCall(PetscOptionsReal("-rd_gamma", "Thermal exponent for diffusion coefficient", "", rd->gamma, &rd->gamma, NULL));
    1059:     PetscCall(PetscOptionsBool("-rd_view_draw", "Draw final solution", "", rd->view_draw, &rd->view_draw, NULL));
    1060:     PetscCall(PetscOptionsBool("-rd_endpoint", "Discretize using endpoints (like trapezoid rule) instead of midpoint", "", rd->endpoint, &rd->endpoint, NULL));
    1061:     PetscCall(PetscOptionsBool("-rd_bcmidpoint", "Impose the boundary condition at the midpoint (Theta) of the interval", "", rd->bcmidpoint, &rd->bcmidpoint, NULL));
    1062:     PetscCall(PetscOptionsBool("-rd_bclimit", "Limit diffusion coefficient in definition of Robin boundary condition", "", rd->bclimit, &rd->bclimit, NULL));
    1063:     PetscCall(PetscOptionsBool("-rd_test_diff", "Test differentiation in constitutive relations", "", rd->test_diff, &rd->test_diff, NULL));
    1064:     PetscCall(PetscOptionsString("-rd_view_binary", "File name to hold final solution", "", rd->view_binary, rd->view_binary, sizeof(rd->view_binary), NULL));
    1065:   }
    1066:   PetscOptionsEnd();

    1068:   switch (rd->initial) {
    1069:   case 1:
    1070:   case 2:
    1071:     rd->rho            = 1.;
    1072:     rd->c              = 1.;
    1073:     rd->K_R            = 1.;
    1074:     rd->K_p            = 1.;
    1075:     rd->sigma_b        = 0.25;
    1076:     rd->MaterialEnergy = RDMaterialEnergy_Reduced;
    1077:     break;
    1078:   case 3:
    1079:     /* Table 2 */
    1080:     rd->rho            = 1.17e-3 * kilogram / (meter * meter * meter); /* density */
    1081:     rd->K_R            = 7.44e18 * PetscPowRealInt(meter, 5) * PetscPowReal(Kelvin, 3.5) * PetscPowRealInt(kilogram, -2);
    1082:     rd->K_p            = 2.33e20 * PetscPowRealInt(meter, 5) * PetscPowReal(Kelvin, 3.5) * PetscPowRealInt(kilogram, -2);
    1083:     rd->I_H            = 2.179e-18 * Joule;                                                         /* Hydrogen ionization potential */
    1084:     rd->m_p            = 1.673e-27 * kilogram;                                                      /* proton mass */
    1085:     rd->m_e            = 9.109e-31 * kilogram;                                                      /* electron mass */
    1086:     rd->h              = 6.626e-34 * Joule * second;                                                /* Planck's constant */
    1087:     rd->k              = 1.381e-23 * Joule / Kelvin;                                                /* Boltzman constant */
    1088:     rd->c              = 3.00e8 * meter / second;                                                   /* speed of light */
    1089:     rd->sigma_b        = 5.67e-8 * Watt * PetscPowRealInt(meter, -2) * PetscPowRealInt(Kelvin, -4); /* Stefan-Boltzman constant */
    1090:     rd->MaterialEnergy = RDMaterialEnergy_Saha;
    1091:     break;
    1092:   }

    1094:   PetscCall(DMDACreate1d(comm, DM_BOUNDARY_NONE, 20, sizeof(RDNode) / sizeof(PetscScalar), 1, NULL, &rd->da));
    1095:   PetscCall(DMSetFromOptions(rd->da));
    1096:   PetscCall(DMSetUp(rd->da));
    1097:   PetscCall(DMDASetFieldName(rd->da, 0, "E"));
    1098:   PetscCall(DMDASetFieldName(rd->da, 1, "T"));
    1099:   PetscCall(DMDASetUniformCoordinates(rd->da, 0., 1., 0., 0., 0., 0.));

    1101:   *inrd = rd;
    1102:   PetscFunctionReturn(PETSC_SUCCESS);
    1103: }

    1105: int main(int argc, char *argv[])
    1106: {
    1107:   RD        rd;
    1108:   TS        ts;
    1109:   SNES      snes;
    1110:   Vec       X;
    1111:   Mat       A, B;
    1112:   PetscInt  steps;
    1113:   PetscReal ftime;

    1115:   PetscFunctionBeginUser;
    1116:   PetscCall(PetscInitialize(&argc, &argv, 0, NULL));
    1117:   PetscCall(RDCreate(PETSC_COMM_WORLD, &rd));
    1118:   PetscCall(DMCreateGlobalVector(rd->da, &X));
    1119:   PetscCall(DMSetMatType(rd->da, MATAIJ));
    1120:   PetscCall(DMCreateMatrix(rd->da, &B));
    1121:   PetscCall(RDInitialState(rd, X));

    1123:   PetscCall(TSCreate(PETSC_COMM_WORLD, &ts));
    1124:   PetscCall(TSSetProblemType(ts, TS_NONLINEAR));
    1125:   PetscCall(TSSetType(ts, TSTHETA));
    1126:   PetscCall(TSSetDM(ts, rd->da));
    1127:   switch (rd->discretization) {
    1128:   case DISCRETIZATION_FD:
    1129:     PetscCall(TSSetIFunction(ts, NULL, RDIFunction_FD, rd));
    1130:     if (rd->jacobian == JACOBIAN_ANALYTIC) PetscCall(TSSetIJacobian(ts, B, B, RDIJacobian_FD, rd));
    1131:     break;
    1132:   case DISCRETIZATION_FE:
    1133:     PetscCall(TSSetIFunction(ts, NULL, RDIFunction_FE, rd));
    1134:     if (rd->jacobian == JACOBIAN_ANALYTIC) PetscCall(TSSetIJacobian(ts, B, B, RDIJacobian_FE, rd));
    1135:     break;
    1136:   }
    1137:   PetscCall(TSSetMaxTime(ts, rd->final_time));
    1138:   PetscCall(TSSetTimeStep(ts, 1e-3));
    1139:   PetscCall(TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER));
    1140:   PetscCall(TSSetFromOptions(ts));

    1142:   A = B;
    1143:   PetscCall(TSGetSNES(ts, &snes));
    1144:   switch (rd->jacobian) {
    1145:   case JACOBIAN_ANALYTIC:
    1146:     break;
    1147:   case JACOBIAN_MATRIXFREE:
    1148:     break;
    1149:   case JACOBIAN_FD_COLORING: {
    1150:     PetscCall(SNESSetJacobian(snes, A, B, SNESComputeJacobianDefaultColor, 0));
    1151:   } break;
    1152:   case JACOBIAN_FD_FULL:
    1153:     PetscCall(SNESSetJacobian(snes, A, B, SNESComputeJacobianDefault, ts));
    1154:     break;
    1155:   }

    1157:   if (rd->test_diff) PetscCall(RDTestDifferentiation(rd));
    1158:   PetscCall(TSSolve(ts, X));
    1159:   PetscCall(TSGetSolveTime(ts, &ftime));
    1160:   PetscCall(TSGetStepNumber(ts, &steps));
    1161:   PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Steps %" PetscInt_FMT "  final time %g\n", steps, (double)ftime));
    1162:   if (rd->view_draw) PetscCall(RDView(rd, X, PETSC_VIEWER_DRAW_WORLD));
    1163:   if (rd->view_binary[0]) {
    1164:     PetscViewer viewer;
    1165:     PetscCall(PetscViewerBinaryOpen(PETSC_COMM_WORLD, rd->view_binary, FILE_MODE_WRITE, &viewer));
    1166:     PetscCall(RDView(rd, X, viewer));
    1167:     PetscCall(PetscViewerDestroy(&viewer));
    1168:   }
    1169:   PetscCall(VecDestroy(&X));
    1170:   PetscCall(MatDestroy(&B));
    1171:   PetscCall(RDDestroy(&rd));
    1172:   PetscCall(TSDestroy(&ts));
    1173:   PetscCall(PetscFinalize());
    1174:   return 0;
    1175: }
    1176: /*TEST

    1178:     test:
    1179:       args: -da_grid_x 20 -rd_initial 1 -rd_discretization fd -rd_jacobian fd_coloring -rd_endpoint -ts_max_time 1 -ts_time_step 2e-1 -ts_theta_initial_guess_extrapolate 0 -ts_monitor -snes_monitor_short -ksp_monitor_short
    1180:       requires: !single

    1182:     test:
    1183:       suffix: 2
    1184:       args: -da_grid_x 20 -rd_initial 1 -rd_discretization fe -rd_quadrature lobatto2 -rd_jacobian fd_coloring -rd_endpoint -ts_max_time 1 -ts_time_step 2e-1 -ts_theta_initial_guess_extrapolate 0 -ts_monitor -snes_monitor_short -ksp_monitor_short
    1185:       requires: !single

    1187:     test:
    1188:       suffix: 3
    1189:       nsize: 2
    1190:       args: -da_grid_x 20 -rd_initial 1 -rd_discretization fd -rd_jacobian analytic -rd_endpoint -ts_max_time 3 -ts_time_step 1e-1 -ts_theta_initial_guess_extrapolate 0 -ts_monitor -snes_monitor_short -ksp_monitor_short
    1191:       requires: !single

    1193: TEST*/