Actual source code: ex10.c
petsc-3.13.6 2020-09-29
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      1: static const char help[] = "1D nonequilibrium radiation diffusion with Saha ionization model.\n\n";

      3: /*
      4:   This example implements the model described in

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

      9:   The paper discusses three examples, the first two are nondimensional with a simple
     10:   ionization model.  The third example is fully dimensional and uses the Saha ionization
     11:   model with realistic parameters.
     12: */

     14:  #include <petscts.h>
     15:  #include <petscdm.h>
     16:  #include <petscdmda.h>

     18: typedef enum {BC_DIRICHLET,BC_NEUMANN,BC_ROBIN} BCType;
     19: static const char *const BCTypes[] = {"DIRICHLET","NEUMANN","ROBIN","BCType","BC_",0};
     20: typedef enum {JACOBIAN_ANALYTIC,JACOBIAN_MATRIXFREE,JACOBIAN_FD_COLORING,JACOBIAN_FD_FULL} JacobianType;
     21: static const char *const JacobianTypes[] = {"ANALYTIC","MATRIXFREE","FD_COLORING","FD_FULL","JacobianType","FD_",0};
     22: typedef enum {DISCRETIZATION_FD,DISCRETIZATION_FE} DiscretizationType;
     23: static const char *const DiscretizationTypes[] = {"FD","FE","DiscretizationType","DISCRETIZATION_",0};
     24: typedef enum {QUADRATURE_GAUSS1,QUADRATURE_GAUSS2,QUADRATURE_GAUSS3,QUADRATURE_GAUSS4,QUADRATURE_LOBATTO2,QUADRATURE_LOBATTO3} QuadratureType;
     25: static const char *const QuadratureTypes[] = {"GAUSS1","GAUSS2","GAUSS3","GAUSS4","LOBATTO2","LOBATTO3","QuadratureType","QUADRATURE_",0};

     27: typedef struct {
     28:   PetscScalar E;                /* radiation energy */
     29:   PetscScalar T;                /* material temperature */
     30: } RDNode;

     32: typedef struct {
     33:   PetscReal meter,kilogram,second,Kelvin; /* Fundamental units */
     34:   PetscReal Joule,Watt;                   /* Derived units */
     35: } RDUnit;

     37: typedef struct _n_RD *RD;

     39: struct _n_RD {
     40:   void               (*MaterialEnergy)(RD,const RDNode*,PetscScalar*,RDNode*);
     41:   DM                 da;
     42:   PetscBool          monitor_residual;
     43:   DiscretizationType discretization;
     44:   QuadratureType     quadrature;
     45:   JacobianType       jacobian;
     46:   PetscInt           initial;
     47:   BCType             leftbc;
     48:   PetscBool          view_draw;
     49:   char               view_binary[PETSC_MAX_PATH_LEN];
     50:   PetscBool          test_diff;
     51:   PetscBool          endpoint;
     52:   PetscBool          bclimit;
     53:   PetscBool          bcmidpoint;
     54:   RDUnit             unit;

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

     59:   /* Domain and boundary conditions */
     60:   PetscReal Eapplied;           /* Radiation flux from the left */
     61:   PetscReal L;                  /* Length of domain */
     62:   PetscReal final_time;
     63: };

     65: static PetscErrorCode RDDestroy(RD *rd)
     66: {

     70:   DMDestroy(&(*rd)->da);
     71:   PetscFree(*rd);
     72:   return(0);
     73: }

     75: /* The paper has a time derivative for material energy (Eq 2) which is a dependent variable (computable from temperature
     76:  * and density through an uninvertible relation).  Computing this derivative is trivial for trapezoid rule (used in the
     77:  * paper), but does not generalize nicely to higher order integrators.  Here we use the implicit form which provides
     78:  * time derivatives of the independent variables (radiation energy and temperature), so we must compute the time
     79:  * derivative of material energy ourselves (could be done using AD).
     80:  *
     81:  * There are multiple ionization models, this interface dispatches to the one currently in use.
     82:  */
     83: static void RDMaterialEnergy(RD rd,const RDNode *n,PetscScalar *Em,RDNode *dEm) { rd->MaterialEnergy(rd,n,Em,dEm); }

     85: /* Solves a quadratic equation while propagating tangents */
     86: static void QuadraticSolve(PetscScalar a,PetscScalar a_t,PetscScalar b,PetscScalar b_t,PetscScalar c,PetscScalar c_t,PetscScalar *x,PetscScalar *x_t)
     87: {
     88:   PetscScalar
     89:     disc   = b*b - 4.*a*c,
     90:     disc_t = 2.*b*b_t - 4.*a_t*c - 4.*a*c_t,
     91:     num    = -b + PetscSqrtScalar(disc), /* choose positive sign */
     92:     num_t  = -b_t + 0.5/PetscSqrtScalar(disc)*disc_t,
     93:     den    = 2.*a,
     94:     den_t  = 2.*a_t;
     95:   *x   = num/den;
     96:   *x_t = (num_t*den - num*den_t) / PetscSqr(den);
     97: }

     99: /* The primary model presented in the paper */
    100: static void RDMaterialEnergy_Saha(RD rd,const RDNode *n,PetscScalar *inEm,RDNode *dEm)
    101: {
    102:   PetscScalar Em,alpha,alpha_t,
    103:               T     = n->T,
    104:               T_t   = 1.,
    105:               chi   = rd->I_H / (rd->k * T),
    106:               chi_t = -chi / T * T_t,
    107:               a     = 1.,
    108:               a_t   = 0,
    109:               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 */
    110:               b_t   = -b*chi_t + 1.5*b/chi*chi_t,
    111:               c     = -b,
    112:               c_t   = -b_t;
    113:   QuadraticSolve(a,a_t,b,b_t,c,c_t,&alpha,&alpha_t);       /* Solve Eq 7 for alpha */
    114:   Em = rd->k * T / rd->m_p * (1.5*(1.+alpha) + alpha*chi); /* Eq 6 */
    115:   if (inEm) *inEm = Em;
    116:   if (dEm) {
    117:     dEm->E = 0;
    118:     dEm->T = Em / T * T_t + rd->k * T / rd->m_p * (1.5*alpha_t + alpha_t*chi + alpha*chi_t);
    119:   }
    120: }
    121: /* Reduced ionization model, Eq 30 */
    122: static void RDMaterialEnergy_Reduced(RD rd,const RDNode *n,PetscScalar *Em,RDNode *dEm)
    123: {
    124:   PetscScalar alpha,alpha_t,
    125:               T     = n->T,
    126:               T_t   = 1.,
    127:               chi   = -0.3 / T,
    128:               chi_t = -chi / T * T_t,
    129:               a     = 1.,
    130:               a_t   = 0.,
    131:               b     = PetscExpScalar(chi),
    132:               b_t   = b*chi_t,
    133:               c     = -b,
    134:               c_t   = -b_t;
    135:   QuadraticSolve(a,a_t,b,b_t,c,c_t,&alpha,&alpha_t);
    136:   if (Em) *Em = (1.+alpha)*T + 0.3*alpha;
    137:   if (dEm) {
    138:     dEm->E = 0;
    139:     dEm->T = alpha_t*T + (1.+alpha)*T_t + 0.3*alpha_t;
    140:   }
    141: }

    143: /* Eq 5 */
    144: static void RDSigma_R(RD rd,RDNode *n,PetscScalar *sigma_R,RDNode *dsigma_R)
    145: {
    146:   *sigma_R    = rd->K_R * rd->rho * PetscPowScalar(n->T,-rd->gamma);
    147:   dsigma_R->E = 0;
    148:   dsigma_R->T = -rd->gamma * (*sigma_R) / n->T;
    149: }

    151: /* Eq 4 */
    152: static void RDDiffusionCoefficient(RD rd,PetscBool limit,RDNode *n,RDNode *nx,PetscScalar *D_R,RDNode *dD_R,RDNode *dxD_R)
    153: {
    154:   PetscScalar sigma_R,denom;
    155:   RDNode      dsigma_R,ddenom,dxdenom;

    157:   RDSigma_R(rd,n,&sigma_R,&dsigma_R);
    158:   denom     = 3. * rd->rho * sigma_R + (int)limit * PetscAbsScalar(nx->E) / n->E;
    159:   ddenom.E  = -(int)limit * PetscAbsScalar(nx->E) / PetscSqr(n->E);
    160:   ddenom.T  = 3. * rd->rho * dsigma_R.T;
    161:   dxdenom.E = (int)limit * (PetscRealPart(nx->E)<0 ? -1. : 1.) / n->E;
    162:   dxdenom.T = 0;
    163:   *D_R      = rd->c / denom;
    164:   if (dD_R) {
    165:     dD_R->E = -rd->c / PetscSqr(denom) * ddenom.E;
    166:     dD_R->T = -rd->c / PetscSqr(denom) * ddenom.T;
    167:   }
    168:   if (dxD_R) {
    169:     dxD_R->E = -rd->c / PetscSqr(denom) * dxdenom.E;
    170:     dxD_R->T = -rd->c / PetscSqr(denom) * dxdenom.T;
    171:   }
    172: }

    174: static PetscErrorCode RDStateView(RD rd,Vec X,Vec Xdot,Vec F)
    175: {
    177:   DMDALocalInfo  info;
    178:   PetscInt       i;
    179:   const RDNode   *x,*xdot,*f;
    180:   MPI_Comm       comm;

    183:   PetscObjectGetComm((PetscObject)rd->da,&comm);
    184:   DMDAGetLocalInfo(rd->da,&info);
    185:   DMDAVecGetArrayRead(rd->da,X,(void*)&x);
    186:   DMDAVecGetArrayRead(rd->da,Xdot,(void*)&xdot);
    187:   DMDAVecGetArrayRead(rd->da,F,(void*)&f);
    188:   for (i=info.xs; i<info.xs+info.xm; i++) {
    189:     PetscSynchronizedPrintf(comm,"x[%D] (%10.2G,%10.2G) (%10.2G,%10.2G) (%10.2G,%10.2G)\n",i,PetscRealPart(x[i].E),PetscRealPart(x[i].T),
    190:                                    PetscRealPart(xdot[i].E),PetscRealPart(xdot[i].T), PetscRealPart(f[i].E),PetscRealPart(f[i].T));
    191:   }
    192:   DMDAVecRestoreArrayRead(rd->da,X,(void*)&x);
    193:   DMDAVecRestoreArrayRead(rd->da,Xdot,(void*)&xdot);
    194:   DMDAVecRestoreArrayRead(rd->da,F,(void*)&f);
    195:   PetscSynchronizedFlush(comm,PETSC_STDOUT);
    196:   return(0);
    197: }

    199: static PetscScalar RDRadiation(RD rd,const RDNode *n,RDNode *dn)
    200: {
    201:   PetscScalar sigma_p   = rd->K_p * rd->rho * PetscPowScalar(n->T,-rd->beta),
    202:               sigma_p_T = -rd->beta * sigma_p / n->T,
    203:               tmp       = 4.* rd->sigma_b*PetscSqr(PetscSqr(n->T)) / rd->c - n->E,
    204:               tmp_E     = -1.,
    205:               tmp_T     = 4. * rd->sigma_b * 4 * n->T*(PetscSqr(n->T)) / rd->c,
    206:               rad       = sigma_p * rd->c * rd->rho * tmp,
    207:               rad_E     = sigma_p * rd->c * rd->rho * tmp_E,
    208:               rad_T     = rd->c * rd->rho * (sigma_p_T * tmp + sigma_p * tmp_T);
    209:   if (dn) {
    210:     dn->E = rad_E;
    211:     dn->T = rad_T;
    212:   }
    213:   return rad;
    214: }

    216: static PetscScalar RDDiffusion(RD rd,PetscReal hx,const RDNode x[],PetscInt i,RDNode d[])
    217: {
    218:   PetscReal   ihx = 1./hx;
    219:   RDNode      n_L,nx_L,n_R,nx_R,dD_L,dxD_L,dD_R,dxD_R,dfluxL[2],dfluxR[2];
    220:   PetscScalar D_L,D_R,fluxL,fluxR;

    222:   n_L.E  = 0.5*(x[i-1].E + x[i].E);
    223:   n_L.T  = 0.5*(x[i-1].T + x[i].T);
    224:   nx_L.E = (x[i].E - x[i-1].E)/hx;
    225:   nx_L.T = (x[i].T - x[i-1].T)/hx;
    226:   RDDiffusionCoefficient(rd,PETSC_TRUE,&n_L,&nx_L,&D_L,&dD_L,&dxD_L);
    227:   fluxL       = D_L*nx_L.E;
    228:   dfluxL[0].E = -ihx*D_L + (0.5*dD_L.E - ihx*dxD_L.E)*nx_L.E;
    229:   dfluxL[1].E = +ihx*D_L + (0.5*dD_L.E + ihx*dxD_L.E)*nx_L.E;
    230:   dfluxL[0].T = (0.5*dD_L.T - ihx*dxD_L.T)*nx_L.E;
    231:   dfluxL[1].T = (0.5*dD_L.T + ihx*dxD_L.T)*nx_L.E;

    233:   n_R.E  = 0.5*(x[i].E + x[i+1].E);
    234:   n_R.T  = 0.5*(x[i].T + x[i+1].T);
    235:   nx_R.E = (x[i+1].E - x[i].E)/hx;
    236:   nx_R.T = (x[i+1].T - x[i].T)/hx;
    237:   RDDiffusionCoefficient(rd,PETSC_TRUE,&n_R,&nx_R,&D_R,&dD_R,&dxD_R);
    238:   fluxR       = D_R*nx_R.E;
    239:   dfluxR[0].E = -ihx*D_R + (0.5*dD_R.E - ihx*dxD_R.E)*nx_R.E;
    240:   dfluxR[1].E = +ihx*D_R + (0.5*dD_R.E + ihx*dxD_R.E)*nx_R.E;
    241:   dfluxR[0].T = (0.5*dD_R.T - ihx*dxD_R.T)*nx_R.E;
    242:   dfluxR[1].T = (0.5*dD_R.T + ihx*dxD_R.T)*nx_R.E;

    244:   if (d) {
    245:     d[0].E = -ihx*dfluxL[0].E;
    246:     d[0].T = -ihx*dfluxL[0].T;
    247:     d[1].E =  ihx*(dfluxR[0].E - dfluxL[1].E);
    248:     d[1].T =  ihx*(dfluxR[0].T - dfluxL[1].T);
    249:     d[2].E =  ihx*dfluxR[1].E;
    250:     d[2].T =  ihx*dfluxR[1].T;
    251:   }
    252:   return ihx*(fluxR - fluxL);
    253: }

    255: 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)
    256: {
    258:   PetscBool      istheta;

    261:   DMGetLocalVector(rd->da,X0loc);
    262:   DMGetLocalVector(rd->da,Xloc);
    263:   DMGetLocalVector(rd->da,Xloc_t);

    265:   DMGlobalToLocalBegin(rd->da,X,INSERT_VALUES,*Xloc);
    266:   DMGlobalToLocalEnd(rd->da,X,INSERT_VALUES,*Xloc);
    267:   DMGlobalToLocalBegin(rd->da,Xdot,INSERT_VALUES,*Xloc_t);
    268:   DMGlobalToLocalEnd(rd->da,Xdot,INSERT_VALUES,*Xloc_t);

    270:   /*
    271:     The following is a hack to subvert TSTHETA which is like an implicit midpoint method to behave more like a trapezoid
    272:     rule.  These methods have equivalent linear stability, but the nonlinear stability is somewhat different.  The
    273:     radiation system is inconvenient to write in explicit form because the ionization model is "on the left".
    274:    */
    275:   PetscObjectTypeCompare((PetscObject)ts,TSTHETA,&istheta);
    276:   if (istheta && rd->endpoint) {
    277:     TSThetaGetTheta(ts,Theta);
    278:   } else *Theta = 1.;

    280:   TSGetTimeStep(ts,dt);
    281:   VecWAXPY(*X0loc,-(*Theta)*(*dt),*Xloc_t,*Xloc); /* back out the value at the start of this step */
    282:   if (rd->endpoint) {
    283:     VecWAXPY(*Xloc,*dt,*Xloc_t,*X0loc);      /* move the abscissa to the end of the step */
    284:   }

    286:   DMDAVecGetArray(rd->da,*X0loc,x0);
    287:   DMDAVecGetArray(rd->da,*Xloc,x);
    288:   DMDAVecGetArray(rd->da,*Xloc_t,xdot);
    289:   return(0);
    290: }

    292: static PetscErrorCode RDRestoreLocalArrays(RD rd,Vec *X0loc,RDNode **x0,Vec *Xloc,RDNode **x,Vec *Xloc_t,RDNode **xdot)
    293: {

    297:   DMDAVecRestoreArray(rd->da,*X0loc,x0);
    298:   DMDAVecRestoreArray(rd->da,*Xloc,x);
    299:   DMDAVecRestoreArray(rd->da,*Xloc_t,xdot);
    300:   DMRestoreLocalVector(rd->da,X0loc);
    301:   DMRestoreLocalVector(rd->da,Xloc);
    302:   DMRestoreLocalVector(rd->da,Xloc_t);
    303:   return(0);
    304: }

    306: static PetscErrorCode RDCheckDomain_Private(RD rd,TS ts,Vec X,PetscBool  *in)
    307: {
    309:   PetscInt       minloc;
    310:   PetscReal      min;

    313:   VecMin(X,&minloc,&min);
    314:   if (min < 0) {
    315:     SNES snes;
    316:     *in  = PETSC_FALSE;
    317:     TSGetSNES(ts,&snes);
    318:     SNESSetFunctionDomainError(snes);
    319:     PetscInfo3(ts,"Domain violation at %D field %D value %g\n",minloc/2,minloc%2,(double)min);
    320:   } else *in = PETSC_TRUE;
    321:   return(0);
    322: }

    324: /* Energy and temperature must remain positive */
    325: #define RDCheckDomain(rd,ts,X) do {                                \
    326:     PetscErrorCode _ierr;                                          \
    327:     PetscBool      _in;                                                \
    328:     _RDCheckDomain_Private(rd,ts,X,&_in);CHKERRQ(_ierr);    \
    329:     if (!_in) return(0);                              \
    330:   } while (0)

    332: static PetscErrorCode RDIFunction_FD(TS ts,PetscReal t,Vec X,Vec Xdot,Vec F,void *ctx)
    333: {
    335:   RD             rd = (RD)ctx;
    336:   RDNode         *x,*x0,*xdot,*f;
    337:   Vec            X0loc,Xloc,Xloc_t;
    338:   PetscReal      hx,Theta,dt;
    339:   DMDALocalInfo  info;
    340:   PetscInt       i;

    343:   RDCheckDomain(rd,ts,X);
    344:   RDGetLocalArrays(rd,ts,X,Xdot,&Theta,&dt,&X0loc,&x0,&Xloc,&x,&Xloc_t,&xdot);
    345:   DMDAVecGetArray(rd->da,F,&f);
    346:   DMDAGetLocalInfo(rd->da,&info);
    347:   VecZeroEntries(F);

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

    351:   for (i=info.xs; i<info.xs+info.xm; i++) {
    352:     PetscReal   rho = rd->rho;
    353:     PetscScalar Em_t,rad;

    355:     rad = (1.-Theta)*RDRadiation(rd,&x0[i],0) + Theta*RDRadiation(rd,&x[i],0);
    356:     if (rd->endpoint) {
    357:       PetscScalar Em0,Em1;
    358:       RDMaterialEnergy(rd,&x0[i],&Em0,NULL);
    359:       RDMaterialEnergy(rd,&x[i],&Em1,NULL);
    360:       Em_t = (Em1 - Em0) / dt;
    361:     } else {
    362:       RDNode dEm;
    363:       RDMaterialEnergy(rd,&x[i],NULL,&dEm);
    364:       Em_t = dEm.E * xdot[i].E + dEm.T * xdot[i].T;
    365:     }
    366:     /* Residuals are multiplied by the volume element (hx).  */
    367:     /* The temperature equation does not have boundary conditions */
    368:     f[i].T = hx*(rho*Em_t + rad);

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

    374:       n.E  =  (1.-bcTheta)*x0[0].E + bcTheta*x[0].E;
    375:       n.T  =  (1.-bcTheta)*x0[0].T + bcTheta*x[0].T;
    376:       nx.E = ((1.-bcTheta)*(x0[1].E-x0[0].E) + bcTheta*(x[1].E-x[0].E))/hx;
    377:       nx.T = ((1.-bcTheta)*(x0[1].T-x0[0].T) + bcTheta*(x[1].T-x[0].T))/hx;
    378:       switch (rd->leftbc) {
    379:       case BC_ROBIN:
    380:         RDDiffusionCoefficient(rd,rd->bclimit,&n,&nx,&D_R,0,0);
    381:         f[0].E = hx*(n.E - 2. * D_R * nx.E - rd->Eapplied);
    382:         break;
    383:       case BC_NEUMANN:
    384:         f[0].E = x[1].E - x[0].E;
    385:         break;
    386:       default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Case %D",rd->initial);
    387:       }
    388:     } else if (i == info.mx-1) { /* Right boundary */
    389:       f[i].E = x[i].E - x[i-1].E; /* Homogeneous Neumann */
    390:     } else {
    391:       PetscScalar diff = (1.-Theta)*RDDiffusion(rd,hx,x0,i,0) + Theta*RDDiffusion(rd,hx,x,i,0);
    392:       f[i].E = hx*(xdot[i].E - diff - rad);
    393:     }
    394:   }
    395:   RDRestoreLocalArrays(rd,&X0loc,&x0,&Xloc,&x,&Xloc_t,&xdot);
    396:   DMDAVecRestoreArray(rd->da,F,&f);
    397:   if (rd->monitor_residual) {RDStateView(rd,X,Xdot,F);}
    398:   return(0);
    399: }

    401: static PetscErrorCode RDIJacobian_FD(TS ts,PetscReal t,Vec X,Vec Xdot,PetscReal a,Mat A,Mat B,void *ctx)
    402: {
    404:   RD             rd = (RD)ctx;
    405:   RDNode         *x,*x0,*xdot;
    406:   Vec            X0loc,Xloc,Xloc_t;
    407:   PetscReal      hx,Theta,dt;
    408:   DMDALocalInfo  info;
    409:   PetscInt       i;

    412:   RDCheckDomain(rd,ts,X);
    413:   RDGetLocalArrays(rd,ts,X,Xdot,&Theta,&dt,&X0loc,&x0,&Xloc,&x,&Xloc_t,&xdot);
    414:   DMDAGetLocalInfo(rd->da,&info);
    415:   hx   = rd->L / (info.mx-1);
    416:   MatZeroEntries(B);

    418:   for (i=info.xs; i<info.xs+info.xm; i++) {
    419:     PetscInt                  col[3];
    420:     PetscReal                 rho = rd->rho;
    421:     PetscScalar /*Em_t,rad,*/ K[2][6];
    422:     RDNode                    dEm_t,drad;

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

    426:     if (rd->endpoint) {
    427:       PetscScalar Em0,Em1;
    428:       RDNode      dEm1;
    429:       RDMaterialEnergy(rd,&x0[i],&Em0,NULL);
    430:       RDMaterialEnergy(rd,&x[i],&Em1,&dEm1);
    431:       /*Em_t = (Em1 - Em0) / (Theta*dt);*/
    432:       dEm_t.E = dEm1.E / (Theta*dt);
    433:       dEm_t.T = dEm1.T / (Theta*dt);
    434:     } else {
    435:       const PetscScalar epsilon = x[i].T * PETSC_SQRT_MACHINE_EPSILON;
    436:       RDNode            n1;
    437:       RDNode            dEm,dEm1;
    438:       PetscScalar       Em_TT;

    440:       n1.E = x[i].E;
    441:       n1.T = x[i].T+epsilon;
    442:       RDMaterialEnergy(rd,&x[i],NULL,&dEm);
    443:       RDMaterialEnergy(rd,&n1,NULL,&dEm1);
    444:       /* The Jacobian needs another derivative.  We finite difference here instead of
    445:        * propagating second derivatives through the ionization model. */
    446:       Em_TT = (dEm1.T - dEm.T) / epsilon;
    447:       /*Em_t = dEm.E * xdot[i].E + dEm.T * xdot[i].T;*/
    448:       dEm_t.E = dEm.E * a;
    449:       dEm_t.T = dEm.T * a + Em_TT * xdot[i].T;
    450:     }

    452:     PetscMemzero(K,sizeof(K));
    453:     /* Residuals are multiplied by the volume element (hx).  */
    454:     if (i == 0) {
    455:       PetscScalar D,bcTheta = rd->bcmidpoint ? Theta : 1.;
    456:       RDNode      n, nx;
    457:       RDNode      dD,dxD;

    459:       n.E  = (1.-bcTheta)*x0[0].E + bcTheta*x[0].E;
    460:       n.T  = (1.-bcTheta)*x0[0].T + bcTheta*x[0].T;
    461:       nx.E = ((1.-bcTheta)*(x0[1].E-x0[0].E) + bcTheta*(x[1].E-x[0].E))/hx;
    462:       nx.T = ((1.-bcTheta)*(x0[1].T-x0[0].T) + bcTheta*(x[1].T-x[0].T))/hx;
    463:       switch (rd->leftbc) {
    464:       case BC_ROBIN:
    465:         RDDiffusionCoefficient(rd,rd->bclimit,&n,&nx,&D,&dD,&dxD);
    466:         K[0][1*2+0] = (bcTheta/Theta)*hx*(1. -2.*D*(-1./hx) - 2.*nx.E*dD.E + 2.*nx.E*dxD.E/hx);
    467:         K[0][1*2+1] = (bcTheta/Theta)*hx*(-2.*nx.E*dD.T);
    468:         K[0][2*2+0] = (bcTheta/Theta)*hx*(-2.*D*(1./hx) - 2.*nx.E*dD.E - 2.*nx.E*dxD.E/hx);
    469:         break;
    470:       case BC_NEUMANN:
    471:         K[0][1*2+0] = -1./Theta;
    472:         K[0][2*2+0] = 1./Theta;
    473:         break;
    474:       default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Case %D",rd->initial);
    475:       }
    476:     } else if (i == info.mx-1) {
    477:       K[0][0*2+0] = -1./Theta;
    478:       K[0][1*2+0] = 1./Theta;
    479:     } else {
    480:       /*PetscScalar diff;*/
    481:       RDNode ddiff[3];
    482:       /*diff = (1.-Theta)*RDDiffusion(rd,hx,x0,i,0) + Theta* */ RDDiffusion(rd,hx,x,i,ddiff);
    483:       K[0][0*2+0] = -hx*ddiff[0].E;
    484:       K[0][0*2+1] = -hx*ddiff[0].T;
    485:       K[0][1*2+0] = hx*(a - ddiff[1].E - drad.E);
    486:       K[0][1*2+1] = hx*(-ddiff[1].T - drad.T);
    487:       K[0][2*2+0] = -hx*ddiff[2].E;
    488:       K[0][2*2+1] = -hx*ddiff[2].T;
    489:     }

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

    494:     col[0] = i-1;
    495:     col[1] = i;
    496:     col[2] = i+1<info.mx ? i+1 : -1;
    497:     MatSetValuesBlocked(B,1,&i,3,col,&K[0][0],INSERT_VALUES);
    498:   }
    499:   RDRestoreLocalArrays(rd,&X0loc,&x0,&Xloc,&x,&Xloc_t,&xdot);
    500:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
    501:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
    502:   if (A != B) {
    503:     MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
    504:     MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
    505:   }
    506:   return(0);
    507: }

    509: /* Evaluate interpolants and derivatives at a select quadrature point */
    510: static void RDEvaluate(PetscReal interp[][2],PetscReal deriv[][2],PetscInt q,const RDNode x[],PetscInt i,RDNode *n,RDNode *nx)
    511: {
    512:   PetscInt j;
    513:   n->E = 0; n->T = 0; nx->E = 0; nx->T = 0;
    514:   for (j=0; j<2; j++) {
    515:     n->E  += interp[q][j] * x[i+j].E;
    516:     n->T  += interp[q][j] * x[i+j].T;
    517:     nx->E += deriv[q][j] * x[i+j].E;
    518:     nx->T += deriv[q][j] * x[i+j].T;
    519:   }
    520: }

    522: /*
    523:  Various quadrature rules.  The nonlinear terms are non-polynomial so no standard quadrature will be exact.
    524: */
    525: static PetscErrorCode RDGetQuadrature(RD rd,PetscReal hx,PetscInt *nq,PetscReal weight[],PetscReal interp[][2],PetscReal deriv[][2])
    526: {
    527:   PetscInt        q,j;
    528:   const PetscReal *refweight,(*refinterp)[2],(*refderiv)[2];

    531:   switch (rd->quadrature) {
    532:   case QUADRATURE_GAUSS1: {
    533:     static const PetscReal ww[1] = {1.},ii[1][2] = {{0.5,0.5}},dd[1][2] = {{-1.,1.}};
    534:     *nq = 1; refweight = ww; refinterp = ii; refderiv = dd;
    535:   } break;
    536:   case QUADRATURE_GAUSS2: {
    537:     static const PetscReal ii[2][2] = {{0.78867513459481287,0.21132486540518713},{0.21132486540518713,0.78867513459481287}},dd[2][2] = {{-1.,1.},{-1.,1.}},ww[2] = {0.5,0.5};
    538:     *nq = 2; refweight = ww; refinterp = ii; refderiv = dd;
    539:   } break;
    540:   case QUADRATURE_GAUSS3: {
    541:     static const PetscReal ii[3][2] = {{0.8872983346207417,0.1127016653792583},{0.5,0.5},{0.1127016653792583,0.8872983346207417}},
    542:                            dd[3][2] = {{-1,1},{-1,1},{-1,1}},ww[3] = {5./18,8./18,5./18};
    543:     *nq = 3; refweight = ww; refinterp = ii; refderiv = dd;
    544:   } break;
    545:   case QUADRATURE_GAUSS4: {
    546:     static const PetscReal ii[][2] = {{0.93056815579702623,0.069431844202973658},
    547:                                       {0.66999052179242813,0.33000947820757187},
    548:                                       {0.33000947820757187,0.66999052179242813},
    549:                                       {0.069431844202973658,0.93056815579702623}},
    550:                            dd[][2] = {{-1,1},{-1,1},{-1,1},{-1,1}},ww[] = {0.17392742256872692,0.3260725774312731,0.3260725774312731,0.17392742256872692};

    552:     *nq = 4; refweight = ww; refinterp = ii; refderiv = dd;
    553:   } break;
    554:   case QUADRATURE_LOBATTO2: {
    555:     static const PetscReal ii[2][2] = {{1.,0.},{0.,1.}},dd[2][2] = {{-1.,1.},{-1.,1.}},ww[2] = {0.5,0.5};
    556:     *nq = 2; refweight = ww; refinterp = ii; refderiv = dd;
    557:   } break;
    558:   case QUADRATURE_LOBATTO3: {
    559:     static const PetscReal ii[3][2] = {{1,0},{0.5,0.5},{0,1}},dd[3][2] = {{-1,1},{-1,1},{-1,1}},ww[3] = {1./6,4./6,1./6};
    560:     *nq = 3; refweight = ww; refinterp = ii; refderiv = dd;
    561:   } break;
    562:   default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unknown quadrature %d",(int)rd->quadrature);
    563:   }

    565:   for (q=0; q<*nq; q++) {
    566:     weight[q] = refweight[q] * hx;
    567:     for (j=0; j<2; j++) {
    568:       interp[q][j] = refinterp[q][j];
    569:       deriv[q][j]  = refderiv[q][j] / hx;
    570:     }
    571:   }
    572:   return(0);
    573: }

    575: /*
    576:  Finite element version
    577: */
    578: static PetscErrorCode RDIFunction_FE(TS ts,PetscReal t,Vec X,Vec Xdot,Vec F,void *ctx)
    579: {
    581:   RD             rd = (RD)ctx;
    582:   RDNode         *x,*x0,*xdot,*f;
    583:   Vec            X0loc,Xloc,Xloc_t,Floc;
    584:   PetscReal      hx,Theta,dt,weight[5],interp[5][2],deriv[5][2];
    585:   DMDALocalInfo  info;
    586:   PetscInt       i,j,q,nq;

    589:   RDCheckDomain(rd,ts,X);
    590:   RDGetLocalArrays(rd,ts,X,Xdot,&Theta,&dt,&X0loc,&x0,&Xloc,&x,&Xloc_t,&xdot);

    592:   DMGetLocalVector(rd->da,&Floc);
    593:   VecZeroEntries(Floc);
    594:   DMDAVecGetArray(rd->da,Floc,&f);
    595:   DMDAGetLocalInfo(rd->da,&info);

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

    601:   for (i=info.xs; i<PetscMin(info.xs+info.xm,info.mx-1); i++) {
    602:     for (q=0; q<nq; q++) {
    603:       PetscReal   rho = rd->rho;
    604:       PetscScalar Em_t,rad,D_R,D0_R;
    605:       RDNode      n,n0,nx,n0x,nt,ntx;
    606:       RDEvaluate(interp,deriv,q,x,i,&n,&nx);
    607:       RDEvaluate(interp,deriv,q,x0,i,&n0,&n0x);
    608:       RDEvaluate(interp,deriv,q,xdot,i,&nt,&ntx);

    610:       rad = (1.-Theta)*RDRadiation(rd,&n0,0) + Theta*RDRadiation(rd,&n,0);
    611:       if (rd->endpoint) {
    612:         PetscScalar Em0,Em1;
    613:         RDMaterialEnergy(rd,&n0,&Em0,NULL);
    614:         RDMaterialEnergy(rd,&n,&Em1,NULL);
    615:         Em_t = (Em1 - Em0) / dt;
    616:       } else {
    617:         RDNode dEm;
    618:         RDMaterialEnergy(rd,&n,NULL,&dEm);
    619:         Em_t = dEm.E * nt.E + dEm.T * nt.T;
    620:       }
    621:       RDDiffusionCoefficient(rd,PETSC_TRUE,&n0,&n0x,&D0_R,0,0);
    622:       RDDiffusionCoefficient(rd,PETSC_TRUE,&n,&nx,&D_R,0,0);
    623:       for (j=0; j<2; j++) {
    624:         f[i+j].E += (deriv[q][j] * weight[q] * ((1.-Theta)*D0_R*n0x.E + Theta*D_R*nx.E)
    625:                      + interp[q][j] * weight[q] * (nt.E - rad));
    626:         f[i+j].T += interp[q][j] * weight[q] * (rho * Em_t + rad);
    627:       }
    628:     }
    629:   }
    630:   if (info.xs == 0) {
    631:     switch (rd->leftbc) {
    632:     case BC_ROBIN: {
    633:       PetscScalar D_R,D_R_bc;
    634:       PetscReal   ratio,bcTheta = rd->bcmidpoint ? Theta : 1.;
    635:       RDNode      n, nx;

    637:       n.E  = (1-bcTheta)*x0[0].E + bcTheta*x[0].E;
    638:       n.T  = (1-bcTheta)*x0[0].T + bcTheta*x[0].T;
    639:       nx.E = (x[1].E-x[0].E)/hx;
    640:       nx.T = (x[1].T-x[0].T)/hx;
    641:       RDDiffusionCoefficient(rd,PETSC_TRUE,&n,&nx,&D_R,0,0);
    642:       RDDiffusionCoefficient(rd,rd->bclimit,&n,&nx,&D_R_bc,0,0);
    643:       ratio = PetscRealPart(D_R/D_R_bc);
    644:       if (ratio > 1.) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Limited diffusivity is greater than unlimited");
    645:       if (ratio < 1e-3) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Heavily limited diffusivity");
    646:       f[0].E += -ratio*0.5*(rd->Eapplied - n.E);
    647:     } break;
    648:     case BC_NEUMANN:
    649:       /* homogeneous Neumann is the natural condition */
    650:       break;
    651:     default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Case %D",rd->initial);
    652:     }
    653:   }

    655:   RDRestoreLocalArrays(rd,&X0loc,&x0,&Xloc,&x,&Xloc_t,&xdot);
    656:   DMDAVecRestoreArray(rd->da,Floc,&f);
    657:   VecZeroEntries(F);
    658:   DMLocalToGlobalBegin(rd->da,Floc,ADD_VALUES,F);
    659:   DMLocalToGlobalEnd(rd->da,Floc,ADD_VALUES,F);
    660:   DMRestoreLocalVector(rd->da,&Floc);

    662:   if (rd->monitor_residual) {RDStateView(rd,X,Xdot,F);}
    663:   return(0);
    664: }

    666: static PetscErrorCode RDIJacobian_FE(TS ts,PetscReal t,Vec X,Vec Xdot,PetscReal a,Mat A,Mat B,void *ctx)
    667: {
    669:   RD             rd = (RD)ctx;
    670:   RDNode         *x,*x0,*xdot;
    671:   Vec            X0loc,Xloc,Xloc_t;
    672:   PetscReal      hx,Theta,dt,weight[5],interp[5][2],deriv[5][2];
    673:   DMDALocalInfo  info;
    674:   PetscInt       i,j,k,q,nq;
    675:   PetscScalar    K[4][4];

    678:   RDCheckDomain(rd,ts,X);
    679:   RDGetLocalArrays(rd,ts,X,Xdot,&Theta,&dt,&X0loc,&x0,&Xloc,&x,&Xloc_t,&xdot);
    680:   DMDAGetLocalInfo(rd->da,&info);
    681:   hx   = rd->L / (info.mx-1);
    682:   RDGetQuadrature(rd,hx,&nq,weight,interp,deriv);
    683:   MatZeroEntries(B);
    684:   for (i=info.xs; i<PetscMin(info.xs+info.xm,info.mx-1); i++) {
    685:     PetscInt rc[2];

    687:     rc[0] = i; rc[1] = i+1;
    688:     PetscMemzero(K,sizeof(K));
    689:     for (q=0; q<nq; q++) {
    690:       PetscScalar              D_R;
    691:       PETSC_UNUSED PetscScalar rad;
    692:       RDNode                   n,nx,nt,ntx,drad,dD_R,dxD_R,dEm;
    693:       RDEvaluate(interp,deriv,q,x,i,&n,&nx);
    694:       RDEvaluate(interp,deriv,q,xdot,i,&nt,&ntx);
    695:       rad = RDRadiation(rd,&n,&drad);
    696:       RDDiffusionCoefficient(rd,PETSC_TRUE,&n,&nx,&D_R,&dD_R,&dxD_R);
    697:       RDMaterialEnergy(rd,&n,NULL,&dEm);
    698:       for (j=0; j<2; j++) {
    699:         for (k=0; k<2; k++) {
    700:           K[j*2+0][k*2+0] += (+interp[q][j] * weight[q] * (a - drad.E) * interp[q][k]
    701:                               + deriv[q][j] * weight[q] * ((D_R + dxD_R.E * nx.E) * deriv[q][k] + dD_R.E * nx.E * interp[q][k]));
    702:           K[j*2+0][k*2+1] += (+interp[q][j] * weight[q] * (-drad.T * interp[q][k])
    703:                               + deriv[q][j] * weight[q] * (dxD_R.T * deriv[q][k] + dD_R.T * interp[q][k]) * nx.E);
    704:           K[j*2+1][k*2+0] +=   interp[q][j] * weight[q] * drad.E * interp[q][k];
    705:           K[j*2+1][k*2+1] +=   interp[q][j] * weight[q] * (a * rd->rho * dEm.T + drad.T) * interp[q][k];
    706:         }
    707:       }
    708:     }
    709:     MatSetValuesBlocked(B,2,rc,2,rc,&K[0][0],ADD_VALUES);
    710:   }
    711:   if (info.xs == 0) {
    712:     switch (rd->leftbc) {
    713:     case BC_ROBIN: {
    714:       PetscScalar D_R,D_R_bc;
    715:       PetscReal   ratio;
    716:       RDNode      n, nx;

    718:       n.E  = (1-Theta)*x0[0].E + Theta*x[0].E;
    719:       n.T  = (1-Theta)*x0[0].T + Theta*x[0].T;
    720:       nx.E = (x[1].E-x[0].E)/hx;
    721:       nx.T = (x[1].T-x[0].T)/hx;
    722:       RDDiffusionCoefficient(rd,PETSC_TRUE,&n,&nx,&D_R,0,0);
    723:       RDDiffusionCoefficient(rd,rd->bclimit,&n,&nx,&D_R_bc,0,0);
    724:       ratio = PetscRealPart(D_R/D_R_bc);
    725:       MatSetValue(B,0,0,ratio*0.5,ADD_VALUES);
    726:     } break;
    727:     case BC_NEUMANN:
    728:       /* homogeneous Neumann is the natural condition */
    729:       break;
    730:     default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Case %D",rd->initial);
    731:     }
    732:   }

    734:   RDRestoreLocalArrays(rd,&X0loc,&x0,&Xloc,&x,&Xloc_t,&xdot);
    735:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
    736:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
    737:   if (A != B) {
    738:     MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
    739:     MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
    740:   }
    741:   return(0);
    742: }

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

    747: static PetscErrorCode RDInitialState(RD rd,Vec X)
    748: {
    749:   DMDALocalInfo  info;
    750:   PetscInt       i;
    751:   RDNode         *x;

    755:   DMDAGetLocalInfo(rd->da,&info);
    756:   DMDAVecGetArray(rd->da,X,&x);
    757:   for (i=info.xs; i<info.xs+info.xm; i++) {
    758:     PetscReal coord = i*rd->L/(info.mx-1);
    759:     switch (rd->initial) {
    760:     case 1:
    761:       x[i].E = 0.001;
    762:       x[i].T = RDRadiationTemperature(rd,x[i].E);
    763:       break;
    764:     case 2:
    765:       x[i].E = 0.001 + 100.*PetscExpReal(-PetscSqr(coord/0.1));
    766:       x[i].T = RDRadiationTemperature(rd,x[i].E);
    767:       break;
    768:     case 3:
    769:       x[i].E = 7.56e-2 * rd->unit.Joule / PetscPowScalarInt(rd->unit.meter,3);
    770:       x[i].T = RDRadiationTemperature(rd,x[i].E);
    771:       break;
    772:     default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"No initial state %D",rd->initial);
    773:     }
    774:   }
    775:   DMDAVecRestoreArray(rd->da,X,&x);
    776:   return(0);
    777: }

    779: static PetscErrorCode RDView(RD rd,Vec X,PetscViewer viewer)
    780: {
    782:   Vec            Y;
    783:   const RDNode   *x;
    784:   PetscScalar    *y;
    785:   PetscInt       i,m,M;
    786:   const PetscInt *lx;
    787:   DM             da;
    788:   MPI_Comm       comm;

    791:   /*
    792:     Create a DMDA (one dof per node, zero stencil width, same layout) to hold Trad
    793:     (radiation temperature).  It is not necessary to create a DMDA for this, but this way
    794:     output and visualization will have meaningful variable names and correct scales.
    795:   */
    796:   DMDAGetInfo(rd->da,0, &M,0,0, 0,0,0, 0,0,0,0,0,0);
    797:   DMDAGetOwnershipRanges(rd->da,&lx,0,0);
    798:   PetscObjectGetComm((PetscObject)rd->da,&comm);
    799:   DMDACreate1d(comm,DM_BOUNDARY_NONE,M,1,0,lx,&da);
    800:   DMSetFromOptions(da);
    801:   DMSetUp(da);
    802:   DMDASetUniformCoordinates(da,0.,rd->L,0.,0.,0.,0.);
    803:   DMDASetFieldName(da,0,"T_rad");
    804:   DMCreateGlobalVector(da,&Y);

    806:   /* Compute the radiation temperature from the solution at each node */
    807:   VecGetLocalSize(Y,&m);
    808:   VecGetArrayRead(X,(const PetscScalar **)&x);
    809:   VecGetArray(Y,&y);
    810:   for (i=0; i<m; i++) y[i] = RDRadiationTemperature(rd,x[i].E);
    811:   VecRestoreArrayRead(X,(const PetscScalar**)&x);
    812:   VecRestoreArray(Y,&y);

    814:   VecView(Y,viewer);
    815:   VecDestroy(&Y);
    816:   DMDestroy(&da);
    817:   return(0);
    818: }

    820: static PetscErrorCode RDTestDifferentiation(RD rd)
    821: {
    822:   MPI_Comm       comm;
    824:   RDNode         n,nx;
    825:   PetscScalar    epsilon;

    828:   PetscObjectGetComm((PetscObject)rd->da,&comm);
    829:   epsilon = 1e-8;
    830:   {
    831:     RDNode      dEm,fdEm;
    832:     PetscScalar T0 = 1000.,T1 = T0*(1.+epsilon),Em0,Em1;
    833:     n.E = 1.;
    834:     n.T = T0;
    835:     rd->MaterialEnergy(rd,&n,&Em0,&dEm);
    836:     n.E = 1.+epsilon;
    837:     n.T = T0;
    838:     rd->MaterialEnergy(rd,&n,&Em1,0);
    839:     fdEm.E = (Em1-Em0)/epsilon;
    840:     n.E = 1.;
    841:     n.T = T1;
    842:     rd->MaterialEnergy(rd,&n,&Em1,0);
    843:     fdEm.T = (Em1-Em0)/(T0*epsilon);
    844:     PetscPrintf(comm,"dEm {%g,%g}, fdEm {%g,%g}, diff {%g,%g}\n",(double)PetscRealPart(dEm.E),(double)PetscRealPart(dEm.T),
    845:                        (double)PetscRealPart(fdEm.E),(double)PetscRealPart(fdEm.T),(double)PetscRealPart(dEm.E-fdEm.E),(double)PetscRealPart(dEm.T-fdEm.T));
    846:   }
    847:   {
    848:     PetscScalar D0,D;
    849:     RDNode      dD,dxD,fdD,fdxD;
    850:     n.E = 1.;          n.T = 1.;           nx.E = 1.;          n.T = 1.;
    851:     RDDiffusionCoefficient(rd,rd->bclimit,&n,&nx,&D0,&dD,&dxD);
    852:     n.E = 1.+epsilon;  n.T = 1.;           nx.E = 1.;          n.T = 1.;
    853:     RDDiffusionCoefficient(rd,rd->bclimit,&n,&nx,&D,0,0); fdD.E = (D-D0)/epsilon;
    854:     n.E = 1;           n.T = 1.+epsilon;   nx.E = 1.;          n.T = 1.;
    855:     RDDiffusionCoefficient(rd,rd->bclimit,&n,&nx,&D,0,0); fdD.T = (D-D0)/epsilon;
    856:     n.E = 1;           n.T = 1.;           nx.E = 1.+epsilon;  n.T = 1.;
    857:     RDDiffusionCoefficient(rd,rd->bclimit,&n,&nx,&D,0,0); fdxD.E = (D-D0)/epsilon;
    858:     n.E = 1;           n.T = 1.;           nx.E = 1.;          n.T = 1.+epsilon;
    859:     RDDiffusionCoefficient(rd,rd->bclimit,&n,&nx,&D,0,0); fdxD.T = (D-D0)/epsilon;
    860:     PetscPrintf(comm,"dD {%g,%g}, fdD {%g,%g}, diff {%g,%g}\n",(double)PetscRealPart(dD.E),(double)PetscRealPart(dD.T),
    861:                        (double)PetscRealPart(fdD.E),(double)PetscRealPart(fdD.T),(double)PetscRealPart(dD.E-fdD.E),(double)PetscRealPart(dD.T-fdD.T));
    862:     PetscPrintf(comm,"dxD {%g,%g}, fdxD {%g,%g}, diffx {%g,%g}\n",(double)PetscRealPart(dxD.E),(double)PetscRealPart(dxD.T),
    863:                        (double)PetscRealPart(fdxD.E),(double)PetscRealPart(fdxD.T),(double)PetscRealPart(dxD.E-fdxD.E),(double)PetscRealPart(dxD.T-fdxD.T));
    864:   }
    865:   {
    866:     PetscInt    i;
    867:     PetscReal   hx = 1.;
    868:     PetscScalar a0;
    869:     RDNode      n0[3],n1[3],d[3],fd[3];

    871:     n0[0].E = 1.;
    872:     n0[0].T = 1.;
    873:     n0[1].E = 5.;
    874:     n0[1].T = 3.;
    875:     n0[2].E = 4.;
    876:     n0[2].T = 2.;
    877:     a0 = RDDiffusion(rd,hx,n0,1,d);
    878:     for (i=0; i<3; i++) {
    879:       PetscMemcpy(n1,n0,sizeof(n0)); n1[i].E += epsilon;
    880:       fd[i].E = (RDDiffusion(rd,hx,n1,1,0)-a0)/epsilon;
    881:       PetscMemcpy(n1,n0,sizeof(n0)); n1[i].T += epsilon;
    882:       fd[i].T = (RDDiffusion(rd,hx,n1,1,0)-a0)/epsilon;
    883:       PetscPrintf(comm,"ddiff[%D] {%g,%g}, fd {%g %g}, diff {%g,%g}\n",i,(double)PetscRealPart(d[i].E),(double)PetscRealPart(d[i].T),
    884:                             (double)PetscRealPart(fd[i].E),(double)PetscRealPart(fd[i].T),(double)PetscRealPart(d[i].E-fd[i].E),(double)PetscRealPart(d[i].T-fd[i].T));
    885:     }
    886:   }
    887:   {
    888:     PetscScalar rad0,rad;
    889:     RDNode      drad,fdrad;
    890:     n.E  = 1.;         n.T = 1.;
    891:     rad0 = RDRadiation(rd,&n,&drad);
    892:     n.E  = 1.+epsilon; n.T = 1.;
    893:     rad  = RDRadiation(rd,&n,0); fdrad.E = (rad-rad0)/epsilon;
    894:     n.E  = 1.;         n.T = 1.+epsilon;
    895:     rad  = RDRadiation(rd,&n,0); fdrad.T = (rad-rad0)/epsilon;
    896:     PetscPrintf(comm,"drad {%g,%g}, fdrad {%g,%g}, diff {%g,%g}\n",(double)PetscRealPart(drad.E),(double)PetscRealPart(drad.T),
    897:                        (double)PetscRealPart(fdrad.E),(double)PetscRealPart(fdrad.T),(double)PetscRealPart(drad.E-drad.E),(double)PetscRealPart(drad.T-fdrad.T));
    898:   }
    899:   return(0);
    900: }

    902: static PetscErrorCode RDCreate(MPI_Comm comm,RD *inrd)
    903: {
    905:   RD             rd;
    906:   PetscReal      meter=0,kilogram=0,second=0,Kelvin=0,Joule=0,Watt=0;

    909:   *inrd = 0;
    910:   PetscNew(&rd);

    912:   PetscOptionsBegin(comm,NULL,"Options for nonequilibrium radiation-diffusion with RD ionization",NULL);
    913:   {
    914:     rd->initial = 1;
    915:     PetscOptionsInt("-rd_initial","Initial condition (1=Marshak, 2=Blast, 3=Marshak+)","",rd->initial,&rd->initial,0);
    916:     switch (rd->initial) {
    917:     case 1:
    918:     case 2:
    919:       rd->unit.kilogram = 1.;
    920:       rd->unit.meter    = 1.;
    921:       rd->unit.second   = 1.;
    922:       rd->unit.Kelvin   = 1.;
    923:       break;
    924:     case 3:
    925:       rd->unit.kilogram = 1.e12;
    926:       rd->unit.meter    = 1.;
    927:       rd->unit.second   = 1.e9;
    928:       rd->unit.Kelvin   = 1.;
    929:       break;
    930:     default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unknown initial condition %d",rd->initial);
    931:     }
    932:     /* Fundamental units */
    933:     PetscOptionsReal("-rd_unit_meter","Length of 1 meter in nondimensional units","",rd->unit.meter,&rd->unit.meter,0);
    934:     PetscOptionsReal("-rd_unit_kilogram","Mass of 1 kilogram in nondimensional units","",rd->unit.kilogram,&rd->unit.kilogram,0);
    935:     PetscOptionsReal("-rd_unit_second","Time of a second in nondimensional units","",rd->unit.second,&rd->unit.second,0);
    936:     PetscOptionsReal("-rd_unit_Kelvin","Temperature of a Kelvin in nondimensional units","",rd->unit.Kelvin,&rd->unit.Kelvin,0);
    937:     /* Derived units */
    938:     rd->unit.Joule = rd->unit.kilogram*PetscSqr(rd->unit.meter/rd->unit.second);
    939:     rd->unit.Watt  = rd->unit.Joule/rd->unit.second;
    940:     /* Local aliases */
    941:     meter    = rd->unit.meter;
    942:     kilogram = rd->unit.kilogram;
    943:     second   = rd->unit.second;
    944:     Kelvin   = rd->unit.Kelvin;
    945:     Joule    = rd->unit.Joule;
    946:     Watt     = rd->unit.Watt;

    948:     PetscOptionsBool("-rd_monitor_residual","Display residuals every time they are evaluated","",rd->monitor_residual,&rd->monitor_residual,NULL);
    949:     PetscOptionsEnum("-rd_discretization","Discretization type","",DiscretizationTypes,(PetscEnum)rd->discretization,(PetscEnum*)&rd->discretization,NULL);
    950:     if (rd->discretization == DISCRETIZATION_FE) {
    951:       rd->quadrature = QUADRATURE_GAUSS2;
    952:       PetscOptionsEnum("-rd_quadrature","Finite element quadrature","",QuadratureTypes,(PetscEnum)rd->quadrature,(PetscEnum*)&rd->quadrature,NULL);
    953:     }
    954:     PetscOptionsEnum("-rd_jacobian","Type of finite difference Jacobian","",JacobianTypes,(PetscEnum)rd->jacobian,(PetscEnum*)&rd->jacobian,NULL);
    955:     switch (rd->initial) {
    956:     case 1:
    957:       rd->leftbc     = BC_ROBIN;
    958:       rd->Eapplied   = 4 * rd->unit.Joule / PetscPowRealInt(rd->unit.meter,3);
    959:       rd->L          = 1. * rd->unit.meter;
    960:       rd->beta       = 3.0;
    961:       rd->gamma      = 3.0;
    962:       rd->final_time = 3 * second;
    963:       break;
    964:     case 2:
    965:       rd->leftbc     = BC_NEUMANN;
    966:       rd->Eapplied   = 0.;
    967:       rd->L          = 1. * rd->unit.meter;
    968:       rd->beta       = 3.0;
    969:       rd->gamma      = 3.0;
    970:       rd->final_time = 1 * second;
    971:       break;
    972:     case 3:
    973:       rd->leftbc     = BC_ROBIN;
    974:       rd->Eapplied   = 7.503e6 * rd->unit.Joule / PetscPowRealInt(rd->unit.meter,3);
    975:       rd->L          = 5. * rd->unit.meter;
    976:       rd->beta       = 3.5;
    977:       rd->gamma      = 3.5;
    978:       rd->final_time = 20e-9 * second;
    979:       break;
    980:     default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Initial %D",rd->initial);
    981:     }
    982:     PetscOptionsEnum("-rd_leftbc","Left boundary condition","",BCTypes,(PetscEnum)rd->leftbc,(PetscEnum*)&rd->leftbc,NULL);
    983:     PetscOptionsReal("-rd_E_applied","Radiation flux at left end of domain","",rd->Eapplied,&rd->Eapplied,NULL);
    984:     PetscOptionsReal("-rd_beta","Thermal exponent for photon absorption","",rd->beta,&rd->beta,NULL);
    985:     PetscOptionsReal("-rd_gamma","Thermal exponent for diffusion coefficient","",rd->gamma,&rd->gamma,NULL);
    986:     PetscOptionsBool("-rd_view_draw","Draw final solution","",rd->view_draw,&rd->view_draw,NULL);
    987:     PetscOptionsBool("-rd_endpoint","Discretize using endpoints (like trapezoid rule) instead of midpoint","",rd->endpoint,&rd->endpoint,NULL);
    988:     PetscOptionsBool("-rd_bcmidpoint","Impose the boundary condition at the midpoint (Theta) of the interval","",rd->bcmidpoint,&rd->bcmidpoint,NULL);
    989:     PetscOptionsBool("-rd_bclimit","Limit diffusion coefficient in definition of Robin boundary condition","",rd->bclimit,&rd->bclimit,NULL);
    990:     PetscOptionsBool("-rd_test_diff","Test differentiation in constitutive relations","",rd->test_diff,&rd->test_diff,NULL);
    991:     PetscOptionsString("-rd_view_binary","File name to hold final solution","",rd->view_binary,rd->view_binary,sizeof(rd->view_binary),NULL);
    992:   }
    993:   PetscOptionsEnd();

    995:   switch (rd->initial) {
    996:   case 1:
    997:   case 2:
    998:     rd->rho            = 1.;
    999:     rd->c              = 1.;
    1000:     rd->K_R            = 1.;
    1001:     rd->K_p            = 1.;
    1002:     rd->sigma_b        = 0.25;
    1003:     rd->MaterialEnergy = RDMaterialEnergy_Reduced;
    1004:     break;
    1005:   case 3:
    1006:     /* Table 2 */
    1007:     rd->rho     = 1.17e-3 * kilogram / (meter*meter*meter);                      /* density */
    1008:     rd->K_R     = 7.44e18 * PetscPowRealInt(meter,5) * PetscPowReal(Kelvin,3.5) * PetscPowRealInt(kilogram,-2); /*  */
    1009:     rd->K_p     = 2.33e20 * PetscPowRealInt(meter,5) * PetscPowReal(Kelvin,3.5) * PetscPowRealInt(kilogram,-2); /*  */
    1010:     rd->I_H     = 2.179e-18 * Joule;                                             /* Hydrogen ionization potential */
    1011:     rd->m_p     = 1.673e-27 * kilogram;                                          /* proton mass */
    1012:     rd->m_e     = 9.109e-31 * kilogram;                                          /* electron mass */
    1013:     rd->h       = 6.626e-34 * Joule * second;                                    /* Planck's constant */
    1014:     rd->k       = 1.381e-23 * Joule / Kelvin;                                    /* Boltzman constant */
    1015:     rd->c       = 3.00e8 * meter / second;                                       /* speed of light */
    1016:     rd->sigma_b = 5.67e-8 * Watt * PetscPowRealInt(meter,-2) * PetscPowRealInt(Kelvin,-4);             /* Stefan-Boltzman constant */
    1017:     rd->MaterialEnergy = RDMaterialEnergy_Saha;
    1018:     break;
    1019:   }

    1021:   DMDACreate1d(comm,DM_BOUNDARY_NONE,20,sizeof(RDNode)/sizeof(PetscScalar),1,NULL,&rd->da);
    1022:   DMSetFromOptions(rd->da);
    1023:   DMSetUp(rd->da);
    1024:   DMDASetFieldName(rd->da,0,"E");
    1025:   DMDASetFieldName(rd->da,1,"T");
    1026:   DMDASetUniformCoordinates(rd->da,0.,1.,0.,0.,0.,0.);

    1028:   *inrd = rd;
    1029:   return(0);
    1030: }

    1032: int main(int argc, char *argv[])
    1033: {
    1035:   RD             rd;
    1036:   TS             ts;
    1037:   SNES           snes;
    1038:   Vec            X;
    1039:   Mat            A,B;
    1040:   PetscInt       steps;
    1041:   PetscReal      ftime;

    1043:   PetscInitialize(&argc,&argv,0,help);if (ierr) return ierr;
    1044:   RDCreate(PETSC_COMM_WORLD,&rd);
    1045:   DMCreateGlobalVector(rd->da,&X);
    1046:   DMSetMatType(rd->da,MATAIJ);
    1047:   DMCreateMatrix(rd->da,&B);
    1048:   RDInitialState(rd,X);

    1050:   TSCreate(PETSC_COMM_WORLD,&ts);
    1051:   TSSetProblemType(ts,TS_NONLINEAR);
    1052:   TSSetType(ts,TSTHETA);
    1053:   TSSetDM(ts,rd->da);
    1054:   switch (rd->discretization) {
    1055:   case DISCRETIZATION_FD:
    1056:     TSSetIFunction(ts,NULL,RDIFunction_FD,rd);
    1057:     if (rd->jacobian == JACOBIAN_ANALYTIC) TSSetIJacobian(ts,B,B,RDIJacobian_FD,rd);
    1058:     break;
    1059:   case DISCRETIZATION_FE:
    1060:     TSSetIFunction(ts,NULL,RDIFunction_FE,rd);
    1061:     if (rd->jacobian == JACOBIAN_ANALYTIC) TSSetIJacobian(ts,B,B,RDIJacobian_FE,rd);
    1062:     break;
    1063:   }
    1064:   TSSetMaxTime(ts,rd->final_time);
    1065:   TSSetTimeStep(ts,1e-3);
    1066:   TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);
    1067:   TSSetFromOptions(ts);

    1069:   A = B;
    1070:   TSGetSNES(ts,&snes);
    1071:   switch (rd->jacobian) {
    1072:   case JACOBIAN_ANALYTIC:
    1073:     break;
    1074:   case JACOBIAN_MATRIXFREE:
    1075:     break;
    1076:   case JACOBIAN_FD_COLORING: {
    1077:     SNESSetJacobian(snes,A,B,SNESComputeJacobianDefaultColor,0);
    1078:   } break;
    1079:   case JACOBIAN_FD_FULL:
    1080:     SNESSetJacobian(snes,A,B,SNESComputeJacobianDefault,ts);
    1081:     break;
    1082:   }

    1084:   if (rd->test_diff) {
    1085:     RDTestDifferentiation(rd);
    1086:   }
    1087:   TSSolve(ts,X);
    1088:   TSGetSolveTime(ts,&ftime);
    1089:   TSGetStepNumber(ts,&steps);
    1090:   PetscPrintf(PETSC_COMM_WORLD,"Steps %D  final time %g\n",steps,(double)ftime);
    1091:   if (rd->view_draw) {
    1092:     RDView(rd,X,PETSC_VIEWER_DRAW_WORLD);
    1093:   }
    1094:   if (rd->view_binary[0]) {
    1095:     PetscViewer viewer;
    1096:     PetscViewerBinaryOpen(PETSC_COMM_WORLD,rd->view_binary,FILE_MODE_WRITE,&viewer);
    1097:     RDView(rd,X,viewer);
    1098:     PetscViewerDestroy(&viewer);
    1099:   }
    1100:   VecDestroy(&X);
    1101:   MatDestroy(&B);
    1102:   RDDestroy(&rd);
    1103:   TSDestroy(&ts);
    1104:   PetscFinalize();
    1105:   return ierr;
    1106: }
    1107: /*TEST

    1109:     test:
    1110:       args: -da_grid_x 20 -rd_initial 1 -rd_discretization fd -rd_jacobian fd_coloring -rd_endpoint -ts_max_time 1 -ts_dt 2e-1 -ts_theta_initial_guess_extrapolate 0 -ts_monitor -snes_monitor_short -ksp_monitor_short
    1111:       requires: !single

    1113:     test:
    1114:       suffix: 2
    1115:       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_dt 2e-1 -ts_theta_initial_guess_extrapolate 0 -ts_monitor -snes_monitor_short -ksp_monitor_short
    1116:       requires: !single

    1118:     test:
    1119:       suffix: 3
    1120:       nsize: 2
    1121:       args: -da_grid_x 20 -rd_initial 1 -rd_discretization fd -rd_jacobian analytic -rd_endpoint -ts_max_time 3 -ts_dt 1e-1 -ts_theta_initial_guess_extrapolate 0 -ts_monitor -snes_monitor_short -ksp_monitor_short
    1122:       requires: !single

    1124: TEST*/