Actual source code: ex14.c

petsc-master 2017-11-22
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  1: static const char help[] = "Toy hydrostatic ice flow with multigrid in 3D.\n\
  2: \n\
  3: Solves the hydrostatic (aka Blatter/Pattyn/First Order) equations for ice sheet flow\n\
  4: using multigrid.  The ice uses a power-law rheology with \"Glen\" exponent 3 (corresponds\n\
  5: to p=4/3 in a p-Laplacian).  The focus is on ISMIP-HOM experiments which assume periodic\n\
  6: boundary conditions in the x- and y-directions.\n\
  7: \n\
  8: Equations are rescaled so that the domain size and solution are O(1), details of this scaling\n\
  9: can be controlled by the options -units_meter, -units_second, and -units_kilogram.\n\
 10: \n\
 11: A VTK StructuredGrid output file can be written using the option -o filename.vts\n\
 12: \n\n";

 14: /*
 15: The equations for horizontal velocity (u,v) are

 17:   - [eta (4 u_x + 2 v_y)]_x - [eta (u_y + v_x)]_y - [eta u_z]_z + rho g s_x = 0
 18:   - [eta (4 v_y + 2 u_x)]_y - [eta (u_y + v_x)]_x - [eta v_z]_z + rho g s_y = 0

 20: where

 22:   eta = B/2 (epsilon + gamma)^((p-2)/2)

 24: is the nonlinear effective viscosity with regularization epsilon and hardness parameter B,
 25: written in terms of the second invariant

 27:   gamma = u_x^2 + v_y^2 + u_x v_y + (1/4) (u_y + v_x)^2 + (1/4) u_z^2 + (1/4) v_z^2

 29: The surface boundary conditions are the natural conditions.  The basal boundary conditions
 30: are either no-slip, or Navier (linear) slip with spatially variant friction coefficient beta^2.

 32: In the code, the equations for (u,v) are multiplied through by 1/(rho g) so that residuals are O(1).

 34: The discretization is Q1 finite elements, managed by a DMDA.  The grid is never distorted in the
 35: map (x,y) plane, but the bed and surface may be bumpy.  This is handled as usual in FEM, through
 36: the Jacobian of the coordinate transformation from a reference element to the physical element.

 38: Since ice-flow is tightly coupled in the z-direction (within columns), the DMDA is managed
 39: specially so that columns are never distributed, and are always contiguous in memory.
 40: This amounts to reversing the meaning of X,Y,Z compared to the DMDA's internal interpretation,
 41: and then indexing as vec[i][j][k].  The exotic coarse spaces require 2D DMDAs which are made to
 42: use compatible domain decomposition relative to the 3D DMDAs.

 44: */

 46:  #include <petscts.h>
 47:  #include <petscdm.h>
 48:  #include <petscdmda.h>
 49:  #include <petscdmcomposite.h>
 50: #include <ctype.h>              /* toupper() */
 51:  #include <petsc/private/petscimpl.h>

 53: #if defined __SSE2__
 54: #  include <emmintrin.h>
 55: #endif

 57: /* The SSE2 kernels are only for PetscScalar=double on architectures that support it */
 58: #define USE_SSE2_KERNELS (!defined NO_SSE2                              \
 59:                           && !defined PETSC_USE_COMPLEX                 \
 60:                           && !defined PETSC_USE_REAL_SINGLE           \
 61:                           && defined __SSE2__)

 63: #if !defined __STDC_VERSION__ || __STDC_VERSION__ < 199901L
 64: #  if defined __cplusplus       /* C++ restrict is nonstandard and compilers have inconsistent rules about where it can be used */
 65: #    define restrict
 66: #  else
 67: #    define restrict PETSC_RESTRICT
 68: #  endif
 69: #endif

 71: static PetscClassId THI_CLASSID;

 73: typedef enum {QUAD_GAUSS,QUAD_LOBATTO} QuadratureType;
 74: static const char *QuadratureTypes[] = {"gauss","lobatto","QuadratureType","QUAD_",0};
 75: static const PetscReal HexQWeights[8] = {1,1,1,1,1,1,1,1};
 76: static const PetscReal HexQNodes[]    = {-0.57735026918962573, 0.57735026918962573};
 77: #define G 0.57735026918962573
 78: #define H (0.5*(1.+G))
 79: #define L (0.5*(1.-G))
 80: #define M (-0.5)
 81: #define P (0.5)
 82: /* Special quadrature: Lobatto in horizontal, Gauss in vertical */
 83: static const PetscReal HexQInterp_Lobatto[8][8] = {{H,0,0,0,L,0,0,0},
 84:                                                    {0,H,0,0,0,L,0,0},
 85:                                                    {0,0,H,0,0,0,L,0},
 86:                                                    {0,0,0,H,0,0,0,L},
 87:                                                    {L,0,0,0,H,0,0,0},
 88:                                                    {0,L,0,0,0,H,0,0},
 89:                                                    {0,0,L,0,0,0,H,0},
 90:                                                    {0,0,0,L,0,0,0,H}};
 91: static const PetscReal HexQDeriv_Lobatto[8][8][3] = {
 92:   {{M*H,M*H,M},{P*H,0,0}  ,{0,0,0}    ,{0,P*H,0}  ,{M*L,M*L,P},{P*L,0,0}  ,{0,0,0}    ,{0,P*L,0}  },
 93:   {{M*H,0,0}  ,{P*H,M*H,M},{0,P*H,0}  ,{0,0,0}    ,{M*L,0,0}  ,{P*L,M*L,P},{0,P*L,0}  ,{0,0,0}    },
 94:   {{0,0,0}    ,{0,M*H,0}  ,{P*H,P*H,M},{M*H,0,0}  ,{0,0,0}    ,{0,M*L,0}  ,{P*L,P*L,P},{M*L,0,0}  },
 95:   {{0,M*H,0}  ,{0,0,0}    ,{P*H,0,0}  ,{M*H,P*H,M},{0,M*L,0}  ,{0,0,0}    ,{P*L,0,0}  ,{M*L,P*L,P}},
 96:   {{M*L,M*L,M},{P*L,0,0}  ,{0,0,0}    ,{0,P*L,0}  ,{M*H,M*H,P},{P*H,0,0}  ,{0,0,0}    ,{0,P*H,0}  },
 97:   {{M*L,0,0}  ,{P*L,M*L,M},{0,P*L,0}  ,{0,0,0}    ,{M*H,0,0}  ,{P*H,M*H,P},{0,P*H,0}  ,{0,0,0}    },
 98:   {{0,0,0}    ,{0,M*L,0}  ,{P*L,P*L,M},{M*L,0,0}  ,{0,0,0}    ,{0,M*H,0}  ,{P*H,P*H,P},{M*H,0,0}  },
 99:   {{0,M*L,0}  ,{0,0,0}    ,{P*L,0,0}  ,{M*L,P*L,M},{0,M*H,0}  ,{0,0,0}    ,{P*H,0,0}  ,{M*H,P*H,P}}};
100: /* Stanndard Gauss */
101: static const PetscReal HexQInterp_Gauss[8][8] = {{H*H*H,L*H*H,L*L*H,H*L*H, H*H*L,L*H*L,L*L*L,H*L*L},
102:                                                  {L*H*H,H*H*H,H*L*H,L*L*H, L*H*L,H*H*L,H*L*L,L*L*L},
103:                                                  {L*L*H,H*L*H,H*H*H,L*H*H, L*L*L,H*L*L,H*H*L,L*H*L},
104:                                                  {H*L*H,L*L*H,L*H*H,H*H*H, H*L*L,L*L*L,L*H*L,H*H*L},
105:                                                  {H*H*L,L*H*L,L*L*L,H*L*L, H*H*H,L*H*H,L*L*H,H*L*H},
106:                                                  {L*H*L,H*H*L,H*L*L,L*L*L, L*H*H,H*H*H,H*L*H,L*L*H},
107:                                                  {L*L*L,H*L*L,H*H*L,L*H*L, L*L*H,H*L*H,H*H*H,L*H*H},
108:                                                  {H*L*L,L*L*L,L*H*L,H*H*L, H*L*H,L*L*H,L*H*H,H*H*H}};
109: static const PetscReal HexQDeriv_Gauss[8][8][3] = {
110:   {{M*H*H,H*M*H,H*H*M},{P*H*H,L*M*H,L*H*M},{P*L*H,L*P*H,L*L*M},{M*L*H,H*P*H,H*L*M}, {M*H*L,H*M*L,H*H*P},{P*H*L,L*M*L,L*H*P},{P*L*L,L*P*L,L*L*P},{M*L*L,H*P*L,H*L*P}},
111:   {{M*H*H,L*M*H,L*H*M},{P*H*H,H*M*H,H*H*M},{P*L*H,H*P*H,H*L*M},{M*L*H,L*P*H,L*L*M}, {M*H*L,L*M*L,L*H*P},{P*H*L,H*M*L,H*H*P},{P*L*L,H*P*L,H*L*P},{M*L*L,L*P*L,L*L*P}},
112:   {{M*L*H,L*M*H,L*L*M},{P*L*H,H*M*H,H*L*M},{P*H*H,H*P*H,H*H*M},{M*H*H,L*P*H,L*H*M}, {M*L*L,L*M*L,L*L*P},{P*L*L,H*M*L,H*L*P},{P*H*L,H*P*L,H*H*P},{M*H*L,L*P*L,L*H*P}},
113:   {{M*L*H,H*M*H,H*L*M},{P*L*H,L*M*H,L*L*M},{P*H*H,L*P*H,L*H*M},{M*H*H,H*P*H,H*H*M}, {M*L*L,H*M*L,H*L*P},{P*L*L,L*M*L,L*L*P},{P*H*L,L*P*L,L*H*P},{M*H*L,H*P*L,H*H*P}},
114:   {{M*H*L,H*M*L,H*H*M},{P*H*L,L*M*L,L*H*M},{P*L*L,L*P*L,L*L*M},{M*L*L,H*P*L,H*L*M}, {M*H*H,H*M*H,H*H*P},{P*H*H,L*M*H,L*H*P},{P*L*H,L*P*H,L*L*P},{M*L*H,H*P*H,H*L*P}},
115:   {{M*H*L,L*M*L,L*H*M},{P*H*L,H*M*L,H*H*M},{P*L*L,H*P*L,H*L*M},{M*L*L,L*P*L,L*L*M}, {M*H*H,L*M*H,L*H*P},{P*H*H,H*M*H,H*H*P},{P*L*H,H*P*H,H*L*P},{M*L*H,L*P*H,L*L*P}},
116:   {{M*L*L,L*M*L,L*L*M},{P*L*L,H*M*L,H*L*M},{P*H*L,H*P*L,H*H*M},{M*H*L,L*P*L,L*H*M}, {M*L*H,L*M*H,L*L*P},{P*L*H,H*M*H,H*L*P},{P*H*H,H*P*H,H*H*P},{M*H*H,L*P*H,L*H*P}},
117:   {{M*L*L,H*M*L,H*L*M},{P*L*L,L*M*L,L*L*M},{P*H*L,L*P*L,L*H*M},{M*H*L,H*P*L,H*H*M}, {M*L*H,H*M*H,H*L*P},{P*L*H,L*M*H,L*L*P},{P*H*H,L*P*H,L*H*P},{M*H*H,H*P*H,H*H*P}}};
118: static const PetscReal (*HexQInterp)[8],(*HexQDeriv)[8][3];
119: /* Standard 2x2 Gauss quadrature for the bottom layer. */
120: static const PetscReal QuadQInterp[4][4] = {{H*H,L*H,L*L,H*L},
121:                                             {L*H,H*H,H*L,L*L},
122:                                             {L*L,H*L,H*H,L*H},
123:                                             {H*L,L*L,L*H,H*H}};
124: static const PetscReal QuadQDeriv[4][4][2] = {
125:   {{M*H,M*H},{P*H,M*L},{P*L,P*L},{M*L,P*H}},
126:   {{M*H,M*L},{P*H,M*H},{P*L,P*H},{M*L,P*L}},
127:   {{M*L,M*L},{P*L,M*H},{P*H,P*H},{M*H,P*L}},
128:   {{M*L,M*H},{P*L,M*L},{P*H,P*L},{M*H,P*H}}};
129: #undef G
130: #undef H
131: #undef L
132: #undef M
133: #undef P

135: #define HexExtract(x,i,j,k,n) do {              \
136:     (n)[0] = (x)[i][j][k];                      \
137:     (n)[1] = (x)[i+1][j][k];                    \
138:     (n)[2] = (x)[i+1][j+1][k];                  \
139:     (n)[3] = (x)[i][j+1][k];                    \
140:     (n)[4] = (x)[i][j][k+1];                    \
141:     (n)[5] = (x)[i+1][j][k+1];                  \
142:     (n)[6] = (x)[i+1][j+1][k+1];                \
143:     (n)[7] = (x)[i][j+1][k+1];                  \
144:   } while (0)

146: #define HexExtractRef(x,i,j,k,n) do {           \
147:     (n)[0] = &(x)[i][j][k];                     \
148:     (n)[1] = &(x)[i+1][j][k];                   \
149:     (n)[2] = &(x)[i+1][j+1][k];                 \
150:     (n)[3] = &(x)[i][j+1][k];                   \
151:     (n)[4] = &(x)[i][j][k+1];                   \
152:     (n)[5] = &(x)[i+1][j][k+1];                 \
153:     (n)[6] = &(x)[i+1][j+1][k+1];               \
154:     (n)[7] = &(x)[i][j+1][k+1];                 \
155:   } while (0)

157: #define QuadExtract(x,i,j,n) do {               \
158:     (n)[0] = (x)[i][j];                         \
159:     (n)[1] = (x)[i+1][j];                       \
160:     (n)[2] = (x)[i+1][j+1];                     \
161:     (n)[3] = (x)[i][j+1];                       \
162:   } while (0)

164: static PetscScalar Sqr(PetscScalar a) {return a*a;}

166: static void HexGrad(const PetscReal dphi[][3],const PetscReal zn[],PetscReal dz[])
167: {
168:   PetscInt i;
169:   dz[0] = dz[1] = dz[2] = 0;
170:   for (i=0; i<8; i++) {
171:     dz[0] += dphi[i][0] * zn[i];
172:     dz[1] += dphi[i][1] * zn[i];
173:     dz[2] += dphi[i][2] * zn[i];
174:   }
175: }

177: static void HexComputeGeometry(PetscInt q,PetscReal hx,PetscReal hy,const PetscReal dz[restrict],PetscReal phi[restrict],PetscReal dphi[restrict][3],PetscReal *restrict jw)
178: {
179:   const PetscReal
180:     jac[3][3] = {{hx/2,0,0}, {0,hy/2,0}, {dz[0],dz[1],dz[2]}}
181:   ,ijac[3][3] = {{1/jac[0][0],0,0}, {0,1/jac[1][1],0}, {-jac[2][0]/(jac[0][0]*jac[2][2]),-jac[2][1]/(jac[1][1]*jac[2][2]),1/jac[2][2]}}
182:   ,jdet = jac[0][0]*jac[1][1]*jac[2][2];
183:   PetscInt i;

185:   for (i=0; i<8; i++) {
186:     const PetscReal *dphir = HexQDeriv[q][i];
187:     phi[i] = HexQInterp[q][i];
188:     dphi[i][0] = dphir[0]*ijac[0][0] + dphir[1]*ijac[1][0] + dphir[2]*ijac[2][0];
189:     dphi[i][1] = dphir[0]*ijac[0][1] + dphir[1]*ijac[1][1] + dphir[2]*ijac[2][1];
190:     dphi[i][2] = dphir[0]*ijac[0][2] + dphir[1]*ijac[1][2] + dphir[2]*ijac[2][2];
191:   }
192:   *jw = 1.0 * jdet;
193: }

195: typedef struct _p_THI   *THI;
196: typedef struct _n_Units *Units;

198: typedef struct {
199:   PetscScalar u,v;
200: } Node;

202: typedef struct {
203:   PetscScalar b;                /* bed */
204:   PetscScalar h;                /* thickness */
205:   PetscScalar beta2;            /* friction */
206: } PrmNode;

208: #define FieldSize(ntype) ((PetscInt)(sizeof(ntype)/sizeof(PetscScalar)))
209: #define FieldOffset(ntype,member) ((PetscInt)(offsetof(ntype,member)/sizeof(PetscScalar)))
210: #define FieldIndex(ntype,i,member) ((PetscInt)((i)*FieldSize(ntype) + FieldOffset(ntype,member)))
211: #define NODE_SIZE FieldSize(Node)
212: #define PRMNODE_SIZE FieldSize(PrmNode)

214: typedef struct {
215:   PetscReal min,max,cmin,cmax;
216: } PRange;

218: struct _p_THI {
219:   PETSCHEADER(int);
220:   void      (*initialize)(THI,PetscReal x,PetscReal y,PrmNode *p);
221:   PetscInt  nlevels;
222:   PetscInt  zlevels;
223:   PetscReal Lx,Ly,Lz;           /* Model domain */
224:   PetscReal alpha;              /* Bed angle */
225:   Units     units;
226:   PetscReal dirichlet_scale;
227:   PetscReal ssa_friction_scale;
228:   PetscReal inertia;
229:   PRange    eta;
230:   PRange    beta2;
231:   struct {
232:     PetscReal Bd2,eps,exponent,glen_n;
233:   } viscosity;
234:   struct {
235:     PetscReal irefgam,eps2,exponent;
236:   } friction;
237:   struct {
238:     PetscReal rate,exponent,refvel;
239:   } erosion;
240:   PetscReal rhog;
241:   PetscBool no_slip;
242:   PetscBool verbose;
243:   char      *mattype;
244:   char      *monitor_basename;
245:   PetscInt  monitor_interval;
246: };

248: struct _n_Units {
249:   /* fundamental */
250:   PetscReal meter;
251:   PetscReal kilogram;
252:   PetscReal second;
253:   /* derived */
254:   PetscReal Pascal;
255:   PetscReal year;
256: };

258: static void PrmHexGetZ(const PrmNode pn[],PetscInt k,PetscInt zm,PetscReal zn[])
259: {
260:   const PetscScalar zm1 = zm-1,
261:     znl[8] = {pn[0].b + pn[0].h*(PetscScalar)k/zm1,
262:               pn[1].b + pn[1].h*(PetscScalar)k/zm1,
263:               pn[2].b + pn[2].h*(PetscScalar)k/zm1,
264:               pn[3].b + pn[3].h*(PetscScalar)k/zm1,
265:               pn[0].b + pn[0].h*(PetscScalar)(k+1)/zm1,
266:               pn[1].b + pn[1].h*(PetscScalar)(k+1)/zm1,
267:               pn[2].b + pn[2].h*(PetscScalar)(k+1)/zm1,
268:               pn[3].b + pn[3].h*(PetscScalar)(k+1)/zm1};
269:   PetscInt i;
270:   for (i=0; i<8; i++) zn[i] = PetscRealPart(znl[i]);
271: }

273: /* Compute a gradient of all the 2D fields at four quadrature points.  Output for [quadrature_point][direction].field_name */
274: static PetscErrorCode QuadComputeGrad4(const PetscReal dphi[][4][2],PetscReal hx,PetscReal hy,const PrmNode pn[4],PrmNode dp[4][2])
275: {
277:   PetscInt       q,i,f;
278:   const PetscScalar (*restrict pg)[PRMNODE_SIZE] = (const PetscScalar(*)[PRMNODE_SIZE])pn; /* Get generic array pointers to the node */
279:   PetscScalar (*restrict dpg)[2][PRMNODE_SIZE]   = (PetscScalar(*)[2][PRMNODE_SIZE])dp;

282:   PetscMemzero(dpg,4*sizeof(dpg[0]));
283:   for (q=0; q<4; q++) {
284:     for (i=0; i<4; i++) {
285:       for (f=0; f<PRMNODE_SIZE; f++) {
286:         dpg[q][0][f] += dphi[q][i][0]/hx * pg[i][f];
287:         dpg[q][1][f] += dphi[q][i][1]/hy * pg[i][f];
288:       }
289:     }
290:   }
291:   return(0);
292: }

294: static inline PetscReal StaggeredMidpoint2D(PetscScalar a,PetscScalar b,PetscScalar c,PetscScalar d)
295: {return 0.5*PetscRealPart(0.75*a + 0.75*b + 0.25*c + 0.25*d);}
296: static inline PetscReal UpwindFlux1D(PetscReal u,PetscReal hL,PetscReal hR)
297: {return (u > 0) ? hL*u : hR*u;}

299: #define UpwindFluxXW(x3,x2,h,i,j,k,dj) UpwindFlux1D(StaggeredMidpoint2D(x3[i][j][k].u,x3[i-1][j][k].u, x3[i-1][j+dj][k].u,x3[i][k+dj][k].u), \
300:                                                     PetscRealPart(0.75*x2[i-1][j  ].h+0.25*x2[i-1][j+dj].h), PetscRealPart(0.75*x2[i  ][j  ].h+0.25*x2[i  ][j+dj].h))
301: #define UpwindFluxXE(x3,x2,h,i,j,k,dj) UpwindFlux1D(StaggeredMidpoint2D(x3[i][j][k].u,x3[i+1][j][k].u, x3[i+1][j+dj][k].u,x3[i][k+dj][k].u), \
302:                                                     PetscRealPart(0.75*x2[i  ][j  ].h+0.25*x2[i  ][j+dj].h), PetscRealPart(0.75*x2[i+1][j  ].h+0.25*x2[i+1][j+dj].h))
303: #define UpwindFluxYS(x3,x2,h,i,j,k,di) UpwindFlux1D(StaggeredMidpoint2D(x3[i][j][k].v,x3[i][j-1][k].v, x3[i+di][j-1][k].v,x3[i+di][j][k].v), \
304:                                                     PetscRealPart(0.75*x2[i  ][j-1].h+0.25*x2[i+di][j-1].h), PetscRealPart(0.75*x2[i  ][j  ].h+0.25*x2[i+di][j  ].h))
305: #define UpwindFluxYN(x3,x2,h,i,j,k,di) UpwindFlux1D(StaggeredMidpoint2D(x3[i][j][k].v,x3[i][j+1][k].v, x3[i+di][j+1][k].v,x3[i+di][j][k].v), \
306:                                                     PetscRealPart(0.75*x2[i  ][j  ].h+0.25*x2[i+di][j  ].h), PetscRealPart(0.75*x2[i  ][j+1].h+0.25*x2[i+di][j+1].h))

308: static void PrmNodeGetFaceMeasure(const PrmNode **p,PetscInt i,PetscInt j,PetscScalar h[])
309: {
310:   /* West */
311:   h[0] = StaggeredMidpoint2D(p[i][j].h,p[i-1][j].h,p[i-1][j-1].h,p[i][j-1].h);
312:   h[1] = StaggeredMidpoint2D(p[i][j].h,p[i-1][j].h,p[i-1][j+1].h,p[i][j+1].h);
313:   /* East */
314:   h[2] = StaggeredMidpoint2D(p[i][j].h,p[i+1][j].h,p[i+1][j+1].h,p[i][j+1].h);
315:   h[3] = StaggeredMidpoint2D(p[i][j].h,p[i+1][j].h,p[i+1][j-1].h,p[i][j-1].h);
316:   /* South */
317:   h[4] = StaggeredMidpoint2D(p[i][j].h,p[i][j-1].h,p[i+1][j-1].h,p[i+1][j].h);
318:   h[5] = StaggeredMidpoint2D(p[i][j].h,p[i][j-1].h,p[i-1][j-1].h,p[i-1][j].h);
319:   /* North */
320:   h[6] = StaggeredMidpoint2D(p[i][j].h,p[i][j+1].h,p[i-1][j+1].h,p[i-1][j].h);
321:   h[7] = StaggeredMidpoint2D(p[i][j].h,p[i][j+1].h,p[i+1][j+1].h,p[i+1][j].h);
322: }

324: /* Tests A and C are from the ISMIP-HOM paper (Pattyn et al. 2008) */
325: static void THIInitialize_HOM_A(THI thi,PetscReal x,PetscReal y,PrmNode *p)
326: {
327:   Units units = thi->units;
328:   PetscReal s = -x*PetscSinReal(thi->alpha);
329:   p->b = s - 1000*units->meter + 500*units->meter * PetscSinReal(x*2*PETSC_PI/thi->Lx) * PetscSinReal(y*2*PETSC_PI/thi->Ly);
330:   p->h = s - p->b;
331:   p->beta2 = -1e-10;             /* This value is not used, but it should not be huge because that would change the finite difference step size  */
332: }

334: static void THIInitialize_HOM_C(THI thi,PetscReal x,PetscReal y,PrmNode *p)
335: {
336:   Units units = thi->units;
337:   PetscReal s = -x*PetscSinReal(thi->alpha);
338:   p->b = s - 1000*units->meter;
339:   p->h = s - p->b;
340:   /* tau_b = beta2 v   is a stress (Pa).
341:    * This is a big number in our units (it needs to balance the driving force from the surface), so we scale it by 1/rhog, just like the residual. */
342:   p->beta2 = 1000 * (1 + PetscSinReal(x*2*PETSC_PI/thi->Lx)*PetscSinReal(y*2*PETSC_PI/thi->Ly)) * units->Pascal * units->year / units->meter / thi->rhog;
343: }

345: /* These are just toys */

347: /* From Fred Herman */
348: static void THIInitialize_HOM_F(THI thi,PetscReal x,PetscReal y,PrmNode *p)
349: {
350:   Units units = thi->units;
351:   PetscReal s = -x*PetscSinReal(thi->alpha);
352:   p->b = s - 1000*units->meter + 100*units->meter * PetscSinReal(x*2*PETSC_PI/thi->Lx);/* * sin(y*2*PETSC_PI/thi->Ly); */
353:   p->h = s - p->b;
354:   p->h = (1-(atan((x-thi->Lx/2)/1.)+PETSC_PI/2.)/PETSC_PI)*500*units->meter+1*units->meter;
355:   s = PetscRealPart(p->b + p->h);
356:   p->beta2 = -1e-10;
357:   /*  p->beta2 = 1000 * units->Pascal * units->year / units->meter; */
358: }

360: /* Same bed as test A, free slip everywhere except for a discontinuous jump to a circular sticky region in the middle. */
361: static void THIInitialize_HOM_X(THI thi,PetscReal xx,PetscReal yy,PrmNode *p)
362: {
363:   Units units = thi->units;
364:   PetscReal x = xx*2*PETSC_PI/thi->Lx - PETSC_PI,y = yy*2*PETSC_PI/thi->Ly - PETSC_PI; /* [-pi,pi] */
365:   PetscReal r = PetscSqrtReal(x*x + y*y),s = -x*PetscSinReal(thi->alpha);
366:   p->b = s - 1000*units->meter + 500*units->meter * PetscSinReal(x + PETSC_PI) * PetscSinReal(y + PETSC_PI);
367:   p->h = s - p->b;
368:   p->beta2 = 1000 * (r < 1 ? 2 : 0) * units->Pascal * units->year / units->meter / thi->rhog;
369: }

371: /* Like Z, but with 200 meter cliffs */
372: static void THIInitialize_HOM_Y(THI thi,PetscReal xx,PetscReal yy,PrmNode *p)
373: {
374:   Units units = thi->units;
375:   PetscReal x = xx*2*PETSC_PI/thi->Lx - PETSC_PI,y = yy*2*PETSC_PI/thi->Ly - PETSC_PI; /* [-pi,pi] */
376:   PetscReal r = PetscSqrtReal(x*x + y*y),s = -x*PetscSinReal(thi->alpha);
377:   p->b = s - 1000*units->meter + 500*units->meter * PetscSinReal(x + PETSC_PI) * PetscSinReal(y + PETSC_PI);
378:   if (PetscRealPart(p->b) > -700*units->meter) p->b += 200*units->meter;
379:   p->h = s - p->b;
380:   p->beta2 = 1000 * (1. + PetscSinReal(PetscSqrtReal(16*r))/PetscSqrtReal(1e-2 + 16*r)*PetscCosReal(x*3/2)*PetscCosReal(y*3/2)) * units->Pascal * units->year / units->meter / thi->rhog;
381: }

383: /* Same bed as A, smoothly varying slipperiness, similar to MATLAB's "sombrero" (uncorrelated with bathymetry) */
384: static void THIInitialize_HOM_Z(THI thi,PetscReal xx,PetscReal yy,PrmNode *p)
385: {
386:   Units units = thi->units;
387:   PetscReal x = xx*2*PETSC_PI/thi->Lx - PETSC_PI,y = yy*2*PETSC_PI/thi->Ly - PETSC_PI; /* [-pi,pi] */
388:   PetscReal r = PetscSqrtReal(x*x + y*y),s = -x*PetscSinReal(thi->alpha);
389:   p->b = s - 1000*units->meter + 500*units->meter * PetscSinReal(x + PETSC_PI) * PetscSinReal(y + PETSC_PI);
390:   p->h = s - p->b;
391:   p->beta2 = 1000 * (1. + PetscSinReal(PetscSqrtReal(16*r))/PetscSqrtReal(1e-2 + 16*r)*PetscCosReal(x*3/2)*PetscCosReal(y*3/2)) * units->Pascal * units->year / units->meter / thi->rhog;
392: }

394: static void THIFriction(THI thi,PetscReal rbeta2,PetscReal gam,PetscReal *beta2,PetscReal *dbeta2)
395: {
396:   if (thi->friction.irefgam == 0) {
397:     Units units = thi->units;
398:     thi->friction.irefgam = 1./(0.5*PetscSqr(100 * units->meter / units->year));
399:     thi->friction.eps2 = 0.5*PetscSqr(1.e-4 / thi->friction.irefgam);
400:   }
401:   if (thi->friction.exponent == 0) {
402:     *beta2  = rbeta2;
403:     *dbeta2 = 0;
404:   } else {
405:     *beta2  = rbeta2 * PetscPowReal(thi->friction.eps2 + gam*thi->friction.irefgam,thi->friction.exponent);
406:     *dbeta2 = thi->friction.exponent * *beta2 / (thi->friction.eps2 + gam*thi->friction.irefgam) * thi->friction.irefgam;
407:   }
408: }

410: static void THIViscosity(THI thi,PetscReal gam,PetscReal *eta,PetscReal *deta)
411: {
412:   PetscReal Bd2,eps,exponent;
413:   if (thi->viscosity.Bd2 == 0) {
414:     Units units = thi->units;
415:     const PetscReal
416:       n = thi->viscosity.glen_n,                        /* Glen exponent */
417:       p = 1. + 1./n,                                    /* for Stokes */
418:       A = 1.e-16 * PetscPowReal(units->Pascal,-n) / units->year, /* softness parameter (Pa^{-n}/s) */
419:       B = PetscPowReal(A,-1./n);                                 /* hardness parameter */
420:     thi->viscosity.Bd2      = B/2;
421:     thi->viscosity.exponent = (p-2)/2;
422:     thi->viscosity.eps      = 0.5*PetscSqr(1e-5 / units->year);
423:   }
424:   Bd2      = thi->viscosity.Bd2;
425:   exponent = thi->viscosity.exponent;
426:   eps      = thi->viscosity.eps;
427:   *eta     = Bd2 * PetscPowReal(eps + gam,exponent);
428:   *deta    = exponent * (*eta) / (eps + gam);
429: }

431: static void THIErosion(THI thi,const Node *vel,PetscScalar *erate,Node *derate)
432: {
433:   const PetscScalar magref2 = 1.e-10 + (PetscSqr(vel->u) + PetscSqr(vel->v)) / PetscSqr(thi->erosion.refvel),
434:                     rate    = -thi->erosion.rate*PetscPowScalar(magref2, 0.5*thi->erosion.exponent);
435:   if (erate) *erate = rate;
436:   if (derate) {
437:     if (thi->erosion.exponent == 1) {
438:       derate->u = 0;
439:       derate->v = 0;
440:     } else {
441:       derate->u = 0.5*thi->erosion.exponent * rate / magref2 * 2. * vel->u / PetscSqr(thi->erosion.refvel);
442:       derate->v = 0.5*thi->erosion.exponent * rate / magref2 * 2. * vel->v / PetscSqr(thi->erosion.refvel);
443:     }
444:   }
445: }

447: static void RangeUpdate(PetscReal *min,PetscReal *max,PetscReal x)
448: {
449:   if (x < *min) *min = x;
450:   if (x > *max) *max = x;
451: }

453: static void PRangeClear(PRange *p)
454: {
455:   p->cmin = p->min = 1e100;
456:   p->cmax = p->max = -1e100;
457: }

459: static PetscErrorCode PRangeMinMax(PRange *p,PetscReal min,PetscReal max)
460: {

463:   p->cmin = min;
464:   p->cmax = max;
465:   if (min < p->min) p->min = min;
466:   if (max > p->max) p->max = max;
467:   return(0);
468: }

470: static PetscErrorCode THIDestroy(THI *thi)
471: {

475:   if (--((PetscObject)(*thi))->refct > 0) return(0);
476:   PetscFree((*thi)->units);
477:   PetscFree((*thi)->mattype);
478:   PetscFree((*thi)->monitor_basename);
479:   PetscHeaderDestroy(thi);
480:   return(0);
481: }

483: static PetscErrorCode THICreate(MPI_Comm comm,THI *inthi)
484: {
485:   static PetscBool registered = PETSC_FALSE;
486:   THI              thi;
487:   Units            units;
488:   char             monitor_basename[PETSC_MAX_PATH_LEN] = "thi-";
489:   PetscErrorCode   ierr;

492:   *inthi = 0;
493:   if (!registered) {
494:     PetscClassIdRegister("Toy Hydrostatic Ice",&THI_CLASSID);
495:     registered = PETSC_TRUE;
496:   }
497:   PetscHeaderCreate(thi,THI_CLASSID,"THI","Toy Hydrostatic Ice","THI",comm,THIDestroy,0);

499:   PetscNew(&thi->units);

501:   units           = thi->units;
502:   units->meter    = 1e-2;
503:   units->second   = 1e-7;
504:   units->kilogram = 1e-12;

506:   PetscOptionsBegin(comm,NULL,"Scaled units options","");
507:   {
508:     PetscOptionsReal("-units_meter","1 meter in scaled length units","",units->meter,&units->meter,NULL);
509:     PetscOptionsReal("-units_second","1 second in scaled time units","",units->second,&units->second,NULL);
510:     PetscOptionsReal("-units_kilogram","1 kilogram in scaled mass units","",units->kilogram,&units->kilogram,NULL);
511:   }
512:   PetscOptionsEnd();
513:   units->Pascal = units->kilogram / (units->meter * PetscSqr(units->second));
514:   units->year   = 31556926. * units->second, /* seconds per year */

516:   thi->Lx              = 10.e3;
517:   thi->Ly              = 10.e3;
518:   thi->Lz              = 1000;
519:   thi->nlevels         = 1;
520:   thi->dirichlet_scale = 1;
521:   thi->verbose         = PETSC_FALSE;

523:   thi->viscosity.glen_n = 3.;
524:   thi->erosion.rate     = 1e-3; /* m/a */
525:   thi->erosion.exponent = 1.;
526:   thi->erosion.refvel   = 1.;   /* m/a */

528:   PetscOptionsBegin(comm,NULL,"Toy Hydrostatic Ice options","");
529:   {
530:     QuadratureType quad       = QUAD_GAUSS;
531:     char           homexp[]   = "A";
532:     char           mtype[256] = MATSBAIJ;
533:     PetscReal      L,m = 1.0;
534:     PetscBool      flg;
535:     L    = thi->Lx;
536:     PetscOptionsReal("-thi_L","Domain size (m)","",L,&L,&flg);
537:     if (flg) thi->Lx = thi->Ly = L;
538:     PetscOptionsReal("-thi_Lx","X Domain size (m)","",thi->Lx,&thi->Lx,NULL);
539:     PetscOptionsReal("-thi_Ly","Y Domain size (m)","",thi->Ly,&thi->Ly,NULL);
540:     PetscOptionsReal("-thi_Lz","Z Domain size (m)","",thi->Lz,&thi->Lz,NULL);
541:     PetscOptionsString("-thi_hom","ISMIP-HOM experiment (A or C)","",homexp,homexp,sizeof(homexp),NULL);
542:     switch (homexp[0] = toupper(homexp[0])) {
543:     case 'A':
544:       thi->initialize = THIInitialize_HOM_A;
545:       thi->no_slip    = PETSC_TRUE;
546:       thi->alpha      = 0.5;
547:       break;
548:     case 'C':
549:       thi->initialize = THIInitialize_HOM_C;
550:       thi->no_slip    = PETSC_FALSE;
551:       thi->alpha      = 0.1;
552:       break;
553:     case 'F':
554:       thi->initialize = THIInitialize_HOM_F;
555:       thi->no_slip    = PETSC_FALSE;
556:       thi->alpha      = 0.5;
557:       break;
558:     case 'X':
559:       thi->initialize = THIInitialize_HOM_X;
560:       thi->no_slip    = PETSC_FALSE;
561:       thi->alpha      = 0.3;
562:       break;
563:     case 'Y':
564:       thi->initialize = THIInitialize_HOM_Y;
565:       thi->no_slip    = PETSC_FALSE;
566:       thi->alpha      = 0.5;
567:       break;
568:     case 'Z':
569:       thi->initialize = THIInitialize_HOM_Z;
570:       thi->no_slip    = PETSC_FALSE;
571:       thi->alpha      = 0.5;
572:       break;
573:     default:
574:       SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"HOM experiment '%c' not implemented",homexp[0]);
575:     }
576:     PetscOptionsEnum("-thi_quadrature","Quadrature to use for 3D elements","",QuadratureTypes,(PetscEnum)quad,(PetscEnum*)&quad,NULL);
577:     switch (quad) {
578:     case QUAD_GAUSS:
579:       HexQInterp = HexQInterp_Gauss;
580:       HexQDeriv  = HexQDeriv_Gauss;
581:       break;
582:     case QUAD_LOBATTO:
583:       HexQInterp = HexQInterp_Lobatto;
584:       HexQDeriv  = HexQDeriv_Lobatto;
585:       break;
586:     }
587:     PetscOptionsReal("-thi_alpha","Bed angle (degrees)","",thi->alpha,&thi->alpha,NULL);
588:     PetscOptionsReal("-thi_viscosity_glen_n","Exponent in Glen flow law, 1=linear, infty=ideal plastic",NULL,thi->viscosity.glen_n,&thi->viscosity.glen_n,NULL);
589:     PetscOptionsReal("-thi_friction_m","Friction exponent, 0=Coulomb, 1=Navier","",m,&m,NULL);
590:     thi->friction.exponent = (m-1)/2;
591:     PetscOptionsReal("-thi_erosion_rate","Rate of erosion relative to sliding velocity at reference velocity (m/a)",NULL,thi->erosion.rate,&thi->erosion.rate,NULL);
592:     PetscOptionsReal("-thi_erosion_exponent","Power of sliding velocity appearing in erosion relation",NULL,thi->erosion.exponent,&thi->erosion.exponent,NULL);
593:     PetscOptionsReal("-thi_erosion_refvel","Reference sliding velocity for erosion (m/a)",NULL,thi->erosion.refvel,&thi->erosion.refvel,NULL);
594:     thi->erosion.rate   *= units->meter / units->year;
595:     thi->erosion.refvel *= units->meter / units->year;
596:     PetscOptionsReal("-thi_dirichlet_scale","Scale Dirichlet boundary conditions by this factor","",thi->dirichlet_scale,&thi->dirichlet_scale,NULL);
597:     PetscOptionsReal("-thi_ssa_friction_scale","Scale slip boundary conditions by this factor in SSA (2D) assembly","",thi->ssa_friction_scale,&thi->ssa_friction_scale,NULL);
598:     PetscOptionsReal("-thi_inertia","Coefficient of accelaration term in velocity system, physical is almost zero",NULL,thi->inertia,&thi->inertia,NULL);
599:     PetscOptionsInt("-thi_nlevels","Number of levels of refinement","",thi->nlevels,&thi->nlevels,NULL);
600:     PetscOptionsFList("-thi_mat_type","Matrix type","MatSetType",MatList,mtype,(char*)mtype,sizeof(mtype),NULL);
601:     PetscStrallocpy(mtype,&thi->mattype);
602:     PetscOptionsBool("-thi_verbose","Enable verbose output (like matrix sizes and statistics)","",thi->verbose,&thi->verbose,NULL);
603:     PetscOptionsString("-thi_monitor","Basename to write state files to",NULL,monitor_basename,monitor_basename,sizeof(monitor_basename),&flg);
604:     if (flg) {
605:       PetscStrallocpy(monitor_basename,&thi->monitor_basename);
606:       thi->monitor_interval = 1;
607:       PetscOptionsInt("-thi_monitor_interval","Frequency at which to write state files",NULL,thi->monitor_interval,&thi->monitor_interval,NULL);
608:     }
609:   }
610:   PetscOptionsEnd();

612:   /* dimensionalize */
613:   thi->Lx    *= units->meter;
614:   thi->Ly    *= units->meter;
615:   thi->Lz    *= units->meter;
616:   thi->alpha *= PETSC_PI / 180;

618:   PRangeClear(&thi->eta);
619:   PRangeClear(&thi->beta2);

621:   {
622:     PetscReal u       = 1000*units->meter/(3e7*units->second),
623:               gradu   = u / (100*units->meter),eta,deta,
624:               rho     = 910 * units->kilogram/PetscPowRealInt(units->meter,3),
625:               grav    = 9.81 * units->meter/PetscSqr(units->second),
626:               driving = rho * grav * PetscSinReal(thi->alpha) * 1000*units->meter;
627:     THIViscosity(thi,0.5*gradu*gradu,&eta,&deta);
628:     thi->rhog = rho * grav;
629:     if (thi->verbose) {
630:       PetscPrintf(PetscObjectComm((PetscObject)thi),"Units: meter %8.2g  second %8.2g  kg %8.2g  Pa %8.2g\n",units->meter,units->second,units->kilogram,units->Pascal);
631:       PetscPrintf(PetscObjectComm((PetscObject)thi),"Domain (%6.2g,%6.2g,%6.2g), pressure %8.2g, driving stress %8.2g\n",thi->Lx,thi->Ly,thi->Lz,rho*grav*1e3*units->meter,driving);
632:       PetscPrintf(PetscObjectComm((PetscObject)thi),"Large velocity 1km/a %8.2g, velocity gradient %8.2g, eta %8.2g, stress %8.2g, ratio %8.2g\n",u,gradu,eta,2*eta*gradu,2*eta*gradu/driving);
633:       THIViscosity(thi,0.5*PetscSqr(1e-3*gradu),&eta,&deta);
634:       PetscPrintf(PetscObjectComm((PetscObject)thi),"Small velocity 1m/a  %8.2g, velocity gradient %8.2g, eta %8.2g, stress %8.2g, ratio %8.2g\n",1e-3*u,1e-3*gradu,eta,2*eta*1e-3*gradu,2*eta*1e-3*gradu/driving);
635:     }
636:   }

638:   *inthi = thi;
639:   return(0);
640: }

642: /* Our problem is periodic, but the domain has a mean slope of alpha so the bed does not line up between the upstream
643:  * and downstream ends of the domain.  This function fixes the ghost values so that the domain appears truly periodic in
644:  * the horizontal. */
645: static PetscErrorCode THIFixGhosts(THI thi,DM da3,DM da2,Vec X3,Vec X2)
646: {
648:   DMDALocalInfo  info;
649:   PrmNode        **x2;
650:   PetscInt       i,j;

653:   DMDAGetLocalInfo(da3,&info);
654:   /* VecView(X2,PETSC_VIEWER_STDOUT_WORLD); */
655:   DMDAVecGetArray(da2,X2,&x2);
656:   for (i=info.gzs; i<info.gzs+info.gzm; i++) {
657:     if (i > -1 && i < info.mz) continue;
658:     for (j=info.gys; j<info.gys+info.gym; j++) {
659:       x2[i][j].b += PetscSinReal(thi->alpha) * thi->Lx * (i<0 ? 1.0 : -1.0);
660:     }
661:   }
662:   DMDAVecRestoreArray(da2,X2,&x2);
663:   /* VecView(X2,PETSC_VIEWER_STDOUT_WORLD); */
664:   return(0);
665: }

667: static PetscErrorCode THIInitializePrm(THI thi,DM da2prm,PrmNode **p)
668: {
669:   PetscInt       i,j,xs,xm,ys,ym,mx,my;

673:   DMDAGetGhostCorners(da2prm,&ys,&xs,0,&ym,&xm,0);
674:   DMDAGetInfo(da2prm,0, &my,&mx,0, 0,0,0, 0,0,0,0,0,0);
675:   for (i=xs; i<xs+xm; i++) {
676:     for (j=ys; j<ys+ym; j++) {
677:       PetscReal xx = thi->Lx*i/mx,yy = thi->Ly*j/my;
678:       thi->initialize(thi,xx,yy,&p[i][j]);
679:     }
680:   }
681:   return(0);
682: }

684: static PetscErrorCode THIInitial(THI thi,DM pack,Vec X)
685: {
686:   DM             da3,da2;
687:   PetscInt       i,j,k,xs,xm,ys,ym,zs,zm,mx,my;
688:   PetscReal      hx,hy;
689:   PrmNode        **prm;
690:   Node           ***x;
691:   Vec            X3g,X2g,X2;

695:   DMCompositeGetEntries(pack,&da3,&da2);
696:   DMCompositeGetAccess(pack,X,&X3g,&X2g);
697:   DMGetLocalVector(da2,&X2);

699:   DMDAGetInfo(da3,0, 0,&my,&mx, 0,0,0, 0,0,0,0,0,0);
700:   DMDAGetCorners(da3,&zs,&ys,&xs,&zm,&ym,&xm);
701:   DMDAVecGetArray(da3,X3g,&x);
702:   DMDAVecGetArray(da2,X2,&prm);

704:   THIInitializePrm(thi,da2,prm);

706:   hx = thi->Lx / mx;
707:   hy = thi->Ly / my;
708:   for (i=xs; i<xs+xm; i++) {
709:     for (j=ys; j<ys+ym; j++) {
710:       for (k=zs; k<zs+zm; k++) {
711:         const PetscScalar zm1      = zm-1,
712:                           drivingx = thi->rhog * (prm[i+1][j].b+prm[i+1][j].h - prm[i-1][j].b-prm[i-1][j].h) / (2*hx),
713:                           drivingy = thi->rhog * (prm[i][j+1].b+prm[i][j+1].h - prm[i][j-1].b-prm[i][j-1].h) / (2*hy);
714:         x[i][j][k].u = 0. * drivingx * prm[i][j].h*(PetscScalar)k/zm1;
715:         x[i][j][k].v = 0. * drivingy * prm[i][j].h*(PetscScalar)k/zm1;
716:       }
717:     }
718:   }

720:   DMDAVecRestoreArray(da3,X3g,&x);
721:   DMDAVecRestoreArray(da2,X2,&prm);

723:   DMLocalToGlobalBegin(da2,X2,INSERT_VALUES,X2g);
724:   DMLocalToGlobalEnd  (da2,X2,INSERT_VALUES,X2g);
725:   DMRestoreLocalVector(da2,&X2);

727:   DMCompositeRestoreAccess(pack,X,&X3g,&X2g);
728:   return(0);
729: }

731: static void PointwiseNonlinearity(THI thi,const Node n[restrict 8],const PetscReal phi[restrict 3],PetscReal dphi[restrict 8][3],PetscScalar *restrict u,PetscScalar *restrict v,PetscScalar du[restrict 3],PetscScalar dv[restrict 3],PetscReal *eta,PetscReal *deta)
732: {
733:   PetscInt    l,ll;
734:   PetscScalar gam;

736:   du[0] = du[1] = du[2] = 0;
737:   dv[0] = dv[1] = dv[2] = 0;
738:   *u    = 0;
739:   *v    = 0;
740:   for (l=0; l<8; l++) {
741:     *u += phi[l] * n[l].u;
742:     *v += phi[l] * n[l].v;
743:     for (ll=0; ll<3; ll++) {
744:       du[ll] += dphi[l][ll] * n[l].u;
745:       dv[ll] += dphi[l][ll] * n[l].v;
746:     }
747:   }
748:   gam = Sqr(du[0]) + Sqr(dv[1]) + du[0]*dv[1] + 0.25*Sqr(du[1]+dv[0]) + 0.25*Sqr(du[2]) + 0.25*Sqr(dv[2]);
749:   THIViscosity(thi,PetscRealPart(gam),eta,deta);
750: }

752: static PetscErrorCode THIFunctionLocal_3D(DMDALocalInfo *info,const Node ***x,const PrmNode **prm,const Node ***xdot,Node ***f,THI thi)
753: {
754:   PetscInt       xs,ys,xm,ym,zm,i,j,k,q,l;
755:   PetscReal      hx,hy,etamin,etamax,beta2min,beta2max;

759:   xs = info->zs;
760:   ys = info->ys;
761:   xm = info->zm;
762:   ym = info->ym;
763:   zm = info->xm;
764:   hx = thi->Lx / info->mz;
765:   hy = thi->Ly / info->my;

767:   etamin   = 1e100;
768:   etamax   = 0;
769:   beta2min = 1e100;
770:   beta2max = 0;

772:   for (i=xs; i<xs+xm; i++) {
773:     for (j=ys; j<ys+ym; j++) {
774:       PrmNode pn[4],dpn[4][2];
775:       QuadExtract(prm,i,j,pn);
776:       QuadComputeGrad4(QuadQDeriv,hx,hy,pn,dpn);
777:       for (k=0; k<zm-1; k++) {
778:         PetscInt  ls = 0;
779:         Node      n[8],ndot[8],*fn[8];
780:         PetscReal zn[8],etabase = 0;
781:         PrmHexGetZ(pn,k,zm,zn);
782:         HexExtract(x,i,j,k,n);
783:         HexExtract(xdot,i,j,k,ndot);
784:         HexExtractRef(f,i,j,k,fn);
785:         if (thi->no_slip && k == 0) {
786:           for (l=0; l<4; l++) n[l].u = n[l].v = 0;
787:           /* The first 4 basis functions lie on the bottom layer, so their contribution is exactly 0, hence we can skip them */
788:           ls = 4;
789:         }
790:         for (q=0; q<8; q++) {
791:           PetscReal   dz[3],phi[8],dphi[8][3],jw,eta,deta;
792:           PetscScalar du[3],dv[3],u,v,udot=0,vdot=0;
793:           for (l=ls; l<8; l++) {
794:             udot += HexQInterp[q][l]*ndot[l].u;
795:             vdot += HexQInterp[q][l]*ndot[l].v;
796:           }
797:           HexGrad(HexQDeriv[q],zn,dz);
798:           HexComputeGeometry(q,hx,hy,dz,phi,dphi,&jw);
799:           PointwiseNonlinearity(thi,n,phi,dphi,&u,&v,du,dv,&eta,&deta);
800:           jw /= thi->rhog;      /* scales residuals to be O(1) */
801:           if (q == 0) etabase = eta;
802:           RangeUpdate(&etamin,&etamax,eta);
803:           for (l=ls; l<8; l++) { /* test functions */
804:             const PetscScalar ds[2] = {dpn[q%4][0].h+dpn[q%4][0].b, dpn[q%4][1].h+dpn[q%4][1].b};
805:             const PetscReal   pp    = phi[l],*dp = dphi[l];
806:             fn[l]->u += dp[0]*jw*eta*(4.*du[0]+2.*dv[1]) + dp[1]*jw*eta*(du[1]+dv[0]) + dp[2]*jw*eta*du[2] + pp*jw*thi->rhog*ds[0];
807:             fn[l]->v += dp[1]*jw*eta*(2.*du[0]+4.*dv[1]) + dp[0]*jw*eta*(du[1]+dv[0]) + dp[2]*jw*eta*dv[2] + pp*jw*thi->rhog*ds[1];
808:             fn[l]->u += pp*jw*udot*thi->inertia*pp;
809:             fn[l]->v += pp*jw*vdot*thi->inertia*pp;
810:           }
811:         }
812:         if (k == 0) { /* we are on a bottom face */
813:           if (thi->no_slip) {
814:             /* Note: Non-Galerkin coarse grid operators are very sensitive to the scaling of Dirichlet boundary
815:             * conditions.  After shenanigans above, etabase contains the effective viscosity at the closest quadrature
816:             * point to the bed.  We want the diagonal entry in the Dirichlet condition to have similar magnitude to the
817:             * diagonal entry corresponding to the adjacent node.  The fundamental scaling of the viscous part is in
818:             * diagu, diagv below.  This scaling is easy to recognize by considering the finite difference operator after
819:             * scaling by element size.  The no-slip Dirichlet condition is scaled by this factor, and also in the
820:             * assembled matrix (see the similar block in THIJacobianLocal).
821:             *
822:             * Note that the residual at this Dirichlet node is linear in the state at this node, but also depends
823:             * (nonlinearly in general) on the neighboring interior nodes through the local viscosity.  This will make
824:             * a matrix-free Jacobian have extra entries in the corresponding row.  We assemble only the diagonal part,
825:             * so the solution will exactly satisfy the boundary condition after the first linear iteration.
826:             */
827:             const PetscReal   hz    = PetscRealPart(pn[0].h)/(zm-1.);
828:             const PetscScalar diagu = 2*etabase/thi->rhog*(hx*hy/hz + hx*hz/hy + 4*hy*hz/hx),diagv = 2*etabase/thi->rhog*(hx*hy/hz + 4*hx*hz/hy + hy*hz/hx);
829:             fn[0]->u = thi->dirichlet_scale*diagu*x[i][j][k].u;
830:             fn[0]->v = thi->dirichlet_scale*diagv*x[i][j][k].v;
831:           } else {              /* Integrate over bottom face to apply boundary condition */
832:             for (q=0; q<4; q++) { /* We remove the explicit scaling of the residual by 1/rhog because beta2 already has that scaling to be O(1) */
833:               const PetscReal jw = 0.25*hx*hy,*phi = QuadQInterp[q];
834:               PetscScalar     u  =0,v=0,rbeta2=0;
835:               PetscReal       beta2,dbeta2;
836:               for (l=0; l<4; l++) {
837:                 u     += phi[l]*n[l].u;
838:                 v     += phi[l]*n[l].v;
839:                 rbeta2 += phi[l]*pn[l].beta2;
840:               }
841:               THIFriction(thi,PetscRealPart(rbeta2),PetscRealPart(u*u+v*v)/2,&beta2,&dbeta2);
842:               RangeUpdate(&beta2min,&beta2max,beta2);
843:               for (l=0; l<4; l++) {
844:                 const PetscReal pp = phi[l];
845:                 fn[ls+l]->u += pp*jw*beta2*u;
846:                 fn[ls+l]->v += pp*jw*beta2*v;
847:               }
848:             }
849:           }
850:         }
851:       }
852:     }
853:   }

855:   PRangeMinMax(&thi->eta,etamin,etamax);
856:   PRangeMinMax(&thi->beta2,beta2min,beta2max);
857:   return(0);
858: }

860: static PetscErrorCode THIFunctionLocal_2D(DMDALocalInfo *info,const Node ***x,const PrmNode **prm,const PrmNode **prmdot,PrmNode **f,THI thi)
861: {
862:   PetscInt xs,ys,xm,ym,zm,i,j,k;

865:   xs = info->zs;
866:   ys = info->ys;
867:   xm = info->zm;
868:   ym = info->ym;
869:   zm = info->xm;

871:   for (i=xs; i<xs+xm; i++) {
872:     for (j=ys; j<ys+ym; j++) {
873:       PetscScalar div = 0,erate,h[8];
874:       PrmNodeGetFaceMeasure(prm,i,j,h);
875:       for (k=0; k<zm; k++) {
876:         PetscScalar weight = (k==0 || k == zm-1) ? 0.5/(zm-1) : 1.0/(zm-1);
877:         if (0) {                /* centered flux */
878:           div += (- weight*h[0] * StaggeredMidpoint2D(x[i][j][k].u,x[i-1][j][k].u, x[i-1][j-1][k].u,x[i][j-1][k].u)
879:                   - weight*h[1] * StaggeredMidpoint2D(x[i][j][k].u,x[i-1][j][k].u, x[i-1][j+1][k].u,x[i][j+1][k].u)
880:                   + weight*h[2] * StaggeredMidpoint2D(x[i][j][k].u,x[i+1][j][k].u, x[i+1][j+1][k].u,x[i][j+1][k].u)
881:                   + weight*h[3] * StaggeredMidpoint2D(x[i][j][k].u,x[i+1][j][k].u, x[i+1][j-1][k].u,x[i][j-1][k].u)
882:                   - weight*h[4] * StaggeredMidpoint2D(x[i][j][k].v,x[i][j-1][k].v, x[i+1][j-1][k].v,x[i+1][j][k].v)
883:                   - weight*h[5] * StaggeredMidpoint2D(x[i][j][k].v,x[i][j-1][k].v, x[i-1][j-1][k].v,x[i-1][j][k].v)
884:                   + weight*h[6] * StaggeredMidpoint2D(x[i][j][k].v,x[i][j+1][k].v, x[i-1][j+1][k].v,x[i-1][j][k].v)
885:                   + weight*h[7] * StaggeredMidpoint2D(x[i][j][k].v,x[i][j+1][k].v, x[i+1][j+1][k].v,x[i+1][j][k].v));
886:         } else {                /* Upwind flux */
887:           div += weight*(-UpwindFluxXW(x,prm,h,i,j,k, 1)
888:                          -UpwindFluxXW(x,prm,h,i,j,k,-1)
889:                          +UpwindFluxXE(x,prm,h,i,j,k, 1)
890:                          +UpwindFluxXE(x,prm,h,i,j,k,-1)
891:                          -UpwindFluxYS(x,prm,h,i,j,k, 1)
892:                          -UpwindFluxYS(x,prm,h,i,j,k,-1)
893:                          +UpwindFluxYN(x,prm,h,i,j,k, 1)
894:                          +UpwindFluxYN(x,prm,h,i,j,k,-1));
895:         }
896:       }
897:       /* printf("div[%d][%d] %g\n",i,j,div); */
898:       THIErosion(thi,&x[i][j][0],&erate,NULL);
899:       f[i][j].b     = prmdot[i][j].b - erate;
900:       f[i][j].h     = prmdot[i][j].h + div;
901:       f[i][j].beta2 = prmdot[i][j].beta2;
902:     }
903:   }
904:   return(0);
905: }

907: static PetscErrorCode THIFunction(TS ts,PetscReal t,Vec X,Vec Xdot,Vec F,void *ctx)
908: {
910:   THI            thi = (THI)ctx;
911:   DM             pack,da3,da2;
912:   Vec            X3,X2,Xdot3,Xdot2,F3,F2,F3g,F2g;
913:   const Node     ***x3,***xdot3;
914:   const PrmNode  **x2,**xdot2;
915:   Node           ***f3;
916:   PrmNode        **f2;
917:   DMDALocalInfo  info3;

920:   TSGetDM(ts,&pack);
921:   DMCompositeGetEntries(pack,&da3,&da2);
922:   DMDAGetLocalInfo(da3,&info3);
923:   DMCompositeGetLocalVectors(pack,&X3,&X2);
924:   DMCompositeGetLocalVectors(pack,&Xdot3,&Xdot2);
925:   DMCompositeScatter(pack,X,X3,X2);
926:   THIFixGhosts(thi,da3,da2,X3,X2);
927:   DMCompositeScatter(pack,Xdot,Xdot3,Xdot2);

929:   DMGetLocalVector(da3,&F3);
930:   DMGetLocalVector(da2,&F2);
931:   VecZeroEntries(F3);

933:   DMDAVecGetArray(da3,X3,&x3);
934:   DMDAVecGetArray(da2,X2,&x2);
935:   DMDAVecGetArray(da3,Xdot3,&xdot3);
936:   DMDAVecGetArray(da2,Xdot2,&xdot2);
937:   DMDAVecGetArray(da3,F3,&f3);
938:   DMDAVecGetArray(da2,F2,&f2);

940:   THIFunctionLocal_3D(&info3,x3,x2,xdot3,f3,thi);
941:   THIFunctionLocal_2D(&info3,x3,x2,xdot2,f2,thi);

943:   DMDAVecRestoreArray(da3,X3,&x3);
944:   DMDAVecRestoreArray(da2,X2,&x2);
945:   DMDAVecRestoreArray(da3,Xdot3,&xdot3);
946:   DMDAVecRestoreArray(da2,Xdot2,&xdot2);
947:   DMDAVecRestoreArray(da3,F3,&f3);
948:   DMDAVecRestoreArray(da2,F2,&f2);

950:   DMCompositeRestoreLocalVectors(pack,&X3,&X2);
951:   DMCompositeRestoreLocalVectors(pack,&Xdot3,&Xdot2);

953:   VecZeroEntries(F);
954:   DMCompositeGetAccess(pack,F,&F3g,&F2g);
955:   DMLocalToGlobalBegin(da3,F3,ADD_VALUES,F3g);
956:   DMLocalToGlobalEnd  (da3,F3,ADD_VALUES,F3g);
957:   DMLocalToGlobalBegin(da2,F2,INSERT_VALUES,F2g);
958:   DMLocalToGlobalEnd  (da2,F2,INSERT_VALUES,F2g);

960:   if (thi->verbose) {
961:     PetscViewer viewer;
962:     PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)thi),&viewer);
963:     PetscViewerASCIIPrintf(viewer,"3D_Velocity residual (bs=2):\n");
964:     PetscViewerASCIIPushTab(viewer);
965:     VecView(F3,viewer);
966:     PetscViewerASCIIPopTab(viewer);
967:     PetscViewerASCIIPrintf(viewer,"2D_Fields residual (bs=3):\n");
968:     PetscViewerASCIIPushTab(viewer);
969:     VecView(F2,viewer);
970:     PetscViewerASCIIPopTab(viewer);
971:   }

973:   DMCompositeRestoreAccess(pack,F,&F3g,&F2g);

975:   DMRestoreLocalVector(da3,&F3);
976:   DMRestoreLocalVector(da2,&F2);
977:   return(0);
978: }

980: static PetscErrorCode THIMatrixStatistics(THI thi,Mat B,PetscViewer viewer)
981: {
983:   PetscReal      nrm;
984:   PetscInt       m;
985:   PetscMPIInt    rank;

988:   MatNorm(B,NORM_FROBENIUS,&nrm);
989:   MatGetSize(B,&m,0);
990:   MPI_Comm_rank(PetscObjectComm((PetscObject)B),&rank);
991:   if (!rank) {
992:     PetscScalar val0,val2;
993:     MatGetValue(B,0,0,&val0);
994:     MatGetValue(B,2,2,&val2);
995:     PetscViewerASCIIPrintf(viewer,"Matrix dim %8d  norm %8.2e, (0,0) %8.2e  (2,2) %8.2e, eta [%8.2e,%8.2e] beta2 [%8.2e,%8.2e]\n",m,nrm,PetscRealPart(val0),PetscRealPart(val2),thi->eta.cmin,thi->eta.cmax,thi->beta2.cmin,thi->beta2.cmax);
996:   }
997:   return(0);
998: }

1000: static PetscErrorCode THISurfaceStatistics(DM pack,Vec X,PetscReal *min,PetscReal *max,PetscReal *mean)
1001: {
1003:   DM             da3,da2;
1004:   Vec            X3,X2;
1005:   Node           ***x;
1006:   PetscInt       i,j,xs,ys,zs,xm,ym,zm,mx,my,mz;
1007:   PetscReal      umin = 1e100,umax=-1e100;
1008:   PetscScalar    usum =0.0,gusum;

1011:   DMCompositeGetEntries(pack,&da3,&da2);
1012:   DMCompositeGetAccess(pack,X,&X3,&X2);
1013:   *min = *max = *mean = 0;
1014:   DMDAGetInfo(da3,0, &mz,&my,&mx, 0,0,0, 0,0,0,0,0,0);
1015:   DMDAGetCorners(da3,&zs,&ys,&xs,&zm,&ym,&xm);
1016:   if (zs != 0 || zm != mz) SETERRQ(PETSC_COMM_SELF,1,"Unexpected decomposition");
1017:   DMDAVecGetArray(da3,X3,&x);
1018:   for (i=xs; i<xs+xm; i++) {
1019:     for (j=ys; j<ys+ym; j++) {
1020:       PetscReal u = PetscRealPart(x[i][j][zm-1].u);
1021:       RangeUpdate(&umin,&umax,u);
1022:       usum += u;
1023:     }
1024:   }
1025:   DMDAVecRestoreArray(da3,X3,&x);
1026:   DMCompositeRestoreAccess(pack,X,&X3,&X2);

1028:   MPI_Allreduce(&umin,min,1,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)da3));
1029:   MPI_Allreduce(&umax,max,1,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)da3));
1030:   MPI_Allreduce(&usum,&gusum,1,MPIU_SCALAR,MPIU_SUM,PetscObjectComm((PetscObject)da3));
1031:   *mean = PetscRealPart(gusum) / (mx*my);
1032:   return(0);
1033: }

1035: static PetscErrorCode THISolveStatistics(THI thi,TS ts,PetscInt coarsened,const char name[])
1036: {
1037:   MPI_Comm       comm;
1038:   DM             pack;
1039:   Vec            X,X3,X2;

1043:   PetscObjectGetComm((PetscObject)thi,&comm);
1044:   TSGetDM(ts,&pack);
1045:   TSGetSolution(ts,&X);
1046:   DMCompositeGetAccess(pack,X,&X3,&X2);
1047:   PetscPrintf(comm,"Solution statistics after solve: %s\n",name);
1048:   {
1049:     PetscInt            its,lits;
1050:     SNESConvergedReason reason;
1051:     SNES                snes;
1052:     TSGetSNES(ts,&snes);
1053:     SNESGetIterationNumber(snes,&its);
1054:     SNESGetConvergedReason(snes,&reason);
1055:     SNESGetLinearSolveIterations(snes,&lits);
1056:     PetscPrintf(comm,"%s: Number of SNES iterations = %d, total linear iterations = %d\n",SNESConvergedReasons[reason],its,lits);
1057:   }
1058:   {
1059:     PetscReal   nrm2,tmin[3]={1e100,1e100,1e100},tmax[3]={-1e100,-1e100,-1e100},min[3],max[3];
1060:     PetscInt    i,j,m;
1061:     PetscScalar *x;
1062:     VecNorm(X3,NORM_2,&nrm2);
1063:     VecGetLocalSize(X3,&m);
1064:     VecGetArray(X3,&x);
1065:     for (i=0; i<m; i+=2) {
1066:       PetscReal u = PetscRealPart(x[i]),v = PetscRealPart(x[i+1]),c = PetscSqrtReal(u*u+v*v);
1067:       tmin[0] = PetscMin(u,tmin[0]);
1068:       tmin[1] = PetscMin(v,tmin[1]);
1069:       tmin[2] = PetscMin(c,tmin[2]);
1070:       tmax[0] = PetscMax(u,tmax[0]);
1071:       tmax[1] = PetscMax(v,tmax[1]);
1072:       tmax[2] = PetscMax(c,tmax[2]);
1073:     }
1074:     VecRestoreArray(X,&x);
1075:     MPI_Allreduce(tmin,min,3,MPIU_REAL,MPIU_MIN,PetscObjectComm((PetscObject)thi));
1076:     MPI_Allreduce(tmax,max,3,MPIU_REAL,MPIU_MAX,PetscObjectComm((PetscObject)thi));
1077:     /* Dimensionalize to meters/year */
1078:     nrm2 *= thi->units->year / thi->units->meter;
1079:     for (j=0; j<3; j++) {
1080:       min[j] *= thi->units->year / thi->units->meter;
1081:       max[j] *= thi->units->year / thi->units->meter;
1082:     }
1083:     PetscPrintf(comm,"|X|_2 %g   u in [%g, %g]   v in [%g, %g]   c in [%g, %g] \n",nrm2,min[0],max[0],min[1],max[1],min[2],max[2]);
1084:     {
1085:       PetscReal umin,umax,umean;
1086:       THISurfaceStatistics(pack,X,&umin,&umax,&umean);
1087:       umin  *= thi->units->year / thi->units->meter;
1088:       umax  *= thi->units->year / thi->units->meter;
1089:       umean *= thi->units->year / thi->units->meter;
1090:       PetscPrintf(comm,"Surface statistics: u in [%12.6e, %12.6e] mean %12.6e\n",umin,umax,umean);
1091:     }
1092:     /* These values stay nondimensional */
1093:     PetscPrintf(comm,"Global eta range   [%g, %g], converged range [%g, %g]\n",thi->eta.min,thi->eta.max,thi->eta.cmin,thi->eta.cmax);
1094:     PetscPrintf(comm,"Global beta2 range [%g, %g], converged range [%g, %g]\n",thi->beta2.min,thi->beta2.max,thi->beta2.cmin,thi->beta2.cmax);
1095:   }
1096:   PetscPrintf(comm,"\n");
1097:   DMCompositeRestoreAccess(pack,X,&X3,&X2);
1098:   return(0);
1099: }

1101: static inline PetscInt DMDALocalIndex3D(DMDALocalInfo *info,PetscInt i,PetscInt j,PetscInt k)
1102: {return ((i-info->gzs)*info->gym + (j-info->gys))*info->gxm + (k-info->gxs);}
1103: static inline PetscInt DMDALocalIndex2D(DMDALocalInfo *info,PetscInt i,PetscInt j)
1104: {return (i-info->gzs)*info->gym + (j-info->gys);}

1106: static PetscErrorCode THIJacobianLocal_Momentum(DMDALocalInfo *info,const Node ***x,const PrmNode **prm,Mat B,Mat Bcpl,THI thi)
1107: {
1108:   PetscInt       xs,ys,xm,ym,zm,i,j,k,q,l,ll;
1109:   PetscReal      hx,hy;

1113:   xs = info->zs;
1114:   ys = info->ys;
1115:   xm = info->zm;
1116:   ym = info->ym;
1117:   zm = info->xm;
1118:   hx = thi->Lx / info->mz;
1119:   hy = thi->Ly / info->my;

1121:   for (i=xs; i<xs+xm; i++) {
1122:     for (j=ys; j<ys+ym; j++) {
1123:       PrmNode pn[4],dpn[4][2];
1124:       QuadExtract(prm,i,j,pn);
1125:       QuadComputeGrad4(QuadQDeriv,hx,hy,pn,dpn);
1126:       for (k=0; k<zm-1; k++) {
1127:         Node        n[8];
1128:         PetscReal   zn[8],etabase = 0;
1129:         PetscScalar Ke[8*NODE_SIZE][8*NODE_SIZE],Kcpl[8*NODE_SIZE][4*PRMNODE_SIZE];
1130:         PetscInt    ls = 0;

1132:         PrmHexGetZ(pn,k,zm,zn);
1133:         HexExtract(x,i,j,k,n);
1134:         PetscMemzero(Ke,sizeof(Ke));
1135:         PetscMemzero(Kcpl,sizeof(Kcpl));
1136:         if (thi->no_slip && k == 0) {
1137:           for (l=0; l<4; l++) n[l].u = n[l].v = 0;
1138:           ls = 4;
1139:         }
1140:         for (q=0; q<8; q++) {
1141:           PetscReal   dz[3],phi[8],dphi[8][3],jw,eta,deta;
1142:           PetscScalar du[3],dv[3],u,v;
1143:           HexGrad(HexQDeriv[q],zn,dz);
1144:           HexComputeGeometry(q,hx,hy,dz,phi,dphi,&jw);
1145:           PointwiseNonlinearity(thi,n,phi,dphi,&u,&v,du,dv,&eta,&deta);
1146:           jw /= thi->rhog;      /* residuals are scaled by this factor */
1147:           if (q == 0) etabase = eta;
1148:           for (l=ls; l<8; l++) { /* test functions */
1149:             const PetscReal pp=phi[l],*restrict dp = dphi[l];
1150:             for (ll=ls; ll<8; ll++) { /* trial functions */
1151:               const PetscReal *restrict dpl = dphi[ll];
1152:               PetscScalar dgdu,dgdv;
1153:               dgdu = 2.*du[0]*dpl[0] + dv[1]*dpl[0] + 0.5*(du[1]+dv[0])*dpl[1] + 0.5*du[2]*dpl[2];
1154:               dgdv = 2.*dv[1]*dpl[1] + du[0]*dpl[1] + 0.5*(du[1]+dv[0])*dpl[0] + 0.5*dv[2]*dpl[2];
1155:               /* Picard part */
1156:               Ke[l*2+0][ll*2+0] += dp[0]*jw*eta*4.*dpl[0] + dp[1]*jw*eta*dpl[1] + dp[2]*jw*eta*dpl[2];
1157:               Ke[l*2+0][ll*2+1] += dp[0]*jw*eta*2.*dpl[1] + dp[1]*jw*eta*dpl[0];
1158:               Ke[l*2+1][ll*2+0] += dp[1]*jw*eta*2.*dpl[0] + dp[0]*jw*eta*dpl[1];
1159:               Ke[l*2+1][ll*2+1] += dp[1]*jw*eta*4.*dpl[1] + dp[0]*jw*eta*dpl[0] + dp[2]*jw*eta*dpl[2];
1160:               /* extra Newton terms */
1161:               Ke[l*2+0][ll*2+0] += dp[0]*jw*deta*dgdu*(4.*du[0]+2.*dv[1]) + dp[1]*jw*deta*dgdu*(du[1]+dv[0]) + dp[2]*jw*deta*dgdu*du[2];
1162:               Ke[l*2+0][ll*2+1] += dp[0]*jw*deta*dgdv*(4.*du[0]+2.*dv[1]) + dp[1]*jw*deta*dgdv*(du[1]+dv[0]) + dp[2]*jw*deta*dgdv*du[2];
1163:               Ke[l*2+1][ll*2+0] += dp[1]*jw*deta*dgdu*(4.*dv[1]+2.*du[0]) + dp[0]*jw*deta*dgdu*(du[1]+dv[0]) + dp[2]*jw*deta*dgdu*dv[2];
1164:               Ke[l*2+1][ll*2+1] += dp[1]*jw*deta*dgdv*(4.*dv[1]+2.*du[0]) + dp[0]*jw*deta*dgdv*(du[1]+dv[0]) + dp[2]*jw*deta*dgdv*dv[2];
1165:               /* inertial part */
1166:               Ke[l*2+0][ll*2+0] += pp*jw*thi->inertia*pp;
1167:               Ke[l*2+1][ll*2+1] += pp*jw*thi->inertia*pp;
1168:             }
1169:             for (ll=0; ll<4; ll++) { /* Trial functions for surface/bed */
1170:               const PetscReal dpl[] = {QuadQDeriv[q%4][ll][0]/hx, QuadQDeriv[q%4][ll][1]/hy}; /* surface = h + b */
1171:               Kcpl[FieldIndex(Node,l,u)][FieldIndex(PrmNode,ll,h)] += pp*jw*thi->rhog*dpl[0];
1172:               Kcpl[FieldIndex(Node,l,u)][FieldIndex(PrmNode,ll,b)] += pp*jw*thi->rhog*dpl[0];
1173:               Kcpl[FieldIndex(Node,l,v)][FieldIndex(PrmNode,ll,h)] += pp*jw*thi->rhog*dpl[1];
1174:               Kcpl[FieldIndex(Node,l,v)][FieldIndex(PrmNode,ll,b)] += pp*jw*thi->rhog*dpl[1];
1175:             }
1176:           }
1177:         }
1178:         if (k == 0) { /* on a bottom face */
1179:           if (thi->no_slip) {
1180:             const PetscReal   hz    = PetscRealPart(pn[0].h)/(zm-1);
1181:             const PetscScalar diagu = 2*etabase/thi->rhog*(hx*hy/hz + hx*hz/hy + 4*hy*hz/hx),diagv = 2*etabase/thi->rhog*(hx*hy/hz + 4*hx*hz/hy + hy*hz/hx);
1182:             Ke[0][0] = thi->dirichlet_scale*diagu;
1183:             Ke[0][1] = 0;
1184:             Ke[1][0] = 0;
1185:             Ke[1][1] = thi->dirichlet_scale*diagv;
1186:           } else {
1187:             for (q=0; q<4; q++) { /* We remove the explicit scaling by 1/rhog because beta2 already has that scaling to be O(1) */
1188:               const PetscReal jw = 0.25*hx*hy,*phi = QuadQInterp[q];
1189:               PetscScalar     u  =0,v=0,rbeta2=0;
1190:               PetscReal       beta2,dbeta2;
1191:               for (l=0; l<4; l++) {
1192:                 u      += phi[l]*n[l].u;
1193:                 v      += phi[l]*n[l].v;
1194:                 rbeta2 += phi[l]*pn[l].beta2;
1195:               }
1196:               THIFriction(thi,PetscRealPart(rbeta2),PetscRealPart(u*u+v*v)/2,&beta2,&dbeta2);
1197:               for (l=0; l<4; l++) {
1198:                 const PetscReal pp = phi[l];
1199:                 for (ll=0; ll<4; ll++) {
1200:                   const PetscReal ppl = phi[ll];
1201:                   Ke[l*2+0][ll*2+0] += pp*jw*beta2*ppl + pp*jw*dbeta2*u*u*ppl;
1202:                   Ke[l*2+0][ll*2+1] +=                   pp*jw*dbeta2*u*v*ppl;
1203:                   Ke[l*2+1][ll*2+0] +=                   pp*jw*dbeta2*v*u*ppl;
1204:                   Ke[l*2+1][ll*2+1] += pp*jw*beta2*ppl + pp*jw*dbeta2*v*v*ppl;
1205:                 }
1206:               }
1207:             }
1208:           }
1209:         }
1210:         {
1211:           const PetscInt rc3blocked[8] = {
1212:             DMDALocalIndex3D(info,i+0,j+0,k+0),
1213:             DMDALocalIndex3D(info,i+1,j+0,k+0),
1214:             DMDALocalIndex3D(info,i+1,j+1,k+0),
1215:             DMDALocalIndex3D(info,i+0,j+1,k+0),
1216:             DMDALocalIndex3D(info,i+0,j+0,k+1),
1217:             DMDALocalIndex3D(info,i+1,j+0,k+1),
1218:             DMDALocalIndex3D(info,i+1,j+1,k+1),
1219:             DMDALocalIndex3D(info,i+0,j+1,k+1)
1220:           },col2blocked[PRMNODE_SIZE*4] = {
1221:             DMDALocalIndex2D(info,i+0,j+0),
1222:             DMDALocalIndex2D(info,i+1,j+0),
1223:             DMDALocalIndex2D(info,i+1,j+1),
1224:             DMDALocalIndex2D(info,i+0,j+1)
1225:           };
1226: #if !defined COMPUTE_LOWER_TRIANGULAR /* fill in lower-triangular part, this is really cheap compared to computing the entries */
1227:           for (l=0; l<8; l++) {
1228:             for (ll=l+1; ll<8; ll++) {
1229:               Ke[ll*2+0][l*2+0] = Ke[l*2+0][ll*2+0];
1230:               Ke[ll*2+1][l*2+0] = Ke[l*2+0][ll*2+1];
1231:               Ke[ll*2+0][l*2+1] = Ke[l*2+1][ll*2+0];
1232:               Ke[ll*2+1][l*2+1] = Ke[l*2+1][ll*2+1];
1233:             }
1234:           }
1235: #endif
1236:           MatSetValuesBlockedLocal(B,8,rc3blocked,8,rc3blocked,&Ke[0][0],ADD_VALUES); /* velocity-velocity coupling can use blocked insertion */
1237:           {                     /* The off-diagonal part cannot (yet) */
1238:             PetscInt row3scalar[NODE_SIZE*8],col2scalar[PRMNODE_SIZE*4];
1239:             for (l=0; l<8; l++) for (ll=0; ll<NODE_SIZE; ll++) row3scalar[l*NODE_SIZE+ll] = rc3blocked[l]*NODE_SIZE+ll;
1240:             for (l=0; l<4; l++) for (ll=0; ll<PRMNODE_SIZE; ll++) col2scalar[l*PRMNODE_SIZE+ll] = col2blocked[l]*PRMNODE_SIZE+ll;
1241:             MatSetValuesLocal(Bcpl,8*NODE_SIZE,row3scalar,4*PRMNODE_SIZE,col2scalar,&Kcpl[0][0],ADD_VALUES);
1242:           }
1243:         }
1244:       }
1245:     }
1246:   }
1247:   return(0);
1248: }

1250: static PetscErrorCode THIJacobianLocal_2D(DMDALocalInfo *info,const Node ***x3,const PrmNode **x2,const PrmNode **xdot2,PetscReal a,Mat B22,Mat B21,THI thi)
1251: {
1253:   PetscInt       xs,ys,xm,ym,zm,i,j,k;

1256:   xs = info->zs;
1257:   ys = info->ys;
1258:   xm = info->zm;
1259:   ym = info->ym;
1260:   zm = info->xm;

1262:   if (zm > 1024) SETERRQ(((PetscObject)info->da)->comm,PETSC_ERR_SUP,"Need to allocate more space");
1263:   for (i=xs; i<xs+xm; i++) {
1264:     for (j=ys; j<ys+ym; j++) {
1265:       {                         /* Self-coupling */
1266:         const PetscInt    row[]  = {DMDALocalIndex2D(info,i,j)};
1267:         const PetscInt    col[]  = {DMDALocalIndex2D(info,i,j)};
1268:         const PetscScalar vals[] = {
1269:           a,0,0,
1270:           0,a,0,
1271:           0,0,a
1272:         };
1273:         MatSetValuesBlockedLocal(B22,1,row,1,col,vals,INSERT_VALUES);
1274:       }
1275:       for (k=0; k<zm; k++) {    /* Coupling to velocity problem */
1276:         /* Use a cheaper quadrature than for residual evaluation, because it is much sparser */
1277:         const PetscInt row[]  = {FieldIndex(PrmNode,DMDALocalIndex2D(info,i,j),h)};
1278:         const PetscInt cols[] = {
1279:           FieldIndex(Node,DMDALocalIndex3D(info,i-1,j,k),u),
1280:           FieldIndex(Node,DMDALocalIndex3D(info,i  ,j,k),u),
1281:           FieldIndex(Node,DMDALocalIndex3D(info,i+1,j,k),u),
1282:           FieldIndex(Node,DMDALocalIndex3D(info,i,j-1,k),v),
1283:           FieldIndex(Node,DMDALocalIndex3D(info,i,j  ,k),v),
1284:           FieldIndex(Node,DMDALocalIndex3D(info,i,j+1,k),v)
1285:         };
1286:         const PetscScalar
1287:           w  = (k && k<zm-1) ? 0.5 : 0.25,
1288:           hW = w*(x2[i-1][j  ].h+x2[i  ][j  ].h)/(zm-1.),
1289:           hE = w*(x2[i  ][j  ].h+x2[i+1][j  ].h)/(zm-1.),
1290:           hS = w*(x2[i  ][j-1].h+x2[i  ][j  ].h)/(zm-1.),
1291:           hN = w*(x2[i  ][j  ].h+x2[i  ][j+1].h)/(zm-1.);
1292:         PetscScalar *vals,
1293:                      vals_upwind[] = {((PetscRealPart(x3[i][j][k].u) > 0) ? -hW : 0),
1294:                                       ((PetscRealPart(x3[i][j][k].u) > 0) ? +hE : -hW),
1295:                                       ((PetscRealPart(x3[i][j][k].u) > 0) ?  0  : +hE),
1296:                                       ((PetscRealPart(x3[i][j][k].v) > 0) ? -hS : 0),
1297:                                       ((PetscRealPart(x3[i][j][k].v) > 0) ? +hN : -hS),
1298:                                       ((PetscRealPart(x3[i][j][k].v) > 0) ?  0  : +hN)},
1299:                      vals_centered[] = {-0.5*hW, 0.5*(-hW+hE), 0.5*hE,
1300:                                         -0.5*hS, 0.5*(-hS+hN), 0.5*hN};
1301:         vals = 1 ? vals_upwind : vals_centered;
1302:         if (k == 0) {
1303:           Node derate;
1304:           THIErosion(thi,&x3[i][j][0],NULL,&derate);
1305:           vals[1] -= derate.u;
1306:           vals[4] -= derate.v;
1307:         }
1308:         MatSetValuesLocal(B21,1,row,6,cols,vals,INSERT_VALUES);
1309:       }
1310:     }
1311:   }
1312:   return(0);
1313: }

1315: static PetscErrorCode THIJacobian(TS ts,PetscReal t,Vec X,Vec Xdot,PetscReal a,Mat A,Mat B,void *ctx)
1316: {
1318:   THI            thi = (THI)ctx;
1319:   DM             pack,da3,da2;
1320:   Vec            X3,X2,Xdot2;
1321:   Mat            B11,B12,B21,B22;
1322:   DMDALocalInfo  info3;
1323:   IS             *isloc;
1324:   const Node     ***x3;
1325:   const PrmNode  **x2,**xdot2;

1328:   TSGetDM(ts,&pack);
1329:   DMCompositeGetEntries(pack,&da3,&da2);
1330:   DMDAGetLocalInfo(da3,&info3);
1331:   DMCompositeGetLocalVectors(pack,&X3,&X2);
1332:   DMCompositeGetLocalVectors(pack,NULL,&Xdot2);
1333:   DMCompositeScatter(pack,X,X3,X2);
1334:   THIFixGhosts(thi,da3,da2,X3,X2);
1335:   DMCompositeScatter(pack,Xdot,NULL,Xdot2);

1337:   MatZeroEntries(B);

1339:   DMCompositeGetLocalISs(pack,&isloc);
1340:   MatGetLocalSubMatrix(B,isloc[0],isloc[0],&B11);
1341:   MatGetLocalSubMatrix(B,isloc[0],isloc[1],&B12);
1342:   MatGetLocalSubMatrix(B,isloc[1],isloc[0],&B21);
1343:   MatGetLocalSubMatrix(B,isloc[1],isloc[1],&B22);

1345:   DMDAVecGetArray(da3,X3,&x3);
1346:   DMDAVecGetArray(da2,X2,&x2);
1347:   DMDAVecGetArray(da2,Xdot2,&xdot2);

1349:   THIJacobianLocal_Momentum(&info3,x3,x2,B11,B12,thi);

1351:   /* Need to switch from ADD_VALUES to INSERT_VALUES */
1352:   MatAssemblyBegin(B,MAT_FLUSH_ASSEMBLY);
1353:   MatAssemblyEnd(B,MAT_FLUSH_ASSEMBLY);

1355:   THIJacobianLocal_2D(&info3,x3,x2,xdot2,a,B22,B21,thi);

1357:   DMDAVecRestoreArray(da3,X3,&x3);
1358:   DMDAVecRestoreArray(da2,X2,&x2);
1359:   DMDAVecRestoreArray(da2,Xdot2,&xdot2);

1361:   MatRestoreLocalSubMatrix(B,isloc[0],isloc[0],&B11);
1362:   MatRestoreLocalSubMatrix(B,isloc[0],isloc[1],&B12);
1363:   MatRestoreLocalSubMatrix(B,isloc[1],isloc[0],&B21);
1364:   MatRestoreLocalSubMatrix(B,isloc[1],isloc[1],&B22);
1365:   ISDestroy(&isloc[0]);
1366:   ISDestroy(&isloc[1]);
1367:   PetscFree(isloc);

1369:   DMCompositeRestoreLocalVectors(pack,&X3,&X2);
1370:   DMCompositeRestoreLocalVectors(pack,0,&Xdot2);

1372:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
1373:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
1374:   if (A != B) {
1375:     MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
1376:     MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
1377:   }
1378:   if (thi->verbose) {THIMatrixStatistics(thi,B,PETSC_VIEWER_STDOUT_WORLD);}
1379:   return(0);
1380: }

1382: /* VTK's XML formats are so brain-dead that they can't handle multiple grids in the same file.  Since the communication
1383:  * can be shared between the two grids, we write two files at once, one for velocity (living on a 3D grid defined by
1384:  * h=thickness and b=bed) and another for all properties living on the 2D grid.
1385:  */
1386: static PetscErrorCode THIDAVecView_VTK_XML(THI thi,DM pack,Vec X,const char filename[],const char filename2[])
1387: {
1388:   const PetscInt dof   = NODE_SIZE,dof2 = PRMNODE_SIZE;
1389:   Units          units = thi->units;
1390:   MPI_Comm       comm;
1392:   PetscViewer    viewer3,viewer2;
1393:   PetscMPIInt    rank,size,tag,nn,nmax,nn2,nmax2;
1394:   PetscInt       mx,my,mz,r,range[6];
1395:   PetscScalar    *x,*x2;
1396:   DM             da3,da2;
1397:   Vec            X3,X2;

1400:   PetscObjectGetComm((PetscObject)thi,&comm);
1401:   DMCompositeGetEntries(pack,&da3,&da2);
1402:   DMCompositeGetAccess(pack,X,&X3,&X2);
1403:   DMDAGetInfo(da3,0, &mz,&my,&mx, 0,0,0, 0,0,0,0,0,0);
1404:   MPI_Comm_size(comm,&size);
1405:   MPI_Comm_rank(comm,&rank);
1406:   PetscViewerASCIIOpen(comm,filename,&viewer3);
1407:   PetscViewerASCIIOpen(comm,filename2,&viewer2);
1408:   PetscViewerASCIIPrintf(viewer3,"<VTKFile type=\"StructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\">\n");
1409:   PetscViewerASCIIPrintf(viewer2,"<VTKFile type=\"StructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\">\n");
1410:   PetscViewerASCIIPrintf(viewer3,"  <StructuredGrid WholeExtent=\"%d %d %d %d %d %d\">\n",0,mz-1,0,my-1,0,mx-1);
1411:   PetscViewerASCIIPrintf(viewer2,"  <StructuredGrid WholeExtent=\"%d %d %d %d %d %d\">\n",0,0,0,my-1,0,mx-1);

1413:   DMDAGetCorners(da3,range,range+1,range+2,range+3,range+4,range+5);
1414:   PetscMPIIntCast(range[3]*range[4]*range[5]*dof,&nn);
1415:   MPI_Reduce(&nn,&nmax,1,MPI_INT,MPI_MAX,0,comm);
1416:   PetscMPIIntCast(range[4]*range[5]*dof2,&nn2);
1417:   MPI_Reduce(&nn2,&nmax2,1,MPI_INT,MPI_MAX,0,comm);
1418:   tag  = ((PetscObject)viewer3)->tag;
1419:   VecGetArrayRead(X3,(const PetscScalar**)&x);
1420:   VecGetArrayRead(X2,(const PetscScalar**)&x2);
1421:   if (!rank) {
1422:     PetscScalar *array,*array2;
1423:     PetscMalloc2(nmax,&array,nmax2,&array2);
1424:     for (r=0; r<size; r++) {
1425:       PetscInt i,j,k,f,xs,xm,ys,ym,zs,zm;
1426:       Node     *y3;
1427:       PetscScalar (*y2)[PRMNODE_SIZE];
1428:       MPI_Status status;
1429:       if (r) {
1430:         MPI_Recv(range,6,MPIU_INT,r,tag,comm,MPI_STATUS_IGNORE);
1431:       }
1432:       zs = range[0];ys = range[1];xs = range[2];zm = range[3];ym = range[4];xm = range[5];
1433:       if (xm*ym*zm*dof > nmax) SETERRQ(PETSC_COMM_SELF,1,"should not happen");
1434:       if (r) {
1435:         MPI_Recv(array,nmax,MPIU_SCALAR,r,tag,comm,&status);
1436:         MPI_Get_count(&status,MPIU_SCALAR,&nn);
1437:         if (nn != xm*ym*zm*dof) SETERRQ(PETSC_COMM_SELF,1,"corrupt da3 send");
1438:         y3   = (Node*)array;
1439:         MPI_Recv(array2,nmax2,MPIU_SCALAR,r,tag,comm,&status);
1440:         MPI_Get_count(&status,MPIU_SCALAR,&nn2);
1441:         if (nn2 != xm*ym*dof2) SETERRQ(PETSC_COMM_SELF,1,"corrupt da2 send");
1442:         y2 = (PetscScalar(*)[PRMNODE_SIZE])array2;
1443:       } else {
1444:         y3 = (Node*)x;
1445:         y2 = (PetscScalar(*)[PRMNODE_SIZE])x2;
1446:       }
1447:       PetscViewerASCIIPrintf(viewer3,"    <Piece Extent=\"%d %d %d %d %d %d\">\n",zs,zs+zm-1,ys,ys+ym-1,xs,xs+xm-1);
1448:       PetscViewerASCIIPrintf(viewer2,"    <Piece Extent=\"%d %d %d %d %d %d\">\n",0,0,ys,ys+ym-1,xs,xs+xm-1);

1450:       PetscViewerASCIIPrintf(viewer3,"      <Points>\n");
1451:       PetscViewerASCIIPrintf(viewer2,"      <Points>\n");
1452:       PetscViewerASCIIPrintf(viewer3,"        <DataArray type=\"Float32\" NumberOfComponents=\"3\" format=\"ascii\">\n");
1453:       PetscViewerASCIIPrintf(viewer2,"        <DataArray type=\"Float32\" NumberOfComponents=\"3\" format=\"ascii\">\n");
1454:       for (i=xs; i<xs+xm; i++) {
1455:         for (j=ys; j<ys+ym; j++) {
1456:           PetscReal
1457:             xx = thi->Lx*i/mx,
1458:             yy = thi->Ly*j/my,
1459:             b  = PetscRealPart(y2[i*ym+j][FieldOffset(PrmNode,b)]),
1460:             h  = PetscRealPart(y2[i*ym+j][FieldOffset(PrmNode,h)]);
1461:           for (k=zs; k<zs+zm; k++) {
1462:             PetscReal zz = b + h*k/(mz-1.);
1463:             PetscViewerASCIIPrintf(viewer3,"%f %f %f\n",xx,yy,zz);
1464:           }
1465:           PetscViewerASCIIPrintf(viewer2,"%f %f %f\n",xx,yy,(double)0.0);
1466:         }
1467:       }
1468:       PetscViewerASCIIPrintf(viewer3,"        </DataArray>\n");
1469:       PetscViewerASCIIPrintf(viewer2,"        </DataArray>\n");
1470:       PetscViewerASCIIPrintf(viewer3,"      </Points>\n");
1471:       PetscViewerASCIIPrintf(viewer2,"      </Points>\n");

1473:       {                         /* Velocity and rank (3D) */
1474:         PetscViewerASCIIPrintf(viewer3,"      <PointData>\n");
1475:         PetscViewerASCIIPrintf(viewer3,"        <DataArray type=\"Float32\" Name=\"velocity\" NumberOfComponents=\"3\" format=\"ascii\">\n");
1476:         for (i=0; i<nn/dof; i++) {
1477:           PetscViewerASCIIPrintf(viewer3,"%f %f %f\n",PetscRealPart(y3[i].u)*units->year/units->meter,PetscRealPart(y3[i].v)*units->year/units->meter,0.0);
1478:         }
1479:         PetscViewerASCIIPrintf(viewer3,"        </DataArray>\n");

1481:         PetscViewerASCIIPrintf(viewer3,"        <DataArray type=\"Int32\" Name=\"rank\" NumberOfComponents=\"1\" format=\"ascii\">\n");
1482:         for (i=0; i<nn; i+=dof) {
1483:           PetscViewerASCIIPrintf(viewer3,"%d\n",r);
1484:         }
1485:         PetscViewerASCIIPrintf(viewer3,"        </DataArray>\n");
1486:         PetscViewerASCIIPrintf(viewer3,"      </PointData>\n");
1487:       }

1489:       {                         /* 2D */
1490:         PetscViewerASCIIPrintf(viewer2,"      <PointData>\n");
1491:         for (f=0; f<PRMNODE_SIZE; f++) {
1492:           const char *fieldname;
1493:           DMDAGetFieldName(da2,f,&fieldname);
1494:           PetscViewerASCIIPrintf(viewer2,"        <DataArray type=\"Float32\" Name=\"%s\" format=\"ascii\">\n",fieldname);
1495:           for (i=0; i<nn2/PRMNODE_SIZE; i++) {
1496:             PetscViewerASCIIPrintf(viewer2,"%g\n",y2[i][f]);
1497:           }
1498:           PetscViewerASCIIPrintf(viewer2,"        </DataArray>\n");
1499:         }
1500:         PetscViewerASCIIPrintf(viewer2,"      </PointData>\n");
1501:       }

1503:       PetscViewerASCIIPrintf(viewer3,"    </Piece>\n");
1504:       PetscViewerASCIIPrintf(viewer2,"    </Piece>\n");
1505:     }
1506:     PetscFree2(array,array2);
1507:   } else {
1508:     MPI_Send(range,6,MPIU_INT,0,tag,comm);
1509:     MPI_Send(x,nn,MPIU_SCALAR,0,tag,comm);
1510:     MPI_Send(x2,nn2,MPIU_SCALAR,0,tag,comm);
1511:   }
1512:   VecRestoreArrayRead(X3,(const PetscScalar**)&x);
1513:   VecRestoreArrayRead(X2,(const PetscScalar**)&x2);
1514:   PetscViewerASCIIPrintf(viewer3,"  </StructuredGrid>\n");
1515:   PetscViewerASCIIPrintf(viewer2,"  </StructuredGrid>\n");

1517:   DMCompositeRestoreAccess(pack,X,&X3,&X2);
1518:   PetscViewerASCIIPrintf(viewer3,"</VTKFile>\n");
1519:   PetscViewerASCIIPrintf(viewer2,"</VTKFile>\n");
1520:   PetscViewerDestroy(&viewer3);
1521:   PetscViewerDestroy(&viewer2);
1522:   return(0);
1523: }

1525: static PetscErrorCode THITSMonitor(TS ts,PetscInt step,PetscReal t,Vec X,void *ctx)
1526: {
1528:   THI            thi = (THI)ctx;
1529:   DM             pack;
1530:   char           filename3[PETSC_MAX_PATH_LEN],filename2[PETSC_MAX_PATH_LEN];

1533:   if (step < 0) return(0); /* negative one is used to indicate an interpolated solution */
1534:   PetscPrintf(PetscObjectComm((PetscObject)ts),"%3D: t=%g\n",step,(double)t);
1535:   if (thi->monitor_interval && step % thi->monitor_interval) return(0);
1536:   TSGetDM(ts,&pack);
1537:   PetscSNPrintf(filename3,sizeof(filename3),"%s-3d-%03d.vts",thi->monitor_basename,step);
1538:   PetscSNPrintf(filename2,sizeof(filename2),"%s-2d-%03d.vts",thi->monitor_basename,step);
1539:   THIDAVecView_VTK_XML(thi,pack,X,filename3,filename2);
1540:   return(0);
1541: }


1544: static PetscErrorCode THICreateDM3d(THI thi,DM *dm3d)
1545: {
1546:   MPI_Comm       comm;
1547:   PetscInt       M    = 3,N = 3,P = 2;
1548:   DM             da;

1552:   PetscObjectGetComm((PetscObject)thi,&comm);
1553:   PetscOptionsBegin(comm,NULL,"Grid resolution options","");
1554:   {
1555:     PetscOptionsInt("-M","Number of elements in x-direction on coarse level","",M,&M,NULL);
1556:     N    = M;
1557:     PetscOptionsInt("-N","Number of elements in y-direction on coarse level (if different from M)","",N,&N,NULL);
1558:     PetscOptionsInt("-P","Number of elements in z-direction on coarse level","",P,&P,NULL);
1559:   }
1560:   PetscOptionsEnd();
1561:   DMDACreate3d(comm,DM_BOUNDARY_NONE,DM_BOUNDARY_PERIODIC,DM_BOUNDARY_PERIODIC,DMDA_STENCIL_BOX,P,N,M,1,PETSC_DETERMINE,PETSC_DETERMINE,sizeof(Node)/sizeof(PetscScalar),1,0,0,0,&da);
1562:   DMSetFromOptions(da);
1563:   DMSetUp(da);
1564:   DMDASetFieldName(da,0,"x-velocity");
1565:   DMDASetFieldName(da,1,"y-velocity");
1566:   *dm3d = da;
1567:   return(0);
1568: }

1570: int main(int argc,char *argv[])
1571: {
1572:   MPI_Comm       comm;
1573:   DM             pack,da3,da2;
1574:   TS             ts;
1575:   THI            thi;
1576:   Vec            X;
1577:   Mat            B;
1578:   PetscInt       i,steps;
1579:   PetscReal      ftime;

1582:   PetscInitialize(&argc,&argv,0,help);
1583:   comm = PETSC_COMM_WORLD;

1585:   THICreate(comm,&thi);
1586:   THICreateDM3d(thi,&da3);
1587:   {
1588:     PetscInt        Mx,My,mx,my,s;
1589:     DMDAStencilType st;
1590:     DMDAGetInfo(da3,0, 0,&My,&Mx, 0,&my,&mx, 0,&s,0,0,0,&st);
1591:     DMDACreate2d(PetscObjectComm((PetscObject)thi),DM_BOUNDARY_PERIODIC,DM_BOUNDARY_PERIODIC,st,My,Mx,my,mx,sizeof(PrmNode)/sizeof(PetscScalar),s,0,0,&da2);
1592:     DMSetUp(da2);
1593:   }

1595:   PetscObjectSetName((PetscObject)da3,"3D_Velocity");
1596:   DMSetOptionsPrefix(da3,"f3d_");
1597:   DMDASetFieldName(da3,0,"u");
1598:   DMDASetFieldName(da3,1,"v");
1599:   PetscObjectSetName((PetscObject)da2,"2D_Fields");
1600:   DMSetOptionsPrefix(da2,"f2d_");
1601:   DMDASetFieldName(da2,0,"b");
1602:   DMDASetFieldName(da2,1,"h");
1603:   DMDASetFieldName(da2,2,"beta2");
1604:   DMCompositeCreate(comm,&pack);
1605:   DMCompositeAddDM(pack,da3);
1606:   DMCompositeAddDM(pack,da2);
1607:   DMDestroy(&da3);
1608:   DMDestroy(&da2);
1609:   DMSetUp(pack);
1610:   DMCreateMatrix(pack,&B);
1611:   MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);
1612:   MatSetOptionsPrefix(B,"thi_");

1614:   for (i=0; i<thi->nlevels; i++) {
1615:     PetscReal Lx = thi->Lx / thi->units->meter,Ly = thi->Ly / thi->units->meter,Lz = thi->Lz / thi->units->meter;
1616:     PetscInt  Mx,My,Mz;
1617:     DMCompositeGetEntries(pack,&da3,&da2);
1618:     DMDAGetInfo(da3,0, &Mz,&My,&Mx, 0,0,0, 0,0,0,0,0,0);
1619:     PetscPrintf(PetscObjectComm((PetscObject)thi),"Level %d domain size (m) %8.2g x %8.2g x %8.2g, num elements %3d x %3d x %3d (%8d), size (m) %g x %g x %g\n",i,Lx,Ly,Lz,Mx,My,Mz,Mx*My*Mz,Lx/Mx,Ly/My,1000./(Mz-1));
1620:   }

1622:   DMCreateGlobalVector(pack,&X);
1623:   THIInitial(thi,pack,X);

1625:   TSCreate(comm,&ts);
1626:   TSSetDM(ts,pack);
1627:   TSSetProblemType(ts,TS_NONLINEAR);
1628:   TSMonitorSet(ts,THITSMonitor,thi,NULL);
1629:   TSSetType(ts,TSTHETA);
1630:   TSSetIFunction(ts,NULL,THIFunction,thi);
1631:   TSSetIJacobian(ts,B,B,THIJacobian,thi);
1632:   TSSetMaxTime(ts,10.0);
1633:   TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);
1634:   TSSetSolution(ts,X);
1635:   TSSetTimeStep(ts,1e-3);
1636:   TSSetFromOptions(ts);

1638:   TSSolve(ts,X);
1639:   TSGetSolveTime(ts,&ftime);
1640:   TSGetStepNumber(ts,&steps);
1641:   PetscPrintf(PETSC_COMM_WORLD,"Steps %D  final time %g\n",steps,(double)ftime);

1643:   if (0) {THISolveStatistics(thi,ts,0,"Full");}

1645:   {
1646:     PetscBool flg;
1647:     char      filename[PETSC_MAX_PATH_LEN] = "";
1648:     PetscOptionsGetString(NULL,NULL,"-o",filename,sizeof(filename),&flg);
1649:     if (flg) {
1650:       THIDAVecView_VTK_XML(thi,pack,X,filename,NULL);
1651:     }
1652:   }

1654:   VecDestroy(&X);
1655:   MatDestroy(&B);
1656:   DMDestroy(&pack);
1657:   TSDestroy(&ts);
1658:   THIDestroy(&thi);
1659:   PetscFinalize();
1660:   return ierr;
1661: }