/usr/lib/petscdir/3.4.2/include/sieve/UFC.hh is in libpetsc3.4.2-dev 3.4.2.dfsg1-8.1+b1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 | /*
Routines for linking UFC to Sieve and PETSc
*/
#include "Mesh.hh"
#include <petscmat.h>
#include <ufc.h>
//we SHOULD have some overlying "problem" object. Let's do that here!
#if 0
namespace ALE {
class sieve_mesh_wrapper : ufc::mesh {
public:
Obj<PETSC_MESH_TYPE> m;
sieve_mesh_wrapper(Obj<PETSC_MESH_TYPE> mesh) {
m = mesh;
Obj<PETSC_MESH_TYPE::real_section_type> coordinates = m->getRealSection("coordinates");
int dim = m->getDimension();
topological_dimension = dim;
geometric_dimension = m->getFiberDimension(*m->depthStratum(0)->begin());
num_entities = new unsigned int[dim+1];
int depth = m->depth();
for (int i = 0; i < depth; i++) {
num_entities[i] = 0;
}
if (depth == 1) {
num_entities[0] = m->depthStratum(0);
num_entities[dim] = m->heightStratum(0);
} else {
if (depth != dim+1) throw Exception("Cannot handle partially interpolated sieves.");
for (int i = 0; i < dim+1; i++) {
num_entities[i] = m->getDepthStratum(i)->size();
}
}
}
};
class sieve_cell_wrapper : ufc::cell {
public:
Obj<PETSC_MESH_TYPE> m; // the presently associated mesh
int num_corners; //for the sake of clarity; the number of vertices
PETSC_MESH_TYPE::point_type current_point; // the presently associated sieve cell
sieve_cell_wrapper() {
}
sieve_cell_wrapper(ufc::finite_element finite_element) {
//properly initialize the cell from the form
int geometric_dimension = m->getRealSection("coordinates")->getFiberDimension(m->depthStratum(0)->begin());
if (finite_element->cell_shape() == ufc::interval) {
num_corners = 2;
topological_dimension = m->getDimension(); //we must clarify what this means in the mesh library
element_entities = new int *[2];
element_entities[0] = new int[2]; //vertices
element_entities[1] = new int[1]; //line
double * tmpcoords = new double[coorddim*2];
coordinates = new double *[2];
for (int i = 0; i < 2; i++) {
coordinates[i] = &tmpcoords[coorddim*i];
}
} else if (finite_element->cell_shape() == ufc::triangle) {
num_corners = 3;
element_entities = new int *[3];
element_entities[0] = new int[3]; //vertices
element_entities[1] = new int[3]; //edges
element_entities[2] = new int[1]; //cell
double * tmpcoords = new double[coorddim*3];
coordinates = new double *[3];
for (int i = 0; i < 3; i++) {
coordinates[i] = &tmpcoords[coorddim*i];
}
} else if (finite_element->cell_shape() == ufc::tetrahedron) {
num_corners = 4;
element_entities = new int *[2];
element_entities[0] = new int[4]; //vertices
element_entities[1] = new int[6]; //edges
element_entities[2] = new int[4]; //faces
element_entities[3] = new int[1]; //tetrahedron
double * tmpcoords = new double[coorddim*4];
coordinates = new double *[4];
for (int i = 0; i < 4; i++) {
coordinates[i] = &tmpcoords[coorddim*i];
}
} else throw Exception("Unsupported geometry");
}
~sieve_cell_wrapper() {
}
void setMesh(Obj<PETSC_MESH_TYPE> mesh) {
m = mesh;
}
Obj<PETSC_MESH_TYPE> getMesh() {
return m;
}
void setCell(PETSC_MESH_TYPE::point_type p) {
if (m->height(p) != 0) throw Exception("sieve_cell_wrapper: the point must be a cell");
current_point = p;
//copy over the coordinates through the restrictClosure and copy
const double * coords = m->;
for (int i = 0; i < num_corners; i++) {
for (int j = 0; j < dim; j++) {
coordinates[i][j] = coords[i*coordim+j];
}
}
//copy over the entity indices such that they're consistent with the
}
void reorientSieveCell(PETSC_MESH_TYPE::point_type p) {
//changing the orientation will be hard; keep it the same for now as it should orient normals right
//this will not be so bad in the long run
}
Obj<PETSC_MESH_TYPE::sieve_type::oConeArray> reorderSieveClosure(PETSC_MESH_TYPE::point_type p) {
//return m->getSieve()->closure(p); //null reorder for now. NEI! the oriented closure!
return PETSC_MESH_TYPE::sieve_alg_type::orientedClosure(m, m->getArrowSection("orientation"), p);
}
void reorderSieveRestrictClosure(const double * coefficients) {
//order the restricted closure given in coefficients based upon the cell mapping here
}
};
class sieve_function_wrapper : ufc::function {
public:
(*_func)(double * values, const double * coords); //the simple function that computes the value based on the coordinates.
int _rank; //the number of values returned by the function
sieve_function_wrapper(){};
sieve_function_wrapper(const double * (*func)(const double * coords), int rank) {
_func = func;
_rank = rank;
}
const double * (*)(const double *) getFunction() {
return _func;
}
void setFunction(const double * (*func)(const double * coords), int rank) {
_func = func;
}
void evaluate(double * values, const double * coordinates, ufc::cell &cell) {
_func(values, coordinates);
}
};
//this class takes coordinates in a cell and produces output based upon those coordinates and the section over the mesh in that cell
//might come in handy for generalized MG, etc.
class section_wrapper_function : ufc::function {
public:
ALE::Obj<PETSC_MESH_TYPE> _m;
ALE::Obj<PETSC_MESH_TYPE::section_type> _s;
//PETSC_MESH_TYPE::point_type c;
ufc::form * _form;
ufc::finite_element * _finite_element;
ufc::cell_integral * _cell_integral;
section_wrapper_function(){};
section_wrapper_function(Obj<PETSC_MESH_TYPE> m, Obj<PETSC_MESH_TYPE::section_type> s, ufc::form form, ufc::finite_element finite_element, ufc::cell_integral::cell_integral){
_m = m;
_s = s;
_form = form;
_finite_element = finite_element;
_cell_integral = cell_integral;
}
void evaluate(double * values, const double * coordinates, ufc::cell &cell)
{
//evaluate the degrees of freedom on the interior of the given cell; note that this requires that coordinates be within the cell to really make sense.
//note for the future: we could wrap this easily into the multigrid routines
//we need an additional aggregation array of size value_rank;
const double * coefficients = m->restrictClosure(_s, cell->current_point);
const double * tmp_values = new double[_finite_element->value_rank()];
for (int i = 0; i < _finite_element->value_rank(); i++) {
values[i] = 0.;
}
for (int i = 0; i < _finite_element->value_dimension(); i++) { //loop over basis functions
_finite_element->evaluate_basis(i, tmp_values, coordinates, cell);
for (int j = 0; j < _finite_element->value_rank()+1; i++) {
values[i] += coefficients[i*(finite_element->value_rank()+1)+j]*tmp_values[j];
}
}
delete tmp_values;
}
};
class boundary_condition {
public:
PetscBool (*_func)(PETSC_MESH_TYPE::point_type, const double *);
int marker;
int cellmarker;
boundary_condition(){};
boundary_condition (PetscBool (*func)(PETSC_MESH_TYPE::point_type, const double *), int mark = 1, int cellmark = 2) {
}
void applyBC(Obj<PETSC_MESH_TYPE> m) {
}
};
PetscBool Scalar_Dirichlet_Pred(PETSC_MESH_TYPE::point_type p, const double * coords) {
//set up the marker
//if anything in the star of the thing has support size 1 but not height 0 then the thing's on the boundary! mark it!
Obj<PETSC_MESH_TYPE::sieve_type::supportArray> star =
}
class UFCProblem : ALE::ParallelObject {
public:
//sieve parts
Obj<PETSC_MESH_TYPE> _mesh;
//UFC parts
//Forms:
ufc::form * _bform;
ufc::form * _lform;
//Coefficients:
int _num_bcoefficients;
double * b_w;
int _num_lcoefficients;
double * l_w;
//Finite Elements:
int _num_finite_elements;
ufc::finite_element ** _finite_elements;
//"Coefficient" elements from the RHS linear forms
int _num_coefficient_elements;
ufc::finite_element ** _coefficient_elements;
//Cell types; perhaps not
int _num_cell_types;
ufc::cell ** _cell;
//Cell integrals
int _num_cell_integrals;
ufc::cell_integral * _cell_integrals;
//Functions:
// - The RHS Function
ufc::function * _rhs_funct;
// - The "Exact Solution"
ufc::function * _exact_solution;
//We also need to define some sort of predicate system for the boundary like dolfin;
//This will involve some setting of the boundary marker, not necessarily based upon the topological boundary, but usually that.
//Initialization
UFCProblem(){};
//give it a mesh, give it a form, mark boundary segments through some f
UFCProblem(Obj<PETSC_MESH_TYPE> m, ufc::form * bform, ufc::form * lform){
_mesh = m;
_bform = bform;
_lform = lform;
//set up the bilinear form finite elements, and cell integral.
_num_finite_elements = bform->num_finite_elements();
_finite_elements = new ufc::finite_element *[_num_finite_elements];
for (int i = 0; i < _num_finite_elements; i++) {
}
//set up the linear form finite elements and cell integrals.
//set up the
}
~UFCProblem(){};
//Accessors
void setMesh(Obj<PETSC_MESH_TYPE> m){mesh = m;}
Obj<PETSC_MESH_TYPE> getMesh() {return mesh;}
Mesh getPetscMesh() {
return NULL;
}
void setForm(ufc::form * f) {form = f;}
ufc::form * getForm() {}
void setRHSFunction(ufc::function * f){rhs_funct = f;}
ufc::function * getRHSFunction();
void setExactSolution(ufc::function * f) {exact_solution = f;}
ufc::function * getExactSolution() {
return exact_solution;
}
//Misc
void setupUFC(){
//initialize the cell, function, and finite element structures for this given problem
finite_element = form->create_finite_element(0);
dof_map = form->create_dof_map(0);
cell_integrals = form->create_cell_integral(0);
cell = new ();
};
void setCell(PETSC_MESH_TYPE::point_type c) {
}
void setupFields(Obj<PETSC_MESH_TYPE> m, Obj<PETSC_MESH_TYPE::real_section_type> s, ufc::form form, ufc::function function){
setCell
};
void assembleMatrix() {
//use the bform to create the matrix
//partial assembly?
}
void assembleRHS() {
//use the lform on the interior and the bform on the boundaries to assemble the RHS
}
void setFieldfromFunction(Obj<PETSC_MESH_TYPE> m, Obj<PETSC_MESH_TYPE::real_section_type> s, ufc::form form, ufc::function function) {
}
};
}
#endif
/*
Wrapper to ufc::function for double * func(double * coords)
*/
class function_wrapper_scalar : public ufc::function {
private:
PetscScalar (*function)(const double * coords);
public:
void setFunction(PetscScalar (*func)(const double *)) {
function = func;
}
virtual void evaluate(double * values, const double * coordinates, const ufc::cell &c) const {
values[0] = (*function)(coordinates);
}
};
/*
Do we even need this one if we're not going to be assembling ourselves?
*/
#undef __FUNCT__
#define __FUNCT__ "Map_SieveCell_UFCCell"
void Map_SieveCell_UFCCell(ALE::Obj<PETSC_MESH_TYPE> m, PETSC_MESH_TYPE::point_type c, ufc::form * form, ufc::cell * cell, const PETSC_MESH_TYPE::point_type * _oPoints = NULL, const int _num_oPoints= -1) {
//set up the ufc cell to be equivalent to the sieve cell given by c; Assume that the # of dofs is constant
//PetscErrorCode ierr;
const ALE::Obj<PETSC_MESH_TYPE::sieve_type> s = m->getSieve();
ALE::Obj<PETSC_MESH_TYPE::real_section_type> coordinates = m->getRealSection("coordinates");
int dim = m->getDimension();
PetscPrintf(m->comm(), "cell of dimension: %d\n", cell->topological_dimension);
if ((int)cell->topological_dimension != m->getDimension() - m->height(c)) throw ALE::Exception("Wrong element dimension for this UFC form");
// ALE::Obj<PETSC_MESH_TYPE::oConeArray> cell_closure = PETSC_MESH_TYPE::sieve_alg_type::orientedClosure(m, m->getArrowSection("orientation"), c);
const PETSC_MESH_TYPE::point_type * oPoints = _oPoints;
int num_oPoints = _num_oPoints;
if (oPoints == NULL) {
ALE::ISieveVisitor::PointRetriever<PETSC_MESH_TYPE::sieve_type> oC((int) pow(m->getSieve()->getMaxConeSize(), m->depth())+1, true);
ALE::ISieveTraversal<PETSC_MESH_TYPE::sieve_type>::orientedClosure(*s, c, oC);
PetscPrintf(m->comm(), "Got the orientedClosure\n");
oPoints = oC.getPoints();
num_oPoints = oC.getSize();
}
//PETSC_MESH_TYPE::oConeArray::iterator cc_iter = cell_closure->begin();
//PETSC_MESH_TYPE::oConeArray::iterator cc_iter_end = cell_closure->end();
int vertex_index = 0;
for (int t = 0; t < num_oPoints; t++) {
//PetscPrintf(PETSC_COMM_WORLD, "%d is in the closure\n", oPoints[t]);
//while (cc_iter != cc_iter_end) {
//FOR NOW: first order lagrange; if you have vertices then put 'em in. This should be ordered
// (and declare victory!)
if (m->depth(oPoints[t]) == 0) {
//"entities"
//PetscPrintf(m->comm(), "%d is vertex %d\n", cc_iter->first, vertex_index);
cell->entity_indices[0][vertex_index] = oPoints[t];
//PetscPrintf(m->comm(), "%d: ", cc_iter->first);
//and coordinates
const double * tmpcoords = coordinates->restrictPoint(oPoints[t]);
for (int i = 0; i < dim; i++) {
cell->coordinates[vertex_index][i] = tmpcoords[i];
}
vertex_index++;
}
}
PetscPrintf(m->comm(), "done with cell map\n");
}
#undef __FUNCT__
#define __FUNCT__ "Assemble_Mat_UFC"
PetscErrorCode Assemble_Mat_UFC(Mesh mesh, SectionReal section, Mat A, ufc::form * form) {
PetscErrorCode ierr;
//get, from the mesh, the assorted structures we need to do this. (numberings)
PetscFunctionBegin;
Obj<PETSC_MESH_TYPE::real_section_type> s;
ierr = SectionRealGetSection(section, s);CHKERRQ(ierr);
Obj<PETSC_MESH_TYPE> m;
ierr = MeshGetMesh(mesh, m);CHKERRQ(ierr);
PetscPrintf(m->comm(), "Beginning Matrix assembly.\n");
ALE::Obj<PETSC_MESH_TYPE::real_section_type> coordinates = m->getRealSection("coordinates");
ALE::Obj<PETSC_MESH_TYPE::label_sequence> cells = m->heightStratum(0);
const Obj<PETSC_MESH_TYPE::order_type>& order = m->getFactory()->getGlobalOrder(m, "default", s);
int dim = m->getDimension();
ufc::cell cell;
ufc::finite_element * finite_element = form->create_finite_element(0);
//initialize the ufc infrastructure
cell.geometric_dimension = dim; //might be different; check the fiberdimension of the coordinates
cell.topological_dimension = dim;
cell.entity_indices = new unsigned int *[dim+1];
cell.entity_indices[0] = new unsigned int[dim+1];
double * tmpcellcoords = new double [(dim+1)*dim];
int space_dimension = finite_element->space_dimension();
//allow both our functions and theirs to use it!
double * localTensor = new double[space_dimension*space_dimension];
//double ** localTensor = new double*[space_dimension];
//for(int i = 0; i < space_dimension; i++) {
// localTensor[i] = &localTensor_pointer[space_dimension*i];
//}
cell.coordinates = new double *[dim+1];
for (int i = 0; i < dim+1; i++) {
cell.coordinates[i] = &tmpcellcoords[i*dim];
}
ufc::cell_integral** cell_integrals;
cell_integrals = new ufc::cell_integral*[form->num_cell_integrals()];
if (form->num_cell_integrals() <= 0) throw ALE::Exception("Number of cell integrals in UFC form is 0.");
for (unsigned int i = 0; i < form->num_cell_integrals(); i++){
cell_integrals[i] = form->create_cell_integral(i);
}
ierr = MatZeroEntries(A);CHKERRQ(ierr);
PETSC_MESH_TYPE::label_sequence::iterator c_iter = cells->begin();
PETSC_MESH_TYPE::label_sequence::iterator c_iter_end = cells->end();
while (c_iter != c_iter_end) {
Map_SieveCell_UFCCell(m, *c_iter, form, &cell);
//for now just do the first cell integral. Fix when you talk to someone about what exactly having more than one means.
//todo: coefficients.... ask if they're global and if yes ask why.
cell_integrals[0]->tabulate_tensor(localTensor, (double * const *)NULL, cell);
//see what the local tensor coming out looks like:
if (1) {
//maybe print the local tensor?
}
ierr = updateOperator(A, m, s, order, *c_iter, localTensor, ADD_VALUES);CHKERRQ(ierr);
c_iter++;
}
MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
if (1) {
ierr = MatView(A, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
//throw ALE::Exception("Finished the jacobian assembly for UFC; aborting for now in case it's messed up.");
PetscFunctionReturn(0);
}
#if 0
//GET THE NEW RHS_UNSTRUCTURED FOR THIS
PetscErrorCode Assemble_RHS_UFC(Mesh mesh, ufc::form * bform, ufc::form * lform, SectionReal X, SectionReal section, PetscScalar (*exactFunc)(const double *)) {
Obj<PETSC_MESH_TYPE> m;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MeshGetMesh(mesh, m);CHKERRQ(ierr);
//const Obj<PETSC_MESH_TYPE::real_section_type>& coordinates = m->getRealSection("coordinates");
const Obj<PETSC_MESH_TYPE::label_sequence>& cells = m->heightStratum(0);
const int dim = m->getDimension();
ufc::finite_element * finite_element = lform->create_finite_element(0);
ufc::cell cell;
cell.geometric_dimension = dim;
cell.topological_dimension = dim;
cell.entity_indices = new unsigned int *[dim+1];
cell.entity_indices[0] = new unsigned int[dim];
cell.coordinates = new double *[dim+1];
double * tmpcellcoords = new double[dim*(dim+1)];
for (int i = 0; i < dim+1; i++) {
cell.coordinates[i] = &tmpcellcoords[i*dim];
}
ufc::cell_integral** cell_integrals;
cell_integrals = new ufc::cell_integral*[bform->num_cell_integrals()];
if (bform->num_cell_integrals() <= 0) throw ALE::Exception("Number of cell integrals in UFC form is 0.");
for (unsigned int i = 0; i < bform->num_cell_integrals(); i++){
cell_integrals[i] = bform->create_cell_integral(i);
}
ufc::cell_integral** cell_integrals_linear = new ufc::cell_integral*[lform->num_cell_integrals()];
for (unsigned int i = 0; i < lform->num_cell_integrals(); i++) {
cell_integrals_linear[i] = lform->create_cell_integral(i);
}
const int numBasisFuncs = finite_element->space_dimension();
//double *t_der, *b_der, *coords, *v0, *J, *invJ, detJ;
PetscScalar *elemVec, *elemMat;
ierr = SectionRealZero(section);CHKERRQ(ierr);
ierr = PetscMalloc2(numBasisFuncs,PetscScalar,&elemVec,numBasisFuncs*numBasisFuncs,PetscScalar,&elemMat);CHKERRQ(ierr);
// ierr = PetscMalloc6(dim,double,&t_der,dim,double,&b_der,dim,double,&coords,dim,double,&v0,dim*dim,double,&J,dim*dim,double,&invJ);CHKERRQ(ierr);
// Loop over cells
Obj<PETSC_MESH_TYPE::real_section_type> xSection;
Obj<PETSC_MESH_TYPE::real_section_type> fSection;
int c = 0;
double ** w = new double *[lform->num_coefficients()];
function_wrapper_scalar sf;
sf.setFunction(exactFunc);
for(PETSC_MESH_TYPE::label_sequence::iterator c_iter = cells->begin(); c_iter != cells->end(); ++c_iter, ++c) {
ierr = PetscMemzero(elemVec, numBasisFuncs * sizeof(PetscScalar));CHKERRQ(ierr);
ierr = PetscMemzero(elemMat, numBasisFuncs*numBasisFuncs * sizeof(PetscScalar));CHKERRQ(ierr);
//set up the weight vector to be 0.
//three steps for this:
//build B in the finite element space
// involves calling the
//construct A local to the boundary
//subtract AX from the boundary
//create the "neumann" RHS and put it in the vector
//m->computeElementGeometry(coordinates, *c_iter, v0, J, invJ, detJ);
Map_SieveCell_UFCCell(m, *c_iter, bform, &cell);
PetscScalar *x;
ierr = SectionRealRestrict(X, *c_iter, &x);CHKERRQ(ierr);
for (int f = 0; f < numBasisFuncs; f++) {
elemVec[f] = 0. - finite_element->evaluate_dof(f, sf, cell);
//PetscPrintf(m->comm(), "Elemvec[f](before): %f\n", elemVec[f]);
}
for(unsigned int i = 0; i < lform->num_coefficients(); i++) {
w[i] = new double[numBasisFuncs];
for (int j = 0; j < numBasisFuncs; j++){
w[i][j] = elemVec[j];
}
}
cell_integrals_linear[0]->tabulate_tensor(elemVec, w, cell);
cell_integrals[0]->tabulate_tensor(elemMat, w, cell);
for(int f = 0; f < numBasisFuncs; ++f) {
for(int g = 0; g < numBasisFuncs; ++g) {
elemVec[f] += elemMat[f*numBasisFuncs+g]*x[g];
}
//PetscPrintf(m->comm(), "x[f]: %f\n", x[f]);
//PetscPrintf(m->comm(), "elemVec[f]: %f\n", elemVec[f]);
}
ierr = SectionRealUpdateAdd(section, *c_iter, elemVec);
//m->updateAdd(fSection, c, elemVec);
}
ierr = PetscFree2(elemVec,elemMat);CHKERRQ(ierr);
//ierr = PetscFree6(t_der,b_der,coords,v0,J,invJ);CHKERRQ(ierr);
// Exchange neighbors
ierr = SectionRealComplete(section);CHKERRQ(ierr);
// Subtract the constant
if (m->hasRealSection("constant")) {
const Obj<PETSC_MESH_TYPE::real_section_type>& constant = m->getRealSection("constant");
Obj<PETSC_MESH_TYPE::real_section_type> s;
ierr = SectionRealGetSection(section, s);CHKERRQ(ierr);
s->axpy(-1.0, constant);
}
PetscFunctionReturn(0);
}
#endif
PetscErrorCode Assemble_RHS_UFC(Mesh mesh, ufc::form * bform, ufc::form * lform, SectionReal X, SectionReal section, PetscScalar (*exactFunc)(const double *)) {
Obj<PETSC_MESH_TYPE> m;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MeshGetMesh(mesh, m);CHKERRQ(ierr);
const Obj<ALE::Discretization>& disc = m->getDiscretization("u");
const Obj<PETSC_MESH_TYPE::label_sequence>& cells = m->heightStratum(0);
const int dim = m->getDimension();
PetscScalar *elemVec, *elemMat;
ufc::finite_element * finite_element = lform->create_finite_element(0);
ufc::cell cell;
cell.geometric_dimension = dim;
cell.topological_dimension = dim;
cell.entity_indices = new unsigned int *[dim+1];
cell.entity_indices[0] = new unsigned int[dim];
cell.coordinates = new double *[dim+1];
double * tmpcellcoords = new double[dim*(dim+1)];
for (int i = 0; i < dim+1; i++) {
cell.coordinates[i] = &tmpcellcoords[i*dim];
}
ufc::cell_integral** cell_integrals;
cell_integrals = new ufc::cell_integral*[bform->num_cell_integrals()];
if (bform->num_cell_integrals() <= 0) throw ALE::Exception("Number of cell integrals in UFC form is 0.");
for (unsigned int i = 0; i < bform->num_cell_integrals(); i++){
cell_integrals[i] = bform->create_cell_integral(i);
}
ufc::cell_integral** cell_integrals_linear = new ufc::cell_integral*[lform->num_cell_integrals()];
for (unsigned int i = 0; i < lform->num_cell_integrals(); i++) {
cell_integrals_linear[i] = lform->create_cell_integral(i);
}
double ** w = new double *[lform->num_coefficients()];
function_wrapper_scalar sf;
sf.setFunction(exactFunc);
const int numBasisFuncs = finite_element->space_dimension();
ierr = SectionRealZero(section);CHKERRQ(ierr);
ierr = PetscMalloc2(numBasisFuncs,PetscScalar,&elemVec,numBasisFuncs*numBasisFuncs,PetscScalar,&elemMat);CHKERRQ(ierr);
//ierr = PetscMalloc6(dim,double,&t_der,dim,double,&b_der,dim,double,&coords,dim,double,&v0,dim*dim,double,&J,dim*dim,double,&invJ);CHKERRQ(ierr);
// Loop over cells
for(PETSC_MESH_TYPE::label_sequence::iterator c_iter = cells->begin(); c_iter != cells->end(); ++c_iter) {
ierr = PetscMemzero(elemVec, numBasisFuncs * sizeof(PetscScalar));CHKERRQ(ierr);
ierr = PetscMemzero(elemMat, numBasisFuncs*numBasisFuncs * sizeof(PetscScalar));CHKERRQ(ierr);
//m->computeElementGeometry(coordinates, *c_iter, v0, J, invJ, detJ);
Map_SieveCell_UFCCell(m, *c_iter, bform, &cell);
//if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, *c_iter);
PetscScalar *x;
ierr = SectionRealRestrict(X, *c_iter, &x);CHKERRQ(ierr);
for (int f = 0; f < numBasisFuncs; f++) {
elemVec[f] = 0. - finite_element->evaluate_dof(f, sf, cell);
//PetscPrintf(m->comm(), "Elemvec[f](before): %f\n", elemVec[f]);
}
for(unsigned int i = 0; i < lform->num_coefficients(); i++) {
w[i] = new double[numBasisFuncs];
for (int j = 0; j < numBasisFuncs; j++){
w[i][j] = elemVec[j];
}
}
cell_integrals_linear[0]->tabulate_tensor(elemVec, w, cell);
cell_integrals[0]->tabulate_tensor(elemMat, w, cell);
for(int f = 0; f < numBasisFuncs; ++f) {
for(int g = 0; g < numBasisFuncs; ++g) {
elemVec[f] += elemMat[f*numBasisFuncs+g]*x[g];
}
//PetscPrintf(m->comm(), "x[f]: %f\n", x[f]);
//PetscPrintf(m->comm(), "elemVec[f]: %f\n", elemVec[f]);
}
ierr = SectionRealUpdateAdd(section, *c_iter, elemVec);CHKERRQ(ierr);
}
ierr = PetscFree2(elemVec,elemMat);CHKERRQ(ierr);
//ierr = PetscFree6(t_der,b_der,coords,v0,J,invJ);CHKERRQ(ierr);
// Exchange neighbors
ierr = SectionRealComplete(section);CHKERRQ(ierr);
// Subtract the constant
if (m->hasRealSection("constant")) {
const Obj<PETSC_MESH_TYPE::real_section_type>& constant = m->getRealSection("constant");
Obj<PETSC_MESH_TYPE::real_section_type> s;
ierr = SectionRealGetSection(section, s);CHKERRQ(ierr);
s->axpy(-1.0, constant);
}
PetscFunctionReturn(0);
}
//Integrator function based upon a given UFC:
//Takes a mesh, cell, and a UFC and integrate for all the unknowns on the cell
#undef __FUNCT__
#define __FUNCT__ "IntegrateDualBasis_UFC"
PetscErrorCode IntegrateDualBasis_UFC(ALE::Obj<PETSC_MESH_TYPE> m, PETSC_MESH_TYPE::point_type c, ufc::form & f) {
}
//you still have to wrap this one as the fields are set up on the basis of the discretizations; you have to set up the discretization as it would be from the form, so we have to at least fill in the fiberdimension parts of the discretization type such that setupFields can do its work. This will be equivalent to the CreateProblem_gen_0 stuff that FIAT + Generator spits out.
//CreateProblem_UFC
//Takes a UFC form and generates the entire problem from it. This involves building a discretization object within the mesh corresponding to what is sent to UFC. Unfortunately UFC handles all the element/vectorish stuff on its own, but
PetscErrorCode CreateProblem_UFC(DM dm, const char * name, ufc::form * form, const int numBC, const int *markers, double (**bcFuncs)(const double * coords), double(*exactFunc)(const double * coords)) {
Mesh mesh = (Mesh) dm;
ALE::Obj<PETSC_MESH_TYPE> m;
PetscErrorCode ierr = 0;
//you need some finite element information from the form.
ufc::finite_element * finite_element = form->create_finite_element(0);
//needed information from the form.
PetscFunctionBegin;
ierr = MeshGetMesh(mesh, m);CHKERRQ(ierr);
//int dim = m->getDimension();
const ALE::Obj<ALE::Discretization>& d = new ALE::Discretization(m->comm(), m->debug()); //create the UFC
//for now handle only vertex unknowns; complain about the fact that Dofs per dimension isn't in the release version of UFC.
d->setNumDof(0, 1);
/*
for (int i = 0; i < dim+1; i++) {
//for each element level; find the fiberdimension from the discretization and set it in the discretization.
d->setNumDof(
}
*/
d->setQuadratureSize(finite_element->space_dimension());
//boundary conditions
for (int c = 0; c < numBC; c++) {
const ALE::Obj<ALE::BoundaryCondition>& b = new ALE::BoundaryCondition(m->comm(), m->debug());
ostringstream n;
b->setLabelName("marker");
b->setMarker(markers[c]);
b->setFunction(bcFuncs[c]);
//b->setDualIntegrator(IntegrateDualBasis_gen_2);
n << c;
d->setBoundaryCondition(n.str(), b);
if (exactFunc) {
const ALE::Obj<ALE::BoundaryCondition>& e = new ALE::BoundaryCondition(m->comm(), m->debug());
e->setLabelName("marker");
e->setFunction(exactFunc);
e->setDualIntegrator(NULL); //TODO
d->setExactSolution(e);
}
}
m->setDiscretization(name, d);
PetscFunctionReturn(0);
}
#undef __FUNCT__
#define __FUNCT__ "SetupDiscretization_UFC"
void SetupDiscretization_UFC(ALE::Obj<PETSC_MESH_TYPE> m, ufc::form * form) {
ALE::Obj<PETSC_MESH_TYPE::sieve_type> s = m->getSieve();
//we will treat the thing arising from the UFC form as a SINGLE discretization such that the separation of forms is handled transparent of sieve;
//watch out if this screws up stuff involving the eventual output of a solution; we may have to reprocess or something silly like that.
//also, where there are multiple forms what should we do?
ALE::Obj<ALE::Discretization> d = m->getDiscretization("ufc_u");
}
//Comment: we shouldn't need to do this! Tie this in properly with the discretization object and then setupfield with noupdate; write a separate routine for setting the boundary values given a wrapped function.
#undef __FUNCT__
#define __FUNCT__ "SetupField_UFC"
/*
This is essentially a copy of m->setupField(s) such that it can use the UFC dualintegrator from the associated form.
*/
#if 0
void SetupField_UFC(ALE::Obj<PETSC_MESH_TYPE> m, const ALE::Obj<PETSC_MESH_TYPE::real_section_type>& s, ufc::form * form, const int cellMarker = 2, const bool noUpdate = false){
const ALE::Obj<PETSC_MESH_TYPE::names_type>& discs = m->getDiscretizations();
const int debug = s->debug();
PETSC_MESH_TYPE::names_type bcLabels;
int maxDof;
//setup the necessary UFC structures here
ufc::finite_element * finite_element = form->create_finite_element(0);
function_wrapper_scalar sf;
ufc::cell cell;
int dim = m->getDimension();
int embeddim = m->getRealSection("coordinates")->getFiberDimension(*m->depthStratum(0)->begin());
cell.geometric_dimension = embeddim;
cell.topological_dimension = dim;
cell.entity_indices = new unsigned int *[dim+1];
cell.entity_indices[0] = new unsigned int[dim];
cell.coordinates = new double *[dim+1];
double * coordpointer = new double[(dim+1)*dim];
for (int i = 0; i < dim+1; i++) {
cell.coordinates[i] = &coordpointer[dim*i];
}
s->setChart(m->getSieve()->getChart());
PetscPrintf(m->comm(), "Set the chart\n");
maxDof = m->setFiberDimensions(s, discs, bcLabels);
PetscPrintf(m->comm(), "Set the max dof\n");
m->calculateIndices();
PetscPrintf(m->comm(), "Calculated the indices\n");
m->calculateIndicesExcluded(s, discs);
PetscPrintf(m->comm(), "Calculated the excluded indices\n");
m->allocate(s);
PetscPrintf(m->comm(), "Allocated\n");
s->defaultConstraintDof();
PetscPrintf(m->comm(), "Set the default constraint DOF");
const ALE::Obj<PETSC_MESH_TYPE::label_type>& cellExclusion = m->getLabel("cellExclusion");
PetscPrintf(m->comm(), "Cell exclusion\n");
if (debug > 1) {std::cout << "Setting boundary values" << std::endl;}
PetscPrintf(m->comm(), "At the boundary condition loop\n");
for(PETSC_MESH_TYPE::names_type::const_iterator n_iter = bcLabels.begin(); n_iter != bcLabels.end(); ++n_iter) {
const ALE::Obj<PETSC_MESH_TYPE::label_sequence>& boundaryCells = m->getLabelStratum(*n_iter, cellMarker);
// const ALE::Obj<PETSC_MESH_TYPE::real_section_type>& coordinates = m->getRealSection("coordinates");
const ALE::Obj<PETSC_MESH_TYPE::names_type>& discs = m->getDiscretizations();
ALE::Obj<PETSC_MESH_TYPE::sieve_type> sieve = m->getSieve();
const PETSC_MESH_TYPE::point_type firstCell = *boundaryCells->begin();
const int numFields = discs->size();
PETSC_MESH_TYPE::real_section_type::value_type *values = new PETSC_MESH_TYPE::real_section_type::value_type[m->sizeWithBC(s, firstCell)];
int *dofs = new int[maxDof];
int *v = new int[numFields];
//double *v0 = new double[m->getDimension()];
//double *J = new double[m->getDimension()*m->getDimension()];
//double detJ;
ALE::ISieveVisitor::PointRetriever<PETSC_MESH_TYPE::sieve_type> oC((int) pow(m->getSieve()->getMaxConeSize(), m->depth())+1, true);
for(PETSC_MESH_TYPE::label_sequence::iterator c_iter = boundaryCells->begin(); c_iter != boundaryCells->end(); ++c_iter) {
//const Obj<PETSC_MESH_TYPE::coneArray> closure = PETSC_MESH_TYPE::sieve_alg_type::closure(m, m->getArrowSection("orientation"), *c_iter);
//const PETSC_MESH_TYPE::coneArray::iterator end = closure->end();
if (debug > 1) {std::cout << " Boundary cell " << *c_iter << std::endl;}
ALE::ISieveTraversal<PETSC_MESH_TYPE::sieve_type>::orientedClosure(sieve, *c_iter, oC);
const PETSC_MESH_TYPE::point_type * oPoints = oC.getPoints();
const int num_oPoints = oC.getSize();
Map_SieveCell_UFCCell(m, *c_iter, form, &cell, oPoints, num_oPoints);
PetscPrintf(m->comm(), "successfully quit the cell map\n");
//m->computeElementGeometry(coordinates, *c_iter, v0, J, NULL, detJ);
for(int f = 0; f < numFields; ++f) v[f] = 0;
for(int t = 0; t < num_oPoints; t++) {
const int cDim = s->getConstraintDimension(oPoints[t]);
int off = 0;
int f = 0;
int i = -1;
if (debug > 1) {std::cout << " point " << oPoints[t] << std::endl;}
if (cDim) {
if (debug > 1) {std::cout << " constrained excMarker: " << m->getValue(cellExclusion, *c_iter) << std::endl;}
for(PETSC_MESH_TYPE::names_type::const_iterator f_iter = discs->begin(); f_iter != discs->end(); ++f_iter, ++f) {
const ALE::Obj<ALE::Discretization>& disc = m->getDiscretization(*f_iter);
const ALE::Obj<PETSC_MESH_TYPE::names_type> bcs = disc->getBoundaryConditions();
const int fDim = s->getFiberDimension(oPoints[t], f);//disc->getNumDof(m->depth(*cl_iter));
const int *indices = disc->getIndices(m->getValue(cellExclusion, *c_iter));
int b = 0;
for(PETSC_MESH_TYPE::names_type::const_iterator bc_iter = bcs->begin(); bc_iter != bcs->end(); ++bc_iter, ++b) {
const ALE::Obj<ALE::BoundaryCondition>& bc = disc->getBoundaryCondition(*bc_iter);
const int value = m->getValue(m->getLabel(bc->getLabelName()), oPoints[t]);
if (b > 0) v[f] -= fDim;
if (value == bc->getMarker()) {
if (debug > 1) {std::cout << " field " << *f_iter << " marker " << value << std::endl;}
//instead, we use the form's dual integrator (evaluation
sf.setFunction(bc->getFunction());
/*
for(int d = 0; d < fDim; ++d, ++v[f]) {
dofs[++i] = off+d;
if (!noUpdate) values[indices[v[f]]] = (*bc->getDualIntegrator())(v0, J, v[f], bc->getFunction());
if (debug > 1) {std::cout << " setting values["<<indices[v[f]]<<"] = " << values[indices[v[f]]] << std::endl;}
}
*/
for (int d = 0; d < fDim; ++d, ++v[f]) {
dofs[++i] = off+d;
if (!noUpdate) {
values[indices[v[f]]] = finite_element->evaluate_dof(v[f], sf, cell);
PetscPrintf(m->comm(), "evaluated DOF %d\n", f);
}
}
++b;
break;
} else {
if (debug > 1) {std::cout << " field " << *f_iter << std::endl;}
for(int d = 0; d < fDim; ++d, ++v[f]) {
values[indices[v[f]]] = 0.0;
if (debug > 1) {std::cout << " setting values["<<indices[v[f]]<<"] = " << values[indices[v[f]]] << std::endl;}
}
}
}
if (b == 0) {
if (debug > 1) {std::cout << " field " << *f_iter << std::endl;}
for(int d = 0; d < fDim; ++d, ++v[f]) {
values[indices[v[f]]] = 0.0;
if (debug > 1) {std::cout << " setting values["<<indices[v[f]]<<"] = " << values[indices[v[f]]] << std::endl;}
}
}
off += fDim;
}
if (i != cDim-1) {throw ALE::Exception("Invalid constraint initialization");}
s->setConstraintDof(oPoints[t], dofs);
} else {
if (debug > 1) {std::cout << " unconstrained" << std::endl;}
for(PETSC_MESH_TYPE::names_type::const_iterator f_iter = discs->begin(); f_iter != discs->end(); ++f_iter, ++f) {
const Obj<ALE::Discretization>& disc = m->getDiscretization(*f_iter);
const int fDim = s->getFiberDimension(oPoints[t], f);//disc->getNumDof(m->depth(*cl_iter));
const int *indices = disc->getIndices(m->getValue(cellExclusion, *c_iter));
if (debug > 1) {std::cout << " field " << *f_iter << std::endl;}
for(int d = 0; d < fDim; ++d, ++v[f]) {
values[indices[v[f]]] = 0.0;
if (debug > 1) {std::cout << " setting values["<<indices[v[f]]<<"] = " << values[indices[v[f]]] << std::endl;}
}
}
}
}
#if 0
if (debug > 1) {
const Obj<PETSC_MESH_TYPE::sieve_type::coneArray> closure = PETSC_MESH_TYPE::sieve_alg_type::closure(m, m->getArrowSection("orientation"), *c_iter);
const PETSC_MESH_TYPE::sieve_type::coneArray::iterator end = closure->end();
for(int f = 0; f < numFields; ++f) v[f] = 0;
for(PETSC_MESH_TYPE::sieve_type::coneArray::iterator cl_iter = closure->begin(); cl_iter != end; ++cl_iter) {
int f = 0;
for(PETSC_MESH_TYPE::names_type::const_iterator f_iter = discs->begin(); f_iter != discs->end(); ++f_iter, ++f) {
const Obj<ALE::Discretization>& disc = m->getDiscretization(*f_iter);
const int fDim = s->getFiberDimension(*cl_iter, f);
const int *indices = disc->getIndices(m->getValue(cellExclusion, *c_iter));
for(int d = 0; d < fDim; ++d, ++v[f]) {
std::cout << " "<<*f_iter<<"-value["<<indices[v[f]]<<"] " << values[indices[v[f]]] << std::endl;
}
}
}
}
#endif
if (!noUpdate) {
m->updateAll(s, *c_iter, values);
}
}
PetscPrintf(m->comm(), "Done with the cell loop.\n");
delete [] dofs;
delete [] values;
}
if (debug > 1) {s->view("");}
}
#endif
void SetupField_UFC(ALE::Obj<PETSC_MESH_TYPE> m, const ALE::Obj<PETSC_MESH_TYPE::real_section_type>& s, ufc::form * form, const int cellMarker = 2, const bool noUpdate = false) {
typedef ALE::ISieveVisitor::PointRetriever<PETSC_MESH_TYPE::sieve_type> Visitor;
const ALE::Obj<PETSC_MESH_TYPE::names_type>& discs = m->getDiscretizations();
const int debug = s->debug();
PETSC_MESH_TYPE::names_type bcLabels;
s->setChart(m->getSieve()->getChart());
int maxdof = m->setFiberDimensions(s, discs, bcLabels);
m->calculateIndices();
m->calculateIndicesExcluded(s, discs);
m->allocate(s);
s->defaultConstraintDof();
const ALE::Obj<PETSC_MESH_TYPE::label_type>& cellExclusion = m->getLabel("cellExclusion");
ufc::finite_element * finite_element = form->create_finite_element(0);
function_wrapper_scalar sf;
ufc::cell cell;
int dim = m->getDimension();
int embeddim = m->getRealSection("coordinates")->getFiberDimension(*m->depthStratum(0)->begin());
cell.geometric_dimension = embeddim;
cell.topological_dimension = dim;
cell.entity_indices = new unsigned int *[dim+1];
cell.entity_indices[0] = new unsigned int[dim];
cell.coordinates = new double *[dim+1];
double * coordpointer = new double[(dim+1)*dim];
for (int i = 0; i < dim+1; i++) {
cell.coordinates[i] = &coordpointer[dim*i];
}
if (debug > 1) {std::cout << "Setting boundary values" << std::endl;}
for(PETSC_MESH_TYPE::names_type::const_iterator n_iter = bcLabels.begin(); n_iter != bcLabels.end(); ++n_iter) {
function_wrapper_scalar sf;
const ALE::Obj<PETSC_MESH_TYPE::label_sequence>& boundaryCells = m->getLabelStratum(*n_iter, cellMarker);
const ALE::Obj<PETSC_MESH_TYPE::real_section_type>& coordinates = m->getRealSection("coordinates");
const ALE::Obj<PETSC_MESH_TYPE::names_type>& discs = m->getDiscretizations();
const PETSC_MESH_TYPE::point_type firstCell = *boundaryCells->begin();
const int numFields = discs->size();
PETSC_MESH_TYPE::real_section_type::value_type *values = new PETSC_MESH_TYPE::real_section_type::value_type[m->sizeWithBC(s, firstCell)];
int *dofs = new int[maxdof];
int *v = new int[numFields];
double *v0 = new double[m->getDimension()];
double *J = new double[m->getDimension()*m->getDimension()];
double detJ;
Visitor pV((int) pow(m->getSieve()->getMaxConeSize(), m->depth())+1, true);
for(PETSC_MESH_TYPE::label_sequence::iterator c_iter = boundaryCells->begin(); c_iter != boundaryCells->end(); ++c_iter) {
ALE::ISieveTraversal<PETSC_MESH_TYPE::sieve_type>::orientedClosure(*m->getSieve(), *c_iter, pV);
const Visitor::point_type *oPoints = pV.getPoints();
const int oSize = pV.getSize();
if (debug > 1) {std::cout << " Boundary cell " << *c_iter << std::endl;}
m->computeElementGeometry(coordinates, *c_iter, v0, J, NULL, detJ);
for(int f = 0; f < numFields; ++f) v[f] = 0;
for(int cl = 0; cl < oSize; ++cl) {
const int cDim = s->getConstraintDimension(oPoints[cl]);
int off = 0;
int f = 0;
int i = -1;
if (debug > 1) {std::cout << " point " << oPoints[cl] << std::endl;}
if (cDim) {
if (debug > 1) {std::cout << " constrained excMarker: " << m->getValue(cellExclusion, *c_iter) << std::endl;}
for(PETSC_MESH_TYPE::names_type::const_iterator f_iter = discs->begin(); f_iter != discs->end(); ++f_iter, ++f) {
const Obj<ALE::Discretization>& disc = m->getDiscretization(*f_iter);
const Obj<PETSC_MESH_TYPE::names_type> bcs = disc->getBoundaryConditions();
const int fDim = s->getFiberDimension(oPoints[cl], f);//disc->getNumDof(this->depth(oPoints[cl]));
const int *indices = disc->getIndices(m->getValue(cellExclusion, *c_iter));
int b = 0;
for(PETSC_MESH_TYPE::names_type::const_iterator bc_iter = bcs->begin(); bc_iter != bcs->end(); ++bc_iter, ++b) {
const Obj<ALE::BoundaryCondition>& bc = disc->getBoundaryCondition(*bc_iter);
const int value = m->getValue(m->getLabel(bc->getLabelName()), oPoints[cl]);
sf.setFunction(bc->getFunction());
if (b > 0) v[f] -= fDim;
if (value == bc->getMarker()) {
if (debug > 1) {std::cout << " field " << *f_iter << " marker " << value << std::endl;}
for (int d = 0; d < fDim; ++d, ++v[f]) {
dofs[++i] = off+d;
if (!noUpdate) {
values[indices[v[f]]] = finite_element->evaluate_dof(v[f], sf, cell);
PetscPrintf(m->comm(), "evaluated DOF %d\n", f);
}
}
/*
for(int d = 0; d < fDim; ++d, ++v[f]) {
dofs[++i] = off+d;
if (!noUpdate) values[indices[v[f]]] = (*bc->getDualIntegrator())(v0, J, v[f], bc->getFunction());
if (debug > 1) {std::cout << " setting values["<<indices[v[f]]<<"] = " << values[indices[v[f]]] << std::endl;}
}
*/
// Allow only one condition per point
++b;
break;
} else {
if (debug > 1) {std::cout << " field " << *f_iter << std::endl;}
for(int d = 0; d < fDim; ++d, ++v[f]) {
values[indices[v[f]]] = 0.0;
if (debug > 1) {std::cout << " setting values["<<indices[v[f]]<<"] = " << values[indices[v[f]]] << std::endl;}
}
}
}
if (b == 0) {
if (debug > 1) {std::cout << " field " << *f_iter << std::endl;}
for(int d = 0; d < fDim; ++d, ++v[f]) {
values[indices[v[f]]] = 0.0;
if (debug > 1) {std::cout << " setting values["<<indices[v[f]]<<"] = " << values[indices[v[f]]] << std::endl;}
}
}
off += fDim;
}
if (i != cDim-1) {throw ALE::Exception("Invalid constraint initialization");}
s->setConstraintDof(oPoints[cl], dofs);
} else {
if (debug > 1) {std::cout << " unconstrained" << std::endl;}
for(PETSC_MESH_TYPE::names_type::const_iterator f_iter = discs->begin(); f_iter != discs->end(); ++f_iter, ++f) {
const Obj<ALE::Discretization>& disc = m->getDiscretization(*f_iter);
const int fDim = s->getFiberDimension(oPoints[cl], f);//disc->getNumDof(this->depth(oPoints[cl]));
const int *indices = disc->getIndices(m->getValue(cellExclusion, *c_iter));
if (debug > 1) {std::cout << " field " << *f_iter << std::endl;}
for(int d = 0; d < fDim; ++d, ++v[f]) {
values[indices[v[f]]] = 0.0;
if (debug > 1) {std::cout << " setting values["<<indices[v[f]]<<"] = " << values[indices[v[f]]] << std::endl;}
}
}
}
}
if (debug > 1) {
for(int f = 0; f < numFields; ++f) v[f] = 0;
for(int cl = 0; cl < oSize; ++cl) {
int f = 0;
for(PETSC_MESH_TYPE::names_type::const_iterator f_iter = discs->begin(); f_iter != discs->end(); ++f_iter, ++f) {
const Obj<ALE::Discretization>& disc = m->getDiscretization(*f_iter);
const int fDim = s->getFiberDimension(oPoints[cl], f);
const int *indices = disc->getIndices(m->getValue(cellExclusion, *c_iter));
for(int d = 0; d < fDim; ++d, ++v[f]) {
std::cout << " "<<*f_iter<<"-value["<<indices[v[f]]<<"] " << values[indices[v[f]]] << std::endl;
}
}
}
}
if (!noUpdate) {
m->updateAll(s, *c_iter, values);
}
pV.clear();
}
delete [] dofs;
delete [] values;
delete [] v0;
delete [] J;
}
if (debug > 1) {s->view("");}
}
#undef __FUNCT__
#define __FUNCT__ "CreateExactSolution_UFC"
PetscErrorCode CreateExactSolution_UFC(Obj<PETSC_MESH_TYPE> m, Obj<PETSC_MESH_TYPE::real_section_type> s, ufc::form * form, PetscScalar (*exactSolution)(const double *))
{
const int dim = m->getDimension();
//PetscBool flag;
//PetscErrorCode ierr;
PetscFunctionBegin;
SetupField_UFC(m, s, form);
ufc::finite_element * finite_element = form->create_finite_element(0);
ufc::cell cell;
cell.geometric_dimension = dim;
cell.topological_dimension = dim;
cell.entity_indices = new unsigned int *[dim+1];
cell.entity_indices[0] = new unsigned int[dim];
cell.coordinates = new double *[dim+1];
double * tmpcellcoords = new double[dim*(dim+1)];
for (int i = 0; i < dim+1; i++) {
cell.coordinates[i] = &tmpcellcoords[i*dim];
}
const Obj<PETSC_MESH_TYPE::label_sequence>& cells = m->heightStratum(0);
//const Obj<PETSC_MESH_TYPE::real_section_type>& coordinates = m->getRealSection("coordinates");
const int localDof = m->sizeWithBC(s, *cells->begin());
PETSC_MESH_TYPE::real_section_type::value_type *values = new PETSC_MESH_TYPE::real_section_type::value_type[localDof];
function_wrapper_scalar sf;
sf.setFunction(exactSolution);
for(PETSC_MESH_TYPE::label_sequence::iterator c_iter = cells->begin(); c_iter != cells->end(); ++c_iter) {
const Obj<PETSC_MESH_TYPE::coneArray> closure = ALE::SieveAlg<ALE::Mesh>::closure(m, *c_iter);
const PETSC_MESH_TYPE::coneArray::iterator end = closure->end();
int v = 0;
//m->computeElementGeometry(coordinates, *c_iter, v0, J, NULL, detJ);
Map_SieveCell_UFCCell(m, *c_iter, form, &cell);
for(PETSC_MESH_TYPE::coneArray::iterator cl_iter = closure->begin(); cl_iter != end; ++cl_iter) {
const int pointDim = s->getFiberDimension(*cl_iter);
//FOR NOW: keep this, only get rid of the integration routine.
if (pointDim) {
for(int d = 0; d < pointDim; ++d, ++v) {
values[v] = finite_element->evaluate_dof(v, sf, cell);
//values[v] = (*options->integrate)(v0, J, v, options->exactFunc);
}
}
}
m->updateAll(s, *c_iter, values);
}
s->view("setup field");
PetscFunctionReturn(0);
}
|