PolyFEM
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ElasticVarForm.cpp
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1#include "ElasticVarForm.hpp"
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30
31#include <algorithm>
32#include <map>
33#include <ostream>
34
35#include <igl/Timer.h>
36
37#include <spdlog/fmt/fmt.h>
38
39namespace polyfem::varform
40{
43 const Eigen::MatrixXd &solution,
44 const io::CheckpointMetadata &metadata) const
45 {
46 VarForm::serialize_checkpoint(writer, solution, metadata);
47 write_checkpoint_ordering(writer, "primary", space_);
48 }
49
51 const io::CheckpointReader &reader,
52 Eigen::MatrixXd &solution)
53 {
54 VarForm::deserialize_checkpoint(reader, solution);
57 reader, "primary", space_,
58 mesh_->dimension(), 0, solution);
59 }
60
62 {
64 space_.reset();
69 rhs_assembler_ = nullptr;
70 mass_.resize(0, 0);
71 pure_mass_.resize(0, 0);
72 avg_mass_ = 0;
73 rhs_.resize(0, 0);
74 primary_assembler_ = nullptr;
75 mass_assembler_ = nullptr;
76 pure_mass_assembler_ = nullptr;
77 t0 = 0;
78 time_steps = 0;
79 dt = 0;
80 }
81
82 void ElasticVarForm::init(const std::string &formulation, const Units &units, const json &args, const std::string &out_path)
83 {
84 VarForm::init(formulation, units, args, out_path);
85 const bool is_time_dependent = args.contains("time") && !args["time"].is_null();
86
88 assert(primary_assembler_->name() == formulation);
89 if (args["solver"]["advanced"]["check_inversion"] == "Conservative")
90 {
91 if (auto elastic_assembler = std::dynamic_pointer_cast<assembler::ElasticityAssembler>(primary_assembler_))
92 elastic_assembler->set_use_robust_jacobian();
93 }
94 mass_assembler_ = std::make_shared<assembler::Mass>();
95 pure_mass_assembler_ = std::make_shared<assembler::HRZMass>();
96
97 if (!args.contains("preset_problem"))
98 {
99 problem = std::make_shared<assembler::GenericTensorProblem>("GenericTensor");
100
101 problem->clear();
102 json tmp;
103 tmp["is_time_dependent"] = is_time_dependent;
104 problem->set_parameters(tmp, resources_);
105
106 // important for the BC
107
108 auto bc = args["boundary_conditions"];
109 problem->set_parameters(bc, resources_);
110 problem->set_parameters(args["initial_conditions"], resources_);
111 problem->set_parameters(args["output"], resources_);
112 }
113 else
114 {
115 if (args["preset_problem"]["type"] == "Kernel")
116 {
117 problem = std::make_shared<problem::KernelProblem>("Kernel", *primary_assembler_);
118 problem->clear();
119 problem::KernelProblem &kprob = *dynamic_cast<problem::KernelProblem *>(problem.get());
120 }
121 else
122 {
123 problem = problem::ProblemFactory::factory().get_problem(args["preset_problem"]["type"]);
124 problem->clear();
125 }
126 // important for the BC
127 problem->set_parameters(args["preset_problem"], resources_);
128 }
129
130 problem->set_units(*primary_assembler_, units);
131
132 t0 = is_time_dependent ? args["time"]["t0"].get<double>() : 0.0;
133 time_steps = is_time_dependent ? args["time"]["time_steps"].get<int>() : 0;
134 dt = is_time_dependent ? args["time"]["dt"].get<double>() : 0.0;
135 }
136
137 void ElasticVarForm::load_mesh(const mesh::Mesh &mesh, const json &args)
138 {
141 pure_mass_assembler_->set_size(mass_assembler_->size());
142
143 problem->init(mesh);
144
145 if (assembler::MultiModel *mm = dynamic_cast<assembler::MultiModel *>(primary_assembler_.get()))
146 {
147 assert(args["materials"].is_array());
148
149 std::vector<std::string> materials(mesh.n_elements());
150
151 std::map<int, std::string> mats;
152
153 for (const auto &m : args["materials"])
154 mats[m["id"].get<int>()] = m["type"];
155
156 for (int i = 0; i < materials.size(); ++i)
157 materials[i] = mats.at(mesh.get_body_id(i));
158
159 mm->init_multimodels(materials);
160 }
161 }
162
163 void ElasticVarForm::build_basis(mesh::Mesh &mesh, const bool iso_parametric, const json &args)
164 {
165 build_elastic_basis(mesh, iso_parametric, args, -1);
166 }
167
168 void ElasticVarForm::build_elastic_basis(mesh::Mesh &mesh, const bool iso_parametric, const json &args, const int fe_space_id)
169 {
170 assert(problem);
171 assert(primary_assembler_);
172 assert(mass_assembler_);
173 assert(pure_mass_assembler_);
174
175 Eigen::VectorXi space_disc_orders, space_disc_ordersq;
176 assign_discr_orders(args["space"], fe_space_id, mesh, space_disc_orders, space_disc_ordersq);
177
178 if (args["space"]["use_p_ref"])
179 {
181 mesh,
182 args["space"]["advanced"]["B"],
183 args["space"]["advanced"]["h1_formula"],
184 args["space"]["discr_order"],
185 args["space"]["advanced"]["discr_order_max"],
186 stats,
187 space_disc_orders);
188
189 logger().info("min p: {} max p: {}", space_disc_orders.minCoeff(), space_disc_orders.maxCoeff());
190 }
191
193 mesh,
194 iso_parametric,
195 space_disc_orders,
196 space_disc_ordersq,
197 args["space"]["basis_type"],
198 args["space"]["poly_basis_type"],
200 mesh.dimension(),
201 args["space"]["advanced"]["quadrature_order"],
202 args["space"]["advanced"]["mass_quadrature_order"],
203 args["space"]["advanced"]["use_corner_quadrature"],
204 args["space"]["advanced"]["n_harmonic_samples"],
205 args["space"]["advanced"]["integral_constraints"],
206 space_,
207 boundary_);
208
209 problem->update_nodes(space_.space_in_node_to_node);
211
213 for (const auto &lb : boundary_.total_local_boundary)
214 boundary_.local_boundary.emplace_back(lb);
215
216 std::vector<basis::ElementBases> empty_pressure_bases;
217 std::vector<int> empty_pressure_boundary_nodes;
218 problem->setup_bc(
219 mesh, space_.n_bases,
220 space_.basis_list(), space_.geometry_basis_list(), empty_pressure_bases,
226 empty_pressure_boundary_nodes,
228
231
232 const auto &current_bases = space_.geometry_basis_list();
233 if (args["space"]["advanced"]["count_flipped_els"])
234 stats.count_flipped_elements(mesh, current_bases);
235
236 const int n_samples = 10;
237 stats.compute_mesh_size(mesh, current_bases, n_samples, args["output"]["advanced"]["curved_mesh_size"]);
238
239 logger().info("flipped elements {}", stats.n_flipped);
240 logger().info("h: {}", stats.mesh_size);
241
242 if (space_.n_bases <= args["solver"]["advanced"]["cache_size"])
243 {
244 igl::Timer timer;
245 timer.start();
246 logger().info("Building cache...");
247 ass_vals_cache_.init(mesh.is_volume(), space_.basis_list(), current_bases);
248 mass_ass_vals_cache_.init(mesh.is_volume(), space_.basis_list(), current_bases, true);
249 pure_mass_ass_vals_cache_.init(mesh.is_volume(), space_.basis_list(), current_bases, true);
250 logger().info(" took {}s", timer.getElapsedTime());
251 }
252 else
253 {
257 }
258 }
259
261 {
262 json rhs_solver_params = args["solver"]["linear"];
263 if (!rhs_solver_params.contains("Pardiso"))
264 rhs_solver_params["Pardiso"] = {};
265 rhs_solver_params["Pardiso"]["mtype"] = -2;
266
267 rhs_assembler_ = std::make_shared<assembler::RhsAssembler>(
268 *primary_assembler_, *mesh_, nullptr,
272 args["space"]["advanced"]["bc_method"],
273 rhs_solver_params,
274 /*fe_space_id=*/-1);
275 }
276
278 {
279 igl::Timer timer;
280 json p_params = {};
281 p_params["formulation"] = primary_assembler_->name();
282 {
283 RowVectorNd min, max, delta;
284 mesh.bounding_box(min, max);
285 delta = (max - min) / 2. + min;
286 if (mesh.is_volume())
287 p_params["bbox_center"] = {delta(0), delta(1), delta(2)};
288 else
289 p_params["bbox_center"] = {delta(0), delta(1)};
290 }
291 problem->set_parameters(p_params, resources_);
292
293 rhs_.resize(0, 0);
294
295 timer.start();
296 logger().info("Assigning rhs...");
297
299 assert(rhs_assembler_ != nullptr);
300 rhs_assembler_->assemble(mass_assembler_->density(), rhs_);
301 rhs_ *= -1;
302
303 timings.assigning_rhs_time = timer.getElapsedTime();
304 logger().info(" took {}s", timings.assigning_rhs_time);
305 }
306
307 void ElasticVarForm::assemble_mass_mat(const mesh::Mesh &mesh, const json &args)
308 {
309 if (!problem->is_time_dependent())
310 {
311 avg_mass_ = 1;
313 if (!primary_assembler_->is_linear())
315 return;
316 }
317
318 mass_.resize(0, 0);
319
320 igl::Timer timer;
321 timer.start();
322 logger().info("Assembling mass mat...");
323
325 if (!primary_assembler_->is_linear())
327
328 assert(mass_.size() > 0);
329
330 avg_mass_ = 0;
331 for (int k = 0; k < mass_.outerSize(); ++k)
332 for (StiffnessMatrix::InnerIterator it(mass_, k); it; ++it)
333 {
334 assert(it.col() == k);
335 avg_mass_ += it.value();
336 }
337
338 avg_mass_ /= mass_.rows();
339 logger().info("average mass {}", avg_mass_);
340
341 if (args["solver"]["advanced"]["lump_mass_matrix"])
343
344 timer.stop();
345 timings.assembling_mass_mat_time = timer.getElapsedTime();
346 logger().info(" took {}s", timings.assembling_mass_mat_time);
347
348 stats.nn_zero = mass_.nonZeros();
349 stats.num_dofs = mass_.rows();
350 stats.mat_size = (long long)mass_.rows() * (long long)mass_.cols();
351 logger().info("sparsity: {}/{}", stats.nn_zero, stats.mat_size);
352 }
353
355 Eigen::MatrixXd &velocity,
356 const InitialConditionOverride *override,
357 const std::string &state_prefix) const
358 {
359 assert(rhs_assembler_ != nullptr);
360 if (override && override->velocity.size() != 0)
361 {
362 velocity = override->velocity;
363 assert(
364 velocity.rows() == space_.ndof() && velocity.cols() >= 1
365 && "Initial velocity override must match the simulation DOFs");
366 return;
367 }
368
369 rhs_assembler_->initial_velocity(velocity);
370 }
371
373 Eigen::MatrixXd &acceleration,
374 const InitialConditionOverride *override,
375 const std::string &state_prefix) const
376 {
377 assert(rhs_assembler_ != nullptr);
378 if (override && override->acceleration.size() != 0)
379 {
380 acceleration = override->acceleration;
381 assert(
382 acceleration.rows() == space_.ndof() && acceleration.cols() >= 1
383 && "Initial acceleration override must match the simulation DOFs");
384 return;
385 }
386
387 rhs_assembler_->initial_acceleration(acceleration);
388 }
389
391 Eigen::MatrixXd &solution,
392 const InitialConditionOverride *override,
393 const std::string &state_prefix) const
394 {
395 assert(rhs_assembler_ != nullptr);
396 if (override && override->solution.size() != 0)
397 {
398 solution = override->solution;
399 assert(
400 solution.rows() == space_.ndof() && solution.cols() >= 1
401 && "Initial solution override must match the simulation DOFs");
402 return;
403 }
404
405 if (problem->is_time_dependent())
406 rhs_assembler_->initial_solution(solution);
407 else
408 {
409 solution.resize(rhs_.size(), 1);
410 solution.setZero();
411 }
412 }
413
415 {
416 const int gdiscr_order = mesh_->orders().size() <= 0 ? 1 : mesh_->orders().maxCoeff();
417 return n_boundary_samples(space_.disc_orders.maxCoeff(), space_.disc_ordersq.maxCoeff(), gdiscr_order);
418 }
419
421 {
422 if (!mesh_ || !space_.geometry)
423 return {};
424
425 const auto &nodes = space_.is_iso_parametric() ? space_.mesh_nodes : space_.geometry->mesh_nodes;
426 if (!nodes)
427 return {};
428
429 auto indices = nodes->primitive_to_node();
430 indices.resize(mesh_->n_vertices());
431 return indices;
432 }
433
435 {
436 const auto p2n = elastic_primitive_to_node();
437 const int n_geometry_bases = space_.geometry ? space_.geometry->n_bases : 0;
438 std::vector<int> indices(n_geometry_bases, -1);
439 for (int i = 0; i < int(p2n.size()); ++i)
440 {
441 if (p2n[i] >= 0 && p2n[i] < int(indices.size()))
442 indices[p2n[i]] = i;
443 }
444 return indices;
445 }
446
447 std::vector<io::OutputField> ElasticVarForm::elastic_output_fields(
448 const io::OutputSample &sample,
449 const Eigen::MatrixXd &solution,
450 const io::OutputFieldOptions &options,
451 const mesh::Obstacle *obstacle,
452 const time_integrator::ImplicitTimeIntegrator *time_integrator,
453 const std::vector<std::pair<std::string, std::shared_ptr<solver::Form>>> &named_forms,
454 const solver::Form *elastic_form,
455 const solver::ContactForm *contact_form) const
456 {
457 std::vector<io::OutputField> fields;
458 if (!mesh_ || !problem || solution.size() <= 0)
459 return fields;
460
461 const bool has_element_samples = sample.local_points.rows() > 0 && sample.local_points.rows() == sample.element_ids.size();
462 const int output_rows = sample.points.rows() > 0 ? sample.points.rows() : std::max<int>(sample.local_points.rows(), sample.node_ids.size());
463
464 const int actual_dim = problem->is_scalar() ? 1 : mesh_->dimension();
465 const auto &paraview_options = args["output"]["paraview"]["options"];
466 const bool material_params = paraview_options["material"];
467 const bool body_ids = paraview_options["body_ids"];
468 const bool velocity = paraview_options["velocity"];
469 const bool acceleration = paraview_options["acceleration"];
470 const bool forces = paraview_options["forces"] && !problem->is_scalar();
471 const bool tensor_values = paraview_options["tensor_values"] && !problem->is_scalar();
472 const bool scalar_values = paraview_options["scalar_values"];
473 const bool use_spline = args["space"]["basis_type"] == "Spline";
474 const bool explicit_fields = !options.fields.empty();
475
476 const auto resize_to_output_rows = [&](Eigen::MatrixXd &values) {
477 if (output_rows <= values.rows())
478 return;
479
480 const int previous_rows = values.rows();
481 values.conservativeResize(output_rows, values.cols());
482 values.bottomRows(output_rows - previous_rows).setZero();
483 };
484
485 const auto append_obstacle_values = [&](Eigen::MatrixXd &sampled_values, const Eigen::MatrixXd &dof_values) -> bool {
486 if (!obstacle || obstacle->n_vertices() <= 0)
487 {
488 resize_to_output_rows(sampled_values);
489 return sample.points.rows() == 0 || sample.points.rows() == sampled_values.rows();
490 }
491
492 const bool has_obstacle_rows =
493 sample.points.rows() == sampled_values.rows() + obstacle->n_vertices()
494 && sample.points.cols() == obstacle->v().cols()
495 && sample.points.bottomRows(obstacle->n_vertices()).isApprox(obstacle->v());
496
497 if (!has_obstacle_rows)
498 return sample.points.rows() == 0 || sample.points.rows() == sampled_values.rows();
499
500 sampled_values.conservativeResize(sampled_values.rows() + obstacle->n_vertices(), sampled_values.cols());
501 if (dof_values.rows() >= obstacle->ndof())
502 {
503 const Eigen::MatrixXd obstacle_values =
504 utils::unflatten(dof_values.bottomRows(obstacle->ndof()), sampled_values.cols());
505 if (obstacle_values.rows() == obstacle->n_vertices()
506 && obstacle_values.cols() == sampled_values.cols())
507 sampled_values.bottomRows(obstacle->n_vertices()) = obstacle_values;
508 else
509 sampled_values.bottomRows(obstacle->n_vertices()).setZero();
510 }
511 else
512 sampled_values.bottomRows(obstacle->n_vertices()).setZero();
513 return true;
514 };
515
516 const auto sample_dof_field = [&](const Eigen::MatrixXd &dof_values, const int field_dim, Eigen::MatrixXd &values) -> bool {
517 if (dof_values.size() <= 0 || field_dim <= 0)
518 return false;
519
520 if (has_element_samples)
521 {
522 values.resize(sample.local_points.rows(), field_dim);
523 for (int i = 0; i < sample.local_points.rows(); ++i)
524 {
525 const int element_id = sample.element_ids(i);
526 if (element_id < 0)
527 {
528 values.row(i).setZero();
529 continue;
530 }
531
532 Eigen::MatrixXd local_sol, local_grad;
535 element_id, sample.local_points.row(i), dof_values, local_sol, local_grad);
536
537 for (int d = 0; d < field_dim; ++d)
538 values(i, d) = local_sol(d);
539 }
540
541 return append_obstacle_values(values, dof_values);
542 }
543
544 if (sample.node_ids.size() > 0)
545 {
546 values.resize(sample.node_ids.size(), field_dim);
547 for (int i = 0; i < sample.node_ids.size(); ++i)
548 {
549 const int node_id = sample.node_ids(i);
550 for (int d = 0; d < field_dim; ++d)
551 {
552 const int dof = node_id * field_dim + d;
553 if (dof < 0 || dof >= dof_values.rows())
554 return false;
555 values(i, d) = dof_values(dof);
556 }
557 }
558
559 return sample.points.rows() == 0 || sample.points.rows() == values.rows();
560 }
561
562 return false;
563 };
564
565 const auto append_sampled_dof_field = [&](const std::string &name, const Eigen::MatrixXd &dof_values, const int field_dim) {
566 Eigen::MatrixXd values;
567 if (sample_dof_field(dof_values, field_dim, values))
568 fields.push_back({name, values, io::OutputField::Association::Point});
569 };
570
571 const auto append_scalar_values = [&]() {
572 if (!scalar_values || problem->is_scalar() || !has_element_samples)
573 return;
574
575 const bool wants_scalar = options.fields.empty()
576 || options.export_field("von_mises")
577 || options.export_field("von_mises_avg");
578 if (!wants_scalar)
579 return;
580
581 std::vector<assembler::Assembler::NamedMatrix> point_values;
582 for (int i = 0; i < sample.local_points.rows(); ++i)
583 {
584 const int element_id = sample.element_ids(i);
585 if (element_id < 0)
586 continue;
587
588 std::vector<assembler::Assembler::NamedMatrix> local_values;
589 primary_assembler_->compute_scalar_value(
590 assembler::OutputData(sample.time, element_id, space_.basis_list()[element_id], space_.geometry_basis_list()[element_id], sample.local_points.row(i), solution),
591 local_values);
592
593 if (point_values.empty())
594 {
595 point_values.resize(local_values.size());
596 for (int k = 0; k < local_values.size(); ++k)
597 {
598 point_values[k].first = local_values[k].first;
599 point_values[k].second.setZero(output_rows, local_values[k].second.cols());
600 }
601 }
602
603 for (int k = 0; k < local_values.size(); ++k)
604 point_values[k].second.row(i) = local_values[k].second;
605 }
606
607 for (const auto &[name, values] : point_values)
608 {
609 if (options.export_field(name))
610 fields.push_back({name, values, io::OutputField::Association::Point});
611 }
612 };
613
614 const auto append_tensor_values = [&]() {
615 if (!tensor_values || problem->is_scalar() || !has_element_samples)
616 return;
617
618 const bool wants_tensor = options.fields.empty()
619 || options.export_field("cauchy_stess")
620 || options.export_field("pk1_stess")
621 || options.export_field("pk2_stess")
622 || options.export_field("F");
623 if (!wants_tensor)
624 return;
625
626 std::vector<assembler::Assembler::NamedMatrix> point_values;
627 for (int i = 0; i < sample.local_points.rows(); ++i)
628 {
629 const int element_id = sample.element_ids(i);
630 if (element_id < 0)
631 continue;
632
633 std::vector<assembler::Assembler::NamedMatrix> local_values;
634 primary_assembler_->compute_tensor_value(
635 assembler::OutputData(sample.time, element_id, space_.basis_list()[element_id], space_.geometry_basis_list()[element_id], sample.local_points.row(i), solution),
636 local_values);
637
638 if (point_values.empty())
639 {
640 point_values.resize(local_values.size());
641 for (int k = 0; k < local_values.size(); ++k)
642 {
643 point_values[k].first = local_values[k].first;
644 point_values[k].second.setZero(output_rows, local_values[k].second.cols());
645 }
646 }
647
648 for (int k = 0; k < local_values.size(); ++k)
649 point_values[k].second.row(i) = local_values[k].second;
650 }
651
652 for (const auto &[name, values] : point_values)
653 {
654 if (!options.export_field(name))
655 continue;
656
657 const int stride = mesh_->dimension();
658 assert(values.cols() % stride == 0);
659 for (int i = 0; i < values.cols(); i += stride)
660 {
661 const int ii = (i / stride) + 1;
662 fields.push_back({fmt::format("{:s}_{:d}", name, ii), values.middleCols(i, stride), io::OutputField::Association::Point});
663 }
664 }
665 };
666
667 const auto append_averaged_values = [&]() {
668 if (use_spline || problem->is_scalar() || !has_element_samples || (!scalar_values && !tensor_values))
669 return;
670
671 const bool wants_avg = options.fields.empty()
672 || options.export_field("von_mises_avg")
673 || options.export_field("cauchy_stess_avg")
674 || options.export_field("pk1_stess_avg")
675 || options.export_field("pk2_stess_avg")
676 || options.export_field("F_avg");
677 if (!wants_avg)
678 return;
679
680 Eigen::MatrixXd areas(space_.n_bases, 1);
681 areas.setZero();
682 std::vector<assembler::Assembler::NamedMatrix> tmp_s, tmp_t;
683 std::vector<Eigen::MatrixXd> avg_scalar, avg_tensor;
684
685 for (int e = 0; e < int(space_.basis_list().size()); ++e)
686 {
687 Eigen::MatrixXd local_pts;
688 if (mesh_->is_simplex(e))
689 {
690 if (mesh_->dimension() == 3)
691 autogen::p_nodes_3d(space_.disc_orders(e), local_pts);
692 else
693 autogen::p_nodes_2d(space_.disc_orders(e), local_pts);
694 }
695 else if (mesh_->is_cube(e))
696 {
697 if (mesh_->dimension() == 3)
698 autogen::q_nodes_3d(space_.disc_orders(e), local_pts);
699 else
700 autogen::q_nodes_2d(space_.disc_orders(e), local_pts);
701 }
702 else if (mesh_->is_prism(e))
703 {
704 autogen::prism_nodes_3d(space_.disc_orders(e), space_.disc_ordersq(e), local_pts);
705 }
706 else
707 {
708 continue;
709 }
710
711 const basis::ElementBases &bs = space_.basis_list()[e];
712 const basis::ElementBases &gbs = space_.geometry_basis_list()[e];
713
714 assembler::ElementAssemblyValues vals;
715 vals.compute(e, mesh_->is_volume(), bs, gbs);
716 const double area = (vals.det.array() * vals.quadrature.weights.array()).sum();
717
718 if (scalar_values)
719 primary_assembler_->compute_scalar_value(assembler::OutputData(sample.time, e, bs, gbs, local_pts, solution), tmp_s);
720 if (tensor_values)
721 primary_assembler_->compute_tensor_value(assembler::OutputData(sample.time, e, bs, gbs, local_pts, solution), tmp_t);
722
723 if (avg_scalar.empty() && !tmp_s.empty())
724 {
725 avg_scalar.resize(tmp_s.size());
726 for (auto &m : avg_scalar)
727 m.setZero(space_.n_bases, 1);
728 }
729 if (avg_tensor.empty() && !tmp_t.empty())
730 {
731 avg_tensor.resize(tmp_t.size());
732 for (auto &m : avg_tensor)
733 m.setZero(space_.n_bases, actual_dim * actual_dim);
734 }
735
736 for (size_t j = 0; j < bs.bases.size(); ++j)
737 {
738 const basis::Basis &b = bs.bases[j];
739 if (b.global().size() > 1)
740 continue;
741
742 const int index = b.global().front().index;
743 areas(index) += area;
744 for (int k = 0; k < tmp_s.size(); ++k)
745 avg_scalar[k](index) += tmp_s[k].second(j) * area;
746 for (int k = 0; k < tmp_t.size(); ++k)
747 avg_tensor[k].row(index) += tmp_t[k].second.row(j) * area;
748 }
749 }
750
751 for (auto &m : avg_scalar)
752 for (int i = 0; i < m.rows(); ++i)
753 if (areas(i) > 0)
754 m(i) /= areas(i);
755 for (auto &m : avg_tensor)
756 for (int i = 0; i < m.rows(); ++i)
757 if (areas(i) > 0)
758 m.row(i) /= areas(i);
759
760 for (int k = 0; k < tmp_s.size(); ++k)
761 {
762 const std::string name = fmt::format("{:s}_avg", tmp_s[k].first);
763 if (!options.export_field(name))
764 continue;
765
766 Eigen::MatrixXd sampled;
767 if (sample_dof_field(avg_scalar[k], 1, sampled))
768 fields.push_back({name, sampled, io::OutputField::Association::Point});
769 }
770
771 for (int k = 0; k < tmp_t.size(); ++k)
772 {
773 const std::string base_name = fmt::format("{:s}_avg", tmp_t[k].first);
774 if (!options.export_field(base_name))
775 continue;
776
777 Eigen::MatrixXd sampled;
778 if (!sample_dof_field(utils::flatten(avg_tensor[k]), actual_dim * actual_dim, sampled))
779 continue;
780
781 const int stride = mesh_->dimension();
782 for (int i = 0; i < sampled.cols(); i += stride)
783 {
784 const int ii = (i / stride) + 1;
785 fields.push_back({fmt::format("{:s}_{:d}", base_name, ii), sampled.middleCols(i, stride), io::OutputField::Association::Point});
786 }
787 }
788 };
789
790 const auto append_material_fields = [&]() {
791 if (!material_params || !has_element_samples)
792 return;
793
794 const auto &params = primary_assembler_->parameters();
795 std::map<std::string, Eigen::MatrixXd> param_values;
796 for (const auto &[p, _] : params)
797 param_values[p].setZero(output_rows, 1);
798 Eigen::MatrixXd rhos = Eigen::MatrixXd::Zero(output_rows, 1);
799
800 const auto &density = mass_assembler_->density();
801 for (int i = 0; i < sample.local_points.rows(); ++i)
802 {
803 const int element_id = sample.element_ids(i);
804 if (element_id < 0)
805 continue;
806
807 for (const auto &[p, func] : params)
808 param_values.at(p)(i) = func(sample.local_points.row(i), sample.points.row(i), sample.time, element_id);
809 rhos(i) = density(sample.local_points.row(i), sample.points.row(i), sample.time, element_id);
810 }
811
812 for (const auto &[name, values] : param_values)
813 if (options.export_field(name))
814 fields.push_back({name, values, io::OutputField::Association::Point});
815 if (options.export_field("rho"))
816 fields.push_back({"rho", rhos, io::OutputField::Association::Point});
817 };
818
819 const auto append_body_ids = [&]() {
820 if (!body_ids || !options.export_field("body_ids") || !has_element_samples)
821 return;
822
823 Eigen::MatrixXd ids = Eigen::MatrixXd::Zero(output_rows, 1);
824 for (int i = 0; i < sample.element_ids.size(); ++i)
825 {
826 const int element_id = sample.element_ids(i);
827 if (element_id >= 0)
828 ids(i) = mesh_->get_body_id(element_id);
829 }
830 fields.push_back({"body_ids", ids, io::OutputField::Association::Point});
831 };
832
833 const auto compute_traction_forces = [&]() {
834 Eigen::MatrixXd traction_forces;
835 traction_forces.setZero(space_.n_bases * actual_dim, 1);
836
837 Eigen::MatrixXd uv, points, normals;
838 Eigen::VectorXd weights;
839 Eigen::VectorXi global_primitive_ids;
840 assembler::ElementAssemblyValues vals;
841
842 for (const auto &lb : boundary_.total_local_boundary)
843 {
844 const int e = lb.element_id();
845 const bool has_samples = utils::BoundarySampler::boundary_quadrature(
846 lb, elastic_boundary_samples(), *mesh_, false, uv, points, normals, weights, global_primitive_ids);
847 if (!has_samples)
848 continue;
849
850 const basis::ElementBases &bs = space_.basis_list()[e];
851 const basis::ElementBases &gbs = space_.geometry_basis_list()[e];
852 vals.compute(e, mesh_->is_volume(), points, bs, gbs);
853
854 for (int n = 0; n < normals.rows(); ++n)
855 {
856 Eigen::MatrixXd deform_mat = Eigen::MatrixXd::Zero(actual_dim, actual_dim);
857 for (const auto &b : vals.basis_values)
858 {
859 for (const auto &g : b.global)
860 {
861 for (int d = 0; d < actual_dim; ++d)
862 deform_mat.row(d) += solution(g.index * actual_dim + d) * b.grad.row(n);
863 }
864 }
865
866 Eigen::MatrixXd trafo = vals.jac_it[n].inverse() + deform_mat;
867 normals.row(n) = normals.row(n) * trafo.inverse();
868 normals.row(n).normalize();
869 }
870
871 std::vector<assembler::Assembler::NamedMatrix> tensor_flat;
872 primary_assembler_->compute_tensor_value(assembler::OutputData(sample.time, e, bs, gbs, points, solution), tensor_flat);
873
874 for (long n = 0; n < vals.basis_values.size(); ++n)
875 {
876 const assembler::AssemblyValues &v = vals.basis_values[n];
877 const int g_index = v.global[0].index * actual_dim;
878 for (int q = 0; q < points.rows(); ++q)
879 {
880 assert(tensor_flat[0].first == "cauchy_stess");
881 Eigen::MatrixXd stress_tensor = utils::unflatten(tensor_flat[0].second.row(q), actual_dim);
882 traction_forces.block(g_index, 0, actual_dim, 1) += stress_tensor * normals.row(q).transpose() * v.val(q) * weights(q);
883 }
884 }
885 }
886
887 return traction_forces;
888 };
889
890 const auto append_traction_force = [&]() {
891 if (problem->is_scalar() || !explicit_fields || !options.export_field("traction_force"))
892 return;
893
894 if (has_element_samples && sample.normals.rows() == sample.local_points.rows() && sample.primitive_ids.size() == sample.local_points.rows())
895 {
896 const Eigen::MatrixXd displaced_normals = displaced_output_normals(sample, solution);
897 const Eigen::MatrixXd &normals = displaced_normals.rows() == sample.normals.rows() ? displaced_normals : sample.normals;
898 Eigen::MatrixXd values = Eigen::MatrixXd::Zero(output_rows, actual_dim);
899 for (int i = 0; i < sample.local_points.rows(); ++i)
900 {
901 const int element_id = sample.element_ids(i);
902 if (element_id < 0)
903 continue;
904
905 std::vector<assembler::Assembler::NamedMatrix> tensor_flat;
906 primary_assembler_->compute_tensor_value(
907 assembler::OutputData(sample.time, element_id, space_.basis_list()[element_id], space_.geometry_basis_list()[element_id], sample.local_points.row(i), solution),
908 tensor_flat);
909
910 assert(tensor_flat[0].first == "cauchy_stess");
911 Eigen::Map<Eigen::MatrixXd> tensor(tensor_flat[0].second.data(), actual_dim, actual_dim);
912 values.row(i) = normals.row(i) * tensor;
913
914 double area = 0;
915 const int primitive_id = sample.primitive_ids(i);
916 if (mesh_->is_volume())
917 {
918 if (mesh_->is_simplex(element_id))
919 area = mesh_->tri_area(primitive_id);
920 else if (mesh_->is_cube(element_id))
921 area = mesh_->quad_area(primitive_id);
922 else if (mesh_->is_prism(element_id))
923 area = mesh_->n_face_vertices(primitive_id) == 4 ? mesh_->quad_area(primitive_id) : mesh_->tri_area(primitive_id);
924 }
925 else
926 {
927 area = mesh_->edge_length(primitive_id);
928 }
929 values.row(i) *= area;
930 }
931 fields.push_back({"traction_force", values, io::OutputField::Association::Point});
932 return;
933 }
934
935 append_sampled_dof_field("traction_force", compute_traction_forces(), actual_dim);
936 };
937
938 append_scalar_values();
939 append_tensor_values();
940 append_averaged_values();
941 append_material_fields();
942 append_body_ids();
943
944 if ((paraview_options["jacobian_validity"] || (explicit_fields && options.export_field("validity")))
945 && has_element_samples
946 && sample.primitive_ids.size() == 0)
947 {
948 const auto invalid_elements = utils::count_invalid(
949 mesh_->dimension(), space_.basis_list(), space_.geometry_basis_list(), solution);
950 Eigen::MatrixXd validity = Eigen::MatrixXd::Zero(output_rows, 1);
951 for (int i = 0; i < sample.element_ids.size(); ++i)
952 {
953 validity(i) = std::find(
954 invalid_elements.begin(), invalid_elements.end(), sample.element_ids(i))
955 != invalid_elements.end();
956 }
957 fields.push_back({"validity", validity, io::OutputField::Association::Point});
958 }
959
960 if (problem->is_time_dependent())
961 {
962 if (velocity && options.export_field("velocity"))
963 append_sampled_dof_field(
964 "velocity",
965 time_integrator ? time_integrator->v_prev() : Eigen::VectorXd::Zero(solution.size()),
966 actual_dim);
967 if (acceleration && options.export_field("acceleration"))
968 append_sampled_dof_field(
969 "acceleration",
970 time_integrator ? time_integrator->a_prev() : Eigen::VectorXd::Zero(solution.size()),
971 actual_dim);
972 }
973
974 if (forces)
975 {
976 const double s = time_integrator ? time_integrator->acceleration_scaling() : 1;
977 for (const auto &[name, form] : named_forms)
978 {
979 const std::string field_name = name + "_forces";
980 if (!options.export_field(field_name))
981 continue;
982
983 Eigen::VectorXd force;
984 if (form && form->enabled())
985 {
986 form->first_derivative(solution, force);
987 force *= -1.0 / s;
988 }
989 else
990 {
991 force.setZero(solution.size());
992 }
993 append_sampled_dof_field(field_name, force, actual_dim);
994 }
995 }
996
997 append_traction_force();
998
999 if (explicit_fields && options.export_field("gradient_of_elastic_potential") && elastic_form)
1000 {
1001 Eigen::VectorXd potential_grad;
1002 elastic_form->first_derivative(solution, potential_grad);
1003 append_sampled_dof_field("gradient_of_elastic_potential", potential_grad, actual_dim);
1004 }
1005
1006 if (explicit_fields && options.export_field("gradient_of_contact_potential") && contact_form && contact_form->weight() > 0)
1007 {
1008 Eigen::VectorXd potential_grad;
1009 contact_form->first_derivative(solution, potential_grad);
1010 potential_grad *= -contact_form->barrier_stiffness() / contact_form->weight();
1011 append_sampled_dof_field("gradient_of_contact_potential", potential_grad, actual_dim);
1012 }
1013
1014 append_primary_output_fields(fields, sample, solution, options, obstacle);
1015 return fields;
1016 }
1017
1018 void ElasticVarForm::append_primary_output_fields(
1019 std::vector<io::OutputField> &fields,
1020 const io::OutputSample &sample,
1021 const Eigen::MatrixXd &solution,
1022 const io::OutputFieldOptions &options,
1023 const mesh::Obstacle *obstacle) const
1024 {
1025 if (!mesh_ || solution.size() <= 0)
1026 return;
1027
1028 const int dim = mesh_->dimension();
1029 const bool has_element_samples =
1030 sample.local_points.rows() > 0
1031 && sample.local_points.rows() == sample.element_ids.size();
1032 const bool export_solution_gradient =
1033 !options.fields.empty() && options.export_field("solution_gradient");
1034
1035 Eigen::MatrixXd values, gradients;
1036 if (has_element_samples)
1037 {
1038 values.resize(sample.local_points.rows(), dim);
1039 if (export_solution_gradient)
1040 gradients.resize(sample.local_points.rows(), dim * mesh_->dimension());
1041 for (int i = 0; i < sample.local_points.rows(); ++i)
1042 {
1043 const int element_id = sample.element_ids(i);
1044 if (element_id < 0)
1045 {
1046 values.row(i).setZero();
1047 if (gradients.rows() > 0)
1048 gradients.row(i).setZero();
1049 continue;
1050 }
1051
1052 Eigen::MatrixXd local_value, local_gradient;
1054 *mesh_, dim, space_.basis_list(), space_.geometry_basis_list(),
1055 element_id, sample.local_points.row(i), solution,
1056 local_value, local_gradient);
1057 values.row(i) = local_value;
1058 if (gradients.rows() > 0)
1059 gradients.row(i) = local_gradient;
1060 }
1061
1062 if (obstacle && obstacle->n_vertices() > 0
1063 && sample.points.rows() == values.rows() + obstacle->n_vertices()
1064 && sample.points.cols() == obstacle->v().cols()
1065 && sample.points.bottomRows(obstacle->n_vertices()).isApprox(obstacle->v()))
1066 {
1067 values.conservativeResize(values.rows() + obstacle->n_vertices(), Eigen::NoChange);
1068 if (solution.rows() >= obstacle->ndof())
1069 values.bottomRows(obstacle->n_vertices()) =
1070 utils::unflatten(solution.bottomRows(obstacle->ndof()), dim);
1071 else
1072 values.bottomRows(obstacle->n_vertices()).setZero();
1073 if (gradients.rows() > 0)
1074 {
1075 gradients.conservativeResize(values.rows(), Eigen::NoChange);
1076 gradients.bottomRows(obstacle->n_vertices()).setZero();
1077 }
1078 }
1079 }
1080 else if (sample.node_ids.size() > 0)
1081 {
1082 values.resize(sample.node_ids.size(), dim);
1083 for (int i = 0; i < sample.node_ids.size(); ++i)
1084 {
1085 for (int d = 0; d < dim; ++d)
1086 {
1087 const int dof = sample.node_ids(i) * dim + d;
1088 if (dof < 0 || dof >= solution.rows())
1089 return;
1090 values(i, d) = solution(dof);
1091 }
1092 }
1093 }
1094 else
1095 {
1096 return;
1097 }
1098
1099 if (sample.points.rows() > 0 && values.rows() != sample.points.rows())
1100 return;
1101 if (options.export_field("displacement"))
1102 fields.push_back({"displacement", values, io::OutputField::Association::Point});
1103 if (options.export_field("solution"))
1104 fields.push_back({"solution", values, io::OutputField::Association::Point});
1105 if (export_solution_gradient && gradients.rows() == values.rows())
1106 fields.push_back({"solution_gradient", gradients, io::OutputField::Association::Point});
1107
1108 if (options.export_field("displaced_normals"))
1109 {
1110 Eigen::MatrixXd normals = displaced_output_normals(sample, solution);
1111 if (normals.rows() == values.rows())
1112 fields.push_back({"displaced_normals", normals, io::OutputField::Association::Point});
1113 }
1114 }
1115
1116 Eigen::MatrixXd ElasticVarForm::displaced_output_normals(
1117 const io::OutputSample &sample,
1118 const Eigen::MatrixXd &solution) const
1119 {
1120 if (!mesh_
1121 || sample.normals.rows() == 0
1122 || sample.normals.rows() != sample.local_points.rows()
1123 || sample.local_points.rows() != sample.element_ids.size())
1124 return {};
1125
1126 const int dim = mesh_->dimension();
1127 Eigen::MatrixXd displaced_normals = sample.normals;
1128 for (int i = 0; i < sample.local_points.rows(); ++i)
1129 {
1130 const int element_id = sample.element_ids(i);
1131 if (element_id < 0)
1132 continue;
1133
1134 Eigen::MatrixXd local_value, local_gradient;
1136 *mesh_, dim, space_.basis_list(), space_.geometry_basis_list(),
1137 element_id, sample.local_points.row(i), solution,
1138 local_value, local_gradient);
1139
1140 Eigen::MatrixXd deformation = Eigen::MatrixXd::Identity(dim, dim);
1141 for (int d = 0; d < dim; ++d)
1142 deformation.row(d) += local_gradient.block(0, d * dim, 1, dim);
1143 displaced_normals.row(i) = sample.normals.row(i) * deformation.inverse();
1144 displaced_normals.row(i).normalize();
1145 }
1146 return displaced_normals;
1147 }
1148
1149 io::OutputSpace ElasticVarForm::output_space() const
1150 {
1151 Eigen::VectorXi output_orders = space_.disc_orders;
1152 if (mesh_ && space_.disc_ordersq.size() == space_.disc_orders.size())
1153 {
1154 for (int e = 0; e < output_orders.size(); ++e)
1155 {
1156 if (mesh_->is_prism(e))
1157 output_orders(e) = std::max(space_.disc_orders(e), space_.disc_ordersq(e));
1158 }
1159 }
1160
1161 return {
1162 mesh_.get(),
1163 &space_.geometry_basis_list(),
1164 output_orders,
1165 &space_.polys,
1166 &space_.polys_3d,
1167 &boundary_.total_local_boundary,
1168 nullptr,
1169 nullptr,
1170 &boundary_.dirichlet_nodes,
1171 &boundary_.dirichlet_nodes_position};
1172 }
1173
1174 io::OutStatsData ElasticVarForm::compute_errors(const Eigen::MatrixXd &solution)
1175 {
1176 if (!args["output"]["advanced"]["compute_error"])
1177 return stats;
1178
1179 double tend = 0;
1180 if (!args["time"].is_null())
1181 tend = args["time"]["tend"];
1182
1183 stats.compute_errors(space_.n_bases, space_.basis_list(), space_.geometry_basis_list(), *mesh_, *problem, tend, solution);
1184 return stats;
1185 }
1186
1187 void ElasticVarForm::export_data(const Eigen::MatrixXd &solution) const
1188 {
1189 const io::OutputSpace space = output_space();
1190 if (!space.mesh)
1191 {
1192 logger().error("Load the mesh first!");
1193 return;
1194 }
1195 if (solution.size() <= 0)
1196 {
1197 logger().error("Solve the problem first!");
1198 return;
1199 }
1200
1201 ensure_output_sampler();
1202
1203 const std::string vis_mesh_path = resolve_output_path(args["output"]["paraview"]["file_name"]);
1204 const bool has_time = args.contains("time") && !args["time"].is_null();
1205 double tend = has_time ? args["time"]["tend"].get<double>() : 1.0;
1206 double dt = 1;
1207 if (has_time)
1208 dt = args["time"]["dt"];
1209
1210 const auto opts = export_options(space);
1211 output_geometry_.export_data(
1212 space,
1213 output_field_function(solution, opts),
1214 has_time,
1215 tend, dt,
1216 opts,
1217 vis_mesh_path);
1218
1219 const std::string solution_path = resolve_output_path(args["output"]["data"]["solution"]);
1220 if (!solution_path.empty())
1221 {
1222 const int dim = mesh_->dimension();
1223 const int primary_ndof = std::min<int>(solution.rows(), space_.n_bases * dim);
1224 const Eigen::MatrixXd primary_solution = solution.topRows(primary_ndof);
1225 if (opts.reorder_output && space_.space_in_node_to_node.size() > 0)
1226 {
1227 const Eigen::MatrixXd nodal_solution = utils::unflatten(primary_solution, dim);
1228 Eigen::MatrixXd reordered = Eigen::MatrixXd::Zero(nodal_solution.rows(), nodal_solution.cols());
1229 for (int input_node = 0; input_node < space_.space_in_node_to_node.size(); ++input_node)
1230 {
1231 const int node = space_.space_in_node_to_node(input_node);
1232 if (node >= 0 && node < nodal_solution.rows() && input_node < reordered.rows())
1233 reordered.row(input_node) = nodal_solution.row(node);
1234 }
1235 io::write_matrix(solution_path, reordered);
1236 }
1237 else
1238 {
1239 io::write_matrix(solution_path, primary_solution);
1240 }
1241 }
1242
1243 const std::string nodes_path = resolve_output_path(args["output"]["data"]["nodes"]);
1244 if (!nodes_path.empty())
1245 {
1246 Eigen::MatrixXd nodes = Eigen::MatrixXd::Zero(space_.n_bases, mesh_->dimension());
1247 for (const basis::ElementBases &element_bases : space_.basis_list())
1248 for (const basis::Basis &basis : element_bases.bases)
1249 for (const auto &global : basis.global())
1250 nodes.row(global.index) = global.node;
1251 io::write_matrix(nodes_path, nodes);
1252 }
1253
1254 const std::string stress_path = resolve_output_path(args["output"]["data"]["stress_mat"]);
1255 const std::string mises_path = resolve_output_path(args["output"]["data"]["mises"]);
1256 if ((!stress_path.empty() || !mises_path.empty()) && primary_assembler_)
1257 {
1258 Eigen::MatrixXd stress;
1259 Eigen::VectorXd mises;
1261 *mesh_, problem->is_scalar(), space_.basis_list(), space_.geometry_basis_list(),
1262 space_.disc_orders, space_.disc_ordersq, *primary_assembler_, solution, tend,
1263 stress, mises);
1264 if (!stress_path.empty())
1265 io::write_matrix(stress_path, stress);
1266 if (!mises_path.empty())
1267 io::write_matrix(mises_path, mises);
1268 }
1269 }
1270
1271 void ElasticVarForm::save_json(const Eigen::MatrixXd &solution, std::ostream &out) const
1272 {
1273 if (!mesh_)
1274 {
1275 logger().error("Load the mesh first!");
1276 return;
1277 }
1278 if (solution.size() <= 0)
1279 {
1280 logger().error("Solve the problem first!");
1281 return;
1282 }
1283
1284 logger().info("Saving json...");
1285 const int primary_size = space_.n_bases * mesh_->dimension();
1286 const Eigen::MatrixXd stats_solution =
1287 solution.rows() >= primary_size
1288 ? solution.topRows(primary_size).eval()
1289 : solution;
1290
1291 nlohmann::json j;
1292 stats.save_json(
1293 args, space_.n_bases, 0,
1294 stats_solution, *mesh_, space_.disc_orders, space_.disc_ordersq, *problem,
1295 timings, primary_assembler_ ? primary_assembler_->name() : name(), space_.is_iso_parametric(),
1296 args["output"]["advanced"]["sol_at_node"], j);
1297 out << j.dump(4) << std::endl;
1298 }
1299
1300 void ElasticVarForm::save_elastic_step_state(
1301 const double t0,
1302 const double dt,
1303 const int t,
1304 const Eigen::MatrixXd &solution,
1305 const time_integrator::ImplicitTimeIntegrator *time_integrator) const
1306 {
1307 if (!mesh_)
1308 return;
1309 save_step_state(t0, dt, t, solution, time_integrator);
1310 }
1311
1312 void ElasticVarForm::build_mesh_matrices(Eigen::MatrixXd &V, Eigen::MatrixXi &F) const
1313 {
1314 assert(mesh_);
1315 assert(space_.basis_list().size() == mesh_->n_elements());
1316 const size_t n_vertices = space_.n_bases - n_obstacle_vertices();
1317 const int dim = mesh_->dimension();
1318
1319 V.resize(n_vertices, dim);
1320 F.resize(space_.basis_list().size(), dim + 1);
1321
1322 for (int i = 0; i < space_.basis_list().size(); i++)
1323 {
1324 const basis::ElementBases &element = space_.basis_list()[i];
1325 for (int j = 0; j < element.bases.size(); j++)
1326 {
1327 const basis::Basis &basis = element.bases[j];
1328 assert(basis.global().size() == 1);
1329 V.row(basis.global()[0].index) = basis.global()[0].node;
1330 if (j < F.cols())
1331 F(i, j) = basis.global()[0].index;
1332 }
1333 }
1334 }
1335
1336} // namespace polyfem::varform
int V
ElementAssemblyValues vals
Definition Assembler.cpp:26
std::vector< std::pair< int, double > > weights
std::array< Matrix< int, 3, 3 >, 3 > space_
static std::shared_ptr< Assembler > make_assembler(const std::string &formulation)
void init(const bool is_volume, const std::vector< basis::ElementBases > &bases, const std::vector< basis::ElementBases > &gbases, const bool is_mass=false)
computes the basis evaluation and geometric mapping for each of the given ElementBases in bases initi...
void init_empty(const bool is_mass=false)
initialize an empty cache.
void compute(const int el_index, const bool is_volume, const Eigen::MatrixXd &pts, const basis::ElementBases &basis, const basis::ElementBases &gbasis)
computes the per element values at the local (ref el) points (pts) sets basis_values,...
std::vector< Eigen::Matrix< double, Eigen::Dynamic, Eigen::Dynamic, 0, 3, 3 > > jac_it
Represents one basis function and its gradient.
Definition Basis.hpp:44
Stores the basis functions for a given element in a mesh (facet in 2d, cell in 3d).
std::vector< Basis > bases
one basis function per node in the element
static void interpolate_at_local_vals(const mesh::Mesh &mesh, const bool is_problem_scalar, const std::vector< basis::ElementBases > &bases, const std::vector< basis::ElementBases > &gbases, const int el_index, const Eigen::MatrixXd &local_pts, const Eigen::MatrixXd &fun, Eigen::MatrixXd &result, Eigen::MatrixXd &result_grad)
interpolate solution and gradient at element (calls interpolate_at_local_vals with sol)
static void compute_stress_at_quadrature_points(const mesh::Mesh &mesh, const bool is_problem_scalar, const std::vector< basis::ElementBases > &bases, const std::vector< basis::ElementBases > &gbases, const Eigen::VectorXi &disc_orders, const Eigen::VectorXi &disc_ordersq, const assembler::Assembler &assembler, const Eigen::MatrixXd &fun, const double t, Eigen::MatrixXd &result, Eigen::VectorXd &von_mises)
compute von mises stress at quadrature points for the function fun, also compute the interpolated fun...
double assigning_rhs_time
time to computing the rhs
double assembling_mass_mat_time
time to assembly mass
all stats from polyfem
int n_flipped
number of flipped elements, compute only when using count_flipped_els (false by default)
void count_flipped_elements(const polyfem::mesh::Mesh &mesh, const std::vector< polyfem::basis::ElementBases > &gbases)
counts the number of flipped elements
Definition OutData.cpp:2815
void compute_mesh_size(const polyfem::mesh::Mesh &mesh_in, const std::vector< polyfem::basis::ElementBases > &bases_in, const int n_samples, const bool use_curved_mesh_size)
computes the mesh size, it samples every edges n_samples times uses curved_mesh_size (false by defaul...
Definition OutData.cpp:2732
long long nn_zero
non zeros and sytem matrix size num dof is the total dof in the system
double mesh_size
max edge lenght
Abstract mesh class to capture 2d/3d conforming and non-conforming meshes.
Definition Mesh.hpp:50
int n_elements() const
utitlity to return the number of elements, cells or faces in 3d and 2d
Definition Mesh.hpp:148
virtual int get_body_id(const int primitive) const
Get the volume selection of an element (cell in 3d, face in 2d)
Definition Mesh.hpp:492
virtual void bounding_box(RowVectorNd &min, RowVectorNd &max) const =0
computes the bbox of the mesh
virtual bool is_volume() const =0
checks if mesh is volume
void update_nodes(const Eigen::VectorXi &in_node_to_node)
Update the node ids to reorder them.
Definition Mesh.cpp:346
int dimension() const
utily for dimension
Definition Mesh.hpp:138
const Eigen::MatrixXd & v() const
Definition Obstacle.hpp:42
static const ProblemFactory & factory()
std::shared_ptr< assembler::Problem > get_problem(const std::string &problem) const
static void p_refine(const mesh::Mesh &mesh, const double B, const bool h1_formula, const int base_p, const int discr_order_max, io::OutStatsData &stats, Eigen::VectorXi &disc_orders)
compute a priori prefinement
Definition APriori.cpp:242
Form representing the contact potential and forces.
Implicit time integrator of a second order ODE (equivently a system of coupled first order ODEs).
static bool boundary_quadrature(const mesh::LocalBoundary &local_boundary, const QuadratureOrders &order, const mesh::Mesh &mesh, const bool skip_computation, Eigen::MatrixXd &uv, Eigen::MatrixXd &points, Eigen::MatrixXd &normals, Eigen::VectorXd &weights, Eigen::VectorXi &global_primitive_ids)
void build_basis(mesh::Mesh &mesh, const bool iso_parametric, const json &args) override
assembler::AssemblyValsCache pure_mass_ass_vals_cache_
void serialize_checkpoint(io::CheckpointWriter &writer, const Eigen::MatrixXd &solution, const io::CheckpointMetadata &metadata) const override
void build_elastic_basis(mesh::Mesh &mesh, const bool iso_parametric, const json &args, const int fe_space_id)
std::vector< int > elastic_primitive_to_node() const
void assemble_mass_mat(const mesh::Mesh &mesh, const json &args) override
std::shared_ptr< assembler::Assembler > primary_assembler_
void init(const std::string &formulation, const Units &units, const json &args, const std::string &out_path) override
Initialize the variational formulation with the given parameters.
std::vector< int > elastic_node_to_primitive() const
QuadratureOrders elastic_boundary_samples() const
assembler::AssemblyValsCache ass_vals_cache_
void deserialize_checkpoint(const io::CheckpointReader &reader, Eigen::MatrixXd &solution) override
std::vector< io::OutputField > elastic_output_fields(const io::OutputSample &sample, const Eigen::MatrixXd &solution, const io::OutputFieldOptions &options, const mesh::Obstacle *obstacle, const time_integrator::ImplicitTimeIntegrator *time_integrator, const std::vector< std::pair< std::string, std::shared_ptr< solver::Form > > > &named_forms, const solver::Form *elastic_form, const solver::ContactForm *contact_form=nullptr) const
std::shared_ptr< assembler::HRZMass > pure_mass_assembler_
std::shared_ptr< assembler::Mass > mass_assembler_
std::shared_ptr< assembler::RhsAssembler > rhs_assembler_
assembler::AssemblyValsCache mass_ass_vals_cache_
void initial_velocity(Eigen::MatrixXd &velocity, const InitialConditionOverride *override=nullptr, const std::string &state_prefix="") const
void load_mesh(const mesh::Mesh &mesh, const json &args) override
void initial_acceleration(Eigen::MatrixXd &acceleration, const InitialConditionOverride *override=nullptr, const std::string &state_prefix="") const
void initial_solution(Eigen::MatrixXd &solution, const InitialConditionOverride *override=nullptr, const std::string &state_prefix="") const
void assemble_rhs(const mesh::Mesh &mesh) override
const std::vector< basis::ElementBases > & geometry_basis_list() const
Definition FESpace.hpp:115
std::shared_ptr< GeometryMapping > geometry
Geometric mapping used to integrate this FE space.
Definition FESpace.hpp:89
Eigen::VectorXi disc_orders
Primary polynomial degree for each mesh element.
Definition FESpace.hpp:71
Eigen::VectorXi disc_ordersq
Secondary polynomial degree for anisotropic bases, e.g. prisms.
Definition FESpace.hpp:74
int n_bases
Number of globally indexed scalar basis functions in the space.
Definition FESpace.hpp:65
Eigen::VectorXi space_in_node_to_node
Definition FESpace.hpp:91
const std::vector< basis::ElementBases > & basis_list() const
Definition FESpace.hpp:109
bool is_iso_parametric() const
Definition FESpace.hpp:104
std::shared_ptr< mesh::MeshNodes > mesh_nodes
Optional primitive-to-node mapping for this FE space.
Definition FESpace.hpp:86
void reorder_checkpoint_block(const io::CheckpointReader &reader, const std::string &name, const FESpace &space, int block_size, int row_offset, Eigen::MatrixXd &value) const
Definition VarForm.cpp:981
static void rebuild_node_positions(const std::vector< basis::ElementBases > &bases, const std::vector< int > &node_ids, std::vector< RowVectorNd > &positions)
Definition VarForm.cpp:1125
std::shared_ptr< assembler::Problem > problem
current problem, it contains rhs and bc
Definition VarForm.hpp:261
virtual std::string name() const =0
Get the name of the variational formulation.
void write_checkpoint_ordering(io::CheckpointWriter &writer, const std::string &name, const FESpace &space) const
Definition VarForm.cpp:938
virtual void deserialize_checkpoint(const io::CheckpointReader &reader, Eigen::MatrixXd &solution)
Definition VarForm.cpp:905
std::unique_ptr< mesh::Mesh > mesh_
Definition VarForm.hpp:273
void assign_discr_orders(const json &space_args, const mesh::Mesh &mesh, Eigen::VectorXi &disc_orders, Eigen::VectorXi &disc_ordersq)
Definition VarForm.cpp:684
io::OutStatsData stats
Definition VarForm.hpp:265
virtual void serialize_checkpoint(io::CheckpointWriter &writer, const Eigen::MatrixXd &solution, const io::CheckpointMetadata &metadata) const
Definition VarForm.cpp:897
QuadratureOrders n_boundary_samples(const int discr_order, const int discr_orderq, const int gdiscr_order) const
Definition VarForm.cpp:185
void build_fe_space(mesh::Mesh &mesh, const bool iso_parametric, const Eigen::VectorXi &disc_orders, const Eigen::VectorXi &disc_ordersq, const std::string &basis_type, const std::string &poly_basis_type, const assembler::Assembler &space_assembler, const int value_dim, const int quadrature_order, const int mass_quadrature_order, const bool use_corner_quadrature, const int n_harmonic_samples, const int integral_constraints, FESpace &space, VarFormBoundaryState &boundary, std::shared_ptr< GeometryMapping > geometry=nullptr)
Definition VarForm.cpp:274
virtual void init(const std::string &formulation, const Units &units, const json &args, const std::string &out_path)
Initialize the variational formulation with the given parameters.
Definition VarForm.cpp:208
void validate_checkpoint_solution(const Eigen::MatrixXd &solution, int expected_rows) const
Definition VarForm.cpp:1037
io::OutRuntimeData timings
runtime statistics
Definition VarForm.hpp:268
const io::ResourceIO & resources_
Definition VarForm.hpp:283
void set_materials(assembler::Assembler &assembler, const int size) const
Definition VarForm.cpp:806
virtual void reset()=0
Definition VarForm.cpp:194
str func
Definition p_bases.py:417
void q_nodes_2d(const int q, Eigen::MatrixXd &val)
void prism_nodes_3d(const int p, const int q, Eigen::MatrixXd &val)
void p_nodes_2d(const int p, Eigen::MatrixXd &val)
void p_nodes_3d(const int p, Eigen::MatrixXd &val)
void q_nodes_3d(const int q, Eigen::MatrixXd &val)
bool write_matrix(const std::string &path, const Mat &mat)
Writes a matrix to a file. Determines the file format based on the path's extension.
Definition MatrixIO.cpp:43
Eigen::SparseMatrix< double > lump_matrix(const Eigen::SparseMatrix< double > &M)
Lump each row of a matrix into the diagonal.
Eigen::MatrixXd unflatten(const Eigen::VectorXd &x, int dim)
Unflatten rowwises, so every dim elements in x become a row.
std::vector< int > count_invalid(const int dim, const std::vector< basis::ElementBases > &bases, const std::vector< basis::ElementBases > &gbases, const Eigen::VectorXd &u, const unsigned max_iter)
Definition Jacobian.cpp:122
Eigen::VectorXd flatten(const Eigen::MatrixXd &X)
Flatten rowwises.
spdlog::logger & logger()
Retrieves the current logger.
Definition Logger.cpp:44
std::array< int, 2 > QuadratureOrders
Definition Types.hpp:19
nlohmann::json json
Definition Common.hpp:9
Eigen::Matrix< double, 1, Eigen::Dynamic, Eigen::RowMajor, 1, 3 > RowVectorNd
Definition Types.hpp:13
bool export_field(const std::string &field) const
Definition OutData.cpp:56
std::vector< std::string > fields
Eigen::VectorXi node_ids
Eigen::MatrixXd normals
Eigen::VectorXi element_ids
Eigen::MatrixXd local_points
const mesh::Mesh * mesh
std::vector< RowVectorNd > neumann_nodes_position
Definition FESpace.hpp:163
std::vector< mesh::LocalBoundary > local_boundary
Definition FESpace.hpp:155
std::vector< mesh::LocalBoundary > local_neumann_boundary
Definition FESpace.hpp:156
std::vector< mesh::LocalBoundary > total_local_boundary
Definition FESpace.hpp:154
std::vector< RowVectorNd > dirichlet_nodes_position
Definition FESpace.hpp:161
std::vector< mesh::LocalBoundary > local_pressure_boundary
Definition FESpace.hpp:157
std::unordered_map< int, std::vector< mesh::LocalBoundary > > local_pressure_cavity
Definition FESpace.hpp:158