Flow123d  JS_before_hm-1804-gf2ad740aa
darcy_flow_mh.cc
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1 /*!
2  *
3  * Copyright (C) 2015 Technical University of Liberec. All rights reserved.
4  *
5  * This program is free software; you can redistribute it and/or modify it under
6  * the terms of the GNU General Public License version 3 as published by the
7  * Free Software Foundation. (http://www.gnu.org/licenses/gpl-3.0.en.html)
8  *
9  * This program is distributed in the hope that it will be useful, but WITHOUT
10  * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
11  * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
12  *
13  *
14  * @file darcy_flow_mh.cc
15  * @ingroup flow
16  * @brief Setup and solve linear system of mixed-hybrid discretization of the linear
17  * porous media flow with possible preferential flow in fractures and chanels.
18  */
19 
20 //#include <limits>
21 #include <vector>
22 //#include <iostream>
23 //#include <iterator>
24 //#include <algorithm>
25 #include <armadillo>
26 
27 #include "petscmat.h"
28 #include "petscviewer.h"
29 #include "petscerror.h"
30 #include "mpi.h"
31 
32 #include "system/system.hh"
33 #include "system/sys_profiler.hh"
34 #include "system/index_types.hh"
35 #include "input/factory.hh"
36 
37 #include "mesh/mesh.h"
38 #include "mesh/bc_mesh.hh"
39 #include "mesh/partitioning.hh"
40 #include "mesh/accessors.hh"
41 #include "mesh/range_wrapper.hh"
42 #include "la/distribution.hh"
43 #include "la/linsys.hh"
44 #include "la/linsys_PETSC.hh"
45 #include "la/linsys_BDDC.hh"
46 #include "la/schur.hh"
47 //#include "la/sparse_graph.hh"
49 #include "la/vector_mpi.hh"
50 
51 #include "flow/assembly_mh.hh"
52 #include "flow/darcy_flow_mh.hh"
54 
55 #include "tools/time_governor.hh"
57 #include "fields/field.hh"
58 #include "fields/field_values.hh"
60 #include "fields/field_fe.hh"
61 #include "fields/field_divide.hh"
62 
63 #include "coupling/balance.hh"
64 
67 
68 #include "fem/fe_p.hh"
69 
70 
71 FLOW123D_FORCE_LINK_IN_CHILD(darcy_flow_mh)
72 
73 
74 
75 
76 namespace it = Input::Type;
77 
79  return it::Selection("MH_MortarMethod")
80  .add_value(NoMortar, "None", "No Mortar method is applied.")
81  .add_value(MortarP0, "P0", "Mortar space: P0 on elements of lower dimension.")
82  .add_value(MortarP1, "P1", "Mortar space: P1 on intersections, using non-conforming pressures.")
83  .close();
84 }
85 
86 
88  return it::Selection("Flow_Darcy_BC_Type")
89  .add_value(none, "none",
90  "Homogeneous Neumann boundary condition\n(zero normal flux over the boundary).")
91  .add_value(dirichlet, "dirichlet",
92  "Dirichlet boundary condition. "
93  "Specify the pressure head through the ``bc_pressure`` field "
94  "or the piezometric head through the ``bc_piezo_head`` field.")
95  .add_value(total_flux, "total_flux", "Flux boundary condition (combines Neumann and Robin type). "
96  "Water inflow equal to (($ \\delta_d(q_d^N + \\sigma_d (h_d^R - h_d) )$)). "
97  "Specify the water inflow by the ``bc_flux`` field, the transition coefficient by ``bc_robin_sigma`` "
98  "and the reference pressure head or piezometric head through ``bc_pressure`` or ``bc_piezo_head`` respectively.")
99  .add_value(seepage, "seepage",
100  "Seepage face boundary condition. Pressure and inflow bounded from above. Boundary with potential seepage flow "
101  "is described by the pair of inequalities: "
102  "(($h_d \\le h_d^D$)) and (($ -\\boldsymbol q_d\\cdot\\boldsymbol n \\le \\delta q_d^N$)), where the equality holds in at least one of them. "
103  "Caution: setting (($q_d^N$)) strictly negative "
104  "may lead to an ill posed problem since a positive outflow is enforced. "
105  "Parameters (($h_d^D$)) and (($q_d^N$)) are given by the fields ``bc_switch_pressure`` (or ``bc_switch_piezo_head``) and ``bc_flux`` respectively."
106  )
107  .add_value(river, "river",
108  "River boundary condition. For the water level above the bedrock, (($H_d > H_d^S$)), the Robin boundary condition is used with the inflow given by: "
109  "(( $ \\delta_d(q_d^N + \\sigma_d(H_d^D - H_d) )$)). For the water level under the bedrock, constant infiltration is used: "
110  "(( $ \\delta_d(q_d^N + \\sigma_d(H_d^D - H_d^S) )$)). Parameters: ``bc_pressure``, ``bc_switch_pressure``, "
111  " ``bc_sigma``, ``bc_flux``."
112  )
113  .close();
114 }
115 
117 
118  const it::Record &field_descriptor =
119  it::Record("Flow_Darcy_MH_Data",FieldCommon::field_descriptor_record_description("Flow_Darcy_MH_Data") )
120  .copy_keys( DarcyMH::EqData().make_field_descriptor_type("Flow_Darcy_MH_Data_aux") )
121  .declare_key("bc_piezo_head", FieldAlgorithmBase< 3, FieldValue<3>::Scalar >::get_input_type_instance(),
122  "Boundary piezometric head for BC types: dirichlet, robin, and river." )
123  .declare_key("bc_switch_piezo_head", FieldAlgorithmBase< 3, FieldValue<3>::Scalar >::get_input_type_instance(),
124  "Boundary switch piezometric head for BC types: seepage, river." )
125  .declare_key("init_piezo_head", FieldAlgorithmBase< 3, FieldValue<3>::Scalar >::get_input_type_instance(),
126  "Initial condition for the pressure given as the piezometric head." )
127  .close();
128  return field_descriptor;
129 }
130 
132 
133  it::Record ns_rec = Input::Type::Record("NonlinearSolver", "Non-linear solver settings.")
134  .declare_key("linear_solver", LinSys::get_input_type(), it::Default("{}"),
135  "Linear solver for MH problem.")
136  .declare_key("tolerance", it::Double(0.0), it::Default("1E-6"),
137  "Residual tolerance.")
138  .declare_key("min_it", it::Integer(0), it::Default("1"),
139  "Minimum number of iterations (linear solutions) to use.\nThis is usefull if the convergence criteria "
140  "does not characterize your goal well enough so it converges prematurely, possibly even without a single linear solution."
141  "If greater then 'max_it' the value is set to 'max_it'.")
142  .declare_key("max_it", it::Integer(0), it::Default("100"),
143  "Maximum number of iterations (linear solutions) of the non-linear solver.")
144  .declare_key("converge_on_stagnation", it::Bool(), it::Default("false"),
145  "If a stagnation of the nonlinear solver is detected the solver stops. "
146  "A divergence is reported by default, forcing the end of the simulation. By setting this flag to 'true', the solver "
147  "ends with convergence success on stagnation, but it reports warning about it.")
148  .close();
149 
150  DarcyMH::EqData eq_data;
151 
152  return it::Record("Flow_Darcy_MH", "Mixed-Hybrid solver for saturated Darcy flow.")
155  .declare_key("gravity", it::Array(it::Double(), 3,3), it::Default("[ 0, 0, -1]"),
156  "Vector of the gravity force. Dimensionless.")
158  "Input data for Darcy flow model.")
159  .declare_key("nonlinear_solver", ns_rec, it::Default("{}"),
160  "Non-linear solver for MH problem.")
161  .declare_key("output_stream", OutputTime::get_input_type(), it::Default("{}"),
162  "Output stream settings.\n Specify file format, precision etc.")
163 
164  .declare_key("output", DarcyFlowMHOutput::get_input_type(eq_data, "Flow_Darcy_MH"),
165  IT::Default("{ \"fields\": [ \"pressure_p0\", \"velocity_p0\" ] }"),
166  "Specification of output fields and output times.")
168  "Output settings specific to Darcy flow model.\n"
169  "Includes raw output and some experimental functionality.")
170  .declare_key("balance", Balance::get_input_type(), it::Default("{}"),
171  "Settings for computing mass balance.")
172  .declare_key("n_schurs", it::Integer(0,2), it::Default("2"),
173  "Number of Schur complements to perform when solving MH system.")
174  .declare_key("mortar_method", get_mh_mortar_selection(), it::Default("\"None\""),
175  "Method for coupling Darcy flow between dimensions on incompatible meshes. [Experimental]" )
176  .close();
177 }
178 
179 
180 const int DarcyMH::registrar =
181  Input::register_class< DarcyMH, Mesh &, const Input::Record >("Flow_Darcy_MH") +
183 
184 
185 
187 {
188  mortar_method_=NoMortar;
189 
190  *this += field_ele_pressure.name("pressure_p0")
191  .units(UnitSI().m())
193  .description("Pressure solution - P0 interpolation.");
194 
195  *this += field_edge_pressure.name("pressure_edge")
196  .units(UnitSI().m())
197  .flags(FieldFlag::input_copy)
198  .description("Pressure solution - Crouzeix-Raviart interpolation.");
199 
200  *this += field_ele_piezo_head.name("piezo_head_p0")
201  .units(UnitSI().m())
203  .description("Piezo head solution - P0 interpolation.");
204 
205  *this += field_ele_velocity.name("velocity_p0")
206  .units(UnitSI().m().s(-1))
208  .description("Velocity solution - P0 interpolation.");
209 
210  *this += flux.name("flux")
211  .units(UnitSI().m().s(-1))
213  .description("Darcy flow flux.");
214 
215  *this += anisotropy.name("anisotropy")
216  .description("Anisotropy of the conductivity tensor.")
217  .input_default("1.0")
218  .units( UnitSI::dimensionless() );
219 
220  *this += cross_section.name("cross_section")
221  .description("Complement dimension parameter (cross section for 1D, thickness for 2D).")
222  .input_default("1.0")
223  .units( UnitSI().m(3).md() );
224 
225  *this += conductivity.name("conductivity")
226  .description("Isotropic conductivity scalar.")
227  .input_default("1.0")
228  .units( UnitSI().m().s(-1) )
229  .set_limits(0.0);
230 
231  *this += sigma.name("sigma")
232  .description("Transition coefficient between dimensions.")
233  .input_default("1.0")
234  .units( UnitSI::dimensionless() );
235 
236  *this += water_source_density.name("water_source_density")
237  .description("Water source density.")
238  .input_default("0.0")
239  .units( UnitSI().s(-1) );
240 
241  *this += bc_type.name("bc_type")
242  .description("Boundary condition type.")
243  .input_selection( get_bc_type_selection() )
244  .input_default("\"none\"")
245  .units( UnitSI::dimensionless() );
246 
247  *this += bc_pressure
248  .disable_where(bc_type, {none, seepage} )
249  .name("bc_pressure")
250  .description("Prescribed pressure value on the boundary. Used for all values of ``bc_type`` except ``none`` and ``seepage``. "
251  "See documentation of ``bc_type`` for exact meaning of ``bc_pressure`` in individual boundary condition types.")
252  .input_default("0.0")
253  .units( UnitSI().m() );
254 
255  *this += bc_flux
256  .disable_where(bc_type, {none, dirichlet} )
257  .name("bc_flux")
258  .description("Incoming water boundary flux. Used for bc_types : ``total_flux``, ``seepage``, ``river``.")
259  .input_default("0.0")
260  .units( UnitSI().m().s(-1) );
261 
262  *this += bc_robin_sigma
263  .disable_where(bc_type, {none, dirichlet, seepage} )
264  .name("bc_robin_sigma")
265  .description("Conductivity coefficient in the ``total_flux`` or the ``river`` boundary condition type.")
266  .input_default("0.0")
267  .units( UnitSI().s(-1) );
268 
269  *this += bc_switch_pressure
270  .disable_where(bc_type, {none, dirichlet, total_flux} )
271  .name("bc_switch_pressure")
272  .description("Critical switch pressure for ``seepage`` and ``river`` boundary conditions.")
273  .input_default("0.0")
274  .units( UnitSI().m() );
275 
276 
277  //these are for unsteady
278  *this += init_pressure.name("init_pressure")
279  .description("Initial condition for pressure in time dependent problems.")
280  .input_default("0.0")
281  .units( UnitSI().m() );
282 
283  *this += storativity.name("storativity")
284  .description("Storativity (in time dependent problems).")
285  .input_default("0.0")
286  .units( UnitSI().m(-1) );
287 
288  *this += extra_storativity.name("extra_storativity")
289  .description("Storativity added from upstream equation.")
290  .units( UnitSI().m(-1) )
291  .input_default("0.0")
292  .flags( input_copy );
293 
294  *this += extra_source.name("extra_water_source_density")
295  .description("Water source density added from upstream equation.")
296  .input_default("0.0")
297  .units( UnitSI().s(-1) )
298  .flags( input_copy );
299 
300  //time_term_fields = this->subset({"storativity"});
301  //main_matrix_fields = this->subset({"anisotropy", "conductivity", "cross_section", "sigma", "bc_type", "bc_robin_sigma"});
302  //rhs_fields = this->subset({"water_source_density", "bc_pressure", "bc_flux"});
303 }
304 
305 
306 
307 //=============================================================================
308 // CREATE AND FILL GLOBAL MH MATRIX OF THE WATER MODEL
309 // - do it in parallel:
310 // - initial distribution of elements, edges
311 //
312 /*! @brief CREATE AND FILL GLOBAL MH MATRIX OF THE WATER MODEL
313  *
314  * Parameters {Solver,NSchurs} number of performed Schur
315  * complements (0,1,2) for water flow MH-system
316  *
317  */
318 //=============================================================================
319 DarcyMH::DarcyMH(Mesh &mesh_in, const Input::Record in_rec, TimeGovernor *tm)
320 : DarcyFlowInterface(mesh_in, in_rec),
321  output_object(nullptr),
322  data_changed_(false),
323  schur0(nullptr),
324  steady_diagonal(nullptr),
325  steady_rhs(nullptr),
326  new_diagonal(nullptr),
327  previous_solution(nullptr)
328 {
329 
330  START_TIMER("Darcy constructor");
331  {
332  auto time_rec = in_rec.val<Input::Record>("time");
333  if (tm == nullptr)
334  {
335  time_ = new TimeGovernor(time_rec);
336  }
337  else
338  {
339  TimeGovernor tm_from_rec(time_rec);
340  if (!tm_from_rec.is_default()) // is_default() == false when time record is present in input file
341  {
342  MessageOut() << "Duplicate key 'time', time in flow equation is already initialized from parent class!";
343  ASSERT(false);
344  }
345  time_ = tm;
346  }
347  }
348 
349  data_ = make_shared<EqData>();
351 
352  data_->is_linear=true;
353 
354  size = mesh_->n_elements() + mesh_->n_sides() + mesh_->n_edges();
355  n_schur_compls = in_rec.val<int>("n_schurs");
356  data_->mortar_method_= in_rec.val<MortarMethod>("mortar_method");
357  if (data_->mortar_method_ != NoMortar) {
359  }
360 
361 
362 
363  //side_ds->view( std::cout );
364  //el_ds->view( std::cout );
365  //edge_ds->view( std::cout );
366  //rows_ds->view( std::cout );
367 
368 }
369 
370 
371 
373 //connecting data fields with mesh
374 {
375 
376  START_TIMER("data init");
377  data_->mesh = mesh_;
378  data_->set_mesh(*mesh_);
379 
380  auto gravity_array = input_record_.val<Input::Array>("gravity");
381  std::vector<double> gvec;
382  gravity_array.copy_to(gvec);
383  gvec.push_back(0.0); // zero pressure shift
384  data_->gravity_ = arma::vec(gvec);
385  data_->gravity_vec_ = data_->gravity_.subvec(0,2);
386 
387  data_->bc_pressure.add_factory(
388  std::make_shared<FieldAddPotential<3, FieldValue<3>::Scalar>::FieldFactory>
389  (data_->gravity_, "bc_piezo_head") );
390  data_->bc_switch_pressure.add_factory(
391  std::make_shared<FieldAddPotential<3, FieldValue<3>::Scalar>::FieldFactory>
392  (data_->gravity_, "bc_switch_piezo_head") );
393  data_->init_pressure.add_factory(
394  std::make_shared<FieldAddPotential<3, FieldValue<3>::Scalar>::FieldFactory>
395  (data_->gravity_, "init_piezo_head") );
396 
397 
398  data_->set_input_list( this->input_record_.val<Input::Array>("input_fields"), *time_ );
399  // Check that the time step was set for the transient simulation.
400  if (! zero_time_term(true) && time_->is_default() ) {
401  //THROW(ExcAssertMsg());
402  //THROW(ExcMissingTimeGovernor() << input_record_.ei_address());
403  MessageOut() << "Missing the key 'time', obligatory for the transient problems." << endl;
404  ASSERT(false);
405  }
406 
407  data_->mark_input_times(*time_);
408 }
409 
410 
411 
413 
414  { // init DOF handler for pressure fields
415 // std::shared_ptr< FiniteElement<0> > fe0_rt = std::make_shared<FE_RT0_disc<0>>();
416  std::shared_ptr< FiniteElement<1> > fe1_rt = std::make_shared<FE_RT0_disc<1>>();
417  std::shared_ptr< FiniteElement<2> > fe2_rt = std::make_shared<FE_RT0_disc<2>>();
418  std::shared_ptr< FiniteElement<3> > fe3_rt = std::make_shared<FE_RT0_disc<3>>();
419  std::shared_ptr< FiniteElement<0> > fe0_disc = std::make_shared<FE_P_disc<0>>(0);
420  std::shared_ptr< FiniteElement<1> > fe1_disc = std::make_shared<FE_P_disc<1>>(0);
421  std::shared_ptr< FiniteElement<2> > fe2_disc = std::make_shared<FE_P_disc<2>>(0);
422  std::shared_ptr< FiniteElement<3> > fe3_disc = std::make_shared<FE_P_disc<3>>(0);
423  std::shared_ptr< FiniteElement<0> > fe0_cr = std::make_shared<FE_CR<0>>();
424  std::shared_ptr< FiniteElement<1> > fe1_cr = std::make_shared<FE_CR<1>>();
425  std::shared_ptr< FiniteElement<2> > fe2_cr = std::make_shared<FE_CR<2>>();
426  std::shared_ptr< FiniteElement<3> > fe3_cr = std::make_shared<FE_CR<3>>();
427 // static FiniteElement<0> fe0_sys = FE_P_disc<0>(0); //TODO fix and use solution with FESystem<0>( {fe0_rt, fe0_disc, fe0_cr} )
428  FESystem<0> fe0_sys( {fe0_disc, fe0_disc, fe0_cr} );
429  FESystem<1> fe1_sys( {fe1_rt, fe1_disc, fe1_cr} );
430  FESystem<2> fe2_sys( {fe2_rt, fe2_disc, fe2_cr} );
431  FESystem<3> fe3_sys( {fe3_rt, fe3_disc, fe3_cr} );
432  MixedPtr<FESystem> fe_sys( std::make_shared<FESystem<0>>(fe0_sys), std::make_shared<FESystem<1>>(fe1_sys),
433  std::make_shared<FESystem<2>>(fe2_sys), std::make_shared<FESystem<3>>(fe3_sys) );
434  std::shared_ptr<DiscreteSpace> ds = std::make_shared<EqualOrderDiscreteSpace>( mesh_, fe_sys);
435  data_->dh_ = std::make_shared<DOFHandlerMultiDim>(*mesh_);
436  data_->dh_->distribute_dofs(ds);
437  }
438 
439  init_eq_data();
440  this->data_->multidim_assembler = AssemblyBase::create< AssemblyMH >(data_);
442 
443  { // construct pressure, velocity and piezo head fields
444  uint rt_component = 0;
445  data_->full_solution = data_->dh_->create_vector();
446  auto ele_flux_ptr = create_field_fe<3, FieldValue<3>::VectorFixed>(data_->dh_, &data_->full_solution, rt_component);
447  data_->flux.set(ele_flux_ptr, 0.0);
448 
449  auto ele_velocity_ptr = std::make_shared< FieldDivide<3, FieldValue<3>::VectorFixed> >(ele_flux_ptr, data_->cross_section);
450  data_->field_ele_velocity.set(ele_velocity_ptr, 0.0);
451 
452  uint p_ele_component = 1;
453  auto ele_pressure_ptr = create_field_fe<3, FieldValue<3>::Scalar>(data_->dh_, &data_->full_solution, p_ele_component);
454  data_->field_ele_pressure.set(ele_pressure_ptr, 0.0);
455 
456  uint p_edge_component = 2;
457  auto edge_pressure_ptr = create_field_fe<3, FieldValue<3>::Scalar>(data_->dh_, &data_->full_solution, p_edge_component);
458  data_->field_edge_pressure.set(edge_pressure_ptr, 0.0);
459 
460  arma::vec4 gravity = (-1) * data_->gravity_;
461  auto ele_piezo_head_ptr = std::make_shared< FieldAddPotential<3, FieldValue<3>::Scalar> >(gravity, ele_pressure_ptr);
462  data_->field_ele_piezo_head.set(ele_piezo_head_ptr, 0.0);
463  }
464 
465  { // init DOF handlers represents edge DOFs
466  uint p_edge_component = 2;
467  data_->dh_cr_ = std::make_shared<SubDOFHandlerMultiDim>(data_->dh_,p_edge_component);
468  }
469 
470  { // init DOF handlers represents side DOFs
471  MixedPtr<FE_CR_disc> fe_cr_disc;
472  std::shared_ptr<DiscreteSpace> ds_cr_disc = std::make_shared<EqualOrderDiscreteSpace>( mesh_, fe_cr_disc);
473  data_->dh_cr_disc_ = std::make_shared<DOFHandlerMultiDim>(*mesh_);
474  data_->dh_cr_disc_->distribute_dofs(ds_cr_disc);
475  }
476 
477  // Initialize bc_switch_dirichlet to size of global boundary.
478  data_->bc_switch_dirichlet.resize(mesh_->n_elements()+mesh_->get_bc_mesh()->n_elements(), 1);
479 
480 
483  .val<Input::Record>("nonlinear_solver")
484  .val<Input::AbstractRecord>("linear_solver");
485 
486  // auxiliary set_time call since allocation assembly evaluates fields as well
489 
490 
491 
492  // allocate time term vectors
493  VecDuplicate(schur0->get_solution(), &previous_solution);
494  VecCreateMPI(PETSC_COMM_WORLD, data_->dh_->distr()->lsize(),PETSC_DETERMINE,&(steady_diagonal));
495  VecDuplicate(steady_diagonal,& new_diagonal);
496  VecZeroEntries(new_diagonal);
497  VecDuplicate(steady_diagonal, &steady_rhs);
498 
499 
500  // initialization of balance object
501  balance_ = std::make_shared<Balance>("water", mesh_);
502  balance_->init_from_input(input_record_.val<Input::Record>("balance"), time());
503  data_->water_balance_idx = balance_->add_quantity("water_volume");
504  balance_->allocate(data_->dh_->distr()->lsize(), 1);
505  balance_->units(UnitSI().m(3));
506 
507 
508  data_->balance = balance_;
509  data_->lin_sys = schur0;
510 
511 
513 }
514 
516 {}
517 
519 {
520 
521  /* TODO:
522  * - Allow solution reconstruction (pressure and velocity) from initial condition on user request.
523  * - Steady solution as an intitial condition may be forced by setting inti_time =-1, and set data for the steady solver in that time.
524  * Solver should be able to switch from and to steady case depending on the zero time term.
525  */
526 
528 
529  // zero_time_term means steady case
530  bool zero_time_term_from_right = zero_time_term();
531 
532 
533  if (zero_time_term_from_right) {
534  // steady case
535  VecZeroEntries(schur0->get_solution());
536  //read_initial_condition(); // Possible solution guess for steady case.
537  use_steady_assembly_ = true;
538  solve_nonlinear(); // with right limit data
539  } else {
540  VecZeroEntries(schur0->get_solution());
541  VecZeroEntries(previous_solution);
543  assembly_linear_system(); // in particular due to balance
544 // print_matlab_matrix("matrix_zero");
545  // TODO: reconstruction of solution in zero time.
546  }
547  //solution_output(T,right_limit); // data for time T in any case
548  output_data();
549 }
550 
551 //=============================================================================
552 // COMPOSE and SOLVE WATER MH System possibly through Schur complements
553 //=============================================================================
555 {
556  START_TIMER("Solving MH system");
557 
558  time_->next_time();
559 
560  time_->view("DARCY"); //time governor information output
561 
562  solve_time_step();
563 
564  data_->full_solution.local_to_ghost_begin();
565  data_->full_solution.local_to_ghost_end();
566 }
567 
568 
569 void DarcyMH::solve_time_step(bool output)
570 {
572 
573  bool zero_time_term_from_left=zero_time_term();
574 
575  bool jump_time = data_->storativity.is_jump_time();
576  if (! zero_time_term_from_left) {
577  // time term not treated as zero
578  // Unsteady solution up to the T.
579 
580  // this flag is necesssary for switching BC to avoid setting zero neumann on the whole boundary in the steady case
581  use_steady_assembly_ = false;
582 
584  solve_nonlinear(); // with left limit data
585  if (jump_time) {
586  WarningOut() << "Output of solution discontinuous in time not supported yet.\n";
587  //solution_output(T, left_limit); // output use time T- delta*dt
588  //output_data();
589  }
590  }
591 
592  if (time_->is_end()) {
593  // output for unsteady case, end_time should not be the jump time
594  // but rether check that
595  if (! zero_time_term_from_left && ! jump_time && output) output_data();
596  return;
597  }
598 
600  bool zero_time_term_from_right=zero_time_term();
601  if (zero_time_term_from_right) {
602  // this flag is necesssary for switching BC to avoid setting zero neumann on the whole boundary in the steady case
603  use_steady_assembly_ = true;
604  solve_nonlinear(); // with right limit data
605 
606  } else if (! zero_time_term_from_left && jump_time) {
607  WarningOut() << "Discontinuous time term not supported yet.\n";
608  //solution_transfer(); // internally call set_time(T, left) and set_time(T,right) again
609  //solve_nonlinear(); // with right limit data
610  }
611 
612  //solution_output(T,right_limit); // data for time T in any case
613  if (output) output_data();
614 }
615 
616 
617 bool DarcyMH::zero_time_term(bool time_global) {
618  if (time_global) {
619  return (data_->storativity.input_list_size() == 0);
620  } else {
621  return data_->storativity.field_result(mesh_->region_db().get_region_set("BULK")) == result_zeros;
622  }
623 }
624 
625 
627 {
628 
630  double residual_norm = schur0->compute_residual();
632  MessageOut().fmt("[nonlinear solver] norm of initial residual: {}\n", residual_norm);
633 
634  // Reduce is_linear flag.
635  int is_linear_common;
636  MPI_Allreduce(&(data_->is_linear), &is_linear_common,1, MPI_INT ,MPI_MIN,PETSC_COMM_WORLD);
637 
638  Input::Record nl_solver_rec = input_record_.val<Input::Record>("nonlinear_solver");
639  this->tolerance_ = nl_solver_rec.val<double>("tolerance");
640  this->max_n_it_ = nl_solver_rec.val<unsigned int>("max_it");
641  this->min_n_it_ = nl_solver_rec.val<unsigned int>("min_it");
642  if (this->min_n_it_ > this->max_n_it_) this->min_n_it_ = this->max_n_it_;
643 
644  if (! is_linear_common) {
645  // set tolerances of the linear solver unless they are set by user.
646  schur0->set_tolerances(0.1*this->tolerance_, 0.01*this->tolerance_, 100);
647  }
648  vector<double> convergence_history;
649 
650  Vec save_solution;
651  VecDuplicate(schur0->get_solution(), &save_solution);
652  while (nonlinear_iteration_ < this->min_n_it_ ||
653  (residual_norm > this->tolerance_ && nonlinear_iteration_ < this->max_n_it_ )) {
654  OLD_ASSERT_EQUAL( convergence_history.size(), nonlinear_iteration_ );
655  convergence_history.push_back(residual_norm);
656 
657  // stagnation test
658  if (convergence_history.size() >= 5 &&
659  convergence_history[ convergence_history.size() - 1]/convergence_history[ convergence_history.size() - 2] > 0.9 &&
660  convergence_history[ convergence_history.size() - 1]/convergence_history[ convergence_history.size() - 5] > 0.8) {
661  // stagnation
662  if (input_record_.val<Input::Record>("nonlinear_solver").val<bool>("converge_on_stagnation")) {
663  WarningOut().fmt("Accept solution on stagnation. Its: {} Residual: {}\n", nonlinear_iteration_, residual_norm);
664  break;
665  } else {
666  THROW(ExcSolverDiverge() << EI_Reason("Stagnation."));
667  }
668  }
669 
670  if (! is_linear_common)
671  VecCopy( schur0->get_solution(), save_solution);
674 
675  // hack to make BDDC work with empty compute_residual
676  if (is_linear_common){
677  // we want to print this info in linear (and steady) case
678  residual_norm = schur0->compute_residual();
679  MessageOut().fmt("[nonlinear solver] lin. it: {}, reason: {}, residual: {}\n",
680  si.n_iterations, si.converged_reason, residual_norm);
681  break;
682  }
683  data_changed_=true; // force reassembly for non-linear case
684 
685  double alpha = 1; // how much of new solution
686  VecAXPBY(schur0->get_solution(), (1-alpha), alpha, save_solution);
687 
688  //LogOut().fmt("Linear solver ended with reason: {} \n", si.converged_reason );
689  //OLD_ASSERT( si.converged_reason >= 0, "Linear solver failed to converge. Convergence reason %d \n", si.converged_reason );
691 
692  residual_norm = schur0->compute_residual();
693  MessageOut().fmt("[nonlinear solver] it: {} lin. it: {}, reason: {}, residual: {}\n",
694  nonlinear_iteration_, si.n_iterations, si.converged_reason, residual_norm);
695  }
696  chkerr(VecDestroy(&save_solution));
697  this -> postprocess();
698 
699  // adapt timestep
700  if (! this->zero_time_term()) {
701  double mult = 1.0;
702  if (nonlinear_iteration_ < 3) mult = 1.6;
703  if (nonlinear_iteration_ > 7) mult = 0.7;
704  time_->set_upper_constraint(time_->dt() * mult, "Darcy adaptivity.");
705  // int result = time_->set_upper_constraint(time_->dt() * mult, "Darcy adaptivity.");
706  //DebugOut().fmt("time adaptivity, res: {} it: {} m: {} dt: {} edt: {}\n", result, nonlinear_iteration_, mult, time_->dt(), time_->estimate_dt());
707  }
708 }
709 
711 {
713 }
714 
716 {
717  START_TIMER("postprocess");
718 
719  //fix velocity when mortar method is used
720  if(data_->mortar_method_ != MortarMethod::NoMortar){
721  auto multidim_assembler = AssemblyBase::create< AssemblyMH >(data_);
722  for ( DHCellAccessor dh_cell : data_->dh_->own_range() ) {
723  unsigned int dim = dh_cell.dim();
724  multidim_assembler[dim-1]->fix_velocity(dh_cell);
725  }
726  }
727  //ElementAccessor<3> ele;
728 
729  // modify side fluxes in parallel
730  // for every local edge take time term on digonal and add it to the corresponding flux
731  /*
732  for (unsigned int i_loc = 0; i_loc < el_ds->lsize(); i_loc++) {
733  ele = mesh_->element_accessor(el_4_loc[i_loc]);
734  for (unsigned int i=0; i<ele->n_sides(); i++) {
735  side_rows[i] = side_row_4_id[ mh_dh.side_dof( ele_ac.side(i) ) ];
736  values[i] = -1.0 * ele_ac.measure() *
737  data.cross_section.value(ele_ac.centre(), ele_ac.element_accessor()) *
738  data.water_source_density.value(ele_ac.centre(), ele_ac.element_accessor()) /
739  ele_ac.n_sides();
740  }
741  VecSetValues(schur0->get_solution(), ele_ac.n_sides(), side_rows, values, ADD_VALUES);
742  }
743  VecAssemblyBegin(schur0->get_solution());
744  VecAssemblyEnd(schur0->get_solution());
745  */
746 }
747 
748 
750  START_TIMER("Darcy output data");
751 
752  //print_matlab_matrix("matrix_" + std::to_string(time_->step().index()));
753 
754  //time_->view("DARCY"); //time governor information output
755  this->output_object->output();
756 
757 
758  START_TIMER("Darcy balance output");
759  balance_->calculate_cumulative(data_->water_balance_idx, schur0->get_solution());
760  balance_->calculate_instant(data_->water_balance_idx, schur0->get_solution());
761  balance_->output();
762 }
763 
764 
766 {
767  return schur0->get_solution_precision();
768 }
769 
770 
771 // ===========================================================================================
772 //
773 // MATRIX ASSEMBLY - we use abstract assembly routine, where LS Mat/Vec SetValues
774 // are in fact pointers to allocating or filling functions - this is governed by Linsystem roitunes
775 //
776 // =======================================================================================
778 {
779  START_TIMER("DarcyFlowMHy::assembly_mh_matrix");
780 
781  // set auxiliary flag for switchting Dirichlet like BC
782  data_->force_no_neumann_bc = use_steady_assembly_ && (nonlinear_iteration_ == 0);
783  data_->n_schur_compls = n_schur_compls;
784 
785 
786  balance_->start_flux_assembly(data_->water_balance_idx);
787 
788  // TODO: try to move this into balance, or have it in the generic assembler class, that should perform the cell loop
789  // including various pre- and post-actions
790  for ( DHCellAccessor dh_cell : data_->dh_->own_range() ) {
791  unsigned int dim = dh_cell.dim();
792  assembler[dim-1]->assemble(dh_cell);
793  }
794 
795 
796  balance_->finish_flux_assembly(data_->water_balance_idx);
797 
798 }
799 
800 
802 {
803  START_TIMER("DarcyFlowMH::allocate_mh_matrix");
804 
805  // set auxiliary flag for switchting Dirichlet like BC
806  data_->n_schur_compls = n_schur_compls;
807  LinSys *ls = schur0;
808 
809  // to make space for second schur complement, max. 10 neighbour edges of one el.
810  double zeros[100000];
811  for(int i=0; i<100000; i++) zeros[i] = 0.0;
812 
813  std::vector<LongIdx> tmp_rows;
814  tmp_rows.reserve(200);
815 
816  std::vector<LongIdx> dofs, dofs_ngh;
817  dofs.reserve(data_->dh_->max_elem_dofs());
818  dofs_ngh.reserve(data_->dh_->max_elem_dofs());
819 
820  for ( DHCellAccessor dh_cell : data_->dh_->own_range() ) {
821  ElementAccessor<3> ele = dh_cell.elm();
822 
823  const uint ndofs = dh_cell.n_dofs();
824  dofs.resize(ndofs);
825  dh_cell.get_dof_indices(dofs);
826 
827  // whole local MH matrix
828  ls->mat_set_values(ndofs, dofs.data(), ndofs, dofs.data(), zeros);
829 
830  tmp_rows.clear();
831 
832  // compatible neighborings rows
833  unsigned int n_neighs = ele->n_neighs_vb();
834  for ( DHCellSide neighb_side : dh_cell.neighb_sides() ) {
835  // every compatible connection adds a 2x2 matrix involving
836  // current element pressure and a connected edge pressure
837 
838  // read neighbor dofs (dh dofhandler)
839  // neighbor cell owning neighb_side
840  DHCellAccessor dh_neighb_cell = neighb_side.cell();
841 
842  const uint ndofs_ngh = dh_neighb_cell.n_dofs();
843  dofs_ngh.resize(ndofs_ngh);
844  dh_neighb_cell.get_dof_indices(dofs_ngh);
845 
846  // local index of pedge dof on neighboring cell
847  // (dim+1) is number of edges of higher dim element
848  // TODO: replace with DHCell getter when available for FESystem component
849  const unsigned int t = dh_neighb_cell.n_dofs() - (dh_neighb_cell.dim()+1) + neighb_side.side().side_idx();
850  tmp_rows.push_back(dofs_ngh[t]);
851  }
852 
853  const uint nsides = ele->n_sides();
854  LongIdx * edge_rows = dofs.data() + nsides; // pointer to start of ele
855  // allocate always also for schur 2
856  ls->mat_set_values(nsides+1, edge_rows, n_neighs, tmp_rows.data(), zeros); // (edges, ele) x (neigh edges)
857  ls->mat_set_values(n_neighs, tmp_rows.data(), nsides+1, edge_rows, zeros); // (neigh edges) x (edges, ele)
858  ls->mat_set_values(n_neighs, tmp_rows.data(), n_neighs, tmp_rows.data(), zeros); // (neigh edges) x (neigh edges)
859 
860  tmp_rows.clear();
861 
862  if (data_->mortar_method_ != NoMortar) {
863  auto &isec_list = mesh_->mixed_intersections().element_intersections_[ele.idx()];
864  for(auto &isec : isec_list ) {
865  IntersectionLocalBase *local = isec.second;
866  DHCellAccessor dh_cell_slave = data_->dh_->cell_accessor_from_element(local->bulk_ele_idx());
867 
868  const uint ndofs_slave = dh_cell_slave.n_dofs();
869  dofs_ngh.resize(ndofs_slave);
870  dh_cell_slave.get_dof_indices(dofs_ngh);
871 
872  //DebugOut().fmt("Alloc: {} {}", ele.idx(), local->bulk_ele_idx());
873  for(unsigned int i_side=0; i_side < dh_cell_slave.elm()->n_sides(); i_side++) {
874  // TODO: replace with DHCell getter when available for FESystem component
875  tmp_rows.push_back( dofs_ngh[(ndofs_slave+1)/2+i_side] );
876  //DebugOut() << "aedge" << print_var(tmp_rows[tmp_rows.size()-1]);
877  }
878  }
879  }
880  /*
881  for(unsigned int i_side=0; i_side < ele->n_sides(); i_side++) {
882  DebugOut() << "aedge:" << print_var(edge_rows[i_side]);
883  }*/
884 
885  edge_rows = dofs.data() + nsides +1; // pointer to start of edges
886  ls->mat_set_values(nsides, edge_rows, tmp_rows.size(), tmp_rows.data(), zeros); // master edges x neigh edges
887  ls->mat_set_values(tmp_rows.size(), tmp_rows.data(), nsides, edge_rows, zeros); // neigh edges x master edges
888  ls->mat_set_values(tmp_rows.size(), tmp_rows.data(), tmp_rows.size(), tmp_rows.data(), zeros); // neigh edges x neigh edges
889 
890  }
891 /*
892  // alloc edge diagonal entries
893  if(rank == 0)
894  for( vector<Edge>::iterator edg = mesh_->edges.begin(); edg != mesh_->edges.end(); ++edg) {
895  int edg_idx = mh_dh.row_4_edge[edg->side(0)->edge_idx()];
896 
897 // for( vector<Edge>::iterator edg2 = mesh_->edges.begin(); edg2 != mesh_->edges.end(); ++edg2){
898 // int edg_idx2 = mh_dh.row_4_edge[edg2->side(0)->edge_idx()];
899 // if(edg_idx == edg_idx2){
900 // DBGCOUT(<< "P[ " << rank << " ] " << "edg alloc: " << edg_idx << " " << edg_idx2 << "\n");
901  ls->mat_set_value(edg_idx, edg_idx, 0.0);
902 // }
903 // }
904  }
905  */
906  /*
907  if (mortar_method_ == MortarP0) {
908  P0_CouplingAssembler(*this).assembly(*ls);
909  } else if (mortar_method_ == MortarP1) {
910  P1_CouplingAssembler(*this).assembly(*ls);
911  }*/
912 }
913 
915 {
916  START_TIMER("assembly source term");
917  balance_->start_source_assembly(data_->water_balance_idx);
918 
919  std::vector<LongIdx> global_dofs(data_->dh_->max_elem_dofs());
920 
921  for ( DHCellAccessor dh_cell : data_->dh_->own_range() ) {
922  ElementAccessor<3> ele = dh_cell.elm();
923 
924  const uint ndofs = dh_cell.n_dofs();
925  global_dofs.resize(ndofs);
926  dh_cell.get_dof_indices(global_dofs);
927 
928  double cs = data_->cross_section.value(ele.centre(), ele);
929 
930  // set sources
931  double source = ele.measure() * cs *
932  (data_->water_source_density.value(ele.centre(), ele)
933  +data_->extra_source.value(ele.centre(), ele));
934  // TODO: replace with DHCell getter when available for FESystem component
935  schur0->rhs_set_value(global_dofs[ndofs/2], -1.0 * source );
936 
937  balance_->add_source_values(data_->water_balance_idx, ele.region().bulk_idx(),
938  {dh_cell.get_loc_dof_indices()[ndofs/2]}, {0}, {source});
939  }
940 
941  balance_->finish_source_assembly(data_->water_balance_idx);
942 }
943 
944 
945 
946 
947 /*******************************************************************************
948  * COMPOSE WATER MH MATRIX WITHOUT SCHUR COMPLEMENT
949  ******************************************************************************/
950 
952 
953  START_TIMER("preallocation");
954 
955  if (schur0 == NULL) { // create Linear System for MH matrix
956 
957  if (in_rec.type() == LinSys_BDDC::get_input_type()) {
958 #ifdef FLOW123D_HAVE_BDDCML
959  WarningOut() << "For BDDC no Schur complements are used.";
960  n_schur_compls = 0;
961  LinSys_BDDC *ls = new LinSys_BDDC(&(*data_->dh_->distr()),
962  true); // swap signs of matrix and rhs to make the matrix SPD
963  ls->set_from_input(in_rec);
964  ls->set_solution( data_->full_solution.petsc_vec() );
965  // possible initialization particular to BDDC
966  START_TIMER("BDDC set mesh data");
968  schur0=ls;
969  END_TIMER("BDDC set mesh data");
970 #else
971  //Exception
972  THROW( ExcBddcmlNotSupported() );
973 #endif // FLOW123D_HAVE_BDDCML
974  }
975  else if (in_rec.type() == LinSys_PETSC::get_input_type()) {
976  // use PETSC for serial case even when user wants BDDC
977  if (n_schur_compls > 2) {
978  WarningOut() << "Invalid number of Schur Complements. Using 2.";
979  n_schur_compls = 2;
980  }
981 
982  LinSys_PETSC *schur1, *schur2;
983 
984  if (n_schur_compls == 0) {
985  LinSys_PETSC *ls = new LinSys_PETSC( &(*data_->dh_->distr()) );
986 
987  // temporary solution; we have to set precision also for sequantial case of BDDC
988  // final solution should be probably call of direct solver for oneproc case
989  if (in_rec.type() != LinSys_BDDC::get_input_type()) ls->set_from_input(in_rec);
990  else {
991  ls->LinSys::set_from_input(in_rec); // get only common options
992  }
993 
994  ls->set_solution( data_->full_solution.petsc_vec() );
995  schur0=ls;
996  } else {
997  IS is;
998  auto side_dofs_vec = get_component_indices_vec(0);
999 
1000  ISCreateGeneral(PETSC_COMM_SELF, side_dofs_vec.size(), &(side_dofs_vec[0]), PETSC_COPY_VALUES, &is);
1001  //ISView(is, PETSC_VIEWER_STDOUT_SELF);
1002  //OLD_ASSERT(err == 0,"Error in ISCreateStride.");
1003 
1004  SchurComplement *ls = new SchurComplement(&(*data_->dh_->distr()), is);
1005 
1006  // make schur1
1008  if (n_schur_compls==1) {
1009  schur1 = new LinSys_PETSC(ds);
1010  schur1->set_positive_definite();
1011  } else {
1012  IS is;
1013  auto elem_dofs_vec = get_component_indices_vec(1);
1014 
1015  const PetscInt *b_indices;
1016  ISGetIndices(ls->IsB, &b_indices);
1017  uint b_size = ls->loc_size_B;
1018  for(uint i_b=0, i_bb=0; i_b < b_size && i_bb < elem_dofs_vec.size(); i_b++) {
1019  if (b_indices[i_b] == elem_dofs_vec[i_bb])
1020  elem_dofs_vec[i_bb++] = i_b + ds->begin();
1021  }
1022  ISRestoreIndices(ls->IsB, &b_indices);
1023 
1024 
1025  ISCreateGeneral(PETSC_COMM_SELF, elem_dofs_vec.size(), &(elem_dofs_vec[0]), PETSC_COPY_VALUES, &is);
1026  //ISView(is, PETSC_VIEWER_STDOUT_SELF);
1027  //OLD_ASSERT(err == 0,"Error in ISCreateStride.");
1028  SchurComplement *ls1 = new SchurComplement(ds, is); // is is deallocated by SchurComplement
1029  ls1->set_negative_definite();
1030 
1031  // make schur2
1032  schur2 = new LinSys_PETSC( ls1->make_complement_distribution() );
1033  schur2->set_positive_definite();
1034  ls1->set_complement( schur2 );
1035  schur1 = ls1;
1036  }
1037  ls->set_complement( schur1 );
1038  ls->set_from_input(in_rec);
1039  ls->set_solution( data_->full_solution.petsc_vec() );
1040  schur0=ls;
1041  }
1042 
1043  START_TIMER("PETSC PREALLOCATION");
1044  schur0->set_symmetric();
1046 
1048 
1049  VecZeroEntries(schur0->get_solution());
1050  END_TIMER("PETSC PREALLOCATION");
1051  }
1052  else {
1053  THROW( ExcUnknownSolver() );
1054  }
1055 
1056  END_TIMER("preallocation");
1057  }
1058 
1059 }
1060 
1061 
1062 
1063 
1065  START_TIMER("DarcyFlowMH_Steady::assembly_linear_system");
1066 
1067  data_->is_linear=true;
1068  bool is_steady = zero_time_term();
1069  //DebugOut() << "Assembly linear system\n";
1070  if (data_changed_) {
1071  data_changed_ = false;
1072  //DebugOut() << "Data changed\n";
1073  // currently we have no optimization for cases when just time term data or RHS data are changed
1074  START_TIMER("full assembly");
1075  if (typeid(*schur0) != typeid(LinSys_BDDC)) {
1076  schur0->start_add_assembly(); // finish allocation and create matrix
1077  }
1078 
1081 
1083 
1084 
1085  assembly_mh_matrix( data_->multidim_assembler ); // fill matrix
1086 
1088 // print_matlab_matrix("matrix");
1090  //MatView( *const_cast<Mat*>(schur0->get_matrix()), PETSC_VIEWER_STDOUT_WORLD );
1091  //VecView( *const_cast<Vec*>(schur0->get_rhs()), PETSC_VIEWER_STDOUT_WORLD);
1092 
1093  if (! is_steady) {
1094  START_TIMER("fix time term");
1095  //DebugOut() << "setup time term\n";
1096  // assembly time term and rhs
1097  setup_time_term();
1098  modify_system();
1099  }
1100  else
1101  {
1102  balance_->start_mass_assembly(data_->water_balance_idx);
1103  balance_->finish_mass_assembly(data_->water_balance_idx);
1104  }
1105  END_TIMER("full assembly");
1106  } else {
1107  START_TIMER("modify system");
1108  if (! is_steady) {
1109  modify_system();
1110  } else {
1111  //Should be replaced with exception if error will be switched on.
1112  //ASSERT(false).error("Planned computation time for steady solver, but data are not changed.\n");
1113  }
1114  END_TIMER("modiffy system");
1115  }
1116 
1117 }
1118 
1119 
1120 void DarcyMH::print_matlab_matrix(std::string matlab_file)
1121 {
1122  std::string output_file;
1123 
1124  if ( typeid(*schur0) == typeid(LinSys_BDDC) ){
1125 // WarningOut() << "Can output matrix only on a single processor.";
1126 // output_file = FilePath(matlab_file + "_bddc.m", FilePath::output_file);
1127 // ofstream os( output_file );
1128 // auto bddc = static_cast<LinSys_BDDC*>(schur0);
1129 // bddc->print_matrix(os);
1130  }
1131  else {//if ( typeid(*schur0) == typeid(LinSys_PETSC) ){
1132  output_file = FilePath(matlab_file + ".m", FilePath::output_file);
1133  PetscViewer viewer;
1134  PetscViewerASCIIOpen(PETSC_COMM_WORLD, output_file.c_str(), &viewer);
1135  PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_MATLAB);
1136  MatView( *const_cast<Mat*>(schur0->get_matrix()), viewer);
1137  VecView( *const_cast<Vec*>(schur0->get_rhs()), viewer);
1138  VecView( *const_cast<Vec*>(schur0->get_rhs()), viewer);
1139  VecView( *const_cast<Vec*>(&(schur0->get_solution())), viewer);
1140  }
1141 // else{
1142 // WarningOut() << "No matrix output available for the current solver.";
1143 // return;
1144 // }
1145 
1146  // compute h_min for different dimensions
1147  double d_max = std::numeric_limits<double>::max();
1148  double h1 = d_max, h2 = d_max, h3 = d_max;
1149  double he2 = d_max, he3 = d_max;
1150  for (auto ele : mesh_->elements_range()) {
1151  switch(ele->dim()){
1152  case 1: h1 = std::min(h1,ele.measure()); break;
1153  case 2: h2 = std::min(h2,ele.measure()); break;
1154  case 3: h3 = std::min(h3,ele.measure()); break;
1155  }
1156 
1157  for (unsigned int j=0; j<ele->n_sides(); j++) {
1158  switch(ele->dim()){
1159  case 2: he2 = std::min(he2, ele.side(j)->measure()); break;
1160  case 3: he3 = std::min(he3, ele.side(j)->measure()); break;
1161  }
1162  }
1163  }
1164  if(h1 == d_max) h1 = 0;
1165  if(h2 == d_max) h2 = 0;
1166  if(h3 == d_max) h3 = 0;
1167  if(he2 == d_max) he2 = 0;
1168  if(he3 == d_max) he3 = 0;
1169 
1170  FILE * file;
1171  file = fopen(output_file.c_str(),"a");
1172  fprintf(file, "nA = %d;\n", data_->dh_cr_disc_->distr()->size());
1173  fprintf(file, "nB = %d;\n", data_->dh_->mesh()->get_el_ds()->size());
1174  fprintf(file, "nBF = %d;\n", data_->dh_cr_->distr()->size());
1175  fprintf(file, "h1 = %e;\nh2 = %e;\nh3 = %e;\n", h1, h2, h3);
1176  fprintf(file, "he2 = %e;\nhe3 = %e;\n", he2, he3);
1177  fclose(file);
1178 }
1179 
1180 
1181 //template <int dim>
1182 //std::vector<arma::vec3> dof_points(DHCellAccessor cell, const Mapping<dim, 3> &mapping) {
1183 //
1184 //
1185 // vector<arma::vec::fixed<dim+1>> bary_dof_points = cell->fe()->dof_points();
1186 //
1187 // std::vector<arma::vec3> points(20);
1188 // points.resize(0);
1189 //
1190 //}
1191 //
1192 
1194  START_TIMER("DarcyFlowMH_Steady::set_mesh_data_for_bddc");
1195  // prepare mesh for BDDCML
1196  // initialize arrays
1197  // auxiliary map for creating coordinates of local dofs and global-to-local numbering
1198  std::map<int, arma::vec3> localDofMap;
1199  // connectivity for the subdomain, i.e. global dof numbers on element, stored element-by-element
1200  // Indices of Nodes on Elements
1201  std::vector<int> inet;
1202  // number of degrees of freedom on elements - determines elementwise chunks of INET array
1203  // Number of Nodes on Elements
1204  std::vector<int> nnet;
1205  // Indices of Subdomain Elements in Global Numbering - for local elements, their global indices
1206  std::vector<int> isegn;
1207 
1208  // This array is currently not used in BDDCML, it was used as an interface scaling alternative to scaling
1209  // by diagonal. It corresponds to the rho-scaling.
1210  std::vector<double> element_permeability;
1211 
1212  // maximal and minimal dimension of elements
1213  uint elDimMax = 1;
1214  uint elDimMin = 3;
1215  std::vector<LongIdx> cell_dofs_global(10);
1216 
1217 
1218 
1219  for ( DHCellAccessor dh_cell : data_->dh_->own_range() ) {
1220  // for each element, create local numbering of dofs as fluxes (sides), pressure (element centre), Lagrange multipliers (edges), compatible connections
1221 
1222  dh_cell.get_dof_indices(cell_dofs_global);
1223 
1224  inet.insert(inet.end(), cell_dofs_global.begin(), cell_dofs_global.end());
1225  uint n_inet = cell_dofs_global.size();
1226 
1227 
1228  uint dim = dh_cell.elm().dim();
1229  elDimMax = std::max( elDimMax, dim );
1230  elDimMin = std::min( elDimMin, dim );
1231 
1232  // TODO: this is consistent with previous implementation, but may be wrong as it use global element numbering
1233  // used in sequential mesh, do global numbering of distributed elements.
1234  isegn.push_back( dh_cell.elm_idx());
1235 
1236  // TODO: use FiniteElement::dof_points
1237  for (unsigned int si=0; si<dh_cell.elm()->n_sides(); si++) {
1238  arma::vec3 coord = dh_cell.elm().side(si)->centre();
1239  // TODO: replace with DHCell getter when available for FESystem component
1240  // flux dof points
1241  localDofMap.insert( std::make_pair( cell_dofs_global[si], coord ) );
1242  // pressure trace dof points
1243  localDofMap.insert( std::make_pair( cell_dofs_global[si+dim+2], coord ) );
1244  }
1245  // pressure dof points
1246  arma::vec3 elm_centre = dh_cell.elm().centre();
1247  localDofMap.insert( std::make_pair( cell_dofs_global[dim+1], elm_centre ) );
1248 
1249  // insert dofs related to compatible connections
1250  //const Element *ele = dh_cell.elm().element();
1251  for(DHCellSide side : dh_cell.neighb_sides()) {
1252  uint neigh_dim = side.cell().elm().dim();
1253  side.cell().get_dof_indices(cell_dofs_global);
1254  int edge_row = cell_dofs_global[neigh_dim+2+side.side_idx()];
1255  localDofMap.insert( std::make_pair( edge_row, side.centre() ) );
1256  inet.push_back( edge_row );
1257  n_inet++;
1258  }
1259  nnet.push_back(n_inet);
1260 
1261 
1262  // version for rho scaling
1263  // trace computation
1264  double conduct = data_->conductivity.value( elm_centre , dh_cell.elm() );
1265  auto aniso = data_->anisotropy.value( elm_centre , dh_cell.elm() );
1266 
1267  // compute mean on the diagonal
1268  double coef = 0.;
1269  for ( int i = 0; i < 3; i++) {
1270  coef = coef + aniso.at(i,i);
1271  }
1272  // Maybe divide by cs
1273  coef = conduct*coef / 3;
1274 
1275  OLD_ASSERT( coef > 0.,
1276  "Zero coefficient of hydrodynamic resistance %f . \n ", coef );
1277  element_permeability.push_back( 1. / coef );
1278  }
1279 // uint i_inet = 0;
1280 // for(int n_dofs : nnet) {
1281 // DebugOut() << "nnet: " << n_dofs;
1282 // for(int j=0; j < n_dofs; j++, i_inet++) {
1283 // DebugOut() << "inet: " << inet[i_inet];
1284 // }
1285 // }
1286 
1287  auto distr = data_->dh_->distr();
1288 // for(auto pair : localDofMap) {
1289 // DebugOut().every_proc() << "r: " << distr->myp() << " gi: " << pair.first << "xyz: " << pair.second[0];
1290 //
1291 // }
1292 
1293 
1294  //convert set of dofs to vectors
1295  // number of nodes (= dofs) on the subdomain
1296  int numNodeSub = localDofMap.size();
1297  //ASSERT_EQ( (unsigned int)numNodeSub, data_->dh_->lsize() );
1298  // Indices of Subdomain Nodes in Global Numbering - for local nodes, their global indices
1299  std::vector<int> isngn( numNodeSub );
1300  // pseudo-coordinates of local nodes (i.e. dofs)
1301  // they need not be exact, they are used just for some geometrical considerations in BDDCML,
1302  // such as selection of corners maximizing area of a triangle, bounding boxes fro subdomains to
1303  // find candidate neighbours etc.
1304  std::vector<double> xyz( numNodeSub * 3 ) ;
1305  int ind = 0;
1306  std::map<int,arma::vec3>::iterator itB = localDofMap.begin();
1307  for ( ; itB != localDofMap.end(); ++itB ) {
1308  isngn[ind] = itB -> first;
1309 
1310  arma::vec3 coord = itB -> second;
1311  for ( int j = 0; j < 3; j++ ) {
1312  xyz[ j*numNodeSub + ind ] = coord[j];
1313  }
1314 
1315  ind++;
1316  }
1317  localDofMap.clear();
1318 
1319  // Number of Nodal Degrees of Freedom
1320  // nndf is trivially one - dofs coincide with nodes
1321  std::vector<int> nndf( numNodeSub, 1 );
1322 
1323  // prepare auxiliary map for renumbering nodes
1324  typedef std::map<int,int> Global2LocalMap_; //! type for storage of global to local map
1325  Global2LocalMap_ global2LocalNodeMap;
1326  for ( unsigned ind = 0; ind < isngn.size(); ++ind ) {
1327  global2LocalNodeMap.insert( std::make_pair( static_cast<unsigned>( isngn[ind] ), ind ) );
1328  }
1329 
1330  // renumber nodes in the inet array to locals
1331  int indInet = 0;
1332  for ( unsigned int iEle = 0; iEle < isegn.size(); iEle++ ) {
1333  int nne = nnet[ iEle ];
1334  for ( int ien = 0; ien < nne; ien++ ) {
1335 
1336  int indGlob = inet[indInet];
1337  // map it to local node
1338  Global2LocalMap_::iterator pos = global2LocalNodeMap.find( indGlob );
1339  OLD_ASSERT( pos != global2LocalNodeMap.end(),
1340  "Cannot remap node index %d to local indices. \n ", indGlob );
1341  int indLoc = static_cast<int> ( pos -> second );
1342 
1343  // store the node
1344  inet[ indInet++ ] = indLoc;
1345  }
1346  }
1347 
1348  int numNodes = size;
1349  int numDofsInt = size;
1350  int spaceDim = 3; // TODO: what is the proper value here?
1351  int meshDim = elDimMax;
1352 
1353  /**
1354  * We need:
1355  * - local to global element map (possibly mesh->el_4_loc
1356  * - inet, nnet - local dof numbers per element, local numbering of only those dofs that are on owned elements
1357  * 1. collect DH local dof indices on elements, manage map from DH local indices to BDDC local dof indices
1358  * 2. map collected DH indices to BDDC indices using the map
1359  * - local BDDC dofs to global dofs, use DH to BDDC map with DH local to global map
1360  * - XYZ - permuted, collect in main loop into array of size of all DH local dofs, compress and rearrange latter
1361  * - element_permeability - in main loop
1362  */
1363  bddc_ls -> load_mesh( LinSys_BDDC::BDDCMatrixType::SPD_VIA_SYMMETRICGENERAL, spaceDim, numNodes, numDofsInt, inet, nnet, nndf, isegn, isngn, isngn, xyz, element_permeability, meshDim );
1364 }
1365 
1366 
1367 
1368 
1369 //=============================================================================
1370 // DESTROY WATER MH SYSTEM STRUCTURE
1371 //=============================================================================
1373  if (previous_solution != nullptr) chkerr(VecDestroy(&previous_solution));
1374  if (steady_diagonal != nullptr) chkerr(VecDestroy(&steady_diagonal));
1375  if (new_diagonal != nullptr) chkerr(VecDestroy(&new_diagonal));
1376  if (steady_rhs != nullptr) chkerr(VecDestroy(&steady_rhs));
1377 
1378 
1379  if (schur0 != NULL) {
1380  delete schur0;
1381  }
1382 
1383  if (output_object) delete output_object;
1384 
1385  if(time_ != nullptr)
1386  delete time_;
1387 
1388 }
1389 
1390 
1391 /*
1392 void mat_count_off_proc_values(Mat m, Vec v) {
1393  int n, first, last;
1394  const PetscInt *cols;
1395  Distribution distr(v);
1396 
1397  int n_off = 0;
1398  int n_on = 0;
1399  int n_off_rows = 0;
1400  MatGetOwnershipRange(m, &first, &last);
1401  for (int row = first; row < last; row++) {
1402  MatGetRow(m, row, &n, &cols, PETSC_NULL);
1403  bool exists_off = false;
1404  for (int i = 0; i < n; i++)
1405  if (distr.get_proc(cols[i]) != distr.myp())
1406  n_off++, exists_off = true;
1407  else
1408  n_on++;
1409  if (exists_off)
1410  n_off_rows++;
1411  MatRestoreRow(m, row, &n, &cols, PETSC_NULL);
1412  }
1413 }
1414 */
1415 
1416 
1417 
1418 
1419 
1420 
1421 
1422 
1423 
1424 
1425 
1426 
1428 {
1429  double *local_sol = schur0->get_solution_array();
1430 
1431  // cycle over local element rows
1432 
1433  DebugOut().fmt("Setup with dt: {}\n", time_->dt());
1434  for ( DHCellAccessor dh_cell : data_->dh_->own_range() ) {
1435  ElementAccessor<3> ele = dh_cell.elm();
1436  // set initial condition
1437  // TODO: replace with DHCell getter when available for FESystem component
1438  const IntIdx p_ele_dof = dh_cell.get_loc_dof_indices()[dh_cell.n_dofs()/2];
1439  local_sol[p_ele_dof] = data_->init_pressure.value(ele.centre(),ele);
1440  }
1441 }
1442 
1444  // save diagonal of steady matrix
1445  MatGetDiagonal(*( schur0->get_matrix() ), steady_diagonal);
1446  // save RHS
1447  VecCopy(*( schur0->get_rhs()), steady_rhs);
1448 
1449 
1450  PetscScalar *local_diagonal;
1451  VecGetArray(new_diagonal,& local_diagonal);
1452 
1453  DebugOut().fmt("Setup with dt: {}\n", time_->dt());
1454 
1455  balance_->start_mass_assembly(data_->water_balance_idx);
1456 
1457  std::vector<LongIdx> dofs;
1458  dofs.reserve(data_->dh_->max_elem_dofs());
1459 
1460  for ( DHCellAccessor dh_cell : data_->dh_->own_range() ) {
1461  ElementAccessor<3> ele = dh_cell.elm();
1462  dofs.resize(dh_cell.n_dofs());
1463  dh_cell.get_dof_indices(dofs);
1464 
1465  // TODO: replace with DHCell getter when available for FESystem component
1466  const uint p_ele_dof = dh_cell.n_dofs() / 2;
1467  // set new diagonal
1468  double diagonal_coeff = data_->cross_section.value(ele.centre(), ele)
1469  * ( data_->storativity.value(ele.centre(), ele)
1470  +data_->extra_storativity.value(ele.centre(), ele))
1471  * ele.measure();
1472  local_diagonal[dh_cell.get_loc_dof_indices()[p_ele_dof]]= - diagonal_coeff / time_->dt();
1473 
1474  balance_->add_mass_values(data_->water_balance_idx, dh_cell,
1475  {dh_cell.get_loc_dof_indices()[p_ele_dof]},
1476  {diagonal_coeff}, 0.0);
1477  }
1478  VecRestoreArray(new_diagonal,& local_diagonal);
1479  MatDiagonalSet(*( schur0->get_matrix() ), new_diagonal, ADD_VALUES);
1480 
1481  schur0->set_matrix_changed();
1482 
1483  balance_->finish_mass_assembly(data_->water_balance_idx);
1484 }
1485 
1487  START_TIMER("modify system");
1488  if (time_->is_changed_dt() && time_->step().index()>0) {
1489  double scale_factor=time_->step(-2).length()/time_->step().length();
1490  if (scale_factor != 1.0) {
1491  // if time step has changed and setup_time_term not called
1492  MatDiagonalSet(*( schur0->get_matrix() ),steady_diagonal, INSERT_VALUES);
1493 
1494  VecScale(new_diagonal, time_->last_dt()/time_->dt());
1495  MatDiagonalSet(*( schur0->get_matrix() ),new_diagonal, ADD_VALUES);
1497  }
1498  }
1499 
1500  // modify RHS - add previous solution
1501  VecPointwiseMult(*( schur0->get_rhs()), new_diagonal, previous_solution);
1502 // VecPointwiseMult(*( schur0->get_rhs()), new_diagonal, schur0->get_solution());
1503  VecAXPY(*( schur0->get_rhs()), 1.0, steady_rhs);
1505 
1506  //VecSwap(previous_solution, schur0->get_solution());
1507 }
1508 
1509 
1510 /// Helper method fills range (min and max) of given component
1511 void dofs_range(unsigned int n_dofs, unsigned int &min, unsigned int &max, unsigned int component) {
1512  if (component==0) {
1513  min = 0;
1514  max = n_dofs/2;
1515  } else if (component==1) {
1516  min = n_dofs/2;
1517  max = (n_dofs+1)/2;
1518  } else {
1519  min = (n_dofs+1)/2;
1520  max = n_dofs;
1521  }
1522 }
1523 
1524 
1526  ASSERT_LT_DBG(component, 3).error("Invalid component!");
1527  unsigned int i, n_dofs, min, max;
1528  std::vector<int> dof_vec;
1529  std::vector<LongIdx> dof_indices(data_->dh_->max_elem_dofs());
1530  for ( DHCellAccessor dh_cell : data_->dh_->own_range() ) {
1531  n_dofs = dh_cell.get_dof_indices(dof_indices);
1532  dofs_range(n_dofs, min, max, component);
1533  for (i=min; i<max; ++i) dof_vec.push_back(dof_indices[i]);
1534  }
1535  return dof_vec;
1536 }
1537 
1538 
1539 //-----------------------------------------------------------------------------
1540 // vim: set cindent:
LimitSide::right
@ right
OLD_ASSERT_EQUAL
#define OLD_ASSERT_EQUAL(a, b)
Definition: global_defs.h:110
Element::n_neighs_vb
unsigned int n_neighs_vb() const
Return number of neighbours.
Definition: elements.h:68
DarcyMH::balance_
std::shared_ptr< Balance > balance_
Definition: darcy_flow_mh.hh:341
EquationBase::mesh_
Mesh * mesh_
Definition: equation.hh:218
linsys_BDDC.hh
Solver based on Multilevel BDDC - using corresponding class of OpenFTL package.
Input::Type::Bool
Class for declaration of the input of type Bool.
Definition: type_base.hh:452
result_zeros
@ result_zeros
Definition: field_algo_base.hh:74
LinSys::get_solution
const Vec & get_solution()
Definition: linsys.hh:282
MPI_MIN
#define MPI_MIN
Definition: mpi.h:198
DarcyMH::previous_solution
Vec previous_solution
Definition: darcy_flow_mh.hh:365
DarcyMH::solution_precision
virtual double solution_precision() const
Definition: darcy_flow_mh.cc:765
DarcyMH::init_eq_data
void init_eq_data()
Definition: darcy_flow_mh.cc:372
LinSys::SolveInfo::n_iterations
int n_iterations
Definition: linsys.hh:110
Armor::vec
ArmaVec< double, N > vec
Definition: armor.hh:885
DarcyMH::solve_nonlinear
void solve_nonlinear()
Solve method common to zero_time_step and update solution.
Definition: darcy_flow_mh.cc:626
DarcyFlowMHOutput::output
void output()
Calculate values for output.
Definition: darcy_flow_mh_output.cc:242
TimeGovernor::dt
double dt() const
Definition: time_governor.hh:558
DarcyMH::use_steady_assembly_
bool use_steady_assembly_
Definition: darcy_flow_mh.hh:350
UnitSI::dimensionless
static UnitSI & dimensionless()
Returns dimensionless unit.
Definition: unit_si.cc:55
SchurComplement::set_complement
void set_complement(LinSys_PETSC *ls)
Set complement LinSys object.
Definition: schur.cc:287
factory.hh
LinSys
Definition: la_linsys_new.hh:169
vector_mpi.hh
time_governor.hh
Basic time management class.
field_add_potential.hh
DarcyMH::size
int size
Definition: darcy_flow_mh.hh:345
DarcyMH::EqData::dirichlet
@ dirichlet
Definition: darcy_flow_mh.hh:154
DarcyMH::steady_rhs
Vec steady_rhs
Definition: darcy_flow_mh.hh:363
field_algo_base.hh
DarcyMH::solve_time_step
void solve_time_step(bool output=true)
Solve the problem without moving to next time and without output.
Definition: darcy_flow_mh.cc:569
DarcyMH::update_solution
void update_solution() override
Definition: darcy_flow_mh.cc:554
LinSys::SolveInfo
Definition: linsys.hh:105
ASSERT
#define ASSERT(expr)
Allow use shorter versions of macro names if these names is not used with external library.
Definition: asserts.hh:347
DarcyMH::type_field_descriptor
static const Input::Type::Record & type_field_descriptor()
Definition: darcy_flow_mh.cc:116
LinSys::set_symmetric
void set_symmetric(bool flag=true)
Definition: linsys.hh:561
Mesh::elements_range
virtual Range< ElementAccessor< 3 > > elements_range() const
Returns range of bulk elements.
Definition: mesh.cc:1130
DarcyMH::postprocess
virtual void postprocess()
postprocess velocity field (add sources)
Definition: darcy_flow_mh.cc:715
Mesh::n_sides
unsigned int n_sides() const
Definition: mesh.cc:238
DarcyFlowInterface::MortarP1
@ MortarP1
Definition: darcy_flow_interface.hh:33
EquationBase::time_
TimeGovernor * time_
Definition: equation.hh:219
DarcyMH::setup_time_term
virtual void setup_time_term()
Definition: darcy_flow_mh.cc:1443
distribution.hh
Support classes for parallel programing.
LinSys_BDDC::get_input_type
static const Input::Type::Record & get_input_type()
Definition: linsys_BDDC.cc:39
bc_mesh.hh
Input::Type::Integer
Class for declaration of the integral input data.
Definition: type_base.hh:483
Input::Record::val
const Ret val(const string &key) const
Definition: accessors_impl.hh:31
DHCellAccessor::get_dof_indices
unsigned int get_dof_indices(std::vector< LongIdx > &indices) const
Fill vector of the global indices of dofs associated to the cell.
Definition: dh_cell_accessor.hh:80
TimeGovernor::set_upper_constraint
int set_upper_constraint(double upper, std::string message)
Sets upper constraint for the next time step estimating.
Definition: time_governor.cc:552
IntIdx
int IntIdx
Definition: index_types.hh:25
EquationBase::time
TimeGovernor & time()
Definition: equation.hh:149
Input::Type::Selection::close
const Selection & close() const
Close the Selection, no more values can be added.
Definition: type_selection.cc:65
fmt::fprintf
FMT_FUNC int fprintf(std::ostream &os, CStringRef format, ArgList args)
Definition: ostream.cc:56
FilePath
Dedicated class for storing path to input and output files.
Definition: file_path.hh:54
linsys.hh
Wrappers for linear systems based on MPIAIJ and MATIS format.
Input::Type::Double
Class for declaration of the input data that are floating point numbers.
Definition: type_base.hh:534
LinSys::rhs_zero_entries
virtual PetscErrorCode rhs_zero_entries()
Definition: linsys.hh:273
chkerr
void chkerr(unsigned int ierr)
Replacement of new/delete operator in the spirit of xmalloc.
Definition: system.hh:142
DarcyMH::create_linear_system
void create_linear_system(Input::AbstractRecord rec)
Definition: darcy_flow_mh.cc:951
FLOW123D_FORCE_LINK_IN_CHILD
#define FLOW123D_FORCE_LINK_IN_CHILD(x)
Definition: global_defs.h:157
LinSys_PETSC
Definition: linsys_PETSC.hh:43
LinSys::mat_zero_entries
virtual PetscErrorCode mat_zero_entries()
Definition: linsys.hh:264
THROW
#define THROW(whole_exception_expr)
Wrapper for throw. Saves the throwing point.
Definition: exceptions.hh:53
LinSys::SolveInfo::converged_reason
int converged_reason
Definition: linsys.hh:109
std::vector< double >
Mesh::n_edges
unsigned int n_edges() const
Definition: mesh.h:178
ElementAccessor< 3 >
DarcyMH::output_data
virtual void output_data() override
Write computed fields.
Definition: darcy_flow_mh.cc:749
DarcyMH::~DarcyMH
virtual ~DarcyMH() override
Definition: darcy_flow_mh.cc:1372
DarcyMH::EqData::total_flux
@ total_flux
Definition: darcy_flow_mh.hh:155
system.hh
arma::vec3
Definition: doxy_dummy_defs.hh:17
LinSys::set_rhs_changed
void set_rhs_changed()
Definition: linsys.hh:218
SchurComplement::make_complement_distribution
Distribution * make_complement_distribution()
get distribution of complement object if complement is defined
Definition: schur.cc:294
DHCellAccessor::dim
unsigned int dim() const
Return dimension of element appropriate to cell.
Definition: dh_cell_accessor.hh:101
DarcyMH::get_mh_mortar_selection
static const Input::Type::Selection & get_mh_mortar_selection()
Selection for enum MortarMethod.
Definition: darcy_flow_mh.cc:78
FieldAddPotential
Definition: field_add_potential.hh:38
LinSys::solve
virtual SolveInfo solve()=0
field_fe.hh
uint
unsigned int uint
Definition: mh_dofhandler.hh:101
Input::AbstractRecord::type
Input::Type::Record type() const
Definition: accessors.cc:273
linsys_PETSC.hh
Solver based on the original PETSc solver using MPIAIJ matrix and succesive Schur complement construc...
DarcyMH::max_n_it_
unsigned int max_n_it_
Definition: darcy_flow_mh.hh:356
dofs_range
void dofs_range(unsigned int n_dofs, unsigned int &min, unsigned int &max, unsigned int component)
Helper method fills range (min and max) of given component.
Definition: darcy_flow_mh.cc:1511
LinSys::set_negative_definite
void set_negative_definite(bool flag=true)
Definition: linsys.hh:588
index_types.hh
LinSys::set_positive_definite
void set_positive_definite(bool flag=true)
Definition: linsys.hh:576
Mesh::n_elements
virtual unsigned int n_elements() const
Returns count of boundary or bulk elements.
Definition: mesh.h:398
DarcyMH::allocate_mh_matrix
void allocate_mh_matrix()
Definition: darcy_flow_mh.cc:801
LinSys::set_matrix_changed
void set_matrix_changed()
Definition: linsys.hh:212
fe_p.hh
Definitions of basic Lagrangean finite elements with polynomial shape functions.
DarcyMH::prepare_new_time_step
void prepare_new_time_step()
Definition: darcy_flow_mh.cc:710
DarcyMH::assembly_mh_matrix
void assembly_mh_matrix(MultidimAssembly &assembler)
Definition: darcy_flow_mh.cc:777
DarcyMH::EqData
Definition: darcy_flow_mh.hh:146
LinSys::start_allocation
virtual void start_allocation()
Definition: linsys.hh:333
DarcyMH::EqData::none
@ none
Definition: darcy_flow_mh.hh:153
DarcyFlowMHOutput::get_input_type
static const Input::Type::Instance & get_input_type(FieldSet &eq_data, const std::string &equation_name)
Definition: darcy_flow_mh_output.cc:62
Input::Type::Record::size
unsigned int size() const
Returns number of keys in the Record.
Definition: type_record.hh:602
SchurComplement
Definition: schur.hh:64
TimeGovernor::is_end
bool is_end() const
Returns true if the actual time is greater than or equal to the end time.
Definition: time_governor.hh:588
SchurComplement::set_from_input
void set_from_input(const Input::Record in_rec) override
Definition: schur.cc:138
Input::Type::Default
Class Input::Type::Default specifies default value of keys of a Input::Type::Record.
Definition: type_record.hh:61
DHCellSide
Side accessor allows to iterate over sides of DOF handler cell.
Definition: dh_cell_accessor.hh:176
Input::Type::Record::derive_from
virtual Record & derive_from(Abstract &parent)
Method to derive new Record from an AbstractRecord parent.
Definition: type_record.cc:196
Distribution
Definition: distribution.hh:50
DarcyMH::output_object
DarcyFlowMHOutput * output_object
Definition: darcy_flow_mh.hh:343
LimitSide::left
@ left
LinSys::compute_residual
virtual double compute_residual()=0
DarcyMH::EqData::river
@ river
Definition: darcy_flow_mh.hh:157
DarcyFlowInterface::NoMortar
@ NoMortar
Definition: darcy_flow_interface.hh:31
accessors.hh
LinSys::set_tolerances
virtual void set_tolerances(double r_tol, double a_tol, unsigned int max_it)=0
Input::Record
Accessor to the data with type Type::Record.
Definition: accessors.hh:291
LinSys::rhs_set_value
void rhs_set_value(int row, double val)
Definition: linsys.hh:381
FieldFlag::equation_result
static constexpr Mask equation_result
Match result fields. These are never given by input or copy of input.
Definition: field_flag.hh:55
sys_profiler.hh
darcy_flow_mh_output.hh
Output class for darcy_flow_mh model.
DarcyMH::assembly_source_term
virtual void assembly_source_term()
Source term is implemented differently in LMH version.
Definition: darcy_flow_mh.cc:914
DarcyMH::DarcyFlowMHOutput
friend class DarcyFlowMHOutput
Definition: darcy_flow_mh.hh:369
LinSys::get_matrix
virtual const Mat * get_matrix()
Definition: linsys.hh:187
Mesh::get_bc_mesh
BCMesh * get_bc_mesh()
Create boundary mesh if doesn't exist and return it.
Definition: mesh.cc:1265
mpi.h
mixed_mesh_intersections.hh
schur.hh
Assembly explicit Schur complement for the given linear system. Provides method for resolution of the...
DarcyMH::modify_system
void modify_system()
Definition: darcy_flow_mh.cc:1486
DarcyMH::min_n_it_
unsigned int min_n_it_
Definition: darcy_flow_mh.hh:355
TimeGovernor
Basic time management functionality for unsteady (and steady) solvers (class Equation).
Definition: time_governor.hh:310
TimeGovernor::step
const TimeStep & step(int index=-1) const
Definition: time_governor.cc:753
DarcyMH::zero_time_term
virtual bool zero_time_term(bool time_global=false)
Definition: darcy_flow_mh.cc:617
DarcyMH::steady_diagonal
Vec steady_diagonal
Definition: darcy_flow_mh.hh:362
DHCellAccessor::elm
const ElementAccessor< 3 > elm() const
Return ElementAccessor to element of loc_ele_idx_.
Definition: dh_cell_accessor.hh:71
field_values.hh
Input::AbstractRecord
Accessor to the polymorphic input data of a type given by an AbstracRecord object.
Definition: accessors.hh:458
Input::Type::Default::obligatory
static Default obligatory()
The factory function to make an empty default value which is obligatory.
Definition: type_record.hh:110
SchurComplement::IsB
IS IsB
Definition: schur.hh:138
UnitSI
Class for representation SI units of Fields.
Definition: unit_si.hh:40
Mesh::region_db
const RegionDB & region_db() const
Definition: mesh.h:187
LinSys_BDDC
Definition: linsys_BDDC.hh:39
DarcyMH::print_matlab_matrix
void print_matlab_matrix(string matlab_file)
Print darcy flow matrix in matlab format into a file.
Definition: darcy_flow_mh.cc:1120
EquationBase::input_record_
Input::Record input_record_
Definition: equation.hh:220
RegionDB::get_region_set
RegionSet get_region_set(const std::string &set_name) const
Definition: region.cc:328
FieldCommon::field_descriptor_record_description
static const std::string field_descriptor_record_description(const string &record_name)
Definition: field_common.cc:73
Input::Type::Record::declare_key
Record & declare_key(const string &key, std::shared_ptr< TypeBase > type, const Default &default_value, const string &description, TypeBase::attribute_map key_attributes=TypeBase::attribute_map())
Declares a new key of the Record.
Definition: type_record.cc:503
MPI_INT
#define MPI_INT
Definition: mpi.h:160
DarcyMH::EqData::get_bc_type_selection
static const Input::Type::Selection & get_bc_type_selection()
Return a Selection corresponding to enum BC_Type.
Definition: darcy_flow_mh.cc:87
DarcyFlowMHOutput::get_input_type_specific
static const Input::Type::Instance & get_input_type_specific()
Definition: darcy_flow_mh_output.cc:69
DarcyMH::schur0
LinSys * schur0
Definition: darcy_flow_mh.hh:360
mesh.h
DHCellAccessor::n_dofs
unsigned int n_dofs() const
Return number of dofs on given cell.
Definition: dh_cell_accessor.hh:420
Input::Type::Selection
Template for classes storing finite set of named values.
Definition: type_selection.hh:65
std::map
Definition: doxy_dummy_defs.hh:11
DarcyFlowInterface::MortarMethod
MortarMethod
Type of experimental Mortar-like method for non-compatible 1d-2d interaction.
Definition: darcy_flow_interface.hh:30
DarcyFlowInterface::get_input_type
static Input::Type::Abstract & get_input_type()
Definition: darcy_flow_interface.hh:23
LinSys::start_add_assembly
virtual void start_add_assembly()
Definition: linsys.hh:341
DarcyMH::n_schur_compls
int n_schur_compls
Definition: darcy_flow_mh.hh:346
TimeGovernor::view
void view(const char *name="") const
Definition: time_governor.cc:769
FieldFlag::input_copy
static constexpr Mask input_copy
Definition: field_flag.hh:44
Input::Type::Record::close
Record & close() const
Close the Record for further declarations of keys.
Definition: type_record.cc:304
LinSys_BDDC::set_from_input
void set_from_input(const Input::Record in_rec) override
Definition: linsys_BDDC.cc:279
SchurComplement::loc_size_B
int loc_size_B
Definition: schur.hh:137
Input::Type
Definition: balance.hh:41
MixedMeshIntersections::element_intersections_
std::vector< std::vector< ILpair > > element_intersections_
Definition: mixed_mesh_intersections.hh:83
partitioning.hh
Input::Type::Record
Record type proxy class.
Definition: type_record.hh:182
DarcyMH::data_
std::shared_ptr< EqData > data_
Definition: darcy_flow_mh.hh:367
DarcyMH::new_diagonal
Vec new_diagonal
Definition: darcy_flow_mh.hh:364
DarcyMH::get_component_indices_vec
std::vector< int > get_component_indices_vec(unsigned int component) const
Get vector of all DOF indices of given component (0..side, 1..element, 2..edge)
Definition: darcy_flow_mh.cc:1525
LongIdx
int LongIdx
Define type that represents indices of large arrays (elements, nodes, dofs etc.)
Definition: index_types.hh:24
LinSys_PETSC::set_from_input
void set_from_input(const Input::Record in_rec) override
Definition: linsys_PETSC.cc:470
Mesh
Definition: mesh.h:98
OutputTime::get_input_type
static const Input::Type::Record & get_input_type()
The specification of output stream.
Definition: output_time.cc:38
Element::n_sides
unsigned int n_sides() const
Definition: elements.h:138
DarcyMH::nonlinear_iteration_
unsigned int nonlinear_iteration_
Definition: darcy_flow_mh.hh:357
Input::Type::Record::copy_keys
Record & copy_keys(const Record &other)
Copy keys from other record.
Definition: type_record.cc:216
FieldAlgorithmBase
Definition: field_algo_base.hh:112
Input::Type::Array
Class for declaration of inputs sequences.
Definition: type_base.hh:339
DarcyMH::tolerance_
double tolerance_
Definition: darcy_flow_mh.hh:354
OLD_ASSERT
#define OLD_ASSERT(...)
Definition: global_defs.h:108
DarcyMH::set_mesh_data_for_bddc
void set_mesh_data_for_bddc(LinSys_BDDC *bddc_ls)
Definition: darcy_flow_mh.cc:1193
DarcyMH::get_input_type
static const Input::Type::Record & get_input_type()
Definition: darcy_flow_mh.cc:131
DHCellAccessor
Cell accessor allow iterate over DOF handler cells.
Definition: dh_cell_accessor.hh:43
LinSys::finish_assembly
virtual void finish_assembly()=0
LinSys::get_rhs
virtual const Vec * get_rhs()
Definition: linsys.hh:203
MPI_Allreduce
#define MPI_Allreduce(sendbuf, recvbuf, count, datatype, op, comm)
Definition: mpi.h:612
Input::Array
Accessor to input data conforming to declared Array.
Definition: accessors.hh:566
DarcyMH::assembly_linear_system
virtual void assembly_linear_system()
Definition: darcy_flow_mh.cc:1064
DarcyMH::DarcyMH
DarcyMH(Mesh &mesh, const Input::Record in_rec, TimeGovernor *tm=nullptr)
CREATE AND FILL GLOBAL MH MATRIX OF THE WATER MODEL.
Definition: darcy_flow_mh.cc:319
WarningOut
#define WarningOut()
Macro defining 'warning' record of log.
Definition: logger.hh:278
ElementAccessor::region
Region region() const
Definition: accessors.hh:201
EquationBase::record_template
static Input::Type::Record & record_template()
Template Record with common keys for derived equations.
Definition: equation.cc:35
LinSys::get_solution_precision
virtual double get_solution_precision()=0
MixedPtr
Definition: mixed.hh:247
SchurComplement
SchurComplement SchurComplement
Definition: linsys.hh:92
TimeGovernor::is_default
bool is_default()
Definition: time_governor.hh:381
darcy_flow_mh.hh
mixed-hybrid model of linear Darcy flow, possibly unsteady.
LinSys::set_solution
void set_solution(Vec sol_vec)
Definition: linsys.hh:290
ASSERT_LT_DBG
#define ASSERT_LT_DBG(a, b)
Definition of comparative assert macro (Less Than) only for debug mode.
Definition: asserts.hh:300
DarcyMH::initialize_specific
virtual void initialize_specific()
Definition: darcy_flow_mh.cc:515
std::vector::data
T data
Definition: doxy_dummy_defs.hh:7
assembly_mh.hh
LinSys::get_input_type
static Input::Type::Abstract & get_input_type()
Definition: linsys.cc:29
ElementAccessor::idx
unsigned int idx() const
Return local idx of element in boundary / bulk part of element vector.
Definition: accessors.hh:223
FilePath::output_file
@ output_file
Definition: file_path.hh:69
EquationBase::eq_fieldset_
FieldSet * eq_fieldset_
Definition: equation.hh:227
TimeGovernor::is_changed_dt
bool is_changed_dt() const
Definition: time_governor.hh:522
field_divide.hh
DarcyFlowInterface::MortarP0
@ MortarP0
Definition: darcy_flow_interface.hh:32
balance.hh
local_to_global_map.hh
DarcyMH::data_changed_
bool data_changed_
Definition: darcy_flow_mh.hh:351
TimeStep::index
unsigned int index() const
Definition: time_governor.hh:159
DarcyMH::EqData::seepage
@ seepage
Definition: darcy_flow_mh.hh:156
IntersectionLocalBase::bulk_ele_idx
unsigned int bulk_ele_idx() const
Returns index of bulk element.
Definition: intersection_local.hh:77
Mesh::mixed_intersections
MixedMeshIntersections & mixed_intersections()
Definition: mesh.cc:800
DebugOut
#define DebugOut()
Macro defining 'debug' record of log.
Definition: logger.hh:284
Input::Type::Selection::add_value
Selection & add_value(const int value, const std::string &key, const std::string &description="", TypeBase::attribute_map attributes=TypeBase::attribute_map())
Adds one new value with name given by key to the Selection.
Definition: type_selection.cc:50
TimeGovernor::next_time
void next_time()
Proceed to the next time according to current estimated time step.
Definition: time_governor.cc:667
TimeStep::length
double length() const
Definition: time_governor.hh:160
LinSys::get_solution_array
double * get_solution_array()
Definition: linsys.hh:325
Input::Type::Default::optional
static Default optional()
The factory function to make an empty default value which is optional.
Definition: type_record.hh:124
DarcyMH::read_initial_condition
virtual void read_initial_condition()
Definition: darcy_flow_mh.cc:1427
BCMesh::n_elements
unsigned int n_elements() const override
Returns count of boundary elements of parent mesh.
Definition: bc_mesh.cc:53
RegionIdx::bulk_idx
unsigned int bulk_idx() const
Returns index of the region in the bulk set.
Definition: region.hh:91
START_TIMER
#define START_TIMER(tag)
Starts a timer with specified tag.
Definition: sys_profiler.hh:115
FESystem
Compound finite element on dim dimensional simplex.
Definition: fe_system.hh:101
DarcyMH::registrar
static const int registrar
Registrar of class to factory.
Definition: darcy_flow_mh.hh:375
DarcyMH::initialize
void initialize() override
Definition: darcy_flow_mh.cc:412
LinSys_PETSC::get_input_type
static const Input::Type::Record & get_input_type()
Definition: linsys_PETSC.cc:32
DarcyMH::zero_time_step
void zero_time_step() override
Definition: darcy_flow_mh.cc:518
field.hh
DarcyFlowInterface
Definition: darcy_flow_interface.hh:15
Balance::get_input_type
static const Input::Type::Record & get_input_type()
Main balance input record type.
Definition: balance.cc:50
IntersectionResult::none
@ none
ElementAccessor::measure
double measure() const
Computes the measure of the element.
Definition: accessors_impl.hh:67
END_TIMER
#define END_TIMER(tag)
Ends a timer with specified tag.
Definition: sys_profiler.hh:149
TimeGovernor::last_dt
double last_dt() const
Definition: time_governor.hh:541
FieldValue
Definition: field_values.hh:645
range_wrapper.hh
Implementation of range helper class.
ElementAccessor::centre
arma::vec::fixed< spacedim > centre() const
Computes the barycenter.
Definition: accessors_impl.hh:89
IntersectionLocalBase
Common base for intersection object.
Definition: intersection_local.hh:48
Distribution::begin
unsigned int begin(int proc) const
get starting local index
Definition: distribution.hh:109
DarcyMH::EqData::EqData
EqData()
Creation of all fields.
Definition: darcy_flow_mh.cc:186
MessageOut
#define MessageOut()
Macro defining 'message' record of log.
Definition: logger.hh:275
LinSys::mat_set_values
virtual void mat_set_values(int nrow, int *rows, int ncol, int *cols, double *vals)=0
intersection_local.hh
Classes with algorithms for computation of intersections of meshes.