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electro_physio.cpp
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1#include <stdlib.h>
2#include <BasicFiniteElements.hpp>
3#include <EP_Operators.hpp>
4
5using namespace MoFEM;
6using namespace ElecPhys;
7
8static char help[] = "...\n\n";
9
10const double init_u = 0;
11const double init_v = 0;
12const double init_w = 1;
13const double init_s = 0.02155;
14
15struct ElectroPhysioProblem {
16public:
17 ElectroPhysioProblem(MoFEM::Core &core, const int order)
18 : m_field(core), order(order)
19 , cOmm(m_field.get_comm())
20 , rAnk(m_field.get_comm_rank())
21 {
22 vol_ele_slow_rhs = boost::shared_ptr<VolEle>(new VolEle(m_field));
23 natural_bdry_ele_slow_rhs =
24 boost::shared_ptr<FaceEle>(new FaceEle(m_field));
25 vol_ele_stiff_rhs = boost::shared_ptr<VolEle>(new VolEle(m_field));
26 vol_ele_stiff_lhs = boost::shared_ptr<VolEle>(new VolEle(m_field));
27 post_proc = boost::shared_ptr<PostProcVolumeOnRefinedMesh>(
28 new PostProcVolumeOnRefinedMesh(m_field));
29
30 data_u = boost::shared_ptr<PreviousData>(new PreviousData());
31 data_v = boost::shared_ptr<PreviousData>(new PreviousData());
32 data_w = boost::shared_ptr<PreviousData>(new PreviousData());
33 data_s = boost::shared_ptr<PreviousData>(new PreviousData());
34
35 flux_u_ptr =
36 boost::shared_ptr<MatrixDouble>(data_u, &data_u->flux_values);
37 divs_u_ptr =
38 boost::shared_ptr<VectorDouble>(data_u, &data_u->flux_divs);
39 values_u_ptr =
40 boost::shared_ptr<VectorDouble>(data_u, &data_u->mass_values);
41 dots_u_ptr =
42 boost::shared_ptr<VectorDouble>(data_u, &data_u->mass_dots);
43
44 flux_v_ptr =
45 boost::shared_ptr<MatrixDouble>(data_v, &data_v->flux_values);
46 divs_v_ptr =
47 boost::shared_ptr<VectorDouble>(data_v, &data_v->flux_divs);
48 values_v_ptr =
49 boost::shared_ptr<VectorDouble>(data_v, &data_v->mass_values);
50 dots_v_ptr =
51 boost::shared_ptr<VectorDouble>(data_v, &data_v->mass_dots);
52
53
54 flux_w_ptr =
55 boost::shared_ptr<MatrixDouble>(data_w, &data_w->flux_values);
56 divs_w_ptr =
57 boost::shared_ptr<VectorDouble>(data_w, &data_w->flux_divs);
58 values_w_ptr =
59 boost::shared_ptr<VectorDouble>(data_w, &data_w->mass_values);
60 dots_w_ptr =
61 boost::shared_ptr<VectorDouble>(data_w, &data_w->mass_dots);
62
63 flux_s_ptr =
64 boost::shared_ptr<MatrixDouble>(data_s, &data_s->flux_values);
65 divs_s_ptr =
66 boost::shared_ptr<VectorDouble>(data_s, &data_s->flux_divs);
67 values_s_ptr =
68 boost::shared_ptr<VectorDouble>(data_s, &data_s->mass_values);
69 dots_s_ptr =
70 boost::shared_ptr<VectorDouble>(data_s, &data_s->mass_dots);
71 }
72 MoFEMErrorCode run_analysis();
73
74private:
75 MoFEMErrorCode setup_system();
76 MoFEMErrorCode add_fe();
77 MoFEMErrorCode extract_bd_ents(std::string ESSENTIAL, std::string NATURAL);
78
79 MoFEMErrorCode extract_initial_ents(int block_id, Range &surface);
80
81 MoFEMErrorCode update_slow_rhs(std::string mass_field,
82 boost::shared_ptr<VectorDouble> &value_ptr);
83 MoFEMErrorCode push_slow_rhs(boost::shared_ptr<PreviousData> &data_u,
84 boost::shared_ptr<PreviousData> &data_v,
85 boost::shared_ptr<PreviousData> &data_w,
86 boost::shared_ptr<PreviousData> &data_s);
87
88 MoFEMErrorCode update_stiff_rhs(std::string mass_field,
89 boost::shared_ptr<VectorDouble> &mass_ptr,
90 boost::shared_ptr<VectorDouble> &mass_dot_ptr);
91 MoFEMErrorCode push_stiff_rhs(boost::shared_ptr<PreviousData> &data_u,
92 boost::shared_ptr<PreviousData> &data_v,
93 boost::shared_ptr<PreviousData> &data_w,
94 boost::shared_ptr<PreviousData> &data_s);
95 MoFEMErrorCode update_stiff_lhs(std::string mass_fiedl,
96 boost::shared_ptr<VectorDouble> &mass_ptr);
97 MoFEMErrorCode push_stiff_lhs();
98
99 MoFEMErrorCode set_integration_rule();
100 MoFEMErrorCode apply_IC(std::string mass_field, Range &surface,
101 boost::shared_ptr<VolEle> &initial_ele,
102 double init_val);
103 MoFEMErrorCode apply_BC();
104 MoFEMErrorCode loop_fe();
105 MoFEMErrorCode post_proc_fields(std::string mass_field);
106 MoFEMErrorCode output_result();
107 MoFEMErrorCode solve();
108
109 MoFEM::Interface &m_field;
110 Simple *simple_interface;
111 SmartPetscObj<DM> dm;
112 SmartPetscObj<TS> ts;
113
114 Range essential_bdry_ents;
115 Range natural_bdry_ents;
116
117 Range inner_surface_u; // nb_species times
118 Range inner_surface_v;
119 Range inner_surface_w;
120 Range inner_surface_s;
121
122 MPI_Comm cOmm;
123 const int rAnk;
124
125 int order;
126
127 boost::shared_ptr<VolEle> vol_ele_slow_rhs;
128 boost::shared_ptr<VolEle> vol_ele_stiff_rhs;
129 boost::shared_ptr<VolEle> vol_ele_stiff_lhs;
130 boost::shared_ptr<FaceEle> natural_bdry_ele_slow_rhs;
131 boost::shared_ptr<PostProcVolumeOnRefinedMesh> post_proc;
132 boost::shared_ptr<Monitor> monitor_ptr;
133
134 boost::shared_ptr<PreviousData> data_u; // nb_species times
135 boost::shared_ptr<PreviousData> data_v;
136 boost::shared_ptr<PreviousData> data_w;
137 boost::shared_ptr<PreviousData> data_s;
138
139 boost::shared_ptr<MatrixDouble> flux_u_ptr; // nb_species times
140 boost::shared_ptr<MatrixDouble> flux_v_ptr;
141 boost::shared_ptr<MatrixDouble> flux_w_ptr;
142 boost::shared_ptr<MatrixDouble> flux_s_ptr;
143
144 boost::shared_ptr<VectorDouble> divs_u_ptr; // nb_species times
145 boost::shared_ptr<VectorDouble> divs_v_ptr;
146 boost::shared_ptr<VectorDouble> divs_w_ptr;
147 boost::shared_ptr<VectorDouble> divs_s_ptr;
148
149 boost::shared_ptr<VectorDouble> values_u_ptr; // nb_species times
150 boost::shared_ptr<VectorDouble> values_v_ptr;
151 boost::shared_ptr<VectorDouble> values_w_ptr;
152 boost::shared_ptr<VectorDouble> values_s_ptr;
153
154 boost::shared_ptr<VectorDouble> dots_u_ptr;
155 boost::shared_ptr<VectorDouble> dots_v_ptr;
156 boost::shared_ptr<VectorDouble> dots_w_ptr;
157 boost::shared_ptr<VectorDouble> dots_s_ptr;
158
159 boost::shared_ptr<ForcesAndSourcesCore> null;
160};
161
162MoFEMErrorCode ElectroPhysioProblem::setup_system() {
163 MoFEMFunctionBegin;
164 CHKERR m_field.getInterface(simple_interface);
165 CHKERR simple_interface->getOptions();
166 CHKERR simple_interface->loadFile();
167 MoFEMFunctionReturn(0);
168}
169
170MoFEMErrorCode ElectroPhysioProblem::add_fe() {
171 MoFEMFunctionBegin;
172 CHKERR simple_interface->addDomainField("u", L2,
173 AINSWORTH_LEGENDRE_BASE, 1);
174
175 CHKERR simple_interface->addDomainField("f", HDIV, DEMKOWICZ_JACOBI_BASE,
176 1);
177
178 CHKERR simple_interface->addBoundaryField("f", HDIV, DEMKOWICZ_JACOBI_BASE,
179 1);
180
181 CHKERR simple_interface->addDataField("U", L2, AINSWORTH_LEGENDRE_BASE, 1);
182 CHKERR simple_interface->addDataField("V", L2, AINSWORTH_LEGENDRE_BASE, 1);
183 CHKERR simple_interface->addDataField("W", L2, AINSWORTH_LEGENDRE_BASE, 1);
184 CHKERR simple_interface->addDataField("S", L2, AINSWORTH_LEGENDRE_BASE, 1);
185
186 CHKERR simple_interface->setFieldOrder("u", order - 1);
187 CHKERR simple_interface->setFieldOrder("f", order);
188
189 CHKERR simple_interface->setFieldOrder("U", order - 1);
190 CHKERR simple_interface->setFieldOrder("V", order - 1);
191 CHKERR simple_interface->setFieldOrder("W", order - 1);
192 CHKERR simple_interface->setFieldOrder("S", order - 1);
193
194 MoFEMFunctionReturn(0);
195}
196MoFEMErrorCode ElectroPhysioProblem::extract_bd_ents(std::string essential,
197 std::string natural) {
198 MoFEMFunctionBegin;
199 for (_IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_(m_field, BLOCKSET, it)) {
200 string name = it->getName();
201 if (name.compare(0, 14, natural) == 0) {
202
203 CHKERR it->getMeshsetIdEntitiesByDimension(m_field.get_moab(), 2,
204 natural_bdry_ents, true);
205 } else if (name.compare(0, 14, essential) == 0) {
206 CHKERR it->getMeshsetIdEntitiesByDimension(m_field.get_moab(), 2,
207 essential_bdry_ents, true);
208 }
209 }
210 MoFEMFunctionReturn(0);
211}
212MoFEMErrorCode ElectroPhysioProblem::extract_initial_ents(int block_id,
213 Range &surface) {
214 MoFEMFunctionBegin;
215 if (m_field.getInterface<MeshsetsManager>()->checkMeshset(block_id,
216 BLOCKSET)) {
217 CHKERR m_field.getInterface<MeshsetsManager>()->getEntitiesByDimension(
218 block_id, BLOCKSET, 3, surface, true);
219 }
220 MoFEMFunctionReturn(0);
221}
222
223MoFEMErrorCode ElectroPhysioProblem::update_slow_rhs(
224 std::string mass_field, boost::shared_ptr<VectorDouble> &mass_ptr) {
225 MoFEMFunctionBegin;
226 vol_ele_slow_rhs->getOpPtrVector().push_back(
227 new OpCalculateScalarFieldValues(mass_field, mass_ptr));
228 MoFEMFunctionReturn(0);
229}
230
231MoFEMErrorCode
232ElectroPhysioProblem::push_slow_rhs(boost::shared_ptr<PreviousData> &data_u,
233 boost::shared_ptr<PreviousData> &data_v,
234 boost::shared_ptr<PreviousData> &data_w,
235 boost::shared_ptr<PreviousData> &data_s) {
236 MoFEMFunctionBegin;
237
238 vol_ele_slow_rhs->getOpPtrVector().push_back(
239 new OpAssembleSlowRhsV(data_u, data_v, data_w, data_s));
240
241 // natural_bdry_ele_slow_rhs->getOpPtrVector().push_back(
242 // new OpAssembleNaturalBCRhsTau(natural_bdry_ents));
243
244 natural_bdry_ele_slow_rhs->getOpPtrVector().push_back(
245 new OpEssentialBC(essential_bdry_ents));
246 MoFEMFunctionReturn(0);
247}
248
249MoFEMErrorCode ElectroPhysioProblem::update_stiff_rhs(
250 std::string mass_field,
251 boost::shared_ptr<VectorDouble> &mass_ptr,
252 boost::shared_ptr<VectorDouble> &mass_dot_ptr) {
253
254 MoFEMFunctionBegin;
255
256 vol_ele_stiff_rhs->getOpPtrVector().push_back(
257 new OpCalculateScalarFieldValues(mass_field, mass_ptr));
258 vol_ele_stiff_rhs->getOpPtrVector().push_back(
259 new OpCalculateScalarValuesDot(mass_field, mass_dot_ptr));
260 MoFEMFunctionReturn(0);
261}
262
263MoFEMErrorCode
264ElectroPhysioProblem::push_stiff_rhs(boost::shared_ptr<PreviousData> &data_u,
265 boost::shared_ptr<PreviousData> &data_v,
266 boost::shared_ptr<PreviousData> &data_w,
267 boost::shared_ptr<PreviousData> &data_s) {
268 MoFEMFunctionBegin;
269 vol_ele_stiff_rhs->getOpPtrVector().push_back(
270 new OpAssembleStiffRhsTau<3>(data_u, data_v, data_w, data_s));
271
272 vol_ele_stiff_rhs->getOpPtrVector().push_back(
273 new OpAssembleStiffRhsV<3>(data_u, data_v, data_w, data_s));
274 MoFEMFunctionReturn(0);
275}
276
277MoFEMErrorCode ElectroPhysioProblem::update_stiff_lhs(
278 std::string mass_field,
279 boost::shared_ptr<VectorDouble> &mass_ptr) {
280 MoFEMFunctionBegin;
281 vol_ele_stiff_lhs->getOpPtrVector().push_back(
282 new OpCalculateScalarFieldValues(mass_field, mass_ptr));
283
284
285 MoFEMFunctionReturn(0);
286}
287
288MoFEMErrorCode
289ElectroPhysioProblem::push_stiff_lhs() {
290 MoFEMFunctionBegin;
291 vol_ele_stiff_lhs->getOpPtrVector().push_back(
292 new OpAssembleLhsTauTau<3>());
293
294 vol_ele_stiff_lhs->getOpPtrVector().push_back(
295 new OpAssembleLhsVV());
296
297 vol_ele_stiff_lhs->getOpPtrVector().push_back(
298 new OpAssembleLhsTauV<3>());
299
300 vol_ele_stiff_lhs->getOpPtrVector().push_back(
301 new OpAssembleLhsVTau());
302
303 vol_ele_stiff_lhs->getOpPtrVector().push_back(
304 new OpDamp_dofs_to_field_data("U"));
305
306 vol_ele_stiff_lhs->getOpPtrVector().push_back(
307 new OpDamp_dofs_to_field_data("V"));
308
309 vol_ele_stiff_lhs->getOpPtrVector().push_back(
310 new OpDamp_dofs_to_field_data("W"));
311
312 vol_ele_stiff_lhs->getOpPtrVector().push_back(
313 new OpDamp_dofs_to_field_data("S"));
314 MoFEMFunctionReturn(0);
315}
316
317MoFEMErrorCode ElectroPhysioProblem::set_integration_rule() {
318 MoFEMFunctionBegin;
319 auto vol_rule = [](int, int, int p) -> int { return 2 * p + 1; };
320 vol_ele_slow_rhs->getRuleHook = vol_rule;
321 natural_bdry_ele_slow_rhs->getRuleHook = vol_rule;
322
323 vol_ele_stiff_rhs->getRuleHook = vol_rule;
324
325 vol_ele_stiff_lhs->getRuleHook = vol_rule;
326 MoFEMFunctionReturn(0);
327}
328
329MoFEMErrorCode
330ElectroPhysioProblem::apply_IC(std::string mass_field, Range &surface,
331 boost::shared_ptr<VolEle> &initial_ele, double init_val) {
332 MoFEMFunctionBegin;
333 initial_ele->getOpPtrVector().push_back(
334 new OpInitialMass(mass_field, surface, init_val));
335 MoFEMFunctionReturn(0);
336}
337
338MoFEMErrorCode ElectroPhysioProblem::apply_BC() {
339 MoFEMFunctionBegin;
340 CHKERR m_field.getInterface<ProblemsManager>()->removeDofsOnEntities(
341 "SimpleProblem", "f", essential_bdry_ents);
342
343 MoFEMFunctionReturn(0);
344}
345MoFEMErrorCode ElectroPhysioProblem::loop_fe() {
346 MoFEMFunctionBegin;
347 CHKERR TSSetType(ts, TSARKIMEX);
348 CHKERR TSARKIMEXSetType(ts, TSARKIMEXA2);
349
350 CHKERR DMMoFEMTSSetIJacobian(dm, simple_interface->getDomainFEName(),
351 vol_ele_stiff_lhs, null, null);
352
353 CHKERR DMMoFEMTSSetIFunction(dm, simple_interface->getDomainFEName(),
354 vol_ele_stiff_rhs, null, null);
355
356 CHKERR DMMoFEMTSSetRHSFunction(dm, simple_interface->getDomainFEName(),
357 vol_ele_slow_rhs, null, null);
358 CHKERR DMMoFEMTSSetRHSFunction(dm, simple_interface->getBoundaryFEName(),
359 natural_bdry_ele_slow_rhs, null, null);
360 MoFEMFunctionReturn(0);
361}
362
363MoFEMErrorCode ElectroPhysioProblem::post_proc_fields(std::string mass_field) {
364 MoFEMFunctionBegin;
365 post_proc->addFieldValuesPostProc(mass_field);
366 MoFEMFunctionReturn(0);
367}
368
369MoFEMErrorCode ElectroPhysioProblem::output_result() {
370 MoFEMFunctionBegin;
371 CHKERR DMMoFEMTSSetMonitor(dm, ts, simple_interface->getDomainFEName(),
372 monitor_ptr, null, null);
373 MoFEMFunctionReturn(0);
374}
375
376MoFEMErrorCode ElectroPhysioProblem::solve() {
377 MoFEMFunctionBegin;
378 // Create solution vector
379 SmartPetscObj<Vec> X;
380 CHKERR DMCreateGlobalVector_MoFEM(dm, X);
381 CHKERR DMoFEMMeshToLocalVector(dm, X, INSERT_VALUES, SCATTER_FORWARD);
382 // Solve problem
383 double ftime = 1;
384 CHKERR TSSetDM(ts, dm);
385 CHKERR TSSetDuration(ts, PETSC_DEFAULT, ftime);
386 CHKERR TSSetSolution(ts, X);
387 CHKERR TSSetFromOptions(ts);
388 CHKERR TSSolve(ts, X);
389 MoFEMFunctionReturn(0);
390}
391
392MoFEMErrorCode ElectroPhysioProblem::run_analysis() {
393 MoFEMFunctionBegin;
394
395 CHKERR setup_system(); // only once
396 CHKERR add_fe(); // nb_species times
397
398
399 CHKERR simple_interface->setUp();
400
401
402
403
404 CHKERR update_slow_rhs("U", values_u_ptr);
405 CHKERR update_slow_rhs("V", values_v_ptr);
406 CHKERR update_slow_rhs("W", values_w_ptr);
407 CHKERR update_slow_rhs("S", values_s_ptr);
408
409 CHKERR push_slow_rhs(data_u, data_v, data_w, data_s);
410
411 // natural_bdry_ele_slow_rhs->getOpPtrVector().push_back(
412 // new OpSetContrariantPiolaTransformOnEdge());
413
414 CHKERR extract_bd_ents("ESSENTIAL", "NATURAL"); // nb_species times
415
416
417
418
419
420
421 CHKERR update_stiff_rhs("U", values_u_ptr, dots_u_ptr);
422 CHKERR update_stiff_rhs("V", values_v_ptr, dots_v_ptr);
423 CHKERR update_stiff_rhs("W", values_w_ptr, dots_w_ptr);
424 CHKERR update_stiff_rhs("S", values_s_ptr, dots_s_ptr);
425
426 vol_ele_stiff_rhs->getOpPtrVector().push_back(
427 new OpCalculateHVecVectorField<3>("f", flux_u_ptr));
428 vol_ele_stiff_rhs->getOpPtrVector().push_back(
429 new OpCalculateHVecVectorField<3>("f", flux_v_ptr));
430 vol_ele_stiff_rhs->getOpPtrVector().push_back(
431 new OpCalculateHVecVectorField<3>("f", flux_w_ptr));
432 vol_ele_stiff_rhs->getOpPtrVector().push_back(
433 new OpCalculateHVecVectorField<3>("f", flux_s_ptr));
434
435 vol_ele_stiff_rhs->getOpPtrVector().push_back(
436 new OpCalculateHdivVectorDivergence<3, 3>("f", divs_u_ptr));
437 vol_ele_stiff_rhs->getOpPtrVector().push_back(
438 new OpCalculateHdivVectorDivergence<3, 3>("f", divs_v_ptr));
439 vol_ele_stiff_rhs->getOpPtrVector().push_back(
440 new OpCalculateHdivVectorDivergence<3, 3>("f", divs_w_ptr));
441 vol_ele_stiff_rhs->getOpPtrVector().push_back(
442 new OpCalculateHdivVectorDivergence<3, 3>("f", divs_s_ptr));
443
444 CHKERR push_stiff_rhs(data_u, data_v, data_w, data_s);
445
446
447
448
449
450 CHKERR update_stiff_lhs("U", values_u_ptr);
451 CHKERR update_stiff_lhs("V", values_v_ptr);
452 CHKERR update_stiff_lhs("W", values_w_ptr);
453 CHKERR update_stiff_lhs("S", values_s_ptr);
454
455 vol_ele_stiff_lhs->getOpPtrVector().push_back(
456 new OpCalculateHVecVectorField<3>("f", flux_u_ptr));
457 vol_ele_stiff_lhs->getOpPtrVector().push_back(
458 new OpCalculateHVecVectorField<3>("f", flux_v_ptr));
459 vol_ele_stiff_lhs->getOpPtrVector().push_back(
460 new OpCalculateHVecVectorField<3>("f", flux_w_ptr));
461 vol_ele_stiff_lhs->getOpPtrVector().push_back(
462 new OpCalculateHVecVectorField<3>("f", flux_s_ptr));
463
464
465
466 CHKERR push_stiff_lhs();
467
468
469
470
471 CHKERR set_integration_rule();
472 dm = simple_interface->getDM();
473 ts = createTS(m_field.get_comm());
474
475 boost::shared_ptr<VolEle> initial_mass_ele(new VolEle(m_field));
476
477 CHKERR apply_IC("u", inner_surface_u, initial_mass_ele, init_u);
478 CHKERR apply_IC("U", inner_surface_u, initial_mass_ele, init_u); // nb_species times
479 CHKERR apply_IC("V", inner_surface_u, initial_mass_ele, init_v);
480 CHKERR apply_IC("W", inner_surface_u, initial_mass_ele, init_w);
481 CHKERR apply_IC("S", inner_surface_u, initial_mass_ele, init_s);
482
483
484
485 CHKERR DMoFEMLoopFiniteElements(
486 dm, simple_interface->getDomainFEName(), initial_mass_ele);
487
488 CHKERR apply_BC();
489
490
491 CHKERR loop_fe(); // only once
492 post_proc->generateReferenceElementMesh(); // only once
493
494 CHKERR post_proc_fields("U");
495 CHKERR post_proc_fields("V");
496 CHKERR post_proc_fields("W");
497 CHKERR post_proc_fields("S");
498
499 monitor_ptr = boost::shared_ptr<Monitor>(
500 new Monitor(cOmm, rAnk, dm, post_proc));
501 CHKERR output_result();
502 CHKERR solve();
503 MoFEMFunctionReturn(0);
504 }
505
506int main(int argc, char *argv[]) {
507 const char param_file[] = "param_file.petsc";
508 MoFEM::Core::Initialize(&argc, &argv, param_file, help);
509 // for(int nsteps = 0; nsteps < 20; ++nsteps){
510 // if(((nsteps + 0) % 4) == 0){
511 // cout << "U" << nsteps << endl;
512 // } else if (((nsteps + 3) % 4) == 0) {
513 // cout << "V" << nsteps << endl;
514 // } else if (((nsteps + 2) % 4) == 0) {
515 // cout << "W" << nsteps << endl;
516 // } else if (((nsteps + 1) % 4) == 0) {
517 // cout << "S" << nsteps << endl;
518 // }
519 // }
520 try {
521 moab::Core mb_instance;
522 moab::Interface &moab = mb_instance;
523 MoFEM::Core core(moab);
524 DMType dm_name = "DMMOFEM";
525 CHKERR DMRegister_MoFEM(dm_name);
526
527 int order = 1;
528 CHKERR PetscOptionsGetInt(PETSC_NULL, "", "-order", &order, PETSC_NULL);
529 ElectroPhysioProblem electro_physio_problem(core, order + 1);
530 CHKERR electro_physio_problem.run_analysis();
531 }
532 CATCH_ERRORS;
533 MoFEM::Core::Finalize();
534 return 0;
535}
p
static Index< 'p', 3 > p
Definition: BasicFeTools.hpp:90
param_file
std::string param_file
Definition: DefaultParams.hpp:113
EP_Operators.hpp
main
int main()
Definition: adol-c_atom.cpp:46
FaceEle
MoFEM::FaceElementForcesAndSourcesCore FaceEle
Definition: boundary_marker.cpp:16
CATCH_ERRORS
#define CATCH_ERRORS
Catch errors.
Definition: definitions.h:372
AINSWORTH_LEGENDRE_BASE
@ AINSWORTH_LEGENDRE_BASE
Ainsworth Cole (Legendre) approx. base .
Definition: definitions.h:60
DEMKOWICZ_JACOBI_BASE
@ DEMKOWICZ_JACOBI_BASE
Definition: definitions.h:66
L2
@ L2
field with C-1 continuity
Definition: definitions.h:88
HDIV
@ HDIV
field with continuous normal traction
Definition: definitions.h:87
MoFEMFunctionBegin
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:346
BLOCKSET
@ BLOCKSET
Definition: definitions.h:148
MoFEMFunctionReturn
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:416
CHKERR
#define CHKERR
Inline error check.
Definition: definitions.h:535
init_w
const double init_w
Definition: electro_physio.cpp:12
help
static char help[]
Definition: electro_physio.cpp:8
init_v
const double init_v
Definition: electro_physio.cpp:11
init_u
const double init_u
Definition: electro_physio.cpp:10
init_s
const double init_s
Definition: electro_physio.cpp:13
order
int order
Definition: fluid_structure_eigenproblem.cpp:84
MoFEM::DMMoFEMTSSetIFunction
PetscErrorCode DMMoFEMTSSetIFunction(DM dm, const char fe_name[], MoFEM::FEMethod *method, MoFEM::BasicMethod *pre_only, MoFEM::BasicMethod *post_only)
set TS implicit function evaluation function
Definition: DMMoFEM.cpp:786
MoFEM::DMoFEMMeshToLocalVector
PetscErrorCode DMoFEMMeshToLocalVector(DM dm, Vec l, InsertMode mode, ScatterMode scatter_mode)
set local (or ghosted) vector values on mesh for partition only
Definition: DMMoFEM.cpp:509
MoFEM::DMRegister_MoFEM
PetscErrorCode DMRegister_MoFEM(const char sname[])
Register MoFEM problem.
Definition: DMMoFEM.cpp:47
MoFEM::DMoFEMLoopFiniteElements
PetscErrorCode DMoFEMLoopFiniteElements(DM dm, const char fe_name[], MoFEM::FEMethod *method, CacheTupleWeakPtr cache_ptr=CacheTupleSharedPtr())
Executes FEMethod for finite elements in DM.
Definition: DMMoFEM.cpp:572
MoFEM::DMMoFEMTSSetIJacobian
PetscErrorCode DMMoFEMTSSetIJacobian(DM dm, const std::string fe_name, boost::shared_ptr< MoFEM::FEMethod > method, boost::shared_ptr< MoFEM::BasicMethod > pre_only, boost::shared_ptr< MoFEM::BasicMethod > post_only)
set TS Jacobian evaluation function
Definition: DMMoFEM.cpp:839
MoFEM::DMCreateGlobalVector_MoFEM
PetscErrorCode DMCreateGlobalVector_MoFEM(DM dm, Vec *g)
DMShellSetCreateGlobalVector.
Definition: DMMoFEM.cpp:1153
MoFEM::MeshsetsManager::checkMeshset
bool checkMeshset(const int ms_id, const CubitBCType cubit_bc_type) const
check for CUBIT Id and CUBIT type
Definition: MeshsetsManager.cpp:271
_IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_
#define _IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_(MESHSET_MANAGER, CUBITBCTYPE, IT)
Iterator that loops over a specific Cubit MeshSet having a particular BC meshset in a moFEM field.
Definition: MeshsetsManager.hpp:71
MoFEM::Exceptions::MoFEMErrorCode
PetscErrorCode MoFEMErrorCode
MoFEM/PETSc error code.
Definition: Exceptions.hpp:56
MoFEM
implementation of Data Operators for Forces and Sources
Definition: Common.hpp:10
MoFEM::DMMoFEMTSSetMonitor
PetscErrorCode DMMoFEMTSSetMonitor(DM dm, TS ts, const std::string fe_name, boost::shared_ptr< MoFEM::FEMethod > method, boost::shared_ptr< MoFEM::BasicMethod > pre_only, boost::shared_ptr< MoFEM::BasicMethod > post_only)
Set Monitor To TS solver.
Definition: DMMoFEM.cpp:1042
MoFEM::DMMoFEMTSSetRHSFunction
PetscErrorCode DMMoFEMTSSetRHSFunction(DM dm, const std::string fe_name, boost::shared_ptr< MoFEM::FEMethod > method, boost::shared_ptr< MoFEM::BasicMethod > pre_only, boost::shared_ptr< MoFEM::BasicMethod > post_only)
set TS the right hand side function
Definition: DMMoFEM.cpp:868
MoFEM::PetscOptionsGetInt
PetscErrorCode PetscOptionsGetInt(PetscOptions *, const char pre[], const char name[], PetscInt *ivalue, PetscBool *set)
Definition: DeprecatedPetsc.hpp:142
MoFEM::OpCalculateScalarValuesDot
OpCalculateScalarFieldValuesDot OpCalculateScalarValuesDot
Definition: UserDataOperators.hpp:281
MoFEM::createTS
auto createTS(MPI_Comm comm)
Definition: PetscSmartObj.hpp:245
ElecPhys::OpDamp_dofs_to_field_data
Definition: EP_Operators.hpp:851
ElectroPhysioProblem::post_proc_fields
MoFEMErrorCode post_proc_fields(std::string mass_field)
Definition: electro_physio.cpp:363
ElectroPhysioProblem::solve
MoFEMErrorCode solve()
Definition: electro_physio.cpp:376
ElectroPhysioProblem::extract_bd_ents
MoFEMErrorCode extract_bd_ents(std::string ESSENTIAL, std::string NATURAL)
Definition: electro_physio.cpp:196
ElectroPhysioProblem::divs_w_ptr
boost::shared_ptr< VectorDouble > divs_w_ptr
Definition: electro_physio.cpp:146
ElectroPhysioProblem::dm
SmartPetscObj< DM > dm
Definition: electro_physio.cpp:111
ElectroPhysioProblem::output_result
MoFEMErrorCode output_result()
Definition: electro_physio.cpp:369
ElectroPhysioProblem::data_s
boost::shared_ptr< PreviousData > data_s
Definition: electro_physio.cpp:137
ElectroPhysioProblem::values_u_ptr
boost::shared_ptr< VectorDouble > values_u_ptr
Definition: electro_physio.cpp:149
ElectroPhysioProblem::run_analysis
MoFEMErrorCode run_analysis()
Definition: electro_physio.cpp:392
ElectroPhysioProblem::divs_v_ptr
boost::shared_ptr< VectorDouble > divs_v_ptr
Definition: electro_physio.cpp:145
ElectroPhysioProblem::null
boost::shared_ptr< ForcesAndSourcesCore > null
Definition: electro_physio.cpp:159
ElectroPhysioProblem::apply_IC
MoFEMErrorCode apply_IC(std::string mass_field, Range &surface, boost::shared_ptr< VolEle > &initial_ele, double init_val)
Definition: electro_physio.cpp:330
ElectroPhysioProblem::dots_s_ptr
boost::shared_ptr< VectorDouble > dots_s_ptr
Definition: electro_physio.cpp:157
ElectroPhysioProblem::update_stiff_rhs
MoFEMErrorCode update_stiff_rhs(std::string mass_field, boost::shared_ptr< VectorDouble > &mass_ptr, boost::shared_ptr< VectorDouble > &mass_dot_ptr)
Definition: electro_physio.cpp:249
ElectroPhysioProblem::add_fe
MoFEMErrorCode add_fe()
Definition: electro_physio.cpp:170
ElectroPhysioProblem::values_w_ptr
boost::shared_ptr< VectorDouble > values_w_ptr
Definition: electro_physio.cpp:151
ElectroPhysioProblem::setup_system
MoFEMErrorCode setup_system()
Definition: electro_physio.cpp:162
ElectroPhysioProblem::loop_fe
MoFEMErrorCode loop_fe()
Definition: electro_physio.cpp:345
ElectroPhysioProblem::extract_initial_ents
MoFEMErrorCode extract_initial_ents(int block_id, Range &surface)
Definition: electro_physio.cpp:212
ElectroPhysioProblem::dots_u_ptr
boost::shared_ptr< VectorDouble > dots_u_ptr
Definition: electro_physio.cpp:154
ElectroPhysioProblem::divs_s_ptr
boost::shared_ptr< VectorDouble > divs_s_ptr
Definition: electro_physio.cpp:147
ElectroPhysioProblem::flux_u_ptr
boost::shared_ptr< MatrixDouble > flux_u_ptr
Definition: electro_physio.cpp:139
ElectroPhysioProblem::ts
SmartPetscObj< TS > ts
Definition: electro_physio.cpp:112
ElectroPhysioProblem::ElectroPhysioProblem
ElectroPhysioProblem(MoFEM::Core &core, const int order)
Definition: electro_physio.cpp:17
ElectroPhysioProblem::natural_bdry_ele_slow_rhs
boost::shared_ptr< FaceEle > natural_bdry_ele_slow_rhs
Definition: electro_physio.cpp:130
ElectroPhysioProblem::values_v_ptr
boost::shared_ptr< VectorDouble > values_v_ptr
Definition: electro_physio.cpp:150
ElectroPhysioProblem::data_w
boost::shared_ptr< PreviousData > data_w
Definition: electro_physio.cpp:136
ElectroPhysioProblem::vol_ele_stiff_lhs
boost::shared_ptr< VolEle > vol_ele_stiff_lhs
Definition: electro_physio.cpp:129
ElectroPhysioProblem::update_stiff_lhs
MoFEMErrorCode update_stiff_lhs(std::string mass_fiedl, boost::shared_ptr< VectorDouble > &mass_ptr)
Definition: electro_physio.cpp:277
ElectroPhysioProblem::flux_w_ptr
boost::shared_ptr< MatrixDouble > flux_w_ptr
Definition: electro_physio.cpp:141
ElectroPhysioProblem::apply_BC
MoFEMErrorCode apply_BC()
Definition: electro_physio.cpp:338
ElectroPhysioProblem::monitor_ptr
boost::shared_ptr< Monitor > monitor_ptr
Definition: electro_physio.cpp:132
ElectroPhysioProblem::push_slow_rhs
MoFEMErrorCode push_slow_rhs(boost::shared_ptr< PreviousData > &data_u, boost::shared_ptr< PreviousData > &data_v, boost::shared_ptr< PreviousData > &data_w, boost::shared_ptr< PreviousData > &data_s)
Definition: electro_physio.cpp:232
ElectroPhysioProblem::set_integration_rule
MoFEMErrorCode set_integration_rule()
Definition: electro_physio.cpp:317
ElectroPhysioProblem::data_v
boost::shared_ptr< PreviousData > data_v
Definition: electro_physio.cpp:135
ElectroPhysioProblem::dots_v_ptr
boost::shared_ptr< VectorDouble > dots_v_ptr
Definition: electro_physio.cpp:155
ElectroPhysioProblem::divs_u_ptr
boost::shared_ptr< VectorDouble > divs_u_ptr
Definition: electro_physio.cpp:144
ElectroPhysioProblem::vol_ele_slow_rhs
boost::shared_ptr< VolEle > vol_ele_slow_rhs
Definition: electro_physio.cpp:127
ElectroPhysioProblem::flux_s_ptr
boost::shared_ptr< MatrixDouble > flux_s_ptr
Definition: electro_physio.cpp:142
ElectroPhysioProblem::vol_ele_stiff_rhs
boost::shared_ptr< VolEle > vol_ele_stiff_rhs
Definition: electro_physio.cpp:128
ElectroPhysioProblem::m_field
MoFEM::Interface & m_field
Definition: electro_physio.cpp:109
ElectroPhysioProblem::post_proc
boost::shared_ptr< PostProcVolumeOnRefinedMesh > post_proc
Definition: electro_physio.cpp:131
ElectroPhysioProblem::push_stiff_rhs
MoFEMErrorCode push_stiff_rhs(boost::shared_ptr< PreviousData > &data_u, boost::shared_ptr< PreviousData > &data_v, boost::shared_ptr< PreviousData > &data_w, boost::shared_ptr< PreviousData > &data_s)
Definition: electro_physio.cpp:264
ElectroPhysioProblem::update_slow_rhs
MoFEMErrorCode update_slow_rhs(std::string mass_field, boost::shared_ptr< VectorDouble > &value_ptr)
Definition: electro_physio.cpp:223
ElectroPhysioProblem::data_u
boost::shared_ptr< PreviousData > data_u
Definition: electro_physio.cpp:134
ElectroPhysioProblem::dots_w_ptr
boost::shared_ptr< VectorDouble > dots_w_ptr
Definition: electro_physio.cpp:156
ElectroPhysioProblem::values_s_ptr
boost::shared_ptr< VectorDouble > values_s_ptr
Definition: electro_physio.cpp:152
ElectroPhysioProblem::flux_v_ptr
boost::shared_ptr< MatrixDouble > flux_v_ptr
Definition: electro_physio.cpp:140
ElectroPhysioProblem::push_stiff_lhs
MoFEMErrorCode push_stiff_lhs()
Definition: electro_physio.cpp:289
MoFEM::CoreInterface::get_moab
virtual moab::Interface & get_moab()=0
MoFEM::CoreInterface::get_comm
virtual MPI_Comm & get_comm() const =0
MoFEM::CoreTmp< 0 >
Core (interface) class.
Definition: Core.hpp:82
MoFEM::CoreTmp< 0 >::Initialize
static MoFEMErrorCode Initialize(int *argc, char ***args, const char file[], const char help[])
Initializes the MoFEM database PETSc, MOAB and MPI.
Definition: Core.cpp:72
MoFEM::CoreTmp< 0 >::Finalize
static MoFEMErrorCode Finalize()
Checks for options to be called at the conclusion of the program.
Definition: Core.cpp:112
MoFEM::DeprecatedCoreInterface
Deprecated interface functions.
Definition: DeprecatedCoreInterface.hpp:16
MoFEM::MeshsetsManager
Interface for managing meshsets containing materials and boundary conditions.
Definition: MeshsetsManager.hpp:104
MoFEM::OpCalculateHVecVectorField
Get vector field for H-div approximation.
Definition: UserDataOperators.hpp:2081
MoFEM::OpCalculateHdivVectorDivergence
Calculate divergence of vector field.
Definition: UserDataOperators.hpp:2179
MoFEM::OpCalculateScalarFieldValues
Get value at integration points for scalar field.
Definition: UserDataOperators.hpp:83
MoFEM::ProblemsManager
Problem manager is used to build and partition problems.
Definition: ProblemsManager.hpp:21
MoFEM::Simple
Simple interface for fast problem set-up.
Definition: Simple.hpp:27
MoFEM::Simple::getBoundaryFEName
const std::string getBoundaryFEName() const
Get the Boundary FE Name.
Definition: Simple.hpp:334
MoFEM::Simple::addDataField
MoFEMErrorCode addDataField(const std::string &name, const FieldSpace space, const FieldApproximationBase base, const FieldCoefficientsNumber nb_of_coefficients, const TagType tag_type=MB_TAG_SPARSE, const enum MoFEMTypes bh=MF_ZERO, int verb=-1)
Add field on domain.
Definition: Simple.cpp:320
MoFEM::Simple::addDomainField
MoFEMErrorCode addDomainField(const std::string &name, const FieldSpace space, const FieldApproximationBase base, const FieldCoefficientsNumber nb_of_coefficients, const TagType tag_type=MB_TAG_SPARSE, const enum MoFEMTypes bh=MF_ZERO, int verb=-1)
Add field on domain.
Definition: Simple.cpp:264
MoFEM::Simple::getOptions
MoFEMErrorCode getOptions()
get options
Definition: Simple.cpp:180
MoFEM::Simple::getDM
MoFEMErrorCode getDM(DM *dm)
Get DM.
Definition: Simple.cpp:667
MoFEM::Simple::loadFile
MoFEMErrorCode loadFile(const std::string options, const std::string mesh_file_name)
Load mesh file.
Definition: Simple.cpp:194
MoFEM::Simple::setFieldOrder
MoFEMErrorCode setFieldOrder(const std::string field_name, const int order, const Range *ents=NULL)
Set field order.
Definition: Simple.cpp:473
MoFEM::Simple::addBoundaryField
MoFEMErrorCode addBoundaryField(const std::string &name, const FieldSpace space, const FieldApproximationBase base, const FieldCoefficientsNumber nb_of_coefficients, const TagType tag_type=MB_TAG_SPARSE, const enum MoFEMTypes bh=MF_ZERO, int verb=-1)
Add field on boundary.
Definition: Simple.cpp:282
MoFEM::Simple::setUp
MoFEMErrorCode setUp(const PetscBool is_partitioned=PETSC_TRUE)
Setup problem.
Definition: Simple.cpp:611
MoFEM::Simple::getDomainFEName
const std::string getDomainFEName() const
Get the Domain FE Name.
Definition: Simple.hpp:327
MoFEM::SmartPetscObj
intrusive_ptr for managing petsc objects
Definition: PetscSmartObj.hpp:79
MoFEM::UnknownInterface::getInterface
MoFEMErrorCode getInterface(IFACE *&iface) const
Get interface refernce to pointer of interface.
Definition: UnknownInterface.hpp:93
PostProcVolumeOnRefinedMesh
Post processing.
Definition: PostProcOnRefMesh.hpp:957
VolEle
VolumeElementForcesAndSourcesCore VolEle
Definition: test_cache_on_entities.cpp:22
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