v0.13.2
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Functions | Variables
mass_calculation.cpp File Reference
#include <MoFEM.hpp>
#include <Projection10NodeCoordsOnField.hpp>
#include <metaImage.h>
#include <moab/Skinner.hpp>
#include <moab/AdaptiveKDTree.hpp>
#include <cholesky.hpp>
#include <DensityMaps.hpp>
#include <PostProcOnRefMesh.hpp>

Go to the source code of this file.

Functions

int main (int argc, char *argv[])
 

Variables

static char help [] = "\n"
 

Function Documentation

◆ main()

int main ( int  argc,
char *  argv[] 
)

Definition at line 42 of file mass_calculation.cpp.

42 {
43 MoFEM::Core::Initialize(&argc, &argv, (char *)0, help);
44
45 try {
46
47 moab::Core mb_instance;
48 moab::Interface& moab = mb_instance;
49
50 char mesh_file_name[255];
51 PetscBool flg_file = PETSC_FALSE;
52 char meta_file_name[255];
53 PetscBool meta_flg_file = PETSC_FALSE;
54 PetscInt order = 1;
55 PetscBool is_atom_test = PETSC_FALSE;
56 // char approximation_base[255];
57
58 ierr = PetscOptionsBegin(PETSC_COMM_WORLD,"","Bone remodeling","none"); CHKERRQ(ierr);
59 ierr = PetscOptionsString(
60 "-my_file",
61 "mesh file name","",
62 "mesh.h5m",mesh_file_name,255,&flg_file
63 ); CHKERRQ(ierr);
64
65 ierr = PetscOptionsString(
66 "-meta_image",
67 "meta image name","",
68 "file.mhd",meta_file_name,255,&meta_flg_file
69 ); CHKERRQ(ierr);
70
71 // ierr = PetscOptionsString(
72 // "-base",
73 // "approximation base name","",
74 // "",approximation_base,255,PETSC_NULL
75 // ); CHKERRQ(ierr);
76
77 ierr = PetscOptionsBool(
78 "-my_is_atom_test",
79 "is used with testing, exit with error when diverged","",
80 PETSC_FALSE,&is_atom_test,PETSC_NULL
81 ); CHKERRQ(ierr);
82
83 ierr = PetscOptionsInt(
84 "-my_order",
85 "default approximation order","",
86 1,&order,PETSC_NULL
87 ); CHKERRQ(ierr);
88
89 ierr = PetscOptionsEnd(); CHKERRQ(ierr);
90
91 // #ifdef WITH_METAIO
92
93 MetaImage meta_file(meta_file_name);
94 cout << "Quantity " << meta_file.Quantity() << endl;
95 const int *dim_size = meta_file.DimSize();
96 cout << "Image dimension: " << dim_size[0] << " " << dim_size[1] << " " << dim_size[2] << endl;
97 const double *elemet_size = meta_file.ElementSize();
98 cout << "Image element size: " << elemet_size[0] << " " << elemet_size[1] << " " << elemet_size[2] << endl;
99 const double *offset = meta_file.Offset();
100 cout << "Image offset: " << offset[0] << " " << offset[1] << " " << offset[2] << endl;
101 const double * transform_matrix = meta_file.TransformMatrix();
102 cout << "Image Transform Matrix:\n";
103 for(int rr = 0;rr<3;rr++) {
104 for(int cc = 0;cc<3;cc++) {
105 cout << transform_matrix[rr*3+cc] << " ";
106 }
107 cout << endl;
108 }
109
110 //Read parameters from line command
111 if(flg_file != PETSC_TRUE) {
112 SETERRQ(PETSC_COMM_SELF,1,"*** ERROR -my_file (MESH FILE NEEDED)");
113 }
114 const char *option;
115 option = "";
116 rval = moab.load_file(mesh_file_name, 0, option); CHKERRQ_MOAB(rval);
117 ParallelComm* pcomm = ParallelComm::get_pcomm(&moab,MYPCOMM_INDEX);
118 if(pcomm == NULL) pcomm = new ParallelComm(&moab,PETSC_COMM_WORLD);
119
120 MoFEM::Core core(moab);
121 MoFEM::Interface& m_field = core;
122 //meshset consisting all entities in mesh
123 EntityHandle root_set = moab.get_root_set();
124 // Seed all mesh entities to MoFEM database, those entities can be potentially used as finite elements
125 // or as entities which carry some approximation field.
126 BitRefLevel bit_level0;
127 bit_level0.set(0);
128 ierr = m_field.seed_ref_level_3D(root_set,bit_level0); CHKERRQ(ierr);
129 // Add field
130 ierr = m_field.add_field("RHO",H1,AINSWORTH_LEGENDRE_BASE,1); CHKERRQ(ierr);
131 ierr = m_field.add_field("MESH_NODE_POSITIONS",H1,AINSWORTH_LEGENDRE_BASE,3); CHKERRQ(ierr);
132
133 // Add meshsets with material and boundary conditions
134 auto *meshsets_manager_ptr = m_field.getInterface<MeshsetsManager>();
135 ierr = meshsets_manager_ptr->setMeshsetFromFile(); CHKERRQ(ierr);
136
137 PetscPrintf(PETSC_COMM_WORLD,"Read meshset. Added meshsets for bc.cfg\n");
138 for(_IT_CUBITMESHSETS_FOR_LOOP_(m_field,it)) {
139 PetscPrintf(
140 PETSC_COMM_WORLD,
141 "%s",static_cast<std::ostringstream&>(std::ostringstream().seekp(0) << *it << endl).str().c_str()
142 );
143 cerr << *it << endl;
144 }
145
146 Range tets_all;
147 rval = m_field.get_moab().get_entities_by_type(0,MBTET,tets_all); CHKERRQ_MOAB(rval);
148
149 for(_IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_(m_field,BLOCKSET,it)) {
150 string name = it->getName();
151 if (name.compare(0,14,"NO_REMODELLING") == 0) {
152 //nOremodellingBlock = true;
153 EntityHandle meshset = it->getMeshset();
154 Range tets_block;
155 rval = m_field.get_moab().get_entities_by_type(
156 meshset,MBTET,tets_block,true
157 ); CHKERRQ_MOAB(rval);
158 tets_all = subtract(tets_all,tets_block);
159 }
160 }
161
162
163 // if ( strcmp(approximation_base, "lobatto") == 0){
164 // ierr = m_field.add_field("RHO",L2,AINSWORTH_LOBATTO_BASE,1); CHKERRQ(ierr);
165 // } else if ( strcmp(approximation_base, "berstein") == 0){ //not implemented yet
166 // ierr = m_field.add_field("RHO",L2,AINSOWRTH_BERNSTEIN_BEZIER_BASE,1); CHKERRQ(ierr);
167 // }
168 // else {
169 // ierr = m_field.add_field("RHO",L2,AINSWORTH_LEGENDRE_BASE,1); CHKERRQ(ierr);
170 // }
171 // Add entities to field (root_mesh, i.e. on all mesh entities fields are approx.)
172 // On those entities and lower dimension entities approximation is spaned,
173 ierr = m_field.add_ents_to_field_by_type(tets_all,MBTET,"RHO"); CHKERRQ(ierr);
174 ierr = m_field.add_ents_to_field_by_type(root_set,MBTET,"MESH_NODE_POSITIONS"); CHKERRQ(ierr);
175
176
177 {
178 ierr = m_field.add_field("DISTANCE_FROM_SURFACE",H1,AINSWORTH_LEGENDRE_BASE,1); CHKERRQ(ierr);
179 Range vertices;
180 rval = moab.get_entities_by_type(root_set,MBVERTEX,vertices); CHKERRQ_MOAB(rval);
181 ierr = m_field.add_ents_to_field_by_type(vertices,MBTET,"DISTANCE_FROM_SURFACE"); CHKERRQ(ierr);
182 Range tets;
183 rval = moab.get_entities_by_type(root_set,MBTET,tets); CHKERRQ_MOAB(rval);
184 Range edges;
185 rval = moab.get_adjacencies(tets,1,true,edges,moab::Interface::UNION); CHKERRQ_MOAB(rval);
186 ierr = m_field.add_ents_to_field_by_type(edges,MBEDGE,"DISTANCE_FROM_SURFACE"); CHKERRQ(ierr);
187 }
188
189 // Set approximation oder
190 ierr = m_field.set_field_order(root_set,MBVERTEX,"RHO",1); CHKERRQ(ierr);
191 ierr = m_field.set_field_order(root_set,MBEDGE,"RHO",order); CHKERRQ(ierr);
192 ierr = m_field.set_field_order(root_set,MBTRI,"RHO",order); CHKERRQ(ierr);
193 ierr = m_field.set_field_order(root_set,MBTET,"RHO",order); CHKERRQ(ierr);
194 ierr = m_field.set_field_order(root_set,MBEDGE,"DISTANCE_FROM_SURFACE",2); CHKERRQ(ierr);
195 ierr = m_field.set_field_order(root_set,MBVERTEX,"DISTANCE_FROM_SURFACE",1); CHKERRQ(ierr);
196
197 // Apply 2nd order geometry approximation only on skin
198 {
199
200 Skinner skin(&moab);
201 Range faces,tets;
202 rval = moab.get_entities_by_type(0,MBTET,tets); CHKERRQ_MOAB(rval);
203 rval = skin.find_skin(0,tets,false,faces); CHKERRQ_MOAB(rval);
204 Range edges;
205 rval = moab.get_adjacencies(
206 faces,1,false,edges,moab::Interface::UNION
207 ); CHKERRQ_MOAB(rval);
208 ierr = m_field.set_field_order(edges,"MESH_NODE_POSITIONS",2); CHKERRQ(ierr);
209 }
210 ierr = m_field.set_field_order(root_set,MBVERTEX,"MESH_NODE_POSITIONS",1); CHKERRQ(ierr);
211
212 ierr = m_field.build_fields(); CHKERRQ(ierr);
213
214 {
215 Projection10NodeCoordsOnField ent_method_material(m_field,"MESH_NODE_POSITIONS");
216 ierr = m_field.loop_dofs("MESH_NODE_POSITIONS",ent_method_material); CHKERRQ(ierr);
217 }
218
219 SurfaceKDTree surface_distance(m_field);
220 {
221 Range tets;
222 rval = moab.get_entities_by_type(root_set,MBTET,tets); CHKERRQ_MOAB(rval);
223 ierr = surface_distance.takeASkin(tets); CHKERRQ(ierr);
224 ierr = surface_distance.buildTree(); CHKERRQ(ierr);
225 ierr = surface_distance.setDistanceFromSurface("DISTANCE_FROM_SURFACE"); CHKERRQ(ierr);
226 }
227
228 // Add finite element (this defines element declaration comes later)
229 ierr = m_field.add_finite_element("DENSITY_MAP_ELEMENT"); CHKERRQ(ierr);
230 ierr = m_field.modify_finite_element_add_field_row("DENSITY_MAP_ELEMENT","RHO"); CHKERRQ(ierr);
231 ierr = m_field.modify_finite_element_add_field_col("DENSITY_MAP_ELEMENT","RHO"); CHKERRQ(ierr);
232 ierr = m_field.modify_finite_element_add_field_data("DENSITY_MAP_ELEMENT","RHO"); CHKERRQ(ierr);
233 ierr = m_field.modify_finite_element_add_field_data("DENSITY_MAP_ELEMENT","DISTANCE_FROM_SURFACE"); CHKERRQ(ierr);
234 ierr = m_field.modify_finite_element_add_field_data("DENSITY_MAP_ELEMENT","MESH_NODE_POSITIONS"); CHKERRQ(ierr);
235
236 // Add entities to that element
237 ierr = m_field.add_ents_to_finite_element_by_type(tets_all,MBTET,"DENSITY_MAP_ELEMENT"); CHKERRQ(ierr);
238
239 //build finite elements
240 ierr = m_field.build_finite_elements(); CHKERRQ(ierr);
241 //build adjacencies between elements and degrees of freedom
242 ierr = m_field.build_adjacencies(bit_level0); CHKERRQ(ierr);
243
244 DM dm_rho;
245 DMType dm_name = "DM_RHO";
246 // Register DM problem
247 ierr = DMRegister_MoFEM(dm_name); CHKERRQ(ierr);
248 ierr = DMCreate(PETSC_COMM_WORLD,&dm_rho);CHKERRQ(ierr);
249 ierr = DMSetType(dm_rho,dm_name);CHKERRQ(ierr);
250 // Create DM instance
251 ierr = DMMoFEMCreateMoFEM(dm_rho,&m_field,dm_name,bit_level0); CHKERRQ(ierr);
252 // Configure DM form line command options (DM itself, solvers, pre-conditioners, ... )
253 ierr = DMSetFromOptions(dm_rho); CHKERRQ(ierr);
254 // Add elements to dm (only one here)
255 ierr = DMMoFEMAddElement(dm_rho,"DENSITY_MAP_ELEMENT"); CHKERRQ(ierr);
256 // Set up problem (number dofs, partition mesh, etc.)
257 //ierr = DMSetUp(dm_rho); CHKERRQ(ierr);
258
259 {
260 ierr = DMSetUp(dm_rho); CHKERRQ(ierr);
261 // Do serial matrix
262 // const MoFEM::Problem *problem_ptr;
263 // ierr = DMMoFEMGetProblemPtr(dm_rho,&problem_ptr); CHKERRQ(ierr);
264 // ierr = m_field.build_problem(problem_ptr->getName()); CHKERRQ(ierr);
265 // // FIXME: That is not optimal partitioning
266 // ierr = m_field.partition_simple_problem(problem_ptr->getName()); CHKERRQ(ierr);
267 // ierr = m_field.partition_finite_elements(problem_ptr->getName());
268 // ierr = m_field.partition_ghost_dofs(problem_ptr->getName()); CHKERRQ(ierr);
269 }
270
271 Vec volume_vec;
272 int volume_vec_ghost[] = { 0 };
273 ierr = VecCreateGhost(
274 PETSC_COMM_WORLD,(!m_field.get_comm_rank())?1:0,1,1,volume_vec_ghost,&volume_vec
275 ); CHKERRQ(ierr);
276 ierr = VecZeroEntries(volume_vec); CHKERRQ(ierr);
277 Vec mass_vec;
278 ierr = VecDuplicate(volume_vec,&mass_vec); CHKERRQ(ierr);
279 Vec mass_vec_approx;
280 ierr = VecDuplicate(volume_vec,&mass_vec_approx); CHKERRQ(ierr);
281
282 DensityMapFe fe_volume(m_field);
283 auto &list_of_operators = fe_volume.getOpPtrVector();
284 list_of_operators.push_back(new OpVolumeCalculation("RHO",volume_vec));
285 DataFromMetaIO data_from_meta_io(meta_file);
286 ierr = data_from_meta_io.fromOptions(); CHKERRQ(ierr);
287 list_of_operators.push_back(new OpMassCalculation("RHO",mass_vec,data_from_meta_io));
288 ierr = DMoFEMLoopFiniteElements(dm_rho,"DENSITY_MAP_ELEMENT",&fe_volume); CHKERRQ(ierr);
289
290 ierr = VecAssemblyBegin(volume_vec); CHKERRQ(ierr);
291 ierr = VecAssemblyEnd(volume_vec); CHKERRQ(ierr);
292 double volume;
293 ierr = VecSum(volume_vec,&volume); CHKERRQ(ierr);
294 ierr = PetscPrintf(PETSC_COMM_WORLD,"Volume %0.32g\n",volume); CHKERRQ(ierr);
295
296 ierr = VecAssemblyBegin(mass_vec); CHKERRQ(ierr);
297 ierr = VecAssemblyEnd(mass_vec); CHKERRQ(ierr);
298 double mass;
299 ierr = VecSum(mass_vec,&mass); CHKERRQ(ierr);
300 ierr = PetscPrintf(PETSC_COMM_WORLD,"Mass %0.32g\n",mass); CHKERRQ(ierr);
301
302 ierr = VecDestroy(&volume_vec); CHKERRQ(ierr);
303 ierr = VecDestroy(&mass_vec); CHKERRQ(ierr);
304
305
306 Mat A;
307 Vec F,D;
308 ierr = DMCreateMatrix(dm_rho,&A); CHKERRQ(ierr);
309 ierr = m_field.getInterface<VecManager>()->vecCreateGhost("DM_RHO",ROW,&F); CHKERRQ(ierr);
310 ierr = m_field.getInterface<VecManager>()->vecCreateGhost("DM_RHO",COL,&D); CHKERRQ(ierr);
311
312 ierr = MatZeroEntries(A); CHKERRQ(ierr);
313 ierr = VecZeroEntries(F); CHKERRQ(ierr);
314
315 CommonData common_data;
316 common_data.globA = A;
317 common_data.globF = F;
318
319 common_data.distanceValue = boost::shared_ptr<VectorDouble>(new VectorDouble());
320 common_data.distanceGradient = boost::shared_ptr<MatrixDouble>(new MatrixDouble());
321 boost::shared_ptr<VectorDouble> dist_value = common_data.distanceValue;
322 boost::shared_ptr<MatrixDouble> grad_value = common_data.distanceGradient;
323
324 DensityMapFe fe_density_approximation(m_field);
325
326 fe_density_approximation.getOpPtrVector().push_back
327 (new OpCalculateScalarFieldValues("DISTANCE_FROM_SURFACE",dist_value));
328 fe_density_approximation.getOpPtrVector().push_back
329 (new OpCalculateScalarFieldGradient<3>("DISTANCE_FROM_SURFACE",grad_value));
330 fe_density_approximation.getOpPtrVector().push_back
331 (new OpCalculateLhs("RHO","RHO",common_data,data_from_meta_io));
332 fe_density_approximation.getOpPtrVector().push_back
333 (new OpCalulatefRhoAtGaussPts("RHO",common_data,data_from_meta_io,surface_distance));
334 fe_density_approximation.getOpPtrVector().push_back
335 (new OpAssmbleRhs("RHO",common_data));
336 ierr = DMoFEMLoopFiniteElements(dm_rho,"DENSITY_MAP_ELEMENT",&fe_density_approximation); CHKERRQ(ierr);
337
338 ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
339 ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
340 ierr = VecGhostUpdateBegin(F,ADD_VALUES,SCATTER_REVERSE);
341 ierr = VecGhostUpdateEnd(F,ADD_VALUES,SCATTER_REVERSE);
342 ierr = VecAssemblyBegin(F); CHKERRQ(ierr);
343 ierr = VecAssemblyEnd(F); CHKERRQ(ierr);
344
345 // MatView(A,PETSC_VIEWER_DRAW_WORLD);
346 // std::string wait;
347 // std::cin >> wait;
348
349 {
350 KSP ksp;
351 ierr = KSPCreate(PETSC_COMM_WORLD,&ksp); CHKERRQ(ierr);
352 ierr = KSPSetOperators(ksp,A,A); CHKERRQ(ierr);
353 ierr = KSPSetFromOptions(ksp); CHKERRQ(ierr);
354 ierr = KSPSolve(ksp,F,D); CHKERRQ(ierr); CHKERRQ(ierr);
355 }
356
357 ierr = VecGhostUpdateBegin(D,INSERT_VALUES,SCATTER_FORWARD); CHKERRQ(ierr);
358 ierr = VecGhostUpdateEnd(D,INSERT_VALUES,SCATTER_FORWARD); CHKERRQ(ierr);
359 ierr = m_field.getInterface<VecManager>()->setGlobalGhostVector("DM_RHO",COL,D,INSERT_VALUES,SCATTER_REVERSE); CHKERRQ(ierr);
360
361 DensityMapFe fe_post_process_calulations(m_field);
362
363 fe_post_process_calulations.getOpPtrVector().push_back(
364 new OpMassCalculationFromApprox("RHO",mass_vec_approx)
365 );
366 ierr = DMoFEMLoopFiniteElements(dm_rho,"DENSITY_MAP_ELEMENT",&fe_post_process_calulations); CHKERRQ(ierr);
367
368 ierr = VecAssemblyBegin(mass_vec_approx); CHKERRQ(ierr);
369 ierr = VecAssemblyEnd(mass_vec_approx); CHKERRQ(ierr);
370 double mass_approx;
371 ierr = VecSum(mass_vec_approx,&mass_approx); CHKERRQ(ierr);
372 ierr = PetscPrintf(PETSC_COMM_WORLD,"Mass after approximation %0.32g\n",mass_approx); CHKERRQ(ierr);
373 if(is_atom_test) {
374 if( abs(mass_approx - volume) > 1.0e-2) {
375 SETERRQ(PETSC_COMM_SELF,MOFEM_ATOM_TEST_INVALID,"atom test diverged");
376 }
377 }
378 ierr = VecDestroy(&mass_vec_approx); CHKERRQ(ierr);
379
380 PostProcVolumeOnRefinedMesh post_proc(m_field);
381 ierr = post_proc.generateReferenceElementMesh(); CHKERRQ(ierr);
382 ierr = post_proc.addFieldValuesPostProc("MESH_NODE_POSITIONS"); CHKERRQ(ierr);
383 ierr = post_proc.addFieldValuesPostProc("RHO"); CHKERRQ(ierr);
384 ierr = post_proc.addFieldValuesPostProc("DISTANCE_FROM_SURFACE"); CHKERRQ(ierr);
385 ierr = post_proc.addFieldValuesGradientPostProc("RHO"); CHKERRQ(ierr);
386 ierr = post_proc.addFieldValuesGradientPostProc("DISTANCE_FROM_SURFACE"); CHKERRQ(ierr);
387 ierr = DMoFEMLoopFiniteElements(dm_rho,"DENSITY_MAP_ELEMENT",&post_proc); CHKERRQ(ierr);
388 ierr = post_proc.writeFile("out.h5m"); CHKERRQ(ierr);
389
390 ierr = VecDestroy(&F); CHKERRQ(ierr);
391 ierr = VecDestroy(&D); CHKERRQ(ierr);
392 ierr = MatDestroy(&A); CHKERRQ(ierr);
393 ierr = DMDestroy(&dm_rho);
394
395 // Delete element which will be no longer used
396 ierr = m_field.delete_finite_element("DENSITY_MAP_ELEMENT",2); CHKERRQ(ierr);
397 if (m_field.get_comm_rank() == 0)
398 CHKERR moab.write_file("analysis_mesh.h5m");
399
400
401 } CATCH_ERRORS;
402
403 MoFEM::Core::Finalize();
404
405 return (0);
406}
COL
@ COL
Definition: definitions.h:123
ROW
@ ROW
Definition: definitions.h:123
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
H1
@ H1
continuous field
Definition: definitions.h:85
MYPCOMM_INDEX
#define MYPCOMM_INDEX
default communicator number PCOMM
Definition: definitions.h:215
BLOCKSET
@ BLOCKSET
Definition: definitions.h:148
CHKERRQ_MOAB
#define CHKERRQ_MOAB(a)
check error code of MoAB function
Definition: definitions.h:454
MOFEM_ATOM_TEST_INVALID
@ MOFEM_ATOM_TEST_INVALID
Definition: definitions.h:40
CHKERR
#define CHKERR
Inline error check.
Definition: definitions.h:535
order
int order
Definition: fluid_structure_eigenproblem.cpp:84
F
@ F
Definition: free_surface.cpp:401
MoFEM::DMMoFEMAddElement
PetscErrorCode DMMoFEMAddElement(DM dm, std::string fe_name)
add element to dm
Definition: DMMoFEM.cpp:483
MoFEM::DMMoFEMCreateMoFEM
PetscErrorCode DMMoFEMCreateMoFEM(DM dm, MoFEM::Interface *m_field_ptr, const char problem_name[], const MoFEM::BitRefLevel bit_level, const MoFEM::BitRefLevel bit_mask=MoFEM::BitRefLevel().set())
Must be called by user to set MoFEM data structures.
Definition: DMMoFEM.cpp:118
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::CoreInterface::add_finite_element
virtual MoFEMErrorCode add_finite_element(const std::string &fe_name, enum MoFEMTypes bh=MF_EXCL, int verb=DEFAULT_VERBOSITY)=0
add finite element
MoFEM::CoreInterface::build_finite_elements
virtual MoFEMErrorCode build_finite_elements(int verb=DEFAULT_VERBOSITY)=0
Build finite elements.
MoFEM::CoreInterface::modify_finite_element_add_field_col
virtual MoFEMErrorCode modify_finite_element_add_field_col(const std::string &fe_name, const std::string name_row)=0
set field col which finite element use
MoFEM::CoreInterface::add_ents_to_finite_element_by_type
virtual MoFEMErrorCode add_ents_to_finite_element_by_type(const EntityHandle entities, const EntityType type, const std::string &name, const bool recursive=true)=0
add entities to finite element
MoFEM::CoreInterface::modify_finite_element_add_field_data
virtual MoFEMErrorCode modify_finite_element_add_field_data(const std::string &fe_name, const std::string name_filed)=0
set finite element field data
MoFEM::CoreInterface::modify_finite_element_add_field_row
virtual MoFEMErrorCode modify_finite_element_add_field_row(const std::string &fe_name, const std::string name_row)=0
set field row which finite element use
MoFEM::CoreInterface::build_fields
virtual MoFEMErrorCode build_fields(int verb=DEFAULT_VERBOSITY)=0
MoFEM::CoreInterface::set_field_order
virtual MoFEMErrorCode set_field_order(const EntityHandle meshset, const EntityType type, const std::string &name, const ApproximationOrder order, int verb=DEFAULT_VERBOSITY)=0
Set order approximation of the entities in the field.
MoFEM::CoreInterface::add_ents_to_field_by_type
virtual MoFEMErrorCode add_ents_to_field_by_type(const Range &ents, const EntityType type, const std::string &name, int verb=DEFAULT_VERBOSITY)=0
Add entities to field meshset.
MoFEM::CoreInterface::loop_dofs
virtual MoFEMErrorCode loop_dofs(const Problem *problem_ptr, const std::string &field_name, RowColData rc, DofMethod &method, int lower_rank, int upper_rank, int verb=DEFAULT_VERBOSITY)=0
Make a loop over dofs.
_IT_CUBITMESHSETS_FOR_LOOP_
#define _IT_CUBITMESHSETS_FOR_LOOP_(MESHSET_MANAGER, IT)
Iterator that loops over all the Cubit MeshSets in a moFEM field.
Definition: MeshsetsManager.hpp:34
_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
D
double D
Definition: initial_diffusion.cpp:44
help
static char help[]
Definition: mass_calculation.cpp:34
mesh_file_name
char mesh_file_name[255]
Definition: mesh_smoothing.cpp:23
EigenMatrix::Vec
const FTensor::Tensor2< T, Dim, Dim > Vec
Definition: MatrixFunction.hpp:66
MoFEM::Exceptions::ierr
static MoFEMErrorCodeGeneric< PetscErrorCode > ierr
Definition: Exceptions.hpp:76
MoFEM::Exceptions::rval
static MoFEMErrorCodeGeneric< moab::ErrorCode > rval
Definition: Exceptions.hpp:74
MoFEM::Types::MatrixDouble
UBlasMatrix< double > MatrixDouble
Definition: Types.hpp:77
MoFEM::Types::BitRefLevel
std::bitset< BITREFLEVEL_SIZE > BitRefLevel
Bit structure attached to each entity identifying to what mesh entity is attached.
Definition: Types.hpp:40
MoFEM::Types::VectorDouble
UBlasVector< double > VectorDouble
Definition: Types.hpp:68
A
constexpr AssemblyType A
Definition: operators_tests.cpp:30
BoneRemodeling::DataFromMetaIO
Load data from MetaImage file, translate grayscale values to densities.
Definition: DensityMaps.hpp:205
BoneRemodeling::OpAssmbleRhs
Assemble RHS vector f.
Definition: DensityMaps.hpp:902
BoneRemodeling::OpCalculateLhs
Assemble LHS matrix K.
Definition: DensityMaps.hpp:689
BoneRemodeling::OpCalulatefRhoAtGaussPts
Assemble local vector containing density data.
Definition: DensityMaps.hpp:769
BoneRemodeling::OpMassCalculationFromApprox
Calculate mass after approximation.
Definition: DensityMaps.hpp:1050
BoneRemodeling::OpMassCalculation
Calculate mass before approximation.
Definition: DensityMaps.hpp:957
BoneRemodeling::SurfaceKDTree
Create KDTree on surface of the mesh and calculate distance.
Definition: DensityMaps.hpp:32
MoFEM::CoreInterface::get_moab
virtual moab::Interface & get_moab()=0
MoFEM::CoreInterface::build_adjacencies
virtual MoFEMErrorCode build_adjacencies(const Range &ents, int verb=DEFAULT_VERBOSITY)=0
build adjacencies
MoFEM::CoreInterface::delete_finite_element
virtual MoFEMErrorCode delete_finite_element(const std::string name, int verb=DEFAULT_VERBOSITY)=0
delete finite element from mofem database
MoFEM::CoreInterface::add_field
virtual MoFEMErrorCode add_field(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_EXCL, int verb=DEFAULT_VERBOSITY)=0
Add field.
MoFEM::CoreInterface::get_comm_rank
virtual int get_comm_rank() 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::DeprecatedCoreInterface::seed_ref_level_3D
DEPRECATED MoFEMErrorCode seed_ref_level_3D(const EntityHandle meshset, const BitRefLevel &bit, int verb=-1)
seed 2D entities in the meshset and their adjacencies (only TETs adjacencies) in a particular BitRefL...
Definition: DeprecatedCoreInterface.cpp:18
MoFEM::MeshsetsManager
Interface for managing meshsets containing materials and boundary conditions.
Definition: MeshsetsManager.hpp:104
MoFEM::OpCalculateScalarFieldGradient
Get field gradients at integration pts for scalar filed rank 0, i.e. vector field.
Definition: UserDataOperators.hpp:1291
MoFEM::OpCalculateScalarFieldValues
Get value at integration points for scalar field.
Definition: UserDataOperators.hpp:83
MoFEM::Projection10NodeCoordsOnField
Projection of edge entities with one mid-node on hierarchical basis.
Definition: Projection10NodeCoordsOnField.hpp:24
MoFEM::UnknownInterface::getInterface
MoFEMErrorCode getInterface(IFACE *&iface) const
Get interface refernce to pointer of interface.
Definition: UnknownInterface.hpp:93
MoFEM::VecManager
Vector manager is used to create vectors \mofem_vectors.
Definition: VecManager.hpp:23
PostProcVolumeOnRefinedMesh
Post processing.
Definition: PostProcOnRefMesh.hpp:957

Variable Documentation

◆ help

char help[] = "\n"
static

Definition at line 34 of file mass_calculation.cpp.

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