v0.14.0
nonlinear_elastic.cpp
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1 /** \file nonlinear_elastic.cpp
2 
3  \brief Atom test for linear elastic dynamics.
4 
5  This is not exactly procedure for linear elastic dynamics, since jacobian is
6  evaluated at every time step and snes procedure is involved. However it is
7  implemented like that, to test methodology for general nonlinear problem.
8 
9 */
10 
11 
12 
13 #include <BasicFiniteElements.hpp>
14 using namespace MoFEM;
15 
16 namespace bio = boost::iostreams;
17 using bio::stream;
18 using bio::tee_device;
19 
20 static char help[] = "...\n\n";
21 
22 int main(int argc, char *argv[]) {
23 
24  MoFEM::Core::Initialize(&argc, &argv, (char *)0, help);
25 
26  try {
27 
28  moab::Core mb_instance;
29  moab::Interface &moab = mb_instance;
30  int rank;
31  MPI_Comm_rank(PETSC_COMM_WORLD, &rank);
32 
33  PetscBool flg = PETSC_TRUE;
34  char mesh_file_name[255];
35  CHKERR PetscOptionsGetString(PETSC_NULL, PETSC_NULL, "-my_file",
36  mesh_file_name, 255, &flg);
37  if (flg != PETSC_TRUE) {
38  SETERRQ(PETSC_COMM_SELF, 1, "*** ERROR -my_file (MESH FILE NEEDED)");
39  }
40 
41  const char *option;
42  option = ""; //"PARALLEL=BCAST;";//;DEBUG_IO";
43  CHKERR moab.load_file(mesh_file_name, 0, option);
44 
45  MoFEM::Core core(moab);
46  MoFEM::Interface &m_field = core;
47 
48  // ref meshset ref level 0
49  BitRefLevel bit_level0;
50  bit_level0.set(0);
51  EntityHandle meshset_level0;
52  CHKERR moab.create_meshset(MESHSET_SET, meshset_level0);
53  CHKERR m_field.getInterface<BitRefManager>()->setBitRefLevelByDim(
54  0, 3, bit_level0);
55  CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByRefLevel(
56  bit_level0, BitRefLevel().set(), meshset_level0);
57 
58  // Fields
59  CHKERR m_field.add_field("SPATIAL_POSITION", H1, AINSWORTH_LEGENDRE_BASE,
60  3);
61  // add entitities (by tets) to the field
62  CHKERR m_field.add_ents_to_field_by_type(0, MBTET, "SPATIAL_POSITION");
63  // set app. order
64  PetscInt order;
65  CHKERR PetscOptionsGetInt(PETSC_NULL, PETSC_NULL, "-my_order", &order,
66  &flg);
67  if (flg != PETSC_TRUE) {
68  order = 1;
69  }
70  CHKERR m_field.set_field_order(0, MBTET, "SPATIAL_POSITION", order);
71  CHKERR m_field.set_field_order(0, MBTRI, "SPATIAL_POSITION", order);
72  CHKERR m_field.set_field_order(0, MBEDGE, "SPATIAL_POSITION", order);
73  CHKERR m_field.set_field_order(0, MBVERTEX, "SPATIAL_POSITION", 1);
74 
75  NonlinearElasticElement elastic(m_field, 1);
76  boost::shared_ptr<
77  NonlinearElasticElement::FunctionsToCalculatePiolaKirchhoffI<double>>
78  double_kirchhoff_material_ptr(
79  new NonlinearElasticElement::FunctionsToCalculatePiolaKirchhoffI<
80  double>());
81  boost::shared_ptr<
82  NonlinearElasticElement::FunctionsToCalculatePiolaKirchhoffI<adouble>>
83  adouble_kirchhoff_material_ptr(
84  new NonlinearElasticElement::FunctionsToCalculatePiolaKirchhoffI<
85  adouble>());
86  CHKERR elastic.setBlocks(double_kirchhoff_material_ptr,
87  adouble_kirchhoff_material_ptr);
88  CHKERR elastic.addElement("ELASTIC", "SPATIAL_POSITION");
89  CHKERR elastic.setOperators("SPATIAL_POSITION");
90 
91  // define problems
92  CHKERR m_field.add_problem("ELASTIC_MECHANICS");
93  // set refinement level for problem
94  CHKERR m_field.modify_problem_ref_level_add_bit("ELASTIC_MECHANICS",
95  bit_level0);
96  // set finite elements for problems
97  CHKERR m_field.modify_problem_add_finite_element("ELASTIC_MECHANICS",
98  "ELASTIC");
99 
100  // build field
101  CHKERR m_field.build_fields();
102 
103  // use this to apply some strain field to the body (testing only)
104  double scale_positions = 2;
105  {
106  EntityHandle node = 0;
107  double coords[3];
108  for (_IT_GET_DOFS_FIELD_BY_NAME_FOR_LOOP_(m_field, "SPATIAL_POSITION",
109  dof_ptr)) {
110  if (dof_ptr->get()->getEntType() != MBVERTEX)
111  continue;
112  EntityHandle ent = dof_ptr->get()->getEnt();
113  int dof_rank = dof_ptr->get()->getDofCoeffIdx();
114  double &fval = dof_ptr->get()->getFieldData();
115  if (node != ent) {
116  CHKERR moab.get_coords(&ent, 1, coords);
117  node = ent;
118  }
119  fval = scale_positions * coords[dof_rank];
120  }
121  }
122 
123  // build finite elemnts
124  CHKERR m_field.build_finite_elements();
125  // build adjacencies
126  CHKERR m_field.build_adjacencies(bit_level0);
127 
128  ProblemsManager *prb_mng_ptr;
129  CHKERR m_field.getInterface(prb_mng_ptr);
130  // build problem
131  CHKERR prb_mng_ptr->buildProblem("ELASTIC_MECHANICS", true);
132  // partition
133  CHKERR prb_mng_ptr->partitionProblem("ELASTIC_MECHANICS");
134  CHKERR prb_mng_ptr->partitionFiniteElements("ELASTIC_MECHANICS");
135  CHKERR prb_mng_ptr->partitionGhostDofs("ELASTIC_MECHANICS");
136 
137  // create matrices
138  Vec F;
139  CHKERR m_field.getInterface<VecManager>()->vecCreateGhost(
140  "ELASTIC_MECHANICS", COL, &F);
141  Mat Aij;
142  CHKERR m_field.getInterface<MatrixManager>()
143  ->createMPIAIJWithArrays<PetscGlobalIdx_mi_tag>("ELASTIC_MECHANICS",
144  &Aij);
145 
146  elastic.getLoopFeRhs().snes_f = F;
147  elastic.getLoopFeLhs().snes_B = Aij;
148 
149  CHKERR m_field.loop_finite_elements("ELASTIC_MECHANICS", "ELASTIC",
150  elastic.getLoopFeRhs());
151  CHKERR VecGhostUpdateBegin(F, ADD_VALUES, SCATTER_REVERSE);
152  CHKERR VecGhostUpdateEnd(F, ADD_VALUES, SCATTER_REVERSE);
153  CHKERR VecAssemblyBegin(F);
154  CHKERR VecAssemblyEnd(F);
155 
156  CHKERR m_field.loop_finite_elements("ELASTIC_MECHANICS", "ELASTIC",
157  elastic.getLoopFeLhs());
158  CHKERR MatAssemblyBegin(Aij, MAT_FINAL_ASSEMBLY);
159  CHKERR MatAssemblyEnd(Aij, MAT_FINAL_ASSEMBLY);
160 
161  double sum = 0;
162  CHKERR VecSum(F, &sum);
163  CHKERR PetscPrintf(PETSC_COMM_WORLD, "sum = %4.3e\n", sum);
164  double fnorm;
165  CHKERR VecNorm(F, NORM_2, &fnorm);
166  CHKERR PetscPrintf(PETSC_COMM_WORLD, "fnorm = %9.8e\n", fnorm);
167 
168  double mnorm;
169  CHKERR MatNorm(Aij, NORM_1, &mnorm);
170  CHKERR PetscPrintf(PETSC_COMM_WORLD, "mnorm = %9.8e\n", mnorm);
171 
172  if (fabs(sum) > 1e-8) {
173  SETERRQ(PETSC_COMM_WORLD, MOFEM_ATOM_TEST_INVALID, "Failed to pass test");
174  }
175  if (fabs(fnorm - 5.12196914e+00) > 1e-6) {
176  SETERRQ(PETSC_COMM_WORLD, MOFEM_ATOM_TEST_INVALID, "Failed to pass test");
177  }
178  if (fabs(mnorm - 5.48280139e+01) > 1e-6) {
179  SETERRQ(PETSC_COMM_WORLD, MOFEM_ATOM_TEST_INVALID, "Failed to pass test");
180  }
181 
182  CHKERR VecDestroy(&F);
183  CHKERR MatDestroy(&Aij);
184  }
185  CATCH_ERRORS;
186 
187  MoFEM::Core::Finalize();
188 
189  return 0;
190 }
MoFEM::UnknownInterface::getInterface
MoFEMErrorCode getInterface(IFACE *&iface) const
Get interface reference to pointer of interface.
Definition: UnknownInterface.hpp:93
MoFEM::CoreInterface::loop_finite_elements
virtual MoFEMErrorCode loop_finite_elements(const std::string problem_name, const std::string &fe_name, FEMethod &method, boost::shared_ptr< NumeredEntFiniteElement_multiIndex > fe_ptr=nullptr, MoFEMTypes bh=MF_EXIST, CacheTupleWeakPtr cache_ptr=CacheTupleSharedPtr(), int verb=DEFAULT_VERBOSITY)=0
Make a loop over finite elements.
MoFEM::ProblemsManager::buildProblem
MoFEMErrorCode buildProblem(const std::string name, const bool square_matrix, int verb=VERBOSE)
build problem data structures
Definition: ProblemsManager.cpp:87
MoFEM::CoreTmp< 0 >
Core (interface) class.
Definition: Core.hpp:82
H1
@ H1
continuous field
Definition: definitions.h:85
EntityHandle
MoFEM::ProblemsManager
Problem manager is used to build and partition problems.
Definition: ProblemsManager.hpp:21
NonlinearElasticElement::FunctionsToCalculatePiolaKirchhoffI< double >
NonlinearElasticElement
structure grouping operators and data used for calculation of nonlinear elastic element
Definition: HookeElement.hpp:27
help
static char help[]
Definition: nonlinear_elastic.cpp:20
BasicFiniteElements.hpp
MoFEM::CoreTmp< 0 >::Finalize
static MoFEMErrorCode Finalize()
Checks for options to be called at the conclusion of the program.
Definition: Core.cpp:112
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.
order
constexpr int order
Definition: dg_projection.cpp:18
MoFEM::DeprecatedCoreInterface
Deprecated interface functions.
Definition: DeprecatedCoreInterface.hpp:16
MoFEM::Interface
DeprecatedCoreInterface Interface
Definition: Interface.hpp:2010
CHKERR
#define CHKERR
Inline error check.
Definition: definitions.h:548
MoFEM
implementation of Data Operators for Forces and Sources
Definition: Common.hpp:10
MoFEM::CoreInterface::build_finite_elements
virtual MoFEMErrorCode build_finite_elements(int verb=DEFAULT_VERBOSITY)=0
Build finite elements.
main
int main(int argc, char *argv[])
Definition: nonlinear_elastic.cpp:511
COL
@ COL
Definition: definitions.h:136
NonlinearElasticElement::addElement
MoFEMErrorCode addElement(const std::string element_name, const std::string spatial_position_field_name, const std::string material_position_field_name="MESH_NODE_POSITIONS", const bool ale=false)
Definition: NonLinearElasticElement.cpp:1120
MoFEM::ProblemsManager::partitionFiniteElements
MoFEMErrorCode partitionFiniteElements(const std::string name, bool part_from_moab=false, int low_proc=-1, int hi_proc=-1, int verb=VERBOSE)
partition finite elements
Definition: ProblemsManager.cpp:2167
MoFEM::CoreInterface::modify_problem_ref_level_add_bit
virtual MoFEMErrorCode modify_problem_ref_level_add_bit(const std::string &name_problem, const BitRefLevel &bit)=0
add ref level to problem
MoFEM::VecManager
Vector manager is used to create vectors \mofem_vectors.
Definition: VecManager.hpp:23
NonlinearElasticElement::setOperators
MoFEMErrorCode setOperators(const std::string spatial_position_field_name, const std::string material_position_field_name="MESH_NODE_POSITIONS", const bool ale=false, const bool field_disp=false)
Set operators to calculate left hand tangent matrix and right hand residual.
Definition: NonLinearElasticElement.cpp:1153
mesh_file_name
char mesh_file_name[255]
Definition: mesh_smoothing.cpp:22
MoFEM::MatrixManager
Matrix manager is used to build and partition problems.
Definition: MatrixManager.hpp:21
adouble
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
CATCH_ERRORS
#define CATCH_ERRORS
Catch errors.
Definition: definitions.h:385
_IT_GET_DOFS_FIELD_BY_NAME_FOR_LOOP_
#define _IT_GET_DOFS_FIELD_BY_NAME_FOR_LOOP_(MFIELD, NAME, IT)
Definition: Interface.hpp:1878
MoFEM::Core
CoreTmp< 0 > Core
Definition: Core.hpp:1148
AINSWORTH_LEGENDRE_BASE
@ AINSWORTH_LEGENDRE_BASE
Ainsworth Cole (Legendre) approx. base .
Definition: definitions.h:60
EigenMatrix::Vec
const FTensor::Tensor2< T, Dim, Dim > Vec
Definition: MatrixFunction.hpp:66
MoFEM::PetscOptionsGetString
PetscErrorCode PetscOptionsGetString(PetscOptions *, const char pre[], const char name[], char str[], size_t size, PetscBool *set)
Definition: DeprecatedPetsc.hpp:172
MoFEM::CoreInterface::build_fields
virtual MoFEMErrorCode build_fields(int verb=DEFAULT_VERBOSITY)=0
MoFEM::BitRefManager
Managing BitRefLevels.
Definition: BitRefManager.hpp:21
MoFEM::CoreInterface::modify_problem_add_finite_element
virtual MoFEMErrorCode modify_problem_add_finite_element(const std::string name_problem, const std::string &fe_name)=0
add finite element to problem, this add entities assigned to finite element to a particular problem
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_ATOM_TEST_INVALID
@ MOFEM_ATOM_TEST_INVALID
Definition: definitions.h:40
MoFEM::CoreInterface::build_adjacencies
virtual MoFEMErrorCode build_adjacencies(const Range &ents, int verb=DEFAULT_VERBOSITY)=0
build adjacencies
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::ProblemsManager::partitionGhostDofs
MoFEMErrorCode partitionGhostDofs(const std::string name, int verb=VERBOSE)
determine ghost nodes
Definition: ProblemsManager.cpp:2339
MoFEM::CoreInterface::add_problem
virtual MoFEMErrorCode add_problem(const std::string &name, enum MoFEMTypes bh=MF_EXCL, int verb=DEFAULT_VERBOSITY)=0
Add problem.
MoFEM::PetscOptionsGetInt
PetscErrorCode PetscOptionsGetInt(PetscOptions *, const char pre[], const char name[], PetscInt *ivalue, PetscBool *set)
Definition: DeprecatedPetsc.hpp:142
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.
NonlinearElasticElement::setBlocks
MoFEMErrorCode setBlocks(boost::shared_ptr< FunctionsToCalculatePiolaKirchhoffI< double >> materialDoublePtr, boost::shared_ptr< FunctionsToCalculatePiolaKirchhoffI< adouble >> materialAdoublePtr)
Definition: NonLinearElasticElement.cpp:1086
MoFEM::ProblemsManager::partitionProblem
MoFEMErrorCode partitionProblem(const std::string name, int verb=VERBOSE)
partition problem dofs (collective)
Definition: ProblemsManager.cpp:1683
F
@ F
Definition: free_surface.cpp:394
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