v0.14.0
simple_interface.cpp
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1 /**
2  * \file simple_interface.cpp
3  * \ingroup mofem_simple_interface
4  * \example simple_interface.cpp
5  *
6  * Calculate volume by integrating volume elements and using divergence theorem
7  * by integrating surface elements.
8  *
9  */
10 
11 
12 
13 #include <MoFEM.hpp>
14 using namespace MoFEM;
15 
16 static char help[] = "...\n\n";
17 
18 struct OpVolume : public VolumeElementForcesAndSourcesCore::UserDataOperator {
19  Vec vOl;
20  OpVolume(const std::string &field_name, Vec vol)
21  : VolumeElementForcesAndSourcesCore::UserDataOperator(field_name, OPROW),
22  vOl(vol) {}
23  MoFEMErrorCode doWork(int side, EntityType type,
24  EntitiesFieldData::EntData &data) {
25 
26  MoFEMFunctionBegin;
27  if (type != MBVERTEX)
28  MoFEMFunctionReturnHot(0);
29  const int nb_int_pts = getGaussPts().size2();
30  // cerr << nb_int_pts << endl;
31  auto t_w = getFTensor0IntegrationWeight();
32  double v = getMeasure();
33  double vol = 0;
34  for (int gg = 0; gg != nb_int_pts; gg++) {
35  vol += t_w * v;
36  ++t_w;
37  }
38  CHKERR VecSetValue(vOl, 0, vol, ADD_VALUES);
39  MoFEMFunctionReturn(0);
40  }
41  MoFEMErrorCode doWork(int row_side, int col_side, EntityType row_type,
42  EntityType col_type,
43  EntitiesFieldData::EntData &row_data,
44  EntitiesFieldData::EntData &col_data) {
45  MoFEMFunctionBeginHot;
46  // PetscPrintf(PETSC_COMM_WORLD,"domain: calculate matrix\n");
47  MoFEMFunctionReturnHot(0);
48  }
49 };
50 
51 struct OpFace : public FaceElementForcesAndSourcesCore::UserDataOperator {
52  Vec vOl;
53  OpFace(const std::string &field_name, Vec vol)
54  : FaceElementForcesAndSourcesCore::UserDataOperator(field_name, OPROW),
55  vOl(vol) {}
56  MoFEMErrorCode doWork(int side, EntityType type,
57  EntitiesFieldData::EntData &data) {
58 
59  MoFEMFunctionBegin;
60  if (type != MBVERTEX)
61  MoFEMFunctionReturnHot(0);
62  const int nb_int_pts = getGaussPts().size2();
63  auto t_normal = getFTensor1NormalsAtGaussPts();
64  auto t_w = getFTensor0IntegrationWeight();
65  auto t_coords = getFTensor1CoordsAtGaussPts();
66  FTensor::Index<'i', 3> i;
67  double vol = 0;
68  for (int gg = 0; gg != nb_int_pts; gg++) {
69  vol += (t_coords(i) * t_normal(i)) * t_w;
70  ++t_normal;
71  ++t_w;
72  ++t_coords;
73  }
74  vol /= 6;
75  CHKERR VecSetValue(vOl, 0, vol, ADD_VALUES);
76  MoFEMFunctionReturn(0);
77  }
78  MoFEMErrorCode doWork(int row_side, int col_side, EntityType row_type,
79  EntityType col_type,
80  EntitiesFieldData::EntData &row_data,
81  EntitiesFieldData::EntData &col_data) {
82  MoFEMFunctionBeginHot;
83  // PetscPrintf(PETSC_COMM_WORLD,"boundary: calculate matrix\n");
84  MoFEMFunctionReturnHot(0);
85  }
86 };
87 
88 struct VolRule {
89  int operator()(int, int, int) const { return 2; }
90 };
91 struct FaceRule {
92  int operator()(int, int, int) const { return 4; }
93 };
94 
95 int main(int argc, char *argv[]) {
96 
97  // initialize petsc
98  MoFEM::Core::Initialize(&argc, &argv, (char *)0, help);
99 
100  try {
101 
102  // Create MoAB database
103  moab::Core moab_core;
104  moab::Interface &moab = moab_core;
105 
106  // Create MoFEM database and link it to MoAB
107  MoFEM::Core mofem_core(moab);
108  MoFEM::Interface &m_field = mofem_core;
109 
110  // Register DM Manager
111  DMType dm_name = "DMMOFEM";
112  CHKERR DMRegister_MoFEM(dm_name);
113 
114  // Simple interface
115  Simple *simple_interface;
116  CHKERR m_field.getInterface(simple_interface);
117  {
118  // get options from command line
119  CHKERR simple_interface->getOptions();
120  // load mesh file
121  CHKERR simple_interface->loadFile();
122  // add fields
123  CHKERR simple_interface->addDomainField("MESH_NODE_POSITIONS", H1,
124  AINSWORTH_LEGENDRE_BASE, 3);
125  CHKERR simple_interface->addBoundaryField("MESH_NODE_POSITIONS", H1,
126  AINSWORTH_LEGENDRE_BASE, 3);
127  CHKERR simple_interface->addSkeletonField("MESH_NODE_POSITIONS", H1,
128  AINSWORTH_LEGENDRE_BASE, 3);
129 
130  // set fields order
131  CHKERR simple_interface->setFieldOrder("MESH_NODE_POSITIONS", 1);
132  // setup problem
133  CHKERR simple_interface->setUp();
134  // Project mesh coordinate on mesh
135  Projection10NodeCoordsOnField ent_method(m_field, "MESH_NODE_POSITIONS");
136  CHKERR m_field.loop_dofs("MESH_NODE_POSITIONS", ent_method);
137  // get dm
138  auto dm = simple_interface->getDM();
139  // create elements
140  auto domain_fe =
141  boost::make_shared<VolumeElementForcesAndSourcesCore>(m_field);
142  auto boundary_fe =
143  boost::make_shared<FaceElementForcesAndSourcesCore>(m_field);
144 
145  // set integration rule
146  domain_fe->getRuleHook = VolRule();
147  boundary_fe->getRuleHook = FaceRule();
148  // create distributed vector to accumulate values from processors.
149  int ghosts[] = {0};
150 
151  auto vol = createGhostVector(
152  PETSC_COMM_WORLD, m_field.get_comm_rank() == 0 ? 1 : 0, 1,
153  m_field.get_comm_rank() == 0 ? 0 : 1, ghosts);
154  auto surf_vol = vectorDuplicate(vol);
155 
156  // set operator to the volume element
157  auto material_grad_mat = boost::make_shared<MatrixDouble>();
158  auto material_det_vec = boost::make_shared<VectorDouble>();
159 
160  domain_fe->getOpPtrVector().push_back(
161  new OpCalculateVectorFieldGradient<3, 3>("MESH_NODE_POSITIONS",
162  material_grad_mat));
163  domain_fe->getOpPtrVector().push_back(new OpInvertMatrix<3>(
164  material_grad_mat, material_det_vec, nullptr));
165  domain_fe->getOpPtrVector().push_back(
166  new OpSetHOWeights(material_det_vec));
167  domain_fe->getOpPtrVector().push_back(
168  new OpCalculateHOCoords("MESH_NODE_POSITIONS"));
169  domain_fe->getOpPtrVector().push_back(
170  new OpVolume("MESH_NODE_POSITIONS", vol));
171  // set operator to the face element
172  boundary_fe->getOpPtrVector().push_back(
173  new OpCalculateHOCoords("MESH_NODE_POSITIONS"));
174  boundary_fe->getOpPtrVector().push_back(
175  new OpFace("MESH_NODE_POSITIONS", surf_vol));
176  // make integration in volume (here real calculations starts)
177  CHKERR DMoFEMLoopFiniteElements(dm, simple_interface->getDomainFEName(),
178  domain_fe);
179  // make integration on boundary
180  CHKERR DMoFEMLoopFiniteElements(dm, simple_interface->getBoundaryFEName(),
181  boundary_fe);
182 
183  auto skeleton_fe = boost::make_shared<FEMethod>();
184  auto A = createDMMatrix(dm);
185  auto B = createDMMatrix(dm);
186  auto f = createDMVector(dm);
187  auto x = createDMVector(dm);
188  auto x_t = createDMVector(dm);
189  auto x_tt = createDMVector(dm);
190  skeleton_fe->f = f;
191  skeleton_fe->A = A;
192  skeleton_fe->B = B;
193  skeleton_fe->x = x;
194  skeleton_fe->x_t = x_t;
195  skeleton_fe->x_tt = x_tt;
196 
197  skeleton_fe->preProcessHook = [&]() {
198  MoFEMFunctionBegin;
199  if (f != skeleton_fe->ts_F)
200  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "Wrong ptr");
201  if (A != skeleton_fe->ts_A)
202  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "Wrong ptr");
203  if (B != skeleton_fe->ts_B)
204  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "Wrong ptr");
205  if (x != skeleton_fe->ts_u)
206  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "Wrong ptr");
207  if (x_t != skeleton_fe->ts_u_t)
208  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "Wrong ptr");
209  if (x_tt != skeleton_fe->ts_u_tt)
210  SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "Wrong ptr");
211  MoFEMFunctionReturn(0);
212  };
213 
214  skeleton_fe->postProcessHook = []() { return 0; };
215  skeleton_fe->operatorHook = []() { return 0; };
216 
217  CHKERR DMoFEMLoopFiniteElements(dm, simple_interface->getSkeletonFEName(),
218  skeleton_fe);
219 
220  // assemble volumes from processors and accumulate on processor of rank 0
221  CHKERR VecAssemblyBegin(vol);
222  CHKERR VecAssemblyEnd(vol);
223  CHKERR VecGhostUpdateBegin(vol, ADD_VALUES, SCATTER_REVERSE);
224  CHKERR VecGhostUpdateEnd(vol, ADD_VALUES, SCATTER_REVERSE);
225  CHKERR VecAssemblyBegin(surf_vol);
226  CHKERR VecAssemblyEnd(surf_vol);
227  CHKERR VecGhostUpdateBegin(surf_vol, ADD_VALUES, SCATTER_REVERSE);
228  CHKERR VecGhostUpdateEnd(surf_vol, ADD_VALUES, SCATTER_REVERSE);
229  if (m_field.get_comm_rank() == 0) {
230  double *a_vol;
231  CHKERR VecGetArray(vol, &a_vol);
232  double *a_surf_vol;
233  CHKERR VecGetArray(surf_vol, &a_surf_vol);
234  cout << "Volume = " << a_vol[0] << endl;
235  cout << "Surf Volume = " << a_surf_vol[0] << endl;
236  if (fabs(a_vol[0] - a_surf_vol[0]) > 1e-12) {
237  SETERRQ(PETSC_COMM_SELF, MOFEM_ATOM_TEST_INVALID, "Should be zero");
238  }
239  CHKERR VecRestoreArray(vol, &a_vol);
240  CHKERR VecRestoreArray(vol, &a_surf_vol);
241  }
242 
243  }
244  }
245  CATCH_ERRORS;
246 
247  // finish work cleaning memory, getting statistics, etc.
248  MoFEM::Core::Finalize();
249 
250  return 0;
251 }
MoFEMFunctionReturnHot
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:460
MoFEM::UnknownInterface::getInterface
MoFEMErrorCode getInterface(IFACE *&iface) const
Get interface reference to pointer of interface.
Definition: UnknownInterface.hpp:93
MoFEM::EntitiesFieldData::EntData
Data on single entity (This is passed as argument to DataOperator::doWork)
Definition: EntitiesFieldData.hpp:128
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.
MoFEM::CoreTmp< 0 >
Core (interface) class.
Definition: Core.hpp:82
H1
@ H1
continuous field
Definition: definitions.h:85
OpFace::doWork
MoFEMErrorCode doWork(int side, EntityType type, EntitiesFieldData::EntData &data)
Operator for linear form, usually to calculate values on right hand side.
Definition: simple_interface.cpp:56
OpFace::vOl
Vec vOl
Definition: simple_interface.cpp:52
MoFEM::Exceptions::MoFEMErrorCode
PetscErrorCode MoFEMErrorCode
MoFEM/PETSc error code.
Definition: Exceptions.hpp:56
FaceRule::operator()
int operator()(int, int, int) const
Definition: simple_interface.cpp:92
MoFEM::CoreInterface::get_comm_rank
virtual int get_comm_rank() const =0
MoFEM::Simple::getSkeletonFEName
const std::string getSkeletonFEName() const
Get the Skeleton FE Name.
Definition: Simple.hpp:382
main
int main(int argc, char *argv[])
Definition: simple_interface.cpp:95
MoFEM::Simple::loadFile
MoFEMErrorCode loadFile(const std::string options, const std::string mesh_file_name, LoadFileFunc loadFunc=defaultLoadFileFunc)
Load mesh file.
Definition: Simple.cpp:194
MoFEM.hpp
A
constexpr AssemblyType A
Definition: operators_tests.cpp:30
VolRule
Set integration rule to volume elements.
Definition: simple_interface.cpp:88
MoFEM::Projection10NodeCoordsOnField
Projection of edge entities with one mid-node on hierarchical basis.
Definition: Projection10NodeCoordsOnField.hpp:24
MoFEM::CoreTmp< 0 >::Finalize
static MoFEMErrorCode Finalize()
Checks for options to be called at the conclusion of the program.
Definition: Core.cpp:112
MoFEM::Simple
Simple interface for fast problem set-up.
Definition: Simple.hpp:27
MoFEM::OpCalculateHOCoords
Calculate HO coordinates at gauss points.
Definition: HODataOperators.hpp:41
MoFEM::createDMMatrix
auto createDMMatrix(DM dm)
Get smart matrix from DM.
Definition: DMMoFEM.hpp:1056
MoFEM::DeprecatedCoreInterface
Deprecated interface functions.
Definition: DeprecatedCoreInterface.hpp:16
MoFEM::Simple::addSkeletonField
MoFEMErrorCode addSkeletonField(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 skeleton.
Definition: Simple.cpp:372
MoFEM::Interface
DeprecatedCoreInterface Interface
Definition: Interface.hpp:2010
MoFEM::Simple::getOptions
MoFEMErrorCode getOptions()
get options
Definition: Simple.cpp:180
MoFEM::Simple::getDM
MoFEMErrorCode getDM(DM *dm)
Get DM.
Definition: Simple.cpp:747
CHKERR
#define CHKERR
Inline error check.
Definition: definitions.h:548
MoFEM::createDMVector
auto createDMVector(DM dm)
Get smart vector from DM.
Definition: DMMoFEM.hpp:1099
MoFEM::createGhostVector
auto createGhostVector(MPI_Comm comm, PetscInt n, PetscInt N, PetscInt nghost, const PetscInt ghosts[])
Create smart ghost vector.
Definition: PetscSmartObj.hpp:179
MoFEM
implementation of Data Operators for Forces and Sources
Definition: Common.hpp:10
MoFEM::ForcesAndSourcesCore::UserDataOperator
Definition: ForcesAndSourcesCore.hpp:549
MoFEM::FaceElementForcesAndSourcesCore::UserDataOperator
default operator for TRI element
Definition: FaceElementForcesAndSourcesCore.hpp:94
convert.type
type
Definition: convert.py:64
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::DMRegister_MoFEM
PetscErrorCode DMRegister_MoFEM(const char sname[])
Register MoFEM problem.
Definition: DMMoFEM.cpp:43
OpFace
Definition: boundary_marker.cpp:19
MoFEM::Simple::getDomainFEName
const std::string getDomainFEName() const
Get the Domain FE Name.
Definition: Simple.hpp:368
MoFEM::FaceElementForcesAndSourcesCore
Face finite element.
Definition: FaceElementForcesAndSourcesCore.hpp:23
OpVolume::doWork
MoFEMErrorCode doWork(int row_side, int col_side, EntityType row_type, EntityType col_type, EntitiesFieldData::EntData &row_data, EntitiesFieldData::EntData &col_data)
Operator for bi-linear form, usually to calculate values on left hand side.
Definition: simple_interface.cpp:41
FaceRule
Set integration rule to boundary elements.
Definition: simple_interface.cpp:91
VolRule::operator()
int operator()(int, int, int) const
Definition: simple_interface.cpp:89
MoFEM::VolumeElementForcesAndSourcesCore
Volume finite element base.
Definition: VolumeElementForcesAndSourcesCore.hpp:26
i
FTensor::Index< 'i', SPACE_DIM > i
Definition: hcurl_divergence_operator_2d.cpp:27
help
static char help[]
Definition: simple_interface.cpp:16
MoFEM::VolumeElementForcesAndSourcesCore::UserDataOperator
Definition: VolumeElementForcesAndSourcesCore.hpp:108
field_name
constexpr auto field_name
Definition: poisson_2d_homogeneous.cpp:13
FTensor::Index< 'i', 3 >
MoFEM::Simple::setFieldOrder
MoFEMErrorCode setFieldOrder(const std::string field_name, const int order, const Range *ents=NULL)
Set field order.
Definition: Simple.cpp:545
MoFEM::OpCalculateVectorFieldGradient
Get field gradients at integration pts for scalar filed rank 0, i.e. vector field.
Definition: UserDataOperators.hpp:1535
OpVolume::vOl
Vec vOl
Definition: simple_interface.cpp:19
OpFace::OpFace
OpFace(const std::string &field_name, Vec vol)
Definition: simple_interface.cpp:53
v
const double v
phase velocity of light in medium (cm/ns)
Definition: initial_diffusion.cpp:40
OpVolume::OpVolume
OpVolume(const std::string &field_name, Vec vol)
Definition: simple_interface.cpp:20
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::vectorDuplicate
SmartPetscObj< Vec > vectorDuplicate(Vec vec)
Create duplicate vector of smart vector.
Definition: PetscSmartObj.hpp:221
CATCH_ERRORS
#define CATCH_ERRORS
Catch errors.
Definition: definitions.h:385
MoFEM::Core
CoreTmp< 0 > Core
Definition: Core.hpp:1148
OpVolume::doWork
MoFEMErrorCode doWork(int side, EntityType type, EntitiesFieldData::EntData &data)
Operator for linear form, usually to calculate values on right hand side.
Definition: simple_interface.cpp:23
HenckyOps::f
auto f
Definition: HenckyOps.hpp:15
MoFEM::OpSetHOWeights
Set inverse jacobian to base functions.
Definition: HODataOperators.hpp:159
AINSWORTH_LEGENDRE_BASE
@ AINSWORTH_LEGENDRE_BASE
Ainsworth Cole (Legendre) approx. base .
Definition: definitions.h:60
MoFEM::Simple::getBoundaryFEName
const std::string getBoundaryFEName() const
Get the Boundary FE Name.
Definition: Simple.hpp:375
EigenMatrix::Vec
const FTensor::Tensor2< T, Dim, Dim > Vec
Definition: MatrixFunction.hpp:66
MOFEM_DATA_INCONSISTENCY
@ MOFEM_DATA_INCONSISTENCY
Definition: definitions.h:31
MoFEM::OpInvertMatrix
Definition: UserDataOperators.hpp:3249
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:354
MOFEM_ATOM_TEST_INVALID
@ MOFEM_ATOM_TEST_INVALID
Definition: definitions.h:40
MoFEMFunctionBeginHot
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:453
MoFEM::Simple::setUp
MoFEMErrorCode setUp(const PetscBool is_partitioned=PETSC_TRUE)
Setup problem.
Definition: Simple.cpp:683
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:586
MoFEMFunctionReturn
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:429
OpVolume
Definition: simple_interface.cpp:18
MoFEMFunctionBegin
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:359
OpFace::doWork
MoFEMErrorCode doWork(int row_side, int col_side, EntityType row_type, EntityType col_type, EntitiesFieldData::EntData &row_data, EntitiesFieldData::EntData &col_data)
Operator for bi-linear form, usually to calculate values on left hand side.
Definition: simple_interface.cpp:78
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