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dm_build_partitioned_mesh.cpp
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1/** \file dm_build_partitioned_mesh.cpp
2 \example dm_build_partitioned_mesh.cpp
3 \brief Testing problem for partitioned mesh
4
5*/
6
7#include <MoFEM.hpp>
8
9using namespace MoFEM;
10
11static char help[] = "...\n\n";
12
13struct CountUp : FEMethod {
14
15 CountUp(int &counter) : FEMethod(), cOunter(counter) {}
16 MoFEMErrorCode preProcess() { return 0; }
18 ++cOunter;
19 return 0;
20 }
22
23private:
24 int &cOunter;
25};
26
28
29 CountDown(int &counter) : FEMethod(), cOunter(counter) {}
30 MoFEMErrorCode preProcess() { return 0; }
32 --cOunter;
33 return 0;
34 }
36
37private:
38 int &cOunter;
39};
40
41int main(int argc, char *argv[]) {
42 // initialize petsc
43 MoFEM::Core::Initialize(&argc, &argv, (char *)0, help);
44
45 try {
46
47 PetscBool flg = PETSC_TRUE;
48 char mesh_file_name[255];
49#if PETSC_VERSION_GE(3, 6, 4)
50 CHKERR PetscOptionsGetString(PETSC_NULL, "", "-my_file", mesh_file_name,
51 255, &flg);
52#else
53 CHKERR PetscOptionsGetString(PETSC_NULL, PETSC_NULL, "-my_file",
54 mesh_file_name, 255, &flg);
55#endif
56 if (flg != PETSC_TRUE) {
57 SETERRQ(PETSC_COMM_SELF, 1, "*** ERROR -my_file (MESH FILE NEEDED)");
58 }
59
60 // register new dm type, i.e. mofem
61 DMType dm_name = "DMMOFEM";
62 CHKERR DMRegister_MoFEM(dm_name);
63
64 // create dm instance
65 DM dm;
66 CHKERR DMCreate(PETSC_COMM_WORLD, &dm);
67 CHKERR DMSetType(dm, dm_name);
68
69 // read mesh and create moab and mofem data structures
70 moab::Core mb_instance;
71 moab::Interface &moab = mb_instance;
72
73 ParallelComm *pcomm = ParallelComm::get_pcomm(&moab, MYPCOMM_INDEX);
74 auto moab_comm_wrap =
75 boost::make_shared<WrapMPIComm>(PETSC_COMM_WORLD, false);
76 if (pcomm == NULL)
77 pcomm = new ParallelComm(&moab, moab_comm_wrap->get_comm());
78
79 const char *option;
80 option = "PARALLEL=BCAST_DELETE;PARALLEL_RESOLVE_SHARED_ENTS;PARTITION="
81 "PARALLEL_PARTITION;";
82 CHKERR moab.load_file(mesh_file_name, 0, option);
83
84 MoFEM::Core core(moab, PETSC_COMM_WORLD);
85 MoFEM::Interface &m_field = core;
86
87 EntityHandle root_set = moab.get_root_set();
88 // add all entities to database, all of them will be used
89 BitRefLevel bit_level0;
90 bit_level0.set(0);
91 CHKERR m_field.getInterface<BitRefManager>()->setBitRefLevelByDim(
92 root_set, 3, bit_level0);
93 // define & build field
94 int field_rank = 3;
95#if PETSC_VERSION_GE(3, 6, 4)
96 CHKERR PetscOptionsGetInt(PETSC_NULL, "", "-my_field_rank", &field_rank,
97 &flg);
98#else
99 CHKERR PetscOptionsGetInt(PETSC_NULL, PETSC_NULL, "-my_field_rank",
100 &field_rank, &flg);
101#endif
102 CHKERR m_field.add_field("FIELD1", H1, AINSWORTH_LEGENDRE_BASE, field_rank);
103 CHKERR m_field.add_field("FIELD2", L2, AINSWORTH_LEGENDRE_BASE, 1);
104
105 // add entities to field
106 CHKERR m_field.add_ents_to_field_by_type(root_set, MBTET, "FIELD1");
107 CHKERR m_field.add_ents_to_field_by_type(root_set, MBTET, "FIELD2");
108
109 // set app. order
110 int order = 4;
111 CHKERR m_field.set_field_order(root_set, MBTET, "FIELD1", order);
112 CHKERR m_field.set_field_order(root_set, MBTRI, "FIELD1", order);
113 CHKERR m_field.set_field_order(root_set, MBEDGE, "FIELD1", order);
114 CHKERR m_field.set_field_order(root_set, MBVERTEX, "FIELD1", 1);
115 CHKERR m_field.set_field_order(root_set, MBTET, "FIELD2", order);
116
117 // build data structures for fields
118 CHKERR m_field.build_fields();
119
120 // define & build finite elements
121 CHKERR m_field.add_finite_element("FE");
122 // Define rows/cols and element data
123 CHKERR m_field.modify_finite_element_add_field_row("FE", "FIELD1");
124 CHKERR m_field.modify_finite_element_add_field_col("FE", "FIELD1");
125 CHKERR m_field.modify_finite_element_add_field_data("FE", "FIELD1");
126 CHKERR m_field.modify_finite_element_add_field_row("FE", "FIELD2");
127 CHKERR m_field.modify_finite_element_add_field_col("FE", "FIELD2");
128 CHKERR m_field.modify_finite_element_add_field_data("FE", "FIELD2");
129 // Only data
130 CHKERR m_field.add_finite_element("FE_ONLY_DATA");
131 CHKERR m_field.modify_finite_element_add_field_data("FE_ONLY_DATA",
132 "FIELD1");
133 CHKERR m_field.modify_finite_element_add_field_data("FE_ONLY_DATA",
134 "FIELD2");
135 // Add entities to finite element
136 CHKERR m_field.add_ents_to_finite_element_by_type(root_set, MBTET, "FE");
137 CHKERR m_field.add_ents_to_finite_element_by_type(root_set, MBTET,
138 "FE_ONLY_DATA");
139 // build finite elemnts
141 // build adjacencies
142 CHKERR m_field.build_adjacencies(bit_level0);
143
144 // set dm data structure which created mofem data structures
145 CHKERR DMMoFEMCreateMoFEM(dm, &m_field, "TEST_PROBLEM", bit_level0);
146 CHKERR DMMoFEMSetIsPartitioned(dm, PETSC_TRUE);
148 dm, PETSC_FALSE); // this is for testing (this problem has the same rows
149 // and cols)
150 CHKERR DMSetFromOptions(dm);
151 CHKERR DMMoFEMAddElement(dm, "FE");
152 CHKERR DMMoFEMAddElement(dm, "FE_ONLY_DATA");
153 CHKERR DMSetUp(dm);
154
155 // dump data to file, just to check if something was changed
158
160 ->checkMPIAIJWithArraysMatrixFillIn<PetscGlobalIdx_mi_tag>(
161 "TEST_PROBLEM", -1, -1, 1);
162
164 ->checkMPIAIJMatrixFillIn<PetscGlobalIdx_mi_tag>("TEST_PROBLEM", -1, -1,
165 1);
166
167 std::vector<std::string> fields_list;
168 fields_list.push_back("FIELD1");
169
170 // PetscSection section;
171 PetscSection section;
172 CHKERR m_field.getInterface<ISManager>()->sectionCreate("TEST_PROBLEM",
173 &section);
174 CHKERR PetscSectionView(section, PETSC_VIEWER_STDOUT_WORLD);
175 CHKERR DMSetSection(dm, section);
176 CHKERR PetscSectionDestroy(&section);
177
178 PetscBool save_file = PETSC_TRUE;
179#if PETSC_VERSION_GE(3, 6, 4)
180 CHKERR PetscOptionsGetBool(PETSC_NULL, "", "-my_save_file", &save_file,
181 &flg);
182#else
183 CHKERR PetscOptionsGetBool(PETSC_NULL, PETSC_NULL, "-my_save_file",
184 &save_file, &flg);
185#endif
186 if (save_file) {
187 PetscViewer viewer;
188 CHKERR PetscViewerASCIIOpen(PETSC_COMM_WORLD,
189 "dm_build_partitioned_mesh.txt", &viewer);
190 CHKERR PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_INFO);
191 MatView(m, viewer);
192 CHKERR PetscViewerDestroy(&viewer);
193 }
194
195 int count = 0;
197 boost::make_shared<CountUp>(count));
198 CHKERR DMoFEMLoopFiniteElements(dm, "FE_ONLY_DATA",
199 boost::make_shared<CountDown>(count));
200 if (count)
201 SETERRQ1(PETSC_COMM_SELF, MOFEM_ATOM_TEST_INVALID, "Should be zero %d",
202 count);
203
204 auto check_consistency_of_uids = [&]() {
206 auto field_ents_ptr = m_field.get_field_ents();
207 for (auto &fe : *field_ents_ptr) {
208 if (fe->getOwnerProc() !=
209 (FieldEntity::getOwnerFromUniqueId(fe->getGlobalUniqueId()))) {
210 MOFEM_LOG("SELF", Sev::error) << *fe;
211 MOFEM_LOG("SELF", Sev::error)
212 << "UId owner proc "
213 << FieldEntity::getOwnerFromUniqueId(fe->getGlobalUniqueId());
214 MOFEM_LOG("SELF", Sev::error)
215 << "Entity owner proc " << fe->getOwnerProc();
216 SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
217 "UId and entity handle inconsistency");
218 }
219 if (fe->getEnt() !=
220 FieldEntity::getHandleFromUniqueId(fe->getLocalUniqueId())) {
221 MOFEM_LOG("SELF", Sev::error) << *fe;
222 MOFEM_LOG("SELF", Sev::error)
223 << "UId handle "
224 << FieldEntity::getHandleFromUniqueId(fe->getLocalUniqueId());
225 MOFEM_LOG("SELF", Sev::error) << "Entity handle " << fe->getEnt();
226 SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
227 "UId and entity handle inconsistency");
228 }
229 const auto field_bit_number_from_uid =
230 FieldEntity::getFieldBitNumberFromUniqueId(fe->getLocalUniqueId());
231 if (fe->getBitNumber() != field_bit_number_from_uid) {
232 MOFEM_LOG("SELF", Sev::error) << *fe;
233 MOFEM_LOG("SELF", Sev::error)
234 << "UId field bit " << field_bit_number_from_uid;
235 MOFEM_LOG("SELF", Sev::error)
236 << "Entity owner proc " << fe->getBitNumber();
237 SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
238 "UId and entity handle inconsistency");
239 }
240 if (fe->getName() != m_field.get_field_name(BitFieldId().set(
241 field_bit_number_from_uid - 1))) {
242 MOFEM_LOG("SELF", Sev::error) << *fe;
243 MOFEM_LOG("SELF", Sev::error)
244 << "UId field bit "
245 << m_field.get_field_name(
246 BitFieldId().set(field_bit_number_from_uid - 1));
247 MOFEM_LOG("SELF", Sev::error)
248 << "Entity owner proc " << fe->getName();
249 SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
250 "UId and entity handle inconsistency");
251 }
252 }
253
255 };
256
257 CHKERR check_consistency_of_uids();
258
259 // destry dm
260 CHKERR DMDestroy(&dm);
261 }
263
264 // finish work cleaning memory, getting statistics, ect.
266
267 return 0;
268}
int main()
Definition: adol-c_atom.cpp:46
#define CATCH_ERRORS
Catch errors.
Definition: definitions.h:372
@ AINSWORTH_LEGENDRE_BASE
Ainsworth Cole (Legendre) approx. base .
Definition: definitions.h:60
@ L2
field with C-1 continuity
Definition: definitions.h:88
@ H1
continuous field
Definition: definitions.h:85
#define MYPCOMM_INDEX
default communicator number PCOMM
Definition: definitions.h:215
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:346
@ MOFEM_ATOM_TEST_INVALID
Definition: definitions.h:40
@ MOFEM_DATA_INCONSISTENCY
Definition: definitions.h:31
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:416
#define CHKERR
Inline error check.
Definition: definitions.h:535
static char help[]
FTensor::Index< 'm', SPACE_DIM > m
PetscErrorCode DMMoFEMSetIsPartitioned(DM dm, PetscBool is_partitioned)
Definition: DMMoFEM.cpp:1109
PetscErrorCode DMMoFEMAddElement(DM dm, std::string fe_name)
add element to dm
Definition: DMMoFEM.cpp:483
PetscErrorCode DMMoFEMSetSquareProblem(DM dm, PetscBool square_problem)
set squared problem
Definition: DMMoFEM.cpp:442
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
PetscErrorCode DMCreateMatrix_MoFEM(DM dm, Mat *M)
Definition: DMMoFEM.cpp:1183
PetscErrorCode DMRegister_MoFEM(const char sname[])
Register MoFEM problem.
Definition: DMMoFEM.cpp:47
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
virtual const FieldEntity_multiIndex * get_field_ents() const =0
Get the field ents object.
virtual MoFEMErrorCode add_finite_element(const std::string &fe_name, enum MoFEMTypes bh=MF_EXCL, int verb=DEFAULT_VERBOSITY)=0
add finite element
virtual MoFEMErrorCode build_finite_elements(int verb=DEFAULT_VERBOSITY)=0
Build finite elements.
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
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
virtual MoFEMErrorCode modify_finite_element_add_field_data(const std::string &fe_name, const std::string name_filed)=0
set finite element field data
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
virtual MoFEMErrorCode build_fields(int verb=DEFAULT_VERBOSITY)=0
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.
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.
#define MOFEM_LOG(channel, severity)
Log.
Definition: LogManager.hpp:308
char mesh_file_name[255]
PetscErrorCode MoFEMErrorCode
MoFEM/PETSc error code.
Definition: Exceptions.hpp:56
std::bitset< BITFIELDID_SIZE > BitFieldId
Field Id.
Definition: Types.hpp:42
std::bitset< BITREFLEVEL_SIZE > BitRefLevel
Bit structure attached to each entity identifying to what mesh entity is attached.
Definition: Types.hpp:40
implementation of Data Operators for Forces and Sources
Definition: Common.hpp:10
PetscErrorCode PetscOptionsGetInt(PetscOptions *, const char pre[], const char name[], PetscInt *ivalue, PetscBool *set)
PetscErrorCode PetscOptionsGetBool(PetscOptions *, const char pre[], const char name[], PetscBool *bval, PetscBool *set)
PetscErrorCode PetscOptionsGetString(PetscOptions *, const char pre[], const char name[], char str[], size_t size, PetscBool *set)
MoFEMErrorCode preProcess()
function is run at the beginning of loop
MoFEMErrorCode operator()()
function is run for every finite element
MoFEMErrorCode postProcess()
function is run at the end of loop
CountDown(int &counter)
MoFEMErrorCode postProcess()
function is run at the end of loop
MoFEMErrorCode preProcess()
function is run at the beginning of loop
CountUp(int &counter)
MoFEMErrorCode operator()()
function is run for every finite element
Managing BitRefLevels.
virtual MoFEMErrorCode build_adjacencies(const Range &ents, int verb=DEFAULT_VERBOSITY)=0
build adjacencies
virtual std::string get_field_name(const BitFieldId id) const =0
get field name from id
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.
Core (interface) class.
Definition: Core.hpp:82
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
static MoFEMErrorCode Finalize()
Checks for options to be called at the conclusion of the program.
Definition: Core.cpp:112
Deprecated interface functions.
structure for User Loop Methods on finite elements
static auto getHandleFromUniqueId(const UId uid)
Get the Handle From Unique Id.
static auto getFieldBitNumberFromUniqueId(const UId uid)
Get the Field Bit Number From Unique Id.
static auto getOwnerFromUniqueId(const UId uid)
Section manager is used to create indexes and sections.
Definition: ISManager.hpp:23
Matrix manager is used to build and partition problems.
intrusive_ptr for managing petsc objects
MoFEMErrorCode getInterface(IFACE *&iface) const
Get interface refernce to pointer of interface.