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Public Member Functions | Public Attributes | List of all members
BoneRemodeling::MonitorPostProc Struct Reference

#include "users_modules/bone_remodelling/src/Remodeling.hpp"

Inheritance diagram for BoneRemodeling::MonitorPostProc:
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Collaboration diagram for BoneRemodeling::MonitorPostProc:
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Public Member Functions

 MonitorPostProc (MoFEM::Interface &m_field, Remodeling::CommonData &common_data)
 
MoFEMErrorCode preProcess ()
 
MoFEMErrorCode operator() ()
 
MoFEMErrorCode postProcess ()
 

Public Attributes

MoFEM::Interface & mField
 
Remodeling::CommonData & commonData
 
PostProcVolumeOnRefinedMesh postProc
 
PostProcVolumeOnRefinedMesh postProcElastic
 
PetscBool mass_postproc
 
PetscBool equilibrium_flg
 
double rate
 
bool iNit
 
int pRT
 

Detailed Description

Element used to post-process results at each time step

Definition at line 553 of file Remodeling.hpp.

Constructor & Destructor Documentation

◆ MonitorPostProc()

MonitorPostProc::MonitorPostProc ( MoFEM::Interface & m_field,
Remodeling::CommonData & common_data )
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 1386 of file Remodeling.cpp.

1388 : mField(m_field), commonData(common_data), postProc(m_field),
1389 postProcElastic(m_field),
1390 // densityMaps(m_field),
1391 iNit(false) {}
BoneRemodeling::MonitorPostProc::commonData
Remodeling::CommonData & commonData
Definition Remodeling.hpp:556
BoneRemodeling::MonitorPostProc::postProcElastic
PostProcVolumeOnRefinedMesh postProcElastic
Definition Remodeling.hpp:558
BoneRemodeling::MonitorPostProc::postProc
PostProcVolumeOnRefinedMesh postProc
Definition Remodeling.hpp:557

Member Function Documentation

◆ operator()()

MoFEMErrorCode MonitorPostProc::operator() ( )
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 1398 of file Remodeling.cpp.

1398 {
1399 MoFEMFunctionBeginHot;
1400 MoFEMFunctionReturnHot(0);
1401}
MoFEMFunctionReturnHot
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition definitions.h:463
MoFEMFunctionBeginHot
#define MoFEMFunctionBeginHot
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition definitions.h:456

◆ postProcess()

MoFEMErrorCode MonitorPostProc::postProcess ( )
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 1403 of file Remodeling.cpp.

1403 {
1404 MoFEMFunctionBegin;
1405
1406 PetscBool mass_postproc = PETSC_FALSE;
1407 PetscBool equilibrium_flg = PETSC_FALSE;
1408 PetscBool analysis_mesh_flg = PETSC_FALSE;
1409 rate = 1;
1410
1411 PetscOptionsBegin(PETSC_COMM_WORLD, "", "Bone remodeling post-process",
1412 "none");
1413
1414 CHKERR PetscOptionsBool(
1415 "-mass_postproc",
1416 "is used for testing, calculates mass and energy at each time step", "",
1417 mass_postproc, &mass_postproc, PETSC_NULL);
1418
1419 CHKERR PetscOptionsBool("-analysis_mesh",
1420 "saves analysis mesh at each time step", "",
1421 analysis_mesh_flg, &analysis_mesh_flg, PETSC_NULL);
1422
1423 CHKERR PetscOptionsScalar(
1424 "-equilibrium_stop_rate",
1425 "is used to stop calculations when equilibium state is achieved", "",
1426 rate, &rate, &equilibrium_flg);
1427 PetscOptionsEnd();
1428
1429 if (!iNit) {
1430
1431 PetscOptionsBegin(PETSC_COMM_WORLD, "",
1432 "Bone remodeling post-process", "none");
1433
1434 pRT = 1;
1435 CHKERR PetscOptionsInt("-my_output_prt",
1436 "frequncy how often results are dumped on hard disk",
1437 "", 1, &pRT, NULL);
1438 PetscOptionsEnd();
1439
1440 CHKERR postProc.generateReferenceElementMesh();
1441 CHKERR postProc.addFieldValuesPostProc("DISPLACEMENTS");
1442 CHKERR postProc.addFieldValuesPostProc("MESH_NODE_POSITIONS");
1443 if (!commonData.less_post_proc) {
1444 CHKERR postProc.addFieldValuesGradientPostProc("DISPLACEMENTS");
1445 }
1446 // CHKERR postProc.addFieldValuesPostProc("RHO");
1447 // CHKERR postProc.addFieldValuesGradientPostProc("RHO");
1448
1449 {
1450 auto &list_of_operators = postProc.getOpPtrVector();
1451
1452 list_of_operators.push_back(
1453 new OpCalculateScalarFieldValues("RHO", commonData.data.rhoPtr));
1454 list_of_operators.push_back(new OpCalculateScalarFieldGradient<3>(
1455 "RHO", commonData.data.gradRhoPtr));
1456 // Get displacement gradient at integration points
1457 list_of_operators.push_back(new OpCalculateVectorFieldGradient<3, 3>(
1458 "DISPLACEMENTS", commonData.data.gradDispPtr));
1459 list_of_operators.push_back(new OpCalculateStress(commonData));
1460 list_of_operators.push_back(new OpPostProcStress(
1461 postProc.postProcMesh, postProc.mapGaussPts, commonData));
1462 }
1463
1464 CHKERR postProcElastic.generateReferenceElementMesh();
1465 CHKERR postProcElastic.addFieldValuesPostProc("DISPLACEMENTS");
1466 CHKERR postProcElastic.addFieldValuesPostProc("MESH_NODE_POSITIONS");
1467 CHKERR postProcElastic.addFieldValuesGradientPostProc("DISPLACEMENTS");
1468 std::map<int, NonlinearElasticElement::BlockData>::iterator sit =
1469 commonData.elasticPtr->setOfBlocks.begin();
1470 for (; sit != commonData.elasticPtr->setOfBlocks.end(); sit++) {
1471 postProcElastic.getOpPtrVector().push_back(new PostProcStress(
1472 postProcElastic.postProcMesh, postProcElastic.mapGaussPts,
1473 "DISPLACEMENTS", sit->second, postProcElastic.commonData));
1474 }
1475
1476 iNit = true;
1477 }
1478
1479 if (mass_postproc) {
1480 Vec mass_vec;
1481 Vec energ_vec;
1482 int mass_vec_ghost[] = {0};
1483 CHKERR VecCreateGhost(PETSC_COMM_WORLD, (!mField.get_comm_rank()) ? 1 : 0,
1484 1, 1, mass_vec_ghost, &mass_vec);
1485
1486 CHKERR VecZeroEntries(mass_vec);
1487 CHKERR VecDuplicate(mass_vec, &energ_vec);
1488
1489 Remodeling::Fe energyCalc(mField);
1490 CHKERR addHOOpsVol("MESH_NODE_POSITIONS", energyCalc, true, false, false,
1491 true);
1492 energyCalc.getOpPtrVector().push_back(
1493 new OpCalculateScalarFieldValues("RHO", commonData.data.rhoPtr));
1494 energyCalc.getOpPtrVector().push_back(new OpCalculateScalarFieldGradient<3>(
1495 "RHO", commonData.data.gradRhoPtr));
1496 energyCalc.getOpPtrVector().push_back(
1497 new OpCalculateVectorFieldGradient<3, 3>("DISPLACEMENTS",
1498 commonData.data.gradDispPtr));
1499 energyCalc.getOpPtrVector().push_back(new OpCalculateStress(commonData));
1500 energyCalc.getOpPtrVector().push_back(
1501 new OpMassAndEnergyCalculation("RHO", commonData, energ_vec, mass_vec));
1502 CHKERR DMoFEMLoopFiniteElements(commonData.dm, "FE_REMODELLING",
1503 &energyCalc);
1504
1505 CHKERR VecAssemblyBegin(mass_vec);
1506 CHKERR VecAssemblyEnd(mass_vec);
1507 double mass_sum;
1508 CHKERR VecSum(mass_vec, &mass_sum);
1509
1510 CHKERR VecAssemblyBegin(energ_vec);
1511 CHKERR VecAssemblyEnd(energ_vec);
1512 double energ_sum;
1513 CHKERR VecSum(energ_vec, &energ_sum);
1514
1515 CHKERR PetscPrintf(PETSC_COMM_WORLD,
1516 "Time: %g Mass: %6.5g Elastic energy: %6.5g \n", ts_t,
1517 mass_sum, energ_sum);
1518 CHKERR VecDestroy(&mass_vec);
1519 CHKERR VecDestroy(&energ_vec);
1520
1521 if (equilibrium_flg) {
1522 double equilibrium_rate =
1523 fabs(energ_sum - commonData.cUrrent_psi) / energ_sum;
1524 double equilibrium_mass_rate =
1525 fabs(mass_sum - commonData.cUrrent_mass) / mass_sum;
1526 if (equilibrium_rate < rate) {
1527 CHKERR PetscPrintf(
1528 PETSC_COMM_WORLD,
1529 "Energy equilibrium state is achieved! Difference = %0.6g %%. \n",
1530 equilibrium_rate * 100);
1531 }
1532 if (equilibrium_mass_rate < rate) {
1533 CHKERR PetscPrintf(
1534 PETSC_COMM_WORLD,
1535 "Mass equilibrium state is achieved! Difference = %0.6g %%. \n",
1536 equilibrium_mass_rate * 100);
1537 }
1538 commonData.cUrrent_psi = energ_sum;
1539 commonData.cUrrent_mass = mass_sum;
1540 }
1541 }
1542
1543 int step;
1544#if PETSC_VERSION_LE(3, 8, 0)
1545 CHKERR TSGetTimeStepNumber(ts, &step);
1546#else
1547 CHKERR TSGetStepNumber(ts, &step);
1548#endif
1549
1550 if ((step) % pRT == 0) {
1551
1552 ostringstream sss;
1553 sss << "out_" << step << ".h5m";
1554 CHKERR DMoFEMLoopFiniteElements(commonData.dm, "FE_REMODELLING", &postProc);
1555 CHKERR postProc.postProcMesh.write_file(sss.str().c_str(), "MOAB",
1556 "PARALLEL=WRITE_PART");
1557 if (analysis_mesh_flg) {
1558 ostringstream ttt;
1559 ttt << "analysis_mesh_" << step << ".h5m";
1560 CHKERR mField.get_moab().write_file(ttt.str().c_str(), "MOAB",
1561 "PARALLEL=WRITE_PART");
1562 }
1563
1564 if (commonData.nOremodellingBlock) {
1565 CHKERR DMoFEMLoopFiniteElements(commonData.dm, "ELASTIC",
1566 &postProcElastic);
1567 ostringstream ss;
1568 ss << "out_elastic_" << step << ".h5m";
1569 CHKERR postProcElastic.postProcMesh.write_file(ss.str().c_str(), "MOAB",
1570 "PARALLEL=WRITE_PART");
1571 }
1572 }
1573 MoFEMFunctionReturn(0);
1574}
MoFEMFunctionBegin
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition definitions.h:359
MoFEMFunctionReturn
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition definitions.h:432
CHKERR
#define CHKERR
Inline error check.
Definition definitions.h:551
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:576
PostProcTemplateOnRefineMesh::addFieldValuesPostProc
MoFEMErrorCode addFieldValuesPostProc(const std::string field_name, Vec v=PETSC_NULLPTR)
Add operator to post-process L2, H1, Hdiv, Hcurl field value.
Definition PostProcOnRefMesh.hpp:153
PostProcTemplateOnRefineMesh::addFieldValuesGradientPostProc
MoFEMErrorCode addFieldValuesGradientPostProc(const std::string field_name, Vec v=PETSC_NULLPTR)
Add operator to post-process L2 or H1 field gradient.
Definition PostProcOnRefMesh.hpp:195
MoFEM::addHOOpsVol
MoFEMErrorCode addHOOpsVol(const std::string field, E &e, bool h1, bool hcurl, bool hdiv, bool l2)
Definition HODataOperators.hpp:678
BoneRemodeling::Remodeling::CommonData::DataContainers::gradDispPtr
boost::shared_ptr< MatrixDouble > gradDispPtr
Ptr to gradient of displacements matrix container.
Definition Remodeling.hpp:185
BoneRemodeling::Remodeling::CommonData::DataContainers::rhoPtr
boost::shared_ptr< VectorDouble > rhoPtr
Ptr to density matrix container.
Definition Remodeling.hpp:187
BoneRemodeling::Remodeling::CommonData::DataContainers::gradRhoPtr
boost::shared_ptr< MatrixDouble > gradRhoPtr
Gradient of density field.
Definition Remodeling.hpp:188
BoneRemodeling::Remodeling::CommonData::less_post_proc
PetscBool less_post_proc
reduce file size
Definition Remodeling.hpp:163
BoneRemodeling::Remodeling::CommonData::cUrrent_psi
double cUrrent_psi
current free energy for evaluating equilibrium state
Definition Remodeling.hpp:158
BoneRemodeling::Remodeling::CommonData::elasticPtr
boost::shared_ptr< NonlinearElasticElement > elasticPtr
Definition Remodeling.hpp:140
BoneRemodeling::Remodeling::CommonData::cUrrent_mass
double cUrrent_mass
current free energy for evaluating equilibrium state
Definition Remodeling.hpp:160
MoFEM::CoreInterface::get_moab
virtual moab::Interface & get_moab()=0
MoFEM::CoreInterface::get_comm_rank
virtual int get_comm_rank() const =0
MoFEM::ForcesAndSourcesCore::getOpPtrVector
boost::ptr_deque< UserDataOperator > & getOpPtrVector()
Use to push back operator for row operator.
Definition ForcesAndSourcesCore.hpp:83
MoFEM::OpCalculateScalarFieldGradient
Get field gradients at integration pts for scalar field rank 0, i.e. vector field.
Definition UserDataOperators.hpp:1321
MoFEM::OpCalculateScalarFieldValues
Get value at integration points for scalar field.
Definition UserDataOperators.hpp:83
MoFEM::OpCalculateVectorFieldGradient
Get field gradients at integration pts for scalar field rank 0, i.e. vector field.
Definition UserDataOperators.hpp:1576
PostProcTemplateOnRefineMesh::mapGaussPts
std::vector< EntityHandle > mapGaussPts
Definition PostProcOnRefMesh.hpp:125
PostProcTemplateVolumeOnRefinedMesh::generateReferenceElementMesh
MoFEMErrorCode generateReferenceElementMesh()
Generate reference mesh on single element.
Definition PostProcOnRefMesh.hpp:301

◆ preProcess()

MoFEMErrorCode MonitorPostProc::preProcess ( )
Examples
Remodeling.cpp, and Remodeling.hpp.

Definition at line 1393 of file Remodeling.cpp.

1393 {
1394 MoFEMFunctionBeginHot;
1395 MoFEMFunctionReturnHot(0);
1396}

Member Data Documentation

◆ commonData

Remodeling::CommonData& BoneRemodeling::MonitorPostProc::commonData
Examples
Remodeling.hpp.

Definition at line 556 of file Remodeling.hpp.

◆ equilibrium_flg

PetscBool BoneRemodeling::MonitorPostProc::equilibrium_flg
Examples
Remodeling.hpp.

Definition at line 561 of file Remodeling.hpp.

◆ iNit

bool BoneRemodeling::MonitorPostProc::iNit
Examples
Remodeling.hpp.

Definition at line 563 of file Remodeling.hpp.

◆ mass_postproc

PetscBool BoneRemodeling::MonitorPostProc::mass_postproc
Examples
Remodeling.hpp.

Definition at line 560 of file Remodeling.hpp.

◆ mField

MoFEM::Interface& BoneRemodeling::MonitorPostProc::mField
Examples
Remodeling.hpp.

Definition at line 555 of file Remodeling.hpp.

◆ postProc

PostProcVolumeOnRefinedMesh BoneRemodeling::MonitorPostProc::postProc
Examples
Remodeling.hpp.

Definition at line 557 of file Remodeling.hpp.

◆ postProcElastic

PostProcVolumeOnRefinedMesh BoneRemodeling::MonitorPostProc::postProcElastic
Examples
Remodeling.hpp.

Definition at line 558 of file Remodeling.hpp.

◆ pRT

int BoneRemodeling::MonitorPostProc::pRT
Examples
Remodeling.hpp.

Definition at line 564 of file Remodeling.hpp.

◆ rate

double BoneRemodeling::MonitorPostProc::rate
Examples
Remodeling.hpp.

Definition at line 562 of file Remodeling.hpp.

The documentation for this struct was generated from the following files:
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