map_disp.cpp

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/* This file is part of MoFEM.
* \ingroup bone_remodelling
 
* MoFEM is free software: you can redistribute it and/or modify it under
* the terms of the GNU Lesser General Public License as published by the
* Free Software Foundation, either version 3 of the License, or (at your
* option) any later version.
*
* MoFEM is distributed in the hope that it will be useful, but WITHOUT
* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
* FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
* License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with MoFEM. If not, see <http://www.gnu.org/licenses/>. */
 
#include <MoFEM.hpp>
using namespace MoFEM;
 
#include <iostream>
#include <fstream> // fstream
#include <vector>
#include <string>
#include <algorithm> // copy
#include <iterator>  // ostream_operator
#include <boost/tokenizer.hpp>
#include <PostProcOnRefMesh.hpp>
#include <DispMap.hpp>
 
using namespace boost;
using namespace CellEngineering;
 
static char help[] = "\n";
 
int main(int argc, char *argv[]) {
  MoFEM::Core::Initialize(&argc, &argv, (char *)0, help);
 
  try {
 
    moab::Core mb_instance;
    moab::Interface &moab = mb_instance;
 
    // global variables
    char mesh_file_name[255];
    char data_file_name1[255];
    char data_file_name2[255];
    PetscBool flg_file = PETSC_FALSE;
    PetscInt order = 1;
    PetscBool flg_n_part = PETSC_FALSE;
    PetscInt n_partas = 1;
 
    CHKERR PetscOptionsBegin(PETSC_COMM_WORLD, "", "none", "none");
    CHKERR PetscOptionsString("-my_file", "mesh file name", "", "mesh.h5m",
                              mesh_file_name, 255, &flg_file);
 
    CHKERR PetscOptionsString("-my_data_x", "data file name", "", "data_x.h5m",
                              data_file_name1, 255, PETSC_NULL);
 
    CHKERR PetscOptionsString("-my_data_y", "data file name", "", "data_y.h5m",
                              data_file_name2, 255, PETSC_NULL);
 
    CHKERR PetscOptionsInt("-my_order", "default approximation order", "", 1,
                           &order, PETSC_NULL);
 
    CHKERR PetscOptionsInt("-my_nparts", "number of parts", "", 1, &n_partas,
                           &flg_n_part);
 
    ierr = PetscOptionsEnd();
    CHKERRQ(ierr);
 
    if (flg_file != PETSC_TRUE) {
      SETERRQ(PETSC_COMM_SELF, 1, "*** ERROR -my_file (MESH FILE NEEDED)");
    }
 
    if (flg_n_part != PETSC_TRUE) {
      SETERRQ(PETSC_COMM_SELF, 1, "*** ERROR partitioning number not given");
    }
 
    const char *option;
    option = "";
    CHKERR moab.load_file(mesh_file_name, 0, option);
    ParallelComm *pcomm = ParallelComm::get_pcomm(&moab, MYPCOMM_INDEX);
    if (pcomm == NULL)
      pcomm = new ParallelComm(&moab, PETSC_COMM_WORLD);
 
    MoFEM::Core core(moab);
    MoFEM::Interface &m_field = core;
    // meshset consisting all entities in mesh
    EntityHandle root_set = moab.get_root_set();
 
    // Seed all mesh entities to MoFEM database, those entities can be
    // potentially used as finite elements or as entities which carry some
    // approximation field.
    BitRefLevel bit_level0;
    bit_level0.set(0);
    CHKERR m_field.seed_ref_level_3D(root_set, bit_level0);
    // Add field
    CHKERR m_field.add_field("DISP_X", H1, AINSWORTH_LEGENDRE_BASE, 1);
    CHKERR m_field.add_field("DISP_Y", H1, AINSWORTH_LEGENDRE_BASE, 1);
 
    MeshsetsManager *meshsets_manager_ptr;
    CHKERR m_field.query_interface(meshsets_manager_ptr);
 
    Range surface;
    CHKERR meshsets_manager_ptr->getEntitiesByDimension(101, SIDESET, 2,
                                                        surface, true);
    CHKERR m_field.add_ents_to_field_by_type(surface, MBTRI, "DISP_X");
    CHKERR m_field.add_ents_to_field_by_type(surface, MBTRI, "DISP_Y");
 
    CHKERR m_field.set_field_order(0, MBVERTEX, "DISP_X", 1);
    CHKERR m_field.set_field_order(0, MBEDGE, "DISP_X", order);
    CHKERR m_field.set_field_order(0, MBTRI, "DISP_X", order);
 
    CHKERR m_field.set_field_order(0, MBVERTEX, "DISP_Y", 1);
    CHKERR m_field.set_field_order(0, MBEDGE, "DISP_Y", order);
    CHKERR m_field.set_field_order(0, MBTRI, "DISP_Y", order);
 
    CHKERR m_field.build_fields();
 
    CHKERR m_field.add_finite_element("DISP_MAP_ELEMENT");
    CHKERR m_field.modify_finite_element_add_field_row("DISP_MAP_ELEMENT",
                                                       "DISP_X");
    CHKERR m_field.modify_finite_element_add_field_col("DISP_MAP_ELEMENT",
                                                       "DISP_X");
    CHKERR m_field.modify_finite_element_add_field_data("DISP_MAP_ELEMENT",
                                                        "DISP_X");
    CHKERR m_field.modify_finite_element_add_field_data("DISP_MAP_ELEMENT",
                                                        "DISP_Y");
 
    // Add entities to that element
    CHKERR m_field.add_ents_to_finite_element_by_type(surface, MBTRI,
                                                      "DISP_MAP_ELEMENT");
 
    // build finite elements
    CHKERR m_field.build_finite_elements();
    // build adjacencies between elements and degrees of freedom
    CHKERR m_field.build_adjacencies(bit_level0);
 
    // set discrete manager
    DM dm_disp;
    DMType dm_name = "DM_DISP";
    // Register DM problem
    CHKERR DMRegister_MoFEM(dm_name);
    CHKERR DMCreate(PETSC_COMM_WORLD, &dm_disp);
    CHKERR DMSetType(dm_disp, dm_name);
    // Create DM instance
    CHKERR DMMoFEMCreateMoFEM(dm_disp, &m_field, dm_name, bit_level0);
    // Configure DM form line command options (DM itself, solvers,
    // pre-conditioners, ... )
    CHKERR DMSetFromOptions(dm_disp);
    // Add elements to dm (only one here)
    CHKERR DMMoFEMAddElement(dm_disp, "DISP_MAP_ELEMENT");
    // Set up problem (number dofs, partition mesh, etc.)
    CHKERR DMSetUp(dm_disp);
 
    DispMapFe fe_face(m_field);
 
    // string file(argv[1]); cout << "argument 1:" << argv[1] <<endl;
    // string file2(argv[2]); cout << "argument 2:" << argv[2] <<endl;
 
    string file1(data_file_name1);
    DataFromFiles data_from_files(file1);
    CHKERR data_from_files.fromOptions();
    CHKERR data_from_files.loadFileData();
 
    string file2(data_file_name2);
    DataFromFiles data_from_files2(file2);
    CHKERR data_from_files2.fromOptions();
    CHKERR data_from_files2.loadFileData();
 
    boost::ptr_vector<MoFEM::ForcesAndSourcesCore::UserDataOperator>
        &list_of_operators = fe_face.getOpPtrVector();
 
    Mat A;
    Vec Fx, Dx;
    CHKERR DMCreateMatrix(dm_disp, &A);
    CHKERR m_field.query_interface<VecManager>()->vecCreateGhost("DM_DISP", ROW,
                                                                 &Fx);
    CHKERR m_field.query_interface<VecManager>()->vecCreateGhost("DM_DISP", COL,
                                                                 &Dx);
    Vec Fy, Dy;
    CHKERR VecDuplicate(Fx, &Fy);
    CHKERR VecDuplicate(Dx, &Dy);
 
    CHKERR MatZeroEntries(A);
    CHKERR VecZeroEntries(Fx);
    CHKERR VecZeroEntries(Fy);
 
    CommonData common_data;
    common_data.globA = A;
 
    common_data.globF = Fx;
    list_of_operators.push_back(
        new OpCalculateInvJacForFace(common_data.invJac));
    list_of_operators.push_back(new OpSetInvJacH1ForFace(common_data.invJac));
    list_of_operators.push_back(
        new OpCalculateLhs("DISP_X", "DISP_X", common_data, data_from_files));
    list_of_operators.push_back(
        new OpCalulatefRhoAtGaussPts("DISP_X", common_data, data_from_files));
    list_of_operators.push_back(new OpAssmbleRhs("DISP_X", common_data));
 
    CHKERR DMoFEMLoopFiniteElements(dm_disp, "DISP_MAP_ELEMENT", &fe_face);
 
    // cout << "error.no !" <<error++ << endl;
    CHKERR MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
    CHKERR MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
    CHKERR VecGhostUpdateBegin(Fx, ADD_VALUES, SCATTER_REVERSE);
    CHKERR VecGhostUpdateEnd(Fx, ADD_VALUES, SCATTER_REVERSE);
    CHKERR VecAssemblyBegin(Fx);
    CHKERR VecAssemblyEnd(Fx);
 
    // int error=1;
    common_data.globF = Fy;
    list_of_operators.clear();
    list_of_operators.push_back(
        new OpCalculateInvJacForFace(common_data.invJac));
    list_of_operators.push_back(new OpSetInvJacH1ForFace(common_data.invJac));
    list_of_operators.push_back(
        new OpCalulatefRhoAtGaussPts("DISP_X", common_data, data_from_files2));
    list_of_operators.push_back(new OpAssmbleRhs("DISP_X", common_data));
    // cout << "error.no !"<< error++<< endl;
 
    CHKERR DMoFEMLoopFiniteElements(dm_disp, "DISP_MAP_ELEMENT", &fe_face);
    // cout << "error.no !" <<error++ << endl;
    CHKERR VecGhostUpdateBegin(Fy, ADD_VALUES, SCATTER_REVERSE);
    CHKERR VecGhostUpdateEnd(Fy, ADD_VALUES, SCATTER_REVERSE);
    CHKERR VecAssemblyBegin(Fy);
    CHKERR VecAssemblyEnd(Fy);
 
    // VecView(F,PETSC_VIEWER_DRAW_WORLD);
    // MatView(A,PETSC_VIEWER_DRAW_WORLD);
    // std::string wait;
    // std::cin >> wait;
 
    // solve
    {
      KSP ksp;
      CHKERR KSPCreate(PETSC_COMM_WORLD, &ksp);
      CHKERR KSPSetOperators(ksp, A, A);
      CHKERR KSPSetFromOptions(ksp);
      CHKERR KSPSolve(ksp, Fx, Dx);
      CHKERR KSPSolve(ksp, Fy, Dy);
    }
 
    CHKERR VecGhostUpdateBegin(Dx, INSERT_VALUES, SCATTER_FORWARD);
    CHKERR VecGhostUpdateEnd(Dx, INSERT_VALUES, SCATTER_FORWARD);
    CHKERR m_field.query_interface<VecManager>()->setGlobalGhostVector(
        "DM_DISP", COL, Dx, INSERT_VALUES, SCATTER_REVERSE);
    CHKERR VecGhostUpdateBegin(Dy, INSERT_VALUES, SCATTER_FORWARD);
    CHKERR VecGhostUpdateEnd(Dy, INSERT_VALUES, SCATTER_FORWARD);
    CHKERR m_field.query_interface<VecManager>()->setOtherGlobalGhostVector(
        "DM_DISP", "DISP_X", "DISP_Y", COL, Dy, INSERT_VALUES, SCATTER_REVERSE);
 
    // Remove rigid translation
    double sum_dx = 0;
    int nb_dx = 0;
    for (_IT_GET_DOFS_FIELD_BY_NAME_AND_TYPE_FOR_LOOP_(m_field, "DISP_X",
                                                       MBVERTEX, dof)) {
      sum_dx += (*dof)->getFieldData();
      nb_dx++;
    }
    sum_dx /= nb_dx;
    for (_IT_GET_DOFS_FIELD_BY_NAME_AND_TYPE_FOR_LOOP_(m_field, "DISP_X",
                                                       MBVERTEX, dof)) {
      (*dof)->getFieldData() -= sum_dx;
    }
    double sum_dy = 0;
    int nb_dy = 0;
    for (_IT_GET_DOFS_FIELD_BY_NAME_AND_TYPE_FOR_LOOP_(m_field, "DISP_Y",
                                                       MBVERTEX, dof)) {
      sum_dy += (*dof)->getFieldData();
      nb_dy++;
    }
    sum_dy /= nb_dy;
    for (_IT_GET_DOFS_FIELD_BY_NAME_AND_TYPE_FOR_LOOP_(m_field, "DISP_Y",
                                                       MBVERTEX, dof)) {
      (*dof)->getFieldData() -= sum_dy;
    }
 
    PostProcFaceOnRefinedMesh post_proc(m_field);
    CHKERR post_proc.generateReferenceElementMesh();
    CHKERR post_proc.addFieldValuesPostProc("DISP_X");
    CHKERR post_proc.addFieldValuesPostProc("DISP_Y");
    CHKERR DMoFEMLoopFiniteElements(dm_disp, "DISP_MAP_ELEMENT", &post_proc);
 
    CHKERR post_proc.postProcMesh.write_file("out_disp.h5m", "MOAB",
                                             "PARALLEL=WRITE_PART");
 
    CHKERR VecDestroy(&Fx);
    CHKERR VecDestroy(&Fy);
    CHKERR VecDestroy(&Dx);
    CHKERR VecDestroy(&Dy);
    CHKERR MatDestroy(&A);
    CHKERR DMDestroy(&dm_disp);
 
    // Delete element which will be no longer used
    CHKERR m_field.delete_finite_element("DISP_MAP_ELEMENT");
 
    {
      // Add one node to fix
      MeshsetsManager *mmanager_ptr;
      CHKERR m_field.query_interface(mmanager_ptr);
      Range ents_1st_layer;
      CHKERR mmanager_ptr->getEntitiesByDimension(202, SIDESET, 2,
                                                  ents_1st_layer, true);
      int num_nodes;
      const EntityHandle *conn;
      CHKERR moab.get_connectivity(ents_1st_layer[0], conn, num_nodes);
      Skinner skin(&moab);
      Range skin_edges;
      CHKERR skin.find_skin(0, ents_1st_layer, false, skin_edges);
      Range edges;
      CHKERR moab.get_adjacencies(&*ents_1st_layer.begin(), 1, 1, false, edges);
      EntityHandle meshset;
      CHKERR mmanager_ptr->getMeshset(202, SIDESET, meshset);
      CHKERR moab.add_entities(meshset, conn, 1);
      CHKERR moab.add_entities(meshset, skin_edges);
    }
 
    {
      Range tets;
      CHKERR moab.get_entities_by_type(0, MBTET, tets, false);
      CHKERR m_field.partition_mesh(tets, 3, 2, n_partas);
    }
 
    CHKERR moab.write_file("analysis_mesh.h5m");
  }
  CATCH_ERRORS;
 
  MoFEM::Core::Finalize();
 
  return 0;
}