unsaturated_transport.cpp

/** \file unsaturated_transport.cpp
\brief Implementation of unsaturated flow problem
\example unsaturated_transport.cpp

\ingroup mofem_mix_transport_elem
*/

/* This file is part of MoFEM.
 * 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 <boost/program_options.hpp>
using namespace std;
namespace po = boost::program_options;

#include <BasicFiniteElements.hpp>
#include <MixTransportElement.hpp>
#include <UnsaturatedFlow.hpp>
#include <MaterialUnsaturatedFlow.hpp>

#ifndef WITH_ADOL_C
#error "MoFEM need to be compiled with ADOL-C"
#endif

using namespace MoFEM;
using namespace MixTransport;
static char help[] = "...\n\n";

double GenericMaterial::ePsilon0 = 0;
double GenericMaterial::ePsilon1 = 0;

map<std::string, CommonMaterialData::RegisterHook>
    RegisterMaterials::mapOfRegistredMaterials;

int main(int argc, char *argv[]) {

  const string default_options = "-ksp_type fgmres \n"
                                 "-pc_type lu \n"
                                 "-pc_factor_mat_solver_package mumps \n"
                                 "-ksp_monitor\n";

  string param_file = "param_file.petsc";
  if (!static_cast<bool>(ifstream(param_file))) {
    std::ofstream file(param_file.c_str(), std::ios::ate);
    if (file.is_open()) {
      file << default_options;
      file.close();
    }
  }

  MoFEM::Core::Initialize(&argc, &argv, param_file.c_str(), help);

  // Register DM Manager
  CHKERR DMRegister_MoFEM("DMMOFEM"); // register MoFEM DM in PETSc
  // Register materials
  CHKERR RegisterMaterials()();

  PetscBool test_mat = PETSC_FALSE;
  CHKERR PetscOptionsGetBool(PETSC_NULL, "", "-test_mat", &test_mat,
                             PETSC_NULL);

  if (test_mat == PETSC_TRUE) {
    CommonMaterialData data;
    // Testing van_genuchten
    MaterialVanGenuchten van_genuchten(data);
    van_genuchten.printMatParameters(-1, "testing");
    van_genuchten.printTheta(-1e-16, -1e4, -1e-12, "hTheta");
    van_genuchten.printKappa(-1e-16, -1, -1e-12, "hK");
    van_genuchten.printC(-1e-16, -1, -1e-12, "hC");
    CHKERR PetscFinalize();
    return 0;
  }

  try {

    moab::Core mb_instance;
    moab::Interface &moab = mb_instance;

    // get file name form command line
    PetscBool flg_mesh_file_name = PETSC_TRUE;
    char mesh_file_name[255];
    PetscBool flg_conf_file_name = PETSC_TRUE;
    char conf_file_name[255];

    int order = 1;

    ierr = PetscOptionsBegin(PETSC_COMM_WORLD, "", "Unsaturated flow options",
                             "none");
    CHKERRG(ierr);
    ierr = PetscOptionsString("-my_file", "mesh file name", "", "mesh.h5m",
                              mesh_file_name, 255, &flg_mesh_file_name);
    CHKERRG(ierr);
    ierr = PetscOptionsString(
        "-configure", "material and bc configuration file name", "",
        "unsaturated.cfg", conf_file_name, 255, &flg_conf_file_name);
    CHKERRG(ierr);
    ierr = PetscOptionsInt("-my_order", "default approximation order", "",
                           order, &order, PETSC_NULL);
    CHKERRG(ierr);
    ierr = PetscOptionsEnd();
    CHKERRG(ierr);

    if (flg_mesh_file_name != PETSC_TRUE) {
      SETERRQ(PETSC_COMM_SELF, MOFEM_INVALID_DATA,
              "File name not set (e.g. -my_name mesh.h5m)");
    }
    if (flg_conf_file_name != PETSC_TRUE) {
      SETERRQ(PETSC_COMM_SELF, MOFEM_INVALID_DATA,
              "File name not set (e.g. -config unsaturated.cfg)");
    }

    // Create MOAB communicator
    MPI_Comm moab_comm_world;
    MPI_Comm_dup(PETSC_COMM_WORLD, &moab_comm_world);
    ParallelComm *pcomm = ParallelComm::get_pcomm(&moab, MYPCOMM_INDEX);
    if (pcomm == NULL)
      pcomm = new ParallelComm(&moab, moab_comm_world);

    const char *option;
    option = "PARALLEL=READ_PART;"
             "PARALLEL_RESOLVE_SHARED_ENTS;"
             "PARTITION=PARALLEL_PARTITION;";
    CHKERR moab.load_file(mesh_file_name, 0, option);

    // Create mofem interface
    MoFEM::Core core(moab);
    MoFEM::Interface &m_field = core;

    // Add meshsets with material and boundary conditions
    MeshsetsManager *meshsets_manager_ptr;
    CHKERR m_field.getInterface(meshsets_manager_ptr);
    CHKERR meshsets_manager_ptr->setMeshsetFromFile();

    PetscPrintf(PETSC_COMM_WORLD,
                "Read meshsets and added meshsets from bc.cfg\n");
    for (_IT_CUBITMESHSETS_FOR_LOOP_(m_field, it)) {
      PetscPrintf(PETSC_COMM_WORLD, "%s",
                  static_cast<std::ostringstream &>(
                      std::ostringstream().seekp(0) << *it << endl)
                      .str()
                      .c_str());
    }

    // Set entities bit level
    CHKERR m_field.getInterface<BitRefManager>()->setBitRefLevelByDim(
        0, 3, BitRefLevel().set(0));

    UnsaturatedFlowElement uf(m_field);

    ifstream ini_file(conf_file_name);
    po::variables_map vm;
    po::options_description config_file_options;
    Range domain_ents, bc_boundary_ents;

    map<int, CommonMaterialData> material_blocks;
    map<int, double> head_blocks;
    map<int, double> flux_blocks;
    // Set material blocks
    for (_IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_(m_field, BLOCKSET, it)) {
      if (it->getName().compare(0, 4, "SOIL") != 0)
        continue;
      // get block id
      const int block_id = it->getMeshsetId();
      std::string block_name =
          "mat_block_" + boost::lexical_cast<std::string>(block_id);
      material_blocks[block_id].blockId = block_id;
      material_blocks[block_id].addOptions(config_file_options, block_name);
    }
    for (_IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_(m_field, BLOCKSET, it)) {
      if (it->getName().compare(0, 4, "HEAD") != 0)
        continue;
      // get block id
      const int block_id = it->getMeshsetId();
      std::string block_name =
          "head_block_" + boost::lexical_cast<std::string>(block_id);
      config_file_options.add_options()(
          (block_name + ".head").c_str(),
          po::value<double>(&head_blocks[block_id])->default_value(0));
    }
    for (_IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_(m_field, BLOCKSET, it)) {
      if (it->getName().compare(0, 4, "FLUX") != 0)
        continue;
      // get block id
      const int block_id = it->getMeshsetId();
      std::string block_name =
          "flux_block_" + boost::lexical_cast<std::string>(block_id);
      config_file_options.add_options()(
          (block_name + ".flux").c_str(),
          po::value<double>(&head_blocks[block_id])->default_value(0));
    }
    po::parsed_options parsed =
        parse_config_file(ini_file, config_file_options, true);
    store(parsed, vm);
    po::notify(vm);
    for (_IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_(m_field, BLOCKSET, it)) {
      if (it->getName().compare(0, 4, "SOIL") != 0)
        continue;
      const int block_id = it->getMeshsetId();
      uf.dMatMap[block_id] = RegisterMaterials::mapOfRegistredMaterials.at(
          material_blocks[block_id].matName)(material_blocks.at(block_id));
      if (!uf.dMatMap.at(block_id)) {
        SETERRQ(PETSC_COMM_WORLD, MOFEM_DATA_INCONSISTENCY,
                "Material block not set");
      }
      // get block test
      CHKERR m_field.get_moab().get_entities_by_type(
          it->meshset, MBTET, uf.dMatMap.at(block_id)->tEts, true);
      domain_ents.merge(uf.dMatMap.at(block_id)->tEts);
      uf.dMatMap.at(block_id)->printMatParameters(block_id, "Read material");
    }
    std::vector<std::string> additional_parameters;
    additional_parameters =
        collect_unrecognized(parsed.options, po::include_positional);
    for (std::vector<std::string>::iterator vit = additional_parameters.begin();
         vit != additional_parameters.end(); vit++) {
      CHKERR PetscPrintf(m_field.get_comm(),
                         "** WARNING Unrecognized option %s\n", vit->c_str());
    }
    // Set capillary pressure bc data
    for (_IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_(m_field, BLOCKSET, it)) {
      if (it->getName().compare(0, 4, "HEAD") != 0)
        continue;
      // get block id
      const int block_id = it->getMeshsetId();
      // create block data instance
      uf.bcValueMap[block_id] =
          boost::shared_ptr<UnsaturatedFlowElement::BcData>(
              new UnsaturatedFlowElement::BcData());
      // get bc value
      std::vector<double> attributes;
      CHKERR it->getAttributes(attributes);
      uf.bcValueMap[block_id]->fixValue = attributes[0];
      std::string block_name =
          "head_block_" + boost::lexical_cast<std::string>(block_id);
      if (vm.count((block_name) + ".head")) {
        uf.bcValueMap[block_id]->fixValue = head_blocks[block_id];
      }
      // cerr << uf.bcValueMap[block_id]->fixValue  << endl;
      // CHKERR it->printAttributes(std::cout);
      // get faces in the block
      CHKERR m_field.get_moab().get_entities_by_type(
          it->meshset, MBTRI, uf.bcValueMap[block_id]->eNts, true);
      bc_boundary_ents.merge(uf.bcValueMap[block_id]->eNts);
    }

    int max_flux_id = 0;
    // Set water flux bc data
    for (_IT_CUBITMESHSETS_BY_SET_TYPE_FOR_LOOP_(m_field, BLOCKSET, it)) {
      if (it->getName().compare(0, 4, "FLUX") != 0)
        continue;
      // get block id
      const int block_id = it->getMeshsetId();
      // create block data instance
      uf.bcFluxMap[block_id] =
          boost::shared_ptr<UnsaturatedFlowElement::BcData>(
              new UnsaturatedFlowElement::BcData());
      // get bc value
      std::vector<double> attributes;
      CHKERR it->getAttributes(attributes);
      // CHKERR it->printAttributes(std::cout);
      uf.bcFluxMap[block_id]->fixValue = attributes[0];
      std::string block_name =
          "flux_block_" + boost::lexical_cast<std::string>(block_id);
      if (vm.count((block_name) + ".flux")) {
        uf.bcValueMap[block_id]->fixValue = head_blocks[block_id];
      }
      // get faces in the block
      CHKERR m_field.get_moab().get_entities_by_type(
          it->meshset, MBTRI, uf.bcFluxMap[block_id]->eNts, true);
      bc_boundary_ents.merge(uf.bcFluxMap[block_id]->eNts);
      max_flux_id = max_flux_id > block_id ? max_flux_id : block_id + 1;
    }

    // Add zero flux on the rest of the boundary
    Range zero_flux_ents;
    {
      Skinner skin(&m_field.get_moab());
      Range domain_skin;
      CHKERR skin.find_skin(0, domain_ents, false, domain_skin);
      // filter not owned entities, those are not on boundary
      CHKERR pcomm->filter_pstatus(domain_skin,
                                   PSTATUS_SHARED | PSTATUS_MULTISHARED,
                                   PSTATUS_NOT, -1, &zero_flux_ents);
      zero_flux_ents = subtract(zero_flux_ents, bc_boundary_ents);
      uf.bcFluxMap[max_flux_id] =
          boost::shared_ptr<UnsaturatedFlowElement::BcData>(
              new UnsaturatedFlowElement::BcData());
      uf.bcFluxMap[max_flux_id]->fixValue = 0;
      uf.bcFluxMap[max_flux_id]->eNts = zero_flux_ents;
    }

    CHKERR uf.addFields("VALUES", "FLUXES", order);
    CHKERR uf.addFiniteElements("FLUXES", "VALUES");
    CHKERR m_field.add_ents_to_finite_element_by_type(zero_flux_ents, MBTRI,
                                                      "MIX_BCFLUX");
    CHKERR uf.buildProblem();
    CHKERR uf.createMatrices();
    CHKERR uf.setFiniteElements();
    CHKERR uf.calculateEssentialBc();
    CHKERR uf.calculateInitialPc();
    CHKERR uf.solveProblem();
    CHKERR uf.destroyMatrices();

    MPI_Comm_free(&moab_comm_world);
  }
  CATCH_ERRORS;

  CHKERR MoFEM::Core::Finalize();

  return 0;
}