source: src/Jobs/VMGJob.cpp@ 8b58ac

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2012 University of Bonn. All rights reserved.
 * 
 *
 *   This file is part of MoleCuilder.
 *
 *    MoleCuilder is free software: you can redistribute it and/or modify
 *    it under the terms of the GNU General Public License as published by
 *    the Free Software Foundation, either version 2 of the License, or
 *    (at your option) any later version.
 *
 *    MoleCuilder 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 General Public License for more details.
 *
 *    You should have received a copy of the GNU General Public License
 *    along with MoleCuilder.  If not, see <http://www.gnu.org/licenses/>.
 */

/*
 * VMGJob.cpp
 *
 *  Created on: Jul 13, 2012
 *      Author: heber
 */


// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#ifdef HAVE_MPI
#include "mpi.h"
#endif

// include headers that implement a archive in simple text format
// otherwise BOOST_CLASS_EXPORT_IMPLEMENT has no effect
#include <boost/archive/text_oarchive.hpp>
#include <boost/archive/text_iarchive.hpp>

#include "CodePatterns/MemDebug.hpp"

#include "Jobs/VMGJob.hpp"

#include "mg.hpp"
#include "base/object.hpp"
#include "base/defs.hpp"

#ifdef HAVE_MPI
#include "comm/comm_mpi.hpp"
#include "comm/domain_decomposition_mpi.hpp"
#else
#include "comm/comm_serial.hpp"
#endif
#include "cycles/cycle_cs_periodic.hpp"
#include "grid/multigrid.hpp"
//#include "grid/tempgrid.hpp"
#include "level/level_operator_cs.hpp"
#include "level/stencils.hpp"
#include "samples/discretization_poisson_fd.hpp"
#include "smoother/gsrb_poisson_4.hpp"
#include "solver/givens.hpp"
//#include "solver/solver_regular.hpp"
#include "solver/solver_singular.hpp"
//#include "units/particle/comm_mpi_particle.hpp"

#include "LinearAlgebra/defs.hpp"
#include "Jobs/InterfaceVMGJob.hpp"

using namespace VMG;

VMGJob::VMGJob(
    const JobId_t _JobId,
    const SamplingGrid &_density_grid,
    const std::vector< std::vector< double > > &_particle_positions,
    const std::vector< double > &_particle_charges) :
  FragmentJob(_JobId),
  density_grid(_density_grid),
  potential_grid(static_cast<const SamplingGridProperties &>(_density_grid)),
  particle_positions(_particle_positions),
  particle_charges(_particle_charges)
{}

VMGJob::VMGJob() :
  FragmentJob(JobId::IllegalJob)
{}

VMGJob::~VMGJob()
{}

FragmentResult::ptr VMGJob::Work()
{
  // initialize VMG library solver
  InitVMG();

  /*
   * Start the multigrid solver
   */
  MG::Solve();

  /// create and fill result object
  // place into returnstream
  std::stringstream returnstream;
  boost::archive::text_oarchive oa(returnstream);
  oa << potential_grid;

  FragmentResult::ptr ptr( new FragmentResult(getId(), returnstream.str()) );

  /*
   * Delete all data.
   */
  MG::Destroy();

  return ptr;
}

/** Initialization of VMG library.
 *
 * The contents is heavily inspired from interface_fcs.cpp: VMG_fcs_init() of
 * the ScaFaCoS project.
 *
 */
void VMGJob::InitVMG()
{
  // TODO: As a matter of fact should use open boundary conditions
  const Boundary boundary(Periodic, Periodic, Periodic);
  int near_field_cells = 10;

  /*
   * Choose multigrid components (self-registering)
   */
#ifdef HAVE_MPI
  new CommMPI(boundary, new DomainDecompositionMPI());
#else
  new CommSerial(boundary);
#endif
  new DiscretizationPoissonFD(4);
  new VMGInterfaces::InterfaceVMGJob(
      density_grid.sampled_grid,
      potential_grid.sampled_grid,
      particle_positions,
      particle_charges,
      boundary,
      2,
      density_grid.level,
      Vector(density_grid.begin),
      density_grid.size,
      near_field_cells);
  new LevelOperatorCS(Stencils::RestrictionFullWeight, Stencils::InterpolationTrilinear);
  new Givens<SolverSingular>();
  const int cycle_type = 1; // V-type
  new CycleCSPeriodic(cycle_type);
  new GaussSeidelRBPoisson4();

  /*
   * Register required parameters
   */
  new ObjectStorage<int>("PRESMOOTHSTEPS", 3);
  new ObjectStorage<int>("POSTSMOOTHSTEPS", 3);
  new ObjectStorage<vmg_float>("PRECISION", 1.0e-10);
  new ObjectStorage<int>("MAX_ITERATION", 15);
  new ObjectStorage<int>("PARTICLE_NEAR_FIELD_CELLS", near_field_cells);
  new ObjectStorage<int>("PARTICLE_INTERPOLATION_DEGREE", 3);

  /*
   * Post init
   */
  MG::PostInit();

  /*
   * Check whether the library is correctly initialized now.
   */
  MG::IsInitialized();
}

// we need to explicitly instantiate the serialization functions as
// its is only serialized through its base class FragmentJob
BOOST_CLASS_EXPORT_IMPLEMENT(VMGJob)