source: src/Jobs/VMGJob.cpp@ 052c10

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2012 University of Bonn. All rights reserved.
 * Copyright (C)  2013 Frederik Heber. 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 "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
// periodic boundary conditions
#include "cycles/cycle_cs_periodic.hpp"
#include "discretization/discretization_poisson_fd.hpp"
#include "level/level_operator_cs.hpp"
#include "smoother/gsrb_poisson_4.hpp"
#include "solver/solver_singular.hpp"
// open boundary conditions
#include "cycles/cycle_fas_dirichlet.hpp"
#include "discretization/discretization_poisson_fv.hpp"
#include "grid/multigrid.hpp"
//#include "grid/tempgrid.hpp"
#include "level/level_operator_fas.hpp"
#include "level/stencils.hpp"
#include "smoother/gsrb_poisson_2.hpp"
#include "solver/givens.hpp"
#include "solver/solver_regular.hpp"
#include "units/particle/comm_mpi_particle.hpp"

#include "CodePatterns/MemDebug.hpp"

#include "Jobs/VMGJob.hpp"

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

#include "CodePatterns/Assert.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,
    const size_t _near_field_cells,
    const size_t _interpolation_degree,
    const bool _DoImportParticles,
    const bool _DoPrintDebug,
    const bool _OpenBoundaryConditions) :
  FragmentJob(_JobId),
  density_grid(_density_grid),
  particle_positions(_particle_positions),
  particle_charges(_particle_charges),
  near_field_cells(_near_field_cells),
  interpolation_degree(_interpolation_degree),
  DoImportParticles(_DoImportParticles),
  DoPrintDebug(_DoPrintDebug),
  OpenBoundaryConditions(_OpenBoundaryConditions),
  returndata(static_cast<const SamplingGridProperties &>(_density_grid)),
  particles()
{}

VMGJob::VMGJob() :
  FragmentJob(JobId::IllegalJob),
  near_field_cells(3),
  interpolation_degree(3),
  DoImportParticles(true),
  DoPrintDebug(false),
  OpenBoundaryConditions(false),
  particles()
{}

VMGJob::~VMGJob()
{
}


VMGJob::particle_arrays::particle_arrays() :
  num_particles(0),
  f(NULL),
  x(NULL),
  p(NULL),
  q(NULL)
{}

VMGJob::particle_arrays::~particle_arrays()
{
  delete[] f;
  delete[] x;
  delete[] p;
  delete[] q;
}

void VMGJob::particle_arrays::init(const size_t _num_particles)
{
  num_particles = _num_particles;
  f = new double[num_particles*3];
  x = new double[num_particles*3];
  p = new double[num_particles];
  q = new double[num_particles];
}

void VMGJob::InitVMGArrays()
{
  particles.init(particle_charges.size());

  {
    size_t index=0;
    for (std::vector< std::vector< double > >::const_iterator iter = particle_positions.begin();
        iter != particle_positions.end(); ++iter) {
      for (std::vector< double >::const_iterator positer = (*iter).begin();
          positer != (*iter).end(); ++positer) {
        particles.f[index] = 0.;
        particles.x[index++] = *positer;
      }
    }
    ASSERT( index == particles.num_particles*3,
        "VMGJob::VMGJob() - too many particles or components in particle_positions.");
  }
  {
    size_t index = 0;
    for (std::vector< double >::const_iterator iter = particle_charges.begin();
        iter != particle_charges.end(); ++iter) {
      particles.p[index] = 0.;
      particles.q[index++] = *iter;
    }
    ASSERT( index == particles.num_particles,
        "VMGJob::VMGJob() - too many charges in particle_charges.");
  }
}


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;
  {
    const VMGData archivedata(returndata);
    boost::archive::text_oarchive oa(returnstream);
    oa << archivedata;
  }

  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()
{
  Boundary *boundary = NULL;
  if (OpenBoundaryConditions)
    boundary = new Boundary(Open, Open, Open);
  else
    boundary = new Boundary(Periodic, Periodic, Periodic);

  /*
   * Choose multigrid components (self-registering)
   */

#ifdef HAVE_MPI
  new Particle::CommMPI(*boundary, new DomainDecompositionMPI());
#else
  new CommSerial(*boundary);
#endif
  if (OpenBoundaryConditions)
    new DiscretizationPoissonFV(2);
  else
    new DiscretizationPoissonFD(4);
  new VMGInterfaces::InterfaceVMGJob(
      density_grid,
      returndata,
      particle_positions,
      particle_charges,
      *boundary,
      2,
      density_grid.level,
      Vector(density_grid.begin),
      density_grid.end[0]-density_grid.begin[0],
      near_field_cells,
      DoImportParticles ?
          VMGInterfaces::InterfaceVMGJob::DoImportParticles
          : VMGInterfaces::InterfaceVMGJob::DontImportParticles,
      DoPrintDebug);
  const int cycle_type = 1; // V-type
  if (OpenBoundaryConditions) {
    new LevelOperatorFAS(Stencils::RestrictionFullWeight, Stencils::Injection, Stencils::InterpolationTrilinear);
    new Givens<SolverRegular>();
    new CycleFASDirichlet(cycle_type);
    new GaussSeidelRBPoisson2();
  } else {
    new LevelOperatorCS(Stencils::RestrictionFullWeight, Stencils::InterpolationTrilinear);
    new Givens<SolverSingular>();
    new CycleCSPeriodic(cycle_type);
    new GaussSeidelRBPoisson4();
  }
  delete boundary;

  /*
   * 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", interpolation_degree);

  // first initialize f,x,p,q,... from STL vectors
  InitVMGArrays();
  // then initialize as objects with VMG's storage
  new ObjectStorage<vmg_float*>("PARTICLE_POS_ARRAY", particles.x);
  new ObjectStorage<vmg_float*>("PARTICLE_CHARGE_ARRAY", particles.q);
  new ObjectStorage<vmg_float*>("PARTICLE_POTENTIAL_ARRAY", particles.p);
  new ObjectStorage<vmg_float*>("PARTICLE_FIELD_ARRAY", particles.f);
  new ObjectStorage<vmg_int>("PARTICLE_NUM_LOCAL", particles.num_particles);

  /*
   * 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)