/*
* 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 .
*/
/*
* InterfaceVMGJob.cpp
*
* Created on: 10.06.2012
* Author: Frederik Heber
*/
#ifdef HAVE_CONFIG_H
#include
#endif
#ifdef HAVE_MPI
#include "mpi.h"
#endif
#include "CodePatterns/MemDebug.hpp"
#include
#include
#include "CodePatterns/Log.hpp"
#include "base/vector.hpp"
#include "base/math.hpp"
#include "comm/comm.hpp"
#include "grid/grid.hpp"
#include "grid/multigrid.hpp"
#include "mg.hpp"
#include "InterfaceVMGJob.hpp"
using namespace VMG;
using VMGInterfaces::InterfaceVMGJob;
InterfaceVMGJob::InterfaceVMGJob(const std::vector< double > &_sampled_input,
VMGData &_returndata,
const std::vector< std::vector > &_particle_positions,
const std::vector< double > &_particle_charges,
VMG::Boundary boundary,
int levelMin,
int levelMax,
const VMG::Vector &box_begin,
vmg_float box_end,
const int& near_field_cells,
int coarseningSteps,
double alpha) :
VMG::Interface(boundary, levelMin, levelMax,
box_begin, box_end, coarseningSteps, alpha),
spl(near_field_cells, Extent(MaxLevel()).MeshWidth().Max()),
sampled_input(_sampled_input),
returndata(_returndata),
level(levelMax)
{
std::vector< std::vector >::const_iterator positer = _particle_positions.begin();
std::vector::const_iterator chargeiter = _particle_charges.begin();
double pos[3];
for (; positer != _particle_positions.end(); ++positer, ++chargeiter) {
ASSERT( (*positer).size() == 3,
"InterfaceVMGJob::InterfaceVMGJob() - particle "
+toString(distance(_particle_positions.begin(), positer))+" has not exactly 3 coordinates.");
for (size_t i=0;i<3;++i)
pos[i] = (*positer)[i];
particles.push_back(Particle::Particle(pos, *chargeiter));
}
}
InterfaceVMGJob::~InterfaceVMGJob()
{}
void InterfaceVMGJob::ImportRightHandSide(Multigrid& multigrid)
{
Index i;
Vector pos;
// VMG::TempGrid *temp_grid = new VMG::TempGrid(129, 0, 0., 1.);
Grid& grid = multigrid(multigrid.MaxLevel());
//grid.ClearBoundary(); // we don't have a boundary under periodic boundary conditions
// print debugging info on grid size
LOG(1, "INFO: Mesh has extent " << grid.Extent().MeshWidth() << ".");
const int gridpoints = pow(2, level);
LOG(1, "INFO: gridpoints on finest level are " << gridpoints << ".");
LOG(1, "INFO: "
<< "X in [" << grid.Local().Begin().X() << "," << grid.Local().End().X() << "],"
<< "Y in [" << grid.Local().Begin().Y() << "," << grid.Local().End().Y() << "],"
<< "Z in [" << grid.Local().Begin().Z() << "," << grid.Local().End().Z() << "].");
/// 1. assign nuclei as smeared-out charges to the grid
/*
* Charge assignment on the grid
*/
Comm& comm = *MG::GetComm();
Grid& particle_grid = comm.GetParticleGrid();
particle_grid.Clear();
assert(particle_grid.Global().LocalSize().IsComponentwiseGreater(
VMG::MG::GetFactory().GetObjectStorageVal("PARTICLE_NEAR_FIELD_CELLS")));
// create smeared-out particle charges on particle_grid via splines
LOG(1, "INFO: Creating particle grid for " << particles.size() << " particles.");
for (std::list::iterator iter = particles.begin();
iter != particles.end(); ++iter) {
LOG(2, "DEBUG: Current particle is at " << (*iter).Pos()
<< " with charge " << (*iter).Charge() << ".");
spl.SetSpline(particle_grid, *iter);
}
// Communicate charges over halo
comm.CommFromGhosts(particle_grid);
// print nuclei grid to vtk
comm.PrintGrid(particle_grid, "Sampled Nuclei Density");
// add sampled electron charge density onto grid
std::vector::const_iterator sample_iter = sampled_input.begin();
for (Grid::iterator iter = grid.Iterators().Local().Begin();
iter != grid.Iterators().Local().End();
++iter)
grid(*iter) = -1. * (*sample_iter++);
assert( sample_iter == sampled_input.end() );
// print electron grid to vtk
comm.PrintGrid(grid, "Sampled Electron Density");
// add particle_grid onto grid
for (int i=0; i(MG::GetComm());
returndata.e_long = potential_sum;
}