Action_Thermostats
        Add_AtomRandomPerturbation
        Add_SelectAtomByNameAction
        Adding_Graph_to_ChangeBondActions
        Adding_MD_integration_tests
        Adding_StructOpt_integration_tests
        AutomationFragmentation_failures
        Candidate_v1.6.1
        Candidate_v1.7.0
        ChangeBugEmailaddress
        ChemicalSpaceEvaluator
        EmpiricalPotential_contain_HomologyGraph_documentation
        Enhance_userguide
        Enhanced_StructuralOptimization
        Enhanced_StructuralOptimization_continued
        Example_ManyWaysToTranslateAtom
        Exclude_Hydrogens_annealWithBondGraph
        Fix_Verbose_Codepatterns
        ForceAnnealing_oldresults
        ForceAnnealing_with_BondGraph
        ForceAnnealing_with_BondGraph_continued
        ForceAnnealing_with_BondGraph_continued_betteresults
        ForceAnnealing_with_BondGraph_contraction-expansion
        GeometryObjects
        Gui_displays_atomic_force_velocity
        IndependentFragmentGrids_IntegrationTest
        JobMarket_RobustOnKillsSegFaults
        JobMarket_StableWorkerPool
        PythonUI_with_named_parameters
        QtGui_reactivate_TimeChanged_changes
        Recreated_GuiChecks
        StoppableMakroAction
        TremoloParser_IncreasedPrecision
        TremoloParser_MultipleTimesteps
        stable
      
      
      
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| 1 | /*
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| 2 |  *    vmg - a versatile multigrid solver
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| 3 |  *    Copyright (C) 2012 Institute for Numerical Simulation, University of Bonn
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| 4 |  *
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| 5 |  *  vmg is free software: you can redistribute it and/or modify
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| 6 |  *  it under the terms of the GNU General Public License as published by
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| 7 |  *  the Free Software Foundation, either version 3 of the License, or
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| 8 |  *  (at your option) any later version.
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| 9 |  *
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| 10 |  *  vmg is distributed in the hope that it will be useful,
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| 11 |  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 12 |  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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| 13 |  *  GNU General Public License for more details.
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| 14 |  *
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| 15 |  *  You should have received a copy of the GNU General Public License
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| 16 |  *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
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| 17 |  */
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| 18 | 
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| 19 | /**
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| 20 |  * @file   stencil.cpp
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| 21 |  * @author Julian Iseringhausen <isering@ins.uni-bonn.de>
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| 22 |  * @date   Mon Apr 18 12:25:05 2011
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| 23 |  *
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| 24 |  * @brief  VMG::Stencil
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| 25 |  *
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| 26 |  */
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| 27 | 
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| 28 | #ifdef HAVE_CONFIG_H
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| 29 | #include <libvmg_config.h>
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| 30 | #endif
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| 31 | 
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| 32 | #ifdef HAVE_MPI
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| 33 | #include <mpi.h>
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| 34 | #endif
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| 35 | 
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| 36 | #include "base/stencil.hpp"
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| 37 | #include "comm/comm.hpp"
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| 38 | #include "grid/grid.hpp"
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| 39 | #include "grid/tempgrid.hpp"
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| 40 | #include "mg.hpp"
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| 41 | 
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| 42 | using namespace VMG;
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| 43 | 
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| 44 | void Stencil::Apply(Grid& grid) const
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| 45 | {
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| 46 |   Grid::iterator grid_iter;
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| 47 |   Stencil::iterator stencil_iter;
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| 48 | 
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| 49 |   TempGrid& temp = *MG::GetTempGrid();
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| 50 |   temp.SetProperties(grid);
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| 51 | 
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| 52 |   MG::GetComm()->CommToGhosts(grid);
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| 53 | 
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| 54 |   for (grid_iter=grid.Iterators().Local().Begin(); grid_iter!=grid.Iterators().Local().End(); ++grid_iter) {
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| 55 |     temp(*grid_iter) = diag * grid.GetVal(*grid_iter);
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| 56 |     for (stencil_iter=disp.begin(); stencil_iter!=disp.end(); ++stencil_iter)
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| 57 |       temp(*grid_iter) += stencil_iter->Val() * grid.GetVal(*grid_iter + stencil_iter->Disp());
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| 58 |   }
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| 59 | 
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| 60 |   grid.SetGrid(temp);
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| 61 | }
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