[b123a5] | 1 | /*
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| 2 | * Project: MoleCuilder
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| 3 | * Description: creates and alters molecular systems
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| 4 | * Copyright (C) 2012 University of Bonn. All rights reserved.
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[5aaa43] | 5 | * Copyright (C) 2013 Frederik Heber. All rights reserved.
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[b123a5] | 6 | * Please see the COPYING file or "Copyright notice" in builder.cpp for details.
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| 7 | *
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| 8 | *
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| 9 | * This file is part of MoleCuilder.
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| 10 | *
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| 11 | * MoleCuilder is free software: you can redistribute it and/or modify
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| 12 | * it under the terms of the GNU General Public License as published by
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| 13 | * the Free Software Foundation, either version 2 of the License, or
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| 14 | * (at your option) any later version.
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| 15 | *
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| 16 | * MoleCuilder is distributed in the hope that it will be useful,
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| 17 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 18 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 19 | * GNU General Public License for more details.
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| 20 | *
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| 21 | * You should have received a copy of the GNU General Public License
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| 22 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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| 23 | */
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| 24 |
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| 25 | /*
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| 26 | * WindowGrid_converter.cpp
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| 27 | *
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| 28 | * Created on: Dec 20, 2012
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| 29 | * Author: heber
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| 30 | */
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| 31 |
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| 32 |
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| 33 | // include config.h
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| 34 | #ifdef HAVE_CONFIG_H
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| 35 | #include <config.h>
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| 36 | #endif
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| 37 |
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| 38 | #include "grid/grid.hpp"
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| 39 |
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| 40 | #include "WindowGrid_converter.hpp"
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| 41 |
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| 42 | #include "CodePatterns/MemDebug.hpp"
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| 43 |
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| 44 | #include <iostream>
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| 45 | #include <iterator>
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| 46 | #include <limits>
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| 47 |
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| 48 | #include "CodePatterns/Assert.hpp"
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| 49 | #include "CodePatterns/Log.hpp"
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| 50 |
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[fbf143] | 51 | #include "Fragmentation/Summation/SetValues/SamplingGrid.hpp"
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[b123a5] | 52 |
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| 53 | void WindowGrid_converter::addGridOntoWindow(
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| 54 | VMG::Grid &grid,
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| 55 | SamplingGrid &window,
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[d9d028] | 56 | const double prefactor,
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| 57 | const bool OpenBoundaryConditions)
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[b123a5] | 58 | {
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| 59 | #ifndef NDEBUG
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| 60 | for(size_t index=0;index<3;++index) {
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| 61 | ASSERT( window.begin[index] >= window.begin_window[index],
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| 62 | "InterfaceVMGJob::addGridOntoWindow() - given grid starts earlier than window in component "
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| 63 | +toString(index)+".");
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| 64 | ASSERT( window.end[index] <= window.end_window[index],
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| 65 | "InterfaceVMGJob::addGridOntoWindow() - given grid ends later than window in component "
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| 66 | +toString(index)+".");
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| 67 | }
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| 68 | #endif
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| 69 | // the only issue are indices
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| 70 | const size_t gridpoints_axis = window.getGridPointsPerAxis();
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| 71 | size_t pre_offset[3];
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| 72 | size_t post_offset[3];
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| 73 | size_t length[3];
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| 74 | size_t total[3];
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| 75 | const double round_offset =
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| 76 | (std::numeric_limits<size_t>::round_style == std::round_toward_zero) ?
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| 77 | 0.5 : 0.; // need offset to get to round_toward_nearest behavior
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| 78 | for(size_t index=0;index<3;++index) {
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| 79 | const double delta = (double)gridpoints_axis/(window.end[index] - window.begin[index]);
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| 80 | // delta is conversion factor from box length to discrete length, i.e. number of points
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| 81 | pre_offset[index] = delta*(window.begin[index] - window.begin_window[index])+round_offset;
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| 82 | length[index] = delta*(window.end[index] - window.begin[index])+round_offset;
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| 83 | post_offset[index] = delta*(window.end_window[index] - window.end[index])+round_offset;
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| 84 | total[index] = delta*(window.end_window[index] - window.begin_window[index])+round_offset;
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| 85 | // total is used as safe-guard against loss due to discrete conversion
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| 86 | ASSERT( pre_offset[index]+post_offset[index]+length[index] == total[index],
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| 87 | "InterfaceVMGJob::addGridOntoWindow() - pre, post, and length don't sum up to total for "
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| 88 | +toString(index)+"th component.");
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| 89 | }
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| 90 | #ifndef NDEBUG
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| 91 | const size_t calculated_size = length[0]*length[1]*length[2];
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| 92 | // const size_t given_size = std::distance(grid_begin, grid_end);
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| 93 | // ASSERT( calculated_size == given_size,
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| 94 | // "InterfaceVMGJob::addGridOntoWindow() - not enough sampled values given: "
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| 95 | // +toString(calculated_size)+" != "+toString(given_size)+".");
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| 96 | ASSERT( calculated_size <= window.sampled_grid.size(),
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| 97 | "InterfaceVMGJob::addGridOntoWindow() - not enough sampled values available: "
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| 98 | +toString(calculated_size)+" <= "+toString(window.sampled_grid.size())+".");
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| 99 | const size_t total_size = total[0]*total[1]*total[2];
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| 100 | ASSERT( total_size == window.sampled_grid.size(),
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| 101 | "InterfaceVMGJob::addGridOntoWindow() - total size is not equal to number of present points: "
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| 102 | +toString(total_size)+" != "+toString(window.sampled_grid.size())+".");
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| 103 | #endif
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| 104 | size_t N[3];
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| 105 | SamplingGrid::sampledvalues_t::iterator griditer = window.sampled_grid.begin();
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| 106 | std::advance(griditer, pre_offset[0]*total[1]*total[2]);
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[d9d028] | 107 |
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[b123a5] | 108 | VMG::Grid::iterator copyiter = grid.Iterators().Local().Begin();
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[d9d028] | 109 | const VMG::Index size = grid.Local().Size();
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| 110 | if (OpenBoundaryConditions)
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[a2a2f7] | 111 | for(N[0]=(size_t)0; N[0] < (size_t)size[0]/(size_t)4; ++N[0])
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| 112 | for(N[1]=(size_t)0; N[1] < (size_t)size[1]; ++N[1])
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| 113 | for(N[2]=(size_t)0; N[2] < (size_t)size[2]; ++N[2]) {
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[d9d028] | 114 | ASSERT( copyiter != grid.Iterators().Local().End(),
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| 115 | "InterfaceVMGJob::addGridOntoWindow() - copyiter is already at end of window.");
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| 116 | ++copyiter;
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| 117 | }
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[a2a2f7] | 118 | for(N[0]=(size_t)0; N[0] < length[0]; ++N[0]) {
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[b123a5] | 119 | std::advance(griditer, pre_offset[1]*total[2]);
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[d9d028] | 120 | if (OpenBoundaryConditions)
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[a2a2f7] | 121 | for(N[1]=(size_t)0; N[1] < (size_t)size[1]/(size_t)4; ++N[1])
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| 122 | for(N[2]=(size_t)0; N[2] < (size_t)size[2]; ++N[2]) {
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[d9d028] | 123 | ASSERT( copyiter != grid.Iterators().Local().End(),
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| 124 | "InterfaceVMGJob::addGridOntoWindow() - copyiter is already at end of window.");
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| 125 | ++copyiter;
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| 126 | }
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[a2a2f7] | 127 | for(N[1]=(size_t)0; N[1] < length[1]; ++N[1]) {
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[b123a5] | 128 | std::advance(griditer, pre_offset[2]);
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[d9d028] | 129 | if (OpenBoundaryConditions)
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[a2a2f7] | 130 | for(N[2]=(size_t)0; N[2] < (size_t)size[2]/(size_t)4; ++N[2]) {
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[d9d028] | 131 | ASSERT( copyiter != grid.Iterators().Local().End(),
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| 132 | "InterfaceVMGJob::addGridOntoWindow() - copyiter is already at end of window.");
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| 133 | ++copyiter;
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| 134 | }
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[a2a2f7] | 135 | for(N[2]=(size_t)0; N[2] < length[2]; ++N[2]) {
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[b123a5] | 136 | ASSERT( griditer != window.sampled_grid.end(),
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| 137 | "InterfaceVMGJob::addGridOntoWindow() - griditer is already at end of window.");
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| 138 | ASSERT( copyiter != grid.Iterators().Local().End(),
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[d9d028] | 139 | "InterfaceVMGJob::addGridOntoWindow() - copyiter is already at end of window.");
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[b123a5] | 140 | *griditer++ += prefactor*grid(*copyiter++);
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| 141 | }
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| 142 | std::advance(griditer, post_offset[2]);
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[d9d028] | 143 | if (OpenBoundaryConditions)
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[a2a2f7] | 144 | for(N[2]=(size_t)0; N[2] < (size_t)size[2] - (size_t)size[2]/(size_t)4 - length[2]; ++N[2]) {
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[d9d028] | 145 | ASSERT( copyiter != grid.Iterators().Local().End(),
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| 146 | "InterfaceVMGJob::addGridOntoWindow() - copyiter is already at end of window.");
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| 147 | ++copyiter;
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| 148 | }
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[b123a5] | 149 | }
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| 150 | std::advance(griditer, post_offset[1]*total[2]);
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[d9d028] | 151 | if (OpenBoundaryConditions)
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[a2a2f7] | 152 | for(N[1]=(size_t)0; N[1] < (size_t)size[1] - (size_t)size[1]/(size_t)4 - length[1]; ++N[1])
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| 153 | for(N[2]=(size_t)0; N[2] < (size_t)size[2]; ++N[2]) {
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[d9d028] | 154 | ASSERT( copyiter != grid.Iterators().Local().End(),
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| 155 | "InterfaceVMGJob::addGridOntoWindow() - copyiter is already at end of window.");
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| 156 | ++copyiter;
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| 157 | }
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[b123a5] | 158 | }
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[d9d028] | 159 | if (OpenBoundaryConditions)
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[a2a2f7] | 160 | for(N[0]=(size_t)0; N[0] < (size_t)size[0] - (size_t)size[0]/(size_t)4 - length[0]; ++N[0])
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| 161 | for(N[1]=(size_t)0; N[1] < (size_t)size[1]; ++N[1])
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| 162 | for(N[2]=(size_t)0; N[2] < (size_t)size[2]; ++N[2]) {
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[d9d028] | 163 | ASSERT( copyiter != grid.Iterators().Local().End(),
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| 164 | "InterfaceVMGJob::addGridOntoWindow() - copyiter is already at end of window.");
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| 165 | ++copyiter;
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| 166 | }
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[b123a5] | 167 | #ifndef NDEBUG
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| 168 | std::advance(griditer, post_offset[0]*total[1]*total[2]);
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| 169 | ASSERT( griditer == window.sampled_grid.end(),
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| 170 | "InterfaceVMGJob::addGridOntoWindow() - griditer is not at end of window.");
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| 171 | ASSERT( copyiter == grid.Iterators().Local().End(),
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| 172 | "InterfaceVMGJob::addGridOntoWindow() - copyiter is not at end of window.");
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| 173 | #endif
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| 174 | }
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| 175 |
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| 176 | void WindowGrid_converter::addWindowOntoGrid(
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| 177 | VMG::Grid& window,
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| 178 | const SamplingGrid &grid,
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[27ef5c] | 179 | const double prefactor,
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| 180 | const bool OpenBoundaryConditions)
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[b123a5] | 181 | {
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| 182 | #ifndef NDEBUG
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| 183 | for(size_t index=0;index<3;++index) {
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| 184 | ASSERT( grid.begin_window[index] >= grid.begin[index],
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| 185 | "InterfaceVMGJob::addWindowOntoGrid() - given window starts earlier than grid in component "
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| 186 | +toString(index)+".");
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| 187 | ASSERT( grid.end_window[index] <= grid.end[index],
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| 188 | "InterfaceVMGJob::addWindowOntoGrid() - given window ends later than grid in component "
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| 189 | +toString(index)+".");
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| 190 | }
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| 191 | #endif
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| 192 | // the only issue are indices
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| 193 | const size_t gridpoints_axis = grid.getGridPointsPerAxis();
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| 194 | size_t pre_offset[3];
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| 195 | size_t post_offset[3];
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| 196 | size_t length[3];
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| 197 | size_t total[3];
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| 198 | const double round_offset =
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| 199 | (std::numeric_limits<size_t>::round_style == std::round_toward_zero) ?
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| 200 | 0.5 : 0.; // need offset to get to round_toward_nearest behavior
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| 201 | for(size_t index=0;index<3;++index) {
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| 202 | const double delta = (double)gridpoints_axis/(grid.end[index] - grid.begin[index]);
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| 203 | // delta is conversion factor from box length to discrete length, i.e. number of points
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| 204 | pre_offset[index] = delta*(grid.begin_window[index] - grid.begin[index])+round_offset;
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| 205 | length[index] = delta*(grid.end_window[index] - grid.begin_window[index])+round_offset;
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| 206 | post_offset[index] = delta*(grid.end[index] - grid.end_window[index])+round_offset;
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| 207 | total[index] = delta*(grid.end[index] - grid.begin[index])+round_offset;
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| 208 | // total is used as safe-guard against loss due to discrete conversion
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| 209 | ASSERT( pre_offset[index]+post_offset[index]+length[index] == total[index],
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| 210 | "InterfaceVMGJob::addWindowOntoGrid() - pre, post, and length don't sum up to total for "
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| 211 | +toString(index)+"th component.");
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| 212 | }
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| 213 | #ifndef NDEBUG
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| 214 | const size_t calculated_size = length[0]*length[1]*length[2];
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| 215 | ASSERT( calculated_size == grid.sampled_grid.size(),
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| 216 | "InterfaceVMGJob::addWindowOntoGrid() - not enough sampled values given: "
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| 217 | +toString(calculated_size)+" != "+toString(grid.sampled_grid.size())+".");
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| 218 | // ASSERT( calculated_size <= given_size,
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| 219 | // "InterfaceVMGJob::addWindowOntoGrid() - not enough sampled values available: "
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| 220 | // +toString(calculated_size)+" <= "+toString(given_size)+".");
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| 221 | // const size_t total_size = total[0]*total[1]*total[2];
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| 222 | // ASSERT( total_size == given_size,
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| 223 | // "InterfaceVMGJob::addWindowOntoGrid() - total size is not equal to number of present points: "
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| 224 | // +toString(total_size)+" != "+toString(given_size)+".");
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| 225 | #endif
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| 226 | size_t N[3];
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[27ef5c] | 227 | // in open boundary case grid.Local() contains more than just the inner area. The grid
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| 228 | // is actually twice as large to allow for the FV discretization to work. Hence, we first
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| 229 | // have to seek our starting point ... see VMG::Grid::GetSpatialPos()
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| 230 | if (OpenBoundaryConditions) {
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| 231 | const VMG::Index size = window.Local().Size();
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[a2a2f7] | 232 | // const VMG::Index boundary1size = window.Local().BoundarySize1();
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| 233 | // const VMG::Index boundary2size = window.Local().BoundarySize2();
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| 234 | // const VMG::Index halo1size = window.Local().HaloSize1();
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| 235 | // const VMG::Index halo2size = window.Local().HaloSize2();
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[b47f9c] | 236 | // this mimicks VMG::GridIndexTranslations::EndOffset()
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| 237 | const size_t off = OpenBoundaryConditions ? 1 : 0;
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[27ef5c] | 238 | for (size_t i=0;i<3;++i)
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[a2a2f7] | 239 | pre_offset[i] += ((size_t)size[i] - off) / 4;
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[27ef5c] | 240 | for (size_t i=0;i<3;++i)
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[a2a2f7] | 241 | total[i] = ((size_t)size[i]);
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[27ef5c] | 242 | for (size_t i=0;i<3;++i)
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[a2a2f7] | 243 | post_offset[i] = ((size_t)size[i]) - pre_offset[i] - length[i];
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[27ef5c] | 244 | }
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| 245 |
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[b123a5] | 246 | VMG::Grid::iterator griditer = window.Iterators().Local().Begin();
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| 247 | // griditer.advance(pre_offset[0]*total[1]*total[2]);
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| 248 | for(N[0]=0; N[0] < pre_offset[0]; ++N[0])
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| 249 | for(N[1]=0; N[1] < total[1]; ++N[1])
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| 250 | for(N[2]=0; N[2] < total[2]; ++N[2]) {
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| 251 | ASSERT( griditer != window.Iterators().Local().End(),
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| 252 | "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
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| 253 | window(*griditer++) = 0.;
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| 254 | }
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| 255 | SamplingGrid::sampledvalues_t::const_iterator copyiter = grid.sampled_grid.begin();
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| 256 | for(N[0]=0; N[0] < length[0]; ++N[0]) {
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| 257 | // griditer.advance(pre_offset[1]*total[2]);
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| 258 | for(N[1]=0; N[1] < pre_offset[1]; ++N[1])
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| 259 | for(N[2]=0; N[2] < total[2]; ++N[2]) {
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| 260 | ASSERT( griditer != window.Iterators().Local().End(),
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| 261 | "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
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| 262 | window(*griditer++) = 0.;
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| 263 | }
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| 264 | for(N[1]=0; N[1] < length[1]; ++N[1]) {
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| 265 | // griditer.advance(pre_offset[2]);
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[27ef5c] | 266 | for(N[2]=0; N[2] < pre_offset[2]; ++N[2])
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| 267 | window(*griditer++) = 0.;
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[b123a5] | 268 | for(N[2]=0; N[2] < length[2]; ++N[2]) {
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| 269 | ASSERT( griditer != window.Iterators().Local().End(),
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| 270 | "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
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| 271 | ASSERT( copyiter != grid.sampled_grid.end(),
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| 272 | "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
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| 273 | window(*griditer++) += prefactor*(*copyiter++);
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| 274 | }
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| 275 | // griditer.advance(post_offset[2]);
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| 276 | for(N[2]=0; N[2] < post_offset[2]; ++N[2]) {
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| 277 | ASSERT( griditer != window.Iterators().Local().End(),
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| 278 | "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
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| 279 | window(*griditer++) = 0.;
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| 280 | }
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| 281 | }
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| 282 | // griditer.advance(post_offset[1]*total[2]);
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| 283 | for(N[1]=0; N[1] < post_offset[1]; ++N[1])
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| 284 | for(N[2]=0; N[2] < total[2]; ++N[2]) {
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| 285 | ASSERT( griditer != window.Iterators().Local().End(),
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| 286 | "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
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| 287 | window(*griditer++) = 0.;
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| 288 | }
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| 289 | }
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[27ef5c] | 290 | // griditer.advance(post_offset[0]*total[1]*total[2]);
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[b123a5] | 291 | for(N[0]=0; N[0] < post_offset[0]; ++N[0])
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| 292 | for(N[1]=0; N[1] < total[1]; ++N[1])
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| 293 | for(N[2]=0; N[2] < total[2]; ++N[2]) {
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| 294 | ASSERT( griditer != window.Iterators().Local().End(),
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| 295 | "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
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| 296 | window(*griditer++) = 0.;
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| 297 | }
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| 298 | #ifndef NDEBUG
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| 299 | ASSERT( griditer == window.Iterators().Local().End(),
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| 300 | "InterfaceVMGJob::addWindowOntoGrid() - griditer is not at end of window.");
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| 301 | ASSERT( copyiter == grid.sampled_grid.end(),
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| 302 | "InterfaceVMGJob::addWindowOntoGrid() - copyiter is not at end of window.");
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| 303 | #endif
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| 304 | // LOG(2, "DEBUG: Grid after adding other is " << grid << ".");
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| 305 | }
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