[fea945] | 1 | /*
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| 2 | * Project: MoleCuilder
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| 3 | * Description: creates and alters molecular systems
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[0aa122] | 4 | * Copyright (C) 2012 University of Bonn. All rights reserved.
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[fea945] | 5 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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| 6 | */
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| 7 |
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| 8 | /*
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| 9 | * LinkedCell_Controller.cpp
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| 10 | *
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| 11 | * Created on: Nov 15, 2011
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| 12 | * Author: heber
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| 13 | */
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| 14 |
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| 15 | // include config.h
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| 16 | #ifdef HAVE_CONFIG_H
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| 17 | #include <config.h>
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| 18 | #endif
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| 19 |
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| 20 | #include "CodePatterns/MemDebug.hpp"
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| 21 |
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[4a8169] | 22 | #include <set>
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| 23 |
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[fea945] | 24 | #include "Box.hpp"
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[fe8253] | 25 | #include "CodePatterns/Assert.hpp"
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[4a8169] | 26 | #include "CodePatterns/Log.hpp"
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| 27 | #include "CodePatterns/Observer/Notification.hpp"
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[fe8253] | 28 | #include "CodePatterns/Range.hpp"
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[fea945] | 29 | #include "LinkedCell_Controller.hpp"
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| 30 | #include "LinkedCell_Model.hpp"
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| 31 | #include "LinkedCell_View.hpp"
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[cbdcb1] | 32 | #include "LinkedCell_View_ModelWrapper.hpp"
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[c80643] | 33 | #include "IPointCloud.hpp"
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[ce81e76] | 34 | #include "WorldTime.hpp"
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[fea945] | 35 |
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| 36 |
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| 37 | using namespace LinkedCell;
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| 38 |
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[fe8253] | 39 | double LinkedCell_Controller::lower_threshold = 1.;
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| 40 | double LinkedCell_Controller::upper_threshold = 20.;
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| 41 |
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[fea945] | 42 | /** Constructor of class LinkedCell_Controller.
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| 43 | *
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| 44 | */
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| 45 | LinkedCell_Controller::LinkedCell_Controller(const Box &_domain) :
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[4a8169] | 46 | Observer("LinkedCell_Controller"),
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[fea945] | 47 | domain(_domain)
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[fe8253] | 48 | {
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[5e2864] | 49 | // sign on to specific notifications
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| 50 | domain.signOn(this, Box::MatrixChanged);
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[ce81e76] | 51 | WorldTime::getInstance().signOn(this, WorldTime::TimeChanged);
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[5e2864] | 52 |
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[fe8253] | 53 | /// Check that upper_threshold fits within half the box.
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| 54 | Vector diagonal(1.,1.,1.);
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| 55 | diagonal.Scale(upper_threshold);
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| 56 | Vector diagonal_transformed = domain.getMinv() * diagonal;
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| 57 | double max_factor = 1.;
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| 58 | for (size_t i=0; i<NDIM; ++i)
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| 59 | if (diagonal_transformed.at(i) > 1./max_factor)
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| 60 | max_factor = 1./diagonal_transformed.at(i);
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| 61 | upper_threshold *= max_factor;
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| 62 |
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| 63 | /// Check that lower_threshold is still lower, if not set to half times upper_threshold.
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| 64 | if (lower_threshold > upper_threshold)
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| 65 | lower_threshold = 0.5*upper_threshold;
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| 66 | }
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[fea945] | 67 |
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| 68 | /** Destructor of class LinkedCell_Controller.
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| 69 | *
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| 70 | * Here, we free all LinkedCell_Model instances again.
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| 71 | *
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| 72 | */
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| 73 | LinkedCell_Controller::~LinkedCell_Controller()
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| 74 | {
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[5e2864] | 75 | // sign off
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| 76 | domain.signOff(this, Box::MatrixChanged);
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[ce81e76] | 77 | WorldTime::getInstance().signOff(this, WorldTime::TimeChanged);
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[5e2864] | 78 |
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[fe8253] | 79 | /// we free all LinkedCell_Model instances again.
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[fea945] | 80 | for(MapEdgelengthModel::iterator iter = ModelsMap.begin();
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| 81 | !ModelsMap.empty(); iter = ModelsMap.begin()) {
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| 82 | delete iter->second;
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| 83 | ModelsMap.erase(iter);
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| 84 | }
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| 85 | }
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| 86 |
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[fe8253] | 87 | /** Internal function to obtain the range within which an model is suitable.
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| 88 | *
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| 89 | * \note We use statics lower_threshold and upper_threshold as min and max
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| 90 | * boundaries.
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| 91 | *
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| 92 | * @param distance desired egde length
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| 93 | * @return range within which model edge length is acceptable
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| 94 | */
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| 95 | const range<double> LinkedCell_Controller::getHeuristicRange(const double distance) const
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| 96 | {
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| 97 | const double lower = 0.5*distance < lower_threshold ? lower_threshold : 0.5*distance;
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| 98 | const double upper = 2.*distance > upper_threshold ? upper_threshold : 2.*distance;
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| 99 | range<double> HeuristicInterval(lower, upper);
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| 100 | return HeuristicInterval;
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| 101 | }
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| 102 |
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[fea945] | 103 | /** Internal function to decide whether a suitable model is present or not.
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| 104 | *
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| 105 | * Here, the heuristic for deciding whether a new linked cell structure has to
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[fe8253] | 106 | * be constructed or not is implemented. The current heuristic is as follows:
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| 107 | * -# the best model should have at least half the desired length (such
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| 108 | * that most we have to look two neighbor shells wide and not one).
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| 109 | * -# the best model should have at most twice the desired length but
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| 110 | * no less than 1 angstroem.
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[fea945] | 111 | *
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| 112 | * \note Dealing out a pointer is here (hopefully) safe because the function is
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| 113 | * internal and we - inside this class - know what we are doing.
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| 114 | *
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| 115 | * @param distance edge length of the requested linked cell structure
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| 116 | * @return NULL - there is no fitting LinkedCell_Model, else - pointer to instance
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| 117 | */
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[fe8253] | 118 | const LinkedCell_Model *LinkedCell_Controller::getBestModel(double distance) const
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[fea945] | 119 | {
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[fe8253] | 120 | /// Bound distance to be within [lower_threshold, upper_threshold).
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| 121 | /// Note that we need to stay away from upper boundary a bit,
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| 122 | /// otherwise the distance will end up outside of the interval.
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| 123 | if (distance < lower_threshold)
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| 124 | distance = lower_threshold;
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| 125 | if (distance > upper_threshold)
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| 126 | distance = upper_threshold - std::numeric_limits<double>::round_error();
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| 127 |
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| 128 | /// Look for all models within [0.5 distance, 2. distance).
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| 129 | MapEdgelengthModel::const_iterator bestmatch = ModelsMap.end();
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| 130 | if (!ModelsMap.empty()) {
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| 131 | for(MapEdgelengthModel::const_iterator iter = ModelsMap.begin();
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| 132 | iter != ModelsMap.end(); ++iter) {
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| 133 | // check that we are truely within range
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| 134 | range<double> HeuristicInterval(getHeuristicRange(iter->first));
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| 135 | if (HeuristicInterval.isInRange(distance)) {
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| 136 | // if it's the first match or a closer one, pick
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| 137 | if ((bestmatch == ModelsMap.end())
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| 138 | || (fabs(bestmatch->first - distance) > fabs(iter->first - distance)))
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| 139 | bestmatch = iter;
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| 140 | }
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[fea945] | 141 | }
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| 142 | }
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[fe8253] | 143 |
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| 144 | /// Return best match or NULL if none found.
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| 145 | if (bestmatch != ModelsMap.end())
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| 146 | return bestmatch->second;
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| 147 | else
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| 148 | return NULL;
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| 149 | }
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| 150 |
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| 151 | /** Internal function to insert a new model and check for valid insertion.
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| 152 | *
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| 153 | * @param distance edge length of new model
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| 154 | * @param instance pointer to model
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| 155 | */
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[455043] | 156 | void LinkedCell_Controller::insertNewModel(const double edgelength, const LinkedCell_Model* instance)
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[fe8253] | 157 | {
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| 158 | std::pair< MapEdgelengthModel::iterator, bool> inserter =
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| 159 | ModelsMap.insert( std::make_pair(edgelength, instance) );
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| 160 | ASSERT(inserter.second,
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| 161 | "LinkedCell_Controller::getView() - LinkedCell_Model instance with distance "
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| 162 | +toString(edgelength)+" already present.");
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[fea945] | 163 | }
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| 164 |
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| 165 | /** Returns the a suitable LinkedCell_Model contained in a LinkedCell_View
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| 166 | * for the requested \a distance.
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| 167 | *
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| 168 | * \sa getBestModel()
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| 169 | *
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| 170 | * @param distance edge length of the requested linked cell structure
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[c80643] | 171 | * @param set of initial points to insert when new model is created (not always), should be World's
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[fea945] | 172 | * @return LinkedCell_View wrapping the best LinkedCell_Model
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| 173 | */
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[c80643] | 174 | LinkedCell_View LinkedCell_Controller::getView(const double distance, IPointCloud &set)
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[fea945] | 175 | {
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[fe8253] | 176 | /// Look for best instance.
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[455043] | 177 | const LinkedCell_Model * const LCModel_best = getBestModel(distance);
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[fea945] | 178 |
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[fe8253] | 179 | /// Construct new instance if none found,
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[fea945] | 180 | if (LCModel_best == NULL) {
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[455043] | 181 | LinkedCell_Model * const LCModel_new = new LinkedCell_Model(distance, domain);
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[c80643] | 182 | LCModel_new->insertPointCloud(set);
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[fe8253] | 183 | insertNewModel(distance, LCModel_new);
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[455043] | 184 | LinkedCell_View view(*LCModel_new);
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[fe8253] | 185 | return view;
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[fea945] | 186 | } else {
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[fe8253] | 187 | /// else construct interface and return.
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| 188 | LinkedCell_View view(*LCModel_best);
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| 189 | return view;
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[fea945] | 190 | }
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| 191 | }
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[4a8169] | 192 |
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| 193 | /** Internal function to re-create all present and used models for the new Box.
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[ce81e76] | 194 | *
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| 195 | * This is necessary in the following cases:
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| 196 | * -# the Box is changed
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| 197 | * -# we step on to a different time step, i.e. all atomic positions change
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[4a8169] | 198 | *
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| 199 | * The main problem are the views currently in use.
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[cbdcb1] | 200 | *
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[4a8169] | 201 | * We make use of LinkedCell:LinkedCell_View::RAIIMap as there all present are
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| 202 | * listed. We go through the list, create a map with old model ref as keys to
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| 203 | * just newly created ones, and finally go again through each view and exchange
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| 204 | * the model against the new ones via a simple map lookup.
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| 205 | *
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| 206 | */
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[ce81e76] | 207 | void LinkedCell_Controller::updateModels()
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[4a8169] | 208 | {
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[cbdcb1] | 209 | LOG(1, "INFO: Updating all models.");
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| 210 |
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[4a8169] | 211 | typedef std::map<const LinkedCell_Model *, LinkedCell_Model *> ModelLookup;
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| 212 | ModelLookup models;
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| 213 |
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| 214 | // set up map, for now with NULL pointers
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| 215 | for (LinkedCell_View::ModelInstanceMap::const_iterator iter = LinkedCell_View::RAIIMap.begin();
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| 216 | iter != LinkedCell_View::RAIIMap.end(); ++iter) {
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| 217 | #ifndef NDEBUG
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| 218 | std::pair< ModelLookup::iterator, bool > inserter =
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| 219 | #endif
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[cbdcb1] | 220 | models.insert( std::pair<const LinkedCell_Model *, LinkedCell_Model *>( (*iter)->LC->getModel(), NULL) );
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| 221 | LOG(2, "INFO: Added " << (*iter)->LC->getModel() << " to list of models to replace.");
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[4a8169] | 222 | ASSERT( inserter.second,
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| 223 | "LinkedCell_Controller::updateModelsForNewBoxMatrix() - failed to insert old model "
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[cbdcb1] | 224 | +toString( (*iter)->LC->getModel() )+","+toString(NULL)+" into models, is already present");
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[4a8169] | 225 | }
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| 226 |
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| 227 | // invert MapEdgelengthModel
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[cbdcb1] | 228 | LOG(2, "INFO: ModelsMap is " << ModelsMap << ".");
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[4a8169] | 229 | typedef std::map<const LinkedCell_Model*, double > MapEdgelengthModel_inverted;
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| 230 | MapEdgelengthModel_inverted ModelsMap_inverted;
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| 231 | for (MapEdgelengthModel::const_iterator iter = ModelsMap.begin();
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| 232 | iter != ModelsMap.end(); ++iter) {
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| 233 | #ifndef NDEBUG
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| 234 | MapEdgelengthModel_inverted::const_iterator assertiter = ModelsMap_inverted.find(iter->second);
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[cbdcb1] | 235 | ASSERT( assertiter == ModelsMap_inverted.end(),
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[4a8169] | 236 | "LinkedCell_Controller::updateModelsForNewBoxMatrix() - ModelsMap is not invertible, value "
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| 237 | +toString(iter->second)+" is already present.");
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| 238 | #endif
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| 239 | ModelsMap_inverted.insert( std::make_pair(iter->second, iter->first) );
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| 240 | }
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[cbdcb1] | 241 | LOG(2, "INFO: Inverted ModelsMap is " << ModelsMap_inverted << ".");
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[4a8169] | 242 |
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| 243 | // go through map and re-create models
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| 244 | for (ModelLookup::iterator iter = models.begin(); iter != models.end(); ++iter) {
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| 245 | // delete old model
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| 246 | const LinkedCell_Model * const oldref = iter->first;
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| 247 | #ifndef NDEBUG
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| 248 | MapEdgelengthModel_inverted::const_iterator assertiter = ModelsMap_inverted.find(oldref);
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| 249 | ASSERT( assertiter != ModelsMap_inverted.end(),
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| 250 | "LinkedCell_Controller::updateModelsForNewBoxMatrix() - ModelsMap_inverted does not contain old model "
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| 251 | +toString(oldref)+".");
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| 252 | #endif
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| 253 | const double distance = ModelsMap_inverted[oldref];
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[429069] | 254 | // create new one, afterwards erase old model (this is for unit test to get different memory addresses)
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[4a8169] | 255 | LinkedCell_Model * const newref = new LinkedCell_Model(distance, domain);
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[429069] | 256 | MapEdgelengthModel::iterator oldmodeliter = ModelsMap.find(distance);
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| 257 | delete oldmodeliter->second;
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| 258 | ModelsMap.erase(oldmodeliter);
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[cbdcb1] | 259 | LOG(2, "INFO: oldref is " << oldref << ", newref is " << newref << ".");
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[4a8169] | 260 | iter->second = newref;
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| 261 | // replace in ModelsMap
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| 262 | #ifndef NDEBUG
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| 263 | std::pair< MapEdgelengthModel::iterator, bool > inserter =
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| 264 | #endif
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| 265 | ModelsMap.insert( std::make_pair(distance, newref) );
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| 266 | ASSERT( inserter.second,
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| 267 | "LinkedCell_Controller::updateModelsForNewBoxMatrix() - failed to insert new model "
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| 268 | +toString(distance)+","+toString(newref)+" into ModelsMap, is already present");
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| 269 | }
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[429069] | 270 |
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| 271 | // remove all remaining active models (also those that don't have an active View on them)
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| 272 | for (MapEdgelengthModel::iterator iter = ModelsMap.begin();
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| 273 | !ModelsMap.empty();
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| 274 | iter = ModelsMap.begin()) {
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| 275 | delete iter->second;
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| 276 | ModelsMap.erase(iter);
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| 277 | }
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| 278 |
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[4a8169] | 279 |
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| 280 | // delete inverted map for safety (values are gone)
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| 281 | ModelsMap_inverted.clear();
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| 282 |
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| 283 | // go through views and exchange the models
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| 284 | for (LinkedCell_View::ModelInstanceMap::const_iterator iter = LinkedCell_View::RAIIMap.begin();
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| 285 | iter != LinkedCell_View::RAIIMap.end(); ++iter) {
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[cbdcb1] | 286 | ModelLookup::const_iterator modeliter = models.find((*iter)->LC->getModel());
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[4a8169] | 287 | ASSERT( modeliter != models.end(),
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| 288 | "LinkedCell_Controller::updateModelsForNewBoxMatrix() - we miss a model "
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[cbdcb1] | 289 | +toString((*iter)->LC->getModel())+" in ModelLookup.");
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[4a8169] | 290 | // this is ugly but the only place where we have to set ourselves over the constness of the member variable
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[cbdcb1] | 291 | if (modeliter != models.end()) {
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| 292 | LOG(2, "INFO: Setting model to " << modeliter->second << " in view " << *iter << ".");
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| 293 | (*iter)->LC->setModel(modeliter->second);
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| 294 | }
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[4a8169] | 295 | }
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| 296 | }
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| 297 |
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| 298 | /** Callback function for Observer mechanism.
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| 299 | *
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| 300 | * @param publisher reference to the Observable that calls
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| 301 | */
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| 302 | void LinkedCell_Controller::update(Observable *publisher)
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| 303 | {
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| 304 | ELOG(2, "LinkedCell_Model received inconclusive general update from "
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| 305 | << publisher << ".");
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| 306 | }
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| 307 |
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| 308 | /** Callback function for the Notifications mechanism.
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| 309 | *
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| 310 | * @param publisher reference to the Observable that calls
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| 311 | * @param notification specific notification as cause of the call
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| 312 | */
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| 313 | void LinkedCell_Controller::recieveNotification(Observable *publisher, Notification_ptr notification)
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| 314 | {
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[ce81e76] | 315 | if (publisher == &domain) {
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| 316 | switch(notification->getChannelNo()) {
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| 317 | case Box::MatrixChanged:
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| 318 | LOG(1, "INFO: LinkedCell_Controller got update from Box.");
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| 319 | updateModels();
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| 320 | break;
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| 321 | default:
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| 322 | ASSERT(0,
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| 323 | "LinkedCell_Controller::recieveNotification() - unwanted notification from Box "
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| 324 | +toString(notification->getChannelNo())+" received.");
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| 325 | break;
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| 326 | }
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| 327 | } else if (publisher == WorldTime::getPointer()) {
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| 328 | switch(notification->getChannelNo()) {
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| 329 | case WorldTime::TimeChanged:
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| 330 | LOG(1, "INFO: LinkedCell_Controller got update from WorldTime.");
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| 331 | updateModels();
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| 332 | break;
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| 333 | default:
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| 334 | ASSERT(0,
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| 335 | "LinkedCell_Controller::recieveNotification() - unwanted notification from WorldTime "
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| 336 | +toString(notification->getChannelNo())+" received.");
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| 337 | break;
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| 338 | }
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| 339 | } else {
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| 340 | ELOG(1, "Notification " << notification->getChannelNo()
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| 341 | << " from unknown publisher " << publisher << ".");
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[4a8169] | 342 | }
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| 343 | }
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| 344 |
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| 345 | /** Callback function when an Observer dies.
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| 346 | *
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| 347 | * @param publisher reference to the Observable that calls
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| 348 | */
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| 349 | void LinkedCell_Controller::subjectKilled(Observable *publisher)
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| 350 | {}
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| 351 |
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