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) 2010-2012 University of Bonn. All rights reserved.
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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 | * FillVoidWithMoleculeAction.cpp
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10 | *
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11 | * Created on: May 10, 2010
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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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22 | #include "Atom/atom.hpp"
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23 | #include "CodePatterns/Verbose.hpp"
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24 | #include "Descriptors/MoleculeIdDescriptor.hpp"
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25 | #include "Descriptors/MoleculeOrderDescriptor.hpp"
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26 | #include "Graph/BondGraph.hpp"
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27 | #include "molecule.hpp"
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28 | #include "MoleculeListClass.hpp"
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29 | #include "Parser/FormatParserInterface.hpp"
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30 | #include "Parser/FormatParserStorage.hpp"
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31 | #include "Tesselation/boundary.hpp"
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32 | #include "World.hpp"
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33 |
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34 |
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35 | #include <algorithm>
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36 | #include <iostream>
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37 | #include <string>
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38 |
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39 | #include "Actions/MoleculeAction/FillVoidWithMoleculeAction.hpp"
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40 |
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41 | using namespace MoleCuilder;
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42 |
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43 | // and construct the stuff
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44 | #include "FillVoidWithMoleculeAction.def"
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45 | #include "Action_impl_pre.hpp"
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46 | /** =========== define the function ====================== */
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47 | Action::state_ptr MoleculeFillVoidWithMoleculeAction::performCall() {
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48 | if (!boost::filesystem::exists(params.fillername.get())) {
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49 | ELOG(1, "File with filler molecule " << params.fillername.get() << " does not exist!");
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50 | return Action::failure;
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51 | }
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52 |
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53 | LOG(1, "INFO: Filling Box with water molecules, "
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54 | << " minimum distance to molecules" << params.boundary.get()
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55 | << ", random atom displacement " << params.RandAtomDisplacement.get()
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56 | << ", random molecule displacement " << params.RandMoleculeDisplacement.get()
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57 | << ", distances between fillers (" << params.distances.get()[0] << "," << params.distances.get()[1] << "," << params.distances.get()[2]
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58 | << "), MinDistance " << params.MinDistance.get()
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59 | << ", DoRotate " << params.DoRotate.get() << ".");
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60 | // construct water molecule
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61 | std::vector<molecule *> presentmolecules = World::getInstance().getAllMolecules();
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62 | // LOG(0, presentmolecules.size() << " molecules initially are present.");
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63 | std::string FilenameSuffix = params.fillername.get().string().substr(params.fillername.get().string().find_last_of('.')+1, params.fillername.get().string().length());
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64 | ifstream input;
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65 | input.open(params.fillername.get().string().c_str());
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66 | ParserTypes type = FormatParserStorage::getInstance().getTypeFromSuffix(FilenameSuffix);
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67 | FormatParserInterface &parser = FormatParserStorage::getInstance().get(type);
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68 | parser.load(&input);
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69 |
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70 | // search the filler molecule that has been just parsed
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71 | molecule *filler = World::getInstance().getMolecule(MoleculeByOrder(-1)); // get last molecule
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72 | ASSERT(filler != NULL,
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73 | "MoleculeFillVoidWithMoleculeAction::performCall() - no last molecule found, nothing parsed?.");
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74 | filler->SetNameFromFilename(params.fillername.get().string().c_str());
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75 | World::AtomComposite Set = filler->getAtomSet();
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76 | World::getInstance().getBondGraph()->CreateAdjacency(Set);
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77 |
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78 | // call routine
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79 | double distance[NDIM];
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80 | for (int i=0;i<NDIM;i++)
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81 | distance[i] = params.distances.get()[i];
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82 | FillVoidWithMolecule(
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83 | filler,
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84 | *(World::getInstance().getConfig()),
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85 | distance,
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86 | params.boundary.get(),
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87 | params.RandAtomDisplacement.get(),
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88 | params.RandMoleculeDisplacement.get(),
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89 | params.MinDistance.get(),
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90 | params.DoRotate.get());
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91 |
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92 | // generate list of newly created molecules
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93 | // (we can in general remove more quickly from a list than a vector)
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94 | std::vector<molecule *> fillermolecules = World::getInstance().getAllMolecules();
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95 | // LOG(0, fillermolecules.size() << " molecules are present.");
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96 | std::list<molecule *> fillermolecules_list;
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97 | std::copy( fillermolecules.begin(), fillermolecules.end(), std::back_inserter( fillermolecules_list ));
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98 | // LOG(0, fillermolecules_list.size() << " molecules have been copied.");
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99 | for (std::vector<molecule *>::const_iterator iter = presentmolecules.begin();
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100 | iter != presentmolecules.end();
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101 | ++iter) {
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102 | fillermolecules_list.remove(*iter);
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103 | }
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104 | // LOG(0, fillermolecules_list.size() << " molecules left after removal.");
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105 | fillermolecules.clear();
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106 | std::copy(fillermolecules_list.begin(), fillermolecules_list.end(), std::back_inserter( fillermolecules ));
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107 |
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108 | // LOG(0, fillermolecules.size() << " molecules have been inserted.");
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109 |
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110 | return Action::state_ptr(new MoleculeFillVoidWithMoleculeState(fillermolecules,params));
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111 | }
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112 |
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113 | Action::state_ptr MoleculeFillVoidWithMoleculeAction::performUndo(Action::state_ptr _state) {
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114 | MoleculeFillVoidWithMoleculeState *state = assert_cast<MoleculeFillVoidWithMoleculeState*>(_state.get());
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115 |
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116 | MoleculeListClass *MolList = World::getInstance().getMolecules();
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117 |
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118 | BOOST_FOREACH(molecule *_mol, state->fillermolecules) {
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119 | MolList->erase(_mol);
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120 | if ((_mol != NULL) && (!(World::getInstance().getAllMolecules(MoleculeById(_mol->getId()))).empty())) {
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121 | for(molecule::iterator iter = _mol->begin();
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122 | !_mol->empty();
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123 | iter = _mol->begin()) {
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124 | atom *Walker = *iter;
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125 | World::getInstance().destroyAtom(Walker);
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126 | }
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127 | World::getInstance().destroyMolecule(_mol);
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128 | }
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129 | }
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130 |
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131 | // as molecules and atoms from state are removed, we have to create a new one
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132 | std::vector<molecule *> fillermolecules;
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133 | return Action::state_ptr(new MoleculeFillVoidWithMoleculeState(fillermolecules,state->params));
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134 | }
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135 |
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136 | Action::state_ptr MoleculeFillVoidWithMoleculeAction::performRedo(Action::state_ptr _state){
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137 | //MoleculeFillVoidWithMoleculeState *state = assert_cast<MoleculeFillVoidWithMoleculeState*>(_state.get());
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138 |
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139 | return Action::failure;
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140 | //return Action::state_ptr(_state);
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141 | }
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142 |
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143 | bool MoleculeFillVoidWithMoleculeAction::canUndo() {
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144 | return true;
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145 | }
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146 |
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147 | bool MoleculeFillVoidWithMoleculeAction::shouldUndo() {
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148 | return true;
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149 | }
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150 | /** =========== end of function ====================== */
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