source: src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp@ eb0d77

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Last change on this file since eb0d77 was f10b0c, checked in by Frederik Heber <heber@…>, 13 years ago

disastrously big and ugly commit

  • using new Parameter<T> classes:
    • Actions
    • Queries (all UIs)
  • TODO:
    • actions crash cause Value is unset
    • no query<BoxVector>
  • Property mode set to 100644
File size: 5.8 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
8/*
9 * FillVoidWithMoleculeAction.cpp
10 *
11 * Created on: May 10, 2010
12 * Author: heber
13 */
14
15// include config.h
16#ifdef HAVE_CONFIG_H
17#include <config.h>
18#endif
19
20#include "CodePatterns/MemDebug.hpp"
21
22#include "Atom/atom.hpp"
23#include "CodePatterns/Verbose.hpp"
24#include "Descriptors/MoleculeIdDescriptor.hpp"
25#include "Descriptors/MoleculeOrderDescriptor.hpp"
26#include "Graph/BondGraph.hpp"
27#include "molecule.hpp"
28#include "MoleculeListClass.hpp"
29#include "Parser/FormatParserInterface.hpp"
30#include "Parser/FormatParserStorage.hpp"
31#include "Tesselation/boundary.hpp"
32#include "World.hpp"
33
34
35#include <algorithm>
36#include <iostream>
37#include <string>
38
39#include "Actions/MoleculeAction/FillVoidWithMoleculeAction.hpp"
40
41using namespace MoleCuilder;
42
43// and construct the stuff
44#include "FillVoidWithMoleculeAction.def"
45#include "Action_impl_pre.hpp"
46/** =========== define the function ====================== */
47Action::state_ptr MoleculeFillVoidWithMoleculeAction::performCall() {
48 if (!boost::filesystem::exists(params.fillername.get())) {
49 ELOG(1, "File with filler molecule " << params.fillername.get() << " does not exist!");
50 return Action::failure;
51 }
52
53 LOG(1, "INFO: Filling Box with water molecules, "
54 << " minimum distance to molecules" << params.boundary.get()
55 << ", random atom displacement " << params.RandAtomDisplacement.get()
56 << ", random molecule displacement " << params.RandMoleculeDisplacement.get()
57 << ", distances between fillers (" << params.distances.get()[0] << "," << params.distances.get()[1] << "," << params.distances.get()[2]
58 << "), MinDistance " << params.MinDistance.get()
59 << ", DoRotate " << params.DoRotate.get() << ".");
60 // construct water molecule
61 std::vector<molecule *> presentmolecules = World::getInstance().getAllMolecules();
62// LOG(0, presentmolecules.size() << " molecules initially are present.");
63 std::string FilenameSuffix = params.fillername.get().string().substr(params.fillername.get().string().find_last_of('.')+1, params.fillername.get().string().length());
64 ifstream input;
65 input.open(params.fillername.get().string().c_str());
66 ParserTypes type = FormatParserStorage::getInstance().getTypeFromSuffix(FilenameSuffix);
67 FormatParserInterface &parser = FormatParserStorage::getInstance().get(type);
68 parser.load(&input);
69
70 // search the filler molecule that has been just parsed
71 molecule *filler = World::getInstance().getMolecule(MoleculeByOrder(-1)); // get last molecule
72 ASSERT(filler != NULL,
73 "MoleculeFillVoidWithMoleculeAction::performCall() - no last molecule found, nothing parsed?.");
74 filler->SetNameFromFilename(params.fillername.get().string().c_str());
75 World::AtomComposite Set = filler->getAtomSet();
76 World::getInstance().getBondGraph()->CreateAdjacency(Set);
77
78 // call routine
79 double distance[NDIM];
80 for (int i=0;i<NDIM;i++)
81 distance[i] = params.distances.get()[i];
82 FillVoidWithMolecule(
83 filler,
84 *(World::getInstance().getConfig()),
85 distance,
86 params.boundary.get(),
87 params.RandAtomDisplacement.get(),
88 params.RandMoleculeDisplacement.get(),
89 params.MinDistance.get(),
90 params.DoRotate.get());
91
92 // generate list of newly created molecules
93 // (we can in general remove more quickly from a list than a vector)
94 std::vector<molecule *> fillermolecules = World::getInstance().getAllMolecules();
95// LOG(0, fillermolecules.size() << " molecules are present.");
96 std::list<molecule *> fillermolecules_list;
97 std::copy( fillermolecules.begin(), fillermolecules.end(), std::back_inserter( fillermolecules_list ));
98// LOG(0, fillermolecules_list.size() << " molecules have been copied.");
99 for (std::vector<molecule *>::const_iterator iter = presentmolecules.begin();
100 iter != presentmolecules.end();
101 ++iter) {
102 fillermolecules_list.remove(*iter);
103 }
104// LOG(0, fillermolecules_list.size() << " molecules left after removal.");
105 fillermolecules.clear();
106 std::copy(fillermolecules_list.begin(), fillermolecules_list.end(), std::back_inserter( fillermolecules ));
107
108// LOG(0, fillermolecules.size() << " molecules have been inserted.");
109
110 return Action::state_ptr(new MoleculeFillVoidWithMoleculeState(fillermolecules,params));
111}
112
113Action::state_ptr MoleculeFillVoidWithMoleculeAction::performUndo(Action::state_ptr _state) {
114 MoleculeFillVoidWithMoleculeState *state = assert_cast<MoleculeFillVoidWithMoleculeState*>(_state.get());
115
116 MoleculeListClass *MolList = World::getInstance().getMolecules();
117
118 BOOST_FOREACH(molecule *_mol, state->fillermolecules) {
119 MolList->erase(_mol);
120 if ((_mol != NULL) && (!(World::getInstance().getAllMolecules(MoleculeById(_mol->getId()))).empty())) {
121 for(molecule::iterator iter = _mol->begin();
122 !_mol->empty();
123 iter = _mol->begin()) {
124 atom *Walker = *iter;
125 World::getInstance().destroyAtom(Walker);
126 }
127 World::getInstance().destroyMolecule(_mol);
128 }
129 }
130
131 // as molecules and atoms from state are removed, we have to create a new one
132 std::vector<molecule *> fillermolecules;
133 return Action::state_ptr(new MoleculeFillVoidWithMoleculeState(fillermolecules,state->params));
134}
135
136Action::state_ptr MoleculeFillVoidWithMoleculeAction::performRedo(Action::state_ptr _state){
137 //MoleculeFillVoidWithMoleculeState *state = assert_cast<MoleculeFillVoidWithMoleculeState*>(_state.get());
138
139 return Action::failure;
140 //return Action::state_ptr(_state);
141}
142
143bool MoleculeFillVoidWithMoleculeAction::canUndo() {
144 return true;
145}
146
147bool MoleculeFillVoidWithMoleculeAction::shouldUndo() {
148 return true;
149}
150/** =========== end of function ====================== */
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