source: src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp@ 360c8b

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Last change on this file since 360c8b was 360c8b, checked in by Frederik Heber <heber@…>, 13 years ago

Merge branch 'Adding_Psi3Parser' into stable

Conflicts:

src/Parser/FormatParser.hpp
src/Parser/unittests/ParserTremoloUnitTest.cpp

Issues:

  • Element and periodentafel have been moved to folder src/Element.
  • 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 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.hpp"
23#include "Graph/BondGraph.hpp"
24#include "Tesselation/boundary.hpp"
25#include "CodePatterns/Verbose.hpp"
26#include "config.hpp"
27#include "Descriptors/MoleculeIdDescriptor.hpp"
28#include "Descriptors/MoleculeOrderDescriptor.hpp"
29#include "molecule.hpp"
30#include "Parser/FormatParserInterface.hpp"
31#include "Parser/FormatParserStorage.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 // obtain information
49 getParametersfromValueStorage();
50
51 if (!boost::filesystem::exists(params.fillername)) {
52 DoeLog(1) && (eLog() << Verbose(1) << "File with filler molecule " << params.fillername << " does not exist!" << endl);
53 return Action::failure;
54 }
55
56 DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules, "
57 << " minimum distance to molecules" << params.boundary
58 << ", random atom displacement " << params.RandAtomDisplacement
59 << ", random molecule displacement " << params.RandMoleculeDisplacement
60 << ", distances between fillers (" << params.distances[0] << "," << params.distances[1] << "," << params.distances[2]
61 << "), MinDistance " << params.MinDistance
62 << ", DoRotate " << params.DoRotate << "." << endl);
63 // construct water molecule
64 std::vector<molecule *> presentmolecules = World::getInstance().getAllMolecules();
65// DoLog(0) && (Log() << Verbose(0) << presentmolecules.size() << " molecules initially are present." << std::endl);
66 std::string FilenameSuffix = params.fillername.string().substr(params.fillername.string().find_last_of('.')+1, params.fillername.string().length());
67 ifstream input;
68 input.open(params.fillername.string().c_str());
69 ParserTypes type = FormatParserStorage::getInstance().getTypeFromSuffix(FilenameSuffix);
70 FormatParserInterface &parser = FormatParserStorage::getInstance().get(type);
71 parser.load(&input);
72
73 // search the filler molecule that has been just parsed
74 molecule *filler = World::getInstance().getMolecule(MoleculeByOrder(-1)); // get last molecule
75 filler->SetNameFromFilename(params.fillername.string().c_str());
76 World::AtomComposite Set = filler->getAtomSet();
77 World::getInstance().getBondGraph()->CreateAdjacency(Set);
78
79 // call routine
80 double distance[NDIM];
81 for (int i=0;i<NDIM;i++)
82 distance[i] = params.distances[i];
83 FillVoidWithMolecule(
84 filler,
85 *(World::getInstance().getConfig()),
86 distance,
87 params.boundary,
88 params.RandAtomDisplacement,
89 params.RandMoleculeDisplacement,
90 params.MinDistance,
91 params.DoRotate);
92
93 // generate list of newly created molecules
94 // (we can in general remove more quickly from a list than a vector)
95 std::vector<molecule *> fillermolecules = World::getInstance().getAllMolecules();
96// DoLog(0) && (Log() << Verbose(0) << fillermolecules.size() << " molecules are present." << std::endl);
97 std::list<molecule *> fillermolecules_list;
98 std::copy( fillermolecules.begin(), fillermolecules.end(), std::back_inserter( fillermolecules_list ));
99// DoLog(0) && (Log() << Verbose(0) << fillermolecules_list.size() << " molecules have been copied." << std::endl);
100 for (std::vector<molecule *>::const_iterator iter = presentmolecules.begin();
101 iter != presentmolecules.end();
102 ++iter) {
103 fillermolecules_list.remove(*iter);
104 }
105// DoLog(0) && (Log() << Verbose(0) << fillermolecules_list.size() << " molecules left after removal." << std::endl);
106 fillermolecules.clear();
107 std::copy(fillermolecules_list.begin(), fillermolecules_list.end(), std::back_inserter( fillermolecules ));
108
109// DoLog(0) && (Log() << Verbose(0) << fillermolecules.size() << " molecules have been inserted." << std::endl);
110
111 return Action::state_ptr(new MoleculeFillVoidWithMoleculeState(fillermolecules,params));
112}
113
114Action::state_ptr MoleculeFillVoidWithMoleculeAction::performUndo(Action::state_ptr _state) {
115 MoleculeFillVoidWithMoleculeState *state = assert_cast<MoleculeFillVoidWithMoleculeState*>(_state.get());
116
117 MoleculeListClass *MolList = World::getInstance().getMolecules();
118
119 BOOST_FOREACH(molecule *_mol, state->fillermolecules) {
120 MolList->erase(_mol);
121 if ((_mol != NULL) && (!(World::getInstance().getAllMolecules(MoleculeById(_mol->getId()))).empty())) {
122 for(molecule::iterator iter = _mol->begin();
123 !_mol->empty();
124 iter = _mol->begin()) {
125 atom *Walker = *iter;
126 World::getInstance().destroyAtom(Walker);
127 }
128 World::getInstance().destroyMolecule(_mol);
129 }
130 }
131
132 // as molecules and atoms from state are removed, we have to create a new one
133 std::vector<molecule *> fillermolecules;
134 return Action::state_ptr(new MoleculeFillVoidWithMoleculeState(fillermolecules,state->params));
135}
136
137Action::state_ptr MoleculeFillVoidWithMoleculeAction::performRedo(Action::state_ptr _state){
138 //MoleculeFillVoidWithMoleculeState *state = assert_cast<MoleculeFillVoidWithMoleculeState*>(_state.get());
139
140 return Action::failure;
141 //return Action::state_ptr(_state);
142}
143
144bool MoleculeFillVoidWithMoleculeAction::canUndo() {
145 return true;
146}
147
148bool MoleculeFillVoidWithMoleculeAction::shouldUndo() {
149 return true;
150}
151/** =========== end of function ====================== */
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