source: src/Actions/WorldAction/RepeatBoxAction.cpp@ 1024cb

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Last change on this file since 1024cb was 1024cb, checked in by Frederik Heber <heber@…>, 15 years ago

Merge commit 'jupiter/MoleculeStartEndSwitch' into CommandLineActionMapping

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/helpers.hpp
molecuilder/src/molecule.cpp
molecuilder/src/molecule_dynamics.cpp
molecuilder/src/molecule_fragmentation.cpp
molecuilder/src/molecule_geometry.cpp
molecuilder/src/molecule_graph.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp
molecuilder/src/unittests/listofbondsunittest.cpp

Integration of MoleculeStartEndSwitch had the following consequences:

  • no more AtomCount -> getAtomCount()
  • no more start/end -> begin(), end() and iterator
  • no more decent ordering in atomic ids (hence, Simple_configuration/8 and Domain/5, Domain/6 now check by comparing sorted xyz, not confs)

There is still a huge problem with bonds. One test runs into an endless loop.

Signed-off-by: Frederik Heber <heber@…>

  • Property mode set to 100644
File size: 4.0 KB
Line 
1/*
2 * RepeatBoxAction.cpp
3 *
4 * Created on: May 12, 2010
5 * Author: heber
6 */
7
8#include "Actions/WorldAction/RepeatBoxAction.hpp"
9#include "CommandLineParser.hpp"
10#include "atom.hpp"
11#include "log.hpp"
12#include "molecule.hpp"
13#include "vector.hpp"
14#include "verbose.hpp"
15#include "World.hpp"
16
17#include <iostream>
18#include <string>
19
20using namespace std;
21
22#include "UIElements/UIFactory.hpp"
23#include "UIElements/Dialog.hpp"
24#include "Actions/MapOfActions.hpp"
25
26const char WorldRepeatBoxAction::NAME[] = "repeat-box";
27
28WorldRepeatBoxAction::WorldRepeatBoxAction() :
29 Action(NAME)
30{}
31
32WorldRepeatBoxAction::~WorldRepeatBoxAction()
33{}
34
35Action::state_ptr WorldRepeatBoxAction::performCall() {
36 Dialog *dialog = UIFactory::getInstance().makeDialog();
37 Vector Repeater;
38 int count;
39 const element ** Elements;
40 molecule *mol = NULL;
41 int j = 0;
42 atom *Walker = NULL;
43
44 dialog->queryVector(NAME, &Repeater, World::getInstance().getDomain(), false, MapOfActions::getInstance().getDescription(NAME));
45 dialog->queryMolecule("molecule-by-id", &mol,MapOfActions::getInstance().getDescription("molecule-by-id"));
46
47 if(dialog->display()) {
48 double * const cell_size = World::getInstance().getDomain();
49 Vector x,y;
50 for (int axis = 1; axis <= NDIM; axis++) {
51 Vector ** vectors;
52 Repeater[axis] = floor(Repeater[axis]);
53 if (Repeater[axis] < 1) {
54 DoeLog(1) && (eLog()<< Verbose(1) << "Repetition factor must be greater than 1!" << endl);
55 Repeater[axis] = 1;
56 }
57 if (mol->getAtomCount() != 0) { // if there is more than none
58 count = mol->getAtomCount(); // is changed becausing of adding, thus has to be stored away beforehand
59 Elements = new const element *[count];
60 vectors = new Vector *[count];
61 j = 0;
62 for(molecule::iterator AtomRunner = mol->begin(); AtomRunner != mol->end(); ++AtomRunner) {
63 Elements[j] = (*AtomRunner)->type;
64 vectors[j] = &(*AtomRunner)->x;
65 j++;
66 }
67 if (count != j)
68 DoeLog(1) && (eLog()<< Verbose(1) << "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!" << endl);
69 x.Zero();
70 y.Zero();
71 y[abs(axis)-1] = cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] * abs(axis)/axis; // last term is for sign, first is for magnitude
72 for (int i=1;i<Repeater[axis];i++) { // then add this list with respective translation factor times
73 x += y; // per factor one cell width further
74 for (int k=count;k--;) { // go through every atom of the original cell
75 Walker = World::getInstance().createAtom(); // create a new body
76 Walker->x = (*vectors[k]) + x;
77 Walker->type = Elements[k]; // insert original element
78 mol->AddAtom(Walker); // and add to the molecule (which increments ElementsInMolecule, AtomCount, ...)
79 }
80 }
81 // free memory
82 delete[](Elements);
83 delete[](vectors);
84 // correct cell size
85 if (axis < 0) { // if sign was negative, we have to translate everything
86 x =(-(Repeater[axis]-1)) * y;
87 mol->Translate(&x);
88 }
89 cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] *= Repeater[axis];
90 }
91 }
92 delete dialog;
93 return Action::success;
94 } else {
95 delete dialog;
96 return Action::failure;
97 }
98}
99
100Action::state_ptr WorldRepeatBoxAction::performUndo(Action::state_ptr _state) {
101// ParserLoadXyzState *state = assert_cast<ParserLoadXyzState*>(_state.get());
102
103 return Action::failure;
104// string newName = state->mol->getName();
105// state->mol->setName(state->lastName);
106//
107// return Action::state_ptr(new ParserLoadXyzState(state->mol,newName));
108}
109
110Action::state_ptr WorldRepeatBoxAction::performRedo(Action::state_ptr _state){
111 return Action::failure;
112}
113
114bool WorldRepeatBoxAction::canUndo() {
115 return false;
116}
117
118bool WorldRepeatBoxAction::shouldUndo() {
119 return false;
120}
121
122const string WorldRepeatBoxAction::getName() {
123 return NAME;
124}
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