source: src/Actions/AtomAction/ChangeElementAction.cpp@ d93d2c

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since d93d2c was f01769, checked in by Frederik Heber <heber@…>, 9 years ago

Replaced World::getAtom() wherever possible by const version.

  • some AtomSet member functions now have const atom ptr instead of atom ptr.
  • molecule can return const and non-const AtomSet.
  • added FromIdToConstAtom to allow iterate through atoms in molecule (which are stored by id, not by ptr) in const fashion.
  • in molecule::isInMolecule() is now const, ::CopyMolecule..() is non-const (because copying involves father atom who is stored non-const).
  • Property mode set to 100644
File size: 3.4 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 *
6 *
7 * This file is part of MoleCuilder.
8 *
9 * MoleCuilder is free software: you can redistribute it and/or modify
10 * it under the terms of the GNU General Public License as published by
11 * the Free Software Foundation, either version 2 of the License, or
12 * (at your option) any later version.
13 *
14 * MoleCuilder is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 * GNU General Public License for more details.
18 *
19 * You should have received a copy of the GNU General Public License
20 * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
21 */
22
23/*
24 * ChangeElementAction.cpp
25 *
26 * Created on: May 9, 2010
27 * Author: heber
28 */
29
30// include config.h
31#ifdef HAVE_CONFIG_H
32#include <config.h>
33#endif
34
35#include "CodePatterns/MemDebug.hpp"
36
37#include "Descriptors/AtomIdDescriptor.hpp"
38#include "Atom/atom.hpp"
39#include "Element/element.hpp"
40#include "CodePatterns/Log.hpp"
41#include "LinearAlgebra/Vector.hpp"
42#include "CodePatterns/Verbose.hpp"
43#include "molecule.hpp"
44#include "World.hpp"
45
46#include <iostream>
47#include <map>
48#include <string>
49
50#include "Actions/AtomAction/ChangeElementAction.hpp"
51
52using namespace MoleCuilder;
53
54// and construct the stuff
55#include "ChangeElementAction.def"
56#include "Action_impl_pre.hpp"
57/** =========== define the function ====================== */
58ActionState::ptr AtomChangeElementAction::performCall() {
59 // create undo state
60 ElementMap Elements;
61 for (World::AtomSelectionIterator iter = World::getInstance().beginAtomSelection(); iter != World::getInstance().endAtomSelection(); ++iter) {
62 Elements.insert(std::pair<int, const element *> (iter->second->getId(), iter->second->getType()));
63 }
64 AtomChangeElementState *UndoState = new AtomChangeElementState(Elements, params);
65
66 for (World::AtomSelectionIterator iter = World::getInstance().beginAtomSelection(); iter != World::getInstance().endAtomSelection(); ++iter) {
67 atom *first = iter->second;
68 LOG(1, "Changing atom " << *first << " to element " << *params.elemental.get() << ".");
69 first->setType(params.elemental.get());
70 }
71 return ActionState::ptr(UndoState);
72}
73
74ActionState::ptr AtomChangeElementAction::performUndo(ActionState::ptr _state) {
75 AtomChangeElementState *state = assert_cast<AtomChangeElementState*>(_state.get());
76 for(ElementMap::const_iterator iter = state->Elements.begin(); iter != state->Elements.end(); ++iter) {
77 atom *first = World::getInstance().getAtom(AtomById(iter->first));
78 first->setType(iter->second);
79 }
80
81 return ActionState::ptr(_state);
82}
83
84ActionState::ptr AtomChangeElementAction::performRedo(ActionState::ptr _state){
85 AtomChangeElementState *state = assert_cast<AtomChangeElementState*>(_state.get());
86
87 for(ElementMap::const_iterator iter = state->Elements.begin(); iter != state->Elements.end(); ++iter) {
88 atom *first = World::getInstance().getAtom(AtomById(iter->first));
89 first->setType(state->params.elemental.get());
90 }
91
92 return ActionState::ptr(_state);
93}
94
95bool AtomChangeElementAction::canUndo() {
96 return true;
97}
98
99bool AtomChangeElementAction::shouldUndo() {
100 return true;
101}
102/** =========== end of function ====================== */
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