source: src/Actions/FragmentationAction/StructuralOptimizationAction.cpp@ 94232b

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 94232b was cd5aa0, checked in by Frederik Heber <heber@…>, 10 years ago

Added correct-bonddegree to MolDyn and StructOpt Actions.

  • this is not really necessary as FragmentationAction will correct bond degrees but it is nonetheless cleaner this way.
  • Property mode set to 100644
File size: 4.8 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2014 Frederik Heber. 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 * StructuralOptimizationAction.cpp
25 *
26 * Created on: Aug 02, 2014
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 "CodePatterns/Chronos.hpp"
38
39#include "Actions/FragmentationAction/AnalyseFragmentationResultsAction.hpp"
40#include "Actions/FragmentationAction/FragmentationAutomationAction.hpp"
41#include "Actions/FragmentationAction/StructuralOptimizationAction.hpp"
42#include "Actions/MoleculeAction/ForceAnnealingAction.hpp"
43#include "Actions/ActionQueue.hpp"
44#include "Actions/ActionSequence.hpp"
45
46#include "Descriptors/AtomDescriptor.hpp"
47
48using namespace MoleCuilder;
49
50// and construct the stuff
51#include "StructuralOptimizationAction.def"
52#include "MakroAction_impl_pre.hpp"
53/** =========== define the function ====================== */
54
55// static instances
56ActionSequence FragmentationStructuralOptimizationAction::prototype_actions;
57bool FragmentationStructuralOptimizationAction::isPrepared = false;
58
59void FragmentationStructuralOptimizationAction::prepare(ActionRegistry &AR)
60{
61 // perform a verlet-integration first, if there are already forces or velocities
62 // present. If not, we still copy the position cleanly into a new step where then
63 // forces are set according to summed fragmentary contributions. This is much cleaner.
64 prototype_actions.addAction(AR.getActionByName(std::string("destroy-adjacency")));
65 prototype_actions.addAction(AR.getActionByName(std::string("create-adjacency")));
66 prototype_actions.addAction(AR.getActionByName(std::string("correct-bonddegree")));
67 prototype_actions.addAction(AR.getActionByName(std::string("update-molecules")));
68 prototype_actions.addAction(AR.getActionByName(std::string("fragment-molecule")));
69 prototype_actions.addAction(AR.getActionByName(std::string("fragment-automation")));
70 prototype_actions.addAction(AR.getActionByName(std::string("analyse-fragment-results")));
71 prototype_actions.addAction(AR.getActionByName(std::string("force-annealing")));
72 prototype_actions.addAction(AR.getActionByName(std::string("output")));
73 prototype_actions.addAction(AR.getActionByName(std::string("clear-fragment-results")));
74 isPrepared = true;
75}
76
77void FragmentationStructuralOptimizationAction::unprepare(ActionRegistry &AR)
78{
79 // empty sequence
80 while (prototype_actions.removeLastAction() != NULL);
81 isPrepared = false;
82}
83
84ActionState::ptr FragmentationStructuralOptimizationAction::performCall(){
85
86 // set number of steps
87 setLoop(params.steps.get());
88 // remove output from sequence if not desired.
89 if (!params.DoOutput.get()) {
90#ifndef NDEBUG
91 bool status =
92#endif
93 removeAction(std::string("output"));
94 ASSERT( status,
95 "FragmentationStructuralOptimizationAction::performCall() - output not found in ActionSequence.");
96 }
97 // don't recreate bond graph if not desired
98 if (params.DontCreateGraphEachStep.get()) {
99#ifndef NDEBUG
100 bool status = true;
101 status &=
102#endif
103 removeAction(std::string("destroy-adjacency"));
104
105#ifndef NDEBUG
106 status &=
107#endif
108 removeAction(std::string("create-adjacency"));
109
110#ifndef NDEBUG
111 status &=
112#endif
113 removeAction(std::string("correct-bonddegree"));
114
115#ifndef NDEBUG
116 status &=
117#endif
118 removeAction(std::string("update-molecules"));
119 ASSERT( status,
120 "FragmentationStructuralOptimizationAction::performCall() - at least one graph action not found in ActionSequence.");
121 }
122 // and call
123 ActionState::ptr state(MakroAction::performCall());
124
125 return state;
126}
127
128ActionState::ptr FragmentationStructuralOptimizationAction::performUndo(ActionState::ptr _state) {
129 ActionState::ptr state(MakroAction::performUndo(_state));
130
131 return state;
132}
133
134ActionState::ptr FragmentationStructuralOptimizationAction::performRedo(ActionState::ptr _state){
135 ActionState::ptr state(MakroAction::performRedo(_state));
136
137 return state;
138}
139
140bool FragmentationStructuralOptimizationAction::canUndo(){
141 return true;
142}
143
144bool FragmentationStructuralOptimizationAction::shouldUndo(){
145 return true;
146}
Note: See TracBrowser for help on using the repository browser.