source: src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp@ 41ea3c

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 41ea3c was 35b698, checked in by Frederik Heber <heber@…>, 15 years ago

BIG CHANGE: config::load and config::save in ParseCommandLineOptions() and main() replaced with FormatParser replacements.

Fragmentation:

  • FIX: MoleculeFillWithMoleculeAction: filler atoms have to be removed before the system can be stored to file.
  • FIX: PcpParser::load() - has to put the molecule also into World's MoleculeListClass (otherwise the name cannot be set right after loading)
  • new Libparser.a
  • all sources from PARSER subdir are compiled into libparser such that only ParserUnitTest is recompiled.

Testfixes:

  • testsuite-fragmentation - changes to due to different -f calling syntax.
  • most of the xyz files had to be replaced due to a single whitespace at the end of each entry: Domain/6, Simple_configuration/2, Simple_configuration/3, Simple_configuration/4, Simple_configuration/5, Simple_configuration/8
  • in many cases were the number orbitals (and thus MaxMinStopStep) wrong: Filling/1, Simple_configuration/4, Simple_configuration/5

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

  • Property mode set to 100644
File size: 3.4 KB
Line 
1/*
2 * LinearInterpolationofTrajectoriesAction.cpp
3 *
4 * Created on: May 10, 2010
5 * Author: heber
6 */
7
8#include "Helpers/MemDebug.hpp"
9
10#include "Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp"
11
12#include <iostream>
13#include <fstream>
14#include <string>
15
16using namespace std;
17
18#include "UIElements/UIFactory.hpp"
19#include "UIElements/Dialog.hpp"
20#include "Actions/MapOfActions.hpp"
21
22#include "atom.hpp"
23#include "defs.hpp"
24#include "log.hpp"
25#include "molecule.hpp"
26#include "verbose.hpp"
27#include "World.hpp"
28
29/****** MoleculeLinearInterpolationofTrajectoriesAction *****/
30
31// memento to remember the state when undoing
32
33//class MoleculeLinearInterpolationofTrajectoriesState : public ActionState {
34//public:
35// MoleculeLinearInterpolationofTrajectoriesState(molecule* _mol,std::string _lastName) :
36// mol(_mol),
37// lastName(_lastName)
38// {}
39// molecule* mol;
40// std::string lastName;
41//};
42
43const char MoleculeLinearInterpolationofTrajectoriesAction::NAME[] = "linear-interpolate";
44
45MoleculeLinearInterpolationofTrajectoriesAction::MoleculeLinearInterpolationofTrajectoriesAction() :
46 Action(NAME)
47{}
48
49MoleculeLinearInterpolationofTrajectoriesAction::~MoleculeLinearInterpolationofTrajectoriesAction()
50{}
51
52Action::state_ptr MoleculeLinearInterpolationofTrajectoriesAction::performCall() {
53 string filename;
54 Dialog *dialog = UIFactory::getInstance().makeDialog();
55 molecule *mol = NULL;
56 int start = -1;
57 int end = -1;
58 bool IdMapping = true;
59
60
61 dialog->queryString(NAME, &filename, MapOfActions::getInstance().getDescription(NAME));
62 dialog->queryInt("start-step", &start, MapOfActions::getInstance().getDescription("start-step"));
63 dialog->queryInt("end-step", &end, MapOfActions::getInstance().getDescription("end-step"));
64 dialog->queryMolecule("molecule-by-id", &mol, MapOfActions::getInstance().getDescription("molecule-by-id"));
65 dialog->queryBoolean("id-mapping", &IdMapping, MapOfActions::getInstance().getDescription("id-mapping"));
66
67 if(dialog->display()) {
68 DoLog(1) && (Log() << Verbose(1) << "Linear interpolation between configuration " << start << " and " << end << "." << endl);
69 if (IdMapping)
70 DoLog(1) && (Log() << Verbose(1) << "Using Identity for the permutation map." << endl);
71 if (!mol->LinearInterpolationBetweenConfiguration(start, end, filename, *(World::getInstance().getConfig()), IdMapping))
72 DoLog(2) && (Log() << Verbose(2) << "Could not store " << filename << " files." << endl);
73 else
74 DoLog(2) && (Log() << Verbose(2) << "Steps created and " << filename << " files stored." << endl);
75 delete dialog;
76 return Action::success;
77 }
78 delete dialog;
79 return Action::failure;
80}
81
82Action::state_ptr MoleculeLinearInterpolationofTrajectoriesAction::performUndo(Action::state_ptr _state) {
83// MoleculeLinearInterpolationofTrajectoriesState *state = assert_cast<MoleculeLinearInterpolationofTrajectoriesState*>(_state.get());
84
85// string newName = state->mol->getName();
86// state->mol->setName(state->lastName);
87
88 return Action::failure;
89}
90
91Action::state_ptr MoleculeLinearInterpolationofTrajectoriesAction::performRedo(Action::state_ptr _state){
92 // Undo and redo have to do the same for this action
93 return performUndo(_state);
94}
95
96bool MoleculeLinearInterpolationofTrajectoriesAction::canUndo() {
97 return false;
98}
99
100bool MoleculeLinearInterpolationofTrajectoriesAction::shouldUndo() {
101 return false;
102}
103
104const string MoleculeLinearInterpolationofTrajectoriesAction::getName() {
105 return NAME;
106}
Note: See TracBrowser for help on using the repository browser.