source: src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp@ 2aad5a

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Last change on this file since 2aad5a was f10b0c, checked in by Frederik Heber <heber@…>, 13 years ago

disastrously big and ugly commit

  • using new Parameter<T> classes:
    • Actions
    • Queries (all UIs)
  • TODO:
    • actions crash cause Value is unset
    • no query<BoxVector>
  • Property mode set to 100644
File size: 4.9 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 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
8/*
9 * DipoleAngularCorrelationAction.cpp
10 *
11 * Created on: Feb 11, 2011
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 "Analysis/analysis_correlation.hpp"
23#include "CodePatterns/Log.hpp"
24#include "Descriptors/AtomOfMoleculeSelectionDescriptor.hpp"
25#include "Descriptors/MoleculeFormulaDescriptor.hpp"
26#include "Element/element.hpp"
27#include "Element/periodentafel.hpp"
28#include "LinearAlgebra/Vector.hpp"
29#include "molecule.hpp"
30#include "World.hpp"
31#include "WorldTime.hpp"
32
33#include <iostream>
34#include <map>
35#include <string>
36
37#include "Actions/AnalysisAction/DipoleAngularCorrelationAction.hpp"
38
39using namespace MoleCuilder;
40
41// and construct the stuff
42#include "DipoleAngularCorrelationAction.def"
43#include "Action_impl_pre.hpp"
44
45/** =========== define the function ====================== */
46Action::state_ptr AnalysisDipoleAngularCorrelationAction::performCall() {
47 //int ranges[3] = {1, 1, 1};
48 string type;
49
50 // get selected atoms
51 std::vector<atom*> old_atom_selection = World::getInstance().getSelectedAtoms();
52 std::vector<molecule*> old_molecule_selection = World::getInstance().getSelectedMolecules();
53
54 // get current time step
55 const unsigned int oldtime = WorldTime::getTime();
56
57 // select atoms and obtain zero dipole orientation
58 Formula DipoleFormula(params.DipoleFormula.get());
59 World::getInstance().setTime(params.timestepzero.get());
60 World::getInstance().clearMoleculeSelection(); // TODO: This should be done in setTime or where molecules are re-done
61 World::getInstance().selectAllMolecules(MoleculeByFormula(DipoleFormula));
62 std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
63 std::map<atomId_t, Vector> ZeroVector = CalculateZeroAngularDipole(molecules);
64
65 // go through each step of common trajectory of all atoms in set
66 World::getInstance().clearAtomSelection();
67 World::getInstance().selectAllAtoms(AtomsByMoleculeSelection());
68 std::vector<atom *> atoms = World::getInstance().getSelectedAtoms();
69 ASSERT(!atoms.empty(),
70 "AnalysisDipoleAngularCorrelationAction::performCall() - "
71 +toString(DipoleFormula)+" selects no atoms.");
72 range<size_t> timesteps = getMaximumTrajectoryBounds(atoms);
73 ASSERT(params.timestepzero.get() < timesteps.first,
74 "AnalysisDipoleAngularCorrelationAction::performCall() - time step zero "
75 +toString(params.timestepzero.get())+" is beyond trajectory range ("
76 +toString(timesteps.first)+") of some atoms.");
77 for (size_t step = params.timestepzero.get(); step < timesteps.first; ++step) {
78 // calculate dipoles relative to zero orientation
79 DipoleAngularCorrelationMap *correlationmap = NULL;
80 correlationmap = DipoleAngularCorrelation(DipoleFormula, step, ZeroVector, DontResetTime);
81
82 // prepare step string in filename
83 std::stringstream stepstream;
84 stepstream << std::setw(4) << std::setfill('0') << step;
85 const std::string stepname(stepstream.str());
86
87 // output correlation map
88 ofstream output;
89 std::string filename = params.outputname.get().string()+"."+stepname+".dat";
90 output.open(filename.c_str());
91 OutputCorrelationMap<DipoleAngularCorrelationMap>(&output, correlationmap, OutputDipoleAngularCorrelation_Header, OutputDipoleAngularCorrelation_Value);
92 output.close();
93
94 // bin map
95 BinPairMap *binmap = BinData( correlationmap, params.BinWidth.get(), params.BinStart.get(), params.BinEnd.get() );
96
97 // free correlation map
98 delete(correlationmap);
99
100 // output binned map
101 ofstream binoutput;
102 std::string binfilename = params.binoutputname.get().string()+"."+stepname+".dat";
103 binoutput.open(binfilename.c_str());
104 OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
105 binoutput.close();
106
107 // free binned map
108 delete(binmap);
109 }
110
111 // reset to old time step
112 World::getInstance().setTime(oldtime);
113
114 // reset to old selections
115 World::getInstance().clearAtomSelection();
116 BOOST_FOREACH(atom *_atom, old_atom_selection) {
117 World::getInstance().selectAtom(_atom);
118 }
119 World::getInstance().clearMoleculeSelection();
120 BOOST_FOREACH(molecule *_mol, old_molecule_selection) {
121 World::getInstance().selectMolecule(_mol);
122 }
123
124 // exit
125 return Action::success;
126}
127
128Action::state_ptr AnalysisDipoleAngularCorrelationAction::performUndo(Action::state_ptr _state) {
129 return Action::success;
130}
131
132Action::state_ptr AnalysisDipoleAngularCorrelationAction::performRedo(Action::state_ptr _state){
133 return Action::success;
134}
135
136bool AnalysisDipoleAngularCorrelationAction::canUndo() {
137 return true;
138}
139
140bool AnalysisDipoleAngularCorrelationAction::shouldUndo() {
141 return true;
142}
143/** =========== end of function ====================== */
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