source: src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp@ c8f12e

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Last change on this file since c8f12e was 94d5ac6, checked in by Frederik Heber <heber@…>, 12 years ago

FIX: As we use GSL internally, we are as of now required to use GPL v2 license.

  • GNU Scientific Library is used at every place in the code, especially the sub-package LinearAlgebra is based on it which in turn is used really everywhere in the remainder of MoleCuilder. Hence, we have to use the GPL license for the whole of MoleCuilder. In effect, GPL's COPYING was present all along and stated the terms of the GPL v2 license.
  • Hence, I added the default GPL v2 disclaimer to every source file and removed the note about a (actually missing) LICENSE file.
  • also, I added a help-redistribute action which again gives the disclaimer of the GPL v2.
  • also, I changed in the disclaimer that is printed at every program start in builder_init.cpp.
  • TEST: Added check on GPL statement present in every module to test CodeChecks project-disclaimer.
  • Property mode set to 100644
File size: 5.6 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 * DipoleAngularCorrelationAction.cpp
25 *
26 * Created on: Feb 11, 2011
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 "Analysis/analysis_correlation.hpp"
38#include "CodePatterns/Log.hpp"
39#include "Descriptors/AtomOfMoleculeSelectionDescriptor.hpp"
40#include "Descriptors/MoleculeFormulaDescriptor.hpp"
41#include "Element/element.hpp"
42#include "Element/periodentafel.hpp"
43#include "LinearAlgebra/Vector.hpp"
44#include "molecule.hpp"
45#include "World.hpp"
46#include "WorldTime.hpp"
47
48#include <iostream>
49#include <map>
50#include <string>
51
52#include "Actions/AnalysisAction/DipoleAngularCorrelationAction.hpp"
53
54using namespace MoleCuilder;
55
56// and construct the stuff
57#include "DipoleAngularCorrelationAction.def"
58#include "Action_impl_pre.hpp"
59
60/** =========== define the function ====================== */
61Action::state_ptr AnalysisDipoleAngularCorrelationAction::performCall() {
62 //int ranges[3] = {1, 1, 1};
63 string type;
64
65 // get selected atoms
66 std::vector<atom*> old_atom_selection = World::getInstance().getSelectedAtoms();
67 std::vector<molecule*> old_molecule_selection = World::getInstance().getSelectedMolecules();
68
69 // get current time step
70 const unsigned int oldtime = WorldTime::getTime();
71
72 // select atoms and obtain zero dipole orientation
73 Formula DipoleFormula(params.DipoleFormula.get());
74 World::getInstance().setTime(params.timestepzero.get());
75 World::getInstance().clearMoleculeSelection(); // TODO: This should be done in setTime or where molecules are re-done
76 World::getInstance().selectAllMolecules(MoleculeByFormula(DipoleFormula));
77 std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
78 std::map<atomId_t, Vector> ZeroVector = CalculateZeroAngularDipole(molecules);
79
80 // go through each step of common trajectory of all atoms in set
81 World::getInstance().clearAtomSelection();
82 World::getInstance().selectAllAtoms(AtomsByMoleculeSelection());
83 std::vector<atom *> atoms = World::getInstance().getSelectedAtoms();
84 ASSERT(!atoms.empty(),
85 "AnalysisDipoleAngularCorrelationAction::performCall() - "
86 +toString(DipoleFormula)+" selects no atoms.");
87 range<size_t> timesteps = getMaximumTrajectoryBounds(atoms);
88 ASSERT(params.timestepzero.get() < timesteps.first,
89 "AnalysisDipoleAngularCorrelationAction::performCall() - time step zero "
90 +toString(params.timestepzero.get())+" is beyond trajectory range ("
91 +toString(timesteps.first)+") of some atoms.");
92 for (size_t step = params.timestepzero.get(); step < timesteps.first; ++step) {
93 // calculate dipoles relative to zero orientation
94 DipoleAngularCorrelationMap *correlationmap = NULL;
95 correlationmap = DipoleAngularCorrelation(DipoleFormula, step, ZeroVector, DontResetTime);
96
97 // prepare step string in filename
98 std::stringstream stepstream;
99 stepstream << std::setw(4) << std::setfill('0') << step;
100 const std::string stepname(stepstream.str());
101
102 // output correlation map
103 ofstream output;
104 std::string filename = params.outputname.get().string()+"."+stepname+".dat";
105 output.open(filename.c_str());
106 OutputCorrelationMap<DipoleAngularCorrelationMap>(&output, correlationmap, OutputDipoleAngularCorrelation_Header, OutputDipoleAngularCorrelation_Value);
107 output.close();
108
109 // bin map
110 BinPairMap *binmap = BinData( correlationmap, params.BinWidth.get(), params.BinStart.get(), params.BinEnd.get() );
111
112 // free correlation map
113 delete(correlationmap);
114
115 // output binned map
116 ofstream binoutput;
117 std::string binfilename = params.binoutputname.get().string()+"."+stepname+".dat";
118 binoutput.open(binfilename.c_str());
119 OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
120 binoutput.close();
121
122 // free binned map
123 delete(binmap);
124 }
125
126 // reset to old time step
127 World::getInstance().setTime(oldtime);
128
129 // reset to old selections
130 World::getInstance().clearAtomSelection();
131 BOOST_FOREACH(atom *_atom, old_atom_selection) {
132 World::getInstance().selectAtom(_atom);
133 }
134 World::getInstance().clearMoleculeSelection();
135 BOOST_FOREACH(molecule *_mol, old_molecule_selection) {
136 World::getInstance().selectMolecule(_mol);
137 }
138
139 // exit
140 return Action::success;
141}
142
143Action::state_ptr AnalysisDipoleAngularCorrelationAction::performUndo(Action::state_ptr _state) {
144 return Action::success;
145}
146
147Action::state_ptr AnalysisDipoleAngularCorrelationAction::performRedo(Action::state_ptr _state){
148 return Action::success;
149}
150
151bool AnalysisDipoleAngularCorrelationAction::canUndo() {
152 return true;
153}
154
155bool AnalysisDipoleAngularCorrelationAction::shouldUndo() {
156 return true;
157}
158/** =========== end of function ====================== */
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