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Comparing trunk/src/applications/staticProps/GofAngle2.cpp (file contents):
Revision 1041 by gezelter, Wed Sep 20 20:13:40 2006 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include <algorithm>
# Line 44 | Line 45
45   #include "applications/staticProps/GofAngle2.hpp"
46   #include "utils/simError.h"
47  
48 < namespace oopse {
48 > namespace OpenMD {
49  
50    GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1,
51                         const std::string& sele2, int nangleBins)
# Line 66 | Line 67 | namespace oopse {
67  
68    void GofAngle2::preProcess() {
69  
70 <    for (int i = 0; i < avgGofr_.size(); ++i) {
70 >    for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
71        std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
72      }
73    }
74  
75 <  void GofAngle2::initalizeHistogram() {
75 >  void GofAngle2::initializeHistogram() {
76      npairs_ = 0;
77 <    for (int i = 0; i < histogram_.size(); ++i)
77 >    for (unsigned int i = 0; i < histogram_.size(); ++i)
78        std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
79    }
80  
# Line 93 | Line 94 | namespace oopse {
94      Vector3d pos1 = sd1->getPos();
95      Vector3d pos2 = sd2->getPos();
96      Vector3d r12 = pos1 - pos2;
97 <    currentSnapshot_->wrapVector(r12);
97 >    if (usePeriodicBoundaryConditions_)
98 >      currentSnapshot_->wrapVector(r12);
99      Vector3d dipole1 = sd1->getElectroFrame().getColumn(2);
100      Vector3d dipole2 = sd2->getElectroFrame().getColumn(2);
101      
# Line 120 | Line 122 | namespace oopse {
122        rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
123        rdfStream << "selection2: (" << selectionScript2_ << ")\n";
124        rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
125 <      for (int i = 0; i < avgGofr_.size(); ++i) {
125 >      for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
126          RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
127  
128 <        for(int j = 0; j < avgGofr_[i].size(); ++j) {
128 >        for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
129            RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_;
130            rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t";
131          }

Comparing trunk/src/applications/staticProps/GofAngle2.cpp (property svn:keywords):
Revision 1041 by gezelter, Wed Sep 20 20:13:40 2006 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC

# Line 0 | Line 1
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