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Comparing trunk/src/applications/staticProps/GofXyz.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #include <algorithm>
# Line 44 | Line 44
44   #include "applications/staticProps/GofXyz.hpp"
45   #include "utils/simError.h"
46   #include "primitives/Molecule.hpp"
47 < namespace oopse {
47 > namespace OpenMD {
48  
49    GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, RealType len, int nrbins)
50      : RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) {
# Line 106 | Line 106 | namespace oopse {
106        Vector3d r3 =sd3->getPos();
107        Vector3d r1 = sd1->getPos();
108        Vector3d v1 =  r3 - r1;
109 <      info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
109 >      if (usePeriodicBoundaryConditions_)
110 >        info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
111        Vector3d zaxis = sd1->getElectroFrame().getColumn(2);
112        Vector3d xaxis = cross(v1, zaxis);
113        Vector3d yaxis = cross(zaxis, xaxis);
# Line 130 | Line 131 | namespace oopse {
131      Vector3d pos1 = sd1->getPos();
132      Vector3d pos2 = sd2->getPos();
133      Vector3d r12 = pos2 - pos1;
134 <    currentSnapshot_->wrapVector(r12);
134 >    if (usePeriodicBoundaryConditions_)
135 >      currentSnapshot_->wrapVector(r12);
136  
137      std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
138      assert(i != rotMats_.end());

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