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root/OpenMD/trunk/src/applications/staticProps/NanoLength.cpp
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Comparing trunk/src/applications/staticProps/NanoLength.cpp (file contents):
Revision 1585 by gezelter, Sun Jun 19 17:51:15 2011 UTC vs.
Revision 1942 by gezelter, Tue Nov 5 18:33:42 2013 UTC

# Line 34 | Line 34
34   *                                                                      
35   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
36   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
37 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 < * [4]  Vardeman & Gezelter, in progress (2009).                        
37 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
38 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
39 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
40   */
41  
42   #include "applications/staticProps/NanoLength.hpp"
# Line 53 | Line 54 | NanoLength::NanoLength(SimInfo* info,
54   NanoLength::NanoLength(SimInfo* info,
55                         const std::string& filename,
56                         const std::string& sele)
57 <  : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info) {
57 >  : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info),
58 >    seleMan_(info) {
59    setOutputName(getPrefix(filename) + ".length");
60    
61    osq.open(getOutputFileName().c_str());
# Line 67 | Line 69 | void NanoLength::process() {
69  
70   void NanoLength::process() {
71    Molecule* mol;
70 –  Atom* atom;
72    RigidBody* rb;
72 –  int myIndex;
73    SimInfo::MoleculeIterator mi;
74    Molecule::RigidBodyIterator rbIter;
75 –  Molecule::AtomIterator ai;
75    StuntDouble* sd;
76    Vector3d vec;
77 <  int i,j;
77 >  int i;
78    
79    DumpReader reader(info_, dumpFilename_);
80    int nFrames = reader.getNFrames();
# Line 120 | Line 119 | void NanoLength::process() {
119        osq << time << "\t" << rodLength << std::endl;      
120      }
121    }
122 +  osq.close();
123   }
124      
125   RealType NanoLength::getLength(std::vector<StuntDouble*> atoms) {

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