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root/OpenMD/branches/development/src/visitors/OtherVisitor.cpp
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Comparing branches/development/src/visitors/OtherVisitor.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1871 by gezelter, Fri May 10 14:59:13 2013 UTC

# Line 35 | Line 35
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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   #include "selection/SelectionManager.hpp"
43   #include "visitors/OtherVisitor.hpp"
# Line 44 | Line 45
45   #include "primitives/RigidBody.hpp"
46   #include "primitives/Molecule.hpp"
47   #include "brains/SimInfo.hpp"
48 + #include "brains/Thermo.hpp"
49 +
50   namespace OpenMD {
51  
52    void WrappingVisitor::visit(Atom *atom) {
# Line 76 | Line 79 | namespace OpenMD {
79  
80      Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
81      
82 <    for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
82 >    for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
83 >         atomInfo = atomData->nextAtomInfo(i) ) {
84 >
85        Vector3d newPos = atomInfo->pos - origin_;
86        currSnapshot->wrapVector(newPos);
87        atomInfo->pos = newPos;
88 +
89      }
90    }
91  
92    void WrappingVisitor::update() {
93      if (useCom_){
94 <      origin_ = info->getCom();
94 >      Thermo thermo(info);
95 >      origin_ = thermo.getCom();
96      }
97    }
98    
# Line 326 | Line 333 | namespace OpenMD {
333                  atomInfo->frc[1], atomInfo->frc[2]);
334          line += buffer;
335        }      
336 +      if (doElectricFields_ && atomInfo->hasElectricField) {
337 +        sprintf(buffer, "%15.8f%15.8f%15.8f", atomInfo->eField[0],
338 +                atomInfo->eField[1], atomInfo->eField[2]);
339 +        line += buffer;
340 +      }      
341        frame.push_back(line);
342      }    
343    }

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