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root/OpenMD/branches/development/src/nonbonded/GB.cpp
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Comparing branches/development/src/nonbonded/GB.cpp (file contents):
Revision 1483 by gezelter, Tue Jul 27 21:17:31 2010 UTC vs.
Revision 1485 by gezelter, Wed Jul 28 19:52:00 2010 UTC

# Line 106 | Line 106 | namespace OpenMD {
106    }
107  
108    void GB::initialize() {    
109 +
110 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
111 +    mu_ = fopts.getGayBerneMu();
112 +    nu_ = fopts.getGayBerneNu();
113      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
114      ForceField::AtomTypeContainer::MapTypeIterator i;
115      AtomType* at;
# Line 282 | Line 286 | namespace OpenMD {
286      RealType xpap2  = mixer.xpap2;
287      RealType xpapi2 = mixer.xpapi2;
288  
289 <    Vector3d ul1 = A1.getColumn(2);
290 <    Vector3d ul2 = A2.getColumn(2);
289 >    Vector3d ul1 = A1.getRow(2);
290 >    Vector3d ul2 = A2.getRow(2);
291  
292      RealType a, b, g;
293  
# Line 391 | Line 395 | namespace OpenMD {
395      // will disappear, as will the transpose below:
396  
397      calcForce(atype1, atype2, disp, *r, *r2, *sw, *vdwMult, *vpair, *pot,
398 <              Ai.transpose(), Aj.transpose(), frc, trq1, trq1);
398 >              Ai, Aj, frc, trq1, trq1);
399        
400      f1[0] = frc.x();
401      f1[1] = frc.y();

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