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Comparing branches/development/src/primitives/DirectionalAtom.cpp (file contents):
Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC vs.
Revision 1850 by gezelter, Wed Feb 20 15:39:39 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).          
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   */
# Line 54 | Line 54 | namespace OpenMD {
54      I_ = da.getI();
55  
56      MultipoleAdapter ma = MultipoleAdapter(dAtomType);
57 <    if (ma.isMultipole()) {
58 <      electroBodyFrame_ = ma.getElectroBodyFrame();
57 >    if (ma.isDipole()) {
58 >      dipole_ = ma.getDipole();
59      }
60 +    if (ma.isQuadrupole()) {
61 +      quadrupole_ = ma.getQuadrupole();
62 +    }
63  
64      // Check if one of the diagonal inertia tensor of this directional
65      // atom is zero:
# Line 86 | Line 89 | namespace OpenMD {
89    
90    void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
91      ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
92 +
93      if (atomType_->isMultipole()) {
94 <      ((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
94 >      RotMat3x3d atrans = a.transpose();
95 >      
96 >      if (atomType_->isDipole()) {
97 >        ((snapshotMan_->getPrevSnapshot())->*storage_).dipole[localIndex_] = atrans * dipole_;
98 >      }
99 >
100 >      if (atomType_->isQuadrupole()) {
101 >        ((snapshotMan_->getPrevSnapshot())->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a;
102 >      }
103      }
104    }
105    
106    
107    void DirectionalAtom::setA(const RotMat3x3d& a) {
108      ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
109 <    
109 >
110      if (atomType_->isMultipole()) {
111 <      ((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
111 >      RotMat3x3d atrans = a.transpose();
112 >
113 >      if (atomType_->isDipole()) {
114 >        ((snapshotMan_->getCurrentSnapshot())->*storage_).dipole[localIndex_] = atrans * dipole_;
115 >      }
116 >
117 >      if (atomType_->isQuadrupole()) {
118 >        ((snapshotMan_->getCurrentSnapshot())->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a;
119 >      }
120      }
121 +  
122    }    
123    
124    void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
125      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
126 <    
126 >
127      if (atomType_->isMultipole()) {
128 <      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;    
128 >      RotMat3x3d atrans = a.transpose();
129 >      
130 >      if (atomType_->isDipole()) {
131 >        ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).dipole[localIndex_] = atrans * dipole_;
132 >      }
133 >
134 >      if (atomType_->isQuadrupole()) {
135 >        ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a;
136 >      }
137      }
138 +
139    }    
140    
141    void DirectionalAtom::rotateBy(const RotMat3x3d& m) {
# Line 117 | Line 147 | namespace OpenMD {
147      Vector3d force;
148      Vector3d torque;
149      Vector3d myEuler;
150 <    RealType phi, theta, psi;
150 >    RealType phi, theta;
151 >    // RealType psi;
152      RealType cphi, sphi, ctheta, stheta;
153      Vector3d ephi;
154      Vector3d etheta;
# Line 129 | Line 160 | namespace OpenMD {
160      
161      phi = myEuler[0];
162      theta = myEuler[1];
163 <    psi = myEuler[2];
163 >    // psi = myEuler[2];
164      
165      cphi = cos(phi);
166      sphi = sin(phi);

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