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root/OpenMD/branches/development/src/visitors/AtomVisitor.cpp
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Comparing:
trunk/src/visitors/AtomVisitor.cpp (file contents), Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (file contents), Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

# Line 36 | Line 36
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).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include <cstring>
# Line 79 | Line 80 | namespace OpenMD {
80      AtomData *atomData;
81      AtomInfo *atomInfo;
82      Vector3d  pos;
83 <    
83 >    Vector3d  vel;
84 >    Vector3d  frc;
85 >    Vector3d  u;
86 >
87      if (isVisited(atom))
88        return;
89      
# Line 89 | Line 93 | namespace OpenMD {
93      atomData->setID("ATOMDATA");
94      
95      pos = atom->getPos();
96 +    vel = atom->getVel();
97 +    frc = atom->getFrc();
98      atomInfo->atomTypeName = atom->getType();
99      atomInfo->pos[0] = pos[0];
100      atomInfo->pos[1] = pos[1];
101      atomInfo->pos[2] = pos[2];
102 <    atomInfo->dipole[0] = 0.0;
103 <    atomInfo->dipole[1] = 0.0;
104 <    atomInfo->dipole[2] = 0.0;
102 >    atomInfo->vel[0] = vel[0];
103 >    atomInfo->vel[1] = vel[1];
104 >    atomInfo->vel[2] = vel[2];
105 >    atomInfo->hasVelocity = true;
106 >    atomInfo->frc[0] = frc[0];
107 >    atomInfo->frc[1] = frc[1];
108 >    atomInfo->frc[2] = frc[2];
109 >    atomInfo->hasForce = true;
110 >    atomInfo->vec[0] = 0.0;
111 >    atomInfo->vec[1] = 0.0;
112 >    atomInfo->vec[2] = 0.0;
113      
114      atomData->addAtomInfo(atomInfo);
115      
# Line 108 | Line 122 | namespace OpenMD {
122      AtomData *atomData;
123      AtomInfo *atomInfo;
124      Vector3d  pos;
125 +    Vector3d  vel;
126 +    Vector3d  frc;
127      Vector3d  u;
128  
129      if (isVisited(datom))
130        return;
131 <
131 >    
132      pos = datom->getPos();
133 +    vel = datom->getVel();
134 +    frc = datom->getFrc();
135      if (datom->getAtomType()->isGayBerne()) {
136          u = datom->getA().transpose()*V3Z;        
137      } else if (datom->getAtomType()->isMultipole()) {
# Line 127 | Line 145 | namespace OpenMD {
145      atomInfo->pos[0] = pos[0];
146      atomInfo->pos[1] = pos[1];
147      atomInfo->pos[2] = pos[2];
148 <    atomInfo->dipole[0] = u[0];
149 <    atomInfo->dipole[1] = u[1];
150 <    atomInfo->dipole[2] = u[2];
148 >    atomInfo->vel[0] = vel[0];
149 >    atomInfo->vel[1] = vel[1];
150 >    atomInfo->vel[2] = vel[2];
151 >    atomInfo->hasVelocity = true;
152 >    atomInfo->frc[0] = frc[0];
153 >    atomInfo->frc[1] = frc[1];
154 >    atomInfo->frc[2] = frc[2];
155 >    atomInfo->hasForce = true;
156 >    atomInfo->vec[0] = u[0];
157 >    atomInfo->vec[1] = u[1];
158 >    atomInfo->vec[2] = u[2];
159 >    atomInfo->hasVector = true;
160  
161      atomData->addAtomInfo(atomInfo);
162  

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