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Comparing trunk/src/primitives/DirectionalAtom.cpp (file contents):
Revision 642 by tim, Mon Oct 3 15:54:23 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
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).                        
40   */
41  
42   #include "primitives/DirectionalAtom.hpp"
43   #include "utils/simError.h"
44 < namespace oopse {
45 <
44 > namespace OpenMD {
45 >  
46    DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType)
47      : Atom(dAtomType){
48 <      objType_= otDAtom;
49 <      if (dAtomType->isMultipole()) {
50 <        electroBodyFrame_ = dAtomType->getElectroBodyFrame();
48 >    objType_= otDAtom;
49 >    if (dAtomType->isMultipole()) {
50 >      electroBodyFrame_ = dAtomType->getElectroBodyFrame();
51 >    }
52 >    
53 >    // Check if one of the diagonal inertia tensor of this directional
54 >    // atom is zero:
55 >    int nLinearAxis = 0;
56 >    Mat3x3d inertiaTensor = getI();
57 >    for (int i = 0; i < 3; i++) {    
58 >      if (fabs(inertiaTensor(i, i)) < OpenMD::epsilon) {
59 >        linear_ = true;
60 >        linearAxis_ = i;
61 >        ++ nLinearAxis;
62        }
52 –
53 –      //check if one of the diagonal inertia tensor of this directional atom  is zero
54 –      int nLinearAxis = 0;
55 –      Mat3x3d inertiaTensor = getI();
56 –      for (int i = 0; i < 3; i++) {    
57 –        if (fabs(inertiaTensor(i, i)) < oopse::epsilon) {
58 –          linear_ = true;
59 –          linearAxis_ = i;
60 –          ++ nLinearAxis;
61 –        }
62 –      }
63 –
64 –      if (nLinearAxis > 1) {
65 –        sprintf( painCave.errMsg,
66 –                 "Directional Atom error.\n"
67 –                 "\tOOPSE found more than one axis in this directional atom with a vanishing \n"
68 –                 "\tmoment of inertia.");
69 –        painCave.isFatal = 1;
70 –        simError();
71 –      }
72 –      
63      }
64  
65 +    if (nLinearAxis > 1) {
66 +      sprintf( painCave.errMsg,
67 +               "Directional Atom warning.\n"
68 +               "\tOpenMD found more than one axis in this directional atom with a vanishing \n"
69 +               "\tmoment of inertia.");
70 +      painCave.isFatal = 0;
71 +      simError();
72 +    }    
73 +  }
74 +  
75    Mat3x3d DirectionalAtom::getI() {
76      return static_cast<DirectionalAtomType*>(getAtomType())->getI();
77    }    
78 <
78 >  
79    void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
80      ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
81      if (atomType_->isMultipole()) {
82        ((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
83      }
84    }
85 <
86 <      
85 >  
86 >  
87    void DirectionalAtom::setA(const RotMat3x3d& a) {
88      ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
89 <
89 >    
90      if (atomType_->isMultipole()) {
91        ((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
92      }
93    }    
94 <    
94 >  
95    void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
96      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
97 <
97 >    
98      if (atomType_->isMultipole()) {
99        ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;    
100      }
101    }    
102 <
102 >  
103    void DirectionalAtom::rotateBy(const RotMat3x3d& m) {
104      setA(m *getA());
105    }
106 <
107 <  std::vector<double> DirectionalAtom::getGrad() {
108 <    std::vector<double> grad(6, 0.0);
106 >  
107 >  std::vector<RealType> DirectionalAtom::getGrad() {
108 >    std::vector<RealType> grad(6, 0.0);
109      Vector3d force;
110      Vector3d torque;
111      Vector3d myEuler;
112 <    double phi, theta, psi;
113 <    double cphi, sphi, ctheta, stheta;
112 >    RealType phi, theta, psi;
113 >    RealType cphi, sphi, ctheta, stheta;
114      Vector3d ephi;
115      Vector3d etheta;
116      Vector3d epsi;
117 <
117 >    
118      force = getFrc();
119      torque =getTrq();
120      myEuler = getA().toEulerAngles();
121 <
121 >    
122      phi = myEuler[0];
123      theta = myEuler[1];
124      psi = myEuler[2];
125 <
125 >    
126      cphi = cos(phi);
127      sphi = sin(phi);
128      ctheta = cos(theta);
129      stheta = sin(theta);
130 <
130 >    
131      // get unit vectors along the phi, theta and psi rotation axes
132 <
132 >    
133      ephi[0] = 0.0;
134      ephi[1] = 0.0;
135      ephi[2] = 1.0;
136 <
137 <    etheta[0] = cphi;
138 <    etheta[1] = sphi;
139 <    etheta[2] = 0.0;
140 <
136 >    
137 >    etheta[0] = -sphi;
138 >    etheta[1] =  cphi;
139 >    etheta[2] =  0.0;
140 >    
141      epsi[0] = stheta * cphi;
142      epsi[1] = stheta * sphi;
143      epsi[2] = ctheta;
144 <
144 >    
145      //gradient is equal to -force
146      for (int j = 0 ; j<3; j++)
147        grad[j] = -force[j];
148 <
149 <    for (int j = 0; j < 3; j++ ) {
150 <
148 >    
149 >    for (int j = 0; j < 3; j++ ) {      
150        grad[3] -= torque[j]*ephi[j];
151        grad[4] -= torque[j]*etheta[j];
152 <      grad[5] -= torque[j]*epsi[j];
154 <
152 >      grad[5] -= torque[j]*epsi[j];      
153      }
154      
155      return grad;
156    }    
157 <
157 >  
158    void DirectionalAtom::accept(BaseVisitor* v) {
159      v->visit(this);
160 <  }    
163 <
160 >  }
161   }
162  

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