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root/OpenMD/trunk/src/utils/MoLocator.cpp
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Comparing trunk/src/utils/MoLocator.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 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 <iostream>
# Line 48 | Line 48
48   #include "utils/MoLocator.hpp"
49   #include "types/AtomType.hpp"
50  
51 < namespace oopse {
51 > namespace OpenMD {
52    MoLocator::MoLocator( MoleculeStamp* theStamp, ForceField* theFF){
53      
54      myStamp = theStamp;
# Line 58 | Line 58 | namespace oopse {
58    }
59    
60    void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){
61 +
62      Vector3d newCoor;
63      Vector3d curRefCoor;  
64      RotMat3x3d rotMat = latVec2RotMat(ort);
# Line 78 | Line 79 | namespace oopse {
79        
80        newCoor = rotMat * refCoords[i];
81        newCoor += offset;
82 <      
83 <      integrableObject->setPos( newCoor);
82 >    
83 >      integrableObject->setPos(newCoor);
84        integrableObject->setVel(V3Zero);
85        
86        if(integrableObject->isDirectional()){
# Line 94 | Line 95 | namespace oopse {
95      RigidBodyStamp* rbStamp;
96      int nAtoms;
97      int nRigidBodies;
98 <    std::vector<double> mass;
98 >    std::vector<RealType> mass;
99      Vector3d coor;
100      Vector3d refMolCom;  
101      int nAtomsInRb;
102 <    double totMassInRb;
103 <    double currAtomMass;
104 <    double molMass;
102 >    RealType totMassInRb;
103 >    RealType currAtomMass;
104 >    RealType molMass;
105      
106      nAtoms= myStamp->getNAtoms();
107      nRigidBodies = myStamp->getNRigidBodies();
108      
109      for(size_t i=0; i<nAtoms; i++){
110        
111 <      currAtomStamp = myStamp->getAtom(i);
111 >      currAtomStamp = myStamp->getAtomStamp(i);
112        
113        if( !currAtomStamp->havePosition() ){
114          sprintf( painCave.errMsg,
115                   "MoLocator error.\n"
116                   "  Component %s, atom %s does not have a position specified.\n"
117                   "  This means MoLocator cannot initalize it's position.\n",
118 <                 myStamp->getID(),
119 <                 currAtomStamp->getType() );
118 >                 myStamp->getName().c_str(),
119 >                 currAtomStamp->getType().c_str());
120          
121          painCave.isFatal = 1;
122          simError();
# Line 138 | Line 139 | namespace oopse {
139      
140      for(int i = 0; i < nRigidBodies; i++){
141        
142 <      rbStamp = myStamp->getRigidBody(i);
142 >      rbStamp = myStamp->getRigidBodyStamp(i);
143        nAtomsInRb = rbStamp->getNMembers();
144        
145        coor.x() = 0.0;
# Line 148 | Line 149 | namespace oopse {
149        
150        for(int j = 0; j < nAtomsInRb; j++){
151          
152 <        currAtomStamp = myStamp->getAtom(rbStamp->getMember(j));
152 >        currAtomStamp = myStamp->getAtomStamp(rbStamp->getMemberAt(j));
153          currAtomMass = getAtomMass(currAtomStamp->getType(), myFF);
154          totMassInRb +=  currAtomMass;
155          
# Line 182 | Line 183 | namespace oopse {
183        refCoords[i] -= refMolCom;
184    }
185    
186 <  double getAtomMass(const std::string& at, ForceField* myFF) {
187 <    double mass;
186 >  RealType getAtomMass(const std::string& at, ForceField* myFF) {
187 >    RealType mass;
188      AtomType* atomType= myFF->getAtomType(at);
189      if (atomType != NULL) {
190        mass =     atomType->getMass();
# Line 194 | Line 195 | namespace oopse {
195      return mass;
196    }
197    
198 <  double getMolMass(MoleculeStamp *molStamp, ForceField *myFF) {
198 >  RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF) {
199      int nAtoms;
200 <    double totMass = 0;
200 >    RealType totMass = 0;
201      nAtoms = molStamp->getNAtoms();
202      
203      for(size_t i = 0; i < nAtoms; i++) {
204 <      AtomStamp *currAtomStamp = molStamp->getAtom(i);
204 >      AtomStamp *currAtomStamp = molStamp->getAtomStamp(i);
205        totMass += getAtomMass(currAtomStamp->getType(), myFF);        
206      }
207      return totMass;
208    }
209    RotMat3x3d latVec2RotMat(const Vector3d& lv){
210      
211 <    double theta =acos(lv[2]);
212 <    double phi = atan2(lv[1], lv[0]);
213 <    double psi = 0;
211 >    RealType theta =acos(lv[2]);
212 >    RealType phi = atan2(lv[1], lv[0]);
213 >    RealType psi = 0;
214      
215      return RotMat3x3d(phi, theta, psi);
216      

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