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Comparing trunk/src/primitives/Molecule.cpp (file contents):
Revision 1211 by gezelter, Wed Jan 23 16:38:22 2008 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   /**
# Line 53 | Line 53
53   #include "utils/MemoryUtils.hpp"
54   #include "utils/simError.h"
55  
56 < namespace oopse {
56 > namespace OpenMD {
57    Molecule::Molecule(int stampId, int globalIndex, const std::string& molName)
58      : stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) {
59    }
# Line 64 | Line 64 | namespace oopse {
64      MemoryUtils::deletePointers(bonds_);
65      MemoryUtils::deletePointers(bends_);
66      MemoryUtils::deletePointers(torsions_);
67 +    MemoryUtils::deletePointers(inversions_);
68      MemoryUtils::deletePointers(rigidBodies_);
69      MemoryUtils::deletePointers(cutoffGroups_);
70      MemoryUtils::deletePointers(constraintPairs_);
# Line 97 | Line 98 | namespace oopse {
98        torsions_.push_back(torsion);
99      }
100    }
101 +
102 +  void Molecule::addInversion(Inversion* inversion) {
103 +    if (std::find(inversions_.begin(), inversions_.end(), inversion) ==
104 +        inversions_.end()) {
105 +      inversions_.push_back(inversion);
106 +    }
107 +  }
108    
109    void Molecule::addRigidBody(RigidBody *rb) {
110      if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) ==
# Line 237 | Line 245 | namespace oopse {
245      Bond* bond;
246      Bend* bend;
247      Torsion* torsion;
248 +    Inversion* inversion;
249      Molecule::BondIterator bondIter;;
250      Molecule::BendIterator  bendIter;
251      Molecule::TorsionIterator  torsionIter;
252 +    Molecule::InversionIterator  inversionIter;
253  
254      RealType potential = 0.0;
255  
# Line 256 | Line 266 | namespace oopse {
266        potential += torsion->getPotential();
267      }
268      
269 +    for (inversion = beginInversion(inversionIter); torsion != NULL;
270 +         inversion =  nextInversion(inversionIter)) {
271 +      potential += inversion->getPotential();
272 +    }
273 +    
274      return potential;
275      
276    }
277    
278 +  void Molecule::addProperty(GenericData* genData) {
279 +    properties_.addProperty(genData);  
280 +  }
281 +
282 +  void Molecule::removeProperty(const std::string& propName) {
283 +    properties_.removeProperty(propName);  
284 +  }
285 +
286 +  void Molecule::clearProperties() {
287 +    properties_.clearProperties();
288 +  }
289 +
290 +  std::vector<std::string> Molecule::getPropertyNames() {
291 +    return properties_.getPropertyNames();  
292 +  }
293 +      
294 +  std::vector<GenericData*> Molecule::getProperties() {
295 +    return properties_.getProperties();
296 +  }
297 +
298 +  GenericData* Molecule::getPropertyByName(const std::string& propName) {
299 +    return properties_.getPropertyByName(propName);
300 +  }
301 +
302 +
303 +
304 +
305    std::ostream& operator <<(std::ostream& o, Molecule& mol) {
306      o << std::endl;
307      o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl;
# Line 267 | Line 309 | namespace oopse {
309      o << mol.getNBonds() << " bonds" << std::endl;
310      o << mol.getNBends() << " bends" << std::endl;
311      o << mol.getNTorsions() << " torsions" << std::endl;
312 +    o << mol.getNInversions() << " inversions" << std::endl;
313      o << mol.getNRigidBodies() << " rigid bodies" << std::endl;
314      o << mol.getNIntegrableObjects() << "integrable objects" << std::endl;
315      o << mol.getNCutoffGroups() << "cutoff groups" << std::endl;
# Line 274 | Line 317 | namespace oopse {
317      return o;
318    }
319    
320 < }//end namespace oopse
320 > }//end namespace OpenMD

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