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root/OpenMD/trunk/src/primitives/Molecule.hpp
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Comparing trunk/src/primitives/Molecule.hpp (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 58 | Line 58
58   #include "primitives/Bond.hpp"
59   #include "primitives/Bend.hpp"
60   #include "primitives/Torsion.hpp"
61 + #include "primitives/Inversion.hpp"
62   #include "primitives/CutoffGroup.hpp"
63 + #include "utils/PropertyMap.hpp"
64  
65 < namespace oopse{
65 > namespace OpenMD{
66  
67    class Constraint;
68  
# Line 75 | Line 77 | namespace oopse{
77      typedef std::vector<Bond*>::iterator BondIterator;
78      typedef std::vector<Bend*>::iterator BendIterator;
79      typedef std::vector<Torsion*>::iterator TorsionIterator;
80 +    typedef std::vector<Inversion*>::iterator InversionIterator;
81      typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
82      typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
83      typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
# Line 129 | Line 132 | namespace oopse{
132      
133      /** add a torsion into this molecule*/
134      void addTorsion(Torsion* torsion);
135 +
136 +    /** add an improper torsion into this molecule*/
137 +    void addInversion(Inversion* inversion);
138      
139      /** add a rigidbody into this molecule */
140      void addRigidBody(RigidBody *rb);
# Line 162 | Line 168 | namespace oopse{
168      unsigned int getNTorsions() {
169        return torsions_.size();
170      }
171 +
172 +    /** Returns the total number of improper torsions in this molecule */
173 +    unsigned int getNInversions() {
174 +      return inversions_.size();
175 +    }
176      
177      /** Returns the total number of rigid bodies in this molecule */        
178      unsigned int getNRigidBodies() {
# Line 232 | Line 243 | namespace oopse{
243      Torsion* nextTorsion(std::vector<Torsion*>::iterator& i) {
244        ++i;
245        return (i == torsions_.end()) ? NULL : *i;    
246 +    }    
247 +
248 +    Inversion* beginInversion(std::vector<Inversion*>::iterator& i) {
249 +      i = inversions_.begin();
250 +      return (i == inversions_.end()) ? NULL : *i;
251 +    }
252 +    
253 +    Inversion* nextInversion(std::vector<Inversion*>::iterator& i) {
254 +      ++i;
255 +      return (i == inversions_.end()) ? NULL : *i;    
256      }    
257      
258      RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i) {
# Line 283 | Line 304 | namespace oopse{
304        ++i;
305        return (i == constraintElems_.end()) ? NULL : *i;    
306      }
307 <    
307 >        
308      /**
309       * Returns the total potential energy of short range interaction
310       * of this molecule
# Line 307 | Line 328 | namespace oopse{
328      }
329          
330      friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
331 +
332 +    //below functions are just forward functions
333 +    /**
334 +     * Adds property into property map
335 +     * @param genData GenericData to be added into PropertyMap
336 +     */
337 +    void addProperty(GenericData* genData);
338 +
339 +    /**
340 +     * Removes property from PropertyMap by name
341 +     * @param propName the name of property to be removed
342 +     */
343 +    void removeProperty(const std::string& propName);
344 +
345 +    /**
346 +     * clear all of the properties
347 +     */
348 +    void clearProperties();
349 +
350 +    /**
351 +     * Returns all names of properties
352 +     * @return all names of properties
353 +     */
354 +    std::vector<std::string> getPropertyNames();
355 +
356 +    /**
357 +     * Returns all of the properties in PropertyMap
358 +     * @return all of the properties in PropertyMap
359 +     */      
360 +    std::vector<GenericData*> getProperties();
361 +
362 +    /**
363 +     * Returns property
364 +     * @param propName name of property
365 +     * @return a pointer point to property with propName. If no property named propName
366 +     * exists, return NULL
367 +     */      
368 +    GenericData* getPropertyByName(const std::string& propName);
369      
370    private:
371      
# Line 316 | Line 375 | namespace oopse{
375      std::vector<Bond*> bonds_;
376      std::vector<Bend*> bends_;
377      std::vector<Torsion*> torsions_;
378 +    std::vector<Inversion*> inversions_;
379      std::vector<RigidBody*> rigidBodies_;
380      std::vector<StuntDouble*> integrableObjects_;
381      std::vector<CutoffGroup*> cutoffGroups_;
# Line 323 | Line 383 | namespace oopse{
383      std::vector<ConstraintElem*> constraintElems_;
384      int stampId_;
385      std::string moleculeName_;
386 +    PropertyMap properties_;
387 +
388    };
389  
390 < } //namespace oopse
390 > } //namespace OpenMD
391   #endif //

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