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Comparing trunk/src/primitives/Molecule.hpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1407 by cli2, Wed Jan 20 16:04:40 2010 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;        
83 >    typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;
84      typedef std::vector<ConstraintPair*>::iterator ConstraintPairIterator;
85      typedef std::vector<ConstraintElem*>::iterator ConstraintElemIterator;
86 <        
87 <
86 >    
87 >    
88      Molecule(int stampId, int globalIndex, const std::string& molName);
89      virtual ~Molecule();
90  
# Line 92 | Line 95 | namespace oopse{
95      int getGlobalIndex() {
96        return globalIndex_;
97      }
98 <
98 >    
99      /**
100       * Returns the stamp id of this molecule
101 <     * @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
102 <     * stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
101 >     * @note Ideally, every molecule should keep a pointer of its
102 >     * molecule stamp instead of its stamp id. However, the pointer
103 >     * will become invalid, if the molecule migrate to other
104 >     * processor.
105       */
106      int getStampId() {
107        return stampId_;
108      }
109 <
109 >    
110      /** Returns the name of the molecule */
111      std::string getType() {
112        return moleculeName_;
113      }
114 <        
114 >    
115      /**
116       * Sets the global index of this molecule.
117       * @param new global index to be set
# Line 114 | Line 119 | namespace oopse{
119      void setGlobalIndex(int index) {
120        globalIndex_ = index;
121      }
122 <
123 <        
122 >    
123 >    
124      /** add an atom into this molecule */
125      void addAtom(Atom* atom);
126 <
126 >    
127      /** add a bond into this molecule */
128      void addBond(Bond* bond);
129 <
129 >    
130      /** add a bend into this molecule */
131      void addBend(Bend* bend);
132 <
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);
141 <
141 >    
142      /** add a cutoff group into this molecule */
143      void addCutoffGroup(CutoffGroup* cp);    
144 <
144 >    
145      void addConstraintPair(ConstraintPair* consPair);
146 <        
146 >    
147      void addConstraintElem(ConstraintElem* consElem);
148 <
148 >    
149      /** */
150      void complete();
151 <
151 >    
152      /** Returns the total number of atoms in this molecule */
153      unsigned int getNAtoms() {
154        return atoms_.size();
155      }
156 <
156 >    
157      /** Returns the total number of bonds in this molecule */        
158      unsigned int getNBonds(){
159        return bonds_.size();
160      }
161 <
161 >    
162      /** Returns the total number of bends in this molecule */        
163      unsigned int getNBends() {
164        return bends_.size();
165      }
166 <
166 >    
167      /** Returns the total number of torsions in this molecule */        
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() {
179        return rigidBodies_.size();
180      }
181 <
181 >    
182      /** Returns the total number of integrable objects in this molecule */
183      unsigned int getNIntegrableObjects() {
184        return integrableObjects_.size();
185      }
186 <
186 >    
187      /** Returns the total number of cutoff groups in this molecule */
188      unsigned int getNCutoffGroups() {
189        return cutoffGroups_.size();
190      }
191 <
191 >    
192      /** Returns the total number of constraints in this molecule */
193      unsigned int getNConstraintPairs() {
194        return constraintPairs_.size();
195      }
196 <
196 >    
197      Atom* getAtomAt(unsigned int i) {
198        assert(i < atoms_.size());
199        return atoms_[i];
200      }
201 <
201 >    
202      RigidBody* getRigidBodyAt(unsigned int i) {
203        assert(i < rigidBodies_.size());
204        return rigidBodies_[i];
205      }
206 <        
206 >    
207      Atom* beginAtom(std::vector<Atom*>::iterator& i) {
208        i = atoms_.begin();
209        return (i == atoms_.end()) ? NULL : *i;
210      }
211 <
211 >    
212      Atom* nextAtom(std::vector<Atom*>::iterator& i) {
213        ++i;
214        return (i == atoms_.end()) ? NULL : *i;    
215      }
216 <
216 >    
217      Bond* beginBond(std::vector<Bond*>::iterator& i) {
218        i = bonds_.begin();
219        return (i == bonds_.end()) ? NULL : *i;
220      }
221 <
221 >    
222      Bond* nextBond(std::vector<Bond*>::iterator& i) {
223        ++i;
224        return (i == bonds_.end()) ? NULL : *i;    
225 <
225 >      
226      }
227 <
227 >    
228      Bend* beginBend(std::vector<Bend*>::iterator& i) {
229        i = bends_.begin();
230        return (i == bends_.end()) ? NULL : *i;
231      }
232 <
232 >    
233      Bend* nextBend(std::vector<Bend*>::iterator& i) {
234        ++i;
235        return (i == bends_.end()) ? NULL : *i;    
236      }
237 <
237 >    
238      Torsion* beginTorsion(std::vector<Torsion*>::iterator& i) {
239        i = torsions_.begin();
240        return (i == torsions_.end()) ? NULL : *i;
241      }
242 <
242 >    
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) {
259        i = rigidBodies_.begin();
260        return (i == rigidBodies_.end()) ? NULL : *i;
261      }
262 <
262 >    
263      RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i) {
264        ++i;
265        return (i == rigidBodies_.end()) ? NULL : *i;    
266      }
267 <
267 >    
268      StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
269        i = integrableObjects_.begin();
270        return (i == integrableObjects_.end()) ? NULL : *i;
271      }
272 <
272 >    
273      StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i) {
274        ++i;
275        return (i == integrableObjects_.end()) ? NULL : *i;    
276      }    
277 <
277 >    
278      CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
279        i = cutoffGroups_.begin();
280        return (i == cutoffGroups_.end()) ? NULL : *i;
281      }
282  
283 <    CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {            
283 >    CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i) {
284        ++i;
285        return (i == cutoffGroups_.end()) ? NULL : *i;    
286      }
287 <
287 >    
288      ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i) {
289        i = constraintPairs_.begin();
290        return (i == constraintPairs_.end()) ? NULL : *i;
291      }
292 <
292 >    
293      ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i) {            
294        ++i;
295        return (i == constraintPairs_.end()) ? NULL : *i;    
296      }        
297 <
297 >    
298      ConstraintElem* beginConstraintElem(std::vector<ConstraintElem*>::iterator& i) {
299        i = constraintElems_.begin();
300        return (i == constraintElems_.end()) ? NULL : *i;
301      }
302 <
302 >    
303      ConstraintElem* nextConstraintElem(std::vector<ConstraintElem*>::iterator& i) {            
304        ++i;
305        return (i == constraintElems_.end()) ? NULL : *i;    
306      }
307          
308 <    /** return the total potential energy of short range interaction of this molecule */
308 >    /**
309 >     * Returns the total potential energy of short range interaction
310 >     * of this molecule
311 >     */    
312      RealType getPotential();
313 <
313 >    
314      /** get total mass of this molecule */        
315      RealType getMass();
316 <
316 >    
317      /** return the center of mass of this molecule */
318      Vector3d getCom();
319 <
319 >    
320      /** Moves the center of this molecule */
321      void moveCom(const Vector3d& delta);
322 <
322 >    
323      /** Returns the velocity of center of mass of this molecule */
324      Vector3d getComVel();
325  
# Line 302 | Line 328 | namespace oopse{
328      }
329          
330      friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
331 <        
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 <        
371 >    
372      int globalIndex_;
373 <
373 >    
374      std::vector<Atom*> atoms_;
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 318 | 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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