1 |
/* |
2 |
* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
3 |
* |
4 |
* Contact: oopse@oopse.org |
5 |
* |
6 |
* This program is free software; you can redistribute it and/or |
7 |
* modify it under the terms of the GNU Lesser General Public License |
8 |
* as published by the Free Software Foundation; either version 2.1 |
9 |
* of the License, or (at your option) any later version. |
10 |
* All we ask is that proper credit is given for our work, which includes |
11 |
* - but is not limited to - adding the above copyright notice to the beginning |
12 |
* of your source code files, and to any copyright notice that you may distribute |
13 |
* with programs based on this work. |
14 |
* |
15 |
* This program is distributed in the hope that it will be useful, |
16 |
* but WITHOUT ANY WARRANTY; without even the implied warranty of |
17 |
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
18 |
* GNU Lesser General Public License for more details. |
19 |
* |
20 |
* You should have received a copy of the GNU Lesser General Public License |
21 |
* along with this program; if not, write to the Free Software |
22 |
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
23 |
* |
24 |
*/ |
25 |
|
26 |
/** |
27 |
* @file Molecule.hpp |
28 |
* @author tlin |
29 |
* @date 10/25/2004 |
30 |
* @version 1.0 |
31 |
*/ |
32 |
|
33 |
#ifndef PRIMITIVES_MOLECULE_HPP |
34 |
#define PRIMITIVES_MOLECULE_HPP |
35 |
#include <vector> |
36 |
#include <iostream> |
37 |
|
38 |
#include "math/Vector3.hpp" |
39 |
#include "primitives/Atom.hpp" |
40 |
#include "primitives/RigidBody.hpp" |
41 |
//#include "primitives/Bond.hpp" |
42 |
//#include "primitives/Bend.hpp" |
43 |
//#include "primitives/Torsion.hpp" |
44 |
#include "primitives/SRI.hpp" |
45 |
#include "primitives/CutoffGroup.hpp" |
46 |
|
47 |
namespace oopse{ |
48 |
|
49 |
class Constraint; |
50 |
|
51 |
/** |
52 |
* @class Molecule Molecule.hpp "primitives/Molecule.hpp" |
53 |
* @brief |
54 |
*/ |
55 |
class Molecule { |
56 |
public: |
57 |
|
58 |
typedef std::vector<Atom*>::iterator AtomIterator; |
59 |
typedef std::vector<Bond*>::iterator BondIterator; |
60 |
typedef std::vector<Bend*>::iterator BendIterator; |
61 |
typedef std::vector<Torsion*>::iterator TorsionIterator; |
62 |
typedef std::vector<RigidBody*>::iterator RigidBodyIterator; |
63 |
typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator; |
64 |
typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator; |
65 |
|
66 |
Molecule(int stampId, int globalIndex); |
67 |
virtual ~Molecule(); |
68 |
|
69 |
/** |
70 |
* Returns the global index of this molecule. |
71 |
* @return the global index of this molecule |
72 |
*/ |
73 |
int getGlobalIndex() { |
74 |
return globalIndex_; |
75 |
} |
76 |
|
77 |
/** |
78 |
* Sets the global index of this molecule. |
79 |
* @param new global index to be set |
80 |
*/ |
81 |
int setGlobalIndex(int index) { |
82 |
return globalIndex_; |
83 |
} |
84 |
|
85 |
/** add an atom into this molecule */ |
86 |
void addAtom(Atom* atom); |
87 |
|
88 |
/** add a bond into this molecule */ |
89 |
void addBond(Bond* bond); |
90 |
|
91 |
/** add a bend into this molecule */ |
92 |
void addBend(Bend* bend); |
93 |
|
94 |
/** add a torsion into this molecule*/ |
95 |
void addTorsion(Torsion* torsion); |
96 |
|
97 |
/** add a rigidbody into this molecule */ |
98 |
void addRigidBody(RigidBody *rb); |
99 |
|
100 |
/** add a cutoff group into this molecule */ |
101 |
void addCutoffGroup(CutoffGroup* cp); |
102 |
|
103 |
/** */ |
104 |
void complete(); |
105 |
|
106 |
/** Returns the total number of atoms in this molecule */ |
107 |
unsigned int getNAtoms() { |
108 |
return atoms_.size(); |
109 |
} |
110 |
|
111 |
/** Returns the total number of bonds in this molecule */ |
112 |
unsigned int getNBonds(){ |
113 |
return bonds_.size(); |
114 |
} |
115 |
|
116 |
/** Returns the total number of bends in this molecule */ |
117 |
unsigned int getNBends() { |
118 |
return bends_.size(); |
119 |
} |
120 |
|
121 |
/** Returns the total number of torsions in this molecule */ |
122 |
unsigned int getNTorsions() { |
123 |
return torsions_.size(); |
124 |
} |
125 |
|
126 |
/** Returns the total number of rigid bodies in this molecule */ |
127 |
unsigned int getNRigidBodies() { |
128 |
return rigidBodies_.size(); |
129 |
} |
130 |
|
131 |
/** Returns the total number of integrable objects in this molecule */ |
132 |
unsigned int getNIntegrableObjects() { |
133 |
return integrableObjects_.size(); |
134 |
} |
135 |
|
136 |
/** Returns the total number of cutoff groups in this molecule */ |
137 |
unsigned int getNCutoffGroups() { |
138 |
return cutoffGroups_.size(); |
139 |
} |
140 |
|
141 |
/** Returns the total number of constraints in this molecule */ |
142 |
unsigned int getNConstraints() { |
143 |
return constraints_.size(); |
144 |
} |
145 |
|
146 |
Atom* getAtomAt(unsigned int i) { |
147 |
assert(i < atoms_.size()); |
148 |
return atoms_[i]; |
149 |
} |
150 |
/** |
151 |
* Returns the first atom in this molecule and initialize the iterator. |
152 |
* @return the first atom, return NULL if there is not cut off group in this molecule |
153 |
* @param i iteraotr |
154 |
*/ |
155 |
Atom* beginAtom(std::vector<Atom*>::iterator& i); |
156 |
|
157 |
Atom* nextAtom(std::vector<Atom*>::iterator& i); |
158 |
|
159 |
/** |
160 |
* Returns the first bond in this molecule and initialize the iterator. |
161 |
* @return the first bond, return NULL if there is not cut off group in this molecule |
162 |
* @param i iteraotr |
163 |
*/ |
164 |
Bond* beginBond(std::vector<Bond*>::iterator& i); |
165 |
|
166 |
Bond* nextBond(std::vector<Bond*>::iterator& i); |
167 |
|
168 |
/** |
169 |
* Returns the first bend in this molecule and initialize the iterator. |
170 |
* @return the first bend, return NULL if there is not cut off group in this molecule |
171 |
* @param i iteraotr |
172 |
*/ |
173 |
Bend* beginBend(std::vector<Bend*>::iterator& i); |
174 |
|
175 |
Bend* nextBend(std::vector<Bend*>::iterator& i); |
176 |
|
177 |
/** |
178 |
* Returns the first torsion in this molecule and initialize the iterator. |
179 |
* @return the first torsion, return NULL if there is not cut off group in this molecule |
180 |
* @param i iteraotr |
181 |
*/ |
182 |
Torsion* beginTorsion(std::vector<Torsion*>::iterator& i); |
183 |
Torsion* nextTorsion(std::vector<Torsion*>::iterator& i); |
184 |
|
185 |
/** |
186 |
* Returns the first rigid body in this molecule and initialize the iterator. |
187 |
* @return the first rigid body, return NULL if there is not cut off group in this molecule |
188 |
* @param i iteraotr |
189 |
*/ |
190 |
RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i); |
191 |
|
192 |
RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i); |
193 |
|
194 |
/** |
195 |
* Returns the first integrable object in this molecule and initialize the iterator. |
196 |
* @return the first integrable object, return NULL if there is not cut off group in this molecule |
197 |
* @param i iteraotr |
198 |
*/ |
199 |
StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i); |
200 |
|
201 |
StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i); |
202 |
|
203 |
/** |
204 |
* Returns the first cutoff group in this molecule and initialize the iterator. |
205 |
* @return the first cutoff group, return NULL if there is not cut off group in this molecule |
206 |
* @param i iteraotr |
207 |
*/ |
208 |
CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i); |
209 |
|
210 |
/** |
211 |
* Returns next cutoff group based on the iterator |
212 |
* @return next cutoff group |
213 |
* @param i |
214 |
*/ |
215 |
CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i); |
216 |
|
217 |
Constraint* beginConstraint(std::vector<Constraint*>::iterator& i); |
218 |
|
219 |
Constraint* nextConstraint(std::vector<Constraint*>::iterator& i); |
220 |
|
221 |
//void setStampID( int info ) {stampID = info;} |
222 |
|
223 |
void calcForces( void ); |
224 |
|
225 |
void atoms2rigidBodies( void ); |
226 |
|
227 |
/** return the total potential energy of short range interaction of this molecule */ |
228 |
double getPotential(); |
229 |
|
230 |
|
231 |
/** return the center of mass of this molecule */ |
232 |
Vector3d getCom(); |
233 |
|
234 |
/** Moves the center of this molecule */ |
235 |
void moveCom(const Vector3d& delta); |
236 |
|
237 |
/** Returns the velocity of center of mass of this molecule */ |
238 |
Vector3d getComVel(); |
239 |
|
240 |
/** Returns the total mass of this molecule */ |
241 |
double getTotalMass(); |
242 |
|
243 |
friend std::ostream& operator <<(std::ostream& o, Molecule& mol); |
244 |
|
245 |
private: |
246 |
|
247 |
int globalIndex_; |
248 |
|
249 |
std::vector<Atom*> atoms_; |
250 |
std::vector<Bond*> bonds_; |
251 |
std::vector<Bend*> bends_; |
252 |
std::vector<Torsion*> torsions_; |
253 |
std::vector<RigidBody*> rigidBodies_; |
254 |
std::vector<StuntDouble*> integrableObjects_; |
255 |
std::vector<CutoffGroup*> cutoffGroups_; |
256 |
std::vector<Constraint*> constraints_; |
257 |
|
258 |
int stampID; |
259 |
}; |
260 |
|
261 |
} //namespace oopse |
262 |
#endif // |