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 |
|
42 |
namespace oopse{ |
43 |
|
44 |
/** |
45 |
* @class Molecule Molecule.hpp "primitives/Molecule.hpp" |
46 |
* @brief |
47 |
*/ |
48 |
class Molecule { |
49 |
public: |
50 |
|
51 |
Molecule(); |
52 |
virtual ~Molecule(); |
53 |
|
54 |
/** |
55 |
* Returns the global index of this molecule. |
56 |
* @return the global index of this molecule |
57 |
*/ |
58 |
int getGlobalIndex() { |
59 |
return globalIndex_; |
60 |
} |
61 |
|
62 |
/** |
63 |
* Sets the global index of this molecule. |
64 |
* @param new global index to be set |
65 |
*/ |
66 |
void setGlobalIndex(int index) { |
67 |
return globalIndex_; |
68 |
} |
69 |
|
70 |
/** |
71 |
* Returns the local index of this molecule |
72 |
* @return the local index of this molecule |
73 |
*/ |
74 |
int getLocalIndex() { |
75 |
return localIndex_; |
76 |
} |
77 |
|
78 |
/** add an atom into this molecule */ |
79 |
void addAtom(Atom* atom); |
80 |
|
81 |
/** add a bond into this molecule */ |
82 |
void addBond(Bond* bond); |
83 |
|
84 |
/** add a bend into this molecule */ |
85 |
void addBend(Bend* bend); |
86 |
|
87 |
/** add a torsion into this molecule*/ |
88 |
void addTorsion(Torsion* torsion); |
89 |
|
90 |
/** add a rigidbody into this molecule */ |
91 |
void addRigidBody(RigidBody *rb); |
92 |
|
93 |
/** add a cutoff group into this molecule */ |
94 |
void addCutoffGroup(CutoffGroup* cp); |
95 |
|
96 |
/** */ |
97 |
void complete(); |
98 |
|
99 |
/** Returns the total number of atoms in this molecule */ |
100 |
unsigned int getNAtoms() { |
101 |
return atoms_.size(); |
102 |
} |
103 |
|
104 |
/** Returns the total number of bonds in this molecule */ |
105 |
unsigned int getNBonds(){ |
106 |
return bonds_.size(); |
107 |
} |
108 |
|
109 |
/** Returns the total number of bends in this molecule */ |
110 |
unsigned int getNBends() { |
111 |
return bends_.size(); |
112 |
} |
113 |
|
114 |
/** Returns the total number of torsions in this molecule */ |
115 |
unsigned int getNTorsions() { |
116 |
return torsions_.size(); |
117 |
} |
118 |
|
119 |
/** Returns the total number of rigid bodies in this molecule */ |
120 |
unsigned int getNRigidBodies() { |
121 |
return rigidBodies_.size(); |
122 |
} |
123 |
|
124 |
/** Returns the total number of integrable objects in this molecule */ |
125 |
unsigned int getNIntegrableObjects() { |
126 |
return integrableObjects_.size(); |
127 |
} |
128 |
|
129 |
/** Returns the total number of cutoff groups in this molecule */ |
130 |
unsigned int getNCutoffGroups() { |
131 |
return cutoffGroups_.size(); |
132 |
} |
133 |
|
134 |
/** |
135 |
* Returns the first atom in this molecule and initialize the iterator. |
136 |
* @return the first atom, return NULL if there is not cut off group in this molecule |
137 |
* @param i iteraotr |
138 |
*/ |
139 |
Atom* beginAtom(std::vector<Atom*>::iterator& i); |
140 |
|
141 |
Atom* nextAtom(std::vector<Atom*>::iterator& i); |
142 |
|
143 |
/** |
144 |
* Returns the first bond in this molecule and initialize the iterator. |
145 |
* @return the first bond, return NULL if there is not cut off group in this molecule |
146 |
* @param i iteraotr |
147 |
*/ |
148 |
Bond* beginBond(std::vector<Bond*>::iterator& i); |
149 |
|
150 |
Bond* nextBond(std::vector<Bond*>::iterator& i); |
151 |
|
152 |
/** |
153 |
* Returns the first bend in this molecule and initialize the iterator. |
154 |
* @return the first bend, return NULL if there is not cut off group in this molecule |
155 |
* @param i iteraotr |
156 |
*/ |
157 |
Bend* beginBend(std::vector<Bend*>::iterator& i); |
158 |
|
159 |
Bend* nextBend(std::vector<Bend*>::iterator& i); |
160 |
|
161 |
/** |
162 |
* Returns the first torsion in this molecule and initialize the iterator. |
163 |
* @return the first torsion, return NULL if there is not cut off group in this molecule |
164 |
* @param i iteraotr |
165 |
*/ |
166 |
Torsion* beginTorsion(std::vector<Torsion*>::iterator& i); |
167 |
Torsion* nextTorsion(std::vector<Torsion*>::iterator& i); |
168 |
|
169 |
/** |
170 |
* Returns the first rigid body in this molecule and initialize the iterator. |
171 |
* @return the first rigid body, return NULL if there is not cut off group in this molecule |
172 |
* @param i iteraotr |
173 |
*/ |
174 |
RigidBody* beginRigidBody(std::vector<RigidBody*>::iterator& i); |
175 |
|
176 |
RigidBody* nextRigidBody(std::vector<RigidBody*>::iterator& i); |
177 |
|
178 |
/** |
179 |
* Returns the first integrable object in this molecule and initialize the iterator. |
180 |
* @return the first integrable object, return NULL if there is not cut off group in this molecule |
181 |
* @param i iteraotr |
182 |
*/ |
183 |
StuntDouble* beginIntegrableObject(std::vector<StuntDouble*>::iterator& i); |
184 |
|
185 |
StuntDouble* nextIntegrableObject(std::vector<StuntDouble*>::iterator& i); |
186 |
|
187 |
/** |
188 |
* Returns the first cutoff group in this molecule and initialize the iterator. |
189 |
* @return the first cutoff group, return NULL if there is not cut off group in this molecule |
190 |
* @param i iteraotr |
191 |
*/ |
192 |
CutoffGroup* beginCutoffGroup(std::vector<CutoffGroup*>::iterator& i); |
193 |
|
194 |
/** |
195 |
* Returns next cutoff group based on the iterator |
196 |
* @return next cutoff group |
197 |
* @param i |
198 |
*/ |
199 |
CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i); |
200 |
|
201 |
//void setStampID( int info ) {stampID = info;} |
202 |
|
203 |
void calcForces( void ); |
204 |
|
205 |
void atoms2rigidBodies( void ); |
206 |
|
207 |
/** return the total potential energy of short range interaction of this molecule */ |
208 |
double getPotential(); |
209 |
|
210 |
|
211 |
/** return the center of mass of this molecule */ |
212 |
Vector3d getCom(); |
213 |
|
214 |
/** Moves the center of this molecule */ |
215 |
void moveCom(const Vetor3d& delta); |
216 |
|
217 |
/** Returns the velocity of center of mass of this molecule */ |
218 |
Vector3d getComVel(); |
219 |
|
220 |
/** Returns the total mass of this molecule */ |
221 |
double getTotalMass(); |
222 |
|
223 |
friend std::ostream& operator <<(std::ostream& o, const Molecule& mol); |
224 |
|
225 |
private: |
226 |
int localIndex_; |
227 |
int globalIndex_; |
228 |
|
229 |
std::vector<Atom*> atoms_; |
230 |
std::vector<Bond*> bonds_; |
231 |
std::vector<Bend*> bends_; |
232 |
std::vector<Torsion*> torsions_; |
233 |
std::vector<RigidBody*> rigidBodies_; |
234 |
std::vector<StuntDouble*> integrableObjects_; |
235 |
std::vector<CutoffGroup*> cutoffGroups_; |
236 |
}; |
237 |
|
238 |
} //namespace oopse |
239 |
#endif // |