1 |
< |
/* |
1 |
> |
/* |
2 |
|
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
3 |
|
* |
4 |
|
* The University of Notre Dame grants you ("Licensee") a |
54 |
|
#include "utils/simError.h" |
55 |
|
|
56 |
|
namespace oopse { |
57 |
< |
Molecule::Molecule(int stampId, int globalIndex, const std::string& molName) |
57 |
> |
Molecule::Molecule(int stampId, int globalIndex, const std::string& molName) |
58 |
|
: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) { |
59 |
|
|
60 |
< |
} |
60 |
> |
} |
61 |
|
|
62 |
< |
Molecule::~Molecule() { |
62 |
> |
Molecule::~Molecule() { |
63 |
|
|
64 |
< |
MemoryUtils::deleteVectorOfPointer(atoms_); |
65 |
< |
MemoryUtils::deleteVectorOfPointer(bonds_); |
66 |
< |
MemoryUtils::deleteVectorOfPointer(bends_); |
67 |
< |
MemoryUtils::deleteVectorOfPointer(torsions_); |
68 |
< |
MemoryUtils::deleteVectorOfPointer(rigidBodies_); |
69 |
< |
MemoryUtils::deleteVectorOfPointer(cutoffGroups_); |
70 |
< |
MemoryUtils::deleteVectorOfPointer(constraintPairs_); |
71 |
< |
MemoryUtils::deleteVectorOfPointer(constraintElems_); |
64 |
> |
MemoryUtils::deletePointers(atoms_); |
65 |
> |
MemoryUtils::deletePointers(bonds_); |
66 |
> |
MemoryUtils::deletePointers(bends_); |
67 |
> |
MemoryUtils::deletePointers(torsions_); |
68 |
> |
MemoryUtils::deletePointers(rigidBodies_); |
69 |
> |
MemoryUtils::deletePointers(cutoffGroups_); |
70 |
> |
MemoryUtils::deletePointers(constraintPairs_); |
71 |
> |
MemoryUtils::deletePointers(constraintElems_); |
72 |
|
//integrableObjects_ don't own the objects |
73 |
|
integrableObjects_.clear(); |
74 |
|
|
75 |
< |
} |
75 |
> |
} |
76 |
|
|
77 |
< |
void Molecule::addAtom(Atom* atom) { |
77 |
> |
void Molecule::addAtom(Atom* atom) { |
78 |
|
if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) { |
79 |
< |
atoms_.push_back(atom); |
79 |
> |
atoms_.push_back(atom); |
80 |
|
} |
81 |
< |
} |
81 |
> |
} |
82 |
|
|
83 |
< |
void Molecule::addBond(Bond* bond) { |
83 |
> |
void Molecule::addBond(Bond* bond) { |
84 |
|
if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) { |
85 |
< |
bonds_.push_back(bond); |
85 |
> |
bonds_.push_back(bond); |
86 |
|
} |
87 |
< |
} |
87 |
> |
} |
88 |
|
|
89 |
< |
void Molecule::addBend(Bend* bend) { |
89 |
> |
void Molecule::addBend(Bend* bend) { |
90 |
|
if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) { |
91 |
< |
bends_.push_back(bend); |
91 |
> |
bends_.push_back(bend); |
92 |
|
} |
93 |
< |
} |
93 |
> |
} |
94 |
|
|
95 |
< |
void Molecule::addTorsion(Torsion* torsion) { |
95 |
> |
void Molecule::addTorsion(Torsion* torsion) { |
96 |
|
if (std::find(torsions_.begin(), torsions_.end(), torsion) == torsions_.end()) { |
97 |
< |
torsions_.push_back(torsion); |
97 |
> |
torsions_.push_back(torsion); |
98 |
|
} |
99 |
< |
} |
99 |
> |
} |
100 |
|
|
101 |
< |
void Molecule::addRigidBody(RigidBody *rb) { |
101 |
> |
void Molecule::addRigidBody(RigidBody *rb) { |
102 |
|
if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == rigidBodies_.end()) { |
103 |
< |
rigidBodies_.push_back(rb); |
103 |
> |
rigidBodies_.push_back(rb); |
104 |
|
} |
105 |
< |
} |
105 |
> |
} |
106 |
|
|
107 |
< |
void Molecule::addCutoffGroup(CutoffGroup* cp) { |
107 |
> |
void Molecule::addCutoffGroup(CutoffGroup* cp) { |
108 |
|
if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) == cutoffGroups_.end()) { |
109 |
< |
cutoffGroups_.push_back(cp); |
109 |
> |
cutoffGroups_.push_back(cp); |
110 |
|
} |
111 |
|
|
112 |
< |
} |
112 |
> |
} |
113 |
|
|
114 |
< |
void Molecule::addConstraintPair(ConstraintPair* cp) { |
114 |
> |
void Molecule::addConstraintPair(ConstraintPair* cp) { |
115 |
|
if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) == constraintPairs_.end()) { |
116 |
< |
constraintPairs_.push_back(cp); |
116 |
> |
constraintPairs_.push_back(cp); |
117 |
|
} |
118 |
|
|
119 |
< |
} |
119 |
> |
} |
120 |
|
|
121 |
< |
void Molecule::addConstraintElem(ConstraintElem* cp) { |
121 |
> |
void Molecule::addConstraintElem(ConstraintElem* cp) { |
122 |
|
if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) == constraintElems_.end()) { |
123 |
< |
constraintElems_.push_back(cp); |
123 |
> |
constraintElems_.push_back(cp); |
124 |
|
} |
125 |
|
|
126 |
< |
} |
126 |
> |
} |
127 |
|
|
128 |
< |
void Molecule::complete() { |
128 |
> |
void Molecule::complete() { |
129 |
|
|
130 |
|
std::set<Atom*> rigidAtoms; |
131 |
|
RigidBody* rb; |
133 |
|
|
134 |
|
|
135 |
|
for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
136 |
< |
rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter()); |
136 |
> |
rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter()); |
137 |
|
} |
138 |
|
|
139 |
|
Atom* atom; |
140 |
|
AtomIterator ai; |
141 |
|
for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { |
142 |
|
|
143 |
< |
if (rigidAtoms.find(*ai) == rigidAtoms.end()) { |
144 |
< |
//if an atom does not belong to a rigid body, it is an integrable object |
145 |
< |
integrableObjects_.push_back(*ai); |
146 |
< |
} |
143 |
> |
if (rigidAtoms.find(*ai) == rigidAtoms.end()) { |
144 |
> |
//if an atom does not belong to a rigid body, it is an integrable object |
145 |
> |
integrableObjects_.push_back(*ai); |
146 |
> |
} |
147 |
|
} |
148 |
|
|
149 |
|
//find all free atoms (which do not belong to rigid bodies) |
164 |
|
integrableObjects_.push_back(rb); |
165 |
|
} |
166 |
|
//integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end()); |
167 |
< |
} |
167 |
> |
} |
168 |
|
|
169 |
< |
double Molecule::getMass() { |
169 |
> |
RealType Molecule::getMass() { |
170 |
|
StuntDouble* sd; |
171 |
|
std::vector<StuntDouble*>::iterator i; |
172 |
< |
double mass = 0.0; |
172 |
> |
RealType mass = 0.0; |
173 |
|
|
174 |
|
for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
175 |
< |
mass += sd->getMass(); |
175 |
> |
mass += sd->getMass(); |
176 |
|
} |
177 |
|
|
178 |
|
return mass; |
179 |
|
|
180 |
< |
} |
180 |
> |
} |
181 |
|
|
182 |
< |
Vector3d Molecule::getCom() { |
182 |
> |
Vector3d Molecule::getCom() { |
183 |
|
StuntDouble* sd; |
184 |
|
std::vector<StuntDouble*>::iterator i; |
185 |
|
Vector3d com; |
186 |
< |
double totalMass = 0; |
187 |
< |
double mass; |
186 |
> |
RealType totalMass = 0; |
187 |
> |
RealType mass; |
188 |
|
|
189 |
|
for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
190 |
< |
mass = sd->getMass(); |
191 |
< |
totalMass += mass; |
192 |
< |
com += sd->getPos() * mass; |
190 |
> |
mass = sd->getMass(); |
191 |
> |
totalMass += mass; |
192 |
> |
com += sd->getPos() * mass; |
193 |
|
} |
194 |
|
|
195 |
|
com /= totalMass; |
196 |
|
|
197 |
|
return com; |
198 |
< |
} |
198 |
> |
} |
199 |
|
|
200 |
< |
void Molecule::moveCom(const Vector3d& delta) { |
200 |
> |
void Molecule::moveCom(const Vector3d& delta) { |
201 |
|
StuntDouble* sd; |
202 |
|
std::vector<StuntDouble*>::iterator i; |
203 |
|
|
204 |
|
for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
205 |
< |
sd->setPos(sd->getPos() + delta); |
205 |
> |
sd->setPos(sd->getPos() + delta); |
206 |
|
} |
207 |
|
|
208 |
< |
} |
208 |
> |
} |
209 |
|
|
210 |
< |
Vector3d Molecule::getComVel() { |
210 |
> |
Vector3d Molecule::getComVel() { |
211 |
|
StuntDouble* sd; |
212 |
|
std::vector<StuntDouble*>::iterator i; |
213 |
|
Vector3d velCom; |
214 |
< |
double totalMass = 0; |
215 |
< |
double mass; |
214 |
> |
RealType totalMass = 0; |
215 |
> |
RealType mass; |
216 |
|
|
217 |
|
for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
218 |
< |
mass = sd->getMass(); |
219 |
< |
totalMass += mass; |
220 |
< |
velCom += sd->getVel() * mass; |
218 |
> |
mass = sd->getMass(); |
219 |
> |
totalMass += mass; |
220 |
> |
velCom += sd->getVel() * mass; |
221 |
|
} |
222 |
|
|
223 |
|
velCom /= totalMass; |
224 |
|
|
225 |
|
return velCom; |
226 |
< |
} |
226 |
> |
} |
227 |
|
|
228 |
< |
double Molecule::getPotential() { |
228 |
> |
RealType Molecule::getPotential() { |
229 |
|
|
230 |
|
Bond* bond; |
231 |
|
Bend* bend; |
234 |
|
Molecule::BendIterator bendIter; |
235 |
|
Molecule::TorsionIterator torsionIter; |
236 |
|
|
237 |
< |
double potential = 0.0; |
237 |
> |
RealType potential = 0.0; |
238 |
|
|
239 |
|
for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) { |
240 |
< |
potential += bond->getPotential(); |
240 |
> |
potential += bond->getPotential(); |
241 |
|
} |
242 |
|
|
243 |
|
for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) { |
244 |
< |
potential += bend->getPotential(); |
244 |
> |
potential += bend->getPotential(); |
245 |
|
} |
246 |
|
|
247 |
|
for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) { |
248 |
< |
potential += torsion->getPotential(); |
248 |
> |
potential += torsion->getPotential(); |
249 |
|
} |
250 |
|
|
251 |
|
return potential; |
252 |
|
|
253 |
< |
} |
253 |
> |
} |
254 |
|
|
255 |
< |
std::ostream& operator <<(std::ostream& o, Molecule& mol) { |
255 |
> |
std::ostream& operator <<(std::ostream& o, Molecule& mol) { |
256 |
|
o << std::endl; |
257 |
|
o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl; |
258 |
|
o << mol.getNAtoms() << " atoms" << std::endl; |
264 |
|
o << mol.getNCutoffGroups() << "cutoff groups" << std::endl; |
265 |
|
o << mol.getNConstraintPairs() << "constraint pairs" << std::endl; |
266 |
|
return o; |
267 |
< |
} |
267 |
> |
} |
268 |
|
|
269 |
|
}//end namespace oopse |