| 1 |
|
/* |
| 2 |
< |
* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
| 2 |
> |
* Copyright (C) 2000-2009 The Open Molecular Dynamics Engine (OpenMD) project |
| 3 |
|
* |
| 4 |
< |
* Contact: oopse@oopse.org |
| 4 |
> |
* Contact: gezelter@openscience.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 |
| 24 |
|
*/ |
| 25 |
|
|
| 26 |
|
/** |
| 27 |
< |
* @file Molecule.hpp |
| 27 |
> |
* @file Molecule.cpp |
| 28 |
|
* @author tlin |
| 29 |
< |
* @date 10/25/2004 |
| 29 |
> |
* @date 10/28/2004 |
| 30 |
|
* @version 1.0 |
| 31 |
|
*/ |
| 32 |
|
|
| 33 |
|
#include "primitives/Molecule.hpp" |
| 34 |
+ |
#include <algorithm> |
| 35 |
|
|
| 36 |
< |
namespace oopse { |
| 36 |
> |
namespace OpenMD { |
| 37 |
|
|
| 38 |
|
Molecule::~Molecule() { |
| 39 |
|
|
| 48 |
|
|
| 49 |
|
} |
| 50 |
|
|
| 51 |
+ |
void Molecule::addAtom(Atom* atom) { |
| 52 |
+ |
if (atoms_.find(atom) == atoms_.end()) { |
| 53 |
+ |
atoms_.push_back(atom); |
| 54 |
+ |
} |
| 55 |
+ |
} |
| 56 |
|
|
| 57 |
+ |
void Molecule::addBond(Bond* bond) { |
| 58 |
+ |
if (bonds_.find(bond) == bonds_.end()) { |
| 59 |
+ |
bonds_.push_back(bond); |
| 60 |
+ |
} |
| 61 |
+ |
} |
| 62 |
+ |
|
| 63 |
+ |
void Molecule::addBend(Bend* bend) { |
| 64 |
+ |
if (bends_.find(bend) == bends_.end()) { |
| 65 |
+ |
bends_.push_back(bend); |
| 66 |
+ |
} |
| 67 |
+ |
} |
| 68 |
+ |
|
| 69 |
+ |
void Molecule::addTorsion(Torsion* torsion) { |
| 70 |
+ |
if (torsions_.find(torsion) == torsions_.end()) { |
| 71 |
+ |
torsions_.push_back(torsion); |
| 72 |
+ |
} |
| 73 |
+ |
} |
| 74 |
+ |
|
| 75 |
+ |
void Molecule::addRigidBody(RigidBody *rb) { |
| 76 |
+ |
if (rigidBodies_.find(bond) == bonds_.end()) { |
| 77 |
+ |
rigidBodies_.push_back(rb); |
| 78 |
+ |
} |
| 79 |
+ |
} |
| 80 |
+ |
|
| 81 |
+ |
void Molecule::addCutoffGroup(CutoffGroup* cp) { |
| 82 |
+ |
if (cutoffGroups_.find(bond) == bonds_.end()) { |
| 83 |
+ |
cutoffGroups_.push_back(cp); |
| 84 |
+ |
} |
| 85 |
+ |
|
| 86 |
+ |
} |
| 87 |
+ |
|
| 88 |
+ |
void Molecule::complete() { |
| 89 |
+ |
|
| 90 |
+ |
std::set<Atom*> allAtoms; |
| 91 |
+ |
allAtoms.insert(atoms_.begin(), atoms_.end()); |
| 92 |
+ |
|
| 93 |
+ |
std::set<Atom*> rigidAtoms; |
| 94 |
+ |
RigidBody* rb; |
| 95 |
+ |
std::vector<RigidBody*> rbIter; |
| 96 |
+ |
|
| 97 |
+ |
|
| 98 |
+ |
for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
| 99 |
+ |
rigidAtoms.insert(rb->beginAtomIter(), rb->endAtomIter()); |
| 100 |
+ |
} |
| 101 |
+ |
|
| 102 |
+ |
//find all free atoms (which do not belong to rigid bodies) |
| 103 |
+ |
//performs the "difference" operation from set theory, the output range contains a copy of every |
| 104 |
+ |
//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in |
| 105 |
+ |
//[rigidAtoms.begin(), rigidAtoms.end()). |
| 106 |
+ |
std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(), |
| 107 |
+ |
std::back_inserter(integrableObjects_)); |
| 108 |
+ |
|
| 109 |
+ |
if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) { |
| 110 |
+ |
//Some atoms in rigidAtoms are not in allAtoms, something must be wrong |
| 111 |
+ |
} |
| 112 |
+ |
|
| 113 |
+ |
integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end()); |
| 114 |
+ |
} |
| 115 |
+ |
|
| 116 |
|
Atom* Molecule::beginAtom(std::vector<Atom*>::iterator& i) { |
| 117 |
|
i = atoms_.begin(); |
| 118 |
|
return (i == atoms_.end()) ? NULL : *i; |
| 213 |
|
|
| 214 |
|
} |
| 215 |
|
|
| 216 |
< |
}//end namespace oopse |
| 216 |
> |
double Molecule::getPotential() { |
| 217 |
> |
//RigidBody* rb; |
| 218 |
> |
Bond* bond; |
| 219 |
> |
Bend* bend; |
| 220 |
> |
Torsion* torsion; |
| 221 |
> |
//std::vector<RigidBody*> rbIter; |
| 222 |
> |
std::vector<Bond*> bondIter;; |
| 223 |
> |
std::vector<Bend*> bendIter; |
| 224 |
> |
std::vector<Torsion*> torsionIter; |
| 225 |
> |
|
| 226 |
> |
double potential = 0; |
| 227 |
> |
|
| 228 |
> |
//for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
| 229 |
> |
// rb->updateAtoms(); |
| 230 |
> |
//} |
| 231 |
> |
|
| 232 |
> |
for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) { |
| 233 |
> |
potential += bond->getPotential(); |
| 234 |
> |
} |
| 235 |
> |
|
| 236 |
> |
for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) { |
| 237 |
> |
potential += bend->getPotential(); |
| 238 |
> |
} |
| 239 |
> |
|
| 240 |
> |
for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = nextTorsion(torsionIter)) { |
| 241 |
> |
potential += torsion->getPotential(); |
| 242 |
> |
} |
| 243 |
> |
|
| 244 |
> |
return potential; |
| 245 |
> |
} |
| 246 |
> |
|
| 247 |
> |
Vector3d Molecule::getCom() { |
| 248 |
> |
StuntDouble* sd; |
| 249 |
> |
std::vector<StuntDouble*>::iterator i; |
| 250 |
> |
Vector3d com; |
| 251 |
> |
double totalMass = 0; |
| 252 |
> |
double mass; |
| 253 |
> |
|
| 254 |
> |
for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
| 255 |
> |
mass = sd->getMass(); |
| 256 |
> |
totalMass += mass; |
| 257 |
> |
com += sd->getPos() * mass; |
| 258 |
> |
} |
| 259 |
> |
|
| 260 |
> |
com /= totalMass; |
| 261 |
> |
|
| 262 |
> |
return com; |
| 263 |
> |
} |
| 264 |
> |
|
| 265 |
> |
void Molecule::moveCom(const Vetor3d& delta) { |
| 266 |
> |
StuntDouble* sd; |
| 267 |
> |
std::vector<StuntDouble*>::iterator i; |
| 268 |
> |
|
| 269 |
> |
for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
| 270 |
> |
s->setPos(sd->getPos() + delta); |
| 271 |
> |
} |
| 272 |
> |
|
| 273 |
> |
} |
| 274 |
> |
|
| 275 |
> |
Vector3d Molecule::getComVel() { |
| 276 |
> |
StuntDouble* sd; |
| 277 |
> |
std::vector<StuntDouble*>::iterator i; |
| 278 |
> |
Vector3d velCom; |
| 279 |
> |
double totalMass = 0; |
| 280 |
> |
double mass; |
| 281 |
> |
|
| 282 |
> |
for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){ |
| 283 |
> |
mass = sd->getMass(); |
| 284 |
> |
totalMass += mass; |
| 285 |
> |
velCom += sd->getVel() * mass; |
| 286 |
> |
} |
| 287 |
> |
|
| 288 |
> |
velCom /= totalMass; |
| 289 |
> |
|
| 290 |
> |
return velCom; |
| 291 |
> |
} |
| 292 |
> |
|
| 293 |
> |
std::ostream& operator <<(std::ostream& o, const Molecule& mol) { |
| 294 |
> |
o << std::endl; |
| 295 |
> |
o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl; |
| 296 |
> |
o << mol.getNAtoms() << " atoms" << std::endl; |
| 297 |
> |
o << mol.getNBonds() << " bonds" << std::endl; |
| 298 |
> |
o << mol.getNBends() << " bends" << std::endl; |
| 299 |
> |
o << mol.getNTorsions() << " torsions" << std::endl; |
| 300 |
> |
o << mol.getNRigidBodies() << " rigid bodies" << std::endl; |
| 301 |
> |
o << mol.getNIntegrableObjects() << "integrable objects" << std::endl; |
| 302 |
> |
o << mol.getNCutoffGroups() << "cutoff groups" << std::endl; |
| 303 |
> |
|
| 304 |
> |
return o; |
| 305 |
> |
} |
| 306 |
> |
|
| 307 |
> |
}//end namespace OpenMD |
