| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 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. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 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, 234107 (2008). |
| 39 |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
*/ |
| 42 |
|
| 43 |
/** |
| 44 |
* @file Molecule.cpp |
| 45 |
* @author tlin |
| 46 |
* @date 10/28/2004 |
| 47 |
* @version 1.0 |
| 48 |
*/ |
| 49 |
|
| 50 |
#include <algorithm> |
| 51 |
#include <set> |
| 52 |
|
| 53 |
#include "primitives/Molecule.hpp" |
| 54 |
#include "utils/MemoryUtils.hpp" |
| 55 |
#include "utils/simError.h" |
| 56 |
#include "utils/ElementsTable.hpp" |
| 57 |
|
| 58 |
namespace OpenMD { |
| 59 |
Molecule::Molecule(int stampId, int globalIndex, const std::string& molName, |
| 60 |
int region) : stampId_(stampId), |
| 61 |
globalIndex_(globalIndex), |
| 62 |
moleculeName_(molName), |
| 63 |
region_(region), |
| 64 |
constrainTotalCharge_(false) { |
| 65 |
} |
| 66 |
|
| 67 |
Molecule::~Molecule() { |
| 68 |
|
| 69 |
MemoryUtils::deletePointers(atoms_); |
| 70 |
MemoryUtils::deletePointers(bonds_); |
| 71 |
MemoryUtils::deletePointers(bends_); |
| 72 |
MemoryUtils::deletePointers(torsions_); |
| 73 |
MemoryUtils::deletePointers(inversions_); |
| 74 |
MemoryUtils::deletePointers(rigidBodies_); |
| 75 |
MemoryUtils::deletePointers(cutoffGroups_); |
| 76 |
MemoryUtils::deletePointers(constraintPairs_); |
| 77 |
MemoryUtils::deletePointers(constraintElems_); |
| 78 |
|
| 79 |
// integrableObjects_ don't own the objects |
| 80 |
integrableObjects_.clear(); |
| 81 |
fluctuatingCharges_.clear(); |
| 82 |
|
| 83 |
} |
| 84 |
|
| 85 |
void Molecule::addAtom(Atom* atom) { |
| 86 |
if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) { |
| 87 |
atoms_.push_back(atom); |
| 88 |
} |
| 89 |
} |
| 90 |
|
| 91 |
void Molecule::addBond(Bond* bond) { |
| 92 |
if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) { |
| 93 |
bonds_.push_back(bond); |
| 94 |
} |
| 95 |
} |
| 96 |
|
| 97 |
void Molecule::addBend(Bend* bend) { |
| 98 |
if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) { |
| 99 |
bends_.push_back(bend); |
| 100 |
} |
| 101 |
} |
| 102 |
|
| 103 |
void Molecule::addTorsion(Torsion* torsion) { |
| 104 |
if (std::find(torsions_.begin(), torsions_.end(), torsion) == |
| 105 |
torsions_.end()) { |
| 106 |
torsions_.push_back(torsion); |
| 107 |
} |
| 108 |
} |
| 109 |
|
| 110 |
void Molecule::addInversion(Inversion* inversion) { |
| 111 |
if (std::find(inversions_.begin(), inversions_.end(), inversion) == |
| 112 |
inversions_.end()) { |
| 113 |
inversions_.push_back(inversion); |
| 114 |
} |
| 115 |
} |
| 116 |
|
| 117 |
void Molecule::addRigidBody(RigidBody *rb) { |
| 118 |
if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == |
| 119 |
rigidBodies_.end()) { |
| 120 |
rigidBodies_.push_back(rb); |
| 121 |
} |
| 122 |
} |
| 123 |
|
| 124 |
void Molecule::addCutoffGroup(CutoffGroup* cp) { |
| 125 |
if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) == |
| 126 |
cutoffGroups_.end()) { |
| 127 |
cutoffGroups_.push_back(cp); |
| 128 |
} |
| 129 |
} |
| 130 |
|
| 131 |
void Molecule::addConstraintPair(ConstraintPair* cp) { |
| 132 |
if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) == |
| 133 |
constraintPairs_.end()) { |
| 134 |
constraintPairs_.push_back(cp); |
| 135 |
} |
| 136 |
} |
| 137 |
|
| 138 |
void Molecule::addConstraintElem(ConstraintElem* cp) { |
| 139 |
if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) == |
| 140 |
constraintElems_.end()) { |
| 141 |
constraintElems_.push_back(cp); |
| 142 |
} |
| 143 |
} |
| 144 |
|
| 145 |
void Molecule::complete() { |
| 146 |
|
| 147 |
std::set<Atom*> rigidAtoms; |
| 148 |
Atom* atom; |
| 149 |
Atom* atom1; |
| 150 |
Atom* atom2; |
| 151 |
AtomIterator ai, aj; |
| 152 |
RigidBody* rb; |
| 153 |
RigidBodyIterator rbIter; |
| 154 |
Bond* bond; |
| 155 |
BondIterator bi; |
| 156 |
|
| 157 |
// Get list of all the atoms that are part of rigid bodies |
| 158 |
|
| 159 |
for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
| 160 |
rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter()); |
| 161 |
} |
| 162 |
|
| 163 |
// add any atom that wasn't part of a rigid body to the list of integrableObjects |
| 164 |
|
| 165 |
for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { |
| 166 |
|
| 167 |
if (rigidAtoms.find(atom) == rigidAtoms.end()) { |
| 168 |
|
| 169 |
// If an atom does not belong to a rigid body, it is an |
| 170 |
// integrable object |
| 171 |
|
| 172 |
integrableObjects_.push_back(atom); |
| 173 |
} |
| 174 |
} |
| 175 |
|
| 176 |
// then add the rigid bodies themselves to the integrableObjects |
| 177 |
|
| 178 |
for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
| 179 |
integrableObjects_.push_back(rb); |
| 180 |
} |
| 181 |
|
| 182 |
// find the atoms that are fluctuating charges and add them to the |
| 183 |
// fluctuatingCharges_ vector |
| 184 |
|
| 185 |
for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { |
| 186 |
if ( atom->isFluctuatingCharge() ) |
| 187 |
fluctuatingCharges_.push_back( atom ); |
| 188 |
} |
| 189 |
|
| 190 |
|
| 191 |
// find the electronegative atoms and add them to the |
| 192 |
// hBondAcceptors_ vector: |
| 193 |
|
| 194 |
for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { |
| 195 |
AtomType* at = atom->getAtomType(); |
| 196 |
// get the chain of base types for this atom type: |
| 197 |
std::vector<AtomType*> ayb = at->allYourBase(); |
| 198 |
// use the last type in the chain of base types for the name: |
| 199 |
std::string bn = ayb[ayb.size()-1]->getName(); |
| 200 |
|
| 201 |
int obanum = etab.GetAtomicNum(bn.c_str()); |
| 202 |
if (obanum != 0) { |
| 203 |
RealType eneg = etab.GetElectroNeg(obanum); |
| 204 |
if (eneg > 3.01) { |
| 205 |
hBondAcceptors_.push_back( atom ); |
| 206 |
} |
| 207 |
} |
| 208 |
} |
| 209 |
|
| 210 |
// find electronegative atoms that are either bonded to hydrogens or are |
| 211 |
// present in the same rigid bodies: |
| 212 |
|
| 213 |
for (bond = beginBond(bi); bond != NULL; bond = nextBond(bi)) { |
| 214 |
Atom* atom1 = bond->getAtomA(); |
| 215 |
Atom* atom2 = bond->getAtomB(); |
| 216 |
AtomType* at1 = atom1->getAtomType(); |
| 217 |
AtomType* at2 = atom1->getAtomType(); |
| 218 |
// get the chain of base types for this atom type: |
| 219 |
std::vector<AtomType*> ayb1 = at1->allYourBase(); |
| 220 |
std::vector<AtomType*> ayb2 = at2->allYourBase(); |
| 221 |
// use the last type in the chain of base types for the name: |
| 222 |
std::string bn1 = ayb1[ayb1.size()-1]->getName(); |
| 223 |
std::string bn2 = ayb2[ayb2.size()-1]->getName(); |
| 224 |
int obanum1 = etab.GetAtomicNum(bn1.c_str()); |
| 225 |
int obanum2 = etab.GetAtomicNum(bn2.c_str()); |
| 226 |
|
| 227 |
if (obanum1 == 1) { |
| 228 |
if (obanum2 != 0) { |
| 229 |
RealType eneg = etab.GetElectroNeg(obanum2); |
| 230 |
if (eneg > 3.01) { |
| 231 |
HBondDonor* donor = new HBondDonor(); |
| 232 |
donor->donorAtom = atom2; |
| 233 |
donor->donatedHydrogen = atom1; |
| 234 |
hBondDonors_.push_back( donor ); |
| 235 |
} |
| 236 |
} |
| 237 |
} |
| 238 |
if (obanum2 == 1) { |
| 239 |
if (obanum1 != 0) { |
| 240 |
RealType eneg = etab.GetElectroNeg(obanum1); |
| 241 |
if (eneg > 3.01) { |
| 242 |
HBondDonor* donor = new HBondDonor(); |
| 243 |
donor->donorAtom = atom1; |
| 244 |
donor->donatedHydrogen = atom2; |
| 245 |
hBondDonors_.push_back( donor ); |
| 246 |
} |
| 247 |
} |
| 248 |
} |
| 249 |
} |
| 250 |
|
| 251 |
for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
| 252 |
for(atom1 = rb->beginAtom(ai); atom1 != NULL; atom1 = rb->nextAtom(ai)) { |
| 253 |
AtomType* at1 = atom1->getAtomType(); |
| 254 |
// get the chain of base types for this atom type: |
| 255 |
std::vector<AtomType*> ayb1 = at1->allYourBase(); |
| 256 |
// use the last type in the chain of base types for the name: |
| 257 |
std::string bn1 = ayb1[ayb1.size()-1]->getName(); |
| 258 |
int obanum1 = etab.GetAtomicNum(bn1.c_str()); |
| 259 |
if (obanum1 != 0) { |
| 260 |
RealType eneg = etab.GetElectroNeg(obanum1); |
| 261 |
if (eneg > 3.01) { |
| 262 |
for(atom2 = rb->beginAtom(aj); atom2 != NULL; |
| 263 |
atom2 = rb->nextAtom(aj)) { |
| 264 |
AtomType* at2 = atom2->getAtomType(); |
| 265 |
// get the chain of base types for this atom type: |
| 266 |
std::vector<AtomType*> ayb2 = at2->allYourBase(); |
| 267 |
// use the last type in the chain of base types for the name: |
| 268 |
std::string bn2 = ayb2[ayb2.size()-1]->getName(); |
| 269 |
int obanum2 = etab.GetAtomicNum(bn2.c_str()); |
| 270 |
if (obanum2 == 1) { |
| 271 |
HBondDonor* donor = new HBondDonor(); |
| 272 |
donor->donorAtom = atom1; |
| 273 |
donor->donatedHydrogen = atom2; |
| 274 |
hBondDonors_.push_back( donor ); |
| 275 |
} |
| 276 |
} |
| 277 |
} |
| 278 |
} |
| 279 |
} |
| 280 |
} |
| 281 |
} |
| 282 |
|
| 283 |
RealType Molecule::getMass() { |
| 284 |
StuntDouble* sd; |
| 285 |
std::vector<StuntDouble*>::iterator i; |
| 286 |
RealType mass = 0.0; |
| 287 |
|
| 288 |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 289 |
nextIntegrableObject(i)){ |
| 290 |
mass += sd->getMass(); |
| 291 |
} |
| 292 |
|
| 293 |
return mass; |
| 294 |
} |
| 295 |
|
| 296 |
Vector3d Molecule::getCom() { |
| 297 |
StuntDouble* sd; |
| 298 |
std::vector<StuntDouble*>::iterator i; |
| 299 |
Vector3d com; |
| 300 |
RealType totalMass = 0; |
| 301 |
RealType mass; |
| 302 |
|
| 303 |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 304 |
nextIntegrableObject(i)){ |
| 305 |
mass = sd->getMass(); |
| 306 |
totalMass += mass; |
| 307 |
com += sd->getPos() * mass; |
| 308 |
} |
| 309 |
|
| 310 |
com /= totalMass; |
| 311 |
|
| 312 |
return com; |
| 313 |
} |
| 314 |
|
| 315 |
Vector3d Molecule::getCom(int snapshotNo) { |
| 316 |
StuntDouble* sd; |
| 317 |
std::vector<StuntDouble*>::iterator i; |
| 318 |
Vector3d com; |
| 319 |
RealType totalMass = 0; |
| 320 |
RealType mass; |
| 321 |
|
| 322 |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 323 |
nextIntegrableObject(i)){ |
| 324 |
mass = sd->getMass(); |
| 325 |
totalMass += mass; |
| 326 |
com += sd->getPos(snapshotNo) * mass; |
| 327 |
} |
| 328 |
|
| 329 |
com /= totalMass; |
| 330 |
|
| 331 |
return com; |
| 332 |
} |
| 333 |
|
| 334 |
void Molecule::moveCom(const Vector3d& delta) { |
| 335 |
StuntDouble* sd; |
| 336 |
std::vector<StuntDouble*>::iterator i; |
| 337 |
|
| 338 |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 339 |
nextIntegrableObject(i)){ |
| 340 |
sd->setPos(sd->getPos() + delta); |
| 341 |
} |
| 342 |
} |
| 343 |
|
| 344 |
Vector3d Molecule::getComVel() { |
| 345 |
StuntDouble* sd; |
| 346 |
std::vector<StuntDouble*>::iterator i; |
| 347 |
Vector3d velCom; |
| 348 |
RealType totalMass = 0; |
| 349 |
RealType mass; |
| 350 |
|
| 351 |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 352 |
nextIntegrableObject(i)){ |
| 353 |
mass = sd->getMass(); |
| 354 |
totalMass += mass; |
| 355 |
velCom += sd->getVel() * mass; |
| 356 |
} |
| 357 |
|
| 358 |
velCom /= totalMass; |
| 359 |
|
| 360 |
return velCom; |
| 361 |
} |
| 362 |
|
| 363 |
RealType Molecule::getPotential() { |
| 364 |
|
| 365 |
Bond* bond; |
| 366 |
Bend* bend; |
| 367 |
Torsion* torsion; |
| 368 |
Inversion* inversion; |
| 369 |
Molecule::BondIterator bondIter;; |
| 370 |
Molecule::BendIterator bendIter; |
| 371 |
Molecule::TorsionIterator torsionIter; |
| 372 |
Molecule::InversionIterator inversionIter; |
| 373 |
|
| 374 |
RealType potential = 0.0; |
| 375 |
|
| 376 |
for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) { |
| 377 |
potential += bond->getPotential(); |
| 378 |
} |
| 379 |
|
| 380 |
for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) { |
| 381 |
potential += bend->getPotential(); |
| 382 |
} |
| 383 |
|
| 384 |
for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = |
| 385 |
nextTorsion(torsionIter)) { |
| 386 |
potential += torsion->getPotential(); |
| 387 |
} |
| 388 |
|
| 389 |
for (inversion = beginInversion(inversionIter); torsion != NULL; |
| 390 |
inversion = nextInversion(inversionIter)) { |
| 391 |
potential += inversion->getPotential(); |
| 392 |
} |
| 393 |
|
| 394 |
return potential; |
| 395 |
|
| 396 |
} |
| 397 |
|
| 398 |
void Molecule::addProperty(GenericData* genData) { |
| 399 |
properties_.addProperty(genData); |
| 400 |
} |
| 401 |
|
| 402 |
void Molecule::removeProperty(const std::string& propName) { |
| 403 |
properties_.removeProperty(propName); |
| 404 |
} |
| 405 |
|
| 406 |
void Molecule::clearProperties() { |
| 407 |
properties_.clearProperties(); |
| 408 |
} |
| 409 |
|
| 410 |
std::vector<std::string> Molecule::getPropertyNames() { |
| 411 |
return properties_.getPropertyNames(); |
| 412 |
} |
| 413 |
|
| 414 |
std::vector<GenericData*> Molecule::getProperties() { |
| 415 |
return properties_.getProperties(); |
| 416 |
} |
| 417 |
|
| 418 |
GenericData* Molecule::getPropertyByName(const std::string& propName) { |
| 419 |
return properties_.getPropertyByName(propName); |
| 420 |
} |
| 421 |
|
| 422 |
std::ostream& operator <<(std::ostream& o, Molecule& mol) { |
| 423 |
o << std::endl; |
| 424 |
o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl; |
| 425 |
o << mol.getNAtoms() << " atoms" << std::endl; |
| 426 |
o << mol.getNBonds() << " bonds" << std::endl; |
| 427 |
o << mol.getNBends() << " bends" << std::endl; |
| 428 |
o << mol.getNTorsions() << " torsions" << std::endl; |
| 429 |
o << mol.getNInversions() << " inversions" << std::endl; |
| 430 |
o << mol.getNRigidBodies() << " rigid bodies" << std::endl; |
| 431 |
o << mol.getNIntegrableObjects() << " integrable objects" << std::endl; |
| 432 |
o << mol.getNCutoffGroups() << " cutoff groups" << std::endl; |
| 433 |
o << mol.getNConstraintPairs() << " constraint pairs" << std::endl; |
| 434 |
o << mol.getNFluctuatingCharges() << " fluctuating charges" << std::endl; |
| 435 |
return o; |
| 436 |
} |
| 437 |
|
| 438 |
}//end namespace OpenMD |
