| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 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. |
| 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 |
|
/** |
| 53 |
|
#include "primitives/Molecule.hpp" |
| 54 |
|
#include "utils/MemoryUtils.hpp" |
| 55 |
|
#include "utils/simError.h" |
| 56 |
+ |
#include "utils/ElementsTable.hpp" |
| 57 |
|
|
| 58 |
< |
namespace oopse { |
| 59 |
< |
Molecule::Molecule(int stampId, int globalIndex, const std::string& molName) |
| 60 |
< |
: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) { |
| 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() { |
| 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 |
|
|
| 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) == |
| 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 |
< |
std::vector<RigidBody*>::iterator rbIter; |
| 153 |
> |
RigidBodyIterator rbIter; |
| 154 |
> |
Bond* bond; |
| 155 |
> |
BondIterator bi; |
| 156 |
|
|
| 157 |
< |
|
| 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 |
< |
Atom* atom; |
| 164 |
< |
AtomIterator ai; |
| 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(*ai) == rigidAtoms.end()) { |
| 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(*ai); |
| 172 |
> |
integrableObjects_.push_back(atom); |
| 173 |
|
} |
| 174 |
|
} |
| 175 |
|
|
| 176 |
< |
//find all free atoms (which do not belong to rigid bodies) |
| 154 |
< |
// performs the "difference" operation from set theory, the output |
| 155 |
< |
// range contains a copy of every element that is contained in |
| 156 |
< |
// [allAtoms.begin(), allAtoms.end()) and not contained in |
| 157 |
< |
// [rigidAtoms.begin(), rigidAtoms.end()). |
| 158 |
< |
//std::set_difference(allAtoms.begin(), allAtoms.end(), rigidAtoms.begin(), rigidAtoms.end(), |
| 159 |
< |
// std::back_inserter(integrableObjects_)); |
| 176 |
> |
// then add the rigid bodies themselves to the integrableObjects |
| 177 |
|
|
| 161 |
– |
//if (integrableObjects_.size() != allAtoms.size() - rigidAtoms.size()) { |
| 162 |
– |
// //Some atoms in rigidAtoms are not in allAtoms, something must be wrong |
| 163 |
– |
// sprintf(painCave.errMsg, "Atoms in rigidbody are not in the atom list of the same molecule"); |
| 164 |
– |
// |
| 165 |
– |
// painCave.isFatal = 1; |
| 166 |
– |
// simError(); |
| 167 |
– |
//} |
| 178 |
|
for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
| 179 |
|
integrableObjects_.push_back(rb); |
| 180 |
|
} |
| 171 |
– |
//integrableObjects_.insert(integrableObjects_.end(), rigidBodies_.begin(), rigidBodies_.end()); |
| 172 |
– |
} |
| 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 |
+ |
if (bn.compare("O")==0 || bn.compare("N")==0 || bn.compare("F")==0) |
| 202 |
+ |
hBondAcceptors_.push_back( atom ); |
| 203 |
+ |
|
| 204 |
+ |
} |
| 205 |
+ |
|
| 206 |
+ |
// find electronegative atoms that are either bonded to |
| 207 |
+ |
// hydrogens or are present in the same rigid bodies: |
| 208 |
+ |
|
| 209 |
+ |
for (bond = beginBond(bi); bond != NULL; bond = nextBond(bi)) { |
| 210 |
+ |
Atom* atom1 = bond->getAtomA(); |
| 211 |
+ |
Atom* atom2 = bond->getAtomB(); |
| 212 |
+ |
AtomType* at1 = atom1->getAtomType(); |
| 213 |
+ |
AtomType* at2 = atom1->getAtomType(); |
| 214 |
+ |
// get the chain of base types for this atom type: |
| 215 |
+ |
std::vector<AtomType*> ayb1 = at1->allYourBase(); |
| 216 |
+ |
std::vector<AtomType*> ayb2 = at2->allYourBase(); |
| 217 |
+ |
// use the last type in the chain of base types for the name: |
| 218 |
+ |
std::string bn1 = ayb1[ayb1.size()-1]->getName(); |
| 219 |
+ |
std::string bn2 = ayb2[ayb2.size()-1]->getName(); |
| 220 |
+ |
|
| 221 |
+ |
if (bn1.compare("H")==0) { |
| 222 |
+ |
if (bn2.compare("O")==0 || bn2.compare("N")==0 |
| 223 |
+ |
|| bn2.compare("F")==0) { |
| 224 |
+ |
HBondDonor* donor = new HBondDonor(); |
| 225 |
+ |
donor->donorAtom = atom2; |
| 226 |
+ |
donor->donatedHydrogen = atom1; |
| 227 |
+ |
hBondDonors_.push_back( donor ); |
| 228 |
+ |
} |
| 229 |
+ |
} |
| 230 |
+ |
if (bn2.compare("H")==0) { |
| 231 |
+ |
if (bn1.compare("O")==0 || bn1.compare("N")==0 |
| 232 |
+ |
|| bn1.compare("F")==0) { |
| 233 |
+ |
HBondDonor* donor = new HBondDonor(); |
| 234 |
+ |
donor->donorAtom = atom1; |
| 235 |
+ |
donor->donatedHydrogen = atom2; |
| 236 |
+ |
hBondDonors_.push_back( donor ); |
| 237 |
+ |
} |
| 238 |
+ |
} |
| 239 |
+ |
} |
| 240 |
+ |
|
| 241 |
+ |
for (rb = beginRigidBody(rbIter); rb != NULL; |
| 242 |
+ |
rb = nextRigidBody(rbIter)) { |
| 243 |
+ |
for(atom1 = rb->beginAtom(ai); atom1 != NULL; |
| 244 |
+ |
atom1 = rb->nextAtom(ai)) { |
| 245 |
+ |
AtomType* at1 = atom1->getAtomType(); |
| 246 |
+ |
// get the chain of base types for this atom type: |
| 247 |
+ |
std::vector<AtomType*> ayb1 = at1->allYourBase(); |
| 248 |
+ |
// use the last type in the chain of base types for the name: |
| 249 |
+ |
std::string bn1 = ayb1[ayb1.size()-1]->getName(); |
| 250 |
+ |
|
| 251 |
+ |
if (bn1.compare("O")==0 || bn1.compare("N")==0 |
| 252 |
+ |
|| bn1.compare("F")==0) { |
| 253 |
+ |
for(atom2 = rb->beginAtom(aj); atom2 != NULL; |
| 254 |
+ |
atom2 = rb->nextAtom(aj)) { |
| 255 |
+ |
AtomType* at2 = atom2->getAtomType(); |
| 256 |
+ |
// get the chain of base types for this atom type: |
| 257 |
+ |
std::vector<AtomType*> ayb2 = at2->allYourBase(); |
| 258 |
+ |
// use the last type in the chain of base types for the name: |
| 259 |
+ |
std::string bn2 = ayb2[ayb2.size()-1]->getName(); |
| 260 |
+ |
if (bn2.compare("H")==0) { |
| 261 |
+ |
HBondDonor* donor = new HBondDonor(); |
| 262 |
+ |
donor->donorAtom = atom1; |
| 263 |
+ |
donor->donatedHydrogen = atom2; |
| 264 |
+ |
hBondDonors_.push_back( donor ); |
| 265 |
+ |
} |
| 266 |
+ |
} |
| 267 |
+ |
} |
| 268 |
+ |
} |
| 269 |
+ |
} |
| 270 |
+ |
} |
| 271 |
+ |
|
| 272 |
|
RealType Molecule::getMass() { |
| 273 |
|
StuntDouble* sd; |
| 274 |
|
std::vector<StuntDouble*>::iterator i; |
| 300 |
|
|
| 301 |
|
return com; |
| 302 |
|
} |
| 303 |
+ |
|
| 304 |
+ |
Vector3d Molecule::getCom(int snapshotNo) { |
| 305 |
+ |
StuntDouble* sd; |
| 306 |
+ |
std::vector<StuntDouble*>::iterator i; |
| 307 |
+ |
Vector3d com; |
| 308 |
+ |
RealType totalMass = 0; |
| 309 |
+ |
RealType mass; |
| 310 |
+ |
|
| 311 |
+ |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 312 |
+ |
nextIntegrableObject(i)){ |
| 313 |
+ |
mass = sd->getMass(); |
| 314 |
+ |
totalMass += mass; |
| 315 |
+ |
com += sd->getPos(snapshotNo) * mass; |
| 316 |
+ |
} |
| 317 |
+ |
|
| 318 |
+ |
com /= totalMass; |
| 319 |
|
|
| 320 |
+ |
return com; |
| 321 |
+ |
} |
| 322 |
+ |
|
| 323 |
|
void Molecule::moveCom(const Vector3d& delta) { |
| 324 |
|
StuntDouble* sd; |
| 325 |
|
std::vector<StuntDouble*>::iterator i; |
| 354 |
|
Bond* bond; |
| 355 |
|
Bend* bend; |
| 356 |
|
Torsion* torsion; |
| 357 |
+ |
Inversion* inversion; |
| 358 |
|
Molecule::BondIterator bondIter;; |
| 359 |
|
Molecule::BendIterator bendIter; |
| 360 |
|
Molecule::TorsionIterator torsionIter; |
| 361 |
+ |
Molecule::InversionIterator inversionIter; |
| 362 |
|
|
| 363 |
|
RealType potential = 0.0; |
| 364 |
|
|
| 375 |
|
potential += torsion->getPotential(); |
| 376 |
|
} |
| 377 |
|
|
| 378 |
+ |
for (inversion = beginInversion(inversionIter); torsion != NULL; |
| 379 |
+ |
inversion = nextInversion(inversionIter)) { |
| 380 |
+ |
potential += inversion->getPotential(); |
| 381 |
+ |
} |
| 382 |
+ |
|
| 383 |
|
return potential; |
| 384 |
|
|
| 385 |
|
} |
| 386 |
|
|
| 387 |
+ |
void Molecule::addProperty(GenericData* genData) { |
| 388 |
+ |
properties_.addProperty(genData); |
| 389 |
+ |
} |
| 390 |
+ |
|
| 391 |
+ |
void Molecule::removeProperty(const std::string& propName) { |
| 392 |
+ |
properties_.removeProperty(propName); |
| 393 |
+ |
} |
| 394 |
+ |
|
| 395 |
+ |
void Molecule::clearProperties() { |
| 396 |
+ |
properties_.clearProperties(); |
| 397 |
+ |
} |
| 398 |
+ |
|
| 399 |
+ |
std::vector<std::string> Molecule::getPropertyNames() { |
| 400 |
+ |
return properties_.getPropertyNames(); |
| 401 |
+ |
} |
| 402 |
+ |
|
| 403 |
+ |
std::vector<GenericData*> Molecule::getProperties() { |
| 404 |
+ |
return properties_.getProperties(); |
| 405 |
+ |
} |
| 406 |
+ |
|
| 407 |
+ |
GenericData* Molecule::getPropertyByName(const std::string& propName) { |
| 408 |
+ |
return properties_.getPropertyByName(propName); |
| 409 |
+ |
} |
| 410 |
+ |
|
| 411 |
|
std::ostream& operator <<(std::ostream& o, Molecule& mol) { |
| 412 |
|
o << std::endl; |
| 413 |
|
o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl; |
| 415 |
|
o << mol.getNBonds() << " bonds" << std::endl; |
| 416 |
|
o << mol.getNBends() << " bends" << std::endl; |
| 417 |
|
o << mol.getNTorsions() << " torsions" << std::endl; |
| 418 |
+ |
o << mol.getNInversions() << " inversions" << std::endl; |
| 419 |
|
o << mol.getNRigidBodies() << " rigid bodies" << std::endl; |
| 420 |
< |
o << mol.getNIntegrableObjects() << "integrable objects" << std::endl; |
| 421 |
< |
o << mol.getNCutoffGroups() << "cutoff groups" << std::endl; |
| 422 |
< |
o << mol.getNConstraintPairs() << "constraint pairs" << std::endl; |
| 420 |
> |
o << mol.getNIntegrableObjects() << " integrable objects" << std::endl; |
| 421 |
> |
o << mol.getNCutoffGroups() << " cutoff groups" << std::endl; |
| 422 |
> |
o << mol.getNConstraintPairs() << " constraint pairs" << std::endl; |
| 423 |
> |
o << mol.getNFluctuatingCharges() << " fluctuating charges" << std::endl; |
| 424 |
|
return o; |
| 425 |
|
} |
| 426 |
|
|
| 427 |
< |
}//end namespace oopse |
| 427 |
> |
}//end namespace OpenMD |
