| 1 |
< |
#include <stdlib.h> |
| 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, 24107 (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 |
|
|
| 57 |
+ |
namespace OpenMD { |
| 58 |
+ |
Molecule::Molecule(int stampId, int globalIndex, const std::string& molName) |
| 59 |
+ |
: stampId_(stampId), globalIndex_(globalIndex), moleculeName_(molName) { |
| 60 |
+ |
} |
| 61 |
+ |
|
| 62 |
+ |
Molecule::~Molecule() { |
| 63 |
+ |
|
| 64 |
+ |
MemoryUtils::deletePointers(atoms_); |
| 65 |
+ |
MemoryUtils::deletePointers(bonds_); |
| 66 |
+ |
MemoryUtils::deletePointers(bends_); |
| 67 |
+ |
MemoryUtils::deletePointers(torsions_); |
| 68 |
+ |
MemoryUtils::deletePointers(inversions_); |
| 69 |
+ |
MemoryUtils::deletePointers(rigidBodies_); |
| 70 |
+ |
MemoryUtils::deletePointers(cutoffGroups_); |
| 71 |
+ |
MemoryUtils::deletePointers(constraintPairs_); |
| 72 |
+ |
MemoryUtils::deletePointers(constraintElems_); |
| 73 |
|
|
| 74 |
< |
|
| 75 |
< |
Molecule::Molecule( void ){ |
| 76 |
< |
|
| 77 |
< |
myAtoms = NULL; |
| 78 |
< |
myBonds = NULL; |
| 13 |
< |
myBends = NULL; |
| 14 |
< |
myTorsions = NULL; |
| 15 |
< |
} |
| 16 |
< |
|
| 17 |
< |
Molecule::~Molecule( void ){ |
| 18 |
< |
int i; |
| 19 |
< |
CutoffGroup* cg; |
| 20 |
< |
vector<CutoffGroup*>::iterator iter; |
| 74 |
> |
// integrableObjects_ don't own the objects |
| 75 |
> |
integrableObjects_.clear(); |
| 76 |
> |
fluctuatingCharges_.clear(); |
| 77 |
> |
|
| 78 |
> |
} |
| 79 |
|
|
| 80 |
< |
if( myAtoms != NULL ){ |
| 81 |
< |
for(i=0; i<nAtoms; i++) if(myAtoms[i] != NULL ) delete myAtoms[i]; |
| 82 |
< |
delete[] myAtoms; |
| 80 |
> |
void Molecule::addAtom(Atom* atom) { |
| 81 |
> |
if (std::find(atoms_.begin(), atoms_.end(), atom) == atoms_.end()) { |
| 82 |
> |
atoms_.push_back(atom); |
| 83 |
> |
} |
| 84 |
|
} |
| 85 |
< |
|
| 86 |
< |
if( myBonds != NULL ){ |
| 87 |
< |
for(i=0; i<nBonds; i++) if(myBonds[i] != NULL ) delete myBonds[i]; |
| 88 |
< |
delete[] myBonds; |
| 85 |
> |
|
| 86 |
> |
void Molecule::addBond(Bond* bond) { |
| 87 |
> |
if (std::find(bonds_.begin(), bonds_.end(), bond) == bonds_.end()) { |
| 88 |
> |
bonds_.push_back(bond); |
| 89 |
> |
} |
| 90 |
|
} |
| 91 |
< |
|
| 92 |
< |
if( myBends != NULL ){ |
| 93 |
< |
for(i=0; i<nBends; i++) if(myBends[i] != NULL ) delete myBends[i]; |
| 94 |
< |
delete[] myBends; |
| 91 |
> |
|
| 92 |
> |
void Molecule::addBend(Bend* bend) { |
| 93 |
> |
if (std::find(bends_.begin(), bends_.end(), bend) == bends_.end()) { |
| 94 |
> |
bends_.push_back(bend); |
| 95 |
> |
} |
| 96 |
|
} |
| 97 |
< |
|
| 98 |
< |
if( myTorsions != NULL ){ |
| 99 |
< |
for(i=0; i<nTorsions; i++) if(myTorsions[i] != NULL ) delete myTorsions[i]; |
| 100 |
< |
delete[] myTorsions; |
| 97 |
> |
|
| 98 |
> |
void Molecule::addTorsion(Torsion* torsion) { |
| 99 |
> |
if (std::find(torsions_.begin(), torsions_.end(), torsion) == |
| 100 |
> |
torsions_.end()) { |
| 101 |
> |
torsions_.push_back(torsion); |
| 102 |
> |
} |
| 103 |
|
} |
| 104 |
|
|
| 105 |
< |
for(cg = beginCutoffGroup(iter); cg != NULL; cg = nextCutoffGroup(iter)) |
| 106 |
< |
delete cg; |
| 107 |
< |
myCutoffGroups.clear(); |
| 105 |
> |
void Molecule::addInversion(Inversion* inversion) { |
| 106 |
> |
if (std::find(inversions_.begin(), inversions_.end(), inversion) == |
| 107 |
> |
inversions_.end()) { |
| 108 |
> |
inversions_.push_back(inversion); |
| 109 |
> |
} |
| 110 |
> |
} |
| 111 |
|
|
| 112 |
< |
} |
| 113 |
< |
|
| 114 |
< |
|
| 115 |
< |
void Molecule::initialize( molInit &theInit ){ |
| 116 |
< |
|
| 117 |
< |
CutoffGroup* curCutoffGroup; |
| 52 |
< |
vector<CutoffGroup*>::iterator iterCutoff; |
| 53 |
< |
Atom* cutoffAtom; |
| 54 |
< |
vector<Atom*>::iterator iterAtom; |
| 55 |
< |
int atomIndex; |
| 112 |
> |
void Molecule::addRigidBody(RigidBody *rb) { |
| 113 |
> |
if (std::find(rigidBodies_.begin(), rigidBodies_.end(), rb) == |
| 114 |
> |
rigidBodies_.end()) { |
| 115 |
> |
rigidBodies_.push_back(rb); |
| 116 |
> |
} |
| 117 |
> |
} |
| 118 |
|
|
| 119 |
< |
nAtoms = theInit.nAtoms; |
| 120 |
< |
nMembers = nAtoms; |
| 121 |
< |
nBonds = theInit.nBonds; |
| 122 |
< |
nBends = theInit.nBends; |
| 123 |
< |
nTorsions = theInit.nTorsions; |
| 124 |
< |
nRigidBodies = theInit.nRigidBodies; |
| 63 |
< |
nOriented = theInit.nOriented; |
| 64 |
< |
|
| 65 |
< |
myAtoms = theInit.myAtoms; |
| 66 |
< |
myBonds = theInit.myBonds; |
| 67 |
< |
myBends = theInit.myBends; |
| 68 |
< |
myTorsions = theInit.myTorsions; |
| 69 |
< |
myRigidBodies = theInit.myRigidBodies; |
| 70 |
< |
|
| 71 |
< |
myIntegrableObjects = theInit.myIntegrableObjects; |
| 72 |
< |
|
| 73 |
< |
for (int i = 0; i < myRigidBodies.size(); i++) |
| 74 |
< |
myRigidBodies[i]->calcRefCoords(); |
| 75 |
< |
|
| 76 |
< |
myCutoffGroups = theInit.myCutoffGroups; |
| 77 |
< |
nCutoffGroups = myCutoffGroups.size(); |
| 78 |
< |
|
| 79 |
< |
} |
| 80 |
< |
|
| 81 |
< |
void Molecule::calcForces( void ){ |
| 119 |
> |
void Molecule::addCutoffGroup(CutoffGroup* cp) { |
| 120 |
> |
if (std::find(cutoffGroups_.begin(), cutoffGroups_.end(), cp) == |
| 121 |
> |
cutoffGroups_.end()) { |
| 122 |
> |
cutoffGroups_.push_back(cp); |
| 123 |
> |
} |
| 124 |
> |
} |
| 125 |
|
|
| 126 |
< |
int i; |
| 127 |
< |
double com[3]; |
| 128 |
< |
|
| 129 |
< |
for(i=0; i<myRigidBodies.size(); i++) { |
| 130 |
< |
myRigidBodies[i]->updateAtoms(); |
| 126 |
> |
void Molecule::addConstraintPair(ConstraintPair* cp) { |
| 127 |
> |
if (std::find(constraintPairs_.begin(), constraintPairs_.end(), cp) == |
| 128 |
> |
constraintPairs_.end()) { |
| 129 |
> |
constraintPairs_.push_back(cp); |
| 130 |
> |
} |
| 131 |
|
} |
| 132 |
< |
|
| 133 |
< |
for(i=0; i<nBonds; i++){ |
| 134 |
< |
myBonds[i]->calc_forces(); |
| 132 |
> |
|
| 133 |
> |
void Molecule::addConstraintElem(ConstraintElem* cp) { |
| 134 |
> |
if (std::find(constraintElems_.begin(), constraintElems_.end(), cp) == |
| 135 |
> |
constraintElems_.end()) { |
| 136 |
> |
constraintElems_.push_back(cp); |
| 137 |
> |
} |
| 138 |
|
} |
| 139 |
+ |
|
| 140 |
+ |
void Molecule::complete() { |
| 141 |
+ |
|
| 142 |
+ |
std::set<Atom*> rigidAtoms; |
| 143 |
+ |
Atom* atom; |
| 144 |
+ |
AtomIterator ai; |
| 145 |
+ |
RigidBody* rb; |
| 146 |
+ |
RigidBodyIterator rbIter; |
| 147 |
|
|
| 148 |
< |
for(i=0; i<nBends; i++){ |
| 95 |
< |
myBends[i]->calc_forces(); |
| 96 |
< |
} |
| 148 |
> |
// Get list of all the atoms that are part of rigid bodies |
| 149 |
|
|
| 150 |
< |
for(i=0; i<nTorsions; i++){ |
| 151 |
< |
myTorsions[i]->calc_forces(); |
| 152 |
< |
} |
| 150 |
> |
for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
| 151 |
> |
rigidAtoms.insert(rb->getBeginAtomIter(), rb->getEndAtomIter()); |
| 152 |
> |
} |
| 153 |
> |
|
| 154 |
> |
// add any atom that wasn't part of a rigid body to the list of integrableObjects |
| 155 |
|
|
| 156 |
< |
// Rigid Body forces and torques are done after the fortran force loop |
| 156 |
> |
for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { |
| 157 |
> |
|
| 158 |
> |
if (rigidAtoms.find(atom) == rigidAtoms.end()) { |
| 159 |
|
|
| 160 |
< |
} |
| 160 |
> |
// If an atom does not belong to a rigid body, it is an |
| 161 |
> |
// integrable object |
| 162 |
|
|
| 163 |
+ |
integrableObjects_.push_back(atom); |
| 164 |
+ |
} |
| 165 |
+ |
} |
| 166 |
+ |
|
| 167 |
+ |
// then add the rigid bodies themselves to the integrableObjects |
| 168 |
|
|
| 169 |
< |
double Molecule::getPotential( void ){ |
| 170 |
< |
|
| 171 |
< |
int i; |
| 110 |
< |
double myPot = 0.0; |
| 169 |
> |
for (rb = beginRigidBody(rbIter); rb != NULL; rb = nextRigidBody(rbIter)) { |
| 170 |
> |
integrableObjects_.push_back(rb); |
| 171 |
> |
} |
| 172 |
|
|
| 173 |
< |
for(i=0; i<myRigidBodies.size(); i++) { |
| 174 |
< |
myRigidBodies[i]->updateAtoms(); |
| 114 |
< |
} |
| 115 |
< |
|
| 116 |
< |
for(i=0; i<nBonds; i++){ |
| 117 |
< |
myPot += myBonds[i]->get_potential(); |
| 118 |
< |
} |
| 173 |
> |
// find the atoms that are fluctuating charges and add them to the |
| 174 |
> |
// fluctuatingCharges_ vector |
| 175 |
|
|
| 176 |
< |
for(i=0; i<nBends; i++){ |
| 177 |
< |
myPot += myBends[i]->get_potential(); |
| 176 |
> |
for (atom = beginAtom(ai); atom != NULL; atom = nextAtom(ai)) { |
| 177 |
> |
if ( atom->isFluctuatingCharge() ) |
| 178 |
> |
fluctuatingCharges_.push_back( atom ); |
| 179 |
> |
} |
| 180 |
> |
|
| 181 |
|
} |
| 182 |
|
|
| 183 |
< |
for(i=0; i<nTorsions; i++){ |
| 184 |
< |
myPot += myTorsions[i]->get_potential(); |
| 183 |
> |
RealType Molecule::getMass() { |
| 184 |
> |
StuntDouble* sd; |
| 185 |
> |
std::vector<StuntDouble*>::iterator i; |
| 186 |
> |
RealType mass = 0.0; |
| 187 |
> |
|
| 188 |
> |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 189 |
> |
nextIntegrableObject(i)){ |
| 190 |
> |
mass += sd->getMass(); |
| 191 |
> |
} |
| 192 |
> |
|
| 193 |
> |
return mass; |
| 194 |
|
} |
| 195 |
|
|
| 196 |
< |
return myPot; |
| 197 |
< |
} |
| 196 |
> |
Vector3d Molecule::getCom() { |
| 197 |
> |
StuntDouble* sd; |
| 198 |
> |
std::vector<StuntDouble*>::iterator i; |
| 199 |
> |
Vector3d com; |
| 200 |
> |
RealType totalMass = 0; |
| 201 |
> |
RealType mass; |
| 202 |
> |
|
| 203 |
> |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 204 |
> |
nextIntegrableObject(i)){ |
| 205 |
> |
mass = sd->getMass(); |
| 206 |
> |
totalMass += mass; |
| 207 |
> |
com += sd->getPos() * mass; |
| 208 |
> |
} |
| 209 |
> |
|
| 210 |
> |
com /= totalMass; |
| 211 |
|
|
| 212 |
< |
void Molecule::printMe( void ){ |
| 132 |
< |
|
| 133 |
< |
int i; |
| 134 |
< |
|
| 135 |
< |
for(i=0; i<nBonds; i++){ |
| 136 |
< |
myBonds[i]->printMe(); |
| 212 |
> |
return com; |
| 213 |
|
} |
| 214 |
|
|
| 215 |
< |
for(i=0; i<nBends; i++){ |
| 216 |
< |
myBends[i]->printMe(); |
| 215 |
> |
void Molecule::moveCom(const Vector3d& delta) { |
| 216 |
> |
StuntDouble* sd; |
| 217 |
> |
std::vector<StuntDouble*>::iterator i; |
| 218 |
> |
|
| 219 |
> |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 220 |
> |
nextIntegrableObject(i)){ |
| 221 |
> |
sd->setPos(sd->getPos() + delta); |
| 222 |
> |
} |
| 223 |
|
} |
| 224 |
|
|
| 225 |
< |
for(i=0; i<nTorsions; i++){ |
| 226 |
< |
myTorsions[i]->printMe(); |
| 225 |
> |
Vector3d Molecule::getComVel() { |
| 226 |
> |
StuntDouble* sd; |
| 227 |
> |
std::vector<StuntDouble*>::iterator i; |
| 228 |
> |
Vector3d velCom; |
| 229 |
> |
RealType totalMass = 0; |
| 230 |
> |
RealType mass; |
| 231 |
> |
|
| 232 |
> |
for (sd = beginIntegrableObject(i); sd != NULL; sd = |
| 233 |
> |
nextIntegrableObject(i)){ |
| 234 |
> |
mass = sd->getMass(); |
| 235 |
> |
totalMass += mass; |
| 236 |
> |
velCom += sd->getVel() * mass; |
| 237 |
> |
} |
| 238 |
> |
|
| 239 |
> |
velCom /= totalMass; |
| 240 |
> |
|
| 241 |
> |
return velCom; |
| 242 |
|
} |
| 243 |
|
|
| 244 |
< |
} |
| 244 |
> |
RealType Molecule::getPotential() { |
| 245 |
|
|
| 246 |
< |
void Molecule::moveCOM(double delta[3]){ |
| 247 |
< |
double aPos[3]; |
| 248 |
< |
int i, j; |
| 246 |
> |
Bond* bond; |
| 247 |
> |
Bend* bend; |
| 248 |
> |
Torsion* torsion; |
| 249 |
> |
Inversion* inversion; |
| 250 |
> |
Molecule::BondIterator bondIter;; |
| 251 |
> |
Molecule::BendIterator bendIter; |
| 252 |
> |
Molecule::TorsionIterator torsionIter; |
| 253 |
> |
Molecule::InversionIterator inversionIter; |
| 254 |
|
|
| 255 |
< |
for(i=0; i<myIntegrableObjects.size(); i++) { |
| 154 |
< |
if(myIntegrableObjects[i] != NULL ) { |
| 155 |
< |
|
| 156 |
< |
myIntegrableObjects[i]->getPos( aPos ); |
| 157 |
< |
|
| 158 |
< |
for (j=0; j< 3; j++) |
| 159 |
< |
aPos[j] += delta[j]; |
| 255 |
> |
RealType potential = 0.0; |
| 256 |
|
|
| 257 |
< |
myIntegrableObjects[i]->setPos( aPos ); |
| 257 |
> |
for (bond = beginBond(bondIter); bond != NULL; bond = nextBond(bondIter)) { |
| 258 |
> |
potential += bond->getPotential(); |
| 259 |
|
} |
| 163 |
– |
} |
| 260 |
|
|
| 261 |
< |
for(i=0; i<myRigidBodies.size(); i++) { |
| 261 |
> |
for (bend = beginBend(bendIter); bend != NULL; bend = nextBend(bendIter)) { |
| 262 |
> |
potential += bend->getPotential(); |
| 263 |
> |
} |
| 264 |
|
|
| 265 |
< |
myRigidBodies[i]->getPos( aPos ); |
| 266 |
< |
|
| 267 |
< |
for (j=0; j< 3; j++) |
| 170 |
< |
aPos[j] += delta[j]; |
| 171 |
< |
|
| 172 |
< |
myRigidBodies[i]->setPos( aPos ); |
| 265 |
> |
for (torsion = beginTorsion(torsionIter); torsion != NULL; torsion = |
| 266 |
> |
nextTorsion(torsionIter)) { |
| 267 |
> |
potential += torsion->getPotential(); |
| 268 |
|
} |
| 269 |
< |
} |
| 269 |
> |
|
| 270 |
> |
for (inversion = beginInversion(inversionIter); torsion != NULL; |
| 271 |
> |
inversion = nextInversion(inversionIter)) { |
| 272 |
> |
potential += inversion->getPotential(); |
| 273 |
> |
} |
| 274 |
> |
|
| 275 |
> |
return potential; |
| 276 |
> |
|
| 277 |
> |
} |
| 278 |
> |
|
| 279 |
> |
void Molecule::addProperty(GenericData* genData) { |
| 280 |
> |
properties_.addProperty(genData); |
| 281 |
> |
} |
| 282 |
|
|
| 283 |
< |
void Molecule::atoms2rigidBodies( void ) { |
| 284 |
< |
int i; |
| 178 |
< |
for (i = 0; i < myRigidBodies.size(); i++) { |
| 179 |
< |
myRigidBodies[i]->calcForcesAndTorques(); |
| 283 |
> |
void Molecule::removeProperty(const std::string& propName) { |
| 284 |
> |
properties_.removeProperty(propName); |
| 285 |
|
} |
| 181 |
– |
} |
| 286 |
|
|
| 287 |
< |
void Molecule::getCOM( double COM[3] ) { |
| 287 |
> |
void Molecule::clearProperties() { |
| 288 |
> |
properties_.clearProperties(); |
| 289 |
> |
} |
| 290 |
|
|
| 291 |
< |
double mass, mtot; |
| 292 |
< |
double aPos[3]; |
| 293 |
< |
int i, j; |
| 188 |
< |
|
| 189 |
< |
for (j=0; j<3; j++) |
| 190 |
< |
COM[j] = 0.0; |
| 191 |
< |
|
| 192 |
< |
mtot = 0.0; |
| 193 |
< |
|
| 194 |
< |
for (i=0; i < myIntegrableObjects.size(); i++) { |
| 195 |
< |
if (myIntegrableObjects[i] != NULL) { |
| 196 |
< |
|
| 197 |
< |
mass = myIntegrableObjects[i]->getMass(); |
| 198 |
< |
mtot += mass; |
| 291 |
> |
std::vector<std::string> Molecule::getPropertyNames() { |
| 292 |
> |
return properties_.getPropertyNames(); |
| 293 |
> |
} |
| 294 |
|
|
| 295 |
< |
myIntegrableObjects[i]->getPos( aPos ); |
| 296 |
< |
|
| 202 |
< |
for( j = 0; j < 3; j++) |
| 203 |
< |
COM[j] += aPos[j] * mass; |
| 204 |
< |
|
| 205 |
< |
} |
| 295 |
> |
std::vector<GenericData*> Molecule::getProperties() { |
| 296 |
> |
return properties_.getProperties(); |
| 297 |
|
} |
| 298 |
|
|
| 299 |
< |
for (j = 0; j < 3; j++) |
| 300 |
< |
COM[j] /= mtot; |
| 210 |
< |
} |
| 211 |
< |
|
| 212 |
< |
double Molecule::getCOMvel( double COMvel[3] ) { |
| 213 |
< |
|
| 214 |
< |
double mass, mtot; |
| 215 |
< |
double aVel[3]; |
| 216 |
< |
int i, j; |
| 217 |
< |
|
| 218 |
< |
|
| 219 |
< |
for (j=0; j<3; j++) |
| 220 |
< |
COMvel[j] = 0.0; |
| 221 |
< |
|
| 222 |
< |
mtot = 0.0; |
| 223 |
< |
|
| 224 |
< |
for (i=0; i < myIntegrableObjects.size(); i++) { |
| 225 |
< |
if (myIntegrableObjects[i] != NULL) { |
| 226 |
< |
|
| 227 |
< |
mass = myIntegrableObjects[i]->getMass(); |
| 228 |
< |
mtot += mass; |
| 229 |
< |
|
| 230 |
< |
myIntegrableObjects[i]->getVel(aVel); |
| 231 |
< |
|
| 232 |
< |
for (j=0; j<3; j++) |
| 233 |
< |
COMvel[j] += aVel[j]*mass; |
| 234 |
< |
|
| 235 |
< |
} |
| 299 |
> |
GenericData* Molecule::getPropertyByName(const std::string& propName) { |
| 300 |
> |
return properties_.getPropertyByName(propName); |
| 301 |
|
} |
| 302 |
|
|
| 303 |
< |
for (j=0; j<3; j++) |
| 304 |
< |
COMvel[j] /= mtot; |
| 305 |
< |
|
| 306 |
< |
return mtot; |
| 307 |
< |
|
| 308 |
< |
} |
| 309 |
< |
|
| 310 |
< |
double Molecule::getTotalMass() |
| 311 |
< |
{ |
| 312 |
< |
|
| 313 |
< |
double totalMass; |
| 314 |
< |
|
| 315 |
< |
totalMass = 0; |
| 316 |
< |
for(int i =0; i < myIntegrableObjects.size(); i++){ |
| 252 |
< |
totalMass += myIntegrableObjects[i]->getMass(); |
| 303 |
> |
std::ostream& operator <<(std::ostream& o, Molecule& mol) { |
| 304 |
> |
o << std::endl; |
| 305 |
> |
o << "Molecule " << mol.getGlobalIndex() << "has: " << std::endl; |
| 306 |
> |
o << mol.getNAtoms() << " atoms" << std::endl; |
| 307 |
> |
o << mol.getNBonds() << " bonds" << std::endl; |
| 308 |
> |
o << mol.getNBends() << " bends" << std::endl; |
| 309 |
> |
o << mol.getNTorsions() << " torsions" << std::endl; |
| 310 |
> |
o << mol.getNInversions() << " inversions" << std::endl; |
| 311 |
> |
o << mol.getNRigidBodies() << " rigid bodies" << std::endl; |
| 312 |
> |
o << mol.getNIntegrableObjects() << " integrable objects" << std::endl; |
| 313 |
> |
o << mol.getNCutoffGroups() << " cutoff groups" << std::endl; |
| 314 |
> |
o << mol.getNConstraintPairs() << " constraint pairs" << std::endl; |
| 315 |
> |
o << mol.getNFluctuatingCharges() << " fluctuating charges" << std::endl; |
| 316 |
> |
return o; |
| 317 |
|
} |
| 318 |
< |
|
| 319 |
< |
return totalMass; |
| 256 |
< |
} |
| 318 |
> |
|
| 319 |
> |
}//end namespace OpenMD |
