| 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). |
| 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 |
|
*/ |
| 233 |
|
|
| 234 |
|
kinetic *= 0.5; |
| 235 |
|
eTemp = (2.0 * kinetic) / |
| 236 |
< |
(info_->getNFluctuatingCharges() * PhysicalConstants::kb ); |
| 236 |
> |
(info_->getNFluctuatingCharges() * PhysicalConstants::kb ); |
| 237 |
|
|
| 238 |
|
snap->setElectronicTemperature(eTemp); |
| 239 |
|
} |
| 324 |
|
Molecule* mol; |
| 325 |
|
Atom* atom; |
| 326 |
|
RealType charge; |
| 327 |
– |
RealType moment(0.0); |
| 327 |
|
Vector3d ri(0.0); |
| 328 |
|
Vector3d dipoleVector(0.0); |
| 329 |
|
Vector3d nPos(0.0); |
| 371 |
|
pCount++; |
| 372 |
|
} |
| 373 |
|
|
| 374 |
< |
MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType()); |
| 375 |
< |
if (ma.isDipole() ) { |
| 377 |
< |
Vector3d u_i = atom->getElectroFrame().getColumn(2); |
| 378 |
< |
moment = ma.getDipoleMoment(); |
| 379 |
< |
moment *= debyeToCm; |
| 380 |
< |
dipoleVector += u_i * moment; |
| 374 |
> |
if (atom->isDipole()) { |
| 375 |
> |
dipoleVector += atom->getDipole() * debyeToCm; |
| 376 |
|
} |
| 377 |
|
} |
| 378 |
|
} |
| 439 |
|
RealType kinetic; |
| 440 |
|
RealType potential; |
| 441 |
|
RealType eatom; |
| 447 |
– |
RealType AvgE_a_ = 0; |
| 442 |
|
// Convective portion of the heat flux |
| 443 |
|
Vector3d heatFluxJc = V3Zero; |
| 444 |
|
|
| 619 |
|
} |
| 620 |
|
|
| 621 |
|
/** |
| 622 |
< |
* Return intertia tensor for entire system and angular momentum |
| 623 |
< |
* Vector. |
| 622 |
> |
* \brief Return inertia tensor for entire system and angular momentum |
| 623 |
> |
* Vector. |
| 624 |
|
* |
| 625 |
|
* |
| 626 |
|
* |
| 700 |
|
|
| 701 |
|
return; |
| 702 |
|
} |
| 703 |
+ |
|
| 704 |
|
|
| 705 |
+ |
Mat3x3d Thermo::getBoundingBox(){ |
| 706 |
+ |
|
| 707 |
+ |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 708 |
+ |
|
| 709 |
+ |
if (!(snap->hasBoundingBox)) { |
| 710 |
+ |
|
| 711 |
+ |
SimInfo::MoleculeIterator i; |
| 712 |
+ |
Molecule::RigidBodyIterator ri; |
| 713 |
+ |
Molecule::AtomIterator ai; |
| 714 |
+ |
Molecule* mol; |
| 715 |
+ |
RigidBody* rb; |
| 716 |
+ |
Atom* atom; |
| 717 |
+ |
Vector3d pos, bMax, bMin; |
| 718 |
+ |
int index = 0; |
| 719 |
+ |
|
| 720 |
+ |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 721 |
+ |
mol = info_->nextMolecule(i)) { |
| 722 |
+ |
|
| 723 |
+ |
//change the positions of atoms which belong to the rigidbodies |
| 724 |
+ |
for (rb = mol->beginRigidBody(ri); rb != NULL; |
| 725 |
+ |
rb = mol->nextRigidBody(ri)) { |
| 726 |
+ |
rb->updateAtoms(); |
| 727 |
+ |
} |
| 728 |
+ |
|
| 729 |
+ |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 730 |
+ |
atom = mol->nextAtom(ai)) { |
| 731 |
+ |
|
| 732 |
+ |
pos = atom->getPos(); |
| 733 |
+ |
|
| 734 |
+ |
if (index == 0) { |
| 735 |
+ |
bMax = pos; |
| 736 |
+ |
bMin = pos; |
| 737 |
+ |
} else { |
| 738 |
+ |
for (int i = 0; i < 3; i++) { |
| 739 |
+ |
bMax[i] = max(bMax[i], pos[i]); |
| 740 |
+ |
bMin[i] = min(bMin[i], pos[i]); |
| 741 |
+ |
} |
| 742 |
+ |
} |
| 743 |
+ |
index++; |
| 744 |
+ |
} |
| 745 |
+ |
} |
| 746 |
+ |
|
| 747 |
+ |
#ifdef IS_MPI |
| 748 |
+ |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bMax[0], 3, MPI::REALTYPE, |
| 749 |
+ |
MPI::MAX); |
| 750 |
+ |
|
| 751 |
+ |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bMin[0], 3, MPI::REALTYPE, |
| 752 |
+ |
MPI::MIN); |
| 753 |
+ |
#endif |
| 754 |
+ |
Mat3x3d bBox = Mat3x3d(0.0); |
| 755 |
+ |
for (int i = 0; i < 3; i++) { |
| 756 |
+ |
bBox(i,i) = bMax[i] - bMin[i]; |
| 757 |
+ |
} |
| 758 |
+ |
snap->setBoundingBox(bBox); |
| 759 |
+ |
} |
| 760 |
+ |
|
| 761 |
+ |
return snap->getBoundingBox(); |
| 762 |
+ |
} |
| 763 |
+ |
|
| 764 |
+ |
|
| 765 |
|
// Returns the angular momentum of the system |
| 766 |
|
Vector3d Thermo::getAngularMomentum(){ |
| 767 |
|
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 887 |
|
data[0] = pos1.x(); |
| 888 |
|
data[1] = pos1.y(); |
| 889 |
|
data[2] = pos1.z(); |
| 890 |
< |
MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD); |
| 890 |
> |
MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc1); |
| 891 |
|
} else { |
| 892 |
< |
MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD); |
| 892 |
> |
MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc1); |
| 893 |
|
pos1 = Vector3d(data); |
| 894 |
|
} |
| 895 |
|
|
| 898 |
|
pos2 = sd2->getPos(); |
| 899 |
|
data[0] = pos2.x(); |
| 900 |
|
data[1] = pos2.y(); |
| 901 |
< |
data[2] = pos2.z(); |
| 902 |
< |
MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD); |
| 901 |
> |
data[2] = pos2.z(); |
| 902 |
> |
MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc2); |
| 903 |
|
} else { |
| 904 |
< |
MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD); |
| 904 |
> |
MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc2); |
| 905 |
|
pos2 = Vector3d(data); |
| 906 |
|
} |
| 907 |
|
#else |
| 920 |
|
} |
| 921 |
|
|
| 922 |
|
RealType Thermo::getHullVolume(){ |
| 868 |
– |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 869 |
– |
|
| 923 |
|
#ifdef HAVE_QHULL |
| 924 |
+ |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 925 |
|
if (!snap->hasHullVolume) { |
| 926 |
|
Hull* surfaceMesh_; |
| 927 |
< |
|
| 927 |
> |
|
| 928 |
|
Globals* simParams = info_->getSimParams(); |
| 929 |
|
const std::string ht = simParams->getHULL_Method(); |
| 930 |
|
|
| 956 |
|
// Compute surface Mesh |
| 957 |
|
surfaceMesh_->computeHull(localSites_); |
| 958 |
|
snap->setHullVolume(surfaceMesh_->getVolume()); |
| 959 |
+ |
|
| 960 |
+ |
delete surfaceMesh_; |
| 961 |
|
} |
| 962 |
+ |
|
| 963 |
|
return snap->getHullVolume(); |
| 964 |
|
#else |
| 965 |
|
return 0.0; |
| 966 |
|
#endif |
| 967 |
|
} |
| 968 |
+ |
|
| 969 |
+ |
|
| 970 |
|
} |
