| 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 |
|
*/ |
| 54 |
|
#include "types/FixedChargeAdapter.hpp" |
| 55 |
|
#include "types/FluctuatingChargeAdapter.hpp" |
| 56 |
|
#include "types/MultipoleAdapter.hpp" |
| 57 |
+ |
#ifdef HAVE_QHULL |
| 58 |
|
#include "math/ConvexHull.hpp" |
| 59 |
|
#include "math/AlphaHull.hpp" |
| 60 |
+ |
#endif |
| 61 |
|
|
| 62 |
|
using namespace std; |
| 63 |
|
namespace OpenMD { |
| 324 |
|
Molecule* mol; |
| 325 |
|
Atom* atom; |
| 326 |
|
RealType charge; |
| 325 |
– |
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() ) { |
| 375 |
< |
Vector3d u_i = atom->getElectroFrame().getColumn(2); |
| 376 |
< |
moment = ma.getDipoleMoment(); |
| 377 |
< |
moment *= debyeToCm; |
| 378 |
< |
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; |
| 445 |
– |
RealType AvgE_a_ = 0; |
| 442 |
|
// Convective portion of the heat flux |
| 443 |
|
Vector3d heatFluxJc = V3Zero; |
| 444 |
|
|
| 826 |
|
data[0] = pos1.x(); |
| 827 |
|
data[1] = pos1.y(); |
| 828 |
|
data[2] = pos1.z(); |
| 829 |
< |
MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD); |
| 829 |
> |
MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc1); |
| 830 |
|
} else { |
| 831 |
< |
MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD); |
| 831 |
> |
MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc1); |
| 832 |
|
pos1 = Vector3d(data); |
| 833 |
|
} |
| 834 |
|
|
| 837 |
|
pos2 = sd2->getPos(); |
| 838 |
|
data[0] = pos2.x(); |
| 839 |
|
data[1] = pos2.y(); |
| 840 |
< |
data[2] = pos2.z(); |
| 841 |
< |
MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD); |
| 840 |
> |
data[2] = pos2.z(); |
| 841 |
> |
MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc2); |
| 842 |
|
} else { |
| 843 |
< |
MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD); |
| 843 |
> |
MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc2); |
| 844 |
|
pos2 = Vector3d(data); |
| 845 |
|
} |
| 846 |
|
#else |
| 860 |
|
|
| 861 |
|
RealType Thermo::getHullVolume(){ |
| 862 |
|
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 867 |
– |
|
| 868 |
– |
if (!snap->hasHullVolume) { |
| 863 |
|
|
| 864 |
+ |
#ifdef HAVE_QHULL |
| 865 |
+ |
if (!snap->hasHullVolume) { |
| 866 |
|
Hull* surfaceMesh_; |
| 867 |
|
|
| 868 |
|
Globals* simParams = info_->getSimParams(); |
| 898 |
|
snap->setHullVolume(surfaceMesh_->getVolume()); |
| 899 |
|
} |
| 900 |
|
return snap->getHullVolume(); |
| 901 |
< |
} |
| 901 |
> |
#else |
| 902 |
> |
return 0.0; |
| 903 |
> |
#endif |
| 904 |
> |
} |
| 905 |
|
} |
