| 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] Vardeman & Gezelter, in progress (2009). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
#include <fstream> |
| 43 |
|
#include <iostream> |
| 47 |
|
#include "hydrodynamics/Sphere.hpp" |
| 48 |
|
#include "hydrodynamics/Ellipsoid.hpp" |
| 49 |
|
#include "utils/ElementsTable.hpp" |
| 50 |
+ |
#include "types/LennardJonesAdapter.hpp" |
| 51 |
+ |
#include "types/GayBerneAdapter.hpp" |
| 52 |
|
|
| 53 |
|
namespace OpenMD { |
| 54 |
|
|
| 159 |
|
if (integrableObject->isAtom()){ |
| 160 |
|
Atom* atom = static_cast<Atom*>(integrableObject); |
| 161 |
|
AtomType* atomType = atom->getAtomType(); |
| 162 |
< |
if (atomType->isGayBerne()) { |
| 163 |
< |
DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
| 164 |
< |
GenericData* data = dAtomType->getPropertyByName("GayBerne"); |
| 165 |
< |
if (data != NULL) { |
| 166 |
< |
GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data); |
| 164 |
< |
|
| 165 |
< |
if (gayBerneData != NULL) { |
| 166 |
< |
GayBerneParam gayBerneParam = gayBerneData->getData(); |
| 167 |
< |
currShape = new Ellipsoid(V3Zero, |
| 168 |
< |
gayBerneParam.GB_l / 2.0, |
| 169 |
< |
gayBerneParam.GB_d / 2.0, |
| 170 |
< |
Mat3x3d::identity()); |
| 171 |
< |
} else { |
| 172 |
< |
sprintf( painCave.errMsg, |
| 173 |
< |
"Can not cast GenericData to GayBerneParam\n"); |
| 174 |
< |
painCave.severity = OPENMD_ERROR; |
| 175 |
< |
painCave.isFatal = 1; |
| 176 |
< |
simError(); |
| 177 |
< |
} |
| 178 |
< |
} else { |
| 179 |
< |
sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n"); |
| 180 |
< |
painCave.severity = OPENMD_ERROR; |
| 181 |
< |
painCave.isFatal = 1; |
| 182 |
< |
simError(); |
| 183 |
< |
} |
| 162 |
> |
GayBerneAdapter gba = GayBerneAdapter(atomType); |
| 163 |
> |
if (gba.isGayBerne()) { |
| 164 |
> |
currShape = new Ellipsoid(V3Zero, gba.getL() / 2.0, |
| 165 |
> |
gba.getD() / 2.0, |
| 166 |
> |
Mat3x3d::identity()); |
| 167 |
|
} else { |
| 168 |
< |
if (atomType->isLennardJones()){ |
| 169 |
< |
GenericData* data = atomType->getPropertyByName("LennardJones"); |
| 170 |
< |
if (data != NULL) { |
| 188 |
< |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 189 |
< |
if (ljData != NULL) { |
| 190 |
< |
LJParam ljParam = ljData->getData(); |
| 191 |
< |
currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0); |
| 192 |
< |
} else { |
| 193 |
< |
sprintf( painCave.errMsg, |
| 194 |
< |
"Can not cast GenericData to LJParam\n"); |
| 195 |
< |
painCave.severity = OPENMD_ERROR; |
| 196 |
< |
painCave.isFatal = 1; |
| 197 |
< |
simError(); |
| 198 |
< |
} |
| 199 |
< |
} |
| 168 |
> |
LennardJonesAdapter lja = LennardJonesAdapter(atomType); |
| 169 |
> |
if (lja.isLennardJones()){ |
| 170 |
> |
currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0); |
| 171 |
|
} else { |
| 172 |
|
int aNum = etab.GetAtomicNum((atom->getType()).c_str()); |
| 173 |
|
if (aNum != 0) { |
