| 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 |
|
#include "applications/hydrodynamics/ShapeBuilder.hpp" |
| 43 |
|
#include "hydrodynamics/Sphere.hpp" |
| 44 |
|
#include "hydrodynamics/Ellipsoid.hpp" |
| 45 |
|
#include "applications/hydrodynamics/CompositeShape.hpp" |
| 46 |
< |
namespace oopse { |
| 46 |
> |
#include "types/LennardJonesAdapter.hpp" |
| 47 |
> |
#include "types/GayBerneAdapter.hpp" |
| 48 |
> |
|
| 49 |
> |
namespace OpenMD { |
| 50 |
|
|
| 51 |
|
Shape* ShapeBuilder::createShape(StuntDouble* sd) { |
| 52 |
|
Shape* currShape = NULL; |
| 63 |
|
Shape* ShapeBuilder::internalCreateShape(Atom* atom) { |
| 64 |
|
AtomType* atomType = atom->getAtomType(); |
| 65 |
|
Shape* currShape = NULL; |
| 66 |
< |
if (atomType->isLennardJones()){ |
| 67 |
< |
GenericData* data = atomType->getPropertyByName("LennardJones"); |
| 68 |
< |
if (data != NULL) { |
| 65 |
< |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 66 |
< |
|
| 67 |
< |
if (ljData != NULL) { |
| 68 |
< |
LJParam ljParam = ljData->getData(); |
| 69 |
< |
currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0); |
| 70 |
< |
} else { |
| 71 |
< |
sprintf( painCave.errMsg, |
| 72 |
< |
"Can not cast GenericData to LJParam\n"); |
| 73 |
< |
painCave.severity = OOPSE_ERROR; |
| 74 |
< |
painCave.isFatal = 1; |
| 75 |
< |
simError(); |
| 76 |
< |
} |
| 77 |
< |
} |
| 66 |
> |
LennardJonesAdapter lja = LennardJonesAdapter(atomType); |
| 67 |
> |
if (lja.isLennardJones()){ |
| 68 |
> |
currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0); |
| 69 |
|
} else { |
| 70 |
|
int obanum = etab.GetAtomicNum((atom->getType()).c_str()); |
| 71 |
|
if (obanum != 0) { |
| 73 |
|
} else { |
| 74 |
|
sprintf( painCave.errMsg, |
| 75 |
|
"Could not find atom type in default element.txt\n"); |
| 76 |
< |
painCave.severity = OOPSE_ERROR; |
| 76 |
> |
painCave.severity = OPENMD_ERROR; |
| 77 |
|
painCave.isFatal = 1; |
| 78 |
|
simError(); |
| 79 |
|
} |
| 84 |
|
Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) { |
| 85 |
|
AtomType* atomType = datom->getAtomType(); |
| 86 |
|
Shape* currShape = NULL; |
| 87 |
< |
if (atomType->isGayBerne()) { |
| 88 |
< |
DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
| 89 |
< |
|
| 90 |
< |
GenericData* data = dAtomType->getPropertyByName("GayBerne"); |
| 91 |
< |
if (data != NULL) { |
| 92 |
< |
GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data); |
| 93 |
< |
|
| 94 |
< |
if (gayBerneData != NULL) { |
| 95 |
< |
GayBerneParam gayBerneParam = gayBerneData->getData(); |
| 96 |
< |
currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_l/2.0, |
| 97 |
< |
gayBerneParam.GB_d/2.0, datom->getA()); |
| 107 |
< |
} else { |
| 108 |
< |
sprintf( painCave.errMsg, |
| 109 |
< |
"Can not cast GenericData to GayBerneParam\n"); |
| 110 |
< |
painCave.severity = OOPSE_ERROR; |
| 111 |
< |
painCave.isFatal = 1; |
| 112 |
< |
simError(); |
| 113 |
< |
} |
| 87 |
> |
LennardJonesAdapter lja = LennardJonesAdapter(atomType); |
| 88 |
> |
GayBerneAdapter gba = GayBerneAdapter(atomType); |
| 89 |
> |
if (gba.isGayBerne()) { |
| 90 |
> |
currShape = new Ellipsoid(datom->getPos(), gba.getL()/2.0, |
| 91 |
> |
gba.getD()/2.0, datom->getA()); |
| 92 |
> |
} else if (lja.isLennardJones()) { |
| 93 |
> |
currShape = new Sphere(datom->getPos(), lja.getSigma()/2.0); |
| 94 |
> |
} else { |
| 95 |
> |
int obanum = etab.GetAtomicNum((datom->getType()).c_str()); |
| 96 |
> |
if (obanum != 0) { |
| 97 |
> |
currShape = new Sphere(datom->getPos(), etab.GetVdwRad(obanum)); |
| 98 |
|
} else { |
| 99 |
< |
sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n"); |
| 100 |
< |
painCave.severity = OOPSE_ERROR; |
| 99 |
> |
sprintf( painCave.errMsg, |
| 100 |
> |
"Could not find atom type in default element.txt\n"); |
| 101 |
> |
painCave.severity = OPENMD_ERROR; |
| 102 |
|
painCave.isFatal = 1; |
| 103 |
< |
simError(); |
| 104 |
< |
} |
| 105 |
< |
} else if (atomType->isLennardJones()) { |
| 121 |
< |
GenericData* data = atomType->getPropertyByName("LennardJones"); |
| 122 |
< |
if (data != NULL) { |
| 123 |
< |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 124 |
< |
|
| 125 |
< |
if (ljData != NULL) { |
| 126 |
< |
LJParam ljParam = ljData->getData(); |
| 127 |
< |
currShape = new Sphere(datom->getPos(), ljParam.sigma/2.0); |
| 128 |
< |
} else { |
| 129 |
< |
sprintf( painCave.errMsg, |
| 130 |
< |
"Can not cast GenericData to LJParam\n"); |
| 131 |
< |
painCave.severity = OOPSE_ERROR; |
| 132 |
< |
painCave.isFatal = 1; |
| 133 |
< |
simError(); |
| 134 |
< |
} |
| 135 |
< |
} else { |
| 136 |
< |
int obanum = etab.GetAtomicNum((datom->getType()).c_str()); |
| 137 |
< |
if (obanum != 0) { |
| 138 |
< |
currShape = new Sphere(datom->getPos(), etab.GetVdwRad(obanum)); |
| 139 |
< |
} else { |
| 140 |
< |
sprintf( painCave.errMsg, |
| 141 |
< |
"Could not find atom type in default element.txt\n"); |
| 142 |
< |
painCave.severity = OOPSE_ERROR; |
| 143 |
< |
painCave.isFatal = 1; |
| 144 |
< |
simError(); |
| 145 |
< |
} |
| 146 |
< |
} |
| 147 |
< |
} |
| 103 |
> |
simError(); |
| 104 |
> |
} |
| 105 |
> |
} |
| 106 |
|
return currShape; |
| 107 |
|
} |
| 108 |
|
|
