| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* 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, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
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|
|
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|
#include "primitives/DirectionalAtom.hpp" |
| 43 |
|
#include "utils/simError.h" |
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
|
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|
DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType) |
| 47 |
|
: Atom(dAtomType){ |
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|
int nLinearAxis = 0; |
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Mat3x3d inertiaTensor = getI(); |
| 57 |
|
for (int i = 0; i < 3; i++) { |
| 58 |
< |
if (fabs(inertiaTensor(i, i)) < oopse::epsilon) { |
| 58 |
> |
if (fabs(inertiaTensor(i, i)) < OpenMD::epsilon) { |
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|
linear_ = true; |
| 60 |
|
linearAxis_ = i; |
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++ nLinearAxis; |
| 65 |
|
if (nLinearAxis > 1) { |
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sprintf( painCave.errMsg, |
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|
"Directional Atom warning.\n" |
| 68 |
< |
"\tOOPSE found more than one axis in this directional atom with a vanishing \n" |
| 68 |
> |
"\tOpenMD found more than one axis in this directional atom with a vanishing \n" |
| 69 |
|
"\tmoment of inertia."); |
| 70 |
|
painCave.isFatal = 0; |
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|
simError(); |
| 134 |
|
ephi[1] = 0.0; |
| 135 |
|
ephi[2] = 1.0; |
| 136 |
|
|
| 137 |
+ |
//etheta[0] = -sphi; |
| 138 |
+ |
//etheta[1] = cphi; |
| 139 |
+ |
//etheta[2] = 0.0; |
| 140 |
+ |
|
| 141 |
|
etheta[0] = cphi; |
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|
etheta[1] = sphi; |
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|
etheta[2] = 0.0; |
