| 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 |
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* 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). |
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*/ |
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|
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|
#include "hydrodynamics/HydroProp.hpp" |
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|
#include "utils/StringTokenizer.hpp" |
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|
#include "math/CholeskyDecomposition.hpp" |
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|
|
| 47 |
< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
|
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< |
HydroProp::HydroProp(){ |
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< |
hasCOR = false; |
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< |
hasXi = false; |
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> |
HydroProp::HydroProp() : hasCOR(false), hasXi(false) { |
| 50 |
|
} |
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|
|
| 52 |
< |
HydroProp::HydroProp(Vector3d cor, Mat6x6d Xi, Mat6x6d D) : cor_(cor), Xi_(Xi), D_(D){ |
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< |
hasCOR = true; |
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< |
hasXi = true; |
| 52 |
> |
HydroProp::HydroProp(Vector3d cor, Mat6x6d Xi, Mat6x6d D) : cor_(cor), |
| 53 |
> |
Xi_(Xi), D_(D), |
| 54 |
> |
hasCOR(true), |
| 55 |
> |
hasXi(true) { |
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|
} |
| 57 |
|
|
| 58 |
< |
HydroProp::HydroProp(const std::string frictionLine) { |
| 58 |
> |
HydroProp::HydroProp(const std::string &frictionLine) : hasCOR(false), |
| 59 |
> |
hasXi(false) { |
| 60 |
|
|
| 61 |
|
StringTokenizer tokenizer(frictionLine); |
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|
if (tokenizer.countTokens() >= 40) { |
| 65 |
|
cor_[1] = tokenizer.nextTokenAsDouble(); |
| 66 |
|
cor_[2] = tokenizer.nextTokenAsDouble(); |
| 67 |
|
|
| 68 |
+ |
hasCOR = true; |
| 69 |
+ |
|
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|
Xitt_(0,0) = tokenizer.nextTokenAsDouble(); |
| 71 |
|
Xitt_(0,1) = tokenizer.nextTokenAsDouble(); |
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Xitt_(0,2) = tokenizer.nextTokenAsDouble(); |
| 112 |
|
Xi_.setSubMatrix(3, 0, Xitr_); |
| 113 |
|
Xi_.setSubMatrix(3, 3, Xirr_); |
| 114 |
|
|
| 115 |
+ |
hasXi = true; |
| 116 |
+ |
|
| 117 |
|
CholeskyDecomposition(Xi_, S_); |
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|
|
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|
} |
