| 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, 24107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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*/ |
| 42 |
|
|
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|
#include "constraints/Rattle.hpp" |
| 44 |
|
#include "primitives/Molecule.hpp" |
| 45 |
|
#include "utils/simError.h" |
| 46 |
< |
namespace oopse { |
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> |
namespace OpenMD { |
| 47 |
|
|
| 48 |
< |
Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6) { |
| 48 |
> |
Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6), doRattle_(false) { |
| 49 |
|
|
| 50 |
+ |
if (info_->getNConstraints() > 0) |
| 51 |
+ |
doRattle_ = true; |
| 52 |
+ |
|
| 53 |
+ |
|
| 54 |
|
if (info_->getSimParams()->haveDt()) { |
| 55 |
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dt_ = info_->getSimParams()->getDt(); |
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} else { |
| 64 |
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} |
| 65 |
|
|
| 66 |
|
void Rattle::constraintA() { |
| 67 |
< |
if (info_->getNConstraints() > 0) { |
| 68 |
< |
doConstraint(&Rattle::constraintPairA); |
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< |
} |
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> |
if (!doRattle_) return; |
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> |
doConstraint(&Rattle::constraintPairA); |
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} |
| 70 |
|
void Rattle::constraintB() { |
| 71 |
< |
if (info_->getNConstraints() > 0) { |
| 72 |
< |
doConstraint(&Rattle::constraintPairB); |
| 69 |
< |
} |
| 71 |
> |
if (!doRattle_) return; |
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> |
doConstraint(&Rattle::constraintPairB); |
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} |
| 74 |
|
|
| 75 |
|
void Rattle::doConstraint(ConstraintPairFuncPtr func) { |
| 76 |
+ |
if (!doRattle_) return; |
| 77 |
+ |
|
| 78 |
|
Molecule* mol; |
| 79 |
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SimInfo::MoleculeIterator mi; |
| 80 |
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ConstraintElem* consElem; |
| 153 |
|
} |
| 154 |
|
|
| 155 |
|
int Rattle::constraintPairA(ConstraintPair* consPair){ |
| 156 |
+ |
|
| 157 |
|
ConstraintElem* consElem1 = consPair->getConsElem1(); |
| 158 |
|
ConstraintElem* consElem2 = consPair->getConsElem2(); |
| 159 |
|
|
