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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
| 12 |
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* the article in which the program was described (Matthew |
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< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
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< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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< |
* |
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* 2. Redistributions of source code must retain the above copyright |
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> |
* 1. Redistributions of source code must retain the above copyright |
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|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
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* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
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* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
| 29 |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
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+ |
* |
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+ |
* 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). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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+ |
* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include "constraints/Rattle.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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> |
namespace OpenMD { |
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|
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Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6) { |
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|
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|
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currentSnapshot_->wrapVector(pab); |
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|
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double pabsq = pab.lengthSquare(); |
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> |
RealType pabsq = pab.lengthSquare(); |
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|
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< |
double rabsq = consPair->getConsDistSquare(); |
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double diffsq = rabsq - pabsq; |
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> |
RealType rabsq = consPair->getConsDistSquare(); |
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> |
RealType diffsq = rabsq - pabsq; |
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|
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// the original rattle code from alan tidesley |
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if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){ |
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|
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currentSnapshot_->wrapVector(rab); |
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|
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< |
double rpab = dot(rab, pab); |
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< |
double rpabsq = rpab * rpab; |
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> |
RealType rpab = dot(rab, pab); |
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> |
RealType rpabsq = rpab * rpab; |
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|
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if (rpabsq < (rabsq * -diffsq)){ |
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return consFail; |
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} |
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|
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< |
double rma = 1.0 / consElem1->getMass(); |
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< |
double rmb = 1.0 / consElem2->getMass(); |
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> |
RealType rma = 1.0 / consElem1->getMass(); |
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> |
RealType rmb = 1.0 / consElem2->getMass(); |
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|
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< |
double gab = diffsq / (2.0 * (rma + rmb) * rpab); |
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> |
RealType gab = diffsq / (2.0 * (rma + rmb) * rpab); |
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|
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Vector3d delta = rab * gab; |
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|
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|
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currentSnapshot_->wrapVector(rab); |
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|
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< |
double rma = 1.0 / consElem1->getMass(); |
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< |
double rmb = 1.0 / consElem2->getMass(); |
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> |
RealType rma = 1.0 / consElem1->getMass(); |
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> |
RealType rmb = 1.0 / consElem2->getMass(); |
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|
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< |
double rvab = dot(rab, dv); |
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> |
RealType rvab = dot(rab, dv); |
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|
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< |
double gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare()); |
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> |
RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare()); |
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|
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if (fabs(gab) > consTolerance_){ |
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Vector3d delta = rab * gab; |
