| 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, 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 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include "constraints/Rattle.hpp" |
| 44 |
|
#include "primitives/Molecule.hpp" |
| 45 |
|
#include "utils/simError.h" |
| 46 |
< |
namespace oopse { |
| 46 |
> |
namespace OpenMD { |
| 47 |
|
|
| 48 |
|
Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6) { |
| 49 |
|
|
| 161 |
|
|
| 162 |
|
currentSnapshot_->wrapVector(pab); |
| 163 |
|
|
| 164 |
< |
double pabsq = pab.lengthSquare(); |
| 164 |
> |
RealType pabsq = pab.lengthSquare(); |
| 165 |
|
|
| 166 |
< |
double rabsq = consPair->getConsDistSquare(); |
| 167 |
< |
double diffsq = rabsq - pabsq; |
| 166 |
> |
RealType rabsq = consPair->getConsDistSquare(); |
| 167 |
> |
RealType diffsq = rabsq - pabsq; |
| 168 |
|
|
| 169 |
|
// the original rattle code from alan tidesley |
| 170 |
|
if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){ |
| 176 |
|
|
| 177 |
|
currentSnapshot_->wrapVector(rab); |
| 178 |
|
|
| 179 |
< |
double rpab = dot(rab, pab); |
| 180 |
< |
double rpabsq = rpab * rpab; |
| 179 |
> |
RealType rpab = dot(rab, pab); |
| 180 |
> |
RealType rpabsq = rpab * rpab; |
| 181 |
|
|
| 182 |
|
if (rpabsq < (rabsq * -diffsq)){ |
| 183 |
|
return consFail; |
| 184 |
|
} |
| 185 |
|
|
| 186 |
< |
double rma = 1.0 / consElem1->getMass(); |
| 187 |
< |
double rmb = 1.0 / consElem2->getMass(); |
| 186 |
> |
RealType rma = 1.0 / consElem1->getMass(); |
| 187 |
> |
RealType rmb = 1.0 / consElem2->getMass(); |
| 188 |
|
|
| 189 |
< |
double gab = diffsq / (2.0 * (rma + rmb) * rpab); |
| 189 |
> |
RealType gab = diffsq / (2.0 * (rma + rmb) * rpab); |
| 190 |
|
|
| 191 |
|
Vector3d delta = rab * gab; |
| 192 |
|
|
| 235 |
|
|
| 236 |
|
currentSnapshot_->wrapVector(rab); |
| 237 |
|
|
| 238 |
< |
double rma = 1.0 / consElem1->getMass(); |
| 239 |
< |
double rmb = 1.0 / consElem2->getMass(); |
| 238 |
> |
RealType rma = 1.0 / consElem1->getMass(); |
| 239 |
> |
RealType rmb = 1.0 / consElem2->getMass(); |
| 240 |
|
|
| 241 |
< |
double rvab = dot(rab, dv); |
| 241 |
> |
RealType rvab = dot(rab, dv); |
| 242 |
|
|
| 243 |
< |
double gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare()); |
| 243 |
> |
RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare()); |
| 244 |
|
|
| 245 |
|
if (fabs(gab) > consTolerance_){ |
| 246 |
|
Vector3d delta = rab * gab; |
