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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: |
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* |
| 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 |
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< |
* 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 |
< |
* |
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* 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 |
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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. |
| 28 |
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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. |
| 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). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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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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> |
Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6), doRattle_(false) { |
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|
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+ |
if (info_->getNConstraints() > 0) |
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+ |
doRattle_ = true; |
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+ |
|
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+ |
|
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if (info_->getSimParams()->haveDt()) { |
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dt_ = info_->getSimParams()->getDt(); |
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} else { |
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} |
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|
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void Rattle::constraintA() { |
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< |
if (info_->getNConstraints() > 0) { |
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< |
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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} |
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void Rattle::constraintB() { |
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< |
if (info_->getNConstraints() > 0) { |
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< |
doConstraint(&Rattle::constraintPairB); |
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} |
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> |
if (!doRattle_) return; |
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> |
doConstraint(&Rattle::constraintPairB); |
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} |
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|
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void Rattle::doConstraint(ConstraintPairFuncPtr func) { |
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if (!doRattle_) return; |
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|
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Molecule* mol; |
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SimInfo::MoleculeIterator mi; |
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ConstraintElem* consElem; |
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} |
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|
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int Rattle::constraintPairA(ConstraintPair* consPair){ |
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+ |
|
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ConstraintElem* consElem1 = consPair->getConsElem1(); |
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ConstraintElem* consElem2 = consPair->getConsElem2(); |
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|
| 166 |
|
|
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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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|
|
| 171 |
< |
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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|
|
| 174 |
|
// 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); |
| 183 |
|
|
| 184 |
< |
double rpab = dot(rab, pab); |
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< |
double rpabsq = rpab * rpab; |
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> |
RealType rpab = dot(rab, pab); |
| 185 |
> |
RealType rpabsq = rpab * rpab; |
| 186 |
|
|
| 187 |
|
if (rpabsq < (rabsq * -diffsq)){ |
| 188 |
|
return consFail; |
| 189 |
|
} |
| 190 |
|
|
| 191 |
< |
double rma = 1.0 / consElem1->getMass(); |
| 192 |
< |
double rmb = 1.0 / consElem2->getMass(); |
| 191 |
> |
RealType rma = 1.0 / consElem1->getMass(); |
| 192 |
> |
RealType rmb = 1.0 / consElem2->getMass(); |
| 193 |
|
|
| 194 |
< |
double gab = diffsq / (2.0 * (rma + rmb) * rpab); |
| 194 |
> |
RealType gab = diffsq / (2.0 * (rma + rmb) * rpab); |
| 195 |
|
|
| 196 |
|
Vector3d delta = rab * gab; |
| 197 |
|
|
| 240 |
|
|
| 241 |
|
currentSnapshot_->wrapVector(rab); |
| 242 |
|
|
| 243 |
< |
double rma = 1.0 / consElem1->getMass(); |
| 244 |
< |
double rmb = 1.0 / consElem2->getMass(); |
| 243 |
> |
RealType rma = 1.0 / consElem1->getMass(); |
| 244 |
> |
RealType rmb = 1.0 / consElem2->getMass(); |
| 245 |
|
|
| 246 |
< |
double rvab = dot(rab, dv); |
| 246 |
> |
RealType rvab = dot(rab, dv); |
| 247 |
|
|
| 248 |
< |
double gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare()); |
| 248 |
> |
RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare()); |
| 249 |
|
|
| 250 |
|
if (fabs(gab) > consTolerance_){ |
| 251 |
|
Vector3d delta = rab * gab; |
