| 71 |
|
RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info), |
| 72 |
|
evaluatorA_(info), seleManA_(info), |
| 73 |
|
commonA_(info), evaluatorB_(info), |
| 74 |
< |
seleManB_(info), commonB_(info), |
| 74 |
> |
seleManB_(info), commonB_(info), |
| 75 |
> |
hasData_(false), |
| 76 |
|
usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) { |
| 77 |
|
|
| 78 |
|
trialCount_ = 0; |
| 604 |
|
#ifdef IS_MPI |
| 605 |
|
} |
| 606 |
|
#endif |
| 607 |
+ |
|
| 608 |
+ |
// delete all of the objects we created: |
| 609 |
+ |
delete areaAccumulator_; |
| 610 |
+ |
data_.clear(); |
| 611 |
|
} |
| 612 |
|
|
| 613 |
|
void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) { |
| 1735 |
|
int isd; |
| 1736 |
|
StuntDouble* sd; |
| 1737 |
|
vector<StuntDouble*> aSites; |
| 1733 |
– |
ConvexHull* surfaceMeshA = new ConvexHull(); |
| 1738 |
|
seleManA_.setSelectionSet(evaluatorA_.evaluate()); |
| 1739 |
|
for (sd = seleManA_.beginSelected(isd); sd != NULL; |
| 1740 |
|
sd = seleManA_.nextSelected(isd)) { |
| 1741 |
|
aSites.push_back(sd); |
| 1742 |
|
} |
| 1743 |
< |
|
| 1743 |
> |
ConvexHull* surfaceMeshA = new ConvexHull(); |
| 1744 |
|
surfaceMeshA->computeHull(aSites); |
| 1745 |
|
areaA = surfaceMeshA->getArea(); |
| 1746 |
+ |
delete surfaceMeshA; |
| 1747 |
+ |
|
| 1748 |
|
} else { |
| 1749 |
|
if (usePeriodicBoundaryConditions_) { |
| 1750 |
|
// in periodic boundaries, the surface area is twice the x-y |
| 1764 |
|
int isd; |
| 1765 |
|
StuntDouble* sd; |
| 1766 |
|
vector<StuntDouble*> bSites; |
| 1761 |
– |
|
| 1767 |
|
seleManB_.setSelectionSet(evaluatorB_.evaluate()); |
| 1763 |
– |
|
| 1768 |
|
for (sd = seleManB_.beginSelected(isd); sd != NULL; |
| 1769 |
|
sd = seleManB_.nextSelected(isd)) { |
| 1770 |
|
bSites.push_back(sd); |
| 1771 |
|
} |
| 1772 |
< |
|
| 1769 |
< |
ConvexHull* surfaceMeshB = new ConvexHull(); |
| 1770 |
< |
|
| 1772 |
> |
ConvexHull* surfaceMeshB = new ConvexHull(); |
| 1773 |
|
surfaceMeshB->computeHull(bSites); |
| 1774 |
|
areaB = surfaceMeshB->getArea(); |
| 1775 |
+ |
delete surfaceMeshB; |
| 1776 |
+ |
|
| 1777 |
|
} else { |
| 1778 |
|
if (usePeriodicBoundaryConditions_) { |
| 1779 |
|
// in periodic boundaries, the surface area is twice the x-y |
| 2013 |
|
} |
| 2014 |
|
} |
| 2015 |
|
} |
| 2016 |
+ |
hasData_ = true; |
| 2017 |
|
} |
| 2018 |
|
|
| 2019 |
|
void RNEMD::getStarted() { |
| 2046 |
|
|
| 2047 |
|
void RNEMD::writeOutputFile() { |
| 2048 |
|
if (!doRNEMD_) return; |
| 2049 |
+ |
if (!hasData_) return; |
| 2050 |
|
|
| 2051 |
|
#ifdef IS_MPI |
| 2052 |
|
// If we're the root node, should we print out the results |
| 2068 |
|
RealType time = currentSnap_->getTime(); |
| 2069 |
|
RealType avgArea; |
| 2070 |
|
areaAccumulator_->getAverage(avgArea); |
| 2071 |
< |
RealType Jz = kineticExchange_ / (time * avgArea) |
| 2072 |
< |
/ PhysicalConstants::energyConvert; |
| 2073 |
< |
Vector3d JzP = momentumExchange_ / (time * avgArea); |
| 2074 |
< |
Vector3d JzL = angularMomentumExchange_ / (time * avgArea); |
| 2071 |
> |
|
| 2072 |
> |
RealType Jz(0.0); |
| 2073 |
> |
Vector3d JzP(V3Zero); |
| 2074 |
> |
Vector3d JzL(V3Zero); |
| 2075 |
> |
if (time >= info_->getSimParams()->getDt()) { |
| 2076 |
> |
Jz = kineticExchange_ / (time * avgArea) |
| 2077 |
> |
/ PhysicalConstants::energyConvert; |
| 2078 |
> |
JzP = momentumExchange_ / (time * avgArea); |
| 2079 |
> |
JzL = angularMomentumExchange_ / (time * avgArea); |
| 2080 |
> |
} |
| 2081 |
|
|
| 2082 |
|
rnemdFile_ << "#######################################################\n"; |
| 2083 |
|
rnemdFile_ << "# RNEMD {\n"; |
