| 873 |
|
|
| 874 |
|
// Setup number of neighbors in neighbor list if present |
| 875 |
|
if (simParams_->haveNeighborListNeighbors()) { |
| 876 |
< |
setNeighbors(simParams_->getNeighborListNeighbors()); |
| 876 |
> |
int nlistNeighbors = simParams_->getNeighborListNeighbors(); |
| 877 |
> |
setNeighbors(&nlistNeighbors); |
| 878 |
|
} |
| 879 |
|
|
| 880 |
|
|
| 1454 |
|
|
| 1455 |
|
void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) { |
| 1456 |
|
IOIndexToIntegrableObject= v; |
| 1457 |
+ |
} |
| 1458 |
+ |
|
| 1459 |
+ |
/* Returns the Volume of the simulation based on a ellipsoid with semi-axes |
| 1460 |
+ |
based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3 |
| 1461 |
+ |
where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to |
| 1462 |
+ |
V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536. |
| 1463 |
+ |
*/ |
| 1464 |
+ |
void SimInfo::getGyrationalVolume(RealType &volume){ |
| 1465 |
+ |
Mat3x3d intTensor; |
| 1466 |
+ |
RealType det; |
| 1467 |
+ |
Vector3d dummyAngMom; |
| 1468 |
+ |
RealType sysconstants; |
| 1469 |
+ |
RealType geomCnst; |
| 1470 |
+ |
|
| 1471 |
+ |
geomCnst = 3.0/2.0; |
| 1472 |
+ |
/* Get the inertial tensor and angular momentum for free*/ |
| 1473 |
+ |
getInertiaTensor(intTensor,dummyAngMom); |
| 1474 |
+ |
|
| 1475 |
+ |
det = intTensor.determinant(); |
| 1476 |
+ |
sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
| 1477 |
+ |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det); |
| 1478 |
+ |
return; |
| 1479 |
|
} |
| 1480 |
|
|
| 1481 |
+ |
void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){ |
| 1482 |
+ |
Mat3x3d intTensor; |
| 1483 |
+ |
Vector3d dummyAngMom; |
| 1484 |
+ |
RealType sysconstants; |
| 1485 |
+ |
RealType geomCnst; |
| 1486 |
+ |
|
| 1487 |
+ |
geomCnst = 3.0/2.0; |
| 1488 |
+ |
/* Get the inertial tensor and angular momentum for free*/ |
| 1489 |
+ |
getInertiaTensor(intTensor,dummyAngMom); |
| 1490 |
+ |
|
| 1491 |
+ |
detI = intTensor.determinant(); |
| 1492 |
+ |
sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_; |
| 1493 |
+ |
volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI); |
| 1494 |
+ |
return; |
| 1495 |
+ |
} |
| 1496 |
|
/* |
| 1497 |
|
void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) { |
| 1498 |
|
assert( v.size() == nAtoms_ + nRigidBodies_); |
