| 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] Vardeman & Gezelter, in progress (2009). |
| 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 |
|
/** |
| 59 |
|
* @class DataStorage |
| 60 |
|
* @warning do not try to insert element into (or ease element from) private member data |
| 61 |
|
* of DataStorage directly. |
| 62 |
< |
* @todo DataStorage may need refactoring. Every std::vector can inherit from the same base class |
| 62 |
> |
* @todo DataStorage may need refactoring. Every vector can inherit from the same base class |
| 63 |
|
* which will make it easy to maintain |
| 64 |
|
*/ |
| 65 |
|
class DataStorage { |
| 78 |
|
dslDensity = 512, |
| 79 |
|
dslFunctional = 1024, |
| 80 |
|
dslFunctionalDerivative = 2048, |
| 81 |
< |
dslElectricField = 4096 |
| 81 |
> |
dslElectricField = 4096, |
| 82 |
> |
dslSkippedCharge = 8192 |
| 83 |
|
}; |
| 84 |
|
|
| 83 |
– |
|
| 85 |
|
DataStorage(); |
| 86 |
< |
DataStorage(int size, int storageLayout = 8191); |
| 86 |
> |
DataStorage(int size, int storageLayout = 16383); |
| 87 |
|
/** return the size of this DataStorage. */ |
| 88 |
|
int getSize(); |
| 89 |
|
/** |
| 95 |
|
* Reallocates memory manually. |
| 96 |
|
* |
| 97 |
|
* The main reason for using reserve() is efficiency if you know |
| 98 |
< |
* the capacity to which your std::vector must eventually grow, |
| 98 |
> |
* the capacity to which your vector must eventually grow, |
| 99 |
|
* then it is usually more efficient to allocate that memory all |
| 100 |
|
* at once. |
| 101 |
|
*/ |
| 103 |
|
/** |
| 104 |
|
* Copies data inside DataStorage class. |
| 105 |
|
* |
| 106 |
< |
* Copy function actually call std::copy for every std::vector in |
| 107 |
< |
* DataStorage class. One Precondition of std::copy is that |
| 108 |
< |
* target is not within the range [soruce, soruce + num] |
| 106 |
> |
* Copy function actually call copy for every vector in |
| 107 |
> |
* DataStorage class. One Precondition of copy is that |
| 108 |
> |
* target is not within the range [source, soruce + num] |
| 109 |
|
* |
| 110 |
|
* @param souce |
| 111 |
|
* @param num number of element to be moved |
| 122 |
|
std::vector<Vector3d> position; /** position array */ |
| 123 |
|
std::vector<Vector3d> velocity; /** velocity array */ |
| 124 |
|
std::vector<RotMat3x3d> aMat; /** rotation matrix array */ |
| 125 |
< |
std::vector<Vector3d> angularMomentum; /** angular momentum array |
| 126 |
< |
(body-fixed) */ |
| 126 |
< |
std::vector<Mat3x3d> electroFrame; /** the lab frame unit vector array*/ |
| 125 |
> |
std::vector<Vector3d> angularMomentum; /** angular momentum array (body-fixed) */ |
| 126 |
> |
std::vector<Mat3x3d> electroFrame; /** the lab frame unit std::vector array*/ |
| 127 |
|
std::vector<RealType> zAngle; /** z-angle array */ |
| 128 |
|
std::vector<Vector3d> force; /** force array */ |
| 129 |
|
std::vector<Vector3d> torque; /** torque array */ |
| 132 |
|
std::vector<RealType> functional; /** density functional */ |
| 133 |
|
std::vector<RealType> functionalDerivative; /** derivative of functional */ |
| 134 |
|
std::vector<Vector3d> electricField; /** local electric field */ |
| 135 |
+ |
std::vector<RealType> skippedCharge; /** charge skipped during normal pairwise calculation */ |
| 136 |
|
|
| 137 |
|
static int getBytesPerStuntDouble(int layout); |
| 138 |
|
|
