| 6 |
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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: |
| 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 |
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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 |
|
* 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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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/** |
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#include <math/Vector3.hpp> |
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#include <math/SquareMatrix3.hpp> |
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|
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< |
namespace oopse { |
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> |
using namespace std; |
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> |
namespace OpenMD { |
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/** |
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* @class DataStorage |
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* @warning do not try to insert element into (or ease element from) private member data |
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* of DataStorage directly. |
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< |
* @todo DataStorage may need refactoring. Every std::vector can inherit from the same base class |
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> |
* @todo DataStorage may need refactoring. Every vector can inherit from the same base class |
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* which will make it easy to maintain |
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*/ |
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class DataStorage { |
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enum{ |
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|
dslPosition = 1, |
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|
dslVelocity = 2, |
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< |
dslAmat = 4, |
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< |
dslAngularMomentum = 8, |
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< |
dslElectroFrame = 16, |
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< |
dslZAngle = 32, |
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< |
dslForce = 64, |
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< |
dslTorque = 128, |
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< |
dslParticlePot = 256 |
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> |
dslForce = 4, |
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> |
dslAmat = 8, |
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> |
dslAngularMomentum = 16, |
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> |
dslTorque = 32, |
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> |
dslParticlePot = 64, |
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> |
dslDensity = 128, |
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> |
dslFunctional = 256, |
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> |
dslFunctionalDerivative = 512, |
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> |
dslDipole = 1024, |
| 81 |
> |
dslQuadrupole = 2048, |
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> |
dslElectricField = 4096, |
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> |
dslSkippedCharge = 8192, |
| 84 |
> |
dslFlucQPosition = 16384, |
| 85 |
> |
dslFlucQVelocity = 32768, |
| 86 |
> |
dslFlucQForce = 65536, |
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> |
dslSitePotential = 131072 |
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|
}; |
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|
|
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– |
|
| 90 |
|
DataStorage(); |
| 91 |
< |
DataStorage(int size, int storageLayout = 511); |
| 91 |
> |
DataStorage(int size, int storageLayout = 0); |
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/** return the size of this DataStorage. */ |
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int getSize(); |
| 94 |
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/** |
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* Changes the size of this DataStorage. |
| 96 |
< |
* @param size new size of this DataStorage |
| 96 |
> |
* @param newSize new size of this DataStorage |
| 97 |
|
*/ |
| 98 |
|
void resize(int newSize); |
| 99 |
|
/** |
| 100 |
< |
* Reallocates memory manually. The main reason for using reserve() is efficiency |
| 101 |
< |
* if you know the capacity to which your std::vector must eventually grow, then it is usually more |
| 102 |
< |
* efficient to allocate that memory all at once. |
| 100 |
> |
* Reallocates memory manually. |
| 101 |
> |
* |
| 102 |
> |
* The main reason for using reserve() is efficiency if you know |
| 103 |
> |
* the capacity to which your vector must eventually grow, |
| 104 |
> |
* then it is usually more efficient to allocate that memory all |
| 105 |
> |
* at once. |
| 106 |
|
*/ |
| 107 |
|
void reserve(int size); |
| 108 |
|
/** |
| 109 |
|
* Copies data inside DataStorage class. |
| 110 |
< |
* Copy function actually call std::copy for every std::vector in DataStorage class. |
| 111 |
< |
* One Precondition of std::copy is that target is not within the range [soruce, soruce + num] |
| 112 |
< |
* @param souce |
| 110 |
> |
* |
| 111 |
> |
* Copy function actually calls copy for every vector in |
| 112 |
> |
* DataStorage class. One Precondition of copy is that |
| 113 |
> |
* target is not within the range [source, soruce + num] |
| 114 |
> |
* |
| 115 |
> |
* @param source |
| 116 |
|
* @param num number of element to be moved |
| 117 |
|
* @param target |
| 118 |
|
*/ |
| 124 |
|
/** Returns the pointer of internal array */ |
| 125 |
|
RealType *getArrayPointer(int whichArray); |
| 126 |
|
|
| 127 |
< |
std::vector<Vector3d> position; /** position array */ |
| 128 |
< |
std::vector<Vector3d> velocity; /** velocity array */ |
| 129 |
< |
std::vector<RotMat3x3d> aMat; /** rotation matrix array */ |
| 130 |
< |
std::vector<Vector3d> angularMomentum;/** angular momentum array (body-fixed) */ |
| 131 |
< |
std::vector<Mat3x3d> electroFrame; /** the lab frame unit std::vector array*/ |
| 132 |
< |
std::vector<RealType> zAngle; /** z -angle array */ |
| 133 |
< |
std::vector<Vector3d> force; /** force array */ |
| 134 |
< |
std::vector<Vector3d> torque; /** torque array */ |
| 135 |
< |
std::vector<RealType> particlePot; /** pair potential arrray */ |
| 127 |
> |
vector<Vector3d> position; /** position array */ |
| 128 |
> |
vector<Vector3d> velocity; /** velocity array */ |
| 129 |
> |
vector<Vector3d> force; /** force array */ |
| 130 |
> |
vector<RotMat3x3d> aMat; /** rotation matrix array */ |
| 131 |
> |
vector<Vector3d> angularMomentum; /** angular momentum array (body-fixed) */ |
| 132 |
> |
vector<Vector3d> torque; /** torque array */ |
| 133 |
> |
vector<RealType> particlePot; /** particle potential arrray */ |
| 134 |
> |
vector<RealType> density; /** electron density */ |
| 135 |
> |
vector<RealType> functional; /** density functional */ |
| 136 |
> |
vector<RealType> functionalDerivative; /** derivative of functional */ |
| 137 |
> |
vector<Vector3d> dipole; /** space-frame dipole vector */ |
| 138 |
> |
vector<Mat3x3d> quadrupole; /** space-frame quadrupole tensor */ |
| 139 |
> |
vector<Vector3d> electricField; /** local electric field */ |
| 140 |
> |
vector<RealType> skippedCharge; /** charge skipped during normal pairwise calculation */ |
| 141 |
> |
vector<RealType> flucQPos; /** fluctuating charges */ |
| 142 |
> |
vector<RealType> flucQVel; /** fluctuating charge velocities */ |
| 143 |
> |
vector<RealType> flucQFrc; /** fluctuating charge forces */ |
| 144 |
> |
vector<RealType> sitePotential; /** electrostatic site potentials */ |
| 145 |
|
|
| 146 |
|
static int getBytesPerStuntDouble(int layout); |
| 147 |
|
|
| 148 |
|
private: |
| 149 |
|
|
| 150 |
< |
RealType* internalGetArrayPointer(std::vector<Vector3d>& v); |
| 150 |
> |
RealType* internalGetArrayPointer(vector<Vector3d>& v); |
| 151 |
> |
RealType* internalGetArrayPointer(vector<Mat3x3d>& v); |
| 152 |
> |
RealType* internalGetArrayPointer(vector<RealType>& v); |
| 153 |
|
|
| 127 |
– |
RealType* internalGetArrayPointer(std::vector<RotMat3x3d>& v); |
| 128 |
– |
RealType* internalGetArrayPointer(std::vector<RealType>& v); |
| 129 |
– |
|
| 130 |
– |
|
| 154 |
|
template<typename T> |
| 155 |
|
void internalResize(std::vector<T>& v, int newSize); |
| 156 |
|
|
