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Comparing branches/development/src/brains/DataStorage.hpp (file contents):
Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC vs.
Revision 1711 by gezelter, Sat May 19 02:58:35 2012 UTC

# Line 54 | Line 54
54   #include <math/Vector3.hpp>
55   #include <math/SquareMatrix3.hpp>
56  
57 + using namespace std;
58   namespace OpenMD {
59    /**
60     * @class DataStorage
# Line 71 | Line 72 | namespace OpenMD {
72        dslAmat = 4,
73        dslAngularMomentum = 8,
74        dslElectroFrame = 16,
75 <      dslZAngle = 32,
76 <      dslForce = 64,
77 <      dslTorque = 128,
78 <      dslParticlePot = 256,
79 <      dslDensity = 512,
80 <      dslFunctional = 1024,
81 <      dslFunctionalDerivative = 2048,
82 <      dslElectricField = 4096,
83 <      dslSkippedCharge = 8192
75 >      dslForce = 32,
76 >      dslTorque = 64,
77 >      dslParticlePot = 128,
78 >      dslDensity = 256,
79 >      dslFunctional = 512,
80 >      dslFunctionalDerivative = 1024,
81 >      dslElectricField = 2048,
82 >      dslSkippedCharge = 4096,
83 >      dslFlucQPosition = 8192,
84 >      dslFlucQVelocity = 16384,
85 >      dslFlucQForce = 32768
86      };
87  
88      DataStorage();
89 <    DataStorage(int size, int storageLayout = 16383);
89 >    DataStorage(int size, int storageLayout = 0);
90      /** return the size of this DataStorage. */
91      int getSize();
92      /**
# Line 103 | Line 106 | namespace OpenMD {
106      /**
107       * Copies data inside DataStorage class.
108       *
109 <     * Copy function actually call copy for every vector in
109 >     * Copy function actually calls copy for every vector in
110       * DataStorage class.  One Precondition of copy is that
111       * target is not within the range [source, soruce + num]
112       *
113 <     * @param souce
113 >     * @param source
114       * @param num number of element to be moved
115       * @param target
116       */
# Line 119 | Line 122 | namespace OpenMD {
122      /** Returns the pointer of internal array */
123      RealType *getArrayPointer(int whichArray);
124  
125 <    std::vector<Vector3d> position;        /** position array */
126 <    std::vector<Vector3d> velocity;        /** velocity array */
127 <    std::vector<RotMat3x3d> aMat;          /** rotation matrix array */
128 <    std::vector<Vector3d> angularMomentum; /** angular momentum array (body-fixed) */
129 <    std::vector<Mat3x3d> electroFrame;     /** the lab frame unit std::vector array*/
130 <    std::vector<RealType> zAngle;          /** z-angle array */        
131 <    std::vector<Vector3d> force;           /** force array */
132 <    std::vector<Vector3d> torque;          /** torque array */
133 <    std::vector<RealType> particlePot;     /** particle potential arrray */
134 <    std::vector<RealType> density;         /** electron density */
135 <    std::vector<RealType> functional;      /** density functional */
136 <    std::vector<RealType> functionalDerivative; /** derivative of functional */
137 <    std::vector<Vector3d> electricField;   /** local electric field */
138 <    std::vector<RealType> skippedCharge;   /** charge skipped during normal pairwise calculation */
125 >    vector<Vector3d> position;        /** position array */
126 >    vector<Vector3d> velocity;        /** velocity array */
127 >    vector<RotMat3x3d> aMat;          /** rotation matrix array */
128 >    vector<Vector3d> angularMomentum; /** angular momentum array (body-fixed) */
129 >    vector<Mat3x3d> electroFrame;     /** the lab frame unit vector array*/
130 >    vector<Vector3d> force;           /** force array */
131 >    vector<Vector3d> torque;          /** torque array */
132 >    vector<RealType> particlePot;     /** particle potential arrray */
133 >    vector<RealType> density;         /** electron density */
134 >    vector<RealType> functional;      /** density functional */
135 >    vector<RealType> functionalDerivative; /** derivative of functional */
136 >    vector<Vector3d> electricField;   /** local electric field */
137 >    vector<RealType> skippedCharge;   /** charge skipped during normal pairwise calculation */
138 >    vector<RealType> flucQPos;        /** fluctuating charges */
139 >    vector<RealType> flucQVel;        /** fluctuating charge velocities */
140 >    vector<RealType> flucQFrc;        /** fluctuating charge forces */
141  
142      static int getBytesPerStuntDouble(int layout);
143  
144    private:
145  
146 <    RealType* internalGetArrayPointer(std::vector<Vector3d>& v);            
147 <    RealType* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
148 <    RealType* internalGetArrayPointer(std::vector<RealType>& v);
146 >    RealType* internalGetArrayPointer(vector<Vector3d>& v);            
147 >    RealType* internalGetArrayPointer(vector<RotMat3x3d>& v);
148 >    RealType* internalGetArrayPointer(vector<RealType>& v);
149  
150              
151      template<typename T>

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