src/brains/DataStorage.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @file Vector.hpp
 * @author Teng Lin
 * @date 09/14/2004
 * @version 1.0
 */

#ifndef BRAINS_DATASTORAGE_HPP
#define BRAINS_DATASTORAGE_HPP

#include <vector>
#include <math/Vector3.hpp>
#include <math/SquareMatrix3.hpp>

using namespace std;
namespace OpenMD {
  /**
   * @class DataStorage
   * @warning do not try to insert element into (or ease element from) private member data 
   * of DataStorage directly.
   * @todo DataStorage may need refactoring. Every vector can inherit from the same base class
   * which will make it easy to maintain
   */
  class DataStorage {
  public:

    enum{
      dslPosition = 1,
      dslVelocity = 2,
      dslForce = 4, 
      dslAmat = 8, 
      dslAngularMomentum = 16,
      dslTorque = 32,
      dslParticlePot = 64,
      dslDensity = 128,
      dslFunctional = 256,
      dslFunctionalDerivative = 512,
      dslDipole = 1024,
      dslQuadrupole = 2048,
      dslElectricField = 4096,
      dslSkippedCharge = 8192,
      dslFlucQPosition = 16384,
      dslFlucQVelocity = 32768,
      dslFlucQForce = 65536,
      dslSitePotential = 131072
    };

    DataStorage();
    DataStorage(int size, int storageLayout = 0);
    /** return the size of this DataStorage. */
    int getSize();
    /**
     * Changes the size of this DataStorage.
     * @param newSize new size of this DataStorage
     */
    void resize(int newSize);
    /**
     * Reallocates memory manually. 
     *
     * The main reason for using reserve() is efficiency if you know
     * the capacity to which your vector must eventually grow,
     * then it is usually more efficient to allocate that memory all
     * at once.
     */
    void reserve(int size);
    /**
     * Copies data inside DataStorage class.
     *
     * Copy function actually calls copy for every vector in
     * DataStorage class.  One Precondition of copy is that
     * target is not within the range [source, soruce + num]
     *
     * @param source 
     * @param num number of element to be moved
     * @param target
     */
    void copy(int source, int num, int target);
    /** Returns the storage layout  */
    int getStorageLayout();
    /** Sets the storage layout  */
    void setStorageLayout(int layout);
    /** Returns the pointer of internal array */
    RealType *getArrayPointer(int whichArray);

    vector<Vector3d> position;        /** position array */
    vector<Vector3d> velocity;        /** velocity array */
    vector<Vector3d> force;           /** force array */
    vector<RotMat3x3d> aMat;          /** rotation matrix array */
    vector<Vector3d> angularMomentum; /** angular momentum array (body-fixed) */
    vector<Vector3d> torque;          /** torque array */
    vector<RealType> particlePot;     /** particle potential arrray */
    vector<RealType> density;         /** electron density */
    vector<RealType> functional;      /** density functional */
    vector<RealType> functionalDerivative; /** derivative of functional */
    vector<Vector3d> dipole;          /** space-frame dipole vector */
    vector<Mat3x3d>  quadrupole;      /** space-frame quadrupole tensor */
    vector<Vector3d> electricField;   /** local electric field */
    vector<RealType> skippedCharge;   /** charge skipped during normal pairwise calculation */
    vector<RealType> flucQPos;        /** fluctuating charges */
    vector<RealType> flucQVel;        /** fluctuating charge velocities */
    vector<RealType> flucQFrc;        /** fluctuating charge forces */
    vector<RealType> sitePotential;   /** electrostatic site potentials */

    static int getBytesPerStuntDouble(int layout);

  private:

    RealType* internalGetArrayPointer(vector<Vector3d>& v);
    RealType* internalGetArrayPointer(vector<Mat3x3d>& v);
    RealType* internalGetArrayPointer(vector<RealType>& v);
            
    template<typename T>
    void internalResize(std::vector<T>& v, int newSize);

    template<typename T>
    void internalCopy(std::vector<T>& v, int source,  int num, int target);
            
    int size_;
    int storageLayout_;

  };

}
#endif //BRAINS_DATASTORAGE_HPP
Revision:	1993
Committed:	Tue Apr 29 17:32:31 2014 UTC (11 years ago) by gezelter
File size:	6292 byte(s)
Log Message:	Added sitePotentials for the Choi et al. potential-frequency maps for nitriles
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* 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).
41	*/
42
43	/**
44	* @file Vector.hpp
45	* @author Teng Lin
46	* @date 09/14/2004
47	* @version 1.0
48	*/
49
50	#ifndef BRAINS_DATASTORAGE_HPP
51	#define BRAINS_DATASTORAGE_HPP
52
53	#include <vector>
54	#include <math/Vector3.hpp>
55	#include <math/SquareMatrix3.hpp>
56
57	using namespace std;
58	namespace OpenMD {
59	/**
60	* @class DataStorage
61	* @warning do not try to insert element into (or ease element from) private member data
62	* of DataStorage directly.
63	* @todo DataStorage may need refactoring. Every vector can inherit from the same base class
64	* which will make it easy to maintain
65	*/
66	class DataStorage {
67	public:
68
69	enum{
70	dslPosition = 1,
71	dslVelocity = 2,
72	dslForce = 4,
73	dslAmat = 8,
74	dslAngularMomentum = 16,
75	dslTorque = 32,
76	dslParticlePot = 64,
77	dslDensity = 128,
78	dslFunctional = 256,
79	dslFunctionalDerivative = 512,
80	dslDipole = 1024,
81	dslQuadrupole = 2048,
82	dslElectricField = 4096,
83	dslSkippedCharge = 8192,
84	dslFlucQPosition = 16384,
85	dslFlucQVelocity = 32768,
86	dslFlucQForce = 65536,
87	dslSitePotential = 131072
88	};
89
90	DataStorage();
91	DataStorage(int size, int storageLayout = 0);
92	/** return the size of this DataStorage. */
93	int getSize();
94	/**
95	* Changes the size of this DataStorage.
96	* @param newSize new size of this DataStorage
97	*/
98	void resize(int newSize);
99	/**
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	*
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	*/
119	void copy(int source, int num, int target);
120	/** Returns the storage layout */
121	int getStorageLayout();
122	/** Sets the storage layout */
123	void setStorageLayout(int layout);
124	/** Returns the pointer of internal array */
125	RealType *getArrayPointer(int whichArray);
126
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(vector<Vector3d>& v);
151	RealType* internalGetArrayPointer(vector<Mat3x3d>& v);
152	RealType* internalGetArrayPointer(vector<RealType>& v);
153
154	template<typename T>
155	void internalResize(std::vector<T>& v, int newSize);
156
157	template<typename T>
158	void internalCopy(std::vector<T>& v, int source, int num, int target);
159
160	int size_;
161	int storageLayout_;
162
163	};
164
165	}
166	#endif //BRAINS_DATASTORAGE_HPP