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
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	tim	155	*
4	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	155	*/
42	gezelter	246
43	tim	155	/**
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	gezelter	1782	using namespace std;
58	gezelter	1390	namespace OpenMD {
59	gezelter	507	/**
60			* @class DataStorage
61			* @warning do not try to insert element into (or ease element from) private member data
62			* of DataStorage directly.
63	gezelter	1782	* @todo DataStorage may need refactoring. Every vector can inherit from the same base class
64	gezelter	507	* which will make it easy to maintain
65			*/
66			class DataStorage {
67			public:
68	tim	155
69	gezelter	507	enum{
70			dslPosition = 1,
71			dslVelocity = 2,
72	gezelter	1879	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	gezelter	1993	dslFlucQForce = 65536,
87			dslSitePotential = 131072
88	gezelter	507	};
89	tim	155
90	gezelter	507	DataStorage();
91	gezelter	1782	DataStorage(int size, int storageLayout = 0);
92	gezelter	507	/** return the size of this DataStorage. */
93			int getSize();
94			/**
95			* Changes the size of this DataStorage.
96	gezelter	1879	* @param newSize new size of this DataStorage
97	gezelter	507	*/
98			void resize(int newSize);
99			/**
100	gezelter	1782	* 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	gezelter	507	*/
107			void reserve(int size);
108			/**
109			* Copies data inside DataStorage class.
110	gezelter	1782	*
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	gezelter	507	* @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	tim	963	RealType *getArrayPointer(int whichArray);
126	gezelter	246
127	gezelter	1782	vector<Vector3d> position; /** position array */
128			vector<Vector3d> velocity; /** velocity array */
129	gezelter	1879	vector<Vector3d> force; /** force array */
130	gezelter	1782	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	gezelter	1879	vector<Vector3d> dipole; /** space-frame dipole vector */
138			vector<Mat3x3d> quadrupole; /** space-frame quadrupole tensor */
139	gezelter	1782	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	gezelter	1993	vector<RealType> sitePotential; /** electrostatic site potentials */
145	gezelter	246
146	gezelter	507	static int getBytesPerStuntDouble(int layout);
147	tim	323
148	gezelter	507	private:
149	tim	155
150	gezelter	1879	RealType* internalGetArrayPointer(vector<Vector3d>& v);
151			RealType* internalGetArrayPointer(vector<Mat3x3d>& v);
152	gezelter	1782	RealType* internalGetArrayPointer(vector<RealType>& v);
153	tim	155
154	gezelter	507	template<typename T>
155			void internalResize(std::vector<T>& v, int newSize);
156	tim	155
157	gezelter	507	template<typename T>
158			void internalCopy(std::vector<T>& v, int source, int num, int target);
159	tim	155
160	gezelter	507	int size_;
161			int storageLayout_;
162	gezelter	246
163	gezelter	507	};
164	tim	155
165	tim	323	}
166	tim	155	#endif //BRAINS_DATASTORAGE_HPP