src/brains/DataStorage.cpp

/*
 * 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, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @file DataStorage.cpp
 * @author tlin
 * @date 10/26/2004
 * @version 1.0
 */

#include "brains/DataStorage.hpp"
using namespace std;
namespace OpenMD {

  DataStorage::DataStorage() : size_(0), storageLayout_(0){

  }

  DataStorage::DataStorage(int size, int storageLayout) : size_(size){
    setStorageLayout(storageLayout);
    resize(size);
  }

  int DataStorage::getSize() {

    if (storageLayout_ & dslPosition && position.size() != size_) {
      //error
      cerr << "size does not match"<< endl;
    }

    if (storageLayout_ & dslVelocity && velocity.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslForce && force.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslAmat && aMat.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslTorque && torque.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslDensity && density.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslFunctional && functional.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslDipole && dipole.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslQuadrupole && quadrupole.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslElectricField && electricField.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslFlucQPosition && flucQPos.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslFlucQVelocity && flucQVel.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslFlucQForce && flucQFrc.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }
    
    return size_;

  }

  void DataStorage::resize(int newSize) {

    if (storageLayout_ & dslPosition) {
      internalResize(position, newSize);
    }

    if (storageLayout_ & dslVelocity) {
      internalResize(velocity, newSize);
    }

    if (storageLayout_ & dslForce) {
      internalResize(force, newSize);
    }

    if (storageLayout_ & dslAmat) {
      internalResize(aMat, newSize);
    }

    if (storageLayout_ & dslAngularMomentum) {
      internalResize(angularMomentum, newSize);
    }
    
    if (storageLayout_ & dslTorque) {
      internalResize(torque, newSize);
    }

    if (storageLayout_ & dslParticlePot) {
      internalResize(particlePot, newSize);
    }

    if (storageLayout_ & dslDensity) {
      internalResize(density, newSize);
    }

    if (storageLayout_ & dslFunctional) {
      internalResize(functional, newSize);
    }

    if (storageLayout_ & dslFunctionalDerivative) {
      internalResize(functionalDerivative, newSize);
    }

    if (storageLayout_ & dslDipole) {
      internalResize(dipole, newSize);
    }

    if (storageLayout_ & dslQuadrupole) {
      internalResize(quadrupole, newSize);
    }

    if (storageLayout_ & dslElectricField) {
      internalResize(electricField, newSize);
    }

    if (storageLayout_ & dslSkippedCharge) {
      internalResize(skippedCharge, newSize);
    }

    if (storageLayout_ & dslFlucQPosition) {
      internalResize(flucQPos, newSize);
    }

    if (storageLayout_ & dslFlucQVelocity) {
      internalResize(flucQVel, newSize);
    }

    if (storageLayout_ & dslFlucQForce) {
      internalResize(flucQFrc, newSize);
    }

    size_ = newSize;
  }

  void DataStorage::reserve(int size) {
    if (storageLayout_ & dslPosition) {
      position.reserve(size);
    } 

    if (storageLayout_ & dslVelocity) {
      velocity.reserve(size);
    } 

    if (storageLayout_ & dslForce) {
      force.reserve(size);
    } 

    if (storageLayout_ & dslAmat) {
      aMat.reserve(size);
    } 

    if (storageLayout_ & dslAngularMomentum) {
      angularMomentum.reserve(size);
    } 

    if (storageLayout_ & dslTorque) {
      torque.reserve(size);
    }
    
    if (storageLayout_ & dslParticlePot) {
      particlePot.reserve(size);
    }

    if (storageLayout_ & dslDensity) {
      density.reserve(size);
    }

    if (storageLayout_ & dslFunctional) {
      functional.reserve(size);
    }

    if (storageLayout_ & dslFunctionalDerivative) {
      functionalDerivative.reserve(size);
    }

    if (storageLayout_ & dslDipole) {
      dipole.reserve(size);
    }

    if (storageLayout_ & dslQuadrupole) {
      quadrupole.reserve(size);
    }

    if (storageLayout_ & dslElectricField) {
      electricField.reserve(size);
    }

    if (storageLayout_ & dslSkippedCharge) {
      skippedCharge.reserve(size);
    }

    if (storageLayout_ & dslFlucQPosition) {
      flucQPos.reserve(size);
    }

    if (storageLayout_ & dslFlucQVelocity) {
      flucQVel.reserve(size);
    }

    if (storageLayout_ & dslFlucQForce) {
      flucQFrc.reserve(size);
    }
  }

  void DataStorage::copy(int source, int num, int target) {
    if (num + target > size_ ) {
      //error
    }
    
    if (storageLayout_ & dslPosition) {
      internalCopy(position, source, num, target);
    } 

    if (storageLayout_ & dslVelocity) {
      internalCopy(velocity, source, num, target);
    } 

    if (storageLayout_ & dslForce) {
      internalCopy(force, source, num, target);
    } 

    if (storageLayout_ & dslAmat) {
      internalCopy(aMat, source, num, target);
    } 

    if (storageLayout_ & dslAngularMomentum) {
      internalCopy(angularMomentum, source, num, target);
    } 

    if (storageLayout_ & dslTorque) {
      internalCopy(torque, source, num, target); 
    }

    if (storageLayout_ & dslParticlePot) {
      internalCopy(particlePot, source, num, target); 
    }

    if (storageLayout_ & dslDensity) {
      internalCopy(density, source, num, target);
    }

    if (storageLayout_ & dslFunctional) {
      internalCopy(functional, source, num, target);
    }

    if (storageLayout_ & dslFunctionalDerivative) {
      internalCopy(functionalDerivative, source, num, target);
    }

    if (storageLayout_ & dslDipole) {
      internalCopy(dipole, source, num, target);
    }

    if (storageLayout_ & dslQuadrupole) {
      internalCopy(quadrupole, source, num, target);
    }

    if (storageLayout_ & dslElectricField) {
      internalCopy(electricField, source, num, target);
    }

    if (storageLayout_ & dslSkippedCharge) {
      internalCopy(skippedCharge, source, num, target);
    }

    if (storageLayout_ & dslFlucQPosition) {
      internalCopy(flucQPos, source, num, target);
    }

    if (storageLayout_ & dslFlucQVelocity) {
      internalCopy(flucQVel, source, num, target);
    }
    if (storageLayout_ & dslFlucQForce) {
      internalCopy(flucQFrc, source, num, target);
    }
  }

  int DataStorage::getStorageLayout() {
    return storageLayout_;
  }

  void DataStorage::setStorageLayout(int layout) {
    storageLayout_ = layout;
    resize(size_);
  }

  RealType* DataStorage::getArrayPointer(int whichArray) {

    switch (whichArray) {
    case dslPosition:
      return internalGetArrayPointer(position);
      break;
            
    case dslVelocity:
      return internalGetArrayPointer(velocity);
      break;
            
    case dslForce:
      return internalGetArrayPointer(force);
      break;            

    case dslAmat:
      return internalGetArrayPointer(aMat);
      break;            
            
    case dslAngularMomentum:
      return internalGetArrayPointer(angularMomentum);
      break;
            
    case dslTorque:
      return internalGetArrayPointer(torque);
      break;

    case dslParticlePot:
      return internalGetArrayPointer(particlePot);
      break;

    case dslDensity:
      return internalGetArrayPointer(density);
      break;

    case dslFunctional:
      return internalGetArrayPointer(functional);
      break;

    case dslFunctionalDerivative:
      return internalGetArrayPointer(functionalDerivative);
      break;

    case dslDipole:
      return internalGetArrayPointer(dipole);
      break;

    case dslQuadrupole:
      return internalGetArrayPointer(quadrupole);
      break;

    case dslElectricField:
      return internalGetArrayPointer(electricField);
      break;

    case dslSkippedCharge:
      return internalGetArrayPointer(skippedCharge);
      break;

    case dslFlucQPosition:
      return internalGetArrayPointer(flucQPos);
      break;

    case dslFlucQVelocity:
      return internalGetArrayPointer(flucQVel);
      break;
           
    case dslFlucQForce:
      return internalGetArrayPointer(flucQFrc);
      break;
           
    default:
      //error message
      return NULL;

    }
  }    

  RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
    if (v.size() == 0) {
      return NULL;
    } else {
      return v[0].getArrayPointer();
    }
  }

  RealType* DataStorage::internalGetArrayPointer(std::vector<Mat3x3d>& v) {
    if (v.size() == 0) {
      return NULL;
    } else {
      return v[0].getArrayPointer();
    }

  }

  RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
    if (v.size() == 0) {
      return NULL;
    } else {
      return &(v[0]);
    }

  }    

  template<typename T>
  void DataStorage::internalResize(std::vector<T>& v, int newSize){
    int oldSize = v.size();

    if (oldSize == newSize) {
      return;
    } else if (oldSize < newSize) {
      v.insert(v.end(), newSize-oldSize, T());
    } else {
      typename std::vector<T>::iterator i;
      i = v.begin();
      std::advance(i, newSize);        
      v.erase(i, v.end());
    }
  }

  template<typename T>
  void DataStorage::internalCopy(std::vector<T>& v, int source,  int num, int target) {
    typename std::vector<T>::iterator first;
    typename std::vector<T>::iterator last;
    typename std::vector<T>::iterator result;

    first = v.begin();
    last = v.begin();
    result = v.begin();

    std::advance(first, source);
    //STL algorithm use half opened range
    std::advance(last, num + 1);
    std::advance(result, target );

    std::copy(first, last, result);
  }

  int DataStorage::getBytesPerStuntDouble(int layout) {
    int bytes = 0;
    if (layout & dslPosition) {
      bytes += sizeof(Vector3d);
    }
    if (layout & dslVelocity) {
      bytes += sizeof(Vector3d);
    }
    if (layout & dslForce) {
      bytes += sizeof(Vector3d);
    }
    if (layout & dslAmat) {
      bytes += sizeof(RotMat3x3d);    
    }
    if (layout & dslAngularMomentum) {
      bytes += sizeof(Vector3d);
    }
    if (layout & dslTorque) {
      bytes += sizeof(Vector3d);
    }
    if (layout & dslParticlePot) {
      bytes += sizeof(RealType);
    }
    if (layout & dslDensity) {
      bytes += sizeof(RealType);
    }
    if (layout & dslFunctional) {
      bytes += sizeof(RealType);
    }
    if (layout & dslFunctionalDerivative) {
      bytes += sizeof(RealType);
    }
    if (layout & dslDipole) {
      bytes += sizeof(Vector3d);
    }
    if (layout & dslQuadrupole) {
      bytes += sizeof(Mat3x3d);
    }
    if (layout & dslElectricField) {
      bytes += sizeof(Vector3d);
    }
    if (layout & dslSkippedCharge) {
      bytes += sizeof(RealType);
    }
    if (layout & dslFlucQPosition) {
      bytes += sizeof(RealType);
    }
    if (layout & dslFlucQVelocity) {
      bytes += sizeof(RealType);
    }
    if (layout & dslFlucQForce) {
      bytes += sizeof(RealType);
    }

    return bytes;
  }

}
Revision:	1808
Committed:	Mon Oct 22 20:42:10 2012 UTC (12 years, 6 months ago) by gezelter
File size:	14658 byte(s)
Log Message:	A bug fix in the electric field for the new electrostatic code. Also comment fixes for Doxygen
#	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, 24107 (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 DataStorage.cpp
45	* @author tlin
46	* @date 10/26/2004
47	* @version 1.0
48	*/
49
50	#include "brains/DataStorage.hpp"
51	using namespace std;
52	namespace OpenMD {
53
54	DataStorage::DataStorage() : size_(0), storageLayout_(0){
55
56	}
57
58	DataStorage::DataStorage(int size, int storageLayout) : size_(size){
59	setStorageLayout(storageLayout);
60	resize(size);
61	}
62
63	int DataStorage::getSize() {
64
65	if (storageLayout_ & dslPosition && position.size() != size_) {
66	//error
67	cerr << "size does not match"<< endl;
68	}
69
70	if (storageLayout_ & dslVelocity && velocity.size() != size_) {
71	//error
72	cerr << "size does not match"<< endl;
73	}
74
75	if (storageLayout_ & dslForce && force.size() != size_) {
76	//error
77	cerr << "size does not match"<< endl;
78	}
79
80	if (storageLayout_ & dslAmat && aMat.size() != size_) {
81	//error
82	cerr << "size does not match"<< endl;
83	}
84
85	if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
86	//error
87	cerr << "size does not match"<< endl;
88	}
89
90	if (storageLayout_ & dslTorque && torque.size() != size_) {
91	//error
92	cerr << "size does not match"<< endl;
93	}
94
95	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
96	//error
97	cerr << "size does not match"<< endl;
98	}
99
100	if (storageLayout_ & dslDensity && density.size() != size_) {
101	//error
102	cerr << "size does not match"<< endl;
103	}
104
105	if (storageLayout_ & dslFunctional && functional.size() != size_) {
106	//error
107	cerr << "size does not match"<< endl;
108	}
109
110	if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
111	//error
112	cerr << "size does not match"<< endl;
113	}
114
115	if (storageLayout_ & dslDipole && dipole.size() != size_) {
116	//error
117	cerr << "size does not match"<< endl;
118	}
119
120	if (storageLayout_ & dslQuadrupole && quadrupole.size() != size_) {
121	//error
122	cerr << "size does not match"<< endl;
123	}
124
125	if (storageLayout_ & dslElectricField && electricField.size() != size_) {
126	//error
127	cerr << "size does not match"<< endl;
128	}
129
130	if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
131	//error
132	cerr << "size does not match"<< endl;
133	}
134
135	if (storageLayout_ & dslFlucQPosition && flucQPos.size() != size_) {
136	//error
137	cerr << "size does not match"<< endl;
138	}
139
140	if (storageLayout_ & dslFlucQVelocity && flucQVel.size() != size_) {
141	//error
142	cerr << "size does not match"<< endl;
143	}
144
145	if (storageLayout_ & dslFlucQForce && flucQFrc.size() != size_) {
146	//error
147	cerr << "size does not match"<< endl;
148	}
149
150	return size_;
151
152	}
153
154	void DataStorage::resize(int newSize) {
155
156	if (storageLayout_ & dslPosition) {
157	internalResize(position, newSize);
158	}
159
160	if (storageLayout_ & dslVelocity) {
161	internalResize(velocity, newSize);
162	}
163
164	if (storageLayout_ & dslForce) {
165	internalResize(force, newSize);
166	}
167
168	if (storageLayout_ & dslAmat) {
169	internalResize(aMat, newSize);
170	}
171
172	if (storageLayout_ & dslAngularMomentum) {
173	internalResize(angularMomentum, newSize);
174	}
175
176	if (storageLayout_ & dslTorque) {
177	internalResize(torque, newSize);
178	}
179
180	if (storageLayout_ & dslParticlePot) {
181	internalResize(particlePot, newSize);
182	}
183
184	if (storageLayout_ & dslDensity) {
185	internalResize(density, newSize);
186	}
187
188	if (storageLayout_ & dslFunctional) {
189	internalResize(functional, newSize);
190	}
191
192	if (storageLayout_ & dslFunctionalDerivative) {
193	internalResize(functionalDerivative, newSize);
194	}
195
196	if (storageLayout_ & dslDipole) {
197	internalResize(dipole, newSize);
198	}
199
200	if (storageLayout_ & dslQuadrupole) {
201	internalResize(quadrupole, newSize);
202	}
203
204	if (storageLayout_ & dslElectricField) {
205	internalResize(electricField, newSize);
206	}
207
208	if (storageLayout_ & dslSkippedCharge) {
209	internalResize(skippedCharge, newSize);
210	}
211
212	if (storageLayout_ & dslFlucQPosition) {
213	internalResize(flucQPos, newSize);
214	}
215
216	if (storageLayout_ & dslFlucQVelocity) {
217	internalResize(flucQVel, newSize);
218	}
219
220	if (storageLayout_ & dslFlucQForce) {
221	internalResize(flucQFrc, newSize);
222	}
223
224	size_ = newSize;
225	}
226
227	void DataStorage::reserve(int size) {
228	if (storageLayout_ & dslPosition) {
229	position.reserve(size);
230	}
231
232	if (storageLayout_ & dslVelocity) {
233	velocity.reserve(size);
234	}
235
236	if (storageLayout_ & dslForce) {
237	force.reserve(size);
238	}
239
240	if (storageLayout_ & dslAmat) {
241	aMat.reserve(size);
242	}
243
244	if (storageLayout_ & dslAngularMomentum) {
245	angularMomentum.reserve(size);
246	}
247
248	if (storageLayout_ & dslTorque) {
249	torque.reserve(size);
250	}
251
252	if (storageLayout_ & dslParticlePot) {
253	particlePot.reserve(size);
254	}
255
256	if (storageLayout_ & dslDensity) {
257	density.reserve(size);
258	}
259
260	if (storageLayout_ & dslFunctional) {
261	functional.reserve(size);
262	}
263
264	if (storageLayout_ & dslFunctionalDerivative) {
265	functionalDerivative.reserve(size);
266	}
267
268	if (storageLayout_ & dslDipole) {
269	dipole.reserve(size);
270	}
271
272	if (storageLayout_ & dslQuadrupole) {
273	quadrupole.reserve(size);
274	}
275
276	if (storageLayout_ & dslElectricField) {
277	electricField.reserve(size);
278	}
279
280	if (storageLayout_ & dslSkippedCharge) {
281	skippedCharge.reserve(size);
282	}
283
284	if (storageLayout_ & dslFlucQPosition) {
285	flucQPos.reserve(size);
286	}
287
288	if (storageLayout_ & dslFlucQVelocity) {
289	flucQVel.reserve(size);
290	}
291
292	if (storageLayout_ & dslFlucQForce) {
293	flucQFrc.reserve(size);
294	}
295	}
296
297	void DataStorage::copy(int source, int num, int target) {
298	if (num + target > size_ ) {
299	//error
300	}
301
302	if (storageLayout_ & dslPosition) {
303	internalCopy(position, source, num, target);
304	}
305
306	if (storageLayout_ & dslVelocity) {
307	internalCopy(velocity, source, num, target);
308	}
309
310	if (storageLayout_ & dslForce) {
311	internalCopy(force, source, num, target);
312	}
313
314	if (storageLayout_ & dslAmat) {
315	internalCopy(aMat, source, num, target);
316	}
317
318	if (storageLayout_ & dslAngularMomentum) {
319	internalCopy(angularMomentum, source, num, target);
320	}
321
322	if (storageLayout_ & dslTorque) {
323	internalCopy(torque, source, num, target);
324	}
325
326	if (storageLayout_ & dslParticlePot) {
327	internalCopy(particlePot, source, num, target);
328	}
329
330	if (storageLayout_ & dslDensity) {
331	internalCopy(density, source, num, target);
332	}
333
334	if (storageLayout_ & dslFunctional) {
335	internalCopy(functional, source, num, target);
336	}
337
338	if (storageLayout_ & dslFunctionalDerivative) {
339	internalCopy(functionalDerivative, source, num, target);
340	}
341
342	if (storageLayout_ & dslDipole) {
343	internalCopy(dipole, source, num, target);
344	}
345
346	if (storageLayout_ & dslQuadrupole) {
347	internalCopy(quadrupole, source, num, target);
348	}
349
350	if (storageLayout_ & dslElectricField) {
351	internalCopy(electricField, source, num, target);
352	}
353
354	if (storageLayout_ & dslSkippedCharge) {
355	internalCopy(skippedCharge, source, num, target);
356	}
357
358	if (storageLayout_ & dslFlucQPosition) {
359	internalCopy(flucQPos, source, num, target);
360	}
361
362	if (storageLayout_ & dslFlucQVelocity) {
363	internalCopy(flucQVel, source, num, target);
364	}
365	if (storageLayout_ & dslFlucQForce) {
366	internalCopy(flucQFrc, source, num, target);
367	}
368	}
369
370	int DataStorage::getStorageLayout() {
371	return storageLayout_;
372	}
373
374	void DataStorage::setStorageLayout(int layout) {
375	storageLayout_ = layout;
376	resize(size_);
377	}
378
379	RealType* DataStorage::getArrayPointer(int whichArray) {
380
381	switch (whichArray) {
382	case dslPosition:
383	return internalGetArrayPointer(position);
384	break;
385
386	case dslVelocity:
387	return internalGetArrayPointer(velocity);
388	break;
389
390	case dslForce:
391	return internalGetArrayPointer(force);
392	break;
393
394	case dslAmat:
395	return internalGetArrayPointer(aMat);
396	break;
397
398	case dslAngularMomentum:
399	return internalGetArrayPointer(angularMomentum);
400	break;
401
402	case dslTorque:
403	return internalGetArrayPointer(torque);
404	break;
405
406	case dslParticlePot:
407	return internalGetArrayPointer(particlePot);
408	break;
409
410	case dslDensity:
411	return internalGetArrayPointer(density);
412	break;
413
414	case dslFunctional:
415	return internalGetArrayPointer(functional);
416	break;
417
418	case dslFunctionalDerivative:
419	return internalGetArrayPointer(functionalDerivative);
420	break;
421
422	case dslDipole:
423	return internalGetArrayPointer(dipole);
424	break;
425
426	case dslQuadrupole:
427	return internalGetArrayPointer(quadrupole);
428	break;
429
430	case dslElectricField:
431	return internalGetArrayPointer(electricField);
432	break;
433
434	case dslSkippedCharge:
435	return internalGetArrayPointer(skippedCharge);
436	break;
437
438	case dslFlucQPosition:
439	return internalGetArrayPointer(flucQPos);
440	break;
441
442	case dslFlucQVelocity:
443	return internalGetArrayPointer(flucQVel);
444	break;
445
446	case dslFlucQForce:
447	return internalGetArrayPointer(flucQFrc);
448	break;
449
450	default:
451	//error message
452	return NULL;
453
454	}
455	}
456
457	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
458	if (v.size() == 0) {
459	return NULL;
460	} else {
461	return v[0].getArrayPointer();
462	}
463	}
464
465	RealType* DataStorage::internalGetArrayPointer(std::vector<Mat3x3d>& v) {
466	if (v.size() == 0) {
467	return NULL;
468	} else {
469	return v[0].getArrayPointer();
470	}
471
472	}
473
474	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
475	if (v.size() == 0) {
476	return NULL;
477	} else {
478	return &(v[0]);
479	}
480
481	}
482
483	template<typename T>
484	void DataStorage::internalResize(std::vector<T>& v, int newSize){
485	int oldSize = v.size();
486
487	if (oldSize == newSize) {
488	return;
489	} else if (oldSize < newSize) {
490	v.insert(v.end(), newSize-oldSize, T());
491	} else {
492	typename std::vector<T>::iterator i;
493	i = v.begin();
494	std::advance(i, newSize);
495	v.erase(i, v.end());
496	}
497	}
498
499	template<typename T>
500	void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
501	typename std::vector<T>::iterator first;
502	typename std::vector<T>::iterator last;
503	typename std::vector<T>::iterator result;
504
505	first = v.begin();
506	last = v.begin();
507	result = v.begin();
508
509	std::advance(first, source);
510	//STL algorithm use half opened range
511	std::advance(last, num + 1);
512	std::advance(result, target );
513
514	std::copy(first, last, result);
515	}
516
517	int DataStorage::getBytesPerStuntDouble(int layout) {
518	int bytes = 0;
519	if (layout & dslPosition) {
520	bytes += sizeof(Vector3d);
521	}
522	if (layout & dslVelocity) {
523	bytes += sizeof(Vector3d);
524	}
525	if (layout & dslForce) {
526	bytes += sizeof(Vector3d);
527	}
528	if (layout & dslAmat) {
529	bytes += sizeof(RotMat3x3d);
530	}
531	if (layout & dslAngularMomentum) {
532	bytes += sizeof(Vector3d);
533	}
534	if (layout & dslTorque) {
535	bytes += sizeof(Vector3d);
536	}
537	if (layout & dslParticlePot) {
538	bytes += sizeof(RealType);
539	}
540	if (layout & dslDensity) {
541	bytes += sizeof(RealType);
542	}
543	if (layout & dslFunctional) {
544	bytes += sizeof(RealType);
545	}
546	if (layout & dslFunctionalDerivative) {
547	bytes += sizeof(RealType);
548	}
549	if (layout & dslDipole) {
550	bytes += sizeof(Vector3d);
551	}
552	if (layout & dslQuadrupole) {
553	bytes += sizeof(Mat3x3d);
554	}
555	if (layout & dslElectricField) {
556	bytes += sizeof(Vector3d);
557	}
558	if (layout & dslSkippedCharge) {
559	bytes += sizeof(RealType);
560	}
561	if (layout & dslFlucQPosition) {
562	bytes += sizeof(RealType);
563	}
564	if (layout & dslFlucQVelocity) {
565	bytes += sizeof(RealType);
566	}
567	if (layout & dslFlucQForce) {
568	bytes += sizeof(RealType);
569	}
570
571	return bytes;
572	}
573
574	}