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
 * @time 11:56am
 * @version 1.0
 */

#include "brains/DataStorage.hpp"

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
      std::cerr << "size does not match"<< std::endl;
    }

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

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

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

    if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
      //error
      std::cerr << "size does not match"<< std::endl;        
    }

    if (storageLayout_ & dslZAngle && zAngle.size() != size_) {
      //error
      std::cerr << "size does not match"<< std::endl;        
    }

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

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

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

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

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

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

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

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

  }

  void DataStorage::resize(int newSize) {

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

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

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

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

    if (storageLayout_ & dslElectroFrame) {
      internalResize(electroFrame, newSize);
    }
    
    if (storageLayout_ & dslZAngle) {
      internalResize(zAngle, newSize);
    }

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

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

    size_ = newSize;
  }

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

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

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

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

    if (storageLayout_ & dslElectroFrame) {
      electroFrame.reserve(size);
    }
    
    if (storageLayout_ & dslZAngle) {
      zAngle.reserve(size);
    }

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

    if (storageLayout_ & dslSkippedCharge) {
      skippedCharge.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_ & dslAmat) {
      internalCopy(aMat, source, num, target);
    } 

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

    if (storageLayout_ & dslElectroFrame) {
      internalCopy(electroFrame, source, num, target);
    }
    
    if (storageLayout_ & dslZAngle) {
      internalCopy(zAngle, source, num, target);
    }

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

    if (storageLayout_ & dslSkippedCharge) {
      internalCopy(skippedCharge, 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 dslAmat:
      return internalGetArrayPointer(aMat);
      break;            
            
    case dslAngularMomentum:
      return internalGetArrayPointer(angularMomentum);
      break;
            
    case dslElectroFrame:
      return internalGetArrayPointer(electroFrame);
      break;
            
    case dslZAngle:
      return internalGetArrayPointer(zAngle);
      break;

    case dslForce:
      return internalGetArrayPointer(force);
      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 dslElectricField:
      return internalGetArrayPointer(electricField);
      break;

    case dslSkippedCharge:
      return internalGetArrayPointer(skippedCharge);
      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<RotMat3x3d>& 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 & dslAmat) {
      bytes += sizeof(RotMat3x3d);    
    }
    if (layout & dslAngularMomentum) {
      bytes += sizeof(Vector3d);
    }
    if (layout & dslElectroFrame) {
      bytes += sizeof(Mat3x3d);
    }
    if (layout & dslZAngle) {
      bytes += sizeof(RealType);
    }
    if (layout & dslForce) {
      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 & dslElectricField) {
      bytes += sizeof(Vector3d);
    }
    if (layout & dslSkippedCharge) {
      bytes += sizeof(RealType);
    }

    return bytes;
  }

}
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 6 months ago) by gezelter
File size:	13082 byte(s)
Log Message:	updated copyright notices
#	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	* @time 11:56am
48	* @version 1.0
49	*/
50
51	#include "brains/DataStorage.hpp"
52
53	namespace OpenMD {
54
55	DataStorage::DataStorage() : size_(0), storageLayout_(0){
56
57	}
58
59	DataStorage::DataStorage(int size, int storageLayout) : size_(size){
60	setStorageLayout(storageLayout);
61	resize(size);
62	}
63
64	int DataStorage::getSize() {
65
66	if (storageLayout_ & dslPosition && position.size() != size_) {
67	//error
68	std::cerr << "size does not match"<< std::endl;
69	}
70
71	if (storageLayout_ & dslVelocity && velocity.size() != size_) {
72	//error
73	std::cerr << "size does not match"<< std::endl;
74	}
75
76	if (storageLayout_ & dslAmat && aMat.size() != size_) {
77	//error
78	std::cerr << "size does not match"<< std::endl;
79	}
80
81	if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
82	//error
83	std::cerr << "size does not match"<< std::endl;
84	}
85
86	if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
87	//error
88	std::cerr << "size does not match"<< std::endl;
89	}
90
91	if (storageLayout_ & dslZAngle && zAngle.size() != size_) {
92	//error
93	std::cerr << "size does not match"<< std::endl;
94	}
95
96	if (storageLayout_ & dslForce && force.size() != size_) {
97	//error
98	std::cerr << "size does not match"<< std::endl;
99	}
100
101	if (storageLayout_ & dslTorque && torque.size() != size_) {
102	//error
103	std::cerr << "size does not match"<< std::endl;
104	}
105
106	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
107	//error
108	std::cerr << "size does not match"<< std::endl;
109	}
110
111	if (storageLayout_ & dslDensity && density.size() != size_) {
112	//error
113	std::cerr << "size does not match"<< std::endl;
114	}
115
116	if (storageLayout_ & dslFunctional && functional.size() != size_) {
117	//error
118	std::cerr << "size does not match"<< std::endl;
119	}
120
121	if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
122	//error
123	std::cerr << "size does not match"<< std::endl;
124	}
125
126	if (storageLayout_ & dslElectricField && electricField.size() != size_) {
127	//error
128	std::cerr << "size does not match"<< std::endl;
129	}
130
131	if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
132	//error
133	std::cerr << "size does not match"<< std::endl;
134	}
135
136	return size_;
137
138	}
139
140	void DataStorage::resize(int newSize) {
141
142	if (storageLayout_ & dslPosition) {
143	internalResize(position, newSize);
144	}
145
146	if (storageLayout_ & dslVelocity) {
147	internalResize(velocity, newSize);
148	}
149
150	if (storageLayout_ & dslAmat) {
151	internalResize(aMat, newSize);
152	}
153
154	if (storageLayout_ & dslAngularMomentum) {
155	internalResize(angularMomentum, newSize);
156	}
157
158	if (storageLayout_ & dslElectroFrame) {
159	internalResize(electroFrame, newSize);
160	}
161
162	if (storageLayout_ & dslZAngle) {
163	internalResize(zAngle, newSize);
164	}
165
166	if (storageLayout_ & dslForce) {
167	internalResize(force, newSize);
168	}
169
170	if (storageLayout_ & dslTorque) {
171	internalResize(torque, newSize);
172	}
173
174	if (storageLayout_ & dslParticlePot) {
175	internalResize(particlePot, newSize);
176	}
177
178	if (storageLayout_ & dslDensity) {
179	internalResize(density, newSize);
180	}
181
182	if (storageLayout_ & dslFunctional) {
183	internalResize(functional, newSize);
184	}
185
186	if (storageLayout_ & dslFunctionalDerivative) {
187	internalResize(functionalDerivative, newSize);
188	}
189
190	if (storageLayout_ & dslElectricField) {
191	internalResize(electricField, newSize);
192	}
193
194	if (storageLayout_ & dslSkippedCharge) {
195	internalResize(skippedCharge, newSize);
196	}
197
198	size_ = newSize;
199	}
200
201	void DataStorage::reserve(int size) {
202	if (storageLayout_ & dslPosition) {
203	position.reserve(size);
204	}
205
206	if (storageLayout_ & dslVelocity) {
207	velocity.reserve(size);
208	}
209
210	if (storageLayout_ & dslAmat) {
211	aMat.reserve(size);
212	}
213
214	if (storageLayout_ & dslAngularMomentum) {
215	angularMomentum.reserve(size);
216	}
217
218	if (storageLayout_ & dslElectroFrame) {
219	electroFrame.reserve(size);
220	}
221
222	if (storageLayout_ & dslZAngle) {
223	zAngle.reserve(size);
224	}
225
226	if (storageLayout_ & dslForce) {
227	force.reserve(size);
228	}
229
230	if (storageLayout_ & dslTorque) {
231	torque.reserve(size);
232	}
233
234	if (storageLayout_ & dslParticlePot) {
235	particlePot.reserve(size);
236	}
237
238	if (storageLayout_ & dslDensity) {
239	density.reserve(size);
240	}
241
242	if (storageLayout_ & dslFunctional) {
243	functional.reserve(size);
244	}
245
246	if (storageLayout_ & dslFunctionalDerivative) {
247	functionalDerivative.reserve(size);
248	}
249
250	if (storageLayout_ & dslElectricField) {
251	electricField.reserve(size);
252	}
253
254	if (storageLayout_ & dslSkippedCharge) {
255	skippedCharge.reserve(size);
256	}
257
258	}
259
260	void DataStorage::copy(int source, int num, int target) {
261	if (num + target > size_ ) {
262	//error
263	}
264
265	if (storageLayout_ & dslPosition) {
266	internalCopy(position, source, num, target);
267	}
268
269	if (storageLayout_ & dslVelocity) {
270	internalCopy(velocity, source, num, target);
271	}
272
273	if (storageLayout_ & dslAmat) {
274	internalCopy(aMat, source, num, target);
275	}
276
277	if (storageLayout_ & dslAngularMomentum) {
278	internalCopy(angularMomentum, source, num, target);
279	}
280
281	if (storageLayout_ & dslElectroFrame) {
282	internalCopy(electroFrame, source, num, target);
283	}
284
285	if (storageLayout_ & dslZAngle) {
286	internalCopy(zAngle, source, num, target);
287	}
288
289	if (storageLayout_ & dslForce) {
290	internalCopy(force, source, num, target);
291	}
292
293	if (storageLayout_ & dslTorque) {
294	internalCopy(torque, source, num, target);
295	}
296
297	if (storageLayout_ & dslParticlePot) {
298	internalCopy(particlePot, source, num, target);
299	}
300
301	if (storageLayout_ & dslDensity) {
302	internalCopy(density, source, num, target);
303	}
304
305	if (storageLayout_ & dslFunctional) {
306	internalCopy(functional, source, num, target);
307	}
308
309	if (storageLayout_ & dslFunctionalDerivative) {
310	internalCopy(functionalDerivative, source, num, target);
311	}
312
313	if (storageLayout_ & dslElectricField) {
314	internalCopy(electricField, source, num, target);
315	}
316
317	if (storageLayout_ & dslSkippedCharge) {
318	internalCopy(skippedCharge, source, num, target);
319	}
320	}
321
322	int DataStorage::getStorageLayout() {
323	return storageLayout_;
324	}
325
326	void DataStorage::setStorageLayout(int layout) {
327	storageLayout_ = layout;
328	resize(size_);
329	}
330
331	RealType* DataStorage::getArrayPointer(int whichArray) {
332
333	switch (whichArray) {
334	case dslPosition:
335	return internalGetArrayPointer(position);
336	break;
337
338	case dslVelocity:
339	return internalGetArrayPointer(velocity);
340	break;
341
342	case dslAmat:
343	return internalGetArrayPointer(aMat);
344	break;
345
346	case dslAngularMomentum:
347	return internalGetArrayPointer(angularMomentum);
348	break;
349
350	case dslElectroFrame:
351	return internalGetArrayPointer(electroFrame);
352	break;
353
354	case dslZAngle:
355	return internalGetArrayPointer(zAngle);
356	break;
357
358	case dslForce:
359	return internalGetArrayPointer(force);
360	break;
361
362	case dslTorque:
363	return internalGetArrayPointer(torque);
364	break;
365
366	case dslParticlePot:
367	return internalGetArrayPointer(particlePot);
368	break;
369
370	case dslDensity:
371	return internalGetArrayPointer(density);
372	break;
373
374	case dslFunctional:
375	return internalGetArrayPointer(functional);
376	break;
377
378	case dslFunctionalDerivative:
379	return internalGetArrayPointer(functionalDerivative);
380	break;
381
382	case dslElectricField:
383	return internalGetArrayPointer(electricField);
384	break;
385
386	case dslSkippedCharge:
387	return internalGetArrayPointer(skippedCharge);
388	break;
389
390	default:
391	//error message
392	return NULL;
393
394	}
395	}
396
397	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
398	if (v.size() == 0) {
399	return NULL;
400	} else {
401	return v[0].getArrayPointer();
402	}
403	}
404
405	RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
406	if (v.size() == 0) {
407	return NULL;
408	} else {
409	return v[0].getArrayPointer();
410	}
411
412	}
413
414	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
415	if (v.size() == 0) {
416	return NULL;
417	} else {
418	return &(v[0]);
419	}
420
421	}
422
423	template<typename T>
424	void DataStorage::internalResize(std::vector<T>& v, int newSize){
425	int oldSize = v.size();
426
427	if (oldSize == newSize) {
428	return;
429	} else if (oldSize < newSize) {
430	v.insert(v.end(), newSize-oldSize, T());
431	} else {
432	typename std::vector<T>::iterator i;
433	i = v.begin();
434	std::advance(i, newSize);
435	v.erase(i, v.end());
436	}
437	}
438
439	template<typename T>
440	void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
441	typename std::vector<T>::iterator first;
442	typename std::vector<T>::iterator last;
443	typename std::vector<T>::iterator result;
444
445	first = v.begin();
446	last = v.begin();
447	result = v.begin();
448
449	std::advance(first, source);
450	//STL algorithm use half opened range
451	std::advance(last, num + 1);
452	std::advance(result, target );
453
454	std::copy(first, last, result);
455	}
456
457	int DataStorage::getBytesPerStuntDouble(int layout) {
458	int bytes = 0;
459	if (layout & dslPosition) {
460	bytes += sizeof(Vector3d);
461	}
462	if (layout & dslVelocity) {
463	bytes += sizeof(Vector3d);
464	}
465	if (layout & dslAmat) {
466	bytes += sizeof(RotMat3x3d);
467	}
468	if (layout & dslAngularMomentum) {
469	bytes += sizeof(Vector3d);
470	}
471	if (layout & dslElectroFrame) {
472	bytes += sizeof(Mat3x3d);
473	}
474	if (layout & dslZAngle) {
475	bytes += sizeof(RealType);
476	}
477	if (layout & dslForce) {
478	bytes += sizeof(Vector3d);
479	}
480	if (layout & dslTorque) {
481	bytes += sizeof(Vector3d);
482	}
483	if (layout & dslParticlePot) {
484	bytes += sizeof(RealType);
485	}
486	if (layout & dslDensity) {
487	bytes += sizeof(RealType);
488	}
489	if (layout & dslFunctional) {
490	bytes += sizeof(RealType);
491	}
492	if (layout & dslFunctionalDerivative) {
493	bytes += sizeof(RealType);
494	}
495	if (layout & dslElectricField) {
496	bytes += sizeof(Vector3d);
497	}
498	if (layout & dslSkippedCharge) {
499	bytes += sizeof(RealType);
500	}
501
502	return bytes;
503	}
504
505	}