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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
/**
 * @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;        
    }
    
    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);
    }

    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);
    }

  }

  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);
    }
  }

  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;
           
    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);
    }

    return bytes;
  }

}
Revision:	1583
Committed:	Thu Jun 16 22:00:08 2011 UTC (13 years, 10 months ago) by gezelter
File size:	12392 byte(s)
Log Message:	Bug squashing
#	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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	155	*/
41
42	gezelter	507	/**
43			* @file DataStorage.cpp
44			* @author tlin
45			* @date 10/26/2004
46			* @time 11:56am
47			* @version 1.0
48			*/
49	tim	155
50			#include "brains/DataStorage.hpp"
51
52	gezelter	1390	namespace OpenMD {
53	tim	155
54	gezelter	507	DataStorage::DataStorage() : size_(0), storageLayout_(0){
55	tim	155
56	gezelter	507	}
57	tim	155
58	gezelter	507	DataStorage::DataStorage(int size, int storageLayout) : size_(size){
59	tim	155	setStorageLayout(storageLayout);
60			resize(size);
61	gezelter	507	}
62	tim	155
63	gezelter	507	int DataStorage::getSize() {
64	tim	155
65			if (storageLayout_ & dslPosition && position.size() != size_) {
66	gezelter	507	//error
67			std::cerr << "size does not match"<< std::endl;
68	tim	155	}
69
70			if (storageLayout_ & dslVelocity && velocity.size() != size_) {
71	gezelter	507	//error
72			std::cerr << "size does not match"<< std::endl;
73	tim	155	}
74
75			if (storageLayout_ & dslAmat && aMat.size() != size_) {
76	gezelter	507	//error
77			std::cerr << "size does not match"<< std::endl;
78	tim	155	}
79
80			if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
81	gezelter	507	//error
82			std::cerr << "size does not match"<< std::endl;
83	tim	155	}
84
85	gezelter	246	if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
86	gezelter	507	//error
87			std::cerr << "size does not match"<< std::endl;
88	tim	155	}
89
90			if (storageLayout_ & dslZAngle && zAngle.size() != size_) {
91	gezelter	507	//error
92			std::cerr << "size does not match"<< std::endl;
93	tim	155	}
94
95			if (storageLayout_ & dslForce && force.size() != size_) {
96	gezelter	507	//error
97			std::cerr << "size does not match"<< std::endl;
98	tim	155	}
99
100			if (storageLayout_ & dslTorque && torque.size() != size_) {
101	gezelter	507	//error
102			std::cerr << "size does not match"<< std::endl;
103	tim	155	}
104	gezelter	1583
105	chuckv	1245	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
106			//error
107			std::cerr << "size does not match"<< std::endl;
108			}
109	gezelter	1583
110			if (storageLayout_ & dslDensity && density.size() != size_) {
111			//error
112			std::cerr << "size does not match"<< std::endl;
113			}
114
115			if (storageLayout_ & dslFunctional && functional.size() != size_) {
116			//error
117			std::cerr << "size does not match"<< std::endl;
118			}
119
120			if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
121			//error
122			std::cerr << "size does not match"<< std::endl;
123			}
124
125			if (storageLayout_ & dslElectricField && electricField.size() != size_) {
126			//error
127			std::cerr << "size does not match"<< std::endl;
128			}
129	chuckv	1245
130	tim	155	return size_;
131
132	gezelter	507	}
133	tim	155
134	gezelter	507	void DataStorage::resize(int newSize) {
135	tim	155
136			if (storageLayout_ & dslPosition) {
137	gezelter	507	internalResize(position, newSize);
138	tim	155	}
139
140			if (storageLayout_ & dslVelocity) {
141	gezelter	507	internalResize(velocity, newSize);
142	tim	155	}
143
144			if (storageLayout_ & dslAmat) {
145	gezelter	507	internalResize(aMat, newSize);
146	tim	155	}
147
148			if (storageLayout_ & dslAngularMomentum) {
149	gezelter	507	internalResize(angularMomentum, newSize);
150	tim	155	}
151
152	gezelter	246	if (storageLayout_ & dslElectroFrame) {
153	gezelter	507	internalResize(electroFrame, newSize);
154	tim	155	}
155
156			if (storageLayout_ & dslZAngle) {
157	gezelter	507	internalResize(zAngle, newSize);
158	tim	155	}
159
160			if (storageLayout_ & dslForce) {
161	gezelter	507	internalResize(force, newSize);
162	tim	155	}
163
164			if (storageLayout_ & dslTorque) {
165	gezelter	507	internalResize(torque, newSize);
166	tim	155	}
167
168	chuckv	1245	if (storageLayout_ & dslParticlePot) {
169			internalResize(particlePot, newSize);
170			}
171
172	gezelter	1583	if (storageLayout_ & dslDensity) {
173			internalResize(density, newSize);
174			}
175
176			if (storageLayout_ & dslFunctional) {
177			internalResize(functional, newSize);
178			}
179
180			if (storageLayout_ & dslFunctionalDerivative) {
181			internalResize(functionalDerivative, newSize);
182			}
183
184			if (storageLayout_ & dslElectricField) {
185			internalResize(electricField, newSize);
186			}
187
188	tim	155	size_ = newSize;
189	gezelter	507	}
190	tim	155
191	gezelter	507	void DataStorage::reserve(int size) {
192	tim	155	if (storageLayout_ & dslPosition) {
193	gezelter	507	position.reserve(size);
194	tim	155	}
195
196			if (storageLayout_ & dslVelocity) {
197	gezelter	507	velocity.reserve(size);
198	tim	155	}
199
200			if (storageLayout_ & dslAmat) {
201	gezelter	507	aMat.reserve(size);
202	tim	155	}
203
204			if (storageLayout_ & dslAngularMomentum) {
205	gezelter	507	angularMomentum.reserve(size);
206	tim	155	}
207
208	gezelter	246	if (storageLayout_ & dslElectroFrame) {
209	gezelter	507	electroFrame.reserve(size);
210	tim	155	}
211
212			if (storageLayout_ & dslZAngle) {
213	gezelter	507	zAngle.reserve(size);
214	tim	155	}
215
216			if (storageLayout_ & dslForce) {
217	gezelter	507	force.reserve(size);
218	tim	155	}
219
220			if (storageLayout_ & dslTorque) {
221	gezelter	507	torque.reserve(size);
222	tim	155	}
223	chuckv	1245
224			if (storageLayout_ & dslParticlePot) {
225			particlePot.reserve(size);
226			}
227	tim	155
228	gezelter	1583	if (storageLayout_ & dslDensity) {
229			density.reserve(size);
230			}
231
232			if (storageLayout_ & dslFunctional) {
233			functional.reserve(size);
234			}
235
236			if (storageLayout_ & dslFunctionalDerivative) {
237			functionalDerivative.reserve(size);
238			}
239
240			if (storageLayout_ & dslElectricField) {
241			electricField.reserve(size);
242			}
243
244	gezelter	507	}
245	tim	155
246	gezelter	507	void DataStorage::copy(int source, int num, int target) {
247	tim	155	if (num + target > size_ ) {
248	gezelter	507	//error
249	tim	155	}
250
251			if (storageLayout_ & dslPosition) {
252	gezelter	507	internalCopy(position, source, num, target);
253	tim	155	}
254
255			if (storageLayout_ & dslVelocity) {
256	gezelter	507	internalCopy(velocity, source, num, target);
257			}
258	tim	155
259			if (storageLayout_ & dslAmat) {
260	gezelter	507	internalCopy(aMat, source, num, target);
261			}
262	tim	155
263			if (storageLayout_ & dslAngularMomentum) {
264	gezelter	507	internalCopy(angularMomentum, source, num, target);
265	tim	155	}
266
267	gezelter	246	if (storageLayout_ & dslElectroFrame) {
268	gezelter	507	internalCopy(electroFrame, source, num, target);
269	tim	155	}
270
271			if (storageLayout_ & dslZAngle) {
272	gezelter	507	internalCopy(zAngle, source, num, target);
273	tim	155	}
274
275			if (storageLayout_ & dslForce) {
276	gezelter	507	internalCopy(force, source, num, target);
277	tim	155	}
278
279			if (storageLayout_ & dslTorque) {
280	gezelter	507	internalCopy(torque, source, num, target);
281	tim	155	}
282	chuckv	1245
283			if (storageLayout_ & dslParticlePot) {
284			internalCopy(particlePot, source, num, target);
285			}
286	tim	155
287	gezelter	1583	if (storageLayout_ & dslDensity) {
288			internalCopy(density, source, num, target);
289			}
290
291			if (storageLayout_ & dslFunctional) {
292			internalCopy(functional, source, num, target);
293			}
294
295			if (storageLayout_ & dslFunctionalDerivative) {
296			internalCopy(functionalDerivative, source, num, target);
297			}
298
299			if (storageLayout_ & dslElectricField) {
300			internalCopy(electricField, source, num, target);
301			}
302	gezelter	507	}
303	tim	155
304	gezelter	507	int DataStorage::getStorageLayout() {
305	tim	155	return storageLayout_;
306	gezelter	507	}
307	tim	155
308	gezelter	507	void DataStorage::setStorageLayout(int layout) {
309	tim	155	storageLayout_ = layout;
310			resize(size_);
311	gezelter	507	}
312	tim	155
313	tim	963	RealType* DataStorage::getArrayPointer(int whichArray) {
314	tim	155
315			switch (whichArray) {
316	gezelter	507	case dslPosition:
317			return internalGetArrayPointer(position);
318			break;
319	tim	155
320	gezelter	507	case dslVelocity:
321			return internalGetArrayPointer(velocity);
322			break;
323	tim	155
324	gezelter	507	case dslAmat:
325			return internalGetArrayPointer(aMat);
326			break;
327	tim	155
328	gezelter	507	case dslAngularMomentum:
329			return internalGetArrayPointer(angularMomentum);
330			break;
331	tim	155
332	gezelter	507	case dslElectroFrame:
333			return internalGetArrayPointer(electroFrame);
334			break;
335	tim	155
336	gezelter	507	case dslZAngle:
337			return internalGetArrayPointer(zAngle);
338			break;
339	tim	155
340	gezelter	507	case dslForce:
341			return internalGetArrayPointer(force);
342			break;
343	tim	155
344	gezelter	507	case dslTorque:
345			return internalGetArrayPointer(torque);
346	gezelter	1104	break;
347	chuckv	1245
348			case dslParticlePot:
349			return internalGetArrayPointer(particlePot);
350			break;
351	gezelter	1583
352			case dslDensity:
353			return internalGetArrayPointer(density);
354			break;
355
356			case dslFunctional:
357			return internalGetArrayPointer(functional);
358			break;
359
360			case dslFunctionalDerivative:
361			return internalGetArrayPointer(functionalDerivative);
362			break;
363
364			case dslElectricField:
365			return internalGetArrayPointer(electricField);
366			break;
367
368	gezelter	507	default:
369			//error message
370			return NULL;
371	tim	155
372			}
373	gezelter	507	}
374	tim	155
375	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
376	tim	155	if (v.size() == 0) {
377	gezelter	507	return NULL;
378	tim	155	} else {
379	gezelter	507	return v[0].getArrayPointer();
380	tim	155	}
381	gezelter	507	}
382	tim	155
383	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
384	tim	155	if (v.size() == 0) {
385	gezelter	507	return NULL;
386	tim	155	} else {
387	gezelter	507	return v[0].getArrayPointer();
388	tim	155	}
389
390	gezelter	507	}
391	tim	155
392	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
393	tim	155	if (v.size() == 0) {
394	gezelter	507	return NULL;
395	tim	155	} else {
396	gezelter	507	return &(v[0]);
397	tim	155	}
398
399	gezelter	507	}
400	tim	155
401	gezelter	507	template<typename T>
402			void DataStorage::internalResize(std::vector<T>& v, int newSize){
403	tim	155	int oldSize = v.size();
404
405			if (oldSize == newSize) {
406	gezelter	507	return;
407	tim	155	} else if (oldSize < newSize) {
408	gezelter	507	v.insert(v.end(), newSize-oldSize, T());
409	tim	155	} else {
410	gezelter	507	typename std::vector<T>::iterator i;
411			i = v.begin();
412			std::advance(i, newSize);
413			v.erase(i, v.end());
414	tim	155	}
415	gezelter	507	}
416	tim	155
417	gezelter	507	template<typename T>
418			void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
419	tim	155	typename std::vector<T>::iterator first;
420			typename std::vector<T>::iterator last;
421			typename std::vector<T>::iterator result;
422
423			first = v.begin();
424			last = v.begin();
425			result = v.begin();
426
427			std::advance(first, source);
428			//STL algorithm use half opened range
429			std::advance(last, num + 1);
430			std::advance(result, target );
431
432			std::copy(first, last, result);
433	gezelter	507	}
434	tim	323
435	gezelter	507	int DataStorage::getBytesPerStuntDouble(int layout) {
436	tim	323	int bytes = 0;
437			if (layout & dslPosition) {
438	gezelter	507	bytes += sizeof(Vector3d);
439	tim	331	}
440			if (layout & dslVelocity) {
441	gezelter	507	bytes += sizeof(Vector3d);
442	tim	331	}
443			if (layout & dslAmat) {
444	chuckv	1245	bytes += sizeof(RotMat3x3d);
445	tim	331	}
446			if (layout & dslAngularMomentum) {
447	gezelter	507	bytes += sizeof(Vector3d);
448	tim	331	}
449			if (layout & dslElectroFrame) {
450	gezelter	507	bytes += sizeof(Mat3x3d);
451	tim	331	}
452			if (layout & dslZAngle) {
453	chuckv	1245	bytes += sizeof(RealType);
454	tim	331	}
455			if (layout & dslForce) {
456	gezelter	507	bytes += sizeof(Vector3d);
457	tim	331	}
458			if (layout & dslTorque) {
459	gezelter	507	bytes += sizeof(Vector3d);
460	tim	323	}
461	chuckv	1245	if (layout & dslParticlePot) {
462			bytes += sizeof(RealType);
463			}
464	gezelter	1583	if (layout & dslDensity) {
465			bytes += sizeof(RealType);
466			}
467			if (layout & dslFunctional) {
468			bytes += sizeof(RealType);
469			}
470			if (layout & dslFunctionalDerivative) {
471			bytes += sizeof(RealType);
472			}
473			if (layout & dslElectricField) {
474			bytes += sizeof(Vector3d);
475			}
476
477	tim	323	return bytes;
478	gezelter	507	}
479	tim	323
480			}