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, 5 months ago) by gezelter
File size:	13082 byte(s)
Log Message:	updated copyright notices
#	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	gezelter	1665	* [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
43	gezelter	507	/**
44			* @file DataStorage.cpp
45			* @author tlin
46			* @date 10/26/2004
47			* @time 11:56am
48			* @version 1.0
49			*/
50	tim	155
51			#include "brains/DataStorage.hpp"
52
53	gezelter	1390	namespace OpenMD {
54	tim	155
55	gezelter	507	DataStorage::DataStorage() : size_(0), storageLayout_(0){
56	tim	155
57	gezelter	507	}
58	tim	155
59	gezelter	507	DataStorage::DataStorage(int size, int storageLayout) : size_(size){
60	tim	155	setStorageLayout(storageLayout);
61			resize(size);
62	gezelter	507	}
63	tim	155
64	gezelter	507	int DataStorage::getSize() {
65	tim	155
66			if (storageLayout_ & dslPosition && position.size() != size_) {
67	gezelter	507	//error
68			std::cerr << "size does not match"<< std::endl;
69	tim	155	}
70
71			if (storageLayout_ & dslVelocity && velocity.size() != size_) {
72	gezelter	507	//error
73			std::cerr << "size does not match"<< std::endl;
74	tim	155	}
75
76			if (storageLayout_ & dslAmat && aMat.size() != size_) {
77	gezelter	507	//error
78			std::cerr << "size does not match"<< std::endl;
79	tim	155	}
80
81			if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
82	gezelter	507	//error
83			std::cerr << "size does not match"<< std::endl;
84	tim	155	}
85
86	gezelter	246	if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
87	gezelter	507	//error
88			std::cerr << "size does not match"<< std::endl;
89	tim	155	}
90
91			if (storageLayout_ & dslZAngle && zAngle.size() != size_) {
92	gezelter	507	//error
93			std::cerr << "size does not match"<< std::endl;
94	tim	155	}
95
96			if (storageLayout_ & dslForce && force.size() != size_) {
97	gezelter	507	//error
98			std::cerr << "size does not match"<< std::endl;
99	tim	155	}
100
101			if (storageLayout_ & dslTorque && torque.size() != size_) {
102	gezelter	507	//error
103			std::cerr << "size does not match"<< std::endl;
104	tim	155	}
105	gezelter	1583
106	chuckv	1245	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
107			//error
108			std::cerr << "size does not match"<< std::endl;
109			}
110	gezelter	1583
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	gezelter	1584
131			if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
132			//error
133			std::cerr << "size does not match"<< std::endl;
134			}
135	chuckv	1245
136	tim	155	return size_;
137
138	gezelter	507	}
139	tim	155
140	gezelter	507	void DataStorage::resize(int newSize) {
141	tim	155
142			if (storageLayout_ & dslPosition) {
143	gezelter	507	internalResize(position, newSize);
144	tim	155	}
145
146			if (storageLayout_ & dslVelocity) {
147	gezelter	507	internalResize(velocity, newSize);
148	tim	155	}
149
150			if (storageLayout_ & dslAmat) {
151	gezelter	507	internalResize(aMat, newSize);
152	tim	155	}
153
154			if (storageLayout_ & dslAngularMomentum) {
155	gezelter	507	internalResize(angularMomentum, newSize);
156	tim	155	}
157
158	gezelter	246	if (storageLayout_ & dslElectroFrame) {
159	gezelter	507	internalResize(electroFrame, newSize);
160	tim	155	}
161
162			if (storageLayout_ & dslZAngle) {
163	gezelter	507	internalResize(zAngle, newSize);
164	tim	155	}
165
166			if (storageLayout_ & dslForce) {
167	gezelter	507	internalResize(force, newSize);
168	tim	155	}
169
170			if (storageLayout_ & dslTorque) {
171	gezelter	507	internalResize(torque, newSize);
172	tim	155	}
173
174	chuckv	1245	if (storageLayout_ & dslParticlePot) {
175			internalResize(particlePot, newSize);
176			}
177
178	gezelter	1583	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	gezelter	1584	if (storageLayout_ & dslSkippedCharge) {
195			internalResize(skippedCharge, newSize);
196			}
197
198	tim	155	size_ = newSize;
199	gezelter	507	}
200	tim	155
201	gezelter	507	void DataStorage::reserve(int size) {
202	tim	155	if (storageLayout_ & dslPosition) {
203	gezelter	507	position.reserve(size);
204	tim	155	}
205
206			if (storageLayout_ & dslVelocity) {
207	gezelter	507	velocity.reserve(size);
208	tim	155	}
209
210			if (storageLayout_ & dslAmat) {
211	gezelter	507	aMat.reserve(size);
212	tim	155	}
213
214			if (storageLayout_ & dslAngularMomentum) {
215	gezelter	507	angularMomentum.reserve(size);
216	tim	155	}
217
218	gezelter	246	if (storageLayout_ & dslElectroFrame) {
219	gezelter	507	electroFrame.reserve(size);
220	tim	155	}
221
222			if (storageLayout_ & dslZAngle) {
223	gezelter	507	zAngle.reserve(size);
224	tim	155	}
225
226			if (storageLayout_ & dslForce) {
227	gezelter	507	force.reserve(size);
228	tim	155	}
229
230			if (storageLayout_ & dslTorque) {
231	gezelter	507	torque.reserve(size);
232	tim	155	}
233	chuckv	1245
234			if (storageLayout_ & dslParticlePot) {
235			particlePot.reserve(size);
236			}
237	tim	155
238	gezelter	1583	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	gezelter	1584	if (storageLayout_ & dslSkippedCharge) {
255			skippedCharge.reserve(size);
256			}
257
258	gezelter	507	}
259	tim	155
260	gezelter	507	void DataStorage::copy(int source, int num, int target) {
261	tim	155	if (num + target > size_ ) {
262	gezelter	507	//error
263	tim	155	}
264
265			if (storageLayout_ & dslPosition) {
266	gezelter	507	internalCopy(position, source, num, target);
267	tim	155	}
268
269			if (storageLayout_ & dslVelocity) {
270	gezelter	507	internalCopy(velocity, source, num, target);
271			}
272	tim	155
273			if (storageLayout_ & dslAmat) {
274	gezelter	507	internalCopy(aMat, source, num, target);
275			}
276	tim	155
277			if (storageLayout_ & dslAngularMomentum) {
278	gezelter	507	internalCopy(angularMomentum, source, num, target);
279	tim	155	}
280
281	gezelter	246	if (storageLayout_ & dslElectroFrame) {
282	gezelter	507	internalCopy(electroFrame, source, num, target);
283	tim	155	}
284
285			if (storageLayout_ & dslZAngle) {
286	gezelter	507	internalCopy(zAngle, source, num, target);
287	tim	155	}
288
289			if (storageLayout_ & dslForce) {
290	gezelter	507	internalCopy(force, source, num, target);
291	tim	155	}
292
293			if (storageLayout_ & dslTorque) {
294	gezelter	507	internalCopy(torque, source, num, target);
295	tim	155	}
296	chuckv	1245
297			if (storageLayout_ & dslParticlePot) {
298			internalCopy(particlePot, source, num, target);
299			}
300	tim	155
301	gezelter	1583	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	gezelter	1584
317			if (storageLayout_ & dslSkippedCharge) {
318			internalCopy(skippedCharge, source, num, target);
319			}
320	gezelter	507	}
321	tim	155
322	gezelter	507	int DataStorage::getStorageLayout() {
323	tim	155	return storageLayout_;
324	gezelter	507	}
325	tim	155
326	gezelter	507	void DataStorage::setStorageLayout(int layout) {
327	tim	155	storageLayout_ = layout;
328			resize(size_);
329	gezelter	507	}
330	tim	155
331	tim	963	RealType* DataStorage::getArrayPointer(int whichArray) {
332	tim	155
333			switch (whichArray) {
334	gezelter	507	case dslPosition:
335			return internalGetArrayPointer(position);
336			break;
337	tim	155
338	gezelter	507	case dslVelocity:
339			return internalGetArrayPointer(velocity);
340			break;
341	tim	155
342	gezelter	507	case dslAmat:
343			return internalGetArrayPointer(aMat);
344			break;
345	tim	155
346	gezelter	507	case dslAngularMomentum:
347			return internalGetArrayPointer(angularMomentum);
348			break;
349	tim	155
350	gezelter	507	case dslElectroFrame:
351			return internalGetArrayPointer(electroFrame);
352			break;
353	tim	155
354	gezelter	507	case dslZAngle:
355			return internalGetArrayPointer(zAngle);
356			break;
357	tim	155
358	gezelter	507	case dslForce:
359			return internalGetArrayPointer(force);
360			break;
361	tim	155
362	gezelter	507	case dslTorque:
363			return internalGetArrayPointer(torque);
364	gezelter	1104	break;
365	chuckv	1245
366			case dslParticlePot:
367			return internalGetArrayPointer(particlePot);
368			break;
369	gezelter	1583
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	gezelter	1584
386			case dslSkippedCharge:
387			return internalGetArrayPointer(skippedCharge);
388			break;
389	gezelter	1583
390	gezelter	507	default:
391			//error message
392			return NULL;
393	tim	155
394			}
395	gezelter	507	}
396	tim	155
397	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
398	tim	155	if (v.size() == 0) {
399	gezelter	507	return NULL;
400	tim	155	} else {
401	gezelter	507	return v[0].getArrayPointer();
402	tim	155	}
403	gezelter	507	}
404	tim	155
405	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
406	tim	155	if (v.size() == 0) {
407	gezelter	507	return NULL;
408	tim	155	} else {
409	gezelter	507	return v[0].getArrayPointer();
410	tim	155	}
411
412	gezelter	507	}
413	tim	155
414	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
415	tim	155	if (v.size() == 0) {
416	gezelter	507	return NULL;
417	tim	155	} else {
418	gezelter	507	return &(v[0]);
419	tim	155	}
420
421	gezelter	507	}
422	tim	155
423	gezelter	507	template<typename T>
424			void DataStorage::internalResize(std::vector<T>& v, int newSize){
425	tim	155	int oldSize = v.size();
426
427			if (oldSize == newSize) {
428	gezelter	507	return;
429	tim	155	} else if (oldSize < newSize) {
430	gezelter	507	v.insert(v.end(), newSize-oldSize, T());
431	tim	155	} else {
432	gezelter	507	typename std::vector<T>::iterator i;
433			i = v.begin();
434			std::advance(i, newSize);
435			v.erase(i, v.end());
436	tim	155	}
437	gezelter	507	}
438	tim	155
439	gezelter	507	template<typename T>
440			void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
441	tim	155	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	gezelter	507	}
456	tim	323
457	gezelter	507	int DataStorage::getBytesPerStuntDouble(int layout) {
458	tim	323	int bytes = 0;
459			if (layout & dslPosition) {
460	gezelter	507	bytes += sizeof(Vector3d);
461	tim	331	}
462			if (layout & dslVelocity) {
463	gezelter	507	bytes += sizeof(Vector3d);
464	tim	331	}
465			if (layout & dslAmat) {
466	chuckv	1245	bytes += sizeof(RotMat3x3d);
467	tim	331	}
468			if (layout & dslAngularMomentum) {
469	gezelter	507	bytes += sizeof(Vector3d);
470	tim	331	}
471			if (layout & dslElectroFrame) {
472	gezelter	507	bytes += sizeof(Mat3x3d);
473	tim	331	}
474			if (layout & dslZAngle) {
475	chuckv	1245	bytes += sizeof(RealType);
476	tim	331	}
477			if (layout & dslForce) {
478	gezelter	507	bytes += sizeof(Vector3d);
479	tim	331	}
480			if (layout & dslTorque) {
481	gezelter	507	bytes += sizeof(Vector3d);
482	tim	323	}
483	chuckv	1245	if (layout & dslParticlePot) {
484			bytes += sizeof(RealType);
485			}
486	gezelter	1583	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	gezelter	1584	if (layout & dslSkippedCharge) {
499			bytes += sizeof(RealType);
500			}
501	gezelter	1583
502	tim	323	return bytes;
503	gezelter	507	}
504	tim	323
505			}