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

    if (storageLayout_ & dslForce && force.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_ & 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_ & dslAmat) {
      internalResize(aMat, newSize);
    }

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

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

    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_ & dslAmat) {
      aMat.reserve(size);
    } 

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

    if (storageLayout_ & dslElectroFrame) {
      electroFrame.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);
    }

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

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

    if (storageLayout_ & dslElectroFrame) {
      internalCopy(electroFrame, 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);
    }

    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);
            
    case dslVelocity:
      return internalGetArrayPointer(velocity);
            
    case dslAmat:
      return internalGetArrayPointer(aMat);
            
    case dslAngularMomentum:
      return internalGetArrayPointer(angularMomentum);
            
    case dslElectroFrame:
      return internalGetArrayPointer(electroFrame);
            
    case dslForce:
      return internalGetArrayPointer(force);

    case dslTorque:
      return internalGetArrayPointer(torque);

    case dslParticlePot:
      return internalGetArrayPointer(particlePot);

    case dslDensity:
      return internalGetArrayPointer(density);

    case dslFunctional:
      return internalGetArrayPointer(functional);

    case dslFunctionalDerivative:
      return internalGetArrayPointer(functionalDerivative);

    case dslElectricField:
      return internalGetArrayPointer(electricField);

    case dslSkippedCharge:
      return internalGetArrayPointer(skippedCharge);

    case dslFlucQPosition:
      return internalGetArrayPointer(flucQPos);

    case dslFlucQVelocity:
      return internalGetArrayPointer(flucQVel);
           
    case dslFlucQForce:
      return internalGetArrayPointer(flucQFrc);
           
    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 & 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);
    }
    if (layout & dslFlucQPosition) {
      bytes += sizeof(RealType);
    }
    if (layout & dslFlucQVelocity) {
      bytes += sizeof(RealType);
    }
    if (layout & dslFlucQForce) {
      bytes += sizeof(RealType);
    }

    return bytes;
  }

}
Revision:	1793
Committed:	Fri Aug 31 21:16:10 2012 UTC (13 years, 2 months ago) by gezelter
File size:	13951 byte(s)
Log Message:	Cleaning up some warning messages on linux
#	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	using namespace std;
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	cerr << "size does not match"<< endl;
69	}
70
71	if (storageLayout_ & dslVelocity && velocity.size() != size_) {
72	//error
73	cerr << "size does not match"<< endl;
74	}
75
76	if (storageLayout_ & dslAmat && aMat.size() != size_) {
77	//error
78	cerr << "size does not match"<< endl;
79	}
80
81	if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
82	//error
83	cerr << "size does not match"<< endl;
84	}
85
86	if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
87	//error
88	cerr << "size does not match"<< endl;
89	}
90
91	if (storageLayout_ & dslForce && force.size() != size_) {
92	//error
93	cerr << "size does not match"<< endl;
94	}
95
96	if (storageLayout_ & dslTorque && torque.size() != size_) {
97	//error
98	cerr << "size does not match"<< endl;
99	}
100
101	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
102	//error
103	cerr << "size does not match"<< endl;
104	}
105
106	if (storageLayout_ & dslDensity && density.size() != size_) {
107	//error
108	cerr << "size does not match"<< endl;
109	}
110
111	if (storageLayout_ & dslFunctional && functional.size() != size_) {
112	//error
113	cerr << "size does not match"<< endl;
114	}
115
116	if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
117	//error
118	cerr << "size does not match"<< endl;
119	}
120
121	if (storageLayout_ & dslElectricField && electricField.size() != size_) {
122	//error
123	cerr << "size does not match"<< endl;
124	}
125
126	if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
127	//error
128	cerr << "size does not match"<< endl;
129	}
130
131	if (storageLayout_ & dslFlucQPosition && flucQPos.size() != size_) {
132	//error
133	cerr << "size does not match"<< endl;
134	}
135
136	if (storageLayout_ & dslFlucQVelocity && flucQVel.size() != size_) {
137	//error
138	cerr << "size does not match"<< endl;
139	}
140
141	if (storageLayout_ & dslFlucQForce && flucQFrc.size() != size_) {
142	//error
143	cerr << "size does not match"<< endl;
144	}
145
146	return size_;
147
148	}
149
150	void DataStorage::resize(int newSize) {
151
152	if (storageLayout_ & dslPosition) {
153	internalResize(position, newSize);
154	}
155
156	if (storageLayout_ & dslVelocity) {
157	internalResize(velocity, newSize);
158	}
159
160	if (storageLayout_ & dslAmat) {
161	internalResize(aMat, newSize);
162	}
163
164	if (storageLayout_ & dslAngularMomentum) {
165	internalResize(angularMomentum, newSize);
166	}
167
168	if (storageLayout_ & dslElectroFrame) {
169	internalResize(electroFrame, newSize);
170	}
171
172	if (storageLayout_ & dslForce) {
173	internalResize(force, 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_ & dslElectricField) {
197	internalResize(electricField, newSize);
198	}
199
200	if (storageLayout_ & dslSkippedCharge) {
201	internalResize(skippedCharge, newSize);
202	}
203
204	if (storageLayout_ & dslFlucQPosition) {
205	internalResize(flucQPos, newSize);
206	}
207
208	if (storageLayout_ & dslFlucQVelocity) {
209	internalResize(flucQVel, newSize);
210	}
211
212	if (storageLayout_ & dslFlucQForce) {
213	internalResize(flucQFrc, newSize);
214	}
215
216	size_ = newSize;
217	}
218
219	void DataStorage::reserve(int size) {
220	if (storageLayout_ & dslPosition) {
221	position.reserve(size);
222	}
223
224	if (storageLayout_ & dslVelocity) {
225	velocity.reserve(size);
226	}
227
228	if (storageLayout_ & dslAmat) {
229	aMat.reserve(size);
230	}
231
232	if (storageLayout_ & dslAngularMomentum) {
233	angularMomentum.reserve(size);
234	}
235
236	if (storageLayout_ & dslElectroFrame) {
237	electroFrame.reserve(size);
238	}
239
240	if (storageLayout_ & dslForce) {
241	force.reserve(size);
242	}
243
244	if (storageLayout_ & dslTorque) {
245	torque.reserve(size);
246	}
247
248	if (storageLayout_ & dslParticlePot) {
249	particlePot.reserve(size);
250	}
251
252	if (storageLayout_ & dslDensity) {
253	density.reserve(size);
254	}
255
256	if (storageLayout_ & dslFunctional) {
257	functional.reserve(size);
258	}
259
260	if (storageLayout_ & dslFunctionalDerivative) {
261	functionalDerivative.reserve(size);
262	}
263
264	if (storageLayout_ & dslElectricField) {
265	electricField.reserve(size);
266	}
267
268	if (storageLayout_ & dslSkippedCharge) {
269	skippedCharge.reserve(size);
270	}
271
272	if (storageLayout_ & dslFlucQPosition) {
273	flucQPos.reserve(size);
274	}
275
276	if (storageLayout_ & dslFlucQVelocity) {
277	flucQVel.reserve(size);
278	}
279
280	if (storageLayout_ & dslFlucQForce) {
281	flucQFrc.reserve(size);
282	}
283	}
284
285	void DataStorage::copy(int source, int num, int target) {
286	if (num + target > size_ ) {
287	//error
288	}
289
290	if (storageLayout_ & dslPosition) {
291	internalCopy(position, source, num, target);
292	}
293
294	if (storageLayout_ & dslVelocity) {
295	internalCopy(velocity, source, num, target);
296	}
297
298	if (storageLayout_ & dslAmat) {
299	internalCopy(aMat, source, num, target);
300	}
301
302	if (storageLayout_ & dslAngularMomentum) {
303	internalCopy(angularMomentum, source, num, target);
304	}
305
306	if (storageLayout_ & dslElectroFrame) {
307	internalCopy(electroFrame, source, num, target);
308	}
309
310	if (storageLayout_ & dslForce) {
311	internalCopy(force, source, num, target);
312	}
313
314	if (storageLayout_ & dslTorque) {
315	internalCopy(torque, source, num, target);
316	}
317
318	if (storageLayout_ & dslParticlePot) {
319	internalCopy(particlePot, source, num, target);
320	}
321
322	if (storageLayout_ & dslDensity) {
323	internalCopy(density, source, num, target);
324	}
325
326	if (storageLayout_ & dslFunctional) {
327	internalCopy(functional, source, num, target);
328	}
329
330	if (storageLayout_ & dslFunctionalDerivative) {
331	internalCopy(functionalDerivative, source, num, target);
332	}
333
334	if (storageLayout_ & dslElectricField) {
335	internalCopy(electricField, source, num, target);
336	}
337
338	if (storageLayout_ & dslSkippedCharge) {
339	internalCopy(skippedCharge, source, num, target);
340	}
341
342	if (storageLayout_ & dslFlucQPosition) {
343	internalCopy(flucQPos, source, num, target);
344	}
345
346	if (storageLayout_ & dslFlucQVelocity) {
347	internalCopy(flucQVel, source, num, target);
348	}
349	if (storageLayout_ & dslFlucQForce) {
350	internalCopy(flucQFrc, source, num, target);
351	}
352	}
353
354	int DataStorage::getStorageLayout() {
355	return storageLayout_;
356	}
357
358	void DataStorage::setStorageLayout(int layout) {
359	storageLayout_ = layout;
360	resize(size_);
361	}
362
363	RealType* DataStorage::getArrayPointer(int whichArray) {
364
365	switch (whichArray) {
366	case dslPosition:
367	return internalGetArrayPointer(position);
368
369	case dslVelocity:
370	return internalGetArrayPointer(velocity);
371
372	case dslAmat:
373	return internalGetArrayPointer(aMat);
374
375	case dslAngularMomentum:
376	return internalGetArrayPointer(angularMomentum);
377
378	case dslElectroFrame:
379	return internalGetArrayPointer(electroFrame);
380
381	case dslForce:
382	return internalGetArrayPointer(force);
383
384	case dslTorque:
385	return internalGetArrayPointer(torque);
386
387	case dslParticlePot:
388	return internalGetArrayPointer(particlePot);
389
390	case dslDensity:
391	return internalGetArrayPointer(density);
392
393	case dslFunctional:
394	return internalGetArrayPointer(functional);
395
396	case dslFunctionalDerivative:
397	return internalGetArrayPointer(functionalDerivative);
398
399	case dslElectricField:
400	return internalGetArrayPointer(electricField);
401
402	case dslSkippedCharge:
403	return internalGetArrayPointer(skippedCharge);
404
405	case dslFlucQPosition:
406	return internalGetArrayPointer(flucQPos);
407
408	case dslFlucQVelocity:
409	return internalGetArrayPointer(flucQVel);
410
411	case dslFlucQForce:
412	return internalGetArrayPointer(flucQFrc);
413
414	default:
415	//error message
416	return NULL;
417
418	}
419	}
420
421	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
422	if (v.size() == 0) {
423	return NULL;
424	} else {
425	return v[0].getArrayPointer();
426	}
427	}
428
429	RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
430	if (v.size() == 0) {
431	return NULL;
432	} else {
433	return v[0].getArrayPointer();
434	}
435
436	}
437
438	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
439	if (v.size() == 0) {
440	return NULL;
441	} else {
442	return &(v[0]);
443	}
444
445	}
446
447	template<typename T>
448	void DataStorage::internalResize(std::vector<T>& v, int newSize){
449	int oldSize = v.size();
450
451	if (oldSize == newSize) {
452	return;
453	} else if (oldSize < newSize) {
454	v.insert(v.end(), newSize-oldSize, T());
455	} else {
456	typename std::vector<T>::iterator i;
457	i = v.begin();
458	std::advance(i, newSize);
459	v.erase(i, v.end());
460	}
461	}
462
463	template<typename T>
464	void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
465	typename std::vector<T>::iterator first;
466	typename std::vector<T>::iterator last;
467	typename std::vector<T>::iterator result;
468
469	first = v.begin();
470	last = v.begin();
471	result = v.begin();
472
473	std::advance(first, source);
474	//STL algorithm use half opened range
475	std::advance(last, num + 1);
476	std::advance(result, target );
477
478	std::copy(first, last, result);
479	}
480
481	int DataStorage::getBytesPerStuntDouble(int layout) {
482	int bytes = 0;
483	if (layout & dslPosition) {
484	bytes += sizeof(Vector3d);
485	}
486	if (layout & dslVelocity) {
487	bytes += sizeof(Vector3d);
488	}
489	if (layout & dslAmat) {
490	bytes += sizeof(RotMat3x3d);
491	}
492	if (layout & dslAngularMomentum) {
493	bytes += sizeof(Vector3d);
494	}
495	if (layout & dslElectroFrame) {
496	bytes += sizeof(Mat3x3d);
497	}
498	if (layout & dslForce) {
499	bytes += sizeof(Vector3d);
500	}
501	if (layout & dslTorque) {
502	bytes += sizeof(Vector3d);
503	}
504	if (layout & dslParticlePot) {
505	bytes += sizeof(RealType);
506	}
507	if (layout & dslDensity) {
508	bytes += sizeof(RealType);
509	}
510	if (layout & dslFunctional) {
511	bytes += sizeof(RealType);
512	}
513	if (layout & dslFunctionalDerivative) {
514	bytes += sizeof(RealType);
515	}
516	if (layout & dslElectricField) {
517	bytes += sizeof(Vector3d);
518	}
519	if (layout & dslSkippedCharge) {
520	bytes += sizeof(RealType);
521	}
522	if (layout & dslFlucQPosition) {
523	bytes += sizeof(RealType);
524	}
525	if (layout & dslFlucQVelocity) {
526	bytes += sizeof(RealType);
527	}
528	if (layout & dslFlucQForce) {
529	bytes += sizeof(RealType);
530	}
531
532	return bytes;
533	}
534
535	}