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_ & dslZAngle && zAngle.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_ & 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);
    }

    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_ & 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);
    }

    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_ & 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);
    }

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

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

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

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

  RealType* DataStorage::getArrayPointer(int whichArray) {

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

    case dslFlucQPosition:
      return internalGetArrayPointer(flucQPos);
      break;

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

    }
  }    

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

  RealType* DataStorage::internalGetArrayPointer(std::vector<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);
    }
    if (layout & dslFlucQPosition) {
      bytes += sizeof(RealType);
    }
    if (layout & dslFlucQVelocity) {
      bytes += sizeof(RealType);
    }
    if (layout & dslFlucQForce) {
      bytes += sizeof(RealType);
    }

    return bytes;
  }

}
Revision:	1710
Committed:	Fri May 18 21:44:02 2012 UTC (12 years, 11 months ago) by gezelter
File size:	14720 byte(s)
Log Message:	Added an adapter layer between the AtomType and the rest of the code to handle the bolt-on capabilities of new types. Fixed a long-standing bug in how storageLayout was being set to the maximum possible value. Started to add infrastructure for Polarizable and fluc-Q calculations.
#	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_ & dslZAngle && zAngle.size() != size_) {
92	//error
93	cerr << "size does not match"<< endl;
94	}
95
96	if (storageLayout_ & dslForce && force.size() != size_) {
97	//error
98	cerr << "size does not match"<< endl;
99	}
100
101	if (storageLayout_ & dslTorque && torque.size() != size_) {
102	//error
103	cerr << "size does not match"<< endl;
104	}
105
106	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
107	//error
108	cerr << "size does not match"<< endl;
109	}
110
111	if (storageLayout_ & dslDensity && density.size() != size_) {
112	//error
113	cerr << "size does not match"<< endl;
114	}
115
116	if (storageLayout_ & dslFunctional && functional.size() != size_) {
117	//error
118	cerr << "size does not match"<< endl;
119	}
120
121	if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
122	//error
123	cerr << "size does not match"<< endl;
124	}
125
126	if (storageLayout_ & dslElectricField && electricField.size() != size_) {
127	//error
128	cerr << "size does not match"<< endl;
129	}
130
131	if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
132	//error
133	cerr << "size does not match"<< endl;
134	}
135
136	if (storageLayout_ & dslFlucQPosition && flucQPos.size() != size_) {
137	//error
138	cerr << "size does not match"<< endl;
139	}
140
141	if (storageLayout_ & dslFlucQVelocity && flucQVel.size() != size_) {
142	//error
143	cerr << "size does not match"<< endl;
144	}
145
146	if (storageLayout_ & dslFlucQForce && flucQFrc.size() != size_) {
147	//error
148	cerr << "size does not match"<< endl;
149	}
150
151	return size_;
152
153	}
154
155	void DataStorage::resize(int newSize) {
156
157	if (storageLayout_ & dslPosition) {
158	internalResize(position, newSize);
159	}
160
161	if (storageLayout_ & dslVelocity) {
162	internalResize(velocity, newSize);
163	}
164
165	if (storageLayout_ & dslAmat) {
166	internalResize(aMat, newSize);
167	}
168
169	if (storageLayout_ & dslAngularMomentum) {
170	internalResize(angularMomentum, newSize);
171	}
172
173	if (storageLayout_ & dslElectroFrame) {
174	internalResize(electroFrame, newSize);
175	}
176
177	if (storageLayout_ & dslZAngle) {
178	internalResize(zAngle, newSize);
179	}
180
181	if (storageLayout_ & dslForce) {
182	internalResize(force, newSize);
183	}
184
185	if (storageLayout_ & dslTorque) {
186	internalResize(torque, newSize);
187	}
188
189	if (storageLayout_ & dslParticlePot) {
190	internalResize(particlePot, newSize);
191	}
192
193	if (storageLayout_ & dslDensity) {
194	internalResize(density, newSize);
195	}
196
197	if (storageLayout_ & dslFunctional) {
198	internalResize(functional, newSize);
199	}
200
201	if (storageLayout_ & dslFunctionalDerivative) {
202	internalResize(functionalDerivative, newSize);
203	}
204
205	if (storageLayout_ & dslElectricField) {
206	internalResize(electricField, newSize);
207	}
208
209	if (storageLayout_ & dslSkippedCharge) {
210	internalResize(skippedCharge, newSize);
211	}
212
213	if (storageLayout_ & dslFlucQPosition) {
214	internalResize(flucQPos, newSize);
215	}
216
217	if (storageLayout_ & dslFlucQVelocity) {
218	internalResize(flucQVel, newSize);
219	}
220
221	if (storageLayout_ & dslFlucQForce) {
222	internalResize(flucQFrc, newSize);
223	}
224
225	size_ = newSize;
226	}
227
228	void DataStorage::reserve(int size) {
229	if (storageLayout_ & dslPosition) {
230	position.reserve(size);
231	}
232
233	if (storageLayout_ & dslVelocity) {
234	velocity.reserve(size);
235	}
236
237	if (storageLayout_ & dslAmat) {
238	aMat.reserve(size);
239	}
240
241	if (storageLayout_ & dslAngularMomentum) {
242	angularMomentum.reserve(size);
243	}
244
245	if (storageLayout_ & dslElectroFrame) {
246	electroFrame.reserve(size);
247	}
248
249	if (storageLayout_ & dslZAngle) {
250	zAngle.reserve(size);
251	}
252
253	if (storageLayout_ & dslForce) {
254	force.reserve(size);
255	}
256
257	if (storageLayout_ & dslTorque) {
258	torque.reserve(size);
259	}
260
261	if (storageLayout_ & dslParticlePot) {
262	particlePot.reserve(size);
263	}
264
265	if (storageLayout_ & dslDensity) {
266	density.reserve(size);
267	}
268
269	if (storageLayout_ & dslFunctional) {
270	functional.reserve(size);
271	}
272
273	if (storageLayout_ & dslFunctionalDerivative) {
274	functionalDerivative.reserve(size);
275	}
276
277	if (storageLayout_ & dslElectricField) {
278	electricField.reserve(size);
279	}
280
281	if (storageLayout_ & dslSkippedCharge) {
282	skippedCharge.reserve(size);
283	}
284
285	if (storageLayout_ & dslFlucQPosition) {
286	flucQPos.reserve(size);
287	}
288
289	if (storageLayout_ & dslFlucQVelocity) {
290	flucQVel.reserve(size);
291	}
292
293	if (storageLayout_ & dslFlucQForce) {
294	flucQFrc.reserve(size);
295	}
296	}
297
298	void DataStorage::copy(int source, int num, int target) {
299	if (num + target > size_ ) {
300	//error
301	}
302
303	if (storageLayout_ & dslPosition) {
304	internalCopy(position, source, num, target);
305	}
306
307	if (storageLayout_ & dslVelocity) {
308	internalCopy(velocity, source, num, target);
309	}
310
311	if (storageLayout_ & dslAmat) {
312	internalCopy(aMat, source, num, target);
313	}
314
315	if (storageLayout_ & dslAngularMomentum) {
316	internalCopy(angularMomentum, source, num, target);
317	}
318
319	if (storageLayout_ & dslElectroFrame) {
320	internalCopy(electroFrame, source, num, target);
321	}
322
323	if (storageLayout_ & dslZAngle) {
324	internalCopy(zAngle, source, num, target);
325	}
326
327	if (storageLayout_ & dslForce) {
328	internalCopy(force, source, num, target);
329	}
330
331	if (storageLayout_ & dslTorque) {
332	internalCopy(torque, source, num, target);
333	}
334
335	if (storageLayout_ & dslParticlePot) {
336	internalCopy(particlePot, source, num, target);
337	}
338
339	if (storageLayout_ & dslDensity) {
340	internalCopy(density, source, num, target);
341	}
342
343	if (storageLayout_ & dslFunctional) {
344	internalCopy(functional, source, num, target);
345	}
346
347	if (storageLayout_ & dslFunctionalDerivative) {
348	internalCopy(functionalDerivative, source, num, target);
349	}
350
351	if (storageLayout_ & dslElectricField) {
352	internalCopy(electricField, source, num, target);
353	}
354
355	if (storageLayout_ & dslSkippedCharge) {
356	internalCopy(skippedCharge, source, num, target);
357	}
358
359	if (storageLayout_ & dslFlucQPosition) {
360	internalCopy(flucQPos, source, num, target);
361	}
362
363	if (storageLayout_ & dslFlucQVelocity) {
364	internalCopy(flucQVel, source, num, target);
365	}
366	if (storageLayout_ & dslFlucQForce) {
367	internalCopy(flucQFrc, source, num, target);
368	}
369	}
370
371	int DataStorage::getStorageLayout() {
372	return storageLayout_;
373	}
374
375	void DataStorage::setStorageLayout(int layout) {
376	storageLayout_ = layout;
377	resize(size_);
378	}
379
380	RealType* DataStorage::getArrayPointer(int whichArray) {
381
382	switch (whichArray) {
383	case dslPosition:
384	return internalGetArrayPointer(position);
385	break;
386
387	case dslVelocity:
388	return internalGetArrayPointer(velocity);
389	break;
390
391	case dslAmat:
392	return internalGetArrayPointer(aMat);
393	break;
394
395	case dslAngularMomentum:
396	return internalGetArrayPointer(angularMomentum);
397	break;
398
399	case dslElectroFrame:
400	return internalGetArrayPointer(electroFrame);
401	break;
402
403	case dslZAngle:
404	return internalGetArrayPointer(zAngle);
405	break;
406
407	case dslForce:
408	return internalGetArrayPointer(force);
409	break;
410
411	case dslTorque:
412	return internalGetArrayPointer(torque);
413	break;
414
415	case dslParticlePot:
416	return internalGetArrayPointer(particlePot);
417	break;
418
419	case dslDensity:
420	return internalGetArrayPointer(density);
421	break;
422
423	case dslFunctional:
424	return internalGetArrayPointer(functional);
425	break;
426
427	case dslFunctionalDerivative:
428	return internalGetArrayPointer(functionalDerivative);
429	break;
430
431	case dslElectricField:
432	return internalGetArrayPointer(electricField);
433	break;
434
435	case dslSkippedCharge:
436	return internalGetArrayPointer(skippedCharge);
437	break;
438
439	case dslFlucQPosition:
440	return internalGetArrayPointer(flucQPos);
441	break;
442
443	case dslFlucQVelocity:
444	return internalGetArrayPointer(flucQVel);
445	break;
446
447	case dslFlucQForce:
448	return internalGetArrayPointer(flucQFrc);
449	break;
450
451	default:
452	//error message
453	return NULL;
454
455	}
456	}
457
458	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
459	if (v.size() == 0) {
460	return NULL;
461	} else {
462	return v[0].getArrayPointer();
463	}
464	}
465
466	RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
467	if (v.size() == 0) {
468	return NULL;
469	} else {
470	return v[0].getArrayPointer();
471	}
472
473	}
474
475	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
476	if (v.size() == 0) {
477	return NULL;
478	} else {
479	return &(v[0]);
480	}
481
482	}
483
484	template<typename T>
485	void DataStorage::internalResize(std::vector<T>& v, int newSize){
486	int oldSize = v.size();
487
488	if (oldSize == newSize) {
489	return;
490	} else if (oldSize < newSize) {
491	v.insert(v.end(), newSize-oldSize, T());
492	} else {
493	typename std::vector<T>::iterator i;
494	i = v.begin();
495	std::advance(i, newSize);
496	v.erase(i, v.end());
497	}
498	}
499
500	template<typename T>
501	void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
502	typename std::vector<T>::iterator first;
503	typename std::vector<T>::iterator last;
504	typename std::vector<T>::iterator result;
505
506	first = v.begin();
507	last = v.begin();
508	result = v.begin();
509
510	std::advance(first, source);
511	//STL algorithm use half opened range
512	std::advance(last, num + 1);
513	std::advance(result, target );
514
515	std::copy(first, last, result);
516	}
517
518	int DataStorage::getBytesPerStuntDouble(int layout) {
519	int bytes = 0;
520	if (layout & dslPosition) {
521	bytes += sizeof(Vector3d);
522	}
523	if (layout & dslVelocity) {
524	bytes += sizeof(Vector3d);
525	}
526	if (layout & dslAmat) {
527	bytes += sizeof(RotMat3x3d);
528	}
529	if (layout & dslAngularMomentum) {
530	bytes += sizeof(Vector3d);
531	}
532	if (layout & dslElectroFrame) {
533	bytes += sizeof(Mat3x3d);
534	}
535	if (layout & dslZAngle) {
536	bytes += sizeof(RealType);
537	}
538	if (layout & dslForce) {
539	bytes += sizeof(Vector3d);
540	}
541	if (layout & dslTorque) {
542	bytes += sizeof(Vector3d);
543	}
544	if (layout & dslParticlePot) {
545	bytes += sizeof(RealType);
546	}
547	if (layout & dslDensity) {
548	bytes += sizeof(RealType);
549	}
550	if (layout & dslFunctional) {
551	bytes += sizeof(RealType);
552	}
553	if (layout & dslFunctionalDerivative) {
554	bytes += sizeof(RealType);
555	}
556	if (layout & dslElectricField) {
557	bytes += sizeof(Vector3d);
558	}
559	if (layout & dslSkippedCharge) {
560	bytes += sizeof(RealType);
561	}
562	if (layout & dslFlucQPosition) {
563	bytes += sizeof(RealType);
564	}
565	if (layout & dslFlucQVelocity) {
566	bytes += sizeof(RealType);
567	}
568	if (layout & dslFlucQForce) {
569	bytes += sizeof(RealType);
570	}
571
572	return bytes;
573	}
574
575	}