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, 234107 (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
 * @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_ & dslForce && force.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_ & 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_ & dslDipole && dipole.size() != size_) {
      //error
      cerr << "size does not match"<< endl;        
    }

    if (storageLayout_ & dslQuadrupole && quadrupole.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;        
    }

    if (storageLayout_ & dslSitePotential && sitePotential.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_ & dslForce) {
      internalResize(force, newSize);
    }

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

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

    if (storageLayout_ & dslQuadrupole) {
      internalResize(quadrupole, 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);
    }

    if (storageLayout_ & dslSitePotential) {
      internalResize(sitePotential, newSize);
    }

    size_ = newSize;
  }

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

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

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

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

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

    if (storageLayout_ & dslQuadrupole) {
      quadrupole.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);
    }

    if (storageLayout_ & dslSitePotential) {
      sitePotential.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_ & dslForce) {
      internalCopy(force, source, num, target);
    } 

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

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

    if (storageLayout_ & dslQuadrupole) {
      internalCopy(quadrupole, 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);
    }

    if (storageLayout_ & dslSitePotential) {
      internalCopy(sitePotential, 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 dslForce:
      return internalGetArrayPointer(force);

    case dslAmat:
      return internalGetArrayPointer(aMat);
            
    case dslAngularMomentum:
      return internalGetArrayPointer(angularMomentum);
            
    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 dslDipole:
      return internalGetArrayPointer(dipole);

    case dslQuadrupole:
      return internalGetArrayPointer(quadrupole);

    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);
           
    case dslSitePotential:
      return internalGetArrayPointer(sitePotential);
           
    default:
      //error message
      return NULL;
    }
  }    

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

  RealType* DataStorage::internalGetArrayPointer(std::vector<Mat3x3d>& v) {
    if (v.empty()) {
      return NULL;
    } else {
      return v[0].getArrayPointer();
    }

  }

  RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
    if (v.empty()) {
      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 & dslForce) {
      bytes += sizeof(Vector3d);
    }
    if (layout & dslAmat) {
      bytes += sizeof(RotMat3x3d);    
    }
    if (layout & dslAngularMomentum) {
      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 & dslDipole) {
      bytes += sizeof(Vector3d);
    }
    if (layout & dslQuadrupole) {
      bytes += sizeof(Mat3x3d);
    }
    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);
    }
    if (layout & dslSitePotential) {
      bytes += sizeof(RealType);
    }

    return bytes;
  }

}
Revision:	1993
Committed:	Tue Apr 29 17:32:31 2014 UTC (11 years ago) by gezelter
File size:	15013 byte(s)
Log Message:	Added sitePotentials for the Choi et al. potential-frequency maps for nitriles
#	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, 234107 (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	* @version 1.0
48	*/
49
50	#include "brains/DataStorage.hpp"
51	using namespace std;
52	namespace OpenMD {
53
54	DataStorage::DataStorage() : size_(0), storageLayout_(0){
55
56	}
57
58	DataStorage::DataStorage(int size, int storageLayout) : size_(size){
59	setStorageLayout(storageLayout);
60	resize(size);
61	}
62
63	int DataStorage::getSize() {
64
65	if (storageLayout_ & dslPosition && position.size() != size_) {
66	//error
67	cerr << "size does not match"<< endl;
68	}
69
70	if (storageLayout_ & dslVelocity && velocity.size() != size_) {
71	//error
72	cerr << "size does not match"<< endl;
73	}
74
75	if (storageLayout_ & dslForce && force.size() != size_) {
76	//error
77	cerr << "size does not match"<< endl;
78	}
79
80	if (storageLayout_ & dslAmat && aMat.size() != size_) {
81	//error
82	cerr << "size does not match"<< endl;
83	}
84
85	if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
86	//error
87	cerr << "size does not match"<< endl;
88	}
89
90	if (storageLayout_ & dslTorque && torque.size() != size_) {
91	//error
92	cerr << "size does not match"<< endl;
93	}
94
95	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
96	//error
97	cerr << "size does not match"<< endl;
98	}
99
100	if (storageLayout_ & dslDensity && density.size() != size_) {
101	//error
102	cerr << "size does not match"<< endl;
103	}
104
105	if (storageLayout_ & dslFunctional && functional.size() != size_) {
106	//error
107	cerr << "size does not match"<< endl;
108	}
109
110	if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
111	//error
112	cerr << "size does not match"<< endl;
113	}
114
115	if (storageLayout_ & dslDipole && dipole.size() != size_) {
116	//error
117	cerr << "size does not match"<< endl;
118	}
119
120	if (storageLayout_ & dslQuadrupole && quadrupole.size() != size_) {
121	//error
122	cerr << "size does not match"<< endl;
123	}
124
125	if (storageLayout_ & dslElectricField && electricField.size() != size_) {
126	//error
127	cerr << "size does not match"<< endl;
128	}
129
130	if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
131	//error
132	cerr << "size does not match"<< endl;
133	}
134
135	if (storageLayout_ & dslFlucQPosition && flucQPos.size() != size_) {
136	//error
137	cerr << "size does not match"<< endl;
138	}
139
140	if (storageLayout_ & dslFlucQVelocity && flucQVel.size() != size_) {
141	//error
142	cerr << "size does not match"<< endl;
143	}
144
145	if (storageLayout_ & dslFlucQForce && flucQFrc.size() != size_) {
146	//error
147	cerr << "size does not match"<< endl;
148	}
149
150	if (storageLayout_ & dslSitePotential && sitePotential.size() != size_) {
151	//error
152	cerr << "size does not match"<< endl;
153	}
154
155	return size_;
156
157	}
158
159	void DataStorage::resize(int newSize) {
160
161	if (storageLayout_ & dslPosition) {
162	internalResize(position, newSize);
163	}
164
165	if (storageLayout_ & dslVelocity) {
166	internalResize(velocity, newSize);
167	}
168
169	if (storageLayout_ & dslForce) {
170	internalResize(force, newSize);
171	}
172
173	if (storageLayout_ & dslAmat) {
174	internalResize(aMat, newSize);
175	}
176
177	if (storageLayout_ & dslAngularMomentum) {
178	internalResize(angularMomentum, newSize);
179	}
180
181	if (storageLayout_ & dslTorque) {
182	internalResize(torque, newSize);
183	}
184
185	if (storageLayout_ & dslParticlePot) {
186	internalResize(particlePot, newSize);
187	}
188
189	if (storageLayout_ & dslDensity) {
190	internalResize(density, newSize);
191	}
192
193	if (storageLayout_ & dslFunctional) {
194	internalResize(functional, newSize);
195	}
196
197	if (storageLayout_ & dslFunctionalDerivative) {
198	internalResize(functionalDerivative, newSize);
199	}
200
201	if (storageLayout_ & dslDipole) {
202	internalResize(dipole, newSize);
203	}
204
205	if (storageLayout_ & dslQuadrupole) {
206	internalResize(quadrupole, newSize);
207	}
208
209	if (storageLayout_ & dslElectricField) {
210	internalResize(electricField, newSize);
211	}
212
213	if (storageLayout_ & dslSkippedCharge) {
214	internalResize(skippedCharge, newSize);
215	}
216
217	if (storageLayout_ & dslFlucQPosition) {
218	internalResize(flucQPos, newSize);
219	}
220
221	if (storageLayout_ & dslFlucQVelocity) {
222	internalResize(flucQVel, newSize);
223	}
224
225	if (storageLayout_ & dslFlucQForce) {
226	internalResize(flucQFrc, newSize);
227	}
228
229	if (storageLayout_ & dslSitePotential) {
230	internalResize(sitePotential, newSize);
231	}
232
233	size_ = newSize;
234	}
235
236	void DataStorage::reserve(int size) {
237	if (storageLayout_ & dslPosition) {
238	position.reserve(size);
239	}
240
241	if (storageLayout_ & dslVelocity) {
242	velocity.reserve(size);
243	}
244
245	if (storageLayout_ & dslForce) {
246	force.reserve(size);
247	}
248
249	if (storageLayout_ & dslAmat) {
250	aMat.reserve(size);
251	}
252
253	if (storageLayout_ & dslAngularMomentum) {
254	angularMomentum.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_ & dslDipole) {
278	dipole.reserve(size);
279	}
280
281	if (storageLayout_ & dslQuadrupole) {
282	quadrupole.reserve(size);
283	}
284
285	if (storageLayout_ & dslElectricField) {
286	electricField.reserve(size);
287	}
288
289	if (storageLayout_ & dslSkippedCharge) {
290	skippedCharge.reserve(size);
291	}
292
293	if (storageLayout_ & dslFlucQPosition) {
294	flucQPos.reserve(size);
295	}
296
297	if (storageLayout_ & dslFlucQVelocity) {
298	flucQVel.reserve(size);
299	}
300
301	if (storageLayout_ & dslFlucQForce) {
302	flucQFrc.reserve(size);
303	}
304
305	if (storageLayout_ & dslSitePotential) {
306	sitePotential.reserve(size);
307	}
308	}
309
310	void DataStorage::copy(int source, int num, int target) {
311	if (num + target > size_ ) {
312	//error
313	}
314
315	if (storageLayout_ & dslPosition) {
316	internalCopy(position, source, num, target);
317	}
318
319	if (storageLayout_ & dslVelocity) {
320	internalCopy(velocity, source, num, target);
321	}
322
323	if (storageLayout_ & dslForce) {
324	internalCopy(force, source, num, target);
325	}
326
327	if (storageLayout_ & dslAmat) {
328	internalCopy(aMat, source, num, target);
329	}
330
331	if (storageLayout_ & dslAngularMomentum) {
332	internalCopy(angularMomentum, source, num, target);
333	}
334
335	if (storageLayout_ & dslTorque) {
336	internalCopy(torque, source, num, target);
337	}
338
339	if (storageLayout_ & dslParticlePot) {
340	internalCopy(particlePot, source, num, target);
341	}
342
343	if (storageLayout_ & dslDensity) {
344	internalCopy(density, source, num, target);
345	}
346
347	if (storageLayout_ & dslFunctional) {
348	internalCopy(functional, source, num, target);
349	}
350
351	if (storageLayout_ & dslFunctionalDerivative) {
352	internalCopy(functionalDerivative, source, num, target);
353	}
354
355	if (storageLayout_ & dslDipole) {
356	internalCopy(dipole, source, num, target);
357	}
358
359	if (storageLayout_ & dslQuadrupole) {
360	internalCopy(quadrupole, source, num, target);
361	}
362
363	if (storageLayout_ & dslElectricField) {
364	internalCopy(electricField, source, num, target);
365	}
366
367	if (storageLayout_ & dslSkippedCharge) {
368	internalCopy(skippedCharge, source, num, target);
369	}
370
371	if (storageLayout_ & dslFlucQPosition) {
372	internalCopy(flucQPos, source, num, target);
373	}
374
375	if (storageLayout_ & dslFlucQVelocity) {
376	internalCopy(flucQVel, source, num, target);
377	}
378	if (storageLayout_ & dslFlucQForce) {
379	internalCopy(flucQFrc, source, num, target);
380	}
381
382	if (storageLayout_ & dslSitePotential) {
383	internalCopy(sitePotential, source, num, target);
384	}
385	}
386
387	int DataStorage::getStorageLayout() {
388	return storageLayout_;
389	}
390
391	void DataStorage::setStorageLayout(int layout) {
392	storageLayout_ = layout;
393	resize(size_);
394	}
395
396	RealType* DataStorage::getArrayPointer(int whichArray) {
397
398	switch (whichArray) {
399	case dslPosition:
400	return internalGetArrayPointer(position);
401
402	case dslVelocity:
403	return internalGetArrayPointer(velocity);
404
405	case dslForce:
406	return internalGetArrayPointer(force);
407
408	case dslAmat:
409	return internalGetArrayPointer(aMat);
410
411	case dslAngularMomentum:
412	return internalGetArrayPointer(angularMomentum);
413
414	case dslTorque:
415	return internalGetArrayPointer(torque);
416
417	case dslParticlePot:
418	return internalGetArrayPointer(particlePot);
419
420	case dslDensity:
421	return internalGetArrayPointer(density);
422
423	case dslFunctional:
424	return internalGetArrayPointer(functional);
425
426	case dslFunctionalDerivative:
427	return internalGetArrayPointer(functionalDerivative);
428
429	case dslDipole:
430	return internalGetArrayPointer(dipole);
431
432	case dslQuadrupole:
433	return internalGetArrayPointer(quadrupole);
434
435	case dslElectricField:
436	return internalGetArrayPointer(electricField);
437
438	case dslSkippedCharge:
439	return internalGetArrayPointer(skippedCharge);
440
441	case dslFlucQPosition:
442	return internalGetArrayPointer(flucQPos);
443
444	case dslFlucQVelocity:
445	return internalGetArrayPointer(flucQVel);
446
447	case dslFlucQForce:
448	return internalGetArrayPointer(flucQFrc);
449
450	case dslSitePotential:
451	return internalGetArrayPointer(sitePotential);
452
453	default:
454	//error message
455	return NULL;
456	}
457	}
458
459	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
460	if (v.empty()) {
461	return NULL;
462	} else {
463	return v[0].getArrayPointer();
464	}
465	}
466
467	RealType* DataStorage::internalGetArrayPointer(std::vector<Mat3x3d>& v) {
468	if (v.empty()) {
469	return NULL;
470	} else {
471	return v[0].getArrayPointer();
472	}
473
474	}
475
476	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
477	if (v.empty()) {
478	return NULL;
479	} else {
480	return &(v[0]);
481	}
482
483	}
484
485	template<typename T>
486	void DataStorage::internalResize(std::vector<T>& v, int newSize){
487	int oldSize = v.size();
488
489	if (oldSize == newSize) {
490	return;
491	} else if (oldSize < newSize) {
492	v.insert(v.end(), newSize-oldSize, T());
493	} else {
494	typename std::vector<T>::iterator i;
495	i = v.begin();
496	std::advance(i, newSize);
497	v.erase(i, v.end());
498	}
499	}
500
501	template<typename T>
502	void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
503	typename std::vector<T>::iterator first;
504	typename std::vector<T>::iterator last;
505	typename std::vector<T>::iterator result;
506
507	first = v.begin();
508	last = v.begin();
509	result = v.begin();
510
511	std::advance(first, source);
512	//STL algorithm use half opened range
513	std::advance(last, num + 1);
514	std::advance(result, target );
515
516	std::copy(first, last, result);
517	}
518
519	int DataStorage::getBytesPerStuntDouble(int layout) {
520	int bytes = 0;
521	if (layout & dslPosition) {
522	bytes += sizeof(Vector3d);
523	}
524	if (layout & dslVelocity) {
525	bytes += sizeof(Vector3d);
526	}
527	if (layout & dslForce) {
528	bytes += sizeof(Vector3d);
529	}
530	if (layout & dslAmat) {
531	bytes += sizeof(RotMat3x3d);
532	}
533	if (layout & dslAngularMomentum) {
534	bytes += sizeof(Vector3d);
535	}
536	if (layout & dslTorque) {
537	bytes += sizeof(Vector3d);
538	}
539	if (layout & dslParticlePot) {
540	bytes += sizeof(RealType);
541	}
542	if (layout & dslDensity) {
543	bytes += sizeof(RealType);
544	}
545	if (layout & dslFunctional) {
546	bytes += sizeof(RealType);
547	}
548	if (layout & dslFunctionalDerivative) {
549	bytes += sizeof(RealType);
550	}
551	if (layout & dslDipole) {
552	bytes += sizeof(Vector3d);
553	}
554	if (layout & dslQuadrupole) {
555	bytes += sizeof(Mat3x3d);
556	}
557	if (layout & dslElectricField) {
558	bytes += sizeof(Vector3d);
559	}
560	if (layout & dslSkippedCharge) {
561	bytes += sizeof(RealType);
562	}
563	if (layout & dslFlucQPosition) {
564	bytes += sizeof(RealType);
565	}
566	if (layout & dslFlucQVelocity) {
567	bytes += sizeof(RealType);
568	}
569	if (layout & dslFlucQForce) {
570	bytes += sizeof(RealType);
571	}
572	if (layout & dslSitePotential) {
573	bytes += sizeof(RealType);
574	}
575
576	return bytes;
577	}
578
579	}