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);
      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 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 & 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:	1711
Committed:	Sat May 19 02:58:35 2012 UTC (12 years, 11 months ago) by gezelter
File size:	14183 byte(s)
Log Message:	Some fixes for DataStorage issues. Removed outdated zangle stuff that has been replaced by the more modern restraints.
#	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	gezelter	1710	using namespace std;
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	gezelter	1710	cerr << "size does not match"<< endl;
69	tim	155	}
70
71			if (storageLayout_ & dslVelocity && velocity.size() != size_) {
72	gezelter	507	//error
73	gezelter	1710	cerr << "size does not match"<< endl;
74	tim	155	}
75
76			if (storageLayout_ & dslAmat && aMat.size() != size_) {
77	gezelter	507	//error
78	gezelter	1710	cerr << "size does not match"<< endl;
79	tim	155	}
80
81			if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
82	gezelter	507	//error
83	gezelter	1710	cerr << "size does not match"<< endl;
84	tim	155	}
85
86	gezelter	246	if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
87	gezelter	507	//error
88	gezelter	1710	cerr << "size does not match"<< endl;
89	tim	155	}
90
91			if (storageLayout_ & dslForce && force.size() != size_) {
92	gezelter	507	//error
93	gezelter	1710	cerr << "size does not match"<< endl;
94	tim	155	}
95
96			if (storageLayout_ & dslTorque && torque.size() != size_) {
97	gezelter	507	//error
98	gezelter	1710	cerr << "size does not match"<< endl;
99	tim	155	}
100	gezelter	1583
101	chuckv	1245	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
102			//error
103	gezelter	1710	cerr << "size does not match"<< endl;
104	chuckv	1245	}
105	gezelter	1583
106			if (storageLayout_ & dslDensity && density.size() != size_) {
107			//error
108	gezelter	1710	cerr << "size does not match"<< endl;
109	gezelter	1583	}
110
111			if (storageLayout_ & dslFunctional && functional.size() != size_) {
112			//error
113	gezelter	1710	cerr << "size does not match"<< endl;
114	gezelter	1583	}
115
116			if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
117			//error
118	gezelter	1710	cerr << "size does not match"<< endl;
119	gezelter	1583	}
120
121			if (storageLayout_ & dslElectricField && electricField.size() != size_) {
122			//error
123	gezelter	1710	cerr << "size does not match"<< endl;
124	gezelter	1583	}
125	gezelter	1584
126			if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
127			//error
128	gezelter	1710	cerr << "size does not match"<< endl;
129	gezelter	1584	}
130	gezelter	1710
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	chuckv	1245
146	tim	155	return size_;
147
148	gezelter	507	}
149	tim	155
150	gezelter	507	void DataStorage::resize(int newSize) {
151	tim	155
152			if (storageLayout_ & dslPosition) {
153	gezelter	507	internalResize(position, newSize);
154	tim	155	}
155
156			if (storageLayout_ & dslVelocity) {
157	gezelter	507	internalResize(velocity, newSize);
158	tim	155	}
159
160			if (storageLayout_ & dslAmat) {
161	gezelter	507	internalResize(aMat, newSize);
162	tim	155	}
163
164			if (storageLayout_ & dslAngularMomentum) {
165	gezelter	507	internalResize(angularMomentum, newSize);
166	tim	155	}
167
168	gezelter	246	if (storageLayout_ & dslElectroFrame) {
169	gezelter	507	internalResize(electroFrame, newSize);
170	tim	155	}
171
172			if (storageLayout_ & dslForce) {
173	gezelter	507	internalResize(force, newSize);
174	tim	155	}
175
176			if (storageLayout_ & dslTorque) {
177	gezelter	507	internalResize(torque, newSize);
178	tim	155	}
179
180	chuckv	1245	if (storageLayout_ & dslParticlePot) {
181			internalResize(particlePot, newSize);
182			}
183
184	gezelter	1583	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	gezelter	1584	if (storageLayout_ & dslSkippedCharge) {
201			internalResize(skippedCharge, newSize);
202			}
203
204	gezelter	1710	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	tim	155	size_ = newSize;
217	gezelter	507	}
218	tim	155
219	gezelter	507	void DataStorage::reserve(int size) {
220	tim	155	if (storageLayout_ & dslPosition) {
221	gezelter	507	position.reserve(size);
222	tim	155	}
223
224			if (storageLayout_ & dslVelocity) {
225	gezelter	507	velocity.reserve(size);
226	tim	155	}
227
228			if (storageLayout_ & dslAmat) {
229	gezelter	507	aMat.reserve(size);
230	tim	155	}
231
232			if (storageLayout_ & dslAngularMomentum) {
233	gezelter	507	angularMomentum.reserve(size);
234	tim	155	}
235
236	gezelter	246	if (storageLayout_ & dslElectroFrame) {
237	gezelter	507	electroFrame.reserve(size);
238	tim	155	}
239
240			if (storageLayout_ & dslForce) {
241	gezelter	507	force.reserve(size);
242	tim	155	}
243
244			if (storageLayout_ & dslTorque) {
245	gezelter	507	torque.reserve(size);
246	tim	155	}
247	chuckv	1245
248			if (storageLayout_ & dslParticlePot) {
249			particlePot.reserve(size);
250			}
251	tim	155
252	gezelter	1583	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	gezelter	1584	if (storageLayout_ & dslSkippedCharge) {
269			skippedCharge.reserve(size);
270			}
271
272	gezelter	1710	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	gezelter	507	}
284	tim	155
285	gezelter	507	void DataStorage::copy(int source, int num, int target) {
286	tim	155	if (num + target > size_ ) {
287	gezelter	507	//error
288	tim	155	}
289
290			if (storageLayout_ & dslPosition) {
291	gezelter	507	internalCopy(position, source, num, target);
292	tim	155	}
293
294			if (storageLayout_ & dslVelocity) {
295	gezelter	507	internalCopy(velocity, source, num, target);
296			}
297	tim	155
298			if (storageLayout_ & dslAmat) {
299	gezelter	507	internalCopy(aMat, source, num, target);
300			}
301	tim	155
302			if (storageLayout_ & dslAngularMomentum) {
303	gezelter	507	internalCopy(angularMomentum, source, num, target);
304	tim	155	}
305
306	gezelter	246	if (storageLayout_ & dslElectroFrame) {
307	gezelter	507	internalCopy(electroFrame, source, num, target);
308	tim	155	}
309
310			if (storageLayout_ & dslForce) {
311	gezelter	507	internalCopy(force, source, num, target);
312	tim	155	}
313
314			if (storageLayout_ & dslTorque) {
315	gezelter	507	internalCopy(torque, source, num, target);
316	tim	155	}
317	chuckv	1245
318			if (storageLayout_ & dslParticlePot) {
319			internalCopy(particlePot, source, num, target);
320			}
321	tim	155
322	gezelter	1583	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	gezelter	1584
338			if (storageLayout_ & dslSkippedCharge) {
339			internalCopy(skippedCharge, source, num, target);
340			}
341	gezelter	1710
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	gezelter	507	}
353	tim	155
354	gezelter	507	int DataStorage::getStorageLayout() {
355	tim	155	return storageLayout_;
356	gezelter	507	}
357	tim	155
358	gezelter	507	void DataStorage::setStorageLayout(int layout) {
359	tim	155	storageLayout_ = layout;
360			resize(size_);
361	gezelter	507	}
362	tim	155
363	tim	963	RealType* DataStorage::getArrayPointer(int whichArray) {
364	tim	155
365			switch (whichArray) {
366	gezelter	507	case dslPosition:
367			return internalGetArrayPointer(position);
368			break;
369	tim	155
370	gezelter	507	case dslVelocity:
371			return internalGetArrayPointer(velocity);
372			break;
373	tim	155
374	gezelter	507	case dslAmat:
375			return internalGetArrayPointer(aMat);
376			break;
377	tim	155
378	gezelter	507	case dslAngularMomentum:
379			return internalGetArrayPointer(angularMomentum);
380			break;
381	tim	155
382	gezelter	507	case dslElectroFrame:
383			return internalGetArrayPointer(electroFrame);
384			break;
385	tim	155
386	gezelter	507	case dslForce:
387			return internalGetArrayPointer(force);
388			break;
389	tim	155
390	gezelter	507	case dslTorque:
391			return internalGetArrayPointer(torque);
392	gezelter	1104	break;
393	chuckv	1245
394			case dslParticlePot:
395			return internalGetArrayPointer(particlePot);
396			break;
397	gezelter	1583
398			case dslDensity:
399			return internalGetArrayPointer(density);
400			break;
401
402			case dslFunctional:
403			return internalGetArrayPointer(functional);
404			break;
405
406			case dslFunctionalDerivative:
407			return internalGetArrayPointer(functionalDerivative);
408			break;
409
410			case dslElectricField:
411			return internalGetArrayPointer(electricField);
412			break;
413	gezelter	1584
414			case dslSkippedCharge:
415			return internalGetArrayPointer(skippedCharge);
416			break;
417	gezelter	1710
418			case dslFlucQPosition:
419			return internalGetArrayPointer(flucQPos);
420			break;
421
422			case dslFlucQVelocity:
423			return internalGetArrayPointer(flucQVel);
424			break;
425	gezelter	1583
426	gezelter	1710	case dslFlucQForce:
427			return internalGetArrayPointer(flucQFrc);
428			break;
429
430	gezelter	507	default:
431			//error message
432			return NULL;
433	tim	155
434			}
435	gezelter	507	}
436	tim	155
437	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
438	tim	155	if (v.size() == 0) {
439	gezelter	507	return NULL;
440	tim	155	} else {
441	gezelter	507	return v[0].getArrayPointer();
442	tim	155	}
443	gezelter	507	}
444	tim	155
445	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
446	tim	155	if (v.size() == 0) {
447	gezelter	507	return NULL;
448	tim	155	} else {
449	gezelter	507	return v[0].getArrayPointer();
450	tim	155	}
451
452	gezelter	507	}
453	tim	155
454	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
455	tim	155	if (v.size() == 0) {
456	gezelter	507	return NULL;
457	tim	155	} else {
458	gezelter	507	return &(v[0]);
459	tim	155	}
460
461	gezelter	507	}
462	tim	155
463	gezelter	507	template<typename T>
464			void DataStorage::internalResize(std::vector<T>& v, int newSize){
465	tim	155	int oldSize = v.size();
466
467			if (oldSize == newSize) {
468	gezelter	507	return;
469	tim	155	} else if (oldSize < newSize) {
470	gezelter	507	v.insert(v.end(), newSize-oldSize, T());
471	tim	155	} else {
472	gezelter	507	typename std::vector<T>::iterator i;
473			i = v.begin();
474			std::advance(i, newSize);
475			v.erase(i, v.end());
476	tim	155	}
477	gezelter	507	}
478	tim	155
479	gezelter	507	template<typename T>
480			void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
481	tim	155	typename std::vector<T>::iterator first;
482			typename std::vector<T>::iterator last;
483			typename std::vector<T>::iterator result;
484
485			first = v.begin();
486			last = v.begin();
487			result = v.begin();
488
489			std::advance(first, source);
490			//STL algorithm use half opened range
491			std::advance(last, num + 1);
492			std::advance(result, target );
493
494			std::copy(first, last, result);
495	gezelter	507	}
496	tim	323
497	gezelter	507	int DataStorage::getBytesPerStuntDouble(int layout) {
498	tim	323	int bytes = 0;
499			if (layout & dslPosition) {
500	gezelter	507	bytes += sizeof(Vector3d);
501	tim	331	}
502			if (layout & dslVelocity) {
503	gezelter	507	bytes += sizeof(Vector3d);
504	tim	331	}
505			if (layout & dslAmat) {
506	chuckv	1245	bytes += sizeof(RotMat3x3d);
507	tim	331	}
508			if (layout & dslAngularMomentum) {
509	gezelter	507	bytes += sizeof(Vector3d);
510	tim	331	}
511			if (layout & dslElectroFrame) {
512	gezelter	507	bytes += sizeof(Mat3x3d);
513	tim	331	}
514			if (layout & dslForce) {
515	gezelter	507	bytes += sizeof(Vector3d);
516	tim	331	}
517			if (layout & dslTorque) {
518	gezelter	507	bytes += sizeof(Vector3d);
519	tim	323	}
520	chuckv	1245	if (layout & dslParticlePot) {
521			bytes += sizeof(RealType);
522			}
523	gezelter	1583	if (layout & dslDensity) {
524			bytes += sizeof(RealType);
525			}
526			if (layout & dslFunctional) {
527			bytes += sizeof(RealType);
528			}
529			if (layout & dslFunctionalDerivative) {
530			bytes += sizeof(RealType);
531			}
532			if (layout & dslElectricField) {
533			bytes += sizeof(Vector3d);
534			}
535	gezelter	1584	if (layout & dslSkippedCharge) {
536			bytes += sizeof(RealType);
537			}
538	gezelter	1710	if (layout & dslFlucQPosition) {
539			bytes += sizeof(RealType);
540			}
541			if (layout & dslFlucQVelocity) {
542			bytes += sizeof(RealType);
543			}
544			if (layout & dslFlucQForce) {
545			bytes += sizeof(RealType);
546			}
547	gezelter	1583
548	tim	323	return bytes;
549	gezelter	507	}
550	tim	323
551			}