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.
#	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_ & dslZAngle && zAngle.size() != size_) {
92	gezelter	507	//error
93	gezelter	1710	cerr << "size does not match"<< endl;
94	tim	155	}
95
96			if (storageLayout_ & dslForce && force.size() != size_) {
97	gezelter	507	//error
98	gezelter	1710	cerr << "size does not match"<< endl;
99	tim	155	}
100
101			if (storageLayout_ & dslTorque && torque.size() != size_) {
102	gezelter	507	//error
103	gezelter	1710	cerr << "size does not match"<< endl;
104	tim	155	}
105	gezelter	1583
106	chuckv	1245	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
107			//error
108	gezelter	1710	cerr << "size does not match"<< endl;
109	chuckv	1245	}
110	gezelter	1583
111			if (storageLayout_ & dslDensity && density.size() != size_) {
112			//error
113	gezelter	1710	cerr << "size does not match"<< endl;
114	gezelter	1583	}
115
116			if (storageLayout_ & dslFunctional && functional.size() != size_) {
117			//error
118	gezelter	1710	cerr << "size does not match"<< endl;
119	gezelter	1583	}
120
121			if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
122			//error
123	gezelter	1710	cerr << "size does not match"<< endl;
124	gezelter	1583	}
125
126			if (storageLayout_ & dslElectricField && electricField.size() != size_) {
127			//error
128	gezelter	1710	cerr << "size does not match"<< endl;
129	gezelter	1583	}
130	gezelter	1584
131			if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
132			//error
133	gezelter	1710	cerr << "size does not match"<< endl;
134	gezelter	1584	}
135	gezelter	1710
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	chuckv	1245
151	tim	155	return size_;
152
153	gezelter	507	}
154	tim	155
155	gezelter	507	void DataStorage::resize(int newSize) {
156	tim	155
157			if (storageLayout_ & dslPosition) {
158	gezelter	507	internalResize(position, newSize);
159	tim	155	}
160
161			if (storageLayout_ & dslVelocity) {
162	gezelter	507	internalResize(velocity, newSize);
163	tim	155	}
164
165			if (storageLayout_ & dslAmat) {
166	gezelter	507	internalResize(aMat, newSize);
167	tim	155	}
168
169			if (storageLayout_ & dslAngularMomentum) {
170	gezelter	507	internalResize(angularMomentum, newSize);
171	tim	155	}
172
173	gezelter	246	if (storageLayout_ & dslElectroFrame) {
174	gezelter	507	internalResize(electroFrame, newSize);
175	tim	155	}
176
177			if (storageLayout_ & dslZAngle) {
178	gezelter	507	internalResize(zAngle, newSize);
179	tim	155	}
180
181			if (storageLayout_ & dslForce) {
182	gezelter	507	internalResize(force, newSize);
183	tim	155	}
184
185			if (storageLayout_ & dslTorque) {
186	gezelter	507	internalResize(torque, newSize);
187	tim	155	}
188
189	chuckv	1245	if (storageLayout_ & dslParticlePot) {
190			internalResize(particlePot, newSize);
191			}
192
193	gezelter	1583	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	gezelter	1584	if (storageLayout_ & dslSkippedCharge) {
210			internalResize(skippedCharge, newSize);
211			}
212
213	gezelter	1710	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	tim	155	size_ = newSize;
226	gezelter	507	}
227	tim	155
228	gezelter	507	void DataStorage::reserve(int size) {
229	tim	155	if (storageLayout_ & dslPosition) {
230	gezelter	507	position.reserve(size);
231	tim	155	}
232
233			if (storageLayout_ & dslVelocity) {
234	gezelter	507	velocity.reserve(size);
235	tim	155	}
236
237			if (storageLayout_ & dslAmat) {
238	gezelter	507	aMat.reserve(size);
239	tim	155	}
240
241			if (storageLayout_ & dslAngularMomentum) {
242	gezelter	507	angularMomentum.reserve(size);
243	tim	155	}
244
245	gezelter	246	if (storageLayout_ & dslElectroFrame) {
246	gezelter	507	electroFrame.reserve(size);
247	tim	155	}
248
249			if (storageLayout_ & dslZAngle) {
250	gezelter	507	zAngle.reserve(size);
251	tim	155	}
252
253			if (storageLayout_ & dslForce) {
254	gezelter	507	force.reserve(size);
255	tim	155	}
256
257			if (storageLayout_ & dslTorque) {
258	gezelter	507	torque.reserve(size);
259	tim	155	}
260	chuckv	1245
261			if (storageLayout_ & dslParticlePot) {
262			particlePot.reserve(size);
263			}
264	tim	155
265	gezelter	1583	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	gezelter	1584	if (storageLayout_ & dslSkippedCharge) {
282			skippedCharge.reserve(size);
283			}
284
285	gezelter	1710	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	gezelter	507	}
297	tim	155
298	gezelter	507	void DataStorage::copy(int source, int num, int target) {
299	tim	155	if (num + target > size_ ) {
300	gezelter	507	//error
301	tim	155	}
302
303			if (storageLayout_ & dslPosition) {
304	gezelter	507	internalCopy(position, source, num, target);
305	tim	155	}
306
307			if (storageLayout_ & dslVelocity) {
308	gezelter	507	internalCopy(velocity, source, num, target);
309			}
310	tim	155
311			if (storageLayout_ & dslAmat) {
312	gezelter	507	internalCopy(aMat, source, num, target);
313			}
314	tim	155
315			if (storageLayout_ & dslAngularMomentum) {
316	gezelter	507	internalCopy(angularMomentum, source, num, target);
317	tim	155	}
318
319	gezelter	246	if (storageLayout_ & dslElectroFrame) {
320	gezelter	507	internalCopy(electroFrame, source, num, target);
321	tim	155	}
322
323			if (storageLayout_ & dslZAngle) {
324	gezelter	507	internalCopy(zAngle, source, num, target);
325	tim	155	}
326
327			if (storageLayout_ & dslForce) {
328	gezelter	507	internalCopy(force, source, num, target);
329	tim	155	}
330
331			if (storageLayout_ & dslTorque) {
332	gezelter	507	internalCopy(torque, source, num, target);
333	tim	155	}
334	chuckv	1245
335			if (storageLayout_ & dslParticlePot) {
336			internalCopy(particlePot, source, num, target);
337			}
338	tim	155
339	gezelter	1583	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	gezelter	1584
355			if (storageLayout_ & dslSkippedCharge) {
356			internalCopy(skippedCharge, source, num, target);
357			}
358	gezelter	1710
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	gezelter	507	}
370	tim	155
371	gezelter	507	int DataStorage::getStorageLayout() {
372	tim	155	return storageLayout_;
373	gezelter	507	}
374	tim	155
375	gezelter	507	void DataStorage::setStorageLayout(int layout) {
376	tim	155	storageLayout_ = layout;
377			resize(size_);
378	gezelter	507	}
379	tim	155
380	tim	963	RealType* DataStorage::getArrayPointer(int whichArray) {
381	tim	155
382			switch (whichArray) {
383	gezelter	507	case dslPosition:
384			return internalGetArrayPointer(position);
385			break;
386	tim	155
387	gezelter	507	case dslVelocity:
388			return internalGetArrayPointer(velocity);
389			break;
390	tim	155
391	gezelter	507	case dslAmat:
392			return internalGetArrayPointer(aMat);
393			break;
394	tim	155
395	gezelter	507	case dslAngularMomentum:
396			return internalGetArrayPointer(angularMomentum);
397			break;
398	tim	155
399	gezelter	507	case dslElectroFrame:
400			return internalGetArrayPointer(electroFrame);
401			break;
402	tim	155
403	gezelter	507	case dslZAngle:
404			return internalGetArrayPointer(zAngle);
405			break;
406	tim	155
407	gezelter	507	case dslForce:
408			return internalGetArrayPointer(force);
409			break;
410	tim	155
411	gezelter	507	case dslTorque:
412			return internalGetArrayPointer(torque);
413	gezelter	1104	break;
414	chuckv	1245
415			case dslParticlePot:
416			return internalGetArrayPointer(particlePot);
417			break;
418	gezelter	1583
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	gezelter	1584
435			case dslSkippedCharge:
436			return internalGetArrayPointer(skippedCharge);
437			break;
438	gezelter	1710
439			case dslFlucQPosition:
440			return internalGetArrayPointer(flucQPos);
441			break;
442
443			case dslFlucQVelocity:
444			return internalGetArrayPointer(flucQVel);
445			break;
446	gezelter	1583
447	gezelter	1710	case dslFlucQForce:
448			return internalGetArrayPointer(flucQFrc);
449			break;
450
451	gezelter	507	default:
452			//error message
453			return NULL;
454	tim	155
455			}
456	gezelter	507	}
457	tim	155
458	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
459	tim	155	if (v.size() == 0) {
460	gezelter	507	return NULL;
461	tim	155	} else {
462	gezelter	507	return v[0].getArrayPointer();
463	tim	155	}
464	gezelter	507	}
465	tim	155
466	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
467	tim	155	if (v.size() == 0) {
468	gezelter	507	return NULL;
469	tim	155	} else {
470	gezelter	507	return v[0].getArrayPointer();
471	tim	155	}
472
473	gezelter	507	}
474	tim	155
475	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
476	tim	155	if (v.size() == 0) {
477	gezelter	507	return NULL;
478	tim	155	} else {
479	gezelter	507	return &(v[0]);
480	tim	155	}
481
482	gezelter	507	}
483	tim	155
484	gezelter	507	template<typename T>
485			void DataStorage::internalResize(std::vector<T>& v, int newSize){
486	tim	155	int oldSize = v.size();
487
488			if (oldSize == newSize) {
489	gezelter	507	return;
490	tim	155	} else if (oldSize < newSize) {
491	gezelter	507	v.insert(v.end(), newSize-oldSize, T());
492	tim	155	} else {
493	gezelter	507	typename std::vector<T>::iterator i;
494			i = v.begin();
495			std::advance(i, newSize);
496			v.erase(i, v.end());
497	tim	155	}
498	gezelter	507	}
499	tim	155
500	gezelter	507	template<typename T>
501			void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
502	tim	155	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	gezelter	507	}
517	tim	323
518	gezelter	507	int DataStorage::getBytesPerStuntDouble(int layout) {
519	tim	323	int bytes = 0;
520			if (layout & dslPosition) {
521	gezelter	507	bytes += sizeof(Vector3d);
522	tim	331	}
523			if (layout & dslVelocity) {
524	gezelter	507	bytes += sizeof(Vector3d);
525	tim	331	}
526			if (layout & dslAmat) {
527	chuckv	1245	bytes += sizeof(RotMat3x3d);
528	tim	331	}
529			if (layout & dslAngularMomentum) {
530	gezelter	507	bytes += sizeof(Vector3d);
531	tim	331	}
532			if (layout & dslElectroFrame) {
533	gezelter	507	bytes += sizeof(Mat3x3d);
534	tim	331	}
535			if (layout & dslZAngle) {
536	chuckv	1245	bytes += sizeof(RealType);
537	tim	331	}
538			if (layout & dslForce) {
539	gezelter	507	bytes += sizeof(Vector3d);
540	tim	331	}
541			if (layout & dslTorque) {
542	gezelter	507	bytes += sizeof(Vector3d);
543	tim	323	}
544	chuckv	1245	if (layout & dslParticlePot) {
545			bytes += sizeof(RealType);
546			}
547	gezelter	1583	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	gezelter	1584	if (layout & dslSkippedCharge) {
560			bytes += sizeof(RealType);
561			}
562	gezelter	1710	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	gezelter	1583
572	tim	323	return bytes;
573	gezelter	507	}
574	tim	323
575			}