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
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [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			* @version 1.0
48			*/
49	tim	155
50			#include "brains/DataStorage.hpp"
51	gezelter	1782	using namespace std;
52	gezelter	1390	namespace OpenMD {
53	tim	155
54	gezelter	507	DataStorage::DataStorage() : size_(0), storageLayout_(0){
55	tim	155
56	gezelter	507	}
57	tim	155
58	gezelter	507	DataStorage::DataStorage(int size, int storageLayout) : size_(size){
59	tim	155	setStorageLayout(storageLayout);
60			resize(size);
61	gezelter	507	}
62	tim	155
63	gezelter	507	int DataStorage::getSize() {
64	tim	155
65			if (storageLayout_ & dslPosition && position.size() != size_) {
66	gezelter	507	//error
67	gezelter	1782	cerr << "size does not match"<< endl;
68	tim	155	}
69
70			if (storageLayout_ & dslVelocity && velocity.size() != size_) {
71	gezelter	507	//error
72	gezelter	1782	cerr << "size does not match"<< endl;
73	tim	155	}
74
75	gezelter	1879	if (storageLayout_ & dslForce && force.size() != size_) {
76			//error
77			cerr << "size does not match"<< endl;
78			}
79
80	tim	155	if (storageLayout_ & dslAmat && aMat.size() != size_) {
81	gezelter	507	//error
82	gezelter	1782	cerr << "size does not match"<< endl;
83	tim	155	}
84
85			if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
86	gezelter	507	//error
87	gezelter	1782	cerr << "size does not match"<< endl;
88	tim	155	}
89
90	gezelter	1879	if (storageLayout_ & dslTorque && torque.size() != size_) {
91	gezelter	507	//error
92	gezelter	1782	cerr << "size does not match"<< endl;
93	tim	155	}
94
95	gezelter	1879	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
96	gezelter	507	//error
97	gezelter	1782	cerr << "size does not match"<< endl;
98	tim	155	}
99
100	gezelter	1879	if (storageLayout_ & dslDensity && density.size() != size_) {
101	gezelter	507	//error
102	gezelter	1782	cerr << "size does not match"<< endl;
103	tim	155	}
104	gezelter	1782
105	gezelter	1879	if (storageLayout_ & dslFunctional && functional.size() != size_) {
106	chuckv	1245	//error
107	gezelter	1782	cerr << "size does not match"<< endl;
108	chuckv	1245	}
109	gezelter	1782
110	gezelter	1879	if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
111	gezelter	1782	//error
112			cerr << "size does not match"<< endl;
113			}
114
115	gezelter	1879	if (storageLayout_ & dslDipole && dipole.size() != size_) {
116	gezelter	1782	//error
117			cerr << "size does not match"<< endl;
118			}
119
120	gezelter	1879	if (storageLayout_ & dslQuadrupole && quadrupole.size() != size_) {
121	gezelter	1782	//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	gezelter	1993
150			if (storageLayout_ & dslSitePotential && sitePotential.size() != size_) {
151			//error
152			cerr << "size does not match"<< endl;
153			}
154	chuckv	1245
155	tim	155	return size_;
156
157	gezelter	507	}
158	tim	155
159	gezelter	507	void DataStorage::resize(int newSize) {
160	tim	155
161			if (storageLayout_ & dslPosition) {
162	gezelter	507	internalResize(position, newSize);
163	tim	155	}
164
165			if (storageLayout_ & dslVelocity) {
166	gezelter	507	internalResize(velocity, newSize);
167	tim	155	}
168
169	gezelter	1879	if (storageLayout_ & dslForce) {
170			internalResize(force, newSize);
171			}
172
173	tim	155	if (storageLayout_ & dslAmat) {
174	gezelter	507	internalResize(aMat, newSize);
175	tim	155	}
176
177			if (storageLayout_ & dslAngularMomentum) {
178	gezelter	507	internalResize(angularMomentum, newSize);
179	tim	155	}
180
181			if (storageLayout_ & dslTorque) {
182	gezelter	507	internalResize(torque, newSize);
183	tim	155	}
184
185	chuckv	1245	if (storageLayout_ & dslParticlePot) {
186			internalResize(particlePot, newSize);
187			}
188
189	gezelter	1782	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	gezelter	1879	if (storageLayout_ & dslDipole) {
202			internalResize(dipole, newSize);
203			}
204
205			if (storageLayout_ & dslQuadrupole) {
206			internalResize(quadrupole, newSize);
207			}
208
209	gezelter	1782	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	gezelter	1993	if (storageLayout_ & dslSitePotential) {
230			internalResize(sitePotential, newSize);
231			}
232
233	tim	155	size_ = newSize;
234	gezelter	507	}
235	tim	155
236	gezelter	507	void DataStorage::reserve(int size) {
237	tim	155	if (storageLayout_ & dslPosition) {
238	gezelter	507	position.reserve(size);
239	tim	155	}
240
241			if (storageLayout_ & dslVelocity) {
242	gezelter	507	velocity.reserve(size);
243	tim	155	}
244
245	gezelter	1879	if (storageLayout_ & dslForce) {
246			force.reserve(size);
247			}
248
249	tim	155	if (storageLayout_ & dslAmat) {
250	gezelter	507	aMat.reserve(size);
251	tim	155	}
252
253			if (storageLayout_ & dslAngularMomentum) {
254	gezelter	507	angularMomentum.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	1782	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	gezelter	1879	if (storageLayout_ & dslDipole) {
278			dipole.reserve(size);
279			}
280
281			if (storageLayout_ & dslQuadrupole) {
282			quadrupole.reserve(size);
283			}
284
285	gezelter	1782	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	gezelter	1993
305			if (storageLayout_ & dslSitePotential) {
306			sitePotential.reserve(size);
307			}
308	gezelter	507	}
309	tim	155
310	gezelter	507	void DataStorage::copy(int source, int num, int target) {
311	tim	155	if (num + target > size_ ) {
312	gezelter	507	//error
313	tim	155	}
314
315			if (storageLayout_ & dslPosition) {
316	gezelter	507	internalCopy(position, source, num, target);
317	tim	155	}
318
319			if (storageLayout_ & dslVelocity) {
320	gezelter	507	internalCopy(velocity, source, num, target);
321			}
322	tim	155
323	gezelter	1879	if (storageLayout_ & dslForce) {
324			internalCopy(force, source, num, target);
325			}
326
327	tim	155	if (storageLayout_ & dslAmat) {
328	gezelter	507	internalCopy(aMat, source, num, target);
329			}
330	tim	155
331			if (storageLayout_ & dslAngularMomentum) {
332	gezelter	507	internalCopy(angularMomentum, source, num, target);
333	tim	155	}
334
335			if (storageLayout_ & dslTorque) {
336	gezelter	507	internalCopy(torque, source, num, target);
337	tim	155	}
338	chuckv	1245
339			if (storageLayout_ & dslParticlePot) {
340			internalCopy(particlePot, source, num, target);
341			}
342	tim	155
343	gezelter	1782	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	gezelter	1879	if (storageLayout_ & dslDipole) {
356			internalCopy(dipole, source, num, target);
357			}
358
359			if (storageLayout_ & dslQuadrupole) {
360			internalCopy(quadrupole, source, num, target);
361			}
362
363	gezelter	1782	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	gezelter	1993
382			if (storageLayout_ & dslSitePotential) {
383			internalCopy(sitePotential, source, num, target);
384			}
385	gezelter	507	}
386	tim	155
387	gezelter	507	int DataStorage::getStorageLayout() {
388	tim	155	return storageLayout_;
389	gezelter	507	}
390	tim	155
391	gezelter	507	void DataStorage::setStorageLayout(int layout) {
392	tim	155	storageLayout_ = layout;
393			resize(size_);
394	gezelter	507	}
395	tim	155
396	tim	963	RealType* DataStorage::getArrayPointer(int whichArray) {
397	tim	155
398			switch (whichArray) {
399	gezelter	507	case dslPosition:
400			return internalGetArrayPointer(position);
401	tim	155
402	gezelter	507	case dslVelocity:
403			return internalGetArrayPointer(velocity);
404	tim	155
405	gezelter	1879	case dslForce:
406			return internalGetArrayPointer(force);
407
408	gezelter	507	case dslAmat:
409			return internalGetArrayPointer(aMat);
410	tim	155
411	gezelter	507	case dslAngularMomentum:
412			return internalGetArrayPointer(angularMomentum);
413	tim	155
414	gezelter	507	case dslTorque:
415			return internalGetArrayPointer(torque);
416	chuckv	1245
417			case dslParticlePot:
418			return internalGetArrayPointer(particlePot);
419	gezelter	1782
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	gezelter	1879	case dslDipole:
430			return internalGetArrayPointer(dipole);
431
432			case dslQuadrupole:
433			return internalGetArrayPointer(quadrupole);
434
435	gezelter	1782	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	gezelter	1993	case dslSitePotential:
451			return internalGetArrayPointer(sitePotential);
452
453	gezelter	507	default:
454			//error message
455			return NULL;
456	tim	155	}
457	gezelter	507	}
458	tim	155
459	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
460	gezelter	1879	if (v.empty()) {
461	gezelter	507	return NULL;
462	tim	155	} else {
463	gezelter	507	return v[0].getArrayPointer();
464	tim	155	}
465	gezelter	507	}
466	tim	155
467	gezelter	1879	RealType* DataStorage::internalGetArrayPointer(std::vector<Mat3x3d>& v) {
468			if (v.empty()) {
469	gezelter	507	return NULL;
470	tim	155	} else {
471	gezelter	507	return v[0].getArrayPointer();
472	tim	155	}
473
474	gezelter	507	}
475	tim	155
476	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
477	gezelter	1879	if (v.empty()) {
478	gezelter	507	return NULL;
479	tim	155	} else {
480	gezelter	507	return &(v[0]);
481	tim	155	}
482
483	gezelter	507	}
484	tim	155
485	gezelter	507	template<typename T>
486			void DataStorage::internalResize(std::vector<T>& v, int newSize){
487	tim	155	int oldSize = v.size();
488
489			if (oldSize == newSize) {
490	gezelter	507	return;
491	tim	155	} else if (oldSize < newSize) {
492	gezelter	507	v.insert(v.end(), newSize-oldSize, T());
493	tim	155	} else {
494	gezelter	507	typename std::vector<T>::iterator i;
495			i = v.begin();
496			std::advance(i, newSize);
497			v.erase(i, v.end());
498	tim	155	}
499	gezelter	507	}
500	tim	155
501	gezelter	507	template<typename T>
502			void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
503	tim	155	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	gezelter	507	}
518	tim	323
519	gezelter	507	int DataStorage::getBytesPerStuntDouble(int layout) {
520	tim	323	int bytes = 0;
521			if (layout & dslPosition) {
522	gezelter	507	bytes += sizeof(Vector3d);
523	tim	331	}
524			if (layout & dslVelocity) {
525	gezelter	507	bytes += sizeof(Vector3d);
526	tim	331	}
527	gezelter	1879	if (layout & dslForce) {
528			bytes += sizeof(Vector3d);
529			}
530	tim	331	if (layout & dslAmat) {
531	chuckv	1245	bytes += sizeof(RotMat3x3d);
532	tim	331	}
533			if (layout & dslAngularMomentum) {
534	gezelter	507	bytes += sizeof(Vector3d);
535	tim	331	}
536			if (layout & dslTorque) {
537	gezelter	507	bytes += sizeof(Vector3d);
538	tim	323	}
539	chuckv	1245	if (layout & dslParticlePot) {
540			bytes += sizeof(RealType);
541			}
542	gezelter	1782	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	gezelter	1879	if (layout & dslDipole) {
552			bytes += sizeof(Vector3d);
553			}
554			if (layout & dslQuadrupole) {
555			bytes += sizeof(Mat3x3d);
556			}
557	gezelter	1782	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	gezelter	1993	if (layout & dslSitePotential) {
573			bytes += sizeof(RealType);
574			}
575	gezelter	1782
576	tim	323	return bytes;
577	gezelter	507	}
578	tim	323
579			}