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
 * @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;        
    }
    
    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);
    }

    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);
    }
  }

  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);
    }
  }

  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 dslForce:
      return internalGetArrayPointer(force);
      break;            

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

    case dslQuadrupole:
      return internalGetArrayPointer(quadrupole);
      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<Mat3x3d>& 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 & 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);
    }

    return bytes;
  }

}
Revision:	1808
Committed:	Mon Oct 22 20:42:10 2012 UTC (12 years, 6 months ago) by gezelter
File size:	14658 byte(s)
Log Message:	A bug fix in the electric field for the new electrostatic code. Also comment fixes for Doxygen
#	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			* @version 1.0
48			*/
49	tim	155
50			#include "brains/DataStorage.hpp"
51	gezelter	1710	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	1710	cerr << "size does not match"<< endl;
68	tim	155	}
69
70			if (storageLayout_ & dslVelocity && velocity.size() != size_) {
71	gezelter	507	//error
72	gezelter	1710	cerr << "size does not match"<< endl;
73	tim	155	}
74
75	gezelter	1787	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	1710	cerr << "size does not match"<< endl;
83	tim	155	}
84
85			if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
86	gezelter	507	//error
87	gezelter	1710	cerr << "size does not match"<< endl;
88	tim	155	}
89
90	gezelter	1787	if (storageLayout_ & dslTorque && torque.size() != size_) {
91	gezelter	507	//error
92	gezelter	1710	cerr << "size does not match"<< endl;
93	tim	155	}
94
95	gezelter	1787	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
96	gezelter	507	//error
97	gezelter	1710	cerr << "size does not match"<< endl;
98	tim	155	}
99
100	gezelter	1787	if (storageLayout_ & dslDensity && density.size() != size_) {
101	gezelter	507	//error
102	gezelter	1710	cerr << "size does not match"<< endl;
103	tim	155	}
104	gezelter	1583
105	gezelter	1787	if (storageLayout_ & dslFunctional && functional.size() != size_) {
106	chuckv	1245	//error
107	gezelter	1710	cerr << "size does not match"<< endl;
108	chuckv	1245	}
109	gezelter	1583
110	gezelter	1787	if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
111	gezelter	1583	//error
112	gezelter	1710	cerr << "size does not match"<< endl;
113	gezelter	1583	}
114
115	gezelter	1787	if (storageLayout_ & dslDipole && dipole.size() != size_) {
116	gezelter	1583	//error
117	gezelter	1710	cerr << "size does not match"<< endl;
118	gezelter	1583	}
119
120	gezelter	1787	if (storageLayout_ & dslQuadrupole && quadrupole.size() != size_) {
121	gezelter	1583	//error
122	gezelter	1710	cerr << "size does not match"<< endl;
123	gezelter	1583	}
124
125			if (storageLayout_ & dslElectricField && electricField.size() != size_) {
126			//error
127	gezelter	1710	cerr << "size does not match"<< endl;
128	gezelter	1583	}
129	gezelter	1584
130			if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
131			//error
132	gezelter	1710	cerr << "size does not match"<< endl;
133	gezelter	1584	}
134	gezelter	1710
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	chuckv	1245
150	tim	155	return size_;
151
152	gezelter	507	}
153	tim	155
154	gezelter	507	void DataStorage::resize(int newSize) {
155	tim	155
156			if (storageLayout_ & dslPosition) {
157	gezelter	507	internalResize(position, newSize);
158	tim	155	}
159
160			if (storageLayout_ & dslVelocity) {
161	gezelter	507	internalResize(velocity, newSize);
162	tim	155	}
163
164	gezelter	1787	if (storageLayout_ & dslForce) {
165			internalResize(force, newSize);
166			}
167
168	tim	155	if (storageLayout_ & dslAmat) {
169	gezelter	507	internalResize(aMat, newSize);
170	tim	155	}
171
172			if (storageLayout_ & dslAngularMomentum) {
173	gezelter	507	internalResize(angularMomentum, 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	gezelter	1787	if (storageLayout_ & dslDipole) {
197			internalResize(dipole, newSize);
198			}
199
200			if (storageLayout_ & dslQuadrupole) {
201			internalResize(quadrupole, newSize);
202			}
203
204	gezelter	1583	if (storageLayout_ & dslElectricField) {
205			internalResize(electricField, newSize);
206			}
207
208	gezelter	1584	if (storageLayout_ & dslSkippedCharge) {
209			internalResize(skippedCharge, newSize);
210			}
211
212	gezelter	1710	if (storageLayout_ & dslFlucQPosition) {
213			internalResize(flucQPos, newSize);
214			}
215
216			if (storageLayout_ & dslFlucQVelocity) {
217			internalResize(flucQVel, newSize);
218			}
219
220			if (storageLayout_ & dslFlucQForce) {
221			internalResize(flucQFrc, newSize);
222			}
223
224	tim	155	size_ = newSize;
225	gezelter	507	}
226	tim	155
227	gezelter	507	void DataStorage::reserve(int size) {
228	tim	155	if (storageLayout_ & dslPosition) {
229	gezelter	507	position.reserve(size);
230	tim	155	}
231
232			if (storageLayout_ & dslVelocity) {
233	gezelter	507	velocity.reserve(size);
234	tim	155	}
235
236	gezelter	1787	if (storageLayout_ & dslForce) {
237			force.reserve(size);
238			}
239
240	tim	155	if (storageLayout_ & dslAmat) {
241	gezelter	507	aMat.reserve(size);
242	tim	155	}
243
244			if (storageLayout_ & dslAngularMomentum) {
245	gezelter	507	angularMomentum.reserve(size);
246	tim	155	}
247
248			if (storageLayout_ & dslTorque) {
249	gezelter	507	torque.reserve(size);
250	tim	155	}
251	chuckv	1245
252			if (storageLayout_ & dslParticlePot) {
253			particlePot.reserve(size);
254			}
255	tim	155
256	gezelter	1583	if (storageLayout_ & dslDensity) {
257			density.reserve(size);
258			}
259
260			if (storageLayout_ & dslFunctional) {
261			functional.reserve(size);
262			}
263
264			if (storageLayout_ & dslFunctionalDerivative) {
265			functionalDerivative.reserve(size);
266			}
267
268	gezelter	1787	if (storageLayout_ & dslDipole) {
269			dipole.reserve(size);
270			}
271
272			if (storageLayout_ & dslQuadrupole) {
273			quadrupole.reserve(size);
274			}
275
276	gezelter	1583	if (storageLayout_ & dslElectricField) {
277			electricField.reserve(size);
278			}
279
280	gezelter	1584	if (storageLayout_ & dslSkippedCharge) {
281			skippedCharge.reserve(size);
282			}
283
284	gezelter	1710	if (storageLayout_ & dslFlucQPosition) {
285			flucQPos.reserve(size);
286			}
287
288			if (storageLayout_ & dslFlucQVelocity) {
289			flucQVel.reserve(size);
290			}
291
292			if (storageLayout_ & dslFlucQForce) {
293			flucQFrc.reserve(size);
294			}
295	gezelter	507	}
296	tim	155
297	gezelter	507	void DataStorage::copy(int source, int num, int target) {
298	tim	155	if (num + target > size_ ) {
299	gezelter	507	//error
300	tim	155	}
301
302			if (storageLayout_ & dslPosition) {
303	gezelter	507	internalCopy(position, source, num, target);
304	tim	155	}
305
306			if (storageLayout_ & dslVelocity) {
307	gezelter	507	internalCopy(velocity, source, num, target);
308			}
309	tim	155
310	gezelter	1787	if (storageLayout_ & dslForce) {
311			internalCopy(force, source, num, target);
312			}
313
314	tim	155	if (storageLayout_ & dslAmat) {
315	gezelter	507	internalCopy(aMat, source, num, target);
316			}
317	tim	155
318			if (storageLayout_ & dslAngularMomentum) {
319	gezelter	507	internalCopy(angularMomentum, source, num, target);
320	tim	155	}
321
322			if (storageLayout_ & dslTorque) {
323	gezelter	507	internalCopy(torque, source, num, target);
324	tim	155	}
325	chuckv	1245
326			if (storageLayout_ & dslParticlePot) {
327			internalCopy(particlePot, source, num, target);
328			}
329	tim	155
330	gezelter	1583	if (storageLayout_ & dslDensity) {
331			internalCopy(density, source, num, target);
332			}
333
334			if (storageLayout_ & dslFunctional) {
335			internalCopy(functional, source, num, target);
336			}
337
338			if (storageLayout_ & dslFunctionalDerivative) {
339			internalCopy(functionalDerivative, source, num, target);
340			}
341
342	gezelter	1787	if (storageLayout_ & dslDipole) {
343			internalCopy(dipole, source, num, target);
344			}
345
346			if (storageLayout_ & dslQuadrupole) {
347			internalCopy(quadrupole, source, num, target);
348			}
349
350	gezelter	1583	if (storageLayout_ & dslElectricField) {
351			internalCopy(electricField, source, num, target);
352			}
353	gezelter	1584
354			if (storageLayout_ & dslSkippedCharge) {
355			internalCopy(skippedCharge, source, num, target);
356			}
357	gezelter	1710
358			if (storageLayout_ & dslFlucQPosition) {
359			internalCopy(flucQPos, source, num, target);
360			}
361
362			if (storageLayout_ & dslFlucQVelocity) {
363			internalCopy(flucQVel, source, num, target);
364			}
365			if (storageLayout_ & dslFlucQForce) {
366			internalCopy(flucQFrc, source, num, target);
367			}
368	gezelter	507	}
369	tim	155
370	gezelter	507	int DataStorage::getStorageLayout() {
371	tim	155	return storageLayout_;
372	gezelter	507	}
373	tim	155
374	gezelter	507	void DataStorage::setStorageLayout(int layout) {
375	tim	155	storageLayout_ = layout;
376			resize(size_);
377	gezelter	507	}
378	tim	155
379	tim	963	RealType* DataStorage::getArrayPointer(int whichArray) {
380	tim	155
381			switch (whichArray) {
382	gezelter	507	case dslPosition:
383			return internalGetArrayPointer(position);
384			break;
385	tim	155
386	gezelter	507	case dslVelocity:
387			return internalGetArrayPointer(velocity);
388			break;
389	tim	155
390	gezelter	1787	case dslForce:
391			return internalGetArrayPointer(force);
392			break;
393
394	gezelter	507	case dslAmat:
395			return internalGetArrayPointer(aMat);
396			break;
397	tim	155
398	gezelter	507	case dslAngularMomentum:
399			return internalGetArrayPointer(angularMomentum);
400			break;
401	tim	155
402	gezelter	507	case dslTorque:
403			return internalGetArrayPointer(torque);
404	gezelter	1104	break;
405	chuckv	1245
406			case dslParticlePot:
407			return internalGetArrayPointer(particlePot);
408			break;
409	gezelter	1583
410			case dslDensity:
411			return internalGetArrayPointer(density);
412			break;
413
414			case dslFunctional:
415			return internalGetArrayPointer(functional);
416			break;
417
418			case dslFunctionalDerivative:
419			return internalGetArrayPointer(functionalDerivative);
420			break;
421
422	gezelter	1787	case dslDipole:
423			return internalGetArrayPointer(dipole);
424			break;
425
426			case dslQuadrupole:
427			return internalGetArrayPointer(quadrupole);
428			break;
429
430	gezelter	1583	case dslElectricField:
431			return internalGetArrayPointer(electricField);
432			break;
433	gezelter	1584
434			case dslSkippedCharge:
435			return internalGetArrayPointer(skippedCharge);
436			break;
437	gezelter	1710
438			case dslFlucQPosition:
439			return internalGetArrayPointer(flucQPos);
440			break;
441
442			case dslFlucQVelocity:
443			return internalGetArrayPointer(flucQVel);
444			break;
445	gezelter	1583
446	gezelter	1710	case dslFlucQForce:
447			return internalGetArrayPointer(flucQFrc);
448			break;
449
450	gezelter	507	default:
451			//error message
452			return NULL;
453	tim	155
454			}
455	gezelter	507	}
456	tim	155
457	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
458	tim	155	if (v.size() == 0) {
459	gezelter	507	return NULL;
460	tim	155	} else {
461	gezelter	507	return v[0].getArrayPointer();
462	tim	155	}
463	gezelter	507	}
464	tim	155
465	gezelter	1787	RealType* DataStorage::internalGetArrayPointer(std::vector<Mat3x3d>& v) {
466	tim	155	if (v.size() == 0) {
467	gezelter	507	return NULL;
468	tim	155	} else {
469	gezelter	507	return v[0].getArrayPointer();
470	tim	155	}
471
472	gezelter	507	}
473	tim	155
474	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
475	tim	155	if (v.size() == 0) {
476	gezelter	507	return NULL;
477	tim	155	} else {
478	gezelter	507	return &(v[0]);
479	tim	155	}
480
481	gezelter	507	}
482	tim	155
483	gezelter	507	template<typename T>
484			void DataStorage::internalResize(std::vector<T>& v, int newSize){
485	tim	155	int oldSize = v.size();
486
487			if (oldSize == newSize) {
488	gezelter	507	return;
489	tim	155	} else if (oldSize < newSize) {
490	gezelter	507	v.insert(v.end(), newSize-oldSize, T());
491	tim	155	} else {
492	gezelter	507	typename std::vector<T>::iterator i;
493			i = v.begin();
494			std::advance(i, newSize);
495			v.erase(i, v.end());
496	tim	155	}
497	gezelter	507	}
498	tim	155
499	gezelter	507	template<typename T>
500			void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
501	tim	155	typename std::vector<T>::iterator first;
502			typename std::vector<T>::iterator last;
503			typename std::vector<T>::iterator result;
504
505			first = v.begin();
506			last = v.begin();
507			result = v.begin();
508
509			std::advance(first, source);
510			//STL algorithm use half opened range
511			std::advance(last, num + 1);
512			std::advance(result, target );
513
514			std::copy(first, last, result);
515	gezelter	507	}
516	tim	323
517	gezelter	507	int DataStorage::getBytesPerStuntDouble(int layout) {
518	tim	323	int bytes = 0;
519			if (layout & dslPosition) {
520	gezelter	507	bytes += sizeof(Vector3d);
521	tim	331	}
522			if (layout & dslVelocity) {
523	gezelter	507	bytes += sizeof(Vector3d);
524	tim	331	}
525	gezelter	1787	if (layout & dslForce) {
526			bytes += sizeof(Vector3d);
527			}
528	tim	331	if (layout & dslAmat) {
529	chuckv	1245	bytes += sizeof(RotMat3x3d);
530	tim	331	}
531			if (layout & dslAngularMomentum) {
532	gezelter	507	bytes += sizeof(Vector3d);
533	tim	331	}
534			if (layout & dslTorque) {
535	gezelter	507	bytes += sizeof(Vector3d);
536	tim	323	}
537	chuckv	1245	if (layout & dslParticlePot) {
538			bytes += sizeof(RealType);
539			}
540	gezelter	1583	if (layout & dslDensity) {
541			bytes += sizeof(RealType);
542			}
543			if (layout & dslFunctional) {
544			bytes += sizeof(RealType);
545			}
546			if (layout & dslFunctionalDerivative) {
547			bytes += sizeof(RealType);
548			}
549	gezelter	1787	if (layout & dslDipole) {
550			bytes += sizeof(Vector3d);
551			}
552			if (layout & dslQuadrupole) {
553			bytes += sizeof(Mat3x3d);
554			}
555	gezelter	1583	if (layout & dslElectricField) {
556			bytes += sizeof(Vector3d);
557			}
558	gezelter	1584	if (layout & dslSkippedCharge) {
559			bytes += sizeof(RealType);
560			}
561	gezelter	1710	if (layout & dslFlucQPosition) {
562			bytes += sizeof(RealType);
563			}
564			if (layout & dslFlucQVelocity) {
565			bytes += sizeof(RealType);
566			}
567			if (layout & dslFlucQForce) {
568			bytes += sizeof(RealType);
569			}
570	gezelter	1583
571	tim	323	return bytes;
572	gezelter	507	}
573	tim	323
574			}