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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
/**
 * @file DataStorage.cpp
 * @author tlin
 * @date 10/26/2004
 * @time 11:56am
 * @version 1.0
 */

#include "brains/DataStorage.hpp"

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
      std::cerr << "size does not match"<< std::endl;
    }

    if (storageLayout_ & dslVelocity && velocity.size() != size_) {
      //error
      std::cerr << "size does not match"<< std::endl;        
    }

    if (storageLayout_ & dslAmat && aMat.size() != size_) {
      //error
      std::cerr << "size does not match"<< std::endl;        
    }

    if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
      //error
      std::cerr << "size does not match"<< std::endl;        
    }

    if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
      //error
      std::cerr << "size does not match"<< std::endl;        
    }

    if (storageLayout_ & dslZAngle && zAngle.size() != size_) {
      //error
      std::cerr << "size does not match"<< std::endl;        
    }

    if (storageLayout_ & dslForce && force.size() != size_) {
      //error
      std::cerr << "size does not match"<< std::endl;        
    }

    if (storageLayout_ & dslTorque && torque.size() != size_) {
      //error
      std::cerr << "size does not match"<< std::endl;        
    }

    if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
      //error
      std::cerr << "size does not match"<< std::endl;        
    }

    if (storageLayout_ & dslDensity && density.size() != size_) {
      //error
      std::cerr << "size does not match"<< std::endl;        
    }

    if (storageLayout_ & dslFunctional && functional.size() != size_) {
      //error
      std::cerr << "size does not match"<< std::endl;        
    }

    if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
      //error
      std::cerr << "size does not match"<< std::endl;        
    }

    if (storageLayout_ & dslElectricField && electricField.size() != size_) {
      //error
      std::cerr << "size does not match"<< std::endl;        
    }

    if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
      //error
      std::cerr << "size does not match"<< std::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);
    }

    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);
    }

  }

  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);
    }
  }

  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;
           
    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);
    }

    return bytes;
  }

}
Revision:	1584
Committed:	Fri Jun 17 20:16:35 2011 UTC (14 years, 4 months ago) by gezelter
File size:	13016 byte(s)
Log Message:	bug fixes.
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	155	*/
41
42	gezelter	507	/**
43			* @file DataStorage.cpp
44			* @author tlin
45			* @date 10/26/2004
46			* @time 11:56am
47			* @version 1.0
48			*/
49	tim	155
50			#include "brains/DataStorage.hpp"
51
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			std::cerr << "size does not match"<< std::endl;
68	tim	155	}
69
70			if (storageLayout_ & dslVelocity && velocity.size() != size_) {
71	gezelter	507	//error
72			std::cerr << "size does not match"<< std::endl;
73	tim	155	}
74
75			if (storageLayout_ & dslAmat && aMat.size() != size_) {
76	gezelter	507	//error
77			std::cerr << "size does not match"<< std::endl;
78	tim	155	}
79
80			if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
81	gezelter	507	//error
82			std::cerr << "size does not match"<< std::endl;
83	tim	155	}
84
85	gezelter	246	if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
86	gezelter	507	//error
87			std::cerr << "size does not match"<< std::endl;
88	tim	155	}
89
90			if (storageLayout_ & dslZAngle && zAngle.size() != size_) {
91	gezelter	507	//error
92			std::cerr << "size does not match"<< std::endl;
93	tim	155	}
94
95			if (storageLayout_ & dslForce && force.size() != size_) {
96	gezelter	507	//error
97			std::cerr << "size does not match"<< std::endl;
98	tim	155	}
99
100			if (storageLayout_ & dslTorque && torque.size() != size_) {
101	gezelter	507	//error
102			std::cerr << "size does not match"<< std::endl;
103	tim	155	}
104	gezelter	1583
105	chuckv	1245	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
106			//error
107			std::cerr << "size does not match"<< std::endl;
108			}
109	gezelter	1583
110			if (storageLayout_ & dslDensity && density.size() != size_) {
111			//error
112			std::cerr << "size does not match"<< std::endl;
113			}
114
115			if (storageLayout_ & dslFunctional && functional.size() != size_) {
116			//error
117			std::cerr << "size does not match"<< std::endl;
118			}
119
120			if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
121			//error
122			std::cerr << "size does not match"<< std::endl;
123			}
124
125			if (storageLayout_ & dslElectricField && electricField.size() != size_) {
126			//error
127			std::cerr << "size does not match"<< std::endl;
128			}
129	gezelter	1584
130			if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
131			//error
132			std::cerr << "size does not match"<< std::endl;
133			}
134	chuckv	1245
135	tim	155	return size_;
136
137	gezelter	507	}
138	tim	155
139	gezelter	507	void DataStorage::resize(int newSize) {
140	tim	155
141			if (storageLayout_ & dslPosition) {
142	gezelter	507	internalResize(position, newSize);
143	tim	155	}
144
145			if (storageLayout_ & dslVelocity) {
146	gezelter	507	internalResize(velocity, newSize);
147	tim	155	}
148
149			if (storageLayout_ & dslAmat) {
150	gezelter	507	internalResize(aMat, newSize);
151	tim	155	}
152
153			if (storageLayout_ & dslAngularMomentum) {
154	gezelter	507	internalResize(angularMomentum, newSize);
155	tim	155	}
156
157	gezelter	246	if (storageLayout_ & dslElectroFrame) {
158	gezelter	507	internalResize(electroFrame, newSize);
159	tim	155	}
160
161			if (storageLayout_ & dslZAngle) {
162	gezelter	507	internalResize(zAngle, newSize);
163	tim	155	}
164
165			if (storageLayout_ & dslForce) {
166	gezelter	507	internalResize(force, newSize);
167	tim	155	}
168
169			if (storageLayout_ & dslTorque) {
170	gezelter	507	internalResize(torque, newSize);
171	tim	155	}
172
173	chuckv	1245	if (storageLayout_ & dslParticlePot) {
174			internalResize(particlePot, newSize);
175			}
176
177	gezelter	1583	if (storageLayout_ & dslDensity) {
178			internalResize(density, newSize);
179			}
180
181			if (storageLayout_ & dslFunctional) {
182			internalResize(functional, newSize);
183			}
184
185			if (storageLayout_ & dslFunctionalDerivative) {
186			internalResize(functionalDerivative, newSize);
187			}
188
189			if (storageLayout_ & dslElectricField) {
190			internalResize(electricField, newSize);
191			}
192
193	gezelter	1584	if (storageLayout_ & dslSkippedCharge) {
194			internalResize(skippedCharge, newSize);
195			}
196
197	tim	155	size_ = newSize;
198	gezelter	507	}
199	tim	155
200	gezelter	507	void DataStorage::reserve(int size) {
201	tim	155	if (storageLayout_ & dslPosition) {
202	gezelter	507	position.reserve(size);
203	tim	155	}
204
205			if (storageLayout_ & dslVelocity) {
206	gezelter	507	velocity.reserve(size);
207	tim	155	}
208
209			if (storageLayout_ & dslAmat) {
210	gezelter	507	aMat.reserve(size);
211	tim	155	}
212
213			if (storageLayout_ & dslAngularMomentum) {
214	gezelter	507	angularMomentum.reserve(size);
215	tim	155	}
216
217	gezelter	246	if (storageLayout_ & dslElectroFrame) {
218	gezelter	507	electroFrame.reserve(size);
219	tim	155	}
220
221			if (storageLayout_ & dslZAngle) {
222	gezelter	507	zAngle.reserve(size);
223	tim	155	}
224
225			if (storageLayout_ & dslForce) {
226	gezelter	507	force.reserve(size);
227	tim	155	}
228
229			if (storageLayout_ & dslTorque) {
230	gezelter	507	torque.reserve(size);
231	tim	155	}
232	chuckv	1245
233			if (storageLayout_ & dslParticlePot) {
234			particlePot.reserve(size);
235			}
236	tim	155
237	gezelter	1583	if (storageLayout_ & dslDensity) {
238			density.reserve(size);
239			}
240
241			if (storageLayout_ & dslFunctional) {
242			functional.reserve(size);
243			}
244
245			if (storageLayout_ & dslFunctionalDerivative) {
246			functionalDerivative.reserve(size);
247			}
248
249			if (storageLayout_ & dslElectricField) {
250			electricField.reserve(size);
251			}
252
253	gezelter	1584	if (storageLayout_ & dslSkippedCharge) {
254			skippedCharge.reserve(size);
255			}
256
257	gezelter	507	}
258	tim	155
259	gezelter	507	void DataStorage::copy(int source, int num, int target) {
260	tim	155	if (num + target > size_ ) {
261	gezelter	507	//error
262	tim	155	}
263
264			if (storageLayout_ & dslPosition) {
265	gezelter	507	internalCopy(position, source, num, target);
266	tim	155	}
267
268			if (storageLayout_ & dslVelocity) {
269	gezelter	507	internalCopy(velocity, source, num, target);
270			}
271	tim	155
272			if (storageLayout_ & dslAmat) {
273	gezelter	507	internalCopy(aMat, source, num, target);
274			}
275	tim	155
276			if (storageLayout_ & dslAngularMomentum) {
277	gezelter	507	internalCopy(angularMomentum, source, num, target);
278	tim	155	}
279
280	gezelter	246	if (storageLayout_ & dslElectroFrame) {
281	gezelter	507	internalCopy(electroFrame, source, num, target);
282	tim	155	}
283
284			if (storageLayout_ & dslZAngle) {
285	gezelter	507	internalCopy(zAngle, source, num, target);
286	tim	155	}
287
288			if (storageLayout_ & dslForce) {
289	gezelter	507	internalCopy(force, source, num, target);
290	tim	155	}
291
292			if (storageLayout_ & dslTorque) {
293	gezelter	507	internalCopy(torque, source, num, target);
294	tim	155	}
295	chuckv	1245
296			if (storageLayout_ & dslParticlePot) {
297			internalCopy(particlePot, source, num, target);
298			}
299	tim	155
300	gezelter	1583	if (storageLayout_ & dslDensity) {
301			internalCopy(density, source, num, target);
302			}
303
304			if (storageLayout_ & dslFunctional) {
305			internalCopy(functional, source, num, target);
306			}
307
308			if (storageLayout_ & dslFunctionalDerivative) {
309			internalCopy(functionalDerivative, source, num, target);
310			}
311
312			if (storageLayout_ & dslElectricField) {
313			internalCopy(electricField, source, num, target);
314			}
315	gezelter	1584
316			if (storageLayout_ & dslSkippedCharge) {
317			internalCopy(skippedCharge, source, num, target);
318			}
319	gezelter	507	}
320	tim	155
321	gezelter	507	int DataStorage::getStorageLayout() {
322	tim	155	return storageLayout_;
323	gezelter	507	}
324	tim	155
325	gezelter	507	void DataStorage::setStorageLayout(int layout) {
326	tim	155	storageLayout_ = layout;
327			resize(size_);
328	gezelter	507	}
329	tim	155
330	tim	963	RealType* DataStorage::getArrayPointer(int whichArray) {
331	tim	155
332			switch (whichArray) {
333	gezelter	507	case dslPosition:
334			return internalGetArrayPointer(position);
335			break;
336	tim	155
337	gezelter	507	case dslVelocity:
338			return internalGetArrayPointer(velocity);
339			break;
340	tim	155
341	gezelter	507	case dslAmat:
342			return internalGetArrayPointer(aMat);
343			break;
344	tim	155
345	gezelter	507	case dslAngularMomentum:
346			return internalGetArrayPointer(angularMomentum);
347			break;
348	tim	155
349	gezelter	507	case dslElectroFrame:
350			return internalGetArrayPointer(electroFrame);
351			break;
352	tim	155
353	gezelter	507	case dslZAngle:
354			return internalGetArrayPointer(zAngle);
355			break;
356	tim	155
357	gezelter	507	case dslForce:
358			return internalGetArrayPointer(force);
359			break;
360	tim	155
361	gezelter	507	case dslTorque:
362			return internalGetArrayPointer(torque);
363	gezelter	1104	break;
364	chuckv	1245
365			case dslParticlePot:
366			return internalGetArrayPointer(particlePot);
367			break;
368	gezelter	1583
369			case dslDensity:
370			return internalGetArrayPointer(density);
371			break;
372
373			case dslFunctional:
374			return internalGetArrayPointer(functional);
375			break;
376
377			case dslFunctionalDerivative:
378			return internalGetArrayPointer(functionalDerivative);
379			break;
380
381			case dslElectricField:
382			return internalGetArrayPointer(electricField);
383			break;
384	gezelter	1584
385			case dslSkippedCharge:
386			return internalGetArrayPointer(skippedCharge);
387			break;
388	gezelter	1583
389	gezelter	507	default:
390			//error message
391			return NULL;
392	tim	155
393			}
394	gezelter	507	}
395	tim	155
396	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
397	tim	155	if (v.size() == 0) {
398	gezelter	507	return NULL;
399	tim	155	} else {
400	gezelter	507	return v[0].getArrayPointer();
401	tim	155	}
402	gezelter	507	}
403	tim	155
404	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
405	tim	155	if (v.size() == 0) {
406	gezelter	507	return NULL;
407	tim	155	} else {
408	gezelter	507	return v[0].getArrayPointer();
409	tim	155	}
410
411	gezelter	507	}
412	tim	155
413	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
414	tim	155	if (v.size() == 0) {
415	gezelter	507	return NULL;
416	tim	155	} else {
417	gezelter	507	return &(v[0]);
418	tim	155	}
419
420	gezelter	507	}
421	tim	155
422	gezelter	507	template<typename T>
423			void DataStorage::internalResize(std::vector<T>& v, int newSize){
424	tim	155	int oldSize = v.size();
425
426			if (oldSize == newSize) {
427	gezelter	507	return;
428	tim	155	} else if (oldSize < newSize) {
429	gezelter	507	v.insert(v.end(), newSize-oldSize, T());
430	tim	155	} else {
431	gezelter	507	typename std::vector<T>::iterator i;
432			i = v.begin();
433			std::advance(i, newSize);
434			v.erase(i, v.end());
435	tim	155	}
436	gezelter	507	}
437	tim	155
438	gezelter	507	template<typename T>
439			void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
440	tim	155	typename std::vector<T>::iterator first;
441			typename std::vector<T>::iterator last;
442			typename std::vector<T>::iterator result;
443
444			first = v.begin();
445			last = v.begin();
446			result = v.begin();
447
448			std::advance(first, source);
449			//STL algorithm use half opened range
450			std::advance(last, num + 1);
451			std::advance(result, target );
452
453			std::copy(first, last, result);
454	gezelter	507	}
455	tim	323
456	gezelter	507	int DataStorage::getBytesPerStuntDouble(int layout) {
457	tim	323	int bytes = 0;
458			if (layout & dslPosition) {
459	gezelter	507	bytes += sizeof(Vector3d);
460	tim	331	}
461			if (layout & dslVelocity) {
462	gezelter	507	bytes += sizeof(Vector3d);
463	tim	331	}
464			if (layout & dslAmat) {
465	chuckv	1245	bytes += sizeof(RotMat3x3d);
466	tim	331	}
467			if (layout & dslAngularMomentum) {
468	gezelter	507	bytes += sizeof(Vector3d);
469	tim	331	}
470			if (layout & dslElectroFrame) {
471	gezelter	507	bytes += sizeof(Mat3x3d);
472	tim	331	}
473			if (layout & dslZAngle) {
474	chuckv	1245	bytes += sizeof(RealType);
475	tim	331	}
476			if (layout & dslForce) {
477	gezelter	507	bytes += sizeof(Vector3d);
478	tim	331	}
479			if (layout & dslTorque) {
480	gezelter	507	bytes += sizeof(Vector3d);
481	tim	323	}
482	chuckv	1245	if (layout & dslParticlePot) {
483			bytes += sizeof(RealType);
484			}
485	gezelter	1583	if (layout & dslDensity) {
486			bytes += sizeof(RealType);
487			}
488			if (layout & dslFunctional) {
489			bytes += sizeof(RealType);
490			}
491			if (layout & dslFunctionalDerivative) {
492			bytes += sizeof(RealType);
493			}
494			if (layout & dslElectricField) {
495			bytes += sizeof(Vector3d);
496			}
497	gezelter	1584	if (layout & dslSkippedCharge) {
498			bytes += sizeof(RealType);
499			}
500	gezelter	1583
501	tim	323	return bytes;
502	gezelter	507	}
503	tim	323
504			}