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;        
    }
    
    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);
    }

    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);
    }

  }

  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); 
    }
    

  }

  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;
            
    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);
    }
    return bytes;
  }

}
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
File size:	9923 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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	chuckv	1245	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
105			//error
106			std::cerr << "size does not match"<< std::endl;
107			}
108
109	tim	155	return size_;
110
111	gezelter	507	}
112	tim	155
113	gezelter	507	void DataStorage::resize(int newSize) {
114	tim	155
115			if (storageLayout_ & dslPosition) {
116	gezelter	507	internalResize(position, newSize);
117	tim	155	}
118
119			if (storageLayout_ & dslVelocity) {
120	gezelter	507	internalResize(velocity, newSize);
121	tim	155	}
122
123			if (storageLayout_ & dslAmat) {
124	gezelter	507	internalResize(aMat, newSize);
125	tim	155	}
126
127			if (storageLayout_ & dslAngularMomentum) {
128	gezelter	507	internalResize(angularMomentum, newSize);
129	tim	155	}
130
131	gezelter	246	if (storageLayout_ & dslElectroFrame) {
132	gezelter	507	internalResize(electroFrame, newSize);
133	tim	155	}
134
135			if (storageLayout_ & dslZAngle) {
136	gezelter	507	internalResize(zAngle, newSize);
137	tim	155	}
138
139			if (storageLayout_ & dslForce) {
140	gezelter	507	internalResize(force, newSize);
141	tim	155	}
142
143			if (storageLayout_ & dslTorque) {
144	gezelter	507	internalResize(torque, newSize);
145	tim	155	}
146
147	chuckv	1245	if (storageLayout_ & dslParticlePot) {
148			internalResize(particlePot, newSize);
149			}
150
151	tim	155	size_ = newSize;
152	gezelter	507	}
153	tim	155
154	gezelter	507	void DataStorage::reserve(int size) {
155	tim	155	if (storageLayout_ & dslPosition) {
156	gezelter	507	position.reserve(size);
157	tim	155	}
158
159			if (storageLayout_ & dslVelocity) {
160	gezelter	507	velocity.reserve(size);
161	tim	155	}
162
163			if (storageLayout_ & dslAmat) {
164	gezelter	507	aMat.reserve(size);
165	tim	155	}
166
167			if (storageLayout_ & dslAngularMomentum) {
168	gezelter	507	angularMomentum.reserve(size);
169	tim	155	}
170
171	gezelter	246	if (storageLayout_ & dslElectroFrame) {
172	gezelter	507	electroFrame.reserve(size);
173	tim	155	}
174
175			if (storageLayout_ & dslZAngle) {
176	gezelter	507	zAngle.reserve(size);
177	tim	155	}
178
179			if (storageLayout_ & dslForce) {
180	gezelter	507	force.reserve(size);
181	tim	155	}
182
183			if (storageLayout_ & dslTorque) {
184	gezelter	507	torque.reserve(size);
185	tim	155	}
186	chuckv	1245
187			if (storageLayout_ & dslParticlePot) {
188			particlePot.reserve(size);
189			}
190	tim	155
191	gezelter	507	}
192	tim	155
193	gezelter	507	void DataStorage::copy(int source, int num, int target) {
194	tim	155	if (num + target > size_ ) {
195	gezelter	507	//error
196	tim	155	}
197
198			if (storageLayout_ & dslPosition) {
199	gezelter	507	internalCopy(position, source, num, target);
200	tim	155	}
201
202			if (storageLayout_ & dslVelocity) {
203	gezelter	507	internalCopy(velocity, source, num, target);
204			}
205	tim	155
206			if (storageLayout_ & dslAmat) {
207	gezelter	507	internalCopy(aMat, source, num, target);
208			}
209	tim	155
210			if (storageLayout_ & dslAngularMomentum) {
211	gezelter	507	internalCopy(angularMomentum, source, num, target);
212	tim	155	}
213
214	gezelter	246	if (storageLayout_ & dslElectroFrame) {
215	gezelter	507	internalCopy(electroFrame, source, num, target);
216	tim	155	}
217
218			if (storageLayout_ & dslZAngle) {
219	gezelter	507	internalCopy(zAngle, source, num, target);
220	tim	155	}
221
222			if (storageLayout_ & dslForce) {
223	gezelter	507	internalCopy(force, source, num, target);
224	tim	155	}
225
226			if (storageLayout_ & dslTorque) {
227	gezelter	507	internalCopy(torque, source, num, target);
228	tim	155	}
229	chuckv	1245
230			if (storageLayout_ & dslParticlePot) {
231			internalCopy(particlePot, source, num, target);
232			}
233	tim	155
234
235	gezelter	507	}
236	tim	155
237	gezelter	507	int DataStorage::getStorageLayout() {
238	tim	155	return storageLayout_;
239	gezelter	507	}
240	tim	155
241	gezelter	507	void DataStorage::setStorageLayout(int layout) {
242	tim	155	storageLayout_ = layout;
243			resize(size_);
244	gezelter	507	}
245	tim	155
246	tim	963	RealType* DataStorage::getArrayPointer(int whichArray) {
247	tim	155
248			switch (whichArray) {
249	gezelter	507	case dslPosition:
250			return internalGetArrayPointer(position);
251			break;
252	tim	155
253	gezelter	507	case dslVelocity:
254			return internalGetArrayPointer(velocity);
255			break;
256	tim	155
257	gezelter	507	case dslAmat:
258			return internalGetArrayPointer(aMat);
259			break;
260	tim	155
261	gezelter	507	case dslAngularMomentum:
262			return internalGetArrayPointer(angularMomentum);
263			break;
264	tim	155
265	gezelter	507	case dslElectroFrame:
266			return internalGetArrayPointer(electroFrame);
267			break;
268	tim	155
269	gezelter	507	case dslZAngle:
270			return internalGetArrayPointer(zAngle);
271			break;
272	tim	155
273	gezelter	507	case dslForce:
274			return internalGetArrayPointer(force);
275			break;
276	tim	155
277	gezelter	507	case dslTorque:
278			return internalGetArrayPointer(torque);
279	gezelter	1104	break;
280	chuckv	1245
281			case dslParticlePot:
282			return internalGetArrayPointer(particlePot);
283			break;
284	tim	155
285	gezelter	507	default:
286			//error message
287			return NULL;
288	tim	155
289			}
290	gezelter	507	}
291	tim	155
292	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
293	tim	155	if (v.size() == 0) {
294	gezelter	507	return NULL;
295	tim	155	} else {
296	gezelter	507	return v[0].getArrayPointer();
297	tim	155	}
298	gezelter	507	}
299	tim	155
300	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
301	tim	155	if (v.size() == 0) {
302	gezelter	507	return NULL;
303	tim	155	} else {
304	gezelter	507	return v[0].getArrayPointer();
305	tim	155	}
306
307	gezelter	507	}
308	tim	155
309	tim	963	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
310	tim	155	if (v.size() == 0) {
311	gezelter	507	return NULL;
312	tim	155	} else {
313	gezelter	507	return &(v[0]);
314	tim	155	}
315
316	gezelter	507	}
317	tim	155
318	gezelter	507	template<typename T>
319			void DataStorage::internalResize(std::vector<T>& v, int newSize){
320	tim	155	int oldSize = v.size();
321
322			if (oldSize == newSize) {
323	gezelter	507	return;
324	tim	155	} else if (oldSize < newSize) {
325	gezelter	507	v.insert(v.end(), newSize-oldSize, T());
326	tim	155	} else {
327	gezelter	507	typename std::vector<T>::iterator i;
328			i = v.begin();
329			std::advance(i, newSize);
330			v.erase(i, v.end());
331	tim	155	}
332	gezelter	507	}
333	tim	155
334	gezelter	507	template<typename T>
335			void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
336	tim	155	typename std::vector<T>::iterator first;
337			typename std::vector<T>::iterator last;
338			typename std::vector<T>::iterator result;
339
340			first = v.begin();
341			last = v.begin();
342			result = v.begin();
343
344			std::advance(first, source);
345			//STL algorithm use half opened range
346			std::advance(last, num + 1);
347			std::advance(result, target );
348
349			std::copy(first, last, result);
350	gezelter	507	}
351	tim	323
352	gezelter	507	int DataStorage::getBytesPerStuntDouble(int layout) {
353	tim	323	int bytes = 0;
354			if (layout & dslPosition) {
355	gezelter	507	bytes += sizeof(Vector3d);
356	tim	331	}
357			if (layout & dslVelocity) {
358	gezelter	507	bytes += sizeof(Vector3d);
359	tim	331	}
360			if (layout & dslAmat) {
361	chuckv	1245	bytes += sizeof(RotMat3x3d);
362	tim	331	}
363			if (layout & dslAngularMomentum) {
364	gezelter	507	bytes += sizeof(Vector3d);
365	tim	331	}
366			if (layout & dslElectroFrame) {
367	gezelter	507	bytes += sizeof(Mat3x3d);
368	tim	331	}
369			if (layout & dslZAngle) {
370	chuckv	1245	bytes += sizeof(RealType);
371	tim	331	}
372			if (layout & dslForce) {
373	gezelter	507	bytes += sizeof(Vector3d);
374	tim	331	}
375			if (layout & dslTorque) {
376	gezelter	507	bytes += sizeof(Vector3d);
377	tim	323	}
378	chuckv	1245	if (layout & dslParticlePot) {
379			bytes += sizeof(RealType);
380			}
381	tim	323	return bytes;
382	gezelter	507	}
383	tim	323
384			}