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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
/**
 * @file DataStorage.cpp
 * @author tlin
 * @date 10/26/2004
 * @time 11:56am
 * @version 1.0
 */

#include "brains/DataStorage.hpp"

namespace oopse {

  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:	1245
Committed:	Tue May 27 16:39:06 2008 UTC (17 years, 5 months ago) by chuckv
File size:	9881 byte(s)
Log Message:	Checking in changes for Hefland moment calculations
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* 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	* 1. Acknowledgement of the program authors must be made in any
10	* publication of scientific results based in part on use of the
11	* program. An acceptable form of acknowledgement is citation of
12	* the article in which the program was described (Matthew
13	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	* Parallel Simulation Engine for Molecular Dynamics,"
16	* J. Comput. Chem. 26, pp. 252-271 (2005))
17	*
18	* 2. Redistributions of source code must retain the above copyright
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	/**
43	* @file DataStorage.cpp
44	* @author tlin
45	* @date 10/26/2004
46	* @time 11:56am
47	* @version 1.0
48	*/
49
50	#include "brains/DataStorage.hpp"
51
52	namespace oopse {
53
54	DataStorage::DataStorage() : size_(0), storageLayout_(0){
55
56	}
57
58	DataStorage::DataStorage(int size, int storageLayout) : size_(size){
59	setStorageLayout(storageLayout);
60	resize(size);
61	}
62
63	int DataStorage::getSize() {
64
65	if (storageLayout_ & dslPosition && position.size() != size_) {
66	//error
67	std::cerr << "size does not match"<< std::endl;
68	}
69
70	if (storageLayout_ & dslVelocity && velocity.size() != size_) {
71	//error
72	std::cerr << "size does not match"<< std::endl;
73	}
74
75	if (storageLayout_ & dslAmat && aMat.size() != size_) {
76	//error
77	std::cerr << "size does not match"<< std::endl;
78	}
79
80	if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
81	//error
82	std::cerr << "size does not match"<< std::endl;
83	}
84
85	if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
86	//error
87	std::cerr << "size does not match"<< std::endl;
88	}
89
90	if (storageLayout_ & dslZAngle && zAngle.size() != size_) {
91	//error
92	std::cerr << "size does not match"<< std::endl;
93	}
94
95	if (storageLayout_ & dslForce && force.size() != size_) {
96	//error
97	std::cerr << "size does not match"<< std::endl;
98	}
99
100	if (storageLayout_ & dslTorque && torque.size() != size_) {
101	//error
102	std::cerr << "size does not match"<< std::endl;
103	}
104	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
105	//error
106	std::cerr << "size does not match"<< std::endl;
107	}
108
109	return size_;
110
111	}
112
113	void DataStorage::resize(int newSize) {
114
115	if (storageLayout_ & dslPosition) {
116	internalResize(position, newSize);
117	}
118
119	if (storageLayout_ & dslVelocity) {
120	internalResize(velocity, newSize);
121	}
122
123	if (storageLayout_ & dslAmat) {
124	internalResize(aMat, newSize);
125	}
126
127	if (storageLayout_ & dslAngularMomentum) {
128	internalResize(angularMomentum, newSize);
129	}
130
131	if (storageLayout_ & dslElectroFrame) {
132	internalResize(electroFrame, newSize);
133	}
134
135	if (storageLayout_ & dslZAngle) {
136	internalResize(zAngle, newSize);
137	}
138
139	if (storageLayout_ & dslForce) {
140	internalResize(force, newSize);
141	}
142
143	if (storageLayout_ & dslTorque) {
144	internalResize(torque, newSize);
145	}
146
147	if (storageLayout_ & dslParticlePot) {
148	internalResize(particlePot, newSize);
149	}
150
151	size_ = newSize;
152	}
153
154	void DataStorage::reserve(int size) {
155	if (storageLayout_ & dslPosition) {
156	position.reserve(size);
157	}
158
159	if (storageLayout_ & dslVelocity) {
160	velocity.reserve(size);
161	}
162
163	if (storageLayout_ & dslAmat) {
164	aMat.reserve(size);
165	}
166
167	if (storageLayout_ & dslAngularMomentum) {
168	angularMomentum.reserve(size);
169	}
170
171	if (storageLayout_ & dslElectroFrame) {
172	electroFrame.reserve(size);
173	}
174
175	if (storageLayout_ & dslZAngle) {
176	zAngle.reserve(size);
177	}
178
179	if (storageLayout_ & dslForce) {
180	force.reserve(size);
181	}
182
183	if (storageLayout_ & dslTorque) {
184	torque.reserve(size);
185	}
186
187	if (storageLayout_ & dslParticlePot) {
188	particlePot.reserve(size);
189	}
190
191	}
192
193	void DataStorage::copy(int source, int num, int target) {
194	if (num + target > size_ ) {
195	//error
196	}
197
198	if (storageLayout_ & dslPosition) {
199	internalCopy(position, source, num, target);
200	}
201
202	if (storageLayout_ & dslVelocity) {
203	internalCopy(velocity, source, num, target);
204	}
205
206	if (storageLayout_ & dslAmat) {
207	internalCopy(aMat, source, num, target);
208	}
209
210	if (storageLayout_ & dslAngularMomentum) {
211	internalCopy(angularMomentum, source, num, target);
212	}
213
214	if (storageLayout_ & dslElectroFrame) {
215	internalCopy(electroFrame, source, num, target);
216	}
217
218	if (storageLayout_ & dslZAngle) {
219	internalCopy(zAngle, source, num, target);
220	}
221
222	if (storageLayout_ & dslForce) {
223	internalCopy(force, source, num, target);
224	}
225
226	if (storageLayout_ & dslTorque) {
227	internalCopy(torque, source, num, target);
228	}
229
230	if (storageLayout_ & dslParticlePot) {
231	internalCopy(particlePot, source, num, target);
232	}
233
234
235	}
236
237	int DataStorage::getStorageLayout() {
238	return storageLayout_;
239	}
240
241	void DataStorage::setStorageLayout(int layout) {
242	storageLayout_ = layout;
243	resize(size_);
244	}
245
246	RealType* DataStorage::getArrayPointer(int whichArray) {
247
248	switch (whichArray) {
249	case dslPosition:
250	return internalGetArrayPointer(position);
251	break;
252
253	case dslVelocity:
254	return internalGetArrayPointer(velocity);
255	break;
256
257	case dslAmat:
258	return internalGetArrayPointer(aMat);
259	break;
260
261	case dslAngularMomentum:
262	return internalGetArrayPointer(angularMomentum);
263	break;
264
265	case dslElectroFrame:
266	return internalGetArrayPointer(electroFrame);
267	break;
268
269	case dslZAngle:
270	return internalGetArrayPointer(zAngle);
271	break;
272
273	case dslForce:
274	return internalGetArrayPointer(force);
275	break;
276
277	case dslTorque:
278	return internalGetArrayPointer(torque);
279	break;
280
281	case dslParticlePot:
282	return internalGetArrayPointer(particlePot);
283	break;
284
285	default:
286	//error message
287	return NULL;
288
289	}
290	}
291
292	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
293	if (v.size() == 0) {
294	return NULL;
295	} else {
296	return v[0].getArrayPointer();
297	}
298	}
299
300	RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
301	if (v.size() == 0) {
302	return NULL;
303	} else {
304	return v[0].getArrayPointer();
305	}
306
307	}
308
309	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
310	if (v.size() == 0) {
311	return NULL;
312	} else {
313	return &(v[0]);
314	}
315
316	}
317
318	template<typename T>
319	void DataStorage::internalResize(std::vector<T>& v, int newSize){
320	int oldSize = v.size();
321
322	if (oldSize == newSize) {
323	return;
324	} else if (oldSize < newSize) {
325	v.insert(v.end(), newSize-oldSize, T());
326	} else {
327	typename std::vector<T>::iterator i;
328	i = v.begin();
329	std::advance(i, newSize);
330	v.erase(i, v.end());
331	}
332	}
333
334	template<typename T>
335	void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
336	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	}
351
352	int DataStorage::getBytesPerStuntDouble(int layout) {
353	int bytes = 0;
354	if (layout & dslPosition) {
355	bytes += sizeof(Vector3d);
356	}
357	if (layout & dslVelocity) {
358	bytes += sizeof(Vector3d);
359	}
360	if (layout & dslAmat) {
361	bytes += sizeof(RotMat3x3d);
362	}
363	if (layout & dslAngularMomentum) {
364	bytes += sizeof(Vector3d);
365	}
366	if (layout & dslElectroFrame) {
367	bytes += sizeof(Mat3x3d);
368	}
369	if (layout & dslZAngle) {
370	bytes += sizeof(RealType);
371	}
372	if (layout & dslForce) {
373	bytes += sizeof(Vector3d);
374	}
375	if (layout & dslTorque) {
376	bytes += sizeof(Vector3d);
377	}
378	if (layout & dslParticlePot) {
379	bytes += sizeof(RealType);
380	}
381	return bytes;
382	}
383
384	}