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;        
    }

    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);
    }

    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);
    }

}

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); 
    }
    

}

int DataStorage::getStorageLayout() {
    return storageLayout_;
}

void DataStorage::setStorageLayout(int layout) {
    storageLayout_ = layout;
    resize(size_);
}

double* 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;  
            
        default:
            //error message
            return NULL;

    }
}    

double* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
    if (v.size() == 0) {
        return NULL;
    } else {
        return v[0].getArrayPointer();
    }
}

double* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
    if (v.size() == 0) {
        return NULL;
    } else {
        return v[0].getArrayPointer();
    }

}

double* DataStorage::internalGetArrayPointer(std::vector<double>& 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(Mat3x3d);    
    }
    if (layout & dslAngularMomentum) {
        bytes += sizeof(Vector3d);
    }
    if (layout & dslElectroFrame) {
        bytes += sizeof(Mat3x3d);
    }
    if (layout & dslZAngle) {
        bytes += sizeof(Vector3d);
    }
    if (layout & dslForce) {
        bytes += sizeof(Vector3d);
    }
    if (layout & dslTorque) {
        bytes += sizeof(Vector3d);
    }
    return bytes;
}

}
Revision:	2015
Committed:	Sun Feb 13 21:18:27 2005 UTC (19 years, 4 months ago) by tim
File size:	9467 byte(s)
Log Message:	fix a bug in calculating bytes per stuntdouble
#	User	Rev	Content
1	gezelter	1930	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	tim	1648	*
4	gezelter	1930	* 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	tim	1648	*/
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	tim	2007	namespace oopse {
53	tim	1648
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	gezelter	1930	if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
86	tim	1648	//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
105			return size_;
106
107			}
108
109			void DataStorage::resize(int newSize) {
110
111			if (storageLayout_ & dslPosition) {
112			internalResize(position, newSize);
113			}
114
115			if (storageLayout_ & dslVelocity) {
116			internalResize(velocity, newSize);
117			}
118
119			if (storageLayout_ & dslAmat) {
120			internalResize(aMat, newSize);
121			}
122
123			if (storageLayout_ & dslAngularMomentum) {
124			internalResize(angularMomentum, newSize);
125			}
126
127	gezelter	1930	if (storageLayout_ & dslElectroFrame) {
128			internalResize(electroFrame, newSize);
129	tim	1648	}
130
131			if (storageLayout_ & dslZAngle) {
132			internalResize(zAngle, newSize);
133			}
134
135			if (storageLayout_ & dslForce) {
136			internalResize(force, newSize);
137			}
138
139			if (storageLayout_ & dslTorque) {
140			internalResize(torque, newSize);
141			}
142
143			size_ = newSize;
144			}
145
146			void DataStorage::reserve(int size) {
147			if (storageLayout_ & dslPosition) {
148			position.reserve(size);
149			}
150
151			if (storageLayout_ & dslVelocity) {
152			velocity.reserve(size);
153			}
154
155			if (storageLayout_ & dslAmat) {
156			aMat.reserve(size);
157			}
158
159			if (storageLayout_ & dslAngularMomentum) {
160			angularMomentum.reserve(size);
161			}
162
163	gezelter	1930	if (storageLayout_ & dslElectroFrame) {
164			electroFrame.reserve(size);
165	tim	1648	}
166
167			if (storageLayout_ & dslZAngle) {
168			zAngle.reserve(size);
169			}
170
171			if (storageLayout_ & dslForce) {
172			force.reserve(size);
173			}
174
175			if (storageLayout_ & dslTorque) {
176			torque.reserve(size);
177			}
178
179			}
180
181			void DataStorage::copy(int source, int num, int target) {
182			if (num + target > size_ ) {
183			//error
184			}
185
186			if (storageLayout_ & dslPosition) {
187	gezelter	1930	internalCopy(position, source, num, target);
188	tim	1648	}
189
190			if (storageLayout_ & dslVelocity) {
191	gezelter	1930	internalCopy(velocity, source, num, target);
192	tim	1648	}
193
194			if (storageLayout_ & dslAmat) {
195	gezelter	1930	internalCopy(aMat, source, num, target);
196	tim	1648	}
197
198			if (storageLayout_ & dslAngularMomentum) {
199	gezelter	1930	internalCopy(angularMomentum, source, num, target);
200	tim	1648	}
201
202	gezelter	1930	if (storageLayout_ & dslElectroFrame) {
203			internalCopy(electroFrame, source, num, target);
204	tim	1648	}
205
206			if (storageLayout_ & dslZAngle) {
207	gezelter	1930	internalCopy(zAngle, source, num, target);
208	tim	1648	}
209
210			if (storageLayout_ & dslForce) {
211	gezelter	1930	internalCopy(force, source, num, target);
212	tim	1648	}
213
214			if (storageLayout_ & dslTorque) {
215	gezelter	1930	internalCopy(torque, source, num, target);
216	tim	1648	}
217
218
219			}
220
221			int DataStorage::getStorageLayout() {
222			return storageLayout_;
223			}
224
225			void DataStorage::setStorageLayout(int layout) {
226			storageLayout_ = layout;
227			resize(size_);
228			}
229
230			double* DataStorage::getArrayPointer(int whichArray) {
231
232			switch (whichArray) {
233			case dslPosition:
234	gezelter	1930	return internalGetArrayPointer(position);
235	tim	1648	break;
236
237			case dslVelocity:
238			return internalGetArrayPointer(velocity);
239			break;
240
241			case dslAmat:
242			return internalGetArrayPointer(aMat);
243			break;
244
245			case dslAngularMomentum:
246			return internalGetArrayPointer(angularMomentum);
247			break;
248
249	gezelter	1930	case dslElectroFrame:
250			return internalGetArrayPointer(electroFrame);
251	tim	1648	break;
252
253			case dslZAngle:
254			return internalGetArrayPointer(zAngle);
255			break;
256
257			case dslForce:
258			return internalGetArrayPointer(force);
259			break;
260
261			case dslTorque:
262			return internalGetArrayPointer(torque);
263			break;
264
265			default:
266			//error message
267			return NULL;
268
269			}
270			}
271
272			double* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
273			if (v.size() == 0) {
274			return NULL;
275			} else {
276			return v[0].getArrayPointer();
277			}
278			}
279
280			double* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
281			if (v.size() == 0) {
282			return NULL;
283			} else {
284			return v[0].getArrayPointer();
285			}
286
287			}
288
289			double* DataStorage::internalGetArrayPointer(std::vector<double>& v) {
290			if (v.size() == 0) {
291			return NULL;
292			} else {
293			return &(v[0]);
294			}
295
296			}
297
298			template<typename T>
299			void DataStorage::internalResize(std::vector<T>& v, int newSize){
300			int oldSize = v.size();
301
302			if (oldSize == newSize) {
303			return;
304			} else if (oldSize < newSize) {
305			v.insert(v.end(), newSize-oldSize, T());
306			} else {
307			typename std::vector<T>::iterator i;
308			i = v.begin();
309			std::advance(i, newSize);
310			v.erase(i, v.end());
311			}
312			}
313
314			template<typename T>
315	gezelter	1930	void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
316	tim	1648	typename std::vector<T>::iterator first;
317			typename std::vector<T>::iterator last;
318			typename std::vector<T>::iterator result;
319
320			first = v.begin();
321			last = v.begin();
322			result = v.begin();
323
324			std::advance(first, source);
325			//STL algorithm use half opened range
326			std::advance(last, num + 1);
327			std::advance(result, target );
328
329			std::copy(first, last, result);
330			}
331	tim	2007
332			int DataStorage::getBytesPerStuntDouble(int layout) {
333			int bytes = 0;
334			if (layout & dslPosition) {
335			bytes += sizeof(Vector3d);
336	tim	2015	}
337			if (layout & dslVelocity) {
338	tim	2007	bytes += sizeof(Vector3d);
339	tim	2015	}
340			if (layout & dslAmat) {
341	tim	2007	bytes += sizeof(Mat3x3d);
342	tim	2015	}
343			if (layout & dslAngularMomentum) {
344	tim	2007	bytes += sizeof(Vector3d);
345	tim	2015	}
346			if (layout & dslElectroFrame) {
347	tim	2007	bytes += sizeof(Mat3x3d);
348	tim	2015	}
349			if (layout & dslZAngle) {
350	tim	2007	bytes += sizeof(Vector3d);
351	tim	2015	}
352			if (layout & dslForce) {
353	tim	2007	bytes += sizeof(Vector3d);
354	tim	2015	}
355			if (layout & dslTorque) {
356	tim	2007	bytes += sizeof(Vector3d);
357			}
358			return bytes;
359			}
360
361			}