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"


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);
}
Revision:	246
Committed:	Wed Jan 12 22:41:40 2005 UTC (20 years, 3 months ago) by gezelter
File size:	8766 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	246	/*
2			* 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			* 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	155	*/
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
53			DataStorage::DataStorage() : size_(0), storageLayout_(0){
54
55			}
56
57			DataStorage::DataStorage(int size, int storageLayout) : size_(size){
58			setStorageLayout(storageLayout);
59			resize(size);
60			}
61
62			int DataStorage::getSize() {
63
64			if (storageLayout_ & dslPosition && position.size() != size_) {
65			//error
66			std::cerr << "size does not match"<< std::endl;
67			}
68
69			if (storageLayout_ & dslVelocity && velocity.size() != size_) {
70			//error
71			std::cerr << "size does not match"<< std::endl;
72			}
73
74			if (storageLayout_ & dslAmat && aMat.size() != size_) {
75			//error
76			std::cerr << "size does not match"<< std::endl;
77			}
78
79			if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
80			//error
81			std::cerr << "size does not match"<< std::endl;
82			}
83
84	gezelter	246	if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
85	tim	155	//error
86			std::cerr << "size does not match"<< std::endl;
87			}
88
89			if (storageLayout_ & dslZAngle && zAngle.size() != size_) {
90			//error
91			std::cerr << "size does not match"<< std::endl;
92			}
93
94			if (storageLayout_ & dslForce && force.size() != size_) {
95			//error
96			std::cerr << "size does not match"<< std::endl;
97			}
98
99			if (storageLayout_ & dslTorque && torque.size() != size_) {
100			//error
101			std::cerr << "size does not match"<< std::endl;
102			}
103
104			return size_;
105
106			}
107
108			void DataStorage::resize(int newSize) {
109
110			if (storageLayout_ & dslPosition) {
111			internalResize(position, newSize);
112			}
113
114			if (storageLayout_ & dslVelocity) {
115			internalResize(velocity, newSize);
116			}
117
118			if (storageLayout_ & dslAmat) {
119			internalResize(aMat, newSize);
120			}
121
122			if (storageLayout_ & dslAngularMomentum) {
123			internalResize(angularMomentum, newSize);
124			}
125
126	gezelter	246	if (storageLayout_ & dslElectroFrame) {
127			internalResize(electroFrame, newSize);
128	tim	155	}
129
130			if (storageLayout_ & dslZAngle) {
131			internalResize(zAngle, newSize);
132			}
133
134			if (storageLayout_ & dslForce) {
135			internalResize(force, newSize);
136			}
137
138			if (storageLayout_ & dslTorque) {
139			internalResize(torque, newSize);
140			}
141
142			size_ = newSize;
143			}
144
145			void DataStorage::reserve(int size) {
146			if (storageLayout_ & dslPosition) {
147			position.reserve(size);
148			}
149
150			if (storageLayout_ & dslVelocity) {
151			velocity.reserve(size);
152			}
153
154			if (storageLayout_ & dslAmat) {
155			aMat.reserve(size);
156			}
157
158			if (storageLayout_ & dslAngularMomentum) {
159			angularMomentum.reserve(size);
160			}
161
162	gezelter	246	if (storageLayout_ & dslElectroFrame) {
163			electroFrame.reserve(size);
164	tim	155	}
165
166			if (storageLayout_ & dslZAngle) {
167			zAngle.reserve(size);
168			}
169
170			if (storageLayout_ & dslForce) {
171			force.reserve(size);
172			}
173
174			if (storageLayout_ & dslTorque) {
175			torque.reserve(size);
176			}
177
178			}
179
180			void DataStorage::copy(int source, int num, int target) {
181			if (num + target > size_ ) {
182			//error
183			}
184
185			if (storageLayout_ & dslPosition) {
186	gezelter	246	internalCopy(position, source, num, target);
187	tim	155	}
188
189			if (storageLayout_ & dslVelocity) {
190	gezelter	246	internalCopy(velocity, source, num, target);
191	tim	155	}
192
193			if (storageLayout_ & dslAmat) {
194	gezelter	246	internalCopy(aMat, source, num, target);
195	tim	155	}
196
197			if (storageLayout_ & dslAngularMomentum) {
198	gezelter	246	internalCopy(angularMomentum, source, num, target);
199	tim	155	}
200
201	gezelter	246	if (storageLayout_ & dslElectroFrame) {
202			internalCopy(electroFrame, source, num, target);
203	tim	155	}
204
205			if (storageLayout_ & dslZAngle) {
206	gezelter	246	internalCopy(zAngle, source, num, target);
207	tim	155	}
208
209			if (storageLayout_ & dslForce) {
210	gezelter	246	internalCopy(force, source, num, target);
211	tim	155	}
212
213			if (storageLayout_ & dslTorque) {
214	gezelter	246	internalCopy(torque, source, num, target);
215	tim	155	}
216
217
218			}
219
220			int DataStorage::getStorageLayout() {
221			return storageLayout_;
222			}
223
224			void DataStorage::setStorageLayout(int layout) {
225			storageLayout_ = layout;
226			resize(size_);
227			}
228
229			double* DataStorage::getArrayPointer(int whichArray) {
230
231			switch (whichArray) {
232			case dslPosition:
233	gezelter	246	return internalGetArrayPointer(position);
234	tim	155	break;
235
236			case dslVelocity:
237			return internalGetArrayPointer(velocity);
238			break;
239
240			case dslAmat:
241			return internalGetArrayPointer(aMat);
242			break;
243
244			case dslAngularMomentum:
245			return internalGetArrayPointer(angularMomentum);
246			break;
247
248	gezelter	246	case dslElectroFrame:
249			return internalGetArrayPointer(electroFrame);
250	tim	155	break;
251
252			case dslZAngle:
253			return internalGetArrayPointer(zAngle);
254			break;
255
256			case dslForce:
257			return internalGetArrayPointer(force);
258			break;
259
260			case dslTorque:
261			return internalGetArrayPointer(torque);
262			break;
263
264			default:
265			//error message
266			return NULL;
267
268			}
269			}
270
271			double* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
272			if (v.size() == 0) {
273			return NULL;
274			} else {
275			return v[0].getArrayPointer();
276			}
277			}
278
279			double* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
280			if (v.size() == 0) {
281			return NULL;
282			} else {
283			return v[0].getArrayPointer();
284			}
285
286			}
287
288			double* DataStorage::internalGetArrayPointer(std::vector<double>& v) {
289			if (v.size() == 0) {
290			return NULL;
291			} else {
292			return &(v[0]);
293			}
294
295			}
296
297			template<typename T>
298			void DataStorage::internalResize(std::vector<T>& v, int newSize){
299			int oldSize = v.size();
300
301			if (oldSize == newSize) {
302			return;
303			} else if (oldSize < newSize) {
304			v.insert(v.end(), newSize-oldSize, T());
305			} else {
306			typename std::vector<T>::iterator i;
307			i = v.begin();
308			std::advance(i, newSize);
309			v.erase(i, v.end());
310			}
311			}
312
313			template<typename T>
314	gezelter	246	void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
315	tim	155	typename std::vector<T>::iterator first;
316			typename std::vector<T>::iterator last;
317			typename std::vector<T>::iterator result;
318
319			first = v.begin();
320			last = v.begin();
321			result = v.begin();
322
323			std::advance(first, source);
324			//STL algorithm use half opened range
325			std::advance(last, num + 1);
326			std::advance(result, target );
327
328			std::copy(first, last, result);
329			}