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, 9 months ago) by gezelter
File size:	8766 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	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
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	if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
85	//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	if (storageLayout_ & dslElectroFrame) {
127	internalResize(electroFrame, newSize);
128	}
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	if (storageLayout_ & dslElectroFrame) {
163	electroFrame.reserve(size);
164	}
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	internalCopy(position, source, num, target);
187	}
188
189	if (storageLayout_ & dslVelocity) {
190	internalCopy(velocity, source, num, target);
191	}
192
193	if (storageLayout_ & dslAmat) {
194	internalCopy(aMat, source, num, target);
195	}
196
197	if (storageLayout_ & dslAngularMomentum) {
198	internalCopy(angularMomentum, source, num, target);
199	}
200
201	if (storageLayout_ & dslElectroFrame) {
202	internalCopy(electroFrame, source, num, target);
203	}
204
205	if (storageLayout_ & dslZAngle) {
206	internalCopy(zAngle, source, num, target);
207	}
208
209	if (storageLayout_ & dslForce) {
210	internalCopy(force, source, num, target);
211	}
212
213	if (storageLayout_ & dslTorque) {
214	internalCopy(torque, source, num, target);
215	}
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	return internalGetArrayPointer(position);
234	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	case dslElectroFrame:
249	return internalGetArrayPointer(electroFrame);
250	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	void DataStorage::internalCopy(std::vector<T>& v, int source, int num, int target) {
315	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	}