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root/OpenMD/trunk/src/brains/DataStorage.cpp

Comparing trunk/src/brains/DataStorage.cpp (file contents):
Revision 323 by tim, Sun Feb 13 15:56:10 2005 UTC vs.
Revision 1793 by gezelter, Fri Aug 31 21:16:10 2012 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
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	+	*
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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	<	/**
44	<	* @file DataStorage.cpp
45	<	* @author tlin
46	<	* @date 10/26/2004
47	<	* @time 11:56am
48	<	* @version 1.0
49	<	*/
43	>	/**
44	>	* @file DataStorage.cpp
45	>	* @author tlin
46	>	* @date 10/26/2004
47	>	* @time 11:56am
48	>	* @version 1.0
49	>	*/
50
51		#include "brains/DataStorage.hpp"
52	+	using namespace std;
53	+	namespace OpenMD {
54
55	<	namespace oopse {
55	>	DataStorage::DataStorage() : size_(0), storageLayout_(0){
56
57	<	DataStorage::DataStorage() : size_(0), storageLayout_(0){
57	>	}
58
59	<	}
57	<
58	<	DataStorage::DataStorage(int size, int storageLayout) : size_(size){
59	>	DataStorage::DataStorage(int size, int storageLayout) : size_(size){
60		setStorageLayout(storageLayout);
61		resize(size);
62	<	}
62	>	}
63
64	<	int DataStorage::getSize() {
64	>	int DataStorage::getSize() {
65
66		if (storageLayout_ & dslPosition && position.size() != size_) {
67	<	//error
68	<	std::cerr << "size does not match"<< std::endl;
67	>	//error
68	>	cerr << "size does not match"<< endl;
69		}
70
71		if (storageLayout_ & dslVelocity && velocity.size() != size_) {
72	<	//error
73	<	std::cerr << "size does not match"<< std::endl;
72	>	//error
73	>	cerr << "size does not match"<< endl;
74		}
75
76		if (storageLayout_ & dslAmat && aMat.size() != size_) {
77	<	//error
78	<	std::cerr << "size does not match"<< std::endl;
77	>	//error
78	>	cerr << "size does not match"<< endl;
79		}
80
81		if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
82	<	//error
83	<	std::cerr << "size does not match"<< std::endl;
82	>	//error
83	>	cerr << "size does not match"<< endl;
84		}
85
86		if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
87	<	//error
88	<	std::cerr << "size does not match"<< std::endl;
87	>	//error
88	>	cerr << "size does not match"<< endl;
89		}
90
90	–	if (storageLayout_ & dslZAngle && zAngle.size() != size_) {
91	–	//error
92	–	std::cerr << "size does not match"<< std::endl;
93	–	}
94	–
91		if (storageLayout_ & dslForce && force.size() != size_) {
92	<	//error
93	<	std::cerr << "size does not match"<< std::endl;
92	>	//error
93	>	cerr << "size does not match"<< endl;
94		}
95
96		if (storageLayout_ & dslTorque && torque.size() != size_) {
97	<	//error
98	<	std::cerr << "size does not match"<< std::endl;
97	>	//error
98	>	cerr << "size does not match"<< endl;
99		}
100
101	+	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
102	+	//error
103	+	cerr << "size does not match"<< endl;
104	+	}
105	+
106	+	if (storageLayout_ & dslDensity && density.size() != size_) {
107	+	//error
108	+	cerr << "size does not match"<< endl;
109	+	}
110	+
111	+	if (storageLayout_ & dslFunctional && functional.size() != size_) {
112	+	//error
113	+	cerr << "size does not match"<< endl;
114	+	}
115	+
116	+	if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
117	+	//error
118	+	cerr << "size does not match"<< endl;
119	+	}
120	+
121	+	if (storageLayout_ & dslElectricField && electricField.size() != size_) {
122	+	//error
123	+	cerr << "size does not match"<< endl;
124	+	}
125	+
126	+	if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
127	+	//error
128	+	cerr << "size does not match"<< endl;
129	+	}
130	+
131	+	if (storageLayout_ & dslFlucQPosition && flucQPos.size() != size_) {
132	+	//error
133	+	cerr << "size does not match"<< endl;
134	+	}
135	+
136	+	if (storageLayout_ & dslFlucQVelocity && flucQVel.size() != size_) {
137	+	//error
138	+	cerr << "size does not match"<< endl;
139	+	}
140	+
141	+	if (storageLayout_ & dslFlucQForce && flucQFrc.size() != size_) {
142	+	//error
143	+	cerr << "size does not match"<< endl;
144	+	}
145	+
146		return size_;
147
148	<	}
148	>	}
149
150	<	void DataStorage::resize(int newSize) {
150	>	void DataStorage::resize(int newSize) {
151
152		if (storageLayout_ & dslPosition) {
153	<	internalResize(position, newSize);
153	>	internalResize(position, newSize);
154		}
155
156		if (storageLayout_ & dslVelocity) {
157	<	internalResize(velocity, newSize);
157	>	internalResize(velocity, newSize);
158		}
159
160		if (storageLayout_ & dslAmat) {
161	<	internalResize(aMat, newSize);
161	>	internalResize(aMat, newSize);
162		}
163
164		if (storageLayout_ & dslAngularMomentum) {
165	<	internalResize(angularMomentum, newSize);
165	>	internalResize(angularMomentum, newSize);
166		}
167
168		if (storageLayout_ & dslElectroFrame) {
169	<	internalResize(electroFrame, newSize);
169	>	internalResize(electroFrame, newSize);
170		}
171
131	–	if (storageLayout_ & dslZAngle) {
132	–	internalResize(zAngle, newSize);
133	–	}
134	–
172		if (storageLayout_ & dslForce) {
173	<	internalResize(force, newSize);
173	>	internalResize(force, newSize);
174		}
175
176		if (storageLayout_ & dslTorque) {
177	<	internalResize(torque, newSize);
177	>	internalResize(torque, newSize);
178		}
179
180	<	size_ = newSize;
181	<	}
180	>	if (storageLayout_ & dslParticlePot) {
181	>	internalResize(particlePot, newSize);
182	>	}
183
184	<	void DataStorage::reserve(int size) {
184	>	if (storageLayout_ & dslDensity) {
185	>	internalResize(density, newSize);
186	>	}
187	>
188	>	if (storageLayout_ & dslFunctional) {
189	>	internalResize(functional, newSize);
190	>	}
191	>
192	>	if (storageLayout_ & dslFunctionalDerivative) {
193	>	internalResize(functionalDerivative, newSize);
194	>	}
195	>
196	>	if (storageLayout_ & dslElectricField) {
197	>	internalResize(electricField, newSize);
198	>	}
199	>
200	>	if (storageLayout_ & dslSkippedCharge) {
201	>	internalResize(skippedCharge, newSize);
202	>	}
203	>
204	>	if (storageLayout_ & dslFlucQPosition) {
205	>	internalResize(flucQPos, newSize);
206	>	}
207	>
208	>	if (storageLayout_ & dslFlucQVelocity) {
209	>	internalResize(flucQVel, newSize);
210	>	}
211	>
212	>	if (storageLayout_ & dslFlucQForce) {
213	>	internalResize(flucQFrc, newSize);
214	>	}
215	>
216	>	size_ = newSize;
217	>	}
218	>
219	>	void DataStorage::reserve(int size) {
220		if (storageLayout_ & dslPosition) {
221	<	position.reserve(size);
221	>	position.reserve(size);
222		}
223
224		if (storageLayout_ & dslVelocity) {
225	<	velocity.reserve(size);
225	>	velocity.reserve(size);
226		}
227
228		if (storageLayout_ & dslAmat) {
229	<	aMat.reserve(size);
229	>	aMat.reserve(size);
230		}
231
232		if (storageLayout_ & dslAngularMomentum) {
233	<	angularMomentum.reserve(size);
233	>	angularMomentum.reserve(size);
234		}
235
236		if (storageLayout_ & dslElectroFrame) {
237	<	electroFrame.reserve(size);
237	>	electroFrame.reserve(size);
238		}
239
167	–	if (storageLayout_ & dslZAngle) {
168	–	zAngle.reserve(size);
169	–	}
170	–
240		if (storageLayout_ & dslForce) {
241	<	force.reserve(size);
241	>	force.reserve(size);
242		}
243
244		if (storageLayout_ & dslTorque) {
245	<	torque.reserve(size);
245	>	torque.reserve(size);
246		}
247	+
248	+	if (storageLayout_ & dslParticlePot) {
249	+	particlePot.reserve(size);
250	+	}
251
252	<	}
252	>	if (storageLayout_ & dslDensity) {
253	>	density.reserve(size);
254	>	}
255
256	<	void DataStorage::copy(int source, int num, int target) {
256	>	if (storageLayout_ & dslFunctional) {
257	>	functional.reserve(size);
258	>	}
259	>
260	>	if (storageLayout_ & dslFunctionalDerivative) {
261	>	functionalDerivative.reserve(size);
262	>	}
263	>
264	>	if (storageLayout_ & dslElectricField) {
265	>	electricField.reserve(size);
266	>	}
267	>
268	>	if (storageLayout_ & dslSkippedCharge) {
269	>	skippedCharge.reserve(size);
270	>	}
271	>
272	>	if (storageLayout_ & dslFlucQPosition) {
273	>	flucQPos.reserve(size);
274	>	}
275	>
276	>	if (storageLayout_ & dslFlucQVelocity) {
277	>	flucQVel.reserve(size);
278	>	}
279	>
280	>	if (storageLayout_ & dslFlucQForce) {
281	>	flucQFrc.reserve(size);
282	>	}
283	>	}
284	>
285	>	void DataStorage::copy(int source, int num, int target) {
286		if (num + target > size_ ) {
287	<	//error
287	>	//error
288		}
289
290		if (storageLayout_ & dslPosition) {
291	<	internalCopy(position, source, num, target);
291	>	internalCopy(position, source, num, target);
292		}
293
294		if (storageLayout_ & dslVelocity) {
295	<	internalCopy(velocity, source, num, target);
296	<	}
295	>	internalCopy(velocity, source, num, target);
296	>	}
297
298		if (storageLayout_ & dslAmat) {
299	<	internalCopy(aMat, source, num, target);
300	<	}
299	>	internalCopy(aMat, source, num, target);
300	>	}
301
302		if (storageLayout_ & dslAngularMomentum) {
303	<	internalCopy(angularMomentum, source, num, target);
303	>	internalCopy(angularMomentum, source, num, target);
304		}
305
306		if (storageLayout_ & dslElectroFrame) {
307	<	internalCopy(electroFrame, source, num, target);
307	>	internalCopy(electroFrame, source, num, target);
308		}
309
206	–	if (storageLayout_ & dslZAngle) {
207	–	internalCopy(zAngle, source, num, target);
208	–	}
209	–
310		if (storageLayout_ & dslForce) {
311	<	internalCopy(force, source, num, target);
311	>	internalCopy(force, source, num, target);
312		}
313
314		if (storageLayout_ & dslTorque) {
315	<	internalCopy(torque, source, num, target);
315	>	internalCopy(torque, source, num, target);
316		}
217	–
317
318	<	}
318	>	if (storageLayout_ & dslParticlePot) {
319	>	internalCopy(particlePot, source, num, target);
320	>	}
321
322	<	int DataStorage::getStorageLayout() {
323	<	return storageLayout_;
324	<	}
322	>	if (storageLayout_ & dslDensity) {
323	>	internalCopy(density, source, num, target);
324	>	}
325
326	<	void DataStorage::setStorageLayout(int layout) {
326	>	if (storageLayout_ & dslFunctional) {
327	>	internalCopy(functional, source, num, target);
328	>	}
329	>
330	>	if (storageLayout_ & dslFunctionalDerivative) {
331	>	internalCopy(functionalDerivative, source, num, target);
332	>	}
333	>
334	>	if (storageLayout_ & dslElectricField) {
335	>	internalCopy(electricField, source, num, target);
336	>	}
337	>
338	>	if (storageLayout_ & dslSkippedCharge) {
339	>	internalCopy(skippedCharge, source, num, target);
340	>	}
341	>
342	>	if (storageLayout_ & dslFlucQPosition) {
343	>	internalCopy(flucQPos, source, num, target);
344	>	}
345	>
346	>	if (storageLayout_ & dslFlucQVelocity) {
347	>	internalCopy(flucQVel, source, num, target);
348	>	}
349	>	if (storageLayout_ & dslFlucQForce) {
350	>	internalCopy(flucQFrc, source, num, target);
351	>	}
352	>	}
353	>
354	>	int DataStorage::getStorageLayout() {
355	>	return storageLayout_;
356	>	}
357	>
358	>	void DataStorage::setStorageLayout(int layout) {
359		storageLayout_ = layout;
360		resize(size_);
361	<	}
361	>	}
362
363	<	double* DataStorage::getArrayPointer(int whichArray) {
363	>	RealType* DataStorage::getArrayPointer(int whichArray) {
364
365		switch (whichArray) {
366	<	case dslPosition:
367	<	return internalGetArrayPointer(position);
235	<	break;
366	>	case dslPosition:
367	>	return internalGetArrayPointer(position);
368
369	<	case dslVelocity:
370	<	return internalGetArrayPointer(velocity);
239	<	break;
369	>	case dslVelocity:
370	>	return internalGetArrayPointer(velocity);
371
372	<	case dslAmat:
373	<	return internalGetArrayPointer(aMat);
243	<	break;
372	>	case dslAmat:
373	>	return internalGetArrayPointer(aMat);
374
375	<	case dslAngularMomentum:
376	<	return internalGetArrayPointer(angularMomentum);
247	<	break;
375	>	case dslAngularMomentum:
376	>	return internalGetArrayPointer(angularMomentum);
377
378	<	case dslElectroFrame:
379	<	return internalGetArrayPointer(electroFrame);
251	<	break;
378	>	case dslElectroFrame:
379	>	return internalGetArrayPointer(electroFrame);
380
381	<	case dslZAngle:
382	<	return internalGetArrayPointer(zAngle);
255	<	break;
381	>	case dslForce:
382	>	return internalGetArrayPointer(force);
383
384	<	case dslForce:
385	<	return internalGetArrayPointer(force);
259	<	break;
384	>	case dslTorque:
385	>	return internalGetArrayPointer(torque);
386
387	<	case dslTorque:
388	<	return internalGetArrayPointer(torque);
263	<	break;
264	<
265	<	default:
266	<	//error message
267	<	return NULL;
387	>	case dslParticlePot:
388	>	return internalGetArrayPointer(particlePot);
389
390	+	case dslDensity:
391	+	return internalGetArrayPointer(density);
392	+
393	+	case dslFunctional:
394	+	return internalGetArrayPointer(functional);
395	+
396	+	case dslFunctionalDerivative:
397	+	return internalGetArrayPointer(functionalDerivative);
398	+
399	+	case dslElectricField:
400	+	return internalGetArrayPointer(electricField);
401	+
402	+	case dslSkippedCharge:
403	+	return internalGetArrayPointer(skippedCharge);
404	+
405	+	case dslFlucQPosition:
406	+	return internalGetArrayPointer(flucQPos);
407	+
408	+	case dslFlucQVelocity:
409	+	return internalGetArrayPointer(flucQVel);
410	+
411	+	case dslFlucQForce:
412	+	return internalGetArrayPointer(flucQFrc);
413	+
414	+	default:
415	+	//error message
416	+	return NULL;
417	+
418		}
419	<	}
419	>	}
420
421	<	double* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
421	>	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
422		if (v.size() == 0) {
423	<	return NULL;
423	>	return NULL;
424		} else {
425	<	return v[0].getArrayPointer();
425	>	return v[0].getArrayPointer();
426		}
427	<	}
427	>	}
428
429	<	double* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
429	>	RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
430		if (v.size() == 0) {
431	<	return NULL;
431	>	return NULL;
432		} else {
433	<	return v[0].getArrayPointer();
433	>	return v[0].getArrayPointer();
434		}
435
436	<	}
436	>	}
437
438	<	double* DataStorage::internalGetArrayPointer(std::vector<double>& v) {
438	>	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
439		if (v.size() == 0) {
440	<	return NULL;
440	>	return NULL;
441		} else {
442	<	return &(v[0]);
442	>	return &(v[0]);
443		}
444
445	<	}
445	>	}
446
447	<	template<typename T>
448	<	void DataStorage::internalResize(std::vector<T>& v, int newSize){
447	>	template<typename T>
448	>	void DataStorage::internalResize(std::vector<T>& v, int newSize){
449		int oldSize = v.size();
450
451		if (oldSize == newSize) {
452	<	return;
452	>	return;
453		} else if (oldSize < newSize) {
454	<	v.insert(v.end(), newSize-oldSize, T());
454	>	v.insert(v.end(), newSize-oldSize, T());
455		} else {
456	<	typename std::vector<T>::iterator i;
457	<	i = v.begin();
458	<	std::advance(i, newSize);
459	<	v.erase(i, v.end());
456	>	typename std::vector<T>::iterator i;
457	>	i = v.begin();
458	>	std::advance(i, newSize);
459	>	v.erase(i, v.end());
460		}
461	<	}
461	>	}
462
463	<	template<typename T>
464	<	void DataStorage::internalCopy(std::vector<T>& v, int source,  int num, int target) {
463	>	template<typename T>
464	>	void DataStorage::internalCopy(std::vector<T>& v, int source,  int num, int target) {
465		typename std::vector<T>::iterator first;
466		typename std::vector<T>::iterator last;
467		typename std::vector<T>::iterator result;
#	Line 327 | Line 476 | void DataStorage::internalCopy(std::vector<T>& v, int
476		std::advance(result, target );
477
478		std::copy(first, last, result);
479	<	}
479	>	}
480
481	<	int DataStorage::getBytesPerStuntDouble(int layout) {
481	>	int DataStorage::getBytesPerStuntDouble(int layout) {
482		int bytes = 0;
483		if (layout & dslPosition) {
484	<	bytes += sizeof(Vector3d);
336	<	} else if (layout & dslVelocity) {
337	<	bytes += sizeof(Vector3d);
338	<	} else if (layout & dslAmat) {
339	<	bytes += sizeof(Mat3x3d);
340	<	} else if (layout & dslAngularMomentum) {
341	<	bytes += sizeof(Vector3d);
342	<	} else if (layout & dslElectroFrame) {
343	<	bytes += sizeof(Mat3x3d);
344	<	} else if (layout & dslZAngle) {
345	<	bytes += sizeof(Vector3d);
346	<	} else if (layout & dslForce) {
347	<	bytes += sizeof(Vector3d);
348	<	} else if (layout & dslTorque) {
349	<	bytes += sizeof(Vector3d);
484	>	bytes += sizeof(Vector3d);
485		}
486	+	if (layout & dslVelocity) {
487	+	bytes += sizeof(Vector3d);
488	+	}
489	+	if (layout & dslAmat) {
490	+	bytes += sizeof(RotMat3x3d);
491	+	}
492	+	if (layout & dslAngularMomentum) {
493	+	bytes += sizeof(Vector3d);
494	+	}
495	+	if (layout & dslElectroFrame) {
496	+	bytes += sizeof(Mat3x3d);
497	+	}
498	+	if (layout & dslForce) {
499	+	bytes += sizeof(Vector3d);
500	+	}
501	+	if (layout & dslTorque) {
502	+	bytes += sizeof(Vector3d);
503	+	}
504	+	if (layout & dslParticlePot) {
505	+	bytes += sizeof(RealType);
506	+	}
507	+	if (layout & dslDensity) {
508	+	bytes += sizeof(RealType);
509	+	}
510	+	if (layout & dslFunctional) {
511	+	bytes += sizeof(RealType);
512	+	}
513	+	if (layout & dslFunctionalDerivative) {
514	+	bytes += sizeof(RealType);
515	+	}
516	+	if (layout & dslElectricField) {
517	+	bytes += sizeof(Vector3d);
518	+	}
519	+	if (layout & dslSkippedCharge) {
520	+	bytes += sizeof(RealType);
521	+	}
522	+	if (layout & dslFlucQPosition) {
523	+	bytes += sizeof(RealType);
524	+	}
525	+	if (layout & dslFlucQVelocity) {
526	+	bytes += sizeof(RealType);
527	+	}
528	+	if (layout & dslFlucQForce) {
529	+	bytes += sizeof(RealType);
530	+	}
531	+
532		return bytes;
533	<	}
533	>	}
534
535		}

Comparing trunk/src/brains/DataStorage.cpp (property svn:keywords):
Revision 323 by tim, Sun Feb 13 15:56:10 2005 UTC vs.
Revision 1793 by gezelter, Fri Aug 31 21:16:10 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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