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

Comparing trunk/src/brains/DataStorage.cpp (file contents):
Revision 331 by tim, Sun Feb 13 21:18:27 2005 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 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	<	return size_;
101	>	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
102	>	//error
103	>	cerr << "size does not match"<< endl;
104	>	}
105
106	<	}
106	>	if (storageLayout_ & dslDensity && density.size() != size_) {
107	>	//error
108	>	cerr << "size does not match"<< endl;
109	>	}
110
111	<	void DataStorage::resize(int newSize) {
112	<
113	<	if (storageLayout_ & dslPosition) {
112	<	internalResize(position, newSize);
111	>	if (storageLayout_ & dslFunctional && functional.size() != size_) {
112	>	//error
113	>	cerr << "size does not match"<< endl;
114		}
115
116	<	if (storageLayout_ & dslVelocity) {
117	<	internalResize(velocity, newSize);
116	>	if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
117	>	//error
118	>	cerr << "size does not match"<< endl;
119		}
120
121	<	if (storageLayout_ & dslAmat) {
122	<	internalResize(aMat, newSize);
121	>	if (storageLayout_ & dslElectricField && electricField.size() != size_) {
122	>	//error
123	>	cerr << "size does not match"<< endl;
124		}
125
126	<	if (storageLayout_ & dslAngularMomentum) {
127	<	internalResize(angularMomentum, newSize);
126	>	if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
127	>	//error
128	>	cerr << "size does not match"<< endl;
129		}
130
131	<	if (storageLayout_ & dslElectroFrame) {
132	<	internalResize(electroFrame, newSize);
131	>	if (storageLayout_ & dslFlucQPosition && flucQPos.size() != size_) {
132	>	//error
133	>	cerr << "size does not match"<< endl;
134		}
130	–
131	–	if (storageLayout_ & dslZAngle) {
132	–	internalResize(zAngle, newSize);
133	–	}
135
136	<	if (storageLayout_ & dslForce) {
137	<	internalResize(force, newSize);
136	>	if (storageLayout_ & dslFlucQVelocity && flucQVel.size() != size_) {
137	>	//error
138	>	cerr << "size does not match"<< endl;
139		}
140
141	<	if (storageLayout_ & dslTorque) {
142	<	internalResize(torque, newSize);
141	>	if (storageLayout_ & dslFlucQForce && flucQFrc.size() != size_) {
142	>	//error
143	>	cerr << "size does not match"<< endl;
144		}
145	+
146	+	return size_;
147
148	<	size_ = newSize;
144	<	}
148	>	}
149
150	<	void DataStorage::reserve(int size) {
150	>	void DataStorage::resize(int newSize) {
151	>
152		if (storageLayout_ & dslPosition) {
153	<	position.reserve(size);
154	<	}
153	>	internalResize(position, newSize);
154	>	}
155
156		if (storageLayout_ & dslVelocity) {
157	<	velocity.reserve(size);
158	<	}
157	>	internalResize(velocity, newSize);
158	>	}
159
160		if (storageLayout_ & dslAmat) {
161	<	aMat.reserve(size);
162	<	}
161	>	internalResize(aMat, newSize);
162	>	}
163
164		if (storageLayout_ & dslAngularMomentum) {
165	<	angularMomentum.reserve(size);
166	<	}
165	>	internalResize(angularMomentum, newSize);
166	>	}
167
168		if (storageLayout_ & dslElectroFrame) {
169	<	electroFrame.reserve(size);
169	>	internalResize(electroFrame, newSize);
170		}
171
172	<	if (storageLayout_ & dslZAngle) {
173	<	zAngle.reserve(size);
172	>	if (storageLayout_ & dslForce) {
173	>	internalResize(force, newSize);
174	>	}
175	>
176	>	if (storageLayout_ & dslTorque) {
177	>	internalResize(torque, newSize);
178	>	}
179	>
180	>	if (storageLayout_ & dslParticlePot) {
181	>	internalResize(particlePot, newSize);
182	>	}
183	>
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);
222	+	}
223	+
224	+	if (storageLayout_ & dslVelocity) {
225	+	velocity.reserve(size);
226	+	}
227	+
228	+	if (storageLayout_ & dslAmat) {
229	+	aMat.reserve(size);
230	+	}
231	+
232	+	if (storageLayout_ & dslAngularMomentum) {
233	+	angularMomentum.reserve(size);
234	+	}
235	+
236	+	if (storageLayout_ & dslElectroFrame) {
237	+	electroFrame.reserve(size);
238	+	}
239	+
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) {
327	<	storageLayout_ = layout;
328	<	resize(size_);
228	<	}
326	>	if (storageLayout_ & dslFunctional) {
327	>	internalCopy(functional, source, num, target);
328	>	}
329
330	<	double* DataStorage::getArrayPointer(int whichArray) {
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	+	}
362	+
363	+	RealType* DataStorage::getArrayPointer(int whichArray) {
364	+
365		switch (whichArray) {
366	<	case dslPosition:
367	<	return internalGetArrayPointer(position);
368	<	break;
366	>	case dslPosition:
367	>	return internalGetArrayPointer(position);
368	>	break;
369
370	<	case dslVelocity:
371	<	return internalGetArrayPointer(velocity);
372	<	break;
370	>	case dslVelocity:
371	>	return internalGetArrayPointer(velocity);
372	>	break;
373
374	<	case dslAmat:
375	<	return internalGetArrayPointer(aMat);
376	<	break;
374	>	case dslAmat:
375	>	return internalGetArrayPointer(aMat);
376	>	break;
377
378	<	case dslAngularMomentum:
379	<	return internalGetArrayPointer(angularMomentum);
380	<	break;
378	>	case dslAngularMomentum:
379	>	return internalGetArrayPointer(angularMomentum);
380	>	break;
381
382	<	case dslElectroFrame:
383	<	return internalGetArrayPointer(electroFrame);
384	<	break;
382	>	case dslElectroFrame:
383	>	return internalGetArrayPointer(electroFrame);
384	>	break;
385
386	<	case dslZAngle:
387	<	return internalGetArrayPointer(zAngle);
388	<	break;
386	>	case dslForce:
387	>	return internalGetArrayPointer(force);
388	>	break;
389
390	<	case dslForce:
391	<	return internalGetArrayPointer(force);
392	<	break;
390	>	case dslTorque:
391	>	return internalGetArrayPointer(torque);
392	>	break;
393
394	<	case dslTorque:
395	<	return internalGetArrayPointer(torque);
396	<	break;
264	<
265	<	default:
266	<	//error message
267	<	return NULL;
394	>	case dslParticlePot:
395	>	return internalGetArrayPointer(particlePot);
396	>	break;
397
398	+	case dslDensity:
399	+	return internalGetArrayPointer(density);
400	+	break;
401	+
402	+	case dslFunctional:
403	+	return internalGetArrayPointer(functional);
404	+	break;
405	+
406	+	case dslFunctionalDerivative:
407	+	return internalGetArrayPointer(functionalDerivative);
408	+	break;
409	+
410	+	case dslElectricField:
411	+	return internalGetArrayPointer(electricField);
412	+	break;
413	+
414	+	case dslSkippedCharge:
415	+	return internalGetArrayPointer(skippedCharge);
416	+	break;
417	+
418	+	case dslFlucQPosition:
419	+	return internalGetArrayPointer(flucQPos);
420	+	break;
421	+
422	+	case dslFlucQVelocity:
423	+	return internalGetArrayPointer(flucQVel);
424	+	break;
425	+
426	+	case dslFlucQForce:
427	+	return internalGetArrayPointer(flucQFrc);
428	+	break;
429	+
430	+	default:
431	+	//error message
432	+	return NULL;
433	+
434		}
435	<	}
435	>	}
436
437	<	double* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
437	>	RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
438		if (v.size() == 0) {
439	<	return NULL;
439	>	return NULL;
440		} else {
441	<	return v[0].getArrayPointer();
441	>	return v[0].getArrayPointer();
442		}
443	<	}
443	>	}
444
445	<	double* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
445	>	RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
446		if (v.size() == 0) {
447	<	return NULL;
447	>	return NULL;
448		} else {
449	<	return v[0].getArrayPointer();
449	>	return v[0].getArrayPointer();
450		}
451
452	<	}
452	>	}
453
454	<	double* DataStorage::internalGetArrayPointer(std::vector<double>& v) {
454	>	RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
455		if (v.size() == 0) {
456	<	return NULL;
456	>	return NULL;
457		} else {
458	<	return &(v[0]);
458	>	return &(v[0]);
459		}
460
461	<	}
461	>	}
462
463	<	template<typename T>
464	<	void DataStorage::internalResize(std::vector<T>& v, int newSize){
463	>	template<typename T>
464	>	void DataStorage::internalResize(std::vector<T>& v, int newSize){
465		int oldSize = v.size();
466
467		if (oldSize == newSize) {
468	<	return;
468	>	return;
469		} else if (oldSize < newSize) {
470	<	v.insert(v.end(), newSize-oldSize, T());
470	>	v.insert(v.end(), newSize-oldSize, T());
471		} else {
472	<	typename std::vector<T>::iterator i;
473	<	i = v.begin();
474	<	std::advance(i, newSize);
475	<	v.erase(i, v.end());
472	>	typename std::vector<T>::iterator i;
473	>	i = v.begin();
474	>	std::advance(i, newSize);
475	>	v.erase(i, v.end());
476		}
477	<	}
477	>	}
478
479	<	template<typename T>
480	<	void DataStorage::internalCopy(std::vector<T>& v, int source,  int num, int target) {
479	>	template<typename T>
480	>	void DataStorage::internalCopy(std::vector<T>& v, int source,  int num, int target) {
481		typename std::vector<T>::iterator first;
482		typename std::vector<T>::iterator last;
483		typename std::vector<T>::iterator result;
#	Line 327 | Line 492 | void DataStorage::internalCopy(std::vector<T>& v, int
492		std::advance(result, target );
493
494		std::copy(first, last, result);
495	<	}
495	>	}
496
497	<	int DataStorage::getBytesPerStuntDouble(int layout) {
497	>	int DataStorage::getBytesPerStuntDouble(int layout) {
498		int bytes = 0;
499		if (layout & dslPosition) {
500	<	bytes += sizeof(Vector3d);
500	>	bytes += sizeof(Vector3d);
501		}
502		if (layout & dslVelocity) {
503	<	bytes += sizeof(Vector3d);
503	>	bytes += sizeof(Vector3d);
504		}
505		if (layout & dslAmat) {
506	<	bytes += sizeof(Mat3x3d);
506	>	bytes += sizeof(RotMat3x3d);
507		}
508		if (layout & dslAngularMomentum) {
509	<	bytes += sizeof(Vector3d);
509	>	bytes += sizeof(Vector3d);
510		}
511		if (layout & dslElectroFrame) {
512	<	bytes += sizeof(Mat3x3d);
512	>	bytes += sizeof(Mat3x3d);
513		}
349	–	if (layout & dslZAngle) {
350	–	bytes += sizeof(Vector3d);
351	–	}
514		if (layout & dslForce) {
515	<	bytes += sizeof(Vector3d);
515	>	bytes += sizeof(Vector3d);
516		}
517		if (layout & dslTorque) {
518	<	bytes += sizeof(Vector3d);
518	>	bytes += sizeof(Vector3d);
519		}
520	+	if (layout & dslParticlePot) {
521	+	bytes += sizeof(RealType);
522	+	}
523	+	if (layout & dslDensity) {
524	+	bytes += sizeof(RealType);
525	+	}
526	+	if (layout & dslFunctional) {
527	+	bytes += sizeof(RealType);
528	+	}
529	+	if (layout & dslFunctionalDerivative) {
530	+	bytes += sizeof(RealType);
531	+	}
532	+	if (layout & dslElectricField) {
533	+	bytes += sizeof(Vector3d);
534	+	}
535	+	if (layout & dslSkippedCharge) {
536	+	bytes += sizeof(RealType);
537	+	}
538	+	if (layout & dslFlucQPosition) {
539	+	bytes += sizeof(RealType);
540	+	}
541	+	if (layout & dslFlucQVelocity) {
542	+	bytes += sizeof(RealType);
543	+	}
544	+	if (layout & dslFlucQForce) {
545	+	bytes += sizeof(RealType);
546	+	}
547	+
548		return bytes;
549	<	}
549	>	}
550
551		}

Comparing trunk/src/brains/DataStorage.cpp (property svn:keywords):
Revision 331 by tim, Sun Feb 13 21:18:27 2005 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

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

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