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

Comparing trunk/src/brains/DataStorage.cpp (file contents):
Revision 1245 by chuckv, Tue May 27 16:39:06 2008 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	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, 234107 (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
46	–	* @time 11:56am
47		* @version 1.0
48		*/
49
50		#include "brains/DataStorage.hpp"
51	+	using namespace std;
52	+	namespace OpenMD {
53
52	–	namespace oopse {
53	–
54		DataStorage::DataStorage() : size_(0), storageLayout_(0){
55
56		}
#	Line 64 | Line 64 | namespace oopse {
64
65		if (storageLayout_ & dslPosition && position.size() != size_) {
66		//error
67	<	std::cerr << "size does not match"<< std::endl;
67	>	cerr << "size does not match"<< endl;
68		}
69
70		if (storageLayout_ & dslVelocity && velocity.size() != size_) {
71		//error
72	<	std::cerr << "size does not match"<< std::endl;
72	>	cerr << "size does not match"<< endl;
73		}
74
75	+	if (storageLayout_ & dslForce && force.size() != size_) {
76	+	//error
77	+	cerr << "size does not match"<< endl;
78	+	}
79	+
80		if (storageLayout_ & dslAmat && aMat.size() != size_) {
81		//error
82	<	std::cerr << "size does not match"<< std::endl;
82	>	cerr << "size does not match"<< endl;
83		}
84
85		if (storageLayout_ & dslAngularMomentum && angularMomentum.size() != size_) {
86		//error
87	<	std::cerr << "size does not match"<< std::endl;
87	>	cerr << "size does not match"<< endl;
88		}
89
90	<	if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
90	>	if (storageLayout_ & dslTorque && torque.size() != size_) {
91		//error
92	<	std::cerr << "size does not match"<< std::endl;
92	>	cerr << "size does not match"<< endl;
93		}
94
95	<	if (storageLayout_ & dslZAngle && zAngle.size() != size_) {
95	>	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
96		//error
97	<	std::cerr << "size does not match"<< std::endl;
97	>	cerr << "size does not match"<< endl;
98		}
99
100	<	if (storageLayout_ & dslForce && force.size() != size_) {
100	>	if (storageLayout_ & dslDensity && density.size() != size_) {
101		//error
102	<	std::cerr << "size does not match"<< std::endl;
102	>	cerr << "size does not match"<< endl;
103		}
104
105	<	if (storageLayout_ & dslTorque && torque.size() != size_) {
105	>	if (storageLayout_ & dslFunctional && functional.size() != size_) {
106		//error
107	<	std::cerr << "size does not match"<< std::endl;
107	>	cerr << "size does not match"<< endl;
108		}
109	<	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
109	>
110	>	if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
111		//error
112	<	std::cerr << "size does not match"<< std::endl;
112	>	cerr << "size does not match"<< endl;
113		}
114	+
115	+	if (storageLayout_ & dslDipole && dipole.size() != size_) {
116	+	//error
117	+	cerr << "size does not match"<< endl;
118	+	}
119	+
120	+	if (storageLayout_ & dslQuadrupole && quadrupole.size() != size_) {
121	+	//error
122	+	cerr << "size does not match"<< endl;
123	+	}
124	+
125	+	if (storageLayout_ & dslElectricField && electricField.size() != size_) {
126	+	//error
127	+	cerr << "size does not match"<< endl;
128	+	}
129	+
130	+	if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
131	+	//error
132	+	cerr << "size does not match"<< endl;
133	+	}
134	+
135	+	if (storageLayout_ & dslFlucQPosition && flucQPos.size() != size_) {
136	+	//error
137	+	cerr << "size does not match"<< endl;
138	+	}
139	+
140	+	if (storageLayout_ & dslFlucQVelocity && flucQVel.size() != size_) {
141	+	//error
142	+	cerr << "size does not match"<< endl;
143	+	}
144	+
145	+	if (storageLayout_ & dslFlucQForce && flucQFrc.size() != size_) {
146	+	//error
147	+	cerr << "size does not match"<< endl;
148	+	}
149
150		return size_;
151
#	Line 120 | Line 161 | namespace oopse {
161		internalResize(velocity, newSize);
162		}
163
164	+	if (storageLayout_ & dslForce) {
165	+	internalResize(force, newSize);
166	+	}
167	+
168		if (storageLayout_ & dslAmat) {
169		internalResize(aMat, newSize);
170		}
#	Line 127 | Line 172 | namespace oopse {
172		if (storageLayout_ & dslAngularMomentum) {
173		internalResize(angularMomentum, newSize);
174		}
175	+
176	+	if (storageLayout_ & dslTorque) {
177	+	internalResize(torque, newSize);
178	+	}
179
180	<	if (storageLayout_ & dslElectroFrame) {
181	<	internalResize(electroFrame, newSize);
180	>	if (storageLayout_ & dslParticlePot) {
181	>	internalResize(particlePot, newSize);
182		}
183	<
184	<	if (storageLayout_ & dslZAngle) {
185	<	internalResize(zAngle, newSize);
183	>
184	>	if (storageLayout_ & dslDensity) {
185	>	internalResize(density, newSize);
186		}
187
188	<	if (storageLayout_ & dslForce) {
189	<	internalResize(force, newSize);
188	>	if (storageLayout_ & dslFunctional) {
189	>	internalResize(functional, newSize);
190		}
191
192	<	if (storageLayout_ & dslTorque) {
193	<	internalResize(torque, newSize);
192	>	if (storageLayout_ & dslFunctionalDerivative) {
193	>	internalResize(functionalDerivative, newSize);
194		}
195
196	<	if (storageLayout_ & dslParticlePot) {
197	<	internalResize(particlePot, newSize);
196	>	if (storageLayout_ & dslDipole) {
197	>	internalResize(dipole, newSize);
198		}
199
200	+	if (storageLayout_ & dslQuadrupole) {
201	+	internalResize(quadrupole, newSize);
202	+	}
203	+
204	+	if (storageLayout_ & dslElectricField) {
205	+	internalResize(electricField, newSize);
206	+	}
207	+
208	+	if (storageLayout_ & dslSkippedCharge) {
209	+	internalResize(skippedCharge, newSize);
210	+	}
211	+
212	+	if (storageLayout_ & dslFlucQPosition) {
213	+	internalResize(flucQPos, newSize);
214	+	}
215	+
216	+	if (storageLayout_ & dslFlucQVelocity) {
217	+	internalResize(flucQVel, newSize);
218	+	}
219	+
220	+	if (storageLayout_ & dslFlucQForce) {
221	+	internalResize(flucQFrc, newSize);
222	+	}
223	+
224		size_ = newSize;
225		}
226
#	Line 160 | Line 233 | namespace oopse {
233		velocity.reserve(size);
234		}
235
236	+	if (storageLayout_ & dslForce) {
237	+	force.reserve(size);
238	+	}
239	+
240		if (storageLayout_ & dslAmat) {
241		aMat.reserve(size);
242		}
#	Line 168 | Line 245 | namespace oopse {
245		angularMomentum.reserve(size);
246		}
247
171	–	if (storageLayout_ & dslElectroFrame) {
172	–	electroFrame.reserve(size);
173	–	}
174	–
175	–	if (storageLayout_ & dslZAngle) {
176	–	zAngle.reserve(size);
177	–	}
178	–
179	–	if (storageLayout_ & dslForce) {
180	–	force.reserve(size);
181	–	}
182	–
248		if (storageLayout_ & dslTorque) {
249		torque.reserve(size);
250		}
251
252		if (storageLayout_ & dslParticlePot) {
253		particlePot.reserve(size);
254	+	}
255	+
256	+	if (storageLayout_ & dslDensity) {
257	+	density.reserve(size);
258	+	}
259	+
260	+	if (storageLayout_ & dslFunctional) {
261	+	functional.reserve(size);
262	+	}
263	+
264	+	if (storageLayout_ & dslFunctionalDerivative) {
265	+	functionalDerivative.reserve(size);
266	+	}
267	+
268	+	if (storageLayout_ & dslDipole) {
269	+	dipole.reserve(size);
270	+	}
271	+
272	+	if (storageLayout_ & dslQuadrupole) {
273	+	quadrupole.reserve(size);
274		}
275
276	+	if (storageLayout_ & dslElectricField) {
277	+	electricField.reserve(size);
278	+	}
279	+
280	+	if (storageLayout_ & dslSkippedCharge) {
281	+	skippedCharge.reserve(size);
282	+	}
283	+
284	+	if (storageLayout_ & dslFlucQPosition) {
285	+	flucQPos.reserve(size);
286	+	}
287	+
288	+	if (storageLayout_ & dslFlucQVelocity) {
289	+	flucQVel.reserve(size);
290	+	}
291	+
292	+	if (storageLayout_ & dslFlucQForce) {
293	+	flucQFrc.reserve(size);
294	+	}
295		}
296
297		void DataStorage::copy(int source, int num, int target) {
#	Line 203 | Line 307 | namespace oopse {
307		internalCopy(velocity, source, num, target);
308		}
309
310	+	if (storageLayout_ & dslForce) {
311	+	internalCopy(force, source, num, target);
312	+	}
313	+
314		if (storageLayout_ & dslAmat) {
315		internalCopy(aMat, source, num, target);
316		}
#	Line 211 | Line 319 | namespace oopse {
319		internalCopy(angularMomentum, source, num, target);
320		}
321
214	–	if (storageLayout_ & dslElectroFrame) {
215	–	internalCopy(electroFrame, source, num, target);
216	–	}
217	–
218	–	if (storageLayout_ & dslZAngle) {
219	–	internalCopy(zAngle, source, num, target);
220	–	}
221	–
222	–	if (storageLayout_ & dslForce) {
223	–	internalCopy(force, source, num, target);
224	–	}
225	–
322		if (storageLayout_ & dslTorque) {
323		internalCopy(torque, source, num, target);
324		}
#	Line 230 | Line 326 | namespace oopse {
326		if (storageLayout_ & dslParticlePot) {
327		internalCopy(particlePot, source, num, target);
328		}
233	–
329
330	+	if (storageLayout_ & dslDensity) {
331	+	internalCopy(density, source, num, target);
332	+	}
333	+
334	+	if (storageLayout_ & dslFunctional) {
335	+	internalCopy(functional, source, num, target);
336	+	}
337	+
338	+	if (storageLayout_ & dslFunctionalDerivative) {
339	+	internalCopy(functionalDerivative, source, num, target);
340	+	}
341	+
342	+	if (storageLayout_ & dslDipole) {
343	+	internalCopy(dipole, source, num, target);
344	+	}
345	+
346	+	if (storageLayout_ & dslQuadrupole) {
347	+	internalCopy(quadrupole, source, num, target);
348	+	}
349	+
350	+	if (storageLayout_ & dslElectricField) {
351	+	internalCopy(electricField, source, num, target);
352	+	}
353	+
354	+	if (storageLayout_ & dslSkippedCharge) {
355	+	internalCopy(skippedCharge, source, num, target);
356	+	}
357	+
358	+	if (storageLayout_ & dslFlucQPosition) {
359	+	internalCopy(flucQPos, source, num, target);
360	+	}
361	+
362	+	if (storageLayout_ & dslFlucQVelocity) {
363	+	internalCopy(flucQVel, source, num, target);
364	+	}
365	+	if (storageLayout_ & dslFlucQForce) {
366	+	internalCopy(flucQFrc, source, num, target);
367	+	}
368		}
369
370		int DataStorage::getStorageLayout() {
#	Line 248 | Line 381 | namespace oopse {
381		switch (whichArray) {
382		case dslPosition:
383		return internalGetArrayPointer(position);
251	–	break;
384
385		case dslVelocity:
386		return internalGetArrayPointer(velocity);
255	–	break;
387
388	+	case dslForce:
389	+	return internalGetArrayPointer(force);
390	+
391		case dslAmat:
392		return internalGetArrayPointer(aMat);
259	–	break;
393
394		case dslAngularMomentum:
395		return internalGetArrayPointer(angularMomentum);
263	–	break;
396
265	–	case dslElectroFrame:
266	–	return internalGetArrayPointer(electroFrame);
267	–	break;
268	–
269	–	case dslZAngle:
270	–	return internalGetArrayPointer(zAngle);
271	–	break;
272	–
273	–	case dslForce:
274	–	return internalGetArrayPointer(force);
275	–	break;
276	–
397		case dslTorque:
398		return internalGetArrayPointer(torque);
279	–	break;
399
400		case dslParticlePot:
401		return internalGetArrayPointer(particlePot);
402	<	break;
403	<
402	>
403	>	case dslDensity:
404	>	return internalGetArrayPointer(density);
405	>
406	>	case dslFunctional:
407	>	return internalGetArrayPointer(functional);
408	>
409	>	case dslFunctionalDerivative:
410	>	return internalGetArrayPointer(functionalDerivative);
411	>
412	>	case dslDipole:
413	>	return internalGetArrayPointer(dipole);
414	>
415	>	case dslQuadrupole:
416	>	return internalGetArrayPointer(quadrupole);
417	>
418	>	case dslElectricField:
419	>	return internalGetArrayPointer(electricField);
420	>
421	>	case dslSkippedCharge:
422	>	return internalGetArrayPointer(skippedCharge);
423	>
424	>	case dslFlucQPosition:
425	>	return internalGetArrayPointer(flucQPos);
426	>
427	>	case dslFlucQVelocity:
428	>	return internalGetArrayPointer(flucQVel);
429	>
430	>	case dslFlucQForce:
431	>	return internalGetArrayPointer(flucQFrc);
432	>
433		default:
434		//error message
435		return NULL;
288	–
436		}
437		}
438
439		RealType* DataStorage::internalGetArrayPointer(std::vector<Vector3d>& v) {
440	<	if (v.size() == 0) {
440	>	if (v.empty()) {
441		return NULL;
442		} else {
443		return v[0].getArrayPointer();
444		}
445		}
446
447	<	RealType* DataStorage::internalGetArrayPointer(std::vector<RotMat3x3d>& v) {
448	<	if (v.size() == 0) {
447	>	RealType* DataStorage::internalGetArrayPointer(std::vector<Mat3x3d>& v) {
448	>	if (v.empty()) {
449		return NULL;
450		} else {
451		return v[0].getArrayPointer();
#	Line 307 | Line 454 | namespace oopse {
454		}
455
456		RealType* DataStorage::internalGetArrayPointer(std::vector<RealType>& v) {
457	<	if (v.size() == 0) {
457	>	if (v.empty()) {
458		return NULL;
459		} else {
460		return &(v[0]);
#	Line 357 | Line 504 | namespace oopse {
504		if (layout & dslVelocity) {
505		bytes += sizeof(Vector3d);
506		}
507	+	if (layout & dslForce) {
508	+	bytes += sizeof(Vector3d);
509	+	}
510		if (layout & dslAmat) {
511		bytes += sizeof(RotMat3x3d);
512		}
513		if (layout & dslAngularMomentum) {
514		bytes += sizeof(Vector3d);
515		}
516	<	if (layout & dslElectroFrame) {
517	<	bytes += sizeof(Mat3x3d);
516	>	if (layout & dslTorque) {
517	>	bytes += sizeof(Vector3d);
518		}
519	<	if (layout & dslZAngle) {
519	>	if (layout & dslParticlePot) {
520		bytes += sizeof(RealType);
521		}
522	<	if (layout & dslForce) {
522	>	if (layout & dslDensity) {
523	>	bytes += sizeof(RealType);
524	>	}
525	>	if (layout & dslFunctional) {
526	>	bytes += sizeof(RealType);
527	>	}
528	>	if (layout & dslFunctionalDerivative) {
529	>	bytes += sizeof(RealType);
530	>	}
531	>	if (layout & dslDipole) {
532		bytes += sizeof(Vector3d);
533		}
534	<	if (layout & dslTorque) {
534	>	if (layout & dslQuadrupole) {
535	>	bytes += sizeof(Mat3x3d);
536	>	}
537	>	if (layout & dslElectricField) {
538		bytes += sizeof(Vector3d);
539		}
540	<	if (layout & dslParticlePot) {
540	>	if (layout & dslSkippedCharge) {
541		bytes += sizeof(RealType);
542		}
543	+	if (layout & dslFlucQPosition) {
544	+	bytes += sizeof(RealType);
545	+	}
546	+	if (layout & dslFlucQVelocity) {
547	+	bytes += sizeof(RealType);
548	+	}
549	+	if (layout & dslFlucQForce) {
550	+	bytes += sizeof(RealType);
551	+	}
552	+
553		return bytes;
554		}
555

Comparing trunk/src/brains/DataStorage.cpp (property svn:keywords):
Revision 1245 by chuckv, Tue May 27 16:39:06 2008 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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

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+	Added lines
<	Changed lines
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