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root/OpenMD/branches/development/src/brains/DataStorage.cpp

Comparing:
trunk/src/brains/DataStorage.cpp (file contents), Revision 1104 by gezelter, Fri Dec 29 21:43:18 2006 UTC vs.
branches/development/src/brains/DataStorage.cpp (file contents), Revision 1710 by gezelter, Fri May 18 21:44:02 2012 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, 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		/**
#	Line 48 | Line 49
49		*/
50
51		#include "brains/DataStorage.hpp"
52	+	using namespace std;
53	+	namespace OpenMD {
54
52	–	namespace oopse {
53	–
55		DataStorage::DataStorage() : size_(0), storageLayout_(0){
56
57		}
#	Line 64 | Line 65 | namespace oopse {
65
66		if (storageLayout_ & dslPosition && position.size() != size_) {
67		//error
68	<	std::cerr << "size does not match"<< std::endl;
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;
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;
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;
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;
88	>	cerr << "size does not match"<< endl;
89		}
90
91		if (storageLayout_ & dslZAngle && zAngle.size() != size_) {
92		//error
93	<	std::cerr << "size does not match"<< std::endl;
93	>	cerr << "size does not match"<< endl;
94		}
95
96		if (storageLayout_ & dslForce && force.size() != size_) {
97		//error
98	<	std::cerr << "size does not match"<< std::endl;
98	>	cerr << "size does not match"<< endl;
99		}
100
101		if (storageLayout_ & dslTorque && torque.size() != size_) {
102		//error
103	<	std::cerr << "size does not match"<< std::endl;
103	>	cerr << "size does not match"<< endl;
104		}
105
106	+	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
107	+	//error
108	+	cerr << "size does not match"<< endl;
109	+	}
110	+
111	+	if (storageLayout_ & dslDensity && density.size() != size_) {
112	+	//error
113	+	cerr << "size does not match"<< endl;
114	+	}
115	+
116	+	if (storageLayout_ & dslFunctional && functional.size() != size_) {
117	+	//error
118	+	cerr << "size does not match"<< endl;
119	+	}
120	+
121	+	if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
122	+	//error
123	+	cerr << "size does not match"<< endl;
124	+	}
125	+
126	+	if (storageLayout_ & dslElectricField && electricField.size() != size_) {
127	+	//error
128	+	cerr << "size does not match"<< endl;
129	+	}
130	+
131	+	if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
132	+	//error
133	+	cerr << "size does not match"<< endl;
134	+	}
135	+
136	+	if (storageLayout_ & dslFlucQPosition && flucQPos.size() != size_) {
137	+	//error
138	+	cerr << "size does not match"<< endl;
139	+	}
140	+
141	+	if (storageLayout_ & dslFlucQVelocity && flucQVel.size() != size_) {
142	+	//error
143	+	cerr << "size does not match"<< endl;
144	+	}
145	+
146	+	if (storageLayout_ & dslFlucQForce && flucQFrc.size() != size_) {
147	+	//error
148	+	cerr << "size does not match"<< endl;
149	+	}
150	+
151		return size_;
152
153		}
#	Line 140 | Line 186 | namespace oopse {
186		internalResize(torque, newSize);
187		}
188
189	+	if (storageLayout_ & dslParticlePot) {
190	+	internalResize(particlePot, newSize);
191	+	}
192	+
193	+	if (storageLayout_ & dslDensity) {
194	+	internalResize(density, newSize);
195	+	}
196	+
197	+	if (storageLayout_ & dslFunctional) {
198	+	internalResize(functional, newSize);
199	+	}
200	+
201	+	if (storageLayout_ & dslFunctionalDerivative) {
202	+	internalResize(functionalDerivative, newSize);
203	+	}
204	+
205	+	if (storageLayout_ & dslElectricField) {
206	+	internalResize(electricField, newSize);
207	+	}
208	+
209	+	if (storageLayout_ & dslSkippedCharge) {
210	+	internalResize(skippedCharge, newSize);
211	+	}
212	+
213	+	if (storageLayout_ & dslFlucQPosition) {
214	+	internalResize(flucQPos, newSize);
215	+	}
216	+
217	+	if (storageLayout_ & dslFlucQVelocity) {
218	+	internalResize(flucQVel, newSize);
219	+	}
220	+
221	+	if (storageLayout_ & dslFlucQForce) {
222	+	internalResize(flucQFrc, newSize);
223	+	}
224	+
225		size_ = newSize;
226		}
227
#	Line 174 | Line 256 | namespace oopse {
256
257		if (storageLayout_ & dslTorque) {
258		torque.reserve(size);
259	+	}
260	+
261	+	if (storageLayout_ & dslParticlePot) {
262	+	particlePot.reserve(size);
263	+	}
264	+
265	+	if (storageLayout_ & dslDensity) {
266	+	density.reserve(size);
267	+	}
268	+
269	+	if (storageLayout_ & dslFunctional) {
270	+	functional.reserve(size);
271		}
272
273	+	if (storageLayout_ & dslFunctionalDerivative) {
274	+	functionalDerivative.reserve(size);
275	+	}
276	+
277	+	if (storageLayout_ & dslElectricField) {
278	+	electricField.reserve(size);
279	+	}
280	+
281	+	if (storageLayout_ & dslSkippedCharge) {
282	+	skippedCharge.reserve(size);
283	+	}
284	+
285	+	if (storageLayout_ & dslFlucQPosition) {
286	+	flucQPos.reserve(size);
287	+	}
288	+
289	+	if (storageLayout_ & dslFlucQVelocity) {
290	+	flucQVel.reserve(size);
291	+	}
292	+
293	+	if (storageLayout_ & dslFlucQForce) {
294	+	flucQFrc.reserve(size);
295	+	}
296		}
297
298		void DataStorage::copy(int source, int num, int target) {
#	Line 214 | Line 331 | namespace oopse {
331		if (storageLayout_ & dslTorque) {
332		internalCopy(torque, source, num, target);
333		}
217	–
334
335	+	if (storageLayout_ & dslParticlePot) {
336	+	internalCopy(particlePot, source, num, target);
337	+	}
338	+
339	+	if (storageLayout_ & dslDensity) {
340	+	internalCopy(density, source, num, target);
341	+	}
342	+
343	+	if (storageLayout_ & dslFunctional) {
344	+	internalCopy(functional, source, num, target);
345	+	}
346	+
347	+	if (storageLayout_ & dslFunctionalDerivative) {
348	+	internalCopy(functionalDerivative, source, num, target);
349	+	}
350	+
351	+	if (storageLayout_ & dslElectricField) {
352	+	internalCopy(electricField, source, num, target);
353	+	}
354	+
355	+	if (storageLayout_ & dslSkippedCharge) {
356	+	internalCopy(skippedCharge, source, num, target);
357	+	}
358	+
359	+	if (storageLayout_ & dslFlucQPosition) {
360	+	internalCopy(flucQPos, source, num, target);
361	+	}
362	+
363	+	if (storageLayout_ & dslFlucQVelocity) {
364	+	internalCopy(flucQVel, source, num, target);
365	+	}
366	+	if (storageLayout_ & dslFlucQForce) {
367	+	internalCopy(flucQFrc, source, num, target);
368	+	}
369		}
370
371		int DataStorage::getStorageLayout() {
#	Line 261 | Line 411 | namespace oopse {
411		case dslTorque:
412		return internalGetArrayPointer(torque);
413		break;
414	<
414	>
415	>	case dslParticlePot:
416	>	return internalGetArrayPointer(particlePot);
417	>	break;
418	>
419	>	case dslDensity:
420	>	return internalGetArrayPointer(density);
421	>	break;
422	>
423	>	case dslFunctional:
424	>	return internalGetArrayPointer(functional);
425	>	break;
426	>
427	>	case dslFunctionalDerivative:
428	>	return internalGetArrayPointer(functionalDerivative);
429	>	break;
430	>
431	>	case dslElectricField:
432	>	return internalGetArrayPointer(electricField);
433	>	break;
434	>
435	>	case dslSkippedCharge:
436	>	return internalGetArrayPointer(skippedCharge);
437	>	break;
438	>
439	>	case dslFlucQPosition:
440	>	return internalGetArrayPointer(flucQPos);
441	>	break;
442	>
443	>	case dslFlucQVelocity:
444	>	return internalGetArrayPointer(flucQVel);
445	>	break;
446	>
447	>	case dslFlucQForce:
448	>	return internalGetArrayPointer(flucQFrc);
449	>	break;
450	>
451		default:
452		//error message
453		return NULL;
#	Line 338 | Line 524 | namespace oopse {
524		bytes += sizeof(Vector3d);
525		}
526		if (layout & dslAmat) {
527	<	bytes += sizeof(Mat3x3d);
527	>	bytes += sizeof(RotMat3x3d);
528		}
529		if (layout & dslAngularMomentum) {
530		bytes += sizeof(Vector3d);
#	Line 347 | Line 533 | namespace oopse {
533		bytes += sizeof(Mat3x3d);
534		}
535		if (layout & dslZAngle) {
536	<	bytes += sizeof(Vector3d);
536	>	bytes += sizeof(RealType);
537		}
538		if (layout & dslForce) {
539		bytes += sizeof(Vector3d);
#	Line 355 | Line 541 | namespace oopse {
541		if (layout & dslTorque) {
542		bytes += sizeof(Vector3d);
543		}
544	+	if (layout & dslParticlePot) {
545	+	bytes += sizeof(RealType);
546	+	}
547	+	if (layout & dslDensity) {
548	+	bytes += sizeof(RealType);
549	+	}
550	+	if (layout & dslFunctional) {
551	+	bytes += sizeof(RealType);
552	+	}
553	+	if (layout & dslFunctionalDerivative) {
554	+	bytes += sizeof(RealType);
555	+	}
556	+	if (layout & dslElectricField) {
557	+	bytes += sizeof(Vector3d);
558	+	}
559	+	if (layout & dslSkippedCharge) {
560	+	bytes += sizeof(RealType);
561	+	}
562	+	if (layout & dslFlucQPosition) {
563	+	bytes += sizeof(RealType);
564	+	}
565	+	if (layout & dslFlucQVelocity) {
566	+	bytes += sizeof(RealType);
567	+	}
568	+	if (layout & dslFlucQForce) {
569	+	bytes += sizeof(RealType);
570	+	}
571	+
572		return bytes;
573		}
574

Comparing:
trunk/src/brains/DataStorage.cpp (property svn:keywords), Revision 1104 by gezelter, Fri Dec 29 21:43:18 2006 UTC vs.
branches/development/src/brains/DataStorage.cpp (property svn:keywords), Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

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

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