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

Comparing:
trunk/src/brains/DataStorage.cpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/DataStorage.cpp (file contents), Revision 1583 by gezelter, Thu Jun 16 22:00:08 2011 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 49 | Line 49
49
50		#include "brains/DataStorage.hpp"
51
52	<	namespace oopse {
52	>	namespace OpenMD {
53
54		DataStorage::DataStorage() : size_(0), storageLayout_(0){
55
#	Line 102 | Line 102 | namespace oopse {
102		std::cerr << "size does not match"<< std::endl;
103		}
104
105	+	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
106	+	//error
107	+	std::cerr << "size does not match"<< std::endl;
108	+	}
109	+
110	+	if (storageLayout_ & dslDensity && density.size() != size_) {
111	+	//error
112	+	std::cerr << "size does not match"<< std::endl;
113	+	}
114	+
115	+	if (storageLayout_ & dslFunctional && functional.size() != size_) {
116	+	//error
117	+	std::cerr << "size does not match"<< std::endl;
118	+	}
119	+
120	+	if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
121	+	//error
122	+	std::cerr << "size does not match"<< std::endl;
123	+	}
124	+
125	+	if (storageLayout_ & dslElectricField && electricField.size() != size_) {
126	+	//error
127	+	std::cerr << "size does not match"<< std::endl;
128	+	}
129	+
130		return size_;
131
132		}
#	Line 140 | Line 165 | namespace oopse {
165		internalResize(torque, newSize);
166		}
167
168	+	if (storageLayout_ & dslParticlePot) {
169	+	internalResize(particlePot, newSize);
170	+	}
171	+
172	+	if (storageLayout_ & dslDensity) {
173	+	internalResize(density, newSize);
174	+	}
175	+
176	+	if (storageLayout_ & dslFunctional) {
177	+	internalResize(functional, newSize);
178	+	}
179	+
180	+	if (storageLayout_ & dslFunctionalDerivative) {
181	+	internalResize(functionalDerivative, newSize);
182	+	}
183	+
184	+	if (storageLayout_ & dslElectricField) {
185	+	internalResize(electricField, newSize);
186	+	}
187	+
188		size_ = newSize;
189		}
190
#	Line 175 | Line 220 | namespace oopse {
220		if (storageLayout_ & dslTorque) {
221		torque.reserve(size);
222		}
223	+
224	+	if (storageLayout_ & dslParticlePot) {
225	+	particlePot.reserve(size);
226	+	}
227
228	+	if (storageLayout_ & dslDensity) {
229	+	density.reserve(size);
230	+	}
231	+
232	+	if (storageLayout_ & dslFunctional) {
233	+	functional.reserve(size);
234	+	}
235	+
236	+	if (storageLayout_ & dslFunctionalDerivative) {
237	+	functionalDerivative.reserve(size);
238	+	}
239	+
240	+	if (storageLayout_ & dslElectricField) {
241	+	electricField.reserve(size);
242	+	}
243	+
244		}
245
246		void DataStorage::copy(int source, int num, int target) {
#	Line 214 | Line 279 | namespace oopse {
279		if (storageLayout_ & dslTorque) {
280		internalCopy(torque, source, num, target);
281		}
217	–
282
283	+	if (storageLayout_ & dslParticlePot) {
284	+	internalCopy(particlePot, source, num, target);
285	+	}
286	+
287	+	if (storageLayout_ & dslDensity) {
288	+	internalCopy(density, source, num, target);
289	+	}
290	+
291	+	if (storageLayout_ & dslFunctional) {
292	+	internalCopy(functional, source, num, target);
293	+	}
294	+
295	+	if (storageLayout_ & dslFunctionalDerivative) {
296	+	internalCopy(functionalDerivative, source, num, target);
297	+	}
298	+
299	+	if (storageLayout_ & dslElectricField) {
300	+	internalCopy(electricField, source, num, target);
301	+	}
302		}
303
304		int DataStorage::getStorageLayout() {
#	Line 260 | Line 343 | namespace oopse {
343
344		case dslTorque:
345		return internalGetArrayPointer(torque);
346	<	break;
347	<
346	>	break;
347	>
348	>	case dslParticlePot:
349	>	return internalGetArrayPointer(particlePot);
350	>	break;
351	>
352	>	case dslDensity:
353	>	return internalGetArrayPointer(density);
354	>	break;
355	>
356	>	case dslFunctional:
357	>	return internalGetArrayPointer(functional);
358	>	break;
359	>
360	>	case dslFunctionalDerivative:
361	>	return internalGetArrayPointer(functionalDerivative);
362	>	break;
363	>
364	>	case dslElectricField:
365	>	return internalGetArrayPointer(electricField);
366	>	break;
367	>
368		default:
369		//error message
370		return NULL;
#	Line 338 | Line 441 | namespace oopse {
441		bytes += sizeof(Vector3d);
442		}
443		if (layout & dslAmat) {
444	<	bytes += sizeof(Mat3x3d);
444	>	bytes += sizeof(RotMat3x3d);
445		}
446		if (layout & dslAngularMomentum) {
447		bytes += sizeof(Vector3d);
#	Line 347 | Line 450 | namespace oopse {
450		bytes += sizeof(Mat3x3d);
451		}
452		if (layout & dslZAngle) {
453	<	bytes += sizeof(Vector3d);
453	>	bytes += sizeof(RealType);
454		}
455		if (layout & dslForce) {
456		bytes += sizeof(Vector3d);
#	Line 355 | Line 458 | namespace oopse {
458		if (layout & dslTorque) {
459		bytes += sizeof(Vector3d);
460		}
461	+	if (layout & dslParticlePot) {
462	+	bytes += sizeof(RealType);
463	+	}
464	+	if (layout & dslDensity) {
465	+	bytes += sizeof(RealType);
466	+	}
467	+	if (layout & dslFunctional) {
468	+	bytes += sizeof(RealType);
469	+	}
470	+	if (layout & dslFunctionalDerivative) {
471	+	bytes += sizeof(RealType);
472	+	}
473	+	if (layout & dslElectricField) {
474	+	bytes += sizeof(Vector3d);
475	+	}
476	+
477		return bytes;
478		}
479

Comparing:
trunk/src/brains/DataStorage.cpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/DataStorage.cpp (property svn:keywords), Revision 1583 by gezelter, Thu Jun 16 22:00:08 2011 UTC

#	Line 0 | Line 1
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