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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 1665 by gezelter, Tue Nov 22 20:38:56 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 49 | Line 50
50
51		#include "brains/DataStorage.hpp"
52
53	<	namespace oopse {
53	>	namespace OpenMD {
54
55		DataStorage::DataStorage() : size_(0), storageLayout_(0){
56
#	Line 102 | Line 103 | namespace oopse {
103		std::cerr << "size does not match"<< std::endl;
104		}
105
106	+	if (storageLayout_ & dslParticlePot && particlePot.size() != size_) {
107	+	//error
108	+	std::cerr << "size does not match"<< std::endl;
109	+	}
110	+
111	+	if (storageLayout_ & dslDensity && density.size() != size_) {
112	+	//error
113	+	std::cerr << "size does not match"<< std::endl;
114	+	}
115	+
116	+	if (storageLayout_ & dslFunctional && functional.size() != size_) {
117	+	//error
118	+	std::cerr << "size does not match"<< std::endl;
119	+	}
120	+
121	+	if (storageLayout_ & dslFunctionalDerivative && functionalDerivative.size() != size_) {
122	+	//error
123	+	std::cerr << "size does not match"<< std::endl;
124	+	}
125	+
126	+	if (storageLayout_ & dslElectricField && electricField.size() != size_) {
127	+	//error
128	+	std::cerr << "size does not match"<< std::endl;
129	+	}
130	+
131	+	if (storageLayout_ & dslSkippedCharge && skippedCharge.size() != size_) {
132	+	//error
133	+	std::cerr << "size does not match"<< std::endl;
134	+	}
135	+
136		return size_;
137
138		}
#	Line 140 | Line 171 | namespace oopse {
171		internalResize(torque, newSize);
172		}
173
174	+	if (storageLayout_ & dslParticlePot) {
175	+	internalResize(particlePot, newSize);
176	+	}
177	+
178	+	if (storageLayout_ & dslDensity) {
179	+	internalResize(density, newSize);
180	+	}
181	+
182	+	if (storageLayout_ & dslFunctional) {
183	+	internalResize(functional, newSize);
184	+	}
185	+
186	+	if (storageLayout_ & dslFunctionalDerivative) {
187	+	internalResize(functionalDerivative, newSize);
188	+	}
189	+
190	+	if (storageLayout_ & dslElectricField) {
191	+	internalResize(electricField, newSize);
192	+	}
193	+
194	+	if (storageLayout_ & dslSkippedCharge) {
195	+	internalResize(skippedCharge, newSize);
196	+	}
197	+
198		size_ = newSize;
199		}
200
#	Line 174 | Line 229 | namespace oopse {
229
230		if (storageLayout_ & dslTorque) {
231		torque.reserve(size);
232	+	}
233	+
234	+	if (storageLayout_ & dslParticlePot) {
235	+	particlePot.reserve(size);
236	+	}
237	+
238	+	if (storageLayout_ & dslDensity) {
239	+	density.reserve(size);
240	+	}
241	+
242	+	if (storageLayout_ & dslFunctional) {
243	+	functional.reserve(size);
244		}
245
246	+	if (storageLayout_ & dslFunctionalDerivative) {
247	+	functionalDerivative.reserve(size);
248	+	}
249	+
250	+	if (storageLayout_ & dslElectricField) {
251	+	electricField.reserve(size);
252	+	}
253	+
254	+	if (storageLayout_ & dslSkippedCharge) {
255	+	skippedCharge.reserve(size);
256	+	}
257	+
258		}
259
260		void DataStorage::copy(int source, int num, int target) {
#	Line 214 | Line 293 | namespace oopse {
293		if (storageLayout_ & dslTorque) {
294		internalCopy(torque, source, num, target);
295		}
217	–
296
297	+	if (storageLayout_ & dslParticlePot) {
298	+	internalCopy(particlePot, source, num, target);
299	+	}
300	+
301	+	if (storageLayout_ & dslDensity) {
302	+	internalCopy(density, source, num, target);
303	+	}
304	+
305	+	if (storageLayout_ & dslFunctional) {
306	+	internalCopy(functional, source, num, target);
307	+	}
308	+
309	+	if (storageLayout_ & dslFunctionalDerivative) {
310	+	internalCopy(functionalDerivative, source, num, target);
311	+	}
312	+
313	+	if (storageLayout_ & dslElectricField) {
314	+	internalCopy(electricField, source, num, target);
315	+	}
316	+
317	+	if (storageLayout_ & dslSkippedCharge) {
318	+	internalCopy(skippedCharge, source, num, target);
319	+	}
320		}
321
322		int DataStorage::getStorageLayout() {
#	Line 261 | Line 362 | namespace oopse {
362		case dslTorque:
363		return internalGetArrayPointer(torque);
364		break;
365	<
365	>
366	>	case dslParticlePot:
367	>	return internalGetArrayPointer(particlePot);
368	>	break;
369	>
370	>	case dslDensity:
371	>	return internalGetArrayPointer(density);
372	>	break;
373	>
374	>	case dslFunctional:
375	>	return internalGetArrayPointer(functional);
376	>	break;
377	>
378	>	case dslFunctionalDerivative:
379	>	return internalGetArrayPointer(functionalDerivative);
380	>	break;
381	>
382	>	case dslElectricField:
383	>	return internalGetArrayPointer(electricField);
384	>	break;
385	>
386	>	case dslSkippedCharge:
387	>	return internalGetArrayPointer(skippedCharge);
388	>	break;
389	>
390		default:
391		//error message
392		return NULL;
#	Line 338 | Line 463 | namespace oopse {
463		bytes += sizeof(Vector3d);
464		}
465		if (layout & dslAmat) {
466	<	bytes += sizeof(Mat3x3d);
466	>	bytes += sizeof(RotMat3x3d);
467		}
468		if (layout & dslAngularMomentum) {
469		bytes += sizeof(Vector3d);
#	Line 347 | Line 472 | namespace oopse {
472		bytes += sizeof(Mat3x3d);
473		}
474		if (layout & dslZAngle) {
475	<	bytes += sizeof(Vector3d);
475	>	bytes += sizeof(RealType);
476		}
477		if (layout & dslForce) {
478		bytes += sizeof(Vector3d);
#	Line 355 | Line 480 | namespace oopse {
480		if (layout & dslTorque) {
481		bytes += sizeof(Vector3d);
482		}
483	+	if (layout & dslParticlePot) {
484	+	bytes += sizeof(RealType);
485	+	}
486	+	if (layout & dslDensity) {
487	+	bytes += sizeof(RealType);
488	+	}
489	+	if (layout & dslFunctional) {
490	+	bytes += sizeof(RealType);
491	+	}
492	+	if (layout & dslFunctionalDerivative) {
493	+	bytes += sizeof(RealType);
494	+	}
495	+	if (layout & dslElectricField) {
496	+	bytes += sizeof(Vector3d);
497	+	}
498	+	if (layout & dslSkippedCharge) {
499	+	bytes += sizeof(RealType);
500	+	}
501	+
502		return bytes;
503		}
504

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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
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