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root/OpenMD/branches/development/src/brains/Snapshot.hpp

Comparing:
trunk/src/brains/Snapshot.hpp (file contents), Revision 1287 by gezelter, Wed Sep 10 18:11:32 2008 UTC vs.
branches/development/src/brains/Snapshot.hpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 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 57 | Line 57
57		#include "UseTheForce/DarkSide/simulation_interface.h"
58
59
60	<	namespace oopse{
60	>	namespace OpenMD{
61
62		/**
63		* @class Snapshot Snapshot.hpp "brains/Snapshot.hpp"
#	Line 77 | Line 77 | namespace oopse{
77		chi_(0.0),
78		integralOfChiDt_(0.0),
79		eta_(0.0), id_(-1),
80	<	hasCOM_(false) {
80	>	hasCOM_(false), hasVolume_(false), volume_(0.0) {
81
82		}
83
#	Line 85 | Line 85 | namespace oopse{
85		: atomData(nAtoms, storageLayout),
86		rigidbodyData(nRigidbodies, storageLayout),
87		currentTime_(0), orthoTolerance_(1e-6), orthoRhombic_(0), chi_(0.0),
88	<	integralOfChiDt_(0.0), eta_(0.0), id_(-1), hasCOM_(false)  {
88	>	integralOfChiDt_(0.0), eta_(0.0), id_(-1), hasCOM_(false), hasVolume_(false),volume_(0.0)  {
89
90		}
91
#	Line 122 | Line 122 | namespace oopse{
122		void setHmat(const Mat3x3d& m);
123
124		RealType getVolume() {
125	<	return hmat_.determinant();
125	>	if (hasVolume_){
126	>	return volume_;
127	>	}else{
128	>	return hmat_.determinant();
129	>	}
130		}
131
132	+	void setVolume(RealType volume){
133	+	hasVolume_=true;
134	+	volume_ = volume;
135	+	}
136	+
137		/** Returns the inverse H-Matrix */
138		Mat3x3d getInvHmat() {
139		return invHmat_;
#	Line 201 | Line 210 | namespace oopse{
210		Mat3x3d invHmat_;
211		RealType orthoTolerance_;
212		int orthoRhombic_;
213	+	RealType volume_;
214
215		RealType chi_;
216		RealType integralOfChiDt_;
#	Line 210 | Line 220 | namespace oopse{
220		Vector3d COMw_;
221		int id_; /**< identification number of the snapshot */
222		bool hasCOM_;
223	+	bool hasVolume_;
224
225		};
226

Comparing:
trunk/src/brains/Snapshot.hpp (property svn:keywords), Revision 1287 by gezelter, Wed Sep 10 18:11:32 2008 UTC vs.
branches/development/src/brains/Snapshot.hpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 0 | Line 1
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