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root/OpenMD/branches/development/src/primitives/CutoffGroup.hpp

Comparing:
trunk/src/primitives/CutoffGroup.hpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/primitives/CutoffGroup.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		#ifndef PRIMITIVES_CUTOFFGROUP_HPP
#	Line 46 | Line 46
46		#include "primitives/Atom.hpp"
47		#include "math/Vector3.hpp"
48
49	<	namespace oopse {
49	>	namespace OpenMD {
50		class CutoffGroup {
51		public:
52	<
52	>
53		CutoffGroup() {
54		haveTotalMass = false;
55		totalMass = 0.0;
56		}
57	<
57	>
58		void addAtom(Atom *atom) {
59		cutoffAtomList.push_back(atom);
60		}
61	<
61	>
62		Atom *beginAtom(std::vector<Atom *>::iterator & i) {
63		i = cutoffAtomList.begin();
64		return i != cutoffAtomList.end() ? *i : NULL;
65		}
66	<
66	>
67		Atom *nextAtom(std::vector<Atom *>::iterator & i) {
68		i++;
69		return i != cutoffAtomList.end() ? *i : NULL;
#	Line 74 | Line 74 | namespace oopse {
74		std::vector<Atom *>::iterator i;
75		Atom * atom;
76		RealType mass;
77	<
77	>
78		if (!haveTotalMass) {
79		totalMass = 0;
80	<
80	>
81		for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
82		mass = atom->getMass();
83		totalMass += mass;
84		}
85	<
85	>
86		haveTotalMass = true;
87		}
88	<
88	>
89		return totalMass;
90		}
91	<
91	>
92		void getCOM(Vector3d & com) {
93		std::vector<Atom *>::iterator i;
94		Atom * atom;
95		Vector3d pos;
96		RealType mass;
97	<
97	>
98		com[0] = 0;
99		com[1] = 0;
100		com[2] = 0;
101		totalMass = getMass();
102	<
102	>
103		if (cutoffAtomList.size() == 1) {
104		com = beginAtom(i)->getPos();
105		} else {
#	Line 108 | Line 108 | namespace oopse {
108		pos = atom->getPos();
109		com += pos * mass;
110		}
111	<
111	>
112		com /= totalMass;
113		}
114		}
115	<
115	>
116		int getNumAtom() {
117		return cutoffAtomList.size();
118		}
119	<
119	>
120		int getGlobalIndex() {
121		return globalIndex;
122		}
123	<
123	>
124		void setGlobalIndex(int id) {
125		this->globalIndex = id;
126		}
127	<
127	>
128		private:
129	<
129	>
130		std::vector<Atom *>cutoffAtomList;
131		bool haveTotalMass;
132		RealType totalMass;
133		int globalIndex;
134	<	};
135	<
136	<	}      //end namespace oopse
137	<
134	>	};
135	>	} //end namespace OpenMD
136		#endif //PRIMITIVES_CUTOFFGROUP_HPP

Comparing:
trunk/src/primitives/CutoffGroup.hpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/primitives/CutoffGroup.hpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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