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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 1581 by gezelter, Mon Jun 13 22:13:12 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		#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	+
53	+	CutoffGroup() :  snapshotMan_(NULL) {
54
55	<	CutoffGroup() {
55	>	storage_ = &Snapshot::cgData;
56		haveTotalMass = false;
57		totalMass = 0.0;
58		}
59	+
60	+	/**
61	+	* Sets the Snapshot Manager of this cutoffGroup
62	+	*/
63	+	void setSnapshotManager(SnapshotManager* sman) {
64	+	snapshotMan_ = sman;
65	+	}
66
67	+
68		void addAtom(Atom *atom) {
69		cutoffAtomList.push_back(atom);
70		}
71	<
71	>
72		Atom *beginAtom(std::vector<Atom *>::iterator & i) {
73		i = cutoffAtomList.begin();
74		return i != cutoffAtomList.end() ? *i : NULL;
75		}
76	<
76	>
77		Atom *nextAtom(std::vector<Atom *>::iterator & i) {
78		i++;
79		return i != cutoffAtomList.end() ? *i : NULL;
#	Line 74 | Line 84 | namespace oopse {
84		std::vector<Atom *>::iterator i;
85		Atom * atom;
86		RealType mass;
87	<
87	>
88		if (!haveTotalMass) {
89		totalMass = 0;
90	<
90	>
91		for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
92		mass = atom->getMass();
93		totalMass += mass;
94		}
95	<
95	>
96		haveTotalMass = true;
97		}
98	<
98	>
99		return totalMass;
100		}
101	<
102	<	void getCOM(Vector3d & com) {
101	>
102	>	void updateCOM() {
103		std::vector<Atom *>::iterator i;
104		Atom * atom;
95	–	Vector3d pos;
96	–	RealType mass;
105
106	<	com[0] = 0;
107	<	com[1] = 0;
100	<	com[2] = 0;
106	>	DataStorage&  data = snapshotMan_->getCurrentSnapshot()->*storage_;
107	>
108		totalMass = getMass();
109	<
109	>
110		if (cutoffAtomList.size() == 1) {
111	<	com = beginAtom(i)->getPos();
111	>	data.position[localIndex_] = beginAtom(i)->getPos();
112		} else {
113	+	data.position[localIndex_] = V3Zero;
114		for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
115	<	mass = atom->getMass();
116	<	pos = atom->getPos();
117	<	com += pos * mass;
110	<	}
111	<
112	<	com /= totalMass;
115	>	data.position[localIndex_] += atom->getMass() * atom->getPos();
116	>	}
117	>	data.position[localIndex_] /= totalMass;
118		}
119		}
120
121	+
122	+	Vector3d getPos() {
123	+	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
124	+	}
125	+
126		int getNumAtom() {
127		return cutoffAtomList.size();
128		}
129	<
129	>
130		int getGlobalIndex() {
131		return globalIndex;
132		}
133	<
133	>
134		void setGlobalIndex(int id) {
135		this->globalIndex = id;
136		}
137
138	<	private:
138	>	/**
139	>	* Returns the local index of this cutoffGroup
140	>	* @return the local index of this cutoffGroup
141	>	*/
142	>	int getLocalIndex() {
143	>	return localIndex_;
144	>	}
145
146	+	/**
147	+	* Sets the local index of this cutoffGroup
148	+	* @param index new index to be set
149	+	*/
150	+	void setLocalIndex(int index) {
151	+	localIndex_ = index;
152	+	}
153	+
154	+	private:
155	+
156		std::vector<Atom *>cutoffAtomList;
157		bool haveTotalMass;
158		RealType totalMass;
159	<	int globalIndex;
134	<	};
159	>	int globalIndex;
160
161	<	}      //end namespace oopse
161	>	int localIndex_;
162	>	DataStoragePointer storage_;
163	>	SnapshotManager* snapshotMan_;
164
165	+	};
166	+	} //end namespace OpenMD
167		#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 1581 by gezelter, Mon Jun 13 22:13:12 2011 UTC

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