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

Comparing:
trunk/src/primitives/CutoffGroup.hpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/primitives/CutoffGroup.hpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 36 | Line 36
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).
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		#ifndef PRIMITIVES_CUTOFFGROUP_HPP
#	Line 50 | Line 51 | namespace OpenMD {
51		class CutoffGroup {
52		public:
53
54	<	CutoffGroup() {
54	>	CutoffGroup() :  snapshotMan_(NULL) {
55	>
56	>	storage_ = &Snapshot::cgData;
57		haveTotalMass = false;
58		totalMass = 0.0;
59		}
60
61	+	/**
62	+	* Sets the Snapshot Manager of this cutoffGroup
63	+	*/
64	+	void setSnapshotManager(SnapshotManager* sman) {
65	+	snapshotMan_ = sman;
66	+	}
67	+
68	+
69		void addAtom(Atom *atom) {
70		cutoffAtomList.push_back(atom);
71		}
#	Line 89 | Line 100 | namespace OpenMD {
100		return totalMass;
101		}
102
103	<	void getCOM(Vector3d & com) {
103	>	void updateCOM() {
104		std::vector<Atom *>::iterator i;
105		Atom * atom;
106	<	Vector3d pos;
107	<	RealType mass;
108	<
98	<	com[0] = 0;
99	<	com[1] = 0;
100	<	com[2] = 0;
106	>
107	>	DataStorage&  data = snapshotMan_->getCurrentSnapshot()->*storage_;
108	>
109		totalMass = getMass();
110
111		if (cutoffAtomList.size() == 1) {
112	<	com = beginAtom(i)->getPos();
112	>	data.position[localIndex_] = beginAtom(i)->getPos();
113		} else {
114	+	data.position[localIndex_] = V3Zero;
115		for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
116	<	mass = atom->getMass();
117	<	pos = atom->getPos();
118	<	com += pos * mass;
110	<	}
111	<
112	<	com /= totalMass;
116	>	data.position[localIndex_] += atom->getMass() * atom->getPos();
117	>	}
118	>	data.position[localIndex_] /= totalMass;
119		}
120		}
121	+
122	+
123	+	Vector3d getPos() {
124	+	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
125	+	}
126
127		int getNumAtom() {
128		return cutoffAtomList.size();
#	Line 124 | Line 135 | namespace OpenMD {
135		void setGlobalIndex(int id) {
136		this->globalIndex = id;
137		}
138	+
139	+	/**
140	+	* Returns the local index of this cutoffGroup
141	+	* @return the local index of this cutoffGroup
142	+	*/
143	+	int getLocalIndex() {
144	+	return localIndex_;
145	+	}
146	+
147	+	/**
148	+	* Sets the local index of this cutoffGroup
149	+	* @param index new index to be set
150	+	*/
151	+	void setLocalIndex(int index) {
152	+	localIndex_ = index;
153	+	}
154
155		private:
156
157		std::vector<Atom *>cutoffAtomList;
158		bool haveTotalMass;
159		RealType totalMass;
160	<	int globalIndex;
160	>	int globalIndex;
161	>
162	>	int localIndex_;
163	>	DataStoragePointer storage_;
164	>	SnapshotManager* snapshotMan_;
165	>
166		};
167		} //end namespace OpenMD
168		#endif //PRIMITIVES_CUTOFFGROUP_HPP

Comparing:
trunk/src/primitives/CutoffGroup.hpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/primitives/CutoffGroup.hpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
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