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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 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

#	Line 35 | Line 35
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).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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		#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	<
109	<	com[0] = 0;
99	<	com[1] = 0;
100	<	com[2] = 0;
106	>
107	>	DataStorage&  data = snapshotMan_->getCurrentSnapshot()->*storage_;
108	>	int storageLayout = data.getStorageLayout();
109	>
110		totalMass = getMass();
111
112		if (cutoffAtomList.size() == 1) {
113	<	com = beginAtom(i)->getPos();
113	>	data.position[localIndex_] = beginAtom(i)->getPos();
114		} else {
115	+	data.position[localIndex_] = V3Zero;
116		for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
117	<	mass = atom->getMass();
118	<	pos = atom->getPos();
119	<	com += pos * mass;
110	<	}
111	<
112	<	com /= totalMass;
117	>	data.position[localIndex_] += atom->getMass() * atom->getPos();
118	>	}
119	>	data.position[localIndex_] /= totalMass;
120		}
121	+
122	+	if (storageLayout & DataStorage::dslVelocity) {
123	+	if (cutoffAtomList.size() == 1) {
124	+	data.velocity[localIndex_] = beginAtom(i)->getVel();
125	+	} else {
126	+	data.velocity[localIndex_] = V3Zero;
127	+	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
128	+	data.velocity[localIndex_] += atom->getMass() * atom->getVel();
129	+	}
130	+	data.velocity[localIndex_] /= totalMass;
131	+	}
132	+	}
133		}
134	+
135	+
136	+	Vector3d getPos() {
137	+	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
138	+	}
139	+	Vector3d getVel() {
140	+	return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_];
141	+	}
142
143		int getNumAtom() {
144		return cutoffAtomList.size();
#	Line 124 | Line 151 | namespace OpenMD {
151		void setGlobalIndex(int id) {
152		this->globalIndex = id;
153		}
154	+
155	+	/**
156	+	* Returns the local index of this cutoffGroup
157	+	* @return the local index of this cutoffGroup
158	+	*/
159	+	int getLocalIndex() {
160	+	return localIndex_;
161	+	}
162	+
163	+	/**
164	+	* Sets the local index of this cutoffGroup
165	+	* @param index new index to be set
166	+	*/
167	+	void setLocalIndex(int index) {
168	+	localIndex_ = index;
169	+	}
170
171		private:
172
173		std::vector<Atom *>cutoffAtomList;
174		bool haveTotalMass;
175		RealType totalMass;
176	<	int globalIndex;
176	>	int globalIndex;
177	>
178	>	int localIndex_;
179	>	DataStoragePointer storage_;
180	>	SnapshotManager* snapshotMan_;
181	>
182		};
183		} //end namespace OpenMD
184		#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 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

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