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root/OpenMD/trunk/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.
Revision 2065 by gezelter, Thu Mar 5 15:11:00 2015 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), globalIndex(-1), localIndex_(-1) {
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 71 | Line 82 | namespace OpenMD {
82
83		std::vector<Atom*> getAtoms() { return cutoffAtomList; }
84		RealType getMass() {
74	–	std::vector<Atom *>::iterator i;
75	–	Atom * atom;
76	–	RealType mass;
85
86		if (!haveTotalMass) {
87	<	totalMass = 0;
87	>	totalMass = 0.0;
88
89	<	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
90	<	mass = atom->getMass();
89	>	std::vector<Atom *>::iterator i;
90	>	for(Atom* atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
91	>	RealType mass = atom->getMass();
92		totalMass += mass;
93		}
94
#	Line 89 | Line 98 | namespace OpenMD {
98		return totalMass;
99		}
100
101	<	void getCOM(Vector3d & com) {
102	<	std::vector<Atom *>::iterator i;
103	<	Atom * atom;
104	<	Vector3d pos;
105	<	RealType mass;
106	<
98	<	com[0] = 0;
99	<	com[1] = 0;
100	<	com[2] = 0;
101	<	totalMass = getMass();
102	<
101	>	void updateCOM() {
102	>
103	>	DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_;
104	>	bool needsVel = false;
105	>	if (data.getStorageLayout() & DataStorage::dslVelocity) needsVel = true;
106	>
107		if (cutoffAtomList.size() == 1) {
108	<	com = beginAtom(i)->getPos();
108	>	data.position[localIndex_] = cutoffAtomList[0]->getPos();
109	>	if (needsVel)
110	>	data.velocity[localIndex_] = cutoffAtomList[0]->getVel();
111		} else {
112	<	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
113	<	mass = atom->getMass();
114	<	pos = atom->getPos();
115	<	com += pos * mass;
116	<	}
112	>	std::vector<Atom *>::iterator i;
113	>	Atom * atom;
114	>	RealType totalMass = getMass();
115	>	data.position[localIndex_] = V3Zero;
116	>	if (needsVel) data.velocity[localIndex_] = V3Zero;
117
118	<	com /= totalMass;
119	<	}
118	>	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
119	>	data.position[localIndex_] += atom->getMass() * atom->getPos();
120	>	if (needsVel)
121	>	data.velocity[localIndex_] += atom->getMass() * atom->getVel();
122	>	}
123	>	data.position[localIndex_] /= totalMass;
124	>	if (needsVel) data.velocity[localIndex_] /= totalMass;
125	>	}
126		}
127	+
128	+
129	+	Vector3d getPos() {
130	+	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
131	+	}
132	+	Vector3d getVel() {
133	+	return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_];
134	+	}
135
136		int getNumAtom() {
137		return cutoffAtomList.size();
#	Line 124 | Line 144 | namespace OpenMD {
144		void setGlobalIndex(int id) {
145		this->globalIndex = id;
146		}
147	+
148	+	/**
149	+	* Returns the local index of this cutoffGroup
150	+	* @return the local index of this cutoffGroup
151	+	*/
152	+	int getLocalIndex() {
153	+	return localIndex_;
154	+	}
155	+
156	+	/**
157	+	* Sets the local index of this cutoffGroup
158	+	* @param index new index to be set
159	+	*/
160	+	void setLocalIndex(int index) {
161	+	localIndex_ = index;
162	+	}
163
164		private:
165
166		std::vector<Atom *>cutoffAtomList;
167		bool haveTotalMass;
168		RealType totalMass;
169	<	int globalIndex;
169	>	int globalIndex;
170	>
171	>	int localIndex_;
172	>	DataStoragePointer storage_;
173	>	SnapshotManager* snapshotMan_;
174	>
175		};
176		} //end namespace OpenMD
177		#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.
Revision 2065 by gezelter, Thu Mar 5 15:11:00 2015 UTC

#	Line 0 | Line 1
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