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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 1874 by gezelter, Wed May 15 15:09:35 2013 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, 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 46 | Line 47
47		#include "primitives/Atom.hpp"
48		#include "math/Vector3.hpp"
49
50	<	namespace oopse {
50	>	namespace OpenMD {
51		class CutoffGroup {
52		public:
53	+
54	+	CutoffGroup() :  snapshotMan_(NULL), globalIndex(-1), localIndex_(-1) {
55
56	<	CutoffGroup() {
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		}
72	<
72	>
73		Atom *beginAtom(std::vector<Atom *>::iterator & i) {
74		i = cutoffAtomList.begin();
75		return i != cutoffAtomList.end() ? *i : NULL;
76		}
77	<
77	>
78		Atom *nextAtom(std::vector<Atom *>::iterator & i) {
79		i++;
80		return i != cutoffAtomList.end() ? *i : NULL;
#	Line 74 | Line 85 | namespace oopse {
85		std::vector<Atom *>::iterator i;
86		Atom * atom;
87		RealType mass;
88	<
88	>
89		if (!haveTotalMass) {
90		totalMass = 0;
91	<
91	>
92		for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
93		mass = atom->getMass();
94		totalMass += mass;
95		}
96	<
96	>
97		haveTotalMass = true;
98		}
99	<
99	>
100		return totalMass;
101		}
102	<
103	<	void getCOM(Vector3d & com) {
102	>
103	>	void updateCOM() {
104		std::vector<Atom *>::iterator i;
105		Atom * atom;
95	–	Vector3d pos;
96	–	RealType mass;
106
107	<	com[0] = 0;
108	<	com[1] = 0;
109	<	com[2] = 0;
107	>	DataStorage&  data = snapshotMan_->getCurrentSnapshot()->*storage_;
108	>	int storageLayout = data.getStorageLayout();
109	>
110		totalMass = getMass();
111	<
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;
120	<	}
117	>	data.position[localIndex_] += atom->getMass() * atom->getPos();
118	>	}
119	>	data.position[localIndex_] /= totalMass;
120	>	}
121
122	<	com /= totalMass;
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();
145		}
146	<
146	>
147		int getGlobalIndex() {
148		return globalIndex;
149		}
150	<
150	>
151		void setGlobalIndex(int id) {
152		this->globalIndex = id;
153		}
154
155	<	private:
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;
134	<	};
176	>	int globalIndex;
177
178	<	}      //end namespace oopse
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 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/primitives/CutoffGroup.hpp (property svn:keywords), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

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