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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 1540 by gezelter, Mon Jan 17 21:34:36 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	>	#ifdef IS_MPI
57	>	iStorage_ = &Snapshot::cgIData;
58	>	jStorage_ = &Snapshot::cgJData;
59	>	#endif
60		haveTotalMass = false;
61		totalMass = 0.0;
62		}
63	+
64	+	/**
65	+	* Sets the Snapshot Manager of this cutoffGroup
66	+	*/
67	+	void setSnapshotManager(SnapshotManager* sman) {
68	+	snapshotMan_ = sman;
69	+	}
70
71	+
72		void addAtom(Atom *atom) {
73		cutoffAtomList.push_back(atom);
74		}
75	<
75	>
76		Atom *beginAtom(std::vector<Atom *>::iterator & i) {
77		i = cutoffAtomList.begin();
78		return i != cutoffAtomList.end() ? *i : NULL;
79		}
80	<
80	>
81		Atom *nextAtom(std::vector<Atom *>::iterator & i) {
82		i++;
83		return i != cutoffAtomList.end() ? *i : NULL;
#	Line 74 | Line 88 | namespace oopse {
88		std::vector<Atom *>::iterator i;
89		Atom * atom;
90		RealType mass;
91	<
91	>
92		if (!haveTotalMass) {
93		totalMass = 0;
94	<
94	>
95		for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
96		mass = atom->getMass();
97		totalMass += mass;
98		}
99	<
99	>
100		haveTotalMass = true;
101		}
102	<
102	>
103		return totalMass;
104		}
105	<
106	<	void getCOM(Vector3d & com) {
105	>
106	>	void updateCOM() {
107		std::vector<Atom *>::iterator i;
108		Atom * atom;
95	–	Vector3d pos;
96	–	RealType mass;
109
110	<	com[0] = 0;
111	<	com[1] = 0;
100	<	com[2] = 0;
110	>	DataStorage&  data = snapshotMan_->getCurrentSnapshot()->*storage_;
111	>
112		totalMass = getMass();
113	<
113	>
114		if (cutoffAtomList.size() == 1) {
115	<	com = beginAtom(i)->getPos();
115	>	std::cerr << "YO!\n";
116	>	std::cerr << "atipos = " << beginAtom(i)->getPos() << "\n";
117	>	std::cerr << "lI = " << localIndex_ << "\n";
118	>
119	>	data.position[localIndex_] = beginAtom(i)->getPos();
120	>	std::cerr << "YOYO!\n";
121		} else {
122	+	data.position[localIndex_] = V3Zero;
123		for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
124	<	mass = atom->getMass();
125	<	pos = atom->getPos();
126	<	com += pos * mass;
110	<	}
111	<
112	<	com /= totalMass;
124	>	data.position[localIndex_] += atom->getMass() * atom->getPos();
125	>	}
126	>	data.position[localIndex_] /= totalMass;
127		}
128		}
129
130	+
131	+	/**
132	+	* Returns the current position of this cutoffGroup for the outer
133	+	* iteration over the cutoff groups.  For Force decomposition,
134	+	* this is the position of the cutoff groups ordered by row index.
135	+	* For serial calculations, this is just the position of the
136	+	* cutoff group.
137	+	*/
138	+	Vector3d getPosI() {
139	+	#ifdef IS_MPI
140	+	return ((snapshotMan_->getCurrentSnapshot())->*iStorage_).position[iIndex_];
141	+	#else
142	+	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
143	+	#endif
144	+	}
145	+
146	+	/**
147	+	* Returns the current position of this cutoffGroup for the inner
148	+	* iteration over the cutoff groups.  For Force decomposition,
149	+	* this is the position of the cutoff groups ordered by column
150	+	* index.  For serial calculations, this is just the position of
151	+	* the cutoff group.
152	+	*/
153	+	Vector3d getPosJ() {
154	+	#ifdef IS_MPI
155	+	return ((snapshotMan_->getCurrentSnapshot())->*jStorage_).position[jIndex_];
156	+	#else
157	+	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
158	+	#endif
159	+	}
160	+
161		int getNumAtom() {
162		return cutoffAtomList.size();
163		}
164	<
164	>
165		int getGlobalIndex() {
166		return globalIndex;
167		}
168	<
168	>
169		void setGlobalIndex(int id) {
170		this->globalIndex = id;
171		}
172
173	<	private:
173	>	/**
174	>	* Returns the local index of this cutoffGroup
175	>	* @return the local index of this cutoffGroup
176	>	*/
177	>	int getLocalIndex() {
178	>	return localIndex_;
179	>	}
180
181	+	/**
182	+	* Sets the local index of this cutoffGroup
183	+	* @param index new index to be set
184	+	*/
185	+	void setLocalIndex(int index) {
186	+	localIndex_ = index;
187	+	}
188	+
189	+	private:
190	+
191		std::vector<Atom *>cutoffAtomList;
192		bool haveTotalMass;
193		RealType totalMass;
194	<	int globalIndex;
134	<	};
194	>	int globalIndex;
195
196	<	}      //end namespace oopse
196	>	int localIndex_;
197	>	DataStoragePointer storage_;
198	>	SnapshotManager* snapshotMan_;
199	>	#ifdef IS_MPI
200	>	int iIndex_;
201	>	int jIndex_;
202	>	DataStoragePointer iStorage_;
203	>	DataStoragePointer jStorage_;
204	>	#endif
205
206	+	};
207	+	} //end namespace OpenMD
208		#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 1540 by gezelter, Mon Jan 17 21:34:36 2011 UTC

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