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Comparing:
trunk/src/primitives/CutoffGroup.hpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/primitives/CutoffGroup.hpp (file contents), Revision 1540 by gezelter, Mon Jan 17 21:34:36 2011 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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 {
50	<	class CutoffGroup {
51	<	public:
49	>	namespace OpenMD {
50	>	class CutoffGroup {
51	>	public:
52	>
53	>	CutoffGroup() :  snapshotMan_(NULL) {
54
55	<	CutoffGroup() {
56	<	haveTotalMass = false;
57	<	totalMass = 0.0;
58	<	}
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
58	–	void addAtom(Atom *atom) {
59	–	cutoffAtomList.push_back(atom);
60	–	}
71
72	<	Atom *beginAtom(std::vector<Atom *>::iterator & i) {
73	<	i = cutoffAtomList.begin();
74	<	return i != cutoffAtomList.end() ? *i : NULL;
75	<	}
72	>	void addAtom(Atom *atom) {
73	>	cutoffAtomList.push_back(atom);
74	>	}
75	>
76	>	Atom *beginAtom(std::vector<Atom *>::iterator & i) {
77	>	i = cutoffAtomList.begin();
78	>	return i != cutoffAtomList.end() ? *i : NULL;
79	>	}
80	>
81	>	Atom *nextAtom(std::vector<Atom *>::iterator & i) {
82	>	i++;
83	>	return i != cutoffAtomList.end() ? *i : NULL;
84	>	}
85
86	<	Atom *nextAtom(std::vector<Atom *>::iterator & i) {
87	<	i++;
88	<	return i != cutoffAtomList.end() ? *i : NULL;
89	<	}
86	>	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
87	>	RealType getMass() {
88	>	std::vector<Atom *>::iterator i;
89	>	Atom * atom;
90	>	RealType mass;
91	>
92	>	if (!haveTotalMass) {
93	>	totalMass = 0;
94	>
95	>	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
96	>	mass = atom->getMass();
97	>	totalMass += mass;
98	>	}
99	>
100	>	haveTotalMass = true;
101	>	}
102	>
103	>	return totalMass;
104	>	}
105	>
106	>	void updateCOM() {
107	>	std::vector<Atom *>::iterator i;
108	>	Atom * atom;
109
110	<	double getMass() {
111	<	std::vector<Atom *>::iterator i;
112	<	Atom * atom;
113	<	double mass;
110	>	DataStorage&  data = snapshotMan_->getCurrentSnapshot()->*storage_;
111	>
112	>	totalMass = getMass();
113	>
114	>	if (cutoffAtomList.size() == 1) {
115	>	std::cerr << "YO!\n";
116	>	std::cerr << "atipos = " << beginAtom(i)->getPos() << "\n";
117	>	std::cerr << "lI = " << localIndex_ << "\n";
118
119	<	if (!haveTotalMass) {
120	<	totalMass = 0;
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	>	data.position[localIndex_] += atom->getMass() * atom->getPos();
125	>	}
126	>	data.position[localIndex_] /= totalMass;
127	>	}
128	>	}
129
80	–	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
81	–	mass = atom->getMass();
82	–	totalMass += mass;
83	–	}
130
131	<	haveTotalMass = true;
132	<	}
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	<	return totalMass;
147	<	}
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	>
165	>	int getGlobalIndex() {
166	>	return globalIndex;
167	>	}
168	>
169	>	void setGlobalIndex(int id) {
170	>	this->globalIndex = id;
171	>	}
172
173	<	void getCOM(Vector3d & com) {
174	<	std::vector<Atom *>::iterator i;
175	<	Atom * atom;
176	<	Vector3d pos;
177	<	double mass;
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	<	com[0] = 0;
182	<	com[1] = 0;
183	<	com[2] = 0;
184	<	totalMass = getMass();
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;
195
196	<	if (cutoffAtomList.size() == 1) {
197	<	com = beginAtom(i)->getPos();
198	<	} else {
199	<	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
200	<	mass = atom->getMass();
201	<	pos = atom->getPos();
202	<	com += pos * mass;
203	<	}
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	<	com /= totalMass;
207	<	}
113	<	}
114	<
115	<	int getNumAtom() {
116	<	return cutoffAtomList.size();
117	<	}
118	<
119	<	int getGlobalIndex() {
120	<	return globalIndex;
121	<	}
122	<
123	<	void setGlobalIndex(int id) {
124	<	this->globalIndex = id;
125	<	}
126	<
127	<	private:
128	<
129	<	std::vector<Atom *>cutoffAtomList;
130	<	bool haveTotalMass;
131	<	double totalMass;
132	<	int globalIndex;
133	<	};
134	<
135	<	}      //end namespace oopse
136	<
206	>	};
207	>	} //end namespace OpenMD
208		#endif //PRIMITIVES_CUTOFFGROUP_HPP

Comparing:
trunk/src/primitives/CutoffGroup.hpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 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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