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root/OpenMD/branches/development/src/primitives/CutoffGroup.hpp

Comparing:
trunk/src/primitives/CutoffGroup.hpp (file contents), Revision 430 by tim, Thu Mar 10 23:56:42 2005 UTC vs.
branches/development/src/primitives/CutoffGroup.hpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 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() {
54	>	haveTotalMass = false;
55	>	totalMass = 0.0;
56	>	}
57	>
58	>	void addAtom(Atom *atom) {
59	>	cutoffAtomList.push_back(atom);
60	>	}
61	>
62	>	Atom *beginAtom(std::vector<Atom *>::iterator & i) {
63	>	i = cutoffAtomList.begin();
64	>	return i != cutoffAtomList.end() ? *i : NULL;
65	>	}
66	>
67	>	Atom *nextAtom(std::vector<Atom *>::iterator & i) {
68	>	i++;
69	>	return i != cutoffAtomList.end() ? *i : NULL;
70	>	}
71
72	<	CutoffGroup() {
73	<	haveTotalMass = false;
74	<	totalMass = 0.0;
75	<	}
76	<
77	<	void addAtom(Atom *atom) {
78	<	cutoffAtomList.push_back(atom);
79	<	}
80	<
81	<	Atom *beginAtom(std::vector<Atom *>::iterator & i) {
82	<	i = cutoffAtomList.begin();
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	<	}
90	<
91	<	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
92	<	double getMass() {
93	<	std::vector<Atom *>::iterator i;
94	<	Atom * atom;
95	<	double mass;
96	<
97	<	if (!haveTotalMass) {
98	<	totalMass = 0;
99	<
100	<	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
101	<	mass = atom->getMass();
102	<	totalMass += mass;
103	<	}
104	<
105	<	haveTotalMass = true;
106	<	}
107	<
108	<	return totalMass;
109	<	}
110	<
111	<	void getCOM(Vector3d & com) {
112	<	std::vector<Atom *>::iterator i;
113	<	Atom * atom;
114	<	Vector3d pos;
115	<	double mass;
116	<
117	<	com[0] = 0;
118	<	com[1] = 0;
119	<	com[2] = 0;
120	<	totalMass = getMass();
121	<
122	<	if (cutoffAtomList.size() == 1) {
123	<	com = beginAtom(i)->getPos();
124	<	} else {
125	<	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
126	<	mass = atom->getMass();
127	<	pos = atom->getPos();
128	<	com += pos * mass;
129	<	}
130	<
131	<	com /= totalMass;
132	<	}
133	<	}
134	<
135	<	int getNumAtom() {
117	<	return cutoffAtomList.size();
118	<	}
119	<
120	<	int getGlobalIndex() {
121	<	return globalIndex;
122	<	}
123	<
124	<	void setGlobalIndex(int id) {
125	<	this->globalIndex = id;
126	<	}
127	<
128	<	private:
129	<
130	<	std::vector<Atom *>cutoffAtomList;
131	<	bool haveTotalMass;
132	<	double totalMass;
133	<	int globalIndex;
134	<	};
135	<
136	<	}      //end namespace oopse
137	<
72	>	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
73	>	RealType getMass() {
74	>	std::vector<Atom *>::iterator i;
75	>	Atom * atom;
76	>	RealType mass;
77	>
78	>	if (!haveTotalMass) {
79	>	totalMass = 0;
80	>
81	>	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
82	>	mass = atom->getMass();
83	>	totalMass += mass;
84	>	}
85	>
86	>	haveTotalMass = true;
87	>	}
88	>
89	>	return totalMass;
90	>	}
91	>
92	>	void getCOM(Vector3d & com) {
93	>	std::vector<Atom *>::iterator i;
94	>	Atom * atom;
95	>	Vector3d pos;
96	>	RealType mass;
97	>
98	>	com[0] = 0;
99	>	com[1] = 0;
100	>	com[2] = 0;
101	>	totalMass = getMass();
102	>
103	>	if (cutoffAtomList.size() == 1) {
104	>	com = beginAtom(i)->getPos();
105	>	} else {
106	>	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
107	>	mass = atom->getMass();
108	>	pos = atom->getPos();
109	>	com += pos * mass;
110	>	}
111	>
112	>	com /= totalMass;
113	>	}
114	>	}
115	>
116	>	int getNumAtom() {
117	>	return cutoffAtomList.size();
118	>	}
119	>
120	>	int getGlobalIndex() {
121	>	return globalIndex;
122	>	}
123	>
124	>	void setGlobalIndex(int id) {
125	>	this->globalIndex = id;
126	>	}
127	>
128	>	private:
129	>
130	>	std::vector<Atom *>cutoffAtomList;
131	>	bool haveTotalMass;
132	>	RealType totalMass;
133	>	int globalIndex;
134	>	};
135	>	} //end namespace OpenMD
136		#endif //PRIMITIVES_CUTOFFGROUP_HPP

Comparing:
trunk/src/primitives/CutoffGroup.hpp (property svn:keywords), Revision 430 by tim, Thu Mar 10 23:56:42 2005 UTC vs.
branches/development/src/primitives/CutoffGroup.hpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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