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

Comparing:
trunk/src/primitives/CutoffGroup.hpp (file contents), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 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	<	#ifndef _CUTOFFGROUP_H_
2	<	#define _CUTOFFGROUP_H_
3	<	#include "Atom.hpp"
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
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.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
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
43
44	<	class CutoffGroup{
6	<	public:
7	<
8	<	CutoffGroup() {
9	<	haveTotalMass = false;
10	<	totalMass = 0.0;
11	<	}
12	<
13	<	void addAtom(Atom* atom) {cutoffAtomList.push_back(atom);}
14	<
15	<	Atom* beginAtom(vector<Atom*>::iterator& i){
16	<	i = cutoffAtomList.begin();
17	<	return i != cutoffAtomList.end()? *i : NULL;
18	<	}
19	<
20	<	Atom* nextAtom(vector<Atom*>::iterator& i){
21	<	i++;
22	<	return i != cutoffAtomList.end()? *i : NULL;
23	<	}
24	<
25	<	double getMass(){
26	<	vector<Atom*>::iterator i;
27	<	Atom* atom;
28	<	double mass;
29	<
30	<	if (!haveTotalMass) {
44	>	#define PRIMITIVES_CUTOFFGROUP_HPP
45
46	<	totalMass = 0;
47	<
34	<	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){
35	<	mass = atom->getMass();
36	<	totalMass += mass;
37	<	}
46	>	#include "primitives/Atom.hpp"
47	>	#include "math/Vector3.hpp"
48
49	<	haveTotalMass = true;
49	>	namespace OpenMD {
50	>	class CutoffGroup {
51	>	public:
52	>
53	>	CutoffGroup() {
54	>	haveTotalMass = false;
55	>	totalMass = 0.0;
56		}
57
58	<	return totalMass;
59	<	}
60	<
45	<	void getCOM(double com[3]){
46	<
47	<	vector<Atom*>::iterator i;
48	<	Atom* atom;
49	<	double pos[3];
50	<	double mass;
58	>	void addAtom(Atom *atom) {
59	>	cutoffAtomList.push_back(atom);
60	>	}
61
62	<	com[0] = 0;
63	<	com[1] = 0;
64	<	com[2] = 0;
65	<	totalMass = getMass();
62	>	Atom *beginAtom(std::vector<Atom *>::iterator & i) {
63	>	i = cutoffAtomList.begin();
64	>	return i != cutoffAtomList.end() ? *i : NULL;
65	>	}
66
67	<	if (cutoffAtomList.size() == 1) {
67	>	Atom *nextAtom(std::vector<Atom *>::iterator & i) {
68	>	i++;
69	>	return i != cutoffAtomList.end() ? *i : NULL;
70	>	}
71	>
72	>	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
73	>	RealType getMass() {
74	>	std::vector<Atom *>::iterator i;
75	>	Atom * atom;
76	>	RealType mass;
77
78	<	beginAtom(i)->getPos(com);
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	<	} else {
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	<	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){
99	<	mass = atom->getMass();
100	<	atom->getPos(pos);
101	<	com[0] += pos[0] * mass;
67	<	com[1] += pos[1] * mass;
68	<	com[2] += pos[2] * mass;
69	<	}
98	>	com[0] = 0;
99	>	com[1] = 0;
100	>	com[2] = 0;
101	>	totalMass = getMass();
102
103	<	com[0] /= totalMass;
104	<	com[1] /= totalMass;
105	<	com[2] /= totalMass;
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	<	}
117	<
118	<	int getNumAtom() {return cutoffAtomList.size();}
119	<
120	<	int getGlobalIndex() {return globalIndex;}
121	<	void setGlobalIndex(int id) {this->globalIndex = id;}
122	<	private:
123	<	vector<Atom*> cutoffAtomList;
124	<	bool haveTotalMass;
125	<	double totalMass;
126	<	int globalIndex;
127	<
128	<	};
129	<
130	<	#endif
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 2 by gezelter, Fri Sep 24 04:16:43 2004 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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