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root/OpenMD/branches/devel_omp/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/devel_omp/src/primitives/CutoffGroup.hpp (file contents), Revision 1598 by mciznick, Wed Jul 27 14:26:53 2011 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	<	class CutoffGroup{
42	>	#ifndef PRIMITIVES_CUTOFFGROUP_HPP
43	>
44	>	#define PRIMITIVES_CUTOFFGROUP_HPP
45	>
46	>	#include "primitives/Atom.hpp"
47	>	#include "math/Vector3.hpp"
48	>
49	>	namespace OpenMD {
50	>	class CutoffGroup {
51		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) {
52
53	<	totalMass = 0;
54	<
34	<	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){
35	<	mass = atom->getMass();
36	<	totalMass += mass;
37	<	}
53	>	CutoffGroup() :
54	>	snapshotMan_(NULL) {
55
56	<	haveTotalMass = true;
57	<	}
58	<
59	<	return totalMass;
43	<	}
44	<
45	<	void getCOM(double com[3]){
56	>	storage_ = &Snapshot::cgData;
57	>	haveTotalMass = false;
58	>	totalMass = 0.0;
59	>	}
60
61	<	vector<Atom*>::iterator i;
62	<	Atom* atom;
63	<	double pos[3];
64	<	double mass;
65	<
66	<	com[0] = 0;
53	<	com[1] = 0;
54	<	com[2] = 0;
55	<	totalMass = getMass();
56	<
57	<	if (cutoffAtomList.size() == 1) {
58	<
59	<	beginAtom(i)->getPos(com);
60	<
61	<	} else {
62	<
63	<	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){
64	<	mass = atom->getMass();
65	<	atom->getPos(pos);
66	<	com[0] += pos[0] * mass;
67	<	com[1] += pos[1] * mass;
68	<	com[2] += pos[2] * mass;
69	<	}
70	<
71	<	com[0] /= totalMass;
72	<	com[1] /= totalMass;
73	<	com[2] /= totalMass;
74	<	}
75	<
76	<	}
77	<
78	<	int getNumAtom() {return cutoffAtomList.size();}
61	>	/**
62	>	* Sets the Snapshot Manager of this cutoffGroup
63	>	*/
64	>	void setSnapshotManager(SnapshotManager* sman) {
65	>	snapshotMan_ = sman;
66	>	}
67
68	<	int getGlobalIndex() {return globalIndex;}
69	<	void setGlobalIndex(int id) {this->globalIndex = id;}
68	>	void addAtom(Atom *atom) {
69	>	cutoffAtomList.push_back(atom);
70	>	}
71	>
72	>	Atom *beginAtom(std::vector<Atom *>::iterator & i) {
73	>	i = cutoffAtomList.begin();
74	>	return i != cutoffAtomList.end() ? *i : NULL;
75	>	}
76	>
77	>	Atom *nextAtom(std::vector<Atom *>::iterator & i) {
78	>	i++;
79	>	return i != cutoffAtomList.end() ? *i : NULL;
80	>	}
81	>
82	>	std::vector<Atom*> getAtoms() {
83	>	return cutoffAtomList;
84	>	}
85	>	RealType getMass() {
86	>	std::vector<Atom *>::iterator i;
87	>	Atom * atom;
88	>	RealType mass;
89	>
90	>	if (!haveTotalMass)
91	>	{
92	>	totalMass = 0;
93	>
94	>	for (atom = beginAtom(i); atom != NULL; atom = nextAtom(i))
95	>	{
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	>	DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_;
111	>
112	>	totalMass = getMass();
113	>
114	>	if (cutoffAtomList.size() == 1)
115	>	{
116	>	data.position[localIndex_] = beginAtom(i)->getPos();
117	>	} else
118	>	{
119	>	data.position[localIndex_] = V3Zero;
120	>	for (atom = beginAtom(i); atom != NULL; atom = nextAtom(i))
121	>	{
122	>	data.position[localIndex_] += atom->getMass() * atom->getPos();
123	>	}
124	>	data.position[localIndex_] /= totalMass;
125	>	}
126	>	}
127	>
128	>	Vector3d getPos() {
129	>	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
130	>	}
131	>
132	>	int getNumAtom() {
133	>	return cutoffAtomList.size();
134	>	}
135	>
136	>	int getGlobalIndex() {
137	>	return globalIndex;
138	>	}
139	>
140	>	void setGlobalIndex(int id) {
141	>	this->globalIndex = id;
142	>	}
143	>
144	>	/**
145	>	* Returns the local index of this cutoffGroup
146	>	* @return the local index of this cutoffGroup
147	>	*/
148	>	int getLocalIndex() {
149	>	return localIndex_;
150	>	}
151	>
152	>	/**
153	>	* Sets the local index of this cutoffGroup
154	>	* @param index new index to be set
155	>	*/
156	>	void setLocalIndex(int index) {
157	>	localIndex_ = index;
158	>	}
159	>
160		private:
83	–	vector<Atom*> cutoffAtomList;
84	–	bool haveTotalMass;
85	–	double totalMass;
86	–	int globalIndex;
161
162	<	};
162	>	std::vector<Atom *> cutoffAtomList;
163	>	bool haveTotalMass;
164	>	RealType totalMass;
165	>	int globalIndex;
166
167	<	#endif
167	>	int localIndex_;
168	>	DataStoragePointer storage_;
169	>	SnapshotManager* snapshotMan_;
170	>
171	>	};
172	>	} //end namespace OpenMD
173	>	#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/devel_omp/src/primitives/CutoffGroup.hpp (property svn:keywords), Revision 1598 by mciznick, Wed Jul 27 14:26:53 2011 UTC

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