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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 1874 by gezelter, Wed May 15 15:09:35 2013 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, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#ifndef PRIMITIVES_CUTOFFGROUP_HPP
#	Line 46 | Line 47
47		#include "primitives/Atom.hpp"
48		#include "math/Vector3.hpp"
49
50	<	namespace oopse {
51	<	class CutoffGroup {
52	<	public:
50	>	namespace OpenMD {
51	>	class CutoffGroup {
52	>	public:
53	>
54	>	CutoffGroup() :  snapshotMan_(NULL), globalIndex(-1), localIndex_(-1) {
55
56	<	CutoffGroup() {
57	<	haveTotalMass = false;
58	<	totalMass = 0.0;
59	<	}
56	>	storage_ = &Snapshot::cgData;
57	>	haveTotalMass = false;
58	>	totalMass = 0.0;
59	>	}
60	>
61	>	/**
62	>	* Sets the Snapshot Manager of this cutoffGroup
63	>	*/
64	>	void setSnapshotManager(SnapshotManager* sman) {
65	>	snapshotMan_ = sman;
66	>	}
67
58	–	void addAtom(Atom *atom) {
59	–	cutoffAtomList.push_back(atom);
60	–	}
68
69	<	Atom *beginAtom(std::vector<Atom *>::iterator & i) {
70	<	i = cutoffAtomList.begin();
71	<	return i != cutoffAtomList.end() ? *i : NULL;
72	<	}
69	>	void addAtom(Atom *atom) {
70	>	cutoffAtomList.push_back(atom);
71	>	}
72	>
73	>	Atom *beginAtom(std::vector<Atom *>::iterator & i) {
74	>	i = cutoffAtomList.begin();
75	>	return i != cutoffAtomList.end() ? *i : NULL;
76	>	}
77	>
78	>	Atom *nextAtom(std::vector<Atom *>::iterator & i) {
79	>	i++;
80	>	return i != cutoffAtomList.end() ? *i : NULL;
81	>	}
82
83	<	Atom *nextAtom(std::vector<Atom *>::iterator & i) {
84	<	i++;
85	<	return i != cutoffAtomList.end() ? *i : NULL;
86	<	}
83	>	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
84	>	RealType getMass() {
85	>	std::vector<Atom *>::iterator i;
86	>	Atom * atom;
87	>	RealType mass;
88	>
89	>	if (!haveTotalMass) {
90	>	totalMass = 0;
91	>
92	>	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
93	>	mass = atom->getMass();
94	>	totalMass += mass;
95	>	}
96	>
97	>	haveTotalMass = true;
98	>	}
99	>
100	>	return totalMass;
101	>	}
102	>
103	>	void updateCOM() {
104	>	std::vector<Atom *>::iterator i;
105	>	Atom * atom;
106
107	<	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
108	<	double getMass() {
109	<	std::vector<Atom *>::iterator i;
110	<	Atom * atom;
111	<	double mass;
107	>	DataStorage&  data = snapshotMan_->getCurrentSnapshot()->*storage_;
108	>	int storageLayout = data.getStorageLayout();
109	>
110	>	totalMass = getMass();
111	>
112	>	if (cutoffAtomList.size() == 1) {
113	>	data.position[localIndex_] = beginAtom(i)->getPos();
114	>	} else {
115	>	data.position[localIndex_] = V3Zero;
116	>	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
117	>	data.position[localIndex_] += atom->getMass() * atom->getPos();
118	>	}
119	>	data.position[localIndex_] /= totalMass;
120	>	}
121
122	<	if (!haveTotalMass) {
123	<	totalMass = 0;
124	<
125	<	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
126	<	mass = atom->getMass();
127	<	totalMass += mass;
128	<	}
129	<
130	<	haveTotalMass = true;
87	<	}
88	<
89	<	return totalMass;
122	>	if (storageLayout & DataStorage::dslVelocity) {
123	>	if (cutoffAtomList.size() == 1) {
124	>	data.velocity[localIndex_] = beginAtom(i)->getVel();
125	>	} else {
126	>	data.velocity[localIndex_] = V3Zero;
127	>	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
128	>	data.velocity[localIndex_] += atom->getMass() * atom->getVel();
129	>	}
130	>	data.velocity[localIndex_] /= totalMass;
131		}
132	+	}
133	+	}
134
92	–	void getCOM(Vector3d & com) {
93	–	std::vector<Atom *>::iterator i;
94	–	Atom * atom;
95	–	Vector3d pos;
96	–	double mass;
135
136	<	com[0] = 0;
137	<	com[1] = 0;
138	<	com[2] = 0;
139	<	totalMass = getMass();
136	>	Vector3d getPos() {
137	>	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
138	>	}
139	>	Vector3d getVel() {
140	>	return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_];
141	>	}
142	>
143	>	int getNumAtom() {
144	>	return cutoffAtomList.size();
145	>	}
146	>
147	>	int getGlobalIndex() {
148	>	return globalIndex;
149	>	}
150	>
151	>	void setGlobalIndex(int id) {
152	>	this->globalIndex = id;
153	>	}
154
155	<	if (cutoffAtomList.size() == 1) {
156	<	com = beginAtom(i)->getPos();
157	<	} else {
158	<	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
159	<	mass = atom->getMass();
160	<	pos = atom->getPos();
161	<	com += pos * mass;
110	<	}
155	>	/**
156	>	* Returns the local index of this cutoffGroup
157	>	* @return the local index of this cutoffGroup
158	>	*/
159	>	int getLocalIndex() {
160	>	return localIndex_;
161	>	}
162
163	<	com /= totalMass;
164	<	}
165	<	}
163	>	/**
164	>	* Sets the local index of this cutoffGroup
165	>	* @param index new index to be set
166	>	*/
167	>	void setLocalIndex(int index) {
168	>	localIndex_ = index;
169	>	}
170	>
171	>	private:
172	>
173	>	std::vector<Atom *>cutoffAtomList;
174	>	bool haveTotalMass;
175	>	RealType totalMass;
176	>	int globalIndex;
177
178	<	int getNumAtom() {
179	<	return cutoffAtomList.size();
180	<	}
178	>	int localIndex_;
179	>	DataStoragePointer storage_;
180	>	SnapshotManager* snapshotMan_;
181
182	<	int getGlobalIndex() {
183	<	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	<
182	>	};
183	>	} //end namespace OpenMD
184		#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 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

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