ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/trunk/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.
Revision 2065 by gezelter, Thu Mar 5 15:11:00 2015 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	>
86	>	if (!haveTotalMass) {
87	>	totalMass = 0.0;
88	>
89	>	std::vector<Atom *>::iterator i;
90	>	for(Atom* atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
91	>	RealType mass = atom->getMass();
92	>	totalMass += mass;
93	>	}
94	>
95	>	haveTotalMass = true;
96	>	}
97	>
98	>	return totalMass;
99	>	}
100	>
101	>	void updateCOM() {
102
103	<	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
104	<	double getMass() {
105	<	std::vector<Atom *>::iterator i;
75	<	Atom * atom;
76	<	double mass;
103	>	DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_;
104	>	bool needsVel = false;
105	>	if (data.getStorageLayout() & DataStorage::dslVelocity) needsVel = true;
106
107	<	if (!haveTotalMass) {
108	<	totalMass = 0;
107	>	if (cutoffAtomList.size() == 1) {
108	>	data.position[localIndex_] = cutoffAtomList[0]->getPos();
109	>	if (needsVel)
110	>	data.velocity[localIndex_] = cutoffAtomList[0]->getVel();
111	>	} else {
112	>	std::vector<Atom *>::iterator i;
113	>	Atom * atom;
114	>	RealType totalMass = getMass();
115	>	data.position[localIndex_] = V3Zero;
116	>	if (needsVel) data.velocity[localIndex_] = V3Zero;
117	>
118	>	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
119	>	data.position[localIndex_] += atom->getMass() * atom->getPos();
120	>	if (needsVel)
121	>	data.velocity[localIndex_] += atom->getMass() * atom->getVel();
122	>	}
123	>	data.position[localIndex_] /= totalMass;
124	>	if (needsVel) data.velocity[localIndex_] /= totalMass;
125	>	}
126	>	}
127
81	–	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
82	–	mass = atom->getMass();
83	–	totalMass += mass;
84	–	}
128
129	<	haveTotalMass = true;
130	<	}
129	>	Vector3d getPos() {
130	>	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
131	>	}
132	>	Vector3d getVel() {
133	>	return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_];
134	>	}
135	>
136	>	int getNumAtom() {
137	>	return cutoffAtomList.size();
138	>	}
139	>
140	>	int getGlobalIndex() {
141	>	return globalIndex;
142	>	}
143	>
144	>	void setGlobalIndex(int id) {
145	>	this->globalIndex = id;
146	>	}
147
148	<	return totalMass;
149	<	}
148	>	/**
149	>	* Returns the local index of this cutoffGroup
150	>	* @return the local index of this cutoffGroup
151	>	*/
152	>	int getLocalIndex() {
153	>	return localIndex_;
154	>	}
155
156	<	void getCOM(Vector3d & com) {
157	<	std::vector<Atom *>::iterator i;
158	<	Atom * atom;
159	<	Vector3d pos;
160	<	double mass;
156	>	/**
157	>	* Sets the local index of this cutoffGroup
158	>	* @param index new index to be set
159	>	*/
160	>	void setLocalIndex(int index) {
161	>	localIndex_ = index;
162	>	}
163	>
164	>	private:
165	>
166	>	std::vector<Atom *>cutoffAtomList;
167	>	bool haveTotalMass;
168	>	RealType totalMass;
169	>	int globalIndex;
170
171	<	com[0] = 0;
172	<	com[1] = 0;
173	<	com[2] = 0;
101	<	totalMass = getMass();
171	>	int localIndex_;
172	>	DataStoragePointer storage_;
173	>	SnapshotManager* snapshotMan_;
174
175	<	if (cutoffAtomList.size() == 1) {
176	<	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	<	double totalMass;
133	<	int globalIndex;
134	<	};
135	<
136	<	}      //end namespace oopse
137	<
175	>	};
176	>	} //end namespace OpenMD
177		#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.
Revision 2065 by gezelter, Thu Mar 5 15:11:00 2015 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines