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root/OpenMD/trunk/src/primitives/CutoffGroup.hpp

Comparing trunk/src/primitives/CutoffGroup.hpp (file contents):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 2065 by gezelter, Thu Mar 5 15:11:00 2015 UTC

#	Line 1 | Line 1
1	<	#ifndef _CUTOFFGROUP_H_
2	<	#define _CUTOFFGROUP_H_
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, 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
44	>
45	>	#define PRIMITIVES_CUTOFFGROUP_HPP
46	>
47		#include "primitives/Atom.hpp"
48	+	#include "math/Vector3.hpp"
49
50	<	class CutoffGroup{
51	<	public:
52	<
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;
50	>	namespace OpenMD {
51	>	class CutoffGroup {
52	>	public:
53
54	<	if (!haveTotalMass) {
54	>	CutoffGroup() :  snapshotMan_(NULL), globalIndex(-1), localIndex_(-1) {
55
56	<	totalMass = 0;
57	<
58	<	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){
35	<	mass = atom->getMass();
36	<	totalMass += mass;
37	<	}
38	<
39	<	haveTotalMass = true;
56	>	storage_ = &Snapshot::cgData;
57	>	haveTotalMass = false;
58	>	totalMass = 0.0;
59		}
60
61	<	return totalMass;
62	<	}
63	<
64	<	void getCOM(double com[3]){
61	>	/**
62	>	* Sets the Snapshot Manager of this cutoffGroup
63	>	*/
64	>	void setSnapshotManager(SnapshotManager* sman) {
65	>	snapshotMan_ = sman;
66	>	}
67
68	<	vector<Atom*>::iterator i;
69	<	Atom* atom;
70	<	double pos[3];
71	<	double mass;
68	>
69	>	void addAtom(Atom *atom) {
70	>	cutoffAtomList.push_back(atom);
71	>	}
72
73	<	com[0] = 0;
74	<	com[1] = 0;
75	<	com[2] = 0;
76	<	totalMass = getMass();
73	>	Atom *beginAtom(std::vector<Atom *>::iterator & i) {
74	>	i = cutoffAtomList.begin();
75	>	return i != cutoffAtomList.end() ? *i : NULL;
76	>	}
77
78	<	if (cutoffAtomList.size() == 1) {
78	>	Atom *nextAtom(std::vector<Atom *>::iterator & i) {
79	>	i++;
80	>	return i != cutoffAtomList.end() ? *i : NULL;
81	>	}
82	>
83	>	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
84	>	RealType getMass() {
85
86	<	beginAtom(i)->getPos(com);
87	<
88	<	} else {
89	<
90	<	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){
91	<	mass = atom->getMass();
92	<	atom->getPos(pos);
93	<	com[0] += pos[0] * mass;
94	<	com[1] += pos[1] * mass;
95	<	com[2] += pos[2] * mass;
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	<	com[0] /= totalMass;
72	<	com[1] /= totalMass;
73	<	com[2] /= totalMass;
98	>	return totalMass;
99		}
100
101	<	}
77	<
78	<	int getNumAtom() {return cutoffAtomList.size();}
101	>	void updateCOM() {
102
103	<	int getGlobalIndex() {return globalIndex;}
104	<	void setGlobalIndex(int id) {this->globalIndex = id;}
105	<	private:
83	<	vector<Atom*> cutoffAtomList;
84	<	bool haveTotalMass;
85	<	double totalMass;
86	<	int globalIndex;
103	>	DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_;
104	>	bool needsVel = false;
105	>	if (data.getStorageLayout() & DataStorage::dslVelocity) needsVel = true;
106
107	<	};
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
128	<	#endif
128	>
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	>	/**
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	>	/**
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	>	int localIndex_;
172	>	DataStoragePointer storage_;
173	>	SnapshotManager* snapshotMan_;
174	>
175	>	};
176	>	} //end namespace OpenMD
177	>	#endif //PRIMITIVES_CUTOFFGROUP_HPP

Comparing trunk/src/primitives/CutoffGroup.hpp (property svn:keywords):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 2065 by gezelter, Thu Mar 5 15:11:00 2015 UTC

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