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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 1540 by gezelter, Mon Jan 17 21:34:36 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	>	#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() :  snapshotMan_(NULL) {
54	>
55	>	storage_ = &Snapshot::cgData;
56	>	#ifdef IS_MPI
57	>	iStorage_ = &Snapshot::cgIData;
58	>	jStorage_ = &Snapshot::cgJData;
59	>	#endif
60	>	haveTotalMass = false;
61	>	totalMass = 0.0;
62		}
63
64	<	return totalMass;
65	<	}
66	<
67	<	void getCOM(double com[3]){
64	>	/**
65	>	* Sets the Snapshot Manager of this cutoffGroup
66	>	*/
67	>	void setSnapshotManager(SnapshotManager* sman) {
68	>	snapshotMan_ = sman;
69	>	}
70
71	<	vector<Atom*>::iterator i;
72	<	Atom* atom;
73	<	double pos[3];
74	<	double mass;
71	>
72	>	void addAtom(Atom *atom) {
73	>	cutoffAtomList.push_back(atom);
74	>	}
75
76	<	com[0] = 0;
77	<	com[1] = 0;
78	<	com[2] = 0;
79	<	totalMass = getMass();
76	>	Atom *beginAtom(std::vector<Atom *>::iterator & i) {
77	>	i = cutoffAtomList.begin();
78	>	return i != cutoffAtomList.end() ? *i : NULL;
79	>	}
80
81	<	if (cutoffAtomList.size() == 1) {
81	>	Atom *nextAtom(std::vector<Atom *>::iterator & i) {
82	>	i++;
83	>	return i != cutoffAtomList.end() ? *i : NULL;
84	>	}
85	>
86	>	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
87	>	RealType getMass() {
88	>	std::vector<Atom *>::iterator i;
89	>	Atom * atom;
90	>	RealType mass;
91
92	<	beginAtom(i)->getPos(com);
92	>	if (!haveTotalMass) {
93	>	totalMass = 0;
94	>
95	>	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
96	>	mass = atom->getMass();
97	>	totalMass += mass;
98	>	}
99	>
100	>	haveTotalMass = true;
101	>	}
102
103	<	} else {
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	<	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)){
115	<	mass = atom->getMass();
116	<	atom->getPos(pos);
117	<	com[0] += pos[0] * mass;
118	<	com[1] += pos[1] * mass;
119	<	com[2] += pos[2] * mass;
114	>	if (cutoffAtomList.size() == 1) {
115	>	std::cerr << "YO!\n";
116	>	std::cerr << "atipos = " << beginAtom(i)->getPos() << "\n";
117	>	std::cerr << "lI = " << localIndex_ << "\n";
118	>
119	>	data.position[localIndex_] = beginAtom(i)->getPos();
120	>	std::cerr << "YOYO!\n";
121	>	} else {
122	>	data.position[localIndex_] = V3Zero;
123	>	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
124	>	data.position[localIndex_] += atom->getMass() * atom->getPos();
125	>	}
126	>	data.position[localIndex_] /= totalMass;
127		}
70	–
71	–	com[0] /= totalMass;
72	–	com[1] /= totalMass;
73	–	com[2] /= totalMass;
128		}
129	+
130	+
131	+	/**
132	+	* Returns the current position of this cutoffGroup for the outer
133	+	* iteration over the cutoff groups.  For Force decomposition,
134	+	* this is the position of the cutoff groups ordered by row index.
135	+	* For serial calculations, this is just the position of the
136	+	* cutoff group.
137	+	*/
138	+	Vector3d getPosI() {
139	+	#ifdef IS_MPI
140	+	return ((snapshotMan_->getCurrentSnapshot())->*iStorage_).position[iIndex_];
141	+	#else
142	+	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
143	+	#endif
144	+	}
145	+
146	+	/**
147	+	* Returns the current position of this cutoffGroup for the inner
148	+	* iteration over the cutoff groups.  For Force decomposition,
149	+	* this is the position of the cutoff groups ordered by column
150	+	* index.  For serial calculations, this is just the position of
151	+	* the cutoff group.
152	+	*/
153	+	Vector3d getPosJ() {
154	+	#ifdef IS_MPI
155	+	return ((snapshotMan_->getCurrentSnapshot())->*jStorage_).position[jIndex_];
156	+	#else
157	+	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
158	+	#endif
159	+	}
160
161	<	}
162	<
163	<	int getNumAtom() {return cutoffAtomList.size();}
161	>	int getNumAtom() {
162	>	return cutoffAtomList.size();
163	>	}
164	>
165	>	int getGlobalIndex() {
166	>	return globalIndex;
167	>	}
168	>
169	>	void setGlobalIndex(int id) {
170	>	this->globalIndex = id;
171	>	}
172
173	<	int getGlobalIndex() {return globalIndex;}
174	<	void setGlobalIndex(int id) {this->globalIndex = id;}
175	<	private:
176	<	vector<Atom*> cutoffAtomList;
177	<	bool haveTotalMass;
178	<	double totalMass;
179	<	int globalIndex;
173	>	/**
174	>	* Returns the local index of this cutoffGroup
175	>	* @return the local index of this cutoffGroup
176	>	*/
177	>	int getLocalIndex() {
178	>	return localIndex_;
179	>	}
180
181	<	};
181	>	/**
182	>	* Sets the local index of this cutoffGroup
183	>	* @param index new index to be set
184	>	*/
185	>	void setLocalIndex(int index) {
186	>	localIndex_ = index;
187	>	}
188	>
189	>	private:
190	>
191	>	std::vector<Atom *>cutoffAtomList;
192	>	bool haveTotalMass;
193	>	RealType totalMass;
194	>	int globalIndex;
195
196	+	int localIndex_;
197	+	DataStoragePointer storage_;
198	+	SnapshotManager* snapshotMan_;
199	+	#ifdef IS_MPI
200	+	int iIndex_;
201	+	int jIndex_;
202	+	DataStoragePointer iStorage_;
203	+	DataStoragePointer jStorage_;
204		#endif
205	+
206	+	};
207	+	} //end namespace OpenMD
208	+	#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 1540 by gezelter, Mon Jan 17 21:34:36 2011 UTC

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