ViewVC Help

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

root/OpenMD/branches/development/src/primitives/CutoffGroup.hpp

Comparing:
trunk/src/primitives/CutoffGroup.hpp (file contents), Revision 1211 by gezelter, Wed Jan 23 16:38:22 2008 UTC vs.
branches/development/src/primitives/CutoffGroup.hpp (file contents), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

#	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 {
50	>	namespace OpenMD {
51		class CutoffGroup {
52		public:
53
54	<	CutoffGroup() {
54	>	CutoffGroup() :  snapshotMan_(NULL), globalIndex(-1), localIndex_(-1) {
55	>
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	+
68	+
69		void addAtom(Atom *atom) {
70		cutoffAtomList.push_back(atom);
71		}
#	Line 72 | Line 83 | namespace oopse {
83		std::vector<Atom*> getAtoms() { return cutoffAtomList; }
84		RealType getMass() {
85		std::vector<Atom *>::iterator i;
75	–	Atom * atom;
76	–	RealType mass;
86
87		if (!haveTotalMass) {
88		totalMass = 0;
89
90	<	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
91	<	mass = atom->getMass();
90	>	for(Atom* atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
91	>	RealType mass = atom->getMass();
92		totalMass += mass;
93		}
94
#	Line 89 | Line 98 | namespace oopse {
98		return totalMass;
99		}
100
101	<	void getCOM(Vector3d & com) {
101	>	void updateCOM() {
102		std::vector<Atom *>::iterator i;
103		Atom * atom;
104	<	Vector3d pos;
105	<	RealType mass;
106	<
107	<	com[0] = 0;
99	<	com[1] = 0;
100	<	com[2] = 0;
104	>
105	>	DataStorage&  data = snapshotMan_->getCurrentSnapshot()->*storage_;
106	>	int storageLayout = data.getStorageLayout();
107	>
108		totalMass = getMass();
109
110		if (cutoffAtomList.size() == 1) {
111	<	com = beginAtom(i)->getPos();
111	>	data.position[localIndex_] = beginAtom(i)->getPos();
112		} else {
113	+	data.position[localIndex_] = V3Zero;
114		for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
115	<	mass = atom->getMass();
116	<	pos = atom->getPos();
117	<	com += pos * mass;
110	<	}
111	<
112	<	com /= totalMass;
115	>	data.position[localIndex_] += atom->getMass() * atom->getPos();
116	>	}
117	>	data.position[localIndex_] /= totalMass;
118		}
119	+
120	+	if (storageLayout & DataStorage::dslVelocity) {
121	+	if (cutoffAtomList.size() == 1) {
122	+	data.velocity[localIndex_] = beginAtom(i)->getVel();
123	+	} else {
124	+	data.velocity[localIndex_] = V3Zero;
125	+	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
126	+	data.velocity[localIndex_] += atom->getMass() * atom->getVel();
127	+	}
128	+	data.velocity[localIndex_] /= totalMass;
129	+	}
130	+	}
131		}
132	+
133	+
134	+	Vector3d getPos() {
135	+	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
136	+	}
137	+	Vector3d getVel() {
138	+	return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_];
139	+	}
140
141		int getNumAtom() {
142		return cutoffAtomList.size();
#	Line 124 | Line 149 | namespace oopse {
149		void setGlobalIndex(int id) {
150		this->globalIndex = id;
151		}
152	+
153	+	/**
154	+	* Returns the local index of this cutoffGroup
155	+	* @return the local index of this cutoffGroup
156	+	*/
157	+	int getLocalIndex() {
158	+	return localIndex_;
159	+	}
160	+
161	+	/**
162	+	* Sets the local index of this cutoffGroup
163	+	* @param index new index to be set
164	+	*/
165	+	void setLocalIndex(int index) {
166	+	localIndex_ = index;
167	+	}
168
169		private:
170
171		std::vector<Atom *>cutoffAtomList;
172		bool haveTotalMass;
173		RealType totalMass;
174	<	int globalIndex;
174	>	int globalIndex;
175	>
176	>	int localIndex_;
177	>	DataStoragePointer storage_;
178	>	SnapshotManager* snapshotMan_;
179	>
180		};
181	<	} //end namespace oopse
181	>	} //end namespace OpenMD
182		#endif //PRIMITIVES_CUTOFFGROUP_HPP

Comparing:
trunk/src/primitives/CutoffGroup.hpp (property svn:keywords), Revision 1211 by gezelter, Wed Jan 23 16:38:22 2008 UTC vs.
branches/development/src/primitives/CutoffGroup.hpp (property svn:keywords), Revision 1875 by gezelter, Fri May 17 14:41:42 2013 UTC

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

Diff Legend

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