src/primitives/CutoffGroup.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */

#ifndef PRIMITIVES_CUTOFFGROUP_HPP

#define PRIMITIVES_CUTOFFGROUP_HPP

#include "primitives/Atom.hpp"
#include "math/Vector3.hpp"

namespace OpenMD {
class CutoffGroup {
public:

        CutoffGroup() :
                snapshotMan_(NULL) {

                storage_ = &Snapshot::cgData;
                haveTotalMass = false;
                totalMass = 0.0;
        }

        /**
         * Sets the Snapshot Manager of this cutoffGroup
         */
        void setSnapshotManager(SnapshotManager* sman) {
                snapshotMan_ = sman;
        }

        void addAtom(Atom *atom) {
                cutoffAtomList.push_back(atom);
        }

        Atom *beginAtom(std::vector<Atom *>::iterator & i) {
                i = cutoffAtomList.begin();
                return i != cutoffAtomList.end() ? *i : NULL;
        }

        Atom *nextAtom(std::vector<Atom *>::iterator & i) {
                i++;
                return i != cutoffAtomList.end() ? *i : NULL;
        }

        std::vector<Atom*> getAtoms() {
                return cutoffAtomList;
        }
        RealType getMass() {
                std::vector<Atom *>::iterator i;
                Atom * atom;
                RealType mass;

                if (!haveTotalMass)
                {
                        totalMass = 0;

                        for (atom = beginAtom(i); atom != NULL; atom = nextAtom(i))
                        {
                                mass = atom->getMass();
                                totalMass += mass;
                        }

                        haveTotalMass = true;
                }

                return totalMass;
        }

        void updateCOM() {
                std::vector<Atom *>::iterator i;
                Atom * atom;

                DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_;

                totalMass = getMass();

                if (cutoffAtomList.size() == 1)
                {
                        data.position[localIndex_] = beginAtom(i)->getPos();
                } else
                {
                        data.position[localIndex_] = V3Zero;
                        for (atom = beginAtom(i); atom != NULL; atom = nextAtom(i))
                        {
                                data.position[localIndex_] += atom->getMass() * atom->getPos();
                        }
                        data.position[localIndex_] /= totalMass;
                }
        }

        Vector3d getPos() {
                return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
        }

        int getNumAtom() {
                return cutoffAtomList.size();
        }

        int getGlobalIndex() {
                return globalIndex;
        }

        void setGlobalIndex(int id) {
                this->globalIndex = id;
        }

        /**
         * Returns the local index of this cutoffGroup
         * @return the local index of this cutoffGroup
         */
        int getLocalIndex() {
                return localIndex_;
        }

        /**
         * Sets the local index of this cutoffGroup
         * @param index new index to be set
         */
        void setLocalIndex(int index) {
                localIndex_ = index;
        }

private:

        std::vector<Atom *> cutoffAtomList;
        bool haveTotalMass;
        RealType totalMass;
        int globalIndex;

        int localIndex_;
        DataStoragePointer storage_;
        SnapshotManager* snapshotMan_;

};
} //end namespace OpenMD
#endif //PRIMITIVES_CUTOFFGROUP_HPP  
Revision:	1598
Committed:	Wed Jul 27 14:26:53 2011 UTC (13 years, 11 months ago) by mciznick
File size:	4586 byte(s)
Log Message:	Updated ordered neighbor list generation.
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	gezelter	246	*/
41	mciznick	1598
42	gezelter	246	#ifndef PRIMITIVES_CUTOFFGROUP_HPP
43
44			#define PRIMITIVES_CUTOFFGROUP_HPP
45
46	tim	3	#include "primitives/Atom.hpp"
47	gezelter	246	#include "math/Vector3.hpp"
48	gezelter	2
49	gezelter	1390	namespace OpenMD {
50	mciznick	1598	class CutoffGroup {
51			public:
52	gezelter	1540
53	mciznick	1598	CutoffGroup() :
54			snapshotMan_(NULL) {
55	gezelter	1540
56	mciznick	1598	storage_ = &Snapshot::cgData;
57			haveTotalMass = false;
58			totalMass = 0.0;
59			}
60	gezelter	1540
61	mciznick	1598	/**
62			* Sets the Snapshot Manager of this cutoffGroup
63			*/
64			void setSnapshotManager(SnapshotManager* sman) {
65			snapshotMan_ = sman;
66			}
67	gezelter	2
68	mciznick	1598	void addAtom(Atom *atom) {
69			cutoffAtomList.push_back(atom);
70	gezelter	507	}
71	gezelter	1540
72	mciznick	1598	Atom beginAtom(std::vector<Atom >::iterator & i) {
73			i = cutoffAtomList.begin();
74			return i != cutoffAtomList.end() ? *i : NULL;
75			}
76	gezelter	1540
77	mciznick	1598	Atom nextAtom(std::vector<Atom >::iterator & i) {
78			i++;
79			return i != cutoffAtomList.end() ? *i : NULL;
80			}
81	gezelter	1540
82	mciznick	1598	std::vector<Atom*> getAtoms() {
83			return cutoffAtomList;
84			}
85			RealType getMass() {
86			std::vector<Atom *>::iterator i;
87			Atom * atom;
88			RealType mass;
89	gezelter	1540
90	mciznick	1598	if (!haveTotalMass)
91			{
92			totalMass = 0;
93	gezelter	1540
94	mciznick	1598	for (atom = beginAtom(i); atom != NULL; atom = nextAtom(i))
95			{
96			mass = atom->getMass();
97			totalMass += mass;
98			}
99	gezelter	1540
100	mciznick	1598	haveTotalMass = true;
101			}
102	gezelter	1540
103	mciznick	1598	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			if (cutoffAtomList.size() == 1)
115			{
116			data.position[localIndex_] = beginAtom(i)->getPos();
117			} else
118			{
119			data.position[localIndex_] = V3Zero;
120			for (atom = beginAtom(i); atom != NULL; atom = nextAtom(i))
121			{
122			data.position[localIndex_] += atom->getMass() * atom->getPos();
123			}
124			data.position[localIndex_] /= totalMass;
125			}
126			}
127
128			Vector3d getPos() {
129			return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
130			}
131
132			int getNumAtom() {
133			return cutoffAtomList.size();
134			}
135
136			int getGlobalIndex() {
137			return globalIndex;
138			}
139
140			void setGlobalIndex(int id) {
141			this->globalIndex = id;
142			}
143
144			/**
145			* Returns the local index of this cutoffGroup
146			* @return the local index of this cutoffGroup
147			*/
148			int getLocalIndex() {
149			return localIndex_;
150			}
151
152			/**
153			* Sets the local index of this cutoffGroup
154			* @param index new index to be set
155			*/
156			void setLocalIndex(int index) {
157			localIndex_ = index;
158			}
159
160			private:
161
162			std::vector<Atom *> cutoffAtomList;
163			bool haveTotalMass;
164			RealType totalMass;
165			int globalIndex;
166
167			int localIndex_;
168			DataStoragePointer storage_;
169			SnapshotManager* snapshotMan_;
170
171			};
172	gezelter	1390	} //end namespace OpenMD
173	gezelter	246	#endif //PRIMITIVES_CUTOFFGROUP_HPP