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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#ifndef PRIMITIVES_CUTOFFGROUP_HPP

#define PRIMITIVES_CUTOFFGROUP_HPP

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

namespace oopse {
class CutoffGroup {
    public:

        CutoffGroup() {
            haveTotalMass = false;
            totalMass = 0.0;
        }

        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;
        }

        double getMass() {
            std::vector<Atom *>::iterator i;
            Atom * atom;
            double mass;

            if (!haveTotalMass) {
                totalMass = 0;

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

                haveTotalMass = true;
            }

            return totalMass;
        }

        void getCOM(Vector3d & com) {
            std::vector<Atom *>::iterator i;
            Atom * atom;
            Vector3d pos;
            double mass;

            com[0] = 0;
            com[1] = 0;
            com[2] = 0;
            totalMass = getMass();

            if (cutoffAtomList.size() == 1) {
                com = beginAtom(i)->getPos();
            } else {
                for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
                    mass = atom->getMass();
                    pos = atom->getPos();
                    com += pos * mass;
                }

                com /= totalMass;
            }
        }

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

        int getGlobalIndex() {
            return globalIndex;
        }

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

    private:

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

}      //end namespace oopse

#endif //PRIMITIVES_CUTOFFGROUP_HPP  
Revision:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	4335 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	1930	/*
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. 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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#ifndef PRIMITIVES_CUTOFFGROUP_HPP
43
44			#define PRIMITIVES_CUTOFFGROUP_HPP
45
46	tim	1492	#include "primitives/Atom.hpp"
47	gezelter	1930	#include "math/Vector3.hpp"
48	gezelter	1490
49	gezelter	1930	namespace oopse {
50			class CutoffGroup {
51			public:
52	gezelter	1490
53	gezelter	1930	CutoffGroup() {
54			haveTotalMass = false;
55			totalMass = 0.0;
56			}
57	gezelter	1490
58	gezelter	1930	void addAtom(Atom *atom) {
59			cutoffAtomList.push_back(atom);
60			}
61	gezelter	1490
62	gezelter	1930	Atom beginAtom(std::vector<Atom >::iterator & i) {
63			i = cutoffAtomList.begin();
64			return i != cutoffAtomList.end() ? *i : NULL;
65			}
66	gezelter	1490
67	gezelter	1930	Atom nextAtom(std::vector<Atom >::iterator & i) {
68			i++;
69			return i != cutoffAtomList.end() ? *i : NULL;
70			}
71	gezelter	1490
72	gezelter	1930	double getMass() {
73			std::vector<Atom *>::iterator i;
74			Atom * atom;
75			double mass;
76
77			if (!haveTotalMass) {
78			totalMass = 0;
79
80			for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
81			mass = atom->getMass();
82			totalMass += mass;
83			}
84
85			haveTotalMass = true;
86			}
87
88			return totalMass;
89			}
90
91			void getCOM(Vector3d & com) {
92			std::vector<Atom *>::iterator i;
93			Atom * atom;
94			Vector3d pos;
95			double mass;
96
97			com[0] = 0;
98			com[1] = 0;
99			com[2] = 0;
100			totalMass = getMass();
101
102			if (cutoffAtomList.size() == 1) {
103			com = beginAtom(i)->getPos();
104			} else {
105			for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
106			mass = atom->getMass();
107			pos = atom->getPos();
108			com += pos * mass;
109			}
110
111			com /= totalMass;
112			}
113			}
114
115			int getNumAtom() {
116			return cutoffAtomList.size();
117			}
118
119			int getGlobalIndex() {
120			return globalIndex;
121			}
122
123			void setGlobalIndex(int id) {
124			this->globalIndex = id;
125			}
126
127			private:
128
129			std::vector<Atom *>cutoffAtomList;
130			bool haveTotalMass;
131			double totalMass;
132			int globalIndex;
133	gezelter	1490	};
134
135	gezelter	1930	} //end namespace oopse
136
137			#endif //PRIMITIVES_CUTOFFGROUP_HPP