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;
    }

    std::vector<Atom*> getAtoms() { return cutoffAtomList; }
    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:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 2 months ago) by gezelter
File size:	3940 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	gezelter	2204	class CutoffGroup {
51			public:
52	gezelter	1490
53	gezelter	2204	CutoffGroup() {
54			haveTotalMass = false;
55			totalMass = 0.0;
56			}
57	gezelter	1490
58	gezelter	2204	void addAtom(Atom *atom) {
59			cutoffAtomList.push_back(atom);
60			}
61	gezelter	1490
62	gezelter	2204	Atom beginAtom(std::vector<Atom >::iterator & i) {
63			i = cutoffAtomList.begin();
64			return i != cutoffAtomList.end() ? *i : NULL;
65			}
66	gezelter	1490
67	gezelter	2204	Atom nextAtom(std::vector<Atom >::iterator & i) {
68			i++;
69			return i != cutoffAtomList.end() ? *i : NULL;
70			}
71	gezelter	1490
72	gezelter	2204	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
73			double getMass() {
74			std::vector<Atom *>::iterator i;
75			Atom * atom;
76			double mass;
77	gezelter	1930
78	gezelter	2204	if (!haveTotalMass) {
79			totalMass = 0;
80	gezelter	1930
81	gezelter	2204	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
82			mass = atom->getMass();
83			totalMass += mass;
84			}
85	gezelter	1930
86	gezelter	2204	haveTotalMass = true;
87			}
88	gezelter	1930
89	gezelter	2204	return totalMass;
90			}
91	gezelter	1930
92	gezelter	2204	void getCOM(Vector3d & com) {
93			std::vector<Atom *>::iterator i;
94			Atom * atom;
95			Vector3d pos;
96			double mass;
97	gezelter	1930
98	gezelter	2204	com[0] = 0;
99			com[1] = 0;
100			com[2] = 0;
101			totalMass = getMass();
102	gezelter	1930
103	gezelter	2204	if (cutoffAtomList.size() == 1) {
104			com = beginAtom(i)->getPos();
105			} else {
106			for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
107			mass = atom->getMass();
108			pos = atom->getPos();
109			com += pos * mass;
110			}
111	gezelter	1930
112	gezelter	2204	com /= totalMass;
113			}
114			}
115	gezelter	1930
116	gezelter	2204	int getNumAtom() {
117			return cutoffAtomList.size();
118			}
119	gezelter	1930
120	gezelter	2204	int getGlobalIndex() {
121			return globalIndex;
122			}
123	gezelter	1930
124	gezelter	2204	void setGlobalIndex(int id) {
125			this->globalIndex = id;
126			}
127	gezelter	1930
128	gezelter	2204	private:
129	gezelter	1930
130	gezelter	2204	std::vector<Atom *>cutoffAtomList;
131			bool haveTotalMass;
132			double totalMass;
133			int globalIndex;
134			};
135	gezelter	1490
136	gezelter	1930	} //end namespace oopse
137
138			#endif //PRIMITIVES_CUTOFFGROUP_HPP