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
#	Content
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. 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	#include "primitives/Atom.hpp"
47	#include "math/Vector3.hpp"
48
49	namespace oopse {
50	class CutoffGroup {
51	public:
52
53	CutoffGroup() {
54	haveTotalMass = false;
55	totalMass = 0.0;
56	}
57
58	void addAtom(Atom *atom) {
59	cutoffAtomList.push_back(atom);
60	}
61
62	Atom beginAtom(std::vector<Atom >::iterator & i) {
63	i = cutoffAtomList.begin();
64	return i != cutoffAtomList.end() ? *i : NULL;
65	}
66
67	Atom nextAtom(std::vector<Atom >::iterator & i) {
68	i++;
69	return i != cutoffAtomList.end() ? *i : NULL;
70	}
71
72	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
73	double getMass() {
74	std::vector<Atom *>::iterator i;
75	Atom * atom;
76	double mass;
77
78	if (!haveTotalMass) {
79	totalMass = 0;
80
81	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
82	mass = atom->getMass();
83	totalMass += mass;
84	}
85
86	haveTotalMass = true;
87	}
88
89	return totalMass;
90	}
91
92	void getCOM(Vector3d & com) {
93	std::vector<Atom *>::iterator i;
94	Atom * atom;
95	Vector3d pos;
96	double mass;
97
98	com[0] = 0;
99	com[1] = 0;
100	com[2] = 0;
101	totalMass = getMass();
102
103	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
112	com /= totalMass;
113	}
114	}
115
116	int getNumAtom() {
117	return cutoffAtomList.size();
118	}
119
120	int getGlobalIndex() {
121	return globalIndex;
122	}
123
124	void setGlobalIndex(int id) {
125	this->globalIndex = id;
126	}
127
128	private:
129
130	std::vector<Atom *>cutoffAtomList;
131	bool haveTotalMass;
132	double totalMass;
133	int globalIndex;
134	};
135
136	} //end namespace oopse
137
138	#endif //PRIMITIVES_CUTOFFGROUP_HPP