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() {
      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; }
    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 getCOM(Vector3d & com) {
      std::vector<Atom *>::iterator i;
      Atom * atom;
      Vector3d pos;
      RealType 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;
      }
    }
    
  void getCOMV(Vector3d & comv) {
      std::vector<Atom *>::iterator i;
      Atom * atom;
      Vector3d vel;
      RealType mass;
      
      comv[0] = 0;
      comv[1] = 0;
      comv[2] = 0;
      totalMass = getMass();
      
      if (cutoffAtomList.size() == 1) {
        comv = beginAtom(i)->getVel();
      } else {
        for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
            mass = atom->getMass();
            vel = atom->getVel();
            comv += vel * mass;
        }        
        comv /= totalMass;
      }
    }


    int getNumAtom() {
      return cutoffAtomList.size();
    }
    
    int getGlobalIndex() {
      return globalIndex;
    }
    
    void setGlobalIndex(int id) {
      this->globalIndex = id;
    }
    
  private:
    
    std::vector<Atom *>cutoffAtomList;
    bool haveTotalMass;
    RealType totalMass;
    int globalIndex;
  };  
} //end namespace OpenMD
#endif //PRIMITIVES_CUTOFFGROUP_HPP  
Revision:	1682
Committed:	Tue Feb 28 23:11:22 2012 UTC (13 years, 5 months ago) by chuckv
File size:	4634 byte(s)
Log Message:	Debugging heat flux calculation for rigid bodies.
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
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	*
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	*/
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 OpenMD {
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	RealType getMass() {
74	std::vector<Atom *>::iterator i;
75	Atom * atom;
76	RealType 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	RealType 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	void getCOMV(Vector3d & comv) {
117	std::vector<Atom *>::iterator i;
118	Atom * atom;
119	Vector3d vel;
120	RealType mass;
121
122	comv[0] = 0;
123	comv[1] = 0;
124	comv[2] = 0;
125	totalMass = getMass();
126
127	if (cutoffAtomList.size() == 1) {
128	comv = beginAtom(i)->getVel();
129	} else {
130	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
131	mass = atom->getMass();
132	vel = atom->getVel();
133	comv += vel * mass;
134	}
135	comv /= totalMass;
136	}
137	}
138
139
140
141	int getNumAtom() {
142	return cutoffAtomList.size();
143	}
144
145	int getGlobalIndex() {
146	return globalIndex;
147	}
148
149	void setGlobalIndex(int id) {
150	this->globalIndex = id;
151	}
152
153	private:
154
155	std::vector<Atom *>cutoffAtomList;
156	bool haveTotalMass;
157	RealType totalMass;
158	int globalIndex;
159	};
160	} //end namespace OpenMD
161	#endif //PRIMITIVES_CUTOFFGROUP_HPP