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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#ifndef PRIMITIVES_CUTOFFGROUP_HPP

#define PRIMITIVES_CUTOFFGROUP_HPP

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

namespace OpenMD {
  class CutoffGroup {
  public:
    
    CutoffGroup() :  snapshotMan_(NULL), globalIndex(-1), localIndex_(-1) {

      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;
      
      if (!haveTotalMass) {
        totalMass = 0;
        
        for(Atom* atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
          RealType mass = atom->getMass();
          totalMass += mass;
        }
        
        haveTotalMass = true;
      }
      
      return totalMass;
    }
    
    void updateCOM() {
      std::vector<Atom *>::iterator i;
      Atom * atom;

      DataStorage&  data = snapshotMan_->getCurrentSnapshot()->*storage_;
      int storageLayout = data.getStorageLayout();
     
      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;
      }

      if (storageLayout & DataStorage::dslVelocity) {
        if (cutoffAtomList.size() == 1) {
          data.velocity[localIndex_] = beginAtom(i)->getVel();
        } else {
          data.velocity[localIndex_] = V3Zero;
          for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
            data.velocity[localIndex_] += atom->getMass() * atom->getVel();
          }        
          data.velocity[localIndex_] /= totalMass;
        }
      }
    }


    Vector3d getPos() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];      
    }
    Vector3d getVel() {
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	5643 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#ifndef PRIMITIVES_CUTOFFGROUP_HPP
44
45	#define PRIMITIVES_CUTOFFGROUP_HPP
46
47	#include "primitives/Atom.hpp"
48	#include "math/Vector3.hpp"
49
50	namespace OpenMD {
51	class CutoffGroup {
52	public:
53
54	CutoffGroup() : snapshotMan_(NULL), globalIndex(-1), localIndex_(-1) {
55
56	storage_ = &Snapshot::cgData;
57	haveTotalMass = false;
58	totalMass = 0.0;
59	}
60
61	/**
62	* Sets the Snapshot Manager of this cutoffGroup
63	*/
64	void setSnapshotManager(SnapshotManager* sman) {
65	snapshotMan_ = sman;
66	}
67
68
69	void addAtom(Atom *atom) {
70	cutoffAtomList.push_back(atom);
71	}
72
73	Atom beginAtom(std::vector<Atom >::iterator & i) {
74	i = cutoffAtomList.begin();
75	return i != cutoffAtomList.end() ? *i : NULL;
76	}
77
78	Atom nextAtom(std::vector<Atom >::iterator & i) {
79	i++;
80	return i != cutoffAtomList.end() ? *i : NULL;
81	}
82
83	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
84	RealType getMass() {
85	std::vector<Atom *>::iterator i;
86
87	if (!haveTotalMass) {
88	totalMass = 0;
89
90	for(Atom* atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
91	RealType mass = atom->getMass();
92	totalMass += mass;
93	}
94
95	haveTotalMass = true;
96	}
97
98	return totalMass;
99	}
100
101	void updateCOM() {
102	std::vector<Atom *>::iterator i;
103	Atom * atom;
104
105	DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_;
106	int storageLayout = data.getStorageLayout();
107
108	totalMass = getMass();
109
110	if (cutoffAtomList.size() == 1) {
111	data.position[localIndex_] = beginAtom(i)->getPos();
112	} else {
113	data.position[localIndex_] = V3Zero;
114	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
115	data.position[localIndex_] += atom->getMass() * atom->getPos();
116	}
117	data.position[localIndex_] /= totalMass;
118	}
119
120	if (storageLayout & DataStorage::dslVelocity) {
121	if (cutoffAtomList.size() == 1) {
122	data.velocity[localIndex_] = beginAtom(i)->getVel();
123	} else {
124	data.velocity[localIndex_] = V3Zero;
125	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
126	data.velocity[localIndex_] += atom->getMass() * atom->getVel();
127	}
128	data.velocity[localIndex_] /= totalMass;
129	}
130	}
131	}
132
133
134	Vector3d getPos() {
135	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
136	}
137	Vector3d getVel() {
138	return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_];
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	/**
154	* Returns the local index of this cutoffGroup
155	* @return the local index of this cutoffGroup
156	*/
157	int getLocalIndex() {
158	return localIndex_;
159	}
160
161	/**
162	* Sets the local index of this cutoffGroup
163	* @param index new index to be set
164	*/
165	void setLocalIndex(int index) {
166	localIndex_ = index;
167	}
168
169	private:
170
171	std::vector<Atom *>cutoffAtomList;
172	bool haveTotalMass;
173	RealType totalMass;
174	int globalIndex;
175
176	int localIndex_;
177	DataStoragePointer storage_;
178	SnapshotManager* snapshotMan_;
179
180	};
181	} //end namespace OpenMD
182	#endif //PRIMITIVES_CUTOFFGROUP_HPP