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]  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) {

      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;
      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 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:	1723
Committed:	Thu May 24 20:59:54 2012 UTC (13 years, 5 months ago) by gezelter
File size:	5633 byte(s)
Log Message:	Bug fixes for heat flux import
#	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] 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) {
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	Atom * atom;
87	RealType mass;
88
89	if (!haveTotalMass) {
90	totalMass = 0;
91
92	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
93	mass = atom->getMass();
94	totalMass += mass;
95	}
96
97	haveTotalMass = true;
98	}
99
100	return totalMass;
101	}
102
103	void updateCOM() {
104	std::vector<Atom *>::iterator i;
105	Atom * atom;
106
107	DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_;
108	int storageLayout = data.getStorageLayout();
109
110	totalMass = getMass();
111
112	if (cutoffAtomList.size() == 1) {
113	data.position[localIndex_] = beginAtom(i)->getPos();
114	} else {
115	data.position[localIndex_] = V3Zero;
116	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
117	data.position[localIndex_] += atom->getMass() * atom->getPos();
118	}
119	data.position[localIndex_] /= totalMass;
120	}
121
122	if (storageLayout & DataStorage::dslVelocity) {
123	if (cutoffAtomList.size() == 1) {
124	data.velocity[localIndex_] = beginAtom(i)->getVel();
125	} else {
126	data.velocity[localIndex_] = V3Zero;
127	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
128	data.velocity[localIndex_] += atom->getMass() * atom->getVel();
129	}
130	data.velocity[localIndex_] /= totalMass;
131	}
132	}
133	}
134
135
136	Vector3d getPos() {
137	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
138	}
139	Vector3d getVel() {
140	return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_];
141	}
142
143	int getNumAtom() {
144	return cutoffAtomList.size();
145	}
146
147	int getGlobalIndex() {
148	return globalIndex;
149	}
150
151	void setGlobalIndex(int id) {
152	this->globalIndex = id;
153	}
154
155	/**
156	* Returns the local index of this cutoffGroup
157	* @return the local index of this cutoffGroup
158	*/
159	int getLocalIndex() {
160	return localIndex_;
161	}
162
163	/**
164	* Sets the local index of this cutoffGroup
165	* @param index new index to be set
166	*/
167	void setLocalIndex(int index) {
168	localIndex_ = index;
169	}
170
171	private:
172
173	std::vector<Atom *>cutoffAtomList;
174	bool haveTotalMass;
175	RealType totalMass;
176	int globalIndex;
177
178	int localIndex_;
179	DataStoragePointer storage_;
180	SnapshotManager* snapshotMan_;
181
182	};
183	} //end namespace OpenMD
184	#endif //PRIMITIVES_CUTOFFGROUP_HPP