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 (12 years, 11 months ago) by gezelter
File size:	5633 byte(s)
Log Message:	Bug fixes for heat flux import
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			#ifndef PRIMITIVES_CUTOFFGROUP_HPP
44
45			#define PRIMITIVES_CUTOFFGROUP_HPP
46
47	tim	3	#include "primitives/Atom.hpp"
48	gezelter	246	#include "math/Vector3.hpp"
49	gezelter	2
50	gezelter	1390	namespace OpenMD {
51	gezelter	507	class CutoffGroup {
52			public:
53	gezelter	1211
54	gezelter	1540	CutoffGroup() : snapshotMan_(NULL) {
55
56			storage_ = &Snapshot::cgData;
57	gezelter	507	haveTotalMass = false;
58			totalMass = 0.0;
59			}
60	gezelter	1211
61	gezelter	1540	/**
62			* Sets the Snapshot Manager of this cutoffGroup
63			*/
64			void setSnapshotManager(SnapshotManager* sman) {
65			snapshotMan_ = sman;
66			}
67
68
69	gezelter	507	void addAtom(Atom *atom) {
70			cutoffAtomList.push_back(atom);
71			}
72	gezelter	1211
73	gezelter	507	Atom beginAtom(std::vector<Atom >::iterator & i) {
74			i = cutoffAtomList.begin();
75			return i != cutoffAtomList.end() ? *i : NULL;
76			}
77	gezelter	1211
78	gezelter	507	Atom nextAtom(std::vector<Atom >::iterator & i) {
79			i++;
80			return i != cutoffAtomList.end() ? *i : NULL;
81			}
82	gezelter	2
83	gezelter	507	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
84	tim	963	RealType getMass() {
85	gezelter	507	std::vector<Atom *>::iterator i;
86			Atom * atom;
87	tim	963	RealType mass;
88	gezelter	1211
89	gezelter	507	if (!haveTotalMass) {
90			totalMass = 0;
91	gezelter	1211
92	gezelter	507	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
93			mass = atom->getMass();
94			totalMass += mass;
95			}
96	gezelter	1211
97	gezelter	507	haveTotalMass = true;
98			}
99	gezelter	1211
100	gezelter	507	return totalMass;
101			}
102	gezelter	1211
103	gezelter	1540	void updateCOM() {
104	gezelter	507	std::vector<Atom *>::iterator i;
105			Atom * atom;
106	gezelter	1540
107			DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_;
108	gezelter	1723	int storageLayout = data.getStorageLayout();
109	gezelter	1540
110	gezelter	507	totalMass = getMass();
111	gezelter	1211
112	gezelter	507	if (cutoffAtomList.size() == 1) {
113	gezelter	1540	data.position[localIndex_] = beginAtom(i)->getPos();
114	gezelter	507	} else {
115	gezelter	1540	data.position[localIndex_] = V3Zero;
116	gezelter	507	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
117	gezelter	1540	data.position[localIndex_] += atom->getMass() * atom->getPos();
118			}
119			data.position[localIndex_] /= totalMass;
120	gezelter	507	}
121	gezelter	1723
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	gezelter	507	}
134	gezelter	1540
135
136	gezelter	1551	Vector3d getPos() {
137	gezelter	1540	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
138			}
139	gezelter	1723	Vector3d getVel() {
140			return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_];
141			}
142	gezelter	1211
143	gezelter	507	int getNumAtom() {
144			return cutoffAtomList.size();
145			}
146	gezelter	1211
147	gezelter	507	int getGlobalIndex() {
148			return globalIndex;
149			}
150	gezelter	1211
151	gezelter	507	void setGlobalIndex(int id) {
152			this->globalIndex = id;
153			}
154	gezelter	1540
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	gezelter	1211
171	gezelter	507	private:
172	gezelter	1211
173	gezelter	507	std::vector<Atom *>cutoffAtomList;
174			bool haveTotalMass;
175	tim	963	RealType totalMass;
176	gezelter	1540	int globalIndex;
177
178			int localIndex_;
179			DataStoragePointer storage_;
180			SnapshotManager* snapshotMan_;
181
182	gezelter	1211	};
183	gezelter	1390	} //end namespace OpenMD
184	gezelter	246	#endif //PRIMITIVES_CUTOFFGROUP_HPP