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() {
      
      if (!haveTotalMass) {
        totalMass = 0.0;
        
        std::vector<Atom *>::iterator i;
        for(Atom* atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
          RealType mass = atom->getMass();
          totalMass += mass;
        }
        
        haveTotalMass = true;
      }
      
      return totalMass;
    }
    
    void updateCOM() {

      DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_;
      bool needsVel = (data.getStorageLayout() & DataStorage::dslVelocity);

      if (cutoffAtomList.size() == 1) {
        data.position[localIndex_] = cutoffAtomList[0]->getPos();
        if (needsVel)
          data.velocity[localIndex_] = cutoffAtomList[0]->getVel();
      } else {
        std::vector<Atom *>::iterator i;
        Atom * atom;
        RealType totalMass = getMass();
        data.position[localIndex_] = V3Zero;
        if (needsVel) data.velocity[localIndex_] = V3Zero;
        
        for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
          data.position[localIndex_] += atom->getMass() * atom->getPos();
          if (needsVel)
            data.velocity[localIndex_] += atom->getMass() * atom->getVel();
        }     
        data.position[localIndex_] /= totalMass;
        if (needsVel) 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:	2057
Committed:	Tue Mar 3 15:22:26 2015 UTC (10 years, 2 months ago) by gezelter
File size:	5553 byte(s)
Log Message:	Performance improvements, Removed CutoffPolicy
#	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
86	if (!haveTotalMass) {
87	totalMass = 0.0;
88
89	std::vector<Atom *>::iterator i;
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
103	DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_;
104	bool needsVel = (data.getStorageLayout() & DataStorage::dslVelocity);
105
106	if (cutoffAtomList.size() == 1) {
107	data.position[localIndex_] = cutoffAtomList[0]->getPos();
108	if (needsVel)
109	data.velocity[localIndex_] = cutoffAtomList[0]->getVel();
110	} else {
111	std::vector<Atom *>::iterator i;
112	Atom * atom;
113	RealType totalMass = getMass();
114	data.position[localIndex_] = V3Zero;
115	if (needsVel) data.velocity[localIndex_] = V3Zero;
116
117	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
118	data.position[localIndex_] += atom->getMass() * atom->getPos();
119	if (needsVel)
120	data.velocity[localIndex_] += atom->getMass() * atom->getVel();
121	}
122	data.position[localIndex_] /= totalMass;
123	if (needsVel) data.velocity[localIndex_] /= totalMass;
124	}
125	}
126
127
128	Vector3d getPos() {
129	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
130	}
131	Vector3d getVel() {
132	return ((snapshotMan_->getCurrentSnapshot())->*storage_).velocity[localIndex_];
133	}
134
135	int getNumAtom() {
136	return cutoffAtomList.size();
137	}
138
139	int getGlobalIndex() {
140	return globalIndex;
141	}
142
143	void setGlobalIndex(int id) {
144	this->globalIndex = id;
145	}
146
147	/**
148	* Returns the local index of this cutoffGroup
149	* @return the local index of this cutoffGroup
150	*/
151	int getLocalIndex() {
152	return localIndex_;
153	}
154
155	/**
156	* Sets the local index of this cutoffGroup
157	* @param index new index to be set
158	*/
159	void setLocalIndex(int index) {
160	localIndex_ = index;
161	}
162
163	private:
164
165	std::vector<Atom *>cutoffAtomList;
166	bool haveTotalMass;
167	RealType totalMass;
168	int globalIndex;
169
170	int localIndex_;
171	DataStoragePointer storage_;
172	SnapshotManager* snapshotMan_;
173
174	};
175	} //end namespace OpenMD
176	#endif //PRIMITIVES_CUTOFFGROUP_HPP