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() :  snapshotMan_(NULL) {

      storage_ = &Snapshot::cgData;
#ifdef IS_MPI
      iStorage_ = &Snapshot::cgIData;
      jStorage_ = &Snapshot::cgJData;
#endif
      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_;
     
      totalMass = getMass();
      
      if (cutoffAtomList.size() == 1) {
        std::cerr << "YO!\n";
        std::cerr << "atipos = " << beginAtom(i)->getPos() << "\n";
        std::cerr << "lI = " << localIndex_ << "\n";

        data.position[localIndex_] = beginAtom(i)->getPos();
        std::cerr << "YOYO!\n";
      } 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;
      }
    }


    /**
     * Returns the current position of this cutoffGroup for the outer
     * iteration over the cutoff groups.  For Force decomposition,
     * this is the position of the cutoff groups ordered by row index.
     * For serial calculations, this is just the position of the
     * cutoff group.
     */    
    Vector3d getPosI() {
#ifdef IS_MPI
      return ((snapshotMan_->getCurrentSnapshot())->*iStorage_).position[iIndex_];
#else
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];      
#endif
    }

    /**
     * Returns the current position of this cutoffGroup for the inner
     * iteration over the cutoff groups.  For Force decomposition,
     * this is the position of the cutoff groups ordered by column
     * index.  For serial calculations, this is just the position of
     * the cutoff group.
     */    
    Vector3d getPosJ() {
#ifdef IS_MPI
      return ((snapshotMan_->getCurrentSnapshot())->*jStorage_).position[jIndex_];
#else
      return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];      
#endif
    }
    
    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_;
#ifdef IS_MPI
    int iIndex_;
    int jIndex_;
    DataStoragePointer iStorage_;
    DataStoragePointer jStorage_;
#endif

  };  
} //end namespace OpenMD
#endif //PRIMITIVES_CUTOFFGROUP_HPP  
Revision:	1540
Committed:	Mon Jan 17 21:34:36 2011 UTC (14 years, 3 months ago) by gezelter
File size:	6315 byte(s)
Log Message:	changes for new parallel architecture
#	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() : snapshotMan_(NULL) {
54
55	storage_ = &Snapshot::cgData;
56	#ifdef IS_MPI
57	iStorage_ = &Snapshot::cgIData;
58	jStorage_ = &Snapshot::cgJData;
59	#endif
60	haveTotalMass = false;
61	totalMass = 0.0;
62	}
63
64	/**
65	* Sets the Snapshot Manager of this cutoffGroup
66	*/
67	void setSnapshotManager(SnapshotManager* sman) {
68	snapshotMan_ = sman;
69	}
70
71
72	void addAtom(Atom *atom) {
73	cutoffAtomList.push_back(atom);
74	}
75
76	Atom beginAtom(std::vector<Atom >::iterator & i) {
77	i = cutoffAtomList.begin();
78	return i != cutoffAtomList.end() ? *i : NULL;
79	}
80
81	Atom nextAtom(std::vector<Atom >::iterator & i) {
82	i++;
83	return i != cutoffAtomList.end() ? *i : NULL;
84	}
85
86	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
87	RealType getMass() {
88	std::vector<Atom *>::iterator i;
89	Atom * atom;
90	RealType mass;
91
92	if (!haveTotalMass) {
93	totalMass = 0;
94
95	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
96	mass = atom->getMass();
97	totalMass += mass;
98	}
99
100	haveTotalMass = true;
101	}
102
103	return totalMass;
104	}
105
106	void updateCOM() {
107	std::vector<Atom *>::iterator i;
108	Atom * atom;
109
110	DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_;
111
112	totalMass = getMass();
113
114	if (cutoffAtomList.size() == 1) {
115	std::cerr << "YO!\n";
116	std::cerr << "atipos = " << beginAtom(i)->getPos() << "\n";
117	std::cerr << "lI = " << localIndex_ << "\n";
118
119	data.position[localIndex_] = beginAtom(i)->getPos();
120	std::cerr << "YOYO!\n";
121	} else {
122	data.position[localIndex_] = V3Zero;
123	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
124	data.position[localIndex_] += atom->getMass() * atom->getPos();
125	}
126	data.position[localIndex_] /= totalMass;
127	}
128	}
129
130
131	/**
132	* Returns the current position of this cutoffGroup for the outer
133	* iteration over the cutoff groups. For Force decomposition,
134	* this is the position of the cutoff groups ordered by row index.
135	* For serial calculations, this is just the position of the
136	* cutoff group.
137	*/
138	Vector3d getPosI() {
139	#ifdef IS_MPI
140	return ((snapshotMan_->getCurrentSnapshot())->*iStorage_).position[iIndex_];
141	#else
142	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
143	#endif
144	}
145
146	/**
147	* Returns the current position of this cutoffGroup for the inner
148	* iteration over the cutoff groups. For Force decomposition,
149	* this is the position of the cutoff groups ordered by column
150	* index. For serial calculations, this is just the position of
151	* the cutoff group.
152	*/
153	Vector3d getPosJ() {
154	#ifdef IS_MPI
155	return ((snapshotMan_->getCurrentSnapshot())->*jStorage_).position[jIndex_];
156	#else
157	return ((snapshotMan_->getCurrentSnapshot())->*storage_).position[localIndex_];
158	#endif
159	}
160
161	int getNumAtom() {
162	return cutoffAtomList.size();
163	}
164
165	int getGlobalIndex() {
166	return globalIndex;
167	}
168
169	void setGlobalIndex(int id) {
170	this->globalIndex = id;
171	}
172
173	/**
174	* Returns the local index of this cutoffGroup
175	* @return the local index of this cutoffGroup
176	*/
177	int getLocalIndex() {
178	return localIndex_;
179	}
180
181	/**
182	* Sets the local index of this cutoffGroup
183	* @param index new index to be set
184	*/
185	void setLocalIndex(int index) {
186	localIndex_ = index;
187	}
188
189	private:
190
191	std::vector<Atom *>cutoffAtomList;
192	bool haveTotalMass;
193	RealType totalMass;
194	int globalIndex;
195
196	int localIndex_;
197	DataStoragePointer storage_;
198	SnapshotManager* snapshotMan_;
199	#ifdef IS_MPI
200	int iIndex_;
201	int jIndex_;
202	DataStoragePointer iStorage_;
203	DataStoragePointer jStorage_;
204	#endif
205
206	};
207	} //end namespace OpenMD
208	#endif //PRIMITIVES_CUTOFFGROUP_HPP