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
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41
42			#ifndef PRIMITIVES_CUTOFFGROUP_HPP
43
44			#define PRIMITIVES_CUTOFFGROUP_HPP
45
46	tim	3	#include "primitives/Atom.hpp"
47	gezelter	246	#include "math/Vector3.hpp"
48	gezelter	2
49	gezelter	1390	namespace OpenMD {
50	gezelter	507	class CutoffGroup {
51			public:
52	gezelter	1211
53	gezelter	1540	CutoffGroup() : snapshotMan_(NULL) {
54
55			storage_ = &Snapshot::cgData;
56			#ifdef IS_MPI
57			iStorage_ = &Snapshot::cgIData;
58			jStorage_ = &Snapshot::cgJData;
59			#endif
60	gezelter	507	haveTotalMass = false;
61			totalMass = 0.0;
62			}
63	gezelter	1211
64	gezelter	1540	/**
65			* Sets the Snapshot Manager of this cutoffGroup
66			*/
67			void setSnapshotManager(SnapshotManager* sman) {
68			snapshotMan_ = sman;
69			}
70
71
72	gezelter	507	void addAtom(Atom *atom) {
73			cutoffAtomList.push_back(atom);
74			}
75	gezelter	1211
76	gezelter	507	Atom beginAtom(std::vector<Atom >::iterator & i) {
77			i = cutoffAtomList.begin();
78			return i != cutoffAtomList.end() ? *i : NULL;
79			}
80	gezelter	1211
81	gezelter	507	Atom nextAtom(std::vector<Atom >::iterator & i) {
82			i++;
83			return i != cutoffAtomList.end() ? *i : NULL;
84			}
85	gezelter	2
86	gezelter	507	std::vector<Atom*> getAtoms() { return cutoffAtomList; }
87	tim	963	RealType getMass() {
88	gezelter	507	std::vector<Atom *>::iterator i;
89			Atom * atom;
90	tim	963	RealType mass;
91	gezelter	1211
92	gezelter	507	if (!haveTotalMass) {
93			totalMass = 0;
94	gezelter	1211
95	gezelter	507	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
96			mass = atom->getMass();
97			totalMass += mass;
98			}
99	gezelter	1211
100	gezelter	507	haveTotalMass = true;
101			}
102	gezelter	1211
103	gezelter	507	return totalMass;
104			}
105	gezelter	1211
106	gezelter	1540	void updateCOM() {
107	gezelter	507	std::vector<Atom *>::iterator i;
108			Atom * atom;
109	gezelter	1540
110			DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_;
111
112	gezelter	507	totalMass = getMass();
113	gezelter	1211
114	gezelter	507	if (cutoffAtomList.size() == 1) {
115	gezelter	1540	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	gezelter	507	} else {
122	gezelter	1540	data.position[localIndex_] = V3Zero;
123	gezelter	507	for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
124	gezelter	1540	data.position[localIndex_] += atom->getMass() * atom->getPos();
125			}
126			data.position[localIndex_] /= totalMass;
127	gezelter	507	}
128			}
129	gezelter	1540
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	gezelter	1211
161	gezelter	507	int getNumAtom() {
162			return cutoffAtomList.size();
163			}
164	gezelter	1211
165	gezelter	507	int getGlobalIndex() {
166			return globalIndex;
167			}
168	gezelter	1211
169	gezelter	507	void setGlobalIndex(int id) {
170			this->globalIndex = id;
171			}
172	gezelter	1540
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	gezelter	1211
189	gezelter	507	private:
190	gezelter	1211
191	gezelter	507	std::vector<Atom *>cutoffAtomList;
192			bool haveTotalMass;
193	tim	963	RealType totalMass;
194	gezelter	1540	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	gezelter	1211	};
207	gezelter	1390	} //end namespace OpenMD
208	gezelter	246	#endif //PRIMITIVES_CUTOFFGROUP_HPP