src/selection/DistanceFinder.cpp

/*
 * Copyright (c) 2005, 2010 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).
 */

#include "selection/DistanceFinder.hpp"
#include "primitives/Molecule.hpp"
#ifdef IS_MPI
#include <mpi.h>
#endif

namespace OpenMD {
  
  DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {
    
    nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
    stuntdoubles_.resize(nStuntDoubles_);
    
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::AtomIterator ai;
    Atom* atom;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
    
    
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
        
      for(atom = mol->beginAtom(ai); atom != NULL; 
          atom = mol->nextAtom(ai)) {
        stuntdoubles_[atom->getGlobalIndex()] = atom;
      }

      for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
           rb = mol->nextRigidBody(rbIter)) {
        stuntdoubles_[rb->getGlobalIndex()] = rb;
      }
    }
  }

  OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) {
    StuntDouble * center;
    Vector3d centerPos;
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    OpenMDBitSet bsResult(nStuntDoubles_);   
    assert(bsResult.size() == bs.size());

#ifdef IS_MPI
    int mol;
    int proc;
    RealType data[3];
    int worldRank = MPI::COMM_WORLD.Get_rank();
#endif
 
    for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
      if (stuntdoubles_[j]->isRigidBody()) {
        RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
        rb->updateAtoms();
      }
    }
       
    OpenMDBitSet bsTemp(nStuntDoubles_);
    bsTemp = bs;
    bsTemp.parallelReduce();

    for (int i = bsTemp.firstOnBit(); i != -1; i = bsTemp.nextOnBit(i)) {

      // Now, if we own stuntdouble i, we can use the position, but in
      // parallel, we'll need to let everyone else know what that
      // position is!

#ifdef IS_MPI
      mol = info_->getGlobalMolMembership(i);
      proc = info_->getMolToProc(mol);
     
      if (proc == worldRank) {
        center = stuntdoubles_[i];
        centerPos = center->getPos();
        data[0] = centerPos.x();
        data[1] = centerPos.y();
        data[2] = centerPos.z();          
        MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
      } else {
        MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
        centerPos = Vector3d(data);
      }
#else
      center = stuntdoubles_[i];
      centerPos = center->getPos();
#endif
      
      for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
        Vector3d r =centerPos - stuntdoubles_[j]->getPos();
        currSnapshot->wrapVector(r);
        if (r.length() <= distance) {
          bsResult.setBitOn(j);
        }
      }
    }
    return bsResult;
  }


OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance, int frame ) {
    StuntDouble * center;
    Vector3d centerPos;
    Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
    OpenMDBitSet bsResult(nStuntDoubles_);   
    assert(bsResult.size() == bs.size());

#ifdef IS_MPI
    int mol;
    int proc;
    RealType data[3];
    int worldRank = MPI::COMM_WORLD.Get_rank();
#endif
 
    for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
      if (stuntdoubles_[j]->isRigidBody()) {
        RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
        rb->updateAtoms(frame);
      }
    }
       
    OpenMDBitSet bsTemp(nStuntDoubles_);
    bsTemp = bs;
    bsTemp.parallelReduce();

    for (int i = bsTemp.firstOnBit(); i != -1; i = bsTemp.nextOnBit(i)) {

      // Now, if we own stuntdouble i, we can use the position, but in
      // parallel, we'll need to let everyone else know what that
      // position is!

#ifdef IS_MPI
      mol = info_->getGlobalMolMembership(i);
      proc = info_->getMolToProc(mol);
     
      if (proc == worldRank) {
        center = stuntdoubles_[i];
        centerPos = center->getPos(frame);
        data[0] = centerPos.x();
        data[1] = centerPos.y();
        data[2] = centerPos.z();          
        MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
      } else {
        MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
        centerPos = Vector3d(data);
      }
#else
      center = stuntdoubles_[i];
      centerPos = center->getPos(frame);
#endif
      
      for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
        Vector3d r =centerPos - stuntdoubles_[j]->getPos(frame);
        currSnapshot->wrapVector(r);
        if (r.length() <= distance) {
          bsResult.setBitOn(j);
        }
      }
    }
    return bsResult;
  }
}
Revision:	1816
Committed:	Fri Dec 7 18:33:33 2012 UTC (12 years, 10 months ago) by gezelter
File size:	6737 byte(s)
Log Message:	Updated selections to be frame-addressable (to support selection correlation function).
#	User	Rev	Content
1	tim	295	/*
2	chuckv	1434	* Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
3	tim	295	*
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	tim	295	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	295	* 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	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	295	*/
42
43			#include "selection/DistanceFinder.hpp"
44			#include "primitives/Molecule.hpp"
45	gezelter	1802	#ifdef IS_MPI
46			#include <mpi.h>
47			#endif
48
49	gezelter	1390	namespace OpenMD {
50	gezelter	1811
51	gezelter	507	DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {
52	gezelter	1811
53	tim	295	nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
54			stuntdoubles_.resize(nStuntDoubles_);
55
56			SimInfo::MoleculeIterator mi;
57			Molecule* mol;
58			Molecule::AtomIterator ai;
59			Atom* atom;
60			Molecule::RigidBodyIterator rbIter;
61			RigidBody* rb;
62
63	gezelter	1811
64	gezelter	1801	for (mol = info_->beginMolecule(mi); mol != NULL;
65			mol = info_->nextMolecule(mi)) {
66	tim	295
67	gezelter	1801	for(atom = mol->beginAtom(ai); atom != NULL;
68			atom = mol->nextAtom(ai)) {
69	gezelter	507	stuntdoubles_[atom->getGlobalIndex()] = atom;
70			}
71	tim	295
72	gezelter	1801	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
73			rb = mol->nextRigidBody(rbIter)) {
74	gezelter	507	stuntdoubles_[rb->getGlobalIndex()] = rb;
75			}
76	gezelter	1801	}
77	gezelter	507	}
78	tim	295
79	gezelter	1390	OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) {
80	tim	295	StuntDouble * center;
81			Vector3d centerPos;
82			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
83	gezelter	1802	OpenMDBitSet bsResult(nStuntDoubles_);
84	tim	295	assert(bsResult.size() == bs.size());
85	gezelter	1802
86			#ifdef IS_MPI
87			int mol;
88			int proc;
89			RealType data[3];
90			int worldRank = MPI::COMM_WORLD.Get_rank();
91			#endif
92
93	gezelter	1782	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
94	chuckv	1434	if (stuntdoubles_[j]->isRigidBody()) {
95			RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
96			rb->updateAtoms();
97			}
98			}
99	gezelter	1802
100			OpenMDBitSet bsTemp(nStuntDoubles_);
101			bsTemp = bs;
102			bsTemp.parallelReduce();
103	gezelter	1801
104	gezelter	1802	for (int i = bsTemp.firstOnBit(); i != -1; i = bsTemp.nextOnBit(i)) {
105
106			// Now, if we own stuntdouble i, we can use the position, but in
107			// parallel, we'll need to let everyone else know what that
108			// position is!
109
110			#ifdef IS_MPI
111			mol = info_->getGlobalMolMembership(i);
112			proc = info_->getMolToProc(mol);
113
114			if (proc == worldRank) {
115			center = stuntdoubles_[i];
116			centerPos = center->getPos();
117			data[0] = centerPos.x();
118			data[1] = centerPos.y();
119			data[2] = centerPos.z();
120			MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
121			} else {
122			MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
123			centerPos = Vector3d(data);
124			}
125			#else
126	gezelter	507	center = stuntdoubles_[i];
127			centerPos = center->getPos();
128	gezelter	1802	#endif
129
130	gezelter	1782	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
131	gezelter	507	Vector3d r =centerPos - stuntdoubles_[j]->getPos();
132			currSnapshot->wrapVector(r);
133			if (r.length() <= distance) {
134			bsResult.setBitOn(j);
135			}
136			}
137	tim	295	}
138			return bsResult;
139	gezelter	507	}
140	gezelter	1816
141
142			OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance, int frame ) {
143			StuntDouble * center;
144			Vector3d centerPos;
145			Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
146			OpenMDBitSet bsResult(nStuntDoubles_);
147			assert(bsResult.size() == bs.size());
148
149			#ifdef IS_MPI
150			int mol;
151			int proc;
152			RealType data[3];
153			int worldRank = MPI::COMM_WORLD.Get_rank();
154			#endif
155
156			for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
157			if (stuntdoubles_[j]->isRigidBody()) {
158			RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
159			rb->updateAtoms(frame);
160			}
161			}
162
163			OpenMDBitSet bsTemp(nStuntDoubles_);
164			bsTemp = bs;
165			bsTemp.parallelReduce();
166
167			for (int i = bsTemp.firstOnBit(); i != -1; i = bsTemp.nextOnBit(i)) {
168
169			// Now, if we own stuntdouble i, we can use the position, but in
170			// parallel, we'll need to let everyone else know what that
171			// position is!
172
173			#ifdef IS_MPI
174			mol = info_->getGlobalMolMembership(i);
175			proc = info_->getMolToProc(mol);
176
177			if (proc == worldRank) {
178			center = stuntdoubles_[i];
179			centerPos = center->getPos(frame);
180			data[0] = centerPos.x();
181			data[1] = centerPos.y();
182			data[2] = centerPos.z();
183			MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
184			} else {
185			MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
186			centerPos = Vector3d(data);
187			}
188			#else
189			center = stuntdoubles_[i];
190			centerPos = center->getPos(frame);
191			#endif
192
193			for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
194			Vector3d r =centerPos - stuntdoubles_[j]->getPos(frame);
195			currSnapshot->wrapVector(r);
196			if (r.length() <= distance) {
197			bsResult.setBitOn(j);
198			}
199			}
200			}
201			return bsResult;
202			}
203	tim	295	}