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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#ifdef IS_MPI
#include <mpi.h>
#endif

#include "selection/DistanceFinder.hpp"
#include "primitives/Molecule.hpp"

namespace OpenMD {
  
  DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {
    nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies());
    nObjects_.push_back(info_->getNGlobalBonds());
    nObjects_.push_back(info_->getNGlobalBends());
    nObjects_.push_back(info_->getNGlobalTorsions());
    nObjects_.push_back(info_->getNGlobalInversions());
    nObjects_.push_back(info_->getNGlobalMolecules());

    stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
    bonds_.resize(nObjects_[BOND]);
    bends_.resize(nObjects_[BEND]);
    torsions_.resize(nObjects_[TORSION]);
    inversions_.resize(nObjects_[INVERSION]);
    molecules_.resize(nObjects_[MOLECULE]);
    
    SimInfo::MoleculeIterator mi;
    Molecule::AtomIterator ai;
    Molecule::RigidBodyIterator rbIter;
    Molecule::BondIterator bondIter;
    Molecule::BendIterator bendIter;
    Molecule::TorsionIterator torsionIter;
    Molecule::InversionIterator inversionIter;

    Molecule* mol;
    Atom* atom;
    RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    Inversion* inversion;    
    
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {

      molecules_[mol->getGlobalIndex()] = mol;
      
      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;
      }
      for (bond = mol->beginBond(bondIter); bond != NULL; 
           bond = mol->nextBond(bondIter)) {
        bonds_[bond->getGlobalIndex()] = bond;
      }   
      for (bend = mol->beginBend(bendIter); bend != NULL; 
           bend = mol->nextBend(bendIter)) {
        bends_[bend->getGlobalIndex()] = bend;
      }   
      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; 
           torsion = mol->nextTorsion(torsionIter)) {
        torsions_[torsion->getGlobalIndex()] = torsion;
      }   
      for (inversion = mol->beginInversion(inversionIter); inversion != NULL; 
           inversion = mol->nextInversion(inversionIter)) {
        inversions_[inversion->getGlobalIndex()] = inversion;
      }   

    }
  }

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

#ifdef IS_MPI
    int mol;
    int proc;
    RealType data[3];
    int worldRank;
    MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
#endif
 
    for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
      if (stuntdoubles_[j]->isRigidBody()) {
        RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
        rb->updateAtoms();
      }
    }
            
    SelectionSet bsTemp(nObjects_);
    bsTemp = bs;
    bsTemp.parallelReduce();

    for (int i = bsTemp.bitsets_[STUNTDOUBLE].firstOnBit(); i != -1; 
         i = bsTemp.bitsets_[STUNTDOUBLE].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_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
      } else {
        MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
        centerPos = Vector3d(data);
      }
#else
      center = stuntdoubles_[i];
      centerPos = center->getPos();
#endif
      
      for (unsigned int j = 0; j < molecules_.size(); ++j) {
        Vector3d r =centerPos - molecules_[j]->getCom();
        currSnapshot->wrapVector(r);
        if (r.length() <= distance) {
          bsResult.bitsets_[MOLECULE].setBitOn(j);
        }
      }
      for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
        Vector3d r =centerPos - stuntdoubles_[j]->getPos();
        currSnapshot->wrapVector(r);
        if (r.length() <= distance) {
          bsResult.bitsets_[STUNTDOUBLE].setBitOn(j);
        }
      }
      for (unsigned int j = 0; j < bonds_.size(); ++j) {
        Vector3d loc = bonds_[j]->getAtomA()->getPos();
        loc += bonds_[j]->getAtomB()->getPos();
        loc = loc / 2.0;
        Vector3d r = centerPos - loc;
        currSnapshot->wrapVector(r);
        if (r.length() <= distance) {
          bsResult.bitsets_[BOND].setBitOn(j);
        }
      }
      for (unsigned int j = 0; j < bends_.size(); ++j) {
        Vector3d loc = bends_[j]->getAtomA()->getPos();
        loc += bends_[j]->getAtomB()->getPos();
        loc += bends_[j]->getAtomC()->getPos();
        loc = loc / 3.0;
        Vector3d r = centerPos - loc;
        currSnapshot->wrapVector(r);
        if (r.length() <= distance) {
          bsResult.bitsets_[BEND].setBitOn(j);
        }
      }
      for (unsigned int j = 0; j < torsions_.size(); ++j) {
        Vector3d loc = torsions_[j]->getAtomA()->getPos();
        loc += torsions_[j]->getAtomB()->getPos();
        loc += torsions_[j]->getAtomC()->getPos();
        loc += torsions_[j]->getAtomD()->getPos();
        loc = loc / 4.0;
        Vector3d r = centerPos - loc;
        currSnapshot->wrapVector(r);
        if (r.length() <= distance) {
          bsResult.bitsets_[TORSION].setBitOn(j);
        }
      }
      for (unsigned int j = 0; j < inversions_.size(); ++j) {
        Vector3d loc = inversions_[j]->getAtomA()->getPos();
        loc += inversions_[j]->getAtomB()->getPos();
        loc += inversions_[j]->getAtomC()->getPos();
        loc += inversions_[j]->getAtomD()->getPos();
        loc = loc / 4.0;
        Vector3d r = centerPos - loc;
        currSnapshot->wrapVector(r);
        if (r.length() <= distance) {
          bsResult.bitsets_[INVERSION].setBitOn(j);
        }
      }
    }
    return bsResult;
  }
  
  
  SelectionSet DistanceFinder::find(const SelectionSet& bs, RealType distance, int frame ) {
    StuntDouble * center;
    Vector3d centerPos;
    Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
    SelectionSet bsResult(nObjects_);   
    assert(bsResult.size() == bs.size());

#ifdef IS_MPI
    int mol;
    int proc;
    RealType data[3];
    int worldRank;
    MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
#endif
 
    for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
      if (stuntdoubles_[j]->isRigidBody()) {
        RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
        rb->updateAtoms(frame);
      }
    }
       
    SelectionSet bsTemp(nObjects_);
    bsTemp = bs;
    bsTemp.parallelReduce();

    for (int i = bsTemp.bitsets_[STUNTDOUBLE].firstOnBit(); i != -1; 
         i = bsTemp.bitsets_[STUNTDOUBLE].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_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
      } else {
        MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
        centerPos = Vector3d(data);
      }
#else
      center = stuntdoubles_[i];
      centerPos = center->getPos(frame);
#endif
      for (unsigned int j = 0; j < molecules_.size(); ++j) {
        Vector3d r =centerPos - molecules_[j]->getCom(frame);
        currSnapshot->wrapVector(r);
        if (r.length() <= distance) {
          bsResult.bitsets_[MOLECULE].setBitOn(j);
        }
      }
      
      for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
        Vector3d r =centerPos - stuntdoubles_[j]->getPos(frame);
        currSnapshot->wrapVector(r);
        if (r.length() <= distance) {
          bsResult.bitsets_[STUNTDOUBLE].setBitOn(j);
        }
      }
      for (unsigned int j = 0; j < bonds_.size(); ++j) {       
        Vector3d loc = bonds_[j]->getAtomA()->getPos(frame);
        loc += bonds_[j]->getAtomB()->getPos(frame);
        loc = loc / 2.0;
        Vector3d r = centerPos - loc;
        currSnapshot->wrapVector(r);
        if (r.length() <= distance) {
          bsResult.bitsets_[BOND].setBitOn(j);
        }
      }
      for (unsigned int j = 0; j < bends_.size(); ++j) {
        Vector3d loc = bends_[j]->getAtomA()->getPos(frame);
        loc += bends_[j]->getAtomB()->getPos(frame);
        loc += bends_[j]->getAtomC()->getPos(frame);
        loc = loc / 3.0;
        Vector3d r = centerPos - loc;
        currSnapshot->wrapVector(r);
        if (r.length() <= distance) {
          bsResult.bitsets_[BEND].setBitOn(j);
        }
      }
      for (unsigned int j = 0; j < torsions_.size(); ++j) {
        Vector3d loc = torsions_[j]->getAtomA()->getPos(frame);
        loc += torsions_[j]->getAtomB()->getPos(frame);
        loc += torsions_[j]->getAtomC()->getPos(frame);
        loc += torsions_[j]->getAtomD()->getPos(frame);
        loc = loc / 4.0;
        Vector3d r = centerPos - loc;
        currSnapshot->wrapVector(r);
        if (r.length() <= distance) {
          bsResult.bitsets_[TORSION].setBitOn(j);
        }
      }
      for (unsigned int j = 0; j < inversions_.size(); ++j) {
        Vector3d loc = inversions_[j]->getAtomA()->getPos(frame);
        loc += inversions_[j]->getAtomB()->getPos(frame);
        loc += inversions_[j]->getAtomC()->getPos(frame);
        loc += inversions_[j]->getAtomD()->getPos(frame);
        loc = loc / 4.0;
        Vector3d r = centerPos - loc;
        currSnapshot->wrapVector(r);
        if (r.length() <= distance) {
          bsResult.bitsets_[INVERSION].setBitOn(j);
        }
      }
    }
    return bsResult;
  }
}
Revision:	2052
Committed:	Fri Jan 9 19:06:35 2015 UTC (10 years, 3 months ago) by gezelter
File size:	12178 byte(s)
Log Message:	Updating Hydrogen Bonding structures, and selection syntax to include molecule selections:
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	gezelter	1802	#ifdef IS_MPI
44			#include <mpi.h>
45			#endif
46
47	gezelter	1938	#include "selection/DistanceFinder.hpp"
48			#include "primitives/Molecule.hpp"
49
50	gezelter	1390	namespace OpenMD {
51	gezelter	1811
52	gezelter	507	DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {
53	gezelter	1953	nObjects_.push_back(info_->getNGlobalAtoms()+info_->getNGlobalRigidBodies());
54			nObjects_.push_back(info_->getNGlobalBonds());
55			nObjects_.push_back(info_->getNGlobalBends());
56			nObjects_.push_back(info_->getNGlobalTorsions());
57			nObjects_.push_back(info_->getNGlobalInversions());
58	gezelter	2052	nObjects_.push_back(info_->getNGlobalMolecules());
59	gezelter	1953
60			stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
61			bonds_.resize(nObjects_[BOND]);
62			bends_.resize(nObjects_[BEND]);
63			torsions_.resize(nObjects_[TORSION]);
64			inversions_.resize(nObjects_[INVERSION]);
65	gezelter	2052	molecules_.resize(nObjects_[MOLECULE]);
66	gezelter	1811
67	tim	295	SimInfo::MoleculeIterator mi;
68	gezelter	1953	Molecule::AtomIterator ai;
69			Molecule::RigidBodyIterator rbIter;
70			Molecule::BondIterator bondIter;
71			Molecule::BendIterator bendIter;
72			Molecule::TorsionIterator torsionIter;
73			Molecule::InversionIterator inversionIter;
74
75	tim	295	Molecule* mol;
76			Atom* atom;
77			RigidBody* rb;
78	gezelter	1953	Bond* bond;
79			Bend* bend;
80			Torsion* torsion;
81			Inversion* inversion;
82	tim	295
83	gezelter	1801	for (mol = info_->beginMolecule(mi); mol != NULL;
84			mol = info_->nextMolecule(mi)) {
85	gezelter	2052
86			molecules_[mol->getGlobalIndex()] = mol;
87
88	gezelter	1801	for(atom = mol->beginAtom(ai); atom != NULL;
89			atom = mol->nextAtom(ai)) {
90	gezelter	507	stuntdoubles_[atom->getGlobalIndex()] = atom;
91			}
92	gezelter	1801	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
93			rb = mol->nextRigidBody(rbIter)) {
94	gezelter	507	stuntdoubles_[rb->getGlobalIndex()] = rb;
95			}
96	gezelter	1953	for (bond = mol->beginBond(bondIter); bond != NULL;
97			bond = mol->nextBond(bondIter)) {
98			bonds_[bond->getGlobalIndex()] = bond;
99			}
100			for (bend = mol->beginBend(bendIter); bend != NULL;
101			bend = mol->nextBend(bendIter)) {
102			bends_[bend->getGlobalIndex()] = bend;
103			}
104			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
105			torsion = mol->nextTorsion(torsionIter)) {
106			torsions_[torsion->getGlobalIndex()] = torsion;
107			}
108			for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
109			inversion = mol->nextInversion(inversionIter)) {
110			inversions_[inversion->getGlobalIndex()] = inversion;
111			}
112
113	gezelter	1801	}
114	gezelter	507	}
115	tim	295
116	gezelter	1953	SelectionSet DistanceFinder::find(const SelectionSet& bs, RealType distance) {
117	tim	295	StuntDouble * center;
118			Vector3d centerPos;
119			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
120	gezelter	1953	SelectionSet bsResult(nObjects_);
121	tim	295	assert(bsResult.size() == bs.size());
122	gezelter	1802
123			#ifdef IS_MPI
124			int mol;
125			int proc;
126			RealType data[3];
127	gezelter	1969	int worldRank;
128			MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
129	gezelter	1802	#endif
130
131	gezelter	1782	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
132	chuckv	1434	if (stuntdoubles_[j]->isRigidBody()) {
133			RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
134			rb->updateAtoms();
135			}
136			}
137	gezelter	1953
138			SelectionSet bsTemp(nObjects_);
139	gezelter	1802	bsTemp = bs;
140			bsTemp.parallelReduce();
141	gezelter	1801
142	gezelter	1953	for (int i = bsTemp.bitsets_[STUNTDOUBLE].firstOnBit(); i != -1;
143			i = bsTemp.bitsets_[STUNTDOUBLE].nextOnBit(i)) {
144
145	gezelter	1802	// Now, if we own stuntdouble i, we can use the position, but in
146			// parallel, we'll need to let everyone else know what that
147			// position is!
148	gezelter	1953
149	gezelter	1802	#ifdef IS_MPI
150			mol = info_->getGlobalMolMembership(i);
151			proc = info_->getMolToProc(mol);
152
153			if (proc == worldRank) {
154			center = stuntdoubles_[i];
155			centerPos = center->getPos();
156			data[0] = centerPos.x();
157			data[1] = centerPos.y();
158			data[2] = centerPos.z();
159	gezelter	1969	MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
160	gezelter	1802	} else {
161	gezelter	1969	MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
162	gezelter	1802	centerPos = Vector3d(data);
163			}
164			#else
165	gezelter	507	center = stuntdoubles_[i];
166			centerPos = center->getPos();
167	gezelter	1802	#endif
168
169	gezelter	2052	for (unsigned int j = 0; j < molecules_.size(); ++j) {
170			Vector3d r =centerPos - molecules_[j]->getCom();
171			currSnapshot->wrapVector(r);
172			if (r.length() <= distance) {
173			bsResult.bitsets_[MOLECULE].setBitOn(j);
174			}
175			}
176	gezelter	1782	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
177	gezelter	507	Vector3d r =centerPos - stuntdoubles_[j]->getPos();
178			currSnapshot->wrapVector(r);
179			if (r.length() <= distance) {
180	gezelter	1953	bsResult.bitsets_[STUNTDOUBLE].setBitOn(j);
181	gezelter	507	}
182			}
183	gezelter	1953	for (unsigned int j = 0; j < bonds_.size(); ++j) {
184			Vector3d loc = bonds_[j]->getAtomA()->getPos();
185			loc += bonds_[j]->getAtomB()->getPos();
186			loc = loc / 2.0;
187			Vector3d r = centerPos - loc;
188			currSnapshot->wrapVector(r);
189			if (r.length() <= distance) {
190			bsResult.bitsets_[BOND].setBitOn(j);
191			}
192			}
193			for (unsigned int j = 0; j < bends_.size(); ++j) {
194			Vector3d loc = bends_[j]->getAtomA()->getPos();
195			loc += bends_[j]->getAtomB()->getPos();
196			loc += bends_[j]->getAtomC()->getPos();
197			loc = loc / 3.0;
198			Vector3d r = centerPos - loc;
199			currSnapshot->wrapVector(r);
200			if (r.length() <= distance) {
201			bsResult.bitsets_[BEND].setBitOn(j);
202			}
203			}
204			for (unsigned int j = 0; j < torsions_.size(); ++j) {
205			Vector3d loc = torsions_[j]->getAtomA()->getPos();
206			loc += torsions_[j]->getAtomB()->getPos();
207			loc += torsions_[j]->getAtomC()->getPos();
208			loc += torsions_[j]->getAtomD()->getPos();
209			loc = loc / 4.0;
210			Vector3d r = centerPos - loc;
211			currSnapshot->wrapVector(r);
212			if (r.length() <= distance) {
213			bsResult.bitsets_[TORSION].setBitOn(j);
214			}
215			}
216			for (unsigned int j = 0; j < inversions_.size(); ++j) {
217			Vector3d loc = inversions_[j]->getAtomA()->getPos();
218			loc += inversions_[j]->getAtomB()->getPos();
219			loc += inversions_[j]->getAtomC()->getPos();
220			loc += inversions_[j]->getAtomD()->getPos();
221			loc = loc / 4.0;
222			Vector3d r = centerPos - loc;
223			currSnapshot->wrapVector(r);
224			if (r.length() <= distance) {
225			bsResult.bitsets_[INVERSION].setBitOn(j);
226			}
227			}
228	tim	295	}
229			return bsResult;
230	gezelter	507	}
231	gezelter	1953
232
233			SelectionSet DistanceFinder::find(const SelectionSet& bs, RealType distance, int frame ) {
234	gezelter	1816	StuntDouble * center;
235			Vector3d centerPos;
236			Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
237	gezelter	1953	SelectionSet bsResult(nObjects_);
238	gezelter	1816	assert(bsResult.size() == bs.size());
239
240			#ifdef IS_MPI
241			int mol;
242			int proc;
243			RealType data[3];
244	gezelter	1969	int worldRank;
245			MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
246	gezelter	1816	#endif
247
248			for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
249			if (stuntdoubles_[j]->isRigidBody()) {
250			RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
251			rb->updateAtoms(frame);
252			}
253			}
254
255	gezelter	1953	SelectionSet bsTemp(nObjects_);
256	gezelter	1816	bsTemp = bs;
257			bsTemp.parallelReduce();
258
259	gezelter	1953	for (int i = bsTemp.bitsets_[STUNTDOUBLE].firstOnBit(); i != -1;
260			i = bsTemp.bitsets_[STUNTDOUBLE].nextOnBit(i)) {
261	gezelter	1816
262			// Now, if we own stuntdouble i, we can use the position, but in
263			// parallel, we'll need to let everyone else know what that
264			// position is!
265
266			#ifdef IS_MPI
267			mol = info_->getGlobalMolMembership(i);
268			proc = info_->getMolToProc(mol);
269
270			if (proc == worldRank) {
271			center = stuntdoubles_[i];
272			centerPos = center->getPos(frame);
273			data[0] = centerPos.x();
274			data[1] = centerPos.y();
275			data[2] = centerPos.z();
276	gezelter	1969	MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
277	gezelter	1816	} else {
278	gezelter	1969	MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
279	gezelter	1816	centerPos = Vector3d(data);
280			}
281			#else
282			center = stuntdoubles_[i];
283			centerPos = center->getPos(frame);
284			#endif
285	gezelter	2052	for (unsigned int j = 0; j < molecules_.size(); ++j) {
286			Vector3d r =centerPos - molecules_[j]->getCom(frame);
287			currSnapshot->wrapVector(r);
288			if (r.length() <= distance) {
289			bsResult.bitsets_[MOLECULE].setBitOn(j);
290			}
291			}
292
293	gezelter	1816	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
294			Vector3d r =centerPos - stuntdoubles_[j]->getPos(frame);
295			currSnapshot->wrapVector(r);
296			if (r.length() <= distance) {
297	gezelter	1953	bsResult.bitsets_[STUNTDOUBLE].setBitOn(j);
298	gezelter	1816	}
299			}
300	gezelter	1953	for (unsigned int j = 0; j < bonds_.size(); ++j) {
301			Vector3d loc = bonds_[j]->getAtomA()->getPos(frame);
302			loc += bonds_[j]->getAtomB()->getPos(frame);
303			loc = loc / 2.0;
304			Vector3d r = centerPos - loc;
305			currSnapshot->wrapVector(r);
306			if (r.length() <= distance) {
307			bsResult.bitsets_[BOND].setBitOn(j);
308			}
309			}
310			for (unsigned int j = 0; j < bends_.size(); ++j) {
311			Vector3d loc = bends_[j]->getAtomA()->getPos(frame);
312			loc += bends_[j]->getAtomB()->getPos(frame);
313			loc += bends_[j]->getAtomC()->getPos(frame);
314			loc = loc / 3.0;
315			Vector3d r = centerPos - loc;
316			currSnapshot->wrapVector(r);
317			if (r.length() <= distance) {
318			bsResult.bitsets_[BEND].setBitOn(j);
319			}
320			}
321			for (unsigned int j = 0; j < torsions_.size(); ++j) {
322			Vector3d loc = torsions_[j]->getAtomA()->getPos(frame);
323			loc += torsions_[j]->getAtomB()->getPos(frame);
324			loc += torsions_[j]->getAtomC()->getPos(frame);
325			loc += torsions_[j]->getAtomD()->getPos(frame);
326			loc = loc / 4.0;
327			Vector3d r = centerPos - loc;
328			currSnapshot->wrapVector(r);
329			if (r.length() <= distance) {
330			bsResult.bitsets_[TORSION].setBitOn(j);
331			}
332			}
333			for (unsigned int j = 0; j < inversions_.size(); ++j) {
334			Vector3d loc = inversions_[j]->getAtomA()->getPos(frame);
335			loc += inversions_[j]->getAtomB()->getPos(frame);
336			loc += inversions_[j]->getAtomC()->getPos(frame);
337			loc += inversions_[j]->getAtomD()->getPos(frame);
338			loc = loc / 4.0;
339			Vector3d r = centerPos - loc;
340			currSnapshot->wrapVector(r);
341			if (r.length() <= distance) {
342			bsResult.bitsets_[INVERSION].setBitOn(j);
343			}
344			}
345	gezelter	1816	}
346			return bsResult;
347			}
348	tim	295	}