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());

    stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
    bonds_.resize(nObjects_[BOND]);
    bends_.resize(nObjects_[BEND]);
    torsions_.resize(nObjects_[TORSION]);
    inversions_.resize(nObjects_[INVERSION]);
    
    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)) {
        
      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 < 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 < 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:	1969
Committed:	Wed Feb 26 14:14:50 2014 UTC (11 years, 8 months ago) by gezelter
File size:	11567 byte(s)
Log Message:	Fixes to deal with deprecation of MPI C++ bindings. We've reverted back to the C calls.
#	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
59			stuntdoubles_.resize(nObjects_[STUNTDOUBLE]);
60			bonds_.resize(nObjects_[BOND]);
61			bends_.resize(nObjects_[BEND]);
62			torsions_.resize(nObjects_[TORSION]);
63			inversions_.resize(nObjects_[INVERSION]);
64	gezelter	1811
65	tim	295	SimInfo::MoleculeIterator mi;
66	gezelter	1953	Molecule::AtomIterator ai;
67			Molecule::RigidBodyIterator rbIter;
68			Molecule::BondIterator bondIter;
69			Molecule::BendIterator bendIter;
70			Molecule::TorsionIterator torsionIter;
71			Molecule::InversionIterator inversionIter;
72
73	tim	295	Molecule* mol;
74			Atom* atom;
75			RigidBody* rb;
76	gezelter	1953	Bond* bond;
77			Bend* bend;
78			Torsion* torsion;
79			Inversion* inversion;
80	tim	295
81	gezelter	1801	for (mol = info_->beginMolecule(mi); mol != NULL;
82			mol = info_->nextMolecule(mi)) {
83	tim	295
84	gezelter	1801	for(atom = mol->beginAtom(ai); atom != NULL;
85			atom = mol->nextAtom(ai)) {
86	gezelter	507	stuntdoubles_[atom->getGlobalIndex()] = atom;
87			}
88	gezelter	1801	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
89			rb = mol->nextRigidBody(rbIter)) {
90	gezelter	507	stuntdoubles_[rb->getGlobalIndex()] = rb;
91			}
92	gezelter	1953	for (bond = mol->beginBond(bondIter); bond != NULL;
93			bond = mol->nextBond(bondIter)) {
94			bonds_[bond->getGlobalIndex()] = bond;
95			}
96			for (bend = mol->beginBend(bendIter); bend != NULL;
97			bend = mol->nextBend(bendIter)) {
98			bends_[bend->getGlobalIndex()] = bend;
99			}
100			for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
101			torsion = mol->nextTorsion(torsionIter)) {
102			torsions_[torsion->getGlobalIndex()] = torsion;
103			}
104			for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
105			inversion = mol->nextInversion(inversionIter)) {
106			inversions_[inversion->getGlobalIndex()] = inversion;
107			}
108
109	gezelter	1801	}
110	gezelter	507	}
111	tim	295
112	gezelter	1953	SelectionSet DistanceFinder::find(const SelectionSet& bs, RealType distance) {
113	tim	295	StuntDouble * center;
114			Vector3d centerPos;
115			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
116	gezelter	1953	SelectionSet bsResult(nObjects_);
117	tim	295	assert(bsResult.size() == bs.size());
118	gezelter	1802
119			#ifdef IS_MPI
120			int mol;
121			int proc;
122			RealType data[3];
123	gezelter	1969	int worldRank;
124			MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
125	gezelter	1802	#endif
126
127	gezelter	1782	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
128	chuckv	1434	if (stuntdoubles_[j]->isRigidBody()) {
129			RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
130			rb->updateAtoms();
131			}
132			}
133	gezelter	1953
134			SelectionSet bsTemp(nObjects_);
135	gezelter	1802	bsTemp = bs;
136			bsTemp.parallelReduce();
137	gezelter	1801
138	gezelter	1953	for (int i = bsTemp.bitsets_[STUNTDOUBLE].firstOnBit(); i != -1;
139			i = bsTemp.bitsets_[STUNTDOUBLE].nextOnBit(i)) {
140
141	gezelter	1802	// Now, if we own stuntdouble i, we can use the position, but in
142			// parallel, we'll need to let everyone else know what that
143			// position is!
144	gezelter	1953
145	gezelter	1802	#ifdef IS_MPI
146			mol = info_->getGlobalMolMembership(i);
147			proc = info_->getMolToProc(mol);
148
149			if (proc == worldRank) {
150			center = stuntdoubles_[i];
151			centerPos = center->getPos();
152			data[0] = centerPos.x();
153			data[1] = centerPos.y();
154			data[2] = centerPos.z();
155	gezelter	1969	MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
156	gezelter	1802	} else {
157	gezelter	1969	MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
158	gezelter	1802	centerPos = Vector3d(data);
159			}
160			#else
161	gezelter	507	center = stuntdoubles_[i];
162			centerPos = center->getPos();
163	gezelter	1802	#endif
164
165	gezelter	1782	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
166	gezelter	507	Vector3d r =centerPos - stuntdoubles_[j]->getPos();
167			currSnapshot->wrapVector(r);
168			if (r.length() <= distance) {
169	gezelter	1953	bsResult.bitsets_[STUNTDOUBLE].setBitOn(j);
170	gezelter	507	}
171			}
172	gezelter	1953	for (unsigned int j = 0; j < bonds_.size(); ++j) {
173			Vector3d loc = bonds_[j]->getAtomA()->getPos();
174			loc += bonds_[j]->getAtomB()->getPos();
175			loc = loc / 2.0;
176			Vector3d r = centerPos - loc;
177			currSnapshot->wrapVector(r);
178			if (r.length() <= distance) {
179			bsResult.bitsets_[BOND].setBitOn(j);
180			}
181			}
182			for (unsigned int j = 0; j < bends_.size(); ++j) {
183			Vector3d loc = bends_[j]->getAtomA()->getPos();
184			loc += bends_[j]->getAtomB()->getPos();
185			loc += bends_[j]->getAtomC()->getPos();
186			loc = loc / 3.0;
187			Vector3d r = centerPos - loc;
188			currSnapshot->wrapVector(r);
189			if (r.length() <= distance) {
190			bsResult.bitsets_[BEND].setBitOn(j);
191			}
192			}
193			for (unsigned int j = 0; j < torsions_.size(); ++j) {
194			Vector3d loc = torsions_[j]->getAtomA()->getPos();
195			loc += torsions_[j]->getAtomB()->getPos();
196			loc += torsions_[j]->getAtomC()->getPos();
197			loc += torsions_[j]->getAtomD()->getPos();
198			loc = loc / 4.0;
199			Vector3d r = centerPos - loc;
200			currSnapshot->wrapVector(r);
201			if (r.length() <= distance) {
202			bsResult.bitsets_[TORSION].setBitOn(j);
203			}
204			}
205			for (unsigned int j = 0; j < inversions_.size(); ++j) {
206			Vector3d loc = inversions_[j]->getAtomA()->getPos();
207			loc += inversions_[j]->getAtomB()->getPos();
208			loc += inversions_[j]->getAtomC()->getPos();
209			loc += inversions_[j]->getAtomD()->getPos();
210			loc = loc / 4.0;
211			Vector3d r = centerPos - loc;
212			currSnapshot->wrapVector(r);
213			if (r.length() <= distance) {
214			bsResult.bitsets_[INVERSION].setBitOn(j);
215			}
216			}
217	tim	295	}
218			return bsResult;
219	gezelter	507	}
220	gezelter	1953
221
222			SelectionSet DistanceFinder::find(const SelectionSet& bs, RealType distance, int frame ) {
223	gezelter	1816	StuntDouble * center;
224			Vector3d centerPos;
225			Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
226	gezelter	1953	SelectionSet bsResult(nObjects_);
227	gezelter	1816	assert(bsResult.size() == bs.size());
228
229			#ifdef IS_MPI
230			int mol;
231			int proc;
232			RealType data[3];
233	gezelter	1969	int worldRank;
234			MPI_Comm_rank( MPI_COMM_WORLD, &worldRank);
235	gezelter	1816	#endif
236
237			for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
238			if (stuntdoubles_[j]->isRigidBody()) {
239			RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
240			rb->updateAtoms(frame);
241			}
242			}
243
244	gezelter	1953	SelectionSet bsTemp(nObjects_);
245	gezelter	1816	bsTemp = bs;
246			bsTemp.parallelReduce();
247
248	gezelter	1953	for (int i = bsTemp.bitsets_[STUNTDOUBLE].firstOnBit(); i != -1;
249			i = bsTemp.bitsets_[STUNTDOUBLE].nextOnBit(i)) {
250	gezelter	1816
251			// Now, if we own stuntdouble i, we can use the position, but in
252			// parallel, we'll need to let everyone else know what that
253			// position is!
254
255			#ifdef IS_MPI
256			mol = info_->getGlobalMolMembership(i);
257			proc = info_->getMolToProc(mol);
258
259			if (proc == worldRank) {
260			center = stuntdoubles_[i];
261			centerPos = center->getPos(frame);
262			data[0] = centerPos.x();
263			data[1] = centerPos.y();
264			data[2] = centerPos.z();
265	gezelter	1969	MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
266	gezelter	1816	} else {
267	gezelter	1969	MPI_Bcast(data, 3, MPI_REALTYPE, proc, MPI_COMM_WORLD);
268	gezelter	1816	centerPos = Vector3d(data);
269			}
270			#else
271			center = stuntdoubles_[i];
272			centerPos = center->getPos(frame);
273			#endif
274			for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
275			Vector3d r =centerPos - stuntdoubles_[j]->getPos(frame);
276			currSnapshot->wrapVector(r);
277			if (r.length() <= distance) {
278	gezelter	1953	bsResult.bitsets_[STUNTDOUBLE].setBitOn(j);
279	gezelter	1816	}
280			}
281	gezelter	1953	for (unsigned int j = 0; j < bonds_.size(); ++j) {
282			Vector3d loc = bonds_[j]->getAtomA()->getPos(frame);
283			loc += bonds_[j]->getAtomB()->getPos(frame);
284			loc = loc / 2.0;
285			Vector3d r = centerPos - loc;
286			currSnapshot->wrapVector(r);
287			if (r.length() <= distance) {
288			bsResult.bitsets_[BOND].setBitOn(j);
289			}
290			}
291			for (unsigned int j = 0; j < bends_.size(); ++j) {
292			Vector3d loc = bends_[j]->getAtomA()->getPos(frame);
293			loc += bends_[j]->getAtomB()->getPos(frame);
294			loc += bends_[j]->getAtomC()->getPos(frame);
295			loc = loc / 3.0;
296			Vector3d r = centerPos - loc;
297			currSnapshot->wrapVector(r);
298			if (r.length() <= distance) {
299			bsResult.bitsets_[BEND].setBitOn(j);
300			}
301			}
302			for (unsigned int j = 0; j < torsions_.size(); ++j) {
303			Vector3d loc = torsions_[j]->getAtomA()->getPos(frame);
304			loc += torsions_[j]->getAtomB()->getPos(frame);
305			loc += torsions_[j]->getAtomC()->getPos(frame);
306			loc += torsions_[j]->getAtomD()->getPos(frame);
307			loc = loc / 4.0;
308			Vector3d r = centerPos - loc;
309			currSnapshot->wrapVector(r);
310			if (r.length() <= distance) {
311			bsResult.bitsets_[TORSION].setBitOn(j);
312			}
313			}
314			for (unsigned int j = 0; j < inversions_.size(); ++j) {
315			Vector3d loc = inversions_[j]->getAtomA()->getPos(frame);
316			loc += inversions_[j]->getAtomB()->getPos(frame);
317			loc += inversions_[j]->getAtomC()->getPos(frame);
318			loc += inversions_[j]->getAtomD()->getPos(frame);
319			loc = loc / 4.0;
320			Vector3d r = centerPos - loc;
321			currSnapshot->wrapVector(r);
322			if (r.length() <= distance) {
323			bsResult.bitsets_[INVERSION].setBitOn(j);
324			}
325			}
326	gezelter	1816	}
327			return bsResult;
328			}
329	tim	295	}