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) {
    
    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:	1938
Committed:	Thu Oct 31 15:32:17 2013 UTC (11 years, 6 months ago) by gezelter
File size:	6739 byte(s)
Log Message:	Some MPI include re-ordering to work with the Intel MPI implementation.
#	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	1811
54	tim	295	nStuntDoubles_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
55			stuntdoubles_.resize(nStuntDoubles_);
56
57			SimInfo::MoleculeIterator mi;
58			Molecule* mol;
59			Molecule::AtomIterator ai;
60			Atom* atom;
61			Molecule::RigidBodyIterator rbIter;
62			RigidBody* rb;
63
64	gezelter	1811
65	gezelter	1801	for (mol = info_->beginMolecule(mi); mol != NULL;
66			mol = info_->nextMolecule(mi)) {
67	tim	295
68	gezelter	1801	for(atom = mol->beginAtom(ai); atom != NULL;
69			atom = mol->nextAtom(ai)) {
70	gezelter	507	stuntdoubles_[atom->getGlobalIndex()] = atom;
71			}
72	tim	295
73	gezelter	1801	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
74			rb = mol->nextRigidBody(rbIter)) {
75	gezelter	507	stuntdoubles_[rb->getGlobalIndex()] = rb;
76			}
77	gezelter	1801	}
78	gezelter	507	}
79	tim	295
80	gezelter	1390	OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) {
81	tim	295	StuntDouble * center;
82			Vector3d centerPos;
83			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
84	gezelter	1802	OpenMDBitSet bsResult(nStuntDoubles_);
85	tim	295	assert(bsResult.size() == bs.size());
86	gezelter	1802
87			#ifdef IS_MPI
88			int mol;
89			int proc;
90			RealType data[3];
91			int worldRank = MPI::COMM_WORLD.Get_rank();
92			#endif
93
94	gezelter	1782	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
95	chuckv	1434	if (stuntdoubles_[j]->isRigidBody()) {
96			RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
97			rb->updateAtoms();
98			}
99			}
100	gezelter	1802
101			OpenMDBitSet bsTemp(nStuntDoubles_);
102			bsTemp = bs;
103			bsTemp.parallelReduce();
104	gezelter	1801
105	gezelter	1802	for (int i = bsTemp.firstOnBit(); i != -1; i = bsTemp.nextOnBit(i)) {
106
107			// Now, if we own stuntdouble i, we can use the position, but in
108			// parallel, we'll need to let everyone else know what that
109			// position is!
110
111			#ifdef IS_MPI
112			mol = info_->getGlobalMolMembership(i);
113			proc = info_->getMolToProc(mol);
114
115			if (proc == worldRank) {
116			center = stuntdoubles_[i];
117			centerPos = center->getPos();
118			data[0] = centerPos.x();
119			data[1] = centerPos.y();
120			data[2] = centerPos.z();
121			MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
122			} else {
123			MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
124			centerPos = Vector3d(data);
125			}
126			#else
127	gezelter	507	center = stuntdoubles_[i];
128			centerPos = center->getPos();
129	gezelter	1802	#endif
130
131	gezelter	1782	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
132	gezelter	507	Vector3d r =centerPos - stuntdoubles_[j]->getPos();
133			currSnapshot->wrapVector(r);
134			if (r.length() <= distance) {
135			bsResult.setBitOn(j);
136			}
137			}
138	tim	295	}
139			return bsResult;
140	gezelter	507	}
141	gezelter	1816
142
143			OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance, int frame ) {
144			StuntDouble * center;
145			Vector3d centerPos;
146			Snapshot* currSnapshot = info_->getSnapshotManager()->getSnapshot(frame);
147			OpenMDBitSet bsResult(nStuntDoubles_);
148			assert(bsResult.size() == bs.size());
149
150			#ifdef IS_MPI
151			int mol;
152			int proc;
153			RealType data[3];
154			int worldRank = MPI::COMM_WORLD.Get_rank();
155			#endif
156
157			for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
158			if (stuntdoubles_[j]->isRigidBody()) {
159			RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
160			rb->updateAtoms(frame);
161			}
162			}
163
164			OpenMDBitSet bsTemp(nStuntDoubles_);
165			bsTemp = bs;
166			bsTemp.parallelReduce();
167
168			for (int i = bsTemp.firstOnBit(); i != -1; i = bsTemp.nextOnBit(i)) {
169
170			// Now, if we own stuntdouble i, we can use the position, but in
171			// parallel, we'll need to let everyone else know what that
172			// position is!
173
174			#ifdef IS_MPI
175			mol = info_->getGlobalMolMembership(i);
176			proc = info_->getMolToProc(mol);
177
178			if (proc == worldRank) {
179			center = stuntdoubles_[i];
180			centerPos = center->getPos(frame);
181			data[0] = centerPos.x();
182			data[1] = centerPos.y();
183			data[2] = centerPos.z();
184			MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
185			} else {
186			MPI::COMM_WORLD.Bcast(data, 3, MPI::REALTYPE, proc);
187			centerPos = Vector3d(data);
188			}
189			#else
190			center = stuntdoubles_[i];
191			centerPos = center->getPos(frame);
192			#endif
193
194			for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
195			Vector3d r =centerPos - stuntdoubles_[j]->getPos(frame);
196			currSnapshot->wrapVector(r);
197			if (r.length() <= distance) {
198			bsResult.setBitOn(j);
199			}
200			}
201			}
202			return bsResult;
203			}
204	tim	295	}