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 (12 years ago) by gezelter
File size:	6739 byte(s)
Log Message:	Some MPI include re-ordering to work with the Intel MPI implementation.
#	Content
1	/*
2	* Copyright (c) 2005, 2010 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	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#ifdef IS_MPI
44	#include <mpi.h>
45	#endif
46
47	#include "selection/DistanceFinder.hpp"
48	#include "primitives/Molecule.hpp"
49
50	namespace OpenMD {
51
52	DistanceFinder::DistanceFinder(SimInfo* info) : info_(info) {
53
54	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
65	for (mol = info_->beginMolecule(mi); mol != NULL;
66	mol = info_->nextMolecule(mi)) {
67
68	for(atom = mol->beginAtom(ai); atom != NULL;
69	atom = mol->nextAtom(ai)) {
70	stuntdoubles_[atom->getGlobalIndex()] = atom;
71	}
72
73	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
74	rb = mol->nextRigidBody(rbIter)) {
75	stuntdoubles_[rb->getGlobalIndex()] = rb;
76	}
77	}
78	}
79
80	OpenMDBitSet DistanceFinder::find(const OpenMDBitSet& bs, RealType distance) {
81	StuntDouble * center;
82	Vector3d centerPos;
83	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
84	OpenMDBitSet bsResult(nStuntDoubles_);
85	assert(bsResult.size() == bs.size());
86
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	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
95	if (stuntdoubles_[j]->isRigidBody()) {
96	RigidBody* rb = static_cast<RigidBody*>(stuntdoubles_[j]);
97	rb->updateAtoms();
98	}
99	}
100
101	OpenMDBitSet bsTemp(nStuntDoubles_);
102	bsTemp = bs;
103	bsTemp.parallelReduce();
104
105	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	center = stuntdoubles_[i];
128	centerPos = center->getPos();
129	#endif
130
131	for (unsigned int j = 0; j < stuntdoubles_.size(); ++j) {
132	Vector3d r =centerPos - stuntdoubles_[j]->getPos();
133	currSnapshot->wrapVector(r);
134	if (r.length() <= distance) {
135	bsResult.setBitOn(j);
136	}
137	}
138	}
139	return bsResult;
140	}
141
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	}