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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1538 by chuckv, Tue Jan 11 18:58:12 2011 UTC vs.
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1551 by gezelter, Thu Apr 28 18:38:21 2011 UTC

# Line 1 | Line 1
1 < /**
2 < * @file ForceDecomposition.cpp
3 < * @author Charles Vardeman <cvardema.at.nd.edu>
4 < * @date 08/18/2010
5 < * @time 11:56am
6 < * @version 1.0
1 > /*
2 > * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
8 – * @section LICENSE
9 – * Copyright (c) 2010 The University of Notre Dame. All Rights Reserved.
10 – *
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
# Line 45 | Line 38
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39   * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41 + #include "parallel/ForceMatrixDecomposition.hpp"
42 + #include "math/SquareMatrix3.hpp"
43 + #include "nonbonded/NonBondedInteraction.hpp"
44 + #include "brains/SnapshotManager.hpp"
45  
46 + using namespace std;
47 + namespace OpenMD {
48  
49 +  /**
50 +   * distributeInitialData is essentially a copy of the older fortran
51 +   * SimulationSetup
52 +   */
53 +  
54 +  void ForceMatrixDecomposition::distributeInitialData() {
55 +    snap_ = sman_->getCurrentSnapshot();
56 +    storageLayout_ = sman_->getStorageLayout();
57 + #ifdef IS_MPI    
58 +    int nLocal = snap_->getNumberOfAtoms();
59 +    int nGroups = snap_->getNumberOfCutoffGroups();
60 +    
61 +    AtomCommIntRow = new Communicator<Row,int>(nLocal);
62 +    AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
63 +    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
64 +    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
65  
66 < /*  -*- c++ -*-  */
67 < #include "config.h"
68 < #include <stdlib.h>
66 >    AtomCommIntColumn = new Communicator<Column,int>(nLocal);
67 >    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
68 >    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
69 >    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
70 >
71 >    cgCommIntRow = new Communicator<Row,int>(nGroups);
72 >    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
73 >    cgCommIntColumn = new Communicator<Column,int>(nGroups);
74 >    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
75 >
76 >    int nAtomsInRow = AtomCommIntRow->getSize();
77 >    int nAtomsInCol = AtomCommIntColumn->getSize();
78 >    int nGroupsInRow = cgCommIntRow->getSize();
79 >    int nGroupsInCol = cgCommIntColumn->getSize();
80 >
81 >    // Modify the data storage objects with the correct layouts and sizes:
82 >    atomRowData.resize(nAtomsInRow);
83 >    atomRowData.setStorageLayout(storageLayout_);
84 >    atomColData.resize(nAtomsInCol);
85 >    atomColData.setStorageLayout(storageLayout_);
86 >    cgRowData.resize(nGroupsInRow);
87 >    cgRowData.setStorageLayout(DataStorage::dslPosition);
88 >    cgColData.resize(nGroupsInCol);
89 >    cgColData.setStorageLayout(DataStorage::dslPosition);
90 >    
91 >    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
92 >                                      vector<RealType> (nAtomsInRow, 0.0));
93 >    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
94 >                                      vector<RealType> (nAtomsInCol, 0.0));
95 >
96 >
97 >    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
98 >    
99 >    // gather the information for atomtype IDs (atids):
100 >    vector<int> identsLocal = info_->getIdentArray();
101 >    identsRow.reserve(nAtomsInRow);
102 >    identsCol.reserve(nAtomsInCol);
103 >    
104 >    AtomCommIntRow->gather(identsLocal, identsRow);
105 >    AtomCommIntColumn->gather(identsLocal, identsCol);
106 >    
107 >    AtomLocalToGlobal = info_->getGlobalAtomIndices();
108 >    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
109 >    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
110 >    
111 >    cgLocalToGlobal = info_->getGlobalGroupIndices();
112 >    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
113 >    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
114 >
115 >    // still need:
116 >    // topoDist
117 >    // exclude
118 > #endif
119 >  }
120 >    
121 >
122 >
123 >  void ForceMatrixDecomposition::distributeData()  {
124 >    snap_ = sman_->getCurrentSnapshot();
125 >    storageLayout_ = sman_->getStorageLayout();
126   #ifdef IS_MPI
127 < #include <mpi.h>
127 >    
128 >    // gather up the atomic positions
129 >    AtomCommVectorRow->gather(snap_->atomData.position,
130 >                              atomRowData.position);
131 >    AtomCommVectorColumn->gather(snap_->atomData.position,
132 >                                 atomColData.position);
133 >    
134 >    // gather up the cutoff group positions
135 >    cgCommVectorRow->gather(snap_->cgData.position,
136 >                            cgRowData.position);
137 >    cgCommVectorColumn->gather(snap_->cgData.position,
138 >                               cgColData.position);
139 >    
140 >    // if needed, gather the atomic rotation matrices
141 >    if (storageLayout_ & DataStorage::dslAmat) {
142 >      AtomCommMatrixRow->gather(snap_->atomData.aMat,
143 >                                atomRowData.aMat);
144 >      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
145 >                                   atomColData.aMat);
146 >    }
147 >    
148 >    // if needed, gather the atomic eletrostatic frames
149 >    if (storageLayout_ & DataStorage::dslElectroFrame) {
150 >      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
151 >                                atomRowData.electroFrame);
152 >      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
153 >                                   atomColData.electroFrame);
154 >    }
155 > #endif      
156 >  }
157 >  
158 >  void ForceMatrixDecomposition::collectIntermediateData() {
159 >    snap_ = sman_->getCurrentSnapshot();
160 >    storageLayout_ = sman_->getStorageLayout();
161 > #ifdef IS_MPI
162 >    
163 >    if (storageLayout_ & DataStorage::dslDensity) {
164 >      
165 >      AtomCommRealRow->scatter(atomRowData.density,
166 >                               snap_->atomData.density);
167 >      
168 >      int n = snap_->atomData.density.size();
169 >      std::vector<RealType> rho_tmp(n, 0.0);
170 >      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
171 >      for (int i = 0; i < n; i++)
172 >        snap_->atomData.density[i] += rho_tmp[i];
173 >    }
174   #endif
175 +  }
176 +  
177 +  void ForceMatrixDecomposition::distributeIntermediateData() {
178 +    snap_ = sman_->getCurrentSnapshot();
179 +    storageLayout_ = sman_->getStorageLayout();
180 + #ifdef IS_MPI
181 +    if (storageLayout_ & DataStorage::dslFunctional) {
182 +      AtomCommRealRow->gather(snap_->atomData.functional,
183 +                              atomRowData.functional);
184 +      AtomCommRealColumn->gather(snap_->atomData.functional,
185 +                                 atomColData.functional);
186 +    }
187 +    
188 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
189 +      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
190 +                              atomRowData.functionalDerivative);
191 +      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
192 +                                 atomColData.functionalDerivative);
193 +    }
194 + #endif
195 +  }
196 +  
197 +  
198 +  void ForceMatrixDecomposition::collectData() {
199 +    snap_ = sman_->getCurrentSnapshot();
200 +    storageLayout_ = sman_->getStorageLayout();
201 + #ifdef IS_MPI    
202 +    int n = snap_->atomData.force.size();
203 +    vector<Vector3d> frc_tmp(n, V3Zero);
204 +    
205 +    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
206 +    for (int i = 0; i < n; i++) {
207 +      snap_->atomData.force[i] += frc_tmp[i];
208 +      frc_tmp[i] = 0.0;
209 +    }
210 +    
211 +    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
212 +    for (int i = 0; i < n; i++)
213 +      snap_->atomData.force[i] += frc_tmp[i];
214 +    
215 +    
216 +    if (storageLayout_ & DataStorage::dslTorque) {
217  
218 < #include <iostream>
219 < #include <vector>
60 < #include <algorithm>
61 < #include <cmath>
62 < #include "parallel/ForceDecomposition.hpp"
218 >      int nt = snap_->atomData.force.size();
219 >      vector<Vector3d> trq_tmp(nt, V3Zero);
220  
221 +      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
222 +      for (int i = 0; i < n; i++) {
223 +        snap_->atomData.torque[i] += trq_tmp[i];
224 +        trq_tmp[i] = 0.0;
225 +      }
226 +      
227 +      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
228 +      for (int i = 0; i < n; i++)
229 +        snap_->atomData.torque[i] += trq_tmp[i];
230 +    }
231 +    
232 +    int nLocal = snap_->getNumberOfAtoms();
233  
234 < using namespace std;
235 < using namespace OpenMD;
234 >    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
235 >                                       vector<RealType> (nLocal, 0.0));
236 >    
237 >    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
238 >      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
239 >      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
240 >        pot_local[i] += pot_temp[i][ii];
241 >      }
242 >    }
243 > #endif
244 >  }
245  
246 < //__static
246 >  
247 >  Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
248 >    Vector3d d;
249 >    
250   #ifdef IS_MPI
251 < static vector<MPI:Comm> communictors;
251 >    d = cgColData.position[cg2] - cgRowData.position[cg1];
252 > #else
253 >    d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
254   #endif
255 +    
256 +    snap_->wrapVector(d);
257 +    return d;    
258 +  }
259  
73 – //____ MPITypeTraits
74 – template<typename T>
75 – struct MPITypeTraits;
260  
261 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
262 +
263 +    Vector3d d;
264 +    
265   #ifdef IS_MPI
266 < template<>
267 < struct MPITypeTraits<RealType> {
268 <  static const MPI::Datatype datatype;
269 < };
82 < const MPI_Datatype MPITypeTraits<RealType>::datatype = MY_MPI_REAL;
266 >    d = cgRowData.position[cg1] - atomRowData.position[atom1];
267 > #else
268 >    d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
269 > #endif
270  
271 < template<>
272 < struct MPITypeTraits<int> {
273 <  static const MPI::Datatype datatype;
274 < };
275 < const MPI::Datatype MPITypeTraits<int>::datatype = MPI_INT;
271 >    snap_->wrapVector(d);
272 >    return d;    
273 >  }
274 >  
275 >  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
276 >    Vector3d d;
277 >    
278 > #ifdef IS_MPI
279 >    d = cgColData.position[cg2] - atomColData.position[atom2];
280 > #else
281 >    d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
282   #endif
283 +    
284 +    snap_->wrapVector(d);
285 +    return d;    
286 +  }
287 +    
288 +  Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
289 +    Vector3d d;
290 +    
291 + #ifdef IS_MPI
292 +    d = atomColData.position[atom2] - atomRowData.position[atom1];
293 + #else
294 +    d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
295 + #endif
296  
297 < /**
298 < * Constructor for ForceDecomposition Parallel Decomposition Method
299 < * Will try to construct a symmetric grid of processors. Ideally, the
94 < * number of processors will be a square ex: 4, 9, 16, 25.
95 < *
96 < */
297 >    snap_->wrapVector(d);
298 >    return d;    
299 >  }
300  
301 < ForceDecomposition::ForceDecomposition() {
301 >  void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
302 > #ifdef IS_MPI
303 >    atomRowData.force[atom1] += fg;
304 > #else
305 >    snap_->atomData.force[atom1] += fg;
306 > #endif
307 >  }
308  
309 +  void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
310   #ifdef IS_MPI
311 <  int nProcs = MPI::COMM_WORLD.Get_size();
312 <  int worldRank = MPI::COMM_WORLD.Get_rank();
311 >    atomColData.force[atom2] += fg;
312 > #else
313 >    snap_->atomData.force[atom2] += fg;
314   #endif
315  
105 –  // First time through, construct column stride.
106 –  if (communicators.size() == 0)
107 –  {
108 –    int nColumnsMax = (int) round(sqrt((float) nProcs));
109 –    for (int i = 0; i < nProcs; ++i)
110 –    {
111 –      if (nProcs%i==0) nColumns=i;
112 –    }
113 –
114 –    int nRows = nProcs/nColumns;    
115 –    myRank_ = (int) worldRank%nColumns;
316    }
117 –  else
118 –  {
119 –    myRank_ = myRank/nColumns;
120 –  }
121 –  MPI::Comm newComm = MPI:COMM_WORLD.Split(myRank_,0);
122 –  
123 –  isColumn_ = false;
124 –  
125 – }
317  
318 < ForceDecomposition::gather(sendbuf, receivebuf){
319 <  communicators(myIndex_).Allgatherv();
129 < }
318 >    // filling interaction blocks with pointers
319 >  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
320  
321 +    InteractionData idat;
322 + #ifdef IS_MPI
323 +    if (storageLayout_ & DataStorage::dslAmat) {
324 +      idat.A1 = atomRowData.aMat[atom1];
325 +      idat.A2 = atomColData.aMat[atom2];
326 +    }
327  
328 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
329 +      idat.eFrame1 = atomRowData.electroFrame[atom1];
330 +      idat.eFrame2 = atomColData.electroFrame[atom2];
331 +    }
332  
333 < ForceDecomposition::scatter(sbuffer, rbuffer){
334 <  communicators(myIndex_).Reduce_scatter(sbuffer, recevbuf. recvcounts, MPI::DOUBLE, MPI::SUM);
335 < }
333 >    if (storageLayout_ & DataStorage::dslTorque) {
334 >      idat.t1 = atomRowData.torque[atom1];
335 >      idat.t2 = atomColData.torque[atom2];
336 >    }
337  
338 +    if (storageLayout_ & DataStorage::dslDensity) {
339 +      idat.rho1 = atomRowData.density[atom1];
340 +      idat.rho2 = atomColData.density[atom2];
341 +    }
342  
343 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
344 +      idat.dfrho1 = atomRowData.functionalDerivative[atom1];
345 +      idat.dfrho2 = atomColData.functionalDerivative[atom2];
346 +    }
347 + #endif
348 +    
349 +  }
350 +  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
351 +  }
352 +  SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
353 +  }
354 +
355 +  
356 + } //end namespace OpenMD

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