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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC vs.
Revision 1554 by gezelter, Sat Apr 30 02:54:02 2011 UTC

# Line 52 | Line 52 | namespace OpenMD {
52     */
53    
54    void ForceMatrixDecomposition::distributeInitialData() {
55 +    snap_ = sman_->getCurrentSnapshot();
56 +    storageLayout_ = sman_->getStorageLayout();
57   #ifdef IS_MPI    
58 <    Snapshot* snap = sman_->getCurrentSnapshot();
59 <    int nLocal = snap->getNumberOfAtoms();
60 <    int nGroups = snap->getNumberOfCutoffGroups();
59 <
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);
# Line 76 | Line 77 | namespace OpenMD {
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 <    
95 >
96 >
97      vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
98      
99      // gather the information for atomtype IDs (atids):
# Line 109 | Line 121 | namespace OpenMD {
121  
122  
123    void ForceMatrixDecomposition::distributeData()  {
124 +    snap_ = sman_->getCurrentSnapshot();
125 +    storageLayout_ = sman_->getStorageLayout();
126   #ifdef IS_MPI
113 –    Snapshot* snap = sman_->getCurrentSnapshot();
127      
128      // gather up the atomic positions
129 <    AtomCommVectorRow->gather(snap->atomData.position,
130 <                            snap->atomIData.position);
131 <    AtomCommVectorColumn->gather(snap->atomData.position,
132 <                            snap->atomJData.position);
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 <                          snap->cgIData.position);
137 <    cgCommVectorColumn->gather(snap->cgData.position,
138 <                          snap->cgJData.position);
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 (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
142 <      AtomCommMatrixRow->gather(snap->atomData.aMat,
143 <                              snap->atomIData.aMat);
144 <      AtomCommMatrixColumn->gather(snap->atomData.aMat,
145 <                              snap->atomJData.aMat);
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 (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
150 <      AtomCommMatrixRow->gather(snap->atomData.electroFrame,
151 <                              snap->atomIData.electroFrame);
152 <      AtomCommMatrixColumn->gather(snap->atomData.electroFrame,
153 <                              snap->atomJData.electroFrame);
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
147 –    Snapshot* snap = sman_->getCurrentSnapshot();
162      
163 <    if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
164 <
165 <      AtomCommRealRow->scatter(snap->atomIData.density,
166 <                             snap->atomData.density);
167 <
168 <      int n = snap->atomData.density.size();
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(snap->atomJData.density, rho_tmp);
170 >      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
171        for (int i = 0; i < n; i++)
172 <        snap->atomData.density[i] += rho_tmp[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 <    Snapshot* snap = sman_->getCurrentSnapshot();
182 <    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
183 <      AtomCommRealRow->gather(snap->atomData.functional,
184 <                            snap->atomIData.functional);
185 <      AtomCommRealColumn->gather(snap->atomData.functional,
170 <                            snap->atomJData.functional);
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 (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
189 <      AtomCommRealRow->gather(snap->atomData.functionalDerivative,
190 <                            snap->atomIData.functionalDerivative);
191 <      AtomCommRealColumn->gather(snap->atomData.functionalDerivative,
192 <                            snap->atomJData.functionalDerivative);
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 < #ifdef IS_MPI
200 <    Snapshot* snap = sman_->getCurrentSnapshot();
201 <    
202 <    int n = snap->atomData.force.size();
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(snap->atomIData.force, frc_tmp);
205 >    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
206      for (int i = 0; i < n; i++) {
207 <      snap->atomData.force[i] += frc_tmp[i];
207 >      snap_->atomData.force[i] += frc_tmp[i];
208        frc_tmp[i] = 0.0;
209      }
210      
211 <    AtomCommVectorColumn->scatter(snap->atomJData.force, frc_tmp);
211 >    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
212      for (int i = 0; i < n; i++)
213 <      snap->atomData.force[i] += frc_tmp[i];
213 >      snap_->atomData.force[i] += frc_tmp[i];
214      
215      
216 <    if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
216 >    if (storageLayout_ & DataStorage::dslTorque) {
217  
218 <      int nt = snap->atomData.force.size();
218 >      int nt = snap_->atomData.force.size();
219        vector<Vector3d> trq_tmp(nt, V3Zero);
220  
221 <      AtomCommVectorRow->scatter(snap->atomIData.torque, trq_tmp);
221 >      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
222        for (int i = 0; i < n; i++) {
223 <        snap->atomData.torque[i] += trq_tmp[i];
223 >        snap_->atomData.torque[i] += trq_tmp[i];
224          trq_tmp[i] = 0.0;
225        }
226        
227 <      AtomCommVectorColumn->scatter(snap->atomJData.torque, trq_tmp);
227 >      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
228        for (int i = 0; i < n; i++)
229 <        snap->atomData.torque[i] += trq_tmp[i];
229 >        snap_->atomData.torque[i] += trq_tmp[i];
230      }
231      
232 <    int nLocal = snap->getNumberOfAtoms();
232 >    int nLocal = snap_->getNumberOfAtoms();
233  
234      vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
235                                         vector<RealType> (nLocal, 0.0));
# Line 227 | Line 242 | namespace OpenMD {
242      }
243   #endif
244    }
245 +
246    
247 +  Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
248 +    Vector3d d;
249 +    
250 + #ifdef IS_MPI
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 +
260 +
261 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
262 +
263 +    Vector3d d;
264 +    
265 + #ifdef IS_MPI
266 +    d = cgRowData.position[cg1] - atomRowData.position[atom1];
267 + #else
268 +    d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
269 + #endif
270 +
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 +    snap_->wrapVector(d);
298 +    return d;    
299 +  }
300 +
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 +    atomColData.force[atom2] += fg;
312 + #else
313 +    snap_->atomData.force[atom2] += fg;
314 + #endif
315 +
316 +  }
317 +
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 +    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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