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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1547 by gezelter, Mon Apr 11 18:44:16 2011 UTC vs.
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC

# Line 38 | Line 38
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39   * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41 < #include "parallel/ForceDecomposition.hpp"
41 > #include "parallel/ForceMatrixDecomposition.hpp"
42   #include "math/SquareMatrix3.hpp"
43   #include "nonbonded/NonBondedInteraction.hpp"
44   #include "brains/SnapshotManager.hpp"
# Line 51 | Line 51 | namespace OpenMD {
51     * SimulationSetup
52     */
53    
54 <  void ForceDecomposition::distributeInitialData() {
54 >  void ForceMatrixDecomposition::distributeInitialData() {
55   #ifdef IS_MPI    
56      Snapshot* snap = sman_->getCurrentSnapshot();
57      int nLocal = snap->getNumberOfAtoms();
58      int nGroups = snap->getNumberOfCutoffGroups();
59  
60 <    AtomCommIntI = new Communicator<Row,int>(nLocal);
61 <    AtomCommRealI = new Communicator<Row,RealType>(nLocal);
62 <    AtomCommVectorI = new Communicator<Row,Vector3d>(nLocal);
63 <    AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nLocal);
60 >    AtomCommIntRow = new Communicator<Row,int>(nLocal);
61 >    AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
62 >    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
63 >    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
64  
65 <    AtomCommIntJ = new Communicator<Column,int>(nLocal);
66 <    AtomCommRealJ = new Communicator<Column,RealType>(nLocal);
67 <    AtomCommVectorJ = new Communicator<Column,Vector3d>(nLocal);
68 <    AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nLocal);
65 >    AtomCommIntColumn = new Communicator<Column,int>(nLocal);
66 >    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
67 >    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
68 >    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
69  
70 <    cgCommIntI = new Communicator<Row,int>(nGroups);
71 <    cgCommVectorI = new Communicator<Row,Vector3d>(nGroups);
72 <    cgCommIntJ = new Communicator<Column,int>(nGroups);
73 <    cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups);
70 >    cgCommIntRow = new Communicator<Row,int>(nGroups);
71 >    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
72 >    cgCommIntColumn = new Communicator<Column,int>(nGroups);
73 >    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
74  
75 <    int nAtomsInRow = AtomCommIntI->getSize();
76 <    int nAtomsInCol = AtomCommIntJ->getSize();
77 <    int nGroupsInRow = cgCommIntI->getSize();
78 <    int nGroupsInCol = cgCommIntJ->getSize();
79 <
75 >    int nAtomsInRow = AtomCommIntRow->getSize();
76 >    int nAtomsInCol = AtomCommIntColumn->getSize();
77 >    int nGroupsInRow = cgCommIntRow->getSize();
78 >    int nGroupsInCol = cgCommIntColumn->getSize();
79 >    
80      vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
81                                        vector<RealType> (nAtomsInRow, 0.0));
82      vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
83                                        vector<RealType> (nAtomsInCol, 0.0));
84      
85      vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
86 <
86 >    
87      // gather the information for atomtype IDs (atids):
88      vector<int> identsLocal = info_->getIdentArray();
89      identsRow.reserve(nAtomsInRow);
90      identsCol.reserve(nAtomsInCol);
91 +    
92 +    AtomCommIntRow->gather(identsLocal, identsRow);
93 +    AtomCommIntColumn->gather(identsLocal, identsCol);
94 +    
95 +    AtomLocalToGlobal = info_->getGlobalAtomIndices();
96 +    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
97 +    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
98 +    
99 +    cgLocalToGlobal = info_->getGlobalGroupIndices();
100 +    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
101 +    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
102  
92 –    AtomCommIntI->gather(identsLocal, identsRow);
93 –    AtomCommIntJ->gather(identsLocal, identsCol);
94 –
95 –    AtomLocalToGlobal = info_->getLocalToGlobalAtomIndex();
96 –    AtomCommIntI->gather(AtomLocalToGlobal, AtomRowToGlobal);
97 –    AtomCommIntJ->gather(AtomLocalToGlobal, AtomColToGlobal);
98 –
99 –    cgLocalToGlobal = info_->getLocalToGlobalCutoffGroupIndex();
100 –    cgCommIntI->gather(cgLocalToGlobal, cgRowToGlobal);
101 –    cgCommIntJ->gather(cgLocalToGlobal, cgColToGlobal);
102 –
103 –    
104 –
103      // still need:
104      // topoDist
105      // exclude
# Line 110 | Line 108 | namespace OpenMD {
108      
109  
110  
111 <  void ForceDecomposition::distributeData()  {
111 >  void ForceMatrixDecomposition::distributeData()  {
112   #ifdef IS_MPI
113      Snapshot* snap = sman_->getCurrentSnapshot();
114      
115      // gather up the atomic positions
116 <    AtomCommVectorI->gather(snap->atomData.position,
116 >    AtomCommVectorRow->gather(snap->atomData.position,
117                              snap->atomIData.position);
118 <    AtomCommVectorJ->gather(snap->atomData.position,
118 >    AtomCommVectorColumn->gather(snap->atomData.position,
119                              snap->atomJData.position);
120      
121      // gather up the cutoff group positions
122 <    cgCommVectorI->gather(snap->cgData.position,
122 >    cgCommVectorRow->gather(snap->cgData.position,
123                            snap->cgIData.position);
124 <    cgCommVectorJ->gather(snap->cgData.position,
124 >    cgCommVectorColumn->gather(snap->cgData.position,
125                            snap->cgJData.position);
126      
127      // if needed, gather the atomic rotation matrices
128      if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
129 <      AtomCommMatrixI->gather(snap->atomData.aMat,
129 >      AtomCommMatrixRow->gather(snap->atomData.aMat,
130                                snap->atomIData.aMat);
131 <      AtomCommMatrixJ->gather(snap->atomData.aMat,
131 >      AtomCommMatrixColumn->gather(snap->atomData.aMat,
132                                snap->atomJData.aMat);
133      }
134      
135      // if needed, gather the atomic eletrostatic frames
136      if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
137 <      AtomCommMatrixI->gather(snap->atomData.electroFrame,
137 >      AtomCommMatrixRow->gather(snap->atomData.electroFrame,
138                                snap->atomIData.electroFrame);
139 <      AtomCommMatrixJ->gather(snap->atomData.electroFrame,
139 >      AtomCommMatrixColumn->gather(snap->atomData.electroFrame,
140                                snap->atomJData.electroFrame);
141      }
142   #endif      
143    }
144    
145 <  void ForceDecomposition::collectIntermediateData() {
145 >  void ForceMatrixDecomposition::collectIntermediateData() {
146   #ifdef IS_MPI
147      Snapshot* snap = sman_->getCurrentSnapshot();
148      
149      if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
150  
151 <      AtomCommRealI->scatter(snap->atomIData.density,
151 >      AtomCommRealRow->scatter(snap->atomIData.density,
152                               snap->atomData.density);
153  
154        int n = snap->atomData.density.size();
155        std::vector<RealType> rho_tmp(n, 0.0);
156 <      AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
156 >      AtomCommRealColumn->scatter(snap->atomJData.density, rho_tmp);
157        for (int i = 0; i < n; i++)
158          snap->atomData.density[i] += rho_tmp[i];
159      }
160   #endif
161    }
162    
163 <  void ForceDecomposition::distributeIntermediateData() {
163 >  void ForceMatrixDecomposition::distributeIntermediateData() {
164   #ifdef IS_MPI
165      Snapshot* snap = sman_->getCurrentSnapshot();
166      if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
167 <      AtomCommRealI->gather(snap->atomData.functional,
167 >      AtomCommRealRow->gather(snap->atomData.functional,
168                              snap->atomIData.functional);
169 <      AtomCommRealJ->gather(snap->atomData.functional,
169 >      AtomCommRealColumn->gather(snap->atomData.functional,
170                              snap->atomJData.functional);
171      }
172      
173      if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
174 <      AtomCommRealI->gather(snap->atomData.functionalDerivative,
174 >      AtomCommRealRow->gather(snap->atomData.functionalDerivative,
175                              snap->atomIData.functionalDerivative);
176 <      AtomCommRealJ->gather(snap->atomData.functionalDerivative,
176 >      AtomCommRealColumn->gather(snap->atomData.functionalDerivative,
177                              snap->atomJData.functionalDerivative);
178      }
179   #endif
180    }
181    
182    
183 <  void ForceDecomposition::collectData() {
183 >  void ForceMatrixDecomposition::collectData() {
184   #ifdef IS_MPI
185      Snapshot* snap = sman_->getCurrentSnapshot();
186      
187      int n = snap->atomData.force.size();
188      vector<Vector3d> frc_tmp(n, V3Zero);
189      
190 <    AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp);
190 >    AtomCommVectorRow->scatter(snap->atomIData.force, frc_tmp);
191      for (int i = 0; i < n; i++) {
192        snap->atomData.force[i] += frc_tmp[i];
193        frc_tmp[i] = 0.0;
194      }
195      
196 <    AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp);
196 >    AtomCommVectorColumn->scatter(snap->atomJData.force, frc_tmp);
197      for (int i = 0; i < n; i++)
198        snap->atomData.force[i] += frc_tmp[i];
199      
# Line 205 | Line 203 | namespace OpenMD {
203        int nt = snap->atomData.force.size();
204        vector<Vector3d> trq_tmp(nt, V3Zero);
205  
206 <      AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp);
206 >      AtomCommVectorRow->scatter(snap->atomIData.torque, trq_tmp);
207        for (int i = 0; i < n; i++) {
208          snap->atomData.torque[i] += trq_tmp[i];
209          trq_tmp[i] = 0.0;
210        }
211        
212 <      AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp);
212 >      AtomCommVectorColumn->scatter(snap->atomJData.torque, trq_tmp);
213        for (int i = 0; i < n; i++)
214          snap->atomData.torque[i] += trq_tmp[i];
215      }
# Line 222 | Line 220 | namespace OpenMD {
220                                         vector<RealType> (nLocal, 0.0));
221      
222      for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
223 <      AtomCommRealI->scatter(pot_row[i], pot_temp[i]);
223 >      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
224        for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
225          pot_local[i] += pot_temp[i][ii];
226        }

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