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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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Comparing:
branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1539 by gezelter, Fri Jan 14 22:31:31 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"
42 < #include "parallel/Communicator.hpp"
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 <  void ForceDecomposition::distributeInitialData() {
50 < #ifdef IS_MPI
49 >  /**
50 >   * distributeInitialData is essentially a copy of the older fortran
51 >   * SimulationSetup
52 >   */
53 >  
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 <    int nAtoms;
61 <    int nGroups;
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 <    AtomCommRealI = new Comm<I,RealType>(nAtoms);
66 <    AtomCommVectorI = new Comm<I,Vector3d>(nAtoms);
67 <    AtomCommMatrixI = new Comm<I,Mat3x3d>(nAtoms);
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 <    AtomCommRealJ = new Comm<J,RealType>(nAtoms);
71 <    AtomCommVectorJ = new Comm<J,Vector3d>(nAtoms);
72 <    AtomCommMatrixJ = new Comm<J,Mat3x3d>(nAtoms);
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 <    cgCommVectorI = new Comm<I,Vector3d>(nGroups);
76 <    cgCommVectorJ = new Comm<J,Vector3d>(nGroups);
77 <    // more to come
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 >    
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 >
103 >    // still need:
104 >    // topoDist
105 >    // exclude
106   #endif
107    }
108      
109  
110  
111 <  void ForceDecomposition::distributeData()  {
111 >  void ForceMatrixDecomposition::distributeData()  {
112   #ifdef IS_MPI
113      Snapshot* snap = sman_->getCurrentSnapshot();
114 <
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,
119 <                           snap->atomJData.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,
123 <                         snap->cgIData.position);
124 <    cgCommVectorJ->gather(snap->cgData.position,
125 <                         snap->cgJData.position);
122 >    cgCommVectorRow->gather(snap->cgData.position,
123 >                          snap->cgIData.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,
130 <                             snap->atomIData.aMat);
131 <      AtomCommMatrixJ->gather(snap->atomData.aMat,
132 <                             snap->atomJData.aMat);
129 >      AtomCommMatrixRow->gather(snap->atomData.aMat,
130 >                              snap->atomIData.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,
138 <                             snap->atomIData.electroFrame);
139 <      AtomCommMatrixJ->gather(snap->atomData.electroFrame,
140 <                             snap->atomJData.electroFrame);
137 >      AtomCommMatrixRow->gather(snap->atomData.electroFrame,
138 >                              snap->atomIData.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();
106 –    // gather up the atomic positions
148      
149      if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
150 <      AtomCommRealI->scatter(snap->atomIData.density,
151 <                            snap->atomData.density);
152 <      std::vector<RealType> rho_tmp;
153 <      int n = snap->getNumberOfAtoms();
154 <      rho_tmp.reserve( n );
155 <      AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
150 >
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 >      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,
168 <                           snap->atomIData.functional);
169 <      AtomCommRealJ->gather(snap->atomData.functional,
170 <                           snap->atomJData.functional);
167 >      AtomCommRealRow->gather(snap->atomData.functional,
168 >                            snap->atomIData.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,
175 <                           snap->atomIData.functionalDerivative);
176 <      AtomCommRealJ->gather(snap->atomData.functionalDerivative,
177 <                           snap->atomJData.functionalDerivative);
174 >      AtomCommRealRow->gather(snap->atomData.functionalDerivative,
175 >                            snap->atomIData.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 +    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 +    AtomCommVectorColumn->scatter(snap->atomJData.force, frc_tmp);
197 +    for (int i = 0; i < n; i++)
198 +      snap->atomData.force[i] += frc_tmp[i];
199 +    
200 +    
201 +    if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
202 +
203 +      int nt = snap->atomData.force.size();
204 +      vector<Vector3d> trq_tmp(nt, V3Zero);
205 +
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 +      AtomCommVectorColumn->scatter(snap->atomJData.torque, trq_tmp);
213 +      for (int i = 0; i < n; i++)
214 +        snap->atomData.torque[i] += trq_tmp[i];
215 +    }
216 +    
217 +    int nLocal = snap->getNumberOfAtoms();
218 +
219 +    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
220 +                                       vector<RealType> (nLocal, 0.0));
221 +    
222 +    for (int i = 0; i < N_INTERACTION_FAMILIES; 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 +      }
227 +    }
228   #endif
229    }
230    

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