[ViewVC] Diff of: OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs.
Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC

+          nTopos++;
-<
+    }
->
+    }
->
-+
+  void ForceMatrixDecomposition::createGtypeCutoffMap() {
-+
-+
+    RealType tol = 1e-6;
-+
+    RealType rc;
-+
+    int atid;
-+
+    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
-+
+    vector<RealType> atypeCutoff;
-+
+    atypeCutoff.reserve( atypes.size() );
-+
-+
+    for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
-+
+      rc = interactionMan_->getSuggestedCutoffRadius(*at);
-+
+      atid = (*at)->getIdent();
-+
+      atypeCutoff[atid] = rc;
-+
+    }
-+
-+
+    vector<RealType> gTypeCutoffs;
-+
-+
+    // first we do a single loop over the cutoff groups to find the
-+
+    // largest cutoff for any atypes present in this group.
-+
+#ifdef IS_MPI
-+
+    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
-+
+    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
-+
+      vector<int> atomListRow = getAtomsInGroupRow(cg1);
-+
+      for (vector<int>::iterator ia = atomListRow.begin();
-+
+           ia != atomListRow.end(); ++ia) {
-+
+        int atom1 = (*ia);
-+
+        atid = identsRow[atom1];
-+
+        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
-+
+          groupCutoffRow[cg1] = atypeCutoff[atid];
-+
+        }
-+
+      }
-+
-+
+      bool gTypeFound = false;
-+
+      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
-+
+        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
-+
+          groupRowToGtype[cg1] = gt;
-+
+          gTypeFound = true;
-+
+        }
-+
+      }
-+
+      if (!gTypeFound) {
-+
+        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
-+
+        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
-+
+      }
-+
-+
+    }
-+
+    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
-+
+    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
-+
+      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
-+
+      for (vector<int>::iterator jb = atomListCol.begin();
-+
+           jb != atomListCol.end(); ++jb) {
-+
+        int atom2 = (*jb);
-+
+        atid = identsCol[atom2];
-+
+        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
-+
+          groupCutoffCol[cg2] = atypeCutoff[atid];
-+
+        }
-+
+      }
-+
+      bool gTypeFound = false;
-+
+      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
-+
+        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
-+
+          groupColToGtype[cg2] = gt;
-+
+          gTypeFound = true;
-+
+        }
-+
+      }
-+
+      if (!gTypeFound) {
-+
+        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
-+
+        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
-+
+      }
-+
+    }
-+
+#else
-+
+    vector<RealType> groupCutoff(nGroups_, 0.0);
-+
+    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
-+
+      groupCutoff[cg1] = 0.0;
-+
+      vector<int> atomList = getAtomsInGroupRow(cg1);
-+
+      for (vector<int>::iterator ia = atomList.begin();
-+
+           ia != atomList.end(); ++ia) {
-+
+        int atom1 = (*ia);
-+
+        atid = identsLocal[atom1];
-+
+        if (atypeCutoff[atid] > groupCutoff[cg1]) {
-+
+          groupCutoff[cg1] = atypeCutoff[atid];
-+
+        }
-+
+      }
-+
-+
+      bool gTypeFound = false;
-+
+      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
-+
+        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
-+
+          groupToGtype[cg1] = gt;
-+
+          gTypeFound = true;
-+
+        }
-+
+      }
-+
+      if (!gTypeFound) {
-+
+        gTypeCutoffs.push_back( groupCutoff[cg1] );
-+
+        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
-+
+      }
-+
+    }
-+
+#endif
-+
-+
+    // Now we find the maximum group cutoff value present in the simulation
-+
-+
+    vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
-+
+    RealType groupMax = *groupMaxLoc;
-+
-+
+#ifdef IS_MPI
-+
+    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
-+
+#endif
-+
-+
+    RealType tradRcut = groupMax;
-+
-+
+    for (int i = 0; i < gTypeCutoffs.size();  i++) {
-+
+      for (int j = 0; j < gTypeCutoffs.size();  j++) {
-+
-+
+        RealType thisRcut;
-+
+        switch(cutoffPolicy_) {
-+
+        case TRADITIONAL:
-+
+          thisRcut = tradRcut;
-+
+        case MIX:
-+
+          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
-+
+        case MAX:
-+
+          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
-+
+        default:
-+
+          sprintf(painCave.errMsg,
-+
+                  "ForceMatrixDecomposition::createGtypeCutoffMap "
-+
+                  "hit an unknown cutoff policy!\n");
-+
+          painCave.severity = OPENMD_ERROR;
-+
+          painCave.isFatal = 1;
-+
+          simError();
-+
+        }
-+
-+
+        pair<int,int> key = make_pair(i,j);
-+
+        gTypeCutoffMap[key].first = thisRcut;
-+
-+
+        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
-+
-+
+        gTypeCutoffMap[key].second = thisRcut*thisRcut;
-+
-+
+        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
-+
-+
+        // sanity check
-+
-+
+        if (userChoseCutoff_) {
-+
+          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
-+
+            sprintf(painCave.errMsg,
-+
+                    "ForceMatrixDecomposition::createGtypeCutoffMap "
-+
+                    "user-specified rCut does not match computed group Cutoff\n");
-+
+            painCave.severity = OPENMD_ERROR;
-+
+            painCave.isFatal = 1;
-+
+            simError();
-+
+          }
-+
+        }
-+
+      }
-+
+    }
-+
+  }
-+
-+
-+
+  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
-+
+    int i, j;
-+
-+
+#ifdef IS_MPI
-+
+    i = groupRowToGtype[cg1];
-+
+    j = groupColToGtype[cg2];
-+
+#else
-+
+    i = groupToGtype[cg1];
-+
+    j = groupToGtype[cg2];
-+
+#endif
-+
-+
+    return gTypeCutoffMap[make_pair(i,j)];
-+
+  }
-+
-+
+  void ForceMatrixDecomposition::zeroWorkArrays() {
+    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
+  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
+    vector<pair<int, int> > neighborList;
-+
+    groupCutoffs cuts;
+#ifdef IS_MPI
+    cellListRow_.clear();
+    cellListCol_.clear();
+    cellList_.clear();
+#endif
-<
+    // dangerous to not do error checking.
-<
+    RealType rCut_;
-<
-<
+    RealType rList_ = (rCut_ + skinThickness_);
->
+    RealType rList_ = (largestRcut_ + skinThickness_);
+    RealType rl2 = rList_ * rList_;
+    Snapshot* snap_ = sman_->getCurrentSnapshot();
+    Mat3x3d Hmat = snap_->getHmat();
+                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
+                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
+                  snap_->wrapVector(dr);
-<
+                  if (dr.lengthSquare() < rl2) {
->
+                  cuts = getGroupCutoffs( (*j1), (*j2) );
->
+                  if (dr.lengthSquare() < cuts.third) {
+                    neighborList.push_back(make_pair((*j1), (*j2)));
+                if (m2 != m1 || (*j2) < (*j1)) {
+                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
+                  snap_->wrapVector(dr);
-<
+                  if (dr.lengthSquare() < rl2) {
->
+                  cuts = getGroupCutoffs( (*j1), (*j2) );
->
+                  if (dr.lengthSquare() < cuts.third) {
+                    neighborList.push_back(make_pair((*j1), (*j2)));

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents): Revision 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs. Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC

Diff Legend

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs.
Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC