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

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1561 by gezelter, Sat Apr 30 02:54:02 2011 UTC vs.
Revision 1562 by gezelter, Thu May 12 17:00:14 2011 UTC

+    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
+      idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
+      idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
-+
+    }
-+
+#else
-+
+    if (storageLayout_ & DataStorage::dslAmat) {
-+
+      idat.A1 = &(snap_->atomData.aMat[atom1]);
-+
+      idat.A2 = &(snap_->atomData.aMat[atom2]);
-+
+    }
-+
-+
+    if (storageLayout_ & DataStorage::dslElectroFrame) {
-+
+      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
-+
+      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
-+
+    }
-+
-+
+    if (storageLayout_ & DataStorage::dslTorque) {
-+
+      idat.t1 = &(snap_->atomData.torque[atom1]);
-+
+      idat.t2 = &(snap_->atomData.torque[atom2]);
-+
+    }
-+
-+
+    if (storageLayout_ & DataStorage::dslDensity) {
-+
+      idat.rho1 = &(snap_->atomData.density[atom1]);
-+
+      idat.rho2 = &(snap_->atomData.density[atom2]);
-+
-+
+    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
-+
+      idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
-+
+      idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
-+
+    }
+#endif
+  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
-+
+    InteractionData idat;
-+
+    skippedCharge1
-+
+      skippedCharge2
-+
+      rij
-+
+      d
-+
+    electroMult
-+
+    sw
-+
+    f
-+
+#ifdef IS_MPI
-+
-+
+    if (storageLayout_ & DataStorage::dslElectroFrame) {
-+
+      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
-+
+      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
-+
+    }
-+
+    if (storageLayout_ & DataStorage::dslTorque) {
-+
+      idat.t1 = &(atomRowData.torque[atom1]);
-+
+      idat.t2 = &(atomColData.torque[atom2]);
-+
+    }
-+
-+
+  SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
-+
+  }
-+
-+
-+
+  /*
-+
+   * buildNeighborList
-+
+   *
-+
+   * first element of pair is row-indexed CutoffGroup
-+
+   * second element of pair is column-indexed CutoffGroup
-+
+   */
-+
+  vector<pair<int, int> >  buildNeighborList() {
-+
+    Vector3d dr, invWid, rs, shift;
-+
+    Vector3i cc, m1v, m2s;
-+
+    RealType rrNebr;
-+
+    int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset;
-+
-+
-+
+    vector<pair<int, int> > neighborList;
-+
+    Vector3i nCells;
-+
+    Vector3d invWid, r;
-+
-+
+    rList_ = (rCut_ + skinThickness_);
-+
+    rl2 = rList_ * rList_;
-+
-+
+    snap_ = sman_->getCurrentSnapshot();
-+
+    Mat3x3d Hmat = snap_->getHmat();
-+
+    Vector3d Hx = Hmat.getColumn(0);
-+
+    Vector3d Hy = Hmat.getColumn(1);
-+
+    Vector3d Hz = Hmat.getColumn(2);
-+
-+
+    nCells.x() = (int) ( Hx.length() )/ rList_;
-+
+    nCells.y() = (int) ( Hy.length() )/ rList_;
-+
+    nCells.z() = (int) ( Hz.length() )/ rList_;
-+
-+
+    for (i = 0; i < nGroupsInRow; i++) {
-+
+      rs = cgRowData.position[i];
-+
+      snap_->scaleVector(rs);
-+
+    }
-+
-+
-+
+    VDiv (invWid, cells, region);
-+
+    for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1;
-+
+    for (n = 0; n < nMol; n ++) {
-+
+      VSAdd (rs, mol[n].r, 0.5, region);
-+
+      VMul (cc, rs, invWid);
-+
+      c = VLinear (cc, cells) + nMol;
-+
+      cellList[n] = cellList[c];
-+
+      cellList[c] = n;
-+
+    }
-+
+    nebrTabLen = 0;
-+
+    for (m1z = 0; m1z < cells.z(); m1z++) {
-+
+      for (m1y = 0; m1y < cells.y(); m1y++) {
-+
+        for (m1x = 0; m1x < cells.x(); m1x++) {
-+
+          Vector3i m1v(m1x, m1y, m1z);
-+
+          m1 = VLinear(m1v, cells) + nMol;
-+
+          for (offset = 0; offset < nOffset_; offset++) {
-+
+            m2v = m1v + cellOffsets_[offset];
-+
+            shift = V3Zero();
-+
-+
+            if (m2v.x() >= cells.x) {
-+
+              m2v.x() = 0;
-+
+              shift.x() = region.x();
-+
+            } else if (m2v.x() < 0) {
-+
+              m2v.x() = cells.x() - 1;
-+
+              shift.x() = - region.x();
-+
+            }
-+
-+
+            if (m2v.y() >= cells.y()) {
-+
+              m2v.y() = 0;
-+
+              shift.y() = region.y();
-+
+            } else if (m2v.y() < 0) {
-+
+              m2v.y() = cells.y() - 1;
-+
+              shift.y() = - region.y();
-+
+            }
-+
-+
+            m2 = VLinear (m2v, cells) + nMol;
-+
+            for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) {
-+
+              for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) {
-+
+                if (m1 != m2 || j2 < j1) {
-+
+                  dr = mol[j1].r - mol[j2].r;
-+
+                  VSub (dr, mol[j1].r, mol[j2].r);
-+
+                  VVSub (dr, shift);
-+
+                  if (VLenSq (dr) < rrNebr) {
-+
+                    neighborList.push_back(make_pair(j1, j2));
-+
+                  }
-+
+                }
-+
+              }
-+
+            }
-+
+          }
-+
+        }
-+
+      }
-+
+    }

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents): Revision 1561 by gezelter, Sat Apr 30 02:54:02 2011 UTC vs. Revision 1562 by gezelter, Thu May 12 17:00:14 2011 UTC

Diff Legend

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1561 by gezelter, Sat Apr 30 02:54:02 2011 UTC vs.
Revision 1562 by gezelter, Thu May 12 17:00:14 2011 UTC