adding molecular dynamics sources/app/utility

2025-11-28 03:28:01 +00:00 · 2008-05-22 15:03:46 +01:00
parent b5a7c032c6
commit 4a9f21ba18
131 changed files with 15306 additions and 0 deletions
--- a/applications/utilities/preProcessing/molConfig/latticeStructures/BCC.H
+++ b/applications/utilities/preProcessing/molConfig/latticeStructures/BCC.H
@ -0,0 +1,179 @@
+labelVector iN(0,0,0);
+
+vector gap = (vector::one)*pow((numberDensity/2.0),-(1.0/3.0));
+
+#include "origin.H"
+
+// Info<< "gap = " << gap << endl;
+
+// Special treatment is required for the first position, i.e. iteration zero.
+
+if (n == 0)
+{
+    latticePosition.x() = (iN.x()*gap.x());
+
+    latticePosition.y() = (iN.y()*gap.y());
+
+    latticePosition.z() = (iN.z()*gap.z());
+
+    // Placing 2 molecules in each unit cell, using the algorithm from
+    // D. Rapaport, The Art of Molecular Dynamics Simulation, 2nd Ed, p68
+
+    for (label iU = 0; iU < 2; iU++)
+    {
+        vector unitCellLatticePosition = latticePosition;
+
+        if (iU == 1)
+        {
+            unitCellLatticePosition += 0.5 * gap;
+        }
+
+        if (originSpecifies == "corner")
+        {
+            unitCellLatticePosition -= 0.25*gap;
+        }
+
+//         Info << nl << n << ", " << unitCellLatticePosition;
+
+        globalPosition =
+            origin + transform(latticeToGlobal,unitCellLatticePosition);
+
+        partOfLayerInBounds = mesh_.bounds().contains(globalPosition);
+
+        if
+        (
+             findIndex(mesh_.cellZones()[cZ], mesh_.findCell(globalPosition))
+           != -1
+        )
+        {
+            molsPlacedThisIteration++;
+
+            initialPositions.append(globalPosition);
+
+            initialCelli.append(mesh_.findCell(globalPosition));
+        }
+    }
+}
+else
+{
+    // Place top and bottom caps.
+
+    for (iN.z() = -n; iN.z() <= n; iN.z() += 2*n)
+    {
+        for (iN.y() = -n; iN.y() <= n; iN.y()++)
+        {
+            for (iN.x() = -n; iN.x() <= n; iN.x()++)
+            {
+                latticePosition.x() = (iN.x() * gap.x());
+
+                latticePosition.y() = (iN.y() * gap.y());
+
+                latticePosition.z() = (iN.z() * gap.z());
+
+                for (label iU = 0; iU < 2; iU++)
+                {
+                    vector unitCellLatticePosition = latticePosition;
+
+                    if (iU == 1)
+                    {
+                        unitCellLatticePosition += 0.5*gap;
+                    }
+
+                    if(originSpecifies == "corner")
+                    {
+                        unitCellLatticePosition -= 0.25*gap;
+                    }
+
+//                     Info << nl << iN << ", " << unitCellLatticePosition;
+
+                    globalPosition =
+                        origin
+                      + transform(latticeToGlobal,unitCellLatticePosition);
+
+                    partOfLayerInBounds =
+                        mesh_.bounds().contains(globalPosition);
+
+                    if
+                    (
+                        findIndex
+                        (
+                             mesh_.cellZones()[cZ],
+                             mesh_.findCell(globalPosition)
+                        )
+                     != -1)
+                    {
+                        molsPlacedThisIteration++;
+
+                        initialPositions.append(globalPosition);
+
+                        initialCelli.append(mesh_.findCell(globalPosition));
+                    }
+                }
+            }
+        }
+    }
+
+//     Placing sides
+
+    for (iN.z() = -(n-1); iN.z() <= (n-1); iN.z()++)
+    {
+        for (label iR = 0; iR <= 2*n -1; iR++)
+        {
+            latticePosition.x() = (n*gap.x());
+
+            latticePosition.y() = ((-n + (iR + 1))*gap.y());
+
+            latticePosition.z() = (iN.z() * gap.z());
+
+            for (label iK = 0; iK < 4; iK++)
+            {
+                for (label iU = 0; iU < 2; iU++)
+                {
+                    vector unitCellLatticePosition = latticePosition;
+
+                    if (iU == 1)
+                    {
+                        unitCellLatticePosition += 0.5 * gap;
+                    }
+
+                    if (originSpecifies == "corner")
+                    {
+                        unitCellLatticePosition -= 0.25*gap;
+                    }
+
+                    globalPosition =
+                        origin
+                      + transform(latticeToGlobal,unitCellLatticePosition);
+
+                    partOfLayerInBounds =
+                        mesh_.bounds().contains(globalPosition);
+
+                    if
+                    (
+                        findIndex
+                         (
+                             mesh_.cellZones()[cZ],
+                             mesh_.findCell(globalPosition)
+                         )
+                      != -1
+                    )
+                    {
+                        molsPlacedThisIteration++;
+
+                        initialPositions.append(globalPosition);
+
+                        initialCelli.append(mesh_.findCell(globalPosition));
+                    }
+                }
+
+                latticePosition =
+                    vector
+                    (
+                      - latticePosition.y(),
+                        latticePosition.x(),
+                        latticePosition.z()
+                    );
+            }
+        }
+    }
+}