// two molecules
private Boolean CheckForClashes(int im1, int im2)
{
Molecule m1 = _molecules[im1];
Molecule m2 = _molecules[im2];
Vector3 dcm = translation[im1] - translation[im2], rc1, rc2;
// check clusters
Vector3[] rc2cache = new Vector3[m2.AtomClusters.Length];
double sumr, dsq, dx2, dy2, dz2;
Vector3 sumrv;
AtomCluster c1, c2;
Matrix3 rot1to2 = Matrix3.Transpose(rotation[im2]) * rotation[im1];
Matrix3 rot2to1 = Matrix3.Transpose(rot1to2);
Vector3 dcm1t = Matrix3.Transpose(rotation[im1]) * dcm;
Vector3 dcm2t = Matrix3.Transpose(rotation[im2]) * dcm;
int[] c2tocheck = new int[m2.AtomClusters.Length];
int j2, n2tocheck;
int[] mustbechecked1 = new int[m1.AtomClusters.Length];
int[] mustbechecked2 = new int[m2.AtomClusters.Length];
// check if we can skip some of m2
n2tocheck = 0;
for (int j = 0; j < m2.AtomClusters.Length; j++)
{
c2 = m2.AtomClusters[j];
rc2 = rot2to1 * c2 - dcm1t;
dx2 = rc2.X * rc2.X;
dy2 = rc2.Y * rc2.Y;
dz2 = rc2.Z * rc2.Z;
sumrv = m1.MaxRadius + c2.ClusterRadius;
if ((dy2 + dz2 <= sumrv.X * sumrv.X) && (dx2 + dz2 <= sumrv.Y * sumrv.Y) && (dx2 + dy2 <= sumrv.Z * sumrv.Z))
{
rc2cache[n2tocheck] = c2;
c2tocheck[n2tocheck++] = j;
}
}
for (int i = 0; i < m1.AtomClusters.Length; i++)
{
c1 = m1.AtomClusters[i];
rc1 = rot1to2 * c1 + dcm2t;
// if completely out of reach, skip the check
dx2 = rc1.X * rc1.X;
dy2 = rc1.Y * rc1.Y;
dz2 = rc1.Z * rc1.Z;
sumrv = m2.MaxRadius + c1.ClusterRadius;
if ((dy2 + dz2 > sumrv.X * sumrv.X) || (dx2 + dz2 > sumrv.Y * sumrv.Y) || (dx2 + dy2 > sumrv.Z * sumrv.Z))
{
continue;
}
// otherwise check selected clusters from m2
for (int j = 0; j < n2tocheck; j++)
{
j2 = c2tocheck[j];
rc2 = rc2cache[j];
c2 = m2.AtomClusters[j2];
dsq = Vector3.SquareNormDiff(rc1, rc2);
sumr = c1.ClusterRadius + c2.ClusterRadius;
if (dsq < sumr * sumr) // clusters overlap, check all atoms
{
mustbechecked1[i] = 1;
mustbechecked2[j2] = 1;
// clash |= CheckForClashes(c1, c2, im1, im2, dcm); // => replaced with unmanaged
}
}
}
// this runs in m1's coordinate system!
Vector3 fclash = new Vector3(), tclash1 = new Vector3(), tclash2 = new Vector3();
double dEClash = FpsNativeWrapper.CheckForClashes(FpsNativeWrapper.Aligned16(m1.XYZvdwRVectorArray),
FpsNativeWrapper.Aligned16(m2.XYZvdwRVectorArray), m1.AtomClusters, m2.AtomClusters,
m1.AtomClusters.Length, m2.AtomClusters.Length, mustbechecked1, mustbechecked2,
rot2to1, -dcm1t, kclash, ref fclash, ref tclash1, ref tclash2);
force[im1] += rotation[im1] * fclash;
force[im2] -= rotation[im1] * fclash;
torque[im1] += rotation[im1] * tclash1;
torque[im2] += rotation[im1] * tclash2;
Eclash += dEClash;
return(dEClash > 1.0e-8);
}
