private void PrepareSimulation()
{
// molecules
Nmolecules = _molecules.Count;
int maxatomsincluster = 0;
for (int i = 0; i < Nmolecules; i++)
{
minmass = Math.Min(minmass, _molecules[i].Mass);
maxatomsincluster = Math.Max(maxatomsincluster, _molecules[i].MaxAtomsInCluster);
}
// labeling positions
int im;
labelingpos_cm = new LabelingPositionList();
labelingpos_cm.AddRange(this._labelingpositions);
lpossim = new Vector3[labelingpos_cm.Count];
LtoM = new int[labelingpos_cm.Count];
// convert to local coordinates
for (int i = 0; i < labelingpos_cm.Count; i++)
{
im = _molecules.FindIndex(labelingpos_cm[i].Molecule);
LtoM[i] = im;
labelingpos_cm[i] -= _molecules[im].CM;
lpossim[i] = labelingpos_cm[i];
}
// distances
Distance dist_i;
DtoL1 = new int[_distances.Count];
DtoM1 = new int[_distances.Count];
DtoL2 = new int[_distances.Count];
DtoM2 = new int[_distances.Count];
kplus = new double[_distances.Count];
kminus = new double[_distances.Count];
drmaxplus = new double[_distances.Count];
drmaxminus = new double[_distances.Count];
double minerror = double.MaxValue;
for (int i = 0; i < _distances.Count; i++)
{
DtoL1[i] = labelingpos_cm.FindIndex(_distances[i].Position1);
DtoM1[i] = _molecules.FindIndex(labelingpos_cm.Find(_distances[i].Position1).Molecule);
DtoL2[i] = labelingpos_cm.FindIndex(_distances[i].Position2);
DtoM2[i] = _molecules.FindIndex(labelingpos_cm.Find(_distances[i].Position2).Molecule);
// check if bond
dist_i = _distances[i];
dist_i.IsBond = (labelingpos_cm[DtoL1[i]].Dye == DyeType.Unknown && labelingpos_cm[DtoL1[i]].AVData.AtomID > 0 &&
labelingpos_cm[DtoL1[i]].AVData.AVType == AVSimlationType.None && labelingpos_cm[DtoL2[i]].Dye == DyeType.Unknown &&
labelingpos_cm[DtoL2[i]].AVData.AtomID > 0 && labelingpos_cm[DtoL2[i]].AVData.AVType == AVSimlationType.None);
_distances[i] = dist_i;
// if bond, set small vdW radii to "exclude" from clashing
if (dist_i.IsBond)
{
foreach (var lp in new[] { labelingpos_cm[DtoL1[i]], labelingpos_cm[DtoL2[i]] })
{
int m = _molecules.FindIndex(lp.Molecule);
int natom = Array.BinarySearch <int>(_molecules[m].OriginalAtomID, lp.AVData.AtomID);
_molecules[m].vdWR[natom] = AtomData.vdWRNoClash;
int natom_cluster = Array.FindIndex <int>(_molecules[m].ClusteredAtomOriginalIndex, n => n == natom);
if (natom_cluster >= 0)
{
_molecules[m].ClusteredAtomvdwR[natom_cluster] = AtomData.vdWRNoClash;
System.Runtime.InteropServices.Marshal.Copy(new[] { (float)AtomData.vdWRNoClash }, 0,
FpsNativeWrapper.Aligned16(_molecules[m].XYZvdwRVectorArray) + (4 * natom_cluster + 3) * sizeof(float), 1);
}
}
}
// "spring constants"
kplus[i] = 2.0 / _distances[i].ErrPlus / _distances[i].ErrPlus;
kminus[i] = 2.0 / _distances[i].ErrMinus / _distances[i].ErrMinus;
//Console.Out.WriteLine("distance#" + i + " k+= " + kplus[i] + " k-= " + kminus[i] + " err+ " + _distances[i].ErrPlus + " err- " + _distances[i].ErrMinus);
drmaxplus[i] = SimulationParameters.MaxForce / kplus[i];
drmaxminus[i] = -SimulationParameters.MaxForce / kminus[i];
minerror = Math.Min(minerror, Math.Min(_distances[i].ErrPlus, _distances[i].ErrMinus));
}
// simulation parameters
kclash = 2.0 / SimulationParameters.ClashTolerance / SimulationParameters.ClashTolerance;
drmaxclash = -SimulationParameters.MaxForce / kclash;
dr4dt = Math.Min(SimulationParameters.ClashTolerance * 0.5, minerror);
}
/// <summary>
/// Calculate some additional parameters needed for simulations
/// </summary>
public void Prepare()
{
if (Error != "")
{
return;
}
// min/max values of local coordinates
double xmin = 1.0e6, xmax = -1.0e6, ymin = 1.0e6, ymax = -1.0e6, zmin = 1.0e6, zmax = -1.0e6;
for (int i = 0; i < NAtoms; i++)
{
xmin = Math.Min(xmin, XLocal[i]);
xmax = Math.Max(xmax, XLocal[i]);
ymin = Math.Min(ymin, YLocal[i]);
ymax = Math.Max(ymax, YLocal[i]);
zmin = Math.Min(zmin, ZLocal[i]);
zmax = Math.Max(zmax, ZLocal[i]);
MaxRadius = new Vector3(Math.Max(MaxRadius.X, Math.Sqrt(YLocal[i] * YLocal[i] + ZLocal[i] * ZLocal[i]) + vdWR[i]),
Math.Max(MaxRadius.Y, Math.Sqrt(XLocal[i] * XLocal[i] + ZLocal[i] * ZLocal[i]) + vdWR[i]),
Math.Max(MaxRadius.Z, Math.Sqrt(XLocal[i] * XLocal[i] + YLocal[i] * YLocal[i]) + vdWR[i]));
}
// moment(s) of inertia
double ixx = 0.0, iyy = 0.0, izz = 0.0, ixy = 0.0, ixz = 0.0, iyz = 0.0;
double m = 0.0, x2, y2, z2;
for (int i = 0; i < NAtoms; i++)
{
m = AtomMass[i];
x2 = XLocal[i] * XLocal[i]; y2 = YLocal[i] * YLocal[i]; z2 = ZLocal[i] * ZLocal[i];
ixx += m * (y2 + z2);
iyy += m * (x2 + z2);
izz += m * (x2 + y2);
ixy -= m * XLocal[i] * YLocal[i];
ixz -= m * XLocal[i] * ZLocal[i];
iyz -= m * YLocal[i] * ZLocal[i];
}
SimpleI = Math.Max(Math.Max(ixx, ixy), ixz);
FullI = new Matrix3(ixx, ixy, ixz, ixy, iyy, iyz, ixz, iyz, izz);
// clusters of clustersize^3 angstrom
const double clustersize = 10.0;
int nx, ny, nz, nxoff, nyoff, nzoff;
nx = (int)(Math.Ceiling(xmax / clustersize) + Math.Ceiling(-xmin / clustersize));
ny = (int)(Math.Ceiling(ymax / clustersize) + Math.Ceiling(-ymin / clustersize));
nz = (int)(Math.Ceiling(zmax / clustersize) + Math.Ceiling(-zmin / clustersize));
nxoff = (int)Math.Ceiling(-xmin / clustersize);
nyoff = (int)Math.Ceiling(-ymin / clustersize);
nzoff = (int)Math.Ceiling(-zmin / clustersize);
int nclusters = nx * ny * nz;
AtomCluster[] atomcluster_tmp = new AtomCluster[nx * ny * nz];
// sort atoms
// first run: count atoms in each cluster
int nc, cNAtomsmax = 0;
double rcsize = 1.0 / clustersize;
for (int i = 0; i < NAtoms; i++)
{
nc = (int)(ZLocal[i] * rcsize + nzoff) + nz * ((int)(YLocal[i] * rcsize + nyoff)
+ ny * ((int)(XLocal[i] * rcsize + nxoff)));
atomcluster_tmp[nc].NAtoms++;
cNAtomsmax = Math.Max(cNAtomsmax, atomcluster_tmp[nc].NAtoms);
}
// allocate index arrays
int ncfull = 0;
int[][] originalatomindex = new int[nclusters][];
for (nc = 0; nc < nclusters; nc++)
{
if (atomcluster_tmp[nc].NAtoms > 0)
{
originalatomindex[nc] = new int[atomcluster_tmp[nc].NAtoms];
ncfull++;
}
}
// fill
int[] atomcounters = new int[nclusters];
for (int i = 0; i < NAtoms; i++)
{
nc = (int)(ZLocal[i] * rcsize + nzoff) + nz * ((int)(YLocal[i] * rcsize + nyoff)
+ ny * ((int)(XLocal[i] * rcsize + nxoff)));
originalatomindex[nc][atomcounters[nc]++] = i;
}
// remove empty
AtomClusters = new AtomCluster[ncfull];
ncfull = 0;
for (nc = 0; nc < nclusters; nc++)
{
if (atomcluster_tmp[nc].NAtoms > 0)
{
originalatomindex[ncfull] = originalatomindex[nc];
AtomClusters[ncfull++] = atomcluster_tmp[nc];
}
}
// optimize each
double rmax, cx, cy, cz;
int ilocal;
Vector3 rlocal;
for (nc = 0; nc < AtomClusters.Length; nc++)
{
// get the center
cx = 0.0; cy = 0.0; cz = 0.0;
for (int i = 0; i < AtomClusters[nc].NAtoms; i++)
{
ilocal = originalatomindex[nc][i];
cx += XLocal[ilocal]; cy += YLocal[ilocal]; cz += ZLocal[ilocal];
}
cx /= (double)AtomClusters[nc].NAtoms;
cy /= (double)AtomClusters[nc].NAtoms;
cz /= (double)AtomClusters[nc].NAtoms;
AtomClusters[nc].ClusterCenter = new Vector3(cx, cy, cz);
// find the most distant atom
rmax = -1.0;
for (int i = 0; i < AtomClusters[nc].NAtoms; i++)
{
ilocal = originalatomindex[nc][i];
rlocal = new Vector3(cx - XLocal[ilocal], cy - YLocal[ilocal], cz - ZLocal[ilocal]);
rmax = Math.Max(Vector3.Abs(rlocal) + vdWR[ilocal], rmax);
}
AtomClusters[nc].ClusterRadius = rmax;
}
// try an alternative method : find a pair of most distant atoms for each dimension, try as a center
int jlocal;
double absr;
for (nc = 0; nc < AtomClusters.Length; nc++)
{
rmax = -1.0;
rlocal = AtomClusters[nc];
for (int i = 0; i < AtomClusters[nc].NAtoms; i++)
{
ilocal = originalatomindex[nc][i];
cx = XLocal[ilocal]; cy = YLocal[ilocal]; cz = ZLocal[ilocal];
for (int j = i + 1; j < AtomClusters[nc].NAtoms; j++)
{
jlocal = originalatomindex[nc][j];
rlocal = new Vector3(XLocal[jlocal] - cx, YLocal[jlocal] - cy, ZLocal[jlocal] - cz);
absr = Vector3.Abs(rlocal);
if (rmax < absr + vdWR[ilocal] + vdWR[jlocal])
{
rmax = absr + vdWR[ilocal] + vdWR[jlocal];
rlocal = (absr == 0.0) ? new Vector3(cx, cy, cz) :
new Vector3(cx, cy, cz) + rlocal * ((0.5 * rmax - vdWR[ilocal]) / absr);
}
}
}
// find the most distant atom
rmax = -1.0;
cx = rlocal.X; cy = rlocal.Y; cz = rlocal.Z;
for (int i = 0; i < AtomClusters[nc].NAtoms; i++)
{
ilocal = originalatomindex[nc][i];
rlocal = new Vector3(cx - XLocal[ilocal], cy - YLocal[ilocal], cz - ZLocal[ilocal]);
rmax = Math.Max(Vector3.Abs(rlocal) + vdWR[ilocal], rmax);
}
if (rmax < AtomClusters[nc].ClusterRadius)
{
AtomClusters[nc].ClusterCenter = new Vector3(cx, cy, cz);
AtomClusters[nc].ClusterRadius = rmax;
}
}
#if DEBUG
if (DebugData.SaveAtomClusters)
{
// for debugging: save clusters xyz
using (StreamWriter sw = new StreamWriter(this.Name + ".cluster.xyz", false))
{
sw.WriteLine(AtomClusters.Length.ToString());
sw.WriteLine("cluster");
for (int i = 0; i < AtomClusters.Length; i++)
{
sw.WriteLine("L" + i.ToString() + " " + AtomClusters[i].ClusterCenter.X.ToString("F3") + " "
+ AtomClusters[i].ClusterCenter.Y.ToString("F3") + " " + AtomClusters[i].ClusterCenter.Z.ToString("F3"));
}
sw.Close();
}
using (StreamWriter sw = new StreamWriter(this.Name + ".cluster.pml", false))
{
sw.WriteLine("select all");
sw.WriteLine("translate [" + CM.X.ToString("F3") + "," + CM.Y.ToString("F3")
+ "," + CM.Z.ToString("F3") + "]");
sw.WriteLine("deselect");
for (int i = 0; i < AtomClusters.Length; i++)
{
sw.WriteLine("alter (name L" + i.ToString() + "), vdw=" + AtomClusters[i].ClusterRadius.ToString("F3"));
}
sw.Close();
}
}
#endif
/////////////////////////////////////////////////////////////////////////////////////////
// remove atoms which can never be approached
int nnbr, nblocked = 0;
double[] xLocalnbr = new double[NAtoms];
double[] yLocalnbr = new double[NAtoms];
double[] zLocalnbr = new double[NAtoms];
double[] rthresh2 = new double[NAtoms];
double[] z2plus = new double[NAtoms];
double[] z2minus = new double[NAtoms];
double x0, y0, z0, rmin = AtomData.vdWRMin;
Boolean[] atom_blocked = new Boolean[NAtoms];
Boolean accesible, zplus_blocked, zminus_blocked;
double xg, yg, zg, rg, rxy, drmax, dtheta, dphi;
for (int i = 0; i < NAtoms; i++)
{
accesible = false;
x0 = XLocal[i]; y0 = YLocal[i]; z0 = ZLocal[i];
rmax = 2.0 * rmin + vdWR[i];
// select neighbours within r1 + r2 + 2rmin
nnbr = 0;
for (int j = 0; j < NAtoms; j++)
{
x2 = (XLocal[j] - x0) * (XLocal[j] - x0);
y2 = (YLocal[j] - y0) * (YLocal[j] - y0);
z2 = (ZLocal[j] - z0) * (ZLocal[j] - z0);
if (x2 + y2 + z2 < (rmax + vdWR[j]) * (rmax + vdWR[j]))
{
xLocalnbr[nnbr] = XLocal[j] - x0;
yLocalnbr[nnbr] = YLocal[j] - y0;
zLocalnbr[nnbr] = ZLocal[j] - z0;
rthresh2[nnbr++] = (0.9 * rmin + vdWR[j]) * (0.9 * rmin + vdWR[j]);
}
}
// spherical grid
rg = vdWR[i] + rmin;
drmax = 0.1 * rmin / rg;
nz = (int)Math.Ceiling(Math.PI / drmax);
dtheta = Math.PI / nz;
for (double theta = Math.PI / 2.0; theta >= 0.0; theta -= dtheta)
{
zg = rg * Math.Sin(theta);
for (int j = 0; j < nnbr; j++)
{
z2plus[j] = (zLocalnbr[j] - zg) * (zLocalnbr[j] - zg);
z2minus[j] = (zLocalnbr[j] + zg) * (zLocalnbr[j] + zg);
}
rxy = rg * Math.Cos(theta);
dphi = (rxy > 0.05 * rmin / Math.PI) ? 0.1 * rmin / rxy : 2.0 * Math.PI;
for (double phi = 0.0; phi <= 2.0 * Math.PI; phi += dphi)
{
xg = rxy * Math.Cos(phi);
yg = rxy * Math.Sin(phi);
// check all neighbours at zg and -zg
zplus_blocked = false;
zminus_blocked = false;
for (int j = 0; j < nnbr; j++)
{
x2 = (xLocalnbr[j] - xg) * (xLocalnbr[j] - xg);
y2 = (yLocalnbr[j] - yg) * (yLocalnbr[j] - yg);
zplus_blocked = zplus_blocked || (x2 + y2 + z2plus[j] < rthresh2[j]);
zminus_blocked = zminus_blocked || (x2 + y2 + z2minus[j] < rthresh2[j]);
if (zplus_blocked && zminus_blocked)
{
break;
}
}
accesible = accesible || (!zplus_blocked) || (!zminus_blocked);
if (accesible)
{
break;
}
}
if (accesible)
{
break;
}
}
atom_blocked[i] = !accesible;
nblocked = accesible ? nblocked : nblocked + 1;
}
// finally remove blocked atoms and reorder
int ai = 0, unblocked = NAtoms - nblocked;
MaxAtomsInCluster = 0;
for (nc = 0; nc < AtomClusters.Length; nc++)
{
// first run: count blocked atoms
nblocked = 0; // now in cluster nc
for (int i = 0; i < AtomClusters[nc].NAtoms; i++)
{
nblocked = atom_blocked[originalatomindex[nc][i]] ? nblocked + 1 : nblocked;
}
// second run: fill
ai = 0;
for (int i = 0; i < AtomClusters[nc].NAtoms; i++)
{
ilocal = originalatomindex[nc][i];
if (!atom_blocked[ilocal])
{
originalatomindex[nc][ai++] = ilocal;
}
}
AtomClusters[nc].NAtoms -= nblocked;
MaxAtomsInCluster = Math.Max(MaxAtomsInCluster, AtomClusters[nc].NAtoms);
}
// fill cluster arrays
this.ClusteredAtomXYZ = new Vector3[unblocked];
this.ClusteredAtomvdwR = new double[unblocked];
this.ClusteredAtomOriginalIndex = new int[unblocked];
if (XYZvdwRVectorArray != IntPtr.Zero)
{
Marshal.FreeHGlobal(XYZvdwRVectorArray);
}
XYZvdwRVectorArray = Marshal.AllocHGlobal((unblocked + 1) * sizeof(float) * 4);
float[] XYZvdwRdata = new float[unblocked * 4];
int idata = 0, idata4 = 0, oi;
for (nc = 0; nc < AtomClusters.Length; nc++)
{
AtomClusters[nc].StartIndexInClusterArrays = idata;
for (int i = 0; i < AtomClusters[nc].NAtoms; i++)
{
oi = originalatomindex[nc][i];
ClusteredAtomXYZ[idata] = new Vector3(XLocal[oi], YLocal[oi], ZLocal[oi]);
ClusteredAtomvdwR[idata] = vdWR[oi];
ClusteredAtomOriginalIndex[idata++] = oi;
XYZvdwRdata[idata4++] = (float)XLocal[oi];
XYZvdwRdata[idata4++] = (float)YLocal[oi];
XYZvdwRdata[idata4++] = (float)ZLocal[oi];
XYZvdwRdata[idata4++] = (float)vdWR[oi];
}
}
Marshal.Copy(XYZvdwRdata, 0, FpsNativeWrapper.Aligned16(XYZvdwRVectorArray), XYZvdwRdata.Length);
Prepared = true;
}
// 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);
}
