// calculate angle forces
void calcAngleForces(AngleTerm angle)
{
if (LogLevel >= 1000)
{
FFlog.WriteLine("calcAngleForces for {0} - {1} - {2}", angle.Atom1, angle.Atom2, angle.Atom3);
}
Vector3 rb1 = position[angle.Atom1] - position[angle.Atom2];
Vector3 rb2 = position[angle.Atom3] - position[angle.Atom2];
float cosAlpha = (Vector3.Dot(rb1, rb2)) / (Vector3.Magnitude(rb1) * Vector3.Magnitude(rb2));
//float angleAlpha = Mathf.Acos(cosAlpha) * (180 / Mathf.PI);
float mAlpha = angle.kAngle * (Mathf.Acos(cosAlpha) * (180.0f / Mathf.PI) - angle.Aeq);
Vector3 fI = (mAlpha / (Vector3.Magnitude(rb1) * Mathf.Sqrt(1.0f - cosAlpha * cosAlpha))) * ((rb2 / Vector3.Magnitude(rb2)) - cosAlpha * (rb1 / Vector3.Magnitude(rb1)));
Vector3 fK = (mAlpha / (Vector3.Magnitude(rb2) * Mathf.Sqrt(1.0f - cosAlpha * cosAlpha))) * ((rb1 / Vector3.Magnitude(rb1)) - cosAlpha * (rb2 / Vector3.Magnitude(rb2)));
Vector3 fJ = -fI - fK;
if (LogLevel >= 1000)
{
FFlog.WriteLine("angle: {0,12:f3} angle0: {1,12:f3} -- moment = {2,14:f5} ", Mathf.Acos(cosAlpha) * (180.0f / Mathf.PI), angle.Aeq, mAlpha);
}
if (LogLevel >= 10000)
{
FFlog.WriteLine(string.Format("force for atom {0,3}: ( {1,14:f6} ; {2,14:f6} ; {3,14:f6} )", angle.Atom1, fI.x, fI.y, fI.z));
FFlog.WriteLine(string.Format("force for atom {0,3}: ( {1,14:f6} ; {2,14:f6} ; {3,14:f6} )", angle.Atom2, fJ.x, fJ.y, fJ.z));
FFlog.WriteLine(string.Format("force for atom {0,3}: ( {1,14:f6} ; {2,14:f6} ; {3,14:f6} )", angle.Atom3, fK.x, fK.y, fK.z));
}
forces[angle.Atom1] += fI;
forces[angle.Atom2] += fJ;
forces[angle.Atom3] += fK;
if (LogLevel >= 10000)
{
FFlog.WriteLine("Updated forces:");
for (int iAtom = 0; iAtom < nAtoms; iAtom++)
{
FFlog.WriteLine(string.Format(" {0,4:d} - {1,5:d} {2,14:f6} {3,14:f6} {4,14:f6}",
iAtom, atomList[iAtom],
forces[iAtom].x, forces[iAtom].y, forces[iAtom].z));
}
}
}
void generateFF()
{
bondList.Clear();
angleList.Clear();
// set topology array
bool[,] topo = new bool[nAtoms, nAtoms];
for (int iAtom = 0; iAtom < nAtoms; iAtom++)
{
for (int jAtom = 0; jAtom < nAtoms; jAtom++)
{
topo[iAtom, jAtom] = false;
}
}
{
int iAtom = 0;
foreach (Atom At1 in GetComponent <GlobalCtrl>().list_curAtoms)
{
// cycle through connection points
foreach (ConnectionStatus conPoint in At1.getAllConPoints())
{
// get current atom index by comparison to entries in atomList
int jAtom = -1;
for (int kAtom = 0; kAtom < nAtoms; kAtom++)
{
if (atomList[kAtom] == conPoint.otherAtomID)
{
jAtom = kAtom;
break;
}
}
if (jAtom >= 0)
{
topo[iAtom, jAtom] = true;
topo[jAtom, iAtom] = true;
}
}
iAtom++;
}
}
// now set all FF terms
// pairwise terms, run over unique atom pairs
for (int iAtom = 0; iAtom < nAtoms; iAtom++)
{
for (int jAtom = 0; jAtom < iAtom; jAtom++)
{
if (topo[iAtom, jAtom])
{
BondTerm newBond = new BondTerm();
newBond.Atom1 = jAtom;
newBond.Atom2 = iAtom;
if (atomType[iAtom] == "C" && atomType[jAtom] == "C")
{
newBond.kBond = kbCC;
newBond.Req = reqCC;
}
else if (atomType[iAtom] == "C" && atomType[jAtom] == "H" ||
atomType[iAtom] == "H" && atomType[jAtom] == "C")
{
newBond.kBond = kbCH;
newBond.Req = reqCH;
}
// RENEW THIS LATER
else if (atomType[iAtom] == "C" && atomType[jAtom] == "DUMMY" ||
atomType[iAtom] == "DUMMY" && atomType[jAtom] == "C")
{
newBond.kBond = kbCX;
newBond.Req = reqCX;
//newBond.kBond = kbCH;
//newBond.Req = reqCH;
}
else if (atomType[iAtom] == "H" && atomType[jAtom] == "H")
{
newBond.kBond = kb;
newBond.Req = reqHH;
}
else if (atomType[iAtom] == "H" && atomType[jAtom] == "DUMMY" ||
atomType[iAtom] == "DUMMY" && atomType[jAtom] == "H")
{
newBond.kBond = kbCX;
newBond.Req = reqHX;
//newBond.kBond = kb;
//newBond.Req = reqHH;
}
else // take defaults for the time being
{
newBond.kBond = kb;
newBond.Req = reqStd;
}
bondList.Add(newBond);
}
// else ... set here non-bonded interactions
}
}
if (LogLevel >= 1000)
{
FFlog.WriteLine("Bond terms:");
FFlog.WriteLine(" Atom1 Atom2 kBond Req");
foreach (BondTerm bond in bondList)
{
FFlog.WriteLine(string.Format(" {0,4} - {1,4} {2,12:f3} {3,12:f3}",
bond.Atom1, bond.Atom2, bond.kBond, bond.Req));
}
}
// angle terms
// run over unique bond pairs
foreach (BondTerm bond1 in bondList)
{
foreach (BondTerm bond2 in bondList)
{
// if we reached the same atom pair, we can skip
if (bond1.Atom1 == bond2.Atom1 && bond1.Atom2 == bond2.Atom2)
{
break;
}
int idx = -1, jdx = -1, kdx = -1;
if (bond1.Atom1 == bond2.Atom1)
{
idx = bond1.Atom2; jdx = bond1.Atom1; kdx = bond2.Atom2;
}
else if (bond1.Atom1 == bond2.Atom2)
{
idx = bond1.Atom2; jdx = bond1.Atom1; kdx = bond2.Atom1;
}
else if (bond1.Atom2 == bond2.Atom1)
{
idx = bond1.Atom1; jdx = bond1.Atom2; kdx = bond2.Atom2;
}
else if (bond1.Atom2 == bond2.Atom2)
{
idx = bond1.Atom1; jdx = bond1.Atom2; kdx = bond2.Atom1;
}
if (idx > -1) // if anything was found: set term
{
AngleTerm newAngle = new AngleTerm();
newAngle.Atom1 = kdx; // I put kdx->Atom1 and idx->Atom3 just for aesthetical reasons ;)
newAngle.Atom2 = jdx;
newAngle.Atom3 = idx;
// currently only this angle type:
newAngle.kAngle = ka;
newAngle.Aeq = alphaNull;
angleList.Add(newAngle);
}
}
}
if (LogLevel >= 1000)
{
FFlog.WriteLine("Angle terms:");
FFlog.WriteLine(" Atom1 Atom2 Atom3 kAngle Aeq");
foreach (AngleTerm angle in angleList)
{
FFlog.WriteLine(string.Format(" {0,4} - {1,4} - {2,4} {3,12:f3} {4,12:f3}",
angle.Atom1, angle.Atom2, angle.Atom3, angle.kAngle, angle.Aeq));
}
}
}
