public MatrixByArr[,] GetHess4PwIntrAct(List <ForceField.IForceField> frcflds, double frcfactor)
{
if (GetHess4PwIntrAct_doselftest)
{
GetHess4PwIntrAct_doselftest = false;
HDebug.Assert(GetHess4PwIntrAct_selftest(frcflds, frcfactor));
}
Vector[] coords = GetCoords();
Dictionary <Pair <int, int>, ForceField.PwIntrActInfo> pwintractinfos = new Dictionary <Pair <int, int>, ForceField.PwIntrActInfo>();
for (int i = 0; i < size - 1; i++)
{
for (int j = i + 1; j < size; j++)
{
pwintractinfos.Add(new Pair <int, int>(i, j), new ForceField.PwIntrActInfo());
}
}
GetHess4PwIntrActBonds(frcflds, coords, pwintractinfos);
GetHess4PwIntrActAngles(frcflds, coords, pwintractinfos);
GetHess4PwIntrActImpropers(frcflds, coords, pwintractinfos);
GetHess4PwIntrActNonbondeds(frcflds, coords, pwintractinfos);
MatrixByArr[,] hessblk = new MatrixByArr[size, size];
Vector[] frcs = new Vector[size];
for (int i = 0; i < size; i++)
{
hessblk[i, i] = new double[3, 3];
frcs[i] = new double[3];
}
foreach (Pair <int, int> key in pwintractinfos.Keys)
{
int i = key.Item1;
int j = key.Item2;
ForceField.PwIntrActInfo pwintractinfo = pwintractinfos[key];
double fij = pwintractinfo.Fij * frcfactor;
double kij = pwintractinfo.Kij;
hessblk[i, j] = ForceField.GetHessianBlock(coords[i], coords[j], kij, fij);
hessblk[j, i] = ForceField.GetHessianBlock(coords[i], coords[j], kij, fij);
hessblk[i, i] -= hessblk[i, j];
hessblk[j, j] -= hessblk[j, i];
/////////////////////////////////////////
Vector uvec_ij = (coords[j] - coords[i]).UnitVector();
frcs[i] += uvec_ij * fij;
frcs[j] += -uvec_ij * fij;
}
double[] frcmags = new double[size];
for (int i = 0; i < size; i++)
{
frcmags[i] = frcs[i].Dist;
}
double frcmag_max = frcmags.Max();
double frcmag_avg = frcmags.Average();
double frcmag_med = frcmags.Median();
return(hessblk);
}
public virtual void Compute(Universe.Atom atom1, Universe.Atom atom2, Vector[] coords, ref double energy, ref Vector[] forces, ref MatrixByArr[,] hessian, double[,] pwfrc = null, double[,] pwspr = null)
{
HDebug.Depreciated("check idx1 and idx2");
int idx1 = 0; // nonbonded.atoms[0].ID;
int idx2 = 1; // nonbonded.atoms[1].ID;
Vector diff = (coords[idx2] - coords[idx1]);
double dx = diff[0];
double dy = diff[1];
double dz = diff[2];
double pchi = atom1.Charge;
double pchj = atom2.Charge;
double ee = 80;
///////////////////////////////////////////////////////////////////////////////
// energy
double lenergy = EnergyEs(dx, dy, dz, pchi, pchj, ee);
energy += lenergy;
///////////////////////////////////////////////////////////////////////////////
// force
if (forces != null)
{
Vector f12 = ForceEs(dx, dy, dz, pchi, pchj, ee);
forces[idx1] += f12;
forces[idx2] += -f12;
}
///////////////////////////////////////////////////////////////////////////////
// hessian
if (hessian != null)
{
//string option = "Spring+Force";
//Vector diff01 = (coords[1] - coords[0]);
//Vector diff10 = (coords[0] - coords[1]);
//hessian[0, 1] += SprngEs(diff01, pchi, pchj, ee, option);
//hessian[1, 0] += SprngEs(diff10, pchi, pchj, ee, option);
{
// !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
// !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
// !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
//
// V(rij) = (332 * pchij / ee) * rij^-1
// F(rij) = ( -1) * (332 * pchij / ee) * rij^-2
// K(rij) = (-2*-1) * (332 * pchij / ee) * rij^-3
double pchij = pchi * pchj;
double rij2 = dx * dx + dy * dy + dz * dz;
double rij = Math.Sqrt(rij2);
double rij3 = rij2 * rij;
double fij = (-1) * (332 * pchij / ee) / rij2;
double kij = (-2 * -1) * (332 * pchij / ee) / rij3;
fij *= optHessianForceFactor;
//Matrix Hij = ForceField.GetHessianBlock(coords[0], coords[1], kij, fij);
hessian[0, 1] += ForceField.GetHessianBlock(coords[0], coords[1], kij, fij);
hessian[1, 0] += ForceField.GetHessianBlock(coords[1], coords[0], kij, fij);
}
}
}
public virtual void Compute(Universe.Atom atom1, Universe.Atom atom2, Vector[] coords, ref double energy, ref Vector[] forces, ref MatrixByArr[,] hessian, double[,] pwfrc = null, double[,] pwspr = null)
{
Vector pos0 = coords[0];
Vector pos1 = coords[1];
double pchi = atom1.Charge;
double pchj = atom2.Charge;
double ee = 80;
double pchij = pchi * pchj;
double lenergy, forceij, springij;
Compute(coords, out lenergy, out forceij, out springij, pchij, ee);
double abs_forceij = Math.Abs(forceij);
if (pwfrc != null)
{
pwfrc[0, 1] = pwfrc[1, 0] = forceij;
}
if (pwspr != null)
{
pwspr[0, 1] = pwspr[1, 0] = springij;
}
///////////////////////////////////////////////////////////////////////////////
// energy
energy += lenergy;
///////////////////////////////////////////////////////////////////////////////
// force
if (forces != null)
{
Vector frc0, frc1;
GetForceVector(pos0, pos1, forceij, out frc0, out frc1);
forces[0] += frc0;
forces[1] += frc1;
}
///////////////////////////////////////////////////////////////////////////////
// hessian
if (hessian != null)
{
hessian[0, 1] += ForceField.GetHessianBlock(coords[0], coords[1], springij, forceij);
hessian[1, 0] += ForceField.GetHessianBlock(coords[1], coords[0], springij, forceij);
}
}
public static void GetPotential_SelfTest(string rootpath, string[] args)
{
if (GetPotential_SelfTest_do == false)
{
return;
}
GetPotential_SelfTest_do = false;
Namd.Psf psf = Namd.Psf.FromFile(rootpath + @"\Sample\alanin.psf");
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\alanin.pdb");
Namd.Prm prm = Namd.Prm.FromFileXPlor(rootpath + @"\Sample\alanin.params", new TextLogger());
Universe univ = Universe.Build(psf, prm, pdb, false);
List <ForceField.IForceField> frcflds = ForceField.GetMindyForceFields();
Vector[] forces = univ.GetVectorsZero();
MatrixByArr hessian = null;
Dictionary <string, object> cache = new Dictionary <string, object>();
double energy = univ.GetPotential(frcflds, ref forces, ref hessian, cache);
double toler = 0.000005;
HDebug.AssertTolerance(toler, SelfTest_alanin_energy - energy);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_bonds - (double)cache["energy_bonds "]);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_angles - (double)cache["energy_angles "]);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_dihedrals - (double)cache["energy_dihedrals "]);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_impropers - (double)cache["energy_impropers "]);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_nonbondeds - (double)cache["energy_nonbondeds"]);
HDebug.AssertTolerance(toler, SelfTest_alanin_energy_unknowns - (double)cache["energy_customs "]);
HDebug.AssertTolerance(toler, SelfTest_alanin_forces.GetLength(0) - forces.Length);
for (int i = 0; i < forces.Length; i++)
{
HDebug.Assert(forces[i].Size == 3);
HDebug.AssertTolerance(toler, SelfTest_alanin_forces[i, 0] - forces[i][0]);
HDebug.AssertTolerance(toler, SelfTest_alanin_forces[i, 1] - forces[i][1]);
HDebug.AssertTolerance(toler, SelfTest_alanin_forces[i, 2] - forces[i][2]);
}
}
public static void SelfTest(string rootpath, string[] args)
{
//{
// Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g.pdb");
// HTLib2.Bioinfo.Universe.Build(pdb);
//}
GetPotential_SelfTest(rootpath, args);
Universe univ = null;
string sample = null;
//sample = "1a6g_autopsf.unfolded";
//sample = "1a6g_autopsf";
switch (sample)
{
case "alanin":
{
List <ForceField.IForceField> frcflds = ForceField.GetMindyForceFields();
double k = 0.0001;
double threshold = 0.001;
//int iter = univ.Minimize_ConjugateGradient_v0(frcflds, k, threshold);
int randomPurturb = 0; // no random purturbation
bool[] atomsMovable = null; // update all atoms
int iter_conjgrad;
{
Namd.Psf psf = Namd.Psf.FromFile(rootpath + @"\Sample\alanin.psf");
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\alanin.pdb");
Namd.Prm prm = Namd.Prm.FromFileXPlor(rootpath + @"\Sample\alanin.params", new TextLogger());
univ = Universe.Build(psf, prm, pdb, false);
//frcflds = new List<ForceField.IForceField>();
//frcflds.Add(new ForceField.MindyBond());
//frcflds.Add(new ForceField.MindyAngle());
//frcflds.Add(new ForceField.MindyDihedral());
//frcflds.Add(new ForceField.MindyImproper());
//frcflds.Add(new ForceField.MindyNonbondedLennardJones());
//frcflds.Add(new ForceField.MindyNonbondedElectrostatic());
//iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
//frcflds = new List<ForceField.IForceField>();
//frcflds.Add(new ForceField.MindyBond());
//frcflds.Add(new ForceField.MindyAngle());
//frcflds.Add(new ForceField.MindyImproper());
//frcflds.Add(new ForceField.MindyNonbondedLennardJones());
//frcflds.Add(new ForceField.MindyNonbondedElectrostatic());
//iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k*0.1, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
frcflds = new List <ForceField.IForceField>();
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyBond());
}
else
{
frcflds.Add(new ForceField.PwBond());
}
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyAngle());
}
else
{
frcflds.Add(new ForceField.PwAngle());
}
frcflds.Add(new ForceField.MindyDihedral());
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyImproper());
}
else
{
frcflds.Add(new ForceField.PwImproper());
}
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyNonbondedElectrostatic());
}
else
{
frcflds.Add(new ForceField.PwElec());
}
if (HDebug.False)
{
frcflds.Add(new ForceField.MindyNonbondedLennardJones());
}
else
{
frcflds.Add(new ForceField.PwVdw());
}
univ.LoadCoords(@"D:\xxxx.coords");
iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.01, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
univ.SaveCoords(@"D:\xxxx.coords");
System.Console.WriteLine("=======================================================================");
System.Console.WriteLine("=======================================================================");
System.Console.WriteLine("=======================================================================");
}
{
//Psf psf = Psf.FromFile(rootpath + @"\Sample\alanin.psf");
//Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\alanin.pdb");
//Prm prm = Prm.FromFileXPlor(rootpath + @"\Sample\alanin.params", new TextLogger());
//univ = Universe.Build(psf, prm, pdb);
//frcflds = new List<ForceField.IForceField>();
//if(true) frcflds.Add(new ForceField.MindyBond()); else frcflds.Add(new ForceField.PwBond());
//if(true) frcflds.Add(new ForceField.MindyAngle()); else frcflds.Add(new ForceField.PwAngle());
//frcflds.Add(new ForceField.MindyDihedral());
//if(true) frcflds.Add(new ForceField.MindyImproper()); else frcflds.Add(new ForceField.PwImproper());
//if(true) frcflds.Add(new ForceField.MindyNonbondedElectrostatic()); else frcflds.Add(new ForceField.PwElec());
//if(true) frcflds.Add(new ForceField.MindyNonbondedLennardJones()); else frcflds.Add(new ForceField.PwVdw());
univ.atoms[0].Coord += new Vector(0.1, 0.1, 0.1);
//iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.001, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
iter_conjgrad = univ.Minimize_ConjugateGradient_AtomwiseUpdate(frcflds,
threshold: threshold,
k: k,
max_atom_movement: 0.001,
max_iteration: null,
atomsMovable: atomsMovable,
logger: new MinimizeLogger_PrintEnergyForceMag()
);
}
k = 0.0005;
HDebug.Assert(false);
//int iter_stepdsnt = univ.Minimize_SteepestDescent(frcflds, k, threshold, System.Console.Error);
}
break;
case "1a6g_autopsf":
{
Namd.Psf psf = Namd.Psf.FromFile(rootpath + @"\Sample\1a6g_autopsf.psf");
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g_autopsf.pdb");
Namd.Prm prm = Namd.Prm.FromFile(rootpath + @"\Sample\1a6g_autopsf.prm", new TextLogger());
univ = Universe.Build(psf, prm, pdb, false);
List <ForceField.IForceField> frcflds = ForceField.GetMindyForceFields();
double threshold = 0.001;
string minimize_ver = "v1";
switch (minimize_ver)
{
//case "v2":
// {
// double atom_max_move = 0.03;
// int iter_conjgrad = univ.Minimize_ConjugateGradient_v2(frcflds, atom_max_move, threshold, System.Console.Error);
// break;
// }
case "v1":
{
double k = 0.0001;
int randomPurturb = 0; // no random purturbation
bool[] atomsMovable = null; // update all atoms
int iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
break;
}
default:
goto case "v1";
}
//atom_max_move = 0.03;
//int iter_stepdsnt = univ.Minimize_SteepestDescent(frcflds, atom_max_move, threshold, System.Console.Error);
}
break;
case "1a6g_autopsf.unfolded":
{
Namd.Psf psf = Namd.Psf.FromFile(rootpath + @"\Sample\1a6g_autopsf.psf");
Pdb pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g_autopsf.pdb");
{
Random rand = new Random(1);
List <Vector> coords = pdb.atoms.ListCoord();
for (int i = 0; i < coords.Count; i++)
{
double x = i * 0.1 + rand.NextDouble() * 0.01;
double y = i * 0.1 + rand.NextDouble() * 0.01;
double z = i * 0.1 + rand.NextDouble() * 0.01;
coords[i] = new Vector(x, y, z);
}
pdb.ToFile(rootpath + @"\Sample\1a6g_autopsf.unfolded.pdb", coords);
pdb = Pdb.FromFile(rootpath + @"\Sample\1a6g_autopsf.unfolded.pdb");
}
Namd.Prm prm = Namd.Prm.FromFile(rootpath + @"\Sample\1a6g_autopsf.prm", new TextLogger());
univ = Universe.Build(psf, prm, pdb, false);
List <ForceField.IForceField> frcflds = ForceField.GetMindyForceFields();
double threshold = 0.01;
string minimize_ver = "v1";
switch (minimize_ver)
{
//case "v2":
// {
// double atom_max_move = 0.1;
// int iter_conjgrad = univ.Minimize_ConjugateGradient_v2(frcflds, atom_max_move, threshold, System.Console.Error);
// break;
// }
case "v1":
{
double k = 0.0001;
int randomPurturb = 100;
bool[] atomsMovable = null; // updates all atoms
int iter_conjgrad = univ.Minimize_ConjugateGradient_v1(0, frcflds, k, 0.1, null, threshold, randomPurturb, atomsMovable, new MinimizeLogger_PrintEnergyForceMag(), null, null);
break;
}
default:
goto case "v1";
}
//atom_max_move = 0.03;
//int iter_stepdsnt = univ.Minimize_SteepestDescent(frcflds, atom_max_move, threshold, System.Console.Error);
}
break;
default:
goto case "alanin";
}
}
public virtual void Compute(Universe.AtomPack nonbonded, Vector[] coords, ref double energy, ref Vector[] forces, ref MatrixByArr[,] hessian
, double radi, double radj, double epsi, double epsj, double[,] pwfrc = null, double[,] pwspr = null)
{
HDebug.Depreciated("check idx1 and idx2");
int idx1 = 0; // nonbonded.atoms[0].ID;
int idx2 = 1; // nonbonded.atoms[1].ID;
Universe.Atom atom1 = nonbonded.atoms[0];
Universe.Atom atom2 = nonbonded.atoms[1];
Vector diff = (coords[idx2] - coords[idx1]);
double dx = diff[0];
double dy = diff[1];
double dz = diff[2];
//double radi = atom1.Rmin2;
//double radj = atom2.Rmin2;
//double epsi = atom1.epsilon;
//double epsj = atom2.epsilon;
///////////////////////////////////////////////////////////////////////////////
// energy
energy += EnergyVdw(dx, dy, dz, radi, radj, epsi, epsj);
///////////////////////////////////////////////////////////////////////////////
// force
if (forces != null)
{
Vector f12 = ForceVdw(dx, dy, dz, radi, radj, epsi, epsj);
forces[idx1] += f12;
forces[idx2] += -f12;
}
///////////////////////////////////////////////////////////////////////////////
// hessian
if (hessian != null)
{
//string option = "Spring+Force";
//Vector diff01 = (coords[1] - coords[0]);
//Vector diff10 = (coords[0] - coords[1]);
//hessian[0, 1] += SprngVdw(diff01, radi, radj, epsi, epsj, option);
//hessian[1, 0] += SprngVdw(diff10, radi, radj, epsi, epsj, option);
{
// !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
// !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
// !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
//
// V(r) = epsij * r0^12 * rij^-12 - 2 * epsij * r0^6 * rij^-6
// F(r) = -12 * epsij * r0^12 * rij^-13 - -6*2 * epsij * r0^6 * rij^-7
// K(r) = -13*-12 * epsij * r0^12 * rij^-14 - -7*-6*2 * epsij * r0^6 * rij^-8
double r = (radi + radj);
double r6 = Math.Pow(r, 6);
double r12 = Math.Pow(r, 12);
double rij2 = (dx * dx + dy * dy + dz * dz);
double rij = Math.Sqrt(rij2);
double rij7 = Math.Pow(rij2, 3) * rij;
double rij8 = Math.Pow(rij2, 4);
double rij13 = Math.Pow(rij2, 6) * rij;
double rij14 = Math.Pow(rij2, 7);
double epsij = epsi * epsj;
double fij = (-12) * epsij * r12 / rij13 - (-6 * 2) * epsij * r6 / rij7;
double kij = (-13 * -12) * epsij * r12 / rij14 - (-7 * -6 * 2) * epsij * r6 / rij8;
fij *= optHessianForceFactor;
//Matrix Hij = ForceField.GetHessianBlock(coords[0], coords[1], kij, fij);
hessian[0, 1] += ForceField.GetHessianBlock(coords[0], coords[1], kij, fij);
hessian[1, 0] += ForceField.GetHessianBlock(coords[1], coords[0], kij, fij);
}
}
}