public void GetForceElements(Vector[] coords
, ForceField.INonbonded ffnonbond
, double nonbonds_maxdist
, out Tuple <int[], Vector[]>[] frcnonbond
, out Tuple <int[], Vector[]>[] frcnonbond14
)
{
double energy = 0;
MatrixByArr[,] lhess = null;
//lfrcfld = new List<ForceField.IForceField>(); lfrcfld.Add(new ForceField.MindyNonbondedLennardJones(false));
//lfrcfld = new List<ForceField.IForceField>(); lfrcfld.Add(new ForceField.MindyNonbondedElectrostatic());
List <Tuple <int[], Vector[]> > _frcnonbond = new List <Tuple <int[], Vector[]> >();
List <Tuple <int[], Vector[]> > _frcnonbond14 = new List <Tuple <int[], Vector[]> >();
{
//List<ForceField.IForceField> frcfld_nonbondeds = new List<ForceField.IForceField>();
//frcfld_nonbondeds.Add(new ForceField.MindyNonbondedLennardJones(false));
//frcfld_nonbondeds.Add(new ForceField.MindyNonbondedElectrostatic());
Universe.Nonbondeds_v1 nonbondeds = new Universe.Nonbondeds_v1(atoms, size, nonbonds_maxdist);
nonbondeds.UpdateNonbondeds(coords, 0);
foreach (Universe.Nonbonded nonbond in nonbondeds)
{
int[] ids = new int[2];
Vector[] lcoords = new Vector[2];
ids[0] = nonbond.atoms[0].ID; lcoords[0] = coords[ids[0]];
ids[1] = nonbond.atoms[1].ID; lcoords[1] = coords[ids[1]];
Vector[] lforces = new Vector[2] {
new double[3], new double[3]
};
ffnonbond.Compute(nonbond, lcoords, ref energy, ref lforces, ref lhess);
//if((lforces[0].Dist2 == 0) || (lforces[1].Dist2 == 0))
// continue;
_frcnonbond.Add(new Tuple <int[], Vector[]>(ids, lforces));
}
foreach (Universe.Nonbonded14 nonbond in nonbonded14s)
{
int[] ids = new int[2];
Vector[] lcoords = new Vector[2];
ids[0] = nonbond.atoms[0].ID; lcoords[0] = coords[ids[0]];
ids[1] = nonbond.atoms[1].ID; lcoords[1] = coords[ids[1]];
Vector[] lforces = new Vector[2] {
new double[3], new double[3]
};
ffnonbond.Compute(nonbond, lcoords, ref energy, ref lforces, ref lhess);
//if((lforces[0].Dist2 == 0) || (lforces[1].Dist2 == 0))
// continue;
_frcnonbond14.Add(new Tuple <int[], Vector[]>(ids, lforces));
}
}
frcnonbond = _frcnonbond.ToArray();
frcnonbond14 = _frcnonbond14.ToArray();
}
public static HessMatrix GetHess(Universe univ)
{
Vector[] coords = univ.GetCoords();
HessMatrix hessian_spr = HessMatrixSparse.ZerosSparse(univ.size * 3, univ.size * 3);
Universe.Nonbondeds_v1 nonbondeds = new Universe.Nonbondeds_v1(univ.atoms, univ.size, 12);
nonbondeds.UpdateNonbondeds(coords, 0);
hessian_spr = STeM.GetHessBond(coords, univ.bonds, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with bond"));
hessian_spr = STeM.GetHessAngle(coords, univ.angles, true, null, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with angle"));
hessian_spr = STeM.GetHessImproper(coords, univ.impropers, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with improper"));
hessian_spr = STeM.GetHessDihedral(coords, univ.dihedrals, null, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with dihedral"));
hessian_spr = STeM.GetHessVdw(coords, univ.nonbonded14s.GetEnumerable(), null, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with vdw14"));
hessian_spr = STeM.GetHessElec(coords, univ.nonbonded14s.GetEnumerable(), hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with elec14"));
hessian_spr = STeM.GetHessVdw(coords, nonbondeds.GetEnumerable(), null, null, hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with vdw"));
hessian_spr = STeM.GetHessElec(coords, nonbondeds.GetEnumerable(), hessian: hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr with elec"));
//hessian_spr = GetHessSprElec(coords, nonbondeds , hessian: hessian_spr); Debug.Verify(Hess.CheckHessDiag(hessian_spr));
//hessian_spr = GetHessSprVdw(coords, nonbondeds , hessian: hessian_spr); Debug.Verify(Hess.CheckHessDiag(hessian_spr));
hessian_spr = Hess.CorrectHessDiag(hessian_spr); HDebug.Verify(Hess.CheckHessDiag(hessian_spr, 0.000001, "non-computable exception while generating STeM hess_spr"));
return(hessian_spr);
}
