private static void FourthTerm(IList <Vector> caArray, double Epsilon, HessMatrix hessian, int i, int j)
{
int[] idx = new int[] { i, j };
Vector[] lcaArray = new Vector[] { caArray[idx[0]], caArray[idx[1]] };
Matrix lhess = FourthTerm(lcaArray, Epsilon);
for (int c = 0; c < 2; c++)
{
for (int dc = 0; dc < 3; dc++)
{
for (int r = 0; r < 2; r++)
{
for (int dr = 0; dr < 3; dr++)
{
hessian[idx[c] * 3 + dc, idx[r] * 3 + dr] += lhess[c * 3 + dc, r *3 + dr];
}
}
}
}
if (HDebug.IsDebuggerAttachedWithProb(0.1))
{
if (caArray.Count == 2)
{
// avoid stack overflow
return;
}
HessMatrix lhess0 = new double[6, 6];
FourthTerm(lcaArray, Epsilon, lhess0, 0, 1);
FourthTerm(lcaArray, Epsilon, lhess0, 1, 0);
double r2 = (lcaArray[0] - lcaArray[1]).Dist2;
Matrix dhess0 = (120 * Epsilon / r2) * Hess.GetHessAnm(lcaArray, double.PositiveInfinity);
HDebug.AssertToleranceMatrix(0.00000001, lhess0 - dhess0);
}
}
static double GetPotentialUpdated_ProbToCheckWithGetPotential = 0;//1;//0.1;
public double GetPotentialUpdated(List <ForceField.IForceField> frcflds
, double?energy0, Vector[] coords0, Vector[] forces0
, Vector[] coords, Vector[] forces
, ref Nonbondeds_v1 nonbondeds
)
{
if (GetPotentialUpdated_SelfTestDo == true)
#region selftest
{
GetPotentialUpdated_SelfTest(frcflds, energy0, coords0, forces0, coords, forces);
}
#endregion
bool[] updated = new bool[size];
if ((energy0 == null) || (nonbondeds == null))
{
HDebug.AssertIf(energy0 == null, coords0 == null);
HDebug.AssertIf(energy0 == null, forces0 == null);
energy0 = 0;
coords0 = null;
forces0 = null;
for (int i = 0; i < size; i++)
{
forces[i] = new double[3];
}
for (int i = 0; i < size; i++)
{
updated[i] = true;
}
}
else
{
HDebug.Assert(size == coords0.Length);
HDebug.Assert(size == forces0.Length);
HDebug.Assert(size == coords.Length);
HDebug.Assert(size == forces.Length);
for (int i = 0; i < size; i++)
{
forces[i] = forces0[i].Clone();
}
int countskip = 0;
//double[] dist2s = new double[size];
//for(int i=0; i<size; i++)
// dist2s[i] = (coords0[i] - coords[i]).Dist2;
//int[] idxsorted = dist2s.IdxSorted();
//for(int i=0; i<size; i++)
// updated[i] = (dist2s[i] > (0.000001*0.000001));
//for(int i=size/2; i<size; i++)
// updated[idxsorted[i]] = true;
for (int i = 0; i < size; i++)
{
updated[i] = (coords0[i] != coords[i]);
}
for (int i = 0; i < size; i++)
{
countskip += (updated[i] == false) ? 1 : 0;
}
if ((size - countskip) * 10 > size)
{
energy0 = 0;
coords0 = null;
forces0 = null;
for (int i = 0; i < size; i++)
{
forces[i] = new double[3];
}
for (int i = 0; i < size; i++)
{
updated[i] = true;
}
}
System.Console.Write(" countskip({0:000}) ", countskip);
}
Vector[] dforces = GetVectorsZero();
double denergy = 0;
denergy += GetPotentialUpdated_ComputeCustomsBond(frcflds, updated, 0, coords0, coords, dforces);
denergy += GetPotentialUpdated_ComputeCustomsAngle(frcflds, updated, 0, coords0, coords, dforces);
denergy += GetPotentialUpdated_ComputeCustomsDihedral(frcflds, updated, 0, coords0, coords, dforces);
denergy += GetPotentialUpdated_ComputeCustomsImproper(frcflds, updated, 0, coords0, coords, dforces);
denergy += GetPotentialUpdated_ComputeCustomsNonbonded(frcflds, updated, 0, coords0, coords, dforces, ref nonbondeds);
//energy += GetPotentialUpdated_ComputeCustomsCustoms (frcflds, updated, 0, coords0, forces0, coords, forces);
double energy = energy0.Value + denergy;
for (int i = 0; i < size; i++)
{
forces[i] += dforces[i];
}
#region commented from threading
//Nonbondeds lnonbondeds = nonbondeds;
//
//double energy = energy0.Value;
//
//object lockobj = new object();
//System.Threading.Tasks.ParallelOptions parallelOptions = new ParallelOptions();
////parallelOptions.MaxDegreeOfParallelism = 1;
//Parallel.ForEach(compunits_bonded, parallelOptions, delegate(GetForcesCompUnit compunit)
//{
// if(compunit == null)
// {
// // in the first iteration, collect nonbonded components
// GetForces_CollectCompUnitNonbonded(frcflds, updated, coords0, coords, ref lnonbondeds, compunits_nonbonded);
// }
// else
// {
// Triple<double, int[], Vector[]> denergy_idx_dforces = compunit.Compute(coords0, coords);
// double denergy = denergy_idx_dforces.first;
// int[] idx = denergy_idx_dforces.second;
// Vector[] dforces = denergy_idx_dforces.third;
// Debug.Assert(idx.Length == dforces.Length);
// lock(lockobj)
// {
// energy += denergy;
// for(int i=0; i<idx.Length; i++)
// forces[idx[i]] += dforces[i];
// }
// }
//});
//nonbondeds = lnonbondeds;
//Parallel.ForEach(compunits_nonbonded, parallelOptions, delegate(GetForcesCompUnit compunit)
//{
// Triple<double, int[], Vector[]> denergy_idx_dforces = compunit.Compute(coords0, coords);
// double denergy = denergy_idx_dforces.first;
// int[] idx = denergy_idx_dforces.second;
// Vector[] dforces = denergy_idx_dforces.third;
// Debug.Assert(idx.Length == dforces.Length);
// lock(lockobj)
// {
// energy += denergy;
// for(int i=0; i<idx.Length; i++)
// forces[idx[i]] += dforces[i];
// }
//});
#endregion
if (HDebug.IsDebuggerAttachedWithProb(GetPotentialUpdated_ProbToCheckWithGetPotential))
#region check force with GetPotential(...)
{
//Vector[] _forces0 = GetVectorsZero();
//Matrix _hessian0 = null;
//double _energy0 = GetPotential(frcflds, coords0, ref _forces0, ref _hessian0, new Dictionary<string,object>());
//Debug.AssertTolerance(0.00000001, energy0 - _energy0);
//Debug.AssertTolerance(0.00000001, Vector.Sub(forces0, _forces0));
Vector[] _forces = GetVectorsZero();
MatrixByArr _hessian = null;
double _energy = GetPotential(frcflds, coords, ref _forces, ref _hessian, new Dictionary <string, object>());
HDebug.AssertTolerance(0.00000001, energy - _energy);
HDebug.AssertToleranceVector(0.00000001, Vector.Sub(forces, _forces));
}
#endregion
//if(cache != null)
//{
// if(cache.ContainsKey("energy_bonds ") == false) cache.Add("energy_bonds ", 0); cache["energy_bonds "] = energy_bonds ;
// if(cache.ContainsKey("energy_angles ") == false) cache.Add("energy_angles ", 0); cache["energy_angles "] = energy_angles ;
// if(cache.ContainsKey("energy_dihedrals ") == false) cache.Add("energy_dihedrals ", 0); cache["energy_dihedrals "] = energy_dihedrals ;
// if(cache.ContainsKey("energy_impropers ") == false) cache.Add("energy_impropers ", 0); cache["energy_impropers "] = energy_impropers ;
// if(cache.ContainsKey("energy_nonbondeds") == false) cache.Add("energy_nonbondeds", 0); cache["energy_nonbondeds"] = energy_nonbondeds;
// if(cache.ContainsKey("energy_customs ") == false) cache.Add("energy_customs ", 0); cache["energy_customs "] = energy_customs ;
//}
return(energy);
}