public bool GetHess4PwIntrAct_selftest(List <ForceField.IForceField> frcflds, double frcfactor)
{
Vector[] coords = GetCoords();
Vector[] forces = GetVectorsZero();
MatrixByArr[,] hessian = new MatrixByArr[size, size];
{
for (int c = 0; c < size; c++)
{
for (int r = 0; r < size; r++)
{
hessian[c, r] = new double[3, 3];
}
}
}
Dictionary <string, object> cache = new Dictionary <string, object>();
cache.Add("all nonbondeds", null);
PwForceDecomposer forceij = null;
double energy = GetPotentialNonbondeds(frcflds, coords, ref forces, ref hessian, cache, forceij);
List <ForceField.IForceField> frcflds_nonbondeds = new List <ForceField.IForceField>();
foreach (ForceField.INonbonded frcfld_nonbonded in SelectInFrcflds(frcflds, new List <ForceField.INonbonded>()))
{
frcflds_nonbondeds.Add(frcfld_nonbonded);
}
MatrixByArr[,] hess = GetHess4PwIntrAct(frcflds_nonbondeds, frcfactor);
if (hess.GetLength(0) != hessian.GetLength(0))
{
return(false);
}
if (hess.GetLength(1) != hessian.GetLength(1))
{
return(false);
}
for (int i = 0; i < hess.GetLength(0); i++)
{
for (int j = 0; j < hess.GetLength(1); j++)
{
if (i == j)
{
continue;
}
if (hess[i, j].ColSize != hessian[i, j].ColSize)
{
return(false);
}
if (hess[i, j].RowSize != hessian[i, j].RowSize)
{
return(false);
}
if (HDebug.CheckTolerance(0.00000001, hess[i, j] - hessian[i, j]) == false)
{
return(false);
}
}
}
return(true);
}
public double GetPotentialBonds(List <ForceField.IForceField> frcflds, Vector[] coords, ref Vector[] forces, ref MatrixByArr[,] hessian,
Dictionary <string, object> cache, PwForceDecomposer forceij, double[,] pwfrc = null, double[,] pwspr = null)
{
List <ForceField.IBond> frcfld_bonds = SelectInFrcflds(frcflds, new List <ForceField.IBond>());
double energy = 0;
if (frcfld_bonds.Count == 0)
{
return(energy);
}
double stat_min = double.MaxValue;
double stat_max = double.MinValue;
double netstat_min = double.MaxValue;
double netstat_max = double.MinValue;
Vector[] lcoords = new Vector[2];
Vector[] lforces = (forces == null) ? null : new Vector[2];
for (int i = 0; i < bonds.Count; i++)
{
int id0 = bonds[i].atoms[0].ID; lcoords[0] = coords[id0];
int id1 = bonds[i].atoms[1].ID; lcoords[1] = coords[id1];
foreach (ForceField.IBond frcfld in frcfld_bonds)
{
if (forces != null)
{
lforces[0] = new double[3];
lforces[1] = new double[3];
}
MatrixByArr[,] lhess = (hessian == null) ? null : LinAlg.CreateMatrixArray(2, 2, new double[3, 3]);
frcfld.Compute(bonds[i], lcoords, ref energy, ref lforces, ref lhess, pwfrc, pwspr);
HDebug.Assert(double.IsNaN(energy) == false, double.IsInfinity(energy) == false);
if (forces != null)
{
forces[id0] += lforces[0];
forces[id1] += lforces[1];
forceij.AddBond(id0, id1, lcoords, lforces);
HDebug.AssertTolerance(0.00000001, lforces[0].Dist2 - lforces[1].Dist2);
double netstat = lforces[0].Dist2 + lforces[1].Dist2;
netstat_min = Math.Min(netstat_min, netstat);
netstat_max = Math.Max(netstat_max, netstat);
stat_min = Math.Min(stat_min, lforces[0].Dist);
stat_max = Math.Max(stat_max, lforces[0].Dist);
stat_min = Math.Min(stat_min, lforces[1].Dist);
stat_max = Math.Max(stat_max, lforces[1].Dist);
}
if (hessian != null)
{
hessian[id0, id0] += lhess[0, 0]; hessian[id0, id1] += lhess[0, 1];
hessian[id1, id0] += lhess[1, 0]; hessian[id1, id1] += lhess[1, 1];
}
}
}
return(energy);
}
public double GetPotentialCustoms(List <ForceField.IForceField> frcflds, Vector[] coords, ref Vector[] forces, ref MatrixByArr[,] hessian,
Dictionary <string, object> cache, PwForceDecomposer forceij, double[,] pwfrc = null, double[,] pwspr = null)
{
List <ForceField.ICustom> frcfld_customs = SelectInFrcflds(frcflds, new List <ForceField.ICustom>());
double energy = 0;
foreach (ForceField.ICustom frcfld in frcfld_customs)
{
Vector[] lforces = (forces == null) ? null : GetVectorsZero();
frcfld.Compute(atoms, coords, ref energy, ref lforces, ref hessian, pwfrc, pwspr);
HDebug.Assert(double.IsNaN(energy) == false, double.IsInfinity(energy) == false);
if (forces != null)
{
for (int i = 0; i < size; i++)
{
forces[i] += lforces[i];
}
forceij.AddCustom(coords, lforces);
}
}
return(energy);
}
public double GetPotentialNonbondeds(List <ForceField.IForceField> frcflds, Vector[] coords, ref Vector[] forces, ref MatrixByArr[,] hessian,
Dictionary <string, object> cache, PwForceDecomposer forceij, double[,] pwfrc = null, double[,] pwspr = null)
{
List <ForceField.INonbonded> frcfld_nonbondeds = SelectInFrcflds(frcflds, new List <ForceField.INonbonded>());
double energy = 0;
if (frcfld_nonbondeds.Count == 0)
{
return(energy);
}
Vector[] lcoords = new Vector[2];
Vector[] lforces = (forces == null) ? null : new Vector[2];
Nonbondeds_v1 nonbondeds = null;
if (cache == null)
{
cache = new Dictionary <string, object>();
}
if (cache.ContainsKey("all nonbondeds"))
{
// compute all non-bondeds
double nonbondeds_maxdist = double.PositiveInfinity;
nonbondeds = new Nonbondeds_v1(atoms, size, nonbondeds_maxdist);
nonbondeds.UpdateNonbondeds(coords, 0);
cache.Add("nonbondeds", nonbondeds);
}
else if (cache.ContainsKey("nonbondeds"))
{
// use existing cached nonbondeds, but update it as well
nonbondeds = (Nonbondeds_v1)cache["nonbondeds"];
nonbondeds.UpdateNonbondeds(coords, 0.01);
}
else
{
// create default nonbondeds, and add it into cache
nonbondeds = new Nonbondeds_v1(atoms, size, 12);
nonbondeds.UpdateNonbondeds(coords, 0);
cache.Add("nonbondeds", nonbondeds);
}
double stat_min = double.MaxValue;
double stat_max = double.MinValue;
double netstat_min = double.MaxValue;
double netstat_max = double.MinValue;
foreach (Nonbonded nonbond in nonbondeds)
{
///{ // this removes interactions in-between rigid atoms.
/// Atom atom0 = nonbond.atoms[0];
/// Atom atom1 = nonbond.atoms[1];
/// HashSet<Atom> atomsInRigid0 = GetAtomsInRigid(atom0);
/// if(atomsInRigid0.Contains(atom1))
/// continue;
///}
int id0 = nonbond.atoms[0].ID; lcoords[0] = coords[id0];
int id1 = nonbond.atoms[1].ID; lcoords[1] = coords[id1];
foreach (ForceField.INonbonded frcfld in frcfld_nonbondeds)
{
if (forces != null)
{
lforces[0] = new double[3];
lforces[1] = new double[3];
}
MatrixByArr[,] lhess = (hessian == null) ? null : LinAlg.CreateMatrixArray(2, 2, new double[3, 3]);
double[,] lpwfrc = new double[2, 2];
double[,] lpwspr = new double[2, 2];
frcfld.Compute(nonbond, lcoords, ref energy, ref lforces, ref lhess, lpwfrc, lpwspr);
HDebug.Assert(double.IsNaN(energy) == false, double.IsInfinity(energy) == false);
if (forces != null)
{
forces[id0] += lforces[0];
forces[id1] += lforces[1];
if (forceij != null)
{
forceij.AddNonbonded(id0, id1, lcoords, lforces);
}
HDebug.AssertTolerance(0.00000001, lforces[0].Dist2 - lforces[1].Dist2);
double netstat = lforces[0].Dist2 + lforces[1].Dist2;
netstat_min = Math.Min(netstat_min, netstat);
netstat_max = Math.Max(netstat_max, netstat);
stat_min = Math.Min(stat_min, lforces[0].Dist);
stat_max = Math.Max(stat_max, lforces[0].Dist);
stat_min = Math.Min(stat_min, lforces[1].Dist);
stat_max = Math.Max(stat_max, lforces[1].Dist);
}
if (hessian != null)
{
hessian[id0, id0] += lhess[0, 0]; hessian[id0, id1] += lhess[0, 1];
hessian[id1, id0] += lhess[1, 0]; hessian[id1, id1] += lhess[1, 1];
}
if (pwfrc != null)
{
pwfrc[id0, id0] += lpwfrc[0, 0]; pwfrc[id0, id1] += lpwfrc[0, 1];
pwfrc[id1, id0] += lpwfrc[1, 0]; pwfrc[id1, id1] += lpwfrc[1, 1];
}
if (pwspr != null)
{
pwspr[id0, id0] += lpwspr[0, 0]; pwspr[id0, id1] += lpwspr[0, 1];
pwspr[id1, id0] += lpwspr[1, 0]; pwspr[id1, id1] += lpwspr[1, 1];
}
}
}
double stat14_min = double.MaxValue;
double stat14_max = double.MinValue;
double netstat14_min = double.MaxValue;
double netstat14_max = double.MinValue;
foreach (Nonbonded14 nonbond in nonbonded14s)
{
int id0 = nonbond.atoms[0].ID; lcoords[0] = coords[id0];
int id1 = nonbond.atoms[1].ID; lcoords[1] = coords[id1];
foreach (ForceField.INonbonded frcfld in frcfld_nonbondeds)
{
if (forces != null)
{
lforces[0] = new double[3];
lforces[1] = new double[3];
}
MatrixByArr[,] lhess = (hessian == null) ? null : LinAlg.CreateMatrixArray(2, 2, new double[3, 3]);
double[,] lpwfrc = new double[2, 2];
double[,] lpwspr = new double[2, 2];
frcfld.Compute(nonbond, lcoords, ref energy, ref lforces, ref lhess, pwfrc, pwspr);
HDebug.Assert(double.IsNaN(energy) == false, double.IsInfinity(energy) == false);
if (forces != null)
{
forces[id0] += lforces[0];
forces[id1] += lforces[1];
if (forceij != null)
{
forceij.AddNonbonded14(id0, id1, lcoords, lforces);
}
HDebug.AssertTolerance(0.00000001, lforces[0].Dist2 - lforces[1].Dist2);
double netstat = lforces[0].Dist2 + lforces[1].Dist2;
netstat14_min = Math.Min(netstat14_min, netstat);
netstat14_max = Math.Max(netstat14_max, netstat);
stat14_min = Math.Min(stat14_min, lforces[0].Dist);
stat14_max = Math.Max(stat14_max, lforces[0].Dist);
stat14_min = Math.Min(stat14_min, lforces[1].Dist);
stat14_max = Math.Max(stat14_max, lforces[1].Dist);
}
if (hessian != null)
{
hessian[id0, id0] += lhess[0, 0]; hessian[id0, id1] += lhess[0, 1];
hessian[id1, id0] += lhess[1, 0]; hessian[id1, id1] += lhess[1, 1];
}
if (pwfrc != null)
{
pwfrc[id0, id0] += lpwfrc[0, 0]; pwfrc[id0, id1] += lpwfrc[0, 1];
pwfrc[id1, id0] += lpwfrc[1, 0]; pwfrc[id1, id1] += lpwfrc[1, 1];
}
if (pwspr != null)
{
pwspr[id0, id0] += lpwspr[0, 0]; pwspr[id0, id1] += lpwspr[0, 1];
pwspr[id1, id0] += lpwspr[1, 0]; pwspr[id1, id1] += lpwspr[1, 1];
}
}
}
return(energy);
}
