public static HessMatrix GetHessElec(IList <Vector> coords, IEnumerable <Universe.Nonbonded14> nonbonded14s, HessMatrix hessian, double ee)
{
int size = coords.Count;
if (hessian == null)
{
hessian = HessMatrixSparse.ZerosSparse(size * 3, size * 3);
}
foreach (Universe.Nonbonded14 nonbonded14 in nonbonded14s)
{
Universe.Atom atom0 = nonbonded14.atoms[0];
Universe.Atom atom1 = nonbonded14.atoms[1];
int idx0 = atom0.ID; if (coords[idx0] == null)
{
continue;
}
int idx1 = atom1.ID; if (coords[idx1] == null)
{
continue;
}
double pch0 = atom0.Charge;
double pch1 = atom1.Charge;
TermElec(coords, pch0, pch1, ee, hessian, idx0, idx1);
TermElec(coords, pch0, pch1, ee, hessian, idx1, idx0);
}
return(hessian);
}
static public void MV(HessMatrixSparse M, Vector V, Vector mv, Vector bvec, Vector bmv)
{
HDebug.Exception(V.Size == M.RowSize);
HDebug.Exception(mv.Size == M.ColSize); //Vector mv = new double[M.ColSize];
HDebug.Exception(bvec.Size == 3); //Vector bvec = new double[3];
HDebug.Exception(bmv.Size == 3); //Vector bmv = new double[3];
foreach (ValueTuple <int, int, MatrixByArr> bc_br_bval in M.EnumBlocks())
{
int bc = bc_br_bval.Item1;
int br = bc_br_bval.Item2;
var bmat = bc_br_bval.Item3;
bvec[0] = V[br * 3 + 0];
bvec[1] = V[br * 3 + 1];
bvec[2] = V[br * 3 + 2];
HTLib2.LinAlg.MV(bmat, bvec, bmv);
mv[bc * 3 + 0] += bmv[0];
mv[bc * 3 + 1] += bmv[1];
mv[bc * 3 + 2] += bmv[2];
}
if (HDebug.Selftest())
{
Matlab.Clear();
Matlab.PutSparseMatrix("M", M.GetMatrixSparse(), 3, 3);
Matlab.PutVector("V", V);
Matlab.Execute("MV = M*V;");
Matlab.PutVector("MV1", mv);
Vector err = Matlab.GetVector("MV-MV1");
double err_max = err.ToArray().HAbs().Max();
HDebug.Assert(err_max < 0.00000001);
}
}
public static HessMatrix GetHessAngle
(IList <Vector> coords, IEnumerable <Universe.Angle> angles, bool useUreybrad, double?K_theta, double?K_ub, HessMatrix hessian
, Matrix pwspr
, Action <Universe.Atom, Vector, Universe.Atom, Vector, Universe.Atom, Vector, double, double> collector
)
{
int size = coords.Count;
if (hessian == null)
{
hessian = HessMatrixSparse.ZerosSparse(size * 3, size * 3);
}
foreach (Universe.Angle angle in angles)
{
int idx0 = angle.atoms[0].ID; if (coords[idx0] == null)
{
continue;
}
int idx1 = angle.atoms[1].ID; if (coords[idx1] == null)
{
continue;
}
int idx2 = angle.atoms[2].ID; if (coords[idx2] == null)
{
continue;
}
double lK_theta = (K_theta != null)? K_theta.Value : angle.Ktheta;
HDebug.Assert(lK_theta >= 0);
SecondTerm(coords, lK_theta, hessian, idx0, idx1, idx2);
double lK_ub = 0;
if (useUreybrad)
{
HDebug.Assert(angle.Kub >= 0);
lK_ub = (K_ub != null)? K_ub.Value : angle.Kub;
FirstTerm(coords, lK_ub, hessian, idx0, idx2);
if (pwspr != null)
{
pwspr[idx0, idx1] += lK_ub;
pwspr[idx1, idx0] += lK_ub;
}
}
if (collector != null)
{
collector
(angle.atoms[0], coords[idx0]
, angle.atoms[1], coords[idx1]
, angle.atoms[2], coords[idx2]
, lK_theta, lK_ub);
}
}
return(hessian);
}
static public Vector MV(HessMatrixSparse M, Vector V)
{
Vector mv = new double[M.ColSize];
Vector bvec = new double[3];
Vector bmv = new double[3];
MV(M, V, mv, bvec, bmv);
return(mv);
}
public static HessMatrix GetMulImpl(ILinAlg ila, bool warning, params HessMatrix[] mats)
{
if (ila != null)
{
if (HDebug.Selftest())
{
Matrix h0 = new double[, ] {
{ 0, 1, 2, 3, 4, 5 }
, { 1, 2, 3, 4, 5, 6 }
, { 2, 3, 4, 5, 6, 7 }
, { 3, 4, 5, 6, 7, 8 }
, { 4, 5, 6, 7, 8, 9 }
, { 5, 6, 7, 8, 9, 0 }
};
HessMatrix h1 = HessMatrixDense.FromMatrix(h0);
HessMatrix h2 = HessMatrixSparse.FromMatrix(h0);
Matrix t0 = Matrix.GetMul(Matrix.GetMul(h1, h1), h1);
{
Matrix t1 = GetMulImpl(ila, false, h1, h1, h1); double d1 = (t0 - t1).HAbsMax(); HDebug.Assert(0 == d1);
Matrix t2 = GetMulImpl(ila, false, h1, h1, h2); double d2 = (t0 - t2).HAbsMax(); HDebug.Assert(0 == d2);
Matrix t3 = GetMulImpl(ila, false, h1, h2, h1); double d3 = (t0 - t3).HAbsMax(); HDebug.Assert(0 == d3);
Matrix t4 = GetMulImpl(ila, false, h1, h2, h2); double d4 = (t0 - t4).HAbsMax(); HDebug.Assert(0 == d4);
Matrix t5 = GetMulImpl(ila, false, h2, h1, h1); double d5 = (t0 - t5).HAbsMax(); HDebug.Assert(0 == d5);
Matrix t6 = GetMulImpl(ila, false, h2, h1, h2); double d6 = (t0 - t6).HAbsMax(); HDebug.Assert(0 == d6);
Matrix t7 = GetMulImpl(ila, false, h2, h2, h1); double d7 = (t0 - t7).HAbsMax(); HDebug.Assert(0 == d7);
Matrix t8 = GetMulImpl(ila, false, h2, h2, h2); double d8 = (t0 - t8).HAbsMax(); HDebug.Assert(0 == d8);
}
{
Matrix t1 = GetMulImpl(null, false, h1, h1, h1); double d1 = (t0 - t1).HAbsMax(); HDebug.Assert(0 == d1);
Matrix t2 = GetMulImpl(null, false, h1, h1, h2); double d2 = (t0 - t2).HAbsMax(); HDebug.Assert(0 == d2);
Matrix t3 = GetMulImpl(null, false, h1, h2, h1); double d3 = (t0 - t3).HAbsMax(); HDebug.Assert(0 == d3);
Matrix t4 = GetMulImpl(null, false, h1, h2, h2); double d4 = (t0 - t4).HAbsMax(); HDebug.Assert(0 == d4);
Matrix t5 = GetMulImpl(null, false, h2, h1, h1); double d5 = (t0 - t5).HAbsMax(); HDebug.Assert(0 == d5);
Matrix t6 = GetMulImpl(null, false, h2, h1, h2); double d6 = (t0 - t6).HAbsMax(); HDebug.Assert(0 == d6);
Matrix t7 = GetMulImpl(null, false, h2, h2, h1); double d7 = (t0 - t7).HAbsMax(); HDebug.Assert(0 == d7);
Matrix t8 = GetMulImpl(null, false, h2, h2, h2); double d8 = (t0 - t8).HAbsMax(); HDebug.Assert(0 == d8);
}
}
}
HessMatrix mul = null;
foreach (HessMatrix mat in mats)
{
if (mul == null)
{
mul = mat;
}
else
{
mul = GetMulImpl(mul, mat, ila, warning);
}
}
return(mul);
}
public static HessMatrix GetHessVdw(IList <Vector> coords, IEnumerable <Universe.Nonbonded14> nonbonded14s, double?Epsilon, string opt, HessMatrix hessian)
{
int size = coords.Count;
if (hessian == null)
{
hessian = HessMatrixSparse.ZerosSparse(size * 3, size * 3);
}
foreach (Universe.Nonbonded14 nonbonded14 in nonbonded14s)
{
Universe.Atom atom0 = nonbonded14.atoms[0];
Universe.Atom atom1 = nonbonded14.atoms[1];
int idx0 = atom0.ID; if (coords[idx0] == null)
{
continue;
}
int idx1 = atom1.ID; if (coords[idx1] == null)
{
continue;
}
double lEpsilon;
if (Epsilon != null)
{
lEpsilon = Epsilon.Value;
}
else
{
switch (opt)
{
case "gromacs":
{
var nbndpar0 = atom0.ConvertGromacsToCharmm;
var nbndpar1 = atom1.ConvertGromacsToCharmm;
double eps0_14 = nbndpar0.eps_14; eps0_14 = (double.IsNaN(eps0_14) == false) ? eps0_14 : nbndpar0.eps;
double eps1_14 = nbndpar1.eps_14; eps1_14 = (double.IsNaN(eps1_14) == false) ? eps1_14 : nbndpar1.eps;
lEpsilon = Math.Sqrt(eps0_14 * eps1_14);
}
break;
default:
{
double eps0_14 = atom0.eps_14; eps0_14 = (double.IsNaN(eps0_14) == false) ? eps0_14 : atom0.epsilon;
double eps1_14 = atom1.eps_14; eps1_14 = (double.IsNaN(eps1_14) == false) ? eps1_14 : atom1.epsilon;
lEpsilon = Math.Sqrt(eps0_14 * eps1_14);
}
break;
}
}
FourthTerm(coords, lEpsilon, hessian, idx0, idx1);
FourthTerm(coords, lEpsilon, hessian, idx1, idx0);
}
return(hessian);
}
public static HessMatrix GetHessImproper
(IList <Vector> coords, IEnumerable <Universe.Improper> impropers, double?K_psi, HessMatrix hessian
, Action <Universe.Atom, Vector, Universe.Atom, Vector, Universe.Atom, Vector, Universe.Atom, Vector, double, double> collector
, bool useArnaud96 = false
)
{
int size = coords.Count;
if (hessian == null)
{
hessian = HessMatrixSparse.ZerosSparse(size * 3, size * 3);
}
double sqrt2 = Math.Sqrt(2);
foreach (Universe.Improper improper in impropers)
{
int idx0 = improper.atoms[0].ID; if (coords[idx0] == null)
{
continue;
}
int idx1 = improper.atoms[1].ID; if (coords[idx1] == null)
{
continue;
}
int idx2 = improper.atoms[2].ID; if (coords[idx2] == null)
{
continue;
}
int idx3 = improper.atoms[3].ID; if (coords[idx3] == null)
{
continue;
}
double lK_psi = (K_psi != null)? K_psi.Value : improper.Kpsi;
double n = sqrt2; // make (K_chi * n^2 / 2 == K_chi) when calling ThirdTermN(IList<Vector> caArray, double K_phi, double n)
lK_psi = lK_psi * 2;
n = 1;
HDebug.Assert(lK_psi >= 0);
ThirdTermN(coords, lK_psi, n, hessian, idx0, idx1, idx2, idx3, useArnaud96: useArnaud96);
if (collector != null)
{
collector
(improper.atoms[0], coords[idx0]
, improper.atoms[1], coords[idx1]
, improper.atoms[2], coords[idx2]
, improper.atoms[3], coords[idx3]
, lK_psi, n);
}
}
return(hessian);
}
public static HessMatrix GetHessVdw(IList <Vector> coords, IEnumerable <Universe.AtomPack> pairs, double?Epsilon, string opt, HessMatrix hessian)
{
int size = coords.Count;
if (hessian == null)
{
hessian = HessMatrixSparse.ZerosSparse(size * 3, size * 3);
}
foreach (Universe.AtomPack pair in pairs)
{
Universe.Atom atom0 = pair.atoms.First();
Universe.Atom atom1 = pair.atoms.Last();
int idx0 = atom0.ID; if (coords[idx0] == null)
{
continue;
}
int idx1 = atom1.ID; if (coords[idx1] == null)
{
continue;
}
double lEpsilon;
if (Epsilon != null)
{
lEpsilon = Epsilon.Value;
}
else
{
switch (opt)
{
case "gromacs":
{
double eps0 = atom0.ConvertGromacsToCharmm.eps;
double eps1 = atom1.ConvertGromacsToCharmm.eps;
lEpsilon = Math.Sqrt(eps0 * eps1);
}
break;
default:
{
double eps0 = atom0.epsilon;
double eps1 = atom1.epsilon;
lEpsilon = Math.Sqrt(eps0 * eps1);
}
break;
}
}
FourthTerm(coords, lEpsilon, hessian, idx0, idx1);
FourthTerm(coords, lEpsilon, hessian, idx1, idx0);
}
return(hessian);
}
public IMatrixSparse <MatrixByArr> GetMatrixSparse()
{
if (this is HessMatrixSparse)
{
return((this as HessMatrixSparse).GetMatrixSparse());
}
if (this is HessMatrixDense)
{
return(HessMatrixSparse.FromMatrix(this).GetMatrixSparse());
}
if (this is HessMatrixLayeredArray)
{
return(this as IMatrixSparse <MatrixByArr>);
}
throw new NotImplementedException();
}
public static HessMatrix GetHessBond
(IList <Vector> coords, IEnumerable <Universe.Bond> bonds, double?K_r, HessMatrix hessian, Matrix pwspr
, Action <Universe.Atom, Vector, Universe.Atom, Vector, double> collector
)
{
int size = coords.Count;
if (hessian == null)
{
hessian = HessMatrixSparse.ZerosSparse(size * 3, size * 3);
}
foreach (Universe.Bond bond in bonds)
{
int idx0 = bond.atoms[0].ID; if (coords[idx0] == null)
{
continue;
}
int idx1 = bond.atoms[1].ID; if (coords[idx1] == null)
{
continue;
}
double lK_r = (K_r != null)? K_r.Value : bond.Kb;
HDebug.Assert(lK_r >= 0);
FirstTerm(coords, lK_r, hessian, idx0, idx1);
if (pwspr != null)
{
pwspr[idx0, idx1] += lK_r;
pwspr[idx1, idx0] += lK_r;
}
if (collector != null)
{
collector
(bond.atoms[0], coords[idx0]
, bond.atoms[1], coords[idx1]
, lK_r);
}
}
return(hessian);
}
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);
}
public static HessMatrixSparse ZerosSparse(int colsize, int rowsize)
{
if (ZerosSparse_selftest)
{
ZerosSparse_selftest = false;
HessMatrixSparse tmat = ZerosSparse(300, 300);
bool bzero = true;
for (int c = 0; c < tmat.ColSize; c++)
{
for (int r = 0; r < tmat.ColSize; r++)
{
if (tmat[c, r] != 0)
{
bzero = false;
}
}
}
HDebug.Assert(bzero);
}
HessMatrixSparse mat = new HessMatrixSparse(colsize, rowsize);
return(mat);
}
private static HessMatrix GetHessCoarseResiIterImpl_Matlab_IterLowerTri_Get_BInvDC
(HessMatrix A
, HessMatrix C
, HessMatrix D
, bool process_disp_console
, string[] options
, double?thld_BinvDC = null
, bool parallel = false
)
{
HessMatrix B_invD_C;
Dictionary <int, int> Cbr_CCbr = new Dictionary <int, int>();
List <int> CCbr_Cbr = new List <int>();
foreach (ValueTuple <int, int, MatrixByArr> bc_br_bval in C.EnumBlocks())
{
int Cbr = bc_br_bval.Item2;
if (Cbr_CCbr.ContainsKey(Cbr) == false)
{
HDebug.Assert(Cbr_CCbr.Count == CCbr_Cbr.Count);
int CCbr = Cbr_CCbr.Count;
Cbr_CCbr.Add(Cbr, CCbr);
CCbr_Cbr.Add(Cbr);
HDebug.Assert(CCbr_Cbr[CCbr] == Cbr);
}
}
HessMatrix CC = HessMatrixSparse.ZerosSparse(C.ColSize, Cbr_CCbr.Count * 3);
{
Action <ValueTuple <int, int, MatrixByArr> > func = delegate(ValueTuple <int, int, MatrixByArr> bc_br_bval)
{
int Cbc = bc_br_bval.Item1; int CCbc = Cbc;
int Cbr = bc_br_bval.Item2; int CCbr = Cbr_CCbr[Cbr];
var bval = bc_br_bval.Item3;
lock (CC)
CC.SetBlock(CCbc, CCbr, bval);
};
if (parallel)
{
Parallel.ForEach(C.EnumBlocks(), func);
}
else
{
foreach (var bc_br_bval in C.EnumBlocks())
{
func(bc_br_bval);
}
}
}
if (process_disp_console)
{
System.Console.Write("squeezeC({0,6}->{1,6} blk), ", C.RowBlockSize, CC.RowBlockSize);
}
{
/// If a diagonal element of D is null, that row and column should be empty.
/// This assume that the atom is removed. In this case, the removed diagonal block
/// is replace as the 3x3 identity matrix.
///
/// [B1 0] [ A 0 ]^-1 [C1 C2 C3] = [B1 0] [ A^-1 0 ] [C1 C2 C3]
/// [B2 0] [ 0 I ] [ 0 0 0] [B2 0] [ 0 I^-1 ] [ 0 0 0]
/// [B3 0] [B3 0]
/// = [B1.invA 0] [C1 C2 C3]
/// [B2.invA 0] [ 0 0 0]
/// [B3.invA 0]
/// = [B1.invA.C1 B1.invA.C2 B1.invA.C3]
/// [B2.invA.C1 B2.invA.C2 B2.invA.C3]
/// [B3.invA.C1 B3.invA.C2 B3.invA.C3]
///
{
//HDebug.Exception(D.ColBlockSize == D.RowBlockSize);
for (int bi = 0; bi < D.ColBlockSize; bi++)
{
if (D.HasBlock(bi, bi) == true)
{
continue;
}
//for(int bc=0; bc< D.ColBlockSize; bc++) HDebug.Exception( D.HasBlock(bc, bi) == false);
//for(int br=0; br< D.RowBlockSize; br++) HDebug.Exception( D.HasBlock(bi, br) == false);
//for(int br=0; br<CC.RowBlockSize; br++) HDebug.Exception(CC.HasBlock(bi, br) == false);
D.SetBlock(bi, bi, new double[3, 3] {
{ 1, 0, 0 }, { 0, 1, 0 }, { 0, 0, 1 }
});
}
}
HessMatrix BB_invDD_CC;
using (new Matlab.NamedLock(""))
{
Matlab.Execute("clear;"); if (process_disp_console)
{
System.Console.Write("matlab(");
}
Matlab.PutMatrix("C", CC); if (process_disp_console)
{
System.Console.Write("C"); //Matlab.PutSparseMatrix("C", CC.GetMatrixSparse(), 3, 3);
}
Matlab.PutMatrix("D", D); if (process_disp_console)
{
System.Console.Write("D");
}
{ // Matlab.Execute("BinvDC = (C' / D) * C;");
if (options != null && options.Contains("pinv(D)"))
{
string msg = Matlab.Execute("BinvDC = (C' / D) * C;", true);
if (msg != "")
{
Matlab.Execute("BinvDC = C' * pinv(D) * C;");
}
}
else
{
Matlab.Execute("BinvDC = (C' / D) * C;");
}
} if (process_disp_console)
{
System.Console.Write("X");
}
/// » whos
/// Name Size Bytes Class Attributes
/// // before compressing C matrix
/// C 1359x507 5512104 double // C 1359x1545 16797240 double
/// CC 1359x507 198464 double sparse // CC 1359x1545 206768 double sparse
/// D 1359x1359 14775048 double // D 1359x1359 14775048 double
/// DD 1359x1359 979280 double sparse // DD 1359x1359 979280 double sparse
/// ans 1x1 8 double
///
/// » tic; for i=1:30; A=(C' / D) * C; end; toc dense * dense * dense => 8.839463 seconds. (win)
/// Elapsed time is 8.839463 seconds.
/// » tic; for i=1:30; AA=(CC' / DD) * CC; end; toc sparse * sparse * sparse => 27.945534 seconds.
/// Elapsed time is 27.945534 seconds.
/// » tic; for i=1:30; AAA=(C' / DD) * C; end; toc sparse * dense * sparse => 29.136144 seconds.
/// Elapsed time is 29.136144 seconds.
/// »
/// » tic; for i=1:30; A=(C' / D) * C; end; toc dense * dense * dense => 8.469071 seconds. (win)
/// Elapsed time is 8.469071 seconds.
/// » tic; for i=1:30; AA=(CC' / DD) * CC; end; toc sparse * sparse * sparse => 28.309953 seconds.
/// Elapsed time is 28.309953 seconds.
/// » tic; for i=1:30; AAA=(C' / DD) * C; end; toc sparse * dense * sparse => 28.586375 seconds.
/// Elapsed time is 28.586375 seconds.
//Matrix BBinvDDCC = Matlab.GetMatrix("BinvDC", true);
if (thld_BinvDC != null)
{
Matlab.Execute("BinvDC(find(BinvDC < " + thld_BinvDC.ToString() + ")) = 0;");
}
if (Matlab.GetValue("nnz(BinvDC)/numel(BinvDC)") > 0.5)
{
double[,] arr = Matlab.GetMatrix("BinvDC", true);
BB_invDD_CC = HessMatrixDense.FromMatrix(arr);
if (process_disp_console)
{
System.Console.Write("Y), ");
}
}
else
{
Matlab.Execute("[i,j,s] = find(sparse(BinvDC));");
TVector <int> listi = Matlab.GetVectorLargeInt("i", true);
TVector <int> listj = Matlab.GetVectorLargeInt("j", true);
TVector <double> lists = Matlab.GetVectorLarge("s", true);
int colsize = Matlab.GetValueInt("size(BinvDC,1)");
int rowsize = Matlab.GetValueInt("size(BinvDC,2)");
Dictionary <ValueTuple <int, int>, MatrixByArr> lst_bc_br_bval = new Dictionary <ValueTuple <int, int>, MatrixByArr>();
for (long i = 0; i < listi.SizeLong; i++)
{
int c = listi[i] - 1; int bc = c / 3; int ic = c % 3;
int r = listj[i] - 1; int br = r / 3; int ir = r % 3;
double v = lists[i];
ValueTuple <int, int> bc_br = new ValueTuple <int, int>(bc, br);
if (lst_bc_br_bval.ContainsKey(bc_br) == false)
{
lst_bc_br_bval.Add(bc_br, new double[3, 3]);
}
lst_bc_br_bval[bc_br][ic, ir] = v;
}
// Matrix BBinvDDCC = Matrix.Zeros(colsize, rowsize);
// for(int i=0; i<listi.Length; i++)
// BBinvDDCC[listi[i]-1, listj[i]-1] = lists[i];
// //GC.Collect(0);
BB_invDD_CC = HessMatrixSparse.ZerosSparse(colsize, rowsize);
foreach (var bc_br_bval in lst_bc_br_bval)
{
int bc = bc_br_bval.Key.Item1;
int br = bc_br_bval.Key.Item2;
var bval = bc_br_bval.Value;
BB_invDD_CC.SetBlock(bc, br, bval);
}
if (process_disp_console)
{
System.Console.Write("Z), ");
}
if (HDebug.IsDebuggerAttached)
{
for (int i = 0; i < listi.Size; i++)
{
int c = listi[i] - 1;
int r = listj[i] - 1;
double v = lists[i];
HDebug.Assert(BB_invDD_CC[c, r] == v);
}
}
}
Matlab.Execute("clear;");
}
//GC.Collect(0);
B_invD_C = HessMatrixSparse.ZerosSparse(C.RowSize, C.RowSize);
{
// for(int bcc=0; bcc<CCbr_Cbr.Count; bcc++)
// {
// int bc = CCbr_Cbr[bcc];
// for(int brr=0; brr<CCbr_Cbr.Count; brr++)
// {
// int br = CCbr_Cbr[brr];
// HDebug.Assert(B_invD_C.HasBlock(bc, br) == false);
// if(BB_invDD_CC.HasBlock(bcc, brr) == false)
// continue;
// var bval = BB_invDD_CC.GetBlock(bcc, brr);
// B_invD_C.SetBlock(bc, br, bval);
// HDebug.Exception(A.HasBlock(bc, bc));
// HDebug.Exception(A.HasBlock(br, br));
// }
// }
Action <ValueTuple <int, int, MatrixByArr> > func = delegate(ValueTuple <int, int, MatrixByArr> bcc_brr_bval)
{
int bcc = bcc_brr_bval.Item1;
int brr = bcc_brr_bval.Item2;
var bval = bcc_brr_bval.Item3;
int bc = CCbr_Cbr[bcc];
int br = CCbr_Cbr[brr];
lock (B_invD_C)
B_invD_C.SetBlock(bc, br, bval);
};
if (parallel)
{
Parallel.ForEach(BB_invDD_CC.EnumBlocks(), func);
}
else
{
foreach (var bcc_brr_bval in BB_invDD_CC.EnumBlocks())
{
func(bcc_brr_bval);
}
}
}
}
GC.Collect(0);
return(B_invD_C);
}
public static HessMatrix GetHessAnm(IList <Vector> coords, IEnumerable <Tuple <int, int, double> > enumKij)
{
if (GetHessAnm_selftest)
{
GetHessAnm_selftest = false;
Vector[] tcoords = new Vector[]
{
new Vector(0, 0, 0),
new Vector(1, 0, 0),
new Vector(0, 2, 0),
new Vector(0, 0, 3),
new Vector(4, 5, 0),
new Vector(0, 6, 7),
new Vector(8, 0, 9),
new Vector(-1, -1, -1),
};
Matrix tKij = Matrix.Ones(8, 8);
for (int i = 0; i < 8; i++)
{
tKij[i, i] = 0;
}
HessMatrix hess0 = GetHessAnm_debug(tcoords, tKij);
HessMatrix hess1 = GetHessAnm(tcoords, tKij.HEnumNonZeros());
HDebug.Assert((hess0 - hess1).HAbsMax() == 0);
}
//Debug.Assert(AnmHessianSelfTest());
int n = coords.Count;
HessMatrix hess = null;
if (n < 100)
{
hess = HessMatrixDense.ZerosDense(n * 3, n * 3);
}
else
{
hess = HessMatrixSparse.ZerosSparse(n * 3, n * 3);
}
int numset = 0;
foreach (var kij in enumKij)
{
int i = kij.Item1;
int j = kij.Item2;
double k_ij = kij.Item3;
{
if (i == j)
{
HDebug.Assert(k_ij == 0);
continue;
}
if (coords[j] == null)
{
continue;
}
Vector vec_ij = coords[j] - coords[i];
Vector unit_ij = vec_ij.UnitVector();
HDebug.Assert(double.IsNaN(k_ij) == false);
if (k_ij == 0)
{
continue;
}
MatrixByArr hessij = new double[3, 3];
hessij[0, 0] = -k_ij * unit_ij[0] * unit_ij[0];
hessij[0, 1] = -k_ij * unit_ij[0] * unit_ij[1];
hessij[0, 2] = -k_ij * unit_ij[0] * unit_ij[2];
hessij[1, 0] = -k_ij * unit_ij[1] * unit_ij[0];
hessij[1, 1] = -k_ij * unit_ij[1] * unit_ij[1];
hessij[1, 2] = -k_ij * unit_ij[1] * unit_ij[2];
hessij[2, 0] = -k_ij * unit_ij[2] * unit_ij[0];
hessij[2, 1] = -k_ij * unit_ij[2] * unit_ij[1];
hessij[2, 2] = -k_ij * unit_ij[2] * unit_ij[2];
hess.SetBlock(i, j, hessij);
MatrixByArr hessii = hess.GetBlock(i, i) - hessij;
hess.SetBlock(i, i, hessii);
numset++;
}
}
return(hess);
}
public static CTesthess ReadHess
(Xyz xyz
, string outputpath
, Dictionary <string, string[]> optOutSource // =null
, Func <int, int, HessMatrix> HessMatrixZeros // =null
)
{
int size = xyz.atoms.Length;
#region format: output.txt
/// ######################################################################
/// ##########################################################################
/// ### ###
/// ### TINKER --- Software Tools for Molecular Design ###
/// ## ##
/// ## Version 6.2 February 2013 ##
/// ## ##
/// ## Copyright (c) Jay William Ponder 1990-2013 ##
/// ### All Rights Reserved ###
/// ### ###
/// ##########################################################################
/// ######################################################################
///
///
/// Atoms with an Unusual Number of Attached Atoms :
///
/// Type Atom Name Atom Type Expected Found
///
/// Valence 1496-NR2 69 2 3
/// Valence 2438-FE 107 6 5
///
/// Diagonal Hessian Elements for Each Atom :
///
/// Atom X Y Z
///
/// 1 1445.9830 1358.3447 1484.8642
/// 2 212.9895 294.4584 604.5062
/// 3 187.1986 751.6727 125.0336
/// 4 813.4799 132.1743 151.5707
/// ...
/// 2507 178.7277 479.7434 243.4103
/// 2508 969.8813 977.2507 1845.6726
/// 2509 390.1648 232.0577 1029.6844
/// 2510 322.3674 337.8749 996.8230
///
/// Sum of Diagonal Hessian Elements : 5209042.9060
///
/// Hessian Matrix written to File : test.hes
#endregion
Tuple <int, double, double, double>[] outDiagHessElems = new Tuple <int, double, double, double> [size];
double?outSumDiagHessElem = null;
string outHessMatFile = null;
string outHessFormat = null;
{
string step = "";
foreach (string _line in HFile.ReadLines(outputpath))
{
string line = _line.Trim();
if (line.Length == 0)
{
continue;
}
if (line.Trim().StartsWith("#"))
{
continue;
}
if (line.Contains(" :"))
{
if (line.Contains("Atoms with an Unusual Number of Attached Atoms"))
{
step = ""; continue;
}
else if (line.Contains("Diagonal Hessian Elements for Each Atom"))
{
step = "hess diagonal"; continue;
}
else if (line.Contains("Sum of Diagonal Hessian Elements"))
{
step = "sum hess diagonal";
}
else if (line.Contains("Hessian Matrix written to File"))
{
step = "full hess file";
}
else if (line.Contains("Hessian Sparse Matrix written to File"))
{
step = "sparse hess file";
}
else if (line.Contains("Select Smaller Size for Sparse Hessian Matrix"))
{
continue;
}
else
{
HDebug.Assert(false);
continue;
}
}
switch (step)
{
case "":
continue;
case "hess diagonal":
{
string[] tokens = line.Split().HRemoveAll("");
if (tokens[0] == "Atom")
{
continue;
}
int Atom = int.Parse(tokens[0]); // ; if( int.TryParse(tokens[0], out Atom) == false) continue;
double X = double.Parse(tokens[1]); // ; if(double.TryParse(tokens[1], out X) == false) continue;
double Y = double.Parse(tokens[2]); // ; if(double.TryParse(tokens[2], out Y) == false) continue;
double Z = double.Parse(tokens[3]); // ; if(double.TryParse(tokens[3], out Z) == false) continue;
HDebug.Assert(outDiagHessElems[Atom - 1] == null);
outDiagHessElems[Atom - 1] = new Tuple <int, double, double, double>(Atom, X, Y, Z);
}
continue;
case "sum hess diagonal":
{
string[] tokens = line.Split().HRemoveAll("");
double sum = double.Parse(tokens.Last()); // if(double.TryParse(tokens.Last(), out sum) == false) continue;
outSumDiagHessElem = sum;
}
step = "";
continue;
case "full hess file": outHessFormat = "full matrix"; goto case "hess file";
case "sparse hess file": outHessFormat = "sparse matrix"; goto case "hess file";
case "hess file":
{
string[] tokens = line.Split().HRemoveAll("");
string outputpath_dir = HFile.GetFileInfo(outputpath).Directory.FullName;
outHessMatFile = outputpath_dir + "\\" + tokens.Last();
}
step = "";
continue;
default:
HDebug.Assert(false);
step = "";
continue;
}
}
}
#region Format: test.hes
/// Diagonal Hessian Elements (3 per Atom)
///
/// 1445.9830 1358.3447 1484.8642 212.9895 294.4584 604.5062
/// 187.1986 751.6727 125.0336 813.4799 132.1743 151.5707
/// 1167.7472 1188.3459 1162.5475 268.8291 498.0188 143.2438
/// ...
/// Off-diagonal Hessian Elements for Atom 1 X
/// 23.0878 14.6380 -214.0545 96.9308 -186.7740 -205.1460
/// -208.7035 -28.9630 -788.9124 39.6748 126.4491 -190.5074
/// ...
/// Off-diagonal Hessian Elements for Atom 1 Y
/// -64.1616 97.2697 -292.3813 264.1922 -184.4701 -728.8687
/// -109.9103 15.4168 -152.5717 -11.7733 18.8369 -188.4875
/// ...
/// Off-diagonal Hessian Elements for Atom 1 Z
/// -155.9409 219.8782 -610.0622 -10.0041 -62.8209 -156.1112
/// 77.0829 -14.2127 -166.0525 53.1834 -97.4207 -347.9315
/// ...
/// Off-diagonal Hessian Elements for Atom 2 X
/// -106.5166 185.8395 19.7546 -10.0094 25.8072 -8.1335
/// 35.8501 -64.8320 3.8761 -13.8893 9.4266 0.1312
/// ...
///
/// ...
///
/// Off-diagonal Hessian Elements for Atom 2508 X
/// 488.4590 -69.2721 -338.4824 -155.1656 253.3732 -297.4214
/// -164.8301 -191.3769
/// Off-diagonal Hessian Elements for Atom 2508 Y
/// 74.0161 -149.1060 -273.4863 176.4975 -170.6527 -341.1639
/// -263.6141
/// Off-diagonal Hessian Elements for Atom 2508 Z
/// 304.9942 223.7496 -851.3028 -242.9481 -310.7953 -821.2532
/// Off-diagonal Hessian Elements for Atom 2509 X
/// 198.4498 -331.6530 78.8172 17.3909 -30.0512
/// Off-diagonal Hessian Elements for Atom 2509 Y
/// -227.5916 25.7235 74.5131 -53.2690
/// Off-diagonal Hessian Elements for Atom 2509 Z
/// 46.7873 20.7615 -168.0704
/// Off-diagonal Hessian Elements for Atom 2510 X
/// 252.6853 247.2963
/// Off-diagonal Hessian Elements for Atom 2510 Y
/// 343.6797
#endregion
HessMatrix hess;
{
if (HessMatrixZeros != null)
{
hess = HessMatrixZeros(size * 3, size * 3);
}
else
{
switch (outHessFormat)
{
case "full matrix": hess = HessMatrixDense.ZerosDense(size * 3, size * 3); break;
case "sparse matrix": hess = HessMatrixSparse.ZerosSparse(size * 3, size * 3); break;
default: hess = null; break;
}
}
//HDebug.SetEpsilon(hess);
string step = "";
int diagidx = -1;
int offidx1 = -1;
int offidx2 = -1;
/// string[] lines = HFile.ReadAllLines(outHessMatFile);
/// GC.WaitForFullGCComplete();
/// object[] tokenss = new object[lines.Length];
///
/// Parallel.For(0, lines.Length, delegate(int i)
/// //for(int i=0; i<lines.Length; i++)
/// {
/// string line = lines[i];
/// string[] stokens = line.Trim().Split().RemoveAll("");
/// if(stokens.Length != 0)
/// {
/// double[] dtokens = new double[stokens.Length];
/// for(int j=0; j<stokens.Length; j++)
/// if(double.TryParse(stokens[j], out dtokens[j]) == false)
/// {
/// tokenss[i] = stokens;
/// goto endfor;
/// }
/// tokenss[i] = dtokens;
/// }
/// endfor: ;
/// });
/// System.IO.StreamReader matreader = HFile.OpenText(outHessMatFile);
/// while(matreader.EndOfStream == false)
/// for(int i=0; i<lines.Length; i++)
/// foreach(string line in lines)
foreach (string line in HFile.HEnumAllLines(outHessMatFile))
{
/// string line = lines[i];
/// string line = matreader.ReadLine();
string[] tokens = line.Trim().Split().HRemoveAll("");
if (tokens.Length == 0)
{
continue;
}
/// if(tokenss[i] == null)
/// continue;
/// string[] stokens = (tokenss[i] as string[]);
if (tokens[0] == "Diagonal" && tokens[1] == "Hessian" && tokens[2] == "Elements")
{
step = "Diagonal"; diagidx = 0; continue;
}
if (tokens[0] == "Off-diagonal" && tokens[1] == "Hessian" && tokens[2] == "Elements")
{
step = "Off-diagonal"; offidx1++; offidx2 = offidx1 + 1; continue;
}
if (tokens[0] == "Off-diagonal" && tokens[1] == "sparse" && tokens[2] == "Hessian" &&
tokens[3] == "Indexes/Elements" && tokens[4] == "for" && tokens[5] == "Atom")
{
step = "Off-diagonal sparse";
offidx1 = (int.Parse(tokens[6]) - 1) * 3;
switch (tokens[7])
{
case "X": break;
case "Y": offidx1 += 1; break;
case "Z": offidx1 += 2; break;
default: throw new HException();
}
continue;
}
/// double[] dtokens = (tokenss[i] as double[]);
/// tokens = new string[20];
/// for(int i=0; i*12<line.Length; i++)
/// tokens[i] = line.Substring(i*12, 12).Trim();
/// tokens = tokens.HRemoveAll("").ToArray();
/// tokens = tokens.HRemoveAll(null).ToArray();
switch (step)
{
case "Diagonal":
{
/// foreach(double val in dtokens)
foreach (string token in tokens)
{
HDebug.Assert(token.Last() != ' ');
double val = double.Parse(token);
HDebug.Assert(hess[diagidx, diagidx] == 0);
hess[diagidx, diagidx] = val;
diagidx++;
}
}
continue;
case "Off-diagonal":
{
/// foreach(double val in dtokens)
foreach (string token in tokens)
{
HDebug.Assert(token.Last() != ' ');
//double val = double.Parse(token);
double val;
bool succ = double.TryParse(token, out val);
if (succ == false)
{
HDebug.Assert(false);
goto case "exception 0";
}
if (size < 3000)
{
HDebug.Assert(hess[offidx1, offidx2] == 0);
HDebug.Assert(hess[offidx2, offidx1] == 0);
}
if (val != 0)
{
hess[offidx1, offidx2] = val;
hess[offidx2, offidx1] = val;
}
offidx2++;
}
}
continue;
case "Off-diagonal sparse":
{
HDebug.Assert(tokens.Length % 2 == 0);
for (int i = 0; i < tokens.Length; i += 2)
{
HDebug.Assert(tokens[i].Last() != ' ');
HDebug.Assert(tokens[i + 1].Last() != ' ');
//double val = double.Parse(token);
double val;
bool succ = true;
succ &= int.TryParse(tokens[i], out offidx2); offidx2--;
succ &= double.TryParse(tokens[i + 1], out val);
if (succ == false)
{
HDebug.Assert(false);
goto case "exception 0";
}
if (size < 3000)
{
HDebug.Assert(hess[offidx1, offidx2] == 0);
HDebug.Assert(hess[offidx2, offidx1] == 0);
}
if (val != 0)
{
hess[offidx1, offidx2] = val;
hess[offidx2, offidx1] = val;
}
}
}
continue;
default:
HDebug.Assert(false);
goto case "exception 1";
case "exception 0":
throw new HException("incomplete hessian file (0)");
case "exception 1":
throw new HException("incomplete hessian file (1)");
}
throw new HException("incomplete hessian file (2)");
}
/// matreader.Close();
if (HDebug.IsDebuggerAttached && size < 3000)
{
//for(int c=0; c<size*3; c++)
// for(int r=0; r<size*3; r++)
// if(hess[c, r] == double.Epsilon)
// throw new Exception("incomplete hessian file (3)");
//
//for(int c=0; c<size*3; c++)
//{
// double sum = 0;
// double max = double.NegativeInfinity;
// for(int r=0; r<size*3; r++)
// {
// max = Math.Max(max, hess[c, r]);
// sum += hess[c, r];
// HDebug.Assert(hess[c, r] != double.Epsilon);
// }
// HDebug.Assert(Math.Abs(sum) < max/1000);
// HDebug.AssertTolerance(0.1, sum);
//}
Hess.CheckHessDiag(hess, 0.1, null);
for (int i = 0; i < size; i++)
{
HDebug.Assert(outDiagHessElems[i].Item1 == i + 1);
HDebug.AssertTolerance(0.000001, outDiagHessElems[i].Item2 - hess[i * 3 + 0, i * 3 + 0]);
HDebug.AssertTolerance(0.000001, outDiagHessElems[i].Item3 - hess[i * 3 + 1, i * 3 + 1]);
HDebug.AssertTolerance(0.000001, outDiagHessElems[i].Item4 - hess[i * 3 + 2, i * 3 + 2]);
}
}
}
if (optOutSource != null)
{
optOutSource.Add("test.hes", HFile.HEnumAllLines(outHessMatFile).ToArray());
}
return(new CTesthess
{
hess = hess,
xyz = xyz,
});
}
public static HessMatrix GetHessAnm(IList <Vector> coords, IList <double> cutoffs, string options = "")
{
if (coords.Count > 10000)
{
HDebug.ToDo("System size is too big. Use EnumHessAnmSpr() and other GetHessAnm()");
}
//Debug.Assert(AnmHessianSelfTest());
HDebug.Assert(coords.Count == cutoffs.Count);
double[] cutoffs2 = new double[cutoffs.Count];
for (int i = 0; i < cutoffs.Count; i++)
{
cutoffs2[i] = cutoffs[i] * cutoffs[i];
}
double Epsilon = 0;// double.Epsilon;
int n = coords.Count;
HessMatrix hess = null;
if (n < 100)
{
hess = HessMatrixDense.ZerosDense(n * 3, n * 3);
}
else
{
hess = HessMatrixSparse.ZerosSparse(n * 3, n * 3);
}
Action <int> comp_hess_i = delegate(int i)
{
if (coords[i] == null)
{
return;
}
//continue;
for (int j = 0; j < n; j++)
{
if (i == j)
{
continue;
}
if (coords[j] == null)
{
continue;
}
Vector vec_ij = coords[j] - coords[i];
double dist2 = vec_ij.Dist2;
double cutoff2 = Math.Max(cutoffs2[i], cutoffs2[j]);
if (dist2 > cutoff2)
{
if (Epsilon == 0)
{
continue;
}
HDebug.Assert(hess[i * 3 + 0, j * 3 + 0] == 0); hess[i * 3 + 0, j *3 + 0] = Epsilon;
HDebug.Assert(hess[i * 3 + 0, j * 3 + 1] == 0); hess[i * 3 + 0, j *3 + 1] = Epsilon;
HDebug.Assert(hess[i * 3 + 0, j * 3 + 2] == 0); hess[i * 3 + 0, j *3 + 2] = Epsilon;
HDebug.Assert(hess[i * 3 + 1, j * 3 + 0] == 0); hess[i * 3 + 1, j *3 + 0] = Epsilon;
HDebug.Assert(hess[i * 3 + 1, j * 3 + 1] == 0); hess[i * 3 + 1, j *3 + 1] = Epsilon;
HDebug.Assert(hess[i * 3 + 1, j * 3 + 2] == 0); hess[i * 3 + 1, j *3 + 2] = Epsilon;
HDebug.Assert(hess[i * 3 + 2, j * 3 + 0] == 0); hess[i * 3 + 2, j *3 + 0] = Epsilon;
HDebug.Assert(hess[i * 3 + 2, j * 3 + 1] == 0); hess[i * 3 + 2, j *3 + 1] = Epsilon;
HDebug.Assert(hess[i * 3 + 2, j * 3 + 2] == 0); hess[i * 3 + 2, j *3 + 2] = Epsilon;
continue;
}
Vector unit_ij = vec_ij.UnitVector();
double k_ij = 1; double val;
val = k_ij * unit_ij[0] * unit_ij[0]; hess[i * 3 + 0, j *3 + 0] = Epsilon - val; hess[i * 3 + 0, i *3 + 0] += val; // hess[i*3+0, j*3+0] = Epsilon - k_ij * unit_ij[0]*unit_ij[0]; hess[i*3+0, i*3+0] += k_ij * unit_ij[0]*unit_ij[0];
val = k_ij * unit_ij[0] * unit_ij[1]; hess[i * 3 + 0, j *3 + 1] = Epsilon - val; hess[i * 3 + 0, i *3 + 1] += val; // hess[i*3+0, j*3+1] = Epsilon - k_ij * unit_ij[0]*unit_ij[1]; hess[i*3+0, i*3+1] += k_ij * unit_ij[0]*unit_ij[1];
val = k_ij * unit_ij[0] * unit_ij[2]; hess[i * 3 + 0, j *3 + 2] = Epsilon - val; hess[i * 3 + 0, i *3 + 2] += val; // hess[i*3+0, j*3+2] = Epsilon - k_ij * unit_ij[0]*unit_ij[2]; hess[i*3+0, i*3+2] += k_ij * unit_ij[0]*unit_ij[2];
val = k_ij * unit_ij[1] * unit_ij[0]; hess[i * 3 + 1, j *3 + 0] = Epsilon - val; hess[i * 3 + 1, i *3 + 0] += val; // hess[i*3+1, j*3+0] = Epsilon - k_ij * unit_ij[1]*unit_ij[0]; hess[i*3+1, i*3+0] += k_ij * unit_ij[1]*unit_ij[0];
val = k_ij * unit_ij[1] * unit_ij[1]; hess[i * 3 + 1, j *3 + 1] = Epsilon - val; hess[i * 3 + 1, i *3 + 1] += val; // hess[i*3+1, j*3+1] = Epsilon - k_ij * unit_ij[1]*unit_ij[1]; hess[i*3+1, i*3+1] += k_ij * unit_ij[1]*unit_ij[1];
val = k_ij * unit_ij[1] * unit_ij[2]; hess[i * 3 + 1, j *3 + 2] = Epsilon - val; hess[i * 3 + 1, i *3 + 2] += val; // hess[i*3+1, j*3+2] = Epsilon - k_ij * unit_ij[1]*unit_ij[2]; hess[i*3+1, i*3+2] += k_ij * unit_ij[1]*unit_ij[2];
val = k_ij * unit_ij[2] * unit_ij[0]; hess[i * 3 + 2, j *3 + 0] = Epsilon - val; hess[i * 3 + 2, i *3 + 0] += val; // hess[i*3+2, j*3+0] = Epsilon - k_ij * unit_ij[2]*unit_ij[0]; hess[i*3+2, i*3+0] += k_ij * unit_ij[2]*unit_ij[0];
val = k_ij * unit_ij[2] * unit_ij[1]; hess[i * 3 + 2, j *3 + 1] = Epsilon - val; hess[i * 3 + 2, i *3 + 1] += val; // hess[i*3+2, j*3+1] = Epsilon - k_ij * unit_ij[2]*unit_ij[1]; hess[i*3+2, i*3+1] += k_ij * unit_ij[2]*unit_ij[1];
val = k_ij * unit_ij[2] * unit_ij[2]; hess[i * 3 + 2, j *3 + 2] = Epsilon - val; hess[i * 3 + 2, i *3 + 2] += val; // hess[i*3+2, j*3+2] = Epsilon - k_ij * unit_ij[2]*unit_ij[2]; hess[i*3+2, i*3+2] += k_ij * unit_ij[2]*unit_ij[2];
}
};
if (options.Split(';').Contains("parallel"))
{
System.Threading.Tasks.Parallel.For(0, n, comp_hess_i);
}
else
{
for (int i = 0; i < n; i++)
{
comp_hess_i(i);
}
}
return(hess);
}
public static bool SelfTest_1AAC()
{
Pdb.Atom[] atoms_ca = new Pdb.Atom[]
{
#region 1AAC text of CA atoms
Pdb.Atom.FromString("ATOM 2 CA ASP A 1 25.378 -18.141 21.012 1.00 23.28 C "),
Pdb.Atom.FromString("ATOM 10 CA LYS A 2 24.390 -18.799 17.407 1.00 12.32 C "),
Pdb.Atom.FromString("ATOM 19 CA ALA A 3 25.772 -15.617 15.840 1.00 10.31 C "),
Pdb.Atom.FromString("ATOM 24 CA THR A 4 28.837 -13.442 16.439 1.00 9.47 C "),
Pdb.Atom.FromString("ATOM 31 CA ILE A 5 28.913 -9.665 15.865 1.00 7.94 C "),
Pdb.Atom.FromString("ATOM 39 CA PRO A 6 31.906 -8.243 13.886 1.00 8.02 C "),
Pdb.Atom.FromString("ATOM 46 CA SER A 7 31.049 -4.632 14.810 1.00 7.70 C "),
Pdb.Atom.FromString("ATOM 52 CA GLU A 8 28.768 -3.589 17.658 1.00 10.01 C "),
Pdb.Atom.FromString("ATOM 73 CA PRO A 10 26.932 0.412 12.498 1.00 7.09 C "),
Pdb.Atom.FromString("ATOM 80 CA PHE A 11 29.488 1.217 9.844 1.00 6.81 C "),
Pdb.Atom.FromString("ATOM 91 CA ALA A 12 29.431 2.815 6.390 1.00 6.76 C "),
Pdb.Atom.FromString("ATOM 96 CA ALA A 13 28.012 1.036 3.320 1.00 8.60 C "),
Pdb.Atom.FromString("ATOM 101 CA ALA A 14 31.392 1.654 1.659 1.00 11.18 C "),
Pdb.Atom.FromString("ATOM 106 CA GLU A 15 33.092 -0.407 4.404 1.00 9.76 C "),
Pdb.Atom.FromString("ATOM 115 CA VAL A 16 31.115 -3.590 3.763 1.00 12.85 C "),
Pdb.Atom.FromString("ATOM 122 CA ALA A 17 33.429 -6.584 3.205 1.00 20.32 C "),
Pdb.Atom.FromString("ATOM 127 CA ASP A 18 34.080 -7.894 -0.306 1.00 27.64 C "),
Pdb.Atom.FromString("ATOM 135 CA GLY A 19 31.708 -10.634 -1.313 1.00 26.92 C "),
Pdb.Atom.FromString("ATOM 139 CA ALA A 20 29.393 -9.683 1.528 1.00 19.57 C "),
Pdb.Atom.FromString("ATOM 144 CA ILE A 21 25.881 -11.238 1.583 1.00 11.70 C "),
Pdb.Atom.FromString("ATOM 152 CA VAL A 22 23.847 -8.061 1.553 1.00 7.77 C "),
Pdb.Atom.FromString("ATOM 159 CA VAL A 23 20.196 -7.501 2.410 1.00 6.37 C "),
Pdb.Atom.FromString("ATOM 166 CA ASP A 24 19.093 -3.982 1.466 1.00 6.66 C "),
Pdb.Atom.FromString("ATOM 174 CA ILE A 25 16.500 -2.121 3.513 1.00 7.21 C "),
Pdb.Atom.FromString("ATOM 182 CA ALA A 26 14.398 0.375 1.556 1.00 8.41 C "),
Pdb.Atom.FromString("ATOM 187 CA LYS A 27 10.724 1.489 1.214 1.00 9.80 C "),
Pdb.Atom.FromString("ATOM 201 CA MET A 28 10.147 0.295 4.838 1.00 8.69 C "),
Pdb.Atom.FromString("ATOM 209 CA LYS A 29 10.882 -3.362 4.004 1.00 9.09 C "),
Pdb.Atom.FromString("ATOM 223 CA TYR A 30 13.753 -5.845 4.132 1.00 6.32 C "),
Pdb.Atom.FromString("ATOM 235 CA GLU A 31 14.275 -6.364 0.381 1.00 9.00 C "),
Pdb.Atom.FromString("ATOM 244 CA THR A 32 15.144 -10.026 0.769 1.00 7.30 C "),
Pdb.Atom.FromString("ATOM 251 CA PRO A 33 12.722 -11.107 3.546 1.00 8.68 C "),
Pdb.Atom.FromString("ATOM 258 CA GLU A 34 13.757 -14.780 3.406 1.00 9.28 C "),
Pdb.Atom.FromString("ATOM 267 CA LEU A 35 17.468 -15.255 2.972 1.00 7.34 C "),
Pdb.Atom.FromString("ATOM 275 CA HIS A 36 19.181 -18.672 2.822 1.00 6.97 C "),
Pdb.Atom.FromString("ATOM 285 CA VAL A 37 22.841 -18.828 3.840 1.00 7.29 C "),
Pdb.Atom.FromString("ATOM 292 CA LYS A 38 25.361 -21.456 5.044 1.00 9.55 C "),
Pdb.Atom.FromString("ATOM 306 CA VAL A 39 26.828 -21.965 8.529 1.00 9.09 C "),
Pdb.Atom.FromString("ATOM 313 CA GLY A 40 29.717 -19.533 8.887 1.00 8.81 C "),
Pdb.Atom.FromString("ATOM 317 CA ASP A 41 28.343 -16.891 6.520 1.00 8.19 C "),
Pdb.Atom.FromString("ATOM 325 CA THR A 42 28.196 -13.227 7.468 1.00 7.95 C "),
Pdb.Atom.FromString("ATOM 332 CA VAL A 43 24.989 -11.395 6.512 1.00 6.02 C "),
Pdb.Atom.FromString("ATOM 339 CA THR A 44 25.158 -7.607 6.224 1.00 5.34 C "),
Pdb.Atom.FromString("ATOM 346 CA TRP A 45 22.054 -5.421 6.244 1.00 4.51 C "),
Pdb.Atom.FromString("ATOM 360 CA ILE A 46 22.453 -1.974 4.623 1.00 5.55 C "),
Pdb.Atom.FromString("ATOM 368 CA ASN A 47 19.890 0.774 5.248 1.00 6.52 C "),
Pdb.Atom.FromString("ATOM 376 CA ARG A 48 19.350 2.559 1.939 1.00 10.21 C "),
Pdb.Atom.FromString("ATOM 387 CA GLU A 49 16.823 5.111 3.196 1.00 12.44 C "),
Pdb.Atom.FromString("ATOM 396 CA ALA A 50 16.764 8.058 5.564 1.00 13.39 C "),
Pdb.Atom.FromString("ATOM 401 CA MET A 51 14.386 6.508 8.133 1.00 12.52 C "),
Pdb.Atom.FromString("ATOM 409 CA PRO A 52 16.509 4.566 10.725 1.00 9.20 C "),
Pdb.Atom.FromString("ATOM 416 CA HIS A 53 16.032 0.778 10.889 1.00 6.43 C "),
Pdb.Atom.FromString("ATOM 426 CA ASN A 54 17.658 -2.107 12.766 1.00 5.06 C "),
Pdb.Atom.FromString("ATOM 434 CA VAL A 55 17.296 -5.891 13.052 1.00 5.44 C "),
Pdb.Atom.FromString("ATOM 441 CA HIS A 56 15.979 -7.379 16.316 1.00 4.53 C "),
Pdb.Atom.FromString("ATOM 451 CA PHE A 57 15.920 -11.061 17.243 1.00 5.94 C "),
Pdb.Atom.FromString("ATOM 462 CA VAL A 58 13.932 -11.794 20.435 1.00 7.60 C "),
Pdb.Atom.FromString("ATOM 469 CA ALA A 59 15.316 -13.765 23.405 1.00 7.37 C "),
Pdb.Atom.FromString("ATOM 474 CA GLY A 60 16.074 -17.393 22.787 1.00 9.00 C "),
Pdb.Atom.FromString("ATOM 478 CA VAL A 61 16.521 -17.029 18.997 1.00 8.51 C "),
Pdb.Atom.FromString("ATOM 485 CA LEU A 62 20.244 -16.290 18.543 1.00 9.65 C "),
Pdb.Atom.FromString("ATOM 493 CA GLY A 63 21.156 -16.644 22.197 1.00 10.26 C "),
Pdb.Atom.FromString("ATOM 497 CA GLU A 64 19.729 -16.413 25.651 1.00 9.18 C "),
Pdb.Atom.FromString("ATOM 506 CA ALA A 65 19.129 -12.671 25.468 1.00 8.86 C "),
Pdb.Atom.FromString("ATOM 511 CA ALA A 66 17.408 -10.687 22.723 1.00 7.22 C "),
Pdb.Atom.FromString("ATOM 516 CA LEU A 67 19.808 -9.283 20.128 1.00 9.01 C "),
Pdb.Atom.FromString("ATOM 524 CA LYS A 68 18.504 -5.777 19.473 1.00 10.06 C "),
Pdb.Atom.FromString("ATOM 533 CA GLY A 69 20.805 -4.416 16.788 1.00 8.06 C "),
Pdb.Atom.FromString("ATOM 537 CA PRO A 70 21.868 -0.715 16.656 1.00 8.23 C "),
Pdb.Atom.FromString("ATOM 544 CA MET A 71 19.807 1.769 14.640 1.00 8.56 C "),
Pdb.Atom.FromString("ATOM 552 CA MET A 72 21.337 2.189 11.156 1.00 8.26 C "),
Pdb.Atom.FromString("ATOM 560 CA LYS A 73 21.086 5.638 9.601 1.00 9.59 C "),
Pdb.Atom.FromString("ATOM 574 CA LYS A 74 21.097 6.084 5.777 1.00 9.46 C "),
Pdb.Atom.FromString("ATOM 588 CA GLU A 75 23.892 4.149 4.097 1.00 9.45 C "),
Pdb.Atom.FromString("ATOM 602 CA GLN A 76 24.997 2.451 7.267 1.00 6.02 C "),
Pdb.Atom.FromString("ATOM 611 CA ALA A 77 25.416 -1.310 7.631 1.00 5.75 C "),
Pdb.Atom.FromString("ATOM 616 CA TYR A 78 25.448 -3.978 10.318 1.00 4.90 C "),
Pdb.Atom.FromString("ATOM 628 CA SER A 79 26.700 -7.612 10.117 1.00 5.13 C "),
Pdb.Atom.FromString("ATOM 634 CA LEU A 80 26.024 -10.884 11.899 1.00 5.65 C "),
Pdb.Atom.FromString("ATOM 642 CA THR A 81 27.969 -14.123 11.320 1.00 6.53 C "),
Pdb.Atom.FromString("ATOM 649 CA PHE A 82 25.693 -17.171 11.780 1.00 5.24 C "),
Pdb.Atom.FromString("ATOM 660 CA THR A 83 27.363 -20.163 13.449 1.00 6.79 C "),
Pdb.Atom.FromString("ATOM 667 CA GLU A 84 24.599 -22.785 13.726 1.00 6.27 C "),
Pdb.Atom.FromString("ATOM 676 CA ALA A 85 21.975 -24.045 11.260 1.00 7.61 C "),
Pdb.Atom.FromString("ATOM 681 CA GLY A 86 18.324 -23.142 11.886 1.00 7.35 C "),
Pdb.Atom.FromString("ATOM 685 CA THR A 87 15.680 -20.519 11.055 1.00 8.50 C "),
Pdb.Atom.FromString("ATOM 692 CA TYR A 88 16.009 -17.145 12.731 1.00 7.35 C "),
Pdb.Atom.FromString("ATOM 704 CA ASP A 89 13.191 -14.620 12.557 1.00 7.28 C "),
Pdb.Atom.FromString("ATOM 712 CA TYR A 90 13.740 -10.922 13.122 1.00 5.26 C "),
Pdb.Atom.FromString("ATOM 724 CA HIS A 91 11.902 -7.619 12.935 1.00 4.80 C "),
Pdb.Atom.FromString("ATOM 734 CA CYS A 92 12.663 -3.894 13.049 1.00 5.44 C "),
Pdb.Atom.FromString("ATOM 740 CA THR A 93 12.228 -2.579 16.647 1.00 6.60 C "),
Pdb.Atom.FromString("ATOM 747 CA PRO A 94 10.460 0.815 15.821 1.00 7.51 C "),
Pdb.Atom.FromString("ATOM 754 CA HIS A 95 8.594 -0.728 12.857 1.00 7.46 C "),
Pdb.Atom.FromString("ATOM 764 CA PRO A 96 7.518 -4.286 13.932 1.00 7.59 C "),
Pdb.Atom.FromString("ATOM 771 CA PHE A 97 5.480 -4.778 10.739 1.00 7.30 C "),
Pdb.Atom.FromString("ATOM 782 CA MET A 98 8.923 -5.104 8.994 1.00 6.57 C "),
Pdb.Atom.FromString("ATOM 790 CA ARG A 99 9.707 -8.821 9.391 1.00 7.91 C "),
Pdb.Atom.FromString("ATOM 808 CA GLY A 100 12.343 -11.105 7.827 1.00 6.39 C "),
Pdb.Atom.FromString("ATOM 812 CA LYS A 101 14.085 -14.438 8.459 1.00 7.31 C "),
Pdb.Atom.FromString("ATOM 826 CA VAL A 102 17.523 -15.900 7.870 1.00 6.58 C "),
Pdb.Atom.FromString("ATOM 833 CA VAL A 103 17.552 -19.658 7.157 1.00 7.20 C "),
Pdb.Atom.FromString("ATOM 840 CA VAL A 104 21.061 -21.012 7.897 1.00 7.28 C "),
Pdb.Atom.FromString("ATOM 847 CA GLU A 105 21.699 -24.347 6.221 1.00 13.74 C "),
#endregion
};
Pdb.Atom[] atoms_r6 = new Pdb.Atom[]
{
Pdb.Atom.FromString("ATOM 42 CB PRO A 6 31.929 -8.271 12.386 1.00 7.98 C "),
Pdb.Atom.FromString("ATOM 43 CG PRO A 6 30.972 -9.378 12.022 1.00 9.48 C "),
Pdb.Atom.FromString("ATOM 44 CD PRO A 6 29.880 -9.313 13.099 1.00 8.27 C "),
};
{
HessMatrix hess = GetHessCa(atoms_ca.ListCoord());
InfoPack extra = new InfoPack();
//Vector bfactors = ENM.BFactorFromHessian(hess, null, 6, extra);
Vector bfactors = Hess.GetBFactor(hess, null, 6, extra);
Vector eigvals = (double[])extra["eigenvalues"];
int[] idxsorted_eigvals = eigvals.ToArray().HAbs().HIdxSorted();
for (int i = 0; i < 6; i++)
{
eigvals[idxsorted_eigvals[i]] = 0;
}
for (int i = 0; i < eigvals.Size; i++)
{
if (eigvals[i] < 0)
{
// return false, if there exists negative eigenvalue
HDebug.Assert(false);
return(false);
}
}
}
{
List <Pdb.Atom> atoms = new List <Pdb.Atom>();
atoms.AddRange(atoms_ca);
atoms.AddRange(atoms_r6);
HDebug.Assert(atoms[5].resSeq == 6);
List <int> idxs_ca = new List <int>(); for (int i = 0; i < atoms_ca.Length; i++)
{
idxs_ca.Add(i);
}
List <int> idxs_r6 = new List <int>(); for (int i = atoms_ca.Length; i < atoms.Count; i++)
{
idxs_r6.Add(i);
}
idxs_r6.InsertRange(0, new int[] { 3, 4, 5 });
List <Tuple <int, int> > list12 = new List <Tuple <int, int> >();
for (int i = 1; i < idxs_ca.Count; i++)
{
list12.Add(new Tuple <int, int>(idxs_ca[i - 1], idxs_ca[i]));
}
for (int i = 3; i < idxs_r6.Count; i++)
{
list12.Add(new Tuple <int, int>(idxs_r6[i - 1], idxs_r6[i]));
}
List <Tuple <int, int, int> > list123 = new List <Tuple <int, int, int> >();
for (int i = 2; i < idxs_ca.Count; i++)
{
list123.Add(new Tuple <int, int, int>(idxs_ca[i - 2], idxs_ca[i - 1], idxs_ca[i]));
}
for (int i = 3; i < idxs_r6.Count; i++)
{
list123.Add(new Tuple <int, int, int>(idxs_r6[i - 2], idxs_r6[i - 1], idxs_r6[i]));
}
List <Tuple <int, int, int, int> > list1234 = new List <Tuple <int, int, int, int> >();
for (int i = 3; i < idxs_ca.Count; i++)
{
list1234.Add(new Tuple <int, int, int, int>(idxs_ca[i - 3], idxs_ca[i - 2], idxs_ca[i - 1], idxs_ca[i]));
}
for (int i = 3; i < idxs_r6.Count; i++)
{
list1234.Add(new Tuple <int, int, int, int>(idxs_r6[i - 3], idxs_r6[i - 2], idxs_r6[i - 1], idxs_r6[i]));
}
List <Tuple <int, int> > listNonbond = new List <Tuple <int, int> >();
for (int i = 0; i < idxs_ca.Count; i++)
{
for (int j = i + 4; j < idxs_ca.Count; j++)
{
listNonbond.Add(new Tuple <int, int>(idxs_ca[i], idxs_ca[j]));
}
}
for (int i = 0; i < idxs_r6.Count; i++)
{
for (int j = i + 4; j < idxs_r6.Count; j++)
{
listNonbond.Add(new Tuple <int, int>(idxs_r6[i], idxs_r6[j]));
}
}
List <Vector> coords = atoms.ListCoord();
HessMatrix hessian = HessMatrixSparse.ZerosSparse(atoms.Count * 3, atoms.Count * 3);
double Epsilon = 0.36;
double K_r = 100 * Epsilon;
double K_theta = 20 * Epsilon;
double K_phi1 = 1 * Epsilon;
double K_phi3 = 0.5 * Epsilon;
for (int i = 0; i < list12.Count; i++)
{
FirstTerm(coords, K_r, hessian, list12[i].Item1, list12[i].Item2);
}
for (int i = 0; i < list123.Count; i++)
{
SecondTerm(coords, K_theta, hessian, list123[i].Item1, list123[i].Item2, list123[i].Item3);
}
for (int i = 0; i < list1234.Count; i++)
{
ThirdTerm(coords, K_phi1, K_phi3, hessian, list1234[i].Item1, list1234[i].Item2, list1234[i].Item3, list1234[i].Item4);
}
for (int i = 0; i < listNonbond.Count; i++)
{
FourthTerm(coords, Epsilon, hessian, listNonbond[i].Item1, listNonbond[i].Item2);
}
InfoPack extra = new InfoPack();
//Vector bfactors = ENM.BFactorFromHessian(hessian, null, 6, extra);
Vector bfactors = Hess.GetBFactor(hessian, null, 6, extra);
Vector eigvals = (double[])extra["eigenvalues"];
int[] idxsorted_eigvals = eigvals.ToArray().HAbs().HIdxSorted();
for (int i = 0; i < 6; i++)
{
eigvals[idxsorted_eigvals[i]] = 0;
}
for (int i = 0; i < eigvals.Size; i++)
{
if (eigvals[i] < 0)
{
// return false, if there exists negative eigenvalue
HDebug.Assert(false);
return(false);
}
}
}
//{
// Debug.Assert(atoms_ca[5].resSeq == 6);
// Pdb.Atom[] atoms_resi6 = new Pdb.Atom[]
// {
// atoms_ca[5],
// Pdb.Atom.FromString("ATOM 42 CB PRO A 6 31.929 -8.271 12.386 1.00 7.98 C "),
// Pdb.Atom.FromString("ATOM 43 CG PRO A 6 30.972 -9.378 12.022 1.00 9.48 C "),
// Pdb.Atom.FromString("ATOM 44 CD PRO A 6 29.880 -9.313 13.099 1.00 8.27 C "),
// };
// Matrix hess_ca = GetHessCa(atoms_ca.ListCoord());
// Matrix hess_resi6 = GetHessCa(atoms_resi6.ListCoord());
//
// int size_ca = atoms_ca.Length;
// int size_r6 = atoms_resi6.Length - 1;
// Matrix hess = new double[(size_ca+size_r6)*3,(size_ca+size_r6)*3];
// for(int c = 0; c < hess.ColSize; c++)
// for(int r = 0; r < hess.RowSize; r++)
// hess[c, r] = double.NaN;
// for(int c = 0; c < hess_ca.ColSize; c++)
// for(int r = 0; r < hess_ca.RowSize; r++)
// hess[c, r] = hess_ca[c, r];
// for(int c = 0; c < hess_resi6.ColSize; c++)
// for(int r = 0; r < hess_resi6.RowSize; r++)
// {
// if(c < 3 && r < 3) { int c0=5 *3+ c ; int r0=5 *3+ r ; Debug.Assert(double.IsNaN(hess[c0, r0]) ==false); hess[c0, r0] = hess_resi6[c, r]; }
// else if(c < 3 && r >= 3) { int c0=5 *3+ c ; int r0=size_ca*3+(r-3); Debug.Assert(double.IsNaN(hess[c0, r0]) == true); hess[c0, r0] = hess_resi6[c, r]; }
// else if(c >= 3 && r < 3) { int c0=size_ca*3+(c-3); int r0=5 *3+ r ; Debug.Assert(double.IsNaN(hess[c0, r0]) == true); hess[c0, r0] = hess_resi6[c, r]; }
// else if(c >= 3 && r >= 3) { int c0=size_ca*3+(c-3); int r0=size_ca*3+(r-3); Debug.Assert(double.IsNaN(hess[c0, r0]) == true); hess[c0, r0] = hess_resi6[c, r]; }
// else Debug.Assert(false);
// }
// for(int j = size_ca * 3; j < (size_ca + size_r6) * 3; j++)
// {
// for(int i = 0; i < 5*3; i++)
// {
// Debug.Assert(double.IsNaN(hess[i, j]) == true); hess[i, j] = 0;
// Debug.Assert(double.IsNaN(hess[j, i]) == true); hess[j, i] = 0;
// }
// for(int i = 6*3; i < size_ca * 3; i++)
// {
// Debug.Assert(double.IsNaN(hess[i, j]) == true); hess[i, j] = 0;
// Debug.Assert(double.IsNaN(hess[j, i]) == true); hess[j, i] = 0;
// }
// }
// for(int c = 0; c < hess.ColSize; c++)
// for(int r = 0; r < hess.RowSize; r++)
// Debug.Assert(double.IsNaN(hess[c, r]) == false);
//
// InfoPack extra = new InfoPack();
// Vector bfactors = ENM.BFactorFromHessian(hess, null, 6, extra);
// Vector eigvals = (double[])extra["eigenvalues"];
// int[] idxsorted_eigvals = eigvals.ToArray().Abs().IdxSorted();
// for(int i = 0; i < 6; i++) eigvals[idxsorted_eigvals[i]] = 0;
// for(int i = 0; i < eigvals.Size; i++)
// if(eigvals[i] < 0)
// {
// // return false, if there exists negative eigenvalue
// Debug.Assert(false);
// return false;
// }
//}
return(true);
}
static HessMatrix GetMulImpl(HessMatrix left, HessMatrix right, ILinAlg ila, bool warning)
{
if (HDebug.Selftest())
{
Matrix h1 = new double[, ] {
{ 0, 1, 2, 3, 4, 5 }
, { 1, 2, 3, 4, 5, 6 }
, { 2, 3, 4, 5, 6, 7 }
, { 3, 4, 5, 6, 7, 8 }
, { 4, 5, 6, 7, 8, 9 }
, { 5, 6, 7, 8, 9, 0 }
};
HessMatrix h2 = HessMatrixSparse.FromMatrix(h1);
Matrix h11 = Matrix.GetMul(h1, h1);
HessMatrix h22 = HessMatrix.GetMulImpl(h2, h2, null, false);
Matrix hdiff = h11 - h22;
HDebug.AssertToleranceMatrix(0, hdiff);
}
if ((left is HessMatrixDense) && (right is HessMatrixDense))
{
if (ila != null)
{
return(new HessMatrixDense {
hess = ila.Mul(left, right)
});
}
if (warning)
{
HDebug.ToDo("Check (HessMatrixDense * HessMatrixDense) !!!");
}
}
Dictionary <int, Dictionary <int, Tuple <int, int, MatrixByArr> > > left_ic_rows = new Dictionary <int, Dictionary <int, Tuple <int, int, MatrixByArr> > >();
foreach (var ic_row in left.EnumRowBlocksAll())
{
left_ic_rows.Add(ic_row.Item1, ic_row.Item2.HToDictionaryWithKeyItem2());
}
Dictionary <int, Dictionary <int, Tuple <int, int, MatrixByArr> > > right_ir_cols = new Dictionary <int, Dictionary <int, Tuple <int, int, MatrixByArr> > >();
foreach (var ir_col in right.EnumColBlocksAll())
{
right_ir_cols.Add(ir_col.Item1, ir_col.Item2.HToDictionaryWithKeyItem1());
}
HessMatrix mul = null;
if ((left is HessMatrixDense) && (right is HessMatrixDense))
{
mul = HessMatrixDense.ZerosDense(left.ColSize, right.RowSize);
}
else
{
mul = HessMatrixSparse.ZerosSparse(left.ColSize, right.RowSize);
}
for (int ic = 0; ic < left.ColBlockSize; ic++)
{
var left_row = left_ic_rows[ic];
if (left_row.Count == 0)
{
continue;
}
for (int ir = 0; ir < right.RowBlockSize; ir++)
{
var right_col = right_ir_cols[ir];
if (right_col.Count == 0)
{
continue;
}
foreach (var left_ck in left_row)
{
int ik = left_ck.Key;
HDebug.Assert(ic == left_ck.Value.Item1);
HDebug.Assert(ik == left_ck.Value.Item2);
if (right_col.ContainsKey(ik))
{
var right_kr = right_col[ik];
HDebug.Assert(ik == right_kr.Item1);
HDebug.Assert(ir == right_kr.Item2);
MatrixByArr mul_ckr = mul.GetBlock(ic, ir) + left_ck.Value.Item3 * right_kr.Item3;
mul.SetBlock(ic, ir, mul_ckr);
}
}
}
}
return(mul);
}
public static HessMatrixSparse FromMatrix(Matrix mat, bool parallel = false)
{
if (mat is HessMatrixSparse)
{
return((mat as HessMatrixSparse).CloneT());
}
HDebug.Assert(mat.ColSize % 3 == 0);
HDebug.Assert(mat.RowSize % 3 == 0);
HessMatrixSparse hess = ZerosSparse(mat.ColSize, mat.RowSize);
{
HessMatrixDense dense = new HessMatrixDense {
hess = mat
};
Action <Tuple <int, int> > func = delegate(Tuple <int, int> bc_br)
{
int bc = bc_br.Item1;
int br = bc_br.Item2;
if (dense.HasBlock(bc, br) == false)
{
return;
}
var bval = dense.GetBlock(bc, br);
lock (hess)
hess.SetBlock(bc, br, bval);
};
if (parallel)
{
Parallel.ForEach(dense.EnumIndicesAll(), func);
}
else
{
foreach (var bc_br_bval in dense.EnumIndicesAll())
{
func(bc_br_bval);
}
}
}
if (HDebug.IsDebuggerAttached)
{
// old version
HessMatrixSparse dhess = ZerosSparse(mat.ColSize, mat.RowSize);
int colsize = mat.ColSize;
int rowsize = mat.RowSize;
for (int c = 0; c < colsize; c++)
{
for (int r = 0; r < rowsize; r++)
{
if (mat[c, r] != 0)
{
dhess[c, r] = mat[c, r];
}
}
}
HDebug.Assert(HessMatrixSparseEqual(hess, dhess));
if (HDebug.IsDebuggerAttached && ((mat.ColSize / 3) < 3000))
{
double maxAbsDiff = mat.HAbsMaxDiffWith(hess);
HDebug.Assert(maxAbsDiff == 0);
}
}
return(hess);
}
public static HessMatrix GetHessDihedral
(IList <Vector> coords, IEnumerable <Universe.Dihedral> dihedrals, double?K_chi, double?n, HessMatrix hessian
, Action <Universe.Atom, Vector, Universe.Atom, Vector, Universe.Atom, Vector, Universe.Atom, Vector, double, double> collector
, bool useAbsSpr = false
, bool useArnaud96 = false
)
{
int size = coords.Count;
if (hessian == null)
{
hessian = HessMatrixSparse.ZerosSparse(size * 3, size * 3);
}
foreach (Universe.Dihedral dihedral in dihedrals)
{
int idx0 = dihedral.atoms[0].ID; if (coords[idx0] == null)
{
continue;
}
int idx1 = dihedral.atoms[1].ID; if (coords[idx1] == null)
{
continue;
}
int idx2 = dihedral.atoms[2].ID; if (coords[idx2] == null)
{
continue;
}
int idx3 = dihedral.atoms[3].ID; if (coords[idx3] == null)
{
continue;
}
double lK_chi = (K_chi != null)? K_chi.Value : dihedral.Kchi;
double ln = (n != null)? n.Value : dihedral.n;
if (useAbsSpr)
{
/// https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=24521
/// ==========================================================================
/// Dear all, Recently I found a parameter file for some carbohydrates, like
/// NAG and FUC, which described the dihedral angle as following:
///
/// OC CC CTS CTS -1.2007 1 0.0
/// OC CC CTS CTS -0.3145 2 0.0
/// OC CC CTS CTS -0.0618 3 0.0
/// CA OSL SL O2L 0.0000 3 0.0
/// CA CA OSL SL 0.0000 3 0.0
///
/// In some entries the values of the Kchi for the dihedral angle are 0 or
/// negatives. But this value usually is a positive. I understand that the
/// kchi value reflect the flexibility of the dihedral, so what do the
/// negatives here mean? Thanks a million.
/// --------------------------------------------------------------------------
/// May I ask where you found these parameters?
///
/// Although the negative values violate the convention, they are not
/// incorrect. Switching the sign of the amplitude is mathematically
/// equivalent to reversing the phase. (See the class I potential energy
/// function, as discussed in any paper or textbook on the subject.) In other
/// words, -1.2 1 0 is equivalent to 1.2 1 180. CHARMM handles this correctly.
/// ==========================================================================
/// htna:
/// Still "taking absolute value" is not a good choice, but because there is
/// no option that I can taek, maybe this is OK in this situation, in order
/// to avoid negative springs.
lK_chi = Math.Abs(lK_chi);
}
HDebug.Assert(lK_chi >= 0);
ThirdTermN(coords, lK_chi, ln, hessian, idx0, idx1, idx2, idx3, useArnaud96: useArnaud96);
if (collector != null)
{
collector
(dihedral.atoms[0], coords[idx0]
, dihedral.atoms[1], coords[idx1]
, dihedral.atoms[2], coords[idx2]
, dihedral.atoms[3], coords[idx3]
, lK_chi, ln);
}
}
return(hessian);
}
