public Mode[] GetModesMassReduced(bool delhess, ILinAlg la)
{
Mode[] modes;
modes = GetModesMassWeighted(delhess, la); // mass-weighted modes
modes.UpdateMassReduced(mass.ToArray()); // mass-reduced modes
return(modes);
}
public static Mode[] GetModeCoarseBlkmat(Matrix hess, IList <int> idx_heavy, ILinAlg ila)
{
HDebug.Depreciated("use GetHessCoarseBlkmat() and GetModesFromHess() separately");
Matrix hess_HH = GetHessCoarseBlkmat(hess, idx_heavy, ila);
//{
// Matlab.PutMatrix("H", hess);
// Matlab.Execute("H = (H + H')/2;");
//
// Matlab.PutVector("idx0", idx_heavy.ToArray());
// Matlab.Execute("idx0 = sort([idx0*3+1; idx0*3+2; idx0*3+3]);");
// Matlab.PutValue("idx1", hess.ColSize);
// Matlab.Execute("idx1 = setdiff(1:idx1, idx0)';");
// HDebug.Assert(Matlab.GetValueInt("length(union(idx0,idx1))") == hess.ColSize*3);
//
// Matlab.Execute("A = full(H(idx0,idx0));");
// Matlab.Execute("B = H(idx0,idx1) ;");
// Matlab.Execute("C = H(idx1,idx0) ;");
// Matlab.Execute("D = full(H(idx1,idx1));");
// Matlab.Execute("clear H;");
//
// Matlab.Execute("bhess = A - B * inv(D) * C;");
// Matlab.Execute("bhess = (bhess + bhess')/2;");
//}
Mode[] modes = GetModesFromHess(hess_HH, ila);
return(modes);
}
public static HessCoarseResiIter.HessInfoCoarseResiIter GetHessCoarseResiIter_BlockWise
(Hess.HessInfo hessinfo
, Vector[] coords
, ILinAlg ila
, int clus_width ///= 18 | (18,500) is good for large sparse proteins
, int num_atom_merge ///= 500 | (14,400) is good for small densely packed globular proteins
, double thres_zeroblk ///= 0.001 | 0.001 could be fairly good for ssNMA (possibly for sbNMA and NMA, too)
, IList <Universe.Atom> keeps
, HessCoarseResiIter.IterOption iteropt
, params string[] options
)
{
if (clus_width <= 0)
{
throw new Exception("clus_width should be > 0");
}
HessCoarseResiIter.FuncGetIdxKeepListRemv GetIdxKeepListRemv = delegate(object[] latoms, Vector[] lcoords)
{
Universe.Atom[] lunivatoms = latoms.HToType(null as Universe.Atom[]);
return(HessCoarseResiIter.GetIdxKeepListRemv_ResiCluster2(lunivatoms, lcoords, clus_width, num_atom_merge, keeps));
};
return(HessCoarseResiIter.GetHessCoarseResiIter
(hessinfo, coords, GetIdxKeepListRemv, ila, thres_zeroblk
, iteropt
, options: options
));
}
public HessInfo GetSubHessInfoByBlockHess(IList <int> idxs, ILinAlg ila)
{
// GetSubHessInfoByBlockHess(idxSele, ila, "pinv")
Vector idxmass = mass.ToArray().HSelectByIndex(idxs);
object[] idxatoms = atoms.HSelectByIndex(idxs);
Vector[] idxcoords = coords.HSelectByIndex(idxs);
HessMatrix idxhess = null;
if (ila != null)
{
idxhess = Hess.GetHessCoarseBlkmat(hess, idxs, ila);
}
else
{
idxhess = Hess.GetHessCoarseBlkmat(hess, idxs);
}
return(new HessInfo
{
mass = idxmass,
atoms = idxatoms,
coords = idxcoords,
hess = idxhess,
numZeroEigval = numZeroEigval,
});
}
public static double[] GetRotAngles(Universe univ
, Vector[] coords
, Vector[] dcoords
, MatrixByArr J
, ILinAlg ila
)
{
Vector dangles;
using (ila.NewDisposables())
{
Vector R = Vector.FromBlockvector(dcoords);
Vector M = univ.GetMasses(3);
var RR = ila.ToILMat(R).AddDisposable();
var MM = ila.ToILMat(M).Diag().AddDisposable();
var JJ = ila.ToILMat(J).AddDisposable();
var invJMJ = ila.Inv(JJ.Tr * MM * JJ).AddDisposable();
var AA = invJMJ * JJ.Tr * MM * RR;
dangles = AA.ToArray().HToArray1D();
}
if (HDebug.False && HDebug.IsDebuggerAttached)
{
Vector tdangles = GetRotAngles(univ, coords, dcoords, J);
HDebug.Assert(0.9999 < (tdangles.Dist / dangles.Dist), (tdangles.Dist / dangles.Dist) < 1.0001);
HDebug.Assert(LinAlg.DotProd(tdangles, dangles) / (tdangles.Dist * dangles.Dist) > 0.9999);
HDebug.Assert((tdangles - dangles).Dist / tdangles.Dist < 0.0001);
}
return(dangles);
}
public Mode[] GetModesMassWeighted(bool delhess, ILinAlg la)
{
Matrix mwhess = GetHessMassWeighted(delhess);
Mode[] mwmodes = Hess.GetModesFromHess(mwhess, la);
return(mwmodes);
}
public static HessCoarseResiIter.HessInfoCoarseResiIter GetHessCoarseResiIter_SymrcmBlockWise
(Hess.HessInfo hessinfo
, Vector[] coords
, double?symrcm_filter_blckwise_interact // null (use 1 as default)
, ILinAlg ila
, int clus_width ///= 18 | (18,500) is good for large sparse proteins
, int num_atom_merge ///= 500 | (14,400) is good for small densely packed globular proteins
, double thres_zeroblk ///= 0.001 | 0.001 could be fairly good for ssNMA (possibly for sbNMA and NMA, too)
, string[] nameToKeep
)
{
if (clus_width <= 0)
{
throw new Exception("clus_width should be > 0");
}
HessCoarseResiIter.FuncGetIdxKeepListRemv GetIdxKeepListRemv = delegate(object[] latoms, Vector[] lcoords)
{
Universe.Atom[] lunivatoms = latoms.HToType(null as Universe.Atom[]);
return(HessCoarseResiIter.GetIdxKeepListRemv_ResiCluster_SymrcmBlockWise(lunivatoms, lcoords, hessinfo.hess, clus_width, num_atom_merge, symrcm_filter_blckwise_interact, nameToKeep));
};
return(HessCoarseResiIter.GetHessCoarseResiIter
(hessinfo, coords, GetIdxKeepListRemv, ila, thres_zeroblk
, HessCoarseResiIter.IterOption.Matlab_experimental
));
}
public Mode[] GetModes(ILinAlg la)
{
if (_modes == null)
{
_modes = Hess.GetModesFromHess(hess, la);
}
return(_modes);
}
public static void Main(string[] args, ILinAlg la)
{
SelfTest_Program20150111_SparsityVsAccuracy.la = la;
string[] hesstypes = new string[] { "NMA", "scrnNMA", "sbNMA", "ssNMA", "eANM", "AA-ANM" };
double[] threszeroblks = new double[] { 0.0001, 0.001, 0.01, 0.1 };
Main(args, hesstypes, threszeroblks);
}
public bool CheckModeWithHess(MatrixByArr hess, double[] masses, ILinAlg la, Mode[] modes = null, double tolerance = 0.00001)
{
if (modes == null)
{
modes = ToModes(masses);
}
HessMatrix ohess = new HessMatrixDense
{
hess = modes.GetHessian(masses, la),
};
double corr = HMath.HCorr(hess.ToArray().HToArray1D(), ohess.ToArray().HToArray1D());
System.Console.Write("corr(TestHess,HessVibr:{0} ", corr);
{
HDebug.Assert(hess.ColSize == ohess.ColSize);
HDebug.Assert(hess.RowSize == ohess.RowSize);
double ltolerance = hess.ToArray().HAbs().HMax() * tolerance;
ltolerance = tolerance;
for (int c = 0; c < ohess.ColSize; c++)
{
for (int r = 0; r < ohess.RowSize; r++)
{
double v = hess[c, r];
double mwv = ohess[c, r];
double diff = Math.Abs(v - mwv);
if (diff >= ltolerance)
{
return(false);
}
}
}
}
//{
// Matrix vhess = hess / hess.ToArray().HToArray1D().HVar();
// Matrix vohess = ohess / ohess.ToArray().HToArray1D().HVar();
//
// HDebug.Assert(hess.ColSize == ohess.ColSize);
// HDebug.Assert(hess.RowSize == ohess.RowSize);
// HDebug.Assert(vhess.Size == vohess.Size);
// for(int c=0; c<vhess.ColSize; c++)
// for(int r=0; r<vhess.RowSize; r++)
// {
// double v = vhess[c,r];
// double vo = vohess[c,r];
// double diff = Math.Abs(v - vo);
// if(diff >= tolerance)
// {
// HDebug.Assert(false);
// return false;
// }
// }
//}
return(true);
}
public static Mode[] PCA(IList <Vector[]> confs, ref Vector[] meanconf, ILinAlg ila)
{
if (meanconf == null)
{
meanconf = new Vector[confs[0].Length];
for (int i = 0; i < meanconf.Length; i++)
{
Vector meancoord = new double[3];
foreach (Vector[] conf in confs)
{
meancoord += conf[i];
}
meancoord /= confs.Count;
meanconf[i] = meancoord;
}
}
int size = meanconf.Length;
int size3 = size * 3;
int num = confs.Count;
Matrix mconfs = Matrix.Zeros(size3, num);
Vector vmeanconf = Vector.FromBlockvector(meanconf);
for (int r = 0; r < num; r++)
{
Vector vconf = Vector.FromBlockvector(confs[r]);
Vector dvconf = vconf - vmeanconf;
for (int c = 0; c < size3; c++)
{
mconfs[c, r] = dvconf[c];
}
}
Matrix cov = null;
{
var CONFS = ila.ToILMat(mconfs);
var COV = CONFS * CONFS.Tr;
cov = COV.ToArray();
CONFS.Dispose();
COV.Dispose();
}
Func <Matrix, Tuple <Matrix, Vector> > fnEig = delegate(Matrix A)
{
var AA = ila.ToILMat(A);
var VVDD = ila.EigSymm(AA);
var VV = VVDD.Item1;
Vector D = VVDD.Item2;
Matrix V = VV.ToArray();
AA.Dispose();
VV.Dispose();
return(new Tuple <Matrix, Vector>(V, D));
};
return(PCA(cov, confs.Count, fnEig));
}
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 Mode[] GetModesFromHess(Matrix hess, ILinAlg la)
{
List <Mode> modes;
{
Matrix V;
Vector D;
switch (la)
{
case null:
using (new Matlab.NamedLock(""))
{
Matlab.PutMatrix("H", hess, true);
Matlab.Execute("H = (H + H')/2;");
Matlab.Execute("[V,D] = eig(H);");
Matlab.Execute("D = diag(D);");
V = Matlab.GetMatrix("V", true);
D = Matlab.GetVector("D", true);
}
break;
default:
{
var H = la.ToILMat(hess);
H = (H + H.Tr) / 2;
var VD = la.EigSymm(H);
V = VD.Item1.ToMatrix();
D = VD.Item2;
H.Dispose();
VD.Item1.Dispose();
}
break;
}
int[] idxs = D.ToArray().HAbs().HIdxSorted();
modes = new List <Mode>(idxs.Length);
//foreach(int idx in idxs)
for (int th = 0; th < idxs.Length; th++)
{
int idx = idxs[th];
Mode mode = new Mode
{
th = (th + 1),
eigval = D[idx],
eigvec = V.GetColVector(idx)
};
modes.Add(mode);
}
}
System.GC.Collect();
return(modes.ToArray());
}
public static Mode[] GetModeMixAnm(IList <Vector> coords
, IList <int> lstIdxCa
, IList <int> lstIdxAll
, ILinAlg la
)
{
double AaCutoff = 6.0; double AaSprcst = 0.64;
double CaCutoff = 13.0; double CaSprcst = 3.10;
return(GetModeMixAnm(coords, lstIdxCa, lstIdxAll
, CaCutoff, CaSprcst
, AaCutoff, AaSprcst
, la
));
}
public static MatrixByArr GetHessian(this IList <Mode> modes, ILinAlg la)
{
Vector[] eigvecs = modes.ListEigvec().ToArray();
Vector eigvals = modes.ListEigval().ToArray();
MatrixByArr hess;
{
var V = la.ToILMat(eigvecs.ToMatrix());
var D = la.ToILMat(eigvals).Diag();
var H = la.Mul(V, D, V.Tr);
hess = H.ToArray();
V.Dispose();
D.Dispose();
H.Dispose();
}
return(hess);
}
public static HessCoarseResiIter.HessInfoCoarseResiIter GetHessCoarseResiIter_SymrcmAtomWise
(Hess.HessInfo hessinfo
, Vector[] coords
, ILinAlg ila
, int num_atom_merge ///= 500 | (14,400) is good for small densely packed globular proteins
, double thres_zeroblk ///= 0.001 | 0.001 could be fairly good for ssNMA (possibly for sbNMA and NMA, too)
, string[] nameToKeep
)
{
HessCoarseResiIter.FuncGetIdxKeepListRemv GetIdxKeepListRemv = delegate(object[] latoms, Vector[] lcoords)
{
Universe.Atom[] lunivatoms = latoms.HToType(null as Universe.Atom[]);
return(HessCoarseResiIter.GetIdxKeepListRemv_ResiCluster_SymrcmAtomWise(lunivatoms, lcoords, hessinfo.hess, num_atom_merge, thres_zeroblk, nameToKeep));
};
return(HessCoarseResiIter.GetHessCoarseResiIter
(hessinfo, coords, GetIdxKeepListRemv, ila, thres_zeroblk
, HessCoarseResiIter.IterOption.Matlab_experimental
));
}
public static Matrix GetInvSprTensorSymm(Matrix H, Matrix S, ILinAlg ila)
{
// check H be symmetric
HDebug.AssertToleranceMatrix(0.00000001, H - H.Tr());
Matrix invK = GetInvSprTensor(H, S, ila);
if (HDebug.IsDebuggerAttached && ila != null)
{
HDebug.AssertToleranceMatrix(0.00000001, invK - invK.Tr()); // check symmetric
var invKK = ila.ToILMat(invK);
var VVDD = ila.EigSymm(invKK);
foreach (double d in VVDD.Item2)
{
HDebug.Assert(d > -0.00000001);
}
}
return(invK);
}
public static HessCoarseResiIter.HessInfoCoarseResiIter GetHessCoarseResiIter_BlockWise
(Hess.HessInfo hessinfo
, Vector[] coords
, ILinAlg ila
, int clus_width ///= 18 | (18,500) is good for large sparse proteins
, int num_atom_merge ///= 500 | (14,400) is good for small densely packed globular proteins
, double thres_zeroblk ///= 0.001 | 0.001 could be fairly good for ssNMA (possibly for sbNMA and NMA, too)
)
{
string[] nameToKeep = new string[] { "CA" };
return(GetHessCoarseResiIter_BlockWise
(hessinfo
, coords
, ila
, clus_width
, num_atom_merge
, thres_zeroblk
, nameToKeep
));
}
public static HessCoarseResiIter.HessInfoCoarseResiIter GetHessCoarseResiIter
(Hess.HessInfo hessinfo
, Vector[] coords
, HessCoarseResiIter.FuncGetIdxKeepListRemv GetIdxKeepListRemv
, ILinAlg ila
, double thres_zeroblk = 0.001
, HessCoarseResiIter.IterOption iteropt = HessCoarseResiIter.IterOption.Matlab_experimental
, string[] options = null
)
{
return(HessCoarseResiIter.GetHessCoarseResiIter
(hessinfo: hessinfo
, coords: coords
, GetIdxKeepListRemv: GetIdxKeepListRemv
, ila: ila
, thres_zeroblk: thres_zeroblk
, iteropt: iteropt
, options: options
));
}
public static Mode[] GetModeMixAnm(IList <Vector> coords
, IList <int> lstIdxCa
, IList <int> lstIdxAll
, double CaCutoff, double CaSprcst
, double AaCutoff, double AaSprcst
, ILinAlg la
)
{
HessInfo hessinfo = GetHessMixAnm(coords, lstIdxCa, lstIdxAll
, CaCutoff, CaSprcst
, AaCutoff, AaSprcst
);
int[] idxMixed = lstIdxCa.HUnionWith(lstIdxAll);
var hessinfoMixed = hessinfo.GetSubHessInfo(idxMixed);
Mode[] modesMixed = hessinfoMixed.GetModesMassReduced(true, la);
Mode[] modes = modesMixed.ToModeEigvecResized(coords.Count, idxMixed);
return(modes);
}
//public static OOverlapWeighted OverlapWeightedByFreq(IList<Mode> modes1, IList<Mode> modes2, ILinAlg ila, bool bResetUnitVector, string optSelectOverlap)
//{
// Vector weights = new double[modes1.Count];
// for(int i=0; i<weights.Size; i++)
// weights[i] = 1/Math.Sqrt(Math.Abs(modes1[i].eigval));
// weights /= weights.Sum();
//
// return OverlapWeighted(modes1, modes2, weights.ToArray(), ila, bResetUnitVector, optSelectOverlap);
//}
public static OOverlapWeighted OverlapWeighted(IList <Mode> modes1, double[] mass1, double[] mass2, IList <Mode> modes2, IList <double> weights, ILinAlg ila, bool bResetUnitVector, string optSelectOverlap)
{
Matrix soverlap = OverlapSigned(modes1, mass1, mass2, modes2, ila, bResetUnitVector);
HDebug.Exception(modes1.Count == weights.Count);
int[] idxOverlap1to2;
switch (optSelectOverlap)
{
case "corresponding index":
if (modes1.Count != modes2.Count)
{
throw new HException();
}
idxOverlap1to2 = HEnum.HEnumCount(modes1.Count).ToArray();
break;
case "best matching overlap":
idxOverlap1to2 = new int[modes1.Count];
for (int im = 0; im < modes1.Count; im++)
{
idxOverlap1to2[im] = 0;
for (int k = 0; k < modes2.Count; k++)
{
if (Math.Abs(soverlap[im, idxOverlap1to2[im]]) < Math.Abs(soverlap[im, k]))
{
idxOverlap1to2[im] = k;
}
}
}
break;
default:
throw new HException();
}
Vector overlap1to2 = new double[modes1.Count];
Vector overlap1to2signed = new double[modes1.Count];
double woverlap = 0;
for (int i = 0; i < modes1.Count; i++)
{
overlap1to2 [i] = Math.Abs(soverlap[i, idxOverlap1to2[i]]);
overlap1to2signed[i] = soverlap[i, idxOverlap1to2[i]];
woverlap += weights[i] * overlap1to2[i];
}
return(new OOverlapWeighted
{
soverlap1to2 = soverlap,
woverlap = woverlap,
weights = weights.ToArray(),
overlaps = overlap1to2.ToArray(),
sgnoverlaps = overlap1to2signed.ToArray(),
idxOverlap1to2 = idxOverlap1to2,
modes1 = modes1.ToArray(),
modes2 = modes2.ToArray(),
});
}
public static OOverlapWeighted OverlapWeightedByEigval(IList <Mode> modes1, double[] mass1, double[] mass2, IList <Mode> modes2, ILinAlg ila, bool bResetUnitVector, string optSelectOverlap)
{
Vector weights = new double[modes1.Count];
for (int i = 0; i < weights.Size; i++)
{
weights[i] = 1 / Math.Abs(modes1[i].eigval);
}
weights /= weights.Sum();
return(OverlapWeighted(modes1, mass1, mass2, modes2, weights.ToArray(), ila, bResetUnitVector, optSelectOverlap));
}
public static OOverlapWeighted OverlapWeightedByEigval(IList <Mode> modes1, IList <Mode> modes2, ILinAlg ila, bool bResetUnitVector, string optSelectOverlap)
{
return(OverlapWeightedByEigval(modes1, null, null, modes2, ila, bResetUnitVector, optSelectOverlap));
}
public static Matrix OverlapSigned(IList <Mode> modes1, double[] mass1, double[] mass2, IList <Mode> modes2, ILinAlg ila, bool bResetUnitVector)
{
Matrix mat1;
Matrix mat2;
string mat12opt = "memory-save";
switch (mat12opt)
{
case "initial":
{
Vector[] eigvecs1 = new Vector[modes1.Count]; for (int i = 0; i < modes1.Count; i++)
{
eigvecs1[i] = modes1[i].eigvec.Clone();
}
Vector[] eigvecs2 = new Vector[modes2.Count]; for (int i = 0; i < modes2.Count; i++)
{
eigvecs2[i] = modes2[i].eigvec.Clone();
}
{
// 1. Hess
// 2. mwHess <- M^-0.5 * H * M^-0.5
// 3. [V,D] <- eig(mwHess)
// 4. mrMode <- M^-0.5 * V
//
// overlap: vi . vj
// 1. vi <- M^0.5 * mrMode_i
// 2. vj <- M^0.5 * mrMode_j
// 3. vi.vj <- dot(vi,vj)
//
// [ 2 ] [4] [2*4] [ 8]
// [ 2 ] [5] [2*5] [10]
// M * v = [ 2 ] * [6] = [2*6] = [12]
// [ 3 ] [7] [3*7] [21]
// [ 3 ] [8] [3*8] [24]
// [ 3 ] [9] [3*9] [27]
//
// V1 <- sqrt(M1) * V1
// V2 <- sqrt(M2) * V2
// 1. get sqrt(mass) 2. for each eigenvector 3 eigveci[j] = eigvec[j] * sqrt_mass[j/3]
if (mass1 != null)
{
double[] mass1sqrt = mass1.HSqrt(); for (int i = 0; i < eigvecs1.Length; i++)
{
for (int j = 0; j < eigvecs1[i].Size; j++)
{
eigvecs1[i][j] *= mass1sqrt[j / 3];
}
}
}
if (mass2 != null)
{
double[] mass2sqrt = mass2.HSqrt(); for (int i = 0; i < eigvecs2.Length; i++)
{
for (int j = 0; j < eigvecs2[i].Size; j++)
{
eigvecs2[i][j] *= mass2sqrt[j / 3];
}
}
}
}
if (bResetUnitVector)
{
for (int i = 0; i < modes1.Count; i++)
{
eigvecs1[i] = eigvecs1[i].UnitVector();
}
for (int i = 0; i < modes2.Count; i++)
{
eigvecs2[i] = eigvecs2[i].UnitVector();
}
}
mat1 = eigvecs1.ToMatrix(false); HDebug.Assert(mat1.ColSize == eigvecs1.Length); eigvecs1 = null; GC.Collect(0);
mat2 = eigvecs2.ToMatrix(true); HDebug.Assert(mat2.RowSize == eigvecs2.Length); eigvecs2 = null; GC.Collect(0);
}
break;
case "memory-save":
{
int vecsize = modes1[0].eigvec.Size;
HDebug.Exception(vecsize == modes1[0].eigvec.Size);
HDebug.Exception(vecsize == modes2[0].eigvec.Size);
//Vector[] eigvecs1 = new Vector[modes1.Count]; for(int i=0; i<modes1.Count; i++) eigvecs1[i] = modes1[i].eigvec.Clone();
//if(mass1 != null) { double[] mass1sqrt = mass1.HSqrt(); for(int i=0; i<modes1.Count; i++) for(int j=0; j<eigvecs1[i].Size; j++) eigvecs1[i][j] *= mass1sqrt[j/3]; }
//if(bResetUnitVector) for(int i=0; i<modes1.Count; i++) eigvecs1[i] = eigvecs1[i].UnitVector();
//mat1 = eigvecs1.ToMatrix(false); HDebug.Assert(mat1.ColSize == modes1.Count); eigvecs1 = null; GC.Collect(0);
mat1 = Matrix.Zeros(modes1.Count, vecsize);
double[] mass1sqrt = null; if (mass1 != null)
{
mass1sqrt = mass1.HSqrt();
}
for (int i = 0; i < modes1.Count; i++)
{
Vector eigvecs1i = modes1[i].eigvec.Clone();
if (mass1 != null)
{
for (int j = 0; j < eigvecs1i.Size; j++)
{
eigvecs1i[j] *= mass1sqrt[j / 3];
}
}
if (bResetUnitVector)
{
eigvecs1i = eigvecs1i.UnitVector();
}
for (int j = 0; j < eigvecs1i.Size; j++)
{
mat1[i, j] = eigvecs1i[j];
}
}
HDebug.Assert(mat1.ColSize == modes1.Count);
GC.Collect(0);
//Vector[] eigvecs2 = new Vector[modes2.Count]; for(int i=0; i<modes2.Count; i++) eigvecs2[i] = modes2[i].eigvec.Clone();
//if(mass2 != null) { double[] mass2sqrt = mass2.HSqrt(); for(int i=0; i<modes2.Count; i++) for(int j=0; j<eigvecs2[i].Size; j++) eigvecs2[i][j] *= mass2sqrt[j/3]; }
//if(bResetUnitVector) for(int i=0; i<modes2.Count; i++) eigvecs2[i] = eigvecs2[i].UnitVector();
//mat2 = eigvecs2.ToMatrix(true ); HDebug.Assert(mat2.RowSize == modes2.Count); eigvecs2 = null; GC.Collect(0);
mat2 = Matrix.Zeros(vecsize, modes2.Count);
double[] mass2sqrt = null; if (mass2 != null)
{
mass2sqrt = mass2.HSqrt();
}
for (int i = 0; i < modes2.Count; i++)
{
Vector eigvecs2i = modes2[i].eigvec.Clone();
if (mass2 != null)
{
for (int j = 0; j < eigvecs2i.Size; j++)
{
eigvecs2i[j] *= mass2sqrt[j / 3];
}
}
if (bResetUnitVector)
{
eigvecs2i = eigvecs2i.UnitVector();
}
for (int j = 0; j < eigvecs2i.Size; j++)
{
mat2[j, i] = eigvecs2i[j];
}
}
HDebug.Assert(mat2.RowSize == modes2.Count);
GC.Collect(0);
}
break;
default:
throw new NotImplementedException();
}
HDebug.Assert(mat1.RowSize == mat2.ColSize);
Matrix overlap = null;
if (ila != null)
{
overlap = ila.Mul(mat1, mat2);
}
else
{
overlap = Matlab.ila.Mul(mat1, mat2);
}
mat1 = mat2 = null;
GC.Collect(0);
//overlap.UpdateAbs();
if (HDebug.IsDebuggerAttached)
{
double[] sum_c2 = new double[overlap.ColSize];
double[] sum_r2 = new double[overlap.RowSize];
for (int c = 0; c < overlap.ColSize; c++)
{
for (int r = 0; r < overlap.RowSize; r++)
{
double v = overlap[c, r];
double v2 = v * v;
HDebug.Assert(v2 <= 1.00000000001);
sum_c2[c] += v2;
sum_r2[r] += v2;
}
}
for (int c = 0; c < overlap.ColSize; c++)
{
HDebug.AssertTolerance(0.00001, sum_c2[c] - 1.0);
}
for (int r = 0; r < overlap.RowSize; r++)
{
HDebug.AssertTolerance(0.00001, sum_r2[r] - 1.0);
}
}
return(overlap);
}
public static Matrix OverlapSigned(IList <Mode> modes1, IList <Mode> modes2, ILinAlg ila, bool bResetUnitVector)
{
return(OverlapSigned(modes1, null, null, modes2, ila, bResetUnitVector));
}
public static (List <(double freq, double dovlp)> freq1_dovlp, List <(double freq, double dovlp)> freq2_dovlp) DegeneratcyOverlap
(IList <Mode> modes1, double[] mass1, double[] mass2, IList <Mode> modes2
, ILinAlg ila, bool bResetUnitVector
, double degeneracy_tolerance // 3.0
, Matrix overlapsigned = null
)
{
if (overlapsigned == null)
{
overlapsigned = HBioinfo.OverlapSigned(modes1, mass1, mass2, modes2, ila, bResetUnitVector);
}
double[] freqs1 = modes1.ListFreq();
double[] freqs2 = modes2.ListFreq();
bool isfreqssorted = true;
{
for (int i = 1; i < freqs1.Length; i++)
{
isfreqssorted = isfreqssorted && (freqs1[i - 1] <= freqs1[i]); // ( sorted ) or ( freqs1[i-1] is close to zero )
}
for (int i = 1; i < freqs2.Length; i++)
{
isfreqssorted = isfreqssorted && (freqs2[i - 1] <= freqs2[i]); // ( sorted ) or ( freqs2[i-1] is close to zero )
}
}
int[] idx1sorted = null;
int[] idx2sorted = null;
if (isfreqssorted == false)
{
idx1sorted = freqs1.HIdxSorted();
idx2sorted = freqs2.HIdxSorted();
modes1 = modes1.HSelectByIndex(idx1sorted);
modes2 = modes2.HSelectByIndex(idx2sorted);
if (mass1 != null)
{
HDebug.Assert(mass1.Length == idx1sorted.Length); mass1 = mass1.HSelectByIndex(idx1sorted);
}
if (mass2 != null)
{
HDebug.Assert(mass2.Length == idx2sorted.Length); mass2 = mass2.HSelectByIndex(idx2sorted);
}
freqs1 = modes1.ListFreq();
freqs2 = modes2.ListFreq();
overlapsigned = HBioinfo.OverlapSigned(modes1, mass1, mass2, modes2, ila, bResetUnitVector);
}
if (HDebug.IsDebuggerAttached)
{
for (int i = 1; i < freqs1.Length; i++)
{
HDebug.Assert(freqs1[i - 1] <= freqs1[i]);
}
for (int i = 1; i < freqs2.Length; i++)
{
HDebug.Assert(freqs2[i - 1] <= freqs2[i]);
}
}
List <(double freq, double dovlp)> freq1_dovlp = new List <(double, double)>();
for (int i1 = 0; i1 < freqs1.Length; i1++)
{
double freq = freqs1[i1];
int i2a = Array.BinarySearch(freqs2, freq - degeneracy_tolerance);
int i2b = Array.BinarySearch(freqs2, freq + degeneracy_tolerance);
if (i2a == i2b)
{
freq1_dovlp.Add((freqs1[i1], 0));
continue;
}
if (i2a < 0)
{
i2a = ~i2a;
}
if (i2b < 0)
{
i2b = ~i2b;
}
HDebug.Assert(i2a < i2b);
double dovlp = 0;
for (int i2 = i2a; i2 < i2b; i2++)
{
dovlp += overlapsigned[i1, i2] * overlapsigned[i1, i2];
}
freq1_dovlp.Add((freqs1[i1], dovlp));
}
List <(double freq, double dovlp)> freq2_dovlp = new List <(double, double)>();
for (int i2 = 0; i2 < freqs2.Length; i2++)
{
double freq = freqs2[i2];
int i1a = Array.BinarySearch(freqs1, freq - degeneracy_tolerance);
int i1b = Array.BinarySearch(freqs1, freq + degeneracy_tolerance);
if (i1a == i1b)
{
freq2_dovlp.Add((freqs2[i2], 0));
continue;
}
if (i1a < 0)
{
i1a = ~i1a;
}
if (i1b < 0)
{
i1b = ~i1b;
}
HDebug.Assert(i1a < i1b);
double dovlp = 0;
for (int i1 = i1a; i1 < i1b; i1++)
{
dovlp += overlapsigned[i1, i2] * overlapsigned[i1, i2];
}
freq2_dovlp.Add((freqs2[i2], dovlp));
}
if (HDebug.IsDebuggerAttached)
{
HDebug.Assert(freqs1.Length == freq1_dovlp.Count);
HDebug.Assert(freqs2.Length == freq2_dovlp.Count);
for (int i = 0; i < freqs1.Length; i++)
{
HDebug.Assert(freqs1[i] == freq1_dovlp[i].freq);
}
for (int i = 0; i < freqs2.Length; i++)
{
HDebug.Assert(freqs2[i] == freq2_dovlp[i].freq);
}
}
return(freq1_dovlp, freq2_dovlp);
}
public static MatrixByArr GetHessian(this IList <Mode> modes, IList <double> masses, ILinAlg la)
{
/// mode.eigval = mweigval
/// mode.eigvec = mass^-0.5 * mweigvec
///
/// W = [mode(1).eigvec, mode(2).eigvec, ... ]
/// M = masses
/// D = diag([mode(1).eigval, mode(2).eigval, ...])
///
/// mwH = M^-0.5 H M^-0.5
/// [V,D] = eig(mwH)
/// mode.eigval == D
/// mode.eigvec == M^-0.5 V = W
///
/// W D W' = M^-0.5 V D V M^-0.5
/// = M^-0.5 mwH M^-0.5
/// = M^-0.5 (M^-0.5 H M^-0.5) M^-0.5
/// = M^-1 H M^-1
/// H = M (M^-1 H M^-1) M
/// = M (W D W') M
/// = (M W) D (M W)'
HDebug.Assert(modes.CheckModeMassReduced(masses.ToArray(), la, 0.000001));
Vector[] mws = modes.ListEigvec().ToArray();
for (int iv = 0; iv < mws.Length; iv++)
{
for (int i = 0; i < mws[iv].Size; i++)
{
mws[iv][i] = mws[iv][i] * masses[i / 3];
}
}
Vector ds = modes.ListEigval().ToArray();
MatrixByArr hess;
{
var MW = la.ToILMat(mws.ToMatrix());
var D = la.ToILMat(ds).Diag();
var H = la.Mul(MW, D, MW.Tr);
hess = H.ToArray();
MW.Dispose();
D.Dispose();
H.Dispose();
}
return(hess);
}
public static CGetHessCoarseResiIterImpl Do
(object[] atoms
, HessMatrix H
, List <int>[] lstNewIdxRemv
, double thres_zeroblk
, ILinAlg ila
, bool cloneH
, string[] options
)
{
//HDebug.ToDo();
ila = null;
cloneH = true;
if (cloneH)
{
H = H.CloneHess();
}
bool process_disp_console = true;
if (options != null && options.Contains("print process"))
{
process_disp_console = true;
}
bool parallel = false;
/// keep only lower triangle of H (lower block triangles)
{
HashSet <Tuple <int, int, MatrixByArr> > lstUppTrig = new HashSet <Tuple <int, int, MatrixByArr> >();
foreach (ValueTuple <int, int, MatrixByArr> bc_br_bval in H.EnumBlocks())
{
int bc = bc_br_bval.Item1;
int br = bc_br_bval.Item2;
if (bc < br)
{
lstUppTrig.Add(bc_br_bval.ToTuple());
}
}
foreach (Tuple <int, int, MatrixByArr> bc_br_bval in lstUppTrig)
{
int bc = bc_br_bval.Item1;
int br = bc_br_bval.Item2;
HDebug.Assert(bc < br);
H.SetBlock(bc, br, null);
}
}
GC.Collect();
DateTime[] process_time = new DateTime[6];
//System.Console.WriteLine("begin coarse-graining");
List <HessCoarseResiIterInfo> iterinfos = new List <HessCoarseResiIterInfo>();
for (int iter = lstNewIdxRemv.Length - 1; iter >= 0; iter--)
{
bool lprocess_disp_console = (process_disp_console && iter % 5 == 0);
lprocess_disp_console = true;
if (lprocess_disp_console)
{
process_time[0] = DateTime.UtcNow;
System.Console.Write(" - {0:000} : ", iter);
}
//int[] ikeep = lstNewIdxRemv[iter].Item1;
HessCoarseResiIterInfo iterinfo = new HessCoarseResiIterInfo();
iterinfo.sizeHessBlkMat = 1;
iterinfo.numAtomsRemoved = 1;
iterinfo.time0 = DateTime.UtcNow;
int _count_update = 0;
{
HDebug.Assert(lstNewIdxRemv[iter].Count == 1);
int iremv = lstNewIdxRemv[iter][0];
HessMatrix A = H;
MatrixByArr D = null;
double D_absmin = 0;
List <int> C_lstbr = new List <int>();
List <MatrixByArr> C_lstbval = new List <MatrixByArr>();
{
// get C and D
foreach (var(bc, br, bval) in H.EnumBlocksInCols(new int[] { iremv }))
{
HDebug.Assert(iremv == bc);
if (bc == br)
{
HDebug.Assert(D == null);
D = bval;
D_absmin = D.HAbsMin();
}
else
{
if (bval.HAbsMin() >= thres_zeroblk)
{
C_lstbr.Add(br);
C_lstbval.Add(bval);
}
}
}
// remove C and D
{
int bc = iremv;
H.SetBlock(bc, bc, null);
foreach (int br in C_lstbr)
{
H.SetBlock(bc, br, null);
}
}
}
if (lprocess_disp_console)
{
process_time[1] = process_time[2] = DateTime.UtcNow;
System.Console.Write("CD({0:00.00} min), ", (process_time[2] - process_time[0]).TotalMinutes);
}
double threshold = thres_zeroblk / lstNewIdxRemv.Length;
// DD ={ { d00,d01,d02},{ d10,d11,d12},{ d20,d21,d22} }; MatrixForm[DD]
// BB ={ { b00,b01,b02},{ b10,b11,b12},{ b20,b21,b22} }; MatrixForm[BB]
// CC ={ { c00,c01,c02},{ c10,c11,c12},{ c20,c21,c22} }; MatrixForm[CC]
// object[] dbginfo = null; // new object[] { iremv, atoms, H, D, C_lstbr, C_lstbval };
Action <ValueTuple <int, int, MatrixByArr, MatrixByArr> > Update_A_B_invD_C = delegate(ValueTuple <int, int, MatrixByArr, MatrixByArr> info)
{
int bc = info.Item1; // bc
int br = info.Item2; // br
MatrixByArr DC = info.Item3; // invDD_CC // XX ={ { x00,x01,x02},{ x10,x11,x12},{ x20,x21,x22} }; MatrixForm[CC]
MatrixByArr B = info.Item4; // BB // BB ={ { b00,b01,b02},{ b10,b11,b12},{ b20,b21,b22} }; MatrixForm[BB]
//var _iremv = (int)dbginfo[0];
//var _atoms = dbginfo[1] as Universe.Atom[] ;
//var _H = dbginfo[2] as HessMatrix ;
//var _D = dbginfo[3] as MatrixByArr ;
//var _C_lstbr = dbginfo[4] as List<int> ;
//var _C_lstbval = dbginfo[5] as List<MatrixByArr>;
//MatrixByArr BB_invDD_CC = BB * invDD_CC;
double _BDC00 = 0 - B[0, 0] * DC[0, 0] - B[0, 1] * DC[1, 0] - B[0, 2] * DC[2, 0]; // { { b00 x00 +b01 x10 + b02 x20
double _BDC01 = 0 - B[0, 0] * DC[0, 1] - B[0, 1] * DC[1, 1] - B[0, 2] * DC[2, 1]; // , b00 x01 +b01 x11 + b02 x21
double _BDC02 = 0 - B[0, 0] * DC[0, 2] - B[0, 1] * DC[1, 2] - B[0, 2] * DC[2, 2]; // , b00 x02 +b01 x12 + b02 x22
double _BDC10 = 0 - B[1, 0] * DC[0, 0] - B[1, 1] * DC[1, 0] - B[1, 2] * DC[2, 0]; // },{ b10 x00 +b11 x10 + b12 x20
double _BDC11 = 0 - B[1, 0] * DC[0, 1] - B[1, 1] * DC[1, 1] - B[1, 2] * DC[2, 1]; // , b10 x01 +b11 x11 + b12 x21
double _BDC12 = 0 - B[1, 0] * DC[0, 2] - B[1, 1] * DC[1, 2] - B[1, 2] * DC[2, 2]; // , b10 x02 +b11 x12 + b12 x22
double _BDC20 = 0 - B[2, 0] * DC[0, 0] - B[2, 1] * DC[1, 0] - B[2, 2] * DC[2, 0]; // },{ b20 x00 +b21 x10 + b22 x20
double _BDC21 = 0 - B[2, 0] * DC[0, 1] - B[2, 1] * DC[1, 1] - B[2, 2] * DC[2, 1]; // , b20 x01 +b21 x11 + b22 x21
double _BDC22 = 0 - B[2, 0] * DC[0, 2] - B[2, 1] * DC[1, 2] - B[2, 2] * DC[2, 2]; // , b20 x02 +b21 x12 + b22 x22 }}
if (A.HasBlockLock(bc, br))
{
MatrixByArr A_bc_br = A.GetBlockLock(bc, br);
A_bc_br[0, 0] += _BDC00; // A = A + (-B.invD.C)
A_bc_br[0, 1] += _BDC01; // A = A + (-B.invD.C)
A_bc_br[0, 2] += _BDC02; // A = A + (-B.invD.C)
A_bc_br[1, 0] += _BDC10; // A = A + (-B.invD.C)
A_bc_br[1, 1] += _BDC11; // A = A + (-B.invD.C)
A_bc_br[1, 2] += _BDC12; // A = A + (-B.invD.C)
A_bc_br[2, 0] += _BDC20; // A = A + (-B.invD.C)
A_bc_br[2, 1] += _BDC21; // A = A + (-B.invD.C)
A_bc_br[2, 2] += _BDC22; // A = A + (-B.invD.C)
// (small && small && small) == !(large || large || large)
bool toosmall = !(Math.Abs(A_bc_br[0, 0]) > threshold || Math.Abs(A_bc_br[0, 1]) > threshold || Math.Abs(A_bc_br[0, 2]) > threshold ||
Math.Abs(A_bc_br[1, 0]) > threshold || Math.Abs(A_bc_br[1, 1]) > threshold || Math.Abs(A_bc_br[1, 2]) > threshold ||
Math.Abs(A_bc_br[2, 0]) > threshold || Math.Abs(A_bc_br[2, 1]) > threshold || Math.Abs(A_bc_br[2, 2]) > threshold);
if (toosmall)
{
HDebug.Assert(bc != br);
A.SetBlockLock(bc, br, null);
}
}
else
{
// (small && small && small) == !(large || large || large)
bool toosmall = !(Math.Abs(_BDC00) > threshold || Math.Abs(_BDC01) > threshold || Math.Abs(_BDC02) > threshold ||
Math.Abs(_BDC10) > threshold || Math.Abs(_BDC11) > threshold || Math.Abs(_BDC12) > threshold ||
Math.Abs(_BDC20) > threshold || Math.Abs(_BDC21) > threshold || Math.Abs(_BDC22) > threshold);
if (!toosmall)
{
MatrixByArr A_bc_br = new double[3, 3]
{
{ _BDC00, _BDC01, _BDC02 } // A = 0 + (-B.invD.C)
, { _BDC10, _BDC11, _BDC12 } // A = 0 + (-B.invD.C)
, { _BDC20, _BDC21, _BDC22 } // A = 0 + (-B.invD.C)
};
A.SetBlockLock(bc, br, A_bc_br);
}
}
System.Threading.Interlocked.Increment(ref _count_update);
};
var lstCompInfo = EnumComput(D, C_lstbr, C_lstbval, threshold);
if (parallel)
{
Parallel.ForEach(lstCompInfo, Update_A_B_invD_C);
}
else
{
foreach (var info in lstCompInfo)
{
Update_A_B_invD_C(info);
}
}
//GC.Collect(0);
if (lprocess_disp_console)
{
process_time[4] = DateTime.UtcNow;
System.Console.Write("B.invD.C({0:00.00} min), ", (process_time[4] - process_time[3]).TotalMinutes);
}
H = A;
}
iterinfo.usedMemoryByte = GC.GetTotalMemory(false);
iterinfo.time1 = DateTime.UtcNow;
iterinfos.Add(iterinfo);
if (lprocess_disp_console)
{
System.Console.WriteLine("summary(makezero {0,5}, nonzero {1,5}, numIgnMul {2,7}, numRemvAtoms {3,3}, {4,5:0.00} sec, {5} mb, {6}x{6}, nzeroBlk/Atom {7:0.00}, cntUpdateBlk({8}))"
, iterinfo.numSetZeroBlock
, iterinfo.numNonZeroBlock
, iterinfo.numAddIgnrBlock
, iterinfo.numAtomsRemoved
, iterinfo.compSec
, iterinfo.usedMemoryByte / (1024 * 1024)
, (0 * 3)
, 0//((double)iterinfo.numNonZeroBlock / idxremv.Length)
, _count_update
);
}
}
int numca = H.ColBlockSize - lstNewIdxRemv.HListCount().Sum();
//System.Console.WriteLine("finish coarse-graining");
{
int[] idxkeep = HEnum.HEnumCount(numca).ToArray();
H = H.SubMatrixByAtoms(false, idxkeep, idxkeep, false);
}
{
H.MakeNearZeroBlockAsZero(thres_zeroblk);
}
GC.Collect(0);
//System.Console.WriteLine("finish resizing");
return(new CGetHessCoarseResiIterImpl
{
iterinfos = iterinfos,
H = H,
});
}
public static CGetHessCoarseResiIterImpl GetHessCoarseResiIterImpl_Matlab_IterLowerTri
(object[] atoms
, HessMatrix H
, List <int>[] lstNewIdxRemv
, double thres_zeroblk
, ILinAlg ila
, bool cloneH
, string[] options // { "pinv(D)" }
)
{
ila = null;
if (cloneH)
{
H = H.CloneHess();
}
bool process_disp_console = true;
if (options != null && options.Contains("print process"))
{
process_disp_console = true;
}
bool parallel = true;
/// keep only lower triangle of H (lower block triangles)
{
HashSet <Tuple <int, int, MatrixByArr> > lstUppTrig = new HashSet <Tuple <int, int, MatrixByArr> >();
foreach (ValueTuple <int, int, MatrixByArr> bc_br_bval in H.EnumBlocks())
{
int bc = bc_br_bval.Item1;
int br = bc_br_bval.Item2;
if (bc < br)
{
lstUppTrig.Add(bc_br_bval.ToTuple());
}
}
foreach (Tuple <int, int, MatrixByArr> bc_br_bval in lstUppTrig)
{
int bc = bc_br_bval.Item1;
int br = bc_br_bval.Item2;
HDebug.Assert(bc < br);
H.SetBlock(bc, br, null);
}
}
GC.Collect();
List <DateTime> process_time = new List <DateTime>();
//System.Console.WriteLine("begin coarse-graining");
List <HessCoarseResiIterInfo> iterinfos = new List <HessCoarseResiIterInfo>();
for (int iter = lstNewIdxRemv.Length - 1; iter >= 0; iter--)
{
process_time.Clear();
if (process_disp_console)
{
process_time.Add(DateTime.UtcNow);
System.Console.Write(" - {0:000} : ", iter);
}
//int[] ikeep = lstNewIdxRemv[iter].Item1;
int[] iremv = lstNewIdxRemv[iter].ToArray();
int iremv_min = iremv.Min();
int iremv_max = iremv.Max();
HDebug.Assert(H.ColBlockSize == H.RowBlockSize);
int blksize = H.ColBlockSize;
//HDebug.Assert(ikeep.Max() < blksize);
//HDebug.Assert(iremv.Max() < blksize);
//HDebug.Assert(iremv.Max()+1 == blksize);
//HDebug.Assert(iremv.Max() - iremv.Min() + 1 == iremv.Length);
int[] idxkeep = HEnum.HEnumFromTo(0, iremv_min - 1).ToArray();
int[] idxremv = HEnum.HEnumFromTo(iremv_min, iremv_max).ToArray();
//HDebug.Assert(idxkeep.HUnionWith(idxremv).Length == blksize);
HessCoarseResiIterInfo iterinfo = new HessCoarseResiIterInfo();
iterinfo.sizeHessBlkMat = idxremv.Max() + 1; // H.ColBlockSize;
iterinfo.numAtomsRemoved = idxremv.Length;
iterinfo.time0 = DateTime.UtcNow;
////////////////////////////////////////////////////////////////////////////////////////
// make C sparse
double C_density0;
double C_density1;
{
double thres_absmax = thres_zeroblk;
C_density0 = 0;
List <Tuple <int, int> > lstIdxToMakeZero = new List <Tuple <int, int> >();
foreach (var bc_br_bval in H.EnumBlocksInCols(idxremv))
{
int bc = bc_br_bval.Item1;
int br = bc_br_bval.Item2;
var bval = bc_br_bval.Item3;
if (br >= iremv_min)
{
// bc_br is in D, not in C
continue;
}
C_density0++;
double absmax_bval = bval.HAbsMax();
if (absmax_bval < thres_absmax)
{
lstIdxToMakeZero.Add(new Tuple <int, int>(bc, br));
}
}
C_density1 = C_density0 - lstIdxToMakeZero.Count;
foreach (var bc_br in lstIdxToMakeZero)
{
int bc = bc_br.Item1;
int br = bc_br.Item2;
HDebug.Assert(bc > br);
var Cval = H.GetBlock(bc, br);
var Dval = H.GetBlock(bc, bc);
var Aval = H.GetBlock(br, br);
var Bval = Cval.Tr();
H.SetBlock(bc, br, null); // nCval = Cval -Cval
H.SetBlock(bc, bc, Dval + Cval); // nDval = Dval - (-Cval) = Dval + Cval
// nBval = Bval -Bval
H.SetBlock(br, br, Aval + Bval); // nAval = Aval - (-Bval) = Aval + Bval
}
iterinfo.numSetZeroBlock = lstIdxToMakeZero.Count;
iterinfo.numNonZeroBlock = (int)C_density1;
C_density0 /= (idxkeep.Length * idxremv.Length);
C_density1 /= (idxkeep.Length * idxremv.Length);
}
////////////////////////////////////////////////////////////////////////////////////////
// get A, B, C, D
HessMatrix A = H; // HessMatrix A = H.SubMatrixByAtoms(false, idxkeep, idxkeep);
// HessMatrix B = H.SubMatrixByAtoms(false, idxkeep, idxremv);
HessMatrix C; // HessMatrix C = H.SubMatrixByAtoms(false, idxremv, idxkeep, parallel:parallel);
HessMatrix D; // HessMatrix D = H.SubMatrixByAtoms(false, idxremv, idxremv, parallel:parallel);
{
C = H.Zeros(idxremv.Length * 3, idxkeep.Length * 3);
D = H.Zeros(idxremv.Length * 3, idxremv.Length * 3);
//List<Tuple<int, int, MatrixByArr>> lst_bc_br_bval = H.EnumBlocksInCols(idxremv).ToList();
//foreach(var bc_br_bval in lst_bc_br_bval)
foreach (var bc_br_bval in H.EnumBlocksInCols(idxremv))
{
int bc = bc_br_bval.Item1;
int br = bc_br_bval.Item2;
var bval = bc_br_bval.Item3;
H.SetBlock(bc, br, null);
if (bc > iremv_max)
{
HDebug.Assert(false); continue;
}
if (br > iremv_max)
{
HDebug.Assert(false); continue;
}
if (br < iremv_min)
{
int nc = bc - iremv_min;
int nr = br;
HDebug.Assert(C.HasBlock(nc, nr) == false);
C.SetBlock(nc, nr, bval.CloneT());
}
else
{
int nc = bc - iremv_min;
int nr = br - iremv_min;
HDebug.Assert(D.HasBlock(nc, nr) == false);
D.SetBlock(nc, nr, bval);
if (nc != nr)
{
HDebug.Assert(D.HasBlock(nr, nc) == false);
D.SetBlock(nr, nc, bval.Tr());
}
}
}
HDebug.Assert(H.EnumBlocksInCols(idxremv).Count() == 0);
}
if (process_disp_console)
{
process_time.Add(DateTime.UtcNow);
int ptc = process_time.Count;
System.Console.Write("CD({0:00.00} min), ", (process_time[ptc - 1] - process_time[ptc - 2]).TotalMinutes);
}
////////////////////////////////////////////////////////////////////////////////////////
// Get B.inv(D).C
HessMatrix B_invD_C;
{
{
B_invD_C = GetHessCoarseResiIterImpl_Matlab_IterLowerTri_Get_BInvDC(A, C, D, process_disp_console
, options
, thld_BinvDC: thres_zeroblk / lstNewIdxRemv.Length
, parallel: parallel
);
}
if (process_disp_console)
{
process_time.Add(DateTime.UtcNow);
int ptc = process_time.Count;
System.Console.Write("B.invD.C({0:00.00} min), ", (process_time[ptc - 1] - process_time[ptc - 2]).TotalMinutes);
}
GC.Collect(0);
}
////////////////////////////////////////////////////////////////////////////////////////
// Get A - B.inv(D).C
/// iterinfo.numAddIgnrBlock = A.UpdateAdd(B_invD_C, -1, null, thres_zeroblk/lstNewIdxRemv.Length, parallel:parallel);
{
HessMatrix __this = A;
HessMatrix other = B_invD_C;
double _thres_NearZeroBlock = thres_zeroblk / lstNewIdxRemv.Length;
int[] _count = new int[1];
int[] _count_ignored = new int[1];
//foreach(var bc_br_bval in other.EnumBlocks())
Action <ValueTuple <int, int, MatrixByArr> > func = delegate(ValueTuple <int, int, MatrixByArr> bc_br_bval)
{
_count[0]++;
int bc = bc_br_bval.Item1;
int br = bc_br_bval.Item2;
MatrixByArr other_bmat = bc_br_bval.Item3;
if (bc < br)
{
return; // continue;
}
if (other_bmat.HAbsMax() <= _thres_NearZeroBlock)
{
/// other_bmat = other_bmat -other_bmat;
/// other_diag = other_diag - (-other_bmat) = other_diag + other_bmat;
/// this_diag = this_diat - B_invD_C
/// = this_diat - other_diag
/// = this_diat - (other_diag + other_bmat)
/// = this_diat - other_diag - other_bmat
/// = (this_diat - other_bmat) - other_diag
/// = (this_diat - other_bmat) - (processed later)
/// = (this_diat - other_bmat)
MatrixByArr this_diag = __this.GetBlock(bc, bc);
MatrixByArr new_diag = this_diag - other_bmat;
__this.SetBlockLock(bc, bc, new_diag);
other_bmat = null;
lock (_count_ignored)
_count_ignored[0]++;
}
if (other_bmat != null)
{
MatrixByArr this_bmat = __this.GetBlock(bc, br);
if (this_bmat == null)
{
this_bmat = new double[3, 3];
}
MatrixByArr new_bmat = this_bmat - other_bmat;
__this.SetBlockLock(bc, br, new_bmat);
}
};
if (parallel)
{
HParallel.ForEach(other.EnumBlocks(), func);
}
else
{
foreach (var bc_br_bval in other.EnumBlocks())
{
func(bc_br_bval);
}
}
iterinfo.numAddIgnrBlock = _count_ignored[0];
}
if (process_disp_console)
{
process_time.Add(DateTime.UtcNow);
int ptc = process_time.Count;
System.Console.Write("A-BinvDC({0:00.00} min), ", (process_time[ptc - 1] - process_time[ptc - 2]).TotalMinutes);
}
//HessMatrix nH = A - B_invD_C;
//nH = ((nH + nH.Tr())/2).ToHessMatrix();
////////////////////////////////////////////////////////////////////////////////////////
// Replace A -> H
H = A;
////////////////////////////////////////////////////////////////////////////////////////
// print iteration log
iterinfo.usedMemoryByte = GC.GetTotalMemory(false);
iterinfo.time1 = DateTime.UtcNow;
iterinfos.Add(iterinfo);
if (process_disp_console)
{
System.Console.Write("summary(makezero {0,5}, nonzero {1,5}, numIgnMul {2,7}, numRemvAtoms {3,3}, {4,5:0.00} min, {5} mb, {6}x{6}, nzeroBlk/Atom {7:0.00}), GC("
, iterinfo.numSetZeroBlock
, iterinfo.numNonZeroBlock
, iterinfo.numAddIgnrBlock
, iterinfo.numAtomsRemoved
, iterinfo.compTime.TotalMinutes
, iterinfo.usedMemoryByte / (1024 * 1024)
, (idxkeep.Length * 3)
, ((double)iterinfo.numNonZeroBlock / idxremv.Length)
);
}
GC.Collect();
if (process_disp_console)
{
System.Console.WriteLine(")");
}
}
int numca = H.ColBlockSize - lstNewIdxRemv.HListCount().Sum();
//System.Console.WriteLine("finish coarse-graining");
{
int[] idxkeep = HEnum.HEnumCount(numca).ToArray();
H = H.SubMatrixByAtoms(false, idxkeep, idxkeep, false);
}
{
H.MakeNearZeroBlockAsZero(thres_zeroblk);
}
GC.Collect();
//System.Console.WriteLine("finish resizing");
return(new CGetHessCoarseResiIterImpl
{
iterinfos = iterinfos,
H = H,
});
}
public static bool CheckModeMassReduced(this IList <Mode> modes, double[] masses, ILinAlg la, double tolerance = 0.000000001)
{
Vector[] mweigvecs = modes.GetMassReduced(masses.HInv()).ListEigvec().ToArray();
MatrixByArr chkmat;
{
var V = la.ToILMat(mweigvecs.ToMatrix());
var VV = V.Tr * V;
chkmat = VV.ToArray();
V.Dispose();
VV.Dispose();
}
HDebug.Assert(chkmat.ColSize == chkmat.RowSize);
for (int i = 0; i < chkmat.ColSize; i++)
{
if (Math.Abs(chkmat[i, i] - 1) >= tolerance)
{
/// not normal
return(false);
}
chkmat[i, i] = 0;
}
for (int c = 0; c < chkmat.ColSize; c++)
{
if (modes[c].eigval == 0)
{
continue;
}
for (int r = 0; r < chkmat.RowSize; r++)
{
if (modes[r].eigval == 0)
{
continue;
}
double v = chkmat[c, r];
if (Math.Abs(v) >= tolerance)
{
/// not orthogonal
return(false);
}
}
}
return(true);
}
