public static CGetHessCoarseResiIterImpl GetHessCoarseResiIterImpl_ILinAlg(HessMatrix H, List <int>[] lstNewIdxRemv, double thres_zeroblk, ILinAlg ila, bool cloneH)
{
if (cloneH)
{
H = H.CloneHess();
}
bool process_disp_console = true;
DateTime[] process_time = new DateTime[7];
//System.Console.WriteLine("begin coarse-graining");
List <HessCoarseResiIterInfo> iterinfos = new List <HessCoarseResiIterInfo>();
for (int iter = lstNewIdxRemv.Length - 1; iter >= 0; iter--)
{
if (process_disp_console)
{
process_time[0] = DateTime.UtcNow; System.Console.Write(" - {0:000} : ", iter);
}
//int[] ikeep = lstNewIdxRemv[iter].Item1;
int[] iremv = lstNewIdxRemv[iter].ToArray();
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;
double C_density0 = double.NaN;
double C_density1 = double.NaN;
{
//HessMatrix A = H.SubMatrixByAtoms(false, idxkeep, idxkeep);
HessMatrix A = H;
//HessMatrix B = H.SubMatrixByAtoms(false, idxkeep, idxremv);
HessMatrix C = H.SubMatrixByAtoms(false, idxremv, idxkeep); if (process_disp_console)
{
process_time[1] = DateTime.UtcNow; System.Console.Write("C({0:00.00} min), ", (process_time[1] - process_time[0]).TotalMinutes);
}
HessMatrix D = H.SubMatrixByAtoms(false, idxremv, idxremv); if (process_disp_console)
{
process_time[2] = DateTime.UtcNow; System.Console.Write("D({0:00.00} min), ", (process_time[2] - process_time[1]).TotalMinutes);
}
HessMatrix invD = new HessMatrixDense {
hess = ila.InvSymm(D)
}; if (process_disp_console)
{
process_time[3] = DateTime.UtcNow; System.Console.Write("invD({0:00.00} min), ", (process_time[3] - process_time[2]).TotalMinutes);
}
// make B,C sparse
//int B_cntzero = B.MakeNearZeroBlockAsZero(thres_zeroblk);
C_density0 = C.RatioUsedBlocks;
iterinfo.numSetZeroBlock = C.MakeNearZeroBlockAsZero(thres_zeroblk); if (process_disp_console)
{
process_time[4] = DateTime.UtcNow; System.Console.Write("sparseC({0:00.00} min), ", (process_time[4] - process_time[3]).TotalMinutes);
}
//int B_nzeros = B.NumUsedBlocks; double B_nzeros_ = Math.Sqrt(B_nzeros);
iterinfo.numNonZeroBlock = C.NumUsedBlocks;
C_density1 = C.RatioUsedBlocks;
HessMatrix B = C.Tr();
HessMatrix B_invD_C = HessMatrix.GetMul(ila, B, invD, C); /* B * invD * C;*/ if (process_disp_console)
{
process_time[5] = DateTime.UtcNow; System.Console.Write("B.invD.C({0:00.00} min), ", (process_time[5] - process_time[4]).TotalMinutes);
}
iterinfo.numAddIgnrBlock = A.UpdateAdd(B_invD_C, -1, null, thres_zeroblk / lstNewIdxRemv.Length); if (process_disp_console)
{
process_time[6] = DateTime.UtcNow; System.Console.Write("A+BinvDC({0:00.00} min), ", (process_time[6] - process_time[5]).TotalMinutes);
}
//HessMatrix nH = A - B_invD_C;
//nH = ((nH + nH.Tr())/2).ToHessMatrix();
H = A;
}
iterinfo.usedMemoryByte = GC.GetTotalMemory(false);
iterinfo.time1 = DateTime.UtcNow;
iterinfos.Add(iterinfo);
if (process_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})"
, iterinfo.numSetZeroBlock
, iterinfo.numNonZeroBlock
, iterinfo.numAddIgnrBlock
, iterinfo.numAtomsRemoved
, iterinfo.compSec
, iterinfo.usedMemoryByte / (1024 * 1024)
, (idxkeep.Length * 3)
, ((double)iterinfo.numNonZeroBlock / idxremv.Length)
);
}
GC.Collect(0);
}
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_ILinAlg_20150329(HessMatrix H, List <int>[] lstNewIdxRemv, double thres_zeroblk, ILinAlg ila, bool cloneH)
{
if (cloneH)
{
H = H.CloneHess();
}
//System.Console.WriteLine("begin coarse-graining");
List <HessCoarseResiIterInfo> iterinfos = new List <HessCoarseResiIterInfo>();
for (int iter = lstNewIdxRemv.Length - 1; iter >= 0; iter--)
{
//int[] ikeep = lstNewIdxRemv[iter].Item1;
int[] iremv = lstNewIdxRemv[iter].ToArray();
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;
{
//HessMatrix A = H.SubMatrixByAtoms(false, idxkeep, idxkeep);
HessMatrix A = H;
//HessMatrix B = H.SubMatrixByAtoms(false, idxkeep, idxremv);
HessMatrix C = H.SubMatrixByAtoms(false, idxremv, idxkeep);
HessMatrix D = H.SubMatrixByAtoms(false, idxremv, idxremv);
HessMatrix invD = new HessMatrixDense {
hess = ila.InvSymm(D)
};
// make B,C sparse
//int B_cntzero = B.MakeNearZeroBlockAsZero(thres_zeroblk);
iterinfo.numSetZeroBlock = C.MakeNearZeroBlockAsZero(thres_zeroblk);
//int B_nzeros = B.NumUsedBlocks; double B_nzeros_ = Math.Sqrt(B_nzeros);
iterinfo.numNonZeroBlock = C.NumUsedBlocks;
HessMatrix B = C.Tr();
HessMatrix B_invD_C = B * invD * C;
iterinfo.numAddIgnrBlock = A.UpdateAdd(B_invD_C, -1, null, thres_zeroblk / lstNewIdxRemv.Length);
//HessMatrix nH = A - B_invD_C;
//nH = ((nH + nH.Tr())/2).ToHessMatrix();
H = A;
}
iterinfo.usedMemoryByte = GC.GetTotalMemory(false);
iterinfo.time1 = DateTime.UtcNow;
iterinfos.Add(iterinfo);
//System.Console.WriteLine(" - {0:000} : makezero {1,5}, nonzero {2,5}, numIgnMul {3,7}, numRemvAtoms {4,3}, {5,5:0.00} sec, {6} mb, {7}x{7}"
// , iter
// , iterinfo.numSetZeroBlock
// , iterinfo.numNonZeroBlock
// , iterinfo.numAddIgnrBlock
// , iterinfo.numAtomsRemoved
// , iterinfo.compSec
// , iterinfo.usedMemoryByte/(1024*1024)
// , (idxkeep.Length*3)
// );
GC.Collect();
}
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 Matrix GetInvSprTensor(Matrix H, Matrix S, ILinAlg ila)
{
Matrix invH;
string optInvH = "EigSymmTol";
optInvH += ((ila == null) ? "-matlab" : "-ilnum");
switch (optInvH)
{
case "InvSymm-ilnum":
HDebug.Assert(false);
invH = ila.InvSymm(H);
break;
case "PInv-ilnum":
invH = ila.PInv(H);
break;
case "EigSymm-ilnum":
{
var HH = ila.ToILMat(H);
var VVDD = ila.EigSymm(HH);
var VV = VVDD.Item1;
for (int i = 0; i < VVDD.Item2.Length; i++)
{
VVDD.Item2[i] = 1 / VVDD.Item2[i];
}
for (int i = 0; i < 6; i++)
{
VVDD.Item2[i] = 0;
}
var DD = ila.ToILMat(VVDD.Item2).Diag();
var invHH = ila.Mul(VV, DD, VV.Tr);
invH = invHH.ToArray();
//var check = (H * invH).ToArray();
GC.Collect();
}
break;
case "EigSymmTol-matlab":
{
using (new Matlab.NamedLock(""))
{
Matlab.PutMatrix("invHH.HH", H);
Matlab.Execute("invHH.HH = (invHH.HH + invHH.HH')/2;");
Matlab.Execute("[invHH.VV, invHH.DD] = eig(invHH.HH);");
Matlab.Execute("invHH.DD = diag(invHH.DD);");
Matlab.Execute("invHH.DD(abs(invHH.DD)<0.00001) = 0;");
Matlab.Execute("invHH.DD = pinv(diag(invHH.DD));");
Matlab.Execute("invHH = invHH.VV * invHH.DD * invHH.VV';");
invH = Matlab.GetMatrix("invHH");
Matlab.Execute("clear invHH;");
}
GC.Collect();
}
break;
case "EigSymmTol-ilnum":
{
var HH = ila.ToILMat(H);
var VVDD = ila.EigSymm(HH);
var VV = VVDD.Item1;
for (int i = 0; i < VVDD.Item2.Length; i++)
{
if (Math.Abs(VVDD.Item2[i]) < 0.00001)
{
VVDD.Item2[i] = 0;
}
else
{
VVDD.Item2[i] = 1 / VVDD.Item2[i];
}
}
var DD = ila.ToILMat(VVDD.Item2).Diag();
var invHH = ila.Mul(VV, DD, VV.Tr);
invH = invHH.ToArray();
//var check = (H * invH).ToArray();
GC.Collect();
}
break;
default:
throw new NotImplementedException();
}
Matrix invkij = 0.5 * (S.Tr() * invH * S);
//HDebug.Assert(invkij >= 0);
return(invkij);
}