private static IEnumerable <ValueTuple <int, int, MatrixByArr, MatrixByArr> > EnumComput
(MatrixByArr D
, List <int> C_lstbr
, List <MatrixByArr> C_lstbval
, double threshold
)
{
MatrixByArr invDD = LinAlg.Inv3x3(D);
HDebug.Assert(invDD.IsComputable());
HDebug.Assert(invDD != null);
List <MatrixByArr> C_lstbval_tr = new List <MatrixByArr>();
List <double> C_lstbval_absmax = new List <double>();
for (int i = 0; i < C_lstbval.Count; i++)
{
C_lstbval_tr.Add(C_lstbval[i].Tr());
C_lstbval_absmax.Add(C_lstbval[i].HAbsMax());
}
for (int c = 0; c < C_lstbr.Count; c++)
{
int bc = C_lstbr[c];
MatrixByArr CC = C_lstbval[c];
MatrixByArr invDD_CC = invDD * CC;
double invDD_CC_absmax = invDD_CC.HAbsMax();
for (int r = 0; r < C_lstbr.Count; r++)
{
int br = C_lstbr[r];
if (bc < br)
{
// upper-triangle
continue;
}
//double BB_absmax = C_lstbval_absmax[r];
//if(BB_absmax*invDD_CC_absmax < threshold)
// continue;
MatrixByArr BB = C_lstbval_tr[r];
yield return
(new ValueTuple <int, int, MatrixByArr, MatrixByArr>
(bc
, br
, invDD_CC
, BB
));
}
}
}
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 CGetHessCoarseResiIterImpl GetHessCoarseResiIterImpl_Matlab_experimental
(object[] atoms
, HessMatrix H
, List <int>[] lstNewIdxRemv
, double thres_zeroblk
, ILinAlg ila
, bool cloneH
, string[] options
)
{
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;
GC.Collect(0);
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--)
{
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, D;
/// HessMatrix C = H.SubMatrixByAtoms(false, idxremv, idxkeep, parallel:parallel);
/// 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);
int iremv_min = iremv.Min();
int iremv_max = iremv.Max();
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 (bc > iremv_max)
{
continue;
}
if (br > iremv_max)
{
continue;
}
if (br < iremv_min)
{
int nc = bc - iremv_min;
int nr = br;
C.SetBlock(nc, nr, bval.CloneT());
}
else
{
int nc = bc - iremv_min;
int nr = br - iremv_min;
D.SetBlock(nc, nr, bval.CloneT());
}
}
}
if (process_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);
}
// make B,C sparse
//int B_cntzero = B.MakeNearZeroBlockAsZero(thres_zeroblk);
C_density0 = C.RatioUsedBlocks;
/// iterinfo.numSetZeroBlock = C.MakeNearZeroBlockAsZero(thres_zeroblk);
{
double thres_absmax = thres_zeroblk;
List <Tuple <int, int> > lstIdxToMakeZero = new List <Tuple <int, int> >();
foreach (var bc_br_bval in C.EnumBlocks())
{
int bc = bc_br_bval.Item1;
int br = bc_br_bval.Item2;
var bval = bc_br_bval.Item3;
double absmax_bval = bval.HAbsMax();
if (absmax_bval < thres_absmax)
{
lstIdxToMakeZero.Add(new Tuple <int, int>(bc, br));
}
}
foreach (var bc_br in lstIdxToMakeZero)
{
int cc = bc_br.Item1;
int cr = bc_br.Item2;
var Cval = C.GetBlock(cc, cr);
C.SetBlock(cc, cr, null);
var Dval = D.GetBlock(cc, cc); // nCval = Cval -Cval
D.SetBlock(cc, cc, Dval + Cval); // nDval = Dval - (-Cval) = Dval + Cval
int bc = cr;
int br = cc;
var Bval = Cval.Tr();
var Aval = A.GetBlock(bc, bc); // nBval = Bval -Bval
A.SetBlock(bc, bc, Aval + Bval); // nAval = Aval - (-Bval) = Aval + Bval
}
iterinfo.numSetZeroBlock = lstIdxToMakeZero.Count;
}
//int B_nzeros = B.NumUsedBlocks; double B_nzeros_ = Math.Sqrt(B_nzeros);
iterinfo.numNonZeroBlock = C.NumUsedBlocks;
C_density1 = C.RatioUsedBlocks;
HessMatrix B_invD_C = Get_BInvDC(A, C, D, process_disp_console
, options
, parallel: parallel
);
if (process_disp_console)
{
process_time[4] = DateTime.UtcNow;
System.Console.Write("B.invD.C({0:00.00} min), ", (process_time[4] - process_time[3]).TotalMinutes);
}
/// 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 = 0;
int count_ignored = 0;
foreach (var bc_br_bval in other.EnumBlocks())
{
count++;
int bc = bc_br_bval.Item1;
int br = bc_br_bval.Item2;
MatrixByArr other_bmat = bc_br_bval.Item3;
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.SetBlock(bc, bc, new_diag);
other_bmat = null;
count_ignored++;
}
if (other_bmat != null)
{
MatrixByArr this_bmat = _this.GetBlock(bc, br);
MatrixByArr new_bmat = this_bmat - other_bmat;
_this.SetBlock(bc, br, new_bmat);
}
}
iterinfo.numAddIgnrBlock = count_ignored;
}
//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 int UpdateAdd(HessMatrix other, double mul_other, IList <int> idxOther, double thres_NearZeroBlock, bool parallel = false)
{
Matrix debug_updateadd = null;
if (UpdateAdd_SelfTest && idxOther == null && thres_NearZeroBlock == 0)
{
if ((100 < ColBlockSize) && (ColBlockSize < 1000) &&
(100 < RowBlockSize) && (RowBlockSize < 1000) &&
(other.NumUsedBlocks > 20))
{
UpdateAdd_SelfTest = false;
debug_updateadd = this.ToArray();
debug_updateadd.UpdateAdd(other, mul_other);
}
}
int[] idx_other;
if (idxOther == null)
{
//HDebug.Exception(ColSize == other.ColSize);
//HDebug.Exception(RowSize == other.RowSize);
idx_other = HEnum.HEnumCount(other.ColSize).ToArray();
}
else
{
idx_other = idxOther.ToArray();
}
int count = 0;
int count_ignored = 0;
object _lock = new object();
object _lock_ignored = new object();
Action <ValueTuple <int, int, MatrixByArr> > func = delegate(ValueTuple <int, int, MatrixByArr> bc_br_bval)
{
count++;
int other_bc = bc_br_bval.Item1;
int other_br = bc_br_bval.Item2;
MatrixByArr other_bmat = bc_br_bval.Item3;
if (other_bmat.HAbsMax() <= thres_NearZeroBlock)
{
lock (_lock_ignored)
count_ignored++;
//continue;
return;
}
int bc = idx_other[other_bc];
int br = idx_other[other_br];
lock (_lock)
{
MatrixByArr this_bmat = GetBlock(bc, br);
MatrixByArr new_bmat;
if (this_bmat == null)
{
if (other_bmat == null)
{
new_bmat = null;
}
else
{
new_bmat = mul_other * other_bmat;
}
}
else
{
if (other_bmat == null)
{
new_bmat = this_bmat.CloneT();
}
else
{
new_bmat = this_bmat + mul_other * other_bmat;
}
}
SetBlock(bc, br, new_bmat);
}
};
if (parallel)
{
Parallel.ForEach(other.EnumBlocks(), func);
}
else
{
foreach (var bc_br_bval in other.EnumBlocks())
{
func(bc_br_bval);
}
}
if (debug_updateadd != null)
{
Matrix debug_diff = debug_updateadd - this;
double debug_absmax = debug_diff.HAbsMax();
HDebug.AssertToleranceMatrix(0, debug_diff);
}
return(count_ignored);
}