private static HessMatrix Get_BInvDC
(HessMatrix A
, HessMatrix C
, HessMatrix D
, bool process_disp_console
, string[] options
, 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 }
});
}
}
HessMatrixSparse 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 (process_disp_console)
{
System.Console.Write("Y");
}
//Matlab.Execute("[i,j,s] = find(sparse(BinvDC));");
//int[] listi = Matlab.GetVectorInt("i");
//int[] listj = Matlab.GetVectorInt("j");
//double[] lists = Matlab.GetVector("s");
//int colsize = Matlab.GetValueInt("size(BinvDC,1)");
//int rowsize = Matlab.GetValueInt("size(BinvDC,2)");
//Matrix BBinvDDCC = Matrix.Zeros(colsize, rowsize);
//for(int i=0; i<listi.Length; i++)
// BBinvDDCC[listi[i], listj[i]] = lists[i];
//GC.Collect(0);
BB_invDD_CC = HessMatrixSparse.FromMatrix(BBinvDDCC, parallel); if (process_disp_console)
{
System.Console.Write("Z), ");
}
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);
}
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
)
{
if (options == null)
{
options = new string[0];
}
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 = C.Zeros(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.Contains("pinv(D)"))
{
Matlab.Execute("BinvDC = C' * pinv(D) * C;");
}
if (options.Contains("/D -> pinv(D)"))
{
string msg = Matlab.Execute("BinvDC = (C' / D) * C;", true);
if (msg != "")
{
Matlab.Execute("BinvDC = C' * pinv(D) * C;");
}
}
else if (options.Contains("/D"))
{
Matlab.Execute("BinvDC = (C' / D) * C;");
}
else
{
Matlab.Execute("BinvDC = (C' / D) * C;");
}
}
if (process_disp_console)
{
System.Console.Write("X");
}
//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 || HDebug.True)
{
Func <int, int, HessMatrix> Zeros = delegate(int colsize, int rowsize)
{
return(HessMatrixDense.ZerosDense(colsize, rowsize));
};
BB_invDD_CC = Matlab.GetMatrix("BinvDC", Zeros, true);
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 = D.Zeros(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 = A.Zeros(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.SetBlockLock(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);
}
private static ValueTuple <HessMatrix, Vector> Get_BInvDC_BInvDG_WithSqueeze
(HessMatrix C
, HessMatrix D
, Vector G
, bool process_disp_console
, string[] options
, double?thld_BinvDC // =null
, bool parallel // =false
)
{
if (options == null)
{
options = new string[0];
}
HessMatrix B_invD_C;
Vector B_invD_G;
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 = C.Zeros(C.ColSize, Cbr_CCbr.Count * 3);
{
Action <ValueTuple <int, int, MatrixByArr>, HessMatrix, Dictionary <int, int> > func =
delegate(ValueTuple <int, int, MatrixByArr> bc_br_bval, HessMatrix _CC, Dictionary <int, int> _Cbr_CCbr)
{
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)
{
HParallel.ForEach(C.EnumBlocks(), func, CC, Cbr_CCbr);
}
else
{
foreach (var bc_br_bval in C.EnumBlocks())
{
func(bc_br_bval, CC, Cbr_CCbr);
}
}
}
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;
Vector BB_invDD_GG;
{
var BBInvDDCC_BBInvDDGG = Get_BInvDC_BInvDG(CC, D, G, process_disp_console, options, thld_BinvDC, parallel);
BB_invDD_CC = BBInvDDCC_BBInvDDGG.Item1;
BB_invDD_GG = BBInvDDCC_BBInvDDGG.Item2;
}
B_invD_C = C.Zeros(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>, HessMatrix, List <int> > func =
delegate(ValueTuple <int, int, MatrixByArr> bcc_brr_bval, HessMatrix _B_invD_C, List <int> _CCbr_Cbr)
{
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.SetBlockLock(bc, br, bval);
};
if (parallel)
{
HParallel.ForEach(BB_invDD_CC.EnumBlocks(), func, B_invD_C, CCbr_Cbr);
}
else
{
foreach (var bcc_brr_bval in BB_invDD_CC.EnumBlocks())
{
func(bcc_brr_bval, B_invD_C, CCbr_Cbr);
}
}
}
B_invD_G = new double[C.RowSize];
{
HDebug.Assert(BB_invDD_GG.Size % 3 == 0);
/////////////////////////////////////////////////////////////////////////////////////
// Double Check Later
if (CCbr_Cbr.Count == 0)
{
// this is the case that a molecule is isolated.
//HDebug.Assert(B_invD_C.NumUsedBlocks == 0);
//HDebug.Assert(B_invD_G.Dist2 == 0);
}
for (int bii = 0; bii < CCbr_Cbr.Count; bii++)
//for(int bii=0; bii<BB_invDD_GG.Size/3; bii++)
/////////////////////////////////////////////////////////////////////////////////////
{
int bi = CCbr_Cbr[bii];
B_invD_G[bi * 3 + 0] = BB_invDD_GG[bii * 3 + 0];
B_invD_G[bi * 3 + 1] = BB_invDD_GG[bii * 3 + 1];
B_invD_G[bi * 3 + 2] = BB_invDD_GG[bii * 3 + 2];
}
}
}
GC.Collect(0);
return(new ValueTuple <HessMatrix, Vector>
(B_invD_C
, B_invD_G
));
}
