public HessInfo GetSubHessInfo(IList <int> idxSele) { Dictionary <int, int> whole2sele = idxSele.HToDictionaryAsValueIndex(); Vector submass = (mass == null) ? null : mass.ToArray().HSelectByIndex(idxSele); object[] subatoms = (atoms == null) ? null : atoms.HSelectByIndex(idxSele); Vector[] subcoords = (coords == null) ? null : coords.HSelectByIndex(idxSele); int subsize = idxSele.Count; HessMatrix subhess = hess.Zeros(subsize * 3, subsize * 3); foreach (var bc_br_bval in hess.EnumBlocks()) { int bc = bc_br_bval.Item1; if (whole2sele.ContainsKey(bc) == false) { continue; } int nbc = whole2sele[bc]; int br = bc_br_bval.Item2; if (whole2sele.ContainsKey(br) == false) { continue; } int nbr = whole2sele[br]; var bval = bc_br_bval.Item3; subhess.SetBlock(nbc, nbr, bval.CloneT()); } return(new HessInfo { mass = submass, atoms = subatoms, coords = subcoords, hess = subhess, numZeroEigval = null, }); }
static void UpdateMassWeightedHess(HessMatrix hess, Vector mass) { if (hess.ColSize < 15000) { if (HDebug.Selftest()) { Matrix tmat0 = hess.ToArray(); UpdateMassWeightedHess(tmat0, mass); HessMatrix tmat1 = hess.CloneHess(); UpdateMassWeightedHess(tmat1, mass); double absmax = (tmat0 - tmat1).HAbsMax(); HDebug.Exception(absmax < 0.00000001); } } HDebug.Exception(mass.Size % 3 == 0); double[] mass03sqrt = new double[mass.Size / 3]; for (int i = 0; i < mass03sqrt.Length; i++) { HDebug.Exception(mass[i * 3 + 0] == mass[i * 3 + 1]); HDebug.Exception(mass[i * 3 + 0] == mass[i * 3 + 2]); mass03sqrt[i] = mass[i * 3 + 0]; } mass03sqrt = mass03sqrt.HSqrt(); foreach (var bc_br_bval in hess.EnumBlocks().ToArray()) { int bc = bc_br_bval.Item1; int br = bc_br_bval.Item2; var bval = bc_br_bval.Item3; bval = bval / (mass03sqrt[bc] * mass03sqrt[br]); hess.SetBlock(bc, br, bval); } }
public static bool HessMatrixSparseEqual(HessMatrix hess, HessMatrix equal) { if (hess.ColSize != equal.ColSize) { return(false); } if (hess.RowSize != equal.RowSize) { return(false); } foreach (var bc_br_bval in hess.EnumBlocks()) { int bc = bc_br_bval.Item1; int br = bc_br_bval.Item2; var bv = bc_br_bval.Item3; var bv0 = equal.GetBlock(bc, br); if (bv0 == null) { return(false); } if ((bv - bv0).HAbsMax() != 0) { return(false); } } foreach (var bc_br_bval in equal.EnumBlocks()) { int bc = bc_br_bval.Item1; int br = bc_br_bval.Item2; var bv = bc_br_bval.Item3; var bv0 = hess.GetBlock(bc, br); if (bv0 == null) { return(false); } if ((bv - bv0).HAbsMax() != 0) { return(false); } } return(true); }
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); }
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 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, }); }
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); }
public static HessInfoCoarseResiIter GetHessCoarseResiIter (Hess.HessInfo hessinfo , Vector[] coords , FuncGetIdxKeepListRemv GetIdxKeepListRemv , ILinAlg ila , double thres_zeroblk = 0.001 , IterOption iteropt = IterOption.Matlab_experimental , string[] options = null ) { bool rediag = true; HessMatrix H = null; List <int>[] lstNewIdxRemv = null; int numca = 0; double[] reMass = null; object[] reAtoms = null; Vector[] reCoords = null; Tuple <int[], int[][]> idxKeepRemv = null; //System.Console.WriteLine("begin re-indexing hess"); { object[] atoms = hessinfo.atoms; idxKeepRemv = GetIdxKeepListRemv(atoms, coords); int[] idxKeep = idxKeepRemv.Item1; int[][] idxsRemv = idxKeepRemv.Item2; { List <int> check = new List <int>(); check.AddRange(idxKeep); foreach (int[] idxRemv in idxsRemv) { check.AddRange(idxRemv); } check = check.HToHashSet().ToList(); if (check.Count != coords.Length) { throw new Exception("the re-index contains the duplicated atoms or the missing atoms"); } } List <int> idxs = new List <int>(); idxs.AddRange(idxKeep); foreach (int[] idxRemv in idxsRemv) { idxs.AddRange(idxRemv); } HDebug.Assert(idxs.Count == idxs.HToHashSet().Count); H = hessinfo.hess.ReshapeByAtom(idxs); numca = idxKeep.Length; reMass = hessinfo.mass.ToArray().HSelectByIndex(idxs); reAtoms = hessinfo.atoms.ToArray().HSelectByIndex(idxs); reCoords = coords.HSelectByIndex(idxs); int nidx = idxKeep.Length; lstNewIdxRemv = new List <int> [idxsRemv.Length]; for (int i = 0; i < idxsRemv.Length; i++) { lstNewIdxRemv[i] = new List <int>(); foreach (var idx in idxsRemv[i]) { lstNewIdxRemv[i].Add(nidx); nidx++; } } HDebug.Assert(nidx == lstNewIdxRemv.Last().Last() + 1); HDebug.Assert(nidx == idxs.Count); } GC.Collect(0); HDebug.Assert(numca == H.ColBlockSize - lstNewIdxRemv.HListCount().Sum()); //if(bool.Parse("false")) { if (bool.Parse("false")) #region { int[] idxKeep = idxKeepRemv.Item1; int[][] idxsRemv = idxKeepRemv.Item2; Pdb.Atom[] pdbatoms = hessinfo.atomsAsUniverseAtom.ListPdbAtoms(); Pdb.ToFile(@"C:\temp\coarse-keeps.pdb", pdbatoms.HSelectByIndex(idxKeep), false); if (HFile.Exists(@"C:\temp\coarse-graining.pdb")) { HFile.Delete(@"C:\temp\coarse-graining.pdb"); } foreach (int[] idxremv in idxsRemv.Reverse()) { List <Pdb.Element> delatoms = new List <Pdb.Element>(); foreach (int idx in idxremv) { if (pdbatoms[idx] == null) { continue; } string line = pdbatoms[idx].GetUpdatedLine(coords[idx]); Pdb.Atom delatom = Pdb.Atom.FromString(line); delatoms.Add(delatom); } Pdb.ToFile(@"C:\temp\coarse-graining.pdb", delatoms.ToArray(), true); } } #endregion if (bool.Parse("false")) #region { // export matrix to matlab, so the matrix can be checked in there. int[] idxca = HEnum.HEnumCount(numca).ToArray(); int[] idxoth = HEnum.HEnumFromTo(numca, coords.Length - 1).ToArray(); Matlab.Register(@"C:\temp\"); Matlab.PutSparseMatrix("H", H.GetMatrixSparse(), 3, 3); Matlab.Execute("figure; spy(H)"); Matlab.Clear(); } #endregion if (bool.Parse("false")) #region { HDirectory.CreateDirectory(@"K:\temp\$coarse-graining\"); { // export original hessian matrix List <int> cs = new List <int>(); List <int> rs = new List <int>(); foreach (ValueTuple <int, int, MatrixByArr> bc_br_bval in hessinfo.hess.EnumBlocks()) { cs.Add(bc_br_bval.Item1); rs.Add(bc_br_bval.Item2); } Matlab.Clear(); Matlab.PutVector("cs", cs.ToArray()); Matlab.PutVector("rs", rs.ToArray()); Matlab.Execute("hess = sparse(cs+1, rs+1, ones(size(cs)));"); Matlab.Execute("hess = float(hess);"); Matlab.Execute("figure; spy(hess)"); Matlab.Execute("cs = int32(cs+1);"); Matlab.Execute("rs = int32(rs+1);"); Matlab.Execute(@"save('K:\temp\$coarse-graining\hess-original.mat', 'cs', 'rs', '-v6');"); Matlab.Clear(); } { // export reshuffled hessian matrix List <int> cs = new List <int>(); List <int> rs = new List <int>(); foreach (ValueTuple <int, int, MatrixByArr> bc_br_bval in H.EnumBlocks()) { cs.Add(bc_br_bval.Item1); rs.Add(bc_br_bval.Item2); } Matlab.Clear(); Matlab.PutVector("cs", cs.ToArray()); Matlab.PutVector("rs", rs.ToArray()); Matlab.Execute("H = sparse(cs+1, rs+1, ones(size(cs)));"); Matlab.Execute("H = float(H);"); Matlab.Execute("figure; spy(H)"); Matlab.Execute("cs = int32(cs+1);"); Matlab.Execute("rs = int32(rs+1);"); Matlab.Execute(@"save('K:\temp\$coarse-graining\hess-reshuffled.mat', 'cs', 'rs', '-v6');"); Matlab.Clear(); } } #endregion if (bool.Parse("false")) #region { int[] idxca = HEnum.HEnumCount(numca).ToArray(); int[] idxoth = HEnum.HEnumFromTo(numca, coords.Length - 1).ToArray(); HessMatrix A = H.SubMatrixByAtoms(false, idxca, idxca); HessMatrix B = H.SubMatrixByAtoms(false, idxca, idxoth); HessMatrix C = H.SubMatrixByAtoms(false, idxoth, idxca); HessMatrix D = H.SubMatrixByAtoms(false, idxoth, idxoth); Matlab.Clear(); Matlab.PutSparseMatrix("A", A.GetMatrixSparse(), 3, 3); Matlab.PutSparseMatrix("B", B.GetMatrixSparse(), 3, 3); Matlab.PutSparseMatrix("C", C.GetMatrixSparse(), 3, 3); Matlab.PutSparseMatrix("D", D.GetMatrixSparse(), 3, 3); Matlab.Clear(); } #endregion } List <HessCoarseResiIterInfo> iterinfos = null; { object[] atoms = reAtoms; // reAtoms.HToType(null as Universe.Atom[]); CGetHessCoarseResiIterImpl info = null; switch (iteropt) { case IterOption.ILinAlg_20150329: info = GetHessCoarseResiIterImpl_ILinAlg_20150329(H, lstNewIdxRemv, thres_zeroblk, ila, false); break; case IterOption.ILinAlg: info = GetHessCoarseResiIterImpl_ILinAlg(H, lstNewIdxRemv, thres_zeroblk, ila, false); break; case IterOption.Matlab: info = GetHessCoarseResiIterImpl_Matlab(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break; case IterOption.Matlab_experimental: info = GetHessCoarseResiIterImpl_Matlab_experimental(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break; case IterOption.Matlab_IterLowerTri: info = GetHessCoarseResiIterImpl_Matlab_IterLowerTri(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break; case IterOption.LinAlg_IterLowerTri: info = GetHessCoarseResiIterImpl_LinAlg_IterLowerTri.Do(atoms, H, lstNewIdxRemv, thres_zeroblk, ila, false, options); break; } ; H = info.H; iterinfos = info.iterinfos; } //{ // var info = GetHessCoarseResiIterImpl_Matlab(H, lstNewIdxRemv, thres_zeroblk); // H = info.H; //} GC.Collect(0); if (HDebug.IsDebuggerAttached) { int nidx = 0; int[] ikeep = idxKeepRemv.Item1; foreach (int idx in ikeep) { bool equal = object.ReferenceEquals(hessinfo.atoms[idx], reAtoms[nidx]); if (equal == false) { HDebug.Assert(false); } HDebug.Assert(equal); nidx++; } } if (rediag) { H = H.CorrectHessDiag(); } //System.Console.WriteLine("finish fixing diag"); return(new HessInfoCoarseResiIter { hess = H, mass = reMass.HSelectCount(numca), atoms = reAtoms.HSelectCount(numca), coords = reCoords.HSelectCount(numca), numZeroEigval = 6, iterinfos = iterinfos, }); }
public static HessInfo GetHessSbNMA (Universe univ , IList <Vector> coords , double nbondMaxDist // =12 , double?maxAbsSpring , bool b_bonds , bool b_angles , bool b_impropers , bool b_dihedrals , bool b_nonbondeds , bool b_nonbonded14s , double?sca_bonds , double?sca_angles , double?sca_impropers , double?sca_dihedrals , double?sca_nonbondeds , double?sca_nonbonded14s , Action <Universe.Atom, Vector, Universe.Atom, Vector, double> collectorBond , Action <Universe.Atom, Vector, Universe.Atom, Vector, Universe.Atom, Vector, double, double> collectorAngle , Action <Universe.Atom, Vector, Universe.Atom, Vector, Universe.Atom, Vector, Universe.Atom, Vector, double, double> collectorImproper , Action <Universe.Atom, Vector, Universe.Atom, Vector, Universe.Atom, Vector, Universe.Atom, Vector, double, double> collectorDihedral , Action <Universe.Atom, Vector, Universe.Atom, Vector, double> collectorNonbonded , Action <Universe.Atom, Vector, Universe.Atom, Vector, double> collectorNonbonded14 , Func <HessSpr.CustomKijInfo, double> GetCustomKij = null , params string[] options ) { IEnumerable <Universe.Nonbonded> nonbondeds = null; IEnumerable <Universe.Nonbonded14> nonbonded14s = univ.nonbonded14s.GetEnumerable(); if (options.Contains("TIP3P: tetrahedral hydrogen bonds")) { nonbondeds = EnumNonbondeds(univ.atoms, coords, univ.size, nbondMaxDist, ListTip3pTetraHBond, options); } else if (options.Contains("TIP3P: near waters")) { nonbondeds = EnumNonbondeds(univ.atoms, coords, univ.size, nbondMaxDist, ListTip3pNears, options); } else { nonbondeds = EnumNonbondeds(univ.atoms, coords, univ.size, nbondMaxDist); } bool vdW = true; // use vdW bool elec = false; // ignore electrostatic double D = double.PositiveInfinity; // dielectric constant for Tinker is "1" bool ignNegSpr = true; // ignore negative spring (do not add the spring into hessian matrix) double?K_r = null; // null for sbNMA, and 340.00 for ssNMA double?K_theta = null; // null for sbNMA, and 45.00 for ssNMA double?K_ub = null; // null for sbNMA, and 10.00 for ssNMA double?K_psi = null; // null for sbNMA, and 70.00 for ssNMA double?K_chi = null; // null for sbNMA, and 1.00 for ssNMA double?n = null; // null for sbNMA, and 1 for ssNMA string K_nbnd = null; // null for sbNMA, and "Unif" for ssNMA if (options.Contains("TIP3P: (vdW+elec) for OH,OO,HH")) { K_nbnd = "TIP3P: (vdW+elec) for OH,OO,HH"; } if (options.Contains("TIP3P: (vdW+elec) for OH")) { K_nbnd = "TIP3P: (vdW+elec) for OH"; } if (options.Contains("vdW:L79")) { K_nbnd = "L79"; } if (options.Contains("vdW:UnifSgn")) { K_nbnd = "UnifSgn"; } if (options.Contains("K_chi:1")) { K_chi = 1; } HessMatrix hess = null; if (b_bonds) { hess = STeM.GetHessBond(coords, univ.bonds, K_r: K_r, hessian: hess, collector: collectorBond); } if (b_angles) { hess = STeM.GetHessAngle(coords, univ.angles, true, K_theta: K_theta, K_ub: K_ub, hessian: hess, collector: collectorAngle); } if (b_impropers) { hess = STeM.GetHessImproper(coords, univ.impropers, K_psi: K_psi, hessian: hess, useArnaud96: true, collector: collectorImproper); } if (b_dihedrals) { hess = STeM.GetHessDihedral(coords, univ.dihedrals, K_chi: K_chi, n: n, hessian: hess, useAbsSpr: true, useArnaud96: true, collector: collectorDihedral); } if (b_nonbondeds) { hess = HessSpr.GetHessNonbond(coords, nonbondeds, D, K_nbnd: K_nbnd, hessian: hess, vdW: vdW, elec: elec, ignNegSpr: ignNegSpr, maxAbsSpring: maxAbsSpring, collector: collectorNonbonded, GetCustomKij: GetCustomKij); } if (b_nonbonded14s) { hess = HessSpr.GetHessNonbond(coords, nonbonded14s, D, K_nbnd: K_nbnd, hessian: hess, vdW: vdW, elec: elec, ignNegSpr: ignNegSpr, maxAbsSpring: maxAbsSpring, collector: collectorNonbonded14, GetCustomKij: GetCustomKij); } if (sca_bonds != null) { if (sca_bonds.Value != 1) { hess += (sca_bonds.Value - 1) * STeM.GetHessBond(coords, univ.bonds, K_r: K_r, hessian: null); } } if (sca_angles != null) { if (sca_angles.Value != 1) { hess += (sca_angles.Value - 1) * STeM.GetHessAngle(coords, univ.angles, true, K_theta: K_theta, K_ub: K_ub, hessian: null); } } if (sca_impropers != null) { if (sca_impropers.Value != 1) { hess += (sca_impropers.Value - 1) * STeM.GetHessImproper(coords, univ.impropers, K_psi: K_psi, hessian: null, useArnaud96: true); } } if (sca_dihedrals != null) { if (sca_dihedrals.Value != 1) { hess += (sca_dihedrals.Value - 1) * STeM.GetHessDihedral(coords, univ.dihedrals, K_chi: K_chi, n: n, hessian: null, useAbsSpr: true, useArnaud96: true); } } if (sca_nonbondeds != null) { if (sca_nonbondeds.Value != 1) { hess += (sca_nonbondeds.Value - 1) * HessSpr.GetHessNonbond(coords, nonbondeds, D, K_nbnd: K_nbnd, hessian: null, vdW: vdW, elec: elec, ignNegSpr: ignNegSpr, maxAbsSpring: maxAbsSpring); } } if (sca_nonbonded14s != null) { if (sca_nonbonded14s.Value != 1) { hess += (sca_nonbonded14s.Value - 1) * HessSpr.GetHessNonbond(coords, nonbonded14s, D, K_nbnd: K_nbnd, hessian: null, vdW: vdW, elec: elec, ignNegSpr: ignNegSpr, maxAbsSpring: maxAbsSpring); } } //Hess.UpdateHessNaN(hess, coords); { foreach (var bc_br_bval in hess.EnumBlocks()) { int bc = bc_br_bval.Item1; int br = bc_br_bval.Item2; var bval = bc_br_bval.Item3; if (coords[bc] == null) { throw new HException("have hess block for null-coord"); } if (coords[br] == null) { throw new HException("have hess block for null-coord"); } if (bval == null) { throw new HException(); } for (int c = 0; c < bval.ColSize; c++) { for (int r = 0; r < bval.RowSize; r++) { double val = bval[c, r]; if (double.IsNaN(val)) { throw new HException("hess has nan element"); } if (double.IsPositiveInfinity(val)) { throw new HException("hess has pos-inf element"); } if (double.IsNegativeInfinity(val)) { throw new HException("hess has neg-inf element"); } } } } } return(new HessInfo { hess = hess, mass = univ.GetMasses(), atoms = univ.atoms.ToArray(), coords = coords.HCloneVectors().ToArray(), numZeroEigval = 6, }); }
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); }
public static double GetSprScalar(Vector[] coords, HessMatrix hess, int atm1, int atm2, IList <int> atms, ILinAlg ila) { HDebug.Assert(atms.Count == atms.HUnion().Length); int[] idxs = atms.HUnion(); idxs = idxs.HRemoveAll(atm1); idxs = idxs.HRemoveAll(atm2); idxs = idxs.HInsert(0, atm2); idxs = idxs.HInsert(0, atm1); HDebug.Assert(idxs.HExcept(atms).HExcept(atm1, atm2).Length == 0); HDebug.Assert(idxs[0] == atm1); HDebug.Assert(idxs[1] == atm2); HessMatrix H = hess.ReshapeByAtom(idxs); H = Hess.GetHessFixDiag(H); HDebug.Assert(H.ColSize == H.RowSize, H.RowSize == idxs.Length * 3); // H should have 6 zero eigenvalues !! // since it is the original hessian matrix. // return "0" spring if there is no connect between atm1 and atm2 { Graph <int, object> g = new Graph <int, object>(); for (int i = 0; i < H.ColBlockSize; i++) { g.AddNode(i); } foreach (var bc_br_bval in H.EnumBlocks()) { int bc = bc_br_bval.Item1; int br = bc_br_bval.Item2; if (bc > br) { continue; } g.AddEdge(bc, br, new object()); //g.AddEdge(br, bc, new object()); // g is bi-directional graph } var paths = g.FindPathShortest(g.GetNode(0), new Graph <int, object> .Node[] { g.GetNode(1) }); if (paths == null) { // if there is no path between 0 <-> 1, then there is no spring return(0); } } Vector u12 = (coords[atm2] - coords[atm1]).UnitVector(); Matrix S12 = new double[idxs.Length * 3, 1]; S12[0, 0] = u12[0]; S12[1, 0] = u12[1]; S12[2, 0] = u12[2]; S12[3, 0] = -u12[0]; S12[4, 0] = -u12[1]; S12[5, 0] = -u12[2]; Matrix invkij = GetInvSprTensorSymm(H, S12, ila); HDebug.Assert(invkij.ColSize == 1, invkij.RowSize == 1); HDebug.Assert(invkij[0, 0] > 0); double kij = 1 / invkij[0, 0]; return(kij); }
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 )); }