public static void SelfTest()
{
if (HDebug.Selftest() == false)
{
return;
}
string temppath = @"K:\temp\";
string tinkerpath_testgrad = "\"" + @"C:\Program Files\Tinker\bin-win64-8.2.1\testgrad.exe" + "\"";
string tinkerpath_testhess = "\"" + @"C:\Program Files\Tinker\bin-win64-8.2.1\testhess.exe" + "\"";
var xyz = Tinker.Xyz.FromLines(SelftestData.lines_1L2Y_xyz);
var prm = Tinker.Prm.FromLines(SelftestData.lines_charmm22_prm);
var univ = Universe.Build(xyz, prm);
var testhess = Tinker.Run.Testhess(tinkerpath_testhess, xyz, prm, temppath
, HessMatrixZeros: HessMatrixLayeredArray.ZerosHessMatrixLayeredArray
);
var testgrad = Tinker.Run.Testgrad(tinkerpath_testgrad, xyz, prm, temppath);
var hessinfo = Hess.HessInfo.FromTinker(xyz, prm, testhess.hess);
var hessforcinfo = HessForc.Coarse.HessForcInfo.From(hessinfo);
hessforcinfo.forc = testgrad.anlyts.GetForces(xyz.atoms);
var coarseinfo_debug = HessForc.Coarse.GetCoarseHessForc
(hessforcinfo
, coords: hessinfo.coords
, GetIdxKeepListRemv: GetIdxKeepListRemv
, ila: null
, thres_zeroblk: double.Epsilon
, options: new string[] { "Debug" }
);
var coarseinfo_simple = HessForc.Coarse.GetCoarseHessForc
(hessforcinfo
, coords: hessinfo.coords
, GetIdxKeepListRemv: GetIdxKeepListRemv
, ila: null
, thres_zeroblk: double.Epsilon
, options: new string[] { "SubSimple" }
);
double absmax_simple = (coarseinfo_debug.hess - coarseinfo_simple.hess).HAbsMax();
HDebug.Assert(Math.Abs(absmax_simple) < 0.00000001);
double absmax_simple_forc = (coarseinfo_debug.forc.ToVector() - coarseinfo_simple.forc.ToVector()).ToArray().MaxAbs();
HDebug.Assert(Math.Abs(absmax_simple_forc) < 0.00000001);
var coarseinfo_1iter = HessForc.Coarse.GetCoarseHessForc
(hessforcinfo
, coords: hessinfo.coords
, GetIdxKeepListRemv: GetIdxKeepListRemv
, ila: null
, thres_zeroblk: double.Epsilon
, options: new string[] { "OneIter" }
);
double absmax_1iter = (coarseinfo_debug.hess - coarseinfo_1iter.hess).HAbsMax();
HDebug.Assert(Math.Abs(absmax_1iter) < 0.00000001);
double absmax_1iter_forc = (coarseinfo_debug.forc.ToVector() - coarseinfo_1iter.forc.ToVector()).ToArray().MaxAbs();
HDebug.Assert(Math.Abs(absmax_1iter_forc) < 0.00000001);
var coarseinfo_iter = HessForc.Coarse.GetCoarseHessForc
(hessforcinfo
, coords: hessinfo.coords
, GetIdxKeepListRemv: GetIdxKeepListRemv
, ila: null
, thres_zeroblk: double.Epsilon
, options: null
);
double absmax_iter = (coarseinfo_debug.hess - coarseinfo_iter.hess).HAbsMax();
HDebug.Assert(Math.Abs(absmax_iter) < 0.00000001);
double absmax_iter_forc = (coarseinfo_debug.forc.ToVector() - coarseinfo_iter.forc.ToVector()).ToArray().MaxAbs();
HDebug.Assert(Math.Abs(absmax_iter_forc) < 0.00000001);
double tolerance = 1.0E-6; // 0.00001;
var coarseinfo_1iter_tolerant = HessForc.Coarse.GetCoarseHessForc
(hessforcinfo
, coords: hessinfo.coords
, GetIdxKeepListRemv: GetIdxKeepListRemv
, ila: null
, thres_zeroblk: tolerance
, options: new string[] { "OneIter" }
);
double absmax_1iter_tolerant = (coarseinfo_debug.hess - coarseinfo_1iter_tolerant.hess).HAbsMax();
HDebug.Assert(Math.Abs(absmax_1iter_tolerant) < tolerance * 10);
double absmax_1iter_tolerant_forc = (coarseinfo_debug.forc.ToVector() - coarseinfo_1iter_tolerant.forc.ToVector()).ToArray().MaxAbs();
HDebug.Assert(Math.Abs(absmax_1iter_tolerant_forc) < tolerance * 10);
var coarseinfo_iter_tolerant = HessForc.Coarse.GetCoarseHessForc
(hessforcinfo
, coords: hessinfo.coords
, GetIdxKeepListRemv: GetIdxKeepListRemv
, ila: null
, thres_zeroblk: tolerance
, options: null
);
double absmax_iter_tolerant = (coarseinfo_debug.hess - coarseinfo_iter_tolerant.hess).HAbsMax();
HDebug.Assert(Math.Abs(absmax_iter_tolerant) < tolerance * 10);
double absmax_iter_tolerant_forc = (coarseinfo_debug.forc.ToVector() - coarseinfo_iter_tolerant.forc.ToVector()).ToArray().MaxAbs();
HDebug.Assert(Math.Abs(absmax_iter_tolerant_forc) < tolerance * 10);
string tempfilepath = HFile.GetTempPath(temppath, "test_serialzation_CoarseHessForc.dat");
HSerialize.Serialize(tempfilepath, null, coarseinfo_iter_tolerant);
var coarseinfo_iter_tolerant2 = HSerialize.Deserialize <HessForcInfo>(tempfilepath, null);
double absmax_iter_tolerant_file = (coarseinfo_iter_tolerant.hess - coarseinfo_iter_tolerant.hess).HAbsMax();
HDebug.Assert(Math.Abs(absmax_iter_tolerant_file) == 0);
double absmax_iter_tolerant_file_forc = (coarseinfo_iter_tolerant.forc.ToVector() - coarseinfo_iter_tolerant.forc.ToVector()).ToArray().MaxAbs();
HDebug.Assert(Math.Abs(absmax_iter_tolerant_file_forc) == 0);
HFile.Delete(tempfilepath);
}
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 void SavePse(string psepath
, bool cartoon
, bool line
, string pngpath // null if not save png
, params string[] pdbpaths)
{
string currpath = HEnvironment.CurrentDirectory;
HEnvironment.CurrentDirectory = HFile.GetFileInfo(psepath).Directory.FullName;
{
Random rand = new Random();
string psename = HFile.GetFileInfo(psepath).Name;
int count = pdbpaths.Length;
string[] pdblnames = new string[count];
string[] pdblpaths = new string[count];
for (int i = 0; i < count; i++)
{
var info = HFile.GetFileInfo(pdbpaths[i]);
pdblnames[i] = info.Name.Replace(".pdb", "").Replace(".PDB", "");
pdblpaths[i] = psepath + info.Name + rand.NextInt(99999).ToString(".rnd00000") + ".pdb";
HFile.Copy(pdbpaths[i], pdblpaths[i]);
}
string pmlpath = psepath + rand.NextInt(99999).ToString(".rnd00000") + ".pml";
List <string> pmltext = new List <string>();
for (int i = 0; i < count; i++)
{
pmltext.Add("load $$path$$, $$name$$;".Replace("$$path$$", pdblpaths[i]).Replace("$$name$$", pdblnames[i]));
}
if (cartoon)
{
pmltext.Add("show cartoon;");
}
else
{
pmltext.Add("hide cartoon");
}
if (line)
{
pmltext.Add("show lines;");
}
else
{
pmltext.Add("hide lines");
}
pmltext.Add("reset;");
pmltext.Add("save $$psepath$$;".Replace("$$psepath$$", psepath));
if (pngpath != null)
{
pmltext.Add("png $$pngpath$$;".Replace("$$pngpath$$", pngpath));
}
pmltext.Add("quit;");
HFile.WriteAllLines(pmlpath, pmltext);
System.Diagnostics.Process pymol;
pymol = System.Diagnostics.Process.Start(@"C:\Program Files (x86)\PyMOL\PyMOL\PymolWin.exe", pmlpath);
pymol.WaitForExit();
for (int i = 0; i < count; i++)
{
HFile.Delete(pdblpaths[i]);
}
HFile.Delete(pmlpath);
}
HEnvironment.CurrentDirectory = currpath;
}
