public static void SelectCommonAtoms <Atom>(ref List <Atom> atoms1, ref List <Atom> atoms2)
where Atom : IAtom
{
List <Atom> _atoms1 = new List <Atom>(atoms1);
List <Atom> _atoms2 = new List <Atom>(atoms2);
_atoms1 = _atoms1.ListCommon(_atoms2);
HPack <List <int> > idxAtom2ToAtom1 = new HPack <List <int> >();
//{
// List<Atom> cas1 = _atoms1.SelectByName("CA");
// List<Atom> cas2 = _atoms2.SelectByName("CA");
// List<int> idx1 = new List<int>();
// List<int> idx2 = new List<int>();
// LCS.LongestCommonSubsequence( cas1 , cas2 , idx1, idx2, Atom.CompareNameResName);
// cas1 = cas1.SelectByIndex(idx1);
// cas2 = cas2.SelectByIndex(idx2);
//}
_atoms2 = _atoms2.ListCommon(_atoms1, idxAtom2ToAtom1);
_atoms1 = _atoms1.HSelectByIndex(idxAtom2ToAtom1.value).ToList();
if (HDebug.IsDebuggerAttached)
{
HDebug.AssertAllEquals(_atoms1.Count, _atoms2.Count);
for (int i = 0; i < _atoms1.Count; i++)
{
HDebug.AssertAllEquals(_atoms1[i].name.Trim(), _atoms2[i].name.Trim());
HDebug.AssertAllEquals(_atoms1[i].resName.Trim(), _atoms1[i].resName.Trim());
HDebug.AssertAllEquals(_atoms1[i].resSeq, _atoms1[i].resSeq);
}
}
atoms1 = _atoms1;
atoms2 = _atoms2;
}
public static void Align(IList <Vector> C1
, IList <Anisou> anisou1
, ref List <Vector> C2
, HPack <List <Vector> > optMoveC2 = null
, HPack <Trans3> outTrans = null
, HPack <double> optEnergy = null
)
{
Trans3 trans = GetTrans(C1, anisou1, C2, optEnergy: optEnergy);
Vector[] nC2 = trans.GetTransformed(C2).ToArray();
if (optMoveC2 != null)
{
optMoveC2.value = new List <Vector>(nC2.Length);
for (int i = 0; i < nC2.Length; i++)
{
optMoveC2.value.Add(nC2[i] - C2[i]);
}
}
if (outTrans != null)
{
outTrans.value = trans;
}
C2 = new List <Vector>(nC2);
}
public static void Align(IList <Vector> C1
, IList <Anisou> anisou1
, ref IList <Vector> C2
, ref IList <Anisou> anisou2
, HPack <Trans3> outTrans = null
, HPack <double> optEnergy = null
)
{
Trans3 trans = GetTrans(C1, anisou1, C2, anisou2, optEnergy: optEnergy);
C2 = new List <Vector>(C2);
anisou2 = new List <Anisou>(anisou2);
Vector[] nC2 = trans.GetTransformed(C2).ToArray();
for (int i = 0; i < C2.Count; i++)
{
Vector p2i = C2[i];
Anisou a2i = anisou2[i];
Vector np2i = trans.DoTransform(p2i);
Anisou na2i = a2i.Clone();
na2i.eigvecs[0] = (trans.DoTransform(p2i + a2i.eigvecs[0]) - np2i).UnitVector();
na2i.eigvecs[1] = (trans.DoTransform(p2i + a2i.eigvecs[1]) - np2i).UnitVector();
na2i.eigvecs[2] = (trans.DoTransform(p2i + a2i.eigvecs[2]) - np2i).UnitVector();
C2[i] = np2i;
anisou2[i] = na2i;
}
if (outTrans != null)
{
outTrans.value = trans;
}
}
public static void Align(IList <Vector> C1
, ref List <Vector> C2
, HPack <List <Vector> > optMoveC2 = null
, HPack <Trans3> outTrans = null
, HPack <double> optRmsd = null
)
{
Trans3 trans = GetTrans(C1, C2);
Vector[] nC2 = trans.GetTransformed(C2).ToArray();
if (optMoveC2 != null)
{
optMoveC2.value = new List <Vector>(nC2.Length);
for (int i = 0; i < nC2.Length; i++)
{
optMoveC2.value[i] = nC2[i] - C2[i];
}
}
if (optRmsd != null)
{
optRmsd.value = 0;
for (int i = 0; i < nC2.Length; i++)
{
optRmsd.value += (nC2[i] - C1[i]).Dist2;
}
optRmsd.value /= nC2.Length;
}
C2 = new List <Vector>(nC2);
if (outTrans != null)
{
outTrans.value = trans.Clone();
}
}
public static List <Atom> ListCommon <Atom>(this IList <Atom> atoms, IList <Atom> atomsToCompare
, HPack <List <int> > outAtomIdx = null // index for the returned list
)
where Atom : IAtom
{
List <Atom> list = new List <Atom>();
if (outAtomIdx != null)
{
outAtomIdx.value = new List <int>();
}
foreach (Atom atom in atoms)
{
int idx = atomsToCompare.IndexOfAtom(atom.name, atom.resSeq);
if (idx == -1)
{
continue;
}
list.Add(atom);
if (outAtomIdx != null)
{
outAtomIdx.value.Add(idx);
}
}
return(list);
}
public static void SelectCommonAtoms <Atom>(ref List <Atom> atoms1, ref List <Atom> atoms2, ref List <Atom> atoms3, ref List <Atom> atoms4, ref List <Atom> atoms5)
where Atom : IAtom
{
List <Atom> _atoms1 = new List <Atom>(atoms1);
List <Atom> _atoms2 = new List <Atom>(atoms2);
List <Atom> _atoms3 = new List <Atom>(atoms3);
List <Atom> _atoms4 = new List <Atom>(atoms4);
List <Atom> _atoms5 = new List <Atom>(atoms5);
_atoms1 = _atoms1.ListCommon(_atoms2);
_atoms1 = _atoms1.ListCommon(_atoms3);
_atoms1 = _atoms1.ListCommon(_atoms4);
_atoms1 = _atoms1.ListCommon(_atoms5);
HPack <List <int> > idxAtom2ToAtom1 = new HPack <List <int> >();
_atoms2 = _atoms2.ListCommon(_atoms1, idxAtom2ToAtom1);
_atoms2 = _atoms2.HSelectByIndex(idxAtom2ToAtom1.value).ToList();
HPack <List <int> > idxAtom3ToAtom1 = new HPack <List <int> >();
_atoms3 = _atoms3.ListCommon(_atoms1, idxAtom3ToAtom1);
_atoms3 = _atoms3.HSelectByIndex(idxAtom3ToAtom1.value).ToList();
HPack <List <int> > idxAtom4ToAtom1 = new HPack <List <int> >();
_atoms4 = _atoms4.ListCommon(_atoms1, idxAtom4ToAtom1);
_atoms4 = _atoms4.HSelectByIndex(idxAtom4ToAtom1.value).ToList();
HPack <List <int> > idxAtom5ToAtom1 = new HPack <List <int> >();
_atoms5 = _atoms5.ListCommon(_atoms1, idxAtom5ToAtom1);
_atoms5 = _atoms5.HSelectByIndex(idxAtom5ToAtom1.value).ToList();
if (HDebug.IsDebuggerAttached)
{
HDebug.AssertAllEquals(_atoms1.Count, _atoms2.Count, _atoms3.Count, _atoms4.Count, _atoms5.Count);
for (int i = 0; i < _atoms1.Count; i++)
{
HDebug.AssertAllEquals(_atoms1[i].name, _atoms2[i].name, _atoms3[i].name, _atoms4[i].name, _atoms5[i].name);
HDebug.AssertAllEquals(_atoms1[i].resName, _atoms1[i].resName, _atoms3[i].resName, _atoms4[i].resName, _atoms5[i].resName);
HDebug.AssertAllEquals(_atoms1[i].resSeq, _atoms1[i].resSeq, _atoms3[i].resSeq, _atoms4[i].resSeq, _atoms5[i].resSeq);
}
}
atoms1 = _atoms1;
atoms2 = _atoms2;
atoms3 = _atoms3;
atoms4 = _atoms4;
atoms5 = _atoms5;
}
public static void Align(IList <Vector> C1
, ref List <Vector> C2
, IList <double> weight
, HPack <Trans3> outTrans = null
)
{
Trans3 trans = GetTrans(C1, C2, weight);
Vector[] nC2 = trans.GetTransformed(C2).ToArray();
C2 = new List <Vector>(nC2);
if (outTrans != null)
{
outTrans.value = trans.Clone();
}
}
public static void Align(ref List <Pdb.Atom>[] ensemble
, int maxiteration = int.MaxValue
, HPack <List <Trans3[]> > outTrajTrans = null
)
{
List <Vector>[] coordss = new List <Vector> [ensemble.Length];
for (int i = 0; i < ensemble.Length; i++)
{
coordss[i] = ensemble[i].ListCoord();
}
Align(ref coordss, maxiteration: maxiteration, outTrajTrans: outTrajTrans);
ensemble = ensemble.HClone <List <Pdb.Atom> >();
for (int i = 0; i < ensemble.Length; i++)
{
ensemble[i] = ensemble[i].CloneByUpdateCoord(coordss[i]);
}
}
public static Trans3 GetTrans(IList <Vector> C1, IList <Vector> C2, HPack <int> optIter = null, HPack <List <double> > optListWeightSum = null)
{
HDebug.Assert(C1.Count == C2.Count);
int size = C1.Count;
if (optIter != null)
{
optIter.value = 0;
}
Trans3 trans0 = new Trans3(new double[3], 1, Quaternion.UnitRotation);
Trans3 trans1 = Geometry.AlignPointPoint.MinRMSD.GetTrans(C2, C1);
if (optListWeightSum != null)
{
optListWeightSum.value = new List <double>();
}
while ((trans0.TransformMatrix - trans1.TransformMatrix).ToArray().HAbs().HMax() > 0.00000001)
{
if (optIter != null)
{
optIter.value++;
}
Vector[] C2trans = trans1.GetTransformed(C2).ToArray();
double[] weight = new double[size];
double[] dist2s = new double[size];
for (int i = 0; i < size; i++)
{
double dist2 = (C1[i] - C2trans[i]).Dist2;
dist2 = HMath.Between(0.001, dist2, double.PositiveInfinity);
weight[i] = 1 / dist2;
dist2s[i] = dist2;
}
if (optListWeightSum != null)
{
optListWeightSum.value.Add(weight.Sum());
}
trans0 = trans1;
trans1 = Geometry.AlignPointPoint.MinRMSD.GetTrans(C2, C1, weight);
}
return(trans1);
}
public static void Align(List <Vector> coords1
, ref List <Vector> coords2
, int maxiteration = int.MaxValue
, HPack <List <Trans3[]> > outTrajTrans = null
)
{
List <Vector>[] ensemble = new List <Vector>[]
{
coords1.HClone(),
coords2.HClone()
};
Align(ref ensemble, maxiteration: maxiteration, outTrajTrans: outTrajTrans);
Trans3 trans = MinRMSD.GetTrans(coords1, ensemble[0]);
Vector[] ensemble0 = trans.GetTransformed(ensemble[0]).ToArray();
Vector[] ensemble1 = trans.GetTransformed(ensemble[1]).ToArray();
coords2 = new List <Vector>(ensemble1);
}
private PreparedHeader(PreparedHeaderName name, string value, byte[] valueEncoded, uint http2StaticIndex)
{
Value = value;
_name = name;
_value = valueEncoded;
int http1EncodedLen = Http1Connection.GetEncodeHeaderLength(name._http1Encoded, valueEncoded);
_http1Encoded = new byte[http1EncodedLen];
Http1Connection.EncodeHeader(name._http1Encoded, valueEncoded, _http1Encoded);
_http2Encoded =
http2StaticIndex != 0 ? HPack.EncodeIndexedHeader(http2StaticIndex) :
name._http2StaticIndex != 0 ? HPack.EncodeHeaderWithoutIndexing(name._http2StaticIndex, valueEncoded) :
HPack.EncodeHeaderWithoutIndexing(name._http2Encoded, valueEncoded);
_http2StaticIndex = http2StaticIndex;
}
public static Mode[] GetModeByTorsional(Universe univ
, Matrix hessian
, List <Universe.RotableInfo> univ_rotinfos = null
, Matrix J = null
, Vector[] coords = null
, HPack <Matrix> optoutJMJ = null // J' M J
, HPack <Matrix> optoutJM = null // J' M
, Func <Matrix, Tuple <Matrix, Vector> > fnEigSymm = null
, Func <Matrix, Matrix, Matrix, Matrix> fnMul = null
)
{
return(GetModeByTorsional(univ
, new HessMatrixDense {
hess = hessian
}
, univ_rotinfos, J
, coords, optoutJMJ, optoutJM
, fnEigSymm, fnMul
));
}
private static double Align(List <Vector>[] ensemble, Vector[] meancoords, Anisou[] meananisous, Trans3[] outTranss)
{
double[] move2s = new double[ensemble.Length];
System.Threading.Tasks.Parallel.For(0, ensemble.Length, delegate(int i)
//for(int i=0; i<ensemble.Length; i++)
{
HPack <List <Vector> > optMoveConf = new HPack <List <Vector> >();
HPack <Trans3> outTrans = new HPack <Trans3>();
MinAnisou.Align(meancoords, meananisous, ref ensemble[i], optMoveConf, outTrans: outTrans);
if (outTranss != null)
{
outTranss[i] = outTrans.value;
}
move2s[i] = optMoveConf.value.Dist2().Average();
}
);
double move2 = move2s.Average();
return(move2);
}
private void GetPotentialAndTorForce(List <ForceField.IForceField> frcflds, Vector[] coords
, out double energy, out Vector[] forces
, Dictionary <string, object> cache)
{
MatrixByArr J;
{
Graph <Universe.Atom[], Universe.Bond> univ_flexgraph = univ.BuildFlexibilityGraph();
List <Universe.RotableInfo> univ_rotinfos = univ.GetRotableInfo(univ_flexgraph);
J = Paper.TNM.GetJ(univ, coords, univ_rotinfos);
}
Vector[] forces0 = univ.GetVectorsZero();
MatrixByArr hessian = null;
energy = univ.GetPotential(frcflds, coords, ref forces0, ref hessian, cache);
HPack <Vector[]> lforces = new HPack <Vector[]>();
double[] dtor = Paper.TNM.GetRotAngles(univ, coords, forces0, 1, J: J, forcesProjectedByTorsional: lforces);
forces = lforces.value;
}
public static Top FromPdb(string pdbpath
, string ff = "charmm27"
, string water = "none"
, HPack <Pdb> optout_confout = null
)
{
Top top;
FileInfo pdbinfo = new FileInfo(pdbpath);
string currdir = HEnvironment.CurrentDirectory;
DirectoryInfo temproot = HDirectory.CreateTempDirectory();
HEnvironment.CurrentDirectory = temproot.FullName;
{
HFile.Copy(pdbinfo.FullName, "protein.pdb");
RunPdb2gmx(f: "protein.pdb"
, o: "confout.pdb"
, p: "topol.top"
, q: "clean.pdb"
, ff: ff
, water: water
, merge: "all"
, lineStderr: null
, lineStdout: null
);
top = Top.FromFile("topol.top");
if (optout_confout != null)
{
optout_confout.value = Pdb.FromFile("confout.pdb");
}
}
HEnvironment.CurrentDirectory = currdir;
Thread.Sleep(100);
try{ temproot.Delete(true); } catch (Exception) {}
return(top);
}
public static Mode[] GetModeByTorsional(Universe univ
, HessMatrix hessian
, List <Universe.RotableInfo> univ_rotinfos = null
, Matrix J = null
, Vector[] coords = null
, HPack <Matrix> optoutJMJ = null // J' M J
, HPack <Matrix> optoutJM = null // J' M
, Func <Matrix, Tuple <Matrix, Vector> > fnEigSymm = null
, Func <Matrix, Matrix, Matrix, Matrix> fnMul = null
)
{
if (univ_rotinfos == null)
{
Graph <Universe.Atom[], Universe.Bond> univ_flexgraph = univ.BuildFlexibilityGraph(null as IList <Bond>);
if (univ_flexgraph.FindLoops().Count > 0)
{
// loop should not exist in the flexibility-graph; no-global loop in backbone
return(null);
}
univ_rotinfos = univ.GetRotableInfo(univ_flexgraph);
}
if (coords == null)
{
coords = univ.GetCoords();
}
if (J == null)
{
J = TNM.GetJ(univ, coords, univ_rotinfos);
}
Vector masses = univ.GetMasses();
Mode[] modes = GetModeByTorsional(hessian, masses, J
, optoutJMJ: optoutJMJ, optoutJM: optoutJM
, fnEigSymm: fnEigSymm, fnMul: fnMul
);
return(modes);
}
////////////////////////////////////////////////////////////////////////////
// Source: Gromacs, g_nmens.c
//
// #define BOLTZ (RGAS/KILO) /* (kJ/(mol K)) */
// #define RGAS (BOLTZMANN*AVOGADRO) /* (J/(mol K)) */
// #define BOLTZMANN (1.380658e-23) /* (J/K) */
// #define AVOGADRO (6.0221367e23) /* () */
// #define KILO (1e3) /* Thousand */
//
// for(s=0; s<nstruct; s++) {
// for(i=0; i<natoms; i++)
// copy_rvec(xav[i],xout1[i]);
// //////////////////////////////////////////////////
// randnorms_mag = 0;
// for(j=0; j<noutvec; j++)
// {
// randnorms[j] = RandNormal();
// randnorms_mag += randnorms[j]*randnorms[j];
// }
// randnorms_mag = sqrt(randnorms_mag);
// for(j=0; j<noutvec; j++)
// {
// randnorms[j] = randnorms[j] / randnorms_mag;
// }
// //////////////////////////////////////////////////
// for(j=0; j<noutvec; j++) {
// v = outvec[j];
// /* (r-0.5) n times: var_n = n * var_1 = n/12
// n=4: var_n = 1/3, so multiply with 3 */
//
// rfac = sqrt(3.0 * BOLTZ*temp/eigval[iout[j]]);
// //rhalf = 2.0*rfac;
// //rfac = rfac/(real)im;
// //
// //jran = (jran*ia+ic) & im;
// //jr = (real)jran;
// //jran = (jran*ia+ic) & im;
// //jr += (real)jran;
// //jran = (jran*ia+ic) & im;
// //jr += (real)jran;
// //jran = (jran*ia+ic) & im;
// //jr += (real)jran;
// //disp = rfac * jr - rhalf;
// disp = rfac*randnorms[j];
//
// for(i=0; i<natoms; i++)
// for(d=0; d<DIM; d++)
// xout1[i][d] += disp*eigvec[v][i][d]*invsqrtm[i];
// }
// for(i=0; i<natoms; i++)
// copy_rvec(xout1[i],xout2[index[i]]);
// t = s+1;
// write_trx(out,natoms,index,atoms,0,t,box,xout2,NULL,NULL);
// fprintf(stderr,"\rGenerated %d structures",s+1);
// }
////////////////////////////////////////////////////////////////////////////
public static Vector[] GenerateEnsemble(IList <Vector> coords, Mode mode, IList <double> mass, double temperature = 300, bool normalize = true, HPack <Vector> optOutRandNorms = null)
{
return(GenerateEnsemble(coords, new Mode[] { mode }, mass, temperature: temperature, normalize: normalize, optOutRandNorms: optOutRandNorms));
}
public int ConjugateGradient(List <ForceField.IForceField> frcflds
, double threshold
, double?k = null
, double max_atom_movement = 0.01
, int?max_iteration = null
, IMinimizeLogger logger = null // logger = new MinimizeLogger_PrintEnergyForceMag(logpath);
, HPack <double> optOutEnergy = null // optional output for final energy
, List <Vector> optOutForces = null // optional output for final force vectors
, HPack <double> optOutForcesNorm1 = null // optional output for norm of final force vectors
, HPack <double> optOutForcesNorm2 = null // optional output for norm of final force vectors
, HPack <double> optOutForcesNormInf = null // optional output for norm of final force vectors
)
{
if (k == null)
{
k = double.MaxValue;
foreach (ForceField.IForceField frcfld in frcflds)
{
double?kk = frcfld.GetDefaultMinimizeStep();
if (kk.HasValue)
{
k = Math.Min(k.Value, kk.Value);
}
}
}
Graph <Universe.Atom[], Universe.Bond> univ_flexgraph = univ.BuildFlexibilityGraph();
List <Universe.RotableInfo> univ_rotinfos = univ.GetRotableInfo(univ_flexgraph);
// double k = 0.0001;
int iter = 0;
// 0. Initial configuration of atoms
Vector[] coords0 = univ.GetCoords();
Vectors coords = univ.GetCoords();
bool[] atomsMovable = null;
if (atomsMovable == null)
{
atomsMovable = new bool[size];
for (int i = 0; i < size; i++)
{
atomsMovable[i] = true;
}
}
Vectors h = univ.GetVectorsZero();
Vectors forces = univ.GetVectorsZero();
Dictionary <string, object> cache;
double energy;
cache = new Dictionary <string, object>();
GetPotentialAndTorForce(frcflds, coords
, out energy, out forces._vecs
, cache);
double forces_NormInf = NormInf(forces, atomsMovable);
double forces_Norm1 = Norm(1, forces, atomsMovable);
double forces_Norm2 = Norm(2, forces, atomsMovable);
Vectors forces0 = forces;
double energy0 = energy;
while (true)
{
if (forces.IsComputable == false)
{
System.Console.Error.WriteLine("non-computable components while doing steepest-descent");
HEnvironment.Exit(0);
}
if (logger != null)
{
logger.log(iter, coords, energy, forces, atomsMovable);
{ // logger.logTrajectory(univ, iter, coords);
Vector[] coordsx = coords._vecs.HClone <Vector>();
Trans3 trans = ICP3.OptimalTransform(coordsx, coords0);
trans.DoTransform(coordsx);
logger.logTrajectory(univ, iter, coordsx);
}
}
// 1. Save the position of atoms
// 2. Calculate the potential energy of system and the net forces on atoms
// 3. Check if every force reaches to zero,
// , and END if yes
bool stopIteration = false;
if (forces_NormInf < threshold)
{
stopIteration = true;
}
if ((max_iteration != null) && (iter >= max_iteration.Value))
{
stopIteration = true;
}
if (stopIteration)
{
// double check
cache = new Dictionary <string, object>(); // reset cache
GetPotentialAndTorForce(frcflds, coords
, out energy, out forces._vecs
, cache);
forces_NormInf = NormInf(forces, atomsMovable);
forces_Norm1 = Norm(1, forces, atomsMovable);
forces_Norm2 = Norm(2, forces, atomsMovable);
if (forces_NormInf < threshold)
{
if (iter != 1)
{
univ.SetCoords((Vector[])coords);
}
{
if (optOutEnergy != null)
{
optOutEnergy.value = energy;
}
if (optOutForces != null)
{
optOutForces.Clear(); optOutForces.AddRange(forces.ToArray());
}
if (optOutForcesNorm1 != null)
{
optOutForcesNorm1.value = forces_Norm1;
}
if (optOutForcesNorm2 != null)
{
optOutForcesNorm2.value = forces_Norm2;
}
if (optOutForcesNormInf != null)
{
optOutForcesNormInf.value = forces_NormInf;
}
}
return(iter);
}
}
// 4. Move atoms with conjugated gradient
Vectors coords_prd;
{
if ((iter > 0) && (iter % 100 == 0))
{
cache = new Dictionary <string, object>(); // reset cache
}
if (iter >= 1)
{
HDebug.Assert(forces0 != null);
double r = Vectors.VtV(forces, forces).Sum() / Vectors.VtV(forces0, forces0).Sum();
h = forces + r * h;
double kk = k.Value;
double hNormInf = NormInf(h, atomsMovable);
if (kk * hNormInf > max_atom_movement)
{
// make the maximum movement as atomsMovable
kk = max_atom_movement / (hNormInf);
}
Vector dangles = Paper.TNM.GetRotAngles(univ, coords, kk * h, 1);
//dangles *= -1;
coords_prd = Paper.TNM.RotateTorsionals(coords, dangles, univ_rotinfos);
}
else
{
// same to the steepest descent for the first iteration
h = forces;
double kk = k.Value;
double hNormInf = NormInf(h, atomsMovable);
if (kk * hNormInf > max_atom_movement)
{
// make the maximum movement as atomsMovable
kk = max_atom_movement / (hNormInf);
}
Vector dangles = Paper.TNM.GetRotAngles(univ, coords, kk * h, 1);
//dangles *= -1;
coords_prd = Paper.TNM.RotateTorsionals(coords, dangles, univ_rotinfos);
}
}
// 5. Predict energy or forces on atoms
iter++;
double energy_prd;
Vectors forces_prd = univ.GetVectorsZero();
GetPotentialAndTorForce(frcflds, coords_prd
, out energy_prd, out forces_prd._vecs
, cache);
// double energy_prd = univ.GetPotential(frcflds, coords_prd, ref forces_prd._vecs, ref hessian_prd, cache);
// Vector[] dcoord_prd = univ.GetVectorsZero();
// double[] dangles_prd = TNM.GetRotAngles(univ, coords_prd, forces_prd, 1, dcoordsRotated: dcoord_prd);
// dangles_prd = TNM.GetRotAngles(univ, coords_prd, hessian_prd, forces_prd, forceProjectedByTorsional: dcoord_prd);
//Vectors coords_prd2 = coords_prd.Clone();
//TNM.RotateTorsionals(coords_prd2, dangles_prd, univ_rotinfos);
double forces_prd_NormInf = NormInf(forces_prd, atomsMovable); // NormInf(forces_prd, atomsMovable);
double forces_prd_Norm1 = Norm(1, forces_prd, atomsMovable); // Norm(1, forces_prd, atomsMovable);
double forces_prd_Norm2 = Norm(2, forces_prd, atomsMovable); // Norm(2, forces_prd, atomsMovable);
// 6. Check if the predicted forces or energy will exceed over the limit
// , and goto 1 if no
if ((energy_prd < energy + 0.1) && (forces_prd_NormInf < forces_NormInf + 0.0001))
{
energy0 = energy;
forces0 = forces;
coords = coords_prd;
forces = forces_prd;
energy = energy_prd;
forces_NormInf = forces_prd_NormInf;
forces_Norm1 = forces_prd_Norm1;
forces_Norm2 = forces_prd_Norm2;
continue;
}
if (logger != null)
{
logger.log(iter, coords_prd, energy_prd, forces_prd, atomsMovable, "will do steepest");
}
// 7. Back to saved configuration
// 8. Move atoms with simple gradient
{
// same to the steepest descent
h = forces;
double kk = k.Value;
double hNormInf = NormInf(h, atomsMovable);
if (kk * hNormInf > max_atom_movement)
{
// make the maximum movement as atomsMovable
kk = max_atom_movement / (hNormInf);
}
Vector dangles = Paper.TNM.GetRotAngles(univ, coords, kk * h, 1);
//dangles *= -1;
coords_prd = Paper.TNM.RotateTorsionals(coords, dangles, univ_rotinfos);
}
forces_prd = univ.GetVectorsZero();
//energy_prd = univ.GetPotential(frcflds, coords_prd, ref forces_prd._vecs, ref hessian_prd, cache);
GetPotentialAndTorForce(frcflds, coords_prd
, out energy_prd, out forces_prd._vecs
, cache);
forces_prd_NormInf = NormInf(forces_prd, atomsMovable);
forces_prd_Norm1 = Norm(1, forces_prd, atomsMovable);
forces_prd_Norm2 = Norm(2, forces_prd, atomsMovable);
energy0 = energy;
forces0 = forces;
coords = coords_prd;
forces = forces_prd;
energy = energy_prd;
forces_NormInf = forces_prd_NormInf;
forces_Norm1 = forces_prd_Norm1;
forces_Norm2 = forces_prd_Norm2;
// 9. goto 1
}
}
public static Trans3 GetTrans(IList <Vector> C1, IList <Anisou> anisou1, IList <Vector> C2, IList <Anisou> anisou2, HPack <double> optEnergy = null)
{
int size = C1.Count;
HDebug.Assert(size == C1.Count, size == C2.Count);
Vector[] srcs = new Vector[size * 3 * 2]; // sources
Vector[] tars = new Vector[size * 3 * 2]; // targets
double[] weis = new double[size * 3 * 2]; // weights
double[] engs = new double[size * 3 * 2]; // energies
//for(int i=0; i<size; i++)
//{
// Debug.Assert(anisou1[i].eigvals[0] >= 0); W1s[i*3+0] = (anisou1[i].eigvals[0] <= 0) ? 0 : 1 / anisou1[i].eigvals[0];
// Debug.Assert(anisou1[i].eigvals[1] >= 0); W1s[i*3+1] = (anisou1[i].eigvals[1] <= 0) ? 0 : 1 / anisou1[i].eigvals[1];
// Debug.Assert(anisou1[i].eigvals[2] >= 0); W1s[i*3+2] = (anisou1[i].eigvals[2] <= 0) ? 0 : 1 / anisou1[i].eigvals[2];
// enrgs[i*3+0] = enrgs[i*3+1] = enrgs[i*3+2] = double.NaN;
//}
//Trans3 trans = ICP3.OptimalTransform(C2, C1);
Trans3 trans = new Trans3(new double[] { 0, 0, 0 }, 1, Quaternion.UnitRotation);// = transICP3.OptimalTransformWeighted(C2, C1, W1s);
int iter = 0;
int iter_max = 1000;
//double enrg = double.NaN;
while (iter < iter_max)
{
iter++;
//for(int i=0; i<size; i++)
System.Threading.Tasks.Parallel.For(0, size, delegate(int i)
{
for (int j = 0; j < 3; j++)
{
Vector p1 = C1[i];
Vector n1 = anisou1[i].axes[j];
double w1 = anisou1[i].eigvals[j]; w1 = (w1 <= 0) ? 0 : 1 / w1;
Vector p2 = trans.DoTransform(C2[i]);
Vector n2 = (trans.DoTransform(C2[i] + anisou2[i].axes[j]) - p2).UnitVector();
double w2 = anisou2[i].eigvals[j]; w2 = (w2 <= 0) ? 0 : 1 / w2;
Vector clo12 = p2 - LinAlg.DotProd(n1, p2 - p1) * n1; // closest point from p1 to plane2
Vector clo21 = p1 - LinAlg.DotProd(n2, p1 - p2) * n2; // closest point from p1 to plane2
HDebug.AssertTolerance(0.00001, LinAlg.DotProd(clo12 - p1, n1));
HDebug.AssertTolerance(0.00001, LinAlg.DotProd(clo21 - p2, n2));
// p2 -> (pt closest to p2 on plane1 with w1)
srcs[(i * 3 + j) * 2 + 0] = p2;
tars[(i * 3 + j) * 2 + 0] = clo12;
weis[(i * 3 + j) * 2 + 0] = w1;
engs[(i * 3 + j) * 2 + 0] = w1 * (p2 - clo12).Dist2;
// inverse of {p1 -> (pt closest to p1 on plane2 with w2)}
// = (pt closest to p1 on plane2 with w2) -> p1
srcs[(i * 3 + j) * 2 + 1] = clo21;
tars[(i * 3 + j) * 2 + 1] = p1;
weis[(i * 3 + j) * 2 + 1] = w2;
engs[(i * 3 + j) * 2 + 1] = w2 * (clo21 - p1).Dist2;
}
});
Trans3 dtrans = ICP3.OptimalTransformWeighted(srcs, tars, weis);
trans = Trans3.AppendTrans(trans, dtrans);
double max_dtrans_matrix = (dtrans.TransformMatrix - LinAlg.Eye(4)).ToArray().HAbs().HMax();
if (max_dtrans_matrix < 0.0000001)
{
break;
}
}
if (optEnergy != null)
{
optEnergy.value = engs.Sum() / size;
}
return(trans);
}
public static double[] GetRotAngles(Universe univ
, Vector[] coords
, MatrixByArr hessian
, Vector[] forces
, MatrixByArr J = null
, Graph <Universe.Atom[], Universe.Bond> univ_flexgraph = null
, List <Universe.RotableInfo> univ_rotinfos = null
, Vector[] forceProjectedByTorsional = null
, HPack <Vector> optEigvalOfTorHessian = null
)
{
Vector mass = univ.GetMasses();
//Vector[] dcoords = new Vector[univ.size];
//double t2 = t*t;
//for(int i=0; i<univ.size; i++)
// dcoords[i] = forces[i] * (0.5*t2/mass[i]);
if (J == null)
{
if (univ_rotinfos == null)
{
if (univ_flexgraph == null)
{
univ_flexgraph = univ.BuildFlexibilityGraph();
}
univ_rotinfos = univ.GetRotableInfo(univ_flexgraph);
}
J = TNM.GetJ(univ, coords, univ_rotinfos);
}
double[] dangles;
using (new Matlab.NamedLock("TEST"))
{
Matlab.Clear("TEST");
Matlab.PutVector("TEST.F", Vector.FromBlockvector(forces));
Matlab.PutMatrix("TEST.J", J);
Matlab.PutMatrix("TEST.H", hessian);
Matlab.PutVector("TEST.M", univ.GetMasses(3));
Matlab.Execute("TEST.M = diag(TEST.M);");
Matlab.Execute("TEST.JHJ = TEST.J' * TEST.H * TEST.J;");
Matlab.Execute("TEST.JMJ = TEST.J' * TEST.M * TEST.J;");
// (J' H J) tor = J' F
// (V' D V) tor = J' F <= (V,D) are (eigvec,eigval) of generalized eigenvalue problem with (A = JHJ, B = JMJ)
// tor = inv(V' D V) J' F
Matlab.Execute("[TEST.V, TEST.D] = eig(TEST.JHJ, TEST.JMJ);");
if (optEigvalOfTorHessian != null)
{
optEigvalOfTorHessian.value = Matlab.GetVector("diag(TEST.D)");
}
{
Matlab.Execute("TEST.D = diag(TEST.D);");
Matlab.Execute("TEST.D(abs(TEST.D)<1) = 0;"); // remove "eigenvalue < 1" because they will increase
// the magnitude of force term too big !!!
Matlab.Execute("TEST.D = diag(TEST.D);");
}
Matlab.Execute("TEST.invJHJ = TEST.V * pinv(TEST.D) * TEST.V';");
Matlab.Execute("TEST.dtor = TEST.invJHJ * TEST.J' * TEST.F;");
/// f = m a
/// d = 1/2 a t^2
/// = 0.5 a : assuming t=1
/// = 0.5 f/m
/// f = m a
/// = 2 m d t^-2
/// = 2 m d : assuming t=1
///
/// coord change
/// dr = 0.5 a t^2
/// = 0.5 f/m : assuming t=1
/// = 0.5 M^-1 F : M is mass matrix, F is the net force of each atom
///
/// torsional angle change
/// dtor = (J' M J)^-1 J' M * dr : (6) of TNM paper
/// = (J' M J)^-1 J' M * 0.5 M^-1 F
/// = 0.5 (J' M J)^-1 J' F
///
/// force filtered by torsional ...
/// F_tor = ma
/// = 2 M (J dtor)
/// = 2 M J 0.5 (J' M J)^-1 J' F
/// = M J (J' M J)^-1 J' F
///
/// H J dtor = F
/// = F_tor : update force as the torsional filtered force
/// = M J (J' M J)^-1 J' F
/// (J' H J) dtor = (J' M J) (J' M J)^-1 J' F
/// (V D V') dtor = (J' M J) (J' M J)^-1 J' F : eigen decomposition of (J' H J) using
/// generalized eigenvalue problem with (J' M J)
/// dtor = (V D^-1 V') (J' M J) (J' M J)^-1 J' F : (J' M J) (J' M J)^-1 = I. However, it has
/// the projection effect of J'F into (J' M J)
/// vector space(?). The projection will be taken
/// care by (V D^-1 V')
/// = (V D^-1 V') J' F
///
dangles = Matlab.GetVector("TEST.dtor");
if (forceProjectedByTorsional != null)
{
HDebug.Assert(forceProjectedByTorsional.Length == forces.Length);
Matlab.Execute("TEST.F_tor = TEST.M * TEST.J * pinv(TEST.JMJ) * TEST.J' * TEST.F;");
Vector lforceProjectedByTorsional = Matlab.GetVector("TEST.F_tor");
HDebug.Assert(lforceProjectedByTorsional.Size == forceProjectedByTorsional.Length * 3);
for (int i = 0; i < forceProjectedByTorsional.Length; i++)
{
int i3 = i * 3;
forceProjectedByTorsional[i] = new double[] { lforceProjectedByTorsional[i3 + 0],
lforceProjectedByTorsional[i3 + 1],
lforceProjectedByTorsional[i3 + 2], };
}
}
Matlab.Clear("TEST");
}
return(dangles);
}
public static double[] GetRotAngles(Universe univ
, Vector[] coords
, Vector[] forces
, double t // 0.1
, MatrixByArr J = null
, Graph <Universe.Atom[], Universe.Bond> univ_flexgraph = null
, List <Universe.RotableInfo> univ_rotinfos = null
, HPack <Vector[]> forcesProjectedByTorsional = null
, HPack <Vector[]> dcoordsProjectedByTorsional = null
)
{
Vector mass = univ.GetMasses();
//Vector[] dcoords = new Vector[univ.size];
double t2 = t * t;
//for(int i=0; i<univ.size; i++)
// dcoords[i] = forces[i] * (0.5*t2/mass[i]);
if (J == null)
{
if (univ_rotinfos == null)
{
if (univ_flexgraph == null)
{
univ_flexgraph = univ.BuildFlexibilityGraph();
}
univ_rotinfos = univ.GetRotableInfo(univ_flexgraph);
}
J = TNM.GetJ(univ, coords, univ_rotinfos);
}
double[] dangles;
using (new Matlab.NamedLock("TEST"))
{
Matlab.Clear("TEST");
Matlab.PutVector("TEST.F", Vector.FromBlockvector(forces));
Matlab.PutValue("TEST.t2", t2);
//Matlab.PutVector("TEST.R", Vector.FromBlockvector(dcoords));
Matlab.PutMatrix("TEST.J", J);
Matlab.PutVector("TEST.M", univ.GetMasses(3));
Matlab.Execute("TEST.M = diag(TEST.M);");
/// f = m a
/// d = 1/2 a t^2
/// = 0.5 f/m t^2
/// f = m a
/// = 2 m d t^-2
///
/// coord change
/// dcoord = 0.5 a t^2
/// = (0.5 t^2) f/m
/// = (0.5 t^2) M^-1 F : M is mass matrix, F is the net force of each atom
///
/// torsional angle change
/// dtor = (J' M J)^-1 J' M * dcoord : (6) of TNM paper
/// = (J' M J)^-1 J' M * (0.5 t^2) M^-1 F
/// = (0.5 t^2) (J' M J)^-1 J' F
/// = (0.5 t^2) (J' M J)^-1 J' F
/// = (0.5 t2) invJMJ JF
///
/// force filtered by torsional ...
/// F_tor = m a
/// = 2 m d t^-2
/// = 2 M (J * dtor) t^-2
/// = 2 M (J * (0.5 t^2) (J' M J)^-1 J' F) t^-2
/// = M J (J' M J)^-1 J' F
/// = MJ invJMJ JF
///
/// coord change filtered by torsional
/// R_tor = (0.5 t^2) M^-1 * F_tor
/// = (0.5 t^2) J (J' M J)^-1 J' F
/// = (0.5 t2) J invJMJ JF
Matlab.Execute("TEST.JMJ = TEST.J' * TEST.M * TEST.J;");
Matlab.Execute("TEST.invJMJ = inv(TEST.JMJ);");
Matlab.Execute("TEST.MJ = TEST.M * TEST.J;");
Matlab.Execute("TEST.JF = TEST.J' * TEST.F;");
Matlab.Execute("TEST.dtor = (0.5 * TEST.t2) * TEST.invJMJ * TEST.JF;"); // (6) of TNM paper
Matlab.Execute("TEST.F_tor = TEST.MJ * TEST.invJMJ * TEST.JF;");
Matlab.Execute("TEST.R_tor = (0.5 * TEST.t2) * TEST.J * TEST.invJMJ * TEST.JF;");
dangles = Matlab.GetVector("TEST.dtor");
if (forcesProjectedByTorsional != null)
{
Vector F_tor = Matlab.GetVector("TEST.F_tor");
HDebug.Assert(F_tor.Size == forces.Length * 3);
forcesProjectedByTorsional.value = new Vector[forces.Length];
for (int i = 0; i < forces.Length; i++)
{
int i3 = i * 3;
forcesProjectedByTorsional.value[i] = new double[] { F_tor[i3 + 0], F_tor[i3 + 1], F_tor[i3 + 2] };
}
}
if (dcoordsProjectedByTorsional != null)
{
Vector R_tor = Matlab.GetVector("TEST.R_tor");
HDebug.Assert(R_tor.Size == coords.Length * 3);
dcoordsProjectedByTorsional.value = new Vector[coords.Length];
for (int i = 0; i < coords.Length; i++)
{
int i3 = i * 3;
dcoordsProjectedByTorsional.value[i] = new double[] { R_tor[i3 + 0], R_tor[i3 + 1], R_tor[i3 + 2] };
}
}
Matlab.Clear("TEST");
}
return(dangles);
}
public int QuasiNewton(List <ForceField.IForceField> frcflds
, double threshold
, double?k = null
, double max_atom_movement = 0.01
, int?max_iteration = null
, IMinimizeLogger logger = null // logger = new MinimizeLogger_PrintEnergyForceMag(logpath);
, HPack <double> optOutEnergy = null // optional output for final energy
, List <Vector> optOutForces = null // optional output for final force vectors
, HPack <double> optOutForcesNorm1 = null // optional output for norm of final force vectors
, HPack <double> optOutForcesNorm2 = null // optional output for norm of final force vectors
, HPack <double> optOutForcesNormInf = null // optional output for norm of final force vectors
)
{
if (k == null)
{
k = double.MaxValue;
foreach (ForceField.IForceField frcfld in frcflds)
{
double?kk = frcfld.GetDefaultMinimizeStep();
if (kk.HasValue)
{
k = Math.Min(k.Value, kk.Value);
}
}
}
Graph <Universe.Atom[], Universe.Bond> univ_flexgraph = univ.BuildFlexibilityGraph();
List <Universe.RotableInfo> univ_rotinfos = univ.GetRotableInfo(univ_flexgraph);
// double k = 0.0001;
int iter = 0;
// 0. Initial configuration of atoms
Vector[] coords = univ.GetCoords();
Vector[] coords0 = univ.GetCoords();
bool[] atomsMovable = null;
{
atomsMovable = new bool[size];
for (int i = 0; i < size; i++)
{
atomsMovable[i] = true;
}
}
Dictionary <string, object> cache = new Dictionary <string, object>();
Vector[] forces = null;
MatrixByArr hessian;
double energy = 0;
double[] dtor;
double forces_NormInf;
double forces_Norm1;
double forces_Norm2;
do
{
if (logger != null)
{
if (forces != null)
{
logger.log(iter, coords, energy, forces, atomsMovable);
}
{
Vector[] coordsx = coords.HClone <Vector>();
Trans3 trans = ICP3.OptimalTransform(coordsx, coords0);
trans.DoTransform(coordsx);
logger.logTrajectory(univ, iter, coordsx);
}
}
//GetPotentialAndTorForce(frcflds, coords
// , out energy, out forces, out hessian, out dtor
// , cache);
{
MatrixByArr J = Paper.TNM.GetJ(univ, coords, univ_rotinfos);
Vector[] forces0 = univ.GetVectorsZero();
hessian = new double[size * 3, size *3];
energy = univ.GetPotential(frcflds, coords, ref forces0, ref hessian, cache);
forces = univ.GetVectorsZero();
dtor = Paper.TNM.GetRotAngles(univ, coords, hessian, forces0, J: J, forceProjectedByTorsional: forces);
for (int i = 0; i < forces0.Length; i++)
{
forces0[i] = forces0[i] * 0.001;
}
dtor = Paper.TNM.GetRotAngles(univ, coords, hessian, forces0, J: J);
}
forces_NormInf = NormInf(forces, atomsMovable); // NormInf(forces_prd, atomsMovable);
forces_Norm1 = Norm(1, forces, atomsMovable); // Norm(1, forces_prd, atomsMovable);
forces_Norm2 = Norm(2, forces, atomsMovable); // Norm(2, forces_prd, atomsMovable);
if (forces_NormInf < 0.0001)
{
System.Environment.Exit(0);
break;
}
coords = Paper.TNM.RotateTorsionals(coords, dtor, univ_rotinfos);
iter++;
}while(true);
while (true)
{
// if(forces.IsComputable == false)
// {
// System.Console.Error.WriteLine("non-computable components while doing steepest-descent");
// Environment.Exit(0);
// }
if (logger != null)
{
logger.log(iter, coords, energy, forces, atomsMovable);
logger.logTrajectory(univ, iter, coords);
//if(iter %10 == 0)
//{
// System.IO.Directory.CreateDirectory("output");
// string pdbname = string.Format("mini.conju.{0:D5}.pdb", iter);
// pdb.ToFile("output\\"+pdbname, coords.ToArray());
// System.IO.File.AppendAllLines("output\\mini.conju.[animation].pml", new string[] { "load "+pdbname+", 1A6G" });
//}
}
// 1. Save the position of atoms
// 2. Calculate the potential energy of system and the net forces on atoms
// 3. Check if every force reaches to zero,
// , and END if yes
bool stopIteration = false;
if (forces_NormInf < threshold)
{
stopIteration = true;
}
if ((max_iteration != null) && (iter >= max_iteration.Value))
{
stopIteration = true;
}
if (stopIteration)
{
// double check
cache = new Dictionary <string, object>(); // reset cache
//energy = GetPotential(frcflds, coords, out forces, cache);
// energy = univ.GetPotential(frcflds, coords, ref forces._vecs, ref hessian, cache);
forces_NormInf = NormInf(forces, atomsMovable);
forces_Norm1 = Norm(1, forces, atomsMovable);
forces_Norm2 = Norm(2, forces, atomsMovable);
if (forces_NormInf < threshold)
{
if (iter != 1)
{
univ.SetCoords(coords);
}
//{
// string pdbname = string.Format("mini.conju.{0:D5}.pdb", iter);
// pdb.ToFile("output\\"+pdbname, coords.ToArray());
// System.IO.File.AppendAllLines("output\\mini.conju.[animation].pml", new string[] { "load "+pdbname+", 1A6G" });
//}
{
if (optOutEnergy != null)
{
optOutEnergy.value = energy;
}
if (optOutForces != null)
{
optOutForces.Clear(); optOutForces.AddRange(forces.ToArray());
}
if (optOutForcesNorm1 != null)
{
optOutForcesNorm1.value = forces_Norm1;
}
if (optOutForcesNorm2 != null)
{
optOutForcesNorm2.value = forces_Norm2;
}
if (optOutForcesNormInf != null)
{
optOutForcesNormInf.value = forces_NormInf;
}
}
return(iter);
}
}
// 4. Move atoms with conjugated gradient
//Vectors coords_prd;
{
if ((iter > 0) && (iter % 100 == 0))
{
cache = new Dictionary <string, object>(); // reset cache
}
if (iter > 1)
{
// Debug.Assert(forces0 != null);
// double r = Vectors.VtV(forces, forces).Sum() / Vectors.VtV(forces0, forces0).Sum();
// h = forces + r * h;
// double kk = k.Value;
// double hNormInf = NormInf(h, atomsMovable);
// if(kk*hNormInf > max_atom_movement)
// // make the maximum movement as atomsMovable
// kk = max_atom_movement/(hNormInf);
// //double kk = (k*h.NormsInf().NormInf() < max_atom_movement) ? k : (max_atom_movement/h.NormsInf().NormInf());
// //double kk = (k.Value*NormInf(h,atomsMovable) < max_atom_movement)? k.Value : (max_atom_movement/NormInf(h,atomsMovable));
// double[] dangles = TNM.GetRotAngles(univ, coords._vecs, hessian, (kk * h)._vecs);
// coords_prd = TNM.RotateTorsionals(coords, dangles, univ_rotinfos);
}
else
{
// // same to the steepest descent for the first iteration
// h = forces;
// double kk = k.Value;
// double hNormInf = NormInf(h, atomsMovable);
// if(kk*hNormInf > max_atom_movement)
// // make the maximum movement as atomsMovable
// kk = max_atom_movement/(hNormInf);
// //double kk = (k*h.NormsInf().NormInf() < max_atom_movement) ? k : (max_atom_movement/h.NormsInf().NormInf());
// //double kk = (k.Value*NormInf(h,atomsMovable) < max_atom_movement)? k.Value : (max_atom_movement/NormInf(h, atomsMovable));
//
// //double[] dangles = TNM.GetRotAngles(this, coords, kk * h, 1);
// double[] dangles = TNM.GetRotAngles(univ, coords._vecs, hessian, (kk * h)._vecs);
// coords_prd = TNM.RotateTorsionals(coords, dangles, univ_rotinfos);
//
// // coords_prd = AddConditional(coords, kk * h, atomsMovable);
}
}
// 5. Predict energy or forces on atoms
iter++;
//double energy_prd;
Vectors forces_prd = univ.GetVectorsZero();
MatrixByArr hessian_prd = new double[size * 3, size *3];
//double energy_prd = GetPotential(frcflds, coords_prd, out forces_prd, cache); iter++;
// GetPotentialAndTorForce(frcflds, coords_prd
// , out energy_prd, out forces_prd._vecs, out hessian_prd
// , cache);
// // double energy_prd = univ.GetPotential(frcflds, coords_prd, ref forces_prd._vecs, ref hessian_prd, cache);
// // Vector[] dcoord_prd = univ.GetVectorsZero();
// // double[] dangles_prd = TNM.GetRotAngles(univ, coords_prd, forces_prd, 1, dcoordsRotated: dcoord_prd);
// // dangles_prd = TNM.GetRotAngles(univ, coords_prd, hessian_prd, forces_prd, forceProjectedByTorsional: dcoord_prd);
// //Vectors coords_prd2 = coords_prd.Clone();
// //TNM.RotateTorsionals(coords_prd2, dangles_prd, univ_rotinfos);
//
// double forces_prd_NormInf = NormInf(forces_prd, atomsMovable); // NormInf(forces_prd, atomsMovable);
// double forces_prd_Norm1 = Norm(1, forces_prd, atomsMovable); // Norm(1, forces_prd, atomsMovable);
// double forces_prd_Norm2 = Norm(2, forces_prd, atomsMovable); // Norm(2, forces_prd, atomsMovable);
// // 6. Check if the predicted forces or energy will exceed over the limit
// // , and goto 1 if no
// // doSteepDeescent = true;
// //if((doSteepDeescent == false) || ((energy_prd <= energy) && (forces_prd_NormInf < forces_NormInf+1.0))
// if((energy_prd < energy+0.1) && (forces_prd_NormInf < forces_NormInf+0.0001))
// {
// energy0 = energy;
// forces0 = forces;
// coords = coords_prd;
// forces = forces_prd;
// hessian = hessian_prd;
// energy = energy_prd;
// forces_NormInf = forces_prd_NormInf;
// forces_Norm1 = forces_prd_Norm1;
// forces_Norm2 = forces_prd_Norm2;
// continue;
// }
// if(logger != null)
// logger.log(iter, coords_prd, energy_prd, forces_prd, atomsMovable, "will do steepest");
// // 7. Back to saved configuration
// // 8. Move atoms with simple gradient
// {
// // same to the steepest descent
// h = forces;
// double kk = k.Value;
// double hNormInf = NormInf(h, atomsMovable);
// if(kk*hNormInf > max_atom_movement)
// // make the maximum movement as atomsMovable
// kk = max_atom_movement/(hNormInf);
// double[] dangles = TNM.GetRotAngles(univ, coords._vecs, hessian, (kk * h)._vecs);
// coords_prd = TNM.RotateTorsionals(coords, dangles, univ_rotinfos);
// }
// forces_prd = univ.GetVectorsZero();
// hessian_prd = new double[size*3, size*3];
// //energy_prd = univ.GetPotential(frcflds, coords_prd, ref forces_prd._vecs, ref hessian_prd, cache);
// GetPotentialAndTorForce(frcflds, coords_prd
// , out energy_prd, out forces_prd._vecs, out hessian_prd
// , cache);
// forces_prd_NormInf = NormInf(forces_prd, atomsMovable);
// forces_prd_Norm1 = Norm(1, forces_prd, atomsMovable);
// forces_prd_Norm2 = Norm(2, forces_prd, atomsMovable);
//
// energy0 = energy;
// forces0 = forces;
// coords = coords_prd;
// forces = forces_prd;
// energy = energy_prd;
// forces_NormInf = forces_prd_NormInf;
// forces_Norm1 = forces_prd_Norm1;
// forces_Norm2 = forces_prd_Norm2;
// // 9. goto 1
}
}
public static List <double> ScaleBFactorComp(List <double> bfactorExpr, List <double> bfactorComp, HPack <double> outScale4BfactorComp)
{
HDebug.Assert(bfactorExpr.Count == bfactorComp.Count);
int size = bfactorComp.Count;
Matrix A = new double[size, 1];
//Matrix A = new double[size, 2];
Vector b = new double[size];
for (int i = 0; i < size; i++)
{
A[i, 0] = bfactorComp[i];
//A[i, 1] = 1;
b[i] = bfactorExpr[i];
}
/// A x = b
/// (A' A) x = (A' b)
/// x = inv(A' A) * (A' b)
Matrix At = A.Tr();
Matrix AtA = At * A;
Vector Atb = LinAlg.MV(At, b); // = At * b;
Matrix invAtA = NumericSolver.Inv(AtA);
Vector x = LinAlg.MV(invAtA, Atb); // = invAtA * Atb;
double scale = x[0];
double add = 0; //= x[1];
double[] bfactorCompScaled = new double[size];
for (int i = 0; i < size; i++)
{
bfactorCompScaled[i] = bfactorComp[i] * scale + add;
}
if (outScale4BfactorComp != null)
{
outScale4BfactorComp.value = scale;
}
return(new List <double>(bfactorCompScaled));
}
public static Tinker.Prm.Atom SelectByXyzAtom(this IList <Tinker.Prm.Atom> prmatoms, Tinker.Xyz.Atom xyzatom, HPack <Dictionary <int, Tinker.Prm.Atom> > cache = null)
{
foreach (var prmatom in prmatoms)
{
if (xyzatom.AtomId == prmatom.Id)
{
return(prmatom);
}
}
return(null);
}
public int Minimize_ConjugateGradient_AtomwiseUpdate(
List <ForceField.IForceField> frcflds
, double threshold = 0.001 // * threshold for forces.NormInf
, double?k = null // * step step
// 0.0001
, double max_atom_movement = 0.1 // * maximum atom movement
, int?max_iteration = null // null for the infinite iteration until converged
, bool[] atomsMovable = null // * selection of movable atoms
// move all atoms if (atomsMovable == null) or (atomsMovable[all] == true)
// move only atom whose (atomsMovable[id] == true)
, IMinimizeLogger logger = null // * write log
// = new MinimizeLogger_PrintEnergyForceMag()
, InfoPack extra = null // get extra information
, bool?doSteepDeescent = null // null or true for default
, HPack <double> optOutEnergy = null // optional output for final energy
, List <Vector> optOutForces = null // optional output for final force vectors
, HPack <double> optOutForcesNorm1 = null // optional output for norm of final force vectors
, HPack <double> optOutForcesNorm2 = null // optional output for norm of final force vectors
, HPack <double> optOutForcesNormInf = null // optional output for norm of final force vectors
)
{
if (doSteepDeescent == null)
{
doSteepDeescent = true;
}
if (k == null)
{
k = double.MaxValue;
foreach (ForceField.IForceField frcfld in frcflds)
{
double?kk = frcfld.GetDefaultMinimizeStep();
if (kk.HasValue)
{
k = Math.Min(k.Value, kk.Value);
}
}
}
int iter = 0;
// 0. Initial configuration of atoms
Vector[] coords = GetCoords();
if (atomsMovable == null)
{
atomsMovable = new bool[size];
for (int i = 0; i < size; i++)
{
atomsMovable[i] = true;
}
}
Vectors h = GetVectorsZero();
Vectors forces = Vector.NewVectors(size, new double[3]);
Vectors moves = Vector.NewVectors(size, new double[3]);
Nonbondeds_v1 nonbondeds = null;
// Dictionary<string,object> cache = new Dictionary<string, object>();
double energy = GetPotentialUpdated(frcflds, null, null, null, coords, forces, ref nonbondeds);
double forces_NormInf = NormInf(forces, atomsMovable);
double forces_Norm1 = Norm(1, forces, atomsMovable);
double forces_Norm2 = Norm(2, forces, atomsMovable);
Vector[] forces0 = forces;
double energy0 = energy;
Vectors moves0 = moves;
double leastMove = 0.000001;
while (true)
{
if (forces.IsComputable == false)
{
System.Console.Error.WriteLine("non-computable components while doing steepest-descent");
HEnvironment.Exit(0);
}
if (logger != null)
{
logger.log(iter, coords, energy, forces, atomsMovable);
logger.logTrajectory(this, iter, coords);
}
// 1. Save the position of atoms
// 2. Calculate the potential energy of system and the net forces on atoms
// 3. Check if every force reaches to zero,
// , and END if yes
bool stopIteration = false;
if (forces_NormInf < threshold)
{
stopIteration = true;
}
if ((max_iteration != null) && (iter >= max_iteration.Value))
{
stopIteration = true;
}
if (stopIteration)
{
// double check
//cache = new Dictionary<string, object>(); // reset cache
//energy = GetPotential(frcflds, coords, out forces, cache);
nonbondeds = null;
energy = GetPotentialUpdated(frcflds, null, null, null, coords, forces, ref nonbondeds);
forces_NormInf = NormInf(forces, atomsMovable);
forces_Norm1 = Norm(1, forces, atomsMovable);
forces_Norm2 = Norm(2, forces, atomsMovable);
if (forces_NormInf < threshold)
{
if (iter != 1)
{
SetCoords(coords);
}
{
if (optOutEnergy != null)
{
optOutEnergy.value = energy;
}
if (optOutForces != null)
{
optOutForces.Clear(); optOutForces.AddRange(forces.ToArray());
}
if (optOutForcesNorm1 != null)
{
optOutForcesNorm1.value = forces_Norm1;
}
if (optOutForcesNorm2 != null)
{
optOutForcesNorm2.value = forces_Norm2;
}
if (optOutForcesNormInf != null)
{
optOutForcesNormInf.value = forces_NormInf;
}
}
return(iter);
}
}
// 4. Move atoms with conjugated gradient
Vectors coords_prd;
double kk;
{
if ((iter > 0) && (iter % 100 == 0))
{
//cache = new Dictionary<string, object>(); // reset cache
nonbondeds = null;
}
if (iter > 1)
{
HDebug.Assert(forces0 != null);
double r = Vectors.VtV(forces, forces).Sum() / Vectors.VtV(forces0, forces0).Sum();
h = forces + r * h;
kk = k.Value;
double hNormInf = NormInf(h, atomsMovable);
if (kk * hNormInf > max_atom_movement)
{
// make the maximum movement as atomsMovable
kk = max_atom_movement / (hNormInf);
}
moves = moves0.Clone();
coords_prd = AddConditional(coords, atomsMovable, moves, kk * h, leastMove);
}
else
{
// same to the steepest descent for the first iteration
h = forces;
kk = k.Value;
double hNormInf = NormInf(h, atomsMovable);
if (kk * hNormInf > max_atom_movement)
{
// make the maximum movement as atomsMovable
kk = max_atom_movement / (hNormInf);
}
//double kk = (k*h.NormsInf().NormInf() < max_atom_movement) ? k : (max_atom_movement/h.NormsInf().NormInf());
//double kk = (k.Value*NormInf(h,atomsMovable) < max_atom_movement)? k.Value : (max_atom_movement/NormInf(h, atomsMovable));
moves = moves0.Clone();
coords_prd = AddConditional(coords, atomsMovable, moves, kk * h, leastMove);
}
}
// 5. Predict energy or forces on atoms
Vectors forces_prd = forces.Clone();
double energy_prd = GetPotentialUpdated(frcflds, energy, coords, forces, coords_prd, forces_prd, ref nonbondeds); iter++;
//double energy_prd = GetPotential(frcflds, coords_prd, out forces_prd, cache); iter++;
double forces_prd_NormInf = NormInf(forces_prd, atomsMovable);
double forces_prd_Norm1 = Norm(1, forces_prd, atomsMovable);
double forces_prd_Norm2 = Norm(2, forces_prd, atomsMovable);
// 6. Check if the predicted forces or energy will exceed over the limit
// , and goto 1 if no
doSteepDeescent = true;
//if((doSteepDeescent == false) || ((energy_prd <= energy) && (forces_prd_NormInf < forces_NormInf+1.0))
if ((energy_prd < energy + 0.1) && (forces_prd_NormInf < forces_NormInf + 0.0001))
{
energy0 = energy;
forces0 = forces;
moves0 = moves;
coords = coords_prd;
forces = forces_prd;
energy = energy_prd;
forces_NormInf = forces_prd_NormInf;
forces_Norm1 = forces_prd_Norm1;
forces_Norm2 = forces_prd_Norm2;
continue;
}
if (logger != null)
{
logger.log(iter, coords_prd, energy_prd, forces_prd, atomsMovable, "will do steepest");
}
// 7. Back to saved configuration
// 8. Move atoms with simple gradient
{
// same to the steepest descent
h = forces;
kk = k.Value;
double hNormInf = NormInf(h, atomsMovable);
if (kk * hNormInf > max_atom_movement)
{
// make the maximum movement as atomsMovable
kk = max_atom_movement / (hNormInf);
}
moves = moves0.Clone();
coords_prd = AddConditional(coords, atomsMovable, moves, kk * h, leastMove);
}
//energy_prd = GetPotential(frcflds, coords_prd, out forces_prd, cache);
energy_prd = GetPotentialUpdated(frcflds, energy, coords, forces, coords_prd, forces_prd, ref nonbondeds);
forces_prd_NormInf = NormInf(forces_prd, atomsMovable);
forces_prd_Norm1 = Norm(1, forces_prd, atomsMovable);
forces_prd_Norm2 = Norm(2, forces_prd, atomsMovable);
energy0 = energy;
forces0 = forces;
moves0 = moves;
coords = coords_prd;
forces = forces_prd;
energy = energy_prd;
forces_NormInf = forces_prd_NormInf;
forces_Norm1 = forces_prd_Norm1;
forces_Norm2 = forces_prd_Norm2;
// 9. goto 1
}
}
public static Mode[] GetModeByTorsional(HessMatrix hessian, Vector masses, Matrix J
, HPack <Matrix> optoutJMJ = null // J' M J
, HPack <Matrix> optoutJM = null // J' M
, Func <Matrix, Tuple <Matrix, Vector> > fnEigSymm = null
, Func <Matrix, Matrix, Matrix, Matrix> fnMul = null
)
{
string opt;
opt = "eig(JMJ^-1/2 * JHJ * JMJ^-1/2)";
//opt = "mwhess->tor->eig(H)->cart->mrmode";
if ((fnEigSymm != null) && (fnMul != null))
{
opt = "fn-" + opt;
}
switch (opt)
{
case "mwhess->tor->eig(H)->cart->mrmode":
/// http://www.lct.jussieu.fr/manuels/Gaussian03/g_whitepap/vib.htm
/// http://www.lct.jussieu.fr/manuels/Gaussian03/g_whitepap/vib/vib.pdf
/// does not work properly.
HDebug.Assert(false);
using (new Matlab.NamedLock("GetModeByTor"))
{
int n = J.ColSize;
int m = J.RowSize;
//Matrix M = massmat; // univ.GetMassMatrix(3);
Vector[] toreigvecs = new Vector[m];
Vector[] tormodes = new Vector[m];
double[] toreigvals = new double[m];
Mode[] modes = new Mode[m];
{
Matlab.Clear("GetModeByTor");
Matlab.PutMatrix("GetModeByTor.H", hessian);
Matlab.PutMatrix("GetModeByTor.J", J);
//Matlab.PutMatrix("GetModeByTor.M", M);
Matlab.PutVector("GetModeByTor.m", masses); // ex: m = [1,2,...,n]
Matlab.Execute("GetModeByTor.m3 = kron(GetModeByTor.m,[1;1;1]);"); // ex: m3 = [1,1,1,2,2,2,...,n,n,n]
Matlab.Execute("GetModeByTor.M = diag(GetModeByTor.m3);");
Matlab.Execute("GetModeByTor.m = diag(1 ./ sqrt(diag(GetModeByTor.M)));");
Matlab.Execute("GetModeByTor.mHm = GetModeByTor.m * GetModeByTor.H * GetModeByTor.m;");
Matlab.Execute("GetModeByTor.JmHmJ = GetModeByTor.J' * GetModeByTor.mHm * GetModeByTor.J;");
Matlab.Execute("[GetModeByTor.V, GetModeByTor.D] = eig(GetModeByTor.JmHmJ);");
Matlab.Execute("GetModeByTor.JV = GetModeByTor.m * GetModeByTor.J * GetModeByTor.V;");
Matrix V = Matlab.GetMatrix("GetModeByTor.V");
Vector D = Matlab.GetVector("diag(GetModeByTor.D)");
Matrix JV = Matlab.GetMatrix("GetModeByTor.JV");
Matlab.Clear("GetModeByTor");
for (int i = 0; i < m; i++)
{
toreigvecs[i] = V.GetColVector(i);
toreigvals[i] = D[i];
tormodes[i] = JV.GetColVector(i);
modes[i] = new Mode();
modes[i].eigval = toreigvals[i];
modes[i].eigvec = tormodes[i];
modes[i].th = i;
}
}
return(modes);
}
case "eig(JMJ^-1/2 * JHJ * JMJ^-1/2)":
/// Solve the problem of using eng(H,M).
///
/// eig(H,M) => H.v = M.v.l
/// H.(M^-1/2 . M^1/2).v = (M^1/2 . M^1/2).v.l
/// M^-1/2 . H.(M^-1/2 . M^1/2).v = M^1/2 .v.l
/// (M^-1/2 . H . M^-1/2) . (M^1/2.v) = (M^1/2.v).l
/// (M^-1/2 . H . M^-1/2) . w = w.l
/// where (M^1/2.v) = w
/// v = M^-1/2 . w
/// where M = V . D . V'
/// M^-1/2 = V . (1/sqrt(D)) . V'
/// M^-1/2 . M^-1/2 . M = (V . (1/sqrt(D)) . V') . (V . (1/sqrt(D)) . V') . (V . D . V')
/// = V . (1/sqrt(D)) . (1/sqrt(D)) . D . V'
/// = V . I . V'
/// = I
using (new Matlab.NamedLock("GetModeByTor"))
{
int n = J.ColSize;
int m = J.RowSize;
//Matrix M = massmat; // univ.GetMassMatrix(3);
Vector[] toreigvecs = new Vector[m];
Vector[] tormodes = new Vector[m];
double[] toreigvals = new double[m];
Mode[] modes = new Mode[m];
{
Matlab.Clear("GetModeByTor");
Matlab.PutMatrix("GetModeByTor.J", J.ToArray(), true);
//Matlab.PutMatrix("GetModeByTor.M", M , true);
//Matlab.PutMatrix("GetModeByTor.H", hessian, true);
Matlab.PutSparseMatrix("GetModeByTor.H", hessian.GetMatrixSparse(), 3, 3);
if (HDebug.IsDebuggerAttached && hessian.ColSize < 10000)
{
Matlab.PutMatrix("GetModeByTor.Htest", hessian.ToArray(), true);
double dHessErr = Matlab.GetValue("max(max(abs(GetModeByTor.H - GetModeByTor.Htest)))");
Matlab.Execute("clear GetModeByTor.Htest");
HDebug.Assert(dHessErr == 0);
}
Matlab.PutVector("GetModeByTor.m", masses); // ex: m = [1,2,...,n]
Matlab.Execute("GetModeByTor.m3 = kron(GetModeByTor.m,[1;1;1]);"); // ex: m3 = [1,1,1,2,2,2,...,n,n,n]
Matlab.Execute("GetModeByTor.M = diag(GetModeByTor.m3);");
Matlab.Execute("GetModeByTor.JMJ = GetModeByTor.J' * GetModeByTor.M * GetModeByTor.J;");
Matlab.Execute("GetModeByTor.JHJ = GetModeByTor.J' * GetModeByTor.H * GetModeByTor.J;");
Matlab.Execute("[GetModeByTor.V, GetModeByTor.D] = eig(GetModeByTor.JMJ);");
Matlab.Execute("GetModeByTor.jmj = GetModeByTor.V * diag(1 ./ sqrt(diag(GetModeByTor.D))) * GetModeByTor.V';"); // jmj = sqrt(JMJ)
//Matlab.Execute("max(max(abs(JMJ*jmj*jmj - eye(size(JMJ)))));"); // for checking
//Matlab.Execute("max(max(abs(jmj*JMJ*jmj - eye(size(JMJ)))));"); // for checking
//Matlab.Execute("max(max(abs(jmj*jmj*JMJ - eye(size(JMJ)))));"); // for checking
Matlab.Execute("[GetModeByTor.V, GetModeByTor.D] = eig(GetModeByTor.jmj * GetModeByTor.JHJ * GetModeByTor.jmj);");
Matlab.Execute("GetModeByTor.D = diag(GetModeByTor.D);");
Matlab.Execute("GetModeByTor.V = GetModeByTor.jmj * GetModeByTor.V;");
Matlab.Execute("GetModeByTor.JV = GetModeByTor.J * GetModeByTor.V;");
Matrix V = Matlab.GetMatrix("GetModeByTor.V", true);
Vector D = Matlab.GetVector("GetModeByTor.D");
Matrix JV = Matlab.GetMatrix("GetModeByTor.JV", true);
if (optoutJMJ != null)
{
optoutJMJ.value = Matlab.GetMatrix("GetModeByTor.JMJ", true);
}
if (optoutJM != null)
{
optoutJM.value = Matlab.GetMatrix("GetModeByTor.J' * GetModeByTor.M", true);
}
Matlab.Clear("GetModeByTor");
for (int i = 0; i < m; i++)
{
toreigvecs[i] = V.GetColVector(i);
toreigvals[i] = D[i];
tormodes[i] = JV.GetColVector(i);
modes[i] = new Mode();
modes[i].eigval = toreigvals[i];
modes[i].eigvec = tormodes[i];
modes[i].th = i;
}
}
return(modes);
}
case "fn-eig(JMJ^-1/2 * JHJ * JMJ^-1/2)":
/// Solve the problem of using eng(H,M).
///
/// eig(H,M) => H.v = M.v.l
/// H.(M^-1/2 . M^1/2).v = (M^1/2 . M^1/2).v.l
/// M^-1/2 . H.(M^-1/2 . M^1/2).v = M^1/2 .v.l
/// (M^-1/2 . H . M^-1/2) . (M^1/2.v) = (M^1/2.v).l
/// (M^-1/2 . H . M^-1/2) . w = w.l
/// where (M^1/2.v) = w
/// v = M^-1/2 . w
/// where M = V . D . V'
/// M^-1/2 = V . (1/sqrt(D)) . V'
/// M^-1/2 . M^-1/2 . M = (V . (1/sqrt(D)) . V') . (V . (1/sqrt(D)) . V') . (V . D . V')
/// = V . (1/sqrt(D)) . (1/sqrt(D)) . D . V'
/// = V . I . V'
/// = I
{
int n = J.ColSize;
int m = J.RowSize;
//Matrix M = massmat; // univ.GetMassMatrix(3);
Vector[] toreigvecs = new Vector[m];
Vector[] tormodes = new Vector[m];
double[] toreigvals = new double[m];
Mode[] modes = new Mode[m];
{
Matrix H = hessian; HDebug.Assert(hessian.ColSize == hessian.RowSize);
Matrix M = Matrix.Zeros(hessian.ColSize, hessian.RowSize); HDebug.Assert(3 * masses.Size == M.ColSize, M.ColSize == M.RowSize);
for (int i = 0; i < M.ColSize; i++)
{
M[i, i] = masses[i / 3];
}
Matrix Jt = J.Tr();
Matrix JMJ = fnMul(Jt, M, J); // JMJ = J' * M * J
Matrix JHJ = fnMul(Jt, H, J); // JHJ = J' * H * J
Matrix V; Vector D; { // [V, D] = eig(JMJ)
var VD = fnEigSymm(JMJ);
V = VD.Item1;
D = VD.Item2;
}
Matrix jmj; { // jmj = sqrt(JMJ)
Vector isD = new double[D.Size];
for (int i = 0; i < isD.Size; i++)
{
isD[i] = 1 / Math.Sqrt(D[i]);
}
jmj = fnMul(V, LinAlg.Diag(isD), V.Tr());
}
{ // [V, D] = eig(jmj * JHJ * jmj)
Matrix jmj_JHJ_jmj = fnMul(jmj, JHJ, jmj);
var VD = fnEigSymm(jmj_JHJ_jmj);
V = VD.Item1;
D = VD.Item2;
}
V = fnMul(jmj, V, null); // V = jmj * V
Matrix JV = fnMul(J, V, null); // JV = J * V
if (optoutJMJ != null)
{
optoutJMJ.value = JMJ;
}
if (optoutJM != null)
{
optoutJM.value = fnMul(Jt, M, null); // J' * M
}
for (int i = 0; i < m; i++)
{
toreigvecs[i] = V.GetColVector(i);
toreigvals[i] = D[i];
tormodes[i] = JV.GetColVector(i);
modes[i] = new Mode();
modes[i].eigval = toreigvals[i];
modes[i].eigvec = tormodes[i];
modes[i].th = i;
}
}
//if(Debug.IsDebuggerAttached)
//{
// Mode[] tmodes = GetModeByTorsional(hessian, masses, J);
// Debug.Assert(modes.Length == tmodes.Length);
// for(int i=0; i<modes.Length; i++)
// {
// Debug.AssertTolerance(0.00001, modes[i].eigval - tmodes[i].eigval);
// Debug.AssertTolerance(0.00001, modes[i].eigvec - tmodes[i].eigvec);
// }
//}
return(modes);
}
case "eig(JHJ,JMJ)":
/// Generalized eigendecomposition does not guarantee that the eigenvalue be normalized.
/// This becomes a problem when a B-factor (determined using eig(H,M)) is compared with another B-factor (determined using eig(M^-1/2 H M^-1/2)).
/// This problem is being solved using case "eig(JMJ^-1/2 * JHJ * JMJ^-1/2)"
using (new Matlab.NamedLock("GetModeByTor"))
{
int n = J.ColSize;
int m = J.RowSize;
//Matrix M = massmat; // univ.GetMassMatrix(3);
Matrix JMJ;
{
Matlab.PutMatrix("GetModeByTor.J", J);
//Matlab.PutMatrix("GetModeByTor.M", M);
Matlab.PutVector("GetModeByTor.m", masses); // ex: m = [1,2,...,n]
Matlab.Execute("GetModeByTor.m3 = kron(GetModeByTor.m,[1;1;1]);"); // ex: m3 = [1,1,1,2,2,2,...,n,n,n]
Matlab.Execute("GetModeByTor.M = diag(GetModeByTor.m3);");
Matlab.Execute("GetModeByTor.JMJ = GetModeByTor.J' * GetModeByTor.M * GetModeByTor.J;");
JMJ = Matlab.GetMatrix("GetModeByTor.JMJ");
Matlab.Clear("GetModeByTor");
}
Matrix JHJ;
{
Matlab.PutMatrix("GetModeByTor.J", J);
Matlab.PutMatrix("GetModeByTor.H", hessian);
Matlab.Execute("GetModeByTor.JHJ = GetModeByTor.J' * GetModeByTor.H * GetModeByTor.J;");
JHJ = Matlab.GetMatrix("GetModeByTor.JHJ");
Matlab.Clear("GetModeByTor");
}
Vector[] toreigvecs = new Vector[m];
Vector[] tormodes = new Vector[m];
double[] toreigvals = new double[m];
Mode[] modes = new Mode[m];
{
Matlab.PutMatrix("GetModeByTor.JHJ", JHJ);
Matlab.PutMatrix("GetModeByTor.JMJ", JMJ);
Matlab.PutMatrix("GetModeByTor.J", J);
Matlab.Execute("[GetModeByTor.V, GetModeByTor.D] = eig(GetModeByTor.JHJ, GetModeByTor.JMJ);");
Matlab.Execute("GetModeByTor.D = diag(GetModeByTor.D);");
Matlab.Execute("GetModeByTor.JV = GetModeByTor.J * GetModeByTor.V;");
Matrix V = Matlab.GetMatrix("GetModeByTor.V");
Vector D = Matlab.GetVector("GetModeByTor.D");
Matrix JV = Matlab.GetMatrix("GetModeByTor.JV");
Matlab.Clear("GetModeByTor");
for (int i = 0; i < m; i++)
{
toreigvecs[i] = V.GetColVector(i);
toreigvals[i] = D[i];
tormodes[i] = JV.GetColVector(i);
modes[i] = new Mode();
modes[i].eigval = toreigvals[i];
modes[i].eigvec = tormodes[i];
modes[i].th = i;
}
}
return(modes);
}
}
return(null);
}
public static Trans3 GetTrans(IList <Vector> C1, IList <Anisou> anisou1, IList <Vector> C2, HPack <double> optEnergy = null)
{
int size = C1.Count;
HDebug.Assert(size == C1.Count, size == C2.Count);
Vector[] C1s = C1.ToArray().Clone(3);
Vector[] C2s = C2.ToArray().Clone(3);
double[] W1s = new double[size * 3];
double[] enrgs = new double[size * 3];
for (int i = 0; i < size; i++)
{
HDebug.Assert(anisou1[i].eigvals[0] >= 0); W1s[i * 3 + 0] = (anisou1[i].eigvals[0] <= 0) ? 0 : 1 / anisou1[i].eigvals[0];
HDebug.Assert(anisou1[i].eigvals[1] >= 0); W1s[i * 3 + 1] = (anisou1[i].eigvals[1] <= 0) ? 0 : 1 / anisou1[i].eigvals[1];
HDebug.Assert(anisou1[i].eigvals[2] >= 0); W1s[i * 3 + 2] = (anisou1[i].eigvals[2] <= 0) ? 0 : 1 / anisou1[i].eigvals[2];
enrgs[i * 3 + 0] = enrgs[i * 3 + 1] = enrgs[i * 3 + 2] = double.NaN;
}
//Trans3 trans = ICP3.OptimalTransform(C2, C1);
Trans3 trans = new Trans3(new double[] { 0, 0, 0 }, 1, Quaternion.UnitRotation);// = transICP3.OptimalTransformWeighted(C2, C1, W1s);
int iter = 0;
int iter_max = 1000;
//double enrg = double.NaN;
while (iter < iter_max)
{
iter++;
Vector[] C2sUpdated = trans.GetTransformed(C2s);
//for(int i=0; i<size; i++)
System.Threading.Tasks.Parallel.For(0, size, delegate(int i)
{
for (int j = 0; j < 3; j++)
{
Vector planeNormal = anisou1[i].axes[j];
Vector planeBase = C1[i];
Vector query = C2sUpdated[i * 3 + j];
Vector closest = query - LinAlg.DotProd(planeNormal, query - planeBase) * planeNormal;
HDebug.AssertTolerance(0.00001, LinAlg.DotProd(closest - planeBase, planeNormal));
C1s[i * 3 + j] = closest;
enrgs[i * 3 + j] = W1s[i * 3 + j] * (query - closest).Dist2;
}
});
Trans3 dtrans = ICP3.OptimalTransformWeighted(C2sUpdated, C1s, W1s);
trans = Trans3.AppendTrans(trans, dtrans);
double max_dtrans_matrix = (dtrans.TransformMatrix - LinAlg.Eye(4)).ToArray().HAbs().HMax();
if (max_dtrans_matrix < 0.0000001)
{
break;
}
}
if (optEnergy != null)
{
optEnergy.value = enrgs.Sum() / size;
}
return(trans);
}
public static void Align(ref List <Vector>[] ensemble
, int maxiteration = int.MaxValue
, HPack <List <Trans3[]> > outTrajTrans = null
)
{
List <Vector>[] lensemble = ensemble.HClone <List <Vector> >();
int size = lensemble[0].Count;
for (int i = 1; i < lensemble.Length; i++)
{
HDebug.Assert(size == lensemble[i].Count);
}
// initial alignment using RMSD
Trans3[] transs = new Trans3[lensemble.Length];
transs[0] = Trans3.UnitTrans;
Vector[] coords = new Vector[size];
Anisou[] anisous = new Anisou[size];
double anisou_eigvalthres = 0.00001 * 0.00001;
double[] bfactors = new double[size];
{
// set ensemble[0] as the initial mean structure
for (int i = 0; i < size; i++)
{
coords[i] = lensemble[0][0].Clone();
}
// set anisou as sphere (with radii as one)
Anisou U0 = Anisou.FromMatrix(new double[3, 3] {
{ 1, 0, 0 }, { 0, 1, 0 }, { 0, 0, 1 }
});
for (int i = 0; i < anisous.Length; i++)
{
anisous[i] = U0;
}
// set bfactor as one
for (int i = 0; i < bfactors.Length; i++)
{
bfactors[i] = 1;
}
}
//List<double>[] bfactorss = new List<double>[ensemble.Length];
//for(int i=0; i<bfactorss.Length; i++)
// bfactorss[i] = new List<double>(bfactors);
//Pdb.ToFile("ensemble.000.pdb", null, lensemble, bfactorss);
System.Console.WriteLine("begin iterative alignment");
double move2 = double.PositiveInfinity;
//double thres = 0.00001;// *size * lensemble.Length;
double thres = 0.00001;// *size * lensemble.Length;
//List<Pdb.Atom> atoms = null;
//while(thres < move2)
for (int iter = 0; iter < maxiteration; iter++)
{
transs = new Trans3[ensemble.Length];
move2 = Align(lensemble, coords, anisous, transs);
if (outTrajTrans != null)
{
outTrajTrans.value.Add(transs);
}
System.Console.WriteLine(iter + "th alignment done: (move " + move2 + " Å)");
if (move2 < thres)
{
break;
}
DetermineMeanConf(lensemble, coords);
DetermineThrmlFluc(lensemble, coords, anisous, null, anisou_eigvalthres);
}
ensemble = lensemble;
}
public static Vector[] GenerateEnsemble(IList <Vector> coords, Mode[] modes, IList <double> mass, double temperature = 300, bool normalize = true, HPack <Vector> optOutRandNorms = null)
{
double[] invsqrtm = new double[mass.Count];
{
for (int i = 0; i < mass.Count; i++)
{
invsqrtm[i] = 1.0 / Math.Sqrt(mass[i]);
}
}
modes = modes.HRemoveAllNull().ToArray();
Vector randnorms;
{
Random rand = new Random();
randnorms = rand.NextNormalVector(modes.Length, 1);
if (normalize)
{
randnorms = randnorms.UnitVector();
}
}
if (optOutRandNorms != null)
{
optOutRandNorms.value = randnorms;
}
int size = mass.Count;
Vector[] ensemble = new Vector[size];
for (int i = 0; i < size; i++)
{
ensemble[i] = coords[i].Clone();
}
for (int m = 0; m < modes.Length; m++)
{
double eigval = modes[m].eigval;
Vector[] eigvec = modes[m].GetEigvecsOfAtoms();
HDebug.Assert(eigvec.Length == size);
double rfac = Math.Sqrt(3.0 * BOLTZ * temperature / eigval);
double disp = rfac * randnorms[m];
//for(int i=0; i<size; i++)
System.Threading.Tasks.Parallel.For(0, size, delegate(int i)
{
ensemble[i] += disp * eigvec[i] * invsqrtm[i];
});
}
return(ensemble);
}
public static Trans3 GetTrans(IList <Vector> C1, IList <Vector> C2, HPack <int> optIter = null, HPack <List <double> > optListWeightSum = null)
{
HDebug.Assert(false);
HDebug.Assert(C1.Count == C2.Count);
int size = C1.Count;
if (optIter != null)
{
optIter.value = 0;
}
int iter = 0;
Trans3 trans0 = new Trans3(new double[3], 1, Quaternion.UnitRotation);
Trans3 trans1 = Geometry.AlignPointPoint.MinRMSD.GetTrans(C2, C1);
if (optListWeightSum != null)
{
optListWeightSum.value = new List <double>();
}
double maxdist = 0;
for (int i = 0; i < size; i++)
{
Vector diff = C1[i] - trans1.DoTransform(C2[i]); maxdist = Math.Max(maxdist, diff.Dist);
}
while ((trans0.TransformMatrix - trans1.TransformMatrix).ToArray().HAbs().HMax() > 0.00000001)
{
iter++;
if (optIter != null)
{
optIter.value++;
}
Vector[] C2trans = trans1.GetTransformed(C2).ToArray();
Vector dist2s = new double[size];
Vector dists = new double[size];
for (int i = 0; i < size; i++)
{
double dist2 = (C1[i] - C2trans[i]).Dist2;
dist2 = HMath.Between(0.00001, dist2, double.PositiveInfinity);
dist2s[i] = dist2;
dists[i] = Math.Sqrt(dist2);
}
//int[] idxsort = dist2s.ToArray().IdxSorted().Reverse();
Vector weight = dists.Clone() / dists.ToArray().Max();
for (int i = 0; i < size; i++)
{
double w = weight[i];
//w = (w*2-1)*4;
w = (w - 1) * 4;
w = 1 / (1 + Math.Exp(-1 * w));
weight[i] = w;
}
//weight[idxsort[i]] = (i <= 6) ? 1 : 0;
if (optListWeightSum != null)
{
optListWeightSum.value.Add(weight.Sum());
}
trans0 = trans1;
trans1 = Geometry.AlignPointPoint.MinRMSD.GetTrans(C2, C1, weight.ToArray());
maxdist = 0;
for (int i = 0; i < size; i++)
{
Vector diff = C1[i] - trans1.DoTransform(C2[i]); maxdist = Math.Max(maxdist, diff.Dist);
}
}
return(trans1);
}
