Example #1
0
   void DCFreeHedron::BuildOld(TrialMol& oldMol, uint molIndex)
   {
      seed.BuildOld(oldMol, molIndex);
      PRNG& prng = data->prng;
      const CalculateEnergy& calc = data->calc;
      const Forcefield& ff = data->ff;
      uint nLJTrials = data->nLJTrialsNth;
      double* ljWeights = data->ljWeights;
      double* inter = data->inter;
	  double* real = data->real;
	  double* self = data->self;
	  double* corr = data->correction;

      //get info about existing geometry
      oldMol.SetBasis(hed.Focus(), hed.Prev());
      //Calculate OldMol Bond Energy &
      //Calculate phi weight for nTrials using actual theta of OldMol
      hed.ConstrainedAnglesOld(data->nAngleTrials - 1, oldMol);
      const XYZ center = oldMol.AtomPosition(hed.Focus());
      XYZArray* positions = data->multiPositions;
      double prevPhi[MAX_BONDS];
      for (uint i = 0; i < hed.NumBond(); ++i)
      {
         //get position and shift to origin
         positions[i].Set(0, oldMol.AtomPosition(hed.Bonded(i)));
         data->axes.UnwrapPBC(positions[i], 0, 1, oldMol.GetBox(), center);
         positions[i].Add(0, -center);
      }
      //add anchor atom
      positions[hed.NumBond()].Set(0, oldMol.AtomPosition(hed.Prev()));
      data->axes.UnwrapPBC(positions[hed.NumBond()], 0, 1,
			   oldMol.GetBox(), center);
      positions[hed.NumBond()].Add(0, -center);

      //counting backward to preserve prototype
      for (uint lj = nLJTrials; lj-- > 1;)
      {
         //convert chosen torsion to 3D positions
         RotationMatrix spin =
            RotationMatrix::UniformRandom(prng(), prng(), prng());
         for (uint b = 0; b < hed.NumBond() + 1; ++b)
         {
            //find positions
            positions[b].Set(lj, spin.Apply(positions[b][0]));
            positions[b].Add(lj, center);
         }
      }

      for (uint b = 0; b < hed.NumBond() + 1; ++b)
      {
         positions[b].Add(0, center);
         data->axes.WrapPBC(positions[b], oldMol.GetBox());
      }

      std::fill_n(inter, nLJTrials, 0.0);
      std::fill_n(real, nLJTrials, 0.0);
      std::fill_n(self, nLJTrials, 0.0);
	  std::fill_n(corr, nLJTrials, 0.0);
      for (uint b = 0; b < hed.NumBond(); ++b)
      {
         calc.ParticleInter(inter, real, positions[b], hed.Bonded(b),
                            molIndex, oldMol.GetBox(), nLJTrials);
		 if(DoEwald){
			 data->calc.SwapSelf(self, molIndex, hed.Bonded(b), oldMol.GetBox(), nLJTrials);
			data->calc.SwapCorrection(corr, oldMol, positions[b], hed.Bonded(b), oldMol.GetBox(), nLJTrials);
		 }
      }
      double stepWeight = 0;
      calc.ParticleInter(inter, real, positions[hed.NumBond()], hed.Prev(),
                         molIndex, oldMol.GetBox(), nLJTrials);
	  if(DoEwald){
		  data->calc.SwapSelf(self, molIndex, hed.Prev(), oldMol.GetBox(), nLJTrials);
		  data->calc.SwapCorrection(corr, oldMol, positions[hed.NumBond()], hed.Prev(), oldMol.GetBox(), nLJTrials);
	  }

      for (uint lj = 0; lj < nLJTrials; ++lj)
      {
         stepWeight += exp(-ff.beta * inter[lj]);
      }
      for(uint b = 0; b < hed.NumBond(); ++b)
      {
         oldMol.ConfirmOldAtom(hed.Bonded(b));
      }
      oldMol.ConfirmOldAtom(hed.Prev());
      oldMol.AddEnergy(Energy(hed.GetEnergy(), 0, inter[0], real[0], 0, self[0], corr[0]));
      oldMol.MultWeight(hed.GetWeight());
      oldMol.MultWeight(stepWeight);
   }
Example #2
0
 void DCLinkNoDih::AlignBasis(TrialMol& mol)
 {
    mol.SetBasis(focus, prev);
 }