C++ Box::BoxY方法代码示例

/** \param boxIn Box coordinates of Frame to image.
  * \param bp Output: Box + boundary.
  * \param bm Output: Box - boundary.
  * \param origin If true, image w.r.t. coordinate origin, otherwise box center.
  * \return 1 if box lengths are zero, 0 if setup completed successfully.
  */
int Image::SetupOrtho(Box const& boxIn, Vec3& bp, Vec3& bm, bool origin) {
  // Set up boundary information for orthorhombic cell
  if (origin) {
    bp = boxIn.Center();
    bm.SetVec( -bp[0], -bp[1], -bp[2] );
  } else {
    bp.SetVec( boxIn.BoxX(), boxIn.BoxY(), boxIn.BoxZ()  );
    bm.Zero();
  }
  if (bp.IsZero()) return 1;
  return 0;
}

// Ewald::Recip_ParticleMesh()
double Ewald_ParticleMesh::Recip_ParticleMesh(Box const& boxIn)
{
  t_recip_.Start();
  // This essentially makes coordsD and chargesD point to arrays.
  Mat coordsD(&coordsD_[0], Charge_.size(), 3);
  Mat chargesD(&Charge_[0], Charge_.size(), 1);
  int nfft1 = nfft_[0];
  int nfft2 = nfft_[1];
  int nfft3 = nfft_[2];
  if ( DetermineNfft(nfft1, nfft2, nfft3, boxIn) ) {
    mprinterr("Error: Could not determine grid spacing.\n");
    return 0.0;
  }
  // Instantiate double precision PME object
  // Args: 1 = Exponent of the distance kernel: 1 for Coulomb
  //       2 = Kappa
  //       3 = Spline order
  //       4 = nfft1
  //       5 = nfft2
  //       6 = nfft3
  //       7 = scale factor to be applied to all computed energies and derivatives thereof
  //       8 = max # threads to use for each MPI instance; 0 = all available threads used.
  // NOTE: Scale factor for Charmm is 332.0716
  // NOTE: The electrostatic constant has been baked into the Charge_ array already.
  //auto pme_object = std::unique_ptr<PMEInstanceD>(new PMEInstanceD());
  pme_object_.setup(1, ew_coeff_, order_, nfft1, nfft2, nfft3, 1.0, 0);
  // Sets the unit cell lattice vectors, with units consistent with those used to specify coordinates.
  // Args: 1 = the A lattice parameter in units consistent with the coordinates.
  //       2 = the B lattice parameter in units consistent with the coordinates.
  //       3 = the C lattice parameter in units consistent with the coordinates.
  //       4 = the alpha lattice parameter in degrees.
  //       5 = the beta lattice parameter in degrees.
  //       6 = the gamma lattice parameter in degrees.
  //       7 = lattice type
  pme_object_.setLatticeVectors(boxIn.BoxX(), boxIn.BoxY(), boxIn.BoxZ(),
                                boxIn.Alpha(), boxIn.Beta(), boxIn.Gamma(),
                                PMEInstanceD::LatticeType::XAligned);
  double erecip = pme_object_.computeERec(0, chargesD, coordsD);

  t_recip_.Stop();
  return erecip;
}

/** Given a box, determine number of FFT grid points in each dimension. */
int Ewald_ParticleMesh::DetermineNfft(int& nfft1, int& nfft2, int& nfft3, Box const& boxIn) const
{
   if (nfft1 < 1) {
    // Need even dimension for X direction
    nfft1 = ComputeNFFT( (boxIn.BoxX() + 1.0) * 0.5 );
    nfft1 *= 2;
  }
  if (nfft2 < 1)
    nfft2 = ComputeNFFT( boxIn.BoxY() );
  if (nfft3 < 1)
    nfft3 = ComputeNFFT( boxIn.BoxZ() );

  if (nfft1 < 1 || nfft2 < 1 || nfft3 < 1) {
    mprinterr("Error: Bad NFFT values: %i %i %i\n", nfft1, nfft2, nfft3);
    return 1;
  }
  if (debug_ > 0) mprintf("DEBUG: NFFTs: %i %i %i\n", nfft1, nfft2, nfft3);

  return 0;
}

/** The LJ PME reciprocal term. */
double Ewald_ParticleMesh::LJ_Recip_ParticleMesh(Box const& boxIn)
{
  t_recip_.Start();
  int nfft1 = nfft_[0];
  int nfft2 = nfft_[1];
  int nfft3 = nfft_[2];
  if ( DetermineNfft(nfft1, nfft2, nfft3, boxIn) ) {
    mprinterr("Error: Could not determine grid spacing.\n");
    return 0.0;
  }

  Mat coordsD(&coordsD_[0], Charge_.size(), 3);
  Mat cparamD(&Cparam_[0], Cparam_.size(), 1);

  //auto pme_vdw = std::unique_ptr<PMEInstanceD>(new PMEInstanceD());
  pme_vdw_.setup(6, lw_coeff_, order_, nfft1, nfft2, nfft3, -1.0, 0);
  pme_vdw_.setLatticeVectors(boxIn.BoxX(), boxIn.BoxY(), boxIn.BoxZ(),
                             boxIn.Alpha(), boxIn.Beta(), boxIn.Gamma(),
                             PMEInstanceD::LatticeType::XAligned);
  double evdwrecip = pme_vdw_.computeERec(0, cparamD, coordsD);
  t_recip_.Stop();
  return evdwrecip;
}