/** \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;
}