C++ Topology::Nonbond方法代码示例

/** Set up the exclusion list based on the given mask and parm.
  * \return the total number of interactions, -1 on error.
  */
int Action_Pairwise::SetupNonbondParm(AtomMask const& maskIn, Topology const& ParmIn) {
  // Check if LJ parameters present - need at least 2 atoms for it to matter.
  if (ParmIn.Natom() > 1 && !ParmIn.Nonbond().HasNonbond()) {
    mprinterr("Error: Topology does not have LJ information.\n");
    return -1;
  }

  // Determine the actual number of pairwise interactions that will be calcd.
  // This is ((N^2 - N) / 2) - SUM[ #excluded atoms]
  int N_interactions = ((maskIn.Nselected() * maskIn.Nselected()) - maskIn.Nselected()) / 2;
  for (AtomMask::const_iterator at = maskIn.begin(); at != maskIn.end(); ++at)
    N_interactions -= ParmIn[ *at ].Nexcluded();

  // DEBUG - Print total number of interactions for this parm
  mprintf("\t%i interactions for this parm.\n",N_interactions);

  // DEBUG - Print exclusion list for each atom
  /*for (unsigned int atom = 0; atom < exclusionList.size(); atom++) {
    mprintf("\t%8u:",atom + 1);
    for (std::vector<int>::iterator eat = exclusionList[atom].begin();
                                    eat != exclusionList[atom].end();
                                    eat++)
    {
      mprintf(" %i",*eat + 1);
    }
    mprintf("\n");
  }*/
  return N_interactions;
}

/** Determine VDW long range correction prefactor. */
void Ewald::Setup_VDW_Correction(Topology const& topIn, AtomMask const& maskIn) {
  Vdw_Recip_term_ = 0.0;
  NB_ = static_cast<NonbondParmType const*>( &(topIn.Nonbond()) );
  if (!NB_->HasNonbond()) {
    mprintf("Warning: '%s' has no nonbonded parameters. Cannot calculate VDW correction.\n",
            topIn.c_str());
    return;
  }
  // Count the number of each unique nonbonded type.
  Iarray N_vdw_type( NB_->Ntypes(), 0 );
  for (AtomMask::const_iterator atm = maskIn.begin(); atm != maskIn.end(); ++atm)
    N_vdw_type[ topIn[*atm].TypeIndex() ]++;
  if (debug_ > 0) {
    mprintf("DEBUG: %zu VDW types.\n", N_vdw_type.size());
    for (Iarray::const_iterator it = N_vdw_type.begin(); it != N_vdw_type.end(); ++it)
      mprintf("\tType %li = %i\n", it-N_vdw_type.begin(), *it);
  }
  // Determine correction term from types and LJ B parameters
  for (unsigned int itype = 0; itype != N_vdw_type.size(); itype++)
  {
    unsigned int offset = N_vdw_type.size() * itype;
    for (unsigned int jtype = 0; jtype != N_vdw_type.size(); jtype++)
    {
      unsigned int idx = offset + jtype;
      int nbidx = NB_->NBindex()[ idx ];
      if (nbidx > -1)
        Vdw_Recip_term_ += N_vdw_type[itype] * N_vdw_type[jtype] * NB_->NBarray()[ nbidx ].B();
    }
  }
}

/** Sets the temporary charge array and makes sure that we have the necessary
  * parameters in our topology to calculate nonbonded energy terms
  */
int Action_LIE::SetupParms(Topology const& ParmIn) {
  if (!ParmIn.Nonbond().HasNonbond()) {
    mprinterr("Error: Topology does not have LJ information.\n");
    return 1;
  }
  // Store the charges
  atom_charge_.clear();
  atom_charge_.reserve( ParmIn.Natom() );
  for (Topology::atom_iterator atom = ParmIn.begin();
                               atom != ParmIn.end(); ++atom)
    atom_charge_.push_back( atom->Charge() * Constants::ELECTOAMBER / sqrt(dielc_) );
  return 0;
}