Ejemplo n.º 1
0
int main () {

  PDBFile pdb ("temp.pdb");

  Molecule * mol = pdb.Molecules(0);
  mol->Name("qtz");
  std::vector<Atom *> atoms = mol->Atoms();

  /* cycle through each atom in order of the pdb file */
  RUN (atoms)
  {
	Atom * atom = atoms[i];
	atom->Residue("qtz");
	VecR pos = atom->Position();

	/* find the surface Oxygens */
	if (atom->Name().find("O") != string::npos && pos[z] > -7.9)
	{
	  /* add H's to the surface */
	  Atom * h = new Atom ("H", pos + VecR (0.0, 0.0, 1.1));
	  mol->AddAtom(h);
	}
  }
  std::vector<Molecule *> mols;
  mols.push_back(mol);
  PDBFile::WritePDB(mols);
}
Ejemplo n.º 2
0
// a copy constructor to do a deep copy of a molecule instead of just referencing a pre-existing one.
Molecule::Molecule (const Molecule& oldMol) :
    _atoms(oldMol._atoms),
    _wanniers(oldMol._wanniers),
    _centerofmass(oldMol._centerofmass),
    _mass(oldMol._mass),
    _name(oldMol._name),
    _ID (oldMol._ID),
    _moltype(oldMol._moltype),
    _DCM (oldMol._DCM) {
    this->Rename(oldMol.Name());
    ++numMolecules;
}
Ejemplo n.º 3
0
// Makes a repeating slab out of a single unit cell by creating copies and shifting
Mol_ptr_vec UnitCellToSlab (GridParams& params) {

  std::vector<Molecule *> mols;
  Molecule * uc = params.unitCell;

  VecR yshift, xshift, zshift;

  yshift.Zero();
  for (int i = 0; i < params.y; i++) {
    zshift.Zero();

    for (int j = 0; j < params.x; j++) {
      xshift.Zero();
      if (!(j % 2))
		xshift += params.x_shift * 0.5;

      for (int k = 0; k < params.z; k++) {

	// make a copy of the unitcell
	Molecule * copy = new Molecule();
	copy->Name(params.name);
	// make copies of all the atoms in the unitcell
	for (Atom_it atom_i = uc->begin(); atom_i != uc->end(); atom_i++) {
	//for (int atom = 0; atom < uc->size(); atom++) {
	  Atom * pa = new Atom (*(*atom_i));
	  copy->AddAtom(pa);
	}

	// shift the new copy to the next lattice point
	copy->Shift(yshift + xshift + zshift);
	mols.push_back(copy);

	xshift += params.x_shift;
      } 

      zshift += params.z_shift;
    } 
    yshift += params.y_shift;
  }

  return mols;
}
Ejemplo n.º 4
0
// Makes a repeating slab out of a single unit cell by creating copies and shifting
Mol_ptr_vec UnitCellToSlab (Molecule * uc, VecR& x_shift,VecR& y_shift, VecR& z_shift) {

  std::vector<Molecule *> mols;
  VecR yshift, xshift, zshift;
  for (int i = 0; i < 1; i++) {
    zshift.Zero();
    yshift.Zero();

    for (int j = 0; j < 6; j++) {
      xshift.Zero();

      for (int k = 0; k < 6; k++) {

	// make a copy of the unitcell
	Molecule * copy = new Molecule();
	copy->Name("qtz");
	// make copies of all the atoms in the unitcell
	for (int atom = 0; atom < uc->size(); atom++) {
	  Atom * pa = new Atom (*uc->Atoms(atom));
	  copy->AddAtom(pa);
	}

	// shift the new copy to the next lattice point
	copy->Shift(yshift + xshift + zshift);
	mols.push_back(copy);

	xshift += x_shift;
      } 

      yshift += y_shift;
    } 
    zshift += z_shift;
  }

  return mols;
}