Chimie Théorique » QMX

class Embed(Atoms):

    #--- constructor of the Embed class ---

        super(Embed, self).__init__()

        # define the atom map

        self.atom_map_sys_cl = []

        # set the cell of the system

        self.set_cell(system.get_cell())

        self.cell_cluster = cell_cluster

        return

    #--- set the cluster ---

        return self.atoms_system

    #--- Embedding ---

        # is the cluster and the host system definied ?

        if self.atoms_cluster is None or self.atoms_system is None:

            return

        self.find_cluster()

        print "link atoms found: ", len(self.linkatoms)

        if self.cell_cluster == "System":

            self.atoms_cluster.set_cell(self.atoms_system.get_cell())

            if bSysOnly:

                self.atom_map_sys_cl[iat_sys] = -1

        # local copies of xyz coordinates to avoid massive copying of xyz objects

        xyzs_cl=[]

        for atom_cl in self.atoms_cluster:

        xyzs_sys=[]

        for atom_sys in self.atoms_system:

            xyzs_sys.append(atom_sys.get_position())

        # number of atoms in the cluster and the system

        nat_cl=len(self.atoms_cluster)

        nat_sys=len(self.atoms_system)

                    r = np.sqrt(np.dot(xyz_diff, xyz_diff))

                    # ratio of the distance to the sum of covalent radius

                    f = r / (r_cl + r_sys)

                    if f <= (1+tol/100.) and f >= (1-2*tol/100.):

                        s = cell_L, self.atom_map_cl_sys[iat_cl], iat_sys, r_cl

                        bonds.append(s)

                    if f <= (1-2*tol/100.):

                        raise RuntimeError("QMX: The cluster atom", iat_cl, " and the system atom", iat_sys, "came too close")

        for bond in bonds:

            cell_L, iat_cl_sys, iat_sys, r_cl = bond

            # assign the tags for the border atoms

            # determine position of the link atom

            xyz_diff += xyzs_sys[iat_cl_sys]

            # create link atom

            # add atom to cluster

            self.atoms_cluster.append(atom)

            # add atom to the linkatoms