def combine_holders(
holder1,
holder2,
holder1_bond_path=".tmp/bonds.dat",
holder2_bond_path=".tmp/bonds.dat",
out_path=".tmp/bonds.dat",
vector=np.zeros(3),
atom_link_list=[],
opt_ids=False,
):
holder1, atom_ids1 = reassign_atom_ids(holder1)
bonds1 = readbond(holder1_bond_path)
holder2, atom_ids2 = reassign_atom_ids(holder2, start_id=holder1.num_atoms)
bonds2 = readbond(holder2_bond_path)
atom_id = 0
holder_new = createHolder(holder1.num_atoms + holder2.num_atoms)
for i in sorted(holder1.pos):
holder_new.pos[atom_id] = holder1.pos[i]
holder_new.el_names[atom_id] = holder1.el_names[i]
holder_new.atom_types[atom_id] = holder1.atom_types[i]
atom_id += 1
for i in sorted(holder2.pos):
holder_new.pos[atom_id] = holder2.pos[i] + vector
holder_new.el_names[atom_id] = holder2.el_names[i]
holder_new.atom_types[atom_id] = holder2.atom_types[i]
atom_id += 1
bonds_file = open(out_path, "w")
bonds_file.write("BONDS\n")
bonds_file.write("\n")
bond_id = 1
for bond in bonds1:
atom1 = bond[0]
atom2 = bond[1]
bonds_file.write("%d 1 %d %d\n" % (bond_id, atom_ids1[atom1], atom_ids1[atom2]))
bond_id += 1
for bond in bonds2:
atom1 = bond[0]
atom2 = bond[1]
bonds_file.write("%d 1 %d %d\n" % (bond_id, atom_ids2[atom1], atom_ids2[atom2]))
bond_id += 1
if atom_link_list:
for link_list in atom_link_list:
bonds_file.write(
"%d 1 %d %d\n"
% (bond_id, atom_ids1[link_list[0]], atom_ids2[link_list[1]])
)
bonds_file.close()
if opt_ids:
return holder_new, atom_ids1, atom_ids2
else:
return holder_new
def reassign_atom_ids(holder, start_id=0):
atom_ids = {}
atom_id = 0
holder_new = createHolder(holder.num_atoms)
for i in sorted(holder.pos):
holder_new.pos[atom_id] = holder.pos[i]
holder_new.el_names[atom_id] = holder.el_names[i]
holder_new.atom_types[atom_id] = holder.atom_types[i]
atom_id += 1
atom_ids[i + 1] = atom_id + start_id
return holder_new, atom_ids
def create_centered_chain(self):
holder = createHolder(self.holder.num_atoms)
array = np.array([self.a / 2, self.b / 2, 0])
chain_cluster = Cluster()
for atom in self.holder.pos:
chain_cluster.add_particle(Sphere(self.holder.pos[atom]))
holder.el_names[atom] = self.holder.el_names[atom]
translator = Translator()
chain_cluster.move(translator, array=array)
for i in range(holder.num_atoms):
holder.pos[i] = chain_cluster.particles[i].center
return holder
def combine_holders(
holder1,
holder2,
holder1_bond_path=".tmp/bonds.dat",
holder2_bond_path=".tmp/bonds.dat",
out_path=".tmp/bonds.dat",
):
holder1, atom_ids1 = reassign_atom_ids(holder1)
bonds1 = readbond(holder1_bond_path)
holder2, atom_ids2 = reassign_atom_ids(holder2, start_id=holder1.num_atoms)
bonds2 = readbond(holder2_bond_path)
atom_id = 0
holder_new = createHolder(holder1.num_atoms + holder2.num_atoms)
for i in sorted(holder1.pos):
holder_new.pos[atom_id] = holder1.pos[i]
holder_new.el_names[atom_id] = holder1.el_names[i]
holder_new.atom_types[atom_id] = holder1.atom_types[i]
atom_id += 1
for i in sorted(holder2.pos):
holder_new.pos[atom_id] = holder2.pos[i]
holder_new.el_names[atom_id] = holder2.el_names[i]
holder_new.atom_types[atom_id] = holder2.atom_types[i]
atom_id += 1
bonds_file = open(out_path, "w")
bonds_file.write("BONDS\n")
bonds_file.write("\n")
bond_id = 1
for bond in bonds1:
atom1 = bond[0]
atom2 = bond[1]
bonds_file.write("%d 1 %d %d\n" %
(bond_id, atom_ids1[atom1], atom_ids1[atom2]))
bond_id += 1
for bond in bonds2:
atom1 = bond[0]
atom2 = bond[1]
bonds_file.write("%d 1 %d %d\n" %
(bond_id, atom_ids2[atom1], atom_ids2[atom2]))
bond_id += 1
bonds_file.close()
return holder_new