def generate_connections(self):
try:
self.atom_labels, self.bonds
except AttributeError:
raise Exception("Simulation has not been assigned atom types and bonds yet")
connect = Connector()
self.bond_types = connect.find_bond_types(self.atom_labels, self.bonds)
self.bond_labels = connect.bond_labels(
self.atom_labels, self.bonds, self.bond_types
)
self.bond_graph = self.generate_bond_graph(self.bonds)
self.angles = connect.angles(self.bonds, self.bond_graph)
self.angle_types = connect.find_angle_types(self.atom_labels, self.angles)
self.angle_labels = connect.angle_labels(
self.atom_labels, self.angles, self.angle_types
)
self.dihedrals = connect.dihedrals(self.bonds, self.bond_graph)
self.dihedral_types = connect.find_dihedral_types(
self.atom_labels, self.dihedrals
)
self.dihedral_labels = connect.dihedral_labels(
self.atom_labels, self.dihedrals, self.dihedral_types
)
self.impropers = connect.impropers(self.bonds, self.bond_graph)
self.improper_types = connect.find_improper_types(
self.atom_labels, self.impropers
)
self.improper_labels = connect.improper_labels(
self.atom_labels, self.impropers, self.improper_types
)
def generate_connections(self):
connect = Connector()
bond_types, angle_types, torsion_types, improper_types = self.molecule.connection_types()
self.bonds = self.molecule.assign_bonds(self.lattice_dimensions)
self.bond_labels = connect.bond_labels(self.atom_labels, self.bonds, bond_types)
self.angles = connect.angles(self.bonds)
self.angle_labels = connect.angle_labels(self.atom_labels, self.angles, angle_types)
self.torsions = connect.torsions(self.bonds)
self.torsion_labels = connect.torsion_labels(self.atom_labels, self.torsions, torsion_types)
self.impropers = connect.impropers(self.bonds)
self.improper_labels = connect.improper_labels(self.atom_labels, self.impropers, improper_types)
[14, 37], [38, 12], [38, 13], [13, 39], [38, 40],
[37, 41], [41, 42], [41, 43], [41, 44], [42, 45],
[42, 46], [42, 47], [45, 46], [45, 48], [45, 49]]))
from connector import Connector
from write_coords import Writer
from params import Parameterise
connect = Connector()
epoxy.bond_types = connect.find_bond_types(epoxy.atom_labels, epoxy.bonds)
epoxy.bond_labels = connect.bond_labels(epoxy.atom_labels, epoxy.bonds,
epoxy.bond_types)
epoxy.angles = connect.angles(epoxy.bonds)
epoxy.angle_types = connect.find_angle_types(epoxy.atom_labels, epoxy.angles)
epoxy.angle_labels = connect.angle_labels(epoxy.atom_labels, epoxy.angles,
epoxy.angle_types)
epoxy.torsions = connect.torsions(epoxy.bonds)
epoxy.torsion_types = connect.find_torsion_types(epoxy.atom_labels,
epoxy.torsions)
epoxy.torsion_labels = connect.torsion_labels(epoxy.atom_labels,
epoxy.torsions,
epoxy.torsion_types)
epoxy.impropers = connect.impropers(epoxy.bonds)
epoxy.improper_types = connect.find_improper_types(epoxy.atom_labels,
epoxy.impropers)
epoxy.improper_labels = connect.improper_labels(epoxy.atom_labels,
epoxy.impropers,
epoxy.improper_types)
epoxy.masses = [0] * len(epoxy.coords)
#output.write_xyz('epoxy.xyz')
from connector import Connector
from write_coords import Writer
from params import Parameterise
connect = Connector()
diamine.bond_types = connect.find_bond_types(diamine.atom_labels,
diamine.bonds)
diamine.bond_labels = connect.bond_labels(diamine.atom_labels, diamine.bonds,
diamine.bond_types)
diamine.angles = connect.angles(diamine.bonds)
diamine.angle_types = connect.find_angle_types(diamine.atom_labels,
diamine.angles)
diamine.angle_labels = connect.angle_labels(diamine.atom_labels,
diamine.angles,
diamine.angle_types)
diamine.torsions = connect.torsions(diamine.bonds)
diamine.torsion_types = connect.find_torsion_types(diamine.atom_labels,
diamine.torsions)
diamine.torsion_labels = connect.torsion_labels(diamine.atom_labels,
diamine.torsions,
diamine.torsion_types)
diamine.impropers = connect.impropers(diamine.bonds)
diamine.improper_types = connect.find_improper_types(diamine.atom_labels,
diamine.impropers)
diamine.improper_labels = connect.improper_labels(diamine.atom_labels,
diamine.impropers,
diamine.improper_types)
diamine.masses = [0] * len(diamine.coords)
from connector import Connector
from write_coords import Writer
from params import Parameterise
connect = Connector()
propanol.bond_types = connect.find_bond_types(propanol.atom_labels,
propanol.bonds)
propanol.bond_labels = connect.bond_labels(propanol.atom_labels,
propanol.bonds, propanol.bond_types)
propanol.angles = connect.angles(propanol.bonds)
propanol.angle_types = connect.find_angle_types(propanol.atom_labels,
propanol.angles)
propanol.angle_labels = connect.angle_labels(propanol.atom_labels,
propanol.angles,
propanol.angle_types)
propanol.torsions = connect.torsions(propanol.bonds)
propanol.torsion_types = connect.find_torsion_types(propanol.atom_labels,
propanol.torsions)
propanol.torsion_labels = connect.torsion_labels(propanol.atom_labels,
propanol.torsions,
propanol.torsion_types)
propanol.impropers = connect.impropers(propanol.bonds)
propanol.improper_types = connect.find_improper_types(propanol.atom_labels,
propanol.impropers)
propanol.improper_labels = connect.improper_labels(propanol.atom_labels,
propanol.impropers,
propanol.improper_types)
propanol.masses = [0] * len(propanol.coords)
from connector import Connector
from write_coords import Writer
from params import Parameterise
connect = Connector()
bp.bond_types = connect.find_bond_types(bp.atom_labels,bp.bonds)
bp.bond_labels = connect.bond_labels(bp.atom_labels,bp.bonds,bp.bond_types)
bp.angles = connect.angles(bp.bonds)
bp.angle_types = connect.find_angle_types(bp.atom_labels,
bp.angles)
bp.angle_labels = connect.angle_labels(bp.atom_labels,bp.angles,
bp.angle_types)
bp.torsions = connect.torsions(bp.bonds)
bp.torsion_types = connect.find_torsion_types(bp.atom_labels,
bp.torsions)
bp.torsion_labels = connect.torsion_labels(bp.atom_labels,bp.torsions,
bp.torsion_types)
bp.impropers = connect.impropers(bp.bonds)
bp.improper_types = connect.find_improper_types(bp.atom_labels,
bp.impropers)
bp.improper_labels = connect.improper_labels(bp.atom_labels,bp.impropers,
bp.improper_types)
bp.masses = [0] * len(bp.coords)
#output.write_xyz('bp.xyz')
p = Parameterise(bp.vdw_defs)