Place molecules on a lattice — MMTK User Guide 2.7.7 documentation

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# Place molecules on a lattice

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    # Example: water molecules on a lattice
    #
    # This example creates a system of water molecules whose centers
    # of mass are positioned simple cubic lattice consisting of
    # 3x4x5 cells, i.e. there are 60 water molecules in total.
    # The molecules are put into a suitably sized periodic universe.
    #

    from MMTK import *
    from Scientific.Geometry.Objects3D import SCLattice
    from MMTK.Visualization import view

    # Define parameters of the lattice
    edge_length = 0.5*Units.nm
    lattice_size = (3, 4, 5)

    # Construct the universe
    universe = OrthorhombicPeriodicUniverse((edge_length*lattice_size[0],
                                             edge_length*lattice_size[1],
                                             edge_length*lattice_size[2]))

    # Add the water molecules
    for point in SCLattice(edge_length, lattice_size):
        universe.addObject(Molecule('water', position = point))

    # Visualization
    view(universe)

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