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chemlab Documentation, Release 0.4
orig: System Original system.
selection: np.ndarray of int or np.ndarray(NA) of bool A boolean array that is True when the ith atom has
to be selected or a set of atomic indices to be included.
Returns:
A new System instance.
chemlab.core.merge_systems(sysa, sysb, bounding=0.2)
Generate a system by merging sysa and sysb.
Overlapping molecules are removed by cutting the molecules of sysa that have atoms near the atoms of sysb.
The cutoff distance is defined by the bounding parameter.
Parameters
sysa: System First system
sysb: System Second system
bounding: float or False Extra space used when cutting molecules in sysa to make space for sysb. If it is False,
no overlap handling will be performed.
3.1.5 Routines to create Systems
chemlab.core.crystal(positions, molecules, group, cellpar=[1.0, 1.0, 1.0, 90, 90, 90], repetitions=[1,
1, 1])
Build a crystal from atomic positions, space group and cell parameters.
Parameters
positions: list of coordinates A list of the atomic positions
molecules: list of Molecule The molecules corresponding to the positions, the molecule will be translated in
all the equivalent positions.
group: int | str Space group given either as its number in International Tables or as its Hermann-Mauguin
symbol.
repetitions: Repetition of the unit cell in each direction
cellpar: Unit cell parameters
This function was taken and adapted from the spacegroup module found in ASE.
The module spacegroup module was originally developed by Jesper Frills.
chemlab.core.random_lattice_box(mol_list, mol_number, size, spacing=<Mock object>)
Make a box by placing the molecules specified in mol_list on random points of an evenly spaced lattice.
Using a lattice automatically ensures that no two molecules are overlapping.
Parameters
mol_list: list of Molecule instances A list of each kind of molecules to add to the system.
mol_number: list of int The number of molecules to place for each kind.
size: np.ndarray((3,), float) The box size in nm
spacing: np.ndarray((3,), float), [0.3 0.3 0.3] The lattice spacing in nm.
3.1. chemlab.core
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