atomman package
Submodules
Classes
Functions and attributes
- atomman.build_lammps_potential(pair_style: str, **kwargs)
Wrapper function for the PotentialLAMMPSBuilder subclasses.
- Parameters:
pair_style (str) – The LAMMPS pair_style setting associated with the potential.
**kwargs (any) – Any keyword parameters supported by PotentialLAMMPSBuilder and the subclass that matches the pair_style.
- atomman.displacement(system_0, system_1, box_reference: str = 'final') ndarray
Compute the displacement vectors between all matching atoms for two systems.
- Parameters:
system_0 (atomman.System) – The initial system to calculate displacements from.
system_1 (atomman.System) – The final system to calculate displacements to.
box_reference (str or None) – Specifies which system’s boundary conditions to use. ‘initial’ uses system_0’s box and pbc. ‘final’ uses system_1’s box and pbc (Default) None computes the straight difference between the positions without accounting for periodic boundaries.
- Returns:
The displacement vectors for all atoms.
- Return type:
numpy.ndarray
- Raises:
ValueError – If the systems have different numbers of atoms or for invalid box_reference values.
- atomman.dmag()
Computes the shortest distance between pos_0 and pos_1 using box dimensions and accounting for periodic boundaries.
- Parameters:
pos_0 (numpy.ndarray, list, or tuple) – Absolute Cartesian vector position(s) to use as reference point(s).
pos_1 (numpy.ndarray, list, or tuple) – Absolute Cartesian vector position(s) to find relative to pos_0.
box (atomman.Box) – Defines the system/box dimensions
pbc (list, tuple, or numpy.ndarray of bool.) – Three Boolean values indicating which of the three box vectors are periodic (True means periodic).
- Returns:
The shortest vector magnitude from each pos_0 to pos_1 positions.
- Return type:
numpy.ndarray
- atomman.dump(style, system, **kwargs)
Convert a System to another format.
- Parameters:
style (str) – Indicates the format of the content to dump the atomman.System as.
system (atomman.System) – The system to convert.
kwargs (any, optional) – Any extra keyword arguments to pass to the underlying dump methods.
- Returns:
Any content returned by the underlying dump methods.
- Return type:
- atomman.dvect()
Computes the shortest vector between pos_0 and pos_1 using box dimensions and accounting for periodic boundaries.
- Parameters:
pos_0 (numpy.ndarray, list, or tuple) – Absolute Cartesian vector position(s) to use as reference point(s).
pos_1 (numpy.ndarray, list, or tuple) – Absolute Cartesian vector position(s) to find relative to pos_0.
box (atomman.Box) – Defines the system/box dimensions
pbc (list, tuple, or numpy.ndarray of bool.) – Three Boolean values indicating which of the three box vectors are periodic (True means periodic).
- Returns:
The shortest vectors from each pos_0 to pos_1 positions.
- Return type:
numpy.ndarray
- atomman.load(style, *args, **kwargs)
Load a System from another format.
- Parameters:
style (str) – Indicates the format of the content to load as an atomman.System
args – Any positional-dependent arguments to pass to the underlying load methods.
kwargs – Any keyword arguments to pass to the underlying load methods.
- Returns:
system – The system object associated with the data model.
- Return type:
- atomman.nlist()
Calculates a neighbor list for all atoms in a System taking periodic boundaries into account.
- Parameters:
system (atomman.System) – The system to calculate the neighbor list for.
cutoff (float) – Radial cutoff distance for identifying neighbors.
initialsize (int, optional) – The number of neighbor positions to initially assign to each atom. Default value is 20.
deltasize (int, optional) – Specifies the number of extra neighbor positions to allow each atom when the number of neighbors exceeds the underlying array size. Default value is 10.
- Returns:
Array listing number of neighbors and neighbor ids for each atom in System. First term in each row is the atom’s coordination number, c. The next c values are the atom’s neighbor ids.
- Return type:
numpy.ndarray of int