LAMMPSSimulation

class narupatools.lammps.simulation.LAMMPSSimulation(lammps: lammps.PyLammps, universe: Optional[MDAnalysis.core.universe.Universe] = None)

Wrapper around a LAMMPS simulation.

Inheritance

Methods

__init__	Initialize self.
add_imd_force	Define an IMD force for the LAMMPS simulation.
clear_imd_force	Clear the IMD force on a specific atom.
command	Run an arbitrary LAMMPS command.
create_atom	Insert an atom into the simulation.
create_box	Create an empty simulation box with the given number of atom types.
create_new	Create a new LAMMPS simulation with the given units system.
create_region	Create a region in the simulation.
eval	Evaluate an arbitrary expression.
extract_compute	Extract value of a compute.
file	Runn all commands found in the provided input file.
from_file	Load LAMMPS simulation from a file.
gather_atoms	Gather a per-atom property from all the processors.
get_frame	Create a Narupa FrameData of the LAMMPS simulation.
get_imd_forces	Get the IMD forces on each atom in kilojoules per mole per angstrom.
run	Run the simulation for a given number of steps.
set_imd_force	Set the IMD force on a specific atom.
set_mass	Set the mass of a specified atom type.
setup_langevin	Setup a Langevin thermostat.

__init__(lammps: lammps.PyLammps, universe: Optional[MDAnalysis.core.universe.Universe] = None)

Initialize self. See help(type(self)) for accurate signature.

add_imd_force() → None

Define an IMD force for the LAMMPS simulation.

clear_imd_force(index: int) → None

Clear the IMD force on a specific atom.

Parameters

index – Index of the particle to clear.

command(command: str, clear_cache: bool = True) → None

Run an arbitrary LAMMPS command.

Running it through this interface means that all previously cached data such as positions etc. are cleared. If you are sure running the command will not affect any data, set clear_cache to False.

Parameters

• command – LAMMPS command to run.

• clear_cache – Should all cached information be cleared.

create_atom(*, type: int, position: numpy.ndarray[Any, numpy.dtype[numpy.float64]]) → None

Insert an atom into the simulation.

Parameters

• type – Type of the atom to insert.

• position – Position of the atom in nanometers.

create_box(n_types: int, region: Union[narupatools.lammps.region.Region, narupatools.lammps.region.RegionSpecification]) → None

Create an empty simulation box with the given number of atom types.

Parameters

• n_types – Number of atom types.

• region – Region to define.

Raises

ValueError – Region does belong to this simulation.

classmethod create_new(units: Literal[lj, real, metal, si, cgs, electron, micro, nano]) → narupatools.lammps.simulation.LAMMPSSimulation

Create a new LAMMPS simulation with the given units system.

This automatically runs the ‘atom_modify map yes’ command required to use atom IDs and hence allow certain operations such as setting positions.

Parameters

units – LAMMPS unit system to use.

Returns

LAMMPS simulation in provided units.

create_region(region: narupatools.lammps.region.RegionSpecification, *, id: Optional[str] = None) → narupatools.lammps.region.Region

Create a region in the simulation.

Parameters

• region – Specification to the region.

• id – Optional id for the region.

Returns

Region object.

eval(expression: str) → Any

Evaluate an arbitrary expression.

Parameters

expression – Expression to be evaluated using the eval command.

extract_compute(key: str, style: narupatools.lammps.constants.VariableStyle, type: Literal[<VariableType.SCALAR: 0>]) → float

extract_compute(key: str, style: narupatools.lammps.constants.VariableStyle, type: Literal[<VariableType.ARRAY: 2>]) → numpy.ndarray

extract_compute(key: str, style: narupatools.lammps.constants.VariableStyle, type: Literal[<VariableType.VECTOR: 1>]) → numpy.ndarray

Extract value of a compute.

Parameters

• key – ID of the compute.

• style – Style of the variable.

• type – Type of the variable.

Raises

• ComputeNotFoundError – Key does not match any known computes.

• InvalidComputeSpecificationError – Compute exists but doesn’t match style and type provided.

Returns

Value of the compute.

file(filename: str) → None

Runn all commands found in the provided input file.

classmethod from_file(filename: str, data_filename: str) → narupatools.lammps.simulation.LAMMPSSimulation

Load LAMMPS simulation from a file.

This automatically runs the ‘atom_modify map yes’ command required to use atom IDs and hence allow certain operations such as setting positions.

Parameters

• filename – Filename of LAMMPS input.

• data_filename – Filename of LAMMPS data file, used to generate MDAnalysis universe.

Returns

LAMMPS simulation based on file.

gather_atoms(key: str, type: narupatools.lammps.constants.PropertyType, dimension: int) → numpy.ndarray

Gather a per-atom property from all the processors.

Parameters

• key – Id of the property.

• type – Type of the variable.

• dimension – Dimension of the variable.

Raises

UnknownAtomPropertyError – Property was not found in the simulation.

Returns

Value of the atom property.

get_frame(*, fields: infinite_sets.infinite_sets.InfiniteSet[str], existing: Optional[narupa.trajectory.frame_data.FrameData] = None) → narupa.trajectory.frame_data.FrameData

Create a Narupa FrameData of the LAMMPS simulation.

Parameters

• fields – Fields to populate of the frame data.

• existing – Preexisting frame data.

Returns

FrameData with the appropriate fields.

get_imd_forces() → numpy.ndarray

Get the IMD forces on each atom in kilojoules per mole per angstrom.

run(steps: int = 1) → None

Run the simulation for a given number of steps.

Parameters

steps – Number of steps to run.

set_imd_force(index: int, force: numpy.ndarray[Any, numpy.dtype[numpy.float64]]) → None

Set the IMD force on a specific atom.

Parameters

• index – Index of the particle to set.

• force – IMD force to apply, in kilojoules per mole per nanometer.

set_mass(*, type: Union[int, slice], mass: float) → None

Set the mass of a specified atom type.

Parameters

• type – Atom type.

• mass – Mass in daltons.

setup_langevin(*, temperature: float, friction: float, seed: int) → None

Setup a Langevin thermostat.

Parameters

• temperature – Temperature in kelvin

• friction – Friction of the thermostat in inverse picoseconds.

• seed – Seed to use for random number generation.

Attributes

atom_ids	ID of each atom.
charges	Charge of each atom in elementary charges.
command_history	List of commands run on the simulation.
computes	Dictionary of computes indexed by their names.
forces	Forces on each atom in kilojoules per mole per nanometer.
kinetic_energy	Kinetic energy of the system in kilojoules per mole.
lammps_packages	List of installed LAMMPS packages.
masses	Masses of each atom in daltons.
positions	Positions of each atom in nanometers.
potential_energy	Potential energy of the system in kilojoules per mole.
pressure	Pressure of the system in kilojoules per nanometers cubed.
region_ids	List of region ids currently in use for the simulation.
temperature	Temperature of the system in kelvin.
timestep	Timestep of the simulation in picoseconds.
universe	An MDAnalysis Universe containing topology information.
velocities	Velocities of each atom in nanometers per picoseconds.

atom_ids

ID of each atom.

charges

Charge of each atom in elementary charges.

command_history

List of commands run on the simulation.

computes

Dictionary of computes indexed by their names.

forces

Forces on each atom in kilojoules per mole per nanometer.

kinetic_energy

Kinetic energy of the system in kilojoules per mole.

lammps_packages

List of installed LAMMPS packages.

masses

Masses of each atom in daltons.

positions

Positions of each atom in nanometers.

potential_energy

Potential energy of the system in kilojoules per mole.

The potential energy is computed using the ‘thermo_pe’ compute which is added to all LAMMPS simulations automatically. This uses the ‘pe’ compute style which includes contributions from pairs, bonds, angles, dihedrals, impropers, kspace and various fixes.

pressure

Pressure of the system in kilojoules per nanometers cubed.

region_ids

List of region ids currently in use for the simulation.

temperature

Temperature of the system in kelvin.

The temperature is computed using the ‘thermo_temp’ compute which is added to all LAMMPS simulations automatically. This uses the ‘temp’ compute style which uses the equation:

\[KE = \frac{D}{2} N k T\]

where \(KE\) is the kinetic energy, \(D\) is the dimension of the system, \(N\) is the number of atoms and \(k\) is the Boltzmann constant.

This removes degrees of freedom due to other fixes that limit molecular motion.

timestep

Timestep of the simulation in picoseconds.

universe

An MDAnalysis Universe containing topology information.

velocities

Velocities of each atom in nanometers per picoseconds.