mythos.simulators.lammps.lammps_oxdna

LAMMPS-based OxDNA simulator for mythos.

Attributes

`REPLACEMENT_MAP`
`REPLACEMENT_MAP`
`LAMMPS_REQUIRED_FIELDS`

Classes

LAMMPSoxDNASimulator

LAMMPS-based OxDNA simulator.

Functions

`_lammps_oxdna_replace_inputs`(→ list[str])
`_replace_parts_in_line`(→ str)
`_transform_param`(→ float)
`_transform_lammps_state`(→ numpy.ndarray)
`_transform_lammps_quat`(→ numpy.ndarray)
`_read_lammps_output`(→ mythos.input.trajectory.Trajectory)	Reads LAMMPS trajectory dump file and extracts the final energy values.

Module Contents

class mythos.simulators.lammps.lammps_oxdna.LAMMPSoxDNASimulator[source]

Bases: mythos.simulators.base.InputDirSimulator

LAMMPS-based OxDNA simulator.

Please note that for LAMMPS simulations of oxDNA, BondedExcludedVolume should be left out of the energy function, as LAMMPS does not implement it (or does not in a compatible way).

Parameters:

input_dir – Path to the directory containing the LAMMPS input files.
overwrite – Whether to overwrite the input directory or copy to a temporary directory.
input_file_name – Name of the LAMMPS input file (default “input”).
energy_fn – Energy function used in the simulation, for updating parameters.
variables – Additional variables to set in the LAMMPS input file before run. These variables must already be defined in the input file using a command of the form “variable name equal value”.

energy_fn: mythos.energy.base.EnergyFunction

input_file_name: str = 'input'

variables: dict[str, Any]

__post_init__() → None[source]

run_simulation(input_dir: pathlib.Path, params: mythos.utils.types.Params, seed: int | None = None) → mythos.simulators.base.SimulatorOutput[source]: Run the simulation in the given input directory.

_replace_parameters(input_dir: pathlib.Path, params: mythos.utils.types.Params, seed: int | None) → None[source]

mythos.simulators.lammps.lammps_oxdna._lammps_oxdna_replace_inputs(input_lines: list[str], params: list[dict[str, float]], seed: int | None, variables: dict[str, Any] | None = None) → list[str][source]

mythos.simulators.lammps.lammps_oxdna._replace_parts_in_line(inputs: str, replacements: tuple[str], params: dict[str, float]) → str[source]

mythos.simulators.lammps.lammps_oxdna.REPLACEMENT_MAP

mythos.simulators.lammps.lammps_oxdna.REPLACEMENT_MAP

mythos.simulators.lammps.lammps_oxdna._transform_param(param: str, value: float) → float[source]

mythos.simulators.lammps.lammps_oxdna.LAMMPS_REQUIRED_FIELDS

mythos.simulators.lammps.lammps_oxdna._transform_lammps_state(state: numpy.ndarray, fields: str) → numpy.ndarray[source]

mythos.simulators.lammps.lammps_oxdna._transform_lammps_quat(quat: numpy.ndarray) → numpy.ndarray[source]

mythos.simulators.lammps.lammps_oxdna._read_lammps_output(output_file: pathlib.Path) → mythos.input.trajectory.Trajectory[source]

Reads LAMMPS trajectory dump file and extracts the final energy values.

The file must have been created by a dump LAMMPS dump command similar to:

compute quat all property/atom quatw quati quatj quatk dump {name} all custom {freq} trajectory.dat x y z vx vy vz &

c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz

noting that the above fields are required, but other fields may also be present in the dump.

Parameters:: output_file – Path to the LAMMPS trajectory dump file.
Returns:: A Trajectory object in mythos format.