mythos.simulators.lammps.lammps_oxdna
=====================================

.. py:module:: mythos.simulators.lammps.lammps_oxdna

.. autoapi-nested-parse::

   LAMMPS-based OxDNA simulator for mythos.



Attributes
----------

.. autoapisummary::

   mythos.simulators.lammps.lammps_oxdna.REPLACEMENT_MAP
   mythos.simulators.lammps.lammps_oxdna.REPLACEMENT_MAP
   mythos.simulators.lammps.lammps_oxdna.LAMMPS_REQUIRED_FIELDS


Classes
-------

.. autoapisummary::

   mythos.simulators.lammps.lammps_oxdna.LAMMPSoxDNASimulator


Functions
---------

.. autoapisummary::

   mythos.simulators.lammps.lammps_oxdna._lammps_oxdna_replace_inputs
   mythos.simulators.lammps.lammps_oxdna._replace_parts_in_line
   mythos.simulators.lammps.lammps_oxdna._transform_param
   mythos.simulators.lammps.lammps_oxdna._transform_lammps_state
   mythos.simulators.lammps.lammps_oxdna._transform_lammps_quat
   mythos.simulators.lammps.lammps_oxdna._read_lammps_output


Module Contents
---------------

.. py:class:: LAMMPSoxDNASimulator

   Bases: :py:obj:`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).

   :param input_dir: Path to the directory containing the LAMMPS input files.
   :param overwrite: Whether to overwrite the input directory or copy to a
                     temporary directory.
   :param input_file_name: Name of the LAMMPS input file (default "input").
   :param energy_fn: Energy function used in the simulation, for updating parameters.
   :param 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".


   .. py:attribute:: energy_fn
      :type:  mythos.energy.base.EnergyFunction


   .. py:attribute:: input_file_name
      :type:  str
      :value: 'input'



   .. py:attribute:: variables
      :type:  dict[str, Any]


   .. py:method:: __post_init__() -> None


   .. py:method:: run_simulation(input_dir: pathlib.Path, params: mythos.utils.types.Params, seed: int | None = None) -> mythos.simulators.base.SimulatorOutput

      Run the simulation in the given input directory.



   .. py:method:: _replace_parameters(input_dir: pathlib.Path, params: mythos.utils.types.Params, seed: int | None) -> None


.. py:function:: _lammps_oxdna_replace_inputs(input_lines: list[str], params: list[dict[str, float]], seed: int | None, variables: dict[str, Any] | None = None) -> list[str]

.. py:function:: _replace_parts_in_line(inputs: str, replacements: tuple[str], params: dict[str, float]) -> str

.. py:data:: REPLACEMENT_MAP

.. py:data:: REPLACEMENT_MAP

.. py:function:: _transform_param(param: str, value: float) -> float

.. py:data:: LAMMPS_REQUIRED_FIELDS

.. py:function:: _transform_lammps_state(state: numpy.ndarray, fields: str) -> numpy.ndarray

.. py:function:: _transform_lammps_quat(quat: numpy.ndarray) -> numpy.ndarray

.. py:function:: _read_lammps_output(output_file: pathlib.Path) -> mythos.input.trajectory.Trajectory

   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.

   :param output_file: Path to the LAMMPS trajectory dump file.

   :returns: A Trajectory object in mythos format.