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".
   :param temperature_variable: Name of the LAMMPS variable that holds the
                                simulation temperature in reduced units (kT). When the corresponding
                                variable is set, it is used to populate the temperature field of the
                                output trajectory.


   .. 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:attribute:: temperature_variable
      :type:  str
      :value: 'kt'



   .. 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.