iphasimulator.trajectory_gromacs_merge
======================================

.. py:module:: iphasimulator.trajectory_gromacs_merge

.. autoapi-nested-parse::

   Merge restarted GROMACS trajectory and energy outputs for one simulation.



Attributes
----------

.. autoapisummary::

   iphasimulator.trajectory_gromacs_merge.Runner
   iphasimulator.trajectory_gromacs_merge.OutputKind
   iphasimulator.trajectory_gromacs_merge.INITIAL_PREFIX
   iphasimulator.trajectory_gromacs_merge.CONTINUATION_PREFIX
   iphasimulator.trajectory_gromacs_merge.TRAJECTORY_OUTPUT_PREFIX


Classes
-------

.. autoapisummary::

   iphasimulator.trajectory_gromacs_merge.DiscoveredGromacsOutputs
   iphasimulator.trajectory_gromacs_merge.GromacsCheckResult
   iphasimulator.trajectory_gromacs_merge.GromacsMergeCommandResult
   iphasimulator.trajectory_gromacs_merge.GromacsMergeOutputsResult


Functions
---------

.. autoapisummary::

   iphasimulator.trajectory_gromacs_merge.discover_gromacs_outputs
   iphasimulator.trajectory_gromacs_merge.maximum_trajectory_part
   iphasimulator.trajectory_gromacs_merge.maximum_energy_part
   iphasimulator.trajectory_gromacs_merge.trajectory_output_filename
   iphasimulator.trajectory_gromacs_merge.energy_output_filename
   iphasimulator.trajectory_gromacs_merge.run_gmx_check
   iphasimulator.trajectory_gromacs_merge.merge_simulation_outputs
   iphasimulator.trajectory_gromacs_merge.build_argument_parser
   iphasimulator.trajectory_gromacs_merge.main


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

.. py:data:: Runner

.. py:data:: OutputKind

.. py:data:: INITIAL_PREFIX
   :value: 'step7_production'


.. py:data:: CONTINUATION_PREFIX
   :value: 'step8_production_2us'


.. py:data:: TRAJECTORY_OUTPUT_PREFIX
   :value: 'production_combined'


.. py:class:: DiscoveredGromacsOutputs

   Raw XTC and EDR files discovered independently.


   .. py:attribute:: simulation_dir
      :type:  pathlib.Path


   .. py:attribute:: xtc_files
      :type:  tuple[pathlib.Path, ...]


   .. py:attribute:: edr_files
      :type:  tuple[pathlib.Path, ...]


.. py:class:: GromacsCheckResult

   Result of one checked ``gmx check`` command.


   .. py:attribute:: kind
      :type:  OutputKind


   .. py:attribute:: path
      :type:  pathlib.Path


   .. py:attribute:: command
      :type:  tuple[str, ...]


   .. py:attribute:: start_time_ps
      :type:  float | None


   .. py:attribute:: end_time_ps
      :type:  float | None


   .. py:attribute:: stdout
      :type:  str


   .. py:attribute:: stderr
      :type:  str


.. py:class:: GromacsMergeCommandResult

   Result of one checked ``gmx trjcat`` or ``gmx eneconv`` command.


   .. py:attribute:: kind
      :type:  OutputKind


   .. py:attribute:: command
      :type:  tuple[str, ...]


   .. py:attribute:: input_files
      :type:  tuple[pathlib.Path, ...]


   .. py:attribute:: output_path
      :type:  pathlib.Path


   .. py:attribute:: stdout
      :type:  str


   .. py:attribute:: stderr
      :type:  str


.. py:class:: GromacsMergeOutputsResult

   Structured discovery, command, and validation results.


   .. py:attribute:: discovered
      :type:  DiscoveredGromacsOutputs


   .. py:attribute:: trajectory_output
      :type:  pathlib.Path


   .. py:attribute:: energy_output
      :type:  pathlib.Path


   .. py:attribute:: input_checks
      :type:  tuple[GromacsCheckResult, ...]


   .. py:attribute:: trajectory_merge
      :type:  GromacsMergeCommandResult | None


   .. py:attribute:: energy_merge
      :type:  GromacsMergeCommandResult | None


   .. py:attribute:: output_checks
      :type:  tuple[GromacsCheckResult, ...]


   .. py:attribute:: energy_skipped_reason
      :type:  str | None


   .. py:attribute:: dry_run
      :type:  bool


.. py:function:: discover_gromacs_outputs(simulation_dir: str | pathlib.Path) -> DiscoveredGromacsOutputs

   Discover ordered raw XTC and EDR files without inferring their times.


.. py:function:: maximum_trajectory_part(xtc_files: Sequence[pathlib.Path]) -> int

   Return the highest continuation number represented by XTC files.


.. py:function:: maximum_energy_part(edr_files: Sequence[pathlib.Path]) -> int

   Return the highest continuation number represented by EDR files.


.. py:function:: trajectory_output_filename(xtc_files: Sequence[pathlib.Path]) -> str

   Build ``production_combined_00X.xtc`` from the highest XTC part.


.. py:function:: energy_output_filename(edr_files: Sequence[pathlib.Path]) -> str

   Build ``production_combined_00X.edr`` from the highest EDR part.


.. py:function:: run_gmx_check(path: str | pathlib.Path, *, kind: OutputKind, gmx_command: str = 'gmx', runner: Runner = subprocess.run) -> GromacsCheckResult

   Run ``gmx check`` with ``-f`` for XTC or ``-e`` for EDR.


.. py:function:: merge_simulation_outputs(simulation_dir: str | pathlib.Path, *, dry_run: bool = False, trajectory_only: bool = False, energy_only: bool = False, skip_check: bool = False, overwrite: bool = False, gmx_command: str = 'gmx', runner: Runner = subprocess.run, stream: TextIO = sys.stdout) -> GromacsMergeOutputsResult

   Discover, check, merge, and validate one simulation directory.


.. py:function:: build_argument_parser() -> argparse.ArgumentParser

   Build the command-line parser for the executable module.


.. py:function:: main(argv: Sequence[str] | None = None) -> int

   Command-line entry point.