.. _user-section-output: The Output section ================== The ``output`` section defines settings for how |pyretis| should create output files. .. pyretis-input-example:: Output .. code-block:: rst Output settings --------------- backup = 'overwrite' pathensemble-file = 1 order-file = 1 energy-file = 1 screen = 10 The following keywords can be set for the output section: .. |output_backup| replace:: :ref:`bakcup ` .. |output_prefix| replace:: :ref:`prefix ` .. |output_energy| replace:: :ref:`energy-file ` .. |output_cross| replace:: :ref:`cross-file ` .. |output_order| replace:: :ref:`order-file ` .. |output_path| replace:: :ref:`pathensemble-file ` .. |output_restart| replace:: :ref:`restart-file ` .. |output_traj| replace:: :ref:`trajectory-file ` .. |output_screen| replace:: :ref:`screen ` .. _table-keywords-file-output: .. table:: Keywords for output to files. :class: table-striped table-hover +------------------+-------------------------------------------------------+ | Keyword | Description | +==================+=======================================================+ | |output_backup| | Determines how we deal with already existing files. | +------------------+-------------------------------------------------------+ | |output_prefix| | Add a prefix to output files. | +------------------+-------------------------------------------------------+ | |output_energy| | Set frequency of output to the energy file. | +------------------+-------------------------------------------------------+ | |output_cross| | Set frequency of output of crossing data. | +------------------+-------------------------------------------------------+ | |output_order| | Set frequency of output of order parameter data. | +------------------+-------------------------------------------------------+ | |output_path| | Set frequency of output of path ensemble data. | +------------------+-------------------------------------------------------+ | |output_restart| | Set frequency of restart files overwriting. | +------------------+-------------------------------------------------------+ | |output_traj| | Set frequency of output of trajectory data. | +------------------+-------------------------------------------------------+ .. _table-keywords-screen-output: .. table:: Keywords for output to the screen. :class: table-striped table-hover +------------------+-------------------------------------------------------+ | Keyword | Description | +==================+=======================================================+ | |output_screen| | Set frequency of output to the screen. | +------------------+-------------------------------------------------------+ Keywords controlling output to files ------------------------------------ For the keywords controlling the frequency of the output to files, e.g. :ref:`energy-file `, writing of such output can be disabled by setting a frequency of ``0`` or less. Note that |pyretis| will create a set of files for each path ensemble in a RETIS (or TIS) simulation. .. _user-section-output-backup: Keyword backup ^^^^^^^^^^^^^^ .. pyretis-keyword:: backup string Determines how we deal with already existing files. This can be set to one of the following: - ``backup = append``: Output will be appended to already existing files. - ``backup = overwrite``: Output will **overwrite** already existing files. - ``backup = backup``: A backup of existing files will be created. Existing files will be renamed with a suffix ``_XXX`` where ``XXX`` is a number. Default The default is ``backup = overwrite``. .. _user-section-output-prefix: Keyword prefix ^^^^^^^^^^^^^^ .. pyretis-keyword:: prefix string The prefix can be used to add names to the output files, that is ``prefix = TEXT`` will prepend ``TEXT`` to output files created by |pyretis|. This can, for instance, be used to organize your output. Default The default is ``None``, that is: no prefix is added by default. .. _user-section-output-keyword-energy-file: Keyword energy-file ^^^^^^^^^^^^^^^^^^^ .. pyretis-keyword:: energy-file integer Determines how often we should write to the energy file. ``energy-file = N`` will make |pyretis| write to the energy file every Nth step. Default The default is ``energy-file = 1``. .. _user-section-output-keyword-cross-file: Keyword cross-file ^^^^^^^^^^^^^^^^^^ .. pyretis-keyword:: cross-file integer Determines how often |pyretis| will try to write to the crossing file. The crossing file will only be written to if an actual crossing has been detected. Note that this only applies to simulations for determining the initial flux. ``cross-file = N`` will make |pyretis| write to the crossing file every Nth step. Normally, this keyword should be set to ``1``. This does not mean that we will write to the crossing file every step, but only that we will check if we can write new crossing data every step. The file will only be written to if a crossing has been made. Default The default is ``cross-file = 1``. .. _user-section-output-keyword-order-file: Keyword order-file ^^^^^^^^^^^^^^^^^^ .. pyretis-keyword:: order-file integer Determines how often we will write out order parameters to the order file. ``order-file = N`` will make |pyretis| write to the order file every Nth step. Default The default is ``order-file = 1``. .. _user-section-output-keyword-restart-file: Keyword restart-file ^^^^^^^^^^^^^^^^^^^^ .. pyretis-keyword:: restart-file integer Determines how often we will write out the restart file. ``restart-file = N`` will make |pyretis| overwrite the restart files every Nth step. The restart files are: ``pyretis.restart`` in the main folder and ``ensemble.restart`` in the ensemble's pathfolders for path ensemble simulations. Default The default is ``restart-file = 1``. .. _user-section-output-keyword-pathensemble-file: Keyword pathensemble-file ^^^^^^^^^^^^^^^^^^^^^^^^^ .. pyretis-keyword:: pathensemble-file integer Determines how often we will write out path data for path ensembles. This file contains the basic information about the paths (length, maximum/minimum order parameter, what kind of move we perform, was the path accepted etc.) and is the **most important** file for the analysis. Normally, the frequency of output should be set to ``1``, but setting ``pathensemble-file = N`` will make |pyretis| write to the order file every Nth step. .. WARNING:: Setting a value different from ``1`` is **not** accounted for in the analysis and is **not** recommended. Default The default is ``pathensemble-file = 1``. .. _user-section-output-keyword-trajectory-file: Keyword trajectory-file ^^^^^^^^^^^^^^^^^^^^^^^ .. pyretis-keyword:: trajectory-file integer Determines how often we should write trajectory data to a trajectory output file. .. WARNING:: Setting this to a *small* value (say 1) is **not** recommended when using external engines as this may quickly use up all the space on your hard drive. Setting ``trajectory-file = N`` means that |pyretis| will store a trajectory every Nth step for each path ensemble in a RETIS/TIS simulation. You are advised to investigate typical sizes for the trajectories before setting this frequency output. Default The default is ``trajectory-file = 100``. Keywords controlling output to the screen ----------------------------------------- Note that if you run the |pyretis| application and choose to use the progress bar, that is: .. code-block:: pyretis pyretisrun -i input.rst -p then writing of results to the screen will be **disabled**. .. _user-section-output-keyword-screen: Keyword screen ^^^^^^^^^^^^^^ .. pyretis-keyword:: screen integer Determines how often output from a simulation should be written to the screen during a simulation. Default The default is ``screen = 10``.