The Output section

The Output section defines settings for how PyRETIS should create output files.

Example Output section:
Output settings
---------------
backup = 'overwrite'
pathensemble-file = 1
order-file = 100
energy-file = 100
screen = 10

The following keywords can be set for the output section:

Table 31 Keywords for output to files.
Keyword Description
bakcup Determines how we deal with already existing files.
prefix Add a prefix to output files.
energy-file Set frequency of output to the energy file.
cross-file Set frequency of output of crossing data.
order-file Set frequency of output of order parameter data.
pathensemble-file Set frequency of output of path ensemble data.
trajectory-file Set frequency of output of trajectory data.
Table 32 Keywords for output to screen.
Keyword Description
screen Set frequency of output to the screen.

Keywords controlling output to files

For the keywords controlling the frequency of output to files, e.g. 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.

Keyword backup

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.

Keyword prefix

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.

Keyword energy-file

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 = 10.

Keyword cross-file

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.

Keyword order-file

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 = 10.

Keyword pathensemble-file

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.

Keyword trajectory-file

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 screen

Note that if you run the PyRETIS application and choose to use the progress bar, that is:

pyretisrun -i input.rst -p

then writing of results to the screen will be disabled.

Keyword screen

screen = integer

Determines how often output from a simulation should be written to the screen during a simulation.

Default
The default is screen = 10.