The Analysis section

The analysis section defines parameters for the analysis.

Example Analysis section:
Analysis settings
-----------------
maxblock = 1000
blockskip = 1
bins = 100
ngrid = 1001
plot = {'plotter': 'mpl', 'output': 'png', 'style': 'pyretis'}
report = ['latex', 'rst', 'html']
maxordermsd = 100
report-dir = report
txt-output = 'txt.gz'
skipcross = 1000

Keywords for the Analysis section

For the analysis section the following keywords can be set:

Table 34 Supported keywords for the analysis section.
Keyword Description
bins Set the number of bins to use when creating histograms.
blockskip Selects certain block lengths to skip in the in the block error analysis
maxblock Set maximum length of blocks to consider in the block error analysis.
maxordermsd Set the maximum number of time origins to consider when calculating a mean square displacement.
ngrid Number of points used for calculating the crossing probability.
plot Settings related to plotting of results.
report Define output format(s) for the report.
report-dir Defines the directory where the analysis results should be written.
skipcross Set time window for initial flux calculation.
txt-output Select format for text-based output.

Keyword bins

bins = integer

The bins keyword defines the number of bins to use when histograms are created.

Default
The default value is: bins = 100

Keyword blockskip

blockskip = integer

The blockskip keyword can be used to skip certain block lengths in the block error analysis. That is:

  • blockskip = 1 will consider all blocks up to the value given in the keyword maxblock
  • blockskip = n will consider every n’th block up to the value given in the keyword maxblock, That is, it will use block lengths equal to 1, 1 + n, 1 + 2*n and so on.
Default
The default value is: blockskip = 1

Keyword maxblock

maxblock = integer

The maxblock keyword defines the maximum length of the blocks to consider for the block error analysis. If a negative number is set, PyRETIS will set maxblock equal to (1/2) * length of the data we are analysing. This is also the maximum length that PyRETIS will consider, even if the input maxblock is set higher.

Default
The default value is: maxblock = 1000

Keyword maxordermsd

maxordermsd = integer

The maxordermsd keyword defines the maximum number of time origins to consider when calculating a mean square displacement. If this is set to a value < 0, PyRETIS will internally set maxordermsd to (1/5) * length of the data for which the mean square displacement will be obtained.

Default
The default value is: maxordermsd = -1

Keyword ngrid

ngrid = integer

The ngrid keyword defines the number of points used for the order parameter when PyRETIS is calculating the crossing probability as a function of the order parameter.

Default
The default value is: ngrid = 1001

Keyword plot

plot = dictionary

The plot keyword defines how plotting should be carried out. It is given as a dictionary, where the following keys can be used:

  • 'plotter': Which selects the kind of plotter to use. Currently, PyRETIS only implements a plotter using matplotlib which is selected by setting plot = {'plotter': 'mpl'}.
  • 'output': Which selects the output format for plots. This can be set to any of the supported output formats by the plotter. Often this will depend on your specific system, but common choices are 'png', 'pdf' and 'svg'.
  • 'style': Selects a style for creating plots. Here you can for instance create your own matplotlib style or use one of the built-in styles. Please see http://matplotlib.org/users/style_sheets.html for more information.
Default
The default value is: plot = {'plotter': 'mpl', 'style': 'pyretis', 'output': 'png'}

Keyword report

report = list of strings

The report keyword defines the output format for the report. This is provided as a list of strings, where each item in the list correspond to a specific format:

  • 'latex' selects latex output.
  • 'rst' selects output in reStructuredText.
  • 'html' selects html output.
Default
The default value is: report = ['latex', 'rst', 'html']

Keyword report-dir

report-dir = string

The report-dir keyword defines where the analysis results should be written.

Default
The default value is a sub-folder named report within the directory where the analysis program was executed.

Keyword skipcross

skipcross = integer

The skipcross keyword defines a time window for which we calculate the initial flux. This is used when analysing a md-flux simulation.

Default
The default value is: skipcross = 1000

Keyword txt-output

txt-output = string

The txt-output keyword defines the format for how text-based output should be written. Valid choices are:

  • txt for writing plain text files.
  • txt.gz for creating gzipped files.
Default
The default value is: txt-output = txt.gz