The Analysis section¶

The analysis section defines parameters for the analysis.

Example Analysis section:

Analysis settings
-----------------
method = 'crossing'
skip_initial_cycles = 0
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

In a TOML input file the same settings are written as a [analysis] table, for example:

[analysis]
method = "wham"
skip_initial_cycles = 100
ngrid = 1001
bins = 100

Choosing the rate-estimation method¶

PyRETIS can estimate the crossing probability and the rate constant with two complementary methods, selected with the method keyword. Both read the sampled paths from the same simulation; they differ in how those paths are combined:

crossing (the default) – the native point-matching analysis. It reads the per-ensemble pathensemble.txt files and matches the per-ensemble crossing-probability curves at the interfaces. This is the classic PyRETIS analysis and is available for every path-sampling task (tis, retis, pptis, repptis).
wham – the weighted-histogram (WHAM) analysis. It reads the infswap_data.txt file written by the infinite-swapping sampler and reweights the shared paths across all ensembles in a single histogram. Use it when you have an infinite-swapping run.
both – run the two analyses and report each. When a run only contains the data file for one method, that method is run and the other is skipped with a warning (method = "wham" instead fails loudly if no infswap_data.txt is present).

The two methods are different estimators of the same physical rate, so on a converged simulation they agree within their statistical error. Comparing them with method = "both" is a useful cross-check.

Regardless of the method, the skip_initial_cycles keyword discards the same number of initial (equilibration) cycles before the statistics are accumulated, so the two estimates are computed over the same production window.

Keywords for the Analysis section¶

For the analysis section the following keywords can be set:

Table 40 Supported keywords for the analysis section.¶
Keyword	Description
method	Select the rate-estimation method.
skip_initial_cycles	Initial cycles to skip (both methods).
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 method¶

method = string

The method keyword selects which rate-estimation method pyretisanalyse runs. See Choosing the rate-estimation method for guidance. Valid choices are:

crossing – the native point-matching analysis of the per-ensemble pathensemble.txt files (the classic PyRETIS analysis).
wham – the weighted-histogram (WHAM) analysis of the infinite-swapping infswap_data.txt file.
both – run both analyses and report each.

Default: The default value is: method = crossing

Keyword skip_initial_cycles¶

skip_initial_cycles = integer

The skip_initial_cycles keyword sets the number of initial (equilibration) cycles to discard before the statistics are accumulated. It applies to both the crossing and the wham methods, so the two estimates are computed over the same production window. When it is left at 0, the legacy skip keyword (if set) is used instead.

Default: The default value is: skip_initial_cycles = 0

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