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:

matched (the default; crossing is accepted as the historical spelling) – the matched / 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); the PPTIS/REPPTIS memory-kernel analyses build on its per-ensemble local probabilities.
wham – the weighted-histogram (WHAM) analysis. It reweights the shared paths across all ensembles in a single histogram, built from the same per-ensemble output every scheduler run writes (a literal infswap_data.txt, if one is present – from an older run, or from merging several runs’ path data – is read directly instead). Use it when you have an infinite-swapping run.
both – run the two analyses and report each. When a run’s data is unusable for one method, that method is run and the other is skipped with a warning (method = "wham" instead fails loudly if no usable path data is found).

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 and skip_final_cycles keywords discard the same cycles at the start and at the end of the sampling before the statistics are accumulated, so the two estimates are computed over the same production window. On the command line they are pyretis analyse -skipb N -skipe M; given neither, everything is kept.

Keywords for the Analysis section¶

For the analysis section the following keywords can be set:

Table 42 Supported keywords for the analysis section.¶
Keyword	Description
method	Select the rate-estimation method.
skip_initial_cycles	Initial cycles to skip (both methods).
skip_final_cycles	Trailing 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 pyretis analyse runs. See Choosing the rate-estimation method for guidance. Valid choices are:

matched – the matched (point-matching) analysis of the per-ensemble pathensemble.txt files (the classic PyRETIS analysis; crossing is accepted as the historical spelling).
wham – the weighted-histogram (WHAM) analysis of an infinite-swapping run’s shared-path data (built from the per-ensemble output, or a literal infswap_data.txt if one is present).
both – run both analyses and report each.

Default: The default value is: method = matched

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

Note

pyretis analyse -skipb N sets this on the command line, overriding the input file. That is usually what you want: how much equilibration to drop is a question you answer after looking at the run, without editing (and re-saving) the input.

Keyword skip_final_cycles¶

skip_final_cycles = integer

The counterpart of skip_initial_cycles: the number of cycles to discard at the end of the sampling. This is what you reach for when a run was stopped part-way – a wall-time kill, a crashed node – and its final cycles are not to be trusted, or when you want to compare two runs over the same number of cycles.

pyretis analyse -skipe N sets it on the command line.

Default: Nothing is discarded.

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 length, in simulation steps, of the time window the initial flux is averaged over in an md-flux analysis.

Note

The name is historical and misleading: nothing is skipped. The keyword is a window length.

The flux is the number of effective crossings of an interface per unit time. Measuring it once over the whole run would give a single number with no way to put an error on it, so the time the system spends in the overall \(A\) state is instead cut into windows of skipcross steps, and the flux is computed in each. That series is what the running-average plot and the block-error estimate are built from.

It does not change the flux itself. The mean over the windows is the total crossing count divided by the total time however the windows are drawn; only the spread of the series changes, and with it the error estimate:

`skipcross`	windows	mean flux	spread
500	200	0.50000	0.313
1000	100	0.50000	0.215
5000	20	0.50000	0.067
20000	5	0.50000	0.039

(the same 500 synthetic crossings over 100000 steps, binned four ways.)

So choose it for the statistics, not for the answer. Too small and each window holds a handful of crossings, so the series is noisy; too large and there are too few windows for a meaningful block analysis. A useful target is enough windows to block over – a few tens – with several crossings in each.

If the run does not contain even one full window, the analysis stops with an explicit error rather than producing an empty flux array: reduce skipcross or run longer.

This keyword affects only the md-flux route. A TIS/RETIS run takes its flux from the [0^-] and [0^+] path lengths instead (see Where each factor comes from in a run), and ignores it.

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