The Analysis section¶
The analysis
section defines parameters for the analysis.
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:
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¶
The bins
keyword defines the number of bins to use when histograms
are created.
- Default
- The default value is:
bins = 100
Keyword blockskip¶
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 maxblockblockskip = n
will consider every n’th block up to the value given in the keyword maxblock, That is, it will use block lengths equal to1
,1 + n
,1 + 2*n
and so on.
- Default
- The default value is:
blockskip = 1
Keyword maxblock¶
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¶
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¶
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¶
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 settingplot = {'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¶
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¶
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¶
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¶
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