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{{DISPLAYTITLE:rst-samples}}
Navigation: [[Documentation]] / [[Methods]] / [[Metadynamics]] / [[MTD:Utilities]] / [[mtd-energy]]
Navigation: [[Documentation]] / [[Methods]] / [[Restrained Dynamics]] / [[RST:Utilities]] / [[rst-samples]]
----
----
{{MTDUtils}}
{{RSTUtils}}
'''Name'''
<div style="text-align: center">rst-samples: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''


mtd-energy
<span style="margin-left: 15px;">rst-samples</span>


'''Synopsis'''
'''Synopsis'''


<span style="color: maroon;">mtd-energy</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input output </span>
<span style="color: maroon; margin-left: 15px;">rst-samples</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname</span> <span style="color: purple;">sname</span>


'''Description'''
'''Description'''


It calculate the free energy surface estimate from the metadynamics restart file.
<p style="text-indent: 1em; text-align: justify;">It prints the number of samples accumulated during RST calculation.</p>


'''Arguments'''
'''Arguments'''


{| style="margin-left: 2em; width: 75%;"
{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">input</span><br/>
| <span style="color: purple;">accuname</span><br/><div style="margin-left: 30px;">File name of the RST histogram file. If the name is '-' then the accumulator is read from the standard input.</div>
<span style="margin-left: 30px;">Name of file containing the metadynamics restart file. If the name is '-' then the file is read from the standard input.</span>
|- style="vertical-align: top;"
|- style="vertical-align: top; "
| <span style="color: purple;">sname</span><br/><div style="margin-left: 30px;">Name of file where the info about samples will be printed. If the name is '-' then the output will be written to the standard output.</div>
| <span style="color: purple;">output</span><br/>
<span style="margin-left: 30px;">Name of file where the resulting free energy surface will be printed. If the name is '-' then the output will be written to the standard output.</span>
|}
|}


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{| style="margin-left: 2em; width: 95%;"
{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-t, --time NUMBER</span><br/><span style="margin-left: 30px;"> Specifies metadynamics time that will be used for the energy calculation.</span><br/>
|<span style="color: blue;">-l, --limit LIMIT</span><br/><div style="margin-left: 30px;">only bins with the number of samples grater than or equal to LIMIT will be printed</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
<span style="color:purple; margin-left: 30px;"> (Default: 0)</span>
|- style="vertical-align: top;"
|- style="vertical-align: top; "
|<span style="color: blue;">--nognuplot</span><br/><div style="margin-left: 30px;">do not print delimiters between records</div>
|<span style="color: blue;">--offset REAL</span><br/><span style="margin-left: 30px;"> Determine position of global minima.</span><br/>
<span style="color:purple; margin-left: 30px;"> (Default: 0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--smooth NUMBER</span><br/><span style="margin-left: 30px;"> Calculate the energy surface average from time interval SMOOTH to TIME.</span><br/>
<span style="color:purple; margin-left: 30px;"> (Default: 0)</span>
|- style="vertical-align: top; "
|<span style="color: blue;">--sd</span><br/><span style="margin-left: 30px;"> Print the standard deviation of the free energy when the smoothing is enabled.</span><br/>
<span style="color:purple; margin-left: 30px;"></span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--output FORMAT</span><br/><span style="margin-left: 30px;"> Output FORMAT, which will be used to print free energy surface. Supported formats are: plain, gnuplot, fes.</span><br/>
<span style="color:purple; margin-left: 30px;"> (Default: gnuplot)</span>
|- style="vertical-align: top; "
|<span style="color: blue;">--noheader</span><br/><span style="margin-left: 30px;"> Do not print header to output file.</span><br/>
<span style="color:purple; margin-left: 30px;"></span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fx FORMAT</span><br/><span style="margin-left: 30px;"> Output FORMAT, which will be used to print values of collective variables.</span><br/>
<span style="color:purple; margin-left: 30px;"> (Default: %15.7le)</span>
|- style="vertical-align: top; "
|<span style="color: blue;">--fe FORMAT</span><br/><span style="margin-left: 30px;"> Output FORMAT, which will be used to print values of free energy.</span><br/>
<span style="color:purple; margin-left: 30px;"> (Default: %15.7le)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fs FORMAT</span><br/><span style="margin-left: 30px;"> Output FORMAT, which will be used to print values of standard deviations.</span><br/>
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of coordinate values</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
<span style="color:purple; margin-left: 30px;"> (Default: %15.7le)</span>
|- style="vertical-align: top;"
|- style="vertical-align: top; "
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of samples</div><span style="color:purple; margin-left: 30px;">(Default: %d)</span>
|<span style="color: blue;">-v, --verbose</span><br/><span style="margin-left: 30px;"> Increase output verbosity.</span><br/>
<span style="color:purple; margin-left: 30px;"></span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><span style="margin-left: 30px;"> Output version information and exit.</span><br/>
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
<span style="color:purple; margin-left: 30px;"></span>
|- style="vertical-align: top;"
|- style="vertical-align: top; "
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
|<span style="color: blue;">-h, --help</span><br/><span style="margin-left: 30px;"> Display this help and exit.</span><br/>
<span style="color:purple; margin-left: 30px;"></span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;"></span><br/><span style="margin-left: 30px;"></span><br/>
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
<span style="color:purple; margin-left: 30px;"></span>
|- style="vertical-align: top; "
|}
|}

Latest revision as of 17:06, 6 March 2020

Navigation: Documentation / Methods / Restrained Dynamics / RST:Utilities / rst-samples

RST Utilities

rst-samples: version 5.271.40980cf (2020-03-02 15:18)

Name

rst-samples

Synopsis

rst-samples [OPTIONS] [--] accuname sname

Description

It prints the number of samples accumulated during RST calculation.

Arguments

accuname
File name of the RST histogram file. If the name is '-' then the accumulator is read from the standard input.
sname
Name of file where the info about samples will be printed. If the name is '-' then the output will be written to the standard output.

Options

-l, --limit LIMIT
only bins with the number of samples grater than or equal to LIMIT will be printed
(Default: 0)
--nognuplot
do not print delimiters between records
--fx FORMAT
output FORMAT of coordinate values
(Default: %15.7le)
--fe FORMAT
output FORMAT of samples
(Default: %d)
-v, --verbose
increase output verbosity
--version
output version information and exit
-h, --help
display this help and exit
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