Rst-samples: Difference between revisions
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{| style="margin-left: 2em; width: 75%;" | {| style="margin-left: 2em; width: 75%;" | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|- style="vertical-align: top;" | |||
| <span style="color: purple;">input</span><br/> | | <span style="color: purple;">input</span><br/> | ||
<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> | <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;" | |||
| <span style="color: purple;">output</span><br/> | | <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> | <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;">-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: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; background-color: #e6e6e6;" | ||
|<span style="color: blue;">--offset REAL</span><br/><span style="margin-left: 30px;"> Determine position of global minima.</span><br/> | |<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> | <span style="color:purple; margin-left: 30px;"> (Default: 0)</span> | ||
|- style="vertical-align: top | |- style="vertical-align: top; " | ||
|<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: 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> | <span style="color:purple; margin-left: 30px;"> (Default: 0)</span> | ||
|- style="vertical-align: top; " | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<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: 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> | <span style="color:purple; margin-left: 30px;"></span> | ||
|- style="vertical-align: top | |- style="vertical-align: top; " | ||
|<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: 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> | <span style="color:purple; margin-left: 30px;"> (Default: gnuplot)</span> | ||
|- style="vertical-align: top; " | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">--noheader</span><br/><span style="margin-left: 30px;"> Do not print header to output file.</span><br/> | |<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> | <span style="color:purple; margin-left: 30px;"></span> | ||
|- style="vertical-align: top | |- style="vertical-align: top; " | ||
|<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: 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> | <span style="color:purple; margin-left: 30px;"> (Default: %15.7le)</span> | ||
|- style="vertical-align: top; " | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<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: 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> | <span style="color:purple; margin-left: 30px;"> (Default: %15.7le)</span> | ||
|- style="vertical-align: top | |- style="vertical-align: top; " | ||
|<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;">--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:purple; margin-left: 30px;"> (Default: %15.7le)</span> | <span style="color:purple; margin-left: 30px;"> (Default: %15.7le)</span> | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |||
|<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; " | |- style="vertical-align: top; " | ||
|<span style="color: blue;">- | |<span style="color: blue;">--version</span><br/><span style="margin-left: 30px;"> Output version information and exit.</span><br/> | ||
<span style="color:purple; margin-left: 30px;"></span> | |||
|- style="vertical-align: top; background-color: #e6e6e6;" | |||
|<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; " | |||
|<span style="color: blue;">help-output source translate-script mandatory arguments and options.</span><br/><span style="margin-left: 30px;"></span><br/> | |||
<span style="color:purple; margin-left: 30px;"></span> | <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 style="color: blue;"></span><br/><span style="margin-left: 30px;"></span><br/> | ||
<span style="color:purple; margin-left: 30px;"></span> | <span style="color:purple; margin-left: 30px;"></span> | ||
|- style="vertical-align: top; " | |- style="vertical-align: top; " | ||
|} | |} | ||