|
|
| Line 1: |
Line 1: |
| Navigation: [[Documentation]] / [[Methods]] / [[Metadynamics]] / [[MTD:Utilities]] / [[mtd-energy]]
| |
| ----
| |
| {{MTDUtils}}
| |
| '''Name'''
| |
|
| |
|
| mtd-energy
| |
|
| |
| '''Synopsis'''
| |
|
| |
| <span style="color: maroon;">mtd-energy</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input output </span>
| |
|
| |
| '''Description'''
| |
|
| |
| It calculate the free energy surface estimate from the metadynamics restart file.
| |
|
| |
| '''Arguments'''
| |
|
| |
| {| style="margin-left: 2em; width: 75%;"
| |
| |- style="vertical-align: top; background-color: #e6e6e6;"
| |
| | <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>
| |
| |- style="vertical-align: top; "
| |
| | <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>
| |
| |}
| |
|
| |
| '''Options'''
| |
|
| |
| {| style="margin-left: 2em; width: 95%;"
| |
| |- 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:purple; margin-left: 30px;"> (Default: 0)</span>
| |
| |- style="vertical-align: top; "
| |
| |<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;"
| |
| |<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>
| |
| |- style="vertical-align: top; "
| |
| |<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;"
| |
| |<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; "
| |
| |<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;"
| |
| |}
| |