Mtd-energy: Difference between revisions
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{{DISPLAYTITLE:mtd-energy}} | |||
Navigation: [[Documentation]] / [[Methods]] / [[Metadynamics]] / [[MTD:Utilities]] / [[mtd-energy]] | Navigation: [[Documentation]] / [[Methods]] / [[Metadynamics]] / [[MTD:Utilities]] / [[mtd-energy]] | ||
---- | ---- | ||
{{MTDUtils}} | {{MTDUtils}} | ||
'''Name''' | <div style="text-align: center">mtd-energy: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name''' | ||
mtd-energy | <span style="margin-left: 15px;">mtd-energy</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;">mtd-energy</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input</span> <span style="color: purple;">output</span> | ||
'''Description''' | '''Description''' | ||
It calculate the free energy surface estimate from the metadynamics restart file. | <p style="text-indent: 1em; text-align: justify;">It calculate the free energy surface estimate from the metadynamics restart file.</p> | ||
'''Arguments''' | '''Arguments''' | ||
{| style="margin-left: 2em; width: | {| 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;">input</span><br/><div 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.</div> | ||
< | |||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| <span style="color: purple;">output</span><br/> | | <span style="color: purple;">output</span><br/><div 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.</div> | ||
< | |||
|} | |} | ||
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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="color: blue;">-t, --time NUMBER</span><br/><div style="margin-left: 30px;">Specifies metadynamics time that will be used for the energy calculation.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span> | ||
|- style="vertical-align: top; " | |- style="vertical-align: top;" | ||
|<span style="color: blue;">--offset REAL</span><br/>< | |<span style="color: blue;">--offset REAL</span><br/><div style="margin-left: 30px;">Determine position of global minima.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span> | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">--smooth NUMBER</span><br/>< | |<span style="color: blue;">--smooth NUMBER</span><br/><div style="margin-left: 30px;">Calculate the energy surface average from time interval SMOOTH to TIME.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span> | ||
|- style="vertical-align: top; " | |- style="vertical-align: top;" | ||
|<span style="color: blue;">--sd</span><br/>< | |<span style="color: blue;">--sd</span><br/><div style="margin-left: 30px;">Print the standard deviation of the free energy when the smoothing is enabled.</div> | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">--output FORMAT</span><br/>< | |<span style="color: blue;">--output FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print free energy surface. Supported formats are: plain, gnuplot, fes.</div><span style="color:purple; margin-left: 30px;">(Default: gnuplot)</span> | ||
|- style="vertical-align: top; " | |- style="vertical-align: top;" | ||
|<span style="color: blue;">--noheader</span><br/>< | |<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print header to output file.</div> | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">--fx FORMAT</span><br/>< | |<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of collective variables.</div><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/>< | |<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of free energy.</div><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="color: blue;">--fs FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of standard deviations.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span> | ||
|- style="vertical-align: top; " | |- style="vertical-align: top;" | ||
|<span style="color: blue;">-v, --verbose</span><br/>< | |<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div> | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">--version</span><br/>< | |<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div> | ||
|- style="vertical-align: top; " | |- style="vertical-align: top;" | ||
|<span style="color: blue;">-h, --help</span><br/>< | |<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div> | ||
|} | |} | ||
Revision as of 17:01, 6 March 2020
Navigation: Documentation / Methods / Metadynamics / MTD:Utilities / mtd-energy
MTD Utilities
mtd-energy: version 5.271.40980cf (2020-03-02 15:18)
Name
mtd-energy
Synopsis
mtd-energy [OPTIONS] [--] input output
Description
It calculate the free energy surface estimate from the metadynamics restart file.
Arguments
| input Name of file containing the metadynamics restart file. If the name is '-' then the file is read from the standard input.
|
| output 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.
|
Options
| -t, --time NUMBER Specifies metadynamics time that will be used for the energy calculation. (Default: 0)
|
| --offset REAL Determine position of global minima. (Default: 0)
|
| --smooth NUMBER Calculate the energy surface average from time interval SMOOTH to TIME. (Default: 0)
|
| --sd Print the standard deviation of the free energy when the smoothing is enabled.
|
| --output FORMAT Output FORMAT, which will be used to print free energy surface. Supported formats are: plain, gnuplot, fes. (Default: gnuplot)
|
| --noheader Do not print header to output file.
|
| --fx FORMAT Output FORMAT, which will be used to print values of collective variables. (Default: %15.7le)
|
| --fe FORMAT Output FORMAT, which will be used to print values of free energy. (Default: %15.7le)
|
| --fs FORMAT Output FORMAT, which will be used to print values of standard deviations. (Default: %15.7le)
|
| -v, --verbose Increase output verbosity.
|
| --version Output version information and exit.
|
| -h, --help Display this help and exit.
|