Revision as of 12:58, 11 April 2016

Navigation: Documentation / Methods / Metadynamics / MTD:Utilities / mtd-energy

MTD Utilities

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.

@@ Line 29: / Line 29: @@
 {| style="margin-left: 2em; width: 95%;"
-|- style="vertical-align: top;
+|- 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; background-color: #e6e6e6;"
+|- 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; "
+|- 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; background-color: #e6e6e6;"
+|- 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; "
+|- 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; background-color: #e6e6e6;"
+|- 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; "
+|- 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; background-color: #e6e6e6;"
+|- 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; "
+|- 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; background-color: #e6e6e6;"
+|- 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; "
+|- 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; background-color: #e6e6e6;"
+|- 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; "
-|<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>
 |- style="vertical-align: top; background-color: #e6e6e6;"

Rst-samples: Difference between revisions

Revision as of 12:58, 11 April 2016

MTD Utilities

Navigation menu

Rst-samples: Difference between revisions

Revision as of 12:58, 11 April 2016

MTD Utilities

Navigation menu

Search