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Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-derivatives]] | Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-derivatives]] | ||
---- | ---- | ||
{{ABFUtils}} | {{ABFUtils}} | ||
'''Name''' | <div style="text-align: center">abf-derivatives: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name''' | ||
abf-derivatives | <span style="margin-left: 15px;">abf-derivatives</span> | ||
'''Synopsis''' | '''Synopsis''' | ||
<span style="color: maroon;">abf-derivatives</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname</span> <span style="color: purple;">dname</span> | <span style="color: maroon; margin-left: 15px;">abf-derivatives</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname</span> <span style="color: purple;">dname</span> | ||
'''Description''' | '''Description''' | ||
<p style="text-indent: 1em; text-align: justify;"><span style="font-style: bold;">abf-derivatives</span> prints selected derivatives of the free energy with respect to given collective variables (mean forces) from the ABF accumulator.</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;">accuname</span><br/> | | <span style="color: purple;">accuname</span><br/><div style="margin-left: 30px;">Name of file containing the ABF accumulator. If the name is '-' then the accumulator is read from the standard input.</div> | ||
< | |||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| <span style="color: purple;">dname</span><br/> | | <span style="color: purple;">dname</span><br/><div style="margin-left: 30px;">Name of file where results 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;">-l, --limit LIMIT</span><br/>< | |<span style="color: blue;">-l, --limit LIMIT</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered as properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span> | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
|<span style="color: blue;">- | |<span style="color: blue;">-c, --ncorr NUMBER</span><br/><div style="margin-left: 30px;">Number of statistically correlated samples.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span> | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">- | |<span style="color: blue;">-i, --item CV</span><br/><div style="margin-left: 30px;">Forces for all CVs are printed (item == 0) unless item is set for given CV index (counted from 1).</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span> | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
|<span style="color: blue;">- | |<span style="color: blue;">-s, --sigma</span><br/><div style="margin-left: 30px;">Print the standard deviation of instanteous forces (fluctuations).</div> | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">-- | |<span style="color: blue;">-e, --error</span><br/><div style="margin-left: 30px;">Print the standard deviation of mean forces (standard error).</div> | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
|<span style="color: blue;">-- | |<span style="color: blue;">--nognuplot</span><br/><div style="margin-left: 30px;">Do not print delimiters between records.</div> | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">-- | |<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print header to the output file.</div> | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
|<span style="color: blue;">-- | |<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: %15.7e)</span> | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">- | |<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print results.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span> | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
|<span style="color: blue;">-- | |<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;">-h, --help</span><br/>< | |<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div> | ||
|- style="vertical-align: top;" | |||
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div> | |||
|} | |} | ||
Latest revision as of 16:20, 6 March 2020
Navigation: Documentation / Methods / Adaptive Biasing Force Method / ABF:Utilities / abf-derivatives
ABF Utilities
abf-derivatives: version 5.271.40980cf (2020-03-02 15:18)
Name
abf-derivatives
Synopsis
abf-derivatives [OPTIONS] [--] accuname dname
Description
abf-derivatives prints selected derivatives of the free energy with respect to given collective variables (mean forces) from the ABF accumulator.
Arguments
| accuname Name of file containing the ABF accumulator. If the name is '-' then the accumulator is read from the standard input.
|
| dname Name of file where results will be printed. If the name is '-' then the output will be written to the standard output.
|
Options
| -l, --limit LIMIT Only bins containing more samples than NUMBER are considered as properly sampled. (Default: 0)
|
| -c, --ncorr NUMBER Number of statistically correlated samples. (Default: 1)
|
| -i, --item CV Forces for all CVs are printed (item == 0) unless item is set for given CV index (counted from 1). (Default: 0)
|
| -s, --sigma Print the standard deviation of instanteous forces (fluctuations).
|
| -e, --error Print the standard deviation of mean forces (standard error).
|
| --nognuplot Do not print delimiters between records.
|
| --noheader Do not print header to the output file.
|
| --fx FORMAT Output FORMAT, which will be used to print values of collective variables. (Default: %15.7e)
|
| --fe FORMAT Output FORMAT, which will be used to print results. (Default: %15.7e)
|
| -v, --verbose Increase output verbosity.
|
| --version Output version information and exit.
|
| -h, --help Display this help and exit.
|