View source for Abf-mask

{{DISPLAYTITLE:abf-mask}}
Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-mask]]
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{{ABFUtils}}
<div style="text-align: center">abf-mask: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">abf-mask</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">abf-mask</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname</span> <span style="color: purple;">mask</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It create the ABF accumulator mask according to user specified criteria.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <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;"
| <span style="color: purple;">mask</span><br/><div style="margin-left: 30px;">Name of file where the info about samples will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-m, --maxene ENERGY</span><br/><div style="margin-left: 30px;">Generate mask with zero weights for bins with the free energy greater than ENERGY.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-l, --limit NUMBER</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: 100)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fdpoints NUMBER</span><br/><div style="margin-left: 30px;">Determines differenciation scheme. Currently implemented schemes use either three or four points.</div><span style="color:purple; margin-left: 30px;">(Default: 3)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-o, --offset NUMBER</span><br/><div style="margin-left: 30px;">Specify an integration constant.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-p, --periodic</span><br/><div style="margin-left: 30px;">Switch on periodicity for collective variables that are periodic.</div>
|- style="vertical-align: top;"
|<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: mask, gnuplot.</div><span style="color:purple; margin-left: 30px;">(Default: mask)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}