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Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-mask]] | Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-mask]] | ||
---- | ---- | ||
{{ABFUtils}} | {{ABFUtils}} | ||
'''Name''' | <div style="text-align: center">abf-mask: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name''' | ||
abf-mask | <span style="margin-left: 15px;">abf-mask</span> | ||
'''Synopsis''' | '''Synopsis''' | ||
<span style="color: maroon;">abf-mask</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname</span> <span style="color: purple;">mask</span> | <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''' | '''Description''' | ||
It create the ABF accumulator mask according to user specified criteria. | <p style="text-indent: 1em; text-align: justify;">It create the ABF accumulator mask according to user specified criteria.</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;">mask</span><br/> | | <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> | ||
< | |||
|} | |} | ||
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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;">-m, --maxene ENERGY</span><br/>< | |<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;" | |- style="vertical-align: top;" | ||
|<span style="color: blue;">-l, --limit NUMBER</span><br/>< | |<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;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">-- | |<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;" | |- style="vertical-align: top;" | ||
|<span style="color: blue;">-o, --offset NUMBER</span><br/>< | |<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;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">-p, --periodic</span><br/>< | |<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;" | |- style="vertical-align: top;" | ||
|<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: mask, gnuplot.</div><span style="color:purple; margin-left: 30px;">(Default: mask)</span> | ||
|- style="vertical-align: top; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<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;" | |- style="vertical-align: top;" | ||
|<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; background-color: #e6e6e6;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<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> | ||
|} | |} | ||
Latest revision as of 16:20, 6 March 2020
Navigation: Documentation / Methods / Adaptive Biasing Force Method / ABF:Utilities / abf-mask
ABF Utilities
abf-mask: version 5.271.40980cf (2020-03-02 15:18)
Name
abf-mask
Synopsis
abf-mask [OPTIONS] [--] accuname mask
Description
It create the ABF accumulator mask according to user specified criteria.
Arguments
| accuname Name of file containing the ABF accumulator. If the name is '-' then the accumulator is read from the standard input.
|
| mask 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.
|
Options
| -m, --maxene ENERGY Generate mask with zero weights for bins with the free energy greater than ENERGY. (Default: 0)
|
| -l, --limit NUMBER Only bins containing more samples than NUMBER are considered as properly sampled. (Default: 100)
|
| --fdpoints NUMBER Determines differenciation scheme. Currently implemented schemes use either three or four points. (Default: 3)
|
| -o, --offset NUMBER Specify an integration constant. (Default: 0)
|
| -p, --periodic Switch on periodicity for collective variables that are periodic.
|
| --output FORMAT Output FORMAT, which will be used to print free energy surface. Supported formats are: mask, gnuplot. (Default: mask)
|
| -v, --verbose Increase output verbosity.
|
| --version Output version information and exit.
|
| -h, --help Display this help and exit.
|