forked from lijiext/lammps
119 lines
4.5 KiB
Plaintext
119 lines
4.5 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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fix plumed command :h3
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[Syntax:]
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fix ID group-ID plumed keyword value ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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plumed = style name of this fix command :l
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keyword = {plumedfile} or {outfile} :l
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{plumedfile} arg = name of PLUMED input file to use (default: NULL)
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{outfile} arg = name of file on which to write the PLUMED log (default: NULL) :pre
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:ule
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[Examples:]
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fix pl all plumed all plumed plumedfile plumed.dat outfile p.log
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[Description:]
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This fix instructs LAMMPS to call the "PLUMED"_plumedhome library, which
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allows one to perform various forms of trajectory analysis on the fly
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and to also use methods such as umbrella sampling and metadynamics to
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enhance the sampling of phase space.
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The documentation included here only describes the fix plumed command
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itself. This command is LAMMPS specific, whereas most of the
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functionality implemented in PLUMED will work with a range of MD codes,
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and when PLUMED is used as a stand alone code for analysis. The full
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"documentation for PLUMED"_plumeddocs is available online and included
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in the PLUMED source code. The PLUMED library development is hosted at
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"https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2
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A detailed discussion of the code can be found in "(PLUMED)"_#PLUMED.
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There is an example input for using this package with LAMMPS in the
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examples/USER/plumed directory.
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:line
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The command to make LAMMPS call PLUMED during a run requires two keyword
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value pairs pointing to the PLUMED input file and an output file for the
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PLUMED log. The user must specify these arguments every time PLUMED is
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to be used. Furthermore, the fix plumed command should appear in the
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LAMMPS input file [after] relevant input parameters (e.g. the timestep)
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have been set.
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The {group-ID} entry is ignored. LAMMPS will always pass all the atoms
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to PLUMED and there can only be one instance of the plumed fix at a
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time. The way the plumed fix is implemented ensures that the minimum
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amount of information required is communicated. Furthermore, PLUMED
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supports multiple, completely independent collective variables, multiple
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independent biases and multiple independent forms of analysis. There is
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thus really no restriction in functionality by only allowing only one
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plumed fix in the LAMMPS input.
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The {plumedfile} keyword allows the user to specify the name of the
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PLUMED input file. Instructions as to what should be included in a
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plumed input file can be found in the "documentation for
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PLUMED"_plumeddocs
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The {outfile} keyword allows the user to specify the name of a file in
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which to output the PLUMED log. This log file normally just repeats the
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information that is contained in the input file to confirm it was
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correctly read and parsed. The names of the files in which the results
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are stored from the various analysis options performed by PLUMED will
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be specified by the user in the PLUMED input file.
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[Restart, fix_modify, output, run start/stop, minimize info:]
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When performing a restart of a calculation that involves PLUMED you must
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include a RESTART command in the PLUMED input file as detailed in the
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"PLUMED documentation"_plumeddocs. When the restart command is found in
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the PLUMED input PLUMED will append to the files that were generated in
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the run that was performed previously. No part of the PLUMED restart
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data is included in the LAMMPS restart files. Furthermore, any history
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dependent bias potentials that were accumulated in previous calculations
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will be read in when the RESTART command is included in the PLUMED
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input.
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The "fix_modify"_fix_modify.html {energy} option is not supported by
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this fix.
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Nothing is computed by this fix that can be accessed by any of the
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"output commands"_Howto_output.html within LAMMPS. All the quantities
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of interest can be output by commands that are native to PLUMED,
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however.
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[Restrictions:]
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This fix is part of the USER-PLUMED package. It is only enabled if
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LAMMPS was built with that package. See the "Build
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package"_Build_package.html doc page for more info.
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There can only be one plumed fix active at a time.
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[Related commands:]
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"fix smd"_fix_smd.html
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"fix colvars"_fix_colvars.html
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[Default:]
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The default options are plumedfile = NULL and outfile = NULL
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:line
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:link(PLUMED)
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[(PLUMED)] G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
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:link(plumeddocs,http://www.plumed.org/doc.html)
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:link(plumedhome,http://www.plumed.org/)
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