forked from lijiext/lammps
Added plumed documentation in a txt file
This commit is contained in:
Gareth Tribello
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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<HR>
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<H3>fix plumed command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID plumed keyword value ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>plumed = style name of this fix command
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<LI>keyword = <I>plumedfile</I> or <I>outfile</I>
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<PRE> <I>plumedfile</I> arg = name of PLUMED input file to use
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<I>outfile </I> arg = name of file on which to write the PLUMED log
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>
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fix pl all plumed all plumed plumedfile plumed.dat outfile p.log
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>
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This fix instructs LAMMPS to call the PLUMED library, which allows one
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to perform various forms of trajectory analysis on the fly and to also use
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methods such as umbrella sampling and metadynamics to enhance the sampling of
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phase space.
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</P>
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<P>The documentation included here only describes the fix plumed command. This command
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is LAMMPS specific whereas most of the functionality implemented in PLUMED will work with a
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range of MD codes and also when PLUMED is used as a stand alone code. The full documentation
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for PLUMED is available at <A HREF="http://www.plumed.org/documentation">this website</A>
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</P>
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<P>The PLUMED library is developed at <A HREF = "https://github.com/plumed/plumed2">https://github.com/plumed/plumed2</A>
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A detailed discussion of the code can be found in <A HREF = "#PLUMED">(PLUMED)</A>.
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</P>
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<P>There are some example scripts for using this package with LAMMPS in the
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examples/USER/plumed directory.
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</P>
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<HR>
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<P>The command to call PLUMED above is reasonably self explanatory. Within the input file
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for lammps the user is required to specify the input file for PLUMED and a file on which
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to output the PLUMED log. The user must specify both of these arguments every time
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PLUMED is to be used. Furthermore, the fix plumed command should appear in the LAMMPS input
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file after the relevant input paramters (e.g. the timestep) have been set.
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</P>
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<P>The <I>group-ID</I> entry is ignored. LAMMPS will always pass all the atoms to PLUMED
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and there can only be one instance of the plumed fix at a time. The plumed fix communicates
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the minimum amount of information required and the PLUMED supports multiple, completely
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independent collective variables, multiple independent biases and multiple independent forms of analysis.
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There is thus really no restriction in functionality by only allowing only one plumed fix in the LAMMPS input.
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</P>
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<P>The <I>plumedfile</I> keyword allows the user to specify the name of the PLUMED input file.
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Instructions as to what should be included in a plumed input file can be found in the
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<A HREF="http://www.plumed.org/documentation">documentation for PLUMED</A>.
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</P>
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<P>The <I>outfile</I> keyword allows the user to specify the name of a file on which to output
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the PLUMED log. This log file normally just parots the information that is contained in the input
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file. The names of the files on which the results from the various analyses that have been performed
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using PLUMED will be specified by the user in the PLUMED input file.
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</P>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>
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When performing a restart of a calculation that involves PLUMED you must include a RESTART command
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in the PLUMED input file as detailed in the <A HREF="http://www.plumed.org/documentation">PLUMED documentation.</A> When the restart
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command is found in the PLUMED input PLUMED will append to the files that were generated in the run
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that was performed previously. Furthermore, any history dependent bias potentials that were accumulated in
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previous calculations will be read in when the restart command is included in the PLUMED input.
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</P>
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<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is not supported by this fix.
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</P>
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<P>Nothing is computed by this fix that can be accessed by any of the
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<A HREF = "Section_howto.html#howto_15">output commands</A> within LAMMPS. All the quantities
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of interest can be output by commands that are native to PLUMED, however.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>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 <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P>There can only be one plumed fix active at a time. Since the interface
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communicates only the minimum amount of information and since the PLUMED module
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itself can handle an arbitrary number of analysis and biasing methods, this is
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not a limitation of functionality.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_smd.html">fix smd</A>
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<P><A HREF = "fix_colvars.html">fix colvars</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The default options are plumedfile = NULL and outfile = NULL
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</P>
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<HR>
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<A NAME = "PLUMED"></A>
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<P><B>(PLUMED)</B> G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014) DOI:https://doi.org/10.1016/j.cpc.2013.09.018
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</P>
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<!-- PAGE BREAK -->
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</HTML>
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@ -0,0 +1,104 @@
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"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 :1
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keyword = {plumedfile} or {outfile} :1
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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)
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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 library, which allows one
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to perform various forms of trajectory analysis on the fly and to also use
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methods such as umbrella sampling and metadynamics to enhance the sampling of
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phase space.
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The documentation included here only describes the fix plumed command. This command
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is LAMMPS specific whereas most of the functionality implemented in PLUMED will work with a
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range of MD codes and also when PLUMED is used as a stand alone code. The full documentation
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for PLUMED is available at "this website"_http://www.plumed.org/documentation
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The PLUMED library is developed at "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 are some example scripts 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 call PLUMED above is reasonably self explanatory. Within the input file
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for lammps the user is required to specify the input file for PLUMED and a file on which
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to output the PLUMED log. The user must specify both of these arguments every time
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PLUMED is to be used. Furthermore, the fix plumed command should appear in the LAMMPS input
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file after the relevant input paramters (e.g. the timestep) have been set.
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The {group-ID} entry is ignored. LAMMPS will always pass all the atoms to PLUMED
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and there can only be one instance of the plumed fix at a time. The plumed fix communicates
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the minimum amount of information required and the PLUMED supports multiple, completely
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independent collective variables, multiple independent biases and multiple independent forms of analysis.
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There is thus really no restriction in functionality by only allowing only one plumed fix in the LAMMPS input.
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The {plumedfile} keyword allows the user to specify the name of the PLUMED input file.
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Instructions as to what should be included in a plumed input file can be found in the
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"documentation for PLUMED"_http://www.plumed.org/documentation.
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The {outfile} keyword allows the user to specify the name of a file on which to output
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the PLUMED log. This log file normally just parots the information that is contained in the input
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file. The names of the files on which the results from the various analyses that have been performed
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using PLUMED will 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 include a RESTART command
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in the PLUMED input file as detailed in the "PLUMED documentation"_http://www.plumed.org/documentation. When the restart
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command is found in the PLUMED input PLUMED will append to the files that were generated in the run
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that was performed previously. Furthermore, any history dependent bias potentials that were accumulated in
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previous calculations will be read in when the restart command is included in the PLUMED input.
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The "fix_modify"_fix_modify.html {energy} option is not supported by 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, 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. Since the interface
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communicates only the minimum amount of information and since the PLUMED module
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itself can handle an arbitrary number of analysis and biasing methods, this is
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not a limitation of functionality.
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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) DOI:https://doi.org/10.1016/j.cpc.2013.09.018
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