142 lines
5.3 KiB
ReStructuredText
142 lines
5.3 KiB
ReStructuredText
.. index:: fix plumed
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fix plumed command
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==================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID plumed keyword value ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* plumed = style name of this fix command
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* keyword = *plumedfile* or *outfile*
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.. parsed-literal::
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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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Examples
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""""""""
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.. code-block:: LAMMPS
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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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"""""""""""
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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 :ref:`(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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----------
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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 PLUMED
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<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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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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When performing a restart of a calculation that involves PLUMED you
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must include a RESTART command in the PLUMED input file as detailed in
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the `PLUMED documentation <plumeddocs_>`_. When the restart command
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is found in the PLUMED input PLUMED will append to the files that were
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generated in the run that was performed previously. No part of the
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PLUMED restart data is included in the LAMMPS restart files.
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Furthermore, any history dependent bias potentials that were
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accumulated in previous calculations will be read in when the RESTART
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command is included in the PLUMED input.
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The :doc:`fix_modify <fix_modify>` *energy* option is supported by
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this fix to add the energy change from the biasing force added by
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PLUMED to the global potential energy of the system as part of
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:doc:`thermodynamic output <thermo_style>`. The default setting for
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this fix is :doc:`fix_modify energy yes <fix_modify>`.
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The :doc:`fix_modify <fix_modify>` *virial* option is supported by
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this fix to add the contribution from the biasing force to the global
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pressure of the system via the :doc:`compute pressure
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<compute_pressure>` command. This can be accessed by
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:doc:`thermodynamic output <thermo_style>`. The default setting for
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this fix is :doc:`fix_modify virial yes <fix_modify>`.
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This fix computes a global scalar which can be accessed by various
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:doc:`output commands <Howto_output>`. The scalar is the PLUMED
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energy mentioned above. The scalar value calculated by this fix is
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"extensive".
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Note that other quantities of interest can be output by commands that
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are native to PLUMED.
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Restrictions
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""""""""""""
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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 :doc:`Build package
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<Build_package>` doc page for more info.
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There can only be one fix plumed command active at a time.
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Related commands
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""""""""""""""""
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:doc:`fix smd <fix_smd>`
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:doc:`fix colvars <fix_colvars>`
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Default
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"""""""
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The default options are plumedfile = NULL and outfile = NULL
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----------
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.. _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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.. _plumeddocs: https://www.plumed.org/doc.html
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.. _plumedhome: https://www.plumed.org/
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