.. index:: fix colvars

fix colvars command
===================

Syntax
""""""

.. code-block:: LAMMPS

   fix ID group-ID colvars *configfile* keyword value ...

* *ID*, *group-ID* are documented in :doc:`fix <fix>` command
* "colvars" = style name of this fix command
* *configfile* = configuration file for Colvars (use "*none*" to provide it inline)
* keyword = *output* or *input* or *unwrap* or *tstat* or *seed*

  .. parsed-literal::
     *output* value = state filename/prefix for Colvars (default: "out")
     *input* value = input state filename/prefix for Colvars (optional, default: "NULL")
     *unwrap* value = "yes" or "no" (default: "yes")
     *tstat* value = fix ID of thermostat applied to relevant atoms (default: "NULL")
     *seed* value = seed for random number generator (default: 1966)

Examples
""""""""

.. code-block:: LAMMPS

   # Create the fix using a config file, set prefix for its output files
   fix Colvars all colvars colvars.inp output ${JOB}

   # Communicate the LAMMPS target temperature to the Colvars module
   fix_modify Colvars tstat NPT

   # Add a new restraint specific to this LAMMPS run
   fix_modify Colvars config """
   harmonic {
       name restraint
       colvars distance1 distance2
       centers ${ref1} ${ref2}
       forceConstant ${kappa}
   }"""

Description
"""""""""""

This fix interfaces LAMMPS to the collective variables `Colvars
<https://colvars.github.io>`_ library, which allows to accelerate
sampling of rare events and the computation of free energy surfaces
and potentials of mean force (PMFs) for any set of collective
variables using a variety of sampling methods (e.g. umbrella-sampling,
metadynamics, ABF...).

This documentation describes only the "fix colvars" command itself in a
LAMMPS script.  The Colvars library is fully documented in the included
`PDF manual <PDF/colvars-refman-lammps.pdf>`_ or in the webpage
`https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html
<https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html>`_.

The Colvars library is developed at `https://github.com/Colvars/colvars
<https://github.com/colvars/colvars>`_.  A detailed discussion of its
implementation is in :ref:`(Fiorin) <Fiorin>`; additional citations for
specific features are printed at runtime if these features are used.

There are example scripts on the `Colvars website
<https://colvars.github.io>`_ as well as in the
``examples/PACKAGES/colvars`` directory in the LAMMPS source tree.

----------

The only required argument to the fix is the name of the Colvars
configuration file.  The contents of this file are independent from the
MD engine in which the Colvars library has been integrated, save for the
units that are specific to each engine.  In LAMMPS, the units used by
Colvars are consistent with those specified by the :doc:`units <units>`
command.

.. versionadded:: Colvars_2023-06-04

   The special value "*none*" (lowercase) initializes an empty Colvars
   module, which allows loading configuration dynamically using
   :doc:`fix_modify <fix_modify>` (see below).

The *group-ID* entry is ignored.  "fix colvars" will always apply to the
entire system, but specific atoms will be selected based on selection
keywords in the Colvars configuration file or files.  There is no need
to define multiple "fix colvars" instances and it is not allowed.

The "output" keyword allows to specify the prefix of output files
generated by Colvars, for example "*output*.colvars.traj" or
"output.pmf".  Supplying an empty string suppresses any file output from
Colvars to file, except for data saved into the LAMMPS :doc:`binary
restart <restart>` files.

The "input" keyword allows to specify an optional state file that
contains the restart information needed to continue a previous
simulation state.  However, because "fix colvars" records its state in
LAMMPS :doc:`binary restart <restart>` files, this is usually not needed
when using the :doc:`read_restart <read_restart>` command.

The *unwrap* keyword controls whether wrapped or unwrapped coordinates
are passed to the Colvars library for calculation of the collective
variables and the resulting forces.  The default is *yes*, i.e. the
image flags are used to reconstruct the absolute atom positions.
Setting this to *no* will use the current local coordinates that are
wrapped back into the simulation cell at each re-neighboring step
instead.  For information about when and how this affects results,
please see
`https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvar_atom_groups_wrapping
<https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvar_atom_groups_wrapping>`_.

The *tstat* keyword can be either "NULL" or the label of a
thermostatting fix that thermostats all atoms in the fix colvars
group. This will be used to provide the colvars module with the current
thermostat target temperature.

The *seed* keyword contains the seed for the random number generator
that will be used in the colvars module.


Restarting
""""""""""

This fix writes the current state of the Colvars module into
:doc:`binary restart files <restart>`.  This is in addition to the
text-mode ".colvars.state" state file that is written by the Colvars
module itself.  The information contained in both files is identical,
and the binary LAMMPS restart file is also used by fix colvars when
:doc:`read_restart <read_restart>` is called in a LAMMPS script.  In
that case, there is typically no need to specify the *input* keyword.

As long as LAMMPS binary restarts will be used to continue a simulation,
it is safe to delete the ".colvars.state" files to save space.  However,
when a LAMMPS simulation is restarted using :doc:`read_data
<read_data>`, the Colvars state file must be available and loaded via
the "input" keyword or via a "fix_modify Colvars load" command (see
below).

When restarting, the fix and the Colvars module should be created and
configured using the original configuration file(s).


Output
""""""

This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`.  The scalar is the energy due to
all external potentials defined in the Colvars configuration.  The
scalar value calculated by this fix is "extensive".

Aside from the state information in a ".colvars.state" file, other
`output files
<https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#sec:colvars_output>`_
are produced by Colvars depending on the type of simulation.  For this
reason, the "output" keyword is required for fix colvars.


Controlling Colvars via `fix_modify`
""""""""""""""""""""""""""""""""""""

.. versionadded:: Colvars_2023-06-04

The :doc:`fix_modify <fix_modify>` command may be used on "fix colvars"
in either one of two ways:

(1) Provide updated values for the fix parameters, such as *output*,
    *input*, *unwrap*, *tstat* and *seed*.  Additionally, the
    :doc:`fix_modify <fix_modify>` *energy* keyword is supported by this fix
    to add the energy change from the biasing force added by Colvars to the
    global potential energy of the system as part of :doc:`thermodynamic
    output <thermo_style>` (the default is :doc:`fix_modify energy no
    <fix_modify>`).  For example, in a multi-step LAMMPS script involving
    multiple thermostats (e.g. fix nvt followed by fix npt), Colvars can
    read a new thermostat's target temperature like this:

   .. code-block:: LAMMPS

      fix NVT all nvt ...
      fix Colvars all colvars <configfile> output equil1 tstat NVT
      run <NUMSTEPS>
      unfix nvt
      fix NPT all n ...
      fix_modify Colvars tstat NPT
      fix_modify Colvars output equil2


(2) Call one of the scripting functions provided by the Colvars module
    itself (a full list is available in the Colvars doc).  The arguments
    to these functions are provided as strings and passed to Colvars.

    LAMMPS variables referenced by their string representation
    "${variable}" will be expanded immediately.  Note also that this
    variable expansion *will also happen within quotes*, similar to what
    the :doc:`mdi <mdi>` command provides.  This feature makes it
    possible to use the values of certain LAMMPS variables in Colvars
    configuration strings.  For example, to synchronize the LAMMPS and
    Colvars dump frequencies:

   .. code-block:: LAMMPS

      variable freq index 10000
      dump myDump all atom/zstd ${freq} dump.atom.zstd
      fix_modify Colvars config "colvarsTrajFrequency ${freq}"

.. note::

   Although it is possible to use :doc:`fix_modify <fix_modify>` at any
   time, its results will only reflect the state of the Colvars module
   at the end of the most recent "run" or "minimize" command.  Any new
   configuration added via "fix_modify Colvars configfile" or
   "fix_modify Colvars config" will only be loaded when the simulation
   resumes.  Configuration files or strings will be parsed in the same
   sequence as they were provided in the LAMMPS script.


Restrictions
""""""""""""

This fix is provided by the COLVARS package and is only available if
LAMMPS was built with that package (default in most builds).  Some of
the features also require code available from the LEPTON package.  See
the :doc:`Build package <Build_package>` page for more info.

There can only be one Colvars instance defined at a time.  Since the
interface communicates only the minimum required amount of information,
and the Colvars module itself can handle an arbitrary number of
collective variables, this is not a limitation of functionality.


Related commands
""""""""""""""""

:doc:`fix smd <fix_smd>`, :doc:`fix spring <fix_spring>`,
:doc:`fix plumed <fix_plumed>`

----------

.. _Fiorin:

**(Fiorin)** Fiorin, Klein, Henin, Mol. Phys. 111, 3345 (2013) https://doi.org/10.1080/00268976.2013.813594

.. _Colvars_LAMMPS_doc:

https://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html
