Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/doc/html/_sources/fix_spring_chunk.txt
b161fbb52a36lammps-icms

Last Change
Raw File

fix_spring_chunk.txt
View Options

.. index:: fix spring/chunk
fix spring/chunk command
========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID spring/chunk K chunkID comID
* ID, group-ID are documented in :doc:`fix <fix>` command
* spring/chunk = style name of this fix command
* K = spring constant for each chunk (force/distance units)
* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
* comID = ID of :doc:`compute com/chunk <compute_com_chunk>` command
Examples
""""""""
.. parsed-literal::
fix restrain all spring/chunk 100 chunkID comID
Description
"""""""""""
Apply a spring force to the center-of-mass (COM) of chunks of atoms as
defined by the :doc:`compute chunk/atom <compute_chunk_atom>` command.
Chunks can be molecules or spatial bins or other groupings of atoms.
This is a way of tethering each chunk to its initial COM coordinates.
The *chunkID* is the ID of a compute chunk/atom command defined in the
input script. It is used to define the chunks. The *comID* is the ID
of a compute com/chunk command defined in the input script. It is
used to compute the COMs of each chunk.
At the beginning of the first :doc:`run <run>` or
:doc:`minimize <minimize>` command after this fix is defined, the
initial COM of each chunk is calculated and stored as R0m, where M is
the chunk number. Thereafter, at every timestep (or minimization
iteration), the current COM of each chunk is calculated as Rm. A
restoring force of magnitude K (Rm - R0m) Mi / Mm is applied to each
atom in each chunk where *K* is the specified spring constant, Mi is
the mass of the atom, and Mm is the total mass of all atoms in the
chunk. Note that *K* thus represents the spring constant for the
total force on each chunk of atoms, not for a spring applied to each
atom.
Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the energy stored in all the springs to the system's potential
energy as part of :doc:`thermodynamic output <thermo_style>`.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
integrator the fix is adding its forces. Default is the outermost level.
This fix computes a global scalar which can be accessed by various
:ref:`output commands <howto_15>`. The scalar is the
energy of all the springs, i.e. 0.5 * K * r^2 per-spring.
The scalar value calculated by this fix is "extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
The forces due to this fix are imposed during an energy minimization,
invoked by the :doc:`minimize <minimize>` command.
.. note::
If you want the spring energies to be included in the total
potential energy of the system (the quantity being minimized), you
MUST enable the :doc:`fix_modify <fix_modify>` *energy* option for this
fix.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`fix spring <fix_spring>`, :doc:`fix spring/self <fix_spring_self>`,
:doc:`fix spring/rg <fix_spring_rg>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
c4science · Help