forked from lijiext/lammps
142 lines
5.5 KiB
Plaintext
142 lines
5.5 KiB
Plaintext
.. index:: fix recenter
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fix recenter 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 recenter x y z keyword value ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* recenter = style name of this fix command
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* x,y,z = constrain center-of-mass to these coords (distance units), any coord can also be NULL or INIT (see below)
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* zero or more keyword/value pairs may be appended
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* keyword = *shift* or *units*
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.. parsed-literal::
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*shift* value = group-ID
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group-ID = group of atoms whose coords are shifted
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*units* value = *box* or *lattice* or *fraction*
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Examples
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""""""""
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.. parsed-literal::
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fix 1 all recenter 0.0 0.5 0.0
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fix 1 all recenter INIT INIT NULL
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fix 1 all recenter INIT 0.0 0.0 units box
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Description
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"""""""""""
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Constrain the center-of-mass position of a group of atoms by adjusting
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the coordinates of the atoms every timestep. This is simply a small
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shift that does not alter the dynamics of the system or change the
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relative coordinates of any pair of atoms in the group. This can be
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used to insure the entire collection of atoms (or a portion of them)
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do not drift during the simulation due to random perturbations
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(e.g. :doc:`fix langevin <fix_langevin>` thermostatting).
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Distance units for the x,y,z values are determined by the setting of
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the *units* keyword, as discussed below. One or more x,y,z values can
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also be specified as NULL, which means exclude that dimension from
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this operation. Or it can be specified as INIT which means to
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constrain the center-of-mass to its initial value at the beginning of
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the run.
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The center-of-mass (COM) is computed for the group specified by the
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fix. If the current COM is different than the specified x,y,z, then a
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group of atoms has their coordinates shifted by the difference. By
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default the shifted group is also the group specified by the fix. A
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different group can be shifted by using the *shift* keyword. For
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example, the COM could be computed on a protein to keep it in the
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center of the simulation box. But the entire system (protein + water)
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could be shifted.
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If the *units* keyword is set to *box*\ , then the distance units of
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x,y,z are defined by the :doc:`units <units>` command - e.g. Angstroms
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for *real* units. A *lattice* value means the distance units are in
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lattice spacings. The :doc:`lattice <lattice>` command must have been
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previously used to define the lattice spacing. A *fraction* value
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means a fractional distance between the lo/hi box boundaries, e.g. 0.5
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= middle of the box. The default is to use lattice units.
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Note that the :doc:`velocity <velocity>` command can be used to create
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velocities with zero aggregate linear and/or angular momentum.
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.. note::
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This fix performs its operations at the same point in the
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timestep as other time integration fixes, such as :doc:`fix nve <fix_nve>`, :doc:`fix nvt <fix_nh>`, or :doc:`fix npt <fix_nh>`.
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Thus fix recenter should normally be the last such fix specified in
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the input script, since the adjustments it makes to atom coordinates
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should come after the changes made by time integration. LAMMPS will
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warn you if your fixes are not ordered this way.
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.. note::
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If you use this fix on a small group of atoms (e.g. a molecule
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in solvent) without using the *shift* keyword to adjust the positions
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of all atoms in the system, then the results can be unpredictable.
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For example, if the molecule is pushed consistently in one direction
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by a flowing solvent, its velocity will increase. But its coordinates
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will be recentered, meaning it is moved back towards the force. Thus
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over time, the velocity and effective temperature of the molecule
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could become very large, though it won't actually be moving due to the
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recentering. If you are thermostatting the entire system, then the
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solvent would be cooled to compensate. A better solution for this
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simulation scenario is to use the :doc:`fix spring <fix_spring>` command
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to tether the molecule in place.
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Restart, fix_modify, output, run start/stop, minimize info
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""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
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are relevant to this fix.
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This fix computes a global scalar which can be accessed by various
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:ref:`output commands <howto_15>`. The scalar is the
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distance the group is moved by fix recenter.
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This fix also computes global 3-vector which can be accessed by
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various :ref:`output commands <howto_15>`. The 3
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quantities in the vector are xyz components of displacement applied to
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the group of atoms by the fix.
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The scalar and vector values calculated by this fix are "extensive".
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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This fix should not be used with an x,y,z setting that causes a large
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shift in the system on the 1st timestep, due to the requested COM
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being very different from the initial COM. This could cause atoms to
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be lost, especially in parallel. Instead, use the
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:doc:`displace_atoms <displace_atoms>` command, which can be used to
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move atoms a large distance.
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Related commands
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""""""""""""""""
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:doc:`fix momentum <fix_momentum>`, :doc:`velocity <velocity>`
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Default
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"""""""
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The option defaults are shift = fix group-ID, and units = lattice.
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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