forked from lijiext/lammps
259 lines
10 KiB
Plaintext
259 lines
10 KiB
Plaintext
.. index:: fix press/berendsen
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fix press/berendsen 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 press/berendsen keyword value ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* press/berendsen = style name of this fix command
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.. parsed-literal::
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one or more keyword value pairs may be appended
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keyword = *iso* or *aniso* or *x* or *y* or *z* or *couple* or *dilate* or *modulus*
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*iso* or *aniso* values = Pstart Pstop Pdamp
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Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
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Pdamp = pressure damping parameter (time units)
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*x* or *y* or *z* values = Pstart Pstop Pdamp
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Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
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Pdamp = stress damping parameter (time units)
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*couple* = *none* or *xyz* or *xy* or *yz* or *xz*
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*modulus* value = bulk modulus of system (pressure units)
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*dilate* value = *all* or *partial*
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Examples
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""""""""
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.. parsed-literal::
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fix 1 all press/berendsen iso 0.0 0.0 1000.0
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fix 2 all press/berendsen aniso 0.0 0.0 1000.0 dilate partial
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Description
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"""""""""""
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Reset the pressure of the system by using a Berendsen barostat
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:ref:`(Berendsen) <Berendsen>`, which rescales the system volume and
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(optionally) the atoms coordinates within the simulation box every
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timestep.
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Regardless of what atoms are in the fix group, a global pressure is
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computed for all atoms. Similarly, when the size of the simulation
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box is changed, all atoms are re-scaled to new positions, unless the
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keyword *dilate* is specified with a value of *partial*\ , in which case
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only the atoms in the fix group are re-scaled. The latter can be
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useful for leaving the coordinates of atoms in a solid substrate
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unchanged and controlling the pressure of a surrounding fluid.
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.. note::
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Unlike the :doc:`fix npt <fix_nh>` or :doc:`fix nph <fix_nh>`
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commands which perform Nose/Hoover barostatting AND time integration,
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this fix does NOT perform time integration. It only modifies the box
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size and atom coordinates to effect barostatting. Thus you must use a
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separate time integration fix, like :doc:`fix nve <fix_nve>` or :doc:`fix nvt <fix_nh>` to actually update the positions and velocities of
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atoms. This fix can be used in conjunction with thermostatting fixes
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to control the temperature, such as :doc:`fix nvt <fix_nh>` or :doc:`fix langevin <fix_langevin>` or :doc:`fix temp/berendsen <fix_temp_berendsen>`.
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See :ref:`this howto section <howto_16>` of the manual for
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a discussion of different ways to compute temperature and perform
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thermostatting and barostatting.
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----------
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The barostat is specified using one or more of the *iso*\ , *aniso*\ ,
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*x*\ , *y*\ , *z*\ , and *couple* keywords. These keywords give you the
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ability to specify the 3 diagonal components of an external stress
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tensor, and to couple various of these components together so that the
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dimensions they represent are varied together during a
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constant-pressure simulation. Unlike the :doc:`fix npt <fix_nh>` and
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:doc:`fix nph <fix_nh>` commands, this fix cannot be used with triclinic
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(non-orthogonal) simulation boxes to control all 6 components of the
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general pressure tensor.
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The target pressures for each of the 3 diagonal components of the
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stress tensor can be specified independently via the *x*\ , *y*\ , *z*\ ,
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keywords, which correspond to the 3 simulation box dimensions. For
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each component, the external pressure or tensor component at each
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timestep is a ramped value during the run from *Pstart* to *Pstop*\ .
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If a target pressure is specified for a component, then the
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corresponding box dimension will change during a simulation. For
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example, if the *y* keyword is used, the y-box length will change. A
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box dimension will not change if that component is not specified,
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although you have the option to change that dimension via the :doc:`fix deform <fix_deform>` command.
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For all barostat keywords, the *Pdamp* parameter determines the time
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scale on which pressure is relaxed. For example, a value of 10.0
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means to relax the pressure in a timespan of (roughly) 10 time units
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(tau or fmsec or psec - see the :doc:`units <units>` command).
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.. note::
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A Berendsen barostat will not work well for arbitrary values of
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*Pdamp*\ . If *Pdamp* is too small, the pressure and volume can
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fluctuate wildly; if it is too large, the pressure will take a very
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long time to equilibrate. A good choice for many models is a *Pdamp*
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of around 1000 timesteps. However, note that *Pdamp* is specified in
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time units, and that timesteps are NOT the same as time units for most
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:doc:`units <units>` settings.
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.. note::
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The relaxation time is actually also a function of the bulk
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modulus of the system (inverse of isothermal compressibility). The
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bulk modulus has units of pressure and is the amount of pressure that
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would need to be applied (isotropically) to reduce the volume of the
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system by a factor of 2 (assuming the bulk modulus was a constant,
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independent of density, which it's not). The bulk modulus can be set
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via the keyword *modulus*\ . The *Pdamp* parameter is effectively
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multiplied by the bulk modulus, so if the pressure is relaxing faster
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than expected or desired, increasing the bulk modulus has the same
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effect as increasing *Pdamp*\ . The converse is also true. LAMMPS does
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not attempt to guess a correct value of the bulk modulus; it just uses
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10.0 as a default value which gives reasonable relaxation for a
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Lennard-Jones liquid, but will be way off for other materials and way
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too small for solids. Thus you should experiment to find appropriate
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values of *Pdamp* and/or the *modulus* when using this fix.
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----------
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The *couple* keyword allows two or three of the diagonal components of
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the pressure tensor to be "coupled" together. The value specified
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with the keyword determines which are coupled. For example, *xz*
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means the *Pxx* and *Pzz* components of the stress tensor are coupled.
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*Xyz* means all 3 diagonal components are coupled. Coupling means two
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things: the instantaneous stress will be computed as an average of the
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corresponding diagonal components, and the coupled box dimensions will
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be changed together in lockstep, meaning coupled dimensions will be
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dilated or contracted by the same percentage every timestep. The
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*Pstart*\ , *Pstop*\ , *Pdamp* parameters for any coupled dimensions must
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be identical. *Couple xyz* can be used for a 2d simulation; the *z*
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dimension is simply ignored.
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----------
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The *iso* and *aniso* keywords are simply shortcuts that are
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equivalent to specifying several other keywords together.
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The keyword *iso* means couple all 3 diagonal components together when
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pressure is computed (hydrostatic pressure), and dilate/contract the
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dimensions together. Using "iso Pstart Pstop Pdamp" is the same as
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specifying these 4 keywords:
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.. parsed-literal::
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x Pstart Pstop Pdamp
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y Pstart Pstop Pdamp
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z Pstart Pstop Pdamp
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couple xyz
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The keyword *aniso* means *x*\ , *y*\ , and *z* dimensions are controlled
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independently using the *Pxx*\ , *Pyy*\ , and *Pzz* components of the
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stress tensor as the driving forces, and the specified scalar external
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pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying
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these 4 keywords:
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.. parsed-literal::
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x Pstart Pstop Pdamp
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y Pstart Pstop Pdamp
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z Pstart Pstop Pdamp
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couple none
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----------
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This fix computes a temperature and pressure each timestep. To do
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this, the fix creates its own computes of style "temp" and "pressure",
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as if these commands had been issued:
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.. parsed-literal::
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compute fix-ID_temp group-ID temp
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compute fix-ID_press group-ID pressure fix-ID_temp
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See the :doc:`compute temp <compute_temp>` and :doc:`compute pressure <compute_pressure>` commands for details. Note that the
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IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
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+ underscore + "press", and the group for the new computes is the same
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as the fix group.
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Note that these are NOT the computes used by thermodynamic output (see
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the :doc:`thermo_style <thermo_style>` command) with ID = *thermo_temp*
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and *thermo_press*\ . This means you can change the attributes of this
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fix's temperature or pressure via the
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:doc:`compute_modify <compute_modify>` command or print this temperature
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or pressure during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` command using the appropriate compute-ID.
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It also means that changing attributes of *thermo_temp* or
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*thermo_press* will have no effect on this fix.
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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>`.
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The :doc:`fix_modify <fix_modify>` *temp* and *press* options are
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supported by this fix. You can use them to assign a
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:doc:`compute <compute>` you have defined to this fix which will be used
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in its temperature and pressure calculations. If you do this, note
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that the kinetic energy derived from the compute temperature should be
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consistent with the virial term computed using all atoms for the
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pressure. LAMMPS will warn you if you choose to compute temperature
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on a subset of atoms.
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No global or per-atom quantities are stored by this fix for access by
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various :ref:`output commands <howto_15>`.
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This fix can ramp its target pressure over multiple runs, using the
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*start* and *stop* keywords of the :doc:`run <run>` command. See the
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:doc:`run <run>` command for details of how to do this.
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This fix is not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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Any dimension being adjusted by this fix must be periodic.
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Related commands
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""""""""""""""""
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:doc:`fix nve <fix_nve>`, :doc:`fix nph <fix_nh>`, :doc:`fix npt <fix_nh>`, :doc:`fix temp/berendsen <fix_temp_berendsen>`,
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:doc:`fix_modify <fix_modify>`
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Default
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"""""""
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The keyword defaults are dilate = all, modulus = 10.0 in units of
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pressure for whatever :doc:`units <units>` are defined.
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----------
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.. _Berendsen:
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**(Berendsen)** Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
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Phys, 81, 3684 (1984).
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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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