forked from lijiext/lammps
182 lines
7.7 KiB
Plaintext
182 lines
7.7 KiB
Plaintext
.. index:: fix npt/body
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fix npt/body 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 npt/body keyword value ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* npt/body = style name of this fix command
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* additional thermostat and barostat related keyword/value pairs from the :doc:`fix npt <fix_nh>` command can be appended
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Examples
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""""""""
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.. parsed-literal::
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fix 1 all npt/body temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
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fix 2 all npt/body temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
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fix 2 all npt/body temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
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fix 2 water npt/body temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial
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Description
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"""""""""""
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Perform constant NPT integration to update position, velocity,
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orientation, and angular velocity each timestep for body
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particles in the group using a Nose/Hoover temperature
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thermostat and Nose/Hoover pressure barostat. P is pressure; T is
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temperature. This creates a system trajectory consistent with the
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isothermal-isobaric ensemble.
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This fix differs from the :doc:`fix npt <fix_nh>` command, which
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assumes point particles and only updates their position and velocity.
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The thermostat is applied to both the translational and rotational
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degrees of freedom for the body particles, assuming a compute is
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used which calculates a temperature that includes the rotational
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degrees of freedom (see below). The translational degrees of freedom
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can also have a bias velocity removed from them before thermostatting
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takes place; see the description below.
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Additional parameters affecting the thermostat and barostat are
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specified by keywords and values documented with the :doc:`fix npt <fix_nh>` command. See, for example, discussion of the *temp*\ ,
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*iso*\ , *aniso*\ , and *dilate* keywords.
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The particles in the fix group are the only ones whose velocities and
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positions are updated by the velocity/position update portion of the
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NPT integration.
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Regardless of what particles are in the fix group, a global pressure is
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computed for all particles. Similarly, when the size of the simulation
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box is changed, all particles 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 particles in the fix group are re-scaled. The latter can be
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useful for leaving the coordinates of particles in a solid substrate
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unchanged and controlling the pressure of a surrounding fluid.
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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/body" and
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"pressure", as if these commands had been issued:
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.. parsed-literal::
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compute fix-ID_temp all temp/body
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compute fix-ID_press all pressure fix-ID_temp
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See the :doc:`compute temp/body <compute_temp_body>` 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 "all"
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since pressure is computed for the entire system.
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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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Like other fixes that perform thermostatting, this fix can be used
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with :doc:`compute commands <compute>` that calculate a temperature
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after removing a "bias" from the atom velocities. E.g. removing the
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center-of-mass velocity from a group of atoms or only calculating
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temperature on the x-component of velocity or only calculating
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temperature for atoms in a geometric region. This is not done by
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default, but only if the :doc:`fix_modify <fix_modify>` command is used
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to assign a temperature compute to this fix that includes such a bias
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term. See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias. In
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this case, the thermostat works in the following manner: the current
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temperature is calculated taking the bias into account, bias is
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removed from each atom, thermostatting is performed on the remaining
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thermal degrees of freedom, and the bias is added back in.
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----------
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Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in :doc:`Section_accelerate <Section_accelerate>`
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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USER-OMP and OPT packages, respectively. They are only enabled if
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LAMMPS was built with those packages. See the :ref:`Making LAMMPS <start_3>` section for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
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use the :doc:`suffix <suffix>` command in your input script.
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See :doc:`Section_accelerate <Section_accelerate>` of the manual for
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more instructions on how to use the accelerated styles effectively.
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Restart, fix_modify, output, run start/stop, minimize info
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""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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This fix writes the state of the Nose/Hoover thermostat and barostat
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to :doc:`binary restart files <restart>`. See the
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:doc:`read_restart <read_restart>` command for info on how to re-specify
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a fix in an input script that reads a restart file, so that the
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operation of the fix continues in an uninterrupted fashion.
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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 thermostatting or barostatting procedure. 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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The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
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fix to add the energy change induced by Nose/Hoover thermostatting and
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barostatting to the system's potential energy as part of
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:doc:`thermodynamic output <thermo_style>`.
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This fix computes the same global scalar and global vector of
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quantities as does the :doc:`fix npt <fix_nh>` command.
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This fix can ramp its target temperature and pressure over multiple
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runs, using the *start* and *stop* keywords of the :doc:`run <run>`
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command. See the :doc:`run <run>` command for details of how to do
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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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This fix is part of the BODY package. It is only enabled if LAMMPS
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was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
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This fix requires that atoms store torque and angular momementum and a
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quaternion as defined by the :doc:`atom_style body <atom_style>`
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command.
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Related commands
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""""""""""""""""
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:doc:`fix npt <fix_nh>`, :doc:`fix nve_body <fix_nve_body>`, :doc:`fix nvt_body <fix_nvt_body>`, :doc:`fix_modify <fix_modify>`
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**Default:** none
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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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