167 lines
6.8 KiB
ReStructuredText
167 lines
6.8 KiB
ReStructuredText
.. index:: fix npt/asphere
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.. index:: fix npt/asphere/omp
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fix npt/asphere command
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=======================
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Accelerator Variants: *npt/asphere/omp*
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID npt/asphere keyword value ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* npt/asphere = 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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.. code-block:: LAMMPS
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fix 1 all npt/asphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
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fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
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fix 2 all npt/asphere 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/asphere 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 aspherical or
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ellipsoidal 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 aspherical 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
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<fix_nh>` command. See, for example, discussion of the *temp*, *iso*,
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*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/asphere" and
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"pressure", as if these commands had been issued:
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.. code-block:: LAMMPS
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compute fix-ID_temp all temp/asphere
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compute fix-ID_press all pressure fix-ID_temp
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See the :doc:`compute temp/asphere <compute_temp_asphere>` 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 remove a "bias" from the
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atom velocities. E.g. to apply the thermostat only to atoms within a
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spatial :doc:`region <region>`, or to remove the center-of-mass
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velocity from a group of atoms, or to remove the x-component of
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velocity from the calculation.
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This is not done by default, but only if the :doc:`fix_modify
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<fix_modify>` command is used to assign a temperature compute to this
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fix that includes such a bias term. See the doc pages for individual
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:doc:`compute temp commands <compute>` to determine which ones include
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a bias. In this case, the thermostat works in the following manner:
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bias is removed from each atom, thermostatting is performed on the
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remaining thermal degrees of freedom, and the bias is added back in.
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----------
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.. include:: accel_styles.rst
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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 cumulative energy change in the system imposed by this fix is
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included in the :doc:`thermodynamic output <thermo_style>` keywords
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*ecouple* and *econserve*. See the :doc:`thermo_style <thermo_style>`
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doc page for details.
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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 ASPHERE package. It is only enabled if LAMMPS
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was built with that package. See the :doc:`Build package <Build_package>` page for more info.
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This fix requires that atoms store torque and angular momentum and a
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quaternion as defined by the :doc:`atom_style ellipsoid <atom_style>`
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command.
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All particles in the group must be finite-size. They cannot be point
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particles, but they can be aspherical or spherical as defined by their
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shape attribute.
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Related commands
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""""""""""""""""
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:doc:`fix npt <fix_nh>`, :doc:`fix nve_asphere <fix_nve_asphere>`, :doc:`fix nvt_asphere <fix_nvt_asphere>`, :doc:`fix_modify <fix_modify>`
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Default
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"""""""
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none
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