185 lines
7.3 KiB
ReStructuredText
185 lines
7.3 KiB
ReStructuredText
.. index:: fix npt/sphere
|
|
.. index:: fix npt/sphere/omp
|
|
|
|
fix npt/sphere command
|
|
======================
|
|
|
|
Accelerator Variants: *npt/sphere/omp*
|
|
|
|
Syntax
|
|
""""""
|
|
|
|
.. parsed-literal::
|
|
|
|
fix ID group-ID npt/sphere keyword value ...
|
|
|
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
|
npt/sphere = style name of this fix command
|
|
zero or more keyword/value pairs may be appended
|
|
* keyword = *disc*
|
|
|
|
.. parsed-literal::
|
|
|
|
*disc* value = none = treat particles as 2d discs, not spheres
|
|
|
|
* NOTE: additional thermostat and barostat and dipole related keyword/value pairs from the :doc:`fix npt <fix_nh>` command can be appended
|
|
|
|
Examples
|
|
""""""""
|
|
|
|
.. code-block:: LAMMPS
|
|
|
|
fix 1 all npt/sphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
|
|
fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
|
|
fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 disc
|
|
fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
|
|
fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 update dipole
|
|
fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial
|
|
|
|
Description
|
|
"""""""""""
|
|
|
|
Perform constant NPT integration to update position, velocity, and
|
|
angular velocity each timestep for finite-sizex spherical particles in
|
|
the group using a Nose/Hoover temperature thermostat and Nose/Hoover
|
|
pressure barostat. P is pressure; T is temperature. This creates a
|
|
system trajectory consistent with the isothermal-isobaric ensemble.
|
|
|
|
This fix differs from the :doc:`fix npt <fix_nh>` command, which
|
|
assumes point particles and only updates their position and velocity.
|
|
|
|
The thermostat is applied to both the translational and rotational
|
|
degrees of freedom for the spherical particles, assuming a compute is
|
|
used which calculates a temperature that includes the rotational
|
|
degrees of freedom (see below). The translational degrees of freedom
|
|
can also have a bias velocity removed from them before thermostatting
|
|
takes place; see the description below.
|
|
|
|
If the *disc* keyword is used, then each particle is treated as a 2d
|
|
disc (circle) instead of as a sphere. This is only possible for 2d
|
|
simulations, as defined by the :doc:`dimension <dimension>` keyword.
|
|
The only difference between discs and spheres in this context is their
|
|
moment of inertia, as used in the time integration.
|
|
|
|
Additional parameters affecting the thermostat and barostat are
|
|
specified by keywords and values documented with the :doc:`fix npt
|
|
<fix_nh>` command. See, for example, discussion of the *temp*, *iso*,
|
|
*aniso*, and *dilate* keywords.
|
|
|
|
The particles in the fix group are the only ones whose velocities and
|
|
positions are updated by the velocity/position update portion of the
|
|
NPT integration.
|
|
|
|
Regardless of what particles are in the fix group, a global pressure is
|
|
computed for all particles. Similarly, when the size of the simulation
|
|
box is changed, all particles are re-scaled to new positions, unless the
|
|
keyword *dilate* is specified with a value of *partial*, in which case
|
|
only the particles in the fix group are re-scaled. The latter can be
|
|
useful for leaving the coordinates of particles in a solid substrate
|
|
unchanged and controlling the pressure of a surrounding fluid.
|
|
|
|
----------
|
|
|
|
This fix computes a temperature and pressure each timestep. To do
|
|
this, the fix creates its own computes of style "temp/sphere" and
|
|
"pressure", as if these commands had been issued:
|
|
|
|
.. code-block:: LAMMPS
|
|
|
|
compute fix-ID_temp all temp/sphere
|
|
compute fix-ID_press all pressure fix-ID_temp
|
|
|
|
See the :doc:`compute temp/sphere <compute_temp_sphere>` and
|
|
:doc:`compute pressure <compute_pressure>` commands for details. Note
|
|
that the IDs of the new computes are the fix-ID + underscore + "temp"
|
|
or fix_ID
|
|
+ underscore + "press", and the group for the new computes is "all"
|
|
since pressure is computed for the entire system.
|
|
|
|
Note that these are NOT the computes used by thermodynamic output (see
|
|
the :doc:`thermo_style <thermo_style>` command) with ID =
|
|
*thermo_temp* and *thermo_press*. This means you can change the
|
|
attributes of this fix's temperature or pressure via the
|
|
:doc:`compute_modify <compute_modify>` command or print this
|
|
temperature or pressure during thermodynamic output via the
|
|
:doc:`thermo_style custom <thermo_style>` command using the
|
|
appropriate compute-ID. It also means that changing attributes of
|
|
*thermo_temp* or *thermo_press* will have no effect on this fix.
|
|
|
|
Like other fixes that perform thermostatting, this fix can be used
|
|
with :doc:`compute commands <compute>` that remove a "bias" from the
|
|
atom velocities. E.g. to apply the thermostat only to atoms within a
|
|
spatial :doc:`region <region>`, or to remove the center-of-mass
|
|
velocity from a group of atoms, or to remove the x-component of
|
|
velocity from the calculation.
|
|
|
|
This is not done by default, but only if the :doc:`fix_modify
|
|
<fix_modify>` command is used to assign a temperature compute to this
|
|
fix that includes such a bias term. See the doc pages for individual
|
|
:doc:`compute temp commands <compute>` to determine which ones include
|
|
a bias. In this case, the thermostat works in the following manner:
|
|
bias is removed from each atom, thermostatting is performed on the
|
|
remaining thermal degrees of freedom, and the bias is added back in.
|
|
|
|
----------
|
|
|
|
.. include:: accel_styles.rst
|
|
|
|
Restart, fix_modify, output, run start/stop, minimize info
|
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
|
|
|
This fix writes the state of the Nose/Hoover thermostat and barostat
|
|
to :doc:`binary restart files <restart>`. See the
|
|
:doc:`read_restart <read_restart>` command for info on how to re-specify
|
|
a fix in an input script that reads a restart file, so that the
|
|
operation of the fix continues in an uninterrupted fashion.
|
|
|
|
The :doc:`fix_modify <fix_modify>` *temp* and *press* options are
|
|
supported by this fix. You can use them to assign a :doc:`compute
|
|
<compute>` you have defined to this fix which will be used in its
|
|
thermostatting or barostatting procedure. If you do this, note that
|
|
the kinetic energy derived from the compute temperature should be
|
|
consistent with the virial term computed using all atoms for the
|
|
pressure. LAMMPS will warn you if you choose to compute temperature
|
|
on a subset of atoms.
|
|
|
|
The cumulative energy change in the system imposed by this fix is
|
|
included in the :doc:`thermodynamic output <thermo_style>` keywords
|
|
*ecouple* and *econserve*. See the :doc:`thermo_style <thermo_style>`
|
|
doc page for details.
|
|
|
|
This fix computes the same global scalar and global vector of
|
|
quantities as does the :doc:`fix npt <fix_nh>` command.
|
|
|
|
This fix can ramp its target temperature and pressure over multiple
|
|
runs, using the *start* and *stop* keywords of the :doc:`run <run>`
|
|
command. See the :doc:`run <run>` command for details of how to do
|
|
this.
|
|
|
|
This fix is not invoked during :doc:`energy minimization <minimize>`.
|
|
|
|
Restrictions
|
|
""""""""""""
|
|
|
|
This fix requires that atoms store torque and angular velocity (omega)
|
|
and a radius as defined by the :doc:`atom_style sphere <atom_style>`
|
|
command.
|
|
|
|
All particles in the group must be finite-size spheres. They cannot
|
|
be point particles.
|
|
|
|
Use of the *disc* keyword is only allowed for 2d simulations, as
|
|
defined by the :doc:`dimension <dimension>` keyword.
|
|
|
|
Related commands
|
|
""""""""""""""""
|
|
|
|
:doc:`fix npt <fix_nh>`, :doc:`fix nve_sphere <fix_nve_sphere>`,
|
|
:doc:`fix nvt_sphere <fix_nvt_sphere>`, :doc:`fix npt_asphere
|
|
<fix_npt_asphere>`, :doc:`fix_modify <fix_modify>`
|
|
|
|
Default
|
|
"""""""
|
|
|
|
none
|