Homec4science
Diffusion lammps (master) Browse

lammps/doc/_sources/fix_nh_eff.txt
9cf43f2a0b7fmaster

Last Change
Raw File

fix_nh_eff.txt
View Options

.. index:: fix nvt/eff
fix nvt/eff command
===================
fix npt/eff command
===================
fix nph/eff command
===================
Syntax
""""""
.. parsed-literal::
fix ID group-ID style_name keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* style_name = *nvt/eff* or *npt/eff* or *nph/eff*
.. parsed-literal::
one or more keyword value pairs may be appended
keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate*
*temp* values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
*iso* or *aniso* or *tri* values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
*x* or *y* or *z* or *xy* or *yz* or *xz* values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
*couple* = *none* or *xyz* or *xy* or *yz* or *xz*
*tchain* value = length of thermostat chain (1 = single thermostat)
*pchain* values = length of thermostat chain on barostat (0 = no thermostat)
*mtk* value = *yes* or *no* = add in MTK adjustment term or not
*tloop* value = number of sub-cycles to perform on thermostat
*ploop* value = number of sub-cycles to perform on barostat thermostat
*nreset* value = reset reference cell every this many timesteps
*drag* value = drag factor added to barostat/thermostat (0.0 = no drag)
*dilate* value = *all* or *partial*
Examples
""""""""
.. parsed-literal::
fix 1 all nvt/eff temp 300.0 300.0 0.1
fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0
fix 2 part npt/eff temp 300.0 300.0 0.1 tri 5.0 5.0 1.0
fix 2 ice nph/eff x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
Description
"""""""""""
These commands perform time integration on Nose-Hoover style
non-Hamiltonian equations of motion for nuclei and electrons in the
group for the :doc:`electron force field <pair_eff>` model. The fixes
are designed to generate positions and velocities sampled from the
canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph)
ensembles. This is achieved by adding some dynamic variables which
are coupled to the particle velocities (thermostatting) and simulation
domain dimensions (barostatting). In addition to basic thermostatting
and barostatting, these fixes can also create a chain of thermostats
coupled to the particle thermostat, and another chain of thermostats
coupled to the barostat variables. The barostat can be coupled to the
overall box volume, or to individual dimensions, including the *xy*,
*xz* and *yz* tilt dimensions. The external pressure of the barostat
can be specified as either a scalar pressure (isobaric ensemble) or as
components of a symmetric stress tensor (constant stress ensemble).
When used correctly, the time-averaged temperature and stress tensor
of the particles will match the target values specified by
Tstart/Tstop and Pstart/Pstop.
The operation of these fixes is exactly like that described by the
:doc:`fix nvt, npt, and nph <fix_nh>` commands, except that the radius
and radial velocity of electrons are also updated. Likewise the
temperature and pressure calculated by the fix, using the computes it
creates (as discussed in the :doc:`fix nvt, npt, and nph <fix_nh>`
doc page), are performed with computes that include the eFF contribution
to the temperature or kinetic energy from the electron radial velocity.
.. note::
there are two different pressures that can be reported for eFF
when defining the pair_style (see :doc:`pair eff/cut <pair_eff_cut>` to
understand these settings), one (default) that considers electrons do
not contribute radial virial components (i.e. electrons treated as
incompressible 'rigid' spheres) and one that does. The radial
electronic contributions to the virials are only tallied if the
flexible pressure option is set, and this will affect both global and
per-atom quantities. In principle, the true pressure of a system is
somewhere in between the rigid and the flexible eFF pressures, but,
for most cases, the difference between these two pressures will not be
significant over long-term averaged runs (i.e. even though the energy
partitioning changes, the total energy remains similar).
.. note::
currently, there is no available option for the user to set or
create temperature distributions that include the radial electronic
degrees of freedom with the :doc:`velocity <velocity>` command, so the
the user must allow for these degrees of freedom to equilibrate
(i.e. equi-partitioning of energy) through time integration.
Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
See the doc page for the :doc:`fix nvt, npt, and nph <fix_nh>` commands
for details.
Restrictions
""""""""""""
This fix is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
Other restriction discussed on the doc page for the :doc:`fix nvt, npt, and nph <fix_nh>` commands also apply.
.. note::
The temperature for systems (regions or groups) with only
electrons and no nuclei is 0.0 (i.e. not defined) in the current
temperature calculations, a practical example would be a uniform
electron gas or a very hot plasma, where electrons remain delocalized
from the nuclei. This is because, even though electron virials are
included in the temperature calculation, these are averaged over the
nuclear degrees of freedom only. In such cases a corrective term must
be added to the pressure to get the correct kinetic contribution.
Related commands
""""""""""""""""
:doc:`fix nvt <fix_nh>`, :doc:`fix nph <fix_nh>`, :doc:`fix npt <fix_nh>`,
:doc:`fix_modify <fix_modify>`, :doc:`run_style <run_style>`
Default
"""""""
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.
----------
.. _Martyna:
**(Martyna)** Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
.. _Parrinello:
**(Parrinello)** Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
.. _Tuckerman:
**(Tuckerman)** Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
Martyna, J Phys A: Math Gen, 39, 5629 (2006).
.. _Shinoda:
**(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
c4science · Help