forked from lijiext/lammps
319 lines
12 KiB
Plaintext
319 lines
12 KiB
Plaintext
.. index:: fix langevin/drude
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fix langevin/drude 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 langevin/drude Tcom damp_com seed_com Tdrude damp_drude seed_drude keyword values ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* langevin/drude = style name of this fix command
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* Tcom = desired temperature of the centers of mass (temperature units)
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* damp_com = damping parameter for the thermostat on centers of mass (time units)
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* seed_com = random number seed to use for white noise of the thermostat on centers of mass (positive integer)
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* Tdrude = desired temperature of the Drude oscillators (temperature units)
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* damp_drude = damping parameter for the thermostat on Drude oscillators (time units)
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* seed_drude = random number seed to use for white noise of the thermostat on Drude oscillators (positive integer)
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* zero or more keyword/value pairs may be appended
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* keyword = *zero*
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.. parsed-literal::
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*zero* value = *no* or *yes*
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*no* = do not set total random force on centers of mass to zero
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*yes* = set total random force on centers of mass to zero
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Examples
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""""""""
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.. parsed-literal::
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fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451
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fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes
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Description
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"""""""""""
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Apply two Langevin thermostats as described in :ref:`(Jiang) <Jiang>` for
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thermalizing the reduced degrees of freedom of Drude oscillators.
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This link describes how to use the :doc:`thermalized Drude oscillator model <tutorial_drude>` in LAMMPS and polarizable models in LAMMPS
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are discussed in :ref:`this Section <howto_25>`.
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Drude oscillators are a way to simulate polarizables atoms, by
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splitting them into a core and a Drude particle bound by a harmonic
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bond. The thermalization works by transforming the particles degrees
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of freedom by these equations. In these equations upper case denotes
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atomic or center of mass values and lower case denotes Drude particle
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or dipole values. Primes denote the transformed (reduced) values,
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while bare letters denote the original values.
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Velocities:
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.. math::
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\begin{equation} V' = \frac {M\, V + m\, v} {M'} \end{equation}
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.. math::
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\begin{equation} v' = v - V \end{equation}
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Masses:
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.. math::
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\begin{equation} M' = M + m \end{equation}
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.. math::
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\begin{equation} m' = \frac {M\, m } {M'} \end{equation}
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The Langevin forces are computed as
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.. math::
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\begin{equation} F' = - \frac {M'} {\mathtt{damp\_com}}\, V' + F_r' \end{equation}
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.. math::
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\begin{equation} f' = - \frac {m'} {\mathtt{damp\_drude}}\, v' + f_r' \end{equation}
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:math:`F_r'` is a random force proportional to
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:math:`\sqrt { \frac {2\, k_B \mathtt{Tcom}\, m'} {\mathrm dt\, \mathtt{damp\_com} } }`. :b:math:`f_r'` is a random force proportional to
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:math:`\sqrt { \frac {2\, k_B \mathtt{Tdrude}\, m'} {\mathrm dt\, \mathtt{damp\_drude} } }`.
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Then the real forces acting on the particles are computed from the inverse
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transform:
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.. math::
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\begin{equation} F = \frac M {M'}\, F' - f' \end{equation}
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.. math::
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\begin{equation} f = \frac m {M'}\, F' + f' \end{equation}
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This fix also thermostates non-polarizable atoms in the group at
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temperature *Tcom*\ , as if they had a massless Drude partner. The
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Drude particles themselves need not be in the group. The center of
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mass and the dipole are thermostated iff the core atom is in the
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group.
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Note that the thermostat effect of this fix is applied to only the
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translational degrees of freedom of the particles, which is an
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important consideration if finite-size particles, which have
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rotational degrees of freedom, are being thermostated. The
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translational degrees of freedom can also have a bias velocity removed
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from them before thermostating takes place; see the description below.
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.. note::
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Like the :doc:`fix langevin <fix_langevin>` command, this fix does
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NOT perform time integration. It only modifies forces to effect
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thermostating. Thus you must use a separate time integration fix, like
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:doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>` to actually update the
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velocities and positions of atoms using the modified forces.
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Likewise, this fix should not normally be used on atoms that also have
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their temperature controlled by another fix - e.g. by :doc:`fix nvt <fix_nh>` or :doc:`fix temp/rescale <fix_temp_rescale>` commands.
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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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thermostating.
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----------
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This fix requires each atom know whether it is a Drude particle or
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not. You must therefore use the :doc:`fix drude <fix_drude>` command to
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specify the Drude status of each atom type.
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.. note::
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only the Drude core atoms need to be in the group specified for
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this fix. A Drude electron will be transformed together with its cores
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even if it is not itself in the group. It is safe to include Drude
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electrons or non-polarizable atoms in the group. The non-polarizable
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atoms will simply be thermostatted as if they had a massless Drude
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partner (electron).
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.. note::
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Ghost atoms need to know their velocity for this fix to act
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correctly. You must use the :doc:`comm_modify <comm_modify>` command to
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enable this, e.g.
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.. parsed-literal::
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comm_modify vel yes
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----------
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*Tcom* is the target temperature of the centers of mass, which would
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be used to thermostate the non-polarizable atoms. *Tdrude* is the
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(normally low) target temperature of the core-Drude particle pairs
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(dipoles). *Tcom* and *Tdrude* can be specified as an equal-style
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:doc:`variable <variable>`. If the value is a variable, it should be
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specified as v_name, where name is the variable name. In this case,
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the variable will be evaluated each timestep, and its value used to
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determine the target temperature.
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Equal-style variables can specify formulas with various mathematical
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functions, and include :doc:`thermo_style <thermo_style>` command
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keywords for the simulation box parameters and timestep and elapsed
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time. Thus it is easy to specify a time-dependent temperature.
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Like other fixes that perform thermostating, this fix can be used with
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:doc:`compute commands <compute>` that remove a "bias" from the atom
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velocities. E.g. removing the center-of-mass velocity from a group of
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atoms. This is not done by default, but only if the
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:doc:`fix_modify <fix_modify>` command is used to assign a temperature
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compute to this fix that includes such a bias term. See the doc pages
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for individual :doc:`compute commands <compute>` to determine which ones
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include a bias. In this case, the thermostat works in the following
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manner: bias is removed from each atom, thermostating is performed on
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the remaining thermal degrees of freedom, and the bias is added back
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in. NOTE: this feature has not been tested.
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Note: The temperature thermostating the core-Drude particle pairs
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should be chosen low enough, so as to mimic as closely as possible the
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self-consistent minimization. It must however be high enough, so that
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the dipoles can follow the local electric field exerted by the
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neighbouring atoms. The optimal value probably depends on the
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temperature of the centers of mass and on the mass of the Drude
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particles.
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*damp_com* is the characteristic time for reaching thermal equilibrium
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of the centers of mass. For example, a value of 100.0 means to relax
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the temperature of the centers of mass in a timespan of (roughly) 100
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time units (tau or fmsec or psec - see the :doc:`units <units>`
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command). *damp_drude* is the characteristic time for reaching
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thermal equilibrium of the dipoles. It is typically a few timesteps.
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The number *seed_com* and *seed_drude* are positive integers. They set
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the seeds of the Marsaglia random number generators used for
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generating the random forces on centers of mass and on the
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dipoles. Each processor uses the input seed to generate its own unique
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seed and its own stream of random numbers. Thus the dynamics of the
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system will not be identical on two runs on different numbers of
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processors.
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The keyword *zero* can be used to eliminate drift due to the
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thermostat on centers of mass. Because the random forces on different
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centers of mass are independent, they do not sum exactly to zero. As
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a result, this fix applies a small random force to the entire system,
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and the momentum of the total center of mass of the system undergoes a
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slow random walk. If the keyword *zero* is set to *yes*\ , the total
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random force on the centers of mass is set exactly to zero by
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subtracting off an equal part of it from each center of mass in the
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group. As a result, the total center of mass of a system with zero
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initial momentum will not drift over time.
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The actual temperatures of cores and Drude particles, in
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center-of-mass and relative coordinates, respectively, can be
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calculated using the :doc:`compute temp/drude <compute_temp_drude>`
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command.
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----------
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Usage example for rigid bodies in the NPT ensemble:
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.. parsed-literal::
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comm_modify vel yes
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fix TEMP all langevin/drude 300. 100. 1256 1. 20. 13977 zero yes
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fix NPH ATOMS rigid/nph/small molecule iso 1. 1. 500.
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fix NVE DRUDES nve
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compute TDRUDE all temp/drude
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thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
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Comments:
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* Drude particles should not be in the rigid group, otherwise the Drude
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oscillators will be frozen and the system will lose its
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polarizability.
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* *zero yes* avoids a drift of the center of mass of
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the system, but is a bit slower.
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* Use two different random seeds to avoid unphysical correlations.
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* Temperature is controlled by the fix *langevin/drude*\ , so the
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time-integration fixes do not thermostate. Don't forget to
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time-integrate both cores and Drude particles.
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* Pressure is time-integrated only once by using *nve* for Drude
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particles and *nph* for atoms/cores (or vice versa). Do not use *nph*
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for both.
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* The temperatures of cores and Drude particles are calculated by
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:doc:`compute temp/drude <compute_temp_drude>`
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* Contrary to the alternative thermostating using Nose-Hoover thermostat
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fix *npt* and :doc:`fix drude/transform <fix_drude_transform>`, the
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*fix_modify* command is not required here, because the fix *nph*
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computes the global pressure even if its group is *ATOMS*\ . This is
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what we want. If we thermostated *ATOMS* using *npt*\ , the pressure
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should be the global one, but the temperature should be only that of
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the cores. That's why the command *fix_modify* should be called in
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that case.
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----------
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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>`. Because the state of the random number generator
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is not saved in restart files, this means you cannot do "exact"
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restarts with this fix, where the simulation continues on the same as
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if no restart had taken place. However, in a statistical sense, a
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restarted simulation should produce the same behavior.
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The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
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fix. You can use it to assign a temperature :doc:`compute <compute>`
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you have defined to this fix which will be used in its thermostating
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procedure, as described above. For consistency, the group used by the
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compute should include the group of this fix and the Drude particles.
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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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none
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Related commands
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""""""""""""""""
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:doc:`fix langevin <fix_langevin>`,
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:doc:`fix drude <fix_drude>`,
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:doc:`fix drude/transform <fix_drude_transform>`,
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:doc:`compute temp/drude <compute_temp_drude>`,
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:doc:`pair_style thole <pair_thole>`
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Default
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"""""""
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The option defaults are zero = no.
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----------
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.. _Jiang:
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**(Jiang)** Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J
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Phys Chem Lett, 2, 87-92 (2011).
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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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