forked from lijiext/lammps
108 lines
4.2 KiB
Plaintext
108 lines
4.2 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute temp/region command :h3
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[Syntax:]
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compute ID group-ID temp/region region-ID :pre
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ID, group-ID are documented in "compute"_compute.html command
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temp/region = style name of this compute command
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region-ID = ID of region to use for choosing atoms :ul
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[Examples:]
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compute mine flow temp/region boundary :pre
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[Description:]
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Define a computation that calculates the temperature of a group of
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atoms in a geometric region. This can be useful for thermostatting
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one portion of the simulation box. E.g. a McDLT simulation where one
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side is cooled, and the other side is heated. A compute of this style
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can be used by any command that computes a temperature,
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e.g. "thermo_modify"_thermo_modify.html, "fix
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temp/rescale"_fix_temp_rescale.html, etc.
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Note that a {region}-style temperature can be used to thermostat with
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"fix temp/rescale"_fix_temp_rescale.html or "fix
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langevin"_fix_langevin.html, but should probably not be used with
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Nose/Hoover style fixes ("fix nvt"_fix_nh.html, "fix
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npt"_fix_nh.html, or "fix nph"_fix_nh.html), if the
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degrees-of-freedom included in the computed T varies with time.
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The temperature is calculated by the formula KE = dim/2 N k T, where
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KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
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dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
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in both the group and region, k = Boltzmann constant, and T =
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temperature.
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A kinetic energy tensor, stored as a 6-element vector, is also
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calculated by this compute for use in the computation of a pressure
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tensor. The formula for the components of the tensor is the same as
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the above formula, except that v^2 is replaced by vx*vy for the xy
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component, etc. The 6 components of the vector are ordered xx, yy,
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zz, xy, xz, yz.
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The number of atoms contributing to the temperature is compute each
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time the temperature is evaluated since it is assumed atoms can
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enter/leave the region. Thus there is no need to use the {dynamic}
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option of the "compute_modify"_compute_modify.html command for this
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compute style.
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The removal of atoms outside the region by this fix is essentially
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computing the temperature after a "bias" has been removed, which in
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this case is the velocity of any atoms outside the region. If this
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compute is used with a fix command that performs thermostatting then
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this bias will be subtracted from each atom, thermostatting of the
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remaining thermal velocity will be performed, and the bias will be
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added back in. Thermostatting fixes that work in this way include
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"fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
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temp/berendsen"_fix_temp_berendsen.html, and "fix
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langevin"_fix_langevin.html. This means any of the thermostatting
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fixes can operate on a geometric region of atoms, as defined by this
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compute.
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Unlike other compute styles that calculate temperature, this compute
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does not subtract out degrees-of-freedom due to fixes that constrain
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molecular motion, such as "fix shake"_fix_shake.html and "fix
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rigid"_fix_rigid.html. This is because those degrees of freedom
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(e.g. a constrained bond) can straddle the region boundary, and hence
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the concept is somewhat ill-defined. If needed the number of
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subtracted degrees-of-freedom can be set explicitly using the {extra}
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option of the "compute_modify"_compute_modify.html command.
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See "this howto section"_Section_howto.html#howto_16 of the manual for
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a discussion of different ways to compute temperature and perform
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thermostatting.
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[Output info:]
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This compute calculates a global scalar (the temperature) and a global
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vector of length 6 (KE tensor), which can be accessed by indices 1-6.
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These values can be used by any command that uses global scalar or
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vector values from a compute as input. See "this
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section"_Section_howto.html#howto_15 for an overview of LAMMPS output
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options.
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The scalar value calculated by this compute is "intensive". The
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vector values are "extensive".
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The scalar value will be in temperature "units"_units.html. The
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vector values will be in energy "units"_units.html.
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[Restrictions:] none
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[Related commands:]
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"compute temp"_compute_temp.html, "compute
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pressure"_compute_pressure.html
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[Default:] none
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