forked from lijiext/lammps
144 lines
5.9 KiB
Plaintext
144 lines
5.9 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/profile command :h3
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[Syntax:]
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compute ID group-ID temp/profile xflag yflag zflag binstyle args :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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temp/profile = style name of this compute command :l
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xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension :l
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binstyle = {x} or {y} or {z} or {xy} or {yz} or {xz} or {xyz} :l
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{x} arg = Nx
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{y} arg = Ny
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{z} arg = Nz
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{xy} args = Nx Ny
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{yz} args = Ny Nz
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{xz} args = Nx Nz
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{xyz} args = Nx Ny Nz
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Nx,Ny,Nz = number of velocity bins in x,y,z dimensions :pre
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:ule
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[Examples:]
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compute myTemp flow temp/profile 1 1 1 x 10
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compute myTemp flow temp/profile 0 1 1 xyz 20 20 20 :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, after subtracting out a spatially-averaged velocity field,
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before computing the kinetic energy. This can be useful for
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thermostatting a collection of atoms undergoing a complex flow,
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e.g. via a profile-unbiased thermostat (PUT) as described in
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"(Evans)"_#Evans. A compute of this style can be used by any command
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that computes a temperature, e.g. "thermo_modify"_thermo_modify.html,
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"fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc.
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The {xflag}, {yflag}, {zflag} settings determine which components of
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average velocity are subtracted out.
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The {binstyle} setting and its {Nx}, {Ny}, {Nz} arguments determine
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how bins are setup to perform spatial averaging. "Bins" can be 1d
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slabs, 2d pencils, or 3d bricks depending on which {binstyle} is used.
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The simulation box is partitioned conceptually into {Nx} by {Ny} by
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{Nz} bins. Depending on the {binstyle}, you may only specify one or
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two of these values; the others are effectively set to 1 (no binning
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in that dimension). For non-orthogonal (triclinic) simulation boxes,
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the bins are "tilted" slabs or pencils or bricks that are parallel to
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the tilted faces of the box. See the "region prism"_region.html
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command for a discussion of the geometry of tilted boxes in LAMMPS.
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When a temperature is computed, the velocity for the set of atoms that
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are both in the compute group and in the same spatial bin is summed to
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compute an average velocity for the bin. This bias velocity is then
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subtracted from the velocities of individual atoms in the bin to yield
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a thermal velocity for each atom. Note that if there is only one
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atom in the bin, it's thermal velocity will thus be 0.0.
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After the spatially-averaged velocity field has been subtracted from
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each atom, the temperature is calculated by the formula KE = dim/2 N k
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T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m
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v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of
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atoms in the group, k = Boltzmann constant, and T = 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 assumed to be
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constant for the duration of the run; use the {dynamic} option of the
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"compute_modify"_compute_modify.html command if this is not the case.
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The removal of the spatially-averaged velocity field by this fix is
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essentially computing the temperature after a "bias" has been removed
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from the velocity of the atoms. If this compute is used with a fix
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command that performs thermostatting then this bias will be subtracted
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from each atom, thermostatting of the remaining thermal velocity will
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be performed, and the bias will be added back in. Thermostatting
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fixes that work in this way include "fix nvt"_fix_nvt.html, "fix
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temp/rescale"_fix_temp_rescale.html, "fix
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temp/berendsen"_fix_temp_berendsen, and "fix
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langevin"_fix_langevin.html.
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This compute subtracts out degrees-of-freedom due to fixes that
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constrain molecular motion, such as "fix shake"_fix_shake.html and
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"fix rigid"_fix_rigid.html. This means the temperature of groups of
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atoms that include these constraints will be computed correctly. If
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needed, the subtracted degrees-of-freedom can be altered using the
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{extra} option of the "compute_modify"_compute_modify.html command.
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See "this howto section"_Section_howto.html#4_16 of the manual for a
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discussion of different ways to compute temperature and perform
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thermostatting. Using this compute in conjunction with a
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thermostatting fix, as explained there, will effectively implement a
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profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans.
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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#4_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", meaning it
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is independent of the number of atoms in the simulation. The vector
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values are "extensive", meaning they scale with the number of atoms in
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the simulation.
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[Restrictions:]
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You should not use too large a velocity-binning grid, especially in
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3d. In the current implementation, the binned velocity averages are
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summed across all processors, so this will be inefficient if the grid
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is too large, and the operation is performed every timestep, as it
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will be for most thermostats.
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[Related commands:]
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"compute temp"_compute_temp.html, "compute
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temp/ramp"_compute_temp_ramp.html, "compute
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temp/deform"_compute_temp_deform.html, "compute
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pressure"_compute_pressure.html
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[Default:]
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The option default is units = lattice.
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:line
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:link(Evans)
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[(Evans)] Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986).
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