forked from lijiext/lammps
156 lines
6.7 KiB
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156 lines
6.7 KiB
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>compute temp/profile command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID temp/profile xflag yflag zflag binstyle args
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>temp/profile = style name of this compute command
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<LI>xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension
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<LI>binstyle = <I>x</I> or <I>y</I> or <I>z</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>xyz</I>
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<PRE> <I>x</I> arg = Nx
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<I>y</I> arg = Ny
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<I>z</I> arg = Nz
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<I>xy</I> args = Nx Ny
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<I>yz</I> args = Ny Nz
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<I>xz</I> args = Nx Nz
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<I>xyz</I> args = Nx Ny Nz
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Nx,Ny,Nz = number of velocity bins in x,y,z dimensions
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>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
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>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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<A HREF = "#Evans">(Evans)</A>. A compute of this style can be used by any command
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that computes a temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</A>,
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<A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
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</P>
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<P>The <I>xflag</I>, <I>yflag</I>, <I>zflag</I> settings determine which components of
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average velocity are subtracted out.
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</P>
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<P>The <I>binstyle</I> setting and its <I>Nx</I>, <I>Ny</I>, <I>Nz</I> 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 <I>binstyle</I> is used.
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The simulation box is partitioned conceptually into <I>Nx</I> by <I>Ny</I> by
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<I>Nz</I> bins. Depending on the <I>binstyle</I>, 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 <A HREF = "region.html">region prism</A>
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command for a discussion of the geometry of tilted boxes in LAMMPS.
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</P>
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<P>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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</P>
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<P>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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</P>
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<P>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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</P>
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<P>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 <I>dynamic</I> option of the
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<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
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</P>
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<P>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 <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
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temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
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temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
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langevin</A>.
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</P>
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<P>This compute subtracts out degrees-of-freedom due to fixes that
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constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
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<A HREF = "fix_rigid.html">fix rigid</A>. 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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<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
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</P>
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<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
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a 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 <A HREF = "#Evans">(Evans)</A>.
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</P>
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<P><B>Output info:</B>
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</P>
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<P>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 <A HREF = "Section_howto.html#howto_15">this
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section</A> for an overview of LAMMPS output
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options.
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</P>
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<P>The scalar value calculated by this compute is "intensive". The
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vector values are "extensive".
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</P>
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<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
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vector values will be in energy <A HREF = "units.html">units</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>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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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_ramp.html">compute
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temp/ramp</A>, <A HREF = "compute_temp_deform.html">compute
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temp/deform</A>, <A HREF = "compute_pressure.html">compute
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pressure</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option default is units = lattice.
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</P>
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<HR>
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<A NAME = "Evans"></A>
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<P><B>(Evans)</B> Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986).
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</P>
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</HTML>
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