2009-04-30 01:29:52 +08:00
|
|
|
<HTML>
|
|
|
|
|
<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>
|
|
|
|
|
</CENTER>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<H3>compute temp/profile command
|
|
|
|
|
</H3>
|
|
|
|
|
<P><B>Syntax:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>compute ID group-ID temp/profile xflag yflag zflag binstyle args
|
|
|
|
|
</PRE>
|
|
|
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
|
|
|
|
|
|
|
|
|
<LI>temp/profile = style name of this compute command
|
|
|
|
|
|
|
|
|
|
<LI>xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension
|
|
|
|
|
|
|
|
|
|
<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>
|
|
|
|
|
|
|
|
|
|
<PRE> <I>x</I> arg = Nx
|
|
|
|
|
<I>y</I> arg = Ny
|
|
|
|
|
<I>z</I> arg = Nz
|
|
|
|
|
<I>xy</I> args = Nx Ny
|
|
|
|
|
<I>yz</I> args = Ny Nz
|
|
|
|
|
<I>xz</I> args = Nx Nz
|
|
|
|
|
<I>xyz</I> args = Nx Ny Nz
|
|
|
|
|
Nx,Ny,Nz = number of velocity bins in x,y,z dimensions
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>compute myTemp flow temp/profile 1 1 1 x 10
|
|
|
|
|
compute myTemp flow temp/profile 0 1 1 xyz 20 20 20
|
|
|
|
|
</PRE>
|
|
|
|
|
<P><B>Description:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>Define a computation that calculates the temperature of a group of
|
|
|
|
|
atoms, after subtracting out a spatially-averaged velocity field,
|
|
|
|
|
before computing the kinetic energy. This can be useful for
|
|
|
|
|
thermostatting a collection of atoms undergoing a complex flow,
|
|
|
|
|
e.g. via a profile-unbiased thermostat (PUT) as described in
|
|
|
|
|
<A HREF = "#Evans">(Evans)</A>. A compute of this style can be used by any command
|
|
|
|
|
that computes a temperature, e.g. <A HREF = "thermo_modify.html">thermo_modify</A>,
|
|
|
|
|
<A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The <I>xflag</I>, <I>yflag</I>, <I>zflag</I> settings determine which components of
|
2009-04-30 01:41:26 +08:00
|
|
|
average velocity are subtracted out.
|
2009-04-30 01:29:52 +08:00
|
|
|
</P>
|
|
|
|
|
<P>The <I>binstyle</I> setting and its <I>Nx</I>, <I>Ny</I>, <I>Nz</I> arguments determine
|
|
|
|
|
how bins are setup to perform spatial averaging. "Bins" can be 1d
|
|
|
|
|
slabs, 2d pencils, or 3d bricks depending on which <I>binstyle</I> is used.
|
|
|
|
|
The simulation box is partitioned conceptually into <I>Nx</I> by <I>Ny</I> by
|
|
|
|
|
<I>Nz</I> bins. Depending on the <I>binstyle</I>, you may only specify one or
|
|
|
|
|
two of these values; the others are effectively set to 1 (no binning
|
|
|
|
|
in that dimension). For non-orthogonal (triclinic) simulation boxes,
|
|
|
|
|
the bins are "tilted" slabs or pencils or bricks that are parallel to
|
|
|
|
|
the tilted faces of the box. See the <A HREF = "region.html">region prism</A>
|
|
|
|
|
command for a discussion of the geometry of tilted boxes in LAMMPS.
|
|
|
|
|
</P>
|
|
|
|
|
<P>When a temperature is computed, the velocity for the set of atoms that
|
|
|
|
|
are both in the compute group and in the same spatial bin is summed to
|
|
|
|
|
compute an average velocity for the bin. This bias velocity is then
|
|
|
|
|
subtracted from the velocities of individual atoms in the bin to yield
|
2009-05-01 00:53:04 +08:00
|
|
|
a thermal velocity for each atom. Note that if there is only one
|
|
|
|
|
atom in the bin, it's thermal velocity will thus be 0.0.
|
2009-04-30 01:29:52 +08:00
|
|
|
</P>
|
|
|
|
|
<P>After the spatially-averaged velocity field has been subtracted from
|
|
|
|
|
each atom, the temperature is calculated by the formula KE = dim/2 N k
|
|
|
|
|
T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m
|
|
|
|
|
v^2), dim = 2 or 3 = dimensionality of the simulation, N = number of
|
|
|
|
|
atoms in the group, k = Boltzmann constant, and T = temperature.
|
|
|
|
|
</P>
|
2009-12-04 07:58:11 +08:00
|
|
|
<P>A kinetic energy tensor, stored as a 6-element vector, is also
|
|
|
|
|
calculated by this compute for use in the computation of a pressure
|
|
|
|
|
tensor. The formula for the components of the tensor is the same as
|
|
|
|
|
the above formula, except that v^2 is replaced by vx*vy for the xy
|
|
|
|
|
component, etc. The 6 components of the vector are ordered xx, yy,
|
|
|
|
|
zz, xy, xz, yz.
|
2009-04-30 01:29:52 +08:00
|
|
|
</P>
|
|
|
|
|
<P>The number of atoms contributing to the temperature is assumed to be
|
|
|
|
|
constant for the duration of the run; use the <I>dynamic</I> option of the
|
|
|
|
|
<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The removal of the spatially-averaged velocity field by this fix is
|
|
|
|
|
essentially computing the temperature after a "bias" has been removed
|
|
|
|
|
from the velocity of the atoms. If this compute is used with a fix
|
|
|
|
|
command that performs thermostatting then this bias will be subtracted
|
|
|
|
|
from each atom, thermostatting of the remaining thermal velocity will
|
|
|
|
|
be performed, and the bias will be added back in. Thermostatting
|
|
|
|
|
fixes that work in this way include <A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
|
|
|
|
|
temp/rescale</A>, <A HREF = "fix_temp_berendsen">fix
|
|
|
|
|
temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
|
|
|
|
|
langevin</A>.
|
|
|
|
|
</P>
|
|
|
|
|
<P>This compute subtracts out degrees-of-freedom due to fixes that
|
|
|
|
|
constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
|
|
|
|
|
<A HREF = "fix_rigid.html">fix rigid</A>. This means the temperature of groups of
|
|
|
|
|
atoms that include these constraints will be computed correctly. If
|
|
|
|
|
needed, the subtracted degrees-of-freedom can be altered using the
|
|
|
|
|
<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
|
|
|
|
|
</P>
|
|
|
|
|
<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
|
|
|
|
|
discussion of different ways to compute temperature and perform
|
|
|
|
|
thermostatting. Using this compute in conjunction with a
|
2009-05-01 00:53:04 +08:00
|
|
|
thermostatting fix, as explained there, will effectively implement a
|
|
|
|
|
profile-unbiased thermostat (PUT), as described in <A HREF = "#Evans">(Evans)</A>.
|
2009-04-30 01:29:52 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Output info:</B>
|
|
|
|
|
</P>
|
2009-12-04 07:58:11 +08:00
|
|
|
<P>This compute calculates a global scalar (the temperature) and a global
|
|
|
|
|
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
|
|
|
|
|
These values can be used by any command that uses global scalar or
|
|
|
|
|
vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
|
|
|
|
|
section</A> for an overview of LAMMPS output
|
|
|
|
|
options.
|
|
|
|
|
</P>
|
2009-04-30 01:29:52 +08:00
|
|
|
<P>The scalar value calculated by this compute is "intensive", meaning it
|
|
|
|
|
is independent of the number of atoms in the simulation. The vector
|
|
|
|
|
values are "extensive", meaning they scale with the number of atoms in
|
|
|
|
|
the simulation.
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Restrictions:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>You should not use too large a velocity-binning grid, especially in
|
|
|
|
|
3d. In the current implementation, the binned velocity averages are
|
|
|
|
|
summed across all processors, so this will be inefficient if the grid
|
|
|
|
|
is too large, and the operation is performed every timestep, as it
|
|
|
|
|
will be for most thermostats.
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_ramp.html">compute
|
|
|
|
|
temp/ramp</A>, <A HREF = "compute_temp_deform.html">compute
|
|
|
|
|
temp/deform</A>, <A HREF = "compute_pressure.html">compute
|
|
|
|
|
pressure</A>
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>The option default is units = lattice.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<A NAME = "Evans"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Evans)</B> Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986).
|
|
|
|
|
</P>
|
|
|
|
|
</HTML>
|
