forked from lijiext/lammps
125 lines
5.7 KiB
HTML
125 lines
5.7 KiB
HTML
<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/deform command
|
|
</H3>
|
|
<P><B>Syntax:</B>
|
|
</P>
|
|
<PRE>compute ID group-ID temp/deform
|
|
</PRE>
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
|
<LI>temp/deform = style name of this compute command
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<PRE>compute myTemp all temp/deform
|
|
</PRE>
|
|
<P><B>Description:</B>
|
|
</P>
|
|
<P>Define a computation that calculates the temperature of a group of
|
|
atoms, after subtracting out a streaming velocity induced by the
|
|
simulation box changing size and/or shape, for example in a
|
|
non-equilibrium MD (NEMD) simulation. The size/shape change is
|
|
induced by use of the <A HREF = "fix_deform.html">fix deform</A> command. A compute
|
|
of this style is created by the <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
|
|
command to compute the thermal temperature of atoms for thermostatting
|
|
purposes. A compute of this style can also 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_nh.html">fix npt</A>, etc.
|
|
</P>
|
|
<P>The deformation fix changes the box size and/or shape over time, so
|
|
each atom in the simulation box can be thought of as having a
|
|
"streaming" velocity. For example, if the box is being sheared in x,
|
|
relative to y, then atoms at the bottom of the box (low y) have a
|
|
small x velocity, while atoms at the top of the box (hi y) have a
|
|
large x velocity. This position-dependent streaming velocity is
|
|
subtracted from each atom's actual velocity to yield a thermal
|
|
velocity which is used to compute the temperature.
|
|
</P>
|
|
<P>IMPORTANT NOTE: <A HREF = "fix_deform.html">Fix deform</A> has an option for
|
|
remapping either atom coordinates or velocities to the changing
|
|
simulation box. When using this compute in conjunction with a
|
|
deforming box, fix deform should NOT remap atom positions, but rather
|
|
should let atoms respond to the changing box by adjusting their own
|
|
velocities (or let <A HREF = "fix_deform.html">fix deform</A> remap the atom
|
|
velocities, see it's remap option). If fix deform does remap atom
|
|
positions, then they appear to move with the box but their velocity is
|
|
not changed, and thus they do NOT have the streaming velocity assumed
|
|
by this compute. LAMMPS will warn you if fix deform is defined and
|
|
its remap setting is not consistent with this compute.
|
|
</P>
|
|
<P>After the streaming velocity 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. Note that v in
|
|
the kinetic energy formula is the atom's thermal velocity.
|
|
</P>
|
|
<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.
|
|
</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 box deformation velocity component 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_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
|
|
temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">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#howto_16">this howto section</A> of the manual for
|
|
a discussion of different ways to compute temperature and perform
|
|
thermostatting.
|
|
</P>
|
|
<P><B>Output info:</B>
|
|
</P>
|
|
<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#howto_15">this
|
|
section</A> for an overview of LAMMPS output
|
|
options.
|
|
</P>
|
|
<P>The scalar value calculated by this compute is "intensive". The
|
|
vector values are "extensive".
|
|
</P>
|
|
<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
|
|
vector values will be in energy <A HREF = "units.html">units</A>.
|
|
</P>
|
|
<P><B>Restrictions:</B> none
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>, <A HREF = "compute_temp_profile.html">compute
|
|
temp/profile</A>, <A HREF = "fix_deform.html">fix deform</A>,
|
|
<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
|
|
</P>
|
|
<P><B>Default:</B> none
|
|
</P>
|
|
</HTML>
|