Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/doc/compute_temp_deform.html
405d4807c2a8lammps-icms

Last Change
Raw File

compute_temp_deform.html
View Options

<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>IMPORTANT NOTE: The temperature calculated by this compute is only
accurate if the atoms are indeed moving with a stream velocity profile
that matches the box deformation. If not, then the compute will
subtract off an incorrect stream velocity, yielding a bogus thermal
temperature. You should NOT assume that your atoms are streaming at
the same rate the box is deforming. Rather, you should monitor their
velocity profile, e.g. via the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>
command. And you can compare the results of this compute to <A HREF = "compute_temp_profile.html">compute
temp/profile</A>, which actually calculates the
stream profile before subtracting it. If the two computes do not give
roughly the same temperature, then your atoms are not streaming
consistent with the box deformation. See the <A HREF = "fix_deform.html">fix
deform</A> command for more details on ways to get atoms
to stream consistently with the box deformation.
</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>
c4science · Help