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<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
velocity are subtracted out.
</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
a thermal velocity.
</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>
<P>A 6-component kinetic energy tensor is also calculated by this compute
for use in the calculation 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.
</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
thermostatting fix will effectively implement a PUT, as described in
<A HREF = "#Evans">(Evans)</A>.
</P>
<P><B>Output info:</B>
</P>
<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>

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute temp/profile command :h3
[Syntax:]
compute ID group-ID temp/profile xflag yflag zflag binstyle args :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
temp/profile = style name of this compute command :l
xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension :l
binstyle = {x} or {y} or {z} or {xy} or {yz} or {xz} or {xyz} :l
{x} arg = Nx
{y} arg = Ny
{z} arg = Nz
{xy} args = Nx Ny
{yz} args = Ny Nz
{xz} args = Nx Nz
{xyz} args = Nx Ny Nz
Nx,Ny,Nz = number of velocity bins in x,y,z dimensions :pre
:ule
[Examples:]
compute myTemp flow temp/profile 1 1 1 x 10
compute myTemp flow temp/profile 0 1 1 xyz 20 20 20 :pre
[Description:]
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
"(Evans)"_#Evans. A compute of this style can be used by any command
that computes a temperature, e.g. "thermo_modify"_thermo_modify.html,
"fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc.
The {xflag}, {yflag}, {zflag} settings determine which components of
velocity are subtracted out.
The {binstyle} setting and its {Nx}, {Ny}, {Nz} arguments determine
how bins are setup to perform spatial averaging. "Bins" can be 1d
slabs, 2d pencils, or 3d bricks depending on which {binstyle} is used.
The simulation box is partitioned conceptually into {Nx} by {Ny} by
{Nz} bins. Depending on the {binstyle}, 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 "region prism"_region.html
command for a discussion of the geometry of tilted boxes in LAMMPS.
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
a thermal velocity.
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.
A 6-component kinetic energy tensor is also calculated by this compute
for use in the calculation 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 number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the {dynamic} option of the
"compute_modify"_compute_modify.html command if this is not the case.
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 "fix nvt"_fix_nvt.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix
temp/berendsen"_fix_temp_berendsen, and "fix
langevin"_fix_langevin.html.
This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as "fix shake"_fix_shake.html and
"fix rigid"_fix_rigid.html. 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
{extra} option of the "compute_modify"_compute_modify.html command.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting. Using this compute in conjunction with a
thermostatting fix will effectively implement a PUT, as described in
"(Evans)"_#Evans.
[Output info:]
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.
[Restrictions:]
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.
[Related commands:]
"compute temp"_compute_temp.html, "compute
temp/ramp"_compute_temp_ramp.html, "compute
temp/deform"_compute_temp_deform.html, "compute
pressure"_compute_pressure.html
[Default:]
The option default is units = lattice.
:line
:link(Evans)
[(Evans)] Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986).