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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10320 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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2013-07-24 14:24:17 +00:00
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20
doc/compute_temp_profile.html
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@ -49,10 +49,10 @@ compute myTemp flow temp/profile 0 1 1 xyz 20 20 20
<P><B>Description:</B> <P><B>Description:</B>
</P> </P>
<P>Define a computation that calculates the temperature of a group of <P>Define a computation that calculates the temperature of a group of
atoms, after subtracting out a spatially-averaged velocity field, atoms, after subtracting out a spatially-averaged center-of-mass
before computing the kinetic energy. This can be useful for velocity field, before computing the kinetic energy. This can be
thermostatting a collection of atoms undergoing a complex flow, useful for thermostatting a collection of atoms undergoing a complex
e.g. via a profile-unbiased thermostat (PUT) as described in 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 <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>, 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. <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
@ -71,12 +71,12 @@ 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> 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. command for a discussion of the geometry of tilted boxes in LAMMPS.
</P> </P>
<P>When a temperature is computed, the velocity for the set of atoms that <P>When a temperature is computed, the center-of-mass velocity for the
are both in the compute group and in the same spatial bin is summed to set of atoms that are both in the compute group and in the same
compute an average velocity for the bin. This bias velocity is then spatial bin is calculated. This bias velocity is then subtracted from
subtracted from the velocities of individual atoms in the bin to yield the velocities of individual atoms in the bin to yield a thermal
a thermal velocity for each atom. Note that if there is only one velocity for each atom. Note that if there is only one atom in the
atom in the bin, it's thermal velocity will thus be 0.0. bin, its thermal velocity will thus be 0.0.
</P> </P>
<P>After the spatially-averaged velocity field has been subtracted from <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 each atom, the temperature is calculated by the formula KE = dim/2 N k

20
doc/compute_temp_profile.txt
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@ -39,10 +39,10 @@ compute myTemp flow temp/profile 0 1 1 xyz 20 20 20 :pre
[Description:] [Description:]
Define a computation that calculates the temperature of a group of Define a computation that calculates the temperature of a group of
atoms, after subtracting out a spatially-averaged velocity field, atoms, after subtracting out a spatially-averaged center-of-mass
before computing the kinetic energy. This can be useful for velocity field, before computing the kinetic energy. This can be
thermostatting a collection of atoms undergoing a complex flow, useful for thermostatting a collection of atoms undergoing a complex
e.g. via a profile-unbiased thermostat (PUT) as described in 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 "(Evans)"_#Evans. A compute of this style can be used by any command
that computes a temperature, e.g. "thermo_modify"_thermo_modify.html, that computes a temperature, e.g. "thermo_modify"_thermo_modify.html,
"fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc. "fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc.
@ -61,12 +61,12 @@ 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 the tilted faces of the box. See the "region prism"_region.html
command for a discussion of the geometry of tilted boxes in LAMMPS. 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 When a temperature is computed, the center-of-mass velocity for the
are both in the compute group and in the same spatial bin is summed to set of atoms that are both in the compute group and in the same
compute an average velocity for the bin. This bias velocity is then spatial bin is calculated. This bias velocity is then subtracted from
subtracted from the velocities of individual atoms in the bin to yield the velocities of individual atoms in the bin to yield a thermal
a thermal velocity for each atom. Note that if there is only one velocity for each atom. Note that if there is only one atom in the
atom in the bin, it's thermal velocity will thus be 0.0. bin, its thermal velocity will thus be 0.0.
After the spatially-averaged velocity field has been subtracted from After the spatially-averaged velocity field has been subtracted from
each atom, the temperature is calculated by the formula KE = dim/2 N k each atom, the temperature is calculated by the formula KE = dim/2 N k