git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1710 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp
2008-04-04 21:15:50 +00:00
parent b9a0d04815
commit a87360587a
32 changed files with 277 additions and 3 deletions

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@ -127,6 +127,8 @@ it gives quick access to documentation for all LAMMPS commands.
4.14 <A HREF = "Section_howto.html#4_14">Aspherical particles</A>
<BR>
4.15 <A HREF = "Section_howto.html#4_15">Output from LAMMPS</A>
<BR>
4.16 <A HREF = "Section_howto.html#4_16">Thermostatting, barostatting, and compute temperature</A>
<BR></UL>
<LI><A HREF = "Section_example.html">Example problems</A>
@ -225,6 +227,8 @@ it gives quick access to documentation for all LAMMPS commands.

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@ -87,7 +87,8 @@ it gives quick access to documentation for all LAMMPS commands.
4.12 "Non-orthogonal simulation boxes"_4_12 :b
4.13 "NEMD simulations"_4_13 :b
4.14 "Aspherical particles"_4_14 :b
4.15 "Output from LAMMPS"_4_15 :ule,b
4.15 "Output from LAMMPS"_4_15 :b
4.16 "Thermostatting, barostatting, and compute temperature"_4_16 :ule,b
"Example problems"_Section_example.html :l
"Performance & scalability"_Section_perf.html :l
"Additional tools"_Section_tools.html :l
@ -137,6 +138,7 @@ it gives quick access to documentation for all LAMMPS commands.
:link(4_13,Section_howto.html#4_13)
:link(4_14,Section_howto.html#4_14)
:link(4_15,Section_howto.html#4_15)
:link(4_16,Section_howto.html#4_16)
:link(9_1,Section_errors.html#9_1)
:link(9_2,Section_errors.html#9_2)

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@ -28,7 +28,8 @@ certain kinds of LAMMPS simulations.
4.12 <A HREF = "#4_12">Non-orthogonal simulation boxes</A><BR>
4.13 <A HREF = "#4_13">NEMD simulations</A><BR>
4.14 <A HREF = "#4_14">Aspherical particles</A><BR>
4.15 <A HREF = "#4_15">Output from LAMMPS</A> <BR>
4.15 <A HREF = "#4_15">Output from LAMMPS</A><BR>
4.16 <A HREF = "#4_16">Thermostatting, barostatting and computing temperature</A> <BR>
<P>The example input scripts included in the LAMMPS distribution and
highlighted in <A HREF = "Section_example.html">this section</A> also show how to
@ -1016,6 +1017,82 @@ frequencies and global vs per-atom attributes are the same.
<HR>
<A NAME = "4_16"></A><H4>4.16 Thermostatting, barostatting, and computing temperature
</H4>
<P> add a HowTo on time integration options and/or thermostat/temperature options
4 thermostats
which do integration, which need fix nve or fix nph
all can be used with press/berendsen
only NVT thermostats rotational degrees of freedom directly
what bias is, how to remove it
howto remove bias for temp/sphere and temp/asphere
which biases can be doubled up via compute_modify bias command
</P>
<P>Enhanced the computes that calculate temperature, thermostatting
fixes, and time integrators that use temperature control to be more
flexible and consistent. This is for point particles, extended
spherical particles, and <A HREF = "doc/Section_howto.html#4_14">aspherical
particles</A>. Also Added new <A HREF = "doc/compute_ke.html">compute
ke</A> and <A HREF = "doc/compute_erotate_asphere.html">compute
erotate/asphere</A> commands.
</P>
<P>These <A HREF = "doc/compute.html">compute commands</A> calculate temperature. All
but the first 3 calculate velocity biases that are removed when
computing a temperature. Temp/sphere and temp/asphere now allow
computes that calculate such a biased temperature to be included as an
additional argument, so that the translational velocity of extended
spherical or aspherical particles can also be altered in prescribed
ways.
</P>
<UL><LI><A HREF = "doc/compute_temp.html">compute temp</A>
<LI><A HREF = "doc/compute_temp_sphere.html">compute temp/sphere</A>
<LI><A HREF = "doc/compute_temp_asphere.html">compute temp/asphere</A>
<LI><A HREF = "doc/compute_temp_com.html">compute temp/com</A>
<LI><A HREF = "doc/compute_temp_deform.html">compute temp/deform</A>
<LI><A HREF = "doc/compute_temp_partial.html">compute temp/partial</A>
<LI><A HREF = "doc/compute_temp_ramp.html">compute temp/ramp</A>
<LI><A HREF = "doc/compute_temp_region.html">compute temp/region</A>
</UL>
<P>Four thermostatting methods are available: Nose-Hoover, Berendsen,
Langevin, and direct rescaling. Nose/Hoover works on rotational
degrees-of-freedom for spherical and aspherical particles; the others
only work on translational degrees of freedom. Any of these methods
can use temperature computes that remove bias for the purpose of
computing the current temperature and performing thermostatting only
on the remaining thermal velocity. For <A HREF = "doc/Section_howto.html#4_13">non-equilibrium MD
simulations</A>., there is also a SLLOD fix
which does NVT thermostatting in conjunction with the SLLOD equations
of motion. These are the relevant <A HREF = "doc/fix.html">fix commands</A>:
</P>
<UL><LI><A HREF = "doc/fix_nvt.html">fix nvt</A>
<LI><A HREF = "doc/fix_nvt_sphere.html">fix nvt/sphere</A>
<LI><A HREF = "doc/fix_nvt_asphere.html">fix nvt/asphere</A>
<LI><A HREF = "doc/fix_nvt_sllod.html">fix nvt/sllod</A>
<LI><A HREF = "doc/fix_temp_berendsen.html">fix temp/berendsen</A>
<LI><A HREF = "doc/fix_langevin.html">fix langevin</A>
<LI><A HREF = "doc/fix_temp_rescale.html">fix temp/rescale</A>
</UL>
<P>Note that only the nvt fixes perform time integration. The others
should be used with an NVE integration fix such as these:
</P>
<UL><LI><A HREF = "doc/fix_nve.html">fix nve</A>
<LI><A HREF = "doc/fix_nve_sphere.html">fix nve/sphere</A>
<LI><A HREF = "doc_fix_nve_asphere.html">fix nve/asphere</A>
</UL>
<P>Two barosttating methods are available: Nose-Hoover and Berendsen.
The fix npt commands include Nose-Hoover thermostatting. Fix nph and
fix press/bernendsen can be used in conjunction with any of the 4
thermostatting methods. These are the relevant <A HREF = "doc/fix.html">fix
commands</A>:
</P>
<UL><LI><A HREF = "doc/fix_npt.html">fix npt</A>
<LI><A HREF = "doc/fix_npt_sphere.html">fix npt/sphere</A>
<LI><A HREF = "doc/fix_npt_asphere.html">fix npt/asphere</A>
<LI><A HREF = "doc/fix_nph.html">fix nph</A>
<LI><A HREF = "doc/fix_press_berendsen.html">fix press/berendsen</A>
</UL>
<HR>
<HR>
<A NAME = "Cornell"></A>

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@ -25,7 +25,8 @@ certain kinds of LAMMPS simulations.
4.12 "Non-orthogonal simulation boxes"_#4_12
4.13 "NEMD simulations"_#4_13
4.14 "Aspherical particles"_#4_14
4.15 "Output from LAMMPS"_#4_15 :all(b)
4.15 "Output from LAMMPS"_#4_15
4.16 "Thermostatting, barostatting and computing temperature"_#4_16 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "this section"_Section_example.html also show how to
@ -1005,6 +1006,84 @@ variable atom: thermo keywords, atom value vx\[123\], atom vector vx\[\], global
print: any variable: N/A: screen, log: between runs
run every: any variable: nevery: screen, log: nevery :tb(s=:)
:line
4.16 Thermostatting, barostatting, and computing temperature :link(4_16),h4
add a HowTo on time integration options and/or thermostat/temperature options
4 thermostats
which do integration, which need fix nve or fix nph
all can be used with press/berendsen
only NVT thermostats rotational degrees of freedom directly
what bias is, how to remove it
howto remove bias for temp/sphere and temp/asphere
which biases can be doubled up via compute_modify bias command
Enhanced the computes that calculate temperature, thermostatting
fixes, and time integrators that use temperature control to be more
flexible and consistent. This is for point particles, extended
spherical particles, and "aspherical
particles"_doc/Section_howto.html#4_14. Also Added new "compute
ke"_doc/compute_ke.html and "compute
erotate/asphere"_doc/compute_erotate_asphere.html commands.
These "compute commands"_doc/compute.html calculate temperature. All
but the first 3 calculate velocity biases that are removed when
computing a temperature. Temp/sphere and temp/asphere now allow
computes that calculate such a biased temperature to be included as an
additional argument, so that the translational velocity of extended
spherical or aspherical particles can also be altered in prescribed
ways.
"compute temp"_doc/compute_temp.html
"compute temp/sphere"_doc/compute_temp_sphere.html
"compute temp/asphere"_doc/compute_temp_asphere.html
"compute temp/com"_doc/compute_temp_com.html
"compute temp/deform"_doc/compute_temp_deform.html
"compute temp/partial"_doc/compute_temp_partial.html
"compute temp/ramp"_doc/compute_temp_ramp.html
"compute temp/region"_doc/compute_temp_region.html :ul
Four thermostatting methods are available: Nose-Hoover, Berendsen,
Langevin, and direct rescaling. Nose/Hoover works on rotational
degrees-of-freedom for spherical and aspherical particles; the others
only work on translational degrees of freedom. Any of these methods
can use temperature computes that remove bias for the purpose of
computing the current temperature and performing thermostatting only
on the remaining thermal velocity. For "non-equilibrium MD
simulations"_doc/Section_howto.html#4_13., there is also a SLLOD fix
which does NVT thermostatting in conjunction with the SLLOD equations
of motion. These are the relevant "fix commands"_doc/fix.html:
"fix nvt"_doc/fix_nvt.html
"fix nvt/sphere"_doc/fix_nvt_sphere.html
"fix nvt/asphere"_doc/fix_nvt_asphere.html
"fix nvt/sllod"_doc/fix_nvt_sllod.html
"fix temp/berendsen"_doc/fix_temp_berendsen.html
"fix langevin"_doc/fix_langevin.html
"fix temp/rescale"_doc/fix_temp_rescale.html :ul
Note that only the nvt fixes perform time integration. The others
should be used with an NVE integration fix such as these:
"fix nve"_doc/fix_nve.html
"fix nve/sphere"_doc/fix_nve_sphere.html
"fix nve/asphere"_doc_fix_nve_asphere.html :ul
Two barosttating methods are available: Nose-Hoover and Berendsen.
The fix npt commands include Nose-Hoover thermostatting. Fix nph and
fix press/bernendsen can be used in conjunction with any of the 4
thermostatting methods. These are the relevant "fix
commands"_doc/fix.html:
"fix npt"_doc/fix_npt.html
"fix npt/sphere"_doc/fix_npt_sphere.html
"fix npt/asphere"_doc/fix_npt_asphere.html
"fix nph"_doc/fix_nph.html
"fix press/berendsen"_doc/fix_press_berendsen.html :ul
:line
:line

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@ -58,6 +58,10 @@ LAMMPS starts up, as if this command were in the input script:
</PRE>
<P>See the "thermo_style" command for more details.
</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.
</P>
<P><B>Output info:</B>
</P>
<P>The scalar value calculated by this compute is "intensive", meaning it

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@ -55,6 +55,10 @@ compute thermo_temp all temp :pre
See the "thermo_style" command for more details.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting.
[Output info:]
The scalar value calculated by this compute is "intensive", meaning it

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@ -65,6 +65,10 @@ 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.
</P>
<P><B>Output info:</B>
</P>
<P>The scalar value calculated by this compute is "intensive", meaning it

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@ -62,6 +62,10 @@ 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.
[Output info:]
The scalar value calculated by this compute is "intensive", meaning it

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@ -87,6 +87,10 @@ 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.
</P>
<P><B>Output info:</B>
</P>
<P>The scalar value calculated by this compute is "intensive", meaning it

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@ -84,6 +84,10 @@ 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.
[Output info:]
The scalar value calculated by this compute is "intensive", meaning it

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@ -66,6 +66,10 @@ 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.
</P>
<P><B>Output info:</B>
</P>
<P>The scalar value calculated by this compute is "intensive", meaning it

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@ -63,6 +63,10 @@ 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.
[Output info:]
The scalar value calculated by this compute is "intensive", meaning it

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@ -78,6 +78,10 @@ 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.
</P>
<P><B>Output info:</B>
</P>
<P>The scalar value calculated by this compute is "intensive", meaning it

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@ -74,6 +74,10 @@ 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.
[Output info:]
The scalar value calculated by this compute is "intensive", meaning it

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@ -77,6 +77,10 @@ constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
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.
</P>
<P><B>Output info:</B>
</P>
<P>The scalar value calculated by this compute is "intensive", meaning it

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@ -74,6 +74,10 @@ constrain molecular motion, such as "fix shake"_fix_shake.html and
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.
[Output info:]
The scalar value calculated by this compute is "intensive", meaning it

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@ -70,6 +70,10 @@ 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.
</P>
<P><B>Output info:</B>
</P>
<P>The scalar value calculated by this compute is "intensive", meaning it

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@ -67,6 +67,10 @@ 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.
[Output info:]
The scalar value calculated by this compute is "intensive", meaning it

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@ -85,6 +85,10 @@ should not normally be used on atoms that also have their temperature
controlled by another fix - e.g. by <A HREF = "fix_nvt.html">fix nvt</A> or <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A> commands.
</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.
</P>
<P>The desired temperature at each timestep is a ramped value during the
run from <I>Tstart</I> to <I>Tstop</I>.
</P>

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@ -76,6 +76,10 @@ should not normally be used on atoms that also have their temperature
controlled by another fix - e.g. by "fix nvt"_fix_nvt.html or "fix
temp/rescale"_fix_temp_rescale.html commands.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting.
The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}.

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@ -81,6 +81,10 @@ nvt</A> on atoms to which this fix is applied. Use <A HREF = "fix_npt.html">fix
npt</A> instead of this fix, if you want to control both
temperature and pressure via Nose/Hoover.
</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 and barostatting.
</P>
<HR>
<P>The pressure can be controlled in one of several styles, as specified

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@ -72,6 +72,10 @@ nvt"_fix_nvt.html on atoms to which this fix is applied. Use "fix
npt"_fix_npt.html instead of this fix, if you want to control both
temperature and pressure via Nose/Hoover.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting and barostatting.
:line
The pressure can be controlled in one of several styles, as specified

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@ -92,6 +92,10 @@ normally be used on atoms that also have their temperature controlled
by another fix - e.g. by <A HREF = "fix_nvt.html">fix langevin</A> or <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A> commands.
</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 and barostatting.
</P>
<HR>
<P>The pressure can be controlled in one of several styles, as specified

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@ -81,6 +81,10 @@ normally be used on atoms that also have their temperature controlled
by another fix - e.g. by "fix langevin"_fix_nvt.html or "fix
temp/rescale"_fix_temp_rescale.html commands.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting and barostatting.
:line
The pressure can be controlled in one of several styles, as specified

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@ -75,6 +75,10 @@ temperature controlled by another fix - e.g. by <A HREF = "fix_nvt.html">fix
langevin</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
commands.
</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.
</P>
<P>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if this command had been
issued:

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@ -66,6 +66,10 @@ temperature controlled by another fix - e.g. by "fix
langevin"_fix_nvt.html or "fix temp/rescale"_fix_temp_rescale.html
commands.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting.
This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if this command had been
issued:

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@ -73,6 +73,10 @@ conjunction with thermostatting fixes to control the temperature, such
as <A HREF = "fix_nvt.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix langevin</A> or <A HREF = "fix_temp_berendsen,html">fix
temp/berendsen</A>.
</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 and barostatting.
</P>
<HR>
<P>The pressure can be controlled in one of several styles, as specified

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@ -64,6 +64,10 @@ conjunction with thermostatting fixes to control the temperature, such
as "fix nvt"_fix_nvt.html or "fix langevin"_fix_langevin.html or "fix
temp/berendsen"_fix_temp_berendsen,html.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting and barostatting.
:line
The pressure can be controlled in one of several styles, as specified

View File

@ -54,6 +54,10 @@ normally be used on atoms that also have their temperature controlled
by another fix - e.g. by <A HREF = "fix_nvt.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
langevin</A> commands.
</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.
</P>
<P>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if this command had been
issued:

View File

@ -51,6 +51,10 @@ normally be used on atoms that also have their temperature controlled
by another fix - e.g. by "fix nvt"_fix_nvt.html or "fix
langevin"_fix_langevin.html commands.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting.
This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if this command had been
issued:

View File

@ -61,6 +61,10 @@ normally be used on atoms that also have their temperature controlled
by another fix - e.g. by <A HREF = "fix_nvt.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
langevin</A> commands.
</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.
</P>
<P>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if one of this command had
been issued:

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@ -58,6 +58,10 @@ normally be used on atoms that also have their temperature controlled
by another fix - e.g. by "fix nvt"_fix_nvt.html or "fix
langevin"_fix_langevin.html commands.
See "this howto section"_Section_howto.html#4_16 of the manual for a
discussion of different ways to compute temperature and perform
thermostatting.
This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if one of this command had
been issued: