Commit a8736058 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1710 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent b9a0d048

doc/Manual.html

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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.

doc/Manual.txt

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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)

doc/Section_howto.html

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@@ -29,6 +29,7 @@ certain kinds of LAMMPS simulations. 
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>

4.16 <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>

doc/Section_howto.txt

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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

doc/compute_temp.html

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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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