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4
doc/_sources/Manual.txt
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@ -5,8 +5,8 @@
LAMMPS Documentation
====================
28 Mar20 2016 version
---------------------
7 Apr 2016 version
------------------
Version info:
-------------

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doc/_sources/fix_nh.txt
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@ -207,8 +207,9 @@ the :doc:`units <units>` command).
of *Pdamp*. If *Pdamp* is too small, the pressure and volume can
fluctuate wildly; if it is too large, the pressure will take a very
long time to equilibrate. A good choice for many models is a *Pdamp*
of around 1000 timesteps. Note that this is NOT the same as 1000 time
units for most :doc:`units <units>` settings.
of around 1000 timesteps. However, note that *Pdamp* is specified in
time units, and that timesteps are NOT the same as time units for most
:doc:`units <units>` settings.
Regardless of what atoms are in the fix group (the only atoms which
are time integrated), a global pressure or stress tensor is computed

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doc/_sources/fix_press_berendsen.txt
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@ -92,10 +92,20 @@ box dimension will not change if that component is not specified,
although you have the option to change that dimension via the :doc:`fix deform <fix_deform>` command.
For all barostat keywords, the *Pdamp* parameter determines the time
scale on which pressure is relaxed. For example, a value of 1000.0
means to relax the pressure in a timespan of (roughly) 1000 time units
scale on which pressure is relaxed. For example, a value of 10.0
means to relax the pressure in a timespan of (roughly) 10 time units
(tau or fmsec or psec - see the :doc:`units <units>` command).
.. note::
A Berendsen barostat will not work well for arbitrary values of
*Pdamp*. If *Pdamp* is too small, the pressure and volume can
fluctuate wildly; if it is too large, the pressure will take a very
long time to equilibrate. A good choice for many models is a *Pdamp*
of around 1000 timesteps. However, note that *Pdamp* is specified in
time units, and that timesteps are NOT the same as time units for most
:doc:`units <units>` settings.
.. note::
The relaxation time is actually also a function of the bulk

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doc/fix_nh.html
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@ -239,12 +239,12 @@ correctly, the time-averaged temperature and stress tensor of the
particles will match the target values specified by Tstart/Tstop and
Pstart/Pstop.</p>
<p>The equations of motion used are those of Shinoda et al in
<a class="reference internal" href="pair_sdk.html#shinoda"><span>(Shinoda)</span></a>, which combine the hydrostatic equations of
Martyna, Tobias and Klein in <a class="reference internal" href="fix_rigid.html#martyna"><span>(Martyna)</span></a> with the strain
<a class="reference internal" href="#shinoda"><span>(Shinoda)</span></a>, which combine the hydrostatic equations of
Martyna, Tobias and Klein in <a class="reference internal" href="#martyna"><span>(Martyna)</span></a> with the strain
energy proposed by Parrinello and Rahman in
<a class="reference internal" href="fix_nh_eff.html#parrinello"><span>(Parrinello)</span></a>. The time integration schemes closely
<a class="reference internal" href="#parrinello"><span>(Parrinello)</span></a>. The time integration schemes closely
follow the time-reversible measure-preserving Verlet and rRESPA
integrators derived by Tuckerman et al in <a class="reference internal" href="run_style.html#tuckerman"><span>(Tuckerman)</span></a>.</p>
integrators derived by Tuckerman et al in <a class="reference internal" href="#tuckerman"><span>(Tuckerman)</span></a>.</p>
<hr class="docutils" />
<p>The thermostat parameters for fix styles <em>nvt</em> and <em>npt</em> is specified
using the <em>temp</em> keyword. Other thermostat-related keywords are
@ -309,8 +309,9 @@ the <a class="reference internal" href="units.html"><em>units</em></a> command).
of <em>Pdamp</em>. If <em>Pdamp</em> is too small, the pressure and volume can
fluctuate wildly; if it is too large, the pressure will take a very
long time to equilibrate. A good choice for many models is a <em>Pdamp</em>
of around 1000 timesteps. Note that this is NOT the same as 1000 time
units for most <a class="reference internal" href="units.html"><em>units</em></a> settings.</p>
of around 1000 timesteps. However, note that <em>Pdamp</em> is specified in
time units, and that timesteps are NOT the same as time units for most
<a class="reference internal" href="units.html"><em>units</em></a> settings.</p>
</div>
<p>Regardless of what atoms are in the fix group (the only atoms which
are time integrated), a global pressure or stress tensor is computed
@ -401,7 +402,7 @@ freedom. A value of 0 corresponds to no thermostatting of the
barostat variables.</p>
<p>The <em>mtk</em> keyword controls whether or not the correction terms due to
Martyna, Tuckerman, and Klein are included in the equations of motion
<a class="reference internal" href="fix_rigid.html#martyna"><span>(Martyna)</span></a>. Specifying <em>no</em> reproduces the original
<a class="reference internal" href="#martyna"><span>(Martyna)</span></a>. Specifying <em>no</em> reproduces the original
Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence
using <em>yes</em> is more correct, but in many cases the difference is
@ -410,7 +411,7 @@ negligible.</p>
scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into <em>tloop</em> substeps, each of
length <em>dt</em>/<em>tloop</em>. This corresponds to using a first-order
Suzuki-Yoshida scheme <a class="reference internal" href="run_style.html#tuckerman"><span>(Tuckerman)</span></a>. The keyword <em>ploop</em>
Suzuki-Yoshida scheme <a class="reference internal" href="#tuckerman"><span>(Tuckerman)</span></a>. The keyword <em>ploop</em>
does the same thing for the barostat thermostat.</p>
<p>The keyword <em>nreset</em> controls how often the reference dimensions used
to define the strain energy are reset. If this keyword is not used,

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doc/fix_nh.txt
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@ -1,4 +1,4 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -173,8 +173,9 @@ NOTE: A Nose-Hoover barostat will not work well for arbitrary values
of {Pdamp}. If {Pdamp} is too small, the pressure and volume can
fluctuate wildly; if it is too large, the pressure will take a very
long time to equilibrate. A good choice for many models is a {Pdamp}
of around 1000 timesteps. Note that this is NOT the same as 1000 time
units for most "units"_units.html settings.
of around 1000 timesteps. However, note that {Pdamp} is specified in
time units, and that timesteps are NOT the same as time units for most
"units"_units.html settings.
Regardless of what atoms are in the fix group (the only atoms which
are time integrated), a global pressure or stress tensor is computed

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doc/fix_press_berendsen.html
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@ -159,7 +159,7 @@ fix 2 all press/berendsen aniso 0.0 0.0 1000.0 dilate partial
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Reset the pressure of the system by using a Berendsen barostat
<a class="reference internal" href="fix_temp_berendsen.html#berendsen"><span>(Berendsen)</span></a>, which rescales the system volume and
<a class="reference internal" href="#berendsen"><span>(Berendsen)</span></a>, which rescales the system volume and
(optionally) the atoms coordinates within the simulation box every
timestep.</p>
<p>Regardless of what atoms are in the fix group, a global pressure is
@ -203,11 +203,21 @@ example, if the <em>y</em> keyword is used, the y-box length will change. A
box dimension will not change if that component is not specified,
although you have the option to change that dimension via the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> command.</p>
<p>For all barostat keywords, the <em>Pdamp</em> parameter determines the time
scale on which pressure is relaxed. For example, a value of 1000.0
means to relax the pressure in a timespan of (roughly) 1000 time units
scale on which pressure is relaxed. For example, a value of 10.0
means to relax the pressure in a timespan of (roughly) 10 time units
(tau or fmsec or psec - see the <a class="reference internal" href="units.html"><em>units</em></a> command).</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">A Berendsen barostat will not work well for arbitrary values of
<em>Pdamp</em>. If <em>Pdamp</em> is too small, the pressure and volume can
fluctuate wildly; if it is too large, the pressure will take a very
long time to equilibrate. A good choice for many models is a <em>Pdamp</em>
of around 1000 timesteps. However, note that <em>Pdamp</em> is specified in
time units, and that timesteps are NOT the same as time units for most
<a class="reference internal" href="units.html"><em>units</em></a> settings.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The relaxation time is actually also a function of the bulk
modulus of the system (inverse of isothermal compressibility). The
bulk modulus has units of pressure and is the amount of pressure that

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doc/fix_press_berendsen.txt
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@ -87,10 +87,18 @@ although you have the option to change that dimension via the "fix
deform"_fix_deform.html command.
For all barostat keywords, the {Pdamp} parameter determines the time
scale on which pressure is relaxed. For example, a value of 1000.0
means to relax the pressure in a timespan of (roughly) 1000 time units
scale on which pressure is relaxed. For example, a value of 10.0
means to relax the pressure in a timespan of (roughly) 10 time units
(tau or fmsec or psec - see the "units"_units.html command).
NOTE: A Berendsen barostat will not work well for arbitrary values of
{Pdamp}. If {Pdamp} is too small, the pressure and volume can
fluctuate wildly; if it is too large, the pressure will take a very
long time to equilibrate. A good choice for many models is a {Pdamp}
of around 1000 timesteps. However, note that {Pdamp} is specified in
time units, and that timesteps are NOT the same as time units for most
"units"_units.html settings.
NOTE: The relaxation time is actually also a function of the bulk
modulus of the system (inverse of isothermal compressibility). The
bulk modulus has units of pressure and is the amount of pressure that

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doc/pair_colloid.html
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@ -163,7 +163,7 @@ Lennard-Jones particle of size sigma.</p>
colloidal particles, and Rc is the cutoff. This equation results from
describing each colloidal particle as an integrated collection of
Lennard-Jones particles of size sigma and is derived in
<a class="reference internal" href="#everaers"><span>(Everaers)</span></a>.</p>
<a class="reference internal" href="pair_resquared.html#everaers"><span>(Everaers)</span></a>.</p>
<p>The colloid-solvent interaction energy is given by</p>
<img alt="_images/pair_colloid_cs.jpg" class="align-center" src="_images/pair_colloid_cs.jpg" />
<p>where A_cs is the Hamaker constant, a is the radius of the colloidal

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doc/searchindex.js
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