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doc/Manual.html
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@ -135,7 +135,7 @@
<H1></H1><div class="section" id="lammps-documentation">
<h1>LAMMPS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline"></a></h1>
<div class="section" id="dec-2015-version">
<h2>19 Dec 2015 version<a class="headerlink" href="#dec-2015-version" title="Permalink to this headline"></a></h2>
<h2>23 Dec 2015 version<a class="headerlink" href="#dec-2015-version" title="Permalink to this headline"></a></h2>
</div>
<div class="section" id="version-info">
<h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline"></a></h2>

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doc/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="19 Dec 2015 version">
<META NAME="docnumber" CONTENT="23 Dec 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
19 Dec 2015 version :c,h4
23 Dec 2015 version :c,h4
Version info: :h4

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doc/fix_nh.html
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@ -235,12 +235,12 @@ 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="#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
<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
energy proposed by Parrinello and Rahman in
<a class="reference internal" href="#parrinello"><span>(Parrinello)</span></a>. The time integration schemes closely
<a class="reference internal" href="fix_nh_eff.html#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="#tuckerman"><span>(Tuckerman)</span></a>.</p>
integrators derived by Tuckerman et al in <a class="reference internal" href="run_style.html#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
@ -397,7 +397,7 @@ 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="#martyna"><span>(Martyna)</span></a>. Specifying <em>no</em> reproduces the original
<a class="reference internal" href="fix_rigid.html#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
@ -406,7 +406,7 @@ 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="#tuckerman"><span>(Tuckerman)</span></a>. The keyword <em>ploop</em>
Suzuki-Yoshida scheme <a class="reference internal" href="run_style.html#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_qeq.html
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@ -172,8 +172,8 @@ fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Perform the charge equilibration (QEq) method as described in <a class="reference internal" href="#rappe"><span>(Rappe and Goddard)</span></a> and formulated in <a class="reference internal" href="#nakano"><span>(Nakano)</span></a> (also known
as the matrix inversion method) and in <a class="reference internal" href="#rick"><span>(Rick and Stuart)</span></a> (also
<p>Perform the charge equilibration (QEq) method as described in <a class="reference internal" href="fix_qeq_reax.html#rappe"><span>(Rappe and Goddard)</span></a> and formulated in <a class="reference internal" href="neb.html#nakano"><span>(Nakano)</span></a> (also known
as the matrix inversion method) and in <a class="reference internal" href="pair_smtbq.html#rick"><span>(Rick and Stuart)</span></a> (also
known as the extended Lagrangian method) based on the
electronegativity equilization principle.</p>
<p>These fixes can be used with any <a class="reference internal" href="pair_style.html"><em>pair style</em></a> in
@ -225,8 +225,8 @@ below, thus the others can be set to 0.0 if desired.</p>
<li><em>chi</em> = electronegativity in energy units</li>
<li><em>eta</em> = self-Coulomb potential in energy units</li>
<li><em>gamma</em> = shielded Coulomb constant defined by <a class="reference internal" href="#vanduin"><span>ReaxFF force field</span></a> in distance units</li>
<li><em>zeta</em> = Slater type orbital exponent defined by the <a class="reference internal" href="#streitz"><span>Streitz-Mintmire</span></a> potential in reverse distance units</li>
<li><em>qcore</em> = charge of the nucleus defined by the <a class="reference internal" href="#streitz"><span>Streitz-Mintmire potential</span></a> potential in charge units</li>
<li><em>zeta</em> = Slater type orbital exponent defined by the <a class="reference internal" href="pair_coul.html#streitz"><span>Streitz-Mintmire</span></a> potential in reverse distance units</li>
<li><em>qcore</em> = charge of the nucleus defined by the <a class="reference internal" href="pair_coul.html#streitz"><span>Streitz-Mintmire potential</span></a> potential in charge units</li>
</ul>
<p>The <em>qeq/point</em> style describes partial charges on atoms as point
charges. Interaction between a pair of charged particles is 1/r,
@ -250,7 +250,7 @@ charge densities centered around atoms via the Slater 1*s* orbital, so
that the interaction between a pair of charged particles is the
product of two Slater 1*s* orbitals. The expression for the Slater
1*s* orbital is given under equation (6) of the
<a class="reference internal" href="#streitz"><span>Streitz-Mintmire</span></a> paper. Only the <em>chi</em>, <em>eta</em>, <em>zeta</em>, and
<a class="reference internal" href="pair_coul.html#streitz"><span>Streitz-Mintmire</span></a> paper. Only the <em>chi</em>, <em>eta</em>, <em>zeta</em>, and
<em>qcore</em> parameters from the <em>qfile</em> file are used. This style solves
partial charges on atoms via the matrix inversion method. A tolerance
of 1.0e-6 is usually a good number. Keyword <em>alpha</em> can be used to

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