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doc/Manual.html
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@ -135,7 +135,7 @@
<H1></H1><div class="section" id="lammps-documentation"> <H1></H1><div class="section" id="lammps-documentation">
<h1>LAMMPS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline"></a></h1> <h1>LAMMPS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline"></a></h1>
<div class="section" id="dec-2015-version"> <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>
<div class="section" id="version-info"> <div class="section" id="version-info">
<h2>Version info:<a class="headerlink" href="#version-info" title="Permalink to this headline"></a></h2> <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 --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS Users Manual</TITLE> <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="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."> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD> </HEAD>
@ -21,7 +21,7 @@
<H1></H1> <H1></H1>
LAMMPS Documentation :c,h3 LAMMPS Documentation :c,h3
19 Dec 2015 version :c,h4 23 Dec 2015 version :c,h4
Version info: :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 particles will match the target values specified by Tstart/Tstop and
Pstart/Pstop.</p> Pstart/Pstop.</p>
<p>The equations of motion used are those of Shinoda et al in <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 <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="#martyna"><span>(Martyna)</span></a> with the strain 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 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 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" /> <hr class="docutils" />
<p>The thermostat parameters for fix styles <em>nvt</em> and <em>npt</em> is specified <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 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> barostat variables.</p>
<p>The <em>mtk</em> keyword controls whether or not the correction terms due to <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 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 Hoover barostat, whose volume probability distribution function
differs from the true NPT and NPH ensembles by a factor of 1/V. Hence 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 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 scheme at little extra cost. The initial and final updates of the
thermostat variables are broken up into <em>tloop</em> substeps, each of 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 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> does the same thing for the barostat thermostat.</p>
<p>The keyword <em>nreset</em> controls how often the reference dimensions used <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, 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>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2> <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 <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="#rick"><span>(Rick and Stuart)</span></a> (also 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 known as the extended Lagrangian method) based on the
electronegativity equilization principle.</p> 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 <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>chi</em> = electronegativity in energy units</li>
<li><em>eta</em> = self-Coulomb potential 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>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>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="#streitz"><span>Streitz-Mintmire potential</span></a> potential in charge 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> </ul>
<p>The <em>qeq/point</em> style describes partial charges on atoms as point <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, 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 that the interaction between a pair of charged particles is the
product of two Slater 1*s* orbitals. The expression for the Slater product of two Slater 1*s* orbitals. The expression for the Slater
1*s* orbital is given under equation (6) of the 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 <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 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 of 1.0e-6 is usually a good number. Keyword <em>alpha</em> can be used to

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