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#	doc/Manual.txt
#	doc/fix_nh.txt
#	src/create_atoms.cpp
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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-ICMS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline"></a></h1> <h1>LAMMPS-ICMS Documentation<a class="headerlink" href="#lammps-documentation" title="Permalink to this headline"></a></h1>
<div class="section" id="jan-2016-version"> <div class="section" id="jan-2016-version">
<h2>14 Jan 2016 version<a class="headerlink" href="#jan-2016-version" title="Permalink to this headline"></a></h2> <h2>15 Jan 2016 version<a class="headerlink" href="#jan-2016-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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@ -1,7 +1,7 @@
<!-- HTML_ONLY --> <!-- HTML_ONLY -->
<HEAD> <HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE> <TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="14 Jan 2016 version"> <META NAME="docnumber" CONTENT="15 Jan 2016 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-ICMS Documentation :c,h3 LAMMPS-ICMS Documentation :c,h3
14 Jan 2016 version :c,h4 15 Jan 2016 version :c,h4
Version info: :h4 Version info: :h4

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doc/Section_commands.html
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@ -1071,7 +1071,7 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="pair_kim.html"><em>kim</em></a></td> <td><a class="reference internal" href="pair_kim.html"><em>kim</em></a></td>
<td><a class="reference internal" href="pair_lcbop.html"><em>lcbop</em></a></td> <td><a class="reference internal" href="pair_lcbop.html"><em>lcbop</em></a></td>
</tr> </tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_line_lj.html"><em>line/lj (o)</em></a></td> <tr class="row-odd"><td><a class="reference internal" href="pair_line_lj.html"><em>line/lj</em></a></td>
<td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/charmm (cko)</em></a></td> <td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/charmm (cko)</em></a></td>
<td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/charmm/implicit (cko)</em></a></td> <td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/charmm/implicit (cko)</em></a></td>
<td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/long (cgiko)</em></a></td> <td><a class="reference internal" href="pair_charmm.html"><em>lj/charmm/coul/long (cgiko)</em></a></td>
@ -1142,7 +1142,7 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
<td><a class="reference internal" href="pair_coul.html"><em>tip4p/cut (o)</em></a></td> <td><a class="reference internal" href="pair_coul.html"><em>tip4p/cut (o)</em></a></td>
</tr> </tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><em>tip4p/long (o)</em></a></td> <tr class="row-odd"><td><a class="reference internal" href="pair_coul.html"><em>tip4p/long (o)</em></a></td>
<td><a class="reference internal" href="pair_tri_lj.html"><em>tri/lj (o)</em></a></td> <td><a class="reference internal" href="pair_tri_lj.html"><em>tri/lj</em></a></td>
<td><a class="reference internal" href="pair_vashishta.html"><em>vashishta (o)</em></a></td> <td><a class="reference internal" href="pair_vashishta.html"><em>vashishta (o)</em></a></td>
<td><a class="reference internal" href="pair_yukawa.html"><em>yukawa (go)</em></a></td> <td><a class="reference internal" href="pair_yukawa.html"><em>yukawa (go)</em></a></td>
</tr> </tr>

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@ -832,7 +832,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html, "hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
"kim"_pair_kim.html, "kim"_pair_kim.html,
"lcbop"_pair_lcbop.html, "lcbop"_pair_lcbop.html,
"line/lj (o)"_pair_line_lj.html, "line/lj"_pair_line_lj.html,
"lj/charmm/coul/charmm (cko)"_pair_charmm.html, "lj/charmm/coul/charmm (cko)"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit (cko)"_pair_charmm.html, "lj/charmm/coul/charmm/implicit (cko)"_pair_charmm.html,
"lj/charmm/coul/long (cgiko)"_pair_charmm.html, "lj/charmm/coul/long (cgiko)"_pair_charmm.html,
@ -888,7 +888,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"tersoff/zbl (ko)"_pair_tersoff_zbl.html, "tersoff/zbl (ko)"_pair_tersoff_zbl.html,
"tip4p/cut (o)"_pair_coul.html, "tip4p/cut (o)"_pair_coul.html,
"tip4p/long (o)"_pair_coul.html, "tip4p/long (o)"_pair_coul.html,
"tri/lj (o)"_pair_tri_lj.html, "tri/lj"_pair_tri_lj.html,
"vashishta (o)"_pair_vashishta.html, "vashishta (o)"_pair_vashishta.html,
"yukawa (go)"_pair_yukawa.html, "yukawa (go)"_pair_yukawa.html,
"yukawa/colloid (go)"_pair_yukawa_colloid.html, "yukawa/colloid (go)"_pair_yukawa_colloid.html,

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@ -296,7 +296,7 @@ simulation domain, not a displacement from the center-of-mass (COM) of
the body particle itself. These values are calculated using the the body particle itself. These values are calculated using the
current COM and orientation of the body particle.</p> current COM and orientation of the body particle.</p>
<p>For images created by the <a class="reference internal" href="dump_image.html"><em>dump image</em></a> command, if the <p>For images created by the <a class="reference internal" href="dump_image.html"><em>dump image</em></a> command, if the
<em>body</em> keyword is set to <em>yes</em>, then each body particle is drawn as a <em>body</em> keyword is set, then each body particle is drawn as a
collection of spheres, one for each sub-particle. The size of each collection of spheres, one for each sub-particle. The size of each
sphere is determined by the <em>bflag1</em> parameter for the <em>body</em> keyword. sphere is determined by the <em>bflag1</em> parameter for the <em>body</em> keyword.
The <em>bflag2</em> argument is ignored.</p> The <em>bflag2</em> argument is ignored.</p>
@ -305,7 +305,7 @@ The <em>bflag2</em> argument is ignored.</p>
<p>The <em>rounded/polygon</em> body style represents body particles as a convex <p>The <em>rounded/polygon</em> body style represents body particles as a convex
polygon with a variable number N &gt; 2 of vertices, which can only be polygon with a variable number N &gt; 2 of vertices, which can only be
used for 2d models. One example use of this body style is for 2d used for 2d models. One example use of this body style is for 2d
discrete element models, as described in <a class="reference internal" href="pair_body_rounded_polygon.html#fraige"><span>Fraige</span></a>. Similar to discrete element models, as described in <a class="reference internal" href="#fraige"><span>Fraige</span></a>. Similar to
body style <em>nparticle</em>, the atom_style body command for this body body style <em>nparticle</em>, the atom_style body command for this body
style takes two additional arguments:</p> style takes two additional arguments:</p>
<div class="highlight-python"><div class="highlight"><pre>atom_style body rounded/polygon Nmin Nmax <div class="highlight-python"><div class="highlight"><pre>atom_style body rounded/polygon Nmin Nmax
@ -374,10 +374,10 @@ simulation domain, not a displacement from the center-of-mass (COM) of
the body particle itself. These values are calculated using the the body particle itself. These values are calculated using the
current COM and orientation of the body particle.</p> current COM and orientation of the body particle.</p>
<p>For images created by the <a class="reference internal" href="dump_image.html"><em>dump image</em></a> command, if the <p>For images created by the <a class="reference internal" href="dump_image.html"><em>dump image</em></a> command, if the
<em>body</em> keyword is set to <em>yes</em>, then each body particle is drawn as a <em>body</em> keyword is set, then each body particle is drawn as a convex
convex polygon consisting of N line segments. Note that the line polygon consisting of N line segments. Note that the line segments
segments are drawn between the N vertices, which does not correspond are drawn between the N vertices, which does not correspond exactly to
exactly to the physical extent of the body (because the <a class="reference external" href="pair_body_rounded_polygon.cpp">pair_style rounded/polygon</a> defines finite-size the physical extent of the body (because the <a class="reference external" href="pair_body_rounded_polygon.cpp">pair_style rounded/polygon</a> defines finite-size
spheres at those point and the line segments between the spheres are spheres at those point and the line segments between the spheres are
tangent to the spheres). The drawn diameter of each line segment is tangent to the spheres). The drawn diameter of each line segment is
determined by the <em>bflag1</em> parameter for the <em>body</em> keyword. The determined by the <em>bflag1</em> parameter for the <em>body</em> keyword. The

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@ -166,7 +166,7 @@ the body particle itself. These values are calculated using the
current COM and orientation of the body particle. current COM and orientation of the body particle.
For images created by the "dump image"_dump_image.html command, if the For images created by the "dump image"_dump_image.html command, if the
{body} keyword is set to {yes}, then each body particle is drawn as a {body} keyword is set, then each body particle is drawn as a
collection of spheres, one for each sub-particle. The size of each collection of spheres, one for each sub-particle. The size of each
sphere is determined by the {bflag1} parameter for the {body} keyword. sphere is determined by the {bflag1} parameter for the {body} keyword.
The {bflag2} argument is ignored. The {bflag2} argument is ignored.
@ -253,10 +253,10 @@ the body particle itself. These values are calculated using the
current COM and orientation of the body particle. current COM and orientation of the body particle.
For images created by the "dump image"_dump_image.html command, if the For images created by the "dump image"_dump_image.html command, if the
{body} keyword is set to {yes}, then each body particle is drawn as a {body} keyword is set, then each body particle is drawn as a convex
convex polygon consisting of N line segments. Note that the line polygon consisting of N line segments. Note that the line segments
segments are drawn between the N vertices, which does not correspond are drawn between the N vertices, which does not correspond exactly to
exactly to the physical extent of the body (because the "pair_style the physical extent of the body (because the "pair_style
rounded/polygon"_pair_body_rounded_polygon.cpp defines finite-size rounded/polygon"_pair_body_rounded_polygon.cpp defines finite-size
spheres at those point and the line segments between the spheres are spheres at those point and the line segments between the spheres are
tangent to the spheres). The drawn diameter of each line segment is tangent to the spheres). The drawn diameter of each line segment is

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@ -170,7 +170,7 @@
<li>one or more keyword/value pairs may be appended</li> <li>one or more keyword/value pairs may be appended</li>
</ul> </ul>
<pre class="literal-block"> <pre class="literal-block">
keyword = <em>temp</em> or <em>iso</em> or <em>aniso</em> or <em>tri</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>yz</em> or <em>xz</em> or <em>couple</em> or <em>tchain</em> or <em>pchain</em> or <em>mtk</em> or <em>tloop</em> or <em>ploop</em> or <em>nreset</em> or <em>drag</em> or <em>dilate</em> or <em>scalexy</em> or <em>scaleyz</em> or <em>scalexz</em> or <em>flip</em> or <em>fixedpoint</em> keyword = <em>temp</em> or <em>iso</em> or <em>aniso</em> or <em>tri</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>yz</em> or <em>xz</em> or <em>couple</em> or <em>tchain</em> or <em>pchain</em> or <em>mtk</em> or <em>tloop</em> or <em>ploop</em> or <em>nreset</em> or <em>drag</em> or <em>dilate</em> or <em>scalexy</em> or <em>scaleyz</em> or <em>scalexz</em> or <em>flip</em> or <em>fixedpoint</em> or <em>update</em>
<em>temp</em> values = Tstart Tstop Tdamp <em>temp</em> values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units) Tdamp = temperature damping parameter (time units)
@ -201,6 +201,7 @@ keyword = <em>temp</em> or <em>iso</em> or <em>aniso</em> or <em>tri</em> or <em
<em>flip</em> value = <em>yes</em> or <em>no</em> = allow or disallow box flips when it becomes highly skewed <em>flip</em> value = <em>yes</em> or <em>no</em> = allow or disallow box flips when it becomes highly skewed
<em>fixedpoint</em> values = x y z <em>fixedpoint</em> values = x y z
x,y,z = perform barostat dilation/contraction around this point (distance units) x,y,z = perform barostat dilation/contraction around this point (distance units)
<em>update</em> value = <em>dipole</em> update dipole orientation (only for sphere variants)
</pre> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
@ -235,12 +236,12 @@ 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="pair_sdk.html#shinoda"><span>(Shinoda)</span></a>, which combine the hydrostatic equations of <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="fix_rigid.html#martyna"><span>(Martyna)</span></a> with the strain 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 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 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" /> <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 +398,7 @@ 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="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 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 +407,7 @@ 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="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> 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,
@ -447,6 +448,11 @@ to <em>fixedpoint</em>, then the lower periodic boundaries will remain at
far. In all cases, the particle trajectories are unaffected by the far. In all cases, the particle trajectories are unaffected by the
chosen value, except for a time-dependent constant translation of chosen value, except for a time-dependent constant translation of
positions.</p> positions.</p>
<p>If the <em>update</em> keyword is used with the <em>dipole</em> value, then the
orientation of the dipole moment of each particle is also updated
during the time integration. This option should be used for models
where a dipole moment is assigned to finite-size particles,
e.g. spheroids via use of the <a class="reference internal" href="atom_style.html"><em>atom_style hybrid sphere dipole</em></a> command.</p>
<hr class="docutils" /> <hr class="docutils" />
<div class="admonition note"> <div class="admonition note">
<p class="first admonition-title">Note</p> <p class="first admonition-title">Note</p>
@ -560,6 +566,18 @@ to undergo a slow random walk. This can be mitigated by resetting
the momentum at infrequent intervals using the the momentum at infrequent intervals using the
<a class="reference internal" href="fix_momentum.html"><em>fix momentum</em></a> command.</p> <a class="reference internal" href="fix_momentum.html"><em>fix momentum</em></a> command.</p>
</div> </div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This implementation has been shown to conserve linear momentum
up to machine precision under NVT dynamics. Under NPT dynamics,
for a system with zero initial total linear momentum, the total
momentum fluctuates close to zero. It may occasionally undergo brief
excursions to non-negligible values, before returning close to zero.
Over long simulations, this has the effect of causing the center-of-mass
to undergo a slow random walk. This can be mitigated by resetting
the momentum at infrequent intervals using the
<a class="reference internal" href="fix_momentum.html"><em>fix momentum</em></a> command.</p>
</div>
<hr class="docutils" /> <hr class="docutils" />
<p>The fix npt and fix nph commands can be used with rigid bodies or <p>The fix npt and fix nph commands can be used with rigid bodies or
mixtures of rigid bodies and non-rigid particles (e.g. solvent). But mixtures of rigid bodies and non-rigid particles (e.g. solvent). But

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@ -331,8 +331,9 @@ positions.
If the {update} keyword is used with the {dipole} value, then the If the {update} keyword is used with the {dipole} value, then the
orientation of the dipole moment of each particle is also updated orientation of the dipole moment of each particle is also updated
during the time integration. This option should be used for models during the time integration. This option should be used for models
where a dipole moment is assigned to extended particles via use of where a dipole moment is assigned to finite-size particles,
the "atom_style hybrid sphere dipole"_atom_style.html command. e.g. spheroids via use of the "atom_style hybrid sphere
dipole"_atom_style.html command.
:line :line
@ -457,6 +458,16 @@ to undergo a slow random walk. This can be mitigated by resetting
the momentum at infrequent intervals using the the momentum at infrequent intervals using the
"fix momentum"_fix_momentum.html command. "fix momentum"_fix_momentum.html command.
NOTE: This implementation has been shown to conserve linear momentum
up to machine precision under NVT dynamics. Under NPT dynamics,
for a system with zero initial total linear momentum, the total
momentum fluctuates close to zero. It may occasionally undergo brief
excursions to non-negligible values, before returning close to zero.
Over long simulations, this has the effect of causing the center-of-mass
to undergo a slow random walk. This can be mitigated by resetting
the momentum at infrequent intervals using the
"fix momentum"_fix_momentum.html command.
:line :line
The fix npt and fix nph commands can be used with rigid bodies or The fix npt and fix nph commands can be used with rigid bodies or

4
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@ -163,8 +163,8 @@ assumes point particles and only updates their position and velocity.</p>
<p>If the <em>update</em> keyword is used with the <em>dipole</em> value, then the <p>If the <em>update</em> keyword is used with the <em>dipole</em> value, then the
orientation of the dipole moment of each particle is also updated orientation of the dipole moment of each particle is also updated
during the time integration. This option should be used for models during the time integration. This option should be used for models
where a dipole moment is assigned to particles via use of the where a dipole moment is assigned to finite-size particles,
<a class="reference internal" href="atom_style.html"><em>atom_style dipole</em></a> command.</p> e.g. spheroids via use of the <a class="reference internal" href="atom_style.html"><em>atom_style hybrid sphere dipole</em></a> command.</p>
<hr class="docutils" /> <hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are <p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix. functionally the same as the corresponding style without the suffix.

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@ -39,8 +39,9 @@ assumes point particles and only updates their position and velocity.
If the {update} keyword is used with the {dipole} value, then the If the {update} keyword is used with the {dipole} value, then the
orientation of the dipole moment of each particle is also updated orientation of the dipole moment of each particle is also updated
during the time integration. This option should be used for models during the time integration. This option should be used for models
where a dipole moment is assigned to particles via use of the where a dipole moment is assigned to finite-size particles,
"atom_style dipole"_atom_style.html command. e.g. spheroids via use of the "atom_style hybrid sphere
dipole"_atom_style.html command.
:line :line

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@ -126,9 +126,6 @@
<div class="section" id="pair-style-line-lj-command"> <div class="section" id="pair-style-line-lj-command">
<span id="index-0"></span><h1>pair_style line/lj command<a class="headerlink" href="#pair-style-line-lj-command" title="Permalink to this headline"></a></h1> <span id="index-0"></span><h1>pair_style line/lj command<a class="headerlink" href="#pair-style-line-lj-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-line-lj-omp-command">
<h1>pair_style line/lj/omp command<a class="headerlink" href="#pair-style-line-lj-omp-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2> <h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style line/lj cutoff <div class="highlight-python"><div class="highlight"><pre>pair_style line/lj cutoff
@ -227,22 +224,6 @@ and a point particle is calculated.</p>
<p>The <em>cutoff</em> coefficient is optional. If not specified, the global <p>The <em>cutoff</em> coefficient is optional. If not specified, the global
cutoff is used.</p> cutoff is used.</p>
<hr class="docutils" /> <hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p> <p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, coeffiecients must be specified. <p>For atom type pairs I,J and I != J, coeffiecients must be specified.
No default mixing rules are used.</p> No default mixing rules are used.</p>

24
doc/pair_line_lj.txt
View File

@ -7,7 +7,6 @@
:line :line
pair_style line/lj command :h3 pair_style line/lj command :h3
pair_style line/lj/omp command :h3
[Syntax:] [Syntax:]
@ -111,29 +110,6 @@ cutoff is used.
:line :line
Styles with a {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section_accelerate"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]: [Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, coeffiecients must be specified. For atom type pairs I,J and I != J, coeffiecients must be specified.

19
doc/pair_tri_lj.html
View File

@ -126,9 +126,6 @@
<div class="section" id="pair-style-tri-lj-command"> <div class="section" id="pair-style-tri-lj-command">
<span id="index-0"></span><h1>pair_style tri/lj command<a class="headerlink" href="#pair-style-tri-lj-command" title="Permalink to this headline"></a></h1> <span id="index-0"></span><h1>pair_style tri/lj command<a class="headerlink" href="#pair-style-tri-lj-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-tri-lj-omp-command">
<h1>pair_style tri/lj/omp command<a class="headerlink" href="#pair-style-tri-lj-omp-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2> <h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style tri/lj cutoff <div class="highlight-python"><div class="highlight"><pre>pair_style tri/lj cutoff
@ -197,22 +194,6 @@ commands:</p>
<p>The last coefficient is optional. If not specified, the global cutoff <p>The last coefficient is optional. If not specified, the global cutoff
is used.</p> is used.</p>
<hr class="docutils" /> <hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p> <p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, the epsilon and sigma coefficients <p>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of this pair style can be mixed. The and cutoff distance for all of this pair style can be mixed. The

24
doc/pair_tri_lj.txt
View File

@ -7,7 +7,6 @@
:line :line
pair_style tri/lj command :h3 pair_style tri/lj command :h3
pair_style tri/lj/omp command :h3
[Syntax:] [Syntax:]
@ -80,29 +79,6 @@ is used.
:line :line
Styles with a {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section_accelerate"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]: [Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients For atom type pairs I,J and I != J, the epsilon and sigma coefficients

2
doc/searchindex.js
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File diff suppressed because one or more lines are too long

2
examples/ASPHERE/line/in.line
View File

@ -13,7 +13,7 @@ neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule all neigh_modify exclude molecule all
pair_style line/lj 2.5 pair_style line/lj 2.5
pair_coeff * * 1.0 0.25 pair_coeff * * 1.0 1.0 1.0 0.25 2.5
fix 2 all rigid molecule langevin 2.0 2.0 1.0 492983 fix 2 all rigid molecule langevin 2.0 2.0 1.0 492983

6
examples/ASPHERE/line/in.line.srd
View File

@ -44,9 +44,9 @@ neigh_modify include big
# no pairwise interactions with small particles # no pairwise interactions with small particles
pair_style line/lj 2.5 pair_style line/lj 2.5
pair_coeff 1 1 1.0 1.0 pair_coeff 1 1 1.0 1.0 1.0 1.0 2.5
pair_coeff 2 2 0.0 1.0 0.0 pair_coeff 2 2 0.0 0.0 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0 pair_coeff 1 2 1.0 0.0 0.0 1.0 0.0
# use fix SRD to push small particles out from inside big ones # use fix SRD to push small particles out from inside big ones
# if comment out, big particles won't see SRD particles # if comment out, big particles won't see SRD particles

5
src/Purge.list
View File

@ -13,6 +13,11 @@ style_kspace.h
style_minimize.h style_minimize.h
style_pair.h style_pair.h
style_region.h style_region.h
# deleted on 15 Jan 2016
pair_line_lj.cpp
pair_line_lj.h
pair_tri_lj.cpp
pair_tri_lj.h
# deleted on 13 May 14 # deleted on 13 May 14
commgrid.cpp commgrid.cpp
commgrid.h commgrid.h

15
src/create_atoms.cpp
View File

@ -416,14 +416,19 @@ void CreateAtoms::command(int narg, char **arg)
} }
// for MOLECULE mode: // for MOLECULE mode:
// set molecule IDs for created atoms if used // molecule can mean just a mol ID or bonds/angles/etc or mol templates
// reset new molecule bond,angle,etc and special values // set molecule IDs for created atoms if atom->molecule_flag is set
// reset new molecule bond,angle,etc and special values if defined
// send atoms to new owning procs via irregular comm // send atoms to new owning procs via irregular comm
// since not all atoms I created will be within my sub-domain // since not all atoms I created will be within my sub-domain
// perform special list build if needed // perform special list build if needed
if (mode == MOLECULE) { if (mode == MOLECULE) {
int molecule_flag = atom->molecule_flag;
int molecular = atom->molecular;
tagint *molecule = atom->molecule;
// molcreate = # of molecules I created // molcreate = # of molecules I created
int molcreate = (atom->nlocal - nlocal_previous) / onemol->natoms; int molcreate = (atom->nlocal - nlocal_previous) / onemol->natoms;
@ -444,8 +449,7 @@ void CreateAtoms::command(int narg, char **arg)
// including molecules existing before this creation // including molecules existing before this creation
tagint moloffset; tagint moloffset;
tagint *molecule = atom->molecule; if (molecule_flag) {
if (atom->molecule_flag) {
tagint max = 0; tagint max = 0;
for (int i = 0; i < nlocal_previous; i++) max = MAX(max,molecule[i]); for (int i = 0; i < nlocal_previous; i++) max = MAX(max,molecule[i]);
tagint maxmol; tagint maxmol;
@ -480,13 +484,12 @@ void CreateAtoms::command(int narg, char **arg)
tagint **improper_atom4 = atom->improper_atom4; tagint **improper_atom4 = atom->improper_atom4;
int **nspecial = atom->nspecial; int **nspecial = atom->nspecial;
tagint **special = atom->special; tagint **special = atom->special;
int molecular = atom->molecular;
int ilocal = nlocal_previous; int ilocal = nlocal_previous;
for (int i = 0; i < molcreate; i++) { for (int i = 0; i < molcreate; i++) {
if (tag) offset = tag[ilocal]-1; if (tag) offset = tag[ilocal]-1;
for (int m = 0; m < natoms; m++) { for (int m = 0; m < natoms; m++) {
if (atom->molecule_flag) molecule[ilocal] = moloffset + i+1; if (molecule_flag) molecule[ilocal] = moloffset + i+1;
if (molecular == 2) { if (molecular == 2) {
atom->molindex[ilocal] = 0; atom->molindex[ilocal] = 0;
atom->molatom[ilocal] = m; atom->molatom[ilocal] = m;

2
src/version.h
View File

@ -1 +1 @@
#define LAMMPS_VERSION "14 Jan 2016" #define LAMMPS_VERSION "15 Jan 2016"