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#	doc/Manual.txt
#	doc/fix_nh.txt
#	src/create_atoms.cpp
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@ -135,7 +135,7 @@
<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>
<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 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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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<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="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-ICMS Documentation :c,h3
14 Jan 2016 version :c,h4
15 Jan 2016 version :c,h4
Version info: :h4

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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_lcbop.html"><em>lcbop</em></a></td>
</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/implicit (cko)</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>
</tr>
<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_yukawa.html"><em>yukawa (go)</em></a></td>
</tr>

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@ -832,7 +832,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
"kim"_pair_kim.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/implicit (cko)"_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,
"tip4p/cut (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,
"yukawa (go)"_pair_yukawa.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
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
<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
sphere is determined by the <em>bflag1</em> parameter for the <em>body</em> keyword.
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
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
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
style takes two additional arguments:</p>
<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
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
<em>body</em> keyword is set to <em>yes</em>, then each body particle is drawn as a
convex polygon consisting of N line segments. Note that the line
segments are drawn between the N vertices, which does not correspond
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
<em>body</em> keyword is set, then each body particle is drawn as a convex
polygon consisting of N line segments. Note that the line segments
are drawn between the N vertices, which does not correspond 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
spheres at those point and the line segments between the spheres are
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

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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.
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
sphere is determined by the {bflag1} parameter for the {body} keyword.
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.
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
convex polygon consisting of N line segments. Note that the line
segments are drawn between the N vertices, which does not correspond
exactly to the physical extent of the body (because the "pair_style
{body} keyword is set, then each body particle is drawn as a convex
polygon consisting of N line segments. Note that the line segments
are drawn between the N vertices, which does not correspond exactly to
the physical extent of the body (because the "pair_style
rounded/polygon"_pair_body_rounded_polygon.cpp defines finite-size
spheres at those point and the line segments between the spheres are
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>
</ul>
<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
Tstart,Tstop = external temperature at start/end of run
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>fixedpoint</em> values = x y z
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>
</div>
<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
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
@ -397,7 +398,7 @@ 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
@ -406,7 +407,7 @@ 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,
@ -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
chosen value, except for a time-dependent constant translation of
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" />
<div class="admonition note">
<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
<a class="reference internal" href="fix_momentum.html"><em>fix momentum</em></a> command.</p>
</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" />
<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

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@ -331,8 +331,9 @@ positions.
If the {update} keyword is used with the {dipole} 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 extended particles via use of
the "atom_style hybrid sphere dipole"_atom_style.html command.
where a dipole moment is assigned to finite-size particles,
e.g. spheroids via use of the "atom_style hybrid sphere
dipole"_atom_style.html command.
:line
@ -457,6 +458,16 @@ 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.
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
The fix npt and fix nph commands can be used with rigid bodies or

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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
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 particles via use of the
<a class="reference internal" href="atom_style.html"><em>atom_style dipole</em></a> command.</p>
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" />
<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.

5
doc/fix_nve_sphere.txt
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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
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 particles via use of the
"atom_style dipole"_atom_style.html command.
where a dipole moment is assigned to finite-size particles,
e.g. spheroids via use of the "atom_style hybrid sphere
dipole"_atom_style.html command.
:line

19
doc/pair_line_lj.html
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@ -126,9 +126,6 @@
<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>
</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">
<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
@ -227,22 +224,6 @@ and a point particle is calculated.</p>
<p>The <em>cutoff</em> coefficient is optional. If not specified, the global
cutoff is used.</p>
<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>For atom type pairs I,J and I != J, coeffiecients must be specified.
No default mixing rules are used.</p>

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@ -7,7 +7,6 @@
:line
pair_style line/lj command :h3
pair_style line/lj/omp command :h3
[Syntax:]
@ -111,29 +110,6 @@ cutoff is used.
: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]:
For atom type pairs I,J and I != J, coeffiecients must be specified.

19
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@ -126,9 +126,6 @@
<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>
</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">
<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
@ -197,22 +194,6 @@ commands:</p>
<p>The last coefficient is optional. If not specified, the global cutoff
is used.</p>
<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>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

24
doc/pair_tri_lj.txt
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@ -7,7 +7,6 @@
:line
pair_style tri/lj command :h3
pair_style tri/lj/omp command :h3
[Syntax:]
@ -80,29 +79,6 @@ is used.
: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]:
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
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@ -13,7 +13,7 @@ neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule all
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

6
examples/ASPHERE/line/in.line.srd
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@ -44,9 +44,9 @@ neigh_modify include big
# no pairwise interactions with small particles
pair_style line/lj 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.0 1.0 0.0
pair_coeff 1 2 0.0 1.0 0.0
pair_coeff 1 1 1.0 1.0 1.0 1.0 2.5
pair_coeff 2 2 0.0 0.0 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
# if comment out, big particles won't see SRD particles

5
src/Purge.list
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@ -13,6 +13,11 @@ style_kspace.h
style_minimize.h
style_pair.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
commgrid.cpp
commgrid.h

15
src/create_atoms.cpp
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@ -416,14 +416,19 @@ void CreateAtoms::command(int narg, char **arg)
}
// for MOLECULE mode:
// set molecule IDs for created atoms if used
// reset new molecule bond,angle,etc and special values
// molecule can mean just a mol ID or bonds/angles/etc or mol templates
// 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
// since not all atoms I created will be within my sub-domain
// perform special list build if needed
if (mode == MOLECULE) {
int molecule_flag = atom->molecule_flag;
int molecular = atom->molecular;
tagint *molecule = atom->molecule;
// molcreate = # of molecules I created
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
tagint moloffset;
tagint *molecule = atom->molecule;
if (atom->molecule_flag) {
if (molecule_flag) {
tagint max = 0;
for (int i = 0; i < nlocal_previous; i++) max = MAX(max,molecule[i]);
tagint maxmol;
@ -480,13 +484,12 @@ void CreateAtoms::command(int narg, char **arg)
tagint **improper_atom4 = atom->improper_atom4;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int molecular = atom->molecular;
int ilocal = nlocal_previous;
for (int i = 0; i < molcreate; i++) {
if (tag) offset = tag[ilocal]-1;
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) {
atom->molindex[ilocal] = 0;
atom->molatom[ilocal] = m;

2
src/version.h
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@ -1 +1 @@
#define LAMMPS_VERSION "14 Jan 2016"
#define LAMMPS_VERSION "15 Jan 2016"