From 206f4e18a64e1874fe884ad9ec496d2862b2c2eb Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Tue, 13 Sep 2016 23:06:23 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15573
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/html/Manual.html | 2 +-
doc/html/Section_commands.html | 12 +-
doc/html/Section_example.html | 20 +--
doc/html/Section_tools.html | 2 +-
doc/html/atom_modify.html | 16 +-
doc/html/atom_style.html | 24 +--
doc/html/body.html | 20 +--
doc/html/change_box.html | 56 +++----
doc/html/compute_dipole_chunk.html | 10 +-
doc/html/compute_inertia_chunk.html | 10 +-
doc/html/compute_ke_atom_eff.html | 10 +-
doc/html/compute_ke_eff.html | 10 +-
doc/html/compute_modify.html | 14 +-
doc/html/compute_pe_atom.html | 10 +-
doc/html/compute_property_atom.html | 38 ++---
doc/html/compute_property_chunk.html | 12 +-
doc/html/compute_reduce.html | 62 ++++----
doc/html/compute_rigid_local.html | 8 +-
doc/html/compute_temp_cs.html | 8 +-
doc/html/compute_temp_eff.html | 10 +-
doc/html/compute_ti.html | 10 +-
doc/html/compute_voronoi_atom.html | 34 ++--
doc/html/delete_bonds.html | 20 +--
doc/html/dihedral_table.html | 46 +++---
doc/html/dump.html | 62 ++++----
doc/html/dump_custom_vtk.html | 12 +-
doc/html/dump_modify.html | 70 ++++-----
doc/html/fix_atom_swap.html | 14 +-
doc/html/fix_ave_atom.html | 52 ++++---
doc/html/fix_ave_chunk.html | 54 +++----
doc/html/fix_ave_correlate_long.html | 30 ++--
doc/html/fix_ave_histo.html | 54 +++----
doc/html/fix_ave_time.html | 52 ++++---
doc/html/fix_bond_break.html | 4 +-
doc/html/fix_bond_create.html | 6 +-
doc/html/fix_colvars.html | 4 +-
doc/html/fix_deform.html | 68 ++++----
doc/html/fix_deposit.html | 4 +-
doc/html/fix_drag.html | 4 +-
doc/html/fix_drude_transform.html | 36 +++--
doc/html/fix_efield.html | 12 +-
doc/html/fix_external.html | 22 +--
doc/html/fix_gcmc.html | 32 ++--
doc/html/fix_gle.html | 6 +-
doc/html/fix_gravity.html | 18 ++-
doc/html/fix_heat.html | 14 +-
doc/html/fix_imd.html | 4 +-
doc/html/fix_ipi.html | 4 +-
doc/html/fix_langevin.html | 4 +-
doc/html/fix_langevin_eff.html | 4 +-
doc/html/fix_lb_momentum.html | 4 +-
doc/html/fix_lb_pc.html | 4 +-
doc/html/fix_lb_rigid_pc_sphere.html | 4 +-
doc/html/fix_lb_viscous.html | 4 +-
doc/html/fix_lineforce.html | 4 +-
doc/html/fix_move.html | 38 ++---
doc/html/fix_msst.html | 30 ++--
doc/html/fix_neb.html | 4 +-
doc/html/fix_nh_eff.html | 10 +-
doc/html/fix_nph_asphere.html | 12 +-
doc/html/fix_nph_sphere.html | 12 +-
doc/html/fix_npt_asphere.html | 12 +-
doc/html/fix_npt_body.html | 12 +-
doc/html/fix_npt_sphere.html | 12 +-
doc/html/fix_nve_asphere.html | 4 +-
doc/html/fix_nve_asphere_noforce.html | 4 +-
doc/html/fix_nve_body.html | 4 +-
doc/html/fix_nve_line.html | 4 +-
doc/html/fix_nve_manifold_rattle.html | 14 +-
doc/html/fix_nve_sphere.html | 4 +-
doc/html/fix_nve_tri.html | 4 +-
doc/html/fix_nvt_asphere.html | 10 +-
doc/html/fix_nvt_body.html | 10 +-
doc/html/fix_nvt_sllod.html | 10 +-
doc/html/fix_nvt_sllod_eff.html | 4 +-
doc/html/fix_nvt_sphere.html | 10 +-
doc/html/fix_phonon.html | 10 +-
doc/html/fix_pour.html | 4 +-
doc/html/fix_qeq.html | 18 ++-
doc/html/fix_qeq_comb.html | 4 +-
doc/html/fix_qeq_reax.html | 4 +-
doc/html/fix_qmmm.html | 4 +-
doc/html/fix_qtb.html | 14 +-
doc/html/fix_reax_bonds.html | 4 +-
doc/html/fix_reaxc_species.html | 4 +-
doc/html/fix_saed_vtk.html | 60 +++----
doc/html/fix_smd.html | 4 +-
doc/html/fix_smd_adjust_dt.html | 16 +-
doc/html/fix_smd_integrate_tlsph.html | 18 ++-
doc/html/fix_smd_integrate_ulsph.html | 24 +--
.../fix_smd_move_triangulated_surface.html | 50 +++---
doc/html/fix_smd_setvel.html | 10 +-
doc/html/fix_smd_wall_surface.html | 16 +-
doc/html/fix_spring.html | 4 +-
doc/html/fix_spring_chunk.html | 4 +-
doc/html/fix_spring_self.html | 4 +-
doc/html/fix_store_state.html | 78 +++++-----
doc/html/fix_temp_rescale_eff.html | 4 +-
doc/html/fix_tfmc.html | 4 +-
doc/html/fix_thermal_conductivity.html | 16 +-
doc/html/fix_viscosity.html | 4 +-
doc/html/fix_viscous.html | 4 +-
doc/html/fix_wall_gran.html | 16 +-
doc/html/fix_wall_piston.html | 4 +-
doc/html/fix_wall_reflect.html | 58 +++----
doc/html/group.html | 36 ++---
doc/html/if.html | 16 +-
doc/html/jump.html | 24 +--
doc/html/kspace_modify.html | 14 +-
doc/html/kspace_style.html | 24 +--
doc/html/lattice.html | 54 +++----
doc/html/min_modify.html | 12 +-
doc/html/min_style.html | 20 +--
doc/html/next.html | 12 +-
doc/html/package.html | 10 +-
doc/html/pair_brownian.html | 16 +-
doc/html/pair_dsmc.html | 28 ++--
doc/html/pair_hybrid.html | 146 +++++++++---------
doc/html/pair_line_lj.html | 18 +--
doc/html/pair_peri.html | 38 ++---
doc/html/pair_quip.html | 16 +-
doc/html/pair_reax.html | 40 ++---
doc/html/pair_reax_c.html | 48 +++---
doc/html/pair_smd_hertz.html | 8 +-
doc/html/pair_smd_triangulated_surface.html | 8 +-
doc/html/pair_style.html | 26 ++--
doc/html/pair_thole.html | 24 +--
doc/html/pair_tri_lj.html | 16 +-
doc/html/prd.html | 32 ++--
doc/html/processors.html | 20 +--
doc/html/python.html | 106 ++++++-------
doc/html/read_dump.html | 30 ++--
doc/html/restart.html | 24 +--
doc/html/run_style.html | 60 +++----
doc/html/set.html | 24 +--
doc/html/special_bonds.html | 38 ++---
doc/html/tad.html | 52 +++----
doc/html/thermo.html | 8 +-
doc/html/thermo_style.html | 58 +++----
doc/html/units.html | 2 +-
doc/html/variable.html | 120 +++++++-------
doc/html/velocity.html | 22 +--
doc/html/write_coeff.html | 12 +-
doc/src/Manual.txt | 4 +-
144 files changed, 1619 insertions(+), 1465 deletions(-)
diff --git a/doc/html/Manual.html b/doc/html/Manual.html
index 2281f57fbd..3e5e1a74a9 100644
--- a/doc/html/Manual.html
+++ b/doc/html/Manual.html
@@ -135,7 +135,7 @@
<H1></H1><div class="section" id="lammps-documentation">
<h1>LAMMPS Documentation</h1>
<div class="section" id="sep-2016-version">
-<h2>7 Sep 2016 version</h2>
+<h2>13 Sep 2016 version</h2>
</div>
<div class="section" id="version-info">
<h2>Version info:</h2>
diff --git a/doc/html/Section_commands.html b/doc/html/Section_commands.html
index 69c6609b6c..88bc54ce5a 100644
--- a/doc/html/Section_commands.html
+++ b/doc/html/Section_commands.html
@@ -247,15 +247,15 @@ inside the parenthesis is treated as an “immediate” variable and
evaluated as an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a>. This is a way
to use numeric formulas in an input script without having to assign
them to variable names. For example, these 3 input script lines:</p>
-<pre class="literal-block">
-variable X equal (xlo+xhi)/2+sqrt(v_area)
+<div class="highlight-default"><div class="highlight"><pre><span></span>variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete
-</pre>
+</pre></div>
+</div>
<p>can be replaced by</p>
-<pre class="literal-block">
-region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span>region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
+</pre></div>
+</div>
<p>so that you do not have to define (or discard) a temporary variable X.</p>
<p>Note that neither the curly-bracket or immediate form of variables can
contain nested $ characters for other variables to substitute for.
diff --git a/doc/html/Section_example.html b/doc/html/Section_example.html
index 9c2e1a0c72..95a590b02f 100644
--- a/doc/html/Section_example.html
+++ b/doc/html/Section_example.html
@@ -303,11 +303,11 @@ longer times, e.g. to measure a particular quantity.</p>
</tbody>
</table>
<p>Here is how you can run and visualize one of the sample problems:</p>
-<pre class="literal-block">
-cd indent
-cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
-lmp_linux -in in.indent # run the problem
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">indent</span>
+<span class="n">cp</span> <span class="o">../../</span><span class="n">src</span><span class="o">/</span><span class="n">lmp_linux</span> <span class="o">.</span> <span class="c1"># copy LAMMPS executable to this dir</span>
+<span class="n">lmp_linux</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">indent</span> <span class="c1"># run the problem</span>
+</pre></div>
+</div>
<p>Running the simulation produces the files <em>dump.indent</em> and
<em>log.lammps</em>. You can visualize the dump file of snapshots with a
variety of 3rd-party tools highlighted on the
@@ -321,17 +321,17 @@ ImageMagick or QuickTime or various Windows-based tools. See the
<a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> doc page for more details. E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
browser.</p>
-<pre class="literal-block">
-% convert -loop 1 *.jpg foo.gif
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">convert</span> <span class="o">-</span><span class="n">loop</span> <span class="mi">1</span> <span class="o">*.</span><span class="n">jpg</span> <span class="n">foo</span><span class="o">.</span><span class="n">gif</span>
+</pre></div>
+</div>
</div>
<hr class="docutils" />
<div class="section" id="uppercase-directories">
<h2>7.2. Uppercase directories</h2>
<table border="1" class="docutils">
<colgroup>
-<col width="11%" />
-<col width="89%" />
+<col width="10%" />
+<col width="90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>ASPHERE</td>
diff --git a/doc/html/Section_tools.html b/doc/html/Section_tools.html
index 1daccc93c4..0e3948b6a0 100644
--- a/doc/html/Section_tools.html
+++ b/doc/html/Section_tools.html
@@ -204,7 +204,7 @@ own sub-directories with their own Makefiles.</p>
<li><a class="reference internal" href="#eff"><span class="std std-ref">eff</span></a></li>
<li><a class="reference internal" href="#emacs"><span class="std std-ref">emacs</span></a></li>
<li><a class="reference internal" href="#fep"><span class="std std-ref">fep</span></a></li>
-<li><a class="reference internal" href="#ipi"><span class="std std-ref">i-pi</span></a></li>
+<li><a class="reference internal" href="fix_ipi.html#ipi"><span class="std std-ref">i-pi</span></a></li>
<li><a class="reference internal" href="#ipp"><span class="std std-ref">ipp</span></a></li>
<li><a class="reference internal" href="#kate"><span class="std std-ref">kate</span></a></li>
<li><a class="reference internal" href="#arc"><span class="std std-ref">lmp2arc</span></a></li>
diff --git a/doc/html/atom_modify.html b/doc/html/atom_modify.html
index 0922591416..b2e3f8585d 100644
--- a/doc/html/atom_modify.html
+++ b/doc/html/atom_modify.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>atom_modify command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-atom_modify keyword values ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_modify</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul class="simple">
<li>one or more keyword/value pairs may be appended</li>
<li>keyword = <em>id</em> or <em>map</em> or <em>first</em> or <em>sort</em></li>
@@ -146,11 +146,11 @@ atom_modify keyword values ...
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-atom_modify map hash
-atom_modify map array sort 10000 2.0
-atom_modify first colloid
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_modify</span> <span class="nb">map</span> <span class="nb">hash</span>
+<span class="n">atom_modify</span> <span class="nb">map</span> <span class="n">array</span> <span class="n">sort</span> <span class="mi">10000</span> <span class="mf">2.0</span>
+<span class="n">atom_modify</span> <span class="n">first</span> <span class="n">colloid</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
diff --git a/doc/html/atom_style.html b/doc/html/atom_style.html
index a2cbd22a72..2ed9ccbab0 100644
--- a/doc/html/atom_style.html
+++ b/doc/html/atom_style.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>atom_style command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-atom_style style args
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">style</span> <span class="n">args</span>
+</pre></div>
+</div>
<ul class="simple">
<li>style = <em>angle</em> or <em>atomic</em> or <em>body</em> or <em>bond</em> or <em>charge</em> or <em>dipole</em> or <em>dpd</em> or <em>electron</em> or <em>ellipsoid</em> or <em>full</em> or <em>line</em> or <em>meso</em> or <em>molecular</em> or <em>peri</em> or <em>smd</em> or <em>sphere</em> or <em>tri</em> or <em>template</em> or <em>hybrid</em></li>
</ul>
@@ -150,15 +150,15 @@ args = none for any style except the following
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-atom_style atomic
-atom_style bond
-atom_style full
-atom_style body nparticle 2 10
-atom_style hybrid charge bond
-atom_style hybrid charge body nparticle 2 5
-atom_style template myMols
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">atomic</span>
+<span class="n">atom_style</span> <span class="n">bond</span>
+<span class="n">atom_style</span> <span class="n">full</span>
+<span class="n">atom_style</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="mi">2</span> <span class="mi">10</span>
+<span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">charge</span> <span class="n">bond</span>
+<span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">charge</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="mi">2</span> <span class="mi">5</span>
+<span class="n">atom_style</span> <span class="n">template</span> <span class="n">myMols</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
diff --git a/doc/html/body.html b/doc/html/body.html
index 5aaa8ec563..6a2be8aff8 100644
--- a/doc/html/body.html
+++ b/doc/html/body.html
@@ -247,11 +247,11 @@ mentioned above, the <a class="reference internal" href="fix_rigid.html"><span c
duplicates its functionality.</p>
<p>The atom_style body command for this body style takes two additional
arguments:</p>
-<pre class="literal-block">
-atom_style body nparticle Nmin Nmax
-Nmin = minimum # of sub-particles in any body in the system
-Nmax = maximum # of sub-particles in any body in the system
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="n">Nmin</span> <span class="n">Nmax</span>
+<span class="n">Nmin</span> <span class="o">=</span> <span class="n">minimum</span> <span class="c1"># of sub-particles in any body in the system</span>
+<span class="n">Nmax</span> <span class="o">=</span> <span class="n">maximum</span> <span class="c1"># of sub-particles in any body in the system</span>
+</pre></div>
+</div>
<p>The Nmin and Nmax arguments are used to bound the size of data
structures used internally by each particle.</p>
<p>When the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command reads a data file for this
@@ -313,11 +313,11 @@ 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="#fraige"><span class="std std-ref">Fraige</span></a>. Similar to
body style <em>nparticle</em>, the atom_style body command for this body
style takes two additional arguments:</p>
-<pre class="literal-block">
-atom_style body rounded/polygon Nmin Nmax
-Nmin = minimum # of vertices in any body in the system
-Nmax = maximum # of vertices in any body in the system
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">body</span> <span class="n">rounded</span><span class="o">/</span><span class="n">polygon</span> <span class="n">Nmin</span> <span class="n">Nmax</span>
+<span class="n">Nmin</span> <span class="o">=</span> <span class="n">minimum</span> <span class="c1"># of vertices in any body in the system</span>
+<span class="n">Nmax</span> <span class="o">=</span> <span class="n">maximum</span> <span class="c1"># of vertices in any body in the system</span>
+</pre></div>
+</div>
<p>The Nmin and Nmax arguments are used to bound the size of data
structures used internally by each particle.</p>
<p>When the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command reads a data file for this
diff --git a/doc/html/change_box.html b/doc/html/change_box.html
index 5fd817925f..fc034cbe2f 100644
--- a/doc/html/change_box.html
+++ b/doc/html/change_box.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>change_box command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-change_box group-ID parameter args ... keyword args ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">parameter</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul class="simple">
<li>group-ID = ID of group of atoms to (optionally) displace</li>
<li>one or more parameter/arg pairs may be appended</li>
@@ -175,10 +175,10 @@ parameter = <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>xz</em>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
-change_box all x scale 1.1 y volume z volume remap
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">xy</span> <span class="n">final</span> <span class="o">-</span><span class="mf">2.0</span> <span class="n">z</span> <span class="n">final</span> <span class="mf">0.0</span> <span class="mf">5.0</span> <span class="n">boundary</span> <span class="n">p</span> <span class="n">p</span> <span class="n">f</span> <span class="n">remap</span> <span class="n">units</span> <span class="n">box</span>
+<span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">y</span> <span class="n">volume</span> <span class="n">z</span> <span class="n">volume</span> <span class="n">remap</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -223,15 +223,15 @@ will be re-shrink-wrapped before the change_box command completes.
Instead you could do something like this, assuming the simulation box
is non-periodic and atoms extend from 0 to 20 in all dimensions:</p>
</div>
-<pre class="literal-block">
-change_box all x final -10 20
-create_atoms 1 single -5 5 5 # this will fail to insert an atom
-</pre>
-<pre class="literal-block">
-change_box all x final -10 20 boundary f s s
-create_atoms 1 single -5 5 5
-change_box boundary s s s # this will work
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">final</span> <span class="o">-</span><span class="mi">10</span> <span class="mi">20</span>
+<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">single</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span> <span class="c1"># this will fail to insert an atom</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">final</span> <span class="o">-</span><span class="mi">10</span> <span class="mi">20</span> <span class="n">boundary</span> <span class="n">f</span> <span class="n">s</span> <span class="n">s</span>
+<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">single</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span>
+<span class="n">change_box</span> <span class="n">boundary</span> <span class="n">s</span> <span class="n">s</span> <span class="n">s</span> <span class="c1"># this will work</span>
+</pre></div>
+</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Unlike the earlier “displace_box” version of this command, atom
@@ -295,30 +295,30 @@ used following a keyword that changed the volume, which is any of the
<em>x</em>, <em>y</em>, <em>z</em> keywords. If the preceding keyword “key” had a <em>volume</em>
style, then both it and the current keyword apply to the keyword
preceding “key”. I.e. this sequence of keywords is allowed:</p>
-<pre class="literal-block">
-change_box all x scale 1.1 y volume z volume
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">y</span> <span class="n">volume</span> <span class="n">z</span> <span class="n">volume</span>
+</pre></div>
+</div>
<p>The <em>volume</em> style changes the associated dimension so that the
overall box volume is unchanged relative to its value before the
preceding keyword was invoked.</p>
<p>If the following command is used, then the z box length will shrink by
the same 1.1 factor the x box length was increased by:</p>
-<pre class="literal-block">
-change_box all x scale 1.1 z volume
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span>
+</pre></div>
+</div>
<p>If the following command is used, then the y,z box lengths will each
shrink by sqrt(1.1) to keep the volume constant. In this case, the
y,z box lengths shrink so as to keep their relative aspect ratio
constant:</p>
-<pre class="literal-block">
-change_box all"x scale 1.1 y volume z volume
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span><span class="s2">"x scale 1.1 y volume z volume</span>
+</pre></div>
+</div>
<p>If the following command is used, then the final box will be a factor
of 10% larger in x and y, and a factor of 21% smaller in z, so as to
keep the volume constant:</p>
-<pre class="literal-block">
-change_box all x scale 1.1 z volume y scale 1.1 z volume
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span> <span class="n">y</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span>
+</pre></div>
+</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">For solids or liquids, when one dimension of the box is
diff --git a/doc/html/compute_dipole_chunk.html b/doc/html/compute_dipole_chunk.html
index efedfa0512..55452e3a0f 100644
--- a/doc/html/compute_dipole_chunk.html
+++ b/doc/html/compute_dipole_chunk.html
@@ -181,11 +181,11 @@ and how they are set for each atom. You can reset the image flags
<p>The simplest way to output the results of the compute com/chunk
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
command, for example:</p>
-<pre class="literal-block">
-compute cc1 all chunk/atom molecule
-compute myChunk all dipole/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">dipole</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
+</pre></div>
+</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global array where the number of rows = the
number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command. The number of columns =
diff --git a/doc/html/compute_inertia_chunk.html b/doc/html/compute_inertia_chunk.html
index d718f90f47..b93575cfc5 100644
--- a/doc/html/compute_inertia_chunk.html
+++ b/doc/html/compute_inertia_chunk.html
@@ -177,11 +177,11 @@ how they are set for each atom. You can reset the image flags
<p>The simplest way to output the results of the compute inertia/chunk
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
command, for example:</p>
-<pre class="literal-block">
-compute cc1 all chunk/atom molecule
-compute myChunk all inertia/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">inertia</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
+</pre></div>
+</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global array where the number of rows = the
number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command. The number of columns =
diff --git a/doc/html/compute_ke_atom_eff.html b/doc/html/compute_ke_atom_eff.html
index 6a017dc79b..00b22b9256 100644
--- a/doc/html/compute_ke_atom_eff.html
+++ b/doc/html/compute_ke_atom_eff.html
@@ -168,11 +168,11 @@ eFF.</p>
thermodynamic output by using the <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a>
command, as shown in the following example:</p>
</div>
-<pre class="literal-block">
-compute effTemp all temp/eff
-thermo_style custom step etotal pe ke temp press
-thermo_modify temp effTemp
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">effTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">eff</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">etotal</span> <span class="n">pe</span> <span class="n">ke</span> <span class="n">temp</span> <span class="n">press</span>
+<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">effTemp</span>
+</pre></div>
+</div>
<p>The value of the kinetic energy will be 0.0 for atoms (nuclei or
electrons) not in the specified compute group.</p>
<p><strong>Output info:</strong></p>
diff --git a/doc/html/compute_ke_eff.html b/doc/html/compute_ke_eff.html
index ff0e0b4e68..b614a9d25b 100644
--- a/doc/html/compute_ke_eff.html
+++ b/doc/html/compute_ke_eff.html
@@ -169,11 +169,11 @@ the <a class="reference internal" href="compute_temp_eff.html"><span class="doc"
printed with thermodynamic output by using the
<a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a> command, as shown in the following
example:</p>
-<pre class="literal-block">
-compute effTemp all temp/eff
-thermo_style custom step etotal pe ke temp press
-thermo_modify temp effTemp
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">effTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">eff</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">etotal</span> <span class="n">pe</span> <span class="n">ke</span> <span class="n">temp</span> <span class="n">press</span>
+<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">effTemp</span>
+</pre></div>
+</div>
<p>See <a class="reference internal" href="compute_temp_eff.html"><span class="doc">compute temp/eff</span></a>.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the KE). This value can be
diff --git a/doc/html/compute_modify.html b/doc/html/compute_modify.html
index 6556686bb9..8c31af05b2 100644
--- a/doc/html/compute_modify.html
+++ b/doc/html/compute_modify.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>compute_modify command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-compute_modify compute-ID keyword value ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute_modify</span> <span class="n">compute</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul class="simple">
<li>compute-ID = ID of the compute to modify</li>
<li>one or more keyword/value pairs may be listed</li>
@@ -145,10 +145,10 @@ compute_modify compute-ID keyword value ...
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-compute_modify myTemp extra 0
-compute_modify newtemp dynamic yes extra 600
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute_modify</span> <span class="n">myTemp</span> <span class="n">extra</span> <span class="mi">0</span>
+<span class="n">compute_modify</span> <span class="n">newtemp</span> <span class="n">dynamic</span> <span class="n">yes</span> <span class="n">extra</span> <span class="mi">600</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
diff --git a/doc/html/compute_pe_atom.html b/doc/html/compute_pe_atom.html
index b5de90dfdb..fafebf006b 100644
--- a/doc/html/compute_pe_atom.html
+++ b/doc/html/compute_pe_atom.html
@@ -185,11 +185,11 @@ command.</p>
<p>As an example of per-atom potential energy compared to total potential
energy, these lines in an input script should yield the same result
in the last 2 columns of thermo output:</p>
-<pre class="literal-block">
-compute peratom all pe/atom
-compute pe all reduce sum c_peratom
-thermo_style custom step temp etotal press pe c_pe
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">peratom</span> <span class="nb">all</span> <span class="n">pe</span><span class="o">/</span><span class="n">atom</span>
+<span class="n">compute</span> <span class="n">pe</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_peratom</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">press</span> <span class="n">pe</span> <span class="n">c_pe</span>
+</pre></div>
+</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The per-atom energy does not any Lennard-Jones tail corrections
diff --git a/doc/html/compute_property_atom.html b/doc/html/compute_property_atom.html
index f91b814e33..9fdc98e352 100644
--- a/doc/html/compute_property_atom.html
+++ b/doc/html/compute_property_atom.html
@@ -136,25 +136,25 @@
<li>property/atom = style name of this compute command</li>
<li>input = one or more atom attributes</li>
</ul>
-<pre class="literal-block">
-possible attributes = id, mol, proc, type, mass,
- x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
- vx, vy, vz, fx, fy, fz,
- q, mux, muy, muz, mu,
- radius, diameter, omegax, omegay, omegaz,
- angmomx, angmomy, angmomz,
- shapex,shapey, shapez,
- quatw, quati, quatj, quatk, tqx, tqy, tqz,
- end1x, end1y, end1z, end2x, end2y, end2z,
- corner1x, corner1y, corner1z,
- corner2x, corner2y, corner2z,
- corner3x, corner3y, corner3z,
- nbonds,
- vfrac, s0,
- spin, eradius, ervel, erforce,
- rho, drho, e, de, cv,
- i_name, d_name
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">possible</span> <span class="n">attributes</span> <span class="o">=</span> <span class="nb">id</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="n">proc</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">mass</span><span class="p">,</span>
+ <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span><span class="p">,</span> <span class="n">xs</span><span class="p">,</span> <span class="n">ys</span><span class="p">,</span> <span class="n">zs</span><span class="p">,</span> <span class="n">xu</span><span class="p">,</span> <span class="n">yu</span><span class="p">,</span> <span class="n">zu</span><span class="p">,</span> <span class="n">ix</span><span class="p">,</span> <span class="n">iy</span><span class="p">,</span> <span class="n">iz</span><span class="p">,</span>
+ <span class="n">vx</span><span class="p">,</span> <span class="n">vy</span><span class="p">,</span> <span class="n">vz</span><span class="p">,</span> <span class="n">fx</span><span class="p">,</span> <span class="n">fy</span><span class="p">,</span> <span class="n">fz</span><span class="p">,</span>
+ <span class="n">q</span><span class="p">,</span> <span class="n">mux</span><span class="p">,</span> <span class="n">muy</span><span class="p">,</span> <span class="n">muz</span><span class="p">,</span> <span class="n">mu</span><span class="p">,</span>
+ <span class="n">radius</span><span class="p">,</span> <span class="n">diameter</span><span class="p">,</span> <span class="n">omegax</span><span class="p">,</span> <span class="n">omegay</span><span class="p">,</span> <span class="n">omegaz</span><span class="p">,</span>
+ <span class="n">angmomx</span><span class="p">,</span> <span class="n">angmomy</span><span class="p">,</span> <span class="n">angmomz</span><span class="p">,</span>
+ <span class="n">shapex</span><span class="p">,</span><span class="n">shapey</span><span class="p">,</span> <span class="n">shapez</span><span class="p">,</span>
+ <span class="n">quatw</span><span class="p">,</span> <span class="n">quati</span><span class="p">,</span> <span class="n">quatj</span><span class="p">,</span> <span class="n">quatk</span><span class="p">,</span> <span class="n">tqx</span><span class="p">,</span> <span class="n">tqy</span><span class="p">,</span> <span class="n">tqz</span><span class="p">,</span>
+ <span class="n">end1x</span><span class="p">,</span> <span class="n">end1y</span><span class="p">,</span> <span class="n">end1z</span><span class="p">,</span> <span class="n">end2x</span><span class="p">,</span> <span class="n">end2y</span><span class="p">,</span> <span class="n">end2z</span><span class="p">,</span>
+ <span class="n">corner1x</span><span class="p">,</span> <span class="n">corner1y</span><span class="p">,</span> <span class="n">corner1z</span><span class="p">,</span>
+ <span class="n">corner2x</span><span class="p">,</span> <span class="n">corner2y</span><span class="p">,</span> <span class="n">corner2z</span><span class="p">,</span>
+ <span class="n">corner3x</span><span class="p">,</span> <span class="n">corner3y</span><span class="p">,</span> <span class="n">corner3z</span><span class="p">,</span>
+ <span class="n">nbonds</span><span class="p">,</span>
+ <span class="n">vfrac</span><span class="p">,</span> <span class="n">s0</span><span class="p">,</span>
+ <span class="n">spin</span><span class="p">,</span> <span class="n">eradius</span><span class="p">,</span> <span class="n">ervel</span><span class="p">,</span> <span class="n">erforce</span><span class="p">,</span>
+ <span class="n">rho</span><span class="p">,</span> <span class="n">drho</span><span class="p">,</span> <span class="n">e</span><span class="p">,</span> <span class="n">de</span><span class="p">,</span> <span class="n">cv</span><span class="p">,</span>
+ <span class="n">i_name</span><span class="p">,</span> <span class="n">d_name</span>
+</pre></div>
+</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">id</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">ID</span>
<span class="n">mol</span> <span class="o">=</span> <span class="n">molecule</span> <span class="n">ID</span>
<span class="n">proc</span> <span class="o">=</span> <span class="n">ID</span> <span class="n">of</span> <span class="n">processor</span> <span class="n">that</span> <span class="n">owns</span> <span class="n">atom</span>
diff --git a/doc/html/compute_property_chunk.html b/doc/html/compute_property_chunk.html
index 7cf73b649d..2012335a47 100644
--- a/doc/html/compute_property_chunk.html
+++ b/doc/html/compute_property_chunk.html
@@ -192,12 +192,12 @@ will be in unitless reduced units (0-1).</p>
<p>The simplest way to output the results of the compute property/chunk
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
command, for example:</p>
-<pre class="literal-block">
-compute cc1 all chunk/atom molecule
-compute myChunk1 all property/chunk cc1 count
-compute myChunk2 all com/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2[*] file tmp.out mode vector
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<span class="n">compute</span> <span class="n">myChunk1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span> <span class="n">count</span>
+<span class="n">compute</span> <span class="n">myChunk2</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk1</span> <span class="n">c_myChunk2</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
+</pre></div>
+</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector or global array depending on
the number of input values. The length of the vector or number of
diff --git a/doc/html/compute_reduce.html b/doc/html/compute_reduce.html
index 56a155c53a..519bc9ff3c 100644
--- a/doc/html/compute_reduce.html
+++ b/doc/html/compute_reduce.html
@@ -148,14 +148,14 @@
<li>one or more inputs can be listed</li>
<li>input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
</ul>
-<pre class="literal-block">
-x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-c_ID = per-atom or local vector calculated by a compute with ID
-c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below)
-f_ID = per-atom or local vector calculated by a fix with ID
-f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID, I can include wildcard (see below)
-v_name = per-atom vector calculated by an atom-style variable with name
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">,</span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">position</span><span class="p">,</span> <span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
+<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
+<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
+<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
+</pre></div>
+</div>
<ul class="simple">
<li>zero or more keyword/args pairs may be appended</li>
<li>keyword = <em>replace</em></li>
@@ -168,13 +168,13 @@ v_name = per-atom vector calculated by an atom-style variable with name
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-compute 1 all reduce sum c_force
-compute 1 all reduce/region subbox sum c_force
-compute 2 all reduce min c_press[2] f_ave v_myKE
-compute 2 all reduce min c_press[*] f_ave v_myKE
-compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_force</span>
+<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">reduce</span><span class="o">/</span><span class="n">region</span> <span class="n">subbox</span> <span class="nb">sum</span> <span class="n">c_force</span>
+<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">c_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">f_ave</span> <span class="n">v_myKE</span>
+<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">c_press</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">f_ave</span> <span class="n">v_myKE</span>
+<span class="n">compute</span> <span class="mi">3</span> <span class="n">fluid</span> <span class="n">reduce</span> <span class="nb">max</span> <span class="n">c_index</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_index</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_dist</span> <span class="n">replace</span> <span class="mi">1</span> <span class="mi">3</span> <span class="n">replace</span> <span class="mi">2</span> <span class="mi">3</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -211,7 +211,7 @@ component) or can be the result of a <a class="reference internal" href="compute
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a>.</p>
<p>Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
-specify multiple values. This takes the form “*” or “*n” or “n*” or
+specify multiple values. This takes the form “*” or “<em>n” or “n</em>” or
“m*n”. If N = the size of the vector (for <em>mode</em> = scalar) or the
number of columns in the array (for <em>mode</em> = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
@@ -222,18 +222,18 @@ means all indices from m to n (inclusive).</p>
had been listed one by one. E.g. these 2 compute reduce commands are
equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
command creates a per-atom array with 6 columns:</p>
-<pre class="literal-block">
-compute myPress all stress/atom NULL
-compute 2 all reduce min myPress[*]
-compute 2 all reduce min myPress[1] myPress[2] myPress[3] &
- myPress[4] myPress[5] myPress[6]
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myPress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
+<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">myPress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
+<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&</span>
+ <span class="n">myPress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
self-explanatory. Note that other atom attributes can be used as
inputs to this fix by using the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command and then specifying
an input value from that compute.</p>
-<p>If a value begins with “c_”, a compute ID must follow which has been
+<p>If a value begins with “<a href="#id1"><span class="problematic" id="id2">c_</span></a>”, a compute ID must follow which has been
previously defined in the input script. Computes can generate
per-atom or local quantities. See the individual
<a class="reference internal" href="compute.html"><span class="doc">compute</span></a> doc page for details. If no bracketed integer
@@ -243,7 +243,7 @@ by the compute is used. Users can also write code for their own
compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.</p>
-<p>If a value begins with “f_”, a fix ID must follow which has been
+<p>If a value begins with “<a href="#id3"><span class="problematic" id="id4">f_</span></a>”, a fix ID must follow which has been
previously defined in the input script. Fixes can generate per-atom
or local quantities. See the individual <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> doc page for
details. Note that some fixes only produce their values on certain
@@ -254,7 +254,7 @@ integer is appended, the Ith column of the array calculated by the fix
is used. Users can also write code for their own fix style and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the discussion above for how
I can be specified with a wildcard asterisk to effectively specify
multiple values.</p>
-<p>If a value begins with “v_”, a variable name must follow which has
+<p>If a value begins with “<a href="#id5"><span class="problematic" id="id6">v_</span></a>”, a variable name must follow which has
been previously defined in the input script. It must be an
<a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a>. Atom-style variables can
reference thermodynamic keywords and various per-atom attributes, or
@@ -271,12 +271,12 @@ Then, instead of performing a min/max on the <em>vec1</em> input vector, the
stored index is used to select the Nth element of the <em>vec1</em> vector.</p>
<p>Thus, for example, if you wish to use this compute to find the bond
with maximum stretch, you can do it as follows:</p>
-<pre class="literal-block">
-compute 1 all property/local batom1 batom2
-compute 2 all bond/local dist
-compute 3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
-thermo_style custom step temp c_3[1] c_3[2] c_3[3]
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">batom1</span> <span class="n">batom2</span>
+<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span>
+<span class="n">compute</span> <span class="mi">3</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">max</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_2</span> <span class="n">replace</span> <span class="mi">1</span> <span class="mi">3</span> <span class="n">replace</span> <span class="mi">2</span> <span class="mi">3</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">c_3</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_3</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_3</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
+</pre></div>
+</div>
<p>The first two input values in the compute reduce command are vectors
with the IDs of the 2 atoms in each bond, using the <a class="reference internal" href="compute_property_local.html"><span class="doc">compute property/local</span></a> command. The last input
value is bond distance, using the <a class="reference internal" href="compute_bond_local.html"><span class="doc">compute bond/local</span></a> command. Instead of taking the
diff --git a/doc/html/compute_rigid_local.html b/doc/html/compute_rigid_local.html
index 7f7d5630fa..154d01a909 100644
--- a/doc/html/compute_rigid_local.html
+++ b/doc/html/compute_rigid_local.html
@@ -202,10 +202,10 @@ there will be no consistent ordering of the entries within the local
vector or array from one timestep to the next.</p>
<p>Here is an example of how to use this compute to dump rigid body info
to a file:</p>
-<pre class="literal-block">
-compute 1 all rigid/local myRigid mol x y z fx fy fz
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7]
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rigid</span><span class="o">/</span><span class="n">local</span> <span class="n">myRigid</span> <span class="n">mol</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span>
+<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">7</span><span class="p">]</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p>This section explains the rigid body attributes that can be specified.</p>
<p>The <em>id</em> attribute is the atomID of the atom which owns the rigid body, which is
diff --git a/doc/html/compute_temp_cs.html b/doc/html/compute_temp_cs.html
index 81927952be..4751726a56 100644
--- a/doc/html/compute_temp_cs.html
+++ b/doc/html/compute_temp_cs.html
@@ -140,10 +140,10 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-compute oxygen_c-s all temp/cs O_core O_shell
-compute core_shells all temp/cs cores shells
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">oxygen_c</span><span class="o">-</span><span class="n">s</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">cs</span> <span class="n">O_core</span> <span class="n">O_shell</span>
+<span class="n">compute</span> <span class="n">core_shells</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">cs</span> <span class="n">cores</span> <span class="n">shells</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
diff --git a/doc/html/compute_temp_eff.html b/doc/html/compute_temp_eff.html
index d11ad256a8..4dadf7de39 100644
--- a/doc/html/compute_temp_eff.html
+++ b/doc/html/compute_temp_eff.html
@@ -170,11 +170,11 @@ reported by LAMMPS in the thermodynamic quantities reported via the
<a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a> command, as shown in the following
example:</p>
</div>
-<pre class="literal-block">
-compute effTemp all temp/eff
-thermo_style custom step etotal pe ke temp press
-thermo_modify temp effTemp
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">effTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">eff</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">etotal</span> <span class="n">pe</span> <span class="n">ke</span> <span class="n">temp</span> <span class="n">press</span>
+<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">effTemp</span>
+</pre></div>
+</div>
<p>A 6-component kinetic energy tensor is also calculated by this compute
for use in the computation of a pressure tensor. The formula for the
components of the tensor is the same as the above formula, except that
diff --git a/doc/html/compute_ti.html b/doc/html/compute_ti.html
index 8d6198637d..5701aeee75 100644
--- a/doc/html/compute_ti.html
+++ b/doc/html/compute_ti.html
@@ -154,10 +154,10 @@ pair style args = atype v_name1 v_name2
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
-compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ti</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mi">1</span> <span class="n">v_lj</span> <span class="n">v_dlj</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mi">2</span> <span class="n">v_c</span> <span class="n">v_dc</span> <span class="n">kspace</span> <span class="mi">1</span> <span class="n">v_ks</span> <span class="n">v_dks</span>
+<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ti</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mi">1</span><span class="o">*</span><span class="mi">3</span> <span class="n">v_lj</span> <span class="n">v_dlj</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="o">*</span> <span class="n">v_c</span> <span class="n">v_dc</span> <span class="n">kspace</span> <span class="o">*</span> <span class="n">v_ks</span> <span class="n">v_dks</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -192,7 +192,7 @@ with respect to <em>lambda</em>.</p>
numeric values can be used, as in the 1st example above. Or a
wildcard asterisk can be used in place of or in conjunction with the
<em>atype</em> argument to select multiple atom types. This takes the form
-“*” or “*n” or “n*” or “m*n”. If N = the number of atom types, then
+“*” or “<em>n” or “n</em>” or “m*n”. If N = the number of atom types, then
an asterisk with no numeric values means all types from 1 to N. A
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
diff --git a/doc/html/compute_voronoi_atom.html b/doc/html/compute_voronoi_atom.html
index ed4cd612a1..630ee3bac6 100644
--- a/doc/html/compute_voronoi_atom.html
+++ b/doc/html/compute_voronoi_atom.html
@@ -158,14 +158,14 @@ or <em>face_threshold</em> or <em>neighbors</em> or <em>peratom</em></li>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-compute 1 all voronoi/atom
-compute 2 precipitate voronoi/atom surface matrix
-compute 3b precipitate voronoi/atom radius v_r
-compute 4 solute voronoi/atom only_group
-compute 5 defects voronoi/atom occupation
-compute 6 all voronoi/atom neighbors yes
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span>
+<span class="n">compute</span> <span class="mi">2</span> <span class="n">precipitate</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">surface</span> <span class="n">matrix</span>
+<span class="n">compute</span> <span class="mi">3</span><span class="n">b</span> <span class="n">precipitate</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">radius</span> <span class="n">v_r</span>
+<span class="n">compute</span> <span class="mi">4</span> <span class="n">solute</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">only_group</span>
+<span class="n">compute</span> <span class="mi">5</span> <span class="n">defects</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">occupation</span>
+<span class="n">compute</span> <span class="mi">6</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">neighbors</span> <span class="n">yes</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -199,11 +199,11 @@ can be obtained by running a “reduce sum” compute on c_2[3]</p>
<p>If the <em>radius</em> keyword is specified with an atom style variable as
the argument, a poly-disperse Voronoi tessellation is
performed. Examples for radius variables are</p>
-<pre class="literal-block">
-variable r1 atom (type==1)*0.1+(type==2)*0.4
-compute radius all property/atom radius
-variable r2 atom c_radius
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">r1</span> <span class="n">atom</span> <span class="p">(</span><span class="nb">type</span><span class="o">==</span><span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="mf">0.1</span><span class="o">+</span><span class="p">(</span><span class="nb">type</span><span class="o">==</span><span class="mi">2</span><span class="p">)</span><span class="o">*</span><span class="mf">0.4</span>
+<span class="n">compute</span> <span class="n">radius</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">radius</span>
+<span class="n">variable</span> <span class="n">r2</span> <span class="n">atom</span> <span class="n">c_radius</span>
+</pre></div>
+</div>
<p>Here v_r1 specifies a per-type radius of 0.1 units for type 1 atoms
and 0.4 units for type 2 atoms, and v_r2 accesses the radius property
present in atom_style sphere for granular models.</p>
@@ -247,10 +247,10 @@ uses local values from a compute as input. See <a class="reference internal" hr
options. More specifically, the array can be accessed by a
<a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> command to write a file containing
all the Voronoi neighbors in a system:</p>
-<pre class="literal-block">
-compute 6 all voronoi/atom neighbors yes
-dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3]
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">6</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">neighbors</span> <span class="n">yes</span>
+<span class="n">dump</span> <span class="n">d2</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1</span> <span class="n">dump</span><span class="o">.</span><span class="n">neighbors</span> <span class="n">index</span> <span class="n">c_6</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_6</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_6</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
+</pre></div>
+</div>
<p>If the <em>face_threshold</em> keyword is used, then only faces
with areas greater than the threshold are stored.</p>
<hr class="docutils" />
diff --git a/doc/html/delete_bonds.html b/doc/html/delete_bonds.html
index b10ff2515d..18e52920f4 100644
--- a/doc/html/delete_bonds.html
+++ b/doc/html/delete_bonds.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>delete_bonds command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-delete_bonds group-ID style arg keyword ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_bonds</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style</span> <span class="n">arg</span> <span class="n">keyword</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul>
<li><p class="first">group-ID = group ID</p>
</li>
@@ -157,12 +157,12 @@ delete_bonds group-ID style arg keyword ...
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-delete_bonds frozen multi remove
-delete_bonds all atom 4 special
-delete_bonds all bond 0*3 special
-delete_bonds all stats
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_bonds</span> <span class="n">frozen</span> <span class="n">multi</span> <span class="n">remove</span>
+<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">4</span> <span class="n">special</span>
+<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">bond</span> <span class="mi">0</span><span class="o">*</span><span class="mi">3</span> <span class="n">special</span>
+<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">stats</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -183,7 +183,7 @@ be an integer from 0 to N, where N is the number of relevant types
(atom types, bond types, etc). A value of 0 is only relevant for
style <em>bond</em>; see details below. In all cases, a wildcard asterisk
can be used in place of or in conjunction with the <em>type</em> argument to
-specify a range of types. This takes the form “*” or “*n” or “n*” or
+specify a range of types. This takes the form “*” or “<em>n” or “n</em>” or
“m*n”. If N = the number of types, then an asterisk with no numeric
values means all types from 0 to N. A leading asterisk means all
types from 0 to n (inclusive). A trailing asterisk means all types
diff --git a/doc/html/dihedral_table.html b/doc/html/dihedral_table.html
index fe30f6ab11..d967731158 100644
--- a/doc/html/dihedral_table.html
+++ b/doc/html/dihedral_table.html
@@ -131,9 +131,9 @@
<h1>dihedral_style table/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-dihedral_style table style Ntable
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">table</span> <span class="n">style</span> <span class="n">Ntable</span>
+</pre></div>
+</div>
<ul class="simple">
<li>style = <em>linear</em> or <em>spline</em> = method of interpolation</li>
<li>Ntable = size of the internal lookup table</li>
@@ -141,12 +141,12 @@ dihedral_style table style Ntable
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-dihedral_style table spline 400
-dihedral_style table linear 1000
-dihedral_coeff 1 file.table DIH_TABLE1
-dihedral_coeff 2 file.table DIH_TABLE2
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">table</span> <span class="n">spline</span> <span class="mi">400</span>
+<span class="n">dihedral_style</span> <span class="n">table</span> <span class="n">linear</span> <span class="mi">1000</span>
+<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="n">file</span><span class="o">.</span><span class="n">table</span> <span class="n">DIH_TABLE1</span>
+<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="n">file</span><span class="o">.</span><span class="n">table</span> <span class="n">DIH_TABLE2</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -185,23 +185,23 @@ or blank lines.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Table of the potential and its negative derivative</span>
</pre></div>
</div>
-<pre class="literal-block">
-DIH_TABLE1 (keyword is the first text on line)
-N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F)
- (blank line)
-1 -168.0 -1.40351172223 0.0423346818422
-2 -156.0 -1.70447981034 0.00811786522531
-3 -144.0 -1.62956100432 -0.0184129719987
-...
-30 180.0 -0.707106781187 0.0719306095245
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">DIH_TABLE1</span> <span class="p">(</span><span class="n">keyword</span> <span class="ow">is</span> <span class="n">the</span> <span class="n">first</span> <span class="n">text</span> <span class="n">on</span> <span class="n">line</span><span class="p">)</span>
+<span class="n">N</span> <span class="mi">30</span> <span class="n">DEGREES</span> <span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="n">NOF</span><span class="p">,</span> <span class="n">DEGREES</span><span class="p">,</span> <span class="n">RADIANS</span><span class="p">,</span> <span class="n">CHECKU</span><span class="o">/</span><span class="n">F</span><span class="p">)</span>
+ <span class="p">(</span><span class="n">blank</span> <span class="n">line</span><span class="p">)</span>
+<span class="mi">1</span> <span class="o">-</span><span class="mf">168.0</span> <span class="o">-</span><span class="mf">1.40351172223</span> <span class="mf">0.0423346818422</span>
+<span class="mi">2</span> <span class="o">-</span><span class="mf">156.0</span> <span class="o">-</span><span class="mf">1.70447981034</span> <span class="mf">0.00811786522531</span>
+<span class="mi">3</span> <span class="o">-</span><span class="mf">144.0</span> <span class="o">-</span><span class="mf">1.62956100432</span> <span class="o">-</span><span class="mf">0.0184129719987</span>
+<span class="o">...</span>
+<span class="mi">30</span> <span class="mf">180.0</span> <span class="o">-</span><span class="mf">0.707106781187</span> <span class="mf">0.0719306095245</span>
+</pre></div>
+</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Example 2: table of the potential. Forces omitted</span>
</pre></div>
</div>
-<pre class="literal-block">
-DIH_TABLE2
-N 30 NOF CHECKU testU.dat CHECKF testF.dat
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">DIH_TABLE2</span>
+<span class="n">N</span> <span class="mi">30</span> <span class="n">NOF</span> <span class="n">CHECKU</span> <span class="n">testU</span><span class="o">.</span><span class="n">dat</span> <span class="n">CHECKF</span> <span class="n">testF</span><span class="o">.</span><span class="n">dat</span>
+</pre></div>
+</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">1</span> <span class="o">-</span><span class="mf">168.0</span> <span class="o">-</span><span class="mf">1.40351172223</span>
<span class="mi">2</span> <span class="o">-</span><span class="mf">156.0</span> <span class="o">-</span><span class="mf">1.70447981034</span>
<span class="mi">3</span> <span class="o">-</span><span class="mf">144.0</span> <span class="o">-</span><span class="mf">1.62956100432</span>
diff --git a/doc/html/dump.html b/doc/html/dump.html
index d76697dbba..b47465bc33 100644
--- a/doc/html/dump.html
+++ b/doc/html/dump.html
@@ -239,19 +239,19 @@ i_name = per-atom integer vector with name, managed by fix property/atom
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-dump myDump all atom 100 dump.atom
-dump myDump all atom/mpiio 100 dump.atom.mpiio
-dump myDump all atom/gz 100 dump.atom.gz
-dump 2 subgroup atom 50 dump.run.bin
-dump 2 subgroup atom 50 dump.run.mpiio.bin
-dump 4a all custom 100 dump.myforce.* id type x y vx fx
-dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
-dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
-dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
-dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
-dump 1 all xtc 1000 file.xtc
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">myDump</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">atom</span>
+<span class="n">dump</span> <span class="n">myDump</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">mpiio</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">atom</span><span class="o">.</span><span class="n">mpiio</span>
+<span class="n">dump</span> <span class="n">myDump</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">gz</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">atom</span><span class="o">.</span><span class="n">gz</span>
+<span class="n">dump</span> <span class="mi">2</span> <span class="n">subgroup</span> <span class="n">atom</span> <span class="mi">50</span> <span class="n">dump</span><span class="o">.</span><span class="n">run</span><span class="o">.</span><span class="n">bin</span>
+<span class="n">dump</span> <span class="mi">2</span> <span class="n">subgroup</span> <span class="n">atom</span> <span class="mi">50</span> <span class="n">dump</span><span class="o">.</span><span class="n">run</span><span class="o">.</span><span class="n">mpiio</span><span class="o">.</span><span class="n">bin</span>
+<span class="n">dump</span> <span class="mi">4</span><span class="n">a</span> <span class="nb">all</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">myforce</span><span class="o">.*</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">x</span> <span class="n">y</span> <span class="n">vx</span> <span class="n">fx</span>
+<span class="n">dump</span> <span class="mi">4</span><span class="n">b</span> <span class="n">flow</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.%.</span><span class="n">myforce</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_myF</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">v_ke</span>
+<span class="n">dump</span> <span class="mi">4</span><span class="n">b</span> <span class="n">flow</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.%.</span><span class="n">myforce</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_myF</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">v_ke</span>
+<span class="n">dump</span> <span class="mi">2</span> <span class="n">inner</span> <span class="n">cfg</span> <span class="mi">10</span> <span class="n">dump</span><span class="o">.</span><span class="n">snap</span><span class="o">.*.</span><span class="n">cfg</span> <span class="n">mass</span> <span class="nb">type</span> <span class="n">xs</span> <span class="n">ys</span> <span class="n">zs</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span>
+<span class="n">dump</span> <span class="n">snap</span> <span class="nb">all</span> <span class="n">cfg</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">config</span><span class="o">.*.</span><span class="n">cfg</span> <span class="n">mass</span> <span class="nb">type</span> <span class="n">xs</span> <span class="n">ys</span> <span class="n">zs</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_Stress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">xtc</span> <span class="mi">1000</span> <span class="n">file</span><span class="o">.</span><span class="n">xtc</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -347,12 +347,12 @@ or m = shrink wrapped with a minimum value. See the
bounding box which encloses the triclinic simulation box is output,
along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
formatted as follows:</p>
-<pre class="literal-block">
-ITEM: BOX BOUNDS xy xz yz xx yy zz
-xlo_bound xhi_bound xy
-ylo_bound yhi_bound xz
-zlo_bound zhi_bound yz
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">ITEM</span><span class="p">:</span> <span class="n">BOX</span> <span class="n">BOUNDS</span> <span class="n">xy</span> <span class="n">xz</span> <span class="n">yz</span> <span class="n">xx</span> <span class="n">yy</span> <span class="n">zz</span>
+<span class="n">xlo_bound</span> <span class="n">xhi_bound</span> <span class="n">xy</span>
+<span class="n">ylo_bound</span> <span class="n">yhi_bound</span> <span class="n">xz</span>
+<span class="n">zlo_bound</span> <span class="n">zhi_bound</span> <span class="n">yz</span>
+</pre></div>
+</div>
<p>The presence of the text “xy xz yz” in the ITEM line indicates that
the 3 tilt factors will be included on each of the 3 following lines.
This bounding box is convenient for many visualization programs. The
@@ -541,7 +541,7 @@ styles.</p>
reference values from a compute or fix, like the <em>custom</em>, <em>cfg</em>, or
<em>local</em> styles, the bracketed index I can be specified using a
wildcard asterisk with the index to effectively specify multiple
-values. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the
+values. This takes the form “*” or “<em>n” or “n</em>” or “m*n”. If N = the
size of the vector (for <em>mode</em> = scalar) or the number of columns in
the array (for <em>mode</em> = vector), then an asterisk with no numeric
values means all indices from 1 to N. A leading asterisk means all
@@ -552,12 +552,12 @@ from m to n (inclusive).</p>
had been listed one by one. E.g. these 2 dump commands are
equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
command creates a per-atom array with 6 columns:</p>
-<pre class="literal-block">
-compute myPress all stress/atom NULL
-dump 2 all custom 100 tmp.dump id myPress[*]
-dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] &
- myPress[4] myPress[5] myPress[6]
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myPress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
+<span class="n">dump</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="nb">id</span> <span class="n">myPress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
+<span class="n">dump</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="nb">id</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&</span>
+ <span class="n">myPress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p>This section explains the local attributes that can be specified as
part of the <em>local</em> style.</p>
@@ -598,11 +598,11 @@ be specified with a wildcard asterisk to effectively specify multiple
values.</p>
<p>Here is an example of how to dump bond info for a system, including
the distance and energy of each bond:</p>
-<pre class="literal-block">
-compute 1 all property/local batom1 batom2 btype
-compute 2 all bond/local dist eng
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">batom1</span> <span class="n">batom2</span> <span class="n">btype</span>
+<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span> <span class="n">eng</span>
+<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p>This section explains the atom attributes that can be specified as
part of the <em>custom</em> and <em>cfg</em> styles.</p>
diff --git a/doc/html/dump_custom_vtk.html b/doc/html/dump_custom_vtk.html
index b77890476a..8bd838f671 100644
--- a/doc/html/dump_custom_vtk.html
+++ b/doc/html/dump_custom_vtk.html
@@ -182,15 +182,15 @@ v_name = per-atom vector calculated by an atom-style variable with name
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
-dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
-dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">dmpvtk</span> <span class="nb">all</span> <span class="n">custom</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">*.</span><span class="n">myforce</span><span class="o">.</span><span class="n">vtk</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">vx</span> <span class="n">fx</span>
+<span class="n">dump</span> <span class="n">dmpvtp</span> <span class="n">flow</span> <span class="n">custom</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">*.%.</span><span class="n">displace</span><span class="o">.</span><span class="n">vtp</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_myD</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myD</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myD</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">v_ke</span>
+<span class="n">dump</span> <span class="n">e_data</span> <span class="nb">all</span> <span class="n">custom</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">*.</span><span class="n">vtu</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">spin</span> <span class="n">eradius</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span> <span class="n">eforce</span>
+</pre></div>
+</div>
<p>The style <em>custom/vtk</em> is similar to the <a class="reference internal" href="dump.html"><span class="doc">custom</span></a> style but
uses the VTK library to write data to VTK simple legacy or XML format
depending on the filename extension specified. This can be either
-<em>*.vtk</em> for the legacy format or <em>*.vtp</em> and <em>*.vtu</em>, respectively,
+<a href="#id1"><span class="problematic" id="id2">**</span></a>.vtk* for the legacy format or <a href="#id3"><span class="problematic" id="id4">**</span></a>.vtp* and <a href="#id5"><span class="problematic" id="id6">**</span></a>.vtu*, respectively,
for the XML format; see the <a class="reference external" href="http://www.vtk.org/VTK/img/file-formats.pdf">VTK homepage</a> for a detailed
description of these formats. Since this naming convention conflicts
with the way binary output is usually specified (see below),
diff --git a/doc/html/dump_modify.html b/doc/html/dump_modify.html
index 08afa5c7c6..492ef0a5f5 100644
--- a/doc/html/dump_modify.html
+++ b/doc/html/dump_modify.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>dump_modify command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-dump_modify dump-ID keyword values ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump_modify</span> <span class="n">dump</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul class="simple">
<li>dump-ID = ID of dump to modify</li>
<li>one or more keyword/value pairs may be appended</li>
@@ -228,16 +228,16 @@ dump_modify dump-ID keyword values ...
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-dump_modify 1 format line "%d %d %20.15g %g %g" scale yes
-dump_modify 1 format float %20.15g scale yes
-dump_modify myDump image yes scale no flush yes
-dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
-dump_modify xtcdump precision 10000 sfactor 0.1
-dump_modify 1 every 1000 nfile 20
-dump_modify 1 every v_myVar
-dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump_modify</span> <span class="mi">1</span> <span class="nb">format</span> <span class="n">line</span> <span class="s2">"</span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%20.15g</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%g</span><span class="s2">"</span> <span class="n">scale</span> <span class="n">yes</span>
+<span class="n">dump_modify</span> <span class="mi">1</span> <span class="nb">format</span> <span class="nb">float</span> <span class="o">%</span><span class="mf">20.15</span><span class="n">g</span> <span class="n">scale</span> <span class="n">yes</span>
+<span class="n">dump_modify</span> <span class="n">myDump</span> <span class="n">image</span> <span class="n">yes</span> <span class="n">scale</span> <span class="n">no</span> <span class="n">flush</span> <span class="n">yes</span>
+<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">region</span> <span class="n">mySphere</span> <span class="n">thresh</span> <span class="n">x</span> <span class="o"><</span> <span class="mf">0.0</span> <span class="n">thresh</span> <span class="n">epair</span> <span class="o">>=</span> <span class="mf">3.2</span>
+<span class="n">dump_modify</span> <span class="n">xtcdump</span> <span class="n">precision</span> <span class="mi">10000</span> <span class="n">sfactor</span> <span class="mf">0.1</span>
+<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="mi">1000</span> <span class="n">nfile</span> <span class="mi">20</span>
+<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="n">v_myVar</span>
+<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">amap</span> <span class="nb">min</span> <span class="nb">max</span> <span class="n">cf</span> <span class="mf">0.0</span> <span class="mi">3</span> <span class="nb">min</span> <span class="n">green</span> <span class="mf">0.5</span> <span class="n">yellow</span> <span class="nb">max</span> <span class="n">blue</span> <span class="n">boxcolor</span> <span class="n">red</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -318,19 +318,19 @@ to the dump file. The <em>every</em> keyword cannot be used with the dump
<em>dcd</em> style.</p>
<p>For example, the following commands will
write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:</p>
-<pre class="literal-block">
-variable s equal logfreq(10,3,10)
-dump 1 all atom 100 tmp.dump
-dump_modify 1 every v_s first yes
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">s</span> <span class="n">equal</span> <span class="n">logfreq</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
+<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span>
+<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="n">v_s</span> <span class="n">first</span> <span class="n">yes</span>
+</pre></div>
+</div>
<p>The following commands would write snapshots at the timesteps listed
in file tmp.times:</p>
-<pre class="literal-block">
-variable f file tmp.times
-variable s equal next(f)
-dump 1 all atom 100 tmp.dump
-dump_modify 1 every v_s
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">f</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">times</span>
+<span class="n">variable</span> <span class="n">s</span> <span class="n">equal</span> <span class="nb">next</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span>
+<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="n">v_s</span>
+</pre></div>
+</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When using a file-style variable with the <em>every</em> keyword, the
@@ -406,11 +406,11 @@ an integer and you wish it to appear in the text dump file as a
(large) integer, then you need to use an appropriate format. For
example, these commands:</p>
</div>
-<pre class="literal-block">
-compute 1 all property/local batom1 batom2
-dump 1 all local 100 tmp.bonds index c_1[1] c_1[2]
-dump_modify 1 format "%d %0.0f %0.0f"
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">batom1</span> <span class="n">batom2</span>
+<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">bonds</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+<span class="n">dump_modify</span> <span class="mi">1</span> <span class="nb">format</span> <span class="s2">"</span><span class="si">%d</span><span class="s2"> </span><span class="si">%0.0f</span><span class="s2"> </span><span class="si">%0.0f</span><span class="s2">"</span>
+</pre></div>
+</div>
<p>will output the two atom IDs for atoms in each bond as integers. If
the dump_modify command were omitted, they would appear as
floating-point values, assuming they were large integers (more than 6
@@ -566,7 +566,7 @@ atoms of each type will be drawn in the image.</p>
<p>The specified <em>type</em> should be an integer from 1 to Ntypes = the
number of atom types. A wildcard asterisk can be used in place of or
in conjunction with the <em>type</em> argument to specify a range of atom
-types. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the
+types. This takes the form “*” or “<em>n” or “n</em>” or “m*n”. If N = the
number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
@@ -689,15 +689,15 @@ color map without having to specify where all the bin boundaries are.</p>
atoms in individual molecules with a different color. See the
examples/pour/in.pour.2d.molecule input script for an example of how
this is used.</p>
-<pre class="literal-block">
-variable colors string &
+<div class="highlight-default"><div class="highlight"><pre><span></span>variable colors string &
"red green blue yellow white &
purple pink orange lime gray"
variable mol atom mol%10
dump 1 all image 250 image.*.jpg v_mol type &
zoom 1.6 adiam 1.5
-dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
-</pre>
+dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
+</pre></div>
+</div>
<p>In this case, 10 colors are defined, and molecule IDs are
mapped to one of the colors, even if there are 1000s of molecules.</p>
<hr class="docutils" />
@@ -711,7 +711,7 @@ set the color that bonds of each type will be drawn in the image.</p>
<p>The specified <em>type</em> should be an integer from 1 to Nbondtypes = the
number of bond types. A wildcard asterisk can be used in place of or
in conjunction with the <em>type</em> argument to specify a range of bond
-types. This takes the form “*” or “*n” or “n*” or “m*n”. If N = the
+types. This takes the form “*” or “<em>n” or “n</em>” or “m*n”. If N = the
number of bond types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
diff --git a/doc/html/fix_atom_swap.html b/doc/html/fix_atom_swap.html
index a56f3b4f8b..862d6932af 100644
--- a/doc/html/fix_atom_swap.html
+++ b/doc/html/fix_atom_swap.html
@@ -156,11 +156,11 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
-fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
-fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">swap</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">29494</span> <span class="mf">300.0</span> <span class="n">ke</span> <span class="n">no</span> <span class="n">types</span> <span class="mi">1</span> <span class="mi">2</span>
+<span class="n">fix</span> <span class="n">myFix</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">swap</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">12345</span> <span class="mf">298.0</span> <span class="n">region</span> <span class="n">my_swap_region</span> <span class="n">types</span> <span class="mi">5</span> <span class="mi">6</span>
+<span class="n">fix</span> <span class="n">SGMC</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">swap</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">345</span> <span class="mf">1.0</span> <span class="n">semi</span><span class="o">-</span><span class="n">grand</span> <span class="n">yes</span> <span class="n">types</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="n">mu</span> <span class="mf">0.0</span> <span class="mf">4.3</span> <span class="o">-</span><span class="mf">5.0</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -250,7 +250,9 @@ system (the quantity used when performing GCMC moves),
you MUST enable the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option for
that fix. The doc pages for individual <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> commands
specify if this should be done.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the state of the fix to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. This includes information about the random
number generator seed, the next timestep for MC exchanges, etc. See
the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to
diff --git a/doc/html/fix_ave_atom.html b/doc/html/fix_ave_atom.html
index 72641a5006..b8459a1d96 100644
--- a/doc/html/fix_ave_atom.html
+++ b/doc/html/fix_ave_atom.html
@@ -140,22 +140,22 @@
one or more input values can be listed</li>
<li>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name</li>
</ul>
-<pre class="literal-block">
-x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-c_ID = per-atom vector calculated by a compute with ID
-c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
-f_ID = per-atom vector calculated by a fix with ID
-f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
-v_name = per-atom vector calculated by an atom-style variable with name
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">,</span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">position</span><span class="p">,</span> <span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
+<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
+<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
+<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
+</pre></div>
+</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 1 all ave/atom 1 100 100 vx vy vz
-fix 1 all ave/atom 10 20 1000 c_my_stress[1]
-fix 1 all ave/atom 10 20 1000 c_my_stress[*]
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">100</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -181,7 +181,7 @@ are the only ones that can be used with this fix since they produce
per-atom vectors.</p>
<p>Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
-specify multiple values. This takes the form “*” or “*n” or “n*” or
+specify multiple values. This takes the form “*” or “<em>n” or “n</em>” or
“m*n”. If N = the size of the vector (for <em>mode</em> = scalar) or the
number of columns in the array (for <em>mode</em> = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
@@ -192,13 +192,13 @@ means all indices from m to n (inclusive).</p>
had been listed one by one. E.g. these 2 fix ave/atom commands are
equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
command creates a per-atom array with 6 columns:</p>
-<pre class="literal-block">
-compute my_stress all stress/atom NULL
-fix 1 all ave/atom 10 20 1000 c_my_stress[*]
-fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[1] &
- c_my_stress[3] c_my_stress[4] &
- c_my_stress[5] c_my_stress[6]
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">my_stress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">&</span>
+ <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="o">&</span>
+ <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
timesteps the input values will be used in order to contribute to the
@@ -228,7 +228,7 @@ this is not what you want, consider averaging unwrapped coordinates,
which can be provided by the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command via its xu,yu,zu
attributes.</p>
</div>
-<p>If a value begins with “c_”, a compute ID must follow which has been
+<p>If a value begins with “<a href="#id1"><span class="problematic" id="id2">c_</span></a>”, a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the per-atom vector calculated by the compute is used. If a
bracketed term containing an index I is appended, the Ith column of
@@ -236,7 +236,7 @@ the per-atom array calculated by the compute is used. Users can also
write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the discussion above for how I can
be specified with a wildcard asterisk to effectively specify multiple
values.</p>
-<p>If a value begins with “f_”, a fix ID must follow which has been
+<p>If a value begins with “<a href="#id3"><span class="problematic" id="id4">f_</span></a>”, a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the per-atom vector calculated by the fix is used. If a
bracketed term containing an index I is appended, the Ith column of
@@ -246,13 +246,15 @@ compatible with <em>Nevery</em>, else an error will result. Users can also
write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the discussion above for how I can
be specified with a wildcard asterisk to effectively specify multiple
values.</p>
-<p>If a value begins with “v_”, a variable name must follow which has
+<p>If a value begins with “<a href="#id5"><span class="problematic" id="id6">v_</span></a>”, a variable name must follow which has
been previously defined in the input script as an <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a> Variables of style <em>atom</em> can reference
thermodynamic keywords, or invoke other computes, fixes, or variables
when they are evaluated, so this is a very general means of generating
per-atom quantities to time average.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global scalar or vector quantities are
stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.</p>
diff --git a/doc/html/fix_ave_chunk.html b/doc/html/fix_ave_chunk.html
index a6293fb62e..564b91e3ef 100644
--- a/doc/html/fix_ave_chunk.html
+++ b/doc/html/fix_ave_chunk.html
@@ -141,16 +141,16 @@
<li>one or more input values can be listed</li>
<li>value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name</li>
</ul>
-<pre class="literal-block">
-vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
-density/number, density/mass = number or mass density
-temp = temperature
-c_ID = per-atom vector calculated by a compute with ID
-c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
-f_ID = per-atom vector calculated by a fix with ID
-f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
-v_name = per-atom vector calculated by an atom-style variable with name
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
+<span class="n">density</span><span class="o">/</span><span class="n">number</span><span class="p">,</span> <span class="n">density</span><span class="o">/</span><span class="n">mass</span> <span class="o">=</span> <span class="n">number</span> <span class="ow">or</span> <span class="n">mass</span> <span class="n">density</span>
+<span class="n">temp</span> <span class="o">=</span> <span class="n">temperature</span>
+<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
+<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
+<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
+</pre></div>
+</div>
<ul class="simple">
<li>zero or more keyword/arg pairs may be appended</li>
<li>keyword = <em>norm</em> or <em>ave</em> or <em>bias</em> or <em>adof</em> or <em>cdof</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
@@ -185,12 +185,12 @@ v_name = per-atom vector calculated by an atom-style variable with name
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values"
-fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
-fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
-fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">10000</span> <span class="mi">1</span> <span class="mi">10000</span> <span class="n">binchunk</span> <span class="n">c_myCentro</span> <span class="n">title1</span> <span class="s2">"My output values"</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="n">molchunk</span> <span class="n">vx</span> <span class="n">vz</span> <span class="n">norm</span> <span class="n">sample</span> <span class="n">file</span> <span class="n">vel</span><span class="o">.</span><span class="n">profile</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">binchunk</span> <span class="n">density</span><span class="o">/</span><span class="n">mass</span> <span class="n">ave</span> <span class="n">running</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">binchunk</span> <span class="n">density</span><span class="o">/</span><span class="n">mass</span> <span class="n">ave</span> <span class="n">running</span>
+</pre></div>
+</div>
<p><strong>NOTE:</strong></p>
<p>If you are trying to replace a deprectated fix ave/spatial command
with the newer, more flexible fix ave/chunk and <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> commands, you simply need to split
@@ -242,7 +242,7 @@ ones that can be used with this fix since all other styles of variable
produce global quantities.</p>
<p>Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
-specify multiple values. This takes the form “*” or “*n” or “n*” or
+specify multiple values. This takes the form “*” or “<em>n” or “n</em>” or
“m*n”. If N = the size of the vector (for <em>mode</em> = scalar) or the
number of columns in the array (for <em>mode</em> = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
@@ -253,11 +253,11 @@ means all indices from m to n (inclusive).</p>
had been listed one by one. E.g. these 2 fix ave/chunk commands are
equivalent, since the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command creates, in this
case, a per-atom array with 3 columns:</p>
-<pre class="literal-block">
-compute myAng all property/atom angmomx angmomy angmomz
-fix 1 all ave/chunk 100 1 100 cc1 c_myAng[*] file tmp.angmom
-fix 2 all ave/chunk 100 1 100 cc1 c_myAng[1] c_myAng[2] c_myAng[3] file tmp.angmom
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myAng</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">angmomx</span> <span class="n">angmomy</span> <span class="n">angmomz</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">cc1</span> <span class="n">c_myAng</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">angmom</span>
+<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">cc1</span> <span class="n">c_myAng</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myAng</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myAng</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">angmom</span>
+</pre></div>
+</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This fix works by creating an array of size <em>Nchunk</em> by Nvalues
@@ -349,7 +349,7 @@ in the chunk on different timesteps were collected together as one set
of atoms to calculate their temperature. The compute allows the
center-of-mass velocity of each chunk to be subtracted before
calculating the temperature; this fix does not.</p>
-<p>If a value begins with “c_”, a compute ID must follow which has been
+<p>If a value begins with “<a href="#id1"><span class="problematic" id="id2">c_</span></a>”, a compute ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the compute is used. If a
bracketed integer is appended, the Ith column of the per-atom array
@@ -357,7 +357,7 @@ calculated by the compute is used. Users can also write code for
their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.
See the discussion above for how I can be specified with a wildcard
asterisk to effectively specify multiple values.</p>
-<p>If a value begins with “f_”, a fix ID must follow which has been
+<p>If a value begins with “<a href="#id3"><span class="problematic" id="id4">f_</span></a>”, a fix ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the fix is used. If a
bracketed integer is appended, the Ith column of the per-atom array
@@ -367,7 +367,7 @@ their values on certain timesteps, which must be compatible with
own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.</p>
-<p>If a value begins with “v_”, a variable name must follow which has
+<p>If a value begins with “<a href="#id5"><span class="problematic" id="id6">v_</span></a>”, a variable name must follow which has
been previously defined in the input script. Variables of style
<em>atom</em> can reference thermodynamic keywords and various per-atom
attributes, or invoke other computes, fixes, or variables when they
@@ -502,8 +502,10 @@ value of the <em>units</em> keyword is <em>reduced</em>, the coordinate values w
be in unitless reduced units (0-1). This is not true for the Coord1 value
of style <em>bin/sphere</em> or <em>bin/cylinder</em> which both represent radial
dimensions. Those values are always in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix computes a global array of values which can be accessed by
diff --git a/doc/html/fix_ave_correlate_long.html b/doc/html/fix_ave_correlate_long.html
index a673143beb..ccd754dbaf 100644
--- a/doc/html/fix_ave_correlate_long.html
+++ b/doc/html/fix_ave_correlate_long.html
@@ -139,13 +139,13 @@
<li>one or more input values can be listed</li>
<li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
</ul>
-<pre class="literal-block">
-c_ID = global scalar calculated by a compute with ID
-c_ID[I] = Ith component of global vector calculated by a compute with ID
-f_ID = global scalar calculated by a fix with ID
-f_ID[I] = Ith component of global vector calculated by a fix with ID
-v_name = global value calculated by an equal-style variable with name
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">c_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">f_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">v_name</span> <span class="o">=</span> <span class="k">global</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
+</pre></div>
+</div>
<ul class="simple">
<li>zero or more keyword/arg pairs may be appended</li>
<li>keyword = <em>type</em> or <em>start</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>ncorr</em> or <em>p</em> or <em>m</em></li>
@@ -177,12 +177,12 @@ v_name = global value calculated by an equal-style variable with name
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
-fix 1 all ave/correlate/long 1 10000 &
- c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
- type upper title1 "My correlation data" nlen 15 ncount 3
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span><span class="o">/</span><span class="n">long</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_myTemp</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">correlate</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span><span class="o">/</span><span class="n">long</span> <span class="mi">1</span> <span class="mi">10000</span> <span class="o">&</span>
+ <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&</span>
+ <span class="nb">type</span> <span class="n">upper</span> <span class="n">title1</span> <span class="s2">"My correlation data"</span> <span class="n">nlen</span> <span class="mi">15</span> <span class="n">ncount</span> <span class="mi">3</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -221,7 +221,9 @@ steps can be calculated.</p>
4*ncorr*nlen*8 bytes. With the default values of the parameters, this
corresponds to about 10 KB.</p>
<p>For the meaning of the additional optional keywords, see the <a class="reference internal" href="fix_ave_correlate.html"><span class="doc">fix ave/correlate</span></a> doc page.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>Since this fix in intended for the calculation of time correlation
functions over very long MD simulations, the information about this
fix is written automatically to binary restart files, so that the time
diff --git a/doc/html/fix_ave_histo.html b/doc/html/fix_ave_histo.html
index bb07687b4a..e8291ddeb4 100644
--- a/doc/html/fix_ave_histo.html
+++ b/doc/html/fix_ave_histo.html
@@ -145,15 +145,15 @@
<li>one or more input values can be listed</li>
<li>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
</ul>
-<pre class="literal-block">
-x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-c_ID = scalar or vector calculated by a compute with ID
-c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below)
-f_ID = scalar or vector calculated by a fix with ID
-f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID, I can include wildcard (see below)
-v_name = value(s) calculated by an equal-style or vector-style or atom-style variable with name
-v_name[I] = value calculated by a vector-style variable with name
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">,</span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">position</span><span class="p">,</span> <span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
+<span class="n">c_ID</span> <span class="o">=</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
+<span class="n">f_ID</span> <span class="o">=</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
+<span class="n">v_name</span> <span class="o">=</span> <span class="n">value</span><span class="p">(</span><span class="n">s</span><span class="p">)</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="ow">or</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="ow">or</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
+<span class="n">v_name</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
+</pre></div>
+</div>
<ul class="simple">
<li>zero or more keyword/arg pairs may be appended</li>
<li>keyword = <em>mode</em> or <em>file</em> or <em>ave</em> or <em>start</em> or <em>beyond</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
@@ -185,13 +185,13 @@ v_name[I] = value calculated by a vector-style variable with name
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
-fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 "My output values"
-fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[*]
-fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
-fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2]
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="mf">0.5</span> <span class="mf">1.5</span> <span class="mi">50</span> <span class="n">c_myTemp</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">histo</span> <span class="n">ave</span> <span class="n">running</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">100</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">title1</span> <span class="s2">"My output values"</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">100</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">1000</span> <span class="o">-</span><span class="mf">2.0</span> <span class="mf">2.0</span> <span class="mi">18</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span> <span class="n">mode</span> <span class="n">vector</span> <span class="n">ave</span> <span class="n">running</span> <span class="n">beyond</span> <span class="n">extra</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span><span class="o">/</span><span class="n">weight</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mi">100</span> <span class="mi">2000</span> <span class="n">c_XRD</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_XRD</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -232,7 +232,7 @@ with a bracketed term appended, indicating the Ith column of the array
is used.</p>
<p>Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
-specify multiple values. This takes the form “*” or “*n” or “n*” or
+specify multiple values. This takes the form “*” or “<em>n” or “n</em>” or
“m*n”. If N = the size of the vector (for <em>mode</em> = scalar) or the
number of columns in the array (for <em>mode</em> = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
@@ -243,11 +243,11 @@ means all indices from m to n (inclusive).</p>
vector or columns of the array had been listed one by one. E.g. these
2 fix ave/histo commands are equivalent, since the <a class="reference internal" href="compute_com_chunk.html"><span class="doc">compute com/chunk</span></a> command creates a global array with
3 columns:</p>
-<pre class="literal-block">
-compute myCOM all com/chunk
-fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector
-fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myCOM</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp1</span><span class="o">.</span><span class="n">com</span> <span class="n">mode</span> <span class="n">vector</span>
+<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp2</span><span class="o">.</span><span class="n">com</span> <span class="n">mode</span> <span class="n">vector</span>
+</pre></div>
+</div>
<p>If the fix ave/histo/weight command is used, exactly two values must
be specified. If the values are vectors, they must be the same
length. The first value (a scalar or vector) is what is histogrammed
@@ -278,7 +278,7 @@ simply generated on timesteps 100,200,etc.</p>
self-explanatory. Note that other atom attributes can be used as
inputs to this fix by using the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command and then specifying
an input value from that compute.</p>
-<p>If a value begins with “c_”, a compute ID must follow which has been
+<p>If a value begins with “<a href="#id1"><span class="problematic" id="id2">c_</span></a>”, a compute ID must follow which has been
previously defined in the input script. If <em>mode</em> = scalar, then if
no bracketed term is appended, the global scalar calculated by the
compute is used. If a bracketed term is appended, the Ith element of
@@ -295,7 +295,7 @@ can thus be accessed by fix ave/histo. Or it can be a compute defined
not in your input script, but by <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a> or other fixes such as <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>. See
the doc pages for these commands which give the IDs of these computes.
Users can also write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If a value begins with “f_”, a fix ID must follow which has been
+<p>If a value begins with “<a href="#id3"><span class="problematic" id="id4">f_</span></a>”, a fix ID must follow which has been
previously defined in the input script. If <em>mode</em> = scalar, then if
no bracketed term is appended, the global scalar calculated by the fix
is used. If a bracketed term is appended, the Ith element of the
@@ -309,7 +309,7 @@ values.</p>
<p>Note that some fixes only produce their values on certain timesteps,
which must be compatible with <em>Nevery</em>, else an error will result.
Users can also write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If a value begins with “v_”, a variable name must follow which has
+<p>If a value begins with “<a href="#id5"><span class="problematic" id="id6">v_</span></a>”, a variable name must follow which has
been previously defined in the input script. If <em>mode</em> = scalar, then
only equal-style or vector-style variables can be used, which both
produce global values. In this mode, a vector-style variable requires
@@ -399,8 +399,10 @@ values for each of these, so they do not need to be specified.</p>
describes the six values that are printed at the first of each section
of output. The third describes the 4 values printed for each bin in
the histogram.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix produces a global vector and global array which can be
diff --git a/doc/html/fix_ave_time.html b/doc/html/fix_ave_time.html
index 2d41fdc0dc..6c6744c5e6 100644
--- a/doc/html/fix_ave_time.html
+++ b/doc/html/fix_ave_time.html
@@ -140,14 +140,14 @@
<li>one or more input values can be listed</li>
<li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
</ul>
-<pre class="literal-block">
-c_ID = global scalar or vector calculated by a compute with ID
-c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
-f_ID = global scalar or vector calculated by a fix with ID
-f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
-v_name = value(s) calculated by an equal-style or vector-style variable with name
-v_name[I] = value calculated by a vector-style variable with name
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">c_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="k">global</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
+<span class="n">f_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="k">global</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
+<span class="n">v_name</span> <span class="o">=</span> <span class="n">value</span><span class="p">(</span><span class="n">s</span><span class="p">)</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="ow">or</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
+<span class="n">v_name</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
+</pre></div>
+</div>
<ul class="simple">
<li>zero or more keyword/arg pairs may be appended</li>
<li>keyword = <em>mode</em> or <em>file</em> or <em>ave</em> or <em>start</em> or <em>off</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
@@ -179,13 +179,13 @@ v_name[I] = value calculated by a vector-style variable with name
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
-fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 &
- title1 "My output values"
-fix 1 all ave/time 100 5 1000 c_thermo_press[*]
-fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_myTemp</span> <span class="n">c_thermo_temp</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">profile</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">ave</span> <span class="n">window</span> <span class="mi">20</span> <span class="o">&</span>
+ <span class="n">title1</span> <span class="s2">"My output values"</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">1000</span> <span class="n">f_indent</span> <span class="n">f_indent</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">indent</span> <span class="n">off</span> <span class="mi">1</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -228,7 +228,7 @@ is used. All vectors must be the same length, which is the length of
the vector or number of rows in the array.</p>
<p>Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
-specify multiple values. This takes the form “*” or “*n” or “n*” or
+specify multiple values. This takes the form “*” or “<em>n” or “n</em>” or
“m*n”. If N = the size of the vector (for <em>mode</em> = scalar) or the
number of columns in the array (for <em>mode</em> = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
@@ -239,11 +239,11 @@ means all indices from m to n (inclusive).</p>
vector or columns of the array had been listed one by one. E.g. these
2 fix ave/time commands are equivalent, since the <a class="reference internal" href="compute_rdf.html"><span class="doc">compute rdf</span></a> command creates, in this case, a global array
with 3 columns, each of length 50:</p>
-<pre class="literal-block">
-compute myRDF all rdf 50 1 2
-fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp1.rdf mode vector
-fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myRDF</span> <span class="nb">all</span> <span class="n">rdf</span> <span class="mi">50</span> <span class="mi">1</span> <span class="mi">2</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp1</span><span class="o">.</span><span class="n">rdf</span> <span class="n">mode</span> <span class="n">vector</span>
+<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp2</span><span class="o">.</span><span class="n">rdf</span> <span class="n">mode</span> <span class="n">vector</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
timesteps the input values will be used in order to contribute to the
@@ -261,7 +261,7 @@ timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
averaging is done; values are simply generated on timesteps
100,200,etc.</p>
<hr class="docutils" />
-<p>If a value begins with “c_”, a compute ID must follow which has been
+<p>If a value begins with “<a href="#id1"><span class="problematic" id="id2">c_</span></a>”, a compute ID must follow which has been
previously defined in the input script. If <em>mode</em> = scalar, then if
no bracketed term is appended, the global scalar calculated by the
compute is used. If a bracketed term is appended, the Ith element of
@@ -277,7 +277,7 @@ can thus be accessed by fix ave/time. Or it can be a compute defined
not in your input script, but by <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a> or other fixes such as <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>. See
the doc pages for these commands which give the IDs of these computes.
Users can also write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If a value begins with “f_”, a fix ID must follow which has been
+<p>If a value begins with “<a href="#id3"><span class="problematic" id="id4">f_</span></a>”, a fix ID must follow which has been
previously defined in the input script. If <em>mode</em> = scalar, then if
no bracketed term is appended, the global scalar calculated by the fix
is used. If a bracketed term is appended, the Ith element of the
@@ -290,7 +290,7 @@ specify multiple values.</p>
<p>Note that some fixes only produce their values on certain timesteps,
which must be compatible with <em>Nevery</em>, else an error will result.
Users can also write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If a value begins with “v_”, a variable name must follow which has
+<p>If a value begins with “<a href="#id5"><span class="problematic" id="id6">v_</span></a>”, a variable name must follow which has
been previously defined in the input script. If <em>mode</em> = scalar, then
only equal-style or vector-style variables can be used, which both
produce global values. In this mode, a vector-style variable requires
@@ -383,8 +383,10 @@ so the <em>title3</em> setting is ignored when <em>mode</em> = scalar.</p>
describes the two values that are printed at the first of each section
of output. In the third line the values are replaced with the
appropriate fields from the fix ave/time command.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix produces a global scalar or global vector or global array
diff --git a/doc/html/fix_bond_break.html b/doc/html/fix_bond_break.html
index ef0c90e2a9..9be191ab77 100644
--- a/doc/html/fix_bond_break.html
+++ b/doc/html/fix_bond_break.html
@@ -224,8 +224,10 @@ dramatically released when the bond is broken. More generally, you
may need to thermostat your system to compensate for energy changes
resulting from broken bonds (and angles, dihedrals, impropers).</p>
</div>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix computes two statistics which it stores in a global vector of
diff --git a/doc/html/fix_bond_create.html b/doc/html/fix_bond_create.html
index 8854f57578..8ab79a00a5 100644
--- a/doc/html/fix_bond_create.html
+++ b/doc/html/fix_bond_create.html
@@ -265,7 +265,7 @@ percolation simulation.</p>
1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
the system) for use in weighting pairwise interactions for bonded
atoms. Note that adding a single bond always adds a new 1st neighbor
-but may also induce *many* new 2nd and 3rd neighbors, depending on the
+but may also induce <em>many</em> new 2nd and 3rd neighbors, depending on the
molecular topology of your system. The “extra special per atom”
parameter must typically be set to allow for the new maximum total
size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 3
@@ -320,8 +320,10 @@ dramatically when the bond is formed. More generally, you may need to
thermostat your system to compensate for energy changes resulting from
created bonds (and angles, dihedrals, impropers).</p>
</div>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix computes two statistics which it stores in a global vector of
diff --git a/doc/html/fix_colvars.html b/doc/html/fix_colvars.html
index 367d9b091c..8ac1624b80 100644
--- a/doc/html/fix_colvars.html
+++ b/doc/html/fix_colvars.html
@@ -200,7 +200,9 @@ wrapped back into the simulation cell at each re-neighboring instead.</p>
fix that thermostats all atoms in the fix colvars group. This will be
used to provide the colvars module with the current thermostat target
temperature.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the current status of the colvars module into
<a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. This is in addition to the text
mode status file that is written by the colvars module itself and the
diff --git a/doc/html/fix_deform.html b/doc/html/fix_deform.html
index d23425a85b..e8ad31ffb0 100644
--- a/doc/html/fix_deform.html
+++ b/doc/html/fix_deform.html
@@ -272,9 +272,9 @@ e.g. picoseconds for “metal” units). Tensile strain is unitless and
is defined as delta/L0, where L0 is the original box length and delta
is the change relative to the original length. The box length L as a
function of time will change as</p>
-<pre class="literal-block">
-L(t) = L0 (1 + erate*dt)
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">L</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">L0</span> <span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="n">erate</span><span class="o">*</span><span class="n">dt</span><span class="p">)</span>
+</pre></div>
+</div>
<p>where dt is the elapsed time (in time units). Thus if <em>erate</em> R is
specified as 0.1 and time units are picoseconds, this means the box
length will increase by 10% of its original length every picosecond.
@@ -295,9 +295,9 @@ e.g. picoseconds for “metal” units). Tensile strain is unitless and
is defined as delta/L0, where L0 is the original box length and delta
is the change relative to the original length.</p>
<p>The box length L as a function of time will change as</p>
-<pre class="literal-block">
-L(t) = L0 exp(trate*dt)
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">L</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">L0</span> <span class="n">exp</span><span class="p">(</span><span class="n">trate</span><span class="o">*</span><span class="n">dt</span><span class="p">)</span>
+</pre></div>
+</div>
<p>where dt is the elapsed time (in time units). Thus if <em>trate</em> R is
specified as ln(1.1) and time units are picoseconds, this means the
box length will increase by 10% of its current (not original) length
@@ -341,9 +341,9 @@ dimensions, so that they respond to the tensile strain dynamically.</p>
<p>The <em>wiggle</em> style oscillates the specified box length dimension
sinusoidally with the specified amplitude and period. I.e. the box
length L as a function of time is given by</p>
-<pre class="literal-block">
-L(t) = L0 + A sin(2*pi t/Tp)
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">L</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">L0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">pi</span> <span class="n">t</span><span class="o">/</span><span class="n">Tp</span><span class="p">)</span>
+</pre></div>
+</div>
<p>where L0 is its initial length. If the amplitude A is a positive
number the box initially expands, then contracts, etc. If A is
negative then the box initially contracts, then expands, etc. The
@@ -370,13 +370,13 @@ arbitrary variable.</p>
<p>Here is an example of using the <em>variable</em> style to perform the same
box deformation as the <em>wiggle</em> style formula listed above, where we
assume that the current timestep = 0.</p>
-<pre class="literal-block">
-variable A equal 5.0
-variable Tp equal 10.0
-variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
-variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
-fix 2 all deform 1 x variable v_displace v_rate remap v
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">A</span> <span class="n">equal</span> <span class="mf">5.0</span>
+<span class="n">variable</span> <span class="n">Tp</span> <span class="n">equal</span> <span class="mf">10.0</span>
+<span class="n">variable</span> <span class="n">displace</span> <span class="n">equal</span> <span class="s2">"v_A * sin(2*PI * step*dt/v_Tp)"</span>
+<span class="n">variable</span> <span class="n">rate</span> <span class="n">equal</span> <span class="s2">"2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"</span>
+<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">deform</span> <span class="mi">1</span> <span class="n">x</span> <span class="n">variable</span> <span class="n">v_displace</span> <span class="n">v_rate</span> <span class="n">remap</span> <span class="n">v</span>
+</pre></div>
+</div>
<p>For the <em>scale</em>, <em>vel</em>, <em>erate</em>, <em>trate</em>, <em>volume</em>, <em>wiggle</em>, and
<em>variable</em> styles, the box length is expanded or compressed around its
mid point.</p>
@@ -413,9 +413,9 @@ to the shear direction (e.g. y box length for xy deformation) and
offset is the displacement distance in the shear direction (e.g. x
direction for xy deformation) from the unstrained orientation.</p>
<p>The tilt factor T as a function of time will change as</p>
-<pre class="literal-block">
-T(t) = T0 + L0*erate*dt
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">T</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">T0</span> <span class="o">+</span> <span class="n">L0</span><span class="o">*</span><span class="n">erate</span><span class="o">*</span><span class="n">dt</span>
+</pre></div>
+</div>
<p>where T0 is the initial tilt factor, L0 is the original length of the
box perpendicular to the shear direction (e.g. y box length for xy
deformation), and dt is the elapsed time (in time units). Thus if
@@ -441,9 +441,9 @@ where length is the box length perpendicular to the shear direction
distance in the shear direction (e.g. x direction for xy deformation)
from the unstrained orientation.</p>
<p>The tilt factor T as a function of time will change as</p>
-<pre class="literal-block">
-T(t) = T0 exp(trate*dt)
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">T</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">T0</span> <span class="n">exp</span><span class="p">(</span><span class="n">trate</span><span class="o">*</span><span class="n">dt</span><span class="p">)</span>
+</pre></div>
+</div>
<p>where T0 is the initial tilt factor and dt is the elapsed time (in
time units). Thus if <em>trate</em> R is specified as ln(1.1) and time units
are picoseconds, this means the shear strain or tilt factor will
@@ -464,9 +464,9 @@ parameter), then this effect on the shear strain is ignored.</p>
<p>The <em>wiggle</em> style oscillates the specified tilt factor sinusoidally
with the specified amplitude and period. I.e. the tilt factor T as a
function of time is given by</p>
-<pre class="literal-block">
-T(t) = T0 + A sin(2*pi t/Tp)
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">T</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">T0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">pi</span> <span class="n">t</span><span class="o">/</span><span class="n">Tp</span><span class="p">)</span>
+</pre></div>
+</div>
<p>where T0 is its initial value. If the amplitude A is a positive
number the tilt factor initially becomes more positive, then more
negative, etc. If A is negative then the tilt factor initially
@@ -492,13 +492,13 @@ arbitrary variable.</p>
<p>Here is an example of using the <em>variable</em> style to perform the same
box deformation as the <em>wiggle</em> style formula listed above, where we
assume that the current timestep = 0.</p>
-<pre class="literal-block">
-variable A equal 5.0
-variable Tp equal 10.0
-variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
-variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
-fix 2 all deform 1 xy variable v_displace v_rate remap v
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">A</span> <span class="n">equal</span> <span class="mf">5.0</span>
+<span class="n">variable</span> <span class="n">Tp</span> <span class="n">equal</span> <span class="mf">10.0</span>
+<span class="n">variable</span> <span class="n">displace</span> <span class="n">equal</span> <span class="s2">"v_A * sin(2*PI * step*dt/v_Tp)"</span>
+<span class="n">variable</span> <span class="n">rate</span> <span class="n">equal</span> <span class="s2">"2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"</span>
+<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">deform</span> <span class="mi">1</span> <span class="n">xy</span> <span class="n">variable</span> <span class="n">v_displace</span> <span class="n">v_rate</span> <span class="n">remap</span> <span class="n">v</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p>All of the tilt styles change the xy, xz, yz tilt factors during a
simulation. In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes
@@ -633,7 +633,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.</p>
diff --git a/doc/html/fix_deposit.html b/doc/html/fix_deposit.html
index 566b353255..6e7e0be54f 100644
--- a/doc/html/fix_deposit.html
+++ b/doc/html/fix_deposit.html
@@ -355,7 +355,9 @@ count is changing due to adding particles, you typically should use
the <a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify dynamic yes</span></a> command for the
temperature compute you are using.</p>
</div>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the state of the deposition to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. This includes information about how many
particles have been depositied, the random number generator seed, the
next timestep for deposition, etc. See the
diff --git a/doc/html/fix_drag.html b/doc/html/fix_drag.html
index 5864fe2ce5..c464c735a2 100644
--- a/doc/html/fix_drag.html
+++ b/doc/html/fix_drag.html
@@ -156,7 +156,9 @@ include that dimension in the distance calculation or force
application.</p>
<p>This command can be used to steer one or more atoms to a new location
in the simulation.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
diff --git a/doc/html/fix_drude_transform.html b/doc/html/fix_drude_transform.html
index 6a078677dc..7134e2dbf5 100644
--- a/doc/html/fix_drude_transform.html
+++ b/doc/html/fix_drude_transform.html
@@ -219,14 +219,14 @@ Nose-Hoover thermostating fixes. The <em>fix drude/transform/inverse</em>
command must appear after any Nose-Hoover thermostating fixes.</p>
</div>
<p>Example:</p>
-<pre class="literal-block">
-fix fDIRECT all drude/transform/direct
-fix fNVT gCORES nvt temp 300.0 300.0 100
-fix fNVT gDRUDES nvt temp 1.0 1.0 100
-fix fINVERSE all drude/transform/inverse
-compute TDRUDE all temp/drude
-thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">fDIRECT</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">direct</span>
+<span class="n">fix</span> <span class="n">fNVT</span> <span class="n">gCORES</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mi">100</span>
+<span class="n">fix</span> <span class="n">fNVT</span> <span class="n">gDRUDES</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mi">100</span>
+<span class="n">fix</span> <span class="n">fINVERSE</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">inverse</span>
+<span class="n">compute</span> <span class="n">TDRUDE</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">drude</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">cpu</span> <span class="n">etotal</span> <span class="n">ke</span> <span class="n">pe</span> <span class="n">ebond</span> <span class="n">ecoul</span> <span class="n">elong</span> <span class="n">press</span> <span class="n">vol</span> <span class="n">temp</span> <span class="n">c_TDRUDE</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_TDRUDE</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+</pre></div>
+</div>
<p>In this example, <em>gCORES</em> is the group of the atom cores and <em>gDRUDES</em>
is the group of the Drude particles (electrons). The centers of mass
of the Drude oscillators will be thermostated at 300.0 and the
@@ -240,14 +240,14 @@ the other one should be <em>nvt</em>. You must add a <em>compute temp/com</em> a
that of its group (the Drude cores) but the pressure be the overall
pressure <em>thermo_press</em>.</p>
<p>Example:</p>
-<pre class="literal-block">
-compute cTEMP_CORE gCORES temp/com
-fix fDIRECT all drude/transform/direct
-fix fNPT gCORES npt temp 298.0 298.0 100 iso 1.0 1.0 500
-fix_modify fNPT temp cTEMP_CORE press thermo_press
-fix fNVT gDRUDES nvt temp 5.0 5.0 100
-fix fINVERSE all drude/transform/inverse
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cTEMP_CORE</span> <span class="n">gCORES</span> <span class="n">temp</span><span class="o">/</span><span class="n">com</span>
+<span class="n">fix</span> <span class="n">fDIRECT</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">direct</span>
+<span class="n">fix</span> <span class="n">fNPT</span> <span class="n">gCORES</span> <span class="n">npt</span> <span class="n">temp</span> <span class="mf">298.0</span> <span class="mf">298.0</span> <span class="mi">100</span> <span class="n">iso</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mi">500</span>
+<span class="n">fix_modify</span> <span class="n">fNPT</span> <span class="n">temp</span> <span class="n">cTEMP_CORE</span> <span class="n">press</span> <span class="n">thermo_press</span>
+<span class="n">fix</span> <span class="n">fNVT</span> <span class="n">gDRUDES</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">5.0</span> <span class="mf">5.0</span> <span class="mi">100</span>
+<span class="n">fix</span> <span class="n">fINVERSE</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">inverse</span>
+</pre></div>
+</div>
<p>In this example, <em>gCORES</em> is the group of the atom cores and <em>gDRUDES</em>
is the group of the Drude particles. The centers of mass of the Drude
oscillators will be thermostated at 298.0 and the internal degrees of
@@ -259,8 +259,10 @@ to add a <em>fix momentum</em> command:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">fMOMENTUM</span> <span class="nb">all</span> <span class="n">momentum</span> <span class="mi">100</span> <span class="n">linear</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span>
</pre></div>
</div>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
</div>
<div class="section" id="restrictions">
diff --git a/doc/html/fix_efield.html b/doc/html/fix_efield.html
index 6ddd5f9067..c724217123 100644
--- a/doc/html/fix_efield.html
+++ b/doc/html/fix_efield.html
@@ -148,10 +148,10 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix kick external-field efield 1.0 0.0 0.0
-fix kick external-field efield 0.0 0.0 v_oscillate
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">kick</span> <span class="n">external</span><span class="o">-</span><span class="n">field</span> <span class="n">efield</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
+<span class="n">fix</span> <span class="n">kick</span> <span class="n">external</span><span class="o">-</span><span class="n">field</span> <span class="n">efield</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="n">v_oscillate</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -218,8 +218,10 @@ variable formulas, i.e. that -Grad(E) = F. For example, if the force
due to the electric field were a spring-like F = kx, then the energy
formula should be E = -0.5kx^2. If you don’t do this correctly, the
minimization will not converge properly.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the potential “energy” inferred by the added force due to
diff --git a/doc/html/fix_external.html b/doc/html/fix_external.html
index 264a4cf9ba..d2a176da50 100644
--- a/doc/html/fix_external.html
+++ b/doc/html/fix_external.html
@@ -167,9 +167,9 @@ in the group, once every <em>Napply</em> steps, similar to the way the <a class=
<em>Napply</em>, the force values produced by one callback will persist, and
be used multiple times to update atom forces.</p>
<p>The callback function “foo” is invoked by the fix as:</p>
-<pre class="literal-block">
-foo(void *ptr, bigint timestep, int nlocal, int *ids, double **x, double **fexternal);
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">foo</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="n">ptr</span><span class="p">,</span> <span class="n">bigint</span> <span class="n">timestep</span><span class="p">,</span> <span class="nb">int</span> <span class="n">nlocal</span><span class="p">,</span> <span class="nb">int</span> <span class="o">*</span><span class="n">ids</span><span class="p">,</span> <span class="n">double</span> <span class="o">**</span><span class="n">x</span><span class="p">,</span> <span class="n">double</span> <span class="o">**</span><span class="n">fexternal</span><span class="p">);</span>
+</pre></div>
+</div>
<p>The arguments are as follows:</p>
<ul class="simple">
<li>ptr = pointer provided by and simply passed back to external driver</li>
@@ -194,9 +194,9 @@ array. The fix adds these forces to each atom in the group, once
every <em>Napply</em> steps, similar to the way the <a class="reference internal" href="fix_addforce.html"><span class="doc">fix addforce</span></a> command works.</p>
<p>The name of the public force array provided by the FixExternal
class is</p>
-<pre class="literal-block">
-double **fexternal;
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">double</span> <span class="o">**</span><span class="n">fexternal</span><span class="p">;</span>
+</pre></div>
+</div>
<p>It is allocated by the FixExternal class as an (N,3) array where N is
the number of atoms owned by a processor. The 3 corresponds to the
fx, fy, fz components of force.</p>
@@ -212,16 +212,18 @@ to the added forces must also be set so as to be consistent with the
added forces. Otherwise the minimization will not converge correctly.</p>
<p>This can be done from the external driver by calling this public
method of the FixExternal class:</p>
-<pre class="literal-block">
-void set_energy(double eng);
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">void</span> <span class="n">set_energy</span><span class="p">(</span><span class="n">double</span> <span class="n">eng</span><span class="p">);</span>
+</pre></div>
+</div>
<p>where eng is the potential energy. Eng is an extensive quantity,
meaning it should be the sum over per-atom energies of all affected
atoms. It should also be provided in <a class="reference internal" href="units.html"><span class="doc">energy units</span></a>
consistent with the simulation. See the details below for how to
insure this energy setting is used appropriately in a minimization.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the potential “energy” set by the external driver to the
diff --git a/doc/html/fix_gcmc.html b/doc/html/fix_gcmc.html
index 2210a5c5c4..02f1da98e6 100644
--- a/doc/html/fix_gcmc.html
+++ b/doc/html/fix_gcmc.html
@@ -168,11 +168,11 @@ keyword = <em>mol</em>, <em>region</em>, <em>maxangle</em>, <em>pressure</em>, <
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
-fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
-fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">2</span> <span class="n">gas</span> <span class="n">gcmc</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="mi">1000</span> <span class="mi">2</span> <span class="mi">29494</span> <span class="mf">298.0</span> <span class="o">-</span><span class="mf">0.5</span> <span class="mf">0.01</span>
+<span class="n">fix</span> <span class="mi">3</span> <span class="n">water</span> <span class="n">gcmc</span> <span class="mi">10</span> <span class="mi">100</span> <span class="mi">100</span> <span class="mi">0</span> <span class="mi">3456543</span> <span class="mf">3.0</span> <span class="o">-</span><span class="mf">2.5</span> <span class="mf">0.1</span> <span class="n">mol</span> <span class="n">my_one_water</span> <span class="n">maxangle</span> <span class="mi">180</span> <span class="n">full_energy</span>
+<span class="n">fix</span> <span class="mi">4</span> <span class="n">my_gas</span> <span class="n">gcmc</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mi">10</span> <span class="mi">1</span> <span class="mi">123456543</span> <span class="mf">300.0</span> <span class="o">-</span><span class="mf">12.5</span> <span class="mf">1.0</span> <span class="n">region</span> <span class="n">disk</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -239,12 +239,12 @@ used in fix nvt. Otherwise, the imaginary reservoir
will not be in thermal equilibrium with the simulation cell. Also,
it is important that the temperature used by fix nvt be dynamic,
which can be achieved as follows:</p>
-<pre class="literal-block">
-compute mdtemp mdatoms temp
-compute_modify mdtemp dynamic yes
-fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
-fix_modify mdnvt temp mdtemp
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">mdtemp</span> <span class="n">mdatoms</span> <span class="n">temp</span>
+<span class="n">compute_modify</span> <span class="n">mdtemp</span> <span class="n">dynamic</span> <span class="n">yes</span>
+<span class="n">fix</span> <span class="n">mdnvt</span> <span class="n">mdatoms</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">10.0</span>
+<span class="n">fix_modify</span> <span class="n">mdnvt</span> <span class="n">temp</span> <span class="n">mdtemp</span>
+</pre></div>
+</div>
<p>Note that neighbor lists are re-built every timestep that this fix is
invoked, so you should not set N to be too small. However, periodic
rebuilds are necessary in order to avoid dangerous rebuilds and missed
@@ -363,9 +363,9 @@ therefore, you will want to use the
<a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a> command to insure that the
current number of atoms is used as a normalizing factor each time
temperature is computed. Here is the necessary command:</p>
-<pre class="literal-block">
-compute_modify thermo_temp dynamic yes
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute_modify</span> <span class="n">thermo_temp</span> <span class="n">dynamic</span> <span class="n">yes</span>
+</pre></div>
+</div>
<p>If LJ units are used, note that a value of 0.18292026 is used by this
fix as the reduced value for Planck’s constant. This value was
derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 *
@@ -375,7 +375,9 @@ mass = 39.948 amu.</p>
of the group-ID value. The <em>grouptype</em> keyword assigns all
inserted atoms of the specified type to the <a class="reference internal" href="group.html"><span class="doc">group</span></a>
of the group-ID value.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the state of the fix to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. This includes information about the random
number generator seed, the next timestep for MC exchanges, etc. See
the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to
diff --git a/doc/html/fix_gle.html b/doc/html/fix_gle.html
index e51ed41bf3..9f9296aea3 100644
--- a/doc/html/fix_gle.html
+++ b/doc/html/fix_gle.html
@@ -145,7 +145,7 @@
<dd><p class="first"><em>noneq</em> Cmatrix = file to read the non-equilibrium covariance matrix from
<em>every</em> stride = apply the GLE once every time steps. Reduces the accuracy</p>
<blockquote class="last">
-<div>of the integration of the GLE, but has *no effect* on the accuracy of equilibrium
+<div>of the integration of the GLE, but has <em>no effect</em> on the accuracy of equilibrium
sampling. It might change sampling properties when used together with <em>noneq</em>.</div></blockquote>
</dd>
</dl>
@@ -207,7 +207,9 @@ Prony series form of the memory kernel used by GLD into an appropriate
input matrix for <a class="reference internal" href="#"><span class="doc">fix gle</span></a>. While the GLE scheme is more
general, the form used by <a class="reference internal" href="fix_gld.html"><span class="doc">fix gld</span></a> can be more directly
related to the representation of an implicit solvent environment.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>The instantaneous values of the extended variables are written to
<a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. Because the state of the random
number generator is not saved in restart files, this means you cannot
diff --git a/doc/html/fix_gravity.html b/doc/html/fix_gravity.html
index f10e0f3416..e770f8e7fe 100644
--- a/doc/html/fix_gravity.html
+++ b/doc/html/fix_gravity.html
@@ -156,13 +156,13 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 1 all gravity 1.0 chute 24.0
-fix 1 all gravity v_increase chute 24.0
-fix 1 all gravity 1.0 spherical 0.0 -180.0
-fix 1 all gravity 10.0 spherical v_phi v_theta
-fix 1 all gravity 100.0 vector 1 1 0
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gravity</span> <span class="mf">1.0</span> <span class="n">chute</span> <span class="mf">24.0</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gravity</span> <span class="n">v_increase</span> <span class="n">chute</span> <span class="mf">24.0</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gravity</span> <span class="mf">1.0</span> <span class="n">spherical</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">180.0</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gravity</span> <span class="mf">10.0</span> <span class="n">spherical</span> <span class="n">v_phi</span> <span class="n">v_theta</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gravity</span> <span class="mf">100.0</span> <span class="n">vector</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">0</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -220,8 +220,10 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the gravitational potential energy of the system to the
diff --git a/doc/html/fix_heat.html b/doc/html/fix_heat.html
index 2e88845d31..fb5b0f55e7 100644
--- a/doc/html/fix_heat.html
+++ b/doc/html/fix_heat.html
@@ -147,11 +147,11 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 3 qin heat 1 1.0
-fix 3 qin heat 10 v_flux
-fix 4 qout heat 1 -1.0 region top
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">3</span> <span class="n">qin</span> <span class="n">heat</span> <span class="mi">1</span> <span class="mf">1.0</span>
+<span class="n">fix</span> <span class="mi">3</span> <span class="n">qin</span> <span class="n">heat</span> <span class="mi">10</span> <span class="n">v_flux</span>
+<span class="n">fix</span> <span class="mi">4</span> <span class="n">qout</span> <span class="n">heat</span> <span class="mi">1</span> <span class="o">-</span><span class="mf">1.0</span> <span class="n">region</span> <span class="n">top</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -219,7 +219,9 @@ their velocities. Thus you must still use an integration fix
(e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>) on the affected atoms. This fix should
not normally be used on atoms that have their temperature controlled
by another fix - e.g. <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> fix.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix computes a global scalar which can be accessed by various
diff --git a/doc/html/fix_imd.html b/doc/html/fix_imd.html
index 3245c8523d..5c92083e88 100644
--- a/doc/html/fix_imd.html
+++ b/doc/html/fix_imd.html
@@ -237,7 +237,9 @@ they were real objects. See the <a class="reference external" href="http://www.k
<p>If IMD control messages are received, a line of text describing the
message and its effect will be printed to the LAMMPS output screen, if
screen output is active.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
diff --git a/doc/html/fix_ipi.html b/doc/html/fix_ipi.html
index 40917601b7..615515d668 100644
--- a/doc/html/fix_ipi.html
+++ b/doc/html/fix_ipi.html
@@ -173,7 +173,9 @@ configurations make sense. It is assumed that the species in the i-PI
input are listed in the same order as in the data file of LAMMPS. The
initial configuration is ignored, as it will be substituted with the
coordinates received from i-PI before forces are ever evaluated.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>There is no restart information associated with this fix, since all
the dynamical parameters are dealt with by i-PI.</p>
</div>
diff --git a/doc/html/fix_langevin.html b/doc/html/fix_langevin.html
index bf67a0e983..40cfbcd9cc 100644
--- a/doc/html/fix_langevin.html
+++ b/doc/html/fix_langevin.html
@@ -375,8 +375,10 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. Because the state of the random number generator
is not saved in restart files, this means you cannot do “exact”
restarts with this fix, where the simulation continues on the same as
diff --git a/doc/html/fix_langevin_eff.html b/doc/html/fix_langevin_eff.html
index dea014ff7b..506e61e35c 100644
--- a/doc/html/fix_langevin_eff.html
+++ b/doc/html/fix_langevin_eff.html
@@ -178,7 +178,9 @@ interactions (<a class="reference internal" href="pair_style.html"><span class="
<p>The operation of this fix is exactly like that described by the <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> command, except that the thermostatting
is also applied to the radial electron velocity for electron
particles.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. Because the state of the random number generator
is not saved in restart files, this means you cannot do “exact”
restarts with this fix, where the simulation continues on the same as
diff --git a/doc/html/fix_lb_momentum.html b/doc/html/fix_lb_momentum.html
index 5ca4e990b6..aefe19517d 100644
--- a/doc/html/fix_lb_momentum.html
+++ b/doc/html/fix_lb_momentum.html
@@ -167,7 +167,9 @@ and the fluid velocities at each lattice site.</p>
be changed by specifying the keyword <em>linear</em>, along with a set of
three flags set to 0/1 in order to exclude/ include the corresponding
dimension.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can be
diff --git a/doc/html/fix_lb_pc.html b/doc/html/fix_lb_pc.html
index 8d27f6cd24..8a5281c6c3 100644
--- a/doc/html/fix_lb_pc.html
+++ b/doc/html/fix_lb_pc.html
@@ -149,7 +149,9 @@ described by <em>group-ID</em>, experiencing velocity-dependent hydrodynamic
forces, using the integration algorithm described in <a class="reference internal" href="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a>. This integration algorithm should only be used if a
user-specified value for the force-coupling constant used in <a class="reference internal" href="fix_lb_fluid.html"><span class="doc">fix lb/fluid</span></a> has been set; do not use this integration
algorithm if the force coupling constant has been set by default.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can be
diff --git a/doc/html/fix_lb_rigid_pc_sphere.html b/doc/html/fix_lb_rigid_pc_sphere.html
index 8bda0b4a82..ca3adc0748 100644
--- a/doc/html/fix_lb_rigid_pc_sphere.html
+++ b/doc/html/fix_lb_rigid_pc_sphere.html
@@ -202,7 +202,9 @@ central atoms interact with one another.</p>
the rigid fix (although it includes fewer optional arguments, and
assumes the constituent atoms are point particles); see
<a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> for a complete documentation.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about the <em>rigid</em> and <em>rigid/nve</em> fixes are written to
<a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>Similar to the <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> command: The rigid
diff --git a/doc/html/fix_lb_viscous.html b/doc/html/fix_lb_viscous.html
index 876c9eb1f0..efc00565c9 100644
--- a/doc/html/fix_lb_viscous.html
+++ b/doc/html/fix_lb_viscous.html
@@ -164,8 +164,10 @@ hydrodynamic forces to the particles.</p>
test runs, see <a class="reference internal" href="#mackay"><span class="std std-ref">Mackay et al.</span></a>. Please include a citation to
this paper if this fix is used in work contributing to published
research.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>As described in the <a class="reference internal" href="fix_viscous.html"><span class="doc">fix viscous</span></a> documentation:</p>
<p>“No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
diff --git a/doc/html/fix_lineforce.html b/doc/html/fix_lineforce.html
index 2734d0ff4e..5ca8460a42 100644
--- a/doc/html/fix_lineforce.html
+++ b/doc/html/fix_lineforce.html
@@ -151,7 +151,9 @@ remains. This is done by subtracting out components of force in the
plane perpendicular to the line.</p>
<p>If the initial velocity of the atom is 0.0 (or along the line), then
it should continue to move along the line thereafter.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
diff --git a/doc/html/fix_move.html b/doc/html/fix_move.html
index ad7177b2bd..66cf61d80e 100644
--- a/doc/html/fix_move.html
+++ b/doc/html/fix_move.html
@@ -160,11 +160,11 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
-fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
-fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="n">boundary</span> <span class="n">move</span> <span class="n">wiggle</span> <span class="mf">3.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="n">units</span> <span class="n">box</span>
+<span class="n">fix</span> <span class="mi">2</span> <span class="n">boundary</span> <span class="n">move</span> <span class="n">rotate</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="mf">5.0</span>
+<span class="n">fix</span> <span class="mi">2</span> <span class="n">boundary</span> <span class="n">move</span> <span class="n">variable</span> <span class="n">v_myx</span> <span class="n">v_myy</span> <span class="n">NULL</span> <span class="n">v_VX</span> <span class="n">v_VY</span> <span class="n">NULL</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -202,9 +202,9 @@ command.</p>
<p>The <em>linear</em> style moves atoms at a constant velocity, so that their
position <em>X</em> = (x,y,z) as a function of time is given in vector
notation as</p>
-<pre class="literal-block">
-X(t) = X0 + V * delta
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">X</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">X0</span> <span class="o">+</span> <span class="n">V</span> <span class="o">*</span> <span class="n">delta</span>
+</pre></div>
+</div>
<p>where <em>X0</em> = (x0,y0,z0) is their position at the time the fix is
specified, <em>V</em> is the specified velocity vector with components
(Vx,Vy,Vz), and <em>delta</em> is the time elapsed since the fix was
@@ -216,17 +216,17 @@ the corresponding force component on the atom.</p>
<p>Note that the <em>linear</em> style is identical to using the <em>variable</em>
style with an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> that uses the
vdisplace() function. E.g.</p>
-<pre class="literal-block">
-variable V equal 10.0
+<div class="highlight-default"><div class="highlight"><pre><span></span>variable V equal 10.0
variable x equal vdisplace(0.0,$V)
fix 1 boundary move variable v_x NULL NULL v_V NULL NULL
-</pre>
+</pre></div>
+</div>
<p>The <em>wiggle</em> style moves atoms in an oscillatory fashion, so that
their position <em>X</em> = (x,y,z) as a function of time is given in vector
notation as</p>
-<pre class="literal-block">
-X(t) = X0 + A sin(omega*delta)
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">X</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">X0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">)</span>
+</pre></div>
+</div>
<p>where <em>X0</em> = (x0,y0,z0) is their position at the time the fix is
specified, <em>A</em> is the specified amplitude vector with components
(Ax,Ay,Az), <em>omega</em> is 2 PI / <em>period</em>, and <em>delta</em> is the time
@@ -239,14 +239,14 @@ corresponding force component on the atom.</p>
<p>Note that the <em>wiggle</em> style is identical to using the <em>variable</em>
style with <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a> that use the
swiggle() and cwiggle() functions. E.g.</p>
-<pre class="literal-block">
-variable A equal 10.0
+<div class="highlight-default"><div class="highlight"><pre><span></span>variable A equal 10.0
variable T equal 5.0
variable omega equal 2.0*PI/$T
variable x equal swiggle(0.0,$A,$T)
variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
fix 1 boundary move variable v_x NULL NULL v_v NULL NULL
-</pre>
+</pre></div>
+</div>
<p>The <em>rotate</em> style rotates atoms around a rotation axis <em>R</em> =
(Rx,Ry,Rz) that goes thru a point <em>P</em> = (Px,Py,Pz). The <em>period</em> of
the rotation is also specified. The direction of rotation for the
@@ -302,8 +302,10 @@ are in lattice spacings. The <a class="reference internal" href="lattice.html">
been previously used to define the lattice spacing. Each of these 3
quantities may be dependent on the x,y,z dimension, since the lattice
spacings can be different in x,y,z.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the original coordinates of moving atoms to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, as well as the initial timestep, so that
the motion can be continuous in a restarted simulation. See the
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify
diff --git a/doc/html/fix_msst.html b/doc/html/fix_msst.html
index c54106e01e..f5a8d09ba8 100644
--- a/doc/html/fix_msst.html
+++ b/doc/html/fix_msst.html
@@ -197,14 +197,16 @@ LAMMPS, but are not implemented for MSST.</p>
<p>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style “temp” and “pressure”,
as if these commands had been issued:</p>
-<pre class="literal-block">
-compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
+<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
+</pre></div>
+</div>
<p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
+ underscore + “press”. The group for the new computes is “all”.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the state of all internal variables to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command
for info on how to re-specify a fix in an input script that reads a
restart file, so that the operation of the fix continues in an
@@ -228,15 +230,15 @@ equations. See also <a class="reference internal" href="thermo_style.html"><span
</ol>
<p>To print these quantities to the log file with descriptive column
headers, the following LAMMPS commands are suggested:</p>
-<pre class="literal-block">
-fix msst all msst z
-fix_modify msst energy yes
-variable dhug equal f_msst[1]
-variable dray equal f_msst[2]
-variable lgr_vel equal f_msst[3]
-variable lgr_pos equal f_msst[4]
-thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">msst</span> <span class="nb">all</span> <span class="n">msst</span> <span class="n">z</span>
+<span class="n">fix_modify</span> <span class="n">msst</span> <span class="n">energy</span> <span class="n">yes</span>
+<span class="n">variable</span> <span class="n">dhug</span> <span class="n">equal</span> <span class="n">f_msst</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+<span class="n">variable</span> <span class="n">dray</span> <span class="n">equal</span> <span class="n">f_msst</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+<span class="n">variable</span> <span class="n">lgr_vel</span> <span class="n">equal</span> <span class="n">f_msst</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
+<span class="n">variable</span> <span class="n">lgr_pos</span> <span class="n">equal</span> <span class="n">f_msst</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">ke</span> <span class="n">pe</span> <span class="n">lz</span> <span class="n">pzz</span> <span class="n">etotal</span> <span class="n">v_dhug</span> <span class="n">v_dray</span> <span class="n">v_lgr_vel</span> <span class="n">v_lgr_pos</span> <span class="n">f_msst</span>
+</pre></div>
+</div>
<p>These fixes compute a global scalar and a global vector of 4
quantities, which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The scalar values calculated
by this fix are “extensive”; the vector values are “intensive”.</p>
diff --git a/doc/html/fix_neb.html b/doc/html/fix_neb.html
index 1e50f393e0..4b5777e1e2 100644
--- a/doc/html/fix_neb.html
+++ b/doc/html/fix_neb.html
@@ -190,7 +190,9 @@ forces on atoms in this replica are described in the
</div>
<p>The inter-replica forces for the other replicas are unchanged from the
first equation.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
diff --git a/doc/html/fix_nh_eff.html b/doc/html/fix_nh_eff.html
index d11bbb105e..5e8d66853c 100644
--- a/doc/html/fix_nh_eff.html
+++ b/doc/html/fix_nh_eff.html
@@ -134,9 +134,9 @@
<h1>fix nph/eff command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-fix ID group-ID style_name keyword value ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style_name</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>style_name = <em>nvt/eff</em> or <em>npt/eff</em> or <em>nph/eff</em></li>
@@ -223,7 +223,9 @@ degrees of freedom with the <a class="reference internal" href="velocity.html"><
the user must allow for these degrees of freedom to equilibrate
(i.e. equi-partitioning of energy) through time integration.</p>
</div>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>See the doc page for the <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt, npt, and nph</span></a> commands
for details.</p>
</div>
diff --git a/doc/html/fix_nph_asphere.html b/doc/html/fix_nph_asphere.html
index 2c2d1a4d0a..d7c91846db 100644
--- a/doc/html/fix_nph_asphere.html
+++ b/doc/html/fix_nph_asphere.html
@@ -175,10 +175,10 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
<p>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style “temp/asphere” and
“pressure”, as if these commands had been issued:</p>
-<pre class="literal-block">
-compute fix-ID_temp all temp/asphere
-compute fix-ID_press all pressure fix-ID_temp
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">asphere</span>
+<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
+</pre></div>
+</div>
<p>See the <a class="reference internal" href="compute_temp_asphere.html"><span class="doc">compute temp/asphere</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
+ underscore + “press”, and the group for the new computes is “all”
@@ -207,7 +207,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the state of the Nose/Hoover barostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nph_sphere.html b/doc/html/fix_nph_sphere.html
index ec7a15a0cd..0529dba9db 100644
--- a/doc/html/fix_nph_sphere.html
+++ b/doc/html/fix_nph_sphere.html
@@ -175,10 +175,10 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
<p>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style “temp/sphere” and
“pressure”, as if these commands had been issued:</p>
-<pre class="literal-block">
-compute fix-ID_temp all temp/sphere
-compute fix-ID_press all pressure fix-ID_temp
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">sphere</span>
+<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
+</pre></div>
+</div>
<p>See the <a class="reference internal" href="compute_temp_sphere.html"><span class="doc">compute temp/sphere</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
+ underscore + “press”, and the group for the new computes is “all”
@@ -207,7 +207,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the state of the Nose/Hoover barostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_npt_asphere.html b/doc/html/fix_npt_asphere.html
index 2216a34678..203bb248e0 100644
--- a/doc/html/fix_npt_asphere.html
+++ b/doc/html/fix_npt_asphere.html
@@ -182,10 +182,10 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
<p>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style “temp/asphere” and
“pressure”, as if these commands had been issued:</p>
-<pre class="literal-block">
-compute fix-ID_temp all temp/asphere
-compute fix-ID_press all pressure fix-ID_temp
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">asphere</span>
+<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
+</pre></div>
+</div>
<p>See the <a class="reference internal" href="compute_temp_asphere.html"><span class="doc">compute temp/asphere</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
+ underscore + “press”, and the group for the new computes is “all”
@@ -227,7 +227,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the state of the Nose/Hoover thermostat and barostat
to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify
diff --git a/doc/html/fix_npt_body.html b/doc/html/fix_npt_body.html
index b037898463..7a21169513 100644
--- a/doc/html/fix_npt_body.html
+++ b/doc/html/fix_npt_body.html
@@ -179,10 +179,10 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
<p>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style “temp/body” and
“pressure”, as if these commands had been issued:</p>
-<pre class="literal-block">
-compute fix-ID_temp all temp/body
-compute fix-ID_press all pressure fix-ID_temp
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">body</span>
+<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
+</pre></div>
+</div>
<p>See the <a class="reference internal" href="compute_temp_body.html"><span class="doc">compute temp/body</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
+ underscore + “press”, and the group for the new computes is “all”
@@ -224,7 +224,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the state of the Nose/Hoover thermostat and barostat
to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify
diff --git a/doc/html/fix_npt_sphere.html b/doc/html/fix_npt_sphere.html
index f05e786221..1d5d6ed867 100644
--- a/doc/html/fix_npt_sphere.html
+++ b/doc/html/fix_npt_sphere.html
@@ -181,10 +181,10 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
<p>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style “temp/sphere” and
“pressure”, as if these commands had been issued:</p>
-<pre class="literal-block">
-compute fix-ID_temp all temp/sphere
-compute fix-ID_press all pressure fix-ID_temp
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">sphere</span>
+<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
+</pre></div>
+</div>
<p>See the <a class="reference internal" href="compute_temp_sphere.html"><span class="doc">compute temp/sphere</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
+ underscore + “press”, and the group for the new computes is “all”
@@ -226,7 +226,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the state of the Nose/Hoover thermostat and barostat
to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify
diff --git a/doc/html/fix_nve_asphere.html b/doc/html/fix_nve_asphere.html
index 88dbabd521..435fea89b4 100644
--- a/doc/html/fix_nve_asphere.html
+++ b/doc/html/fix_nve_asphere.html
@@ -153,7 +153,9 @@ group each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.</p>
<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
assumes point particles and only updates their position and velocity.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
diff --git a/doc/html/fix_nve_asphere_noforce.html b/doc/html/fix_nve_asphere_noforce.html
index dd98e2ce40..75760b0c6a 100644
--- a/doc/html/fix_nve_asphere_noforce.html
+++ b/doc/html/fix_nve_asphere_noforce.html
@@ -150,8 +150,10 @@ angularm momenta are used to update their positions and orientation.</p>
<p>This is useful as an implicit time integrator for Fast Lubrication
Dynamics, since the velocity and angular momentum are updated by the
<a class="reference external" href="pair_lubricateU.txt">pair_style lubricuteU</a> command.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
diff --git a/doc/html/fix_nve_body.html b/doc/html/fix_nve_body.html
index 45816df757..cd459a4379 100644
--- a/doc/html/fix_nve_body.html
+++ b/doc/html/fix_nve_body.html
@@ -151,7 +151,9 @@ consistent with the microcanonical ensemble. See <a class="reference internal"
doc page for more details on using body particles.</p>
<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
assumes point particles and only updates their position and velocity.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
diff --git a/doc/html/fix_nve_line.html b/doc/html/fix_nve_line.html
index 5b6a9bb8ab..5168b08db0 100644
--- a/doc/html/fix_nve_line.html
+++ b/doc/html/fix_nve_line.html
@@ -152,7 +152,9 @@ trajectory consistent with the microcanonical ensemble. See
using line segment particles.</p>
<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
assumes point particles and only updates their position and velocity.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
diff --git a/doc/html/fix_nve_manifold_rattle.html b/doc/html/fix_nve_manifold_rattle.html
index 149e6de046..06d68cd6ae 100644
--- a/doc/html/fix_nve_manifold_rattle.html
+++ b/doc/html/fix_nve_manifold_rattle.html
@@ -159,7 +159,7 @@ keyword = <em>every</em>
atoms constrained to a curved surface (manifold) in the group each
timestep. The constraint is handled by RATTLE <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a>
written out for the special case of single-particle constraints as
-explained in <a class="reference internal" href="#paquay"><span class="std std-ref">(Paquay)</span></a>. V is volume; E is energy. This way,
+explained in <a class="reference internal" href="manifolds.html#paquay"><span class="std std-ref">(Paquay)</span></a>. V is volume; E is energy. This way,
the dynamics of particles constrained to curved surfaces can be
studied. If combined with <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, this
generates Brownian motion of particles constrained to a curved
@@ -172,18 +172,20 @@ manifolds this can be achieved with <em>region</em> and <em>create_atoms</em>
commands, but for more complex surfaces it might be more useful to
write a script.</p>
<p>The manifold args may be equal-style variables, like so:</p>
-<pre class="literal-block">
-variable R equal "ramp(5.0,3.0)"
-fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">R</span> <span class="n">equal</span> <span class="s2">"ramp(5.0,3.0)"</span>
+<span class="n">fix</span> <span class="n">shrink_sphere</span> <span class="nb">all</span> <span class="n">nve</span><span class="o">/</span><span class="n">manifold</span><span class="o">/</span><span class="n">rattle</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">4</span> <span class="mi">10</span> <span class="n">sphere</span> <span class="n">v_R</span>
+</pre></div>
+</div>
<p>In this case, the manifold parameter will change in time according to
the variable. This is not a problem for the time integrator as long
as the change of the manifold is slow with respect to the dynamics of
the particles. Note that if the manifold has to exert work on the
particles because of these changes, the total energy might not be
conserved.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
diff --git a/doc/html/fix_nve_sphere.html b/doc/html/fix_nve_sphere.html
index 2a70998598..e0e8bf5189 100644
--- a/doc/html/fix_nve_sphere.html
+++ b/doc/html/fix_nve_sphere.html
@@ -189,8 +189,10 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
diff --git a/doc/html/fix_nve_tri.html b/doc/html/fix_nve_tri.html
index 1462555ef2..e707401c30 100644
--- a/doc/html/fix_nve_tri.html
+++ b/doc/html/fix_nve_tri.html
@@ -152,7 +152,9 @@ trajectory consistent with the microcanonical ensemble. See
using triangular particles.</p>
<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
assumes point particles and only updates their position and velocity.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
diff --git a/doc/html/fix_nvt_asphere.html b/doc/html/fix_nvt_asphere.html
index 473db13d7f..08a1bea12b 100644
--- a/doc/html/fix_nvt_asphere.html
+++ b/doc/html/fix_nvt_asphere.html
@@ -169,9 +169,9 @@ keywords.</p>
<p>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style “temp/asphere”, as if this command
had been issued:</p>
-<pre class="literal-block">
-compute fix-ID_temp group-ID temp/asphere
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span><span class="o">/</span><span class="n">asphere</span>
+</pre></div>
+</div>
<p>See the <a class="reference internal" href="compute_temp_asphere.html"><span class="doc">compute temp/asphere</span></a> command for
details. Note that the ID of the new compute is the fix-ID +
underscore + “temp”, and the group for the new compute is the same as
@@ -213,7 +213,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nvt_body.html b/doc/html/fix_nvt_body.html
index 57ba66659d..9fecb55fc4 100644
--- a/doc/html/fix_nvt_body.html
+++ b/doc/html/fix_nvt_body.html
@@ -166,9 +166,9 @@ keywords.</p>
<p>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style “temp/body”, as if this command
had been issued:</p>
-<pre class="literal-block">
-compute fix-ID_temp group-ID temp/body
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span><span class="o">/</span><span class="n">body</span>
+</pre></div>
+</div>
<p>See the <a class="reference internal" href="compute_temp_body.html"><span class="doc">compute temp/body</span></a> command for
details. Note that the ID of the new compute is the fix-ID +
underscore + “temp”, and the group for the new compute is the same as
@@ -210,7 +210,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nvt_sllod.html b/doc/html/fix_nvt_sllod.html
index 09875bceb8..a2592ab7e7 100644
--- a/doc/html/fix_nvt_sllod.html
+++ b/doc/html/fix_nvt_sllod.html
@@ -194,9 +194,9 @@ keywords.</p>
<p>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style “temp/deform”, as if this command had
been issued:</p>
-<pre class="literal-block">
-compute fix-ID_temp group-ID temp/deform
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span><span class="o">/</span><span class="n">deform</span>
+</pre></div>
+</div>
<p>See the <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a> command for
details. Note that the ID of the new compute is the fix-ID +
underscore + “temp”, and the group for the new compute is the same as
@@ -238,7 +238,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nvt_sllod_eff.html b/doc/html/fix_nvt_sllod_eff.html
index c175a68bdc..8492983e42 100644
--- a/doc/html/fix_nvt_sllod_eff.html
+++ b/doc/html/fix_nvt_sllod_eff.html
@@ -157,7 +157,9 @@ creates (as discussed in the <a class="reference internal" href="fix_nh.html"><s
page), is performed with a <a class="reference internal" href="compute_temp_deform_eff.html"><span class="doc">compute temp/deform/eff</span></a> commmand that includes
the eFF contribution to the temperature from the electron radial
velocity.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nvt_sphere.html b/doc/html/fix_nvt_sphere.html
index 6a27b967ed..fc5b3ddab1 100644
--- a/doc/html/fix_nvt_sphere.html
+++ b/doc/html/fix_nvt_sphere.html
@@ -169,9 +169,9 @@ keywords.</p>
<p>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style “temp/sphere”, as if this command
had been issued:</p>
-<pre class="literal-block">
-compute fix-ID_temp group-ID temp/sphere
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span><span class="o">/</span><span class="n">sphere</span>
+</pre></div>
+</div>
<p>See the <a class="reference internal" href="compute_temp_sphere.html"><span class="doc">compute temp/sphere</span></a> command for
details. Note that the ID of the new compute is the fix-ID +
underscore + “temp”, and the group for the new compute is the same as
@@ -213,7 +213,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_phonon.html b/doc/html/fix_phonon.html
index 3094e830ae..40d369afee 100644
--- a/doc/html/fix_phonon.html
+++ b/doc/html/fix_phonon.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix phonon command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-fix ID group-ID phonon N Noutput Nwait map_file prefix keyword values ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">phonon</span> <span class="n">N</span> <span class="n">Noutput</span> <span class="n">Nwait</span> <span class="n">map_file</span> <span class="n">prefix</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>phonon = style name of this fix command</li>
@@ -239,7 +239,9 @@ even degrade the performance of lammps in case the unit cell is too large.</p>
<a class="reference internal" href="units.html"><span class="doc">energy/distance^2/mass</span></a> units. The coordinates for <em>q</em>
points in the log file is in the units of the basis vectors of the
corresponding reciprocal lattice.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> option is supported by this
fix. You can use it to change the temperature compute from thermo_temp
diff --git a/doc/html/fix_pour.html b/doc/html/fix_pour.html
index ee3f050be4..ca471ec2c3 100644
--- a/doc/html/fix_pour.html
+++ b/doc/html/fix_pour.html
@@ -316,8 +316,10 @@ can prevent particles from being inserted. The <em>ignore</em> keyword
causes the overlap check to skip any line or triangle particles.
Obviously you should only use it if there is in fact no overlap of the
line or triangle particles with the insertion region.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. This means you must be careful when restarting a
pouring simulation, when the restart file was written in the middle of
the pouring operation. Specifically, you should use a new fix pour
diff --git a/doc/html/fix_qeq.html b/doc/html/fix_qeq.html
index 05e428f671..addd4b9ecf 100644
--- a/doc/html/fix_qeq.html
+++ b/doc/html/fix_qeq.html
@@ -162,13 +162,13 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
-fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
-fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2
-fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
-fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qeq</span><span class="o">/</span><span class="n">point</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mf">1.0e-6</span> <span class="mi">200</span> <span class="n">param</span><span class="o">.</span><span class="n">qeq1</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="n">qeq</span> <span class="n">qeq</span><span class="o">/</span><span class="n">shielded</span> <span class="mi">1</span> <span class="mi">8</span> <span class="mf">1.0e-6</span> <span class="mi">100</span> <span class="n">param</span><span class="o">.</span><span class="n">qeq2</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qeq</span><span class="o">/</span><span class="n">slater</span> <span class="mi">5</span> <span class="mi">10</span> <span class="mf">1.0e-6</span> <span class="mi">100</span> <span class="n">params</span> <span class="n">alpha</span> <span class="mf">0.2</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="n">qeq</span> <span class="n">qeq</span><span class="o">/</span><span class="n">dynamic</span> <span class="mi">1</span> <span class="mi">12</span> <span class="mf">1.0e-3</span> <span class="mi">100</span> <span class="n">my_qeq</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qeq</span><span class="o">/</span><span class="n">fire</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mf">1.0e-3</span> <span class="mi">100</span> <span class="n">my_qeq</span> <span class="n">qdamp</span> <span class="mf">0.2</span> <span class="n">qstep</span> <span class="mf">0.1</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -292,7 +292,9 @@ non-trivial. Charges on atoms are not guaranteed to equilibrate with
arbitrary choices of these parameters. We do not develop these QEq
paramters. See the examples/qeq directory for some examples.</p>
</div>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about these fixes is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. No global scalar or vector or per-atom
quantities are stored by these fixes for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of these fixes
can be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a>
diff --git a/doc/html/fix_qeq_comb.html b/doc/html/fix_qeq_comb.html
index 3bf7a12a5c..c7382d021d 100644
--- a/doc/html/fix_qeq_comb.html
+++ b/doc/html/fix_qeq_comb.html
@@ -195,8 +195,10 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
diff --git a/doc/html/fix_qeq_reax.html b/doc/html/fix_qeq_reax.html
index 665de2e845..cc02c2516a 100644
--- a/doc/html/fix_qeq_reax.html
+++ b/doc/html/fix_qeq_reax.html
@@ -180,7 +180,9 @@ exponent. Note that these 3 quantities are also in the ReaxFF
potential file, except that eta is defined here as twice the eta value
in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
of this fix are hard-coded to be A, eV, and electronic charge.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. No global scalar or vector or per-atom
quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.</p>
diff --git a/doc/html/fix_qmmm.html b/doc/html/fix_qmmm.html
index fa8cf47576..1adbcf6567 100644
--- a/doc/html/fix_qmmm.html
+++ b/doc/html/fix_qmmm.html
@@ -156,7 +156,9 @@ other QM codes. This will allow the LAMMPS side of the implementation
to be adapted if necessary before being finalized.</p>
<p>Details about how to use this fix are currently documented in the
description of the QM/MM interface code itself in lib/qmmm/README.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
diff --git a/doc/html/fix_qtb.html b/doc/html/fix_qtb.html
index cffd9b2764..2f8934ddd0 100644
--- a/doc/html/fix_qtb.html
+++ b/doc/html/fix_qtb.html
@@ -147,12 +147,12 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 1 all nve
-fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100 (liquid methane modeled with the REAX force field, real units)
-fix 2 all nph iso 1.01325 1.01325 1
-fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100 (quartz modeled with the BKS force field, metal units)
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nve</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qtb</span> <span class="n">temp</span> <span class="mi">110</span> <span class="n">damp</span> <span class="mi">200</span> <span class="n">seed</span> <span class="mi">35082</span> <span class="n">f_max</span> <span class="mf">0.3</span> <span class="n">N_f</span> <span class="mi">100</span> <span class="p">(</span><span class="n">liquid</span> <span class="n">methane</span> <span class="n">modeled</span> <span class="k">with</span> <span class="n">the</span> <span class="n">REAX</span> <span class="n">force</span> <span class="n">field</span><span class="p">,</span> <span class="n">real</span> <span class="n">units</span><span class="p">)</span>
+<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">nph</span> <span class="n">iso</span> <span class="mf">1.01325</span> <span class="mf">1.01325</span> <span class="mi">1</span>
+<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">qtb</span> <span class="n">temp</span> <span class="mi">300</span> <span class="n">damp</span> <span class="mi">1</span> <span class="n">seed</span> <span class="mi">47508</span> <span class="n">f_max</span> <span class="mf">120.0</span> <span class="n">N_f</span> <span class="mi">100</span> <span class="p">(</span><span class="n">quartz</span> <span class="n">modeled</span> <span class="k">with</span> <span class="n">the</span> <span class="n">BKS</span> <span class="n">force</span> <span class="n">field</span><span class="p">,</span> <span class="n">metal</span> <span class="n">units</span><span class="p">)</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -219,7 +219,7 @@ runs on different numbers of processors.</p>
vibrational modes with frequencies higher than <em>f_max</em> will not be
modulated. If we denote &Delta;<i>t</i> as the time interval for the
MD integration, <em>f_max</em> is always reset by the code to make
-<i>&alpha;</i> = (int)(2*f_max*&Delta;<i>t</i>)<sup><i>-1</i></sup> a
+<i>&alpha;</i> = (int)(2<em>f_max</em>&Delta;<i>t</i>)<sup><i>-1</i></sup> a
positive integer and print out relative information. An appropriate
value for the cutoff frequency <em>f_max</em> would be around 2~3
<i>f</i><sub>D</sub>, where <i>f</i><sub>D</sub> is the Debye
diff --git a/doc/html/fix_reax_bonds.html b/doc/html/fix_reax_bonds.html
index e8c6d12136..0275b0ad0e 100644
--- a/doc/html/fix_reax_bonds.html
+++ b/doc/html/fix_reax_bonds.html
@@ -157,8 +157,10 @@ written to <em>filename</em> on timesteps that are multiples of <em>Nevery</em>,
including timestep 0. For time-averaged chemical species analysis,
please see the <a class="reference internal" href="fix_reaxc_species.html"><span class="doc">fix reaxc/c/species</span></a> command.</p>
<p>The format of the output file should be self-explantory.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
diff --git a/doc/html/fix_reaxc_species.html b/doc/html/fix_reaxc_species.html
index fb72dd69c4..d4f4f182bd 100644
--- a/doc/html/fix_reaxc_species.html
+++ b/doc/html/fix_reaxc_species.html
@@ -215,8 +215,10 @@ i.e. Nrepeat*Nevery can not exceed Nfreq.</p>
<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order
values on timesteps 90,92,94,96,98,100 will be used to compute the
average bond-order for the species analysis output on timestep 100.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix computes both a global vector of length 2 and a per-atom
diff --git a/doc/html/fix_saed_vtk.html b/doc/html/fix_saed_vtk.html
index 08de66a8eb..29f7570dc9 100644
--- a/doc/html/fix_saed_vtk.html
+++ b/doc/html/fix_saed_vtk.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix saed/vtk command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="n">Nevery</span> <span class="n">Nrepeat</span> <span class="n">Nfreak</span> <span class="n">c_ID</span> <span class="n">attribute</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>saed/vtk = style name of this fix command</li>
@@ -154,14 +154,14 @@ keyword = <em>file</em> or <em>ave</em> or <em>start</em> or <em>file</em> or <e
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
-compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
-</pre>
-<pre class="literal-block">
-fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
-fix saed/vtk 1 1 1 c_2 file Ni_000.saed
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Al</span> <span class="n">O</span> <span class="n">Kmax</span> <span class="mf">1.70</span> <span class="n">Zone</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="n">dR_Ewald</span> <span class="mf">0.01</span> <span class="n">c</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">0.5</span>
+<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Ni</span> <span class="n">Kmax</span> <span class="mf">1.70</span> <span class="n">Zone</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="n">c</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="n">manual</span> <span class="n">echo</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_1</span> <span class="n">file</span> <span class="n">Al2O3_001</span><span class="o">.</span><span class="n">saed</span>
+<span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_2</span> <span class="n">file</span> <span class="n">Ni_000</span><span class="o">.</span><span class="n">saed</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -182,10 +182,10 @@ specified values may represent calculations performed by saed computes
which store their own “group” definitions.</p>
<p>Fix saed/vtk is designed to work only with <a class="reference internal" href="compute_saed.html"><span class="doc">compute saed</span></a>
values, e.g.</p>
-<pre class="literal-block">
-compute 3 top saed 0.0251 Al O
-fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">3</span> <span class="n">top</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Al</span> <span class="n">O</span>
+<span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_3</span> <span class="n">file</span> <span class="n">Al2O3_001</span><span class="o">.</span><span class="n">saed</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
timesteps the input values will be used in order to contribute to the
@@ -209,19 +209,19 @@ vtk image data formatting. The filename assigned by the <em>file</em> keyword i
appended with _N.vtk where N is an index (0,1,2...) to account for multiple
diffraction intensity outputs.</p>
<p>By default the header contains the following information (with example data):</p>
-<pre class="literal-block">
-# vtk DataFile Version 3.0 c_SAED
-Image data set
-ASCII
-DATASET STRUCTURED_POINTS
-DIMENSIONS 337 219 209
-ASPECT_RATIO 0.00507953 0.00785161 0.00821458
-ORIGIN -0.853361 -0.855826 -0.854316
-POINT_DATA 15424827
-SCALARS intensity float
-LOOKUP_TABLE default
-...data
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># vtk DataFile Version 3.0 c_SAED</span>
+<span class="n">Image</span> <span class="n">data</span> <span class="nb">set</span>
+<span class="n">ASCII</span>
+<span class="n">DATASET</span> <span class="n">STRUCTURED_POINTS</span>
+<span class="n">DIMENSIONS</span> <span class="mi">337</span> <span class="mi">219</span> <span class="mi">209</span>
+<span class="n">ASPECT_RATIO</span> <span class="mf">0.00507953</span> <span class="mf">0.00785161</span> <span class="mf">0.00821458</span>
+<span class="n">ORIGIN</span> <span class="o">-</span><span class="mf">0.853361</span> <span class="o">-</span><span class="mf">0.855826</span> <span class="o">-</span><span class="mf">0.854316</span>
+<span class="n">POINT_DATA</span> <span class="mi">15424827</span>
+<span class="n">SCALARS</span> <span class="n">intensity</span> <span class="nb">float</span>
+<span class="n">LOOKUP_TABLE</span> <span class="n">default</span>
+<span class="o">...</span><span class="n">data</span>
+</pre></div>
+</div>
<p>In this example, kspace is sampled across a 337 x 219 x 209 point mesh
where the mesh spacing is approximately 0.005, 0.007, and 0.008
inv(length) units in the k1, k2, and k3 directions, respectively.
@@ -264,7 +264,9 @@ intensity outputs.</p>
<p>The <em>overwrite</em> keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of
output. This option can only be used with the <em>ave running</em> setting.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
diff --git a/doc/html/fix_smd.html b/doc/html/fix_smd.html
index 0c2d9bc519..5be23f5d7b 100644
--- a/doc/html/fix_smd.html
+++ b/doc/html/fix_smd.html
@@ -212,7 +212,9 @@ over the pulling force in direction of the spring is recorded and
can then later be used to compute the potential of mean force (PMF)
by averaging over multiple independent trajectories along the same
pulling path.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>The fix stores the direction of the spring, current pulling target
distance and the running PMF to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.
See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to
diff --git a/doc/html/fix_smd_adjust_dt.html b/doc/html/fix_smd_adjust_dt.html
index 734c433f36..ebf49b94ca 100644
--- a/doc/html/fix_smd_adjust_dt.html
+++ b/doc/html/fix_smd_adjust_dt.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix smd/adjust_dt command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-fix ID group-ID smd/adjust_dt arg
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">smd</span><span class="o">/</span><span class="n">adjust_dt</span> <span class="n">arg</span>
+</pre></div>
+</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>smd/adjust_dt = style name of this fix command</li>
@@ -142,9 +142,9 @@ fix ID group-ID smd/adjust_dt arg
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 1 all smd/adjust_dt 0.1
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">adjust_dt</span> <span class="mf">0.1</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -157,7 +157,9 @@ stable maximum time step.</p>
<p>This fix inquires the minimum stable time increment across all particles contained in the group for which this
fix is defined. An additional safety factor <em>s_fact</em> is applied to the time increment.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to use Smooth Mach Dynamics in LAMMPS.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>Currently, no part of USER-SMD supports restarting nor minimization.</p>
</div>
<div class="section" id="restrictions">
diff --git a/doc/html/fix_smd_integrate_tlsph.html b/doc/html/fix_smd_integrate_tlsph.html
index 04c9db062a..194f99be37 100644
--- a/doc/html/fix_smd_integrate_tlsph.html
+++ b/doc/html/fix_smd_integrate_tlsph.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix smd/integrate_tlsph command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-fix ID group-ID smd/integrate_tlsph keyword values
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_tlsph</span> <span class="n">keyword</span> <span class="n">values</span>
+</pre></div>
+</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>smd/integrate_tlsph = style name of this fix command</li>
@@ -144,10 +144,10 @@ fix ID group-ID smd/integrate_tlsph keyword values
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 1 all smd/integrate_tlsph
-fix 1 all smd/integrate_tlsph limit_velocity 1000
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_tlsph</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_tlsph</span> <span class="n">limit_velocity</span> <span class="mi">1000</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -155,7 +155,9 @@ fix 1 all smd/integrate_tlsph limit_velocity 1000
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
<p>The <em>limit_velocity</em> keyword will control the velocity, scaling the norm of
the velocity vector to max_vel in case it exceeds this velocity limit.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.</p>
</div>
<div class="section" id="restrictions">
diff --git a/doc/html/fix_smd_integrate_ulsph.html b/doc/html/fix_smd_integrate_ulsph.html
index 58bd9fda2c..e45d7d3f31 100644
--- a/doc/html/fix_smd_integrate_ulsph.html
+++ b/doc/html/fix_smd_integrate_ulsph.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix smd/integrate_ulsph command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-fix ID group-ID smd/integrate_ulsph keyword
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_ulsph</span> <span class="n">keyword</span>
+</pre></div>
+</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>smd/integrate_ulsph = style name of this fix command</li>
@@ -148,12 +148,12 @@ max_nn = maximum number of neighbors</dd>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
-</pre>
-<pre class="literal-block">
-fix 1 all smd/integrate_ulsph limit_velocity 1000
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_ulsph</span> <span class="n">adjust_radius</span> <span class="mf">1.02</span> <span class="mi">25</span> <span class="mi">50</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_ulsph</span> <span class="n">limit_velocity</span> <span class="mi">1000</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -161,10 +161,12 @@ fix 1 all smd/integrate_ulsph limit_velocity 1000
See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
<p>The <em>adjust_radius</em> keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains
within the interval <em>min_nn</em> to <em>max_nn</em>. The parameter <em>adjust_radius_factor</em> determines the amount of adjustment per timestep. Typical values are
-<a href="#id1"><span class="problematic" id="id2">*</span></a>adjust_radius_factor*=1.02, <a href="#id3"><span class="problematic" id="id4">*</span></a>min_nn*=15, and <a href="#id5"><span class="problematic" id="id6">*</span></a>max_nn*=20.</p>
+<em>adjust_radius_factor</em>=1.02, <em>min_nn</em>=15, and <em>max_nn</em>=20.</p>
<p>The <em>limit_velocity</em> keyword will control the velocity, scaling the norm of
the velocity vector to max_vel in case it exceeds this velocity limit.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.</p>
</div>
<div class="section" id="restrictions">
diff --git a/doc/html/fix_smd_move_triangulated_surface.html b/doc/html/fix_smd_move_triangulated_surface.html
index e3c04397e7..689017806f 100644
--- a/doc/html/fix_smd_move_triangulated_surface.html
+++ b/doc/html/fix_smd_move_triangulated_surface.html
@@ -128,53 +128,55 @@
<span id="index-0"></span><h1>fix smd/move_tri_surf command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-fix ID group-ID smd/move_tri_surf keyword
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">smd</span><span class="o">/</span><span class="n">move_tri_surf</span> <span class="n">keyword</span>
+</pre></div>
+</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>smd/move_tri_surf keyword = style name of this fix command</li>
-<li>keyword = <em>*LINEAR</em> or <em>*WIGGLE</em> or <em>*ROTATE</em></li>
+<li>keyword = <a href="#id1"><span class="problematic" id="id2">**</span></a>LINEAR* or <a href="#id3"><span class="problematic" id="id4">**</span></a>WIGGLE* or <a href="#id5"><span class="problematic" id="id6">**</span></a>ROTATE*</li>
</ul>
-<pre class="literal-block">
-<em>*LINEAR</em> args = Vx Vy Vz
- Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
-<em>*WIGGLE</em> args = Vx Vy Vz max_travel
- vx,vy,vz = components of velocity vector (velocity units), any component can be specified as NULL
- max_travel = wiggle amplitude
-<em>*ROTATE</em> args = Px Py Pz Rx Ry Rz period
- Px,Py,Pz = origin point of axis of rotation (distance units)
- Rx,Ry,Rz = axis of rotation vector
- period = period of rotation (time units)
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">**</span><span class="n">LINEAR</span><span class="o">*</span> <span class="n">args</span> <span class="o">=</span> <span class="n">Vx</span> <span class="n">Vy</span> <span class="n">Vz</span>
+ <span class="n">Vx</span><span class="p">,</span><span class="n">Vy</span><span class="p">,</span><span class="n">Vz</span> <span class="o">=</span> <span class="n">components</span> <span class="n">of</span> <span class="n">velocity</span> <span class="n">vector</span> <span class="p">(</span><span class="n">velocity</span> <span class="n">units</span><span class="p">),</span> <span class="nb">any</span> <span class="n">component</span> <span class="n">can</span> <span class="n">be</span> <span class="n">specified</span> <span class="k">as</span> <span class="n">NULL</span>
+<span class="o">**</span><span class="n">WIGGLE</span><span class="o">*</span> <span class="n">args</span> <span class="o">=</span> <span class="n">Vx</span> <span class="n">Vy</span> <span class="n">Vz</span> <span class="n">max_travel</span>
+ <span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span> <span class="o">=</span> <span class="n">components</span> <span class="n">of</span> <span class="n">velocity</span> <span class="n">vector</span> <span class="p">(</span><span class="n">velocity</span> <span class="n">units</span><span class="p">),</span> <span class="nb">any</span> <span class="n">component</span> <span class="n">can</span> <span class="n">be</span> <span class="n">specified</span> <span class="k">as</span> <span class="n">NULL</span>
+ <span class="n">max_travel</span> <span class="o">=</span> <span class="n">wiggle</span> <span class="n">amplitude</span>
+<span class="o">**</span><span class="n">ROTATE</span><span class="o">*</span> <span class="n">args</span> <span class="o">=</span> <span class="n">Px</span> <span class="n">Py</span> <span class="n">Pz</span> <span class="n">Rx</span> <span class="n">Ry</span> <span class="n">Rz</span> <span class="n">period</span>
+ <span class="n">Px</span><span class="p">,</span><span class="n">Py</span><span class="p">,</span><span class="n">Pz</span> <span class="o">=</span> <span class="n">origin</span> <span class="n">point</span> <span class="n">of</span> <span class="n">axis</span> <span class="n">of</span> <span class="n">rotation</span> <span class="p">(</span><span class="n">distance</span> <span class="n">units</span><span class="p">)</span>
+ <span class="n">Rx</span><span class="p">,</span><span class="n">Ry</span><span class="p">,</span><span class="n">Rz</span> <span class="o">=</span> <span class="n">axis</span> <span class="n">of</span> <span class="n">rotation</span> <span class="n">vector</span>
+ <span class="n">period</span> <span class="o">=</span> <span class="n">period</span> <span class="n">of</span> <span class="n">rotation</span> <span class="p">(</span><span class="n">time</span> <span class="n">units</span><span class="p">)</span>
+</pre></div>
+</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix 1 tool smd/move_tri_surf *LINEAR 20 20 10
-fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10
-fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="n">tool</span> <span class="n">smd</span><span class="o">/</span><span class="n">move_tri_surf</span> <span class="o">*</span><span class="n">LINEAR</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">10</span>
+<span class="n">fix</span> <span class="mi">2</span> <span class="n">tool</span> <span class="n">smd</span><span class="o">/</span><span class="n">move_tri_surf</span> <span class="o">*</span><span class="n">WIGGLE</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">10</span>
+<span class="n">fix</span> <span class="mi">2</span> <span class="n">tool</span> <span class="n">smd</span><span class="o">/</span><span class="n">move_tri_surf</span> <span class="o">*</span><span class="n">ROTATE</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">5</span> <span class="mi">2</span> <span class="mi">1</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>This fix applies only to rigid surfaces read from .STL files via fix <a class="reference internal" href="fix_smd_wall_surface.html"><span class="doc">smd/wall_surface</span></a> .
It updates position and velocity for the particles in the group each timestep without regard to forces on the particles.
The rigid surfaces can thus be moved along simple trajectories during the simulation.</p>
-<p>The <em>*LINEAR</em> style moves particles with the specified constant velocity
+<p>The <a href="#id19"><span class="problematic" id="id20">**</span></a>LINEAR* style moves particles with the specified constant velocity
vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle
to V = (Vx,Vy,Vz).</p>
-<p>The <em>*WIGGLE</em> style moves particles in an oscillatory fashion.
+<p>The <a href="#id21"><span class="problematic" id="id22">**</span></a>WIGGLE* style moves particles in an oscillatory fashion.
Particles are moved along (vx, vy, vz) with constant velocity until a
displacement of max_travel is reached. Then, the velocity vector is
reversed. This process is repeated.</p>
-<p>The <em>*ROTATE</em> style rotates particles around a rotation axis R = (Rx,Ry,Rz) that
+<p>The <a href="#id23"><span class="problematic" id="id24">**</span></a>ROTATE* style rotates particles around a rotation axis R = (Rx,Ry,Rz) that
goes through a point P = (Px,Py,Pz). The period of the rotation is also
specified. This style also sets the velocity of each particle to (omega cross
Rperp) where omega is its angular velocity around the rotation axis and
Rperp is a perpendicular vector from the rotation axis to the particle.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.</p>
</div>
<div class="section" id="restrictions">
diff --git a/doc/html/fix_smd_setvel.html b/doc/html/fix_smd_setvel.html
index 16fc5abc50..cb8449f1c0 100644
--- a/doc/html/fix_smd_setvel.html
+++ b/doc/html/fix_smd_setvel.html
@@ -146,9 +146,9 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix top_velocity top_group setvel 1.0 0.0 0.0
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">top_velocity</span> <span class="n">top_group</span> <span class="n">setvel</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -174,8 +174,10 @@ coordinates. Thus it is easy to specify a spatially-dependent velocity
field with optional time-dependence as well.</p>
<p>If the <em>region</em> keyword is used, the particle must also be in the
specified geometric <a class="reference internal" href="region.html"><span class="doc">region</span></a> in order to have its velocity set by this command.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>Currently, no part of USER-SMD supports restarting nor minimization
None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
diff --git a/doc/html/fix_smd_wall_surface.html b/doc/html/fix_smd_wall_surface.html
index f51d51f6a6..92d197d542 100644
--- a/doc/html/fix_smd_wall_surface.html
+++ b/doc/html/fix_smd_wall_surface.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix smd/wall_surface command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-fix ID group-ID smd/wall_surface arg type mol-ID
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">smd</span><span class="o">/</span><span class="n">wall_surface</span> <span class="n">arg</span> <span class="nb">type</span> <span class="n">mol</span><span class="o">-</span><span class="n">ID</span>
+</pre></div>
+</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>smd/wall_surface = style name of this fix command</li>
@@ -146,9 +146,9 @@ fix ID group-ID smd/wall_surface arg type mol-ID
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix stl_surf all smd/wall_surface tool.stl 2 65535
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">stl_surf</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">wall_surface</span> <span class="n">tool</span><span class="o">.</span><span class="n">stl</span> <span class="mi">2</span> <span class="mi">65535</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -160,7 +160,9 @@ It is possible to move the triangulated surface via the <a class="reference inte
<p>Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles
in the system. See the “funnel_flow” example in the USER-SMD examples directory.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to use Smooth Mach Dynamics in LAMMPS.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.</p>
</div>
<div class="section" id="restrictions">
diff --git a/doc/html/fix_spring.html b/doc/html/fix_spring.html
index 413066a788..a1d40fbf68 100644
--- a/doc/html/fix_spring.html
+++ b/doc/html/fix_spring.html
@@ -215,7 +215,9 @@ spring command, if the rigid body will cross a periodic boundary.
This is because image flags for rigid bodies are used in a different
way, as explained on the <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> doc page.</p>
</div>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the energy stored in the spring to the system’s potential
diff --git a/doc/html/fix_spring_chunk.html b/doc/html/fix_spring_chunk.html
index 5ea20d8a43..7373fd8e56 100644
--- a/doc/html/fix_spring_chunk.html
+++ b/doc/html/fix_spring_chunk.html
@@ -166,7 +166,9 @@ the mass of the atom, and Mm is the total mass of all atoms in the
chunk. Note that <em>K</em> thus represents the spring constant for the
total force on each chunk of atoms, not for a spring applied to each
atom.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the energy stored in all the springs to the system’s potential
diff --git a/doc/html/fix_spring_self.html b/doc/html/fix_spring_self.html
index 28e33fc5ed..dbc542e600 100644
--- a/doc/html/fix_spring_self.html
+++ b/doc/html/fix_spring_self.html
@@ -160,7 +160,9 @@ spring force is applied. By default, the restraint is applied in all
directions, but it can be limited to the xy-, xz-, yz-plane and the
x-, y-, or z-direction, thus restraining the atoms to a line or a
plane, respectively.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the original coordinates of tethered atoms to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so that the spring effect will be the
same in a restarted simulation. See the
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify
diff --git a/doc/html/fix_store_state.html b/doc/html/fix_store_state.html
index 0a885ed683..9d236aa13f 100644
--- a/doc/html/fix_store_state.html
+++ b/doc/html/fix_store_state.html
@@ -137,43 +137,43 @@
<li>N = store atom attributes every N steps, N = 0 for initial store only</li>
<li>input = one or more atom attributes</li>
</ul>
-<pre class="literal-block">
-possible attributes = id, mol, type, mass,
- x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
- vx, vy, vz, fx, fy, fz,
- q, mux, muy, muz, mu,
- radius, diameter, omegax, omegay, omegaz,
- angmomx, angmomy, angmomz, tqx, tqy, tqz,
- c_ID, c_ID[N], f_ID, f_ID[N], v_name,
- d_name, i_name
-</pre>
-<pre class="literal-block">
-id = atom ID
-mol = molecule ID
-type = atom type
-mass = atom mass
-x,y,z = unscaled atom coordinates
-xs,ys,zs = scaled atom coordinates
-xu,yu,zu = unwrapped atom coordinates
-xsu,ysu,zsu = scaled unwrapped atom coordinates
-ix,iy,iz = box image that the atom is in
-vx,vy,vz = atom velocities
-fx,fy,fz = forces on atoms
-q = atom charge
-mux,muy,muz = orientation of dipolar atom
-mu = magnitued of dipole moment of atom
-radius,diameter = radius.diameter of spherical particle
-omegax,omegay,omegaz = angular velocity of spherical particle
-angmomx,angmomy,angmomz = angular momentum of aspherical particle
-tqx,tqy,tqz = torque on finite-size particles
-c_ID = per-atom vector calculated by a compute with ID
-c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-f_ID = per-atom vector calculated by a fix with ID
-f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-v_name = per-atom vector calculated by an atom-style variable with name
-d_name = per-atom floating point vector name, managed by fix property/atom
-i_name = per-atom integer vector name, managed by fix property/atom
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">possible</span> <span class="n">attributes</span> <span class="o">=</span> <span class="nb">id</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">mass</span><span class="p">,</span>
+ <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span><span class="p">,</span> <span class="n">xs</span><span class="p">,</span> <span class="n">ys</span><span class="p">,</span> <span class="n">zs</span><span class="p">,</span> <span class="n">xu</span><span class="p">,</span> <span class="n">yu</span><span class="p">,</span> <span class="n">zu</span><span class="p">,</span> <span class="n">xsu</span><span class="p">,</span> <span class="n">ysu</span><span class="p">,</span> <span class="n">zsu</span><span class="p">,</span> <span class="n">ix</span><span class="p">,</span> <span class="n">iy</span><span class="p">,</span> <span class="n">iz</span><span class="p">,</span>
+ <span class="n">vx</span><span class="p">,</span> <span class="n">vy</span><span class="p">,</span> <span class="n">vz</span><span class="p">,</span> <span class="n">fx</span><span class="p">,</span> <span class="n">fy</span><span class="p">,</span> <span class="n">fz</span><span class="p">,</span>
+ <span class="n">q</span><span class="p">,</span> <span class="n">mux</span><span class="p">,</span> <span class="n">muy</span><span class="p">,</span> <span class="n">muz</span><span class="p">,</span> <span class="n">mu</span><span class="p">,</span>
+ <span class="n">radius</span><span class="p">,</span> <span class="n">diameter</span><span class="p">,</span> <span class="n">omegax</span><span class="p">,</span> <span class="n">omegay</span><span class="p">,</span> <span class="n">omegaz</span><span class="p">,</span>
+ <span class="n">angmomx</span><span class="p">,</span> <span class="n">angmomy</span><span class="p">,</span> <span class="n">angmomz</span><span class="p">,</span> <span class="n">tqx</span><span class="p">,</span> <span class="n">tqy</span><span class="p">,</span> <span class="n">tqz</span><span class="p">,</span>
+ <span class="n">c_ID</span><span class="p">,</span> <span class="n">c_ID</span><span class="p">[</span><span class="n">N</span><span class="p">],</span> <span class="n">f_ID</span><span class="p">,</span> <span class="n">f_ID</span><span class="p">[</span><span class="n">N</span><span class="p">],</span> <span class="n">v_name</span><span class="p">,</span>
+ <span class="n">d_name</span><span class="p">,</span> <span class="n">i_name</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">id</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">ID</span>
+<span class="n">mol</span> <span class="o">=</span> <span class="n">molecule</span> <span class="n">ID</span>
+<span class="nb">type</span> <span class="o">=</span> <span class="n">atom</span> <span class="nb">type</span>
+<span class="n">mass</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">mass</span>
+<span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span> <span class="o">=</span> <span class="n">unscaled</span> <span class="n">atom</span> <span class="n">coordinates</span>
+<span class="n">xs</span><span class="p">,</span><span class="n">ys</span><span class="p">,</span><span class="n">zs</span> <span class="o">=</span> <span class="n">scaled</span> <span class="n">atom</span> <span class="n">coordinates</span>
+<span class="n">xu</span><span class="p">,</span><span class="n">yu</span><span class="p">,</span><span class="n">zu</span> <span class="o">=</span> <span class="n">unwrapped</span> <span class="n">atom</span> <span class="n">coordinates</span>
+<span class="n">xsu</span><span class="p">,</span><span class="n">ysu</span><span class="p">,</span><span class="n">zsu</span> <span class="o">=</span> <span class="n">scaled</span> <span class="n">unwrapped</span> <span class="n">atom</span> <span class="n">coordinates</span>
+<span class="n">ix</span><span class="p">,</span><span class="n">iy</span><span class="p">,</span><span class="n">iz</span> <span class="o">=</span> <span class="n">box</span> <span class="n">image</span> <span class="n">that</span> <span class="n">the</span> <span class="n">atom</span> <span class="ow">is</span> <span class="ow">in</span>
+<span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">velocities</span>
+<span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">forces</span> <span class="n">on</span> <span class="n">atoms</span>
+<span class="n">q</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">charge</span>
+<span class="n">mux</span><span class="p">,</span><span class="n">muy</span><span class="p">,</span><span class="n">muz</span> <span class="o">=</span> <span class="n">orientation</span> <span class="n">of</span> <span class="n">dipolar</span> <span class="n">atom</span>
+<span class="n">mu</span> <span class="o">=</span> <span class="n">magnitued</span> <span class="n">of</span> <span class="n">dipole</span> <span class="n">moment</span> <span class="n">of</span> <span class="n">atom</span>
+<span class="n">radius</span><span class="p">,</span><span class="n">diameter</span> <span class="o">=</span> <span class="n">radius</span><span class="o">.</span><span class="n">diameter</span> <span class="n">of</span> <span class="n">spherical</span> <span class="n">particle</span>
+<span class="n">omegax</span><span class="p">,</span><span class="n">omegay</span><span class="p">,</span><span class="n">omegaz</span> <span class="o">=</span> <span class="n">angular</span> <span class="n">velocity</span> <span class="n">of</span> <span class="n">spherical</span> <span class="n">particle</span>
+<span class="n">angmomx</span><span class="p">,</span><span class="n">angmomy</span><span class="p">,</span><span class="n">angmomz</span> <span class="o">=</span> <span class="n">angular</span> <span class="n">momentum</span> <span class="n">of</span> <span class="n">aspherical</span> <span class="n">particle</span>
+<span class="n">tqx</span><span class="p">,</span><span class="n">tqy</span><span class="p">,</span><span class="n">tqz</span> <span class="o">=</span> <span class="n">torque</span> <span class="n">on</span> <span class="n">finite</span><span class="o">-</span><span class="n">size</span> <span class="n">particles</span>
+<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
+<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
+<span class="n">d_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">floating</span> <span class="n">point</span> <span class="n">vector</span> <span class="n">name</span><span class="p">,</span> <span class="n">managed</span> <span class="n">by</span> <span class="n">fix</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span>
+<span class="n">i_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">integer</span> <span class="n">vector</span> <span class="n">name</span><span class="p">,</span> <span class="n">managed</span> <span class="n">by</span> <span class="n">fix</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span>
+</pre></div>
+</div>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>com</em></li>
@@ -217,7 +217,9 @@ of the group of atoms, instead of storing the absolute position.</p>
<p>The requested values are stored in a per-atom vector or array as
discussed below. Zeroes are stored for atoms not in the specified
group.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the per-atom values it stores to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so that the values can be restored when a
simulation is restarted. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
command for info on how to re-specify a fix in an input script that
diff --git a/doc/html/fix_temp_rescale_eff.html b/doc/html/fix_temp_rescale_eff.html
index 4a5b09b42a..826fcfb6f4 100644
--- a/doc/html/fix_temp_rescale_eff.html
+++ b/doc/html/fix_temp_rescale_eff.html
@@ -154,7 +154,9 @@ their velocities.</p>
<p>The operation of this fix is exactly like that described by the <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a> command, except that the rescaling
is also applied to the radial electron velocity for electron
particles.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> option is supported by this
fix. You can use it to assign a temperature <a class="reference internal" href="compute.html"><span class="doc">compute</span></a>
diff --git a/doc/html/fix_tfmc.html b/doc/html/fix_tfmc.html
index 32b9de3cbb..1fa84393e7 100644
--- a/doc/html/fix_tfmc.html
+++ b/doc/html/fix_tfmc.html
@@ -228,8 +228,10 @@ translations or rotations of the fix group could be induced by these
external forces, and removing them will lead to a violation of
detailed balance.</p>
</div>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options are relevant to this
fix.</p>
diff --git a/doc/html/fix_thermal_conductivity.html b/doc/html/fix_thermal_conductivity.html
index 05f63ab2de..97325bd91e 100644
--- a/doc/html/fix_thermal_conductivity.html
+++ b/doc/html/fix_thermal_conductivity.html
@@ -180,12 +180,12 @@ of the 2 atoms is performed, to conserve kinetic energy. Over time,
this induces a temperature gradient in the system which can be
measured using commands such as the following, which writes the
temperature profile (assuming z = edim) to the file tmp.profile:</p>
-<pre class="literal-block">
-compute ke all ke/atom
-variable temp atom c_ke/1.5
-compute layers all chunk/atom bin/1d z lower 0.05 units reduced
-fix 3 all ave/chunk 10 100 1000 layers v_temp file tmp.profile
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ke</span> <span class="nb">all</span> <span class="n">ke</span><span class="o">/</span><span class="n">atom</span>
+<span class="n">variable</span> <span class="n">temp</span> <span class="n">atom</span> <span class="n">c_ke</span><span class="o">/</span><span class="mf">1.5</span>
+<span class="n">compute</span> <span class="n">layers</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="nb">bin</span><span class="o">/</span><span class="mi">1</span><span class="n">d</span> <span class="n">z</span> <span class="n">lower</span> <span class="mf">0.05</span> <span class="n">units</span> <span class="n">reduced</span>
+<span class="n">fix</span> <span class="mi">3</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">10</span> <span class="mi">100</span> <span class="mi">1000</span> <span class="n">layers</span> <span class="n">v_temp</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">profile</span>
+</pre></div>
+</div>
<p>Note that by default, Nswap = 1, though this can be changed by the
optional <em>swap</em> keyword. Setting this parameter appropriately, in
conjunction with the swap rate N, allows the heat flux to be adjusted
@@ -221,7 +221,9 @@ not in a regime of linear response. In this case you cannot
accurately infer a thermal conductivity and should try increasing the
Nevery parameter.</p>
</div>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix computes a global scalar which can be accessed by various
diff --git a/doc/html/fix_viscosity.html b/doc/html/fix_viscosity.html
index 16fa977a8f..03773104e4 100644
--- a/doc/html/fix_viscosity.html
+++ b/doc/html/fix_viscosity.html
@@ -226,7 +226,9 @@ deform the simmulation box via the <a class="reference internal" href="fix_defor
command. Thus they cannot be run on a charged system using a <a class="reference internal" href="kspace_style.html"><span class="doc">PPPM solver</span></a> since PPPM does not currently support
non-orthogonal boxes. Using fix viscosity keeps the box orthogonal;
thus it does not suffer from this limitation.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix computes a global scalar which can be accessed by various
diff --git a/doc/html/fix_viscous.html b/doc/html/fix_viscous.html
index e63286eaeb..5bf3e54e0a 100644
--- a/doc/html/fix_viscous.html
+++ b/doc/html/fix_viscous.html
@@ -194,8 +194,10 @@ performing the same operation as fix viscous. Also note that the
gamma of fix viscous is related to the damping parameter of <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, however the former is specified in units
of force/velocity and the latter in units of time, so that it can more
easily be used as a thermostat.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
diff --git a/doc/html/fix_wall_gran.html b/doc/html/fix_wall_gran.html
index b6360f4ffb..08178f888a 100644
--- a/doc/html/fix_wall_gran.html
+++ b/doc/html/fix_wall_gran.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix wall/gran command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-fix ID group-ID wall/gran Kn Kt fstyle gamma_n gamma_t xmu dampflag wallstyle args keyword values ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">wall</span><span class="o">/</span><span class="n">gran</span> <span class="n">Kn</span> <span class="n">Kt</span> <span class="n">fstyle</span> <span class="n">gamma_n</span> <span class="n">gamma_t</span> <span class="n">xmu</span> <span class="n">dampflag</span> <span class="n">wallstyle</span> <span class="n">args</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>wall/gran = style name of this fix command</li>
@@ -241,9 +241,9 @@ is perpendicular to the wall, it is more of a shaking motion. A
<em>zcylinder</em> wall can only be wiggled in the z dimension.</p>
<p>Each timestep, the position of a wiggled wall in the appropriate <em>dim</em>
is set according to this equation:</p>
-<pre class="literal-block">
-position = coord + A - A cos (omega * delta)
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">coord</span> <span class="o">+</span> <span class="n">A</span> <span class="o">-</span> <span class="n">A</span> <span class="n">cos</span> <span class="p">(</span><span class="n">omega</span> <span class="o">*</span> <span class="n">delta</span><span class="p">)</span>
+</pre></div>
+</div>
<p>where <em>coord</em> is the specified initial position of the wall, <em>A</em> is
the <em>amplitude</em>, <em>omega</em> is 2 PI / <em>period</em>, and <em>delta</em> is the time
elapsed since the fix was specified. The velocity of the wall is set
@@ -257,7 +257,9 @@ cylinder is moving in the z-direction along it’s axis. A dimension of
the clockwise direction for <em>vshear</em> > 0 or counter-clockwise for
<em>vshear</em> < 0. In this case, <em>vshear</em> is the tangential velocity of
the wall at whatever <em>radius</em> has been defined.</p>
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+</div>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the shear friction state of atoms interacting with the
wall to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so that a simulation can
continue correctly if granular potentials with shear “history” effects
diff --git a/doc/html/fix_wall_piston.html b/doc/html/fix_wall_piston.html
index baed71d961..ade80b4497 100644
--- a/doc/html/fix_wall_piston.html
+++ b/doc/html/fix_wall_piston.html
@@ -199,8 +199,10 @@ to define a wall position, but only when a numeric constant is used.</p>
A <em>lattice</em> value means the distance units are in lattice spacings.
The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command must have been previously used to
define the lattice spacings.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
diff --git a/doc/html/fix_wall_reflect.html b/doc/html/fix_wall_reflect.html
index 9df5dfe8ef..4c6467cd42 100644
--- a/doc/html/fix_wall_reflect.html
+++ b/doc/html/fix_wall_reflect.html
@@ -162,11 +162,11 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-fix xwalls all wall/reflect xlo EDGE xhi EDGE
-fix walls all wall/reflect xlo 0.0 ylo 10.0 units box
-fix top all wall/reflect zhi v_pressdown
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">xwalls</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="n">EDGE</span> <span class="n">xhi</span> <span class="n">EDGE</span>
+<span class="n">fix</span> <span class="n">walls</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="mf">0.0</span> <span class="n">ylo</span> <span class="mf">10.0</span> <span class="n">units</span> <span class="n">box</span>
+<span class="n">fix</span> <span class="n">top</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">zhi</span> <span class="n">v_pressdown</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -215,22 +215,22 @@ define the lattice spacings.</p>
<p>Here are examples of variable definitions that move the wall position
in a time-dependent fashion using equal-style
<a class="reference internal" href="variable.html"><span class="doc">variables</span></a>.</p>
-<pre class="literal-block">
-variable ramp equal ramp(0,10)
-fix 1 all wall/reflect xlo v_ramp
-</pre>
-<pre class="literal-block">
-variable linear equal vdisplace(0,20)
-fix 1 all wall/reflect xlo v_linear
-</pre>
-<pre class="literal-block">
-variable wiggle equal swiggle(0.0,5.0,3.0)
-fix 1 all wall/reflect xlo v_wiggle
-</pre>
-<pre class="literal-block">
-variable wiggle equal cwiggle(0.0,5.0,3.0)
-fix 1 all wall/reflect xlo v_wiggle
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">ramp</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="n">v_ramp</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">linear</span> <span class="n">equal</span> <span class="n">vdisplace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">20</span><span class="p">)</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="n">v_linear</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">wiggle</span> <span class="n">equal</span> <span class="n">swiggle</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">5.0</span><span class="p">,</span><span class="mf">3.0</span><span class="p">)</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="n">v_wiggle</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">wiggle</span> <span class="n">equal</span> <span class="n">cwiggle</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">5.0</span><span class="p">,</span><span class="mf">3.0</span><span class="p">)</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="n">v_wiggle</span>
+</pre></div>
+</div>
<p>The ramp(lo,hi) function adjusts the wall position linearly from lo to
hi over the course of a run. The vdisplace(c0,velocity) function does
something similar using the equation position = c0 + velocity*delta,
@@ -238,16 +238,16 @@ where delta is the elapsed time.</p>
<p>The swiggle(c0,A,period) function causes the wall position to
oscillate sinusoidally according to this equation, where omega = 2 PI
/ period:</p>
-<pre class="literal-block">
-position = c0 + A sin(omega*delta)
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">)</span>
+</pre></div>
+</div>
<p>The cwiggle(c0,A,period) function causes the wall position to
oscillate sinusoidally according to this equation, which will have an
initial wall velocity of 0.0, and thus may impose a gentler
perturbation on the particles:</p>
-<pre class="literal-block">
-position = c0 + A (1 - cos(omega*delta))
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">cos</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">))</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p>Styles with a <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.
@@ -264,8 +264,10 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
+</div>
<hr class="docutils" />
-<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
+<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
+<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
diff --git a/doc/html/group.html b/doc/html/group.html
index 009ce0deea..d21faf214a 100644
--- a/doc/html/group.html
+++ b/doc/html/group.html
@@ -257,22 +257,22 @@ or exclude from a group.</p>
<p>For example, these lines define a variable “eatom” that calculates the
potential energy of each atom and includes it in the group if its
potential energy is above the threshhold value -3.0.</p>
-<pre class="literal-block">
-compute 1 all pe/atom
-compute 2 all reduce sum c_1
-thermo_style custom step temp pe c_2
-run 0
-</pre>
-<pre class="literal-block">
-variable eatom atom "c_1 > -3.0"
-group hienergy variable eatom
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">pe</span><span class="o">/</span><span class="n">atom</span>
+<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_1</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">pe</span> <span class="n">c_2</span>
+<span class="n">run</span> <span class="mi">0</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">eatom</span> <span class="n">atom</span> <span class="s2">"c_1 > -3.0"</span>
+<span class="n">group</span> <span class="n">hienergy</span> <span class="n">variable</span> <span class="n">eatom</span>
+</pre></div>
+</div>
<p>Note that these lines</p>
-<pre class="literal-block">
-compute 2 all reduce sum c_1
-thermo_style custom step temp pe c_2
-run 0
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_1</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">pe</span> <span class="n">c_2</span>
+<span class="n">run</span> <span class="mi">0</span>
+</pre></div>
+</div>
<p>are necessary to insure that the “eatom” variable is current when the
group command invokes it. Because the eatom variable computes the
per-atom energy via the pe/atom compute, it will only be current if a
@@ -353,8 +353,7 @@ being integrated by using a spherical region with a variable radius
used to model a quench of the system, freezing atoms outside the
shrinking sphere, then converting the remaining atoms to a static
group and running further.</p>
-<pre class="literal-block">
-variable nsteps equal 5000
+<div class="highlight-default"><div class="highlight"><pre><span></span>variable nsteps equal 5000
variable rad equal 18-(step/v_nsteps)*(18-5)
region ss sphere 20 20 0 v_rad
group mobile dynamic all region ss
@@ -362,7 +361,8 @@ fix 1 mobile nve
run ${nsteps}
group mobile static
run ${nsteps}
-</pre>
+</pre></div>
+</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">All fixes and computes take a group ID as an argument, but they
diff --git a/doc/html/if.html b/doc/html/if.html
index fe0350f9d5..f2ba9d34e7 100644
--- a/doc/html/if.html
+++ b/doc/html/if.html
@@ -143,8 +143,7 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-if "${steps} > 1000" then quit
+<div class="highlight-default"><div class="highlight"><pre><span></span>if "${steps} > 1000" then quit
if "${myString} == a10" then quit
if "$x <= $y" then "print X is smaller = $x" else "print Y is smaller = $y"
if "(${eng} > 0.0) || ($n < 1000)" then &
@@ -153,9 +152,10 @@ elif $n<10000 &
"timestep 0.01" &
else &
"timestep 0.02" &
- "print 'Max step reached'"
+ "print 'Max step reached'"
if "${eng} > ${eng_previous}" then "jump file1" else "jump file2"
-</pre>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -249,10 +249,10 @@ clarity, you must enclose the entire expression in quotes.</p>
<p>An expression is built out of numbers (which start with a digit or
period or minus sign) or strings (which start with a letter and can
contain alphanumeric characters or underscores):</p>
-<pre class="literal-block">
-0.2, 100, 1.0e20, -15.4, etc
-InP, myString, a123, ab_23_cd, etc
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mf">0.2</span><span class="p">,</span> <span class="mi">100</span><span class="p">,</span> <span class="mf">1.0e20</span><span class="p">,</span> <span class="o">-</span><span class="mf">15.4</span><span class="p">,</span> <span class="n">etc</span>
+<span class="n">InP</span><span class="p">,</span> <span class="n">myString</span><span class="p">,</span> <span class="n">a123</span><span class="p">,</span> <span class="n">ab_23_cd</span><span class="p">,</span> <span class="n">etc</span>
+</pre></div>
+</div>
<p>and Boolean operators:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>A == B, A != B, A < B, A <= B, A > B, A >= B, A && B, A || B, !A
</pre></div>
diff --git a/doc/html/jump.html b/doc/html/jump.html
index 8b2f4578a4..a87db9100d 100644
--- a/doc/html/jump.html
+++ b/doc/html/jump.html
@@ -158,22 +158,22 @@ script is re-opened and read again.</p>
<p class="last">The SELF option is not guaranteed to work when the current input
script is being read through stdin (standard input), e.g.</p>
</div>
-<pre class="literal-block">
-lmp_g++ < in.script
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_g</span><span class="o">++</span> <span class="o"><</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>
+</pre></div>
+</div>
<p>since the SELF option invokes the C-library rewind() call, which may
not be supported for stdin on some systems or by some MPI
implementations. This can be worked around by using the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-in command-line argument</span></a>, e.g.</p>
-<pre class="literal-block">
-lmp_g++ -in in.script
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>
+</pre></div>
+</div>
<p>or by using the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-var command-line argument</span></a> to pass the script name as a
variable to the input script. In the latter case, a
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a> called “fname” could be used in place of
SELF, e.g.</p>
-<pre class="literal-block">
-lmp_g++ -var fname in.script < in.script
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">var</span> <span class="n">fname</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="o"><</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>
+</pre></div>
+</div>
<p>The 2nd argument to the jump command is optional. If specified, it is
treated as a label and the new file is scanned (without executing
commands) until the label is found, and commands are executed from
@@ -198,9 +198,9 @@ scripts. In this example, LAMMPS is run on 40 processors, with 4
partitions of 10 procs each. An in.file containing the example
variable and jump command will cause each partition to run a different
simulation.</p>
-<pre class="literal-block">
-mpirun -np 40 lmp_ibm -partition 4x10 -in in.file
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">40</span> <span class="n">lmp_ibm</span> <span class="o">-</span><span class="n">partition</span> <span class="mi">4</span><span class="n">x10</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">file</span>
+</pre></div>
+</div>
<div class="highlight-default"><div class="highlight"><pre><span></span>variable f world script.1 script.2 script.3 script.4
jump $f
</pre></div>
diff --git a/doc/html/kspace_modify.html b/doc/html/kspace_modify.html
index 2019d48cff..961ea342d6 100644
--- a/doc/html/kspace_modify.html
+++ b/doc/html/kspace_modify.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>kspace_modify command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-kspace_modify keyword value ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">kspace_modify</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul class="simple">
<li>one or more keyword/value pairs may be listed</li>
</ul>
@@ -174,10 +174,10 @@ keyword = <em>mesh</em> or <em>order</em> or <em>order/disp</em> or <em>mix/disp
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-kspace_modify mesh 24 24 30 order 6
-kspace_modify slab 3.0
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">kspace_modify</span> <span class="n">mesh</span> <span class="mi">24</span> <span class="mi">24</span> <span class="mi">30</span> <span class="n">order</span> <span class="mi">6</span>
+<span class="n">kspace_modify</span> <span class="n">slab</span> <span class="mf">3.0</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
diff --git a/doc/html/kspace_style.html b/doc/html/kspace_style.html
index 5cecc5b41d..53a0c22ce2 100644
--- a/doc/html/kspace_style.html
+++ b/doc/html/kspace_style.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>kspace_style command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-kspace_style style value
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">kspace_style</span> <span class="n">style</span> <span class="n">value</span>
+</pre></div>
+</div>
<ul class="simple">
<li>style = <em>none</em> or <em>ewald</em> or <em>ewald/disp</em> or <em>ewald/omp</em> or <em>pppm</em> or <em>pppm/cg</em> or <em>pppm/disp</em> or <em>pppm/tip4p</em> or <em>pppm/stagger</em> or <em>pppm/disp/tip4p</em> or <em>pppm/gpu</em> or <em>pppm/kk</em> or <em>pppm/omp</em> or <em>pppm/cg/omp</em> or <em>pppm/tip4p/omp</em> or <em>msm</em> or <em>msm/cg</em> or <em>msm/omp</em> or <em>msm/cg/omp</em></li>
</ul>
@@ -179,12 +179,12 @@ kspace_style style value
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-kspace_style pppm 1.0e-4
-kspace_style pppm/cg 1.0e-5 1.0e-6
-kspace style msm 1.0e-4
-kspace_style none
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">kspace_style</span> <span class="n">pppm</span> <span class="mf">1.0e-4</span>
+<span class="n">kspace_style</span> <span class="n">pppm</span><span class="o">/</span><span class="n">cg</span> <span class="mf">1.0e-5</span> <span class="mf">1.0e-6</span>
+<span class="n">kspace</span> <span class="n">style</span> <span class="n">msm</span> <span class="mf">1.0e-4</span>
+<span class="n">kspace_style</span> <span class="n">none</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -422,9 +422,9 @@ must be periodic and the z dimension must be non-periodic.</p>
</div>
<div class="section" id="default">
<h2>Default</h2>
-<pre class="literal-block">
-kspace_style none
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">kspace_style</span> <span class="n">none</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p id="darden"><strong>(Darden)</strong> Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).</p>
<p id="deserno"><strong>(Deserno)</strong> Deserno and Holm, J Chem Phys, 109, 7694 (1998).</p>
diff --git a/doc/html/lattice.html b/doc/html/lattice.html
index 07d659915c..636cba7437 100644
--- a/doc/html/lattice.html
+++ b/doc/html/lattice.html
@@ -135,10 +135,10 @@
<li>style = <em>none</em> or <em>sc</em> or <em>bcc</em> or <em>fcc</em> or <em>hcp</em> or <em>diamond</em> or <em>sq</em> or <em>sq2</em> or <em>hex</em> or <em>custom</em></li>
<li>scale = scale factor between lattice and simulation box</li>
</ul>
-<pre class="literal-block">
-scale = reduced density rho* (for LJ units)
-scale = lattice constant in distance units (for all other units)
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">scale</span> <span class="o">=</span> <span class="n">reduced</span> <span class="n">density</span> <span class="n">rho</span><span class="o">*</span> <span class="p">(</span><span class="k">for</span> <span class="n">LJ</span> <span class="n">units</span><span class="p">)</span>
+<span class="n">scale</span> <span class="o">=</span> <span class="n">lattice</span> <span class="n">constant</span> <span class="ow">in</span> <span class="n">distance</span> <span class="n">units</span> <span class="p">(</span><span class="k">for</span> <span class="nb">all</span> <span class="n">other</span> <span class="n">units</span><span class="p">)</span>
+</pre></div>
+</div>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>origin</em> or <em>orient</em> or <em>spacing</em> or <em>a1</em> or <em>a2</em> or <em>a3</em> or <em>basis</em></li>
@@ -349,21 +349,20 @@ in commands that use the spacings should be decipherable.</p>
<hr class="docutils" />
<p>Example commands for generating a Wurtzite crystal (courtesy
of Aidan Thompson), with its 8 atom unit cell.</p>
-<pre class="literal-block">
-variable a equal 4.340330
+<div class="highlight-default"><div class="highlight"><pre><span></span>variable a equal 4.340330
variable b equal $a*sqrt(3.0)
variable c equal $a*sqrt(8.0/3.0)
-</pre>
-<pre class="literal-block">
-variable 1_3 equal 1.0/3.0
-variable 2_3 equal 2.0/3.0
-variable 1_6 equal 1.0/6.0
-variable 5_6 equal 5.0/6.0
-variable 1_12 equal 1.0/12.0
-variable 5_12 equal 5.0/12.0
-</pre>
-<pre class="literal-block">
-lattice custom 1.0 &
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="mi">1</span><span class="n">_3</span> <span class="n">equal</span> <span class="mf">1.0</span><span class="o">/</span><span class="mf">3.0</span>
+<span class="n">variable</span> <span class="mi">2</span><span class="n">_3</span> <span class="n">equal</span> <span class="mf">2.0</span><span class="o">/</span><span class="mf">3.0</span>
+<span class="n">variable</span> <span class="mi">1</span><span class="n">_6</span> <span class="n">equal</span> <span class="mf">1.0</span><span class="o">/</span><span class="mf">6.0</span>
+<span class="n">variable</span> <span class="mi">5</span><span class="n">_6</span> <span class="n">equal</span> <span class="mf">5.0</span><span class="o">/</span><span class="mf">6.0</span>
+<span class="n">variable</span> <span class="mi">1</span><span class="n">_12</span> <span class="n">equal</span> <span class="mf">1.0</span><span class="o">/</span><span class="mf">12.0</span>
+<span class="n">variable</span> <span class="mi">5</span><span class="n">_12</span> <span class="n">equal</span> <span class="mf">5.0</span><span class="o">/</span><span class="mf">12.0</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span>lattice custom 1.0 &
a1 $a 0.0 0.0 &
a2 0.0 $b 0.0 &
a3 0.0 0.0 $c &
@@ -375,16 +374,17 @@ lattice custom 1.0 &
basis 0.5 0.5 0.625 &
basis ${1_3} 0.0 0.125 &
basis ${5_6} 0.5 0.125
-</pre>
-<pre class="literal-block">
-region myreg block 0 1 0 1 0 1
-create_box 2 myreg
-create_atoms 1 box &
- basis 5 2 &
- basis 6 2 &
- basis 7 2 &
- basis 8 2
-</pre>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">region</span> <span class="n">myreg</span> <span class="n">block</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mi">1</span>
+<span class="n">create_box</span> <span class="mi">2</span> <span class="n">myreg</span>
+<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span> <span class="o">&</span>
+ <span class="n">basis</span> <span class="mi">5</span> <span class="mi">2</span> <span class="o">&</span>
+ <span class="n">basis</span> <span class="mi">6</span> <span class="mi">2</span> <span class="o">&</span>
+ <span class="n">basis</span> <span class="mi">7</span> <span class="mi">2</span> <span class="o">&</span>
+ <span class="n">basis</span> <span class="mi">8</span> <span class="mi">2</span>
+</pre></div>
+</div>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
diff --git a/doc/html/min_modify.html b/doc/html/min_modify.html
index bd9a1f285f..5434586014 100644
--- a/doc/html/min_modify.html
+++ b/doc/html/min_modify.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>min_modify command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-min_modify keyword values ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">min_modify</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul class="simple">
<li>one or more keyword/value pairs may be listed</li>
</ul>
@@ -144,9 +144,9 @@ keyword = <em>dmax</em> or <em>line</em>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-min_modify dmax 0.2
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">min_modify</span> <span class="n">dmax</span> <span class="mf">0.2</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
diff --git a/doc/html/min_style.html b/doc/html/min_style.html
index c2c66e37b9..158cf94d45 100644
--- a/doc/html/min_style.html
+++ b/doc/html/min_style.html
@@ -128,19 +128,19 @@
<span id="index-0"></span><h1>min_style command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-min_style style
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">min_style</span> <span class="n">style</span>
+</pre></div>
+</div>
<ul class="simple">
<li>style = <em>cg</em> or <em>hftn</em> or <em>sd</em> or <em>quickmin</em> or <em>fire</em></li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-min_style cg
-min_style fire
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">min_style</span> <span class="n">cg</span>
+<span class="n">min_style</span> <span class="n">fire</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -206,9 +206,9 @@ involving the electron radius in <a class="reference internal" href="pair_eff.ht
</div>
<div class="section" id="default">
<h2>Default</h2>
-<pre class="literal-block">
-min_style cg
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">min_style</span> <span class="n">cg</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p id="sheppard"><strong>(Sheppard)</strong> Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106
(2008). See ref 1 in this paper for original reference to Qmin in
diff --git a/doc/html/next.html b/doc/html/next.html
index e8b2338450..91a180f677 100644
--- a/doc/html/next.html
+++ b/doc/html/next.html
@@ -196,8 +196,7 @@ see in your directory during and after such a LAMMPS run.</p>
command with an <em>index</em>-style variable. If this input script is named
in.polymer, 8 simulations would be run using data files from
directories run1 thru run8.</p>
-<pre class="literal-block">
-variable d index run1 run2 run3 run4 run5 run6 run7 run8
+<div class="highlight-default"><div class="highlight"><pre><span></span>variable d index run1 run2 run3 run4 run5 run6 run7 run8
shell cd $d
read_data data.polymer
run 10000
@@ -205,7 +204,8 @@ shell cd ..
clear
next d
jump in.polymer
-</pre>
+</pre></div>
+</div>
<p>If the variable “d” were of style <em>universe</em>, and the same in.polymer
input script were run on 3 partitions of processors, then the first 3
simulations would begin, one on each set of processors. Whichever
@@ -214,8 +214,7 @@ and run another simulation, and so forth until all 8 simulations were
finished.</p>
<p>Jump and next commands can also be nested to enable multi-level loops.
For example, this script will run 15 simulations in a double loop.</p>
-<pre class="literal-block">
-variable i loop 3
+<div class="highlight-default"><div class="highlight"><pre><span></span>variable i loop 3
variable j loop 5
clear
...
@@ -226,7 +225,8 @@ variable i loop 3
jump in.script
next i
jump in.script
-</pre>
+</pre></div>
+</div>
<p>Here is an example of a double loop which uses the <a class="reference internal" href="if.html"><span class="doc">if</span></a> and
<a class="reference internal" href="jump.html"><span class="doc">jump</span></a> commands to break out of the inner loop when a
condition is met, then continues iterating thru the outer loop.</p>
diff --git a/doc/html/package.html b/doc/html/package.html
index 7146faef4d..90477fc5ec 100644
--- a/doc/html/package.html
+++ b/doc/html/package.html
@@ -572,11 +572,11 @@ compilers is to use one thread for each available CPU core when
performance.</p>
<p>Here are examples of how to set the environment variable when
launching LAMMPS:</p>
-<pre class="literal-block">
-env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
-env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
-mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">env</span> <span class="n">OMP_NUM_THREADS</span><span class="o">=</span><span class="mi">4</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>
+<span class="n">env</span> <span class="n">OMP_NUM_THREADS</span><span class="o">=</span><span class="mi">2</span> <span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>
+<span class="n">mpirun</span> <span class="o">-</span><span class="n">x</span> <span class="n">OMP_NUM_THREADS</span><span class="o">=</span><span class="mi">2</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>
+</pre></div>
+</div>
<p>or you can set it permanently in your shell’s start-up script.
All three of these examples use a total of 4 CPU cores.</p>
<p>Note that different MPI implementations have different ways of passing
diff --git a/doc/html/pair_brownian.html b/doc/html/pair_brownian.html
index 777cb46f10..eaf0a723c3 100644
--- a/doc/html/pair_brownian.html
+++ b/doc/html/pair_brownian.html
@@ -137,9 +137,9 @@
<h1>pair_style brownian/poly/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">mu</span> <span class="n">flaglog</span> <span class="n">flagfld</span> <span class="n">cutinner</span> <span class="n">cutoff</span> <span class="n">t_target</span> <span class="n">seed</span> <span class="n">flagHI</span> <span class="n">flagVF</span>
+</pre></div>
+</div>
<ul class="simple">
<li>style = <em>brownian</em> or <em>brownian/poly</em></li>
<li>mu = dynamic viscosity (dynamic viscosity units)</li>
@@ -155,11 +155,11 @@ pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1)
-pair_coeff 1 1 2.05 2.8
-pair_coeff * *
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">brownian</span> <span class="mf">1.5</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">2.01</span> <span class="mf">2.5</span> <span class="mf">2.0</span> <span class="mi">5878567</span> <span class="p">(</span><span class="n">assuming</span> <span class="n">radius</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">2.05</span> <span class="mf">2.8</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
diff --git a/doc/html/pair_dsmc.html b/doc/html/pair_dsmc.html
index 4c971f1dd1..5f8ddd5600 100644
--- a/doc/html/pair_dsmc.html
+++ b/doc/html/pair_dsmc.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>pair_style dsmc command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">dsmc</span> <span class="n">max_cell_size</span> <span class="n">seed</span> <span class="n">weighting</span> <span class="n">Tref</span> <span class="n">Nrecompute</span> <span class="n">Nsample</span>
+</pre></div>
+</div>
<ul class="simple">
<li>max_cell_size = global maximum cell size for DSMC interactions (distance units)</li>
<li>seed = random # seed (positive integer)</li>
@@ -142,11 +142,11 @@ pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-pair_style dsmc 2.5 34387 10 1.0 100 20
-pair_coeff * * 1.0
-pair_coeff 1 1 1.0
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">dsmc</span> <span class="mf">2.5</span> <span class="mi">34387</span> <span class="mi">10</span> <span class="mf">1.0</span> <span class="mi">100</span> <span class="mi">20</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span>
+<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -191,12 +191,12 @@ neighboring processors every timestep as they move. This makes it
possible to perform all collisions between pairs of particles that are
on the same processor. To ensure this occurs, you should use
these commands:</p>
-<pre class="literal-block">
-neighbor 0.0 bin
-neigh_modify every 1 delay 0 check no
-atom_modify sort 0 0.0
-communicate single cutoff 0.0
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">neighbor</span> <span class="mf">0.0</span> <span class="nb">bin</span>
+<span class="n">neigh_modify</span> <span class="n">every</span> <span class="mi">1</span> <span class="n">delay</span> <span class="mi">0</span> <span class="n">check</span> <span class="n">no</span>
+<span class="n">atom_modify</span> <span class="n">sort</span> <span class="mi">0</span> <span class="mf">0.0</span>
+<span class="n">communicate</span> <span class="n">single</span> <span class="n">cutoff</span> <span class="mf">0.0</span>
+</pre></div>
+</div>
<p>These commands ensure that LAMMPS communicates particles to
neighboring processors every timestep and that no ghost atoms are
created. The output statistics for a simulation run should indicate
diff --git a/doc/html/pair_hybrid.html b/doc/html/pair_hybrid.html
index 60044d0faf..afe0cebcd6 100644
--- a/doc/html/pair_hybrid.html
+++ b/doc/html/pair_hybrid.html
@@ -137,27 +137,27 @@
<h1>pair_style hybrid/overlay/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-pair_style hybrid style1 args style2 args ...
-pair_style hybrid/overlay style1 args style2 args ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span> <span class="n">style1</span> <span class="n">args</span> <span class="n">style2</span> <span class="n">args</span> <span class="o">...</span>
+<span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">style1</span> <span class="n">args</span> <span class="n">style2</span> <span class="n">args</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul class="simple">
<li>style1,style2 = list of one or more pair styles and their arguments</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0
-pair_coeff 1*2 1*2 eam niu3
-pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
-pair_coeff 1*2 3 lj/cut 0.5 1.2
-</pre>
-<pre class="literal-block">
-pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0
-pair_coeff * * lj/cut 1.0 1.0
-pair_coeff * * coul/long
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span> <span class="n">eam</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">5.0</span>
+<span class="n">pair_coeff</span> <span class="mi">1</span><span class="o">*</span><span class="mi">2</span> <span class="mi">1</span><span class="o">*</span><span class="mi">2</span> <span class="n">eam</span> <span class="n">niu3</span>
+<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="mi">3</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
+<span class="n">pair_coeff</span> <span class="mi">1</span><span class="o">*</span><span class="mi">2</span> <span class="mi">3</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">0.5</span> <span class="mf">1.2</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">2.5</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">2.0</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -218,22 +218,22 @@ these coefficients apply to.</p>
<p>For example, consider a simulation with 3 atom types: types 1 and 2
are Ni atoms, type 3 are LJ atoms with charges. The following
commands would set up a hybrid simulation:</p>
-<pre class="literal-block">
-pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
-pair_coeff * * eam/alloy nialhjea Ni Ni NULL
-pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
-pair_coeff 1*2 3 lj/cut 0.8 1.3
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span> <span class="n">eam</span><span class="o">/</span><span class="n">alloy</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">8.0</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">eam</span><span class="o">/</span><span class="n">alloy</span> <span class="n">nialhjea</span> <span class="n">Ni</span> <span class="n">Ni</span> <span class="n">NULL</span>
+<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="mi">3</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
+<span class="n">pair_coeff</span> <span class="mi">1</span><span class="o">*</span><span class="mi">2</span> <span class="mi">3</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">0.8</span> <span class="mf">1.3</span>
+</pre></div>
+</div>
<p>As an example of using the same pair style multiple times, consider a
simulation with 2 atom types. Type 1 is Si, type 2 is C. The
following commands would model the Si atoms with Tersoff, the C atoms
with Tersoff, and the cross-interactions with Lennard-Jones:</p>
-<pre class="literal-block">
-pair_style hybrid lj/cut 2.5 tersoff tersoff
-pair_coeff * * tersoff 1 Si.tersoff Si NULL
-pair_coeff * * tersoff 2 C.tersoff NULL C
-pair_coeff 1 2 lj/cut 1.0 1.5
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">2.5</span> <span class="n">tersoff</span> <span class="n">tersoff</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">tersoff</span> <span class="mi">1</span> <span class="n">Si</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">Si</span> <span class="n">NULL</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">tersoff</span> <span class="mi">2</span> <span class="n">C</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">NULL</span> <span class="n">C</span>
+<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.0</span> <span class="mf">1.5</span>
+</pre></div>
+</div>
<p>If pair coefficients are specified in the data file read via the
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command, then the same rule applies.
E.g. “eam/alloy” or “lj/cut” must be added after the atom type, for
@@ -266,16 +266,16 @@ sub-style that has already been defined for that pair of atoms, then
the new pair coefficients simply override the previous ones, as in the
normal usage of the pair_coeff command. E.g. these two sets of
commands are the same:</p>
-<pre class="literal-block">
-pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0
-pair_coeff 2 2 1.5 0.8
-</pre>
-<pre class="literal-block">
-pair_style hybrid/overlay lj/cut 2.5
-pair_coeff * * lj/cut 1.0 1.0
-pair_coeff 2 2 lj/cut 1.5 0.8
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">2.5</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
+<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mf">1.5</span> <span class="mf">0.8</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">2.5</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
+<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.5</span> <span class="mf">0.8</span>
+</pre></div>
+</div>
<p>Coefficients must be defined for each pair of atoms types via the
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as described above, or in the
data file or restart files read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or
@@ -293,9 +293,9 @@ command. You can assign it to some sub-style and set the coefficients
so that there is effectively no interaction (e.g. epsilon = 0.0 in a
LJ potential). Or, for <em>hybrid</em> and <em>hybrid/overlay</em> simulations, you
can use this form of the pair_coeff command in your input script:</p>
-<pre class="literal-block">
-pair_coeff 2 3 none
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="n">none</span>
+</pre></div>
+</div>
<p>or this form in the “Pair Coeffs” section of the data file:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">3</span> <span class="n">none</span>
</pre></div>
@@ -321,29 +321,29 @@ described by the different force fields do not mix.</p>
<p>Here is an example for mixing CHARMM and AMBER: The global <em>amber</em>
setting sets the 1-4 interactions to non-zero scaling factors and
then overrides them with 0.0 only for CHARMM:</p>
-<pre class="literal-block">
-special_bonds amber
-pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
-pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="n">amber</span>
+<span class="n">pair_hybrid</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
+<span class="n">pair_modify</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">special</span> <span class="n">lj</span><span class="o">/</span><span class="n">coul</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
+</pre></div>
+</div>
<p>The this input achieves the same effect:</p>
-<pre class="literal-block">
-special_bonds 0.0 0.0 0.1
-pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
-pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
-pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
-pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.1</span>
+<span class="n">pair_hybrid</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
+<span class="n">pair_modify</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">special</span> <span class="n">lj</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.5</span>
+<span class="n">pair_modify</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">special</span> <span class="n">coul</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.83333333</span>
+<span class="n">pair_modify</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">special</span> <span class="n">lj</span><span class="o">/</span><span class="n">coul</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
+</pre></div>
+</div>
<p>Here is an example for mixing Tersoff with OPLS/AA based on
a data file that defines bonds for all atoms where for the
Tersoff part of the system the force constants for the bonded
interactions have been set to 0. Note the global settings are
effectively <em>lj/coul 0.0 0.0 0.5</em> as required for OPLS/AA:</p>
-<pre class="literal-block">
-special_bonds lj/coul 1e-20 1e-20 0.5
-pair_hybrid tersoff lj/cut/coul/long 12.0
-pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="n">lj</span><span class="o">/</span><span class="n">coul</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">20</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">20</span> <span class="mf">0.5</span>
+<span class="n">pair_hybrid</span> <span class="n">tersoff</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">12.0</span>
+<span class="n">pair_modify</span> <span class="n">pair</span> <span class="n">tersoff</span> <span class="n">special</span> <span class="n">lj</span><span class="o">/</span><span class="n">coul</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
+</pre></div>
+</div>
<p>See the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> doc page for details on
the specific syntax, requirements and restrictions.</p>
<hr class="docutils" />
@@ -358,7 +358,7 @@ ReaxFF, etc. The way to think about using these potentials in a
hybrid setting is as follows.</p>
</div>
<p>A subset of atom types is assigned to the many-body potential with a
-single <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command, using “* *” to include
+single <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command, using “* <a href="#id1"><span class="problematic" id="id2">*</span></a>” to include
all types and the NULL keywords described above to exclude specific
types not assigned to that potential. If types 1,3,4 were assigned in
that way (but not type 2), this means that all many-body interactions
@@ -388,16 +388,16 @@ atoms in one surface, and type 2 for atoms in the other, and you wish
to use a Tersoff potential to compute interactions within each
surface, but not between surfaces. Then either of these two command
sequences would implement that model:</p>
-<pre class="literal-block">
-pair_style hybrid tersoff
-pair_coeff * * tersoff SiC.tersoff C C
-pair_coeff 1 2 none
-</pre>
-<pre class="literal-block">
-pair_style tersoff
-pair_coeff * * SiC.tersoff C C
-neigh_modify exclude type 1 2
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span> <span class="n">tersoff</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">tersoff</span> <span class="n">SiC</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">C</span> <span class="n">C</span>
+<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">none</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tersoff</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">SiC</span><span class="o">.</span><span class="n">tersoff</span> <span class="n">C</span> <span class="n">C</span>
+<span class="n">neigh_modify</span> <span class="n">exclude</span> <span class="nb">type</span> <span class="mi">1</span> <span class="mi">2</span>
+</pre></div>
+</div>
<p>Either way, only neighbor lists with 1-1 or 2-2 interactions would be
passed to the Tersoff potential, which means it would compute no
3-body interactions containing both type 1 and 2 atoms.</p>
@@ -406,11 +406,11 @@ potentials together, in an overlapping manner. Imagine you have CNT
(C atoms) on a Si surface. You want to use Tersoff for Si/Si and Si/C
interactions, and AIREBO for C/C interactions. Si atoms are type 1; C
atoms are type 2. Something like this will work:</p>
-<pre class="literal-block">
-pair_style hybrid/overlay tersoff airebo 3.0
-pair_coeff * * tersoff SiC.tersoff.custom Si C
-pair_coeff * * airebo CH.airebo NULL C
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">tersoff</span> <span class="n">airebo</span> <span class="mf">3.0</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">tersoff</span> <span class="n">SiC</span><span class="o">.</span><span class="n">tersoff</span><span class="o">.</span><span class="n">custom</span> <span class="n">Si</span> <span class="n">C</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">airebo</span> <span class="n">CH</span><span class="o">.</span><span class="n">airebo</span> <span class="n">NULL</span> <span class="n">C</span>
+</pre></div>
+</div>
<p>Note that to prevent the Tersoff potential from computing C/C
interactions, you would need to modify the SiC.tersoff file to turn
off C/C interaction, i.e. by setting the appropriate coefficients to
diff --git a/doc/html/pair_line_lj.html b/doc/html/pair_line_lj.html
index c79f73301e..f36f573822 100644
--- a/doc/html/pair_line_lj.html
+++ b/doc/html/pair_line_lj.html
@@ -128,19 +128,19 @@
<span id="index-0"></span><h1>pair_style line/lj command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-pair_style line/lj cutoff
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">line</span><span class="o">/</span><span class="n">lj</span> <span class="n">cutoff</span>
+</pre></div>
+</div>
<p>cutoff = global cutoff for interactions (distance units)</p>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-pair_style line/lj 3.0
-pair_coeff * * 1.0 1.0 1.0 0.8 1.12
-pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0
-pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">line</span><span class="o">/</span><span class="n">lj</span> <span class="mf">3.0</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.8</span> <span class="mf">1.12</span>
+<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mf">1.0</span> <span class="mf">2.0</span> <span class="mf">1.0</span> <span class="mf">1.5</span> <span class="mf">1.12</span> <span class="mf">5.0</span>
+<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
diff --git a/doc/html/pair_peri.html b/doc/html/pair_peri.html
index c2fa31cce8..a57e98bbb1 100644
--- a/doc/html/pair_peri.html
+++ b/doc/html/pair_peri.html
@@ -143,31 +143,31 @@
<h1>pair_style peri/eps command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-pair_style style
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span>
+</pre></div>
+</div>
<ul class="simple">
<li>style = <em>peri/pmb</em> or <em>peri/lps</em> or <em>peri/ves</em> or <em>peri/eps</em></li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-pair_style peri/pmb
-pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
-</pre>
-<pre class="literal-block">
-pair_style peri/lps
-pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
-</pre>
-<pre class="literal-block">
-pair_style peri/ves
-pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
-</pre>
-<pre class="literal-block">
-pair_style peri/eps
-pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">peri</span><span class="o">/</span><span class="n">pmb</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.6863e22</span> <span class="mf">0.0015001</span> <span class="mf">0.0005</span> <span class="mf">0.25</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">peri</span><span class="o">/</span><span class="n">lps</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">14.9e9</span> <span class="mf">14.9e9</span> <span class="mf">0.0015001</span> <span class="mf">0.0005</span> <span class="mf">0.25</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">peri</span><span class="o">/</span><span class="n">ves</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">14.9e9</span> <span class="mf">14.9e9</span> <span class="mf">0.0015001</span> <span class="mf">0.0005</span> <span class="mf">0.25</span> <span class="mf">0.5</span> <span class="mf">0.001</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">peri</span><span class="o">/</span><span class="n">eps</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">14.9e9</span> <span class="mf">14.9e9</span> <span class="mf">0.0015001</span> <span class="mf">0.0005</span> <span class="mf">0.25</span> <span class="mf">118.43</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
diff --git a/doc/html/pair_quip.html b/doc/html/pair_quip.html
index 91f1131efb..e2bae6d90b 100644
--- a/doc/html/pair_quip.html
+++ b/doc/html/pair_quip.html
@@ -128,17 +128,17 @@
<span id="index-0"></span><h1>pair_style quip command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-pair_style quip
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">quip</span>
+</pre></div>
+</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-pair_style quip
-pair_coeff * * gap_example.xml "Potential xml_label=GAP_2014_5_8_60_17_10_38_466" 14
-pair_coeff * * sw_example.xml "IP SW" 14
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">quip</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">gap_example</span><span class="o">.</span><span class="n">xml</span> <span class="s2">"Potential xml_label=GAP_2014_5_8_60_17_10_38_466"</span> <span class="mi">14</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">sw_example</span><span class="o">.</span><span class="n">xml</span> <span class="s2">"IP SW"</span> <span class="mi">14</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
diff --git a/doc/html/pair_reax.html b/doc/html/pair_reax.html
index 3929a8cd0d..3093a0b62b 100644
--- a/doc/html/pair_reax.html
+++ b/doc/html/pair_reax.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>pair_style reax command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-pair_style reax hbcut hbnewflag tripflag precision
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">reax</span> <span class="n">hbcut</span> <span class="n">hbnewflag</span> <span class="n">tripflag</span> <span class="n">precision</span>
+</pre></div>
+</div>
<ul class="simple">
<li>hbcut = hydrogen-bond cutoff (optional) (distance units)</li>
<li>hbnewflag = use old or new hbond function style (0 or 1) (optional)</li>
@@ -140,12 +140,12 @@ pair_style reax hbcut hbnewflag tripflag precision
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-pair_style reax
-pair_style reax 10.0 0 1 1.0e-5
-pair_coeff * * ffield.reax 3 1 2 2
-pair_coeff * * ffield.reax 3 NULL NULL 3
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">reax</span>
+<span class="n">pair_style</span> <span class="n">reax</span> <span class="mf">10.0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mf">1.0e-5</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">ffield</span><span class="o">.</span><span class="n">reax</span> <span class="mi">3</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">2</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">ffield</span><span class="o">.</span><span class="n">reax</span> <span class="mi">3</span> <span class="n">NULL</span> <span class="n">NULL</span> <span class="mi">3</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -238,14 +238,14 @@ names in italics match those used in the ReaxFF FORTRAN library):</p>
</ol>
<p>To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:</p>
-<pre class="literal-block">
-compute reax all pair reax
-variable eb equal c_reax[1]
-variable ea equal c_reax[2]
-...
-variable eqeq equal c_reax[14]
-thermo_style custom step temp epair v_eb v_ea ... v_eqeq
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">reax</span> <span class="nb">all</span> <span class="n">pair</span> <span class="n">reax</span>
+<span class="n">variable</span> <span class="n">eb</span> <span class="n">equal</span> <span class="n">c_reax</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+<span class="n">variable</span> <span class="n">ea</span> <span class="n">equal</span> <span class="n">c_reax</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+<span class="o">...</span>
+<span class="n">variable</span> <span class="n">eqeq</span> <span class="n">equal</span> <span class="n">c_reax</span><span class="p">[</span><span class="mi">14</span><span class="p">]</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">epair</span> <span class="n">v_eb</span> <span class="n">v_ea</span> <span class="o">...</span> <span class="n">v_eqeq</span>
+</pre></div>
+</div>
<p>Only a single pair_coeff command is used with the <em>reax</em> style which
specifies a ReaxFF potential file with parameters for all needed
elements. These are mapped to LAMMPS atom types by specifying N
@@ -286,9 +286,9 @@ enable this.</p>
elements are ordered as C, H, O, N in the <em>ffield</em> file. If you want
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
H, you would use the following pair_coeff command:</p>
-<pre class="literal-block">
-pair_coeff * * ffield.reax 1 1 4 2
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">ffield</span><span class="o">.</span><span class="n">reax</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">4</span> <span class="mi">2</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a>
diff --git a/doc/html/pair_reax_c.html b/doc/html/pair_reax_c.html
index 38e27022b9..bd96471c6b 100644
--- a/doc/html/pair_reax_c.html
+++ b/doc/html/pair_reax_c.html
@@ -131,9 +131,9 @@
<h1>pair_style reax/c/kk command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-pair_style reax/c cfile keyword value
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">cfile</span> <span class="n">keyword</span> <span class="n">value</span>
+</pre></div>
+</div>
<ul class="simple">
<li>cfile = NULL or name of a control file</li>
<li>zero or more keyword/value pairs may be appended</li>
@@ -148,13 +148,13 @@ keyword = <em>checkqeq</em> or <em>lgvdw</em> or <em>safezone</em> or <em>mincap
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-pair_style reax/c NULL
-pair_style reax/c controlfile checkqeq no
-pair_style reax/c NULL lgvdw yes
-pair_style reax/c NULL safezone 1.6 mincap 100
-pair_coeff * * ffield.reax C H O N
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">NULL</span>
+<span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">controlfile</span> <span class="n">checkqeq</span> <span class="n">no</span>
+<span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">NULL</span> <span class="n">lgvdw</span> <span class="n">yes</span>
+<span class="n">pair_style</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span> <span class="n">NULL</span> <span class="n">safezone</span> <span class="mf">1.6</span> <span class="n">mincap</span> <span class="mi">100</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">ffield</span><span class="o">.</span><span class="n">reax</span> <span class="n">C</span> <span class="n">H</span> <span class="n">O</span> <span class="n">N</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -276,14 +276,14 @@ names in italics match those used in the original FORTRAN ReaxFF code):</p>
</ol>
<p>To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:</p>
-<pre class="literal-block">
-compute reax all pair reax/c
-variable eb equal c_reax[1]
-variable ea equal c_reax[2]
-...
-variable eqeq equal c_reax[14]
-thermo_style custom step temp epair v_eb v_ea ... v_eqeq
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">reax</span> <span class="nb">all</span> <span class="n">pair</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span>
+<span class="n">variable</span> <span class="n">eb</span> <span class="n">equal</span> <span class="n">c_reax</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+<span class="n">variable</span> <span class="n">ea</span> <span class="n">equal</span> <span class="n">c_reax</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+<span class="o">...</span>
+<span class="n">variable</span> <span class="n">eqeq</span> <span class="n">equal</span> <span class="n">c_reax</span><span class="p">[</span><span class="mi">14</span><span class="p">]</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">epair</span> <span class="n">v_eb</span> <span class="n">v_ea</span> <span class="o">...</span> <span class="n">v_eqeq</span>
+</pre></div>
+</div>
<p>Only a single pair_coeff command is used with the <em>reax/c</em> style which
specifies a ReaxFF potential file with parameters for all needed
elements. These are mapped to LAMMPS atom types by specifying N
@@ -310,14 +310,14 @@ types that will be used with other potentials.</p>
elements are ordered as C, H, O, N in the <em>ffield</em> file. If you want
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
H, you would use the following pair_coeff command:</p>
-<pre class="literal-block">
-pair_coeff * * ffield.reax C C N H
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">ffield</span><span class="o">.</span><span class="n">reax</span> <span class="n">C</span> <span class="n">C</span> <span class="n">N</span> <span class="n">H</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p>The format of a line in the control file is as follows:</p>
-<pre class="literal-block">
-variable_name value
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable_name</span> <span class="n">value</span>
+</pre></div>
+</div>
<p>and it may be followed by an ”!” character and a trailing comment.</p>
<p>If the value of a control variable is not specified, then default
values are used. What follows is the list of variables along with a
diff --git a/doc/html/pair_smd_hertz.html b/doc/html/pair_smd_hertz.html
index 25cbc618da..52dd7939f6 100644
--- a/doc/html/pair_smd_hertz.html
+++ b/doc/html/pair_smd_hertz.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>pair_style smd/hertz command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-pair_style smd/hertz scale_factor
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">smd</span><span class="o">/</span><span class="n">hertz</span> <span class="n">scale_factor</span>
+</pre></div>
+</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
@@ -146,7 +146,7 @@ The effect is that a particles cannot penetrate into each other.
The parameter <contact_stiffness> has units of pressure and should equal roughly one half
of the Young’s modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles.</p>
<p>The parameter <em>scale_factor</em> can be used to scale the particles’ contact radii. This can be useful to control how close
-particles can approach each other. Usually, <a href="#id1"><span class="problematic" id="id2">*</span></a>scale_factor*=1.0.</p>
+particles can approach each other. Usually, <em>scale_factor</em>=1.0.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>No mixing is performed automatically.
diff --git a/doc/html/pair_smd_triangulated_surface.html b/doc/html/pair_smd_triangulated_surface.html
index 428893dfc3..9f4ba0991d 100644
--- a/doc/html/pair_smd_triangulated_surface.html
+++ b/doc/html/pair_smd_triangulated_surface.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>pair_style smd/tri_surface command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-pair_style smd/tri_surface scale_factor
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">smd</span><span class="o">/</span><span class="n">tri_surface</span> <span class="n">scale_factor</span>
+</pre></div>
+</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
@@ -147,7 +147,7 @@ The effect is that a particle cannot penetrate into the triangular surface.
The parameter <contact_stiffness> has units of pressure and should equal roughly one half
of the Young’s modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle</p>
<p>The parameter <em>scale_factor</em> can be used to scale the particles’ contact radii. This can be useful to control how close
-particles can approach the triangulated surface. Usually, <a href="#id1"><span class="problematic" id="id2">*</span></a>scale_factor*=1.0.</p>
+particles can approach the triangulated surface. Usually, <em>scale_factor</em>=1.0.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>No mixing is performed automatically.
diff --git a/doc/html/pair_style.html b/doc/html/pair_style.html
index 86a80963cc..4dc6adc479 100644
--- a/doc/html/pair_style.html
+++ b/doc/html/pair_style.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>pair_style command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-pair_style style args
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
+</pre></div>
+</div>
<ul class="simple">
<li>style = one of the styles from the list below</li>
<li>args = arguments used by a particular style</li>
@@ -138,13 +138,13 @@ pair_style style args
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-pair_style lj/cut 2.5
-pair_style eam/alloy
-pair_style hybrid lj/charmm/coul/long 10.0 eam
-pair_style table linear 1000
-pair_style none
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">2.5</span>
+<span class="n">pair_style</span> <span class="n">eam</span><span class="o">/</span><span class="n">alloy</span>
+<span class="n">pair_style</span> <span class="n">hybrid</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span> <span class="n">eam</span>
+<span class="n">pair_style</span> <span class="n">table</span> <span class="n">linear</span> <span class="mi">1000</span>
+<span class="n">pair_style</span> <span class="n">none</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -338,9 +338,9 @@ package.</p>
</div>
<div class="section" id="default">
<h2>Default</h2>
-<pre class="literal-block">
-pair_style none
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">none</span>
+</pre></div>
+</div>
</div>
</div>
diff --git a/doc/html/pair_thole.html b/doc/html/pair_thole.html
index 8e8f15daf2..b2742247f9 100644
--- a/doc/html/pair_thole.html
+++ b/doc/html/pair_thole.html
@@ -134,9 +134,9 @@
<h1>pair_style lj/cut/thole/long/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-pair_style style args
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
+</pre></div>
+</div>
<ul class="simple">
<li>style = <em>thole</em> or <em>lj/cut/thole/long</em> or <em>lj/cut/thole/long/omp</em></li>
<li>args = list of arguments for a particular style</li>
@@ -153,15 +153,15 @@ pair_style style args
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-pair_style hybrid/overlay ... thole 2.6 12.0
-pair_coeff 1 1 thole 1.0
-pair_coeff 1 2 thole 1.0 2.6 10.0
-pair_coeff * 2 thole 1.0 2.6
-</pre>
-<pre class="literal-block">
-pair_style lj/cut/thole/long 2.6 12.0
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="o">...</span> <span class="n">thole</span> <span class="mf">2.6</span> <span class="mf">12.0</span>
+<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">thole</span> <span class="mf">1.0</span>
+<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">thole</span> <span class="mf">1.0</span> <span class="mf">2.6</span> <span class="mf">10.0</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="mi">2</span> <span class="n">thole</span> <span class="mf">1.0</span> <span class="mf">2.6</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">thole</span><span class="o">/</span><span class="n">long</span> <span class="mf">2.6</span> <span class="mf">12.0</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
diff --git a/doc/html/pair_tri_lj.html b/doc/html/pair_tri_lj.html
index bdda14e2e2..e6c6b24ddd 100644
--- a/doc/html/pair_tri_lj.html
+++ b/doc/html/pair_tri_lj.html
@@ -128,18 +128,18 @@
<span id="index-0"></span><h1>pair_style tri/lj command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-pair_style tri/lj cutoff
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tri</span><span class="o">/</span><span class="n">lj</span> <span class="n">cutoff</span>
+</pre></div>
+</div>
<p>cutoff = global cutoff for interactions (distance units)</p>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-pair_style tri/lj 3.0
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.5 2.5
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tri</span><span class="o">/</span><span class="n">lj</span> <span class="mf">3.0</span>
+<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
+<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.5</span> <span class="mf">2.5</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
diff --git a/doc/html/prd.html b/doc/html/prd.html
index a32fecfdce..ee0c7948c0 100644
--- a/doc/html/prd.html
+++ b/doc/html/prd.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>prd command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">prd</span> <span class="n">N</span> <span class="n">t_event</span> <span class="n">n_dephase</span> <span class="n">t_dephase</span> <span class="n">t_correlate</span> <span class="n">compute</span><span class="o">-</span><span class="n">ID</span> <span class="n">seed</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul class="simple">
<li>N = # of timesteps to run (not including dephasing/quenching)</li>
<li>t_event = timestep interval between event checks</li>
@@ -200,19 +200,19 @@ potentials, etc should be the same for every replica.</p>
<p>A PRD run has several stages, which are repeated each time an “event”
occurs in one of the replicas, as defined below. The logic for a PRD
run is as follows:</p>
-<pre class="literal-block">
-while (time remains):
- dephase for n_dephase*t_dephase steps
- until (event occurs on some replica):
- run dynamics for t_event steps
- quench
- check for uncorrelated event on any replica
- until (no correlated event occurs):
- run dynamics for t_correlate steps
- quench
- check for correlated event on this replica
- event replica shares state with all replicas
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">while</span> <span class="p">(</span><span class="n">time</span> <span class="n">remains</span><span class="p">):</span>
+ <span class="n">dephase</span> <span class="k">for</span> <span class="n">n_dephase</span><span class="o">*</span><span class="n">t_dephase</span> <span class="n">steps</span>
+ <span class="n">until</span> <span class="p">(</span><span class="n">event</span> <span class="n">occurs</span> <span class="n">on</span> <span class="n">some</span> <span class="n">replica</span><span class="p">):</span>
+ <span class="n">run</span> <span class="n">dynamics</span> <span class="k">for</span> <span class="n">t_event</span> <span class="n">steps</span>
+ <span class="n">quench</span>
+ <span class="n">check</span> <span class="k">for</span> <span class="n">uncorrelated</span> <span class="n">event</span> <span class="n">on</span> <span class="nb">any</span> <span class="n">replica</span>
+ <span class="n">until</span> <span class="p">(</span><span class="n">no</span> <span class="n">correlated</span> <span class="n">event</span> <span class="n">occurs</span><span class="p">):</span>
+ <span class="n">run</span> <span class="n">dynamics</span> <span class="k">for</span> <span class="n">t_correlate</span> <span class="n">steps</span>
+ <span class="n">quench</span>
+ <span class="n">check</span> <span class="k">for</span> <span class="n">correlated</span> <span class="n">event</span> <span class="n">on</span> <span class="n">this</span> <span class="n">replica</span>
+ <span class="n">event</span> <span class="n">replica</span> <span class="n">shares</span> <span class="n">state</span> <span class="k">with</span> <span class="nb">all</span> <span class="n">replicas</span>
+</pre></div>
+</div>
<p>Before this loop begins, the state of the system on replica 0 is
shared with all replicas, so that all replicas begin from the same
initial state. The first potential energy basin is identified by
diff --git a/doc/html/processors.html b/doc/html/processors.html
index 15f24d6340..f0feeb91ba 100644
--- a/doc/html/processors.html
+++ b/doc/html/processors.html
@@ -162,15 +162,15 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-processors * * 5
-processors 2 4 4
-processors * * 8 map xyz
-processors * * * grid numa
-processors * * * grid twolevel 4 * * 1
-processors 4 8 16 grid custom myfile
-processors * * * part 1 2 multiple
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">processors</span> <span class="o">*</span> <span class="o">*</span> <span class="mi">5</span>
+<span class="n">processors</span> <span class="mi">2</span> <span class="mi">4</span> <span class="mi">4</span>
+<span class="n">processors</span> <span class="o">*</span> <span class="o">*</span> <span class="mi">8</span> <span class="nb">map</span> <span class="n">xyz</span>
+<span class="n">processors</span> <span class="o">*</span> <span class="o">*</span> <span class="o">*</span> <span class="n">grid</span> <span class="n">numa</span>
+<span class="n">processors</span> <span class="o">*</span> <span class="o">*</span> <span class="o">*</span> <span class="n">grid</span> <span class="n">twolevel</span> <span class="mi">4</span> <span class="o">*</span> <span class="o">*</span> <span class="mi">1</span>
+<span class="n">processors</span> <span class="mi">4</span> <span class="mi">8</span> <span class="mi">16</span> <span class="n">grid</span> <span class="n">custom</span> <span class="n">myfile</span>
+<span class="n">processors</span> <span class="o">*</span> <span class="o">*</span> <span class="o">*</span> <span class="n">part</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">multiple</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -428,7 +428,7 @@ option.</p>
</div>
<div class="section" id="default">
<h2>Default</h2>
-<p>The option defaults are Px Py Pz = * * *, grid = onelevel, and map =
+<p>The option defaults are Px Py Pz = * * <a href="#id1"><span class="problematic" id="id2">*</span></a>, grid = onelevel, and map =
cart.</p>
</div>
</div>
diff --git a/doc/html/python.html b/doc/html/python.html
index 6700435a9f..f78a9df834 100644
--- a/doc/html/python.html
+++ b/doc/html/python.html
@@ -161,35 +161,35 @@ keyword = <em>invoke</em> or <em>input</em> or <em>return</em> or <em>format</em
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-python pForce input 2 v_x 20.0 return v_f format fff file force.py
-python pForce invoke
-</pre>
-<pre class="literal-block">
-python factorial input 1 myN return v_fac format ii here """
-def factorial(n):
- if n == 1: return n
- return n * factorial(n-1)
- """
-</pre>
-<pre class="literal-block">
-python loop input 1 SELF return v_value format -f here """
-def loop(lmpptr,N,cut0):
- from lammps import lammps
- lmp = lammps(ptr=lmpptr)
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">pForce</span> <span class="nb">input</span> <span class="mi">2</span> <span class="n">v_x</span> <span class="mf">20.0</span> <span class="k">return</span> <span class="n">v_f</span> <span class="nb">format</span> <span class="n">fff</span> <span class="n">file</span> <span class="n">force</span><span class="o">.</span><span class="n">py</span>
+<span class="n">python</span> <span class="n">pForce</span> <span class="n">invoke</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">factorial</span> <span class="nb">input</span> <span class="mi">1</span> <span class="n">myN</span> <span class="k">return</span> <span class="n">v_fac</span> <span class="nb">format</span> <span class="n">ii</span> <span class="n">here</span> <span class="s2">"""</span>
+<span class="s2">def factorial(n):</span>
+<span class="s2"> if n == 1: return n</span>
+<span class="s2"> return n * factorial(n-1)</span>
+<span class="s2"> """</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">loop</span> <span class="nb">input</span> <span class="mi">1</span> <span class="n">SELF</span> <span class="k">return</span> <span class="n">v_value</span> <span class="nb">format</span> <span class="o">-</span><span class="n">f</span> <span class="n">here</span> <span class="s2">"""</span>
+<span class="s2">def loop(lmpptr,N,cut0):</span>
+<span class="s2"> from lammps import lammps</span>
+<span class="s2"> lmp = lammps(ptr=lmpptr)</span>
+</pre></div>
+</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># loop N times, increasing cutoff each time</span>
</pre></div>
</div>
-<pre class="literal-block">
- for i in range(N):
- cut = cut0 + i*0.1
- lmp.set_variable("cut",cut) # set a variable in LAMMPS
- lmp.command("pair_style lj/cut ${cut}") # LAMMPS commands
- lmp.command("pair_coeff * * 1.0 1.0")
- lmp.command("run 100")
-"""
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">N</span><span class="p">):</span>
+ <span class="n">cut</span> <span class="o">=</span> <span class="n">cut0</span> <span class="o">+</span> <span class="n">i</span><span class="o">*</span><span class="mf">0.1</span>
+ <span class="n">lmp</span><span class="o">.</span><span class="n">set_variable</span><span class="p">(</span><span class="s2">"cut"</span><span class="p">,</span><span class="n">cut</span><span class="p">)</span> <span class="c1"># set a variable in LAMMPS</span>
+ <span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">"pair_style lj/cut $</span><span class="si">{cut}</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># LAMMPS commands</span>
+ <span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">"pair_coeff * * 1.0 1.0"</span><span class="p">)</span>
+ <span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">"run 100"</span><span class="p">)</span>
+<span class="s2">"""</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -263,10 +263,10 @@ numeric or string value, as specified by the <em>format</em> keyword.</p>
of a python-style variable associates a Python function name with the
variable. This must match the <em>func</em> setting for this command. For
exampe these two commands would be self-consistent:</p>
-<pre class="literal-block">
-variable foo python myMultiply
-python myMultiply return v_foo format f file funcs.py
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">foo</span> <span class="n">python</span> <span class="n">myMultiply</span>
+<span class="n">python</span> <span class="n">myMultiply</span> <span class="k">return</span> <span class="n">v_foo</span> <span class="nb">format</span> <span class="n">f</span> <span class="n">file</span> <span class="n">funcs</span><span class="o">.</span><span class="n">py</span>
+</pre></div>
+</div>
<p>The two commands can appear in either order in the input script so
long as both are specified before the Python function is invoked for
the first time.</p>
@@ -417,29 +417,29 @@ Python wraps the various functions included in the LAMMPS library
interface.</p>
<p>A more interesting example is in the examples/python/in.python script
which loads and runs the following function from examples/python/funcs.py:</p>
-<pre class="literal-block">
-def loop(N,cut0,thresh,lmpptr):
- print "LOOP ARGS",N,cut0,thresh,lmpptr
- from lammps import lammps
- lmp = lammps(ptr=lmpptr)
- natoms = lmp.get_natoms()
-</pre>
-<pre class="literal-block">
-for i in range(N):
- cut = cut0 + i*0.1
-</pre>
-<pre class="literal-block">
-lmp.set_variable("cut",cut) # set a variable in LAMMPS
-lmp.command("pair_style lj/cut ${cut}") # LAMMPS command
-#lmp.command("pair_style lj/cut %d" % cut) # LAMMPS command option
-</pre>
-<pre class="literal-block">
-lmp.command("pair_coeff * * 1.0 1.0") # ditto
-lmp.command("run 10") # ditto
-pe = lmp.extract_compute("thermo_pe",0,0) # extract total PE from LAMMPS
-print "PE",pe/natoms,thresh
-if pe/natoms < thresh: return
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">def</span> <span class="nf">loop</span><span class="p">(</span><span class="n">N</span><span class="p">,</span><span class="n">cut0</span><span class="p">,</span><span class="n">thresh</span><span class="p">,</span><span class="n">lmpptr</span><span class="p">):</span>
+ <span class="nb">print</span> <span class="s2">"LOOP ARGS"</span><span class="p">,</span><span class="n">N</span><span class="p">,</span><span class="n">cut0</span><span class="p">,</span><span class="n">thresh</span><span class="p">,</span><span class="n">lmpptr</span>
+ <span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span>
+ <span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">ptr</span><span class="o">=</span><span class="n">lmpptr</span><span class="p">)</span>
+ <span class="n">natoms</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">get_natoms</span><span class="p">()</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">N</span><span class="p">):</span>
+ <span class="n">cut</span> <span class="o">=</span> <span class="n">cut0</span> <span class="o">+</span> <span class="n">i</span><span class="o">*</span><span class="mf">0.1</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp</span><span class="o">.</span><span class="n">set_variable</span><span class="p">(</span><span class="s2">"cut"</span><span class="p">,</span><span class="n">cut</span><span class="p">)</span> <span class="c1"># set a variable in LAMMPS</span>
+<span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">"pair_style lj/cut $</span><span class="si">{cut}</span><span class="s2">"</span><span class="p">)</span> <span class="c1"># LAMMPS command</span>
+<span class="c1">#lmp.command("pair_style lj/cut %d" % cut) # LAMMPS command option</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">"pair_coeff * * 1.0 1.0"</span><span class="p">)</span> <span class="c1"># ditto</span>
+<span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="s2">"run 10"</span><span class="p">)</span> <span class="c1"># ditto</span>
+<span class="n">pe</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_compute</span><span class="p">(</span><span class="s2">"thermo_pe"</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">)</span> <span class="c1"># extract total PE from LAMMPS</span>
+<span class="nb">print</span> <span class="s2">"PE"</span><span class="p">,</span><span class="n">pe</span><span class="o">/</span><span class="n">natoms</span><span class="p">,</span><span class="n">thresh</span>
+<span class="k">if</span> <span class="n">pe</span><span class="o">/</span><span class="n">natoms</span> <span class="o"><</span> <span class="n">thresh</span><span class="p">:</span> <span class="k">return</span>
+</pre></div>
+</div>
<p>with these input script commands:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">loop</span> <span class="nb">input</span> <span class="mi">4</span> <span class="mi">10</span> <span class="mf">1.0</span> <span class="o">-</span><span class="mf">4.0</span> <span class="n">SELF</span> <span class="nb">format</span> <span class="n">iffp</span> <span class="n">file</span> <span class="n">funcs</span><span class="o">.</span><span class="n">py</span>
<span class="n">python</span> <span class="n">loop</span> <span class="n">invoke</span>
diff --git a/doc/html/read_dump.html b/doc/html/read_dump.html
index 5e2e9f96eb..603ab46785 100644
--- a/doc/html/read_dump.html
+++ b/doc/html/read_dump.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>read_dump command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-read_dump file Nstep field1 field2 ... keyword values ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">read_dump</span> <span class="n">file</span> <span class="n">Nstep</span> <span class="n">field1</span> <span class="n">field2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul class="simple">
<li>file = name of dump file to read</li>
<li>Nstep = snapshot timestep to read from file</li>
@@ -168,18 +168,18 @@ field = <em>x</em> or <em>y</em> or <em>z</em> or <em>vx</em> or <em>vy</em> or
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-read_dump dump.file 5000 x y z
-read_dump dump.xyz 5 x y z box no format xyz
-read_dump dump.xyz 10 x y z box no format molfile xyz "../plugins"
-read_dump dump.dcd 0 x y z box yes format molfile dcd
-read_dump dump.file 1000 x y z vx vy vz box yes format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
-read_dump dump.file 5000 x y vx vy trim yes
-read_dump ../run7/dump.file.gz 10000 x y z box yes
-read_dump dump.xyz 10 x y z box no format molfile xyz ../plugins
-read_dump dump.dcd 0 x y z format molfile dcd
-read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">file</span> <span class="mi">5000</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span>
+<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">xyz</span> <span class="mi">5</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">box</span> <span class="n">no</span> <span class="nb">format</span> <span class="n">xyz</span>
+<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">xyz</span> <span class="mi">10</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">box</span> <span class="n">no</span> <span class="nb">format</span> <span class="n">molfile</span> <span class="n">xyz</span> <span class="s2">"../plugins"</span>
+<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">dcd</span> <span class="mi">0</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">box</span> <span class="n">yes</span> <span class="nb">format</span> <span class="n">molfile</span> <span class="n">dcd</span>
+<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">file</span> <span class="mi">1000</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span> <span class="n">box</span> <span class="n">yes</span> <span class="nb">format</span> <span class="n">molfile</span> <span class="n">lammpstrj</span> <span class="o">/</span><span class="n">usr</span><span class="o">/</span><span class="n">local</span><span class="o">/</span><span class="n">lib</span><span class="o">/</span><span class="n">vmd</span><span class="o">/</span><span class="n">plugins</span><span class="o">/</span><span class="n">LINUXAMD64</span><span class="o">/</span><span class="n">plugins</span><span class="o">/</span><span class="n">molfile</span>
+<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">file</span> <span class="mi">5000</span> <span class="n">x</span> <span class="n">y</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">trim</span> <span class="n">yes</span>
+<span class="n">read_dump</span> <span class="o">../</span><span class="n">run7</span><span class="o">/</span><span class="n">dump</span><span class="o">.</span><span class="n">file</span><span class="o">.</span><span class="n">gz</span> <span class="mi">10000</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">box</span> <span class="n">yes</span>
+<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">xyz</span> <span class="mi">10</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">box</span> <span class="n">no</span> <span class="nb">format</span> <span class="n">molfile</span> <span class="n">xyz</span> <span class="o">../</span><span class="n">plugins</span>
+<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">dcd</span> <span class="mi">0</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="nb">format</span> <span class="n">molfile</span> <span class="n">dcd</span>
+<span class="n">read_dump</span> <span class="n">dump</span><span class="o">.</span><span class="n">file</span> <span class="mi">1000</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span> <span class="nb">format</span> <span class="n">molfile</span> <span class="n">lammpstrj</span> <span class="o">/</span><span class="n">usr</span><span class="o">/</span><span class="n">local</span><span class="o">/</span><span class="n">lib</span><span class="o">/</span><span class="n">vmd</span><span class="o">/</span><span class="n">plugins</span><span class="o">/</span><span class="n">LINUXAMD64</span><span class="o">/</span><span class="n">plugins</span><span class="o">/</span><span class="n">molfile</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
diff --git a/doc/html/restart.html b/doc/html/restart.html
index 3f169da485..d6fc25f246 100644
--- a/doc/html/restart.html
+++ b/doc/html/restart.html
@@ -150,14 +150,14 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-restart 0
-restart 1000 poly.restart
-restart 1000 poly.restart.mpiio
-restart 1000 restart.*.equil
-restart 10000 poly.%.1 poly.%.2 nfile 10
-restart v_mystep poly.restart
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">restart</span> <span class="mi">0</span>
+<span class="n">restart</span> <span class="mi">1000</span> <span class="n">poly</span><span class="o">.</span><span class="n">restart</span>
+<span class="n">restart</span> <span class="mi">1000</span> <span class="n">poly</span><span class="o">.</span><span class="n">restart</span><span class="o">.</span><span class="n">mpiio</span>
+<span class="n">restart</span> <span class="mi">1000</span> <span class="n">restart</span><span class="o">.*.</span><span class="n">equil</span>
+<span class="n">restart</span> <span class="mi">10000</span> <span class="n">poly</span><span class="o">.%.</span><span class="mi">1</span> <span class="n">poly</span><span class="o">.%.</span><span class="mi">2</span> <span class="n">nfile</span> <span class="mi">10</span>
+<span class="n">restart</span> <span class="n">v_mystep</span> <span class="n">poly</span><span class="o">.</span><span class="n">restart</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -226,10 +226,10 @@ options for <a class="reference internal" href="variable.html"><span class="doc"
<p>For example, the following commands will write restart files
every step from 1100 to 1200, and could be useful for debugging
a simulation where something goes wrong at step 1163:</p>
-<pre class="literal-block">
-variable s equal stride(1100,1200,1)
-restart v_s tmp.restart
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">s</span> <span class="n">equal</span> <span class="n">stride</span><span class="p">(</span><span class="mi">1100</span><span class="p">,</span><span class="mi">1200</span><span class="p">,</span><span class="mi">1</span><span class="p">)</span>
+<span class="n">restart</span> <span class="n">v_s</span> <span class="n">tmp</span><span class="o">.</span><span class="n">restart</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p>See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for information about
what is stored in a restart file.</p>
diff --git a/doc/html/run_style.html b/doc/html/run_style.html
index b00835c7e1..9ef0e69f67 100644
--- a/doc/html/run_style.html
+++ b/doc/html/run_style.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>run_style command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-run_style style args
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run_style</span> <span class="n">style</span> <span class="n">args</span>
+</pre></div>
+</div>
<ul class="simple">
<li>style = <em>verlet</em> or <em>verlet/split</em> or <em>respa</em> or <em>respa/omp</em></li>
</ul>
@@ -175,14 +175,14 @@ run_style style args
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-run_style verlet
-run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
-run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4
-</pre>
-<pre class="literal-block">
-run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run_style</span> <span class="n">verlet</span>
+<span class="n">run_style</span> <span class="n">respa</span> <span class="mi">4</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">bond</span> <span class="mi">1</span> <span class="n">dihedral</span> <span class="mi">2</span> <span class="n">pair</span> <span class="mi">3</span> <span class="n">kspace</span> <span class="mi">4</span>
+<span class="n">run_style</span> <span class="n">respa</span> <span class="mi">4</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">bond</span> <span class="mi">1</span> <span class="n">dihedral</span> <span class="mi">2</span> <span class="n">inner</span> <span class="mi">3</span> <span class="mf">5.0</span> <span class="mf">6.0</span> <span class="n">outer</span> <span class="mi">4</span> <span class="n">kspace</span> <span class="mi">4</span>
+</pre></div>
+</div>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run_style</span> <span class="n">respa</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mi">2</span> <span class="n">bond</span> <span class="mi">1</span> <span class="n">hybrid</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mi">1</span> <span class="n">kspace</span> <span class="mi">3</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -219,9 +219,9 @@ its onn optimal layout, then require the 2nd partition’s layout to
match the integer multiple constraint. See the
<a class="reference internal" href="processors.html"><span class="doc">processors</span></a> command with its <em>part</em> keyword for a way
to control this, e.g.</p>
-<pre class="literal-block">
-procssors * * * part 1 2 multiple
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">procssors</span> <span class="o">*</span> <span class="o">*</span> <span class="o">*</span> <span class="n">part</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">multiple</span>
+</pre></div>
+</div>
<p>You can also use the <a class="reference internal" href="partition.html"><span class="doc">partition</span></a> command to explicitly
specity the processor layout on each partition. E.g. for 2 partitions
of 60 and 15 processors each:</p>
@@ -314,10 +314,10 @@ angstrom “healing distance” (the distance between the outer and inne
cutoffs) works reasonably well. We thus recommend the following
settings for use of the <em>respa</em> style without SHAKE in biomolecular
simulations:</p>
-<pre class="literal-block">
-timestep 4.0
-run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">timestep</span> <span class="mf">4.0</span>
+<span class="n">run_style</span> <span class="n">respa</span> <span class="mi">4</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">inner</span> <span class="mi">2</span> <span class="mf">4.5</span> <span class="mf">6.0</span> <span class="n">middle</span> <span class="mi">3</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="n">outer</span> <span class="mi">4</span>
+</pre></div>
+</div>
<p>With these settings, users can expect good energy conservation and
roughly a 2.5 fold speedup over the <em>verlet</em> style with a 0.5 fmsec
timestep.</p>
@@ -332,11 +332,11 @@ respa in order to freeze out these high frequency motions and increase
the size of the time steps in the respa hierarchy. The following
settings can be used for biomolecular simulations with SHAKE and
rRESPA:</p>
-<pre class="literal-block">
-fix 2 all shake 0.000001 500 0 m 1.0 a 1
-timestep 4.0
-run_style respa 2 2 inner 1 4.0 5.0 outer 2
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">shake</span> <span class="mf">0.000001</span> <span class="mi">500</span> <span class="mi">0</span> <span class="n">m</span> <span class="mf">1.0</span> <span class="n">a</span> <span class="mi">1</span>
+<span class="n">timestep</span> <span class="mf">4.0</span>
+<span class="n">run_style</span> <span class="n">respa</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">inner</span> <span class="mi">1</span> <span class="mf">4.0</span> <span class="mf">5.0</span> <span class="n">outer</span> <span class="mi">2</span>
+</pre></div>
+</div>
<p>With these settings, users can expect good energy conservation and
roughly a 1.5 fold speedup over the <em>verlet</em> style with SHAKE and a
2.0 fmsec timestep.</p>
@@ -348,10 +348,10 @@ keywords. A 2-fold or more speedup can be obtained while maintaining
good energy conservation. In real units, for a pure LJ fluid at
liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1
Kcal/mol, the following settings seem to work well:</p>
-<pre class="literal-block">
-timestep 36.0
-run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">timestep</span> <span class="mf">36.0</span>
+<span class="n">run_style</span> <span class="n">respa</span> <span class="mi">3</span> <span class="mi">3</span> <span class="mi">4</span> <span class="n">inner</span> <span class="mi">1</span> <span class="mf">3.0</span> <span class="mf">4.0</span> <span class="n">middle</span> <span class="mi">2</span> <span class="mf">6.0</span> <span class="mf">7.0</span> <span class="n">outer</span> <span class="mi">3</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p>The <em>respa/omp</em> styles is a variant of <em>respa</em> adapted for use with
pair, bond, angle, dihedral, improper, or kspace styles with an <em>omp</em>
@@ -384,9 +384,9 @@ conserving energy to adequate precision.</p>
</div>
<div class="section" id="default">
<h2>Default</h2>
-<pre class="literal-block">
-run_style verlet
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run_style</span> <span class="n">verlet</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p id="tuckerman"><strong>(Tuckerman)</strong> Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990
(1992).</p>
diff --git a/doc/html/set.html b/doc/html/set.html
index 075dbb3510..89ea2eb1ff 100644
--- a/doc/html/set.html
+++ b/doc/html/set.html
@@ -214,17 +214,17 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-set group solvent type 2
-set group solvent type/fraction 2 0.5 12393
-set group edge bond 4
-set region half charge 0.5
-set type 3 charge 0.5
-set type 1*3 charge 0.5
-set atom * charge v_atomfile
-set atom 100*200 x 0.5 y 1.0
-set atom 1492 type 3
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">set</span> <span class="n">group</span> <span class="n">solvent</span> <span class="nb">type</span> <span class="mi">2</span>
+<span class="nb">set</span> <span class="n">group</span> <span class="n">solvent</span> <span class="nb">type</span><span class="o">/</span><span class="n">fraction</span> <span class="mi">2</span> <span class="mf">0.5</span> <span class="mi">12393</span>
+<span class="nb">set</span> <span class="n">group</span> <span class="n">edge</span> <span class="n">bond</span> <span class="mi">4</span>
+<span class="nb">set</span> <span class="n">region</span> <span class="n">half</span> <span class="n">charge</span> <span class="mf">0.5</span>
+<span class="nb">set</span> <span class="nb">type</span> <span class="mi">3</span> <span class="n">charge</span> <span class="mf">0.5</span>
+<span class="nb">set</span> <span class="nb">type</span> <span class="mi">1</span><span class="o">*</span><span class="mi">3</span> <span class="n">charge</span> <span class="mf">0.5</span>
+<span class="nb">set</span> <span class="n">atom</span> <span class="o">*</span> <span class="n">charge</span> <span class="n">v_atomfile</span>
+<span class="nb">set</span> <span class="n">atom</span> <span class="mi">100</span><span class="o">*</span><span class="mi">200</span> <span class="n">x</span> <span class="mf">0.5</span> <span class="n">y</span> <span class="mf">1.0</span>
+<span class="nb">set</span> <span class="n">atom</span> <span class="mi">1492</span> <span class="nb">type</span> <span class="mi">3</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -252,7 +252,7 @@ style <em>type</em> selects all the atoms in a range of types. The style
<em>mol</em> selects all the atoms in a range of molecule IDs.</p>
<p>In each of the range cases, the range can be specified as a single
numeric value, or a wildcard asterisk can be used to specify a range
-of values. This takes the form “*” or “*n” or “n*” or “m*n”. For
+of values. This takes the form “*” or “<em>n” or “n</em>” or “m*n”. For
example, for the style <em>type</em>, if N = the number of atom types, then
an asterisk with no numeric values means all types from 1 to N. A
leading asterisk means all types from 1 to n (inclusive). A trailing
diff --git a/doc/html/special_bonds.html b/doc/html/special_bonds.html
index d431cc49b3..08a1e3f74c 100644
--- a/doc/html/special_bonds.html
+++ b/doc/html/special_bonds.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>special_bonds command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-special_bonds keyword values ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul class="simple">
<li>one or more keyword/value pairs may be appended</li>
<li>keyword = <em>amber</em> or <em>charmm</em> or <em>dreiding</em> or <em>fene</em> or <em>lj/coul</em> or <em>lj</em> or <em>coul</em> or <em>angle</em> or <em>dihedral</em> or <em>extra</em></li>
@@ -152,14 +152,14 @@ special_bonds keyword values ...
N = number of extra 1-2,1-3,1-4 interactions to save space for
</pre>
<p>Examples:</p>
-<pre class="literal-block">
-special_bonds amber
-special_bonds charmm
-special_bonds fene dihedral no
-special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
-special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
-special_bonds lj/coul 0 1 1 extra 2
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="n">amber</span>
+<span class="n">special_bonds</span> <span class="n">charmm</span>
+<span class="n">special_bonds</span> <span class="n">fene</span> <span class="n">dihedral</span> <span class="n">no</span>
+<span class="n">special_bonds</span> <span class="n">lj</span><span class="o">/</span><span class="n">coul</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.5</span> <span class="n">angle</span> <span class="n">yes</span> <span class="n">dihedral</span> <span class="n">yes</span>
+<span class="n">special_bonds</span> <span class="n">lj</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.5</span> <span class="n">coul</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="n">dihedral</span> <span class="n">yes</span>
+<span class="n">special_bonds</span> <span class="n">lj</span><span class="o">/</span><span class="n">coul</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">extra</span> <span class="mi">2</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -301,7 +301,7 @@ current system has.</p>
the system). If new bonds are created (or molecules added containing
atoms with more special neighbors), the size of this list needs to
grow. Note that adding a single bond always adds a new 1st neighbor
-but may also induce *many* new 2nd and 3rd neighbors, depending on the
+but may also induce <em>many</em> new 2nd and 3rd neighbors, depending on the
molecular topology of your system. Using the <em>extra</em> keyword leaves
empty space in the list for this N additional 1st, 2nd, or 3rd
neighbors to be added. If you do not do this, you may get an error
@@ -325,14 +325,14 @@ Coul: coul 0.0 0.0 1.0</p>
<p>because the LJ settings are reset to their default values
each time the command is issued.</p>
<p>Likewise</p>
-<pre class="literal-block">
-special_bonds amber
-special_bonds extra 2
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="n">amber</span>
+<span class="n">special_bonds</span> <span class="n">extra</span> <span class="mi">2</span>
+</pre></div>
+</div>
<p>is not the same as this single command:</p>
-<pre class="literal-block">
-special_bonds amber extra 2
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">special_bonds</span> <span class="n">amber</span> <span class="n">extra</span> <span class="mi">2</span>
+</pre></div>
+</div>
<p>since in the former case, the 2nd command will reset all the LJ and
Coulombic weights to 0.0 (the default).</p>
<p>One exception to this rule is the <em>extra</em> option itself. It is not
diff --git a/doc/html/tad.html b/doc/html/tad.html
index e4bab3f210..d4f05d75ae 100644
--- a/doc/html/tad.html
+++ b/doc/html/tad.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>tad command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-tad N t_event T_lo T_hi delta tmax compute-ID keyword value ...
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">tad</span> <span class="n">N</span> <span class="n">t_event</span> <span class="n">T_lo</span> <span class="n">T_hi</span> <span class="n">delta</span> <span class="n">tmax</span> <span class="n">compute</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
+</pre></div>
+</div>
<ul class="simple">
<li>N = # of timesteps to run (not including dephasing/quenching)</li>
<li>t_event = timestep interval between event checks</li>
@@ -162,15 +162,15 @@ tad N t_event T_lo T_hi delta tmax compute-ID keyword value ...
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-tad 2000 50 1800 2300 0.01 0.01 event
-tad 2000 50 1800 2300 0.01 0.01 event &
- min 1e-05 1e-05 100 100 &
- neb 0.0 0.01 200 200 20 &
- min_style cg &
- neb_style fire &
- neb_log log.neb
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">tad</span> <span class="mi">2000</span> <span class="mi">50</span> <span class="mi">1800</span> <span class="mi">2300</span> <span class="mf">0.01</span> <span class="mf">0.01</span> <span class="n">event</span>
+<span class="n">tad</span> <span class="mi">2000</span> <span class="mi">50</span> <span class="mi">1800</span> <span class="mi">2300</span> <span class="mf">0.01</span> <span class="mf">0.01</span> <span class="n">event</span> <span class="o">&</span>
+ <span class="nb">min</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">05</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">05</span> <span class="mi">100</span> <span class="mi">100</span> <span class="o">&</span>
+ <span class="n">neb</span> <span class="mf">0.0</span> <span class="mf">0.01</span> <span class="mi">200</span> <span class="mi">200</span> <span class="mi">20</span> <span class="o">&</span>
+ <span class="n">min_style</span> <span class="n">cg</span> <span class="o">&</span>
+ <span class="n">neb_style</span> <span class="n">fire</span> <span class="o">&</span>
+ <span class="n">neb_log</span> <span class="n">log</span><span class="o">.</span><span class="n">neb</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -215,19 +215,19 @@ partitions remain idle. See <a class="reference internal" href="Section_howto.ht
multi-replica simulations.</p>
<p>A TAD run has several stages, which are repeated each time an event is
performed. The logic for a TAD run is as follows:</p>
-<pre class="literal-block">
-while (time remains):
- while (time < tstop):
- until (event occurs):
- run dynamics for t_event steps
- quench
- run neb calculation using all replicas
- compute tlo from energy barrier
- update earliest event
- update tstop
- reflect back into current basin
- execute earliest event
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">while</span> <span class="p">(</span><span class="n">time</span> <span class="n">remains</span><span class="p">):</span>
+ <span class="k">while</span> <span class="p">(</span><span class="n">time</span> <span class="o"><</span> <span class="n">tstop</span><span class="p">):</span>
+ <span class="n">until</span> <span class="p">(</span><span class="n">event</span> <span class="n">occurs</span><span class="p">):</span>
+ <span class="n">run</span> <span class="n">dynamics</span> <span class="k">for</span> <span class="n">t_event</span> <span class="n">steps</span>
+ <span class="n">quench</span>
+ <span class="n">run</span> <span class="n">neb</span> <span class="n">calculation</span> <span class="n">using</span> <span class="nb">all</span> <span class="n">replicas</span>
+ <span class="n">compute</span> <span class="n">tlo</span> <span class="kn">from</span> <span class="nn">energy</span> <span class="n">barrier</span>
+ <span class="n">update</span> <span class="n">earliest</span> <span class="n">event</span>
+ <span class="n">update</span> <span class="n">tstop</span>
+ <span class="n">reflect</span> <span class="n">back</span> <span class="n">into</span> <span class="n">current</span> <span class="n">basin</span>
+ <span class="n">execute</span> <span class="n">earliest</span> <span class="n">event</span>
+</pre></div>
+</div>
<p>Before this outer loop begins, the initial potential energy basin is
identified by quenching (an energy minimization, see below) the
initial state and storing the resulting coordinates for reference.</p>
@@ -298,7 +298,7 @@ at the low temperature.</p>
current basin to the stopping time. This last number can be used to
judge whether the stopping time is too short or too long (see above).</p>
<p><em>t_lo</em> is the low-temperature event time when the current basin was
-entered, in units of timestep. del*t_lo* is the time of each detected
+entered, in units of timestep. del<em>t_lo</em> is the time of each detected
event, measured relative to <em>t_lo</em>. <em>delt_lo</em> is equal to the
high-temperature time since entering the current basin, scaled by an
exponential factor that depends on the hi/lo temperature ratio and the
diff --git a/doc/html/thermo.html b/doc/html/thermo.html
index 7a5cb15c32..8567a3fd63 100644
--- a/doc/html/thermo.html
+++ b/doc/html/thermo.html
@@ -162,10 +162,10 @@ this context. Other similar math functions could easily be added as
options for <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a>.</p>
<p>For example, the following commands will output thermodynamic info at
timesteps 0,10,20,30,100,200,300,1000,2000,etc:</p>
-<pre class="literal-block">
-variable s equal logfreq(10,3,10)
-thermo v_s
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">s</span> <span class="n">equal</span> <span class="n">logfreq</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
+<span class="n">thermo</span> <span class="n">v_s</span>
+</pre></div>
+</div>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
diff --git a/doc/html/thermo_style.html b/doc/html/thermo_style.html
index 4f0f68acae..5a6e41bfc9 100644
--- a/doc/html/thermo_style.html
+++ b/doc/html/thermo_style.html
@@ -128,9 +128,9 @@
<span id="index-0"></span><h1>thermo_style command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-thermo_style style args
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">thermo_style</span> <span class="n">style</span> <span class="n">args</span>
+</pre></div>
+</div>
<ul class="simple">
<li>style = <em>one</em> or <em>multi</em> or <em>custom</em></li>
<li>args = list of arguments for a particular style</li>
@@ -207,12 +207,12 @@ thermo_style style args
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-thermo_style multi
-thermo_style custom step temp pe etotal press vol
-thermo_style custom step temp etotal c_myTemp v_abc
-thermo_style custom step temp etotal c_myTemp[*] v_abc
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">thermo_style</span> <span class="n">multi</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">pe</span> <span class="n">etotal</span> <span class="n">press</span> <span class="n">vol</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">c_myTemp</span> <span class="n">v_abc</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">v_abc</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -260,9 +260,9 @@ the thermo_modify command after it.</p>
computed: “temp”, “press”, “ke”, “etotal”, “enthalpy”, “pxx”, etc. By
default this is done by using a <em>temperature</em> compute which is created
when LAMMPS starts up, as if this command had been issued:</p>
-<pre class="literal-block">
-compute thermo_temp all temp
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_temp</span> <span class="nb">all</span> <span class="n">temp</span>
+</pre></div>
+</div>
<p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command for details. Note
that the ID of this compute is <em>thermo_temp</em> and the group is <em>all</em>.
You can change the attributes of this temperature (e.g. its
@@ -275,9 +275,9 @@ This is done via the <a class="reference internal" href="thermo_modify.html"><sp
computed: “press”, “enthalpy”, “pxx”, etc. By default this is done by
using a <em>pressure</em> compute which is created when LAMMPS starts up, as
if this command had been issued:</p>
-<pre class="literal-block">
-compute thermo_press all pressure thermo_temp
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">thermo_temp</span>
+</pre></div>
+</div>
<p>See the <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> command for details.
Note that the ID of this compute is <em>thermo_press</em> and the group is
<em>all</em>. You can change the attributes of this pressure via the
@@ -290,9 +290,9 @@ that requires a pressure. This is done via the
be computed: “pe”, “etotal”, “ebond”, etc. This is done by using a
<em>pe</em> compute which is created when LAMMPS starts up, as if this
command had been issued:</p>
-<pre class="literal-block">
-compute thermo_pe all pe
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_pe</span> <span class="nb">all</span> <span class="n">pe</span>
+</pre></div>
+</div>
<p>See the <a class="reference internal" href="compute_pe.html"><span class="doc">compute pe</span></a> command for details. Note that
the ID of this compute is <em>thermo_pe</em> and the group is <em>all</em>. You can
change the attributes of this potential energy via the
@@ -394,7 +394,7 @@ of these quantities in terms of the internal LAMMPS cell dimensions
<p>For output values from a compute or fix, the bracketed index I used to
index a vector, as in <em>c_ID[I]</em> or <em>f_ID[I]</em>, can be specified
using a wildcard asterisk with the index to effectively specify
-multiple values. This takes the form “*” or “*n” or “n*” or “m*n”.
+multiple values. This takes the form “*” or “<em>n” or “n</em>” or “m*n”.
If N = the size of the vector (for <em>mode</em> = scalar) or the number of
columns in the array (for <em>mode</em> = vector), then an asterisk with no
numeric values means all indices from 1 to N. A leading asterisk
@@ -405,13 +405,13 @@ indices from m to n (inclusive).</p>
vector had been listed one by one. E.g. these 2 thermo_style commands
are equivalent, since the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command
creates a global vector with 6 values.</p>
-<pre class="literal-block">
-compute myTemp all temp
-thermo_style custom step temp etotal c_myTemp[*]
-thermo_style custom step temp etotal &
- c_myTemp[1] c_myTemp[2] c_myTemp[3] &
- c_myTemp[4] c_myTemp[5] c_myTemp[6]
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myTemp</span> <span class="nb">all</span> <span class="n">temp</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
+<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="o">&</span>
+ <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&</span>
+ <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_myTemp</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
+</pre></div>
+</div>
<hr class="docutils" />
<p>The <em>c_ID</em> and <em>c_ID[I]</em> and <em>c_ID[I][J]</em> keywords allow global
values calculated by a compute to be output. As discussed on the
@@ -490,9 +490,9 @@ division by “natoms” in the variable formula if this is not the case
</div>
<div class="section" id="default">
<h2>Default</h2>
-<pre class="literal-block">
-thermo_style one
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">thermo_style</span> <span class="n">one</span>
+</pre></div>
+</div>
</div>
</div>
diff --git a/doc/html/units.html b/doc/html/units.html
index e80e207a23..9dc8285c6d 100644
--- a/doc/html/units.html
+++ b/doc/html/units.html
@@ -187,7 +187,7 @@ results from a unitless LJ simulation into physical quantities.</p>
<li>pressure = reduced LJ pressure, where P* = P sigma^3 / epsilon</li>
<li>dynamic viscosity = reduced LJ viscosity, where eta* = eta sigma^3 / epsilon / tau</li>
<li>charge = reduced LJ charge, where q* = q / (4 pi perm0 sigma epsilon)^1/2</li>
-<li>dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon)^1/2</li>
+<li>dipole = reduced LJ dipole, moment where <a href="#id1"><span class="problematic" id="id2">*</span></a>mu = mu / (4 pi perm0 sigma^3 epsilon)^1/2</li>
<li>electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon</li>
<li>density = mass/volume, where rho* = rho sigma^dim</li>
</ul>
diff --git a/doc/html/variable.html b/doc/html/variable.html
index f7fd72fac0..f5eb258506 100644
--- a/doc/html/variable.html
+++ b/doc/html/variable.html
@@ -197,8 +197,7 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-variable x index run1 run2 run3 run4 run5 run6 run7 run8
+<div class="highlight-default"><div class="highlight"><pre><span></span>variable x index run1 run2 run3 run4 run5 run6 run7 run8
variable LoopVar loop $n
variable beta equal temp/3.0
variable b1 equal x[234]+0.5*vol
@@ -215,7 +214,8 @@ variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
variable x uloop 15 pad
variable str format x %.6g
variable x delete
-</pre>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -470,10 +470,10 @@ appear in the set, will remain 0.0.</p>
to match a function name specified in a <a class="reference internal" href="python.html"><span class="doc">python</span></a> command
which returns a value to this variable as defined by its <em>return</em>
keyword. For example these two commands would be self-consistent:</p>
-<pre class="literal-block">
-variable foo python myMultiply
-python myMultiply return v_foo format f file funcs.py
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">foo</span> <span class="n">python</span> <span class="n">myMultiply</span>
+<span class="n">python</span> <span class="n">myMultiply</span> <span class="k">return</span> <span class="n">v_foo</span> <span class="nb">format</span> <span class="n">f</span> <span class="n">file</span> <span class="n">funcs</span><span class="o">.</span><span class="n">py</span>
+</pre></div>
+</div>
<p>The two commands can appear in either order so long as both are
specified before the Python function is invoked for the first time.</p>
<p>Each time the variable is evaluated, the associated Python function is
@@ -527,9 +527,9 @@ variety of quantities. The syntax for each kind of quantity is
simple, but multiple quantities can be nested and combined in various
ways to build up formulas of arbitrary complexity. For example, this
is a valid (though strange) variable formula:</p>
-<pre class="literal-block">
-variable x equal "pe + c_MyTemp / vol^(1/3)"
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">x</span> <span class="n">equal</span> <span class="s2">"pe + c_MyTemp / vol^(1/3)"</span>
+</pre></div>
+</div>
<p>Specifically, a formula can contain numbers, constants, thermo
keywords, math operators, math functions, group functions, region
functions, atom values, atom vectors, compute references, fix
@@ -618,9 +618,9 @@ of LAMMPS will be smaller. This can be used to have input scripts
adapt automatically to LAMMPS versions, when non-backwards compatible
syntax changes are introduced. Here is an illustrative example (which
will not work, since the <em>version</em> has been introduced more recently):</p>
-<pre class="literal-block">
-if $(version<20140513) then "communicate vel yes" else "comm_modify vel yes"
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span>if $(version<20140513) then "communicate vel yes" else "comm_modify vel yes"
+</pre></div>
+</div>
<p>The thermo keywords allowed in a formula are those defined by the
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command. Thermo keywords that
require a <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> to calculate their values such as
@@ -719,9 +719,9 @@ is the nearest integer to its argument.</p>
<p>The ramp(x,y) function uses the current timestep to generate a value
linearly intepolated between the specified x,y values over the course
of a run, according to this formula:</p>
-<pre class="literal-block">
-value = x + (y-x) * (timestep-startstep) / (stopstep-startstep)
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">value</span> <span class="o">=</span> <span class="n">x</span> <span class="o">+</span> <span class="p">(</span><span class="n">y</span><span class="o">-</span><span class="n">x</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="n">timestep</span><span class="o">-</span><span class="n">startstep</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">stopstep</span><span class="o">-</span><span class="n">startstep</span><span class="p">)</span>
+</pre></div>
+</div>
<p>The run begins on startstep and ends on stopstep. Startstep and
stopstep can span multiple runs, using the <em>start</em> and <em>stop</em> keywords
of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. See the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command for
@@ -790,9 +790,9 @@ sequence of output timesteps:</p>
velocity, and uses the elapsed time to change the value by a linear
displacement due to the applied velocity over the course of a run,
according to this formula:</p>
-<pre class="literal-block">
-value = value0 + velocity*(timestep-startstep)*dt
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">value</span> <span class="o">=</span> <span class="n">value0</span> <span class="o">+</span> <span class="n">velocity</span><span class="o">*</span><span class="p">(</span><span class="n">timestep</span><span class="o">-</span><span class="n">startstep</span><span class="p">)</span><span class="o">*</span><span class="n">dt</span>
+</pre></div>
+</div>
<p>where dt = the timestep size.</p>
<p>The run begins on startstep. Startstep can span multiple runs, using
the <em>start</em> keyword of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. See the
@@ -803,10 +803,10 @@ timestep-startstep.</p>
x = value0, y = amplitude, z = period. They use the elapsed time to
oscillate the value by a sin() or cos() function over the course of a
run, according to one of these formulas, where omega = 2 PI / period:</p>
-<pre class="literal-block">
-value = value0 + Amplitude * sin(omega*(timestep-startstep)*dt)
-value = value0 + Amplitude * (1 - cos(omega*(timestep-startstep)*dt))
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">value</span> <span class="o">=</span> <span class="n">value0</span> <span class="o">+</span> <span class="n">Amplitude</span> <span class="o">*</span> <span class="n">sin</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="p">(</span><span class="n">timestep</span><span class="o">-</span><span class="n">startstep</span><span class="p">)</span><span class="o">*</span><span class="n">dt</span><span class="p">)</span>
+<span class="n">value</span> <span class="o">=</span> <span class="n">value0</span> <span class="o">+</span> <span class="n">Amplitude</span> <span class="o">*</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">cos</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="p">(</span><span class="n">timestep</span><span class="o">-</span><span class="n">startstep</span><span class="p">)</span><span class="o">*</span><span class="n">dt</span><span class="p">))</span>
+</pre></div>
+</div>
<p>where dt = the timestep size.</p>
<p>The run begins on startstep. Startstep can span multiple runs, using
the <em>start</em> keyword of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. See the
@@ -952,16 +952,16 @@ features or LAMMPS, <em>respa</em> allows to check whether the inner/middle/oute
mode of r-RESPA is supported. In the various style categories,
the checking is also done using suffix flags, if available and enabled.</p>
<p>Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on the CPU concurrently to running the pair style on the GPU), but do use the suffix otherwise (e.g. with USER-OMP).</p>
-<pre class="literal-block">
-pair_style lj/cut/coul/long 14.0
+<div class="highlight-default"><div class="highlight"><pre><span></span>pair_style lj/cut/coul/long 14.0
if $(is_active(package,gpu)) then "suffix off"
kspace_style pppm
-</pre>
+</pre></div>
+</div>
<p>Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, otherwise fall back to using pair and reducing the outer time step</p>
-<pre class="literal-block">
-timestep $(2.0*(1.0+*is_active(pair,respa))
+<div class="highlight-default"><div class="highlight"><pre><span></span>timestep $(2.0*(1.0+*is_active(pair,respa))
if $(is_active(pair,respa)) then "run_style respa 4 3 2 2 improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2 improper 1 pair 2 kspace 3"
-</pre>
+</pre></div>
+</div>
<p>The <em>is_defined()</em> function allows to query categories like <em>compute</em>,
<em>dump</em>, <em>fix</em>, <em>group</em>, <em>region</em>, and <em>variable</em> whether an entry
with the provided name or id is defined.</p>
@@ -1022,8 +1022,8 @@ reference means, since computes only produce either global or per-atom
quantities, never both.</p>
<table border="1" class="docutils">
<colgroup>
-<col width="11%" />
-<col width="89%" />
+<col width="10%" />
+<col width="90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>c_ID</td>
@@ -1046,9 +1046,9 @@ variable refers to a compute that produces both a global scalar and a
global vector. Consider a compute with ID “foo” that does this,
referenced as follows by variable “a”, where “myVec” is another
vector-style variable:</p>
-<pre class="literal-block">
-variable a vector c_foo*v_myVec
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">a</span> <span class="n">vector</span> <span class="n">c_foo</span><span class="o">*</span><span class="n">v_myVec</span>
+</pre></div>
+</div>
<p>The reference “c_foo” could refer to either the global scalar or
global vector produced by compute “foo”. In this case, “c_foo” will
always refer to the global scalar, and “C_foo” can be used to
@@ -1077,14 +1077,14 @@ vector values. A vector value can be a per-atom vector itself, or a
column of an per-atom array. See the doc pages for individual fixes
to see what kind of values they produce.</p>
<p>The different kinds of fix references are exactly the same as the
-compute references listed in the above table, where “c_” is replaced
-by “f_”. Again, there is typically no ambiguity (see exception below)
+compute references listed in the above table, where “<a href="#id1"><span class="problematic" id="id2">c_</span></a>” is replaced
+by “<a href="#id3"><span class="problematic" id="id4">f_</span></a>”. Again, there is typically no ambiguity (see exception below)
as to what a reference means, since fixes only produce either global
or per-atom quantities, never both.</p>
<table border="1" class="docutils">
<colgroup>
-<col width="11%" />
-<col width="89%" />
+<col width="10%" />
+<col width="90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>f_ID</td>
@@ -1152,8 +1152,8 @@ There is no ambiguity as to what a reference means, since variables
produce only a global scalar or global vector or per-atom vector.</p>
<table border="1" class="docutils">
<colgroup>
-<col width="15%" />
-<col width="85%" />
+<col width="14%" />
+<col width="86%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>v_name</td>
@@ -1188,7 +1188,7 @@ same syntax as equal-style variables described on this page. This
effectively evaluates a formula immediately without using the variable
command to define a named variable.</p>
<p>More generally, there is a difference between referencing a variable
-with a leading $ sign (e.g. $x or ${abc}) versus with a leading “v_”
+with a leading $ sign (e.g. $x or ${abc}) versus with a leading “<a href="#id5"><span class="problematic" id="id6">v_</span></a>”
(e.g. v_x or v_abc). The former can be used in any input script
command, including a variable command. The input script parser
evaluates the reference variable immediately and substitutes its value
@@ -1197,7 +1197,7 @@ un-named “immediate” variables for this purpose. For example, a
string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script
command evaluates the string between the parenthesis as an equal-style
variable formula.</p>
-<p>Referencing a variable with a leading “v_” is an optional or required
+<p>Referencing a variable with a leading “<a href="#id7"><span class="problematic" id="id8">v_</span></a>” is an optional or required
kind of argument for some commands (e.g. the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> or <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> or
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> commands) if you wish it to evaluate
a variable periodically during a run. It can also be used in a
@@ -1224,9 +1224,9 @@ variable v0 equal $v
<p>The second command will force “v” to be evaluated (yielding the
initial volume) and assign that value to the variable “v0”. Thus the
command</p>
-<pre class="literal-block">
-thermo_style custom step v_v v_v0
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">v_v</span> <span class="n">v_v0</span>
+</pre></div>
+</div>
<p>would print out both the current and initial volume periodically
during the run.</p>
<p>Note that it is a mistake to enclose a variable formula in double
@@ -1317,13 +1317,13 @@ a 0-timestep run before printing the variable has the desired effect.</p>
<p>(3) The variable may be evaluated incorrectly and LAMMPS may have no
way to detect this has occurred. Consider the following sequence of
commands:</p>
-<pre class="literal-block">
-pair_coeff 1 1 1.0 1.0
-run 1000
-pair_coeff 1 1 1.5 1.0
-variable e equal pe
-print "Final potential energy = $e"
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
+<span class="n">run</span> <span class="mi">1000</span>
+<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.5</span> <span class="mf">1.0</span>
+<span class="n">variable</span> <span class="n">e</span> <span class="n">equal</span> <span class="n">pe</span>
+<span class="nb">print</span> <span class="s2">"Final potential energy = $e"</span>
+</pre></div>
+</div>
<p>The first run is performed using one setting for the pairwise
potential defined by the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> and
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> commands. The potential energy is
@@ -1340,14 +1340,14 @@ perform a 0-timestep run before the variable is evaluated to insure
the system is up-to-date. For example, this sequence of commands
would print a potential energy that reflected the changed pairwise
coefficient:</p>
-<pre class="literal-block">
-pair_coeff 1 1 1.0 1.0
-run 1000
-pair_coeff 1 1 1.5 1.0
-run 0
-variable e equal pe
-print "Final potential energy = $e"
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
+<span class="n">run</span> <span class="mi">1000</span>
+<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.5</span> <span class="mf">1.0</span>
+<span class="n">run</span> <span class="mi">0</span>
+<span class="n">variable</span> <span class="n">e</span> <span class="n">equal</span> <span class="n">pe</span>
+<span class="nb">print</span> <span class="s2">"Final potential energy = $e"</span>
+</pre></div>
+</div>
</div>
</div>
<hr class="docutils" />
diff --git a/doc/html/velocity.html b/doc/html/velocity.html
index af9be7196c..06accf9593 100644
--- a/doc/html/velocity.html
+++ b/doc/html/velocity.html
@@ -172,13 +172,13 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-velocity all create 300.0 4928459 rot yes dist gaussian
-velocity border set NULL 4.0 v_vz sum yes units box
-velocity flow scale 300.0
-velocity flow ramp vx 0.0 5.0 y 5 25 temp mytemp
-velocity all zero linear
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">velocity</span> <span class="nb">all</span> <span class="n">create</span> <span class="mf">300.0</span> <span class="mi">4928459</span> <span class="n">rot</span> <span class="n">yes</span> <span class="n">dist</span> <span class="n">gaussian</span>
+<span class="n">velocity</span> <span class="n">border</span> <span class="nb">set</span> <span class="n">NULL</span> <span class="mf">4.0</span> <span class="n">v_vz</span> <span class="nb">sum</span> <span class="n">yes</span> <span class="n">units</span> <span class="n">box</span>
+<span class="n">velocity</span> <span class="n">flow</span> <span class="n">scale</span> <span class="mf">300.0</span>
+<span class="n">velocity</span> <span class="n">flow</span> <span class="n">ramp</span> <span class="n">vx</span> <span class="mf">0.0</span> <span class="mf">5.0</span> <span class="n">y</span> <span class="mi">5</span> <span class="mi">25</span> <span class="n">temp</span> <span class="n">mytemp</span>
+<span class="n">velocity</span> <span class="nb">all</span> <span class="n">zero</span> <span class="n">linear</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@@ -244,7 +244,7 @@ replace them if sum = no.</p>
<p>The <em>mom</em> and <em>rot</em> keywords are used by <em>create</em>. If mom = yes, the
linear momentum of the newly created ensemble of velocities is zeroed;
if rot = yes, the angular momentum is zeroed.</p>
-<p>*line</p>
+<p><a href="#id1"><span class="problematic" id="id2">*</span></a>line</p>
<p>If specified, the <em>temp</em> keyword is used by <em>create</em> and <em>scale</em> to
specify a <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> that calculates temperature in a
desired way, e.g. by first subtracting out a velocity bias, as
@@ -252,9 +252,9 @@ discussed in <a class="reference internal" href="Section_howto.html#howto-15"><s
pages. If this keyword is not specified, <em>create</em> and <em>scale</em>
calculate temperature using a compute that is defined internally as
follows:</p>
-<pre class="literal-block">
-compute velocity_temp group-ID temp
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">velocity_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
+</pre></div>
+</div>
<p>where group-ID is the same ID used in the velocity command. i.e. the
group of atoms whose velocity is being altered. This compute is
deleted when the velocity command is finished. See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command for details. If the calculated
diff --git a/doc/html/write_coeff.html b/doc/html/write_coeff.html
index d4d15e1ddf..1698ec2615 100644
--- a/doc/html/write_coeff.html
+++ b/doc/html/write_coeff.html
@@ -128,18 +128,18 @@
<span id="index-0"></span><h1>write_coeff command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
-<pre class="literal-block">
-write_coeff file
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">write_coeff</span> <span class="n">file</span>
+</pre></div>
+</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">file</span> <span class="o">=</span> <span class="n">name</span> <span class="n">of</span> <span class="n">data</span> <span class="n">file</span> <span class="n">to</span> <span class="n">write</span> <span class="n">out</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
-<pre class="literal-block">
-write_coeff polymer.coeff
-</pre>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">write_coeff</span> <span class="n">polymer</span><span class="o">.</span><span class="n">coeff</span>
+</pre></div>
+</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index ab82bb0716..e9e6cb9192 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="7 Sep 2016 version">
+<META NAME="docnumber" CONTENT="13 Sep 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 Documentation :c,h3
-7 Sep 2016 version :c,h4
+13 Sep 2016 version :c,h4
Version info: :h4
--
GitLab