git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15317 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/html/_sources/dihedral_spherical.txt

@@ -0,0 +1,101 @@
+.. index:: dihedral_style spherical
+
+dihedral_style spherical command
+================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   dihedral_style spherical
+
+Examples
+""""""""
+
+.. parsed-literal::
+
+   dihedral_coeff 1 1  286.1  1 124 1   1 90.0 0   1 90.0 0   
+   dihedral_coeff 1 3  286.1  1 114 1   1 90  0    1 90.0  0  &
+                       17.3   0 0.0 0   1 158 1    0 0.0   0  &
+                       15.1   0 0.0 0   0 0.0 0    1 167.3 1
+
+Description
+"""""""""""
+
+The *spherical* dihedral style uses the potential:
+
+.. image:: JPG/dihedral_spherical_angles.jpg
+   :align: center
+
+.. image:: Eqs/dihedral_spherical.jpg
+   :align: center
+
+For this dihedral style, the energy can be any function that combines the
+4-body dihedral-angle (phi) and the two 3-body bond-angles (theta1, theta2).
+For this reason, there is usually no need to define 3-body "angle" forces
+separately for the atoms participating in these interactions.
+It is probably more efficient to incorporate 3-body angle forces into
+the dihedral interaction even if it requires adding additional terms to
+the expansion (as was done in the second example).  A careful choice of
+parameters can prevent singularities that occur with traditional
+force-fields whenever theta1 or theta2 approach 0 or 180 degrees.
+The last example above corresponds to an interaction with a single energy
+minima located at phi=114, theta1=158, theta2=167.3 degrees, and it remains
+numerically stable at all angles (phi, theta1, theta2). In this example,
+the coefficients 17.3, and 15.1 can be physically interpreted as the
+harmonic spring constants for theta1 and theta2 around their minima.
+The coefficient 286.1 is the harmonic spring constant for phi after
+division by sin(158)*sin(167.3) (the minima positions for theta1 and theta2).
+
+The following coefficients must be defined for each dihedral type via the
+:doc:`dihedral_coeff <dihedral_coeff>` command as in the example above, or in
+the Dihedral Coeffs section of a data file file read by the
+:doc:`read_data <read_data>` command:
+
+* n (integer >= 1)
+* C1 (energy)
+* K1 (typically an integer)
+* a1 (degrees)
+* u1 (typically 0.0 or 1.0)
+* L1 (typically an integer)
+* b1 (degrees, typically 0.0 or 90.0)
+* v1 (typically 0.0 or 1.0)
+* M1 (typically an integer)
+* c1 (degrees, typically 0.0 or 90.0)
+* w1 (typically 0.0 or 1.0)
+* ....
+* Cn (energy)
+* Kn (typically an integer)
+* an (degrees)
+* un (typically 0.0 or 1.0)
+* Ln (typically an integer)
+* bn (degrees, typically 0.0 or 90.0)
+* vn (typically 0.0 or 1.0)
+* Mn (typically an integer)
+* cn (degrees, typically 0.0 or 90.0)
+* wn (typically 0.0 or 1.0)
+
+
+----------
+
+
+Restrictions
+""""""""""""
+
+
+This dihedral style can only be used if LAMMPS was built with the
+USER_MISC package.  See the :ref:`Making LAMMPS <start_3>` 
+section for more info on packages.
+
+Related commands
+""""""""""""""""
+
+:doc:`dihedral_coeff <dihedral_coeff>`
+
+**Default:** none
+
+
+.. _lws: http://lammps.sandia.gov
+.. _ld: Manual.html
+.. _lc: Section_commands.html#comm

doc/html/_sources/dihedral_style.txt

@@ -57,7 +57,7 @@ In the formulas listed for each dihedral style, *phi* is the torsional
 angle defined by the quadruplet of atoms.  This angle has a sign
 convention as shown in this diagram:
 
-.. image:: Eqs/dihedral_sign.jpg
+.. image:: JPG/dihedral_sign.jpg
    :align: center
 
 where the I,J,K,L ordering of the 4 atoms that define the dihedral

doc/html/_sources/dump_image.txt

@@ -21,7 +21,7 @@ Syntax
 * color = atom attribute that determines color of each atom
 * diameter = atom attribute that determines size of each atom
 * zero or more keyword/value pairs may be appended
-* keyword = *atom* or *adiam* or *bond* or *line* or *tri* or *body* or *size* or *view* or *center* or *up* or *zoom* or *persp* or *box* or *axes* or *subbox* or *shiny* or *ssao*
+* keyword = *atom* or *adiam* or *bond* or *line* or *tri* or *body* or *fix* or *size* or *view* or *center* or *up* or *zoom* or *persp* or *box* or *axes* or *subbox* or *shiny* or *ssao*
 .. parsed-literal::
 
      *atom* = yes/no = do or do not draw atoms
@@ -40,6 +40,10 @@ Syntax
      *body* = color bflag1 bflag2
        color = *type*
        bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
+     *fix* = fixID color fflag1 fflag2
+       fixID = ID of fix that generates objects to dray
+       color = *type*
+       fflag1,fflag2 = 2 numeric flags to affect how fix objects are drawn
      *size* values = width height = size of images
        width = width of image in # of pixels
        height = height of image in # of pixels
@@ -274,6 +278,10 @@ set a single numeric *size*\ .  All atoms will be drawn with that
 diameter, e.g. 1.5, which is in whatever distance :doc:`units <units>`
 the input script defines, e.g. Angstroms.
 
+
+----------
+
+
 The *bond* keyword allows to you to alter how bonds are drawn.  A bond
 is only drawn if both atoms in the bond are being drawn due to being
 in the specified group and due to other selection criteria
@@ -316,6 +324,10 @@ If *type* is specified for the *width* value then the diameter of each
 bond is determined by its bond type.  By default all types have
 diameter 0.5.  This mapping can be changed by the :doc:`dump_modify bdiam <dump_modify>` command.
 
+
+----------
+
+
 The *line* keyword can be used when :doc:`atom_style line <atom_style>`
 is used to define particles as line segments, and will draw them as
 lines.  If this keyword is not used, such particles will be drawn as
@@ -339,6 +351,10 @@ lines will be drawn as cylinders with that diameter, e.g. 1.0, which
 is in whatever distance :doc:`units <units>` the input script defines,
 e.g. Angstroms.
 
+
+----------
+
+
 The *tri* keyword can be used when :doc:`atom_style tri <atom_style>` is
 used to define particles as triangles, and will draw them as triangles
 or edges (3 lines) or both, depending on the setting for *tflag*\ .  If
@@ -359,6 +375,10 @@ default the mapping of types to colors is as follows:
 and repeats itself for types > 6.  There is not yet an option to
 change this via the :doc:`dump_modify <dump_modify>` command.
 
+
+----------
+
+
 The *body* keyword can be used when :doc:`atom_style body <atom_style>`
 is used to define body particles with internal state
 (e.g. sub-particles), and will drawn them in a manner specific to the
@@ -376,6 +396,47 @@ passed to the body style to affect how the drawing of a body particle
 is done.  See the :doc:`body <body>` doc page for a description of what
 these parameters mean for each body style.
 
+The only setting currently allowed for the *color* value is *type*\ ,
+which will color the body particles according to the atom type of the
+particle.  By default the mapping of types to colors is as follows:
+
+* type 1 = red
+* type 2 = green
+* type 3 = blue
+* type 4 = yellow
+* type 5 = aqua
+* type 6 = cyan
+
+and repeats itself for types > 6.  There is not yet an option to
+change this via the :doc:`dump_modify <dump_modify>` command.
+
+
+----------
+
+
+The *fix* keyword can be used with a :doc:`fix <fix>` that produces
+objects to be drawn.  An example is the :doc:`fix surface/global <fix_surface_global>` command which can draw lines
+or triangles for 2d/3d simulations.
+
+The *fflag1* and *fflag2* settings are numerical values which are
+passed to the fix to affect how the drawing of its objects is done.
+See the individual fix doc page for a description of what these
+parameters mean for a particular fix.
+
+The only setting currently allowed for the *color* value is *type*\ ,
+which will color the fix objects according to their type.  By default
+the mapping of types to colors is as follows:
+
+* type 1 = red
+* type 2 = green
+* type 3 = blue
+* type 4 = yellow
+* type 5 = aqua
+* type 6 = cyan
+
+and repeats itself for types > 6.  There is not yet an option to
+change this via the :doc:`dump_modify <dump_modify>` command.
+
 
 ----------
 

doc/html/_sources/fix_addforce.txt

@@ -122,8 +122,9 @@ depending on your available hardware, as discussed in
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.
 
-These accelerated styles are part of the ackage.  They are only
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-enabled if LAMMPS was built with that package.  See the :ref:`Making LAMMPS <start_3>` section for more info.
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :ref:`Making LAMMPS <start_3>` section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can

doc/html/_sources/fix_aveforce.txt

@@ -80,8 +80,9 @@ depending on your available hardware, as discussed in
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.
 
-These accelerated styles are part of the ackage.  They are only
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-enabled if LAMMPS was built with that package.  See the :ref:`Making LAMMPS <start_3>` section for more info.
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :ref:`Making LAMMPS <start_3>` section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can

doc/html/_sources/fix_enforce2d.txt

@@ -38,8 +38,9 @@ depending on your available hardware, as discussed in
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.
 
-These accelerated styles are part of the ackage.  They are only
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-enabled if LAMMPS was built with that package.  See the :ref:`Making LAMMPS <start_3>` section for more info.
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :ref:`Making LAMMPS <start_3>` section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can

doc/html/_sources/fix_freeze.txt

@@ -42,8 +42,9 @@ depending on your available hardware, as discussed in
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.
 
-These accelerated styles are part of the ackage.  They are only
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-enabled if LAMMPS was built with that package.  See the :ref:`Making LAMMPS <start_3>` section for more info.
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :ref:`Making LAMMPS <start_3>` section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can

doc/html/_sources/fix_shake.txt

@@ -169,8 +169,9 @@ depending on your available hardware, as discussed in
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.
 
-These accelerated styles are part of the ackage.  They are only
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-enabled if LAMMPS was built with that package.  See the :ref:`Making LAMMPS <start_3>` section for more info.
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :ref:`Making LAMMPS <start_3>` section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can

doc/html/_sources/replicate.txt

@@ -85,15 +85,6 @@ the time the replicate command is used that require vectors of atom
 information to be stored.  This is because the replicate command does
 not know how to replicate that information for new atoms it creates.
 
-Replicating a system that has rigid bodies (defined via the :doc:`fix rigid <fix_rigid>` command), either currently defined or that
-created the restart file which was read in before replicating, can
-cause problems if there is a bond between a pair of rigid bodies that
-straddle a periodic boundary.  This is because the periodic image
-information for particles in the rigid bodies are set differently than
-for a non-rigid system and can result in a new bond being created that
-spans the periodic box.  Thus you cannot use the replicate command in
-this scenario.
-
 **Related commands:** none
 
 **Default:** none

doc/html/dihedral_spherical.html

@@ -0,0 +1,270 @@
+
+
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+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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+  
+  <title>dihedral_style spherical command &mdash; LAMMPS documentation</title>
+  
+
+  
+  
+
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+  
+  
+    
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+  
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+  
+
+  
+    <link rel="top" title="LAMMPS documentation" href="index.html"/> 
+
+  
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+            <a href="Section_commands.html#comm">Commands</a>
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+           <div itemprop="articleBody">
+            
+  <div class="section" id="dihedral-style-spherical-command">
+<span id="index-0"></span><h1>dihedral_style spherical command</h1>
+<div class="section" id="syntax">
+<h2>Syntax</h2>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">spherical</span>
+</pre></div>
+</div>
+</div>
+<div class="section" id="examples">
+<h2>Examples</h2>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">1</span>  <span class="mf">286.1</span>  <span class="mi">1</span> <span class="mi">124</span> <span class="mi">1</span>   <span class="mi">1</span> <span class="mf">90.0</span> <span class="mi">0</span>   <span class="mi">1</span> <span class="mf">90.0</span> <span class="mi">0</span>
+<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">3</span>  <span class="mf">286.1</span>  <span class="mi">1</span> <span class="mi">114</span> <span class="mi">1</span>   <span class="mi">1</span> <span class="mi">90</span>  <span class="mi">0</span>    <span class="mi">1</span> <span class="mf">90.0</span>  <span class="mi">0</span>  <span class="o">&amp;</span>
+                    <span class="mf">17.3</span>   <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span>   <span class="mi">1</span> <span class="mi">158</span> <span class="mi">1</span>    <span class="mi">0</span> <span class="mf">0.0</span>   <span class="mi">0</span>  <span class="o">&amp;</span>
+                    <span class="mf">15.1</span>   <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span>   <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span>    <span class="mi">1</span> <span class="mf">167.3</span> <span class="mi">1</span>
+</pre></div>
+</div>
+</div>
+<div class="section" id="description">
+<h2>Description</h2>
+<p>The <em>spherical</em> dihedral style uses the potential:</p>
+<img alt="_images/dihedral_spherical_angles.jpg" class="align-center" src="_images/dihedral_spherical_angles.jpg" />
+<img alt="_images/dihedral_spherical.jpg" class="align-center" src="_images/dihedral_spherical.jpg" />
+<p>For this dihedral style, the energy can be any function that combines the
+4-body dihedral-angle (phi) and the two 3-body bond-angles (theta1, theta2).
+For this reason, there is usually no need to define 3-body &#8220;angle&#8221; forces
+separately for the atoms participating in these interactions.
+It is probably more efficient to incorporate 3-body angle forces into
+the dihedral interaction even if it requires adding additional terms to
+the expansion (as was done in the second example).  A careful choice of
+parameters can prevent singularities that occur with traditional
+force-fields whenever theta1 or theta2 approach 0 or 180 degrees.
+The last example above corresponds to an interaction with a single energy
+minima located at phi=114, theta1=158, theta2=167.3 degrees, and it remains
+numerically stable at all angles (phi, theta1, theta2). In this example,
+the coefficients 17.3, and 15.1 can be physically interpreted as the
+harmonic spring constants for theta1 and theta2 around their minima.
+The coefficient 286.1 is the harmonic spring constant for phi after
+division by sin(158)*sin(167.3) (the minima positions for theta1 and theta2).</p>
+<p>The following coefficients must be defined for each dihedral type via the
+<a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a> command as in the example above, or in
+the Dihedral Coeffs section of a data file file read by the
+<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command:</p>
+<ul class="simple">
+<li>n (integer &gt;= 1)</li>
+<li>C1 (energy)</li>
+<li>K1 (typically an integer)</li>
+<li>a1 (degrees)</li>
+<li>u1 (typically 0.0 or 1.0)</li>
+<li>L1 (typically an integer)</li>
+<li>b1 (degrees, typically 0.0 or 90.0)</li>
+<li>v1 (typically 0.0 or 1.0)</li>
+<li>M1 (typically an integer)</li>
+<li>c1 (degrees, typically 0.0 or 90.0)</li>
+<li>w1 (typically 0.0 or 1.0)</li>
+<li></li>
+<li>Cn (energy)</li>
+<li>Kn (typically an integer)</li>
+<li>an (degrees)</li>
+<li>un (typically 0.0 or 1.0)</li>
+<li>Ln (typically an integer)</li>
+<li>bn (degrees, typically 0.0 or 90.0)</li>
+<li>vn (typically 0.0 or 1.0)</li>
+<li>Mn (typically an integer)</li>
+<li>cn (degrees, typically 0.0 or 90.0)</li>
+<li>wn (typically 0.0 or 1.0)</li>
+</ul>
+</div>
+<hr class="docutils" />
+<div class="section" id="restrictions">
+<h2>Restrictions</h2>
+<p>This dihedral style can only be used if LAMMPS was built with the
+USER_MISC package.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a>
+section for more info on packages.</p>
+</div>
+<div class="section" id="related-commands">
+<h2>Related commands</h2>
+<p><a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a></p>
+<p><strong>Default:</strong> none</p>
+</div>
+</div>
+
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+    </script>
+      <script type="text/javascript" src="_static/jquery.js"></script>
+      <script type="text/javascript" src="_static/underscore.js"></script>
+      <script type="text/javascript" src="_static/doctools.js"></script>
+      <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
+      <script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
+
+  
+
+  
+  
+    <script type="text/javascript" src="_static/js/theme.js"></script>
+  
+
+  
+  
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.StickyNav.enable();
+      });
+  </script>
+   
+
+</body>
+</html>

doc/html/dump_image.html

@@ -143,7 +143,7 @@
 <li>color = atom attribute that determines color of each atom</li>
 <li>diameter = atom attribute that determines size of each atom</li>
 <li>zero or more keyword/value pairs may be appended</li>
-<li>keyword = <em>atom</em> or <em>adiam</em> or <em>bond</em> or <em>line</em> or <em>tri</em> or <em>body</em> or <em>size</em> or <em>view</em> or <em>center</em> or <em>up</em> or <em>zoom</em> or <em>persp</em> or <em>box</em> or <em>axes</em> or <em>subbox</em> or <em>shiny</em> or <em>ssao</em></li>
+<li>keyword = <em>atom</em> or <em>adiam</em> or <em>bond</em> or <em>line</em> or <em>tri</em> or <em>body</em> or <em>fix</em> or <em>size</em> or <em>view</em> or <em>center</em> or <em>up</em> or <em>zoom</em> or <em>persp</em> or <em>box</em> or <em>axes</em> or <em>subbox</em> or <em>shiny</em> or <em>ssao</em></li>
 </ul>
 <pre class="literal-block">
 <em>atom</em> = yes/no = do or do not draw atoms
@@ -162,6 +162,10 @@
 <em>body</em> = color bflag1 bflag2
   color = <em>type</em>
   bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
+<em>fix</em> = fixID color fflag1 fflag2
+  fixID = ID of fix that generates objects to dray
+  color = <em>type</em>
+  fflag1,fflag2 = 2 numeric flags to affect how fix objects are drawn
 <em>size</em> values = width height = size of images
   width = width of image in # of pixels
   height = height of image in # of pixels
@@ -366,6 +370,7 @@ if the <em>line</em>, <em>tri</em>, or <em>body</em> keywords are used.</p>
 set a single numeric <em>size</em>.  All atoms will be drawn with that
 diameter, e.g. 1.5, which is in whatever distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>
 the input script defines, e.g. Angstroms.</p>
+<hr class="docutils" />
 <p>The <em>bond</em> keyword allows to you to alter how bonds are drawn.  A bond
 is only drawn if both atoms in the bond are being drawn due to being
 in the specified group and due to other selection criteria
@@ -401,6 +406,7 @@ of the 2 atoms in the bond.</p>
 <p>If <em>type</em> is specified for the <em>width</em> value then the diameter of each
 bond is determined by its bond type.  By default all types have
 diameter 0.5.  This mapping can be changed by the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify bdiam</span></a> command.</p>
+<hr class="docutils" />
 <p>The <em>line</em> keyword can be used when <a class="reference internal" href="atom_style.html"><span class="doc">atom_style line</span></a>
 is used to define particles as line segments, and will draw them as
 lines.  If this keyword is not used, such particles will be drawn as
@@ -422,6 +428,7 @@ change this via the <a class="reference internal" href="dump_modify.html"><span
 lines will be drawn as cylinders with that diameter, e.g. 1.0, which
 is in whatever distance <a class="reference internal" href="units.html"><span class="doc">units</span></a> the input script defines,
 e.g. Angstroms.</p>
+<hr class="docutils" />
 <p>The <em>tri</em> keyword can be used when <a class="reference internal" href="atom_style.html"><span class="doc">atom_style tri</span></a> is
 used to define particles as triangles, and will draw them as triangles
 or edges (3 lines) or both, depending on the setting for <em>tflag</em>.  If
@@ -441,6 +448,7 @@ default the mapping of types to colors is as follows:</p>
 </ul>
 <p>and repeats itself for types &gt; 6.  There is not yet an option to
 change this via the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command.</p>
+<hr class="docutils" />
 <p>The <em>body</em> keyword can be used when <a class="reference internal" href="atom_style.html"><span class="doc">atom_style body</span></a>
 is used to define body particles with internal state
 (e.g. sub-particles), and will drawn them in a manner specific to the
@@ -456,6 +464,40 @@ The <em>bflag1</em> and <em>bflag2</em> settings are numerical values which are
 passed to the body style to affect how the drawing of a body particle
 is done.  See the <a class="reference internal" href="body.html"><span class="doc">body</span></a> doc page for a description of what
 these parameters mean for each body style.</p>
+<p>The only setting currently allowed for the <em>color</em> value is <em>type</em>,
+which will color the body particles according to the atom type of the
+particle.  By default the mapping of types to colors is as follows:</p>
+<ul class="simple">
+<li>type 1 = red</li>
+<li>type 2 = green</li>
+<li>type 3 = blue</li>
+<li>type 4 = yellow</li>
+<li>type 5 = aqua</li>
+<li>type 6 = cyan</li>
+</ul>
+<p>and repeats itself for types &gt; 6.  There is not yet an option to
+change this via the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command.</p>
+<hr class="docutils" />
+<p>The <em>fix</em> keyword can be used with a <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> that produces
+objects to be drawn.  An example is the <span class="xref doc">fix surface/global</span> command which can draw lines
+or triangles for 2d/3d simulations.</p>
+<p>The <em>fflag1</em> and <em>fflag2</em> settings are numerical values which are
+passed to the fix to affect how the drawing of its objects is done.
+See the individual fix doc page for a description of what these
+parameters mean for a particular fix.</p>
+<p>The only setting currently allowed for the <em>color</em> value is <em>type</em>,
+which will color the fix objects according to their type.  By default
+the mapping of types to colors is as follows:</p>
+<ul class="simple">
+<li>type 1 = red</li>
+<li>type 2 = green</li>
+<li>type 3 = blue</li>
+<li>type 4 = yellow</li>
+<li>type 5 = aqua</li>
+<li>type 6 = cyan</li>
+</ul>
+<p>and repeats itself for types &gt; 6.  There is not yet an option to
+change this via the <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> command.</p>
 <hr class="docutils" />
 <p>The <em>size</em> keyword sets the width and height of the created images,
 i.e. the number of pixels in each direction.</p>

doc/html/fix_addforce.html

@@ -224,8 +224,9 @@ depending on your available hardware, as discussed in
 <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual.  The
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.</p>
-<p>These accelerated styles are part of the ackage.  They are only
+<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-enabled if LAMMPS was built with that package.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
 <p>You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>

doc/html/fix_aveforce.html

@@ -190,8 +190,9 @@ depending on your available hardware, as discussed in
 <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual.  The
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.</p>
-<p>These accelerated styles are part of the ackage.  They are only
+<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-enabled if LAMMPS was built with that package.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
 <p>You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>

doc/html/fix_enforce2d.html

@@ -154,8 +154,9 @@ depending on your available hardware, as discussed in
 <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual.  The
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.</p>
-<p>These accelerated styles are part of the ackage.  They are only
+<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-enabled if LAMMPS was built with that package.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
 <p>You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>

doc/html/fix_freeze.html

@@ -158,8 +158,9 @@ depending on your available hardware, as discussed in
 <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual.  The
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.</p>
-<p>These accelerated styles are part of the ackage.  They are only
+<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-enabled if LAMMPS was built with that package.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
 <p>You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>

doc/html/fix_shake.html

@@ -265,8 +265,9 @@ depending on your available hardware, as discussed in
 <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual.  The
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.</p>
-<p>These accelerated styles are part of the ackage.  They are only
+<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-enabled if LAMMPS was built with that package.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
 <p>You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
 use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>

doc/html/genindex.html

@@ -890,6 +890,10 @@
   </dt>
 
       
+  <dt><a href="dihedral_spherical.html#index-0">dihedral_style spherical</a>
+  </dt>
+
+      
   <dt><a href="dihedral_table.html#index-0">dihedral_style table</a>
   </dt>
 

doc/html/replicate.html

@@ -199,14 +199,6 @@ the file for individual atoms.  Similarly, no fixes can be defined at
 the time the replicate command is used that require vectors of atom
 information to be stored.  This is because the replicate command does
 not know how to replicate that information for new atoms it creates.</p>
-<p>Replicating a system that has rigid bodies (defined via the <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> command), either currently defined or that
-created the restart file which was read in before replicating, can
-cause problems if there is a bond between a pair of rigid bodies that
-straddle a periodic boundary.  This is because the periodic image
-information for particles in the rigid bodies are set differently than
-for a non-rigid system and can result in a new bond being created that
-spans the periodic box.  Thus you cannot use the replicate command in
-this scenario.</p>
 <p><strong>Related commands:</strong> none</p>
 <p><strong>Default:</strong> none</p>
 </div>

doc/src/Eqs/dihedral_spherical.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\pagestyle{empty}
+\begin{eqnarray*}
+E(\phi,\theta_1,\theta_2) & = &\sum_{i=1}^N\nolimits\ C_i\ \Phi_i(\phi)\ \Theta_{1i}(\theta_1)\ \Theta_{2i}(\theta_2)\\
+\Phi_{i}(\phi)        & = &  u_i - \mathrm{cos}((\phi   - a_i)K_i) \\
+\Theta_{1i}(\theta_1) & = &  v_i - \mathrm{cos}((\theta_1-b_i)L_i) \\
+\Theta_{2i}(\theta_2) & = &  w_i - \mathrm{cos}((\theta_2-c_i)M_i)
+\end{eqnarray*}
+
+% Check using: http://quicklatex.com/  (24pt font)
+\pagestyle{empty}
+\end{document}
+

doc/src/dihedral_spherical.txt

@@ -0,0 +1,87 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+dihedral_style spherical command :h3
+
+[Syntax:]
+
+dihedral_style spherical :pre
+
+[Examples:]
+
+dihedral_coeff 1 1  286.1  1 124 1   1 90.0 0   1 90.0 0   
+dihedral_coeff 1 3  286.1  1 114 1   1 90  0    1 90.0  0  &
+                    17.3   0 0.0 0   1 158 1    0 0.0   0  &
+                    15.1   0 0.0 0   0 0.0 0    1 167.3 1   :pre
+
+[Description:]
+
+The {spherical} dihedral style uses the potential:
+
+:c,image(JPG/dihedral_spherical_angles.jpg)
+:c,image(Eqs/dihedral_spherical.jpg)
+
+For this dihedral style, the energy can be any function that combines the
+4-body dihedral-angle (phi) and the two 3-body bond-angles (theta1, theta2).
+For this reason, there is usually no need to define 3-body "angle" forces
+separately for the atoms participating in these interactions.
+It is probably more efficient to incorporate 3-body angle forces into
+the dihedral interaction even if it requires adding additional terms to
+the expansion (as was done in the second example).  A careful choice of
+parameters can prevent singularities that occur with traditional
+force-fields whenever theta1 or theta2 approach 0 or 180 degrees.
+The last example above corresponds to an interaction with a single energy
+minima located at phi=114, theta1=158, theta2=167.3 degrees, and it remains
+numerically stable at all angles (phi, theta1, theta2). In this example,
+the coefficients 17.3, and 15.1 can be physically interpreted as the
+harmonic spring constants for theta1 and theta2 around their minima.
+The coefficient 286.1 is the harmonic spring constant for phi after
+division by sin(158)*sin(167.3) (the minima positions for theta1 and theta2).
+
+The following coefficients must be defined for each dihedral type via the
+"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
+the Dihedral Coeffs section of a data file file read by the
+"read_data"_read_data.html command:
+
+n (integer >= 1)
+C1 (energy)
+K1 (typically an integer)
+a1 (degrees)
+u1 (typically 0.0 or 1.0)
+L1 (typically an integer)
+b1 (degrees, typically 0.0 or 90.0)
+v1 (typically 0.0 or 1.0)
+M1 (typically an integer)
+c1 (degrees, typically 0.0 or 90.0)
+w1 (typically 0.0 or 1.0)
+....
+Cn (energy)
+Kn (typically an integer)
+an (degrees)
+un (typically 0.0 or 1.0)
+Ln (typically an integer)
+bn (degrees, typically 0.0 or 90.0)
+vn (typically 0.0 or 1.0)
+Mn (typically an integer)
+cn (degrees, typically 0.0 or 90.0)
+wn (typically 0.0 or 1.0) :ul
+
+:line
+
+[Restrictions:]
+
+This dihedral style can only be used if LAMMPS was built with the
+USER_MISC package.  See the "Making LAMMPS"_Section_start.html#start_3 
+section for more info on packages.
+
+[Related commands:]
+
+"dihedral_coeff"_dihedral_coeff.html
+
+[Default:] none
+

doc/src/dihedral_style.txt

@@ -54,7 +54,7 @@ In the formulas listed for each dihedral style, {phi} is the torsional
 angle defined by the quadruplet of atoms.  This angle has a sign
 convention as shown in this diagram:
 
-:c,image(Eqs/dihedral_sign.jpg)
+:c,image(JPG/dihedral_sign.jpg)
 
 where the I,J,K,L ordering of the 4 atoms that define the dihedral
 is from left to right.

doc/src/fix_addforce.txt

@@ -110,8 +110,9 @@ depending on your available hardware, as discussed in
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.
 
-These accelerated styles are part of the ackage.  They are only
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-enabled if LAMMPS was built with that package.  See the "Making
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script

doc/src/fix_aveforce.txt

@@ -70,8 +70,9 @@ depending on your available hardware, as discussed in
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.
 
-These accelerated styles are part of the ackage.  They are only
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-enabled if LAMMPS was built with that package.  See the "Making
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script

doc/src/fix_enforce2d.txt

@@ -34,8 +34,9 @@ depending on your available hardware, as discussed in
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.
 
-These accelerated styles are part of the ackage.  They are only
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-enabled if LAMMPS was built with that package.  See the "Making
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script

doc/src/fix_freeze.txt

@@ -38,8 +38,9 @@ depending on your available hardware, as discussed in
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.
 
-These accelerated styles are part of the ackage.  They are only
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-enabled if LAMMPS was built with that package.  See the "Making
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script

doc/src/fix_shake.txt

@@ -152,8 +152,9 @@ depending on your available hardware, as discussed in
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.
 
-These accelerated styles are part of the ackage.  They are only
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-enabled if LAMMPS was built with that package.  See the "Making
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script