jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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

This commit is contained in:
sjplimp 2016-07-15 22:33:52 +00:00
parent 1587bdf2f1
commit 10bbb28943
34 changed files with 630 additions and 52 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

BIN
doc/html/_images/dihedral_sign.jpg
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 19 KiB

After

Width:  |  Height:  |  Size: 23 KiB

BIN
doc/html/_images/dihedral_spherical.jpg Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 14 KiB

BIN
doc/html/_images/dihedral_spherical_angles.jpg Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 25 KiB

101
doc/html/_sources/dihedral_spherical.txt Normal file
View File

@ -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

2
doc/html/_sources/dihedral_style.txt
View File

@ -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

63
doc/html/_sources/dump_image.txt
View File

@ -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.
----------

5
doc/html/_sources/fix_addforce.txt
View File

@ -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
enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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

5
doc/html/_sources/fix_aveforce.txt
View File

@ -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
enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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

5
doc/html/_sources/fix_enforce2d.txt
View File

@ -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
enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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

5
doc/html/_sources/fix_freeze.txt
View File

@ -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
enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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

5
doc/html/_sources/fix_shake.txt
View File

@ -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
enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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

9
doc/html/_sources/replicate.txt
View File

@ -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

270
doc/html/dihedral_spherical.html Normal file
View File

@ -0,0 +1,270 @@
<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>dihedral_style spherical command &mdash; LAMMPS documentation</title>
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
</head>
<body class="wy-body-for-nav" role="document">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-nav-search">
<a href="Manual.html" class="icon icon-home"> LAMMPS
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
&nbsp;
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="Manual.html">LAMMPS</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>dihedral_style spherical command</li>
<li class="wy-breadcrumbs-aside">
<a href="http://lammps.sandia.gov">Website</a>
<a href="Section_commands.html#comm">Commands</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<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>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
&copy; Copyright 2013 Sandia Corporation.
</p>
</div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
};
</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>

44
doc/html/dump_image.html
View File

@ -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>

5
doc/html/fix_addforce.html
View File

@ -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
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>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span 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>

5
doc/html/fix_aveforce.html
View File

@ -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
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>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span 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>

5
doc/html/fix_enforce2d.html
View File

@ -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
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>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span 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>

5
doc/html/fix_freeze.html
View File

@ -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
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>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span 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>

5
doc/html/fix_shake.html
View File

@ -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
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>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span 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>

4
doc/html/genindex.html
View File

@ -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>

8
doc/html/replicate.html
View File

@ -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>

2
doc/html/searchindex.js
View File

File diff suppressed because one or more lines are too long

BIN
doc/src/Eqs/dihedral_sign.jpg
View File

Binary file not shown.
Side by Side

Before

Width:  |  Height:  |  Size: 19 KiB

BIN
doc/src/Eqs/dihedral_spherical.jpg Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 14 KiB

15
doc/src/Eqs/dihedral_spherical.tex Normal file
View File

@ -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}

BIN
doc/src/JPG/dihedral_sign.jpg Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 23 KiB

BIN
doc/src/JPG/dihedral_spherical_angles.jpg Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 25 KiB

87
doc/src/dihedral_spherical.txt Normal file
View File

@ -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

2
doc/src/dihedral_style.txt
View File

@ -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.

5
doc/src/fix_addforce.txt
View File

@ -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
enabled if LAMMPS was built with that package. See the "Making
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script

5
doc/src/fix_aveforce.txt
View File

@ -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
enabled if LAMMPS was built with that package. See the "Making
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script

5
doc/src/fix_enforce2d.txt
View File

@ -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
enabled if LAMMPS was built with that package. See the "Making
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script

5
doc/src/fix_freeze.txt
View File

@ -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
enabled if LAMMPS was built with that package. See the "Making
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script

5
doc/src/fix_shake.txt
View File

@ -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
enabled if LAMMPS was built with that package. See the "Making
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script