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23
doc/html/_sources/compute_rigid_local.txt
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@ -14,6 +14,29 @@ Syntax
* rigid/local = style name of this compute command * rigid/local = style name of this compute command
* rigidID = ID of fix rigid/small command or one of its variants * rigidID = ID of fix rigid/small command or one of its variants
* input = one or more rigid body attributes * input = one or more rigid body attributes
.. parsed-literal::
possible attributes = id, mol, mass,
x, y, z, xu, yu, zu, ix, iy, iz
vx, vy, vz, fx, fy, fz,
omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
quatw, quati, quatj, quatk,
tqx, tqy, tqz,
inertiax, inertiay, inertiaz
id = atom ID of atom within body which owns body properties
mol = molecule ID used to define body in :doc:`fix rigid/small <fix_rigid>` command
mass = total mass of body
x,y,z = center of mass coords of body
xu,yu,zu = unwrapped center of mass coords of body
ix,iy,iz = box image that the center of mass is in
vx,vy,vz = center of mass velocities
fx,fy,fz = force of center of mass
omegax,omegay,omegaz = angular velocity of body
angmomx,angmomy,angmomz = angular momentum of body
quatw,quati,quatj,quatk = quaternion components for body
tqx,tqy,tqz = torque on body
inertiax,inertiay,inertiaz = diagonalized moments of inertia of body

18
doc/html/_sources/manifolds.txt
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@ -1,8 +1,18 @@
Description Manifolds (surfacse)
""""""""""" ====================
Below is a list of currently supported manifolds, their parameters and a short description of them. **Overview:**
The parameters listed here are in the same order as they should be passed to the relevant fixes.
This doc page is not about a LAMMPS input script command, but about
manifolds, which are generalized surfaces, as defined and used by the
USER-MANIFOLD package, to track particle motion on the manifolds. See
the src/USER-MANIFOLD/README file for more details about the package
and its commands.
Below is a list of currently supported manifolds by the USER-MANIFOLD
package, their parameters and a short description of them. The
parameters listed here are in the same order as they should be passed
to the relevant fixes.
+---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+ +---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
| *manifold* | *parameters* | *equation* | *description* | | | *manifold* | *parameters* | *equation* | *description* | |

3
doc/html/_sources/pair_modify.txt
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@ -216,9 +216,6 @@ pair style be defined.
---------- ----------
Use of *special* keyword
^^^^^^^^^^^^^^^^^^^^^^^^
The *special* keyword allows to override the 1-2, 1-3, and 1-4 The *special* keyword allows to override the 1-2, 1-3, and 1-4
exclusion settings for individual sub-styles of a exclusion settings for individual sub-styles of a
:doc:`hybrid pair style <pair_hybrid>`. It requires 4 arguments similar :doc:`hybrid pair style <pair_hybrid>`. It requires 4 arguments similar

30
doc/html/_sources/tutorial_github.txt
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@ -1,23 +1,21 @@
LAMMPS GitHub tutorial LAMMPS GitHub tutorial
********************** ======================
written by Stefan Paquay **written by Stefan Paquay**
========================
---------- ----------
This document briefly describes how to use GitHub to merge changes This document briefly describes how to use GitHub to merge changes you
into LAMMPS using GitHub. It assumes that you are familiar with make into LAMMPS, using GitHub. It assumes that you are familiar with
git. You may want to have a look at the `Git book <http://git-scm.com/book/>`_ to reacquaint yourself. git. You may want to have a look at the `Git book <http://git-scm.com/book/>`_ to reacquaint yourself.
---------- ----------
Making an account **Making an account**
*****************
First of all, you need a GitHub account. This is fairly simple, just First of all, you need a GitHub account. This is fairly simple, just
go to `GitHub <https://github.com>`_ and create an account by clicking go to `GitHub <https://github.com>`_ and create an account by clicking
@ -29,8 +27,7 @@ username or e-mail address and password.
---------- ----------
Forking the repository **Forking the repository**
**********************
To get changes into LAMMPS, you need to first fork the repository. At To get changes into LAMMPS, you need to first fork the repository. At
the time of writing, LAMMPS-ICMS is the preferred fork. Go to `LAMMPS on GitHub <https://github.com/lammps/lammps>`_ and make sure branch is the time of writing, LAMMPS-ICMS is the preferred fork. Go to `LAMMPS on GitHub <https://github.com/lammps/lammps>`_ and make sure branch is
@ -54,14 +51,12 @@ can include changes from upstream into your repository.
---------- ----------
Adding changes to your own fork **Adding changes to your own fork**
*******************************
Before adding changes, it is better to first create a new branch that Before adding changes, it is better to first create a new branch that
will contain these changes, a so-called feature branch. will contain these changes, a so-called feature branch.
Feature branches **Feature branches**
================
Since LAMMPS is such a big project and most user contributions come in Since LAMMPS is such a big project and most user contributions come in
small portions, the most ideal workflow for LAMMPS is the so-called small portions, the most ideal workflow for LAMMPS is the so-called
@ -126,8 +121,7 @@ After the files are added, the change should be comitted:
The "-m" switch is used to add a message to the commit. Use this to The "-m" switch is used to add a message to the commit. Use this to
indicate what type of change was commited. indicate what type of change was commited.
Wisdom by Axel: **Wisdom by Axel**
---------------
*"Do not use "git commit -a". the -a flag will automatically include *"Do not use "git commit -a". the -a flag will automatically include
*all* modified or new files. mercurial does that and it find it *all* modified or new files. mercurial does that and it find it
@ -204,8 +198,7 @@ request.
---------- ----------
Additional changes **Additional changes**
******************
Before the pull request is accepted, any additional changes you push Before the pull request is accepted, any additional changes you push
into your repository will automatically become part of the pull into your repository will automatically become part of the pull
@ -215,8 +208,7 @@ request.
---------- ----------
After a merge **After a merge**
*************
When everything is fine the feature branch is merged into the LAMMPS When everything is fine the feature branch is merged into the LAMMPS
repositories: repositories:

23
doc/html/compute_rigid_local.html
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@ -137,6 +137,29 @@
<li>rigidID = ID of fix rigid/small command or one of its variants</li> <li>rigidID = ID of fix rigid/small command or one of its variants</li>
<li>input = one or more rigid body attributes</li> <li>input = one or more rigid body attributes</li>
</ul> </ul>
<pre class="literal-block">
possible attributes = id, mol, mass,
x, y, z, xu, yu, zu, ix, iy, iz
vx, vy, vz, fx, fy, fz,
omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
quatw, quati, quatj, quatk,
tqx, tqy, tqz,
inertiax, inertiay, inertiaz
id = atom ID of atom within body which owns body properties
mol = molecule ID used to define body in <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/small</span></a> command
mass = total mass of body
x,y,z = center of mass coords of body
xu,yu,zu = unwrapped center of mass coords of body
ix,iy,iz = box image that the center of mass is in
vx,vy,vz = center of mass velocities
fx,fy,fz = force of center of mass
omegax,omegay,omegaz = angular velocity of body
angmomx,angmomy,angmomz = angular momentum of body
quatw,quati,quatj,quatk = quaternion components for body
tqx,tqy,tqz = torque on body
inertiax,inertiay,inertiaz = diagonalized moments of inertia of body
</pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>

20
doc/html/manifolds.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Description &mdash; LAMMPS documentation</title> <title>Manifolds (surfacse) &mdash; LAMMPS documentation</title>
@ -109,7 +109,7 @@
<ul class="wy-breadcrumbs"> <ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li> <li><a href="Manual.html">Docs</a> &raquo;</li>
<li>Description</li> <li>Manifolds (surfacse)</li>
<li class="wy-breadcrumbs-aside"> <li class="wy-breadcrumbs-aside">
@ -124,10 +124,18 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody"> <div itemprop="articleBody">
<div class="section" id="description"> <div class="section" id="manifolds-surfacse">
<h1>Description</h1> <h1>Manifolds (surfacse)</h1>
<p>Below is a list of currently supported manifolds, their parameters and a short description of them. <p><strong>Overview:</strong></p>
The parameters listed here are in the same order as they should be passed to the relevant fixes.</p> <p>This doc page is not about a LAMMPS input script command, but about
manifolds, which are generalized surfaces, as defined and used by the
USER-MANIFOLD package, to track particle motion on the manifolds. See
the src/USER-MANIFOLD/README file for more details about the package
and its commands.</p>
<p>Below is a list of currently supported manifolds by the USER-MANIFOLD
package, their parameters and a short description of them. The
parameters listed here are in the same order as they should be passed
to the relevant fixes.</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="5%" /> <col width="5%" />

5
doc/html/pair_modify.html
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@ -228,7 +228,7 @@ see the doc page for individual styles to see which potentials support
these options. If N is non-zero, a table of length 2^N is these options. If N is non-zero, a table of length 2^N is
pre-computed for forces and energies, which can shrink their pre-computed for forces and energies, which can shrink their
computational cost by up to a factor of 2. The table is indexed via a computational cost by up to a factor of 2. The table is indexed via a
bit-mapping technique <a class="reference internal" href="pair_table_rx.html#wolff"><span class="std std-ref">(Wolff)</span></a> and a linear interpolation is bit-mapping technique <a class="reference internal" href="#wolff"><span class="std std-ref">(Wolff)</span></a> and a linear interpolation is
performed between adjacent table values. In our experiments with performed between adjacent table values. In our experiments with
different table styles (lookup, linear, spline), this method typically different table styles (lookup, linear, spline), this method typically
gave the best performance in terms of speed and accuracy.</p> gave the best performance in terms of speed and accuracy.</p>
@ -316,8 +316,6 @@ a pair style will not work, because the
<a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> command requires a Kspace-compatible <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> command requires a Kspace-compatible
pair style be defined.</p> pair style be defined.</p>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="use-of-special-keyword">
<h3>Use of <em>special</em> keyword</h3>
<p>The <em>special</em> keyword allows to override the 1-2, 1-3, and 1-4 <p>The <em>special</em> keyword allows to override the 1-2, 1-3, and 1-4
exclusion settings for individual sub-styles of a exclusion settings for individual sub-styles of a
<a class="reference internal" href="pair_hybrid.html"><span class="doc">hybrid pair style</span></a>. It requires 4 arguments similar <a class="reference internal" href="pair_hybrid.html"><span class="doc">hybrid pair style</span></a>. It requires 4 arguments similar
@ -343,7 +341,6 @@ usually a sufficient workaround in this case without causing a
significant error.</p> significant error.</p>
</div> </div>
</div> </div>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="restrictions"> <div class="section" id="restrictions">
<h2>Restrictions</h2> <h2>Restrictions</h2>

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

36
doc/html/tutorial_github.html
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@ -126,26 +126,20 @@
<div class="section" id="lammps-github-tutorial"> <div class="section" id="lammps-github-tutorial">
<h1>LAMMPS GitHub tutorial</h1> <h1>LAMMPS GitHub tutorial</h1>
<div class="section" id="written-by-stefan-paquay"> <p><strong>written by Stefan Paquay</strong></p>
<h2>written by Stefan Paquay</h2>
<hr class="docutils" /> <hr class="docutils" />
<p>This document briefly describes how to use GitHub to merge changes <p>This document briefly describes how to use GitHub to merge changes you
into LAMMPS using GitHub. It assumes that you are familiar with make into LAMMPS, using GitHub. It assumes that you are familiar with
git. You may want to have a look at the <a class="reference external" href="http://git-scm.com/book/">Git book</a> to reacquaint yourself.</p> git. You may want to have a look at the <a class="reference external" href="http://git-scm.com/book/">Git book</a> to reacquaint yourself.</p>
</div>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="making-an-account"> <p><strong>Making an account</strong></p>
<h1>Making an account</h1>
<p>First of all, you need a GitHub account. This is fairly simple, just <p>First of all, you need a GitHub account. This is fairly simple, just
go to <a class="reference external" href="https://github.com">GitHub</a> and create an account by clicking go to <a class="reference external" href="https://github.com">GitHub</a> and create an account by clicking
the <a href="#id1"><span class="problematic" id="id2">``</span></a>Sign up for GitHub&#8217;&#8217; button. Once your account is created, you the <a href="#id1"><span class="problematic" id="id2">``</span></a>Sign up for GitHub&#8217;&#8217; button. Once your account is created, you
can sign in by clicking the button in the top left and filling in your can sign in by clicking the button in the top left and filling in your
username or e-mail address and password.</p> username or e-mail address and password.</p>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="forking-the-repository"> <p><strong>Forking the repository</strong></p>
<h1>Forking the repository</h1>
<p>To get changes into LAMMPS, you need to first fork the repository. At <p>To get changes into LAMMPS, you need to first fork the repository. At
the time of writing, LAMMPS-ICMS is the preferred fork. Go to <a class="reference external" href="https://github.com/lammps/lammps">LAMMPS on GitHub</a> and make sure branch is the time of writing, LAMMPS-ICMS is the preferred fork. Go to <a class="reference external" href="https://github.com/lammps/lammps">LAMMPS on GitHub</a> and make sure branch is
set to <a href="#id3"><span class="problematic" id="id4">``</span></a>lammps-icms&#8217;&#8216;, see the figure below.</p> set to <a href="#id3"><span class="problematic" id="id4">``</span></a>lammps-icms&#8217;&#8216;, see the figure below.</p>
@ -157,14 +151,11 @@ changes in this fork and later file <em>pull requests</em> to allow the
upstream repository to merge changes from your own fork into the one upstream repository to merge changes from your own fork into the one
we just forked from. At the same time, you can set things up, so you we just forked from. At the same time, you can set things up, so you
can include changes from upstream into your repository.</p> can include changes from upstream into your repository.</p>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="adding-changes-to-your-own-fork"> <p><strong>Adding changes to your own fork</strong></p>
<h1>Adding changes to your own fork</h1>
<p>Before adding changes, it is better to first create a new branch that <p>Before adding changes, it is better to first create a new branch that
will contain these changes, a so-called feature branch.</p> will contain these changes, a so-called feature branch.</p>
<div class="section" id="feature-branches"> <p><strong>Feature branches</strong></p>
<h2>Feature branches</h2>
<p>Since LAMMPS is such a big project and most user contributions come in <p>Since LAMMPS is such a big project and most user contributions come in
small portions, the most ideal workflow for LAMMPS is the so-called small portions, the most ideal workflow for LAMMPS is the so-called
<a href="#id5"><span class="problematic" id="id6">``</span></a>Feature branch&#8217;&#8217; workflow. It is explained in great detail here: <a href="#id5"><span class="problematic" id="id6">``</span></a>Feature branch&#8217;&#8217; workflow. It is explained in great detail here:
@ -210,8 +201,7 @@ $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt
</div> </div>
<p>The &#8220;-m&#8221; switch is used to add a message to the commit. Use this to <p>The &#8220;-m&#8221; switch is used to add a message to the commit. Use this to
indicate what type of change was commited.</p> indicate what type of change was commited.</p>
<div class="section" id="wisdom-by-axel"> <p><strong>Wisdom by Axel</strong></p>
<h3>Wisdom by Axel:</h3>
<p><em>&#8220;Do not use &#8220;git commit -a&#8221;. the -a flag will automatically include <p><em>&#8220;Do not use &#8220;git commit -a&#8221;. the -a flag will automatically include
*all</em> modified or new files. mercurial does that and it find it *all</em> modified or new files. mercurial does that and it find it
hugely annoying and often leading to accidental commits of files you hugely annoying and often leading to accidental commits of files you
@ -262,19 +252,13 @@ is now up to the maintainer(s) of the upstream repository to
incorporate the changes into the repository and to close the pull incorporate the changes into the repository and to close the pull
request.</p> request.</p>
<img alt="_images/tutorial_pull_request4.png" class="align-center" src="_images/tutorial_pull_request4.png" /> <img alt="_images/tutorial_pull_request4.png" class="align-center" src="_images/tutorial_pull_request4.png" />
</div>
</div>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="additional-changes"> <p><strong>Additional changes</strong></p>
<h1>Additional changes</h1>
<p>Before the pull request is accepted, any additional changes you push <p>Before the pull request is accepted, any additional changes you push
into your repository will automatically become part of the pull into your repository will automatically become part of the pull
request.</p> request.</p>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="after-a-merge"> <p><strong>After a merge</strong></p>
<h1>After a merge</h1>
<p>When everything is fine the feature branch is merged into the LAMMPS <p>When everything is fine the feature branch is merged into the LAMMPS
repositories:</p> repositories:</p>
<img alt="_images/tutorial_merged.png" class="align-center" src="_images/tutorial_merged.png" /> <img alt="_images/tutorial_merged.png" class="align-center" src="_images/tutorial_merged.png" />

2
doc/lammps.book
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@ -620,5 +620,3 @@ USER/atc/man_unfix_flux.html
USER/atc/man_unfix_nodes.html USER/atc/man_unfix_nodes.html
USER/atc/man_write_atom_weights.html USER/atc/man_write_atom_weights.html
USER/atc/man_write_restart.html USER/atc/man_write_restart.html