ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14957 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2016-05-09 19:31:29 +00:00
parent 5bc5c6ba93
commit 5b2d4fe6b1
57 changed files with 100 additions and 104 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
doc/html/fix_rigid.html
View File

@ -288,10 +288,10 @@ differences may accumulate to produce divergent trajectories.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">You should not update the atoms in rigid bodies via other
time-integration fixes (e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>), or you will be integrating
time-integration fixes (e.g. <span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>), or you will be integrating
their motion more than once each timestep. When performing a hybrid
simulation with some atoms in rigid bodies, and some not, a separate
time integration fix like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> should be used for the non-rigid particles.</p>
time integration fix like <span class="xref doc">fix nve</span> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> should be used for the non-rigid particles.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
@ -303,7 +303,7 @@ your time integration fix. E.g. use &#8220;fix 1 mobile nve&#8221; instead of
move. You can move atoms with a constant velocity by assigning them
an initial velocity (via the <a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a> command),
setting the force on them to 0.0 (via the <a class="reference internal" href="fix_setforce.html"><span class="doc">fix setforce</span></a> command), and integrating them as usual
(e.g. via the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command).</p>
(e.g. via the <span class="xref doc">fix nve</span> command).</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
@ -685,10 +685,10 @@ also accounted for by this fix.</p>
<hr class="docutils" />
<p>If your simlulation is a hybrid model with a mixture of rigid bodies
and non-rigid particles (e.g. solvent) there are several ways these
rigid fixes can be used in tandem with <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>, and <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
rigid fixes can be used in tandem with <span class="xref doc">fix nve</span>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>, and <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
<p>If you wish to perform NVE dynamics (no thermostatting or
barostatting), use fix rigid or fix rigid/nve to integrate the rigid
bodies, and <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> to integrate the non-rigid
bodies, and <span class="xref doc">fix nve</span> to integrate the non-rigid
particles.</p>
<p>If you wish to perform NVT dynamics (thermostatting, but no
barostatting), you can use fix rigid/nvt for the rigid bodies, and any