From 57b24b566867038b092867cb0c23a880e8467233 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Sat, 27 Aug 2016 23:07:03 +0000
Subject: [PATCH] updated USER-MANIFOLD doc pages
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15516 f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/html/fix_nve_manifold_rattle.html | 7 ++-----
doc/html/fix_nvt_manifold_rattle.html | 7 ++-----
doc/src/fix_nve_manifold_rattle.txt | 6 +-----
doc/src/fix_nvt_manifold_rattle.txt | 6 +-----
4 files changed, 6 insertions(+), 20 deletions(-)
diff --git a/doc/html/fix_nve_manifold_rattle.html b/doc/html/fix_nve_manifold_rattle.html
index dbcf0a2488..3f7633ded4 100644
--- a/doc/html/fix_nve_manifold_rattle.html
+++ b/doc/html/fix_nve_manifold_rattle.html
@@ -158,7 +158,7 @@ keyword = <em>every</em>
<p>Perform constant NVE integration to update position and velocity for
atoms constrained to a curved surface (manifold) in the group each timestep. The constraint
is handled by RATTLE <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a> written out for the special case of
-single-particle constraints as explained in <a class="reference internal" href="manifolds.html#paquay"><span class="std std-ref">(Paquay)</span></a>.
+single-particle constraints as explained in <a class="reference internal" href="fix_nvt_manifold_rattle.html#paquay"><span class="std std-ref">(Paquay)</span></a>.
V is volume; E is energy. This way, the dynamics of particles constrained to
curved surfaces can be studied. If combined with <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, this generates
Brownian motion of particles constrained to a curved surface. For a list of currently supported
@@ -191,9 +191,6 @@ This fix is not invoked during <a class="reference internal" href="minimize.html
<p>This fix is part of the USER-MANIFOLD package. It is 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>Only use this with <em>min_style hftn</em> or <em>min_style quickmin</em>. If not, the constraints
-will not be satisfied very well at all. A warning is generated if the <em>min_style</em> is
-incompatible but no error.</p>
</div>
<hr class="docutils" />
<div class="section" id="related-commands">
@@ -202,7 +199,7 @@ incompatible but no error.</p>
<p><strong>Default:</strong> every = 0, tchain = 3</p>
<hr class="docutils" />
<p id="andersen"><strong>(Andersen)</strong> Andersen, J. Comp. Phys. 52, 24, (1983).</p>
-<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
+<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, 6, (2016).
preprint available at <a class="reference external" href="http://arxiv.org/abs/1411.3019/">arXiv:1411.3019</a>.</p>
</div>
</div>
diff --git a/doc/html/fix_nvt_manifold_rattle.html b/doc/html/fix_nvt_manifold_rattle.html
index 98dd612247..35e6ea6135 100644
--- a/doc/html/fix_nvt_manifold_rattle.html
+++ b/doc/html/fix_nvt_manifold_rattle.html
@@ -157,7 +157,7 @@ keyword = <em>temp</em> or <em>tchain</em> or <em>every</em>
</div>
<div class="section" id="description">
<h2>Description</h2>
-<p>This fix combines the RATTLE-based <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a> time integrator of <a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">fix nve/manifold/rattle</span></a> <a class="reference internal" href="manifolds.html#paquay"><span class="std std-ref">(Paquay)</span></a> with a Nose-Hoover-chain thermostat to sample the
+<p>This fix combines the RATTLE-based <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a> time integrator of <a class="reference internal" href="fix_nve_manifold_rattle.html"><span class="doc">fix nve/manifold/rattle</span></a> <a class="reference internal" href="#paquay"><span class="std std-ref">(Paquay)</span></a> with a Nose-Hoover-chain thermostat to sample the
canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt).
For a list of currently supported manifolds and their parameters, see <a class="reference internal" href="manifolds.html"><span class="doc">manifolds</span></a></p>
</div>
@@ -176,9 +176,6 @@ This fix is not invoked during <a class="reference internal" href="minimize.html
<p>This fix is part of the USER-MANIFOLD package. It is 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>Only use this with <em>min_style hftn</em> or <em>min_style quickmin</em>. If not, the constraints
-will not be satisfied very well at all. A warning is generated if the <em>min_style</em> is
-incompatible but no error.</p>
</div>
<hr class="docutils" />
<div class="section" id="related-commands">
@@ -187,7 +184,7 @@ incompatible but no error.</p>
<strong>Default:</strong> every = 0</p>
<hr class="docutils" />
<p id="andersen"><strong>(Andersen)</strong> Andersen, J. Comp. Phys. 52, 24, (1983).</p>
-<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
+<p id="paquay"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, 6, (2016).
preprint available at <a class="reference external" href="http://arxiv.org/abs/1411.3019/">arXiv:1411.3019</a>.</p>
</div>
</div>
diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/src/fix_nve_manifold_rattle.txt
index 8d0eb8e57c..a35c234e63 100644
--- a/doc/src/fix_nve_manifold_rattle.txt
+++ b/doc/src/fix_nve_manifold_rattle.txt
@@ -76,10 +76,6 @@ This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
-Only use this with {min_style hftn} or {min_style quickmin}. If not, the constraints
-will not be satisfied very well at all. A warning is generated if the {min_style} is
-incompatible but no error.
-
:line
[Related commands:]
@@ -94,7 +90,7 @@ incompatible but no error.
[(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983).
:link(Paquay)
-[(Paquay)] Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
+[(Paquay)] Paquay and Kusters, Biophys. J., 110, 6, (2016).
preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/.
diff --git a/doc/src/fix_nvt_manifold_rattle.txt b/doc/src/fix_nvt_manifold_rattle.txt
index f117d10eb9..42a06d4ed7 100644
--- a/doc/src/fix_nvt_manifold_rattle.txt
+++ b/doc/src/fix_nvt_manifold_rattle.txt
@@ -62,10 +62,6 @@ This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
-Only use this with {min_style hftn} or {min_style quickmin}. If not, the constraints
-will not be satisfied very well at all. A warning is generated if the {min_style} is
-incompatible but no error.
-
:line
@@ -80,6 +76,6 @@ incompatible but no error.
[(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983).
:link(Paquay)
-[(Paquay)] Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
+[(Paquay)] Paquay and Kusters, Biophys. J., 110, 6, (2016).
preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/.
--
GitLab