Merge remote-tracking branch 'lammps-rw/clean-up-docs-for-sphinx' into clean-up-docs-for-sphinx (ace5dc3c) · Commits · 郑智淋 / lammps

doc/html/body.html

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		@@ -302,6 +302,11 @@ sphere is determined by the <em>bflag1</em> parameter for the <em>body</em> keyw
		The <em>bflag2</em> argument is ignored.</p>
		<hr class="docutils" />
		<p><strong>Specifics of body style rounded/polygon:</strong></p>
		<div class="admonition note">
		<p class="first admonition-title">Note</p>
		<p class="last">Aug 2016 - This body style has not yet been added to LAMMPS.
		The info below is a placeholder.</p>
		</div>
		<p>The <em>rounded/polygon</em> body style represents body particles as a convex
		polygon with a variable number N > 2 of vertices, which can only be
		used for 2d models. One example use of this body style is for 2d
		@@ -359,8 +364,9 @@ particles whose edge length is sqrt(2):</p>
		<span class="mf">1.0</span>
		</pre></div>
		</div>
		<p>The <span class="xref doc">pair_style body/rounded/polygon</span> command
		can be used with this body style to compute body/body interactions.</p>
		<p>The <span class="xref doc">pair_style body/rounded/polygon</span>
		command can be used with this body style to compute body/body
		interactions.</p>
		<p>For output purposes via the <a class="reference internal" href="compute_body_local.html"><span class="doc">compute body/local</span></a> and <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>
		commands, this body style produces one datum for each of the N
		sub-particles in a body particle. The datum has 3 values:</p>

doc/html/dump_image.html

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		@@ -481,6 +481,11 @@ change this via the <a class="reference internal" href="dump_modify.html"><span
		<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>
		<div class="admonition note">
		<p class="first admonition-title">Note</p>
		<p class="last">Aug 2016 - The fix surface/global command is not yet added to
		LAMMPS.</p>
		</div>
		<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

doc/html/kspace_style.html

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		@@ -132,7 +132,7 @@
		</pre></div>
		</div>
		<ul class="simple">
		<li>style = <em>none</em> or <em>ewald</em> or <em>ewald/disp</em> or <em>ewald/omp</em> or <em>pppm</em> or <em>pppm/cg</em> or <em>pppm/disp</em> or <em>pppm/tip4p</em> or <em>pppm/stagger</em> or <em>pppm/disp/tip4p</em> or <em>pppm/gpu</em> or <em>pppm/omp</em> or <em>pppm/cg/omp</em> or <em>pppm/tip4p/omp</em> or <em>msm</em> or <em>msm/cg</em> or <em>msm/omp</em> or <em>msm/cg/omp</em></li>
		<li>style = <em>none</em> or <em>ewald</em> or <em>ewald/disp</em> or <em>ewald/omp</em> or <em>pppm</em> or <em>pppm/cg</em> or <em>pppm/disp</em> or <em>pppm/tip4p</em> or <em>pppm/stagger</em> or <em>pppm/disp/tip4p</em> or <em>pppm/gpu</em> or <em>pppm/kk</em> or <em>pppm/omp</em> or <em>pppm/cg/omp</em> or <em>pppm/tip4p/omp</em> or <em>msm</em> or <em>msm/cg</em> or <em>msm/omp</em> or <em>msm/cg/omp</em></li>
		</ul>
		<pre class="literal-block">
		<em>none</em> value = none
		@@ -155,6 +155,8 @@
		accuracy = desired relative error in forces
		<em>pppm/gpu</em> value = accuracy
		accuracy = desired relative error in forces
		<em>pppm/kk</em> value = accuracy
		accuracy = desired relative error in forces
		<em>pppm/omp</em> value = accuracy
		accuracy = desired relative error in forces
		<em>pppm/cg/omp</em> value = accuracy
		@@ -385,6 +387,9 @@ If <em>pppm/gpu</em> is used with a GPU-enabled pair style, part of the PPPM
		calculation can be performed concurrently on the GPU while other
		calculations for non-bonded and bonded force calculation are performed
		on the CPU.</p>
		<p>The <em>pppm/kk</em> style also performs charge assignment and force
		interpolation calculations on the GPU while the FFTs themselves are
		calculated on the CPU in non-threaded mode.</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>
		@@ -406,10 +411,10 @@ the KSPACE package is installed by default.</p>
		<p>For MSM, a simulation must be 3d and one can use any combination of
		periodic, non-periodic, or shrink-wrapped boundaries (specified using
		the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command).</p>
		<p>For Ewald and PPPM, a simulation must be 3d and periodic in all dimensions.
		The only exception is if the slab option is set with <a class="reference internal" href="kspace_modify.html"><span class="doc">kspace_modify</span></a>,
		in which case the xy dimensions must be periodic and the z dimension must be
		non-periodic.</p>
		<p>For Ewald and PPPM, a simulation must be 3d and periodic in all
		dimensions. The only exception is if the slab option is set with
		<a class="reference internal" href="kspace_modify.html"><span class="doc">kspace_modify</span></a>, in which case the xy dimensions
		must be periodic and the z dimension must be non-periodic.</p>
		</div>
		<div class="section" id="related-commands">
		<h2>Related commands</h2>
		@@ -435,9 +440,10 @@ and Computation 5, 2322 (2009)</p>
		<p id="veld"><strong>(Veld)</strong> In ‘t Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).</p>
		<p id="toukmaji"><strong>(Toukmaji)</strong> Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
		10913 (2000).</p>
		<p id="isele-holder"><strong>(Isele-Holder)</strong> Isele-Holder, Mitchell, Ismail, J Chem Phys, 137, 174107 (2012).</p>
		<p id="isele-holder2"><strong>(Isele-Holder2)</strong> Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J Chem Theory
		Comput 9, 5412 (2013).</p>
		<p id="isele-holder"><strong>(Isele-Holder)</strong> Isele-Holder, Mitchell, Ismail, J Chem Phys, 137,
		174107 (2012).</p>
		<p id="isele-holder2"><strong>(Isele-Holder2)</strong> Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail,
		J Chem Theory Comput 9, 5412 (2013).</p>
		<p id="hardy"><strong>(Hardy)</strong> David Hardy thesis: Multilevel Summation for the Fast
		Evaluation of Forces for the Simulation of Biomolecules, University of
		Illinois at Urbana-Champaign, (2006).</p>

doc/src/body.txt

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		@@ -175,6 +175,9 @@ The {bflag2} argument is ignored.

		[Specifics of body style rounded/polygon:]

		NOTE: Aug 2016 - This body style has not yet been added to LAMMPS.
		The info below is a placeholder.

		The {rounded/polygon} body style represents body particles as a convex
		polygon with a variable number N > 2 of vertices, which can only be
		used for 2d models. One example use of this body style is for 2d
		@@ -235,8 +238,9 @@ particles whose edge length is sqrt(2):
		0 1 1 2 2 3 3 0
		1.0 :pre

		The "pair_style body/rounded/polygon"_pair_body_rounded_polygon.html command
		can be used with this body style to compute body/body interactions.
		The "pair_style body/rounded/polygon"_pair_body_rounded_polygon.html
		command can be used with this body style to compute body/body
		interactions.

		For output purposes via the "compute
		body/local"_compute_body_local.html and "dump local"_dump.html

doc/src/dump_image.txt

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Original line number	Diff line number	Diff line
		@@ -388,6 +388,9 @@ objects to be drawn. An example is the "fix
		surface/global"_fix_surface_global.html command which can draw lines
		or triangles for 2d/3d simulations.

		NOTE: Aug 2016 - The fix surface/global command is not yet added to
		LAMMPS.

		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

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