Merge branch 'integration' into fix-flow-gauss (bb721db8) · Commits · 郑智淋 / lammps

.gitignore

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			*~
			*.o
			*.so
			*.cu_o
			*.ptx
			*_ptx.h
			*.a
			*.d
			*.x
			*.exe
			*.dll

			Obj_*
			log.lammps
			log.cite
			*.bz2
			*.gz
			*.tar
			.*.swp
			*.orig
			*.rej
			.vagrant

			.DS_Store
			.DS_Store?
			._*
			.Spotlight-V100
			.Trashes
			ehthumbs.db
			Thumbs.db

doc/.gitignore

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doc/html/Manual.html

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	@@ -135,7 +135,7 @@
	<H1></H1><div class="section" id="lammps-documentation">		<H1></H1><div class="section" id="lammps-documentation">
	<h1>LAMMPS Documentation</h1>		<h1>LAMMPS Documentation</h1>
	<div class="section" id="aug-2016-version">		<div class="section" id="aug-2016-version">
	<h2>20 Aug 2016 version</h2>		<h2>23 Aug 2016 version</h2>
	</div>		</div>
	<div class="section" id="version-info">		<div class="section" id="version-info">
	<h2>Version info:</h2>		<h2>Version info:</h2>

doc/html/Section_commands.html

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	@@ -778,12 +778,12 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
	<a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>		<a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>
	<table border="1" class="docutils">		<table border="1" class="docutils">
	<colgroup>		<colgroup>
	<col width="23%" />		<col width="14%" />
			<col width="22%" />
	<col width="15%" />		<col width="15%" />
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	<col width="20%" />		<col width="20%" />
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	<tbody valign="top">		<tbody valign="top">
	<tr class="row-odd"><td><a class="reference internal" href="fix_adapt_fep.html"><span class="doc">adapt/fep</span></a></td>		<tr class="row-odd"><td><a class="reference internal" href="fix_adapt_fep.html"><span class="doc">adapt/fep</span></a></td>
	@@ -798,56 +798,63 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p>
	<td><a class="reference internal" href="fix_eos_cv.html"><span class="doc">eos/cv</span></a></td>		<td><a class="reference internal" href="fix_eos_cv.html"><span class="doc">eos/cv</span></a></td>
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			<td> </td>
			<td> </td>
			<td> </td>
			<td> </td>
			<td> </td>
	</tr>		</tr>
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doc/html/Section_start.html

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	@@ -1769,15 +1769,17 @@ computation. These thread timings are taking from the first MPI rank
	only and and thus, as the breakdown for MPI tasks can change from MPI		only and and thus, as the breakdown for MPI tasks can change from MPI
	rank to MPI rank, this breakdown can be very different for individual		rank to MPI rank, this breakdown can be very different for individual
	ranks. Here is an example output for this section:</p>		ranks. Here is an example output for this section:</p>
	<p>Thread timings breakdown (MPI rank 0):		<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Thread</span> <span class="n">timings</span> <span class="n">breakdown</span> <span class="p">(</span><span class="n">MPI</span> <span class="n">rank</span> <span class="mi">0</span><span class="p">):</span>
	Total threaded time 0.6846 / 90.6%		<span class="n">Total</span> <span class="n">threaded</span> <span class="n">time</span> <span class="mf">0.6846</span> <span class="o">/</span> <span class="mf">90.6</span><span class="o">%</span>
	Section \| min time \| avg time \| max time <a href="#id37"><span class="problematic" id="id38">\|%varavg\|</span></a> %total		<span class="n">Section</span> <span class="o">\|</span> <span class="nb">min</span> <span class="n">time</span> <span class="o">\|</span> <span class="n">avg</span> <span class="n">time</span> <span class="o">\|</span> <span class="nb">max</span> <span class="n">time</span> <span class="o">\|%</span><span class="n">varavg</span><span class="o">\|</span> <span class="o">%</span><span class="n">total</span>
	—————————————————————		<span class="o">---------------------------------------------------------------</span>
	Pair \| 0.5127 \| 0.5147 \| 0.5167 \| 0.3 \| 75.18		<span class="n">Pair</span> <span class="o">\|</span> <span class="mf">0.5127</span> <span class="o">\|</span> <span class="mf">0.5147</span> <span class="o">\|</span> <span class="mf">0.5167</span> <span class="o">\|</span> <span class="mf">0.3</span> <span class="o">\|</span> <span class="mf">75.18</span>
	Bond \| 0.0043139 \| 0.0046779 \| 0.0050418 \| 0.5 \| 0.68		<span class="n">Bond</span> <span class="o">\|</span> <span class="mf">0.0043139</span> <span class="o">\|</span> <span class="mf">0.0046779</span> <span class="o">\|</span> <span class="mf">0.0050418</span> <span class="o">\|</span> <span class="mf">0.5</span> <span class="o">\|</span> <span class="mf">0.68</span>
	Kspace \| 0.070572 \| 0.074541 \| 0.07851 \| 1.5 \| 10.89		<span class="n">Kspace</span> <span class="o">\|</span> <span class="mf">0.070572</span> <span class="o">\|</span> <span class="mf">0.074541</span> <span class="o">\|</span> <span class="mf">0.07851</span> <span class="o">\|</span> <span class="mf">1.5</span> <span class="o">\|</span> <span class="mf">10.89</span>
	Neigh \| 0.084778 \| 0.086969 \| 0.089161 \| 0.7 \| 12.70		<span class="n">Neigh</span> <span class="o">\|</span> <span class="mf">0.084778</span> <span class="o">\|</span> <span class="mf">0.086969</span> <span class="o">\|</span> <span class="mf">0.089161</span> <span class="o">\|</span> <span class="mf">0.7</span> <span class="o">\|</span> <span class="mf">12.70</span>
	Reduce \| 0.0036485 \| 0.003737 \| 0.0038254 \| 0.1 \| 0.55</p>		<span class="n">Reduce</span> <span class="o">\|</span> <span class="mf">0.0036485</span> <span class="o">\|</span> <span class="mf">0.003737</span> <span class="o">\|</span> <span class="mf">0.0038254</span> <span class="o">\|</span> <span class="mf">0.1</span> <span class="o">\|</span> <span class="mf">0.55</span>
			</pre></div>
			</div>
	<p>The third section lists the number of owned atoms (Nlocal), ghost atoms		<p>The third section lists the number of owned atoms (Nlocal), ghost atoms
	(Nghost), and pair-wise neighbors stored per processor. The max and min		(Nghost), and pair-wise neighbors stored per processor. The max and min
	values give the spread of these values across processors with a 10-bin		values give the spread of these values across processors with a 10-bin

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