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@14349 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2015-12-10 17:23:56 +00:00
parent 8550cacf18
commit 28bf73fbf7
688 changed files with 6410 additions and 6513 deletions
Download Patch File Download Diff File Expand all files Collapse all files

73
doc/Section_start.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>2. Getting Started &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>2. Getting Started &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<link rel="next" title="3. Commands" href="Section_commands.html"/>
<link rel="prev" title="1. Introduction" href="Section_intro.html"/>
@ -397,10 +397,10 @@ within the LAMMPS code. The options that are currently recogized are:</p>
compile with -DLAMMPS_GZIP. It requires that your machine supports
the &#8220;popen()&#8221; function in the standard runtime library and that a gzip
executable can be found by LAMMPS during a run.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">on some clusters with high-speed networks, using the
fork() library calls (required by popen()) can interfere with the fast
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">on some clusters with high-speed networks, using the fork()
library calls (required by popen()) can interfere with the fast
communication library and lead to simulations using compressed output
or input to hang or crash. For selected operations, compressed file
I/O is also available using a compression library instead, which are
@ -420,10 +420,10 @@ will be available to support on-the-fly generation of rendered movies
the need to store intermediate image files. It requires that your
machines supports the &#8220;popen&#8221; function in the standard runtime library
and that an FFmpeg executable can be found by LAMMPS during the run.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Similar to the note above, this option can conflict
with high-speed networks, because it uses popen().</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Similar to the note above, this option can conflict with
high-speed networks, because it uses popen().</p>
</div>
<p>Using -DLAMMPS_MEMALIGN=&lt;bytes&gt; enables the use of the
posix_memalign() call instead of malloc() when large chunks or memory
@ -588,17 +588,16 @@ gmake foo
<p>You should get the executable lmp_foo when the build is complete.</p>
<hr class="docutils" />
<p id="start-2-3"><strong>*Errors that can occur when making LAMMPS:*</strong></p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If an error occurs when building LAMMPS, the compiler
or linker will state very explicitly what the problem is. The error
message should give you a hint as to which of the steps above has
failed, and what you need to do in order to fix it. Building a code
with a Makefile is a very logical process. The compiler and linker
need to find the appropriate files and those files need to be
compatible with LAMMPS source files. When a make fails, there is
usually a very simple reason, which you or a local expert will need to
fix.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If an error occurs when building LAMMPS, the compiler or linker
will state very explicitly what the problem is. The error message
should give you a hint as to which of the steps above has failed, and
what you need to do in order to fix it. Building a code with a
Makefile is a very logical process. The compiler and linker need to
find the appropriate files and those files need to be compatible with
LAMMPS source files. When a make fails, there is usually a very
simple reason, which you or a local expert will need to fix.</p>
</div>
<p>Here are two non-obvious errors that can occur:</p>
<p>(1) If the make command breaks immediately with errors that indicate
@ -769,13 +768,13 @@ make g++
make g++
</pre></div>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">You should NOT include/exclude packages and build
LAMMPS in a single make command using multiple targets, e.g. make
yes-colloid g++. This is because the make procedure creates a list of
source files that will be out-of-date for the build if the package
configuration changes within the same command.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">You should NOT include/exclude packages and build LAMMPS in a
single make command using multiple targets, e.g. make yes-colloid g++.
This is because the make procedure creates a list of source files that
will be out-of-date for the build if the package configuration changes
within the same command.</p>
</div>
<p>Some packages have individual files that depend on other packages
being included. LAMMPS checks for this and does the right thing.
@ -799,13 +798,13 @@ no-standard&#8221;, &#8220;make yes-std&#8221;, &#8220;make no-std&#8221;, &#822
no-user&#8221;, &#8220;make yes-all&#8221; or &#8220;make no-all&#8221; to include/exclude various
sets of packages. Type &#8220;make package&#8221; to see the all of the
package-related make options.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Inclusion/exclusion of a package works by simply
moving files back and forth between the main src directory and
sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
so that the files are seen or not seen when LAMMPS is built. After
you have included or excluded a package, you must re-build LAMMPS.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Inclusion/exclusion of a package works by simply moving files
back and forth between the main src directory and sub-directories with
the package name (e.g. src/KSPACE, src/USER-ATC), so that the files
are seen or not seen when LAMMPS is built. After you have included or
excluded a package, you must re-build LAMMPS.</p>
</div>
<p>Additional package-related make options exist to help manage LAMMPS
files that exist in both the src directory and in package
@ -1935,7 +1934,7 @@ close if you have setup the problem for both codes the same.</p>
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; Copyright 2013 Sandia Corporation.
</p>
</div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
@ -1956,7 +1955,7 @@ close if you have setup the problem for both codes the same.</p>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true