Commit b12ad2ce authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

Merge branch 'integration' into vashishta-tabulation

parents cdf06646 fb2c18ee

doc/Makefile

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@@ -43,6 +43,8 @@ html: $(OBJECTS) 
		sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\

		deactivate ;\

	)

	-rm html/searchindex.js

	-rm -rf html/_sources

	@echo "Build finished. The HTML pages are in doc/html."



pdf: utils/txt2html/txt2html.exe

doc/README.md

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@@ -14,8 +14,8 @@ make clean-all # remove entire build folder and any cached data 


## Installing prerequisites



To run the documention build toolchain Python 3 and virtualenv have to be

installed. Here are instructions for common setups:

To run the documention build toolchain, Python 3 and virtualenv have

to be installed. Here are instructions for common setups:



### Ubuntu
@@ -23,10 +23,16 @@ installed. Here are instructions for common setups: 
sudo apt-get install python-virtualenv

```



### Fedora

### Fedora (up to version 21), Red Hat Enterprise Linux or CentOS (up to version 7.x)



```bash

sudo yum install python3-virtualenv

```

sudo yum install python-virtualenv



### Fedora (since version 22)



```bash

sudo dnf install python3-virtualenv

```



### MacOS X

doc/html/.gitignore

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.buildinfo

objects.inv

searchindex.js

_sources

doc/html/Section_howto.html

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@@ -2333,20 +2333,20 @@ velocity:</p> 
</ol>

<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>

<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>

<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>

<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>

</pre></div>

</div>

<ol class="arabic simple" start="4">

<li>Total force on each molecule and ave/max across all molecules:</li>

</ol>

<pre class="literal-block">

compute cc1 all chunk/atom molecule

fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out

variable xave equal ave(f_1<strong>2</strong>)

variable xmax equal max(f_1<strong>2</strong>)

thermo 1000

thermo_style custom step temp v_xave v_xmax

</pre>

<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>

<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">1000</span> <span class="mi">1</span> <span class="mi">1000</span> <span class="n">cc1</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span>

<span class="n">variable</span> <span class="n">xave</span> <span class="n">equal</span> <span class="n">ave</span><span class="p">(</span><span class="n">f_1</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>

<span class="n">variable</span> <span class="n">xmax</span> <span class="n">equal</span> <span class="nb">max</span><span class="p">(</span><span class="n">f_1</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>

<span class="n">thermo</span> <span class="mi">1000</span>

<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">v_xave</span> <span class="n">v_xmax</span>

</pre></div>

</div>

<ol class="arabic simple" start="5">

<li>Histogram of cluster sizes:</li>

</ol>

doc/html/Section_start.html

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@@ -389,6 +389,7 @@ within the LAMMPS code. The options that are currently recogized are:</p> 
<li>-DLAMMPS_BIGBIG</li>

<li>-DLAMMPS_SMALLSMALL</li>

<li>-DLAMMPS_LONGLONG_TO_LONG</li>

<li>-DLAMMPS_EXCEPTIONS</li>

<li>-DPACK_ARRAY</li>

<li>-DPACK_POINTER</li>

<li>-DPACK_MEMCPY</li>
@@ -457,6 +458,13 @@ be compiled with the same setting, or the link will fail.</p> 
MPI version does not recognize &#8220;long long&#8221; data types.  In this case a

&#8220;long&#8221; data type is likely already 64-bits, in which case this setting

will convert to that data type.</p>

<p>The -DLAMMPS_EXCEPTIONS setting can be used to activate alternative

versions of error handling inside of LAMMPS.  This is useful when

external codes drive LAMMPS as a library.  Using this option, LAMMPS

errors do not kill the caller.  Instead, the call stack is unwound and

control returns to the caller.  The library interface provides the

lammps_has_error() and lammps_get_last_error_message() functions to

detect and find out more about a LAMMPS error.</p>

<p>Using one of the -DPACK_ARRAY, -DPACK_POINTER, and -DPACK_MEMCPY

options can make for faster parallel FFTs (in the PPPM solver) on some

platforms.  The -DPACK_ARRAY setting is the default.  See the

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