Unverified Commit 54740a06 authored by Steve Plimpton's avatar Steve Plimpton Committed by GitHub
Browse files

Merge pull request #804 from akohlmey/collected-small-changes 

Collected small changes for next patch release
parents 7e78738c 9f7b837f

doc/Makefile

+1 −1
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@@ -21,7 +21,7 @@ HAS_VIRTUALENV = YES 
endif



SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')

SOURCES=$(wildcard src/*.txt)

SOURCES=$(filter-out src/lammps_commands.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))

OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)



.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check

doc/src/Manual.txt

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@@ -176,11 +176,11 @@ END_RST --> 
  5.1 "Measuring performance"_acc_1 :ulb,b

  5.2 "Algorithms and code options to boost performace"_acc_2 :b

  5.3 "Accelerator packages with optimized styles"_acc_3 :b

    5.3.1 "GPU package"_accelerate_gpu.html :ulb,b

    5.3.1 "GPU package"_accelerate_gpu.html :b

    5.3.2 "USER-INTEL package"_accelerate_intel.html :b

    5.3.3 "KOKKOS package"_accelerate_kokkos.html :b

    5.3.4 "USER-OMP package"_accelerate_omp.html :b

    5.3.5 "OPT package"_accelerate_opt.html :ule,b

    5.3.5 "OPT package"_accelerate_opt.html :b

  5.4 "Comparison of various accelerator packages"_acc_4 :ule,b

"How-to discussions"_Section_howto.html :l

  6.1 "Restarting a simulation"_howto_1 :ulb,b

doc/src/Section_intro.txt

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@@ -507,11 +507,15 @@ we'll be pleased to add them to the 
"Movies"_http://lammps.sandia.gov/movies.html pages of the LAMMPS WWW

site.



The core group of LAMMPS developers is at Sandia National Labs:

The primary LAMMPS developers are at Sandia National Labs and Temple University:



Steve Plimpton, sjplimp at sandia.gov

Aidan Thompson, athomps at sandia.gov

Paul Crozier, pscrozi at sandia.gov :ul

Stan Moore, stamoor at sandia.gov

Axel Kohlmeyer, akohlmey at gmail.com :ul



Past primary developers include Paul Crozier and Mark Stevens,

both at Sandia, and Ray Shan, now at Materials Design.



The following folks are responsible for significant contributions to

the code, or other aspects of the LAMMPS development effort.  Many of
@@ -519,19 +523,20 @@ the packages they have written are somewhat unique to LAMMPS and the 
code would not be as general-purpose as it is without their expertise

and efforts.



Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK and USER-OMP packages

Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM, USER-TALLY, and COMPRESS packages

Roy Pollock (LLNL), Ewald and PPPM solvers

Mike Brown (ORNL), brownw at ornl.gov, GPU package

Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL package

Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential

Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics

Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion

Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling

Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD

Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package

Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages

Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field

Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling

Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF

Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package :ul

Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages

Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul



As discussed in "Section 13"_Section_history.html, LAMMPS

originated as a cooperative project between DOE labs and industrial

doc/src/Section_tools.txt

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@@ -184,7 +184,7 @@ doxygen tool :h4,link(doxygen) 


The tools/doxygen directory contains a shell script called

doxygen.sh which can generate a call graph and API lists using

the "Doxygen"_http://doxygen.org software.

the "Doxygen software"_http://doxygen.org.



See the included README file for details.

doc/src/USER/atc/man_add_molecule.html

+22 −24
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@@ -7,24 +7,22 @@ 
<link href="doxygen.css" rel="stylesheet" type="text/css"/>

</head>

<body>

<center>

  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;

  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;

  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;

  <a href="../../Section_commands.html#comm">Commands</a>

</center>



<hr>





<!-- Generated by Doxygen 1.6.1 -->

<div class="navigation" id="top">

  <div class="tabs">

    <ul>

      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>

      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>

      <li><a href="namespaces.html"><span>Namespaces</span></a></li>

      <li><a href="annotated.html"><span>Classes</span></a></li>

      <li><a href="files.html"><span>Files</span></a></li>

      <li><a href="dirs.html"><span>Directories</span></a></li>

    </ul>

  </div>

</div>

<div class="contents">





<h1><a class="anchor" id="man_add_molecule">fix_modify AtC add_molecule </a></h1><h2><a class="anchor" id="syntax">

syntax</a></h2>

<h3><a class="anchor" id="man_add_molecule">fix_modify AtC add_molecule </a></h3><h4><a class="anchor" id="syntax">

syntax</a></h4>

<p>fix_modify_AtC add_molecule &lt;small|large&gt; &lt;TAG&gt; &lt;GROUP_NAME&gt; <br/>

</p>

<ul>
@@ -35,21 +33,21 @@ syntax</a></h2> 
<li>&lt;GROUP_NAME&gt; = name of group that tracking will be applied to <br/>

 </li>

</ul>

<h2><a class="anchor" id="examples">

examples</a></h2>

<h4><a class="anchor" id="examples">

examples</a></h4>

<p><code> group WATERGROUP type 1 2 </code> <br/>

 <code> fix_modify AtC add_molecule small water WATERGROUP </code> <br/>

 </p>

<h2><a class="anchor" id="description">

description</a></h2>

<h4><a class="anchor" id="description">

description</a></h4>

<p>Associates a tag with all molecules corresponding to a specified group. <br/>

 </p>

<h2><a class="anchor" id="restrictions">

restrictions</a></h2>

<h2><a class="anchor" id="related">

related</a></h2>

<h2><a class="anchor" id="default">

default</a></h2>

<h4><a class="anchor" id="restrictions">

restrictions</a></h4>

<h4><a class="anchor" id="related">

related</a></h4>

<h4><a class="anchor" id="default">

default</a></h4>

<p>No defaults for this command. </p>

</div>

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